Multiple sequence alignment - TraesCS5D01G248500

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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 TraesCS5D01G248500 chr5D 100.000 2954 0 0 1 2954 355462951 355459998 0.000000e+00 5456.0
1 TraesCS5D01G248500 chr5D 92.484 306 21 2 2589 2892 460730666 460730971 1.260000e-118 436.0
2 TraesCS5D01G248500 chr5D 76.259 417 77 16 1096 1509 355797707 355797310 4.990000e-48 202.0
3 TraesCS5D01G248500 chr5D 77.689 251 43 7 2636 2884 460731023 460731262 1.100000e-29 141.0
4 TraesCS5D01G248500 chr5A 90.130 1388 82 33 705 2066 457717828 457719186 0.000000e+00 1753.0
5 TraesCS5D01G248500 chr5A 85.871 637 74 13 1 623 439181130 439181764 0.000000e+00 664.0
6 TraesCS5D01G248500 chr5A 76.651 424 77 16 1089 1509 457511682 457512086 6.410000e-52 215.0
7 TraesCS5D01G248500 chr5A 78.723 329 55 11 1093 1420 457086419 457086733 3.860000e-49 206.0
8 TraesCS5D01G248500 chr5B 95.833 1080 38 4 993 2069 420182220 420181145 0.000000e+00 1738.0
9 TraesCS5D01G248500 chr5B 76.960 421 75 17 1092 1509 420732868 420732467 1.380000e-53 220.0
10 TraesCS5D01G248500 chr5B 75.735 408 84 10 1093 1499 419727582 419727975 1.080000e-44 191.0
11 TraesCS5D01G248500 chr7A 93.750 848 39 8 2062 2904 709369713 709370551 0.000000e+00 1260.0
12 TraesCS5D01G248500 chr7A 93.803 823 40 9 2059 2874 30299438 30300256 0.000000e+00 1227.0
13 TraesCS5D01G248500 chr7A 85.086 637 79 12 3 625 245935020 245935654 1.150000e-178 636.0
14 TraesCS5D01G248500 chr7A 76.667 270 52 7 2636 2903 709370597 709370857 3.970000e-29 139.0
15 TraesCS5D01G248500 chr7A 98.148 54 1 0 2901 2954 709370593 709370646 8.720000e-16 95.3
16 TraesCS5D01G248500 chr2B 92.332 626 38 7 2282 2904 776527621 776527003 0.000000e+00 881.0
17 TraesCS5D01G248500 chr2B 92.683 451 31 2 2454 2904 776508155 776507707 0.000000e+00 649.0
18 TraesCS5D01G248500 chr2B 85.335 641 71 17 1 625 658992892 658993525 2.480000e-180 641.0
19 TraesCS5D01G248500 chr2B 97.368 228 5 1 2070 2297 776529175 776528949 1.280000e-103 387.0
20 TraesCS5D01G248500 chr2B 77.647 255 48 6 2636 2888 776507661 776507414 2.370000e-31 147.0
21 TraesCS5D01G248500 chr2B 77.647 255 48 6 2636 2888 776526957 776526710 2.370000e-31 147.0
22 TraesCS5D01G248500 chr2B 98.148 54 1 0 2901 2954 776507665 776507612 8.720000e-16 95.3
23 TraesCS5D01G248500 chr2B 98.148 54 1 0 2901 2954 776526961 776526908 8.720000e-16 95.3
24 TraesCS5D01G248500 chr2B 100.000 29 0 0 2069 2097 55547580 55547608 1.000000e-03 54.7
25 TraesCS5D01G248500 chr3D 91.483 634 38 13 1 624 113454826 113455453 0.000000e+00 857.0
26 TraesCS5D01G248500 chr3D 91.683 517 36 7 3 514 156728893 156728379 0.000000e+00 710.0
27 TraesCS5D01G248500 chr3D 85.404 644 76 14 1 628 31867241 31867882 0.000000e+00 652.0
28 TraesCS5D01G248500 chr3D 90.476 84 7 1 2636 2719 22123140 22123222 3.110000e-20 110.0
29 TraesCS5D01G248500 chr3D 88.889 54 5 1 2065 2118 578316684 578316736 6.830000e-07 65.8
30 TraesCS5D01G248500 chr6A 80.821 975 150 24 1007 1955 16444399 16443436 0.000000e+00 730.0
31 TraesCS5D01G248500 chr6A 100.000 33 0 0 2901 2933 184950549 184950581 8.840000e-06 62.1
32 TraesCS5D01G248500 chr6D 87.152 646 64 13 1 633 379093049 379092410 0.000000e+00 715.0
33 TraesCS5D01G248500 chr6B 80.083 969 160 19 1008 1955 28063436 28064392 0.000000e+00 689.0
