Multiple sequence alignment - TraesCS2A01G370000

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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 TraesCS2A01G370000 chr2A 100.000 2344 0 0 865 3208 612835420 612833077 0.000000e+00 4329.0
1 TraesCS2A01G370000 chr2A 100.000 380 0 0 1 380 612836284 612835905 0.000000e+00 702.0
2 TraesCS2A01G370000 chr2A 87.097 124 16 0 1270 1393 185285018 185285141 1.200000e-29 141.0
3 TraesCS2A01G370000 chr2B 90.337 2432 103 51 865 3205 550214596 550212206 0.000000e+00 3068.0
4 TraesCS2A01G370000 chr2B 83.060 366 22 26 20 380 550215025 550214695 2.420000e-76 296.0
5 TraesCS2A01G370000 chr2D 90.042 1426 55 44 865 2225 471056380 471054977 0.000000e+00 1766.0
6 TraesCS2A01G370000 chr2D 85.167 627 37 17 2593 3180 471053177 471052568 2.760000e-165 592.0
7 TraesCS2A01G370000 chr2D 93.611 360 13 5 2249 2601 471054989 471054633 2.190000e-146 529.0
8 TraesCS2A01G370000 chr2D 88.372 301 12 13 82 380 471056758 471056479 1.100000e-89 340.0
9 TraesCS2A01G370000 chr2D 85.714 140 20 0 1257 1396 165468259 165468120 7.170000e-32 148.0
10 TraesCS2A01G370000 chr2D 95.402 87 4 0 3119 3205 471052572 471052486 4.320000e-29 139.0
11 TraesCS2A01G370000 chr6D 76.114 561 58 48 1617 2157 309719548 309720052 1.160000e-54 224.0
12 TraesCS2A01G370000 chr6D 92.105 152 11 1 1243 1393 309719045 309719196 2.510000e-51 213.0
13 TraesCS2A01G370000 chr6B 94.483 145 7 1 1250 1393 477689717 477689861 4.170000e-54 222.0
14 TraesCS2A01G370000 chr6B 75.579 561 61 47 1617 2157 477691822 477692326 1.170000e-49 207.0
15 TraesCS2A01G370000 chr6A 94.483 145 7 1 1250 1393 446521222 446521366 4.170000e-54 222.0
16 TraesCS2A01G370000 chr6A 75.666 563 63 44 1617 2157 446521693 446522203 2.510000e-51 213.0
17 TraesCS2A01G370000 chr6A 100.000 28 0 0 2853 2880 492287256 492287283 6.000000e-03 52.8
18 TraesCS2A01G370000 chr1D 88.421 95 9 2 1617 1710 449982995 449982902 2.620000e-21 113.0
19 TraesCS2A01G370000 chr1D 87.368 95 10 2 1617 1710 449660778 449660871 1.220000e-19 108.0
20 TraesCS2A01G370000 chr1A 87.368 95 10 2 1617 1710 544928194 544928287 1.220000e-19 108.0
21 TraesCS2A01G370000 chr1A 87.368 95 10 2 1617 1710 545009107 545009014 1.220000e-19 108.0
22 TraesCS2A01G370000 chr7B 80.576 139 25 2 1253 1390 77432152 77432289 4.380000e-19 106.0
23 TraesCS2A01G370000 chr5A 80.292 137 23 4 1256 1390 663379367 663379501 2.040000e-17 100.0
24 TraesCS2A01G370000 chr3A 79.710 138 20 8 2853 2985 25489294 25489428 3.410000e-15 93.5


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 TraesCS2A01G370000 chr2A 612833077 612836284 3207 True 2515.5 4329 100.0000 1 3208 2 chr2A.!!$R1 3207
1 TraesCS2A01G370000 chr2B 550212206 550215025 2819 True 1682.0 3068 86.6985 20 3205 2 chr2B.!!$R1 3185
2 TraesCS2A01G370000 chr2D 471052486 471056758 4272 True 673.2 1766 90.5188 82 3205 5 chr2D.!!$R2 3123
3 TraesCS2A01G370000 chr6D 309719045 309720052 1007 False 218.5 224 84.1095 1243 2157 2 chr6D.!!$F1 914
4 TraesCS2A01G370000 chr6B 477689717 477692326 2609 False 214.5 222 85.0310 1250 2157 2 chr6B.!!$F1 907
