Multiple sequence alignment - TraesCS2B01G009100

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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 TraesCS2B01G009100 chr2B 100.000 3684 0 0 1 3684 5043778 5040095 0.000000e+00 6804.0
1 TraesCS2B01G009100 chr2B 91.641 1651 111 12 1902 3537 5335623 5333985 0.000000e+00 2259.0
2 TraesCS2B01G009100 chr2D 93.889 1980 104 4 1706 3677 6206332 6208302 0.000000e+00 2970.0
3 TraesCS2B01G009100 chr2D 90.591 1201 40 28 14 1161 6204517 6205697 0.000000e+00 1524.0
4 TraesCS2B01G009100 chr2D 96.970 363 11 0 1318 1680 6205694 6206056 8.750000e-171 610.0
5 TraesCS2B01G009100 chr2D 93.293 164 11 0 1156 1319 362930971 362930808 3.680000e-60 243.0
6 TraesCS2B01G009100 chr5A 81.970 599 80 20 549 1147 640400304 640400874 1.990000e-132 483.0
7 TraesCS2B01G009100 chr5A 79.886 701 85 30 2354 3042 640403407 640404063 2.590000e-126 462.0
8 TraesCS2B01G009100 chr5A 89.773 264 27 0 1407 1670 640401596 640401859 4.560000e-89 339.0
9 TraesCS2B01G009100 chr5B 80.201 596 86 22 2435 3016 702757677 702757100 5.690000e-113 418.0
10 TraesCS2B01G009100 chr5B 80.067 597 85 24 2435 3016 702644587 702644010 2.650000e-111 412.0
11 TraesCS2B01G009100 chr5B 79.128 642 98 24 2435 3060 702606800 702606179 9.520000e-111 411.0
12 TraesCS2B01G009100 chr5B 79.128 642 98 22 2435 3060 702739394 702738773 9.520000e-111 411.0
13 TraesCS2B01G009100 chr5B 79.698 596 89 21 2435 3016 702625437 702624860 5.730000e-108 401.0
14 TraesCS2B01G009100 chr5B 79.698 596 89 20 2435 3016 702796231 702795654 5.730000e-108 401.0
15 TraesCS2B01G009100 chr5B 91.566 249 21 0 1404 1652 702607969 702607721 9.790000e-91 344.0
16 TraesCS2B01G009100 chr5B 91.165 249 22 0 1404 1652 702797323 702797075 4.560000e-89 339.0
17 TraesCS2B01G009100 chr5B 90.763 249 23 0 1404 1652 702740570 702740322 2.120000e-87 333.0
18 TraesCS2B01G009100 chr5B 90.763 249 23 0 1404 1652 702758757 702758509 2.120000e-87 333.0
19 TraesCS2B01G009100 chr5B 85.882 170 21 2 1936 2105 702607253 702607087 1.050000e-40 178.0
20 TraesCS2B01G009100 chr5B 85.549 173 19 5 1936 2105 702645043 702644874 3.780000e-40 176.0
21 TraesCS2B01G009100 chr5B 85.549 173 19 5 1936 2105 702796687 702796518 3.780000e-40 176.0
22 TraesCS2B01G009100 chr5B 89.209 139 12 2 1936 2074 702625885 702625750 1.760000e-38 171.0
23 TraesCS2B01G009100 chr5B 89.209 139 12 2 1936 2074 702758125 702757990 1.760000e-38 171.0
24 TraesCS2B01G009100 chrUn 78.519 675 102 23 2400 3055 110464998 110465648 1.590000e-108 403.0
25 TraesCS2B01G009100 chrUn 87.823 271 33 0 1401 1671 224673465 224673735 5.940000e-83 318.0
26 TraesCS2B01G009100 chrUn 89.062 256 28 0 1416 1671 340347148 340346893 5.940000e-83 318.0
27 TraesCS2B01G009100 chrUn 87.823 271 33 0 1401 1671 351702987 351703257 5.940000e-83 318.0
28 TraesCS2B01G009100 chrUn 86.561 253 26 2 236 488 224672306 224672550 4.690000e-69 272.0
29 TraesCS2B01G009100 chrUn 88.444 225 26 0 264 488 340348302 340348078 4.690000e-69 272.0
30 TraesCS2B01G009100 chrUn 86.166 253 27 2 236 488 327006599 327006843 2.180000e-67 267.0
31 TraesCS2B01G009100 chrUn 89.600 125 13 0 1950 2074 110464560 110464684 3.810000e-35 159.0
32 TraesCS2B01G009100 chrUn 83.871 155 25 0 992 1146 224673174 224673328 8.240000e-32 148.0
33 TraesCS2B01G009100 chrUn 84.211 152 24 0 995 1146 340347451 340347300 8.240000e-32 148.0
