Multiple sequence alignment - TraesCS1A01G157400

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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 TraesCS1A01G157400 chr1A 100.000 2455 0 0 1 2455 278537404 278539858 0.000000e+00 4534.0
1 TraesCS1A01G157400 chr1A 97.623 2188 52 0 1 2188 94770220 94768033 0.000000e+00 3753.0
2 TraesCS1A01G157400 chr1A 97.863 234 4 1 2222 2455 278541832 278541600 1.060000e-108 403.0
3 TraesCS1A01G157400 chr1A 96.667 240 6 2 2216 2455 290057572 290057809 4.920000e-107 398.0
4 TraesCS1A01G157400 chr1A 97.436 234 5 1 2222 2455 481835303 481835071 4.920000e-107 398.0
5 TraesCS1A01G157400 chr1A 96.250 240 8 1 2216 2455 69367425 69367663 2.290000e-105 392.0
6 TraesCS1A01G157400 chr7A 97.579 2189 50 3 1 2188 563575919 563573733 0.000000e+00 3746.0
7 TraesCS1A01G157400 chr7A 97.980 1634 33 0 555 2188 699893405 699895038 0.000000e+00 2835.0
8 TraesCS1A01G157400 chr7A 97.487 557 14 0 3 559 699873062 699873618 0.000000e+00 952.0
9 TraesCS1A01G157400 chr1B 97.532 2188 48 2 1 2188 471874186 471876367 0.000000e+00 3736.0
10 TraesCS1A01G157400 chr1B 97.840 2083 43 2 107 2188 638737913 638735832 0.000000e+00 3596.0
11 TraesCS1A01G157400 chr1B 100.000 30 0 0 2194 2223 49797808 49797779 3.410000e-04 56.5
12 TraesCS1A01G157400 chr3B 98.079 2082 40 0 107 2188 201624235 201622154 0.000000e+00 3624.0
13 TraesCS1A01G157400 chr6A 98.080 2083 35 2 107 2188 64698998 64696920 0.000000e+00 3620.0
14 TraesCS1A01G157400 chr5B 97.651 2086 45 1 107 2188 127817701 127815616 0.000000e+00 3578.0
15 TraesCS1A01G157400 chr6B 96.552 1943 45 3 1 1942 388123228 388125149 0.000000e+00 3197.0
16 TraesCS1A01G157400 chr2B 95.631 1465 38 2 1 1460 357194775 357193332 0.000000e+00 2327.0
17 TraesCS1A01G157400 chr2B 97.569 288 7 0 1901 2188 391202114 391202401 6.100000e-136 494.0
18 TraesCS1A01G157400 chr2B 96.281 242 8 1 2214 2455 662739931 662740171 1.770000e-106 396.0
19 TraesCS1A01G157400 chr4B 97.436 234 5 1 2222 2455 302837182 302837414 4.920000e-107 398.0
20 TraesCS1A01G157400 chr3A 97.436 234 5 1 2222 2455 260693472 260693240 4.920000e-107 398.0
21 TraesCS1A01G157400 chr3A 97.436 234 5 1 2222 2455 313195171 313194939 4.920000e-107 398.0
22 TraesCS1A01G157400 chr7D 96.250 240 8 1 2216 2455 158183852 158184090 2.290000e-105 392.0
23 TraesCS1A01G157400 chr2D 100.000 50 0 0 39 88 47618796 47618747 2.600000e-15 93.5
24 TraesCS1A01G157400 chr3D 94.828 58 3 0 28 85 193426684 193426741 9.350000e-15 91.6
25 TraesCS1A01G157400 chrUn 100.000 29 0 0 2195 2223 40085246 40085218 1.000000e-03 54.7
26 TraesCS1A01G157400 chrUn 100.000 29 0 0 2195 2223 223707549 223707577 1.000000e-03 54.7
27 TraesCS1A01G157400 chrUn 100.000 29 0 0 2195 2223 266188696 266188724 1.000000e-03 54.7
28 TraesCS1A01G157400 chr6D 100.000 29 0 0 2195 2223 430481142 430481114 1.000000e-03 54.7
29 TraesCS1A01G157400 chr5D 100.000 29 0 0 2195 2223 3134314 3134286 1.000000e-03 54.7
30 TraesCS1A01G157400 chr4D 100.000 29 0 0 2195 2223 135036572 135036600 1.000000e-03 54.7
31 TraesCS1A01G157400 chr1D 100.000 29 0 0 2195 2223 141345368 141345396 1.000000e-03 54.7
32 TraesCS1A01G157400 chr1D 100.000 29 0 0 2195 2223 141345482 141345510 1.000000e-03 54.7


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 TraesCS1A01G157400 chr1A 278537404 278539858 2454 False 4534 4534 100.000 1 2455 1 chr1A.!!$F2 2454
1 TraesCS1A01G157400 chr1A 94768033 94770220 2187 True 3753 3753 97.623 1 2188 1 chr1A.!!$R1 2187
2 TraesCS1A01G157400 chr7A 563573733 563575919 2186 True 3746 3746 97.579 1 2188 1 chr7A.!!$R1 2187
3 TraesCS1A01G157400 chr7A 699893405 699895038 1633 False 2835 2835 97.980 555 2188 1 chr7A.!!$F2 1633
4 TraesCS1A01G157400 chr7A 699873062 699873618 556 False 952 952 97.487 3 559 1 chr7A.!!$F1 556
5 TraesCS1A01G157400 chr1B 471874186 471876367 2181 False 3736 3736 97.532 1 2188 1 chr1B.!!$F1 2187
6 TraesCS1A01G157400 chr1B 638735832 638737913 2081 True 3596 3596 97.840 107 2188 1 chr1B.!!$R2 2081
7 TraesCS1A01G157400 chr3B 201622154 201624235 2081 True 3624 3624 98.079 107 2188 1 chr3B.!!$R1 2081
8 TraesCS1A01G157400 chr6A 64696920 64698998 2078 True 3620 3620 98.080 107 2188 1 chr6A.!!$R1 2081
9 TraesCS1A01G157400 chr5B 127815616 127817701 2085 True 3578 3578 97.651 107 2188 1 chr5B.!!$R1 2081
10 TraesCS1A01G157400 chr6B 388123228 388125149 1921 False 3197 3197 96.552 1 1942 1 chr6B.!!$F1 1941
11 TraesCS1A01G157400 chr2B 357193332 357194775 1443 True 2327 2327 95.631 1 1460 1 chr2B.!!$R1 1459

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
467 521 1.737793 CCAATACGCTTCGCTTTCCTT 59.262 47.619 0.0 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2445 0.254747 TTTCCAATAGGACCCCGCTG 59.745 55.0 0.0 0.0 45.73 5.18 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
138 144 4.809193 ACTTCCCTCTAGCATCACTCATA 58.191 43.478 0.00 0.00 0.00 2.15
