Multiple sequence alignment - TraesCS7D01G407400

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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 TraesCS7D01G407400 chr7D 100.000 3133 0 0 1 3133 524872767 524869635 0.000000e+00 5786.0
1 TraesCS7D01G407400 chr7D 90.937 662 35 16 2185 2821 549781759 549781098 0.000000e+00 867.0
2 TraesCS7D01G407400 chr7D 84.485 709 107 2 1204 1909 524993373 524992665 0.000000e+00 697.0
3 TraesCS7D01G407400 chr7D 92.157 204 8 6 2185 2383 615354680 615354480 6.620000e-72 281.0
4 TraesCS7D01G407400 chr7D 88.889 81 6 1 2128 2205 59375142 59375222 2.570000e-16 97.1
5 TraesCS7D01G407400 chr7D 80.583 103 17 2 213 313 582507902 582508003 3.350000e-10 76.8
6 TraesCS7D01G407400 chr7B 90.502 2011 141 27 55 2033 561140607 561138615 0.000000e+00 2610.0
7 TraesCS7D01G407400 chr7B 87.107 1210 137 14 936 2131 561372611 561371407 0.000000e+00 1352.0
8 TraesCS7D01G407400 chr7B 79.026 267 43 11 618 877 399791726 399791986 1.490000e-38 171.0
9 TraesCS7D01G407400 chr7B 95.327 107 5 0 2025 2131 561135343 561135237 1.490000e-38 171.0
10 TraesCS7D01G407400 chr7B 89.286 84 7 2 485 566 54729942 54730025 1.540000e-18 104.0
11 TraesCS7D01G407400 chr7B 83.146 89 6 8 488 569 48342853 48342767 4.330000e-09 73.1
12 TraesCS7D01G407400 chr7B 97.143 35 1 0 408 442 217783386 217783352 3.370000e-05 60.2
13 TraesCS7D01G407400 chr7A 95.521 1228 51 3 904 2131 604824835 604823612 0.000000e+00 1960.0
14 TraesCS7D01G407400 chr7A 86.930 834 101 6 946 1775 605176568 605175739 0.000000e+00 929.0
15 TraesCS7D01G407400 chr7A 87.952 332 38 2 1801 2131 605175531 605175201 1.050000e-104 390.0
16 TraesCS7D01G407400 chr7A 81.208 298 19 11 2115 2377 190879039 190879334 4.100000e-49 206.0
17 TraesCS7D01G407400 chr5D 96.719 762 23 2 2372 3133 3790800 3790041 0.000000e+00 1267.0
18 TraesCS7D01G407400 chr5D 93.701 762 25 8 2372 3133 498089241 498089979 0.000000e+00 1120.0
19 TraesCS7D01G407400 chr5D 93.557 388 23 2 2350 2735 510380302 510379915 7.530000e-161 577.0
20 TraesCS7D01G407400 chr5D 90.464 388 25 2 2350 2725 510376081 510375694 4.660000e-138 501.0
21 TraesCS7D01G407400 chr5D 91.700 253 13 5 2128 2377 507167481 507167728 8.320000e-91 344.0
22 TraesCS7D01G407400 chr5D 88.931 262 10 6 2128 2375 557786983 557787239 3.930000e-79 305.0
23 TraesCS7D01G407400 chr5D 83.453 278 20 5 2125 2377 16797795 16798071 5.220000e-58 235.0
24 TraesCS7D01G407400 chr5D 83.624 287 10 9 2126 2377 24164121 24164405 5.220000e-58 235.0
25 TraesCS7D01G407400 chr5D 78.755 273 18 12 2127 2383 547969766 547969518 2.520000e-31 147.0
26 TraesCS7D01G407400 chr5D 91.250 80 6 1 492 570 500221087 500221008 1.190000e-19 108.0
27 TraesCS7D01G407400 chr6D 96.073 764 28 2 2372 3133 453589935 453589172 0.000000e+00 1243.0
28 TraesCS7D01G407400 chr6D 95.300 766 19 10 2372 3133 112446649 112447401 0.000000e+00 1199.0
29 TraesCS7D01G407400 chr6D 87.681 276 13 3 2127 2383 445998397 445998124 5.080000e-78 302.0
30 TraesCS7D01G407400 chr6D 84.672 274 18 3 2126 2375 32236304 32236031 5.190000e-63 252.0
31 TraesCS7D01G407400 chr6D 84.192 291 8 9 2124 2377 21996519 21996808 6.710000e-62 248.0
32 TraesCS7D01G407400 chr6D 84.559 272 14 5 2124 2377 112446313 112446574 8.680000e-61 244.0
33 TraesCS7D01G407400 chr6D 79.336 271 26 10 2127 2377 410068162 410068422 2.500000e-36 163.0
34 TraesCS7D01G407400 chr6D 84.314 153 6 1 2126 2260 447757667 447757515 1.960000e-27 134.0
35 TraesCS7D01G407400 chr6D 83.212 137 4 4 2124 2241 447979353 447979489 1.190000e-19 108.0
36 TraesCS7D01G407400 chr2D 96.073 764 24 6 2372 3133 620827661 620828420 0.000000e+00 1240.0
37 TraesCS7D01G407400 chr2D 92.462 199 8 5 2185 2377 603985591 603985788 8.560000e-71 278.0
