Multiple sequence alignment - TraesCS3D01G027000

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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 TraesCS3D01G027000 chr3D 100.000 3442 0 0 1 3442 9133192 9129751 0.000000e+00 6357.0
1 TraesCS3D01G027000 chr3D 91.478 575 27 4 14 570 55366131 55365561 0.000000e+00 771.0
2 TraesCS3D01G027000 chr3D 96.514 459 15 1 4 461 606928039 606927581 0.000000e+00 758.0
3 TraesCS3D01G027000 chr3D 78.811 774 118 33 1125 1870 9199567 9200322 2.400000e-131 479.0
4 TraesCS3D01G027000 chr3A 87.337 1532 74 40 622 2108 11864799 11866255 0.000000e+00 1644.0
5 TraesCS3D01G027000 chr3A 94.175 618 30 2 2826 3437 44440283 44439666 0.000000e+00 937.0
6 TraesCS3D01G027000 chr3A 88.446 502 32 12 2125 2604 11866619 11867116 1.780000e-162 582.0
7 TraesCS3D01G027000 chr3A 94.898 196 8 1 2586 2779 11869823 11870018 4.320000e-79 305.0
8 TraesCS3D01G027000 chr3A 95.833 48 2 0 2780 2827 11870077 11870124 1.020000e-10 78.7
9 TraesCS3D01G027000 chr3B 92.818 1100 71 4 969 2062 11475485 11474388 0.000000e+00 1587.0
10 TraesCS3D01G027000 chr3B 93.730 622 32 3 2826 3442 620824364 620824983 0.000000e+00 926.0
11 TraesCS3D01G027000 chr3B 77.778 1044 178 40 1100 2108 11561656 11562680 8.220000e-166 593.0
12 TraesCS3D01G027000 chr3B 75.000 1016 182 44 1125 2108 11511047 11512022 1.490000e-108 403.0
13 TraesCS3D01G027000 chr3B 74.529 1009 178 45 1125 2108 3205430 3206384 1.950000e-97 366.0
14 TraesCS3D01G027000 chr3B 79.213 356 47 18 622 972 11501407 11501074 4.470000e-54 222.0
15 TraesCS3D01G027000 chr3B 85.470 117 1 1 3267 3383 620824925 620825025 1.310000e-19 108.0
16 TraesCS3D01G027000 chr3B 93.750 48 3 0 2780 2827 11472923 11472876 4.760000e-09 73.1
17 TraesCS3D01G027000 chr3B 95.238 42 2 0 2391 2432 3206878 3206919 2.220000e-07 67.6
18 TraesCS3D01G027000 chr7D 98.551 621 7 2 2823 3442 608564900 608565519 0.000000e+00 1096.0
19 TraesCS3D01G027000 chr7D 91.115 574 29 4 14 569 31108490 31107921 0.000000e+00 758.0
20 TraesCS3D01G027000 chr7D 76.657 1041 186 41 1100 2108 44538293 44539308 1.090000e-144 523.0
21 TraesCS3D01G027000 chr7D 78.893 488 79 17 1100 1576 44530526 44531000 3.340000e-80 309.0
22 TraesCS3D01G027000 chr7D 78.643 398 69 10 1722 2108 43168789 43168397 2.050000e-62 250.0
23 TraesCS3D01G027000 chr7D 94.737 38 2 0 2390 2427 44702093 44702130 3.710000e-05 60.2
24 TraesCS3D01G027000 chr2D 98.544 618 8 1 2825 3442 589476904 589477520 0.000000e+00 1090.0
25 TraesCS3D01G027000 chr2D 94.771 612 30 2 1 611 189689693 189689083 0.000000e+00 952.0
26 TraesCS3D01G027000 chr2D 91.667 576 25 4 14 570 406204145 406204716 0.000000e+00 776.0
27 TraesCS3D01G027000 chr2D 82.500 200 31 4 1104 1301 19016129 19016326 4.570000e-39 172.0
28 TraesCS3D01G027000 chr1D 97.407 617 15 1 2826 3442 257429351 257429966 0.000000e+00 1050.0
29 TraesCS3D01G027000 chr4D 94.780 613 29 3 1 611 400894243 400894854 0.000000e+00 952.0
30 TraesCS3D01G027000 chr4D 94.617 613 29 4 1 611 472924960 472925570 0.000000e+00 946.0
31 TraesCS3D01G027000 chr2B 91.722 604 32 5 1 586 547098206 547098809 0.000000e+00 822.0
32 TraesCS3D01G027000 chr7B 92.389 565 21 5 2825 3384 322399941 322399394 0.000000e+00 785.0
33 TraesCS3D01G027000 chr6D 91.840 576 28 6 14 570 49804276 49803701 0.000000e+00 785.0
