Multiple sequence alignment - TraesCS1A01G161200

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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 TraesCS1A01G161200 chr1A 100.000 6142 0 0 1 6142 290122284 290128425 0.000000e+00 11343.0
1 TraesCS1A01G161200 chr1A 84.957 1170 124 28 3966 5120 338594104 338592972 0.000000e+00 1138.0
2 TraesCS1A01G161200 chr1A 83.868 998 134 22 2198 3176 294039437 294040426 0.000000e+00 926.0
3 TraesCS1A01G161200 chr1A 82.759 928 103 35 3966 4877 293737306 293738192 0.000000e+00 774.0
4 TraesCS1A01G161200 chr1A 83.562 730 87 22 3323 4039 294040637 294041346 0.000000e+00 652.0
5 TraesCS1A01G161200 chr1A 86.792 530 65 5 3292 3819 338594685 338594159 2.470000e-163 586.0
6 TraesCS1A01G161200 chr1A 84.565 609 72 19 2684 3290 338595359 338594771 8.870000e-163 584.0
7 TraesCS1A01G161200 chr1A 95.205 146 7 0 5162 5307 290142250 290142105 1.330000e-56 231.0
8 TraesCS1A01G161200 chr1A 100.000 62 0 0 799 860 290123021 290123082 1.400000e-21 115.0
9 TraesCS1A01G161200 chr1A 100.000 62 0 0 738 799 290123082 290123143 1.400000e-21 115.0
10 TraesCS1A01G161200 chr1A 94.000 50 2 1 2015 2063 338595864 338595815 2.370000e-09 75.0
11 TraesCS1A01G161200 chr1B 95.284 4156 133 37 881 4997 322472229 322476360 0.000000e+00 6530.0
12 TraesCS1A01G161200 chr1B 85.500 1131 128 16 2684 3806 350443391 350442289 0.000000e+00 1147.0
13 TraesCS1A01G161200 chr1B 85.359 1045 107 23 3966 4996 350442223 350441211 0.000000e+00 1040.0
14 TraesCS1A01G161200 chr1B 85.657 1004 116 19 2199 3176 327227633 327228634 0.000000e+00 1031.0
15 TraesCS1A01G161200 chr1B 83.008 1024 107 30 4134 5113 327229594 327230594 0.000000e+00 865.0
16 TraesCS1A01G161200 chr1B 84.045 890 93 27 4149 5008 326914156 326915026 0.000000e+00 811.0
17 TraesCS1A01G161200 chr1B 83.627 739 89 22 3314 4039 327228833 327229552 0.000000e+00 665.0
18 TraesCS1A01G161200 chr1B 84.945 631 75 15 2198 2812 326912205 326912831 6.760000e-174 621.0
19 TraesCS1A01G161200 chr1B 85.390 616 71 14 2562 3171 327340953 327341555 6.760000e-174 621.0
20 TraesCS1A01G161200 chr1B 85.106 376 44 9 2198 2562 327339348 327339722 2.090000e-99 374.0
21 TraesCS1A01G161200 chr1B 95.833 120 5 0 5043 5162 322476371 322476490 1.750000e-45 195.0
22 TraesCS1A01G161200 chr1B 82.710 214 24 8 1055 1267 327226216 327226417 1.760000e-40 178.0
23 TraesCS1A01G161200 chr1B 82.326 215 27 9 1055 1269 326911102 326911305 6.330000e-40 176.0
24 TraesCS1A01G161200 chr1B 96.078 51 2 0 2085 2135 350443851 350443801 3.950000e-12 84.2
25 TraesCS1A01G161200 chr1D 92.854 4198 173 56 881 5002 223161021 223165167 0.000000e+00 5973.0
26 TraesCS1A01G161200 chr1D 86.649 1131 116 16 2684 3806 261723255 261724358 0.000000e+00 1219.0
27 TraesCS1A01G161200 chr1D 91.152 825 46 10 1 800 122530018 122530840 0.000000e+00 1094.0
28 TraesCS1A01G161200 chr1D 84.930 1002 125 16 2198 3176 226943121 226944119 0.000000e+00 990.0
29 TraesCS1A01G161200 chr1D 85.246 976 113 20 2199 3147 227373575 227374546 0.000000e+00 976.0
30 TraesCS1A01G161200 chr1D 87.317 820 78 17 4264 5060 226827594 226828410 0.000000e+00 915.0
31 TraesCS1A01G161200 chr1D 85.111 900 89 19 3314 4180 227648728 227649615 0.000000e+00 878.0
32 TraesCS1A01G161200 chr1D 84.994 893 93 24 4149 5008 226945063 226945947 0.000000e+00 869.0
33 TraesCS1A01G161200 chr1D 82.817 1001 120 22 2199 3171 226825346 226826322 0.000000e+00 848.0
34 TraesCS1A01G161200 chr1D 83.402 976 94 31 4134 5064 227375619 227376571 0.000000e+00 843.0
35 TraesCS1A01G161200 chr1D 82.740 927 105 33 3966 4877 226468912 226469798 0.000000e+00 774.0
36 TraesCS1A01G161200 chr1D 86.817 622 70 9 2562 3176 208416420 208415804 0.000000e+00 684.0
