Multiple sequence alignment - TraesCS2A01G172600

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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 TraesCS2A01G172600 chr2A 100.000 3380 0 0 1 3380 129106699 129103320 0.000000e+00 6242
1 TraesCS2A01G172600 chr2A 89.944 358 29 4 786 1142 129873596 129873947 3.980000e-124 455
2 TraesCS2A01G172600 chr2A 76.744 559 105 19 130 677 15726461 15725917 4.270000e-74 289
3 TraesCS2A01G172600 chr2D 90.520 2173 92 53 786 2903 123811723 123809610 0.000000e+00 2767
4 TraesCS2A01G172600 chr2B 91.681 1791 79 22 786 2522 176415135 176413361 0.000000e+00 2418
5 TraesCS2A01G172600 chr2B 87.270 597 69 6 81 675 714327847 714327256 0.000000e+00 675
6 TraesCS2A01G172600 chr2B 87.145 599 67 7 81 675 714270977 714270385 0.000000e+00 671
7 TraesCS2A01G172600 chr2B 84.795 513 41 16 2618 3098 176412980 176412473 6.560000e-132 481
8 TraesCS2A01G172600 chr2B 80.769 156 20 3 3193 3348 176412322 176412177 2.760000e-21 113
9 TraesCS2A01G172600 chr3D 85.799 676 91 5 1 674 489529238 489528566 0.000000e+00 712
10 TraesCS2A01G172600 chr7B 84.172 676 94 11 3 675 162991090 162990425 0.000000e+00 643
11 TraesCS2A01G172600 chr5A 83.704 675 100 9 1 673 389165562 389164896 2.210000e-176 628
12 TraesCS2A01G172600 chr5D 83.456 677 93 14 1 673 308627517 308628178 2.230000e-171 612
13 TraesCS2A01G172600 chr3A 83.043 631 89 11 1 628 632612401 632611786 1.060000e-154 556
14 TraesCS2A01G172600 chr1A 87.000 300 37 2 1 299 512858012 512858310 1.500000e-88 337
15 TraesCS2A01G172600 chr6A 76.534 554 113 16 130 677 107680000 107680542 1.530000e-73 287
16 TraesCS2A01G172600 chr4B 87.500 128 15 1 3 129 671680178 671680305 2.720000e-31 147
17 TraesCS2A01G172600 chr7D 72.442 606 110 33 1 574 611759540 611758960 1.260000e-29 141
18 TraesCS2A01G172600 chr7D 87.179 117 14 1 8 123 536970947 536970831 7.610000e-27 132
19 TraesCS2A01G172600 chr7A 85.437 103 11 4 1 102 192891887 192891788 1.660000e-18 104


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 TraesCS2A01G172600 chr2A 129103320 129106699 3379 True 6242 6242 100.000000 1 3380 1 chr2A.!!$R2 3379
1 TraesCS2A01G172600 chr2A 15725917 15726461 544 True 289 289 76.744000 130 677 1 chr2A.!!$R1 547
2 TraesCS2A01G172600 chr2D 123809610 123811723 2113 True 2767 2767 90.520000 786 2903 1 chr2D.!!$R1 2117
3 TraesCS2A01G172600 chr2B 176412177 176415135 2958 True 1004 2418 85.748333 786 3348 3 chr2B.!!$R3 2562
4 TraesCS2A01G172600 chr2B 714327256 714327847 591 True 675 675 87.270000 81 675 1 chr2B.!!$R2 594
5 TraesCS2A01G172600 chr2B 714270385 714270977 592 True 671 671 87.145000 81 675 1 chr2B.!!$R1 594
6 TraesCS2A01G172600 chr3D 489528566 489529238 672 True 712 712 85.799000 1 674 1 chr3D.!!$R1 673
7 TraesCS2A01G172600 chr7B 162990425 162991090 665 True 643 643 84.172000 3 675 1 chr7B.!!$R1 672
8 TraesCS2A01G172600 chr5A 389164896 389165562 666 True 628 628 83.704000 1 673 1 chr5A.!!$R1 672
9 TraesCS2A01G172600 chr5D 308627517 308628178 661 False 612 612 83.456000 1 673 1 chr5D.!!$F1 672
10 TraesCS2A01G172600 chr3A 632611786 632612401 615 True 556 556 83.043000 1 628 1 chr3A.!!$R1 627
11 TraesCS2A01G172600 chr6A 107680000 107680542 542 False 287 287 76.534000 130 677 1 chr6A.!!$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
721 736 0.038251 TGTCAGTCACACGATGCTCC 60.038 55.0 0.0 0.0 0.0 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2622 3016 0.457443 GCCAAGCACAATTAGCCCTC 59.543 55.0 0.0 0.0 0.0 4.3 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
22 23 0.259065 TCTGATCTACCGTCCCAGCT 59.741 55.000 0.00 0.00 0.00 4.24
26 27 2.308690 GATCTACCGTCCCAGCTAGTT 58.691 52.381 0.00 0.00 0.00 2.24
29 30 2.032620 CTACCGTCCCAGCTAGTTGAT 58.967 52.381 8.34 0.00 0.00 2.57
32 33 1.414181 CCGTCCCAGCTAGTTGATGAT 59.586 52.381 8.34 0.00 33.12 2.45
37 38 5.451937 CGTCCCAGCTAGTTGATGATCTTTA 60.452 44.000 8.34 0.00 33.12 1.85
211 217 0.388649 GCACAACGACGACCTCTCAT 60.389 55.000 0.00 0.00 0.00 2.90
225 231 3.781770 CTCATGTCGGGCGCTCCTC 62.782 68.421 7.64 0.00 0.00 3.71
265 271 6.265196 ACTGGAGCTATGTTTTTGAAACATGA 59.735 34.615 22.54 10.41 40.70 3.07
289 295 3.294493 TTGCAAAGTCTGGCCGCC 61.294 61.111 1.04 1.04 0.00 6.13
301 307 3.400054 GCCGCCCACTCCCTAACT 61.400 66.667 0.00 0.00 0.00 2.24
306 312 1.760613 CGCCCACTCCCTAACTATGAA 59.239 52.381 0.00 0.00 0.00 2.57
315 321 5.138758 TCCCTAACTATGAAGTGCTCCTA 57.861 43.478 0.00 0.00 35.62 2.94
352 360 6.522761 CAACTCGGACTATGTTTCTAAAACG 58.477 40.000 0.00 0.00 0.00 3.60
450 462 8.802267 CAGAAACCTTTTGAAATAAGACCCATA 58.198 33.333 0.00 0.00 0.00 2.74
