Multiple sequence alignment - TraesCS1D01G044700

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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 TraesCS1D01G044700 chr1D 100.000 2906 0 0 1 2906 24126713 24123808 0.000000e+00 5367.0
1 TraesCS1D01G044700 chr1D 95.425 1399 48 4 635 2019 23999175 23997779 0.000000e+00 2215.0
2 TraesCS1D01G044700 chr1D 96.512 516 17 1 2 516 23999678 23999163 0.000000e+00 852.0
3 TraesCS1D01G044700 chr1D 85.675 733 48 27 2225 2906 23997294 23996568 0.000000e+00 719.0
4 TraesCS1D01G044700 chr1D 95.946 74 3 0 2829 2902 23435654 23435727 1.410000e-23 121.0
5 TraesCS1D01G044700 chr1A 92.928 1414 64 11 635 2025 24945087 24943687 0.000000e+00 2025.0
6 TraesCS1D01G044700 chr1A 89.163 526 46 7 2 516 24945600 24945075 0.000000e+00 645.0
7 TraesCS1D01G044700 chr1A 89.205 352 17 7 2571 2902 24942797 24942447 1.250000e-113 420.0
8 TraesCS1D01G044700 chr1A 92.857 154 10 1 2571 2724 24943170 24943018 3.770000e-54 222.0
9 TraesCS1D01G044700 chr1A 81.022 274 32 12 2088 2342 24943688 24943416 1.770000e-47 200.0
10 TraesCS1D01G044700 chr1A 92.135 89 5 1 2509 2595 24943256 24943168 1.090000e-24 124.0
11 TraesCS1D01G044700 chr1A 95.946 74 3 0 2829 2902 24561678 24561751 1.410000e-23 121.0
12 TraesCS1D01G044700 chr1A 93.243 74 5 0 2829 2902 24773104 24773031 3.060000e-20 110.0
13 TraesCS1D01G044700 chr1A 95.588 68 1 1 2024 2089 566654363 566654430 1.100000e-19 108.0
14 TraesCS1D01G044700 chr1A 95.522 67 2 1 2024 2089 516154144 516154078 3.960000e-19 106.0
15 TraesCS1D01G044700 chr1A 96.491 57 2 0 2539 2595 24942851 24942795 8.570000e-16 95.3
16 TraesCS1D01G044700 chr1A 96.491 57 2 0 2539 2595 24943014 24942958 8.570000e-16 95.3
17 TraesCS1D01G044700 chr1B 94.592 980 38 3 635 1602 39656774 39655798 0.000000e+00 1502.0
18 TraesCS1D01G044700 chr1B 95.930 516 20 1 2 516 39657277 39656762 0.000000e+00 835.0
19 TraesCS1D01G044700 chr1B 98.204 167 3 0 1436 1602 39582056 39582222 2.830000e-75 292.0
20 TraesCS1D01G044700 chr1B 94.286 70 2 1 2021 2090 512159346 512159279 3.960000e-19 106.0
21 TraesCS1D01G044700 chr5A 87.511 1161 119 13 798 1935 656937018 656935861 0.000000e+00 1317.0
22 TraesCS1D01G044700 chr5A 95.522 67 1 1 2023 2089 625031363 625031299 3.960000e-19 106.0
23 TraesCS1D01G044700 chr5B 86.942 1187 120 18 798 1962 665811659 665810486 0.000000e+00 1301.0
24 TraesCS1D01G044700 chr5B 90.411 73 7 0 2024 2096 618253273 618253201 2.380000e-16 97.1
25 TraesCS1D01G044700 chr3D 88.645 1048 94 7 932 1964 108571255 108572292 0.000000e+00 1253.0
26 TraesCS1D01G044700 chr3D 92.000 125 9 1 515 639 384001173 384001050 1.070000e-39 174.0
27 TraesCS1D01G044700 chr3D 92.000 125 9 1 515 639 471419929 471419806 1.070000e-39 174.0
28 TraesCS1D01G044700 chr3D 96.970 66 1 1 2024 2089 36571511 36571447 3.060000e-20 110.0
29 TraesCS1D01G044700 chr3B 88.149 886 91 4 1059 1932 160138195 160139078 0.000000e+00 1042.0
30 TraesCS1D01G044700 chr3B 89.744 78 4 3 2020 2093 765604972 765604895 2.380000e-16 97.1
31 TraesCS1D01G044700 chr7D 95.489 133 4 2 508 639 550890975 550890844 8.160000e-51 211.0
32 TraesCS1D01G044700 chr2A 93.600 125 7 1 515 639 307690462 307690585 4.950000e-43 185.0
33 TraesCS1D01G044700 chr7A 92.000 125 9 1 515 639 40536464 40536341 1.070000e-39 174.0
34 TraesCS1D01G044700 chr7A 90.625 128 10 2 515 641 567451277 567451151 4.980000e-38 169.0
35 TraesCS1D01G044700 chr4B 91.200 125 10 1 515 639 174700685 174700808 4.980000e-38 169.0
36 TraesCS1D01G044700 chr4A 91.200 125 10 1 515 639 617221885 617221762 4.980000e-38 169.0
37 TraesCS1D01G044700 chr3A 90.476 126 10 2 515 639 323392883 323393007 6.440000e-37 165.0
38 TraesCS1D01G044700 chr2B 97.059 68 0 1 2024 2089 440816007 440815940 2.370000e-21 113.0
39 TraesCS1D01G044700 chrUn 92.208 77 4 2 2024 2099 188193928 188193853 1.100000e-19 108.0


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 TraesCS1D01G044700 chr1D 24123808 24126713 2905 True 5367.000 5367 100.000000 1 2906 1 chr1D.!!$R1 2905
1 TraesCS1D01G044700 chr1D 23996568 23999678 3110 True 1262.000 2215 92.537333 2 2906 3 chr1D.!!$R2 2904
2 TraesCS1D01G044700 chr1A 24942447 24945600 3153 True 478.325 2025 91.286500 2 2902 8 chr1A.!!$R3 2900
3 TraesCS1D01G044700 chr1B 39655798 39657277 1479 True 1168.500 1502 95.261000 2 1602 2 chr1B.!!$R2 1600
4 TraesCS1D01G044700 chr5A 656935861 656937018 1157 True 1317.000 1317 87.511000 798 1935 1 chr5A.!!$R2 1137
5 TraesCS1D01G044700 chr5B 665810486 665811659 1173 True 1301.000 1301 86.942000 798 1962 1 chr5B.!!$R2 1164
6 TraesCS1D01G044700 chr3D 108571255 108572292 1037 False 1253.000 1253 88.645000 932 1964 1 chr3D.!!$F1 1032
7 TraesCS1D01G044700 chr3B 160138195 160139078 883 False 1042.000 1042 88.149000 1059 1932 1 chr3B.!!$F1 873

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
