Multiple sequence alignment - TraesCS6B01G200700

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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 TraesCS6B01G200700 chr6B 100.000 3975 0 0 1 3975 240334252 240330278 0.000000e+00 7341.0
1 TraesCS6B01G200700 chrUn 98.767 892 9 2 1 891 165317852 165318742 0.000000e+00 1585.0
2 TraesCS6B01G200700 chrUn 98.544 893 10 3 1 891 327649291 327650182 0.000000e+00 1574.0
3 TraesCS6B01G200700 chrUn 98.506 803 9 3 91 891 165286337 165287138 0.000000e+00 1413.0
4 TraesCS6B01G200700 chrUn 98.506 803 9 3 91 891 328807919 328808720 0.000000e+00 1413.0
5 TraesCS6B01G200700 chrUn 99.424 521 2 1 371 891 370721145 370720626 0.000000e+00 944.0
6 TraesCS6B01G200700 chr7B 98.655 892 9 3 1 891 734810977 734810088 0.000000e+00 1578.0
7 TraesCS6B01G200700 chr7B 98.543 892 11 2 1 891 734835924 734835034 0.000000e+00 1574.0
8 TraesCS6B01G200700 chr7B 98.430 892 12 2 1 891 734881293 734880403 0.000000e+00 1568.0
9 TraesCS6B01G200700 chr7B 99.424 521 2 1 371 891 734860067 734859548 0.000000e+00 944.0
10 TraesCS6B01G200700 chr7B 88.333 720 64 8 2970 3686 129548380 129547678 0.000000e+00 846.0
11 TraesCS6B01G200700 chr1B 95.648 988 34 4 2988 3975 143632537 143633515 0.000000e+00 1578.0
12 TraesCS6B01G200700 chr1B 93.114 1002 55 4 2987 3974 127037683 127036682 0.000000e+00 1456.0
13 TraesCS6B01G200700 chr1B 93.219 988 67 0 2988 3975 524297384 524298371 0.000000e+00 1454.0
14 TraesCS6B01G200700 chr1B 88.562 612 39 22 2982 3587 328126260 328125674 0.000000e+00 713.0
15 TraesCS6B01G200700 chr1B 93.151 219 13 2 2982 3200 519650785 519651001 1.780000e-83 320.0
16 TraesCS6B01G200700 chr3B 95.344 988 45 1 2988 3975 203965686 203964700 0.000000e+00 1568.0
17 TraesCS6B01G200700 chr3B 92.901 986 70 0 2990 3975 824661679 824662664 0.000000e+00 1434.0
18 TraesCS6B01G200700 chr3B 87.651 996 105 7 2982 3975 691361851 691360872 0.000000e+00 1142.0
19 TraesCS6B01G200700 chr3B 95.833 120 5 0 3856 3975 368101433 368101314 1.130000e-45 195.0
20 TraesCS6B01G200700 chr3B 93.333 120 8 0 3856 3975 203647518 203647637 1.140000e-40 178.0
21 TraesCS6B01G200700 chr3B 93.277 119 8 0 2741 2859 189150393 189150275 4.080000e-40 176.0
22 TraesCS6B01G200700 chr3B 95.370 108 5 0 2749 2856 702857819 702857712 5.280000e-39 172.0
23 TraesCS6B01G200700 chr3A 92.698 986 72 0 2990 3975 750065855 750064870 0.000000e+00 1423.0
24 TraesCS6B01G200700 chr3A 72.981 1325 273 50 1348 2614 627996532 627997829 6.230000e-103 385.0
25 TraesCS6B01G200700 chr5B 92.799 986 61 2 2990 3975 204179142 204178167 0.000000e+00 1419.0
26 TraesCS6B01G200700 chr5B 91.126 879 64 3 2989 3867 293187483 293188347 0.000000e+00 1179.0
27 TraesCS6B01G200700 chr5B 81.694 366 42 21 2988 3341 253183235 253182883 8.410000e-72 281.0
28 TraesCS6B01G200700 chr5B 93.043 115 7 1 2745 2858 126153742 126153856 2.460000e-37 167.0
29 TraesCS6B01G200700 chr6A 92.155 956 43 10 890 1819 184888501 184887552 0.000000e+00 1321.0
30 TraesCS6B01G200700 chr6A 93.543 635 26 2 2133 2752 184821867 184821233 0.000000e+00 931.0
31 TraesCS6B01G200700 chr6A 95.046 323 13 3 1816 2137 184827697 184827377 4.580000e-139 505.0
32 TraesCS6B01G200700 chr6A 98.837 86 1 0 2855 2940 184821235 184821150 1.910000e-33 154.0
33 TraesCS6B01G200700 chr6D 92.919 918 33 7 1 887 131632500 131633416 0.000000e+00 1306.0
34 TraesCS6B01G200700 chr6D 93.333 345 15 2 891 1233 140222175 140221837 1.650000e-138 503.0
35 TraesCS6B01G200700 chr7D 92.316 885 33 6 1 850 498230915 498230031 0.000000e+00 1225.0
