Multiple sequence alignment - TraesCS6D01G162100

Loading Multiple Alignment...

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 TraesCS6D01G162100 chr6D 100.000 3284 0 0 1 3284 140218604 140221887 0.000000e+00 6065.0
1 TraesCS6D01G162100 chr6A 92.500 1720 85 14 834 2539 184818807 184820496 0.000000e+00 2422.0
2 TraesCS6D01G162100 chr6A 96.078 51 2 0 3234 3284 184888159 184888209 2.100000e-12 84.2
3 TraesCS6D01G162100 chr6B 94.011 1603 63 9 968 2539 240323362 240324962 0.000000e+00 2398.0
4 TraesCS6D01G162100 chr6B 94.737 209 10 1 653 860 240323114 240323322 1.140000e-84 324.0
5 TraesCS6D01G162100 chr6B 96.078 51 2 0 3234 3284 240333020 240333070 2.100000e-12 84.2
6 TraesCS6D01G162100 chr2B 95.948 617 23 2 2538 3154 158438259 158437645 0.000000e+00 1000.0
7 TraesCS6D01G162100 chr2B 85.258 563 69 10 2 558 59095552 59096106 4.760000e-158 568.0
8 TraesCS6D01G162100 chr2B 84.801 579 62 20 13 585 324658951 324659509 2.860000e-155 558.0
9 TraesCS6D01G162100 chr2B 83.765 579 75 15 13 585 782289990 782290555 6.240000e-147 531.0
10 TraesCS6D01G162100 chr2B 90.123 81 7 1 2537 2617 47203156 47203235 1.610000e-18 104.0
11 TraesCS6D01G162100 chr1B 95.527 626 25 3 2537 3162 115775056 115774434 0.000000e+00 998.0
12 TraesCS6D01G162100 chr1B 85.133 565 66 13 1 558 23973651 23973098 2.210000e-156 562.0
13 TraesCS6D01G162100 chr4D 95.238 630 25 4 2537 3166 469071212 469071836 0.000000e+00 992.0
14 TraesCS6D01G162100 chr7D 94.695 622 18 5 2537 3158 399428394 399427788 0.000000e+00 952.0
15 TraesCS6D01G162100 chr7D 84.356 326 42 7 2064 2381 580003352 580003676 8.850000e-81 311.0
16 TraesCS6D01G162100 chr7D 85.000 220 29 3 2079 2295 580005515 580005733 1.530000e-53 220.0
17 TraesCS6D01G162100 chr2D 90.271 627 44 5 2554 3165 523650009 523649385 0.000000e+00 804.0
18 TraesCS6D01G162100 chr4B 90.113 617 56 5 2537 3151 518139701 518140314 0.000000e+00 797.0
19 TraesCS6D01G162100 chr1D 89.773 616 63 0 2544 3159 345403787 345404402 0.000000e+00 789.0
20 TraesCS6D01G162100 chr1D 89.677 620 56 6 2539 3151 315638983 315639601 0.000000e+00 784.0
21 TraesCS6D01G162100 chr1D 89.482 599 53 9 1 593 87668711 87668117 0.000000e+00 749.0
22 TraesCS6D01G162100 chr5D 89.836 610 59 2 2538 3145 448446697 448446089 0.000000e+00 780.0
23 TraesCS6D01G162100 chr3D 86.401 603 64 15 1 594 586308913 586308320 0.000000e+00 643.0
24 TraesCS6D01G162100 chrUn 86.082 582 61 15 1 575 50298505 50297937 2.800000e-170 608.0
25 TraesCS6D01G162100 chr1A 85.763 583 67 13 1 575 281387418 281387992 1.300000e-168 603.0
26 TraesCS6D01G162100 chr4A 85.179 587 74 10 13 594 537741637 537741059 1.010000e-164 590.0
27 TraesCS6D01G162100 chr7A 84.308 325 44 5 2064 2381 671500409 671500733 8.850000e-81 311.0
28 TraesCS6D01G162100 chr7B 83.333 324 45 7 2077 2393 646369018 646369339 1.150000e-74 291.0
29 TraesCS6D01G162100 chr7B 85.268 224 31 2 2065 2286 646371002 646371225 2.550000e-56 230.0


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 TraesCS6D01G162100 chr6D 140218604 140221887 3283 False 6065.0 6065 100.0000 1 3284 1 chr6D.!!$F1 3283
1 TraesCS6D01G162100 chr6A 184818807 184820496 1689 False 2422.0 2422 92.5000 834 2539 1 chr6A.!!$F1 1705
2 TraesCS6D01G162100 chr6B 240323114 240324962 1848 False 1361.0 2398 94.3740 653 2539 2 chr6B.!!$F2 1886
3 TraesCS6D01G162100 chr2B 158437645 158438259 614 True 1000.0 1000 95.9480 2538 3154 1 chr2B.!!$R1 616
4 TraesCS6D01G162100 chr2B 59095552 59096106 554 False 568.0 568 85.2580 2 558 1 chr2B.!!$F2 556
5 TraesCS6D01G162100 chr2B 324658951 324659509 558 False 558.0 558 84.8010 13 585 1 chr2B.!!$F3 572
6 TraesCS6D01G162100 chr2B 782289990 782290555 565 False 531.0 531 83.7650 13 585 1 chr2B.!!$F4 572
7 TraesCS6D01G162100 chr1B 115774434 115775056 622 True 998.0 998 95.5270 2537 3162 1 chr1B.!!$R2 625
8 TraesCS6D01G162100 chr1B 23973098 23973651 553 True 562.0 562 85.1330 1 558 1 chr1B.!!$R1 557
9 TraesCS6D01G162100 chr4D 469071212 469071836 624 False 992.0 992 95.2380 2537 3166 1 chr4D.!!$F1 629
10 TraesCS6D01G162100 chr7D 399427788 399428394 606 True 952.0 952 94.6950 2537 3158 1 chr7D.!!$R1 621
11 TraesCS6D01G162100 chr7D 580003352 580005733 2381 False 265.5 311 84.6780 2064 2381 2 chr7D.!!$F1 317
12 TraesCS6D01G162100 chr2D 523649385 523650009 624 True 804.0 804 90.2710 2554 3165 1 chr2D.!!$R1 611
13 TraesCS6D01G162100 chr4B 518139701 518140314 613 False 797.0 797 90.1130 2537 3151 1 chr4B.!!$F1 614
