Multiple sequence alignment - TraesCS2D01G087200

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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 TraesCS2D01G087200 chr2D 100.000 2096 0 0 1 2096 37533521 37531426 0.000000e+00 3871.0
1 TraesCS2D01G087200 chr2D 95.276 889 32 8 1176 2060 651641880 651640998 0.000000e+00 1400.0
2 TraesCS2D01G087200 chr2D 95.421 546 22 3 299 842 651642454 651641910 0.000000e+00 867.0
3 TraesCS2D01G087200 chr2D 97.444 313 7 1 840 1152 334226189 334226500 1.100000e-147 532.0
4 TraesCS2D01G087200 chr2D 82.709 561 36 11 301 842 37926460 37925942 1.910000e-120 442.0
5 TraesCS2D01G087200 chr2D 95.652 46 1 1 306 350 646827966 646827921 2.880000e-09 73.1
6 TraesCS2D01G087200 chr2D 95.652 46 1 1 306 350 646846327 646846282 2.880000e-09 73.1
7 TraesCS2D01G087200 chr7D 96.552 1798 32 11 303 2096 87755550 87757321 0.000000e+00 2950.0
8 TraesCS2D01G087200 chr7D 95.339 944 31 9 1156 2096 122527010 122526077 0.000000e+00 1487.0
9 TraesCS2D01G087200 chr7D 96.252 507 17 2 337 842 122527533 122527028 0.000000e+00 830.0
10 TraesCS2D01G087200 chr7D 78.584 551 66 28 308 839 134489234 134489751 1.210000e-82 316.0
11 TraesCS2D01G087200 chr7A 94.726 948 37 10 1153 2096 704840652 704841590 0.000000e+00 1461.0
12 TraesCS2D01G087200 chr7A 90.698 946 66 15 1153 2090 630551292 630552223 0.000000e+00 1240.0
13 TraesCS2D01G087200 chr7A 89.706 952 77 15 1153 2096 411539079 411540017 0.000000e+00 1195.0
14 TraesCS2D01G087200 chr7A 90.643 513 39 8 354 863 411538574 411539080 0.000000e+00 673.0
15 TraesCS2D01G087200 chr6B 92.850 951 48 15 1156 2096 345630811 345629871 0.000000e+00 1362.0
16 TraesCS2D01G087200 chr6B 91.897 543 25 12 324 863 345631339 345630813 0.000000e+00 741.0
17 TraesCS2D01G087200 chr5B 94.305 878 33 11 1158 2027 507996095 507995227 0.000000e+00 1328.0
18 TraesCS2D01G087200 chr5B 88.649 555 46 11 313 863 571508706 571508165 0.000000e+00 660.0
19 TraesCS2D01G087200 chr4D 91.309 932 59 19 1153 2080 368504806 368505719 0.000000e+00 1253.0
20 TraesCS2D01G087200 chr4D 88.696 575 40 15 306 863 368504241 368504807 0.000000e+00 678.0
21 TraesCS2D01G087200 chr3D 88.713 567 33 15 299 863 93971883 93972420 0.000000e+00 664.0
22 TraesCS2D01G087200 chr2B 87.057 564 45 14 303 863 723051662 723051124 1.370000e-171 612.0
23 TraesCS2D01G087200 chr2B 90.506 316 13 4 1 300 65313876 65313562 3.240000e-108 401.0
24 TraesCS2D01G087200 chrUn 98.095 315 4 1 840 1152 404958504 404958818 3.930000e-152 547.0
25 TraesCS2D01G087200 chrUn 98.697 307 4 0 846 1152 317472914 317472608 1.410000e-151 545.0
26 TraesCS2D01G087200 chr3B 98.089 314 5 1 840 1152 201506845 201507158 1.410000e-151 545.0
27 TraesCS2D01G087200 chr3B 83.429 350 36 13 493 840 60858467 60858796 2.610000e-79 305.0
28 TraesCS2D01G087200 chr6D 97.764 313 7 0 840 1152 431400294 431400606 6.580000e-150 540.0
29 TraesCS2D01G087200 chr6D 95.918 49 1 1 303 350 455296040 455296088 6.200000e-11 78.7
30 TraesCS2D01G087200 chr5D 98.371 307 4 1 846 1152 6207547 6207242 2.370000e-149 538.0
31 TraesCS2D01G087200 chr1D 97.764 313 6 1 840 1152 254489969 254490280 2.370000e-149 538.0
32 TraesCS2D01G087200 chr1D 97.152 316 6 1 840 1152 394179180 394179495 3.960000e-147 531.0
33 TraesCS2D01G087200 chr2A 91.213 239 12 3 65 303 42397778 42397549 1.210000e-82 316.0
34 TraesCS2D01G087200 chr2A 95.833 48 1 1 306 352 13427650 13427697 2.230000e-10 76.8
35 TraesCS2D01G087200 chr4B 89.091 55 4 2 298 351 37145072 37145125 1.340000e-07 67.6