5 TraesCS2A01G370000 chr6A 446521222 446522203 981 False 217.5 222 85.0745 1250 2157 2 chr6A.!!$F2 907

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
981 989 0.092351 CGTGTACATTTCGTCGGTGC 59.908 55.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2928 6279 0.389817 CCGGAGTTGTTCATCGCTGA 60.39 55.0 0.0 0.0 0.0 4.26 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
17 18 3.226242 TGGGCAAGACGTGTCACT 58.774 55.556 0.00 0.00 31.37 3.41
18 19 1.069090 TGGGCAAGACGTGTCACTC 59.931 57.895 0.00 0.00 31.37 3.51
50 51 1.855360 GGAGTGATCGCGAGTTGATTC 59.145 52.381 16.66 6.57 0.00 2.52
51 52 2.480416 GGAGTGATCGCGAGTTGATTCT 60.480 50.000 16.66 5.73 0.00 2.40
52 53 3.182967 GAGTGATCGCGAGTTGATTCTT 58.817 45.455 16.66 0.00 0.00 2.52
53 54 3.589988 AGTGATCGCGAGTTGATTCTTT 58.410 40.909 16.66 0.00 0.00 2.52
54 55 3.614616 AGTGATCGCGAGTTGATTCTTTC 59.385 43.478 16.66 3.28 0.00 2.62
55 56 3.614616 GTGATCGCGAGTTGATTCTTTCT 59.385 43.478 16.66 0.00 0.00 2.52
62 63 5.561873 CGCGAGTTGATTCTTTCTTTCTTTC 59.438 40.000 0.00 0.00 0.00 2.62
63 64 6.564873 CGCGAGTTGATTCTTTCTTTCTTTCT 60.565 38.462 0.00 0.00 0.00 2.52
66 67 9.163903 CGAGTTGATTCTTTCTTTCTTTCTTTC 57.836 33.333 0.00 0.00 0.00 2.62
78 79 8.970859 TCTTTCTTTCTTTCTTTCTGATGACT 57.029 30.769 0.00 0.00 0.00 3.41
102 103 4.859629 AGATCGCGAGTTGATTTTTACC 57.140 40.909 16.66 0.00 0.00 2.85
108 109 3.500680 GCGAGTTGATTTTTACCACTCCA 59.499 43.478 0.00 0.00 0.00 3.86
109 110 4.612939 GCGAGTTGATTTTTACCACTCCAC 60.613 45.833 0.00 0.00 0.00 4.02
110 111 4.755123 CGAGTTGATTTTTACCACTCCACT 59.245 41.667 0.00 0.00 0.00 4.00
111 112 5.107065 CGAGTTGATTTTTACCACTCCACTC 60.107 44.000 0.00 0.00 30.87 3.51
112 113 5.070685 AGTTGATTTTTACCACTCCACTCC 58.929 41.667 0.00 0.00 0.00 3.85
113 114 4.715534 TGATTTTTACCACTCCACTCCA 57.284 40.909 0.00 0.00 0.00 3.86
114 115 4.394729 TGATTTTTACCACTCCACTCCAC 58.605 43.478 0.00 0.00 0.00 4.02
115 116 4.104102 TGATTTTTACCACTCCACTCCACT 59.896 41.667 0.00 0.00 0.00 4.00
116 117 3.764237 TTTTACCACTCCACTCCACTC 57.236 47.619 0.00 0.00 0.00 3.51
117 118 1.640917 TTACCACTCCACTCCACTCC 58.359 55.000 0.00 0.00 0.00 3.85
118 119 0.784495 TACCACTCCACTCCACTCCT 59.216 55.000 0.00 0.00 0.00 3.69
147 148 1.371267 TCGTCCAGTTGAGAACGCG 60.371 57.895 3.53 3.53 35.22 6.01
148 149 2.853914 GTCCAGTTGAGAACGCGC 59.146 61.111 5.73 0.00 36.23 6.86
149 150 1.954146 GTCCAGTTGAGAACGCGCA 60.954 57.895 5.73 0.00 36.23 6.09
150 151 1.954146 TCCAGTTGAGAACGCGCAC 60.954 57.895 5.73 0.00 36.23 5.34
151 152 1.956170 CCAGTTGAGAACGCGCACT 60.956 57.895 5.73 5.51 36.23 4.40
152 153 1.202568 CAGTTGAGAACGCGCACTG 59.797 57.895 5.73 7.88 36.23 3.66
193 194 3.041351 TGGCGCAGTTGTAGCACG 61.041 61.111 10.83 0.00 0.00 5.34
243 247 2.695147 CCTACCCAAGGCATTGAATTCC 59.305 50.000 13.66 0.00 38.97 3.01
255 261 2.009302 GAATTCCCCCTGGCCCTCT 61.009 63.158 0.00 0.00 0.00 3.69
265 271 3.755628 GGCCCTCTCGTGCGTGTA 61.756 66.667 0.00 0.00 0.00 2.90
266 272 2.506438 GCCCTCTCGTGCGTGTAC 60.506 66.667 0.00 0.00 0.00 2.90
267 273 2.991076 GCCCTCTCGTGCGTGTACT 61.991 63.158 0.00 0.00 0.00 2.73
268 274 1.585006 CCCTCTCGTGCGTGTACTT 59.415 57.895 0.00 0.00 0.00 2.24
