Multiple sequence alignment - TraesCS2A01G574600

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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 TraesCS2A01G574600 chr2A 100.000 4762 0 0 1 4762 769493669 769498430 0.000000e+00 8794.0
1 TraesCS2A01G574600 chr2A 98.182 110 2 0 2115 2224 706218251 706218142 4.860000e-45 193.0
2 TraesCS2A01G574600 chr2A 85.124 121 17 1 390 509 769493925 769494045 6.470000e-24 122.0
3 TraesCS2A01G574600 chr2A 85.124 121 17 1 257 377 769494058 769494177 6.470000e-24 122.0
4 TraesCS2A01G574600 chr2A 84.906 106 16 0 704 809 728750692 728750587 1.810000e-19 108.0
5 TraesCS2A01G574600 chr2B 92.818 3091 134 26 848 3892 791481551 791478503 0.000000e+00 4397.0
6 TraesCS2A01G574600 chr2B 90.551 254 20 2 4228 4477 791478377 791478124 2.750000e-87 333.0
7 TraesCS2A01G574600 chr2B 93.151 146 7 3 4044 4187 791478515 791478371 1.340000e-50 211.0
8 TraesCS2A01G574600 chr2B 97.391 115 1 2 2115 2227 275319217 275319103 1.350000e-45 195.0
9 TraesCS2A01G574600 chr2B 78.095 315 46 9 543 837 759258535 759258846 1.360000e-40 178.0
10 TraesCS2A01G574600 chr2B 85.542 166 14 5 4573 4735 791477892 791477734 1.060000e-36 165.0
11 TraesCS2A01G574600 chr2B 78.088 251 42 5 596 839 754609320 754609564 3.840000e-31 147.0
12 TraesCS2A01G574600 chr2D 90.806 1860 104 28 2336 4149 644331268 644333106 0.000000e+00 2425.0
13 TraesCS2A01G574600 chr2D 91.416 1759 73 24 388 2108 644329405 644331123 0.000000e+00 2340.0
14 TraesCS2A01G574600 chr2D 89.086 394 33 6 1 384 644329141 644329534 9.270000e-132 481.0
15 TraesCS2A01G574600 chr2D 92.788 208 11 3 4142 4346 644360364 644360570 1.000000e-76 298.0
16 TraesCS2A01G574600 chr2D 89.209 139 12 1 4403 4541 644361494 644361629 2.280000e-38 171.0
17 TraesCS2A01G574600 chr1D 84.823 481 52 11 1047 1518 490035087 490034619 9.330000e-127 464.0
18 TraesCS2A01G574600 chr1D 78.014 282 46 8 541 809 483527558 483527280 3.810000e-36 163.0
19 TraesCS2A01G574600 chr7D 79.683 315 46 9 519 818 180068133 180068444 1.340000e-50 211.0
20 TraesCS2A01G574600 chr7D 85.333 75 11 0 1374 1448 583282115 583282041 1.420000e-10 78.7
21 TraesCS2A01G574600 chr5B 79.868 303 45 5 551 837 488849527 488849225 1.740000e-49 207.0
22 TraesCS2A01G574600 chr5B 98.198 111 2 0 2112 2222 75535660 75535770 1.350000e-45 195.0
23 TraesCS2A01G574600 chr5B 78.025 314 47 7 543 836 445632792 445632481 1.360000e-40 178.0
24 TraesCS2A01G574600 chr5B 77.586 290 53 6 543 820 595668109 595667820 1.060000e-36 165.0
25 TraesCS2A01G574600 chr5B 75.258 291 45 10 543 809 560660788 560661075 3.890000e-21 113.0
26 TraesCS2A01G574600 chr1B 80.069 291 42 7 543 819 204398644 204398356 8.080000e-48 202.0
27 TraesCS2A01G574600 chr1B 80.303 264 39 5 557 809 610300709 610300448 2.260000e-43 187.0
28 TraesCS2A01G574600 chr1B 75.399 313 56 11 543 836 384039016 384039326 1.080000e-26 132.0
29 TraesCS2A01G574600 chr6B 100.000 107 0 0 2112 2218 548130725 548130619 1.050000e-46 198.0
30 TraesCS2A01G574600 chr5A 98.198 111 2 0 2112 2222 219578962 219579072 1.350000e-45 195.0
31 TraesCS2A01G574600 chr5A 99.074 108 1 0 2115 2222 457431784 457431677 1.350000e-45 195.0
32 TraesCS2A01G574600 chr7B 79.016 305 46 10 543 836 546546967 546547264 4.860000e-45 193.0
33 TraesCS2A01G574600 chr7B 77.049 305 43 12 543 837 510166694 510166981 2.970000e-32 150.0
34 TraesCS2A01G574600 chr7A 97.345 113 3 0 2112 2224 76122929 76123041 4.860000e-45 193.0
35 TraesCS2A01G574600 chr4A 95.868 121 1 3 2115 2232 546624951 546624832 4.860000e-45 193.0
36 TraesCS2A01G574600 chr4B 78.710 310 49 5 543 835 86365273 86364964 1.750000e-44 191.0
37 TraesCS2A01G574600 chr4B 78.387 310 46 8 543 833 68653449 68653756 1.050000e-41 182.0
38 TraesCS2A01G574600 chr3B 76.518 247 38 11 543 773 513663111 513662869 3.010000e-22 117.0
39 TraesCS2A01G574600 chr4D 84.685 111 17 0 704 814 215393773 215393663 1.400000e-20 111.0


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 TraesCS2A01G574600 chr2A 769493669 769498430 4761 False 8794.000000 8794 100.0000 1 4762 1 chr2A.!!$F1 4761
1 TraesCS2A01G574600 chr2B 791477734 791481551 3817 True 1276.500000 4397 90.5155 848 4735 4 chr2B.!!$R2 3887
2 TraesCS2A01G574600 chr2D 644329141 644333106 3965 False 1748.666667 2425 90.4360 1 4149 3 chr2D.!!$F1 4148
3 TraesCS2A01G574600 chr2D 644360364 644361629 1265 False 234.500000 298 90.9985 4142 4541 2 chr2D.!!$F2 399

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
728 755 0.039618 ATTTCATGCTGGGTTCGGGT 59.960 50.000 0.0 0.0 0.00 5.28 F
741 768 0.248702 TTCGGGTTTGAAAACAGCGC 60.249 50.000 0.0 0.0 40.63 5.92 F
2218 2294 0.398318 GCACTGGGTCTGTCCTTTCT 59.602 55.000 0.0 0.0 36.25 2.52 F
3113 3223 1.768870 ACCACTTACCTGTGCTGTCTT 59.231 47.619 0.0 0.0 36.68 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1579 1632 0.332972 ATTCCCAGAACAGAAGGCCC 59.667 55.000 0.00 0.0 0.00 5.80 R
2691 2800 1.376037 AGCTAAAGACACAGCGCCC 60.376 57.895 2.29 0.0 42.74 6.13 R
3147 3257 0.037697 CTGGAATGTCGGACACGGAA 60.038 55.000 13.92 0.0 41.39 4.30 R
4583 5840 0.179156 GCCAAATGCATGGACTGTCG 60.179 55.000 10.63 0.0 43.54 4.35 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
46 47 7.756722 GCTAATTTGATGTGTGCTAGTGAAATT 59.243 33.333 0.00 0.00 0.00 1.82