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 TraesCS2D01G087200 chr2D 37531426 37533521 2095 True 3871.0 3871 100.0000 1 2096 1 chr2D.!!$R1 2095
1 TraesCS2D01G087200 chr2D 651640998 651642454 1456 True 1133.5 1400 95.3485 299 2060 2 chr2D.!!$R5 1761
2 TraesCS2D01G087200 chr2D 37925942 37926460 518 True 442.0 442 82.7090 301 842 1 chr2D.!!$R2 541
3 TraesCS2D01G087200 chr7D 87755550 87757321 1771 False 2950.0 2950 96.5520 303 2096 1 chr7D.!!$F1 1793
4 TraesCS2D01G087200 chr7D 122526077 122527533 1456 True 1158.5 1487 95.7955 337 2096 2 chr7D.!!$R1 1759
5 TraesCS2D01G087200 chr7D 134489234 134489751 517 False 316.0 316 78.5840 308 839 1 chr7D.!!$F2 531
6 TraesCS2D01G087200 chr7A 704840652 704841590 938 False 1461.0 1461 94.7260 1153 2096 1 chr7A.!!$F2 943
7 TraesCS2D01G087200 chr7A 630551292 630552223 931 False 1240.0 1240 90.6980 1153 2090 1 chr7A.!!$F1 937
8 TraesCS2D01G087200 chr7A 411538574 411540017 1443 False 934.0 1195 90.1745 354 2096 2 chr7A.!!$F3 1742
9 TraesCS2D01G087200 chr6B 345629871 345631339 1468 True 1051.5 1362 92.3735 324 2096 2 chr6B.!!$R1 1772
10 TraesCS2D01G087200 chr5B 507995227 507996095 868 True 1328.0 1328 94.3050 1158 2027 1 chr5B.!!$R1 869
11 TraesCS2D01G087200 chr5B 571508165 571508706 541 True 660.0 660 88.6490 313 863 1 chr5B.!!$R2 550
12 TraesCS2D01G087200 chr4D 368504241 368505719 1478 False 965.5 1253 90.0025 306 2080 2 chr4D.!!$F1 1774
13 TraesCS2D01G087200 chr3D 93971883 93972420 537 False 664.0 664 88.7130 299 863 1 chr3D.!!$F1 564
14 TraesCS2D01G087200 chr2B 723051124 723051662 538 True 612.0 612 87.0570 303 863 1 chr2B.!!$R2 560

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
135 136 0.03889 TGGATTGGTTGGATTGGCGA 59.961 50.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1574 1667 0.468648 GAGCCGGCCCAAGTAGTTAT 59.531 55.0 26.15 0.0 0.0 1.89 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 4.514577 CTCGAGGTTCGGCGGCAT 62.515 66.667 10.53 0.00 40.88 4.40
22 23 4.508128 TCGAGGTTCGGCGGCATC 62.508 66.667 10.53 7.01 40.88 3.91
23 24 4.514577 CGAGGTTCGGCGGCATCT 62.515 66.667 10.53 0.00 36.00 2.90
24 25 2.125106 GAGGTTCGGCGGCATCTT 60.125 61.111 10.53 0.00 0.00 2.40
25 26 2.125106 AGGTTCGGCGGCATCTTC 60.125 61.111 10.53 0.00 0.00 2.87
26 27 3.564027 GGTTCGGCGGCATCTTCG 61.564 66.667 10.53 0.00 0.00 3.79
69 70 4.103928 GGGTGGGGAGGGGAGCTA 62.104 72.222 0.00 0.00 0.00 3.32
70 71 2.446802 GGTGGGGAGGGGAGCTAG 60.447 72.222 0.00 0.00 0.00 3.42
71 72 2.446802 GTGGGGAGGGGAGCTAGG 60.447 72.222 0.00 0.00 0.00 3.02
72 73 3.779083 TGGGGAGGGGAGCTAGGG 61.779 72.222 0.00 0.00 0.00 3.53
73 74 3.780275 GGGGAGGGGAGCTAGGGT 61.780 72.222 0.00 0.00 0.00 4.34
74 75 2.373100 GGGAGGGGAGCTAGGGTT 59.627 66.667 0.00 0.00 0.00 4.11
75 76 1.307953 GGGAGGGGAGCTAGGGTTT 60.308 63.158 0.00 0.00 0.00 3.27
76 77 0.919780 GGGAGGGGAGCTAGGGTTTT 60.920 60.000 0.00 0.00 0.00 2.43
77 78 0.256177 GGAGGGGAGCTAGGGTTTTG 59.744 60.000 0.00 0.00 0.00 2.44
78 79 0.256177 GAGGGGAGCTAGGGTTTTGG 59.744 60.000 0.00 0.00 0.00 3.28
79 80 1.214992 AGGGGAGCTAGGGTTTTGGG 61.215 60.000 0.00 0.00 0.00 4.12
80 81 1.306633 GGGAGCTAGGGTTTTGGGG 59.693 63.158 0.00 0.00 0.00 4.96
81 82 1.306633 GGAGCTAGGGTTTTGGGGG 59.693 63.158 0.00 0.00 0.00 5.40
116 117 3.489513 GAGGGGCAGCCGGGTTAT 61.490 66.667 1.64 0.00 0.00 1.89
117 118 3.774599 GAGGGGCAGCCGGGTTATG 62.775 68.421 1.64 0.00 0.00 1.90
118 119 4.894896 GGGGCAGCCGGGTTATGG 62.895 72.222 1.64 0.00 0.00 2.74
