Multiple sequence alignment - TraesCS7A01G029800

Loading Multiple Alignment...

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 TraesCS7A01G029800 chr7A 100.000 2351 0 0 1 2351 12126659 12129009 0.000000e+00 4342
1 TraesCS7A01G029800 chr7A 84.734 2214 263 39 20 2200 215575774 215573603 0.000000e+00 2146
2 TraesCS7A01G029800 chr2B 88.959 2228 194 20 2 2200 243358839 243361043 0.000000e+00 2704
3 TraesCS7A01G029800 chr2B 87.685 2225 211 28 2 2200 572267951 572265764 0.000000e+00 2532
4 TraesCS7A01G029800 chr2B 86.343 2204 232 29 20 2200 355882682 355884839 0.000000e+00 2338
5 TraesCS7A01G029800 chr2B 91.083 1727 132 11 486 2200 644137956 644139672 0.000000e+00 2316
6 TraesCS7A01G029800 chr6D 88.834 2230 174 29 1 2200 463789029 463786845 0.000000e+00 2669
7 TraesCS7A01G029800 chr3D 89.016 2185 170 20 7 2167 7403009 7400871 0.000000e+00 2641
8 TraesCS7A01G029800 chr3D 83.005 406 42 9 2 396 429109239 429109628 2.240000e-90 342
9 TraesCS7A01G029800 chr7D 89.400 2132 176 26 2 2109 616482455 616484560 0.000000e+00 2639
10 TraesCS7A01G029800 chr7D 87.706 2188 220 23 2 2171 155728809 155726653 0.000000e+00 2505
11 TraesCS7A01G029800 chr7D 87.288 2242 196 39 1 2200 412230164 412232358 0.000000e+00 2479
12 TraesCS7A01G029800 chr7B 86.884 2211 227 29 19 2200 71247737 71245561 0.000000e+00 2418
13 TraesCS7A01G029800 chr7B 81.504 492 49 24 20 491 414092238 414092707 1.330000e-97 366
14 TraesCS7A01G029800 chr2D 86.087 2221 234 34 20 2200 127267872 127265687 0.000000e+00 2320
15 TraesCS7A01G029800 chr6A 89.854 1784 149 16 435 2202 595914696 595916463 0.000000e+00 2263
16 TraesCS7A01G029800 chr6A 96.104 154 6 0 2198 2351 114475828 114475981 3.880000e-63 252
17 TraesCS7A01G029800 chr6A 94.479 163 7 1 2191 2351 86321719 86321557 1.390000e-62 250
18 TraesCS7A01G029800 chr6B 85.242 2209 254 39 20 2200 486084831 486086995 0.000000e+00 2207
19 TraesCS7A01G029800 chr6B 82.218 523 68 15 20 534 405058309 405057804 6.000000e-116 427
20 TraesCS7A01G029800 chr5D 82.893 795 76 22 2 772 217057245 217058003 0.000000e+00 660
21 TraesCS7A01G029800 chr2A 97.403 154 4 0 2198 2351 65955217 65955064 1.790000e-66 263
22 TraesCS7A01G029800 chrUn 96.753 154 5 0 2198 2351 465238949 465239102 8.340000e-65 257
23 TraesCS7A01G029800 chr3A 96.753 154 5 0 2198 2351 17513029 17513182 8.340000e-65 257
24 TraesCS7A01G029800 chr3A 96.753 154 5 0 2198 2351 536623416 536623569 8.340000e-65 257
25 TraesCS7A01G029800 chr5A 96.104 154 6 0 2198 2351 516829783 516829630 3.880000e-63 252
26 TraesCS7A01G029800 chr5A 96.104 154 6 0 2198 2351 528561034 528560881 3.880000e-63 252
27 TraesCS7A01G029800 chr1A 96.104 154 6 0 2198 2351 61701524 61701677 3.880000e-63 252


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 TraesCS7A01G029800 chr7A 12126659 12129009 2350 False 4342 4342 100.000 1 2351 1 chr7A.!!$F1 2350
1 TraesCS7A01G029800 chr7A 215573603 215575774 2171 True 2146 2146 84.734 20 2200 1 chr7A.!!$R1 2180
2 TraesCS7A01G029800 chr2B 243358839 243361043 2204 False 2704 2704 88.959 2 2200 1 chr2B.!!$F1 2198
3 TraesCS7A01G029800 chr2B 572265764 572267951 2187 True 2532 2532 87.685 2 2200 1 chr2B.!!$R1 2198
4 TraesCS7A01G029800 chr2B 355882682 355884839 2157 False 2338 2338 86.343 20 2200 1 chr2B.!!$F2 2180
5 TraesCS7A01G029800 chr2B 644137956 644139672 1716 False 2316 2316 91.083 486 2200 1 chr2B.!!$F3 1714
6 TraesCS7A01G029800 chr6D 463786845 463789029 2184 True 2669 2669 88.834 1 2200 1 chr6D.!!$R1 2199