36 TraesCS6B01G200700 chr7D 72.533 841 163 38 1829 2617 60486743 60485919 1.120000e-50 211.0
37 TraesCS6B01G200700 chr7D 94.495 109 6 0 2750 2858 556642493 556642385 6.830000e-38 169.0
38 TraesCS6B01G200700 chr4B 88.194 864 78 17 3056 3910 199749924 199750772 0.000000e+00 1009.0
39 TraesCS6B01G200700 chr4B 95.455 110 5 0 2750 2859 413733956 413734065 4.080000e-40 176.0
40 TraesCS6B01G200700 chr4B 94.595 111 6 0 2750 2860 330778909 330778799 5.280000e-39 172.0
41 TraesCS6B01G200700 chr4B 93.750 112 7 0 2748 2859 654206459 654206348 6.830000e-38 169.0
42 TraesCS6B01G200700 chr3D 72.302 1668 343 82 1028 2633 485140515 485142125 1.030000e-110 411.0
43 TraesCS6B01G200700 chr2A 72.906 1373 270 68 1304 2619 58360826 58362153 8.060000e-102 381.0
44 TraesCS6B01G200700 chr2A 78.909 275 50 8 2324 2593 58982884 58983155 3.160000e-41 180.0
45 TraesCS6B01G200700 chr2A 75.198 379 77 13 1829 2200 59050817 59051185 3.180000e-36 163.0
46 TraesCS6B01G200700 chr2A 80.952 105 20 0 1832 1936 58982388 58982492 2.550000e-12 84.2
47 TraesCS6B01G200700 chr2D 72.401 1395 274 77 1277 2619 57107903 57109238 1.370000e-89 340.0
48 TraesCS6B01G200700 chr2D 74.251 668 119 36 1035 1683 57334003 57333370 8.590000e-57 231.0
49 TraesCS6B01G200700 chr2D 84.951 206 23 6 2395 2593 58650027 58650231 6.740000e-48 202.0
50 TraesCS6B01G200700 chr2D 80.349 229 45 0 2368 2596 58748832 58748604 1.470000e-39 174.0
51 TraesCS6B01G200700 chr2D 95.370 108 4 1 2749 2856 405626803 405626909 1.900000e-38 171.0
52 TraesCS6B01G200700 chr2D 81.683 202 29 8 2324 2520 57970116 57970314 1.140000e-35 161.0
53 TraesCS6B01G200700 chr2D 75.000 364 72 16 1833 2188 58649429 58649781 2.470000e-32 150.0
54 TraesCS6B01G200700 chr2B 73.622 762 149 30 1833 2571 90396236 90396968 3.070000e-61 246.0
55 TraesCS6B01G200700 chr2B 79.336 271 49 7 2331 2596 91206784 91206516 2.440000e-42 183.0
56 TraesCS6B01G200700 chr2B 79.048 105 22 0 1832 1936 91207294 91207190 5.510000e-09 73.1
57 TraesCS6B01G200700 chr2B 93.023 43 3 0 1832 1874 91084579 91084537 3.320000e-06 63.9
58 TraesCS6B01G200700 chr4A 86.758 219 14 7 2982 3199 157328961 157329165 3.090000e-56 230.0
59 TraesCS6B01G200700 chr5D 94.545 110 6 0 2749 2858 257163169 257163278 1.900000e-38 171.0


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 TraesCS6B01G200700 chr6B 240330278 240334252 3974 True 7341.0 7341 100.000 1 3975 1 chr6B.!!$R1 3974
1 TraesCS6B01G200700 chrUn 165317852 165318742 890 False 1585.0 1585 98.767 1 891 1 chrUn.!!$F2 890
2 TraesCS6B01G200700 chrUn 327649291 327650182 891 False 1574.0 1574 98.544 1 891 1 chrUn.!!$F3 890
3 TraesCS6B01G200700 chrUn 165286337 165287138 801 False 1413.0 1413 98.506 91 891 1 chrUn.!!$F1 800
4 TraesCS6B01G200700 chrUn 328807919 328808720 801 False 1413.0 1413 98.506 91 891 1 chrUn.!!$F4 800
5 TraesCS6B01G200700 chrUn 370720626 370721145 519 True 944.0 944 99.424 371 891 1 chrUn.!!$R1 520
6 TraesCS6B01G200700 chr7B 734810088 734810977 889 True 1578.0 1578 98.655 1 891 1 chr7B.!!$R2 890
7 TraesCS6B01G200700 chr7B 734835034 734835924 890 True 1574.0 1574 98.543 1 891 1 chr7B.!!$R3 890
8 TraesCS6B01G200700 chr7B 734880403 734881293 890 True 1568.0 1568 98.430 1 891 1 chr7B.!!$R5 890
9 TraesCS6B01G200700 chr7B 734859548 734860067 519 True 944.0 944 99.424 371 891 1 chr7B.!!$R4 520
10 TraesCS6B01G200700 chr7B 129547678 129548380 702 True 846.0 846 88.333 2970 3686 1 chr7B.!!$R1 716
11 TraesCS6B01G200700 chr1B 143632537 143633515 978 False 1578.0 1578 95.648 2988 3975 1 chr1B.!!$F1 987
