Multiple sequence alignment - TraesCS5D01G367100

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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 TraesCS5D01G367100 chr5D 100.000 3498 0 0 1 3498 443520667 443524164 0.000000e+00 6460.0
1 TraesCS5D01G367100 chr5D 96.977 1555 36 2 1951 3498 351321395 351322945 0.000000e+00 2601.0
2 TraesCS5D01G367100 chr7D 97.051 1560 36 3 1947 3498 530866188 530864631 0.000000e+00 2617.0
3 TraesCS5D01G367100 chr7D 96.923 1560 40 2 1947 3498 498406735 498408294 0.000000e+00 2608.0
4 TraesCS5D01G367100 chr7D 96.729 1559 43 2 1947 3497 596121821 596120263 0.000000e+00 2590.0
5 TraesCS5D01G367100 chr7D 96.538 1560 43 4 1947 3498 70679822 70678266 0.000000e+00 2571.0
6 TraesCS5D01G367100 chr7D 94.185 1582 45 15 1947 3498 11643490 11645054 0.000000e+00 2368.0
7 TraesCS5D01G367100 chr7D 96.807 1284 36 4 588 1869 592400973 592402253 0.000000e+00 2139.0
8 TraesCS5D01G367100 chr7D 96.651 1284 32 4 588 1869 530867456 530866182 0.000000e+00 2122.0
9 TraesCS5D01G367100 chr7D 87.477 543 25 20 2965 3498 58114068 58113560 1.400000e-163 586.0
10 TraesCS5D01G367100 chr7D 91.304 368 17 3 3146 3498 592402694 592403061 4.060000e-134 488.0
11 TraesCS5D01G367100 chr4D 95.727 1568 50 9 1947 3498 440464178 440462612 0.000000e+00 2508.0
12 TraesCS5D01G367100 chr4D 97.512 1286 29 3 586 1869 440465456 440464172 0.000000e+00 2194.0
13 TraesCS5D01G367100 chr7A 94.540 1575 59 5 1947 3498 164738017 164736447 0.000000e+00 2407.0
14 TraesCS5D01G367100 chr7A 94.311 1582 57 5 1947 3498 642166746 642168324 0.000000e+00 2392.0
15 TraesCS5D01G367100 chr7A 93.986 1563 67 9 1950 3498 134462998 134464547 0.000000e+00 2340.0
16 TraesCS5D01G367100 chr7A 94.652 1178 55 5 589 1759 47492055 47490879 0.000000e+00 1820.0
17 TraesCS5D01G367100 chr7A 91.537 1288 59 14 585 1869 675422255 675423495 0.000000e+00 1729.0
18 TraesCS5D01G367100 chr7A 87.594 266 18 10 1605 1867 707671468 707671721 9.500000e-76 294.0
19 TraesCS5D01G367100 chr7A 87.405 262 18 10 1608 1867 13132434 13132186 1.590000e-73 287.0
20 TraesCS5D01G367100 chr2A 95.035 1289 58 6 585 1869 458970806 458969520 0.000000e+00 2021.0
21 TraesCS5D01G367100 chr2A 94.601 1278 54 5 594 1869 514763732 514764996 0.000000e+00 1964.0
22 TraesCS5D01G367100 chr2A 94.276 1188 52 12 582 1759 764066991 764068172 0.000000e+00 1803.0
23 TraesCS5D01G367100 chr2A 87.405 262 19 9 1608 1867 2767026 2766777 4.420000e-74 289.0
24 TraesCS5D01G367100 chr2A 87.023 262 20 9 1608 1867 734934048 734933799 2.060000e-72 283.0
25 TraesCS5D01G367100 chr6A 94.741 1179 54 5 588 1759 134201700 134202877 0.000000e+00 1827.0
26 TraesCS5D01G367100 chr6A 96.875 96 2 1 1857 1952 262052040 262052134 3.610000e-35 159.0
27 TraesCS5D01G367100 chr5A 94.496 1181 56 6 587 1759 402974415 402975594 0.000000e+00 1812.0
28 TraesCS5D01G367100 chr5A 94.228 1178 57 9 588 1759 513856834 513858006 0.000000e+00 1788.0
29 TraesCS5D01G367100 chr5A 91.583 499 34 5 1 499 559787719 559788209 0.000000e+00 682.0
30 TraesCS5D01G367100 chr5A 97.872 94 2 0 1860 1953 523751671 523751764 2.790000e-36 163.0
31 TraesCS5D01G367100 chr5A 91.525 59 3 1 531 587 559788216 559788274 2.890000e-11 80.5
32 TraesCS5D01G367100 chr2D 87.048 525 44 10 2998 3498 102989460 102988936 3.920000e-159 571.0
33 TraesCS5D01G367100 chr2B 97.849 93 2 0 1865 1957 738486658 738486750 1.000000e-35 161.0
34 TraesCS5D01G367100 chr6D 96.875 96 2 1 1857 1952 221219306 221219400 3.610000e-35 159.0
35 TraesCS5D01G367100 chr5B 96.875 96 2 1 1859 1953 621231937 621232032 3.610000e-35 159.0
36 TraesCS5D01G367100 chr4A 96.809 94 3 0 1867 1960 661959874 661959781 1.300000e-34 158.0
37 TraesCS5D01G367100 chr4A 90.517 116 8 3 1838 1952 735658299 735658186 2.180000e-32 150.0
38 TraesCS5D01G367100 chr6B 94.118 102 4 2 1853 1952 342268377 342268478 1.680000e-33 154.0
39 TraesCS5D01G367100 chr4B 90.179 112 8 3 1843 1952 31522751 31522641 3.640000e-30 143.0


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 TraesCS5D01G367100 chr5D 443520667 443524164 3497 False 6460.00 6460 100.0000 1 3498 1 chr5D.!!$F2 3497
1 TraesCS5D01G367100 chr5D 351321395 351322945 1550 False 2601.00 2601 96.9770 1951 3498 1 chr5D.!!$F1 1547
2 TraesCS5D01G367100 chr7D 498406735 498408294 1559 False 2608.00 2608 96.9230 1947 3498 1 chr7D.!!$F2 1551
3 TraesCS5D01G367100 chr7D 596120263 596121821 1558 True 2590.00 2590 96.7290 1947 3497 1 chr7D.!!$R3 1550
4 TraesCS5D01G367100 chr7D 70678266 70679822 1556 True 2571.00 2571 96.5380 1947 3498 1 chr7D.!!$R2 1551
5 TraesCS5D01G367100 chr7D 530864631 530867456 2825 True 2369.50 2617 96.8510 588 3498 2 chr7D.!!$R4 2910
6 TraesCS5D01G367100 chr7D 11643490 11645054 1564 False 2368.00 2368 94.1850 1947 3498 1 chr7D.!!$F1 1551
7 TraesCS5D01G367100 chr7D 592400973 592403061 2088 False 1313.50 2139 94.0555 588 3498 2 chr7D.!!$F3 2910
8 TraesCS5D01G367100 chr7D 58113560 58114068 508 True 586.00 586 87.4770 2965 3498 1 chr7D.!!$R1 533
9 TraesCS5D01G367100 chr4D 440462612 440465456 2844 True 2351.00 2508 96.6195 586 3498 2 chr4D.!!$R1 2912
10 TraesCS5D01G367100 chr7A 164736447 164738017 1570 True 2407.00 2407 94.5400 1947 3498 1 chr7A.!!$R3 1551
11 TraesCS5D01G367100 chr7A 642166746 642168324 1578 False 2392.00 2392 94.3110 1947 3498 1 chr7A.!!$F2 1551
12 TraesCS5D01G367100 chr7A 134462998 134464547 1549 False 2340.00 2340 93.9860 1950 3498 1 chr7A.!!$F1 1548
13 TraesCS5D01G367100 chr7A 47490879 47492055 1176 True 1820.00 1820 94.6520 589 1759 1 chr7A.!!$R2 1170
