Multiple sequence alignment - TraesCS5D01G217400

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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 TraesCS5D01G217400 chr5D 100.000 4337 0 0 1 4337 326401791 326406127 0.000000e+00 8010.0
1 TraesCS5D01G217400 chr5D 95.183 1038 40 6 948 1976 326384674 326383638 0.000000e+00 1631.0
2 TraesCS5D01G217400 chr5D 88.927 1156 86 22 2057 3194 326383339 326382208 0.000000e+00 1387.0
3 TraesCS5D01G217400 chr5D 97.698 695 8 6 3648 4337 533655194 533654503 0.000000e+00 1188.0
4 TraesCS5D01G217400 chr5D 97.114 693 15 3 3647 4337 391737569 391738258 0.000000e+00 1164.0
5 TraesCS5D01G217400 chr5D 90.115 698 53 13 3648 4337 456027019 456026330 0.000000e+00 893.0
6 TraesCS5D01G217400 chr5D 91.071 56 2 2 3193 3248 326404903 326404955 6.020000e-09 73.1
7 TraesCS5D01G217400 chr5D 91.071 56 2 2 3113 3165 326404983 326405038 6.020000e-09 73.1
8 TraesCS5D01G217400 chr5A 91.299 1655 82 24 758 2387 429998473 429996856 0.000000e+00 2202.0
9 TraesCS5D01G217400 chr5A 91.411 1269 83 16 2387 3646 429996808 429995557 0.000000e+00 1716.0
10 TraesCS5D01G217400 chr5A 92.361 1152 63 13 2048 3190 430042549 430043684 0.000000e+00 1616.0
11 TraesCS5D01G217400 chr5A 93.981 1080 36 13 952 2010 430041485 430042556 0.000000e+00 1607.0
12 TraesCS5D01G217400 chr5A 96.254 694 13 7 3648 4336 680598795 680599480 0.000000e+00 1125.0
13 TraesCS5D01G217400 chr5A 83.919 939 132 15 1044 1971 419830892 419829962 0.000000e+00 880.0
14 TraesCS5D01G217400 chr5A 90.152 396 26 6 1 391 430000236 429999849 1.800000e-138 503.0
15 TraesCS5D01G217400 chr5A 92.079 101 8 0 389 489 577946067 577945967 4.520000e-30 143.0
16 TraesCS5D01G217400 chr5A 88.073 109 13 0 389 497 125228006 125228114 3.520000e-26 130.0
17 TraesCS5D01G217400 chr5B 92.971 1437 68 20 626 2036 378902936 378904365 0.000000e+00 2063.0
18 TraesCS5D01G217400 chr5B 92.998 1114 50 15 948 2046 378853391 378852291 0.000000e+00 1600.0
19 TraesCS5D01G217400 chr5B 92.881 885 56 6 2387 3266 378904720 378905602 0.000000e+00 1279.0
20 TraesCS5D01G217400 chr5B 87.281 1140 106 27 2079 3194 378852294 378851170 0.000000e+00 1266.0
21 TraesCS5D01G217400 chr5B 84.115 938 132 13 1044 1971 375224965 375224035 0.000000e+00 891.0
22 TraesCS5D01G217400 chr5B 87.619 315 29 5 2076 2387 378904365 378904672 1.480000e-94 357.0
23 TraesCS5D01G217400 chr5B 82.824 425 27 15 1 391 378902312 378902724 5.370000e-89 339.0
24 TraesCS5D01G217400 chr5B 92.118 203 16 0 3262 3464 378906927 378907129 1.970000e-73 287.0
25 TraesCS5D01G217400 chr5B 94.444 108 6 0 389 496 45943859 45943966 2.680000e-37 167.0
26 TraesCS5D01G217400 chr5B 90.741 108 10 0 389 496 354169336 354169443 1.260000e-30 145.0
27 TraesCS5D01G217400 chr3D 97.309 706 8 4 3643 4337 302923009 302922304 0.000000e+00 1188.0
28 TraesCS5D01G217400 chr3D 97.391 690 13 3 3648 4337 442860586 442859902 0.000000e+00 1170.0
29 TraesCS5D01G217400 chr2D 96.871 703 9 8 3648 4337 610369865 610370567 0.000000e+00 1164.0
30 TraesCS5D01G217400 chr2D 96.464 707 13 5 3643 4337 572697018 572697724 0.000000e+00 1157.0
31 TraesCS5D01G217400 chr2D 83.494 933 143 6 1040 1971 538597492 538598414 0.000000e+00 859.0
32 TraesCS5D01G217400 chr6B 96.248 693 22 3 3648 4337 36201232 36200541 0.000000e+00 1133.0
33 TraesCS5D01G217400 chr6B 95.745 47 2 0 450 496 447113659 447113613 4.650000e-10 76.8
34 TraesCS5D01G217400 chr2B 82.851 933 149 7 1040 1971 641193378 641194300 0.000000e+00 826.0
35 TraesCS5D01G217400 chr2A 82.315 933 154 7 1040 1971 680548122 680549044 0.000000e+00 798.0
36 TraesCS5D01G217400 chr1B 83.055 838 124 12 1134 1971 52293653 52294472 0.000000e+00 745.0
37 TraesCS5D01G217400 chr7D 76.978 847 168 23 1131 1968 13698302 13697474 3.950000e-125 459.0
38 TraesCS5D01G217400 chr7D 75.967 724 146 26 1131 1848 13681530 13680829 8.930000e-92 348.0
39 TraesCS5D01G217400 chr7D 80.108 186 33 4 3463 3646 496169437 496169254 7.570000e-28 135.0
40 TraesCS5D01G217400 chr4B 91.803 122 7 2 389 507 312267174 312267053 2.680000e-37 167.0
41 TraesCS5D01G217400 chr4B 90.909 110 8 1 389 496 11718301 11718192 3.500000e-31 147.0
42 TraesCS5D01G217400 chr4B 88.235 85 10 0 389 473 666049710 666049626 7.670000e-18 102.0
43 TraesCS5D01G217400 chr7B 92.857 112 8 0 386 497 201497288 201497399 3.470000e-36 163.0
44 TraesCS5D01G217400 chr7B 77.912 249 42 8 3399 3646 39097199 39096963 4.520000e-30 143.0
45 TraesCS5D01G217400 chr1D 79.134 254 38 13 3399 3646 217975409 217975653 1.250000e-35 161.0
46 TraesCS5D01G217400 chr3B 78.226 248 54 0 3399 3646 33846288 33846535 4.490000e-35 159.0
47 TraesCS5D01G217400 chr4D 84.277 159 25 0 3488 3646 116786229 116786071 5.810000e-34 156.0
48 TraesCS5D01G217400 chr4D 81.865 193 28 6 3457 3646 505966924 505966736 5.810000e-34 156.0
49 TraesCS5D01G217400 chr4D 89.908 109 10 1 388 496 209212243 209212136 5.850000e-29 139.0
50 TraesCS5D01G217400 chr4A 78.000 250 49 6 3399 3646 527900211 527900456 7.510000e-33 152.0
51 TraesCS5D01G217400 chr3A 90.826 109 10 0 388 496 533087669 533087777 3.500000e-31 147.0
52 TraesCS5D01G217400 chr1A 82.609 161 25 2 3489 3646 451854131 451854291 5.850000e-29 139.0
53 TraesCS5D01G217400 chr6D 80.447 179 31 3 3470 3646 354989370 354989194 2.720000e-27 134.0
54 TraesCS5D01G217400 chr7A 79.293 198 33 6 3451 3646 510156588 510156779 9.790000e-27 132.0
55 TraesCS5D01G217400 chr6A 90.526 95 9 0 405 499 383077982 383078076 4.550000e-25 126.0


