Multiple sequence alignment - TraesCS5D01G534400

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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 TraesCS5D01G534400 chr5D 100.000 3803 0 0 1 3803 548486474 548482672 0.000000e+00 7023
1 TraesCS5D01G534400 chr5D 85.806 1550 155 32 1526 3064 548536123 548534628 0.000000e+00 1583
2 TraesCS5D01G534400 chr5D 88.752 729 54 14 5 727 27512839 27513545 0.000000e+00 867
3 TraesCS5D01G534400 chr5D 100.000 250 0 0 4226 4475 548482249 548482000 3.150000e-126 462
4 TraesCS5D01G534400 chr4A 93.490 2980 152 21 846 3803 619375577 619372618 0.000000e+00 4390
5 TraesCS5D01G534400 chr4A 88.694 911 90 7 2543 3452 619384940 619384042 0.000000e+00 1099
6 TraesCS5D01G534400 chr4A 92.966 725 34 8 4 727 690216247 690216955 0.000000e+00 1040
7 TraesCS5D01G534400 chr4A 84.522 743 83 13 1547 2275 619418125 619417401 0.000000e+00 706
8 TraesCS5D01G534400 chr4A 89.908 436 40 4 2631 3064 619407753 619407320 3.910000e-155 558
9 TraesCS5D01G534400 chr4A 95.652 253 8 2 4226 4475 619372586 619372334 1.940000e-108 403
10 TraesCS5D01G534400 chr4A 88.760 258 23 2 3498 3755 619384045 619383794 1.210000e-80 311
11 TraesCS5D01G534400 chr4A 90.863 197 17 1 2868 3064 619490695 619490500 3.430000e-66 263
12 TraesCS5D01G534400 chr4A 90.863 197 17 1 2868 3064 619551152 619550957 3.430000e-66 263
13 TraesCS5D01G534400 chr4A 87.805 205 23 1 4271 4475 619383706 619383504 5.790000e-59 239
14 TraesCS5D01G534400 chr4A 87.113 194 19 2 1809 2002 619385124 619384937 9.750000e-52 215
15 TraesCS5D01G534400 chr4A 91.089 101 9 0 2782 2882 619490811 619490711 2.170000e-28 137
16 TraesCS5D01G534400 chr4A 91.089 101 9 0 2782 2882 619551268 619551168 2.170000e-28 137
17 TraesCS5D01G534400 chr4A 93.333 90 6 0 2367 2456 619416745 619416656 2.810000e-27 134
18 TraesCS5D01G534400 chr4A 89.011 91 5 3 2442 2527 619407846 619407756 1.700000e-19 108
19 TraesCS5D01G534400 chr4A 80.556 108 12 7 1351 1451 619418303 619418198 1.730000e-09 75
20 TraesCS5D01G534400 chr5B 93.456 2980 153 21 846 3803 692697183 692694224 0.000000e+00 4385
21 TraesCS5D01G534400 chr5B 88.474 911 92 4 2543 3452 692706215 692705317 0.000000e+00 1088
22 TraesCS5D01G534400 chr5B 98.008 251 4 1 4226 4475 692694192 692693942 6.870000e-118 435
23 TraesCS5D01G534400 chr5B 91.234 308 27 0 2757 3064 692747298 692746991 1.920000e-113 420
24 TraesCS5D01G534400 chr5B 82.857 490 61 10 1526 2010 692748406 692747935 6.920000e-113 418
25 TraesCS5D01G534400 chr5B 88.599 307 23 3 2458 2752 692747920 692747614 3.290000e-96 363
26 TraesCS5D01G534400 chr5B 88.372 258 24 2 3498 3755 692705320 692705069 5.620000e-79 305
27 TraesCS5D01G534400 chr5B 88.293 205 22 1 4271 4475 692704981 692704779 1.240000e-60 244
28 TraesCS5D01G534400 chr5B 87.629 194 18 2 1809 2002 692706399 692706212 2.100000e-53 220
29 TraesCS5D01G534400 chr6A 94.932 730 18 8 1 727 528992969 528992256 0.000000e+00 1125
30 TraesCS5D01G534400 chr6A 89.617 732 52 14 1 724 12311413 12312128 0.000000e+00 909
31 TraesCS5D01G534400 chr3A 90.220 726 52 9 5 727 654206160 654206869 0.000000e+00 929
32 TraesCS5D01G534400 chr3A 89.459 740 51 13 1 729 724583907 724584630 0.000000e+00 909
33 TraesCS5D01G534400 chr3A 89.569 719 55 13 13 727 671354259 671354961 0.000000e+00 894
34 TraesCS5D01G534400 chr3A 86.035 623 56 14 5 620 711533938 711534536 1.360000e-179 640
35 TraesCS5D01G534400 chr3A 85.554 623 59 15 5 620 662901726 662901128 1.370000e-174 623
36 TraesCS5D01G534400 chr3A 87.175 538 47 11 5 537 647746949 647746429 3.850000e-165 592
37 TraesCS5D01G534400 chr5A 89.632 733 51 13 1 724 490856268 490856984 0.000000e+00 909
