Multiple sequence alignment - TraesCS4B01G089900

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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 TraesCS4B01G089900 chr4B 100.000 3415 0 0 1 3415 91326440 91329854 0.000000e+00 6307.0
1 TraesCS4B01G089900 chr4B 97.264 731 19 1 1492 2222 91227971 91228700 0.000000e+00 1238.0
2 TraesCS4B01G089900 chr4B 92.191 858 29 16 621 1470 91190332 91191159 0.000000e+00 1179.0
3 TraesCS4B01G089900 chr4B 88.438 320 26 7 1 320 91190040 91190348 3.220000e-100 375.0
4 TraesCS4B01G089900 chr4B 97.727 44 1 0 379 422 132047285 132047242 3.650000e-10 76.8
5 TraesCS4B01G089900 chr4D 92.707 2756 129 34 621 3322 61595344 61592607 0.000000e+00 3910.0
6 TraesCS4B01G089900 chr4D 89.105 257 16 3 72 324 61595571 61595323 3.310000e-80 309.0
7 TraesCS4B01G089900 chr4A 91.458 1756 70 36 804 2524 534792167 534790457 0.000000e+00 2338.0
8 TraesCS4B01G089900 chr4A 93.511 524 21 3 2557 3077 534790458 534789945 0.000000e+00 767.0
9 TraesCS4B01G089900 chr4A 89.590 317 17 3 3099 3415 534789880 534789580 4.130000e-104 388.0
10 TraesCS4B01G089900 chr4A 100.000 43 0 0 380 422 329317906 329317864 2.820000e-11 80.5
11 TraesCS4B01G089900 chr4A 100.000 28 0 0 3081 3108 534789928 534789901 6.000000e-03 52.8
12 TraesCS4B01G089900 chr6D 92.571 175 13 0 1828 2002 358216793 358216619 5.660000e-63 252.0
13 TraesCS4B01G089900 chr6D 90.741 54 4 1 370 422 463154748 463154695 1.700000e-08 71.3
14 TraesCS4B01G089900 chrUn 92.398 171 13 0 1832 2002 209272496 209272326 9.470000e-61 244.0
15 TraesCS4B01G089900 chr7B 92.398 171 13 0 1832 2002 642232629 642232459 9.470000e-61 244.0
16 TraesCS4B01G089900 chr7B 86.076 79 9 2 1567 1644 730809815 730809892 2.180000e-12 84.2
17 TraesCS4B01G089900 chr7B 100.000 43 0 0 380 422 139478619 139478661 2.820000e-11 80.5
18 TraesCS4B01G089900 chr7D 84.043 94 13 2 1567 1659 628219389 628219297 4.690000e-14 89.8
19 TraesCS4B01G089900 chr7D 82.979 94 14 2 1567 1659 628223630 628223538 2.180000e-12 84.2
20 TraesCS4B01G089900 chr7D 92.727 55 4 0 321 375 612341718 612341772 2.820000e-11 80.5
21 TraesCS4B01G089900 chr1A 94.643 56 3 0 320 375 559405695 559405750 1.690000e-13 87.9
22 TraesCS4B01G089900 chr6B 92.982 57 4 0 322 378 479872870 479872814 2.180000e-12 84.2
23 TraesCS4B01G089900 chr6B 92.727 55 4 0 321 375 479869382 479869436 2.820000e-11 80.5
24 TraesCS4B01G089900 chr7A 86.667 75 8 2 1567 1640 724947557 724947630 7.850000e-12 82.4
25 TraesCS4B01G089900 chr7A 84.810 79 10 2 1567 1644 724951590 724951667 1.020000e-10 78.7
26 TraesCS4B01G089900 chr7A 97.727 44 1 0 379 422 514778322 514778365 3.650000e-10 76.8
27 TraesCS4B01G089900 chr5D 100.000 43 0 0 380 422 433503036 433502994 2.820000e-11 80.5
28 TraesCS4B01G089900 chr5B 100.000 43 0 0 380 422 620768183 620768141 2.820000e-11 80.5
29 TraesCS4B01G089900 chr2A 100.000 43 0 0 380 422 211459240 211459282 2.820000e-11 80.5
30 TraesCS4B01G089900 chr6A 97.727 44 1 0 379 422 66429416 66429459 3.650000e-10 76.8
31 TraesCS4B01G089900 chr1B 85.000 60 4 2 321 375 667705139 667705080 4.760000e-04 56.5


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 TraesCS4B01G089900 chr4B 91326440 91329854 3414 False 6307.00 6307 100.00000 1 3415 1 chr4B.!!$F2 3414
1 TraesCS4B01G089900 chr4B 91227971 91228700 729 False 1238.00 1238 97.26400 1492 2222 1 chr4B.!!$F1 730
2 TraesCS4B01G089900 chr4B 91190040 91191159 1119 False 777.00 1179 90.31450 1 1470 2 chr4B.!!$F3 1469
3 TraesCS4B01G089900 chr4D 61592607 61595571 2964 True 2109.50 3910 90.90600 72 3322 2 chr4D.!!$R1 3250
4 TraesCS4B01G089900 chr4A 534789580 534792167 2587 True 886.45 2338 93.63975 804 3415 4 chr4A.!!$R2 2611

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
419 423 0.036765 GTGTGCGTTCATAGGGGTGA 60.037 55.0 0.0 0.0 0.00 4.02 F
552 556 0.243907 ATACAGACGTGCAGAAGCGT 59.756 50.0 0.0 0.0 46.23 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1405 1458 0.742990 CGGCCGCCTTGTTCTTGATA 60.743 55.0 14.67 0.0 0.0 2.15 R
2535 2602 0.396435 ACACCCTTCTTGTCGATGCA 59.604 50.0 0.00 0.0 0.0 3.96 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
20 21 1.202687 CCAATATGGAGCTCGCCTTCA 60.203 52.381 7.83 0.00 40.96 3.02
21 22 2.564771 CAATATGGAGCTCGCCTTCAA 58.435 47.619 7.83 0.00 31.30 2.69
35 36 2.289133 GCCTTCAACGAGACTTCCTCTT 60.289 50.000 0.00 0.00 39.78 2.85
36 37 3.321497 CCTTCAACGAGACTTCCTCTTG 58.679 50.000 0.00 0.00 39.78 3.02
39 40 3.223435 TCAACGAGACTTCCTCTTGTCT 58.777 45.455 0.00 0.00 42.21 3.41
49 50 0.107945 CCTCTTGTCTGGCTGTAGGC 60.108 60.000 0.00 0.00 41.50 3.93
70 71 0.969894 AGACATATCAGCGCCCCTAC 59.030 55.000 2.29 0.00 0.00 3.18
81 82 1.829096 GCCCCTACGAGGACTCCTC 60.829 68.421 14.52 14.52 46.44 3.71
178 182 1.046472 ATCGTGAGGCCCGGTATCAA 61.046 55.000 0.00 0.00 0.00 2.57
191 195 1.641577 GTATCAACCTGCCTCACGTC 58.358 55.000 0.00 0.00 0.00 4.34
192 196 1.067142 GTATCAACCTGCCTCACGTCA 60.067 52.381 0.00 0.00 0.00 4.35
198 202 1.576421 CTGCCTCACGTCAAAAGCC 59.424 57.895 0.00 0.00 0.00 4.35
206 210 2.811431 TCACGTCAAAAGCCTAACATGG 59.189 45.455 0.00 0.00 0.00 3.66
250 254 6.897259 ATTGAAGAACAAATGTATGCATGC 57.103 33.333 11.82 11.82 42.03 4.06
288 292 7.099266 TCTTCATTTCTTCAGTTTTCAGCAA 57.901 32.000 0.00 0.00 0.00 3.91
293 297 6.949352 TTTCTTCAGTTTTCAGCAATCTCT 57.051 33.333 0.00 0.00 0.00 3.10
356 360 8.748412 TCATTTTACTCCACTGAATAAAATGGG 58.252 33.333 20.16 5.45 45.98 4.00
