Multiple sequence alignment - TraesCS5D01G227800

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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 TraesCS5D01G227800 chr5D 100.000 7095 0 0 1 7095 335127476 335134570 0.000000e+00 13103.0
1 TraesCS5D01G227800 chr5D 81.925 1953 278 41 1580 3485 335216572 335218496 0.000000e+00 1581.0
2 TraesCS5D01G227800 chr5D 81.184 1419 185 50 4795 6169 335219662 335221042 0.000000e+00 1066.0
3 TraesCS5D01G227800 chr5D 87.990 408 44 3 4201 4604 335219015 335219421 1.790000e-130 477.0
4 TraesCS5D01G227800 chr5D 85.423 343 37 11 966 1299 335215877 335216215 1.890000e-90 344.0
5 TraesCS5D01G227800 chr5D 78.977 176 31 5 4268 4440 334698328 334698500 1.620000e-21 115.0
6 TraesCS5D01G227800 chr5D 83.721 129 13 7 3557 3684 335218493 335218614 1.620000e-21 115.0
7 TraesCS5D01G227800 chr5B 95.069 2819 107 20 4289 7095 392137403 392140201 0.000000e+00 4407.0
8 TraesCS5D01G227800 chr5B 97.460 2323 42 7 1753 4061 392127911 392130230 0.000000e+00 3947.0
9 TraesCS5D01G227800 chr5B 97.245 2323 47 7 1753 4061 392087874 392090193 0.000000e+00 3919.0
10 TraesCS5D01G227800 chr5B 96.630 1365 27 6 368 1720 392126444 392127801 0.000000e+00 2248.0
11 TraesCS5D01G227800 chr5B 96.484 1365 29 6 368 1720 392086407 392087764 0.000000e+00 2237.0
12 TraesCS5D01G227800 chr5B 86.155 1524 186 13 2202 3704 392147950 392149469 0.000000e+00 1622.0
13 TraesCS5D01G227800 chr5B 81.812 1413 170 53 4807 6151 392150740 392152133 0.000000e+00 1105.0
14 TraesCS5D01G227800 chr5B 86.752 468 47 10 4201 4666 392150075 392150529 2.280000e-139 507.0
15 TraesCS5D01G227800 chr5B 91.837 294 18 5 975 1264 392146398 392146689 8.570000e-109 405.0
16 TraesCS5D01G227800 chr5B 90.875 263 6 1 4059 4303 392090474 392090736 3.170000e-88 337.0
17 TraesCS5D01G227800 chr5B 90.875 263 6 1 4059 4303 392130511 392130773 3.170000e-88 337.0
18 TraesCS5D01G227800 chr5B 98.235 170 3 0 172 341 392086080 392086249 1.500000e-76 298.0
19 TraesCS5D01G227800 chr5B 97.647 170 4 0 172 341 392126117 392126286 6.960000e-75 292.0
20 TraesCS5D01G227800 chr5B 98.039 102 2 0 76 177 671343382 671343281 2.030000e-40 178.0
21 TraesCS5D01G227800 chr5B 96.262 107 4 0 76 182 425884668 425884562 7.310000e-40 176.0
22 TraesCS5D01G227800 chr5B 77.698 278 44 12 1924 2190 392147568 392147838 3.430000e-33 154.0
23 TraesCS5D01G227800 chr5B 98.718 78 1 0 1 78 392086004 392086081 9.600000e-29 139.0
24 TraesCS5D01G227800 chr5B 98.718 78 1 0 1 78 392126041 392126118 9.600000e-29 139.0
25 TraesCS5D01G227800 chr5B 80.000 180 30 5 4264 4440 391639343 391639519 2.080000e-25 128.0
26 TraesCS5D01G227800 chr5B 100.000 46 0 0 325 370 392086259 392086304 1.270000e-12 86.1
27 TraesCS5D01G227800 chr5B 100.000 46 0 0 325 370 392126296 392126341 1.270000e-12 86.1
28 TraesCS5D01G227800 chrUn 96.944 2323 44 9 1753 4061 267452976 267455285 0.000000e+00 3871.0
29 TraesCS5D01G227800 chrUn 96.630 1365 28 6 368 1720 267451508 267452866 0.000000e+00 2250.0
30 TraesCS5D01G227800 chrUn 96.630 1365 28 6 368 1720 340254876 340256234 0.000000e+00 2250.0
31 TraesCS5D01G227800 chrUn 96.422 587 13 4 1753 2333 340256344 340256928 0.000000e+00 961.0
