Multiple sequence alignment - TraesCS3B01G341900

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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 TraesCS3B01G341900 chr3B 100.000 2264 0 0 1 2264 548879091 548881354 0.000000e+00 4181.0
1 TraesCS3B01G341900 chr3B 91.061 179 15 1 2086 2264 570512092 570512269 8.080000e-60 241.0
2 TraesCS3B01G341900 chr3B 86.486 74 4 2 709 776 548879733 548879806 2.410000e-10 76.8
3 TraesCS3B01G341900 chr2B 92.086 2047 141 8 1 2039 71643479 71641446 0.000000e+00 2863.0
4 TraesCS3B01G341900 chr2B 91.160 1448 106 13 678 2111 292848079 292849518 0.000000e+00 1945.0
5 TraesCS3B01G341900 chr2B 91.697 1096 54 15 678 1750 430231792 430230711 0.000000e+00 1485.0
6 TraesCS3B01G341900 chr2B 90.893 1109 84 7 785 1889 15207721 15206626 0.000000e+00 1472.0
7 TraesCS3B01G341900 chr2B 91.975 785 50 5 1 773 215847198 215847981 0.000000e+00 1088.0
8 TraesCS3B01G341900 chr2B 91.465 785 55 2 1 773 430232433 430231649 0.000000e+00 1068.0
9 TraesCS3B01G341900 chr2B 94.479 163 8 1 2103 2264 701818392 701818230 1.340000e-62 250.0
10 TraesCS3B01G341900 chr2B 92.617 149 8 3 1841 1988 71641301 71641447 6.340000e-51 211.0
11 TraesCS3B01G341900 chr5D 92.755 1753 95 5 1 1749 358006659 358004935 0.000000e+00 2505.0
12 TraesCS3B01G341900 chr5D 91.784 779 52 2 1 767 520878627 520879405 0.000000e+00 1074.0
13 TraesCS3B01G341900 chr1B 90.826 1417 80 22 711 2113 449941597 449942977 0.000000e+00 1851.0
14 TraesCS3B01G341900 chr1B 93.880 719 41 1 1 716 449940950 449941668 0.000000e+00 1081.0
15 TraesCS3B01G341900 chr1B 84.926 272 33 6 1844 2113 449943071 449942806 3.710000e-68 268.0
16 TraesCS3B01G341900 chr6A 92.546 1194 74 6 767 1947 607999744 607998553 0.000000e+00 1698.0
17 TraesCS3B01G341900 chr6A 92.593 54 1 1 1956 2009 607998475 607998425 8.670000e-10 75.0
18 TraesCS3B01G341900 chr3D 91.088 1268 70 21 706 1955 116062240 116063482 0.000000e+00 1676.0
19 TraesCS3B01G341900 chr3D 93.001 743 52 0 1 743 116061565 116062307 0.000000e+00 1085.0
20 TraesCS3B01G341900 chr3D 91.210 785 54 4 1 773 310406123 310406904 0.000000e+00 1053.0
21 TraesCS3B01G341900 chr6B 92.077 1199 78 9 767 1951 702946726 702945531 0.000000e+00 1672.0
22 TraesCS3B01G341900 chr6B 90.664 1189 80 20 767 1947 703064115 703062950 0.000000e+00 1552.0
23 TraesCS3B01G341900 chr6B 89.558 1245 97 19 709 1947 703008265 703007048 0.000000e+00 1548.0
24 TraesCS3B01G341900 chr6B 96.154 156 6 0 2109 2264 352998588 352998743 2.890000e-64 255.0
25 TraesCS3B01G341900 chr6B 93.413 167 9 2 2100 2264 467050064 467050230 1.740000e-61 246.0
26 TraesCS3B01G341900 chr6B 90.741 54 2 1 1956 2009 703006969 703006919 4.040000e-08 69.4
27 TraesCS3B01G341900 chr6B 89.474 57 3 1 1953 2009 703013824 703013771 4.040000e-08 69.4
28 TraesCS3B01G341900 chr6B 89.474 57 3 1 1953 2009 703062872 703062819 4.040000e-08 69.4
29 TraesCS3B01G341900 chr1D 89.561 1322 79 26 678 1955 198509269 198510575 0.000000e+00 1622.0
30 TraesCS3B01G341900 chr2A 87.334 1279 114 23 706 1955 14628808 14627549 0.000000e+00 1421.0
31 TraesCS3B01G341900 chr2A 92.090 177 11 3 2089 2264 397744842 397745016 1.740000e-61 246.0
32 TraesCS3B01G341900 chr2A 93.413 167 10 1 2099 2264 399550536 399550370 1.740000e-61 246.0
33 TraesCS3B01G341900 chr4B 93.700 746 46 1 1 746 644536049 644535305 0.000000e+00 1116.0
34 TraesCS3B01G341900 chr4B 97.419 155 4 0 2110 2264 458030899 458031053 4.790000e-67 265.0