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 TraesCS5D01G217400 chr5D 326401791 326406127 4336 False 2718.733333 8010 94.047333 1 4337 3 chr5D.!!$F2 4336
1 TraesCS5D01G217400 chr5D 326382208 326384674 2466 True 1509.000000 1631 92.055000 948 3194 2 chr5D.!!$R3 2246
2 TraesCS5D01G217400 chr5D 533654503 533655194 691 True 1188.000000 1188 97.698000 3648 4337 1 chr5D.!!$R2 689
3 TraesCS5D01G217400 chr5D 391737569 391738258 689 False 1164.000000 1164 97.114000 3647 4337 1 chr5D.!!$F1 690
4 TraesCS5D01G217400 chr5D 456026330 456027019 689 True 893.000000 893 90.115000 3648 4337 1 chr5D.!!$R1 689
5 TraesCS5D01G217400 chr5A 430041485 430043684 2199 False 1611.500000 1616 93.171000 952 3190 2 chr5A.!!$F3 2238
6 TraesCS5D01G217400 chr5A 429995557 430000236 4679 True 1473.666667 2202 90.954000 1 3646 3 chr5A.!!$R3 3645
7 TraesCS5D01G217400 chr5A 680598795 680599480 685 False 1125.000000 1125 96.254000 3648 4336 1 chr5A.!!$F2 688
8 TraesCS5D01G217400 chr5A 419829962 419830892 930 True 880.000000 880 83.919000 1044 1971 1 chr5A.!!$R1 927
9 TraesCS5D01G217400 chr5B 378851170 378853391 2221 True 1433.000000 1600 90.139500 948 3194 2 chr5B.!!$R2 2246
10 TraesCS5D01G217400 chr5B 375224035 375224965 930 True 891.000000 891 84.115000 1044 1971 1 chr5B.!!$R1 927
11 TraesCS5D01G217400 chr5B 378902312 378907129 4817 False 865.000000 2063 89.682600 1 3464 5 chr5B.!!$F3 3463
12 TraesCS5D01G217400 chr3D 302922304 302923009 705 True 1188.000000 1188 97.309000 3643 4337 1 chr3D.!!$R1 694
13 TraesCS5D01G217400 chr3D 442859902 442860586 684 True 1170.000000 1170 97.391000 3648 4337 1 chr3D.!!$R2 689
14 TraesCS5D01G217400 chr2D 610369865 610370567 702 False 1164.000000 1164 96.871000 3648 4337 1 chr2D.!!$F3 689
15 TraesCS5D01G217400 chr2D 572697018 572697724 706 False 1157.000000 1157 96.464000 3643 4337 1 chr2D.!!$F2 694
16 TraesCS5D01G217400 chr2D 538597492 538598414 922 False 859.000000 859 83.494000 1040 1971 1 chr2D.!!$F1 931
17 TraesCS5D01G217400 chr6B 36200541 36201232 691 True 1133.000000 1133 96.248000 3648 4337 1 chr6B.!!$R1 689
18 TraesCS5D01G217400 chr2B 641193378 641194300 922 False 826.000000 826 82.851000 1040 1971 1 chr2B.!!$F1 931
19 TraesCS5D01G217400 chr2A 680548122 680549044 922 False 798.000000 798 82.315000 1040 1971 1 chr2A.!!$F1 931
20 TraesCS5D01G217400 chr1B 52293653 52294472 819 False 745.000000 745 83.055000 1134 1971 1 chr1B.!!$F1 837
21 TraesCS5D01G217400 chr7D 13697474 13698302 828 True 459.000000 459 76.978000 1131 1968 1 chr7D.!!$R2 837
22 TraesCS5D01G217400 chr7D 13680829 13681530 701 True 348.000000 348 75.967000 1131 1848 1 chr7D.!!$R1 717

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
843 2205 0.244994 GGACGTCAGCATCAGTGTCT 59.755 55.0 18.91 0.0 0.00 3.41 F
2005 3451 0.250901 TGCTTTCCTTCCCTGCACTC 60.251 55.0 0.00 0.0 0.00 3.51 F
2952 4730 0.776810 TTGGGCTGAAGGTGATCCAA 59.223 50.0 0.00 0.0 35.89 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2334 4057 0.538746 GTCACGGTCCAATTTGGGGT 60.539 55.0 15.37 8.43 38.32 4.95 R
3122 4900 0.813610 CTCAACACACGAGGGCACAA 60.814 55.0 0.00 0.00 0.00 3.33 R
4293 7450 1.741528 TACGACGATGAGTAGCACCA 58.258 50.0 0.00 0.00 0.00 4.17 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
42 43 1.203052 GCTGGTAGTTGCGGTGTACTA 59.797 52.381 0.00 0.00 0.00 1.82
43 44 2.734492 GCTGGTAGTTGCGGTGTACTAG 60.734 54.545 0.00 0.00 0.00 2.57
44 45 1.203052 TGGTAGTTGCGGTGTACTAGC 59.797 52.381 0.00 0.00 42.66 3.42
50 51 0.809385 TGCGGTGTACTAGCTCAGAC 59.191 55.000 0.00 0.00 0.00 3.51
96 97 3.669251 ACAGCTAGCTTAATCGGATCC 57.331 47.619 16.46 0.00 0.00 3.36
120 121 3.966215 CAGCGTCCGGTGAAATGT 58.034 55.556 13.15 0.00 45.42 2.71
121 122 3.131326 CAGCGTCCGGTGAAATGTA 57.869 52.632 13.15 0.00 45.42 2.29
122 123 0.719465 CAGCGTCCGGTGAAATGTAC 59.281 55.000 13.15 0.00 45.42 2.90
123 124 0.606604 AGCGTCCGGTGAAATGTACT 59.393 50.000 0.00 0.00 0.00 2.73
179 180 1.377725 AAGAAGTGGCCGGCATCTG 60.378 57.895 30.85 0.00 0.00 2.90
180 181 2.825836 GAAGTGGCCGGCATCTGG 60.826 66.667 30.85 0.00 0.00 3.86
181 182 3.628646 GAAGTGGCCGGCATCTGGT 62.629 63.158 30.85 11.23 0.00 4.00
182 183 2.252072 GAAGTGGCCGGCATCTGGTA 62.252 60.000 30.85 1.53 0.00 3.25
183 184 1.847798 AAGTGGCCGGCATCTGGTAA 61.848 55.000 30.85 0.00 0.00 2.85
184 185 1.152963 GTGGCCGGCATCTGGTAAT 60.153 57.895 30.85 0.00 0.00 1.89
197 198 3.052329 TCTGGTAATGGTATGATGGGCA 58.948 45.455 0.00 0.00 0.00 5.36
247 280 2.745821 CCATGATGGGCTTGATGTATCG 59.254 50.000 2.79 0.00 32.67 2.92
274 307 1.812922 GTGGCCATCAGCGTCAGAG 60.813 63.158 9.72 0.00 45.17 3.35
310 345 4.173256 GCCATTAAACTTGTCGGATTTGG 58.827 43.478 0.00 0.00 0.00 3.28
314 349 0.898326 AACTTGTCGGATTTGGCCCC 60.898 55.000 0.00 0.00 0.00 5.80
315 350 2.360600 TTGTCGGATTTGGCCCCG 60.361 61.111 11.56 11.56 46.57 5.73
337 372 1.138883 CATGCCTGATGTGCTGTGC 59.861 57.895 0.00 0.00 0.00 4.57
338 373 2.404186 ATGCCTGATGTGCTGTGCG 61.404 57.895 0.00 0.00 0.00 5.34
344 379 2.281002 ATGTGCTGTGCGTGCTCA 60.281 55.556 0.00 0.00 38.11 4.26
391 433 3.742369 CCACGTACAACGACCAAAATACT 59.258 43.478 6.44 0.00 46.05 2.12
392 434 4.143263 CCACGTACAACGACCAAAATACTC 60.143 45.833 6.44 0.00 46.05 2.59
393 435 3.989817 ACGTACAACGACCAAAATACTCC 59.010 43.478 6.44 0.00 46.05 3.85
394 436 3.368843 CGTACAACGACCAAAATACTCCC 59.631 47.826 0.00 0.00 46.05 4.30
395 437 3.782656 ACAACGACCAAAATACTCCCT 57.217 42.857 0.00 0.00 0.00 4.20
396 438 3.671716 ACAACGACCAAAATACTCCCTC 58.328 45.455 0.00 0.00 0.00 4.30
