Multiple sequence alignment - TraesCS5D01G004000

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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 TraesCS5D01G004000 chr5D 100.000 2495 0 0 1 2495 3570184 3572678 0.000000e+00 4608
1 TraesCS5D01G004000 chr5B 91.678 2283 127 31 1 2247 5056447 5058702 0.000000e+00 3105
2 TraesCS5D01G004000 chr5A 91.964 1904 105 21 1 1864 2413707 2415602 0.000000e+00 2625
3 TraesCS5D01G004000 chr2B 86.220 254 25 5 2248 2495 253703609 253703858 1.470000e-67 267
4 TraesCS5D01G004000 chr7D 89.720 107 10 1 957 1062 610764561 610764455 4.330000e-28 135


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 TraesCS5D01G004000 chr5D 3570184 3572678 2494 False 4608 4608 100.000 1 2495 1 chr5D.!!$F1 2494
1 TraesCS5D01G004000 chr5B 5056447 5058702 2255 False 3105 3105 91.678 1 2247 1 chr5B.!!$F1 2246
2 TraesCS5D01G004000 chr5A 2413707 2415602 1895 False 2625 2625 91.964 1 1864 1 chr5A.!!$F1 1863

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
845 858 1.225376 TTCGGTGCACGGAACATCAC 61.225 55.0 29.53 4.95 44.45 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2258 2306 0.037232 CGCCTCCCTTCTTTCTTCGT 60.037 55.0 0.0 0.0 0.0 3.85 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
27 28 7.462571 ACCTTGATTCTAACAATTTGGGTAC 57.537 36.000 0.78 0.00 0.00 3.34
161 165 3.197549 AGTCCTTGGTGCACAATGTTTTT 59.802 39.130 20.43 0.00 38.65 1.94
295 306 2.671130 TTCGTATGCATCACAGAGCA 57.329 45.000 0.19 0.00 45.92 4.26
372 383 8.063200 ACTACTAACACATAAGACACATGCTA 57.937 34.615 0.00 0.00 0.00 3.49
388 399 9.632807 GACACATGCTATAACAAATTTTTGGTA 57.367 29.630 3.45 3.45 43.74 3.25
665 676 5.638657 GTGGAAGATGACATCTAGATGCATC 59.361 44.000 34.31 34.31 43.91 3.91
681 692 9.702494 CTAGATGCATCACTTATCATGTTCTAA 57.298 33.333 27.81 0.00 0.00 2.10
807 820 5.873164 GGAATAACATTACACGTGGTCTCTT 59.127 40.000 21.57 7.79 0.00 2.85
829 842 4.340894 TTCGAGGAAAATTGCAGATTCG 57.659 40.909 0.00 0.00 0.00 3.34
837 850 2.741985 TGCAGATTCGGTGCACGG 60.742 61.111 17.69 17.69 45.96 4.94
845 858 1.225376 TTCGGTGCACGGAACATCAC 61.225 55.000 29.53 4.95 44.45 3.06
851 864 1.271325 TGCACGGAACATCACCTCAAT 60.271 47.619 0.00 0.00 0.00 2.57
895 931 9.590451 CATCCAACTAAATTTGTAAGCATTCAT 57.410 29.630 0.00 0.00 0.00 2.57
906 942 5.698832 TGTAAGCATTCATAAGCAACACAC 58.301 37.500 0.00 0.00 0.00 3.82
1065 1101 1.948834 ACTGCTATTGCGCAATATGCA 59.051 42.857 36.57 36.57 45.36 3.96
1177 1213 1.023513 CGAGGAAGAGCAGCCAAAGG 61.024 60.000 0.00 0.00 0.00 3.11
1240 1276 0.394565 GGATATGCCGCTCTCTTGGT 59.605 55.000 0.00 0.00 0.00 3.67
1318 1354 0.040425 GCAATTGAGGCAAACGACGT 60.040 50.000 10.34 0.00 0.00 4.34
1435 1471 2.356667 CCAAGAGCCTTCCCACCC 59.643 66.667 0.00 0.00 0.00 4.61
1452 1488 0.452987 CCCAGTGCAACATTGATCCG 59.547 55.000 0.00 0.00 41.43 4.18
1457 1493 4.487948 CAGTGCAACATTGATCCGAAATT 58.512 39.130 0.00 0.00 41.43 1.82
1490 1526 4.223032 CCCCATCACTAGCGGATATTACTT 59.777 45.833 0.00 0.00 0.00 2.24
1689 1729 2.165167 AGGAATGTGTGGAAGTGCATG 58.835 47.619 0.00 0.00 0.00 4.06
1701 1741 0.108615 AGTGCATGTACGCCTCTCAC 60.109 55.000 8.36 0.00 0.00 3.51
1705 1745 0.108662 CATGTACGCCTCTCACTGCA 60.109 55.000 0.00 0.00 0.00 4.41
1761 1802 7.448469 GGATAATTAGGGCATACTTGTGAACAT 59.552 37.037 0.00 0.00 0.00 2.71
1812 1853 4.154918 CAGAATCGAAGAACCCTCAAAAGG 59.845 45.833 0.00 0.00 43.58 3.11
1884 1929 5.008019 CACATTTCATGAGTTTAGGGATCCG 59.992 44.000 5.45 0.00 0.00 4.18
1885 1930 3.838244 TTCATGAGTTTAGGGATCCGG 57.162 47.619 5.45 0.00 0.00 5.14
1938 1983 3.120095 TGCATGCTCAAGTGATTTCTTCG 60.120 43.478 20.33 0.00 0.00 3.79
1965 2010 0.486879 AGCCTTCCCATCCACCAAAA 59.513 50.000 0.00 0.00 0.00 2.44
2024 2070 4.634004 TCTTCTTGTCAAAGTGCTTCGAAA 59.366 37.500 0.00 0.00 34.78 3.46
2026 2072 6.481976 TCTTCTTGTCAAAGTGCTTCGAAATA 59.518 34.615 0.00 0.00 34.78 1.40
2035 2081 1.203758 TGCTTCGAAATAGCTGTCCGA 59.796 47.619 8.90 0.00 39.38 4.55
2077 2125 2.092049 TGCATGCTGATCTGAATTCCCT 60.092 45.455 20.33 0.00 0.00 4.20
2089 2137 6.387192 TCTGAATTCCCTTTAGACCATTCA 57.613 37.500 2.27 0.00 0.00 2.57
2102 2150 0.824109 CCATTCAGGCACTACTCCGA 59.176 55.000 0.00 0.00 36.02 4.55
2111 2159 1.672145 GCACTACTCCGAACCAAGTCC 60.672 57.143 0.00 0.00 0.00 3.85
2113 2161 2.036733 CACTACTCCGAACCAAGTCCAA 59.963 50.000 0.00 0.00 0.00 3.53
2131 2179 1.130777 AAGGTTGCTTGGTTTGGCAT 58.869 45.000 0.00 0.00 38.30 4.40
2141 2189 0.667184 GGTTTGGCATTGAACCAGCG 60.667 55.000 13.42 0.00 43.75 5.18
2144 2192 1.851021 TTGGCATTGAACCAGCGTCG 61.851 55.000 0.00 0.00 38.73 5.12
2148 2196 2.890766 ATTGAACCAGCGTCGGGGT 61.891 57.895 0.00 0.00 39.65 4.95
2149 2197 3.818121 TTGAACCAGCGTCGGGGTG 62.818 63.158 0.00 0.45 43.78 4.61