14 TraesCS6D01G162100 chr1D 345403787 345404402 615 False 789.0 789 89.7730 2544 3159 1 chr1D.!!$F2 615
15 TraesCS6D01G162100 chr1D 315638983 315639601 618 False 784.0 784 89.6770 2539 3151 1 chr1D.!!$F1 612
16 TraesCS6D01G162100 chr1D 87668117 87668711 594 True 749.0 749 89.4820 1 593 1 chr1D.!!$R1 592
17 TraesCS6D01G162100 chr5D 448446089 448446697 608 True 780.0 780 89.8360 2538 3145 1 chr5D.!!$R1 607
18 TraesCS6D01G162100 chr3D 586308320 586308913 593 True 643.0 643 86.4010 1 594 1 chr3D.!!$R1 593
19 TraesCS6D01G162100 chrUn 50297937 50298505 568 True 608.0 608 86.0820 1 575 1 chrUn.!!$R1 574
20 TraesCS6D01G162100 chr1A 281387418 281387992 574 False 603.0 603 85.7630 1 575 1 chr1A.!!$F1 574
21 TraesCS6D01G162100 chr4A 537741059 537741637 578 True 590.0 590 85.1790 13 594 1 chr4A.!!$R1 581
22 TraesCS6D01G162100 chr7B 646369018 646371225 2207 False 260.5 291 84.3005 2065 2393 2 chr7B.!!$F1 328

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
432 437 0.105593 GCCTGATCAAGAGGATGCGA 59.894 55.0 3.71 0.0 36.00 5.10 F
626 640 0.110192 GCACTTGTTTAGTCCGCTGC 60.110 55.0 0.00 0.0 33.85 5.25 F
1423 1459 0.033405 AGCCAGCAGAATGAAGCCAT 60.033 50.0 0.00 0.0 39.69 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1418 1454 0.040058 TCAGAACCAATGGCATGGCT 59.960 50.0 21.08 3.03 44.75 4.75 R
1660 1714 0.167470 CACAGGCACTCAAGCAATCG 59.833 55.0 0.00 0.00 34.60 3.34 R
3224 5454 0.466189 CAGCCCTTCGCACCCATAAT 60.466 55.0 0.00 0.00 41.38 1.28 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
95 100 2.125106 GGCGGAGGAGATTTGCGT 60.125 61.111 0.00 0.00 0.00 5.24
131 136 2.289631 TGCCTGTGTCAGATCGATTTGT 60.290 45.455 14.90 0.00 32.44 2.83
134 139 4.320494 GCCTGTGTCAGATCGATTTGTTTT 60.320 41.667 14.90 0.00 32.44 2.43
176 181 1.272769 GAGACTTGGTCGTTGTAGGCT 59.727 52.381 0.00 0.00 37.67 4.58
278 283 1.338107 TGTCTGTGGTCTCCGTCATT 58.662 50.000 0.00 0.00 0.00 2.57
421 426 1.134521 GTGGATGTTACCGCCTGATCA 60.135 52.381 0.00 0.00 34.73 2.92
432 437 0.105593 GCCTGATCAAGAGGATGCGA 59.894 55.000 3.71 0.00 36.00 5.10
463 472 2.406616 GCGGCGAATGGTGTGGAAT 61.407 57.895 12.98 0.00 0.00 3.01
502 511 6.891908 AGGCTCTGATTACCAAATTGTAATGT 59.108 34.615 6.03 0.00 40.57 2.71
544 557 1.944177 TGGGTGAGGAAGGAGAGAAG 58.056 55.000 0.00 0.00 0.00 2.85
549 562 2.564947 GTGAGGAAGGAGAGAAGCAGAA 59.435 50.000 0.00 0.00 0.00 3.02
570 584 2.118403 AGGTGAGGGAAGACTTGGAA 57.882 50.000 0.00 0.00 0.00 3.53
575 589 3.325135 GTGAGGGAAGACTTGGAAGAAGA 59.675 47.826 0.00 0.00 0.00 2.87
585 599 6.237154 AGACTTGGAAGAAGAGAAAGGATTG 58.763 40.000 0.00 0.00 0.00 2.67
590 604 5.776716 TGGAAGAAGAGAAAGGATTGCATTT 59.223 36.000 0.00 0.00 0.00 2.32
594 608 8.820153 AAGAAGAGAAAGGATTGCATTTATCT 57.180 30.769 2.57 2.57 45.05 1.98
595 609 8.223177 AGAAGAGAAAGGATTGCATTTATCTG 57.777 34.615 8.08 0.00 43.14 2.90
596 610 8.051535 AGAAGAGAAAGGATTGCATTTATCTGA 58.948 33.333 8.08 0.00 43.14 3.27
597 611 8.585471 AAGAGAAAGGATTGCATTTATCTGAA 57.415 30.769 8.08 0.00 43.14 3.02
598 612 8.763984 AGAGAAAGGATTGCATTTATCTGAAT 57.236 30.769 6.81 0.00 42.57 2.57
599 613 9.857656 AGAGAAAGGATTGCATTTATCTGAATA 57.142 29.630 6.81 0.00 42.57 1.75
600 614 9.890352 GAGAAAGGATTGCATTTATCTGAATAC 57.110 33.333 0.00 0.00 34.32 1.89
601 615 9.638176 AGAAAGGATTGCATTTATCTGAATACT 57.362 29.630 0.00 0.00 0.00 2.12
602 616 9.674824 GAAAGGATTGCATTTATCTGAATACTG 57.325 33.333 0.00 0.00 0.00 2.74
603 617 8.985315 AAGGATTGCATTTATCTGAATACTGA 57.015 30.769 0.00 0.00 0.00 3.41
604 618 8.985315 AGGATTGCATTTATCTGAATACTGAA 57.015 30.769 0.00 0.00 0.00 3.02
605 619 8.844244 AGGATTGCATTTATCTGAATACTGAAC 58.156 33.333 0.00 0.00 0.00 3.18
606 620 8.844244 GGATTGCATTTATCTGAATACTGAACT 58.156 33.333 0.00 0.00 0.00 3.01
607 621 9.661187 GATTGCATTTATCTGAATACTGAACTG 57.339 33.333 0.00 0.00 0.00 3.16
608 622 7.019774 TGCATTTATCTGAATACTGAACTGC 57.980 36.000 0.00 0.00 0.00 4.40
609 623 6.598850 TGCATTTATCTGAATACTGAACTGCA 59.401 34.615 0.00 0.00 32.25 4.41
610 624 6.909357 GCATTTATCTGAATACTGAACTGCAC 59.091 38.462 0.00 0.00 0.00 4.57
611 625 7.201679 GCATTTATCTGAATACTGAACTGCACT 60.202 37.037 0.00 0.00 0.00 4.40
612 626 8.671921 CATTTATCTGAATACTGAACTGCACTT 58.328 33.333 0.00 0.00 0.00 3.16
613 627 7.601073 TTATCTGAATACTGAACTGCACTTG 57.399 36.000 0.00 0.00 0.00 3.16
614 628 4.960938 TCTGAATACTGAACTGCACTTGT 58.039 39.130 0.00 0.00 0.00 3.16
615 629 5.368145 TCTGAATACTGAACTGCACTTGTT 58.632 37.500 0.00 0.00 0.00 2.83
616 630 5.822519 TCTGAATACTGAACTGCACTTGTTT 59.177 36.000 0.00 0.00 0.00 2.83