397 439 3.326880 ACAACGACCAAAATACTCCCTCT 59.673 43.478 0.00 0.00 0.00 3.69
398 440 4.529377 ACAACGACCAAAATACTCCCTCTA 59.471 41.667 0.00 0.00 0.00 2.43
399 441 5.189145 ACAACGACCAAAATACTCCCTCTAT 59.811 40.000 0.00 0.00 0.00 1.98
400 442 5.952347 ACGACCAAAATACTCCCTCTATT 57.048 39.130 0.00 0.00 0.00 1.73
401 443 5.915175 ACGACCAAAATACTCCCTCTATTC 58.085 41.667 0.00 0.00 0.00 1.75
402 444 5.424252 ACGACCAAAATACTCCCTCTATTCA 59.576 40.000 0.00 0.00 0.00 2.57
403 445 6.099845 ACGACCAAAATACTCCCTCTATTCAT 59.900 38.462 0.00 0.00 0.00 2.57
404 446 6.992715 CGACCAAAATACTCCCTCTATTCATT 59.007 38.462 0.00 0.00 0.00 2.57
405 447 7.499232 CGACCAAAATACTCCCTCTATTCATTT 59.501 37.037 0.00 0.00 0.00 2.32
406 448 9.190317 GACCAAAATACTCCCTCTATTCATTTT 57.810 33.333 0.00 0.00 0.00 1.82
407 449 9.547279 ACCAAAATACTCCCTCTATTCATTTTT 57.453 29.630 0.00 0.00 0.00 1.94
414 456 8.926092 ACTCCCTCTATTCATTTTTATAAGGC 57.074 34.615 0.00 0.00 0.00 4.35
415 457 8.728098 ACTCCCTCTATTCATTTTTATAAGGCT 58.272 33.333 0.00 0.00 0.00 4.58
416 458 9.579932 CTCCCTCTATTCATTTTTATAAGGCTT 57.420 33.333 4.58 4.58 0.00 4.35
417 459 9.936329 TCCCTCTATTCATTTTTATAAGGCTTT 57.064 29.630 4.45 0.00 0.00 3.51
434 476 7.856145 AAGGCTTTATAGATGTTTCAGACAG 57.144 36.000 0.00 0.00 42.62 3.51
435 477 6.951971 AGGCTTTATAGATGTTTCAGACAGT 58.048 36.000 0.00 0.00 42.62 3.55
436 478 6.820656 AGGCTTTATAGATGTTTCAGACAGTG 59.179 38.462 0.00 0.00 42.62 3.66
437 479 6.595716 GGCTTTATAGATGTTTCAGACAGTGT 59.404 38.462 0.00 0.00 42.62 3.55
438 480 7.413438 GGCTTTATAGATGTTTCAGACAGTGTG 60.413 40.741 0.00 0.00 42.62 3.82
439 481 6.968131 TTATAGATGTTTCAGACAGTGTGC 57.032 37.500 0.00 0.00 42.62 4.57
440 482 3.198409 AGATGTTTCAGACAGTGTGCA 57.802 42.857 0.00 0.00 42.62 4.57
441 483 3.544684 AGATGTTTCAGACAGTGTGCAA 58.455 40.909 0.00 0.00 42.62 4.08
442 484 3.947196 AGATGTTTCAGACAGTGTGCAAA 59.053 39.130 0.00 0.00 42.62 3.68
443 485 4.398988 AGATGTTTCAGACAGTGTGCAAAA 59.601 37.500 0.00 0.00 42.62 2.44
444 486 3.832276 TGTTTCAGACAGTGTGCAAAAC 58.168 40.909 0.00 8.57 33.40 2.43
445 487 3.254411 TGTTTCAGACAGTGTGCAAAACA 59.746 39.130 16.68 16.68 33.98 2.83
446 488 4.233789 GTTTCAGACAGTGTGCAAAACAA 58.766 39.130 0.00 0.00 41.57 2.83
447 489 3.485947 TCAGACAGTGTGCAAAACAAC 57.514 42.857 0.00 0.00 41.57 3.32
448 490 2.816672 TCAGACAGTGTGCAAAACAACA 59.183 40.909 0.00 0.00 41.57 3.33
449 491 3.443329 TCAGACAGTGTGCAAAACAACAT 59.557 39.130 0.00 0.00 41.57 2.71
450 492 4.637977 TCAGACAGTGTGCAAAACAACATA 59.362 37.500 0.00 0.00 41.57 2.29
451 493 5.124617 TCAGACAGTGTGCAAAACAACATAA 59.875 36.000 0.00 0.00 41.57 1.90
452 494 5.978919 CAGACAGTGTGCAAAACAACATAAT 59.021 36.000 0.00 0.00 41.57 1.28
453 495 6.476380 CAGACAGTGTGCAAAACAACATAATT 59.524 34.615 0.00 0.00 41.57 1.40
454 496 7.010367 CAGACAGTGTGCAAAACAACATAATTT 59.990 33.333 0.00 0.00 41.57 1.82
455 497 7.548780 AGACAGTGTGCAAAACAACATAATTTT 59.451 29.630 0.00 0.00 41.57 1.82
456 498 8.709386 ACAGTGTGCAAAACAACATAATTTTA 57.291 26.923 0.00 0.00 41.57 1.52
457 499 8.599774 ACAGTGTGCAAAACAACATAATTTTAC 58.400 29.630 0.00 0.00 41.57 2.01
458 500 8.816144 CAGTGTGCAAAACAACATAATTTTACT 58.184 29.630 0.00 0.00 41.57 2.24
459 501 9.377312 AGTGTGCAAAACAACATAATTTTACTT 57.623 25.926 0.00 0.00 41.57 2.24
460 502 9.419737 GTGTGCAAAACAACATAATTTTACTTG 57.580 29.630 0.00 0.00 41.57 3.16
461 503 9.155975 TGTGCAAAACAACATAATTTTACTTGT 57.844 25.926 0.00 0.00 35.24 3.16
462 504 9.631639 GTGCAAAACAACATAATTTTACTTGTC 57.368 29.630 0.00 0.00 0.00 3.18
463 505 9.593134 TGCAAAACAACATAATTTTACTTGTCT 57.407 25.926 0.00 0.00 0.00 3.41
464 506 9.848172 GCAAAACAACATAATTTTACTTGTCTG 57.152 29.630 0.00 0.00 0.00 3.51
469 511 9.445786 ACAACATAATTTTACTTGTCTGAAACG 57.554 29.630 0.00 0.00 0.00 3.60
470 512 9.658475 CAACATAATTTTACTTGTCTGAAACGA 57.342 29.630 0.00 0.00 0.00 3.85
471 513 9.659830 AACATAATTTTACTTGTCTGAAACGAC 57.340 29.630 0.00 0.00 34.52 4.34
472 514 9.052759 ACATAATTTTACTTGTCTGAAACGACT 57.947 29.630 0.00 0.00 35.00 4.18
473 515 9.878599 CATAATTTTACTTGTCTGAAACGACTT 57.121 29.630 0.00 0.00 35.00 3.01
474 516 9.878599 ATAATTTTACTTGTCTGAAACGACTTG 57.121 29.630 0.00 0.00 35.00 3.16
475 517 6.730960 TTTTACTTGTCTGAAACGACTTGT 57.269 33.333 0.00 0.00 35.00 3.16
476 518 7.830940 TTTTACTTGTCTGAAACGACTTGTA 57.169 32.000 0.00 0.00 35.00 2.41
477 519 7.830940 TTTACTTGTCTGAAACGACTTGTAA 57.169 32.000 0.00 0.00 34.25 2.41
478 520 7.830940 TTACTTGTCTGAAACGACTTGTAAA 57.169 32.000 0.00 0.00 33.75 2.01
479 521 6.730960 ACTTGTCTGAAACGACTTGTAAAA 57.269 33.333 0.00 0.00 35.00 1.52
480 522 6.772078 ACTTGTCTGAAACGACTTGTAAAAG 58.228 36.000 0.00 0.00 35.00 2.27
481 523 6.370718 ACTTGTCTGAAACGACTTGTAAAAGT 59.629 34.615 0.00 0.00 35.00 2.66
482 524 6.102006 TGTCTGAAACGACTTGTAAAAGTG 57.898 37.500 2.08 0.00 35.00 3.16
483 525 5.870433 TGTCTGAAACGACTTGTAAAAGTGA 59.130 36.000 2.08 0.00 35.00 3.41
484 526 6.369340 TGTCTGAAACGACTTGTAAAAGTGAA 59.631 34.615 2.08 0.00 35.00 3.18
485 527 6.681599 GTCTGAAACGACTTGTAAAAGTGAAC 59.318 38.462 2.08 0.00 32.22 3.18
486 528 5.552807 TGAAACGACTTGTAAAAGTGAACG 58.447 37.500 2.08 3.44 32.22 3.95
487 529 4.525411 AACGACTTGTAAAAGTGAACGG 57.475 40.909 2.08 0.00 32.22 4.44
488 530 3.784338 ACGACTTGTAAAAGTGAACGGA 58.216 40.909 2.08 0.00 32.22 4.69
489 531 4.374399 ACGACTTGTAAAAGTGAACGGAT 58.626 39.130 2.08 0.00 32.22 4.18
490 532 4.210537 ACGACTTGTAAAAGTGAACGGATG 59.789 41.667 2.08 0.00 32.22 3.51
491 533 4.377022 CGACTTGTAAAAGTGAACGGATGG 60.377 45.833 2.08 0.00 32.22 3.51