34 TraesCS2B01G009100 chrUn 83.871 155 25 0 992 1146 351702696 351702850 8.240000e-32 148.0
35 TraesCS2B01G009100 chrUn 83.871 155 25 0 992 1146 351725196 351725350 8.240000e-32 148.0
36 TraesCS2B01G009100 chrUn 84.211 152 24 0 995 1146 407255765 407255614 8.240000e-32 148.0
37 TraesCS2B01G009100 chr4A 87.352 253 24 2 236 488 629110455 629110699 2.170000e-72 283.0
38 TraesCS2B01G009100 chr4A 89.529 191 18 2 1147 1336 517406643 517406454 1.320000e-59 241.0
39 TraesCS2B01G009100 chr4A 90.909 176 14 2 1153 1326 671507018 671507193 6.150000e-58 235.0
40 TraesCS2B01G009100 chr4A 83.974 156 25 0 992 1147 629118415 629118570 2.290000e-32 150.0
41 TraesCS2B01G009100 chr4B 80.682 352 60 7 551 898 660489793 660490140 2.180000e-67 267.0
42 TraesCS2B01G009100 chr4B 94.152 171 9 1 1151 1320 664170929 664170759 3.650000e-65 259.0
43 TraesCS2B01G009100 chr4B 94.512 164 9 0 1157 1320 93739381 93739218 1.700000e-63 254.0
44 TraesCS2B01G009100 chr4B 87.671 146 15 3 1928 2073 660491297 660491439 2.280000e-37 167.0
45 TraesCS2B01G009100 chr7B 93.939 165 10 0 1157 1321 384970820 384970656 2.200000e-62 250.0
46 TraesCS2B01G009100 chr7B 91.813 171 14 0 1150 1320 114143494 114143324 4.750000e-59 239.0
47 TraesCS2B01G009100 chr6B 93.865 163 10 0 1158 1320 720912056 720912218 2.840000e-61 246.0
48 TraesCS2B01G009100 chr6B 82.353 68 5 6 1292 1355 688866012 688866076 7.000000e-03 52.8
49 TraesCS2B01G009100 chr1B 91.860 172 13 1 1158 1329 414091029 414090859 4.750000e-59 239.0


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 TraesCS2B01G009100 chr2B 5040095 5043778 3683 True 6804.000000 6804 100.000000 1 3684 1 chr2B.!!$R1 3683
1 TraesCS2B01G009100 chr2B 5333985 5335623 1638 True 2259.000000 2259 91.641000 1902 3537 1 chr2B.!!$R2 1635
2 TraesCS2B01G009100 chr2D 6204517 6208302 3785 False 1701.333333 2970 93.816667 14 3677 3 chr2D.!!$F1 3663
3 TraesCS2B01G009100 chr5A 640400304 640404063 3759 False 428.000000 483 83.876333 549 3042 3 chr5A.!!$F1 2493
4 TraesCS2B01G009100 chr5B 702738773 702740570 1797 True 372.000000 411 84.945500 1404 3060 2 chr5B.!!$R4 1656
5 TraesCS2B01G009100 chr5B 702606179 702607969 1790 True 311.000000 411 85.525333 1404 3060 3 chr5B.!!$R1 1656
6 TraesCS2B01G009100 chr5B 702757100 702758757 1657 True 307.333333 418 86.724333 1404 3016 3 chr5B.!!$R5 1612
7 TraesCS2B01G009100 chr5B 702795654 702797323 1669 True 305.333333 401 85.470667 1404 3016 3 chr5B.!!$R6 1612
8 TraesCS2B01G009100 chr5B 702644010 702645043 1033 True 294.000000 412 82.808000 1936 3016 2 chr5B.!!$R3 1080
9 TraesCS2B01G009100 chr5B 702624860 702625885 1025 True 286.000000 401 84.453500 1936 3016 2 chr5B.!!$R2 1080
10 TraesCS2B01G009100 chrUn 110464560 110465648 1088 False 281.000000 403 84.059500 1950 3055 2 chrUn.!!$F3 1105
11 TraesCS2B01G009100 chrUn 224672306 224673735 1429 False 246.000000 318 86.085000 236 1671 3 chrUn.!!$F4 1435
12 TraesCS2B01G009100 chrUn 340346893 340348302 1409 True 246.000000 318 87.239000 264 1671 3 chrUn.!!$R2 1407
13 TraesCS2B01G009100 chrUn 351702696 351703257 561 False 233.000000 318 85.847000 992 1671 2 chrUn.!!$F5 679
14 TraesCS2B01G009100 chr4B 660489793 660491439 1646 False 217.000000 267 84.176500 551 2073 2 chr4B.!!$F1 1522

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
