Multiple sequence alignment - TraesCS5B01G226200

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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 TraesCS5B01G226200 chr5B 100.000 3010 0 0 1 3010 402846525 402843516 0.000000e+00 5559
1 TraesCS5B01G226200 chr5B 92.143 560 33 3 1 549 22356393 22355834 0.000000e+00 780
2 TraesCS5B01G226200 chr5B 81.585 429 63 6 1704 2131 673374933 673374520 1.030000e-89 340
3 TraesCS5B01G226200 chr5B 91.489 141 11 1 2470 2609 606968125 606967985 3.060000e-45 193
4 TraesCS5B01G226200 chr5B 91.429 105 9 0 2607 2711 606967956 606967852 8.700000e-31 145
5 TraesCS5B01G226200 chr6D 91.304 966 65 14 750 1703 806744 807702 0.000000e+00 1301
6 TraesCS5B01G226200 chr6B 89.609 972 71 18 750 1703 3386079 3387038 0.000000e+00 1208
7 TraesCS5B01G226200 chr6B 88.153 574 54 8 1703 2276 710669166 710669725 0.000000e+00 671
8 TraesCS5B01G226200 chr6B 89.810 422 40 3 1699 2120 710670036 710670454 3.410000e-149 538
9 TraesCS5B01G226200 chr6B 81.993 572 80 11 1704 2273 597988188 597988738 5.880000e-127 464
10 TraesCS5B01G226200 chr6B 83.236 513 63 11 1765 2273 100933638 100934131 1.650000e-122 449
11 TraesCS5B01G226200 chr6A 89.609 972 71 18 750 1703 289469 290428 0.000000e+00 1208
12 TraesCS5B01G226200 chr2D 93.929 560 23 3 1 549 592104935 592105494 0.000000e+00 835
13 TraesCS5B01G226200 chr5D 93.226 561 26 4 1 549 503526557 503525997 0.000000e+00 815
14 TraesCS5B01G226200 chr5D 87.392 579 59 8 1699 2277 471127147 471127711 0.000000e+00 652
15 TraesCS5B01G226200 chr7B 93.214 560 27 6 1 549 68749099 68748540 0.000000e+00 813
16 TraesCS5B01G226200 chr7B 91.055 559 37 5 2 549 690403577 690404133 0.000000e+00 743
17 TraesCS5B01G226200 chrUn 92.832 558 31 2 1 549 8489885 8490442 0.000000e+00 800
18 TraesCS5B01G226200 chrUn 96.067 178 4 1 542 719 8502189 8502363 1.370000e-73 287
19 TraesCS5B01G226200 chr1B 92.500 560 31 3 1 549 635878566 635878007 0.000000e+00 791
20 TraesCS5B01G226200 chr1B 86.192 717 63 16 2315 3010 113539783 113540484 0.000000e+00 743
21 TraesCS5B01G226200 chr4B 91.771 559 34 6 2 549 564328968 564329525 0.000000e+00 767
22 TraesCS5B01G226200 chr4B 91.055 559 38 6 2 549 564274556 564275113 0.000000e+00 745
23 TraesCS5B01G226200 chr4A 96.571 175 6 0 545 719 566050950 566050776 1.060000e-74 291
24 TraesCS5B01G226200 chr7A 96.571 175 5 1 545 719 709598000 709597827 3.800000e-74 289
25 TraesCS5B01G226200 chr5A 95.531 179 7 1 542 719 36207302 36207480 4.910000e-73 285
26 TraesCS5B01G226200 chr5A 95.455 176 8 0 542 717 36115587 36115762 6.350000e-72 281
27 TraesCS5B01G226200 chr5A 95.455 176 8 0 542 717 36149291 36149466 6.350000e-72 281
28 TraesCS5B01G226200 chr5A 95.455 176 8 0 542 717 36177696 36177871 6.350000e-72 281
29 TraesCS5B01G226200 chr5A 94.318 176 10 0 542 717 36060295 36060470 1.380000e-68 270
30 TraesCS5B01G226200 chr5A 94.318 176 10 0 542 717 36086973 36087148 1.380000e-68 270
31 TraesCS5B01G226200 chr3B 81.784 269 44 5 1704 1971 685831018 685830754 1.400000e-53 220


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 TraesCS5B01G226200 chr5B 402843516 402846525 3009 True 5559.0 5559 100.0000 1 3010 1 chr5B.!!$R2 3009
1 TraesCS5B01G226200 chr5B 22355834 22356393 559 True 780.0 780 92.1430 1 549 1 chr5B.!!$R1 548
2 TraesCS5B01G226200 chr6D 806744 807702 958 False 1301.0 1301 91.3040 750 1703 1 chr6D.!!$F1 953
3 TraesCS5B01G226200 chr6B 3386079 3387038 959 False 1208.0 1208 89.6090 750 1703 1 chr6B.!!$F1 953
4 TraesCS5B01G226200 chr6B 710669166 710670454 1288 False 604.5 671 88.9815 1699 2276 2 chr6B.!!$F4 577
5 TraesCS5B01G226200 chr6B 597988188 597988738 550 False 464.0 464 81.9930 1704 2273 1 chr6B.!!$F3 569
6 TraesCS5B01G226200 chr6A 289469 290428 959 False 1208.0 1208 89.6090 750 1703 1 chr6A.!!$F1 953
7 TraesCS5B01G226200 chr2D 592104935 592105494 559 False 835.0 835 93.9290 1 549 1 chr2D.!!$F1 548
8 TraesCS5B01G226200 chr5D 503525997 503526557 560 True 815.0 815 93.2260 1 549 1 chr5D.!!$R1 548
9 TraesCS5B01G226200 chr5D 471127147 471127711 564 False 652.0 652 87.3920 1699 2277 1 chr5D.!!$F1 578
10 TraesCS5B01G226200 chr7B 68748540 68749099 559 True 813.0 813 93.2140 1 549 1 chr7B.!!$R1 548
11 TraesCS5B01G226200 chr7B 690403577 690404133 556 False 743.0 743 91.0550 2 549 1 chr7B.!!$F1 547
12 TraesCS5B01G226200 chrUn 8489885 8490442 557 False 800.0 800 92.8320 1 549 1 chrUn.!!$F1 548
13 TraesCS5B01G226200 chr1B 635878007 635878566 559 True 791.0 791 92.5000 1 549 1 chr1B.!!$R1 548
14 TraesCS5B01G226200 chr1B 113539783 113540484 701 False 743.0 743 86.1920 2315 3010 1 chr1B.!!$F1 695
15 TraesCS5B01G226200 chr4B 564328968 564329525 557 False 767.0 767 91.7710 2 549 1 chr4B.!!$F2 547
16 TraesCS5B01G226200 chr4B 564274556 564275113 557 False 745.0 745 91.0550 2 549 1 chr4B.!!$F1 547

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
134 136 0.843309 TTGGGTTCAGAGCACCTTCA 59.157 50.0 0.0 0.0 34.36 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2100 2129 0.620556 GGGGAGGAGTCAAGCAATGA 59.379 55.0 0.0 0.0 35.05 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
102 104 6.547141 TGTTGATGAGAGTTTCTCCATGTTTT 59.453 34.615 3.81 0.00 42.73 2.43
