Multiple sequence alignment - TraesCS3B01G078800

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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 TraesCS3B01G078800 chr3B 100.000 2918 0 0 1 2918 49859791 49856874 0.000000e+00 5389.0
1 TraesCS3B01G078800 chr3B 85.392 1109 110 26 1038 2111 49780328 49779237 0.000000e+00 1103.0
2 TraesCS3B01G078800 chr3B 88.305 590 49 13 2332 2918 49778916 49778344 0.000000e+00 689.0
3 TraesCS3B01G078800 chr3B 81.900 221 22 11 1931 2143 49775123 49774913 1.390000e-38 171.0
4 TraesCS3B01G078800 chr3A 87.925 1234 83 21 939 2143 38538333 38537137 0.000000e+00 1393.0
5 TraesCS3B01G078800 chr3A 89.637 936 64 10 19 923 38539251 38538318 0.000000e+00 1160.0
6 TraesCS3B01G078800 chr3A 84.864 1143 119 21 1038 2143 38436081 38434956 0.000000e+00 1103.0
7 TraesCS3B01G078800 chr3A 84.677 1129 116 27 1038 2127 38474403 38473293 0.000000e+00 1074.0
8 TraesCS3B01G078800 chr3A 87.927 439 43 7 2482 2917 38536968 38536537 2.590000e-140 508.0
9 TraesCS3B01G078800 chr3A 91.111 90 8 0 2141 2230 572334519 572334430 3.950000e-24 122.0
10 TraesCS3B01G078800 chr3A 90.909 88 7 1 2141 2228 649834829 649834915 1.840000e-22 117.0
11 TraesCS3B01G078800 chr3D 90.909 1034 63 11 1 1012 29276243 29275219 0.000000e+00 1360.0
12 TraesCS3B01G078800 chr3D 86.643 1138 100 19 1038 2143 29250383 29249266 0.000000e+00 1212.0
13 TraesCS3B01G078800 chr3D 90.230 696 33 12 2226 2918 29249267 29248604 0.000000e+00 876.0
14 TraesCS3B01G078800 chr3D 87.135 342 31 9 2570 2908 29217774 29217443 2.750000e-100 375.0
15 TraesCS3B01G078800 chr3D 87.500 264 23 6 1139 1394 29227782 29227521 2.200000e-76 296.0
16 TraesCS3B01G078800 chr3D 78.947 247 36 13 2484 2727 29226416 29226183 1.400000e-33 154.0
17 TraesCS3B01G078800 chr5D 85.461 564 50 12 1311 1858 412359323 412358776 2.540000e-155 558.0
18 TraesCS3B01G078800 chr5B 93.182 88 6 0 2141 2228 209635155 209635242 2.360000e-26 130.0
19 TraesCS3B01G078800 chr5B 90.426 94 8 1 2136 2228 469290990 469291083 3.950000e-24 122.0
20 TraesCS3B01G078800 chr5B 85.841 113 13 3 2141 2252 550149093 550148983 1.840000e-22 117.0
21 TraesCS3B01G078800 chr6A 93.023 86 6 0 2142 2227 616974535 616974620 3.050000e-25 126.0
22 TraesCS3B01G078800 chr7A 90.426 94 8 1 2136 2228 689907081 689907174 3.950000e-24 122.0
23 TraesCS3B01G078800 chr7A 89.583 96 9 1 2133 2227 581849907 581850002 1.420000e-23 121.0
24 TraesCS3B01G078800 chr2A 88.000 100 9 2 2142 2238 758604218 758604119 6.610000e-22 115.0
25 TraesCS3B01G078800 chr2B 89.855 69 7 0 298 366 326478845 326478913 4.010000e-14 89.8


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 TraesCS3B01G078800 chr3B 49856874 49859791 2917 True 5389.000000 5389 100.000000 1 2918 1 chr3B.!!$R1 2917
1 TraesCS3B01G078800 chr3B 49774913 49780328 5415 True 654.333333 1103 85.199000 1038 2918 3 chr3B.!!$R2 1880
2 TraesCS3B01G078800 chr3A 38434956 38436081 1125 True 1103.000000 1103 84.864000 1038 2143 1 chr3A.!!$R1 1105