927 1060 0.032813 CCATCCCCTTCCTGCAATGT 60.033 55.0 0.0 0.0 0.00 2.71 F
1675 2646 0.322546 GCTCCAGGTTGGTTGGTAGG 60.323 60.0 0.0 0.0 39.03 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 4149 1.538512 GTTTTGCATGCAGCTCTCAGA 59.461 47.619 21.5 0.0 45.94 3.27 R
3491 5879 0.888619 TGTACTCTGGTCCAAGAGCG 59.111 55.000 14.7 0.0 46.46 5.03 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
52 53 1.468520 CATTACCTGCCCTGACAAACG 59.531 52.381 0.00 0.00 0.00 3.60
84 85 1.067212 CGATACCAGCCAGACACCTAC 59.933 57.143 0.00 0.00 0.00 3.18
86 87 0.412244 TACCAGCCAGACACCTACCT 59.588 55.000 0.00 0.00 0.00 3.08
87 88 0.412244 ACCAGCCAGACACCTACCTA 59.588 55.000 0.00 0.00 0.00 3.08
90 91 2.093447 CCAGCCAGACACCTACCTAAAG 60.093 54.545 0.00 0.00 0.00 1.85
91 92 2.567615 CAGCCAGACACCTACCTAAAGT 59.432 50.000 0.00 0.00 0.00 2.66
92 93 3.767673 CAGCCAGACACCTACCTAAAGTA 59.232 47.826 0.00 0.00 0.00 2.24
93 94 4.024670 AGCCAGACACCTACCTAAAGTAG 58.975 47.826 0.00 0.00 46.99 2.57
94 95 3.768215 GCCAGACACCTACCTAAAGTAGT 59.232 47.826 0.00 0.00 46.15 2.73
113 114 9.617975 AAAGTAGTTAATAGAAGTCACACGTAC 57.382 33.333 0.00 0.00 0.00 3.67
114 115 7.459486 AGTAGTTAATAGAAGTCACACGTACG 58.541 38.462 15.01 15.01 0.00 3.67
115 116 6.246420 AGTTAATAGAAGTCACACGTACGT 57.754 37.500 16.72 16.72 0.00 3.57
116 117 6.310197 AGTTAATAGAAGTCACACGTACGTC 58.690 40.000 19.94 7.38 0.00 4.34
118 119 2.396160 AGAAGTCACACGTACGTCAC 57.604 50.000 19.94 15.03 0.00 3.67
119 120 1.002033 AGAAGTCACACGTACGTCACC 60.002 52.381 19.94 6.85 0.00 4.02
120 121 1.002033 GAAGTCACACGTACGTCACCT 60.002 52.381 19.94 9.15 0.00 4.00
121 122 1.882912 AGTCACACGTACGTCACCTA 58.117 50.000 19.94 0.00 0.00 3.08
122 123 2.430465 AGTCACACGTACGTCACCTAT 58.570 47.619 19.94 0.01 0.00 2.57
123 124 2.161012 AGTCACACGTACGTCACCTATG 59.839 50.000 19.94 8.13 0.00 2.23
124 125 2.160219 GTCACACGTACGTCACCTATGA 59.840 50.000 19.94 12.11 0.00 2.15
125 126 2.813172 TCACACGTACGTCACCTATGAA 59.187 45.455 19.94 0.00 36.31 2.57
126 127 3.441222 TCACACGTACGTCACCTATGAAT 59.559 43.478 19.94 0.00 36.31 2.57
127 128 4.082625 TCACACGTACGTCACCTATGAATT 60.083 41.667 19.94 0.00 36.31 2.17
135 136 7.593644 CGTACGTCACCTATGAATTAATCATCA 59.406 37.037 7.22 0.00 45.91 3.07
216 230 3.243234 CCAACAATCCGCACACAACTAAA 60.243 43.478 0.00 0.00 0.00 1.85
217 231 3.619233 ACAATCCGCACACAACTAAAC 57.381 42.857 0.00 0.00 0.00 2.01
218 232 2.292292 ACAATCCGCACACAACTAAACC 59.708 45.455 0.00 0.00 0.00 3.27
220 234 1.301423 TCCGCACACAACTAAACCAC 58.699 50.000 0.00 0.00 0.00 4.16
221 235 1.018148 CCGCACACAACTAAACCACA 58.982 50.000 0.00 0.00 0.00 4.17
223 237 1.268335 CGCACACAACTAAACCACACC 60.268 52.381 0.00 0.00 0.00 4.16
225 239 1.679153 CACACAACTAAACCACACCCC 59.321 52.381 0.00 0.00 0.00 4.95
226 240 1.567175 ACACAACTAAACCACACCCCT 59.433 47.619 0.00 0.00 0.00 4.79
642 720 0.255033 AGCCCAACCGGTTTATCCTC 59.745 55.000 19.55 3.94 0.00 3.71
751 829 2.009774 CCATCCACAAGTTCATCCGTC 58.990 52.381 0.00 0.00 0.00 4.79
867 945 4.373116 ATGCCCAGCGTCGACGTT 62.373 61.111 35.48 29.35 42.22 3.99
915 1048 2.054453 GCCTTGTTGCTCCATCCCC 61.054 63.158 0.00 0.00 0.00 4.81
926 1059 0.259647 TCCATCCCCTTCCTGCAATG 59.740 55.000 0.00 0.00 0.00 2.82
927 1060 0.032813 CCATCCCCTTCCTGCAATGT 60.033 55.000 0.00 0.00 0.00 2.71
928 1061 1.620524 CCATCCCCTTCCTGCAATGTT 60.621 52.381 0.00 0.00 0.00 2.71