134 136 0.843309 TTGGGTTCAGAGCACCTTCA 59.157 50.000 0.00 0.00 34.36 3.02
302 304 2.680429 GTTGGACGTCGTTCAACCA 58.320 52.632 31.05 17.13 43.90 3.67
323 325 2.046507 CTCTGGCACCCACTGAGC 60.047 66.667 0.00 0.00 0.00 4.26
325 327 2.113774 CTGGCACCCACTGAGCAA 59.886 61.111 0.00 0.00 0.00 3.91
369 371 1.759445 GTGAGCTGCATCTTCCTCCTA 59.241 52.381 1.02 0.00 0.00 2.94
549 562 5.183530 TGGATGGTCATTTCTGATGAGTT 57.816 39.130 0.00 0.00 32.98 3.01
550 563 5.573219 TGGATGGTCATTTCTGATGAGTTT 58.427 37.500 0.00 0.00 32.98 2.66
551 564 5.416639 TGGATGGTCATTTCTGATGAGTTTG 59.583 40.000 0.00 0.00 32.98 2.93
552 565 5.416952 GGATGGTCATTTCTGATGAGTTTGT 59.583 40.000 0.00 0.00 32.98 2.83
553 566 5.947228 TGGTCATTTCTGATGAGTTTGTC 57.053 39.130 0.00 0.00 32.98 3.18
554 567 5.624159 TGGTCATTTCTGATGAGTTTGTCT 58.376 37.500 0.00 0.00 32.98 3.41
555 568 6.768483 TGGTCATTTCTGATGAGTTTGTCTA 58.232 36.000 0.00 0.00 32.98 2.59
556 569 7.397221 TGGTCATTTCTGATGAGTTTGTCTAT 58.603 34.615 0.00 0.00 32.98 1.98
557 570 7.550551 TGGTCATTTCTGATGAGTTTGTCTATC 59.449 37.037 0.00 0.00 32.98 2.08
558 571 7.768120 GGTCATTTCTGATGAGTTTGTCTATCT 59.232 37.037 0.00 0.00 32.98 1.98
559 572 8.602328 GTCATTTCTGATGAGTTTGTCTATCTG 58.398 37.037 0.00 0.00 32.98 2.90
560 573 8.534496 TCATTTCTGATGAGTTTGTCTATCTGA 58.466 33.333 0.00 0.00 0.00 3.27
561 574 9.159364 CATTTCTGATGAGTTTGTCTATCTGAA 57.841 33.333 0.00 0.00 36.42 3.02
562 575 8.539770 TTTCTGATGAGTTTGTCTATCTGAAC 57.460 34.615 0.00 0.00 37.29 3.18
563 576 7.473735 TCTGATGAGTTTGTCTATCTGAACT 57.526 36.000 0.00 0.00 35.22 3.01
564 577 7.901029 TCTGATGAGTTTGTCTATCTGAACTT 58.099 34.615 0.00 0.00 32.85 2.66
565 578 8.370940 TCTGATGAGTTTGTCTATCTGAACTTT 58.629 33.333 0.00 0.00 32.85 2.66
566 579 9.645059 CTGATGAGTTTGTCTATCTGAACTTTA 57.355 33.333 0.00 0.00 32.85 1.85
570 583 9.219603 TGAGTTTGTCTATCTGAACTTTATTGG 57.780 33.333 0.00 0.00 32.85 3.16
571 584 8.045176 AGTTTGTCTATCTGAACTTTATTGGC 57.955 34.615 0.00 0.00 0.00 4.52
572 585 7.665559 AGTTTGTCTATCTGAACTTTATTGGCA 59.334 33.333 0.00 0.00 0.00 4.92
573 586 6.985188 TGTCTATCTGAACTTTATTGGCAC 57.015 37.500 0.00 0.00 0.00 5.01
574 587 6.711277 TGTCTATCTGAACTTTATTGGCACT 58.289 36.000 0.00 0.00 0.00 4.40
575 588 6.595326 TGTCTATCTGAACTTTATTGGCACTG 59.405 38.462 0.00 0.00 0.00 3.66
576 589 6.818644 GTCTATCTGAACTTTATTGGCACTGA 59.181 38.462 0.00 0.00 0.00 3.41
577 590 7.334421 GTCTATCTGAACTTTATTGGCACTGAA 59.666 37.037 0.00 0.00 0.00 3.02
578 591 6.899393 ATCTGAACTTTATTGGCACTGAAA 57.101 33.333 0.00 0.00 0.00 2.69
579 592 6.899393 TCTGAACTTTATTGGCACTGAAAT 57.101 33.333 0.00 0.00 0.00 2.17
580 593 7.288810 TCTGAACTTTATTGGCACTGAAATT 57.711 32.000 0.00 0.00 0.00 1.82
581 594 8.402798 TCTGAACTTTATTGGCACTGAAATTA 57.597 30.769 0.00 0.00 0.00 1.40
582 595 9.023962 TCTGAACTTTATTGGCACTGAAATTAT 57.976 29.630 0.00 0.00 0.00 1.28
583 596 9.294030 CTGAACTTTATTGGCACTGAAATTATC 57.706 33.333 0.00 0.00 0.00 1.75
584 597 9.023962 TGAACTTTATTGGCACTGAAATTATCT 57.976 29.630 0.00 0.00 0.00 1.98
585 598 9.508567 GAACTTTATTGGCACTGAAATTATCTC 57.491 33.333 0.00 0.00 0.00 2.75
586 599 7.697691 ACTTTATTGGCACTGAAATTATCTCG 58.302 34.615 0.00 0.00 0.00 4.04
587 600 7.552687 ACTTTATTGGCACTGAAATTATCTCGA 59.447 33.333 0.00 0.00 0.00 4.04
588 601 8.450578 TTTATTGGCACTGAAATTATCTCGAT 57.549 30.769 0.00 0.00 0.00 3.59
589 602 5.739752 TTGGCACTGAAATTATCTCGATG 57.260 39.130 0.00 0.00 0.00 3.84
590 603 5.022282 TGGCACTGAAATTATCTCGATGA 57.978 39.130 0.00 0.00 0.00 2.92
591 604 4.811024 TGGCACTGAAATTATCTCGATGAC 59.189 41.667 0.00 0.00 0.00 3.06
592 605 5.053145 GGCACTGAAATTATCTCGATGACT 58.947 41.667 0.00 0.00 0.00 3.41
593 606 5.050499 GGCACTGAAATTATCTCGATGACTG 60.050 44.000 0.00 0.00 0.00 3.51
594 607 5.750547 GCACTGAAATTATCTCGATGACTGA 59.249 40.000 0.00 0.00 0.00 3.41
595 608 6.423302 GCACTGAAATTATCTCGATGACTGAT 59.577 38.462 0.00 0.00 0.00 2.90
596 609 7.596621 GCACTGAAATTATCTCGATGACTGATA 59.403 37.037 0.00 0.00 0.00 2.15
597 610 9.636879 CACTGAAATTATCTCGATGACTGATAT 57.363 33.333 0.00 0.00 0.00 1.63
607 620 8.171164 TCTCGATGACTGATATTATCTGTTGT 57.829 34.615 14.96 8.69 40.84 3.32
608 621 9.284968 TCTCGATGACTGATATTATCTGTTGTA 57.715 33.333 14.96 7.69 40.84 2.41
609 622 9.899226 CTCGATGACTGATATTATCTGTTGTAA 57.101 33.333 14.96 5.31 40.84 2.41
610 623 9.678941 TCGATGACTGATATTATCTGTTGTAAC 57.321 33.333 14.96 5.47 40.84 2.50
611 624 9.463443 CGATGACTGATATTATCTGTTGTAACA 57.537 33.333 14.96 9.73 40.84 2.41
620 633 6.971527 TTATCTGTTGTAACATACGTTGGG 57.028 37.500 0.00 0.00 38.41 4.12
621 634 4.603989 TCTGTTGTAACATACGTTGGGA 57.396 40.909 0.00 0.00 38.41 4.37
622 635 5.155278 TCTGTTGTAACATACGTTGGGAT 57.845 39.130 0.00 0.00 38.41 3.85
623 636 6.283544 TCTGTTGTAACATACGTTGGGATA 57.716 37.500 0.00 0.00 38.41 2.59
624 637 6.699366 TCTGTTGTAACATACGTTGGGATAA 58.301 36.000 0.00 0.00 38.41 1.75
625 638 7.160049 TCTGTTGTAACATACGTTGGGATAAA 58.840 34.615 0.00 0.00 38.41 1.40
626 639 7.825270 TCTGTTGTAACATACGTTGGGATAAAT 59.175 33.333 0.00 0.00 38.41 1.40
627 640 9.100554 CTGTTGTAACATACGTTGGGATAAATA 57.899 33.333 0.00 0.00 38.41 1.40
628 641 9.445878 TGTTGTAACATACGTTGGGATAAATAA 57.554 29.630 0.00 0.00 36.52 1.40
