Multiple sequence alignment - TraesCS4B01G074900

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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 TraesCS4B01G074900 chr4B 100.000 2555 0 0 1 2555 70574831 70577385 0.000000e+00 4719.0
1 TraesCS4B01G074900 chr4D 96.508 1661 49 5 901 2555 47990877 47992534 0.000000e+00 2737.0
2 TraesCS4B01G074900 chr4D 90.496 484 32 8 1 472 47990285 47990766 6.000000e-176 627.0
3 TraesCS4B01G074900 chr4A 94.124 885 48 2 909 1790 549800229 549799346 0.000000e+00 1343.0
4 TraesCS4B01G074900 chr4A 81.513 119 19 3 338 455 607264790 607264906 7.530000e-16 95.3
5 TraesCS4B01G074900 chr4A 93.182 44 2 1 516 559 549800278 549800236 2.120000e-06 63.9
6 TraesCS4B01G074900 chr1A 90.941 287 18 3 558 844 507839299 507839021 1.860000e-101 379.0
7 TraesCS4B01G074900 chr1A 90.780 282 18 3 560 841 515274304 515274577 1.120000e-98 370.0
8 TraesCS4B01G074900 chr1A 79.675 123 20 5 338 458 445940975 445940856 1.630000e-12 84.2
9 TraesCS4B01G074900 chr3B 90.426 282 19 3 560 841 9309507 9309780 5.200000e-97 364.0
10 TraesCS4B01G074900 chr3B 89.310 290 21 5 552 841 687632932 687633211 3.130000e-94 355.0
11 TraesCS4B01G074900 chr3B 89.362 282 22 3 560 841 576172053 576172326 5.230000e-92 348.0
12 TraesCS4B01G074900 chr3B 89.062 64 7 0 138 201 525232876 525232939 2.110000e-11 80.5
13 TraesCS4B01G074900 chr3B 100.000 35 0 0 203 237 440135777 440135743 5.900000e-07 65.8
14 TraesCS4B01G074900 chr7B 89.547 287 22 3 557 843 427292578 427292300 8.690000e-95 357.0
15 TraesCS4B01G074900 chr7B 86.275 102 12 2 352 453 427697220 427697121 2.690000e-20 110.0
16 TraesCS4B01G074900 chr5B 88.927 289 23 4 554 841 318877926 318878206 5.230000e-92 348.0
17 TraesCS4B01G074900 chr5B 86.735 98 11 2 344 440 707437703 707437607 9.670000e-20 108.0
18 TraesCS4B01G074900 chr1B 88.542 288 23 3 557 844 106386412 106386689 8.750000e-90 340.0
19 TraesCS4B01G074900 chr1B 88.153 287 25 4 557 843 191954780 191955057 1.460000e-87 333.0
20 TraesCS4B01G074900 chr1D 86.607 112 8 1 125 229 211684191 211684080 1.610000e-22 117.0
21 TraesCS4B01G074900 chr5D 85.714 112 7 4 125 228 546298269 546298159 2.690000e-20 110.0
22 TraesCS4B01G074900 chr2B 90.000 80 5 3 125 202 445257286 445257208 1.620000e-17 100.0
23 TraesCS4B01G074900 chr2D 90.667 75 5 2 125 199 375149126 375149054 5.820000e-17 99.0
24 TraesCS4B01G074900 chr2D 85.714 84 10 2 121 203 195298066 195298148 1.260000e-13 87.9
25 TraesCS4B01G074900 chr7A 84.112 107 10 4 126 229 22917681 22917579 2.090000e-16 97.1
26 TraesCS4B01G074900 chr7D 85.106 94 12 1 338 431 634043434 634043525 7.530000e-16 95.3
27 TraesCS4B01G074900 chr5A 80.488 123 21 2 334 456 417306426 417306545 9.730000e-15 91.6
28 TraesCS4B01G074900 chr5A 80.328 122 21 3 336 456 644116152 644116033 3.500000e-14 89.8
29 TraesCS4B01G074900 chr6B 82.178 101 18 0 336 436 182577217 182577117 1.260000e-13 87.9
30 TraesCS4B01G074900 chr6B 84.416 77 11 1 125 201 16960332 16960407 9.800000e-10 75.0


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 TraesCS4B01G074900 chr4B 70574831 70577385 2554 False 4719.00 4719 100.000 1 2555 1 chr4B.!!$F1 2554
1 TraesCS4B01G074900 chr4D 47990285 47992534 2249 False 1682.00 2737 93.502 1 2555 2 chr4D.!!$F1 2554
2 TraesCS4B01G074900 chr4A 549799346 549800278 932 True 703.45 1343 93.653 516 1790 2 chr4A.!!$R1 1274

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
880 898 0.377203 CGCCTTAAACTCCCGATTGC 59.623 55.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2202 2226 0.749454 GATTGCATCCAAGAGGGCGT 60.749 55.0 0.0 0.0 36.21 5.68 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
257 264 8.526147 ACATCAATAGAAAATCACTCCAAAAGG 58.474 33.333 0.00 0.00 0.00 3.11
270 277 8.017418 TCACTCCAAAAGGTGATGTAAAATTT 57.983 30.769 0.00 0.00 37.52 1.82
271 278 9.137459 TCACTCCAAAAGGTGATGTAAAATTTA 57.863 29.630 0.00 0.00 37.52 1.40
272 279 9.927668 CACTCCAAAAGGTGATGTAAAATTTAT 57.072 29.630 0.00 0.00 35.69 1.40
281 288 7.760750 GTGATGTAAAATTTATATCACCGCG 57.239 36.000 29.37 0.00 40.89 6.46
282 289 7.569297 GTGATGTAAAATTTATATCACCGCGA 58.431 34.615 29.37 8.36 40.89 5.87
284 291 8.613482 TGATGTAAAATTTATATCACCGCGAAA 58.387 29.630 17.39 0.00 0.00 3.46
309 316 4.994471 TGGTGAGGTGCGCTGCAG 62.994 66.667 10.11 10.11 40.08 4.41
342 349 1.672854 CGCGGGGGTCTGAGTGATTA 61.673 60.000 0.00 0.00 0.00 1.75
356 363 5.295152 TGAGTGATTATAGTCGTCGCTAGA 58.705 41.667 0.00 0.00 33.24 2.43
