Multiple sequence alignment - TraesCS5A01G156700

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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 TraesCS5A01G156700 chr5A 100.000 4324 0 0 1 4324 335673776 335678099 0.000000e+00 7986.0
1 TraesCS5A01G156700 chr5D 96.947 2227 60 6 1 2223 253179527 253181749 0.000000e+00 3729.0
2 TraesCS5A01G156700 chr5D 93.641 2013 65 18 2345 4324 253181746 253183728 0.000000e+00 2950.0
3 TraesCS5A01G156700 chr5B 95.191 2225 89 7 1 2223 285500705 285502913 0.000000e+00 3500.0
4 TraesCS5A01G156700 chr5B 93.965 2005 66 15 2345 4321 285502910 285504887 0.000000e+00 2981.0
5 TraesCS5A01G156700 chr5B 98.519 135 1 1 2213 2346 341535185 341535319 2.010000e-58 237.0
6 TraesCS5A01G156700 chr5B 100.000 127 0 0 2220 2346 697172536 697172410 7.230000e-58 235.0
7 TraesCS5A01G156700 chrUn 85.163 337 39 7 2358 2687 224667066 224666734 6.930000e-88 335.0
8 TraesCS5A01G156700 chrUn 79.574 235 22 6 2565 2799 67091782 67091990 1.250000e-30 145.0
9 TraesCS5A01G156700 chr4B 99.242 132 1 0 2215 2346 642978710 642978579 5.590000e-59 239.0
10 TraesCS5A01G156700 chr4B 84.615 91 13 1 1295 1385 68662506 68662417 5.960000e-14 89.8
11 TraesCS5A01G156700 chr7A 100.000 128 0 0 2220 2347 295905599 295905472 2.010000e-58 237.0
12 TraesCS5A01G156700 chr7A 99.242 132 0 1 2217 2347 721227146 721227277 2.010000e-58 237.0
13 TraesCS5A01G156700 chr4A 97.810 137 2 1 2213 2348 626166212 626166348 7.230000e-58 235.0
14 TraesCS5A01G156700 chr2B 100.000 127 0 0 2220 2346 111069154 111069028 7.230000e-58 235.0
15 TraesCS5A01G156700 chr1B 99.225 129 1 0 2219 2347 436213094 436213222 2.600000e-57 233.0
16 TraesCS5A01G156700 chr3B 95.714 140 6 0 2212 2351 763346121 763345982 4.350000e-55 226.0
17 TraesCS5A01G156700 chr1D 89.610 77 7 1 1307 1383 375958800 375958875 3.560000e-16 97.1
18 TraesCS5A01G156700 chr1D 86.047 86 11 1 1299 1384 196479021 196479105 1.660000e-14 91.6
19 TraesCS5A01G156700 chr1D 84.444 90 14 0 1298 1387 372835753 372835842 5.960000e-14 89.8
20 TraesCS5A01G156700 chr2D 84.946 93 14 0 1292 1384 522984065 522984157 1.280000e-15 95.3
21 TraesCS5A01G156700 chr2A 83.871 93 13 2 1292 1384 668047894 668047984 2.140000e-13 87.9
22 TraesCS5A01G156700 chr6B 84.091 88 12 2 1298 1384 27938510 27938424 2.770000e-12 84.2


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 TraesCS5A01G156700 chr5A 335673776 335678099 4323 False 7986.0 7986 100.000 1 4324 1 chr5A.!!$F1 4323
1 TraesCS5A01G156700 chr5D 253179527 253183728 4201 False 3339.5 3729 95.294 1 4324 2 chr5D.!!$F1 4323
2 TraesCS5A01G156700 chr5B 285500705 285504887 4182 False 3240.5 3500 94.578 1 4321 2 chr5B.!!$F2 4320

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
378 379 0.036875 ACTTCCTTCTTGCCCTTCCG 59.963 55.0 0.0 0.0 0.00 4.30 F
1581 1586 1.177401 CTCCTGTGACCAGATGACGA 58.823 55.0 0.0 0.0 41.50 4.20 F
1943 1948 0.960364 TTTCAGATCCTGTTGCCGCC 60.960 55.0 0.0 0.0 32.61 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1621 1626 0.034059 GCCATCATAGGACAGACGGG 59.966 60.0 0.00 0.00 0.0 5.28 R
2867 2884 0.329261 TTGGAGACTGGAATGCAGGG 59.671 55.0 6.73 0.00 0.0 4.45 R