639 652 9.326413 ACGTTGGGATAAATAATTCTAGACAAG 57.674 33.333 0.00 0.00 0.00 3.16
640 653 9.326413 CGTTGGGATAAATAATTCTAGACAAGT 57.674 33.333 0.00 0.00 0.00 3.16
642 655 9.627123 TTGGGATAAATAATTCTAGACAAGTGG 57.373 33.333 0.00 0.00 0.00 4.00
643 656 8.998814 TGGGATAAATAATTCTAGACAAGTGGA 58.001 33.333 0.00 0.00 0.00 4.02
651 664 6.678568 ATTCTAGACAAGTGGATATGAGGG 57.321 41.667 0.00 0.00 0.00 4.30
652 665 5.403558 TCTAGACAAGTGGATATGAGGGA 57.596 43.478 0.00 0.00 0.00 4.20
653 666 5.970289 TCTAGACAAGTGGATATGAGGGAT 58.030 41.667 0.00 0.00 0.00 3.85
654 667 7.103745 TCTAGACAAGTGGATATGAGGGATA 57.896 40.000 0.00 0.00 0.00 2.59
655 668 7.535738 TCTAGACAAGTGGATATGAGGGATAA 58.464 38.462 0.00 0.00 0.00 1.75
656 669 8.010697 TCTAGACAAGTGGATATGAGGGATAAA 58.989 37.037 0.00 0.00 0.00 1.40
657 670 7.639062 AGACAAGTGGATATGAGGGATAAAT 57.361 36.000 0.00 0.00 0.00 1.40
658 671 8.742125 AGACAAGTGGATATGAGGGATAAATA 57.258 34.615 0.00 0.00 0.00 1.40
659 672 9.170890 AGACAAGTGGATATGAGGGATAAATAA 57.829 33.333 0.00 0.00 0.00 1.40
660 673 9.965902 GACAAGTGGATATGAGGGATAAATAAT 57.034 33.333 0.00 0.00 0.00 1.28
679 692 8.438676 AAATAATATAATAGATGAGGGCGTGC 57.561 34.615 0.00 0.00 0.00 5.34
680 693 5.683876 AATATAATAGATGAGGGCGTGCT 57.316 39.130 0.00 0.00 0.00 4.40
681 694 5.683876 ATATAATAGATGAGGGCGTGCTT 57.316 39.130 0.00 0.00 0.00 3.91
682 695 6.791867 ATATAATAGATGAGGGCGTGCTTA 57.208 37.500 0.00 0.00 0.00 3.09
683 696 3.838244 AATAGATGAGGGCGTGCTTAA 57.162 42.857 0.00 0.00 0.00 1.85
684 697 2.890808 TAGATGAGGGCGTGCTTAAG 57.109 50.000 0.00 0.00 0.00 1.85
685 698 1.195115 AGATGAGGGCGTGCTTAAGA 58.805 50.000 6.67 0.00 0.00 2.10
686 699 1.765314 AGATGAGGGCGTGCTTAAGAT 59.235 47.619 6.67 0.00 0.00 2.40
687 700 2.171448 AGATGAGGGCGTGCTTAAGATT 59.829 45.455 6.67 0.00 0.00 2.40
688 701 2.489938 TGAGGGCGTGCTTAAGATTT 57.510 45.000 6.67 0.00 0.00 2.17
689 702 2.790433 TGAGGGCGTGCTTAAGATTTT 58.210 42.857 6.67 0.00 0.00 1.82
690 703 3.153919 TGAGGGCGTGCTTAAGATTTTT 58.846 40.909 6.67 0.00 0.00 1.94
728 741 7.696992 AATCATTACTAAATTTGTCACGGGT 57.303 32.000 0.00 0.00 0.00 5.28
729 742 8.795842 AATCATTACTAAATTTGTCACGGGTA 57.204 30.769 0.00 0.00 0.00 3.69
730 743 8.795842 ATCATTACTAAATTTGTCACGGGTAA 57.204 30.769 0.00 0.00 0.00 2.85
731 744 8.618702 TCATTACTAAATTTGTCACGGGTAAA 57.381 30.769 0.00 0.00 0.00 2.01
732 745 9.233649 TCATTACTAAATTTGTCACGGGTAAAT 57.766 29.630 0.00 0.00 0.00 1.40
733 746 9.849166 CATTACTAAATTTGTCACGGGTAAATT 57.151 29.630 0.00 8.78 36.02 1.82
734 747 9.849166 ATTACTAAATTTGTCACGGGTAAATTG 57.151 29.630 13.36 7.14 35.05 2.32
735 748 7.279750 ACTAAATTTGTCACGGGTAAATTGT 57.720 32.000 13.36 7.60 35.05 2.71
736 749 8.393671 ACTAAATTTGTCACGGGTAAATTGTA 57.606 30.769 13.36 8.84 35.05 2.41
737 750 8.291740 ACTAAATTTGTCACGGGTAAATTGTAC 58.708 33.333 13.36 0.00 35.05 2.90
738 751 5.632244 ATTTGTCACGGGTAAATTGTACC 57.368 39.130 0.00 0.00 36.88 3.34
739 752 3.766068 TGTCACGGGTAAATTGTACCA 57.234 42.857 5.40 0.00 39.31 3.25
740 753 3.666274 TGTCACGGGTAAATTGTACCAG 58.334 45.455 5.40 3.64 39.31 4.00
741 754 3.071312 TGTCACGGGTAAATTGTACCAGT 59.929 43.478 5.40 4.28 44.69 4.00
742 755 3.681417 GTCACGGGTAAATTGTACCAGTC 59.319 47.826 5.90 0.00 42.58 3.51
743 756 3.004862 CACGGGTAAATTGTACCAGTCC 58.995 50.000 5.90 0.00 42.58 3.85
744 757 2.638855 ACGGGTAAATTGTACCAGTCCA 59.361 45.455 5.40 0.00 41.03 4.02
745 758 3.004862 CGGGTAAATTGTACCAGTCCAC 58.995 50.000 5.40 0.00 39.31 4.02
746 759 3.557475 CGGGTAAATTGTACCAGTCCACA 60.557 47.826 5.40 0.00 39.31 4.17
747 760 3.754850 GGGTAAATTGTACCAGTCCACAC 59.245 47.826 5.40 0.00 39.31 3.82
748 761 4.391155 GGTAAATTGTACCAGTCCACACA 58.609 43.478 0.00 0.00 37.53 3.72
820 833 1.428448 CACACGGCTCGAGAAATTCA 58.572 50.000 18.75 0.00 0.00 2.57
859 872 1.202604 ACCTGCCCATACCGATTTACG 60.203 52.381 0.00 0.00 42.18 3.18
900 913 7.377928 GTGTCAGCTATTTATGCATTTGATGTC 59.622 37.037 3.54 0.00 0.00 3.06
903 916 6.576313 CAGCTATTTATGCATTTGATGTCGAC 59.424 38.462 9.11 9.11 0.00 4.20
909 922 8.839947 TTTATGCATTTGATGTCGACTTAATG 57.160 30.769 17.92 17.19 0.00 1.90
952 968 2.186903 CCGCGTATGGCCAGTTCT 59.813 61.111 13.05 0.00 38.94 3.01
976 992 2.357836 CCAATGGTGAGCAGCCCT 59.642 61.111 0.00 0.00 0.00 5.19
1151 1168 0.034089 AACAGATAAGCCTGCACCCC 60.034 55.000 0.00 0.00 37.68 4.95
1167 1184 2.738521 CCGTGCTGGACAAGACGG 60.739 66.667 0.00 0.00 42.00 4.79
1173 1190 1.585006 CTGGACAAGACGGCGTACT 59.415 57.895 14.74 9.49 0.00 2.73
1178 1195 2.009774 GACAAGACGGCGTACTACCTA 58.990 52.381 14.74 0.00 0.00 3.08
1196 1213 2.367567 CCTAATAAACCCTGAGCGGCTA 59.632 50.000 0.60 0.00 0.00 3.93
1213 1233 1.626686 CTAGCGATGATGGAGGAGGT 58.373 55.000 0.00 0.00 0.00 3.85
1218 1238 2.311463 CGATGATGGAGGAGGTAGTGT 58.689 52.381 0.00 0.00 0.00 3.55
1226 1246 2.572104 GGAGGAGGTAGTGTTGGTGAAT 59.428 50.000 0.00 0.00 0.00 2.57
1260 1280 0.460284 GGTGATCGACGAGGTTGCAT 60.460 55.000 3.01 0.00 0.00 3.96
1285 1305 2.244117 GAGCACCTGAGGGCGAATCA 62.244 60.000 2.38 0.00 35.63 2.57
1286 1306 1.153086 GCACCTGAGGGCGAATCAT 60.153 57.895 2.38 0.00 35.63 2.45
1294 1314 2.437651 TGAGGGCGAATCATATGTTCCA 59.562 45.455 1.90 0.00 0.00 3.53
1304 1324 3.979911 TCATATGTTCCATGTTGGCCTT 58.020 40.909 3.32 0.00 37.47 4.35