34 TraesCS5D01G248500 chr6B 80.405 939 146 26 1041 1955 27904007 27903083 0.000000e+00 680.0
35 TraesCS5D01G248500 chr6B 84.700 634 77 15 1 616 63260969 63261600 1.500000e-172 616.0
36 TraesCS5D01G248500 chr2D 86.115 641 73 12 1 627 505640530 505639892 0.000000e+00 676.0
37 TraesCS5D01G248500 chr2D 89.796 49 5 0 2070 2118 22108181 22108133 2.460000e-06 63.9
38 TraesCS5D01G248500 chr2D 100.000 33 0 0 2901 2933 37496800 37496768 8.840000e-06 62.1
39 TraesCS5D01G248500 chr2D 100.000 33 0 0 2901 2933 522758229 522758197 8.840000e-06 62.1
40 TraesCS5D01G248500 chr7D 90.536 317 27 3 2589 2904 229876209 229876523 1.640000e-112 416.0
41 TraesCS5D01G248500 chr7D 77.083 384 77 11 1034 1413 125856372 125856748 8.300000e-51 211.0
42 TraesCS5D01G248500 chr7D 78.491 265 45 6 2636 2899 80497669 80497416 2.360000e-36 163.0
43 TraesCS5D01G248500 chr7D 92.727 110 6 2 2640 2748 65631793 65631901 1.100000e-34 158.0
44 TraesCS5D01G248500 chr7D 76.493 268 50 8 2634 2899 80497221 80496965 1.850000e-27 134.0
45 TraesCS5D01G248500 chr7D 75.375 333 50 23 1092 1419 125887912 125888217 6.640000e-27 132.0
46 TraesCS5D01G248500 chr7D 86.364 88 11 1 2636 2723 175914482 175914568 8.720000e-16 95.3
47 TraesCS5D01G248500 chr7D 95.918 49 2 0 2906 2954 229876574 229876622 2.440000e-11 80.5
48 TraesCS5D01G248500 chr7D 100.000 33 0 0 2901 2933 65635005 65635037 8.840000e-06 62.1
49 TraesCS5D01G248500 chr7D 96.970 33 1 0 2901 2933 610690185 610690217 4.110000e-04 56.5
50 TraesCS5D01G248500 chr2A 88.013 317 32 5 2589 2904 42013786 42013475 1.290000e-98 370.0
51 TraesCS5D01G248500 chr2A 100.000 49 0 0 2901 2949 42013433 42013385 1.130000e-14 91.6
52 TraesCS5D01G248500 chr2A 100.000 45 0 0 2905 2949 760386678 760386634 1.890000e-12 84.2
53 TraesCS5D01G248500 chr7B 90.909 110 9 1 2640 2748 572616730 572616839 2.370000e-31 147.0
54 TraesCS5D01G248500 chr7B 84.722 72 10 1 2067 2137 731895246 731895175 1.470000e-08 71.3
55 TraesCS5D01G248500 chr3A 81.633 147 21 5 2636 2782 617012487 617012347 1.860000e-22 117.0
56 TraesCS5D01G248500 chr3A 90.278 72 6 1 2070 2140 719800246 719800175 3.130000e-15 93.5
57 TraesCS5D01G248500 chr3A 100.000 33 0 0 2901 2933 466103088 466103120 8.840000e-06 62.1
58 TraesCS5D01G248500 chr1D 96.970 33 1 0 2901 2933 229058302 229058334 4.110000e-04 56.5


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 TraesCS5D01G248500 chr5D 355459998 355462951 2953 True 5456.000 5456 100.000000 1 2954 1 chr5D.!!$R1 2953
1 TraesCS5D01G248500 chr5D 460730666 460731262 596 False 288.500 436 85.086500 2589 2892 2 chr5D.!!$F1 303
2 TraesCS5D01G248500 chr5A 457717828 457719186 1358 False 1753.000 1753 90.130000 705 2066 1 chr5A.!!$F4 1361
3 TraesCS5D01G248500 chr5A 439181130 439181764 634 False 664.000 664 85.871000 1 623 1 chr5A.!!$F1 622
4 TraesCS5D01G248500 chr5B 420181145 420182220 1075 True 1738.000 1738 95.833000 993 2069 1 chr5B.!!$R1 1076
5 TraesCS5D01G248500 chr7A 30299438 30300256 818 False 1227.000 1227 93.803000 2059 2874 1 chr7A.!!$F1 815
6 TraesCS5D01G248500 chr7A 245935020 245935654 634 False 636.000 636 85.086000 3 625 1 chr7A.!!$F2 622
7 TraesCS5D01G248500 chr7A 709369713 709370857 1144 False 498.100 1260 89.521667 2062 2954 3 chr7A.!!$F3 892