3637 3676 1.128513 TTGATATTAGACTGCGCGCG 58.871 50.0 28.44 28.44 0.0 6.86 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
163 164 4.339247 ACAATGAATACAATGGGCTACTGC 59.661 41.667 0.00 0.00 31.86 4.40
224 225 8.116651 TCCAGATCTATGATACTCTACAAAGC 57.883 38.462 0.00 0.00 0.00 3.51
262 263 3.447586 TGAGTACTGATGAGGTTAGCCAC 59.552 47.826 0.00 0.00 37.19 5.01
378 379 0.036875 ACTTCCTTCTTGCCCTTCCG 59.963 55.000 0.00 0.00 0.00 4.30
396 397 3.093814 TCCGTTGCATCTACCAGTCTAA 58.906 45.455 0.00 0.00 0.00 2.10
439 440 1.896122 GCACAAGGGCCTAGGTACGT 61.896 60.000 6.41 2.77 0.00 3.57
545 548 8.465273 AGGAAAAGTAAGTTAGCACTTTGAAT 57.535 30.769 3.58 0.00 42.62 2.57
612 615 8.587608 TGATCAACCTTCAAAATTCAGCTAAAT 58.412 29.630 0.00 0.00 0.00 1.40
763 768 5.714333 TGGTTTCATGCACATACCTGTAATT 59.286 36.000 9.64 0.00 33.14 1.40
785 790 6.716934 TTTCCATTAAAAAGCACACACCTA 57.283 33.333 0.00 0.00 0.00 3.08
809 814 6.426980 TGTTTTATTGTGCTCTGCTCATAG 57.573 37.500 0.00 0.00 32.16 2.23
1327 1332 7.603784 TCACTCCGATCCATAATAATTGTCATG 59.396 37.037 0.00 0.00 0.00 3.07
1411 1416 6.323482 TCCCAAGAATGACACTTCAAATCAAA 59.677 34.615 0.00 0.00 34.61 2.69
1532 1537 4.174009 CTGGTTTAGATACCACACGTGAG 58.826 47.826 25.01 15.20 43.14 3.51
1581 1586 1.177401 CTCCTGTGACCAGATGACGA 58.823 55.000 0.00 0.00 41.50 4.20
1943 1948 0.960364 TTTCAGATCCTGTTGCCGCC 60.960 55.000 0.00 0.00 32.61 6.13
1962 1967 1.603678 CCGCATTCAAAAGCAGCTGTT 60.604 47.619 16.64 6.37 0.00 3.16
2022 2027 2.744202 CACTGGAACACAAGGTATGCTC 59.256 50.000 0.00 0.00 0.00 4.26
2038 2043 8.396272 AGGTATGCTCATGTTGTTTAATATCC 57.604 34.615 0.00 0.00 0.00 2.59
2045 2050 7.184800 TCATGTTGTTTAATATCCGGATTCG 57.815 36.000 24.71 0.00 0.00 3.34
2110 2115 5.762218 AGAATGGCAAAGATCATACTACAGC 59.238 40.000 0.00 0.00 0.00 4.40
2152 2157 6.864685 TCACTTACAGTTACGTTCTTATGGTG 59.135 38.462 0.00 0.00 0.00 4.17
2206 2212 6.172136 TGCCAATTTGTTATCCCATAATGG 57.828 37.500 0.00 0.00 37.25 3.16
2227 2233 8.697507 AATGGTGATGAAAATTATACTCCCTC 57.302 34.615 0.00 0.00 0.00 4.30
2228 2234 6.601332 TGGTGATGAAAATTATACTCCCTCC 58.399 40.000 0.00 0.00 0.00 4.30
2229 2235 5.701290 GGTGATGAAAATTATACTCCCTCCG 59.299 44.000 0.00 0.00 0.00 4.63
2231 2237 6.766467 GTGATGAAAATTATACTCCCTCCGTT 59.234 38.462 0.00 0.00 0.00 4.44
2232 2238 6.990349 TGATGAAAATTATACTCCCTCCGTTC 59.010 38.462 0.00 0.00 0.00 3.95
2233 2239 5.677567 TGAAAATTATACTCCCTCCGTTCC 58.322 41.667 0.00 0.00 0.00 3.62
2234 2240 4.332428 AAATTATACTCCCTCCGTTCCG 57.668 45.455 0.00 0.00 0.00 4.30
2235 2241 2.734755 TTATACTCCCTCCGTTCCGA 57.265 50.000 0.00 0.00 0.00 4.55
2236 2242 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
2237 2243 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
2238 2244 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
2239 2245 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
2240 2246 1.479730 ACTCCCTCCGTTCCGAATTAC 59.520 52.381 0.00 0.00 0.00 1.89
2241 2247 1.755380 CTCCCTCCGTTCCGAATTACT 59.245 52.381 0.00 0.00 0.00 2.24
2242 2248 2.167900 CTCCCTCCGTTCCGAATTACTT 59.832 50.000 0.00 0.00 0.00 2.24
2243 2249 2.093869 TCCCTCCGTTCCGAATTACTTG 60.094 50.000 0.00 0.00 0.00 3.16
2244 2250 2.354403 CCCTCCGTTCCGAATTACTTGT 60.354 50.000 0.00 0.00 0.00 3.16