205 211 2.026262 TCCTCATGGAACTAGGGTTTGC 60.026 50.000 0.00 0.00 39.87 3.68
304 342 9.221933 CATTCATTTTCCTTTCCATGAATTTGA 57.778 29.630 0.00 0.00 41.51 2.69
467 521 1.737793 CCAATACGCTTCGCTTTCCTT 59.262 47.619 0.00 0.00 0.00 3.36
729 789 4.265056 ACCTGTGCGGACCAACCC 62.265 66.667 4.04 0.00 36.31 4.11
736 796 2.675075 CGGACCAACCCGGCAATT 60.675 61.111 0.00 0.00 45.43 2.32
889 949 7.773489 TTATCATCCTGTTGTTTCCATGAAA 57.227 32.000 0.00 0.00 0.00 2.69
998 1058 7.154435 AGTTACTCGCTCATTAGTAGTGAAA 57.846 36.000 0.00 0.00 33.34 2.69
1333 1393 5.680619 TGAAAAAGAGAGTCAAGCAAGGTA 58.319 37.500 0.00 0.00 0.00 3.08
1473 1533 8.190888 AGCTTAAGATCTTCGTATTTCAAGTG 57.809 34.615 12.24 0.00 0.00 3.16
1586 1646 3.380637 GCTCTAGTCGAACTCCATACCAA 59.619 47.826 0.00 0.00 0.00 3.67
1614 1674 1.878088 GAGAACCCTTTCCGTTGGAAC 59.122 52.381 0.00 0.00 41.87 3.62
1767 1827 4.143986 AGAAAGATCGATGGAAAGGGAC 57.856 45.455 0.54 0.00 0.00 4.46
1904 1964 5.888161 GCCTTTGATTCTCTTTAAGGATCCA 59.112 40.000 15.82 0.00 39.05 3.41
2188 2248 3.578716 TGCTAGCTAGGAAACTGTCTGTT 59.421 43.478 22.10 0.00 43.88 3.16
2189 2249 4.770531 TGCTAGCTAGGAAACTGTCTGTTA 59.229 41.667 22.10 0.00 43.88 2.41
2190 2250 5.422331 TGCTAGCTAGGAAACTGTCTGTTAT 59.578 40.000 22.10 0.00 43.88 1.89
2191 2251 5.751028 GCTAGCTAGGAAACTGTCTGTTATG 59.249 44.000 22.10 0.00 43.88 1.90
2192 2252 4.508662 AGCTAGGAAACTGTCTGTTATGC 58.491 43.478 0.00 0.00 43.88 3.14
2193 2253 4.223923 AGCTAGGAAACTGTCTGTTATGCT 59.776 41.667 0.00 0.00 43.88 3.79
2194 2254 5.422331 AGCTAGGAAACTGTCTGTTATGCTA 59.578 40.000 0.00 2.15 43.88 3.49
2195 2255 5.751028 GCTAGGAAACTGTCTGTTATGCTAG 59.249 44.000 17.80 17.80 43.88 3.42
2196 2256 6.405953 GCTAGGAAACTGTCTGTTATGCTAGA 60.406 42.308 21.83 0.00 43.88 2.43
2197 2257 5.971763 AGGAAACTGTCTGTTATGCTAGAG 58.028 41.667 0.00 0.00 41.13 2.43
2198 2258 5.482175 AGGAAACTGTCTGTTATGCTAGAGT 59.518 40.000 0.00 0.00 41.13 3.24
2199 2259 5.808030 GGAAACTGTCTGTTATGCTAGAGTC 59.192 44.000 0.00 0.00 38.03 3.36
2200 2260 5.984695 AACTGTCTGTTATGCTAGAGTCA 57.015 39.130 0.00 0.00 37.07 3.41
2201 2261 5.574891 ACTGTCTGTTATGCTAGAGTCAG 57.425 43.478 0.00 0.00 0.00 3.51
2202 2262 5.013547 ACTGTCTGTTATGCTAGAGTCAGT 58.986 41.667 0.00 0.00 30.16 3.41
2203 2263 6.181190 ACTGTCTGTTATGCTAGAGTCAGTA 58.819 40.000 0.00 0.00 32.06 2.74
2204 2264 6.317642 ACTGTCTGTTATGCTAGAGTCAGTAG 59.682 42.308 0.00 1.56 32.06 2.57
2205 2265 6.415573 TGTCTGTTATGCTAGAGTCAGTAGA 58.584 40.000 0.00 0.00 0.00 2.59
2206 2266 6.316640 TGTCTGTTATGCTAGAGTCAGTAGAC 59.683 42.308 0.00 0.00 45.31 2.59
2207 2267 5.823570 TCTGTTATGCTAGAGTCAGTAGACC 59.176 44.000 0.00 0.00 46.15 3.85
2208 2268 5.756918 TGTTATGCTAGAGTCAGTAGACCT 58.243 41.667 0.00 0.00 46.15 3.85
2209 2269 6.188407 TGTTATGCTAGAGTCAGTAGACCTT 58.812 40.000 0.00 0.00 46.15 3.50
2210 2270 7.344134 TGTTATGCTAGAGTCAGTAGACCTTA 58.656 38.462 0.00 0.00 46.15 2.69
2211 2271 7.282675 TGTTATGCTAGAGTCAGTAGACCTTAC 59.717 40.741 0.00 0.00 46.15 2.34
2212 2272 5.438698 TGCTAGAGTCAGTAGACCTTACT 57.561 43.478 0.00 0.00 46.15 2.24
2213 2273 5.817784 TGCTAGAGTCAGTAGACCTTACTT 58.182 41.667 0.00 0.00 46.15 2.24
2214 2274 6.246919 TGCTAGAGTCAGTAGACCTTACTTT 58.753 40.000 0.00 0.00 46.15 2.66
2215 2275 7.400439 TGCTAGAGTCAGTAGACCTTACTTTA 58.600 38.462 0.00 0.00 46.15 1.85
2216 2276 7.553402 TGCTAGAGTCAGTAGACCTTACTTTAG 59.447 40.741 0.00 0.00 46.15 1.85
2217 2277 7.553760 GCTAGAGTCAGTAGACCTTACTTTAGT 59.446 40.741 0.00 0.00 46.15 2.24
2218 2278 7.690952 AGAGTCAGTAGACCTTACTTTAGTG 57.309 40.000 0.00 0.00 46.15 2.74
2219 2279 7.232910 AGAGTCAGTAGACCTTACTTTAGTGT 58.767 38.462 0.00 0.00 46.15 3.55
2220 2280 8.381636 AGAGTCAGTAGACCTTACTTTAGTGTA 58.618 37.037 0.00 0.00 46.15 2.90
2221 2281 8.564509 AGTCAGTAGACCTTACTTTAGTGTAG 57.435 38.462 0.00 0.00 46.15 2.74
2222 2282 7.611079 AGTCAGTAGACCTTACTTTAGTGTAGG 59.389 40.741 9.86 9.86 46.15 3.18
2223 2283 7.609532 GTCAGTAGACCTTACTTTAGTGTAGGA 59.390 40.741 15.55 0.00 38.89 2.94
2224 2284 8.334734 TCAGTAGACCTTACTTTAGTGTAGGAT 58.665 37.037 15.55 8.85 35.81 3.24
2225 2285 8.407064 CAGTAGACCTTACTTTAGTGTAGGATG 58.593 40.741 15.55 6.34 35.81 3.51
2226 2286 8.334734 AGTAGACCTTACTTTAGTGTAGGATGA 58.665 37.037 15.55 2.70 35.81 2.92
2227 2287 7.648039 AGACCTTACTTTAGTGTAGGATGAG 57.352 40.000 15.55 0.00 35.81 2.90
2228 2288 7.183460 AGACCTTACTTTAGTGTAGGATGAGT 58.817 38.462 15.55 0.00 35.81 3.41
2229 2289 7.674772 AGACCTTACTTTAGTGTAGGATGAGTT 59.325 37.037 15.55 0.00 35.81 3.01
2230 2290 8.890410 ACCTTACTTTAGTGTAGGATGAGTTA 57.110 34.615 15.55 0.00 35.81 2.24
2231 2291 9.490083 ACCTTACTTTAGTGTAGGATGAGTTAT 57.510 33.333 15.55 0.00 35.81 1.89
2232 2292 9.751542 CCTTACTTTAGTGTAGGATGAGTTATG 57.248 37.037 6.93 0.00 34.86 1.90
2233 2293 9.250624 CTTACTTTAGTGTAGGATGAGTTATGC 57.749 37.037 0.00 0.00 0.00 3.14
2234 2294 6.583562 ACTTTAGTGTAGGATGAGTTATGCC 58.416 40.000 0.00 0.00 0.00 4.40