34 TraesCS3D01G027000 chr7A 91.681 565 42 5 2823 3383 679208615 679209178 0.000000e+00 778.0
35 TraesCS3D01G027000 chr7A 91.358 567 41 6 2823 3383 679216454 679217018 0.000000e+00 769.0
36 TraesCS3D01G027000 chr7A 90.861 569 43 5 2823 3383 679200778 679201345 0.000000e+00 754.0
37 TraesCS3D01G027000 chr7A 76.227 1039 194 35 1100 2108 47007273 47008288 5.130000e-138 501.0
38 TraesCS3D01G027000 chr7A 86.824 425 36 12 206 611 219167861 219167438 1.130000e-124 457.0
39 TraesCS3D01G027000 chr7A 78.586 481 88 8 1100 1575 47283116 47283586 1.550000e-78 303.0
40 TraesCS3D01G027000 chr7A 77.664 488 85 17 1100 1576 47000518 47000992 3.380000e-70 276.0
41 TraesCS3D01G027000 chr7A 77.453 479 90 12 1103 1575 47225317 47224851 1.570000e-68 270.0
42 TraesCS3D01G027000 chr7A 76.908 511 92 19 1613 2107 47283657 47284157 2.040000e-67 267.0
43 TraesCS3D01G027000 chr5D 95.864 411 16 1 206 616 72364490 72364081 0.000000e+00 664.0
44 TraesCS3D01G027000 chr4A 75.575 1044 192 46 1100 2108 656249757 656250772 1.130000e-124 457.0
45 TraesCS3D01G027000 chr4A 74.495 1039 212 35 1100 2108 656030007 656031022 5.350000e-108 401.0
46 TraesCS3D01G027000 chr4A 73.900 1023 199 50 1123 2106 656550842 656551835 7.070000e-92 348.0
47 TraesCS3D01G027000 chr4A 76.054 735 128 29 1402 2108 655659099 655659813 4.250000e-89 339.0
48 TraesCS3D01G027000 chr4A 77.344 512 92 20 1613 2108 655442948 655443451 7.270000e-72 281.0
49 TraesCS3D01G027000 chr4A 76.628 522 97 21 1601 2108 656472933 656473443 7.320000e-67 265.0
50 TraesCS3D01G027000 chr5B 82.791 430 38 15 206 611 860390 860807 5.470000e-93 351.0


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 TraesCS3D01G027000 chr3D 9129751 9133192 3441 True 6357.000 6357 100.0000 1 3442 1 chr3D.!!$R1 3441
1 TraesCS3D01G027000 chr3D 55365561 55366131 570 True 771.000 771 91.4780 14 570 1 chr3D.!!$R2 556
2 TraesCS3D01G027000 chr3D 9199567 9200322 755 False 479.000 479 78.8110 1125 1870 1 chr3D.!!$F1 745
3 TraesCS3D01G027000 chr3A 44439666 44440283 617 True 937.000 937 94.1750 2826 3437 1 chr3A.!!$R1 611
4 TraesCS3D01G027000 chr3A 11864799 11870124 5325 False 652.425 1644 91.6285 622 2827 4 chr3A.!!$F1 2205
5 TraesCS3D01G027000 chr3B 11472876 11475485 2609 True 830.050 1587 93.2840 969 2827 2 chr3B.!!$R2 1858
6 TraesCS3D01G027000 chr3B 11561656 11562680 1024 False 593.000 593 77.7780 1100 2108 1 chr3B.!!$F2 1008
7 TraesCS3D01G027000 chr3B 620824364 620825025 661 False 517.000 926 89.6000 2826 3442 2 chr3B.!!$F4 616
8 TraesCS3D01G027000 chr3B 11511047 11512022 975 False 403.000 403 75.0000 1125 2108 1 chr3B.!!$F1 983
9 TraesCS3D01G027000 chr3B 3205430 3206919 1489 False 216.800 366 84.8835 1125 2432 2 chr3B.!!$F3 1307
10 TraesCS3D01G027000 chr7D 608564900 608565519 619 False 1096.000 1096 98.5510 2823 3442 1 chr7D.!!$F4 619
11 TraesCS3D01G027000 chr7D 31107921 31108490 569 True 758.000 758 91.1150 14 569 1 chr7D.!!$R1 555
12 TraesCS3D01G027000 chr7D 44538293 44539308 1015 False 523.000 523 76.6570 1100 2108 1 chr7D.!!$F2 1008
13 TraesCS3D01G027000 chr2D 589476904 589477520 616 False 1090.000 1090 98.5440 2825 3442 1 chr2D.!!$F3 617
14 TraesCS3D01G027000 chr2D 189689083 189689693 610 True 952.000 952 94.7710 1 611 1 chr2D.!!$R1 610