38 TraesCS7D01G407400 chr2D 90.865 208 8 4 2185 2383 471707158 471706953 5.150000e-68 268.0
39 TraesCS7D01G407400 chr2D 77.099 262 41 13 2121 2377 22441760 22442007 1.960000e-27 134.0
40 TraesCS7D01G407400 chr3D 95.282 763 32 4 2372 3133 522395516 522396275 0.000000e+00 1206.0
41 TraesCS7D01G407400 chr3D 95.182 768 28 6 2372 3133 345210772 345210008 0.000000e+00 1205.0
42 TraesCS7D01G407400 chr3D 88.210 687 33 20 2185 2839 586304985 586305655 0.000000e+00 776.0
43 TraesCS7D01G407400 chr3D 89.384 471 23 7 2350 2797 19862119 19862585 4.530000e-158 568.0
44 TraesCS7D01G407400 chr3D 90.881 329 27 1 2350 2678 79444571 79444246 3.710000e-119 438.0
45 TraesCS7D01G407400 chr3D 82.724 301 14 9 2118 2383 533383310 533383013 1.880000e-57 233.0
46 TraesCS7D01G407400 chr3D 83.045 289 11 11 2123 2377 571921490 571921774 8.740000e-56 228.0
47 TraesCS7D01G407400 chr3D 93.590 78 4 1 488 564 125688094 125688171 7.100000e-22 115.0
48 TraesCS7D01G407400 chr4D 94.825 773 23 6 2376 3133 480465484 480464714 0.000000e+00 1190.0
49 TraesCS7D01G407400 chr4D 94.372 764 30 6 2372 3133 460780441 460779689 0.000000e+00 1160.0
50 TraesCS7D01G407400 chr2A 85.466 461 41 13 2204 2642 759121058 759121514 1.020000e-124 457.0
51 TraesCS7D01G407400 chr2A 78.481 316 46 15 580 877 775084372 775084683 1.480000e-43 187.0
52 TraesCS7D01G407400 chr5A 87.395 357 38 7 2345 2697 457271583 457271936 1.350000e-108 403.0
53 TraesCS7D01G407400 chr3B 84.962 399 52 8 2306 2701 739018727 739018334 6.300000e-107 398.0
54 TraesCS7D01G407400 chr3B 82.500 120 13 6 2128 2239 5804040 5804159 7.150000e-17 99.0
55 TraesCS7D01G407400 chr3B 82.407 108 14 2 2128 2235 812502344 812502242 4.300000e-14 89.8
56 TraesCS7D01G407400 chr1D 83.834 433 40 16 2348 2758 28229331 28228907 4.900000e-103 385.0
57 TraesCS7D01G407400 chr1D 95.980 199 5 2 2185 2383 2352919 2352724 1.400000e-83 320.0
58 TraesCS7D01G407400 chr1D 80.827 266 41 10 618 877 31698552 31698291 1.910000e-47 200.0
59 TraesCS7D01G407400 chr2B 92.079 202 10 4 2185 2383 124271006 124270808 2.380000e-71 279.0
60 TraesCS7D01G407400 chrUn 87.037 216 9 6 2185 2383 39122365 39122152 3.140000e-55 226.0
61 TraesCS7D01G407400 chrUn 84.135 208 21 5 2185 2383 22525741 22525537 1.150000e-44 191.0
62 TraesCS7D01G407400 chrUn 95.918 98 4 0 2185 2282 294263956 294264053 3.230000e-35 159.0
63 TraesCS7D01G407400 chrUn 95.918 98 4 0 2185 2282 333014416 333014513 3.230000e-35 159.0
64 TraesCS7D01G407400 chrUn 96.809 94 3 0 2186 2279 92979387 92979480 1.160000e-34 158.0
65 TraesCS7D01G407400 chrUn 94.898 98 5 0 2185 2282 75804703 75804606 1.500000e-33 154.0
66 TraesCS7D01G407400 chrUn 86.614 127 15 1 2185 2311 114583045 114583169 4.210000e-29 139.0
67 TraesCS7D01G407400 chrUn 90.000 70 6 1 2116 2185 92502712 92502644 4.300000e-14 89.8
68 TraesCS7D01G407400 chr5B 81.570 293 29 7 2115 2383 698902933 698902642 5.260000e-53 219.0
69 TraesCS7D01G407400 chr5B 80.064 311 15 10 2118 2383 516521647 516521339 1.480000e-43 187.0
70 TraesCS7D01G407400 chr5B 82.243 214 29 7 671 877 301216860 301216649 3.210000e-40 176.0
71 TraesCS7D01G407400 chr4A 78.358 268 45 11 618 877 634731927 634732189 8.990000e-36 161.0
72 TraesCS7D01G407400 chr4A 77.465 142 18 8 286 421 628609340 628609207 4.330000e-09 73.1
73 TraesCS7D01G407400 chr4A 86.207 58 6 2 215 271 39065178 39065234 9.380000e-06 62.1
74 TraesCS7D01G407400 chr1A 88.119 101 7 5 485 581 47793782 47793881 7.100000e-22 115.0
75 TraesCS7D01G407400 chr1B 84.483 116 13 3 2128 2239 29240221 29240335 3.300000e-20 110.0
76 TraesCS7D01G407400 chr1B 87.059 85 7 4 498 580 556098616 556098698 3.330000e-15 93.5
77 TraesCS7D01G407400 chr1B 91.304 46 4 0 211 256 491767954 491767909 2.610000e-06 63.9