38 TraesCS5D01G534400 chr2A 89.495 733 55 13 1 727 49755786 49755070 0.000000e+00 907
39 TraesCS5D01G534400 chr6D 88.599 728 57 12 5 727 222717815 222717109 0.000000e+00 861
40 TraesCS5D01G534400 chr7D 88.219 730 54 17 5 727 63877092 63876388 0.000000e+00 843
41 TraesCS5D01G534400 chr7D 91.455 433 26 5 296 727 169035422 169035000 6.450000e-163 584
42 TraesCS5D01G534400 chr2B 87.175 616 49 16 5 615 46464120 46464710 0.000000e+00 673
43 TraesCS5D01G534400 chr2B 84.272 426 47 14 5 415 677510554 677510134 9.020000e-107 398
44 TraesCS5D01G534400 chr1A 86.334 622 55 20 5 620 249341928 249342525 0.000000e+00 651
45 TraesCS5D01G534400 chr1A 82.329 249 28 7 1796 2034 566584051 566584293 7.590000e-48 202


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 TraesCS5D01G534400 chr5D 548482000 548486474 4474 True 3742.500000 7023 100.000000 1 4475 2 chr5D.!!$R2 4474
1 TraesCS5D01G534400 chr5D 548534628 548536123 1495 True 1583.000000 1583 85.806000 1526 3064 1 chr5D.!!$R1 1538
2 TraesCS5D01G534400 chr5D 27512839 27513545 706 False 867.000000 867 88.752000 5 727 1 chr5D.!!$F1 722
3 TraesCS5D01G534400 chr4A 619372334 619375577 3243 True 2396.500000 4390 94.571000 846 4475 2 chr4A.!!$R1 3629
4 TraesCS5D01G534400 chr4A 690216247 690216955 708 False 1040.000000 1040 92.966000 4 727 1 chr4A.!!$F1 723
5 TraesCS5D01G534400 chr4A 619383504 619385124 1620 True 466.000000 1099 88.093000 1809 4475 4 chr4A.!!$R2 2666
6 TraesCS5D01G534400 chr4A 619407320 619407846 526 True 333.000000 558 89.459500 2442 3064 2 chr4A.!!$R3 622
7 TraesCS5D01G534400 chr4A 619416656 619418303 1647 True 305.000000 706 86.137000 1351 2456 3 chr4A.!!$R4 1105
8 TraesCS5D01G534400 chr5B 692693942 692697183 3241 True 2410.000000 4385 95.732000 846 4475 2 chr5B.!!$R1 3629
9 TraesCS5D01G534400 chr5B 692704779 692706399 1620 True 464.250000 1088 88.192000 1809 4475 4 chr5B.!!$R2 2666
10 TraesCS5D01G534400 chr5B 692746991 692748406 1415 True 400.333333 420 87.563333 1526 3064 3 chr5B.!!$R3 1538
11 TraesCS5D01G534400 chr6A 528992256 528992969 713 True 1125.000000 1125 94.932000 1 727 1 chr6A.!!$R1 726
12 TraesCS5D01G534400 chr6A 12311413 12312128 715 False 909.000000 909 89.617000 1 724 1 chr6A.!!$F1 723
13 TraesCS5D01G534400 chr3A 654206160 654206869 709 False 929.000000 929 90.220000 5 727 1 chr3A.!!$F1 722
14 TraesCS5D01G534400 chr3A 724583907 724584630 723 False 909.000000 909 89.459000 1 729 1 chr3A.!!$F4 728
15 TraesCS5D01G534400 chr3A 671354259 671354961 702 False 894.000000 894 89.569000 13 727 1 chr3A.!!$F2 714
16 TraesCS5D01G534400 chr3A 711533938 711534536 598 False 640.000000 640 86.035000 5 620 1 chr3A.!!$F3 615
17 TraesCS5D01G534400 chr3A 662901128 662901726 598 True 623.000000 623 85.554000 5 620 1 chr3A.!!$R2 615
18 TraesCS5D01G534400 chr3A 647746429 647746949 520 True 592.000000 592 87.175000 5 537 1 chr3A.!!$R1 532
19 TraesCS5D01G534400 chr5A 490856268 490856984 716 False 909.000000 909 89.632000 1 724 1 chr5A.!!$F1 723
20 TraesCS5D01G534400 chr2A 49755070 49755786 716 True 907.000000 907 89.495000 1 727 1 chr2A.!!$R1 726
21 TraesCS5D01G534400 chr6D 222717109 222717815 706 True 861.000000 861 88.599000 5 727 1 chr6D.!!$R1 722
22 TraesCS5D01G534400 chr7D 63876388 63877092 704 True 843.000000 843 88.219000 5 727 1 chr7D.!!$R1 722
23 TraesCS5D01G534400 chr2B 46464120 46464710 590 False 673.000000 673 87.175000 5 615 1 chr2B.!!$F1 610
24 TraesCS5D01G534400 chr1A 249341928 249342525 597 False 651.000000 651 86.334000 5 620 1 chr1A.!!$F1 615

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
766 795 0.386731 ATGCGCGTGGTAGTTTTTGC 60.387 50.0 8.43 0.0 0.0 3.68 F
1427 1469 0.110486 CTGTAAGTGCACAAGGGGGT 59.890 55.0 21.04 0.0 0.0 4.95 F
