Multiple sequence alignment - TraesCS2A01G366200

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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 TraesCS2A01G366200 chr2A 100.000 5361 0 0 1 5361 610716597 610711237 0.000000e+00 9901.0
1 TraesCS2A01G366200 chr2A 97.577 2806 54 7 2004 4803 587754722 587751925 0.000000e+00 4793.0
2 TraesCS2A01G366200 chr2A 90.173 1384 109 14 86 1461 587756079 587754715 0.000000e+00 1777.0
3 TraesCS2A01G366200 chr2A 97.500 560 13 1 1450 2009 750713175 750712617 0.000000e+00 955.0
4 TraesCS2A01G366200 chr2A 97.491 558 13 1 1452 2008 733527434 733527991 0.000000e+00 952.0
5 TraesCS2A01G366200 chr2A 94.810 578 13 5 4788 5361 587751986 587751422 0.000000e+00 885.0
6 TraesCS2A01G366200 chr2A 92.254 568 37 7 1454 2016 556060173 556059608 0.000000e+00 798.0
7 TraesCS2A01G366200 chr2A 84.211 171 22 5 2004 2173 70046391 70046557 1.550000e-35 161.0
8 TraesCS2A01G366200 chr2A 92.593 81 3 3 1 80 604957464 604957542 4.390000e-21 113.0
9 TraesCS2A01G366200 chr2A 100.000 61 0 0 4743 4803 610711810 610711750 4.390000e-21 113.0
10 TraesCS2A01G366200 chr2A 100.000 61 0 0 4788 4848 610711855 610711795 4.390000e-21 113.0
11 TraesCS2A01G366200 chr2D 97.634 2621 56 5 2187 4803 445400130 445397512 0.000000e+00 4492.0
12 TraesCS2A01G366200 chr2D 94.409 1395 59 11 74 1461 445401657 445400275 0.000000e+00 2126.0
13 TraesCS2A01G366200 chr2D 94.148 581 13 7 4788 5361 445397572 445397006 0.000000e+00 865.0
14 TraesCS2A01G366200 chr2D 90.603 564 51 2 1451 2013 435146601 435146039 0.000000e+00 747.0
15 TraesCS2A01G366200 chr2D 97.059 170 5 0 2004 2173 445400282 445400113 2.440000e-73 287.0
16 TraesCS2A01G366200 chr2D 85.161 155 21 1 2021 2173 588542965 588542811 2.000000e-34 158.0
17 TraesCS2A01G366200 chr2D 90.769 65 6 0 2189 2253 321240569 321240505 2.660000e-13 87.9
18 TraesCS2A01G366200 chr2D 86.420 81 8 2 1 80 596782180 596782102 9.570000e-13 86.1
19 TraesCS2A01G366200 chr2D 92.453 53 4 0 2004 2056 169639123 169639071 5.760000e-10 76.8
20 TraesCS2A01G366200 chr2D 92.453 53 4 0 2004 2056 298716777 298716829 5.760000e-10 76.8
21 TraesCS2A01G366200 chr2B 94.970 2624 108 11 2187 4803 523764340 523761734 0.000000e+00 4093.0
22 TraesCS2A01G366200 chr2B 86.352 762 50 14 729 1461 523765221 523764485 0.000000e+00 782.0
23 TraesCS2A01G366200 chr2B 86.927 589 32 21 4800 5361 523761782 523761212 2.120000e-173 619.0
24 TraesCS2A01G366200 chr2B 94.706 170 9 0 2004 2173 523764492 523764323 1.140000e-66 265.0
25 TraesCS2A01G366200 chr5A 98.535 546 8 0 1460 2005 311004531 311003986 0.000000e+00 965.0
26 TraesCS2A01G366200 chr5A 97.679 560 12 1 1453 2011 472461043 472460484 0.000000e+00 961.0
27 TraesCS2A01G366200 chr5A 96.791 561 18 0 1453 2013 430046502 430047062 0.000000e+00 937.0
28 TraesCS2A01G366200 chr5A 96.733 551 17 1 1463 2013 402217388 402216839 0.000000e+00 917.0
29 TraesCS2A01G366200 chr5A 88.800 125 12 2 2049 2173 464197386 464197264 9.300000e-33 152.0
30 TraesCS2A01G366200 chr1A 98.172 547 10 0 1459 2005 516145731 516145185 0.000000e+00 955.0
31 TraesCS2A01G366200 chr1A 97.468 553 13 1 1453 2005 516081760 516081209 0.000000e+00 942.0
32 TraesCS2A01G366200 chr6A 98.343 543 9 0 1462 2004 222690949 222690407 0.000000e+00 953.0
33 TraesCS2A01G366200 chr6A 97.455 550 11 2 1454 2003 34419657 34420203 0.000000e+00 935.0
34 TraesCS2A01G366200 chr6A 97.075 547 16 0 1466 2012 162983915 162983369 0.000000e+00 922.0
35 TraesCS2A01G366200 chr6A 91.071 560 47 3 1455 2012 351219371 351218813 0.000000e+00 754.0
36 TraesCS2A01G366200 chr7A 97.653 554 11 2 1452 2005 511519603 511519052 0.000000e+00 950.0
37 TraesCS2A01G366200 chr7A 84.659 176 24 2 2001 2173 40999105 40999280 7.140000e-39 172.0