2245 2251 2.928116 CCTCCGTTCCGAATTACTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
2246 2252 3.368116 CCTCCGTTCCGAATTACTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
2247 2253 4.243270 CTCCGTTCCGAATTACTTGTCTT 58.757 43.478 0.00 0.00 0.00 3.01
2248 2254 3.991773 TCCGTTCCGAATTACTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
2249 2255 3.124636 CCGTTCCGAATTACTTGTCTTGG 59.875 47.826 0.00 0.00 0.00 3.61
2250 2256 3.991773 CGTTCCGAATTACTTGTCTTGGA 59.008 43.478 0.00 0.00 0.00 3.53
2251 2257 4.630069 CGTTCCGAATTACTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
2252 2258 5.121768 CGTTCCGAATTACTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
2253 2259 6.348213 CGTTCCGAATTACTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
2254 2260 6.494893 TCCGAATTACTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
2255 2261 6.001460 TCCGAATTACTTGTCTTGGATTTGT 58.999 36.000 0.00 0.00 0.00 2.83
2256 2262 6.148811 TCCGAATTACTTGTCTTGGATTTGTC 59.851 38.462 0.00 0.00 0.00 3.18
2257 2263 6.149474 CCGAATTACTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
2258 2264 7.333423 CCGAATTACTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
2259 2265 8.383619 CGAATTACTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
2260 2266 9.436957 GAATTACTTGTCTTGGATTTGTCTAGA 57.563 33.333 0.00 0.00 0.00 2.43
2261 2267 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2263 2269 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
2264 2270 7.907389 ACTTGTCTTGGATTTGTCTAGATACA 58.093 34.615 0.00 0.00 0.00 2.29
2265 2271 8.037758 ACTTGTCTTGGATTTGTCTAGATACAG 58.962 37.037 0.00 0.00 0.00 2.74
2266 2272 7.718334 TGTCTTGGATTTGTCTAGATACAGA 57.282 36.000 0.00 0.00 0.00 3.41
2267 2273 8.311395 TGTCTTGGATTTGTCTAGATACAGAT 57.689 34.615 0.00 0.00 0.00 2.90
2268 2274 8.200120 TGTCTTGGATTTGTCTAGATACAGATG 58.800 37.037 0.00 0.00 0.00 2.90
2269 2275 8.200792 GTCTTGGATTTGTCTAGATACAGATGT 58.799 37.037 0.00 0.00 0.00 3.06
2270 2276 9.421399 TCTTGGATTTGTCTAGATACAGATGTA 57.579 33.333 0.00 0.00 34.67 2.29
2289 2295 9.190858 CAGATGTATCTAGACTCATTTTAGTGC 57.809 37.037 11.25 0.69 34.85 4.40
2290 2296 9.142014 AGATGTATCTAGACTCATTTTAGTGCT 57.858 33.333 11.25 2.44 34.85 4.40
2293 2299 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
2297 2303 9.854668 TCTAGACTCATTTTAGTGCTAGATACT 57.145 33.333 0.00 0.00 34.69 2.12
2300 2306 9.196139 AGACTCATTTTAGTGCTAGATACTTCT 57.804 33.333 5.55 0.00 35.90 2.85
2301 2307 9.243637 GACTCATTTTAGTGCTAGATACTTCTG 57.756 37.037 5.55 1.01 33.17 3.02
2302 2308 8.754080 ACTCATTTTAGTGCTAGATACTTCTGT 58.246 33.333 5.55 0.00 33.17 3.41
2320 2326 8.367660 ACTTCTGTATCTAGACAAATCCAAGA 57.632 34.615 0.00 0.00 0.00 3.02
2321 2327 8.254508 ACTTCTGTATCTAGACAAATCCAAGAC 58.745 37.037 0.00 0.00 0.00 3.01
2322 2328 7.718334 TCTGTATCTAGACAAATCCAAGACA 57.282 36.000 0.00 0.00 0.00 3.41
2323 2329 8.134202 TCTGTATCTAGACAAATCCAAGACAA 57.866 34.615 0.00 0.00 0.00 3.18
2324 2330 8.253810 TCTGTATCTAGACAAATCCAAGACAAG 58.746 37.037 0.00 0.00 0.00 3.16
2325 2331 7.907389 TGTATCTAGACAAATCCAAGACAAGT 58.093 34.615 0.00 0.00 0.00 3.16
2326 2332 9.031537 TGTATCTAGACAAATCCAAGACAAGTA 57.968 33.333 0.00 0.00 0.00 2.24