55 56 6.040278 TGTGTGCTAGTGAAATTTTTGGATGA 59.960 34.615 0.00 0.00 0.00 2.92
105 106 3.275617 TTGATGGCCGCTTAGTACAAT 57.724 42.857 0.00 0.00 0.00 2.71
110 111 4.167554 TGGCCGCTTAGTACAATTTTTG 57.832 40.909 0.00 0.00 0.00 2.44
114 115 4.791676 GCCGCTTAGTACAATTTTTGTAGC 59.208 41.667 0.00 2.38 45.99 3.58
138 139 6.595716 GCGGTATAGATTGATGGCTTAGAATT 59.404 38.462 0.00 0.00 0.00 2.17
172 183 5.692115 ACACATGGATGTTGTAGATGGTA 57.308 39.130 0.00 0.00 39.39 3.25
175 186 6.945435 ACACATGGATGTTGTAGATGGTAAAA 59.055 34.615 0.00 0.00 39.39 1.52
183 194 5.472137 TGTTGTAGATGGTAAAAGTGAAGGC 59.528 40.000 0.00 0.00 0.00 4.35
209 220 6.151985 ACCGAAAACTATTGATGCCAATAACA 59.848 34.615 0.00 0.00 42.71 2.41
214 225 2.937469 TTGATGCCAATAACAAGCCG 57.063 45.000 0.00 0.00 0.00 5.52
235 246 4.561105 CGAAAAGAACTGTCTCTTAGCCT 58.439 43.478 5.92 0.00 34.49 4.58
238 249 4.965200 AAGAACTGTCTCTTAGCCTTGT 57.035 40.909 4.24 0.00 33.81 3.16
255 266 7.601705 AGCCTTGTATGCATATGGTTTTAAT 57.398 32.000 10.16 0.00 0.00 1.40
363 374 5.047235 GCCGTTTACATCCCTATGAGTAGAT 60.047 44.000 0.00 0.00 36.54 1.98
377 388 3.181468 TGAGTAGATCTGAGCATTGGCAG 60.181 47.826 5.18 0.00 44.61 4.85
378 389 2.104451 AGTAGATCTGAGCATTGGCAGG 59.896 50.000 5.18 0.00 44.61 4.85
379 390 0.465824 AGATCTGAGCATTGGCAGGC 60.466 55.000 0.00 5.21 44.61 4.85
380 391 1.453762 GATCTGAGCATTGGCAGGCC 61.454 60.000 2.62 2.62 44.61 5.19
381 392 3.515286 CTGAGCATTGGCAGGCCG 61.515 66.667 5.74 0.00 44.61 6.13
382 393 3.982316 CTGAGCATTGGCAGGCCGA 62.982 63.158 2.03 2.03 44.61 5.54
383 394 3.512516 GAGCATTGGCAGGCCGAC 61.513 66.667 1.47 0.00 44.61 4.79
391 402 4.699522 GCAGGCCGACCCGACTTT 62.700 66.667 0.00 0.00 39.21 2.66
392 403 2.975536 CAGGCCGACCCGACTTTA 59.024 61.111 0.00 0.00 39.21 1.85
393 404 1.153628 CAGGCCGACCCGACTTTAG 60.154 63.158 0.00 0.00 39.21 1.85
394 405 1.608627 AGGCCGACCCGACTTTAGT 60.609 57.895 0.00 0.00 39.21 2.24
395 406 1.190178 AGGCCGACCCGACTTTAGTT 61.190 55.000 0.00 0.00 39.21 2.24
396 407 0.532115 GGCCGACCCGACTTTAGTTA 59.468 55.000 0.00 0.00 0.00 2.24
397 408 1.470458 GGCCGACCCGACTTTAGTTAG 60.470 57.143 0.00 0.00 0.00 2.34
398 409 1.918595 CCGACCCGACTTTAGTTAGC 58.081 55.000 0.00 0.00 0.00 3.09
399 410 1.475682 CCGACCCGACTTTAGTTAGCT 59.524 52.381 0.00 0.00 0.00 3.32
400 411 2.094338 CCGACCCGACTTTAGTTAGCTT 60.094 50.000 0.00 0.00 0.00 3.74
401 412 3.129287 CCGACCCGACTTTAGTTAGCTTA 59.871 47.826 0.00 0.00 0.00 3.09
402 413 4.349501 CGACCCGACTTTAGTTAGCTTAG 58.650 47.826 0.00 0.00 0.00 2.18
403 414 4.111198 GACCCGACTTTAGTTAGCTTAGC 58.889 47.826 0.00 0.00 0.00 3.09
404 415 3.768215 ACCCGACTTTAGTTAGCTTAGCT 59.232 43.478 12.67 12.67 43.41 3.32
405 416 4.952335 ACCCGACTTTAGTTAGCTTAGCTA 59.048 41.667 10.21 10.21 40.44 3.32
406 417 5.067544 ACCCGACTTTAGTTAGCTTAGCTAG 59.932 44.000 13.93 6.00 42.34 3.42
423 434 9.841880 GCTTAGCTAGCTTAATAGTTTGTTTTT 57.158 29.630 24.88 0.00 46.77 1.94
462 473 8.786826 TTAAACTGTTAGATCATTAGTGGGTG 57.213 34.615 0.00 0.00 0.00 4.61
463 474 6.374417 AACTGTTAGATCATTAGTGGGTGT 57.626 37.500 0.00 0.00 0.00 4.16
464 475 7.490657 AACTGTTAGATCATTAGTGGGTGTA 57.509 36.000 0.00 0.00 0.00 2.90
465 476 7.490657 ACTGTTAGATCATTAGTGGGTGTAA 57.509 36.000 0.00 0.00 0.00 2.41
466 477 7.913789 ACTGTTAGATCATTAGTGGGTGTAAA 58.086 34.615 0.00 0.00 0.00 2.01
467 478 7.822822 ACTGTTAGATCATTAGTGGGTGTAAAC 59.177 37.037 0.00 0.00 0.00 2.01
468 479 6.814644 TGTTAGATCATTAGTGGGTGTAAACG 59.185 38.462 0.00 0.00 0.00 3.60
469 480 4.766375 AGATCATTAGTGGGTGTAAACGG 58.234 43.478 0.00 0.00 0.00 4.44
470 481 3.337694 TCATTAGTGGGTGTAAACGGG 57.662 47.619 0.00 0.00 0.00 5.28
471 482 2.027007 TCATTAGTGGGTGTAAACGGGG 60.027 50.000 0.00 0.00 0.00 5.73
472 483 1.433121 TTAGTGGGTGTAAACGGGGT 58.567 50.000 0.00 0.00 0.00 4.95
473 484 1.433121 TAGTGGGTGTAAACGGGGTT 58.567 50.000 0.00 0.00 0.00 4.11
474 485 0.179012 AGTGGGTGTAAACGGGGTTG 60.179 55.000 0.00 0.00 0.00 3.77
475 486 0.466007 GTGGGTGTAAACGGGGTTGT 60.466 55.000 0.00 0.00 0.00 3.32
476 487 0.258194 TGGGTGTAAACGGGGTTGTT 59.742 50.000 0.00 0.00 0.00 2.83
477 488 1.341778 TGGGTGTAAACGGGGTTGTTT 60.342 47.619 0.00 0.00 43.95 2.83
478 489 2.092212 TGGGTGTAAACGGGGTTGTTTA 60.092 45.455 0.00 0.00 41.92 2.01
495 506 8.883954 GGTTGTTTACATCCCTATAAGTAGAC 57.116 38.462 0.00 0.00 31.18 2.59
496 507 8.702819 GGTTGTTTACATCCCTATAAGTAGACT 58.297 37.037 0.00 0.00 31.18 3.24
499 510 9.483489 TGTTTACATCCCTATAAGTAGACTTGA 57.517 33.333 5.15 0.00 37.40 3.02
500 511 9.968870 GTTTACATCCCTATAAGTAGACTTGAG 57.031 37.037 5.15 2.83 37.40 3.02
501 512 6.658188 ACATCCCTATAAGTAGACTTGAGC 57.342 41.667 5.15 0.00 37.40 4.26
502 513 6.136857 ACATCCCTATAAGTAGACTTGAGCA 58.863 40.000 5.15 0.00 37.40 4.26
503 514 6.784969 ACATCCCTATAAGTAGACTTGAGCAT 59.215 38.462 5.15 0.00 37.40 3.79
504 515 7.291182 ACATCCCTATAAGTAGACTTGAGCATT 59.709 37.037 5.15 0.00 37.40 3.56
505 516 8.807118 CATCCCTATAAGTAGACTTGAGCATTA 58.193 37.037 5.15 0.00 37.40 1.90
506 517 8.410673 TCCCTATAAGTAGACTTGAGCATTAG 57.589 38.462 5.15 0.00 37.40 1.73
507 518 7.039644 TCCCTATAAGTAGACTTGAGCATTAGC 60.040 40.741 5.15 0.00 37.99 3.09
508 519 7.255977 CCCTATAAGTAGACTTGAGCATTAGCA 60.256 40.741 5.15 0.00 39.21 3.49
509 520 8.144478 CCTATAAGTAGACTTGAGCATTAGCAA 58.856 37.037 5.15 0.00 39.21 3.91
513 524 2.040278 AGACTTGAGCATTAGCAACCCA 59.960 45.455 0.00 0.00 45.49 4.51