8 TraesCS5D01G248500 chr2B 658992892 658993525 633 False 641.000 641 85.335000 1 625 1 chr2B.!!$F2 624
9 TraesCS5D01G248500 chr2B 776526710 776529175 2465 True 377.575 881 91.373750 2070 2954 4 chr2B.!!$R2 884
10 TraesCS5D01G248500 chr2B 776507414 776508155 741 True 297.100 649 89.492667 2454 2954 3 chr2B.!!$R1 500
11 TraesCS5D01G248500 chr3D 113454826 113455453 627 False 857.000 857 91.483000 1 624 1 chr3D.!!$F3 623
12 TraesCS5D01G248500 chr3D 156728379 156728893 514 True 710.000 710 91.683000 3 514 1 chr3D.!!$R1 511
13 TraesCS5D01G248500 chr3D 31867241 31867882 641 False 652.000 652 85.404000 1 628 1 chr3D.!!$F2 627
14 TraesCS5D01G248500 chr6A 16443436 16444399 963 True 730.000 730 80.821000 1007 1955 1 chr6A.!!$R1 948
15 TraesCS5D01G248500 chr6D 379092410 379093049 639 True 715.000 715 87.152000 1 633 1 chr6D.!!$R1 632
16 TraesCS5D01G248500 chr6B 28063436 28064392 956 False 689.000 689 80.083000 1008 1955 1 chr6B.!!$F1 947
17 TraesCS5D01G248500 chr6B 27903083 27904007 924 True 680.000 680 80.405000 1041 1955 1 chr6B.!!$R1 914
18 TraesCS5D01G248500 chr6B 63260969 63261600 631 False 616.000 616 84.700000 1 616 1 chr6B.!!$F2 615
19 TraesCS5D01G248500 chr2D 505639892 505640530 638 True 676.000 676 86.115000 1 627 1 chr2D.!!$R3 626

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
773 843 0.179081 GTGGGAGGGCTGTAATCGTC 60.179 60.0 0.0 0.0 0.00 4.20 F
786 856 0.320771 AATCGTCAACGCCAGAAGCT 60.321 50.0 0.0 0.0 40.39 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1851 1977 0.325203 GCTCTCCTCCCTTGGACTCT 60.325 60.0 0.00 0.0 31.94 3.24 R
2344 3820 0.958382 ACGGCAATTAAGAGCGGCAA 60.958 50.0 1.45 0.0 34.83 4.52 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
125 130 6.014840 ACAACTCTCTCTTTTACCCGAACATA 60.015 38.462 0.00 0.00 0.00 2.29
129 134 7.549488 ACTCTCTCTTTTACCCGAACATATTTG 59.451 37.037 0.00 0.00 0.00 2.32
133 138 8.852135 TCTCTTTTACCCGAACATATTTGTTTT 58.148 29.630 2.94 0.00 46.01 2.43
134 139 8.804688 TCTTTTACCCGAACATATTTGTTTTG 57.195 30.769 2.94 0.15 46.01 2.44
136 141 3.920446 ACCCGAACATATTTGTTTTGCC 58.080 40.909 2.94 0.00 46.01 4.52
137 142 3.322254 ACCCGAACATATTTGTTTTGCCA 59.678 39.130 2.94 0.00 46.01 4.92
138 143 4.020662 ACCCGAACATATTTGTTTTGCCAT 60.021 37.500 2.94 0.00 46.01 4.40
139 144 4.329528 CCCGAACATATTTGTTTTGCCATG 59.670 41.667 2.94 0.00 46.01 3.66
141 146 4.201705 CGAACATATTTGTTTTGCCATGCC 60.202 41.667 2.94 0.00 46.01 4.40
248 260 1.820519 CCATACATGGCAACTGCAGTT 59.179 47.619 26.36 26.36 41.75 3.16
319 383 1.606668 GACATGGCAACCGAAGTTCAA 59.393 47.619 3.32 0.00 32.45 2.69
362 426 0.741221 GAACATGGACGAGGGTCTGC 60.741 60.000 0.00 0.00 42.97 4.26
496 561 0.395862 GTGTGAGAGGGATCGGGAGA 60.396 60.000 0.00 0.00 46.90 3.71
536 605 4.384940 ACATTATTTGTTTTGCCCACACC 58.615 39.130 0.00 0.00 33.74 4.16
559 628 0.685097 GTGTGTGGGCTGTTCCTCTA 59.315 55.000 0.00 0.00 34.39 2.43
635 705 1.576356 TTGGCGTCCAATGTTTTTGC 58.424 45.000 7.15 0.00 38.75 3.68
636 706 0.749649 TGGCGTCCAATGTTTTTGCT 59.250 45.000 0.00 0.00 0.00 3.91
637 707 1.139163 GGCGTCCAATGTTTTTGCTG 58.861 50.000 0.00 0.00 0.00 4.41
638 708 0.508213 GCGTCCAATGTTTTTGCTGC 59.492 50.000 0.00 0.00 0.00 5.25
639 709 1.139163 CGTCCAATGTTTTTGCTGCC 58.861 50.000 0.00 0.00 0.00 4.85