495 537 5.471556 TGTAAAAGTGAACGGATGGAGTA 57.528 39.130 0.00 0.00 0.00 2.59
521 563 6.293081 CCAAATATTTGTCAGAGCGTCCATAG 60.293 42.308 23.24 2.39 36.45 2.23
524 566 0.684479 TGTCAGAGCGTCCATAGCCT 60.684 55.000 0.00 0.00 34.64 4.58
565 607 2.504175 TCCATACACTTTAGGTCTGGGC 59.496 50.000 0.00 0.00 0.00 5.36
578 620 3.020984 GGTCTGGGCGAAATGGAAATAA 58.979 45.455 0.00 0.00 0.00 1.40
618 671 4.936685 AAAAAGGCTGGACTCCTAGAAT 57.063 40.909 0.00 0.00 32.65 2.40
620 673 6.388619 AAAAAGGCTGGACTCCTAGAATAA 57.611 37.500 0.00 0.00 32.65 1.40
628 778 6.481644 GCTGGACTCCTAGAATAAACTGAATG 59.518 42.308 0.00 0.00 0.00 2.67
686 1997 7.775053 TTCCTAGACAAAAACATAGCCAAAT 57.225 32.000 0.00 0.00 0.00 2.32
688 1999 7.826690 TCCTAGACAAAAACATAGCCAAATTC 58.173 34.615 0.00 0.00 0.00 2.17
691 2002 9.643693 CTAGACAAAAACATAGCCAAATTCAAT 57.356 29.630 0.00 0.00 0.00 2.57
693 2004 9.341078 AGACAAAAACATAGCCAAATTCAATTT 57.659 25.926 0.00 0.00 0.00 1.82
694 2005 9.384682 GACAAAAACATAGCCAAATTCAATTTG 57.615 29.630 14.99 14.99 46.98 2.32
695 2006 8.901793 ACAAAAACATAGCCAAATTCAATTTGT 58.098 25.926 19.35 6.65 46.22 2.83
696 2007 9.171701 CAAAAACATAGCCAAATTCAATTTGTG 57.828 29.630 19.35 13.75 46.22 3.33
723 2085 7.484641 CGTGCATGTTTAGTTGCTAAATTACAT 59.515 33.333 0.00 2.84 38.07 2.29
724 2086 9.139174 GTGCATGTTTAGTTGCTAAATTACATT 57.861 29.630 4.88 0.00 38.07 2.71
735 2097 9.884465 GTTGCTAAATTACATTAGTCATGATCC 57.116 33.333 0.00 0.00 36.24 3.36
736 2098 8.621532 TGCTAAATTACATTAGTCATGATCCC 57.378 34.615 0.00 0.00 36.24 3.85
737 2099 8.217111 TGCTAAATTACATTAGTCATGATCCCA 58.783 33.333 0.00 0.00 36.24 4.37
738 2100 9.236006 GCTAAATTACATTAGTCATGATCCCAT 57.764 33.333 0.00 0.00 36.24 4.00
747 2109 1.297689 ATGATCCCATGATCCCGCG 59.702 57.895 0.00 0.00 45.74 6.46
748 2110 1.483595 ATGATCCCATGATCCCGCGT 61.484 55.000 4.92 0.00 45.74 6.01
749 2111 1.071471 GATCCCATGATCCCGCGTT 59.929 57.895 4.92 0.00 41.37 4.84
750 2112 1.227943 ATCCCATGATCCCGCGTTG 60.228 57.895 4.92 0.00 0.00 4.10
751 2113 1.983119 ATCCCATGATCCCGCGTTGT 61.983 55.000 4.92 0.00 0.00 3.32
752 2114 1.145156 CCCATGATCCCGCGTTGTA 59.855 57.895 4.92 0.00 0.00 2.41
753 2115 0.250295 CCCATGATCCCGCGTTGTAT 60.250 55.000 4.92 0.00 0.00 2.29
754 2116 0.867746 CCATGATCCCGCGTTGTATG 59.132 55.000 4.92 3.07 0.00 2.39
755 2117 1.581934 CATGATCCCGCGTTGTATGT 58.418 50.000 4.92 0.00 0.00 2.29
756 2118 2.547007 CCATGATCCCGCGTTGTATGTA 60.547 50.000 4.92 0.00 0.00 2.29
757 2119 3.325870 CATGATCCCGCGTTGTATGTAT 58.674 45.455 4.92 0.00 0.00 2.29
758 2120 4.490743 CATGATCCCGCGTTGTATGTATA 58.509 43.478 4.92 0.00 0.00 1.47
759 2121 3.904571 TGATCCCGCGTTGTATGTATAC 58.095 45.455 4.92 0.00 0.00 1.47
760 2122 3.318557 TGATCCCGCGTTGTATGTATACA 59.681 43.478 8.27 8.27 41.19 2.29
764 2126 2.453080 CGCGTTGTATGTATACACCGT 58.547 47.619 18.64 0.00 46.47 4.83
768 2130 4.672413 GCGTTGTATGTATACACCGTCTAC 59.328 45.833 18.64 7.13 46.47 2.59
814 2176 4.809426 CAGTAAACTCTCACCACGTTTTCT 59.191 41.667 0.00 0.00 33.40 2.52
843 2205 0.244994 GGACGTCAGCATCAGTGTCT 59.755 55.000 18.91 0.00 0.00 3.41
867 2229 6.262193 TCGTCAAGTTTTCCAAGTCTTTTT 57.738 33.333 0.00 0.00 0.00 1.94
897 2261 2.781595 CTACTTTCCCACCACGCGCT 62.782 60.000 5.73 0.00 0.00 5.92
904 2268 4.680237 CACCACGCGCTCCTTCCA 62.680 66.667 5.73 0.00 0.00 3.53
905 2269 4.681978 ACCACGCGCTCCTTCCAC 62.682 66.667 5.73 0.00 0.00 4.02
907 2271 4.379243 CACGCGCTCCTTCCACCT 62.379 66.667 5.73 0.00 0.00 4.00
908 2272 4.070552 ACGCGCTCCTTCCACCTC 62.071 66.667 5.73 0.00 0.00 3.85
914 2279 3.649277 CTCCTTCCACCTCGCCACG 62.649 68.421 0.00 0.00 0.00 4.94
915 2280 3.691342 CCTTCCACCTCGCCACGA 61.691 66.667 0.00 0.00 0.00 4.35
950 2315 4.056125 CCGCACGCAGTCTGAGGA 62.056 66.667 3.32 0.00 41.61 3.71
1006 2371 1.532868 GAACACATCACTCAGCCACAC 59.467 52.381 0.00 0.00 0.00 3.82
1062 2450 2.556114 CCCAATGGAGCTTCCTCAACTT 60.556 50.000 0.00 0.00 39.96 2.66
1108 2496 0.514691 CACGGTGCTCTTCTTCAAGC 59.485 55.000 0.00 0.00 39.02 4.01
1272 2666 3.702048 TTCGGCTCCTTCCCGGTG 61.702 66.667 0.00 0.00 45.60 4.94
1674 3086 2.879462 GTGATCACGACGCCCGAC 60.879 66.667 10.69 0.00 41.76 4.79
2005 3451 0.250901 TGCTTTCCTTCCCTGCACTC 60.251 55.000 0.00 0.00 0.00 3.51
2009 3455 2.978156 TTCCTTCCCTGCACTCAATT 57.022 45.000 0.00 0.00 0.00 2.32
2011 3457 4.380843 TTCCTTCCCTGCACTCAATTTA 57.619 40.909 0.00 0.00 0.00 1.40
2013 3459 4.934356 TCCTTCCCTGCACTCAATTTAAT 58.066 39.130 0.00 0.00 0.00 1.40
2015 3461 6.489603 TCCTTCCCTGCACTCAATTTAATTA 58.510 36.000 0.00 0.00 0.00 1.40
2016 3462 6.377146 TCCTTCCCTGCACTCAATTTAATTAC 59.623 38.462 0.00 0.00 0.00 1.89
2017 3463 6.378280 CCTTCCCTGCACTCAATTTAATTACT 59.622 38.462 0.00 0.00 0.00 2.24
2018 3464 6.757897 TCCCTGCACTCAATTTAATTACTG 57.242 37.500 0.00 0.00 0.00 2.74
2019 3465 5.125417 TCCCTGCACTCAATTTAATTACTGC 59.875 40.000 6.50 6.50 0.00 4.40
2022 3468 7.201812 CCCTGCACTCAATTTAATTACTGCATA 60.202 37.037 13.07 0.00 33.19 3.14
2151 3861 1.406903 AAGCAGAAAAGCCAGCAAGT 58.593 45.000 0.00 0.00 34.23 3.16
2174 3896 8.123639 AGTATATTATGTCCTGTTGCTATCGT 57.876 34.615 0.00 0.00 0.00 3.73
2175 3897 8.244802 AGTATATTATGTCCTGTTGCTATCGTC 58.755 37.037 0.00 0.00 0.00 4.20
2176 3898 5.537300 ATTATGTCCTGTTGCTATCGTCT 57.463 39.130 0.00 0.00 0.00 4.18
2177 3899 2.654749 TGTCCTGTTGCTATCGTCTG 57.345 50.000 0.00 0.00 0.00 3.51
2178 3900 1.893137 TGTCCTGTTGCTATCGTCTGT 59.107 47.619 0.00 0.00 0.00 3.41
2179 3901 2.299013 TGTCCTGTTGCTATCGTCTGTT 59.701 45.455 0.00 0.00 0.00 3.16
