Multiple sequence alignment - TraesCS2B01G344400

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 TraesCS2B01G344400 chr2B 100.000 3416 0 0 1 3416 491026140 491022725 0.000000e+00 6309
1 TraesCS2B01G344400 chr2D 95.298 1999 84 8 1424 3415 419026935 419024940 0.000000e+00 3162
2 TraesCS2B01G344400 chr2D 90.134 598 24 18 846 1425 419027566 419026986 0.000000e+00 745
3 TraesCS2B01G344400 chr2A 89.705 1729 126 27 848 2542 571147756 571149466 0.000000e+00 2159
4 TraesCS2B01G344400 chr2A 90.878 888 64 7 2530 3416 571149481 571150352 0.000000e+00 1175
5 TraesCS2B01G344400 chr1A 94.576 590 29 2 1 588 494176123 494175535 0.000000e+00 909
6 TraesCS2B01G344400 chr5D 92.386 591 40 5 5 593 254010418 254009831 0.000000e+00 837
7 TraesCS2B01G344400 chr5D 90.556 593 48 6 1 588 527818544 527817955 0.000000e+00 778
8 TraesCS2B01G344400 chr5D 88.583 254 24 2 589 842 465087287 465087535 1.540000e-78 303
9 TraesCS2B01G344400 chr1B 91.032 591 50 2 1 589 651443995 651443406 0.000000e+00 795
10 TraesCS2B01G344400 chr3D 90.541 592 48 7 1 588 549754977 549755564 0.000000e+00 776
11 TraesCS2B01G344400 chr4D 90.236 594 48 9 1 588 321825443 321826032 0.000000e+00 767
12 TraesCS2B01G344400 chr4D 85.581 215 21 6 640 845 433395456 433395669 2.060000e-52 217
13 TraesCS2B01G344400 chr6A 90.084 595 48 9 1 588 59944525 59943935 0.000000e+00 761
14 TraesCS2B01G344400 chr4A 89.933 596 48 9 1 588 242785149 242785740 0.000000e+00 758
15 TraesCS2B01G344400 chr4A 89.351 601 54 7 1 596 690857901 690857306 0.000000e+00 747
16 TraesCS2B01G344400 chr1D 90.157 254 20 2 589 842 54924248 54924496 3.290000e-85 326
17 TraesCS2B01G344400 chr1D 89.764 254 21 2 589 842 113863835 113864083 1.530000e-83 320
18 TraesCS2B01G344400 chr1D 88.372 258 23 2 589 846 162055074 162055324 1.540000e-78 303
19 TraesCS2B01G344400 chr7B 88.803 259 27 2 589 846 119631807 119632064 1.980000e-82 316
20 TraesCS2B01G344400 chr7A 89.147 258 22 3 589 846 447285009 447285260 1.980000e-82 316
21 TraesCS2B01G344400 chr7D 88.327 257 25 2 589 845 634749337 634749588 1.540000e-78 303
22 TraesCS2B01G344400 chr3A 88.933 253 19 3 589 841 425512508 425512751 1.540000e-78 303
23 TraesCS2B01G344400 chr3A 87.549 257 31 1 589 845 24974684 24974939 2.580000e-76 296


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 TraesCS2B01G344400 chr2B 491022725 491026140 3415 True 6309.0 6309 100.0000 1 3416 1 chr2B.!!$R1 3415
1 TraesCS2B01G344400 chr2D 419024940 419027566 2626 True 1953.5 3162 92.7160 846 3415 2 chr2D.!!$R1 2569
2 TraesCS2B01G344400 chr2A 571147756 571150352 2596 False 1667.0 2159 90.2915 848 3416 2 chr2A.!!$F1 2568
3 TraesCS2B01G344400 chr1A 494175535 494176123 588 True 909.0 909 94.5760 1 588 1 chr1A.!!$R1 587
4 TraesCS2B01G344400 chr5D 254009831 254010418 587 True 837.0 837 92.3860 5 593 1 chr5D.!!$R1 588
5 TraesCS2B01G344400 chr5D 527817955 527818544 589 True 778.0 778 90.5560 1 588 1 chr5D.!!$R2 587
6 TraesCS2B01G344400 chr1B 651443406 651443995 589 True 795.0 795 91.0320 1 589 1 chr1B.!!$R1 588
7 TraesCS2B01G344400 chr3D 549754977 549755564 587 False 776.0 776 90.5410 1 588 1 chr3D.!!$F1 587
8 TraesCS2B01G344400 chr4D 321825443 321826032 589 False 767.0 767 90.2360 1 588 1 chr4D.!!$F1 587
9 TraesCS2B01G344400 chr6A 59943935 59944525 590 True 761.0 761 90.0840 1 588 1 chr6A.!!$R1 587
10 TraesCS2B01G344400 chr4A 242785149 242785740 591 False 758.0 758 89.9330 1 588 1 chr4A.!!$F1 587
11 TraesCS2B01G344400 chr4A 690857306 690857901 595 True 747.0 747 89.3510 1 596 1 chr4A.!!$R1 595

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
686 699 0.037232 AACTGGCTCCTAACTCGTGC 60.037 55.0 0.00 0.00 0.0 5.34 F
767 780 0.106149 ATTATGGTTCGAGGCCGACC 59.894 55.0 12.06 12.06 45.5 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2190 2291 0.327924 ATTGCCACCGATCCAAGACA 59.672 50.0 0.0 0.0 0.0 3.41 R
2551 2678 0.884704 TCTCGTTTCAGCCAAGCACC 60.885 55.0 0.0 0.0 0.0 5.01 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
137 138 2.196997 CTTTGGCGATCCAGGGTCCA 62.197 60.000 0.00 0.00 44.53 4.02
201 202 1.005289 ATCTCCACCATCCTGGGCT 59.995 57.895 0.00 0.00 43.37 5.19
230 231 1.258445 CGGTGTTGTCTAGGAGCCCT 61.258 60.000 0.00 0.00 37.71 5.19
273 275 3.069318 GGAGGACCCGCGTCTTCT 61.069 66.667 11.53 0.00 43.04 2.85
306 308 2.936919 TCCTCTTGCAAGCTTCTCAA 57.063 45.000 21.99 3.15 0.00 3.02