14 TraesCS5D01G367100 chr7A 675422255 675423495 1240 False 1729.00 1729 91.5370 585 1869 1 chr7A.!!$F3 1284
15 TraesCS5D01G367100 chr2A 458969520 458970806 1286 True 2021.00 2021 95.0350 585 1869 1 chr2A.!!$R2 1284
16 TraesCS5D01G367100 chr2A 514763732 514764996 1264 False 1964.00 1964 94.6010 594 1869 1 chr2A.!!$F1 1275
17 TraesCS5D01G367100 chr2A 764066991 764068172 1181 False 1803.00 1803 94.2760 582 1759 1 chr2A.!!$F2 1177
18 TraesCS5D01G367100 chr6A 134201700 134202877 1177 False 1827.00 1827 94.7410 588 1759 1 chr6A.!!$F1 1171
19 TraesCS5D01G367100 chr5A 402974415 402975594 1179 False 1812.00 1812 94.4960 587 1759 1 chr5A.!!$F1 1172
20 TraesCS5D01G367100 chr5A 513856834 513858006 1172 False 1788.00 1788 94.2280 588 1759 1 chr5A.!!$F2 1171
21 TraesCS5D01G367100 chr5A 559787719 559788274 555 False 381.25 682 91.5540 1 587 2 chr5A.!!$F4 586
22 TraesCS5D01G367100 chr2D 102988936 102989460 524 True 571.00 571 87.0480 2998 3498 1 chr2D.!!$R1 500

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
525 526 0.249120 CCATAGGTGCCTCGTTGTCA 59.751 55.0 0.00 0.00 0.0 3.58 F
529 530 0.396435 AGGTGCCTCGTTGTCAATGA 59.604 50.0 7.27 7.27 0.0 2.57 F
1318 1331 0.694444 ACTCCTGGGTTGTCCTGTGT 60.694 55.0 0.00 0.00 36.2 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1945 1975 1.002087 CCACAGTTCACACCTACTCCC 59.998 57.143 0.0 0.0 0.0 4.30 R
1946 1976 1.002087 CCCACAGTTCACACCTACTCC 59.998 57.143 0.0 0.0 0.0 3.85 R
2546 2578 0.742505 ATGCATGACATTCCAAGGCG 59.257 50.000 0.0 0.0 34.4 5.52 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
18 19 2.029743 CCACACAACCCCAACGAAG 58.970 57.895 0.00 0.00 0.00 3.79
146 147 3.141488 CACCGACGGGAGGAGGAG 61.141 72.222 20.00 0.00 36.97 3.69
148 149 4.124943 CCGACGGGAGGAGGAGGA 62.125 72.222 5.81 0.00 34.06 3.71
150 151 1.681327 CGACGGGAGGAGGAGGAAA 60.681 63.158 0.00 0.00 0.00 3.13
151 152 1.668101 CGACGGGAGGAGGAGGAAAG 61.668 65.000 0.00 0.00 0.00 2.62
152 153 0.324460 GACGGGAGGAGGAGGAAAGA 60.324 60.000 0.00 0.00 0.00 2.52
153 154 0.615261 ACGGGAGGAGGAGGAAAGAC 60.615 60.000 0.00 0.00 0.00 3.01
204 205 6.799441 TGTCGGATTTTAAACATGACAAATCG 59.201 34.615 0.00 4.97 36.77 3.34
215 216 8.955061 AAACATGACAAATCGAGTCTTTTATG 57.045 30.769 0.00 3.33 36.94 1.90
242 243 0.776810 ATGGTTGTGTGGGGATGACA 59.223 50.000 0.00 0.00 0.00 3.58
249 250 5.469479 GTTGTGTGGGGATGACAAATTTAG 58.531 41.667 0.00 0.00 31.62 1.85
308 309 3.899734 TGAAACGGATTTGTCATGCTTG 58.100 40.909 0.00 0.00 0.00 4.01
330 331 8.817100 GCTTGCCAACTAAATATAAATTTCCAC 58.183 33.333 0.00 0.00 36.67 4.02
349 350 9.920946 ATTTCCACATAAAAAGGCTCTATTAGA 57.079 29.630 0.00 0.00 0.00 2.10
350 351 8.964476 TTCCACATAAAAAGGCTCTATTAGAG 57.036 34.615 15.17 15.17 45.04 2.43
351 352 8.090788 TCCACATAAAAAGGCTCTATTAGAGT 57.909 34.615 19.40 4.07 44.12 3.24
352 353 8.204836 TCCACATAAAAAGGCTCTATTAGAGTC 58.795 37.037 16.02 16.02 46.94 3.36
393 394 9.787532 AACATTTATGTGCAAATACATACACTC 57.212 29.630 0.00 0.00 41.75 3.51
394 395 8.122330 ACATTTATGTGCAAATACATACACTCG 58.878 33.333 0.00 0.00 41.75 4.18
395 396 6.597262 TTATGTGCAAATACATACACTCGG 57.403 37.500 0.00 0.00 41.75 4.63
396 397 3.932822 TGTGCAAATACATACACTCGGT 58.067 40.909 0.00 0.00 34.14 4.69
397 398 3.930229 TGTGCAAATACATACACTCGGTC 59.070 43.478 0.00 0.00 34.14 4.79
398 399 3.930229 GTGCAAATACATACACTCGGTCA 59.070 43.478 0.00 0.00 0.00 4.02
399 400 4.570772 GTGCAAATACATACACTCGGTCAT 59.429 41.667 0.00 0.00 0.00 3.06
400 401 5.751509 GTGCAAATACATACACTCGGTCATA 59.248 40.000 0.00 0.00 0.00 2.15
401 402 5.751509 TGCAAATACATACACTCGGTCATAC 59.248 40.000 0.00 0.00 0.00 2.39
402 403 5.751509 GCAAATACATACACTCGGTCATACA 59.248 40.000 0.00 0.00 0.00 2.29
403 404 6.292168 GCAAATACATACACTCGGTCATACAC 60.292 42.308 0.00 0.00 0.00 2.90
404 405 6.459670 AATACATACACTCGGTCATACACA 57.540 37.500 0.00 0.00 0.00 3.72
405 406 4.106029 ACATACACTCGGTCATACACAC 57.894 45.455 0.00 0.00 0.00 3.82
406 407 3.508402 ACATACACTCGGTCATACACACA 59.492 43.478 0.00 0.00 0.00 3.72
407 408 2.724977 ACACTCGGTCATACACACAG 57.275 50.000 0.00 0.00 0.00 3.66
408 409 1.961394 ACACTCGGTCATACACACAGT 59.039 47.619 0.00 0.00 0.00 3.55
409 410 3.151554 ACACTCGGTCATACACACAGTA 58.848 45.455 0.00 0.00 37.06 2.74
410 411 3.762288 ACACTCGGTCATACACACAGTAT 59.238 43.478 0.00 0.00 44.20 2.12
444 445 9.830975 AACACAATACATATACAGATGCTTACA 57.169 29.630 0.00 0.00 0.00 2.41
450 451 9.788960 ATACATATACAGATGCTTACATACACG 57.211 33.333 0.00 0.00 36.35 4.49
451 452 6.586463 ACATATACAGATGCTTACATACACGC 59.414 38.462 0.00 0.00 36.35 5.34
452 453 3.245518 ACAGATGCTTACATACACGCA 57.754 42.857 0.00 0.00 36.35 5.24
453 454 3.797039 ACAGATGCTTACATACACGCAT 58.203 40.909 0.00 0.00 44.97 4.73
454 455 4.944048 ACAGATGCTTACATACACGCATA 58.056 39.130 0.00 0.00 42.60 3.14
455 456 5.541845 ACAGATGCTTACATACACGCATAT 58.458 37.500 0.00 0.00 42.60 1.78
456 457 6.687604 ACAGATGCTTACATACACGCATATA 58.312 36.000 0.00 0.00 42.60 0.86
457 458 6.586463 ACAGATGCTTACATACACGCATATAC 59.414 38.462 0.00 0.00 42.60 1.47
458 459 6.586082 CAGATGCTTACATACACGCATATACA 59.414 38.462 0.00 0.00 42.60 2.29
459 460 6.586463 AGATGCTTACATACACGCATATACAC 59.414 38.462 0.00 0.00 42.60 2.90
460 461 5.838529 TGCTTACATACACGCATATACACT 58.161 37.500 0.00 0.00 0.00 3.55
461 462 5.918576 TGCTTACATACACGCATATACACTC 59.081 40.000 0.00 0.00 0.00 3.51
462 463 5.918576 GCTTACATACACGCATATACACTCA 59.081 40.000 0.00 0.00 0.00 3.41
463 464 6.586463 GCTTACATACACGCATATACACTCAT 59.414 38.462 0.00 0.00 0.00 2.90