78 TraesCS7D01G407400 chr6B 86.207 87 10 2 485 570 708855918 708856003 3.330000e-15 93.5
79 TraesCS7D01G407400 chr3A 92.308 65 4 1 2121 2185 702187734 702187797 1.200000e-14 91.6


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 TraesCS7D01G407400 chr7D 524869635 524872767 3132 True 5786.0 5786 100.0000 1 3133 1 chr7D.!!$R1 3132
1 TraesCS7D01G407400 chr7D 549781098 549781759 661 True 867.0 867 90.9370 2185 2821 1 chr7D.!!$R3 636
2 TraesCS7D01G407400 chr7D 524992665 524993373 708 True 697.0 697 84.4850 1204 1909 1 chr7D.!!$R2 705
3 TraesCS7D01G407400 chr7B 561135237 561140607 5370 True 1390.5 2610 92.9145 55 2131 2 chr7B.!!$R4 2076
4 TraesCS7D01G407400 chr7B 561371407 561372611 1204 True 1352.0 1352 87.1070 936 2131 1 chr7B.!!$R3 1195
5 TraesCS7D01G407400 chr7A 604823612 604824835 1223 True 1960.0 1960 95.5210 904 2131 1 chr7A.!!$R1 1227
6 TraesCS7D01G407400 chr7A 605175201 605176568 1367 True 659.5 929 87.4410 946 2131 2 chr7A.!!$R2 1185
7 TraesCS7D01G407400 chr5D 3790041 3790800 759 True 1267.0 1267 96.7190 2372 3133 1 chr5D.!!$R1 761
8 TraesCS7D01G407400 chr5D 498089241 498089979 738 False 1120.0 1120 93.7010 2372 3133 1 chr5D.!!$F3 761
9 TraesCS7D01G407400 chr5D 510375694 510380302 4608 True 539.0 577 92.0105 2350 2735 2 chr5D.!!$R4 385
10 TraesCS7D01G407400 chr6D 453589172 453589935 763 True 1243.0 1243 96.0730 2372 3133 1 chr6D.!!$R4 761
11 TraesCS7D01G407400 chr6D 112446313 112447401 1088 False 721.5 1199 89.9295 2124 3133 2 chr6D.!!$F4 1009
12 TraesCS7D01G407400 chr2D 620827661 620828420 759 False 1240.0 1240 96.0730 2372 3133 1 chr2D.!!$F3 761
13 TraesCS7D01G407400 chr3D 522395516 522396275 759 False 1206.0 1206 95.2820 2372 3133 1 chr3D.!!$F3 761
14 TraesCS7D01G407400 chr3D 345210008 345210772 764 True 1205.0 1205 95.1820 2372 3133 1 chr3D.!!$R2 761
15 TraesCS7D01G407400 chr3D 586304985 586305655 670 False 776.0 776 88.2100 2185 2839 1 chr3D.!!$F5 654
16 TraesCS7D01G407400 chr4D 480464714 480465484 770 True 1190.0 1190 94.8250 2376 3133 1 chr4D.!!$R2 757
17 TraesCS7D01G407400 chr4D 460779689 460780441 752 True 1160.0 1160 94.3720 2372 3133 1 chr4D.!!$R1 761

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
58 59 0.031857 TGCACAAATTTGCTCCCGTG 59.968 50.0 18.12 8.75 43.41 4.94 F
922 950 0.240945 ATTTCGCAAAAGCCGGACAG 59.759 50.0 5.05 0.00 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1847 2063 0.188587 TAGGCCGTCATCTCTCCCAT 59.811 55.0 0.00 0.0 0.00 4.00 R
2139 5643 1.428718 AACCGGGTCAAAAGCCCCTA 61.429 55.0 6.32 0.0 43.18 3.53 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
21 22 1.512926 TTTTTCTGCGAGAGAGGCAC 58.487 50.000 0.00 0.00 36.24 5.01
22 23 0.392706 TTTTCTGCGAGAGAGGCACA 59.607 50.000 0.00 0.00 36.24 4.57
23 24 0.392706 TTTCTGCGAGAGAGGCACAA 59.607 50.000 0.00 0.00 36.24 3.33
24 25 0.037882 TTCTGCGAGAGAGGCACAAG 60.038 55.000 0.00 0.00 36.24 3.16
25 26 1.181741 TCTGCGAGAGAGGCACAAGT 61.182 55.000 0.00 0.00 36.24 3.16
26 27 0.320247 CTGCGAGAGAGGCACAAGTT 60.320 55.000 0.00 0.00 36.24 2.66
27 28 0.966179 TGCGAGAGAGGCACAAGTTA 59.034 50.000 0.00 0.00 35.04 2.24
28 29 1.336887 TGCGAGAGAGGCACAAGTTAC 60.337 52.381 0.00 0.00 35.04 2.50
29 30 1.067495 GCGAGAGAGGCACAAGTTACT 60.067 52.381 0.00 0.00 0.00 2.24
30 31 2.610727 GCGAGAGAGGCACAAGTTACTT 60.611 50.000 0.00 0.00 0.00 2.24
31 32 3.246619 CGAGAGAGGCACAAGTTACTTC 58.753 50.000 0.00 0.00 0.00 3.01
32 33 3.057174 CGAGAGAGGCACAAGTTACTTCT 60.057 47.826 0.00 0.00 0.00 2.85
33 34 4.490743 GAGAGAGGCACAAGTTACTTCTC 58.509 47.826 0.00 0.00 0.00 2.87
34 35 3.057174 AGAGAGGCACAAGTTACTTCTCG 60.057 47.826 0.00 0.00 0.00 4.04
35 36 2.628657 AGAGGCACAAGTTACTTCTCGT 59.371 45.455 0.00 0.00 0.00 4.18
