Multiple sequence alignment - TraesCS3A01G042800

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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 TraesCS3A01G042800 chr3A 100.000 2979 0 0 1 2979 23144050 23141072 0.000000e+00 5502
1 TraesCS3A01G042800 chr3A 93.600 500 31 1 83 582 696879149 696879647 0.000000e+00 745
2 TraesCS3A01G042800 chr7A 96.406 2365 75 4 586 2949 134461737 134464092 0.000000e+00 3888
3 TraesCS3A01G042800 chr7A 93.843 2274 90 14 586 2852 675422258 675424488 0.000000e+00 3378
4 TraesCS3A01G042800 chr7A 90.669 1211 63 17 1782 2949 133613052 133611849 0.000000e+00 1565
5 TraesCS3A01G042800 chr7A 93.281 506 33 1 84 589 495187228 495186724 0.000000e+00 745
6 TraesCS3A01G042800 chr7A 95.714 70 3 0 2880 2949 255925387 255925456 2.430000e-21 113
7 TraesCS3A01G042800 chr7A 88.636 88 3 7 2868 2949 675424456 675424542 1.890000e-17 100
8 TraesCS3A01G042800 chr2A 94.849 2388 101 14 592 2979 514763732 514766097 0.000000e+00 3709
9 TraesCS3A01G042800 chr2A 93.922 2073 111 6 586 2645 458970802 458968732 0.000000e+00 3116
10 TraesCS3A01G042800 chr4D 94.032 2396 113 12 575 2949 440465466 440463080 0.000000e+00 3605
11 TraesCS3A01G042800 chr7D 93.708 2384 111 13 586 2949 530867456 530865092 0.000000e+00 3535
12 TraesCS3A01G042800 chr7D 93.082 2385 118 15 586 2949 596123081 596120723 0.000000e+00 3446
13 TraesCS3A01G042800 chr7D 93.474 1701 93 6 586 2272 592400973 592402669 0.000000e+00 2510
14 TraesCS3A01G042800 chr7D 94.075 1654 68 12 1316 2949 70680369 70678726 0.000000e+00 2484
15 TraesCS3A01G042800 chr7D 94.681 94 3 2 1 93 416264302 416264210 8.610000e-31 145
16 TraesCS3A01G042800 chr7D 93.617 94 4 2 1 93 633967809 633967901 4.000000e-29 139
17 TraesCS3A01G042800 chr6A 93.501 2385 109 15 586 2949 508298181 508300540 0.000000e+00 3504
18 TraesCS3A01G042800 chr6A 90.158 2408 145 46 580 2949 134201694 134204047 0.000000e+00 3049
19 TraesCS3A01G042800 chr6A 93.788 499 30 1 84 582 302029207 302029704 0.000000e+00 749
20 TraesCS3A01G042800 chr6A 92.786 499 35 1 84 582 302024864 302025361 0.000000e+00 721
21 TraesCS3A01G042800 chr5A 96.018 1959 76 2 586 2543 633045665 633043708 0.000000e+00 3184
22 TraesCS3A01G042800 chr5A 93.849 504 27 3 84 584 515821687 515821185 0.000000e+00 756
23 TraesCS3A01G042800 chr5A 92.871 505 32 3 84 585 634039196 634038693 0.000000e+00 730
24 TraesCS3A01G042800 chr5A 92.871 505 30 5 84 585 515826008 515825507 0.000000e+00 728
25 TraesCS3A01G042800 chr5A 92.534 509 33 4 81 585 634045725 634045218 0.000000e+00 725
26 TraesCS3A01G042800 chr5D 93.767 1476 60 12 1494 2949 351321021 351322484 0.000000e+00 2187
27 TraesCS3A01G042800 chr5D 94.081 1284 61 4 586 1856 443521254 443522535 0.000000e+00 1936
28 TraesCS3A01G042800 chr5D 93.617 94 4 2 1 93 430721070 430720978 4.000000e-29 139
29 TraesCS3A01G042800 chr1D 93.028 502 33 1 84 585 224816112 224816611 0.000000e+00 732
30 TraesCS3A01G042800 chr7B 94.681 94 3 2 1 93 673647718 673647626 8.610000e-31 145
31 TraesCS3A01G042800 chr6D 93.617 94 4 2 1 93 425333401 425333493 4.000000e-29 139
32 TraesCS3A01G042800 chr6D 93.617 94 4 2 1 93 464708534 464708626 4.000000e-29 139
33 TraesCS3A01G042800 chr6B 93.617 94 4 2 1 93 658753413 658753505 4.000000e-29 139
34 TraesCS3A01G042800 chr6B 93.617 94 4 2 1 93 658755934 658756026 4.000000e-29 139
35 TraesCS3A01G042800 chr1B 93.617 94 4 2 1 93 269309578 269309670 4.000000e-29 139


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 TraesCS3A01G042800 chr3A 23141072 23144050 2978 True 5502 5502 100.0000 1 2979 1 chr3A.!!$R1 2978
1 TraesCS3A01G042800 chr7A 134461737 134464092 2355 False 3888 3888 96.4060 586 2949 1 chr7A.!!$F1 2363
2 TraesCS3A01G042800 chr7A 675422258 675424542 2284 False 1739 3378 91.2395 586 2949 2 chr7A.!!$F3 2363
3 TraesCS3A01G042800 chr7A 133611849 133613052 1203 True 1565 1565 90.6690 1782 2949 1 chr7A.!!$R1 1167
4 TraesCS3A01G042800 chr7A 495186724 495187228 504 True 745 745 93.2810 84 589 1 chr7A.!!$R2 505
5 TraesCS3A01G042800 chr2A 514763732 514766097 2365 False 3709 3709 94.8490 592 2979 1 chr2A.!!$F1 2387
6 TraesCS3A01G042800 chr2A 458968732 458970802 2070 True 3116 3116 93.9220 586 2645 1 chr2A.!!$R1 2059
7 TraesCS3A01G042800 chr4D 440463080 440465466 2386 True 3605 3605 94.0320 575 2949 1 chr4D.!!$R1 2374
8 TraesCS3A01G042800 chr7D 530865092 530867456 2364 True 3535 3535 93.7080 586 2949 1 chr7D.!!$R3 2363
9 TraesCS3A01G042800 chr7D 596120723 596123081 2358 True 3446 3446 93.0820 586 2949 1 chr7D.!!$R4 2363
10 TraesCS3A01G042800 chr7D 592400973 592402669 1696 False 2510 2510 93.4740 586 2272 1 chr7D.!!$F1 1686
11 TraesCS3A01G042800 chr7D 70678726 70680369 1643 True 2484 2484 94.0750 1316 2949 1 chr7D.!!$R1 1633
12 TraesCS3A01G042800 chr6A 508298181 508300540 2359 False 3504 3504 93.5010 586 2949 1 chr6A.!!$F2 2363
13 TraesCS3A01G042800 chr6A 134201694 134204047 2353 False 3049 3049 90.1580 580 2949 1 chr6A.!!$F1 2369
14 TraesCS3A01G042800 chr6A 302024864 302029704 4840 False 735 749 93.2870 84 582 2 chr6A.!!$F3 498