1360 1380 2.641305 GCTGGCTGAGATGAAGAATGT 58.359 47.619 0.00 0.00 0.00 2.71
1385 1405 1.810853 CGTGCCTCACATCGCATCA 60.811 57.895 0.00 0.00 37.33 3.07
1386 1406 1.360931 CGTGCCTCACATCGCATCAA 61.361 55.000 0.00 0.00 37.33 2.57
1398 1418 3.558931 TCGCATCAACATCCAAGGTAT 57.441 42.857 0.00 0.00 0.00 2.73
1402 1422 4.096231 CGCATCAACATCCAAGGTATGAAA 59.904 41.667 5.82 0.00 0.00 2.69
1404 1424 6.017192 CGCATCAACATCCAAGGTATGAAATA 60.017 38.462 5.82 0.00 0.00 1.40
1453 1477 6.038050 GGATTCAACTGAAGTGAAGATGGATC 59.962 42.308 0.00 0.00 37.48 3.36
1494 1518 1.977056 TTGCCATGCATCCTCTGATC 58.023 50.000 0.00 0.00 38.76 2.92
1513 1537 6.483307 TCTGATCGATTTCTCTGTTTGTTTGT 59.517 34.615 0.00 0.00 0.00 2.83
1521 1545 6.817765 TTCTCTGTTTGTTTGTTTGACTCT 57.182 33.333 0.00 0.00 0.00 3.24
1533 1557 3.132111 TGTTTGACTCTGTGTGCTCAGTA 59.868 43.478 0.00 0.00 36.85 2.74
1588 1612 1.583054 ACGTGCTTGTGAGTTTCCTC 58.417 50.000 0.00 0.00 38.27 3.71
1600 1624 3.706086 TGAGTTTCCTCGGATGATGATCA 59.294 43.478 0.00 0.00 40.85 2.92
1631 1655 8.561738 TCAATCAAGTGGTCCTTAAGTTTATC 57.438 34.615 0.97 0.00 0.00 1.75
1633 1657 7.923414 ATCAAGTGGTCCTTAAGTTTATCAC 57.077 36.000 0.97 3.69 0.00 3.06
1748 1777 3.243177 CCTCTTCGTGTCTAAATAAGCGC 59.757 47.826 0.00 0.00 0.00 5.92
1753 1782 0.458889 TGTCTAAATAAGCGCGCGGT 60.459 50.000 30.98 30.98 0.00 5.68
1880 1909 6.064060 ACTCATCACTGAAAGGATTTTGACA 58.936 36.000 0.00 0.00 39.27 3.58
1882 1911 5.474532 TCATCACTGAAAGGATTTTGACAGG 59.525 40.000 0.00 0.00 39.27 4.00
1885 1914 3.571401 ACTGAAAGGATTTTGACAGGCAG 59.429 43.478 0.00 0.00 39.27 4.85
1958 1987 5.078949 TGGTATGATTTCCCTGCATTATGG 58.921 41.667 0.00 0.00 0.00 2.74
1978 2007 4.769688 TGGAGCACCATCATTAGTACTTG 58.230 43.478 0.00 0.00 41.77 3.16
1996 2025 8.307582 AGTACTTGCAACTCTATACCAGTATT 57.692 34.615 0.00 0.00 0.00 1.89
2025 2054 8.408743 AGAAGTTTAAAGTTTCGATCTATCCG 57.591 34.615 9.60 0.00 0.00 4.18
2047 2076 8.089625 TCCGTGGATATATATTCCAATGATGT 57.910 34.615 14.45 0.00 35.05 3.06
2048 2077 7.986889 TCCGTGGATATATATTCCAATGATGTG 59.013 37.037 14.45 3.99 35.05 3.21
2070 2099 5.982516 GTGATGTTAGCTCCATTCTCAGTAG 59.017 44.000 0.00 0.00 0.00 2.57
2100 2129 3.642848 AGCTTTGGTTTTGGATGTGATGT 59.357 39.130 0.00 0.00 0.00 3.06
2120 2149 0.394899 CATTGCTTGACTCCTCCCCC 60.395 60.000 0.00 0.00 0.00 5.40
2147 2176 6.455360 TTGGAAAATGGTGCTCTTCATATC 57.545 37.500 0.00 0.00 0.00 1.63
2256 2285 5.376625 CAATAGCTTGGCATTTACCTCCTA 58.623 41.667 0.00 0.00 0.00 2.94
2262 2291 6.329197 AGCTTGGCATTTACCTCCTAGTTATA 59.671 38.462 0.00 0.00 0.00 0.98
2277 2306 8.767478 TCCTAGTTATACCAAAACTTTCTTCG 57.233 34.615 0.00 0.00 38.18 3.79
2278 2307 7.332678 TCCTAGTTATACCAAAACTTTCTTCGC 59.667 37.037 0.00 0.00 38.18 4.70
2279 2308 7.333672 CCTAGTTATACCAAAACTTTCTTCGCT 59.666 37.037 0.00 0.00 38.18 4.93
2282 2311 7.227910 AGTTATACCAAAACTTTCTTCGCTTGA 59.772 33.333 0.00 0.00 33.39 3.02
2298 2327 5.872635 TCGCTTGAAGATAAGAATGCTTTG 58.127 37.500 0.00 0.00 35.56 2.77
2299 2328 5.643348 TCGCTTGAAGATAAGAATGCTTTGA 59.357 36.000 0.00 0.00 35.56 2.69
2303 2432 7.431668 GCTTGAAGATAAGAATGCTTTGATGAC 59.568 37.037 0.00 0.00 35.56 3.06
2304 2433 7.926674 TGAAGATAAGAATGCTTTGATGACA 57.073 32.000 0.00 0.00 35.56 3.58
2310 2439 4.264253 AGAATGCTTTGATGACATCCGAA 58.736 39.130 12.90 7.01 0.00 4.30
2313 2442 5.587388 ATGCTTTGATGACATCCGAATTT 57.413 34.783 12.90 0.00 0.00 1.82
2323 2452 8.020819 TGATGACATCCGAATTTTAGTTTGTTC 58.979 33.333 12.90 0.00 0.00 3.18
2333 2462 9.257865 CGAATTTTAGTTTGTTCGTTAGTATGG 57.742 33.333 0.00 0.00 38.77 2.74
2337 2466 7.493743 TTAGTTTGTTCGTTAGTATGGCAAA 57.506 32.000 0.00 0.00 0.00 3.68
2354 2483 0.831711 AAAGGGTGCCATTGTGGTCC 60.832 55.000 0.00 1.58 40.46 4.46
2390 2519 4.514401 AGCTCGTCCCCTATTTTAGTTTG 58.486 43.478 0.00 0.00 0.00 2.93
2474 2621 8.735315 TCTCTCTCTCTATGTTCAAAGTGTAAG 58.265 37.037 0.00 0.00 0.00 2.34
2489 2636 9.320295 TCAAAGTGTAAGGGAAATAAAATGGAT 57.680 29.630 0.00 0.00 0.00 3.41
2501 2648 3.837213 AAAATGGATGTGTCTTCTGCG 57.163 42.857 0.00 0.00 0.00 5.18
2510 2657 4.251543 TGTGTCTTCTGCGTTATCTTCA 57.748 40.909 0.00 0.00 0.00 3.02
2514 2661 5.050363 GTGTCTTCTGCGTTATCTTCAAACA 60.050 40.000 0.00 0.00 0.00 2.83
2549 2696 2.814805 AGCAATGCCTATGTGGAAGT 57.185 45.000 0.00 0.00 38.35 3.01
2554 2701 4.321899 GCAATGCCTATGTGGAAGTTTTGA 60.322 41.667 0.00 0.00 38.35 2.69
2557 2704 5.643379 TGCCTATGTGGAAGTTTTGATTC 57.357 39.130 0.00 0.00 38.35 2.52
2559 2706 5.716228 TGCCTATGTGGAAGTTTTGATTCAT 59.284 36.000 0.00 0.00 38.35 2.57
2569 2716 7.927629 TGGAAGTTTTGATTCATTTTCCTCTTG 59.072 33.333 14.62 0.00 34.98 3.02
2570 2717 7.928167 GGAAGTTTTGATTCATTTTCCTCTTGT 59.072 33.333 9.77 0.00 32.02 3.16
2571 2718 9.317936 GAAGTTTTGATTCATTTTCCTCTTGTT 57.682 29.630 0.00 0.00 0.00 2.83
2572 2719 8.877808 AGTTTTGATTCATTTTCCTCTTGTTC 57.122 30.769 0.00 0.00 0.00 3.18
2621 2784 7.866729 TGATATGTTAAAAGAAGTTTGACGCA 58.133 30.769 0.00 0.00 38.28 5.24
2625 2788 6.734137 TGTTAAAAGAAGTTTGACGCATCAT 58.266 32.000 0.00 0.00 38.28 2.45
2637 2800 9.060347 AGTTTGACGCATCATAATATTCAAGAT 57.940 29.630 0.00 0.00 33.85 2.40
2675 2839 4.249638 TCATGGTTTCCCCCAGATTTAG 57.750 45.455 0.00 0.00 38.07 1.85
