Multiple sequence alignment - TraesCS1A01G214800

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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 TraesCS1A01G214800 chr1A 100.000 2543 0 0 1 2543 379139354 379136812 0.000000e+00 4697.0
1 TraesCS1A01G214800 chr1A 95.788 926 38 1 561 1486 379616354 379617278 0.000000e+00 1493.0
2 TraesCS1A01G214800 chr1A 94.223 952 44 6 1 945 379146930 379145983 0.000000e+00 1443.0
3 TraesCS1A01G214800 chr1A 92.444 900 62 5 1345 2240 379145986 379145089 0.000000e+00 1280.0
4 TraesCS1A01G214800 chr1A 90.572 594 54 2 1649 2240 379626980 379627573 0.000000e+00 785.0
5 TraesCS1A01G214800 chr1A 94.175 309 16 2 2237 2543 593114148 593114456 1.070000e-128 470.0
6 TraesCS1A01G214800 chr1B 89.450 2237 213 10 7 2237 402502320 402504539 0.000000e+00 2802.0
7 TraesCS1A01G214800 chr1B 77.901 181 34 5 82 259 642053671 642053494 9.620000e-20 108.0
8 TraesCS1A01G214800 chr5A 96.764 309 7 2 2237 2543 365049150 365049457 1.740000e-141 512.0
9 TraesCS1A01G214800 chr5A 94.534 311 12 3 2237 2543 8685323 8685632 2.290000e-130 475.0
10 TraesCS1A01G214800 chr7A 96.117 309 9 2 2237 2543 195351707 195351400 3.780000e-138 501.0
11 TraesCS1A01G214800 chr7A 95.455 308 11 3 2237 2543 119957024 119956719 2.940000e-134 488.0
12 TraesCS1A01G214800 chr7A 94.788 307 16 0 2237 2543 645836913 645836607 1.770000e-131 479.0
13 TraesCS1A01G214800 chr6A 96.587 293 7 3 2253 2543 573265395 573265104 1.370000e-132 483.0
14 TraesCS1A01G214800 chr6A 94.822 309 13 2 2237 2543 448991121 448991428 1.770000e-131 479.0
15 TraesCS1A01G214800 chr6A 86.250 80 10 1 4 83 44768311 44768233 4.510000e-13 86.1
16 TraesCS1A01G214800 chr2A 94.788 307 15 1 2238 2543 388032569 388032875 6.370000e-131 477.0
17 TraesCS1A01G214800 chr6B 89.873 79 6 1 1 79 570525411 570525335 1.610000e-17 100.0


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 TraesCS1A01G214800 chr1A 379136812 379139354 2542 True 4697.0 4697 100.0000 1 2543 1 chr1A.!!$R1 2542
1 TraesCS1A01G214800 chr1A 379616354 379617278 924 False 1493.0 1493 95.7880 561 1486 1 chr1A.!!$F1 925
2 TraesCS1A01G214800 chr1A 379145089 379146930 1841 True 1361.5 1443 93.3335 1 2240 2 chr1A.!!$R2 2239
3 TraesCS1A01G214800 chr1A 379626980 379627573 593 False 785.0 785 90.5720 1649 2240 1 chr1A.!!$F2 591
4 TraesCS1A01G214800 chr1B 402502320 402504539 2219 False 2802.0 2802 89.4500 7 2237 1 chr1B.!!$F1 2230

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
146 150 1.067635 GCAAGCATTCGGTGTCCATTT 60.068 47.619 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2040 2065 0.184211 TGATGATGTGCCATCCCCAG 59.816 55.0 11.25 0.0 41.6 4.45 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