32 TraesCS5D01G227800 chrUn 90.494 263 7 1 4059 4303 267455566 267455828 1.480000e-86 331.0
33 TraesCS5D01G227800 chrUn 98.235 170 3 0 172 341 267451181 267451350 1.500000e-76 298.0
34 TraesCS5D01G227800 chrUn 98.235 170 3 0 172 341 340254549 340254718 1.500000e-76 298.0
35 TraesCS5D01G227800 chrUn 98.101 158 3 0 172 329 339807900 339807743 7.010000e-70 276.0
36 TraesCS5D01G227800 chrUn 98.718 78 1 0 1 78 339807976 339807899 9.600000e-29 139.0
37 TraesCS5D01G227800 chrUn 97.436 78 2 0 1 78 267451105 267451182 4.470000e-27 134.0
38 TraesCS5D01G227800 chrUn 98.529 68 1 0 11 78 340254483 340254550 3.480000e-23 121.0
39 TraesCS5D01G227800 chrUn 100.000 46 0 0 325 370 267451360 267451405 1.270000e-12 86.1
40 TraesCS5D01G227800 chrUn 100.000 46 0 0 325 370 340254728 340254773 1.270000e-12 86.1
41 TraesCS5D01G227800 chr5A 94.418 2329 91 16 4794 7095 436621769 436624085 0.000000e+00 3544.0
42 TraesCS5D01G227800 chr5A 94.295 1928 81 12 1789 3710 436618646 436620550 0.000000e+00 2924.0
43 TraesCS5D01G227800 chr5A 95.667 900 33 5 385 1281 436617226 436618122 0.000000e+00 1441.0
44 TraesCS5D01G227800 chr5A 89.350 939 53 22 3877 4800 436620789 436621695 0.000000e+00 1136.0
45 TraesCS5D01G227800 chr5A 88.991 327 20 6 1313 1623 436618310 436618636 2.400000e-104 390.0
46 TraesCS5D01G227800 chr5A 94.059 202 11 1 172 373 436615605 436615805 8.940000e-79 305.0
47 TraesCS5D01G227800 chr5A 96.154 78 3 0 1 78 436615529 436615606 2.080000e-25 128.0
48 TraesCS5D01G227800 chr5A 79.769 173 29 5 4271 4440 436259633 436259802 3.480000e-23 121.0
49 TraesCS5D01G227800 chr5A 97.917 48 1 0 3710 3757 436620577 436620624 4.560000e-12 84.2
50 TraesCS5D01G227800 chr5A 90.909 44 4 0 3734 3777 436620676 436620719 7.690000e-05 60.2
51 TraesCS5D01G227800 chr5A 94.286 35 2 0 335 369 585406053 585406019 4.000000e-03 54.7
52 TraesCS5D01G227800 chr7B 90.138 1014 61 13 5675 6677 141007941 141006956 0.000000e+00 1282.0
53 TraesCS5D01G227800 chr7B 84.259 108 16 1 199 305 494735447 494735554 3.500000e-18 104.0
54 TraesCS5D01G227800 chr7A 89.917 724 46 12 5955 6671 177343273 177342570 0.000000e+00 907.0
55 TraesCS5D01G227800 chr7A 91.111 270 16 4 5675 5941 177343689 177343425 6.770000e-95 359.0
56 TraesCS5D01G227800 chr7D 90.767 574 29 6 5675 6243 175661139 175660585 0.000000e+00 745.0
57 TraesCS5D01G227800 chr7D 88.760 258 15 6 6427 6677 175659044 175658794 3.220000e-78 303.0
58 TraesCS5D01G227800 chr2B 100.000 100 0 0 74 173 752488069 752488168 1.220000e-42 185.0
59 TraesCS5D01G227800 chr3B 94.828 116 5 1 58 173 490924672 490924558 5.650000e-41 180.0
60 TraesCS5D01G227800 chr3B 96.262 107 4 0 68 174 826648901 826649007 7.310000e-40 176.0
61 TraesCS5D01G227800 chr3B 92.500 120 7 2 77 194 245963055 245962936 3.400000e-38 171.0
62 TraesCS5D01G227800 chr4B 98.058 103 1 1 72 173 498378507 498378609 2.030000e-40 178.0
63 TraesCS5D01G227800 chr4B 83.186 113 19 0 199 311 388623468 388623580 3.500000e-18 104.0
64 TraesCS5D01G227800 chr1B 93.388 121 6 2 55 173 429610614 429610734 2.030000e-40 178.0
65 TraesCS5D01G227800 chr6B 96.296 108 3 1 74 180 283316621 283316728 7.310000e-40 176.0