2235 2295 6.156256 ACTTTAGTGTAGGATGAGTTATGCCA 59.844 38.462 0.00 0.00 0.00 4.92
2236 2296 4.679373 AGTGTAGGATGAGTTATGCCAG 57.321 45.455 0.00 0.00 0.00 4.85
2237 2297 4.290093 AGTGTAGGATGAGTTATGCCAGA 58.710 43.478 0.00 0.00 0.00 3.86
2238 2298 4.904251 AGTGTAGGATGAGTTATGCCAGAT 59.096 41.667 0.00 0.00 0.00 2.90
2239 2299 4.993584 GTGTAGGATGAGTTATGCCAGATG 59.006 45.833 0.00 0.00 0.00 2.90
2240 2300 3.137446 AGGATGAGTTATGCCAGATGC 57.863 47.619 0.00 0.00 41.77 3.91
2241 2301 1.802960 GGATGAGTTATGCCAGATGCG 59.197 52.381 0.00 0.00 45.60 4.73
2242 2302 1.802960 GATGAGTTATGCCAGATGCGG 59.197 52.381 0.00 0.00 45.60 5.69
2243 2303 0.541392 TGAGTTATGCCAGATGCGGT 59.459 50.000 0.00 0.00 45.60 5.68
2244 2304 1.065491 TGAGTTATGCCAGATGCGGTT 60.065 47.619 0.00 0.00 45.60 4.44
2245 2305 1.599542 GAGTTATGCCAGATGCGGTTC 59.400 52.381 0.00 0.00 45.60 3.62
2246 2306 1.065491 AGTTATGCCAGATGCGGTTCA 60.065 47.619 0.00 0.00 45.60 3.18
2247 2307 1.949525 GTTATGCCAGATGCGGTTCAT 59.050 47.619 0.00 0.00 45.60 2.57
2258 2318 3.052455 TGCGGTTCATCATGTAACAGT 57.948 42.857 0.00 0.00 0.00 3.55
2259 2319 3.000041 TGCGGTTCATCATGTAACAGTC 59.000 45.455 0.00 0.00 0.00 3.51
2260 2320 3.000041 GCGGTTCATCATGTAACAGTCA 59.000 45.455 0.00 0.00 0.00 3.41
2261 2321 3.623060 GCGGTTCATCATGTAACAGTCAT 59.377 43.478 0.00 0.00 0.00 3.06
2262 2322 4.808895 GCGGTTCATCATGTAACAGTCATA 59.191 41.667 0.00 0.00 0.00 2.15
2263 2323 5.293324 GCGGTTCATCATGTAACAGTCATAA 59.707 40.000 0.00 0.00 0.00 1.90
2264 2324 6.705782 CGGTTCATCATGTAACAGTCATAAC 58.294 40.000 0.00 0.00 0.00 1.89
2265 2325 6.312672 CGGTTCATCATGTAACAGTCATAACA 59.687 38.462 0.00 0.00 0.00 2.41
2266 2326 7.011389 CGGTTCATCATGTAACAGTCATAACAT 59.989 37.037 0.00 0.00 32.91 2.71
2267 2327 9.325198 GGTTCATCATGTAACAGTCATAACATA 57.675 33.333 0.00 0.00 31.55 2.29
2269 2329 9.546428 TTCATCATGTAACAGTCATAACATAGG 57.454 33.333 0.00 0.00 31.55 2.57
2270 2330 8.150296 TCATCATGTAACAGTCATAACATAGGG 58.850 37.037 0.00 0.00 31.55 3.53
2271 2331 7.432148 TCATGTAACAGTCATAACATAGGGT 57.568 36.000 0.00 0.00 31.55 4.34
2272 2332 7.272244 TCATGTAACAGTCATAACATAGGGTG 58.728 38.462 0.00 0.00 31.55 4.61
2273 2333 6.860790 TGTAACAGTCATAACATAGGGTGA 57.139 37.500 0.00 0.00 0.00 4.02
2274 2334 6.636705 TGTAACAGTCATAACATAGGGTGAC 58.363 40.000 0.00 0.00 40.87 3.67
2275 2335 5.755409 AACAGTCATAACATAGGGTGACA 57.245 39.130 10.82 0.00 42.51 3.58
2276 2336 5.086104 ACAGTCATAACATAGGGTGACAC 57.914 43.478 10.82 0.00 42.51 3.67
2277 2337 4.530553 ACAGTCATAACATAGGGTGACACA 59.469 41.667 8.08 0.00 42.51 3.72
2278 2338 5.111989 CAGTCATAACATAGGGTGACACAG 58.888 45.833 8.08 0.00 42.51 3.66
2279 2339 5.023452 AGTCATAACATAGGGTGACACAGA 58.977 41.667 8.08 0.00 42.51 3.41
2280 2340 5.483937 AGTCATAACATAGGGTGACACAGAA 59.516 40.000 8.08 0.00 42.51 3.02
2281 2341 5.581085 GTCATAACATAGGGTGACACAGAAC 59.419 44.000 8.08 0.00 40.41 3.01
2282 2342 5.483937 TCATAACATAGGGTGACACAGAACT 59.516 40.000 8.08 2.56 0.00 3.01
2283 2343 6.666113 TCATAACATAGGGTGACACAGAACTA 59.334 38.462 8.08 4.69 0.00 2.24
2284 2344 5.407407 AACATAGGGTGACACAGAACTAG 57.593 43.478 8.08 0.00 0.00 2.57
2285 2345 3.195825 ACATAGGGTGACACAGAACTAGC 59.804 47.826 8.08 0.00 0.00 3.42
2286 2346 2.016905 AGGGTGACACAGAACTAGCT 57.983 50.000 8.08 0.00 0.00 3.32
2287 2347 1.896465 AGGGTGACACAGAACTAGCTC 59.104 52.381 8.08 0.00 0.00 4.09
2288 2348 1.066787 GGGTGACACAGAACTAGCTCC 60.067 57.143 8.08 0.00 0.00 4.70
2289 2349 1.618837 GGTGACACAGAACTAGCTCCA 59.381 52.381 8.08 0.00 0.00 3.86
2290 2350 2.353208 GGTGACACAGAACTAGCTCCAG 60.353 54.545 8.08 0.00 0.00 3.86
2291 2351 2.297597 GTGACACAGAACTAGCTCCAGT 59.702 50.000 0.00 0.00 0.00 4.00
2292 2352 2.965831 TGACACAGAACTAGCTCCAGTT 59.034 45.455 1.40 1.40 41.44 3.16
2301 2361 4.833478 ACTAGCTCCAGTTCATCAATGT 57.167 40.909 0.00 0.00 0.00 2.71
2302 2362 5.939764 ACTAGCTCCAGTTCATCAATGTA 57.060 39.130 0.00 0.00 0.00 2.29
2303 2363 6.299805 ACTAGCTCCAGTTCATCAATGTAA 57.700 37.500 0.00 0.00 0.00 2.41
2304 2364 6.893583 ACTAGCTCCAGTTCATCAATGTAAT 58.106 36.000 0.00 0.00 0.00 1.89
2305 2365 6.765036 ACTAGCTCCAGTTCATCAATGTAATG 59.235 38.462 0.00 0.00 0.00 1.90
2306 2366 5.503927 AGCTCCAGTTCATCAATGTAATGT 58.496 37.500 0.00 0.00 0.00 2.71
2307 2367 6.653020 AGCTCCAGTTCATCAATGTAATGTA 58.347 36.000 0.00 0.00 0.00 2.29
2308 2368 6.765036 AGCTCCAGTTCATCAATGTAATGTAG 59.235 38.462 0.00 0.00 0.00 2.74
2309 2369 6.017605 GCTCCAGTTCATCAATGTAATGTAGG 60.018 42.308 0.00 0.00 0.00 3.18
2310 2370 5.822519 TCCAGTTCATCAATGTAATGTAGGC 59.177 40.000 0.00 0.00 0.00 3.93
2311 2371 5.589855 CCAGTTCATCAATGTAATGTAGGCA 59.410 40.000 0.00 0.00 0.00 4.75
2312 2372 6.263842 CCAGTTCATCAATGTAATGTAGGCAT 59.736 38.462 0.00 0.00 36.80 4.40
2313 2373 7.136772 CAGTTCATCAATGTAATGTAGGCATG 58.863 38.462 0.00 0.00 35.15 4.06
2314 2374 6.830324 AGTTCATCAATGTAATGTAGGCATGT 59.170 34.615 0.00 0.00 35.15 3.21