43 44 9.685828 TTTTTAAATGAAATACCTCGGTTTGAG 57.314 29.630 0.00 0.00 44.83 3.02
60 61 5.009610 GGTTTGAGCAAAGGTGAAATGAGTA 59.990 40.000 0.00 0.00 0.00 2.59
132 136 5.767665 TCATTGTTTCTAGGTAAAGCAAGCA 59.232 36.000 0.00 0.00 0.00 3.91
146 150 1.067635 GCAAGCATTCGGTGTCCATTT 60.068 47.619 0.00 0.00 0.00 2.32
148 152 2.198827 AGCATTCGGTGTCCATTTGA 57.801 45.000 0.00 0.00 0.00 2.69
258 262 7.321271 CGAGTTTGAAAAGTGCTACAATAACTG 59.679 37.037 0.00 0.00 0.00 3.16
280 284 6.733160 CTGCCCTCAATTGGGGATTATCAAG 61.733 48.000 26.78 7.27 46.61 3.02
342 346 6.676950 CACAATACATTGAGCAAGGTTGTTA 58.323 36.000 5.82 0.00 40.14 2.41
886 906 6.338146 TCTACATGTGTGAGGTGCTATTAAC 58.662 40.000 9.11 0.00 0.00 2.01
934 954 8.842280 CATTTAATTATTGATTTGGCAGCCAAT 58.158 29.630 27.89 17.06 43.55 3.16
1047 1067 4.349663 TTGAAACACACCGCATATTAGC 57.650 40.909 0.00 0.00 0.00 3.09
1141 1161 3.073798 TCTTTTTGGTGGCTCTCATGGTA 59.926 43.478 0.00 0.00 0.00 3.25
1334 1354 2.412421 AGGACTAACGACGTGTGTTC 57.588 50.000 0.00 2.36 0.00 3.18
1374 1394 3.432186 GCAGATGCAATACCACTACCTGA 60.432 47.826 0.00 0.00 41.59 3.86
1448 1468 0.704076 TTGCATAAACCCTGGAGGCT 59.296 50.000 0.00 0.00 40.58 4.58
1486 1506 5.954752 TGATTATTGTTGTTGCCCTATGGAA 59.045 36.000 0.00 0.00 0.00 3.53
1543 1563 5.826737 TGGGTTGTCGTTTTTAACCTATGAA 59.173 36.000 0.00 0.00 42.65 2.57
1786 1808 1.284841 CCCCTCCTCCTTGGCAAGAT 61.285 60.000 28.18 0.00 35.26 2.40
1804 1826 7.235399 TGGCAAGATTTTTAAAGGGAATTCTCT 59.765 33.333 0.61 0.61 0.00 3.10
1819 1842 6.836242 GGAATTCTCTACTCTTCCCATTCAT 58.164 40.000 5.23 0.00 32.67 2.57
1876 1900 3.455910 TGCCTATTGGAGTAGAGCACAAT 59.544 43.478 0.00 0.00 37.34 2.71
1877 1901 4.653801 TGCCTATTGGAGTAGAGCACAATA 59.346 41.667 0.00 0.00 35.40 1.90
1880 1904 6.742644 GCCTATTGGAGTAGAGCACAATACAT 60.743 42.308 0.00 0.00 35.40 2.29
1886 1910 8.885693 TGGAGTAGAGCACAATACATCTATAT 57.114 34.615 0.00 0.00 0.00 0.86
1914 1938 2.753043 GGTCATGTGCTGCCCCTG 60.753 66.667 0.00 0.00 0.00 4.45
1915 1940 3.446570 GTCATGTGCTGCCCCTGC 61.447 66.667 0.00 0.00 38.26 4.85
1950 1975 3.376935 CTACCTGGGACTGCCGCTG 62.377 68.421 0.00 0.00 33.83 5.18
1987 2012 2.580322 TCCCTTGGACTAATGATGCCAA 59.420 45.455 0.00 0.00 38.02 4.52
1989 2014 3.571401 CCCTTGGACTAATGATGCCAATC 59.429 47.826 0.00 0.00 39.46 2.67
1991 2016 4.037208 CCTTGGACTAATGATGCCAATCAC 59.963 45.833 0.00 0.00 45.51 3.06
2018 2043 5.761234 AGCGTGTTGACAAAAGGTTATTAGA 59.239 36.000 0.32 0.00 0.00 2.10
2020 2045 6.073440 GCGTGTTGACAAAAGGTTATTAGAGA 60.073 38.462 0.32 0.00 0.00 3.10
2034 2059 1.195115 TAGAGAGGCATGCGACCTTT 58.805 50.000 12.44 6.28 37.77 3.11