2092 2157 0.393537 TCGACGACCTCTTCTACCCC 60.394 60.0 0.00 0.0 0.0 4.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1732 1789 0.175760 TGGAGACGAACATAGGCTGC 59.824 55.000 0.0 0.0 35.48 5.25 R
3304 4281 0.034186 TGATTGTCATGCCCTGGTCC 60.034 55.000 0.0 0.0 0.00 4.46 R
3675 4652 2.430332 CAGGAAAAGGTTGCCACTTCAA 59.570 45.455 0.0 0.0 0.00 2.69 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
43 45 6.876789 CGGTTATGGGTGCTTGTATTATCATA 59.123 38.462 0.00 0.00 0.00 2.15
196 204 4.016444 TCAGGGGTATGTTTCAGCAAATC 58.984 43.478 0.00 0.00 0.00 2.17
244 257 9.444600 AAACTTATCATGGTGTTTAGTTATCGT 57.555 29.630 0.00 0.00 31.85 3.73
271 285 8.685427 AGTGCATATGTTTTTCATGCTATTACA 58.315 29.630 4.29 0.00 44.27 2.41
272 286 8.745837 GTGCATATGTTTTTCATGCTATTACAC 58.254 33.333 4.29 0.00 44.27 2.90
274 288 8.961092 GCATATGTTTTTCATGCTATTACACAG 58.039 33.333 4.29 0.00 41.44 3.66
496 514 9.693739 TGGTTAAAGATACCATGATGTTTGTAT 57.306 29.630 0.00 0.00 40.65 2.29
655 684 1.340248 CGACTCCGGTGCTTATATGGT 59.660 52.381 0.00 0.00 0.00 3.55
729 758 3.242248 GTGGTGCGTTAGTTATCGTGATC 59.758 47.826 0.00 0.00 0.00 2.92
730 759 2.466571 GGTGCGTTAGTTATCGTGATCG 59.533 50.000 0.00 0.00 38.55 3.69
731 760 2.466571 GTGCGTTAGTTATCGTGATCGG 59.533 50.000 0.00 0.00 37.69 4.18
732 761 2.355444 TGCGTTAGTTATCGTGATCGGA 59.645 45.455 0.00 0.00 37.69 4.55
733 762 3.004002 TGCGTTAGTTATCGTGATCGGAT 59.996 43.478 4.70 4.70 37.69 4.18
734 763 3.602915 GCGTTAGTTATCGTGATCGGATC 59.397 47.826 11.07 11.07 37.69 3.36
735 764 4.613167 GCGTTAGTTATCGTGATCGGATCT 60.613 45.833 18.16 1.49 37.69 2.75
736 765 4.846677 CGTTAGTTATCGTGATCGGATCTG 59.153 45.833 18.16 11.09 37.69 2.90
737 766 5.333875 CGTTAGTTATCGTGATCGGATCTGA 60.334 44.000 18.16 6.72 37.69 3.27
738 767 4.491234 AGTTATCGTGATCGGATCTGAC 57.509 45.455 18.16 8.65 37.69 3.51
739 768 3.058846 AGTTATCGTGATCGGATCTGACG 60.059 47.826 19.17 19.17 37.69 4.35
740 769 0.593618 ATCGTGATCGGATCTGACGG 59.406 55.000 22.66 10.46 37.69 4.79
741 770 1.658717 CGTGATCGGATCTGACGGC 60.659 63.158 18.16 0.13 0.00 5.68
742 771 1.658717 GTGATCGGATCTGACGGCG 60.659 63.158 18.16 4.80 0.00 6.46
743 772 2.731348 GATCGGATCTGACGGCGC 60.731 66.667 6.90 0.00 0.00 6.53
744 773 3.200887 GATCGGATCTGACGGCGCT 62.201 63.158 6.90 0.00 0.00 5.92
745 774 1.853114 GATCGGATCTGACGGCGCTA 61.853 60.000 6.90 0.00 0.00 4.26
746 775 1.857318 ATCGGATCTGACGGCGCTAG 61.857 60.000 6.90 5.62 0.00 3.42
747 776 2.543802 CGGATCTGACGGCGCTAGA 61.544 63.158 6.90 11.78 0.00 2.43
748 777 1.857318 CGGATCTGACGGCGCTAGAT 61.857 60.000 21.51 21.51 34.06 1.98
749 778 0.387878 GGATCTGACGGCGCTAGATG 60.388 60.000 24.91 4.31 31.67 2.90
750 779 1.006314 GATCTGACGGCGCTAGATGC 61.006 60.000 24.91 15.15 31.67 3.91
759 788 3.923614 GCTAGATGCGCGTGGTAG 58.076 61.111 6.97 9.06 0.00 3.18
760 789 1.065928 GCTAGATGCGCGTGGTAGT 59.934 57.895 6.97 0.00 0.00 2.73
761 790 0.527817 GCTAGATGCGCGTGGTAGTT 60.528 55.000 6.97 0.00 0.00 2.24
762 791 1.922570 CTAGATGCGCGTGGTAGTTT 58.077 50.000 6.97 0.00 0.00 2.66
763 792 2.268298 CTAGATGCGCGTGGTAGTTTT 58.732 47.619 6.97 0.00 0.00 2.43
764 793 1.519408 AGATGCGCGTGGTAGTTTTT 58.481 45.000 6.97 0.00 0.00 1.94
765 794 1.196808 AGATGCGCGTGGTAGTTTTTG 59.803 47.619 6.97 0.00 0.00 2.44
766 795 0.386731 ATGCGCGTGGTAGTTTTTGC 60.387 50.000 8.43 0.00 0.00 3.68
767 796 1.009449 GCGCGTGGTAGTTTTTGCA 60.009 52.632 8.43 0.00 0.00 4.08
768 797 0.592754 GCGCGTGGTAGTTTTTGCAA 60.593 50.000 8.43 0.00 0.00 4.08
769 798 1.928595 GCGCGTGGTAGTTTTTGCAAT 60.929 47.619 8.43 0.00 0.00 3.56
770 799 1.976045 CGCGTGGTAGTTTTTGCAATC 59.024 47.619 0.00 0.00 0.00 2.67
771 800 2.350388 CGCGTGGTAGTTTTTGCAATCT 60.350 45.455 0.00 2.25 0.00 2.40