119 120 3.804329 GGGCAGCCGGGTTATGGA 61.804 66.667 1.64 0.00 0.00 3.41
120 121 2.515901 GGCAGCCGGGTTATGGAT 59.484 61.111 1.64 0.00 0.00 3.41
121 122 1.152756 GGCAGCCGGGTTATGGATT 60.153 57.895 1.64 0.00 0.00 3.01
122 123 1.455383 GGCAGCCGGGTTATGGATTG 61.455 60.000 1.64 0.00 0.00 2.67
123 124 1.455383 GCAGCCGGGTTATGGATTGG 61.455 60.000 1.64 0.00 0.00 3.16
124 125 0.106719 CAGCCGGGTTATGGATTGGT 60.107 55.000 1.64 0.00 0.00 3.67
125 126 0.629058 AGCCGGGTTATGGATTGGTT 59.371 50.000 0.00 0.00 0.00 3.67
126 127 0.744281 GCCGGGTTATGGATTGGTTG 59.256 55.000 2.18 0.00 0.00 3.77
127 128 1.398692 CCGGGTTATGGATTGGTTGG 58.601 55.000 0.00 0.00 0.00 3.77
128 129 1.064314 CCGGGTTATGGATTGGTTGGA 60.064 52.381 0.00 0.00 0.00 3.53
129 130 2.424234 CCGGGTTATGGATTGGTTGGAT 60.424 50.000 0.00 0.00 0.00 3.41
130 131 3.295973 CGGGTTATGGATTGGTTGGATT 58.704 45.455 0.00 0.00 0.00 3.01
131 132 3.068024 CGGGTTATGGATTGGTTGGATTG 59.932 47.826 0.00 0.00 0.00 2.67
132 133 3.387699 GGGTTATGGATTGGTTGGATTGG 59.612 47.826 0.00 0.00 0.00 3.16
133 134 3.181466 GGTTATGGATTGGTTGGATTGGC 60.181 47.826 0.00 0.00 0.00 4.52
134 135 1.113788 ATGGATTGGTTGGATTGGCG 58.886 50.000 0.00 0.00 0.00 5.69
135 136 0.038890 TGGATTGGTTGGATTGGCGA 59.961 50.000 0.00 0.00 0.00 5.54
136 137 0.740737 GGATTGGTTGGATTGGCGAG 59.259 55.000 0.00 0.00 0.00 5.03
137 138 0.101219 GATTGGTTGGATTGGCGAGC 59.899 55.000 0.00 0.00 0.00 5.03
138 139 1.656818 ATTGGTTGGATTGGCGAGCG 61.657 55.000 0.00 0.00 0.00 5.03
139 140 2.435938 GGTTGGATTGGCGAGCGA 60.436 61.111 0.00 0.00 0.00 4.93
140 141 2.464459 GGTTGGATTGGCGAGCGAG 61.464 63.158 0.00 0.00 0.00 5.03
141 142 2.819595 TTGGATTGGCGAGCGAGC 60.820 61.111 0.00 0.00 0.00 5.03
142 143 3.315142 TTGGATTGGCGAGCGAGCT 62.315 57.895 0.00 0.00 37.29 4.09
143 144 3.267860 GGATTGGCGAGCGAGCTG 61.268 66.667 0.84 0.00 37.29 4.24
144 145 3.934684 GATTGGCGAGCGAGCTGC 61.935 66.667 0.84 6.64 46.98 5.25
153 154 3.965701 GCGAGCTGCGAATCGACG 61.966 66.667 6.91 4.68 44.57 5.12
154 155 2.277310 CGAGCTGCGAATCGACGA 60.277 61.111 6.91 0.00 44.57 4.20
155 156 1.655654 CGAGCTGCGAATCGACGAT 60.656 57.895 6.91 4.05 44.57 3.73
156 157 1.842686 GAGCTGCGAATCGACGATG 59.157 57.895 11.83 0.60 35.09 3.84
157 158 0.867753 GAGCTGCGAATCGACGATGT 60.868 55.000 11.83 1.65 35.09 3.06
158 159 1.142185 AGCTGCGAATCGACGATGTG 61.142 55.000 11.83 8.10 35.09 3.21
159 160 1.920051 CTGCGAATCGACGATGTGG 59.080 57.895 11.83 4.98 35.09 4.17
160 161 0.525455 CTGCGAATCGACGATGTGGA 60.525 55.000 11.83 7.32 35.09 4.02
161 162 0.525455 TGCGAATCGACGATGTGGAG 60.525 55.000 11.83 2.87 35.09 3.86
162 163 1.209275 GCGAATCGACGATGTGGAGG 61.209 60.000 11.83 0.00 35.09 4.30
163 164 0.595053 CGAATCGACGATGTGGAGGG 60.595 60.000 11.83 0.00 35.09 4.30
164 165 0.249489 GAATCGACGATGTGGAGGGG 60.249 60.000 11.83 0.00 0.00 4.79
165 166 2.311688 AATCGACGATGTGGAGGGGC 62.312 60.000 11.83 0.00 0.00 5.80
166 167 4.530857 CGACGATGTGGAGGGGCC 62.531 72.222 0.00 0.00 37.10 5.80
167 168 4.530857 GACGATGTGGAGGGGCCG 62.531 72.222 0.00 0.00 40.66 6.13
169 170 4.838152 CGATGTGGAGGGGCCGTG 62.838 72.222 2.05 0.00 40.66 4.94
170 171 4.489771 GATGTGGAGGGGCCGTGG 62.490 72.222 2.05 0.00 40.66 4.94
174 175 4.000620 TGGAGGGGCCGTGGAGTA 62.001 66.667 2.05 0.00 40.66 2.59
175 176 3.468140 GGAGGGGCCGTGGAGTAC 61.468 72.222 2.05 0.00 0.00 2.73
185 186 3.908737 GTGGAGTACGTGAGCCTTT 57.091 52.632 0.00 0.00 0.00 3.11
186 187 2.165319 GTGGAGTACGTGAGCCTTTT 57.835 50.000 0.00 0.00 0.00 2.27