269 275 0.732880 CCCTCTCGTGCGTGTACTTG 60.733 60.000 0.00 0.00 0.00 3.16
270 276 1.344942 CCTCTCGTGCGTGTACTTGC 61.345 60.000 0.00 0.00 0.00 4.01
271 277 0.663269 CTCTCGTGCGTGTACTTGCA 60.663 55.000 8.27 8.27 39.13 4.08
272 278 0.249114 TCTCGTGCGTGTACTTGCAA 60.249 50.000 13.02 0.00 43.75 4.08
273 279 0.161658 CTCGTGCGTGTACTTGCAAG 59.838 55.000 24.84 24.84 43.75 4.01
274 280 0.249114 TCGTGCGTGTACTTGCAAGA 60.249 50.000 32.50 18.72 45.08 3.02
280 286 3.242608 TGCGTGTACTTGCAAGAAAGAAC 60.243 43.478 32.50 19.61 38.34 3.01
332 338 4.154347 CCTCTGCCCGTCAGCTCC 62.154 72.222 0.00 0.00 42.56 4.70
347 353 3.958147 TCAGCTCCACCACTTATTATCGA 59.042 43.478 0.00 0.00 0.00 3.59
350 356 3.050619 CTCCACCACTTATTATCGACGC 58.949 50.000 0.00 0.00 0.00 5.19
357 363 3.493503 CACTTATTATCGACGCCCCTTTC 59.506 47.826 0.00 0.00 0.00 2.62
358 364 2.825861 TATTATCGACGCCCCTTTCC 57.174 50.000 0.00 0.00 0.00 3.13
909 916 2.508887 GCTCACTCTCGCTGCCTG 60.509 66.667 0.00 0.00 0.00 4.85
911 918 4.074526 TCACTCTCGCTGCCTGCC 62.075 66.667 0.00 0.00 38.78 4.85
915 922 3.602513 CTCTCGCTGCCTGCCACTT 62.603 63.158 0.00 0.00 38.78 3.16
981 989 0.092351 CGTGTACATTTCGTCGGTGC 59.908 55.000 0.00 0.00 0.00 5.01
1170 1183 2.840572 GCCATCCCCATGCATGCA 60.841 61.111 25.04 25.04 0.00 3.96
1171 1184 2.214216 GCCATCCCCATGCATGCAT 61.214 57.895 27.46 27.46 37.08 3.96
1172 1185 1.972198 CCATCCCCATGCATGCATC 59.028 57.895 30.07 0.00 33.90 3.91
1173 1186 1.584495 CATCCCCATGCATGCATCG 59.416 57.895 30.07 23.47 33.90 3.84
1174 1187 2.273179 ATCCCCATGCATGCATCGC 61.273 57.895 30.07 12.44 33.90 4.58
1177 1190 1.897137 CCCATGCATGCATCGCTCT 60.897 57.895 30.07 6.83 33.90 4.09
1180 1193 1.197036 CCATGCATGCATCGCTCTTAG 59.803 52.381 30.07 15.79 33.90 2.18
1183 1196 2.358957 TGCATGCATCGCTCTTAGTTT 58.641 42.857 18.46 0.00 0.00 2.66
1184 1197 2.749076 TGCATGCATCGCTCTTAGTTTT 59.251 40.909 18.46 0.00 0.00 2.43
1185 1198 3.181507 TGCATGCATCGCTCTTAGTTTTC 60.182 43.478 18.46 0.00 0.00 2.29
1186 1199 3.064545 GCATGCATCGCTCTTAGTTTTCT 59.935 43.478 14.21 0.00 0.00 2.52
1187 1200 4.784710 GCATGCATCGCTCTTAGTTTTCTC 60.785 45.833 14.21 0.00 0.00 2.87
1188 1201 3.262420 TGCATCGCTCTTAGTTTTCTCC 58.738 45.455 0.00 0.00 0.00 3.71
1189 1202 2.609916 GCATCGCTCTTAGTTTTCTCCC 59.390 50.000 0.00 0.00 0.00 4.30
1190 1203 3.680196 GCATCGCTCTTAGTTTTCTCCCT 60.680 47.826 0.00 0.00 0.00 4.20
1192 1205 2.496470 TCGCTCTTAGTTTTCTCCCTCC 59.504 50.000 0.00 0.00 0.00 4.30
1195 1208 4.563786 CGCTCTTAGTTTTCTCCCTCCTTT 60.564 45.833 0.00 0.00 0.00 3.11
1196 1209 4.697828 GCTCTTAGTTTTCTCCCTCCTTTG 59.302 45.833 0.00 0.00 0.00 2.77
1198 1211 6.509523 TCTTAGTTTTCTCCCTCCTTTGAA 57.490 37.500 0.00 0.00 0.00 2.69
1199 1212 6.906848 TCTTAGTTTTCTCCCTCCTTTGAAA 58.093 36.000 0.00 0.00 0.00 2.69
1200 1213 7.526918 TCTTAGTTTTCTCCCTCCTTTGAAAT 58.473 34.615 0.00 0.00 0.00 2.17
1202 1215 4.762251 AGTTTTCTCCCTCCTTTGAAATCG 59.238 41.667 0.00 0.00 0.00 3.34
1203 1216 4.367039 TTTCTCCCTCCTTTGAAATCGT 57.633 40.909 0.00 0.00 0.00 3.73
1204 1217 3.334583 TCTCCCTCCTTTGAAATCGTG 57.665 47.619 0.00 0.00 0.00 4.35
1206 1219 3.835978 TCTCCCTCCTTTGAAATCGTGTA 59.164 43.478 0.00 0.00 0.00 2.90
