Multiple sequence alignment - TraesCS5D01G459000

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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 TraesCS5D01G459000 chr5D 100.000 2678 0 0 1 2678 503331544 503328867 0.000000e+00 4946.0
1 TraesCS5D01G459000 chr5D 98.411 2392 36 2 287 2678 6235554 6237943 0.000000e+00 4205.0
2 TraesCS5D01G459000 chr5D 98.606 287 4 0 1 287 503308928 503308642 2.380000e-140 508.0
3 TraesCS5D01G459000 chr5D 98.611 288 1 2 1 287 6257847 6258132 8.550000e-140 507.0
4 TraesCS5D01G459000 chr1D 98.537 2393 32 3 287 2678 254477345 254474955 0.000000e+00 4222.0
5 TraesCS5D01G459000 chr1D 97.324 2392 62 2 287 2678 180356048 180358437 0.000000e+00 4061.0
6 TraesCS5D01G459000 chr1D 96.493 2395 67 10 287 2678 244768825 244766445 0.000000e+00 3941.0
7 TraesCS5D01G459000 chr1D 96.321 2392 82 4 287 2678 244201637 244199252 0.000000e+00 3925.0
8 TraesCS5D01G459000 chr1D 99.303 287 1 1 1 287 254452059 254451774 3.950000e-143 518.0
9 TraesCS5D01G459000 chr1A 98.796 2326 25 3 287 2612 554447599 554449921 0.000000e+00 4137.0
10 TraesCS5D01G459000 chr1A 100.000 287 0 0 1 287 554477495 554477209 5.080000e-147 531.0
11 TraesCS5D01G459000 chr3B 98.496 2327 32 3 287 2612 201493350 201491026 0.000000e+00 4100.0
12 TraesCS5D01G459000 chr3B 96.354 192 7 0 372 563 430241126 430240935 1.550000e-82 316.0
13 TraesCS5D01G459000 chr3B 99.296 142 1 0 287 428 201493700 201493559 9.510000e-65 257.0
14 TraesCS5D01G459000 chr3B 95.652 69 3 0 555 623 636832265 636832197 7.840000e-21 111.0
15 TraesCS5D01G459000 chr3B 100.000 32 0 0 287 318 374245283 374245314 2.880000e-05 60.2
16 TraesCS5D01G459000 chr2D 99.010 1717 15 2 897 2612 33929969 33931684 0.000000e+00 3075.0
17 TraesCS5D01G459000 chr4A 97.554 1758 38 4 921 2678 309374680 309376432 0.000000e+00 3003.0
18 TraesCS5D01G459000 chrUn 100.000 287 0 0 1 287 387441240 387441526 5.080000e-147 531.0
19 TraesCS5D01G459000 chr7B 100.000 287 0 0 1 287 663104838 663104552 5.080000e-147 531.0
20 TraesCS5D01G459000 chr7B 98.955 287 2 1 1 287 137681916 137681631 1.840000e-141 512.0
21 TraesCS5D01G459000 chr1B 98.258 287 3 2 1 287 633712223 633711939 3.980000e-138 501.0
22 TraesCS5D01G459000 chr5A 97.561 287 4 3 1 287 85548004 85547721 3.100000e-134 488.0


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 TraesCS5D01G459000 chr5D 503328867 503331544 2677 True 4946.0 4946 100.000 1 2678 1 chr5D.!!$R2 2677
1 TraesCS5D01G459000 chr5D 6235554 6237943 2389 False 4205.0 4205 98.411 287 2678 1 chr5D.!!$F1 2391
2 TraesCS5D01G459000 chr1D 254474955 254477345 2390 True 4222.0 4222 98.537 287 2678 1 chr1D.!!$R4 2391
3 TraesCS5D01G459000 chr1D 180356048 180358437 2389 False 4061.0 4061 97.324 287 2678 1 chr1D.!!$F1 2391
4 TraesCS5D01G459000 chr1D 244766445 244768825 2380 True 3941.0 3941 96.493 287 2678 1 chr1D.!!$R2 2391
5 TraesCS5D01G459000 chr1D 244199252 244201637 2385 True 3925.0 3925 96.321 287 2678 1 chr1D.!!$R1 2391
6 TraesCS5D01G459000 chr1A 554447599 554449921 2322 False 4137.0 4137 98.796 287 2612 1 chr1A.!!$F1 2325
7 TraesCS5D01G459000 chr3B 201491026 201493700 2674 True 2178.5 4100 98.896 287 2612 2 chr3B.!!$R3 2325