627 639 1.488812 TGAGGGTGTTGCAGTTAGTGT 59.511 47.619 0.0 0.0 0.0 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2358 2811 0.034186 GCCATGGACACCCTGAATGA 60.034 55.0 18.4 0.0 0.0 2.57 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
113 122 5.877012 AGTTGTGATGTTGATGATACTGTCC 59.123 40.000 0.00 0.00 0.00 4.02
205 214 3.127721 GCCTTATTGCTGTCTTGTCCTTC 59.872 47.826 0.00 0.00 0.00 3.46
206 215 4.326826 CCTTATTGCTGTCTTGTCCTTCA 58.673 43.478 0.00 0.00 0.00 3.02
293 302 1.901159 TGCCAATCACAATTTCCCTGG 59.099 47.619 0.00 0.00 0.00 4.45
364 374 8.606830 ACTATGGGAGAAGAGAAACAAGTTAAT 58.393 33.333 0.00 0.00 0.00 1.40
485 497 7.961326 ATTAGGCTAATTTTGTCACAGGATT 57.039 32.000 13.96 0.00 0.00 3.01
541 553 7.718272 TTTTCCAGAAAATGCAGAAGATTTG 57.282 32.000 1.45 0.00 35.57 2.32
542 554 4.813027 TCCAGAAAATGCAGAAGATTTGC 58.187 39.130 0.00 0.00 41.86 3.68
543 555 3.611113 CCAGAAAATGCAGAAGATTTGCG 59.389 43.478 0.00 0.00 44.40 4.85
544 556 4.232221 CAGAAAATGCAGAAGATTTGCGT 58.768 39.130 0.00 0.00 44.40 5.24
548 560 3.921119 ATGCAGAAGATTTGCGTTTCA 57.079 38.095 0.00 0.00 44.40 2.69
549 561 3.921119 TGCAGAAGATTTGCGTTTCAT 57.079 38.095 0.00 0.00 44.40 2.57
550 562 4.241590 TGCAGAAGATTTGCGTTTCATT 57.758 36.364 0.00 0.00 44.40 2.57
551 563 3.982701 TGCAGAAGATTTGCGTTTCATTG 59.017 39.130 0.00 0.00 44.40 2.82
552 564 3.181537 GCAGAAGATTTGCGTTTCATTGC 60.182 43.478 0.00 0.00 0.00 3.56
553 565 3.982701 CAGAAGATTTGCGTTTCATTGCA 59.017 39.130 0.00 0.00 39.81 4.08
554 566 4.624024 CAGAAGATTTGCGTTTCATTGCAT 59.376 37.500 0.00 0.00 41.42 3.96
555 567 5.119588 CAGAAGATTTGCGTTTCATTGCATT 59.880 36.000 0.00 0.00 41.42 3.56
556 568 4.914312 AGATTTGCGTTTCATTGCATTG 57.086 36.364 2.08 2.08 41.42 2.82
557 569 4.558178 AGATTTGCGTTTCATTGCATTGA 58.442 34.783 7.19 7.19 41.42 2.57
558 570 4.989797 AGATTTGCGTTTCATTGCATTGAA 59.010 33.333 17.74 17.74 41.42 2.69
559 571 5.466058 AGATTTGCGTTTCATTGCATTGAAA 59.534 32.000 25.34 25.34 41.92 2.69
560 572 5.475273 TTTGCGTTTCATTGCATTGAAAA 57.525 30.435 28.82 16.62 44.71 2.29
561 573 4.712191 TGCGTTTCATTGCATTGAAAAG 57.288 36.364 29.50 29.50 44.71 2.27
562 574 3.493877 TGCGTTTCATTGCATTGAAAAGG 59.506 39.130 31.90 26.38 44.71 3.11
563 575 3.740321 GCGTTTCATTGCATTGAAAAGGA 59.260 39.130 31.90 16.11 44.71 3.36
564 576 4.210955 GCGTTTCATTGCATTGAAAAGGAA 59.789 37.500 31.90 15.84 44.71 3.36
565 577 5.613142 GCGTTTCATTGCATTGAAAAGGAAG 60.613 40.000 31.90 22.66 44.71 3.46
566 578 5.107375 CGTTTCATTGCATTGAAAAGGAAGG 60.107 40.000 28.82 14.73 44.71 3.46
567 579 4.540359 TCATTGCATTGAAAAGGAAGGG 57.460 40.909 8.80 0.00 0.00 3.95
568 580 3.261390 TCATTGCATTGAAAAGGAAGGGG 59.739 43.478 8.80 0.00 0.00 4.79
569 581 2.397044 TGCATTGAAAAGGAAGGGGT 57.603 45.000 0.00 0.00 0.00 4.95
570 582 2.688477 TGCATTGAAAAGGAAGGGGTT 58.312 42.857 0.00 0.00 0.00 4.11
571 583 3.044894 TGCATTGAAAAGGAAGGGGTTT 58.955 40.909 0.00 0.00 0.00 3.27
572 584 3.457749 TGCATTGAAAAGGAAGGGGTTTT 59.542 39.130 0.00 0.00 0.00 2.43
573 585 4.065088 GCATTGAAAAGGAAGGGGTTTTC 58.935 43.478 0.00 0.00 41.22 2.29
574 586 4.444164 GCATTGAAAAGGAAGGGGTTTTCA 60.444 41.667 6.22 6.22 46.11 2.69
576 588 3.989056 TGAAAAGGAAGGGGTTTTCAGT 58.011 40.909 6.22 0.00 44.07 3.41
577 589 4.358214 TGAAAAGGAAGGGGTTTTCAGTT 58.642 39.130 6.22 0.00 44.07 3.16
578 590 5.520751 TGAAAAGGAAGGGGTTTTCAGTTA 58.479 37.500 6.22 0.00 44.07 2.24
579 591 5.361571 TGAAAAGGAAGGGGTTTTCAGTTAC 59.638 40.000 6.22 0.00 44.07 2.50
580 592 4.529716 AAGGAAGGGGTTTTCAGTTACA 57.470 40.909 0.00 0.00 0.00 2.41
581 593 4.741928 AGGAAGGGGTTTTCAGTTACAT 57.258 40.909 0.00 0.00 0.00 2.29
582 594 4.663334 AGGAAGGGGTTTTCAGTTACATC 58.337 43.478 0.00 0.00 0.00 3.06
583 595 4.105697 AGGAAGGGGTTTTCAGTTACATCA 59.894 41.667 0.00 0.00 0.00 3.07
584 596 5.016831 GGAAGGGGTTTTCAGTTACATCAT 58.983 41.667 0.00 0.00 0.00 2.45
585 597 5.125578 GGAAGGGGTTTTCAGTTACATCATC 59.874 44.000 0.00 0.00 0.00 2.92
586 598 4.600062 AGGGGTTTTCAGTTACATCATCC 58.400 43.478 0.00 0.00 0.00 3.51
587 599 4.292306 AGGGGTTTTCAGTTACATCATCCT 59.708 41.667 0.00 0.00 0.00 3.24
588 600 5.491078 AGGGGTTTTCAGTTACATCATCCTA 59.509 40.000 0.00 0.00 0.00 2.94
589 601 5.823045 GGGGTTTTCAGTTACATCATCCTAG 59.177 44.000 0.00 0.00 0.00 3.02
590 602 5.823045 GGGTTTTCAGTTACATCATCCTAGG 59.177 44.000 0.82 0.82 0.00 3.02
591 603 6.352737 GGGTTTTCAGTTACATCATCCTAGGA 60.353 42.308 15.46 15.46 0.00 2.94
592 604 6.763610 GGTTTTCAGTTACATCATCCTAGGAG 59.236 42.308 18.34 9.54 0.00 3.69
593 605 6.485830 TTTCAGTTACATCATCCTAGGAGG 57.514 41.667 17.55 17.55 36.46 4.30
594 606 3.898123 TCAGTTACATCATCCTAGGAGGC 59.102 47.826 18.79 3.52 34.61 4.70
595 607 3.643320 CAGTTACATCATCCTAGGAGGCA 59.357 47.826 18.79 8.18 34.61 4.75
596 608 4.101585 CAGTTACATCATCCTAGGAGGCAA 59.898 45.833 18.79 2.69 34.61 4.52
597 609 4.910304 AGTTACATCATCCTAGGAGGCAAT 59.090 41.667 18.79 5.18 34.61 3.56
598 610 5.012561 AGTTACATCATCCTAGGAGGCAATC 59.987 44.000 18.79 6.78 34.61 2.67
599 611 3.321039 ACATCATCCTAGGAGGCAATCA 58.679 45.455 18.79 1.09 34.61 2.57