15 TraesCS3D01G027000 chr2D 406204145 406204716 571 False 776.000 776 91.6670 14 570 1 chr2D.!!$F2 556
16 TraesCS3D01G027000 chr1D 257429351 257429966 615 False 1050.000 1050 97.4070 2826 3442 1 chr1D.!!$F1 616
17 TraesCS3D01G027000 chr4D 400894243 400894854 611 False 952.000 952 94.7800 1 611 1 chr4D.!!$F1 610
18 TraesCS3D01G027000 chr4D 472924960 472925570 610 False 946.000 946 94.6170 1 611 1 chr4D.!!$F2 610
19 TraesCS3D01G027000 chr2B 547098206 547098809 603 False 822.000 822 91.7220 1 586 1 chr2B.!!$F1 585
20 TraesCS3D01G027000 chr7B 322399394 322399941 547 True 785.000 785 92.3890 2825 3384 1 chr7B.!!$R1 559
21 TraesCS3D01G027000 chr6D 49803701 49804276 575 True 785.000 785 91.8400 14 570 1 chr6D.!!$R1 556
22 TraesCS3D01G027000 chr7A 679208615 679209178 563 False 778.000 778 91.6810 2823 3383 1 chr7A.!!$F4 560
23 TraesCS3D01G027000 chr7A 679216454 679217018 564 False 769.000 769 91.3580 2823 3383 1 chr7A.!!$F5 560
24 TraesCS3D01G027000 chr7A 679200778 679201345 567 False 754.000 754 90.8610 2823 3383 1 chr7A.!!$F3 560
25 TraesCS3D01G027000 chr7A 47007273 47008288 1015 False 501.000 501 76.2270 1100 2108 1 chr7A.!!$F2 1008
26 TraesCS3D01G027000 chr7A 47283116 47284157 1041 False 285.000 303 77.7470 1100 2107 2 chr7A.!!$F6 1007
27 TraesCS3D01G027000 chr4A 656249757 656250772 1015 False 457.000 457 75.5750 1100 2108 1 chr4A.!!$F4 1008
28 TraesCS3D01G027000 chr4A 656030007 656031022 1015 False 401.000 401 74.4950 1100 2108 1 chr4A.!!$F3 1008
29 TraesCS3D01G027000 chr4A 656550842 656551835 993 False 348.000 348 73.9000 1123 2106 1 chr4A.!!$F6 983
30 TraesCS3D01G027000 chr4A 655659099 655659813 714 False 339.000 339 76.0540 1402 2108 1 chr4A.!!$F2 706
31 TraesCS3D01G027000 chr4A 655442948 655443451 503 False 281.000 281 77.3440 1613 2108 1 chr4A.!!$F1 495
32 TraesCS3D01G027000 chr4A 656472933 656473443 510 False 265.000 265 76.6280 1601 2108 1 chr4A.!!$F5 507

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
901 961 0.037232 AGAAGTAGCACGGCTCAACC 60.037 55.0 1.46 0.0 40.44 3.77 F
1035 1099 0.028505 TACGTAGATCGCCGAAGCAC 59.971 55.0 12.95 0.0 44.19 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2338 2994 0.532862 CCACCACTACATCGATGCCC 60.533 60.0 25.11 0.0 0.00 5.36 R
2648 6130 0.719465 CGCCAGCGGTAAACTAACAG 59.281 55.0 3.61 0.0 35.56 3.16 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
348 350 3.051479 CACGCTGCTGCATCCACA 61.051 61.111 16.29 0.00 39.64 4.17
356 359 1.761784 TGCTGCATCCACAAAGGTTTT 59.238 42.857 0.00 0.00 39.02 2.43
557 579 1.071385 GGATCTGACGATGCAAGGGAT 59.929 52.381 0.00 0.00 37.85 3.85
570 592 2.034878 CAAGGGATCAGATCTGACGGA 58.965 52.381 27.37 5.89 43.11 4.69
571 593 1.698506 AGGGATCAGATCTGACGGAC 58.301 55.000 27.37 16.94 43.11 4.79
573 595 0.318275 GGATCAGATCTGACGGACGC 60.318 60.000 27.37 12.08 43.11 5.19
574 596 0.382158 GATCAGATCTGACGGACGCA 59.618 55.000 27.37 3.10 43.11 5.24
591 613 2.048877 AGTTGGACCGGCGTAACG 60.049 61.111 6.01 0.00 0.00 3.18
592 614 2.049248 GTTGGACCGGCGTAACGA 60.049 61.111 6.01 0.00 35.47 3.85
593 615 2.049248 TTGGACCGGCGTAACGAC 60.049 61.111 6.01 0.00 35.47 4.34
595 617 2.202531 GGACCGGCGTAACGACTC 60.203 66.667 6.01 0.00 35.47 3.36
603 625 2.202531 GTAACGACTCGGCCGGTC 60.203 66.667 27.83 27.38 0.00 4.79