35 TraesCS3B01G341900 chr7D 97.351 151 4 0 2114 2264 625131932 625132082 8.020000e-65 257.0
36 TraesCS3B01G341900 chr4A 95.031 161 6 2 2102 2262 659008188 659008030 3.730000e-63 252.0
37 TraesCS3B01G341900 chr5B 100.000 28 0 0 2013 2040 529282505 529282532 4.000000e-03 52.8


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 TraesCS3B01G341900 chr3B 548879091 548881354 2263 False 2128.9 4181 93.2430 1 2264 2 chr3B.!!$F2 2263
1 TraesCS3B01G341900 chr2B 71641446 71643479 2033 True 2863.0 2863 92.0860 1 2039 1 chr2B.!!$R2 2038
2 TraesCS3B01G341900 chr2B 292848079 292849518 1439 False 1945.0 1945 91.1600 678 2111 1 chr2B.!!$F3 1433
3 TraesCS3B01G341900 chr2B 15206626 15207721 1095 True 1472.0 1472 90.8930 785 1889 1 chr2B.!!$R1 1104
4 TraesCS3B01G341900 chr2B 430230711 430232433 1722 True 1276.5 1485 91.5810 1 1750 2 chr2B.!!$R4 1749
5 TraesCS3B01G341900 chr2B 215847198 215847981 783 False 1088.0 1088 91.9750 1 773 1 chr2B.!!$F2 772
6 TraesCS3B01G341900 chr5D 358004935 358006659 1724 True 2505.0 2505 92.7550 1 1749 1 chr5D.!!$R1 1748
7 TraesCS3B01G341900 chr5D 520878627 520879405 778 False 1074.0 1074 91.7840 1 767 1 chr5D.!!$F1 766
8 TraesCS3B01G341900 chr1B 449940950 449942977 2027 False 1466.0 1851 92.3530 1 2113 2 chr1B.!!$F1 2112
9 TraesCS3B01G341900 chr6A 607998425 607999744 1319 True 886.5 1698 92.5695 767 2009 2 chr6A.!!$R1 1242
10 TraesCS3B01G341900 chr3D 116061565 116063482 1917 False 1380.5 1676 92.0445 1 1955 2 chr3D.!!$F2 1954
11 TraesCS3B01G341900 chr3D 310406123 310406904 781 False 1053.0 1053 91.2100 1 773 1 chr3D.!!$F1 772
12 TraesCS3B01G341900 chr6B 702945531 702946726 1195 True 1672.0 1672 92.0770 767 1951 1 chr6B.!!$R1 1184
13 TraesCS3B01G341900 chr6B 703062819 703064115 1296 True 810.7 1552 90.0690 767 2009 2 chr6B.!!$R4 1242
14 TraesCS3B01G341900 chr6B 703006919 703008265 1346 True 808.7 1548 90.1495 709 2009 2 chr6B.!!$R3 1300
15 TraesCS3B01G341900 chr1D 198509269 198510575 1306 False 1622.0 1622 89.5610 678 1955 1 chr1D.!!$F1 1277
16 TraesCS3B01G341900 chr2A 14627549 14628808 1259 True 1421.0 1421 87.3340 706 1955 1 chr2A.!!$R1 1249
17 TraesCS3B01G341900 chr4B 644535305 644536049 744 True 1116.0 1116 93.7000 1 746 1 chr4B.!!$R1 745

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
90 91 1.210155 GCGCGCAAGTCTTCCAAAT 59.79 52.632 29.1 0.0 41.68 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 2052 0.106819 GCCCCTCATCTGAGCACAAT 60.107 55.0 1.51 0.0 40.75 2.71 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
90 91 1.210155 GCGCGCAAGTCTTCCAAAT 59.790 52.632 29.10 0.00 41.68 2.32
183 184 3.197116 CGGTAGGTCTTATGGTGGAGTTT 59.803 47.826 0.00 0.00 0.00 2.66
349 350 3.888930 ACATTGGAACGAACAAGGTTGAT 59.111 39.130 0.00 0.00 39.49 2.57
389 390 2.309755 TCCTTTCCTTGATGCCTCACAT 59.690 45.455 0.00 0.00 43.54 3.21
437 441 1.596477 GCCAGATCCCGCACTCATC 60.596 63.158 0.00 0.00 0.00 2.92
474 478 6.465178 GGGAAGAAGAAGAAAGAAGAGGTTCT 60.465 42.308 0.00 0.00 45.56 3.01
506 510 4.482990 TGGATGATCTAGCTGGATACACA 58.517 43.478 13.16 7.45 46.17 3.72
507 511 4.901250 TGGATGATCTAGCTGGATACACAA 59.099 41.667 13.16 0.00 46.17 3.33
587 591 5.010820 TGGAGAATGCAATGAAACATGACAA 59.989 36.000 0.00 0.00 28.48 3.18
596 600 7.011189 GCAATGAAACATGACAAAACATTAGC 58.989 34.615 0.00 5.87 0.00 3.09
677 681 1.619363 CCTTGGAGGGGGTCATGGA 60.619 63.158 0.00 0.00 32.03 3.41