12 TraesCS6B01G200700 chr1B 127036682 127037683 1001 True 1456.0 1456 93.114 2987 3974 1 chr1B.!!$R1 987
13 TraesCS6B01G200700 chr1B 524297384 524298371 987 False 1454.0 1454 93.219 2988 3975 1 chr1B.!!$F3 987
14 TraesCS6B01G200700 chr1B 328125674 328126260 586 True 713.0 713 88.562 2982 3587 1 chr1B.!!$R2 605
15 TraesCS6B01G200700 chr3B 203964700 203965686 986 True 1568.0 1568 95.344 2988 3975 1 chr3B.!!$R2 987
16 TraesCS6B01G200700 chr3B 824661679 824662664 985 False 1434.0 1434 92.901 2990 3975 1 chr3B.!!$F2 985
17 TraesCS6B01G200700 chr3B 691360872 691361851 979 True 1142.0 1142 87.651 2982 3975 1 chr3B.!!$R4 993
18 TraesCS6B01G200700 chr3A 750064870 750065855 985 True 1423.0 1423 92.698 2990 3975 1 chr3A.!!$R1 985
19 TraesCS6B01G200700 chr3A 627996532 627997829 1297 False 385.0 385 72.981 1348 2614 1 chr3A.!!$F1 1266
20 TraesCS6B01G200700 chr5B 204178167 204179142 975 True 1419.0 1419 92.799 2990 3975 1 chr5B.!!$R1 985
21 TraesCS6B01G200700 chr5B 293187483 293188347 864 False 1179.0 1179 91.126 2989 3867 1 chr5B.!!$F2 878
22 TraesCS6B01G200700 chr6A 184887552 184888501 949 True 1321.0 1321 92.155 890 1819 1 chr6A.!!$R2 929
23 TraesCS6B01G200700 chr6A 184821150 184821867 717 True 542.5 931 96.190 2133 2940 2 chr6A.!!$R3 807
24 TraesCS6B01G200700 chr6D 131632500 131633416 916 False 1306.0 1306 92.919 1 887 1 chr6D.!!$F1 886
25 TraesCS6B01G200700 chr7D 498230031 498230915 884 True 1225.0 1225 92.316 1 850 1 chr7D.!!$R2 849
26 TraesCS6B01G200700 chr7D 60485919 60486743 824 True 211.0 211 72.533 1829 2617 1 chr7D.!!$R1 788
27 TraesCS6B01G200700 chr4B 199749924 199750772 848 False 1009.0 1009 88.194 3056 3910 1 chr4B.!!$F1 854
28 TraesCS6B01G200700 chr3D 485140515 485142125 1610 False 411.0 411 72.302 1028 2633 1 chr3D.!!$F1 1605
29 TraesCS6B01G200700 chr2A 58360826 58362153 1327 False 381.0 381 72.906 1304 2619 1 chr2A.!!$F1 1315
30 TraesCS6B01G200700 chr2D 57107903 57109238 1335 False 340.0 340 72.401 1277 2619 1 chr2D.!!$F1 1342
31 TraesCS6B01G200700 chr2D 57333370 57334003 633 True 231.0 231 74.251 1035 1683 1 chr2D.!!$R1 648
32 TraesCS6B01G200700 chr2B 90396236 90396968 732 False 246.0 246 73.622 1833 2571 1 chr2B.!!$F1 738

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
110 111 0.038159 GCAGTTGCGAGTCTAGTGGT 60.038 55.0 0.00 0.0 0.00 4.16 F
1993 2110 0.097499 CCACGTCACGTATGCTCGTA 59.903 55.0 0.41 0.0 42.27 3.43 F
2425 2614 0.108992 CGCTGCAGTTCAATGCCAAT 60.109 50.0 16.64 0.0 45.91 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2158 0.386100 CCTCGCCGTAGATGATGTCG 60.386 60.000 0.0 0.0 0.0 4.35 R
2845 3040 0.102481 CGTCCATTGTACTCCCTCCG 59.898 60.000 0.0 0.0 0.0 4.63 R
3935 4162 4.717629 CTGGAAGTGACGGCGCGA 62.718 66.667 12.1 0.0 0.0 5.87 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
58 59 2.519771 ATGAAAATGCAGCTCAGGGA 57.480 45.000 0.00 0.00 0.00 4.20
110 111 0.038159 GCAGTTGCGAGTCTAGTGGT 60.038 55.000 0.00 0.00 0.00 4.16
468 473 4.618965 ACTTTGTCTTCCACGTCTAGTTC 58.381 43.478 0.00 0.00 0.00 3.01
900 948 2.811504 CGGTCCCCGTTTTATAATCCCC 60.812 54.545 0.00 0.00 42.73 4.81
1002 1055 0.529773 TCCTACGCGCATCCATCAAC 60.530 55.000 5.73 0.00 0.00 3.18
1003 1056 0.809636 CCTACGCGCATCCATCAACA 60.810 55.000 5.73 0.00 0.00 3.33
1004 1057 1.220529 CTACGCGCATCCATCAACAT 58.779 50.000 5.73 0.00 0.00 2.71
1007 1060 0.377905 CGCGCATCCATCAACATCAA 59.622 50.000 8.75 0.00 0.00 2.57
1008 1061 1.596220 CGCGCATCCATCAACATCAAG 60.596 52.381 8.75 0.00 0.00 3.02
1009 1062 1.862815 GCGCATCCATCAACATCAAGC 60.863 52.381 0.30 0.00 0.00 4.01