2327 2333 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
2329 2335 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
2330 2336 9.793259 TCTAGACAAATCCAAGACAAGTAATTT 57.207 29.630 0.00 0.00 0.00 1.82
2333 2339 9.793259 AGACAAATCCAAGACAAGTAATTTAGA 57.207 29.630 0.00 0.00 0.00 2.10
2336 2342 9.329913 CAAATCCAAGACAAGTAATTTAGAACG 57.670 33.333 0.00 0.00 0.00 3.95
2337 2343 7.611213 ATCCAAGACAAGTAATTTAGAACGG 57.389 36.000 0.00 0.00 0.00 4.44
2338 2344 6.761312 TCCAAGACAAGTAATTTAGAACGGA 58.239 36.000 0.00 0.00 0.00 4.69
2339 2345 6.872020 TCCAAGACAAGTAATTTAGAACGGAG 59.128 38.462 0.00 0.00 0.00 4.63
2340 2346 6.092259 CCAAGACAAGTAATTTAGAACGGAGG 59.908 42.308 0.00 0.00 0.00 4.30
2341 2347 5.731591 AGACAAGTAATTTAGAACGGAGGG 58.268 41.667 0.00 0.00 0.00 4.30
2342 2348 5.482878 AGACAAGTAATTTAGAACGGAGGGA 59.517 40.000 0.00 0.00 0.00 4.20
2343 2349 5.731591 ACAAGTAATTTAGAACGGAGGGAG 58.268 41.667 0.00 0.00 0.00 4.30
2344 2350 5.247792 ACAAGTAATTTAGAACGGAGGGAGT 59.752 40.000 0.00 0.00 0.00 3.85
2345 2351 6.438425 ACAAGTAATTTAGAACGGAGGGAGTA 59.562 38.462 0.00 0.00 0.00 2.59
2346 2352 6.462552 AGTAATTTAGAACGGAGGGAGTAC 57.537 41.667 0.00 0.00 0.00 2.73
2347 2353 6.193504 AGTAATTTAGAACGGAGGGAGTACT 58.806 40.000 0.00 0.00 0.00 2.73
2348 2354 6.666980 AGTAATTTAGAACGGAGGGAGTACTT 59.333 38.462 0.00 0.00 0.00 2.24
2349 2355 7.836183 AGTAATTTAGAACGGAGGGAGTACTTA 59.164 37.037 0.00 0.00 0.00 2.24
2350 2356 7.672122 AATTTAGAACGGAGGGAGTACTTAT 57.328 36.000 0.00 0.00 0.00 1.73
2351 2357 6.461110 TTTAGAACGGAGGGAGTACTTATG 57.539 41.667 0.00 0.00 0.00 1.90
2352 2358 4.246712 AGAACGGAGGGAGTACTTATGA 57.753 45.455 0.00 0.00 0.00 2.15
2353 2359 4.607239 AGAACGGAGGGAGTACTTATGAA 58.393 43.478 0.00 0.00 0.00 2.57
2354 2360 4.401837 AGAACGGAGGGAGTACTTATGAAC 59.598 45.833 0.00 0.00 0.00 3.18
2355 2361 3.978610 ACGGAGGGAGTACTTATGAACT 58.021 45.455 0.00 0.00 0.00 3.01
2356 2362 5.121380 ACGGAGGGAGTACTTATGAACTA 57.879 43.478 0.00 0.00 0.00 2.24
2375 2382 2.220653 ATGCATTGTGCTACCCTTGT 57.779 45.000 0.00 0.00 45.31 3.16
2377 2384 2.710377 TGCATTGTGCTACCCTTGTAG 58.290 47.619 3.41 0.00 45.31 2.74
2385 2392 2.969628 CTACCCTTGTAGCACTGAGG 57.030 55.000 0.00 0.00 38.20 3.86
2415 2422 5.688176 GCAACTTTGCGGTAAACAAGAAATA 59.312 36.000 0.00 0.00 45.11 1.40
2416 2423 6.199342 GCAACTTTGCGGTAAACAAGAAATAA 59.801 34.615 0.00 0.00 45.11 1.40
2646 2654 3.120627 GCCGCAGCTGCAAAAATAA 57.879 47.368 36.03 0.00 42.21 1.40
2661 2669 6.716628 TGCAAAAATAAGAGGAATGTCTGTCT 59.283 34.615 0.00 0.00 0.00 3.41
2673 2685 4.881019 ATGTCTGTCTGACTAGTTGCTT 57.119 40.909 9.51 0.00 45.54 3.91
2674 2686 4.672587 TGTCTGTCTGACTAGTTGCTTT 57.327 40.909 9.51 0.00 45.54 3.51
2675 2687 4.621991 TGTCTGTCTGACTAGTTGCTTTC 58.378 43.478 9.51 0.00 45.54 2.62
2676 2688 4.342378 TGTCTGTCTGACTAGTTGCTTTCT 59.658 41.667 9.51 0.00 45.54 2.52
2691 2703 7.529158 AGTTGCTTTCTTGATTTTTGTTTTGG 58.471 30.769 0.00 0.00 0.00 3.28
2803 2817 9.612620 CAAGTTACCTACATCTGTTTGAAATTC 57.387 33.333 0.00 0.00 0.00 2.17
2805 2819 5.880054 ACCTACATCTGTTTGAAATTCCG 57.120 39.130 0.00 0.00 0.00 4.30
2815 2829 2.697431 TGAAATTCCGTTTTCAGCCG 57.303 45.000 2.41 0.00 39.91 5.52