617 639 2.509336 GGTCGACCGGCATCAGTG 60.509 66.667 20.85 0.00 0.00 3.66
618 640 2.509336 GTCGACCGGCATCAGTGG 60.509 66.667 3.51 0.00 0.00 4.00
619 641 4.451150 TCGACCGGCATCAGTGGC 62.451 66.667 0.00 0.00 46.68 5.01
638 660 1.611491 GCCAACCAGAAAACCATCGAA 59.389 47.619 0.00 0.00 0.00 3.71
639 661 2.231235 GCCAACCAGAAAACCATCGAAT 59.769 45.455 0.00 0.00 0.00 3.34
640 662 3.306019 GCCAACCAGAAAACCATCGAATT 60.306 43.478 0.00 0.00 0.00 2.17
648 670 6.363357 CCAGAAAACCATCGAATTTCAAACTC 59.637 38.462 14.60 2.02 35.91 3.01
652 674 9.458374 GAAAACCATCGAATTTCAAACTCTAAA 57.542 29.630 0.00 0.00 34.12 1.85
671 694 8.601546 ACTCTAAAGATTCAGTCAAAGAAGGAT 58.398 33.333 0.00 0.00 0.00 3.24
695 718 2.075338 CAAAGAAGTGCAGCCTCTCTC 58.925 52.381 0.00 0.00 0.00 3.20
705 728 2.386779 CAGCCTCTCTCTCTCCATCAA 58.613 52.381 0.00 0.00 0.00 2.57
706 729 2.967201 CAGCCTCTCTCTCTCCATCAAT 59.033 50.000 0.00 0.00 0.00 2.57
707 730 3.388676 CAGCCTCTCTCTCTCCATCAATT 59.611 47.826 0.00 0.00 0.00 2.32
708 731 3.642848 AGCCTCTCTCTCTCCATCAATTC 59.357 47.826 0.00 0.00 0.00 2.17
709 732 3.244181 GCCTCTCTCTCTCCATCAATTCC 60.244 52.174 0.00 0.00 0.00 3.01
710 733 3.966006 CCTCTCTCTCTCCATCAATTCCA 59.034 47.826 0.00 0.00 0.00 3.53
720 743 3.659195 TCCATCAATTCCATCCAGCCTAT 59.341 43.478 0.00 0.00 0.00 2.57
735 758 0.107703 CCTATGCTCCACGGCTGAAA 60.108 55.000 0.00 0.00 0.00 2.69
766 795 1.142748 CAGCTCGTCCAGTCCCATC 59.857 63.158 0.00 0.00 0.00 3.51
812 866 2.158842 CCATCCTGCTCCTCCTTTACTG 60.159 54.545 0.00 0.00 0.00 2.74
816 870 1.002430 CTGCTCCTCCTTTACTGTGCA 59.998 52.381 0.00 0.00 0.00 4.57
839 893 2.264166 GACGAGGCAGCAGCTTCT 59.736 61.111 11.36 0.00 44.03 2.85
842 896 2.511145 GAGGCAGCAGCTTCTCCG 60.511 66.667 5.94 0.00 43.00 4.63
845 899 2.511145 GCAGCAGCTTCTCCGAGG 60.511 66.667 0.00 0.00 37.91 4.63
862 922 1.593750 GGCTTCTCGCTCGCATCAT 60.594 57.895 0.00 0.00 39.13 2.45
865 925 1.130140 CTTCTCGCTCGCATCATCTG 58.870 55.000 0.00 0.00 0.00 2.90
866 926 0.249197 TTCTCGCTCGCATCATCTGG 60.249 55.000 0.00 0.00 0.00 3.86
867 927 2.279717 TCGCTCGCATCATCTGGC 60.280 61.111 0.00 0.00 0.00 4.85
868 928 2.279985 CGCTCGCATCATCTGGCT 60.280 61.111 0.00 0.00 0.00 4.75
869 929 2.308769 CGCTCGCATCATCTGGCTC 61.309 63.158 0.00 0.00 0.00 4.70
886 946 1.919600 CTCTCCCAGGCCCCAAGAAG 61.920 65.000 0.00 0.00 0.00 2.85
892 952 0.678048 CAGGCCCCAAGAAGTAGCAC 60.678 60.000 0.00 0.00 0.00 4.40
894 954 1.745489 GCCCCAAGAAGTAGCACGG 60.745 63.158 0.00 0.00 0.00 4.94
895 955 1.745489 CCCCAAGAAGTAGCACGGC 60.745 63.158 0.00 0.00 0.00 5.68
897 957 0.741221 CCCAAGAAGTAGCACGGCTC 60.741 60.000 1.46 0.00 40.44 4.70
898 958 0.037326 CCAAGAAGTAGCACGGCTCA 60.037 55.000 1.46 0.00 40.44 4.26
899 959 1.608025 CCAAGAAGTAGCACGGCTCAA 60.608 52.381 1.46 0.00 40.44 3.02
900 960 1.461127 CAAGAAGTAGCACGGCTCAAC 59.539 52.381 1.46 0.00 40.44 3.18
901 961 0.037232 AGAAGTAGCACGGCTCAACC 60.037 55.000 1.46 0.00 40.44 3.77
902 962 0.320421 GAAGTAGCACGGCTCAACCA 60.320 55.000 1.46 0.00 40.44 3.67
903 963 0.602905 AAGTAGCACGGCTCAACCAC 60.603 55.000 1.46 0.00 40.44 4.16
904 964 1.301401 GTAGCACGGCTCAACCACA 60.301 57.895 1.46 0.00 40.44 4.17
905 965 0.882927 GTAGCACGGCTCAACCACAA 60.883 55.000 1.46 0.00 40.44 3.33
906 966 0.882927 TAGCACGGCTCAACCACAAC 60.883 55.000 1.46 0.00 40.44 3.32