3 TraesCS3B01G078800 chr3A 38473293 38474403 1110 True 1074.000000 1074 84.677000 1038 2127 1 chr3A.!!$R2 1089
4 TraesCS3B01G078800 chr3A 38536537 38539251 2714 True 1020.333333 1393 88.496333 19 2917 3 chr3A.!!$R4 2898
5 TraesCS3B01G078800 chr3D 29275219 29276243 1024 True 1360.000000 1360 90.909000 1 1012 1 chr3D.!!$R2 1011
6 TraesCS3B01G078800 chr3D 29248604 29250383 1779 True 1044.000000 1212 88.436500 1038 2918 2 chr3D.!!$R4 1880
7 TraesCS3B01G078800 chr3D 29226183 29227782 1599 True 225.000000 296 83.223500 1139 2727 2 chr3D.!!$R3 1588
8 TraesCS3B01G078800 chr5D 412358776 412359323 547 True 558.000000 558 85.461000 1311 1858 1 chr5D.!!$R1 547

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
643 666 0.037232 GGAGGAACACCGGAGAACAG 60.037 60.0 9.46 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2449 3282 0.746659 GCAAGCACAAAGTCCAACCT 59.253 50.0 0.0 0.0 0.0 3.5 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
25 26 3.571828 TGCATCAAACTTCCAATCCGAAA 59.428 39.130 0.00 0.00 0.00 3.46
26 27 4.038522 TGCATCAAACTTCCAATCCGAAAA 59.961 37.500 0.00 0.00 0.00 2.29
28 29 5.527951 CATCAAACTTCCAATCCGAAAACA 58.472 37.500 0.00 0.00 0.00 2.83
30 31 4.884744 TCAAACTTCCAATCCGAAAACAGA 59.115 37.500 0.00 0.00 0.00 3.41
48 49 6.506500 AACAGAGCGATCTTCATCAATTTT 57.493 33.333 0.00 0.00 0.00 1.82
103 104 8.715998 AGCAGAAATATTACTAGAATTGCATCG 58.284 33.333 0.00 0.00 0.00 3.84
105 106 8.498358 CAGAAATATTACTAGAATTGCATCGCA 58.502 33.333 0.00 0.00 36.47 5.10
174 184 0.393077 CCTAACCCGAGCATACCCAG 59.607 60.000 0.00 0.00 0.00 4.45
179 189 1.077787 CCGAGCATACCCAGCCAAA 60.078 57.895 0.00 0.00 0.00 3.28
192 202 0.523072 AGCCAAAATACAGCAGCACG 59.477 50.000 0.00 0.00 0.00 5.34
203 214 0.613260 AGCAGCACGGGAAGAACATA 59.387 50.000 0.00 0.00 0.00 2.29
210 221 0.583438 CGGGAAGAACATATGCAGCG 59.417 55.000 1.58 0.00 0.00 5.18
422 437 0.435008 CGCGGAGAAGAGAAAACACG 59.565 55.000 0.00 0.00 0.00 4.49
567 589 2.517402 CCGACCCTCTCCCTCTCG 60.517 72.222 0.00 0.00 0.00 4.04
640 663 2.280552 CGGGAGGAACACCGGAGAA 61.281 63.158 9.46 0.00 45.08 2.87
641 664 1.295746 GGGAGGAACACCGGAGAAC 59.704 63.158 9.46 0.00 41.07 3.01
643 666 0.037232 GGAGGAACACCGGAGAACAG 60.037 60.000 9.46 0.00 0.00 3.16
645 668 0.969894 AGGAACACCGGAGAACAGAG 59.030 55.000 9.46 0.00 0.00 3.35
680 703 1.271102 GAGCAGAAACAGAGACGGACT 59.729 52.381 0.00 0.00 0.00 3.85
681 704 1.689273 AGCAGAAACAGAGACGGACTT 59.311 47.619 0.00 0.00 0.00 3.01
683 706 2.545952 GCAGAAACAGAGACGGACTTGA 60.546 50.000 0.00 0.00 0.00 3.02
684 707 3.053455 CAGAAACAGAGACGGACTTGAC 58.947 50.000 0.00 0.00 0.00 3.18
685 708 2.959707 AGAAACAGAGACGGACTTGACT 59.040 45.455 0.00 0.00 0.00 3.41
686 709 3.004944 AGAAACAGAGACGGACTTGACTC 59.995 47.826 0.00 0.00 0.00 3.36
687 710 1.982660 ACAGAGACGGACTTGACTCA 58.017 50.000 0.00 0.00 33.87 3.41
696 721 1.202604 GGACTTGACTCAACCGAACCA 60.203 52.381 0.00 0.00 0.00 3.67
857 910 2.377310 CCGTAGCACCCACGAAACG 61.377 63.158 0.00 0.00 41.91 3.60