1207 1220 4.081642 TCTCCCTCCTTTGAAATCGTGTAG 60.082 45.833 0.00 0.00 0.00 2.74
1208 1221 2.678336 CCCTCCTTTGAAATCGTGTAGC 59.322 50.000 0.00 0.00 0.00 3.58
1209 1222 2.348666 CCTCCTTTGAAATCGTGTAGCG 59.651 50.000 0.00 0.00 43.01 4.26
1227 1262 2.096799 CGAAGCGAAGGCATGATTTC 57.903 50.000 0.00 0.00 43.41 2.17
1228 1263 1.268234 CGAAGCGAAGGCATGATTTCC 60.268 52.381 0.00 0.00 43.41 3.13
1240 1275 3.679639 GCATGATTTCCTTGGGCGATTTT 60.680 43.478 0.00 0.00 0.00 1.82
1242 1277 2.270923 GATTTCCTTGGGCGATTTTGC 58.729 47.619 0.00 0.00 0.00 3.68
1248 1283 1.876497 TTGGGCGATTTTGCTGAGGC 61.876 55.000 0.00 0.00 39.26 4.70
1250 1285 2.577911 GCGATTTTGCTGAGGCGC 60.578 61.111 0.00 0.00 42.25 6.53
1251 1286 2.276868 CGATTTTGCTGAGGCGCG 60.277 61.111 0.00 0.00 42.25 6.86
1252 1287 2.870372 GATTTTGCTGAGGCGCGT 59.130 55.556 8.43 0.27 42.25 6.01
1253 1288 1.512734 GATTTTGCTGAGGCGCGTG 60.513 57.895 7.63 0.00 42.25 5.34
1254 1289 3.615536 ATTTTGCTGAGGCGCGTGC 62.616 57.895 13.78 13.78 42.25 5.34
1409 3063 2.137810 AGTCAGTGCTCCTCCTACTC 57.862 55.000 0.00 0.00 0.00 2.59
1412 3066 2.092321 GTCAGTGCTCCTCCTACTCCTA 60.092 54.545 0.00 0.00 0.00 2.94
1413 3067 2.092321 TCAGTGCTCCTCCTACTCCTAC 60.092 54.545 0.00 0.00 0.00 3.18
1414 3068 2.092103 CAGTGCTCCTCCTACTCCTACT 60.092 54.545 0.00 0.00 0.00 2.57
1417 3071 2.442502 TGCTCCTCCTACTCCTACTACC 59.557 54.545 0.00 0.00 0.00 3.18
1418 3072 2.442502 GCTCCTCCTACTCCTACTACCA 59.557 54.545 0.00 0.00 0.00 3.25
1447 3101 7.610397 CACATTTCGTGCTACTACAGTATAG 57.390 40.000 0.00 0.00 39.19 1.31
1448 3102 7.194278 CACATTTCGTGCTACTACAGTATAGT 58.806 38.462 0.00 0.00 39.19 2.12
1449 3103 8.340443 CACATTTCGTGCTACTACAGTATAGTA 58.660 37.037 0.00 0.00 39.19 1.82
1450 3104 8.341173 ACATTTCGTGCTACTACAGTATAGTAC 58.659 37.037 0.00 0.00 32.50 2.73
1452 3106 5.896922 CGTGCTACTACAGTATAGTACGT 57.103 43.478 20.09 0.00 46.16 3.57
1453 3107 6.993175 CGTGCTACTACAGTATAGTACGTA 57.007 41.667 20.09 0.00 46.16 3.57
1454 3108 6.802222 CGTGCTACTACAGTATAGTACGTAC 58.198 44.000 18.10 18.10 46.16 3.67
1455 3109 6.397998 CGTGCTACTACAGTATAGTACGTACG 60.398 46.154 19.49 15.01 46.16 3.67
1456 3110 6.418226 GTGCTACTACAGTATAGTACGTACGT 59.582 42.308 25.98 25.98 0.00 3.57
1485 3139 1.323534 GCGTATCTTTGCACGTACTGG 59.676 52.381 0.00 0.00 40.25 4.00
1497 3336 1.410517 ACGTACTGGATGAGGATGCTG 59.589 52.381 0.00 0.00 0.00 4.41
1509 3348 4.062991 TGAGGATGCTGATTGAATGATCG 58.937 43.478 0.00 0.00 0.00 3.69
2176 4055 2.260434 GTTCTCGCTGTACCCGCA 59.740 61.111 5.29 0.00 0.00 5.69
2221 4100 1.686052 CCAGTGAGGCTAAGCTAGAGG 59.314 57.143 0.00 0.00 0.00 3.69
2222 4101 2.383855 CAGTGAGGCTAAGCTAGAGGT 58.616 52.381 0.00 0.00 0.00 3.85
2223 4102 2.763448 CAGTGAGGCTAAGCTAGAGGTT 59.237 50.000 0.00 0.00 39.33 3.50
2224 4103 3.196685 CAGTGAGGCTAAGCTAGAGGTTT 59.803 47.826 0.00 0.00 37.00 3.27
2344 4223 2.706636 GTGTGGTGCACATGACTGT 58.293 52.632 20.43 0.00 46.32 3.55
2493 4376 5.860941 TTATTTGACTGCTCTAGCTAGCT 57.139 39.130 23.12 23.12 43.19 3.32
2494 4377 3.516981 TTTGACTGCTCTAGCTAGCTG 57.483 47.619 27.68 16.48 43.19 4.24
2543 4426 2.511373 CTGCCGATGCTTGCCGTA 60.511 61.111 0.00 0.00 38.71 4.02