357 361 8.531146 CATTTTACTCCACTGAATAAAATGGGT 58.469 33.333 15.88 0.00 44.16 4.51
358 362 7.461182 TTTACTCCACTGAATAAAATGGGTG 57.539 36.000 0.00 0.00 32.73 4.61
359 363 4.344104 ACTCCACTGAATAAAATGGGTGG 58.656 43.478 0.00 0.00 43.67 4.61
360 364 4.202673 ACTCCACTGAATAAAATGGGTGGT 60.203 41.667 9.30 0.00 43.07 4.16
361 365 4.746466 TCCACTGAATAAAATGGGTGGTT 58.254 39.130 9.30 0.00 43.07 3.67
362 366 4.770010 TCCACTGAATAAAATGGGTGGTTC 59.230 41.667 9.30 0.00 43.07 3.62
363 367 4.526262 CCACTGAATAAAATGGGTGGTTCA 59.474 41.667 0.00 0.00 39.25 3.18
364 368 5.469479 CACTGAATAAAATGGGTGGTTCAC 58.531 41.667 0.00 0.00 0.00 3.18
365 369 5.010516 CACTGAATAAAATGGGTGGTTCACA 59.989 40.000 0.38 0.00 35.86 3.58
366 370 5.779771 ACTGAATAAAATGGGTGGTTCACAT 59.220 36.000 0.38 0.00 42.70 3.21
367 371 6.951198 ACTGAATAAAATGGGTGGTTCACATA 59.049 34.615 0.38 0.00 39.55 2.29
368 372 7.453126 ACTGAATAAAATGGGTGGTTCACATAA 59.547 33.333 0.38 0.00 39.55 1.90
369 373 8.372877 TGAATAAAATGGGTGGTTCACATAAT 57.627 30.769 0.38 0.00 39.55 1.28
370 374 8.474025 TGAATAAAATGGGTGGTTCACATAATC 58.526 33.333 0.38 0.00 39.55 1.75
371 375 5.675684 AAAATGGGTGGTTCACATAATCC 57.324 39.130 0.38 0.00 39.55 3.01
372 376 2.818751 TGGGTGGTTCACATAATCCC 57.181 50.000 0.38 0.00 35.86 3.85
373 377 1.286553 TGGGTGGTTCACATAATCCCC 59.713 52.381 0.38 0.00 35.86 4.81
374 378 1.569072 GGGTGGTTCACATAATCCCCT 59.431 52.381 0.38 0.00 35.86 4.79
375 379 2.781174 GGGTGGTTCACATAATCCCCTA 59.219 50.000 0.38 0.00 35.86 3.53
376 380 3.203487 GGGTGGTTCACATAATCCCCTAA 59.797 47.826 0.38 0.00 35.86 2.69
377 381 4.325501 GGGTGGTTCACATAATCCCCTAAA 60.326 45.833 0.38 0.00 35.86 1.85
378 382 4.887655 GGTGGTTCACATAATCCCCTAAAG 59.112 45.833 0.38 0.00 35.86 1.85
379 383 5.506708 GTGGTTCACATAATCCCCTAAAGT 58.493 41.667 0.00 0.00 34.08 2.66
380 384 5.589050 GTGGTTCACATAATCCCCTAAAGTC 59.411 44.000 0.00 0.00 34.08 3.01
381 385 5.251932 TGGTTCACATAATCCCCTAAAGTCA 59.748 40.000 0.00 0.00 0.00 3.41
382 386 6.069088 TGGTTCACATAATCCCCTAAAGTCAT 60.069 38.462 0.00 0.00 0.00 3.06
383 387 7.128109 TGGTTCACATAATCCCCTAAAGTCATA 59.872 37.037 0.00 0.00 0.00 2.15
384 388 7.661847 GGTTCACATAATCCCCTAAAGTCATAG 59.338 40.741 0.00 0.00 0.00 2.23
385 389 7.316393 TCACATAATCCCCTAAAGTCATAGG 57.684 40.000 0.00 0.00 41.86 2.57
393 397 3.588569 CCTAAAGTCATAGGGCTAGGGT 58.411 50.000 0.00 0.00 39.07 4.34
394 398 3.325135 CCTAAAGTCATAGGGCTAGGGTG 59.675 52.174 0.00 0.00 39.07 4.61
395 399 2.570386 AAGTCATAGGGCTAGGGTGT 57.430 50.000 0.00 0.00 0.00 4.16
396 400 1.794714 AGTCATAGGGCTAGGGTGTG 58.205 55.000 0.00 0.00 0.00 3.82
397 401 0.106894 GTCATAGGGCTAGGGTGTGC 59.893 60.000 0.00 0.00 0.00 4.57
398 402 1.069765 CATAGGGCTAGGGTGTGCG 59.930 63.158 0.00 0.00 0.00 5.34
399 403 1.382695 ATAGGGCTAGGGTGTGCGT 60.383 57.895 0.00 0.00 0.00 5.24
400 404 1.686325 ATAGGGCTAGGGTGTGCGTG 61.686 60.000 0.00 0.00 0.00 5.34
401 405 4.016706 GGGCTAGGGTGTGCGTGT 62.017 66.667 0.00 0.00 0.00 4.49
402 406 2.742372 GGCTAGGGTGTGCGTGTG 60.742 66.667 0.00 0.00 0.00 3.82
403 407 2.030562 GCTAGGGTGTGCGTGTGT 59.969 61.111 0.00 0.00 0.00 3.72
404 408 2.317609 GCTAGGGTGTGCGTGTGTG 61.318 63.158 0.00 0.00 0.00 3.82
405 409 2.280524 TAGGGTGTGCGTGTGTGC 60.281 61.111 0.00 0.00 0.00 4.57
408 412 3.871574 GGTGTGCGTGTGTGCGTT 61.872 61.111 0.00 0.00 37.81 4.84
409 413 2.350760 GTGTGCGTGTGTGCGTTC 60.351 61.111 0.00 0.00 37.81 3.95
410 414 2.815647 TGTGCGTGTGTGCGTTCA 60.816 55.556 0.00 0.00 37.81 3.18
411 415 2.176926 TGTGCGTGTGTGCGTTCAT 61.177 52.632 0.00 0.00 37.81 2.57
412 416 0.876342 TGTGCGTGTGTGCGTTCATA 60.876 50.000 0.00 0.00 37.81 2.15
413 417 0.179250 GTGCGTGTGTGCGTTCATAG 60.179 55.000 0.00 0.00 37.81 2.23
414 418 1.288419 TGCGTGTGTGCGTTCATAGG 61.288 55.000 0.00 0.00 37.81 2.57
415 419 1.966493 GCGTGTGTGCGTTCATAGGG 61.966 60.000 0.00 0.00 0.00 3.53
416 420 1.358725 CGTGTGTGCGTTCATAGGGG 61.359 60.000 0.00 0.00 0.00 4.79
417 421 0.321298 GTGTGTGCGTTCATAGGGGT 60.321 55.000 0.00 0.00 0.00 4.95
418 422 0.321210 TGTGTGCGTTCATAGGGGTG 60.321 55.000 0.00 0.00 0.00 4.61
419 423 0.036765 GTGTGCGTTCATAGGGGTGA 60.037 55.000 0.00 0.00 0.00 4.02
420 424 0.249120 TGTGCGTTCATAGGGGTGAG 59.751 55.000 0.00 0.00 0.00 3.51
421 425 0.249398 GTGCGTTCATAGGGGTGAGT 59.751 55.000 0.00 0.00 0.00 3.41
422 426 0.981183 TGCGTTCATAGGGGTGAGTT 59.019 50.000 0.00 0.00 0.00 3.01
423 427 1.349688 TGCGTTCATAGGGGTGAGTTT 59.650 47.619 0.00 0.00 0.00 2.66
424 428 1.737793 GCGTTCATAGGGGTGAGTTTG 59.262 52.381 0.00 0.00 0.00 2.93
425 429 2.614481 GCGTTCATAGGGGTGAGTTTGA 60.614 50.000 0.00 0.00 0.00 2.69
426 430 3.670625 CGTTCATAGGGGTGAGTTTGAA 58.329 45.455 0.00 0.00 0.00 2.69
427 431 3.435671 CGTTCATAGGGGTGAGTTTGAAC 59.564 47.826 0.00 0.00 39.51 3.18
428 432 3.713826 TCATAGGGGTGAGTTTGAACC 57.286 47.619 0.00 0.00 35.59 3.62
429 433 2.983192 TCATAGGGGTGAGTTTGAACCA 59.017 45.455 0.00 0.00 38.27 3.67
430 434 3.591527 TCATAGGGGTGAGTTTGAACCAT 59.408 43.478 0.00 0.00 38.27 3.55
431 435 2.586648 AGGGGTGAGTTTGAACCATC 57.413 50.000 0.00 0.00 38.27 3.51
432 436 1.075536 AGGGGTGAGTTTGAACCATCC 59.924 52.381 6.25 6.25 38.27 3.51
433 437 1.203001 GGGGTGAGTTTGAACCATCCA 60.203 52.381 13.18 0.00 38.27 3.41
434 438 2.557452 GGGGTGAGTTTGAACCATCCAT 60.557 50.000 13.18 0.00 38.27 3.41
435 439 3.165071 GGGTGAGTTTGAACCATCCATT 58.835 45.455 8.74 0.00 38.27 3.16
436 440 3.578282 GGGTGAGTTTGAACCATCCATTT 59.422 43.478 8.74 0.00 38.27 2.32