424 428 4.293494 TGAGAAGAGGTGGCTCTGATTAT 58.707 43.478 0.00 0.00 33.39 1.28
531 544 8.870879 GCGTACAAGAAGATATACAAGAGTTTT 58.129 33.333 0.00 0.00 0.00 2.43
593 606 6.861065 ACGGCATATATTCTAACACAAAGG 57.139 37.500 0.00 0.00 0.00 3.11
596 609 7.719633 ACGGCATATATTCTAACACAAAGGAAT 59.280 33.333 0.00 0.00 33.69 3.01
597 610 8.567948 CGGCATATATTCTAACACAAAGGAATT 58.432 33.333 0.00 0.00 31.89 2.17
604 617 7.611213 TTCTAACACAAAGGAATTAGCTAGC 57.389 36.000 6.62 6.62 0.00 3.42
605 618 6.947464 TCTAACACAAAGGAATTAGCTAGCT 58.053 36.000 23.12 23.12 0.00 3.32
606 619 8.074613 TCTAACACAAAGGAATTAGCTAGCTA 57.925 34.615 20.67 20.67 0.00 3.32
607 620 6.986904 AACACAAAGGAATTAGCTAGCTAC 57.013 37.500 24.09 12.67 0.00 3.58
608 621 5.429130 ACACAAAGGAATTAGCTAGCTACC 58.571 41.667 24.09 20.63 0.00 3.18
609 622 4.816925 CACAAAGGAATTAGCTAGCTACCC 59.183 45.833 24.09 22.23 0.00 3.69
610 623 4.141459 ACAAAGGAATTAGCTAGCTACCCC 60.141 45.833 24.09 21.91 0.00 4.95
611 624 2.622210 AGGAATTAGCTAGCTACCCCC 58.378 52.381 24.09 21.59 0.00 5.40
612 625 1.275573 GGAATTAGCTAGCTACCCCCG 59.724 57.143 24.09 0.00 0.00 5.73
613 626 0.685660 AATTAGCTAGCTACCCCCGC 59.314 55.000 24.09 0.00 0.00 6.13
614 627 0.178929 ATTAGCTAGCTACCCCCGCT 60.179 55.000 24.09 9.16 41.35 5.52
615 628 1.113517 TTAGCTAGCTACCCCCGCTG 61.114 60.000 24.09 0.00 38.38 5.18
616 629 2.996470 TAGCTAGCTACCCCCGCTGG 62.996 65.000 20.67 0.00 38.38 4.85
617 630 3.930012 CTAGCTACCCCCGCTGGC 61.930 72.222 0.00 0.00 38.38 4.85
618 631 4.789173 TAGCTACCCCCGCTGGCA 62.789 66.667 0.00 0.00 38.38 4.92
621 634 2.762459 CTACCCCCGCTGGCACTA 60.762 66.667 0.00 0.00 0.00 2.74
622 635 2.284773 TACCCCCGCTGGCACTAA 60.285 61.111 0.00 0.00 0.00 2.24
623 636 2.588856 CTACCCCCGCTGGCACTAAC 62.589 65.000 0.00 0.00 0.00 2.34
625 638 4.077184 CCCCGCTGGCACTAACGA 62.077 66.667 0.00 0.00 0.00 3.85
626 639 2.047655 CCCGCTGGCACTAACGAA 60.048 61.111 0.00 0.00 0.00 3.85
627 640 2.388232 CCCGCTGGCACTAACGAAC 61.388 63.158 0.00 0.00 0.00 3.95
628 641 1.374252 CCGCTGGCACTAACGAACT 60.374 57.895 0.00 0.00 0.00 3.01
629 642 0.108992 CCGCTGGCACTAACGAACTA 60.109 55.000 0.00 0.00 0.00 2.24
630 643 1.670674 CCGCTGGCACTAACGAACTAA 60.671 52.381 0.00 0.00 0.00 2.24
631 644 2.268298 CGCTGGCACTAACGAACTAAT 58.732 47.619 0.00 0.00 0.00 1.73
632 645 2.029244 CGCTGGCACTAACGAACTAATG 59.971 50.000 0.00 0.00 0.00 1.90
633 646 3.259064 GCTGGCACTAACGAACTAATGA 58.741 45.455 0.00 0.00 0.00 2.57
634 647 3.062234 GCTGGCACTAACGAACTAATGAC 59.938 47.826 0.00 0.00 0.00 3.06
635 648 4.495422 CTGGCACTAACGAACTAATGACT 58.505 43.478 0.00 0.00 0.00 3.41
636 649 4.491676 TGGCACTAACGAACTAATGACTC 58.508 43.478 0.00 0.00 0.00 3.36
637 650 3.864003 GGCACTAACGAACTAATGACTCC 59.136 47.826 0.00 0.00 0.00 3.85
638 651 4.381718 GGCACTAACGAACTAATGACTCCT 60.382 45.833 0.00 0.00 0.00 3.69
639 652 4.799428 GCACTAACGAACTAATGACTCCTC 59.201 45.833 0.00 0.00 0.00 3.71
640 653 5.393243 GCACTAACGAACTAATGACTCCTCT 60.393 44.000 0.00 0.00 0.00 3.69
641 654 6.030849 CACTAACGAACTAATGACTCCTCTG 58.969 44.000 0.00 0.00 0.00 3.35
642 655 3.512033 ACGAACTAATGACTCCTCTGC 57.488 47.619 0.00 0.00 0.00 4.26
643 656 2.826128 ACGAACTAATGACTCCTCTGCA 59.174 45.455 0.00 0.00 0.00 4.41
644 657 3.258372 ACGAACTAATGACTCCTCTGCAA 59.742 43.478 0.00 0.00 0.00 4.08
645 658 3.614616 CGAACTAATGACTCCTCTGCAAC 59.385 47.826 0.00 0.00 0.00 4.17
646 659 4.569943 GAACTAATGACTCCTCTGCAACA 58.430 43.478 0.00 0.00 0.00 3.33
647 660 4.623932 ACTAATGACTCCTCTGCAACAA 57.376 40.909 0.00 0.00 0.00 2.83
648 661 4.973168 ACTAATGACTCCTCTGCAACAAA 58.027 39.130 0.00 0.00 0.00 2.83
649 662 5.376625 ACTAATGACTCCTCTGCAACAAAA 58.623 37.500 0.00 0.00 0.00 2.44
650 663 4.574599 AATGACTCCTCTGCAACAAAAC 57.425 40.909 0.00 0.00 0.00 2.43
651 664 2.997980 TGACTCCTCTGCAACAAAACA 58.002 42.857 0.00 0.00 0.00 2.83
652 665 2.682856 TGACTCCTCTGCAACAAAACAC 59.317 45.455 0.00 0.00 0.00 3.32
653 666 2.682856 GACTCCTCTGCAACAAAACACA 59.317 45.455 0.00 0.00 0.00 3.72
654 667 3.290710 ACTCCTCTGCAACAAAACACAT 58.709 40.909 0.00 0.00 0.00 3.21
655 668 3.067180 ACTCCTCTGCAACAAAACACATG 59.933 43.478 0.00 0.00 0.00 3.21
656 669 2.129607 CCTCTGCAACAAAACACATGC 58.870 47.619 0.00 0.00 39.22 4.06
657 670 2.481622 CCTCTGCAACAAAACACATGCA 60.482 45.455 0.00 0.00 45.75 3.96
658 671 3.386486 CTCTGCAACAAAACACATGCAT 58.614 40.909 0.00 0.00 46.59 3.96