37 TraesCS1A01G161200 chr1D 86.560 625 69 10 2562 3176 227647998 227648617 0.000000e+00 675.0
38 TraesCS1A01G161200 chr1D 83.784 703 82 24 3314 4007 227374866 227375545 6.710000e-179 638.0
39 TraesCS1A01G161200 chr1D 84.574 376 45 10 2198 2562 227647078 227647451 1.630000e-95 361.0
40 TraesCS1A01G161200 chr1D 89.123 285 29 2 320 604 376276434 376276716 2.720000e-93 353.0
41 TraesCS1A01G161200 chr6A 96.840 981 31 0 5162 6142 582805110 582806090 0.000000e+00 1640.0
42 TraesCS1A01G161200 chr6A 93.617 141 9 0 5163 5303 582809497 582809357 1.730000e-50 211.0
43 TraesCS1A01G161200 chr2D 95.441 987 38 3 5162 6142 630787170 630786185 0.000000e+00 1567.0
44 TraesCS1A01G161200 chr2D 90.476 147 14 0 5161 5307 630778832 630778978 1.750000e-45 195.0
45 TraesCS1A01G161200 chr2D 100.000 30 0 0 2171 2200 476352655 476352684 8.600000e-04 56.5
46 TraesCS1A01G161200 chr6D 93.821 971 27 13 5173 6142 391887057 391886119 0.000000e+00 1430.0
47 TraesCS1A01G161200 chr6D 91.156 147 13 0 5161 5307 391880854 391881000 3.750000e-47 200.0
48 TraesCS1A01G161200 chr2B 90.585 1009 63 17 5162 6142 231244838 231243834 0.000000e+00 1308.0
49 TraesCS1A01G161200 chr2B 89.104 982 73 11 5162 6142 76501168 76500220 0.000000e+00 1190.0
50 TraesCS1A01G161200 chr2B 94.386 766 43 0 5377 6142 326311976 326312741 0.000000e+00 1177.0
51 TraesCS1A01G161200 chr7A 95.734 797 33 1 1 797 657677304 657678099 0.000000e+00 1282.0
52 TraesCS1A01G161200 chr7A 92.857 84 6 0 799 882 657678040 657678123 8.360000e-24 122.0
53 TraesCS1A01G161200 chr5B 88.856 1005 63 20 5163 6142 3572770 3571790 0.000000e+00 1190.0
54 TraesCS1A01G161200 chr5B 90.620 661 31 11 5513 6142 280458082 280457422 0.000000e+00 848.0
55 TraesCS1A01G161200 chr5B 88.339 283 30 3 323 604 547979791 547979511 2.740000e-88 337.0
56 TraesCS1A01G161200 chr5B 87.956 274 23 6 5256 5523 280458301 280458032 1.290000e-81 315.0
57 TraesCS1A01G161200 chr5B 85.915 71 3 5 2130 2198 401008076 401008141 1.100000e-07 69.4
58 TraesCS1A01G161200 chr5B 84.416 77 2 5 2136 2202 661232286 661232210 3.970000e-07 67.6
59 TraesCS1A01G161200 chr6B 87.650 834 55 23 5163 5971 60118491 60117681 0.000000e+00 926.0
60 TraesCS1A01G161200 chr6B 91.878 394 25 3 219 605 93326779 93326386 1.510000e-150 544.0
61 TraesCS1A01G161200 chr6B 93.370 181 12 0 1 181 93326961 93326781 1.010000e-67 268.0
62 TraesCS1A01G161200 chr6B 93.370 181 11 1 620 800 93326331 93326152 3.650000e-67 267.0
63 TraesCS1A01G161200 chr6B 91.489 94 7 1 799 892 93326214 93326122 1.800000e-25 128.0
64 TraesCS1A01G161200 chr6B 86.957 69 7 2 2131 2198 25612787 25612720 6.600000e-10 76.8
65 TraesCS1A01G161200 chr4D 93.709 604 38 0 1 604 366972065 366972668 0.000000e+00 905.0
66 TraesCS1A01G161200 chr4D 88.961 616 46 14 5533 6140 477005985 477005384 0.000000e+00 741.0
67 TraesCS1A01G161200 chr4D 92.135 178 11 3 624 800 366972726 366972901 1.320000e-61 248.0
68 TraesCS1A01G161200 chr4D 91.954 87 5 2 799 884 366972840 366972925 3.010000e-23 121.0
69 TraesCS1A01G161200 chr2A 90.229 655 33 13 5513 6142 617846353 617847001 0.000000e+00 826.0
70 TraesCS1A01G161200 chr2A 88.558 437 41 5 173 604 768055081 768054649 7.060000e-144 521.0
71 TraesCS1A01G161200 chr2A 92.308 52 2 2 2132 2182 741094854 741094904 8.540000e-09 73.1
72 TraesCS1A01G161200 chr7B 89.066 439 37 6 173 604 232211912 232211478 9.060000e-148 534.0
73 TraesCS1A01G161200 chr3B 89.016 437 41 3 173 604 525638024 525638458 9.060000e-148 534.0
74 TraesCS1A01G161200 chr3B 92.308 91 6 1 710 800 813008093 813008004 1.800000e-25 128.0
75 TraesCS1A01G161200 chr3B 89.831 59 4 2 2142 2198 177068011 177068069 2.370000e-09 75.0