2040 2065 0.101219 GGCATGCGACCTTTCATTCC 59.899 55.000 12.44 0.00 0.00 3.01
2113 2138 6.001449 ACTACTGCATGGCCTATTTTCTTA 57.999 37.500 3.32 0.00 0.00 2.10
2171 2196 3.641017 GAGCTTTCCTCTGGCAAGT 57.359 52.632 0.00 0.00 37.60 3.16
2226 2251 0.521735 GCCCGAGACAAACATTCCAC 59.478 55.000 0.00 0.00 0.00 4.02
2240 2265 5.323382 ACATTCCACATGCCTTCCATATA 57.677 39.130 0.00 0.00 31.47 0.86
2241 2266 5.895807 ACATTCCACATGCCTTCCATATAT 58.104 37.500 0.00 0.00 31.47 0.86
2242 2267 7.031415 ACATTCCACATGCCTTCCATATATA 57.969 36.000 0.00 0.00 31.47 0.86
2243 2268 7.645942 ACATTCCACATGCCTTCCATATATAT 58.354 34.615 0.00 0.00 31.47 0.86
2244 2269 8.780977 ACATTCCACATGCCTTCCATATATATA 58.219 33.333 0.00 0.00 31.47 0.86
2245 2270 9.281371 CATTCCACATGCCTTCCATATATATAG 57.719 37.037 0.00 0.00 31.47 1.31
2246 2271 7.379059 TCCACATGCCTTCCATATATATAGG 57.621 40.000 5.86 5.86 31.47 2.57
2247 2272 6.329986 TCCACATGCCTTCCATATATATAGGG 59.670 42.308 15.91 15.91 35.61 3.53
2248 2273 6.101734 CCACATGCCTTCCATATATATAGGGT 59.898 42.308 20.10 0.53 35.76 4.34
2249 2274 7.220030 CACATGCCTTCCATATATATAGGGTC 58.780 42.308 20.10 10.47 35.76 4.46
2250 2275 6.042093 ACATGCCTTCCATATATATAGGGTCG 59.958 42.308 20.10 13.09 35.76 4.79
2251 2276 4.344102 TGCCTTCCATATATATAGGGTCGC 59.656 45.833 20.10 18.58 35.76 5.19
2252 2277 4.558898 GCCTTCCATATATATAGGGTCGCG 60.559 50.000 20.10 0.00 35.76 5.87
2253 2278 4.547532 CTTCCATATATATAGGGTCGCGC 58.452 47.826 20.10 0.00 35.76 6.86
2254 2279 3.828921 TCCATATATATAGGGTCGCGCT 58.171 45.455 20.10 0.00 35.76 5.92
2255 2280 4.976864 TCCATATATATAGGGTCGCGCTA 58.023 43.478 20.10 0.00 35.76 4.26
2256 2281 5.567430 TCCATATATATAGGGTCGCGCTAT 58.433 41.667 20.10 16.35 41.39 2.97
2257 2282 6.008331 TCCATATATATAGGGTCGCGCTATT 58.992 40.000 20.10 10.35 39.65 1.73
2258 2283 6.150641 TCCATATATATAGGGTCGCGCTATTC 59.849 42.308 20.10 0.00 39.65 1.75
2259 2284 2.846039 ATATAGGGTCGCGCTATTCG 57.154 50.000 17.00 0.00 39.65 3.34
2260 2285 1.527034 TATAGGGTCGCGCTATTCGT 58.473 50.000 17.00 0.00 39.65 3.85
2261 2286 0.240411 ATAGGGTCGCGCTATTCGTC 59.760 55.000 5.56 0.00 36.44 4.20
2262 2287 1.096967 TAGGGTCGCGCTATTCGTCA 61.097 55.000 5.56 0.00 41.07 4.35
2263 2288 1.299926 GGGTCGCGCTATTCGTCAT 60.300 57.895 5.56 0.00 41.07 3.06
2264 2289 1.276145 GGGTCGCGCTATTCGTCATC 61.276 60.000 5.56 0.00 41.07 2.92
2265 2290 1.276145 GGTCGCGCTATTCGTCATCC 61.276 60.000 5.56 0.00 41.07 3.51
2266 2291 0.317938 GTCGCGCTATTCGTCATCCT 60.318 55.000 5.56 0.00 41.07 3.24
2267 2292 0.317854 TCGCGCTATTCGTCATCCTG 60.318 55.000 5.56 0.00 41.07 3.86
2268 2293 1.278172 CGCGCTATTCGTCATCCTGG 61.278 60.000 5.56 0.00 41.07 4.45
2269 2294 0.946221 GCGCTATTCGTCATCCTGGG 60.946 60.000 0.00 0.00 41.07 4.45