772 801 2.979813 GCGTGGTAGTTTTTGCAATCTG 59.020 45.455 0.00 0.00 0.00 2.90
773 802 2.979813 CGTGGTAGTTTTTGCAATCTGC 59.020 45.455 0.00 3.33 45.29 4.26
774 803 3.317150 GTGGTAGTTTTTGCAATCTGCC 58.683 45.455 19.11 19.11 44.23 4.85
775 804 2.961741 TGGTAGTTTTTGCAATCTGCCA 59.038 40.909 22.30 22.30 44.23 4.92
776 805 3.243704 TGGTAGTTTTTGCAATCTGCCAC 60.244 43.478 22.30 9.52 44.23 5.01
777 806 3.243704 GGTAGTTTTTGCAATCTGCCACA 60.244 43.478 20.19 0.00 44.23 4.17
778 807 2.825205 AGTTTTTGCAATCTGCCACAC 58.175 42.857 0.00 0.00 44.23 3.82
779 808 2.431782 AGTTTTTGCAATCTGCCACACT 59.568 40.909 0.00 0.00 44.23 3.55
780 809 3.636300 AGTTTTTGCAATCTGCCACACTA 59.364 39.130 0.00 0.00 44.23 2.74
781 810 4.281688 AGTTTTTGCAATCTGCCACACTAT 59.718 37.500 0.00 0.00 44.23 2.12
782 811 4.870123 TTTTGCAATCTGCCACACTATT 57.130 36.364 0.00 0.00 44.23 1.73
783 812 3.853831 TTGCAATCTGCCACACTATTG 57.146 42.857 0.00 0.00 44.23 1.90
784 813 2.199291 GCAATCTGCCACACTATTGC 57.801 50.000 0.00 0.00 45.04 3.56
785 814 1.202336 GCAATCTGCCACACTATTGCC 60.202 52.381 7.48 0.00 45.31 4.52
786 815 2.093890 CAATCTGCCACACTATTGCCA 58.906 47.619 0.00 0.00 0.00 4.92
787 816 1.755179 ATCTGCCACACTATTGCCAC 58.245 50.000 0.00 0.00 0.00 5.01
788 817 0.399833 TCTGCCACACTATTGCCACA 59.600 50.000 0.00 0.00 0.00 4.17
789 818 1.004628 TCTGCCACACTATTGCCACAT 59.995 47.619 0.00 0.00 0.00 3.21
790 819 2.238395 TCTGCCACACTATTGCCACATA 59.762 45.455 0.00 0.00 0.00 2.29
791 820 2.355756 CTGCCACACTATTGCCACATAC 59.644 50.000 0.00 0.00 0.00 2.39
792 821 2.290577 TGCCACACTATTGCCACATACA 60.291 45.455 0.00 0.00 0.00 2.29
793 822 2.951642 GCCACACTATTGCCACATACAT 59.048 45.455 0.00 0.00 0.00 2.29
794 823 4.133820 GCCACACTATTGCCACATACATA 58.866 43.478 0.00 0.00 0.00 2.29
795 824 4.761739 GCCACACTATTGCCACATACATAT 59.238 41.667 0.00 0.00 0.00 1.78
796 825 5.241506 GCCACACTATTGCCACATACATATT 59.758 40.000 0.00 0.00 0.00 1.28
797 826 6.239008 GCCACACTATTGCCACATACATATTT 60.239 38.462 0.00 0.00 0.00 1.40
798 827 7.362662 CCACACTATTGCCACATACATATTTC 58.637 38.462 0.00 0.00 0.00 2.17
799 828 7.071414 CACACTATTGCCACATACATATTTCG 58.929 38.462 0.00 0.00 0.00 3.46
800 829 6.765989 ACACTATTGCCACATACATATTTCGT 59.234 34.615 0.00 0.00 0.00 3.85
801 830 7.282224 ACACTATTGCCACATACATATTTCGTT 59.718 33.333 0.00 0.00 0.00 3.85
802 831 8.128582 CACTATTGCCACATACATATTTCGTTT 58.871 33.333 0.00 0.00 0.00 3.60
803 832 8.682710 ACTATTGCCACATACATATTTCGTTTT 58.317 29.630 0.00 0.00 0.00 2.43
807 836 9.862371 TTGCCACATACATATTTCGTTTTATTT 57.138 25.926 0.00 0.00 0.00 1.40
808 837 9.862371 TGCCACATACATATTTCGTTTTATTTT 57.138 25.926 0.00 0.00 0.00 1.82
831 860 8.438676 TTTTTGAGATTCGAGTCTTTTCTCTT 57.561 30.769 12.12 0.00 35.09 2.85
832 861 7.644986 TTTGAGATTCGAGTCTTTTCTCTTC 57.355 36.000 12.12 0.00 35.09 2.87
833 862 5.394802 TGAGATTCGAGTCTTTTCTCTTCG 58.605 41.667 12.12 0.00 35.09 3.79
834 863 5.181433 TGAGATTCGAGTCTTTTCTCTTCGA 59.819 40.000 12.12 0.00 35.09 3.71
835 864 5.636837 AGATTCGAGTCTTTTCTCTTCGAG 58.363 41.667 4.34 0.00 32.83 4.04
836 865 4.832590 TTCGAGTCTTTTCTCTTCGAGT 57.167 40.909 0.00 0.00 32.83 4.18
837 866 4.148563 TCGAGTCTTTTCTCTTCGAGTG 57.851 45.455 0.00 0.00 32.83 3.51
838 867 2.659279 CGAGTCTTTTCTCTTCGAGTGC 59.341 50.000 0.00 0.00 32.83 4.40
839 868 3.610585 CGAGTCTTTTCTCTTCGAGTGCT 60.611 47.826 0.00 0.00 32.83 4.40
840 869 3.908213 AGTCTTTTCTCTTCGAGTGCTC 58.092 45.455 0.00 0.00 0.00 4.26
841 870 3.572255 AGTCTTTTCTCTTCGAGTGCTCT 59.428 43.478 0.00 0.00 0.00 4.09
842 871 4.038642 AGTCTTTTCTCTTCGAGTGCTCTT 59.961 41.667 0.00 0.00 0.00 2.85
843 872 4.149747 GTCTTTTCTCTTCGAGTGCTCTTG 59.850 45.833 0.00 0.00 0.00 3.02
844 873 3.735237 TTTCTCTTCGAGTGCTCTTGT 57.265 42.857 3.03 0.00 0.00 3.16