861 914 1.017177 TAGCACCCACGAAACGCATC 61.017 55.000 0.00 0.00 0.00 3.91
869 922 3.242608 CCCACGAAACGCATCGATAAAAT 60.243 43.478 16.17 0.00 45.48 1.82
914 967 1.998315 CGCAGATTGATCCATCGATCC 59.002 52.381 11.73 0.05 45.03 3.36
918 971 3.864003 CAGATTGATCCATCGATCCATCG 59.136 47.826 11.73 2.37 45.74 3.84
947 1000 6.368791 TCGTTGTAAACTTCAGATCCATCTTG 59.631 38.462 0.00 0.00 46.99 3.02
959 1012 8.357290 TCAGATCCATCTTGTGATTTGATTTT 57.643 30.769 0.00 0.00 34.22 1.82
982 1035 0.972471 TCTTCTCATGGAGGCAGCGA 60.972 55.000 0.00 0.00 0.00 4.93
1020 1073 1.078567 GCAGTGGGAGAGCAAGGAG 60.079 63.158 0.00 0.00 0.00 3.69
1021 1074 1.601171 CAGTGGGAGAGCAAGGAGG 59.399 63.158 0.00 0.00 0.00 4.30
1022 1075 0.906756 CAGTGGGAGAGCAAGGAGGA 60.907 60.000 0.00 0.00 0.00 3.71
1023 1076 0.617249 AGTGGGAGAGCAAGGAGGAG 60.617 60.000 0.00 0.00 0.00 3.69
1024 1077 1.306482 TGGGAGAGCAAGGAGGAGG 60.306 63.158 0.00 0.00 0.00 4.30
1025 1078 1.002274 GGGAGAGCAAGGAGGAGGA 59.998 63.158 0.00 0.00 0.00 3.71
1026 1079 1.048160 GGGAGAGCAAGGAGGAGGAG 61.048 65.000 0.00 0.00 0.00 3.69
1027 1080 1.685355 GGAGAGCAAGGAGGAGGAGC 61.685 65.000 0.00 0.00 0.00 4.70
1028 1081 0.975040 GAGAGCAAGGAGGAGGAGCA 60.975 60.000 0.00 0.00 0.00 4.26
1029 1082 1.220477 GAGCAAGGAGGAGGAGCAC 59.780 63.158 0.00 0.00 0.00 4.40
1030 1083 2.125350 GCAAGGAGGAGGAGCACG 60.125 66.667 0.00 0.00 0.00 5.34
1031 1084 2.125350 CAAGGAGGAGGAGCACGC 60.125 66.667 0.00 0.00 0.00 5.34
1032 1085 3.764466 AAGGAGGAGGAGCACGCG 61.764 66.667 3.53 3.53 0.00 6.01
1272 1340 4.961511 TGCGGCGTGCTCGAGTTT 62.962 61.111 15.13 0.00 46.63 2.66
1434 1502 2.282180 GGCGCCAAGGACCAGAAA 60.282 61.111 24.80 0.00 0.00 2.52
1513 1584 4.056584 TCGCCGAGGGGGAGAAGA 62.057 66.667 6.35 0.00 42.12 2.87
1728 1808 4.021925 AAGCCCGTGGAGCAGACC 62.022 66.667 0.00 0.00 0.00 3.85
1927 2019 6.296435 AGTATACCCTCTAGAAGACCCAAT 57.704 41.667 0.00 0.00 0.00 3.16
1929 2021 3.786213 ACCCTCTAGAAGACCCAATCT 57.214 47.619 0.00 0.00 40.46 2.40
1945 2040 4.695455 CCCAATCTACGACTGAAACATGTT 59.305 41.667 4.92 4.92 0.00 2.71
1953 2048 3.725740 CGACTGAAACATGTTTGCAGTTC 59.274 43.478 32.87 27.14 39.09 3.01
1976 2071 6.914259 TCATGTTTTGTTGTTAGTGACACAA 58.086 32.000 8.59 0.00 38.18 3.33
1998 2100 3.715628 AGTTCGCCATGGAAAATATGC 57.284 42.857 18.40 0.00 0.00 3.14
2006 2113 3.803778 CCATGGAAAATATGCGGCTTTTC 59.196 43.478 5.56 14.19 39.51 2.29
2081 2190 1.269517 TGGCGAAATTTTCAGTGTGGC 60.270 47.619 9.66 5.51 0.00 5.01
2082 2191 1.418373 GCGAAATTTTCAGTGTGGCC 58.582 50.000 9.66 0.00 0.00 5.36
2083 2192 1.934849 GCGAAATTTTCAGTGTGGCCC 60.935 52.381 0.00 0.00 0.00 5.80
2084 2193 1.665735 CGAAATTTTCAGTGTGGCCCG 60.666 52.381 0.00 0.00 0.00 6.13
2146 2414 9.807386 GTATTGTTTCACGCATATAAATACTCC 57.193 33.333 0.00 0.00 0.00 3.85
2147 2415 6.854496 TGTTTCACGCATATAAATACTCCC 57.146 37.500 0.00 0.00 0.00 4.30
2148 2416 6.588204 TGTTTCACGCATATAAATACTCCCT 58.412 36.000 0.00 0.00 0.00 4.20
2149 2417 6.704493 TGTTTCACGCATATAAATACTCCCTC 59.296 38.462 0.00 0.00 0.00 4.30