76 TraesCS1A01G161200 chr5D 81.716 443 59 10 173 599 565315133 565315569 3.520000e-92 350.0
77 TraesCS1A01G161200 chr5D 94.444 36 1 1 2173 2208 53759127 53759093 3.000000e-03 54.7
78 TraesCS1A01G161200 chr4B 92.308 52 3 1 2131 2182 22844126 22844076 8.540000e-09 73.1
79 TraesCS1A01G161200 chr7D 85.714 70 4 4 2134 2198 312564524 312564456 1.100000e-07 69.4
80 TraesCS1A01G161200 chr5A 96.875 32 0 1 852 882 486845981 486845950 1.100000e-02 52.8


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 TraesCS1A01G161200 chr1A 290122284 290128425 6141 False 11343.000000 11343 100.000000 1 6142 1 chr1A.!!$F1 6141
1 TraesCS1A01G161200 chr1A 294039437 294041346 1909 False 789.000000 926 83.715000 2198 4039 2 chr1A.!!$F4 1841
2 TraesCS1A01G161200 chr1A 293737306 293738192 886 False 774.000000 774 82.759000 3966 4877 1 chr1A.!!$F2 911
3 TraesCS1A01G161200 chr1A 338592972 338595864 2892 True 595.750000 1138 87.578500 2015 5120 4 chr1A.!!$R2 3105
4 TraesCS1A01G161200 chr1B 322472229 322476490 4261 False 3362.500000 6530 95.558500 881 5162 2 chr1B.!!$F1 4281
5 TraesCS1A01G161200 chr1B 350441211 350443851 2640 True 757.066667 1147 88.979000 2085 4996 3 chr1B.!!$R1 2911
6 TraesCS1A01G161200 chr1B 327226216 327230594 4378 False 684.750000 1031 83.750500 1055 5113 4 chr1B.!!$F3 4058
7 TraesCS1A01G161200 chr1B 326911102 326915026 3924 False 536.000000 811 83.772000 1055 5008 3 chr1B.!!$F2 3953
8 TraesCS1A01G161200 chr1B 327339348 327341555 2207 False 497.500000 621 85.248000 2198 3171 2 chr1B.!!$F4 973
9 TraesCS1A01G161200 chr1D 223161021 223165167 4146 False 5973.000000 5973 92.854000 881 5002 1 chr1D.!!$F2 4121
10 TraesCS1A01G161200 chr1D 261723255 261724358 1103 False 1219.000000 1219 86.649000 2684 3806 1 chr1D.!!$F4 1122
11 TraesCS1A01G161200 chr1D 122530018 122530840 822 False 1094.000000 1094 91.152000 1 800 1 chr1D.!!$F1 799
12 TraesCS1A01G161200 chr1D 226943121 226945947 2826 False 929.500000 990 84.962000 2198 5008 2 chr1D.!!$F7 2810
13 TraesCS1A01G161200 chr1D 226825346 226828410 3064 False 881.500000 915 85.067000 2199 5060 2 chr1D.!!$F6 2861
14 TraesCS1A01G161200 chr1D 227373575 227376571 2996 False 819.000000 976 84.144000 2199 5064 3 chr1D.!!$F8 2865
15 TraesCS1A01G161200 chr1D 226468912 226469798 886 False 774.000000 774 82.740000 3966 4877 1 chr1D.!!$F3 911
16 TraesCS1A01G161200 chr1D 208415804 208416420 616 True 684.000000 684 86.817000 2562 3176 1 chr1D.!!$R1 614
17 TraesCS1A01G161200 chr1D 227647078 227649615 2537 False 638.000000 878 85.415000 2198 4180 3 chr1D.!!$F9 1982
18 TraesCS1A01G161200 chr6A 582805110 582806090 980 False 1640.000000 1640 96.840000 5162 6142 1 chr6A.!!$F1 980
19 TraesCS1A01G161200 chr2D 630786185 630787170 985 True 1567.000000 1567 95.441000 5162 6142 1 chr2D.!!$R1 980
20 TraesCS1A01G161200 chr6D 391886119 391887057 938 True 1430.000000 1430 93.821000 5173 6142 1 chr6D.!!$R1 969
21 TraesCS1A01G161200 chr2B 231243834 231244838 1004 True 1308.000000 1308 90.585000 5162 6142 1 chr2B.!!$R2 980
22 TraesCS1A01G161200 chr2B 76500220 76501168 948 True 1190.000000 1190 89.104000 5162 6142 1 chr2B.!!$R1 980
23 TraesCS1A01G161200 chr2B 326311976 326312741 765 False 1177.000000 1177 94.386000 5377 6142 1 chr2B.!!$F1 765
24 TraesCS1A01G161200 chr7A 657677304 657678123 819 False 702.000000 1282 94.295500 1 882 2 chr7A.!!$F1 881
25 TraesCS1A01G161200 chr5B 3571790 3572770 980 True 1190.000000 1190 88.856000 5163 6142 1 chr5B.!!$R1 979
26 TraesCS1A01G161200 chr5B 280457422 280458301 879 True 581.500000 848 89.288000 5256 6142 2 chr5B.!!$R4 886
27 TraesCS1A01G161200 chr6B 60117681 60118491 810 True 926.000000 926 87.650000 5163 5971 1 chr6B.!!$R2 808