617 631 6.989759 TCTGAATACTGAACTGCACTTGTTTA 59.010 34.615 0.00 0.00 0.00 2.01
618 632 7.171508 TCTGAATACTGAACTGCACTTGTTTAG 59.828 37.037 7.34 7.34 37.16 1.85
619 633 6.765989 TGAATACTGAACTGCACTTGTTTAGT 59.234 34.615 15.78 15.78 43.42 2.24
620 634 6.787085 ATACTGAACTGCACTTGTTTAGTC 57.213 37.500 15.18 0.00 41.28 2.59
621 635 3.877508 ACTGAACTGCACTTGTTTAGTCC 59.122 43.478 8.40 0.00 39.09 3.85
622 636 2.869801 TGAACTGCACTTGTTTAGTCCG 59.130 45.455 0.00 0.00 33.85 4.79
623 637 1.226746 ACTGCACTTGTTTAGTCCGC 58.773 50.000 0.00 0.00 33.85 5.54
624 638 1.202651 ACTGCACTTGTTTAGTCCGCT 60.203 47.619 0.00 0.00 33.85 5.52
625 639 1.195448 CTGCACTTGTTTAGTCCGCTG 59.805 52.381 0.00 0.00 33.85 5.18
626 640 0.110192 GCACTTGTTTAGTCCGCTGC 60.110 55.000 0.00 0.00 33.85 5.25
627 641 1.512926 CACTTGTTTAGTCCGCTGCT 58.487 50.000 0.00 0.00 33.85 4.24
628 642 1.195448 CACTTGTTTAGTCCGCTGCTG 59.805 52.381 0.00 0.00 33.85 4.41
629 643 1.202651 ACTTGTTTAGTCCGCTGCTGT 60.203 47.619 0.00 0.00 28.23 4.40
630 644 1.461127 CTTGTTTAGTCCGCTGCTGTC 59.539 52.381 0.00 0.00 0.00 3.51
631 645 0.679505 TGTTTAGTCCGCTGCTGTCT 59.320 50.000 0.00 0.00 0.00 3.41
632 646 1.336887 TGTTTAGTCCGCTGCTGTCTC 60.337 52.381 0.00 0.00 0.00 3.36
633 647 0.966179 TTTAGTCCGCTGCTGTCTCA 59.034 50.000 0.00 0.00 0.00 3.27
634 648 0.528017 TTAGTCCGCTGCTGTCTCAG 59.472 55.000 0.00 0.00 37.15 3.35
645 659 2.222007 CTGTCTCAGCATCAGTAGGC 57.778 55.000 0.00 0.00 0.00 3.93
646 660 0.457443 TGTCTCAGCATCAGTAGGCG 59.543 55.000 0.00 0.00 37.52 5.52
647 661 0.873743 GTCTCAGCATCAGTAGGCGC 60.874 60.000 0.00 0.00 37.52 6.53
648 662 1.948138 CTCAGCATCAGTAGGCGCG 60.948 63.158 0.00 0.00 37.52 6.86
649 663 2.104928 CAGCATCAGTAGGCGCGA 59.895 61.111 12.10 0.00 37.52 5.87
650 664 2.105128 AGCATCAGTAGGCGCGAC 59.895 61.111 12.10 7.34 37.52 5.19
651 665 2.202743 GCATCAGTAGGCGCGACA 60.203 61.111 17.71 0.00 0.00 4.35
669 683 1.419762 ACAACCCCAAGCCCAAAAATC 59.580 47.619 0.00 0.00 0.00 2.17
670 684 0.684535 AACCCCAAGCCCAAAAATCG 59.315 50.000 0.00 0.00 0.00 3.34
671 685 0.471022 ACCCCAAGCCCAAAAATCGT 60.471 50.000 0.00 0.00 0.00 3.73
681 695 3.610821 GCCCAAAAATCGTGTAACTGTCC 60.611 47.826 0.00 0.00 31.75 4.02
692 706 4.400120 GTGTAACTGTCCCATACCCAAAA 58.600 43.478 0.00 0.00 0.00 2.44
738 752 5.567430 AGTAATGGGTAGGAAAACAGTTCC 58.433 41.667 0.00 0.00 38.86 3.62
783 797 3.238108 TGAGCTTTCCTCGATGAGTTC 57.762 47.619 0.00 0.00 43.82 3.01
801 815 3.891977 AGTTCACTGACTTCTGCTGAGTA 59.108 43.478 0.00 0.00 0.00 2.59
860 875 0.813184 CCCACCAGCACATCACATTC 59.187 55.000 0.00 0.00 0.00 2.67
870 885 5.344933 CAGCACATCACATTCAACATTCAAG 59.655 40.000 0.00 0.00 0.00 3.02
914 929 1.207791 AATCTCAAGGTCGCATCCCT 58.792 50.000 0.00 0.00 0.00 4.20
917 932 2.184533 TCTCAAGGTCGCATCCCTAAA 58.815 47.619 0.00 0.00 0.00 1.85
918 933 2.569853 TCTCAAGGTCGCATCCCTAAAA 59.430 45.455 0.00 0.00 0.00 1.52
919 934 3.008594 TCTCAAGGTCGCATCCCTAAAAA 59.991 43.478 0.00 0.00 0.00 1.94
1056 1071 2.022129 CCACGACGTTGAGCAGGTC 61.022 63.158 10.51 0.00 37.00 3.85
1085 1100 1.622173 CCAGCTCTCCTCTTTCTCCCT 60.622 57.143 0.00 0.00 0.00 4.20
1118 1133 2.789092 CGATTTGGTCGCTGAATCTTGC 60.789 50.000 0.00 0.00 44.33 4.01
1139 1154 4.719616 GGCGTCGTGCTCGTTTGC 62.720 66.667 8.17 10.16 45.43 3.68
1354 1380 1.077429 GGGCCAGTGAGGGATGTTC 60.077 63.158 4.39 0.00 38.09 3.18
1399 1425 4.845621 GAAATTGGATGTGCAATTTCGG 57.154 40.909 25.95 0.00 43.37 4.30
1416 1452 0.661552 CGGAATGAGCCAGCAGAATG 59.338 55.000 0.00 0.00 40.87 2.67
1418 1454 2.372264 GGAATGAGCCAGCAGAATGAA 58.628 47.619 0.00 0.00 39.69 2.57
1419 1455 2.358267 GGAATGAGCCAGCAGAATGAAG 59.642 50.000 0.00 0.00 39.69 3.02
1420 1456 1.390565 ATGAGCCAGCAGAATGAAGC 58.609 50.000 0.00 0.00 39.69 3.86
1421 1457 0.679002 TGAGCCAGCAGAATGAAGCC 60.679 55.000 0.00 0.00 39.69 4.35
1422 1458 0.679002 GAGCCAGCAGAATGAAGCCA 60.679 55.000 0.00 0.00 39.69 4.75
1423 1459 0.033405 AGCCAGCAGAATGAAGCCAT 60.033 50.000 0.00 0.00 39.69 4.40
1424 1460 0.102481 GCCAGCAGAATGAAGCCATG 59.898 55.000 0.00 0.00 39.69 3.66
1425 1461 0.102481 CCAGCAGAATGAAGCCATGC 59.898 55.000 0.00 0.00 39.69 4.06
1426 1462 0.102481 CAGCAGAATGAAGCCATGCC 59.898 55.000 0.00 0.00 39.69 4.40
1427 1463 0.323999 AGCAGAATGAAGCCATGCCA 60.324 50.000 0.00 0.00 39.69 4.92
1428 1464 0.750850 GCAGAATGAAGCCATGCCAT 59.249 50.000 0.00 0.00 39.69 4.40
1455 1491 5.930837 TCTGAACCTGGAATTGTGTTTTT 57.069 34.783 0.00 0.00 0.00 1.94
1509 1545 6.047511 AGCATCAAGATGGCCTAGTATTAG 57.952 41.667 3.32 0.00 39.16 1.73
1567 1604 6.593268 TTTCTTCCATTTGCTTGATCATGA 57.407 33.333 12.54 0.00 0.00 3.07
