Multiple sequence alignment - TraesCS1A01G418100

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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 TraesCS1A01G418100 chr1A 100.000 2596 0 0 1 2596 575594062 575596657 0.000000e+00 4795
1 TraesCS1A01G418100 chr1B 89.790 2194 134 46 423 2596 667491028 667493151 0.000000e+00 2728
2 TraesCS1A01G418100 chr1D 94.595 1739 61 15 470 2180 479228050 479229783 0.000000e+00 2660
3 TraesCS1A01G418100 chr1D 89.362 329 21 6 2275 2596 479229779 479230100 4.020000e-108 401
4 TraesCS1A01G418100 chr1D 97.030 202 4 2 1 201 479227537 479227737 3.200000e-89 339
5 TraesCS1A01G418100 chr1D 85.135 222 9 9 208 406 479227824 479228044 3.390000e-49 206


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 TraesCS1A01G418100 chr1A 575594062 575596657 2595 False 4795.0 4795 100.0000 1 2596 1 chr1A.!!$F1 2595
1 TraesCS1A01G418100 chr1B 667491028 667493151 2123 False 2728.0 2728 89.7900 423 2596 1 chr1B.!!$F1 2173
2 TraesCS1A01G418100 chr1D 479227537 479230100 2563 False 901.5 2660 91.5305 1 2596 4 chr1D.!!$F1 2595