2270 2295 0.389391 CGCTATTCGTCATCCTGGGT 59.611 55.000 0.00 0.00 0.00 4.51
2271 2296 1.869754 CGCTATTCGTCATCCTGGGTG 60.870 57.143 0.00 0.00 0.00 4.61
2272 2297 1.412710 GCTATTCGTCATCCTGGGTGA 59.587 52.381 5.31 5.31 0.00 4.02
2273 2298 2.546795 GCTATTCGTCATCCTGGGTGAG 60.547 54.545 10.58 5.05 0.00 3.51
2274 2299 0.833287 ATTCGTCATCCTGGGTGAGG 59.167 55.000 20.81 20.81 44.45 3.86
2288 2313 7.751768 CCTGGGTGAGGAATAATTATTCTTC 57.248 40.000 29.75 29.75 46.33 2.87
2294 2319 7.465900 TGAGGAATAATTATTCTTCACCCCT 57.534 36.000 32.86 22.57 46.85 4.79
2295 2320 7.518188 TGAGGAATAATTATTCTTCACCCCTC 58.482 38.462 32.86 27.10 46.85 4.30
2296 2321 7.350921 TGAGGAATAATTATTCTTCACCCCTCT 59.649 37.037 32.86 20.64 46.85 3.69
2297 2322 7.750655 AGGAATAATTATTCTTCACCCCTCTC 58.249 38.462 28.64 13.44 41.33 3.20
2298 2323 7.574372 AGGAATAATTATTCTTCACCCCTCTCT 59.426 37.037 28.64 15.00 41.33 3.10
2299 2324 8.881262 GGAATAATTATTCTTCACCCCTCTCTA 58.119 37.037 28.64 0.00 41.33 2.43
2304 2329 8.986929 ATTATTCTTCACCCCTCTCTATTTTG 57.013 34.615 0.00 0.00 0.00 2.44
2305 2330 6.642733 ATTCTTCACCCCTCTCTATTTTGA 57.357 37.500 0.00 0.00 0.00 2.69
2306 2331 5.422214 TCTTCACCCCTCTCTATTTTGAC 57.578 43.478 0.00 0.00 0.00 3.18
2307 2332 4.844085 TCTTCACCCCTCTCTATTTTGACA 59.156 41.667 0.00 0.00 0.00 3.58
2308 2333 5.488919 TCTTCACCCCTCTCTATTTTGACAT 59.511 40.000 0.00 0.00 0.00 3.06
2309 2334 5.359194 TCACCCCTCTCTATTTTGACATC 57.641 43.478 0.00 0.00 0.00 3.06
2310 2335 4.782691 TCACCCCTCTCTATTTTGACATCA 59.217 41.667 0.00 0.00 0.00 3.07
2311 2336 5.250543 TCACCCCTCTCTATTTTGACATCAA 59.749 40.000 0.00 0.00 0.00 2.57
2312 2337 6.069440 TCACCCCTCTCTATTTTGACATCAAT 60.069 38.462 0.00 0.00 35.55 2.57
2313 2338 6.039047 CACCCCTCTCTATTTTGACATCAATG 59.961 42.308 0.00 0.00 35.55 2.82
2314 2339 5.009410 CCCCTCTCTATTTTGACATCAATGC 59.991 44.000 0.00 0.00 35.55 3.56
2315 2340 5.591472 CCCTCTCTATTTTGACATCAATGCA 59.409 40.000 0.00 0.00 35.55 3.96
2316 2341 6.459298 CCCTCTCTATTTTGACATCAATGCAC 60.459 42.308 0.00 0.00 35.55 4.57
2317 2342 6.441093 TCTCTATTTTGACATCAATGCACC 57.559 37.500 0.00 0.00 35.55 5.01
2318 2343 5.065090 TCTCTATTTTGACATCAATGCACCG 59.935 40.000 0.00 0.00 35.55 4.94
2319 2344 3.940209 ATTTTGACATCAATGCACCGT 57.060 38.095 0.00 0.00 35.55 4.83
2320 2345 5.877564 TCTATTTTGACATCAATGCACCGTA 59.122 36.000 0.00 0.00 35.55 4.02
2321 2346 5.581126 ATTTTGACATCAATGCACCGTAT 57.419 34.783 0.00 0.00 35.55 3.06
2322 2347 5.384063 TTTTGACATCAATGCACCGTATT 57.616 34.783 0.00 0.00 35.55 1.89
2323 2348 5.384063 TTTGACATCAATGCACCGTATTT 57.616 34.783 0.00 0.00 35.55 1.40
2324 2349 5.384063 TTGACATCAATGCACCGTATTTT 57.616 34.783 0.00 0.00 0.00 1.82