2180 3902 2.924290 GTCCTGTTGCTATCGTCTGTTC 59.076 50.000 0.00 0.00 0.00 3.18
2181 3903 2.826128 TCCTGTTGCTATCGTCTGTTCT 59.174 45.455 0.00 0.00 0.00 3.01
2182 3904 4.014406 TCCTGTTGCTATCGTCTGTTCTA 58.986 43.478 0.00 0.00 0.00 2.10
2183 3905 4.645136 TCCTGTTGCTATCGTCTGTTCTAT 59.355 41.667 0.00 0.00 0.00 1.98
2184 3906 4.979197 CCTGTTGCTATCGTCTGTTCTATC 59.021 45.833 0.00 0.00 0.00 2.08
2185 3907 4.598062 TGTTGCTATCGTCTGTTCTATCG 58.402 43.478 0.00 0.00 0.00 2.92
2210 3932 6.913673 GGTCTAAGCGAGTCAGACTTTAATAG 59.086 42.308 4.05 6.34 38.95 1.73
2233 3956 2.439507 TCCATTATCTGAACTCTGGGGC 59.560 50.000 0.00 0.00 0.00 5.80
2333 4056 6.839124 TGAACTTTTCATATCAGTGGCAAT 57.161 33.333 0.00 0.00 34.08 3.56
2334 4057 7.936496 TGAACTTTTCATATCAGTGGCAATA 57.064 32.000 0.00 0.00 34.08 1.90
2337 4062 5.594317 ACTTTTCATATCAGTGGCAATACCC 59.406 40.000 0.00 0.00 37.83 3.69
2344 4069 2.830923 TCAGTGGCAATACCCCAAATTG 59.169 45.455 0.00 0.00 37.83 2.32
2345 4070 2.093553 CAGTGGCAATACCCCAAATTGG 60.094 50.000 4.74 4.74 37.83 3.16
2347 4072 2.093711 GTGGCAATACCCCAAATTGGAC 60.094 50.000 14.62 0.00 36.43 4.02
2439 4217 8.267620 TCACTCATTTACACATCACCAATAAG 57.732 34.615 0.00 0.00 0.00 1.73
2443 4221 7.402054 TCATTTACACATCACCAATAAGTCCT 58.598 34.615 0.00 0.00 0.00 3.85
2446 4224 5.755409 ACACATCACCAATAAGTCCTACA 57.245 39.130 0.00 0.00 0.00 2.74
2574 4352 4.749310 AAGCCAGAGGTGCTCGCG 62.749 66.667 0.00 0.00 38.34 5.87
2736 4514 2.067091 TTTCACGCGAGGACACGTCT 62.067 55.000 15.93 0.00 41.32 4.18
2952 4730 0.776810 TTGGGCTGAAGGTGATCCAA 59.223 50.000 0.00 0.00 35.89 3.53
3122 4900 4.393062 CGCCGAGGCTTGAATATTTGATAT 59.607 41.667 12.70 0.00 39.32 1.63
3215 5001 2.022764 TTGATACATGTGTGCCCTCG 57.977 50.000 9.11 0.00 0.00 4.63
3234 5020 6.482308 GCCCTCGTGTGTTGAGTAATTATTAT 59.518 38.462 0.00 0.00 0.00 1.28
3412 6527 8.737168 TTCTAGGTTGTGAATATCCATTTCTG 57.263 34.615 0.00 0.00 0.00 3.02
3416 6531 5.357878 GGTTGTGAATATCCATTTCTGAGCA 59.642 40.000 0.00 0.00 0.00 4.26
3417 6532 6.040166 GGTTGTGAATATCCATTTCTGAGCAT 59.960 38.462 0.00 0.00 0.00 3.79
3484 6599 7.247019 ACAAAAACAAATTCAAACAAATCCGG 58.753 30.769 0.00 0.00 0.00 5.14
3485 6600 6.370433 AAAACAAATTCAAACAAATCCGGG 57.630 33.333 0.00 0.00 0.00 5.73
3514 6629 1.063616 CATGGAAGATGCTTCTGTGCG 59.936 52.381 2.39 0.00 35.36 5.34
3516 6631 0.445436 GGAAGATGCTTCTGTGCGTG 59.555 55.000 2.39 0.00 35.36 5.34
3523 6638 1.367471 CTTCTGTGCGTGAGGTCCA 59.633 57.895 0.00 0.00 0.00 4.02
3524 6639 0.946221 CTTCTGTGCGTGAGGTCCAC 60.946 60.000 0.00 0.00 42.30 4.02
3526 6641 1.069765 CTGTGCGTGAGGTCCACTT 59.930 57.895 0.00 0.00 43.53 3.16
3527 6642 0.946221 CTGTGCGTGAGGTCCACTTC 60.946 60.000 0.00 0.00 43.53 3.01
3542 6657 5.279156 GGTCCACTTCAAATTTCAGCTCATT 60.279 40.000 0.00 0.00 0.00 2.57
3550 6665 8.665643 TTCAAATTTCAGCTCATTTGAACATT 57.334 26.923 22.63 9.05 46.87 2.71
3562 6677 7.137490 TCATTTGAACATTTGAGTAGCTCTG 57.863 36.000 0.00 0.00 0.00 3.35
3572 6687 3.919216 TGAGTAGCTCTGAGCAAAAGAC 58.081 45.455 29.49 18.05 45.56 3.01
3574 6689 3.658709 AGTAGCTCTGAGCAAAAGACAC 58.341 45.455 29.49 14.88 45.56 3.67
3575 6690 1.506493 AGCTCTGAGCAAAAGACACG 58.494 50.000 29.49 0.00 45.56 4.49
3594 6709 1.732259 CGTATTGGGTCAGAACAGCAC 59.268 52.381 0.00 0.00 0.00 4.40
3595 6710 2.084546 GTATTGGGTCAGAACAGCACC 58.915 52.381 0.00 0.00 0.00 5.01
3597 6712 0.179020 TTGGGTCAGAACAGCACCTG 60.179 55.000 0.00 0.00 37.52 4.00
3598 6713 1.053835 TGGGTCAGAACAGCACCTGA 61.054 55.000 0.00 0.00 37.11 3.86
3599 6714 0.108585 GGGTCAGAACAGCACCTGAA 59.891 55.000 0.00 0.00 40.64 3.02
3600 6715 1.230324 GGTCAGAACAGCACCTGAAC 58.770 55.000 0.00 0.00 40.64 3.18
3601 6716 1.475034 GGTCAGAACAGCACCTGAACA 60.475 52.381 0.00 0.00 44.32 3.18
3602 6717 1.869767 GTCAGAACAGCACCTGAACAG 59.130 52.381 0.00 0.00 40.64 3.16
3603 6718 1.486310 TCAGAACAGCACCTGAACAGT 59.514 47.619 0.00 0.00 36.58 3.55
3604 6719 2.698274 TCAGAACAGCACCTGAACAGTA 59.302 45.455 0.00 0.00 36.58 2.74
3605 6720 3.133901 TCAGAACAGCACCTGAACAGTAA 59.866 43.478 0.00 0.00 36.58 2.24
3606 6721 3.876914 CAGAACAGCACCTGAACAGTAAA 59.123 43.478 0.00 0.00 35.18 2.01
3607 6722 3.877508 AGAACAGCACCTGAACAGTAAAC 59.122 43.478 0.00 0.00 35.18 2.01
4293 7450 1.532316 TCTTCCGTCCAAGTCGGGT 60.532 57.895 4.58 0.00 46.82 5.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.201647 TCTGAGCTAGTACACCGCAAC 59.798 52.381 0.00 0.00 0.00 4.17
42 43 0.038709 GCGTCTGTCAAGTCTGAGCT 60.039 55.000 0.00 0.00 30.14 4.09
43 44 0.319040 TGCGTCTGTCAAGTCTGAGC 60.319 55.000 0.00 0.00 30.14 4.26
44 45 2.094803 AGATGCGTCTGTCAAGTCTGAG 60.095 50.000 7.89 0.00 32.13 3.35
50 51 0.460987 GGGGAGATGCGTCTGTCAAG 60.461 60.000 14.59 0.00 33.97 3.02
96 97 0.389817 TCACCGGACGCTGATCAAAG 60.390 55.000 9.46 0.00 0.00 2.77
179 180 3.788227 TCTGCCCATCATACCATTACC 57.212 47.619 0.00 0.00 0.00 2.85
180 181 4.910195 TCATCTGCCCATCATACCATTAC 58.090 43.478 0.00 0.00 0.00 1.89
181 182 5.316167 GTTCATCTGCCCATCATACCATTA 58.684 41.667 0.00 0.00 0.00 1.90
182 183 4.147321 GTTCATCTGCCCATCATACCATT 58.853 43.478 0.00 0.00 0.00 3.16
183 184 3.759581 GTTCATCTGCCCATCATACCAT 58.240 45.455 0.00 0.00 0.00 3.55
184 185 2.485302 CGTTCATCTGCCCATCATACCA 60.485 50.000 0.00 0.00 0.00 3.25
197 198 1.220529 CACTGCACACACGTTCATCT 58.779 50.000 0.00 0.00 0.00 2.90
247 280 1.003839 TGATGGCCACACGGAGAAC 60.004 57.895 8.16 0.00 0.00 3.01
274 307 1.369091 AATGGCGCGGACACAAGATC 61.369 55.000 8.83 0.00 0.00 2.75
310 345 1.754234 ATCAGGCATGAAACGGGGC 60.754 57.895 4.62 0.00 39.39 5.80