187 188 3.308438 GTGGAGTACGTGAGCCTTTTA 57.692 47.619 0.00 0.00 0.00 1.52
188 189 3.858247 GTGGAGTACGTGAGCCTTTTAT 58.142 45.455 0.00 0.00 0.00 1.40
189 190 3.617263 GTGGAGTACGTGAGCCTTTTATG 59.383 47.826 0.00 0.00 0.00 1.90
190 191 3.512329 TGGAGTACGTGAGCCTTTTATGA 59.488 43.478 0.00 0.00 0.00 2.15
191 192 4.020928 TGGAGTACGTGAGCCTTTTATGAA 60.021 41.667 0.00 0.00 0.00 2.57
192 193 4.567159 GGAGTACGTGAGCCTTTTATGAAG 59.433 45.833 0.00 0.00 0.00 3.02
193 194 5.401531 AGTACGTGAGCCTTTTATGAAGA 57.598 39.130 0.00 0.00 0.00 2.87
194 195 5.169295 AGTACGTGAGCCTTTTATGAAGAC 58.831 41.667 0.00 0.00 0.00 3.01
195 196 2.993899 ACGTGAGCCTTTTATGAAGACG 59.006 45.455 0.00 0.00 0.00 4.18
196 197 2.222819 CGTGAGCCTTTTATGAAGACGC 60.223 50.000 0.00 0.00 0.00 5.19
197 198 2.096013 GTGAGCCTTTTATGAAGACGCC 59.904 50.000 0.00 0.00 0.00 5.68
198 199 2.290008 TGAGCCTTTTATGAAGACGCCA 60.290 45.455 0.00 0.00 0.00 5.69
199 200 2.747446 GAGCCTTTTATGAAGACGCCAA 59.253 45.455 0.00 0.00 0.00 4.52
200 201 3.153919 AGCCTTTTATGAAGACGCCAAA 58.846 40.909 0.00 0.00 0.00 3.28
201 202 3.057526 AGCCTTTTATGAAGACGCCAAAC 60.058 43.478 0.00 0.00 0.00 2.93
211 212 3.122323 CGCCAAACGGGTATGCGT 61.122 61.111 1.42 0.00 40.33 5.24
212 213 2.483288 GCCAAACGGGTATGCGTG 59.517 61.111 0.00 0.00 39.65 5.34
213 214 2.329614 GCCAAACGGGTATGCGTGT 61.330 57.895 0.00 0.00 39.65 4.49
214 215 1.791662 CCAAACGGGTATGCGTGTC 59.208 57.895 0.00 0.00 0.00 3.67
215 216 1.641123 CCAAACGGGTATGCGTGTCC 61.641 60.000 0.00 0.00 0.00 4.02
216 217 0.951525 CAAACGGGTATGCGTGTCCA 60.952 55.000 0.00 0.00 0.00 4.02
217 218 0.672401 AAACGGGTATGCGTGTCCAG 60.672 55.000 0.00 0.00 0.00 3.86
218 219 2.890474 CGGGTATGCGTGTCCAGC 60.890 66.667 0.00 0.00 0.00 4.85
219 220 2.513897 GGGTATGCGTGTCCAGCC 60.514 66.667 0.00 0.00 0.00 4.85
220 221 2.584608 GGTATGCGTGTCCAGCCT 59.415 61.111 0.00 0.00 0.00 4.58
221 222 1.521681 GGTATGCGTGTCCAGCCTC 60.522 63.158 0.00 0.00 0.00 4.70
222 223 1.878522 GTATGCGTGTCCAGCCTCG 60.879 63.158 0.00 0.00 0.00 4.63
223 224 2.348104 TATGCGTGTCCAGCCTCGT 61.348 57.895 0.00 0.00 0.00 4.18
224 225 2.557059 TATGCGTGTCCAGCCTCGTG 62.557 60.000 0.00 0.00 0.00 4.35
225 226 4.664677 GCGTGTCCAGCCTCGTGT 62.665 66.667 0.00 0.00 0.00 4.49
226 227 2.734723 CGTGTCCAGCCTCGTGTG 60.735 66.667 0.00 0.00 0.00 3.82
227 228 2.357517 GTGTCCAGCCTCGTGTGG 60.358 66.667 0.00 0.00 34.87 4.17
228 229 2.523168 TGTCCAGCCTCGTGTGGA 60.523 61.111 0.00 0.00 40.72 4.02
229 230 1.913262 TGTCCAGCCTCGTGTGGAT 60.913 57.895 0.80 0.00 44.71 3.41
230 231 0.613572 TGTCCAGCCTCGTGTGGATA 60.614 55.000 0.80 0.00 44.71 2.59
231 232 0.179108 GTCCAGCCTCGTGTGGATAC 60.179 60.000 0.80 0.00 44.71 2.24
232 233 2.834685 GTCCAGCCTCGTGTGGATACA 61.835 57.143 0.80 0.00 44.71 2.29
244 245 0.251916 TGGATACAGGTTTCAGCCCG 59.748 55.000 0.00 0.00 46.17 6.13
245 246 0.539986 GGATACAGGTTTCAGCCCGA 59.460 55.000 0.00 0.00 0.00 5.14
246 247 1.141053 GGATACAGGTTTCAGCCCGAT 59.859 52.381 0.00 0.00 0.00 4.18
247 248 2.421529 GGATACAGGTTTCAGCCCGATT 60.422 50.000 0.00 0.00 0.00 3.34
248 249 2.871096 TACAGGTTTCAGCCCGATTT 57.129 45.000 0.00 0.00 0.00 2.17
249 250 2.871096 ACAGGTTTCAGCCCGATTTA 57.129 45.000 0.00 0.00 0.00 1.40
250 251 3.366052 ACAGGTTTCAGCCCGATTTAT 57.634 42.857 0.00 0.00 0.00 1.40
251 252 3.697166 ACAGGTTTCAGCCCGATTTATT 58.303 40.909 0.00 0.00 0.00 1.40
252 253 4.086457 ACAGGTTTCAGCCCGATTTATTT 58.914 39.130 0.00 0.00 0.00 1.40
253 254 4.082245 ACAGGTTTCAGCCCGATTTATTTG 60.082 41.667 0.00 0.00 0.00 2.32