539 551 8.507249 GTTGCATAAATCTACTGAAACAAGACT 58.493 33.333 0.00 0.00 30.23 3.24
606 619 1.153107 TGGGCGCTCAATCAGGATG 60.153 57.895 8.00 0.00 37.54 3.51
652 667 2.964174 CTTTGCTTGCATCCGCCA 59.036 55.556 0.00 0.00 37.32 5.69
677 692 5.926542 GCTGAAGGGTAATGTTTTCCTTTTC 59.073 40.000 0.00 0.00 39.46 2.29
678 693 6.413783 TGAAGGGTAATGTTTTCCTTTTCC 57.586 37.500 0.00 0.00 39.46 3.13
679 694 5.900123 TGAAGGGTAATGTTTTCCTTTTCCA 59.100 36.000 0.00 0.00 39.46 3.53
680 695 6.384305 TGAAGGGTAATGTTTTCCTTTTCCAA 59.616 34.615 0.00 0.00 39.46 3.53
681 696 6.816616 AGGGTAATGTTTTCCTTTTCCAAA 57.183 33.333 0.00 0.00 0.00 3.28
682 697 7.201702 AGGGTAATGTTTTCCTTTTCCAAAA 57.798 32.000 0.00 0.00 0.00 2.44
683 698 7.811282 AGGGTAATGTTTTCCTTTTCCAAAAT 58.189 30.769 0.00 0.00 0.00 1.82
684 699 8.278639 AGGGTAATGTTTTCCTTTTCCAAAATT 58.721 29.630 0.00 0.00 0.00 1.82
685 700 8.564574 GGGTAATGTTTTCCTTTTCCAAAATTC 58.435 33.333 0.00 0.00 0.00 2.17
686 701 9.114952 GGTAATGTTTTCCTTTTCCAAAATTCA 57.885 29.630 0.00 0.00 0.00 2.57
689 704 9.853555 AATGTTTTCCTTTTCCAAAATTCAAAC 57.146 25.926 0.00 0.00 0.00 2.93
690 705 8.628630 TGTTTTCCTTTTCCAAAATTCAAACT 57.371 26.923 10.85 0.00 0.00 2.66
691 706 9.726438 TGTTTTCCTTTTCCAAAATTCAAACTA 57.274 25.926 10.85 0.00 0.00 2.24
694 709 8.810652 TTCCTTTTCCAAAATTCAAACTATCG 57.189 30.769 0.00 0.00 0.00 2.92
695 710 8.172352 TCCTTTTCCAAAATTCAAACTATCGA 57.828 30.769 0.00 0.00 0.00 3.59
696 711 8.634444 TCCTTTTCCAAAATTCAAACTATCGAA 58.366 29.630 0.00 0.00 0.00 3.71
697 712 9.423061 CCTTTTCCAAAATTCAAACTATCGAAT 57.577 29.630 0.00 0.00 33.27 3.34
700 715 8.980143 TTCCAAAATTCAAACTATCGAATTCC 57.020 30.769 0.00 0.00 40.15 3.01
701 716 8.116651 TCCAAAATTCAAACTATCGAATTCCA 57.883 30.769 0.00 0.00 40.15 3.53
702 717 8.748412 TCCAAAATTCAAACTATCGAATTCCAT 58.252 29.630 0.00 0.00 40.15 3.41
703 718 8.810427 CCAAAATTCAAACTATCGAATTCCATG 58.190 33.333 0.00 0.00 40.15 3.66
704 719 9.357652 CAAAATTCAAACTATCGAATTCCATGT 57.642 29.630 0.00 0.00 40.15 3.21
705 720 9.573133 AAAATTCAAACTATCGAATTCCATGTC 57.427 29.630 0.00 0.00 40.15 3.06
706 721 7.864108 ATTCAAACTATCGAATTCCATGTCA 57.136 32.000 0.00 0.00 0.00 3.58
707 722 6.908870 TCAAACTATCGAATTCCATGTCAG 57.091 37.500 0.00 0.00 0.00 3.51
708 723 6.406370 TCAAACTATCGAATTCCATGTCAGT 58.594 36.000 0.00 0.00 0.00 3.41
709 724 6.535150 TCAAACTATCGAATTCCATGTCAGTC 59.465 38.462 0.00 0.00 0.00 3.51
710 725 5.598416 ACTATCGAATTCCATGTCAGTCA 57.402 39.130 0.00 0.00 0.00 3.41
711 726 5.352284 ACTATCGAATTCCATGTCAGTCAC 58.648 41.667 0.00 0.00 0.00 3.67
712 727 3.676291 TCGAATTCCATGTCAGTCACA 57.324 42.857 0.00 0.00 40.18 3.58
713 728 3.325870 TCGAATTCCATGTCAGTCACAC 58.674 45.455 0.00 0.00 38.04 3.82
714 729 2.092681 CGAATTCCATGTCAGTCACACG 59.907 50.000 0.00 0.00 38.04 4.49
715 730 3.325870 GAATTCCATGTCAGTCACACGA 58.674 45.455 0.00 0.00 38.04 4.35
716 731 3.616956 ATTCCATGTCAGTCACACGAT 57.383 42.857 0.00 0.00 38.04 3.73
717 732 2.368655 TCCATGTCAGTCACACGATG 57.631 50.000 0.00 0.00 38.04 3.84
718 733 0.723414 CCATGTCAGTCACACGATGC 59.277 55.000 0.00 0.00 38.04 3.91
719 734 1.673923 CCATGTCAGTCACACGATGCT 60.674 52.381 0.00 0.00 38.04 3.79
720 735 1.657594 CATGTCAGTCACACGATGCTC 59.342 52.381 0.00 0.00 38.04 4.26
721 736 0.038251 TGTCAGTCACACGATGCTCC 60.038 55.000 0.00 0.00 0.00 4.70
722 737 0.038251 GTCAGTCACACGATGCTCCA 60.038 55.000 0.00 0.00 0.00 3.86
723 738 0.897621 TCAGTCACACGATGCTCCAT 59.102 50.000 0.00 0.00 0.00 3.41
724 739 1.134995 TCAGTCACACGATGCTCCATC 60.135 52.381 0.00 0.00 37.50 3.51
725 740 1.134877 CAGTCACACGATGCTCCATCT 60.135 52.381 0.00 0.00 38.59 2.90
726 741 1.552337 AGTCACACGATGCTCCATCTT 59.448 47.619 0.00 0.00 38.59 2.40
727 742 2.027745 AGTCACACGATGCTCCATCTTT 60.028 45.455 0.00 0.00 38.59 2.52
728 743 2.744202 GTCACACGATGCTCCATCTTTT 59.256 45.455 0.00 0.00 38.59 2.27
729 744 3.002791 TCACACGATGCTCCATCTTTTC 58.997 45.455 0.00 0.00 38.59 2.29
730 745 2.002586 ACACGATGCTCCATCTTTTCG 58.997 47.619 0.00 0.00 38.59 3.46
731 746 2.002586 CACGATGCTCCATCTTTTCGT 58.997 47.619 0.00 0.00 38.59 3.85
732 747 2.002586 ACGATGCTCCATCTTTTCGTG 58.997 47.619 0.00 0.00 38.59 4.35
733 748 1.267732 CGATGCTCCATCTTTTCGTGC 60.268 52.381 3.98 0.00 38.59 5.34
734 749 0.729116 ATGCTCCATCTTTTCGTGCG 59.271 50.000 0.00 0.00 0.00 5.34
735 750 0.320334 TGCTCCATCTTTTCGTGCGA 60.320 50.000 0.00 0.00 0.00 5.10
736 751 0.371645 GCTCCATCTTTTCGTGCGAG 59.628 55.000 0.00 0.00 0.00 5.03
737 752 1.714794 CTCCATCTTTTCGTGCGAGT 58.285 50.000 0.00 0.00 0.00 4.18
738 753 2.069273 CTCCATCTTTTCGTGCGAGTT 58.931 47.619 0.00 0.00 0.00 3.01
739 754 1.798223 TCCATCTTTTCGTGCGAGTTG 59.202 47.619 0.00 0.00 0.00 3.16