659 672 3.124560 TCTGCAACAAAACACATGCATG 58.875 40.909 25.09 25.09 46.59 4.06
660 673 2.867368 CTGCAACAAAACACATGCATGT 59.133 40.909 26.61 26.61 46.59 3.21
661 674 2.864946 TGCAACAAAACACATGCATGTC 59.135 40.909 29.23 14.92 43.32 3.06
662 675 2.221517 GCAACAAAACACATGCATGTCC 59.778 45.455 29.23 5.91 39.39 4.02
663 676 3.719924 CAACAAAACACATGCATGTCCT 58.280 40.909 29.23 16.15 39.39 3.85
664 677 4.795635 GCAACAAAACACATGCATGTCCTA 60.796 41.667 29.23 0.00 39.39 2.94
665 678 4.771590 ACAAAACACATGCATGTCCTAG 57.228 40.909 29.23 19.78 39.39 3.02
666 679 4.144297 ACAAAACACATGCATGTCCTAGT 58.856 39.130 29.23 20.44 39.39 2.57
667 680 5.312895 ACAAAACACATGCATGTCCTAGTA 58.687 37.500 29.23 0.00 39.39 1.82
668 681 5.767665 ACAAAACACATGCATGTCCTAGTAA 59.232 36.000 29.23 0.00 39.39 2.24
669 682 5.880054 AAACACATGCATGTCCTAGTAAC 57.120 39.130 29.23 0.00 39.39 2.50
670 683 4.826274 ACACATGCATGTCCTAGTAACT 57.174 40.909 29.23 0.96 39.39 2.24
671 684 4.507710 ACACATGCATGTCCTAGTAACTG 58.492 43.478 29.23 15.94 39.39 3.16
672 685 3.873361 CACATGCATGTCCTAGTAACTGG 59.127 47.826 29.23 9.96 39.39 4.00
673 686 2.691409 TGCATGTCCTAGTAACTGGC 57.309 50.000 0.00 0.00 0.00 4.85
674 687 2.187958 TGCATGTCCTAGTAACTGGCT 58.812 47.619 0.00 0.00 0.00 4.75
675 688 2.168521 TGCATGTCCTAGTAACTGGCTC 59.831 50.000 0.00 0.00 0.00 4.70
676 689 2.483889 GCATGTCCTAGTAACTGGCTCC 60.484 54.545 0.00 0.00 0.00 4.70
677 690 2.921834 TGTCCTAGTAACTGGCTCCT 57.078 50.000 0.00 0.00 0.00 3.69
678 691 4.215908 CATGTCCTAGTAACTGGCTCCTA 58.784 47.826 0.00 0.00 0.00 2.94
679 692 4.326600 TGTCCTAGTAACTGGCTCCTAA 57.673 45.455 0.00 0.00 0.00 2.69
680 693 4.021916 TGTCCTAGTAACTGGCTCCTAAC 58.978 47.826 0.00 0.00 0.00 2.34
681 694 4.264262 TGTCCTAGTAACTGGCTCCTAACT 60.264 45.833 0.00 0.00 0.00 2.24
682 695 4.338964 GTCCTAGTAACTGGCTCCTAACTC 59.661 50.000 0.00 0.00 0.00 3.01
683 696 3.315749 CCTAGTAACTGGCTCCTAACTCG 59.684 52.174 0.00 0.00 0.00 4.18
684 697 2.805194 AGTAACTGGCTCCTAACTCGT 58.195 47.619 0.00 0.00 0.00 4.18
685 698 2.492484 AGTAACTGGCTCCTAACTCGTG 59.508 50.000 0.00 0.00 0.00 4.35
686 699 0.037232 AACTGGCTCCTAACTCGTGC 60.037 55.000 0.00 0.00 0.00 5.34
687 700 1.153549 CTGGCTCCTAACTCGTGCC 60.154 63.158 0.00 0.00 43.49 5.01
688 701 1.608717 CTGGCTCCTAACTCGTGCCT 61.609 60.000 0.00 0.00 43.57 4.75
689 702 1.142097 GGCTCCTAACTCGTGCCTC 59.858 63.158 0.00 0.00 40.36 4.70
690 703 1.226717 GCTCCTAACTCGTGCCTCG 60.227 63.158 0.00 0.00 41.41 4.63
691 704 1.433879 CTCCTAACTCGTGCCTCGG 59.566 63.158 0.00 0.00 40.32 4.63
692 705 1.001764 TCCTAACTCGTGCCTCGGA 60.002 57.895 0.00 0.00 40.32 4.55
693 706 1.030488 TCCTAACTCGTGCCTCGGAG 61.030 60.000 0.00 0.00 40.32 4.63
694 707 1.433879 CTAACTCGTGCCTCGGAGG 59.566 63.158 19.95 19.95 40.32 4.30
695 708 1.303888 TAACTCGTGCCTCGGAGGT 60.304 57.895 24.30 6.14 37.80 3.85
696 709 1.592400 TAACTCGTGCCTCGGAGGTG 61.592 60.000 24.30 14.78 37.80 4.00
697 710 4.135153 CTCGTGCCTCGGAGGTGG 62.135 72.222 24.30 13.94 37.80 4.61
716 729 4.101448 GCGACCCTGCTGACCCAT 62.101 66.667 0.00 0.00 0.00 4.00
717 730 2.671070 CGACCCTGCTGACCCATT 59.329 61.111 0.00 0.00 0.00 3.16
718 731 1.746615 CGACCCTGCTGACCCATTG 60.747 63.158 0.00 0.00 0.00 2.82
719 732 1.379044 GACCCTGCTGACCCATTGG 60.379 63.158 0.00 0.00 37.80 3.16
729 742 3.077907 CCCATTGGGTCAGTCGGT 58.922 61.111 14.10 0.00 38.25 4.69
730 743 1.377202 CCCATTGGGTCAGTCGGTG 60.377 63.158 14.10 0.00 38.25 4.94
731 744 2.040544 CCATTGGGTCAGTCGGTGC 61.041 63.158 0.00 0.00 0.00 5.01
732 745 2.040544 CATTGGGTCAGTCGGTGCC 61.041 63.158 0.00 0.00 0.00 5.01
733 746 3.605749 ATTGGGTCAGTCGGTGCCG 62.606 63.158 3.94 3.94 41.35 5.69
748 761 3.636231 CCGGCTCCACTGACCCAA 61.636 66.667 0.00 0.00 0.00 4.12
749 762 2.671070 CGGCTCCACTGACCCAAT 59.329 61.111 0.00 0.00 0.00 3.16
750 763 1.002134 CGGCTCCACTGACCCAATT 60.002 57.895 0.00 0.00 0.00 2.32
751 764 0.251916 CGGCTCCACTGACCCAATTA 59.748 55.000 0.00 0.00 0.00 1.40
752 765 1.134098 CGGCTCCACTGACCCAATTAT 60.134 52.381 0.00 0.00 0.00 1.28
753 766 2.301346 GGCTCCACTGACCCAATTATG 58.699 52.381 0.00 0.00 0.00 1.90
755 768 2.357154 GCTCCACTGACCCAATTATGGT 60.357 50.000 0.00 0.00 46.01 3.55
756 769 3.877735 GCTCCACTGACCCAATTATGGTT 60.878 47.826 0.72 0.00 46.01 3.67
757 770 3.947834 CTCCACTGACCCAATTATGGTTC 59.052 47.826 0.72 0.00 46.01 3.62
758 771 2.682856 CCACTGACCCAATTATGGTTCG 59.317 50.000 0.72 0.00 46.01 3.95