464 465 7.201359 GCTTACATACACGCATATACACTCATC 60.201 40.741 0.00 0.00 0.00 2.92
465 466 5.470368 ACATACACGCATATACACTCATCC 58.530 41.667 0.00 0.00 0.00 3.51
466 467 5.243954 ACATACACGCATATACACTCATCCT 59.756 40.000 0.00 0.00 0.00 3.24
467 468 4.672587 ACACGCATATACACTCATCCTT 57.327 40.909 0.00 0.00 0.00 3.36
468 469 5.023533 ACACGCATATACACTCATCCTTT 57.976 39.130 0.00 0.00 0.00 3.11
469 470 5.428253 ACACGCATATACACTCATCCTTTT 58.572 37.500 0.00 0.00 0.00 2.27
470 471 5.294306 ACACGCATATACACTCATCCTTTTG 59.706 40.000 0.00 0.00 0.00 2.44
471 472 5.523552 CACGCATATACACTCATCCTTTTGA 59.476 40.000 0.00 0.00 0.00 2.69
472 473 6.037062 CACGCATATACACTCATCCTTTTGAA 59.963 38.462 0.00 0.00 0.00 2.69
473 474 6.767902 ACGCATATACACTCATCCTTTTGAAT 59.232 34.615 0.00 0.00 0.00 2.57
474 475 7.931407 ACGCATATACACTCATCCTTTTGAATA 59.069 33.333 0.00 0.00 0.00 1.75
475 476 8.223769 CGCATATACACTCATCCTTTTGAATAC 58.776 37.037 0.00 0.00 0.00 1.89
476 477 8.507249 GCATATACACTCATCCTTTTGAATACC 58.493 37.037 0.00 0.00 0.00 2.73
477 478 8.712363 CATATACACTCATCCTTTTGAATACCG 58.288 37.037 0.00 0.00 0.00 4.02
478 479 4.261801 ACACTCATCCTTTTGAATACCGG 58.738 43.478 0.00 0.00 0.00 5.28
479 480 3.065371 CACTCATCCTTTTGAATACCGGC 59.935 47.826 0.00 0.00 0.00 6.13
480 481 3.278574 CTCATCCTTTTGAATACCGGCA 58.721 45.455 0.00 0.00 0.00 5.69
481 482 3.278574 TCATCCTTTTGAATACCGGCAG 58.721 45.455 0.00 0.00 0.00 4.85
482 483 3.054728 TCATCCTTTTGAATACCGGCAGA 60.055 43.478 0.00 0.00 0.00 4.26
483 484 3.426787 TCCTTTTGAATACCGGCAGAA 57.573 42.857 0.00 0.00 0.00 3.02
484 485 3.078837 TCCTTTTGAATACCGGCAGAAC 58.921 45.455 0.00 0.00 0.00 3.01
485 486 2.817258 CCTTTTGAATACCGGCAGAACA 59.183 45.455 0.00 0.00 0.00 3.18
486 487 3.443681 CCTTTTGAATACCGGCAGAACAT 59.556 43.478 0.00 0.00 0.00 2.71
487 488 4.414852 CTTTTGAATACCGGCAGAACATG 58.585 43.478 0.00 0.00 0.00 3.21
488 489 2.779755 TGAATACCGGCAGAACATGT 57.220 45.000 0.00 0.00 0.00 3.21
489 490 3.066291 TGAATACCGGCAGAACATGTT 57.934 42.857 11.78 11.78 0.00 2.71
490 491 4.209307 TGAATACCGGCAGAACATGTTA 57.791 40.909 11.95 0.00 0.00 2.41
491 492 4.580868 TGAATACCGGCAGAACATGTTAA 58.419 39.130 11.95 0.00 0.00 2.01
492 493 4.634004 TGAATACCGGCAGAACATGTTAAG 59.366 41.667 11.95 8.19 0.00 1.85
493 494 2.851263 ACCGGCAGAACATGTTAAGA 57.149 45.000 11.95 0.00 0.00 2.10
494 495 3.350219 ACCGGCAGAACATGTTAAGAT 57.650 42.857 11.95 0.00 0.00 2.40
495 496 3.686016 ACCGGCAGAACATGTTAAGATT 58.314 40.909 11.95 0.00 0.00 2.40
496 497 3.440173 ACCGGCAGAACATGTTAAGATTG 59.560 43.478 11.95 6.61 0.00 2.67
497 498 3.689161 CCGGCAGAACATGTTAAGATTGA 59.311 43.478 11.95 0.00 0.00 2.57
498 499 4.437390 CCGGCAGAACATGTTAAGATTGAC 60.437 45.833 11.95 6.67 0.00 3.18
499 500 4.651994 GGCAGAACATGTTAAGATTGACG 58.348 43.478 11.95 0.00 0.00 4.35
500 501 4.391830 GGCAGAACATGTTAAGATTGACGA 59.608 41.667 11.95 0.00 0.00 4.20
501 502 5.106712 GGCAGAACATGTTAAGATTGACGAA 60.107 40.000 11.95 0.00 0.00 3.85
502 503 6.370593 GCAGAACATGTTAAGATTGACGAAA 58.629 36.000 11.95 0.00 0.00 3.46
503 504 7.023575 GCAGAACATGTTAAGATTGACGAAAT 58.976 34.615 11.95 0.00 0.00 2.17
504 505 7.217070 GCAGAACATGTTAAGATTGACGAAATC 59.783 37.037 11.95 7.29 44.44 2.17
505 506 8.229811 CAGAACATGTTAAGATTGACGAAATCA 58.770 33.333 11.95 0.00 46.21 2.57
506 507 8.230486 AGAACATGTTAAGATTGACGAAATCAC 58.770 33.333 11.95 7.53 46.21 3.06
507 508 6.842163 ACATGTTAAGATTGACGAAATCACC 58.158 36.000 14.85 3.99 46.21 4.02
508 509 6.429692 ACATGTTAAGATTGACGAAATCACCA 59.570 34.615 14.85 7.92 46.21 4.17
509 510 7.121168 ACATGTTAAGATTGACGAAATCACCAT 59.879 33.333 14.85 9.27 46.21 3.55
510 511 8.611757 CATGTTAAGATTGACGAAATCACCATA 58.388 33.333 14.85 3.82 46.21 2.74
511 512 8.196802 TGTTAAGATTGACGAAATCACCATAG 57.803 34.615 14.85 0.00 46.21 2.23
512 513 7.279981 TGTTAAGATTGACGAAATCACCATAGG 59.720 37.037 14.85 0.00 46.21 2.57
513 514 5.359194 AGATTGACGAAATCACCATAGGT 57.641 39.130 14.85 0.00 46.21 3.08
523 524 2.372852 ACCATAGGTGCCTCGTTGT 58.627 52.632 0.00 0.00 32.98 3.32
524 525 0.249398 ACCATAGGTGCCTCGTTGTC 59.751 55.000 0.00 0.00 32.98 3.18
525 526 0.249120 CCATAGGTGCCTCGTTGTCA 59.751 55.000 0.00 0.00 0.00 3.58
526 527 1.338674 CCATAGGTGCCTCGTTGTCAA 60.339 52.381 0.00 0.00 0.00 3.18
527 528 2.632377 CATAGGTGCCTCGTTGTCAAT 58.368 47.619 0.00 0.00 0.00 2.57
528 529 2.093306 TAGGTGCCTCGTTGTCAATG 57.907 50.000 0.00 0.00 0.00 2.82
529 530 0.396435 AGGTGCCTCGTTGTCAATGA 59.604 50.000 7.27 7.27 0.00 2.57
530 531 1.202758 AGGTGCCTCGTTGTCAATGAA 60.203 47.619 8.78 0.00 0.00 2.57
531 532 1.606668 GGTGCCTCGTTGTCAATGAAA 59.393 47.619 8.78 0.00 0.00 2.69
532 533 2.604614 GGTGCCTCGTTGTCAATGAAAC 60.605 50.000 8.78 7.42 0.00 2.78
533 534 2.032799 GTGCCTCGTTGTCAATGAAACA 59.967 45.455 8.78 7.03 0.00 2.83
534 535 2.884012 TGCCTCGTTGTCAATGAAACAT 59.116 40.909 8.78 0.00 0.00 2.71
535 536 3.058293 TGCCTCGTTGTCAATGAAACATC 60.058 43.478 8.78 0.00 0.00 3.06
536 537 3.189287 GCCTCGTTGTCAATGAAACATCT 59.811 43.478 8.78 0.00 0.00 2.90
537 538 4.670221 GCCTCGTTGTCAATGAAACATCTC 60.670 45.833 8.78 0.00 0.00 2.75
538 539 4.142816 CCTCGTTGTCAATGAAACATCTCC 60.143 45.833 8.78 0.00 0.00 3.71
539 540 4.641396 TCGTTGTCAATGAAACATCTCCT 58.359 39.130 4.95 0.00 0.00 3.69
540 541 4.690748 TCGTTGTCAATGAAACATCTCCTC 59.309 41.667 4.95 0.00 0.00 3.71
541 542 4.142816 CGTTGTCAATGAAACATCTCCTCC 60.143 45.833 0.00 0.00 0.00 4.30
542 543 3.955471 TGTCAATGAAACATCTCCTCCC 58.045 45.455 0.00 0.00 0.00 4.30