1178 1333 3.944015 GACAGAAAGAAGTCATGGATGGG 59.056 47.826 0.00 0.00 34.93 4.00
1320 1475 9.554724 CAACACTAACATCCATTTTGTATGTAC 57.445 33.333 0.00 0.00 33.59 2.90
1372 1527 4.649692 GTGGATAGATCATGAAGTGCCAT 58.350 43.478 0.00 0.00 0.00 4.40
1380 1535 7.071069 AGATCATGAAGTGCCATAAGATGTA 57.929 36.000 0.00 0.00 0.00 2.29
1433 1588 1.535462 CCAACGGCTGTTCGAAGAAAT 59.465 47.619 8.28 0.00 45.90 2.17
1563 1719 1.505425 CAAGAAAGCTTGCAAAGGCC 58.495 50.000 7.33 0.00 46.35 5.19
1629 1790 2.431057 CCCCGTATGACTCAGTAAAGCT 59.569 50.000 0.00 0.00 0.00 3.74
1790 1987 8.250332 TGAGAACTAAAGTTTGTCAGCAATTTT 58.750 29.630 0.00 0.00 38.56 1.82
1793 1990 7.463544 AACTAAAGTTTGTCAGCAATTTTTGC 58.536 30.769 4.08 4.08 45.79 3.68
1911 2134 3.335729 CCCCCTGGCGGTAGGTTT 61.336 66.667 0.00 0.00 36.02 3.27
1988 2286 4.142966 CGGTTCTGTTACGAGAAAAATCCC 60.143 45.833 0.00 0.00 33.73 3.85
2017 2317 0.758310 GGCGGTAGGGTAAGCCTACT 60.758 60.000 2.36 3.27 45.67 2.57
2028 2328 1.908340 AAGCCTACTGCCAGAGCCTG 61.908 60.000 0.00 0.00 42.71 4.85
2041 2341 4.778143 GCCTGTGGCGGTAGGGTG 62.778 72.222 4.07 0.00 39.62 4.61
2042 2342 3.319198 CCTGTGGCGGTAGGGTGT 61.319 66.667 0.00 0.00 0.00 4.16
2043 2343 2.047274 CTGTGGCGGTAGGGTGTG 60.047 66.667 0.00 0.00 0.00 3.82
2080 2380 4.830600 GGGATGGTTTTTCCTTGTAACAGA 59.169 41.667 0.00 0.00 37.07 3.41
2095 2395 1.077716 CAGAACCGATTCCACCCCC 60.078 63.158 0.00 0.00 35.18 5.40
2117 2417 2.762459 CACCCCCTACCGCTGCTA 60.762 66.667 0.00 0.00 0.00 3.49
2118 2418 2.762875 ACCCCCTACCGCTGCTAC 60.763 66.667 0.00 0.00 0.00 3.58
2119 2419 3.912907 CCCCCTACCGCTGCTACG 61.913 72.222 0.00 0.00 0.00 3.51
2120 2420 3.145551 CCCCTACCGCTGCTACGT 61.146 66.667 0.00 0.00 0.00 3.57
2121 2421 2.412112 CCCTACCGCTGCTACGTC 59.588 66.667 0.00 0.00 0.00 4.34
2122 2422 2.119655 CCCTACCGCTGCTACGTCT 61.120 63.158 0.00 0.00 0.00 4.18
2123 2423 1.664321 CCCTACCGCTGCTACGTCTT 61.664 60.000 0.00 0.00 0.00 3.01
2124 2424 0.525668 CCTACCGCTGCTACGTCTTG 60.526 60.000 0.00 0.00 0.00 3.02
2125 2425 0.450583 CTACCGCTGCTACGTCTTGA 59.549 55.000 0.00 0.00 0.00 3.02
2126 2426 0.450583 TACCGCTGCTACGTCTTGAG 59.549 55.000 0.00 0.00 0.00 3.02
2127 2427 2.161486 CCGCTGCTACGTCTTGAGC 61.161 63.158 0.00 0.00 39.25 4.26
2128 2428 1.153939 CGCTGCTACGTCTTGAGCT 60.154 57.895 9.31 0.00 39.54 4.09
2129 2429 0.734253 CGCTGCTACGTCTTGAGCTT 60.734 55.000 9.31 0.00 39.54 3.74
2130 2430 0.718343 GCTGCTACGTCTTGAGCTTG 59.282 55.000 9.31 4.04 39.54 4.01
2131 2431 1.937108 GCTGCTACGTCTTGAGCTTGT 60.937 52.381 9.31 0.00 39.54 3.16
2132 2432 1.723542 CTGCTACGTCTTGAGCTTGTG 59.276 52.381 9.31 0.00 39.54 3.33
2133 2433 1.068588 TGCTACGTCTTGAGCTTGTGT 59.931 47.619 9.31 0.00 39.54 3.72
2134 2434 2.135933 GCTACGTCTTGAGCTTGTGTT 58.864 47.619 0.00 0.00 35.73 3.32
2135 2435 2.096713 GCTACGTCTTGAGCTTGTGTTG 60.097 50.000 0.00 0.00 35.73 3.33
2136 2436 1.299541 ACGTCTTGAGCTTGTGTTGG 58.700 50.000 0.00 0.00 0.00 3.77
2137 2437 1.299541 CGTCTTGAGCTTGTGTTGGT 58.700 50.000 0.00 0.00 0.00 3.67
2138 2438 1.670811 CGTCTTGAGCTTGTGTTGGTT 59.329 47.619 0.00 0.00 0.00 3.67
2139 2439 2.097466 CGTCTTGAGCTTGTGTTGGTTT 59.903 45.455 0.00 0.00 0.00 3.27
2140 2440 3.427503 CGTCTTGAGCTTGTGTTGGTTTT 60.428 43.478 0.00 0.00 0.00 2.43
2141 2441 4.105486 GTCTTGAGCTTGTGTTGGTTTTC 58.895 43.478 0.00 0.00 0.00 2.29
2142 2442 3.130340 TCTTGAGCTTGTGTTGGTTTTCC 59.870 43.478 0.00 0.00 41.14 3.13