2315 2375 7.992608 AGTTCATCAATGTAATGTAGGCATGTA 59.007 33.333 0.00 0.00 35.15 2.29
2316 2376 8.786898 GTTCATCAATGTAATGTAGGCATGTAT 58.213 33.333 0.00 0.00 35.15 2.29
2317 2377 8.922931 TCATCAATGTAATGTAGGCATGTATT 57.077 30.769 0.00 0.00 35.15 1.89
2318 2378 9.002600 TCATCAATGTAATGTAGGCATGTATTC 57.997 33.333 0.00 0.00 35.15 1.75
2319 2379 7.744087 TCAATGTAATGTAGGCATGTATTCC 57.256 36.000 0.00 0.00 35.15 3.01
2320 2380 6.426633 TCAATGTAATGTAGGCATGTATTCCG 59.573 38.462 0.00 0.00 35.15 4.30
2321 2381 5.284861 TGTAATGTAGGCATGTATTCCGT 57.715 39.130 0.00 0.00 35.15 4.69
2322 2382 6.408107 TGTAATGTAGGCATGTATTCCGTA 57.592 37.500 0.00 0.00 35.15 4.02
2323 2383 6.999950 TGTAATGTAGGCATGTATTCCGTAT 58.000 36.000 0.00 0.00 35.15 3.06
2324 2384 8.124808 TGTAATGTAGGCATGTATTCCGTATA 57.875 34.615 0.00 0.00 35.15 1.47
2325 2385 8.755028 TGTAATGTAGGCATGTATTCCGTATAT 58.245 33.333 0.00 0.00 35.15 0.86
2328 2388 7.949690 TGTAGGCATGTATTCCGTATATAGT 57.050 36.000 0.00 0.00 0.00 2.12
2329 2389 7.993101 TGTAGGCATGTATTCCGTATATAGTC 58.007 38.462 0.00 0.00 0.00 2.59
2330 2390 7.612633 TGTAGGCATGTATTCCGTATATAGTCA 59.387 37.037 0.00 0.00 0.00 3.41
2331 2391 7.661536 AGGCATGTATTCCGTATATAGTCAT 57.338 36.000 0.00 0.00 0.00 3.06
2332 2392 8.762481 AGGCATGTATTCCGTATATAGTCATA 57.238 34.615 0.00 0.00 0.00 2.15
2333 2393 8.630917 AGGCATGTATTCCGTATATAGTCATAC 58.369 37.037 0.00 0.00 0.00 2.39
2345 2405 9.550811 CGTATATAGTCATACGTGCTTATGAAA 57.449 33.333 0.00 0.00 45.48 2.69
2349 2409 8.942338 ATAGTCATACGTGCTTATGAAAAAGA 57.058 30.769 0.00 0.00 39.62 2.52
2350 2410 7.667043 AGTCATACGTGCTTATGAAAAAGAA 57.333 32.000 0.00 0.00 39.62 2.52
2351 2411 7.519002 AGTCATACGTGCTTATGAAAAAGAAC 58.481 34.615 0.00 0.00 39.62 3.01
2352 2412 7.387948 AGTCATACGTGCTTATGAAAAAGAACT 59.612 33.333 0.00 0.00 39.62 3.01
2353 2413 8.015658 GTCATACGTGCTTATGAAAAAGAACTT 58.984 33.333 0.00 0.00 39.62 2.66
2354 2414 8.015087 TCATACGTGCTTATGAAAAAGAACTTG 58.985 33.333 0.00 0.00 35.87 3.16
2355 2415 4.976116 ACGTGCTTATGAAAAAGAACTTGC 59.024 37.500 0.00 0.00 33.44 4.01
2356 2416 4.975502 CGTGCTTATGAAAAAGAACTTGCA 59.024 37.500 0.00 0.00 33.44 4.08
2357 2417 5.630680 CGTGCTTATGAAAAAGAACTTGCAT 59.369 36.000 0.00 0.00 33.44 3.96
2358 2418 6.399249 CGTGCTTATGAAAAAGAACTTGCATG 60.399 38.462 0.00 0.00 33.44 4.06
2359 2419 6.642131 GTGCTTATGAAAAAGAACTTGCATGA 59.358 34.615 6.60 0.00 32.93 3.07
2360 2420 6.642131 TGCTTATGAAAAAGAACTTGCATGAC 59.358 34.615 6.60 0.54 0.00 3.06
2361 2421 6.642131 GCTTATGAAAAAGAACTTGCATGACA 59.358 34.615 6.60 0.00 0.00 3.58
2362 2422 7.330208 GCTTATGAAAAAGAACTTGCATGACAT 59.670 33.333 6.60 0.00 0.00 3.06
2363 2423 8.746922 TTATGAAAAAGAACTTGCATGACATC 57.253 30.769 6.60 2.21 0.00 3.06
2364 2424 6.395426 TGAAAAAGAACTTGCATGACATCT 57.605 33.333 6.60 4.38 0.00 2.90
2365 2425 6.808829 TGAAAAAGAACTTGCATGACATCTT 58.191 32.000 6.60 9.66 0.00 2.40
2366 2426 7.267128 TGAAAAAGAACTTGCATGACATCTTT 58.733 30.769 17.95 17.95 38.40 2.52
2367 2427 7.765360 TGAAAAAGAACTTGCATGACATCTTTT 59.235 29.630 23.24 23.24 44.50 2.27
2368 2428 7.473027 AAAAGAACTTGCATGACATCTTTTG 57.527 32.000 25.48 0.00 42.37 2.44
2369 2429 5.779529 AGAACTTGCATGACATCTTTTGT 57.220 34.783 6.60 0.00 42.79 2.83
2379 2439 3.329929 ACATCTTTTGTCCTACCGTCC 57.670 47.619 0.00 0.00 30.89 4.79
2380 2440 2.027469 ACATCTTTTGTCCTACCGTCCC 60.027 50.000 0.00 0.00 30.89 4.46
2381 2441 0.604578 TCTTTTGTCCTACCGTCCCG 59.395 55.000 0.00 0.00 0.00 5.14
2382 2442 0.319405 CTTTTGTCCTACCGTCCCGT 59.681 55.000 0.00 0.00 0.00 5.28
2383 2443 0.033781 TTTTGTCCTACCGTCCCGTG 59.966 55.000 0.00 0.00 0.00 4.94
2384 2444 1.818959 TTTGTCCTACCGTCCCGTGG 61.819 60.000 0.00 0.00 0.00 4.94
2385 2445 4.139234 GTCCTACCGTCCCGTGGC 62.139 72.222 0.00 0.00 0.00 5.01
2386 2446 4.682334 TCCTACCGTCCCGTGGCA 62.682 66.667 0.00 0.00 0.00 4.92
2387 2447 4.143333 CCTACCGTCCCGTGGCAG 62.143 72.222 0.00 0.00 0.00 4.85
2388 2448 4.814294 CTACCGTCCCGTGGCAGC 62.814 72.222 0.00 0.00 0.00 5.25
2398 2458 3.480133 GTGGCAGCGGGGTCCTAT 61.480 66.667 0.00 0.00 0.00 2.57
2399 2459 2.690881 TGGCAGCGGGGTCCTATT 60.691 61.111 0.00 0.00 0.00 1.73
2400 2460 2.203209 GGCAGCGGGGTCCTATTG 60.203 66.667 0.00 0.00 0.00 1.90
2401 2461 2.203209 GCAGCGGGGTCCTATTGG 60.203 66.667 0.00 0.00 0.00 3.16
2402 2462 2.742116 GCAGCGGGGTCCTATTGGA 61.742 63.158 0.00 0.00 40.69 3.53
2403 2463 1.912220 CAGCGGGGTCCTATTGGAA 59.088 57.895 0.00 0.00 45.18 3.53
2404 2464 0.254747 CAGCGGGGTCCTATTGGAAA 59.745 55.000 0.00 0.00 45.18 3.13
2405 2465 0.255033 AGCGGGGTCCTATTGGAAAC 59.745 55.000 0.00 0.00 45.18 2.78
2406 2466 0.255033 GCGGGGTCCTATTGGAAACT 59.745 55.000 0.00 0.00 45.18 2.66
2407 2467 1.487558 GCGGGGTCCTATTGGAAACTA 59.512 52.381 0.00 0.00 45.18 2.24
2408 2468 2.092807 GCGGGGTCCTATTGGAAACTAA 60.093 50.000 0.00 0.00 45.18 2.24
2409 2469 3.805207 CGGGGTCCTATTGGAAACTAAG 58.195 50.000 0.00 0.00 45.18 2.18