66 TraesCS5D01G227800 chr3D 77.632 152 23 8 170 319 456109763 456109905 1.640000e-11 82.4


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 TraesCS5D01G227800 chr5D 335127476 335134570 7094 False 13103.000000 13103 100.000000 1 7095 1 chr5D.!!$F2 7094
1 TraesCS5D01G227800 chr5D 335215877 335221042 5165 False 716.600000 1581 84.048600 966 6169 5 chr5D.!!$F3 5203
2 TraesCS5D01G227800 chr5B 392137403 392140201 2798 False 4407.000000 4407 95.069000 4289 7095 1 chr5B.!!$F2 2806
3 TraesCS5D01G227800 chr5B 392126041 392130773 4732 False 1174.850000 3947 96.888333 1 4303 6 chr5B.!!$F4 4302
4 TraesCS5D01G227800 chr5B 392086004 392090736 4732 False 1169.350000 3919 96.926167 1 4303 6 chr5B.!!$F3 4302
5 TraesCS5D01G227800 chr5B 392146398 392152133 5735 False 758.600000 1622 84.850800 975 6151 5 chr5B.!!$F5 5176
6 TraesCS5D01G227800 chrUn 267451105 267455828 4723 False 1161.683333 3871 96.623167 1 4303 6 chrUn.!!$F1 4302
7 TraesCS5D01G227800 chrUn 340254483 340256928 2445 False 743.220000 2250 97.963200 11 2333 5 chrUn.!!$F2 2322
8 TraesCS5D01G227800 chr5A 436615529 436624085 8556 False 1112.488889 3544 93.528889 1 7095 9 chr5A.!!$F2 7094
9 TraesCS5D01G227800 chr7B 141006956 141007941 985 True 1282.000000 1282 90.138000 5675 6677 1 chr7B.!!$R1 1002
10 TraesCS5D01G227800 chr7A 177342570 177343689 1119 True 633.000000 907 90.514000 5675 6671 2 chr7A.!!$R1 996
11 TraesCS5D01G227800 chr7D 175658794 175661139 2345 True 524.000000 745 89.763500 5675 6677 2 chr7D.!!$R1 1002

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
89 90 0.106116 ACCAGATACTCCCTCCGTCC 60.106 60.000 0.0 0.0 0.00 4.79 F
90 91 0.186386 CCAGATACTCCCTCCGTCCT 59.814 60.000 0.0 0.0 0.00 3.85 F
1587 3323 1.376466 GCATCAGGACCACAGGTGT 59.624 57.895 0.0 0.0 35.25 4.16 F
1873 3695 0.759959 TACCAGCAAACCACGGAAGA 59.240 50.000 0.0 0.0 0.00 2.87 F
3032 5000 1.067250 GCCGCAGCAAAAGTTGGAA 59.933 52.632 0.0 0.0 39.53 3.53 F
3932 6058 3.308530 GACGCTGTTCATTCCCAAAAAG 58.691 45.455 0.0 0.0 0.00 2.27 F
4670 7316 2.350522 AGAAGCCTCATGCAACTAACG 58.649 47.619 0.0 0.0 44.83 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1587 3323 6.201226 TCATTTACACAGCAACAAAACTGA 57.799 33.333 0.00 0.0 37.35 3.41 R
1741 3482 8.495949 TCGTTTTTCTTCAATTCTACATCTCAC 58.504 33.333 0.00 0.0 0.00 3.51 R
3032 5000 4.274602 TCTGAAATGTGGCATTTGCAAT 57.725 36.364 11.24 0.0 44.36 3.56 R
3843 5959 7.294017 CATGGAATGCATTTAGGGTTATCTT 57.706 36.000 14.33 0.0 37.62 2.40 R
4669 7315 0.317160 TGTGGAGCTGTGTTAGACCG 59.683 55.000 0.00 0.0 0.00 4.79 R
4851 7634 1.168407 TTGCACAAGCTCCTCTGCAC 61.168 55.000 6.97 0.0 39.32 4.57 R
6586 10950 5.085219 AGGTATGCATCTACTAGGTTACCC 58.915 45.833 0.19 0.0 0.00 3.69 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
41 42 9.474920 TTGACTTGCCAAATTATCTTTTGTAAG 57.525 29.630 0.00 0.00 36.26 2.34
81 82 9.574516 ACCAAATAAATGATTACCAGATACTCC 57.425 33.333 0.00 0.00 0.00 3.85
82 83 9.014297 CCAAATAAATGATTACCAGATACTCCC 57.986 37.037 0.00 0.00 0.00 4.30
83 84 9.799106 CAAATAAATGATTACCAGATACTCCCT 57.201 33.333 0.00 0.00 0.00 4.20
85 86 6.441088 AAATGATTACCAGATACTCCCTCC 57.559 41.667 0.00 0.00 0.00 4.30