8 TraesCS5D01G459000 chr2D 33929969 33931684 1715 False 3075.0 3075 99.010 897 2612 1 chr2D.!!$F1 1715
9 TraesCS5D01G459000 chr4A 309374680 309376432 1752 False 3003.0 3003 97.554 921 2678 1 chr4A.!!$F1 1757

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
207 208 0.035247 AGTCCGCCTAGTCGACTTCT 60.035 55.0 25.44 1.49 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1872 2229 1.870064 ATCCCAATCCCCTGCTTTTG 58.13 50.0 0.0 0.0 0.0 2.44 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
33 34 3.773418 TTTCCGTTGAACATAGACCCA 57.227 42.857 0.00 0.00 0.00 4.51
34 35 3.773418 TTCCGTTGAACATAGACCCAA 57.227 42.857 0.00 0.00 0.00 4.12
35 36 3.992943 TCCGTTGAACATAGACCCAAT 57.007 42.857 0.00 0.00 0.00 3.16
36 37 4.295141 TCCGTTGAACATAGACCCAATT 57.705 40.909 0.00 0.00 0.00 2.32
37 38 4.658063 TCCGTTGAACATAGACCCAATTT 58.342 39.130 0.00 0.00 0.00 1.82
38 39 5.074115 TCCGTTGAACATAGACCCAATTTT 58.926 37.500 0.00 0.00 0.00 1.82
39 40 5.536916 TCCGTTGAACATAGACCCAATTTTT 59.463 36.000 0.00 0.00 0.00 1.94
40 41 5.861787 CCGTTGAACATAGACCCAATTTTTC 59.138 40.000 0.00 0.00 0.00 2.29
41 42 5.861787 CGTTGAACATAGACCCAATTTTTCC 59.138 40.000 0.00 0.00 0.00 3.13
42 43 6.294508 CGTTGAACATAGACCCAATTTTTCCT 60.295 38.462 0.00 0.00 0.00 3.36
43 44 7.441836 GTTGAACATAGACCCAATTTTTCCTT 58.558 34.615 0.00 0.00 0.00 3.36
44 45 7.610580 TGAACATAGACCCAATTTTTCCTTT 57.389 32.000 0.00 0.00 0.00 3.11
45 46 8.028652 TGAACATAGACCCAATTTTTCCTTTT 57.971 30.769 0.00 0.00 0.00 2.27
46 47 8.490311 TGAACATAGACCCAATTTTTCCTTTTT 58.510 29.630 0.00 0.00 0.00 1.94
88 89 4.759516 TTTTTGTCTTTCTGGCGGTATC 57.240 40.909 0.00 0.00 0.00 2.24
89 90 3.410631 TTTGTCTTTCTGGCGGTATCA 57.589 42.857 0.00 0.00 0.00 2.15
90 91 3.410631 TTGTCTTTCTGGCGGTATCAA 57.589 42.857 0.00 0.00 0.00 2.57
91 92 3.410631 TGTCTTTCTGGCGGTATCAAA 57.589 42.857 0.00 0.00 0.00 2.69
92 93 3.071479 TGTCTTTCTGGCGGTATCAAAC 58.929 45.455 0.00 0.00 0.00 2.93
93 94 3.071479 GTCTTTCTGGCGGTATCAAACA 58.929 45.455 0.00 0.00 0.00 2.83
94 95 3.125316 GTCTTTCTGGCGGTATCAAACAG 59.875 47.826 0.00 0.00 0.00 3.16
99 100 1.800681 GCGGTATCAAACAGCCACC 59.199 57.895 0.00 0.00 42.75 4.61
100 101 0.676782 GCGGTATCAAACAGCCACCT 60.677 55.000 0.00 0.00 42.75 4.00
101 102 1.406341 GCGGTATCAAACAGCCACCTA 60.406 52.381 0.00 0.00 42.75 3.08
102 103 2.937873 GCGGTATCAAACAGCCACCTAA 60.938 50.000 0.00 0.00 42.75 2.69
103 104 3.541632 CGGTATCAAACAGCCACCTAAT 58.458 45.455 0.00 0.00 0.00 1.73
104 105 4.699637 CGGTATCAAACAGCCACCTAATA 58.300 43.478 0.00 0.00 0.00 0.98
105 106 5.305585 CGGTATCAAACAGCCACCTAATAT 58.694 41.667 0.00 0.00 0.00 1.28
106 107 5.408604 CGGTATCAAACAGCCACCTAATATC 59.591 44.000 0.00 0.00 0.00 1.63
107 108 6.534634 GGTATCAAACAGCCACCTAATATCT 58.465 40.000 0.00 0.00 0.00 1.98
108 109 6.998673 GGTATCAAACAGCCACCTAATATCTT 59.001 38.462 0.00 0.00 0.00 2.40
109 110 8.154856 GGTATCAAACAGCCACCTAATATCTTA 58.845 37.037 0.00 0.00 0.00 2.10
110 111 9.726438 GTATCAAACAGCCACCTAATATCTTAT 57.274 33.333 0.00 0.00 0.00 1.73
111 112 8.854614 ATCAAACAGCCACCTAATATCTTATC 57.145 34.615 0.00 0.00 0.00 1.75
112 113 7.224297 TCAAACAGCCACCTAATATCTTATCC 58.776 38.462 0.00 0.00 0.00 2.59
113 114 5.407407 ACAGCCACCTAATATCTTATCCG 57.593 43.478 0.00 0.00 0.00 4.18