2410 2470 3.433173 CGGGGTCCTATTGGAAACTAAGG 60.433 52.174 0.00 0.00 45.18 2.69
2411 2471 3.117625 GGGGTCCTATTGGAAACTAAGGG 60.118 52.174 0.00 0.00 45.18 3.95
2412 2472 3.784202 GGGTCCTATTGGAAACTAAGGGA 59.216 47.826 0.00 0.00 45.18 4.20
2413 2473 4.415846 GGGTCCTATTGGAAACTAAGGGAT 59.584 45.833 0.00 0.00 45.18 3.85
2414 2474 5.609708 GGGTCCTATTGGAAACTAAGGGATA 59.390 44.000 0.00 0.00 45.18 2.59
2415 2475 6.274908 GGGTCCTATTGGAAACTAAGGGATAT 59.725 42.308 0.00 0.00 45.18 1.63
2416 2476 7.202289 GGGTCCTATTGGAAACTAAGGGATATT 60.202 40.741 0.00 0.00 45.18 1.28
2417 2477 7.665974 GGTCCTATTGGAAACTAAGGGATATTG 59.334 40.741 0.00 0.00 45.18 1.90
2418 2478 8.437575 GTCCTATTGGAAACTAAGGGATATTGA 58.562 37.037 0.00 0.00 45.18 2.57
2419 2479 8.660435 TCCTATTGGAAACTAAGGGATATTGAG 58.340 37.037 0.00 0.00 39.87 3.02
2420 2480 7.885399 CCTATTGGAAACTAAGGGATATTGAGG 59.115 40.741 0.00 0.00 34.57 3.86
2421 2481 5.048846 TGGAAACTAAGGGATATTGAGGC 57.951 43.478 0.00 0.00 0.00 4.70
2422 2482 4.476846 TGGAAACTAAGGGATATTGAGGCA 59.523 41.667 0.00 0.00 0.00 4.75
2423 2483 5.134339 TGGAAACTAAGGGATATTGAGGCAT 59.866 40.000 0.00 0.00 0.00 4.40
2424 2484 5.707764 GGAAACTAAGGGATATTGAGGCATC 59.292 44.000 0.00 0.00 0.00 3.91
2425 2485 4.917906 ACTAAGGGATATTGAGGCATCC 57.082 45.455 0.00 0.00 40.11 3.51
2426 2486 4.507342 ACTAAGGGATATTGAGGCATCCT 58.493 43.478 0.00 0.00 40.57 3.24
2427 2487 4.916424 ACTAAGGGATATTGAGGCATCCTT 59.084 41.667 0.00 0.00 40.57 3.36
2428 2488 4.821532 AAGGGATATTGAGGCATCCTTT 57.178 40.909 0.00 0.00 40.57 3.11
2429 2489 4.821532 AGGGATATTGAGGCATCCTTTT 57.178 40.909 0.00 0.00 40.57 2.27
2430 2490 5.930209 AGGGATATTGAGGCATCCTTTTA 57.070 39.130 0.00 0.00 40.57 1.52
2431 2491 6.279813 AGGGATATTGAGGCATCCTTTTAA 57.720 37.500 0.00 0.00 40.57 1.52
2432 2492 6.867723 AGGGATATTGAGGCATCCTTTTAAT 58.132 36.000 0.00 0.00 40.57 1.40
2433 2493 8.000171 AGGGATATTGAGGCATCCTTTTAATA 58.000 34.615 0.00 0.00 40.57 0.98
2434 2494 8.112183 AGGGATATTGAGGCATCCTTTTAATAG 58.888 37.037 0.00 0.00 40.57 1.73
2435 2495 8.109634 GGGATATTGAGGCATCCTTTTAATAGA 58.890 37.037 0.00 0.00 40.57 1.98
2436 2496 9.171877 GGATATTGAGGCATCCTTTTAATAGAG 57.828 37.037 0.00 0.00 38.16 2.43
2437 2497 9.950496 GATATTGAGGCATCCTTTTAATAGAGA 57.050 33.333 0.00 0.00 31.76 3.10
2439 2499 7.865706 TTGAGGCATCCTTTTAATAGAGAAC 57.134 36.000 0.00 0.00 31.76 3.01
2440 2500 6.357367 TGAGGCATCCTTTTAATAGAGAACC 58.643 40.000 0.00 0.00 31.76 3.62
2441 2501 5.368989 AGGCATCCTTTTAATAGAGAACCG 58.631 41.667 0.00 0.00 0.00 4.44
2442 2502 4.515567 GGCATCCTTTTAATAGAGAACCGG 59.484 45.833 0.00 0.00 0.00 5.28
2443 2503 5.365619 GCATCCTTTTAATAGAGAACCGGA 58.634 41.667 9.46 0.00 0.00 5.14
2444 2504 5.820947 GCATCCTTTTAATAGAGAACCGGAA 59.179 40.000 9.46 0.00 0.00 4.30
2445 2505 6.238402 GCATCCTTTTAATAGAGAACCGGAAC 60.238 42.308 9.46 0.55 0.00 3.62
2446 2506 6.363167 TCCTTTTAATAGAGAACCGGAACA 57.637 37.500 9.46 0.00 0.00 3.18
2447 2507 6.771573 TCCTTTTAATAGAGAACCGGAACAA 58.228 36.000 9.46 0.00 0.00 2.83
2448 2508 7.225725 TCCTTTTAATAGAGAACCGGAACAAA 58.774 34.615 9.46 0.00 0.00 2.83
2449 2509 7.389607 TCCTTTTAATAGAGAACCGGAACAAAG 59.610 37.037 9.46 5.59 0.00 2.77
2450 2510 6.490566 TTTAATAGAGAACCGGAACAAAGC 57.509 37.500 9.46 0.00 0.00 3.51
2451 2511 3.695830 ATAGAGAACCGGAACAAAGCA 57.304 42.857 9.46 0.00 0.00 3.91
2452 2512 2.568623 AGAGAACCGGAACAAAGCAT 57.431 45.000 9.46 0.00 0.00 3.79
2453 2513 2.863809 AGAGAACCGGAACAAAGCATT 58.136 42.857 9.46 0.00 0.00 3.56
2454 2514 4.015872 AGAGAACCGGAACAAAGCATTA 57.984 40.909 9.46 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
138 144 1.755380 GGATGGACTAGTGCCGTAAGT 59.245 52.381 12.28 0.00 0.00 2.24
205 211 5.220117 CGCTCGAAAGTCTTGTCTATGAAAG 60.220 44.000 0.00 0.00 0.00 2.62
467 521 2.031314 CGAACGGAGTCTATACGAGCAA 59.969 50.000 0.00 0.00 45.00 3.91
599 659 8.651589 TCCGTCTGGAACATATAGATAGATTT 57.348 34.615 0.00 0.00 42.85 2.17
729 789 4.065321 AGAATAGACAGGAGAATTGCCG 57.935 45.455 0.00 0.00 0.00 5.69
736 796 7.504238 GTCCAGATAGAAAGAATAGACAGGAGA 59.496 40.741 0.00 0.00 0.00 3.71
998 1058 9.857656 AAACATACTCCTCACAAATGATCATAT 57.142 29.630 9.04 0.00 33.22 1.78
1179 1239 3.387947 ACAACGAGCCCGGGTAGG 61.388 66.667 24.63 13.79 40.78 3.18
1586 1646 3.391626 ACGGAAAGGGTTCTCTTCTCTTT 59.608 43.478 0.00 0.00 33.92 2.52
1614 1674 1.250840 CCCGGCCCCTTTTCTCTTTG 61.251 60.000 0.00 0.00 0.00 2.77
1767 1827 6.489675 AGCGTGCATCTAAAATAGTTTCATG 58.510 36.000 0.00 0.00 0.00 3.07
1904 1964 5.188751 GCTAACTCATCCTTATATGGCTCCT 59.811 44.000 0.00 0.00 0.00 3.69
1948 2008 1.907240 TCCCCTTATTCCCTTCCCAG 58.093 55.000 0.00 0.00 0.00 4.45
2040 2100 3.245371 TGCCATGGATTCTCTTTTCTGGT 60.245 43.478 18.40 0.00 0.00 4.00
2169 2229 5.422331 AGCATAACAGACAGTTTCCTAGCTA 59.578 40.000 0.00 0.00 41.64 3.32
2188 2248 7.139287 AGTAAGGTCTACTGACTCTAGCATA 57.861 40.000 0.00 0.00 35.96 3.14