437 441 4.040339 GGGTGAGTTTGAACCATCCATTTT 59.960 41.667 8.74 0.00 38.27 1.82
438 442 4.990426 GGTGAGTTTGAACCATCCATTTTG 59.010 41.667 0.00 0.00 36.41 2.44
439 443 5.453198 GGTGAGTTTGAACCATCCATTTTGT 60.453 40.000 0.00 0.00 36.41 2.83
440 444 6.048509 GTGAGTTTGAACCATCCATTTTGTT 58.951 36.000 0.00 0.00 0.00 2.83
441 445 6.538381 GTGAGTTTGAACCATCCATTTTGTTT 59.462 34.615 0.00 0.00 0.00 2.83
442 446 7.708752 GTGAGTTTGAACCATCCATTTTGTTTA 59.291 33.333 0.00 0.00 0.00 2.01
443 447 7.925483 TGAGTTTGAACCATCCATTTTGTTTAG 59.075 33.333 0.00 0.00 0.00 1.85
444 448 7.216494 AGTTTGAACCATCCATTTTGTTTAGG 58.784 34.615 0.00 0.00 0.00 2.69
445 449 5.146010 TGAACCATCCATTTTGTTTAGGC 57.854 39.130 0.00 0.00 0.00 3.93
446 450 4.020662 TGAACCATCCATTTTGTTTAGGCC 60.021 41.667 0.00 0.00 0.00 5.19
447 451 3.515562 ACCATCCATTTTGTTTAGGCCA 58.484 40.909 5.01 0.00 0.00 5.36
448 452 3.260632 ACCATCCATTTTGTTTAGGCCAC 59.739 43.478 5.01 0.00 0.00 5.01
449 453 3.510719 CATCCATTTTGTTTAGGCCACG 58.489 45.455 5.01 0.00 0.00 4.94
450 454 1.271102 TCCATTTTGTTTAGGCCACGC 59.729 47.619 5.01 0.00 0.00 5.34
451 455 1.272212 CCATTTTGTTTAGGCCACGCT 59.728 47.619 5.01 0.00 0.00 5.07
452 456 2.288763 CCATTTTGTTTAGGCCACGCTT 60.289 45.455 5.01 0.00 0.00 4.68
453 457 2.500509 TTTTGTTTAGGCCACGCTTG 57.499 45.000 5.01 0.00 0.00 4.01
463 467 3.966215 CACGCTTGGATTGACCGT 58.034 55.556 0.00 0.00 42.61 4.83
464 468 3.131326 CACGCTTGGATTGACCGTA 57.869 52.632 0.00 0.00 42.61 4.02
465 469 1.434555 CACGCTTGGATTGACCGTAA 58.565 50.000 0.00 0.00 42.61 3.18
466 470 1.393539 CACGCTTGGATTGACCGTAAG 59.606 52.381 0.00 0.00 42.61 2.34
467 471 1.001633 ACGCTTGGATTGACCGTAAGT 59.998 47.619 0.00 0.00 42.61 2.24
468 472 2.073816 CGCTTGGATTGACCGTAAGTT 58.926 47.619 0.00 0.00 42.61 2.66
469 473 3.255725 CGCTTGGATTGACCGTAAGTTA 58.744 45.455 0.00 0.00 42.61 2.24
470 474 3.680937 CGCTTGGATTGACCGTAAGTTAA 59.319 43.478 0.00 0.00 42.61 2.01
471 475 4.331717 CGCTTGGATTGACCGTAAGTTAAT 59.668 41.667 0.00 0.00 42.61 1.40
472 476 5.521010 CGCTTGGATTGACCGTAAGTTAATA 59.479 40.000 0.00 0.00 42.61 0.98
473 477 6.509039 CGCTTGGATTGACCGTAAGTTAATAC 60.509 42.308 0.00 0.00 42.61 1.89
474 478 6.509039 GCTTGGATTGACCGTAAGTTAATACG 60.509 42.308 2.32 2.32 46.22 3.06
495 499 9.849166 AATACGGGTTTATCAATTTTACAAGTG 57.151 29.630 0.00 0.00 0.00 3.16
496 500 7.279750 ACGGGTTTATCAATTTTACAAGTGT 57.720 32.000 0.00 0.00 29.75 3.55
497 501 8.393671 ACGGGTTTATCAATTTTACAAGTGTA 57.606 30.769 0.00 0.00 29.75 2.90
498 502 8.291740 ACGGGTTTATCAATTTTACAAGTGTAC 58.708 33.333 0.00 0.00 29.75 2.90
499 503 7.751793 CGGGTTTATCAATTTTACAAGTGTACC 59.248 37.037 0.00 0.00 29.75 3.34
500 504 8.799367 GGGTTTATCAATTTTACAAGTGTACCT 58.201 33.333 0.00 0.00 29.75 3.08
506 510 8.301730 TCAATTTTACAAGTGTACCTTACTCG 57.698 34.615 0.00 0.00 29.75 4.18
507 511 8.143193 TCAATTTTACAAGTGTACCTTACTCGA 58.857 33.333 0.00 0.00 29.75 4.04
508 512 8.932791 CAATTTTACAAGTGTACCTTACTCGAT 58.067 33.333 0.00 0.00 0.00 3.59
509 513 9.498176 AATTTTACAAGTGTACCTTACTCGATT 57.502 29.630 0.00 0.00 0.00 3.34
511 515 9.630098 TTTTACAAGTGTACCTTACTCGATTAG 57.370 33.333 0.00 0.00 0.00 1.73
512 516 8.565896 TTACAAGTGTACCTTACTCGATTAGA 57.434 34.615 0.00 0.00 0.00 2.10
524 528 4.700596 CTCGATTAGAGTGATTTTCGGC 57.299 45.455 0.00 0.00 41.99 5.54
525 529 3.454375 TCGATTAGAGTGATTTTCGGCC 58.546 45.455 0.00 0.00 0.00 6.13
526 530 2.218759 CGATTAGAGTGATTTTCGGCCG 59.781 50.000 22.12 22.12 0.00 6.13
527 531 2.018542 TTAGAGTGATTTTCGGCCGG 57.981 50.000 27.83 6.80 0.00 6.13
528 532 1.187974 TAGAGTGATTTTCGGCCGGA 58.812 50.000 27.83 16.16 0.00 5.14
529 533 0.323629 AGAGTGATTTTCGGCCGGAA 59.676 50.000 27.83 22.66 0.00 4.30
530 534 1.161843 GAGTGATTTTCGGCCGGAAA 58.838 50.000 32.76 32.76 42.75 3.13
531 535 0.879090 AGTGATTTTCGGCCGGAAAC 59.121 50.000 33.28 24.76 44.07 2.78
545 549 1.705256 GGAAACGATACAGACGTGCA 58.295 50.000 0.00 0.00 43.16 4.57
546 550 1.654105 GGAAACGATACAGACGTGCAG 59.346 52.381 0.00 0.00 43.16 4.41
547 551 2.592194 GAAACGATACAGACGTGCAGA 58.408 47.619 0.00 0.00 43.16 4.26
548 552 2.717580 AACGATACAGACGTGCAGAA 57.282 45.000 0.00 0.00 43.16 3.02
549 553 2.264109 ACGATACAGACGTGCAGAAG 57.736 50.000 0.00 0.00 42.37 2.85
550 554 0.917259 CGATACAGACGTGCAGAAGC 59.083 55.000 0.00 0.00 42.57 3.86
551 555 0.917259 GATACAGACGTGCAGAAGCG 59.083 55.000 0.00 0.00 46.23 4.68
552 556 0.243907 ATACAGACGTGCAGAAGCGT 59.756 50.000 0.00 0.00 46.23 5.07
553 557 0.663269 TACAGACGTGCAGAAGCGTG 60.663 55.000 4.69 0.00 46.23 5.34
554 558 1.951130 CAGACGTGCAGAAGCGTGT 60.951 57.895 4.69 0.00 46.23 4.49
555 559 0.663269 CAGACGTGCAGAAGCGTGTA 60.663 55.000 4.69 0.00 46.23 2.90
556 560 0.243907 AGACGTGCAGAAGCGTGTAT 59.756 50.000 4.69 0.00 46.23 2.29
557 561 1.068474 GACGTGCAGAAGCGTGTATT 58.932 50.000 4.69 0.00 46.23 1.89
558 562 1.459592 GACGTGCAGAAGCGTGTATTT 59.540 47.619 4.69 0.00 46.23 1.40
559 563 1.871039 ACGTGCAGAAGCGTGTATTTT 59.129 42.857 0.00 0.00 46.23 1.82
560 564 2.289547 ACGTGCAGAAGCGTGTATTTTT 59.710 40.909 0.00 0.00 46.23 1.94
583 587 8.851541 TTTTTACGGGTGTATCTGTTAGAAAT 57.148 30.769 0.00 0.00 0.00 2.17
584 588 9.941325 TTTTTACGGGTGTATCTGTTAGAAATA 57.059 29.630 0.00 0.00 0.00 1.40
586 590 9.537192 TTTACGGGTGTATCTGTTAGAAATATG 57.463 33.333 0.00 0.00 0.00 1.78
587 591 7.356089 ACGGGTGTATCTGTTAGAAATATGA 57.644 36.000 0.00 0.00 0.00 2.15