640 710 1.139163 GTCCAATGTTTTTGCTGCCG 58.861 50.000 0.00 0.00 0.00 5.69
641 711 0.749649 TCCAATGTTTTTGCTGCCGT 59.250 45.000 0.00 0.00 0.00 5.68
642 712 1.139163 CCAATGTTTTTGCTGCCGTC 58.861 50.000 0.00 0.00 0.00 4.79
643 713 0.777631 CAATGTTTTTGCTGCCGTCG 59.222 50.000 0.00 0.00 0.00 5.12
644 714 0.318614 AATGTTTTTGCTGCCGTCGG 60.319 50.000 6.99 6.99 0.00 4.79
654 724 3.609258 GCCGTCGGCGTATACTTG 58.391 61.111 22.50 0.00 39.62 3.16
655 725 1.064621 GCCGTCGGCGTATACTTGA 59.935 57.895 22.50 0.00 39.62 3.02
656 726 0.933509 GCCGTCGGCGTATACTTGAG 60.934 60.000 22.50 0.00 39.62 3.02
657 727 0.379669 CCGTCGGCGTATACTTGAGT 59.620 55.000 9.28 0.00 36.15 3.41
658 728 1.202222 CCGTCGGCGTATACTTGAGTT 60.202 52.381 9.28 0.00 36.15 3.01
659 729 2.523015 CGTCGGCGTATACTTGAGTTT 58.477 47.619 6.85 0.00 0.00 2.66
660 730 2.919229 CGTCGGCGTATACTTGAGTTTT 59.081 45.455 6.85 0.00 0.00 2.43
661 731 3.365820 CGTCGGCGTATACTTGAGTTTTT 59.634 43.478 6.85 0.00 0.00 1.94
662 732 4.634991 GTCGGCGTATACTTGAGTTTTTG 58.365 43.478 6.85 0.00 0.00 2.44
663 733 3.123959 TCGGCGTATACTTGAGTTTTTGC 59.876 43.478 6.85 0.00 0.00 3.68
664 734 3.124636 CGGCGTATACTTGAGTTTTTGCT 59.875 43.478 0.00 0.00 0.00 3.91
665 735 4.327898 CGGCGTATACTTGAGTTTTTGCTA 59.672 41.667 0.00 0.00 0.00 3.49
666 736 5.500290 CGGCGTATACTTGAGTTTTTGCTAG 60.500 44.000 0.00 0.00 0.00 3.42
667 737 5.579511 GGCGTATACTTGAGTTTTTGCTAGA 59.420 40.000 0.56 0.00 0.00 2.43
668 738 6.455246 GGCGTATACTTGAGTTTTTGCTAGAC 60.455 42.308 0.56 0.00 0.00 2.59
669 739 6.683883 CGTATACTTGAGTTTTTGCTAGACG 58.316 40.000 0.56 0.00 0.00 4.18
670 740 6.307318 CGTATACTTGAGTTTTTGCTAGACGT 59.693 38.462 0.56 0.00 0.00 4.34
671 741 4.795970 ACTTGAGTTTTTGCTAGACGTG 57.204 40.909 0.00 0.00 0.00 4.49
672 742 3.560068 ACTTGAGTTTTTGCTAGACGTGG 59.440 43.478 0.00 0.00 0.00 4.94
673 743 3.188159 TGAGTTTTTGCTAGACGTGGT 57.812 42.857 0.00 0.00 0.00 4.16
674 744 2.869801 TGAGTTTTTGCTAGACGTGGTG 59.130 45.455 0.00 0.00 0.00 4.17
675 745 2.218603 AGTTTTTGCTAGACGTGGTGG 58.781 47.619 0.00 0.00 0.00 4.61
676 746 1.944709 GTTTTTGCTAGACGTGGTGGT 59.055 47.619 0.00 0.00 0.00 4.16
677 747 1.588674 TTTTGCTAGACGTGGTGGTG 58.411 50.000 0.00 0.00 0.00 4.17
678 748 0.882927 TTTGCTAGACGTGGTGGTGC 60.883 55.000 0.00 0.00 0.00 5.01
679 749 2.034048 TTGCTAGACGTGGTGGTGCA 62.034 55.000 0.00 0.00 0.00 4.57
680 750 1.301401 GCTAGACGTGGTGGTGCAA 60.301 57.895 0.00 0.00 0.00 4.08
681 751 1.291877 GCTAGACGTGGTGGTGCAAG 61.292 60.000 0.00 0.00 0.00 4.01
682 752 0.670546 CTAGACGTGGTGGTGCAAGG 60.671 60.000 0.00 0.00 0.00 3.61
683 753 1.116536 TAGACGTGGTGGTGCAAGGA 61.117 55.000 0.00 0.00 0.00 3.36
684 754 2.203153 ACGTGGTGGTGCAAGGAC 60.203 61.111 0.00 0.00 0.00 3.85
685 755 3.345808 CGTGGTGGTGCAAGGACG 61.346 66.667 0.00 0.00 0.00 4.79
686 756 2.978010 GTGGTGGTGCAAGGACGG 60.978 66.667 0.00 0.00 0.00 4.79
687 757 4.947147 TGGTGGTGCAAGGACGGC 62.947 66.667 0.00 0.00 0.00 5.68
705 775 4.803426 GGCGAGCCGGAGACTGTG 62.803 72.222 5.05 0.00 0.00 3.66
706 776 3.749064 GCGAGCCGGAGACTGTGA 61.749 66.667 5.05 0.00 0.00 3.58
707 777 2.179517 CGAGCCGGAGACTGTGAC 59.820 66.667 5.05 0.00 0.00 3.67
708 778 2.179517 GAGCCGGAGACTGTGACG 59.820 66.667 5.05 0.00 0.00 4.35
709 779 3.973267 GAGCCGGAGACTGTGACGC 62.973 68.421 5.05 0.00 0.00 5.19
710 780 4.057428 GCCGGAGACTGTGACGCT 62.057 66.667 5.05 0.00 0.00 5.07