600 612 3.915073 ACATCATCCTAGGAGGCAATCAT 59.085 43.478 18.79 3.66 34.61 2.45
601 613 5.096521 ACATCATCCTAGGAGGCAATCATA 58.903 41.667 18.79 0.00 34.61 2.15
602 614 5.046014 ACATCATCCTAGGAGGCAATCATAC 60.046 44.000 18.79 0.00 34.61 2.39
603 615 4.492646 TCATCCTAGGAGGCAATCATACA 58.507 43.478 18.79 0.00 34.61 2.29
604 616 4.529769 TCATCCTAGGAGGCAATCATACAG 59.470 45.833 18.79 0.00 34.61 2.74
605 617 3.928754 TCCTAGGAGGCAATCATACAGT 58.071 45.455 7.62 0.00 34.61 3.55
606 618 5.074746 TCCTAGGAGGCAATCATACAGTA 57.925 43.478 7.62 0.00 34.61 2.74
607 619 5.655394 TCCTAGGAGGCAATCATACAGTAT 58.345 41.667 7.62 0.00 34.61 2.12
608 620 5.481824 TCCTAGGAGGCAATCATACAGTATG 59.518 44.000 7.62 13.75 37.45 2.39
609 621 6.696708 TCCTAGGAGGCAATCATACAGTATGA 60.697 42.308 22.90 22.90 41.34 2.15
610 622 8.452785 TCCTAGGAGGCAATCATACAGTATGAG 61.453 44.444 24.36 14.94 40.84 2.90
618 630 4.137116 TCATACAGTATGAGGGTGTTGC 57.863 45.455 17.93 0.00 40.09 4.17
619 631 3.517500 TCATACAGTATGAGGGTGTTGCA 59.482 43.478 17.93 0.00 40.09 4.08
620 632 2.479566 ACAGTATGAGGGTGTTGCAG 57.520 50.000 0.00 0.00 39.69 4.41
621 633 1.699634 ACAGTATGAGGGTGTTGCAGT 59.300 47.619 0.00 0.00 39.69 4.40
622 634 2.106511 ACAGTATGAGGGTGTTGCAGTT 59.893 45.455 0.00 0.00 39.69 3.16
623 635 3.326588 ACAGTATGAGGGTGTTGCAGTTA 59.673 43.478 0.00 0.00 39.69 2.24
624 636 3.935203 CAGTATGAGGGTGTTGCAGTTAG 59.065 47.826 0.00 0.00 39.69 2.34
625 637 3.583086 AGTATGAGGGTGTTGCAGTTAGT 59.417 43.478 0.00 0.00 0.00 2.24
626 638 2.254546 TGAGGGTGTTGCAGTTAGTG 57.745 50.000 0.00 0.00 0.00 2.74
627 639 1.488812 TGAGGGTGTTGCAGTTAGTGT 59.511 47.619 0.00 0.00 0.00 3.55
628 640 2.701423 TGAGGGTGTTGCAGTTAGTGTA 59.299 45.455 0.00 0.00 0.00 2.90
629 641 3.064931 GAGGGTGTTGCAGTTAGTGTAC 58.935 50.000 0.00 0.00 0.00 2.90
630 642 2.436542 AGGGTGTTGCAGTTAGTGTACA 59.563 45.455 0.00 0.00 0.00 2.90
631 643 3.072476 AGGGTGTTGCAGTTAGTGTACAT 59.928 43.478 0.00 0.00 0.00 2.29
632 644 3.435671 GGGTGTTGCAGTTAGTGTACATC 59.564 47.826 0.00 0.00 0.00 3.06
633 645 3.435671 GGTGTTGCAGTTAGTGTACATCC 59.564 47.826 0.00 0.00 0.00 3.51
634 646 3.435671 GTGTTGCAGTTAGTGTACATCCC 59.564 47.826 0.00 0.00 0.00 3.85
635 647 3.071747 TGTTGCAGTTAGTGTACATCCCA 59.928 43.478 0.00 0.00 0.00 4.37
636 648 3.610040 TGCAGTTAGTGTACATCCCAG 57.390 47.619 0.00 0.00 0.00 4.45
637 649 2.236146 TGCAGTTAGTGTACATCCCAGG 59.764 50.000 0.00 0.00 0.00 4.45
638 650 2.236395 GCAGTTAGTGTACATCCCAGGT 59.764 50.000 0.00 0.00 0.00 4.00
639 651 3.307480 GCAGTTAGTGTACATCCCAGGTT 60.307 47.826 0.00 0.00 0.00 3.50
640 652 4.806286 GCAGTTAGTGTACATCCCAGGTTT 60.806 45.833 0.00 0.00 0.00 3.27
641 653 5.570034 GCAGTTAGTGTACATCCCAGGTTTA 60.570 44.000 0.00 0.00 0.00 2.01
642 654 6.650120 CAGTTAGTGTACATCCCAGGTTTAT 58.350 40.000 0.00 0.00 0.00 1.40
643 655 7.634210 GCAGTTAGTGTACATCCCAGGTTTATA 60.634 40.741 0.00 0.00 0.00 0.98
644 656 7.709613 CAGTTAGTGTACATCCCAGGTTTATAC 59.290 40.741 0.00 0.00 0.00 1.47
645 657 7.622479 AGTTAGTGTACATCCCAGGTTTATACT 59.378 37.037 0.00 0.00 0.00 2.12
646 658 6.886178 AGTGTACATCCCAGGTTTATACTT 57.114 37.500 0.00 0.00 0.00 2.24
658 670 5.989168 CAGGTTTATACTTGCGATCACCATA 59.011 40.000 0.00 0.00 0.00 2.74
841 861 5.771469 TCCTTATGTTGTGAAATGCAACTG 58.229 37.500 9.16 0.00 44.54 3.16
848 868 4.300189 TGTGAAATGCAACTGTGTTACC 57.700 40.909 0.00 0.00 0.00 2.85
1608 1659 0.915364 GGAGGATGGACTGCTTTCCT 59.085 55.000 5.85 0.00 41.29 3.36
1728 1779 4.451150 GTCATCTGGACCGCGCCA 62.451 66.667 0.00 2.17 40.83 5.69
1866 1917 0.391793 CCCTCTGGAAAGAAGCCGTC 60.392 60.000 0.00 0.00 0.00 4.79
1919 1970 1.217882 CCATAGATGTTCCGCGTTCC 58.782 55.000 4.92 0.00 0.00 3.62
2007 2060 9.283768 AGTGGATTTGATTATCATAATAACGCA 57.716 29.630 0.00 0.00 30.27 5.24
2023 2076 2.434884 CATCCGGTGCTGCGAGTT 60.435 61.111 0.00 0.00 0.00 3.01
2024 2077 1.153647 CATCCGGTGCTGCGAGTTA 60.154 57.895 0.00 0.00 0.00 2.24
2025 2078 1.153628 ATCCGGTGCTGCGAGTTAC 60.154 57.895 0.00 0.00 0.00 2.50
2026 2079 1.605058 ATCCGGTGCTGCGAGTTACT 61.605 55.000 0.00 0.00 0.00 2.24
2027 2080 1.805945 CCGGTGCTGCGAGTTACTC 60.806 63.158 1.64 1.64 0.00 2.59
2028 2081 1.805945 CGGTGCTGCGAGTTACTCC 60.806 63.158 6.80 0.63 0.00 3.85
2029 2082 1.448013 GGTGCTGCGAGTTACTCCC 60.448 63.158 6.80 0.00 0.00 4.30
2030 2083 1.592223 GTGCTGCGAGTTACTCCCT 59.408 57.895 6.80 0.00 0.00 4.20
2031 2084 0.458716 GTGCTGCGAGTTACTCCCTC 60.459 60.000 6.80 0.00 0.00 4.30
2032 2085 1.142097 GCTGCGAGTTACTCCCTCC 59.858 63.158 6.80 0.00 0.00 4.30
2033 2086 1.433879 CTGCGAGTTACTCCCTCCG 59.566 63.158 6.80 0.00 0.00 4.63
2034 2087 1.303888 TGCGAGTTACTCCCTCCGT 60.304 57.895 6.80 0.00 0.00 4.69
2035 2088 0.896940 TGCGAGTTACTCCCTCCGTT 60.897 55.000 6.80 0.00 0.00 4.44
2036 2089 0.179142 GCGAGTTACTCCCTCCGTTC 60.179 60.000 6.80 0.00 0.00 3.95
2037 2090 0.455005 CGAGTTACTCCCTCCGTTCC 59.545 60.000 6.80 0.00 0.00 3.62
2038 2091 1.553706 GAGTTACTCCCTCCGTTCCA 58.446 55.000 0.00 0.00 0.00 3.53