2676 2840 3.052944 TCATGGTTTCCCCCAGATTTAGG 60.053 47.826 0.00 0.00 38.07 2.69
2693 2857 4.698583 TTAGGAACGTAGTGCTTCTCTC 57.301 45.455 0.00 0.00 45.00 3.20
2711 2875 3.772025 CTCTCTTCCTATTGGTGTGAGGT 59.228 47.826 10.60 0.00 31.78 3.85
2750 2914 6.995686 TCTTATGTATTGATGCCGTTATGGTT 59.004 34.615 0.00 0.00 41.21 3.67
2758 2922 4.396790 TGATGCCGTTATGGTTTCCTTTAC 59.603 41.667 0.00 0.00 41.21 2.01
2765 2929 6.420008 CCGTTATGGTTTCCTTTACGAGATAG 59.580 42.308 12.34 0.00 36.35 2.08
2779 2943 8.638685 TTTACGAGATAGTTTTATGTACTGGC 57.361 34.615 0.00 0.00 0.00 4.85
2788 2952 6.485171 AGTTTTATGTACTGGCCATTCTCTT 58.515 36.000 5.51 0.00 0.00 2.85
2836 3000 4.471025 TGGCAGACCATTCTCTTAGATCAA 59.529 41.667 0.00 0.00 42.67 2.57
2893 3367 6.688578 TGATGTAACTTTGTGGTACTCTCTC 58.311 40.000 0.00 0.00 39.50 3.20
2895 3369 6.726490 TGTAACTTTGTGGTACTCTCTCTT 57.274 37.500 0.00 0.00 39.50 2.85
2903 3388 4.707448 TGTGGTACTCTCTCTTTCTCATCC 59.293 45.833 0.00 0.00 0.00 3.51
2921 3406 2.631384 TCCTCTTGGATTCCAGGTCAA 58.369 47.619 13.93 0.00 37.46 3.18
2930 3415 2.270352 TTCCAGGTCAACACCATCAC 57.730 50.000 0.00 0.00 46.68 3.06
2950 3435 1.152525 GGGCGGGATGAGGTCTCTA 60.153 63.158 0.00 0.00 0.00 2.43
2952 3437 1.272536 GGGCGGGATGAGGTCTCTATA 60.273 57.143 0.00 0.00 0.00 1.31
2957 3442 4.566070 GCGGGATGAGGTCTCTATAGTAGT 60.566 50.000 0.00 0.00 0.00 2.73
2989 3474 7.350921 TGGGATCTCCACTAATTTATCTCCTTT 59.649 37.037 0.00 0.00 41.46 3.11
2990 3475 7.663493 GGGATCTCCACTAATTTATCTCCTTTG 59.337 40.741 0.00 0.00 37.91 2.77
2993 3478 8.319057 TCTCCACTAATTTATCTCCTTTGCTA 57.681 34.615 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 8.893727 AGAGTAAGCTTGCGACATATAATTTTT 58.106 29.630 9.86 0.00 0.00 1.94
53 54 7.495934 ACAGAGTAAGCTTGCGACATATAATTT 59.504 33.333 9.86 0.00 0.00 1.82
54 55 6.986817 ACAGAGTAAGCTTGCGACATATAATT 59.013 34.615 9.86 0.00 0.00 1.40
55 56 6.516718 ACAGAGTAAGCTTGCGACATATAAT 58.483 36.000 9.86 0.00 0.00 1.28
102 104 6.461509 GCTCTGAACCCAAATCTTTTCTTCAA 60.462 38.462 0.00 0.00 0.00 2.69
158 160 2.223572 GCTTTGTGACTGACCAACAAGG 60.224 50.000 0.00 0.00 45.67 3.61
216 218 3.147629 CAGGAGCTCATCATTTCCCATC 58.852 50.000 17.19 0.00 0.00 3.51
281 283 0.871163 GTTGAACGACGTCCAACCGA 60.871 55.000 18.15 2.38 35.43 4.69
302 304 1.149174 CAGTGGGTGCCAGAGTTGT 59.851 57.895 0.00 0.00 32.34 3.32
323 325 0.392998 AGGTTGTAGCCGAGGCATTG 60.393 55.000 17.18 0.00 44.88 2.82
325 327 1.522569 GAGGTTGTAGCCGAGGCAT 59.477 57.895 17.18 4.24 44.88 4.40
369 371 1.755380 GTCCCATACAGTAGCCGAAGT 59.245 52.381 0.00 0.00 0.00 3.01
516 529 0.615331 GACCATCCAAGGACAGAGCA 59.385 55.000 0.00 0.00 0.00 4.26
549 562 7.119699 CAGTGCCAATAAAGTTCAGATAGACAA 59.880 37.037 0.00 0.00 0.00 3.18
550 563 6.595326 CAGTGCCAATAAAGTTCAGATAGACA 59.405 38.462 0.00 0.00 0.00 3.41
551 564 6.818644 TCAGTGCCAATAAAGTTCAGATAGAC 59.181 38.462 0.00 0.00 0.00 2.59
552 565 6.946340 TCAGTGCCAATAAAGTTCAGATAGA 58.054 36.000 0.00 0.00 0.00 1.98
553 566 7.615582 TTCAGTGCCAATAAAGTTCAGATAG 57.384 36.000 0.00 0.00 0.00 2.08
554 567 7.994425 TTTCAGTGCCAATAAAGTTCAGATA 57.006 32.000 0.00 0.00 0.00 1.98
555 568 6.899393 TTTCAGTGCCAATAAAGTTCAGAT 57.101 33.333 0.00 0.00 0.00 2.90
556 569 6.899393 ATTTCAGTGCCAATAAAGTTCAGA 57.101 33.333 0.00 0.00 0.00 3.27
557 570 9.294030 GATAATTTCAGTGCCAATAAAGTTCAG 57.706 33.333 0.00 0.00 0.00 3.02
558 571 9.023962 AGATAATTTCAGTGCCAATAAAGTTCA 57.976 29.630 0.00 0.00 0.00 3.18
559 572 9.508567 GAGATAATTTCAGTGCCAATAAAGTTC 57.491 33.333 0.00 0.00 0.00 3.01
560 573 8.184192 CGAGATAATTTCAGTGCCAATAAAGTT 58.816 33.333 0.00 0.00 0.00 2.66
561 574 7.552687 TCGAGATAATTTCAGTGCCAATAAAGT 59.447 33.333 0.00 0.00 0.00 2.66
562 575 7.919690 TCGAGATAATTTCAGTGCCAATAAAG 58.080 34.615 0.00 0.00 0.00 1.85
563 576 7.857734 TCGAGATAATTTCAGTGCCAATAAA 57.142 32.000 0.00 0.00 0.00 1.40
564 577 7.714813 TCATCGAGATAATTTCAGTGCCAATAA 59.285 33.333 0.00 0.00 0.00 1.40
565 578 7.171508 GTCATCGAGATAATTTCAGTGCCAATA 59.828 37.037 0.00 0.00 0.00 1.90
566 579 6.017605 GTCATCGAGATAATTTCAGTGCCAAT 60.018 38.462 0.00 0.00 0.00 3.16
567 580 5.294306 GTCATCGAGATAATTTCAGTGCCAA 59.706 40.000 0.00 0.00 0.00 4.52
568 581 4.811024 GTCATCGAGATAATTTCAGTGCCA 59.189 41.667 0.00 0.00 0.00 4.92
569 582 5.050499 CAGTCATCGAGATAATTTCAGTGCC 60.050 44.000 0.00 0.00 0.00 5.01
570 583 5.750547 TCAGTCATCGAGATAATTTCAGTGC 59.249 40.000 0.00 0.00 0.00 4.40
571 584 7.943413 ATCAGTCATCGAGATAATTTCAGTG 57.057 36.000 0.00 0.00 0.00 3.66
581 594 8.801299 ACAACAGATAATATCAGTCATCGAGAT 58.199 33.333 2.84 0.00 0.00 2.75
582 595 8.171164 ACAACAGATAATATCAGTCATCGAGA 57.829 34.615 2.84 0.00 0.00 4.04
583 596 9.899226 TTACAACAGATAATATCAGTCATCGAG 57.101 33.333 2.84 0.00 0.00 4.04
584 597 9.678941 GTTACAACAGATAATATCAGTCATCGA 57.321 33.333 2.84 0.00 0.00 3.59
585 598 9.463443 TGTTACAACAGATAATATCAGTCATCG 57.537 33.333 2.84 0.00 34.30 3.84
594 607 9.268268 CCCAACGTATGTTACAACAGATAATAT 57.732 33.333 0.00 0.00 43.04 1.28
595 608 8.476447 TCCCAACGTATGTTACAACAGATAATA 58.524 33.333 0.00 0.00 43.04 0.98
596 609 7.332557 TCCCAACGTATGTTACAACAGATAAT 58.667 34.615 0.00 0.00 43.04 1.28
597 610 6.699366 TCCCAACGTATGTTACAACAGATAA 58.301 36.000 0.00 0.00 43.04 1.75
598 611 6.283544 TCCCAACGTATGTTACAACAGATA 57.716 37.500 0.00 0.00 43.04 1.98