2867 2884 1.376553 GACTTCTGGTGAGGCTGCC 60.377 63.158 11.65 11.65 0.00 4.85
2895 2912 1.081892 CCAGTCTCCAACAGAATGCG 58.918 55.000 0.00 0.00 44.50 4.73
3032 3049 2.159170 TGCCCCTTGTGTTTTTCTTTCG 60.159 45.455 0.00 0.00 0.00 3.46
3039 3056 4.920640 TGTGTTTTTCTTTCGGGCATAA 57.079 36.364 0.00 0.00 0.00 1.90
3170 3187 4.262249 GCTACATCATCAACTCCTCTACCC 60.262 50.000 0.00 0.00 0.00 3.69
3357 3374 7.708752 AGAAGAAAGTACAATGCTCTATAGTGC 59.291 37.037 17.86 17.86 35.32 4.40
3470 3509 1.971505 TATCCTTGAGCAGCCGTGGG 61.972 60.000 0.00 0.00 0.00 4.61
3491 3530 6.918022 GTGGGCAAGTATTAGATGTAATTTGC 59.082 38.462 17.52 17.52 39.54 3.68
3492 3531 6.605194 TGGGCAAGTATTAGATGTAATTTGCA 59.395 34.615 23.07 9.53 40.81 4.08
3631 3670 3.815337 TTACAACACACACACACACAC 57.185 42.857 0.00 0.00 0.00 3.82
3632 3671 0.515127 ACAACACACACACACACACG 59.485 50.000 0.00 0.00 0.00 4.49
3633 3672 0.792729 CAACACACACACACACACGC 60.793 55.000 0.00 0.00 0.00 5.34
3634 3673 2.021243 CACACACACACACACGCG 59.979 61.111 3.53 3.53 0.00 6.01
3635 3674 3.860125 ACACACACACACACGCGC 61.860 61.111 5.73 0.00 0.00 6.86
3636 3675 4.918060 CACACACACACACGCGCG 62.918 66.667 30.96 30.96 0.00 6.86
3732 3771 4.447290 GGAGCTCTTCCACCTTAAGATTC 58.553 47.826 14.64 0.00 46.01 2.52
3745 3784 2.674796 AAGATTCTACTCGGCACCAC 57.325 50.000 0.00 0.00 0.00 4.16
3808 3847 5.355071 AGGCAAAGGCAAAGAAAAGAAAAAG 59.645 36.000 0.00 0.00 43.71 2.27
3840 3879 6.273071 ACAAAAGCAAACAACTCTGATAACC 58.727 36.000 0.00 0.00 0.00 2.85
3860 3899 2.159085 CCGTCCTAACCTCCAAGATGTC 60.159 54.545 0.00 0.00 0.00 3.06
3986 4025 5.569355 TCATCTTTCCTTGTATTGGAAGCA 58.431 37.500 0.00 0.00 43.48 3.91
4108 4147 1.557099 AGGTACCTGATGTCTGCGAA 58.443 50.000 15.42 0.00 0.00 4.70
4146 4185 7.169140 CCTGGCAAATTAAAAGTCAAGTGTTAC 59.831 37.037 0.00 0.00 0.00 2.50
4149 4188 6.143278 GCAAATTAAAAGTCAAGTGTTACCCG 59.857 38.462 0.00 0.00 0.00 5.28
4207 4246 8.546597 ACAAAATTATAAAGGTGGAACATTGC 57.453 30.769 0.00 0.00 41.66 3.56
4213 4252 3.525800 AAGGTGGAACATTGCTAGGTT 57.474 42.857 0.00 0.00 40.56 3.50
4214 4253 4.650972 AAGGTGGAACATTGCTAGGTTA 57.349 40.909 0.00 0.00 40.56 2.85
4226 4265 5.366482 TTGCTAGGTTATAAGTGATGCCA 57.634 39.130 0.00 0.00 0.00 4.92
4254 4293 1.486997 ATAGGAGGCATGCCAGCGAT 61.487 55.000 37.18 21.59 38.92 4.58
4288 4327 1.612146 TGGCCTCCTCATGTTCCGA 60.612 57.895 3.32 0.00 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 5.758296 ACATCACAGTGTTTGTTTATCGTCT 59.242 36.000 0.00 0.00 38.16 4.18
163 164 0.872388 GTAAGGGAAACTGCACACCG 59.128 55.000 0.00 0.00 0.00 4.94
218 219 1.675483 TGTCTGCATGTTTCGCTTTGT 59.325 42.857 0.00 0.00 0.00 2.83
224 225 2.138320 ACTCACTGTCTGCATGTTTCG 58.862 47.619 0.00 0.00 0.00 3.46
262 263 3.164026 GGGTTAGGTAAACGCCAGG 57.836 57.895 0.00 0.00 43.40 4.45
378 379 3.118592 AGCCTTAGACTGGTAGATGCAAC 60.119 47.826 0.00 0.00 0.00 4.17
396 397 2.969016 CTCGCTCAGTCACAGCCT 59.031 61.111 0.00 0.00 32.83 4.58
439 440 8.875168 ACAAAAACAATGGAAATATAAGGTCCA 58.125 29.630 5.21 5.21 45.29 4.02
545 548 8.012809 CAGAACATACTAATGTAACAACGCAAA 58.987 33.333 0.00 0.00 45.79 3.68
763 768 6.266558 ACATAGGTGTGTGCTTTTTAATGGAA 59.733 34.615 0.00 0.00 37.14 3.53
785 790 5.909621 ATGAGCAGAGCACAATAAAACAT 57.090 34.783 0.00 0.00 32.39 2.71