2576 4459 4.280929 AGCCCTCTTTGGTTTATTGTGTTC 59.719 41.667 0.00 0.00 0.00 3.18
2628 5975 5.240623 TGTTAAATCTGCAAGGGTACAACTG 59.759 40.000 0.00 0.00 0.00 3.16
2629 5976 1.826385 ATCTGCAAGGGTACAACTGC 58.174 50.000 0.00 0.05 0.00 4.40
2630 5977 0.602638 TCTGCAAGGGTACAACTGCG 60.603 55.000 0.00 0.00 0.00 5.18
2631 5978 0.602638 CTGCAAGGGTACAACTGCGA 60.603 55.000 0.00 0.00 0.00 5.10
2632 5979 0.179043 TGCAAGGGTACAACTGCGAA 60.179 50.000 0.00 0.00 0.00 4.70
2633 5980 0.517316 GCAAGGGTACAACTGCGAAG 59.483 55.000 0.00 0.00 0.00 3.79
2671 6018 2.160417 CCCAGCTTCGACAACATTTCTC 59.840 50.000 0.00 0.00 0.00 2.87
2688 6035 3.124921 CAACACCCGCCACGATCC 61.125 66.667 0.00 0.00 0.00 3.36
2689 6036 3.632080 AACACCCGCCACGATCCA 61.632 61.111 0.00 0.00 0.00 3.41
2690 6037 3.185299 AACACCCGCCACGATCCAA 62.185 57.895 0.00 0.00 0.00 3.53
2691 6038 2.819595 CACCCGCCACGATCCAAG 60.820 66.667 0.00 0.00 0.00 3.61
2770 6117 1.445410 TTGCACCGTCCGATCTTCG 60.445 57.895 0.00 0.00 40.07 3.79
2922 6273 1.348008 CCTGGCCATCCCTCTAAGCA 61.348 60.000 5.51 0.00 0.00 3.91
2928 6279 0.107456 CATCCCTCTAAGCACCGCAT 59.893 55.000 0.00 0.00 0.00 4.73
2949 6301 2.750888 GCGATGAACAACTCCGGCC 61.751 63.158 0.00 0.00 0.00 6.13
2966 6318 3.341629 CATCCCCTGCACCCCACT 61.342 66.667 0.00 0.00 0.00 4.00
2991 6368 6.942005 TCGTAAGATAGATAATGGGTCCGTTA 59.058 38.462 4.36 4.36 45.01 3.18
2992 6369 7.448161 TCGTAAGATAGATAATGGGTCCGTTAA 59.552 37.037 5.85 0.00 45.01 2.01
2993 6370 8.084073 CGTAAGATAGATAATGGGTCCGTTAAA 58.916 37.037 5.85 0.00 43.02 1.52
3024 6411 0.035056 GGCTGCTGCTTCCTCCTAAA 60.035 55.000 15.64 0.00 39.59 1.85
3081 6469 0.318955 AAAAAGTGGCTGACGCATGC 60.319 50.000 7.91 7.91 38.10 4.06
3205 6650 4.446413 CCAGTACACCCGGCGGAC 62.446 72.222 30.79 17.99 0.00 4.79
3206 6651 3.687102 CAGTACACCCGGCGGACA 61.687 66.667 30.79 6.02 0.00 4.02
3207 6652 2.918802 AGTACACCCGGCGGACAA 60.919 61.111 30.79 6.84 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.069090 GAGTGACACGTCTTGCCCA 59.931 57.895 0.00 0.00 0.00 5.36
1 2 2.022129 CGAGTGACACGTCTTGCCC 61.022 63.158 0.00 0.00 0.00 5.36
4 5 0.729478 ATCGCGAGTGACACGTCTTG 60.729 55.000 16.66 0.00 0.00 3.02
5 6 0.454620 GATCGCGAGTGACACGTCTT 60.455 55.000 16.66 0.00 0.00 3.01
6 7 1.134901 GATCGCGAGTGACACGTCT 59.865 57.895 16.66 0.00 0.00 4.18
8 9 0.318360 TTTGATCGCGAGTGACACGT 60.318 50.000 16.66 0.00 0.00 4.49
9 10 0.363512 CTTTGATCGCGAGTGACACG 59.636 55.000 16.66 0.00 0.00 4.49
10 11 0.093705 GCTTTGATCGCGAGTGACAC 59.906 55.000 16.66 0.00 0.00 3.67
11 12 2.445274 GCTTTGATCGCGAGTGACA 58.555 52.632 16.66 9.38 0.00 3.58
30 31 1.855360 GAATCAACTCGCGATCACTCC 59.145 52.381 10.36 0.00 0.00 3.85
39 40 6.663565 AGAAAGAAAGAAAGAATCAACTCGC 58.336 36.000 0.00 0.00 0.00 5.03
52 53 9.401058 AGTCATCAGAAAGAAAGAAAGAAAGAA 57.599 29.630 0.00 0.00 0.00 2.52
53 54 8.970859 AGTCATCAGAAAGAAAGAAAGAAAGA 57.029 30.769 0.00 0.00 0.00 2.52
62 63 7.060518 CGCGATCTATAGTCATCAGAAAGAAAG 59.939 40.741 0.00 0.00 0.00 2.62
63 64 6.858478 CGCGATCTATAGTCATCAGAAAGAAA 59.142 38.462 0.00 0.00 0.00 2.52
66 67 5.932661 TCGCGATCTATAGTCATCAGAAAG 58.067 41.667 3.71 0.00 0.00 2.62