2150 2198 4.309950 GAACCAGCGTCGGGGTGT 62.310 66.667 0.00 0.00 42.62 4.16
2151 2199 4.619227 AACCAGCGTCGGGGTGTG 62.619 66.667 0.00 1.49 42.62 3.82
2154 2202 3.991051 CAGCGTCGGGGTGTGTCT 61.991 66.667 0.00 0.00 39.31 3.41
2161 2209 4.065281 GGGGTGTGTCTCGGGTCG 62.065 72.222 0.00 0.00 0.00 4.79
2187 2235 1.064758 TCTCAATTTGGACCATCCGGG 60.065 52.381 0.00 0.00 40.17 5.73
2211 2259 2.409870 GGCCAATGACCAAGCCGAG 61.410 63.158 0.00 0.00 35.30 4.63
2232 2280 1.560505 CAAGGGCTGGTTTTATGGCT 58.439 50.000 0.00 0.00 0.00 4.75
2237 2285 2.092375 GGGCTGGTTTTATGGCTAGACT 60.092 50.000 0.00 0.00 0.00 3.24
2258 2306 3.532993 CGACGCATCGTGTGTTGA 58.467 55.556 11.28 0.00 43.21 3.18
2259 2307 1.127817 CGACGCATCGTGTGTTGAC 59.872 57.895 11.28 0.00 43.21 3.18
2260 2308 1.127817 GACGCATCGTGTGTTGACG 59.872 57.895 0.00 0.00 41.77 4.35
2268 2316 3.153676 TCGTGTGTTGACGAAGAAAGA 57.846 42.857 0.00 0.00 45.08 2.52
2269 2317 3.513662 TCGTGTGTTGACGAAGAAAGAA 58.486 40.909 0.00 0.00 45.08 2.52
2270 2318 3.550275 TCGTGTGTTGACGAAGAAAGAAG 59.450 43.478 0.00 0.00 45.08 2.85
2271 2319 3.302480 CGTGTGTTGACGAAGAAAGAAGG 60.302 47.826 0.00 0.00 42.10 3.46
2272 2320 3.002348 GTGTGTTGACGAAGAAAGAAGGG 59.998 47.826 0.00 0.00 0.00 3.95
2273 2321 3.118555 TGTGTTGACGAAGAAAGAAGGGA 60.119 43.478 0.00 0.00 0.00 4.20
2274 2322 3.495001 GTGTTGACGAAGAAAGAAGGGAG 59.505 47.826 0.00 0.00 0.00 4.30
2275 2323 3.067833 GTTGACGAAGAAAGAAGGGAGG 58.932 50.000 0.00 0.00 0.00 4.30
2276 2324 1.002087 TGACGAAGAAAGAAGGGAGGC 59.998 52.381 0.00 0.00 0.00 4.70
2277 2325 0.037232 ACGAAGAAAGAAGGGAGGCG 60.037 55.000 0.00 0.00 0.00 5.52
2278 2326 0.246635 CGAAGAAAGAAGGGAGGCGA 59.753 55.000 0.00 0.00 0.00 5.54
2279 2327 1.134670 CGAAGAAAGAAGGGAGGCGAT 60.135 52.381 0.00 0.00 0.00 4.58
2280 2328 2.100916 CGAAGAAAGAAGGGAGGCGATA 59.899 50.000 0.00 0.00 0.00 2.92
2281 2329 3.243907 CGAAGAAAGAAGGGAGGCGATAT 60.244 47.826 0.00 0.00 0.00 1.63
2282 2330 3.760580 AGAAAGAAGGGAGGCGATATG 57.239 47.619 0.00 0.00 0.00 1.78
2283 2331 2.147150 GAAAGAAGGGAGGCGATATGC 58.853 52.381 0.00 0.00 45.38 3.14
2284 2332 1.428869 AAGAAGGGAGGCGATATGCT 58.571 50.000 0.00 0.00 45.43 3.79
2285 2333 2.310779 AGAAGGGAGGCGATATGCTA 57.689 50.000 0.00 0.00 45.43 3.49
2286 2334 2.609747 AGAAGGGAGGCGATATGCTAA 58.390 47.619 0.00 0.00 45.43 3.09
2287 2335 2.972713 AGAAGGGAGGCGATATGCTAAA 59.027 45.455 0.00 0.00 45.43 1.85
2288 2336 2.841442 AGGGAGGCGATATGCTAAAC 57.159 50.000 0.00 0.00 45.43 2.01
2289 2337 1.000955 AGGGAGGCGATATGCTAAACG 59.999 52.381 0.00 0.00 45.43 3.60
2290 2338 1.000506 GGGAGGCGATATGCTAAACGA 59.999 52.381 0.00 0.00 45.43 3.85
2291 2339 2.547218 GGGAGGCGATATGCTAAACGAA 60.547 50.000 0.00 0.00 45.43 3.85
2292 2340 3.128349 GGAGGCGATATGCTAAACGAAA 58.872 45.455 0.00 0.00 45.43 3.46
2293 2341 3.746492 GGAGGCGATATGCTAAACGAAAT 59.254 43.478 0.00 0.00 45.43 2.17
2294 2342 4.377431 GGAGGCGATATGCTAAACGAAATG 60.377 45.833 0.00 0.00 45.43 2.32
2295 2343 4.127171 AGGCGATATGCTAAACGAAATGT 58.873 39.130 0.00 0.00 45.43 2.71
2296 2344 4.574828 AGGCGATATGCTAAACGAAATGTT 59.425 37.500 0.00 0.00 45.43 2.71
2297 2345 5.065988 AGGCGATATGCTAAACGAAATGTTT 59.934 36.000 0.00 0.00 46.31 2.83
2298 2346 5.741982 GGCGATATGCTAAACGAAATGTTTT 59.258 36.000 0.00 0.00 45.62 2.43
2299 2347 6.075572 GGCGATATGCTAAACGAAATGTTTTC 60.076 38.462 0.00 0.00 45.62 2.29
2300 2348 8.870375 GGCGATATGCTAAACGAAATGTTTTCC 61.870 40.741 0.00 0.00 45.62 3.13
2309 2357 5.288804 AACGAAATGTTTTCCATCACTTGG 58.711 37.500 0.00 0.00 42.05 3.61
2310 2358 3.674753 CGAAATGTTTTCCATCACTTGGC 59.325 43.478 0.00 0.00 46.01 4.52
2311 2359 4.630111 GAAATGTTTTCCATCACTTGGCA 58.370 39.130 0.00 0.00 46.01 4.92
2312 2360 3.947910 ATGTTTTCCATCACTTGGCAG 57.052 42.857 0.00 0.00 46.01 4.85
2313 2361 2.665165 TGTTTTCCATCACTTGGCAGT 58.335 42.857 0.00 0.00 46.01 4.40
2321 2369 2.183409 CACTTGGCAGTGGCATACC 58.817 57.895 21.29 0.00 46.10 2.73
2322 2370 0.322816 CACTTGGCAGTGGCATACCT 60.323 55.000 21.29 0.15 46.10 3.08
2323 2371 0.405585 ACTTGGCAGTGGCATACCTT 59.594 50.000 21.29 0.28 43.71 3.50
2324 2372 0.813184 CTTGGCAGTGGCATACCTTG 59.187 55.000 21.29 3.43 43.71 3.61
2325 2373 0.112218 TTGGCAGTGGCATACCTTGT 59.888 50.000 21.29 0.00 43.71 3.16
2326 2374 0.988063 TGGCAGTGGCATACCTTGTA 59.012 50.000 16.56 0.00 43.71 2.41
2327 2375 1.352687 TGGCAGTGGCATACCTTGTAA 59.647 47.619 16.56 0.00 43.71 2.41
2328 2376 2.025416 TGGCAGTGGCATACCTTGTAAT 60.025 45.455 16.56 0.00 43.71 1.89
2329 2377 3.023832 GGCAGTGGCATACCTTGTAATT 58.976 45.455 12.58 0.00 43.71 1.40
2330 2378 3.447229 GGCAGTGGCATACCTTGTAATTT 59.553 43.478 12.58 0.00 43.71 1.82
2331 2379 4.440112 GGCAGTGGCATACCTTGTAATTTC 60.440 45.833 12.58 0.00 43.71 2.17