254 255 4.157656 CAGGTTTCAGCCCGATTTATTTGA 59.842 41.667 0.00 0.00 0.00 2.69
255 256 4.399303 AGGTTTCAGCCCGATTTATTTGAG 59.601 41.667 0.00 0.00 0.00 3.02
256 257 4.157840 GGTTTCAGCCCGATTTATTTGAGT 59.842 41.667 0.00 0.00 0.00 3.41
257 258 5.336451 GGTTTCAGCCCGATTTATTTGAGTT 60.336 40.000 0.00 0.00 0.00 3.01
258 259 6.127842 GGTTTCAGCCCGATTTATTTGAGTTA 60.128 38.462 0.00 0.00 0.00 2.24
259 260 6.431198 TTCAGCCCGATTTATTTGAGTTAC 57.569 37.500 0.00 0.00 0.00 2.50
260 261 4.879545 TCAGCCCGATTTATTTGAGTTACC 59.120 41.667 0.00 0.00 0.00 2.85
261 262 4.881850 CAGCCCGATTTATTTGAGTTACCT 59.118 41.667 0.00 0.00 0.00 3.08
262 263 5.007724 CAGCCCGATTTATTTGAGTTACCTC 59.992 44.000 0.00 0.00 38.27 3.85
263 264 4.275196 GCCCGATTTATTTGAGTTACCTCC 59.725 45.833 0.00 0.00 36.86 4.30
264 265 4.510340 CCCGATTTATTTGAGTTACCTCCG 59.490 45.833 0.00 0.00 36.86 4.63
265 266 5.114081 CCGATTTATTTGAGTTACCTCCGT 58.886 41.667 0.00 0.00 36.86 4.69
266 267 5.006358 CCGATTTATTTGAGTTACCTCCGTG 59.994 44.000 0.00 0.00 36.86 4.94
267 268 5.501897 CGATTTATTTGAGTTACCTCCGTGC 60.502 44.000 0.00 0.00 36.86 5.34
268 269 4.546829 TTATTTGAGTTACCTCCGTGCT 57.453 40.909 0.00 0.00 36.86 4.40
269 270 2.450609 TTTGAGTTACCTCCGTGCTC 57.549 50.000 0.00 0.00 36.86 4.26
270 271 0.242825 TTGAGTTACCTCCGTGCTCG 59.757 55.000 0.14 0.14 36.86 5.03
296 297 9.665264 GGACACCGAAATTAGATATTTGATTTC 57.335 33.333 11.41 11.41 35.95 2.17
427 461 7.780745 TGTCCAAAACTAAAAATTACCTCCTCA 59.219 33.333 0.00 0.00 0.00 3.86
472 509 5.597806 CCTATACGCAAATCTGGTCACTAA 58.402 41.667 0.00 0.00 0.00 2.24
845 914 6.449635 TGGTGAACAATGCTTTATATGACC 57.550 37.500 0.00 0.00 0.00 4.02
1170 1243 7.335924 TCCTGGCACTAAATACACACTATTTTC 59.664 37.037 0.00 0.00 0.00 2.29
1855 1951 1.543871 GCAACTGGGGTAAAAGGTCGA 60.544 52.381 0.00 0.00 0.00 4.20
1894 1990 1.066430 GGTGGACTCGCAATTAGGACA 60.066 52.381 0.00 0.00 0.00 4.02
1987 2086 1.310933 GCGAGTCGAGGGTGGACTTA 61.311 60.000 18.61 0.00 44.41 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 4.514577 ATGCCGCCGAACCTCGAG 62.515 66.667 5.13 5.13 43.74 4.04
6 7 4.514577 AGATGCCGCCGAACCTCG 62.515 66.667 0.00 0.00 40.07 4.63
7 8 2.125106 AAGATGCCGCCGAACCTC 60.125 61.111 0.00 0.00 0.00 3.85
8 9 2.125106 GAAGATGCCGCCGAACCT 60.125 61.111 0.00 0.00 0.00 3.50
9 10 3.564027 CGAAGATGCCGCCGAACC 61.564 66.667 0.00 0.00 0.00 3.62
10 11 4.223964 GCGAAGATGCCGCCGAAC 62.224 66.667 0.00 0.00 46.22 3.95
52 53 4.103928 TAGCTCCCCTCCCCACCC 62.104 72.222 0.00 0.00 0.00 4.61
53 54 2.446802 CTAGCTCCCCTCCCCACC 60.447 72.222 0.00 0.00 0.00 4.61
54 55 2.446802 CCTAGCTCCCCTCCCCAC 60.447 72.222 0.00 0.00 0.00 4.61
55 56 3.779083 CCCTAGCTCCCCTCCCCA 61.779 72.222 0.00 0.00 0.00 4.96
56 57 2.859791 AAACCCTAGCTCCCCTCCCC 62.860 65.000 0.00 0.00 0.00 4.81
57 58 0.919780 AAAACCCTAGCTCCCCTCCC 60.920 60.000 0.00 0.00 0.00 4.30
58 59 0.256177 CAAAACCCTAGCTCCCCTCC 59.744 60.000 0.00 0.00 0.00 4.30
59 60 0.256177 CCAAAACCCTAGCTCCCCTC 59.744 60.000 0.00 0.00 0.00 4.30
60 61 1.214992 CCCAAAACCCTAGCTCCCCT 61.215 60.000 0.00 0.00 0.00 4.79
61 62 1.306633 CCCAAAACCCTAGCTCCCC 59.693 63.158 0.00 0.00 0.00 4.81
62 63 1.306633 CCCCAAAACCCTAGCTCCC 59.693 63.158 0.00 0.00 0.00 4.30
63 64 1.306633 CCCCCAAAACCCTAGCTCC 59.693 63.158 0.00 0.00 0.00 4.70
99 100 3.489513 ATAACCCGGCTGCCCCTC 61.490 66.667 14.12 0.00 0.00 4.30
100 101 3.809013 CATAACCCGGCTGCCCCT 61.809 66.667 14.12 0.00 0.00 4.79
101 102 4.894896 CCATAACCCGGCTGCCCC 62.895 72.222 14.12 0.00 0.00 5.80
102 103 2.640581 AATCCATAACCCGGCTGCCC 62.641 60.000 14.12 0.00 0.00 5.36