2039 2092 1.897802 GAGTTACTCCCTCCGTTCCAA 59.102 52.381 0.00 0.00 0.00 3.53
2040 2093 2.301009 GAGTTACTCCCTCCGTTCCAAA 59.699 50.000 0.00 0.00 0.00 3.28
2041 2094 2.707257 AGTTACTCCCTCCGTTCCAAAA 59.293 45.455 0.00 0.00 0.00 2.44
2042 2095 3.329814 AGTTACTCCCTCCGTTCCAAAAT 59.670 43.478 0.00 0.00 0.00 1.82
2043 2096 4.533311 AGTTACTCCCTCCGTTCCAAAATA 59.467 41.667 0.00 0.00 0.00 1.40
2044 2097 5.013391 AGTTACTCCCTCCGTTCCAAAATAA 59.987 40.000 0.00 0.00 0.00 1.40
2045 2098 4.376225 ACTCCCTCCGTTCCAAAATAAA 57.624 40.909 0.00 0.00 0.00 1.40
2046 2099 4.332828 ACTCCCTCCGTTCCAAAATAAAG 58.667 43.478 0.00 0.00 0.00 1.85
2047 2100 4.202535 ACTCCCTCCGTTCCAAAATAAAGT 60.203 41.667 0.00 0.00 0.00 2.66
2048 2101 4.732065 TCCCTCCGTTCCAAAATAAAGTT 58.268 39.130 0.00 0.00 0.00 2.66
2049 2102 5.878627 TCCCTCCGTTCCAAAATAAAGTTA 58.121 37.500 0.00 0.00 0.00 2.24
2050 2103 5.941647 TCCCTCCGTTCCAAAATAAAGTTAG 59.058 40.000 0.00 0.00 0.00 2.34
2051 2104 5.708697 CCCTCCGTTCCAAAATAAAGTTAGT 59.291 40.000 0.00 0.00 0.00 2.24
2052 2105 6.880529 CCCTCCGTTCCAAAATAAAGTTAGTA 59.119 38.462 0.00 0.00 0.00 1.82
2053 2106 7.148356 CCCTCCGTTCCAAAATAAAGTTAGTAC 60.148 40.741 0.00 0.00 0.00 2.73
2054 2107 7.388500 CCTCCGTTCCAAAATAAAGTTAGTACA 59.612 37.037 0.00 0.00 0.00 2.90
2055 2108 8.674263 TCCGTTCCAAAATAAAGTTAGTACAA 57.326 30.769 0.00 0.00 0.00 2.41
2056 2109 9.118300 TCCGTTCCAAAATAAAGTTAGTACAAA 57.882 29.630 0.00 0.00 0.00 2.83
2057 2110 9.389570 CCGTTCCAAAATAAAGTTAGTACAAAG 57.610 33.333 0.00 0.00 0.00 2.77
2058 2111 9.940166 CGTTCCAAAATAAAGTTAGTACAAAGT 57.060 29.630 0.00 0.00 0.00 2.66
2062 2115 9.471084 CCAAAATAAAGTTAGTACAAAGTTGGG 57.529 33.333 0.00 0.00 0.00 4.12
2065 2118 8.983702 AATAAAGTTAGTACAAAGTTGGGTCA 57.016 30.769 0.00 0.00 0.00 4.02
2066 2119 9.582648 AATAAAGTTAGTACAAAGTTGGGTCAT 57.417 29.630 0.00 0.00 0.00 3.06
2067 2120 7.506328 AAAGTTAGTACAAAGTTGGGTCATC 57.494 36.000 0.00 0.00 0.00 2.92
2068 2121 6.435292 AGTTAGTACAAAGTTGGGTCATCT 57.565 37.500 0.00 0.00 0.00 2.90
2069 2122 7.549147 AGTTAGTACAAAGTTGGGTCATCTA 57.451 36.000 0.00 0.00 0.00 1.98
2070 2123 8.147244 AGTTAGTACAAAGTTGGGTCATCTAT 57.853 34.615 0.00 0.00 0.00 1.98
2071 2124 8.603304 AGTTAGTACAAAGTTGGGTCATCTATT 58.397 33.333 0.00 0.00 0.00 1.73
2072 2125 9.227777 GTTAGTACAAAGTTGGGTCATCTATTT 57.772 33.333 0.00 0.00 0.00 1.40
2073 2126 9.802039 TTAGTACAAAGTTGGGTCATCTATTTT 57.198 29.630 0.00 0.00 0.00 1.82
2074 2127 8.110860 AGTACAAAGTTGGGTCATCTATTTTG 57.889 34.615 0.00 0.00 0.00 2.44
2075 2128 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2076 2129 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2077 2130 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2078 2131 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2079 2132 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2080 2133 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2081 2134 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2082 2135 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2083 2136 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2084 2137 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2085 2138 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2086 2139 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2095 2148 3.228453 GGAACGGAGGGAGTATGTGATA 58.772 50.000 0.00 0.00 0.00 2.15
2113 2166 5.825151 TGTGATAGAATTGTGTTTGTCACCA 59.175 36.000 0.00 0.00 45.61 4.17
2116 2169 3.631250 AGAATTGTGTTTGTCACCACCT 58.369 40.909 0.00 0.00 45.61 4.00
2127 2180 1.748493 GTCACCACCTTTGTTGAAGCA 59.252 47.619 0.00 0.00 33.84 3.91
2138 2191 4.782019 TTGTTGAAGCAGGCGATATTTT 57.218 36.364 0.00 0.00 0.00 1.82
2139 2192 4.355543 TGTTGAAGCAGGCGATATTTTC 57.644 40.909 0.00 0.00 0.00 2.29
2140 2193 3.755905 TGTTGAAGCAGGCGATATTTTCA 59.244 39.130 0.00 0.00 0.00 2.69
2141 2194 4.142622 TGTTGAAGCAGGCGATATTTTCAG 60.143 41.667 0.00 0.00 0.00 3.02
2146 2199 3.118408 AGCAGGCGATATTTTCAGTACCA 60.118 43.478 0.00 0.00 0.00 3.25
2148 2503 4.495844 GCAGGCGATATTTTCAGTACCAAC 60.496 45.833 0.00 0.00 0.00 3.77
2151 2506 4.634443 GGCGATATTTTCAGTACCAACAGT 59.366 41.667 0.00 0.00 0.00 3.55
2152 2507 5.813672 GGCGATATTTTCAGTACCAACAGTA 59.186 40.000 0.00 0.00 0.00 2.74
2163 2518 3.059352 ACCAACAGTACAAGCATCCTC 57.941 47.619 0.00 0.00 0.00 3.71
2198 2579 7.175119 TGTGGTCTATAATCTATCAAGAGGTCG 59.825 40.741 0.00 0.00 34.49 4.79
2210 2591 0.655733 AGAGGTCGTTTGTTGCAACG 59.344 50.000 23.79 13.51 43.14 4.10
2253 2661 1.505353 GAGGTCATGCTGCTGTTGC 59.495 57.895 0.00 0.00 40.20 4.17
2320 2728 7.982224 TGAATAAGCATATATTCATGAGCAGC 58.018 34.615 12.74 1.84 43.72 5.25
2342 2750 2.184385 CTGAACATCAGCGGAATTGC 57.816 50.000 0.00 0.00 37.72 3.56
2344 2752 0.248215 GAACATCAGCGGAATTGCGG 60.248 55.000 21.21 5.38 40.67 5.69
2345 2753 0.676466 AACATCAGCGGAATTGCGGA 60.676 50.000 21.21 10.90 43.05 5.54
2358 2811 2.665649 TTGCGGAACACGTGAGATAT 57.334 45.000 25.01 2.25 46.52 1.63
2378 2831 0.033796 CATTCAGGGTGTCCATGGCT 60.034 55.000 6.96 0.00 34.83 4.75