38 TraesCS2A01G366200 chr7A 93.671 79 5 0 2 80 91381361 91381439 9.430000e-23 119.0
39 TraesCS2A01G366200 chr7A 92.500 80 3 2 1 80 330299304 330299380 1.580000e-20 111.0
40 TraesCS2A01G366200 chr7A 92.405 79 4 2 2 80 649069929 649069853 1.580000e-20 111.0
41 TraesCS2A01G366200 chr7A 92.647 68 3 2 1 68 416427953 416428018 4.420000e-16 97.1
42 TraesCS2A01G366200 chr4A 97.982 545 10 1 1463 2007 183856212 183855669 0.000000e+00 944.0
43 TraesCS2A01G366200 chr4A 96.959 559 15 2 1456 2013 308893583 308894140 0.000000e+00 937.0
44 TraesCS2A01G366200 chr4A 98.113 53 1 0 2 54 74255719 74255667 5.720000e-15 93.5
45 TraesCS2A01G366200 chr4A 90.385 52 4 1 2 53 570235051 570235101 3.470000e-07 67.6
46 TraesCS2A01G366200 chr3B 89.474 133 14 0 2041 2173 413810065 413810197 9.230000e-38 169.0
47 TraesCS2A01G366200 chr3B 94.737 57 3 0 2197 2253 422155930 422155874 7.400000e-14 89.8
48 TraesCS2A01G366200 chr1D 87.970 133 16 0 2041 2173 182699839 182699707 2.000000e-34 158.0
49 TraesCS2A01G366200 chr1D 100.000 40 0 0 26 65 193451842 193451803 2.070000e-09 75.0
50 TraesCS2A01G366200 chr1B 89.412 85 8 1 1 84 667168564 667168480 7.340000e-19 106.0
51 TraesCS2A01G366200 chr1B 89.552 67 7 0 2186 2252 5176628 5176694 9.570000e-13 86.1
52 TraesCS2A01G366200 chr3A 95.000 60 3 0 5 64 328769734 328769675 1.590000e-15 95.3
53 TraesCS2A01G366200 chr7D 89.855 69 7 0 2187 2255 480002925 480002857 7.400000e-14 89.8
54 TraesCS2A01G366200 chr5D 90.769 65 4 1 1 65 374260412 374260474 9.570000e-13 86.1
55 TraesCS2A01G366200 chr5D 88.235 68 8 0 2189 2256 520641830 520641897 1.240000e-11 82.4
56 TraesCS2A01G366200 chr6D 94.340 53 3 0 2004 2056 360056764 360056712 1.240000e-11 82.4
57 TraesCS2A01G366200 chr6B 89.231 65 5 2 2189 2252 102081244 102081307 4.450000e-11 80.5
58 TraesCS2A01G366200 chr6B 92.453 53 4 0 2004 2056 50480777 50480725 5.760000e-10 76.8


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 TraesCS2A01G366200 chr2A 610711237 610716597 5360 True 9901.00 9901 100.000000 1 5361 1 chr2A.!!$R2 5360
1 TraesCS2A01G366200 chr2A 587751422 587756079 4657 True 2485.00 4793 94.186667 86 5361 3 chr2A.!!$R4 5275
2 TraesCS2A01G366200 chr2A 750712617 750713175 558 True 955.00 955 97.500000 1450 2009 1 chr2A.!!$R3 559
3 TraesCS2A01G366200 chr2A 733527434 733527991 557 False 952.00 952 97.491000 1452 2008 1 chr2A.!!$F3 556
4 TraesCS2A01G366200 chr2A 556059608 556060173 565 True 798.00 798 92.254000 1454 2016 1 chr2A.!!$R1 562
5 TraesCS2A01G366200 chr2D 445397006 445401657 4651 True 1942.50 4492 95.812500 74 5361 4 chr2D.!!$R6 5287
6 TraesCS2A01G366200 chr2D 435146039 435146601 562 True 747.00 747 90.603000 1451 2013 1 chr2D.!!$R3 562
7 TraesCS2A01G366200 chr2B 523761212 523765221 4009 True 1439.75 4093 90.738750 729 5361 4 chr2B.!!$R1 4632
8 TraesCS2A01G366200 chr5A 311003986 311004531 545 True 965.00 965 98.535000 1460 2005 1 chr5A.!!$R1 545
9 TraesCS2A01G366200 chr5A 472460484 472461043 559 True 961.00 961 97.679000 1453 2011 1 chr5A.!!$R4 558
10 TraesCS2A01G366200 chr5A 430046502 430047062 560 False 937.00 937 96.791000 1453 2013 1 chr5A.!!$F1 560
11 TraesCS2A01G366200 chr5A 402216839 402217388 549 True 917.00 917 96.733000 1463 2013 1 chr5A.!!$R2 550
12 TraesCS2A01G366200 chr1A 516145185 516145731 546 True 955.00 955 98.172000 1459 2005 1 chr1A.!!$R2 546
13 TraesCS2A01G366200 chr1A 516081209 516081760 551 True 942.00 942 97.468000 1453 2005 1 chr1A.!!$R1 552
14 TraesCS2A01G366200 chr6A 222690407 222690949 542 True 953.00 953 98.343000 1462 2004 1 chr6A.!!$R2 542
15 TraesCS2A01G366200 chr6A 34419657 34420203 546 False 935.00 935 97.455000 1454 2003 1 chr6A.!!$F1 549