543 544 3.330405 TGTCAATGAAACATCTCCTCCCA 59.670 43.478 0.00 0.00 0.00 4.37
544 545 4.018141 TGTCAATGAAACATCTCCTCCCAT 60.018 41.667 0.00 0.00 0.00 4.00
545 546 4.952335 GTCAATGAAACATCTCCTCCCATT 59.048 41.667 0.00 0.00 0.00 3.16
546 547 6.122277 GTCAATGAAACATCTCCTCCCATTA 58.878 40.000 0.00 0.00 0.00 1.90
547 548 6.603201 GTCAATGAAACATCTCCTCCCATTAA 59.397 38.462 0.00 0.00 0.00 1.40
548 549 7.122650 GTCAATGAAACATCTCCTCCCATTAAA 59.877 37.037 0.00 0.00 0.00 1.52
549 550 7.122650 TCAATGAAACATCTCCTCCCATTAAAC 59.877 37.037 0.00 0.00 0.00 2.01
550 551 5.886609 TGAAACATCTCCTCCCATTAAACA 58.113 37.500 0.00 0.00 0.00 2.83
551 552 6.310941 TGAAACATCTCCTCCCATTAAACAA 58.689 36.000 0.00 0.00 0.00 2.83
552 553 6.434028 TGAAACATCTCCTCCCATTAAACAAG 59.566 38.462 0.00 0.00 0.00 3.16
553 554 4.273318 ACATCTCCTCCCATTAAACAAGC 58.727 43.478 0.00 0.00 0.00 4.01
554 555 4.263905 ACATCTCCTCCCATTAAACAAGCA 60.264 41.667 0.00 0.00 0.00 3.91
555 556 4.591321 TCTCCTCCCATTAAACAAGCAT 57.409 40.909 0.00 0.00 0.00 3.79
556 557 4.934356 TCTCCTCCCATTAAACAAGCATT 58.066 39.130 0.00 0.00 0.00 3.56
567 568 3.132863 CAAGCATTGCAGGAAAGGC 57.867 52.632 11.91 0.00 40.39 4.35
568 569 4.858994 AGCATTGCAGGAAAGGCT 57.141 50.000 11.91 0.00 42.01 4.58
569 570 1.820519 CAAGCATTGCAGGAAAGGCTA 59.179 47.619 11.91 0.00 45.75 3.93
570 571 2.220653 AGCATTGCAGGAAAGGCTAA 57.779 45.000 11.91 0.00 44.74 3.09
571 572 2.743553 AGCATTGCAGGAAAGGCTAAT 58.256 42.857 11.91 0.00 44.74 1.73
572 573 3.102204 AGCATTGCAGGAAAGGCTAATT 58.898 40.909 11.91 0.00 44.74 1.40
573 574 4.280819 AGCATTGCAGGAAAGGCTAATTA 58.719 39.130 11.91 0.00 44.74 1.40
574 575 4.711355 AGCATTGCAGGAAAGGCTAATTAA 59.289 37.500 11.91 0.00 44.74 1.40
575 576 5.364735 AGCATTGCAGGAAAGGCTAATTAAT 59.635 36.000 11.91 0.00 44.74 1.40
576 577 5.693555 GCATTGCAGGAAAGGCTAATTAATC 59.306 40.000 3.15 0.00 34.15 1.75
577 578 5.852282 TTGCAGGAAAGGCTAATTAATCC 57.148 39.130 0.00 0.00 0.00 3.01
578 579 4.865905 TGCAGGAAAGGCTAATTAATCCA 58.134 39.130 0.00 0.00 0.00 3.41
579 580 4.889409 TGCAGGAAAGGCTAATTAATCCAG 59.111 41.667 0.00 0.00 0.00 3.86
580 581 5.133221 GCAGGAAAGGCTAATTAATCCAGA 58.867 41.667 0.00 0.00 0.00 3.86
584 585 8.531146 CAGGAAAGGCTAATTAATCCAGAAAAA 58.469 33.333 0.00 0.00 0.00 1.94
739 746 2.512974 CCGCGCTAACCCCGAATT 60.513 61.111 5.56 0.00 0.00 2.17
744 751 1.734163 CGCTAACCCCGAATTTGACT 58.266 50.000 0.00 0.00 0.00 3.41
922 935 1.562008 TCTCACTCGTCCTCATCCTCT 59.438 52.381 0.00 0.00 0.00 3.69
923 936 2.025793 TCTCACTCGTCCTCATCCTCTT 60.026 50.000 0.00 0.00 0.00 2.85
1069 1082 2.609427 TTCAATGGATCCTCAGCTCG 57.391 50.000 14.23 0.00 0.00 5.03
1230 1243 4.563580 GGTTCTTACACTGAATCTGAGCCA 60.564 45.833 0.00 0.00 0.00 4.75
1271 1284 0.909610 AGGCCGAAGAAGATGGTGGA 60.910 55.000 0.00 0.00 0.00 4.02
1300 1313 2.035442 GCTTTGACTGGGAGGCGAC 61.035 63.158 0.00 0.00 0.00 5.19
1318 1331 0.694444 ACTCCTGGGTTGTCCTGTGT 60.694 55.000 0.00 0.00 36.20 3.72
1871 1901 8.894768 AATAATTGCTTCTGTAGGATGTACTC 57.105 34.615 0.00 0.00 0.00 2.59
1872 1902 4.737855 TTGCTTCTGTAGGATGTACTCC 57.262 45.455 0.00 0.00 45.33 3.85
1873 1903 3.031736 TGCTTCTGTAGGATGTACTCCC 58.968 50.000 7.50 2.60 46.27 4.30
1874 1904 3.301274 GCTTCTGTAGGATGTACTCCCT 58.699 50.000 10.65 10.65 46.27 4.20
1875 1905 3.319689 GCTTCTGTAGGATGTACTCCCTC 59.680 52.174 9.41 4.11 46.27 4.30
1876 1906 3.596940 TCTGTAGGATGTACTCCCTCC 57.403 52.381 9.41 3.69 46.27 4.30
1877 1907 2.158652 TCTGTAGGATGTACTCCCTCCG 60.159 54.545 9.41 2.03 46.27 4.63
1878 1908 1.567649 TGTAGGATGTACTCCCTCCGT 59.432 52.381 9.41 0.00 46.27 4.69
1879 1909 2.779430 TGTAGGATGTACTCCCTCCGTA 59.221 50.000 9.41 0.00 46.27 4.02
1880 1910 3.202818 TGTAGGATGTACTCCCTCCGTAA 59.797 47.826 9.41 0.00 46.27 3.18
1881 1911 3.393426 AGGATGTACTCCCTCCGTAAA 57.607 47.619 7.50 0.00 46.27 2.01
1882 1912 3.029570 AGGATGTACTCCCTCCGTAAAC 58.970 50.000 7.50 0.00 46.27 2.01
1883 1913 3.029570 GGATGTACTCCCTCCGTAAACT 58.970 50.000 0.00 0.00 38.19 2.66
1884 1914 4.079558 AGGATGTACTCCCTCCGTAAACTA 60.080 45.833 7.50 0.00 46.27 2.24
1885 1915 4.646492 GGATGTACTCCCTCCGTAAACTAA 59.354 45.833 0.00 0.00 38.19 2.24
1886 1916 5.303845 GGATGTACTCCCTCCGTAAACTAAT 59.696 44.000 0.00 0.00 38.19 1.73
1887 1917 6.491403 GGATGTACTCCCTCCGTAAACTAATA 59.509 42.308 0.00 0.00 38.19 0.98
1888 1918 7.178097 GGATGTACTCCCTCCGTAAACTAATAT 59.822 40.741 0.00 0.00 38.19 1.28
1889 1919 9.236006 GATGTACTCCCTCCGTAAACTAATATA 57.764 37.037 0.00 0.00 0.00 0.86
1890 1920 8.995027 TGTACTCCCTCCGTAAACTAATATAA 57.005 34.615 0.00 0.00 0.00 0.98
1891 1921 9.071276 TGTACTCCCTCCGTAAACTAATATAAG 57.929 37.037 0.00 0.00 0.00 1.73
1892 1922 9.289782 GTACTCCCTCCGTAAACTAATATAAGA 57.710 37.037 0.00 0.00 0.00 2.10
1893 1923 8.406730 ACTCCCTCCGTAAACTAATATAAGAG 57.593 38.462 0.00 0.00 0.00 2.85
1894 1924 7.039853 ACTCCCTCCGTAAACTAATATAAGAGC 60.040 40.741 0.00 0.00 0.00 4.09
1895 1925 6.072286 TCCCTCCGTAAACTAATATAAGAGCG 60.072 42.308 0.00 0.00 0.00 5.03
1896 1926 6.294397 CCCTCCGTAAACTAATATAAGAGCGT 60.294 42.308 0.00 0.00 0.00 5.07
1897 1927 7.144000 CCTCCGTAAACTAATATAAGAGCGTT 58.856 38.462 0.00 0.00 0.00 4.84
1898 1928 7.650903 CCTCCGTAAACTAATATAAGAGCGTTT 59.349 37.037 0.00 0.00 0.00 3.60
1899 1929 9.669353 CTCCGTAAACTAATATAAGAGCGTTTA 57.331 33.333 0.00 0.00 0.00 2.01
1900 1930 9.669353 TCCGTAAACTAATATAAGAGCGTTTAG 57.331 33.333 0.00 0.00 30.36 1.85
1901 1931 9.669353 CCGTAAACTAATATAAGAGCGTTTAGA 57.331 33.333 0.00 0.00 30.36 2.10
1915 1945 9.570488 AAGAGCGTTTAGAATACTAAAGTAGTG 57.430 33.333 0.00 0.00 45.42 2.74