599 612 5.155278 TCCCAACGTATGTTACAACAGAT 57.845 39.130 0.00 0.00 43.04 2.90
600 613 4.603989 TCCCAACGTATGTTACAACAGA 57.396 40.909 0.00 0.00 43.04 3.41
601 614 6.971527 TTATCCCAACGTATGTTACAACAG 57.028 37.500 0.00 0.00 43.04 3.16
602 615 7.925043 ATTTATCCCAACGTATGTTACAACA 57.075 32.000 0.00 0.00 44.06 3.33
613 626 9.326413 CTTGTCTAGAATTATTTATCCCAACGT 57.674 33.333 0.00 0.00 0.00 3.99
614 627 9.326413 ACTTGTCTAGAATTATTTATCCCAACG 57.674 33.333 0.00 0.00 0.00 4.10
616 629 9.627123 CCACTTGTCTAGAATTATTTATCCCAA 57.373 33.333 0.00 0.00 0.00 4.12
617 630 8.998814 TCCACTTGTCTAGAATTATTTATCCCA 58.001 33.333 0.00 0.00 0.00 4.37
625 638 8.820831 CCCTCATATCCACTTGTCTAGAATTAT 58.179 37.037 0.00 0.00 0.00 1.28
626 639 8.010697 TCCCTCATATCCACTTGTCTAGAATTA 58.989 37.037 0.00 0.00 0.00 1.40
627 640 6.846505 TCCCTCATATCCACTTGTCTAGAATT 59.153 38.462 0.00 0.00 0.00 2.17
628 641 6.385443 TCCCTCATATCCACTTGTCTAGAAT 58.615 40.000 0.00 0.00 0.00 2.40
629 642 5.777449 TCCCTCATATCCACTTGTCTAGAA 58.223 41.667 0.00 0.00 0.00 2.10
630 643 5.403558 TCCCTCATATCCACTTGTCTAGA 57.596 43.478 0.00 0.00 0.00 2.43
631 644 7.782897 TTATCCCTCATATCCACTTGTCTAG 57.217 40.000 0.00 0.00 0.00 2.43
632 645 8.742125 ATTTATCCCTCATATCCACTTGTCTA 57.258 34.615 0.00 0.00 0.00 2.59
633 646 7.639062 ATTTATCCCTCATATCCACTTGTCT 57.361 36.000 0.00 0.00 0.00 3.41
634 647 9.965902 ATTATTTATCCCTCATATCCACTTGTC 57.034 33.333 0.00 0.00 0.00 3.18
653 666 9.542462 GCACGCCCTCATCTATTATATTATTTA 57.458 33.333 0.00 0.00 0.00 1.40
654 667 8.267894 AGCACGCCCTCATCTATTATATTATTT 58.732 33.333 0.00 0.00 0.00 1.40
655 668 7.796054 AGCACGCCCTCATCTATTATATTATT 58.204 34.615 0.00 0.00 0.00 1.40
656 669 7.366847 AGCACGCCCTCATCTATTATATTAT 57.633 36.000 0.00 0.00 0.00 1.28
657 670 6.791867 AGCACGCCCTCATCTATTATATTA 57.208 37.500 0.00 0.00 0.00 0.98
658 671 5.683876 AGCACGCCCTCATCTATTATATT 57.316 39.130 0.00 0.00 0.00 1.28
659 672 5.683876 AAGCACGCCCTCATCTATTATAT 57.316 39.130 0.00 0.00 0.00 0.86
660 673 6.436218 TCTTAAGCACGCCCTCATCTATTATA 59.564 38.462 0.00 0.00 0.00 0.98
661 674 5.246203 TCTTAAGCACGCCCTCATCTATTAT 59.754 40.000 0.00 0.00 0.00 1.28
662 675 4.587262 TCTTAAGCACGCCCTCATCTATTA 59.413 41.667 0.00 0.00 0.00 0.98
663 676 3.388024 TCTTAAGCACGCCCTCATCTATT 59.612 43.478 0.00 0.00 0.00 1.73
664 677 2.965831 TCTTAAGCACGCCCTCATCTAT 59.034 45.455 0.00 0.00 0.00 1.98
665 678 2.384828 TCTTAAGCACGCCCTCATCTA 58.615 47.619 0.00 0.00 0.00 1.98
666 679 1.195115 TCTTAAGCACGCCCTCATCT 58.805 50.000 0.00 0.00 0.00 2.90
667 680 2.246719 ATCTTAAGCACGCCCTCATC 57.753 50.000 0.00 0.00 0.00 2.92
668 681 2.717639 AATCTTAAGCACGCCCTCAT 57.282 45.000 0.00 0.00 0.00 2.90
669 682 2.489938 AAATCTTAAGCACGCCCTCA 57.510 45.000 0.00 0.00 0.00 3.86
670 683 3.850122 AAAAATCTTAAGCACGCCCTC 57.150 42.857 0.00 0.00 0.00 4.30
702 715 9.233649 ACCCGTGACAAATTTAGTAATGATTAA 57.766 29.630 0.00 0.00 0.00 1.40
703 716 8.795842 ACCCGTGACAAATTTAGTAATGATTA 57.204 30.769 0.00 0.00 0.00 1.75
704 717 7.696992 ACCCGTGACAAATTTAGTAATGATT 57.303 32.000 0.00 0.00 0.00 2.57
705 718 8.795842 TTACCCGTGACAAATTTAGTAATGAT 57.204 30.769 0.00 0.00 0.00 2.45
706 719 8.618702 TTTACCCGTGACAAATTTAGTAATGA 57.381 30.769 0.00 0.00 0.00 2.57
707 720 9.849166 AATTTACCCGTGACAAATTTAGTAATG 57.151 29.630 0.00 0.00 29.77 1.90
708 721 9.849166 CAATTTACCCGTGACAAATTTAGTAAT 57.151 29.630 0.00 0.00 31.27 1.89
709 722 8.848182 ACAATTTACCCGTGACAAATTTAGTAA 58.152 29.630 0.00 0.00 31.27 2.24
710 723 8.393671 ACAATTTACCCGTGACAAATTTAGTA 57.606 30.769 0.00 0.00 31.27 1.82
711 724 7.279750 ACAATTTACCCGTGACAAATTTAGT 57.720 32.000 0.00 0.00 31.27 2.24
712 725 7.751793 GGTACAATTTACCCGTGACAAATTTAG 59.248 37.037 0.00 0.00 31.27 1.85
713 726 7.230108 TGGTACAATTTACCCGTGACAAATTTA 59.770 33.333 11.79 0.00 36.79 1.40
714 727 6.040616 TGGTACAATTTACCCGTGACAAATTT 59.959 34.615 11.79 0.00 36.79 1.82
715 728 5.535406 TGGTACAATTTACCCGTGACAAATT 59.465 36.000 11.79 0.00 36.79 1.82
716 729 5.071370 TGGTACAATTTACCCGTGACAAAT 58.929 37.500 11.79 0.00 36.79 2.32
717 730 4.458397 TGGTACAATTTACCCGTGACAAA 58.542 39.130 11.79 0.00 36.79 2.83
718 731 4.066490 CTGGTACAATTTACCCGTGACAA 58.934 43.478 11.79 0.00 38.70 3.18
719 732 3.071312 ACTGGTACAATTTACCCGTGACA 59.929 43.478 11.79 0.00 38.70 3.58
720 733 3.667360 ACTGGTACAATTTACCCGTGAC 58.333 45.455 11.79 0.00 38.70 3.67
721 734 3.306919 GGACTGGTACAATTTACCCGTGA 60.307 47.826 14.14 0.00 38.70 4.35
722 735 3.004862 GGACTGGTACAATTTACCCGTG 58.995 50.000 14.14 8.21 38.70 4.94
723 736 2.638855 TGGACTGGTACAATTTACCCGT 59.361 45.455 11.07 11.07 38.70 5.28
724 737 3.004862 GTGGACTGGTACAATTTACCCG 58.995 50.000 11.79 9.18 38.70 5.28
725 738 3.754850 GTGTGGACTGGTACAATTTACCC 59.245 47.826 11.79 0.00 38.70 3.69
726 739 4.391155 TGTGTGGACTGGTACAATTTACC 58.609 43.478 0.00 8.89 38.70 2.85
727 740 4.083484 GCTGTGTGGACTGGTACAATTTAC 60.083 45.833 0.00 0.00 38.70 2.01
728 741 4.069304 GCTGTGTGGACTGGTACAATTTA 58.931 43.478 0.00 0.00 38.70 1.40
729 742 2.884639 GCTGTGTGGACTGGTACAATTT 59.115 45.455 0.00 0.00 38.70 1.82
730 743 2.106511 AGCTGTGTGGACTGGTACAATT 59.893 45.455 0.00 0.00 38.70 2.32
731 744 1.699634 AGCTGTGTGGACTGGTACAAT 59.300 47.619 0.00 0.00 38.70 2.71