372 379 4.887655 TCGCTAGATGGTCTACAGATTTGA 59.112 41.667 0.00 0.00 0.00 2.69
378 385 6.363065 AGATGGTCTACAGATTTGAATGCAT 58.637 36.000 0.00 0.00 0.00 3.96
408 415 8.771920 TGTTACTTCTCATGTTATTGGTACTG 57.228 34.615 0.00 0.00 0.00 2.74
422 432 3.966979 TGGTACTGCCATGATGTTTGAT 58.033 40.909 0.00 0.00 43.61 2.57
423 433 3.695556 TGGTACTGCCATGATGTTTGATG 59.304 43.478 0.00 0.00 43.61 3.07
425 435 4.398988 GGTACTGCCATGATGTTTGATGAA 59.601 41.667 0.00 0.00 37.17 2.57
432 442 6.773685 TGCCATGATGTTTGATGAATAGATCA 59.226 34.615 0.00 0.00 43.67 2.92
472 485 2.675658 AAGCTGCTGGTTTTTCCCTA 57.324 45.000 1.35 0.00 34.77 3.53
473 486 2.675658 AGCTGCTGGTTTTTCCCTAA 57.324 45.000 0.00 0.00 34.77 2.69
474 487 2.957474 AGCTGCTGGTTTTTCCCTAAA 58.043 42.857 0.00 0.00 34.77 1.85
475 488 2.628178 AGCTGCTGGTTTTTCCCTAAAC 59.372 45.455 0.00 0.00 37.30 2.01
476 489 2.364002 GCTGCTGGTTTTTCCCTAAACA 59.636 45.455 0.00 0.00 39.27 2.83
477 490 3.552890 GCTGCTGGTTTTTCCCTAAACAG 60.553 47.826 0.00 0.00 39.27 3.16
478 491 3.636764 CTGCTGGTTTTTCCCTAAACAGT 59.363 43.478 0.00 0.00 39.27 3.55
479 492 3.383185 TGCTGGTTTTTCCCTAAACAGTG 59.617 43.478 0.00 0.00 39.27 3.66
480 493 3.798889 GCTGGTTTTTCCCTAAACAGTGC 60.799 47.826 0.00 0.00 39.27 4.40
481 494 3.636764 CTGGTTTTTCCCTAAACAGTGCT 59.363 43.478 0.00 0.00 39.27 4.40
482 495 3.383185 TGGTTTTTCCCTAAACAGTGCTG 59.617 43.478 0.00 0.00 39.27 4.41
483 496 3.381045 GTTTTTCCCTAAACAGTGCTGC 58.619 45.455 0.00 0.00 37.81 5.25
484 497 2.656947 TTTCCCTAAACAGTGCTGCT 57.343 45.000 0.00 0.00 0.00 4.24
519 532 9.231297 TCTCAAAGAAAAGAAAAGAAAGAGTGA 57.769 29.630 0.00 0.00 0.00 3.41
559 572 2.050350 CGACCGAGCCAGTCCCTAA 61.050 63.158 0.00 0.00 0.00 2.69
560 573 1.817209 GACCGAGCCAGTCCCTAAG 59.183 63.158 0.00 0.00 0.00 2.18
561 574 1.677637 GACCGAGCCAGTCCCTAAGG 61.678 65.000 0.00 0.00 0.00 2.69
562 575 2.435693 CCGAGCCAGTCCCTAAGGG 61.436 68.421 0.00 0.00 46.11 3.95
565 578 3.335711 GCCAGTCCCTAAGGGCAT 58.664 61.111 0.00 0.00 45.70 4.40
567 580 1.068121 GCCAGTCCCTAAGGGCATAT 58.932 55.000 0.00 0.00 45.70 1.78
568 581 2.266279 GCCAGTCCCTAAGGGCATATA 58.734 52.381 0.00 0.00 45.70 0.86
569 582 2.027100 GCCAGTCCCTAAGGGCATATAC 60.027 54.545 0.00 0.00 45.70 1.47
570 583 3.248024 CCAGTCCCTAAGGGCATATACA 58.752 50.000 0.00 0.00 43.94 2.29
571 584 3.650942 CCAGTCCCTAAGGGCATATACAA 59.349 47.826 0.00 0.00 43.94 2.41
572 585 4.289672 CCAGTCCCTAAGGGCATATACAAT 59.710 45.833 0.00 0.00 43.94 2.71
573 586 5.248640 CAGTCCCTAAGGGCATATACAATG 58.751 45.833 0.00 0.00 43.94 2.82
574 587 4.289672 AGTCCCTAAGGGCATATACAATGG 59.710 45.833 0.00 0.00 43.94 3.16
575 588 4.042934 GTCCCTAAGGGCATATACAATGGT 59.957 45.833 0.00 0.00 43.94 3.55
576 589 4.667858 TCCCTAAGGGCATATACAATGGTT 59.332 41.667 0.00 0.00 43.94 3.67
577 590 5.010282 CCCTAAGGGCATATACAATGGTTC 58.990 45.833 0.00 0.00 35.35 3.62
578 591 5.222130 CCCTAAGGGCATATACAATGGTTCT 60.222 44.000 0.00 0.00 35.35 3.01
579 592 6.012858 CCCTAAGGGCATATACAATGGTTCTA 60.013 42.308 0.00 0.00 35.35 2.10
580 593 7.311929 CCCTAAGGGCATATACAATGGTTCTAT 60.312 40.741 0.00 0.00 35.35 1.98
581 594 7.770897 CCTAAGGGCATATACAATGGTTCTATC 59.229 40.741 0.00 0.00 0.00 2.08
582 595 6.959606 AGGGCATATACAATGGTTCTATCT 57.040 37.500 0.00 0.00 0.00 1.98
583 596 7.335127 AGGGCATATACAATGGTTCTATCTT 57.665 36.000 0.00 0.00 0.00 2.40
584 597 8.449423 AGGGCATATACAATGGTTCTATCTTA 57.551 34.615 0.00 0.00 0.00 2.10
585 598 8.543774 AGGGCATATACAATGGTTCTATCTTAG 58.456 37.037 0.00 0.00 0.00 2.18
586 599 7.281100 GGGCATATACAATGGTTCTATCTTAGC 59.719 40.741 0.00 0.00 0.00 3.09
587 600 7.824289 GGCATATACAATGGTTCTATCTTAGCA 59.176 37.037 0.00 0.00 0.00 3.49
588 601 9.219603 GCATATACAATGGTTCTATCTTAGCAA 57.780 33.333 0.00 0.00 0.00 3.91
591 604 6.382869 ACAATGGTTCTATCTTAGCAATGC 57.617 37.500 0.00 0.00 0.00 3.56
592 605 5.300286 ACAATGGTTCTATCTTAGCAATGCC 59.700 40.000 0.00 0.00 0.00 4.40
593 606 4.502105 TGGTTCTATCTTAGCAATGCCA 57.498 40.909 0.00 0.00 0.00 4.92
594 607 5.052693 TGGTTCTATCTTAGCAATGCCAT 57.947 39.130 0.00 0.00 0.00 4.40
595 608 6.186420 TGGTTCTATCTTAGCAATGCCATA 57.814 37.500 0.00 0.00 0.00 2.74
596 609 6.782986 TGGTTCTATCTTAGCAATGCCATAT 58.217 36.000 0.00 0.00 0.00 1.78
597 610 7.917003 TGGTTCTATCTTAGCAATGCCATATA 58.083 34.615 0.00 0.00 0.00 0.86
598 611 8.043113 TGGTTCTATCTTAGCAATGCCATATAG 58.957 37.037 0.00 5.03 0.00 1.31
599 612 7.497249 GGTTCTATCTTAGCAATGCCATATAGG 59.503 40.741 0.00 0.00 41.84 2.57