516 527 2.284754 TGAGCATTAGCAACCCAACA 57.715 45.000 0.00 0.00 45.49 3.33
529 540 0.251297 CCCAACATGAGCCTGACCAA 60.251 55.000 0.00 0.00 0.00 3.67
534 545 3.228188 ACATGAGCCTGACCAAGAAAA 57.772 42.857 0.00 0.00 0.00 2.29
535 546 2.887152 ACATGAGCCTGACCAAGAAAAC 59.113 45.455 0.00 0.00 0.00 2.43
536 547 1.981256 TGAGCCTGACCAAGAAAACC 58.019 50.000 0.00 0.00 0.00 3.27
539 550 2.693074 GAGCCTGACCAAGAAAACCAAA 59.307 45.455 0.00 0.00 0.00 3.28
540 551 2.695147 AGCCTGACCAAGAAAACCAAAG 59.305 45.455 0.00 0.00 0.00 2.77
542 553 3.490933 GCCTGACCAAGAAAACCAAAGTC 60.491 47.826 0.00 0.00 0.00 3.01
543 554 3.243068 CCTGACCAAGAAAACCAAAGTCG 60.243 47.826 0.00 0.00 0.00 4.18
545 556 2.028876 ACCAAGAAAACCAAAGTCGGG 58.971 47.619 0.00 0.00 0.00 5.14
581 607 0.939419 GCTTGGGCTTTGTTTTGCAG 59.061 50.000 0.00 0.00 35.22 4.41
582 608 0.939419 CTTGGGCTTTGTTTTGCAGC 59.061 50.000 0.00 0.00 0.00 5.25
583 609 0.463474 TTGGGCTTTGTTTTGCAGCC 60.463 50.000 2.37 2.37 44.31 4.85
584 610 1.336632 TGGGCTTTGTTTTGCAGCCT 61.337 50.000 10.33 0.00 44.44 4.58
586 612 0.881600 GGCTTTGTTTTGCAGCCTGG 60.882 55.000 3.76 0.00 41.99 4.45
605 631 0.320697 GAAGGTAGTTCGTGCTGGGT 59.679 55.000 0.00 0.00 0.00 4.51
610 636 1.180456 TAGTTCGTGCTGGGTTCGGA 61.180 55.000 0.00 0.00 0.00 4.55
612 638 2.504274 TTCGTGCTGGGTTCGGACT 61.504 57.895 0.00 0.00 0.00 3.85
622 648 2.224450 TGGGTTCGGACTTCTCTTTTCC 60.224 50.000 0.00 0.00 0.00 3.13
627 653 5.480205 GTTCGGACTTCTCTTTTCCTGTAT 58.520 41.667 0.00 0.00 0.00 2.29
628 654 5.740290 TCGGACTTCTCTTTTCCTGTATT 57.260 39.130 0.00 0.00 0.00 1.89
629 655 6.110411 TCGGACTTCTCTTTTCCTGTATTT 57.890 37.500 0.00 0.00 0.00 1.40
630 656 6.531021 TCGGACTTCTCTTTTCCTGTATTTT 58.469 36.000 0.00 0.00 0.00 1.82
631 657 7.673180 TCGGACTTCTCTTTTCCTGTATTTTA 58.327 34.615 0.00 0.00 0.00 1.52
632 658 7.817962 TCGGACTTCTCTTTTCCTGTATTTTAG 59.182 37.037 0.00 0.00 0.00 1.85
633 659 7.064728 CGGACTTCTCTTTTCCTGTATTTTAGG 59.935 40.741 0.00 0.00 36.63 2.69
634 660 7.883833 GGACTTCTCTTTTCCTGTATTTTAGGT 59.116 37.037 0.00 0.00 36.67 3.08
635 661 8.850007 ACTTCTCTTTTCCTGTATTTTAGGTC 57.150 34.615 0.00 0.00 36.67 3.85
636 662 7.603024 ACTTCTCTTTTCCTGTATTTTAGGTCG 59.397 37.037 0.00 0.00 36.67 4.79
637 663 6.403878 TCTCTTTTCCTGTATTTTAGGTCGG 58.596 40.000 0.00 0.00 36.67 4.79
638 664 5.493809 TCTTTTCCTGTATTTTAGGTCGGG 58.506 41.667 0.00 0.00 36.67 5.14
639 665 2.994186 TCCTGTATTTTAGGTCGGGC 57.006 50.000 0.00 0.00 36.67 6.13
640 666 2.474112 TCCTGTATTTTAGGTCGGGCT 58.526 47.619 0.00 0.00 36.67 5.19
641 667 2.841881 TCCTGTATTTTAGGTCGGGCTT 59.158 45.455 0.00 0.00 36.67 4.35
642 668 3.264964 TCCTGTATTTTAGGTCGGGCTTT 59.735 43.478 0.00 0.00 36.67 3.51
643 669 3.626217 CCTGTATTTTAGGTCGGGCTTTC 59.374 47.826 0.00 0.00 0.00 2.62
644 670 3.264104 TGTATTTTAGGTCGGGCTTTCG 58.736 45.455 0.00 0.00 0.00 3.46
645 671 1.746470 ATTTTAGGTCGGGCTTTCGG 58.254 50.000 0.00 0.00 0.00 4.30
646 672 0.321830 TTTTAGGTCGGGCTTTCGGG 60.322 55.000 0.00 0.00 0.00 5.14
650 676 2.330372 GGTCGGGCTTTCGGGTTTC 61.330 63.158 0.00 0.00 0.00 2.78
651 677 2.357760 TCGGGCTTTCGGGTTTCG 60.358 61.111 0.00 0.00 40.90 3.46
654 680 3.744719 GGCTTTCGGGTTTCGGGC 61.745 66.667 0.00 0.00 39.77 6.13
710 736 3.953612 TGTTCACAGACTTTTGGCTTGAT 59.046 39.130 0.00 0.00 33.85 2.57
720 747 3.322211 TTTGGCTTGATTTCATGCTGG 57.678 42.857 15.41 0.00 43.82 4.85
728 755 0.039618 ATTTCATGCTGGGTTCGGGT 59.960 50.000 0.00 0.00 0.00 5.28
736 763 1.537348 GCTGGGTTCGGGTTTGAAAAC 60.537 52.381 0.00 0.00 38.17 2.43
738 765 1.751924 TGGGTTCGGGTTTGAAAACAG 59.248 47.619 8.11 0.00 40.63 3.16
739 766 1.537348 GGGTTCGGGTTTGAAAACAGC 60.537 52.381 8.11 0.00 40.63 4.40
741 768 0.248702 TTCGGGTTTGAAAACAGCGC 60.249 50.000 0.00 0.00 40.63 5.92
779 806 1.223487 GGGCTCGGGCTTGATACAA 59.777 57.895 7.48 0.00 38.73 2.41
783 810 2.159379 GGCTCGGGCTTGATACAAAAAG 60.159 50.000 7.48 0.00 38.73 2.27
786 813 3.492337 TCGGGCTTGATACAAAAAGGTT 58.508 40.909 0.00 0.00 0.00 3.50
799 826 5.182487 ACAAAAAGGTTGGGCTTTTACAAG 58.818 37.500 0.00 0.00 33.11 3.16
807 834 3.284336 CTTTTACAAGCCCGGCCC 58.716 61.111 5.55 0.00 0.00 5.80
808 835 2.673687 TTTTACAAGCCCGGCCCG 60.674 61.111 5.55 0.00 0.00 6.13
844 871 3.726291 TGCCCAAGTTTACTTTTGAGC 57.274 42.857 0.00 0.00 33.11 4.26
846 873 3.640967 TGCCCAAGTTTACTTTTGAGCAT 59.359 39.130 0.00 0.00 33.11 3.79
871 898 1.268386 GCCGTCATCAGTCGTATCGAA 60.268 52.381 0.00 0.00 37.72 3.71
876 903 3.014623 TCATCAGTCGTATCGAACCTGT 58.985 45.455 0.00 0.00 37.72 4.00
1040 1085 2.752238 CGTCCTCCTCCTCGTGCT 60.752 66.667 0.00 0.00 0.00 4.40
1147 1195 3.327404 CCAACTACACCGCCCCCT 61.327 66.667 0.00 0.00 0.00 4.79
1561 1614 6.942532 ATCTGTTCTAGCAAAAACTTCACA 57.057 33.333 0.00 0.00 0.00 3.58
1579 1632 9.507280 AACTTCACATTCGCAAATTAGATTATG 57.493 29.630 0.00 0.00 0.00 1.90
1601 1654 3.563479 GGGCCTTCTGTTCTGGGAATTTA 60.563 47.826 0.84 0.00 0.00 1.40
1846 1907 8.284945 AGTGCATTGAATTAATACTCACACAT 57.715 30.769 0.00 0.00 31.08 3.21
1979 2040 0.821711 CTCGCAGGACCCTAGAGGAG 60.822 65.000 0.00 3.07 39.89 3.69
2178 2254 1.542093 TAATCCCTCCCCAGACCCCA 61.542 60.000 0.00 0.00 0.00 4.96
2218 2294 0.398318 GCACTGGGTCTGTCCTTTCT 59.602 55.000 0.00 0.00 36.25 2.52
2222 2298 2.237392 ACTGGGTCTGTCCTTTCTATGC 59.763 50.000 0.00 0.00 36.25 3.14