740 755 1.798223 CCATCTTTTCGTGCGAGTTGA 59.202 47.619 0.00 0.00 0.00 3.18
741 756 2.416547 CCATCTTTTCGTGCGAGTTGAT 59.583 45.455 0.00 0.00 0.00 2.57
742 757 3.484229 CCATCTTTTCGTGCGAGTTGATC 60.484 47.826 0.00 0.00 0.00 2.92
743 758 3.026630 TCTTTTCGTGCGAGTTGATCT 57.973 42.857 0.00 0.00 0.00 2.75
744 759 2.731451 TCTTTTCGTGCGAGTTGATCTG 59.269 45.455 0.00 0.00 0.00 2.90
745 760 2.432206 TTTCGTGCGAGTTGATCTGA 57.568 45.000 0.00 0.00 0.00 3.27
746 761 2.654749 TTCGTGCGAGTTGATCTGAT 57.345 45.000 0.00 0.00 0.00 2.90
747 762 1.913317 TCGTGCGAGTTGATCTGATG 58.087 50.000 0.00 0.00 0.00 3.07
748 763 0.926155 CGTGCGAGTTGATCTGATGG 59.074 55.000 0.00 0.00 0.00 3.51
749 764 0.654683 GTGCGAGTTGATCTGATGGC 59.345 55.000 0.00 0.00 0.00 4.40
750 765 0.462581 TGCGAGTTGATCTGATGGCC 60.463 55.000 0.00 0.00 0.00 5.36
751 766 0.179062 GCGAGTTGATCTGATGGCCT 60.179 55.000 3.32 0.00 0.00 5.19
752 767 1.579698 CGAGTTGATCTGATGGCCTG 58.420 55.000 3.32 0.00 0.00 4.85
753 768 1.307097 GAGTTGATCTGATGGCCTGC 58.693 55.000 3.32 0.00 0.00 4.85
754 769 0.917533 AGTTGATCTGATGGCCTGCT 59.082 50.000 3.32 0.00 0.00 4.24
755 770 1.284198 AGTTGATCTGATGGCCTGCTT 59.716 47.619 3.32 0.00 0.00 3.91
756 771 1.404391 GTTGATCTGATGGCCTGCTTG 59.596 52.381 3.32 0.00 0.00 4.01
757 772 0.106868 TGATCTGATGGCCTGCTTGG 60.107 55.000 3.32 0.00 39.35 3.61
758 773 0.106819 GATCTGATGGCCTGCTTGGT 60.107 55.000 3.32 0.00 38.35 3.67
759 774 1.141657 GATCTGATGGCCTGCTTGGTA 59.858 52.381 3.32 0.00 38.35 3.25
760 775 0.991146 TCTGATGGCCTGCTTGGTAA 59.009 50.000 3.32 0.00 38.35 2.85
761 776 1.065199 TCTGATGGCCTGCTTGGTAAG 60.065 52.381 3.32 0.00 38.35 2.34
776 791 2.174363 GTAAGCTACCAACAACGGGT 57.826 50.000 0.00 0.00 42.48 5.28
777 792 2.497138 GTAAGCTACCAACAACGGGTT 58.503 47.619 0.00 0.00 41.47 4.11
778 793 2.061509 AAGCTACCAACAACGGGTTT 57.938 45.000 0.00 0.00 37.72 3.27
779 794 2.061509 AGCTACCAACAACGGGTTTT 57.938 45.000 0.00 0.00 37.72 2.43
780 795 3.211718 AGCTACCAACAACGGGTTTTA 57.788 42.857 0.00 0.00 37.72 1.52
781 796 3.553904 AGCTACCAACAACGGGTTTTAA 58.446 40.909 0.00 0.00 37.72 1.52
782 797 3.952967 AGCTACCAACAACGGGTTTTAAA 59.047 39.130 0.00 0.00 37.72 1.52
783 798 4.043750 GCTACCAACAACGGGTTTTAAAC 58.956 43.478 0.00 0.00 37.72 2.01
811 826 2.665185 GCGGCTCACGTTTCCTGT 60.665 61.111 0.00 0.00 46.52 4.00
813 828 0.947180 GCGGCTCACGTTTCCTGTAA 60.947 55.000 0.00 0.00 46.52 2.41
816 831 2.490991 GGCTCACGTTTCCTGTAAGTT 58.509 47.619 0.00 0.00 0.00 2.66
819 834 4.053295 GCTCACGTTTCCTGTAAGTTGTA 58.947 43.478 0.00 0.00 0.00 2.41
895 912 1.739338 CGGTCTCTTCTCCATCGGGG 61.739 65.000 0.00 0.00 38.37 5.73
949 975 0.546122 ACTCAACCAGTGGACAGCAA 59.454 50.000 18.40 0.00 32.26 3.91
968 994 2.656069 CGACCCATCCACCGGAAGT 61.656 63.158 9.46 0.00 34.34 3.01
1238 1264 6.699204 CGATCACTCAGCTTAATTCACTATGT 59.301 38.462 0.00 0.00 0.00 2.29
1242 1268 7.708322 TCACTCAGCTTAATTCACTATGTCATC 59.292 37.037 0.00 0.00 0.00 2.92
1286 1317 0.647410 CATCCGCGCTGTTCTTGTAG 59.353 55.000 5.56 0.00 0.00 2.74
1287 1318 1.084370 ATCCGCGCTGTTCTTGTAGC 61.084 55.000 5.56 0.00 36.60 3.58
1288 1319 2.027073 CCGCGCTGTTCTTGTAGCA 61.027 57.895 5.56 0.00 39.87 3.49
1331 1368 2.324215 GCTGCATGCATCGGTGTAT 58.676 52.632 22.97 0.00 42.31 2.29
1350 1387 6.317857 GTGTATCTGAATTTTGCCTGTTCTC 58.682 40.000 0.00 0.00 0.00 2.87
1386 1424 1.139734 GCGAGACGAAGGATGCAGA 59.860 57.895 0.00 0.00 0.00 4.26
1495 1533 1.117749 TGCCGGAGATGATGGAGGAG 61.118 60.000 5.05 0.00 0.00 3.69
1588 1626 2.910688 ACAACACGGTGAGATCAGTT 57.089 45.000 16.29 0.00 0.00 3.16
1634 1682 2.195683 CACAGGCCCAACACACCT 59.804 61.111 0.00 0.00 0.00 4.00
1661 1709 1.269778 TGGCATCGCTACTGCACTATC 60.270 52.381 4.71 0.00 41.47 2.08
1686 1734 3.487574 CGTGCAAGCTATGAGTAACTAGC 59.512 47.826 0.00 0.00 40.52 3.42
1821 1896 4.622740 GCAATCTTCAATGTACTTTGGTGC 59.377 41.667 18.40 15.53 0.00 5.01
1915 1990 0.036875 ACTTCTGGGCCTTCTTTCCG 59.963 55.000 4.53 0.00 0.00 4.30
2056 2162 6.173339 CAATCCTTCTTGACCTAGTTTGCTA 58.827 40.000 0.00 0.00 0.00 3.49
2057 2163 5.148651 TCCTTCTTGACCTAGTTTGCTAC 57.851 43.478 0.00 0.00 0.00 3.58
2060 2166 4.436242 TCTTGACCTAGTTTGCTACTCG 57.564 45.455 0.00 0.00 38.33 4.18
2063 2169 4.595762 TGACCTAGTTTGCTACTCGTTT 57.404 40.909 0.00 0.00 38.33 3.60
2111 2217 9.642312 CGAATTACTGTAATCAATCACTTCATG 57.358 33.333 13.07 0.00 0.00 3.07
2130 2236 4.156922 TCATGGCCCAAAAACTACATAACG 59.843 41.667 0.00 0.00 0.00 3.18
2390 2496 3.314080 CCTGCAGAGTAGTCAGTAGTAGC 59.686 52.174 17.39 0.00 0.00 3.58
2399 2505 5.710567 AGTAGTCAGTAGTAGCAACACATGA 59.289 40.000 0.00 0.00 0.00 3.07
2463 2571 5.605534 ACTCTGTGTATAAGATGTCCATGC 58.394 41.667 0.00 0.00 0.00 4.06