15 TraesCS3A01G042800 chr5A 633043708 633045665 1957 True 3184 3184 96.0180 586 2543 1 chr5A.!!$R1 1957
16 TraesCS3A01G042800 chr5A 515821185 515826008 4823 True 742 756 93.3600 84 585 2 chr5A.!!$R4 501
17 TraesCS3A01G042800 chr5A 634038693 634039196 503 True 730 730 92.8710 84 585 1 chr5A.!!$R2 501
18 TraesCS3A01G042800 chr5A 634045218 634045725 507 True 725 725 92.5340 81 585 1 chr5A.!!$R3 504
19 TraesCS3A01G042800 chr5D 351321021 351322484 1463 False 2187 2187 93.7670 1494 2949 1 chr5D.!!$F1 1455
20 TraesCS3A01G042800 chr5D 443521254 443522535 1281 False 1936 1936 94.0810 586 1856 1 chr5D.!!$F2 1270

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
576 578 0.171007 TAACACTGTACGGCGGCTAC 59.829 55.0 13.24 6.26 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2401 5865 0.751643 ACCCACACACCAAGCACTTC 60.752 55.0 0.0 0.0 0.0 3.01 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
62 63 8.956533 TGTCGACATTTATTTATCCTCATGAA 57.043 30.769 15.76 0.00 0.00 2.57
63 64 9.559732 TGTCGACATTTATTTATCCTCATGAAT 57.440 29.630 15.76 0.00 0.00 2.57
75 76 9.527157 TTTATCCTCATGAATTGTAAAAGACCA 57.473 29.630 0.00 0.00 0.00 4.02
76 77 9.699410 TTATCCTCATGAATTGTAAAAGACCAT 57.301 29.630 0.00 0.00 0.00 3.55
77 78 7.395190 TCCTCATGAATTGTAAAAGACCATG 57.605 36.000 0.00 0.00 33.32 3.66
78 79 6.377996 TCCTCATGAATTGTAAAAGACCATGG 59.622 38.462 11.19 11.19 33.00 3.66
79 80 6.377996 CCTCATGAATTGTAAAAGACCATGGA 59.622 38.462 21.47 0.00 33.00 3.41
80 81 7.069085 CCTCATGAATTGTAAAAGACCATGGAT 59.931 37.037 21.47 3.12 33.00 3.41
81 82 8.365060 TCATGAATTGTAAAAGACCATGGATT 57.635 30.769 21.47 10.06 33.00 3.01
82 83 8.252417 TCATGAATTGTAAAAGACCATGGATTG 58.748 33.333 21.47 0.00 33.00 2.67
143 145 6.741724 AGATAACTACAATTTTGGGTGGGAT 58.258 36.000 0.00 0.00 0.00 3.85
150 152 2.478872 TTTTGGGTGGGATTTGACCA 57.521 45.000 0.00 0.00 33.48 4.02
210 212 2.158957 ACGACTGATATCCACGGCAATT 60.159 45.455 14.37 0.00 0.00 2.32
229 231 1.045407 TGCTGAACTAACTCCACGGT 58.955 50.000 0.00 0.00 0.00 4.83
314 316 9.643693 AAATCGAAGAACATGCAAGAAAATAAT 57.356 25.926 0.00 0.00 43.58 1.28
316 318 9.941664 ATCGAAGAACATGCAAGAAAATAATAG 57.058 29.630 0.00 0.00 43.58 1.73
317 319 7.910162 TCGAAGAACATGCAAGAAAATAATAGC 59.090 33.333 0.00 0.00 0.00 2.97
318 320 7.166473 CGAAGAACATGCAAGAAAATAATAGCC 59.834 37.037 0.00 0.00 0.00 3.93
319 321 7.408756 AGAACATGCAAGAAAATAATAGCCA 57.591 32.000 0.00 0.00 0.00 4.75
320 322 7.839907 AGAACATGCAAGAAAATAATAGCCAA 58.160 30.769 0.00 0.00 0.00 4.52
321 323 7.977853 AGAACATGCAAGAAAATAATAGCCAAG 59.022 33.333 0.00 0.00 0.00 3.61
322 324 6.044682 ACATGCAAGAAAATAATAGCCAAGC 58.955 36.000 0.00 0.00 0.00 4.01
323 325 5.657826 TGCAAGAAAATAATAGCCAAGCA 57.342 34.783 0.00 0.00 0.00 3.91
324 326 6.035368 TGCAAGAAAATAATAGCCAAGCAA 57.965 33.333 0.00 0.00 0.00 3.91
325 327 6.642430 TGCAAGAAAATAATAGCCAAGCAAT 58.358 32.000 0.00 0.00 0.00 3.56
326 328 6.757947 TGCAAGAAAATAATAGCCAAGCAATC 59.242 34.615 0.00 0.00 0.00 2.67
327 329 6.982724 GCAAGAAAATAATAGCCAAGCAATCT 59.017 34.615 0.00 0.00 0.00 2.40
328 330 7.168804 GCAAGAAAATAATAGCCAAGCAATCTC 59.831 37.037 0.00 0.00 0.00 2.75
329 331 7.886629 AGAAAATAATAGCCAAGCAATCTCA 57.113 32.000 0.00 0.00 0.00 3.27
330 332 8.297470 AGAAAATAATAGCCAAGCAATCTCAA 57.703 30.769 0.00 0.00 0.00 3.02
331 333 8.752187 AGAAAATAATAGCCAAGCAATCTCAAA 58.248 29.630 0.00 0.00 0.00 2.69
332 334 9.369904 GAAAATAATAGCCAAGCAATCTCAAAA 57.630 29.630 0.00 0.00 0.00 2.44
333 335 9.895138 AAAATAATAGCCAAGCAATCTCAAAAT 57.105 25.926 0.00 0.00 0.00 1.82
334 336 9.895138 AAATAATAGCCAAGCAATCTCAAAATT 57.105 25.926 0.00 0.00 0.00 1.82
335 337 8.882415 ATAATAGCCAAGCAATCTCAAAATTG 57.118 30.769 0.00 0.00 39.22 2.32
351 353 8.724229 TCTCAAAATTGCGAATATGATAGATGG 58.276 33.333 0.00 0.00 0.00 3.51
352 354 8.620116 TCAAAATTGCGAATATGATAGATGGA 57.380 30.769 0.00 0.00 0.00 3.41
353 355 9.065798 TCAAAATTGCGAATATGATAGATGGAA 57.934 29.630 0.00 0.00 0.00 3.53
354 356 9.850628 CAAAATTGCGAATATGATAGATGGAAT 57.149 29.630 0.00 0.00 0.00 3.01
372 374 8.381636 AGATGGAATAAATCTCACAAGATAGGG 58.618 37.037 0.00 0.00 41.54 3.53
373 375 7.451731 TGGAATAAATCTCACAAGATAGGGT 57.548 36.000 0.00 0.00 41.54 4.34
374 376 7.872138 TGGAATAAATCTCACAAGATAGGGTT 58.128 34.615 0.00 0.00 41.54 4.11
375 377 7.993183 TGGAATAAATCTCACAAGATAGGGTTC 59.007 37.037 0.00 0.00 41.54 3.62
376 378 7.445707 GGAATAAATCTCACAAGATAGGGTTCC 59.554 40.741 0.00 0.00 41.54 3.62
377 379 4.408182 AATCTCACAAGATAGGGTTCCG 57.592 45.455 0.00 0.00 41.54 4.30
378 380 3.095912 TCTCACAAGATAGGGTTCCGA 57.904 47.619 0.00 0.00 0.00 4.55
379 381 3.643237 TCTCACAAGATAGGGTTCCGAT 58.357 45.455 0.00 0.00 0.00 4.18
380 382 4.800023 TCTCACAAGATAGGGTTCCGATA 58.200 43.478 0.00 0.00 0.00 2.92
381 383 4.827835 TCTCACAAGATAGGGTTCCGATAG 59.172 45.833 0.00 0.00 0.00 2.08
396 398 3.001395 CGATAGGATGTCTTGACGGTC 57.999 52.381 0.00 0.00 0.00 4.79
397 399 2.602456 CGATAGGATGTCTTGACGGTCG 60.602 54.545 3.34 0.00 0.00 4.79
398 400 0.454600 TAGGATGTCTTGACGGTCGC 59.545 55.000 3.34 0.00 0.00 5.19