1916 1946 8.954350 AGAGCGTTTAGAATACTAAAGTAGTGA 58.046 33.333 0.00 0.00 45.42 3.41
1917 1947 9.733219 GAGCGTTTAGAATACTAAAGTAGTGAT 57.267 33.333 0.00 0.00 45.42 3.06
1918 1948 9.733219 AGCGTTTAGAATACTAAAGTAGTGATC 57.267 33.333 0.00 0.00 45.42 2.92
1919 1949 9.733219 GCGTTTAGAATACTAAAGTAGTGATCT 57.267 33.333 0.00 4.67 45.42 2.75
1925 1955 9.733219 AGAATACTAAAGTAGTGATCTAAACGC 57.267 33.333 0.00 0.00 39.81 4.84
1926 1956 9.733219 GAATACTAAAGTAGTGATCTAAACGCT 57.267 33.333 0.00 0.00 39.81 5.07
1927 1957 9.733219 AATACTAAAGTAGTGATCTAAACGCTC 57.267 33.333 0.00 0.00 39.81 5.03
1928 1958 7.393841 ACTAAAGTAGTGATCTAAACGCTCT 57.606 36.000 0.00 0.00 37.69 4.09
1929 1959 7.828712 ACTAAAGTAGTGATCTAAACGCTCTT 58.171 34.615 0.00 0.00 37.69 2.85
1930 1960 8.954350 ACTAAAGTAGTGATCTAAACGCTCTTA 58.046 33.333 0.00 0.00 37.69 2.10
1931 1961 9.953697 CTAAAGTAGTGATCTAAACGCTCTTAT 57.046 33.333 0.00 0.00 0.00 1.73
1937 1967 8.973835 AGTGATCTAAACGCTCTTATATTAGC 57.026 34.615 0.00 0.00 35.33 3.09
1938 1968 8.798402 AGTGATCTAAACGCTCTTATATTAGCT 58.202 33.333 0.00 0.00 36.56 3.32
1939 1969 9.413048 GTGATCTAAACGCTCTTATATTAGCTT 57.587 33.333 0.00 0.00 36.56 3.74
1943 1973 9.894783 TCTAAACGCTCTTATATTAGCTTACAG 57.105 33.333 0.00 0.00 36.56 2.74
1944 1974 9.894783 CTAAACGCTCTTATATTAGCTTACAGA 57.105 33.333 0.00 0.00 36.56 3.41
1945 1975 8.804688 AAACGCTCTTATATTAGCTTACAGAG 57.195 34.615 0.00 0.00 36.56 3.35
1946 1976 6.915349 ACGCTCTTATATTAGCTTACAGAGG 58.085 40.000 0.00 0.00 36.56 3.69
1947 1977 6.071840 ACGCTCTTATATTAGCTTACAGAGGG 60.072 42.308 13.72 13.72 42.53 4.30
1948 1978 6.151312 CGCTCTTATATTAGCTTACAGAGGGA 59.849 42.308 11.57 0.00 40.49 4.20
2058 2088 1.457346 CATGAGCAGAACTTGGGGAC 58.543 55.000 0.00 0.00 0.00 4.46
2136 2167 7.581213 TTGATTTCCTGTCAAACAACTACAT 57.419 32.000 0.00 0.00 32.98 2.29
2410 2442 7.156000 ACCTACTTAAGCAAGAGAAGAAGAAC 58.844 38.462 1.29 0.00 35.60 3.01
3033 3095 7.288389 TGAACCTAGGAACTTACTGAACTTACA 59.712 37.037 17.98 0.00 41.75 2.41
3120 3191 2.909006 TCCTTCTTCAGCATCTTCAGGT 59.091 45.455 0.00 0.00 0.00 4.00
3164 3244 1.002011 GGCCGCCCTCTTCTTCTTT 60.002 57.895 0.00 0.00 0.00 2.52
3168 3248 0.324943 CGCCCTCTTCTTCTTTCCCA 59.675 55.000 0.00 0.00 0.00 4.37
3241 3321 3.148279 GCCGTCTGGGAGATCGGT 61.148 66.667 12.84 0.00 39.44 4.69
3367 3450 1.139734 CGACCTCATCCACCTCGTG 59.860 63.158 0.00 0.00 0.00 4.35
3379 3462 0.966920 ACCTCGTGGTCAGATTCGTT 59.033 50.000 2.61 0.00 44.78 3.85
3401 3485 0.397675 AGGGCTCGTCCTCATCATCA 60.398 55.000 0.00 0.00 29.56 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 4.176752 GTGGAGGATCACGGCCCC 62.177 72.222 0.00 0.00 36.25 5.80
67 68 2.125106 GGTGTGGAGGATCACGGC 60.125 66.667 0.00 0.00 40.31 5.68
71 72 1.114627 CATCGAGGTGTGGAGGATCA 58.885 55.000 0.00 0.00 36.25 2.92
146 147 4.416620 CAGACGACTCTATGTGTCTTTCC 58.583 47.826 0.00 0.00 36.02 3.13
148 149 3.827302 ACCAGACGACTCTATGTGTCTTT 59.173 43.478 0.00 0.00 36.02 2.52
150 151 3.074675 ACCAGACGACTCTATGTGTCT 57.925 47.619 0.00 0.00 37.45 3.41
151 152 3.057456 ACAACCAGACGACTCTATGTGTC 60.057 47.826 0.00 0.00 0.00 3.67
152 153 2.891580 ACAACCAGACGACTCTATGTGT 59.108 45.455 0.00 0.00 0.00 3.72
153 154 3.577649 ACAACCAGACGACTCTATGTG 57.422 47.619 0.00 0.00 0.00 3.21
204 205 8.034804 ACAACCATAAATTGCCATAAAAGACTC 58.965 33.333 0.00 0.00 0.00 3.36
215 216 2.354604 CCCCACACAACCATAAATTGCC 60.355 50.000 0.00 0.00 0.00 4.52
270 271 8.850454 TCCGTTTCAGTTCATTTTTCTTTTAG 57.150 30.769 0.00 0.00 0.00 1.85
272 273 8.716646 AATCCGTTTCAGTTCATTTTTCTTTT 57.283 26.923 0.00 0.00 0.00 2.27
274 275 7.763985 ACAAATCCGTTTCAGTTCATTTTTCTT 59.236 29.630 0.00 0.00 0.00 2.52
276 277 7.221838 TGACAAATCCGTTTCAGTTCATTTTTC 59.778 33.333 0.00 0.00 0.00 2.29
281 282 5.702865 CATGACAAATCCGTTTCAGTTCAT 58.297 37.500 0.00 0.00 0.00 2.57
282 283 4.556501 GCATGACAAATCCGTTTCAGTTCA 60.557 41.667 0.00 0.00 0.00 3.18
283 284 3.914364 GCATGACAAATCCGTTTCAGTTC 59.086 43.478 0.00 0.00 0.00 3.01
326 327 8.090788 ACTCTAATAGAGCCTTTTTATGTGGA 57.909 34.615 16.62 0.00 46.12 4.02
367 368 9.787532 GAGTGTATGTATTTGCACATAAATGTT 57.212 29.630 5.89 0.00 41.74 2.71
368 369 8.122330 CGAGTGTATGTATTTGCACATAAATGT 58.878 33.333 5.89 0.00 41.74 2.71
369 370 7.587392 CCGAGTGTATGTATTTGCACATAAATG 59.413 37.037 5.89 0.00 41.74 2.32
370 371 7.282224 ACCGAGTGTATGTATTTGCACATAAAT 59.718 33.333 1.28 1.28 41.74 1.40
371 372 6.596106 ACCGAGTGTATGTATTTGCACATAAA 59.404 34.615 0.00 0.00 41.74 1.40
372 373 6.110033 ACCGAGTGTATGTATTTGCACATAA 58.890 36.000 0.00 0.00 41.74 1.90
373 374 5.666462 ACCGAGTGTATGTATTTGCACATA 58.334 37.500 0.00 0.00 39.77 2.29
374 375 4.513442 ACCGAGTGTATGTATTTGCACAT 58.487 39.130 0.00 0.00 41.88 3.21
375 376 3.930229 GACCGAGTGTATGTATTTGCACA 59.070 43.478 0.00 0.00 34.59 4.57
376 377 3.930229 TGACCGAGTGTATGTATTTGCAC 59.070 43.478 0.00 0.00 0.00 4.57
377 378 4.195225 TGACCGAGTGTATGTATTTGCA 57.805 40.909 0.00 0.00 0.00 4.08
378 379 5.751509 TGTATGACCGAGTGTATGTATTTGC 59.248 40.000 0.00 0.00 0.00 3.68
379 380 6.754675 TGTGTATGACCGAGTGTATGTATTTG 59.245 38.462 0.00 0.00 0.00 2.32
380 381 6.755141 GTGTGTATGACCGAGTGTATGTATTT 59.245 38.462 0.00 0.00 0.00 1.40
381 382 6.127563 TGTGTGTATGACCGAGTGTATGTATT 60.128 38.462 0.00 0.00 0.00 1.89
382 383 5.358725 TGTGTGTATGACCGAGTGTATGTAT 59.641 40.000 0.00 0.00 0.00 2.29
383 384 4.701171 TGTGTGTATGACCGAGTGTATGTA 59.299 41.667 0.00 0.00 0.00 2.29
384 385 3.508402 TGTGTGTATGACCGAGTGTATGT 59.492 43.478 0.00 0.00 0.00 2.29