28 TraesCS1A01G161200 chr6B 93326122 93326961 839 True 301.750000 544 92.526750 1 892 4 chr6B.!!$R3 891
29 TraesCS1A01G161200 chr4D 477005384 477005985 601 True 741.000000 741 88.961000 5533 6140 1 chr4D.!!$R1 607
30 TraesCS1A01G161200 chr4D 366972065 366972925 860 False 424.666667 905 92.599333 1 884 3 chr4D.!!$F1 883
31 TraesCS1A01G161200 chr2A 617846353 617847001 648 False 826.000000 826 90.229000 5513 6142 1 chr2A.!!$F1 629

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
53 54 0.107557 TGCATCGCATCATGGTCAGT 60.108 50.000 0.00 0.0 31.71 3.41 F
861 887 0.785979 CAACAAAATTCCGCAGCAGC 59.214 50.000 0.00 0.0 37.42 5.25 F
1153 1196 0.179936 CTCCACTTCCTCATGGGAGC 59.820 60.000 0.00 0.0 42.96 4.70 F
2347 2994 0.833287 AATATCAGCCCGTGCACTCT 59.167 50.000 16.19 6.3 41.13 3.24 F
3650 6197 3.578282 ACTTGGACCATGAACAATTTCCC 59.422 43.478 14.05 0.0 0.00 3.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1007 1033 1.005332 TCACCAGTCCTCTCCTCTCTG 59.995 57.143 0.00 0.00 0.00 3.35 R
2337 2984 0.895530 TCTTCCCTAAGAGTGCACGG 59.104 55.000 12.01 5.94 36.80 4.94 R
2527 3174 6.825610 ACATGAATTTTGCAGGTTCCTTTTA 58.174 32.000 0.00 0.00 0.00 1.52 R
4301 7158 1.068753 CTGAGCATGGGTCTAGCCG 59.931 63.158 0.00 0.00 38.44 5.52 R
5331 8251 0.763035 GTAATCCCCCACACGCCTAT 59.237 55.000 0.00 0.00 0.00 2.57 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
53 54 0.107557 TGCATCGCATCATGGTCAGT 60.108 50.000 0.00 0.00 31.71 3.41
93 94 1.586028 GCTTCCAAATCCAGCGCAA 59.414 52.632 11.47 0.00 0.00 4.85
189 190 1.207089 TCTGCCTCTACCCAAACATCG 59.793 52.381 0.00 0.00 0.00 3.84
276 277 1.213296 TCCTGATTCTACTTGGCCCC 58.787 55.000 0.00 0.00 0.00 5.80
277 278 0.918983 CCTGATTCTACTTGGCCCCA 59.081 55.000 0.00 0.00 0.00 4.96
293 294 1.548582 CCCCACTGCATTTTCCTCAGT 60.549 52.381 0.00 0.00 41.29 3.41
297 298 4.326826 CCACTGCATTTTCCTCAGTTAGA 58.673 43.478 0.00 0.00 38.85 2.10
299 300 5.416952 CCACTGCATTTTCCTCAGTTAGATT 59.583 40.000 0.00 0.00 38.85 2.40
349 351 4.839668 TTGATTAGTTCGGTGTTTTGGG 57.160 40.909 0.00 0.00 0.00 4.12
375 377 6.870971 TTACAGTTTGATTGGTTGGACTAC 57.129 37.500 0.00 0.00 0.00 2.73
423 425 4.263462 ACAAGAGATGTGGCTGTCCAATTA 60.263 41.667 0.00 0.00 45.53 1.40
690 716 6.482973 AGGCGTTTCAATTTGTTCAAATCATT 59.517 30.769 10.55 0.00 0.00 2.57
790 816 9.345517 CATTATCATCTTCACGACAACAAAATT 57.654 29.630 0.00 0.00 0.00 1.82
800 826 2.863137 GACAACAAAATTCCGCAGCAAA 59.137 40.909 0.00 0.00 0.00 3.68
801 827 3.265791 ACAACAAAATTCCGCAGCAAAA 58.734 36.364 0.00 0.00 0.00 2.44
803 829 4.335037 ACAACAAAATTCCGCAGCAAAATT 59.665 33.333 0.00 0.00 0.00 1.82
805 831 4.125703 ACAAAATTCCGCAGCAAAATTCA 58.874 34.783 0.00 0.00 0.00 2.57
806 832 4.756135 ACAAAATTCCGCAGCAAAATTCAT 59.244 33.333 0.00 0.00 0.00 2.57
807 833 5.106987 ACAAAATTCCGCAGCAAAATTCATC 60.107 36.000 0.00 0.00 0.00 2.92
808 834 3.872511 ATTCCGCAGCAAAATTCATCA 57.127 38.095 0.00 0.00 0.00 3.07
809 835 3.872511 TTCCGCAGCAAAATTCATCAT 57.127 38.095 0.00 0.00 0.00 2.45
810 836 4.979943 TTCCGCAGCAAAATTCATCATA 57.020 36.364 0.00 0.00 0.00 2.15
811 837 4.979943 TCCGCAGCAAAATTCATCATAA 57.020 36.364 0.00 0.00 0.00 1.90
812 838 5.321959 TCCGCAGCAAAATTCATCATAAA 57.678 34.783 0.00 0.00 0.00 1.40
813 839 5.718146 TCCGCAGCAAAATTCATCATAAAA 58.282 33.333 0.00 0.00 0.00 1.52
814 840 5.806502 TCCGCAGCAAAATTCATCATAAAAG 59.193 36.000 0.00 0.00 0.00 2.27
815 841 5.577945 CCGCAGCAAAATTCATCATAAAAGT 59.422 36.000 0.00 0.00 0.00 2.66
816 842 6.751425 CCGCAGCAAAATTCATCATAAAAGTA 59.249 34.615 0.00 0.00 0.00 2.24
817 843 7.275341 CCGCAGCAAAATTCATCATAAAAGTAA 59.725 33.333 0.00 0.00 0.00 2.24