848 877 4.442706 TCTCTTCGAGTGCTCTTGTTTTT 58.557 39.130 3.03 0.00 0.00 1.94
948 981 9.363763 CATATACACATCAGATCAGATTACACC 57.636 37.037 0.00 0.00 0.00 4.16
949 982 5.946942 ACACATCAGATCAGATTACACCT 57.053 39.130 0.00 0.00 0.00 4.00
951 984 5.163364 ACACATCAGATCAGATTACACCTCC 60.163 44.000 0.00 0.00 0.00 4.30
952 985 4.346418 ACATCAGATCAGATTACACCTCCC 59.654 45.833 0.00 0.00 0.00 4.30
953 986 3.309296 TCAGATCAGATTACACCTCCCC 58.691 50.000 0.00 0.00 0.00 4.81
1040 1075 2.882876 CAGCAGCTGGACAATGCC 59.117 61.111 17.12 0.00 40.89 4.40
1041 1076 1.974875 CAGCAGCTGGACAATGCCA 60.975 57.895 17.12 0.00 40.89 4.92
1050 1085 1.300963 GACAATGCCAGCTCCTCCA 59.699 57.895 0.00 0.00 0.00 3.86
1116 1151 0.336737 CCTCACCTACACCTCCCTCT 59.663 60.000 0.00 0.00 0.00 3.69
1147 1182 2.633488 GCTCCACTATGGTTCTGGTTC 58.367 52.381 0.00 0.00 39.03 3.62
1149 1184 3.866651 CTCCACTATGGTTCTGGTTCTG 58.133 50.000 0.00 0.00 39.03 3.02
1163 1198 1.202818 GGTTCTGGTCTCAGTGCCTTT 60.203 52.381 0.00 0.00 41.59 3.11
1164 1199 2.147150 GTTCTGGTCTCAGTGCCTTTC 58.853 52.381 0.00 0.00 41.59 2.62
1165 1200 1.722034 TCTGGTCTCAGTGCCTTTCT 58.278 50.000 0.00 0.00 41.59 2.52
1166 1201 2.889512 TCTGGTCTCAGTGCCTTTCTA 58.110 47.619 0.00 0.00 41.59 2.10
1167 1202 2.563179 TCTGGTCTCAGTGCCTTTCTAC 59.437 50.000 0.00 0.00 41.59 2.59
1168 1203 2.564947 CTGGTCTCAGTGCCTTTCTACT 59.435 50.000 0.00 0.00 36.30 2.57
1172 1207 4.097286 GGTCTCAGTGCCTTTCTACTCTAG 59.903 50.000 0.00 0.00 0.00 2.43
1193 1228 0.889186 CTAGTGCCCGCAACCTGTTT 60.889 55.000 0.00 0.00 0.00 2.83
1221 1256 2.856988 TCGCCCCCTTCCCTTGTT 60.857 61.111 0.00 0.00 0.00 2.83
1224 1259 2.525592 CCCCCTTCCCTTGTTGCA 59.474 61.111 0.00 0.00 0.00 4.08
1230 1265 1.421382 CTTCCCTTGTTGCATTTGCG 58.579 50.000 0.00 0.00 45.83 4.85
1285 1320 5.163364 CCTCTCAGCTACACATACCAGAAAT 60.163 44.000 0.00 0.00 0.00 2.17
1298 1333 2.015587 CCAGAAATCAGAGCAGCCTTC 58.984 52.381 0.00 0.00 0.00 3.46
1427 1469 0.110486 CTGTAAGTGCACAAGGGGGT 59.890 55.000 21.04 0.00 0.00 4.95
1502 1545 3.309388 CGTCGATGATGGGATACAGAAC 58.691 50.000 0.00 0.00 39.74 3.01
1602 1654 3.755378 AGTGTGCTCCAACTGATGAATTC 59.245 43.478 0.00 0.00 0.00 2.17
1611 1663 4.201980 CCAACTGATGAATTCATGCGTCAT 60.202 41.667 25.37 0.00 36.57 3.06
1617 1670 6.488817 TGATGAATTCATGCGTCATTACTTG 58.511 36.000 25.37 0.00 36.57 3.16
1632 1686 0.940126 ACTTGCTTCTGAACACTGCG 59.060 50.000 0.00 0.00 0.00 5.18
1650 1704 3.398406 TGCGTAACTGAAGATGCTTTCA 58.602 40.909 0.00 0.00 35.83 2.69
1731 1788 5.698089 TCTTTGATCGATCATGCTAATGGAC 59.302 40.000 27.75 0.00 36.56 4.02
1732 1789 3.578688 TGATCGATCATGCTAATGGACG 58.421 45.455 23.99 0.00 35.61 4.79
1745 1805 0.530650 ATGGACGCAGCCTATGTTCG 60.531 55.000 0.00 0.00 0.00 3.95
1752 1812 1.202580 GCAGCCTATGTTCGTCTCCAT 60.203 52.381 0.00 0.00 0.00 3.41
1759 1819 5.046529 CCTATGTTCGTCTCCATCTTCTTG 58.953 45.833 0.00 0.00 0.00 3.02
1765 1825 4.278310 TCGTCTCCATCTTCTTGTATCCA 58.722 43.478 0.00 0.00 0.00 3.41
1780 1840 3.700539 TGTATCCAATGTGCCAATCCAAG 59.299 43.478 0.00 0.00 0.00 3.61
1871 1936 5.705441 ACGCCAAGAATATCTGAAACTGAAA 59.295 36.000 0.00 0.00 0.00 2.69
1872 1937 6.024049 CGCCAAGAATATCTGAAACTGAAAC 58.976 40.000 0.00 0.00 0.00 2.78
1873 1938 6.128172 CGCCAAGAATATCTGAAACTGAAACT 60.128 38.462 0.00 0.00 0.00 2.66
1874 1939 7.025963 GCCAAGAATATCTGAAACTGAAACTG 58.974 38.462 0.00 0.00 0.00 3.16
1875 1940 7.094634 GCCAAGAATATCTGAAACTGAAACTGA 60.095 37.037 0.00 0.00 0.00 3.41
1876 1941 8.786898 CCAAGAATATCTGAAACTGAAACTGAA 58.213 33.333 0.00 0.00 0.00 3.02
2020 2085 1.511850 CTGCTCCGTCATTGTTGTCA 58.488 50.000 0.00 0.00 0.00 3.58
2092 2157 0.393537 TCGACGACCTCTTCTACCCC 60.394 60.000 0.00 0.00 0.00 4.95