2522 2630 8.738106 GGTTCATCTGATTCTTTTTCTTCTGAT 58.262 33.333 0.00 0.00 0.00 2.90
2524 2632 9.511272 TTCATCTGATTCTTTTTCTTCTGATGA 57.489 29.630 13.76 13.76 44.60 2.92
2525 2633 9.511272 TCATCTGATTCTTTTTCTTCTGATGAA 57.489 29.630 14.80 2.19 43.97 2.57
2613 2750 7.628153 GCAAAGAAATGGGTTGTTGTTGAAATT 60.628 33.333 0.00 0.00 0.00 1.82
2614 2751 6.923928 AGAAATGGGTTGTTGTTGAAATTG 57.076 33.333 0.00 0.00 0.00 2.32
2697 3091 1.137086 CGGAAGGTTCCTGACGATCAT 59.863 52.381 7.17 0.00 45.33 2.45
2699 3093 2.168521 GGAAGGTTCCTGACGATCATCA 59.831 50.000 1.16 0.00 44.11 3.07
2700 3094 3.452474 GAAGGTTCCTGACGATCATCAG 58.548 50.000 11.85 11.85 44.91 2.90
2701 3095 1.137872 AGGTTCCTGACGATCATCAGC 59.862 52.381 13.31 0.02 44.12 4.26
2702 3096 1.203928 GTTCCTGACGATCATCAGCG 58.796 55.000 13.31 7.05 44.12 5.18
2746 3140 2.032528 CCACGGCAAGGAAGCAGA 59.967 61.111 0.00 0.00 35.83 4.26
2823 3217 2.362369 CCAGTCGCACTCCATCCCT 61.362 63.158 0.00 0.00 0.00 4.20
2891 3287 1.790838 CGCCGCGTAGTGCTAGATATC 60.791 57.143 4.92 0.00 43.27 1.63
2908 3304 8.723311 GCTAGATATCTTAGTAATCGTCAGTGT 58.277 37.037 11.25 0.00 0.00 3.55
2944 3361 3.692791 TGAAGTGAGGATCGTCGTATG 57.307 47.619 10.63 0.00 38.61 2.39
2955 3372 0.110956 CGTCGTATGCATGCATGAGC 60.111 55.000 37.43 25.86 37.82 4.26
2978 3403 5.914635 GCAATCTGAAGATGAACAACGAAAA 59.085 36.000 0.00 0.00 34.49 2.29
2979 3404 6.087291 GCAATCTGAAGATGAACAACGAAAAG 59.913 38.462 0.00 0.00 34.49 2.27
2980 3405 6.867662 ATCTGAAGATGAACAACGAAAAGT 57.132 33.333 0.00 0.00 32.68 2.66
2997 3423 6.183360 ACGAAAAGTAATTTGAATACGCCGAT 60.183 34.615 0.00 0.00 0.00 4.18
2998 3424 6.353582 CGAAAAGTAATTTGAATACGCCGATC 59.646 38.462 0.00 0.00 0.00 3.69
2999 3425 5.668558 AAGTAATTTGAATACGCCGATCC 57.331 39.130 0.00 0.00 0.00 3.36
3004 3430 1.361271 GAATACGCCGATCCACCGA 59.639 57.895 0.00 0.00 0.00 4.69
3006 3432 0.391597 AATACGCCGATCCACCGAAT 59.608 50.000 0.00 0.00 0.00 3.34
3009 3435 2.504032 GCCGATCCACCGAATCCA 59.496 61.111 0.00 0.00 0.00 3.41
3020 3446 3.605634 CACCGAATCCAGTGATAAACCA 58.394 45.455 0.00 0.00 36.01 3.67
3021 3447 4.199310 CACCGAATCCAGTGATAAACCAT 58.801 43.478 0.00 0.00 36.01 3.55
3026 3452 5.586243 CGAATCCAGTGATAAACCATCAAGT 59.414 40.000 0.00 0.00 45.28 3.16
3042 3468 9.750125 AACCATCAAGTAAGAAAAGTTGATTTC 57.250 29.630 4.56 0.00 43.72 2.17
3053 3479 0.449388 GTTGATTTCTGCGCTCCAGG 59.551 55.000 9.73 0.00 42.05 4.45
3054 3480 0.036732 TTGATTTCTGCGCTCCAGGT 59.963 50.000 9.73 0.00 42.05 4.00
3088 3514 0.834612 TCCCTCACGTTGGTTTGAGT 59.165 50.000 3.97 0.00 38.06 3.41
3090 3516 1.333619 CCCTCACGTTGGTTTGAGTTG 59.666 52.381 3.97 0.00 38.06 3.16
3102 3612 7.255001 CGTTGGTTTGAGTTGTTACCTAGATTT 60.255 37.037 0.00 0.00 0.00 2.17
3103 3613 8.410912 GTTGGTTTGAGTTGTTACCTAGATTTT 58.589 33.333 0.00 0.00 0.00 1.82
3104 3614 7.936584 TGGTTTGAGTTGTTACCTAGATTTTG 58.063 34.615 0.00 0.00 0.00 2.44
3114 3624 7.663827 TGTTACCTAGATTTTGTCGAGAAGAA 58.336 34.615 0.00 0.00 31.86 2.52
3120 3630 8.865001 CCTAGATTTTGTCGAGAAGAAAGTAAG 58.135 37.037 0.00 0.00 31.86 2.34
3126 3636 4.980434 TGTCGAGAAGAAAGTAAGAAACCG 59.020 41.667 0.00 0.00 0.00 4.44
3127 3637 4.981054 GTCGAGAAGAAAGTAAGAAACCGT 59.019 41.667 0.00 0.00 0.00 4.83
3128 3638 4.980434 TCGAGAAGAAAGTAAGAAACCGTG 59.020 41.667 0.00 0.00 0.00 4.94
3129 3639 4.376109 CGAGAAGAAAGTAAGAAACCGTGC 60.376 45.833 0.00 0.00 0.00 5.34
3130 3640 4.448210 AGAAGAAAGTAAGAAACCGTGCA 58.552 39.130 0.00 0.00 0.00 4.57
3131 3641 4.272748 AGAAGAAAGTAAGAAACCGTGCAC 59.727 41.667 6.82 6.82 0.00 4.57
3132 3642 2.876550 AGAAAGTAAGAAACCGTGCACC 59.123 45.455 12.15 0.00 0.00 5.01
3133 3643 2.335316 AAGTAAGAAACCGTGCACCA 57.665 45.000 12.15 0.00 0.00 4.17
3134 3644 2.561478 AGTAAGAAACCGTGCACCAT 57.439 45.000 12.15 0.00 0.00 3.55
3135 3645 2.151202 AGTAAGAAACCGTGCACCATG 58.849 47.619 12.15 2.48 0.00 3.66
3136 3646 2.147958 GTAAGAAACCGTGCACCATGA 58.852 47.619 12.15 0.00 0.00 3.07
3137 3647 1.686355 AAGAAACCGTGCACCATGAA 58.314 45.000 12.15 0.00 0.00 2.57
3138 3648 1.909700 AGAAACCGTGCACCATGAAT 58.090 45.000 12.15 0.00 0.00 2.57
3139 3649 1.812571 AGAAACCGTGCACCATGAATC 59.187 47.619 12.15 2.70 0.00 2.52
3140 3650 0.887933 AAACCGTGCACCATGAATCC 59.112 50.000 12.15 0.00 0.00 3.01
3141 3651 0.251121 AACCGTGCACCATGAATCCA 60.251 50.000 12.15 0.00 0.00 3.41
3142 3652 0.034186 ACCGTGCACCATGAATCCAT 60.034 50.000 12.15 0.00 0.00 3.41
3147 3657 2.953648 GTGCACCATGAATCCATGATGA 59.046 45.455 5.22 0.00 45.30 2.92
3148 3658 3.382227 GTGCACCATGAATCCATGATGAA 59.618 43.478 5.22 0.00 45.30 2.57
3149 3659 3.382227 TGCACCATGAATCCATGATGAAC 59.618 43.478 4.07 0.00 45.30 3.18
3150 3660 3.243636 GCACCATGAATCCATGATGAACC 60.244 47.826 4.07 0.00 45.30 3.62