2150 2418 6.665992 TTCACGCATATAAATACTCCCTCT 57.334 37.500 0.00 0.00 0.00 3.69
2151 2419 6.025749 TCACGCATATAAATACTCCCTCTG 57.974 41.667 0.00 0.00 0.00 3.35
2152 2420 5.538813 TCACGCATATAAATACTCCCTCTGT 59.461 40.000 0.00 0.00 0.00 3.41
2153 2421 5.864474 CACGCATATAAATACTCCCTCTGTC 59.136 44.000 0.00 0.00 0.00 3.51
2154 2422 5.047235 ACGCATATAAATACTCCCTCTGTCC 60.047 44.000 0.00 0.00 0.00 4.02
2155 2423 5.624738 CGCATATAAATACTCCCTCTGTCCC 60.625 48.000 0.00 0.00 0.00 4.46
2156 2424 5.248477 GCATATAAATACTCCCTCTGTCCCA 59.752 44.000 0.00 0.00 0.00 4.37
2157 2425 6.239887 GCATATAAATACTCCCTCTGTCCCAA 60.240 42.308 0.00 0.00 0.00 4.12
2158 2426 7.691791 GCATATAAATACTCCCTCTGTCCCAAA 60.692 40.741 0.00 0.00 0.00 3.28
2159 2427 6.652205 ATAAATACTCCCTCTGTCCCAAAA 57.348 37.500 0.00 0.00 0.00 2.44
2160 2428 5.536497 AAATACTCCCTCTGTCCCAAAAT 57.464 39.130 0.00 0.00 0.00 1.82
2161 2429 6.652205 AAATACTCCCTCTGTCCCAAAATA 57.348 37.500 0.00 0.00 0.00 1.40
2162 2430 5.896073 ATACTCCCTCTGTCCCAAAATAG 57.104 43.478 0.00 0.00 0.00 1.73
2163 2431 3.803340 ACTCCCTCTGTCCCAAAATAGA 58.197 45.455 0.00 0.00 0.00 1.98
2164 2432 4.375313 ACTCCCTCTGTCCCAAAATAGAT 58.625 43.478 0.00 0.00 0.00 1.98
2165 2433 4.164988 ACTCCCTCTGTCCCAAAATAGATG 59.835 45.833 0.00 0.00 0.00 2.90
2166 2434 4.370776 TCCCTCTGTCCCAAAATAGATGA 58.629 43.478 0.00 0.00 0.00 2.92
2167 2435 4.977739 TCCCTCTGTCCCAAAATAGATGAT 59.022 41.667 0.00 0.00 0.00 2.45
2168 2436 5.433051 TCCCTCTGTCCCAAAATAGATGATT 59.567 40.000 0.00 0.00 0.00 2.57
2169 2437 5.767168 CCCTCTGTCCCAAAATAGATGATTC 59.233 44.000 0.00 0.00 0.00 2.52
2170 2438 6.359804 CCTCTGTCCCAAAATAGATGATTCA 58.640 40.000 0.00 0.00 0.00 2.57
2171 2439 6.830324 CCTCTGTCCCAAAATAGATGATTCAA 59.170 38.462 0.00 0.00 0.00 2.69
2172 2440 7.504911 CCTCTGTCCCAAAATAGATGATTCAAT 59.495 37.037 0.00 0.00 0.00 2.57
2173 2441 8.827832 TCTGTCCCAAAATAGATGATTCAATT 57.172 30.769 0.00 0.00 0.00 2.32
2174 2442 9.258629 TCTGTCCCAAAATAGATGATTCAATTT 57.741 29.630 0.00 0.00 0.00 1.82
2175 2443 9.880157 CTGTCCCAAAATAGATGATTCAATTTT 57.120 29.630 0.00 0.00 33.07 1.82
2176 2444 9.656040 TGTCCCAAAATAGATGATTCAATTTTG 57.344 29.630 19.21 19.21 43.77 2.44
2177 2445 9.657419 GTCCCAAAATAGATGATTCAATTTTGT 57.343 29.630 21.88 0.00 43.14 2.83
2216 2484 9.487790 TCAAAATTGGGTCATCTATTTTGAAAC 57.512 29.630 17.65 0.00 46.05 2.78
2217 2485 8.434661 CAAAATTGGGTCATCTATTTTGAAACG 58.565 33.333 14.48 0.00 44.64 3.60
2218 2486 5.637006 TTGGGTCATCTATTTTGAAACGG 57.363 39.130 0.00 0.00 0.00 4.44
2219 2487 4.912586 TGGGTCATCTATTTTGAAACGGA 58.087 39.130 0.00 0.00 0.00 4.69
2220 2488 4.941263 TGGGTCATCTATTTTGAAACGGAG 59.059 41.667 0.00 0.00 0.00 4.63
2221 2489 4.335594 GGGTCATCTATTTTGAAACGGAGG 59.664 45.833 0.00 0.00 0.00 4.30
2222 2490 4.335594 GGTCATCTATTTTGAAACGGAGGG 59.664 45.833 0.00 0.00 0.00 4.30
2223 2491 5.183228 GTCATCTATTTTGAAACGGAGGGA 58.817 41.667 0.00 0.00 0.00 4.20
2224 2492 5.294552 GTCATCTATTTTGAAACGGAGGGAG 59.705 44.000 0.00 0.00 0.00 4.30