588 592 7.208080 ACGGGTGTATCTGTTAGAAATATGAC 58.792 38.462 0.00 0.00 0.00 3.06
589 593 7.147794 ACGGGTGTATCTGTTAGAAATATGACA 60.148 37.037 0.00 0.00 0.00 3.58
590 594 7.709182 CGGGTGTATCTGTTAGAAATATGACAA 59.291 37.037 0.00 0.00 0.00 3.18
591 595 9.561069 GGGTGTATCTGTTAGAAATATGACAAT 57.439 33.333 0.00 0.00 0.00 2.71
597 601 8.213518 TCTGTTAGAAATATGACAATCCAAGC 57.786 34.615 0.00 0.00 0.00 4.01
598 602 7.011389 TCTGTTAGAAATATGACAATCCAAGCG 59.989 37.037 0.00 0.00 0.00 4.68
599 603 6.038161 TGTTAGAAATATGACAATCCAAGCGG 59.962 38.462 0.00 0.00 0.00 5.52
600 604 3.885297 AGAAATATGACAATCCAAGCGGG 59.115 43.478 0.00 0.00 38.37 6.13
601 605 2.276732 ATATGACAATCCAAGCGGGG 57.723 50.000 0.00 0.00 37.22 5.73
602 606 0.465460 TATGACAATCCAAGCGGGGC 60.465 55.000 0.00 0.00 37.22 5.80
603 607 3.140814 GACAATCCAAGCGGGGCC 61.141 66.667 0.00 0.00 37.22 5.80
604 608 3.645268 GACAATCCAAGCGGGGCCT 62.645 63.158 0.84 0.00 37.22 5.19
605 609 2.362889 CAATCCAAGCGGGGCCTT 60.363 61.111 0.84 0.00 37.22 4.35
606 610 1.077068 CAATCCAAGCGGGGCCTTA 60.077 57.895 0.84 0.00 37.22 2.69
607 611 1.103398 CAATCCAAGCGGGGCCTTAG 61.103 60.000 0.84 0.00 37.22 2.18
608 612 2.284515 AATCCAAGCGGGGCCTTAGG 62.285 60.000 0.84 0.00 37.22 2.69
609 613 4.506255 CCAAGCGGGGCCTTAGGG 62.506 72.222 0.84 0.00 0.00 3.53
610 614 3.728373 CAAGCGGGGCCTTAGGGT 61.728 66.667 0.84 0.00 34.45 4.34
611 615 2.041596 AAGCGGGGCCTTAGGGTA 59.958 61.111 0.84 0.00 34.45 3.69
612 616 2.070650 AAGCGGGGCCTTAGGGTAG 61.071 63.158 0.84 0.00 34.45 3.18
613 617 2.767073 GCGGGGCCTTAGGGTAGT 60.767 66.667 0.84 0.00 34.45 2.73
614 618 1.458209 GCGGGGCCTTAGGGTAGTA 60.458 63.158 0.84 0.00 34.45 1.82
615 619 1.050421 GCGGGGCCTTAGGGTAGTAA 61.050 60.000 0.84 0.00 34.45 2.24
616 620 1.499368 CGGGGCCTTAGGGTAGTAAA 58.501 55.000 0.84 0.00 34.45 2.01
617 621 2.052468 CGGGGCCTTAGGGTAGTAAAT 58.948 52.381 0.84 0.00 34.45 1.40
618 622 2.224450 CGGGGCCTTAGGGTAGTAAATG 60.224 54.545 0.84 0.00 34.45 2.32
619 623 2.107726 GGGGCCTTAGGGTAGTAAATGG 59.892 54.545 0.84 0.00 34.45 3.16
620 624 3.050835 GGGCCTTAGGGTAGTAAATGGA 58.949 50.000 0.84 0.00 34.45 3.41
621 625 3.181447 GGGCCTTAGGGTAGTAAATGGAC 60.181 52.174 0.84 0.00 34.45 4.02
622 626 3.715315 GGCCTTAGGGTAGTAAATGGACT 59.285 47.826 0.00 0.00 34.45 3.85
623 627 4.165565 GGCCTTAGGGTAGTAAATGGACTT 59.834 45.833 0.00 0.00 34.45 3.01
624 628 5.339778 GGCCTTAGGGTAGTAAATGGACTTT 60.340 44.000 0.00 0.00 34.45 2.66
625 629 6.185511 GCCTTAGGGTAGTAAATGGACTTTT 58.814 40.000 0.00 0.00 34.45 2.27
626 630 6.662234 GCCTTAGGGTAGTAAATGGACTTTTT 59.338 38.462 0.00 0.00 34.45 1.94
721 731 9.967346 TTATTTAATTTCGTTTTCCATGTGTGA 57.033 25.926 0.00 0.00 0.00 3.58
730 740 6.316640 TCGTTTTCCATGTGTGACTTCTAAAA 59.683 34.615 0.00 0.00 0.00 1.52
731 741 6.970043 CGTTTTCCATGTGTGACTTCTAAAAA 59.030 34.615 0.00 0.00 0.00 1.94
757 767 4.512944 CACCAGATCTTCATTGTATTCCCG 59.487 45.833 0.00 0.00 0.00 5.14
928 950 2.665185 GTTTCCAGCGCCGACTGT 60.665 61.111 2.29 0.00 35.83 3.55
972 1013 4.560128 ACGTGCAACTCCAGCATATATAG 58.440 43.478 0.00 0.00 44.79 1.31
974 1015 5.047021 ACGTGCAACTCCAGCATATATAGAT 60.047 40.000 0.00 0.00 44.79 1.98
979 1020 6.336566 CAACTCCAGCATATATAGATCGCTT 58.663 40.000 2.74 0.00 0.00 4.68
980 1021 5.900425 ACTCCAGCATATATAGATCGCTTG 58.100 41.667 2.74 1.18 0.00 4.01
983 1024 4.442612 CCAGCATATATAGATCGCTTGCCT 60.443 45.833 2.74 0.00 0.00 4.75
1013 1057 2.594654 GCTCGAACACGTCATAGTCTTG 59.405 50.000 0.00 0.00 0.00 3.02
1264 1314 2.666989 GGAAGCACGAGAATCCGAC 58.333 57.895 0.00 0.00 0.00 4.79
1957 2010 1.116536 TGGTGCAGAACGACCTGGTA 61.117 55.000 0.00 0.00 34.82 3.25
1963 2016 1.735559 GAACGACCTGGTACACGCC 60.736 63.158 0.00 0.00 0.00 5.68
2222 2276 4.616835 CGTAGCCGGTGACTAGTAGTTTTT 60.617 45.833 1.90 0.00 0.00 1.94
2223 2277 3.660865 AGCCGGTGACTAGTAGTTTTTG 58.339 45.455 1.90 0.00 0.00 2.44
2224 2278 3.070590 AGCCGGTGACTAGTAGTTTTTGT 59.929 43.478 1.90 0.00 0.00 2.83
2225 2279 3.811497 GCCGGTGACTAGTAGTTTTTGTT 59.189 43.478 1.90 0.00 0.00 2.83
2226 2280 4.084171 GCCGGTGACTAGTAGTTTTTGTTC 60.084 45.833 1.90 0.00 0.00 3.18
2276 2339 7.312657 AGCTTTGAAGTGTACATACATGATG 57.687 36.000 0.00 1.48 41.79 3.07
2281 2344 7.713764 TGAAGTGTACATACATGATGCATAC 57.286 36.000 0.00 0.00 39.39 2.39
2535 2602 7.057894 TGTTCTGTAAACAATACAAGAAGGGT 58.942 34.615 0.00 0.00 0.00 4.34
2536 2603 7.012894 TGTTCTGTAAACAATACAAGAAGGGTG 59.987 37.037 0.00 0.00 0.00 4.61
2537 2604 5.472137 TCTGTAAACAATACAAGAAGGGTGC 59.528 40.000 0.00 0.00 0.00 5.01
2538 2605 5.133941 TGTAAACAATACAAGAAGGGTGCA 58.866 37.500 0.00 0.00 0.00 4.57
2539 2606 5.772672 TGTAAACAATACAAGAAGGGTGCAT 59.227 36.000 0.00 0.00 0.00 3.96
2540 2607 5.391312 AAACAATACAAGAAGGGTGCATC 57.609 39.130 0.00 0.00 0.00 3.91
2541 2608 3.009723 ACAATACAAGAAGGGTGCATCG 58.990 45.455 0.00 0.00 0.00 3.84
2542 2609 3.270027 CAATACAAGAAGGGTGCATCGA 58.730 45.455 0.00 0.00 0.00 3.59
2543 2610 2.380084 TACAAGAAGGGTGCATCGAC 57.620 50.000 0.00 0.00 0.00 4.20
2545 2612 1.202758 ACAAGAAGGGTGCATCGACAA 60.203 47.619 0.00 0.00 0.00 3.18
2546 2613 1.466167 CAAGAAGGGTGCATCGACAAG 59.534 52.381 0.00 0.00 0.00 3.16
2547 2614 0.976641 AGAAGGGTGCATCGACAAGA 59.023 50.000 0.00 0.00 0.00 3.02
2549 2616 1.734465 GAAGGGTGCATCGACAAGAAG 59.266 52.381 0.00 0.00 0.00 2.85
2563 2634 4.513692 CGACAAGAAGGGTGTAAACAATCA 59.486 41.667 0.00 0.00 0.00 2.57
2657 2728 3.126858 GTGACGAAAATGCAGCCATCTTA 59.873 43.478 0.00 0.00 0.00 2.10