2189 2249 6.008696 AGTAAGGTCTACTGACTCTAGCAT 57.991 41.667 0.00 0.00 35.96 3.79
2190 2250 5.438698 AGTAAGGTCTACTGACTCTAGCA 57.561 43.478 0.00 0.00 35.96 3.49
2191 2251 6.762702 AAAGTAAGGTCTACTGACTCTAGC 57.237 41.667 0.00 0.00 40.21 3.42
2192 2252 8.885722 CACTAAAGTAAGGTCTACTGACTCTAG 58.114 40.741 0.00 0.00 40.21 2.43
2193 2253 8.381636 ACACTAAAGTAAGGTCTACTGACTCTA 58.618 37.037 0.00 0.00 40.21 2.43
2194 2254 7.232910 ACACTAAAGTAAGGTCTACTGACTCT 58.767 38.462 0.00 0.00 40.21 3.24
2195 2255 7.451501 ACACTAAAGTAAGGTCTACTGACTC 57.548 40.000 0.00 0.00 40.21 3.36
2196 2256 7.611079 CCTACACTAAAGTAAGGTCTACTGACT 59.389 40.741 0.00 0.00 43.14 3.41
2197 2257 7.609532 TCCTACACTAAAGTAAGGTCTACTGAC 59.390 40.741 9.39 0.00 42.22 3.51
2198 2258 7.693132 TCCTACACTAAAGTAAGGTCTACTGA 58.307 38.462 9.39 0.00 34.05 3.41
2199 2259 7.934855 TCCTACACTAAAGTAAGGTCTACTG 57.065 40.000 9.39 0.00 34.05 2.74
2200 2260 8.334734 TCATCCTACACTAAAGTAAGGTCTACT 58.665 37.037 9.39 0.00 34.05 2.57
2201 2261 8.517062 TCATCCTACACTAAAGTAAGGTCTAC 57.483 38.462 9.39 0.00 34.05 2.59
2202 2262 8.334734 ACTCATCCTACACTAAAGTAAGGTCTA 58.665 37.037 9.39 0.00 34.05 2.59
2203 2263 7.183460 ACTCATCCTACACTAAAGTAAGGTCT 58.817 38.462 9.39 0.00 34.05 3.85
2204 2264 7.407393 ACTCATCCTACACTAAAGTAAGGTC 57.593 40.000 9.39 0.00 34.05 3.85
2205 2265 7.793948 AACTCATCCTACACTAAAGTAAGGT 57.206 36.000 9.39 0.00 34.05 3.50
2206 2266 9.751542 CATAACTCATCCTACACTAAAGTAAGG 57.248 37.037 4.90 4.90 33.81 2.69
2207 2267 9.250624 GCATAACTCATCCTACACTAAAGTAAG 57.749 37.037 0.00 0.00 0.00 2.34
2208 2268 8.202137 GGCATAACTCATCCTACACTAAAGTAA 58.798 37.037 0.00 0.00 0.00 2.24
2209 2269 7.343574 TGGCATAACTCATCCTACACTAAAGTA 59.656 37.037 0.00 0.00 0.00 2.24
2210 2270 6.156256 TGGCATAACTCATCCTACACTAAAGT 59.844 38.462 0.00 0.00 0.00 2.66
2211 2271 6.582636 TGGCATAACTCATCCTACACTAAAG 58.417 40.000 0.00 0.00 0.00 1.85
2212 2272 6.382859 TCTGGCATAACTCATCCTACACTAAA 59.617 38.462 0.00 0.00 0.00 1.85
2213 2273 5.897250 TCTGGCATAACTCATCCTACACTAA 59.103 40.000 0.00 0.00 0.00 2.24
2214 2274 5.454966 TCTGGCATAACTCATCCTACACTA 58.545 41.667 0.00 0.00 0.00 2.74
2215 2275 4.290093 TCTGGCATAACTCATCCTACACT 58.710 43.478 0.00 0.00 0.00 3.55
2216 2276 4.672587 TCTGGCATAACTCATCCTACAC 57.327 45.455 0.00 0.00 0.00 2.90
2217 2277 4.503817 GCATCTGGCATAACTCATCCTACA 60.504 45.833 0.00 0.00 43.97 2.74
2218 2278 3.999663 GCATCTGGCATAACTCATCCTAC 59.000 47.826 0.00 0.00 43.97 3.18
2219 2279 3.306294 CGCATCTGGCATAACTCATCCTA 60.306 47.826 0.00 0.00 45.17 2.94
2220 2280 2.549563 CGCATCTGGCATAACTCATCCT 60.550 50.000 0.00 0.00 45.17 3.24
2221 2281 1.802960 CGCATCTGGCATAACTCATCC 59.197 52.381 0.00 0.00 45.17 3.51
2222 2282 1.802960 CCGCATCTGGCATAACTCATC 59.197 52.381 0.00 0.00 45.17 2.92
2223 2283 1.141657 ACCGCATCTGGCATAACTCAT 59.858 47.619 0.00 0.00 45.17 2.90
2224 2284 0.541392 ACCGCATCTGGCATAACTCA 59.459 50.000 0.00 0.00 45.17 3.41
2225 2285 1.599542 GAACCGCATCTGGCATAACTC 59.400 52.381 0.00 0.00 45.17 3.01
2226 2286 1.065491 TGAACCGCATCTGGCATAACT 60.065 47.619 0.00 0.00 45.17 2.24
2227 2287 1.378531 TGAACCGCATCTGGCATAAC 58.621 50.000 0.00 0.00 45.17 1.89
2228 2288 2.346766 ATGAACCGCATCTGGCATAA 57.653 45.000 0.00 0.00 45.17 1.90
2230 2290 4.993307 ATGAACCGCATCTGGCAT 57.007 50.000 0.00 0.00 45.17 4.40
2237 2297 3.609853 ACTGTTACATGATGAACCGCAT 58.390 40.909 0.00 0.00 40.77 4.73
2238 2298 3.000041 GACTGTTACATGATGAACCGCA 59.000 45.455 0.00 0.00 0.00 5.69
2239 2299 3.000041 TGACTGTTACATGATGAACCGC 59.000 45.455 0.00 0.00 0.00 5.68
2240 2300 6.312672 TGTTATGACTGTTACATGATGAACCG 59.687 38.462 0.00 0.03 0.00 4.44
2241 2301 7.609760 TGTTATGACTGTTACATGATGAACC 57.390 36.000 0.00 0.00 0.00 3.62
2243 2303 9.546428 CCTATGTTATGACTGTTACATGATGAA 57.454 33.333 0.00 0.00 33.58 2.57
2244 2304 8.150296 CCCTATGTTATGACTGTTACATGATGA 58.850 37.037 0.00 0.00 33.58 2.92
2245 2305 7.933577 ACCCTATGTTATGACTGTTACATGATG 59.066 37.037 0.00 0.00 33.58 3.07
2246 2306 7.933577 CACCCTATGTTATGACTGTTACATGAT 59.066 37.037 0.00 0.00 33.58 2.45
2247 2307 7.125053 TCACCCTATGTTATGACTGTTACATGA 59.875 37.037 0.00 0.00 33.58 3.07
2248 2308 7.224753 GTCACCCTATGTTATGACTGTTACATG 59.775 40.741 0.00 0.00 38.72 3.21
2249 2309 7.093068 TGTCACCCTATGTTATGACTGTTACAT 60.093 37.037 4.98 0.00 41.65 2.29
2250 2310 6.211785 TGTCACCCTATGTTATGACTGTTACA 59.788 38.462 4.98 0.00 41.65 2.41
2251 2311 6.534079 GTGTCACCCTATGTTATGACTGTTAC 59.466 42.308 4.98 0.00 41.65 2.50
2252 2312 6.211785 TGTGTCACCCTATGTTATGACTGTTA 59.788 38.462 0.00 0.00 41.65 2.41
2253 2313 5.012664 TGTGTCACCCTATGTTATGACTGTT 59.987 40.000 0.00 0.00 41.65 3.16
2254 2314 4.530553 TGTGTCACCCTATGTTATGACTGT 59.469 41.667 0.00 0.00 41.65 3.55
2255 2315 5.084818 TGTGTCACCCTATGTTATGACTG 57.915 43.478 0.00 0.00 41.65 3.51
2256 2316 5.023452 TCTGTGTCACCCTATGTTATGACT 58.977 41.667 0.00 0.00 41.65 3.41