915 975 2.590575 AACCACAACCAGGCGACG 60.591 61.111 0.00 0.00 0.00 5.12
939 999 3.631127 GAAATCGCCGCTCTCGCC 61.631 66.667 0.00 0.00 0.00 5.54
949 1009 4.824515 CTCTCGCCCGGTCCTCCT 62.825 72.222 0.00 0.00 0.00 3.69
950 1010 4.816984 TCTCGCCCGGTCCTCCTC 62.817 72.222 0.00 0.00 0.00 3.71
957 1017 3.839432 CGGTCCTCCTCCGGCTTC 61.839 72.222 0.00 0.00 43.68 3.86
958 1018 3.471806 GGTCCTCCTCCGGCTTCC 61.472 72.222 0.00 0.00 0.00 3.46
962 1022 4.214327 CTCCTCCGGCTTCCGCTC 62.214 72.222 0.00 0.00 46.86 5.03
1002 1066 1.744320 CTGCCCGTCCATCGTATCCA 61.744 60.000 0.00 0.00 37.94 3.41
1007 1071 3.804411 GCCCGTCCATCGTATCCATTAAA 60.804 47.826 0.00 0.00 37.94 1.52
1035 1099 0.028505 TACGTAGATCGCCGAAGCAC 59.971 55.000 12.95 0.00 44.19 4.40
1061 1127 4.690719 TTGCGCCCAATCCGTCGT 62.691 61.111 4.18 0.00 0.00 4.34
1071 1137 3.431207 CCCAATCCGTCGTACCACTAATT 60.431 47.826 0.00 0.00 0.00 1.40
1385 1461 0.764369 TCCTCCCTGTGCAGTCTTGT 60.764 55.000 0.00 0.00 0.00 3.16
1396 1472 1.512926 CAGTCTTGTCCTTTCGGGTG 58.487 55.000 0.00 0.00 36.25 4.61
1449 1525 2.577059 GTGTCGCGGGAATCCAGA 59.423 61.111 6.13 0.00 0.00 3.86
1461 1537 4.039730 CGGGAATCCAGATTCTACATCTGT 59.960 45.833 17.51 0.00 44.90 3.41
1581 1665 1.760613 GGAGAACACCGGGTGATATGA 59.239 52.381 32.72 0.00 36.96 2.15
1596 1680 9.091784 CGGGTGATATGAATGTTAGAATATCAG 57.908 37.037 4.82 0.00 40.74 2.90
1663 1786 1.243342 CCAGCCAAGACGCATCCAAA 61.243 55.000 0.00 0.00 0.00 3.28
2090 2256 1.967762 CATTGTGACGTTGATGGTGC 58.032 50.000 0.00 0.00 0.00 5.01
2108 2274 0.733150 GCGTTCTTAGGGAATGTGGC 59.267 55.000 0.00 0.00 41.59 5.01
2109 2275 1.379527 CGTTCTTAGGGAATGTGGCC 58.620 55.000 0.00 0.00 36.49 5.36
2110 2276 1.379527 GTTCTTAGGGAATGTGGCCG 58.620 55.000 0.00 0.00 36.24 6.13
2111 2277 0.988832 TTCTTAGGGAATGTGGCCGT 59.011 50.000 0.00 0.00 0.00 5.68
2112 2278 1.868713 TCTTAGGGAATGTGGCCGTA 58.131 50.000 0.00 0.00 0.00 4.02
2113 2279 2.189676 TCTTAGGGAATGTGGCCGTAA 58.810 47.619 0.00 0.00 35.28 3.18
2114 2280 2.093341 TCTTAGGGAATGTGGCCGTAAC 60.093 50.000 0.00 0.00 33.59 2.50
2115 2281 1.575419 TAGGGAATGTGGCCGTAACT 58.425 50.000 0.00 0.00 0.00 2.24
2116 2282 0.696501 AGGGAATGTGGCCGTAACTT 59.303 50.000 0.00 0.00 0.00 2.66
2117 2283 1.092348 GGGAATGTGGCCGTAACTTC 58.908 55.000 0.00 0.00 0.00 3.01
2118 2284 1.339727 GGGAATGTGGCCGTAACTTCT 60.340 52.381 0.00 0.00 0.00 2.85
2119 2285 2.433436 GGAATGTGGCCGTAACTTCTT 58.567 47.619 0.00 0.00 0.00 2.52
2121 2287 3.621715 GGAATGTGGCCGTAACTTCTTAG 59.378 47.826 0.00 0.00 0.00 2.18
2123 2289 1.276989 TGTGGCCGTAACTTCTTAGGG 59.723 52.381 0.00 0.00 39.84 3.53
2275 2912 9.371136 TGATCTTTCATGTTCAGTATACACTTC 57.629 33.333 5.50 0.00 30.46 3.01
2308 2947 1.298157 TTTTGGCATCTGGTCGCTCG 61.298 55.000 0.00 0.00 0.00 5.03
2320 2959 3.793144 CGCTCGGGCTCTTTGTGC 61.793 66.667 5.36 0.00 36.09 4.57
2338 2994 2.092838 GTGCGGAGATGTTTCTTTCTCG 59.907 50.000 0.00 0.00 39.42 4.04
2354 3010 1.739667 TCGGGCATCGATGTAGTGG 59.260 57.895 25.47 11.47 43.74 4.00
2386 3075 6.560711 AGTTTGCGTCTGACAAGTAATTTTT 58.439 32.000 8.73 0.00 0.00 1.94
2389 3078 8.964150 GTTTGCGTCTGACAAGTAATTTTTATT 58.036 29.630 8.73 0.00 0.00 1.40
2485 3240 2.104792 TGAAGAACTGGCAAGCAGTACT 59.895 45.455 0.00 0.00 31.85 2.73
2486 3241 2.938956 AGAACTGGCAAGCAGTACTT 57.061 45.000 0.00 0.00 40.05 2.24