2758 2829 0.798776 CTGTTTTCCGCAGCTCGAAT 59.201 50.000 7.07 0.00 41.67 3.34
2826 2897 1.000274 GTCTGCCGTTTTGCCTGAAAT 60.000 47.619 0.00 0.00 0.00 2.17
2886 2957 5.064834 GGTGAGACGACCAAAAGAAATATCC 59.935 44.000 0.00 0.00 35.88 2.59
2993 3064 1.216710 GACTCGGAGACCCTGCAAG 59.783 63.158 12.86 0.00 0.00 4.01
3018 3089 5.947228 ACATGTAGGTCAATCACACAAAG 57.053 39.130 0.00 0.00 0.00 2.77
3043 3114 8.232513 AGTGCTAACAATATGCATCATAATTCG 58.767 33.333 0.19 0.00 39.00 3.34
3063 3134 5.502153 TCGAAAAGGAGCATCTACTAGAC 57.498 43.478 0.00 0.00 33.73 2.59
3132 3251 1.328279 CTTTGTCCAAACTGGGGGTC 58.672 55.000 0.00 0.00 38.32 4.46
3158 3277 0.037232 AACGCTTCAGTGTAGGGCTC 60.037 55.000 12.82 0.00 37.87 4.70
3199 3319 1.056700 AATACATCCCAGCTCGGCCT 61.057 55.000 0.00 0.00 0.00 5.19
3215 3335 2.092323 GGCCTGAGGTCAATTTACACC 58.908 52.381 0.00 0.00 0.00 4.16
3230 3350 8.372459 TCAATTTACACCTTGAGCTTAGAAGTA 58.628 33.333 0.00 0.00 0.00 2.24
3289 3409 0.538584 ATGCTCGTGAGGCTGAATGA 59.461 50.000 0.00 0.00 0.00 2.57
3292 3412 2.366590 TGCTCGTGAGGCTGAATGATAT 59.633 45.455 0.00 0.00 0.00 1.63
3293 3413 2.735663 GCTCGTGAGGCTGAATGATATG 59.264 50.000 0.00 0.00 0.00 1.78
3329 3449 2.307768 AGATGGGCTCATGAATGCTTG 58.692 47.619 2.16 0.00 32.98 4.01
3354 3474 1.643832 CGCGCAGATAGAAAAGGCC 59.356 57.895 8.75 0.00 0.00 5.19
3366 3486 1.269448 GAAAAGGCCGAATGAGTTGCA 59.731 47.619 0.00 0.00 0.00 4.08
3376 3496 2.995466 ATGAGTTGCATGGTCGTTTG 57.005 45.000 0.00 0.00 35.42 2.93
3391 3511 1.632589 GTTTGGGCCTGAACTTCCAT 58.367 50.000 4.53 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 2.565841 GTTGAAGGCGAGCTCCATATT 58.434 47.619 8.47 0.00 0.00 1.28
20 21 2.297597 CCAGACAAGAGGAAGTCTCGTT 59.702 50.000 0.00 0.00 46.82 3.85
21 22 1.889829 CCAGACAAGAGGAAGTCTCGT 59.110 52.381 0.00 0.00 46.82 4.18
35 36 1.304134 TCTCGCCTACAGCCAGACA 60.304 57.895 0.00 0.00 33.34 3.41
36 37 3.604629 TCTCGCCTACAGCCAGAC 58.395 61.111 0.00 0.00 33.34 3.51
39 40 1.613925 GATATGTCTCGCCTACAGCCA 59.386 52.381 0.00 0.00 38.78 4.75
49 50 1.373497 GGGGCGCTGATATGTCTCG 60.373 63.158 7.64 0.00 0.00 4.04
81 82 1.609555 CTTCTCGAGACCCCCTATTCG 59.390 57.143 16.36 0.00 34.56 3.34
122 126 1.327764 CGAAAGCTATTTGTCCTCGGC 59.672 52.381 0.00 0.00 0.00 5.54
159 163 1.046472 TTGATACCGGGCCTCACGAT 61.046 55.000 6.32 0.00 0.00 3.73
160 164 1.683025 TTGATACCGGGCCTCACGA 60.683 57.895 6.32 0.00 0.00 4.35
191 195 9.487790 TTTTAAGAAATCCATGTTAGGCTTTTG 57.512 29.630 0.00 0.00 27.83 2.44
225 229 7.063662 TGCATGCATACATTTGTTCTTCAATTC 59.936 33.333 18.46 0.00 35.84 2.17
230 234 6.268797 CATGCATGCATACATTTGTTCTTC 57.731 37.500 31.73 0.00 32.87 2.87
246 250 1.816835 AGAAGTTGGAGTGCATGCATG 59.183 47.619 25.64 22.70 0.00 4.06
250 254 4.778534 AATGAAGAAGTTGGAGTGCATG 57.221 40.909 0.00 0.00 0.00 4.06
333 337 7.039363 CCACCCATTTTATTCAGTGGAGTAAAA 60.039 37.037 0.64 7.34 46.15 1.52
334 338 6.435904 CCACCCATTTTATTCAGTGGAGTAAA 59.564 38.462 0.64 0.00 46.15 2.01
335 339 5.949354 CCACCCATTTTATTCAGTGGAGTAA 59.051 40.000 0.64 0.00 46.15 2.24
336 340 5.014755 ACCACCCATTTTATTCAGTGGAGTA 59.985 40.000 13.57 0.00 46.15 2.59
337 341 4.202673 ACCACCCATTTTATTCAGTGGAGT 60.203 41.667 13.57 0.00 46.15 3.85
338 342 4.344104 ACCACCCATTTTATTCAGTGGAG 58.656 43.478 13.57 0.00 46.15 3.86
339 343 4.396357 ACCACCCATTTTATTCAGTGGA 57.604 40.909 13.57 0.00 46.15 4.02
341 345 5.010516 TGTGAACCACCCATTTTATTCAGTG 59.989 40.000 0.00 0.00 32.73 3.66
342 346 5.144100 TGTGAACCACCCATTTTATTCAGT 58.856 37.500 0.00 0.00 32.73 3.41
343 347 5.720371 TGTGAACCACCCATTTTATTCAG 57.280 39.130 0.00 0.00 32.73 3.02
344 348 7.782897 TTATGTGAACCACCCATTTTATTCA 57.217 32.000 0.00 0.00 32.73 2.57
345 349 7.926018 GGATTATGTGAACCACCCATTTTATTC 59.074 37.037 0.00 0.00 32.73 1.75
346 350 7.147567 GGGATTATGTGAACCACCCATTTTATT 60.148 37.037 0.00 0.00 36.27 1.40
347 351 6.326323 GGGATTATGTGAACCACCCATTTTAT 59.674 38.462 0.00 0.00 36.27 1.40
348 352 5.659079 GGGATTATGTGAACCACCCATTTTA 59.341 40.000 0.00 0.00 36.27 1.52
349 353 4.469586 GGGATTATGTGAACCACCCATTTT 59.530 41.667 0.00 0.00 36.27 1.82
350 354 4.030216 GGGATTATGTGAACCACCCATTT 58.970 43.478 0.00 0.00 36.27 2.32
351 355 3.629796 GGGGATTATGTGAACCACCCATT 60.630 47.826 0.00 0.00 37.78 3.16
352 356 2.091333 GGGGATTATGTGAACCACCCAT 60.091 50.000 0.00 0.00 37.78 4.00
353 357 1.286553 GGGGATTATGTGAACCACCCA 59.713 52.381 0.00 0.00 37.78 4.51
354 358 1.569072 AGGGGATTATGTGAACCACCC 59.431 52.381 0.00 0.00 37.17 4.61
355 359 4.513406 TTAGGGGATTATGTGAACCACC 57.487 45.455 0.00 0.00 32.73 4.61
356 360 5.506708 ACTTTAGGGGATTATGTGAACCAC 58.493 41.667 0.00 0.00 34.56 4.16
357 361 5.251932 TGACTTTAGGGGATTATGTGAACCA 59.748 40.000 0.00 0.00 0.00 3.67
358 362 5.751586 TGACTTTAGGGGATTATGTGAACC 58.248 41.667 0.00 0.00 0.00 3.62
359 363 7.661847 CCTATGACTTTAGGGGATTATGTGAAC 59.338 40.741 0.00 0.00 35.96 3.18
360 364 7.745717 CCTATGACTTTAGGGGATTATGTGAA 58.254 38.462 0.00 0.00 35.96 3.18
361 365 7.316393 CCTATGACTTTAGGGGATTATGTGA 57.684 40.000 0.00 0.00 35.96 3.58
372 376 3.325135 CACCCTAGCCCTATGACTTTAGG 59.675 52.174 0.00 0.00 38.82 2.69
373 377 3.967987 ACACCCTAGCCCTATGACTTTAG 59.032 47.826 0.00 0.00 0.00 1.85
374 378 3.709653 CACACCCTAGCCCTATGACTTTA 59.290 47.826 0.00 0.00 0.00 1.85
375 379 2.505819 CACACCCTAGCCCTATGACTTT 59.494 50.000 0.00 0.00 0.00 2.66
376 380 2.119495 CACACCCTAGCCCTATGACTT 58.881 52.381 0.00 0.00 0.00 3.01