3151 3661 4.212716 CACCATGAATCCATGATGAACCT 58.787 43.478 6.95 0.00 45.30 3.50
3152 3662 4.647853 CACCATGAATCCATGATGAACCTT 59.352 41.667 6.95 0.00 45.30 3.50
3153 3663 5.221185 CACCATGAATCCATGATGAACCTTC 60.221 44.000 6.95 0.00 45.30 3.46
3154 3664 8.130401 CACCATGAATCCATGATGAACCTTCC 62.130 46.154 6.95 0.00 45.30 3.46
3155 3665 4.868172 TGAATCCATGATGAACCTTCCT 57.132 40.909 0.00 0.00 0.00 3.36
3156 3666 5.974156 TGAATCCATGATGAACCTTCCTA 57.026 39.130 0.00 0.00 0.00 2.94
3157 3667 5.933617 TGAATCCATGATGAACCTTCCTAG 58.066 41.667 0.00 0.00 0.00 3.02
3166 3676 3.539842 CCTTCCTAGGTCGGCCTC 58.460 66.667 14.54 0.00 45.64 4.70
3167 3677 2.491022 CCTTCCTAGGTCGGCCTCG 61.491 68.421 14.54 6.10 45.64 4.63
3179 3689 0.377203 CGGCCTCGTAAAAATCCAGC 59.623 55.000 0.00 0.00 0.00 4.85
3193 3703 0.599991 TCCAGCGACATGTCACACAC 60.600 55.000 24.93 8.84 0.00 3.82
3196 3706 0.880278 AGCGACATGTCACACACACC 60.880 55.000 24.93 3.27 38.04 4.16
3203 3726 3.814842 ACATGTCACACACACCTGTAATG 59.185 43.478 0.00 0.00 38.04 1.90
3204 3727 2.217750 TGTCACACACACCTGTAATGC 58.782 47.619 0.00 0.00 0.00 3.56
3207 3730 1.946081 CACACACACCTGTAATGCACA 59.054 47.619 0.00 0.00 35.30 4.57
3243 3766 3.870633 GGAACACGACAACTCTATCCT 57.129 47.619 0.00 0.00 0.00 3.24
3255 3778 7.437713 ACAACTCTATCCTCATGGTTGATTA 57.562 36.000 12.27 0.00 37.86 1.75
3256 3779 7.861629 ACAACTCTATCCTCATGGTTGATTAA 58.138 34.615 12.27 0.00 37.86 1.40
3259 3782 8.915057 ACTCTATCCTCATGGTTGATTAAATG 57.085 34.615 0.00 0.00 34.23 2.32
3276 3799 9.531942 TGATTAAATGTTGCATTTGGATGATAC 57.468 29.630 14.99 2.11 35.16 2.24
3279 3802 5.779529 ATGTTGCATTTGGATGATACTCC 57.220 39.130 0.00 0.00 35.16 3.85
3280 3803 4.858850 TGTTGCATTTGGATGATACTCCT 58.141 39.130 0.00 0.00 36.20 3.69
3281 3804 6.000246 TGTTGCATTTGGATGATACTCCTA 58.000 37.500 0.00 0.00 36.20 2.94
3282 3805 6.057533 TGTTGCATTTGGATGATACTCCTAG 58.942 40.000 0.00 0.00 36.20 3.02
3283 3806 5.894298 TGCATTTGGATGATACTCCTAGT 57.106 39.130 0.00 0.00 36.20 2.57
3284 3807 6.252599 TGCATTTGGATGATACTCCTAGTT 57.747 37.500 0.00 0.00 36.20 2.24
3295 3818 3.618690 ACTCCTAGTTCAGATTGGTGC 57.381 47.619 0.00 0.00 0.00 5.01
3299 3822 5.189736 ACTCCTAGTTCAGATTGGTGCATAA 59.810 40.000 0.00 0.00 0.00 1.90
3303 3826 9.100197 TCCTAGTTCAGATTGGTGCATAATATA 57.900 33.333 0.00 0.00 0.00 0.86
3304 3827 9.155975 CCTAGTTCAGATTGGTGCATAATATAC 57.844 37.037 0.00 0.00 0.00 1.47
3306 3829 7.517320 AGTTCAGATTGGTGCATAATATACCA 58.483 34.615 0.00 0.00 42.40 3.25
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 1.214673 ACTAGCTGGGACGGTAGATCA 59.785 52.381 0.85 0.00 36.80 2.92
22 23 9.431887 GGTAGTTGTTGTAAAGATCATCAACTA 57.568 33.333 17.73 17.73 45.58 2.24
26 27 8.322906 CAAGGTAGTTGTTGTAAAGATCATCA 57.677 34.615 0.00 0.00 0.00 3.07
139 142 1.606531 GTGGAGGAGGAGCAGCAAT 59.393 57.895 0.00 0.00 0.00 3.56
184 187 1.299850 CGTCGTTGTGCTGGAGTGA 60.300 57.895 0.00 0.00 0.00 3.41
237 243 6.127479 TGTTTCAAAAACATAGCTCCAGTTGT 60.127 34.615 0.00 0.00 0.00 3.32
265 271 1.610522 GCCAGACTTTGCAACATGAGT 59.389 47.619 0.00 0.00 0.00 3.41
289 295 3.452627 AGCACTTCATAGTTAGGGAGTGG 59.547 47.826 12.64 0.00 30.26 4.00
301 307 5.557576 AAGCATCATAGGAGCACTTCATA 57.442 39.130 0.00 0.00 0.00 2.15
306 312 3.806380 CAGAAAGCATCATAGGAGCACT 58.194 45.455 0.00 0.00 0.00 4.40
410 422 8.514594 CAAAAGGTTTCTGCAATAGACATCTTA 58.485 33.333 0.00 0.00 35.91 2.10
415 427 6.707440 TTCAAAAGGTTTCTGCAATAGACA 57.293 33.333 0.00 0.00 34.43 3.41
497 509 3.215151 TGCAACACGGGACTAATTTCAA 58.785 40.909 0.00 0.00 0.00 2.69
503 515 4.839121 AGATTTATGCAACACGGGACTAA 58.161 39.130 0.00 0.00 0.00 2.24
606 619 1.017387 CTTGCTTAGCCGTTGGATCC 58.983 55.000 4.20 4.20 0.00 3.36
652 667 4.388577 AGGAAAACATTACCCTTCAGCT 57.611 40.909 0.00 0.00 0.00 4.24
677 692 8.810427 CATGGAATTCGATAGTTTGAATTTTGG 58.190 33.333 2.33 0.00 43.19 3.28
678 693 9.357652 ACATGGAATTCGATAGTTTGAATTTTG 57.642 29.630 2.33 4.15 43.19 2.44
679 694 9.573133 GACATGGAATTCGATAGTTTGAATTTT 57.427 29.630 2.33 0.00 43.19 1.82
680 695 8.739039 TGACATGGAATTCGATAGTTTGAATTT 58.261 29.630 2.33 0.00 43.19 1.82
681 696 8.279970 TGACATGGAATTCGATAGTTTGAATT 57.720 30.769 2.33 0.20 44.96 2.17
682 697 7.554118 ACTGACATGGAATTCGATAGTTTGAAT 59.446 33.333 2.33 0.00 37.53 2.57
683 698 6.878923 ACTGACATGGAATTCGATAGTTTGAA 59.121 34.615 2.33 0.00 37.40 2.69
684 699 6.406370 ACTGACATGGAATTCGATAGTTTGA 58.594 36.000 2.33 0.00 37.40 2.69
685 700 6.313658 TGACTGACATGGAATTCGATAGTTTG 59.686 38.462 2.33 0.00 37.40 2.93
686 701 6.313905 GTGACTGACATGGAATTCGATAGTTT 59.686 38.462 2.33 0.00 37.40 2.66
687 702 5.812642 GTGACTGACATGGAATTCGATAGTT 59.187 40.000 2.33 0.00 37.40 2.24