818 844 8.810427 CGCAGCAAAATTCATCATAAAAGTAAT 58.190 29.630 0.00 0.00 0.00 1.89
840 866 9.817365 GTAATTCCAATCATTATCATCTTCACG 57.183 33.333 0.00 0.00 0.00 4.35
841 867 8.681486 AATTCCAATCATTATCATCTTCACGA 57.319 30.769 0.00 0.00 0.00 4.35
842 868 7.482654 TTCCAATCATTATCATCTTCACGAC 57.517 36.000 0.00 0.00 0.00 4.34
843 869 6.581712 TCCAATCATTATCATCTTCACGACA 58.418 36.000 0.00 0.00 0.00 4.35
844 870 7.047271 TCCAATCATTATCATCTTCACGACAA 58.953 34.615 0.00 0.00 0.00 3.18
845 871 7.011389 TCCAATCATTATCATCTTCACGACAAC 59.989 37.037 0.00 0.00 0.00 3.32
846 872 7.201635 CCAATCATTATCATCTTCACGACAACA 60.202 37.037 0.00 0.00 0.00 3.33
847 873 7.848223 ATCATTATCATCTTCACGACAACAA 57.152 32.000 0.00 0.00 0.00 2.83
848 874 7.665561 TCATTATCATCTTCACGACAACAAA 57.334 32.000 0.00 0.00 0.00 2.83
849 875 8.093659 TCATTATCATCTTCACGACAACAAAA 57.906 30.769 0.00 0.00 0.00 2.44
850 876 8.729756 TCATTATCATCTTCACGACAACAAAAT 58.270 29.630 0.00 0.00 0.00 1.82
851 877 9.345517 CATTATCATCTTCACGACAACAAAATT 57.654 29.630 0.00 0.00 0.00 1.82
852 878 8.948853 TTATCATCTTCACGACAACAAAATTC 57.051 30.769 0.00 0.00 0.00 2.17
853 879 5.757886 TCATCTTCACGACAACAAAATTCC 58.242 37.500 0.00 0.00 0.00 3.01
854 880 4.203950 TCTTCACGACAACAAAATTCCG 57.796 40.909 0.00 0.00 0.00 4.30
855 881 2.392933 TCACGACAACAAAATTCCGC 57.607 45.000 0.00 0.00 0.00 5.54
856 882 1.671328 TCACGACAACAAAATTCCGCA 59.329 42.857 0.00 0.00 0.00 5.69
857 883 2.043411 CACGACAACAAAATTCCGCAG 58.957 47.619 0.00 0.00 0.00 5.18
858 884 1.052287 CGACAACAAAATTCCGCAGC 58.948 50.000 0.00 0.00 0.00 5.25
859 885 1.599171 CGACAACAAAATTCCGCAGCA 60.599 47.619 0.00 0.00 0.00 4.41
860 886 2.053627 GACAACAAAATTCCGCAGCAG 58.946 47.619 0.00 0.00 0.00 4.24
861 887 0.785979 CAACAAAATTCCGCAGCAGC 59.214 50.000 0.00 0.00 37.42 5.25
895 921 6.039616 GTCATCTAGTTGTCTTCAGTGATCC 58.960 44.000 0.00 0.00 0.00 3.36
961 987 5.281314 AGAAGCAGAGGGGTAATAAGAGAA 58.719 41.667 0.00 0.00 0.00 2.87
964 990 6.582929 AGCAGAGGGGTAATAAGAGAAAAT 57.417 37.500 0.00 0.00 0.00 1.82
968 994 9.185680 GCAGAGGGGTAATAAGAGAAAATAAAA 57.814 33.333 0.00 0.00 0.00 1.52
1138 1181 1.006519 CCAGGTCTCTCTCTTCCTCCA 59.993 57.143 0.00 0.00 0.00 3.86
1153 1196 0.179936 CTCCACTTCCTCATGGGAGC 59.820 60.000 0.00 0.00 42.96 4.70
1210 1674 2.027192 TGCCATCCTACTGTTCTTCACC 60.027 50.000 0.00 0.00 0.00 4.02
1241 1705 2.150397 AGTCGAGGGTTTTTCAGACG 57.850 50.000 0.00 0.00 34.21 4.18
1565 2082 5.911178 ACCTTTCCCTGAGATATGGTATGAA 59.089 40.000 0.00 0.00 0.00 2.57
1587 2104 7.341030 TGAATTAATCTCATTTGCAGAGGAGA 58.659 34.615 21.84 21.84 40.37 3.71
1589 2106 6.550938 TTAATCTCATTTGCAGAGGAGAGA 57.449 37.500 23.43 15.71 39.53 3.10
1651 2170 4.450976 TCATGTATGTATGCCTGGTCAAC 58.549 43.478 0.00 0.00 0.00 3.18
2078 2709 7.127186 TGAATAACTATTCTGATTGACCAGGGA 59.873 37.037 10.11 0.00 41.93 4.20
2172 2803 8.370940 TCCCACAATATAAGATGTTTTTGCAAA 58.629 29.630 8.05 8.05 0.00 3.68
2244 2878 3.432252 CGGTGGTCGATATTTTATCCTGC 59.568 47.826 0.00 0.00 42.43 4.85
2337 2984 2.094597 TGCACTTGTGCAAATATCAGCC 60.095 45.455 23.78 0.00 42.40 4.85
2347 2994 0.833287 AATATCAGCCCGTGCACTCT 59.167 50.000 16.19 6.30 41.13 3.24
2591 4548 7.905126 CCATCTGGTTTGTTTTGTAGAAAAAC 58.095 34.615 0.00 6.72 39.78 2.43
2817 4825 7.782644 CCCATAATTTCATTTACCAGGTTCCTA 59.217 37.037 0.00 0.00 0.00 2.94
3165 5287 4.975502 TGCTTTGTATTTTCTTTGCTGTCG 59.024 37.500 0.00 0.00 0.00 4.35
3201 5433 4.703093 TCGGACTACATACACATGTTCTCA 59.297 41.667 0.00 0.00 42.98 3.27
3284 5522 4.193240 ACTGGGGTGAAGTTTGGTTATT 57.807 40.909 0.00 0.00 0.00 1.40
3650 6197 3.578282 ACTTGGACCATGAACAATTTCCC 59.422 43.478 14.05 0.00 0.00 3.97
3854 6409 5.847670 AATAGTCGACAGAAACTTCTTGC 57.152 39.130 19.50 0.00 34.74 4.01