385 386 4.104696 TGTGTGTATGACCGAGTGTATG 57.895 45.455 0.00 0.00 0.00 2.39
386 387 3.762288 ACTGTGTGTATGACCGAGTGTAT 59.238 43.478 0.00 0.00 0.00 2.29
387 388 3.151554 ACTGTGTGTATGACCGAGTGTA 58.848 45.455 0.00 0.00 0.00 2.90
388 389 1.961394 ACTGTGTGTATGACCGAGTGT 59.039 47.619 0.00 0.00 0.00 3.55
389 390 2.724977 ACTGTGTGTATGACCGAGTG 57.275 50.000 0.00 0.00 0.00 3.51
418 419 9.830975 TGTAAGCATCTGTATATGTATTGTGTT 57.169 29.630 0.00 0.00 0.00 3.32
424 425 9.788960 CGTGTATGTAAGCATCTGTATATGTAT 57.211 33.333 0.00 0.00 36.58 2.29
425 426 7.753580 GCGTGTATGTAAGCATCTGTATATGTA 59.246 37.037 0.00 0.00 36.58 2.29
426 427 6.586463 GCGTGTATGTAAGCATCTGTATATGT 59.414 38.462 0.00 0.00 36.58 2.29
427 428 6.586082 TGCGTGTATGTAAGCATCTGTATATG 59.414 38.462 0.00 0.00 36.58 1.78
428 429 6.687604 TGCGTGTATGTAAGCATCTGTATAT 58.312 36.000 0.00 0.00 36.58 0.86
429 430 6.079424 TGCGTGTATGTAAGCATCTGTATA 57.921 37.500 0.00 0.00 36.58 1.47
430 431 4.944048 TGCGTGTATGTAAGCATCTGTAT 58.056 39.130 0.00 0.00 36.58 2.29
431 432 4.379339 TGCGTGTATGTAAGCATCTGTA 57.621 40.909 0.00 0.00 36.58 2.74
432 433 3.245518 TGCGTGTATGTAAGCATCTGT 57.754 42.857 0.00 0.00 36.58 3.41
433 434 6.586082 TGTATATGCGTGTATGTAAGCATCTG 59.414 38.462 4.99 0.00 45.97 2.90
434 435 6.586463 GTGTATATGCGTGTATGTAAGCATCT 59.414 38.462 4.99 0.00 45.97 2.90
435 436 6.586463 AGTGTATATGCGTGTATGTAAGCATC 59.414 38.462 4.99 0.00 45.97 3.91
437 438 5.838529 AGTGTATATGCGTGTATGTAAGCA 58.161 37.500 0.00 0.00 44.13 3.91
438 439 5.918576 TGAGTGTATATGCGTGTATGTAAGC 59.081 40.000 0.00 0.00 0.00 3.09
439 440 7.273598 GGATGAGTGTATATGCGTGTATGTAAG 59.726 40.741 0.00 0.00 0.00 2.34
440 441 7.039993 AGGATGAGTGTATATGCGTGTATGTAA 60.040 37.037 0.00 0.00 0.00 2.41
441 442 6.433093 AGGATGAGTGTATATGCGTGTATGTA 59.567 38.462 0.00 0.00 0.00 2.29
442 443 5.243954 AGGATGAGTGTATATGCGTGTATGT 59.756 40.000 0.00 0.00 0.00 2.29
443 444 5.714047 AGGATGAGTGTATATGCGTGTATG 58.286 41.667 0.00 0.00 0.00 2.39
444 445 5.984695 AGGATGAGTGTATATGCGTGTAT 57.015 39.130 0.00 0.00 0.00 2.29
445 446 5.784578 AAGGATGAGTGTATATGCGTGTA 57.215 39.130 0.00 0.00 0.00 2.90
446 447 4.672587 AAGGATGAGTGTATATGCGTGT 57.327 40.909 0.00 0.00 0.00 4.49
447 448 5.523552 TCAAAAGGATGAGTGTATATGCGTG 59.476 40.000 0.00 0.00 0.00 5.34
448 449 5.670485 TCAAAAGGATGAGTGTATATGCGT 58.330 37.500 0.00 0.00 0.00 5.24
449 450 6.603237 TTCAAAAGGATGAGTGTATATGCG 57.397 37.500 0.00 0.00 0.00 4.73
450 451 8.507249 GGTATTCAAAAGGATGAGTGTATATGC 58.493 37.037 0.00 0.00 0.00 3.14
451 452 8.712363 CGGTATTCAAAAGGATGAGTGTATATG 58.288 37.037 0.00 0.00 0.00 1.78
452 453 7.878127 CCGGTATTCAAAAGGATGAGTGTATAT 59.122 37.037 0.00 0.00 0.00 0.86
453 454 7.214381 CCGGTATTCAAAAGGATGAGTGTATA 58.786 38.462 0.00 0.00 0.00 1.47
454 455 6.055588 CCGGTATTCAAAAGGATGAGTGTAT 58.944 40.000 0.00 0.00 0.00 2.29
455 456 5.424757 CCGGTATTCAAAAGGATGAGTGTA 58.575 41.667 0.00 0.00 0.00 2.90
456 457 4.261801 CCGGTATTCAAAAGGATGAGTGT 58.738 43.478 0.00 0.00 0.00 3.55
457 458 3.065371 GCCGGTATTCAAAAGGATGAGTG 59.935 47.826 1.90 0.00 0.00 3.51
458 459 3.279434 GCCGGTATTCAAAAGGATGAGT 58.721 45.455 1.90 0.00 0.00 3.41
459 460 3.278574 TGCCGGTATTCAAAAGGATGAG 58.721 45.455 1.90 0.00 0.00 2.90
460 461 3.054728 TCTGCCGGTATTCAAAAGGATGA 60.055 43.478 1.90 0.00 0.00 2.92
461 462 3.278574 TCTGCCGGTATTCAAAAGGATG 58.721 45.455 1.90 0.00 0.00 3.51
462 463 3.644966 TCTGCCGGTATTCAAAAGGAT 57.355 42.857 1.90 0.00 0.00 3.24
463 464 3.078837 GTTCTGCCGGTATTCAAAAGGA 58.921 45.455 1.90 0.00 0.00 3.36
464 465 2.817258 TGTTCTGCCGGTATTCAAAAGG 59.183 45.455 1.90 0.00 0.00 3.11
465 466 4.082787 ACATGTTCTGCCGGTATTCAAAAG 60.083 41.667 1.90 0.00 0.00 2.27
466 467 3.823873 ACATGTTCTGCCGGTATTCAAAA 59.176 39.130 1.90 0.00 0.00 2.44
467 468 3.417101 ACATGTTCTGCCGGTATTCAAA 58.583 40.909 1.90 0.00 0.00 2.69
468 469 3.066291 ACATGTTCTGCCGGTATTCAA 57.934 42.857 1.90 0.00 0.00 2.69
469 470 2.779755 ACATGTTCTGCCGGTATTCA 57.220 45.000 1.90 0.00 0.00 2.57
470 471 4.873827 TCTTAACATGTTCTGCCGGTATTC 59.126 41.667 15.85 0.00 0.00 1.75
471 472 4.839121 TCTTAACATGTTCTGCCGGTATT 58.161 39.130 15.85 0.00 0.00 1.89
472 473 4.481368 TCTTAACATGTTCTGCCGGTAT 57.519 40.909 15.85 0.00 0.00 2.73
473 474 3.965379 TCTTAACATGTTCTGCCGGTA 57.035 42.857 15.85 0.00 0.00 4.02
474 475 2.851263 TCTTAACATGTTCTGCCGGT 57.149 45.000 15.85 0.00 0.00 5.28
475 476 3.689161 TCAATCTTAACATGTTCTGCCGG 59.311 43.478 15.85 0.00 0.00 6.13
476 477 4.651994 GTCAATCTTAACATGTTCTGCCG 58.348 43.478 15.85 1.03 0.00 5.69
477 478 4.391830 TCGTCAATCTTAACATGTTCTGCC 59.608 41.667 15.85 0.00 0.00 4.85
478 479 5.530519 TCGTCAATCTTAACATGTTCTGC 57.469 39.130 15.85 2.72 0.00 4.26
479 480 8.229811 TGATTTCGTCAATCTTAACATGTTCTG 58.770 33.333 15.85 9.27 41.91 3.02
480 481 8.230486 GTGATTTCGTCAATCTTAACATGTTCT 58.770 33.333 15.85 0.00 41.91 3.01
481 482 7.481798 GGTGATTTCGTCAATCTTAACATGTTC 59.518 37.037 15.85 0.00 41.91 3.18
482 483 7.040755 TGGTGATTTCGTCAATCTTAACATGTT 60.041 33.333 16.68 16.68 41.91 2.71
483 484 6.429692 TGGTGATTTCGTCAATCTTAACATGT 59.570 34.615 0.00 0.00 41.91 3.21
484 485 6.841119 TGGTGATTTCGTCAATCTTAACATG 58.159 36.000 10.22 0.00 41.91 3.21
485 486 7.630242 ATGGTGATTTCGTCAATCTTAACAT 57.370 32.000 10.22 4.38 41.91 2.71
486 487 7.279981 CCTATGGTGATTTCGTCAATCTTAACA 59.720 37.037 10.22 2.67 41.91 2.41
487 488 7.280205 ACCTATGGTGATTTCGTCAATCTTAAC 59.720 37.037 10.22 2.75 41.91 2.01
488 489 7.335627 ACCTATGGTGATTTCGTCAATCTTAA 58.664 34.615 10.22 0.00 41.91 1.85