600 613 7.978099 TCTATCTTAGCAATGCCATATAGGA 57.022 36.000 0.00 0.00 41.22 2.94
601 614 8.558713 TCTATCTTAGCAATGCCATATAGGAT 57.441 34.615 0.00 2.00 41.22 3.24
602 615 9.660544 TCTATCTTAGCAATGCCATATAGGATA 57.339 33.333 0.00 3.09 41.22 2.59
605 618 8.792830 TCTTAGCAATGCCATATAGGATAAAC 57.207 34.615 0.00 0.00 41.22 2.01
606 619 7.549134 TCTTAGCAATGCCATATAGGATAAACG 59.451 37.037 0.00 0.00 41.22 3.60
607 620 5.804639 AGCAATGCCATATAGGATAAACGA 58.195 37.500 0.00 0.00 41.22 3.85
608 621 6.418101 AGCAATGCCATATAGGATAAACGAT 58.582 36.000 0.00 0.00 41.22 3.73
609 622 6.886459 AGCAATGCCATATAGGATAAACGATT 59.114 34.615 0.00 0.00 41.22 3.34
610 623 8.046708 AGCAATGCCATATAGGATAAACGATTA 58.953 33.333 0.00 0.00 41.22 1.75
611 624 8.338259 GCAATGCCATATAGGATAAACGATTAG 58.662 37.037 0.00 0.00 41.22 1.73
612 625 8.830580 CAATGCCATATAGGATAAACGATTAGG 58.169 37.037 0.00 0.00 41.22 2.69
613 626 7.490657 TGCCATATAGGATAAACGATTAGGT 57.509 36.000 0.00 0.00 41.22 3.08
614 627 7.327975 TGCCATATAGGATAAACGATTAGGTG 58.672 38.462 0.00 0.00 41.22 4.00
615 628 7.179516 TGCCATATAGGATAAACGATTAGGTGA 59.820 37.037 0.00 0.00 41.22 4.02
616 629 8.038944 GCCATATAGGATAAACGATTAGGTGAA 58.961 37.037 0.00 0.00 41.22 3.18
617 630 9.587772 CCATATAGGATAAACGATTAGGTGAAG 57.412 37.037 0.00 0.00 41.22 3.02
618 631 9.587772 CATATAGGATAAACGATTAGGTGAAGG 57.412 37.037 0.00 0.00 0.00 3.46
619 632 7.850935 ATAGGATAAACGATTAGGTGAAGGA 57.149 36.000 0.00 0.00 0.00 3.36
620 633 6.163135 AGGATAAACGATTAGGTGAAGGAG 57.837 41.667 0.00 0.00 0.00 3.69
621 634 5.897824 AGGATAAACGATTAGGTGAAGGAGA 59.102 40.000 0.00 0.00 0.00 3.71
622 635 6.041069 AGGATAAACGATTAGGTGAAGGAGAG 59.959 42.308 0.00 0.00 0.00 3.20
623 636 6.040616 GGATAAACGATTAGGTGAAGGAGAGA 59.959 42.308 0.00 0.00 0.00 3.10
624 637 4.993029 AACGATTAGGTGAAGGAGAGAG 57.007 45.455 0.00 0.00 0.00 3.20
625 638 4.237976 ACGATTAGGTGAAGGAGAGAGA 57.762 45.455 0.00 0.00 0.00 3.10
626 639 4.601084 ACGATTAGGTGAAGGAGAGAGAA 58.399 43.478 0.00 0.00 0.00 2.87
627 640 5.205056 ACGATTAGGTGAAGGAGAGAGAAT 58.795 41.667 0.00 0.00 0.00 2.40
628 641 5.659079 ACGATTAGGTGAAGGAGAGAGAATT 59.341 40.000 0.00 0.00 0.00 2.17
629 642 6.183360 ACGATTAGGTGAAGGAGAGAGAATTC 60.183 42.308 0.00 0.00 0.00 2.17
630 643 6.183360 CGATTAGGTGAAGGAGAGAGAATTCA 60.183 42.308 8.44 0.00 0.00 2.57
631 644 7.471260 CGATTAGGTGAAGGAGAGAGAATTCAT 60.471 40.741 8.44 0.00 34.45 2.57
632 645 8.789767 ATTAGGTGAAGGAGAGAGAATTCATA 57.210 34.615 8.44 0.00 34.45 2.15
633 646 8.609617 TTAGGTGAAGGAGAGAGAATTCATAA 57.390 34.615 8.44 0.00 34.45 1.90
634 647 7.123355 AGGTGAAGGAGAGAGAATTCATAAG 57.877 40.000 8.44 0.00 34.45 1.73
635 648 6.900186 AGGTGAAGGAGAGAGAATTCATAAGA 59.100 38.462 8.44 0.00 34.45 2.10
636 649 7.401493 AGGTGAAGGAGAGAGAATTCATAAGAA 59.599 37.037 8.44 0.00 38.31 2.52
637 650 8.043710 GGTGAAGGAGAGAGAATTCATAAGAAA 58.956 37.037 8.44 0.00 37.29 2.52
638 651 9.442047 GTGAAGGAGAGAGAATTCATAAGAAAA 57.558 33.333 8.44 0.00 37.29 2.29
639 652 9.664332 TGAAGGAGAGAGAATTCATAAGAAAAG 57.336 33.333 8.44 0.00 37.29 2.27
640 653 9.883142 GAAGGAGAGAGAATTCATAAGAAAAGA 57.117 33.333 8.44 0.00 37.29 2.52
641 654 9.665719 AAGGAGAGAGAATTCATAAGAAAAGAC 57.334 33.333 8.44 0.00 37.29 3.01
642 655 8.264347 AGGAGAGAGAATTCATAAGAAAAGACC 58.736 37.037 8.44 0.00 37.29 3.85
643 656 8.264347 GGAGAGAGAATTCATAAGAAAAGACCT 58.736 37.037 8.44 0.00 37.29 3.85
644 657 9.097257 GAGAGAGAATTCATAAGAAAAGACCTG 57.903 37.037 8.44 0.00 37.29 4.00
645 658 8.601546 AGAGAGAATTCATAAGAAAAGACCTGT 58.398 33.333 8.44 0.00 37.29 4.00
646 659 8.785329 AGAGAATTCATAAGAAAAGACCTGTC 57.215 34.615 8.44 0.00 37.29 3.51
647 660 8.601546 AGAGAATTCATAAGAAAAGACCTGTCT 58.398 33.333 8.44 0.00 37.25 3.41
678 691 9.877178 TTATTTAAGAGAAGACAAGAGATGACC 57.123 33.333 0.00 0.00 0.00 4.02
679 692 7.546250 TTTAAGAGAAGACAAGAGATGACCT 57.454 36.000 0.00 0.00 0.00 3.85
680 693 5.659440 AAGAGAAGACAAGAGATGACCTC 57.341 43.478 0.00 0.00 42.28 3.85
695 708 8.359060 GAGATGACCTCTTAACACAATATGTC 57.641 38.462 0.00 0.00 38.64 3.06
696 709 8.083828 AGATGACCTCTTAACACAATATGTCT 57.916 34.615 0.00 0.00 42.31 3.41
697 710 8.200792 AGATGACCTCTTAACACAATATGTCTC 58.799 37.037 0.00 0.00 42.31 3.36
698 711 7.239763 TGACCTCTTAACACAATATGTCTCA 57.760 36.000 0.00 0.00 42.31 3.27
699 712 7.097192 TGACCTCTTAACACAATATGTCTCAC 58.903 38.462 0.00 0.00 42.31 3.51
700 713 6.407202 ACCTCTTAACACAATATGTCTCACC 58.593 40.000 0.00 0.00 42.31 4.02