2379 2832 0.033796 ATTCAGGGTGTCCATGGCTG 60.034 55.000 6.96 8.46 34.83 4.85
2380 2833 1.426251 TTCAGGGTGTCCATGGCTGT 61.426 55.000 6.96 0.00 34.83 4.40
2381 2834 1.676635 CAGGGTGTCCATGGCTGTG 60.677 63.158 6.96 0.00 34.83 3.66
2382 2835 2.361610 GGGTGTCCATGGCTGTGG 60.362 66.667 6.96 3.48 40.76 4.17
2383 2836 3.064324 GGTGTCCATGGCTGTGGC 61.064 66.667 6.96 0.00 39.19 5.01
2430 2883 5.535030 AGTTTAACTGAACCCAATTGACTCC 59.465 40.000 7.12 0.00 0.00 3.85
2459 2917 2.892425 GGAGTCTGCGCCCAATCG 60.892 66.667 4.18 0.00 0.00 3.34
2469 2927 1.303317 GCCCAATCGACCCACAGTT 60.303 57.895 0.00 0.00 0.00 3.16
2476 2934 1.145156 CGACCCACAGTTGTCCACA 59.855 57.895 0.00 0.00 0.00 4.17
2512 2970 0.312102 GCCAGACAAGAACAGGCAAC 59.688 55.000 0.00 0.00 44.59 4.17
2513 2971 1.679139 CCAGACAAGAACAGGCAACA 58.321 50.000 0.00 0.00 41.41 3.33
2517 2975 3.859386 CAGACAAGAACAGGCAACAAAAC 59.141 43.478 0.00 0.00 41.41 2.43
2530 2991 2.190841 CAAAACACCGCCCCGAACT 61.191 57.895 0.00 0.00 0.00 3.01
2596 3452 8.918202 ACTATACTCTTGAATTGAAACAACCA 57.082 30.769 0.00 0.00 0.00 3.67
2605 3461 6.795399 TGAATTGAAACAACCAGAGAAAGTC 58.205 36.000 0.00 0.00 0.00 3.01
2624 3480 8.375506 AGAAAGTCATTCTGTTGGAGTATACAA 58.624 33.333 5.50 0.00 46.71 2.41
2835 3711 3.026694 AGAAACTTGAACAAGCCTTGCT 58.973 40.909 13.50 0.00 41.99 3.91
2858 3734 6.239458 GCTTTTCTATACTACTCCTCATGCCT 60.239 42.308 0.00 0.00 0.00 4.75
2865 3741 3.840666 ACTACTCCTCATGCCTTCTTCAA 59.159 43.478 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.032799 TGCAACCGTCAAACAACTGATC 59.967 45.455 0.00 0.00 0.00 2.92
43 44 3.433343 TGGAGATGCATTCAAATGGTGT 58.567 40.909 0.00 0.00 36.90 4.16
293 302 8.196771 TGAGATGGTTTTATTTAATCACATGCC 58.803 33.333 0.00 0.00 0.00 4.40
516 528 7.254863 GCAAATCTTCTGCATTTTCTGGAAAAA 60.255 33.333 11.69 0.00 42.71 1.94
517 529 6.203338 GCAAATCTTCTGCATTTTCTGGAAAA 59.797 34.615 10.33 10.33 43.48 2.29
518 530 5.697633 GCAAATCTTCTGCATTTTCTGGAAA 59.302 36.000 0.00 0.00 39.69 3.13
519 531 5.232463 GCAAATCTTCTGCATTTTCTGGAA 58.768 37.500 0.00 0.00 39.69 3.53
520 532 4.616604 CGCAAATCTTCTGCATTTTCTGGA 60.617 41.667 0.00 0.00 39.91 3.86
521 533 3.611113 CGCAAATCTTCTGCATTTTCTGG 59.389 43.478 0.00 0.00 39.91 3.86
522 534 4.232221 ACGCAAATCTTCTGCATTTTCTG 58.768 39.130 0.00 0.00 39.91 3.02
523 535 4.510038 ACGCAAATCTTCTGCATTTTCT 57.490 36.364 0.00 0.00 39.91 2.52
524 536 5.175491 TGAAACGCAAATCTTCTGCATTTTC 59.825 36.000 10.02 10.02 35.52 2.29
525 537 5.049167 TGAAACGCAAATCTTCTGCATTTT 58.951 33.333 0.00 0.00 35.52 1.82
526 538 4.619973 TGAAACGCAAATCTTCTGCATTT 58.380 34.783 0.00 0.00 37.85 2.32
527 539 4.241590 TGAAACGCAAATCTTCTGCATT 57.758 36.364 0.00 0.00 39.91 3.56
528 540 3.921119 TGAAACGCAAATCTTCTGCAT 57.079 38.095 0.00 0.00 39.91 3.96
529 541 3.921119 ATGAAACGCAAATCTTCTGCA 57.079 38.095 0.00 0.00 39.91 4.41
530 542 3.181537 GCAATGAAACGCAAATCTTCTGC 60.182 43.478 0.00 0.00 36.41 4.26
531 543 3.982701 TGCAATGAAACGCAAATCTTCTG 59.017 39.130 0.00 0.00 34.59 3.02
532 544 4.241590 TGCAATGAAACGCAAATCTTCT 57.758 36.364 0.00 0.00 34.59 2.85
533 545 5.118971 TCAATGCAATGAAACGCAAATCTTC 59.881 36.000 0.85 0.00 42.37 2.87
534 546 4.989797 TCAATGCAATGAAACGCAAATCTT 59.010 33.333 0.85 0.00 42.37 2.40
535 547 4.558178 TCAATGCAATGAAACGCAAATCT 58.442 34.783 0.85 0.00 42.37 2.40
536 548 4.907188 TCAATGCAATGAAACGCAAATC 57.093 36.364 0.85 0.00 42.37 2.17
537 549 5.670149 TTTCAATGCAATGAAACGCAAAT 57.330 30.435 22.92 0.00 42.68 2.32
538 550 5.475273 TTTTCAATGCAATGAAACGCAAA 57.525 30.435 25.73 11.15 46.06 3.68
539 551 4.025061 CCTTTTCAATGCAATGAAACGCAA 60.025 37.500 25.73 12.87 46.06 4.85
540 552 3.493877 CCTTTTCAATGCAATGAAACGCA 59.506 39.130 25.73 13.18 46.06 5.24
541 553 3.740321 TCCTTTTCAATGCAATGAAACGC 59.260 39.130 25.73 0.00 46.06 4.84
542 554 5.107375 CCTTCCTTTTCAATGCAATGAAACG 60.107 40.000 25.73 23.18 46.06 3.60
543 555 5.179929 CCCTTCCTTTTCAATGCAATGAAAC 59.820 40.000 25.73 0.00 46.06 2.78
544 556 5.307204 CCCTTCCTTTTCAATGCAATGAAA 58.693 37.500 22.92 22.92 45.07 2.69
545 557 4.262981 CCCCTTCCTTTTCAATGCAATGAA 60.263 41.667 13.20 13.20 37.53 2.57
546 558 3.261390 CCCCTTCCTTTTCAATGCAATGA 59.739 43.478 0.00 0.00 0.00 2.57
547 559 3.008266 ACCCCTTCCTTTTCAATGCAATG 59.992 43.478 0.00 0.00 0.00 2.82
548 560 3.250617 ACCCCTTCCTTTTCAATGCAAT 58.749 40.909 0.00 0.00 0.00 3.56
549 561 2.688477 ACCCCTTCCTTTTCAATGCAA 58.312 42.857 0.00 0.00 0.00 4.08
550 562 2.397044 ACCCCTTCCTTTTCAATGCA 57.603 45.000 0.00 0.00 0.00 3.96
551 563 3.769739 AAACCCCTTCCTTTTCAATGC 57.230 42.857 0.00 0.00 0.00 3.56
552 564 5.163311 ACTGAAAACCCCTTCCTTTTCAATG 60.163 40.000 6.92 0.82 42.79 2.82
553 565 4.968719 ACTGAAAACCCCTTCCTTTTCAAT 59.031 37.500 6.92 0.00 42.79 2.57
554 566 4.358214 ACTGAAAACCCCTTCCTTTTCAA 58.642 39.130 6.92 0.00 42.79 2.69
555 567 3.989056 ACTGAAAACCCCTTCCTTTTCA 58.011 40.909 5.66 5.66 41.76 2.69
556 568 5.361571 TGTAACTGAAAACCCCTTCCTTTTC 59.638 40.000 0.00 0.00 37.05 2.29