489 490 6.884832 ACCTATGGTGATTTCGTCAATCTTA 58.115 36.000 10.22 0.56 41.91 2.10
490 491 5.745227 ACCTATGGTGATTTCGTCAATCTT 58.255 37.500 10.22 0.00 41.91 2.40
491 492 5.359194 ACCTATGGTGATTTCGTCAATCT 57.641 39.130 10.22 0.00 41.91 2.40
505 506 0.249398 GACAACGAGGCACCTATGGT 59.751 55.000 0.00 0.00 35.62 3.55
506 507 0.249120 TGACAACGAGGCACCTATGG 59.751 55.000 0.00 0.00 0.00 2.74
507 508 2.093306 TTGACAACGAGGCACCTATG 57.907 50.000 0.00 0.00 32.34 2.23
508 509 2.236146 TCATTGACAACGAGGCACCTAT 59.764 45.455 0.00 0.00 32.34 2.57
509 510 1.621317 TCATTGACAACGAGGCACCTA 59.379 47.619 0.00 0.00 32.34 3.08
510 511 0.396435 TCATTGACAACGAGGCACCT 59.604 50.000 0.00 0.00 32.34 4.00
511 512 1.234821 TTCATTGACAACGAGGCACC 58.765 50.000 0.00 0.00 32.34 5.01
512 513 2.032799 TGTTTCATTGACAACGAGGCAC 59.967 45.455 0.00 0.00 32.34 5.01
513 514 2.293170 TGTTTCATTGACAACGAGGCA 58.707 42.857 0.00 0.00 0.00 4.75
514 515 3.189287 AGATGTTTCATTGACAACGAGGC 59.811 43.478 0.00 0.00 0.00 4.70
515 516 4.142816 GGAGATGTTTCATTGACAACGAGG 60.143 45.833 0.00 0.00 0.00 4.63
516 517 4.692625 AGGAGATGTTTCATTGACAACGAG 59.307 41.667 0.00 0.00 0.00 4.18
517 518 4.641396 AGGAGATGTTTCATTGACAACGA 58.359 39.130 0.00 0.00 0.00 3.85
518 519 4.142816 GGAGGAGATGTTTCATTGACAACG 60.143 45.833 0.00 0.00 0.00 4.10
519 520 4.156739 GGGAGGAGATGTTTCATTGACAAC 59.843 45.833 0.00 0.00 0.00 3.32
520 521 4.202556 TGGGAGGAGATGTTTCATTGACAA 60.203 41.667 0.00 0.00 0.00 3.18
521 522 3.330405 TGGGAGGAGATGTTTCATTGACA 59.670 43.478 0.00 0.00 0.00 3.58
522 523 3.955471 TGGGAGGAGATGTTTCATTGAC 58.045 45.455 0.00 0.00 0.00 3.18
523 524 4.868172 ATGGGAGGAGATGTTTCATTGA 57.132 40.909 0.00 0.00 0.00 2.57
524 525 7.093814 TGTTTAATGGGAGGAGATGTTTCATTG 60.094 37.037 0.00 0.00 0.00 2.82
525 526 6.953520 TGTTTAATGGGAGGAGATGTTTCATT 59.046 34.615 0.00 0.00 0.00 2.57
526 527 6.493166 TGTTTAATGGGAGGAGATGTTTCAT 58.507 36.000 0.00 0.00 0.00 2.57
527 528 5.886609 TGTTTAATGGGAGGAGATGTTTCA 58.113 37.500 0.00 0.00 0.00 2.69
528 529 6.625960 GCTTGTTTAATGGGAGGAGATGTTTC 60.626 42.308 0.00 0.00 0.00 2.78
529 530 5.185828 GCTTGTTTAATGGGAGGAGATGTTT 59.814 40.000 0.00 0.00 0.00 2.83
530 531 4.706962 GCTTGTTTAATGGGAGGAGATGTT 59.293 41.667 0.00 0.00 0.00 2.71
531 532 4.263905 TGCTTGTTTAATGGGAGGAGATGT 60.264 41.667 0.00 0.00 0.00 3.06
532 533 4.272489 TGCTTGTTTAATGGGAGGAGATG 58.728 43.478 0.00 0.00 0.00 2.90
533 534 4.591321 TGCTTGTTTAATGGGAGGAGAT 57.409 40.909 0.00 0.00 0.00 2.75
534 535 4.591321 ATGCTTGTTTAATGGGAGGAGA 57.409 40.909 0.00 0.00 0.00 3.71
535 536 4.678840 GCAATGCTTGTTTAATGGGAGGAG 60.679 45.833 0.00 0.00 0.00 3.69
536 537 3.195396 GCAATGCTTGTTTAATGGGAGGA 59.805 43.478 0.00 0.00 0.00 3.71
537 538 3.055963 TGCAATGCTTGTTTAATGGGAGG 60.056 43.478 6.82 0.00 0.00 4.30
538 539 4.178540 CTGCAATGCTTGTTTAATGGGAG 58.821 43.478 6.82 0.00 0.00 4.30
539 540 3.055963 CCTGCAATGCTTGTTTAATGGGA 60.056 43.478 6.82 0.00 0.00 4.37
540 541 3.055963 TCCTGCAATGCTTGTTTAATGGG 60.056 43.478 6.82 0.00 0.00 4.00
541 542 4.191033 TCCTGCAATGCTTGTTTAATGG 57.809 40.909 6.82 0.00 0.00 3.16
542 543 5.121142 CCTTTCCTGCAATGCTTGTTTAATG 59.879 40.000 6.82 0.00 0.00 1.90
543 544 5.240121 CCTTTCCTGCAATGCTTGTTTAAT 58.760 37.500 6.82 0.00 0.00 1.40
544 545 4.630111 CCTTTCCTGCAATGCTTGTTTAA 58.370 39.130 6.82 0.00 0.00 1.52
545 546 3.554752 GCCTTTCCTGCAATGCTTGTTTA 60.555 43.478 6.82 0.00 0.00 2.01
546 547 2.807837 GCCTTTCCTGCAATGCTTGTTT 60.808 45.455 6.82 0.00 0.00 2.83
547 548 1.270465 GCCTTTCCTGCAATGCTTGTT 60.270 47.619 6.82 0.00 0.00 2.83
548 549 0.319405 GCCTTTCCTGCAATGCTTGT 59.681 50.000 6.82 0.00 0.00 3.16
549 550 0.606604 AGCCTTTCCTGCAATGCTTG 59.393 50.000 6.82 0.00 0.00 4.01
550 551 2.220653 TAGCCTTTCCTGCAATGCTT 57.779 45.000 6.82 0.00 0.00 3.91
551 552 2.220653 TTAGCCTTTCCTGCAATGCT 57.779 45.000 6.82 0.00 0.00 3.79
552 553 3.531934 AATTAGCCTTTCCTGCAATGC 57.468 42.857 0.00 0.00 0.00 3.56
553 554 6.183360 TGGATTAATTAGCCTTTCCTGCAATG 60.183 38.462 7.66 0.00 0.00 2.82
554 555 5.898972 TGGATTAATTAGCCTTTCCTGCAAT 59.101 36.000 7.66 0.00 0.00 3.56
555 556 5.268387 TGGATTAATTAGCCTTTCCTGCAA 58.732 37.500 7.66 0.00 0.00 4.08
556 557 4.865905 TGGATTAATTAGCCTTTCCTGCA 58.134 39.130 7.66 0.00 0.00 4.41
557 558 5.133221 TCTGGATTAATTAGCCTTTCCTGC 58.867 41.667 7.66 0.00 0.00 4.85
558 559 7.645058 TTTCTGGATTAATTAGCCTTTCCTG 57.355 36.000 7.66 0.00 0.00 3.86
559 560 8.664669 TTTTTCTGGATTAATTAGCCTTTCCT 57.335 30.769 7.66 0.00 0.00 3.36
560 561 9.317936 CATTTTTCTGGATTAATTAGCCTTTCC 57.682 33.333 7.66 0.00 0.00 3.13
561 562 9.317936 CCATTTTTCTGGATTAATTAGCCTTTC 57.682 33.333 7.66 0.00 38.69 2.62
562 563 9.045745 TCCATTTTTCTGGATTAATTAGCCTTT 57.954 29.630 7.66 0.00 40.43 3.11
563 564 8.608185 TCCATTTTTCTGGATTAATTAGCCTT 57.392 30.769 7.66 0.00 40.43 4.35
564 565 7.841222 ACTCCATTTTTCTGGATTAATTAGCCT 59.159 33.333 7.66 0.00 44.23 4.58
565 566 8.011844 ACTCCATTTTTCTGGATTAATTAGCC 57.988 34.615 0.00 0.72 44.23 3.93
573 574 9.320295 TGGTTAAATACTCCATTTTTCTGGATT 57.680 29.630 0.00 0.00 44.23 3.01
574 575 8.893563 TGGTTAAATACTCCATTTTTCTGGAT 57.106 30.769 0.00 0.00 44.23 3.41
575 576 8.713708 TTGGTTAAATACTCCATTTTTCTGGA 57.286 30.769 0.00 0.00 43.09 3.86
576 577 9.771534 TTTTGGTTAAATACTCCATTTTTCTGG 57.228 29.630 0.00 0.00 37.93 3.86
584 585 8.799367 GTGGTAGTTTTTGGTTAAATACTCCAT 58.201 33.333 0.00 0.00 38.47 3.41
739 746 4.966787 GCGGGCCCAACCAGTCAA 62.967 66.667 24.92 0.00 42.05 3.18
922 935 0.906756 CAGAGCACCAGGGAGAGGAA 60.907 60.000 0.00 0.00 0.00 3.36