2129 2194 2.039405 GCTCAGAACAGGGCAGCTG 61.039 63.158 10.11 10.11 0.00 4.24
2162 2227 5.253330 GGTCATCTAAAACATGGTTCCTGA 58.747 41.667 0.00 0.00 0.00 3.86
2228 2297 0.686441 CTCCCCCGGTGACTACATCA 60.686 60.000 0.00 0.00 33.79 3.07
2231 2300 2.043992 CCCCCGGTGACTACATCATTA 58.956 52.381 0.00 0.00 40.28 1.90
2233 2302 3.835978 CCCCCGGTGACTACATCATTATA 59.164 47.826 0.00 0.00 40.28 0.98
2239 2308 5.619309 CGGTGACTACATCATTATACCTCGG 60.619 48.000 0.00 0.00 40.28 4.63
2365 3019 0.999406 CGTCACAGGTGGATAAAGCG 59.001 55.000 0.00 0.00 0.00 4.68
2472 3126 0.575390 GGTATCGTCGATGTTTGCCG 59.425 55.000 17.98 0.00 0.00 5.69
2597 3263 2.106566 TGCAATCCACACACAAGGTTT 58.893 42.857 0.00 0.00 0.00 3.27
2636 3302 1.202568 CCTCGATGCTTCACATGGCTA 60.203 52.381 0.00 0.00 39.84 3.93
2665 3331 4.910195 TGGTTGATGCAGATAAAGTGAGT 58.090 39.130 0.00 0.00 0.00 3.41
2830 3807 3.458118 TGGTAATCCCAGGGTTATCTGTG 59.542 47.826 5.01 0.00 38.72 3.66
3010 3987 1.946283 GCAGTCAACTTAGGGACCAGC 60.946 57.143 0.00 4.77 34.58 4.85
3046 4023 4.448537 AAAGCTTGTACAGTGTGCAAAA 57.551 36.364 24.18 6.87 37.65 2.44
3067 4044 9.661187 GCAAAACATCTCTCAGATAAATACATG 57.339 33.333 0.00 0.00 32.12 3.21
3141 4118 5.108517 GGATAAGTTCTCTGTCAAGCTGAG 58.891 45.833 0.00 0.00 42.40 3.35
3217 4194 1.680249 GGGGAGATTTGTGGTGAGCTC 60.680 57.143 6.82 6.82 0.00 4.09
3265 4242 0.907704 TGCTGATACCCGGTGAGGTT 60.908 55.000 0.00 0.00 41.58 3.50
3289 4266 4.744795 AACTCAGGATTCGCTGTCTTAT 57.255 40.909 0.00 0.00 0.00 1.73
3304 4281 7.009815 TCGCTGTCTTATTTAATAAACGTCAGG 59.990 37.037 0.00 0.00 0.00 3.86
3429 4406 4.811024 GCAGAGATATTTCGATGGTTCACA 59.189 41.667 0.00 0.00 0.00 3.58
3477 4454 6.243148 TGTATAGTATGAGGGACGATAAGCA 58.757 40.000 0.00 0.00 0.00 3.91
3543 4520 4.888038 AAACTTGTCTAACGGAACAACC 57.112 40.909 0.00 0.00 0.00 3.77
3571 4548 1.093159 GCTTGGCCAGACATTGAGAG 58.907 55.000 5.11 0.00 0.00 3.20
3625 4602 3.853671 GCTACAAGACGATGCCAAAATTG 59.146 43.478 0.00 0.00 0.00 2.32
3660 4637 0.037303 CATGTGGCCTCCTGTGAGTT 59.963 55.000 3.32 0.00 36.86 3.01
3661 4638 0.326264 ATGTGGCCTCCTGTGAGTTC 59.674 55.000 3.32 0.00 36.86 3.01
3675 4652 4.323417 TGTGAGTTCGAAGCATAAACCAT 58.677 39.130 0.00 0.00 0.00 3.55
3791 4768 4.035208 CACCAAGTAACAGTTCCTGTGTTC 59.965 45.833 0.00 0.00 44.62 3.18
4255 5233 0.822811 ATCTGCATCGCTGTGACTCT 59.177 50.000 0.00 0.00 0.00 3.24
4457 5435 8.546597 AATGTAACCACCATTTCTTTATTTGC 57.453 30.769 0.00 0.00 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 45 7.362574 CCCCGAGATTTTGTGTGTGTAAATAAT 60.363 37.037 0.00 0.00 0.00 1.28
501 519 9.784531 CACACCATAGACCTGATAATTTAGAAT 57.215 33.333 0.00 0.00 0.00 2.40
502 520 8.988060 TCACACCATAGACCTGATAATTTAGAA 58.012 33.333 0.00 0.00 0.00 2.10
729 758 1.857318 ATCTAGCGCCGTCAGATCCG 61.857 60.000 2.29 0.00 0.00 4.18
730 759 0.387878 CATCTAGCGCCGTCAGATCC 60.388 60.000 2.29 0.00 0.00 3.36
731 760 1.006314 GCATCTAGCGCCGTCAGATC 61.006 60.000 2.29 0.00 0.00 2.75
732 761 1.006805 GCATCTAGCGCCGTCAGAT 60.007 57.895 2.29 4.59 0.00 2.90
733 762 2.413351 GCATCTAGCGCCGTCAGA 59.587 61.111 2.29 1.93 0.00 3.27
742 771 0.527817 AACTACCACGCGCATCTAGC 60.528 55.000 5.73 0.00 40.87 3.42
743 772 1.922570 AAACTACCACGCGCATCTAG 58.077 50.000 5.73 2.39 0.00 2.43
744 773 2.373540 AAAACTACCACGCGCATCTA 57.626 45.000 5.73 0.00 0.00 1.98
745 774 1.196808 CAAAAACTACCACGCGCATCT 59.803 47.619 5.73 0.00 0.00 2.90
746 775 1.602191 CAAAAACTACCACGCGCATC 58.398 50.000 5.73 0.00 0.00 3.91
747 776 0.386731 GCAAAAACTACCACGCGCAT 60.387 50.000 5.73 0.00 0.00 4.73
748 777 1.009449 GCAAAAACTACCACGCGCA 60.009 52.632 5.73 0.00 0.00 6.09
749 778 0.592754 TTGCAAAAACTACCACGCGC 60.593 50.000 5.73 0.00 0.00 6.86