399 401 1.080093 GGATGTCTTGACGGTCGCA 60.080 57.895 3.34 0.78 0.00 5.10
400 402 1.352156 GGATGTCTTGACGGTCGCAC 61.352 60.000 3.34 0.69 0.00 5.34
401 403 0.388649 GATGTCTTGACGGTCGCACT 60.389 55.000 3.34 0.00 0.00 4.40
402 404 0.885879 ATGTCTTGACGGTCGCACTA 59.114 50.000 3.34 0.00 0.00 2.74
403 405 0.240145 TGTCTTGACGGTCGCACTAG 59.760 55.000 3.34 0.00 0.00 2.57
404 406 0.240411 GTCTTGACGGTCGCACTAGT 59.760 55.000 3.34 0.00 0.00 2.57
405 407 0.520404 TCTTGACGGTCGCACTAGTC 59.480 55.000 3.34 0.00 0.00 2.59
406 408 0.793478 CTTGACGGTCGCACTAGTCG 60.793 60.000 3.34 0.01 36.49 4.18
407 409 2.576317 GACGGTCGCACTAGTCGC 60.576 66.667 0.00 0.00 0.00 5.19
408 410 3.036783 GACGGTCGCACTAGTCGCT 62.037 63.158 13.14 0.00 0.00 4.93
409 411 1.699656 GACGGTCGCACTAGTCGCTA 61.700 60.000 13.14 2.68 0.00 4.26
410 412 1.297451 CGGTCGCACTAGTCGCTAC 60.297 63.158 13.14 12.09 0.00 3.58
411 413 1.297451 GGTCGCACTAGTCGCTACG 60.297 63.158 13.14 4.67 0.00 3.51
412 414 1.699656 GGTCGCACTAGTCGCTACGA 61.700 60.000 13.14 6.57 0.00 3.43
413 415 0.315220 GTCGCACTAGTCGCTACGAG 60.315 60.000 13.14 0.00 36.23 4.18
414 416 1.651730 CGCACTAGTCGCTACGAGC 60.652 63.158 13.14 2.47 36.23 5.03
423 425 3.870606 GCTACGAGCGAAGGCAAA 58.129 55.556 0.00 0.00 43.41 3.68
424 426 2.384203 GCTACGAGCGAAGGCAAAT 58.616 52.632 0.00 0.00 43.41 2.32
425 427 1.567504 GCTACGAGCGAAGGCAAATA 58.432 50.000 0.00 0.00 43.41 1.40
426 428 1.931172 GCTACGAGCGAAGGCAAATAA 59.069 47.619 0.00 0.00 43.41 1.40
427 429 2.350498 GCTACGAGCGAAGGCAAATAAA 59.650 45.455 0.00 0.00 43.41 1.40
428 430 3.181514 GCTACGAGCGAAGGCAAATAAAA 60.182 43.478 0.00 0.00 43.41 1.52
429 431 3.471495 ACGAGCGAAGGCAAATAAAAG 57.529 42.857 0.00 0.00 43.41 2.27
430 432 2.812011 ACGAGCGAAGGCAAATAAAAGT 59.188 40.909 0.00 0.00 43.41 2.66
431 433 3.998341 ACGAGCGAAGGCAAATAAAAGTA 59.002 39.130 0.00 0.00 43.41 2.24
432 434 4.092968 ACGAGCGAAGGCAAATAAAAGTAG 59.907 41.667 0.00 0.00 43.41 2.57
433 435 4.343609 GAGCGAAGGCAAATAAAAGTAGC 58.656 43.478 0.00 0.00 43.41 3.58
434 436 4.010349 AGCGAAGGCAAATAAAAGTAGCT 58.990 39.130 0.00 0.00 43.41 3.32
435 437 5.183228 AGCGAAGGCAAATAAAAGTAGCTA 58.817 37.500 0.00 0.00 43.41 3.32
436 438 5.646360 AGCGAAGGCAAATAAAAGTAGCTAA 59.354 36.000 0.00 0.00 43.41 3.09
437 439 6.150474 AGCGAAGGCAAATAAAAGTAGCTAAA 59.850 34.615 0.00 0.00 43.41 1.85
438 440 6.469275 GCGAAGGCAAATAAAAGTAGCTAAAG 59.531 38.462 0.00 0.00 39.62 1.85
439 441 6.469275 CGAAGGCAAATAAAAGTAGCTAAAGC 59.531 38.462 0.00 0.00 42.49 3.51
458 460 9.946165 GCTAAAGCTAAACTTCTCTAAACAAAA 57.054 29.630 0.00 0.00 37.75 2.44
461 463 7.273320 AGCTAAACTTCTCTAAACAAAACCC 57.727 36.000 0.00 0.00 0.00 4.11
462 464 6.264744 AGCTAAACTTCTCTAAACAAAACCCC 59.735 38.462 0.00 0.00 0.00 4.95
463 465 6.040054 GCTAAACTTCTCTAAACAAAACCCCA 59.960 38.462 0.00 0.00 0.00 4.96
464 466 6.465439 AAACTTCTCTAAACAAAACCCCAG 57.535 37.500 0.00 0.00 0.00 4.45
465 467 5.125367 ACTTCTCTAAACAAAACCCCAGT 57.875 39.130 0.00 0.00 0.00 4.00
466 468 5.131067 ACTTCTCTAAACAAAACCCCAGTC 58.869 41.667 0.00 0.00 0.00 3.51
467 469 5.104067 ACTTCTCTAAACAAAACCCCAGTCT 60.104 40.000 0.00 0.00 0.00 3.24
468 470 6.100714 ACTTCTCTAAACAAAACCCCAGTCTA 59.899 38.462 0.00 0.00 0.00 2.59
469 471 6.503560 TCTCTAAACAAAACCCCAGTCTAA 57.496 37.500 0.00 0.00 0.00 2.10
470 472 6.902408 TCTCTAAACAAAACCCCAGTCTAAA 58.098 36.000 0.00 0.00 0.00 1.85
471 473 6.769341 TCTCTAAACAAAACCCCAGTCTAAAC 59.231 38.462 0.00 0.00 0.00 2.01
472 474 5.829391 TCTAAACAAAACCCCAGTCTAAACC 59.171 40.000 0.00 0.00 0.00 3.27
473 475 2.953453 ACAAAACCCCAGTCTAAACCC 58.047 47.619 0.00 0.00 0.00 4.11
474 476 2.516702 ACAAAACCCCAGTCTAAACCCT 59.483 45.455 0.00 0.00 0.00 4.34
475 477 3.723154 ACAAAACCCCAGTCTAAACCCTA 59.277 43.478 0.00 0.00 0.00 3.53
476 478 4.168479 ACAAAACCCCAGTCTAAACCCTAA 59.832 41.667 0.00 0.00 0.00 2.69
477 479 4.377762 AAACCCCAGTCTAAACCCTAAC 57.622 45.455 0.00 0.00 0.00 2.34
478 480 2.272698 ACCCCAGTCTAAACCCTAACC 58.727 52.381 0.00 0.00 0.00 2.85
479 481 2.157895 ACCCCAGTCTAAACCCTAACCT 60.158 50.000 0.00 0.00 0.00 3.50
480 482 3.079534 ACCCCAGTCTAAACCCTAACCTA 59.920 47.826 0.00 0.00 0.00 3.08
481 483 3.710165 CCCCAGTCTAAACCCTAACCTAG 59.290 52.174 0.00 0.00 0.00 3.02
482 484 4.573520 CCCCAGTCTAAACCCTAACCTAGA 60.574 50.000 0.00 0.00 0.00 2.43
483 485 5.217400 CCCAGTCTAAACCCTAACCTAGAT 58.783 45.833 0.00 0.00 0.00 1.98
484 486 5.666265 CCCAGTCTAAACCCTAACCTAGATT 59.334 44.000 0.00 0.00 0.00 2.40
485 487 6.408206 CCCAGTCTAAACCCTAACCTAGATTG 60.408 46.154 0.00 0.00 31.45 2.67
486 488 6.383147 CCAGTCTAAACCCTAACCTAGATTGA 59.617 42.308 0.00 0.00 32.67 2.57
487 489 7.266400 CAGTCTAAACCCTAACCTAGATTGAC 58.734 42.308 0.00 0.00 32.67 3.18
488 490 7.124448 CAGTCTAAACCCTAACCTAGATTGACT 59.876 40.741 0.00 0.00 32.67 3.41
489 491 8.342270 AGTCTAAACCCTAACCTAGATTGACTA 58.658 37.037 0.00 0.00 0.00 2.59
490 492 9.145442 GTCTAAACCCTAACCTAGATTGACTAT 57.855 37.037 0.00 0.00 0.00 2.12
491 493 9.725206 TCTAAACCCTAACCTAGATTGACTATT 57.275 33.333 0.00 0.00 0.00 1.73