759 772 3.605634 CACTGACCCAATTATGGTTCGA 58.394 45.455 0.72 0.00 46.01 3.71
760 773 3.623060 CACTGACCCAATTATGGTTCGAG 59.377 47.826 0.72 1.56 46.01 4.04
761 774 3.206150 CTGACCCAATTATGGTTCGAGG 58.794 50.000 0.72 0.00 46.01 4.63
762 775 1.947456 GACCCAATTATGGTTCGAGGC 59.053 52.381 0.72 0.00 46.01 4.70
763 776 1.318576 CCCAATTATGGTTCGAGGCC 58.681 55.000 0.00 0.00 46.01 5.19
764 777 0.944386 CCAATTATGGTTCGAGGCCG 59.056 55.000 0.00 0.00 42.18 6.13
765 778 1.474320 CCAATTATGGTTCGAGGCCGA 60.474 52.381 0.00 0.00 42.18 5.54
766 779 1.597663 CAATTATGGTTCGAGGCCGAC 59.402 52.381 0.00 0.00 45.50 4.79
767 780 0.106149 ATTATGGTTCGAGGCCGACC 59.894 55.000 12.06 12.06 45.50 4.79
768 781 1.963464 TTATGGTTCGAGGCCGACCC 61.963 60.000 15.11 5.31 46.10 4.46
770 783 4.754667 GGTTCGAGGCCGACCCAC 62.755 72.222 0.00 0.00 45.35 4.61
771 784 3.998672 GTTCGAGGCCGACCCACA 61.999 66.667 0.00 0.00 45.50 4.17
772 785 3.998672 TTCGAGGCCGACCCACAC 61.999 66.667 0.00 0.00 45.50 3.82
784 797 2.753701 CCACACGGGTCCATTGGA 59.246 61.111 0.00 0.00 0.00 3.53
798 811 4.009675 TCCATTGGACTCGATTTTTCAGG 58.990 43.478 0.00 0.00 0.00 3.86
799 812 3.758554 CCATTGGACTCGATTTTTCAGGT 59.241 43.478 0.00 0.00 0.00 4.00
800 813 4.142600 CCATTGGACTCGATTTTTCAGGTC 60.143 45.833 0.00 0.00 0.00 3.85
801 814 2.683968 TGGACTCGATTTTTCAGGTCG 58.316 47.619 0.00 0.00 36.75 4.79
802 815 2.000447 GGACTCGATTTTTCAGGTCGG 59.000 52.381 0.00 0.00 36.14 4.79
803 816 2.000447 GACTCGATTTTTCAGGTCGGG 59.000 52.381 0.00 0.00 41.41 5.14
804 817 1.346722 ACTCGATTTTTCAGGTCGGGT 59.653 47.619 0.00 0.00 43.60 5.28
805 818 2.000447 CTCGATTTTTCAGGTCGGGTC 59.000 52.381 0.00 0.00 36.14 4.46
806 819 1.345089 TCGATTTTTCAGGTCGGGTCA 59.655 47.619 0.00 0.00 36.14 4.02
807 820 1.732259 CGATTTTTCAGGTCGGGTCAG 59.268 52.381 0.00 0.00 0.00 3.51
808 821 1.468914 GATTTTTCAGGTCGGGTCAGC 59.531 52.381 0.00 0.00 0.00 4.26
809 822 0.882927 TTTTTCAGGTCGGGTCAGCG 60.883 55.000 0.00 0.00 0.00 5.18
810 823 1.750341 TTTTCAGGTCGGGTCAGCGA 61.750 55.000 0.00 0.00 0.00 4.93
811 824 2.430382 TTTCAGGTCGGGTCAGCGAC 62.430 60.000 0.00 0.00 34.71 5.19
837 850 4.506255 CCGACCTGGCCCATTCCC 62.506 72.222 0.00 0.00 0.00 3.97
838 851 3.727258 CGACCTGGCCCATTCCCA 61.727 66.667 0.00 0.00 0.00 4.37
839 852 3.018901 GACCTGGCCCATTCCCAT 58.981 61.111 0.00 0.00 0.00 4.00
840 853 1.152673 GACCTGGCCCATTCCCATC 60.153 63.158 0.00 0.00 0.00 3.51
841 854 2.199535 CCTGGCCCATTCCCATCC 59.800 66.667 0.00 0.00 0.00 3.51
842 855 2.397902 CCTGGCCCATTCCCATCCT 61.398 63.158 0.00 0.00 0.00 3.24
843 856 1.152610 CTGGCCCATTCCCATCCTG 60.153 63.158 0.00 0.00 0.00 3.86
844 857 1.622132 TGGCCCATTCCCATCCTGA 60.622 57.895 0.00 0.00 0.00 3.86
868 881 7.604545 TGACATATGACCAATCGAACTTTGTAA 59.395 33.333 10.38 0.00 0.00 2.41
869 882 8.506168 ACATATGACCAATCGAACTTTGTAAT 57.494 30.769 10.38 0.00 0.00 1.89
870 883 8.397906 ACATATGACCAATCGAACTTTGTAATG 58.602 33.333 10.38 0.00 0.00 1.90
871 884 5.041951 TGACCAATCGAACTTTGTAATGC 57.958 39.130 0.00 0.00 0.00 3.56
872 885 4.759693 TGACCAATCGAACTTTGTAATGCT 59.240 37.500 0.00 0.00 0.00 3.79
958 979 1.408822 CCCTCCAAAAGCGCTTATCCT 60.409 52.381 25.33 4.30 0.00 3.24
966 987 4.925576 CGCTTATCCTCGCCGCGT 62.926 66.667 13.39 0.00 39.07 6.01
1214 1244 4.554363 CGGCGAGGCGTCTTCGAT 62.554 66.667 0.00 0.00 39.71 3.59
1217 1247 2.517450 GCGAGGCGTCTTCGATTGG 61.517 63.158 13.68 0.00 39.71 3.16
1347 1377 6.594937 ACACAAATGTTCACTTTCTTTGCATT 59.405 30.769 0.00 0.00 34.46 3.56
1348 1378 7.119553 ACACAAATGTTCACTTTCTTTGCATTT 59.880 29.630 0.00 0.00 34.46 2.32
1352 1382 3.988379 TCACTTTCTTTGCATTTCGCT 57.012 38.095 0.00 0.00 43.06 4.93
1385 1415 6.734104 TGCAAGCAAATTTTGTACACTTTT 57.266 29.167 10.65 0.00 0.00 2.27
1411 1441 7.672983 TCTGTGAACTGGAGAATCATTTAAC 57.327 36.000 0.00 0.00 36.25 2.01
1414 1444 7.685481 TGTGAACTGGAGAATCATTTAACCTA 58.315 34.615 0.00 0.00 36.25 3.08
1415 1445 7.824289 TGTGAACTGGAGAATCATTTAACCTAG 59.176 37.037 0.00 0.00 36.25 3.02
1416 1446 6.823689 TGAACTGGAGAATCATTTAACCTAGC 59.176 38.462 0.00 0.00 36.25 3.42
1417 1447 6.567602 ACTGGAGAATCATTTAACCTAGCT 57.432 37.500 0.00 0.00 36.25 3.32
1422 1504 7.872993 TGGAGAATCATTTAACCTAGCTAATCG 59.127 37.037 0.00 0.00 36.25 3.34
1430 1512 9.268268 CATTTAACCTAGCTAATCGTTCCATTA 57.732 33.333 0.00 0.00 0.00 1.90
1435 1517 8.747538 ACCTAGCTAATCGTTCCATTAAAAAT 57.252 30.769 0.00 0.00 0.00 1.82