2332 2380 4.157656 GCAGTGGCATACCTTGTAATTTCA 59.842 41.667 0.00 0.00 40.72 2.69
2333 2381 5.640732 CAGTGGCATACCTTGTAATTTCAC 58.359 41.667 0.00 0.00 36.63 3.18
2334 2382 5.415701 CAGTGGCATACCTTGTAATTTCACT 59.584 40.000 0.00 0.00 36.63 3.41
2335 2383 6.597672 CAGTGGCATACCTTGTAATTTCACTA 59.402 38.462 0.00 0.00 36.63 2.74
2336 2384 7.120579 CAGTGGCATACCTTGTAATTTCACTAA 59.879 37.037 0.00 0.00 36.63 2.24
2337 2385 7.668052 AGTGGCATACCTTGTAATTTCACTAAA 59.332 33.333 0.00 0.00 36.63 1.85
2338 2386 7.753580 GTGGCATACCTTGTAATTTCACTAAAC 59.246 37.037 0.00 0.00 36.63 2.01
2339 2387 7.668052 TGGCATACCTTGTAATTTCACTAAACT 59.332 33.333 0.00 0.00 36.63 2.66
2340 2388 8.182227 GGCATACCTTGTAATTTCACTAAACTC 58.818 37.037 0.00 0.00 0.00 3.01
2341 2389 8.182227 GCATACCTTGTAATTTCACTAAACTCC 58.818 37.037 0.00 0.00 0.00 3.85
2342 2390 6.796705 ACCTTGTAATTTCACTAAACTCCG 57.203 37.500 0.00 0.00 0.00 4.63
2343 2391 5.180680 ACCTTGTAATTTCACTAAACTCCGC 59.819 40.000 0.00 0.00 0.00 5.54
2344 2392 4.914312 TGTAATTTCACTAAACTCCGCG 57.086 40.909 0.00 0.00 0.00 6.46
2345 2393 4.309099 TGTAATTTCACTAAACTCCGCGT 58.691 39.130 4.92 0.00 0.00 6.01
2346 2394 4.751098 TGTAATTTCACTAAACTCCGCGTT 59.249 37.500 4.92 0.00 37.47 4.84
2347 2395 4.823790 AATTTCACTAAACTCCGCGTTT 57.176 36.364 4.92 1.33 46.94 3.60
2348 2396 4.823790 ATTTCACTAAACTCCGCGTTTT 57.176 36.364 4.92 4.04 43.06 2.43
2349 2397 5.927954 ATTTCACTAAACTCCGCGTTTTA 57.072 34.783 4.92 5.06 43.06 1.52
2350 2398 4.977741 TTCACTAAACTCCGCGTTTTAG 57.022 40.909 21.38 21.38 43.06 1.85
2351 2399 4.241590 TCACTAAACTCCGCGTTTTAGA 57.758 40.909 26.25 9.68 43.06 2.10
2352 2400 4.232221 TCACTAAACTCCGCGTTTTAGAG 58.768 43.478 26.25 21.27 43.06 2.43
2353 2401 3.367025 CACTAAACTCCGCGTTTTAGAGG 59.633 47.826 26.25 18.03 43.06 3.69
2354 2402 2.825861 AAACTCCGCGTTTTAGAGGA 57.174 45.000 4.92 0.00 43.06 3.71
2355 2403 3.329929 AAACTCCGCGTTTTAGAGGAT 57.670 42.857 4.92 0.00 43.06 3.24
2356 2404 3.329929 AACTCCGCGTTTTAGAGGATT 57.670 42.857 4.92 0.00 39.32 3.01
2357 2405 3.329929 ACTCCGCGTTTTAGAGGATTT 57.670 42.857 4.92 0.00 39.32 2.17
2358 2406 3.671716 ACTCCGCGTTTTAGAGGATTTT 58.328 40.909 4.92 0.00 39.32 1.82
2359 2407 3.435671 ACTCCGCGTTTTAGAGGATTTTG 59.564 43.478 4.92 0.00 39.32 2.44
2360 2408 3.404899 TCCGCGTTTTAGAGGATTTTGT 58.595 40.909 4.92 0.00 35.17 2.83
2361 2409 3.187637 TCCGCGTTTTAGAGGATTTTGTG 59.812 43.478 4.92 0.00 35.17 3.33
2362 2410 3.488489 CGCGTTTTAGAGGATTTTGTGG 58.512 45.455 0.00 0.00 0.00 4.17
2363 2411 3.187637 CGCGTTTTAGAGGATTTTGTGGA 59.812 43.478 0.00 0.00 0.00 4.02
2364 2412 4.669197 CGCGTTTTAGAGGATTTTGTGGAG 60.669 45.833 0.00 0.00 0.00 3.86
2365 2413 4.723248 CGTTTTAGAGGATTTTGTGGAGC 58.277 43.478 0.00 0.00 0.00 4.70
2366 2414 4.215399 CGTTTTAGAGGATTTTGTGGAGCA 59.785 41.667 0.00 0.00 0.00 4.26
2367 2415 5.106157 CGTTTTAGAGGATTTTGTGGAGCAT 60.106 40.000 0.00 0.00 0.00 3.79
2368 2416 6.570378 CGTTTTAGAGGATTTTGTGGAGCATT 60.570 38.462 0.00 0.00 0.00 3.56
2369 2417 5.902613 TTAGAGGATTTTGTGGAGCATTG 57.097 39.130 0.00 0.00 0.00 2.82
2370 2418 3.771216 AGAGGATTTTGTGGAGCATTGT 58.229 40.909 0.00 0.00 0.00 2.71
2371 2419 4.154942 AGAGGATTTTGTGGAGCATTGTT 58.845 39.130 0.00 0.00 0.00 2.83
2372 2420 4.590222 AGAGGATTTTGTGGAGCATTGTTT 59.410 37.500 0.00 0.00 0.00 2.83
2373 2421 4.634199 AGGATTTTGTGGAGCATTGTTTG 58.366 39.130 0.00 0.00 0.00 2.93
2374 2422 4.101430 AGGATTTTGTGGAGCATTGTTTGT 59.899 37.500 0.00 0.00 0.00 2.83
2375 2423 4.448732 GGATTTTGTGGAGCATTGTTTGTC 59.551 41.667 0.00 0.00 0.00 3.18
2376 2424 4.462508 TTTTGTGGAGCATTGTTTGTCA 57.537 36.364 0.00 0.00 0.00 3.58
2377 2425 3.713858 TTGTGGAGCATTGTTTGTCAG 57.286 42.857 0.00 0.00 0.00 3.51
2378 2426 1.337703 TGTGGAGCATTGTTTGTCAGC 59.662 47.619 0.00 0.00 0.00 4.26
2379 2427 1.610522 GTGGAGCATTGTTTGTCAGCT 59.389 47.619 0.00 0.00 38.43 4.24
2380 2428 2.035066 GTGGAGCATTGTTTGTCAGCTT 59.965 45.455 0.00 0.00 35.36 3.74
2381 2429 2.294233 TGGAGCATTGTTTGTCAGCTTC 59.706 45.455 0.00 0.00 35.36 3.86
2382 2430 2.555757 GGAGCATTGTTTGTCAGCTTCT 59.444 45.455 0.00 0.00 35.36 2.85
2383 2431 3.365767 GGAGCATTGTTTGTCAGCTTCTC 60.366 47.826 0.00 0.00 35.36 2.87
2384 2432 3.484407 AGCATTGTTTGTCAGCTTCTCT 58.516 40.909 0.00 0.00 29.98 3.10
2385 2433 4.645535 AGCATTGTTTGTCAGCTTCTCTA 58.354 39.130 0.00 0.00 29.98 2.43
2386 2434 5.065914 AGCATTGTTTGTCAGCTTCTCTAA 58.934 37.500 0.00 0.00 29.98 2.10
2387 2435 5.049129 AGCATTGTTTGTCAGCTTCTCTAAC 60.049 40.000 0.00 0.00 29.98 2.34
2388 2436 5.049129 GCATTGTTTGTCAGCTTCTCTAACT 60.049 40.000 0.00 0.00 0.00 2.24
2389 2437 6.597614 CATTGTTTGTCAGCTTCTCTAACTC 58.402 40.000 0.00 0.00 0.00 3.01
2390 2438 4.632153 TGTTTGTCAGCTTCTCTAACTCC 58.368 43.478 0.00 0.00 0.00 3.85