2143 2443 2.733956 TGAGCTTGTGTTGGTTTTCCT 58.266 42.857 0.00 0.00 41.38 3.36
2144 2444 3.096092 TGAGCTTGTGTTGGTTTTCCTT 58.904 40.909 0.00 0.00 41.38 3.36
2145 2445 3.119173 TGAGCTTGTGTTGGTTTTCCTTG 60.119 43.478 0.00 0.00 41.38 3.61
2146 2446 3.096092 AGCTTGTGTTGGTTTTCCTTGA 58.904 40.909 0.00 0.00 41.38 3.02
2147 2447 3.513515 AGCTTGTGTTGGTTTTCCTTGAA 59.486 39.130 0.00 0.00 41.38 2.69
2148 2448 3.865164 GCTTGTGTTGGTTTTCCTTGAAG 59.135 43.478 0.00 0.00 41.38 3.02
2149 2449 4.381505 GCTTGTGTTGGTTTTCCTTGAAGA 60.382 41.667 0.00 0.00 41.38 2.87
2150 2450 4.981806 TGTGTTGGTTTTCCTTGAAGAG 57.018 40.909 0.00 0.00 41.38 2.85
2163 2463 4.431661 CTTGAAGAGGAAAGGTTGATGC 57.568 45.455 0.00 0.00 0.00 3.91
2164 2464 3.507162 TGAAGAGGAAAGGTTGATGCA 57.493 42.857 0.00 0.00 0.00 3.96
2165 2465 3.831323 TGAAGAGGAAAGGTTGATGCAA 58.169 40.909 0.00 0.00 0.00 4.08
2166 2466 3.569701 TGAAGAGGAAAGGTTGATGCAAC 59.430 43.478 0.00 1.82 42.89 4.17
2167 2467 3.228188 AGAGGAAAGGTTGATGCAACA 57.772 42.857 11.83 0.00 45.11 3.33
2168 2468 3.565307 AGAGGAAAGGTTGATGCAACAA 58.435 40.909 5.14 5.14 45.11 2.83
2169 2469 4.154942 AGAGGAAAGGTTGATGCAACAAT 58.845 39.130 12.87 0.00 45.11 2.71
2170 2470 5.324409 AGAGGAAAGGTTGATGCAACAATA 58.676 37.500 12.87 0.00 45.11 1.90
2171 2471 5.416952 AGAGGAAAGGTTGATGCAACAATAG 59.583 40.000 12.87 0.00 45.11 1.73
2172 2472 5.079643 AGGAAAGGTTGATGCAACAATAGT 58.920 37.500 12.87 0.00 45.11 2.12
2173 2473 6.245408 AGGAAAGGTTGATGCAACAATAGTA 58.755 36.000 12.87 0.00 45.11 1.82
2174 2474 6.375455 AGGAAAGGTTGATGCAACAATAGTAG 59.625 38.462 12.87 0.00 45.11 2.57
2175 2475 5.567138 AAGGTTGATGCAACAATAGTAGC 57.433 39.130 12.87 0.00 45.11 3.58
2176 2476 3.623060 AGGTTGATGCAACAATAGTAGCG 59.377 43.478 12.87 0.00 45.11 4.26
2177 2477 3.374058 GGTTGATGCAACAATAGTAGCGT 59.626 43.478 12.87 0.00 45.11 5.07
2178 2478 4.569162 GGTTGATGCAACAATAGTAGCGTA 59.431 41.667 12.87 0.00 45.11 4.42
2179 2479 5.064198 GGTTGATGCAACAATAGTAGCGTAA 59.936 40.000 12.87 0.00 45.11 3.18
2180 2480 5.966636 TGATGCAACAATAGTAGCGTAAG 57.033 39.130 0.00 0.00 43.44 2.34
2181 2481 5.416083 TGATGCAACAATAGTAGCGTAAGT 58.584 37.500 0.00 0.00 41.68 2.24
2182 2482 6.566141 TGATGCAACAATAGTAGCGTAAGTA 58.434 36.000 0.00 0.00 41.68 2.24
2183 2483 7.207383 TGATGCAACAATAGTAGCGTAAGTAT 58.793 34.615 0.00 0.00 41.68 2.12
2184 2484 7.709182 TGATGCAACAATAGTAGCGTAAGTATT 59.291 33.333 0.00 0.00 41.68 1.89
2185 2485 7.837202 TGCAACAATAGTAGCGTAAGTATTT 57.163 32.000 0.00 0.00 41.68 1.40
2186 2486 7.902032 TGCAACAATAGTAGCGTAAGTATTTC 58.098 34.615 0.00 0.00 41.68 2.17
2187 2487 7.010738 TGCAACAATAGTAGCGTAAGTATTTCC 59.989 37.037 0.00 0.00 41.68 3.13
2188 2488 7.517893 GCAACAATAGTAGCGTAAGTATTTCCC 60.518 40.741 0.00 0.00 41.68 3.97
2189 2489 7.357429 ACAATAGTAGCGTAAGTATTTCCCT 57.643 36.000 0.00 0.00 41.68 4.20
2190 2490 7.432059 ACAATAGTAGCGTAAGTATTTCCCTC 58.568 38.462 0.00 0.00 41.68 4.30
2191 2491 7.069085 ACAATAGTAGCGTAAGTATTTCCCTCA 59.931 37.037 0.00 0.00 41.68 3.86
2192 2492 5.517322 AGTAGCGTAAGTATTTCCCTCAG 57.483 43.478 0.00 0.00 41.68 3.35
2193 2493 4.954826 AGTAGCGTAAGTATTTCCCTCAGT 59.045 41.667 0.00 0.00 41.68 3.41
2194 2494 4.820894 AGCGTAAGTATTTCCCTCAGTT 57.179 40.909 0.00 0.00 41.68 3.16
2195 2495 5.161943 AGCGTAAGTATTTCCCTCAGTTT 57.838 39.130 0.00 0.00 41.68 2.66
2196 2496 5.176592 AGCGTAAGTATTTCCCTCAGTTTC 58.823 41.667 0.00 0.00 41.68 2.78