2325 2350 5.384063 TGACATCAATGCACCGTATTTTT 57.616 34.783 0.00 0.00 0.00 1.94
2326 2351 6.502136 TGACATCAATGCACCGTATTTTTA 57.498 33.333 0.00 0.00 0.00 1.52
2327 2352 7.094508 TGACATCAATGCACCGTATTTTTAT 57.905 32.000 0.00 0.00 0.00 1.40
2328 2353 6.971756 TGACATCAATGCACCGTATTTTTATG 59.028 34.615 0.00 0.00 0.00 1.90
2329 2354 6.862209 ACATCAATGCACCGTATTTTTATGT 58.138 32.000 0.00 0.00 0.00 2.29
2330 2355 7.319646 ACATCAATGCACCGTATTTTTATGTT 58.680 30.769 0.00 0.00 0.00 2.71
2331 2356 7.816995 ACATCAATGCACCGTATTTTTATGTTT 59.183 29.630 0.00 0.00 0.00 2.83
2332 2357 7.804614 TCAATGCACCGTATTTTTATGTTTC 57.195 32.000 0.00 0.00 0.00 2.78
2333 2358 6.524933 TCAATGCACCGTATTTTTATGTTTCG 59.475 34.615 0.00 0.00 0.00 3.46
2334 2359 5.359716 TGCACCGTATTTTTATGTTTCGT 57.640 34.783 0.00 0.00 0.00 3.85
2335 2360 6.477669 TGCACCGTATTTTTATGTTTCGTA 57.522 33.333 0.00 0.00 0.00 3.43
2336 2361 6.895898 TGCACCGTATTTTTATGTTTCGTAA 58.104 32.000 0.00 0.00 0.00 3.18
2337 2362 7.358066 TGCACCGTATTTTTATGTTTCGTAAA 58.642 30.769 0.00 0.00 0.00 2.01
2338 2363 8.021973 TGCACCGTATTTTTATGTTTCGTAAAT 58.978 29.630 0.00 0.00 0.00 1.40
2339 2364 8.852380 GCACCGTATTTTTATGTTTCGTAAATT 58.148 29.630 0.00 0.00 0.00 1.82
2387 2412 8.838452 AGAGAACGTAAGAAAATATGTACTCG 57.162 34.615 0.00 0.00 43.62 4.18
2388 2413 7.431668 AGAGAACGTAAGAAAATATGTACTCGC 59.568 37.037 0.00 0.00 43.62 5.03
2389 2414 6.474751 AGAACGTAAGAAAATATGTACTCGCC 59.525 38.462 0.00 0.00 43.62 5.54
2390 2415 4.736793 ACGTAAGAAAATATGTACTCGCCG 59.263 41.667 0.00 0.00 43.62 6.46
2391 2416 4.736793 CGTAAGAAAATATGTACTCGCCGT 59.263 41.667 0.00 0.00 43.02 5.68
2392 2417 5.909054 CGTAAGAAAATATGTACTCGCCGTA 59.091 40.000 0.00 0.00 43.02 4.02
2393 2418 6.414694 CGTAAGAAAATATGTACTCGCCGTAA 59.585 38.462 0.00 0.00 43.02 3.18
2394 2419 7.044117 CGTAAGAAAATATGTACTCGCCGTAAA 60.044 37.037 0.00 0.00 43.02 2.01
2395 2420 7.599630 AAGAAAATATGTACTCGCCGTAAAA 57.400 32.000 0.00 0.00 0.00 1.52
2396 2421 7.599630 AGAAAATATGTACTCGCCGTAAAAA 57.400 32.000 0.00 0.00 0.00 1.94
2479 2504 9.533831 AATGTGATTTTTCTGGTCTTATAACCT 57.466 29.630 0.00 0.00 40.20 3.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.860898 ATTTTTATACTCATTTCACCTTTGCTC 57.139 29.630 0.00 0.00 0.00 4.26
69 70 7.353525 ACATGTATAAAAGGATTGATGGGTGA 58.646 34.615 0.00 0.00 0.00 4.02
132 136 6.826668 TGATAGTATCAAATGGACACCGAAT 58.173 36.000 10.50 0.00 36.11 3.34
280 284 7.816640 TGACTTGAGTTATATTGTTTGGAAGC 58.183 34.615 0.00 0.00 0.00 3.86
342 346 1.003580 CACTGACAGTGGTGGCCTAAT 59.996 52.381 25.22 0.00 42.35 1.73
364 368 9.449719 ACTAACTATGGGAAAAATCTGTGTTAG 57.550 33.333 0.00 0.00 39.04 2.34