809 814 3.891049 AGAGACTGGGATTGCATTAACC 58.109 45.455 0.00 0.00 0.00 2.85
1532 1537 4.635765 TGTTCTGGATCGATGACCATTTTC 59.364 41.667 0.54 0.00 35.54 2.29
1581 1586 5.007034 TGGTTTGTTGATATCGTGGAATGT 58.993 37.500 0.00 0.00 0.00 2.71
1621 1626 0.034059 GCCATCATAGGACAGACGGG 59.966 60.000 0.00 0.00 0.00 5.28
1943 1948 1.774639 AACAGCTGCTTTTGAATGCG 58.225 45.000 15.27 0.00 32.27 4.73
1962 1967 7.332430 AGTGTTTCCAAATTCATCGACGTAATA 59.668 33.333 0.00 0.00 0.00 0.98
2006 2011 4.216257 ACAACATGAGCATACCTTGTGTTC 59.784 41.667 0.00 0.00 32.54 3.18
2022 2027 7.184800 TCGAATCCGGATATTAAACAACATG 57.815 36.000 19.48 0.00 36.24 3.21
2064 2069 1.063266 ACCCACAACCTCCACATGTTT 60.063 47.619 0.00 0.00 0.00 2.83
2152 2157 4.829064 TGGTGCTTGTTCATAACAGAAC 57.171 40.909 0.00 0.00 46.22 3.01
2206 2212 6.289064 ACGGAGGGAGTATAATTTTCATCAC 58.711 40.000 0.00 0.00 0.00 3.06
2229 2235 6.496338 AATCCAAGACAAGTAATTCGGAAC 57.504 37.500 0.00 0.00 0.00 3.62
2231 2237 6.001460 ACAAATCCAAGACAAGTAATTCGGA 58.999 36.000 0.00 0.00 0.00 4.55
2232 2238 6.149474 AGACAAATCCAAGACAAGTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
2233 2239 7.133891 AGACAAATCCAAGACAAGTAATTCG 57.866 36.000 0.00 0.00 0.00 3.34
2234 2240 9.436957 TCTAGACAAATCCAAGACAAGTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
2235 2241 9.965902 ATCTAGACAAATCCAAGACAAGTAATT 57.034 29.630 0.00 0.00 0.00 1.40
2237 2243 9.871238 GTATCTAGACAAATCCAAGACAAGTAA 57.129 33.333 0.00 0.00 0.00 2.24
2238 2244 9.031537 TGTATCTAGACAAATCCAAGACAAGTA 57.968 33.333 0.00 0.00 0.00 2.24
2239 2245 7.907389 TGTATCTAGACAAATCCAAGACAAGT 58.093 34.615 0.00 0.00 0.00 3.16
2240 2246 8.253810 TCTGTATCTAGACAAATCCAAGACAAG 58.746 37.037 0.00 0.00 0.00 3.16
2241 2247 8.134202 TCTGTATCTAGACAAATCCAAGACAA 57.866 34.615 0.00 0.00 0.00 3.18
2242 2248 7.718334 TCTGTATCTAGACAAATCCAAGACA 57.282 36.000 0.00 0.00 0.00 3.41
2243 2249 8.200792 ACATCTGTATCTAGACAAATCCAAGAC 58.799 37.037 0.00 0.00 0.00 3.01
2244 2250 8.311395 ACATCTGTATCTAGACAAATCCAAGA 57.689 34.615 0.00 0.00 0.00 3.02
2263 2269 9.190858 GCACTAAAATGAGTCTAGATACATCTG 57.809 37.037 12.66 7.80 37.76 2.90
2264 2270 9.142014 AGCACTAAAATGAGTCTAGATACATCT 57.858 33.333 12.66 0.00 40.86 2.90
2267 2273 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
2271 2277 9.854668 AGTATCTAGCACTAAAATGAGTCTAGA 57.145 33.333 11.59 11.59 38.76 2.43
2274 2280 9.196139 AGAAGTATCTAGCACTAAAATGAGTCT 57.804 33.333 0.00 0.00 32.88 3.24
2275 2281 9.243637 CAGAAGTATCTAGCACTAAAATGAGTC 57.756 37.037 0.00 0.00 33.50 3.36
2276 2282 8.754080 ACAGAAGTATCTAGCACTAAAATGAGT 58.246 33.333 0.00 0.00 33.50 3.41
2294 2300 9.475620 TCTTGGATTTGTCTAGATACAGAAGTA 57.524 33.333 0.00 0.00 34.10 2.24
2295 2301 8.254508 GTCTTGGATTTGTCTAGATACAGAAGT 58.745 37.037 0.00 0.00 0.00 3.01
2296 2302 8.253810 TGTCTTGGATTTGTCTAGATACAGAAG 58.746 37.037 0.00 0.00 0.00 2.85
2297 2303 8.134202 TGTCTTGGATTTGTCTAGATACAGAA 57.866 34.615 0.00 0.00 0.00 3.02
2298 2304 7.718334 TGTCTTGGATTTGTCTAGATACAGA 57.282 36.000 0.00 0.00 0.00 3.41
2299 2305 8.037758 ACTTGTCTTGGATTTGTCTAGATACAG 58.962 37.037 0.00 0.00 0.00 2.74
2300 2306 7.907389 ACTTGTCTTGGATTTGTCTAGATACA 58.093 34.615 0.00 0.00 0.00 2.29