2197 2497 5.046520 AGCGTAAGTATTTCCCTCAGTTTCT 60.047 40.000 0.00 0.00 41.68 2.52
2198 2498 5.063564 GCGTAAGTATTTCCCTCAGTTTCTG 59.936 44.000 0.00 0.00 41.68 3.02
2199 2499 6.395629 CGTAAGTATTTCCCTCAGTTTCTGA 58.604 40.000 0.00 0.00 38.25 3.27
2213 2513 6.826668 TCAGTTTCTGAGAACCAAGTTATCA 58.173 36.000 0.00 4.87 40.68 2.15
2214 2514 7.279615 TCAGTTTCTGAGAACCAAGTTATCAA 58.720 34.615 6.30 0.00 42.00 2.57
2215 2515 7.939039 TCAGTTTCTGAGAACCAAGTTATCAAT 59.061 33.333 6.30 0.00 42.00 2.57
2216 2516 8.233190 CAGTTTCTGAGAACCAAGTTATCAATC 58.767 37.037 6.30 0.00 42.00 2.67
2217 2517 7.391833 AGTTTCTGAGAACCAAGTTATCAATCC 59.608 37.037 6.30 0.00 42.00 3.01
2218 2518 6.373005 TCTGAGAACCAAGTTATCAATCCA 57.627 37.500 6.30 0.00 42.00 3.41
2219 2519 6.409704 TCTGAGAACCAAGTTATCAATCCAG 58.590 40.000 6.30 0.00 42.00 3.86
2220 2520 6.013379 TCTGAGAACCAAGTTATCAATCCAGT 60.013 38.462 6.30 0.00 42.00 4.00
2221 2521 7.180229 TCTGAGAACCAAGTTATCAATCCAGTA 59.820 37.037 6.30 0.00 42.00 2.74
2222 2522 7.331026 TGAGAACCAAGTTATCAATCCAGTAG 58.669 38.462 2.50 0.00 40.14 2.57
2223 2523 6.653989 AGAACCAAGTTATCAATCCAGTAGG 58.346 40.000 0.00 0.00 0.00 3.18
2224 2524 7.364762 GAGAACCAAGTTATCAATCCAGTAGGA 60.365 40.741 0.00 0.00 39.66 2.94
2232 2532 3.904717 TCAATCCAGTAGGAGTCTCCTC 58.095 50.000 25.21 15.86 45.66 3.71
2233 2533 3.269643 TCAATCCAGTAGGAGTCTCCTCA 59.730 47.826 25.21 9.08 45.66 3.86
2234 2534 4.026744 CAATCCAGTAGGAGTCTCCTCAA 58.973 47.826 25.21 5.93 45.66 3.02
2235 2535 3.827817 TCCAGTAGGAGTCTCCTCAAA 57.172 47.619 25.21 5.12 45.66 2.69
2236 2536 4.127918 TCCAGTAGGAGTCTCCTCAAAA 57.872 45.455 25.21 4.72 45.66 2.44
2237 2537 4.090090 TCCAGTAGGAGTCTCCTCAAAAG 58.910 47.826 25.21 11.38 45.66 2.27
2238 2538 3.835395 CCAGTAGGAGTCTCCTCAAAAGT 59.165 47.826 25.21 7.77 45.66 2.66
2239 2539 4.081917 CCAGTAGGAGTCTCCTCAAAAGTC 60.082 50.000 25.21 8.10 45.66 3.01
2240 2540 4.081917 CAGTAGGAGTCTCCTCAAAAGTCC 60.082 50.000 25.21 0.00 45.66 3.85
2241 2541 2.261729 AGGAGTCTCCTCAAAAGTCCC 58.738 52.381 16.28 0.00 45.66 4.46
2242 2542 1.978580 GGAGTCTCCTCAAAAGTCCCA 59.021 52.381 12.02 0.00 39.64 4.37
2243 2543 2.289756 GGAGTCTCCTCAAAAGTCCCAC 60.290 54.545 12.02 0.00 39.64 4.61
2244 2544 1.344763 AGTCTCCTCAAAAGTCCCACG 59.655 52.381 0.00 0.00 0.00 4.94
2245 2545 0.034896 TCTCCTCAAAAGTCCCACGC 59.965 55.000 0.00 0.00 0.00 5.34
2246 2546 0.250295 CTCCTCAAAAGTCCCACGCA 60.250 55.000 0.00 0.00 0.00 5.24
2247 2547 0.534203 TCCTCAAAAGTCCCACGCAC 60.534 55.000 0.00 0.00 0.00 5.34
2248 2548 1.515521 CCTCAAAAGTCCCACGCACC 61.516 60.000 0.00 0.00 0.00 5.01
2249 2549 0.535102 CTCAAAAGTCCCACGCACCT 60.535 55.000 0.00 0.00 0.00 4.00
2250 2550 0.759959 TCAAAAGTCCCACGCACCTA 59.240 50.000 0.00 0.00 0.00 3.08
2251 2551 0.872388 CAAAAGTCCCACGCACCTAC 59.128 55.000 0.00 0.00 0.00 3.18
2252 2552 0.470766 AAAAGTCCCACGCACCTACA 59.529 50.000 0.00 0.00 0.00 2.74
2253 2553 0.250166 AAAGTCCCACGCACCTACAC 60.250 55.000 0.00 0.00 0.00 2.90
2254 2554 1.404479 AAGTCCCACGCACCTACACA 61.404 55.000 0.00 0.00 0.00 3.72
2255 2555 1.070105 GTCCCACGCACCTACACAA 59.930 57.895 0.00 0.00 0.00 3.33
2256 2556 0.533308 GTCCCACGCACCTACACAAA 60.533 55.000 0.00 0.00 0.00 2.83
2257 2557 0.533308 TCCCACGCACCTACACAAAC 60.533 55.000 0.00 0.00 0.00 2.93
2258 2558 0.816018 CCCACGCACCTACACAAACA 60.816 55.000 0.00 0.00 0.00 2.83
2259 2559 1.018148 CCACGCACCTACACAAACAA 58.982 50.000 0.00 0.00 0.00 2.83