70 71 4.937696 ACTCGCGATCTATAGTCATCAG 57.062 45.455 10.36 0.00 0.00 2.90
74 75 5.690997 AATCAACTCGCGATCTATAGTCA 57.309 39.130 10.36 0.00 0.00 3.41
75 76 6.994868 AAAATCAACTCGCGATCTATAGTC 57.005 37.500 10.36 0.00 0.00 2.59
76 77 7.381678 GGTAAAAATCAACTCGCGATCTATAGT 59.618 37.037 10.36 0.00 0.00 2.12
77 78 7.381408 TGGTAAAAATCAACTCGCGATCTATAG 59.619 37.037 10.36 0.00 0.00 1.31
78 79 7.168637 GTGGTAAAAATCAACTCGCGATCTATA 59.831 37.037 10.36 0.00 0.00 1.31
79 80 6.018994 GTGGTAAAAATCAACTCGCGATCTAT 60.019 38.462 10.36 0.00 0.00 1.98
102 103 2.223803 AGTAGGAGTGGAGTGGAGTG 57.776 55.000 0.00 0.00 0.00 3.51
108 109 2.379226 ACCTGTGTAGTAGGAGTGGAGT 59.621 50.000 0.00 0.00 38.71 3.85
109 110 3.018149 GACCTGTGTAGTAGGAGTGGAG 58.982 54.545 0.00 0.00 38.71 3.86
110 111 2.617276 CGACCTGTGTAGTAGGAGTGGA 60.617 54.545 0.00 0.00 38.71 4.02
111 112 1.743958 CGACCTGTGTAGTAGGAGTGG 59.256 57.143 0.00 0.00 38.71 4.00
112 113 2.419324 GACGACCTGTGTAGTAGGAGTG 59.581 54.545 0.00 0.00 38.71 3.51
113 114 2.617532 GGACGACCTGTGTAGTAGGAGT 60.618 54.545 0.00 0.00 38.71 3.85
114 115 2.015587 GGACGACCTGTGTAGTAGGAG 58.984 57.143 0.00 0.00 38.71 3.69
115 116 1.352017 TGGACGACCTGTGTAGTAGGA 59.648 52.381 5.33 0.00 38.71 2.94
116 117 1.743958 CTGGACGACCTGTGTAGTAGG 59.256 57.143 5.33 0.00 41.22 3.18
117 118 2.434428 ACTGGACGACCTGTGTAGTAG 58.566 52.381 14.97 0.00 44.59 2.57
118 119 2.555325 CAACTGGACGACCTGTGTAGTA 59.445 50.000 16.24 0.00 45.33 1.82
149 150 3.839353 GAGGGCAGTGCAGTGCAGT 62.839 63.158 39.34 28.62 45.93 4.40
150 151 3.054503 GAGGGCAGTGCAGTGCAG 61.055 66.667 39.34 9.23 45.93 4.41
151 152 3.563224 AGAGGGCAGTGCAGTGCA 61.563 61.111 39.34 15.37 45.93 4.57
152 153 3.054503 CAGAGGGCAGTGCAGTGC 61.055 66.667 33.86 33.86 43.19 4.40
179 180 2.014554 ACGACGTGCTACAACTGCG 61.015 57.895 0.00 0.00 0.00 5.18
193 194 0.316196 GTTGTCTGCTGTTGCACGAC 60.316 55.000 0.00 11.02 45.31 4.34
255 261 0.249114 TCTTGCAAGTACACGCACGA 60.249 50.000 25.19 9.59 38.00 4.35
259 265 3.289076 GTTCTTTCTTGCAAGTACACGC 58.711 45.455 25.19 10.03 0.00 5.34
260 266 3.531982 CGTTCTTTCTTGCAAGTACACG 58.468 45.455 25.19 20.76 0.00 4.49
261 267 3.242608 TGCGTTCTTTCTTGCAAGTACAC 60.243 43.478 25.19 14.45 33.80 2.90
262 268 2.939756 TGCGTTCTTTCTTGCAAGTACA 59.060 40.909 25.19 8.81 33.80 2.90
263 269 3.545633 CTGCGTTCTTTCTTGCAAGTAC 58.454 45.455 25.19 14.77 36.82 2.73
265 271 1.268743 GCTGCGTTCTTTCTTGCAAGT 60.269 47.619 25.19 0.00 36.82 3.16
266 272 1.402511 GCTGCGTTCTTTCTTGCAAG 58.597 50.000 20.81 20.81 36.82 4.01
267 273 0.316937 CGCTGCGTTCTTTCTTGCAA 60.317 50.000 14.93 0.00 36.82 4.08
268 274 1.279539 CGCTGCGTTCTTTCTTGCA 59.720 52.632 14.93 0.00 35.75 4.08
269 275 2.077198 GCGCTGCGTTCTTTCTTGC 61.077 57.895 24.04 0.00 0.00 4.01
270 276 0.110056 ATGCGCTGCGTTCTTTCTTG 60.110 50.000 24.04 0.00 0.00 3.02
271 277 0.166814 GATGCGCTGCGTTCTTTCTT 59.833 50.000 24.04 3.61 0.00 2.52
272 278 0.950555 TGATGCGCTGCGTTCTTTCT 60.951 50.000 24.04 0.60 0.00 2.52
273 279 0.097674 ATGATGCGCTGCGTTCTTTC 59.902 50.000 24.04 13.06 0.00 2.62
274 280 0.179181 CATGATGCGCTGCGTTCTTT 60.179 50.000 24.04 9.84 0.00 2.52