701 714 6.013725 ACCTCTTAACACAATATGTCTCACCA 60.014 38.462 0.00 0.00 42.31 4.17
702 715 6.313905 CCTCTTAACACAATATGTCTCACCAC 59.686 42.308 0.00 0.00 42.31 4.16
703 716 5.867174 TCTTAACACAATATGTCTCACCACG 59.133 40.000 0.00 0.00 42.31 4.94
704 717 3.678056 ACACAATATGTCTCACCACGT 57.322 42.857 0.00 0.00 36.54 4.49
705 718 4.002906 ACACAATATGTCTCACCACGTT 57.997 40.909 0.00 0.00 36.54 3.99
706 719 4.385825 ACACAATATGTCTCACCACGTTT 58.614 39.130 0.00 0.00 36.54 3.60
707 720 4.819630 ACACAATATGTCTCACCACGTTTT 59.180 37.500 0.00 0.00 36.54 2.43
708 721 5.298276 ACACAATATGTCTCACCACGTTTTT 59.702 36.000 0.00 0.00 36.54 1.94
709 722 6.483974 ACACAATATGTCTCACCACGTTTTTA 59.516 34.615 0.00 0.00 36.54 1.52
710 723 7.015289 CACAATATGTCTCACCACGTTTTTAG 58.985 38.462 0.00 0.00 0.00 1.85
711 724 6.148811 ACAATATGTCTCACCACGTTTTTAGG 59.851 38.462 0.00 0.00 0.00 2.69
712 725 3.823281 TGTCTCACCACGTTTTTAGGA 57.177 42.857 0.00 0.00 0.00 2.94
713 726 4.139859 TGTCTCACCACGTTTTTAGGAA 57.860 40.909 0.00 0.00 0.00 3.36
714 727 4.710324 TGTCTCACCACGTTTTTAGGAAT 58.290 39.130 0.00 0.00 0.00 3.01
715 728 5.856156 TGTCTCACCACGTTTTTAGGAATA 58.144 37.500 0.00 0.00 0.00 1.75
716 729 5.929992 TGTCTCACCACGTTTTTAGGAATAG 59.070 40.000 0.00 0.00 0.00 1.73
717 730 4.933400 TCTCACCACGTTTTTAGGAATAGC 59.067 41.667 0.00 0.00 0.00 2.97
718 731 4.901868 TCACCACGTTTTTAGGAATAGCT 58.098 39.130 0.00 0.00 0.00 3.32
719 732 6.040209 TCACCACGTTTTTAGGAATAGCTA 57.960 37.500 0.00 0.00 0.00 3.32
720 733 6.103997 TCACCACGTTTTTAGGAATAGCTAG 58.896 40.000 0.00 0.00 0.00 3.42
721 734 5.873164 CACCACGTTTTTAGGAATAGCTAGT 59.127 40.000 0.00 0.00 0.00 2.57
722 735 6.370718 CACCACGTTTTTAGGAATAGCTAGTT 59.629 38.462 0.00 0.00 0.00 2.24
723 736 7.546667 CACCACGTTTTTAGGAATAGCTAGTTA 59.453 37.037 0.00 0.00 0.00 2.24
724 737 8.262933 ACCACGTTTTTAGGAATAGCTAGTTAT 58.737 33.333 0.00 0.00 0.00 1.89
725 738 9.106070 CCACGTTTTTAGGAATAGCTAGTTATT 57.894 33.333 11.22 11.22 0.00 1.40
726 739 9.916397 CACGTTTTTAGGAATAGCTAGTTATTG 57.084 33.333 15.66 2.20 0.00 1.90
727 740 9.880157 ACGTTTTTAGGAATAGCTAGTTATTGA 57.120 29.630 15.66 0.00 0.00 2.57
765 778 9.606631 AAGACTAAAAGATGATCCATTGTAGAC 57.393 33.333 6.08 1.71 0.00 2.59
766 779 8.762645 AGACTAAAAGATGATCCATTGTAGACA 58.237 33.333 6.08 0.00 0.00 3.41
767 780 9.553064 GACTAAAAGATGATCCATTGTAGACAT 57.447 33.333 6.08 0.00 0.00 3.06
768 781 9.334947 ACTAAAAGATGATCCATTGTAGACATG 57.665 33.333 0.00 0.00 0.00 3.21
769 782 9.334947 CTAAAAGATGATCCATTGTAGACATGT 57.665 33.333 0.00 0.00 0.00 3.21
770 783 8.585471 AAAAGATGATCCATTGTAGACATGTT 57.415 30.769 0.00 0.00 0.00 2.71
771 784 8.585471 AAAGATGATCCATTGTAGACATGTTT 57.415 30.769 0.00 0.00 0.00 2.83
772 785 8.585471 AAGATGATCCATTGTAGACATGTTTT 57.415 30.769 0.00 0.00 0.00 2.43
773 786 8.585471 AGATGATCCATTGTAGACATGTTTTT 57.415 30.769 0.00 0.00 0.00 1.94
803 816 9.624373 ATCATCTCTTAATTACATGCAAGACTT 57.376 29.630 0.00 0.00 0.00 3.01
836 849 9.770097 AGACTATCTTATCAACCATTGTACATG 57.230 33.333 0.00 0.00 0.00 3.21
837 850 8.383318 ACTATCTTATCAACCATTGTACATGC 57.617 34.615 0.00 0.00 0.00 4.06
842 855 4.308526 TCAACCATTGTACATGCCCTAA 57.691 40.909 0.00 0.00 0.00 2.69
868 881 1.671054 GCTCAGGTGTGCGCCTTAA 60.671 57.895 4.18 0.00 36.58 1.85
869 882 1.234615 GCTCAGGTGTGCGCCTTAAA 61.235 55.000 4.18 0.00 36.58 1.52
880 898 0.377203 CGCCTTAAACTCCCGATTGC 59.623 55.000 0.00 0.00 0.00 3.56
881 899 0.738975 GCCTTAAACTCCCGATTGCC 59.261 55.000 0.00 0.00 0.00 4.52
882 900 1.682087 GCCTTAAACTCCCGATTGCCT 60.682 52.381 0.00 0.00 0.00 4.75
883 901 2.289565 CCTTAAACTCCCGATTGCCTC 58.710 52.381 0.00 0.00 0.00 4.70
884 902 2.355716 CCTTAAACTCCCGATTGCCTCA 60.356 50.000 0.00 0.00 0.00 3.86
885 903 3.343617 CTTAAACTCCCGATTGCCTCAA 58.656 45.455 0.00 0.00 0.00 3.02
886 904 2.286365 AAACTCCCGATTGCCTCAAA 57.714 45.000 0.00 0.00 0.00 2.69
887 905 2.286365 AACTCCCGATTGCCTCAAAA 57.714 45.000 0.00 0.00 0.00 2.44
888 906 2.286365 ACTCCCGATTGCCTCAAAAA 57.714 45.000 0.00 0.00 0.00 1.94
889 907 2.162681 ACTCCCGATTGCCTCAAAAAG 58.837 47.619 0.00 0.00 0.00 2.27
890 908 2.224769 ACTCCCGATTGCCTCAAAAAGA 60.225 45.455 0.00 0.00 0.00 2.52
891 909 2.819608 CTCCCGATTGCCTCAAAAAGAA 59.180 45.455 0.00 0.00 0.00 2.52
892 910 3.226777 TCCCGATTGCCTCAAAAAGAAA 58.773 40.909 0.00 0.00 0.00 2.52
893 911 3.639094 TCCCGATTGCCTCAAAAAGAAAA 59.361 39.130 0.00 0.00 0.00 2.29