711 781 2.126307 CCGGAGACTGTGACGCTG 60.126 66.667 0.00 0.00 0.00 5.18
730 800 3.443045 GGATGCCGGCAACCACAG 61.443 66.667 41.50 0.00 38.55 3.66
749 819 4.314440 GACCGTGTGCTGGAGCCA 62.314 66.667 0.00 0.00 41.18 4.75
770 840 1.146263 CGGTGGGAGGGCTGTAATC 59.854 63.158 0.00 0.00 0.00 1.75
771 841 1.146263 GGTGGGAGGGCTGTAATCG 59.854 63.158 0.00 0.00 0.00 3.34
772 842 1.623542 GGTGGGAGGGCTGTAATCGT 61.624 60.000 0.00 0.00 0.00 3.73
773 843 0.179081 GTGGGAGGGCTGTAATCGTC 60.179 60.000 0.00 0.00 0.00 4.20
774 844 0.616395 TGGGAGGGCTGTAATCGTCA 60.616 55.000 0.00 0.00 0.00 4.35
775 845 0.539986 GGGAGGGCTGTAATCGTCAA 59.460 55.000 0.00 0.00 0.00 3.18
776 846 1.653151 GGAGGGCTGTAATCGTCAAC 58.347 55.000 0.00 0.00 0.00 3.18
777 847 1.278238 GAGGGCTGTAATCGTCAACG 58.722 55.000 0.00 0.00 41.45 4.10
778 848 0.739813 AGGGCTGTAATCGTCAACGC 60.740 55.000 0.00 0.00 39.60 4.84
779 849 1.702491 GGGCTGTAATCGTCAACGCC 61.702 60.000 0.00 0.00 39.60 5.68
780 850 1.017177 GGCTGTAATCGTCAACGCCA 61.017 55.000 0.00 0.00 39.60 5.69
781 851 0.370273 GCTGTAATCGTCAACGCCAG 59.630 55.000 0.00 3.00 39.60 4.85
782 852 1.990799 CTGTAATCGTCAACGCCAGA 58.009 50.000 0.00 0.00 39.60 3.86
783 853 2.333926 CTGTAATCGTCAACGCCAGAA 58.666 47.619 0.00 0.00 39.60 3.02
784 854 2.333926 TGTAATCGTCAACGCCAGAAG 58.666 47.619 0.00 0.00 39.60 2.85
785 855 1.060698 GTAATCGTCAACGCCAGAAGC 59.939 52.381 0.00 0.00 39.60 3.86
786 856 0.320771 AATCGTCAACGCCAGAAGCT 60.321 50.000 0.00 0.00 40.39 3.74
787 857 1.016130 ATCGTCAACGCCAGAAGCTG 61.016 55.000 0.00 0.00 40.39 4.24
796 866 2.345244 CAGAAGCTGGAGCCACGT 59.655 61.111 0.00 0.00 43.38 4.49
797 867 2.031516 CAGAAGCTGGAGCCACGTG 61.032 63.158 9.08 9.08 43.38 4.49
798 868 3.426568 GAAGCTGGAGCCACGTGC 61.427 66.667 10.91 5.91 43.38 5.34
810 880 3.737172 ACGTGCTGCAATTCCGGC 61.737 61.111 2.77 0.00 37.61 6.13
840 910 2.626467 AAGGGGATGGCAAGGGGAC 61.626 63.158 0.00 0.00 0.00 4.46
852 931 1.889530 AAGGGGACGAAGAGAAGGCG 61.890 60.000 0.00 0.00 0.00 5.52
866 945 0.674895 AAGGCGCCAGATCTGAACAC 60.675 55.000 31.54 11.22 0.00 3.32
874 953 2.568956 CCAGATCTGAACACTTGGGAGA 59.431 50.000 24.62 0.00 0.00 3.71
884 963 1.726791 CACTTGGGAGACGTTTCATCG 59.273 52.381 8.50 0.00 0.00 3.84
948 1028 3.737824 GCCTAGCGCTGGGAATTC 58.262 61.111 40.44 20.63 32.26 2.17
961 1041 2.849294 GGAATTCCCTAGCTGGCTAG 57.151 55.000 14.03 19.33 44.07 3.42
991 1071 3.842923 CGGGCGCCTCAGTCTCAT 61.843 66.667 28.56 0.00 0.00 2.90
1011 1119 2.842256 GCCAGCAATGGATCCAGCG 61.842 63.158 21.33 14.30 0.00 5.18
1428 1539 4.286320 GCCGCGTCGAGGGATGAT 62.286 66.667 17.13 0.00 34.27 2.45
1605 1728 2.897326 GTTTGGTGGTAAGGAGCCAATT 59.103 45.455 0.00 0.00 40.23 2.32
1657 1780 1.685148 GGAGAAGCTTTGGCCCATAG 58.315 55.000 0.00 0.00 39.73 2.23
1851 1977 3.009115 GGCAGGGTGGAGTGGCTA 61.009 66.667 0.00 0.00 36.35 3.93
1944 2070 4.070552 GTGGTCGCCTTCCTCGCT 62.071 66.667 0.00 0.00 0.00 4.93
1967 2093 3.128242 GGCAATTGATTCAGAGGACACTG 59.872 47.826 10.34 0.00 39.02 3.66
1968 2094 4.005650 GCAATTGATTCAGAGGACACTGA 58.994 43.478 10.34 0.00 43.83 3.41
1970 2096 5.243981 CAATTGATTCAGAGGACACTGACT 58.756 41.667 0.00 0.00 44.94 3.41
1972 2098 6.611613 ATTGATTCAGAGGACACTGACTTA 57.388 37.500 0.00 0.00 44.94 2.24
1973 2099 6.611613 TTGATTCAGAGGACACTGACTTAT 57.388 37.500 0.00 0.00 44.94 1.73