103 104 1.152756 AATCCATAACCCGGCTGCC 60.153 57.895 9.11 9.11 0.00 4.85
104 105 1.455383 CCAATCCATAACCCGGCTGC 61.455 60.000 0.00 0.00 0.00 5.25
105 106 0.106719 ACCAATCCATAACCCGGCTG 60.107 55.000 0.00 0.00 0.00 4.85
106 107 0.629058 AACCAATCCATAACCCGGCT 59.371 50.000 0.00 0.00 0.00 5.52
107 108 0.744281 CAACCAATCCATAACCCGGC 59.256 55.000 0.00 0.00 0.00 6.13
108 109 1.064314 TCCAACCAATCCATAACCCGG 60.064 52.381 0.00 0.00 0.00 5.73
109 110 2.428544 TCCAACCAATCCATAACCCG 57.571 50.000 0.00 0.00 0.00 5.28
110 111 3.387699 CCAATCCAACCAATCCATAACCC 59.612 47.826 0.00 0.00 0.00 4.11
111 112 3.181466 GCCAATCCAACCAATCCATAACC 60.181 47.826 0.00 0.00 0.00 2.85
112 113 3.490761 CGCCAATCCAACCAATCCATAAC 60.491 47.826 0.00 0.00 0.00 1.89
113 114 2.692557 CGCCAATCCAACCAATCCATAA 59.307 45.455 0.00 0.00 0.00 1.90
114 115 2.092158 TCGCCAATCCAACCAATCCATA 60.092 45.455 0.00 0.00 0.00 2.74
115 116 1.113788 CGCCAATCCAACCAATCCAT 58.886 50.000 0.00 0.00 0.00 3.41
116 117 0.038890 TCGCCAATCCAACCAATCCA 59.961 50.000 0.00 0.00 0.00 3.41
117 118 0.740737 CTCGCCAATCCAACCAATCC 59.259 55.000 0.00 0.00 0.00 3.01
118 119 0.101219 GCTCGCCAATCCAACCAATC 59.899 55.000 0.00 0.00 0.00 2.67
119 120 1.656818 CGCTCGCCAATCCAACCAAT 61.657 55.000 0.00 0.00 0.00 3.16
120 121 2.331893 CGCTCGCCAATCCAACCAA 61.332 57.895 0.00 0.00 0.00 3.67
121 122 2.745884 CGCTCGCCAATCCAACCA 60.746 61.111 0.00 0.00 0.00 3.67
122 123 2.435938 TCGCTCGCCAATCCAACC 60.436 61.111 0.00 0.00 0.00 3.77
123 124 3.093278 CTCGCTCGCCAATCCAAC 58.907 61.111 0.00 0.00 0.00 3.77
124 125 2.819595 GCTCGCTCGCCAATCCAA 60.820 61.111 0.00 0.00 0.00 3.53
125 126 3.774528 AGCTCGCTCGCCAATCCA 61.775 61.111 0.00 0.00 0.00 3.41
126 127 3.267860 CAGCTCGCTCGCCAATCC 61.268 66.667 0.00 0.00 0.00 3.01
127 128 3.934684 GCAGCTCGCTCGCCAATC 61.935 66.667 1.48 0.00 37.77 2.67
132 133 3.982360 GATTCGCAGCTCGCTCGC 61.982 66.667 6.58 0.00 39.08 5.03
133 134 3.676348 CGATTCGCAGCTCGCTCG 61.676 66.667 0.00 9.81 39.08 5.03
134 135 2.278206 TCGATTCGCAGCTCGCTC 60.278 61.111 0.00 3.47 39.08 5.03
135 136 2.580867 GTCGATTCGCAGCTCGCT 60.581 61.111 0.00 0.00 39.08 4.93
136 137 3.965701 CGTCGATTCGCAGCTCGC 61.966 66.667 0.00 0.00 38.27 5.03
137 138 1.655654 ATCGTCGATTCGCAGCTCG 60.656 57.895 0.75 0.00 40.15 5.03
138 139 0.867753 ACATCGTCGATTCGCAGCTC 60.868 55.000 4.63 0.00 0.00 4.09
139 140 1.139734 ACATCGTCGATTCGCAGCT 59.860 52.632 4.63 0.00 0.00 4.24
140 141 1.270968 CACATCGTCGATTCGCAGC 59.729 57.895 4.63 0.00 0.00 5.25
141 142 0.525455 TCCACATCGTCGATTCGCAG 60.525 55.000 4.63 0.00 0.00 5.18
142 143 0.525455 CTCCACATCGTCGATTCGCA 60.525 55.000 4.63 0.00 0.00 5.10
143 144 1.209275 CCTCCACATCGTCGATTCGC 61.209 60.000 4.63 0.00 0.00 4.70
144 145 0.595053 CCCTCCACATCGTCGATTCG 60.595 60.000 4.63 0.00 0.00 3.34
145 146 0.249489 CCCCTCCACATCGTCGATTC 60.249 60.000 4.63 0.00 0.00 2.52
146 147 1.823295 CCCCTCCACATCGTCGATT 59.177 57.895 4.63 0.00 0.00 3.34
147 148 2.797278 GCCCCTCCACATCGTCGAT 61.797 63.158 0.75 0.75 0.00 3.59
148 149 3.458163 GCCCCTCCACATCGTCGA 61.458 66.667 0.00 0.00 0.00 4.20
149 150 4.530857 GGCCCCTCCACATCGTCG 62.531 72.222 0.00 0.00 34.01 5.12
150 151 4.530857 CGGCCCCTCCACATCGTC 62.531 72.222 0.00 0.00 34.01 4.20
152 153 4.838152 CACGGCCCCTCCACATCG 62.838 72.222 0.00 0.00 34.01 3.84
153 154 4.489771 CCACGGCCCCTCCACATC 62.490 72.222 0.00 0.00 34.01 3.06
157 158 4.000620 TACTCCACGGCCCCTCCA 62.001 66.667 0.00 0.00 34.01 3.86