1010 1063 1.268896 CGCATCCATCAACATCAAGCC 60.269 52.381 0.00 0.00 0.00 4.35
1011 1064 1.268896 GCATCCATCAACATCAAGCCG 60.269 52.381 0.00 0.00 0.00 5.52
1012 1065 2.291365 CATCCATCAACATCAAGCCGA 58.709 47.619 0.00 0.00 0.00 5.54
1013 1066 2.028420 TCCATCAACATCAAGCCGAG 57.972 50.000 0.00 0.00 0.00 4.63
1014 1067 1.019673 CCATCAACATCAAGCCGAGG 58.980 55.000 0.00 0.00 0.00 4.63
1015 1068 1.679944 CCATCAACATCAAGCCGAGGT 60.680 52.381 0.00 0.00 41.34 3.85
1016 1069 1.667724 CATCAACATCAAGCCGAGGTC 59.332 52.381 0.00 0.00 37.76 3.85
1017 1070 0.976641 TCAACATCAAGCCGAGGTCT 59.023 50.000 0.00 0.00 37.76 3.85
1067 1120 3.528370 CCGCTCTCCCCGACGATT 61.528 66.667 0.00 0.00 0.00 3.34
1100 1153 2.355837 TATCATTCGCGCCCGAGC 60.356 61.111 0.00 0.00 45.35 5.03
1158 1211 4.056125 CACTCTGTGGCGCCGAGA 62.056 66.667 29.37 26.09 0.00 4.04
1201 1254 4.910585 CCCTACATGGCCGCCGAC 62.911 72.222 4.58 0.00 0.00 4.79
1212 1265 3.744719 CGCCGACGAGGGTCAAGA 61.745 66.667 0.00 0.00 43.61 3.02
1250 1303 4.069232 CGCTGGACGCCCTCTTGA 62.069 66.667 0.00 0.00 34.21 3.02
1354 1423 1.347564 CGACGTCGACAGCTCGTAT 59.652 57.895 33.35 0.00 43.02 3.06
1718 1816 2.897350 CGCCGGATTCAGCCTTCC 60.897 66.667 5.05 0.00 0.00 3.46
1787 1897 2.602676 GCCACCACCCTGGAGCTAA 61.603 63.158 0.00 0.00 40.96 3.09
1819 1933 3.844090 GGCGCTGAGGAGGAGGAC 61.844 72.222 7.64 0.00 0.00 3.85
1863 1977 2.511373 CATGCCGAGCCTGCGTTA 60.511 61.111 0.00 0.00 0.00 3.18
1894 2008 2.825836 GGGGACGCCATCAAGCTG 60.826 66.667 3.14 0.00 0.00 4.24
1898 2012 1.738099 GACGCCATCAAGCTGTCGT 60.738 57.895 0.00 0.00 30.73 4.34
1936 2050 1.004277 GTCTGTCAAGCGTCGACCTG 61.004 60.000 10.58 5.31 32.15 4.00
1937 2051 1.170290 TCTGTCAAGCGTCGACCTGA 61.170 55.000 10.58 7.73 32.15 3.86
1947 2061 1.901948 TCGACCTGAACGCCAGTCT 60.902 57.895 4.95 0.00 41.33 3.24
1969 2086 2.125753 GGAGAGCAGTCGCAGTGG 60.126 66.667 0.00 0.00 42.27 4.00
1992 2109 1.154093 CCACGTCACGTATGCTCGT 60.154 57.895 0.41 0.00 45.10 4.18
1993 2110 0.097499 CCACGTCACGTATGCTCGTA 59.903 55.000 0.41 0.00 42.27 3.43
2015 2132 2.134630 CTTCTCCAGCACAAGGGCCT 62.135 60.000 0.00 0.00 0.00 5.19
2027 2144 3.741476 GGGCCTTGAAGCTGCACG 61.741 66.667 0.84 0.00 0.00 5.34
2033 2150 0.940126 CTTGAAGCTGCACGTCAACT 59.060 50.000 0.00 0.00 41.10 3.16
2038 2155 1.441515 GCTGCACGTCAACTGCATG 60.442 57.895 0.00 0.00 43.61 4.06
2039 2156 1.844771 GCTGCACGTCAACTGCATGA 61.845 55.000 0.00 0.00 43.61 3.07
2041 2158 0.307453 TGCACGTCAACTGCATGAAC 59.693 50.000 0.00 0.00 39.76 3.18
2052 2169 4.391405 ACTGCATGAACGACATCATCTA 57.609 40.909 0.00 0.00 37.96 1.98
2053 2170 4.115516 ACTGCATGAACGACATCATCTAC 58.884 43.478 0.00 0.00 37.96 2.59
2054 2171 3.115554 TGCATGAACGACATCATCTACG 58.884 45.455 0.00 0.00 37.96 3.51
2055 2172 2.472861 GCATGAACGACATCATCTACGG 59.527 50.000 0.00 0.00 37.96 4.02
2056 2173 2.203800 TGAACGACATCATCTACGGC 57.796 50.000 0.00 0.00 0.00 5.68
2057 2174 1.121240 GAACGACATCATCTACGGCG 58.879 55.000 4.80 4.80 0.00 6.46
2058 2175 0.736636 AACGACATCATCTACGGCGA 59.263 50.000 16.62 0.00 0.00 5.54
2059 2176 0.308068 ACGACATCATCTACGGCGAG 59.692 55.000 16.62 6.98 0.00 5.03
2060 2177 0.386100 CGACATCATCTACGGCGAGG 60.386 60.000 16.62 5.63 0.00 4.63
2061 2178 0.952280 GACATCATCTACGGCGAGGA 59.048 55.000 16.62 11.64 0.00 3.71
2062 2179 0.955178 ACATCATCTACGGCGAGGAG 59.045 55.000 16.62 7.96 0.00 3.69
2063 2180 0.242286 CATCATCTACGGCGAGGAGG 59.758 60.000 16.62 12.85 0.00 4.30
2064 2181 0.110678 ATCATCTACGGCGAGGAGGA 59.889 55.000 16.62 17.84 0.00 3.71
2065 2182 0.535328 TCATCTACGGCGAGGAGGAG 60.535 60.000 16.62 5.77 0.00 3.69