7 TraesCS7A01G029800 chr3D 7400871 7403009 2138 True 2641 2641 89.016 7 2167 1 chr3D.!!$R1 2160
8 TraesCS7A01G029800 chr7D 616482455 616484560 2105 False 2639 2639 89.400 2 2109 1 chr7D.!!$F2 2107
9 TraesCS7A01G029800 chr7D 155726653 155728809 2156 True 2505 2505 87.706 2 2171 1 chr7D.!!$R1 2169
10 TraesCS7A01G029800 chr7D 412230164 412232358 2194 False 2479 2479 87.288 1 2200 1 chr7D.!!$F1 2199
11 TraesCS7A01G029800 chr7B 71245561 71247737 2176 True 2418 2418 86.884 19 2200 1 chr7B.!!$R1 2181
12 TraesCS7A01G029800 chr2D 127265687 127267872 2185 True 2320 2320 86.087 20 2200 1 chr2D.!!$R1 2180
13 TraesCS7A01G029800 chr6A 595914696 595916463 1767 False 2263 2263 89.854 435 2202 1 chr6A.!!$F2 1767
14 TraesCS7A01G029800 chr6B 486084831 486086995 2164 False 2207 2207 85.242 20 2200 1 chr6B.!!$F1 2180
15 TraesCS7A01G029800 chr6B 405057804 405058309 505 True 427 427 82.218 20 534 1 chr6B.!!$R1 514
16 TraesCS7A01G029800 chr5D 217057245 217058003 758 False 660 660 82.893 2 772 1 chr5D.!!$F1 770

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
424 491 0.654683 GATGAAGCCATCGTGACTGC 59.345 55.0 0.0 0.0 39.7 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2262 2436 0.034756 GGCCCACAAACATTGGTTCC 59.965 55.0 0.0 0.0 35.82 3.62 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
138 147 1.229927 TGGCAGCCACCATAATCCC 59.770 57.895 11.22 0.00 33.75 3.85
139 148 1.531602 GGCAGCCACCATAATCCCC 60.532 63.158 6.55 0.00 0.00 4.81
171 188 1.116536 TTCCCAAAACCCTTTCGCCC 61.117 55.000 0.00 0.00 0.00 6.13
214 243 2.264794 GCCATGGACGACGACCTT 59.735 61.111 18.40 8.33 0.00 3.50
215 244 2.100631 GCCATGGACGACGACCTTG 61.101 63.158 18.40 20.12 33.97 3.61
216 245 1.589630 CCATGGACGACGACCTTGA 59.410 57.895 25.85 5.70 35.48 3.02
217 246 0.736325 CCATGGACGACGACCTTGAC 60.736 60.000 25.85 0.00 35.48 3.18
218 247 0.736325 CATGGACGACGACCTTGACC 60.736 60.000 21.75 6.00 35.48 4.02
219 248 0.898789 ATGGACGACGACCTTGACCT 60.899 55.000 16.98 0.00 0.00 3.85
220 249 1.111116 TGGACGACGACCTTGACCTT 61.111 55.000 16.98 0.00 0.00 3.50
231 260 1.512926 CTTGACCTTGACCTTGACGG 58.487 55.000 0.00 0.00 39.35 4.79
306 368 1.034838 AAAGGCAACACGCAAGACCA 61.035 50.000 0.00 0.00 45.17 4.02
308 374 2.186826 GGCAACACGCAAGACCACT 61.187 57.895 0.00 0.00 45.17 4.00
363 429 2.036890 AGCGGGTAAGGGAGTCGT 59.963 61.111 0.00 0.00 0.00 4.34
424 491 0.654683 GATGAAGCCATCGTGACTGC 59.345 55.000 0.00 0.00 39.70 4.40
425 492 0.745845 ATGAAGCCATCGTGACTGCC 60.746 55.000 0.00 0.00 0.00 4.85
426 493 2.434884 AAGCCATCGTGACTGCCG 60.435 61.111 0.00 0.00 0.00 5.69
651 760 1.298340 CGGCTTCCATGTGTACCCA 59.702 57.895 0.00 0.00 0.00 4.51
680 790 2.685380 CCTCTCCGGGGAGTGCTT 60.685 66.667 29.45 0.00 42.49 3.91
773 907 4.388499 GGGAGGCGCGAGGAAACA 62.388 66.667 12.10 0.00 0.00 2.83
778 912 3.033764 GCGCGAGGAAACACACGA 61.034 61.111 12.10 0.00 0.00 4.35
906 1040 3.917760 GCCGCTGGCTACGATCCT 61.918 66.667 11.61 0.00 46.69 3.24
921 1055 2.351835 CGATCCTGACGAGACACAAAGT 60.352 50.000 0.00 0.00 0.00 2.66
1041 1175 0.682852 TTGACCACGAGTTTCCGGAT 59.317 50.000 4.15 0.00 0.00 4.18
1121 1258 3.741476 GCTCGCCAACCAAGCCAG 61.741 66.667 0.00 0.00 0.00 4.85
1123 1260 4.577677 TCGCCAACCAAGCCAGCA 62.578 61.111 0.00 0.00 0.00 4.41
1232 1372 2.895424 AAGACCCCAAGACCAGCGG 61.895 63.158 0.00 0.00 0.00 5.52
1312 1452 5.318630 AGAAGTTTCCGCCTTACCAAATTA 58.681 37.500 0.00 0.00 0.00 1.40