2298 2578 3.264706 TCAACATCCGAAATTGGGGTCTA 59.735 43.478 0.00 0.00 0.00 2.59
2310 2590 0.183252 GGGGTCTAGCTAGGACTCGT 59.817 60.000 20.58 0.00 35.22 4.18
2329 2609 6.231211 ACTCGTTCATGATTAAGTCTTGGTT 58.769 36.000 0.00 0.00 33.88 3.67
2334 2645 7.330946 CGTTCATGATTAAGTCTTGGTTGACTA 59.669 37.037 0.00 0.00 45.49 2.59
2348 2659 3.322828 GGTTGACTAACGCCATCCCTATA 59.677 47.826 0.00 0.00 37.69 1.31
2362 3177 5.480073 CCATCCCTATATGCTCTAGCCTATC 59.520 48.000 3.43 0.00 41.18 2.08
2439 3260 3.247648 AGTTATGTTGTTGTGTGCTCGTC 59.752 43.478 0.00 0.00 0.00 4.20
2440 3261 0.581529 ATGTTGTTGTGTGCTCGTCG 59.418 50.000 0.00 0.00 0.00 5.12
2449 3282 0.604073 TGTGCTCGTCGGTGGATTTA 59.396 50.000 0.00 0.00 0.00 1.40
2458 3291 2.027469 GTCGGTGGATTTAGGTTGGACT 60.027 50.000 0.00 0.00 0.00 3.85
2459 3292 2.640826 TCGGTGGATTTAGGTTGGACTT 59.359 45.455 0.00 0.00 0.00 3.01
2460 3293 3.073356 TCGGTGGATTTAGGTTGGACTTT 59.927 43.478 0.00 0.00 0.00 2.66
2461 3294 3.190535 CGGTGGATTTAGGTTGGACTTTG 59.809 47.826 0.00 0.00 0.00 2.77
2462 3295 4.149598 GGTGGATTTAGGTTGGACTTTGT 58.850 43.478 0.00 0.00 0.00 2.83
2463 3296 4.022329 GGTGGATTTAGGTTGGACTTTGTG 60.022 45.833 0.00 0.00 0.00 3.33
2464 3297 3.572255 TGGATTTAGGTTGGACTTTGTGC 59.428 43.478 0.00 0.00 0.00 4.57
2465 3298 3.826729 GGATTTAGGTTGGACTTTGTGCT 59.173 43.478 0.00 0.00 0.00 4.40
2466 3299 4.280929 GGATTTAGGTTGGACTTTGTGCTT 59.719 41.667 0.00 0.00 0.00 3.91
2467 3300 4.647424 TTTAGGTTGGACTTTGTGCTTG 57.353 40.909 0.00 0.00 0.00 4.01
2468 3301 0.746659 AGGTTGGACTTTGTGCTTGC 59.253 50.000 0.00 0.00 0.00 4.01
2469 3302 0.459489 GGTTGGACTTTGTGCTTGCA 59.541 50.000 0.00 0.00 0.00 4.08
2470 3303 1.134848 GGTTGGACTTTGTGCTTGCAA 60.135 47.619 0.00 0.00 0.00 4.08
2471 3304 2.483538 GGTTGGACTTTGTGCTTGCAAT 60.484 45.455 0.00 0.00 0.00 3.56
2472 3305 3.197265 GTTGGACTTTGTGCTTGCAATT 58.803 40.909 0.00 0.00 0.00 2.32
2473 3306 3.096489 TGGACTTTGTGCTTGCAATTC 57.904 42.857 0.00 0.00 0.00 2.17
2474 3307 2.224018 TGGACTTTGTGCTTGCAATTCC 60.224 45.455 0.00 0.00 34.23 3.01
2475 3308 2.036346 GGACTTTGTGCTTGCAATTCCT 59.964 45.455 0.00 0.00 32.45 3.36
2476 3309 3.493176 GGACTTTGTGCTTGCAATTCCTT 60.493 43.478 0.00 0.00 32.45 3.36
2477 3310 4.122046 GACTTTGTGCTTGCAATTCCTTT 58.878 39.130 0.00 0.00 0.00 3.11
2478 3311 4.516323 ACTTTGTGCTTGCAATTCCTTTT 58.484 34.783 0.00 0.00 0.00 2.27
2479 3312 4.943093 ACTTTGTGCTTGCAATTCCTTTTT 59.057 33.333 0.00 0.00 0.00 1.94
2546 3380 8.763601 ACTTGCTTCCCTATATATATTGGAGTC 58.236 37.037 20.81 12.76 31.42 3.36
2548 3382 8.311395 TGCTTCCCTATATATATTGGAGTCTG 57.689 38.462 20.81 7.24 31.42 3.51
2561 3395 8.995027 ATATTGGAGTCTGCACCATTTTTATA 57.005 30.769 0.00 0.00 35.34 0.98
2590 3424 8.076781 CACACACACATAGAGGTATATAGTGTC 58.923 40.741 0.00 0.00 36.69 3.67
2673 3508 8.795786 TTACATGAATATTTTTAGGAATGCGC 57.204 30.769 0.00 0.00 0.00 6.09