923 936 1.305633 CAGAGCACCAGGGAGAGGA 60.306 63.158 0.00 0.00 0.00 3.71
981 994 1.344065 TCCTCAACTTCTACCGGCAA 58.656 50.000 0.00 0.00 0.00 4.52
1069 1082 5.048364 TGTTCCACCATTATGCACTTACAAC 60.048 40.000 0.00 0.00 0.00 3.32
1271 1284 3.070015 CCCAGTCAAAGCACCTTCAAAAT 59.930 43.478 0.00 0.00 0.00 1.82
1300 1313 1.276421 CTACACAGGACAACCCAGGAG 59.724 57.143 0.00 0.00 37.41 3.69
1318 1331 6.346096 AGCGTTCAAGATTTAATACCTGCTA 58.654 36.000 0.00 0.00 0.00 3.49
1869 1899 7.314393 GCTCTTATATTAGTTTACGGAGGGAG 58.686 42.308 0.00 0.00 0.00 4.30
1870 1900 6.072286 CGCTCTTATATTAGTTTACGGAGGGA 60.072 42.308 0.00 0.00 34.63 4.20
1871 1901 6.091437 CGCTCTTATATTAGTTTACGGAGGG 58.909 44.000 0.00 0.00 0.00 4.30
1872 1902 6.675987 ACGCTCTTATATTAGTTTACGGAGG 58.324 40.000 0.00 0.00 0.00 4.30
1873 1903 8.571461 AAACGCTCTTATATTAGTTTACGGAG 57.429 34.615 0.00 0.00 31.14 4.63
1874 1904 9.669353 CTAAACGCTCTTATATTAGTTTACGGA 57.331 33.333 0.00 0.00 34.29 4.69
1875 1905 9.669353 TCTAAACGCTCTTATATTAGTTTACGG 57.331 33.333 0.00 0.00 34.29 4.02
1889 1919 9.570488 CACTACTTTAGTATTCTAAACGCTCTT 57.430 33.333 0.76 0.00 40.05 2.85
1890 1920 8.954350 TCACTACTTTAGTATTCTAAACGCTCT 58.046 33.333 0.76 0.00 40.05 4.09
1891 1921 9.733219 ATCACTACTTTAGTATTCTAAACGCTC 57.267 33.333 0.76 0.00 40.05 5.03
1892 1922 9.733219 GATCACTACTTTAGTATTCTAAACGCT 57.267 33.333 0.76 0.00 40.05 5.07
1893 1923 9.733219 AGATCACTACTTTAGTATTCTAAACGC 57.267 33.333 0.76 0.00 40.05 4.84
1899 1929 9.733219 GCGTTTAGATCACTACTTTAGTATTCT 57.267 33.333 0.00 0.00 37.23 2.40
1900 1930 9.733219 AGCGTTTAGATCACTACTTTAGTATTC 57.267 33.333 0.00 0.00 37.23 1.75
1901 1931 9.733219 GAGCGTTTAGATCACTACTTTAGTATT 57.267 33.333 0.00 0.00 37.23 1.89
1902 1932 9.122779 AGAGCGTTTAGATCACTACTTTAGTAT 57.877 33.333 0.00 0.00 37.82 2.12
1903 1933 8.503458 AGAGCGTTTAGATCACTACTTTAGTA 57.497 34.615 0.00 0.00 37.82 1.82
1904 1934 7.393841 AGAGCGTTTAGATCACTACTTTAGT 57.606 36.000 0.00 0.00 37.82 2.24
1905 1935 9.953697 ATAAGAGCGTTTAGATCACTACTTTAG 57.046 33.333 0.00 0.00 37.82 1.85
1912 1942 8.798402 AGCTAATATAAGAGCGTTTAGATCACT 58.202 33.333 0.00 0.00 43.72 3.41
1913 1943 8.973835 AGCTAATATAAGAGCGTTTAGATCAC 57.026 34.615 0.00 0.00 43.72 3.06
1917 1947 9.894783 CTGTAAGCTAATATAAGAGCGTTTAGA 57.105 33.333 3.64 0.00 43.72 2.10
1918 1948 9.894783 TCTGTAAGCTAATATAAGAGCGTTTAG 57.105 33.333 3.64 3.84 43.72 1.85
1919 1949 9.894783 CTCTGTAAGCTAATATAAGAGCGTTTA 57.105 33.333 3.64 0.00 43.72 2.01
1920 1950 7.868415 CCTCTGTAAGCTAATATAAGAGCGTTT 59.132 37.037 3.64 0.00 43.72 3.60
1921 1951 7.371936 CCTCTGTAAGCTAATATAAGAGCGTT 58.628 38.462 3.64 2.76 43.72 4.84
1922 1952 6.071840 CCCTCTGTAAGCTAATATAAGAGCGT 60.072 42.308 0.00 3.96 43.72 5.07
1923 1953 6.151312 TCCCTCTGTAAGCTAATATAAGAGCG 59.849 42.308 0.00 0.00 43.72 5.03
1924 1954 7.177744 ACTCCCTCTGTAAGCTAATATAAGAGC 59.822 40.741 0.00 1.81 39.08 4.09
1925 1955 8.644374 ACTCCCTCTGTAAGCTAATATAAGAG 57.356 38.462 0.00 0.00 0.00 2.85
1926 1956 9.742144 CTACTCCCTCTGTAAGCTAATATAAGA 57.258 37.037 0.00 0.00 0.00 2.10
1927 1957 8.962679 CCTACTCCCTCTGTAAGCTAATATAAG 58.037 40.741 0.00 0.00 0.00 1.73
1928 1958 8.454494 ACCTACTCCCTCTGTAAGCTAATATAA 58.546 37.037 0.00 0.00 0.00 0.98
1929 1959 7.889073 CACCTACTCCCTCTGTAAGCTAATATA 59.111 40.741 0.00 0.00 0.00 0.86
1930 1960 6.722129 CACCTACTCCCTCTGTAAGCTAATAT 59.278 42.308 0.00 0.00 0.00 1.28
1931 1961 6.069331 CACCTACTCCCTCTGTAAGCTAATA 58.931 44.000 0.00 0.00 0.00 0.98
1932 1962 4.896482 CACCTACTCCCTCTGTAAGCTAAT 59.104 45.833 0.00 0.00 0.00 1.73
1933 1963 4.264262 ACACCTACTCCCTCTGTAAGCTAA 60.264 45.833 0.00 0.00 0.00 3.09
1934 1964 3.268856 ACACCTACTCCCTCTGTAAGCTA 59.731 47.826 0.00 0.00 0.00 3.32
1935 1965 2.043252 ACACCTACTCCCTCTGTAAGCT 59.957 50.000 0.00 0.00 0.00 3.74
1936 1966 2.166664 CACACCTACTCCCTCTGTAAGC 59.833 54.545 0.00 0.00 0.00 3.09
1937 1967 3.698289 TCACACCTACTCCCTCTGTAAG 58.302 50.000 0.00 0.00 0.00 2.34
1938 1968 3.820195 TCACACCTACTCCCTCTGTAA 57.180 47.619 0.00 0.00 0.00 2.41
1939 1969 3.075582 AGTTCACACCTACTCCCTCTGTA 59.924 47.826 0.00 0.00 0.00 2.74
1940 1970 2.158295 AGTTCACACCTACTCCCTCTGT 60.158 50.000 0.00 0.00 0.00 3.41
1941 1971 2.232452 CAGTTCACACCTACTCCCTCTG 59.768 54.545 0.00 0.00 0.00 3.35
1942 1972 2.158295 ACAGTTCACACCTACTCCCTCT 60.158 50.000 0.00 0.00 0.00 3.69
1943 1973 2.028930 CACAGTTCACACCTACTCCCTC 60.029 54.545 0.00 0.00 0.00 4.30
1944 1974 1.971357 CACAGTTCACACCTACTCCCT 59.029 52.381 0.00 0.00 0.00 4.20
1945 1975 1.002087 CCACAGTTCACACCTACTCCC 59.998 57.143 0.00 0.00 0.00 4.30
1946 1976 1.002087 CCCACAGTTCACACCTACTCC 59.998 57.143 0.00 0.00 0.00 3.85
1947 1977 1.002087 CCCCACAGTTCACACCTACTC 59.998 57.143 0.00 0.00 0.00 2.59
1948 1978 1.056660 CCCCACAGTTCACACCTACT 58.943 55.000 0.00 0.00 0.00 2.57
2058 2088 1.335872 GGGCTTGTTTGTCATTCACCG 60.336 52.381 0.00 0.00 0.00 4.94
2136 2167 5.311989 TGGATACATCTTCCACCAACTGGA 61.312 45.833 1.86 0.00 45.78 3.86
2410 2442 4.283978 AGATCAGCAATCAGATACTCCAGG 59.716 45.833 0.00 0.00 36.79 4.45
2546 2578 0.742505 ATGCATGACATTCCAAGGCG 59.257 50.000 0.00 0.00 34.40 5.52
2858 2906 6.910536 ACTTGCTACTTGCTACATATGTTC 57.089 37.500 14.77 7.23 43.37 3.18
2898 2960 8.885693 ATGGCAGTACTATCTATCTATGTCAA 57.114 34.615 0.00 0.00 0.00 3.18
3033 3095 4.332819 CAGTTTCGTCAGTCCTGAACTTTT 59.667 41.667 0.00 0.00 41.85 2.27
3367 3450 1.757699 AGCCCTCTAACGAATCTGACC 59.242 52.381 0.00 0.00 0.00 4.02


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

AutoCloner maintained by Alex Coulton.