36 37 2.731976 GAGGCACAAGTTACTTCTCGTG 59.268 50.000 8.96 8.96 0.00 4.35
37 38 1.798813 GGCACAAGTTACTTCTCGTGG 59.201 52.381 13.43 0.00 0.00 4.94
38 39 2.547218 GGCACAAGTTACTTCTCGTGGA 60.547 50.000 13.43 0.00 0.00 4.02
39 40 3.326747 GCACAAGTTACTTCTCGTGGAT 58.673 45.455 13.43 0.00 0.00 3.41
40 41 3.123621 GCACAAGTTACTTCTCGTGGATG 59.876 47.826 13.43 0.00 0.00 3.51
41 42 3.123621 CACAAGTTACTTCTCGTGGATGC 59.876 47.826 0.00 0.00 0.00 3.91
42 43 3.244078 ACAAGTTACTTCTCGTGGATGCA 60.244 43.478 0.00 0.00 0.00 3.96
43 44 2.960819 AGTTACTTCTCGTGGATGCAC 58.039 47.619 7.39 7.39 0.00 4.57
44 45 2.299013 AGTTACTTCTCGTGGATGCACA 59.701 45.455 18.05 3.93 0.00 4.57
45 46 3.064207 GTTACTTCTCGTGGATGCACAA 58.936 45.455 18.05 0.00 0.00 3.33
46 47 2.254546 ACTTCTCGTGGATGCACAAA 57.745 45.000 18.05 7.31 0.00 2.83
47 48 2.783135 ACTTCTCGTGGATGCACAAAT 58.217 42.857 18.05 0.00 0.00 2.32
48 49 3.149196 ACTTCTCGTGGATGCACAAATT 58.851 40.909 18.05 0.29 0.00 1.82
49 50 3.569701 ACTTCTCGTGGATGCACAAATTT 59.430 39.130 18.05 0.00 0.00 1.82
50 51 3.557577 TCTCGTGGATGCACAAATTTG 57.442 42.857 18.05 16.67 0.00 2.32
51 52 1.987770 CTCGTGGATGCACAAATTTGC 59.012 47.619 18.12 6.63 43.31 3.68
52 53 1.612950 TCGTGGATGCACAAATTTGCT 59.387 42.857 18.12 2.95 43.41 3.91
53 54 1.987770 CGTGGATGCACAAATTTGCTC 59.012 47.619 18.12 10.26 43.41 4.26
54 55 2.340337 GTGGATGCACAAATTTGCTCC 58.660 47.619 18.12 17.28 43.41 4.70
55 56 1.275856 TGGATGCACAAATTTGCTCCC 59.724 47.619 18.12 12.12 43.41 4.30
56 57 1.632422 GATGCACAAATTTGCTCCCG 58.368 50.000 18.12 3.33 43.41 5.14
57 58 0.968405 ATGCACAAATTTGCTCCCGT 59.032 45.000 18.12 2.95 43.41 5.28
58 59 0.031857 TGCACAAATTTGCTCCCGTG 59.968 50.000 18.12 8.75 43.41 4.94
59 60 0.313672 GCACAAATTTGCTCCCGTGA 59.686 50.000 18.12 0.00 39.59 4.35
60 61 1.666888 GCACAAATTTGCTCCCGTGAG 60.667 52.381 18.12 0.00 39.59 3.51
61 62 1.879380 CACAAATTTGCTCCCGTGAGA 59.121 47.619 18.12 0.00 41.42 3.27
62 63 2.095567 CACAAATTTGCTCCCGTGAGAG 60.096 50.000 18.12 0.00 41.42 3.20
72 73 4.891566 CGTGAGAGTCGGAAAGGG 57.108 61.111 0.00 0.00 0.00 3.95
115 121 7.881775 ACCTTGAGAGACACAAATTTACTTT 57.118 32.000 0.00 0.00 0.00 2.66
118 124 8.405531 CCTTGAGAGACACAAATTTACTTTTGA 58.594 33.333 4.10 0.00 38.58 2.69
124 130 8.463930 AGACACAAATTTACTTTTGATGGAGA 57.536 30.769 4.10 0.00 38.58 3.71
127 133 7.920682 ACACAAATTTACTTTTGATGGAGACAC 59.079 33.333 4.10 0.00 40.53 3.67
140 146 2.693591 TGGAGACACCTATTAGCTTCCG 59.306 50.000 0.00 0.00 39.86 4.30
141 147 2.546162 GGAGACACCTATTAGCTTCCGC 60.546 54.545 0.00 0.00 35.41 5.54
151 157 2.964389 GCTTCCGCGAGAGGCATC 60.964 66.667 20.89 0.00 46.54 3.91
158 164 1.756375 CGCGAGAGGCATCGGAAAAG 61.756 60.000 0.00 0.00 42.94 2.27
222 228 1.025113 TCCTACCGCGAGAGACACAG 61.025 60.000 8.23 0.00 0.00 3.66
231 237 2.093467 GCGAGAGACACAGATTTGCTTC 59.907 50.000 0.00 0.00 0.00 3.86
313 320 3.123804 GCCACATATGTACTTCTCGTGG 58.876 50.000 8.32 14.80 44.18 4.94
322 329 1.048601 ACTTCTCGTGGAGGCAAAGA 58.951 50.000 0.00 0.00 0.00 2.52
353 360 3.323691 TGCAAGTAAAGCTGTACCTCTCA 59.676 43.478 10.60 1.65 0.00 3.27
369 377 9.362151 TGTACCTCTCAAAAAGGAAAAATACAT 57.638 29.630 0.00 0.00 37.35 2.29
370 378 9.626045 GTACCTCTCAAAAAGGAAAAATACATG 57.374 33.333 0.00 0.00 37.35 3.21
390 398 6.686630 ACATGTTTGTTTTTGTGAGAGACAA 58.313 32.000 0.00 0.00 36.23 3.18
420 428 4.553323 CTTCTTGTGGAGGCAAAGATTTG 58.447 43.478 0.84 0.84 41.03 2.32
425 433 4.692228 TGTGGAGGCAAAGATTTGTTTTC 58.308 39.130 7.12 3.21 40.24 2.29
449 457 4.792087 GGCACAACCTCTTCGGAA 57.208 55.556 0.00 0.00 36.31 4.30
454 462 2.572290 CACAACCTCTTCGGAAAAGGT 58.428 47.619 9.97 9.97 45.32 3.50
464 472 6.126568 TCTTCGGAAAAGGTAAAACAAGTG 57.873 37.500 0.00 0.00 0.00 3.16