86 87 3.497332 TGATTACCAGATACTCCCTCCG 58.503 50.000 0.00 0.00 0.00 4.63
87 88 3.117246 TGATTACCAGATACTCCCTCCGT 60.117 47.826 0.00 0.00 0.00 4.69
88 89 2.653234 TACCAGATACTCCCTCCGTC 57.347 55.000 0.00 0.00 0.00 4.79
89 90 0.106116 ACCAGATACTCCCTCCGTCC 60.106 60.000 0.00 0.00 0.00 4.79
90 91 0.186386 CCAGATACTCCCTCCGTCCT 59.814 60.000 0.00 0.00 0.00 3.85
91 92 1.424302 CCAGATACTCCCTCCGTCCTA 59.576 57.143 0.00 0.00 0.00 2.94
92 93 2.158505 CCAGATACTCCCTCCGTCCTAA 60.159 54.545 0.00 0.00 0.00 2.69
93 94 3.563223 CAGATACTCCCTCCGTCCTAAA 58.437 50.000 0.00 0.00 0.00 1.85
94 95 3.958798 CAGATACTCCCTCCGTCCTAAAA 59.041 47.826 0.00 0.00 0.00 1.52
95 96 4.589374 CAGATACTCCCTCCGTCCTAAAAT 59.411 45.833 0.00 0.00 0.00 1.82
96 97 5.773680 CAGATACTCCCTCCGTCCTAAAATA 59.226 44.000 0.00 0.00 0.00 1.40
97 98 6.267014 CAGATACTCCCTCCGTCCTAAAATAA 59.733 42.308 0.00 0.00 0.00 1.40
98 99 6.494146 AGATACTCCCTCCGTCCTAAAATAAG 59.506 42.308 0.00 0.00 0.00 1.73
99 100 4.359996 ACTCCCTCCGTCCTAAAATAAGT 58.640 43.478 0.00 0.00 0.00 2.24
100 101 4.161754 ACTCCCTCCGTCCTAAAATAAGTG 59.838 45.833 0.00 0.00 0.00 3.16
101 102 4.098894 TCCCTCCGTCCTAAAATAAGTGT 58.901 43.478 0.00 0.00 0.00 3.55
102 103 4.161001 TCCCTCCGTCCTAAAATAAGTGTC 59.839 45.833 0.00 0.00 0.00 3.67
103 104 4.161754 CCCTCCGTCCTAAAATAAGTGTCT 59.838 45.833 0.00 0.00 0.00 3.41
104 105 5.338137 CCCTCCGTCCTAAAATAAGTGTCTT 60.338 44.000 0.00 0.00 0.00 3.01
105 106 5.581085 CCTCCGTCCTAAAATAAGTGTCTTG 59.419 44.000 0.00 0.00 0.00 3.02
106 107 6.349243 TCCGTCCTAAAATAAGTGTCTTGA 57.651 37.500 0.00 0.00 0.00 3.02
107 108 6.395629 TCCGTCCTAAAATAAGTGTCTTGAG 58.604 40.000 0.00 0.00 0.00 3.02
108 109 5.063564 CCGTCCTAAAATAAGTGTCTTGAGC 59.936 44.000 0.00 0.00 0.00 4.26
109 110 5.869888 CGTCCTAAAATAAGTGTCTTGAGCT 59.130 40.000 0.00 0.00 0.00 4.09
110 111 6.369065 CGTCCTAAAATAAGTGTCTTGAGCTT 59.631 38.462 0.00 0.00 0.00 3.74
111 112 7.544566 CGTCCTAAAATAAGTGTCTTGAGCTTA 59.455 37.037 0.00 0.00 0.00 3.09
112 113 8.874816 GTCCTAAAATAAGTGTCTTGAGCTTAG 58.125 37.037 0.00 0.00 0.00 2.18
113 114 8.594550 TCCTAAAATAAGTGTCTTGAGCTTAGT 58.405 33.333 0.00 0.00 0.00 2.24
114 115 9.871238 CCTAAAATAAGTGTCTTGAGCTTAGTA 57.129 33.333 0.00 0.00 0.00 1.82
117 118 9.555727 AAAATAAGTGTCTTGAGCTTAGTACAA 57.444 29.630 0.00 0.00 0.00 2.41
118 119 9.555727 AAATAAGTGTCTTGAGCTTAGTACAAA 57.444 29.630 0.00 0.00 0.00 2.83
119 120 9.726438 AATAAGTGTCTTGAGCTTAGTACAAAT 57.274 29.630 0.00 0.00 0.00 2.32
120 121 9.726438 ATAAGTGTCTTGAGCTTAGTACAAATT 57.274 29.630 0.00 0.00 0.00 1.82
121 122 8.451908 AAGTGTCTTGAGCTTAGTACAAATTT 57.548 30.769 0.00 0.00 0.00 1.82
122 123 7.865707 AGTGTCTTGAGCTTAGTACAAATTTG 58.134 34.615 16.67 16.67 0.00 2.32
123 124 7.499232 AGTGTCTTGAGCTTAGTACAAATTTGT 59.501 33.333 25.99 25.99 44.86 2.83
124 125 8.770828 GTGTCTTGAGCTTAGTACAAATTTGTA 58.229 33.333 23.91 23.91 42.35 2.41
148 149 7.148355 ACTAGAGCTAGTACAAAGTTGAGAC 57.852 40.000 8.35 0.00 43.98 3.36
149 150 6.715718 ACTAGAGCTAGTACAAAGTTGAGACA 59.284 38.462 8.35 0.00 43.98 3.41
150 151 5.774630 AGAGCTAGTACAAAGTTGAGACAC 58.225 41.667 0.00 0.00 0.00 3.67