688 703 5.105351 TGTGACTGACATGGAATTCGATAGT 60.105 40.000 2.33 3.61 37.40 2.12
689 704 5.233050 GTGTGACTGACATGGAATTCGATAG 59.767 44.000 2.33 0.42 36.78 2.08
690 705 5.109210 GTGTGACTGACATGGAATTCGATA 58.891 41.667 2.33 0.00 36.78 2.92
691 706 3.935203 GTGTGACTGACATGGAATTCGAT 59.065 43.478 0.00 0.00 36.78 3.59
692 707 3.325870 GTGTGACTGACATGGAATTCGA 58.674 45.455 0.00 0.00 36.78 3.71
693 708 2.092681 CGTGTGACTGACATGGAATTCG 59.907 50.000 0.00 0.00 37.86 3.34
694 709 3.325870 TCGTGTGACTGACATGGAATTC 58.674 45.455 0.00 0.00 41.37 2.17
695 710 3.401033 TCGTGTGACTGACATGGAATT 57.599 42.857 0.00 0.00 41.37 2.17
696 711 3.264947 CATCGTGTGACTGACATGGAAT 58.735 45.455 0.00 0.00 41.37 3.01
697 712 2.687370 CATCGTGTGACTGACATGGAA 58.313 47.619 0.00 0.00 41.37 3.53
698 713 1.672737 GCATCGTGTGACTGACATGGA 60.673 52.381 0.00 0.00 41.37 3.41
699 714 0.723414 GCATCGTGTGACTGACATGG 59.277 55.000 0.00 0.00 41.37 3.66
700 715 1.657594 GAGCATCGTGTGACTGACATG 59.342 52.381 0.00 0.00 42.28 3.21
701 716 1.404717 GGAGCATCGTGTGACTGACAT 60.405 52.381 0.00 0.00 36.78 3.06
702 717 0.038251 GGAGCATCGTGTGACTGACA 60.038 55.000 0.00 0.00 34.37 3.58
703 718 0.038251 TGGAGCATCGTGTGACTGAC 60.038 55.000 0.00 0.00 34.37 3.51
704 719 0.897621 ATGGAGCATCGTGTGACTGA 59.102 50.000 0.00 0.00 34.37 3.41
705 720 1.134877 AGATGGAGCATCGTGTGACTG 60.135 52.381 0.00 0.00 44.67 3.51
706 721 1.189752 AGATGGAGCATCGTGTGACT 58.810 50.000 0.00 0.00 44.67 3.41
707 722 2.015736 AAGATGGAGCATCGTGTGAC 57.984 50.000 0.00 0.00 44.67 3.67
708 723 2.768253 AAAGATGGAGCATCGTGTGA 57.232 45.000 0.00 0.00 44.67 3.58
709 724 2.222886 CGAAAAGATGGAGCATCGTGTG 60.223 50.000 0.00 0.00 44.67 3.82
710 725 2.002586 CGAAAAGATGGAGCATCGTGT 58.997 47.619 0.00 0.00 44.67 4.49
711 726 2.002586 ACGAAAAGATGGAGCATCGTG 58.997 47.619 0.00 0.00 44.67 4.35
712 727 2.002586 CACGAAAAGATGGAGCATCGT 58.997 47.619 0.00 0.00 44.67 3.73
713 728 1.267732 GCACGAAAAGATGGAGCATCG 60.268 52.381 0.00 0.00 44.67 3.84
714 729 1.267732 CGCACGAAAAGATGGAGCATC 60.268 52.381 0.00 0.00 40.80 3.91
715 730 0.729116 CGCACGAAAAGATGGAGCAT 59.271 50.000 0.00 0.00 0.00 3.79
716 731 0.320334 TCGCACGAAAAGATGGAGCA 60.320 50.000 0.00 0.00 0.00 4.26
717 732 0.371645 CTCGCACGAAAAGATGGAGC 59.628 55.000 0.00 0.00 0.00 4.70
718 733 1.714794 ACTCGCACGAAAAGATGGAG 58.285 50.000 0.00 0.00 0.00 3.86
719 734 1.798223 CAACTCGCACGAAAAGATGGA 59.202 47.619 0.00 0.00 0.00 3.41
720 735 1.798223 TCAACTCGCACGAAAAGATGG 59.202 47.619 0.00 0.00 0.00 3.51
721 736 3.369147 AGATCAACTCGCACGAAAAGATG 59.631 43.478 0.00 0.00 0.00 2.90
722 737 3.369147 CAGATCAACTCGCACGAAAAGAT 59.631 43.478 0.00 0.00 0.00 2.40
723 738 2.731451 CAGATCAACTCGCACGAAAAGA 59.269 45.455 0.00 0.00 0.00 2.52
724 739 2.731451 TCAGATCAACTCGCACGAAAAG 59.269 45.455 0.00 0.00 0.00 2.27
725 740 2.749776 TCAGATCAACTCGCACGAAAA 58.250 42.857 0.00 0.00 0.00 2.29
726 741 2.432206 TCAGATCAACTCGCACGAAA 57.568 45.000 0.00 0.00 0.00 3.46
727 742 2.262211 CATCAGATCAACTCGCACGAA 58.738 47.619 0.00 0.00 0.00 3.85
728 743 1.469767 CCATCAGATCAACTCGCACGA 60.470 52.381 0.00 0.00 0.00 4.35
729 744 0.926155 CCATCAGATCAACTCGCACG 59.074 55.000 0.00 0.00 0.00 5.34
730 745 0.654683 GCCATCAGATCAACTCGCAC 59.345 55.000 0.00 0.00 0.00 5.34
731 746 0.462581 GGCCATCAGATCAACTCGCA 60.463 55.000 0.00 0.00 0.00 5.10
732 747 0.179062 AGGCCATCAGATCAACTCGC 60.179 55.000 5.01 0.00 0.00 5.03
733 748 1.579698 CAGGCCATCAGATCAACTCG 58.420 55.000 5.01 0.00 0.00 4.18
734 749 1.134159 AGCAGGCCATCAGATCAACTC 60.134 52.381 5.01 0.00 0.00 3.01
735 750 0.917533 AGCAGGCCATCAGATCAACT 59.082 50.000 5.01 0.00 0.00 3.16
736 751 1.404391 CAAGCAGGCCATCAGATCAAC 59.596 52.381 5.01 0.00 0.00 3.18
737 752 1.683938 CCAAGCAGGCCATCAGATCAA 60.684 52.381 5.01 0.00 0.00 2.57
738 753 0.106868 CCAAGCAGGCCATCAGATCA 60.107 55.000 5.01 0.00 0.00 2.92
739 754 0.106819 ACCAAGCAGGCCATCAGATC 60.107 55.000 5.01 0.00 43.14 2.75
740 755 1.216064 TACCAAGCAGGCCATCAGAT 58.784 50.000 5.01 0.00 43.14 2.90
741 756 0.991146 TTACCAAGCAGGCCATCAGA 59.009 50.000 5.01 0.00 43.14 3.27
742 757 1.386533 CTTACCAAGCAGGCCATCAG 58.613 55.000 5.01 0.00 43.14 2.90
743 758 3.575506 CTTACCAAGCAGGCCATCA 57.424 52.632 5.01 0.00 43.14 3.07
757 772 2.174363 ACCCGTTGTTGGTAGCTTAC 57.826 50.000 0.00 0.00 33.26 2.34
758 773 2.934886 AACCCGTTGTTGGTAGCTTA 57.065 45.000 0.00 0.00 35.31 3.09
759 774 2.061509 AAACCCGTTGTTGGTAGCTT 57.938 45.000 0.00 0.00 37.23 3.74
760 775 2.061509 AAAACCCGTTGTTGGTAGCT 57.938 45.000 0.00 0.00 37.23 3.32
761 776 3.986442 TTAAAACCCGTTGTTGGTAGC 57.014 42.857 0.00 0.00 37.23 3.58