366 370 7.309194 GCACTAACTATGGGAAAAATCTGTGTT 60.309 37.037 0.00 0.00 0.00 3.32
759 779 6.655003 AGGTAAATCAAATGCCCTATGTATCG 59.345 38.462 0.00 0.00 0.00 2.92
983 1003 8.960591 GTTTATATAGGTGCCTATTGATGCATT 58.039 33.333 15.12 0.00 40.07 3.56
1029 1049 3.078097 TGTGCTAATATGCGGTGTGTTT 58.922 40.909 0.00 0.00 35.36 2.83
1047 1067 6.072838 AGTGACTTCTATGCTCAATTGTTGTG 60.073 38.462 5.13 0.00 0.00 3.33
1067 1087 0.465460 TGGTGAGGCCAACAAGTGAC 60.465 55.000 5.01 0.00 45.94 3.67
1120 1140 2.242043 ACCATGAGAGCCACCAAAAAG 58.758 47.619 0.00 0.00 0.00 2.27
1141 1161 1.838077 GGGGACACAATAGTAGCCAGT 59.162 52.381 0.00 0.00 0.00 4.00
1334 1354 4.989044 TCTGCATGTATCTGCACAAAATG 58.011 39.130 0.00 0.00 46.76 2.32
1365 1385 4.832248 TGGATAGCAACTTTCAGGTAGTG 58.168 43.478 0.00 0.00 0.00 2.74
1374 1394 6.494835 AGGAAACTTCATTGGATAGCAACTTT 59.505 34.615 0.00 0.00 37.44 2.66
1448 1468 8.575589 ACAACAATAATCAACATCTTTGCAGTA 58.424 29.630 0.00 0.00 0.00 2.74
1486 1506 1.271707 CGGGGGTTGAGTGGTGTTTAT 60.272 52.381 0.00 0.00 0.00 1.40
1587 1607 2.783135 ACGTCCAATTCATGAGCAAGT 58.217 42.857 0.00 0.00 0.00 3.16
1651 1671 1.216178 GGTGCATGTTCATGGTGCC 59.784 57.895 13.55 0.00 38.06 5.01
1786 1808 9.516546 GGAAGAGTAGAGAATTCCCTTTAAAAA 57.483 33.333 0.65 0.00 36.08 1.94
1819 1842 4.837093 ATGGAAGTTAATCTCAACCCGA 57.163 40.909 0.00 0.00 0.00 5.14
1876 1900 9.706529 ATGACCTCAGCAATCTATATAGATGTA 57.293 33.333 23.03 8.61 41.96 2.29
1877 1901 8.476447 CATGACCTCAGCAATCTATATAGATGT 58.524 37.037 23.03 15.21 41.96 3.06
1880 1904 7.578380 GCACATGACCTCAGCAATCTATATAGA 60.578 40.741 14.76 14.76 36.65 1.98
1886 1910 2.502947 AGCACATGACCTCAGCAATCTA 59.497 45.455 0.00 0.00 0.00 1.98
1914 1938 2.531522 AGGTGCATGAAAAAGTTGGC 57.468 45.000 0.00 0.00 0.00 4.52
1915 1940 3.573967 AGGTAGGTGCATGAAAAAGTTGG 59.426 43.478 0.00 0.00 0.00 3.77
1950 1975 7.039714 AGTCCAAGGGAAATCTTGTTTATTGAC 60.040 37.037 0.00 0.00 41.72 3.18
1991 2016 2.218603 ACCTTTTGTCAACACGCTAGG 58.781 47.619 0.00 0.00 0.00 3.02
2018 2043 0.254178 ATGAAAGGTCGCATGCCTCT 59.746 50.000 13.15 4.12 34.81 3.69
2020 2045 1.098050 GAATGAAAGGTCGCATGCCT 58.902 50.000 13.15 0.00 38.11 4.75
2034 2059 1.213619 TGTGCCATCCCCAGGAATGA 61.214 55.000 3.86 0.00 34.34 2.57
2040 2065 0.184211 TGATGATGTGCCATCCCCAG 59.816 55.000 11.25 0.00 41.60 4.45
2135 2160 3.118629 AGCTCTCATCGGTCTATTTTGCA 60.119 43.478 0.00 0.00 0.00 4.08
2171 2196 2.170397 CCTACATGGGCATAGTGTGTGA 59.830 50.000 0.00 0.00 0.00 3.58
2226 2251 6.459066 CGACCCTATATATATGGAAGGCATG 58.541 44.000 18.03 0.00 0.00 4.06
2240 2265 2.089980 ACGAATAGCGCGACCCTATAT 58.910 47.619 12.10 0.00 46.04 0.86
2241 2266 1.466167 GACGAATAGCGCGACCCTATA 59.534 52.381 12.10 0.00 46.04 1.31