2008 2137 3.009723 CGGGTTGCAAGTGTAATCAGAT 58.990 45.455 0.00 0.00 0.00 2.90
2013 2142 5.412594 GGTTGCAAGTGTAATCAGATCTCAA 59.587 40.000 0.00 0.00 0.00 3.02
2049 2178 8.081633 TGTATTTGTGAATTCAGAACCATTGAC 58.918 33.333 16.93 9.51 0.00 3.18
2062 2191 7.451255 TCAGAACCATTGACAATAAAGGACAAT 59.549 33.333 9.42 0.00 0.00 2.71
2163 2292 1.867233 GTTGAGATTCGTGTGTGCTGT 59.133 47.619 0.00 0.00 0.00 4.40
2220 2349 1.662122 AGTTGTTTCGTTTCGTCGCTT 59.338 42.857 0.00 0.00 0.00 4.68
2344 3820 4.459337 GCATGTTAGTAGGAAAAGCAACCT 59.541 41.667 0.00 0.00 39.95 3.50
2734 4212 1.747745 GTGACCGTAACCATGGGGC 60.748 63.158 18.09 0.00 37.90 5.80
2736 4214 2.936584 ACCGTAACCATGGGGCCA 60.937 61.111 18.09 0.00 37.90 5.36
2755 4233 2.280592 GGCAAGGGTTGTCGACGT 60.281 61.111 11.62 0.00 0.00 4.34
2815 4294 4.619437 TTTTGTTGTAGTTCCAACCGTC 57.381 40.909 0.00 0.00 43.22 4.79
2818 4297 0.033781 TTGTAGTTCCAACCGTCCCG 59.966 55.000 0.00 0.00 0.00 5.14
2837 4316 1.065401 CGACCCATGCGCAATTGTATT 59.935 47.619 17.11 0.00 0.00 1.89
2866 4345 3.349006 AAGCGCAACTGCAGGTCG 61.349 61.111 19.93 17.70 42.21 4.79
2949 4475 1.732683 CCCGAACGCAATTGCAACC 60.733 57.895 28.77 15.40 42.21 3.77
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
248 260 1.808531 GCAGTTGCCATGGTTGCTCA 61.809 55.000 14.67 0.00 34.31 4.26
251 263 1.373748 CTGCAGTTGCCATGGTTGC 60.374 57.895 14.67 17.56 41.18 4.17
254 266 4.605064 AACTGCAGTTGCCATGGT 57.395 50.000 30.66 4.24 41.18 3.55
319 383 0.819259 AACTGCAGTTGCCATGTCGT 60.819 50.000 30.66 2.58 41.18 4.34
362 426 3.751246 CCCGCAGTTGCCATGGTG 61.751 66.667 14.67 4.51 37.91 4.17
503 570 6.478512 AAACAAATAATGTCCACACACCTT 57.521 33.333 0.00 0.00 42.99 3.50
507 574 5.053145 GGCAAAACAAATAATGTCCACACA 58.947 37.500 0.00 0.00 42.99 3.72
514 583 4.102367 AGGTGTGGGCAAAACAAATAATGT 59.898 37.500 0.00 0.00 46.82 2.71
516 585 4.972751 AGGTGTGGGCAAAACAAATAAT 57.027 36.364 0.00 0.00 0.00 1.28
517 586 4.282195 CCTAGGTGTGGGCAAAACAAATAA 59.718 41.667 0.00 0.00 0.00 1.40
536 605 0.321653 GGAACAGCCCACACACCTAG 60.322 60.000 0.00 0.00 0.00 3.02
559 628 8.948401 TGCCCATATATTTTATGTGGTGTATT 57.052 30.769 8.80 0.00 0.00 1.89
617 687 0.749649 AGCAAAAACATTGGACGCCA 59.250 45.000 0.00 0.00 0.00 5.69
627 697 2.718731 CCGACGGCAGCAAAAACA 59.281 55.556 0.00 0.00 0.00 2.83
637 707 0.933509 CTCAAGTATACGCCGACGGC 60.934 60.000 29.10 29.10 46.75 5.68
638 708 0.379669 ACTCAAGTATACGCCGACGG 59.620 55.000 10.29 10.29 46.04 4.79
640 710 4.634991 CAAAAACTCAAGTATACGCCGAC 58.365 43.478 0.00 0.00 0.00 4.79
641 711 3.123959 GCAAAAACTCAAGTATACGCCGA 59.876 43.478 0.00 0.00 0.00 5.54
642 712 3.124636 AGCAAAAACTCAAGTATACGCCG 59.875 43.478 0.00 0.00 0.00 6.46
643 713 4.680171 AGCAAAAACTCAAGTATACGCC 57.320 40.909 0.00 0.00 0.00 5.68
644 714 6.467648 GTCTAGCAAAAACTCAAGTATACGC 58.532 40.000 0.00 0.00 0.00 4.42
645 715 6.307318 ACGTCTAGCAAAAACTCAAGTATACG 59.693 38.462 0.00 0.00 0.00 3.06
646 716 7.411588 CCACGTCTAGCAAAAACTCAAGTATAC 60.412 40.741 0.00 0.00 0.00 1.47
647 717 6.588756 CCACGTCTAGCAAAAACTCAAGTATA 59.411 38.462 0.00 0.00 0.00 1.47
648 718 5.408604 CCACGTCTAGCAAAAACTCAAGTAT 59.591 40.000 0.00 0.00 0.00 2.12
649 719 4.748102 CCACGTCTAGCAAAAACTCAAGTA 59.252 41.667 0.00 0.00 0.00 2.24
650 720 3.560068 CCACGTCTAGCAAAAACTCAAGT 59.440 43.478 0.00 0.00 0.00 3.16