314 349 0.806868 AGCACATCAGGCATGAAACG 59.193 50.000 4.62 0.00 39.39 3.60
315 350 1.542915 ACAGCACATCAGGCATGAAAC 59.457 47.619 4.62 0.00 39.39 2.78
337 372 1.081892 CATCTCTTTGGGTGAGCACG 58.918 55.000 0.00 0.00 0.00 5.34
338 373 0.807496 GCATCTCTTTGGGTGAGCAC 59.193 55.000 0.00 0.00 0.00 4.40
344 379 1.668419 GCGTATGCATCTCTTTGGGT 58.332 50.000 0.19 0.00 42.15 4.51
380 422 8.753497 AAATGAATAGAGGGAGTATTTTGGTC 57.247 34.615 0.00 0.00 0.00 4.02
391 433 9.936329 AAAGCCTTATAAAAATGAATAGAGGGA 57.064 29.630 0.00 0.00 0.00 4.20
408 450 9.553064 CTGTCTGAAACATCTATAAAGCCTTAT 57.447 33.333 0.00 0.00 37.23 1.73
409 451 8.540388 ACTGTCTGAAACATCTATAAAGCCTTA 58.460 33.333 0.00 0.00 37.23 2.69
410 452 7.335422 CACTGTCTGAAACATCTATAAAGCCTT 59.665 37.037 0.00 0.00 37.23 4.35
411 453 6.820656 CACTGTCTGAAACATCTATAAAGCCT 59.179 38.462 0.00 0.00 37.23 4.58
412 454 6.595716 ACACTGTCTGAAACATCTATAAAGCC 59.404 38.462 0.00 0.00 37.23 4.35
413 455 7.459486 CACACTGTCTGAAACATCTATAAAGC 58.541 38.462 0.00 0.00 37.23 3.51
414 456 7.118245 TGCACACTGTCTGAAACATCTATAAAG 59.882 37.037 0.00 0.00 37.23 1.85
415 457 6.934083 TGCACACTGTCTGAAACATCTATAAA 59.066 34.615 0.00 0.00 37.23 1.40
416 458 6.463360 TGCACACTGTCTGAAACATCTATAA 58.537 36.000 0.00 0.00 37.23 0.98
417 459 6.036577 TGCACACTGTCTGAAACATCTATA 57.963 37.500 0.00 0.00 37.23 1.31
418 460 4.898320 TGCACACTGTCTGAAACATCTAT 58.102 39.130 0.00 0.00 37.23 1.98
419 461 4.335400 TGCACACTGTCTGAAACATCTA 57.665 40.909 0.00 0.00 37.23 1.98
420 462 3.198409 TGCACACTGTCTGAAACATCT 57.802 42.857 0.00 0.00 37.23 2.90
421 463 3.969117 TTGCACACTGTCTGAAACATC 57.031 42.857 0.00 0.00 37.23 3.06
422 464 4.082300 TGTTTTGCACACTGTCTGAAACAT 60.082 37.500 3.99 0.00 37.23 2.71
423 465 3.254411 TGTTTTGCACACTGTCTGAAACA 59.746 39.130 3.99 3.99 34.34 2.83
424 466 3.832276 TGTTTTGCACACTGTCTGAAAC 58.168 40.909 0.00 0.00 0.00 2.78
425 467 4.233789 GTTGTTTTGCACACTGTCTGAAA 58.766 39.130 0.00 0.00 33.98 2.69
426 468 3.254411 TGTTGTTTTGCACACTGTCTGAA 59.746 39.130 0.00 0.00 33.98 3.02
427 469 2.816672 TGTTGTTTTGCACACTGTCTGA 59.183 40.909 0.00 0.00 33.98 3.27
428 470 3.214697 TGTTGTTTTGCACACTGTCTG 57.785 42.857 0.00 0.00 33.98 3.51
429 471 5.574891 TTATGTTGTTTTGCACACTGTCT 57.425 34.783 0.00 0.00 33.98 3.41
430 472 6.826893 AATTATGTTGTTTTGCACACTGTC 57.173 33.333 0.00 0.00 33.98 3.51
431 473 7.608308 AAAATTATGTTGTTTTGCACACTGT 57.392 28.000 0.00 0.00 33.98 3.55
432 474 8.816144 AGTAAAATTATGTTGTTTTGCACACTG 58.184 29.630 0.00 0.00 33.98 3.66
433 475 8.940768 AGTAAAATTATGTTGTTTTGCACACT 57.059 26.923 0.00 0.00 33.98 3.55
434 476 9.419737 CAAGTAAAATTATGTTGTTTTGCACAC 57.580 29.630 0.00 0.00 33.98 3.82
435 477 9.155975 ACAAGTAAAATTATGTTGTTTTGCACA 57.844 25.926 0.00 0.00 33.96 4.57
436 478 9.631639 GACAAGTAAAATTATGTTGTTTTGCAC 57.368 29.630 0.00 0.00 33.96 4.57
437 479 9.593134 AGACAAGTAAAATTATGTTGTTTTGCA 57.407 25.926 0.00 0.00 33.96 4.08
438 480 9.848172 CAGACAAGTAAAATTATGTTGTTTTGC 57.152 29.630 5.74 0.00 31.57 3.68
443 485 9.445786 CGTTTCAGACAAGTAAAATTATGTTGT 57.554 29.630 4.47 4.47 34.08 3.32
444 486 9.658475 TCGTTTCAGACAAGTAAAATTATGTTG 57.342 29.630 0.00 0.00 0.00 3.33
445 487 9.659830 GTCGTTTCAGACAAGTAAAATTATGTT 57.340 29.630 0.00 0.00 40.65 2.71
446 488 9.052759 AGTCGTTTCAGACAAGTAAAATTATGT 57.947 29.630 0.00 0.00 43.24 2.29
447 489 9.878599 AAGTCGTTTCAGACAAGTAAAATTATG 57.121 29.630 0.00 0.00 43.24 1.90
448 490 9.878599 CAAGTCGTTTCAGACAAGTAAAATTAT 57.121 29.630 0.00 0.00 43.24 1.28
449 491 8.885722 ACAAGTCGTTTCAGACAAGTAAAATTA 58.114 29.630 0.00 0.00 43.24 1.40
450 492 7.758495 ACAAGTCGTTTCAGACAAGTAAAATT 58.242 30.769 0.00 0.00 43.24 1.82
451 493 7.316544 ACAAGTCGTTTCAGACAAGTAAAAT 57.683 32.000 0.00 0.00 43.24 1.82
452 494 6.730960 ACAAGTCGTTTCAGACAAGTAAAA 57.269 33.333 0.00 0.00 43.24 1.52
453 495 7.830940 TTACAAGTCGTTTCAGACAAGTAAA 57.169 32.000 9.98 0.00 43.24 2.01
454 496 7.830940 TTTACAAGTCGTTTCAGACAAGTAA 57.169 32.000 0.00 5.44 43.24 2.24
455 497 7.546667 ACTTTTACAAGTCGTTTCAGACAAGTA 59.453 33.333 0.00 0.00 39.15 2.24
456 498 6.370718 ACTTTTACAAGTCGTTTCAGACAAGT 59.629 34.615 0.00 0.84 39.15 3.16
457 499 6.682863 CACTTTTACAAGTCGTTTCAGACAAG 59.317 38.462 0.00 0.00 41.69 3.16
458 500 6.369340 TCACTTTTACAAGTCGTTTCAGACAA 59.631 34.615 0.00 0.00 41.69 3.18
459 501 5.870433 TCACTTTTACAAGTCGTTTCAGACA 59.130 36.000 0.00 0.00 41.69 3.41
460 502 6.340537 TCACTTTTACAAGTCGTTTCAGAC 57.659 37.500 0.00 0.00 41.69 3.51
461 503 6.454583 CGTTCACTTTTACAAGTCGTTTCAGA 60.455 38.462 0.00 0.00 41.69 3.27
462 504 5.671140 CGTTCACTTTTACAAGTCGTTTCAG 59.329 40.000 0.00 0.00 41.69 3.02
463 505 5.446206 CCGTTCACTTTTACAAGTCGTTTCA 60.446 40.000 0.00 0.00 41.69 2.69
464 506 4.959757 CCGTTCACTTTTACAAGTCGTTTC 59.040 41.667 0.00 0.00 41.69 2.78
465 507 4.630940 TCCGTTCACTTTTACAAGTCGTTT 59.369 37.500 0.00 0.00 41.69 3.60
466 508 4.183101 TCCGTTCACTTTTACAAGTCGTT 58.817 39.130 0.00 0.00 41.69 3.85
467 509 3.784338 TCCGTTCACTTTTACAAGTCGT 58.216 40.909 0.00 0.00 41.69 4.34
468 510 4.377022 CCATCCGTTCACTTTTACAAGTCG 60.377 45.833 0.00 0.00 41.69 4.18
469 511 4.753107 TCCATCCGTTCACTTTTACAAGTC 59.247 41.667 0.00 0.00 41.69 3.01
470 512 4.710324 TCCATCCGTTCACTTTTACAAGT 58.290 39.130 0.00 0.00 44.72 3.16
471 513 4.755123 ACTCCATCCGTTCACTTTTACAAG 59.245 41.667 0.00 0.00 35.92 3.16
472 514 4.710324 ACTCCATCCGTTCACTTTTACAA 58.290 39.130 0.00 0.00 0.00 2.41
473 515 4.345859 ACTCCATCCGTTCACTTTTACA 57.654 40.909 0.00 0.00 0.00 2.41