929 1062 1.753073 CATCCCCTTCCTGCAATGTTC 59.247 52.381 0.00 0.00 0.00 3.18
1017 1188 2.380084 TTATGTTCGAGCTGGTGACC 57.620 50.000 0.00 0.00 0.00 4.02
1062 1233 0.979665 CAAAGTCCAGGGAGCTGAGA 59.020 55.000 0.00 0.00 0.00 3.27
1104 1275 1.793994 AGGGCTCTTCTCCTTCCCT 59.206 57.895 0.00 0.00 42.25 4.20
1156 1327 6.036083 CCGATGCATGCAGGTATATAAACTAC 59.964 42.308 26.69 0.00 0.00 2.73
1159 1330 9.088512 GATGCATGCAGGTATATAAACTACTAC 57.911 37.037 26.69 0.00 0.00 2.73
1160 1331 8.190326 TGCATGCAGGTATATAAACTACTACT 57.810 34.615 18.46 0.00 0.00 2.57
1161 1332 8.304596 TGCATGCAGGTATATAAACTACTACTC 58.695 37.037 18.46 0.00 0.00 2.59
1162 1333 8.524487 GCATGCAGGTATATAAACTACTACTCT 58.476 37.037 14.21 0.00 0.00 3.24
1168 1339 8.879227 AGGTATATAAACTACTACTCTCTCCGT 58.121 37.037 0.00 0.00 0.00 4.69
1174 1345 5.690464 ACTACTACTCTCTCCGTTCCTAA 57.310 43.478 0.00 0.00 0.00 2.69
1175 1346 6.059787 ACTACTACTCTCTCCGTTCCTAAA 57.940 41.667 0.00 0.00 0.00 1.85
1177 1348 5.838531 ACTACTCTCTCCGTTCCTAAATG 57.161 43.478 0.00 0.00 0.00 2.32
1178 1349 5.262804 ACTACTCTCTCCGTTCCTAAATGT 58.737 41.667 0.00 0.00 0.00 2.71
1179 1350 6.421485 ACTACTCTCTCCGTTCCTAAATGTA 58.579 40.000 0.00 0.00 0.00 2.29
1180 1351 6.888632 ACTACTCTCTCCGTTCCTAAATGTAA 59.111 38.462 0.00 0.00 0.00 2.41
1181 1352 6.210287 ACTCTCTCCGTTCCTAAATGTAAG 57.790 41.667 0.00 0.00 0.00 2.34
1182 1353 5.715753 ACTCTCTCCGTTCCTAAATGTAAGT 59.284 40.000 0.00 0.00 0.00 2.24
1184 1355 5.126707 TCTCTCCGTTCCTAAATGTAAGTCC 59.873 44.000 0.00 0.00 0.00 3.85
1186 1357 5.482878 TCTCCGTTCCTAAATGTAAGTCCTT 59.517 40.000 0.00 0.00 0.00 3.36
1190 1361 7.820872 TCCGTTCCTAAATGTAAGTCCTTTTAG 59.179 37.037 0.00 0.00 34.38 1.85
1215 1386 9.856488 AGATATTACACTACAAACTATATGCGG 57.144 33.333 0.00 0.00 0.00 5.69
1221 1392 7.667557 ACACTACAAACTATATGCGGATGTAT 58.332 34.615 0.00 0.00 0.00 2.29
1222 1393 8.799367 ACACTACAAACTATATGCGGATGTATA 58.201 33.333 0.00 0.00 0.00 1.47
1223 1394 9.803315 CACTACAAACTATATGCGGATGTATAT 57.197 33.333 0.00 0.00 37.23 0.86
1261 2096 7.093322 AGTGTAGATTCATTCATTTTGCTCC 57.907 36.000 0.00 0.00 0.00 4.70
1262 2097 5.967674 GTGTAGATTCATTCATTTTGCTCCG 59.032 40.000 0.00 0.00 0.00 4.63
1265 2100 6.949352 AGATTCATTCATTTTGCTCCGTAT 57.051 33.333 0.00 0.00 0.00 3.06
1266 2101 6.732154 AGATTCATTCATTTTGCTCCGTATG 58.268 36.000 0.00 0.00 0.00 2.39
1269 2104 6.603237 TCATTCATTTTGCTCCGTATGTAG 57.397 37.500 0.00 0.00 0.00 2.74
1271 2106 6.257849 TCATTCATTTTGCTCCGTATGTAGAC 59.742 38.462 0.00 0.00 0.00 2.59
1272 2107 4.439057 TCATTTTGCTCCGTATGTAGACC 58.561 43.478 0.00 0.00 0.00 3.85
1273 2108 3.965379 TTTTGCTCCGTATGTAGACCA 57.035 42.857 0.00 0.00 0.00 4.02
1274 2109 4.481368 TTTTGCTCCGTATGTAGACCAT 57.519 40.909 0.00 0.00 37.58 3.55
1276 2111 4.848562 TTGCTCCGTATGTAGACCATAG 57.151 45.455 0.00 0.00 36.71 2.23
1277 2112 3.828921 TGCTCCGTATGTAGACCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
1278 2113 3.568430 TGCTCCGTATGTAGACCATAGTG 59.432 47.826 0.00 0.00 36.71 2.74
1279 2114 3.057456 GCTCCGTATGTAGACCATAGTGG 60.057 52.174 0.00 0.00 45.02 4.00
1282 2117 5.391256 TCCGTATGTAGACCATAGTGGAAT 58.609 41.667 2.45 0.00 40.96 3.01
1283 2118 5.475909 TCCGTATGTAGACCATAGTGGAATC 59.524 44.000 2.45 0.00 40.96 2.52
1284 2119 5.477291 CCGTATGTAGACCATAGTGGAATCT 59.523 44.000 2.45 0.00 40.96 2.40