16 TraesCS2A01G366200 chr6A 162983369 162983915 546 True 922.00 922 97.075000 1466 2012 1 chr6A.!!$R1 546
17 TraesCS2A01G366200 chr6A 351218813 351219371 558 True 754.00 754 91.071000 1455 2012 1 chr6A.!!$R3 557
18 TraesCS2A01G366200 chr7A 511519052 511519603 551 True 950.00 950 97.653000 1452 2005 1 chr7A.!!$R1 553
19 TraesCS2A01G366200 chr4A 183855669 183856212 543 True 944.00 944 97.982000 1463 2007 1 chr4A.!!$R2 544
20 TraesCS2A01G366200 chr4A 308893583 308894140 557 False 937.00 937 96.959000 1456 2013 1 chr4A.!!$F1 557

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
77 78 0.102481 CGAATAGCGCGCCCCTATAT 59.898 55.000 30.33 15.94 0.00 0.86 F
84 85 1.269621 GCGCGCCCCTATATATCGATT 60.270 52.381 23.24 0.00 0.00 3.34 F
1241 1268 1.268625 GCGATTTTCGGGAGGTTTTGT 59.731 47.619 0.00 0.00 40.84 2.83 F
1449 1504 1.412710 CTCGCTAGGCAAATACTCCCA 59.587 52.381 0.00 0.00 0.00 4.37 F
3082 3145 1.757118 TCTACTTCCTCAAGATGGGCG 59.243 52.381 0.00 0.00 33.34 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1241 1268 1.719063 AAGCCTGAAGCCCTGGTCAA 61.719 55.000 0.00 0.00 45.47 3.18 R
1363 1418 7.199766 CACACACAAATACACTAAACCACAAT 58.800 34.615 0.00 0.00 0.00 2.71 R
2334 2393 1.515521 CGTGGCCAACTGAAGAACCC 61.516 60.000 7.24 0.00 0.00 4.11 R
3245 3308 1.004628 TGCTGAGCACAATACCACCAT 59.995 47.619 1.40 0.00 31.71 3.55 R
4831 4902 0.321919 AAGATCACCGTGCACAGCAT 60.322 50.000 18.64 0.89 41.91 3.79 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
24 25 7.081526 GTGCATTGATGTCAAAATAGAGAGT 57.918 36.000 0.00 0.00 39.55 3.24
25 26 6.965500 GTGCATTGATGTCAAAATAGAGAGTG 59.035 38.462 0.00 0.00 39.55 3.51
26 27 6.094464 TGCATTGATGTCAAAATAGAGAGTGG 59.906 38.462 0.00 0.00 39.55 4.00
27 28 6.459298 GCATTGATGTCAAAATAGAGAGTGGG 60.459 42.308 0.00 0.00 39.55 4.61
28 29 5.762179 TGATGTCAAAATAGAGAGTGGGT 57.238 39.130 0.00 0.00 0.00 4.51
29 30 5.491070 TGATGTCAAAATAGAGAGTGGGTG 58.509 41.667 0.00 0.00 0.00 4.61
30 31 5.248248 TGATGTCAAAATAGAGAGTGGGTGA 59.752 40.000 0.00 0.00 0.00 4.02
31 32 5.560722 TGTCAAAATAGAGAGTGGGTGAA 57.439 39.130 0.00 0.00 0.00 3.18
32 33 5.551233 TGTCAAAATAGAGAGTGGGTGAAG 58.449 41.667 0.00 0.00 0.00 3.02
33 34 5.306937 TGTCAAAATAGAGAGTGGGTGAAGA 59.693 40.000 0.00 0.00 0.00 2.87
34 35 6.183361 TGTCAAAATAGAGAGTGGGTGAAGAA 60.183 38.462 0.00 0.00 0.00 2.52
35 36 6.881602 GTCAAAATAGAGAGTGGGTGAAGAAT 59.118 38.462 0.00 0.00 0.00 2.40
36 37 8.041323 GTCAAAATAGAGAGTGGGTGAAGAATA 58.959 37.037 0.00 0.00 0.00 1.75
37 38 8.602424 TCAAAATAGAGAGTGGGTGAAGAATAA 58.398 33.333 0.00 0.00 0.00 1.40
38 39 8.669243 CAAAATAGAGAGTGGGTGAAGAATAAC 58.331 37.037 0.00 0.00 0.00 1.89
39 40 7.741554 AATAGAGAGTGGGTGAAGAATAACT 57.258 36.000 0.00 0.00 0.00 2.24
40 41 8.840200 AATAGAGAGTGGGTGAAGAATAACTA 57.160 34.615 0.00 0.00 0.00 2.24
41 42 9.440761 AATAGAGAGTGGGTGAAGAATAACTAT 57.559 33.333 0.00 0.00 0.00 2.12
42 43 7.741554 AGAGAGTGGGTGAAGAATAACTATT 57.258 36.000 0.00 0.00 0.00 1.73
43 44 7.787028 AGAGAGTGGGTGAAGAATAACTATTC 58.213 38.462 1.83 1.83 41.78 1.75
44 45 6.890293 AGAGTGGGTGAAGAATAACTATTCC 58.110 40.000 5.95 0.00 42.29 3.01
45 46 6.674419 AGAGTGGGTGAAGAATAACTATTCCT 59.326 38.462 5.95 0.00 42.29 3.36
46 47 6.890293 AGTGGGTGAAGAATAACTATTCCTC 58.110 40.000 5.95 4.07 42.29 3.71
47 48 6.443849 AGTGGGTGAAGAATAACTATTCCTCA 59.556 38.462 6.65 6.65 42.29 3.86
48 49 7.127955 AGTGGGTGAAGAATAACTATTCCTCAT 59.872 37.037 11.92 0.00 42.09 2.90
49 50 7.442666 GTGGGTGAAGAATAACTATTCCTCATC 59.557 40.741 11.92 11.37 42.09 2.92
50 51 7.348274 TGGGTGAAGAATAACTATTCCTCATCT 59.652 37.037 15.86 0.00 42.09 2.90
51 52 8.871125 GGGTGAAGAATAACTATTCCTCATCTA 58.129 37.037 15.86 0.00 42.09 1.98
52 53 9.921637 GGTGAAGAATAACTATTCCTCATCTAG 57.078 37.037 11.92 0.00 42.09 2.43