474 516 4.628766 GGTACTCCATCCGTTCACTTTTAC 59.371 45.833 0.00 0.00 0.00 2.01
475 517 4.283978 TGGTACTCCATCCGTTCACTTTTA 59.716 41.667 0.00 0.00 39.03 1.52
476 518 3.071892 TGGTACTCCATCCGTTCACTTTT 59.928 43.478 0.00 0.00 39.03 2.27
477 519 2.635915 TGGTACTCCATCCGTTCACTTT 59.364 45.455 0.00 0.00 39.03 2.66
478 520 2.253610 TGGTACTCCATCCGTTCACTT 58.746 47.619 0.00 0.00 39.03 3.16
479 521 1.933021 TGGTACTCCATCCGTTCACT 58.067 50.000 0.00 0.00 39.03 3.41
480 522 2.754946 TTGGTACTCCATCCGTTCAC 57.245 50.000 0.00 0.00 43.91 3.18
481 523 3.992943 ATTTGGTACTCCATCCGTTCA 57.007 42.857 0.00 0.00 43.91 3.18
482 524 6.317893 ACAAATATTTGGTACTCCATCCGTTC 59.682 38.462 27.43 0.00 43.91 3.95
483 525 6.184789 ACAAATATTTGGTACTCCATCCGTT 58.815 36.000 27.43 3.28 43.91 4.44
484 526 5.751586 ACAAATATTTGGTACTCCATCCGT 58.248 37.500 27.43 3.68 43.91 4.69
485 527 5.820423 TGACAAATATTTGGTACTCCATCCG 59.180 40.000 27.43 3.04 43.91 4.18
486 528 7.054124 TCTGACAAATATTTGGTACTCCATCC 58.946 38.462 27.43 7.79 43.91 3.51
487 529 7.254932 GCTCTGACAAATATTTGGTACTCCATC 60.255 40.741 27.43 15.64 43.91 3.51
488 530 6.543831 GCTCTGACAAATATTTGGTACTCCAT 59.456 38.462 27.43 8.03 43.91 3.41
489 531 5.880332 GCTCTGACAAATATTTGGTACTCCA 59.120 40.000 27.43 15.24 42.34 3.86
490 532 5.006746 CGCTCTGACAAATATTTGGTACTCC 59.993 44.000 27.43 13.16 42.34 3.85
491 533 5.581085 ACGCTCTGACAAATATTTGGTACTC 59.419 40.000 27.43 17.72 42.34 2.59
495 537 3.689649 GGACGCTCTGACAAATATTTGGT 59.310 43.478 27.43 15.82 42.34 3.67
504 546 0.175760 GGCTATGGACGCTCTGACAA 59.824 55.000 0.00 0.00 0.00 3.18
540 582 5.360591 CCAGACCTAAAGTGTATGGACATC 58.639 45.833 0.00 0.00 45.74 3.06
555 597 1.281419 TTCCATTTCGCCCAGACCTA 58.719 50.000 0.00 0.00 0.00 3.08
556 598 0.404040 TTTCCATTTCGCCCAGACCT 59.596 50.000 0.00 0.00 0.00 3.85
600 653 5.033522 AGTTTATTCTAGGAGTCCAGCCTT 58.966 41.667 12.86 0.00 36.96 4.35
603 656 5.599999 TCAGTTTATTCTAGGAGTCCAGC 57.400 43.478 12.86 0.00 0.00 4.85
604 657 6.481644 GCATTCAGTTTATTCTAGGAGTCCAG 59.518 42.308 12.86 7.10 0.00 3.86
605 658 6.070251 TGCATTCAGTTTATTCTAGGAGTCCA 60.070 38.462 12.86 0.00 0.00 4.02
606 659 6.349300 TGCATTCAGTTTATTCTAGGAGTCC 58.651 40.000 0.00 0.00 0.00 3.85
607 660 7.268586 TCTGCATTCAGTTTATTCTAGGAGTC 58.731 38.462 0.00 0.00 41.10 3.36
608 661 7.187824 TCTGCATTCAGTTTATTCTAGGAGT 57.812 36.000 0.00 0.00 41.10 3.85
609 662 8.498054 TTTCTGCATTCAGTTTATTCTAGGAG 57.502 34.615 0.00 0.00 41.10 3.69
610 663 7.554118 CCTTTCTGCATTCAGTTTATTCTAGGA 59.446 37.037 0.00 0.00 41.10 2.94
611 664 7.201767 CCCTTTCTGCATTCAGTTTATTCTAGG 60.202 40.741 0.00 0.00 41.10 3.02
612 665 7.680588 GCCCTTTCTGCATTCAGTTTATTCTAG 60.681 40.741 0.00 0.00 41.10 2.43
613 666 6.095440 GCCCTTTCTGCATTCAGTTTATTCTA 59.905 38.462 0.00 0.00 41.10 2.10
614 667 5.105595 GCCCTTTCTGCATTCAGTTTATTCT 60.106 40.000 0.00 0.00 41.10 2.40
615 668 5.105063 GCCCTTTCTGCATTCAGTTTATTC 58.895 41.667 0.00 0.00 41.10 1.75
616 669 4.527816 TGCCCTTTCTGCATTCAGTTTATT 59.472 37.500 0.00 0.00 41.10 1.40
617 670 4.088634 TGCCCTTTCTGCATTCAGTTTAT 58.911 39.130 0.00 0.00 41.10 1.40
618 671 3.495331 TGCCCTTTCTGCATTCAGTTTA 58.505 40.909 0.00 0.00 41.10 2.01
619 672 2.318908 TGCCCTTTCTGCATTCAGTTT 58.681 42.857 0.00 0.00 41.10 2.66
620 673 1.999648 TGCCCTTTCTGCATTCAGTT 58.000 45.000 0.00 0.00 41.10 3.16
628 778 1.030457 CAGATCCATGCCCTTTCTGC 58.970 55.000 0.00 0.00 0.00 4.26
686 1997 2.505628 ACATGCACGCACAAATTGAA 57.494 40.000 0.00 0.00 0.00 2.69
688 1999 3.735240 ACTAAACATGCACGCACAAATTG 59.265 39.130 0.00 0.00 0.00 2.32
691 2002 3.111838 CAACTAAACATGCACGCACAAA 58.888 40.909 0.00 0.00 0.00 2.83
693 2004 1.599171 GCAACTAAACATGCACGCACA 60.599 47.619 0.00 0.00 0.00 4.57
694 2005 1.052287 GCAACTAAACATGCACGCAC 58.948 50.000 0.00 0.00 0.00 5.34
695 2006 0.950836 AGCAACTAAACATGCACGCA 59.049 45.000 0.00 0.00 0.00 5.24
696 2007 2.892373 TAGCAACTAAACATGCACGC 57.108 45.000 0.00 0.00 0.00 5.34
732 2094 1.227943 CAACGCGGGATCATGGGAT 60.228 57.895 12.47 0.00 36.13 3.85
733 2095 1.331399 TACAACGCGGGATCATGGGA 61.331 55.000 12.47 0.00 0.00 4.37
734 2096 0.250295 ATACAACGCGGGATCATGGG 60.250 55.000 12.47 0.00 0.00 4.00
735 2097 0.867746 CATACAACGCGGGATCATGG 59.132 55.000 12.47 0.00 0.00 3.66
736 2098 1.581934 ACATACAACGCGGGATCATG 58.418 50.000 12.47 9.60 0.00 3.07
737 2099 3.678056 ATACATACAACGCGGGATCAT 57.322 42.857 12.47 0.00 0.00 2.45
738 2100 3.318557 TGTATACATACAACGCGGGATCA 59.681 43.478 12.47 0.00 40.08 2.92
739 2101 3.671928 GTGTATACATACAACGCGGGATC 59.328 47.826 12.47 0.00 44.11 3.36
740 2102 3.553508 GGTGTATACATACAACGCGGGAT 60.554 47.826 12.47 0.00 44.11 3.85
741 2103 2.223782 GGTGTATACATACAACGCGGGA 60.224 50.000 12.47 0.00 44.11 5.14
742 2104 2.129607 GGTGTATACATACAACGCGGG 58.870 52.381 12.47 4.46 44.11 6.13
747 2109 6.690098 CACTGTAGACGGTGTATACATACAAC 59.310 42.308 9.18 7.25 45.65 3.32
748 2110 6.788243 CACTGTAGACGGTGTATACATACAA 58.212 40.000 9.18 0.00 45.65 2.41
749 2111 6.367686 CACTGTAGACGGTGTATACATACA 57.632 41.667 9.18 11.65 45.65 2.29
768 2130 1.530293 GCTCAGCAACAGACTTCACTG 59.470 52.381 0.00 0.00 42.78 3.66
843 2205 5.890424 AAAGACTTGGAAAACTTGACGAA 57.110 34.783 0.00 0.00 0.00 3.85
867 2229 2.292653 TGGGAAAGTAGGGAGGAATCGA 60.293 50.000 0.00 0.00 0.00 3.59
897 2261 3.691342 CGTGGCGAGGTGGAAGGA 61.691 66.667 0.00 0.00 0.00 3.36
899 2263 2.432628 GTCGTGGCGAGGTGGAAG 60.433 66.667 0.00 0.00 36.23 3.46
900 2264 4.351938 CGTCGTGGCGAGGTGGAA 62.352 66.667 3.48 0.00 36.23 3.53