2391 2439 4.100963 TGTTTGTCAGCTTCTCTAACTCCA 59.899 41.667 0.00 0.00 0.00 3.86
2392 2440 3.944055 TGTCAGCTTCTCTAACTCCAC 57.056 47.619 0.00 0.00 0.00 4.02
2393 2441 2.563179 TGTCAGCTTCTCTAACTCCACC 59.437 50.000 0.00 0.00 0.00 4.61
2394 2442 1.819288 TCAGCTTCTCTAACTCCACCG 59.181 52.381 0.00 0.00 0.00 4.94
2395 2443 1.819288 CAGCTTCTCTAACTCCACCGA 59.181 52.381 0.00 0.00 0.00 4.69
2396 2444 2.231478 CAGCTTCTCTAACTCCACCGAA 59.769 50.000 0.00 0.00 0.00 4.30
2397 2445 2.897969 AGCTTCTCTAACTCCACCGAAA 59.102 45.455 0.00 0.00 0.00 3.46
2398 2446 3.323979 AGCTTCTCTAACTCCACCGAAAA 59.676 43.478 0.00 0.00 0.00 2.29
2399 2447 4.020128 AGCTTCTCTAACTCCACCGAAAAT 60.020 41.667 0.00 0.00 0.00 1.82
2400 2448 5.187186 AGCTTCTCTAACTCCACCGAAAATA 59.813 40.000 0.00 0.00 0.00 1.40
2401 2449 5.291371 GCTTCTCTAACTCCACCGAAAATAC 59.709 44.000 0.00 0.00 0.00 1.89
2402 2450 5.988310 TCTCTAACTCCACCGAAAATACA 57.012 39.130 0.00 0.00 0.00 2.29
2403 2451 5.717119 TCTCTAACTCCACCGAAAATACAC 58.283 41.667 0.00 0.00 0.00 2.90
2404 2452 5.479375 TCTCTAACTCCACCGAAAATACACT 59.521 40.000 0.00 0.00 0.00 3.55
2405 2453 6.660521 TCTCTAACTCCACCGAAAATACACTA 59.339 38.462 0.00 0.00 0.00 2.74
2406 2454 6.624423 TCTAACTCCACCGAAAATACACTAC 58.376 40.000 0.00 0.00 0.00 2.73
2407 2455 3.841643 ACTCCACCGAAAATACACTACG 58.158 45.455 0.00 0.00 0.00 3.51
2408 2456 3.507233 ACTCCACCGAAAATACACTACGA 59.493 43.478 0.00 0.00 0.00 3.43
2409 2457 3.836949 TCCACCGAAAATACACTACGAC 58.163 45.455 0.00 0.00 0.00 4.34
2410 2458 3.507233 TCCACCGAAAATACACTACGACT 59.493 43.478 0.00 0.00 0.00 4.18
2411 2459 3.855950 CCACCGAAAATACACTACGACTC 59.144 47.826 0.00 0.00 0.00 3.36
2412 2460 3.541130 CACCGAAAATACACTACGACTCG 59.459 47.826 0.00 0.00 0.00 4.18
2413 2461 3.189287 ACCGAAAATACACTACGACTCGT 59.811 43.478 9.45 9.45 44.35 4.18
2414 2462 3.782893 CCGAAAATACACTACGACTCGTC 59.217 47.826 7.52 0.00 41.54 4.20
2415 2463 4.397382 CGAAAATACACTACGACTCGTCA 58.603 43.478 7.52 0.00 41.54 4.35
2416 2464 4.259275 CGAAAATACACTACGACTCGTCAC 59.741 45.833 7.52 0.00 41.54 3.67
2417 2465 3.380486 AATACACTACGACTCGTCACG 57.620 47.619 7.52 0.00 41.54 4.35
2418 2466 2.064573 TACACTACGACTCGTCACGA 57.935 50.000 7.52 0.00 41.54 4.35
2419 2467 0.510359 ACACTACGACTCGTCACGAC 59.490 55.000 7.52 0.00 41.54 4.34
2420 2468 0.788995 CACTACGACTCGTCACGACT 59.211 55.000 7.52 0.00 41.54 4.18
2421 2469 1.194098 CACTACGACTCGTCACGACTT 59.806 52.381 7.52 0.00 41.54 3.01
2422 2470 1.458827 ACTACGACTCGTCACGACTTC 59.541 52.381 7.52 0.00 41.54 3.01
2423 2471 1.725706 CTACGACTCGTCACGACTTCT 59.274 52.381 7.52 0.00 41.54 2.85
2424 2472 0.512085 ACGACTCGTCACGACTTCTC 59.488 55.000 0.00 0.00 33.69 2.87
2425 2473 0.516727 CGACTCGTCACGACTTCTCG 60.517 60.000 0.00 0.00 46.06 4.04
2426 2474 0.788995 GACTCGTCACGACTTCTCGA 59.211 55.000 0.00 0.00 43.06 4.04
2427 2475 1.194098 GACTCGTCACGACTTCTCGAA 59.806 52.381 0.00 0.00 43.06 3.71
2428 2476 1.194997 ACTCGTCACGACTTCTCGAAG 59.805 52.381 0.00 5.17 43.06 3.79
2429 2477 0.110328 TCGTCACGACTTCTCGAAGC 60.110 55.000 0.00 0.00 43.06 3.86
2430 2478 1.066114 CGTCACGACTTCTCGAAGCC 61.066 60.000 6.58 0.00 43.06 4.35
2432 2480 1.801913 CACGACTTCTCGAAGCCGG 60.802 63.158 17.29 0.00 46.24 6.13
2433 2481 2.881352 CGACTTCTCGAAGCCGGC 60.881 66.667 21.89 21.89 43.06 6.13
2434 2482 2.574399 GACTTCTCGAAGCCGGCT 59.426 61.111 27.08 27.08 41.99 5.52
2435 2483 1.079750 GACTTCTCGAAGCCGGCTT 60.080 57.895 40.90 40.90 41.99 4.35
2436 2484 1.079317 GACTTCTCGAAGCCGGCTTC 61.079 60.000 45.39 45.39 46.41 3.86
2442 2490 3.882025 GAAGCCGGCTTCTCACAG 58.118 61.111 46.69 2.61 46.38 3.66
2443 2491 2.359230 AAGCCGGCTTCTCACAGC 60.359 61.111 35.84 0.00 39.28 4.40
2444 2492 2.794820 GAAGCCGGCTTCTCACAGCT 62.795 60.000 46.69 24.74 46.38 4.24
2445 2493 3.123620 GCCGGCTTCTCACAGCTG 61.124 66.667 22.15 13.48 44.71 4.24
2454 2502 1.610363 TCTCACAGCTGAGACGTTCT 58.390 50.000 23.35 0.00 46.79 3.01
2455 2503 1.268079 TCTCACAGCTGAGACGTTCTG 59.732 52.381 23.35 5.45 46.79 3.02
2456 2504 2.257991 CTCACAGCTGAGACGTTCTGC 61.258 57.143 23.35 16.17 46.32 4.26
2459 2507 2.343758 GCTGAGACGTTCTGCCCA 59.656 61.111 14.25 0.00 42.92 5.36
2460 2508 1.739562 GCTGAGACGTTCTGCCCAG 60.740 63.158 14.25 7.58 42.92 4.45
2461 2509 1.739562 CTGAGACGTTCTGCCCAGC 60.740 63.158 0.00 0.00 0.00 4.85
2462 2510 2.164865 CTGAGACGTTCTGCCCAGCT 62.165 60.000 0.00 0.00 0.00 4.24
2463 2511 1.446966 GAGACGTTCTGCCCAGCTC 60.447 63.158 0.00 0.00 0.00 4.09
2464 2512 2.435059 GACGTTCTGCCCAGCTCC 60.435 66.667 0.00 0.00 0.00 4.70
2465 2513 4.379243 ACGTTCTGCCCAGCTCCG 62.379 66.667 0.00 0.00 0.00 4.63
2466 2514 4.379243 CGTTCTGCCCAGCTCCGT 62.379 66.667 0.00 0.00 0.00 4.69