1350 1494 1.999735 GTGTCCATTTCGAAGCGATGA 59.000 47.619 9.40 0.00 35.23 2.92
1409 1553 2.854253 TTGAGAGTGTCAAGGCCCT 58.146 52.632 0.00 0.00 40.45 5.19
1432 1576 4.471908 TGAGCGGCATCGGCATGT 62.472 61.111 1.45 0.00 43.71 3.21
1466 1614 0.676782 TAGCAAGCCGCCCTCTTTTC 60.677 55.000 0.00 0.00 44.04 2.29
1468 1616 1.527433 GCAAGCCGCCCTCTTTTCTT 61.527 55.000 0.00 0.00 32.94 2.52
1802 1966 4.413189 TGGAGGGCATGATGAATAAGAAGA 59.587 41.667 0.00 0.00 0.00 2.87
1886 2051 1.963985 AAGGAGGAGGCTTGAGATGT 58.036 50.000 0.00 0.00 0.00 3.06
1934 2099 0.392998 GATGGAGGCGGAGAAGCAAA 60.393 55.000 0.00 0.00 39.27 3.68
1994 2159 0.320771 GGCGAAAGAAGTGGCTCTCA 60.321 55.000 0.00 0.00 0.00 3.27
2033 2198 3.648067 GGTGGAGATCATGAAGGTGGATA 59.352 47.826 0.00 0.00 0.00 2.59
2065 2230 2.747855 CCAAGGAAGAGGCCGTGC 60.748 66.667 0.00 0.00 36.29 5.34
2069 2234 1.768684 AAGGAAGAGGCCGTGCTTCA 61.769 55.000 26.39 0.00 41.69 3.02
2202 2376 2.254459 CATGGTCGAACTCAAGTCTCG 58.746 52.381 0.33 7.81 33.30 4.04
2203 2377 0.596577 TGGTCGAACTCAAGTCTCGG 59.403 55.000 0.33 0.00 33.07 4.63
2204 2378 0.597072 GGTCGAACTCAAGTCTCGGT 59.403 55.000 0.00 0.00 33.07 4.69
2205 2379 1.000496 GGTCGAACTCAAGTCTCGGTT 60.000 52.381 0.00 0.00 33.07 4.44
2206 2380 2.317684 GTCGAACTCAAGTCTCGGTTC 58.682 52.381 11.83 0.00 35.93 3.62
2208 2382 2.418983 GAACTCAAGTCTCGGTTCGT 57.581 50.000 0.00 0.00 0.00 3.85
2209 2383 2.052157 GAACTCAAGTCTCGGTTCGTG 58.948 52.381 0.00 0.00 0.00 4.35
2210 2384 0.314302 ACTCAAGTCTCGGTTCGTGG 59.686 55.000 0.00 0.00 0.00 4.94
2211 2385 1.006571 TCAAGTCTCGGTTCGTGGC 60.007 57.895 0.00 0.00 0.00 5.01
2212 2386 1.006102 CAAGTCTCGGTTCGTGGCT 60.006 57.895 0.00 0.00 36.89 4.75
2213 2387 1.006102 AAGTCTCGGTTCGTGGCTG 60.006 57.895 0.00 0.00 35.54 4.85
2214 2388 2.432628 GTCTCGGTTCGTGGCTGG 60.433 66.667 0.00 0.00 0.00 4.85
2215 2389 2.599281 TCTCGGTTCGTGGCTGGA 60.599 61.111 0.00 0.00 0.00 3.86
2216 2390 2.204461 TCTCGGTTCGTGGCTGGAA 61.204 57.895 0.00 0.00 0.00 3.53
2217 2391 2.027625 CTCGGTTCGTGGCTGGAAC 61.028 63.158 11.23 11.23 42.32 3.62
2220 2394 3.047877 GTTCGTGGCTGGAACCGG 61.048 66.667 0.00 0.00 38.23 5.28
2221 2395 4.323477 TTCGTGGCTGGAACCGGG 62.323 66.667 6.32 0.00 0.00 5.73
2224 2398 3.637273 GTGGCTGGAACCGGGACT 61.637 66.667 6.32 0.00 0.00 3.85
2225 2399 2.120940 TGGCTGGAACCGGGACTA 59.879 61.111 6.32 0.00 0.00 2.59
2226 2400 1.536907 TGGCTGGAACCGGGACTAA 60.537 57.895 6.32 0.00 0.00 2.24
2227 2401 1.128809 TGGCTGGAACCGGGACTAAA 61.129 55.000 6.32 0.00 0.00 1.85
2228 2402 0.392595 GGCTGGAACCGGGACTAAAG 60.393 60.000 6.32 0.00 0.00 1.85
2229 2403 0.611714 GCTGGAACCGGGACTAAAGA 59.388 55.000 6.32 0.00 0.00 2.52
2230 2404 1.675116 GCTGGAACCGGGACTAAAGAC 60.675 57.143 6.32 0.00 0.00 3.01
2231 2405 0.978907 TGGAACCGGGACTAAAGACC 59.021 55.000 6.32 0.00 0.00 3.85
2232 2406 0.978907 GGAACCGGGACTAAAGACCA 59.021 55.000 6.32 0.00 0.00 4.02
2233 2407 1.066358 GGAACCGGGACTAAAGACCAG 60.066 57.143 6.32 0.00 0.00 4.00
2234 2408 0.323957 AACCGGGACTAAAGACCAGC 59.676 55.000 6.32 0.00 0.00 4.85
2235 2409 1.221021 CCGGGACTAAAGACCAGCC 59.779 63.158 0.00 0.00 0.00 4.85
2236 2410 1.265454 CCGGGACTAAAGACCAGCCT 61.265 60.000 0.00 0.00 0.00 4.58
2237 2411 0.613777 CGGGACTAAAGACCAGCCTT 59.386 55.000 1.07 0.00 0.00 4.35
2238 2412 1.405661 CGGGACTAAAGACCAGCCTTC 60.406 57.143 1.07 0.00 0.00 3.46
2239 2413 1.909986 GGGACTAAAGACCAGCCTTCT 59.090 52.381 1.07 0.00 0.00 2.85
2240 2414 2.355209 GGGACTAAAGACCAGCCTTCTG 60.355 54.545 1.07 0.00 40.02 3.02