2266 2342 8.160521 TGGAATATATGTTAACCCACATTTCG 57.839 34.615 2.48 0.00 38.40 3.46
2871 2980 9.265901 CTGAAATCGAATAAAGGTCATGAGTAT 57.734 33.333 0.00 0.00 0.00 2.12
2979 3088 2.618709 GCAGCATACCCATACAACCTTC 59.381 50.000 0.00 0.00 0.00 3.46
3036 3145 3.274288 CACTTCATTCCTTCCTGTAGCC 58.726 50.000 0.00 0.00 0.00 3.93
3038 3147 4.162320 CACTTCATTCCTTCCTGTAGCCTA 59.838 45.833 0.00 0.00 0.00 3.93
3074 3183 6.927381 GCACTAAACTTGTCTAGTCTTGGTTA 59.073 38.462 0.00 0.00 35.54 2.85
3109 3219 3.214328 AGAAAACCACTTACCTGTGCTG 58.786 45.455 0.00 0.00 36.68 4.41
3113 3223 1.768870 ACCACTTACCTGTGCTGTCTT 59.231 47.619 0.00 0.00 36.68 3.01
3122 3232 5.438761 ACCTGTGCTGTCTTTTATGTTTC 57.561 39.130 0.00 0.00 0.00 2.78
3147 3257 6.656693 CCATGTAGAAATTCTTTGGTCTGAGT 59.343 38.462 0.00 0.00 0.00 3.41
3269 3379 7.079182 TGACTTACAAAATTTTCTCACGTGT 57.921 32.000 16.51 0.00 0.00 4.49
3308 3418 4.371624 TGTTGGATCAGATGTTCAGGTT 57.628 40.909 0.00 0.00 0.00 3.50
3389 3502 3.301794 TTGGTGCCAGCATGATATCTT 57.698 42.857 0.00 0.00 39.69 2.40
3390 3503 2.854963 TGGTGCCAGCATGATATCTTC 58.145 47.619 3.98 0.00 39.69 2.87
3391 3504 2.440627 TGGTGCCAGCATGATATCTTCT 59.559 45.455 3.98 0.00 39.69 2.85
3394 3507 3.501445 GTGCCAGCATGATATCTTCTTCC 59.499 47.826 3.98 0.00 39.69 3.46
3503 3627 0.833834 CCATCCGGATAGACTGGCCT 60.834 60.000 18.63 0.00 44.31 5.19
3515 3639 2.616893 TGGCCTGCTTACCCCCAT 60.617 61.111 3.32 0.00 0.00 4.00
3593 3717 1.221466 TGAACACCTTTGAGAGCGCG 61.221 55.000 0.00 0.00 0.00 6.86
3611 3735 2.265739 GCGAGTGCCATGGAGACA 59.734 61.111 18.40 0.07 39.44 3.41
3713 3840 1.344763 GCGGTACCTGAGCCTCATATT 59.655 52.381 10.90 0.00 0.00 1.28
3719 3846 3.378512 ACCTGAGCCTCATATTGAGTCA 58.621 45.455 0.00 0.00 42.80 3.41
3721 3848 4.040217 ACCTGAGCCTCATATTGAGTCATC 59.960 45.833 0.00 0.42 42.80 2.92
3741 3868 3.020237 GCCGGTGAGGAGGAAGGTC 62.020 68.421 1.90 0.00 45.00 3.85
3765 3892 1.016130 GCGTGTGGATCTGTGAGTGG 61.016 60.000 0.00 0.00 0.00 4.00
3822 3949 5.470098 GGATCACTGCAGTTTTCTTTCAGTA 59.530 40.000 18.94 0.00 38.35 2.74
3832 3959 6.967199 CAGTTTTCTTTCAGTACCAGTTGTTC 59.033 38.462 0.00 0.00 0.00 3.18
3847 3974 2.820197 GTTGTTCCCTCATGTTTCCCTC 59.180 50.000 0.00 0.00 0.00 4.30
3901 4049 9.553064 GATGAATGTAGAGTGTAGGATGAAATT 57.447 33.333 0.00 0.00 0.00 1.82
3906 4054 9.911788 ATGTAGAGTGTAGGATGAAATTCAATT 57.088 29.630 0.00 0.00 0.00 2.32
3928 4076 4.623932 TTACAGATTCAGGAGCTGTTGT 57.376 40.909 4.53 0.00 42.40 3.32
3929 4077 2.775890 ACAGATTCAGGAGCTGTTGTG 58.224 47.619 0.00 0.00 39.69 3.33
3930 4078 1.467734 CAGATTCAGGAGCTGTTGTGC 59.532 52.381 0.00 0.00 32.61 4.57
3965 4113 9.599866 TGTAATACTCTGAAAATACATCACCAG 57.400 33.333 0.00 0.00 0.00 4.00
3966 4114 9.601217 GTAATACTCTGAAAATACATCACCAGT 57.399 33.333 0.00 0.00 0.00 4.00
3968 4116 9.601217 AATACTCTGAAAATACATCACCAGTAC 57.399 33.333 0.00 0.00 0.00 2.73
3969 4117 7.004555 ACTCTGAAAATACATCACCAGTACA 57.995 36.000 0.00 0.00 0.00 2.90
3970 4118 7.624549 ACTCTGAAAATACATCACCAGTACAT 58.375 34.615 0.00 0.00 0.00 2.29
3971 4119 7.766278 ACTCTGAAAATACATCACCAGTACATC 59.234 37.037 0.00 0.00 0.00 3.06
3972 4120 7.619965 TCTGAAAATACATCACCAGTACATCA 58.380 34.615 0.00 0.00 0.00 3.07
3973 4121 7.549134 TCTGAAAATACATCACCAGTACATCAC 59.451 37.037 0.00 0.00 0.00 3.06
3974 4122 6.597672 TGAAAATACATCACCAGTACATCACC 59.402 38.462 0.00 0.00 0.00 4.02
3998 4146 4.701850 GGTTATACCATGTGCCGAGGCA 62.702 54.545 13.49 13.49 43.05 4.75
4025 4192 4.368874 TTTCCACATTGTCAACACACAG 57.631 40.909 0.00 0.00 29.76 3.66
4095 4262 8.141298 TGTATACAGAAATGAAAGTGGGAGTA 57.859 34.615 0.08 0.00 0.00 2.59
4279 4448 2.892425 CTTGGATCTGCCGCGGAC 60.892 66.667 33.48 21.14 40.66 4.79
4316 4485 4.657969 ACCAAACAAAGAAATGGGGAATGA 59.342 37.500 0.00 0.00 37.26 2.57
4322 4491 6.466812 ACAAAGAAATGGGGAATGATTTGAC 58.533 36.000 0.00 0.00 32.28 3.18
4340 4509 2.028658 TGACTGATCTTGCTCAGGTCAC 60.029 50.000 5.76 0.00 45.67 3.67
4359 5376 2.026822 CACCTACATGTTCTGGAAGCCT 60.027 50.000 2.30 0.00 0.00 4.58
4361 5378 3.074538 ACCTACATGTTCTGGAAGCCTTT 59.925 43.478 2.30 0.00 0.00 3.11
4407 5444 3.797353 CCACGGCCCTGCAGGTAT 61.797 66.667 30.63 10.58 38.26 2.73
4430 5467 3.415457 AACTCTGCTTTTCCTCTCCTG 57.585 47.619 0.00 0.00 0.00 3.86
4450 5490 7.944554 TCTCCTGTTCCATTCATCTTTTACTTT 59.055 33.333 0.00 0.00 0.00 2.66
4496 5536 7.933577 CACTGTTTATTATGGCATCTCTTCCTA 59.066 37.037 1.65 0.00 0.00 2.94
4504 5544 6.753913 ATGGCATCTCTTCCTACAGAATTA 57.246 37.500 0.00 0.00 32.82 1.40
4506 5546 5.425217 TGGCATCTCTTCCTACAGAATTACA 59.575 40.000 0.00 0.00 32.82 2.41
4511 5551 7.187824 TCTCTTCCTACAGAATTACAGCATT 57.812 36.000 0.00 0.00 32.82 3.56
4514 5554 9.553064 CTCTTCCTACAGAATTACAGCATTAAT 57.447 33.333 0.00 0.00 32.82 1.40
4555 5595 8.964476 ATTAACAGGGTAATCAACTACATCTG 57.036 34.615 0.00 0.00 34.01 2.90
4567 5607 7.170393 TCAACTACATCTGTTGTACTGCTAT 57.830 36.000 6.52 0.00 43.54 2.97
4583 5840 6.334102 ACTGCTATGTACTAACTGATAGCC 57.666 41.667 14.59 2.56 41.70 3.93
4586 5843 5.048921 TGCTATGTACTAACTGATAGCCGAC 60.049 44.000 14.59 0.00 41.70 4.79
4605 5862 0.892755 CAGTCCATGCATTTGGCTGT 59.107 50.000 16.08 0.00 45.15 4.40
4607 5864 2.691526 CAGTCCATGCATTTGGCTGTAT 59.308 45.455 16.08 0.00 45.15 2.29
4608 5865 2.691526 AGTCCATGCATTTGGCTGTATG 59.308 45.455 0.00 0.00 45.15 2.39