1480 1562 9.586435 AATCATCGATTAATTAGCATCGTGATA 57.414 29.630 21.63 8.38 42.42 2.15
1649 1731 2.859806 GCATTACGGCCATGATTCTTGC 60.860 50.000 2.24 0.00 0.00 4.01
1768 1865 9.216148 ACATTACTTATGGTTATGGGTACAGTA 57.784 33.333 0.00 0.00 38.73 2.74
1822 1923 5.406477 GGCAGAAGGATTGTTCAATTTTGTC 59.594 40.000 0.00 0.00 0.00 3.18
1866 1967 1.227089 CGCTCCTCTTCACGGATGG 60.227 63.158 0.00 0.00 0.00 3.51
1879 1980 1.075450 GGATGGTAGGAGGGACCGT 60.075 63.158 0.00 0.00 44.74 4.83
1883 1984 0.324645 TGGTAGGAGGGACCGTTACC 60.325 60.000 7.78 7.78 44.74 2.85
1897 1998 0.674534 GTTACCAGGGATCGCTCGAT 59.325 55.000 9.74 4.26 37.59 3.59
1963 2064 2.079170 TGACCCAAAATGAACCAGCA 57.921 45.000 0.00 0.00 0.00 4.41
1975 2076 2.170397 TGAACCAGCAGAACAGTTCAGA 59.830 45.455 15.85 0.00 42.61 3.27
2190 2291 2.097825 GCAGATGCTGATTTTGGAGGT 58.902 47.619 0.00 0.00 38.21 3.85
2199 2300 4.338879 CTGATTTTGGAGGTGTCTTGGAT 58.661 43.478 0.00 0.00 0.00 3.41
2266 2367 2.356135 ACGCATTTCTGTGGGACATAC 58.644 47.619 0.00 0.00 44.52 2.39
2329 2430 5.255710 TCTTCAGAATGCGAAACCAAAAA 57.744 34.783 0.00 0.00 34.76 1.94
2709 2836 6.578919 GCTGTTACAGATGCTAAGAAAAACAC 59.421 38.462 17.40 0.00 32.44 3.32
2761 2888 6.683715 ACTCTAGTTTGCAGAAAGTCTAGAC 58.316 40.000 15.41 15.41 33.56 2.59
2776 2903 6.576662 AGTCTAGACGATCTTTTCAGAACA 57.423 37.500 17.07 0.00 36.20 3.18
2912 3039 1.200716 GATGTTGTCAGTGGTGGCATG 59.799 52.381 0.00 0.00 38.36 4.06
2997 3124 4.681978 GCGACGGTGCTTGTCCCT 62.682 66.667 0.00 0.00 32.68 4.20
3037 3164 8.327941 TCAAGACAGTTATTGATTCAAAGAGG 57.672 34.615 2.68 0.00 30.67 3.69
3038 3165 7.391554 TCAAGACAGTTATTGATTCAAAGAGGG 59.608 37.037 2.68 0.00 30.67 4.30
3039 3166 6.784031 AGACAGTTATTGATTCAAAGAGGGT 58.216 36.000 2.68 0.17 0.00 4.34
3056 3183 2.297033 AGGGTTTTCAGTACGTAGCGAA 59.703 45.455 0.00 0.00 0.00 4.70
3057 3184 2.409715 GGGTTTTCAGTACGTAGCGAAC 59.590 50.000 0.00 0.00 0.00 3.95
3083 3215 2.345341 GGCCGAAGAAAATCATTTTGCG 59.655 45.455 0.00 1.65 31.94 4.85
3132 3264 1.571919 CGCTGAGTTATGGTACCTGC 58.428 55.000 14.36 0.56 0.00 4.85
3188 3320 4.704833 GGGAAGGCAGCAGCACGA 62.705 66.667 2.65 0.00 44.61 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 0.263765 TAGAGCCGAACCCCCTGTAT 59.736 55.000 0.00 0.00 0.00 2.29
207 208 0.170561 CTCCTAGACAACACCGACGG 59.829 60.000 13.61 13.61 0.00 4.79
221 222 1.327690 CGCAGGTAACAGGGCTCCTA 61.328 60.000 0.00 0.00 41.41 2.94
230 231 2.048597 CGAGGTGCGCAGGTAACA 60.049 61.111 12.22 0.00 41.41 2.41
264 266 4.555348 ACTTTATCCTCTAGAAGACGCG 57.445 45.455 3.53 3.53 0.00 6.01
424 428 8.311395 AGTAGGACACTTGATATCTTTCATGA 57.689 34.615 3.98 0.00 31.59 3.07
555 568 3.134574 TGCCGTTGTAATCTCAACCTT 57.865 42.857 4.39 0.00 43.02 3.50
593 606 1.337917 GCGGGGGTAGCTAGCTAATTC 60.338 57.143 25.74 16.98 0.00 2.17
596 609 1.113517 CAGCGGGGGTAGCTAGCTAA 61.114 60.000 25.74 7.85 44.06 3.09
597 610 1.530891 CAGCGGGGGTAGCTAGCTA 60.531 63.158 20.67 20.67 44.06 3.32
598 611 2.840102 CAGCGGGGGTAGCTAGCT 60.840 66.667 23.12 23.12 44.06 3.32
599 612 3.930012 CCAGCGGGGGTAGCTAGC 61.930 72.222 14.67 14.67 44.06 3.42
600 613 3.930012 GCCAGCGGGGGTAGCTAG 61.930 72.222 4.64 0.00 44.06 3.42
601 614 4.789173 TGCCAGCGGGGGTAGCTA 62.789 66.667 4.64 0.00 44.06 3.32
604 617 2.363975 TTAGTGCCAGCGGGGGTAG 61.364 63.158 4.64 0.00 37.04 3.18
605 618 2.284773 TTAGTGCCAGCGGGGGTA 60.285 61.111 4.64 0.00 37.04 3.69
606 619 4.029809 GTTAGTGCCAGCGGGGGT 62.030 66.667 4.64 0.00 37.04 4.95
608 621 3.599285 TTCGTTAGTGCCAGCGGGG 62.599 63.158 4.64 0.00 40.85 5.73
609 622 2.047655 TTCGTTAGTGCCAGCGGG 60.048 61.111 0.00 0.00 37.18 6.13
610 623 0.108992 TAGTTCGTTAGTGCCAGCGG 60.109 55.000 0.00 0.00 0.00 5.52
611 624 1.705256 TTAGTTCGTTAGTGCCAGCG 58.295 50.000 0.00 0.00 0.00 5.18
612 625 3.062234 GTCATTAGTTCGTTAGTGCCAGC 59.938 47.826 0.00 0.00 0.00 4.85
613 626 4.495422 AGTCATTAGTTCGTTAGTGCCAG 58.505 43.478 0.00 0.00 0.00 4.85
614 627 4.491676 GAGTCATTAGTTCGTTAGTGCCA 58.508 43.478 0.00 0.00 0.00 4.92
615 628 3.864003 GGAGTCATTAGTTCGTTAGTGCC 59.136 47.826 0.00 0.00 0.00 5.01
616 629 4.745649 AGGAGTCATTAGTTCGTTAGTGC 58.254 43.478 0.00 0.00 0.00 4.40
617 630 6.030849 CAGAGGAGTCATTAGTTCGTTAGTG 58.969 44.000 0.00 0.00 0.00 2.74
618 631 5.393243 GCAGAGGAGTCATTAGTTCGTTAGT 60.393 44.000 0.00 0.00 0.00 2.24
619 632 5.038033 GCAGAGGAGTCATTAGTTCGTTAG 58.962 45.833 0.00 0.00 0.00 2.34