909 2273 1.269621 ACTTATAGATGGCGTCGTGGC 60.270 52.381 0.13 0.00 45.12 5.01
914 2279 2.415625 CGGCCTACTTATAGATGGCGTC 60.416 54.545 0.00 0.00 44.07 5.19
915 2280 1.544691 CGGCCTACTTATAGATGGCGT 59.455 52.381 0.00 0.00 44.07 5.68
950 2315 0.463654 TTGAGCTCGTTGTGGTGCTT 60.464 50.000 9.64 0.00 35.76 3.91
989 2354 0.957395 GGGTGTGGCTGAGTGATGTG 60.957 60.000 0.00 0.00 0.00 3.21
1006 2371 2.321263 ATCAGCTCGATGCAGGTGGG 62.321 60.000 9.09 0.00 45.94 4.61
1674 3086 2.854777 GTCGATCATCCACTTGAACTCG 59.145 50.000 0.00 0.00 32.22 4.18
1973 3391 4.162040 AGGAAAGCAATAGCAGTAGCAT 57.838 40.909 0.00 0.00 45.49 3.79
2009 3455 8.170061 AGCAGGGGATAAATATGCAGTAATTAA 58.830 33.333 0.00 0.00 39.34 1.40
2011 3457 6.555711 AGCAGGGGATAAATATGCAGTAATT 58.444 36.000 0.00 0.00 39.34 1.40
2013 3459 5.582950 AGCAGGGGATAAATATGCAGTAA 57.417 39.130 0.00 0.00 39.34 2.24
2015 3461 4.147321 CAAGCAGGGGATAAATATGCAGT 58.853 43.478 0.00 0.00 39.34 4.40
2016 3462 3.057033 GCAAGCAGGGGATAAATATGCAG 60.057 47.826 0.00 0.00 39.34 4.41
2017 3463 2.892852 GCAAGCAGGGGATAAATATGCA 59.107 45.455 0.00 0.00 39.34 3.96
2018 3464 3.160269 AGCAAGCAGGGGATAAATATGC 58.840 45.455 0.00 0.00 37.15 3.14
2019 3465 3.760684 GGAGCAAGCAGGGGATAAATATG 59.239 47.826 0.00 0.00 0.00 1.78
2022 3468 1.855599 AGGAGCAAGCAGGGGATAAAT 59.144 47.619 0.00 0.00 0.00 1.40
2151 3861 8.244113 CAGACGATAGCAACAGGACATAATATA 58.756 37.037 0.00 0.00 42.67 0.86
2174 3896 3.538591 TCGCTTAGACCGATAGAACAGA 58.461 45.455 0.00 0.00 39.76 3.41
2175 3897 3.312973 ACTCGCTTAGACCGATAGAACAG 59.687 47.826 0.00 0.00 39.76 3.16
2176 3898 3.276857 ACTCGCTTAGACCGATAGAACA 58.723 45.455 0.00 0.00 39.76 3.18
2177 3899 3.311871 TGACTCGCTTAGACCGATAGAAC 59.688 47.826 0.00 0.00 39.76 3.01
2178 3900 3.538591 TGACTCGCTTAGACCGATAGAA 58.461 45.455 0.00 0.00 39.76 2.10
2179 3901 3.132160 CTGACTCGCTTAGACCGATAGA 58.868 50.000 0.00 0.00 39.76 1.98
2180 3902 3.059461 GTCTGACTCGCTTAGACCGATAG 60.059 52.174 0.00 0.00 35.86 2.08
2181 3903 2.871022 GTCTGACTCGCTTAGACCGATA 59.129 50.000 0.00 0.00 35.86 2.92
2182 3904 1.671845 GTCTGACTCGCTTAGACCGAT 59.328 52.381 0.00 0.00 35.86 4.18
2183 3905 1.085091 GTCTGACTCGCTTAGACCGA 58.915 55.000 0.00 0.00 35.86 4.69
2184 3906 1.088306 AGTCTGACTCGCTTAGACCG 58.912 55.000 4.06 0.00 41.26 4.79
2185 3907 3.579335 AAAGTCTGACTCGCTTAGACC 57.421 47.619 11.31 0.00 41.26 3.85
2210 3932 4.455606 CCCCAGAGTTCAGATAATGGAAC 58.544 47.826 0.00 0.00 42.82 3.62
2233 3956 6.925165 GTGCCTATCAACAATCCCATTATTTG 59.075 38.462 0.00 0.00 0.00 2.32
2330 4053 2.165437 CACGGTCCAATTTGGGGTATTG 59.835 50.000 15.37 3.62 38.32 1.90
2331 4054 2.041891 TCACGGTCCAATTTGGGGTATT 59.958 45.455 15.37 0.00 38.32 1.89
2333 4056 1.065647 TCACGGTCCAATTTGGGGTA 58.934 50.000 15.37 0.00 38.32 3.69
2334 4057 0.538746 GTCACGGTCCAATTTGGGGT 60.539 55.000 15.37 8.43 38.32 4.95
2337 4062 2.926159 GCAATGTCACGGTCCAATTTGG 60.926 50.000 9.28 9.28 39.43 3.28
2344 4069 1.539388 TGAATTGCAATGTCACGGTCC 59.461 47.619 13.82 0.00 0.00 4.46
2345 4070 2.987413 TGAATTGCAATGTCACGGTC 57.013 45.000 13.82 5.39 0.00 4.79
2347 4072 5.639757 TCTAAATGAATTGCAATGTCACGG 58.360 37.500 13.82 9.48 0.00 4.94
2439 4217 7.360946 GGTGTTGATTAGTGTGAAATGTAGGAC 60.361 40.741 0.00 0.00 0.00 3.85
2443 4221 7.994425 ATGGTGTTGATTAGTGTGAAATGTA 57.006 32.000 0.00 0.00 0.00 2.29
2446 4224 8.420222 TCAAAATGGTGTTGATTAGTGTGAAAT 58.580 29.630 0.00 0.00 30.08 2.17
2574 4352 0.811281 CCAATTCCTCGGTGGCTTTC 59.189 55.000 0.00 0.00 35.26 2.62
2589 4367 2.434331 CCCACCACACGGTCCAAT 59.566 61.111 0.00 0.00 44.71 3.16
2736 4514 1.338973 GGGATGTCGTAGCCGTTGATA 59.661 52.381 0.00 0.00 34.98 2.15
2922 4700 1.802553 TCAGCCCAAGACTATACCCC 58.197 55.000 0.00 0.00 0.00 4.95
2952 4730 0.896226 GGAGGTTCGCCAGACTTACT 59.104 55.000 0.00 0.00 40.60 2.24
3057 4835 4.988716 TCCACGACGGCCTCCAGT 62.989 66.667 0.00 0.00 33.14 4.00
3122 4900 0.813610 CTCAACACACGAGGGCACAA 60.814 55.000 0.00 0.00 0.00 3.33
3266 6381 9.665264 GACCATCTTTTACACTTTTCTTTACAG 57.335 33.333 0.00 0.00 0.00 2.74
3268 6383 8.553696 TCGACCATCTTTTACACTTTTCTTTAC 58.446 33.333 0.00 0.00 0.00 2.01
3339 6454 4.675671 CGAGGCTTTGATAGAGACGTCTTT 60.676 45.833 21.08 17.13 33.84 2.52
3412 6527 2.733552 CGGTGCATATGAGTACATGCTC 59.266 50.000 6.97 11.61 46.19 4.26
3416 6531 3.578282 TCATCCGGTGCATATGAGTACAT 59.422 43.478 6.97 0.00 40.16 2.29
3417 6532 2.962421 TCATCCGGTGCATATGAGTACA 59.038 45.455 6.97 0.00 0.00 2.90
3494 6609 1.063616 CGCACAGAAGCATCTTCCATG 59.936 52.381 3.20 3.83 32.03 3.66
3498 6613 1.392853 CTCACGCACAGAAGCATCTTC 59.607 52.381 0.00 0.00 32.03 2.87
3514 6629 4.557496 GCTGAAATTTGAAGTGGACCTCAC 60.557 45.833 0.00 0.00 46.39 3.51
3516 6631 3.823304 AGCTGAAATTTGAAGTGGACCTC 59.177 43.478 0.00 0.00 0.00 3.85
3526 6641 8.552865 CAAATGTTCAAATGAGCTGAAATTTGA 58.447 29.630 18.22 18.22 46.06 2.69
3527 6642 8.552865 TCAAATGTTCAAATGAGCTGAAATTTG 58.447 29.630 15.29 15.29 42.53 2.32
3542 6657 4.692625 GCTCAGAGCTACTCAAATGTTCAA 59.307 41.667 15.78 0.00 38.45 2.69
3550 6665 4.202253 TGTCTTTTGCTCAGAGCTACTCAA 60.202 41.667 23.15 6.01 42.97 3.02
3562 6677 2.812011 ACCCAATACGTGTCTTTTGCTC 59.188 45.455 0.00 0.00 0.00 4.26
3572 6687 1.732259 GCTGTTCTGACCCAATACGTG 59.268 52.381 0.00 0.00 0.00 4.49
3574 6689 1.732259 GTGCTGTTCTGACCCAATACG 59.268 52.381 0.00 0.00 0.00 3.06
3575 6690 2.084546 GGTGCTGTTCTGACCCAATAC 58.915 52.381 0.00 0.00 0.00 1.89
4293 7450 1.741528 TACGACGATGAGTAGCACCA 58.258 50.000 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.