1285 2120 6.349445 CCGTATGTAGACCATAGTGGAATCTC 60.349 46.154 2.45 0.00 40.96 2.75
1286 2121 6.431543 CGTATGTAGACCATAGTGGAATCTCT 59.568 42.308 2.45 0.00 40.96 3.10
1287 2122 7.606839 CGTATGTAGACCATAGTGGAATCTCTA 59.393 40.741 2.45 0.00 40.96 2.43
1288 2123 9.298250 GTATGTAGACCATAGTGGAATCTCTAA 57.702 37.037 2.45 0.00 40.96 2.10
1289 2124 8.783660 ATGTAGACCATAGTGGAATCTCTAAA 57.216 34.615 2.45 0.00 40.96 1.85
1290 2125 8.603898 TGTAGACCATAGTGGAATCTCTAAAA 57.396 34.615 2.45 0.00 40.96 1.52
1291 2126 9.042450 TGTAGACCATAGTGGAATCTCTAAAAA 57.958 33.333 2.45 0.00 40.96 1.94
1292 2127 9.535878 GTAGACCATAGTGGAATCTCTAAAAAG 57.464 37.037 2.45 0.00 40.96 2.27
1293 2128 8.380742 AGACCATAGTGGAATCTCTAAAAAGA 57.619 34.615 2.45 0.00 40.96 2.52
1294 2129 8.261522 AGACCATAGTGGAATCTCTAAAAAGAC 58.738 37.037 2.45 0.00 40.96 3.01
1295 2130 8.152023 ACCATAGTGGAATCTCTAAAAAGACT 57.848 34.615 2.45 0.00 40.96 3.24
1296 2131 8.606830 ACCATAGTGGAATCTCTAAAAAGACTT 58.393 33.333 2.45 0.00 40.96 3.01
1402 2373 4.189231 GCAACATAATCTCCTTACGGTGT 58.811 43.478 0.00 0.00 0.00 4.16
1673 2644 1.373435 CGCTCCAGGTTGGTTGGTA 59.627 57.895 0.00 0.00 39.03 3.25
1675 2646 0.322546 GCTCCAGGTTGGTTGGTAGG 60.323 60.000 0.00 0.00 39.03 3.18
1679 2650 1.633432 CCAGGTTGGTTGGTAGGATGA 59.367 52.381 0.00 0.00 31.35 2.92
1693 3561 6.824553 TGGTAGGATGAATGATCTTTCTCTG 58.175 40.000 18.92 0.00 0.00 3.35
1694 3562 5.700373 GGTAGGATGAATGATCTTTCTCTGC 59.300 44.000 18.92 15.72 0.00 4.26
1697 3565 6.761312 AGGATGAATGATCTTTCTCTGCTAG 58.239 40.000 18.92 0.00 0.00 3.42
1754 3940 9.539825 TTCCAGTAGTGTAATTTTTAACGTACA 57.460 29.630 0.00 0.00 0.00 2.90
1879 4099 8.543774 AGTAATACTGTTCTGGTCATCTTCATT 58.456 33.333 0.00 0.00 0.00 2.57
1929 4157 8.572855 AATGAAGGGAGTAAAAAGATTCTGAG 57.427 34.615 0.00 0.00 0.00 3.35
1953 4181 7.098477 AGAGCTGCATGCAAAACAATTAATAA 58.902 30.769 22.88 0.00 45.94 1.40
2020 4256 1.304134 AATGGTCGAAAGGGTGGGC 60.304 57.895 0.00 0.00 0.00 5.36
2107 4353 8.879342 TTAAAAACATTGATTACAACTGGGTG 57.121 30.769 0.00 0.00 38.90 4.61
2113 4359 6.377146 ACATTGATTACAACTGGGTGTATTCC 59.623 38.462 14.22 3.39 38.90 3.01
2268 4601 5.236478 AGTCAATGGTAAACACTCAGAAACG 59.764 40.000 0.00 0.00 0.00 3.60
2332 4669 8.555166 TTTAGTTCAAAATTAAAGCACGACAG 57.445 30.769 0.00 0.00 0.00 3.51
2339 4676 8.020819 TCAAAATTAAAGCACGACAGGAATTAG 58.979 33.333 0.00 0.00 0.00 1.73
2778 5146 2.232756 TGTCAAGCTGCTCGTAACAA 57.767 45.000 1.00 0.00 0.00 2.83
2784 5152 3.328382 AGCTGCTCGTAACAATTACCA 57.672 42.857 0.00 0.00 32.49 3.25
2888 5262 1.888512 GCACGGATGGGATATGCAATT 59.111 47.619 0.00 0.00 36.30 2.32
2937 5312 5.242393 ACACAGATGGGAAGAAATGAAACAG 59.758 40.000 0.00 0.00 0.00 3.16
3020 5401 3.270027 CCCAAGACGATAACTGATGCAA 58.730 45.455 0.00 0.00 0.00 4.08
3042 5423 7.120579 TGCAAACATATACCAACAGGAAACTAG 59.879 37.037 0.00 0.00 40.21 2.57
3055 5436 3.964031 AGGAAACTAGGCCTATGAGACTG 59.036 47.826 14.30 1.78 40.61 3.51
3130 5511 8.277490 TCTATGGACTACTAAGCATTATACCG 57.723 38.462 0.00 0.00 0.00 4.02
3131 5512 8.105197 TCTATGGACTACTAAGCATTATACCGA 58.895 37.037 0.00 0.00 0.00 4.69
3277 5665 4.730966 TGGTATTTAAGTGAGTTTGCCCA 58.269 39.130 0.00 0.00 0.00 5.36
3278 5666 4.521256 TGGTATTTAAGTGAGTTTGCCCAC 59.479 41.667 0.00 0.00 0.00 4.61
3279 5667 3.915437 ATTTAAGTGAGTTTGCCCACG 57.085 42.857 0.00 0.00 38.26 4.94