557 569 5.274015 TGTAACTGAAAACCCCTTCCTTTT 58.726 37.500 0.00 0.00 0.00 2.27
558 570 4.874199 TGTAACTGAAAACCCCTTCCTTT 58.126 39.130 0.00 0.00 0.00 3.11
559 571 4.529716 TGTAACTGAAAACCCCTTCCTT 57.470 40.909 0.00 0.00 0.00 3.36
560 572 4.105697 TGATGTAACTGAAAACCCCTTCCT 59.894 41.667 0.00 0.00 0.00 3.36
561 573 4.403734 TGATGTAACTGAAAACCCCTTCC 58.596 43.478 0.00 0.00 0.00 3.46
562 574 5.125578 GGATGATGTAACTGAAAACCCCTTC 59.874 44.000 0.00 0.00 0.00 3.46
563 575 5.016831 GGATGATGTAACTGAAAACCCCTT 58.983 41.667 0.00 0.00 0.00 3.95
564 576 4.292306 AGGATGATGTAACTGAAAACCCCT 59.708 41.667 0.00 0.00 0.00 4.79
565 577 4.600062 AGGATGATGTAACTGAAAACCCC 58.400 43.478 0.00 0.00 0.00 4.95
566 578 5.823045 CCTAGGATGATGTAACTGAAAACCC 59.177 44.000 1.05 0.00 0.00 4.11
567 579 6.650120 TCCTAGGATGATGTAACTGAAAACC 58.350 40.000 7.62 0.00 0.00 3.27
568 580 6.763610 CCTCCTAGGATGATGTAACTGAAAAC 59.236 42.308 13.12 0.00 37.67 2.43
569 581 6.632672 GCCTCCTAGGATGATGTAACTGAAAA 60.633 42.308 17.48 0.00 37.67 2.29
570 582 5.163301 GCCTCCTAGGATGATGTAACTGAAA 60.163 44.000 17.48 0.00 37.67 2.69
571 583 4.345257 GCCTCCTAGGATGATGTAACTGAA 59.655 45.833 17.48 0.00 37.67 3.02
572 584 3.898123 GCCTCCTAGGATGATGTAACTGA 59.102 47.826 17.48 0.00 37.67 3.41
573 585 3.643320 TGCCTCCTAGGATGATGTAACTG 59.357 47.826 17.48 0.00 37.67 3.16
574 586 3.928754 TGCCTCCTAGGATGATGTAACT 58.071 45.455 17.48 0.00 37.67 2.24
575 587 4.689612 TTGCCTCCTAGGATGATGTAAC 57.310 45.455 17.48 0.00 37.67 2.50
576 588 4.907269 TGATTGCCTCCTAGGATGATGTAA 59.093 41.667 17.48 10.14 37.67 2.41
577 589 4.492646 TGATTGCCTCCTAGGATGATGTA 58.507 43.478 17.48 1.86 37.67 2.29
578 590 3.321039 TGATTGCCTCCTAGGATGATGT 58.679 45.455 17.48 2.29 37.67 3.06
579 591 4.571369 ATGATTGCCTCCTAGGATGATG 57.429 45.455 17.48 3.56 37.67 3.07
580 592 5.096521 TGTATGATTGCCTCCTAGGATGAT 58.903 41.667 17.48 7.07 37.67 2.45
581 593 4.492646 TGTATGATTGCCTCCTAGGATGA 58.507 43.478 17.48 2.48 37.67 2.92
582 594 4.285517 ACTGTATGATTGCCTCCTAGGATG 59.714 45.833 13.12 11.14 37.67 3.51
583 595 4.497516 ACTGTATGATTGCCTCCTAGGAT 58.502 43.478 13.12 0.00 37.67 3.24
584 596 3.928754 ACTGTATGATTGCCTCCTAGGA 58.071 45.455 11.98 11.98 37.67 2.94
585 597 5.481824 TCATACTGTATGATTGCCTCCTAGG 59.518 44.000 23.01 0.82 40.09 3.02
586 598 6.350864 CCTCATACTGTATGATTGCCTCCTAG 60.351 46.154 25.92 12.96 43.66 3.02
587 599 5.481824 CCTCATACTGTATGATTGCCTCCTA 59.518 44.000 25.92 5.01 43.66 2.94
588 600 4.285517 CCTCATACTGTATGATTGCCTCCT 59.714 45.833 25.92 0.00 43.66 3.69
589 601 4.564406 CCCTCATACTGTATGATTGCCTCC 60.564 50.000 25.92 0.00 43.66 4.30
590 602 4.040952 ACCCTCATACTGTATGATTGCCTC 59.959 45.833 25.92 0.00 43.66 4.70
591 603 3.976654 ACCCTCATACTGTATGATTGCCT 59.023 43.478 25.92 8.67 43.66 4.75
592 604 4.067896 CACCCTCATACTGTATGATTGCC 58.932 47.826 25.92 0.00 43.66 4.52
593 605 4.708177 ACACCCTCATACTGTATGATTGC 58.292 43.478 25.92 0.00 43.66 3.56
594 606 5.008019 GCAACACCCTCATACTGTATGATTG 59.992 44.000 25.92 24.67 43.66 2.67
595 607 5.126067 GCAACACCCTCATACTGTATGATT 58.874 41.667 25.92 16.27 43.66 2.57
596 608 4.164030 TGCAACACCCTCATACTGTATGAT 59.836 41.667 25.92 12.48 43.66 2.45
597 609 3.517500 TGCAACACCCTCATACTGTATGA 59.482 43.478 24.61 24.61 42.56 2.15
598 610 3.872696 TGCAACACCCTCATACTGTATG 58.127 45.455 19.37 19.37 37.52 2.39
599 611 3.519510 ACTGCAACACCCTCATACTGTAT 59.480 43.478 0.00 0.00 0.00 2.29
600 612 2.903784 ACTGCAACACCCTCATACTGTA 59.096 45.455 0.00 0.00 0.00 2.74
601 613 1.699634 ACTGCAACACCCTCATACTGT 59.300 47.619 0.00 0.00 0.00 3.55
602 614 2.479566 ACTGCAACACCCTCATACTG 57.520 50.000 0.00 0.00 0.00 2.74
603 615 3.583086 ACTAACTGCAACACCCTCATACT 59.417 43.478 0.00 0.00 0.00 2.12
604 616 3.684788 CACTAACTGCAACACCCTCATAC 59.315 47.826 0.00 0.00 0.00 2.39
605 617 3.326588 ACACTAACTGCAACACCCTCATA 59.673 43.478 0.00 0.00 0.00 2.15
606 618 2.106511 ACACTAACTGCAACACCCTCAT 59.893 45.455 0.00 0.00 0.00 2.90
607 619 1.488812 ACACTAACTGCAACACCCTCA 59.511 47.619 0.00 0.00 0.00 3.86
608 620 2.256117 ACACTAACTGCAACACCCTC 57.744 50.000 0.00 0.00 0.00 4.30
609 621 2.436542 TGTACACTAACTGCAACACCCT 59.563 45.455 0.00 0.00 0.00 4.34
610 622 2.841215 TGTACACTAACTGCAACACCC 58.159 47.619 0.00 0.00 0.00 4.61
611 623 3.435671 GGATGTACACTAACTGCAACACC 59.564 47.826 0.00 0.00 0.00 4.16
612 624 3.435671 GGGATGTACACTAACTGCAACAC 59.564 47.826 0.00 0.00 0.00 3.32
613 625 3.071747 TGGGATGTACACTAACTGCAACA 59.928 43.478 0.00 0.00 0.00 3.33
614 626 3.670625 TGGGATGTACACTAACTGCAAC 58.329 45.455 0.00 0.00 0.00 4.17
615 627 3.307410 CCTGGGATGTACACTAACTGCAA 60.307 47.826 0.00 0.00 0.00 4.08
616 628 2.236146 CCTGGGATGTACACTAACTGCA 59.764 50.000 0.00 0.00 0.00 4.41
617 629 2.236395 ACCTGGGATGTACACTAACTGC 59.764 50.000 0.00 0.00 0.00 4.40
618 630 4.553330 AACCTGGGATGTACACTAACTG 57.447 45.455 0.00 0.00 0.00 3.16
619 631 6.886178 ATAAACCTGGGATGTACACTAACT 57.114 37.500 0.00 0.00 0.00 2.24