3886 6452 3.897141 TGCCAACGGACATTAGTGATA 57.103 42.857 0.00 0.00 0.00 2.15
4106 6707 8.526147 AGCCTATAAAATTTCATGGTCATATGC 58.474 33.333 0.00 0.00 0.00 3.14
4301 7158 3.320826 AGTTGTGTCCAAAGTTAATGGCC 59.679 43.478 0.00 0.00 37.88 5.36
4313 7170 0.766674 TAATGGCCGGCTAGACCCAT 60.767 55.000 28.56 17.08 39.66 4.00
4472 7376 4.253685 TGATTGCCTCAGCTTGTACTTAC 58.746 43.478 0.00 0.00 40.80 2.34
4494 7398 2.036428 CTGGATGCCTCGGATGAGCA 62.036 60.000 0.80 0.80 41.13 4.26
4555 7459 1.060729 TCCTGGACCAAACGAATGGA 58.939 50.000 16.26 0.00 43.54 3.41
4847 7761 8.316946 CAATGATGGCTAGATCTTTACCTCATA 58.683 37.037 0.00 0.00 0.00 2.15
5025 7945 5.900339 TTCGATCGGAAATATGTTACTGC 57.100 39.130 16.41 0.00 0.00 4.40
5026 7946 5.196341 TCGATCGGAAATATGTTACTGCT 57.804 39.130 16.41 0.00 0.00 4.24
5125 8045 5.605534 ACCATGTTATCACTCACTCTATGC 58.394 41.667 0.00 0.00 0.00 3.14
5133 8053 4.941657 TCACTCACTCTATGCATCATGTC 58.058 43.478 0.19 0.00 0.00 3.06
5155 8075 3.053693 CCCCAGTTGATGAATCAGGGTTA 60.054 47.826 12.65 0.00 37.84 2.85
5158 8078 4.396166 CCAGTTGATGAATCAGGGTTACAC 59.604 45.833 0.00 0.00 38.19 2.90
5179 8099 6.218019 ACACGTAGAGTAAAATGCACTACAA 58.782 36.000 8.55 0.00 34.86 2.41
5252 8172 4.178540 CGGTCATTACGGTCACTTTGTAT 58.821 43.478 0.00 0.00 0.00 2.29
5256 8176 6.315393 GGTCATTACGGTCACTTTGTATGATT 59.685 38.462 0.00 0.00 0.00 2.57
5260 8180 4.843728 ACGGTCACTTTGTATGATTGGAT 58.156 39.130 0.00 0.00 0.00 3.41
5299 8219 2.139323 TCACTGTACTGAGCCGGTAT 57.861 50.000 1.90 0.00 0.00 2.73
5880 8866 5.122396 ACCTTGTAGATCATCGTTTTCTTGC 59.878 40.000 0.00 0.00 0.00 4.01
6005 8992 4.526262 GTCAGAGGATAGGTATGCAGATGT 59.474 45.833 0.00 0.00 0.00 3.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 3.898509 GCACCGTGTTGCTTGGCA 61.899 61.111 0.00 0.00 39.59 4.92
93 94 4.988598 CAACACGGCAGCGAGGGT 62.989 66.667 0.00 0.00 0.00 4.34
167 168 1.729586 TGTTTGGGTAGAGGCAGACT 58.270 50.000 0.00 0.00 0.00 3.24
217 218 3.306088 CGTTGAAAAGAGGAGCTCACCTA 60.306 47.826 17.19 0.00 40.73 3.08
276 277 6.149973 TGAATCTAACTGAGGAAAATGCAGTG 59.850 38.462 0.00 0.00 41.65 3.66
277 278 6.240894 TGAATCTAACTGAGGAAAATGCAGT 58.759 36.000 0.00 0.00 44.15 4.40
338 340 1.679153 ACTGTAAAGCCCAAAACACCG 59.321 47.619 0.00 0.00 0.00 4.94
349 351 4.982295 GTCCAACCAATCAAACTGTAAAGC 59.018 41.667 0.00 0.00 0.00 3.51
375 377 4.356405 TCCACATATCCTGGCATAAGTG 57.644 45.455 11.32 11.32 30.84 3.16
423 425 2.824936 TCGACCATTGTTGCCATTGAAT 59.175 40.909 0.00 0.00 0.00 2.57
618 644 3.760151 CCTGAATGCCTTGACTTTCATGA 59.240 43.478 0.00 0.00 34.40 3.07
625 651 2.306805 TGTCATCCTGAATGCCTTGACT 59.693 45.455 0.00 0.00 35.63 3.41
665 691 5.355596 TGATTTGAACAAATTGAAACGCCT 58.644 33.333 12.91 0.00 40.77 5.52
690 716 7.013369 TGTTTTATAACACACAACACTGGCATA 59.987 33.333 0.22 0.00 39.29 3.14
790 816 4.979943 TTATGATGAATTTTGCTGCGGA 57.020 36.364 0.00 0.00 0.00 5.54
814 840 9.817365 CGTGAAGATGATAATGATTGGAATTAC 57.183 33.333 0.00 0.00 0.00 1.89
815 841 9.777297 TCGTGAAGATGATAATGATTGGAATTA 57.223 29.630 0.00 0.00 0.00 1.40
816 842 8.562892 GTCGTGAAGATGATAATGATTGGAATT 58.437 33.333 0.00 0.00 0.00 2.17
817 843 7.716560 TGTCGTGAAGATGATAATGATTGGAAT 59.283 33.333 0.00 0.00 0.00 3.01
818 844 7.047271 TGTCGTGAAGATGATAATGATTGGAA 58.953 34.615 0.00 0.00 0.00 3.53
819 845 6.581712 TGTCGTGAAGATGATAATGATTGGA 58.418 36.000 0.00 0.00 0.00 3.53
820 846 6.849588 TGTCGTGAAGATGATAATGATTGG 57.150 37.500 0.00 0.00 0.00 3.16
821 847 7.687445 TGTTGTCGTGAAGATGATAATGATTG 58.313 34.615 0.00 0.00 0.00 2.67
822 848 7.848223 TGTTGTCGTGAAGATGATAATGATT 57.152 32.000 0.00 0.00 0.00 2.57
823 849 7.848223 TTGTTGTCGTGAAGATGATAATGAT 57.152 32.000 0.00 0.00 0.00 2.45