2687 3522 9.601971 TTTAGGAATGCGCGAATATTTATAAAC 57.398 29.630 12.10 0.00 0.00 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.527951 TGTTTTCGGATTGGAAGTTTGATG 58.472 37.500 0.00 0.00 0.00 3.07
7 8 4.884744 TCTGTTTTCGGATTGGAAGTTTGA 59.115 37.500 0.00 0.00 0.00 2.69
13 14 1.804151 CGCTCTGTTTTCGGATTGGAA 59.196 47.619 0.00 0.00 34.39 3.53
15 16 1.438651 TCGCTCTGTTTTCGGATTGG 58.561 50.000 0.00 0.00 34.39 3.16
17 18 3.252974 AGATCGCTCTGTTTTCGGATT 57.747 42.857 0.00 0.00 34.39 3.01
21 22 3.614176 TGATGAAGATCGCTCTGTTTTCG 59.386 43.478 0.00 0.00 0.00 3.46
25 26 6.149973 TGAAAATTGATGAAGATCGCTCTGTT 59.850 34.615 0.00 0.00 0.00 3.16
26 27 5.645067 TGAAAATTGATGAAGATCGCTCTGT 59.355 36.000 0.00 0.00 0.00 3.41
28 29 6.939132 ATGAAAATTGATGAAGATCGCTCT 57.061 33.333 0.00 0.00 0.00 4.09
30 31 6.255020 GCAAATGAAAATTGATGAAGATCGCT 59.745 34.615 0.00 0.00 0.00 4.93
48 49 1.675310 CTGACCCCTGCGCAAATGA 60.675 57.895 13.05 0.00 0.00 2.57
103 104 7.735500 TGTTGTTATTAAGACTGTACGATTGC 58.264 34.615 0.00 0.00 0.00 3.56
142 151 2.237893 CGGGTTAGGGAAGTGGTTGTAT 59.762 50.000 0.00 0.00 0.00 2.29
174 184 0.456653 CCGTGCTGCTGTATTTTGGC 60.457 55.000 0.00 0.00 0.00 4.52
179 189 0.613260 TCTTCCCGTGCTGCTGTATT 59.387 50.000 0.00 0.00 0.00 1.89
192 202 1.953559 TCGCTGCATATGTTCTTCCC 58.046 50.000 4.29 0.00 0.00 3.97
203 214 1.021390 CCGGTTCTTCTTCGCTGCAT 61.021 55.000 0.00 0.00 0.00 3.96
210 221 0.673956 GACTGGCCCGGTTCTTCTTC 60.674 60.000 0.00 0.00 0.00 2.87
567 589 1.168714 GATTGGATTATCGGGGCTGC 58.831 55.000 0.00 0.00 0.00 5.25
575 597 6.954352 ACCCTAACCCTAGATTGGATTATC 57.046 41.667 0.00 0.00 0.00 1.75
576 598 7.723109 AAACCCTAACCCTAGATTGGATTAT 57.277 36.000 0.00 0.00 0.00 1.28
640 663 2.366570 GCTCCCCTCCTCCTCTGT 59.633 66.667 0.00 0.00 0.00 3.41
641 664 2.063378 GTGCTCCCCTCCTCCTCTG 61.063 68.421 0.00 0.00 0.00 3.35
643 666 3.151022 CGTGCTCCCCTCCTCCTC 61.151 72.222 0.00 0.00 0.00 3.71
645 668 3.151022 CTCGTGCTCCCCTCCTCC 61.151 72.222 0.00 0.00 0.00 4.30
680 703 1.673920 GCTTTGGTTCGGTTGAGTCAA 59.326 47.619 0.08 0.08 0.00 3.18
681 704 1.305201 GCTTTGGTTCGGTTGAGTCA 58.695 50.000 0.00 0.00 0.00 3.41
683 706 0.822121 GGGCTTTGGTTCGGTTGAGT 60.822 55.000 0.00 0.00 0.00 3.41
684 707 1.852067 CGGGCTTTGGTTCGGTTGAG 61.852 60.000 0.00 0.00 0.00 3.02
685 708 1.894756 CGGGCTTTGGTTCGGTTGA 60.895 57.895 0.00 0.00 0.00 3.18
686 709 2.642700 CGGGCTTTGGTTCGGTTG 59.357 61.111 0.00 0.00 0.00 3.77
687 710 2.596338 CCGGGCTTTGGTTCGGTT 60.596 61.111 0.00 0.00 37.92 4.44
691 716 1.365999 CAAACCCGGGCTTTGGTTC 59.634 57.895 27.50 0.00 43.94 3.62
733 777 3.492353 CCCGGGCCTGTCCATGAT 61.492 66.667 8.08 0.00 36.21 2.45
889 942 2.411904 GATGGATCAATCTGCGAGTCC 58.588 52.381 2.52 0.00 0.00 3.85
914 967 5.401376 TCTGAAGTTTACAACGAACTCGATG 59.599 40.000 6.05 6.98 45.70 3.84
918 971 5.694910 TGGATCTGAAGTTTACAACGAACTC 59.305 40.000 0.00 0.00 36.38 3.01
927 980 7.856145 ATCACAAGATGGATCTGAAGTTTAC 57.144 36.000 0.00 0.00 37.19 2.01
947 1000 9.947669 CCATGAGAAGAGATAAAATCAAATCAC 57.052 33.333 0.00 0.00 0.00 3.06