4609 5866 2.689471 GTCCATGCATTTGGCTGTATGA 59.311 45.455 0.00 0.00 45.15 2.15
4610 5867 2.689471 TCCATGCATTTGGCTGTATGAC 59.311 45.455 0.00 0.00 45.15 3.06
4611 5868 2.691526 CCATGCATTTGGCTGTATGACT 59.308 45.455 0.00 0.00 45.15 3.41
4612 5869 3.490249 CCATGCATTTGGCTGTATGACTG 60.490 47.826 0.00 0.00 45.15 3.51
4613 5870 1.473677 TGCATTTGGCTGTATGACTGC 59.526 47.619 0.27 0.27 45.15 4.40
4618 5875 0.983467 TGGCTGTATGACTGCTTCCA 59.017 50.000 8.15 0.00 41.90 3.53
4639 5896 7.654022 TCCAGTTGTTTTTCCTAGAAATTGT 57.346 32.000 0.00 0.00 0.00 2.71
4662 5922 9.444600 TTGTTTGGGAACTAGTACTAATCATTC 57.555 33.333 3.76 5.84 36.70 2.67
4663 5923 8.822805 TGTTTGGGAACTAGTACTAATCATTCT 58.177 33.333 3.76 0.00 36.70 2.40
4681 5941 1.693606 TCTGATGCTTGTGGTGACAGA 59.306 47.619 0.00 0.00 44.46 3.41
4684 5944 1.002430 GATGCTTGTGGTGACAGAGGA 59.998 52.381 0.00 0.00 44.46 3.71
4685 5945 1.059098 TGCTTGTGGTGACAGAGGAT 58.941 50.000 0.00 0.00 44.46 3.24
4723 5983 3.591527 ACATTGTTGGGACTTGGGAGATA 59.408 43.478 0.00 0.00 0.00 1.98
4728 5988 3.129262 TGGGACTTGGGAGATACATGA 57.871 47.619 0.00 0.00 0.00 3.07
4743 6003 7.615039 AGATACATGATCTCCTTCACAAGAT 57.385 36.000 0.00 0.00 41.37 2.40
4744 6004 7.669427 AGATACATGATCTCCTTCACAAGATC 58.331 38.462 0.00 5.60 41.37 2.75
4749 6009 4.640364 GATCTCCTTCACAAGATCATCCC 58.360 47.826 7.34 0.00 44.76 3.85
4750 6010 3.729108 TCTCCTTCACAAGATCATCCCT 58.271 45.455 0.00 0.00 0.00 4.20
4751 6011 3.708631 TCTCCTTCACAAGATCATCCCTC 59.291 47.826 0.00 0.00 0.00 4.30
4752 6012 2.774234 TCCTTCACAAGATCATCCCTCC 59.226 50.000 0.00 0.00 0.00 4.30
4753 6013 2.507058 CCTTCACAAGATCATCCCTCCA 59.493 50.000 0.00 0.00 0.00 3.86
4754 6014 3.054139 CCTTCACAAGATCATCCCTCCAA 60.054 47.826 0.00 0.00 0.00 3.53
4755 6015 4.386088 CCTTCACAAGATCATCCCTCCAAT 60.386 45.833 0.00 0.00 0.00 3.16
4756 6016 5.163163 CCTTCACAAGATCATCCCTCCAATA 60.163 44.000 0.00 0.00 0.00 1.90
4757 6017 5.557576 TCACAAGATCATCCCTCCAATAG 57.442 43.478 0.00 0.00 0.00 1.73
4758 6018 4.070716 CACAAGATCATCCCTCCAATAGC 58.929 47.826 0.00 0.00 0.00 2.97
4759 6019 3.073650 ACAAGATCATCCCTCCAATAGCC 59.926 47.826 0.00 0.00 0.00 3.93
4760 6020 2.995746 AGATCATCCCTCCAATAGCCA 58.004 47.619 0.00 0.00 0.00 4.75
4761 6021 3.330198 AGATCATCCCTCCAATAGCCAA 58.670 45.455 0.00 0.00 0.00 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 7.961351 ACTCCATACAAAACAATCATCCAAAA 58.039 30.769 0.00 0.00 0.00 2.44
65 66 7.500227 CCATCAATCATACAACTTGTACTCCAT 59.500 37.037 3.67 0.00 35.42 3.41
76 77 1.949525 AGCGGCCATCAATCATACAAC 59.050 47.619 2.24 0.00 0.00 3.32
83 84 2.833794 TGTACTAAGCGGCCATCAATC 58.166 47.619 2.24 0.00 0.00 2.67
105 106 6.017440 GCCATCAATCTATACCGCTACAAAAA 60.017 38.462 0.00 0.00 0.00 1.94
110 111 4.457834 AGCCATCAATCTATACCGCTAC 57.542 45.455 0.00 0.00 0.00 3.58
114 115 8.553459 AAATTCTAAGCCATCAATCTATACCG 57.447 34.615 0.00 0.00 0.00 4.02
138 139 7.014711 ACAACATCCATGTGTAAACATACCAAA 59.985 33.333 0.00 0.00 41.61 3.28
172 183 2.758423 AGTTTTCGGTGCCTTCACTTTT 59.242 40.909 0.00 0.00 42.72 2.27
175 186 2.922740 TAGTTTTCGGTGCCTTCACT 57.077 45.000 0.00 0.00 42.72 3.41
183 194 4.433186 TTGGCATCAATAGTTTTCGGTG 57.567 40.909 0.00 0.00 0.00 4.94
209 220 3.477210 AGAGACAGTTCTTTTCGGCTT 57.523 42.857 0.00 0.00 29.47 4.35
214 225 5.760743 ACAAGGCTAAGAGACAGTTCTTTTC 59.239 40.000 0.00 0.00 38.35 2.29
318 329 4.573607 GGCTCCGTTTAAACCTACTAATGG 59.426 45.833 12.66 5.65 0.00 3.16
323 334 2.375173 CGGCTCCGTTTAAACCTACT 57.625 50.000 12.66 0.00 34.35 2.57
338 349 3.039011 ACTCATAGGGATGTAAACGGCT 58.961 45.455 0.00 0.00 34.41 5.52
350 361 5.337410 CCAATGCTCAGATCTACTCATAGGG 60.337 48.000 0.00 1.60 0.00 3.53
363 374 2.044650 GGCCTGCCAATGCTCAGA 60.045 61.111 2.58 0.00 38.71 3.27
377 388 0.532115 TAACTAAAGTCGGGTCGGCC 59.468 55.000 0.00 0.00 28.67 6.13
378 389 1.918595 CTAACTAAAGTCGGGTCGGC 58.081 55.000 0.00 0.00 0.00 5.54
379 390 1.475682 AGCTAACTAAAGTCGGGTCGG 59.524 52.381 0.00 0.00 0.00 4.79
380 391 2.935481 AGCTAACTAAAGTCGGGTCG 57.065 50.000 0.00 0.00 0.00 4.79
381 392 4.111198 GCTAAGCTAACTAAAGTCGGGTC 58.889 47.826 0.00 0.00 0.00 4.46
382 393 3.768215 AGCTAAGCTAACTAAAGTCGGGT 59.232 43.478 0.00 0.00 36.99 5.28
383 394 4.388378 AGCTAAGCTAACTAAAGTCGGG 57.612 45.455 0.00 0.00 36.99 5.14
436 447 9.396022 CACCCACTAATGATCTAACAGTTTAAT 57.604 33.333 0.00 0.00 0.00 1.40
437 448 8.380099 ACACCCACTAATGATCTAACAGTTTAA 58.620 33.333 0.00 0.00 0.00 1.52
438 449 7.913789 ACACCCACTAATGATCTAACAGTTTA 58.086 34.615 0.00 0.00 0.00 2.01
439 450 6.779860 ACACCCACTAATGATCTAACAGTTT 58.220 36.000 0.00 0.00 0.00 2.66
440 451 6.374417 ACACCCACTAATGATCTAACAGTT 57.626 37.500 0.00 0.00 0.00 3.16
441 452 7.490657 TTACACCCACTAATGATCTAACAGT 57.509 36.000 0.00 0.00 0.00 3.55
442 453 7.010183 CGTTTACACCCACTAATGATCTAACAG 59.990 40.741 0.00 0.00 0.00 3.16
443 454 6.814644 CGTTTACACCCACTAATGATCTAACA 59.185 38.462 0.00 0.00 0.00 2.41
444 455 6.257193 CCGTTTACACCCACTAATGATCTAAC 59.743 42.308 0.00 0.00 0.00 2.34
445 456 6.342906 CCGTTTACACCCACTAATGATCTAA 58.657 40.000 0.00 0.00 0.00 2.10
446 457 5.163385 CCCGTTTACACCCACTAATGATCTA 60.163 44.000 0.00 0.00 0.00 1.98
447 458 4.383770 CCCGTTTACACCCACTAATGATCT 60.384 45.833 0.00 0.00 0.00 2.75
448 459 3.875134 CCCGTTTACACCCACTAATGATC 59.125 47.826 0.00 0.00 0.00 2.92