894 912 4.100189 TCCCGATTGCCTCAAAAAGAAAAA 59.900 37.500 0.00 0.00 0.00 1.94
895 913 4.448732 CCCGATTGCCTCAAAAAGAAAAAG 59.551 41.667 0.00 0.00 0.00 2.27
896 914 5.288804 CCGATTGCCTCAAAAAGAAAAAGA 58.711 37.500 0.00 0.00 0.00 2.52
897 915 5.752955 CCGATTGCCTCAAAAAGAAAAAGAA 59.247 36.000 0.00 0.00 0.00 2.52
898 916 6.257630 CCGATTGCCTCAAAAAGAAAAAGAAA 59.742 34.615 0.00 0.00 0.00 2.52
899 917 7.201600 CCGATTGCCTCAAAAAGAAAAAGAAAA 60.202 33.333 0.00 0.00 0.00 2.29
1049 1068 1.693103 GTTCCCTCCCCACCCTAGG 60.693 68.421 0.06 0.06 0.00 3.02
1153 1172 2.222727 AGCTTCAGCACCAGGAGCT 61.223 57.895 5.38 5.38 45.16 4.09
1355 1377 1.752358 ATGGCGCAGGACATCGAGAT 61.752 55.000 10.83 0.00 37.28 2.75
1413 1435 2.567497 GGTGGACACGGACGAGGAA 61.567 63.158 0.00 0.00 0.00 3.36
1416 1438 1.407979 GTGGACACGGACGAGGAATAT 59.592 52.381 0.00 0.00 0.00 1.28
1441 1463 1.765904 TCGCAAGGGATATGCAGGTAA 59.234 47.619 0.00 0.00 44.01 2.85
1509 1531 0.471211 CCATTAGGACCGAGGGGCTA 60.471 60.000 0.00 0.00 36.89 3.93
1518 1540 2.234168 GACCGAGGGGCTAATTCCTATC 59.766 54.545 0.00 0.00 36.48 2.08
1530 1552 6.223852 GCTAATTCCTATCGAAATGGTCAGA 58.776 40.000 0.00 0.00 33.08 3.27
1569 1591 2.673610 GCTGTGAGTTCTGTCTAGGCAG 60.674 54.545 18.61 18.61 37.81 4.85
1656 1678 1.228552 AGCCTGCGGTGGTTGATTT 60.229 52.632 0.00 0.00 0.00 2.17
1673 1695 1.925229 TTTGAGCTTTGTGTTGCTGC 58.075 45.000 0.00 0.00 39.91 5.25
1725 1747 3.502595 GCATGAGCAGAATGTAGCATCAT 59.497 43.478 0.00 0.00 41.58 2.45
1726 1748 4.023107 GCATGAGCAGAATGTAGCATCATT 60.023 41.667 0.00 6.17 41.58 2.57
1733 1755 5.447683 GCAGAATGTAGCATCATTGTTCGAA 60.448 40.000 10.32 0.00 38.03 3.71
1747 1769 4.238761 TGTTCGAACCTGAGACTAACAG 57.761 45.455 24.78 0.00 35.43 3.16
1835 1858 6.403866 TGTATGCACTGGATTTTGTCTTTT 57.596 33.333 0.00 0.00 0.00 2.27
1841 1864 8.402798 TGCACTGGATTTTGTCTTTTATCTTA 57.597 30.769 0.00 0.00 0.00 2.10
1906 1929 2.916502 AAACACCTCACGTCGCTGCA 62.917 55.000 0.00 0.00 0.00 4.41
2202 2226 1.067213 TGCGATCATCGTTGTCCTTCA 60.067 47.619 9.23 0.00 42.81 3.02
2219 2243 1.675310 CACGCCCTCTTGGATGCAA 60.675 57.895 0.00 0.00 35.39 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
178 181 9.143631 GAGATGATGTAAAAATCCACTTTTTGG 57.856 33.333 6.06 0.00 44.70 3.28
189 192 8.859090 TGTTGAAGTTGGAGATGATGTAAAAAT 58.141 29.630 0.00 0.00 0.00 1.82
198 201 5.488262 TCATCTGTTGAAGTTGGAGATGA 57.512 39.130 0.00 0.00 44.23 2.92
232 235 8.526147 ACCTTTTGGAGTGATTTTCTATTGATG 58.474 33.333 0.00 0.00 44.07 3.07
245 248 7.595819 AATTTTACATCACCTTTTGGAGTGA 57.404 32.000 0.00 0.00 46.39 3.41
257 264 7.569297 TCGCGGTGATATAAATTTTACATCAC 58.431 34.615 23.35 23.35 42.98 3.06
281 288 2.409870 CCTCACCATGGCCGCTTTC 61.410 63.158 13.04 0.00 0.00 2.62
282 289 2.361610 CCTCACCATGGCCGCTTT 60.362 61.111 13.04 0.00 0.00 3.51
284 291 4.415150 CACCTCACCATGGCCGCT 62.415 66.667 13.04 0.00 0.00 5.52
304 311 2.730672 GCCACTAACGTCGCTGCAG 61.731 63.158 10.11 10.11 0.00 4.41
324 331 0.759346 ATAATCACTCAGACCCCCGC 59.241 55.000 0.00 0.00 0.00 6.13
333 340 5.295152 TCTAGCGACGACTATAATCACTCA 58.705 41.667 0.00 0.00 0.00 3.41
337 344 5.001874 ACCATCTAGCGACGACTATAATCA 58.998 41.667 0.00 0.00 0.00 2.57
342 349 3.128852 AGACCATCTAGCGACGACTAT 57.871 47.619 0.00 0.00 0.00 2.12
356 363 7.414222 AAATGCATTCAAATCTGTAGACCAT 57.586 32.000 13.38 0.00 0.00 3.55
405 412 6.124340 TCTATTCATCAAACATCATGGCAGT 58.876 36.000 0.00 0.00 0.00 4.40
408 415 7.174426 TCTGATCTATTCATCAAACATCATGGC 59.826 37.037 0.00 0.00 32.24 4.40
412 419 9.676861 AACTTCTGATCTATTCATCAAACATCA 57.323 29.630 0.00 0.00 32.24 3.07
458 471 3.798889 GCACTGTTTAGGGAAAAACCAGC 60.799 47.826 0.00 0.00 38.35 4.85
500 513 9.605955 GCTCTAATCACTCTTTCTTTTCTTTTC 57.394 33.333 0.00 0.00 0.00 2.29
504 517 6.692486 TCGCTCTAATCACTCTTTCTTTTCT 58.308 36.000 0.00 0.00 0.00 2.52
505 518 6.952935 TCGCTCTAATCACTCTTTCTTTTC 57.047 37.500 0.00 0.00 0.00 2.29
506 519 6.128795 CGTTCGCTCTAATCACTCTTTCTTTT 60.129 38.462 0.00 0.00 0.00 2.27
508 521 4.859798 CGTTCGCTCTAATCACTCTTTCTT 59.140 41.667 0.00 0.00 0.00 2.52
509 522 4.156190 TCGTTCGCTCTAATCACTCTTTCT 59.844 41.667 0.00 0.00 0.00 2.52
510 523 4.413087 TCGTTCGCTCTAATCACTCTTTC 58.587 43.478 0.00 0.00 0.00 2.62
511 524 4.082679 ACTCGTTCGCTCTAATCACTCTTT 60.083 41.667 0.00 0.00 0.00 2.52
512 525 3.440872 ACTCGTTCGCTCTAATCACTCTT 59.559 43.478 0.00 0.00 0.00 2.85
513 526 3.011119 ACTCGTTCGCTCTAATCACTCT 58.989 45.455 0.00 0.00 0.00 3.24