2257 2317 5.339008 TCTGTGTCACCCTATGTTATGAC 57.661 43.478 0.00 0.00 41.51 3.06
2258 2318 5.483937 AGTTCTGTGTCACCCTATGTTATGA 59.516 40.000 0.00 0.00 0.00 2.15
2259 2319 5.734720 AGTTCTGTGTCACCCTATGTTATG 58.265 41.667 0.00 0.00 0.00 1.90
2260 2320 6.407074 GCTAGTTCTGTGTCACCCTATGTTAT 60.407 42.308 0.00 0.00 0.00 1.89
2261 2321 5.105473 GCTAGTTCTGTGTCACCCTATGTTA 60.105 44.000 0.00 0.00 0.00 2.41
2262 2322 4.322801 GCTAGTTCTGTGTCACCCTATGTT 60.323 45.833 0.00 0.00 0.00 2.71
2263 2323 3.195825 GCTAGTTCTGTGTCACCCTATGT 59.804 47.826 0.00 0.00 0.00 2.29
2264 2324 3.449018 AGCTAGTTCTGTGTCACCCTATG 59.551 47.826 0.00 0.00 0.00 2.23
2265 2325 3.702045 GAGCTAGTTCTGTGTCACCCTAT 59.298 47.826 0.00 0.00 0.00 2.57
2266 2326 3.090037 GAGCTAGTTCTGTGTCACCCTA 58.910 50.000 0.00 0.00 0.00 3.53
2267 2327 1.896465 GAGCTAGTTCTGTGTCACCCT 59.104 52.381 0.00 0.00 0.00 4.34
2268 2328 1.066787 GGAGCTAGTTCTGTGTCACCC 60.067 57.143 6.54 0.00 0.00 4.61
2269 2329 1.618837 TGGAGCTAGTTCTGTGTCACC 59.381 52.381 6.54 0.00 0.00 4.02
2270 2330 2.297597 ACTGGAGCTAGTTCTGTGTCAC 59.702 50.000 6.54 0.00 0.00 3.67
2271 2331 2.598565 ACTGGAGCTAGTTCTGTGTCA 58.401 47.619 6.54 0.00 0.00 3.58
2272 2332 3.669251 AACTGGAGCTAGTTCTGTGTC 57.331 47.619 6.54 0.00 36.16 3.67
2279 2339 5.171339 ACATTGATGAACTGGAGCTAGTT 57.829 39.130 1.40 1.40 43.24 2.24
2280 2340 4.833478 ACATTGATGAACTGGAGCTAGT 57.167 40.909 0.00 0.00 0.00 2.57
2281 2341 6.765036 ACATTACATTGATGAACTGGAGCTAG 59.235 38.462 0.00 0.00 0.00 3.42
2282 2342 6.653020 ACATTACATTGATGAACTGGAGCTA 58.347 36.000 0.00 0.00 0.00 3.32
2283 2343 5.503927 ACATTACATTGATGAACTGGAGCT 58.496 37.500 0.00 0.00 0.00 4.09
2284 2344 5.824904 ACATTACATTGATGAACTGGAGC 57.175 39.130 0.00 0.00 0.00 4.70
2285 2345 6.017605 GCCTACATTACATTGATGAACTGGAG 60.018 42.308 0.00 0.00 0.00 3.86
2286 2346 5.822519 GCCTACATTACATTGATGAACTGGA 59.177 40.000 0.00 0.00 0.00 3.86
2287 2347 5.589855 TGCCTACATTACATTGATGAACTGG 59.410 40.000 0.00 0.00 0.00 4.00
2288 2348 6.682423 TGCCTACATTACATTGATGAACTG 57.318 37.500 0.00 0.00 0.00 3.16
2289 2349 6.830324 ACATGCCTACATTACATTGATGAACT 59.170 34.615 0.00 0.00 32.87 3.01
2290 2350 7.031226 ACATGCCTACATTACATTGATGAAC 57.969 36.000 0.00 0.00 32.87 3.18
2291 2351 8.922931 ATACATGCCTACATTACATTGATGAA 57.077 30.769 0.00 0.00 32.87 2.57
2292 2352 8.922931 AATACATGCCTACATTACATTGATGA 57.077 30.769 0.00 0.00 32.87 2.92
2293 2353 8.239314 GGAATACATGCCTACATTACATTGATG 58.761 37.037 0.00 0.00 32.87 3.07
2294 2354 7.119699 CGGAATACATGCCTACATTACATTGAT 59.880 37.037 0.00 0.00 32.87 2.57
2295 2355 6.426633 CGGAATACATGCCTACATTACATTGA 59.573 38.462 0.00 0.00 32.87 2.57
2296 2356 6.204688 ACGGAATACATGCCTACATTACATTG 59.795 38.462 0.00 0.00 32.87 2.82
2297 2357 6.296026 ACGGAATACATGCCTACATTACATT 58.704 36.000 0.00 0.00 32.87 2.71
2298 2358 5.865085 ACGGAATACATGCCTACATTACAT 58.135 37.500 0.00 0.00 32.87 2.29
2299 2359 5.284861 ACGGAATACATGCCTACATTACA 57.715 39.130 0.00 0.00 32.87 2.41
2302 2362 8.978472 ACTATATACGGAATACATGCCTACATT 58.022 33.333 0.00 0.00 32.87 2.71
2303 2363 8.534954 ACTATATACGGAATACATGCCTACAT 57.465 34.615 0.00 0.00 36.79 2.29
2304 2364 7.612633 TGACTATATACGGAATACATGCCTACA 59.387 37.037 0.00 0.00 0.00 2.74
2305 2365 7.993101 TGACTATATACGGAATACATGCCTAC 58.007 38.462 0.00 0.00 0.00 3.18
2306 2366 8.762481 ATGACTATATACGGAATACATGCCTA 57.238 34.615 0.00 0.00 0.00 3.93
2307 2367 7.661536 ATGACTATATACGGAATACATGCCT 57.338 36.000 0.00 0.00 0.00 4.75
2308 2368 8.798748 GTATGACTATATACGGAATACATGCC 57.201 38.462 0.00 0.00 0.00 4.40
2324 2384 8.942338 TCTTTTTCATAAGCACGTATGACTAT 57.058 30.769 5.88 0.00 39.62 2.12
2325 2385 8.653338 GTTCTTTTTCATAAGCACGTATGACTA 58.347 33.333 5.88 0.00 39.62 2.59
2326 2386 7.387948 AGTTCTTTTTCATAAGCACGTATGACT 59.612 33.333 5.88 0.00 39.62 3.41
2327 2387 7.519002 AGTTCTTTTTCATAAGCACGTATGAC 58.481 34.615 5.88 0.00 39.62 3.06
2328 2388 7.667043 AGTTCTTTTTCATAAGCACGTATGA 57.333 32.000 2.68 2.68 38.45 2.15
2329 2389 7.201266 GCAAGTTCTTTTTCATAAGCACGTATG 60.201 37.037 0.00 0.00 33.49 2.39
2330 2390 6.801862 GCAAGTTCTTTTTCATAAGCACGTAT 59.198 34.615 0.00 0.00 0.00 3.06
2331 2391 6.140110 GCAAGTTCTTTTTCATAAGCACGTA 58.860 36.000 0.00 0.00 0.00 3.57
2332 2392 4.976116 GCAAGTTCTTTTTCATAAGCACGT 59.024 37.500 0.00 0.00 0.00 4.49
2333 2393 4.975502 TGCAAGTTCTTTTTCATAAGCACG 59.024 37.500 0.00 0.00 0.00 5.34
2334 2394 6.642131 TCATGCAAGTTCTTTTTCATAAGCAC 59.358 34.615 0.00 0.00 0.00 4.40
2335 2395 6.642131 GTCATGCAAGTTCTTTTTCATAAGCA 59.358 34.615 0.00 0.00 0.00 3.91
2336 2396 6.642131 TGTCATGCAAGTTCTTTTTCATAAGC 59.358 34.615 0.00 0.00 0.00 3.09
2337 2397 8.752766 ATGTCATGCAAGTTCTTTTTCATAAG 57.247 30.769 0.00 0.00 0.00 1.73
2338 2398 8.579006 AGATGTCATGCAAGTTCTTTTTCATAA 58.421 29.630 0.00 0.00 0.00 1.90
2339 2399 8.114331 AGATGTCATGCAAGTTCTTTTTCATA 57.886 30.769 0.00 0.00 0.00 2.15
2340 2400 6.989659 AGATGTCATGCAAGTTCTTTTTCAT 58.010 32.000 0.00 0.00 0.00 2.57