2066 2183 1.899534 ATCTACGGCGAGGAGGAGC 60.900 63.158 16.62 0.00 0.00 4.70
2067 2184 2.626255 ATCTACGGCGAGGAGGAGCA 62.626 60.000 16.62 0.00 34.54 4.26
2114 2270 1.715993 GAACCTCAAGCTCCTCGAAC 58.284 55.000 0.00 0.00 0.00 3.95
2121 2277 1.738350 CAAGCTCCTCGAACTAGACGA 59.262 52.381 13.67 13.67 38.11 4.20
2123 2279 2.645802 AGCTCCTCGAACTAGACGAAT 58.354 47.619 14.76 0.00 39.23 3.34
2223 2379 1.722751 GCTCAACTTGAACATGACGCG 60.723 52.381 3.53 3.53 0.00 6.01
2224 2380 0.865111 TCAACTTGAACATGACGCGG 59.135 50.000 12.47 0.00 0.00 6.46
2317 2482 1.145598 CAGGCTCGCATCCATGACT 59.854 57.895 0.00 0.00 0.00 3.41
2425 2614 0.108992 CGCTGCAGTTCAATGCCAAT 60.109 50.000 16.64 0.00 45.91 3.16
2429 2618 2.230508 CTGCAGTTCAATGCCAATGAGT 59.769 45.455 5.25 0.00 45.91 3.41
2523 2715 2.030562 CGGGAACACGTTCTGGCT 59.969 61.111 9.63 0.00 39.45 4.75
2662 2857 3.399330 TCTTAGGAACAAGCAGGAAACG 58.601 45.455 0.00 0.00 0.00 3.60
2664 2859 2.341846 AGGAACAAGCAGGAAACGAA 57.658 45.000 0.00 0.00 0.00 3.85
2752 2947 7.286087 TGGTTACATCCGATGTACAGTAATACT 59.714 37.037 18.90 0.00 44.79 2.12
2753 2948 7.806960 GGTTACATCCGATGTACAGTAATACTC 59.193 40.741 18.90 5.72 44.79 2.59
2754 2949 6.328641 ACATCCGATGTACAGTAATACTCC 57.671 41.667 12.50 0.00 42.78 3.85
2755 2950 5.243283 ACATCCGATGTACAGTAATACTCCC 59.757 44.000 12.50 0.00 42.78 4.30
2756 2951 5.057843 TCCGATGTACAGTAATACTCCCT 57.942 43.478 0.33 0.00 0.00 4.20
2757 2952 5.068636 TCCGATGTACAGTAATACTCCCTC 58.931 45.833 0.33 0.00 0.00 4.30
2758 2953 4.217983 CCGATGTACAGTAATACTCCCTCC 59.782 50.000 0.33 0.00 0.00 4.30
2759 2954 4.083431 CGATGTACAGTAATACTCCCTCCG 60.083 50.000 0.33 0.00 0.00 4.63
2760 2955 4.240881 TGTACAGTAATACTCCCTCCGT 57.759 45.455 0.00 0.00 0.00 4.69
2761 2956 4.603131 TGTACAGTAATACTCCCTCCGTT 58.397 43.478 0.00 0.00 0.00 4.44
2762 2957 4.641989 TGTACAGTAATACTCCCTCCGTTC 59.358 45.833 0.00 0.00 0.00 3.95
2763 2958 2.686915 ACAGTAATACTCCCTCCGTTCG 59.313 50.000 0.00 0.00 0.00 3.95
2764 2959 2.034305 CAGTAATACTCCCTCCGTTCGG 59.966 54.545 4.74 4.74 0.00 4.30
2765 2960 2.092212 AGTAATACTCCCTCCGTTCGGA 60.092 50.000 13.34 13.34 0.00 4.55
2766 2961 1.856629 AATACTCCCTCCGTTCGGAA 58.143 50.000 14.79 0.00 33.41 4.30
2767 2962 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
2768 2963 1.856629 TACTCCCTCCGTTCGGAATT 58.143 50.000 14.79 0.00 33.41 2.17
2769 2964 1.856629 ACTCCCTCCGTTCGGAATTA 58.143 50.000 14.79 2.82 33.41 1.40
2770 2965 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2771 2966 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2772 2967 1.753073 TCCCTCCGTTCGGAATTACTC 59.247 52.381 14.79 0.00 33.41 2.59
2773 2968 1.479323 CCCTCCGTTCGGAATTACTCA 59.521 52.381 14.79 0.00 33.41 3.41
2774 2969 2.102588 CCCTCCGTTCGGAATTACTCAT 59.897 50.000 14.79 0.00 33.41 2.90
2775 2970 3.381949 CCTCCGTTCGGAATTACTCATC 58.618 50.000 14.79 0.00 33.41 2.92
2776 2971 3.381949 CTCCGTTCGGAATTACTCATCC 58.618 50.000 14.79 0.00 33.41 3.51
2777 2972 2.761767 TCCGTTCGGAATTACTCATCCA 59.238 45.455 11.66 0.00 35.34 3.41
2778 2973 3.196039 TCCGTTCGGAATTACTCATCCAA 59.804 43.478 11.66 0.00 35.34 3.53
2779 2974 3.936453 CCGTTCGGAATTACTCATCCAAA 59.064 43.478 5.19 0.00 35.34 3.28
2780 2975 4.393680 CCGTTCGGAATTACTCATCCAAAA 59.606 41.667 5.19 0.00 35.34 2.44
2781 2976 5.106475 CCGTTCGGAATTACTCATCCAAAAA 60.106 40.000 5.19 0.00 35.34 1.94
2821 3016 9.325198 GATGTATTTCAGTTGTACATACATCCA 57.675 33.333 21.98 4.86 44.75 3.41
2822 3017 9.851686 ATGTATTTCAGTTGTACATACATCCAT 57.148 29.630 9.27 0.00 36.68 3.41
2823 3018 9.679661 TGTATTTCAGTTGTACATACATCCATT 57.320 29.630 0.00 0.00 35.89 3.16