114 115 4.184629 CAGCCACCTAATATCTTATCCGC 58.815 47.826 0.00 0.00 0.00 5.54
115 116 3.197983 AGCCACCTAATATCTTATCCGCC 59.802 47.826 0.00 0.00 0.00 6.13
116 117 3.197983 GCCACCTAATATCTTATCCGCCT 59.802 47.826 0.00 0.00 0.00 5.52
117 118 4.680975 GCCACCTAATATCTTATCCGCCTC 60.681 50.000 0.00 0.00 0.00 4.70
118 119 4.712337 CCACCTAATATCTTATCCGCCTCT 59.288 45.833 0.00 0.00 0.00 3.69
119 120 5.187967 CCACCTAATATCTTATCCGCCTCTT 59.812 44.000 0.00 0.00 0.00 2.85
120 121 6.334202 CACCTAATATCTTATCCGCCTCTTC 58.666 44.000 0.00 0.00 0.00 2.87
121 122 6.017192 ACCTAATATCTTATCCGCCTCTTCA 58.983 40.000 0.00 0.00 0.00 3.02
122 123 6.153680 ACCTAATATCTTATCCGCCTCTTCAG 59.846 42.308 0.00 0.00 0.00 3.02
123 124 5.413309 AATATCTTATCCGCCTCTTCAGG 57.587 43.478 0.00 0.00 43.82 3.86
124 125 2.454336 TCTTATCCGCCTCTTCAGGA 57.546 50.000 0.00 0.00 43.65 3.86
125 126 2.747177 TCTTATCCGCCTCTTCAGGAA 58.253 47.619 0.00 0.00 43.65 3.36
126 127 3.104512 TCTTATCCGCCTCTTCAGGAAA 58.895 45.455 0.00 0.00 43.65 3.13
127 128 3.517901 TCTTATCCGCCTCTTCAGGAAAA 59.482 43.478 0.00 0.00 43.65 2.29
128 129 4.164221 TCTTATCCGCCTCTTCAGGAAAAT 59.836 41.667 0.00 0.00 43.65 1.82
129 130 2.113860 TCCGCCTCTTCAGGAAAATG 57.886 50.000 0.00 0.00 43.65 2.32
130 131 1.628340 TCCGCCTCTTCAGGAAAATGA 59.372 47.619 0.00 0.00 43.65 2.57
131 132 2.039746 TCCGCCTCTTCAGGAAAATGAA 59.960 45.455 0.00 0.00 43.65 2.57
132 133 3.019564 CCGCCTCTTCAGGAAAATGAAT 58.980 45.455 0.00 0.00 43.65 2.57
133 134 4.080582 TCCGCCTCTTCAGGAAAATGAATA 60.081 41.667 0.00 0.00 43.65 1.75
134 135 4.823989 CCGCCTCTTCAGGAAAATGAATAT 59.176 41.667 0.00 0.00 43.65 1.28
135 136 5.049129 CCGCCTCTTCAGGAAAATGAATATC 60.049 44.000 0.00 0.00 43.65 1.63
136 137 5.762218 CGCCTCTTCAGGAAAATGAATATCT 59.238 40.000 0.00 0.00 43.65 1.98
137 138 6.073331 CGCCTCTTCAGGAAAATGAATATCTC 60.073 42.308 0.00 0.00 43.65 2.75
138 139 6.206438 GCCTCTTCAGGAAAATGAATATCTCC 59.794 42.308 0.00 0.00 43.65 3.71
139 140 6.426328 CCTCTTCAGGAAAATGAATATCTCCG 59.574 42.308 0.00 0.00 43.65 4.63
140 141 6.291377 TCTTCAGGAAAATGAATATCTCCGG 58.709 40.000 0.00 0.00 38.47 5.14
141 142 5.887214 TCAGGAAAATGAATATCTCCGGA 57.113 39.130 2.93 2.93 0.00 5.14
142 143 6.247229 TCAGGAAAATGAATATCTCCGGAA 57.753 37.500 5.23 0.00 29.08 4.30
143 144 6.658849 TCAGGAAAATGAATATCTCCGGAAA 58.341 36.000 5.23 0.00 29.08 3.13
144 145 7.116075 TCAGGAAAATGAATATCTCCGGAAAA 58.884 34.615 5.23 0.00 29.08 2.29
145 146 7.779798 TCAGGAAAATGAATATCTCCGGAAAAT 59.220 33.333 5.23 4.81 29.08 1.82
146 147 9.066892 CAGGAAAATGAATATCTCCGGAAAATA 57.933 33.333 5.23 7.15 0.00 1.40
147 148 9.813826 AGGAAAATGAATATCTCCGGAAAATAT 57.186 29.630 5.23 9.31 0.00 1.28
154 155 9.627123 TGAATATCTCCGGAAAATATTTTGAGT 57.373 29.630 23.03 10.80 0.00 3.41
157 158 6.753107 TCTCCGGAAAATATTTTGAGTTCC 57.247 37.500 17.98 11.28 35.42 3.62
164 165 6.695713 GGAAAATATTTTGAGTTCCGTATGGC 59.304 38.462 17.98 0.00 34.14 4.40
165 166 7.404671 AAAATATTTTGAGTTCCGTATGGCT 57.595 32.000 12.62 0.00 34.14 4.75
166 167 7.404671 AAATATTTTGAGTTCCGTATGGCTT 57.595 32.000 0.00 0.00 34.14 4.35
167 168 7.404671 AATATTTTGAGTTCCGTATGGCTTT 57.595 32.000 0.00 0.00 34.14 3.51
168 169 5.722021 ATTTTGAGTTCCGTATGGCTTTT 57.278 34.783 0.00 0.00 34.14 2.27