1611 1648 5.682234 TCATGCCCATATAGACATAGTGG 57.318 43.478 0.00 0.00 0.00 4.00
1620 1657 7.095910 CCATATAGACATAGTGGAAGCTGAAG 58.904 42.308 0.00 0.00 31.59 3.02
1626 1663 5.376625 ACATAGTGGAAGCTGAAGTTTTCA 58.623 37.500 0.00 0.00 38.17 2.69
1664 1718 9.757227 TTGATTTGAACTTATTGTTTTCCGATT 57.243 25.926 0.00 0.00 39.30 3.34
1676 1730 0.036732 TTCCGATTGCTTGAGTGCCT 59.963 50.000 0.00 0.00 0.00 4.75
1677 1731 0.674581 TCCGATTGCTTGAGTGCCTG 60.675 55.000 0.00 0.00 0.00 4.85
1695 1749 3.253188 GCCTGTGTTCTGAACTGCAATAA 59.747 43.478 20.18 0.00 0.00 1.40
1702 1756 8.845227 TGTGTTCTGAACTGCAATAATTTTAGA 58.155 29.630 20.18 0.00 0.00 2.10
1717 1771 8.707938 ATAATTTTAGATCAAAGCAAAGCACC 57.292 30.769 0.00 0.00 0.00 5.01
1719 1773 0.242017 AGATCAAAGCAAAGCACCGC 59.758 50.000 0.00 0.00 0.00 5.68
1847 1901 1.206610 CTATCTGCCTGTCTGCACTGT 59.793 52.381 0.00 0.00 36.04 3.55
1861 1915 5.565259 GTCTGCACTGTTTATTTGATTGTCG 59.435 40.000 0.00 0.00 0.00 4.35
1868 1922 8.967218 CACTGTTTATTTGATTGTCGTGAAATT 58.033 29.630 0.00 0.00 0.00 1.82
1872 1926 9.072294 GTTTATTTGATTGTCGTGAAATTAGGG 57.928 33.333 0.00 0.00 0.00 3.53
1962 2019 1.139058 ACACAGTGTCAGTCCTTCCAC 59.861 52.381 0.00 0.00 0.00 4.02
2122 4329 5.543714 TCGAGCAGGAAATACAAACAACTA 58.456 37.500 0.00 0.00 0.00 2.24
2390 4597 4.278310 TCTCTTGCTATACCTAGTGCACA 58.722 43.478 21.04 4.13 35.01 4.57
2504 4711 4.763279 TGTTACTAGTGCTGTACTGCTGTA 59.237 41.667 23.07 16.78 40.65 2.74
2527 4734 8.667463 TGTACATGCCATTGATTTCATATATCG 58.333 33.333 0.00 0.00 0.00 2.92
2531 4738 7.984422 TGCCATTGATTTCATATATCGAAGT 57.016 32.000 0.00 0.00 0.00 3.01
2857 5080 1.616374 TGGTCGTTACTCACTCATGCA 59.384 47.619 0.00 0.00 0.00 3.96
2895 5118 2.105649 TGGATATTGGATGCAACCGCTA 59.894 45.455 8.65 2.83 39.64 4.26
3060 5289 4.894784 TCTTGACTCGGTTTATGAGCTTT 58.105 39.130 0.00 0.00 36.94 3.51
3183 5413 9.798994 ATAAATAAAGCATTTCAGCTCTTTCAG 57.201 29.630 0.00 0.00 45.89 3.02
3184 5414 7.458409 AATAAAGCATTTCAGCTCTTTCAGA 57.542 32.000 0.00 0.00 45.89 3.27
3185 5415 4.762956 AAGCATTTCAGCTCTTTCAGAC 57.237 40.909 0.00 0.00 45.89 3.51
3186 5416 3.080319 AGCATTTCAGCTCTTTCAGACC 58.920 45.455 0.00 0.00 42.18 3.85
3187 5417 2.163211 GCATTTCAGCTCTTTCAGACCC 59.837 50.000 0.00 0.00 0.00 4.46
3188 5418 3.683802 CATTTCAGCTCTTTCAGACCCT 58.316 45.455 0.00 0.00 0.00 4.34
3189 5419 3.864789 TTTCAGCTCTTTCAGACCCTT 57.135 42.857 0.00 0.00 0.00 3.95
3190 5420 3.409026 TTCAGCTCTTTCAGACCCTTC 57.591 47.619 0.00 0.00 0.00 3.46
3191 5421 2.329267 TCAGCTCTTTCAGACCCTTCA 58.671 47.619 0.00 0.00 0.00 3.02
3192 5422 2.705658 TCAGCTCTTTCAGACCCTTCAA 59.294 45.455 0.00 0.00 0.00 2.69
3193 5423 3.328931 TCAGCTCTTTCAGACCCTTCAAT 59.671 43.478 0.00 0.00 0.00 2.57
3194 5424 4.077822 CAGCTCTTTCAGACCCTTCAATT 58.922 43.478 0.00 0.00 0.00 2.32
3195 5425 4.077822 AGCTCTTTCAGACCCTTCAATTG 58.922 43.478 0.00 0.00 0.00 2.32
3196 5426 3.823304 GCTCTTTCAGACCCTTCAATTGT 59.177 43.478 5.13 0.00 0.00 2.71
3197 5427 5.003804 GCTCTTTCAGACCCTTCAATTGTA 58.996 41.667 5.13 0.00 0.00 2.41
3198 5428 5.649831 GCTCTTTCAGACCCTTCAATTGTAT 59.350 40.000 5.13 0.00 0.00 2.29
3199 5429 6.151817 GCTCTTTCAGACCCTTCAATTGTATT 59.848 38.462 5.13 0.00 0.00 1.89
3200 5430 7.309438 GCTCTTTCAGACCCTTCAATTGTATTT 60.309 37.037 5.13 0.00 0.00 1.40
3201 5431 7.885297 TCTTTCAGACCCTTCAATTGTATTTG 58.115 34.615 5.13 0.00 0.00 2.32
3202 5432 5.643379 TCAGACCCTTCAATTGTATTTGC 57.357 39.130 5.13 0.00 0.00 3.68
3203 5433 5.076182 TCAGACCCTTCAATTGTATTTGCA 58.924 37.500 5.13 0.00 0.00 4.08
3204 5434 5.048083 TCAGACCCTTCAATTGTATTTGCAC 60.048 40.000 5.13 0.00 0.00 4.57
3205 5435 5.047802 CAGACCCTTCAATTGTATTTGCACT 60.048 40.000 5.13 0.00 0.00 4.40
3206 5436 5.539955 AGACCCTTCAATTGTATTTGCACTT 59.460 36.000 5.13 0.00 0.00 3.16
3207 5437 6.719370 AGACCCTTCAATTGTATTTGCACTTA 59.281 34.615 5.13 0.00 0.00 2.24
3208 5438 6.924111 ACCCTTCAATTGTATTTGCACTTAG 58.076 36.000 5.13 0.00 0.00 2.18
3209 5439 5.807011 CCCTTCAATTGTATTTGCACTTAGC 59.193 40.000 5.13 0.00 45.96 3.09
3210 5440 6.350445 CCCTTCAATTGTATTTGCACTTAGCT 60.350 38.462 5.13 0.00 45.94 3.32
3211 5441 7.092716 CCTTCAATTGTATTTGCACTTAGCTT 58.907 34.615 5.13 0.00 45.94 3.74
3212 5442 7.062605 CCTTCAATTGTATTTGCACTTAGCTTG 59.937 37.037 5.13 0.00 45.94 4.01
3213 5443 6.389091 TCAATTGTATTTGCACTTAGCTTGG 58.611 36.000 5.13 0.00 45.94 3.61
3214 5444 6.208402 TCAATTGTATTTGCACTTAGCTTGGA 59.792 34.615 5.13 0.00 45.94 3.53
3215 5445 6.588719 ATTGTATTTGCACTTAGCTTGGAA 57.411 33.333 0.00 0.00 45.94 3.53