824 850 7.665561 TTTGTTGTCGTGAAGATGATAATGA 57.334 32.000 0.00 0.00 0.00 2.57
825 851 8.900511 ATTTTGTTGTCGTGAAGATGATAATG 57.099 30.769 0.00 0.00 0.00 1.90
826 852 9.559958 GAATTTTGTTGTCGTGAAGATGATAAT 57.440 29.630 0.00 0.00 0.00 1.28
827 853 8.020819 GGAATTTTGTTGTCGTGAAGATGATAA 58.979 33.333 0.00 0.00 0.00 1.75
828 854 7.526608 GGAATTTTGTTGTCGTGAAGATGATA 58.473 34.615 0.00 0.00 0.00 2.15
829 855 6.381801 GGAATTTTGTTGTCGTGAAGATGAT 58.618 36.000 0.00 0.00 0.00 2.45
830 856 5.559991 CGGAATTTTGTTGTCGTGAAGATGA 60.560 40.000 0.00 0.00 0.00 2.92
831 857 4.612614 CGGAATTTTGTTGTCGTGAAGATG 59.387 41.667 0.00 0.00 0.00 2.90
832 858 4.783242 CGGAATTTTGTTGTCGTGAAGAT 58.217 39.130 0.00 0.00 0.00 2.40
833 859 3.547214 GCGGAATTTTGTTGTCGTGAAGA 60.547 43.478 0.00 0.00 0.00 2.87
834 860 2.719046 GCGGAATTTTGTTGTCGTGAAG 59.281 45.455 0.00 0.00 0.00 3.02
835 861 2.097629 TGCGGAATTTTGTTGTCGTGAA 59.902 40.909 0.00 0.00 0.00 3.18
836 862 1.671328 TGCGGAATTTTGTTGTCGTGA 59.329 42.857 0.00 0.00 0.00 4.35
837 863 2.043411 CTGCGGAATTTTGTTGTCGTG 58.957 47.619 0.00 0.00 0.00 4.35
838 864 1.599419 GCTGCGGAATTTTGTTGTCGT 60.599 47.619 0.00 0.00 0.00 4.34
839 865 1.052287 GCTGCGGAATTTTGTTGTCG 58.948 50.000 0.00 0.00 0.00 4.35
840 866 2.053627 CTGCTGCGGAATTTTGTTGTC 58.946 47.619 1.17 0.00 0.00 3.18
841 867 1.869342 GCTGCTGCGGAATTTTGTTGT 60.869 47.619 13.72 0.00 0.00 3.32
842 868 0.785979 GCTGCTGCGGAATTTTGTTG 59.214 50.000 13.72 0.00 0.00 3.33
843 869 3.199764 GCTGCTGCGGAATTTTGTT 57.800 47.368 13.72 0.00 0.00 2.83
844 870 4.972591 GCTGCTGCGGAATTTTGT 57.027 50.000 13.72 0.00 0.00 2.83
859 885 4.760047 GATGACACCCCACGCGCT 62.760 66.667 5.73 0.00 0.00 5.92
860 886 3.365291 TAGATGACACCCCACGCGC 62.365 63.158 5.73 0.00 0.00 6.86
861 887 1.226974 CTAGATGACACCCCACGCG 60.227 63.158 3.53 3.53 0.00 6.01
862 888 0.249398 AACTAGATGACACCCCACGC 59.751 55.000 0.00 0.00 0.00 5.34
863 889 1.275291 ACAACTAGATGACACCCCACG 59.725 52.381 7.05 0.00 0.00 4.94
864 890 2.567615 AGACAACTAGATGACACCCCAC 59.432 50.000 7.05 0.00 0.00 4.61
865 891 2.902608 AGACAACTAGATGACACCCCA 58.097 47.619 7.05 0.00 0.00 4.96
930 956 2.230660 CCCCTCTGCTTCTTCGTTTTT 58.769 47.619 0.00 0.00 0.00 1.94
931 957 1.143073 ACCCCTCTGCTTCTTCGTTTT 59.857 47.619 0.00 0.00 0.00 2.43
935 961 2.990066 ATTACCCCTCTGCTTCTTCG 57.010 50.000 0.00 0.00 0.00 3.79
936 962 5.364157 TCTCTTATTACCCCTCTGCTTCTTC 59.636 44.000 0.00 0.00 0.00 2.87
939 965 5.615925 TTCTCTTATTACCCCTCTGCTTC 57.384 43.478 0.00 0.00 0.00 3.86
961 987 6.658555 TTCCTCCCCATCTCTCTTTTATTT 57.341 37.500 0.00 0.00 0.00 1.40
964 990 5.570844 CGTTTTCCTCCCCATCTCTCTTTTA 60.571 44.000 0.00 0.00 0.00 1.52
968 994 1.834263 CGTTTTCCTCCCCATCTCTCT 59.166 52.381 0.00 0.00 0.00 3.10
969 995 1.134371 CCGTTTTCCTCCCCATCTCTC 60.134 57.143 0.00 0.00 0.00 3.20
970 996 0.912486 CCGTTTTCCTCCCCATCTCT 59.088 55.000 0.00 0.00 0.00 3.10
971 997 0.909623 TCCGTTTTCCTCCCCATCTC 59.090 55.000 0.00 0.00 0.00 2.75
972 998 0.912486 CTCCGTTTTCCTCCCCATCT 59.088 55.000 0.00 0.00 0.00 2.90
973 999 0.748367 GCTCCGTTTTCCTCCCCATC 60.748 60.000 0.00 0.00 0.00 3.51
974 1000 1.303282 GCTCCGTTTTCCTCCCCAT 59.697 57.895 0.00 0.00 0.00 4.00
1007 1033 1.005332 TCACCAGTCCTCTCCTCTCTG 59.995 57.143 0.00 0.00 0.00 3.35
1138 1181 1.203441 TGCAGCTCCCATGAGGAAGT 61.203 55.000 0.00 0.00 46.94 3.01
1153 1196 2.907910 CAAAGAGACGGGATTTGCAG 57.092 50.000 0.00 0.00 0.00 4.41
1210 1674 4.522722 ACCCTCGACTACAGAAGAAAAG 57.477 45.455 0.00 0.00 0.00 2.27
1241 1705 3.463944 TCGTGAAAAGGAAGAACTGGAC 58.536 45.455 0.00 0.00 0.00 4.02
1383 1855 6.258068 CCGCGAAATAAATAAAGGAGAGAACT 59.742 38.462 8.23 0.00 0.00 3.01
1532 2042 2.768527 CTCAGGGAAAGGTAGCAGATCA 59.231 50.000 0.00 0.00 0.00 2.92