2260 2560 1.402259 CCACGCACCTACACAAACAAA 59.598 47.619 0.00 0.00 0.00 2.83
2261 2561 2.446282 CACGCACCTACACAAACAAAC 58.554 47.619 0.00 0.00 0.00 2.93
2262 2562 2.085320 ACGCACCTACACAAACAAACA 58.915 42.857 0.00 0.00 0.00 2.83
2263 2563 2.488545 ACGCACCTACACAAACAAACAA 59.511 40.909 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
42 43 4.118168 ACAACCAATCCTGAACCTTCAT 57.882 40.909 0.00 0.00 36.46 2.57
44 45 3.552890 GCAACAACCAATCCTGAACCTTC 60.553 47.826 0.00 0.00 0.00 3.46
120 121 4.325741 CGGCTCATCGATTTGATAGATCAC 59.674 45.833 0.00 0.00 36.36 3.06
291 292 0.468226 ACCGTTGTGCCATCGGATAT 59.532 50.000 23.09 6.24 46.01 1.63
312 313 1.333308 CAATGTGAACTCGTGCAACCA 59.667 47.619 0.00 0.00 0.00 3.67
349 350 2.243810 GATTAAACCAAGGCACCCACA 58.756 47.619 0.00 0.00 0.00 4.17
389 390 2.897207 CCGTGATACTCGGGCCAA 59.103 61.111 4.39 0.00 43.68 4.52
437 441 0.830648 TTCTTCCCCTCATAGGCACG 59.169 55.000 0.00 0.00 32.73 5.34
474 478 3.323115 GCTAGATCATCCATGTCACTCCA 59.677 47.826 0.00 0.00 0.00 3.86
506 510 5.539955 ACCACTACCAAATTGCTTCATTCTT 59.460 36.000 0.00 0.00 0.00 2.52
507 511 5.079643 ACCACTACCAAATTGCTTCATTCT 58.920 37.500 0.00 0.00 0.00 2.40
587 591 4.002982 TCTTCGTGCATCTGCTAATGTTT 58.997 39.130 3.53 0.00 42.66 2.83
596 600 3.849911 TCTAGGTTTCTTCGTGCATCTG 58.150 45.455 0.00 0.00 0.00 2.90
677 681 0.971447 GGCTAGTCCTTCCTCCACGT 60.971 60.000 0.00 0.00 0.00 4.49
1178 1333 5.707764 GGGCATACAAAATATCTCCTTCCTC 59.292 44.000 0.00 0.00 0.00 3.71
1320 1475 1.365633 GCATAGAGGAGGCGGTGAG 59.634 63.158 0.00 0.00 0.00 3.51
1372 1527 9.967451 TTCATATTGGTCCTTTTGTACATCTTA 57.033 29.630 0.00 0.00 0.00 2.10
1380 1535 7.671398 AGACAATCTTCATATTGGTCCTTTTGT 59.329 33.333 0.00 0.00 40.48 2.83
1433 1588 2.963101 TCCTCCAAGACTCTTCGAAACA 59.037 45.455 0.00 0.00 0.00 2.83
1445 1600 0.894184 ACGACGCTCTTCCTCCAAGA 60.894 55.000 0.00 0.00 38.95 3.02
1492 1648 4.382541 TGCCCTCTCCTCCTCGCA 62.383 66.667 0.00 0.00 0.00 5.10
1528 1684 0.906756 CTTGCCCTCTCCTCCTCACA 60.907 60.000 0.00 0.00 0.00 3.58
1563 1719 0.607489 CCTCCTCTTGTGCCTTGTGG 60.607 60.000 0.00 0.00 0.00 4.17
1790 1987 5.345472 CACATAAATTGCTGACAAATCGCAA 59.655 36.000 2.71 2.71 43.45 4.85
1793 1990 6.968335 TCATCACATAAATTGCTGACAAATCG 59.032 34.615 0.00 0.00 39.77 3.34
1834 2052 0.106819 GCCCCTCATCTGAGCACAAT 60.107 55.000 1.51 0.00 40.75 2.71
1911 2134 4.020617 CTGGCGGCAGGGTTCAGA 62.021 66.667 30.03 0.00 0.00 3.27
2028 2328 2.047560 GTCACACCCTACCGCCAC 60.048 66.667 0.00 0.00 0.00 5.01
2039 2339 1.375523 CTTGGCGGTAGGGTCACAC 60.376 63.158 0.00 0.00 0.00 3.82
2041 2341 2.267961 CCTTGGCGGTAGGGTCAC 59.732 66.667 0.00 0.00 0.00 3.67
2042 2342 3.006728 CCCTTGGCGGTAGGGTCA 61.007 66.667 10.18 0.00 46.16 4.02
2072 2372 2.289819 GGGTGGAATCGGTTCTGTTACA 60.290 50.000 8.59 0.00 34.68 2.41
2073 2373 2.353323 GGGTGGAATCGGTTCTGTTAC 58.647 52.381 8.59 3.15 34.68 2.50
2080 2380 2.931649 ACGGGGGTGGAATCGGTT 60.932 61.111 0.00 0.00 0.00 4.44
2113 2413 1.068588 ACACAAGCTCAAGACGTAGCA 59.931 47.619 10.48 0.00 41.32 3.49
2114 2414 1.784525 ACACAAGCTCAAGACGTAGC 58.215 50.000 0.00 0.00 39.08 3.58
2115 2415 2.476619 CCAACACAAGCTCAAGACGTAG 59.523 50.000 0.00 0.00 0.00 3.51
2116 2416 2.159014 ACCAACACAAGCTCAAGACGTA 60.159 45.455 0.00 0.00 0.00 3.57
2117 2417 1.299541 CCAACACAAGCTCAAGACGT 58.700 50.000 0.00 0.00 0.00 4.34
2118 2418 1.299541 ACCAACACAAGCTCAAGACG 58.700 50.000 0.00 0.00 0.00 4.18