732 745 1.128200 AGCTGTGTGGACTGGTACAA 58.872 50.000 0.00 0.00 38.70 2.41
733 746 1.893137 CTAGCTGTGTGGACTGGTACA 59.107 52.381 0.00 0.00 34.11 2.90
734 747 2.168496 TCTAGCTGTGTGGACTGGTAC 58.832 52.381 0.00 0.00 34.11 3.34
735 748 2.597578 TCTAGCTGTGTGGACTGGTA 57.402 50.000 0.00 0.00 34.11 3.25
736 749 1.944177 ATCTAGCTGTGTGGACTGGT 58.056 50.000 0.00 0.00 36.01 4.00
737 750 2.234661 TCAATCTAGCTGTGTGGACTGG 59.765 50.000 0.00 0.00 0.00 4.00
738 751 3.519579 CTCAATCTAGCTGTGTGGACTG 58.480 50.000 0.00 0.00 0.00 3.51
739 752 2.499289 CCTCAATCTAGCTGTGTGGACT 59.501 50.000 0.00 0.00 0.00 3.85
740 753 2.419297 CCCTCAATCTAGCTGTGTGGAC 60.419 54.545 0.00 0.00 0.00 4.02
741 754 1.833630 CCCTCAATCTAGCTGTGTGGA 59.166 52.381 0.00 0.00 0.00 4.02
742 755 1.134280 CCCCTCAATCTAGCTGTGTGG 60.134 57.143 0.00 0.00 0.00 4.17
743 756 1.556911 ACCCCTCAATCTAGCTGTGTG 59.443 52.381 0.00 0.00 0.00 3.82
744 757 1.958288 ACCCCTCAATCTAGCTGTGT 58.042 50.000 0.00 0.00 0.00 3.72
745 758 2.237143 TGAACCCCTCAATCTAGCTGTG 59.763 50.000 0.00 0.00 0.00 3.66
746 759 2.551270 TGAACCCCTCAATCTAGCTGT 58.449 47.619 0.00 0.00 0.00 4.40
747 760 3.198635 TCTTGAACCCCTCAATCTAGCTG 59.801 47.826 0.00 0.00 43.20 4.24
748 761 3.454858 TCTTGAACCCCTCAATCTAGCT 58.545 45.455 0.00 0.00 43.20 3.32
859 872 4.878397 AGCTGACACAAGAATAATAGTGCC 59.122 41.667 0.00 0.00 35.47 5.01
900 913 9.502145 AAACATTATTACACATGCATTAAGTCG 57.498 29.630 0.00 0.00 0.00 4.18
936 952 0.739462 TCAAGAACTGGCCATACGCG 60.739 55.000 5.51 3.53 38.94 6.01
952 968 1.614903 CTGCTCACCATTGGCTTTCAA 59.385 47.619 1.54 0.00 40.01 2.69
976 992 2.496899 GAAGCCCTCTTCCATGTCAA 57.503 50.000 0.00 0.00 42.18 3.18
1016 1032 4.567195 TGACCACATCAGCCTCCT 57.433 55.556 0.00 0.00 31.91 3.69
1092 1108 9.911788 ACAGAGTTCCATATCTCAAATGTAATT 57.088 29.630 0.00 0.00 38.98 1.40
1093 1109 9.911788 AACAGAGTTCCATATCTCAAATGTAAT 57.088 29.630 0.00 0.00 33.63 1.89
1108 1124 4.136796 CCATCAACAGAAACAGAGTTCCA 58.863 43.478 0.00 0.00 0.00 3.53
1151 1168 3.414700 GCCGTCTTGTCCAGCACG 61.415 66.667 0.00 0.00 0.00 5.34
1167 1184 5.520376 TCAGGGTTTATTAGGTAGTACGC 57.480 43.478 0.00 0.00 0.00 4.42
1173 1190 2.103601 GCCGCTCAGGGTTTATTAGGTA 59.896 50.000 0.00 0.00 41.48 3.08
1196 1213 1.133325 ACTACCTCCTCCATCATCGCT 60.133 52.381 0.00 0.00 0.00 4.93
1206 1223 3.600388 CATTCACCAACACTACCTCCTC 58.400 50.000 0.00 0.00 0.00 3.71
1213 1233 1.438651 GCTCGCATTCACCAACACTA 58.561 50.000 0.00 0.00 0.00 2.74
1218 1238 2.031919 ACGGCTCGCATTCACCAA 59.968 55.556 0.00 0.00 0.00 3.67
1294 1314 4.503643 CCTCAAAAACATCAAGGCCAACAT 60.504 41.667 5.01 0.00 0.00 2.71
1304 1324 4.038271 AGGCTCATCCTCAAAAACATCA 57.962 40.909 0.00 0.00 43.20 3.07
1360 1380 2.523184 GATGTGAGGCACGACGACGA 62.523 60.000 15.32 0.00 42.66 4.20
1423 1445 6.973843 TCTTCACTTCAGTTGAATCCAATTG 58.026 36.000 0.00 0.00 40.19 2.32
1494 1518 6.747280 AGTCAAACAAACAAACAGAGAAATCG 59.253 34.615 0.00 0.00 0.00 3.34
1513 1537 2.988010 ACTGAGCACACAGAGTCAAA 57.012 45.000 11.41 0.00 40.63 2.69
1521 1545 1.081442 CGCGTCTACTGAGCACACA 60.081 57.895 0.00 0.00 0.00 3.72
1533 1557 2.579201 CCATCCCTTCACGCGTCT 59.421 61.111 9.86 0.00 0.00 4.18
1588 1612 7.662604 TGATTGATTAAGTGATCATCATCCG 57.337 36.000 0.00 0.00 36.05 4.18
1600 1624 8.164070 ACTTAAGGACCACTTGATTGATTAAGT 58.836 33.333 7.53 0.00 40.37 2.24
1616 1640 7.606839 ACTTTAGCAGTGATAAACTTAAGGACC 59.393 37.037 9.46 0.00 36.83 4.46
1645 1669 6.097554 AGGTTCAGATCAGTAATCACCTACTG 59.902 42.308 4.70 4.70 46.85 2.74
1725 1754 3.797256 CGCTTATTTAGACACGAAGAGGG 59.203 47.826 0.00 0.00 0.00 4.30
1748 1777 1.135803 CACCCAACAAAATAGACCGCG 60.136 52.381 0.00 0.00 0.00 6.46
1753 1782 7.175990 GGTTATGAGAACACCCAACAAAATAGA 59.824 37.037 0.00 0.00 0.00 1.98
1853 1882 9.383519 GTCAAAATCCTTTCAGTGATGAGTATA 57.616 33.333 0.00 0.00 0.00 1.47
1880 1909 1.145571 TACCAAACCTGGAACTGCCT 58.854 50.000 0.00 0.00 46.92 4.75
1882 1911 2.271944 AGTACCAAACCTGGAACTGC 57.728 50.000 0.00 0.00 46.92 4.40
1885 1914 7.279750 TCAAAATTAGTACCAAACCTGGAAC 57.720 36.000 0.00 0.00 46.92 3.62
1958 1987 4.191544 TGCAAGTACTAATGATGGTGCTC 58.808 43.478 11.89 0.00 31.96 4.26
1971 2000 7.899648 ATACTGGTATAGAGTTGCAAGTACT 57.100 36.000 6.80 8.83 0.00 2.73
1978 2007 8.718102 TTCTTCAAATACTGGTATAGAGTTGC 57.282 34.615 0.00 0.00 0.00 4.17
2014 2043 8.161425 TGGAATATATATCCACGGATAGATCGA 58.839 37.037 14.88 1.94 41.98 3.59
2023 2052 7.986889 TCACATCATTGGAATATATATCCACGG 59.013 37.037 13.15 9.87 46.37 4.94
2047 2076 5.658634 ACTACTGAGAATGGAGCTAACATCA 59.341 40.000 4.05 0.00 0.00 3.07
2048 2077 6.155475 ACTACTGAGAATGGAGCTAACATC 57.845 41.667 4.05 0.00 0.00 3.06
2053 2082 4.528076 AGGACTACTGAGAATGGAGCTA 57.472 45.455 0.00 0.00 0.00 3.32
2056 2085 5.659463 CTGAAAGGACTACTGAGAATGGAG 58.341 45.833 0.00 0.00 0.00 3.86
2070 2099 3.132111 TCCAAAACCAAAGCTGAAAGGAC 59.868 43.478 0.00 0.00 0.00 3.85
2100 2129 0.620556 GGGGAGGAGTCAAGCAATGA 59.379 55.000 0.00 0.00 35.05 2.57
2120 2149 4.706476 TGAAGAGCACCATTTTCCAATAGG 59.294 41.667 0.00 0.00 0.00 2.57
2147 2176 7.923344 TGAACTTTCTTAAGACAGAAGAGTGAG 59.077 37.037 22.46 0.00 34.22 3.51
2218 2247 2.476619 GCTATTGGCATGCTAGTGTACG 59.523 50.000 18.92 0.63 41.35 3.67