620 632 7.789026 AGTATAAACCTGGGATGTACACTAAC 58.211 38.462 0.00 0.00 0.00 2.34
621 633 7.983166 AGTATAAACCTGGGATGTACACTAA 57.017 36.000 0.00 0.00 0.00 2.24
622 634 7.634210 GCAAGTATAAACCTGGGATGTACACTA 60.634 40.741 0.00 0.00 0.00 2.74
623 635 6.650120 CAAGTATAAACCTGGGATGTACACT 58.350 40.000 0.00 0.00 0.00 3.55
624 636 5.296035 GCAAGTATAAACCTGGGATGTACAC 59.704 44.000 0.00 0.00 0.00 2.90
625 637 5.433526 GCAAGTATAAACCTGGGATGTACA 58.566 41.667 0.00 0.00 0.00 2.90
626 638 4.510340 CGCAAGTATAAACCTGGGATGTAC 59.490 45.833 0.00 0.00 33.05 2.90
627 639 4.406326 TCGCAAGTATAAACCTGGGATGTA 59.594 41.667 0.00 0.00 34.94 2.29
628 640 3.199071 TCGCAAGTATAAACCTGGGATGT 59.801 43.478 0.00 0.00 34.94 3.06
629 641 3.804036 TCGCAAGTATAAACCTGGGATG 58.196 45.455 0.00 0.00 34.94 3.51
630 642 4.102524 TGATCGCAAGTATAAACCTGGGAT 59.897 41.667 6.43 6.43 46.61 3.85
631 643 3.452990 TGATCGCAAGTATAAACCTGGGA 59.547 43.478 0.00 0.00 41.56 4.37
632 644 3.560068 GTGATCGCAAGTATAAACCTGGG 59.440 47.826 0.16 0.00 39.48 4.45
633 645 3.560068 GGTGATCGCAAGTATAAACCTGG 59.440 47.826 8.82 0.00 39.48 4.45
634 646 4.188462 TGGTGATCGCAAGTATAAACCTG 58.812 43.478 8.82 0.00 39.48 4.00
635 647 4.481368 TGGTGATCGCAAGTATAAACCT 57.519 40.909 8.82 0.00 39.48 3.50
636 648 6.854496 TTATGGTGATCGCAAGTATAAACC 57.146 37.500 8.82 0.00 39.48 3.27
641 653 9.719355 TGTTATAATTATGGTGATCGCAAGTAT 57.281 29.630 8.82 5.92 39.48 2.12
642 654 9.549078 TTGTTATAATTATGGTGATCGCAAGTA 57.451 29.630 8.82 0.00 39.48 2.24
643 655 8.445275 TTGTTATAATTATGGTGATCGCAAGT 57.555 30.769 8.82 0.00 39.48 3.16
644 656 7.535258 GCTTGTTATAATTATGGTGATCGCAAG 59.465 37.037 8.82 10.33 0.00 4.01
645 657 7.012799 TGCTTGTTATAATTATGGTGATCGCAA 59.987 33.333 8.82 0.00 0.00 4.85
646 658 6.484977 TGCTTGTTATAATTATGGTGATCGCA 59.515 34.615 8.82 5.64 0.00 5.10
666 678 8.752766 ATAACAAAATGAAATCTGACTGCTTG 57.247 30.769 0.00 0.00 0.00 4.01
731 743 7.899178 TTTGGTACACAAGATACATACACTG 57.101 36.000 0.00 0.00 40.82 3.66
799 811 5.546621 AGGAGCTGAGTTGTTACAGTTAA 57.453 39.130 0.00 0.00 36.62 2.01
841 861 8.718102 ATACAATTCACTGATACAGGTAACAC 57.282 34.615 0.00 0.00 35.51 3.32
848 868 8.599055 ATGCAGTATACAATTCACTGATACAG 57.401 34.615 5.50 0.00 41.80 2.74
1608 1659 1.001764 CCTGTGCATCTGAAGGGCA 60.002 57.895 0.00 0.00 34.70 5.36
1728 1779 0.890996 CCCACTGCTCGCCTTCTTTT 60.891 55.000 0.00 0.00 0.00 2.27
2007 2060 1.153628 GTAACTCGCAGCACCGGAT 60.154 57.895 9.46 0.00 0.00 4.18
2019 2072 1.553706 TGGAACGGAGGGAGTAACTC 58.446 55.000 0.00 0.00 0.00 3.01
2021 2074 2.845363 TTTGGAACGGAGGGAGTAAC 57.155 50.000 0.00 0.00 0.00 2.50
2023 2076 5.013391 ACTTTATTTTGGAACGGAGGGAGTA 59.987 40.000 0.00 0.00 0.00 2.59
2024 2077 4.202535 ACTTTATTTTGGAACGGAGGGAGT 60.203 41.667 0.00 0.00 0.00 3.85
2025 2078 4.332828 ACTTTATTTTGGAACGGAGGGAG 58.667 43.478 0.00 0.00 0.00 4.30
2026 2079 4.376225 ACTTTATTTTGGAACGGAGGGA 57.624 40.909 0.00 0.00 0.00 4.20
2027 2080 5.708697 ACTAACTTTATTTTGGAACGGAGGG 59.291 40.000 0.00 0.00 0.00 4.30
2028 2081 6.812879 ACTAACTTTATTTTGGAACGGAGG 57.187 37.500 0.00 0.00 0.00 4.30
2029 2082 8.314143 TGTACTAACTTTATTTTGGAACGGAG 57.686 34.615 0.00 0.00 0.00 4.63
2030 2083 8.674263 TTGTACTAACTTTATTTTGGAACGGA 57.326 30.769 0.00 0.00 0.00 4.69
2031 2084 9.389570 CTTTGTACTAACTTTATTTTGGAACGG 57.610 33.333 0.00 0.00 0.00 4.44
2032 2085 9.940166 ACTTTGTACTAACTTTATTTTGGAACG 57.060 29.630 0.00 0.00 0.00 3.95
2036 2089 9.471084 CCCAACTTTGTACTAACTTTATTTTGG 57.529 33.333 0.00 0.00 0.00 3.28
2039 2092 9.411189 TGACCCAACTTTGTACTAACTTTATTT 57.589 29.630 0.00 0.00 0.00 1.40
2040 2093 8.983702 TGACCCAACTTTGTACTAACTTTATT 57.016 30.769 0.00 0.00 0.00 1.40
2041 2094 9.227777 GATGACCCAACTTTGTACTAACTTTAT 57.772 33.333 0.00 0.00 0.00 1.40
2042 2095 8.434392 AGATGACCCAACTTTGTACTAACTTTA 58.566 33.333 0.00 0.00 0.00 1.85
2043 2096 7.287810 AGATGACCCAACTTTGTACTAACTTT 58.712 34.615 0.00 0.00 0.00 2.66
2044 2097 6.838382 AGATGACCCAACTTTGTACTAACTT 58.162 36.000 0.00 0.00 0.00 2.66
2045 2098 6.435292 AGATGACCCAACTTTGTACTAACT 57.565 37.500 0.00 0.00 0.00 2.24
2046 2099 8.788325 AATAGATGACCCAACTTTGTACTAAC 57.212 34.615 0.00 0.00 0.00 2.34
2047 2100 9.802039 AAAATAGATGACCCAACTTTGTACTAA 57.198 29.630 0.00 0.00 0.00 2.24
2048 2101 9.226606 CAAAATAGATGACCCAACTTTGTACTA 57.773 33.333 0.00 0.00 0.00 1.82
2049 2102 7.176690 CCAAAATAGATGACCCAACTTTGTACT 59.823 37.037 0.00 0.00 0.00 2.73
2050 2103 7.175990 TCCAAAATAGATGACCCAACTTTGTAC 59.824 37.037 0.00 0.00 0.00 2.90
2051 2104 7.235079 TCCAAAATAGATGACCCAACTTTGTA 58.765 34.615 0.00 0.00 0.00 2.41