465 473 5.881443 TCTTCGGAAAAGGTAAAACAAGTGA 59.119 36.000 0.00 0.00 0.00 3.41
488 496 3.745332 AAAAACGTTCTTTCGGTTCGT 57.255 38.095 0.00 0.00 39.90 3.85
489 497 2.724744 AAACGTTCTTTCGGTTCGTG 57.275 45.000 0.00 0.00 35.83 4.35
518 536 6.961359 AATTCGTCGAAACTATCAACATGA 57.039 33.333 12.40 0.00 0.00 3.07
564 582 6.507023 ACATGAGAAATCCAACAGTGAAAAC 58.493 36.000 0.00 0.00 0.00 2.43
566 584 4.878971 TGAGAAATCCAACAGTGAAAACGA 59.121 37.500 0.00 0.00 0.00 3.85
569 587 6.438763 AGAAATCCAACAGTGAAAACGATTC 58.561 36.000 0.00 0.00 0.00 2.52
572 590 2.546368 CCAACAGTGAAAACGATTCCGA 59.454 45.455 0.00 0.00 39.50 4.55
574 592 4.496673 CCAACAGTGAAAACGATTCCGAAA 60.497 41.667 0.00 0.00 39.50 3.46
580 598 4.615541 GTGAAAACGATTCCGAAATTGGAC 59.384 41.667 0.00 0.00 37.89 4.02
595 613 2.961536 TGGACTCCCTCCATTCCTTA 57.038 50.000 0.00 0.00 44.99 2.69
596 614 2.478292 TGGACTCCCTCCATTCCTTAC 58.522 52.381 0.00 0.00 44.99 2.34
597 615 2.225779 TGGACTCCCTCCATTCCTTACA 60.226 50.000 0.00 0.00 44.99 2.41
598 616 3.049344 GGACTCCCTCCATTCCTTACAT 58.951 50.000 0.00 0.00 39.21 2.29
599 617 3.181450 GGACTCCCTCCATTCCTTACATG 60.181 52.174 0.00 0.00 39.21 3.21
600 618 3.456277 GACTCCCTCCATTCCTTACATGT 59.544 47.826 2.69 2.69 0.00 3.21
602 620 5.227593 ACTCCCTCCATTCCTTACATGTAT 58.772 41.667 6.36 0.00 0.00 2.29
603 621 5.672194 ACTCCCTCCATTCCTTACATGTATT 59.328 40.000 6.36 0.00 0.00 1.89
604 622 6.849697 ACTCCCTCCATTCCTTACATGTATTA 59.150 38.462 6.36 0.00 0.00 0.98
605 623 7.074653 TCCCTCCATTCCTTACATGTATTAC 57.925 40.000 6.36 0.00 0.00 1.89
613 638 5.353938 TCCTTACATGTATTACTTCGGCAC 58.646 41.667 6.36 0.00 0.00 5.01
633 658 6.165659 GCACGGTAAGCCACATAATTATAG 57.834 41.667 0.00 0.00 34.09 1.31
710 735 9.822727 AAATCATTTAGGTTAGGAAAGGAAGAA 57.177 29.630 0.00 0.00 30.10 2.52
726 751 8.817092 AAAGGAAGAAATATAATCAACCGGAA 57.183 30.769 9.46 0.00 0.00 4.30
727 752 7.803279 AGGAAGAAATATAATCAACCGGAAC 57.197 36.000 9.46 0.00 0.00 3.62
731 756 8.438676 AAGAAATATAATCAACCGGAACAGAG 57.561 34.615 9.46 0.00 0.00 3.35
740 765 3.889520 ACCGGAACAGAGATACTTTCC 57.110 47.619 9.46 0.00 35.01 3.13
768 796 7.606858 TTTCTCAACAAGAAGAGATGCATAG 57.393 36.000 0.00 0.00 44.69 2.23
775 803 4.533919 AGAAGAGATGCATAGAATCGGG 57.466 45.455 0.00 0.00 0.00 5.14
786 814 4.461081 GCATAGAATCGGGTGAGAGATACT 59.539 45.833 0.00 0.00 0.00 2.12
798 826 7.298854 GGGTGAGAGATACTTTTTCTTTTTCG 58.701 38.462 0.00 0.00 0.00 3.46
800 828 7.798982 GGTGAGAGATACTTTTTCTTTTTCGTG 59.201 37.037 0.00 0.00 0.00 4.35
803 831 9.587461 GAGAGATACTTTTTCTTTTTCGTGAAG 57.413 33.333 0.00 0.00 0.00 3.02
807 835 6.762702 ACTTTTTCTTTTTCGTGAAGGGTA 57.237 33.333 0.00 0.00 0.00 3.69
839 867 8.956426 AGAAATTACGAGGAATTAGAAATGCAA 58.044 29.630 0.00 0.00 0.00 4.08
844 872 7.073342 ACGAGGAATTAGAAATGCAACTTAC 57.927 36.000 0.00 0.00 0.00 2.34
845 873 6.653320 ACGAGGAATTAGAAATGCAACTTACA 59.347 34.615 0.00 0.00 0.00 2.41
846 874 7.336931 ACGAGGAATTAGAAATGCAACTTACAT 59.663 33.333 0.00 0.00 0.00 2.29
847 875 8.826710 CGAGGAATTAGAAATGCAACTTACATA 58.173 33.333 0.00 0.00 0.00 2.29
887 915 2.781681 AATACACCTGAAACGGAGGG 57.218 50.000 0.00 0.00 34.56 4.30
922 950 0.240945 ATTTCGCAAAAGCCGGACAG 59.759 50.000 5.05 0.00 0.00 3.51
1030 1064 1.522676 GCAGAGCCAAAAAGCGAAAAC 59.477 47.619 0.00 0.00 38.01 2.43
1039 1073 0.534203 AAAGCGAAAACGGCAGGAGA 60.534 50.000 0.00 0.00 0.00 3.71
1192 1226 2.818132 GCACCCAGATCCTCTCCG 59.182 66.667 0.00 0.00 0.00 4.63
1354 1388 2.190981 GGTACGGCTACAAATCTGACG 58.809 52.381 0.00 0.00 0.00 4.35
1461 1495 3.643159 ATTTGCCAGAAACTTCGGTTC 57.357 42.857 0.00 0.00 37.14 3.62
1528 1562 3.615536 CTTTTGCCCAAGCTCCGCG 62.616 63.158 0.00 0.00 40.80 6.46
1545 1579 0.671781 GCGTCCTCAGCATCAAGTGT 60.672 55.000 0.00 0.00 34.19 3.55