2545 3300 1.032014 TGGCTGAAGCTTTTGTGTCC 58.968 50.000 0.00 0.00 41.70 4.02
2563 3318 2.028112 GTCCAGGATTTGGGCCTTTTTC 60.028 50.000 4.53 0.00 46.36 2.29
2577 3334 5.497474 GGCCTTTTTCTGTGTAGGAATAGA 58.503 41.667 0.00 0.00 0.00 1.98
2588 3345 8.144478 TCTGTGTAGGAATAGATTACAAGATGC 58.856 37.037 0.00 0.00 0.00 3.91
2648 6130 4.430007 TGGTGATAGTCTGTTTACGATGC 58.570 43.478 0.00 0.00 0.00 3.91
2660 6142 6.366877 TCTGTTTACGATGCTGTTAGTTTACC 59.633 38.462 0.00 0.00 0.00 2.85
2715 6213 2.224992 TGCAGCCTCTAACCCAAATCAA 60.225 45.455 0.00 0.00 0.00 2.57
2816 6374 4.763279 TGCTGTCTTGAACATCATGTCAAT 59.237 37.500 0.00 0.00 37.23 2.57
2817 6375 5.939296 TGCTGTCTTGAACATCATGTCAATA 59.061 36.000 0.00 0.00 37.23 1.90
2818 6376 6.600427 TGCTGTCTTGAACATCATGTCAATAT 59.400 34.615 0.00 0.00 37.23 1.28
2819 6377 7.121611 TGCTGTCTTGAACATCATGTCAATATT 59.878 33.333 0.00 0.00 37.23 1.28
2820 6378 7.642978 GCTGTCTTGAACATCATGTCAATATTC 59.357 37.037 0.00 0.00 37.23 1.75
2821 6379 8.797350 TGTCTTGAACATCATGTCAATATTCT 57.203 30.769 0.00 0.00 31.20 2.40
2822 6380 9.889128 TGTCTTGAACATCATGTCAATATTCTA 57.111 29.630 0.00 0.00 31.20 2.10
3036 6594 2.904866 GTGGGCTGGTGCGTTTGA 60.905 61.111 0.00 0.00 40.82 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
296 298 2.343758 GGTCGAGGTTGCAGCTCA 59.656 61.111 13.30 0.00 42.53 4.26
356 359 4.801330 ATGTCGTCTTCATGTGGTTCTA 57.199 40.909 0.00 0.00 0.00 2.10
557 579 0.960861 ACTGCGTCCGTCAGATCTGA 60.961 55.000 21.67 21.67 37.24 3.27
573 595 2.377310 CGTTACGCCGGTCCAACTG 61.377 63.158 1.90 0.00 0.00 3.16
574 596 2.048877 CGTTACGCCGGTCCAACT 60.049 61.111 1.90 0.00 0.00 3.16
586 608 2.202531 GACCGGCCGAGTCGTTAC 60.203 66.667 30.73 6.68 0.00 2.50
611 633 1.963515 GTTTTCTGGTTGGCCACTGAT 59.036 47.619 3.88 0.00 40.46 2.90
612 634 1.398692 GTTTTCTGGTTGGCCACTGA 58.601 50.000 3.88 1.06 40.46 3.41
613 635 0.389025 GGTTTTCTGGTTGGCCACTG 59.611 55.000 3.88 0.00 40.46 3.66
614 636 0.032615 TGGTTTTCTGGTTGGCCACT 60.033 50.000 3.88 0.00 40.46 4.00
615 637 1.000843 GATGGTTTTCTGGTTGGCCAC 59.999 52.381 3.88 0.00 40.46 5.01
616 638 1.337118 GATGGTTTTCTGGTTGGCCA 58.663 50.000 0.00 0.00 43.73 5.36
617 639 0.243636 CGATGGTTTTCTGGTTGGCC 59.756 55.000 0.00 0.00 0.00 5.36
618 640 1.243902 TCGATGGTTTTCTGGTTGGC 58.756 50.000 0.00 0.00 0.00 4.52
619 641 4.519540 AATTCGATGGTTTTCTGGTTGG 57.480 40.909 0.00 0.00 0.00 3.77
620 642 5.527951 TGAAATTCGATGGTTTTCTGGTTG 58.472 37.500 10.19 0.00 32.02 3.77
621 643 5.782893 TGAAATTCGATGGTTTTCTGGTT 57.217 34.783 10.19 0.00 32.02 3.67
622 644 5.782893 TTGAAATTCGATGGTTTTCTGGT 57.217 34.783 10.19 0.00 32.02 4.00
623 645 6.215845 AGTTTGAAATTCGATGGTTTTCTGG 58.784 36.000 10.19 0.00 32.02 3.86
624 646 7.141363 AGAGTTTGAAATTCGATGGTTTTCTG 58.859 34.615 10.19 0.00 32.02 3.02
631 653 9.495754 GAATCTTTAGAGTTTGAAATTCGATGG 57.504 33.333 0.00 0.00 0.00 3.51
640 662 9.613428 TCTTTGACTGAATCTTTAGAGTTTGAA 57.387 29.630 0.00 0.00 0.00 2.69
648 670 9.447157 AGAATCCTTCTTTGACTGAATCTTTAG 57.553 33.333 0.00 0.00 36.36 1.85
652 674 7.013823 TGAGAATCCTTCTTTGACTGAATCT 57.986 36.000 0.00 0.00 40.87 2.40
671 694 2.105477 AGAGGCTGCACTTCTTTGAGAA 59.895 45.455 0.50 0.00 32.50 2.87
695 718 3.147629 GCTGGATGGAATTGATGGAGAG 58.852 50.000 0.00 0.00 0.00 3.20
720 743 1.600636 CCTTTTCAGCCGTGGAGCA 60.601 57.895 0.00 0.00 34.23 4.26