959 1012 2.632028 GCTGCCTCCATGAGAAGAGATA 59.368 50.000 0.00 0.00 31.43 1.98
982 1035 4.221422 CGCCGATGATCCACCCGT 62.221 66.667 0.00 0.00 0.00 5.28
986 1039 1.563435 CTGCATCGCCGATGATCCAC 61.563 60.000 29.82 12.44 42.09 4.02
1122 1175 3.046087 TCGCTCTTGCACAGCTGC 61.046 61.111 15.27 1.39 44.52 5.25
1124 1177 2.736236 CGTCGCTCTTGCACAGCT 60.736 61.111 13.64 0.00 39.64 4.24
1125 1178 2.734723 TCGTCGCTCTTGCACAGC 60.735 61.111 6.75 6.75 39.64 4.40
1128 1181 3.470567 CCGTCGTCGCTCTTGCAC 61.471 66.667 0.00 0.00 39.64 4.57
1183 1242 4.760047 CGCCCCAACCGACTGGAG 62.760 72.222 4.45 0.00 38.96 3.86
1447 1515 4.058817 GTGGAGTAGTTCTTCAGGTTGTG 58.941 47.826 0.00 0.00 31.42 3.33
1686 1766 1.745890 CATCCTTATCCCGACGCCA 59.254 57.895 0.00 0.00 0.00 5.69
1754 1834 2.679342 CCCTTGCCCGAAGATCCCA 61.679 63.158 0.00 0.00 32.82 4.37
1927 2019 4.123506 TGCAAACATGTTTCAGTCGTAGA 58.876 39.130 20.85 0.00 0.00 2.59
1929 2021 3.874543 ACTGCAAACATGTTTCAGTCGTA 59.125 39.130 30.14 17.34 36.84 3.43
1945 2040 6.309980 CACTAACAACAAAACATGAACTGCAA 59.690 34.615 0.00 0.00 0.00 4.08
1953 2048 7.573916 TTTGTGTCACTAACAACAAAACATG 57.426 32.000 4.27 0.00 40.31 3.21
1976 2071 4.432712 GCATATTTTCCATGGCGAACTTT 58.567 39.130 6.96 0.00 0.00 2.66
1998 2100 6.820470 TTGTGTCAAAAATAAGAAAAGCCG 57.180 33.333 0.00 0.00 0.00 5.52
2044 2151 4.551388 TCGCCAAAATTTCACCAACATAC 58.449 39.130 0.00 0.00 0.00 2.39
2081 2190 1.059913 AGATCCCTTAATCAGGCGGG 58.940 55.000 0.00 0.00 42.29 6.13
2082 2191 3.261897 ACATAGATCCCTTAATCAGGCGG 59.738 47.826 0.00 0.00 42.29 6.13
2083 2192 4.543590 ACATAGATCCCTTAATCAGGCG 57.456 45.455 0.00 0.00 42.29 5.52
2084 2193 6.014156 ACACTACATAGATCCCTTAATCAGGC 60.014 42.308 0.00 0.00 42.29 4.85
2143 2411 4.410228 TCATCTATTTTGGGACAGAGGGAG 59.590 45.833 0.00 0.00 42.39 4.30
2144 2412 4.370776 TCATCTATTTTGGGACAGAGGGA 58.629 43.478 0.00 0.00 42.39 4.20
2145 2413 4.778213 TCATCTATTTTGGGACAGAGGG 57.222 45.455 0.00 0.00 42.39 4.30
2146 2414 6.359804 TGAATCATCTATTTTGGGACAGAGG 58.640 40.000 0.00 0.00 42.39 3.69
2147 2415 7.870509 TTGAATCATCTATTTTGGGACAGAG 57.129 36.000 0.00 0.00 42.39 3.35
2148 2416 8.827832 AATTGAATCATCTATTTTGGGACAGA 57.172 30.769 0.00 0.00 42.39 3.41
2149 2417 9.880157 AAAATTGAATCATCTATTTTGGGACAG 57.120 29.630 9.18 0.00 44.06 3.51
2191 2459 8.434661 CGTTTCAAAATAGATGACCCAATTTTG 58.565 33.333 11.32 11.32 44.73 2.44
2192 2460 7.602265 CCGTTTCAAAATAGATGACCCAATTTT 59.398 33.333 0.00 0.00 33.07 1.82
2193 2461 7.039363 TCCGTTTCAAAATAGATGACCCAATTT 60.039 33.333 0.00 0.00 0.00 1.82
2194 2462 6.435904 TCCGTTTCAAAATAGATGACCCAATT 59.564 34.615 0.00 0.00 0.00 2.32
2195 2463 5.949354 TCCGTTTCAAAATAGATGACCCAAT 59.051 36.000 0.00 0.00 0.00 3.16
2196 2464 5.317808 TCCGTTTCAAAATAGATGACCCAA 58.682 37.500 0.00 0.00 0.00 4.12
2197 2465 4.912586 TCCGTTTCAAAATAGATGACCCA 58.087 39.130 0.00 0.00 0.00 4.51
2198 2466 4.335594 CCTCCGTTTCAAAATAGATGACCC 59.664 45.833 0.00 0.00 0.00 4.46
2199 2467 4.335594 CCCTCCGTTTCAAAATAGATGACC 59.664 45.833 0.00 0.00 0.00 4.02