449 460 3.371166 CCCCGTTTACACCCACTAATGAT 60.371 47.826 0.00 0.00 0.00 2.45
450 461 2.027007 CCCCGTTTACACCCACTAATGA 60.027 50.000 0.00 0.00 0.00 2.57
451 462 2.290450 ACCCCGTTTACACCCACTAATG 60.290 50.000 0.00 0.00 0.00 1.90
452 463 1.987368 ACCCCGTTTACACCCACTAAT 59.013 47.619 0.00 0.00 0.00 1.73
453 464 1.433121 ACCCCGTTTACACCCACTAA 58.567 50.000 0.00 0.00 0.00 2.24
454 465 1.072015 CAACCCCGTTTACACCCACTA 59.928 52.381 0.00 0.00 0.00 2.74
455 466 0.179012 CAACCCCGTTTACACCCACT 60.179 55.000 0.00 0.00 0.00 4.00
456 467 0.466007 ACAACCCCGTTTACACCCAC 60.466 55.000 0.00 0.00 0.00 4.61
457 468 0.258194 AACAACCCCGTTTACACCCA 59.742 50.000 0.00 0.00 0.00 4.51
458 469 1.401761 AAACAACCCCGTTTACACCC 58.598 50.000 0.00 0.00 37.33 4.61
470 481 8.702819 AGTCTACTTATAGGGATGTAAACAACC 58.297 37.037 0.96 0.96 38.00 3.77
473 484 9.483489 TCAAGTCTACTTATAGGGATGTAAACA 57.517 33.333 0.00 0.00 34.28 2.83
474 485 9.968870 CTCAAGTCTACTTATAGGGATGTAAAC 57.031 37.037 0.00 0.00 34.28 2.01
475 486 8.639761 GCTCAAGTCTACTTATAGGGATGTAAA 58.360 37.037 0.00 0.00 34.28 2.01
476 487 7.783119 TGCTCAAGTCTACTTATAGGGATGTAA 59.217 37.037 0.00 0.00 34.28 2.41
477 488 7.295340 TGCTCAAGTCTACTTATAGGGATGTA 58.705 38.462 0.00 0.00 34.28 2.29
478 489 6.136857 TGCTCAAGTCTACTTATAGGGATGT 58.863 40.000 0.00 0.00 34.28 3.06
479 490 6.656632 TGCTCAAGTCTACTTATAGGGATG 57.343 41.667 0.00 0.00 34.28 3.51
480 491 7.863901 AATGCTCAAGTCTACTTATAGGGAT 57.136 36.000 0.00 0.00 34.28 3.85
481 492 7.039644 GCTAATGCTCAAGTCTACTTATAGGGA 60.040 40.741 0.00 0.00 33.67 4.20
482 493 7.093992 GCTAATGCTCAAGTCTACTTATAGGG 58.906 42.308 0.00 0.00 33.67 3.53
483 494 7.661968 TGCTAATGCTCAAGTCTACTTATAGG 58.338 38.462 0.00 0.00 40.48 2.57
484 495 8.973378 GTTGCTAATGCTCAAGTCTACTTATAG 58.027 37.037 0.00 0.00 40.48 1.31
485 496 7.926555 GGTTGCTAATGCTCAAGTCTACTTATA 59.073 37.037 0.00 0.00 40.48 0.98
486 497 6.763610 GGTTGCTAATGCTCAAGTCTACTTAT 59.236 38.462 0.00 0.00 40.48 1.73
487 498 6.106673 GGTTGCTAATGCTCAAGTCTACTTA 58.893 40.000 0.00 0.00 40.48 2.24
488 499 4.938226 GGTTGCTAATGCTCAAGTCTACTT 59.062 41.667 0.00 0.00 40.48 2.24
489 500 4.508662 GGTTGCTAATGCTCAAGTCTACT 58.491 43.478 0.00 0.00 40.48 2.57
490 501 3.623510 GGGTTGCTAATGCTCAAGTCTAC 59.376 47.826 0.00 0.00 40.48 2.59
491 502 3.263170 TGGGTTGCTAATGCTCAAGTCTA 59.737 43.478 0.00 0.00 40.48 2.59
492 503 2.040278 TGGGTTGCTAATGCTCAAGTCT 59.960 45.455 0.00 0.00 40.48 3.24
493 504 2.436417 TGGGTTGCTAATGCTCAAGTC 58.564 47.619 0.00 0.00 40.48 3.01
494 505 2.558359 GTTGGGTTGCTAATGCTCAAGT 59.442 45.455 0.00 0.00 40.48 3.16
495 506 2.557924 TGTTGGGTTGCTAATGCTCAAG 59.442 45.455 0.00 0.00 40.48 3.02
496 507 2.591923 TGTTGGGTTGCTAATGCTCAA 58.408 42.857 0.00 0.00 40.48 3.02
497 508 2.284754 TGTTGGGTTGCTAATGCTCA 57.715 45.000 0.00 0.00 40.48 4.26
498 509 2.754552 TCATGTTGGGTTGCTAATGCTC 59.245 45.455 0.00 0.00 40.48 4.26
499 510 2.756760 CTCATGTTGGGTTGCTAATGCT 59.243 45.455 0.00 0.00 40.48 3.79
500 511 2.736400 GCTCATGTTGGGTTGCTAATGC 60.736 50.000 0.00 0.00 40.20 3.56
501 512 2.159198 GGCTCATGTTGGGTTGCTAATG 60.159 50.000 0.00 0.00 0.00 1.90
502 513 2.102578 GGCTCATGTTGGGTTGCTAAT 58.897 47.619 0.00 0.00 0.00 1.73
503 514 1.075374 AGGCTCATGTTGGGTTGCTAA 59.925 47.619 0.00 0.00 0.00 3.09
504 515 0.698238 AGGCTCATGTTGGGTTGCTA 59.302 50.000 0.00 0.00 0.00 3.49
505 516 0.896940 CAGGCTCATGTTGGGTTGCT 60.897 55.000 0.00 0.00 0.00 3.91
506 517 0.895100 TCAGGCTCATGTTGGGTTGC 60.895 55.000 0.00 0.00 0.00 4.17
507 518 0.883833 GTCAGGCTCATGTTGGGTTG 59.116 55.000 0.00 0.00 0.00 3.77
508 519 0.251341 GGTCAGGCTCATGTTGGGTT 60.251 55.000 0.00 0.00 0.00 4.11
509 520 1.380302 GGTCAGGCTCATGTTGGGT 59.620 57.895 0.00 0.00 0.00 4.51
513 524 2.957402 TTCTTGGTCAGGCTCATGTT 57.043 45.000 0.00 0.00 0.00 2.71
516 527 2.158475 TGGTTTTCTTGGTCAGGCTCAT 60.158 45.455 0.00 0.00 0.00 2.90
529 540 1.407618 GCAACCCGACTTTGGTTTTCT 59.592 47.619 0.00 0.00 43.52 2.52
534 545 0.469144 AATGGCAACCCGACTTTGGT 60.469 50.000 0.00 0.00 37.85 3.67
535 546 0.038343 CAATGGCAACCCGACTTTGG 60.038 55.000 0.00 0.00 34.77 3.28
536 547 0.038343 CCAATGGCAACCCGACTTTG 60.038 55.000 0.00 0.00 37.49 2.77
539 550 2.035626 CCCAATGGCAACCCGACT 59.964 61.111 0.00 0.00 0.00 4.18
540 551 3.068064 CCCCAATGGCAACCCGAC 61.068 66.667 0.00 0.00 0.00 4.79
581 607 1.019805 GCACGAACTACCTTCCAGGC 61.020 60.000 0.00 0.00 39.63 4.85
582 608 0.608640 AGCACGAACTACCTTCCAGG 59.391 55.000 0.00 0.00 42.49 4.45
583 609 1.673033 CCAGCACGAACTACCTTCCAG 60.673 57.143 0.00 0.00 0.00 3.86
584 610 0.320374 CCAGCACGAACTACCTTCCA 59.680 55.000 0.00 0.00 0.00 3.53
586 612 0.320697 ACCCAGCACGAACTACCTTC 59.679 55.000 0.00 0.00 0.00 3.46
597 623 0.670854 GAGAAGTCCGAACCCAGCAC 60.671 60.000 0.00 0.00 0.00 4.40
605 631 5.740290 ATACAGGAAAAGAGAAGTCCGAA 57.260 39.130 0.00 0.00 36.49 4.30
610 636 7.603024 CGACCTAAAATACAGGAAAAGAGAAGT 59.397 37.037 0.00 0.00 36.61 3.01
612 638 6.877322 CCGACCTAAAATACAGGAAAAGAGAA 59.123 38.462 0.00 0.00 36.61 2.87
622 648 3.308866 CGAAAGCCCGACCTAAAATACAG 59.691 47.826 0.00 0.00 0.00 2.74
627 653 0.321830 CCCGAAAGCCCGACCTAAAA 60.322 55.000 0.00 0.00 0.00 1.52
628 654 1.297364 CCCGAAAGCCCGACCTAAA 59.703 57.895 0.00 0.00 0.00 1.85
629 655 1.482748 AACCCGAAAGCCCGACCTAA 61.483 55.000 0.00 0.00 0.00 2.69