151 152 5.536916 AGAGCTAGTACAAAGTTGAGACACT 59.463 40.000 0.00 0.00 0.00 3.55
152 153 6.041069 AGAGCTAGTACAAAGTTGAGACACTT 59.959 38.462 0.00 0.00 38.74 3.16
153 154 7.230913 AGAGCTAGTACAAAGTTGAGACACTTA 59.769 37.037 0.00 0.00 35.87 2.24
154 155 7.897864 AGCTAGTACAAAGTTGAGACACTTAT 58.102 34.615 0.00 0.00 35.87 1.73
155 156 8.368668 AGCTAGTACAAAGTTGAGACACTTATT 58.631 33.333 0.00 0.00 35.87 1.40
156 157 8.989980 GCTAGTACAAAGTTGAGACACTTATTT 58.010 33.333 0.00 0.00 35.87 1.40
159 160 8.621286 AGTACAAAGTTGAGACACTTATTTTGG 58.379 33.333 0.00 0.00 35.87 3.28
160 161 6.805713 ACAAAGTTGAGACACTTATTTTGGG 58.194 36.000 0.00 0.00 35.87 4.12
161 162 6.605594 ACAAAGTTGAGACACTTATTTTGGGA 59.394 34.615 0.00 0.00 35.87 4.37
162 163 6.635030 AAGTTGAGACACTTATTTTGGGAC 57.365 37.500 0.00 0.00 35.10 4.46
163 164 4.755123 AGTTGAGACACTTATTTTGGGACG 59.245 41.667 0.00 0.00 0.00 4.79
164 165 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
165 166 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
166 167 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
167 168 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
168 169 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
169 170 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
170 171 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
171 172 1.961133 TATTTTGGGACGGAGGGAGT 58.039 50.000 0.00 0.00 0.00 3.85
172 173 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
184 185 6.656270 GGACGGAGGGAGTAAAATCTTAAAAA 59.344 38.462 0.00 0.00 0.00 1.94
377 1816 7.853437 CAGATGTATCTAAGACGTAGTTCACAG 59.147 40.741 0.00 0.00 36.45 3.66
784 2232 3.682858 GCCAATAGAAAAGACGTGCAGTA 59.317 43.478 0.00 0.00 0.00 2.74
1317 2819 4.388485 TCTGTTATGCTGCTGAGAAACAA 58.612 39.130 0.00 0.00 0.00 2.83
1587 3323 1.376466 GCATCAGGACCACAGGTGT 59.624 57.895 0.00 0.00 35.25 4.16
1873 3695 0.759959 TACCAGCAAACCACGGAAGA 59.240 50.000 0.00 0.00 0.00 2.87
1933 3789 7.355101 AGACCTATATGTCTCCTTGTCACTTA 58.645 38.462 4.95 0.00 41.75 2.24
2272 4240 6.537301 ACGATGTTCAACTAAAGTTTGTCTCA 59.463 34.615 0.00 0.00 35.83 3.27
2285 4253 7.878477 AAGTTTGTCTCAATGTGCAATTATG 57.122 32.000 0.00 0.00 0.00 1.90
2500 4468 3.133362 AGGTAAATTGCATTGCCTCCATG 59.867 43.478 6.12 0.00 40.89 3.66
2806 4774 4.964897 TGGATCATGACAGATGGAGTAACT 59.035 41.667 0.00 0.00 0.00 2.24
3032 5000 1.067250 GCCGCAGCAAAAGTTGGAA 59.933 52.632 0.00 0.00 39.53 3.53
3785 5899 4.717233 TCAAACTGAACTTGCACACATT 57.283 36.364 0.00 0.00 0.00 2.71
3792 5906 5.750067 ACTGAACTTGCACACATTTCATTTC 59.250 36.000 0.00 0.00 31.33 2.17
3793 5907 4.739228 TGAACTTGCACACATTTCATTTCG 59.261 37.500 0.00 0.00 0.00 3.46
3843 5959 3.625649 TTGGATGACGATGGATGTTGA 57.374 42.857 0.00 0.00 0.00 3.18
3859 5975 6.321181 TGGATGTTGAAGATAACCCTAAATGC 59.679 38.462 0.00 0.00 0.00 3.56
3886 6012 5.045505 TCCATGCAGTACTGTAAACCCATTA 60.046 40.000 23.44 5.86 0.00 1.90
3932 6058 3.308530 GACGCTGTTCATTCCCAAAAAG 58.691 45.455 0.00 0.00 0.00 2.27
3949 6075 5.452356 CCAAAAAGAAAGAGGATGCTGTGTT 60.452 40.000 0.00 0.00 0.00 3.32
4229 6872 7.928307 ATTTTCTATCTGCTCAGCTAACAAA 57.072 32.000 0.00 0.00 0.00 2.83
4230 6873 7.744087 TTTTCTATCTGCTCAGCTAACAAAA 57.256 32.000 0.00 0.00 0.00 2.44