2850 3045 8.712285 TTATGACAAGTAATTCTAAACGGAGG 57.288 34.615 0.00 0.00 0.00 4.30
2851 3046 5.484715 TGACAAGTAATTCTAAACGGAGGG 58.515 41.667 0.00 0.00 0.00 4.30
2852 3047 5.246656 TGACAAGTAATTCTAAACGGAGGGA 59.753 40.000 0.00 0.00 0.00 4.20
2853 3048 5.731591 ACAAGTAATTCTAAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
2854 3049 5.247792 ACAAGTAATTCTAAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
2855 3050 6.438425 ACAAGTAATTCTAAACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
2856 3051 6.462552 AGTAATTCTAAACGGAGGGAGTAC 57.537 41.667 0.00 0.00 0.00 2.73
2940 3135 1.206578 CTTTGCGCATTCGAACGGT 59.793 52.632 12.75 0.00 38.10 4.83
2941 3136 0.789383 CTTTGCGCATTCGAACGGTC 60.789 55.000 12.75 0.00 38.10 4.79
2942 3137 2.177654 TTTGCGCATTCGAACGGTCC 62.178 55.000 12.75 0.00 38.10 4.46
2943 3138 2.813908 GCGCATTCGAACGGTCCT 60.814 61.111 0.30 0.00 38.10 3.85
2944 3139 2.799540 GCGCATTCGAACGGTCCTC 61.800 63.158 0.30 0.00 38.10 3.71
2945 3140 1.445410 CGCATTCGAACGGTCCTCA 60.445 57.895 0.00 0.00 38.10 3.86
2946 3141 1.413767 CGCATTCGAACGGTCCTCAG 61.414 60.000 0.00 0.00 38.10 3.35
2947 3142 1.084370 GCATTCGAACGGTCCTCAGG 61.084 60.000 0.00 0.00 0.00 3.86
2948 3143 0.246635 CATTCGAACGGTCCTCAGGT 59.753 55.000 0.00 0.00 0.00 4.00
2949 3144 0.531200 ATTCGAACGGTCCTCAGGTC 59.469 55.000 0.00 0.00 0.00 3.85
2950 3145 0.538977 TTCGAACGGTCCTCAGGTCT 60.539 55.000 0.00 0.00 0.00 3.85
2951 3146 1.213013 CGAACGGTCCTCAGGTCTG 59.787 63.158 0.00 0.00 0.00 3.51
2952 3147 1.524863 CGAACGGTCCTCAGGTCTGT 61.525 60.000 0.00 0.00 32.12 3.41
2953 3148 0.038159 GAACGGTCCTCAGGTCTGTG 60.038 60.000 2.83 0.00 31.29 3.66
2954 3149 2.100879 AACGGTCCTCAGGTCTGTGC 62.101 60.000 2.83 0.00 31.29 4.57
2955 3150 2.279069 CGGTCCTCAGGTCTGTGCT 61.279 63.158 0.00 0.00 0.00 4.40
2956 3151 1.294780 GGTCCTCAGGTCTGTGCTG 59.705 63.158 0.00 0.00 0.00 4.41
2957 3152 1.375268 GTCCTCAGGTCTGTGCTGC 60.375 63.158 0.00 0.00 0.00 5.25
2958 3153 1.534959 TCCTCAGGTCTGTGCTGCT 60.535 57.895 0.00 0.00 0.00 4.24
2959 3154 1.079266 CCTCAGGTCTGTGCTGCTC 60.079 63.158 0.00 0.00 0.00 4.26
2960 3155 1.079266 CTCAGGTCTGTGCTGCTCC 60.079 63.158 0.00 0.00 0.00 4.70
2961 3156 1.534959 TCAGGTCTGTGCTGCTCCT 60.535 57.895 0.00 0.00 0.00 3.69
2962 3157 0.251787 TCAGGTCTGTGCTGCTCCTA 60.252 55.000 0.00 0.00 0.00 2.94
2963 3158 0.610174 CAGGTCTGTGCTGCTCCTAA 59.390 55.000 0.00 0.00 0.00 2.69
2964 3159 0.610687 AGGTCTGTGCTGCTCCTAAC 59.389 55.000 0.00 0.00 0.00 2.34
2965 3160 0.391793 GGTCTGTGCTGCTCCTAACC 60.392 60.000 0.00 1.66 0.00 2.85
2966 3161 0.391793 GTCTGTGCTGCTCCTAACCC 60.392 60.000 0.00 0.00 0.00 4.11
2967 3162 0.545309 TCTGTGCTGCTCCTAACCCT 60.545 55.000 0.00 0.00 0.00 4.34
2968 3163 0.392193 CTGTGCTGCTCCTAACCCTG 60.392 60.000 0.00 0.00 0.00 4.45
3019 3215 6.346096 CCGATTTGGTCTATACAAGGAAGAA 58.654 40.000 0.00 0.00 0.00 2.52
3071 3281 6.964464 TGACCCATAAGTTATCTTAGGCAAA 58.036 36.000 0.00 0.00 39.17 3.68
3101 3325 9.695155 TTTTAGGCAAATTATCTTAGGCTAAGT 57.305 29.630 28.40 19.58 44.50 2.24
3240 3464 1.514087 CTAAACCCTAGCCGCGACA 59.486 57.895 8.23 0.00 0.00 4.35
3457 3681 3.636231 CCGCCAACTCCTCCACCA 61.636 66.667 0.00 0.00 0.00 4.17
3459 3683 2.883828 CGCCAACTCCTCCACCACT 61.884 63.158 0.00 0.00 0.00 4.00
3640 3864 1.421268 AGTTCACACAGGAGGCAATGA 59.579 47.619 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
58 59 2.019249 CCGACTGCAATTCATGTCCAT 58.981 47.619 0.00 0.00 0.00 3.41
110 111 8.749354 ACCATGTCGACTATAATTGCATATCTA 58.251 33.333 17.92 0.00 0.00 1.98