620 633 4.461431 TGCAGAGGAGTCATTAGTTCGTTA 59.539 41.667 0.00 0.00 0.00 3.18
621 634 3.258372 TGCAGAGGAGTCATTAGTTCGTT 59.742 43.478 0.00 0.00 0.00 3.85
622 635 2.826128 TGCAGAGGAGTCATTAGTTCGT 59.174 45.455 0.00 0.00 0.00 3.85
623 636 3.510388 TGCAGAGGAGTCATTAGTTCG 57.490 47.619 0.00 0.00 0.00 3.95
624 637 4.569943 TGTTGCAGAGGAGTCATTAGTTC 58.430 43.478 0.00 0.00 0.00 3.01
625 638 4.623932 TGTTGCAGAGGAGTCATTAGTT 57.376 40.909 0.00 0.00 0.00 2.24
626 639 4.623932 TTGTTGCAGAGGAGTCATTAGT 57.376 40.909 0.00 0.00 0.00 2.24
627 640 5.239306 TGTTTTGTTGCAGAGGAGTCATTAG 59.761 40.000 0.00 0.00 0.00 1.73
628 641 5.008613 GTGTTTTGTTGCAGAGGAGTCATTA 59.991 40.000 0.00 0.00 0.00 1.90
629 642 3.953612 TGTTTTGTTGCAGAGGAGTCATT 59.046 39.130 0.00 0.00 0.00 2.57
630 643 3.316308 GTGTTTTGTTGCAGAGGAGTCAT 59.684 43.478 0.00 0.00 0.00 3.06
631 644 2.682856 GTGTTTTGTTGCAGAGGAGTCA 59.317 45.455 0.00 0.00 0.00 3.41
632 645 2.682856 TGTGTTTTGTTGCAGAGGAGTC 59.317 45.455 0.00 0.00 0.00 3.36
633 646 2.722094 TGTGTTTTGTTGCAGAGGAGT 58.278 42.857 0.00 0.00 0.00 3.85
634 647 3.635331 CATGTGTTTTGTTGCAGAGGAG 58.365 45.455 0.00 0.00 0.00 3.69
635 648 2.223782 GCATGTGTTTTGTTGCAGAGGA 60.224 45.455 0.00 0.00 35.22 3.71
636 649 2.129607 GCATGTGTTTTGTTGCAGAGG 58.870 47.619 0.00 0.00 35.22 3.69
637 650 2.811855 TGCATGTGTTTTGTTGCAGAG 58.188 42.857 0.00 0.00 39.98 3.35
638 651 2.955477 TGCATGTGTTTTGTTGCAGA 57.045 40.000 0.00 0.00 39.98 4.26
641 654 2.221517 GGACATGCATGTGTTTTGTTGC 59.778 45.455 35.92 17.60 41.95 4.17
642 655 3.719924 AGGACATGCATGTGTTTTGTTG 58.280 40.909 35.92 6.03 41.95 3.33
643 656 4.584325 ACTAGGACATGCATGTGTTTTGTT 59.416 37.500 35.92 9.61 41.95 2.83
644 657 4.144297 ACTAGGACATGCATGTGTTTTGT 58.856 39.130 35.92 22.38 41.95 2.83
645 658 4.771590 ACTAGGACATGCATGTGTTTTG 57.228 40.909 35.92 21.79 41.95 2.44
646 659 6.003950 AGTTACTAGGACATGCATGTGTTTT 58.996 36.000 35.92 19.32 41.95 2.43
647 660 5.412594 CAGTTACTAGGACATGCATGTGTTT 59.587 40.000 35.92 21.63 41.95 2.83
648 661 4.937620 CAGTTACTAGGACATGCATGTGTT 59.062 41.667 35.92 23.98 41.95 3.32
649 662 4.507710 CAGTTACTAGGACATGCATGTGT 58.492 43.478 35.92 27.00 41.95 3.72
650 663 3.873361 CCAGTTACTAGGACATGCATGTG 59.127 47.826 35.92 22.98 41.95 3.21
651 664 3.682718 GCCAGTTACTAGGACATGCATGT 60.683 47.826 31.82 31.82 45.16 3.21
652 665 2.874701 GCCAGTTACTAGGACATGCATG 59.125 50.000 25.09 25.09 0.00 4.06
653 666 2.774234 AGCCAGTTACTAGGACATGCAT 59.226 45.455 0.00 0.00 0.00 3.96
654 667 2.168521 GAGCCAGTTACTAGGACATGCA 59.831 50.000 0.00 0.00 0.00 3.96
655 668 2.483889 GGAGCCAGTTACTAGGACATGC 60.484 54.545 0.00 0.04 0.00 4.06
656 669 3.034635 AGGAGCCAGTTACTAGGACATG 58.965 50.000 5.30 0.00 0.00 3.21
657 670 3.406512 AGGAGCCAGTTACTAGGACAT 57.593 47.619 5.30 0.00 0.00 3.06
658 671 2.921834 AGGAGCCAGTTACTAGGACA 57.078 50.000 5.30 0.00 0.00 4.02
659 672 4.279982 AGTTAGGAGCCAGTTACTAGGAC 58.720 47.826 5.30 0.00 0.00 3.85
660 673 4.534797 GAGTTAGGAGCCAGTTACTAGGA 58.465 47.826 5.30 0.00 0.00 2.94
661 674 3.315749 CGAGTTAGGAGCCAGTTACTAGG 59.684 52.174 0.00 0.00 0.00 3.02
662 675 3.946558 ACGAGTTAGGAGCCAGTTACTAG 59.053 47.826 0.00 0.00 0.00 2.57
663 676 3.693085 CACGAGTTAGGAGCCAGTTACTA 59.307 47.826 0.00 0.00 0.00 1.82
664 677 2.492484 CACGAGTTAGGAGCCAGTTACT 59.508 50.000 0.00 0.00 0.00 2.24
665 678 2.877335 CACGAGTTAGGAGCCAGTTAC 58.123 52.381 0.00 0.00 0.00 2.50
666 679 1.203994 GCACGAGTTAGGAGCCAGTTA 59.796 52.381 0.00 0.00 0.00 2.24
667 680 0.037232 GCACGAGTTAGGAGCCAGTT 60.037 55.000 0.00 0.00 0.00 3.16
668 681 1.592223 GCACGAGTTAGGAGCCAGT 59.408 57.895 0.00 0.00 0.00 4.00
669 682 1.153549 GGCACGAGTTAGGAGCCAG 60.154 63.158 0.00 0.00 44.59 4.85
670 683 2.978824 GGCACGAGTTAGGAGCCA 59.021 61.111 0.00 0.00 44.59 4.75
671 684 1.142097 GAGGCACGAGTTAGGAGCC 59.858 63.158 0.00 0.00 45.54 4.70
672 685 1.226717 CGAGGCACGAGTTAGGAGC 60.227 63.158 0.00 0.00 45.77 4.70
673 686 1.030488 TCCGAGGCACGAGTTAGGAG 61.030 60.000 5.74 0.00 45.77 3.69
674 687 1.001764 TCCGAGGCACGAGTTAGGA 60.002 57.895 5.74 0.00 45.77 2.94
675 688 1.433879 CTCCGAGGCACGAGTTAGG 59.566 63.158 5.74 0.00 45.77 2.69
676 689 1.313812 ACCTCCGAGGCACGAGTTAG 61.314 60.000 14.86 0.00 45.77 2.34
677 690 1.303888 ACCTCCGAGGCACGAGTTA 60.304 57.895 14.86 0.00 45.77 2.24
678 691 2.600769 ACCTCCGAGGCACGAGTT 60.601 61.111 14.86 0.00 45.77 3.01
679 692 3.374402 CACCTCCGAGGCACGAGT 61.374 66.667 14.86 0.00 45.77 4.18