4384 7029 7.094205 GGGATAGCATAAACAAGAATACATGGG 60.094 40.741 0.00 0.00 0.00 4.00
4669 7315 7.736447 ATTATAGAAGCCTCATGCAACTAAC 57.264 36.000 0.00 0.00 44.83 2.34
4670 7316 2.350522 AGAAGCCTCATGCAACTAACG 58.649 47.619 0.00 0.00 44.83 3.18
4690 7336 2.612972 CGGTCTAACACAGCTCCACAAT 60.613 50.000 0.00 0.00 0.00 2.71
4695 7341 6.016610 GGTCTAACACAGCTCCACAATTTAAA 60.017 38.462 0.00 0.00 0.00 1.52
4745 7407 6.702329 TCAAAACACATTTGGGTAACTTTGT 58.298 32.000 7.91 0.00 46.85 2.83
5092 7875 4.610605 TGGTTTTGACAGGTCGAAGATA 57.389 40.909 2.60 0.00 40.67 1.98
5481 8297 5.006746 CGTAGCCAGATGGATTTACTGAAAC 59.993 44.000 2.18 0.00 37.39 2.78
5496 8326 5.288543 ACTGAAACGTACTACTAAGTCCG 57.711 43.478 0.00 0.00 40.57 4.79
5536 8367 4.483476 ACTTTTACTTGCATCGGACAAC 57.517 40.909 0.00 0.00 0.00 3.32
5677 8518 1.197812 ACGTAACTGGGGGTGATACC 58.802 55.000 0.00 0.00 37.60 2.73
6250 10414 1.620822 AGTCATTTGTGCCAGGGTTC 58.379 50.000 0.00 0.00 0.00 3.62
6375 10539 5.698089 GCTCATCTAATTGGATTCATCGTGA 59.302 40.000 0.83 0.00 0.00 4.35
6479 10840 7.066163 TGTGGTGTCATGAGATATTGATTGAAC 59.934 37.037 0.00 0.00 0.00 3.18
6492 10853 2.290260 TGATTGAACGCCACTCATCCTT 60.290 45.455 0.00 0.00 30.68 3.36
6536 10897 4.716784 AGCATATCCAGACAGAACAGGTTA 59.283 41.667 0.00 0.00 0.00 2.85
6537 10898 5.189736 AGCATATCCAGACAGAACAGGTTAA 59.810 40.000 0.00 0.00 0.00 2.01
6538 10899 5.525378 GCATATCCAGACAGAACAGGTTAAG 59.475 44.000 0.00 0.00 0.00 1.85
6539 10900 4.559862 ATCCAGACAGAACAGGTTAAGG 57.440 45.455 0.00 0.00 0.00 2.69
6540 10901 3.314693 TCCAGACAGAACAGGTTAAGGT 58.685 45.455 0.00 0.00 0.00 3.50
6541 10902 3.714798 TCCAGACAGAACAGGTTAAGGTT 59.285 43.478 0.00 0.00 0.00 3.50
6562 10923 7.633789 AGGTTATTACAGTGAGATGGTGAATT 58.366 34.615 0.00 0.00 0.00 2.17
6586 10950 2.885266 AGCATGCATCCTAGCTGAAATG 59.115 45.455 21.98 0.00 35.72 2.32
6733 11106 4.527038 ACTCTTCCACGTTTCTGATCCTTA 59.473 41.667 0.00 0.00 0.00 2.69
6746 11119 9.869844 GTTTCTGATCCTTAATGTTATGAATCG 57.130 33.333 0.00 0.00 0.00 3.34
6939 11313 9.838975 CATTATAGAGTACTGATTGCTACTGAG 57.161 37.037 0.00 0.00 0.00 3.35
6970 11344 4.084328 GCCTCATGATATTGTACAGCGTTC 60.084 45.833 0.00 0.00 0.00 3.95
7008 11382 5.856455 CCTGCGACTTACCAAAAGTTTTATG 59.144 40.000 0.00 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
78 79 4.161754 ACACTTATTTTAGGACGGAGGGAG 59.838 45.833 0.00 0.00 0.00 4.30
79 80 4.098894 ACACTTATTTTAGGACGGAGGGA 58.901 43.478 0.00 0.00 0.00 4.20
80 81 4.161754 AGACACTTATTTTAGGACGGAGGG 59.838 45.833 0.00 0.00 0.00 4.30
81 82 5.340439 AGACACTTATTTTAGGACGGAGG 57.660 43.478 0.00 0.00 0.00 4.30
82 83 6.395629 TCAAGACACTTATTTTAGGACGGAG 58.604 40.000 0.00 0.00 0.00 4.63
83 84 6.349243 TCAAGACACTTATTTTAGGACGGA 57.651 37.500 0.00 0.00 0.00 4.69
84 85 5.063564 GCTCAAGACACTTATTTTAGGACGG 59.936 44.000 0.00 0.00 0.00 4.79
85 86 5.869888 AGCTCAAGACACTTATTTTAGGACG 59.130 40.000 0.00 0.00 0.00 4.79
86 87 7.674471 AAGCTCAAGACACTTATTTTAGGAC 57.326 36.000 0.00 0.00 0.00 3.85
87 88 8.594550 ACTAAGCTCAAGACACTTATTTTAGGA 58.405 33.333 3.19 0.00 0.00 2.94
88 89 8.779354 ACTAAGCTCAAGACACTTATTTTAGG 57.221 34.615 3.19 0.00 0.00 2.69