1533 2043 3.034635 TCTCAGGGAAAGGTAGCAGATC 58.965 50.000 0.00 0.00 0.00 2.75
1534 2044 3.121929 TCTCAGGGAAAGGTAGCAGAT 57.878 47.619 0.00 0.00 0.00 2.90
1565 2082 7.134362 TCTCTCCTCTGCAAATGAGATTAAT 57.866 36.000 8.63 0.00 33.68 1.40
1575 2092 3.260380 CCTCTTCTTCTCTCCTCTGCAAA 59.740 47.826 0.00 0.00 0.00 3.68
1587 2104 3.182887 TCTGCTCCTTCCTCTTCTTCT 57.817 47.619 0.00 0.00 0.00 2.85
1589 2106 2.771372 GGATCTGCTCCTTCCTCTTCTT 59.229 50.000 0.00 0.00 41.29 2.52
1651 2170 2.813754 AGACACAATCCAAACATCACGG 59.186 45.455 0.00 0.00 0.00 4.94
1706 2304 5.467035 TTGACTTTTGCCAAGGAATTAGG 57.533 39.130 0.00 0.00 0.00 2.69
1918 2517 9.540538 TGAGGATGGGAAAGTAAAAATCAAATA 57.459 29.630 0.00 0.00 0.00 1.40
2172 2803 6.635021 ACTCCCTCTGTCCCATAATATAAGT 58.365 40.000 0.00 0.00 0.00 2.24
2337 2984 0.895530 TCTTCCCTAAGAGTGCACGG 59.104 55.000 12.01 5.94 36.80 4.94
2527 3174 6.825610 ACATGAATTTTGCAGGTTCCTTTTA 58.174 32.000 0.00 0.00 0.00 1.52
2817 4825 6.839124 TCTTTATGCATTGGAATCACTTGT 57.161 33.333 3.54 0.00 0.00 3.16
3165 5287 4.806330 TGTAGTCCGAATCAGACAAACTC 58.194 43.478 0.00 0.00 36.68 3.01
3378 5721 5.757099 AGGTAGCTGCTTTTAGGTAAAGA 57.243 39.130 7.79 0.00 45.00 2.52
3650 6197 4.855388 CGAAGTGCTTCAAATCCAATTCAG 59.145 41.667 11.82 0.00 39.46 3.02
3838 6393 4.024556 ACATTCAGCAAGAAGTTTCTGTCG 60.025 41.667 0.00 0.00 40.15 4.35
3854 6409 4.165779 GTCCGTTGGCATAAAACATTCAG 58.834 43.478 0.00 0.00 0.00 3.02
3886 6452 1.270465 GCCTTGCACAAAAATCTGGCT 60.270 47.619 0.00 0.00 36.52 4.75
4301 7158 1.068753 CTGAGCATGGGTCTAGCCG 59.931 63.158 0.00 0.00 38.44 5.52
4313 7170 2.812358 TCGAAAGTTGTAGCTGAGCA 57.188 45.000 7.39 0.00 0.00 4.26
4472 7376 1.227764 CATCCGAGGCATCCAGGTG 60.228 63.158 0.00 0.00 0.00 4.00
4494 7398 1.344763 CCTTCTTGGACTCGAGTTGGT 59.655 52.381 21.08 0.00 38.35 3.67
4548 7452 6.202954 AGTTCTAGTGAAGTGTTTTCCATTCG 59.797 38.462 0.00 0.00 34.79 3.34
4555 7459 6.415573 ACCTGAAGTTCTAGTGAAGTGTTTT 58.584 36.000 4.17 0.00 36.12 2.43
4619 7523 2.602211 CAGACACTAGCTGCTTGAATCG 59.398 50.000 17.66 5.75 0.00 3.34
4847 7761 1.342819 GCGTTATCTCTCCATCAGGCT 59.657 52.381 0.00 0.00 33.74 4.58
5008 7928 7.578310 AGTACTAGCAGTAACATATTTCCGA 57.422 36.000 0.00 0.00 31.62 4.55
5010 7930 9.250624 CAGAAGTACTAGCAGTAACATATTTCC 57.749 37.037 0.00 0.00 31.62 3.13
5022 7942 4.987285 CCATGCATACAGAAGTACTAGCAG 59.013 45.833 0.00 0.00 38.43 4.24
5025 7945 6.986250 TCATCCATGCATACAGAAGTACTAG 58.014 40.000 0.00 0.00 31.96 2.57
5026 7946 6.976934 TCATCCATGCATACAGAAGTACTA 57.023 37.500 0.00 0.00 31.96 1.82
5125 8045 3.286329 TCATCAACTGGGGACATGATG 57.714 47.619 0.00 8.00 41.51 3.07
5133 8053 1.285962 ACCCTGATTCATCAACTGGGG 59.714 52.381 14.26 11.89 41.61 4.96
5155 8075 5.775686 TGTAGTGCATTTTACTCTACGTGT 58.224 37.500 0.00 0.00 37.07 4.49
5158 8078 6.946229 ACTTGTAGTGCATTTTACTCTACG 57.054 37.500 0.00 0.00 37.07 3.51
5179 8099 1.566018 GCGGCGCAAGTTCAAGTACT 61.566 55.000 29.21 0.00 41.68 2.73
5252 8172 5.989168 GTGACCGTATAATCACATCCAATCA 59.011 40.000 7.74 0.00 43.89 2.57
5256 8176 4.404394 ACAGTGACCGTATAATCACATCCA 59.596 41.667 12.94 0.00 46.34 3.41
5260 8180 5.047590 AGTGAACAGTGACCGTATAATCACA 60.048 40.000 12.94 0.00 46.34 3.58
5299 8219 3.283684 CTGGTCAAAACGGCGGCA 61.284 61.111 13.24 0.00 0.00 5.69
5331 8251 0.763035 GTAATCCCCCACACGCCTAT 59.237 55.000 0.00 0.00 0.00 2.57
5672 8620 3.144657 TGGACACGTAGAACCTCACTA 57.855 47.619 0.00 0.00 0.00 2.74
5821 8807 1.470098 CTCTCCCAATGCCAGAAAACG 59.530 52.381 0.00 0.00 0.00 3.60
5880 8866 2.673043 GCATCAACAACTTCATGCCCAG 60.673 50.000 0.00 0.00 36.44 4.45


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

AutoCloner maintained by Alex Coulton.