2241 2415 2.303311 GGACTAAAGACCAGCCTTCTGT 59.697 50.000 0.00 0.00 38.66 3.41
2242 2416 3.591023 GACTAAAGACCAGCCTTCTGTC 58.409 50.000 0.00 0.00 38.66 3.51
2243 2417 2.303311 ACTAAAGACCAGCCTTCTGTCC 59.697 50.000 0.00 0.00 38.66 4.02
2244 2418 0.402121 AAAGACCAGCCTTCTGTCCC 59.598 55.000 0.00 0.00 38.66 4.46
2245 2419 1.831652 AAGACCAGCCTTCTGTCCCG 61.832 60.000 0.00 0.00 38.66 5.14
2246 2420 3.316573 GACCAGCCTTCTGTCCCGG 62.317 68.421 0.00 0.00 38.66 5.73
2247 2421 3.322466 CCAGCCTTCTGTCCCGGT 61.322 66.667 0.00 0.00 38.66 5.28
2248 2422 2.750350 CAGCCTTCTGTCCCGGTT 59.250 61.111 0.00 0.00 35.61 4.44
2249 2423 1.376037 CAGCCTTCTGTCCCGGTTC 60.376 63.158 0.00 0.00 35.61 3.62
2250 2424 2.434359 GCCTTCTGTCCCGGTTCG 60.434 66.667 0.00 0.00 0.00 3.95
2251 2425 2.939261 GCCTTCTGTCCCGGTTCGA 61.939 63.158 0.00 0.00 0.00 3.71
2252 2426 1.215647 CCTTCTGTCCCGGTTCGAG 59.784 63.158 0.00 0.00 0.00 4.04
2253 2427 1.446272 CTTCTGTCCCGGTTCGAGC 60.446 63.158 0.00 0.00 0.00 5.03
2254 2428 2.837371 CTTCTGTCCCGGTTCGAGCC 62.837 65.000 8.48 8.48 0.00 4.70
2255 2429 3.691342 CTGTCCCGGTTCGAGCCA 61.691 66.667 19.03 0.00 0.00 4.75
2256 2430 3.234630 CTGTCCCGGTTCGAGCCAA 62.235 63.158 19.03 0.00 0.00 4.52
2257 2431 2.434359 GTCCCGGTTCGAGCCAAG 60.434 66.667 19.03 8.60 0.00 3.61
2258 2432 2.602267 TCCCGGTTCGAGCCAAGA 60.602 61.111 19.03 10.90 0.00 3.02
2259 2433 2.211410 TCCCGGTTCGAGCCAAGAA 61.211 57.895 19.03 0.00 0.00 2.52
2260 2434 2.033194 CCCGGTTCGAGCCAAGAAC 61.033 63.158 19.03 7.71 45.16 3.01
2263 2437 3.562635 GTTCGAGCCAAGAACCGG 58.437 61.111 0.00 0.00 41.38 5.28
2264 2438 1.005394 GTTCGAGCCAAGAACCGGA 60.005 57.895 9.46 0.00 41.38 5.14
2265 2439 0.601841 GTTCGAGCCAAGAACCGGAA 60.602 55.000 9.46 0.00 41.38 4.30
2266 2440 0.601841 TTCGAGCCAAGAACCGGAAC 60.602 55.000 9.46 0.55 0.00 3.62
2267 2441 2.033194 CGAGCCAAGAACCGGAACC 61.033 63.158 9.46 0.00 0.00 3.62
2268 2442 1.072505 GAGCCAAGAACCGGAACCA 59.927 57.895 9.46 0.00 0.00 3.67
2269 2443 0.536460 GAGCCAAGAACCGGAACCAA 60.536 55.000 9.46 0.00 0.00 3.67
2270 2444 0.112412 AGCCAAGAACCGGAACCAAT 59.888 50.000 9.46 0.00 0.00 3.16
2271 2445 0.243636 GCCAAGAACCGGAACCAATG 59.756 55.000 9.46 0.00 0.00 2.82
2272 2446 1.616159 CCAAGAACCGGAACCAATGT 58.384 50.000 9.46 0.00 0.00 2.71
2273 2447 1.960689 CCAAGAACCGGAACCAATGTT 59.039 47.619 9.46 0.00 37.42 2.71
2274 2448 2.364002 CCAAGAACCGGAACCAATGTTT 59.636 45.455 9.46 0.00 33.97 2.83
2275 2449 3.380142 CAAGAACCGGAACCAATGTTTG 58.620 45.455 9.46 0.00 33.97 2.93
2276 2450 2.661718 AGAACCGGAACCAATGTTTGT 58.338 42.857 9.46 0.00 33.97 2.83
2277 2451 2.360801 AGAACCGGAACCAATGTTTGTG 59.639 45.455 9.46 0.00 33.97 3.33
2278 2452 1.036707 ACCGGAACCAATGTTTGTGG 58.963 50.000 9.46 0.00 42.28 4.17
2279 2453 0.316841 CCGGAACCAATGTTTGTGGG 59.683 55.000 0.00 0.00 40.75 4.61
2280 2454 0.319469 CGGAACCAATGTTTGTGGGC 60.319 55.000 0.00 0.00 40.75 5.36
2281 2455 0.034756 GGAACCAATGTTTGTGGGCC 59.965 55.000 0.00 0.00 40.75 5.80
2282 2456 0.755686 GAACCAATGTTTGTGGGCCA 59.244 50.000 0.00 0.00 40.75 5.36
2283 2457 0.758123 AACCAATGTTTGTGGGCCAG 59.242 50.000 6.40 0.00 40.75 4.85
2284 2458 1.120795 ACCAATGTTTGTGGGCCAGG 61.121 55.000 6.40 4.20 40.75 4.45
2285 2459 0.831288 CCAATGTTTGTGGGCCAGGA 60.831 55.000 6.40 0.00 32.03 3.86
2286 2460 0.604578 CAATGTTTGTGGGCCAGGAG 59.395 55.000 6.40 0.00 0.00 3.69
2287 2461 1.187567 AATGTTTGTGGGCCAGGAGC 61.188 55.000 6.40 0.47 42.60 4.70