506 508 9.326413 AGATTGACTATTTATTAAAGGTGGACG 57.674 33.333 0.00 0.00 0.00 4.79
507 509 9.106070 GATTGACTATTTATTAAAGGTGGACGT 57.894 33.333 0.00 0.00 0.00 4.34
509 511 8.931385 TGACTATTTATTAAAGGTGGACGTAC 57.069 34.615 0.00 0.00 0.00 3.67
510 512 7.701924 TGACTATTTATTAAAGGTGGACGTACG 59.298 37.037 15.01 15.01 0.00 3.67
511 513 6.980397 ACTATTTATTAAAGGTGGACGTACGG 59.020 38.462 21.06 1.43 0.00 4.02
512 514 2.014335 ATTAAAGGTGGACGTACGGC 57.986 50.000 21.06 17.96 0.00 5.68
514 516 1.240641 TAAAGGTGGACGTACGGCGA 61.241 55.000 21.06 11.81 44.77 5.54
515 517 2.482296 AAAGGTGGACGTACGGCGAG 62.482 60.000 21.06 7.10 44.77 5.03
516 518 3.741476 GGTGGACGTACGGCGAGT 61.741 66.667 21.06 10.79 44.77 4.18
517 519 2.202401 GTGGACGTACGGCGAGTC 60.202 66.667 21.06 18.90 44.77 3.36
528 530 4.395583 GCGAGTCCGTCCGTCGTT 62.396 66.667 0.00 0.00 38.24 3.85
529 531 2.202272 CGAGTCCGTCCGTCGTTC 60.202 66.667 0.00 0.00 37.94 3.95
530 532 2.177778 GAGTCCGTCCGTCGTTCC 59.822 66.667 0.00 0.00 37.94 3.62
531 533 2.595463 AGTCCGTCCGTCGTTCCA 60.595 61.111 0.00 0.00 37.94 3.53
532 534 1.930908 GAGTCCGTCCGTCGTTCCAT 61.931 60.000 0.00 0.00 37.94 3.41
533 535 0.677731 AGTCCGTCCGTCGTTCCATA 60.678 55.000 0.00 0.00 37.94 2.74
534 536 0.248377 GTCCGTCCGTCGTTCCATAG 60.248 60.000 0.00 0.00 37.94 2.23
535 537 1.065273 CCGTCCGTCGTTCCATAGG 59.935 63.158 0.00 0.00 37.94 2.57
536 538 1.378882 CCGTCCGTCGTTCCATAGGA 61.379 60.000 0.00 0.00 37.94 2.94
537 539 0.666913 CGTCCGTCGTTCCATAGGAT 59.333 55.000 0.00 0.00 33.15 3.24
538 540 1.599667 CGTCCGTCGTTCCATAGGATG 60.600 57.143 0.00 0.00 33.15 3.51
539 541 1.407979 GTCCGTCGTTCCATAGGATGT 59.592 52.381 0.00 0.00 33.15 3.06
540 542 2.104967 TCCGTCGTTCCATAGGATGTT 58.895 47.619 0.00 0.00 0.00 2.71
541 543 2.159156 TCCGTCGTTCCATAGGATGTTG 60.159 50.000 0.00 0.00 0.00 3.33
542 544 2.201732 CGTCGTTCCATAGGATGTTGG 58.798 52.381 0.00 0.00 0.00 3.77
543 545 2.561569 GTCGTTCCATAGGATGTTGGG 58.438 52.381 0.00 0.00 33.62 4.12
544 546 1.134220 TCGTTCCATAGGATGTTGGGC 60.134 52.381 0.00 0.00 33.62 5.36
545 547 1.692411 GTTCCATAGGATGTTGGGCC 58.308 55.000 0.00 0.00 33.62 5.80
546 548 0.182537 TTCCATAGGATGTTGGGCCG 59.817 55.000 0.00 0.00 33.62 6.13
547 549 0.986019 TCCATAGGATGTTGGGCCGT 60.986 55.000 0.00 0.00 33.62 5.68
548 550 0.762418 CCATAGGATGTTGGGCCGTA 59.238 55.000 0.00 0.00 0.00 4.02
549 551 1.542547 CCATAGGATGTTGGGCCGTAC 60.543 57.143 0.00 0.00 0.00 3.67
550 552 0.391597 ATAGGATGTTGGGCCGTACG 59.608 55.000 8.69 8.69 0.00 3.67
551 553 0.683828 TAGGATGTTGGGCCGTACGA 60.684 55.000 18.76 0.00 0.00 3.43
552 554 1.145377 GGATGTTGGGCCGTACGAT 59.855 57.895 18.76 0.00 0.00 3.73
553 555 1.157870 GGATGTTGGGCCGTACGATG 61.158 60.000 18.76 1.33 0.00 3.84
554 556 0.179094 GATGTTGGGCCGTACGATGA 60.179 55.000 18.76 0.00 0.00 2.92
555 557 0.461339 ATGTTGGGCCGTACGATGAC 60.461 55.000 18.76 2.19 0.00 3.06
556 558 1.812507 GTTGGGCCGTACGATGACC 60.813 63.158 18.76 13.47 0.00 4.02
557 559 1.985662 TTGGGCCGTACGATGACCT 60.986 57.895 18.76 0.00 0.00 3.85
558 560 0.683828 TTGGGCCGTACGATGACCTA 60.684 55.000 18.76 6.65 0.00 3.08
559 561 0.683828 TGGGCCGTACGATGACCTAA 60.684 55.000 18.76 0.00 0.00 2.69
560 562 0.249197 GGGCCGTACGATGACCTAAC 60.249 60.000 18.76 0.00 0.00 2.34
561 563 0.457035 GGCCGTACGATGACCTAACA 59.543 55.000 18.76 0.00 0.00 2.41
562 564 1.553308 GCCGTACGATGACCTAACAC 58.447 55.000 18.76 0.00 0.00 3.32
563 565 1.133790 GCCGTACGATGACCTAACACT 59.866 52.381 18.76 0.00 0.00 3.55
564 566 2.793933 CCGTACGATGACCTAACACTG 58.206 52.381 18.76 0.00 0.00 3.66
565 567 2.163010 CCGTACGATGACCTAACACTGT 59.837 50.000 18.76 0.00 0.00 3.55
566 568 3.374988 CCGTACGATGACCTAACACTGTA 59.625 47.826 18.76 0.00 0.00 2.74
567 569 4.337763 CGTACGATGACCTAACACTGTAC 58.662 47.826 10.44 0.00 33.92 2.90
568 570 3.482722 ACGATGACCTAACACTGTACG 57.517 47.619 0.00 0.00 0.00 3.67
569 571 2.163010 ACGATGACCTAACACTGTACGG 59.837 50.000 0.00 0.00 0.00 4.02
570 572 2.537401 GATGACCTAACACTGTACGGC 58.463 52.381 0.23 0.00 0.00 5.68
571 573 0.241749 TGACCTAACACTGTACGGCG 59.758 55.000 4.80 4.80 0.00 6.46
572 574 0.457337 GACCTAACACTGTACGGCGG 60.457 60.000 13.24 0.00 0.00 6.13
573 575 1.808390 CCTAACACTGTACGGCGGC 60.808 63.158 13.24 0.00 0.00 6.53
574 576 1.214589 CTAACACTGTACGGCGGCT 59.785 57.895 13.24 0.00 0.00 5.52
575 577 0.452987 CTAACACTGTACGGCGGCTA 59.547 55.000 13.24 0.00 0.00 3.93
576 578 0.171007 TAACACTGTACGGCGGCTAC 59.829 55.000 13.24 6.26 0.00 3.58
577 579 2.578713 CACTGTACGGCGGCTACG 60.579 66.667 13.24 5.09 44.63 3.51
578 580 3.818787 ACTGTACGGCGGCTACGG 61.819 66.667 13.24 13.18 41.36 4.02
582 584 3.372730 TACGGCGGCTACGGTTGT 61.373 61.111 13.24 0.00 41.36 3.32
705 709 2.614983 GACCAAAAACTACCAAGTCGCA 59.385 45.455 0.00 0.00 33.75 5.10
715 719 0.516877 CCAAGTCGCAAAATCGCTCA 59.483 50.000 0.00 0.00 0.00 4.26
723 727 0.798776 CAAAATCGCTCACTTCGGCT 59.201 50.000 0.00 0.00 0.00 5.52
824 829 4.440127 TTAACGCCCCGTCCGCTC 62.440 66.667 0.00 0.00 39.99 5.03
834 957 3.745803 GTCCGCTCTCCGAACGGT 61.746 66.667 12.93 0.00 46.92 4.83