3216 5446 6.398234 TTGTATTTGCACTTAGCTTGGAAA 57.602 33.333 6.10 6.10 45.94 3.13
3217 5447 5.768317 TGTATTTGCACTTAGCTTGGAAAC 58.232 37.500 5.80 0.00 45.94 2.78
3218 5448 5.534654 TGTATTTGCACTTAGCTTGGAAACT 59.465 36.000 5.80 0.38 45.94 2.66
3219 5449 4.568152 TTTGCACTTAGCTTGGAAACTC 57.432 40.909 0.00 0.00 45.94 3.01
3220 5450 3.207265 TGCACTTAGCTTGGAAACTCA 57.793 42.857 0.00 0.00 45.94 3.41
3221 5451 3.141398 TGCACTTAGCTTGGAAACTCAG 58.859 45.455 0.00 0.00 45.94 3.35
3222 5452 2.095516 GCACTTAGCTTGGAAACTCAGC 60.096 50.000 0.00 0.00 41.15 4.26
3223 5453 3.406764 CACTTAGCTTGGAAACTCAGCT 58.593 45.455 0.00 0.00 45.82 4.24
3224 5454 4.569943 CACTTAGCTTGGAAACTCAGCTA 58.430 43.478 0.00 0.00 43.32 3.32
3225 5455 5.181748 CACTTAGCTTGGAAACTCAGCTAT 58.818 41.667 0.00 0.00 44.33 2.97
3226 5456 5.645497 CACTTAGCTTGGAAACTCAGCTATT 59.355 40.000 0.00 0.00 44.33 1.73
3227 5457 6.818644 CACTTAGCTTGGAAACTCAGCTATTA 59.181 38.462 0.00 0.00 44.33 0.98
3228 5458 7.497249 CACTTAGCTTGGAAACTCAGCTATTAT 59.503 37.037 0.00 0.00 44.33 1.28
3229 5459 7.497249 ACTTAGCTTGGAAACTCAGCTATTATG 59.503 37.037 0.00 0.00 44.33 1.90
3230 5460 5.128919 AGCTTGGAAACTCAGCTATTATGG 58.871 41.667 0.00 0.00 43.32 2.74
3231 5461 4.276926 GCTTGGAAACTCAGCTATTATGGG 59.723 45.833 0.00 0.00 35.27 4.00
3232 5462 5.440610 CTTGGAAACTCAGCTATTATGGGT 58.559 41.667 0.00 0.00 30.88 4.51
3233 5463 4.780815 TGGAAACTCAGCTATTATGGGTG 58.219 43.478 1.26 1.26 29.85 4.61
3234 5464 3.565902 GGAAACTCAGCTATTATGGGTGC 59.434 47.826 2.86 0.00 29.85 5.01
3235 5465 2.533266 ACTCAGCTATTATGGGTGCG 57.467 50.000 2.86 0.00 27.65 5.34
3236 5466 2.039418 ACTCAGCTATTATGGGTGCGA 58.961 47.619 4.87 0.00 27.65 5.10
3237 5467 2.434336 ACTCAGCTATTATGGGTGCGAA 59.566 45.455 4.87 0.00 27.65 4.70
3238 5468 3.062763 CTCAGCTATTATGGGTGCGAAG 58.937 50.000 2.86 0.00 32.94 3.79
3239 5469 2.146342 CAGCTATTATGGGTGCGAAGG 58.854 52.381 0.00 0.00 0.00 3.46
3240 5470 1.072331 AGCTATTATGGGTGCGAAGGG 59.928 52.381 0.00 0.00 0.00 3.95
3241 5471 1.523758 CTATTATGGGTGCGAAGGGC 58.476 55.000 0.00 0.00 43.96 5.19
3242 5472 1.072331 CTATTATGGGTGCGAAGGGCT 59.928 52.381 0.00 0.00 44.05 5.19
3243 5473 0.466189 ATTATGGGTGCGAAGGGCTG 60.466 55.000 0.00 0.00 44.05 4.85
3244 5474 1.558167 TTATGGGTGCGAAGGGCTGA 61.558 55.000 0.00 0.00 44.05 4.26
3245 5475 1.344953 TATGGGTGCGAAGGGCTGAT 61.345 55.000 0.00 0.00 44.05 2.90
3246 5476 2.825836 GGGTGCGAAGGGCTGATG 60.826 66.667 0.00 0.00 44.05 3.07
3247 5477 3.512516 GGTGCGAAGGGCTGATGC 61.513 66.667 0.00 0.00 44.05 3.91
3248 5478 3.869272 GTGCGAAGGGCTGATGCG 61.869 66.667 0.00 0.00 44.05 4.73
3250 5480 4.838152 GCGAAGGGCTGATGCGGA 62.838 66.667 0.00 0.00 40.82 5.54
3251 5481 2.587194 CGAAGGGCTGATGCGGAG 60.587 66.667 0.00 0.00 40.82 4.63
3252 5482 2.203126 GAAGGGCTGATGCGGAGG 60.203 66.667 0.00 0.00 40.82 4.30
3253 5483 4.496336 AAGGGCTGATGCGGAGGC 62.496 66.667 0.00 0.00 40.82 4.70
3256 5486 4.496336 GGCTGATGCGGAGGCCTT 62.496 66.667 6.77 0.00 41.20 4.35
3257 5487 3.207669 GCTGATGCGGAGGCCTTG 61.208 66.667 6.77 3.69 38.85 3.61
3258 5488 2.586245 CTGATGCGGAGGCCTTGA 59.414 61.111 6.77 0.00 38.85 3.02
3259 5489 1.817099 CTGATGCGGAGGCCTTGAC 60.817 63.158 6.77 0.00 38.85 3.18
3260 5490 2.514824 GATGCGGAGGCCTTGACC 60.515 66.667 6.77 1.90 38.85 4.02
3261 5491 4.115199 ATGCGGAGGCCTTGACCC 62.115 66.667 6.77 1.44 38.85 4.46
3263 5493 4.475135 GCGGAGGCCTTGACCCTC 62.475 72.222 6.77 0.00 46.54 4.30
3266 5496 2.579738 GAGGCCTTGACCCTCGTC 59.420 66.667 6.77 0.00 39.50 4.20
3267 5497 3.358076 GAGGCCTTGACCCTCGTCG 62.358 68.421 6.77 0.00 42.37 5.12
3268 5498 4.452733 GGCCTTGACCCTCGTCGG 62.453 72.222 0.00 0.00 42.37 4.79
3270 5500 4.796231 CCTTGACCCTCGTCGGCG 62.796 72.222 1.15 1.15 42.37 6.46
3271 5501 4.796231 CTTGACCCTCGTCGGCGG 62.796 72.222 10.62 0.00 42.37 6.13
3278 5508 4.201679 CTCGTCGGCGGCCATGTA 62.202 66.667 20.71 0.15 38.89 2.29
3279 5509 4.201679 TCGTCGGCGGCCATGTAG 62.202 66.667 20.71 1.74 38.89 2.74
3281 5511 4.910585 GTCGGCGGCCATGTAGGG 62.911 72.222 20.71 0.11 38.09 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 9 4.087892 CCTCAGGCTCCCACCACG 62.088 72.222 0.00 0.00 0.00 4.94
40 44 1.152963 GCAACCCCGGTGCATCTAT 60.153 57.895 10.45 0.00 0.00 1.98
48 52 4.660938 GAGGCAAGCAACCCCGGT 62.661 66.667 0.00 0.00 0.00 5.28
95 100 1.225426 GGCAGATGTGGATGAGGCA 59.775 57.895 0.00 0.00 0.00 4.75
197 202 1.079127 CAACCAGAAGACCGCCGAT 60.079 57.895 0.00 0.00 0.00 4.18
421 426 3.390521 TGCCCGTCGCATCCTCTT 61.391 61.111 0.00 0.00 44.64 2.85