2288 2462 3.365265 GTTTGTGGGCCAGGAGCG 61.365 66.667 6.40 0.00 45.17 5.03
2289 2463 3.565214 TTTGTGGGCCAGGAGCGA 61.565 61.111 6.40 0.00 45.17 4.93
2290 2464 3.551496 TTTGTGGGCCAGGAGCGAG 62.551 63.158 6.40 0.00 45.17 5.03
2297 2471 3.801997 CCAGGAGCGAGGCCCATT 61.802 66.667 0.00 0.00 0.00 3.16
2298 2472 2.515523 CAGGAGCGAGGCCCATTG 60.516 66.667 0.00 0.00 0.00 2.82
2299 2473 3.801997 AGGAGCGAGGCCCATTGG 61.802 66.667 0.00 0.00 0.00 3.16
2300 2474 4.115199 GGAGCGAGGCCCATTGGT 62.115 66.667 0.00 0.00 0.00 3.67
2301 2475 2.514824 GAGCGAGGCCCATTGGTC 60.515 66.667 0.00 0.00 36.05 4.02
2302 2476 4.115199 AGCGAGGCCCATTGGTCC 62.115 66.667 0.00 0.00 36.69 4.46
2304 2478 4.856801 CGAGGCCCATTGGTCCCG 62.857 72.222 0.00 0.00 36.69 5.14
2305 2479 4.506255 GAGGCCCATTGGTCCCGG 62.506 72.222 0.00 0.00 36.69 5.73
2307 2481 4.376170 GGCCCATTGGTCCCGGTT 62.376 66.667 0.00 0.00 0.00 4.44
2308 2482 2.754254 GCCCATTGGTCCCGGTTC 60.754 66.667 0.00 0.00 0.00 3.62
2309 2483 2.437716 CCCATTGGTCCCGGTTCG 60.438 66.667 0.00 0.00 0.00 3.95
2310 2484 2.349755 CCATTGGTCCCGGTTCGT 59.650 61.111 0.00 0.00 0.00 3.85
2311 2485 2.038269 CCATTGGTCCCGGTTCGTG 61.038 63.158 0.00 0.00 0.00 4.35
2312 2486 2.359478 ATTGGTCCCGGTTCGTGC 60.359 61.111 0.00 0.00 0.00 5.34
2313 2487 3.912745 ATTGGTCCCGGTTCGTGCC 62.913 63.158 0.00 0.00 0.00 5.01
2315 2489 3.384532 GGTCCCGGTTCGTGCCTA 61.385 66.667 0.00 0.00 0.00 3.93
2316 2490 2.183555 GTCCCGGTTCGTGCCTAG 59.816 66.667 0.00 0.00 0.00 3.02
2317 2491 2.036098 TCCCGGTTCGTGCCTAGA 59.964 61.111 0.00 0.00 0.00 2.43
2318 2492 1.607178 TCCCGGTTCGTGCCTAGAA 60.607 57.895 0.00 0.00 0.00 2.10
2319 2493 1.447314 CCCGGTTCGTGCCTAGAAC 60.447 63.158 0.00 7.30 45.16 3.01
2322 2496 4.180496 GTTCGTGCCTAGAACCGG 57.820 61.111 0.00 0.00 41.38 5.28
2323 2497 1.447314 GTTCGTGCCTAGAACCGGG 60.447 63.158 6.32 0.00 41.38 5.73
2324 2498 1.607178 TTCGTGCCTAGAACCGGGA 60.607 57.895 6.32 0.00 0.00 5.14
2325 2499 1.880819 TTCGTGCCTAGAACCGGGAC 61.881 60.000 6.32 0.00 39.24 4.46
2326 2500 2.642254 CGTGCCTAGAACCGGGACA 61.642 63.158 6.32 0.00 42.32 4.02
2327 2501 1.675219 GTGCCTAGAACCGGGACAA 59.325 57.895 6.32 0.00 41.87 3.18
2328 2502 0.035739 GTGCCTAGAACCGGGACAAA 59.964 55.000 6.32 0.00 41.87 2.83
2329 2503 0.988832 TGCCTAGAACCGGGACAAAT 59.011 50.000 6.32 0.00 0.00 2.32
2330 2504 1.339631 TGCCTAGAACCGGGACAAATG 60.340 52.381 6.32 0.00 0.00 2.32
2331 2505 2.017113 GCCTAGAACCGGGACAAATGG 61.017 57.143 6.32 0.00 0.00 3.16
2332 2506 1.408266 CCTAGAACCGGGACAAATGGG 60.408 57.143 6.32 0.00 0.00 4.00
2333 2507 1.280998 CTAGAACCGGGACAAATGGGT 59.719 52.381 6.32 0.00 0.00 4.51
2334 2508 0.037734 AGAACCGGGACAAATGGGTC 59.962 55.000 6.32 0.00 39.88 4.46
2347 2521 2.502577 GGGTCCATACGAACCGGG 59.497 66.667 6.32 0.00 39.05 5.73
2348 2522 2.059786 GGGTCCATACGAACCGGGA 61.060 63.158 6.32 0.00 39.05 5.14
2349 2523 4.821177 GTCCATACGAACCGGGAC 57.179 61.111 6.32 0.00 42.60 4.46
2350 2524 1.142531 GTCCATACGAACCGGGACC 59.857 63.158 6.32 0.00 43.14 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 3.088532 GCCAGAAATGGGTCAACATACA 58.911 45.455 0.00 0.00 0.00 2.29
13 14 3.737559 AGCCAGAAATGGGTCAACATA 57.262 42.857 0.00 0.00 33.99 2.29
82 91 2.829458 GAGGAGTAGACGGGCGCT 60.829 66.667 7.64 0.00 0.00 5.92
87 96 1.102222 CCGGGAAGAGGAGTAGACGG 61.102 65.000 0.00 0.00 0.00 4.79
89 98 1.393487 GCCCGGGAAGAGGAGTAGAC 61.393 65.000 29.31 0.00 0.00 2.59
90 99 1.076192 GCCCGGGAAGAGGAGTAGA 60.076 63.158 29.31 0.00 0.00 2.59