514 527 3.102276 CACTCGTTCGCTCTAATCACTC 58.898 50.000 0.00 0.00 0.00 3.51
515 528 2.747989 TCACTCGTTCGCTCTAATCACT 59.252 45.455 0.00 0.00 0.00 3.41
516 529 3.102276 CTCACTCGTTCGCTCTAATCAC 58.898 50.000 0.00 0.00 0.00 3.06
517 530 2.747989 ACTCACTCGTTCGCTCTAATCA 59.252 45.455 0.00 0.00 0.00 2.57
518 531 3.102276 CACTCACTCGTTCGCTCTAATC 58.898 50.000 0.00 0.00 0.00 1.75
519 532 2.159366 CCACTCACTCGTTCGCTCTAAT 60.159 50.000 0.00 0.00 0.00 1.73
520 533 1.199327 CCACTCACTCGTTCGCTCTAA 59.801 52.381 0.00 0.00 0.00 2.10
521 534 0.803117 CCACTCACTCGTTCGCTCTA 59.197 55.000 0.00 0.00 0.00 2.43
522 535 1.581954 CCACTCACTCGTTCGCTCT 59.418 57.895 0.00 0.00 0.00 4.09
559 572 6.959606 AGATAGAACCATTGTATATGCCCT 57.040 37.500 0.00 0.00 0.00 5.19
560 573 7.281100 GCTAAGATAGAACCATTGTATATGCCC 59.719 40.741 0.00 0.00 0.00 5.36
561 574 7.824289 TGCTAAGATAGAACCATTGTATATGCC 59.176 37.037 0.00 0.00 0.00 4.40
562 575 8.777865 TGCTAAGATAGAACCATTGTATATGC 57.222 34.615 0.00 0.00 0.00 3.14
565 578 9.219603 GCATTGCTAAGATAGAACCATTGTATA 57.780 33.333 0.16 0.00 0.00 1.47
567 580 6.486657 GGCATTGCTAAGATAGAACCATTGTA 59.513 38.462 8.82 0.00 0.00 2.41
568 581 5.300286 GGCATTGCTAAGATAGAACCATTGT 59.700 40.000 8.82 0.00 0.00 2.71
569 582 5.300034 TGGCATTGCTAAGATAGAACCATTG 59.700 40.000 8.82 0.00 0.00 2.82
570 583 5.448654 TGGCATTGCTAAGATAGAACCATT 58.551 37.500 8.82 0.00 0.00 3.16
571 584 5.052693 TGGCATTGCTAAGATAGAACCAT 57.947 39.130 8.82 0.00 0.00 3.55
572 585 4.502105 TGGCATTGCTAAGATAGAACCA 57.498 40.909 8.82 0.00 0.00 3.67
573 586 7.497249 CCTATATGGCATTGCTAAGATAGAACC 59.503 40.741 19.98 0.00 0.00 3.62
574 587 8.260818 TCCTATATGGCATTGCTAAGATAGAAC 58.739 37.037 19.98 0.00 35.26 3.01
575 588 8.379428 TCCTATATGGCATTGCTAAGATAGAA 57.621 34.615 19.98 5.83 35.26 2.10
576 589 7.978099 TCCTATATGGCATTGCTAAGATAGA 57.022 36.000 19.98 6.24 35.26 1.98
579 592 9.401058 GTTTATCCTATATGGCATTGCTAAGAT 57.599 33.333 4.78 4.18 35.26 2.40
580 593 7.549134 CGTTTATCCTATATGGCATTGCTAAGA 59.451 37.037 4.78 0.00 35.26 2.10
581 594 7.549134 TCGTTTATCCTATATGGCATTGCTAAG 59.451 37.037 4.78 0.00 35.26 2.18
582 595 7.390823 TCGTTTATCCTATATGGCATTGCTAA 58.609 34.615 4.78 0.00 35.26 3.09
583 596 6.941857 TCGTTTATCCTATATGGCATTGCTA 58.058 36.000 4.78 2.16 35.26 3.49
584 597 5.804639 TCGTTTATCCTATATGGCATTGCT 58.195 37.500 4.78 0.00 35.26 3.91
585 598 6.683974 ATCGTTTATCCTATATGGCATTGC 57.316 37.500 4.78 0.00 35.26 3.56
586 599 8.830580 CCTAATCGTTTATCCTATATGGCATTG 58.169 37.037 4.78 0.00 35.26 2.82
587 600 8.548877 ACCTAATCGTTTATCCTATATGGCATT 58.451 33.333 4.78 0.00 35.26 3.56
588 601 7.987458 CACCTAATCGTTTATCCTATATGGCAT 59.013 37.037 4.88 4.88 35.26 4.40
589 602 7.179516 TCACCTAATCGTTTATCCTATATGGCA 59.820 37.037 0.00 0.00 35.26 4.92
590 603 7.553334 TCACCTAATCGTTTATCCTATATGGC 58.447 38.462 0.00 0.00 35.26 4.40
591 604 9.587772 CTTCACCTAATCGTTTATCCTATATGG 57.412 37.037 0.00 0.00 37.10 2.74
592 605 9.587772 CCTTCACCTAATCGTTTATCCTATATG 57.412 37.037 0.00 0.00 0.00 1.78
593 606 9.543231 TCCTTCACCTAATCGTTTATCCTATAT 57.457 33.333 0.00 0.00 0.00 0.86
594 607 8.945195 TCCTTCACCTAATCGTTTATCCTATA 57.055 34.615 0.00 0.00 0.00 1.31
595 608 7.728981 TCTCCTTCACCTAATCGTTTATCCTAT 59.271 37.037 0.00 0.00 0.00 2.57
596 609 7.064866 TCTCCTTCACCTAATCGTTTATCCTA 58.935 38.462 0.00 0.00 0.00 2.94
597 610 5.897824 TCTCCTTCACCTAATCGTTTATCCT 59.102 40.000 0.00 0.00 0.00 3.24
598 611 6.040616 TCTCTCCTTCACCTAATCGTTTATCC 59.959 42.308 0.00 0.00 0.00 2.59
599 612 7.013464 TCTCTCTCCTTCACCTAATCGTTTATC 59.987 40.741 0.00 0.00 0.00 1.75
600 613 6.834451 TCTCTCTCCTTCACCTAATCGTTTAT 59.166 38.462 0.00 0.00 0.00 1.40
601 614 6.185511 TCTCTCTCCTTCACCTAATCGTTTA 58.814 40.000 0.00 0.00 0.00 2.01
602 615 5.017490 TCTCTCTCCTTCACCTAATCGTTT 58.983 41.667 0.00 0.00 0.00 3.60
603 616 4.601084 TCTCTCTCCTTCACCTAATCGTT 58.399 43.478 0.00 0.00 0.00 3.85
604 617 4.237976 TCTCTCTCCTTCACCTAATCGT 57.762 45.455 0.00 0.00 0.00 3.73
605 618 5.782893 ATTCTCTCTCCTTCACCTAATCG 57.217 43.478 0.00 0.00 0.00 3.34
606 619 7.118496 TGAATTCTCTCTCCTTCACCTAATC 57.882 40.000 7.05 0.00 0.00 1.75
607 620 7.688918 ATGAATTCTCTCTCCTTCACCTAAT 57.311 36.000 7.05 0.00 31.00 1.73
608 621 8.609617 TTATGAATTCTCTCTCCTTCACCTAA 57.390 34.615 7.05 0.00 31.00 2.69
609 622 8.061920 TCTTATGAATTCTCTCTCCTTCACCTA 58.938 37.037 7.05 0.00 31.00 3.08
610 623 6.900186 TCTTATGAATTCTCTCTCCTTCACCT 59.100 38.462 7.05 0.00 31.00 4.00