2119 2419 3.782889 AAACCAACACAAGCTCAAGAC 57.217 42.857 0.00 0.00 0.00 3.01
2120 2420 3.130340 GGAAAACCAACACAAGCTCAAGA 59.870 43.478 0.00 0.00 0.00 3.02
2121 2421 3.131046 AGGAAAACCAACACAAGCTCAAG 59.869 43.478 0.00 0.00 0.00 3.02
2122 2422 3.096092 AGGAAAACCAACACAAGCTCAA 58.904 40.909 0.00 0.00 0.00 3.02
2123 2423 2.733956 AGGAAAACCAACACAAGCTCA 58.266 42.857 0.00 0.00 0.00 4.26
2124 2424 3.130340 TCAAGGAAAACCAACACAAGCTC 59.870 43.478 0.00 0.00 0.00 4.09
2125 2425 3.096092 TCAAGGAAAACCAACACAAGCT 58.904 40.909 0.00 0.00 0.00 3.74
2126 2426 3.518634 TCAAGGAAAACCAACACAAGC 57.481 42.857 0.00 0.00 0.00 4.01
2127 2427 5.323371 TCTTCAAGGAAAACCAACACAAG 57.677 39.130 0.00 0.00 0.00 3.16
2128 2428 5.323371 CTCTTCAAGGAAAACCAACACAA 57.677 39.130 0.00 0.00 0.00 3.33
2129 2429 4.981806 CTCTTCAAGGAAAACCAACACA 57.018 40.909 0.00 0.00 0.00 3.72
2141 2441 8.664750 GTTGCATCAACCTTTCCTCTTCAAGG 62.665 46.154 0.00 0.00 44.68 3.61
2142 2442 3.822735 TGCATCAACCTTTCCTCTTCAAG 59.177 43.478 0.00 0.00 0.00 3.02
2143 2443 3.831323 TGCATCAACCTTTCCTCTTCAA 58.169 40.909 0.00 0.00 0.00 2.69
2144 2444 3.507162 TGCATCAACCTTTCCTCTTCA 57.493 42.857 0.00 0.00 0.00 3.02
2145 2445 3.569701 TGTTGCATCAACCTTTCCTCTTC 59.430 43.478 7.17 0.00 42.96 2.87
2146 2446 3.565307 TGTTGCATCAACCTTTCCTCTT 58.435 40.909 7.17 0.00 42.96 2.85
2147 2447 3.228188 TGTTGCATCAACCTTTCCTCT 57.772 42.857 7.17 0.00 42.96 3.69
2148 2448 4.525912 ATTGTTGCATCAACCTTTCCTC 57.474 40.909 12.26 0.00 42.96 3.71
2149 2449 5.079643 ACTATTGTTGCATCAACCTTTCCT 58.920 37.500 12.26 0.00 42.96 3.36
2150 2450 5.391312 ACTATTGTTGCATCAACCTTTCC 57.609 39.130 12.26 0.00 42.96 3.13
2151 2451 6.030228 GCTACTATTGTTGCATCAACCTTTC 58.970 40.000 12.26 0.00 42.96 2.62
2152 2452 5.391950 CGCTACTATTGTTGCATCAACCTTT 60.392 40.000 12.26 0.00 42.96 3.11
2153 2453 4.094887 CGCTACTATTGTTGCATCAACCTT 59.905 41.667 12.26 0.29 42.96 3.50
2154 2454 3.623060 CGCTACTATTGTTGCATCAACCT 59.377 43.478 12.26 0.98 42.96 3.50
2155 2455 3.374058 ACGCTACTATTGTTGCATCAACC 59.626 43.478 12.26 0.00 42.96 3.77
2156 2456 4.600012 ACGCTACTATTGTTGCATCAAC 57.400 40.909 12.26 2.96 43.29 3.18
2157 2457 5.872617 ACTTACGCTACTATTGTTGCATCAA 59.127 36.000 12.39 12.39 43.29 2.57
2158 2458 5.416083 ACTTACGCTACTATTGTTGCATCA 58.584 37.500 13.11 0.00 43.29 3.07
2159 2459 5.968387 ACTTACGCTACTATTGTTGCATC 57.032 39.130 13.11 0.00 43.29 3.91
2160 2460 8.433421 AAATACTTACGCTACTATTGTTGCAT 57.567 30.769 13.11 1.45 43.29 3.96
2161 2461 7.010738 GGAAATACTTACGCTACTATTGTTGCA 59.989 37.037 13.11 0.00 43.29 4.08
2162 2462 7.342942 GGAAATACTTACGCTACTATTGTTGC 58.657 38.462 3.87 3.87 40.56 4.17
2163 2463 7.709613 AGGGAAATACTTACGCTACTATTGTTG 59.290 37.037 0.00 0.00 0.00 3.33
2164 2464 7.789026 AGGGAAATACTTACGCTACTATTGTT 58.211 34.615 0.00 0.00 0.00 2.83
2165 2465 7.069085 TGAGGGAAATACTTACGCTACTATTGT 59.931 37.037 0.00 0.00 0.00 2.71
2166 2466 7.431249 TGAGGGAAATACTTACGCTACTATTG 58.569 38.462 0.00 0.00 0.00 1.90
2167 2467 7.287235 ACTGAGGGAAATACTTACGCTACTATT 59.713 37.037 0.00 0.00 0.00 1.73
2168 2468 6.776603 ACTGAGGGAAATACTTACGCTACTAT 59.223 38.462 0.00 0.00 0.00 2.12
2169 2469 6.125029 ACTGAGGGAAATACTTACGCTACTA 58.875 40.000 0.00 0.00 0.00 1.82
2170 2470 4.954826 ACTGAGGGAAATACTTACGCTACT 59.045 41.667 0.00 0.00 0.00 2.57
2171 2471 5.259832 ACTGAGGGAAATACTTACGCTAC 57.740 43.478 0.00 0.00 0.00 3.58