837 960 4.052229 CGCTCTCCGAACGGTGGT 62.052 66.667 12.93 0.00 40.02 4.16
1178 1307 3.103742 ACTTTCTTTTGCAGGAAACCCA 58.896 40.909 7.25 0.00 0.00 4.51
1289 1419 4.262592 GGTGGATTTTGAAGGTGCTTTGAT 60.263 41.667 0.00 0.00 0.00 2.57
1339 1469 6.828273 TGTGTAGCAGGTATTAAATCTTGCAT 59.172 34.615 15.53 7.06 38.75 3.96
1341 1471 5.779529 AGCAGGTATTAAATCTTGCATGG 57.220 39.130 15.53 0.00 38.75 3.66
1422 1552 2.156917 CATGTGGTGCAGAGATGTGTT 58.843 47.619 0.00 0.00 0.00 3.32
1515 1680 9.204570 TGTGAAAGTAGATCTTTAGTTAACTGC 57.795 33.333 18.56 1.08 45.15 4.40
1521 1686 9.593134 AGTAGATCTTTAGTTAACTGCATTCAG 57.407 33.333 18.56 5.07 45.71 3.02
1564 1729 6.299805 ACACCTACATGCAGAGATCTTTAA 57.700 37.500 0.00 0.00 0.00 1.52
1949 4867 4.385199 GGATTTGGGACATGTACCATGAGA 60.385 45.833 30.59 13.12 44.54 3.27
1976 4993 0.704664 GGGGAGGGTGAAGGACAAAT 59.295 55.000 0.00 0.00 0.00 2.32
2044 5178 5.235850 TCCTGTCAAACAACTATAGCCAA 57.764 39.130 0.00 0.00 0.00 4.52
2286 5457 0.178831 AAGGAAGTGGAGGGGGACAT 60.179 55.000 0.00 0.00 0.00 3.06
2401 5865 5.840243 TCAAGGCAATTATGAATGAGTGG 57.160 39.130 0.00 0.00 0.00 4.00
2717 6433 6.720288 ACAGTAGTGACATAGTTGGAAGTAGT 59.280 38.462 4.09 0.00 0.00 2.73
2723 6439 7.042335 GTGACATAGTTGGAAGTAGTAAGCAT 58.958 38.462 0.00 0.00 0.00 3.79
2949 6774 7.328005 CCTAGGAACTTACTGAACTTACGAAAC 59.672 40.741 1.05 0.00 41.75 2.78
2951 6776 6.700520 AGGAACTTACTGAACTTACGAAACTG 59.299 38.462 0.00 0.00 27.25 3.16
2952 6777 6.698766 GGAACTTACTGAACTTACGAAACTGA 59.301 38.462 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 9.559732 TTCATGAGGATAAATAAATGTCGACAT 57.440 29.630 25.18 25.18 38.41 3.06
37 38 8.956533 TTCATGAGGATAAATAAATGTCGACA 57.043 30.769 22.48 22.48 0.00 4.35
49 50 9.527157 TGGTCTTTTACAATTCATGAGGATAAA 57.473 29.630 0.00 0.00 0.00 1.40
50 51 9.699410 ATGGTCTTTTACAATTCATGAGGATAA 57.301 29.630 0.00 0.00 0.00 1.75
51 52 9.123902 CATGGTCTTTTACAATTCATGAGGATA 57.876 33.333 0.00 0.00 34.26 2.59
52 53 7.069085 CCATGGTCTTTTACAATTCATGAGGAT 59.931 37.037 2.57 0.00 34.26 3.24
53 54 6.377996 CCATGGTCTTTTACAATTCATGAGGA 59.622 38.462 2.57 0.00 34.26 3.71
54 55 6.377996 TCCATGGTCTTTTACAATTCATGAGG 59.622 38.462 12.58 0.00 34.26 3.86
55 56 7.395190 TCCATGGTCTTTTACAATTCATGAG 57.605 36.000 12.58 0.00 34.26 2.90
56 57 7.959658 ATCCATGGTCTTTTACAATTCATGA 57.040 32.000 12.58 0.00 34.26 3.07
57 58 8.036575 ACAATCCATGGTCTTTTACAATTCATG 58.963 33.333 12.58 0.00 0.00 3.07
58 59 8.036575 CACAATCCATGGTCTTTTACAATTCAT 58.963 33.333 12.58 0.00 0.00 2.57
59 60 7.232330 TCACAATCCATGGTCTTTTACAATTCA 59.768 33.333 12.58 0.00 0.00 2.57
60 61 7.601856 TCACAATCCATGGTCTTTTACAATTC 58.398 34.615 12.58 0.00 0.00 2.17
61 62 7.537596 TCACAATCCATGGTCTTTTACAATT 57.462 32.000 12.58 0.00 0.00 2.32
62 63 7.178983 ACATCACAATCCATGGTCTTTTACAAT 59.821 33.333 12.58 0.00 0.00 2.71
63 64 6.493115 ACATCACAATCCATGGTCTTTTACAA 59.507 34.615 12.58 0.00 0.00 2.41
64 65 6.009589 ACATCACAATCCATGGTCTTTTACA 58.990 36.000 12.58 0.00 0.00 2.41
65 66 6.150976 TCACATCACAATCCATGGTCTTTTAC 59.849 38.462 12.58 0.00 0.00 2.01
66 67 6.244654 TCACATCACAATCCATGGTCTTTTA 58.755 36.000 12.58 0.00 0.00 1.52
67 68 5.078949 TCACATCACAATCCATGGTCTTTT 58.921 37.500 12.58 0.00 0.00 2.27
68 69 4.665451 TCACATCACAATCCATGGTCTTT 58.335 39.130 12.58 1.50 0.00 2.52
69 70 4.305539 TCACATCACAATCCATGGTCTT 57.694 40.909 12.58 4.00 0.00 3.01
70 71 4.012374 GTTCACATCACAATCCATGGTCT 58.988 43.478 12.58 0.00 0.00 3.85
71 72 4.012374 AGTTCACATCACAATCCATGGTC 58.988 43.478 12.58 0.00 0.00 4.02
72 73 3.760151 CAGTTCACATCACAATCCATGGT 59.240 43.478 12.58 0.00 0.00 3.55
73 74 3.129813 CCAGTTCACATCACAATCCATGG 59.870 47.826 4.97 4.97 0.00 3.66
74 75 3.129813 CCCAGTTCACATCACAATCCATG 59.870 47.826 0.00 0.00 0.00 3.66
75 76 3.359033 CCCAGTTCACATCACAATCCAT 58.641 45.455 0.00 0.00 0.00 3.41
76 77 2.555006 CCCCAGTTCACATCACAATCCA 60.555 50.000 0.00 0.00 0.00 3.41
77 78 2.094675 CCCCAGTTCACATCACAATCC 58.905 52.381 0.00 0.00 0.00 3.01
78 79 1.474077 GCCCCAGTTCACATCACAATC 59.526 52.381 0.00 0.00 0.00 2.67
79 80 1.549203 GCCCCAGTTCACATCACAAT 58.451 50.000 0.00 0.00 0.00 2.71
80 81 0.539438 GGCCCCAGTTCACATCACAA 60.539 55.000 0.00 0.00 0.00 3.33
81 82 1.074775 GGCCCCAGTTCACATCACA 59.925 57.895 0.00 0.00 0.00 3.58
82 83 1.678970 GGGCCCCAGTTCACATCAC 60.679 63.158 12.23 0.00 0.00 3.06
117 119 5.359860 CCCACCCAAAATTGTAGTTATCTCC 59.640 44.000 0.00 0.00 0.00 3.71
119 121 6.147437 TCCCACCCAAAATTGTAGTTATCT 57.853 37.500 0.00 0.00 0.00 1.98
143 145 0.742990 GCCGGATCGTGATGGTCAAA 60.743 55.000 5.05 0.00 0.00 2.69
150 152 0.104304 GTTGGTAGCCGGATCGTGAT 59.896 55.000 5.05 0.00 0.00 3.06
210 212 1.045407 ACCGTGGAGTTAGTTCAGCA 58.955 50.000 0.00 0.00 0.00 4.41
218 220 2.164219 GGTCGATAACACCGTGGAGTTA 59.836 50.000 10.64 10.64 36.10 2.24
229 231 0.457166 CGTTGGCTCGGTCGATAACA 60.457 55.000 0.00 3.35 0.00 2.41
325 327 8.724229 CCATCTATCATATTCGCAATTTTGAGA 58.276 33.333 0.00 0.00 35.18 3.27
326 328 8.724229 TCCATCTATCATATTCGCAATTTTGAG 58.276 33.333 0.00 0.00 0.00 3.02