53 54 9.921637 GTGAAGAATAACTATTCCTCATCTAGG 57.078 37.037 11.92 0.00 42.09 3.02
54 55 9.094578 TGAAGAATAACTATTCCTCATCTAGGG 57.905 37.037 6.65 0.00 46.55 3.53
55 56 9.095700 GAAGAATAACTATTCCTCATCTAGGGT 57.904 37.037 5.95 0.00 46.55 4.34
56 57 8.429237 AGAATAACTATTCCTCATCTAGGGTG 57.571 38.462 5.95 0.00 46.55 4.61
57 58 8.235230 AGAATAACTATTCCTCATCTAGGGTGA 58.765 37.037 5.95 0.00 46.55 4.02
58 59 7.784470 ATAACTATTCCTCATCTAGGGTGAC 57.216 40.000 0.00 0.00 46.55 3.67
59 60 4.145807 ACTATTCCTCATCTAGGGTGACG 58.854 47.826 0.00 0.00 46.55 4.35
60 61 2.820728 TTCCTCATCTAGGGTGACGA 57.179 50.000 0.00 0.00 46.55 4.20
61 62 2.820728 TCCTCATCTAGGGTGACGAA 57.179 50.000 0.00 0.00 46.55 3.85
62 63 3.314307 TCCTCATCTAGGGTGACGAAT 57.686 47.619 0.00 0.00 46.55 3.34
63 64 4.448720 TCCTCATCTAGGGTGACGAATA 57.551 45.455 0.00 0.00 46.55 1.75
64 65 4.399219 TCCTCATCTAGGGTGACGAATAG 58.601 47.826 0.00 0.00 46.55 1.73
65 66 3.057174 CCTCATCTAGGGTGACGAATAGC 60.057 52.174 0.00 0.00 42.32 2.97
66 67 6.387972 CCTCATCTAGGGTGACGAATAGCG 62.388 54.167 0.00 0.00 42.32 4.26
67 68 0.666913 TCTAGGGTGACGAATAGCGC 59.333 55.000 0.00 0.00 46.04 5.92
68 69 0.660595 CTAGGGTGACGAATAGCGCG 60.661 60.000 0.00 0.00 46.04 6.86
69 70 2.672908 TAGGGTGACGAATAGCGCGC 62.673 60.000 26.66 26.66 46.04 6.86
70 71 3.627218 GGTGACGAATAGCGCGCC 61.627 66.667 30.33 11.74 46.04 6.53
71 72 3.627218 GTGACGAATAGCGCGCCC 61.627 66.667 30.33 13.83 46.04 6.13
72 73 4.884257 TGACGAATAGCGCGCCCC 62.884 66.667 30.33 13.44 46.04 5.80
73 74 4.587189 GACGAATAGCGCGCCCCT 62.587 66.667 30.33 12.78 46.04 4.79
74 75 3.203546 GACGAATAGCGCGCCCCTA 62.204 63.158 30.33 14.92 46.04 3.53
75 76 2.261671 CGAATAGCGCGCCCCTAT 59.738 61.111 30.33 16.75 0.00 2.57
76 77 1.246056 ACGAATAGCGCGCCCCTATA 61.246 55.000 30.33 14.06 46.04 1.31
77 78 0.102481 CGAATAGCGCGCCCCTATAT 59.898 55.000 30.33 15.94 0.00 0.86
84 85 1.269621 GCGCGCCCCTATATATCGATT 60.270 52.381 23.24 0.00 0.00 3.34
190 191 8.810990 AACTGGTAATAAAATTGTTCCCGATA 57.189 30.769 0.00 0.00 0.00 2.92
467 472 6.287525 TGAATGAAGAAAAATGAAACCCCAC 58.712 36.000 0.00 0.00 0.00 4.61
537 545 8.574196 ACAAAACAAAACCGAAGAATATGAAG 57.426 30.769 0.00 0.00 0.00 3.02
542 550 9.810545 AACAAAACCGAAGAATATGAAGAAAAA 57.189 25.926 0.00 0.00 0.00 1.94
625 650 2.029290 ACTATCTTTGGACTCGCGTTGT 60.029 45.455 5.77 6.61 0.00 3.32
686 712 4.418359 GGTTTACCCCAATAACTTCCCAA 58.582 43.478 0.00 0.00 0.00 4.12
726 752 1.600485 TCGTTTCTCCGCTTTGTTTCC 59.400 47.619 0.00 0.00 0.00 3.13
817 843 3.755628 GTGCCCACTCGCCGAGTA 61.756 66.667 20.78 0.60 41.37 2.59
903 929 3.066190 CACCTGAGTCGGCCCGTA 61.066 66.667 1.63 0.00 0.00 4.02
1241 1268 1.268625 GCGATTTTCGGGAGGTTTTGT 59.731 47.619 0.00 0.00 40.84 2.83
1363 1418 9.665719 TGTTTCATCTATGTTATGTCTTTGCTA 57.334 29.630 0.00 0.00 0.00 3.49
1449 1504 1.412710 CTCGCTAGGCAAATACTCCCA 59.587 52.381 0.00 0.00 0.00 4.37
2480 2539 2.728846 CGTTGATGATTCTGGCAAACCG 60.729 50.000 0.00 0.00 39.70 4.44
2485 2544 2.582052 TGATTCTGGCAAACCGAAAGT 58.418 42.857 0.00 0.00 39.70 2.66
2522 2581 2.881111 AAGGAAAGAGGGCTGTAACC 57.119 50.000 0.00 0.00 0.00 2.85
2558 2617 5.952387 TCCTTGAGATGGAAAAAGGAAAGA 58.048 37.500 0.57 0.00 43.99 2.52
2580 2639 5.127845 AGAGAATTTCAGAGAATGACCGCTA 59.872 40.000 0.00 0.00 37.77 4.26
2588 2647 3.769844 AGAGAATGACCGCTAAGGAGAAA 59.230 43.478 0.00 0.00 45.00 2.52
2745 2807 7.495934 ACGTAGCATGATTTTCTAATACTGCTT 59.504 33.333 0.00 0.00 39.91 3.91
3082 3145 1.757118 TCTACTTCCTCAAGATGGGCG 59.243 52.381 0.00 0.00 33.34 6.13
3245 3308 4.283467 TGCCTCAGAGTTAGCAGTTCTAAA 59.717 41.667 0.00 0.00 38.86 1.85
3364 3427 3.189495 GGTTGCACTTCCTAGAAAGAAGC 59.811 47.826 0.00 0.00 43.75 3.86