502 511 6.239430 CCAAATTCCTAGATCGAGATTCAGGA 60.239 42.308 4.15 10.65 32.56 3.86
544 557 2.769095 AGTCTTCCCTCACCTATTCTGC 59.231 50.000 0.00 0.00 0.00 4.26
549 562 3.491766 TCCAAGTCTTCCCTCACCTAT 57.508 47.619 0.00 0.00 0.00 2.57
570 584 8.051535 TCAGATAAATGCAATCCTTTCTCTTCT 58.948 33.333 0.00 0.00 0.00 2.85
575 589 9.638176 AGTATTCAGATAAATGCAATCCTTTCT 57.362 29.630 0.00 0.00 0.00 2.52
585 599 6.909357 GTGCAGTTCAGTATTCAGATAAATGC 59.091 38.462 0.00 0.00 0.00 3.56
590 604 6.701340 ACAAGTGCAGTTCAGTATTCAGATA 58.299 36.000 3.08 0.00 0.00 1.98
594 608 6.765989 ACTAAACAAGTGCAGTTCAGTATTCA 59.234 34.615 3.08 0.00 36.93 2.57
595 609 7.190920 ACTAAACAAGTGCAGTTCAGTATTC 57.809 36.000 3.08 0.00 36.93 1.75
596 610 6.204882 GGACTAAACAAGTGCAGTTCAGTATT 59.795 38.462 3.08 1.74 45.40 1.89
597 611 5.701290 GGACTAAACAAGTGCAGTTCAGTAT 59.299 40.000 3.08 0.00 45.40 2.12
598 612 5.054477 GGACTAAACAAGTGCAGTTCAGTA 58.946 41.667 3.08 0.00 45.40 2.74
599 613 3.877508 GGACTAAACAAGTGCAGTTCAGT 59.122 43.478 3.08 5.53 45.40 3.41
600 614 3.059597 CGGACTAAACAAGTGCAGTTCAG 60.060 47.826 3.08 2.34 46.35 3.02
601 615 2.869801 CGGACTAAACAAGTGCAGTTCA 59.130 45.455 3.08 0.00 46.35 3.18
602 616 2.349532 GCGGACTAAACAAGTGCAGTTC 60.350 50.000 3.08 0.00 46.35 3.01
603 617 1.602377 GCGGACTAAACAAGTGCAGTT 59.398 47.619 0.00 0.00 46.35 3.16
604 618 1.202651 AGCGGACTAAACAAGTGCAGT 60.203 47.619 0.00 0.00 46.35 4.40
605 619 1.195448 CAGCGGACTAAACAAGTGCAG 59.805 52.381 0.00 0.00 46.35 4.41
606 620 1.225855 CAGCGGACTAAACAAGTGCA 58.774 50.000 0.00 0.00 46.35 4.57
607 621 0.110192 GCAGCGGACTAAACAAGTGC 60.110 55.000 0.00 0.00 42.81 4.40
608 622 1.195448 CAGCAGCGGACTAAACAAGTG 59.805 52.381 0.00 0.00 39.07 3.16
609 623 1.202651 ACAGCAGCGGACTAAACAAGT 60.203 47.619 0.00 0.00 42.80 3.16
610 624 1.461127 GACAGCAGCGGACTAAACAAG 59.539 52.381 0.00 0.00 0.00 3.16
611 625 1.070134 AGACAGCAGCGGACTAAACAA 59.930 47.619 0.00 0.00 0.00 2.83
612 626 0.679505 AGACAGCAGCGGACTAAACA 59.320 50.000 0.00 0.00 0.00 2.83
613 627 1.336887 TGAGACAGCAGCGGACTAAAC 60.337 52.381 0.00 0.00 0.00 2.01
614 628 0.966179 TGAGACAGCAGCGGACTAAA 59.034 50.000 0.00 0.00 0.00 1.85
615 629 0.528017 CTGAGACAGCAGCGGACTAA 59.472 55.000 0.00 0.00 0.00 2.24
616 630 2.184323 CTGAGACAGCAGCGGACTA 58.816 57.895 0.00 0.00 0.00 2.59
617 631 2.969016 CTGAGACAGCAGCGGACT 59.031 61.111 0.00 0.00 0.00 3.85
626 640 1.535649 CGCCTACTGATGCTGAGACAG 60.536 57.143 0.00 0.00 37.62 3.51
627 641 0.457443 CGCCTACTGATGCTGAGACA 59.543 55.000 0.00 0.00 0.00 3.41
628 642 0.873743 GCGCCTACTGATGCTGAGAC 60.874 60.000 0.00 0.00 0.00 3.36
629 643 1.439228 GCGCCTACTGATGCTGAGA 59.561 57.895 0.00 0.00 0.00 3.27
630 644 1.948138 CGCGCCTACTGATGCTGAG 60.948 63.158 0.00 0.00 0.00 3.35
631 645 2.104928 CGCGCCTACTGATGCTGA 59.895 61.111 0.00 0.00 0.00 4.26
632 646 2.104928 TCGCGCCTACTGATGCTG 59.895 61.111 0.00 0.00 0.00 4.41
633 647 2.105128 GTCGCGCCTACTGATGCT 59.895 61.111 0.00 0.00 0.00 3.79
634 648 1.809619 TTGTCGCGCCTACTGATGC 60.810 57.895 0.00 0.00 0.00 3.91
635 649 1.421410 GGTTGTCGCGCCTACTGATG 61.421 60.000 0.00 0.00 0.00 3.07
636 650 1.153628 GGTTGTCGCGCCTACTGAT 60.154 57.895 0.00 0.00 0.00 2.90
637 651 2.260434 GGTTGTCGCGCCTACTGA 59.740 61.111 0.00 0.00 0.00 3.41
638 652 2.813908 GGGTTGTCGCGCCTACTG 60.814 66.667 0.00 0.00 0.00 2.74
639 653 4.078516 GGGGTTGTCGCGCCTACT 62.079 66.667 0.00 0.00 38.31 2.57
640 654 3.887335 TTGGGGTTGTCGCGCCTAC 62.887 63.158 0.00 0.00 41.45 3.18
641 655 3.599285 CTTGGGGTTGTCGCGCCTA 62.599 63.158 0.00 0.00 41.45 3.93
646 660 4.966787 TGGGCTTGGGGTTGTCGC 62.967 66.667 0.00 0.00 0.00 5.19
647 661 1.395826 TTTTGGGCTTGGGGTTGTCG 61.396 55.000 0.00 0.00 0.00 4.35
648 662 0.833949 TTTTTGGGCTTGGGGTTGTC 59.166 50.000 0.00 0.00 0.00 3.18
649 663 1.419762 GATTTTTGGGCTTGGGGTTGT 59.580 47.619 0.00 0.00 0.00 3.32
650 664 1.607767 CGATTTTTGGGCTTGGGGTTG 60.608 52.381 0.00 0.00 0.00 3.77
651 665 0.684535 CGATTTTTGGGCTTGGGGTT 59.315 50.000 0.00 0.00 0.00 4.11
670 684 6.552295 CCTTTTGGGTATGGGACAGTTACAC 61.552 48.000 0.00 0.00 37.70 2.90
671 685 4.507691 CCTTTTGGGTATGGGACAGTTACA 60.508 45.833 0.00 0.00 37.70 2.41
705 719 7.743116 TTCCTACCCATTACTACTGATTTGA 57.257 36.000 0.00 0.00 0.00 2.69
738 752 2.322355 ATGGAAGCAAGATCTGGTCG 57.678 50.000 0.00 0.00 33.58 4.79
783 797 6.551385 AAAAATACTCAGCAGAAGTCAGTG 57.449 37.500 0.00 0.00 0.00 3.66
860 875 0.179129 GGATGCGGCCTTGAATGTTG 60.179 55.000 0.00 0.00 0.00 3.33
1085 1100 3.861840 GACCAAATCGATCAGACCAGAA 58.138 45.455 0.00 0.00 0.00 3.02