2467 2515 2.743928 GTTCTGCCCAGCTCCGTG 60.744 66.667 0.00 0.00 0.00 4.94
2468 2516 4.704833 TTCTGCCCAGCTCCGTGC 62.705 66.667 0.00 0.00 43.29 5.34
2477 2525 3.027292 GCTCCGTGCGTTTTTGGA 58.973 55.556 0.00 0.00 0.00 3.53
2479 2527 4.859400 TCCGTGCGTTTTTGGAGA 57.141 50.000 0.00 0.00 0.00 3.71
2480 2528 2.612200 TCCGTGCGTTTTTGGAGAG 58.388 52.632 0.00 0.00 0.00 3.20
2481 2529 1.082104 CCGTGCGTTTTTGGAGAGC 60.082 57.895 0.00 0.00 0.00 4.09
2482 2530 1.438710 CGTGCGTTTTTGGAGAGCG 60.439 57.895 0.00 0.00 0.00 5.03
2483 2531 1.082104 GTGCGTTTTTGGAGAGCGG 60.082 57.895 0.00 0.00 0.00 5.52
2484 2532 1.227704 TGCGTTTTTGGAGAGCGGA 60.228 52.632 0.00 0.00 0.00 5.54
2485 2533 1.227999 TGCGTTTTTGGAGAGCGGAG 61.228 55.000 0.00 0.00 0.00 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 46 9.123902 CATTGACAAGGAAAATCTACCATCATA 57.876 33.333 0.00 0.00 0.00 2.15
45 47 7.616935 ACATTGACAAGGAAAATCTACCATCAT 59.383 33.333 6.88 0.00 0.00 2.45
135 139 4.151883 ACATTGTGCACCAAGGACTAAAT 58.848 39.130 15.69 0.63 36.99 1.40
189 193 4.630069 GCGAGTTATTAGGACAGAAGCAAA 59.370 41.667 0.00 0.00 0.00 3.68
194 198 6.519679 TTGTAGCGAGTTATTAGGACAGAA 57.480 37.500 0.00 0.00 0.00 3.02
197 201 5.522460 GCATTTGTAGCGAGTTATTAGGACA 59.478 40.000 0.00 0.00 0.00 4.02
295 306 2.038164 GTCCTCTTCTACCCGTGGTTTT 59.962 50.000 0.72 0.00 37.09 2.43
388 399 4.934356 TGGATCCACCATTCTTAGCTTTT 58.066 39.130 11.44 0.00 44.64 2.27
412 423 1.259770 GACTTCCGTCGGTTGTTTCAC 59.740 52.381 11.88 0.00 0.00 3.18
423 434 2.067013 GCTAACTTGTGGACTTCCGTC 58.933 52.381 0.00 0.00 39.43 4.79
492 503 6.127758 CCTGCTTTTGGTATTGTATTGCACTA 60.128 38.462 0.00 0.00 0.00 2.74
493 504 5.336690 CCTGCTTTTGGTATTGTATTGCACT 60.337 40.000 0.00 0.00 0.00 4.40
494 505 4.864247 CCTGCTTTTGGTATTGTATTGCAC 59.136 41.667 0.00 0.00 0.00 4.57
495 506 4.769488 TCCTGCTTTTGGTATTGTATTGCA 59.231 37.500 0.00 0.00 0.00 4.08
535 546 8.267620 TGTGGAAACATACAATGAGTAATGAG 57.732 34.615 0.00 0.00 46.14 2.90
735 746 8.147058 TGTGGAACTTAATTTGTAATTGTGCAT 58.853 29.630 0.00 0.00 38.04 3.96
736 747 7.492524 TGTGGAACTTAATTTGTAATTGTGCA 58.507 30.769 0.00 0.00 38.04 4.57
807 820 4.379394 CCGAATCTGCAATTTTCCTCGAAA 60.379 41.667 0.00 0.00 0.00 3.46
829 842 3.263941 GGTGATGTTCCGTGCACC 58.736 61.111 12.15 0.00 43.34 5.01
837 850 5.886960 ACTTTGCTATTGAGGTGATGTTC 57.113 39.130 0.00 0.00 0.00 3.18
845 858 6.206634 TGACCAAAGTTACTTTGCTATTGAGG 59.793 38.462 26.93 15.90 46.44 3.86
851 864 5.626142 TGGATGACCAAAGTTACTTTGCTA 58.374 37.500 26.93 17.04 46.44 3.49
895 931 4.709250 TGTCTACCATTGTGTGTTGCTTA 58.291 39.130 0.00 0.00 0.00 3.09
906 942 9.662947 ATGTGACATGATATATGTCTACCATTG 57.337 33.333 17.74 0.00 46.25 2.82
1065 1101 1.849823 AGCTGGGCTGGGAACTTCT 60.850 57.895 0.00 0.00 37.57 2.85
1177 1213 9.119329 CATAACATAATCGCTACAAGAGTCTAC 57.881 37.037 0.00 0.00 0.00 2.59
1240 1276 0.690762 CCCCAAGTCCGAGGAAAGAA 59.309 55.000 0.00 0.00 0.00 2.52
1297 1333 1.334960 CGTCGTTTGCCTCAATTGCTT 60.335 47.619 0.00 0.00 0.00 3.91
1329 1365 4.436113 TGATGTCCATATAGCCTTGCAA 57.564 40.909 0.00 0.00 0.00 4.08
1395 1431 0.394938 TCTGCACCGTTCTGGCTTTA 59.605 50.000 0.00 0.00 43.94 1.85
1432 1468 1.549203 GGATCAATGTTGCACTGGGT 58.451 50.000 0.00 0.00 0.00 4.51
1435 1471 3.557577 TTTCGGATCAATGTTGCACTG 57.442 42.857 0.00 0.00 0.00 3.66
1452 1488 3.448301 TGATGGGGATGTTGCAGAATTTC 59.552 43.478 0.00 0.00 0.00 2.17
1457 1493 0.994247 AGTGATGGGGATGTTGCAGA 59.006 50.000 0.00 0.00 0.00 4.26
1490 1526 3.008923 TCACCAATGGAAGCTACATCACA 59.991 43.478 6.16 0.00 0.00 3.58
1689 1729 1.726853 AAATGCAGTGAGAGGCGTAC 58.273 50.000 0.00 0.00 0.00 3.67
1701 1741 3.058016 CCGCCATCTATACCAAAATGCAG 60.058 47.826 0.00 0.00 0.00 4.41
1705 1745 6.976934 ATTTTCCGCCATCTATACCAAAAT 57.023 33.333 0.00 0.00 0.00 1.82
1761 1802 4.041938 ACCTTCACGGTTGGGACTAAAATA 59.958 41.667 0.00 0.00 46.37 1.40
1789 1830 4.154918 CCTTTTGAGGGTTCTTCGATTCTG 59.845 45.833 0.00 0.00 0.00 3.02
1812 1853 9.321562 TCTACCGATATTCTTGTGTTATTTTCC 57.678 33.333 0.00 0.00 0.00 3.13
1830 1871 7.793948 AGCCTATAAAATAACCTCTACCGAT 57.206 36.000 0.00 0.00 0.00 4.18
1884 1929 1.761198 ACGTCCCCTCTAAATAGTGCC 59.239 52.381 0.00 0.00 0.00 5.01
1885 1930 2.483188 CCACGTCCCCTCTAAATAGTGC 60.483 54.545 0.00 0.00 0.00 4.40
1965 2010 9.758651 ATTTATAGTCTTTTTCGCTTTGGTTTT 57.241 25.926 0.00 0.00 0.00 2.43
2024 2070 3.347411 GAACGCTTCGGACAGCTAT 57.653 52.632 9.41 0.00 37.68 2.97
2071 2119 3.269381 TGCCTGAATGGTCTAAAGGGAAT 59.731 43.478 0.00 0.00 38.35 3.01
2072 2120 2.647299 TGCCTGAATGGTCTAAAGGGAA 59.353 45.455 0.00 0.00 38.35 3.97
2073 2121 2.026262 GTGCCTGAATGGTCTAAAGGGA 60.026 50.000 0.00 0.00 38.35 4.20
2077 2125 4.081087 GGAGTAGTGCCTGAATGGTCTAAA 60.081 45.833 0.00 0.00 38.35 1.85