788 817 2.771762 GGAGGAGCAGGATGGGCT 60.772 66.667 0.00 0.00 46.07 5.19
789 818 1.931007 AAAGGAGGAGCAGGATGGGC 61.931 60.000 0.00 0.00 35.86 5.36
790 819 1.141858 GTAAAGGAGGAGCAGGATGGG 59.858 57.143 0.00 0.00 35.86 4.00
791 820 2.122768 AGTAAAGGAGGAGCAGGATGG 58.877 52.381 0.00 0.00 35.86 3.51
794 823 1.902508 CACAGTAAAGGAGGAGCAGGA 59.097 52.381 0.00 0.00 0.00 3.86
795 824 1.677217 GCACAGTAAAGGAGGAGCAGG 60.677 57.143 0.00 0.00 0.00 4.85
796 825 1.002430 TGCACAGTAAAGGAGGAGCAG 59.998 52.381 0.00 0.00 0.00 4.24
797 826 1.055849 TGCACAGTAAAGGAGGAGCA 58.944 50.000 0.00 0.00 0.00 4.26
812 866 3.106407 GCCTCGTCTGTCGTGCAC 61.106 66.667 6.82 6.82 40.80 4.57
816 870 3.274455 CTGCTGCCTCGTCTGTCGT 62.274 63.158 0.00 0.00 40.80 4.34
852 912 0.945265 GAGAGCCAGATGATGCGAGC 60.945 60.000 0.00 0.00 0.00 5.03
866 926 4.120755 CTTGGGGCCTGGGAGAGC 62.121 72.222 0.84 0.00 0.00 4.09
867 927 1.919600 CTTCTTGGGGCCTGGGAGAG 61.920 65.000 0.84 0.00 0.00 3.20
868 928 1.925455 CTTCTTGGGGCCTGGGAGA 60.925 63.158 0.84 0.00 0.00 3.71
869 929 0.914417 TACTTCTTGGGGCCTGGGAG 60.914 60.000 0.84 0.36 0.00 4.30
875 935 1.745489 CGTGCTACTTCTTGGGGCC 60.745 63.158 0.00 0.00 0.00 5.80
877 937 1.745489 GCCGTGCTACTTCTTGGGG 60.745 63.158 0.00 0.00 0.00 4.96
886 946 0.882927 TTGTGGTTGAGCCGTGCTAC 60.883 55.000 0.00 0.00 39.88 3.58
892 952 2.260869 CCTGGTTGTGGTTGAGCCG 61.261 63.158 0.00 0.00 41.21 5.52
894 954 2.908073 CGCCTGGTTGTGGTTGAGC 61.908 63.158 0.00 0.00 0.00 4.26
895 955 1.227823 TCGCCTGGTTGTGGTTGAG 60.228 57.895 0.00 0.00 0.00 3.02
897 957 2.892334 CGTCGCCTGGTTGTGGTTG 61.892 63.158 0.00 0.00 0.00 3.77
898 958 2.590575 CGTCGCCTGGTTGTGGTT 60.591 61.111 0.00 0.00 0.00 3.67
954 1014 4.379221 CTTACGTCGGAGCGGAAG 57.621 61.111 9.44 9.44 44.84 3.46
955 1015 2.180017 GCTTACGTCGGAGCGGAA 59.820 61.111 7.05 2.36 35.98 4.30
956 1016 3.818787 GGCTTACGTCGGAGCGGA 61.819 66.667 14.18 0.00 39.78 5.54
957 1017 4.867599 GGGCTTACGTCGGAGCGG 62.868 72.222 14.18 0.00 39.78 5.52
958 1018 3.753070 GAGGGCTTACGTCGGAGCG 62.753 68.421 14.18 0.00 39.78 5.03
959 1019 2.104530 GAGGGCTTACGTCGGAGC 59.895 66.667 12.75 12.75 38.17 4.70
960 1020 1.728672 GAGAGGGCTTACGTCGGAG 59.271 63.158 0.00 0.00 38.94 4.63
961 1021 2.110967 CGAGAGGGCTTACGTCGGA 61.111 63.158 0.00 0.00 38.94 4.55
962 1022 2.408022 CGAGAGGGCTTACGTCGG 59.592 66.667 0.00 0.00 38.94 4.79
990 1050 4.940905 TCGGTTTAATGGATACGATGGA 57.059 40.909 0.00 0.00 42.51 3.41
1002 1066 6.074676 GCGATCTACGTACAAATCGGTTTAAT 60.075 38.462 21.93 0.00 44.60 1.40
1007 1071 2.542411 GGCGATCTACGTACAAATCGGT 60.542 50.000 21.93 0.00 44.60 4.69
1035 1099 1.399791 GATTGGGCGCAAGAAGAGAAG 59.600 52.381 21.44 0.00 43.02 2.85
1071 1137 9.681062 TCTTCTAAGAAAGTGGAAGAAGAAAAA 57.319 29.630 9.91 0.00 45.52 1.94
1085 1151 3.065095 GGCATGCTGCTCTTCTAAGAAAG 59.935 47.826 18.92 0.00 44.28 2.62
1156 1223 1.202313 CGGACAAGGATCTCTTCGACC 60.202 57.143 0.00 0.00 32.41 4.79
1449 1525 2.104281 GGCCGGGTTACAGATGTAGAAT 59.896 50.000 2.18 0.00 0.00 2.40
1578 1662 7.754851 TGCATGCTGATATTCTAACATTCAT 57.245 32.000 20.33 0.00 0.00 2.57
1581 1665 7.664318 TGAGATGCATGCTGATATTCTAACATT 59.336 33.333 20.33 0.00 0.00 2.71
1596 1680 1.530771 AGGGGACTGAGATGCATGC 59.469 57.895 11.82 11.82 41.13 4.06