887 935 5.333568 CGTTCGGAATCGGGGATTATAAAAC 60.334 44.000 0.00 0.00 31.89 2.43
1002 1055 2.670635 CGAAGACCTCGGCTTGATG 58.329 57.895 0.00 0.00 44.20 3.07
1011 1064 3.089117 GTGTCGACACGAAGACCTC 57.911 57.895 31.03 7.09 37.72 3.85
1142 1195 3.753434 CTCTCGGCGCCACAGAGT 61.753 66.667 31.43 0.00 40.99 3.24
1212 1265 3.553095 GAAGGGCTGTTGCGGAGGT 62.553 63.158 0.00 0.00 40.82 3.85
1354 1423 2.504274 GGGGTCGTCCACACTGTCA 61.504 63.158 0.04 0.00 37.04 3.58
1787 1897 2.348888 CGCCCACGGAGTAGGTCTT 61.349 63.158 0.00 0.00 42.67 3.01
1826 1940 3.401411 GAGCTCGATGCCGATGCG 61.401 66.667 0.00 0.00 44.62 4.73
1827 1941 3.401411 CGAGCTCGATGCCGATGC 61.401 66.667 32.06 0.00 44.62 3.91
1880 1994 3.084579 CGACAGCTTGATGGCGTC 58.915 61.111 5.92 0.00 46.75 5.19
1883 1997 1.503542 CCAACGACAGCTTGATGGC 59.496 57.895 0.00 0.00 0.00 4.40
1886 2000 1.089920 GATGCCAACGACAGCTTGAT 58.910 50.000 0.00 0.00 0.00 2.57
1918 2032 1.170290 TCAGGTCGACGCTTGACAGA 61.170 55.000 9.92 0.00 38.10 3.41
1922 2036 1.371267 CGTTCAGGTCGACGCTTGA 60.371 57.895 9.92 10.41 32.11 3.02
1954 2068 2.601666 TCCCACTGCGACTGCTCT 60.602 61.111 0.00 0.00 43.34 4.09
1958 2072 4.767255 GGGCTCCCACTGCGACTG 62.767 72.222 0.00 0.00 35.81 3.51
1969 2086 1.518572 CATACGTGACGTGGGCTCC 60.519 63.158 22.16 0.00 41.39 4.70
2008 2125 1.905354 GTGCAGCTTCAAGGCCCTT 60.905 57.895 0.00 0.00 0.00 3.95
2015 2132 0.657312 CAGTTGACGTGCAGCTTCAA 59.343 50.000 0.00 0.00 35.72 2.69
2027 2144 2.480037 TGATGTCGTTCATGCAGTTGAC 59.520 45.455 0.00 0.00 36.83 3.18
2033 2150 3.115554 CGTAGATGATGTCGTTCATGCA 58.884 45.455 0.00 0.00 36.48 3.96
2038 2155 1.121240 CGCCGTAGATGATGTCGTTC 58.879 55.000 0.00 0.00 0.00 3.95
2039 2156 0.736636 TCGCCGTAGATGATGTCGTT 59.263 50.000 0.00 0.00 0.00 3.85
2041 2158 0.386100 CCTCGCCGTAGATGATGTCG 60.386 60.000 0.00 0.00 0.00 4.35
2121 2277 3.502920 CTGCTCGTGTACTCGAAGAATT 58.497 45.455 19.35 0.00 39.34 2.17
2123 2279 1.401148 GCTGCTCGTGTACTCGAAGAA 60.401 52.381 19.35 8.77 39.34 2.52
2129 2285 2.155194 CGCTGCTGCTCGTGTACTC 61.155 63.158 14.03 0.00 36.97 2.59
2224 2380 3.989566 CTCGTCGTCGCGGTACCAC 62.990 68.421 13.54 0.07 36.96 4.16
2244 2400 1.103398 GGCCGGATCATTGGTCTTGG 61.103 60.000 5.05 1.05 0.00 3.61
2376 2562 1.291588 AGACTCGTCTGCAAGCAGG 59.708 57.895 20.78 8.16 43.75 4.85
2523 2715 0.179020 CTTGTTGCAGAGGTGGTCCA 60.179 55.000 0.00 0.00 35.89 4.02
2597 2789 4.025401 GTGGTGCACCCGAAAGCG 62.025 66.667 32.62 0.00 35.15 4.68
2662 2857 5.883673 ACTCTGAGATGTGGAGTACTACTTC 59.116 44.000 12.44 5.24 38.37 3.01
2664 2859 5.444744 ACTCTGAGATGTGGAGTACTACT 57.555 43.478 12.44 0.00 38.37 2.57
2727 2922 7.655490 AGTATTACTGTACATCGGATGTAACC 58.345 38.462 27.41 18.33 46.36 2.85
2752 2947 1.753073 GAGTAATTCCGAACGGAGGGA 59.247 52.381 15.34 2.49 46.06 4.20
2753 2948 1.479323 TGAGTAATTCCGAACGGAGGG 59.521 52.381 15.34 0.00 46.06 4.30
2754 2949 2.953466 TGAGTAATTCCGAACGGAGG 57.047 50.000 15.34 0.00 46.06 4.30
2755 2950 3.181479 TGGATGAGTAATTCCGAACGGAG 60.181 47.826 15.34 0.00 46.06 4.63
2756 2951 2.761767 TGGATGAGTAATTCCGAACGGA 59.238 45.455 12.04 12.04 43.52 4.69
2757 2952 3.173668 TGGATGAGTAATTCCGAACGG 57.826 47.619 6.94 6.94 34.58 4.44
2758 2953 5.539582 TTTTGGATGAGTAATTCCGAACG 57.460 39.130 0.00 0.00 35.56 3.95
2796 2991 9.851686 ATGGATGTATGTACAACTGAAATACAT 57.148 29.630 13.28 13.28 43.60 2.29
2797 2992 9.679661 AATGGATGTATGTACAACTGAAATACA 57.320 29.630 0.00 2.50 39.99 2.29
2824 3019 9.158233 CCTCCGTTTAGAATTACTTGTCATAAA 57.842 33.333 0.00 0.00 0.00 1.40
2825 3020 7.767198 CCCTCCGTTTAGAATTACTTGTCATAA 59.233 37.037 0.00 0.00 0.00 1.90