3320 5708 5.219633 GTGCATTTGTATTCGGTTGAACTT 58.780 37.500 0.00 0.00 36.81 2.66
3328 5716 5.823570 TGTATTCGGTTGAACTTCCTTTGAA 59.176 36.000 0.00 0.00 36.81 2.69
3405 5793 6.647067 AGTCTATTTATCACCGCATTAGCTTC 59.353 38.462 0.00 0.00 39.10 3.86
3491 5879 0.380378 TGGAAACACGCTCAACTTGC 59.620 50.000 0.00 0.00 33.40 4.01
3573 5961 7.928706 TGAGAGCCTAAACTTATCAAGCTAATC 59.071 37.037 0.00 0.00 0.00 1.75
3579 5967 9.699703 CCTAAACTTATCAAGCTAATCTACCTC 57.300 37.037 0.00 0.00 0.00 3.85
3591 5979 8.202745 AGCTAATCTACCTCAAAATTCTTTCG 57.797 34.615 0.00 0.00 0.00 3.46
3627 6015 4.214310 CCCATCGATCCTGCTATATCTCT 58.786 47.826 0.00 0.00 0.00 3.10
3677 6065 0.898789 TCCCTCGAAGTGTGACCCTC 60.899 60.000 0.00 0.00 0.00 4.30
3678 6066 0.900647 CCCTCGAAGTGTGACCCTCT 60.901 60.000 0.00 0.00 0.00 3.69
3679 6067 0.969894 CCTCGAAGTGTGACCCTCTT 59.030 55.000 0.00 0.00 0.00 2.85
3680 6068 1.337260 CCTCGAAGTGTGACCCTCTTG 60.337 57.143 0.00 0.00 0.00 3.02
3681 6069 0.033504 TCGAAGTGTGACCCTCTTGC 59.966 55.000 0.00 0.00 0.00 4.01
3682 6070 1.284982 CGAAGTGTGACCCTCTTGCG 61.285 60.000 0.00 0.00 0.00 4.85
3683 6071 0.033504 GAAGTGTGACCCTCTTGCGA 59.966 55.000 0.00 0.00 0.00 5.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 8.577048 TGGAGTATTATGTAGGAGTAGCATAC 57.423 38.462 0.00 0.00 43.47 2.39
3 4 9.769677 AATGGAGTATTATGTAGGAGTAGCATA 57.230 33.333 0.00 0.00 0.00 3.14
4 5 8.671987 AATGGAGTATTATGTAGGAGTAGCAT 57.328 34.615 0.00 0.00 0.00 3.79
5 6 8.492415 AAATGGAGTATTATGTAGGAGTAGCA 57.508 34.615 0.00 0.00 0.00 3.49
6 7 8.035984 GGAAATGGAGTATTATGTAGGAGTAGC 58.964 40.741 0.00 0.00 0.00 3.58
7 8 9.090103 TGGAAATGGAGTATTATGTAGGAGTAG 57.910 37.037 0.00 0.00 0.00 2.57
8 9 9.615660 ATGGAAATGGAGTATTATGTAGGAGTA 57.384 33.333 0.00 0.00 0.00 2.59
9 10 7.931015 TGGAAATGGAGTATTATGTAGGAGT 57.069 36.000 0.00 0.00 0.00 3.85
12 13 9.449719 GGTAATGGAAATGGAGTATTATGTAGG 57.550 37.037 0.00 0.00 0.00 3.18
16 17 7.094205 GGCAGGTAATGGAAATGGAGTATTATG 60.094 40.741 0.00 0.00 0.00 1.90
70 71 2.567615 ACTTTAGGTAGGTGTCTGGCTG 59.432 50.000 0.00 0.00 0.00 4.85
84 85 9.286946 CGTGTGACTTCTATTAACTACTTTAGG 57.713 37.037 0.00 0.00 0.00 2.69
87 88 9.617975 GTACGTGTGACTTCTATTAACTACTTT 57.382 33.333 0.00 0.00 0.00 2.66
90 91 7.237173 ACGTACGTGTGACTTCTATTAACTAC 58.763 38.462 22.14 0.00 0.00 2.73
91 92 7.117667 TGACGTACGTGTGACTTCTATTAACTA 59.882 37.037 28.16 0.00 0.00 2.24
92 93 6.073058 TGACGTACGTGTGACTTCTATTAACT 60.073 38.462 28.16 0.00 0.00 2.24
93 94 6.031833 GTGACGTACGTGTGACTTCTATTAAC 59.968 42.308 28.16 5.63 0.00 2.01
94 95 6.079763 GTGACGTACGTGTGACTTCTATTAA 58.920 40.000 28.16 0.00 0.00 1.40
109 110 7.593644 TGATGATTAATTCATAGGTGACGTACG 59.406 37.037 15.01 15.01 45.29 3.67
112 113 9.996554 TTATGATGATTAATTCATAGGTGACGT 57.003 29.630 8.95 0.00 45.29 4.34
216 230 1.779061 AAATGAGCGAGGGGTGTGGT 61.779 55.000 0.00 0.00 0.00 4.16
217 231 1.002134 AAATGAGCGAGGGGTGTGG 60.002 57.895 0.00 0.00 0.00 4.17
218 232 0.321564 TGAAATGAGCGAGGGGTGTG 60.322 55.000 0.00 0.00 0.00 3.82
220 234 1.755179 AATGAAATGAGCGAGGGGTG 58.245 50.000 0.00 0.00 0.00 4.61
221 235 2.369394 GAAATGAAATGAGCGAGGGGT 58.631 47.619 0.00 0.00 0.00 4.95
223 237 2.648059 AGGAAATGAAATGAGCGAGGG 58.352 47.619 0.00 0.00 0.00 4.30
225 239 6.758886 ACTAGTAAGGAAATGAAATGAGCGAG 59.241 38.462 0.00 0.00 0.00 5.03
226 240 6.640518 ACTAGTAAGGAAATGAAATGAGCGA 58.359 36.000 0.00 0.00 0.00 4.93