3466 3529 6.093082 ACACGCACAAAAACTAGTAAAAGACT 59.907 34.615 0.00 0.00 42.69 3.24
3635 3698 4.162509 AGGAAGGGTGTTCTGTATTCTAGC 59.837 45.833 0.00 0.00 0.00 3.42
4149 4213 0.612229 TCAGAGGAGCAAGCAGAAGG 59.388 55.000 0.00 0.00 0.00 3.46
4499 4563 6.732531 TCAAACACTGAGCTGATTCATAAG 57.267 37.500 0.00 0.00 0.00 1.73
4577 4642 3.544834 GCGACTCATGTGATGTTGCATAC 60.545 47.826 0.94 0.00 39.96 2.39
4680 4745 2.304470 TGGTGTTAAGCAGTAGCCATCA 59.696 45.455 0.00 0.00 43.56 3.07
4802 4873 3.582148 CATGCTGTGCACGGTGAT 58.418 55.556 26.00 15.63 43.04 3.06
4803 4874 1.878070 CATGCTGTGCACGGTGATT 59.122 52.632 26.00 6.74 43.04 2.57
4804 4875 1.085893 CATGCTGTGCACGGTGATTA 58.914 50.000 26.00 8.98 43.04 1.75
4805 4876 1.086696 ATGCTGTGCACGGTGATTAC 58.913 50.000 26.00 9.44 43.04 1.89
4806 4877 0.250081 TGCTGTGCACGGTGATTACA 60.250 50.000 26.00 11.97 31.71 2.41
4807 4878 0.443869 GCTGTGCACGGTGATTACAG 59.556 55.000 26.00 24.02 41.15 2.74
4808 4879 1.795768 CTGTGCACGGTGATTACAGT 58.204 50.000 17.96 0.00 35.55 3.55
4809 4880 2.929161 GCTGTGCACGGTGATTACAGTA 60.929 50.000 26.00 0.00 40.52 2.74
4810 4881 2.666508 CTGTGCACGGTGATTACAGTAC 59.333 50.000 17.96 3.96 33.35 2.73
4811 4882 2.297880 TGTGCACGGTGATTACAGTACT 59.702 45.455 13.29 0.00 33.35 2.73
4812 4883 2.666508 GTGCACGGTGATTACAGTACTG 59.333 50.000 21.44 21.44 33.35 2.74
4813 4884 2.297880 TGCACGGTGATTACAGTACTGT 59.702 45.455 30.13 30.13 46.87 3.55
4814 4885 3.506844 TGCACGGTGATTACAGTACTGTA 59.493 43.478 27.99 27.99 44.42 2.74
4815 4886 4.158949 TGCACGGTGATTACAGTACTGTAT 59.841 41.667 31.05 21.82 44.54 2.29
4816 4887 4.503007 GCACGGTGATTACAGTACTGTATG 59.497 45.833 31.05 24.55 44.54 2.39
4817 4888 5.041287 CACGGTGATTACAGTACTGTATGG 58.959 45.833 31.05 19.45 44.54 2.74
4818 4889 4.049186 CGGTGATTACAGTACTGTATGGC 58.951 47.826 31.05 23.03 44.54 4.40
4819 4890 4.202121 CGGTGATTACAGTACTGTATGGCT 60.202 45.833 31.05 18.27 44.54 4.75
4820 4891 5.050490 GGTGATTACAGTACTGTATGGCTG 58.950 45.833 31.05 4.83 44.54 4.85
4821 4892 5.395324 GGTGATTACAGTACTGTATGGCTGT 60.395 44.000 31.05 15.67 44.54 4.40
4822 4893 6.183360 GGTGATTACAGTACTGTATGGCTGTA 60.183 42.308 31.05 17.68 44.54 2.74
4823 4894 6.918569 GTGATTACAGTACTGTATGGCTGTAG 59.081 42.308 31.05 1.93 44.54 2.74
4824 4895 6.605995 TGATTACAGTACTGTATGGCTGTAGT 59.394 38.462 31.05 10.64 44.54 2.73
4825 4896 6.845758 TTACAGTACTGTATGGCTGTAGTT 57.154 37.500 31.05 7.66 44.54 2.24
4826 4897 5.326200 ACAGTACTGTATGGCTGTAGTTC 57.674 43.478 26.91 0.00 42.90 3.01
4827 4898 4.770531 ACAGTACTGTATGGCTGTAGTTCA 59.229 41.667 26.91 0.00 42.90 3.18
4828 4899 5.245301 ACAGTACTGTATGGCTGTAGTTCAA 59.755 40.000 26.91 0.00 42.90 2.69
4829 4900 5.807520 CAGTACTGTATGGCTGTAGTTCAAG 59.192 44.000 15.06 0.00 34.33 3.02
4830 4901 3.600388 ACTGTATGGCTGTAGTTCAAGC 58.400 45.455 0.00 0.00 0.00 4.01
4831 4902 3.007940 ACTGTATGGCTGTAGTTCAAGCA 59.992 43.478 0.00 0.00 0.00 3.91
4832 4903 4.194640 CTGTATGGCTGTAGTTCAAGCAT 58.805 43.478 0.00 0.00 0.00 3.79
4833 4904 3.940852 TGTATGGCTGTAGTTCAAGCATG 59.059 43.478 0.00 0.00 0.00 4.06
4834 4905 1.167851 TGGCTGTAGTTCAAGCATGC 58.832 50.000 10.51 10.51 0.00 4.06
4835 4906 1.271543 TGGCTGTAGTTCAAGCATGCT 60.272 47.619 16.30 16.30 0.00 3.79
4836 4907 1.131883 GGCTGTAGTTCAAGCATGCTG 59.868 52.381 23.48 15.40 0.00 4.41
4837 4908 1.808945 GCTGTAGTTCAAGCATGCTGT 59.191 47.619 23.48 8.82 0.00 4.40
4838 4909 2.413765 GCTGTAGTTCAAGCATGCTGTG 60.414 50.000 23.48 20.19 0.00 3.66
4877 4948 3.133691 TGCATTATGATCGCCTCTTGTC 58.866 45.455 0.00 0.00 0.00 3.18
4881 4952 2.783828 ATGATCGCCTCTTGTCTACG 57.216 50.000 0.00 0.00 0.00 3.51
4922 5012 8.129211 CCACAGTATATAAACCTTAAAAGCAGC 58.871 37.037 0.00 0.00 0.00 5.25