630 656 1.482748 AAACCCGAAAGCCCGACCTA 61.483 55.000 0.00 0.00 0.00 3.08
631 657 2.743126 GAAACCCGAAAGCCCGACCT 62.743 60.000 0.00 0.00 0.00 3.85
632 658 2.281970 AAACCCGAAAGCCCGACC 60.282 61.111 0.00 0.00 0.00 4.79
633 659 2.674084 CGAAACCCGAAAGCCCGAC 61.674 63.158 0.00 0.00 41.76 4.79
634 660 2.357760 CGAAACCCGAAAGCCCGA 60.358 61.111 0.00 0.00 41.76 5.14
635 661 3.428282 CCGAAACCCGAAAGCCCG 61.428 66.667 0.00 0.00 41.76 6.13
636 662 3.060000 CCCGAAACCCGAAAGCCC 61.060 66.667 0.00 0.00 41.76 5.19
637 663 3.744719 GCCCGAAACCCGAAAGCC 61.745 66.667 0.00 0.00 41.76 4.35
638 664 3.744719 GGCCCGAAACCCGAAAGC 61.745 66.667 0.00 0.00 41.76 3.51
684 710 6.265196 TCAAGCCAAAAGTCTGTGAACATATT 59.735 34.615 0.00 0.00 0.00 1.28
685 711 5.769662 TCAAGCCAAAAGTCTGTGAACATAT 59.230 36.000 0.00 0.00 0.00 1.78
686 712 5.129634 TCAAGCCAAAAGTCTGTGAACATA 58.870 37.500 0.00 0.00 0.00 2.29
687 713 3.953612 TCAAGCCAAAAGTCTGTGAACAT 59.046 39.130 0.00 0.00 0.00 2.71
688 714 3.351740 TCAAGCCAAAAGTCTGTGAACA 58.648 40.909 0.00 0.00 0.00 3.18
695 721 4.282703 AGCATGAAATCAAGCCAAAAGTCT 59.717 37.500 6.98 0.00 41.05 3.24
710 736 0.178975 AACCCGAACCCAGCATGAAA 60.179 50.000 0.00 0.00 39.69 2.69
720 747 1.847818 GCTGTTTTCAAACCCGAACC 58.152 50.000 0.00 0.00 38.11 3.62
728 755 2.968006 CGAAATACGCGCTGTTTTCAAA 59.032 40.909 5.73 6.72 32.16 2.69
738 765 0.042448 CTAAAGCCCGAAATACGCGC 60.042 55.000 5.73 0.00 44.74 6.86
739 766 0.580104 CCTAAAGCCCGAAATACGCG 59.420 55.000 3.53 3.53 41.07 6.01
760 787 2.280186 GTATCAAGCCCGAGCCCG 60.280 66.667 0.00 0.00 41.25 6.13
761 788 0.393808 TTTGTATCAAGCCCGAGCCC 60.394 55.000 0.00 0.00 41.25 5.19
762 789 1.459450 TTTTGTATCAAGCCCGAGCC 58.541 50.000 0.00 0.00 41.25 4.70
763 790 2.159379 CCTTTTTGTATCAAGCCCGAGC 60.159 50.000 0.00 0.00 40.32 5.03
764 791 3.081804 ACCTTTTTGTATCAAGCCCGAG 58.918 45.455 0.00 0.00 0.00 4.63
765 792 3.149005 ACCTTTTTGTATCAAGCCCGA 57.851 42.857 0.00 0.00 0.00 5.14
779 806 3.804036 GCTTGTAAAAGCCCAACCTTTT 58.196 40.909 6.34 5.39 44.63 2.27
844 871 1.854743 CGACTGATGACGGCAGTAATG 59.145 52.381 0.00 0.00 45.94 1.90
846 873 0.885879 ACGACTGATGACGGCAGTAA 59.114 50.000 0.00 0.00 45.94 2.24
912 945 2.693250 TTCTGCGCGTGTGCTACACT 62.693 55.000 8.43 0.00 46.46 3.55
966 999 2.358125 TGGTGGTGGTGATTCGCG 60.358 61.111 0.00 0.00 0.00 5.87
1068 1116 1.953138 GATGCAGATGTCCTCGGCG 60.953 63.158 0.00 0.00 46.72 6.46
1561 1614 5.079643 AGGCCCATAATCTAATTTGCGAAT 58.920 37.500 0.00 0.00 0.00 3.34
1579 1632 0.332972 ATTCCCAGAACAGAAGGCCC 59.667 55.000 0.00 0.00 0.00 5.80
1609 1662 7.255139 GCCACAGTAATCAAGTTTAACTGAACT 60.255 37.037 0.00 0.00 41.44 3.01
1846 1907 2.561858 TGCAACATTTCCTGCATAGCAA 59.438 40.909 0.00 0.00 43.44 3.91
1979 2040 1.895707 CCCGGCATCAATGAGCTCC 60.896 63.158 12.15 0.00 0.00 4.70
2009 2070 4.118410 CAGTGACAAGCTCTGATATGGTC 58.882 47.826 0.00 0.00 39.82 4.02
2178 2254 1.729586 TAGAAGCTCCCACACAAGGT 58.270 50.000 0.00 0.00 0.00 3.50
2218 2294 5.293324 CAGTAAACGCAACTATTGGAGCATA 59.707 40.000 0.00 0.00 0.00 3.14
2222 2298 4.250464 TCCAGTAAACGCAACTATTGGAG 58.750 43.478 0.00 0.00 31.15 3.86
2335 2413 6.890268 TCTTCATTAGTCCTAGAGTGCTACAA 59.110 38.462 0.00 0.00 0.00 2.41
2691 2800 1.376037 AGCTAAAGACACAGCGCCC 60.376 57.895 2.29 0.00 42.74 6.13
2871 2980 0.876777 CAACCGTCACCGTGCAGTTA 60.877 55.000 0.00 0.00 0.00 2.24
2979 3088 1.216710 GTCCAAGAGGCCTCTGACG 59.783 63.158 35.77 24.85 40.36 4.35
3036 3145 8.856490 ACAAGTTTAGTGCTTCAAAACAATAG 57.144 30.769 0.00 0.00 35.93 1.73
3038 3147 7.547227 AGACAAGTTTAGTGCTTCAAAACAAT 58.453 30.769 0.00 0.00 35.93 2.71
3074 3183 4.573607 GTGGTTTTCTTTCTCGTGGTAACT 59.426 41.667 0.00 0.00 37.61 2.24
3122 3232 6.656693 ACTCAGACCAAAGAATTTCTACATGG 59.343 38.462 17.65 17.65 35.03 3.66
3147 3257 0.037697 CTGGAATGTCGGACACGGAA 60.038 55.000 13.92 0.00 41.39 4.30
3231 3341 1.078709 AAGTCATGTCATGTTCGCCG 58.921 50.000 12.54 0.00 0.00 6.46
3342 3452 4.469945 AGCCTAGCCATGTCTACTTTAACA 59.530 41.667 0.00 0.00 0.00 2.41
3353 3463 3.290710 CACCAAAATAGCCTAGCCATGT 58.709 45.455 0.00 0.00 0.00 3.21
3389 3502 4.357325 AGATACCAGCTCTTCAAGGAAGA 58.643 43.478 8.27 8.27 45.01 2.87
3390 3503 4.751767 AGATACCAGCTCTTCAAGGAAG 57.248 45.455 0.00 0.00 40.65 3.46
3391 3504 5.505181 AAAGATACCAGCTCTTCAAGGAA 57.495 39.130 0.00 0.00 31.83 3.36
3428 3552 9.060347 CATTGCCACAGATAAGATAACAACTAT 57.940 33.333 0.00 0.00 0.00 2.12
3429 3553 7.012327 GCATTGCCACAGATAAGATAACAACTA 59.988 37.037 0.00 0.00 0.00 2.24
3503 3627 0.923358 CCTGGTAATGGGGGTAAGCA 59.077 55.000 0.00 0.00 0.00 3.91
3515 3639 2.850851 AATCCTCCGGGGCCTGGTAA 62.851 60.000 30.37 17.16 34.39 2.85
3623 3747 3.257561 CTCGCCACATTCTCCGCG 61.258 66.667 0.00 0.00 45.76 6.46
3713 3840 1.607801 CCTCACCGGCAGATGACTCA 61.608 60.000 0.00 0.00 0.00 3.41
3719 3846 1.306141 TTCCTCCTCACCGGCAGAT 60.306 57.895 0.00 0.00 0.00 2.90
3721 3848 2.581354 CTTCCTCCTCACCGGCAG 59.419 66.667 0.00 0.00 0.00 4.85
3741 3868 4.838152 CAGATCCACACGCCGGGG 62.838 72.222 18.33 18.33 0.00 5.73
3755 3882 2.608623 TCTTCCACATCCACTCACAGA 58.391 47.619 0.00 0.00 0.00 3.41
3765 3892 7.334421 TCAAAACTAGTAAGCATCTTCCACATC 59.666 37.037 0.00 0.00 0.00 3.06
3822 3949 3.222603 GAAACATGAGGGAACAACTGGT 58.777 45.455 0.00 0.00 0.00 4.00
3832 3959 0.392998 CACCGAGGGAAACATGAGGG 60.393 60.000 0.00 0.00 0.00 4.30