151 164 0.753867 GGCGAAAGGGTTTTGGGAAA 59.246 50.000 0.00 0.00 0.00 3.13
214 243 1.070786 GCCGTCAAGGTCAAGGTCA 59.929 57.895 0.00 0.00 43.70 4.02
215 244 2.027625 CGCCGTCAAGGTCAAGGTC 61.028 63.158 0.00 0.00 43.70 3.85
216 245 2.030562 CGCCGTCAAGGTCAAGGT 59.969 61.111 0.00 0.00 43.70 3.50
217 246 3.423154 GCGCCGTCAAGGTCAAGG 61.423 66.667 0.00 0.00 43.70 3.61
218 247 3.423154 GGCGCCGTCAAGGTCAAG 61.423 66.667 12.58 0.00 43.70 3.02
295 346 2.943345 GCGACAGTGGTCTTGCGTG 61.943 63.158 0.00 0.00 42.05 5.34
352 418 1.356738 TCCTCTTGGACGACTCCCTTA 59.643 52.381 0.00 0.00 37.46 2.69
363 429 2.606587 GGCCCTGCTTCCTCTTGGA 61.607 63.158 0.00 0.00 41.36 3.53
515 621 2.303549 GACGAGGCTGTGCTGGCTAT 62.304 60.000 0.00 0.00 43.09 2.97
560 669 2.449031 AAACGCAGATGAGCCGGTGA 62.449 55.000 1.90 0.00 0.00 4.02
819 953 0.102481 CGGTCGACATTCCCTCGAAT 59.898 55.000 18.91 0.00 41.64 3.34
906 1040 2.028876 TCCTGACTTTGTGTCTCGTCA 58.971 47.619 0.00 0.00 45.54 4.35
935 1069 4.657824 CGGTCGGCGTGAACACCT 62.658 66.667 6.85 0.00 32.01 4.00
949 1083 2.872388 CGGGATCATAGCCAGCGGT 61.872 63.158 0.00 0.00 0.00 5.68
1020 1154 1.566018 CCGGAAACTCGTGGTCAAGC 61.566 60.000 0.00 0.00 0.00 4.01
1041 1175 0.895530 CTTCCTCTTGCCCGTAGTCA 59.104 55.000 0.00 0.00 0.00 3.41
1232 1372 4.777140 AAAGTTGAATGCTTTTGTTCGC 57.223 36.364 0.00 0.00 32.86 4.70
1324 1464 0.474614 TTCGAAATGGACACCCACCA 59.525 50.000 0.00 0.00 46.98 4.17
1350 1494 2.815589 GCACTCTTGTTGGATCACCCTT 60.816 50.000 0.00 0.00 35.38 3.95
1398 1542 4.974438 ACGGGGAGGGCCTTGACA 62.974 66.667 7.89 0.00 0.00 3.58
1432 1576 4.380531 GCTTGCTAGCATACCATGTCTTA 58.619 43.478 20.13 0.00 46.95 2.10
1802 1966 1.261238 CGCTCCTCCTCCCTTGAGTT 61.261 60.000 0.00 0.00 36.86 3.01
1886 2051 2.125673 GGCTTGCTTCTCCGCGTA 60.126 61.111 4.92 0.00 0.00 4.42
1934 2099 2.890311 CCTCGATCTCTAGCATCTTGGT 59.110 50.000 0.00 0.00 0.00 3.67
1994 2159 2.501128 CCCGGTCATCATGCTCGT 59.499 61.111 0.00 0.00 0.00 4.18
2033 2198 1.078709 CTTGGCGACACGATGTTGAT 58.921 50.000 0.00 0.00 42.67 2.57
2065 2230 0.731417 CGGCCTGCATCTTCTTGAAG 59.269 55.000 0.00 4.13 0.00 3.02
2069 2234 0.254178 ATGTCGGCCTGCATCTTCTT 59.746 50.000 0.00 0.00 0.00 2.52
2183 2357 1.202582 CCGAGACTTGAGTTCGACCAT 59.797 52.381 13.44 0.00 36.49 3.55
2203 2377 3.047877 CCGGTTCCAGCCACGAAC 61.048 66.667 0.00 0.66 39.12 3.95
2204 2378 4.323477 CCCGGTTCCAGCCACGAA 62.323 66.667 0.00 0.00 0.00 3.85
2207 2381 1.833787 TTAGTCCCGGTTCCAGCCAC 61.834 60.000 0.00 0.00 0.00 5.01
2208 2382 1.128809 TTTAGTCCCGGTTCCAGCCA 61.129 55.000 0.00 0.00 0.00 4.75
2209 2383 0.392595 CTTTAGTCCCGGTTCCAGCC 60.393 60.000 0.00 0.00 0.00 4.85
2210 2384 0.611714 TCTTTAGTCCCGGTTCCAGC 59.388 55.000 0.00 0.00 0.00 4.85
2211 2385 1.066358 GGTCTTTAGTCCCGGTTCCAG 60.066 57.143 0.00 0.00 0.00 3.86
2212 2386 0.978907 GGTCTTTAGTCCCGGTTCCA 59.021 55.000 0.00 0.00 0.00 3.53
2213 2387 0.978907 TGGTCTTTAGTCCCGGTTCC 59.021 55.000 0.00 0.00 0.00 3.62
2214 2388 1.675116 GCTGGTCTTTAGTCCCGGTTC 60.675 57.143 0.00 0.00 0.00 3.62
2215 2389 0.323957 GCTGGTCTTTAGTCCCGGTT 59.676 55.000 0.00 0.00 0.00 4.44
2216 2390 1.551019 GGCTGGTCTTTAGTCCCGGT 61.551 60.000 0.00 0.00 0.00 5.28
2217 2391 1.221021 GGCTGGTCTTTAGTCCCGG 59.779 63.158 0.00 0.00 0.00 5.73
2218 2392 0.613777 AAGGCTGGTCTTTAGTCCCG 59.386 55.000 0.00 0.00 0.00 5.14
2219 2393 1.909986 AGAAGGCTGGTCTTTAGTCCC 59.090 52.381 0.00 0.00 0.00 4.46