762 777 4.609947 GGTTTAAAACCCGTTGTTGGTAG 58.390 43.478 0.00 0.00 46.12 3.18
763 778 4.645762 GGTTTAAAACCCGTTGTTGGTA 57.354 40.909 0.00 0.00 46.12 3.25
764 779 3.523606 GGTTTAAAACCCGTTGTTGGT 57.476 42.857 0.00 0.00 46.12 3.67
775 790 4.168014 CCGCCCGATTAAAGGTTTAAAAC 58.832 43.478 0.00 0.00 36.35 2.43
776 791 3.367190 GCCGCCCGATTAAAGGTTTAAAA 60.367 43.478 0.00 0.00 36.35 1.52
777 792 2.164017 GCCGCCCGATTAAAGGTTTAAA 59.836 45.455 0.00 0.00 36.35 1.52
778 793 1.744522 GCCGCCCGATTAAAGGTTTAA 59.255 47.619 0.00 0.00 37.08 1.52
779 794 1.065272 AGCCGCCCGATTAAAGGTTTA 60.065 47.619 0.00 0.00 0.00 2.01
780 795 0.323087 AGCCGCCCGATTAAAGGTTT 60.323 50.000 0.00 0.00 0.00 3.27
781 796 0.746923 GAGCCGCCCGATTAAAGGTT 60.747 55.000 0.00 0.00 0.00 3.50
782 797 1.153229 GAGCCGCCCGATTAAAGGT 60.153 57.895 0.00 0.00 0.00 3.50
783 798 1.153249 TGAGCCGCCCGATTAAAGG 60.153 57.895 0.00 0.00 0.00 3.11
784 799 1.762222 CGTGAGCCGCCCGATTAAAG 61.762 60.000 0.00 0.00 0.00 1.85
807 822 2.484264 GCTGTGGCTTACAACTTACAGG 59.516 50.000 0.00 0.00 39.20 4.00
808 823 3.138304 TGCTGTGGCTTACAACTTACAG 58.862 45.455 0.00 0.00 39.20 2.74
811 826 2.151202 GCTGCTGTGGCTTACAACTTA 58.849 47.619 0.00 0.00 39.20 2.24
813 828 0.179020 TGCTGCTGTGGCTTACAACT 60.179 50.000 0.00 0.00 39.20 3.16
816 831 0.603707 GTCTGCTGCTGTGGCTTACA 60.604 55.000 0.00 0.00 39.59 2.41
819 834 2.667536 CGTCTGCTGCTGTGGCTT 60.668 61.111 0.00 0.00 39.59 4.35
871 888 1.617947 ATGGAGAAGAGACCGGTGCC 61.618 60.000 14.63 2.54 0.00 5.01
895 912 1.946650 GACGCCGCTCTATCTGCAC 60.947 63.158 0.00 0.00 0.00 4.57
932 958 0.813610 CGTTGCTGTCCACTGGTTGA 60.814 55.000 0.00 0.00 0.00 3.18
949 975 2.605295 TTCCGGTGGATGGGTCGT 60.605 61.111 0.00 0.00 0.00 4.34
1238 1264 0.530744 GCGTACACCACTCCTGATGA 59.469 55.000 0.00 0.00 0.00 2.92
1242 1268 0.667487 CACTGCGTACACCACTCCTG 60.667 60.000 0.00 0.00 0.00 3.86
1286 1317 1.734465 AGCGTCTAAAGCTTCATGTGC 59.266 47.619 0.00 1.88 43.24 4.57
1326 1363 6.072508 TGAGAACAGGCAAAATTCAGATACAC 60.073 38.462 0.00 0.00 0.00 2.90
1331 1368 4.889409 AGTTGAGAACAGGCAAAATTCAGA 59.111 37.500 0.00 0.00 0.00 3.27
1350 1387 2.995939 TCGCTAACTGCATCAGAAGTTG 59.004 45.455 0.29 0.00 43.63 3.16
1386 1424 0.250338 GGCTTCCTTCTTGTCACCGT 60.250 55.000 0.00 0.00 0.00 4.83
1588 1626 3.365868 GCAATCGCTTGTTGGTATGAACA 60.366 43.478 0.42 0.00 34.69 3.18
1634 1682 2.009051 CAGTAGCGATGCCAAATCACA 58.991 47.619 0.00 0.00 0.00 3.58
1661 1709 2.293677 TACTCATAGCTTGCACGGTG 57.706 50.000 4.99 3.15 0.00 4.94
1686 1734 0.754217 AGCCAGTGCCATGCCTAATG 60.754 55.000 0.00 0.00 38.69 1.90
1821 1896 3.144506 CCCAAAGGATCGATCAGAATGG 58.855 50.000 25.93 23.63 32.46 3.16
1915 1990 2.985456 CCTGTGAGGTCTCCCTGC 59.015 66.667 0.00 0.00 42.86 4.85
1935 2010 6.544931 AGAAGGGTTCCAAAGTTAGTTTGTAC 59.455 38.462 11.05 8.52 43.68 2.90
1936 2011 6.544564 CAGAAGGGTTCCAAAGTTAGTTTGTA 59.455 38.462 11.05 0.00 43.68 2.41
1937 2012 5.359860 CAGAAGGGTTCCAAAGTTAGTTTGT 59.640 40.000 11.05 0.00 43.68 2.83
1951 2026 1.177401 GGCATTGGACAGAAGGGTTC 58.823 55.000 0.00 0.00 0.00 3.62
2056 2162 7.307219 CCGAGATTTTCAGAAGTTTAAACGAGT 60.307 37.037 12.54 2.56 0.00 4.18
2057 2163 7.010023 CCGAGATTTTCAGAAGTTTAAACGAG 58.990 38.462 12.54 4.69 0.00 4.18
2060 2166 5.564127 CGCCGAGATTTTCAGAAGTTTAAAC 59.436 40.000 10.47 10.47 0.00 2.01
2063 2169 3.124636 GCGCCGAGATTTTCAGAAGTTTA 59.875 43.478 0.00 0.00 0.00 2.01
2111 2217 4.769859 TTCGTTATGTAGTTTTTGGGCC 57.230 40.909 0.00 0.00 0.00 5.80
2390 2496 8.288913 TGTATGTTGTGTATCTTTCATGTGTTG 58.711 33.333 0.00 0.00 0.00 3.33
2399 2505 6.121776 TCACCCTGTATGTTGTGTATCTTT 57.878 37.500 0.00 0.00 0.00 2.52
2463 2571 8.680903 AGCATCTTTACTCAATTCACAATTAGG 58.319 33.333 0.00 0.00 0.00 2.69
2522 2630 5.939883 CAGTTATCATCAAGGTTGGACTTCA 59.060 40.000 0.00 0.00 0.00 3.02
2524 2632 5.880901 ACAGTTATCATCAAGGTTGGACTT 58.119 37.500 0.00 0.00 0.00 3.01
2525 2633 5.505181 ACAGTTATCATCAAGGTTGGACT 57.495 39.130 0.00 0.00 0.00 3.85
2526 2634 5.619981 GCAACAGTTATCATCAAGGTTGGAC 60.620 44.000 0.00 0.00 35.82 4.02
2527 2635 4.458989 GCAACAGTTATCATCAAGGTTGGA 59.541 41.667 0.00 0.00 35.82 3.53
2528 2636 4.380867 GGCAACAGTTATCATCAAGGTTGG 60.381 45.833 0.00 0.00 35.82 3.77
2622 3016 0.457443 GCCAAGCACAATTAGCCCTC 59.543 55.000 0.00 0.00 0.00 4.30
2628 3022 2.275880 GCCCAGCCAAGCACAATTA 58.724 52.632 0.00 0.00 0.00 1.40
2697 3091 2.156098 GTTTTGGATTGTACCCGCTGA 58.844 47.619 0.00 0.00 0.00 4.26
2699 3093 1.541379 GGTTTTGGATTGTACCCGCT 58.459 50.000 0.00 0.00 0.00 5.52
2700 3094 0.528924 GGGTTTTGGATTGTACCCGC 59.471 55.000 0.00 0.00 40.75 6.13
2721 3115 3.305744 GCTTCCTTGCCGTGGAAAAATAA 60.306 43.478 0.00 0.00 42.29 1.40