377 381 1.794714 CACACCCTAGCCCTATGACT 58.205 55.000 0.00 0.00 0.00 3.41
378 382 0.106894 GCACACCCTAGCCCTATGAC 59.893 60.000 0.00 0.00 0.00 3.06
379 383 1.399744 CGCACACCCTAGCCCTATGA 61.400 60.000 0.00 0.00 0.00 2.15
380 384 1.069765 CGCACACCCTAGCCCTATG 59.930 63.158 0.00 0.00 0.00 2.23
381 385 1.382695 ACGCACACCCTAGCCCTAT 60.383 57.895 0.00 0.00 0.00 2.57
382 386 2.038329 ACGCACACCCTAGCCCTA 59.962 61.111 0.00 0.00 0.00 3.53
383 387 3.706373 CACGCACACCCTAGCCCT 61.706 66.667 0.00 0.00 0.00 5.19
384 388 4.016706 ACACGCACACCCTAGCCC 62.017 66.667 0.00 0.00 0.00 5.19
385 389 2.742372 CACACGCACACCCTAGCC 60.742 66.667 0.00 0.00 0.00 3.93
386 390 2.030562 ACACACGCACACCCTAGC 59.969 61.111 0.00 0.00 0.00 3.42
387 391 2.317609 GCACACACGCACACCCTAG 61.318 63.158 0.00 0.00 0.00 3.02
388 392 2.280524 GCACACACGCACACCCTA 60.281 61.111 0.00 0.00 0.00 3.53
391 395 3.783588 GAACGCACACACGCACACC 62.784 63.158 0.00 0.00 36.19 4.16
392 396 2.350760 GAACGCACACACGCACAC 60.351 61.111 0.00 0.00 36.19 3.82
393 397 0.876342 TATGAACGCACACACGCACA 60.876 50.000 0.00 0.00 36.19 4.57
394 398 0.179250 CTATGAACGCACACACGCAC 60.179 55.000 0.00 0.00 36.19 5.34
395 399 1.288419 CCTATGAACGCACACACGCA 61.288 55.000 0.00 0.00 36.19 5.24
396 400 1.419922 CCTATGAACGCACACACGC 59.580 57.895 0.00 0.00 36.19 5.34
397 401 1.358725 CCCCTATGAACGCACACACG 61.359 60.000 0.00 0.00 39.50 4.49
398 402 0.321298 ACCCCTATGAACGCACACAC 60.321 55.000 0.00 0.00 0.00 3.82
399 403 0.321210 CACCCCTATGAACGCACACA 60.321 55.000 0.00 0.00 0.00 3.72
400 404 0.036765 TCACCCCTATGAACGCACAC 60.037 55.000 0.00 0.00 0.00 3.82
401 405 0.249120 CTCACCCCTATGAACGCACA 59.751 55.000 0.00 0.00 0.00 4.57
402 406 0.249398 ACTCACCCCTATGAACGCAC 59.751 55.000 0.00 0.00 0.00 5.34
403 407 0.981183 AACTCACCCCTATGAACGCA 59.019 50.000 0.00 0.00 0.00 5.24
404 408 1.737793 CAAACTCACCCCTATGAACGC 59.262 52.381 0.00 0.00 0.00 4.84
405 409 3.328382 TCAAACTCACCCCTATGAACG 57.672 47.619 0.00 0.00 0.00 3.95
406 410 3.756963 GGTTCAAACTCACCCCTATGAAC 59.243 47.826 7.68 7.68 43.51 3.18
407 411 3.396276 TGGTTCAAACTCACCCCTATGAA 59.604 43.478 0.00 0.00 31.24 2.57
408 412 2.983192 TGGTTCAAACTCACCCCTATGA 59.017 45.455 0.00 0.00 31.24 2.15
409 413 3.433306 TGGTTCAAACTCACCCCTATG 57.567 47.619 0.00 0.00 31.24 2.23
410 414 3.053619 GGATGGTTCAAACTCACCCCTAT 60.054 47.826 0.00 0.00 31.24 2.57
411 415 2.307686 GGATGGTTCAAACTCACCCCTA 59.692 50.000 0.00 0.00 31.24 3.53
412 416 1.075536 GGATGGTTCAAACTCACCCCT 59.924 52.381 0.00 0.00 31.24 4.79
413 417 1.203001 TGGATGGTTCAAACTCACCCC 60.203 52.381 0.00 0.00 31.24 4.95
414 418 2.286365 TGGATGGTTCAAACTCACCC 57.714 50.000 0.00 0.00 31.24 4.61
415 419 4.871933 AAATGGATGGTTCAAACTCACC 57.128 40.909 0.00 0.00 0.00 4.02
416 420 5.600696 ACAAAATGGATGGTTCAAACTCAC 58.399 37.500 0.00 0.00 0.00 3.51
417 421 5.867903 ACAAAATGGATGGTTCAAACTCA 57.132 34.783 0.00 0.00 0.00 3.41
418 422 7.384932 CCTAAACAAAATGGATGGTTCAAACTC 59.615 37.037 0.00 0.00 0.00 3.01
419 423 7.216494 CCTAAACAAAATGGATGGTTCAAACT 58.784 34.615 0.00 0.00 0.00 2.66
420 424 6.073276 GCCTAAACAAAATGGATGGTTCAAAC 60.073 38.462 0.00 0.00 0.00 2.93
421 425 5.994668 GCCTAAACAAAATGGATGGTTCAAA 59.005 36.000 0.00 0.00 0.00 2.69
422 426 5.512232 GGCCTAAACAAAATGGATGGTTCAA 60.512 40.000 0.00 0.00 0.00 2.69
423 427 4.020662 GGCCTAAACAAAATGGATGGTTCA 60.021 41.667 0.00 0.00 0.00 3.18
424 428 4.020662 TGGCCTAAACAAAATGGATGGTTC 60.021 41.667 3.32 0.00 0.00 3.62
425 429 3.906846 TGGCCTAAACAAAATGGATGGTT 59.093 39.130 3.32 0.00 0.00 3.67
426 430 3.260632 GTGGCCTAAACAAAATGGATGGT 59.739 43.478 3.32 0.00 0.00 3.55
427 431 3.675775 CGTGGCCTAAACAAAATGGATGG 60.676 47.826 3.32 0.00 0.00 3.51
428 432 3.510719 CGTGGCCTAAACAAAATGGATG 58.489 45.455 3.32 0.00 0.00 3.51
429 433 2.094234 GCGTGGCCTAAACAAAATGGAT 60.094 45.455 3.32 0.00 0.00 3.41
430 434 1.271102 GCGTGGCCTAAACAAAATGGA 59.729 47.619 3.32 0.00 0.00 3.41
431 435 1.272212 AGCGTGGCCTAAACAAAATGG 59.728 47.619 3.32 0.00 0.00 3.16
432 436 2.723124 AGCGTGGCCTAAACAAAATG 57.277 45.000 3.32 0.00 0.00 2.32
433 437 2.288763 CCAAGCGTGGCCTAAACAAAAT 60.289 45.455 5.51 0.00 38.35 1.82
434 438 1.067821 CCAAGCGTGGCCTAAACAAAA 59.932 47.619 5.51 0.00 38.35 2.44
435 439 0.671251 CCAAGCGTGGCCTAAACAAA 59.329 50.000 5.51 0.00 38.35 2.83
436 440 0.179015 TCCAAGCGTGGCCTAAACAA 60.179 50.000 14.54 0.00 45.54 2.83
437 441 0.037590 ATCCAAGCGTGGCCTAAACA 59.962 50.000 14.54 0.00 45.54 2.83
438 442 1.135402 CAATCCAAGCGTGGCCTAAAC 60.135 52.381 14.54 0.00 45.54 2.01
439 443 1.173043 CAATCCAAGCGTGGCCTAAA 58.827 50.000 14.54 0.00 45.54 1.85
440 444 0.326595 TCAATCCAAGCGTGGCCTAA 59.673 50.000 14.54 0.00 45.54 2.69
441 445 0.392461 GTCAATCCAAGCGTGGCCTA 60.392 55.000 14.54 0.00 45.54 3.93
442 446 1.675641 GTCAATCCAAGCGTGGCCT 60.676 57.895 14.54 0.51 45.54 5.19
443 447 2.700773 GGTCAATCCAAGCGTGGCC 61.701 63.158 14.54 5.14 45.54 5.36
444 448 2.877691 GGTCAATCCAAGCGTGGC 59.122 61.111 14.54 0.00 45.54 5.01
448 452 1.722011 ACTTACGGTCAATCCAAGCG 58.278 50.000 0.00 0.00 42.91 4.68
449 453 5.813080 ATTAACTTACGGTCAATCCAAGC 57.187 39.130 0.00 0.00 35.57 4.01
450 454 6.929896 CGTATTAACTTACGGTCAATCCAAG 58.070 40.000 1.48 0.00 40.90 3.61
451 455 6.890663 CGTATTAACTTACGGTCAATCCAA 57.109 37.500 1.48 0.00 40.90 3.53
469 473 9.849166 CACTTGTAAAATTGATAAACCCGTATT 57.151 29.630 0.00 0.00 0.00 1.89
470 474 9.016438 ACACTTGTAAAATTGATAAACCCGTAT 57.984 29.630 0.00 0.00 0.00 3.06