2242 2267 0.240411 GACGAATAGCGCGACCCTAT 59.760 55.000 12.10 4.35 46.04 2.57
2243 2268 1.096967 TGACGAATAGCGCGACCCTA 61.097 55.000 12.10 1.47 46.04 3.53
2244 2269 1.735376 ATGACGAATAGCGCGACCCT 61.735 55.000 12.10 0.00 46.04 4.34
2245 2270 1.276145 GATGACGAATAGCGCGACCC 61.276 60.000 12.10 0.00 46.04 4.46
2246 2271 1.276145 GGATGACGAATAGCGCGACC 61.276 60.000 12.10 0.00 46.04 4.79
2247 2272 0.317938 AGGATGACGAATAGCGCGAC 60.318 55.000 12.10 0.04 46.04 5.19
2248 2273 0.317854 CAGGATGACGAATAGCGCGA 60.318 55.000 12.10 0.00 46.04 5.87
2249 2274 1.278172 CCAGGATGACGAATAGCGCG 61.278 60.000 0.00 0.00 46.04 6.86
2250 2275 0.946221 CCCAGGATGACGAATAGCGC 60.946 60.000 0.00 0.00 46.04 5.92
2252 2277 1.412710 TCACCCAGGATGACGAATAGC 59.587 52.381 0.00 0.00 39.69 2.97
2253 2278 3.377346 CTCACCCAGGATGACGAATAG 57.623 52.381 0.00 0.00 39.69 1.73
2264 2289 7.290061 TGAAGAATAATTATTCCTCACCCAGG 58.710 38.462 25.58 0.00 42.29 4.45
2270 2295 7.350921 AGAGGGGTGAAGAATAATTATTCCTCA 59.649 37.037 25.58 25.58 42.29 3.86
2271 2296 7.750655 AGAGGGGTGAAGAATAATTATTCCTC 58.249 38.462 27.18 24.55 42.29 3.71
2272 2297 7.574372 AGAGAGGGGTGAAGAATAATTATTCCT 59.426 37.037 27.18 18.76 42.29 3.36
2273 2298 7.750655 AGAGAGGGGTGAAGAATAATTATTCC 58.249 38.462 27.18 17.01 42.29 3.01
2278 2303 9.413734 CAAAATAGAGAGGGGTGAAGAATAATT 57.586 33.333 0.00 0.00 0.00 1.40
2279 2304 8.781951 TCAAAATAGAGAGGGGTGAAGAATAAT 58.218 33.333 0.00 0.00 0.00 1.28
2280 2305 8.047310 GTCAAAATAGAGAGGGGTGAAGAATAA 58.953 37.037 0.00 0.00 0.00 1.40
2281 2306 7.182026 TGTCAAAATAGAGAGGGGTGAAGAATA 59.818 37.037 0.00 0.00 0.00 1.75
2282 2307 6.012508 TGTCAAAATAGAGAGGGGTGAAGAAT 60.013 38.462 0.00 0.00 0.00 2.40
2283 2308 5.309543 TGTCAAAATAGAGAGGGGTGAAGAA 59.690 40.000 0.00 0.00 0.00 2.52
2284 2309 4.844085 TGTCAAAATAGAGAGGGGTGAAGA 59.156 41.667 0.00 0.00 0.00 2.87
2285 2310 5.165961 TGTCAAAATAGAGAGGGGTGAAG 57.834 43.478 0.00 0.00 0.00 3.02
2286 2311 5.250543 TGATGTCAAAATAGAGAGGGGTGAA 59.749 40.000 0.00 0.00 0.00 3.18
2287 2312 4.782691 TGATGTCAAAATAGAGAGGGGTGA 59.217 41.667 0.00 0.00 0.00 4.02
2288 2313 5.102953 TGATGTCAAAATAGAGAGGGGTG 57.897 43.478 0.00 0.00 0.00 4.61
2289 2314 5.779241 TTGATGTCAAAATAGAGAGGGGT 57.221 39.130 0.00 0.00 32.11 4.95
2290 2315 5.009410 GCATTGATGTCAAAATAGAGAGGGG 59.991 44.000 0.00 0.00 39.55 4.79
2291 2316 5.591472 TGCATTGATGTCAAAATAGAGAGGG 59.409 40.000 0.00 0.00 39.55 4.30
2292 2317 6.459298 GGTGCATTGATGTCAAAATAGAGAGG 60.459 42.308 0.00 0.00 39.55 3.69
2293 2318 6.493116 GGTGCATTGATGTCAAAATAGAGAG 58.507 40.000 0.00 0.00 39.55 3.20
2294 2319 5.065090 CGGTGCATTGATGTCAAAATAGAGA 59.935 40.000 0.00 0.00 39.55 3.10