2052 2105 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2053 2106 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2054 2107 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2055 2108 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2056 2109 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2057 2110 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2058 2111 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2059 2112 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2060 2113 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2061 2114 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2062 2115 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2063 2116 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2064 2117 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2065 2118 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2066 2119 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2067 2120 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2068 2121 4.472108 ACATACTCCCTCCGTTCCAAAATA 59.528 41.667 0.00 0.00 0.00 1.40
2069 2122 3.265995 ACATACTCCCTCCGTTCCAAAAT 59.734 43.478 0.00 0.00 0.00 1.82
2070 2123 2.640826 ACATACTCCCTCCGTTCCAAAA 59.359 45.455 0.00 0.00 0.00 2.44
2071 2124 2.027561 CACATACTCCCTCCGTTCCAAA 60.028 50.000 0.00 0.00 0.00 3.28
2072 2125 1.553248 CACATACTCCCTCCGTTCCAA 59.447 52.381 0.00 0.00 0.00 3.53
2073 2126 1.191535 CACATACTCCCTCCGTTCCA 58.808 55.000 0.00 0.00 0.00 3.53
2074 2127 1.481871 TCACATACTCCCTCCGTTCC 58.518 55.000 0.00 0.00 0.00 3.62
2075 2128 4.142790 TCTATCACATACTCCCTCCGTTC 58.857 47.826 0.00 0.00 0.00 3.95
2076 2129 4.180377 TCTATCACATACTCCCTCCGTT 57.820 45.455 0.00 0.00 0.00 4.44
2077 2130 3.878237 TCTATCACATACTCCCTCCGT 57.122 47.619 0.00 0.00 0.00 4.69
2078 2131 5.011125 ACAATTCTATCACATACTCCCTCCG 59.989 44.000 0.00 0.00 0.00 4.63
2079 2132 6.183361 ACACAATTCTATCACATACTCCCTCC 60.183 42.308 0.00 0.00 0.00 4.30
2080 2133 6.821388 ACACAATTCTATCACATACTCCCTC 58.179 40.000 0.00 0.00 0.00 4.30
2081 2134 6.814954 ACACAATTCTATCACATACTCCCT 57.185 37.500 0.00 0.00 0.00 4.20
2082 2135 7.336931 ACAAACACAATTCTATCACATACTCCC 59.663 37.037 0.00 0.00 0.00 4.30
2083 2136 8.268850 ACAAACACAATTCTATCACATACTCC 57.731 34.615 0.00 0.00 0.00 3.85
2084 2137 8.935844 TGACAAACACAATTCTATCACATACTC 58.064 33.333 0.00 0.00 0.00 2.59
2085 2138 8.846943 TGACAAACACAATTCTATCACATACT 57.153 30.769 0.00 0.00 0.00 2.12
2113 2166 0.465460 TCGCCTGCTTCAACAAAGGT 60.465 50.000 0.00 0.00 35.37 3.50
2116 2169 4.782019 AAATATCGCCTGCTTCAACAAA 57.218 36.364 0.00 0.00 0.00 2.83
2127 2180 4.839121 TGTTGGTACTGAAAATATCGCCT 58.161 39.130 0.00 0.00 0.00 5.52
2146 2199 2.093973 CCTCGAGGATGCTTGTACTGTT 60.094 50.000 28.21 0.00 37.39 3.16
2148 2503 1.202463 CCCTCGAGGATGCTTGTACTG 60.202 57.143 33.39 7.31 38.24 2.74
2151 2506 1.568504 AACCCTCGAGGATGCTTGTA 58.431 50.000 33.39 0.00 39.89 2.41
2152 2507 0.693049 AAACCCTCGAGGATGCTTGT 59.307 50.000 33.39 17.61 39.89 3.16
2156 2511 0.804989 CACAAAACCCTCGAGGATGC 59.195 55.000 33.39 0.00 39.89 3.91
2161 2516 3.611766 ATAGACCACAAAACCCTCGAG 57.388 47.619 5.13 5.13 0.00 4.04
2163 2518 5.671493 AGATTATAGACCACAAAACCCTCG 58.329 41.667 0.00 0.00 0.00 4.63
2198 2579 3.507786 AGAAACTTCCGTTGCAACAAAC 58.492 40.909 28.01 10.24 30.52 2.93
2337 2745 1.808411 ATCTCACGTGTTCCGCAATT 58.192 45.000 16.51 0.00 41.42 2.32
2339 2747 2.094442 TGATATCTCACGTGTTCCGCAA 60.094 45.455 16.51 0.00 41.42 4.85
2341 2749 2.203800 TGATATCTCACGTGTTCCGC 57.796 50.000 16.51 3.01 41.42 5.54
2342 2750 4.359706 TGAATGATATCTCACGTGTTCCG 58.640 43.478 16.51 3.15 44.03 4.30
2344 2752 4.747108 CCCTGAATGATATCTCACGTGTTC 59.253 45.833 16.51 9.67 33.22 3.18
2345 2753 4.162320 ACCCTGAATGATATCTCACGTGTT 59.838 41.667 16.51 4.59 33.22 3.32
2358 2811 0.034186 GCCATGGACACCCTGAATGA 60.034 55.000 18.40 0.00 0.00 2.57
2391 2844 5.569059 CAGTTAAACTAAATTTGCTGGCTCG 59.431 40.000 0.00 0.00 34.05 5.03
2430 2883 1.970447 CAGACTCCGACAGAAGTTCG 58.030 55.000 0.00 0.00 0.00 3.95
2459 2917 3.487576 TTGTGGACAACTGTGGGTC 57.512 52.632 4.74 4.74 0.00 4.46
2469 2927 2.280797 GCTGCCGAGTTGTGGACA 60.281 61.111 0.00 0.00 0.00 4.02
2495 2953 3.781079 TTTGTTGCCTGTTCTTGTCTG 57.219 42.857 0.00 0.00 0.00 3.51
2512 2970 2.190841 AGTTCGGGGCGGTGTTTTG 61.191 57.895 0.00 0.00 0.00 2.44
2513 2971 2.190841 CAGTTCGGGGCGGTGTTTT 61.191 57.895 0.00 0.00 0.00 2.43
2530 2991 2.125952 CTCATGTGCTCGCCGTCA 60.126 61.111 0.00 0.00 0.00 4.35
2537 2998 1.156645 GCCGATGGTCTCATGTGCTC 61.157 60.000 0.00 0.00 32.98 4.26
2596 3452 5.559148 ACTCCAACAGAATGACTTTCTCT 57.441 39.130 0.73 0.00 42.98 3.10
2605 3461 9.396022 ACCTTAATTGTATACTCCAACAGAATG 57.604 33.333 4.17 0.00 46.00 2.67
2613 3469 9.613428 CAATGAGAACCTTAATTGTATACTCCA 57.387 33.333 4.17 0.00 0.00 3.86
2624 3480 6.532657 CGTACCGTAACAATGAGAACCTTAAT 59.467 38.462 0.00 0.00 0.00 1.40
2739 3595 2.006169 CGTATGCTGTGTGTAATGCCA 58.994 47.619 0.00 0.00 0.00 4.92
2788 3644 2.169330 TGCTCATGTTATGCAAGGCAA 58.831 42.857 0.00 0.00 43.62 4.52
2835 3711 7.565398 AGAAGGCATGAGGAGTAGTATAGAAAA 59.435 37.037 0.00 0.00 0.00 2.29
2858 3734 3.016031 TGCTGCTCAAAGTGTTGAAGAA 58.984 40.909 0.00 0.00 43.18 2.52
2865 3741 1.736126 CATCGATGCTGCTCAAAGTGT 59.264 47.619 13.37 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.