1663 1786 0.543749 CTTCCTGAATCTTCCGGCCT 59.456 55.000 0.00 0.00 32.30 5.19
2090 2256 1.379527 GGCCACATTCCCTAAGAACG 58.620 55.000 0.00 0.00 37.29 3.95
2108 2274 5.484715 TCAACATTCCCTAAGAAGTTACGG 58.515 41.667 0.00 0.00 38.07 4.02
2109 2275 7.429636 TTTCAACATTCCCTAAGAAGTTACG 57.570 36.000 0.00 0.00 38.07 3.18
2110 2276 7.808381 GCTTTTCAACATTCCCTAAGAAGTTAC 59.192 37.037 0.00 0.00 38.07 2.50
2111 2277 7.504238 TGCTTTTCAACATTCCCTAAGAAGTTA 59.496 33.333 0.00 0.00 38.07 2.24
2112 2278 6.323739 TGCTTTTCAACATTCCCTAAGAAGTT 59.676 34.615 0.00 0.00 38.07 2.66
2113 2279 5.833131 TGCTTTTCAACATTCCCTAAGAAGT 59.167 36.000 0.00 0.00 38.07 3.01
2114 2280 6.331369 TGCTTTTCAACATTCCCTAAGAAG 57.669 37.500 0.00 0.00 38.07 2.85
2115 2281 6.493115 TCATGCTTTTCAACATTCCCTAAGAA 59.507 34.615 0.00 0.00 39.32 2.52
2116 2282 6.009589 TCATGCTTTTCAACATTCCCTAAGA 58.990 36.000 0.00 0.00 0.00 2.10
2117 2283 6.271488 TCATGCTTTTCAACATTCCCTAAG 57.729 37.500 0.00 0.00 0.00 2.18
2118 2284 6.662865 TTCATGCTTTTCAACATTCCCTAA 57.337 33.333 0.00 0.00 0.00 2.69
2119 2285 6.295236 CCTTTCATGCTTTTCAACATTCCCTA 60.295 38.462 0.00 0.00 0.00 3.53
2121 2287 4.692155 CCTTTCATGCTTTTCAACATTCCC 59.308 41.667 0.00 0.00 0.00 3.97
2123 2289 4.751098 TGCCTTTCATGCTTTTCAACATTC 59.249 37.500 0.00 0.00 0.00 2.67
2199 2836 5.176407 TGAACTAACCATTTCAACAACCG 57.824 39.130 0.00 0.00 0.00 4.44
2248 2885 9.896645 AAGTGTATACTGAACATGAAAGATCAT 57.103 29.630 0.00 0.00 41.14 2.45
2308 2947 1.078143 ATCTCCGCACAAAGAGCCC 60.078 57.895 0.00 0.00 0.00 5.19
2320 2959 2.271800 CCCGAGAAAGAAACATCTCCG 58.728 52.381 0.00 0.00 39.09 4.63
2338 2994 0.532862 CCACCACTACATCGATGCCC 60.533 60.000 25.11 0.00 0.00 5.36
2354 3010 2.412089 GTCAGACGCAAACTATCACCAC 59.588 50.000 0.00 0.00 0.00 4.16
2386 3075 8.185506 TCAGACACAAAACAGAGGTAGTAATA 57.814 34.615 0.00 0.00 0.00 0.98
2389 3078 6.665992 ATCAGACACAAAACAGAGGTAGTA 57.334 37.500 0.00 0.00 0.00 1.82
2485 3240 3.442273 GGTGAAGGTCACTGAAACAACAA 59.558 43.478 8.21 0.00 46.19 2.83
2486 3241 3.013921 GGTGAAGGTCACTGAAACAACA 58.986 45.455 8.21 0.00 46.19 3.33
2487 3242 3.013921 TGGTGAAGGTCACTGAAACAAC 58.986 45.455 8.21 0.00 46.19 3.32
2496 3251 2.154462 CTCCAACATGGTGAAGGTCAC 58.846 52.381 13.74 0.00 46.23 3.67
2545 3300 2.634453 ACAGAAAAAGGCCCAAATCCTG 59.366 45.455 0.00 2.95 33.43 3.86
2563 3318 7.115520 CGCATCTTGTAATCTATTCCTACACAG 59.884 40.741 0.00 0.00 0.00 3.66
2588 3345 5.684184 CCACAACATGATGATTAAGATTGCG 59.316 40.000 10.29 0.00 0.00 4.85
2648 6130 0.719465 CGCCAGCGGTAAACTAACAG 59.281 55.000 3.61 0.00 35.56 3.16
2715 6213 6.530019 AAGAAAAAGAACAGACAACATGGT 57.470 33.333 0.00 0.00 0.00 3.55
2817 6375 9.003658 CCAACAGTGTAATTGACTCTTTAGAAT 57.996 33.333 0.00 0.00 29.24 2.40
2818 6376 7.990886 ACCAACAGTGTAATTGACTCTTTAGAA 59.009 33.333 0.00 0.00 29.24 2.10
2819 6377 7.441157 CACCAACAGTGTAATTGACTCTTTAGA 59.559 37.037 0.00 0.00 41.93 2.10
2820 6378 7.576236 CACCAACAGTGTAATTGACTCTTTAG 58.424 38.462 0.00 0.00 41.93 1.85
2821 6379 7.490962 CACCAACAGTGTAATTGACTCTTTA 57.509 36.000 0.00 0.00 41.93 1.85
2822 6380 6.377327 CACCAACAGTGTAATTGACTCTTT 57.623 37.500 0.00 0.00 41.93 2.52
3036 6594 4.145052 GGGGTTTCTGAGAAAACTCATGT 58.855 43.478 21.03 0.00 40.67 3.21


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

AutoCloner maintained by Alex Coulton.