169 170 5.523438 TTTTGAGTTCCGTATGGCTTTTT 57.477 34.783 0.00 0.00 34.14 1.94
188 189 3.830744 TTTTTCTCTTCACTCGGACCA 57.169 42.857 0.00 0.00 0.00 4.02
189 190 3.386768 TTTTCTCTTCACTCGGACCAG 57.613 47.619 0.00 0.00 0.00 4.00
190 191 1.996798 TTCTCTTCACTCGGACCAGT 58.003 50.000 0.00 0.00 0.00 4.00
191 192 1.535833 TCTCTTCACTCGGACCAGTC 58.464 55.000 0.00 0.00 0.00 3.51
192 193 0.528470 CTCTTCACTCGGACCAGTCC 59.472 60.000 6.77 6.77 46.18 3.85
200 201 3.208335 GGACCAGTCCGCCTAGTC 58.792 66.667 0.05 0.00 40.36 2.59
201 202 2.772691 GGACCAGTCCGCCTAGTCG 61.773 68.421 0.05 0.00 40.36 4.18
202 203 1.748122 GACCAGTCCGCCTAGTCGA 60.748 63.158 0.00 0.00 0.00 4.20
203 204 1.991099 GACCAGTCCGCCTAGTCGAC 61.991 65.000 7.70 7.70 0.00 4.20
204 205 1.749638 CCAGTCCGCCTAGTCGACT 60.750 63.158 23.66 23.66 0.00 4.18
205 206 1.313812 CCAGTCCGCCTAGTCGACTT 61.314 60.000 25.44 8.09 0.00 3.01
206 207 0.099082 CAGTCCGCCTAGTCGACTTC 59.901 60.000 25.44 12.26 0.00 3.01
207 208 0.035247 AGTCCGCCTAGTCGACTTCT 60.035 55.000 25.44 1.49 0.00 2.85
208 209 0.810016 GTCCGCCTAGTCGACTTCTT 59.190 55.000 25.44 1.06 0.00 2.52
209 210 0.809385 TCCGCCTAGTCGACTTCTTG 59.191 55.000 25.44 11.60 0.00 3.02
210 211 0.526662 CCGCCTAGTCGACTTCTTGT 59.473 55.000 25.44 0.00 0.00 3.16
211 212 1.741706 CCGCCTAGTCGACTTCTTGTA 59.258 52.381 25.44 2.97 0.00 2.41
212 213 2.358267 CCGCCTAGTCGACTTCTTGTAT 59.642 50.000 25.44 0.00 0.00 2.29
213 214 3.181489 CCGCCTAGTCGACTTCTTGTATT 60.181 47.826 25.44 0.00 0.00 1.89
214 215 4.421948 CGCCTAGTCGACTTCTTGTATTT 58.578 43.478 25.44 0.00 0.00 1.40
215 216 4.863131 CGCCTAGTCGACTTCTTGTATTTT 59.137 41.667 25.44 0.00 0.00 1.82
216 217 5.347907 CGCCTAGTCGACTTCTTGTATTTTT 59.652 40.000 25.44 0.00 0.00 1.94
236 237 6.371809 TTTTTGTGAGTTGTGTATCCACTC 57.628 37.500 0.00 0.00 42.34 3.51
237 238 3.678056 TGTGAGTTGTGTATCCACTCC 57.322 47.619 0.00 0.00 42.34 3.85
238 239 2.969262 TGTGAGTTGTGTATCCACTCCA 59.031 45.455 0.00 0.00 42.34 3.86
239 240 3.389656 TGTGAGTTGTGTATCCACTCCAA 59.610 43.478 0.00 0.00 42.34 3.53
240 241 4.041567 TGTGAGTTGTGTATCCACTCCAAT 59.958 41.667 0.00 0.00 42.34 3.16
241 242 5.247337 TGTGAGTTGTGTATCCACTCCAATA 59.753 40.000 0.00 0.00 42.34 1.90
242 243 6.170506 GTGAGTTGTGTATCCACTCCAATAA 58.829 40.000 0.00 0.00 42.34 1.40
243 244 6.823689 GTGAGTTGTGTATCCACTCCAATAAT 59.176 38.462 0.00 0.00 42.34 1.28
244 245 7.985184 GTGAGTTGTGTATCCACTCCAATAATA 59.015 37.037 0.00 0.00 42.34 0.98
245 246 7.985184 TGAGTTGTGTATCCACTCCAATAATAC 59.015 37.037 0.00 0.00 42.34 1.89
246 247 8.090788 AGTTGTGTATCCACTCCAATAATACT 57.909 34.615 0.00 0.00 42.34 2.12
247 248 9.209048 AGTTGTGTATCCACTCCAATAATACTA 57.791 33.333 0.00 0.00 42.34 1.82
248 249 9.998106 GTTGTGTATCCACTCCAATAATACTAT 57.002 33.333 0.00 0.00 42.34 2.12
250 251 9.996554 TGTGTATCCACTCCAATAATACTATTG 57.003 33.333 0.00 0.00 41.55 1.90
251 252 9.998106 GTGTATCCACTCCAATAATACTATTGT 57.002 33.333 3.45 0.00 39.48 2.71
255 256 9.784531 ATCCACTCCAATAATACTATTGTCAAG 57.215 33.333 3.45 1.33 41.96 3.02
256 257 8.768397 TCCACTCCAATAATACTATTGTCAAGT 58.232 33.333 3.45 1.85 41.96 3.16
270 271 9.213777 ACTATTGTCAAGTATCTTTAGGGATGA 57.786 33.333 0.00 0.00 0.00 2.92
272 273 8.970859 ATTGTCAAGTATCTTTAGGGATGAAG 57.029 34.615 0.00 0.00 0.00 3.02