530 589 1.339055 ACGCATGTGGCAATCAGTACT 60.339 47.619 11.65 0.00 45.17 2.73
625 703 0.621609 TGGAGGATAAACCGGTTGGG 59.378 55.000 23.08 0.00 44.74 4.12
642 720 2.050350 CATGGTGCCTTCCTGCTGG 61.050 63.158 2.58 2.58 0.00 4.85
751 829 0.726827 AACAACATGTAGGCGCATCG 59.273 50.000 10.83 0.00 0.00 3.84
915 1048 6.160684 TGAAATGAATGAACATTGCAGGAAG 58.839 36.000 4.72 0.00 39.85 3.46
926 1059 7.543172 ACAATGCATACACTGAAATGAATGAAC 59.457 33.333 0.00 0.00 0.00 3.18
927 1060 7.604549 ACAATGCATACACTGAAATGAATGAA 58.395 30.769 0.00 0.00 0.00 2.57
928 1061 7.160547 ACAATGCATACACTGAAATGAATGA 57.839 32.000 0.00 0.00 0.00 2.57
1062 1233 2.690326 AAGCGTGTCGAACTTGCTT 58.310 47.368 8.97 8.97 40.79 3.91
1104 1275 7.415004 AAATGGTGTCCCAGGGAAATATATA 57.585 36.000 10.89 0.00 46.15 0.86
1156 1327 5.838531 ACATTTAGGAACGGAGAGAGTAG 57.161 43.478 0.00 0.00 0.00 2.57
1159 1330 6.210287 ACTTACATTTAGGAACGGAGAGAG 57.790 41.667 0.00 0.00 0.00 3.20
1160 1331 5.126707 GGACTTACATTTAGGAACGGAGAGA 59.873 44.000 0.00 0.00 0.00 3.10
1161 1332 5.127356 AGGACTTACATTTAGGAACGGAGAG 59.873 44.000 0.00 0.00 0.00 3.20
1162 1333 5.021458 AGGACTTACATTTAGGAACGGAGA 58.979 41.667 0.00 0.00 0.00 3.71
1190 1361 9.850628 TCCGCATATAGTTTGTAGTGTAATATC 57.149 33.333 0.00 0.00 0.00 1.63
1196 1367 5.914033 ACATCCGCATATAGTTTGTAGTGT 58.086 37.500 0.00 0.00 0.00 3.55
1197 1368 9.803315 ATATACATCCGCATATAGTTTGTAGTG 57.197 33.333 0.00 0.00 0.00 2.74
1241 2076 7.498900 ACATACGGAGCAAAATGAATGAATCTA 59.501 33.333 0.00 0.00 0.00 1.98
1246 2081 6.257849 GTCTACATACGGAGCAAAATGAATGA 59.742 38.462 0.00 0.00 0.00 2.57
1248 2083 5.527582 GGTCTACATACGGAGCAAAATGAAT 59.472 40.000 0.00 0.00 0.00 2.57
1251 2086 4.188462 TGGTCTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 37.09 2.32
1253 2088 3.965379 TGGTCTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 37.09 2.44
1258 2093 4.395625 TCCACTATGGTCTACATACGGAG 58.604 47.826 0.00 0.00 41.03 4.63
1259 2094 4.442401 TCCACTATGGTCTACATACGGA 57.558 45.455 0.00 0.00 41.03 4.69
1261 2096 6.431543 AGAGATTCCACTATGGTCTACATACG 59.568 42.308 0.00 0.00 41.03 3.06
1262 2097 7.768807 AGAGATTCCACTATGGTCTACATAC 57.231 40.000 0.00 0.00 41.03 2.39
1265 2100 8.603898 TTTTAGAGATTCCACTATGGTCTACA 57.396 34.615 0.00 0.00 39.03 2.74
1266 2101 9.535878 CTTTTTAGAGATTCCACTATGGTCTAC 57.464 37.037 0.00 0.00 39.03 2.59
1269 2104 8.261522 AGTCTTTTTAGAGATTCCACTATGGTC 58.738 37.037 0.00 0.00 39.03 4.02
1287 2122 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
1288 2123 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
1289 2124 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
1290 2125 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
1291 2126 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
1292 2127 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
1293 2128 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
1294 2129 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
1295 2130 7.300658 AGTACTCCCTCCGTTCCTAAATATAA 58.699 38.462 0.00 0.00 0.00 0.98
1296 2131 6.856757 AGTACTCCCTCCGTTCCTAAATATA 58.143 40.000 0.00 0.00 0.00 0.86
1297 2132 5.713807 AGTACTCCCTCCGTTCCTAAATAT 58.286 41.667 0.00 0.00 0.00 1.28
1298 2133 5.134725 AGTACTCCCTCCGTTCCTAAATA 57.865 43.478 0.00 0.00 0.00 1.40
1299 2134 3.991683 AGTACTCCCTCCGTTCCTAAAT 58.008 45.455 0.00 0.00 0.00 1.40