5002 5095 2.480073 CCGAATCGCCTTGCAATTTCAT 60.480 45.455 0.00 0.00 0.00 2.57
5003 5096 3.243035 CCGAATCGCCTTGCAATTTCATA 60.243 43.478 0.00 0.00 0.00 2.15
5004 5097 3.725740 CGAATCGCCTTGCAATTTCATAC 59.274 43.478 0.00 0.00 0.00 2.39
5005 5098 4.496341 CGAATCGCCTTGCAATTTCATACT 60.496 41.667 0.00 0.00 0.00 2.12
5006 5099 3.763097 TCGCCTTGCAATTTCATACTG 57.237 42.857 0.00 0.00 0.00 2.74
5067 5160 3.563808 GGCAGAATCCGTTTGCATACATA 59.436 43.478 8.06 0.00 39.54 2.29
5147 5252 7.508296 TCAGTTCAGATATCTCATCCAAGATCA 59.492 37.037 1.03 0.00 37.24 2.92
5326 5431 4.201679 CGGCGCCTGGTCGTCATA 62.202 66.667 26.68 0.00 39.39 2.15
5327 5432 2.585247 GGCGCCTGGTCGTCATAC 60.585 66.667 22.15 0.00 33.72 2.39
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.965500 CACTCTCTATTTTGACATCAATGCAC 59.035 38.462 0.00 0.00 35.55 4.57
2 3 6.459298 CCCACTCTCTATTTTGACATCAATGC 60.459 42.308 0.00 0.00 35.55 3.56
7 8 5.734720 TCACCCACTCTCTATTTTGACATC 58.265 41.667 0.00 0.00 0.00 3.06
9 10 5.306937 TCTTCACCCACTCTCTATTTTGACA 59.693 40.000 0.00 0.00 0.00 3.58
10 11 5.794894 TCTTCACCCACTCTCTATTTTGAC 58.205 41.667 0.00 0.00 0.00 3.18
11 12 6.433847 TTCTTCACCCACTCTCTATTTTGA 57.566 37.500 0.00 0.00 0.00 2.69
12 13 8.669243 GTTATTCTTCACCCACTCTCTATTTTG 58.331 37.037 0.00 0.00 0.00 2.44
13 14 8.606830 AGTTATTCTTCACCCACTCTCTATTTT 58.393 33.333 0.00 0.00 0.00 1.82
14 15 8.152023 AGTTATTCTTCACCCACTCTCTATTT 57.848 34.615 0.00 0.00 0.00 1.40
15 16 7.741554 AGTTATTCTTCACCCACTCTCTATT 57.258 36.000 0.00 0.00 0.00 1.73
16 17 9.440761 AATAGTTATTCTTCACCCACTCTCTAT 57.559 33.333 0.00 0.00 0.00 1.98
17 18 8.840200 AATAGTTATTCTTCACCCACTCTCTA 57.160 34.615 0.00 0.00 0.00 2.43
18 19 7.147637 GGAATAGTTATTCTTCACCCACTCTCT 60.148 40.741 10.71 0.00 41.33 3.10
19 20 6.987404 GGAATAGTTATTCTTCACCCACTCTC 59.013 42.308 10.71 0.00 41.33 3.20
20 21 6.674419 AGGAATAGTTATTCTTCACCCACTCT 59.326 38.462 10.71 0.00 41.33 3.24
21 22 6.890293 AGGAATAGTTATTCTTCACCCACTC 58.110 40.000 10.71 0.00 41.33 3.51
22 23 6.443849 TGAGGAATAGTTATTCTTCACCCACT 59.556 38.462 17.60 3.75 46.85 4.00
23 24 6.650120 TGAGGAATAGTTATTCTTCACCCAC 58.350 40.000 17.60 1.16 46.85 4.61
24 25 6.884472 TGAGGAATAGTTATTCTTCACCCA 57.116 37.500 17.60 2.39 46.85 4.51
43 44 3.057174 GCTATTCGTCACCCTAGATGAGG 60.057 52.174 9.25 9.25 46.25 3.86
44 45 3.365465 CGCTATTCGTCACCCTAGATGAG 60.365 52.174 0.00 0.00 35.17 2.90
45 46 2.552743 CGCTATTCGTCACCCTAGATGA 59.447 50.000 0.00 0.00 0.00 2.92
46 47 2.922758 GCGCTATTCGTCACCCTAGATG 60.923 54.545 0.00 0.00 41.07 2.90
47 48 1.269998 GCGCTATTCGTCACCCTAGAT 59.730 52.381 0.00 0.00 41.07 1.98
48 49 0.666913 GCGCTATTCGTCACCCTAGA 59.333 55.000 0.00 0.00 41.07 2.43
49 50 0.660595 CGCGCTATTCGTCACCCTAG 60.661 60.000 5.56 0.00 41.07 3.02
50 51 1.357690 CGCGCTATTCGTCACCCTA 59.642 57.895 5.56 0.00 41.07 3.53
51 52 2.104331 CGCGCTATTCGTCACCCT 59.896 61.111 5.56 0.00 41.07 4.34
52 53 3.627218 GCGCGCTATTCGTCACCC 61.627 66.667 26.67 0.00 41.07 4.61
53 54 3.627218 GGCGCGCTATTCGTCACC 61.627 66.667 32.29 5.91 41.07 4.02
54 55 3.627218 GGGCGCGCTATTCGTCAC 61.627 66.667 32.29 10.56 41.07 3.67
55 56 4.884257 GGGGCGCGCTATTCGTCA 62.884 66.667 32.29 0.00 41.07 4.35
56 57 2.488087 ATAGGGGCGCGCTATTCGTC 62.488 60.000 32.29 12.21 36.44 4.20
57 58 1.246056 TATAGGGGCGCGCTATTCGT 61.246 55.000 32.29 19.93 39.65 3.85
58 59 0.102481 ATATAGGGGCGCGCTATTCG 59.898 55.000 32.29 0.00 39.65 3.34
59 60 3.576648 GATATATAGGGGCGCGCTATTC 58.423 50.000 32.29 14.29 39.65 1.75
60 61 2.030185 CGATATATAGGGGCGCGCTATT 60.030 50.000 32.29 18.15 39.65 1.73
61 62 1.540267 CGATATATAGGGGCGCGCTAT 59.460 52.381 32.29 22.31 41.39 2.97
62 63 0.949397 CGATATATAGGGGCGCGCTA 59.051 55.000 32.29 16.48 33.62 4.26