273 274 7.733773 TGTCAAGTATCTTTAGGGATGAAGA 57.266 36.000 0.00 0.00 36.43 2.87
274 275 8.324191 TGTCAAGTATCTTTAGGGATGAAGAT 57.676 34.615 4.29 4.29 43.17 2.40
275 276 8.424918 TGTCAAGTATCTTTAGGGATGAAGATC 58.575 37.037 2.19 0.00 40.69 2.75
276 277 8.646900 GTCAAGTATCTTTAGGGATGAAGATCT 58.353 37.037 2.19 0.00 40.69 2.75
277 278 8.865090 TCAAGTATCTTTAGGGATGAAGATCTC 58.135 37.037 0.00 0.00 40.69 2.75
278 279 7.461182 AGTATCTTTAGGGATGAAGATCTCG 57.539 40.000 0.00 0.00 40.69 4.04
279 280 5.736951 ATCTTTAGGGATGAAGATCTCGG 57.263 43.478 0.00 0.00 37.96 4.63
280 281 3.322254 TCTTTAGGGATGAAGATCTCGGC 59.678 47.826 0.00 0.00 33.78 5.54
281 282 2.381752 TAGGGATGAAGATCTCGGCA 57.618 50.000 0.00 0.00 33.78 5.69
282 283 1.500474 AGGGATGAAGATCTCGGCAA 58.500 50.000 0.00 0.00 33.78 4.52
283 284 1.415659 AGGGATGAAGATCTCGGCAAG 59.584 52.381 0.00 0.00 33.78 4.01
284 285 1.414181 GGGATGAAGATCTCGGCAAGA 59.586 52.381 0.00 0.00 38.72 3.02
316 317 5.059833 AGAGAAAGCGAGACAAAGTGAAAT 58.940 37.500 0.00 0.00 0.00 2.17
434 785 7.400599 TGAATCTTTAAAGAAGATGCAGCAT 57.599 32.000 21.26 7.91 37.39 3.79
560 911 9.855021 AATTGAATTGACTAATTTAAGTTCCGG 57.145 29.630 0.00 0.00 35.89 5.14
612 963 8.613060 ATGTTTCTGCTTCACGAATATGATAT 57.387 30.769 0.00 0.00 0.00 1.63
872 1224 6.598850 ACGTATTGGGTGTATCCGTTTTTATT 59.401 34.615 0.00 0.00 37.00 1.40
1037 1393 5.717654 AGTTTCCCTTACTTGACCAAACAAA 59.282 36.000 0.00 0.00 0.00 2.83
1493 1849 3.380320 TCGCGAGAAATAGTTGAGGATCA 59.620 43.478 3.71 0.00 40.28 2.92
1731 2088 4.151883 AGCAGGGCAATCTTTCAAACTTA 58.848 39.130 0.00 0.00 0.00 2.24
1781 2138 4.360889 AGAGGGAGAGATGAAGACAATGT 58.639 43.478 0.00 0.00 0.00 2.71
1872 2229 6.310711 CACCGAGGAATAGAGACTTTACAAAC 59.689 42.308 0.00 0.00 0.00 2.93
2501 2861 5.815233 AGGATGACTCAAAGAAGTTCTCA 57.185 39.130 5.70 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 4.462133 TGGGTCTATGTTCAACGGAAAAA 58.538 39.130 0.00 0.00 34.13 1.94
12 13 4.088056 TGGGTCTATGTTCAACGGAAAA 57.912 40.909 0.00 0.00 34.13 2.29
13 14 3.773418 TGGGTCTATGTTCAACGGAAA 57.227 42.857 0.00 0.00 34.13 3.13
14 15 3.773418 TTGGGTCTATGTTCAACGGAA 57.227 42.857 0.00 0.00 0.00 4.30
15 16 3.992943 ATTGGGTCTATGTTCAACGGA 57.007 42.857 0.00 0.00 0.00 4.69
16 17 5.385509 AAAATTGGGTCTATGTTCAACGG 57.614 39.130 0.00 0.00 0.00 4.44
17 18 5.861787 GGAAAAATTGGGTCTATGTTCAACG 59.138 40.000 0.00 0.00 0.00 4.10
18 19 6.993079 AGGAAAAATTGGGTCTATGTTCAAC 58.007 36.000 0.00 0.00 0.00 3.18
19 20 7.610580 AAGGAAAAATTGGGTCTATGTTCAA 57.389 32.000 0.00 0.00 0.00 2.69
20 21 7.610580 AAAGGAAAAATTGGGTCTATGTTCA 57.389 32.000 0.00 0.00 0.00 3.18
21 22 8.902540 AAAAAGGAAAAATTGGGTCTATGTTC 57.097 30.769 0.00 0.00 0.00 3.18
67 68 4.138290 TGATACCGCCAGAAAGACAAAAA 58.862 39.130 0.00 0.00 0.00 1.94
68 69 3.745799 TGATACCGCCAGAAAGACAAAA 58.254 40.909 0.00 0.00 0.00 2.44
69 70 3.410631 TGATACCGCCAGAAAGACAAA 57.589 42.857 0.00 0.00 0.00 2.83
70 71 3.410631 TTGATACCGCCAGAAAGACAA 57.589 42.857 0.00 0.00 0.00 3.18
71 72 3.071479 GTTTGATACCGCCAGAAAGACA 58.929 45.455 0.00 0.00 0.00 3.41
72 73 3.071479 TGTTTGATACCGCCAGAAAGAC 58.929 45.455 0.00 0.00 0.00 3.01
73 74 3.334691 CTGTTTGATACCGCCAGAAAGA 58.665 45.455 0.00 0.00 0.00 2.52