750 779 1.976045 GATTGCAAAAACTACCACGCG 59.024 47.619 3.53 3.53 0.00 6.01
751 780 2.979813 CAGATTGCAAAAACTACCACGC 59.020 45.455 1.71 0.00 0.00 5.34
752 781 2.979813 GCAGATTGCAAAAACTACCACG 59.020 45.455 1.71 0.00 44.26 4.94
765 794 2.199291 GCAATAGTGTGGCAGATTGC 57.801 50.000 15.97 15.97 45.12 3.56
766 795 2.857592 GGCAATAGTGTGGCAGATTG 57.142 50.000 0.00 0.00 43.33 2.67
772 801 2.364632 TGTATGTGGCAATAGTGTGGC 58.635 47.619 0.00 0.00 44.09 5.01
773 802 6.882610 AATATGTATGTGGCAATAGTGTGG 57.117 37.500 0.00 0.00 0.00 4.17
774 803 7.071414 CGAAATATGTATGTGGCAATAGTGTG 58.929 38.462 0.00 0.00 0.00 3.82
775 804 6.765989 ACGAAATATGTATGTGGCAATAGTGT 59.234 34.615 0.00 0.00 0.00 3.55
776 805 7.189693 ACGAAATATGTATGTGGCAATAGTG 57.810 36.000 0.00 0.00 0.00 2.74
777 806 7.801716 AACGAAATATGTATGTGGCAATAGT 57.198 32.000 0.00 0.00 0.00 2.12
781 810 9.862371 AAATAAAACGAAATATGTATGTGGCAA 57.138 25.926 0.00 0.00 0.00 4.52
782 811 9.862371 AAAATAAAACGAAATATGTATGTGGCA 57.138 25.926 0.00 0.00 0.00 4.92
806 835 8.438676 AAGAGAAAAGACTCGAATCTCAAAAA 57.561 30.769 0.00 0.00 41.25 1.94
807 836 7.096023 CGAAGAGAAAAGACTCGAATCTCAAAA 60.096 37.037 0.00 0.00 41.25 2.44
808 837 6.363626 CGAAGAGAAAAGACTCGAATCTCAAA 59.636 38.462 0.00 0.00 41.25 2.69
809 838 5.859114 CGAAGAGAAAAGACTCGAATCTCAA 59.141 40.000 0.00 0.00 41.25 3.02
810 839 5.181433 TCGAAGAGAAAAGACTCGAATCTCA 59.819 40.000 0.00 0.00 41.25 3.27
811 840 5.632959 TCGAAGAGAAAAGACTCGAATCTC 58.367 41.667 0.00 0.00 41.25 2.75
812 841 5.630661 TCGAAGAGAAAAGACTCGAATCT 57.369 39.130 0.00 0.00 41.25 2.40
932 965 3.309296 GGGGAGGTGTAATCTGATCTGA 58.691 50.000 4.63 4.63 0.00 3.27
953 986 3.934391 GAGTGACGTGCGGGAAGGG 62.934 68.421 0.00 0.00 0.00 3.95
988 1021 2.126071 AAGCATGGTCGGTCGTCG 60.126 61.111 0.00 0.00 40.90 5.12
996 1029 2.637947 GGAGGAAGAAGAAGCATGGTC 58.362 52.381 0.00 0.00 0.00 4.02
997 1030 1.283321 GGGAGGAAGAAGAAGCATGGT 59.717 52.381 0.00 0.00 0.00 3.55
1030 1065 1.300963 GAGGAGCTGGCATTGTCCA 59.699 57.895 11.29 0.88 34.42 4.02
1032 1067 0.747283 CTGGAGGAGCTGGCATTGTC 60.747 60.000 0.00 0.00 0.00 3.18
1034 1069 2.119655 GCTGGAGGAGCTGGCATTG 61.120 63.158 0.00 0.00 45.21 2.82
1035 1070 2.274760 GCTGGAGGAGCTGGCATT 59.725 61.111 0.00 0.00 45.21 3.56
1116 1151 0.963856 TAGTGGAGCGAAGAAGGCGA 60.964 55.000 0.00 0.00 35.00 5.54
1147 1182 2.564947 AGTAGAAAGGCACTGAGACCAG 59.435 50.000 0.00 0.00 45.76 4.00
1149 1184 2.829120 AGAGTAGAAAGGCACTGAGACC 59.171 50.000 0.00 0.00 40.86 3.85
1163 1198 2.485124 GCGGGCACTAGACTAGAGTAGA 60.485 54.545 16.55 0.00 0.00 2.59
1164 1199 1.874872 GCGGGCACTAGACTAGAGTAG 59.125 57.143 16.55 5.52 0.00 2.57
1165 1200 1.211212 TGCGGGCACTAGACTAGAGTA 59.789 52.381 16.55 0.00 0.00 2.59
1166 1201 0.034380 TGCGGGCACTAGACTAGAGT 60.034 55.000 16.55 0.00 0.00 3.24
1167 1202 1.103803 TTGCGGGCACTAGACTAGAG 58.896 55.000 16.55 9.46 0.00 2.43
1168 1203 0.815734 GTTGCGGGCACTAGACTAGA 59.184 55.000 16.55 0.00 0.00 2.43
1172 1207 1.741770 CAGGTTGCGGGCACTAGAC 60.742 63.158 0.00 0.00 0.00 2.59
1207 1242 0.545071 AATGCAACAAGGGAAGGGGG 60.545 55.000 0.00 0.00 0.00 5.40
1209 1244 1.608801 GCAAATGCAACAAGGGAAGGG 60.609 52.381 0.00 0.00 41.59 3.95
1250 1285 4.465446 TGAGAGGAGGAGGCCGGG 62.465 72.222 2.18 0.00 0.00 5.73
1260 1295 3.053619 TCTGGTATGTGTAGCTGAGAGGA 60.054 47.826 0.00 0.00 33.25 3.71
1285 1320 3.011517 GGGGGAAGGCTGCTCTGA 61.012 66.667 0.00 0.00 0.00 3.27
1427 1469 2.738139 CCACGTGAGCACATCGCA 60.738 61.111 19.30 0.00 46.13 5.10
1482 1524 3.243434 ACGTTCTGTATCCCATCATCGAC 60.243 47.826 0.00 0.00 0.00 4.20
1483 1525 2.956333 ACGTTCTGTATCCCATCATCGA 59.044 45.455 0.00 0.00 0.00 3.59
1570 1618 2.876581 TGGAGCACACTAGAACAGAGA 58.123 47.619 0.00 0.00 0.00 3.10