2301 2307 9.871238 TTACTTGTCTTGGATTTGTCTAGATAC 57.129 33.333 0.00 0.00 0.00 2.24
2303 2309 9.965902 AATTACTTGTCTTGGATTTGTCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2304 2310 9.793259 AAATTACTTGTCTTGGATTTGTCTAGA 57.207 29.630 0.00 0.00 0.00 2.43
2307 2313 9.793259 TCTAAATTACTTGTCTTGGATTTGTCT 57.207 29.630 0.00 0.00 0.00 3.41
2310 2316 9.329913 CGTTCTAAATTACTTGTCTTGGATTTG 57.670 33.333 0.00 0.00 0.00 2.32
2311 2317 8.512138 CCGTTCTAAATTACTTGTCTTGGATTT 58.488 33.333 0.00 0.00 0.00 2.17
2312 2318 7.881232 TCCGTTCTAAATTACTTGTCTTGGATT 59.119 33.333 0.00 0.00 0.00 3.01
2313 2319 7.391620 TCCGTTCTAAATTACTTGTCTTGGAT 58.608 34.615 0.00 0.00 0.00 3.41
2314 2320 6.761312 TCCGTTCTAAATTACTTGTCTTGGA 58.239 36.000 0.00 0.00 0.00 3.53
2315 2321 6.092259 CCTCCGTTCTAAATTACTTGTCTTGG 59.908 42.308 0.00 0.00 0.00 3.61
2316 2322 6.092259 CCCTCCGTTCTAAATTACTTGTCTTG 59.908 42.308 0.00 0.00 0.00 3.02
2317 2323 6.013984 TCCCTCCGTTCTAAATTACTTGTCTT 60.014 38.462 0.00 0.00 0.00 3.01
2318 2324 5.482878 TCCCTCCGTTCTAAATTACTTGTCT 59.517 40.000 0.00 0.00 0.00 3.41
2319 2325 5.727434 TCCCTCCGTTCTAAATTACTTGTC 58.273 41.667 0.00 0.00 0.00 3.18
2320 2326 5.247792 ACTCCCTCCGTTCTAAATTACTTGT 59.752 40.000 0.00 0.00 0.00 3.16
2321 2327 5.731591 ACTCCCTCCGTTCTAAATTACTTG 58.268 41.667 0.00 0.00 0.00 3.16
2322 2328 6.666980 AGTACTCCCTCCGTTCTAAATTACTT 59.333 38.462 0.00 0.00 0.00 2.24
2323 2329 6.193504 AGTACTCCCTCCGTTCTAAATTACT 58.806 40.000 0.00 0.00 0.00 2.24
2324 2330 6.462552 AGTACTCCCTCCGTTCTAAATTAC 57.537 41.667 0.00 0.00 0.00 1.89
2325 2331 8.636213 CATAAGTACTCCCTCCGTTCTAAATTA 58.364 37.037 0.00 0.00 0.00 1.40
2326 2332 7.343833 TCATAAGTACTCCCTCCGTTCTAAATT 59.656 37.037 0.00 0.00 0.00 1.82
2327 2333 6.837568 TCATAAGTACTCCCTCCGTTCTAAAT 59.162 38.462 0.00 0.00 0.00 1.40
2328 2334 6.189859 TCATAAGTACTCCCTCCGTTCTAAA 58.810 40.000 0.00 0.00 0.00 1.85
2329 2335 5.759059 TCATAAGTACTCCCTCCGTTCTAA 58.241 41.667 0.00 0.00 0.00 2.10
2330 2336 5.378230 TCATAAGTACTCCCTCCGTTCTA 57.622 43.478 0.00 0.00 0.00 2.10
2331 2337 4.246712 TCATAAGTACTCCCTCCGTTCT 57.753 45.455 0.00 0.00 0.00 3.01
2332 2338 4.401837 AGTTCATAAGTACTCCCTCCGTTC 59.598 45.833 0.00 0.00 0.00 3.95
2333 2339 4.351127 AGTTCATAAGTACTCCCTCCGTT 58.649 43.478 0.00 0.00 0.00 4.44
2334 2340 3.978610 AGTTCATAAGTACTCCCTCCGT 58.021 45.455 0.00 0.00 0.00 4.69
2335 2341 5.565045 GCATAGTTCATAAGTACTCCCTCCG 60.565 48.000 0.00 0.00 0.00 4.63
2336 2342 5.304614 TGCATAGTTCATAAGTACTCCCTCC 59.695 44.000 0.00 0.00 0.00 4.30
2337 2343 6.406692 TGCATAGTTCATAAGTACTCCCTC 57.593 41.667 0.00 0.00 0.00 4.30
2338 2344 7.147479 ACAATGCATAGTTCATAAGTACTCCCT 60.147 37.037 0.00 0.00 0.00 4.20
2339 2345 6.992715 ACAATGCATAGTTCATAAGTACTCCC 59.007 38.462 0.00 0.00 0.00 4.30
2340 2346 7.519008 GCACAATGCATAGTTCATAAGTACTCC 60.519 40.741 0.00 0.00 44.26 3.85
2341 2347 7.348201 GCACAATGCATAGTTCATAAGTACTC 58.652 38.462 0.00 0.00 44.26 2.59
2342 2348 7.251704 GCACAATGCATAGTTCATAAGTACT 57.748 36.000 0.00 0.00 44.26 2.73
2375 2382 0.835971 TTGCAGTCCCCTCAGTGCTA 60.836 55.000 2.19 0.00 42.42 3.49
2377 2384 1.968540 GTTGCAGTCCCCTCAGTGC 60.969 63.158 0.00 0.00 42.29 4.40