74 75 2.159517 GCTGTTTGATACCGCCAGAAAG 60.160 50.000 0.00 0.00 31.47 2.62
75 76 1.810151 GCTGTTTGATACCGCCAGAAA 59.190 47.619 0.00 0.00 31.47 2.52
76 77 1.448985 GCTGTTTGATACCGCCAGAA 58.551 50.000 0.00 0.00 31.47 3.02
77 78 3.153024 GCTGTTTGATACCGCCAGA 57.847 52.632 0.00 0.00 31.47 3.86
81 82 0.676782 AGGTGGCTGTTTGATACCGC 60.677 55.000 0.00 0.00 36.55 5.68
82 83 2.684001 TAGGTGGCTGTTTGATACCG 57.316 50.000 0.00 0.00 36.55 4.02
83 84 6.534634 AGATATTAGGTGGCTGTTTGATACC 58.465 40.000 0.00 0.00 0.00 2.73
84 85 9.726438 ATAAGATATTAGGTGGCTGTTTGATAC 57.274 33.333 0.00 0.00 0.00 2.24
85 86 9.944376 GATAAGATATTAGGTGGCTGTTTGATA 57.056 33.333 0.00 0.00 0.00 2.15
86 87 7.885399 GGATAAGATATTAGGTGGCTGTTTGAT 59.115 37.037 0.00 0.00 0.00 2.57
87 88 7.224297 GGATAAGATATTAGGTGGCTGTTTGA 58.776 38.462 0.00 0.00 0.00 2.69
88 89 6.147821 CGGATAAGATATTAGGTGGCTGTTTG 59.852 42.308 0.00 0.00 0.00 2.93
89 90 6.231211 CGGATAAGATATTAGGTGGCTGTTT 58.769 40.000 0.00 0.00 0.00 2.83
90 91 5.794894 CGGATAAGATATTAGGTGGCTGTT 58.205 41.667 0.00 0.00 0.00 3.16
91 92 4.322801 GCGGATAAGATATTAGGTGGCTGT 60.323 45.833 0.00 0.00 0.00 4.40
92 93 4.184629 GCGGATAAGATATTAGGTGGCTG 58.815 47.826 0.00 0.00 0.00 4.85
93 94 3.197983 GGCGGATAAGATATTAGGTGGCT 59.802 47.826 0.00 0.00 0.00 4.75
94 95 3.197983 AGGCGGATAAGATATTAGGTGGC 59.802 47.826 0.00 0.00 0.00 5.01
95 96 4.712337 AGAGGCGGATAAGATATTAGGTGG 59.288 45.833 0.00 0.00 0.00 4.61
96 97 5.923733 AGAGGCGGATAAGATATTAGGTG 57.076 43.478 0.00 0.00 0.00 4.00
97 98 6.017192 TGAAGAGGCGGATAAGATATTAGGT 58.983 40.000 0.00 0.00 0.00 3.08
98 99 6.406400 CCTGAAGAGGCGGATAAGATATTAGG 60.406 46.154 0.00 0.00 30.52 2.69
99 100 6.378564 TCCTGAAGAGGCGGATAAGATATTAG 59.621 42.308 0.00 0.00 39.57 1.73
100 101 6.253758 TCCTGAAGAGGCGGATAAGATATTA 58.746 40.000 0.00 0.00 39.57 0.98
101 102 5.087323 TCCTGAAGAGGCGGATAAGATATT 58.913 41.667 0.00 0.00 39.57 1.28
102 103 4.678256 TCCTGAAGAGGCGGATAAGATAT 58.322 43.478 0.00 0.00 39.57 1.63
103 104 4.114015 TCCTGAAGAGGCGGATAAGATA 57.886 45.455 0.00 0.00 39.57 1.98
104 105 2.964209 TCCTGAAGAGGCGGATAAGAT 58.036 47.619 0.00 0.00 39.57 2.40
105 106 2.454336 TCCTGAAGAGGCGGATAAGA 57.546 50.000 0.00 0.00 39.57 2.10
106 107 3.543680 TTTCCTGAAGAGGCGGATAAG 57.456 47.619 0.00 0.00 39.57 1.73
107 108 3.992943 TTTTCCTGAAGAGGCGGATAA 57.007 42.857 0.00 0.00 39.57 1.75
108 109 3.454447 TCATTTTCCTGAAGAGGCGGATA 59.546 43.478 0.00 0.00 39.57 2.59
109 110 2.239654 TCATTTTCCTGAAGAGGCGGAT 59.760 45.455 0.00 0.00 39.57 4.18
110 111 1.628340 TCATTTTCCTGAAGAGGCGGA 59.372 47.619 0.00 0.00 39.57 5.54
111 112 2.113860 TCATTTTCCTGAAGAGGCGG 57.886 50.000 0.00 0.00 39.57 6.13
112 113 5.762218 AGATATTCATTTTCCTGAAGAGGCG 59.238 40.000 0.00 0.00 38.47 5.52
113 114 6.206438 GGAGATATTCATTTTCCTGAAGAGGC 59.794 42.308 0.00 0.00 38.47 4.70
114 115 6.426328 CGGAGATATTCATTTTCCTGAAGAGG 59.574 42.308 0.00 0.00 38.47 3.69
115 116 6.426328 CCGGAGATATTCATTTTCCTGAAGAG 59.574 42.308 0.00 0.00 38.47 2.85
116 117 6.099701 TCCGGAGATATTCATTTTCCTGAAGA 59.900 38.462 0.00 0.00 38.47 2.87
117 118 6.291377 TCCGGAGATATTCATTTTCCTGAAG 58.709 40.000 0.00 0.00 38.47 3.02
118 119 6.247229 TCCGGAGATATTCATTTTCCTGAA 57.753 37.500 0.00 0.00 39.35 3.02