2341 2401 6.395426 AGATGTCATGCAAGTTCTTTTTCA 57.605 33.333 0.00 0.00 0.00 2.69
2342 2402 7.704789 AAAGATGTCATGCAAGTTCTTTTTC 57.295 32.000 0.00 0.00 32.88 2.29
2343 2403 7.550196 ACAAAAGATGTCATGCAAGTTCTTTTT 59.450 29.630 18.26 8.01 39.75 1.94
2344 2404 7.043565 ACAAAAGATGTCATGCAAGTTCTTTT 58.956 30.769 16.58 16.58 41.14 2.27
2345 2405 6.576185 ACAAAAGATGTCATGCAAGTTCTTT 58.424 32.000 0.00 1.16 37.96 2.52
2346 2406 6.152932 ACAAAAGATGTCATGCAAGTTCTT 57.847 33.333 0.00 0.00 37.96 2.52
2347 2407 5.779529 ACAAAAGATGTCATGCAAGTTCT 57.220 34.783 0.00 0.00 37.96 3.01
2360 2420 2.629051 GGGACGGTAGGACAAAAGATG 58.371 52.381 0.00 0.00 0.00 2.90
2381 2441 3.043999 AATAGGACCCCGCTGCCAC 62.044 63.158 0.00 0.00 0.00 5.01
2382 2442 2.690881 AATAGGACCCCGCTGCCA 60.691 61.111 0.00 0.00 0.00 4.92
2383 2443 2.203209 CAATAGGACCCCGCTGCC 60.203 66.667 0.00 0.00 0.00 4.85
2384 2444 2.203209 CCAATAGGACCCCGCTGC 60.203 66.667 0.00 0.00 36.89 5.25
2385 2445 0.254747 TTTCCAATAGGACCCCGCTG 59.745 55.000 0.00 0.00 45.73 5.18
2386 2446 0.255033 GTTTCCAATAGGACCCCGCT 59.745 55.000 0.00 0.00 45.73 5.52
2387 2447 0.255033 AGTTTCCAATAGGACCCCGC 59.745 55.000 0.00 0.00 45.73 6.13
2388 2448 3.433173 CCTTAGTTTCCAATAGGACCCCG 60.433 52.174 0.00 0.00 45.73 5.73
2389 2449 3.117625 CCCTTAGTTTCCAATAGGACCCC 60.118 52.174 0.00 0.00 45.73 4.95
2390 2450 3.784202 TCCCTTAGTTTCCAATAGGACCC 59.216 47.826 0.00 0.00 45.73 4.46
2391 2451 5.648330 ATCCCTTAGTTTCCAATAGGACC 57.352 43.478 0.00 0.00 45.73 4.46
2392 2452 8.437575 TCAATATCCCTTAGTTTCCAATAGGAC 58.562 37.037 0.00 0.00 45.73 3.85
2393 2453 8.575736 TCAATATCCCTTAGTTTCCAATAGGA 57.424 34.615 0.00 0.00 43.93 2.94
2394 2454 7.885399 CCTCAATATCCCTTAGTTTCCAATAGG 59.115 40.741 0.00 0.00 0.00 2.57
2395 2455 7.391833 GCCTCAATATCCCTTAGTTTCCAATAG 59.608 40.741 0.00 0.00 0.00 1.73
2396 2456 7.147213 TGCCTCAATATCCCTTAGTTTCCAATA 60.147 37.037 0.00 0.00 0.00 1.90
2397 2457 6.071320 GCCTCAATATCCCTTAGTTTCCAAT 58.929 40.000 0.00 0.00 0.00 3.16
2398 2458 5.044476 TGCCTCAATATCCCTTAGTTTCCAA 60.044 40.000 0.00 0.00 0.00 3.53
2399 2459 4.476846 TGCCTCAATATCCCTTAGTTTCCA 59.523 41.667 0.00 0.00 0.00 3.53
2400 2460 5.048846 TGCCTCAATATCCCTTAGTTTCC 57.951 43.478 0.00 0.00 0.00 3.13
2401 2461 5.707764 GGATGCCTCAATATCCCTTAGTTTC 59.292 44.000 0.00 0.00 37.48 2.78
2402 2462 5.373854 AGGATGCCTCAATATCCCTTAGTTT 59.626 40.000 0.00 0.00 43.12 2.66
2403 2463 4.916424 AGGATGCCTCAATATCCCTTAGTT 59.084 41.667 0.00 0.00 43.12 2.24
2404 2464 4.507342 AGGATGCCTCAATATCCCTTAGT 58.493 43.478 0.00 0.00 43.12 2.24
2405 2465 5.511386 AAGGATGCCTCAATATCCCTTAG 57.489 43.478 0.00 0.00 43.12 2.18
2406 2466 5.930209 AAAGGATGCCTCAATATCCCTTA 57.070 39.130 0.00 0.00 43.12 2.69
2407 2467 4.821532 AAAGGATGCCTCAATATCCCTT 57.178 40.909 0.00 0.00 43.12 3.95
2408 2468 4.821532 AAAAGGATGCCTCAATATCCCT 57.178 40.909 0.00 0.00 43.12 4.20
2409 2469 8.109634 TCTATTAAAAGGATGCCTCAATATCCC 58.890 37.037 0.00 0.00 43.12 3.85
2410 2470 9.171877 CTCTATTAAAAGGATGCCTCAATATCC 57.828 37.037 0.00 0.00 42.56 2.59
2411 2471 9.950496 TCTCTATTAAAAGGATGCCTCAATATC 57.050 33.333 0.00 0.00 30.89 1.63
2413 2473 9.561069 GTTCTCTATTAAAAGGATGCCTCAATA 57.439 33.333 0.00 0.00 30.89 1.90
2414 2474 7.503902 GGTTCTCTATTAAAAGGATGCCTCAAT 59.496 37.037 0.00 0.00 30.89 2.57
2415 2475 6.828785 GGTTCTCTATTAAAAGGATGCCTCAA 59.171 38.462 0.00 0.00 30.89 3.02
2416 2476 6.357367 GGTTCTCTATTAAAAGGATGCCTCA 58.643 40.000 0.00 0.00 30.89 3.86
2417 2477 5.467063 CGGTTCTCTATTAAAAGGATGCCTC 59.533 44.000 0.00 0.00 30.89 4.70
2418 2478 5.368989 CGGTTCTCTATTAAAAGGATGCCT 58.631 41.667 0.00 0.00 33.87 4.75
2419 2479 4.515567 CCGGTTCTCTATTAAAAGGATGCC 59.484 45.833 0.00 0.00 0.00 4.40
2420 2480 5.365619 TCCGGTTCTCTATTAAAAGGATGC 58.634 41.667 0.00 0.00 0.00 3.91
2421 2481 6.821665 TGTTCCGGTTCTCTATTAAAAGGATG 59.178 38.462 0.00 0.00 0.00 3.51
2422 2482 6.954232 TGTTCCGGTTCTCTATTAAAAGGAT 58.046 36.000 0.00 0.00 0.00 3.24
2423 2483 6.363167 TGTTCCGGTTCTCTATTAAAAGGA 57.637 37.500 0.00 0.00 0.00 3.36
2424 2484 7.443259 TTTGTTCCGGTTCTCTATTAAAAGG 57.557 36.000 0.00 0.00 0.00 3.11
2425 2485 7.021790 GCTTTGTTCCGGTTCTCTATTAAAAG 58.978 38.462 0.00 1.97 0.00 2.27
2426 2486 6.487331 TGCTTTGTTCCGGTTCTCTATTAAAA 59.513 34.615 0.00 0.00 0.00 1.52
2427 2487 5.998981 TGCTTTGTTCCGGTTCTCTATTAAA 59.001 36.000 0.00 0.00 0.00 1.52
2428 2488 5.553123 TGCTTTGTTCCGGTTCTCTATTAA 58.447 37.500 0.00 0.00 0.00 1.40
2429 2489 5.155278 TGCTTTGTTCCGGTTCTCTATTA 57.845 39.130 0.00 0.00 0.00 0.98
2430 2490 4.015872 TGCTTTGTTCCGGTTCTCTATT 57.984 40.909 0.00 0.00 0.00 1.73
2431 2491 3.695830 TGCTTTGTTCCGGTTCTCTAT 57.304 42.857 0.00 0.00 0.00 1.98
2432 2492 3.695830 ATGCTTTGTTCCGGTTCTCTA 57.304 42.857 0.00 0.00 0.00 2.43
2433 2493 2.568623 ATGCTTTGTTCCGGTTCTCT 57.431 45.000 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.