2826 3021 7.124599 TCCCTCCGTTTAGAATTACTTGTCATA 59.875 37.037 0.00 0.00 0.00 2.15
2827 3022 6.070424 TCCCTCCGTTTAGAATTACTTGTCAT 60.070 38.462 0.00 0.00 0.00 3.06
2828 3023 5.246656 TCCCTCCGTTTAGAATTACTTGTCA 59.753 40.000 0.00 0.00 0.00 3.58
2829 3024 5.727434 TCCCTCCGTTTAGAATTACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
2830 3025 5.247792 ACTCCCTCCGTTTAGAATTACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
2831 3026 5.731591 ACTCCCTCCGTTTAGAATTACTTG 58.268 41.667 0.00 0.00 0.00 3.16
2832 3027 6.438425 TGTACTCCCTCCGTTTAGAATTACTT 59.562 38.462 0.00 0.00 0.00 2.24
2833 3028 5.954150 TGTACTCCCTCCGTTTAGAATTACT 59.046 40.000 0.00 0.00 0.00 2.24
2834 3029 6.212888 TGTACTCCCTCCGTTTAGAATTAC 57.787 41.667 0.00 0.00 0.00 1.89
2835 3030 6.855763 TTGTACTCCCTCCGTTTAGAATTA 57.144 37.500 0.00 0.00 0.00 1.40
2836 3031 5.750352 TTGTACTCCCTCCGTTTAGAATT 57.250 39.130 0.00 0.00 0.00 2.17
2837 3032 5.396436 CCATTGTACTCCCTCCGTTTAGAAT 60.396 44.000 0.00 0.00 0.00 2.40
2838 3033 4.081309 CCATTGTACTCCCTCCGTTTAGAA 60.081 45.833 0.00 0.00 0.00 2.10
2839 3034 3.449737 CCATTGTACTCCCTCCGTTTAGA 59.550 47.826 0.00 0.00 0.00 2.10
2840 3035 3.449737 TCCATTGTACTCCCTCCGTTTAG 59.550 47.826 0.00 0.00 0.00 1.85
2841 3036 3.196254 GTCCATTGTACTCCCTCCGTTTA 59.804 47.826 0.00 0.00 0.00 2.01
2842 3037 2.027469 GTCCATTGTACTCCCTCCGTTT 60.027 50.000 0.00 0.00 0.00 3.60
2843 3038 1.553704 GTCCATTGTACTCCCTCCGTT 59.446 52.381 0.00 0.00 0.00 4.44
2844 3039 1.192428 GTCCATTGTACTCCCTCCGT 58.808 55.000 0.00 0.00 0.00 4.69
2845 3040 0.102481 CGTCCATTGTACTCCCTCCG 59.898 60.000 0.00 0.00 0.00 4.63
2846 3041 1.481871 TCGTCCATTGTACTCCCTCC 58.518 55.000 0.00 0.00 0.00 4.30
2847 3042 2.959707 AGATCGTCCATTGTACTCCCTC 59.040 50.000 0.00 0.00 0.00 4.30
2848 3043 2.959707 GAGATCGTCCATTGTACTCCCT 59.040 50.000 0.00 0.00 0.00 4.20
2849 3044 2.036089 GGAGATCGTCCATTGTACTCCC 59.964 54.545 0.00 0.00 46.10 4.30
2850 3045 3.372660 GGAGATCGTCCATTGTACTCC 57.627 52.381 0.00 0.00 46.10 3.85
2905 3100 4.423732 GCAAAGCTTTGTTCAACTCTGAA 58.576 39.130 33.47 0.00 40.24 3.02
2940 3135 1.534959 AGCAGCACAGACCTGAGGA 60.535 57.895 4.99 0.00 32.03 3.71
2941 3136 1.079266 GAGCAGCACAGACCTGAGG 60.079 63.158 0.00 0.00 32.03 3.86
2942 3137 1.079266 GGAGCAGCACAGACCTGAG 60.079 63.158 3.76 0.00 32.03 3.35
2943 3138 0.251787 TAGGAGCAGCACAGACCTGA 60.252 55.000 3.76 0.00 32.03 3.86
2944 3139 0.610174 TTAGGAGCAGCACAGACCTG 59.390 55.000 0.00 0.00 32.90 4.00
2945 3140 0.610687 GTTAGGAGCAGCACAGACCT 59.389 55.000 0.00 0.00 35.11 3.85
2946 3141 0.391793 GGTTAGGAGCAGCACAGACC 60.392 60.000 0.00 0.00 0.00 3.85
2947 3142 0.391793 GGGTTAGGAGCAGCACAGAC 60.392 60.000 0.00 0.00 0.00 3.51
2948 3143 0.545309 AGGGTTAGGAGCAGCACAGA 60.545 55.000 0.00 0.00 0.00 3.41
2949 3144 0.392193 CAGGGTTAGGAGCAGCACAG 60.392 60.000 0.00 0.00 0.00 3.66
2950 3145 0.835971 TCAGGGTTAGGAGCAGCACA 60.836 55.000 0.00 0.00 0.00 4.57
2951 3146 0.324943 TTCAGGGTTAGGAGCAGCAC 59.675 55.000 0.00 0.00 0.00 4.40
2952 3147 1.064003 TTTCAGGGTTAGGAGCAGCA 58.936 50.000 0.00 0.00 0.00 4.41
2953 3148 2.200373 TTTTCAGGGTTAGGAGCAGC 57.800 50.000 0.00 0.00 0.00 5.25
2977 3172 4.753516 TCGGTCATAACATGATGAGGTT 57.246 40.909 0.00 0.00 42.04 3.50
2980 3175 5.993891 CCAAATCGGTCATAACATGATGAG 58.006 41.667 0.00 0.00 42.04 2.90
3273 3497 4.954118 TGAGGTGGAGGTGGGCGT 62.954 66.667 0.00 0.00 0.00 5.68
3935 4162 4.717629 CTGGAAGTGACGGCGCGA 62.718 66.667 12.10 0.00 0.00 5.87


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

AutoCloner maintained by Alex Coulton.