2089 2137 0.608640 CTTGGTTCGGAGTAGTGCCT 59.391 55.000 0.00 0.00 0.00 4.75
2102 2150 1.756538 CAAGCAACCTTGGACTTGGTT 59.243 47.619 11.23 7.42 46.33 3.67
2111 2159 0.177604 TGCCAAACCAAGCAACCTTG 59.822 50.000 0.00 0.00 46.38 3.61
2113 2161 1.130777 AATGCCAAACCAAGCAACCT 58.869 45.000 0.00 0.00 43.36 3.50
2131 2179 3.552384 ACCCCGACGCTGGTTCAA 61.552 61.111 1.80 0.00 0.00 2.69
2141 2189 4.065281 CCCGAGACACACCCCGAC 62.065 72.222 0.00 0.00 0.00 4.79
2144 2192 4.065281 CGACCCGAGACACACCCC 62.065 72.222 0.00 0.00 0.00 4.95
2148 2196 2.338620 CAAGCGACCCGAGACACA 59.661 61.111 0.00 0.00 0.00 3.72
2149 2197 2.432628 CCAAGCGACCCGAGACAC 60.433 66.667 0.00 0.00 0.00 3.67
2150 2198 2.915659 ACCAAGCGACCCGAGACA 60.916 61.111 0.00 0.00 0.00 3.41
2151 2199 2.126031 GACCAAGCGACCCGAGAC 60.126 66.667 0.00 0.00 0.00 3.36
2152 2200 2.282958 AGACCAAGCGACCCGAGA 60.283 61.111 0.00 0.00 0.00 4.04
2153 2201 2.154798 TTGAGACCAAGCGACCCGAG 62.155 60.000 0.00 0.00 0.00 4.63
2154 2202 1.541310 ATTGAGACCAAGCGACCCGA 61.541 55.000 0.00 0.00 35.48 5.14
2242 2290 1.127817 CGTCAACACACGATGCGTC 59.872 57.895 0.00 0.00 42.69 5.19
2248 2296 3.153676 TCTTTCTTCGTCAACACACGA 57.846 42.857 0.00 0.00 46.91 4.35
2249 2297 3.302480 CCTTCTTTCTTCGTCAACACACG 60.302 47.826 0.00 0.00 41.36 4.49
2250 2298 3.002348 CCCTTCTTTCTTCGTCAACACAC 59.998 47.826 0.00 0.00 0.00 3.82
2251 2299 3.118555 TCCCTTCTTTCTTCGTCAACACA 60.119 43.478 0.00 0.00 0.00 3.72
2252 2300 3.463944 TCCCTTCTTTCTTCGTCAACAC 58.536 45.455 0.00 0.00 0.00 3.32
2253 2301 3.494398 CCTCCCTTCTTTCTTCGTCAACA 60.494 47.826 0.00 0.00 0.00 3.33
2254 2302 3.067833 CCTCCCTTCTTTCTTCGTCAAC 58.932 50.000 0.00 0.00 0.00 3.18
2255 2303 2.550208 GCCTCCCTTCTTTCTTCGTCAA 60.550 50.000 0.00 0.00 0.00 3.18
2256 2304 1.002087 GCCTCCCTTCTTTCTTCGTCA 59.998 52.381 0.00 0.00 0.00 4.35
2257 2305 1.728068 GCCTCCCTTCTTTCTTCGTC 58.272 55.000 0.00 0.00 0.00 4.20
2258 2306 0.037232 CGCCTCCCTTCTTTCTTCGT 60.037 55.000 0.00 0.00 0.00 3.85
2259 2307 0.246635 TCGCCTCCCTTCTTTCTTCG 59.753 55.000 0.00 0.00 0.00 3.79
2260 2308 2.700722 ATCGCCTCCCTTCTTTCTTC 57.299 50.000 0.00 0.00 0.00 2.87
2261 2309 3.745797 GCATATCGCCTCCCTTCTTTCTT 60.746 47.826 0.00 0.00 32.94 2.52
2262 2310 2.224402 GCATATCGCCTCCCTTCTTTCT 60.224 50.000 0.00 0.00 32.94 2.52
2263 2311 2.147150 GCATATCGCCTCCCTTCTTTC 58.853 52.381 0.00 0.00 32.94 2.62
2264 2312 1.771255 AGCATATCGCCTCCCTTCTTT 59.229 47.619 0.00 0.00 44.04 2.52
2265 2313 1.428869 AGCATATCGCCTCCCTTCTT 58.571 50.000 0.00 0.00 44.04 2.52
2266 2314 2.310779 TAGCATATCGCCTCCCTTCT 57.689 50.000 0.00 0.00 44.04 2.85
2267 2315 3.067833 GTTTAGCATATCGCCTCCCTTC 58.932 50.000 0.00 0.00 44.04 3.46
2268 2316 2.548067 CGTTTAGCATATCGCCTCCCTT 60.548 50.000 0.00 0.00 44.04 3.95
2269 2317 1.000955 CGTTTAGCATATCGCCTCCCT 59.999 52.381 0.00 0.00 44.04 4.20
2270 2318 1.000506 TCGTTTAGCATATCGCCTCCC 59.999 52.381 0.00 0.00 44.04 4.30
2271 2319 2.433868 TCGTTTAGCATATCGCCTCC 57.566 50.000 0.00 0.00 44.04 4.30
2272 2320 4.211374 ACATTTCGTTTAGCATATCGCCTC 59.789 41.667 0.00 0.00 44.04 4.70
2273 2321 4.127171 ACATTTCGTTTAGCATATCGCCT 58.873 39.130 0.00 0.00 44.04 5.52
2274 2322 4.468095 ACATTTCGTTTAGCATATCGCC 57.532 40.909 0.00 0.00 44.04 5.54
2304 2352 0.405585 AAGGTATGCCACTGCCAAGT 59.594 50.000 1.54 0.00 36.98 3.16
2305 2353 0.813184 CAAGGTATGCCACTGCCAAG 59.187 55.000 1.54 0.00 37.19 3.61
2306 2354 0.112218 ACAAGGTATGCCACTGCCAA 59.888 50.000 1.54 0.00 37.19 4.52
2307 2355 0.988063 TACAAGGTATGCCACTGCCA 59.012 50.000 1.54 0.00 37.19 4.92
2308 2356 2.122783 TTACAAGGTATGCCACTGCC 57.877 50.000 1.54 0.00 37.19 4.85
2309 2357 4.157656 TGAAATTACAAGGTATGCCACTGC 59.842 41.667 1.54 0.00 37.19 4.40
2310 2358 5.415701 AGTGAAATTACAAGGTATGCCACTG 59.584 40.000 1.54 1.30 37.19 3.66
2311 2359 5.570320 AGTGAAATTACAAGGTATGCCACT 58.430 37.500 1.54 0.00 37.19 4.00
2312 2360 5.897377 AGTGAAATTACAAGGTATGCCAC 57.103 39.130 1.54 0.00 37.19 5.01
2313 2361 7.668052 AGTTTAGTGAAATTACAAGGTATGCCA 59.332 33.333 1.54 0.00 37.19 4.92
2314 2362 8.051901 AGTTTAGTGAAATTACAAGGTATGCC 57.948 34.615 0.00 0.00 0.00 4.40
2315 2363 8.182227 GGAGTTTAGTGAAATTACAAGGTATGC 58.818 37.037 0.00 0.00 0.00 3.14
2316 2364 8.388103 CGGAGTTTAGTGAAATTACAAGGTATG 58.612 37.037 0.00 0.00 0.00 2.39
2317 2365 7.065443 GCGGAGTTTAGTGAAATTACAAGGTAT 59.935 37.037 0.00 0.00 0.00 2.73
2318 2366 6.369615 GCGGAGTTTAGTGAAATTACAAGGTA 59.630 38.462 0.00 0.00 0.00 3.08
2319 2367 5.180680 GCGGAGTTTAGTGAAATTACAAGGT 59.819 40.000 0.00 0.00 0.00 3.50
2320 2368 5.628134 GCGGAGTTTAGTGAAATTACAAGG 58.372 41.667 0.00 0.00 0.00 3.61
2321 2369 5.107220 ACGCGGAGTTTAGTGAAATTACAAG 60.107 40.000 12.47 0.00 0.00 3.16