2725 3119 0.753479 TGCTTCCTTGCCGTGGAAAA 60.753 50.000 0.00 0.00 42.29 2.29
2746 3140 0.246635 AAACGGCGATGCTCTACTGT 59.753 50.000 16.62 0.00 0.00 3.55
2823 3217 4.639755 TCAGATAATGGCGAAATGCTGAAA 59.360 37.500 0.00 0.00 45.43 2.69
2923 3340 3.551046 GCATACGACGATCCTCACTTCAT 60.551 47.826 0.00 0.00 0.00 2.57
2955 3372 7.134815 ACTTTTCGTTGTTCATCTTCAGATTG 58.865 34.615 0.00 0.00 31.21 2.67
2967 3392 8.145312 GCGTATTCAAATTACTTTTCGTTGTTC 58.855 33.333 0.00 0.00 0.00 3.18
2978 3403 4.510340 GTGGATCGGCGTATTCAAATTACT 59.490 41.667 6.85 0.00 0.00 2.24
2979 3404 4.319261 GGTGGATCGGCGTATTCAAATTAC 60.319 45.833 6.85 0.00 0.00 1.89
2980 3405 3.810941 GGTGGATCGGCGTATTCAAATTA 59.189 43.478 6.85 0.00 0.00 1.40
2991 3417 2.661866 GGATTCGGTGGATCGGCG 60.662 66.667 0.00 0.00 0.00 6.46
2999 3425 7.571786 TTGATGGTTTATCACTGGATTCGGTG 61.572 42.308 6.63 6.63 45.22 4.94
3004 3430 8.328758 TCTTACTTGATGGTTTATCACTGGATT 58.671 33.333 0.00 0.00 45.22 3.01
3006 3432 7.252612 TCTTACTTGATGGTTTATCACTGGA 57.747 36.000 0.00 0.00 45.22 3.86
3009 3435 9.574516 ACTTTTCTTACTTGATGGTTTATCACT 57.425 29.630 0.00 0.00 45.22 3.41
3020 3446 7.805071 CGCAGAAATCAACTTTTCTTACTTGAT 59.195 33.333 0.00 0.00 41.95 2.57
3021 3447 7.132213 CGCAGAAATCAACTTTTCTTACTTGA 58.868 34.615 0.00 0.00 41.95 3.02
3026 3452 5.334879 GGAGCGCAGAAATCAACTTTTCTTA 60.335 40.000 11.47 0.00 41.95 2.10
3043 3469 3.670637 GATCTGCACCTGGAGCGCA 62.671 63.158 11.47 10.22 33.17 6.09
3054 3480 2.040145 TGAGGGAAATGTGTGATCTGCA 59.960 45.455 0.00 0.00 0.00 4.41
3088 3514 7.663827 TCTTCTCGACAAAATCTAGGTAACAA 58.336 34.615 0.00 0.00 41.41 2.83
3090 3516 8.530269 TTTCTTCTCGACAAAATCTAGGTAAC 57.470 34.615 0.00 0.00 0.00 2.50
3102 3612 5.461078 CGGTTTCTTACTTTCTTCTCGACAA 59.539 40.000 0.00 0.00 0.00 3.18
3103 3613 4.980434 CGGTTTCTTACTTTCTTCTCGACA 59.020 41.667 0.00 0.00 0.00 4.35
3104 3614 4.981054 ACGGTTTCTTACTTTCTTCTCGAC 59.019 41.667 0.00 0.00 0.00 4.20
3114 3624 2.335316 TGGTGCACGGTTTCTTACTT 57.665 45.000 11.45 0.00 0.00 2.24
3120 3630 1.135402 GGATTCATGGTGCACGGTTTC 60.135 52.381 11.45 2.88 0.00 2.78
3132 3642 8.442310 CCTAGGAAGGTTCATCATGGATTCATG 61.442 44.444 7.76 7.76 43.43 3.07
3133 3643 5.399052 AGGAAGGTTCATCATGGATTCAT 57.601 39.130 0.00 0.00 0.00 2.57
3134 3644 4.868172 AGGAAGGTTCATCATGGATTCA 57.132 40.909 0.00 0.00 0.00 2.57
3135 3645 5.312079 CCTAGGAAGGTTCATCATGGATTC 58.688 45.833 1.05 0.00 38.19 2.52
3136 3646 5.316158 CCTAGGAAGGTTCATCATGGATT 57.684 43.478 1.05 0.00 38.19 3.01
3137 3647 4.989875 CCTAGGAAGGTTCATCATGGAT 57.010 45.455 1.05 0.00 38.19 3.41
3157 3667 1.012086 GGATTTTTACGAGGCCGACC 58.988 55.000 0.00 0.00 39.50 4.79
3158 3668 1.664151 CTGGATTTTTACGAGGCCGAC 59.336 52.381 0.00 0.00 39.50 4.79
3159 3669 2.010043 GCTGGATTTTTACGAGGCCGA 61.010 52.381 0.00 0.00 39.50 5.54
3160 3670 0.377203 GCTGGATTTTTACGAGGCCG 59.623 55.000 0.00 0.00 42.50 6.13
3161 3671 0.377203 CGCTGGATTTTTACGAGGCC 59.623 55.000 0.00 0.00 0.00 5.19
3162 3672 1.062148 GTCGCTGGATTTTTACGAGGC 59.938 52.381 0.00 0.00 32.76 4.70
3163 3673 2.343101 TGTCGCTGGATTTTTACGAGG 58.657 47.619 0.00 0.00 32.76 4.63
3164 3674 3.370978 ACATGTCGCTGGATTTTTACGAG 59.629 43.478 0.00 0.00 32.76 4.18
3165 3675 3.331150 ACATGTCGCTGGATTTTTACGA 58.669 40.909 0.00 0.00 0.00 3.43
3166 3676 3.124466 TGACATGTCGCTGGATTTTTACG 59.876 43.478 20.54 0.00 0.00 3.18
3167 3677 4.083537 TGTGACATGTCGCTGGATTTTTAC 60.084 41.667 32.89 16.58 40.54 2.01
3179 3689 0.861185 CAGGTGTGTGTGACATGTCG 59.139 55.000 20.54 0.00 36.78 4.35
3203 3726 2.159517 CCGTTTTGGATAAGAGCTGTGC 60.160 50.000 0.00 0.00 42.00 4.57
3204 3727 3.334691 TCCGTTTTGGATAAGAGCTGTG 58.665 45.455 0.00 0.00 43.74 3.66
3237 3760 7.864379 GCAACATTTAATCAACCATGAGGATAG 59.136 37.037 0.00 0.00 39.39 2.08
3238 3761 7.341512 TGCAACATTTAATCAACCATGAGGATA 59.658 33.333 0.00 0.00 39.39 2.59
3243 3766 7.119407 CCAAATGCAACATTTAATCAACCATGA 59.881 33.333 5.30 0.00 40.57 3.07
3255 3778 6.381994 AGGAGTATCATCCAAATGCAACATTT 59.618 34.615 0.00 0.00 42.26 2.32
3256 3779 5.895534 AGGAGTATCATCCAAATGCAACATT 59.104 36.000 0.00 0.00 42.26 2.71
3259 3782 6.058183 ACTAGGAGTATCATCCAAATGCAAC 58.942 40.000 0.00 0.00 42.26 4.17
3276 3799 3.616956 TGCACCAATCTGAACTAGGAG 57.383 47.619 0.00 0.00 0.00 3.69
3279 3802 9.155975 GGTATATTATGCACCAATCTGAACTAG 57.844 37.037 0.00 0.00 32.32 2.57
3280 3803 8.655901 TGGTATATTATGCACCAATCTGAACTA 58.344 33.333 0.00 0.00 39.36 2.24
3281 3804 7.517320 TGGTATATTATGCACCAATCTGAACT 58.483 34.615 0.00 0.00 39.36 3.01
3282 3805 7.744087 TGGTATATTATGCACCAATCTGAAC 57.256 36.000 0.00 0.00 39.36 3.18


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

AutoCloner maintained by Alex Coulton.