158 159 3.468140 GTACTCCACGGCCCCTCC 61.468 72.222 0.00 0.00 0.00 4.30
167 168 2.165319 AAAAGGCTCACGTACTCCAC 57.835 50.000 0.00 0.00 0.00 4.02
168 169 3.512329 TCATAAAAGGCTCACGTACTCCA 59.488 43.478 0.00 0.00 0.00 3.86
169 170 4.119442 TCATAAAAGGCTCACGTACTCC 57.881 45.455 0.00 0.00 0.00 3.85
170 171 5.288952 GTCTTCATAAAAGGCTCACGTACTC 59.711 44.000 0.00 0.00 0.00 2.59
171 172 5.169295 GTCTTCATAAAAGGCTCACGTACT 58.831 41.667 0.00 0.00 0.00 2.73
172 173 4.031426 CGTCTTCATAAAAGGCTCACGTAC 59.969 45.833 0.00 0.00 0.00 3.67
173 174 4.171005 CGTCTTCATAAAAGGCTCACGTA 58.829 43.478 0.00 0.00 0.00 3.57
174 175 2.993899 CGTCTTCATAAAAGGCTCACGT 59.006 45.455 0.00 0.00 0.00 4.49
175 176 2.222819 GCGTCTTCATAAAAGGCTCACG 60.223 50.000 0.00 0.00 0.00 4.35
176 177 2.096013 GGCGTCTTCATAAAAGGCTCAC 59.904 50.000 0.00 0.00 0.00 3.51
177 178 2.290008 TGGCGTCTTCATAAAAGGCTCA 60.290 45.455 0.00 0.00 0.00 4.26
178 179 2.356135 TGGCGTCTTCATAAAAGGCTC 58.644 47.619 0.00 0.00 0.00 4.70
179 180 2.489938 TGGCGTCTTCATAAAAGGCT 57.510 45.000 0.00 0.00 0.00 4.58
180 181 3.242518 GTTTGGCGTCTTCATAAAAGGC 58.757 45.455 0.00 0.00 0.00 4.35
181 182 3.488489 CGTTTGGCGTCTTCATAAAAGG 58.512 45.455 0.00 0.00 35.54 3.11
182 183 3.488489 CCGTTTGGCGTCTTCATAAAAG 58.512 45.455 0.00 0.00 39.32 2.27
183 184 2.226912 CCCGTTTGGCGTCTTCATAAAA 59.773 45.455 0.00 0.00 39.32 1.52
184 185 1.807742 CCCGTTTGGCGTCTTCATAAA 59.192 47.619 0.00 0.00 39.32 1.40
185 186 1.270947 ACCCGTTTGGCGTCTTCATAA 60.271 47.619 0.00 0.00 39.32 1.90
186 187 0.322322 ACCCGTTTGGCGTCTTCATA 59.678 50.000 0.00 0.00 39.32 2.15
187 188 0.322322 TACCCGTTTGGCGTCTTCAT 59.678 50.000 0.00 0.00 39.32 2.57
188 189 0.322322 ATACCCGTTTGGCGTCTTCA 59.678 50.000 0.00 0.00 39.32 3.02
189 190 0.725117 CATACCCGTTTGGCGTCTTC 59.275 55.000 0.00 0.00 39.32 2.87
190 191 1.303091 GCATACCCGTTTGGCGTCTT 61.303 55.000 0.00 0.00 39.32 3.01
191 192 1.743995 GCATACCCGTTTGGCGTCT 60.744 57.895 0.00 0.00 39.32 4.18
192 193 2.789249 GCATACCCGTTTGGCGTC 59.211 61.111 0.00 0.00 39.32 5.19
193 194 3.122323 CGCATACCCGTTTGGCGT 61.122 61.111 0.00 0.00 42.51 5.68
195 196 2.248274 GACACGCATACCCGTTTGGC 62.248 60.000 0.00 0.00 39.83 4.52
196 197 1.641123 GGACACGCATACCCGTTTGG 61.641 60.000 0.00 0.00 39.83 3.28
197 198 0.951525 TGGACACGCATACCCGTTTG 60.952 55.000 0.00 0.00 39.83 2.93
198 199 0.672401 CTGGACACGCATACCCGTTT 60.672 55.000 0.00 0.00 39.83 3.60
199 200 1.079405 CTGGACACGCATACCCGTT 60.079 57.895 0.00 0.00 39.83 4.44
200 201 2.577059 CTGGACACGCATACCCGT 59.423 61.111 0.00 0.00 43.11 5.28
201 202 2.890474 GCTGGACACGCATACCCG 60.890 66.667 0.00 0.00 0.00 5.28
202 203 2.513897 GGCTGGACACGCATACCC 60.514 66.667 0.00 0.00 0.00 3.69
203 204 1.521681 GAGGCTGGACACGCATACC 60.522 63.158 0.00 0.00 0.00 2.73
204 205 1.878522 CGAGGCTGGACACGCATAC 60.879 63.158 0.00 0.00 0.00 2.39
205 206 2.348104 ACGAGGCTGGACACGCATA 61.348 57.895 2.65 0.00 0.00 3.14
206 207 3.695606 ACGAGGCTGGACACGCAT 61.696 61.111 2.65 0.00 0.00 4.73
207 208 4.662961 CACGAGGCTGGACACGCA 62.663 66.667 2.65 0.00 0.00 5.24
208 209 4.664677 ACACGAGGCTGGACACGC 62.665 66.667 2.65 0.00 0.00 5.34
209 210 2.734723 CACACGAGGCTGGACACG 60.735 66.667 2.65 0.00 0.00 4.49
210 211 2.172483 ATCCACACGAGGCTGGACAC 62.172 60.000 2.65 0.00 39.44 3.67
211 212 0.613572 TATCCACACGAGGCTGGACA 60.614 55.000 2.65 0.00 39.44 4.02
212 213 0.179108 GTATCCACACGAGGCTGGAC 60.179 60.000 2.65 0.00 39.44 4.02
213 214 0.613572 TGTATCCACACGAGGCTGGA 60.614 55.000 2.65 0.00 40.92 3.86