1107 1122 1.136147 CGCCACAGCAAGATTCAGC 59.864 57.895 0.00 0.00 39.83 4.26
1139 1154 1.284657 CACTATCCGCTGCACAAGAG 58.715 55.000 0.00 0.00 0.00 2.85
1399 1425 2.223525 GCTTCATTCTGCTGGCTCATTC 60.224 50.000 0.00 0.00 0.00 2.67
1416 1452 1.134907 CAGAACCAATGGCATGGCTTC 60.135 52.381 21.08 14.54 44.75 3.86
1418 1454 0.040058 TCAGAACCAATGGCATGGCT 59.960 50.000 21.08 3.03 44.75 4.75
1419 1455 0.896923 TTCAGAACCAATGGCATGGC 59.103 50.000 13.29 13.29 44.75 4.40
1420 1456 2.660189 GTTCAGAACCAATGGCATGG 57.340 50.000 0.00 7.58 46.38 3.66
1455 1491 3.686016 CAAGGGGCTAAAAAGCTACAGA 58.314 45.455 0.00 0.00 34.73 3.41
1590 1627 5.682234 TCCACTATGTCTATATGGGCATG 57.318 43.478 15.73 8.54 0.00 4.06
1620 1657 9.997482 TCAAATCAAAAGTACAGTACTGAAAAC 57.003 29.630 29.30 21.04 39.39 2.43
1651 1705 4.549458 CACTCAAGCAATCGGAAAACAAT 58.451 39.130 0.00 0.00 0.00 2.71
1656 1710 0.881118 GGCACTCAAGCAATCGGAAA 59.119 50.000 0.00 0.00 35.83 3.13
1660 1714 0.167470 CACAGGCACTCAAGCAATCG 59.833 55.000 0.00 0.00 34.60 3.34
1664 1718 0.181114 AGAACACAGGCACTCAAGCA 59.819 50.000 0.00 0.00 34.60 3.91
1676 1730 8.845227 TCTAAAATTATTGCAGTTCAGAACACA 58.155 29.630 15.85 10.12 0.00 3.72
1677 1731 9.846248 ATCTAAAATTATTGCAGTTCAGAACAC 57.154 29.630 15.85 7.63 0.00 3.32
1695 1749 5.163513 CGGTGCTTTGCTTTGATCTAAAAT 58.836 37.500 0.00 0.00 0.00 1.82
1702 1756 0.242017 GAGCGGTGCTTTGCTTTGAT 59.758 50.000 0.00 0.00 42.60 2.57
1705 1759 1.181098 ATGGAGCGGTGCTTTGCTTT 61.181 50.000 7.84 0.00 42.60 3.51
1717 1771 5.069501 TCTCATCTCATCAATATGGAGCG 57.930 43.478 0.00 0.00 33.61 5.03
1719 1773 8.478877 TCATCATCTCATCTCATCAATATGGAG 58.521 37.037 0.00 0.00 33.61 3.86
1847 1901 8.798402 ACCCTAATTTCACGACAATCAAATAAA 58.202 29.630 0.00 0.00 0.00 1.40
1861 1915 4.055360 GTTGCCACAAACCCTAATTTCAC 58.945 43.478 0.00 0.00 0.00 3.18
1868 1922 0.402504 ATCGGTTGCCACAAACCCTA 59.597 50.000 0.69 0.00 45.83 3.53
1872 1926 0.387565 ACCAATCGGTTGCCACAAAC 59.612 50.000 1.86 0.00 46.31 2.93
1956 2013 2.428890 CTGGCTAGTACTCTGGTGGAAG 59.571 54.545 0.00 0.00 0.00 3.46
1962 2019 5.073428 TCACATATCTGGCTAGTACTCTGG 58.927 45.833 0.00 0.00 0.00 3.86
2122 4329 3.758300 CACTTTTTATTTCCTCGCGCAT 58.242 40.909 8.75 0.00 0.00 4.73
2337 4544 1.367346 TGGAGTTGGGAAGCCACATA 58.633 50.000 0.00 0.00 0.00 2.29
2504 4711 7.926674 TCGATATATGAAATCAATGGCATGT 57.073 32.000 0.00 0.00 0.00 3.21
2527 4734 6.198966 CACAAAAACAGCACCTGAAATACTTC 59.801 38.462 0.00 0.00 35.18 3.01
2531 4738 5.843673 TCACAAAAACAGCACCTGAAATA 57.156 34.783 0.00 0.00 35.18 1.40
2535 4742 3.286353 TGATCACAAAAACAGCACCTGA 58.714 40.909 0.00 0.00 35.18 3.86
2857 5080 7.288621 CCAATATCCAAAAGCTCCCTAAAATCT 59.711 37.037 0.00 0.00 0.00 2.40
2895 5118 4.003788 CCCGTGCAACCGTCTCCT 62.004 66.667 0.00 0.00 0.00 3.69
3060 5289 5.510179 CGTAACAAGGTCTTAGGTTCCAAGA 60.510 44.000 0.00 0.00 0.00 3.02
3175 5405 8.025445 CAAATACAATTGAAGGGTCTGAAAGAG 58.975 37.037 13.59 0.00 36.54 2.85
3176 5406 7.523709 GCAAATACAATTGAAGGGTCTGAAAGA 60.524 37.037 13.59 0.00 34.39 2.52
3177 5407 6.587608 GCAAATACAATTGAAGGGTCTGAAAG 59.412 38.462 13.59 0.00 31.84 2.62
3178 5408 6.041409 TGCAAATACAATTGAAGGGTCTGAAA 59.959 34.615 13.59 0.00 31.84 2.69
3179 5409 5.538053 TGCAAATACAATTGAAGGGTCTGAA 59.462 36.000 13.59 0.00 31.84 3.02
3180 5410 5.048083 GTGCAAATACAATTGAAGGGTCTGA 60.048 40.000 13.59 0.00 31.84 3.27
3181 5411 5.047802 AGTGCAAATACAATTGAAGGGTCTG 60.048 40.000 13.59 1.38 31.84 3.51
3182 5412 5.079643 AGTGCAAATACAATTGAAGGGTCT 58.920 37.500 13.59 0.00 31.84 3.85
3183 5413 5.391312 AGTGCAAATACAATTGAAGGGTC 57.609 39.130 13.59 0.00 31.84 4.46
3184 5414 5.806654 AAGTGCAAATACAATTGAAGGGT 57.193 34.783 13.59 0.00 31.84 4.34
3185 5415 5.807011 GCTAAGTGCAAATACAATTGAAGGG 59.193 40.000 13.59 0.00 42.31 3.95
3186 5416 6.624423 AGCTAAGTGCAAATACAATTGAAGG 58.376 36.000 13.59 0.00 45.94 3.46
3187 5417 7.062605 CCAAGCTAAGTGCAAATACAATTGAAG 59.937 37.037 13.59 0.00 45.94 3.02
3188 5418 6.867816 CCAAGCTAAGTGCAAATACAATTGAA 59.132 34.615 13.59 0.00 45.94 2.69
3189 5419 6.208402 TCCAAGCTAAGTGCAAATACAATTGA 59.792 34.615 13.59 0.00 45.94 2.57
3190 5420 6.389091 TCCAAGCTAAGTGCAAATACAATTG 58.611 36.000 3.24 3.24 45.94 2.32
3191 5421 6.588719 TCCAAGCTAAGTGCAAATACAATT 57.411 33.333 0.00 0.00 45.94 2.32
3192 5422 6.588719 TTCCAAGCTAAGTGCAAATACAAT 57.411 33.333 0.00 0.00 45.94 2.71
3193 5423 6.040391 AGTTTCCAAGCTAAGTGCAAATACAA 59.960 34.615 0.00 0.00 45.94 2.41
3194 5424 5.534654 AGTTTCCAAGCTAAGTGCAAATACA 59.465 36.000 0.00 0.00 45.94 2.29