2220 2394 2.303311 ACAGAAGGCTGGTCTTTAGTCC 59.697 50.000 0.00 0.00 46.60 3.85
2221 2395 3.591023 GACAGAAGGCTGGTCTTTAGTC 58.409 50.000 6.90 5.47 46.60 2.59
2222 2396 2.303311 GGACAGAAGGCTGGTCTTTAGT 59.697 50.000 12.19 0.00 46.60 2.24
2223 2397 2.355209 GGGACAGAAGGCTGGTCTTTAG 60.355 54.545 12.19 0.00 46.60 1.85
2224 2398 1.628846 GGGACAGAAGGCTGGTCTTTA 59.371 52.381 12.19 0.00 46.60 1.85
2225 2399 0.402121 GGGACAGAAGGCTGGTCTTT 59.598 55.000 12.19 0.00 46.60 2.52
2226 2400 1.831652 CGGGACAGAAGGCTGGTCTT 61.832 60.000 12.19 0.00 46.60 3.01
2227 2401 2.286523 CGGGACAGAAGGCTGGTCT 61.287 63.158 12.19 0.00 46.60 3.85
2228 2402 2.266055 CGGGACAGAAGGCTGGTC 59.734 66.667 5.85 5.85 46.60 4.02
2229 2403 3.322466 CCGGGACAGAAGGCTGGT 61.322 66.667 0.00 0.00 46.60 4.00
2230 2404 2.804828 GAACCGGGACAGAAGGCTGG 62.805 65.000 6.32 0.00 46.60 4.85
2232 2406 2.943978 CGAACCGGGACAGAAGGCT 61.944 63.158 6.32 0.00 0.00 4.58
2233 2407 2.434359 CGAACCGGGACAGAAGGC 60.434 66.667 6.32 0.00 0.00 4.35
2234 2408 1.215647 CTCGAACCGGGACAGAAGG 59.784 63.158 6.32 0.00 0.00 3.46
2235 2409 1.446272 GCTCGAACCGGGACAGAAG 60.446 63.158 6.32 0.00 0.00 2.85
2236 2410 2.654877 GCTCGAACCGGGACAGAA 59.345 61.111 6.32 0.00 0.00 3.02
2237 2411 3.379445 GGCTCGAACCGGGACAGA 61.379 66.667 6.32 0.00 34.24 3.41
2238 2412 3.691342 TGGCTCGAACCGGGACAG 61.691 66.667 6.32 0.00 42.08 3.51
2239 2413 3.234630 CTTGGCTCGAACCGGGACA 62.235 63.158 6.32 0.00 46.91 4.02
2240 2414 2.434359 CTTGGCTCGAACCGGGAC 60.434 66.667 6.32 0.00 34.94 4.46
2241 2415 2.211410 TTCTTGGCTCGAACCGGGA 61.211 57.895 6.32 0.00 0.00 5.14
2242 2416 2.033194 GTTCTTGGCTCGAACCGGG 61.033 63.158 6.32 0.00 35.81 5.73
2243 2417 3.562635 GTTCTTGGCTCGAACCGG 58.437 61.111 0.00 0.00 35.81 5.28
2246 2420 0.601841 TTCCGGTTCTTGGCTCGAAC 60.602 55.000 0.00 9.87 39.92 3.95
2247 2421 0.601841 GTTCCGGTTCTTGGCTCGAA 60.602 55.000 0.00 0.00 0.00 3.71
2248 2422 1.005394 GTTCCGGTTCTTGGCTCGA 60.005 57.895 0.00 0.00 0.00 4.04
2249 2423 2.033194 GGTTCCGGTTCTTGGCTCG 61.033 63.158 0.00 0.00 0.00 5.03
2250 2424 0.536460 TTGGTTCCGGTTCTTGGCTC 60.536 55.000 0.00 0.00 0.00 4.70
2251 2425 0.112412 ATTGGTTCCGGTTCTTGGCT 59.888 50.000 0.00 0.00 0.00 4.75
2252 2426 0.243636 CATTGGTTCCGGTTCTTGGC 59.756 55.000 0.00 0.00 0.00 4.52
2253 2427 1.616159 ACATTGGTTCCGGTTCTTGG 58.384 50.000 0.00 0.00 0.00 3.61
2254 2428 3.181480 ACAAACATTGGTTCCGGTTCTTG 60.181 43.478 0.00 0.00 35.82 3.02
2255 2429 3.028130 ACAAACATTGGTTCCGGTTCTT 58.972 40.909 0.00 0.00 35.82 2.52
2256 2430 2.360801 CACAAACATTGGTTCCGGTTCT 59.639 45.455 0.00 0.00 35.82 3.01
2257 2431 2.544903 CCACAAACATTGGTTCCGGTTC 60.545 50.000 0.00 0.00 35.82 3.62
2258 2432 1.410882 CCACAAACATTGGTTCCGGTT 59.589 47.619 0.00 0.00 35.82 4.44
2259 2433 1.036707 CCACAAACATTGGTTCCGGT 58.963 50.000 0.00 0.00 35.82 5.28
2260 2434 0.316841 CCCACAAACATTGGTTCCGG 59.683 55.000 0.00 0.00 35.82 5.14
2261 2435 0.319469 GCCCACAAACATTGGTTCCG 60.319 55.000 0.00 0.00 35.82 4.30
2262 2436 0.034756 GGCCCACAAACATTGGTTCC 59.965 55.000 0.00 0.00 35.82 3.62
2263 2437 0.755686 TGGCCCACAAACATTGGTTC 59.244 50.000 0.00 0.00 35.82 3.62
2264 2438 0.758123 CTGGCCCACAAACATTGGTT 59.242 50.000 0.00 0.00 39.43 3.67
2265 2439 1.120795 CCTGGCCCACAAACATTGGT 61.121 55.000 0.00 0.00 31.46 3.67
2266 2440 0.831288 TCCTGGCCCACAAACATTGG 60.831 55.000 0.00 0.00 34.12 3.16
2267 2441 0.604578 CTCCTGGCCCACAAACATTG 59.395 55.000 0.00 0.00 0.00 2.82
2268 2442 1.187567 GCTCCTGGCCCACAAACATT 61.188 55.000 0.00 0.00 34.27 2.71