2322 2370 4.751098 ACGCGGAGTTTAGTGAAATTACAA 59.249 37.500 12.47 0.00 0.00 2.41
2323 2371 4.309099 ACGCGGAGTTTAGTGAAATTACA 58.691 39.130 12.47 0.00 0.00 2.41
2324 2372 4.916099 ACGCGGAGTTTAGTGAAATTAC 57.084 40.909 12.47 0.00 0.00 1.89
2336 2384 3.329929 AATCCTCTAAAACGCGGAGTT 57.670 42.857 12.47 3.49 46.76 3.01
2337 2385 3.329929 AAATCCTCTAAAACGCGGAGT 57.670 42.857 12.47 0.00 0.00 3.85
2338 2386 3.435671 ACAAAATCCTCTAAAACGCGGAG 59.564 43.478 12.47 6.71 0.00 4.63
2339 2387 3.187637 CACAAAATCCTCTAAAACGCGGA 59.812 43.478 12.47 0.00 0.00 5.54
2340 2388 3.488489 CACAAAATCCTCTAAAACGCGG 58.512 45.455 12.47 0.00 0.00 6.46
2341 2389 3.187637 TCCACAAAATCCTCTAAAACGCG 59.812 43.478 3.53 3.53 0.00 6.01
2342 2390 4.723248 CTCCACAAAATCCTCTAAAACGC 58.277 43.478 0.00 0.00 0.00 4.84
2343 2391 4.215399 TGCTCCACAAAATCCTCTAAAACG 59.785 41.667 0.00 0.00 0.00 3.60
2344 2392 5.705609 TGCTCCACAAAATCCTCTAAAAC 57.294 39.130 0.00 0.00 0.00 2.43
2345 2393 6.267471 ACAATGCTCCACAAAATCCTCTAAAA 59.733 34.615 0.00 0.00 0.00 1.52
2346 2394 5.774690 ACAATGCTCCACAAAATCCTCTAAA 59.225 36.000 0.00 0.00 0.00 1.85
2347 2395 5.324409 ACAATGCTCCACAAAATCCTCTAA 58.676 37.500 0.00 0.00 0.00 2.10
2348 2396 4.922206 ACAATGCTCCACAAAATCCTCTA 58.078 39.130 0.00 0.00 0.00 2.43
2349 2397 3.771216 ACAATGCTCCACAAAATCCTCT 58.229 40.909 0.00 0.00 0.00 3.69
2350 2398 4.525912 AACAATGCTCCACAAAATCCTC 57.474 40.909 0.00 0.00 0.00 3.71
2351 2399 4.101430 ACAAACAATGCTCCACAAAATCCT 59.899 37.500 0.00 0.00 0.00 3.24
2352 2400 4.379652 ACAAACAATGCTCCACAAAATCC 58.620 39.130 0.00 0.00 0.00 3.01
2353 2401 5.049167 TGACAAACAATGCTCCACAAAATC 58.951 37.500 0.00 0.00 0.00 2.17
2354 2402 5.021033 TGACAAACAATGCTCCACAAAAT 57.979 34.783 0.00 0.00 0.00 1.82
2355 2403 4.431809 CTGACAAACAATGCTCCACAAAA 58.568 39.130 0.00 0.00 0.00 2.44
2356 2404 3.737663 GCTGACAAACAATGCTCCACAAA 60.738 43.478 0.00 0.00 0.00 2.83
2357 2405 2.223782 GCTGACAAACAATGCTCCACAA 60.224 45.455 0.00 0.00 0.00 3.33
2358 2406 1.337703 GCTGACAAACAATGCTCCACA 59.662 47.619 0.00 0.00 0.00 4.17
2359 2407 1.610522 AGCTGACAAACAATGCTCCAC 59.389 47.619 0.00 0.00 0.00 4.02
2360 2408 1.985473 AGCTGACAAACAATGCTCCA 58.015 45.000 0.00 0.00 0.00 3.86
2361 2409 2.555757 AGAAGCTGACAAACAATGCTCC 59.444 45.455 0.00 0.00 30.50 4.70
2362 2410 3.501445 AGAGAAGCTGACAAACAATGCTC 59.499 43.478 0.00 0.00 30.50 4.26
2363 2411 3.484407 AGAGAAGCTGACAAACAATGCT 58.516 40.909 0.00 0.00 32.59 3.79
2364 2412 3.911661 AGAGAAGCTGACAAACAATGC 57.088 42.857 0.00 0.00 0.00 3.56
2365 2413 6.348050 GGAGTTAGAGAAGCTGACAAACAATG 60.348 42.308 0.00 0.00 35.68 2.82
2366 2414 5.703130 GGAGTTAGAGAAGCTGACAAACAAT 59.297 40.000 0.00 0.00 35.68 2.71
2367 2415 5.057149 GGAGTTAGAGAAGCTGACAAACAA 58.943 41.667 0.00 0.00 35.68 2.83
2368 2416 4.100963 TGGAGTTAGAGAAGCTGACAAACA 59.899 41.667 0.00 0.00 35.68 2.83
2369 2417 4.449405 GTGGAGTTAGAGAAGCTGACAAAC 59.551 45.833 0.00 0.00 35.68 2.93
2370 2418 4.503296 GGTGGAGTTAGAGAAGCTGACAAA 60.503 45.833 0.00 0.00 35.68 2.83
2371 2419 3.006967 GGTGGAGTTAGAGAAGCTGACAA 59.993 47.826 0.00 0.00 35.68 3.18
2372 2420 2.563179 GGTGGAGTTAGAGAAGCTGACA 59.437 50.000 0.00 0.00 35.68 3.58
2373 2421 2.416162 CGGTGGAGTTAGAGAAGCTGAC 60.416 54.545 0.00 0.00 33.54 3.51
2374 2422 1.819288 CGGTGGAGTTAGAGAAGCTGA 59.181 52.381 0.00 0.00 0.00 4.26
2375 2423 1.819288 TCGGTGGAGTTAGAGAAGCTG 59.181 52.381 0.00 0.00 0.00 4.24
2376 2424 2.217510 TCGGTGGAGTTAGAGAAGCT 57.782 50.000 0.00 0.00 0.00 3.74
2377 2425 3.314541 TTTCGGTGGAGTTAGAGAAGC 57.685 47.619 0.00 0.00 0.00 3.86
2378 2426 6.310711 GTGTATTTTCGGTGGAGTTAGAGAAG 59.689 42.308 0.00 0.00 0.00 2.85
2379 2427 6.014840 AGTGTATTTTCGGTGGAGTTAGAGAA 60.015 38.462 0.00 0.00 0.00 2.87
2380 2428 5.479375 AGTGTATTTTCGGTGGAGTTAGAGA 59.521 40.000 0.00 0.00 0.00 3.10
2381 2429 5.721232 AGTGTATTTTCGGTGGAGTTAGAG 58.279 41.667 0.00 0.00 0.00 2.43
2382 2430 5.733620 AGTGTATTTTCGGTGGAGTTAGA 57.266 39.130 0.00 0.00 0.00 2.10
2383 2431 5.514204 CGTAGTGTATTTTCGGTGGAGTTAG 59.486 44.000 0.00 0.00 0.00 2.34
2384 2432 5.182950 TCGTAGTGTATTTTCGGTGGAGTTA 59.817 40.000 0.00 0.00 0.00 2.24
2385 2433 4.022068 TCGTAGTGTATTTTCGGTGGAGTT 60.022 41.667 0.00 0.00 0.00 3.01
2386 2434 3.507233 TCGTAGTGTATTTTCGGTGGAGT 59.493 43.478 0.00 0.00 0.00 3.85
2387 2435 3.855950 GTCGTAGTGTATTTTCGGTGGAG 59.144 47.826 0.00 0.00 0.00 3.86
2388 2436 3.507233 AGTCGTAGTGTATTTTCGGTGGA 59.493 43.478 0.00 0.00 0.00 4.02
2389 2437 3.841643 AGTCGTAGTGTATTTTCGGTGG 58.158 45.455 0.00 0.00 0.00 4.61
2390 2438 3.541130 CGAGTCGTAGTGTATTTTCGGTG 59.459 47.826 3.82 0.00 0.00 4.94
2391 2439 3.189287 ACGAGTCGTAGTGTATTTTCGGT 59.811 43.478 18.34 0.00 38.73 4.69