2256 2285 7.227910 TCAAGCGAAGAAAGTTTTGGTATAACT 59.772 33.333 0.00 0.00 37.43 2.24
2262 2291 4.712122 TTCAAGCGAAGAAAGTTTTGGT 57.288 36.364 0.00 0.00 0.00 3.67
2277 2306 7.431668 GTCATCAAAGCATTCTTATCTTCAAGC 59.568 37.037 0.00 0.00 31.02 4.01
2278 2307 8.456471 TGTCATCAAAGCATTCTTATCTTCAAG 58.544 33.333 0.00 0.00 31.02 3.02
2279 2308 8.339344 TGTCATCAAAGCATTCTTATCTTCAA 57.661 30.769 0.00 0.00 31.02 2.69
2282 2311 7.255035 CGGATGTCATCAAAGCATTCTTATCTT 60.255 37.037 14.72 0.00 31.02 2.40
2284 2313 6.203530 TCGGATGTCATCAAAGCATTCTTATC 59.796 38.462 14.72 0.00 31.02 1.75
2285 2314 6.057533 TCGGATGTCATCAAAGCATTCTTAT 58.942 36.000 14.72 0.00 31.02 1.73
2287 2316 4.264253 TCGGATGTCATCAAAGCATTCTT 58.736 39.130 14.72 0.00 0.00 2.52
2288 2317 3.877559 TCGGATGTCATCAAAGCATTCT 58.122 40.909 14.72 0.00 0.00 2.40
2289 2318 4.621068 TTCGGATGTCATCAAAGCATTC 57.379 40.909 14.72 0.00 0.00 2.67
2290 2319 5.587388 AATTCGGATGTCATCAAAGCATT 57.413 34.783 14.72 5.07 0.00 3.56
2292 2321 5.389859 AAAATTCGGATGTCATCAAAGCA 57.610 34.783 14.72 0.00 0.00 3.91
2293 2322 6.555315 ACTAAAATTCGGATGTCATCAAAGC 58.445 36.000 14.72 0.00 0.00 3.51
2294 2323 8.853345 CAAACTAAAATTCGGATGTCATCAAAG 58.147 33.333 14.72 5.65 0.00 2.77
2295 2324 8.356657 ACAAACTAAAATTCGGATGTCATCAAA 58.643 29.630 14.72 8.46 0.00 2.69
2298 2327 7.216317 CGAACAAACTAAAATTCGGATGTCATC 59.784 37.037 4.06 4.06 40.11 2.92
2299 2328 7.021196 CGAACAAACTAAAATTCGGATGTCAT 58.979 34.615 0.00 0.00 40.11 3.06
2303 2432 8.013378 ACTAACGAACAAACTAAAATTCGGATG 58.987 33.333 9.69 2.36 46.26 3.51
2304 2433 8.091385 ACTAACGAACAAACTAAAATTCGGAT 57.909 30.769 9.69 1.70 46.26 4.18
2310 2439 8.101654 TGCCATACTAACGAACAAACTAAAAT 57.898 30.769 0.00 0.00 0.00 1.82
2313 2442 7.308109 CCTTTGCCATACTAACGAACAAACTAA 60.308 37.037 0.00 0.00 0.00 2.24
2323 2452 1.400494 GCACCCTTTGCCATACTAACG 59.600 52.381 0.00 0.00 46.63 3.18
2337 2466 2.440599 GGACCACAATGGCACCCT 59.559 61.111 0.00 0.00 42.67 4.34
2354 2483 0.596083 CGAGCTAACATGAGGCTCCG 60.596 60.000 22.66 5.74 46.60 4.63
2438 2585 7.455641 ACATAGAGAGAGAGAGAACGAAAAA 57.544 36.000 0.00 0.00 0.00 1.94
2443 2590 6.429791 TTGAACATAGAGAGAGAGAGAACG 57.570 41.667 0.00 0.00 0.00 3.95
2444 2591 7.754924 CACTTTGAACATAGAGAGAGAGAGAAC 59.245 40.741 0.00 0.00 0.00 3.01
2445 2592 7.450014 ACACTTTGAACATAGAGAGAGAGAGAA 59.550 37.037 0.00 0.00 0.00 2.87
2446 2593 6.945435 ACACTTTGAACATAGAGAGAGAGAGA 59.055 38.462 0.00 0.00 0.00 3.10
2447 2594 7.156876 ACACTTTGAACATAGAGAGAGAGAG 57.843 40.000 0.00 0.00 0.00 3.20
2448 2595 8.637196 TTACACTTTGAACATAGAGAGAGAGA 57.363 34.615 0.00 0.00 0.00 3.10
2449 2596 7.973388 CCTTACACTTTGAACATAGAGAGAGAG 59.027 40.741 0.00 0.00 0.00 3.20
2450 2597 7.093727 CCCTTACACTTTGAACATAGAGAGAGA 60.094 40.741 0.00 0.00 0.00 3.10
2451 2598 7.038659 CCCTTACACTTTGAACATAGAGAGAG 58.961 42.308 0.00 0.00 0.00 3.20
2474 2621 7.260603 CAGAAGACACATCCATTTTATTTCCC 58.739 38.462 0.00 0.00 0.00 3.97
2484 2631 2.479566 AACGCAGAAGACACATCCAT 57.520 45.000 0.00 0.00 0.00 3.41
2489 2636 4.251543 TGAAGATAACGCAGAAGACACA 57.748 40.909 0.00 0.00 0.00 3.72
2514 2661 6.711645 AGGCATTGCTACAAAACAAAATTGAT 59.288 30.769 8.82 0.00 0.00 2.57
2529 2676 3.931907 ACTTCCACATAGGCATTGCTA 57.068 42.857 8.82 0.00 37.29 3.49
2549 2696 9.965824 GTAGAACAAGAGGAAAATGAATCAAAA 57.034 29.630 0.00 0.00 0.00 2.44
2559 2706 8.648693 AGCTTTAGTAGTAGAACAAGAGGAAAA 58.351 33.333 0.00 0.00 0.00 2.29
2611 2758 8.437360 TCTTGAATATTATGATGCGTCAAACT 57.563 30.769 13.65 0.00 38.01 2.66
2637 2800 8.862325 AAACCATGATACTCAAATAAGTGTGA 57.138 30.769 0.00 0.00 0.00 3.58
2659 2822 3.014623 CGTTCCTAAATCTGGGGGAAAC 58.985 50.000 0.00 0.00 39.20 2.78
2675 2839 3.503891 GAAGAGAGAAGCACTACGTTCC 58.496 50.000 0.00 0.00 0.00 3.62
2676 2840 3.191791 AGGAAGAGAGAAGCACTACGTTC 59.808 47.826 0.00 0.00 0.00 3.95
2693 2857 2.571653 TCCACCTCACACCAATAGGAAG 59.428 50.000 0.00 0.00 38.69 3.46
2725 2889 6.530120 ACCATAACGGCATCAATACATAAGA 58.470 36.000 0.00 0.00 39.03 2.10
2729 2893 5.009610 GGAAACCATAACGGCATCAATACAT 59.990 40.000 0.00 0.00 39.03 2.29
2733 2897 3.631250 AGGAAACCATAACGGCATCAAT 58.369 40.909 0.00 0.00 39.03 2.57
2741 2905 6.976925 ACTATCTCGTAAAGGAAACCATAACG 59.023 38.462 0.00 0.00 0.00 3.18
2758 2922 5.597806 TGGCCAGTACATAAAACTATCTCG 58.402 41.667 0.00 0.00 0.00 4.04
2765 2929 6.759497 AAGAGAATGGCCAGTACATAAAAC 57.241 37.500 13.05 0.00 0.00 2.43
2795 2959 8.896921 GGTCTGCCAACATAATGGAACAAAAAC 61.897 40.741 0.00 0.00 43.54 2.43
2866 3340 6.223852 AGAGTACCACAAAGTTACATCAGTG 58.776 40.000 0.00 0.00 0.00 3.66
2879 3353 5.186021 GGATGAGAAAGAGAGAGTACCACAA 59.814 44.000 0.00 0.00 0.00 3.33
2880 3354 4.707448 GGATGAGAAAGAGAGAGTACCACA 59.293 45.833 0.00 0.00 0.00 4.17
2881 3355 4.953579 AGGATGAGAAAGAGAGAGTACCAC 59.046 45.833 0.00 0.00 0.00 4.16
2903 3388 3.077359 GTGTTGACCTGGAATCCAAGAG 58.923 50.000 4.66 0.00 30.80 2.85
2950 3435 5.476983 TGGAGATCCCATCCAAACTACTAT 58.523 41.667 0.00 0.00 43.87 2.12
2952 3437 3.736094 TGGAGATCCCATCCAAACTACT 58.264 45.455 0.00 0.00 43.87 2.57
2989 3474 2.901249 GAGCCTCCGTTTACAATAGCA 58.099 47.619 0.00 0.00 0.00 3.49


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

AutoCloner maintained by Alex Coulton.