1623 1657 1.621301 CCGAACTCAAGCAGCTCACG 61.621 60.000 0.00 0.00 0.00 4.35
1626 1660 0.948141 AACTCAAGCAGCTCACGCTC 60.948 55.000 0.00 0.00 45.15 5.03
1752 1786 2.297698 TCAACTCGTCCACCCTTAGA 57.702 50.000 0.00 0.00 0.00 2.10
1768 1802 1.041447 TAGAAGGCTAGGGGTGTCGC 61.041 60.000 0.00 0.00 0.00 5.19
1847 2063 7.291566 CCTCTCCTAGAGAAGTTGTTCCTATA 58.708 42.308 5.50 0.00 45.07 1.31
1875 2091 1.464376 ATGACGGCCTATCAGTCCGG 61.464 60.000 11.74 0.00 46.78 5.14
1965 2181 5.888724 TGAAACCAATGTTCTTCAGGTAACA 59.111 36.000 0.00 0.00 39.73 2.41
1992 2215 7.095691 GCAGCTTCTTAATTTTTGTGTTATGCA 60.096 33.333 0.00 0.00 0.00 3.96
2003 2226 4.374843 TGTGTTATGCATTGCAGATTCC 57.625 40.909 17.52 5.59 43.65 3.01
2018 2242 2.423538 AGATTCCGTGCTAACCATTTGC 59.576 45.455 0.00 0.00 0.00 3.68
2132 5636 5.255687 AGTGTTGATGATGCCATTCACTAA 58.744 37.500 0.00 0.00 37.53 2.24
2133 5637 5.124457 AGTGTTGATGATGCCATTCACTAAC 59.876 40.000 0.00 0.00 37.53 2.34
2139 5643 6.604396 TGATGATGCCATTCACTAACAGAAAT 59.396 34.615 0.00 0.00 32.09 2.17
2151 5655 5.710099 CACTAACAGAAATAGGGGCTTTTGA 59.290 40.000 0.00 0.00 0.00 2.69
2282 5813 4.566070 CCATCTTTAGTCCCGGTTGGTAAA 60.566 45.833 0.00 0.00 34.77 2.01
2283 5814 4.276058 TCTTTAGTCCCGGTTGGTAAAG 57.724 45.455 0.00 8.40 34.76 1.85
2284 5815 3.903090 TCTTTAGTCCCGGTTGGTAAAGA 59.097 43.478 15.97 15.97 37.71 2.52
2285 5816 4.347583 TCTTTAGTCCCGGTTGGTAAAGAA 59.652 41.667 16.93 6.84 37.39 2.52
2286 5817 4.703379 TTAGTCCCGGTTGGTAAAGAAA 57.297 40.909 0.00 0.00 34.77 2.52
2287 5818 3.581265 AGTCCCGGTTGGTAAAGAAAA 57.419 42.857 0.00 0.00 34.77 2.29
2442 6080 3.790089 ATTCTCCCTCGTTTCCAAGTT 57.210 42.857 0.00 0.00 0.00 2.66
2496 6134 6.846505 AGATGTCAATCCTATTAACCCTCAGA 59.153 38.462 0.00 0.00 32.77 3.27
2510 6148 4.218312 ACCCTCAGAAATTTTGCTTGAGT 58.782 39.130 15.55 3.83 0.00 3.41
2545 6183 7.818930 ACACATTTCACTGTTTGAGTTTGAAAT 59.181 29.630 2.72 2.72 37.60 2.17
2958 6623 6.875972 TTCCACTCTAGATCTTAAAAGCCT 57.124 37.500 0.00 0.00 0.00 4.58
3016 6685 5.158889 TGAAAATGTTTAATGGGGTTCCCT 58.841 37.500 7.87 0.00 45.70 4.20
3017 6686 6.323737 TGAAAATGTTTAATGGGGTTCCCTA 58.676 36.000 7.87 1.70 45.70 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 0.037882 CTTGTGCCTCTCTCGCAGAA 60.038 55.000 0.00 0.00 37.18 3.02
6 7 1.181741 ACTTGTGCCTCTCTCGCAGA 61.182 55.000 0.00 0.00 36.78 4.26
7 8 0.320247 AACTTGTGCCTCTCTCGCAG 60.320 55.000 0.00 0.00 36.78 5.18
8 9 0.966179 TAACTTGTGCCTCTCTCGCA 59.034 50.000 0.00 0.00 0.00 5.10
9 10 1.067495 AGTAACTTGTGCCTCTCTCGC 60.067 52.381 0.00 0.00 0.00 5.03
11 12 4.490743 GAGAAGTAACTTGTGCCTCTCTC 58.509 47.826 0.00 0.00 0.00 3.20
12 13 3.057174 CGAGAAGTAACTTGTGCCTCTCT 60.057 47.826 0.00 0.00 0.00 3.10
13 14 3.246619 CGAGAAGTAACTTGTGCCTCTC 58.753 50.000 0.00 0.00 0.00 3.20
14 15 2.628657 ACGAGAAGTAACTTGTGCCTCT 59.371 45.455 0.00 0.00 33.77 3.69
15 16 2.731976 CACGAGAAGTAACTTGTGCCTC 59.268 50.000 0.00 0.00 42.72 4.70
16 17 2.548067 CCACGAGAAGTAACTTGTGCCT 60.548 50.000 0.00 0.00 45.63 4.75
17 18 1.798813 CCACGAGAAGTAACTTGTGCC 59.201 52.381 0.00 0.00 45.63 5.01
18 19 2.750948 TCCACGAGAAGTAACTTGTGC 58.249 47.619 0.00 0.00 45.63 4.57
19 20 3.123621 GCATCCACGAGAAGTAACTTGTG 59.876 47.826 0.00 0.00 46.19 3.33
20 21 3.244078 TGCATCCACGAGAAGTAACTTGT 60.244 43.478 0.00 0.00 35.17 3.16
21 22 3.123621 GTGCATCCACGAGAAGTAACTTG 59.876 47.826 0.00 0.00 31.34 3.16
22 23 3.244078 TGTGCATCCACGAGAAGTAACTT 60.244 43.478 0.00 0.00 45.04 2.66
23 24 2.299013 TGTGCATCCACGAGAAGTAACT 59.701 45.455 0.00 0.00 45.04 2.24
24 25 2.683968 TGTGCATCCACGAGAAGTAAC 58.316 47.619 0.00 0.00 45.04 2.50
25 26 3.394674 TTGTGCATCCACGAGAAGTAA 57.605 42.857 0.00 0.00 45.04 2.24