119 120 5.887214 TCCGGAGATATTCATTTTCCTGA 57.113 39.130 0.00 0.00 0.00 3.86
120 121 6.942532 TTTCCGGAGATATTCATTTTCCTG 57.057 37.500 3.34 0.00 0.00 3.86
121 122 9.813826 ATATTTTCCGGAGATATTCATTTTCCT 57.186 29.630 3.34 0.00 0.00 3.36
128 129 9.627123 ACTCAAAATATTTTCCGGAGATATTCA 57.373 29.630 24.09 15.35 0.00 2.57
131 132 9.067986 GGAACTCAAAATATTTTCCGGAGATAT 57.932 33.333 23.40 10.20 0.00 1.63
132 133 8.446599 GGAACTCAAAATATTTTCCGGAGATA 57.553 34.615 23.40 8.15 0.00 1.98
133 134 7.334844 GGAACTCAAAATATTTTCCGGAGAT 57.665 36.000 23.40 16.26 0.00 2.75
134 135 6.753107 GGAACTCAAAATATTTTCCGGAGA 57.247 37.500 23.40 12.84 0.00 3.71
139 140 6.695713 GCCATACGGAACTCAAAATATTTTCC 59.304 38.462 10.53 7.95 33.66 3.13
140 141 7.480810 AGCCATACGGAACTCAAAATATTTTC 58.519 34.615 10.53 0.00 0.00 2.29
141 142 7.404671 AGCCATACGGAACTCAAAATATTTT 57.595 32.000 7.64 7.64 0.00 1.82
142 143 7.404671 AAGCCATACGGAACTCAAAATATTT 57.595 32.000 0.00 0.00 0.00 1.40
143 144 7.404671 AAAGCCATACGGAACTCAAAATATT 57.595 32.000 0.00 0.00 0.00 1.28
144 145 7.404671 AAAAGCCATACGGAACTCAAAATAT 57.595 32.000 0.00 0.00 0.00 1.28
145 146 6.827586 AAAAGCCATACGGAACTCAAAATA 57.172 33.333 0.00 0.00 0.00 1.40
146 147 5.722021 AAAAGCCATACGGAACTCAAAAT 57.278 34.783 0.00 0.00 0.00 1.82
147 148 5.523438 AAAAAGCCATACGGAACTCAAAA 57.477 34.783 0.00 0.00 0.00 2.44
168 169 3.134081 ACTGGTCCGAGTGAAGAGAAAAA 59.866 43.478 0.00 0.00 0.00 1.94
169 170 2.698797 ACTGGTCCGAGTGAAGAGAAAA 59.301 45.455 0.00 0.00 0.00 2.29
170 171 2.296471 GACTGGTCCGAGTGAAGAGAAA 59.704 50.000 0.00 0.00 0.00 2.52
171 172 1.887198 GACTGGTCCGAGTGAAGAGAA 59.113 52.381 0.00 0.00 0.00 2.87
172 173 1.535833 GACTGGTCCGAGTGAAGAGA 58.464 55.000 0.00 0.00 0.00 3.10
173 174 0.528470 GGACTGGTCCGAGTGAAGAG 59.472 60.000 3.88 0.00 40.36 2.85
174 175 2.654802 GGACTGGTCCGAGTGAAGA 58.345 57.895 3.88 0.00 40.36 2.87
185 186 2.045131 GTCGACTAGGCGGACTGGT 61.045 63.158 19.96 0.00 44.39 4.00
186 187 1.313812 AAGTCGACTAGGCGGACTGG 61.314 60.000 20.39 0.00 0.00 4.00
187 188 0.099082 GAAGTCGACTAGGCGGACTG 59.901 60.000 20.39 0.00 0.00 3.51
188 189 0.035247 AGAAGTCGACTAGGCGGACT 60.035 55.000 20.39 16.86 0.00 3.85
189 190 0.810016 AAGAAGTCGACTAGGCGGAC 59.190 55.000 20.39 14.79 0.00 4.79
190 191 0.809385 CAAGAAGTCGACTAGGCGGA 59.191 55.000 20.39 1.55 0.00 5.54
191 192 0.526662 ACAAGAAGTCGACTAGGCGG 59.473 55.000 20.39 10.27 0.00 6.13
192 193 3.694535 ATACAAGAAGTCGACTAGGCG 57.305 47.619 20.39 13.16 0.00 5.52
193 194 6.723131 AAAAATACAAGAAGTCGACTAGGC 57.277 37.500 20.39 11.49 0.00 3.93
229 230 9.784531 CTTGACAATAGTATTATTGGAGTGGAT 57.215 33.333 18.84 0.21 46.80 3.41
230 231 8.768397 ACTTGACAATAGTATTATTGGAGTGGA 58.232 33.333 18.84 2.46 46.80 4.02
231 232 8.964476 ACTTGACAATAGTATTATTGGAGTGG 57.036 34.615 18.84 9.43 46.80 4.00
244 245 9.213777 TCATCCCTAAAGATACTTGACAATAGT 57.786 33.333 0.00 0.00 0.00 2.12
247 248 8.772250 TCTTCATCCCTAAAGATACTTGACAAT 58.228 33.333 0.00 0.00 0.00 2.71
248 249 8.146053 TCTTCATCCCTAAAGATACTTGACAA 57.854 34.615 0.00 0.00 0.00 3.18
249 250 7.733773 TCTTCATCCCTAAAGATACTTGACA 57.266 36.000 0.00 0.00 0.00 3.58
250 251 8.646900 AGATCTTCATCCCTAAAGATACTTGAC 58.353 37.037 0.00 0.00 41.20 3.18