327 329 8.620116 TCCATCTATCATATTCGCAATTTTGA 57.380 30.769 0.00 0.00 0.00 2.69
328 330 9.850628 ATTCCATCTATCATATTCGCAATTTTG 57.149 29.630 0.00 0.00 0.00 2.44
346 348 8.381636 CCCTATCTTGTGAGATTTATTCCATCT 58.618 37.037 0.00 0.00 42.55 2.90
347 349 8.160106 ACCCTATCTTGTGAGATTTATTCCATC 58.840 37.037 0.00 0.00 42.55 3.51
348 350 8.050316 ACCCTATCTTGTGAGATTTATTCCAT 57.950 34.615 0.00 0.00 42.55 3.41
349 351 7.451731 ACCCTATCTTGTGAGATTTATTCCA 57.548 36.000 0.00 0.00 42.55 3.53
350 352 7.445707 GGAACCCTATCTTGTGAGATTTATTCC 59.554 40.741 0.00 0.00 42.55 3.01
351 353 7.171678 CGGAACCCTATCTTGTGAGATTTATTC 59.828 40.741 0.00 0.00 42.55 1.75
352 354 6.992715 CGGAACCCTATCTTGTGAGATTTATT 59.007 38.462 0.00 0.00 42.55 1.40
353 355 6.326583 TCGGAACCCTATCTTGTGAGATTTAT 59.673 38.462 0.00 0.00 42.55 1.40
354 356 5.659525 TCGGAACCCTATCTTGTGAGATTTA 59.340 40.000 0.00 0.00 42.55 1.40
355 357 4.469945 TCGGAACCCTATCTTGTGAGATTT 59.530 41.667 0.00 0.00 42.55 2.17
356 358 4.030913 TCGGAACCCTATCTTGTGAGATT 58.969 43.478 0.00 0.00 42.55 2.40
357 359 3.643237 TCGGAACCCTATCTTGTGAGAT 58.357 45.455 0.00 0.00 44.67 2.75
358 360 3.095912 TCGGAACCCTATCTTGTGAGA 57.904 47.619 0.00 0.00 36.09 3.27
359 361 4.021894 CCTATCGGAACCCTATCTTGTGAG 60.022 50.000 0.00 0.00 0.00 3.51
360 362 3.895656 CCTATCGGAACCCTATCTTGTGA 59.104 47.826 0.00 0.00 0.00 3.58
361 363 3.895656 TCCTATCGGAACCCTATCTTGTG 59.104 47.826 0.00 0.00 36.03 3.33
362 364 4.194678 TCCTATCGGAACCCTATCTTGT 57.805 45.455 0.00 0.00 36.03 3.16
363 365 4.528596 ACATCCTATCGGAACCCTATCTTG 59.471 45.833 0.00 0.00 44.02 3.02
364 366 4.753186 ACATCCTATCGGAACCCTATCTT 58.247 43.478 0.00 0.00 44.02 2.40
365 367 4.044825 AGACATCCTATCGGAACCCTATCT 59.955 45.833 0.00 0.00 44.02 1.98
366 368 4.345854 AGACATCCTATCGGAACCCTATC 58.654 47.826 0.00 0.00 44.02 2.08
367 369 4.405756 AGACATCCTATCGGAACCCTAT 57.594 45.455 0.00 0.00 44.02 2.57
368 370 3.895656 CAAGACATCCTATCGGAACCCTA 59.104 47.826 0.00 0.00 44.02 3.53
369 371 2.700897 CAAGACATCCTATCGGAACCCT 59.299 50.000 0.00 0.00 44.02 4.34
370 372 2.698797 TCAAGACATCCTATCGGAACCC 59.301 50.000 0.00 0.00 44.02 4.11
371 373 3.718815 GTCAAGACATCCTATCGGAACC 58.281 50.000 0.00 0.00 44.02 3.62
372 374 3.372954 CGTCAAGACATCCTATCGGAAC 58.627 50.000 0.72 0.00 44.02 3.62
373 375 2.361119 CCGTCAAGACATCCTATCGGAA 59.639 50.000 0.72 0.00 44.02 4.30
374 376 1.954382 CCGTCAAGACATCCTATCGGA 59.046 52.381 0.72 0.00 45.16 4.55
375 377 1.681793 ACCGTCAAGACATCCTATCGG 59.318 52.381 0.72 0.00 37.97 4.18
376 378 2.602456 CGACCGTCAAGACATCCTATCG 60.602 54.545 0.00 0.00 0.00 2.92
377 379 2.859032 GCGACCGTCAAGACATCCTATC 60.859 54.545 0.00 0.00 0.00 2.08
378 380 1.067212 GCGACCGTCAAGACATCCTAT 59.933 52.381 0.00 0.00 0.00 2.57
379 381 0.454600 GCGACCGTCAAGACATCCTA 59.545 55.000 0.00 0.00 0.00 2.94
380 382 1.215647 GCGACCGTCAAGACATCCT 59.784 57.895 0.00 0.00 0.00 3.24
381 383 1.080093 TGCGACCGTCAAGACATCC 60.080 57.895 0.00 0.00 0.00 3.51
382 384 0.388649 AGTGCGACCGTCAAGACATC 60.389 55.000 0.00 0.00 0.00 3.06
383 385 0.885879 TAGTGCGACCGTCAAGACAT 59.114 50.000 0.00 0.00 0.00 3.06
384 386 0.240145 CTAGTGCGACCGTCAAGACA 59.760 55.000 0.00 0.00 0.00 3.41
385 387 0.240411 ACTAGTGCGACCGTCAAGAC 59.760 55.000 0.00 0.00 0.00 3.01
386 388 0.520404 GACTAGTGCGACCGTCAAGA 59.480 55.000 0.00 0.00 0.00 3.02
387 389 0.793478 CGACTAGTGCGACCGTCAAG 60.793 60.000 0.00 0.00 0.00 3.02
388 390 1.208358 CGACTAGTGCGACCGTCAA 59.792 57.895 0.00 0.00 0.00 3.18
389 391 2.865308 CGACTAGTGCGACCGTCA 59.135 61.111 0.00 0.00 0.00 4.35
390 392 1.699656 TAGCGACTAGTGCGACCGTC 61.700 60.000 15.79 3.96 37.44 4.79
391 393 1.742880 TAGCGACTAGTGCGACCGT 60.743 57.895 15.79 1.69 37.44 4.83
392 394 1.297451 GTAGCGACTAGTGCGACCG 60.297 63.158 15.79 7.55 37.44 4.79
393 395 1.297451 CGTAGCGACTAGTGCGACC 60.297 63.158 17.81 8.34 34.93 4.79
394 396 0.315220 CTCGTAGCGACTAGTGCGAC 60.315 60.000 15.79 15.58 37.44 5.19
395 397 2.004445 CTCGTAGCGACTAGTGCGA 58.996 57.895 15.79 9.69 37.44 5.10
396 398 1.651730 GCTCGTAGCGACTAGTGCG 60.652 63.158 0.00 5.20 37.44 5.34
397 399 4.288645 GCTCGTAGCGACTAGTGC 57.711 61.111 0.00 4.54 0.00 4.40
406 408 1.567504 TATTTGCCTTCGCTCGTAGC 58.432 50.000 0.00 0.00 38.02 3.58
407 409 4.092968 ACTTTTATTTGCCTTCGCTCGTAG 59.907 41.667 0.00 0.00 35.36 3.51
408 410 3.998341 ACTTTTATTTGCCTTCGCTCGTA 59.002 39.130 0.00 0.00 35.36 3.43
409 411 2.812011 ACTTTTATTTGCCTTCGCTCGT 59.188 40.909 0.00 0.00 35.36 4.18
410 412 3.471495 ACTTTTATTTGCCTTCGCTCG 57.529 42.857 0.00 0.00 35.36 5.03
411 413 4.095036 AGCTACTTTTATTTGCCTTCGCTC 59.905 41.667 0.00 0.00 35.36 5.03
412 414 4.010349 AGCTACTTTTATTTGCCTTCGCT 58.990 39.130 0.00 0.00 35.36 4.93
413 415 4.357018 AGCTACTTTTATTTGCCTTCGC 57.643 40.909 0.00 0.00 0.00 4.70
414 416 6.469275 GCTTTAGCTACTTTTATTTGCCTTCG 59.531 38.462 0.00 0.00 38.21 3.79
415 417 7.742019 GCTTTAGCTACTTTTATTTGCCTTC 57.258 36.000 0.00 0.00 38.21 3.46
432 434 9.946165 TTTTGTTTAGAGAAGTTTAGCTTTAGC 57.054 29.630 0.00 0.00 37.59 3.09
435 437 8.195436 GGGTTTTGTTTAGAGAAGTTTAGCTTT 58.805 33.333 0.00 0.00 37.59 3.51