2295 2320 5.163723 ACGGTGCATTGATGTCAAAATAGAG 60.164 40.000 0.00 0.00 39.55 2.43
2296 2321 4.699735 ACGGTGCATTGATGTCAAAATAGA 59.300 37.500 0.00 0.00 39.55 1.98
2297 2322 4.985413 ACGGTGCATTGATGTCAAAATAG 58.015 39.130 0.00 0.00 39.55 1.73
2298 2323 6.691754 ATACGGTGCATTGATGTCAAAATA 57.308 33.333 0.00 0.00 39.55 1.40
2299 2324 3.940209 ACGGTGCATTGATGTCAAAAT 57.060 38.095 0.00 0.00 39.55 1.82
2300 2325 5.384063 AATACGGTGCATTGATGTCAAAA 57.616 34.783 0.00 0.00 39.55 2.44
2301 2326 5.384063 AAATACGGTGCATTGATGTCAAA 57.616 34.783 0.00 0.00 39.55 2.69
2302 2327 5.384063 AAAATACGGTGCATTGATGTCAA 57.616 34.783 0.00 0.00 40.51 3.18
2303 2328 5.384063 AAAAATACGGTGCATTGATGTCA 57.616 34.783 0.00 0.00 0.00 3.58
2304 2329 6.972328 ACATAAAAATACGGTGCATTGATGTC 59.028 34.615 0.00 0.00 0.00 3.06
2305 2330 6.862209 ACATAAAAATACGGTGCATTGATGT 58.138 32.000 0.00 0.00 0.00 3.06
2306 2331 7.754069 AACATAAAAATACGGTGCATTGATG 57.246 32.000 0.00 0.00 0.00 3.07
2307 2332 7.219917 CGAAACATAAAAATACGGTGCATTGAT 59.780 33.333 0.00 0.00 0.00 2.57
2308 2333 6.524933 CGAAACATAAAAATACGGTGCATTGA 59.475 34.615 0.00 0.00 0.00 2.57
2309 2334 6.306837 ACGAAACATAAAAATACGGTGCATTG 59.693 34.615 0.00 0.00 0.00 2.82
2310 2335 6.383415 ACGAAACATAAAAATACGGTGCATT 58.617 32.000 0.00 0.00 0.00 3.56
2311 2336 5.945155 ACGAAACATAAAAATACGGTGCAT 58.055 33.333 0.00 0.00 0.00 3.96
2312 2337 5.359716 ACGAAACATAAAAATACGGTGCA 57.640 34.783 0.00 0.00 0.00 4.57
2313 2338 7.778743 TTTACGAAACATAAAAATACGGTGC 57.221 32.000 0.00 0.00 0.00 5.01
2361 2386 9.286946 CGAGTACATATTTTCTTACGTTCTCTT 57.713 33.333 0.00 0.00 0.00 2.85
2362 2387 7.431668 GCGAGTACATATTTTCTTACGTTCTCT 59.568 37.037 0.00 0.00 0.00 3.10
2363 2388 7.305878 GGCGAGTACATATTTTCTTACGTTCTC 60.306 40.741 0.00 0.00 0.00 2.87
2364 2389 6.474751 GGCGAGTACATATTTTCTTACGTTCT 59.525 38.462 0.00 0.00 0.00 3.01
2365 2390 6.559158 CGGCGAGTACATATTTTCTTACGTTC 60.559 42.308 0.00 0.00 0.00 3.95
2366 2391 5.230726 CGGCGAGTACATATTTTCTTACGTT 59.769 40.000 0.00 0.00 0.00 3.99
2367 2392 4.736793 CGGCGAGTACATATTTTCTTACGT 59.263 41.667 0.00 0.00 0.00 3.57
2368 2393 4.736793 ACGGCGAGTACATATTTTCTTACG 59.263 41.667 16.62 0.00 0.00 3.18
2369 2394 7.684062 TTACGGCGAGTACATATTTTCTTAC 57.316 36.000 16.62 0.00 34.56 2.34
2370 2395 8.700722 TTTTACGGCGAGTACATATTTTCTTA 57.299 30.769 16.62 0.00 34.56 2.10
2371 2396 7.599630 TTTTACGGCGAGTACATATTTTCTT 57.400 32.000 16.62 0.00 34.56 2.52
2372 2397 7.599630 TTTTTACGGCGAGTACATATTTTCT 57.400 32.000 16.62 0.00 34.56 2.52
2453 2478 9.533831 AGGTTATAAGACCAGAAAAATCACATT 57.466 29.630 0.00 0.00 42.35 2.71


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

AutoCloner maintained by Alex Coulton.