63 64 0.750546 TCGATATATAGGGGCGCGCT 60.751 55.000 32.29 14.49 0.00 5.92
64 65 0.314302 ATCGATATATAGGGGCGCGC 59.686 55.000 25.94 25.94 0.00 6.86
65 66 2.795175 AATCGATATATAGGGGCGCG 57.205 50.000 0.00 0.00 0.00 6.86
66 67 5.135508 ACATAATCGATATATAGGGGCGC 57.864 43.478 0.00 0.00 0.00 6.53
67 68 7.210718 TGTACATAATCGATATATAGGGGCG 57.789 40.000 0.00 0.00 0.00 6.13
68 69 9.257651 GTTTGTACATAATCGATATATAGGGGC 57.742 37.037 0.00 0.00 0.00 5.80
161 162 9.694137 CGGGAACAATTTTATTACCAGTTTTAA 57.306 29.630 0.00 0.00 0.00 1.52
163 164 7.953752 TCGGGAACAATTTTATTACCAGTTTT 58.046 30.769 0.00 0.00 0.00 2.43
174 175 9.015367 TCTTCACAAATATCGGGAACAATTTTA 57.985 29.630 0.00 0.00 0.00 1.52
339 343 7.642071 ATGACTTGTTTTTCATACACATTGC 57.358 32.000 0.00 0.00 30.41 3.56
447 452 5.683876 TTGTGGGGTTTCATTTTTCTTCA 57.316 34.783 0.00 0.00 0.00 3.02
474 479 1.002251 GTTTCCGCATGGTTTTCACGA 60.002 47.619 0.00 0.00 36.30 4.35
475 480 1.404477 GTTTCCGCATGGTTTTCACG 58.596 50.000 0.00 0.00 36.30 4.35
476 481 1.002251 TCGTTTCCGCATGGTTTTCAC 60.002 47.619 0.00 0.00 36.30 3.18
477 482 1.309950 TCGTTTCCGCATGGTTTTCA 58.690 45.000 0.00 0.00 36.30 2.69
482 490 1.600023 TTTCTTCGTTTCCGCATGGT 58.400 45.000 0.00 0.00 36.30 3.55
503 511 8.560374 TCTTCGGTTTTGTTTTGTTTTTCATTT 58.440 25.926 0.00 0.00 0.00 2.32
504 512 8.089115 TCTTCGGTTTTGTTTTGTTTTTCATT 57.911 26.923 0.00 0.00 0.00 2.57
506 514 7.478520 TTCTTCGGTTTTGTTTTGTTTTTCA 57.521 28.000 0.00 0.00 0.00 2.69
510 518 8.934507 TCATATTCTTCGGTTTTGTTTTGTTT 57.065 26.923 0.00 0.00 0.00 2.83
511 519 8.934507 TTCATATTCTTCGGTTTTGTTTTGTT 57.065 26.923 0.00 0.00 0.00 2.83
625 650 0.881796 CCTGCCGACTATATCTCGCA 59.118 55.000 0.00 0.00 0.00 5.10
686 712 1.683365 GTGCATTGGCCCACTGGAT 60.683 57.895 0.00 0.00 40.13 3.41
817 843 1.485294 TACGGGTGTGGTGAATGGCT 61.485 55.000 0.00 0.00 0.00 4.75
958 984 3.184736 GAGAGTTCGAGAGAGCCCT 57.815 57.895 0.00 0.00 42.90 5.19
1053 1079 3.637273 GGCGGAGGTGGTGAAGGT 61.637 66.667 0.00 0.00 0.00 3.50
1241 1268 1.719063 AAGCCTGAAGCCCTGGTCAA 61.719 55.000 0.00 0.00 45.47 3.18
1356 1411 9.128107 CAAATACACTAAACCACAATAGCAAAG 57.872 33.333 0.00 0.00 0.00 2.77
1363 1418 7.199766 CACACACAAATACACTAAACCACAAT 58.800 34.615 0.00 0.00 0.00 2.71
2318 2377 2.618442 ACCCGTCGTCTTGGTAAAAA 57.382 45.000 0.00 0.00 0.00 1.94
2334 2393 1.515521 CGTGGCCAACTGAAGAACCC 61.516 60.000 7.24 0.00 0.00 4.11
2516 2575 6.381420 TCAAGGATTTCAAAAACCTGGTTACA 59.619 34.615 13.37 0.00 39.90 2.41
2522 2581 6.015180 TCCATCTCAAGGATTTCAAAAACCTG 60.015 38.462 5.20 1.52 39.90 4.00
2558 2617 4.213564 AGCGGTCATTCTCTGAAATTCT 57.786 40.909 0.00 0.00 35.07 2.40
2822 2884 9.809096 GTGAGAGAACATCAGAAACATAGATTA 57.191 33.333 0.00 0.00 0.00 1.75
3245 3308 1.004628 TGCTGAGCACAATACCACCAT 59.995 47.619 1.40 0.00 31.71 3.55
3364 3427 8.065473 ACCATGATAGCAGAGATAGAACATAG 57.935 38.462 0.00 0.00 0.00 2.23
3411 3474 4.323417 ACCTCGCTTCACAATTCATACAA 58.677 39.130 0.00 0.00 0.00 2.41
3466 3529 6.096705 TGTCTTTCTTTGAAATCTTGAAGCCA 59.903 34.615 0.00 0.00 0.00 4.75
3599 3662 4.211920 CACCCTTCCTACCAACTGAAAAA 58.788 43.478 0.00 0.00 0.00 1.94
3635 3698 5.620738 TCTATTTGATCCTGACTTCCTGG 57.379 43.478 0.00 0.00 35.40 4.45
4261 4325 1.026718 CGGGTGAATCTGCCTTGTCC 61.027 60.000 0.00 0.00 0.00 4.02
4499 4563 4.141846 TGGTGGATGCTCTTCAGTAAGATC 60.142 45.833 0.00 0.00 40.92 2.75
4577 4642 8.365399 TGATTGCGATATTTCAGGTTACTAAG 57.635 34.615 0.00 0.00 0.00 2.18
4804 4875 4.770531 TGAACTACAGCCATACAGTACTGT 59.229 41.667 30.13 30.13 46.87 3.55
4805 4876 5.324784 TGAACTACAGCCATACAGTACTG 57.675 43.478 21.44 21.44 36.22 2.74
4806 4877 5.624738 GCTTGAACTACAGCCATACAGTACT 60.625 44.000 0.00 0.00 0.00 2.73
4807 4878 4.567159 GCTTGAACTACAGCCATACAGTAC 59.433 45.833 0.00 0.00 0.00 2.73