2200 2468 5.183228 TCCCTCCGTTTCAAAATAGATGAC 58.817 41.667 0.00 0.00 0.00 3.06
2201 2469 5.045869 ACTCCCTCCGTTTCAAAATAGATGA 60.046 40.000 0.00 0.00 0.00 2.92
2202 2470 5.186198 ACTCCCTCCGTTTCAAAATAGATG 58.814 41.667 0.00 0.00 0.00 2.90
2203 2471 5.437191 ACTCCCTCCGTTTCAAAATAGAT 57.563 39.130 0.00 0.00 0.00 1.98
2204 2472 4.903045 ACTCCCTCCGTTTCAAAATAGA 57.097 40.909 0.00 0.00 0.00 1.98
2205 2473 6.346096 TCATACTCCCTCCGTTTCAAAATAG 58.654 40.000 0.00 0.00 0.00 1.73
2206 2474 6.070424 ACTCATACTCCCTCCGTTTCAAAATA 60.070 38.462 0.00 0.00 0.00 1.40
2207 2475 5.174037 TCATACTCCCTCCGTTTCAAAAT 57.826 39.130 0.00 0.00 0.00 1.82
2208 2476 4.041198 ACTCATACTCCCTCCGTTTCAAAA 59.959 41.667 0.00 0.00 0.00 2.44
2209 2477 3.581332 ACTCATACTCCCTCCGTTTCAAA 59.419 43.478 0.00 0.00 0.00 2.69
2210 2478 3.170717 ACTCATACTCCCTCCGTTTCAA 58.829 45.455 0.00 0.00 0.00 2.69
2211 2479 2.758979 GACTCATACTCCCTCCGTTTCA 59.241 50.000 0.00 0.00 0.00 2.69
2212 2480 2.758979 TGACTCATACTCCCTCCGTTTC 59.241 50.000 0.00 0.00 0.00 2.78
2213 2481 2.816411 TGACTCATACTCCCTCCGTTT 58.184 47.619 0.00 0.00 0.00 3.60
2214 2482 2.526888 TGACTCATACTCCCTCCGTT 57.473 50.000 0.00 0.00 0.00 4.44
2215 2483 2.526888 TTGACTCATACTCCCTCCGT 57.473 50.000 0.00 0.00 0.00 4.69
2216 2484 3.887621 TTTTGACTCATACTCCCTCCG 57.112 47.619 0.00 0.00 0.00 4.63
2217 2485 6.418946 AGAAATTTTGACTCATACTCCCTCC 58.581 40.000 0.00 0.00 0.00 4.30
2218 2486 8.261522 AGTAGAAATTTTGACTCATACTCCCTC 58.738 37.037 0.00 0.00 0.00 4.30
2219 2487 8.043710 CAGTAGAAATTTTGACTCATACTCCCT 58.956 37.037 0.00 0.00 0.00 4.20
2220 2488 7.824779 ACAGTAGAAATTTTGACTCATACTCCC 59.175 37.037 0.00 0.00 0.00 4.30
2221 2489 8.779354 ACAGTAGAAATTTTGACTCATACTCC 57.221 34.615 0.00 0.00 0.00 3.85
2265 2536 7.864108 ATTTCGGATGTTGATAATTCTCACA 57.136 32.000 0.00 0.00 0.00 3.58
2298 2578 5.361285 ACTTAATCATGAACGAGTCCTAGCT 59.639 40.000 0.00 0.00 0.00 3.32
2310 2590 8.999431 GTTAGTCAACCAAGACTTAATCATGAA 58.001 33.333 0.00 0.00 46.26 2.57
2329 2609 3.056107 GCATATAGGGATGGCGTTAGTCA 60.056 47.826 0.00 0.00 35.88 3.41
2334 2645 2.260822 AGAGCATATAGGGATGGCGTT 58.739 47.619 0.00 0.00 0.00 4.84
2348 2659 4.750941 AGGAGAAAGATAGGCTAGAGCAT 58.249 43.478 3.54 0.00 44.36 3.79
2362 3177 6.255453 GTCAAGATCATCGAAGAAGGAGAAAG 59.745 42.308 0.00 0.00 43.58 2.62
2439 3260 2.781681 AGTCCAACCTAAATCCACCG 57.218 50.000 0.00 0.00 0.00 4.94
2440 3261 4.022329 CACAAAGTCCAACCTAAATCCACC 60.022 45.833 0.00 0.00 0.00 4.61
2449 3282 0.746659 GCAAGCACAAAGTCCAACCT 59.253 50.000 0.00 0.00 0.00 3.50
2479 3312 3.065095 GCAAGGAATTGCAAGCACAAAAA 59.935 39.130 4.94 0.00 46.60 1.94
2480 3313 2.613133 GCAAGGAATTGCAAGCACAAAA 59.387 40.909 4.94 0.00 46.60 2.44
2546 3380 6.699204 TGTGTGTGTTTATAAAAATGGTGCAG 59.301 34.615 0.00 0.00 0.00 4.41
2548 3382 6.477033 TGTGTGTGTGTTTATAAAAATGGTGC 59.523 34.615 0.00 0.00 0.00 5.01
2561 3395 8.978472 ACTATATACCTCTATGTGTGTGTGTTT 58.022 33.333 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.