2415 2422 4.508584 GGACCAAGGACACCTAGGATTTTT 60.509 45.833 17.98 0.07 31.13 1.94
2416 2423 3.010250 GGACCAAGGACACCTAGGATTTT 59.990 47.826 17.98 0.00 31.13 1.82
2574 2582 4.901868 TGTTTTCCTGACCATACTGTACC 58.098 43.478 0.00 0.00 0.00 3.34
2661 2669 7.771183 ACAAAAATCAAGAAAGCAACTAGTCA 58.229 30.769 0.00 0.00 0.00 3.41
2673 2685 7.986085 TCCAAACCAAAACAAAAATCAAGAA 57.014 28.000 0.00 0.00 0.00 2.52
2674 2686 7.986085 TTCCAAACCAAAACAAAAATCAAGA 57.014 28.000 0.00 0.00 0.00 3.02
2675 2687 9.074443 CATTTCCAAACCAAAACAAAAATCAAG 57.926 29.630 0.00 0.00 0.00 3.02
2676 2688 8.796475 TCATTTCCAAACCAAAACAAAAATCAA 58.204 25.926 0.00 0.00 0.00 2.57
2691 2703 8.547967 TTGACTAGACATACTCATTTCCAAAC 57.452 34.615 0.00 0.00 0.00 2.93
2803 2817 0.517316 CTCCTTTCGGCTGAAAACGG 59.483 55.000 20.77 18.51 43.21 4.44
2805 2819 2.350868 GCTTCTCCTTTCGGCTGAAAAC 60.351 50.000 20.77 2.55 43.21 2.43
2815 2829 4.670347 GATGCTTGATTGCTTCTCCTTTC 58.330 43.478 0.00 0.00 35.22 2.62
2867 2884 0.329261 TTGGAGACTGGAATGCAGGG 59.671 55.000 6.73 0.00 0.00 4.45
2895 2912 3.391665 CTGCATCCCCAGACGACCC 62.392 68.421 0.00 0.00 34.77 4.46
3032 3049 8.196378 TGTACCCCAAAAATTATATTATGCCC 57.804 34.615 0.00 0.00 0.00 5.36
3039 3056 9.945633 AACTGGTATGTACCCCAAAAATTATAT 57.054 29.630 6.74 0.00 45.87 0.86
3170 3187 5.204833 CAACCACATGTAAACAAGTCTTCG 58.795 41.667 0.00 0.00 0.00 3.79
3319 3336 8.433421 TTGTACTTTCTTCTTTCGTCTTCATT 57.567 30.769 0.00 0.00 0.00 2.57
3385 3402 5.796350 AGCGCTATTGTATTCTTTTTCGT 57.204 34.783 8.99 0.00 0.00 3.85
3470 3509 8.909708 TGTTGCAAATTACATCTAATACTTGC 57.090 30.769 0.00 4.19 36.97 4.01
3483 3522 5.458779 ACGAGCTTCTTTTGTTGCAAATTAC 59.541 36.000 0.00 0.00 0.00 1.89
3491 3530 5.273170 TGATTCAACGAGCTTCTTTTGTTG 58.727 37.500 0.00 0.00 40.85 3.33
3492 3531 5.499139 TGATTCAACGAGCTTCTTTTGTT 57.501 34.783 0.00 0.00 0.00 2.83
3635 3674 2.254671 GATATTAGACTGCGCGCGCG 62.255 60.000 45.73 45.73 45.51 6.86
3636 3675 1.275471 TGATATTAGACTGCGCGCGC 61.275 55.000 45.02 45.02 42.35 6.86
3637 3676 1.128513 TTGATATTAGACTGCGCGCG 58.871 50.000 28.44 28.44 0.00 6.86
3808 3847 4.116961 GTTGTTTGCTTTTGTACCTTCCC 58.883 43.478 0.00 0.00 0.00 3.97
3840 3879 2.479730 CGACATCTTGGAGGTTAGGACG 60.480 54.545 0.00 0.00 0.00 4.79
3860 3899 1.574702 GGAAAGCCCGAAACCTGACG 61.575 60.000 0.00 0.00 0.00 4.35
4048 4087 2.435422 TGTCACATACCCATGCTGTTG 58.565 47.619 0.00 0.00 35.39 3.33
4088 4127 1.557099 TCGCAGACATCAGGTACCTT 58.443 50.000 13.15 0.00 0.00 3.50
4146 4185 0.751643 CCCTTCCCTGTAAATGCGGG 60.752 60.000 0.00 0.00 39.41 6.13
4149 4188 3.017442 GTCTTCCCTTCCCTGTAAATGC 58.983 50.000 0.00 0.00 0.00 3.56
4207 4246 5.930135 AGGTTGGCATCACTTATAACCTAG 58.070 41.667 0.00 0.00 44.29 3.02
4213 4252 3.525609 TGGGAAGGTTGGCATCACTTATA 59.474 43.478 0.00 0.00 0.00 0.98
4214 4253 2.311542 TGGGAAGGTTGGCATCACTTAT 59.688 45.455 0.00 0.00 0.00 1.73
4226 4265 1.496429 CATGCCTCCTATGGGAAGGTT 59.504 52.381 12.85 2.25 41.69 3.50
4254 4293 2.309755 AGGCCACCATCTTCATCTTCAA 59.690 45.455 5.01 0.00 0.00 2.69
4288 4327 4.275810 AGCCAACATTGAATACTGAGCAT 58.724 39.130 0.00 0.00 0.00 3.79


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

AutoCloner maintained by Alex Coulton.