680 693 4.135153 CCACCTCCGAGGCACGAG 62.135 72.222 14.86 1.56 45.77 4.18
699 712 3.628646 AATGGGTCAGCAGGGTCGC 62.629 63.158 0.00 0.00 0.00 5.19
700 713 1.746615 CAATGGGTCAGCAGGGTCG 60.747 63.158 0.00 0.00 0.00 4.79
701 714 1.379044 CCAATGGGTCAGCAGGGTC 60.379 63.158 0.00 0.00 0.00 4.46
702 715 2.765969 CCAATGGGTCAGCAGGGT 59.234 61.111 0.00 0.00 0.00 4.34
703 716 2.043652 CCCAATGGGTCAGCAGGG 60.044 66.667 10.91 0.00 38.25 4.45
713 726 2.040544 GCACCGACTGACCCAATGG 61.041 63.158 0.00 0.00 37.80 3.16
714 727 2.040544 GGCACCGACTGACCCAATG 61.041 63.158 0.00 0.00 0.00 2.82
715 728 2.351276 GGCACCGACTGACCCAAT 59.649 61.111 0.00 0.00 0.00 3.16
716 729 4.308458 CGGCACCGACTGACCCAA 62.308 66.667 2.01 0.00 42.83 4.12
734 747 2.301346 CCATAATTGGGTCAGTGGAGC 58.699 52.381 0.00 0.00 39.56 4.70
735 748 3.968265 AACCATAATTGGGTCAGTGGAG 58.032 45.455 4.32 0.00 39.37 3.86
744 757 2.413862 CGGCCTCGAACCATAATTGGG 61.414 57.143 0.00 0.00 42.55 4.12
745 758 0.944386 CGGCCTCGAACCATAATTGG 59.056 55.000 0.00 0.00 43.35 3.16
746 759 1.948104 TCGGCCTCGAACCATAATTG 58.052 50.000 0.00 0.00 43.03 2.32
747 760 1.474498 GGTCGGCCTCGAACCATAATT 60.474 52.381 0.00 0.00 46.56 1.40
748 761 0.106149 GGTCGGCCTCGAACCATAAT 59.894 55.000 0.00 0.00 46.56 1.28
749 762 1.518774 GGTCGGCCTCGAACCATAA 59.481 57.895 0.00 0.00 46.56 1.90
750 763 3.213264 GGTCGGCCTCGAACCATA 58.787 61.111 0.00 0.00 46.56 2.74
767 780 1.674322 GTCCAATGGACCCGTGTGG 60.674 63.158 21.30 0.00 46.19 4.17
768 781 3.981308 GTCCAATGGACCCGTGTG 58.019 61.111 21.30 0.00 46.19 3.82
776 789 4.009675 CCTGAAAAATCGAGTCCAATGGA 58.990 43.478 0.00 0.00 0.00 3.41
777 790 3.758554 ACCTGAAAAATCGAGTCCAATGG 59.241 43.478 0.00 0.00 0.00 3.16
778 791 4.436050 CGACCTGAAAAATCGAGTCCAATG 60.436 45.833 0.00 0.00 38.10 2.82
779 792 3.684788 CGACCTGAAAAATCGAGTCCAAT 59.315 43.478 0.00 0.00 38.10 3.16
780 793 3.064207 CGACCTGAAAAATCGAGTCCAA 58.936 45.455 0.00 0.00 38.10 3.53
781 794 2.611971 CCGACCTGAAAAATCGAGTCCA 60.612 50.000 0.00 0.00 38.10 4.02
782 795 2.000447 CCGACCTGAAAAATCGAGTCC 59.000 52.381 0.00 0.00 38.10 3.85
783 796 2.000447 CCCGACCTGAAAAATCGAGTC 59.000 52.381 0.00 0.00 38.10 3.36
784 797 1.346722 ACCCGACCTGAAAAATCGAGT 59.653 47.619 0.00 0.00 38.10 4.18
785 798 2.000447 GACCCGACCTGAAAAATCGAG 59.000 52.381 0.00 0.00 38.10 4.04
786 799 1.345089 TGACCCGACCTGAAAAATCGA 59.655 47.619 0.00 0.00 38.10 3.59
787 800 1.732259 CTGACCCGACCTGAAAAATCG 59.268 52.381 0.00 0.00 35.62 3.34
788 801 1.468914 GCTGACCCGACCTGAAAAATC 59.531 52.381 0.00 0.00 0.00 2.17
789 802 1.534729 GCTGACCCGACCTGAAAAAT 58.465 50.000 0.00 0.00 0.00 1.82
790 803 0.882927 CGCTGACCCGACCTGAAAAA 60.883 55.000 0.00 0.00 0.00 1.94
791 804 1.301401 CGCTGACCCGACCTGAAAA 60.301 57.895 0.00 0.00 0.00 2.29
792 805 2.204461 TCGCTGACCCGACCTGAAA 61.204 57.895 0.00 0.00 31.36 2.69
793 806 2.599281 TCGCTGACCCGACCTGAA 60.599 61.111 0.00 0.00 31.36 3.02
820 833 4.506255 GGGAATGGGCCAGGTCGG 62.506 72.222 13.78 0.00 38.11 4.79
821 834 2.965716 GATGGGAATGGGCCAGGTCG 62.966 65.000 13.78 0.00 0.00 4.79
822 835 1.152673 GATGGGAATGGGCCAGGTC 60.153 63.158 13.78 12.01 0.00 3.85
823 836 2.704424 GGATGGGAATGGGCCAGGT 61.704 63.158 13.78 1.32 0.00 4.00
824 837 2.199535 GGATGGGAATGGGCCAGG 59.800 66.667 13.78 0.00 0.00 4.45
825 838 1.152610 CAGGATGGGAATGGGCCAG 60.153 63.158 13.78 0.00 0.00 4.85
826 839 1.622132 TCAGGATGGGAATGGGCCA 60.622 57.895 9.61 9.61 36.16 5.36
827 840 1.152673 GTCAGGATGGGAATGGGCC 60.153 63.158 0.00 0.00 36.16 5.80
828 841 0.186873 ATGTCAGGATGGGAATGGGC 59.813 55.000 0.00 0.00 36.16 5.36
829 842 3.331591 TCATATGTCAGGATGGGAATGGG 59.668 47.826 1.90 0.00 36.16 4.00
830 843 4.330250 GTCATATGTCAGGATGGGAATGG 58.670 47.826 1.90 0.00 36.16 3.16
831 844 4.202493 TGGTCATATGTCAGGATGGGAATG 60.202 45.833 1.90 0.00 36.16 2.67
832 845 3.982730 TGGTCATATGTCAGGATGGGAAT 59.017 43.478 1.90 0.00 36.16 3.01
833 846 3.392730 TGGTCATATGTCAGGATGGGAA 58.607 45.455 1.90 0.00 36.16 3.97
834 847 3.059051 TGGTCATATGTCAGGATGGGA 57.941 47.619 1.90 0.00 36.16 4.37
835 848 3.862877 TTGGTCATATGTCAGGATGGG 57.137 47.619 1.90 0.00 36.16 4.00
836 849 3.999001 CGATTGGTCATATGTCAGGATGG 59.001 47.826 1.90 0.00 36.16 3.51
837 850 4.886579 TCGATTGGTCATATGTCAGGATG 58.113 43.478 1.90 0.00 37.54 3.51
838 851 5.070981 AGTTCGATTGGTCATATGTCAGGAT 59.929 40.000 1.90 0.00 0.00 3.24