91 92 9.555727 TTGTACTAAGCTCAAGACACTTATTTT 57.444 29.630 3.19 0.00 0.00 1.82
92 93 9.555727 TTTGTACTAAGCTCAAGACACTTATTT 57.444 29.630 3.19 0.00 0.00 1.40
93 94 9.726438 ATTTGTACTAAGCTCAAGACACTTATT 57.274 29.630 3.19 0.00 0.00 1.40
94 95 9.726438 AATTTGTACTAAGCTCAAGACACTTAT 57.274 29.630 3.19 0.00 0.00 1.73
95 96 9.555727 AAATTTGTACTAAGCTCAAGACACTTA 57.444 29.630 3.19 0.00 0.00 2.24
96 97 8.345565 CAAATTTGTACTAAGCTCAAGACACTT 58.654 33.333 10.15 0.00 0.00 3.16
97 98 7.499232 ACAAATTTGTACTAAGCTCAAGACACT 59.501 33.333 22.10 0.00 40.16 3.55
98 99 7.639945 ACAAATTTGTACTAAGCTCAAGACAC 58.360 34.615 22.10 2.09 40.16 3.67
99 100 7.801716 ACAAATTTGTACTAAGCTCAAGACA 57.198 32.000 22.10 0.00 40.16 3.41
123 124 7.881751 TGTCTCAACTTTGTACTAGCTCTAGTA 59.118 37.037 11.59 11.59 43.98 1.82
125 126 7.024768 GTGTCTCAACTTTGTACTAGCTCTAG 58.975 42.308 0.00 2.55 39.04 2.43
126 127 6.715718 AGTGTCTCAACTTTGTACTAGCTCTA 59.284 38.462 0.00 0.00 0.00 2.43
127 128 5.536916 AGTGTCTCAACTTTGTACTAGCTCT 59.463 40.000 0.00 0.00 0.00 4.09
128 129 5.774630 AGTGTCTCAACTTTGTACTAGCTC 58.225 41.667 0.00 0.00 0.00 4.09
129 130 5.793030 AGTGTCTCAACTTTGTACTAGCT 57.207 39.130 0.00 0.00 0.00 3.32
130 131 8.535690 AATAAGTGTCTCAACTTTGTACTAGC 57.464 34.615 0.00 0.00 40.77 3.42
133 134 8.621286 CCAAAATAAGTGTCTCAACTTTGTACT 58.379 33.333 0.00 0.00 40.77 2.73
134 135 7.860872 CCCAAAATAAGTGTCTCAACTTTGTAC 59.139 37.037 0.00 0.00 40.77 2.90
135 136 7.776030 TCCCAAAATAAGTGTCTCAACTTTGTA 59.224 33.333 0.00 0.00 40.77 2.41
136 137 6.605594 TCCCAAAATAAGTGTCTCAACTTTGT 59.394 34.615 0.00 0.00 40.77 2.83
137 138 6.918022 GTCCCAAAATAAGTGTCTCAACTTTG 59.082 38.462 0.00 0.00 40.77 2.77
138 139 6.238648 CGTCCCAAAATAAGTGTCTCAACTTT 60.239 38.462 0.00 0.00 40.77 2.66
139 140 5.238650 CGTCCCAAAATAAGTGTCTCAACTT 59.761 40.000 0.00 0.00 42.89 2.66
140 141 4.755123 CGTCCCAAAATAAGTGTCTCAACT 59.245 41.667 0.00 0.00 0.00 3.16
141 142 4.083484 CCGTCCCAAAATAAGTGTCTCAAC 60.083 45.833 0.00 0.00 0.00 3.18
142 143 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
143 144 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
144 145 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
145 146 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
146 147 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
147 148 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
148 149 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
149 150 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
150 151 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
151 152 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
152 153 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
153 154 1.961133 TACTCCCTCCGTCCCAAAAT 58.039 50.000 0.00 0.00 0.00 1.82
154 155 1.732117 TTACTCCCTCCGTCCCAAAA 58.268 50.000 0.00 0.00 0.00 2.44
155 156 1.732117 TTTACTCCCTCCGTCCCAAA 58.268 50.000 0.00 0.00 0.00 3.28
156 157 1.732117 TTTTACTCCCTCCGTCCCAA 58.268 50.000 0.00 0.00 0.00 4.12
157 158 1.835531 GATTTTACTCCCTCCGTCCCA 59.164 52.381 0.00 0.00 0.00 4.37
158 159 2.117051 AGATTTTACTCCCTCCGTCCC 58.883 52.381 0.00 0.00 0.00 4.46