471 475 8.393671 ACACTTGTAAAATTGATAAACCCGTA 57.606 30.769 0.00 0.00 0.00 4.02
472 476 7.279750 ACACTTGTAAAATTGATAAACCCGT 57.720 32.000 0.00 0.00 0.00 5.28
473 477 7.751793 GGTACACTTGTAAAATTGATAAACCCG 59.248 37.037 0.00 0.00 31.52 5.28
474 478 8.799367 AGGTACACTTGTAAAATTGATAAACCC 58.201 33.333 0.00 0.00 31.52 4.11
480 484 8.932791 CGAGTAAGGTACACTTGTAAAATTGAT 58.067 33.333 0.00 0.00 40.37 2.57
481 485 8.143193 TCGAGTAAGGTACACTTGTAAAATTGA 58.857 33.333 0.00 0.00 40.37 2.57
482 486 8.301730 TCGAGTAAGGTACACTTGTAAAATTG 57.698 34.615 0.00 0.00 40.37 2.32
483 487 9.498176 AATCGAGTAAGGTACACTTGTAAAATT 57.502 29.630 0.00 0.00 40.37 1.82
485 489 9.630098 CTAATCGAGTAAGGTACACTTGTAAAA 57.370 33.333 0.00 0.00 40.37 1.52
486 490 9.013229 TCTAATCGAGTAAGGTACACTTGTAAA 57.987 33.333 0.00 0.00 40.37 2.01
487 491 8.565896 TCTAATCGAGTAAGGTACACTTGTAA 57.434 34.615 0.00 0.00 40.37 2.41
488 492 8.206325 CTCTAATCGAGTAAGGTACACTTGTA 57.794 38.462 0.00 0.00 40.37 2.41
489 493 7.086230 CTCTAATCGAGTAAGGTACACTTGT 57.914 40.000 0.00 0.00 40.37 3.16
503 507 3.491267 GGCCGAAAATCACTCTAATCGAG 59.509 47.826 0.00 0.00 45.56 4.04
504 508 3.454375 GGCCGAAAATCACTCTAATCGA 58.546 45.455 0.00 0.00 32.38 3.59
505 509 2.218759 CGGCCGAAAATCACTCTAATCG 59.781 50.000 24.07 0.00 0.00 3.34
506 510 2.544267 CCGGCCGAAAATCACTCTAATC 59.456 50.000 30.73 0.00 0.00 1.75
507 511 2.169769 TCCGGCCGAAAATCACTCTAAT 59.830 45.455 30.73 0.00 0.00 1.73
508 512 1.551430 TCCGGCCGAAAATCACTCTAA 59.449 47.619 30.73 0.00 0.00 2.10
509 513 1.187974 TCCGGCCGAAAATCACTCTA 58.812 50.000 30.73 0.00 0.00 2.43
510 514 0.323629 TTCCGGCCGAAAATCACTCT 59.676 50.000 30.73 0.00 0.00 3.24
511 515 1.135774 GTTTCCGGCCGAAAATCACTC 60.136 52.381 30.73 1.90 42.11 3.51
512 516 0.879090 GTTTCCGGCCGAAAATCACT 59.121 50.000 30.73 0.00 42.11 3.41
513 517 0.453782 CGTTTCCGGCCGAAAATCAC 60.454 55.000 30.73 14.78 42.11 3.06
514 518 0.603172 TCGTTTCCGGCCGAAAATCA 60.603 50.000 30.73 6.66 42.11 2.57
515 519 0.730840 ATCGTTTCCGGCCGAAAATC 59.269 50.000 30.73 17.51 42.11 2.17
516 520 1.667212 GTATCGTTTCCGGCCGAAAAT 59.333 47.619 30.73 17.10 42.11 1.82
517 521 1.077915 GTATCGTTTCCGGCCGAAAA 58.922 50.000 30.73 18.67 42.11 2.29
518 522 0.037512 TGTATCGTTTCCGGCCGAAA 60.038 50.000 30.73 21.50 38.16 3.46
519 523 0.458889 CTGTATCGTTTCCGGCCGAA 60.459 55.000 30.73 16.49 36.57 4.30
520 524 1.140161 CTGTATCGTTTCCGGCCGA 59.860 57.895 30.73 10.38 37.51 5.54
521 525 1.140161 TCTGTATCGTTTCCGGCCG 59.860 57.895 21.04 21.04 33.95 6.13
522 526 1.143969 CGTCTGTATCGTTTCCGGCC 61.144 60.000 0.00 0.00 33.95 6.13
523 527 0.457337 ACGTCTGTATCGTTTCCGGC 60.457 55.000 0.00 0.00 38.38 6.13
524 528 1.265568 CACGTCTGTATCGTTTCCGG 58.734 55.000 0.00 0.00 39.55 5.14
525 529 0.638746 GCACGTCTGTATCGTTTCCG 59.361 55.000 0.00 0.00 39.55 4.30
526 530 1.654105 CTGCACGTCTGTATCGTTTCC 59.346 52.381 0.00 0.00 39.55 3.13
527 531 2.592194 TCTGCACGTCTGTATCGTTTC 58.408 47.619 0.00 0.00 39.55 2.78
528 532 2.717580 TCTGCACGTCTGTATCGTTT 57.282 45.000 0.00 0.00 39.55 3.60
529 533 2.596452 CTTCTGCACGTCTGTATCGTT 58.404 47.619 0.00 0.00 39.55 3.85
530 534 1.732732 GCTTCTGCACGTCTGTATCGT 60.733 52.381 0.00 0.00 42.33 3.73
531 535 0.917259 GCTTCTGCACGTCTGTATCG 59.083 55.000 0.00 0.00 39.41 2.92
532 536 0.917259 CGCTTCTGCACGTCTGTATC 59.083 55.000 0.00 0.00 39.64 2.24
533 537 0.243907 ACGCTTCTGCACGTCTGTAT 59.756 50.000 0.00 0.00 38.28 2.29
534 538 0.663269 CACGCTTCTGCACGTCTGTA 60.663 55.000 0.00 0.00 41.32 2.74
535 539 1.951130 CACGCTTCTGCACGTCTGT 60.951 57.895 0.00 0.00 41.32 3.41
536 540 0.663269 TACACGCTTCTGCACGTCTG 60.663 55.000 0.00 0.00 41.32 3.51
537 541 0.243907 ATACACGCTTCTGCACGTCT 59.756 50.000 0.00 0.00 41.32 4.18
538 542 1.068474 AATACACGCTTCTGCACGTC 58.932 50.000 0.00 0.00 41.32 4.34
539 543 1.508632 AAATACACGCTTCTGCACGT 58.491 45.000 0.00 0.00 44.75 4.49
540 544 2.594529 AAAATACACGCTTCTGCACG 57.405 45.000 0.00 0.00 39.64 5.34
558 562 8.851541 ATTTCTAACAGATACACCCGTAAAAA 57.148 30.769 0.00 0.00 0.00 1.94
560 564 9.537192 CATATTTCTAACAGATACACCCGTAAA 57.463 33.333 0.00 0.00 0.00 2.01
561 565 8.916062 TCATATTTCTAACAGATACACCCGTAA 58.084 33.333 0.00 0.00 0.00 3.18
562 566 8.355169 GTCATATTTCTAACAGATACACCCGTA 58.645 37.037 0.00 0.00 0.00 4.02
563 567 7.147794 TGTCATATTTCTAACAGATACACCCGT 60.148 37.037 0.00 0.00 0.00 5.28
564 568 7.207383 TGTCATATTTCTAACAGATACACCCG 58.793 38.462 0.00 0.00 0.00 5.28
565 569 8.958119 TTGTCATATTTCTAACAGATACACCC 57.042 34.615 0.00 0.00 0.00 4.61
571 575 8.844244 GCTTGGATTGTCATATTTCTAACAGAT 58.156 33.333 0.00 0.00 0.00 2.90
572 576 7.011389 CGCTTGGATTGTCATATTTCTAACAGA 59.989 37.037 0.00 0.00 0.00 3.41
573 577 7.128331 CGCTTGGATTGTCATATTTCTAACAG 58.872 38.462 0.00 0.00 0.00 3.16
574 578 6.038161 CCGCTTGGATTGTCATATTTCTAACA 59.962 38.462 0.00 0.00 33.02 2.41
575 579 6.430451 CCGCTTGGATTGTCATATTTCTAAC 58.570 40.000 0.00 0.00 33.02 2.34
576 580 5.530915 CCCGCTTGGATTGTCATATTTCTAA 59.469 40.000 0.00 0.00 35.39 2.10
577 581 5.063204 CCCGCTTGGATTGTCATATTTCTA 58.937 41.667 0.00 0.00 35.39 2.10
578 582 3.885297 CCCGCTTGGATTGTCATATTTCT 59.115 43.478 0.00 0.00 35.39 2.52
579 583 3.004734 CCCCGCTTGGATTGTCATATTTC 59.995 47.826 0.00 0.00 35.39 2.17
580 584 2.958355 CCCCGCTTGGATTGTCATATTT 59.042 45.455 0.00 0.00 35.39 1.40
581 585 2.586425 CCCCGCTTGGATTGTCATATT 58.414 47.619 0.00 0.00 35.39 1.28