4808 4879 4.221924 TGCTTGAACTACAGCCATACAGTA 59.778 41.667 0.00 0.00 0.00 2.74
4809 4880 3.007940 TGCTTGAACTACAGCCATACAGT 59.992 43.478 0.00 0.00 0.00 3.55
4810 4881 3.599343 TGCTTGAACTACAGCCATACAG 58.401 45.455 0.00 0.00 0.00 2.74
4811 4882 3.694043 TGCTTGAACTACAGCCATACA 57.306 42.857 0.00 0.00 0.00 2.29
4812 4883 3.242870 GCATGCTTGAACTACAGCCATAC 60.243 47.826 11.37 0.00 0.00 2.39
4813 4884 2.945008 GCATGCTTGAACTACAGCCATA 59.055 45.455 11.37 0.00 0.00 2.74
4814 4885 1.747355 GCATGCTTGAACTACAGCCAT 59.253 47.619 11.37 0.00 0.00 4.40
4815 4886 1.167851 GCATGCTTGAACTACAGCCA 58.832 50.000 11.37 0.00 0.00 4.75
4816 4887 1.131883 CAGCATGCTTGAACTACAGCC 59.868 52.381 19.98 0.00 0.00 4.85
4817 4888 1.808945 ACAGCATGCTTGAACTACAGC 59.191 47.619 19.98 0.00 42.53 4.40
4818 4889 3.466712 CACAGCATGCTTGAACTACAG 57.533 47.619 19.98 5.86 42.53 2.74
4830 4901 1.022982 AGATCACCGTGCACAGCATG 61.023 55.000 18.64 8.85 44.25 4.06
4831 4902 0.321919 AAGATCACCGTGCACAGCAT 60.322 50.000 18.64 0.89 41.91 3.79
4832 4903 0.950555 GAAGATCACCGTGCACAGCA 60.951 55.000 18.64 0.00 35.60 4.41
4833 4904 1.639298 GGAAGATCACCGTGCACAGC 61.639 60.000 18.64 0.00 0.00 4.40
4834 4905 1.021390 GGGAAGATCACCGTGCACAG 61.021 60.000 18.64 8.33 0.00 3.66
4835 4906 1.003839 GGGAAGATCACCGTGCACA 60.004 57.895 18.64 0.00 0.00 4.57
4836 4907 0.535335 TAGGGAAGATCACCGTGCAC 59.465 55.000 6.82 6.82 0.00 4.57
4837 4908 1.138859 CATAGGGAAGATCACCGTGCA 59.861 52.381 12.29 0.00 0.00 4.57
4838 4909 1.871080 CATAGGGAAGATCACCGTGC 58.129 55.000 12.29 0.00 0.00 5.34
4839 4910 1.138859 TGCATAGGGAAGATCACCGTG 59.861 52.381 12.29 0.00 0.00 4.94
4840 4911 1.496060 TGCATAGGGAAGATCACCGT 58.504 50.000 0.00 2.50 0.00 4.83
4841 4912 2.847327 ATGCATAGGGAAGATCACCG 57.153 50.000 0.00 0.00 0.00 4.94
4842 4913 5.809001 TCATAATGCATAGGGAAGATCACC 58.191 41.667 0.00 0.00 0.00 4.02
4843 4914 6.257411 CGATCATAATGCATAGGGAAGATCAC 59.743 42.308 0.00 0.00 32.00 3.06
4844 4915 6.343703 CGATCATAATGCATAGGGAAGATCA 58.656 40.000 0.00 0.00 32.00 2.92
4845 4916 5.236047 GCGATCATAATGCATAGGGAAGATC 59.764 44.000 0.00 6.97 0.00 2.75
4877 4948 3.057806 GTGGAAAATTCAACCACCCGTAG 60.058 47.826 13.97 0.00 45.53 3.51
4906 4995 5.782893 ACATGTGCTGCTTTTAAGGTTTA 57.217 34.783 0.00 0.00 0.00 2.01
4908 4997 4.670896 AACATGTGCTGCTTTTAAGGTT 57.329 36.364 0.00 0.00 0.00 3.50
4909 4998 4.670896 AAACATGTGCTGCTTTTAAGGT 57.329 36.364 0.00 0.00 0.00 3.50
4910 4999 4.448732 GGAAAACATGTGCTGCTTTTAAGG 59.551 41.667 0.00 0.00 0.00 2.69
4922 5012 8.946085 AGTGTAATATACTGTGGAAAACATGTG 58.054 33.333 0.00 0.00 38.39 3.21
5002 5095 4.010667 AGTTGCCGTGGAAAATACAGTA 57.989 40.909 0.00 0.00 0.00 2.74
5003 5096 2.858745 AGTTGCCGTGGAAAATACAGT 58.141 42.857 0.00 0.00 0.00 3.55
5004 5097 4.671766 GCTTAGTTGCCGTGGAAAATACAG 60.672 45.833 0.00 0.00 0.00 2.74
5005 5098 3.189702 GCTTAGTTGCCGTGGAAAATACA 59.810 43.478 0.00 0.00 0.00 2.29
5006 5099 3.726782 CGCTTAGTTGCCGTGGAAAATAC 60.727 47.826 0.00 0.00 0.00 1.89
5067 5160 4.549458 AGTAAACTAATACGCGTGTGTGT 58.451 39.130 24.59 14.77 42.59 3.72
5147 5252 3.592546 GGACTACCTCCTCGTTCCT 57.407 57.895 0.00 0.00 35.89 3.36
5322 5427 1.471287 CGACCTGTTCCACGAGTATGA 59.529 52.381 0.00 0.00 0.00 2.15
5323 5428 1.471287 TCGACCTGTTCCACGAGTATG 59.529 52.381 0.00 0.00 0.00 2.39
5324 5429 1.830279 TCGACCTGTTCCACGAGTAT 58.170 50.000 0.00 0.00 0.00 2.12
5325 5430 1.471287 CATCGACCTGTTCCACGAGTA 59.529 52.381 0.00 0.00 38.12 2.59
5326 5431 0.243907 CATCGACCTGTTCCACGAGT 59.756 55.000 0.00 0.00 38.12 4.18
5327 5432 0.243907 ACATCGACCTGTTCCACGAG 59.756 55.000 0.00 0.00 38.12 4.18


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

AutoCloner maintained by Alex Coulton.