2392 2440 3.751621 ACGAGTCGTAGTGTATTTTCGG 58.248 45.455 18.34 0.00 38.73 4.30
2393 2441 4.259275 GTGACGAGTCGTAGTGTATTTTCG 59.741 45.833 19.93 0.00 41.37 3.46
2394 2442 4.259275 CGTGACGAGTCGTAGTGTATTTTC 59.741 45.833 19.93 2.31 41.37 2.29
2395 2443 4.083855 TCGTGACGAGTCGTAGTGTATTTT 60.084 41.667 19.93 0.00 41.37 1.82
2396 2444 3.433274 TCGTGACGAGTCGTAGTGTATTT 59.567 43.478 19.93 0.00 41.37 1.40
2397 2445 2.995939 TCGTGACGAGTCGTAGTGTATT 59.004 45.455 19.93 0.00 41.37 1.89
2398 2446 2.346847 GTCGTGACGAGTCGTAGTGTAT 59.653 50.000 19.93 0.00 41.37 2.29
2399 2447 1.721389 GTCGTGACGAGTCGTAGTGTA 59.279 52.381 19.93 0.44 41.37 2.90
2400 2448 0.510359 GTCGTGACGAGTCGTAGTGT 59.490 55.000 19.93 0.00 41.37 3.55
2401 2449 0.788995 AGTCGTGACGAGTCGTAGTG 59.211 55.000 19.93 10.98 41.37 2.74
2402 2450 1.458827 GAAGTCGTGACGAGTCGTAGT 59.541 52.381 19.93 2.60 41.37 2.73
2403 2451 1.725706 AGAAGTCGTGACGAGTCGTAG 59.274 52.381 19.93 13.11 41.37 3.51
2404 2452 1.723542 GAGAAGTCGTGACGAGTCGTA 59.276 52.381 19.93 0.00 41.37 3.43
2405 2453 0.512085 GAGAAGTCGTGACGAGTCGT 59.488 55.000 20.02 20.02 45.10 4.34
2406 2454 0.516727 CGAGAAGTCGTGACGAGTCG 60.517 60.000 16.35 11.85 38.67 4.18
2407 2455 0.788995 TCGAGAAGTCGTGACGAGTC 59.211 55.000 16.35 12.68 46.85 3.36
2408 2456 1.194997 CTTCGAGAAGTCGTGACGAGT 59.805 52.381 8.41 9.22 46.85 4.18
2409 2457 1.872029 CTTCGAGAAGTCGTGACGAG 58.128 55.000 8.41 0.00 46.85 4.18
2410 2458 0.110328 GCTTCGAGAAGTCGTGACGA 60.110 55.000 2.39 2.39 46.85 4.20
2411 2459 1.066114 GGCTTCGAGAAGTCGTGACG 61.066 60.000 13.58 0.00 46.85 4.35
2412 2460 2.726887 GGCTTCGAGAAGTCGTGAC 58.273 57.895 13.58 0.00 46.85 3.67
2417 2465 1.079317 GAAGCCGGCTTCGAGAAGTC 61.079 60.000 43.97 26.09 42.23 3.01
2418 2466 1.079750 GAAGCCGGCTTCGAGAAGT 60.080 57.895 43.97 22.52 42.23 3.01
2419 2467 3.787458 GAAGCCGGCTTCGAGAAG 58.213 61.111 43.97 8.39 42.23 2.85
2426 2474 2.359230 GCTGTGAGAAGCCGGCTT 60.359 61.111 40.90 40.90 37.20 4.35
2427 2475 3.317571 AGCTGTGAGAAGCCGGCT 61.318 61.111 27.08 27.08 44.68 5.52
2428 2476 3.123620 CAGCTGTGAGAAGCCGGC 61.124 66.667 21.89 21.89 44.68 6.13
2429 2477 2.659016 TCAGCTGTGAGAAGCCGG 59.341 61.111 14.67 0.00 44.68 6.13
2437 2485 0.319040 GCAGAACGTCTCAGCTGTGA 60.319 55.000 14.67 14.47 33.88 3.58
2438 2486 1.287730 GGCAGAACGTCTCAGCTGTG 61.288 60.000 14.67 11.96 36.80 3.66
2439 2487 1.005630 GGCAGAACGTCTCAGCTGT 60.006 57.895 14.67 0.00 36.80 4.40
2440 2488 1.739562 GGGCAGAACGTCTCAGCTG 60.740 63.158 7.63 7.63 36.80 4.24
2441 2489 2.164865 CTGGGCAGAACGTCTCAGCT 62.165 60.000 12.27 0.00 36.80 4.24
2442 2490 1.739562 CTGGGCAGAACGTCTCAGC 60.740 63.158 0.00 0.00 35.87 4.26
2443 2491 1.739562 GCTGGGCAGAACGTCTCAG 60.740 63.158 0.00 0.00 0.00 3.35
2444 2492 2.159819 GAGCTGGGCAGAACGTCTCA 62.160 60.000 0.00 0.00 0.00 3.27
2445 2493 1.446966 GAGCTGGGCAGAACGTCTC 60.447 63.158 0.00 0.00 0.00 3.36
2446 2494 2.659610 GAGCTGGGCAGAACGTCT 59.340 61.111 0.00 0.00 0.00 4.18
2447 2495 2.435059 GGAGCTGGGCAGAACGTC 60.435 66.667 0.00 0.00 0.00 4.34
2448 2496 4.379243 CGGAGCTGGGCAGAACGT 62.379 66.667 0.00 0.00 0.00 3.99
2449 2497 4.379243 ACGGAGCTGGGCAGAACG 62.379 66.667 0.00 0.00 0.00 3.95
2450 2498 2.743928 CACGGAGCTGGGCAGAAC 60.744 66.667 0.00 0.00 0.00 3.01
2451 2499 4.704833 GCACGGAGCTGGGCAGAA 62.705 66.667 0.00 0.00 41.15 3.02
2456 2504 2.551912 AAAAACGCACGGAGCTGGG 61.552 57.895 0.00 0.00 42.61 4.45
2457 2505 1.370414 CAAAAACGCACGGAGCTGG 60.370 57.895 0.00 0.00 42.61 4.85
2458 2506 1.370414 CCAAAAACGCACGGAGCTG 60.370 57.895 0.00 0.00 42.61 4.24
2459 2507 1.507141 CTCCAAAAACGCACGGAGCT 61.507 55.000 0.00 0.00 42.61 4.09
2460 2508 1.082104 CTCCAAAAACGCACGGAGC 60.082 57.895 0.00 0.00 38.74 4.70
2461 2509 0.512952 CTCTCCAAAAACGCACGGAG 59.487 55.000 0.00 0.00 45.40 4.63
2462 2510 1.503818 GCTCTCCAAAAACGCACGGA 61.504 55.000 0.00 0.00 0.00 4.69
2463 2511 1.082104 GCTCTCCAAAAACGCACGG 60.082 57.895 0.00 0.00 0.00 4.94
2464 2512 1.438710 CGCTCTCCAAAAACGCACG 60.439 57.895 0.00 0.00 0.00 5.34
2465 2513 1.082104 CCGCTCTCCAAAAACGCAC 60.082 57.895 0.00 0.00 0.00 5.34
2466 2514 1.227704 TCCGCTCTCCAAAAACGCA 60.228 52.632 0.00 0.00 0.00 5.24
2467 2515 1.497722 CTCCGCTCTCCAAAAACGC 59.502 57.895 0.00 0.00 0.00 4.84
2468 2516 1.497722 GCTCCGCTCTCCAAAAACG 59.502 57.895 0.00 0.00 0.00 3.60
2469 2517 1.876664 GGCTCCGCTCTCCAAAAAC 59.123 57.895 0.00 0.00 0.00 2.43
2470 2518 1.671054 CGGCTCCGCTCTCCAAAAA 60.671 57.895 0.00 0.00 0.00 1.94
2471 2519 2.047274 CGGCTCCGCTCTCCAAAA 60.047 61.111 0.00 0.00 0.00 2.44
2472 2520 4.082523 CCGGCTCCGCTCTCCAAA 62.083 66.667 2.18 0.00 38.24 3.28


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

AutoCloner maintained by Alex Coulton.