214 215 0.179100 CTGTATCCACACGAGGCTGG 60.179 60.000 0.00 0.00 0.00 4.85
215 216 0.179100 CCTGTATCCACACGAGGCTG 60.179 60.000 0.00 0.00 0.00 4.85
216 217 0.614979 ACCTGTATCCACACGAGGCT 60.615 55.000 0.00 0.00 0.00 4.58
217 218 0.249398 AACCTGTATCCACACGAGGC 59.751 55.000 0.00 0.00 0.00 4.70
218 219 2.028476 TGAAACCTGTATCCACACGAGG 60.028 50.000 0.00 0.00 0.00 4.63
219 220 3.254060 CTGAAACCTGTATCCACACGAG 58.746 50.000 0.00 0.00 0.00 4.18
220 221 2.611971 GCTGAAACCTGTATCCACACGA 60.612 50.000 0.00 0.00 0.00 4.35
221 222 1.732259 GCTGAAACCTGTATCCACACG 59.268 52.381 0.00 0.00 0.00 4.49
222 223 2.084546 GGCTGAAACCTGTATCCACAC 58.915 52.381 0.00 0.00 0.00 3.82
223 224 1.004277 GGGCTGAAACCTGTATCCACA 59.996 52.381 0.00 0.00 0.00 4.17
224 225 1.751437 GGGCTGAAACCTGTATCCAC 58.249 55.000 0.00 0.00 0.00 4.02
225 226 0.251916 CGGGCTGAAACCTGTATCCA 59.748 55.000 0.00 0.00 0.00 3.41
226 227 0.539986 TCGGGCTGAAACCTGTATCC 59.460 55.000 0.00 0.00 37.37 2.59
227 228 2.622064 ATCGGGCTGAAACCTGTATC 57.378 50.000 0.00 0.00 37.37 2.24
228 229 3.366052 AAATCGGGCTGAAACCTGTAT 57.634 42.857 0.00 0.00 37.37 2.29
229 230 2.871096 AAATCGGGCTGAAACCTGTA 57.129 45.000 0.00 0.00 37.37 2.74
230 231 2.871096 TAAATCGGGCTGAAACCTGT 57.129 45.000 0.00 0.00 37.37 4.00
231 232 4.157656 TCAAATAAATCGGGCTGAAACCTG 59.842 41.667 0.00 0.00 37.44 4.00
232 233 4.340617 TCAAATAAATCGGGCTGAAACCT 58.659 39.130 0.00 0.00 0.00 3.50
233 234 4.157840 ACTCAAATAAATCGGGCTGAAACC 59.842 41.667 0.00 0.00 0.00 3.27
234 235 5.310720 ACTCAAATAAATCGGGCTGAAAC 57.689 39.130 0.00 0.00 0.00 2.78
235 236 5.975693 AACTCAAATAAATCGGGCTGAAA 57.024 34.783 0.00 0.00 0.00 2.69
236 237 5.355910 GGTAACTCAAATAAATCGGGCTGAA 59.644 40.000 0.00 0.00 0.00 3.02
237 238 4.879545 GGTAACTCAAATAAATCGGGCTGA 59.120 41.667 0.00 0.00 0.00 4.26
238 239 5.169836 GGTAACTCAAATAAATCGGGCTG 57.830 43.478 0.00 0.00 0.00 4.85
270 271 9.665264 GAAATCAAATATCTAATTTCGGTGTCC 57.335 33.333 0.00 0.00 30.91 4.02
289 290 9.967346 CATAGACGGACTCTATTTAGAAATCAA 57.033 33.333 0.00 0.00 39.84 2.57
290 291 9.132923 ACATAGACGGACTCTATTTAGAAATCA 57.867 33.333 0.00 0.00 39.84 2.57
291 292 9.615295 GACATAGACGGACTCTATTTAGAAATC 57.385 37.037 0.00 0.00 39.84 2.17
292 293 9.132923 TGACATAGACGGACTCTATTTAGAAAT 57.867 33.333 0.00 0.00 39.84 2.17
293 294 8.404000 GTGACATAGACGGACTCTATTTAGAAA 58.596 37.037 0.00 0.00 39.84 2.52
294 295 7.555195 TGTGACATAGACGGACTCTATTTAGAA 59.445 37.037 0.00 0.00 39.84 2.10
295 296 7.052248 TGTGACATAGACGGACTCTATTTAGA 58.948 38.462 0.00 0.00 39.84 2.10
296 297 7.260558 TGTGACATAGACGGACTCTATTTAG 57.739 40.000 0.00 0.00 39.84 1.85
297 298 7.720074 AGATGTGACATAGACGGACTCTATTTA 59.280 37.037 0.00 0.00 39.84 1.40
298 299 6.547880 AGATGTGACATAGACGGACTCTATTT 59.452 38.462 0.00 0.00 39.84 1.40
299 300 6.065374 AGATGTGACATAGACGGACTCTATT 58.935 40.000 0.00 0.00 39.84 1.73
403 437 8.802267 CATGAGGAGGTAATTTTTAGTTTTGGA 58.198 33.333 0.00 0.00 0.00 3.53
427 461 3.156714 TGACCAAGGCGGACACAT 58.843 55.556 0.00 0.00 34.28 3.21
845 914 8.103948 AGTGTAAAAGAAAGTGGATTCATCAG 57.896 34.615 0.00 0.00 0.00 2.90
1033 1103 3.883489 GGGGTTATAGTTAAAGCAGCCAG 59.117 47.826 0.00 0.00 0.00 4.85
1139 1209 4.018870 TGTGTATTTAGTGCCAGGAATCCA 60.019 41.667 0.61 0.00 0.00 3.41
1170 1243 6.317789 ACAATGTTCAGTGTGTATTGGAAG 57.682 37.500 5.12 0.00 34.07 3.46
1574 1667 0.468648 GAGCCGGCCCAAGTAGTTAT 59.531 55.000 26.15 0.00 0.00 1.89
1855 1951 0.822164 CCTCGATTCGTAACTGGGGT 59.178 55.000 5.89 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.