582 586 1.819305 GCCCCGCTTGGATTGTCATAT 60.819 52.381 0.00 0.00 35.39 1.78
583 587 0.465460 GCCCCGCTTGGATTGTCATA 60.465 55.000 0.00 0.00 35.39 2.15
584 588 1.754234 GCCCCGCTTGGATTGTCAT 60.754 57.895 0.00 0.00 35.39 3.06
585 589 2.361104 GCCCCGCTTGGATTGTCA 60.361 61.111 0.00 0.00 35.39 3.58
586 590 3.140814 GGCCCCGCTTGGATTGTC 61.141 66.667 0.00 0.00 35.39 3.18
587 591 1.858739 TAAGGCCCCGCTTGGATTGT 61.859 55.000 0.00 0.00 35.39 2.71
588 592 1.077068 TAAGGCCCCGCTTGGATTG 60.077 57.895 0.00 0.00 35.39 2.67
589 593 1.227383 CTAAGGCCCCGCTTGGATT 59.773 57.895 0.00 0.00 35.39 3.01
590 594 2.757124 CCTAAGGCCCCGCTTGGAT 61.757 63.158 0.00 0.00 35.39 3.41
591 595 3.407967 CCTAAGGCCCCGCTTGGA 61.408 66.667 0.00 0.00 35.39 3.53
592 596 4.506255 CCCTAAGGCCCCGCTTGG 62.506 72.222 0.00 0.00 0.00 3.61
593 597 2.325393 CTACCCTAAGGCCCCGCTTG 62.325 65.000 0.00 0.00 36.11 4.01
594 598 2.041596 TACCCTAAGGCCCCGCTT 59.958 61.111 0.00 0.00 36.11 4.68
595 599 1.953100 TACTACCCTAAGGCCCCGCT 61.953 60.000 0.00 0.00 36.11 5.52
596 600 1.050421 TTACTACCCTAAGGCCCCGC 61.050 60.000 0.00 0.00 36.11 6.13
597 601 1.499368 TTTACTACCCTAAGGCCCCG 58.501 55.000 0.00 0.00 36.11 5.73
598 602 2.107726 CCATTTACTACCCTAAGGCCCC 59.892 54.545 0.00 0.00 36.11 5.80
599 603 3.050835 TCCATTTACTACCCTAAGGCCC 58.949 50.000 0.00 0.00 36.11 5.80
600 604 3.715315 AGTCCATTTACTACCCTAAGGCC 59.285 47.826 0.00 0.00 36.11 5.19
601 605 5.369409 AAGTCCATTTACTACCCTAAGGC 57.631 43.478 0.00 0.00 36.11 4.35
721 731 5.584551 AGATCTGGTGGGTTTTTAGAAGT 57.415 39.130 0.00 0.00 0.00 3.01
730 740 3.814504 ACAATGAAGATCTGGTGGGTT 57.185 42.857 0.00 0.00 0.00 4.11
731 741 5.440610 GAATACAATGAAGATCTGGTGGGT 58.559 41.667 0.00 0.00 0.00 4.51
928 950 6.261603 ACGTACATCAAACCGATACTGATCTA 59.738 38.462 0.00 0.00 31.20 1.98
937 959 2.087501 TGCACGTACATCAAACCGAT 57.912 45.000 0.00 0.00 33.27 4.18
943 965 2.412870 CTGGAGTTGCACGTACATCAA 58.587 47.619 0.00 0.00 0.00 2.57
1000 1044 3.878103 AGCGATCTACAAGACTATGACGT 59.122 43.478 0.00 0.00 0.00 4.34
1013 1057 0.461961 AGGTGAGGCAAGCGATCTAC 59.538 55.000 0.00 0.00 0.00 2.59
1405 1458 0.742990 CGGCCGCCTTGTTCTTGATA 60.743 55.000 14.67 0.00 0.00 2.15
1963 2016 1.517832 CTTGTAGTCGAGGCCCCAG 59.482 63.158 0.00 0.00 0.00 4.45
2208 2262 9.886132 AAAAGAGAGAACAAAAACTACTAGTCA 57.114 29.630 0.00 0.00 0.00 3.41
2214 2268 7.220875 CCAGCAAAAAGAGAGAACAAAAACTAC 59.779 37.037 0.00 0.00 0.00 2.73
2222 2276 3.576078 TCCCAGCAAAAAGAGAGAACA 57.424 42.857 0.00 0.00 0.00 3.18
2223 2277 4.520492 TGATTCCCAGCAAAAAGAGAGAAC 59.480 41.667 0.00 0.00 0.00 3.01
2224 2278 4.728772 TGATTCCCAGCAAAAAGAGAGAA 58.271 39.130 0.00 0.00 0.00 2.87
2225 2279 4.202503 ACTGATTCCCAGCAAAAAGAGAGA 60.203 41.667 0.00 0.00 46.81 3.10
2226 2280 4.077822 ACTGATTCCCAGCAAAAAGAGAG 58.922 43.478 0.00 0.00 46.81 3.20
2281 2344 3.337358 TGTGATGATGTACAAGGCAGTG 58.663 45.455 0.00 0.00 0.00 3.66
2529 2596 1.734465 CTTCTTGTCGATGCACCCTTC 59.266 52.381 0.00 0.00 0.00 3.46
2532 2599 1.026718 CCCTTCTTGTCGATGCACCC 61.027 60.000 0.00 0.00 0.00 4.61
2535 2602 0.396435 ACACCCTTCTTGTCGATGCA 59.604 50.000 0.00 0.00 0.00 3.96
2536 2603 2.380084 TACACCCTTCTTGTCGATGC 57.620 50.000 0.00 0.00 0.00 3.91
2537 2604 4.062293 TGTTTACACCCTTCTTGTCGATG 58.938 43.478 0.00 0.00 0.00 3.84
2538 2605 4.345859 TGTTTACACCCTTCTTGTCGAT 57.654 40.909 0.00 0.00 0.00 3.59
2539 2606 3.823281 TGTTTACACCCTTCTTGTCGA 57.177 42.857 0.00 0.00 0.00 4.20
2540 2607 4.513692 TGATTGTTTACACCCTTCTTGTCG 59.486 41.667 0.00 0.00 0.00 4.35
2541 2608 6.039382 AGTTGATTGTTTACACCCTTCTTGTC 59.961 38.462 0.00 0.00 0.00 3.18
2542 2609 5.891551 AGTTGATTGTTTACACCCTTCTTGT 59.108 36.000 0.00 0.00 0.00 3.16
2543 2610 6.391227 AGTTGATTGTTTACACCCTTCTTG 57.609 37.500 0.00 0.00 0.00 3.02
2545 2612 6.002082 GGTAGTTGATTGTTTACACCCTTCT 58.998 40.000 0.00 0.00 0.00 2.85
2546 2613 5.182570 GGGTAGTTGATTGTTTACACCCTTC 59.817 44.000 0.00 0.00 41.02 3.46
2547 2614 5.074804 GGGTAGTTGATTGTTTACACCCTT 58.925 41.667 0.00 0.00 41.02 3.95
2549 2616 4.659115 AGGGTAGTTGATTGTTTACACCC 58.341 43.478 0.00 0.00 43.94 4.61
2563 2634 7.898014 AATTTCAGAAAACTGAAGGGTAGTT 57.102 32.000 11.49 0.00 43.21 2.24
2657 2728 1.139256 CCTGATGCTCTCTGCTGATGT 59.861 52.381 0.00 0.00 43.37 3.06
2826 2897 3.670359 CGATTTGGCGATTTCTCTTTGCA 60.670 43.478 0.00 0.00 0.00 4.08
2886 2957 4.996758 TGCATTGATCGTAATCCCTATGTG 59.003 41.667 0.00 0.00 0.00 3.21
2993 3064 6.795098 TTGTGTGATTGACCTACATGTAAC 57.205 37.500 7.06 0.26 0.00 2.50
3018 3089 8.229811 TCGAATTATGATGCATATTGTTAGCAC 58.770 33.333 0.00 0.00 41.60 4.40
3043 3114 5.251601 ACGTCTAGTAGATGCTCCTTTTC 57.748 43.478 17.69 0.00 34.63 2.29
3063 3134 5.975939 GGTAGTATCCACAACTTAGCTTACG 59.024 44.000 0.00 0.00 0.00 3.18
3132 3251 3.791887 CCTACACTGAAGCGTTCTATTCG 59.208 47.826 0.00 0.00 0.00 3.34
3199 3319 4.072131 GCTCAAGGTGTAAATTGACCTCA 58.928 43.478 4.89 0.00 42.03 3.86
3315 3435 2.223433 GGTAGCACAAGCATTCATGAGC 60.223 50.000 0.00 0.00 45.49 4.26
3319 3439 0.734889 GCGGTAGCACAAGCATTCAT 59.265 50.000 0.00 0.00 45.49 2.57
3329 3449 0.248907 TTCTATCTGCGCGGTAGCAC 60.249 55.000 17.37 0.00 45.49 4.40
3354 3474 1.078709 ACGACCATGCAACTCATTCG 58.921 50.000 0.00 0.00 39.84 3.34
3366 3486 0.893727 GTTCAGGCCCAAACGACCAT 60.894 55.000 0.00 0.00 0.00 3.55
3376 3496 2.054453 GCCATGGAAGTTCAGGCCC 61.054 63.158 18.40 0.00 39.42 5.80


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

AutoCloner maintained by Alex Coulton.