436 438 7.201884 GGGGTTTTGTTTAGAGAAGTTTAGCTT 60.202 37.037 0.00 0.00 40.76 3.74
437 439 6.264744 GGGGTTTTGTTTAGAGAAGTTTAGCT 59.735 38.462 0.00 0.00 0.00 3.32
438 440 6.040054 TGGGGTTTTGTTTAGAGAAGTTTAGC 59.960 38.462 0.00 0.00 0.00 3.09
439 441 7.284716 ACTGGGGTTTTGTTTAGAGAAGTTTAG 59.715 37.037 0.00 0.00 0.00 1.85
440 442 7.120716 ACTGGGGTTTTGTTTAGAGAAGTTTA 58.879 34.615 0.00 0.00 0.00 2.01
441 443 5.955959 ACTGGGGTTTTGTTTAGAGAAGTTT 59.044 36.000 0.00 0.00 0.00 2.66
442 444 5.516044 ACTGGGGTTTTGTTTAGAGAAGTT 58.484 37.500 0.00 0.00 0.00 2.66
443 445 5.104067 AGACTGGGGTTTTGTTTAGAGAAGT 60.104 40.000 0.00 0.00 0.00 3.01
444 446 5.377478 AGACTGGGGTTTTGTTTAGAGAAG 58.623 41.667 0.00 0.00 0.00 2.85
445 447 5.382664 AGACTGGGGTTTTGTTTAGAGAA 57.617 39.130 0.00 0.00 0.00 2.87
446 448 6.503560 TTAGACTGGGGTTTTGTTTAGAGA 57.496 37.500 0.00 0.00 0.00 3.10
447 449 6.016527 GGTTTAGACTGGGGTTTTGTTTAGAG 60.017 42.308 0.00 0.00 0.00 2.43
448 450 5.829391 GGTTTAGACTGGGGTTTTGTTTAGA 59.171 40.000 0.00 0.00 0.00 2.10
449 451 5.010314 GGGTTTAGACTGGGGTTTTGTTTAG 59.990 44.000 0.00 0.00 0.00 1.85
450 452 4.894705 GGGTTTAGACTGGGGTTTTGTTTA 59.105 41.667 0.00 0.00 0.00 2.01
451 453 3.707611 GGGTTTAGACTGGGGTTTTGTTT 59.292 43.478 0.00 0.00 0.00 2.83
452 454 3.052414 AGGGTTTAGACTGGGGTTTTGTT 60.052 43.478 0.00 0.00 0.00 2.83
453 455 2.516702 AGGGTTTAGACTGGGGTTTTGT 59.483 45.455 0.00 0.00 0.00 2.83
454 456 3.238788 AGGGTTTAGACTGGGGTTTTG 57.761 47.619 0.00 0.00 0.00 2.44
455 457 4.448200 GGTTAGGGTTTAGACTGGGGTTTT 60.448 45.833 0.00 0.00 0.00 2.43
456 458 3.074985 GGTTAGGGTTTAGACTGGGGTTT 59.925 47.826 0.00 0.00 0.00 3.27
457 459 2.646297 GGTTAGGGTTTAGACTGGGGTT 59.354 50.000 0.00 0.00 0.00 4.11
458 460 2.157895 AGGTTAGGGTTTAGACTGGGGT 60.158 50.000 0.00 0.00 0.00 4.95
459 461 2.558974 AGGTTAGGGTTTAGACTGGGG 58.441 52.381 0.00 0.00 0.00 4.96
460 462 4.617593 TCTAGGTTAGGGTTTAGACTGGG 58.382 47.826 0.00 0.00 0.00 4.45
461 463 6.383147 TCAATCTAGGTTAGGGTTTAGACTGG 59.617 42.308 0.00 0.00 0.00 4.00
462 464 7.124448 AGTCAATCTAGGTTAGGGTTTAGACTG 59.876 40.741 1.49 0.00 0.00 3.51
463 465 7.190501 AGTCAATCTAGGTTAGGGTTTAGACT 58.809 38.462 0.00 0.00 0.00 3.24
464 466 7.421087 AGTCAATCTAGGTTAGGGTTTAGAC 57.579 40.000 0.00 0.00 0.00 2.59
465 467 9.725206 AATAGTCAATCTAGGTTAGGGTTTAGA 57.275 33.333 0.00 0.00 31.67 2.10
480 482 9.326413 CGTCCACCTTTAATAAATAGTCAATCT 57.674 33.333 0.00 0.00 0.00 2.40
481 483 9.106070 ACGTCCACCTTTAATAAATAGTCAATC 57.894 33.333 0.00 0.00 0.00 2.67
483 485 9.369904 GTACGTCCACCTTTAATAAATAGTCAA 57.630 33.333 0.00 0.00 0.00 3.18
484 486 7.701924 CGTACGTCCACCTTTAATAAATAGTCA 59.298 37.037 7.22 0.00 0.00 3.41
485 487 7.168135 CCGTACGTCCACCTTTAATAAATAGTC 59.832 40.741 15.21 0.00 0.00 2.59
486 488 6.980397 CCGTACGTCCACCTTTAATAAATAGT 59.020 38.462 15.21 0.00 0.00 2.12
487 489 6.074142 GCCGTACGTCCACCTTTAATAAATAG 60.074 42.308 15.21 0.00 0.00 1.73
488 490 5.752955 GCCGTACGTCCACCTTTAATAAATA 59.247 40.000 15.21 0.00 0.00 1.40
489 491 4.571984 GCCGTACGTCCACCTTTAATAAAT 59.428 41.667 15.21 0.00 0.00 1.40
490 492 3.932089 GCCGTACGTCCACCTTTAATAAA 59.068 43.478 15.21 0.00 0.00 1.40
491 493 3.520569 GCCGTACGTCCACCTTTAATAA 58.479 45.455 15.21 0.00 0.00 1.40
492 494 2.479389 CGCCGTACGTCCACCTTTAATA 60.479 50.000 15.21 0.00 36.87 0.98
493 495 1.736696 CGCCGTACGTCCACCTTTAAT 60.737 52.381 15.21 0.00 36.87 1.40
494 496 0.388391 CGCCGTACGTCCACCTTTAA 60.388 55.000 15.21 0.00 36.87 1.52
495 497 1.212490 CGCCGTACGTCCACCTTTA 59.788 57.895 15.21 0.00 36.87 1.85
496 498 2.048877 CGCCGTACGTCCACCTTT 60.049 61.111 15.21 0.00 36.87 3.11
497 499 2.985282 TCGCCGTACGTCCACCTT 60.985 61.111 15.21 0.00 44.19 3.50
498 500 3.437795 CTCGCCGTACGTCCACCT 61.438 66.667 15.21 0.00 44.19 4.00
499 501 3.673867 GACTCGCCGTACGTCCACC 62.674 68.421 15.21 0.00 44.19 4.61
500 502 2.202401 GACTCGCCGTACGTCCAC 60.202 66.667 15.21 0.00 44.19 4.02
501 503 3.434319 GGACTCGCCGTACGTCCA 61.434 66.667 15.21 0.00 45.08 4.02
516 518 4.973023 ATCCTATGGAACGACGGACGGA 62.973 54.545 4.74 0.00 38.95 4.69
517 519 2.688850 ATCCTATGGAACGACGGACGG 61.689 57.143 4.74 0.00 38.95 4.79
518 520 0.666913 ATCCTATGGAACGACGGACG 59.333 55.000 0.00 0.00 39.92 4.79
519 521 1.407979 ACATCCTATGGAACGACGGAC 59.592 52.381 0.00 0.00 34.34 4.79
520 522 1.771565 ACATCCTATGGAACGACGGA 58.228 50.000 0.00 0.00 34.34 4.69
521 523 2.201732 CAACATCCTATGGAACGACGG 58.798 52.381 0.00 0.00 34.34 4.79
522 524 2.201732 CCAACATCCTATGGAACGACG 58.798 52.381 0.00 0.00 39.12 5.12
523 525 2.561569 CCCAACATCCTATGGAACGAC 58.438 52.381 0.00 0.00 39.12 4.34
524 526 1.134220 GCCCAACATCCTATGGAACGA 60.134 52.381 0.00 0.00 39.12 3.85
525 527 1.308998 GCCCAACATCCTATGGAACG 58.691 55.000 0.00 0.00 39.12 3.95
526 528 1.692411 GGCCCAACATCCTATGGAAC 58.308 55.000 0.00 0.00 39.12 3.62
527 529 0.182537 CGGCCCAACATCCTATGGAA 59.817 55.000 0.00 0.00 39.12 3.53
528 530 0.986019 ACGGCCCAACATCCTATGGA 60.986 55.000 0.00 0.00 39.12 3.41
529 531 0.762418 TACGGCCCAACATCCTATGG 59.238 55.000 0.00 0.00 36.42 2.74