3847 3974 3.431856 CAGAATGCAATTGATGTCACCG 58.568 45.455 10.34 0.00 36.07 4.94
3901 4049 6.240894 ACAGCTCCTGAATCTGTAAAATTGA 58.759 36.000 0.00 0.00 39.08 2.57
3906 4054 4.756642 CACAACAGCTCCTGAATCTGTAAA 59.243 41.667 0.00 0.00 39.86 2.01
3909 4057 2.775890 CACAACAGCTCCTGAATCTGT 58.224 47.619 0.00 0.00 42.28 3.41
3921 4069 2.086869 ACATAGTGGATGCACAACAGC 58.913 47.619 20.21 0.00 39.39 4.40
3928 4076 6.976934 TCAGAGTATTACATAGTGGATGCA 57.023 37.500 0.00 0.00 39.39 3.96
3929 4077 8.662781 TTTTCAGAGTATTACATAGTGGATGC 57.337 34.615 0.00 0.00 39.39 3.91
3992 4140 4.142403 ACAATGTGGAAAATACATGCCTCG 60.142 41.667 0.00 0.00 32.66 4.63
3993 4141 5.105797 TGACAATGTGGAAAATACATGCCTC 60.106 40.000 0.00 0.00 32.66 4.70
3994 4142 4.771577 TGACAATGTGGAAAATACATGCCT 59.228 37.500 0.00 0.00 32.66 4.75
3998 4146 6.922957 GTGTGTTGACAATGTGGAAAATACAT 59.077 34.615 0.00 0.00 32.49 2.29
4025 4192 2.861935 GCATCAATTGCCTACACAATGC 59.138 45.455 0.00 4.72 46.15 3.56
4104 4271 5.589831 ACAAAAATAGGGTCCAAGGCTAAT 58.410 37.500 0.00 0.00 0.00 1.73
4175 4342 5.399991 TCTACTTGGAGGGAGTAGACAAAA 58.600 41.667 9.30 0.00 46.43 2.44
4179 4346 3.558033 CCTCTACTTGGAGGGAGTAGAC 58.442 54.545 9.30 0.00 46.43 2.59
4316 4485 4.260170 GACCTGAGCAAGATCAGTCAAAT 58.740 43.478 13.56 0.00 44.35 2.32
4322 4491 1.554160 AGGTGACCTGAGCAAGATCAG 59.446 52.381 1.77 8.29 45.24 2.90
4340 4509 3.356529 AAGGCTTCCAGAACATGTAGG 57.643 47.619 0.00 1.80 0.00 3.18
4359 5376 3.921677 AGAAGACTATTCGCCGACAAAA 58.078 40.909 0.00 0.00 0.00 2.44
4361 5378 3.057104 TGAAGAAGACTATTCGCCGACAA 60.057 43.478 0.00 0.00 0.00 3.18
4407 5444 3.904339 AGGAGAGGAAAAGCAGAGTTACA 59.096 43.478 0.00 0.00 0.00 2.41
4450 5490 7.105588 ACAGTGAAATGTAGCATCAGATTGTA 58.894 34.615 0.00 0.00 0.00 2.41
4541 5581 6.467677 AGCAGTACAACAGATGTAGTTGATT 58.532 36.000 12.42 0.00 44.11 2.57
4542 5582 6.042638 AGCAGTACAACAGATGTAGTTGAT 57.957 37.500 12.42 1.00 44.11 2.57
4543 5583 5.468540 AGCAGTACAACAGATGTAGTTGA 57.531 39.130 12.42 0.00 44.11 3.18
4544 5584 6.813649 ACATAGCAGTACAACAGATGTAGTTG 59.186 38.462 4.66 4.66 44.11 3.16
4545 5585 6.936279 ACATAGCAGTACAACAGATGTAGTT 58.064 36.000 0.00 0.00 44.11 2.24
4546 5586 6.531503 ACATAGCAGTACAACAGATGTAGT 57.468 37.500 0.00 0.00 46.81 2.73
4547 5587 7.708051 AGTACATAGCAGTACAACAGATGTAG 58.292 38.462 14.03 0.00 45.00 2.74
4548 5588 7.640597 AGTACATAGCAGTACAACAGATGTA 57.359 36.000 14.03 2.87 45.25 2.29
4549 5589 6.531503 AGTACATAGCAGTACAACAGATGT 57.468 37.500 14.03 3.75 45.25 3.06
4550 5590 8.191446 AGTTAGTACATAGCAGTACAACAGATG 58.809 37.037 14.03 0.00 45.25 2.90
4551 5591 8.191446 CAGTTAGTACATAGCAGTACAACAGAT 58.809 37.037 14.03 0.00 45.25 2.90
4552 5592 7.392393 TCAGTTAGTACATAGCAGTACAACAGA 59.608 37.037 14.03 13.59 45.25 3.41
4553 5593 7.535997 TCAGTTAGTACATAGCAGTACAACAG 58.464 38.462 14.03 12.23 45.25 3.16
4554 5594 7.457024 TCAGTTAGTACATAGCAGTACAACA 57.543 36.000 14.03 0.31 45.25 3.33
4555 5595 9.666626 CTATCAGTTAGTACATAGCAGTACAAC 57.333 37.037 14.03 14.12 45.25 3.32
4567 5607 4.267536 ACTGTCGGCTATCAGTTAGTACA 58.732 43.478 0.00 0.00 41.33 2.90
4583 5840 0.179156 GCCAAATGCATGGACTGTCG 60.179 55.000 10.63 0.00 43.54 4.35
4586 5843 0.892755 ACAGCCAAATGCATGGACTG 59.107 50.000 20.16 20.16 43.54 3.51
4605 5862 5.009610 GGAAAAACAACTGGAAGCAGTCATA 59.990 40.000 0.00 0.00 37.60 2.15
4607 5864 3.130340 GGAAAAACAACTGGAAGCAGTCA 59.870 43.478 0.00 0.00 37.60 3.41
4608 5865 3.381590 AGGAAAAACAACTGGAAGCAGTC 59.618 43.478 0.00 0.00 37.60 3.51
4609 5866 3.365472 AGGAAAAACAACTGGAAGCAGT 58.635 40.909 0.00 0.00 37.60 4.40
4610 5867 4.821805 TCTAGGAAAAACAACTGGAAGCAG 59.178 41.667 0.00 0.00 37.60 4.24
4611 5868 4.787551 TCTAGGAAAAACAACTGGAAGCA 58.212 39.130 0.00 0.00 37.60 3.91
4612 5869 5.767816 TTCTAGGAAAAACAACTGGAAGC 57.232 39.130 0.00 0.00 37.60 3.86
4613 5870 8.197439 ACAATTTCTAGGAAAAACAACTGGAAG 58.803 33.333 0.00 0.00 42.29 3.46
4618 5875 7.768582 CCCAAACAATTTCTAGGAAAAACAACT 59.231 33.333 0.00 0.00 0.00 3.16
4639 5896 9.042450 TCAGAATGATTAGTACTAGTTCCCAAA 57.958 33.333 0.00 0.00 42.56 3.28
4657 5917 5.337968 CTGTCACCACAAGCATCAGAATGA 61.338 45.833 0.00 0.00 40.56 2.57
4662 5922 2.074576 CTCTGTCACCACAAGCATCAG 58.925 52.381 0.00 0.00 29.82 2.90
4663 5923 1.271001 CCTCTGTCACCACAAGCATCA 60.271 52.381 0.00 0.00 29.82 3.07
4684 5944 2.088104 TGTTGCGGATAGGAGGAGAT 57.912 50.000 0.00 0.00 0.00 2.75
4685 5945 2.088104 ATGTTGCGGATAGGAGGAGA 57.912 50.000 0.00 0.00 0.00 3.71
4689 5949 2.355756 CCAACAATGTTGCGGATAGGAG 59.644 50.000 19.82 0.13 0.00 3.69
4723 5983 5.688814 TGATCTTGTGAAGGAGATCATGT 57.311 39.130 10.95 0.00 41.23 3.21
4728 5988 4.305524 AGGGATGATCTTGTGAAGGAGAT 58.694 43.478 0.00 0.00 0.00 2.75
4735 5995 4.202398 GCTATTGGAGGGATGATCTTGTGA 60.202 45.833 0.00 0.00 0.00 3.58
4736 5996 4.070716 GCTATTGGAGGGATGATCTTGTG 58.929 47.826 0.00 0.00 0.00 3.33
4737 5997 3.073650 GGCTATTGGAGGGATGATCTTGT 59.926 47.826 0.00 0.00 0.00 3.16
4738 5998 3.073503 TGGCTATTGGAGGGATGATCTTG 59.926 47.826 0.00 0.00 0.00 3.02
4739 5999 3.330198 TGGCTATTGGAGGGATGATCTT 58.670 45.455 0.00 0.00 0.00 2.40
4740 6000 2.995746 TGGCTATTGGAGGGATGATCT 58.004 47.619 0.00 0.00 0.00 2.75
4741 6001 3.795688 TTGGCTATTGGAGGGATGATC 57.204 47.619 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.