3195 5425 6.013842 AGTTTCCAAGCTAAGTGCAAATAC 57.986 37.500 0.00 0.00 45.94 1.89
3196 5426 5.767665 TGAGTTTCCAAGCTAAGTGCAAATA 59.232 36.000 0.00 0.00 45.94 1.40
3197 5427 4.584325 TGAGTTTCCAAGCTAAGTGCAAAT 59.416 37.500 0.00 0.00 45.94 2.32
3198 5428 3.951037 TGAGTTTCCAAGCTAAGTGCAAA 59.049 39.130 0.00 0.00 45.94 3.68
3199 5429 3.550820 TGAGTTTCCAAGCTAAGTGCAA 58.449 40.909 0.00 0.00 45.94 4.08
3200 5430 3.141398 CTGAGTTTCCAAGCTAAGTGCA 58.859 45.455 0.00 0.00 45.94 4.57
3201 5431 2.095516 GCTGAGTTTCCAAGCTAAGTGC 60.096 50.000 0.00 0.00 43.29 4.40
3202 5432 3.406764 AGCTGAGTTTCCAAGCTAAGTG 58.593 45.455 0.00 0.00 33.70 3.16
3203 5433 3.778954 AGCTGAGTTTCCAAGCTAAGT 57.221 42.857 0.00 0.00 33.70 2.24
3204 5434 7.041508 CCATAATAGCTGAGTTTCCAAGCTAAG 60.042 40.741 7.62 0.20 40.75 2.18
3205 5435 6.767902 CCATAATAGCTGAGTTTCCAAGCTAA 59.232 38.462 7.62 0.00 40.75 3.09
3206 5436 6.291377 CCATAATAGCTGAGTTTCCAAGCTA 58.709 40.000 6.12 6.12 41.47 3.32
3207 5437 5.128919 CCATAATAGCTGAGTTTCCAAGCT 58.871 41.667 0.00 1.63 39.36 3.74
3208 5438 4.276926 CCCATAATAGCTGAGTTTCCAAGC 59.723 45.833 0.00 0.00 0.00 4.01
3209 5439 5.297776 CACCCATAATAGCTGAGTTTCCAAG 59.702 44.000 0.00 0.00 0.00 3.61
3210 5440 5.192927 CACCCATAATAGCTGAGTTTCCAA 58.807 41.667 0.00 0.00 0.00 3.53
3211 5441 4.780815 CACCCATAATAGCTGAGTTTCCA 58.219 43.478 0.00 0.00 0.00 3.53
3212 5442 3.565902 GCACCCATAATAGCTGAGTTTCC 59.434 47.826 0.00 0.00 0.00 3.13
3213 5443 3.248602 CGCACCCATAATAGCTGAGTTTC 59.751 47.826 0.00 0.00 0.00 2.78
3214 5444 3.118408 TCGCACCCATAATAGCTGAGTTT 60.118 43.478 0.00 0.00 0.00 2.66
3215 5445 2.434336 TCGCACCCATAATAGCTGAGTT 59.566 45.455 0.00 0.00 0.00 3.01
3216 5446 2.039418 TCGCACCCATAATAGCTGAGT 58.961 47.619 0.00 0.00 0.00 3.41
3217 5447 2.820059 TCGCACCCATAATAGCTGAG 57.180 50.000 0.00 0.00 0.00 3.35
3218 5448 2.224281 CCTTCGCACCCATAATAGCTGA 60.224 50.000 0.00 0.00 0.00 4.26
3219 5449 2.146342 CCTTCGCACCCATAATAGCTG 58.854 52.381 0.00 0.00 0.00 4.24
3220 5450 1.072331 CCCTTCGCACCCATAATAGCT 59.928 52.381 0.00 0.00 0.00 3.32
3221 5451 1.523758 CCCTTCGCACCCATAATAGC 58.476 55.000 0.00 0.00 0.00 2.97
3222 5452 1.072331 AGCCCTTCGCACCCATAATAG 59.928 52.381 0.00 0.00 41.38 1.73
3223 5453 1.136828 AGCCCTTCGCACCCATAATA 58.863 50.000 0.00 0.00 41.38 0.98
3224 5454 0.466189 CAGCCCTTCGCACCCATAAT 60.466 55.000 0.00 0.00 41.38 1.28
3225 5455 1.077787 CAGCCCTTCGCACCCATAA 60.078 57.895 0.00 0.00 41.38 1.90
3226 5456 1.344953 ATCAGCCCTTCGCACCCATA 61.345 55.000 0.00 0.00 41.38 2.74
3227 5457 2.683465 ATCAGCCCTTCGCACCCAT 61.683 57.895 0.00 0.00 41.38 4.00
3228 5458 3.329889 ATCAGCCCTTCGCACCCA 61.330 61.111 0.00 0.00 41.38 4.51
3229 5459 2.825836 CATCAGCCCTTCGCACCC 60.826 66.667 0.00 0.00 41.38 4.61
3230 5460 3.512516 GCATCAGCCCTTCGCACC 61.513 66.667 0.00 0.00 41.38 5.01
3231 5461 3.869272 CGCATCAGCCCTTCGCAC 61.869 66.667 0.00 0.00 41.38 5.34
3233 5463 4.838152 TCCGCATCAGCCCTTCGC 62.838 66.667 0.00 0.00 37.52 4.70
3234 5464 2.587194 CTCCGCATCAGCCCTTCG 60.587 66.667 0.00 0.00 37.52 3.79
3235 5465 2.203126 CCTCCGCATCAGCCCTTC 60.203 66.667 0.00 0.00 37.52 3.46
3236 5466 4.496336 GCCTCCGCATCAGCCCTT 62.496 66.667 0.00 0.00 37.52 3.95
3239 5469 4.496336 AAGGCCTCCGCATCAGCC 62.496 66.667 5.23 0.00 46.13 4.85
3240 5470 3.207669 CAAGGCCTCCGCATCAGC 61.208 66.667 5.23 0.00 36.38 4.26
3241 5471 1.817099 GTCAAGGCCTCCGCATCAG 60.817 63.158 5.23 0.00 36.38 2.90
3242 5472 2.268920 GTCAAGGCCTCCGCATCA 59.731 61.111 5.23 0.00 36.38 3.07
3243 5473 2.514824 GGTCAAGGCCTCCGCATC 60.515 66.667 5.23 0.00 36.38 3.91
3244 5474 4.115199 GGGTCAAGGCCTCCGCAT 62.115 66.667 5.23 0.00 36.38 4.73
3246 5476 4.475135 GAGGGTCAAGGCCTCCGC 62.475 72.222 5.23 0.00 0.00 5.54
3247 5477 4.148825 CGAGGGTCAAGGCCTCCG 62.149 72.222 5.23 0.00 0.00 4.63
3248 5478 3.003763 ACGAGGGTCAAGGCCTCC 61.004 66.667 5.23 2.14 0.00 4.30
3249 5479 2.579738 GACGAGGGTCAAGGCCTC 59.420 66.667 5.23 0.00 42.91 4.70
3250 5480 3.382832 CGACGAGGGTCAAGGCCT 61.383 66.667 0.00 0.00 43.61 5.19
3251 5481 4.452733 CCGACGAGGGTCAAGGCC 62.453 72.222 0.00 0.00 43.61 5.19
3253 5483 4.796231 CGCCGACGAGGGTCAAGG 62.796 72.222 0.00 0.00 43.61 3.61
3254 5484 4.796231 CCGCCGACGAGGGTCAAG 62.796 72.222 0.00 0.00 43.61 3.02
3261 5491 4.201679 TACATGGCCGCCGACGAG 62.202 66.667 4.58 0.00 43.93 4.18
3262 5492 4.201679 CTACATGGCCGCCGACGA 62.202 66.667 4.58 0.00 43.93 4.20
3264 5494 4.910585 CCCTACATGGCCGCCGAC 62.911 72.222 4.58 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.