332 338 2.132762 GGGCGTCGATAATAAGTGGTG 58.867 52.381 0.00 0.00 0.00 4.17
868 874 2.310233 CGGTTGGCGACACAGACAG 61.310 63.158 7.28 0.00 42.67 3.51
909 916 0.971447 ACCGGAGTAGGAGAAGTGGC 60.971 60.000 9.46 0.00 34.73 5.01
911 918 0.818296 CCACCGGAGTAGGAGAAGTG 59.182 60.000 9.46 0.00 34.73 3.16
915 922 1.000019 CCACCACCGGAGTAGGAGA 60.000 63.158 9.46 0.00 34.73 3.71
967 975 1.070786 ACCAGCACCGACGAAATGT 59.929 52.632 0.00 0.00 0.00 2.71
1158 1171 2.910479 AGCGATGCATGCATGGGG 60.910 61.111 36.73 24.39 36.70 4.96
1170 1183 3.133183 GGAGGGAGAAAACTAAGAGCGAT 59.867 47.826 0.00 0.00 0.00 4.58
1171 1184 2.496470 GGAGGGAGAAAACTAAGAGCGA 59.504 50.000 0.00 0.00 0.00 4.93
1172 1185 2.498078 AGGAGGGAGAAAACTAAGAGCG 59.502 50.000 0.00 0.00 0.00 5.03
1173 1186 4.561500 AAGGAGGGAGAAAACTAAGAGC 57.438 45.455 0.00 0.00 0.00 4.09
1174 1187 6.115448 TCAAAGGAGGGAGAAAACTAAGAG 57.885 41.667 0.00 0.00 0.00 2.85
1177 1190 6.430000 CGATTTCAAAGGAGGGAGAAAACTAA 59.570 38.462 0.00 0.00 34.13 2.24
1180 1193 4.519350 ACGATTTCAAAGGAGGGAGAAAAC 59.481 41.667 0.00 0.00 34.13 2.43
1183 1196 3.072476 ACACGATTTCAAAGGAGGGAGAA 59.928 43.478 0.00 0.00 0.00 2.87
1184 1197 2.637872 ACACGATTTCAAAGGAGGGAGA 59.362 45.455 0.00 0.00 0.00 3.71
1185 1198 3.059352 ACACGATTTCAAAGGAGGGAG 57.941 47.619 0.00 0.00 0.00 4.30
1186 1199 3.618997 GCTACACGATTTCAAAGGAGGGA 60.619 47.826 0.00 0.00 0.00 4.20
1187 1200 2.678336 GCTACACGATTTCAAAGGAGGG 59.322 50.000 0.00 0.00 0.00 4.30
1202 1215 1.084370 ATGCCTTCGCTTCGCTACAC 61.084 55.000 0.00 0.00 35.36 2.90
1203 1216 1.083806 CATGCCTTCGCTTCGCTACA 61.084 55.000 0.00 0.00 35.36 2.74
1204 1217 0.806102 TCATGCCTTCGCTTCGCTAC 60.806 55.000 0.00 0.00 35.36 3.58
1206 1219 0.745845 AATCATGCCTTCGCTTCGCT 60.746 50.000 0.00 0.00 35.36 4.93
1207 1220 0.099436 AAATCATGCCTTCGCTTCGC 59.901 50.000 0.00 0.00 35.36 4.70
1208 1221 1.268234 GGAAATCATGCCTTCGCTTCG 60.268 52.381 0.00 0.00 35.36 3.79
1209 1222 2.019984 AGGAAATCATGCCTTCGCTTC 58.980 47.619 0.00 0.00 35.36 3.86
1210 1223 2.134789 AGGAAATCATGCCTTCGCTT 57.865 45.000 0.00 0.00 35.36 4.68
1214 1227 1.137675 GCCCAAGGAAATCATGCCTTC 59.862 52.381 0.00 0.00 42.41 3.46
1216 1229 1.039233 CGCCCAAGGAAATCATGCCT 61.039 55.000 0.00 0.00 35.61 4.75
1218 1231 1.035139 ATCGCCCAAGGAAATCATGC 58.965 50.000 0.00 0.00 0.00 4.06
1220 1233 3.679639 GCAAAATCGCCCAAGGAAATCAT 60.680 43.478 0.00 0.00 0.00 2.45
1222 1257 2.094026 AGCAAAATCGCCCAAGGAAATC 60.094 45.455 0.00 0.00 0.00 2.17
1223 1258 1.901833 AGCAAAATCGCCCAAGGAAAT 59.098 42.857 0.00 0.00 0.00 2.17
1227 1262 0.171903 CTCAGCAAAATCGCCCAAGG 59.828 55.000 0.00 0.00 0.00 3.61
1228 1263 0.171903 CCTCAGCAAAATCGCCCAAG 59.828 55.000 0.00 0.00 0.00 3.61
1250 1285 2.979676 TTCAGCCCTGCAAGCACG 60.980 61.111 10.73 2.05 0.00 5.34
1251 1286 2.647297 GTTCAGCCCTGCAAGCAC 59.353 61.111 10.73 0.00 0.00 4.40
1252 1287 2.598394 GGTTCAGCCCTGCAAGCA 60.598 61.111 10.73 0.00 0.00 3.91
1253 1288 3.741476 CGGTTCAGCCCTGCAAGC 61.741 66.667 0.04 0.04 0.00 4.01
1254 1289 3.058160 CCGGTTCAGCCCTGCAAG 61.058 66.667 0.00 0.00 0.00 4.01
1255 1290 3.884774 ACCGGTTCAGCCCTGCAA 61.885 61.111 0.00 0.00 0.00 4.08