1300 2135 3.463048 AGTACTCCCTCCGTTCCTAAA 57.537 47.619 0.00 0.00 0.00 1.85
1301 2136 3.686691 GCTAGTACTCCCTCCGTTCCTAA 60.687 52.174 0.00 0.00 0.00 2.69
1302 2137 2.158696 GCTAGTACTCCCTCCGTTCCTA 60.159 54.545 0.00 0.00 0.00 2.94
1307 2142 2.509131 ACTTAGCTAGTACTCCCTCCGT 59.491 50.000 0.00 0.00 34.56 4.69
1414 2385 5.569059 GCAGTGTCTTGTGAATATTTTTCCG 59.431 40.000 0.00 0.00 0.00 4.30
1673 2644 5.633655 AGCAGAGAAAGATCATTCATCCT 57.366 39.130 12.84 4.42 30.71 3.24
1675 2646 6.225318 AGCTAGCAGAGAAAGATCATTCATC 58.775 40.000 18.83 7.50 0.00 2.92
1679 2650 6.729690 ACTAGCTAGCAGAGAAAGATCATT 57.270 37.500 20.91 0.00 0.00 2.57
1693 3561 7.148103 GGGGTAATACATACTGTACTAGCTAGC 60.148 44.444 20.91 6.62 34.61 3.42
1694 3562 7.065563 CGGGGTAATACATACTGTACTAGCTAG 59.934 44.444 19.44 19.44 34.61 3.42
1697 3565 5.474876 ACGGGGTAATACATACTGTACTAGC 59.525 44.000 0.00 0.00 35.42 3.42
1867 4087 6.148480 GCCATCAGTATACAATGAAGATGACC 59.852 42.308 15.95 6.59 34.79 4.02
1917 4142 3.128938 GCATGCAGCTCTCAGAATCTTTT 59.871 43.478 14.21 0.00 41.15 2.27
1924 4149 1.538512 GTTTTGCATGCAGCTCTCAGA 59.461 47.619 21.50 0.00 45.94 3.27
1929 4157 5.789710 ATTAATTGTTTTGCATGCAGCTC 57.210 34.783 21.50 14.60 45.94 4.09
1958 4186 7.704472 CCTTCTGTGTAAAGTGCATGTTTTTAA 59.296 33.333 2.68 0.00 0.00 1.52
1960 4188 6.042143 CCTTCTGTGTAAAGTGCATGTTTTT 58.958 36.000 2.68 0.00 0.00 1.94
1966 4202 4.623932 TCTCCTTCTGTGTAAAGTGCAT 57.376 40.909 0.00 0.00 0.00 3.96
2121 4367 8.988064 TTTGTCAAATTTACAAAGCTACAACA 57.012 26.923 15.73 0.00 40.83 3.33
2153 4486 7.069331 TGGTCACCTTCATTAAAAGTCAAACAT 59.931 33.333 0.00 0.00 0.00 2.71
2268 4601 6.890979 ACGGAGGGAGTAGTATATTGTAAC 57.109 41.667 0.00 0.00 0.00 2.50
2324 4661 2.092211 CGTTGTCTAATTCCTGTCGTGC 59.908 50.000 0.00 0.00 0.00 5.34
2332 4669 2.500504 ACTCCCTCCGTTGTCTAATTCC 59.499 50.000 0.00 0.00 0.00 3.01
2339 4676 4.732672 AATTACTACTCCCTCCGTTGTC 57.267 45.455 0.00 0.00 0.00 3.18
2888 5262 7.833285 AGGAACTAGGAAGTTAAAATTGCAA 57.167 32.000 0.00 0.00 46.09 4.08
2937 5312 6.214191 TCTCCACTTCTGAATACATCTGTC 57.786 41.667 0.00 0.00 0.00 3.51
3020 5401 6.120220 GCCTAGTTTCCTGTTGGTATATGTT 58.880 40.000 0.00 0.00 34.23 2.71
3055 5436 8.494347 CATTTAGATATTGTGCTAGAACTGAGC 58.506 37.037 1.64 0.00 40.53 4.26
3066 5447 9.616634 CATAACCATGACATTTAGATATTGTGC 57.383 33.333 0.00 0.00 33.67 4.57
3130 5511 3.763897 ACATGAAAGCCCCAAGTAACATC 59.236 43.478 0.00 0.00 0.00 3.06
3131 5512 3.511146 CACATGAAAGCCCCAAGTAACAT 59.489 43.478 0.00 0.00 0.00 2.71
3277 5665 4.320935 GCACACCATGGAAGAAAAATACGT 60.321 41.667 21.47 0.00 0.00 3.57
3278 5666 4.165779 GCACACCATGGAAGAAAAATACG 58.834 43.478 21.47 0.00 0.00 3.06
3279 5667 5.132897 TGCACACCATGGAAGAAAAATAC 57.867 39.130 21.47 0.00 0.00 1.89
3320 5708 5.630661 TTTCTTGTTGTCGTTTCAAAGGA 57.369 34.783 0.00 0.00 0.00 3.36
3328 5716 9.244799 GGAGATTTTTATTTTCTTGTTGTCGTT 57.755 29.630 0.00 0.00 0.00 3.85
3374 5762 4.873827 TGCGGTGATAAATAGACTTGAACC 59.126 41.667 0.00 0.00 0.00 3.62
3433 5821 5.959618 ATACTTTTGGACTTTGGCTACAC 57.040 39.130 0.00 0.00 0.00 2.90
3469 5857 2.325583 AGTTGAGCGTGTTTCCAAGA 57.674 45.000 0.00 0.00 0.00 3.02
3491 5879 0.888619 TGTACTCTGGTCCAAGAGCG 59.111 55.000 14.70 0.00 46.46 5.03
3611 5999 6.550481 TGATGATGGAGAGATATAGCAGGATC 59.450 42.308 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.