1602 1654 3.371898 TCAGAAGCAAGTAATGACGCATG 59.628 43.478 0.00 0.00 0.00 4.06
1611 1663 2.543848 CGCAGTGTTCAGAAGCAAGTAA 59.456 45.455 0.00 0.00 0.00 2.24
1617 1670 2.096713 CAGTTACGCAGTGTTCAGAAGC 60.097 50.000 0.00 0.00 45.73 3.86
1632 1686 7.504818 GCAAATTTGAAAGCATCTTCAGTTAC 58.495 34.615 22.31 0.00 36.69 2.50
1731 1788 0.872021 GGAGACGAACATAGGCTGCG 60.872 60.000 0.00 0.00 0.00 5.18
1732 1789 0.175760 TGGAGACGAACATAGGCTGC 59.824 55.000 0.00 0.00 35.48 5.25
1759 1819 3.068590 CCTTGGATTGGCACATTGGATAC 59.931 47.826 0.00 0.00 39.30 2.24
1765 1825 3.242011 AGAAACCTTGGATTGGCACATT 58.758 40.909 0.00 0.00 39.30 2.71
1780 1840 5.473504 TGATTCCTGCAAGACTAAAGAAACC 59.526 40.000 0.00 0.00 34.07 3.27
1845 1910 3.375299 AGTTTCAGATATTCTTGGCGTGC 59.625 43.478 0.00 0.00 0.00 5.34
2020 2085 2.433436 GTCTCCGTGCCAATAAGGTTT 58.567 47.619 0.00 0.00 40.61 3.27
2092 2157 1.747355 GCATCCAAGATCACACCCTTG 59.253 52.381 0.00 0.00 39.43 3.61
2129 2194 6.385649 TGTTTTAGATGACCCAAACAGTTC 57.614 37.500 0.00 0.00 34.87 3.01
2162 2227 1.515954 CGCAGGTACTCCCGTTGAT 59.484 57.895 0.00 0.00 34.60 2.57
2211 2280 0.837272 AATGATGTAGTCACCGGGGG 59.163 55.000 2.42 0.00 40.28 5.40
2228 2297 5.871396 ATGTGACAGTTCCGAGGTATAAT 57.129 39.130 0.00 0.00 0.00 1.28
2231 2300 4.020573 TGAAATGTGACAGTTCCGAGGTAT 60.021 41.667 21.07 0.00 37.61 2.73
2233 2302 2.104111 TGAAATGTGACAGTTCCGAGGT 59.896 45.455 21.07 0.00 37.61 3.85
2263 2332 4.760047 CCGGACAGAACCAGGGCG 62.760 72.222 0.00 0.00 0.00 6.13
2281 2935 3.386768 ACTATATACTTGGGCACAGCG 57.613 47.619 0.00 0.00 0.00 5.18
2472 3126 2.484742 AACCGGAATGTGTAAGGGAC 57.515 50.000 9.46 0.00 0.00 4.46
2587 3253 3.567478 AGAGAGCTCAAAACCTTGTGT 57.433 42.857 17.77 0.00 33.94 3.72
2597 3263 3.501349 AGGACTGTGTAAGAGAGCTCAA 58.499 45.455 17.77 0.00 0.00 3.02
2636 3302 1.649321 TCTGCATCAACCAGACCTCT 58.351 50.000 0.00 0.00 34.59 3.69
2665 3331 0.322816 GGAGCAACTGGAGGCATTGA 60.323 55.000 0.00 0.00 0.00 2.57
2743 3409 4.750098 TCAAAAGATTTCGAGTTCTCGCTT 59.250 37.500 16.06 10.94 0.00 4.68
2753 3730 4.069304 ACCGGTTCATCAAAAGATTTCGA 58.931 39.130 0.00 0.00 0.00 3.71
2755 3732 4.485163 CCACCGGTTCATCAAAAGATTTC 58.515 43.478 2.97 0.00 0.00 2.17
2830 3807 1.668047 GCAAAGCATGACAAGTCCAGC 60.668 52.381 0.00 6.03 0.00 4.85
3010 3987 3.655276 AGCTTTTGAACATCTTGCCTG 57.345 42.857 0.00 0.00 0.00 4.85
3046 4023 7.871973 GCAGACATGTATTTATCTGAGAGATGT 59.128 37.037 12.72 0.00 40.92 3.06
3067 4044 3.999229 AATCTCGATTCGTTTGCAGAC 57.001 42.857 5.89 0.00 0.00 3.51
3141 4118 2.869101 AAAGAAGGCCTCTCTTGGAC 57.131 50.000 22.77 3.92 31.02 4.02
3217 4194 0.250038 CTGGTGGATACGGGCAGATG 60.250 60.000 0.00 0.00 42.51 2.90
3265 4242 2.826128 AGACAGCGAATCCTGAGTTACA 59.174 45.455 5.89 0.00 36.67 2.41
3289 4266 4.566070 CCCTGGTCCCTGACGTTTATTAAA 60.566 45.833 0.00 0.00 32.65 1.52
3304 4281 0.034186 TGATTGTCATGCCCTGGTCC 60.034 55.000 0.00 0.00 0.00 4.46
3477 4454 2.749044 CTGCTTGGGCTGATGCGT 60.749 61.111 0.00 0.00 40.82 5.24
3571 4548 4.705337 ACTCTTCCTTCACGAGATGTAC 57.295 45.455 0.00 0.00 0.00 2.90
3612 4589 3.443681 ACCCTACTTCAATTTTGGCATCG 59.556 43.478 0.00 0.00 0.00 3.84
3625 4602 3.495100 CCACATGCCATAGACCCTACTTC 60.495 52.174 0.00 0.00 0.00 3.01
3660 4637 4.155826 CCACTTCAATGGTTTATGCTTCGA 59.844 41.667 0.00 0.00 34.77 3.71
3661 4638 4.414852 CCACTTCAATGGTTTATGCTTCG 58.585 43.478 0.00 0.00 34.77 3.79
3675 4652 2.430332 CAGGAAAAGGTTGCCACTTCAA 59.570 45.455 0.00 0.00 0.00 2.69
4255 5233 2.755876 AGCGGATGGTCGAGCTCA 60.756 61.111 16.64 0.59 34.48 4.26
4386 5364 3.441496 TCTTTCGGTACACGTTCAGTT 57.559 42.857 0.00 0.00 44.69 3.16
4421 5399 4.525874 TGGTGGTTACATTTGCAATGATGA 59.474 37.500 16.22 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.