2172 2472 5.927281 AACTGAGGGAAATACTTACGCTA 57.073 39.130 0.00 0.00 0.00 4.26
2173 2473 4.820894 AACTGAGGGAAATACTTACGCT 57.179 40.909 0.00 0.00 0.00 5.07
2174 2474 5.063564 CAGAAACTGAGGGAAATACTTACGC 59.936 44.000 0.00 0.00 32.44 4.42
2175 2475 6.395629 TCAGAAACTGAGGGAAATACTTACG 58.604 40.000 0.00 0.00 35.39 3.18
2189 2489 6.826668 TGATAACTTGGTTCTCAGAAACTGA 58.173 36.000 3.56 0.00 38.25 3.41
2190 2490 7.496529 TTGATAACTTGGTTCTCAGAAACTG 57.503 36.000 3.56 0.00 32.03 3.16
2191 2491 7.391833 GGATTGATAACTTGGTTCTCAGAAACT 59.608 37.037 3.56 0.00 32.03 2.66
2192 2492 7.174946 TGGATTGATAACTTGGTTCTCAGAAAC 59.825 37.037 0.00 0.00 32.03 2.78
2193 2493 7.230747 TGGATTGATAACTTGGTTCTCAGAAA 58.769 34.615 0.00 0.00 32.03 2.52
2194 2494 6.778821 TGGATTGATAACTTGGTTCTCAGAA 58.221 36.000 0.00 0.00 32.03 3.02
2195 2495 6.013379 ACTGGATTGATAACTTGGTTCTCAGA 60.013 38.462 0.00 0.00 32.03 3.27
2196 2496 6.176183 ACTGGATTGATAACTTGGTTCTCAG 58.824 40.000 0.00 0.00 32.03 3.35
2197 2497 6.126863 ACTGGATTGATAACTTGGTTCTCA 57.873 37.500 0.00 0.00 29.16 3.27
2198 2498 6.763610 CCTACTGGATTGATAACTTGGTTCTC 59.236 42.308 0.00 0.00 34.57 2.87
2199 2499 6.443849 TCCTACTGGATTGATAACTTGGTTCT 59.556 38.462 0.00 0.00 37.46 3.01
2200 2500 6.650120 TCCTACTGGATTGATAACTTGGTTC 58.350 40.000 0.00 0.00 37.46 3.62
2201 2501 6.215636 ACTCCTACTGGATTGATAACTTGGTT 59.784 38.462 0.00 0.00 42.29 3.67
2202 2502 5.726793 ACTCCTACTGGATTGATAACTTGGT 59.273 40.000 0.00 0.00 42.29 3.67
2203 2503 6.098982 AGACTCCTACTGGATTGATAACTTGG 59.901 42.308 0.00 0.00 42.29 3.61
2204 2504 7.118496 AGACTCCTACTGGATTGATAACTTG 57.882 40.000 0.00 0.00 42.29 3.16
2205 2505 6.325286 GGAGACTCCTACTGGATTGATAACTT 59.675 42.308 14.72 0.00 42.29 2.66
2206 2506 5.836358 GGAGACTCCTACTGGATTGATAACT 59.164 44.000 14.72 0.00 42.29 2.24
2207 2507 6.091718 GGAGACTCCTACTGGATTGATAAC 57.908 45.833 14.72 0.00 42.29 1.89
2225 2525 1.797025 CGTGGGACTTTTGAGGAGAC 58.203 55.000 0.00 0.00 0.00 3.36
2226 2526 0.034896 GCGTGGGACTTTTGAGGAGA 59.965 55.000 0.00 0.00 0.00 3.71
2227 2527 0.250295 TGCGTGGGACTTTTGAGGAG 60.250 55.000 0.00 0.00 0.00 3.69
2228 2528 0.534203 GTGCGTGGGACTTTTGAGGA 60.534 55.000 0.00 0.00 0.00 3.71
2229 2529 1.515521 GGTGCGTGGGACTTTTGAGG 61.516 60.000 0.00 0.00 0.00 3.86
2230 2530 0.535102 AGGTGCGTGGGACTTTTGAG 60.535 55.000 0.00 0.00 0.00 3.02
2231 2531 0.759959 TAGGTGCGTGGGACTTTTGA 59.240 50.000 0.00 0.00 0.00 2.69
2232 2532 0.872388 GTAGGTGCGTGGGACTTTTG 59.128 55.000 0.00 0.00 0.00 2.44
2233 2533 0.470766 TGTAGGTGCGTGGGACTTTT 59.529 50.000 0.00 0.00 0.00 2.27
2234 2534 0.250166 GTGTAGGTGCGTGGGACTTT 60.250 55.000 0.00 0.00 0.00 2.66
2235 2535 1.370064 GTGTAGGTGCGTGGGACTT 59.630 57.895 0.00 0.00 0.00 3.01
2236 2536 1.404479 TTGTGTAGGTGCGTGGGACT 61.404 55.000 0.00 0.00 0.00 3.85
2237 2537 0.533308 TTTGTGTAGGTGCGTGGGAC 60.533 55.000 0.00 0.00 0.00 4.46
2238 2538 0.533308 GTTTGTGTAGGTGCGTGGGA 60.533 55.000 0.00 0.00 0.00 4.37
2239 2539 0.816018 TGTTTGTGTAGGTGCGTGGG 60.816 55.000 0.00 0.00 0.00 4.61
2240 2540 1.018148 TTGTTTGTGTAGGTGCGTGG 58.982 50.000 0.00 0.00 0.00 4.94
2241 2541 2.159503 TGTTTGTTTGTGTAGGTGCGTG 60.160 45.455 0.00 0.00 0.00 5.34
2242 2542 2.085320 TGTTTGTTTGTGTAGGTGCGT 58.915 42.857 0.00 0.00 0.00 5.24
2243 2543 2.834574 TGTTTGTTTGTGTAGGTGCG 57.165 45.000 0.00 0.00 0.00 5.34


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

AutoCloner maintained by Alex Coulton.