611 624 7.118496 TCTTATGAATTCTCTCTCCTTCACC 57.882 40.000 7.05 0.00 31.00 4.02
612 625 9.442047 TTTTCTTATGAATTCTCTCTCCTTCAC 57.558 33.333 7.05 0.00 31.00 3.18
613 626 9.664332 CTTTTCTTATGAATTCTCTCTCCTTCA 57.336 33.333 7.05 0.00 32.63 3.02
614 627 9.883142 TCTTTTCTTATGAATTCTCTCTCCTTC 57.117 33.333 7.05 0.00 31.56 3.46
615 628 9.665719 GTCTTTTCTTATGAATTCTCTCTCCTT 57.334 33.333 7.05 0.00 31.56 3.36
616 629 8.264347 GGTCTTTTCTTATGAATTCTCTCTCCT 58.736 37.037 7.05 0.00 31.56 3.69
617 630 8.264347 AGGTCTTTTCTTATGAATTCTCTCTCC 58.736 37.037 7.05 0.00 31.56 3.71
618 631 9.097257 CAGGTCTTTTCTTATGAATTCTCTCTC 57.903 37.037 7.05 0.00 31.56 3.20
619 632 8.601546 ACAGGTCTTTTCTTATGAATTCTCTCT 58.398 33.333 7.05 0.00 31.56 3.10
620 633 8.785329 ACAGGTCTTTTCTTATGAATTCTCTC 57.215 34.615 7.05 0.00 31.56 3.20
621 634 8.601546 AGACAGGTCTTTTCTTATGAATTCTCT 58.398 33.333 7.05 0.00 36.31 3.10
622 635 8.785329 AGACAGGTCTTTTCTTATGAATTCTC 57.215 34.615 7.05 0.00 36.31 2.87
652 665 9.877178 GGTCATCTCTTGTCTTCTCTTAAATAA 57.123 33.333 0.00 0.00 0.00 1.40
653 666 9.261035 AGGTCATCTCTTGTCTTCTCTTAAATA 57.739 33.333 0.00 0.00 0.00 1.40
654 667 8.144862 AGGTCATCTCTTGTCTTCTCTTAAAT 57.855 34.615 0.00 0.00 0.00 1.40
655 668 7.546250 AGGTCATCTCTTGTCTTCTCTTAAA 57.454 36.000 0.00 0.00 0.00 1.52
656 669 7.164230 GAGGTCATCTCTTGTCTTCTCTTAA 57.836 40.000 0.00 0.00 39.38 1.85
657 670 6.767524 GAGGTCATCTCTTGTCTTCTCTTA 57.232 41.667 0.00 0.00 39.38 2.10
658 671 5.659440 GAGGTCATCTCTTGTCTTCTCTT 57.341 43.478 0.00 0.00 39.38 2.85
668 681 8.543774 ACATATTGTGTTAAGAGGTCATCTCTT 58.456 33.333 5.28 5.28 46.73 2.85
669 682 8.083828 ACATATTGTGTTAAGAGGTCATCTCT 57.916 34.615 0.00 0.00 46.35 3.10
670 683 8.200792 AGACATATTGTGTTAAGAGGTCATCTC 58.799 37.037 0.00 0.00 42.36 2.75
671 684 8.083828 AGACATATTGTGTTAAGAGGTCATCT 57.916 34.615 0.00 0.00 42.36 2.90
672 685 7.981789 TGAGACATATTGTGTTAAGAGGTCATC 59.018 37.037 0.00 0.00 42.36 2.92
673 686 7.766278 GTGAGACATATTGTGTTAAGAGGTCAT 59.234 37.037 0.00 0.00 42.36 3.06
674 687 7.097192 GTGAGACATATTGTGTTAAGAGGTCA 58.903 38.462 0.00 0.00 42.36 4.02
675 688 6.535508 GGTGAGACATATTGTGTTAAGAGGTC 59.464 42.308 0.00 0.00 42.36 3.85
676 689 6.013725 TGGTGAGACATATTGTGTTAAGAGGT 60.014 38.462 0.00 0.00 42.36 3.85
677 690 6.313905 GTGGTGAGACATATTGTGTTAAGAGG 59.686 42.308 0.00 0.00 42.36 3.69
678 691 6.035005 CGTGGTGAGACATATTGTGTTAAGAG 59.965 42.308 0.00 0.00 42.36 2.85
679 692 5.867174 CGTGGTGAGACATATTGTGTTAAGA 59.133 40.000 0.00 0.00 42.36 2.10
680 693 5.637810 ACGTGGTGAGACATATTGTGTTAAG 59.362 40.000 0.00 0.00 42.36 1.85
681 694 5.543714 ACGTGGTGAGACATATTGTGTTAA 58.456 37.500 0.00 0.00 42.36 2.01
682 695 5.142061 ACGTGGTGAGACATATTGTGTTA 57.858 39.130 0.00 0.00 42.36 2.41
683 696 4.002906 ACGTGGTGAGACATATTGTGTT 57.997 40.909 0.00 0.00 42.36 3.32
684 697 3.678056 ACGTGGTGAGACATATTGTGT 57.322 42.857 0.00 0.00 45.83 3.72
685 698 5.356882 AAAACGTGGTGAGACATATTGTG 57.643 39.130 0.00 0.00 0.00 3.33
686 699 6.148811 CCTAAAAACGTGGTGAGACATATTGT 59.851 38.462 0.00 0.00 0.00 2.71
687 700 6.370442 TCCTAAAAACGTGGTGAGACATATTG 59.630 38.462 0.00 0.00 0.00 1.90
688 701 6.469410 TCCTAAAAACGTGGTGAGACATATT 58.531 36.000 0.00 0.00 0.00 1.28
689 702 6.045072 TCCTAAAAACGTGGTGAGACATAT 57.955 37.500 0.00 0.00 0.00 1.78
690 703 5.471556 TCCTAAAAACGTGGTGAGACATA 57.528 39.130 0.00 0.00 0.00 2.29
691 704 4.345859 TCCTAAAAACGTGGTGAGACAT 57.654 40.909 0.00 0.00 0.00 3.06
692 705 3.823281 TCCTAAAAACGTGGTGAGACA 57.177 42.857 0.00 0.00 0.00 3.41
693 706 5.163884 GCTATTCCTAAAAACGTGGTGAGAC 60.164 44.000 0.00 0.00 0.00 3.36
694 707 4.933400 GCTATTCCTAAAAACGTGGTGAGA 59.067 41.667 0.00 0.00 0.00 3.27
695 708 4.935808 AGCTATTCCTAAAAACGTGGTGAG 59.064 41.667 0.00 0.00 0.00 3.51
696 709 4.901868 AGCTATTCCTAAAAACGTGGTGA 58.098 39.130 0.00 0.00 0.00 4.02
697 710 5.873164 ACTAGCTATTCCTAAAAACGTGGTG 59.127 40.000 0.00 0.00 0.00 4.17
698 711 6.046290 ACTAGCTATTCCTAAAAACGTGGT 57.954 37.500 0.00 0.00 0.00 4.16
699 712 6.980051 AACTAGCTATTCCTAAAAACGTGG 57.020 37.500 0.00 0.00 0.00 4.94
700 713 9.916397 CAATAACTAGCTATTCCTAAAAACGTG 57.084 33.333 0.00 0.00 0.00 4.49
701 714 9.880157 TCAATAACTAGCTATTCCTAAAAACGT 57.120 29.630 0.00 0.00 0.00 3.99
739 752 9.606631 GTCTACAATGGATCATCTTTTAGTCTT 57.393 33.333 0.00 0.00 0.00 3.01
740 753 8.762645 TGTCTACAATGGATCATCTTTTAGTCT 58.237 33.333 0.00 0.00 0.00 3.24
741 754 8.948631 TGTCTACAATGGATCATCTTTTAGTC 57.051 34.615 0.00 0.00 0.00 2.59