651 721 3.560068 ACCACGTCTAGCAAAAACTCAAG 59.440 43.478 0.00 0.00 0.00 3.02
652 722 3.311322 CACCACGTCTAGCAAAAACTCAA 59.689 43.478 0.00 0.00 0.00 3.02
653 723 2.869801 CACCACGTCTAGCAAAAACTCA 59.130 45.455 0.00 0.00 0.00 3.41
654 724 2.223377 CCACCACGTCTAGCAAAAACTC 59.777 50.000 0.00 0.00 0.00 3.01
655 725 2.218603 CCACCACGTCTAGCAAAAACT 58.781 47.619 0.00 0.00 0.00 2.66
656 726 1.944709 ACCACCACGTCTAGCAAAAAC 59.055 47.619 0.00 0.00 0.00 2.43
657 727 1.944024 CACCACCACGTCTAGCAAAAA 59.056 47.619 0.00 0.00 0.00 1.94
658 728 1.588674 CACCACCACGTCTAGCAAAA 58.411 50.000 0.00 0.00 0.00 2.44
659 729 0.882927 GCACCACCACGTCTAGCAAA 60.883 55.000 0.00 0.00 0.00 3.68
660 730 1.301401 GCACCACCACGTCTAGCAA 60.301 57.895 0.00 0.00 0.00 3.91
661 731 2.034048 TTGCACCACCACGTCTAGCA 62.034 55.000 0.00 0.00 0.00 3.49
662 732 1.291877 CTTGCACCACCACGTCTAGC 61.292 60.000 0.00 0.00 0.00 3.42
663 733 0.670546 CCTTGCACCACCACGTCTAG 60.671 60.000 0.00 0.00 0.00 2.43
664 734 1.116536 TCCTTGCACCACCACGTCTA 61.117 55.000 0.00 0.00 0.00 2.59
665 735 2.111043 CCTTGCACCACCACGTCT 59.889 61.111 0.00 0.00 0.00 4.18
666 736 2.110213 TCCTTGCACCACCACGTC 59.890 61.111 0.00 0.00 0.00 4.34
667 737 2.203153 GTCCTTGCACCACCACGT 60.203 61.111 0.00 0.00 0.00 4.49
668 738 3.345808 CGTCCTTGCACCACCACG 61.346 66.667 0.00 0.00 0.00 4.94
669 739 2.978010 CCGTCCTTGCACCACCAC 60.978 66.667 0.00 0.00 0.00 4.16
670 740 4.947147 GCCGTCCTTGCACCACCA 62.947 66.667 0.00 0.00 0.00 4.17
688 758 4.803426 CACAGTCTCCGGCTCGCC 62.803 72.222 0.00 0.00 0.00 5.54
689 759 3.749064 TCACAGTCTCCGGCTCGC 61.749 66.667 0.00 0.00 0.00 5.03
690 760 2.179517 GTCACAGTCTCCGGCTCG 59.820 66.667 0.00 0.00 0.00 5.03
691 761 2.179517 CGTCACAGTCTCCGGCTC 59.820 66.667 0.00 0.00 0.00 4.70
692 762 4.057428 GCGTCACAGTCTCCGGCT 62.057 66.667 0.00 0.00 0.00 5.52
693 763 4.057428 AGCGTCACAGTCTCCGGC 62.057 66.667 0.00 0.00 0.00 6.13
694 764 2.126307 CAGCGTCACAGTCTCCGG 60.126 66.667 0.00 0.00 0.00 5.14
695 765 2.126307 CCAGCGTCACAGTCTCCG 60.126 66.667 0.00 0.00 0.00 4.63
696 766 2.262915 CCCAGCGTCACAGTCTCC 59.737 66.667 0.00 0.00 0.00 3.71
697 767 1.608717 ATCCCCAGCGTCACAGTCTC 61.609 60.000 0.00 0.00 0.00 3.36
698 768 1.610673 ATCCCCAGCGTCACAGTCT 60.611 57.895 0.00 0.00 0.00 3.24
699 769 1.448540 CATCCCCAGCGTCACAGTC 60.449 63.158 0.00 0.00 0.00 3.51
700 770 2.665000 CATCCCCAGCGTCACAGT 59.335 61.111 0.00 0.00 0.00 3.55
701 771 2.821366 GCATCCCCAGCGTCACAG 60.821 66.667 0.00 0.00 0.00 3.66
702 772 4.408821 GGCATCCCCAGCGTCACA 62.409 66.667 0.00 0.00 0.00 3.58
729 799 2.737180 CTCCAGCACACGGTCACT 59.263 61.111 0.00 0.00 0.00 3.41
730 800 3.044305 GCTCCAGCACACGGTCAC 61.044 66.667 0.00 0.00 41.59 3.67
749 819 2.833151 TTACAGCCCTCCCACCGGAT 62.833 60.000 9.46 0.00 37.60 4.18
753 823 1.146263 CGATTACAGCCCTCCCACC 59.854 63.158 0.00 0.00 0.00 4.61
763 833 1.990799 TCTGGCGTTGACGATTACAG 58.009 50.000 7.85 9.12 43.02 2.74
770 840 2.671177 CCAGCTTCTGGCGTTGACG 61.671 63.158 0.00 0.00 45.13 4.35
771 841 3.257933 CCAGCTTCTGGCGTTGAC 58.742 61.111 0.00 0.00 45.13 3.18
779 849 2.031516 CACGTGGCTCCAGCTTCTG 61.032 63.158 7.95 0.00 41.70 3.02
780 850 2.345244 CACGTGGCTCCAGCTTCT 59.655 61.111 7.95 0.00 41.70 2.85
781 851 3.426568 GCACGTGGCTCCAGCTTC 61.427 66.667 18.88 0.00 41.70 3.86