26 27 3.394674 TTTGTGCATCCACGAGAAGTA 57.605 42.857 0.00 0.00 45.04 2.24
27 28 2.254546 TTTGTGCATCCACGAGAAGT 57.745 45.000 0.00 0.00 45.04 3.01
28 29 3.837213 AATTTGTGCATCCACGAGAAG 57.163 42.857 0.00 0.00 45.04 2.85
29 30 3.856638 GCAAATTTGTGCATCCACGAGAA 60.857 43.478 19.03 0.00 45.04 2.87
30 31 2.351641 GCAAATTTGTGCATCCACGAGA 60.352 45.455 19.03 0.00 45.04 4.04
31 32 1.987770 GCAAATTTGTGCATCCACGAG 59.012 47.619 19.03 0.00 45.04 4.18
32 33 2.063156 GCAAATTTGTGCATCCACGA 57.937 45.000 19.03 0.00 45.04 4.35
40 41 0.313672 TCACGGGAGCAAATTTGTGC 59.686 50.000 19.03 7.03 45.28 4.57
41 42 1.879380 TCTCACGGGAGCAAATTTGTG 59.121 47.619 19.03 8.68 41.13 3.33
42 43 2.154462 CTCTCACGGGAGCAAATTTGT 58.846 47.619 19.03 6.52 41.13 2.83
43 44 2.154462 ACTCTCACGGGAGCAAATTTG 58.846 47.619 10.68 14.03 41.13 2.32
44 45 2.427506 GACTCTCACGGGAGCAAATTT 58.572 47.619 10.68 0.00 41.13 1.82
45 46 1.673033 CGACTCTCACGGGAGCAAATT 60.673 52.381 10.68 0.00 41.13 1.82
46 47 0.108615 CGACTCTCACGGGAGCAAAT 60.109 55.000 10.68 0.00 41.13 2.32
47 48 1.289066 CGACTCTCACGGGAGCAAA 59.711 57.895 10.68 0.00 41.13 3.68
48 49 2.636412 CCGACTCTCACGGGAGCAA 61.636 63.158 10.68 0.00 45.65 3.91
49 50 3.062466 CCGACTCTCACGGGAGCA 61.062 66.667 10.68 0.00 45.65 4.26
55 56 0.601558 TTCCCTTTCCGACTCTCACG 59.398 55.000 0.00 0.00 0.00 4.35
56 57 2.833631 TTTCCCTTTCCGACTCTCAC 57.166 50.000 0.00 0.00 0.00 3.51
57 58 3.849563 TTTTTCCCTTTCCGACTCTCA 57.150 42.857 0.00 0.00 0.00 3.27
81 82 9.793259 TTTGTGTCTCTCAAGGTAGAAAAATAT 57.207 29.630 0.00 0.00 0.00 1.28
88 94 7.963532 AGTAAATTTGTGTCTCTCAAGGTAGA 58.036 34.615 0.00 0.00 0.00 2.59
94 100 9.734620 CATCAAAAGTAAATTTGTGTCTCTCAA 57.265 29.630 0.00 0.00 40.40 3.02
95 101 8.352201 CCATCAAAAGTAAATTTGTGTCTCTCA 58.648 33.333 0.00 0.00 40.40 3.27
115 121 5.163301 GGAAGCTAATAGGTGTCTCCATCAA 60.163 44.000 4.35 0.00 39.02 2.57
118 124 3.322254 CGGAAGCTAATAGGTGTCTCCAT 59.678 47.826 8.77 0.00 39.02 3.41
136 142 4.207281 CCGATGCCTCTCGCGGAA 62.207 66.667 6.13 0.00 46.29 4.30
140 146 1.432270 CCTTTTCCGATGCCTCTCGC 61.432 60.000 0.00 0.00 37.33 5.03
141 147 0.175760 TCCTTTTCCGATGCCTCTCG 59.824 55.000 0.00 0.00 38.37 4.04
168 174 3.934457 TTTTTCCTTTTCCGATGCCTC 57.066 42.857 0.00 0.00 0.00 4.70
204 210 1.025113 TCTGTGTCTCTCGCGGTAGG 61.025 60.000 6.13 0.00 34.79 3.18
211 217 2.670414 GGAAGCAAATCTGTGTCTCTCG 59.330 50.000 0.00 0.00 0.00 4.04
231 237 0.596083 CATAGTTCTGCCTCTCGCGG 60.596 60.000 6.13 0.00 46.15 6.46
277 284 2.052104 TGGCTCTCGCGGATGAGAA 61.052 57.895 22.00 10.73 44.03 2.87
279 286 2.279120 GTGGCTCTCGCGGATGAG 60.279 66.667 6.13 12.92 36.88 2.90
301 308 2.029290 TCTTTGCCTCCACGAGAAGTAC 60.029 50.000 0.00 0.00 0.00 2.73
334 341 6.486993 CCTTTTTGAGAGGTACAGCTTTACTT 59.513 38.462 9.78 2.02 0.00 2.24
337 344 6.182507 TCCTTTTTGAGAGGTACAGCTTTA 57.817 37.500 0.00 0.00 35.71 1.85
342 349 8.846211 TGTATTTTTCCTTTTTGAGAGGTACAG 58.154 33.333 0.00 0.00 35.71 2.74
379 387 6.455360 AGAAGCAAAATTTTGTCTCTCACA 57.545 33.333 27.13 0.00 40.24 3.58
390 398 3.134442 TGCCTCCACAAGAAGCAAAATTT 59.866 39.130 0.00 0.00 39.02 1.82
393 401 1.774110 TGCCTCCACAAGAAGCAAAA 58.226 45.000 0.00 0.00 39.02 2.44
420 428 3.321271 AGGTTGTGCCTCTCACGAAAAC 61.321 50.000 0.00 0.00 46.96 2.43
471 479 1.925229 TCACGAACCGAAAGAACGTT 58.075 45.000 0.00 0.00 35.05 3.99
496 514 6.330278 TCTCATGTTGATAGTTTCGACGAAT 58.670 36.000 11.71 0.00 41.10 3.34
539 557 6.713762 TTTCACTGTTGGATTTCTCATGTT 57.286 33.333 0.00 0.00 0.00 2.71
543 561 4.878971 TCGTTTTCACTGTTGGATTTCTCA 59.121 37.500 0.00 0.00 0.00 3.27
547 565 5.528870 GGAATCGTTTTCACTGTTGGATTT 58.471 37.500 3.88 0.00 0.00 2.17
566 584 2.092375 GGAGGGAGTCCAATTTCGGAAT 60.092 50.000 12.30 0.00 46.10 3.01
569 587 3.478540 GGAGGGAGTCCAATTTCGG 57.521 57.895 12.30 0.00 46.10 4.30