839 852 4.405680 AGTTCGATTGGTCATATGTCAGGA 59.594 41.667 1.90 0.50 0.00 3.86
840 853 4.697514 AGTTCGATTGGTCATATGTCAGG 58.302 43.478 1.90 0.00 0.00 3.86
841 854 6.092670 ACAAAGTTCGATTGGTCATATGTCAG 59.907 38.462 1.90 0.00 32.02 3.51
842 855 5.937540 ACAAAGTTCGATTGGTCATATGTCA 59.062 36.000 1.90 0.18 32.02 3.58
843 856 6.422776 ACAAAGTTCGATTGGTCATATGTC 57.577 37.500 1.90 0.00 32.02 3.06
844 857 7.915293 TTACAAAGTTCGATTGGTCATATGT 57.085 32.000 1.90 0.00 32.02 2.29
871 884 4.624364 TCTGGGCACGCCACACAG 62.624 66.667 10.83 8.32 37.98 3.66
872 885 3.490031 ATTCTGGGCACGCCACACA 62.490 57.895 10.83 0.00 37.98 3.72
1320 1350 7.093354 TGCAAAGAAAGTGAACATTTGTGTTA 58.907 30.769 0.00 0.00 34.22 2.41
1347 1377 1.739466 CTTGCATTGGAGCTAAGCGAA 59.261 47.619 0.00 0.00 34.99 4.70
1348 1378 1.372582 CTTGCATTGGAGCTAAGCGA 58.627 50.000 0.00 0.00 34.99 4.93
1352 1382 4.540359 AATTTGCTTGCATTGGAGCTAA 57.460 36.364 9.40 8.30 39.60 3.09
1385 1415 8.567948 GTTAAATGATTCTCCAGTTCACAGAAA 58.432 33.333 0.00 0.00 30.07 2.52
1401 1431 7.990886 TGGAACGATTAGCTAGGTTAAATGATT 59.009 33.333 0.00 0.00 0.00 2.57
1430 1512 8.729805 TTGGTGCACTTTCTTTTCATATTTTT 57.270 26.923 17.98 0.00 0.00 1.94
1435 1517 6.647334 TGATTGGTGCACTTTCTTTTCATA 57.353 33.333 17.98 0.00 0.00 2.15
1480 1562 2.034066 CACAATGGGTCGCCCTGT 59.966 61.111 14.76 9.46 45.70 4.00
1492 1574 1.959042 CTTGCGAGATAGCCCACAAT 58.041 50.000 0.00 0.00 36.02 2.71
1649 1731 1.027357 ACACTGCCAAGCAAACTCAG 58.973 50.000 0.00 0.00 38.41 3.35
1768 1865 4.377022 GCAACGACTGACGAATTAACACAT 60.377 41.667 6.52 0.00 45.77 3.21
1822 1923 0.892358 ACAGCAGTGTCCAGGCAATG 60.892 55.000 6.88 6.88 37.49 2.82
1866 1967 1.109609 CTGGTAACGGTCCCTCCTAC 58.890 60.000 0.00 0.00 42.51 3.18
1879 1980 2.281539 TATCGAGCGATCCCTGGTAA 57.718 50.000 8.84 0.00 36.17 2.85
1883 1984 2.230025 ACAAGATATCGAGCGATCCCTG 59.770 50.000 8.84 5.66 36.17 4.45
1897 1998 1.951209 TCTGACAGCCCCACAAGATA 58.049 50.000 0.00 0.00 0.00 1.98
2095 2196 1.226974 CTACACCGGATGCACCTCG 60.227 63.158 9.46 0.00 36.31 4.63
2106 2207 1.651987 CACCAGTTATGCCTACACCG 58.348 55.000 0.00 0.00 0.00 4.94
2169 2270 1.407979 CCTCCAAAATCAGCATCTGCC 59.592 52.381 0.00 0.00 43.38 4.85
2190 2291 0.327924 ATTGCCACCGATCCAAGACA 59.672 50.000 0.00 0.00 0.00 3.41
2199 2300 2.124942 TGCGCATATTGCCACCGA 60.125 55.556 5.66 0.00 41.12 4.69
2244 2345 2.093306 TGTCCCACAGAAATGCGTAG 57.907 50.000 0.00 0.00 0.00 3.51
2247 2348 2.352651 CAGTATGTCCCACAGAAATGCG 59.647 50.000 0.00 0.00 30.43 4.73
2266 2367 4.158579 TGGCTGGAATATCGAGTATAGCAG 59.841 45.833 10.08 0.00 0.00 4.24
2316 2417 3.942748 ACTCTGTAGTTTTTGGTTTCGCA 59.057 39.130 0.00 0.00 29.00 5.10
2329 2430 5.853936 TGCTACATTCACAAACTCTGTAGT 58.146 37.500 9.11 0.00 40.74 2.73
2545 2672 3.678806 CGTTTCAGCCAAGCACCTATCTA 60.679 47.826 0.00 0.00 0.00 1.98
2551 2678 0.884704 TCTCGTTTCAGCCAAGCACC 60.885 55.000 0.00 0.00 0.00 5.01
2648 2775 5.294552 GTGGTTGAAGGAGTAATATGCTCAC 59.705 44.000 9.05 0.00 34.83 3.51
2709 2836 6.771749 TCCTAGAGAACTTAGTTATTCCCTCG 59.228 42.308 0.00 0.00 0.00 4.63
2761 2888 5.062809 GGCTTCTAGTGTTCTGAAAAGATCG 59.937 44.000 0.00 0.00 0.00 3.69
2776 2903 4.072839 GGCAACAGTTTTAGGCTTCTAGT 58.927 43.478 0.00 0.00 0.00 2.57
2893 3020 1.250328 CATGCCACCACTGACAACAT 58.750 50.000 0.00 0.00 0.00 2.71
2981 3108 2.432628 GAGGGACAAGCACCGTCG 60.433 66.667 0.00 0.00 33.70 5.12
2988 3115 0.251634 CTCCTTCCAGAGGGACAAGC 59.748 60.000 0.00 0.00 44.89 4.01
3037 3164 2.409715 GGTTCGCTACGTACTGAAAACC 59.590 50.000 6.37 5.84 0.00 3.27
3038 3165 2.409715 GGGTTCGCTACGTACTGAAAAC 59.590 50.000 6.37 3.95 0.00 2.43
3039 3166 2.610232 GGGGTTCGCTACGTACTGAAAA 60.610 50.000 6.37 0.00 0.00 2.29
3056 3183 0.323451 GATTTTCTTCGGCCAGGGGT 60.323 55.000 2.24 0.00 0.00 4.95
3057 3184 0.323360 TGATTTTCTTCGGCCAGGGG 60.323 55.000 2.24 0.00 0.00 4.79
3083 3215 0.389391 TCCATCCGCGATCTCTTTCC 59.611 55.000 8.23 0.00 0.00 3.13
3097 3229 2.035193 TCAGCGCTGAATACTCTCCATC 59.965 50.000 36.62 0.00 36.53 3.51
3145 3277 3.606662 CTCGATGTCCCCGCCGAT 61.607 66.667 0.00 0.00 0.00 4.18
3156 3288 1.667154 TTCCCTCTGCCGACTCGATG 61.667 60.000 0.00 0.00 0.00 3.84
3163 3295 3.393970 CTGCCTTCCCTCTGCCGA 61.394 66.667 0.00 0.00 0.00 5.54
3188 3320 2.736995 CGTGAACATGTCCCGCGT 60.737 61.111 19.58 0.00 0.00 6.01


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

AutoCloner maintained by Alex Coulton.