2269 2443 1.607467 GCTCCTGGCCCACAAACAT 60.607 57.895 0.00 0.00 34.27 2.71
2270 2444 2.203480 GCTCCTGGCCCACAAACA 60.203 61.111 0.00 0.00 34.27 2.83
2271 2445 3.365265 CGCTCCTGGCCCACAAAC 61.365 66.667 0.00 0.00 37.74 2.93
2272 2446 3.551496 CTCGCTCCTGGCCCACAAA 62.551 63.158 0.00 0.00 37.74 2.83
2273 2447 4.020617 CTCGCTCCTGGCCCACAA 62.021 66.667 0.00 0.00 37.74 3.33
2280 2454 3.801997 AATGGGCCTCGCTCCTGG 61.802 66.667 4.53 0.00 0.00 4.45
2281 2455 2.515523 CAATGGGCCTCGCTCCTG 60.516 66.667 4.53 0.00 0.00 3.86
2282 2456 3.801997 CCAATGGGCCTCGCTCCT 61.802 66.667 4.53 0.00 0.00 3.69
2283 2457 4.115199 ACCAATGGGCCTCGCTCC 62.115 66.667 4.53 0.00 37.90 4.70
2284 2458 2.514824 GACCAATGGGCCTCGCTC 60.515 66.667 4.53 0.00 37.90 5.03
2291 2465 2.754254 GAACCGGGACCAATGGGC 60.754 66.667 6.32 0.00 37.90 5.36
2292 2466 2.437716 CGAACCGGGACCAATGGG 60.438 66.667 6.32 0.00 41.29 4.00
2293 2467 2.038269 CACGAACCGGGACCAATGG 61.038 63.158 6.32 0.00 28.17 3.16
2294 2468 2.686816 GCACGAACCGGGACCAATG 61.687 63.158 6.32 0.00 28.17 2.82
2295 2469 2.359478 GCACGAACCGGGACCAAT 60.359 61.111 6.32 0.00 28.17 3.16
2296 2470 4.629523 GGCACGAACCGGGACCAA 62.630 66.667 6.32 0.00 28.34 3.67
2298 2472 3.366739 CTAGGCACGAACCGGGACC 62.367 68.421 6.32 0.00 40.38 4.46
2299 2473 1.880819 TTCTAGGCACGAACCGGGAC 61.881 60.000 6.32 0.00 39.41 4.46
2300 2474 1.607178 TTCTAGGCACGAACCGGGA 60.607 57.895 6.32 0.00 28.17 5.14
2301 2475 1.447314 GTTCTAGGCACGAACCGGG 60.447 63.158 6.32 0.00 35.81 5.73
2302 2476 4.180496 GTTCTAGGCACGAACCGG 57.820 61.111 0.00 0.00 35.81 5.28
2305 2479 1.447314 CCCGGTTCTAGGCACGAAC 60.447 63.158 0.00 9.57 39.92 3.95
2306 2480 1.607178 TCCCGGTTCTAGGCACGAA 60.607 57.895 0.00 0.00 0.00 3.85
2307 2481 2.036098 TCCCGGTTCTAGGCACGA 59.964 61.111 0.00 0.00 0.00 4.35
2308 2482 2.162338 TTGTCCCGGTTCTAGGCACG 62.162 60.000 0.00 0.00 0.00 5.34
2309 2483 0.035739 TTTGTCCCGGTTCTAGGCAC 59.964 55.000 0.00 0.00 0.00 5.01
2310 2484 0.988832 ATTTGTCCCGGTTCTAGGCA 59.011 50.000 0.00 0.00 0.00 4.75
2311 2485 1.379527 CATTTGTCCCGGTTCTAGGC 58.620 55.000 0.00 0.00 0.00 3.93
2312 2486 1.408266 CCCATTTGTCCCGGTTCTAGG 60.408 57.143 0.00 0.00 0.00 3.02
2313 2487 1.280998 ACCCATTTGTCCCGGTTCTAG 59.719 52.381 0.00 0.00 0.00 2.43
2314 2488 1.279846 GACCCATTTGTCCCGGTTCTA 59.720 52.381 0.00 0.00 0.00 2.10
2315 2489 0.037734 GACCCATTTGTCCCGGTTCT 59.962 55.000 0.00 0.00 0.00 3.01
2316 2490 2.563297 GACCCATTTGTCCCGGTTC 58.437 57.895 0.00 0.00 0.00 3.62
2317 2491 4.834911 GACCCATTTGTCCCGGTT 57.165 55.556 0.00 0.00 0.00 4.44
2323 2497 2.681344 GGTTCGTATGGACCCATTTGTC 59.319 50.000 6.88 0.00 37.82 3.18
2324 2498 2.718563 GGTTCGTATGGACCCATTTGT 58.281 47.619 6.88 0.00 37.82 2.83
2325 2499 1.668751 CGGTTCGTATGGACCCATTTG 59.331 52.381 6.84 0.84 37.82 2.32
2326 2500 1.407712 CCGGTTCGTATGGACCCATTT 60.408 52.381 6.84 0.00 37.82 2.32
2327 2501 0.179468 CCGGTTCGTATGGACCCATT 59.821 55.000 6.84 0.00 37.82 3.16
2328 2502 1.692173 CCCGGTTCGTATGGACCCAT 61.692 60.000 6.84 6.77 40.19 4.00
2329 2503 2.360767 CCCGGTTCGTATGGACCCA 61.361 63.158 6.84 0.00 0.00 4.51
2330 2504 2.059786 TCCCGGTTCGTATGGACCC 61.060 63.158 6.84 0.00 0.00 4.46
2331 2505 1.142531 GTCCCGGTTCGTATGGACC 59.857 63.158 1.74 1.74 41.14 4.46
2332 2506 1.142531 GGTCCCGGTTCGTATGGAC 59.857 63.158 0.00 0.00 45.25 4.02
2333 2507 3.619938 GGTCCCGGTTCGTATGGA 58.380 61.111 0.00 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.