580 598 5.832539 ATACATGTAAGGAATGGAGGGAG 57.167 43.478 10.14 0.00 0.00 4.30
595 613 2.093869 ACCGTGCCGAAGTAATACATGT 60.094 45.455 2.69 2.69 0.00 3.21
596 614 2.546778 ACCGTGCCGAAGTAATACATG 58.453 47.619 0.00 0.00 0.00 3.21
597 615 2.973694 ACCGTGCCGAAGTAATACAT 57.026 45.000 0.00 0.00 0.00 2.29
598 616 3.772932 CTTACCGTGCCGAAGTAATACA 58.227 45.455 0.00 0.00 0.00 2.29
599 617 2.537214 GCTTACCGTGCCGAAGTAATAC 59.463 50.000 0.00 0.00 0.00 1.89
600 618 2.481795 GGCTTACCGTGCCGAAGTAATA 60.482 50.000 0.00 0.00 41.03 0.98
602 620 0.390209 GGCTTACCGTGCCGAAGTAA 60.390 55.000 0.00 0.00 41.03 2.24
603 621 1.216178 GGCTTACCGTGCCGAAGTA 59.784 57.895 0.00 0.00 41.03 2.24
604 622 2.047560 GGCTTACCGTGCCGAAGT 60.048 61.111 0.00 0.00 41.03 3.01
613 638 7.956420 TTGTCTATAATTATGTGGCTTACCG 57.044 36.000 8.28 0.00 39.70 4.02
676 701 9.474313 TTCCTAACCTAAATGATTTACTTGCAT 57.526 29.630 0.00 0.00 0.00 3.96
677 702 8.871629 TTCCTAACCTAAATGATTTACTTGCA 57.128 30.769 0.00 0.00 0.00 4.08
678 703 9.788960 CTTTCCTAACCTAAATGATTTACTTGC 57.211 33.333 0.00 0.00 0.00 4.01
710 735 8.871125 AGTATCTCTGTTCCGGTTGATTATATT 58.129 33.333 0.00 0.00 0.00 1.28
716 741 5.420409 GAAAGTATCTCTGTTCCGGTTGAT 58.580 41.667 0.00 0.46 0.00 2.57
717 742 4.322499 GGAAAGTATCTCTGTTCCGGTTGA 60.322 45.833 0.00 0.00 30.85 3.18
721 746 4.473477 AAGGAAAGTATCTCTGTTCCGG 57.527 45.455 0.00 0.00 43.60 5.14
764 792 6.582677 AAGTATCTCTCACCCGATTCTATG 57.417 41.667 0.00 0.00 0.00 2.23
768 796 6.342111 AGAAAAAGTATCTCTCACCCGATTC 58.658 40.000 0.00 0.00 0.00 2.52
775 803 8.548721 TCACGAAAAAGAAAAAGTATCTCTCAC 58.451 33.333 0.00 0.00 0.00 3.51
786 814 8.828688 TTTTTACCCTTCACGAAAAAGAAAAA 57.171 26.923 0.00 0.00 0.00 1.94
813 841 8.506168 TGCATTTCTAATTCCTCGTAATTTCT 57.494 30.769 0.00 0.00 31.63 2.52
821 849 7.072177 TGTAAGTTGCATTTCTAATTCCTCG 57.928 36.000 0.00 0.00 0.00 4.63
1354 1388 2.921754 CGTTCAGTAATGGGAAGACGTC 59.078 50.000 7.70 7.70 0.00 4.34
1476 1510 2.817834 GGCAGCGCATACGGAACA 60.818 61.111 11.47 0.00 40.57 3.18
1528 1562 2.234908 AGGTACACTTGATGCTGAGGAC 59.765 50.000 0.00 0.00 0.00 3.85
1545 1579 3.181469 GGAAATGGATCACGTAGCAGGTA 60.181 47.826 0.00 0.00 0.00 3.08
1623 1657 0.318784 AGACGACGACACCTTTGAGC 60.319 55.000 0.00 0.00 0.00 4.26
1626 1660 1.002250 CCGAGACGACGACACCTTTG 61.002 60.000 0.00 0.00 35.09 2.77
1752 1786 3.400054 GGCGACACCCCTAGCCTT 61.400 66.667 0.00 0.00 45.67 4.35
1768 1802 0.764890 TCTGTCCAACCAGAACCAGG 59.235 55.000 0.00 0.00 38.49 4.45
1847 2063 0.188587 TAGGCCGTCATCTCTCCCAT 59.811 55.000 0.00 0.00 0.00 4.00
1965 2181 7.116805 GCATAACACAAAAATTAAGAAGCTGCT 59.883 33.333 0.00 0.00 0.00 4.24
1992 2215 2.017049 GGTTAGCACGGAATCTGCAAT 58.983 47.619 0.00 0.00 37.08 3.56
2003 2226 1.863012 CGCGCAAATGGTTAGCACG 60.863 57.895 8.75 0.00 0.00 5.34
2018 2242 6.780706 ATTCCCTGAATTAAGTAATACGCG 57.219 37.500 3.53 3.53 0.00 6.01
2132 5636 3.431415 GGTCAAAAGCCCCTATTTCTGT 58.569 45.455 0.00 0.00 0.00 3.41
2133 5637 2.760650 GGGTCAAAAGCCCCTATTTCTG 59.239 50.000 0.00 0.00 40.26 3.02
2139 5643 1.428718 AACCGGGTCAAAAGCCCCTA 61.429 55.000 6.32 0.00 43.18 3.53
2262 5793 3.903090 TCTTTACCAACCGGGACTAAAGA 59.097 43.478 6.32 13.09 39.80 2.52
2442 6080 3.256879 TGTCAGGAAAACAACAAGTGCAA 59.743 39.130 0.00 0.00 0.00 4.08
2496 6134 7.649306 GTGTCACTTCATACTCAAGCAAAATTT 59.351 33.333 0.00 0.00 0.00 1.82
2608 6246 4.950475 TGGTCAAACTGTGGTCAAACAATA 59.050 37.500 0.00 0.00 0.00 1.90
3016 6685 9.421806 TCGAAAAGTTACATCCGAATTTAACTA 57.578 29.630 0.00 0.00 37.38 2.24
3017 6686 8.314143 TCGAAAAGTTACATCCGAATTTAACT 57.686 30.769 0.00 0.00 39.12 2.24


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

AutoCloner maintained by Alex Coulton.