742 755 9.334947 CATGTCTACAATGGATCATCTTTTAGT 57.665 33.333 0.00 0.00 0.00 2.24
743 756 9.334947 ACATGTCTACAATGGATCATCTTTTAG 57.665 33.333 0.00 0.00 0.00 1.85
744 757 9.685276 AACATGTCTACAATGGATCATCTTTTA 57.315 29.630 0.00 0.00 0.00 1.52
745 758 8.585471 AACATGTCTACAATGGATCATCTTTT 57.415 30.769 0.00 0.00 0.00 2.27
746 759 8.585471 AAACATGTCTACAATGGATCATCTTT 57.415 30.769 0.00 0.00 0.00 2.52
747 760 8.585471 AAAACATGTCTACAATGGATCATCTT 57.415 30.769 0.00 0.00 0.00 2.40
748 761 8.585471 AAAAACATGTCTACAATGGATCATCT 57.415 30.769 0.00 0.00 0.00 2.90
777 790 9.624373 AAGTCTTGCATGTAATTAAGAGATGAT 57.376 29.630 0.00 0.00 30.38 2.45
810 823 9.770097 CATGTACAATGGTTGATAAGATAGTCT 57.230 33.333 0.00 0.00 0.00 3.24
811 824 8.499162 GCATGTACAATGGTTGATAAGATAGTC 58.501 37.037 0.00 0.00 0.00 2.59
812 825 7.445402 GGCATGTACAATGGTTGATAAGATAGT 59.555 37.037 0.00 0.00 0.00 2.12
813 826 7.094634 GGGCATGTACAATGGTTGATAAGATAG 60.095 40.741 0.00 0.00 0.00 2.08
814 827 6.714810 GGGCATGTACAATGGTTGATAAGATA 59.285 38.462 0.00 0.00 0.00 1.98
815 828 5.536161 GGGCATGTACAATGGTTGATAAGAT 59.464 40.000 0.00 0.00 0.00 2.40
816 829 4.887071 GGGCATGTACAATGGTTGATAAGA 59.113 41.667 0.00 0.00 0.00 2.10
817 830 4.889409 AGGGCATGTACAATGGTTGATAAG 59.111 41.667 0.00 0.00 0.00 1.73
818 831 4.865905 AGGGCATGTACAATGGTTGATAA 58.134 39.130 0.00 0.00 0.00 1.75
819 832 4.518278 AGGGCATGTACAATGGTTGATA 57.482 40.909 0.00 0.00 0.00 2.15
820 833 3.386932 AGGGCATGTACAATGGTTGAT 57.613 42.857 0.00 0.00 0.00 2.57
821 834 2.897271 AGGGCATGTACAATGGTTGA 57.103 45.000 0.00 0.00 0.00 3.18
822 835 4.202141 CCATTAGGGCATGTACAATGGTTG 60.202 45.833 10.95 1.39 40.39 3.77
823 836 3.960102 CCATTAGGGCATGTACAATGGTT 59.040 43.478 10.95 0.00 40.39 3.67
824 837 3.565307 CCATTAGGGCATGTACAATGGT 58.435 45.455 10.95 0.00 40.39 3.55
864 877 2.985896 TGAGGCAATCGGGAGTTTAAG 58.014 47.619 0.00 0.00 0.00 1.85
865 878 3.426787 TTGAGGCAATCGGGAGTTTAA 57.573 42.857 0.00 0.00 0.00 1.52
868 881 2.286365 TTTTGAGGCAATCGGGAGTT 57.714 45.000 0.00 0.00 0.00 3.01
869 882 2.162681 CTTTTTGAGGCAATCGGGAGT 58.837 47.619 0.00 0.00 0.00 3.85
897 915 4.079730 AGAGGACTCCTTTCACTGGTTTTT 60.080 41.667 0.00 0.00 31.76 1.94
898 916 3.459969 AGAGGACTCCTTTCACTGGTTTT 59.540 43.478 0.00 0.00 31.76 2.43
899 917 3.049344 AGAGGACTCCTTTCACTGGTTT 58.951 45.455 0.00 0.00 31.76 3.27
939 957 2.200092 TCAGGGGTTTGGGTTGCC 59.800 61.111 0.00 0.00 0.00 4.52
1045 1064 4.261701 CGGGAGGTGAGACCCTAG 57.738 66.667 0.00 0.00 43.57 3.02
1126 1145 2.350514 GCTGAAGCTGCAGGAGGT 59.649 61.111 23.61 0.00 36.41 3.85
1153 1172 4.243008 TCGAACGGTTGGCCTGCA 62.243 61.111 3.32 0.00 0.00 4.41
1182 1204 1.380112 GCCTGGGACGTAGGTCTCT 60.380 63.158 16.01 0.00 44.40 3.10
1279 1301 2.586792 GATGAGCGGCACCTTCCT 59.413 61.111 1.45 0.00 0.00 3.36
1413 1435 4.256920 GCATATCCCTTGCGAACTCATAT 58.743 43.478 0.00 0.00 0.00 1.78
1416 1438 1.209261 TGCATATCCCTTGCGAACTCA 59.791 47.619 0.00 0.00 43.10 3.41
1441 1463 4.335647 CAGCGTTGGCAGTCCCCT 62.336 66.667 0.00 0.00 43.41 4.79
1492 1514 2.417719 ATTAGCCCCTCGGTCCTAAT 57.582 50.000 0.00 0.00 0.00 1.73
1509 1531 6.884295 TGTTTCTGACCATTTCGATAGGAATT 59.116 34.615 5.44 0.00 43.33 2.17
1518 1540 4.329801 TCGATGATGTTTCTGACCATTTCG 59.670 41.667 12.00 12.00 0.00 3.46
1569 1591 5.752892 TGTAGCTACTACAGACACTATGC 57.247 43.478 23.84 0.00 41.33 3.14
1656 1678 2.797837 AGCAGCAACACAAAGCTCA 58.202 47.368 0.00 0.00 39.50 4.26
1725 1747 4.340097 TCTGTTAGTCTCAGGTTCGAACAA 59.660 41.667 28.24 12.91 34.15 2.83
1726 1748 3.887110 TCTGTTAGTCTCAGGTTCGAACA 59.113 43.478 28.24 8.56 34.15 3.18
1733 1755 4.841246 AGAACCAATCTGTTAGTCTCAGGT 59.159 41.667 0.00 0.00 36.88 4.00
1747 1769 5.591877 AGAATGGTGCAATAGAGAACCAATC 59.408 40.000 0.00 0.00 45.40 2.67
1841 1864 7.279981 TGCATCTAAAGTCAATTTATACGCAGT 59.720 33.333 0.00 0.00 37.07 4.40
1890 1913 3.406361 GTGCAGCGACGTGAGGTG 61.406 66.667 13.50 13.50 39.81 4.00
2014 2037 4.155733 CGGTATGAGCGGTGGCCA 62.156 66.667 0.00 0.00 41.24 5.36
2202 2226 0.749454 GATTGCATCCAAGAGGGCGT 60.749 55.000 0.00 0.00 36.21 5.68
2219 2243 2.672996 GCAAGTGGTGGCGGTGAT 60.673 61.111 0.00 0.00 0.00 3.06
2290 2314 2.563179 GCGGATATAAGAGGAAGGCTGA 59.437 50.000 0.00 0.00 0.00 4.26
2325 2349 4.680237 TCAAGCAGCCCACGGACG 62.680 66.667 0.00 0.00 0.00 4.79
2421 2445 2.564062 CTCTTTCCGTGGTTACCCTGTA 59.436 50.000 0.00 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.