1409 3063 7.000575 CACGAAATGTGTTAATGGTAGTAGG 57.999 40.000 0.00 0.00 43.88 3.18
1458 3112 0.986270 TGCAAAGATACGCACGTACG 59.014 50.000 15.01 15.01 39.50 3.67
1482 3136 3.487120 TCAATCAGCATCCTCATCCAG 57.513 47.619 0.00 0.00 0.00 3.86
1485 3139 5.163844 CGATCATTCAATCAGCATCCTCATC 60.164 44.000 0.00 0.00 0.00 2.92
1509 3348 4.904154 GCTTAATAAATGGCATCGTTCGTC 59.096 41.667 0.00 0.00 0.00 4.20
1581 3420 0.098200 TCGAGCACCACGATAGAACG 59.902 55.000 0.00 0.00 41.38 3.95
2221 4100 3.724295 CTAGGCGAGCTACAAACAAAC 57.276 47.619 0.00 0.00 0.00 2.93
2291 4170 4.360027 CGCGGACGCATGCATAGC 62.360 66.667 19.57 15.42 42.06 2.97
2350 4229 1.599518 GGCAACACACGACATGGGA 60.600 57.895 0.00 0.00 34.14 4.37
2352 4231 2.250939 ACGGCAACACACGACATGG 61.251 57.895 0.00 0.00 0.00 3.66
2476 4359 2.136298 ACAGCTAGCTAGAGCAGTCA 57.864 50.000 25.15 0.00 45.43 3.41
2493 4376 4.333690 GTGTCCTGTCCTAGACTTCTACA 58.666 47.826 0.00 0.00 34.02 2.74
2494 4377 3.374678 CGTGTCCTGTCCTAGACTTCTAC 59.625 52.174 0.00 0.00 34.02 2.59
2495 4378 3.607741 CGTGTCCTGTCCTAGACTTCTA 58.392 50.000 0.00 0.00 34.02 2.10
2496 4379 2.438411 CGTGTCCTGTCCTAGACTTCT 58.562 52.381 0.00 0.00 34.02 2.85
2497 4380 1.473278 CCGTGTCCTGTCCTAGACTTC 59.527 57.143 0.00 0.00 34.02 3.01
2498 4381 1.546961 CCGTGTCCTGTCCTAGACTT 58.453 55.000 0.00 0.00 34.02 3.01
2543 4426 1.548269 CAAAGAGGGCTCGAGAAGTCT 59.452 52.381 18.75 10.72 34.09 3.24
2576 4459 4.824301 TGAAAAGTAAGCAAACGTACACG 58.176 39.130 0.00 0.00 46.33 4.49
2628 5975 2.551270 CTGTGTTGTCGCCTTCGC 59.449 61.111 0.00 0.00 35.26 4.70
2629 5976 2.243957 TGCTGTGTTGTCGCCTTCG 61.244 57.895 0.00 0.00 0.00 3.79
2630 5977 1.279840 GTGCTGTGTTGTCGCCTTC 59.720 57.895 0.00 0.00 0.00 3.46
2631 5978 2.534019 CGTGCTGTGTTGTCGCCTT 61.534 57.895 0.00 0.00 0.00 4.35
2632 5979 2.967076 CGTGCTGTGTTGTCGCCT 60.967 61.111 0.00 0.00 0.00 5.52
2633 5980 4.666532 GCGTGCTGTGTTGTCGCC 62.667 66.667 0.00 0.00 40.83 5.54
2671 6018 3.124921 GGATCGTGGCGGGTGTTG 61.125 66.667 0.00 0.00 0.00 3.33
2688 6035 2.224426 TGGTAGGGTGTGTACTTGCTTG 60.224 50.000 0.00 0.00 0.00 4.01
2689 6036 2.051692 TGGTAGGGTGTGTACTTGCTT 58.948 47.619 0.00 0.00 0.00 3.91
2690 6037 1.724545 TGGTAGGGTGTGTACTTGCT 58.275 50.000 0.00 0.00 0.00 3.91
2691 6038 2.781681 ATGGTAGGGTGTGTACTTGC 57.218 50.000 0.00 0.00 0.00 4.01
2770 6117 5.048713 CCAGACCTATTTTCAACTGTTGGAC 60.049 44.000 19.55 3.37 0.00 4.02
2928 6279 0.389817 CCGGAGTTGTTCATCGCTGA 60.390 55.000 0.00 0.00 0.00 4.26
2949 6301 3.341629 AGTGGGGTGCAGGGGATG 61.342 66.667 0.00 0.00 0.00 3.51
2966 6318 5.319453 ACGGACCCATTATCTATCTTACGA 58.681 41.667 0.00 0.00 0.00 3.43
2991 6368 3.069158 GCAGCAGCCCAATGATCTATTTT 59.931 43.478 0.00 0.00 33.58 1.82
2992 6369 2.626743 GCAGCAGCCCAATGATCTATTT 59.373 45.455 0.00 0.00 33.58 1.40
2993 6370 2.158505 AGCAGCAGCCCAATGATCTATT 60.159 45.455 0.00 0.00 43.56 1.73
3024 6411 3.173965 TCACCGGAGAAGAAGAATCCTT 58.826 45.455 9.46 0.00 34.81 3.36
3128 6573 1.139989 CGGGCATCACATATGACGAC 58.860 55.000 10.38 0.00 37.79 4.34


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

AutoCloner maintained by Alex Coulton.