530 532 1.872237 CGTACGGCCCAACATCCTATG 60.872 57.143 7.57 0.00 0.00 2.23
531 533 0.391597 CGTACGGCCCAACATCCTAT 59.608 55.000 7.57 0.00 0.00 2.57
532 534 0.683828 TCGTACGGCCCAACATCCTA 60.684 55.000 16.52 0.00 0.00 2.94
533 535 1.335132 ATCGTACGGCCCAACATCCT 61.335 55.000 16.52 0.00 0.00 3.24
534 536 1.145377 ATCGTACGGCCCAACATCC 59.855 57.895 16.52 0.00 0.00 3.51
535 537 0.179094 TCATCGTACGGCCCAACATC 60.179 55.000 16.52 0.00 0.00 3.06
536 538 0.461339 GTCATCGTACGGCCCAACAT 60.461 55.000 16.52 0.00 0.00 2.71
537 539 1.079681 GTCATCGTACGGCCCAACA 60.080 57.895 16.52 0.00 0.00 3.33
538 540 1.812507 GGTCATCGTACGGCCCAAC 60.813 63.158 16.52 6.99 0.00 3.77
539 541 0.683828 TAGGTCATCGTACGGCCCAA 60.684 55.000 16.52 0.00 0.00 4.12
540 542 0.683828 TTAGGTCATCGTACGGCCCA 60.684 55.000 16.52 0.00 0.00 5.36
541 543 0.249197 GTTAGGTCATCGTACGGCCC 60.249 60.000 16.52 10.04 0.00 5.80
542 544 0.457035 TGTTAGGTCATCGTACGGCC 59.543 55.000 16.52 12.44 0.00 6.13
543 545 1.133790 AGTGTTAGGTCATCGTACGGC 59.866 52.381 16.52 3.61 0.00 5.68
544 546 2.163010 ACAGTGTTAGGTCATCGTACGG 59.837 50.000 16.52 0.00 0.00 4.02
545 547 3.482722 ACAGTGTTAGGTCATCGTACG 57.517 47.619 9.53 9.53 0.00 3.67
546 548 4.337763 CGTACAGTGTTAGGTCATCGTAC 58.662 47.826 0.00 0.00 0.00 3.67
547 549 3.374988 CCGTACAGTGTTAGGTCATCGTA 59.625 47.826 0.00 0.00 0.00 3.43
548 550 2.163010 CCGTACAGTGTTAGGTCATCGT 59.837 50.000 0.00 0.00 0.00 3.73
549 551 2.793933 CCGTACAGTGTTAGGTCATCG 58.206 52.381 0.00 0.00 0.00 3.84
550 552 2.537401 GCCGTACAGTGTTAGGTCATC 58.463 52.381 0.00 0.00 0.00 2.92
551 553 1.135199 CGCCGTACAGTGTTAGGTCAT 60.135 52.381 0.00 0.00 0.00 3.06
552 554 0.241749 CGCCGTACAGTGTTAGGTCA 59.758 55.000 0.00 0.00 0.00 4.02
553 555 0.457337 CCGCCGTACAGTGTTAGGTC 60.457 60.000 0.00 1.67 0.00 3.85
554 556 1.588082 CCGCCGTACAGTGTTAGGT 59.412 57.895 0.00 0.00 0.00 3.08
555 557 1.808390 GCCGCCGTACAGTGTTAGG 60.808 63.158 0.00 6.72 0.00 2.69
556 558 0.452987 TAGCCGCCGTACAGTGTTAG 59.547 55.000 0.00 0.00 0.00 2.34
557 559 0.171007 GTAGCCGCCGTACAGTGTTA 59.829 55.000 0.00 0.00 0.00 2.41
558 560 1.080298 GTAGCCGCCGTACAGTGTT 60.080 57.895 0.00 0.00 0.00 3.32
559 561 2.570181 GTAGCCGCCGTACAGTGT 59.430 61.111 0.00 0.00 0.00 3.55
560 562 2.578713 CGTAGCCGCCGTACAGTG 60.579 66.667 0.00 0.00 0.00 3.66
561 563 3.818787 CCGTAGCCGCCGTACAGT 61.819 66.667 0.00 0.00 0.00 3.55
562 564 3.346631 AACCGTAGCCGCCGTACAG 62.347 63.158 0.00 0.00 0.00 2.74
563 565 3.372730 AACCGTAGCCGCCGTACA 61.373 61.111 0.00 0.00 0.00 2.90
564 566 2.882301 CAACCGTAGCCGCCGTAC 60.882 66.667 0.00 0.00 0.00 3.67
565 567 2.433231 AAACAACCGTAGCCGCCGTA 62.433 55.000 0.00 0.00 0.00 4.02
566 568 3.812865 AAACAACCGTAGCCGCCGT 62.813 57.895 0.00 0.00 0.00 5.68
567 569 3.045492 AAACAACCGTAGCCGCCG 61.045 61.111 0.00 0.00 0.00 6.46
568 570 1.908066 CTCAAACAACCGTAGCCGCC 61.908 60.000 0.00 0.00 0.00 6.13
569 571 1.226030 ACTCAAACAACCGTAGCCGC 61.226 55.000 0.00 0.00 0.00 6.53
570 572 2.068837 TACTCAAACAACCGTAGCCG 57.931 50.000 0.00 0.00 0.00 5.52
571 573 6.309436 GTTAAATACTCAAACAACCGTAGCC 58.691 40.000 0.00 0.00 0.00 3.93
572 574 6.073112 TGGTTAAATACTCAAACAACCGTAGC 60.073 38.462 0.00 0.00 38.59 3.58
573 575 7.424227 TGGTTAAATACTCAAACAACCGTAG 57.576 36.000 0.00 0.00 38.59 3.51
574 576 7.798596 TTGGTTAAATACTCAAACAACCGTA 57.201 32.000 0.00 0.00 38.59 4.02
575 577 6.696441 TTGGTTAAATACTCAAACAACCGT 57.304 33.333 0.00 0.00 38.59 4.83
576 578 7.988904 TTTTGGTTAAATACTCAAACAACCG 57.011 32.000 0.00 0.00 38.59 4.44
577 579 9.373603 AGTTTTTGGTTAAATACTCAAACAACC 57.626 29.630 0.00 0.00 34.37 3.77
705 709 0.798776 CAGCCGAAGTGAGCGATTTT 59.201 50.000 0.00 0.00 0.00 1.82
723 727 1.153449 CAGATTCGGGGTTAGCGCA 60.153 57.895 11.47 0.00 0.00 6.09
824 829 2.019951 CGACAACCACCGTTCGGAG 61.020 63.158 18.28 9.90 0.00 4.63
834 957 1.780107 TATTGGCCCACCGACAACCA 61.780 55.000 0.00 0.00 39.70 3.67
837 960 0.402504 ACTTATTGGCCCACCGACAA 59.597 50.000 0.00 0.00 39.70 3.18
886 1013 1.452145 GAGAGCGAGCGAGGAGGAAT 61.452 60.000 0.00 0.00 0.00 3.01
1178 1307 0.843309 TGGTTCCACCACACTGTCAT 59.157 50.000 0.00 0.00 44.79 3.06
1289 1419 0.326238 ACCTAGGAATCGCCTCCCAA 60.326 55.000 17.98 0.00 46.97 4.12
1339 1469 2.428890 CCACCAGCAAAACAAGTTACCA 59.571 45.455 0.00 0.00 0.00 3.25
1341 1471 3.630312 TCTCCACCAGCAAAACAAGTTAC 59.370 43.478 0.00 0.00 0.00 2.50
1422 1552 4.006780 ACAACACACATCTCTGCACATA 57.993 40.909 0.00 0.00 0.00 2.29
1521 1686 4.686554 GTGTTCTCAGGTTCAGTCATGTAC 59.313 45.833 0.00 0.00 0.00 2.90
1949 4867 1.425448 CTTCACCCTCCCCAAGTTCTT 59.575 52.381 0.00 0.00 0.00 2.52
1976 4993 2.239654 CCACCTCTTTCTCATGGGCTTA 59.760 50.000 0.00 0.00 0.00 3.09
2286 5457 5.084519 TCTTCTCTTGCTTAAGTAGGTCCA 58.915 41.667 4.02 0.00 0.00 4.02
2376 5838 6.040054 CCACTCATTCATAATTGCCTTGATCA 59.960 38.462 0.00 0.00 0.00 2.92
2401 5865 0.751643 ACCCACACACCAAGCACTTC 60.752 55.000 0.00 0.00 0.00 3.01
2882 6637 9.008965 CACTATCTACTTGCTATCTATGTCAGT 57.991 37.037 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.