790 860 2.126346 GGAATTGCAGCACGTGGC 60.126 61.111 18.88 13.75 45.30 5.01
791 861 2.176546 CGGAATTGCAGCACGTGG 59.823 61.111 18.88 2.10 0.00 4.94
792 862 2.176546 CCGGAATTGCAGCACGTG 59.823 61.111 12.28 12.28 0.00 4.49
793 863 3.737172 GCCGGAATTGCAGCACGT 61.737 61.111 5.05 0.00 0.00 4.49
794 864 4.817063 CGCCGGAATTGCAGCACG 62.817 66.667 5.05 0.00 0.00 5.34
795 865 4.481112 CCGCCGGAATTGCAGCAC 62.481 66.667 5.05 0.00 0.00 4.40
821 891 2.042639 CCCCTTGCCATCCCCTTG 60.043 66.667 0.00 0.00 0.00 3.61
822 892 2.204448 TCCCCTTGCCATCCCCTT 60.204 61.111 0.00 0.00 0.00 3.95
826 896 1.452108 CTTCGTCCCCTTGCCATCC 60.452 63.158 0.00 0.00 0.00 3.51
840 910 0.873743 GATCTGGCGCCTTCTCTTCG 60.874 60.000 29.70 5.67 0.00 3.79
852 931 1.003580 TCCCAAGTGTTCAGATCTGGC 59.996 52.381 22.42 15.47 0.00 4.85
866 945 2.080286 ACGATGAAACGTCTCCCAAG 57.920 50.000 0.00 0.00 43.02 3.61
884 963 3.116531 GTCGTGCCTTGGCCGTAC 61.117 66.667 17.27 12.30 0.00 3.67
943 1023 2.177394 GCTAGCCAGCTAGGGAATTC 57.823 55.000 24.24 0.00 44.93 2.17
958 1038 1.142748 CCGAACAGGCCAGAGCTAG 59.857 63.158 5.01 0.00 39.73 3.42
960 1040 3.710722 CCCGAACAGGCCAGAGCT 61.711 66.667 5.01 0.00 39.73 4.09
983 1063 0.656259 CATTGCTGGCGATGAGACTG 59.344 55.000 15.54 0.00 39.55 3.51
990 1070 0.536687 CTGGATCCATTGCTGGCGAT 60.537 55.000 16.63 0.00 42.80 4.58
991 1071 1.153107 CTGGATCCATTGCTGGCGA 60.153 57.895 16.63 0.00 42.80 5.54
1011 1119 1.390463 GAGTCGAATCGCAGTTTGGTC 59.610 52.381 0.00 0.00 0.00 4.02
1369 1477 4.867599 GTCGTAGGCCGCGGGAAG 62.868 72.222 29.38 0.38 36.19 3.46
1542 1665 0.105039 CCTCAATCCGTACTCCTGGC 59.895 60.000 0.00 0.00 0.00 4.85
1681 1807 1.401318 TTCAACCTCGGGTCGTCCAA 61.401 55.000 0.04 0.00 33.12 3.53
1838 1964 1.331399 GGACTCTAGCCACTCCACCC 61.331 65.000 0.00 0.00 0.00 4.61
1851 1977 0.325203 GCTCTCCTCCCTTGGACTCT 60.325 60.000 0.00 0.00 31.94 3.24
1944 2070 3.084039 GTGTCCTCTGAATCAATTGCCA 58.916 45.455 0.00 0.00 0.00 4.92
1967 2093 4.680171 CGAAGGGGAACACAAATAAGTC 57.320 45.455 0.00 0.00 0.00 3.01
1990 2119 6.486253 TTGAGATCTGATTACACTTGCAAC 57.514 37.500 0.00 0.00 0.00 4.17
2008 2137 6.094742 TCACAAATACAAGTGTGCTTTTGAGA 59.905 34.615 16.52 13.11 43.91 3.27
2013 2142 7.264221 TGAATTCACAAATACAAGTGTGCTTT 58.736 30.769 3.38 0.00 43.91 3.51
2220 2349 2.202946 TGCAGCGTGGACAAACGA 60.203 55.556 0.17 0.00 46.49 3.85
2344 3820 0.958382 ACGGCAATTAAGAGCGGCAA 60.958 50.000 1.45 0.00 34.83 4.52
2350 3826 7.382218 AGAAACATTTTTCACGGCAATTAAGAG 59.618 33.333 7.08 0.00 43.29 2.85
2386 3863 1.544686 AACAACAAAAGAACGCAGCG 58.455 45.000 14.82 14.82 0.00 5.18
2637 4115 3.312828 GGCGATTGCAACAACAACAATA 58.687 40.909 0.00 0.00 45.35 1.90
2646 4124 2.569354 GGTTGGGGCGATTGCAACA 61.569 57.895 0.00 1.77 45.35 3.33
2734 4212 2.672996 CGACAACCCTTGCCCTGG 60.673 66.667 0.00 0.00 0.00 4.45
2736 4214 2.430367 GTCGACAACCCTTGCCCT 59.570 61.111 11.55 0.00 0.00 5.19
2815 4294 3.140141 AATTGCGCATGGGTCGGG 61.140 61.111 12.75 0.00 0.00 5.14
2818 4297 2.869233 AATACAATTGCGCATGGGTC 57.131 45.000 12.75 4.58 0.00 4.46
2837 4316 3.286751 GCGCTTGGGTGTGCTGAA 61.287 61.111 0.00 0.00 40.01 3.02
2866 4345 1.595794 CCGGTTGCGGTCACATTATAC 59.404 52.381 0.00 0.00 0.00 1.47


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

AutoCloner maintained by Alex Coulton.