251 252 8.789767 AGATCTTCATCCCTAAAGATACTTGA 57.210 34.615 0.00 0.00 41.20 3.02
252 253 7.812191 CGAGATCTTCATCCCTAAAGATACTTG 59.188 40.741 0.00 0.00 41.20 3.16
253 254 7.039363 CCGAGATCTTCATCCCTAAAGATACTT 60.039 40.741 0.00 0.00 41.20 2.24
254 255 6.435904 CCGAGATCTTCATCCCTAAAGATACT 59.564 42.308 0.00 0.00 41.20 2.12
255 256 6.626302 CCGAGATCTTCATCCCTAAAGATAC 58.374 44.000 0.00 0.00 41.20 2.24
256 257 5.186021 GCCGAGATCTTCATCCCTAAAGATA 59.814 44.000 0.00 0.00 41.20 1.98
257 258 4.020662 GCCGAGATCTTCATCCCTAAAGAT 60.021 45.833 0.00 0.00 43.23 2.40
258 259 3.322254 GCCGAGATCTTCATCCCTAAAGA 59.678 47.826 0.00 0.00 36.05 2.52
259 260 3.070159 TGCCGAGATCTTCATCCCTAAAG 59.930 47.826 0.00 0.00 0.00 1.85
260 261 3.038280 TGCCGAGATCTTCATCCCTAAA 58.962 45.455 0.00 0.00 0.00 1.85
261 262 2.677914 TGCCGAGATCTTCATCCCTAA 58.322 47.619 0.00 0.00 0.00 2.69
262 263 2.381752 TGCCGAGATCTTCATCCCTA 57.618 50.000 0.00 0.00 0.00 3.53
263 264 1.415659 CTTGCCGAGATCTTCATCCCT 59.584 52.381 0.00 0.00 0.00 4.20
264 265 1.414181 TCTTGCCGAGATCTTCATCCC 59.586 52.381 0.00 0.00 0.00 3.85
265 266 2.898729 TCTTGCCGAGATCTTCATCC 57.101 50.000 0.00 0.00 0.00 3.51
266 267 5.384063 TCTATCTTGCCGAGATCTTCATC 57.616 43.478 0.00 0.00 44.04 2.92
267 268 5.999205 ATCTATCTTGCCGAGATCTTCAT 57.001 39.130 0.00 0.00 44.04 2.57
268 269 5.538053 AGAATCTATCTTGCCGAGATCTTCA 59.462 40.000 0.00 0.00 44.04 3.02
269 270 6.024552 AGAATCTATCTTGCCGAGATCTTC 57.975 41.667 0.00 1.50 44.04 2.87
270 271 6.945435 TCTAGAATCTATCTTGCCGAGATCTT 59.055 38.462 0.00 0.00 44.04 2.40
271 272 6.480763 TCTAGAATCTATCTTGCCGAGATCT 58.519 40.000 0.00 0.00 44.04 2.75
272 273 6.597672 TCTCTAGAATCTATCTTGCCGAGATC 59.402 42.308 0.00 0.00 44.04 2.75
273 274 6.480763 TCTCTAGAATCTATCTTGCCGAGAT 58.519 40.000 0.00 0.00 46.74 2.75
274 275 5.870706 TCTCTAGAATCTATCTTGCCGAGA 58.129 41.667 0.00 0.00 39.71 4.04
275 276 6.567687 TTCTCTAGAATCTATCTTGCCGAG 57.432 41.667 0.00 0.00 39.71 4.63
276 277 6.515862 GCTTTCTCTAGAATCTATCTTGCCGA 60.516 42.308 0.00 0.00 39.71 5.54
277 278 5.633182 GCTTTCTCTAGAATCTATCTTGCCG 59.367 44.000 0.00 0.00 39.71 5.69
278 279 5.633182 CGCTTTCTCTAGAATCTATCTTGCC 59.367 44.000 0.00 0.00 39.71 4.52
279 280 6.442952 TCGCTTTCTCTAGAATCTATCTTGC 58.557 40.000 0.00 0.00 39.71 4.01
280 281 7.803189 GTCTCGCTTTCTCTAGAATCTATCTTG 59.197 40.741 0.00 0.00 39.71 3.02
281 282 7.500892 TGTCTCGCTTTCTCTAGAATCTATCTT 59.499 37.037 0.00 0.00 39.71 2.40
282 283 6.995686 TGTCTCGCTTTCTCTAGAATCTATCT 59.004 38.462 0.00 0.00 42.48 1.98
283 284 7.197071 TGTCTCGCTTTCTCTAGAATCTATC 57.803 40.000 0.00 0.00 33.54 2.08
284 285 7.575414 TTGTCTCGCTTTCTCTAGAATCTAT 57.425 36.000 0.00 0.00 33.54 1.98
285 286 7.121463 ACTTTGTCTCGCTTTCTCTAGAATCTA 59.879 37.037 0.00 0.00 33.54 1.98
434 785 6.653740 GCTTAGTTTAGCCTTTGTTTCCTCTA 59.346 38.462 0.00 0.00 35.06 2.43
560 911 6.296026 TGTACTCCCATTAATGTGGAATAGC 58.704 40.000 19.82 12.61 42.02 2.97
872 1224 3.988379 AGCACGAAAATCAAAGCTTCA 57.012 38.095 0.00 0.00 0.00 3.02
1781 2138 5.690865 CCAATTAGATAACCAACCCTGCTA 58.309 41.667 0.00 0.00 0.00 3.49
1872 2229 1.870064 ATCCCAATCCCCTGCTTTTG 58.130 50.000 0.00 0.00 0.00 2.44
2501 2861 1.601166 GCGGTACAAAGTTCCTGGTT 58.399 50.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.