159 160 3.908643 AAGATTTTACTCCCTCCGTCC 57.091 47.619 0.00 0.00 0.00 4.79
160 161 7.677454 TTTTTAAGATTTTACTCCCTCCGTC 57.323 36.000 0.00 0.00 0.00 4.79
161 162 8.645814 AATTTTTAAGATTTTACTCCCTCCGT 57.354 30.769 0.00 0.00 0.00 4.69
585 2033 2.224867 ACATGTCCAACTTGGGAGAAGG 60.225 50.000 8.01 0.00 38.32 3.46
784 2232 1.063183 AAAGCAGGTCAGAGGCTTCT 58.937 50.000 0.00 0.00 46.39 2.85
1587 3323 6.201226 TCATTTACACAGCAACAAAACTGA 57.799 33.333 0.00 0.00 37.35 3.41
1730 3471 9.421806 CAATTCTACATCTCACTAATCTCATCC 57.578 37.037 0.00 0.00 0.00 3.51
1740 3481 8.499162 CGTTTTTCTTCAATTCTACATCTCACT 58.501 33.333 0.00 0.00 0.00 3.41
1741 3482 8.495949 TCGTTTTTCTTCAATTCTACATCTCAC 58.504 33.333 0.00 0.00 0.00 3.51
1933 3789 9.477484 CTGCTTTATATTTCAGAATAGTACCGT 57.523 33.333 0.00 0.00 31.58 4.83
2165 4031 5.493133 AGCGTGTGTTTTCAGAAATGTTA 57.507 34.783 0.00 0.00 0.00 2.41
2238 4206 8.280497 ACTTTAGTTGAACATCGTACATTGAAC 58.720 33.333 0.00 0.00 0.00 3.18
3032 5000 4.274602 TCTGAAATGTGGCATTTGCAAT 57.725 36.364 11.24 0.00 44.36 3.56
3843 5959 7.294017 CATGGAATGCATTTAGGGTTATCTT 57.706 36.000 14.33 0.00 37.62 2.40
3886 6012 6.656693 CCTCAAAAGTAGTGAAGGATGACAAT 59.343 38.462 0.00 0.00 0.00 2.71
3932 6058 2.095364 CAGCAACACAGCATCCTCTTTC 60.095 50.000 0.00 0.00 36.85 2.62
3949 6075 6.655078 TGAGACTAGCATATATGAACAGCA 57.345 37.500 17.10 2.57 0.00 4.41
4384 7029 4.822350 AGGTTCTAGTGGCTTCAAGAAAAC 59.178 41.667 0.00 0.00 30.24 2.43
4669 7315 0.317160 TGTGGAGCTGTGTTAGACCG 59.683 55.000 0.00 0.00 0.00 4.79
4670 7316 2.543777 TTGTGGAGCTGTGTTAGACC 57.456 50.000 0.00 0.00 0.00 3.85
4695 7341 7.881232 AGAAATTTCACATGCATTCCTCATTTT 59.119 29.630 19.99 0.00 0.00 1.82
4701 7347 5.988310 TGAGAAATTTCACATGCATTCCT 57.012 34.783 19.99 0.00 0.00 3.36
4702 7348 7.041916 TGTTTTGAGAAATTTCACATGCATTCC 60.042 33.333 19.99 5.38 0.00 3.01
4851 7634 1.168407 TTGCACAAGCTCCTCTGCAC 61.168 55.000 6.97 0.00 39.32 4.57
5092 7875 4.731929 TCTTCAGGGGAATTATAGGGCTTT 59.268 41.667 0.00 0.00 31.34 3.51
5677 8518 9.817809 ATCCATTTCTTCTCAATTTGAATCATG 57.182 29.630 0.01 0.00 0.00 3.07
6127 9126 7.004691 AGGGAGCTAAAAATGTACTGAACTTT 58.995 34.615 0.00 0.00 0.00 2.66
6250 10414 8.627487 TGCAGTTCTAATTGTTTACAAGTTTG 57.373 30.769 0.64 0.00 39.47 2.93
6375 10539 8.037166 GGATCATAAAGAAGCAGTTTGGAAATT 58.963 33.333 0.00 0.00 0.00 1.82
6536 10897 6.620877 TCACCATCTCACTGTAATAACCTT 57.379 37.500 0.00 0.00 0.00 3.50
6537 10898 6.620877 TTCACCATCTCACTGTAATAACCT 57.379 37.500 0.00 0.00 0.00 3.50
6538 10899 7.865706 AATTCACCATCTCACTGTAATAACC 57.134 36.000 0.00 0.00 0.00 2.85
6541 10902 9.929180 GCTATAATTCACCATCTCACTGTAATA 57.071 33.333 0.00 0.00 0.00 0.98
6562 10923 5.488262 TTTCAGCTAGGATGCATGCTATA 57.512 39.130 25.82 9.31 34.10 1.31
6586 10950 5.085219 AGGTATGCATCTACTAGGTTACCC 58.915 45.833 0.19 0.00 0.00 3.69
6733 11106 6.924111 AGTTCAAAAGGCGATTCATAACATT 58.076 32.000 0.00 0.00 0.00 2.71
6746 11119 6.131544 TGACAAGTAGAAAGTTCAAAAGGC 57.868 37.500 0.00 0.00 0.00 4.35
6939 11313 6.707608 TGTACAATATCATGAGGCTGATGAAC 59.292 38.462 20.36 12.93 36.55 3.18


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

AutoCloner maintained by Alex Coulton.