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
667 771 0.037326 ATGTGTGGTACTGAGGCACG 60.037 55.0 0.0 0.0 33.23 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2084 2213 0.254462 TGGCTACATTCCAATCGGCA 59.746 50.0 0.0 0.0 0.0 5.69 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
33 34 6.459573 GCTTTCATTTCTGACACACCAGTTTA 60.460 38.462 0.00 0.00 35.71 2.01
34 35 6.371809 TTCATTTCTGACACACCAGTTTAC 57.628 37.500 0.00 0.00 35.71 2.01
153 154 4.119862 TGACTACTCAGTTGTGAACTTGC 58.880 43.478 0.00 0.00 40.46 4.01
166 167 2.290008 TGAACTTGCGATGGTACCACAT 60.290 45.455 19.09 1.04 0.00 3.21
167 168 1.737838 ACTTGCGATGGTACCACATG 58.262 50.000 19.09 14.97 0.00 3.21
168 169 1.277842 ACTTGCGATGGTACCACATGA 59.722 47.619 19.09 0.00 0.00 3.07
253 334 4.793201 ACCAACTTGTCTAAAGAAGCCTT 58.207 39.130 0.00 0.00 28.90 4.35
268 349 8.497910 AAAGAAGCCTTGGAGACATATAGATA 57.502 34.615 0.00 0.00 42.32 1.98
271 352 7.898100 AGAAGCCTTGGAGACATATAGATATGA 59.102 37.037 14.96 0.00 42.05 2.15
275 356 7.978975 GCCTTGGAGACATATAGATATGACTTC 59.021 40.741 14.96 12.93 42.70 3.01
295 376 8.590204 TGACTTCTTTTCTTTTAAAAAGGTGGT 58.410 29.630 1.66 6.02 43.38 4.16
353 457 8.871862 GCTACATTATCAGATCTAGCTGAAATG 58.128 37.037 19.69 19.69 46.94 2.32
406 510 7.277319 CCTACACATGCATCATACATCACTATC 59.723 40.741 0.00 0.00 0.00 2.08
407 511 5.936372 ACACATGCATCATACATCACTATCC 59.064 40.000 0.00 0.00 0.00 2.59
409 513 7.038799 ACACATGCATCATACATCACTATCCTA 60.039 37.037 0.00 0.00 0.00 2.94
410 514 7.985752 CACATGCATCATACATCACTATCCTAT 59.014 37.037 0.00 0.00 0.00 2.57
411 515 9.205513 ACATGCATCATACATCACTATCCTATA 57.794 33.333 0.00 0.00 0.00 1.31
415 519 9.833182 GCATCATACATCACTATCCTATATACG 57.167 37.037 0.00 0.00 0.00 3.06
418 522 9.557061 TCATACATCACTATCCTATATACGTCC 57.443 37.037 0.00 0.00 0.00 4.79
419 523 9.562408 CATACATCACTATCCTATATACGTCCT 57.438 37.037 0.00 0.00 0.00 3.85
420 524 7.867305 ACATCACTATCCTATATACGTCCTG 57.133 40.000 0.00 0.00 0.00 3.86
421 525 6.319152 ACATCACTATCCTATATACGTCCTGC 59.681 42.308 0.00 0.00 0.00 4.85
452 556 1.536940 TGTGTTGGATGCCATGACAG 58.463 50.000 0.00 0.00 31.53 3.51
467 571 3.057969 TGACAGCCACATCCTAACAAG 57.942 47.619 0.00 0.00 0.00 3.16
499 603 1.901591 ATTCACACCAGGCACAAGAG 58.098 50.000 0.00 0.00 0.00 2.85
500 604 0.819259 TTCACACCAGGCACAAGAGC 60.819 55.000 0.00 0.00 0.00 4.09
506 610 2.204059 AGGCACAAGAGCTCCCCT 60.204 61.111 10.93 5.91 34.17 4.79
619 723 4.130255 GGAGTGTACAGCTCCCCA 57.870 61.111 23.43 0.00 45.05 4.96
627 731 1.562672 TACAGCTCCCCAAAGGCCTC 61.563 60.000 5.23 0.00 34.51 4.70
667 771 0.037326 ATGTGTGGTACTGAGGCACG 60.037 55.000 0.00 0.00 33.23 5.34
712 816 0.397675 TCAGGGTGATCTCCGAGCAT 60.398 55.000 7.70 0.00 28.52 3.79
775 879 0.546747 AAGTCCCCCGGATGTTCTCA 60.547 55.000 0.73 0.00 32.73 3.27
960 1064 8.260114 CCTAGTGTGATTGGATATATGTATGCA 58.740 37.037 0.00 0.00 36.94 3.96
991 1095 1.202794 TGCTGGATGAACTGAGTTGCA 60.203 47.619 0.90 1.69 0.00 4.08
1137 1241 2.287117 ATCCCATGGCCTGGTCCA 60.287 61.111 6.09 11.41 44.30 4.02
1227 1331 7.623770 CATTGCACAAGGTAAATATTTCATGC 58.376 34.615 3.39 7.45 0.00 4.06
1252 1356 5.717078 AGTTCTCGTGGTTCTGTATACAA 57.283 39.130 7.06 0.00 0.00 2.41
1258 1362 9.661563 TTCTCGTGGTTCTGTATACAAATTATT 57.338 29.630 7.06 0.00 0.00 1.40
1367 1496 7.525688 TTGTGACATCGCAAACAAAAATTAA 57.474 28.000 5.41 0.00 42.60 1.40
1371 1500 9.432077 GTGACATCGCAAACAAAAATTAAAAAT 57.568 25.926 0.00 0.00 0.00 1.82
1452 1581 3.763897 AGTTTTGCAGGTGTATTCCATCC 59.236 43.478 0.00 0.00 0.00 3.51
1476 1605 0.694444 TGGGGCTATTCTCAGGGGAC 60.694 60.000 0.00 0.00 0.00 4.46
1488 1617 0.684479 CAGGGGACGAGATGGTCAGA 60.684 60.000 0.00 0.00 38.70 3.27
1652 1781 6.785191 ACTTAATTTGGTCTGATATGCAACG 58.215 36.000 0.00 0.00 0.00 4.10
1720 1849 2.491693 CGTGGGTTTAATCTGTGGCATT 59.508 45.455 0.00 0.00 0.00 3.56
1773 1902 6.630071 GGAAGCATCCAAAGTAAGCAATTAA 58.370 36.000 2.32 0.00 45.79 1.40
1774 1903 7.096551 GGAAGCATCCAAAGTAAGCAATTAAA 58.903 34.615 2.32 0.00 45.79 1.52
1855 1984 6.930068 ACTGAGTCCATATCATCATCATCA 57.070 37.500 0.00 0.00 0.00 3.07
1856 1985 7.497773 ACTGAGTCCATATCATCATCATCAT 57.502 36.000 0.00 0.00 0.00 2.45
1857 1986 7.557724 ACTGAGTCCATATCATCATCATCATC 58.442 38.462 0.00 0.00 0.00 2.92
1863 1992 8.994170 GTCCATATCATCATCATCATCATCATC 58.006 37.037 0.00 0.00 0.00 2.92
1933 2062 3.251729 CACTGCCTTGAATTGATATCCCG 59.748 47.826 0.00 0.00 0.00 5.14
2035 2164 3.980775 CCAGCTACAAAATGAAAACACGG 59.019 43.478 0.00 0.00 0.00 4.94
2048 2177 5.175859 TGAAAACACGGCATTTAAAACCAA 58.824 33.333 10.32 0.00 0.00 3.67
2084 2213 6.331369 AGTTTGTTGTTGCATAACTAGCAT 57.669 33.333 13.45 0.00 42.33 3.79
2116 2247 5.221925 GGAATGTAGCCAAGGAATCTGGATA 60.222 44.000 0.00 0.00 0.00 2.59
2129 2260 6.069963 AGGAATCTGGATAGGGCATATTGTAC 60.070 42.308 0.00 0.00 0.00 2.90
2171 2387 9.191995 GTTACAACCTCCAAACAGAATATTTTG 57.808 33.333 4.50 4.50 33.30 2.44
2180 2396 8.075593 CCAAACAGAATATTTTGGTTGAGTTG 57.924 34.615 29.06 14.33 43.06 3.16
2181 2397 7.925483 CCAAACAGAATATTTTGGTTGAGTTGA 59.075 33.333 29.06 0.00 43.06 3.18
2182 2398 9.311916 CAAACAGAATATTTTGGTTGAGTTGAA 57.688 29.630 25.22 0.00 43.06 2.69
2184 2400 9.480053 AACAGAATATTTTGGTTGAGTTGAATG 57.520 29.630 10.46 0.00 0.00 2.67
2185 2401 8.641541 ACAGAATATTTTGGTTGAGTTGAATGT 58.358 29.630 10.46 0.00 0.00 2.71
2186 2402 9.132521 CAGAATATTTTGGTTGAGTTGAATGTC 57.867 33.333 0.00 0.00 0.00 3.06
2187 2403 9.082313 AGAATATTTTGGTTGAGTTGAATGTCT 57.918 29.630 0.00 0.00 0.00 3.41
2191 2407 8.641498 ATTTTGGTTGAGTTGAATGTCTATCT 57.359 30.769 0.00 0.00 0.00 1.98
2192 2408 9.739276 ATTTTGGTTGAGTTGAATGTCTATCTA 57.261 29.630 0.00 0.00 0.00 1.98
2193 2409 9.739276 TTTTGGTTGAGTTGAATGTCTATCTAT 57.261 29.630 0.00 0.00 0.00 1.98
2195 2411 9.817809 TTGGTTGAGTTGAATGTCTATCTATAC 57.182 33.333 0.00 0.00 0.00 1.47
2196 2412 9.201989 TGGTTGAGTTGAATGTCTATCTATACT 57.798 33.333 0.00 0.00 0.00 2.12
2205 2421 9.982651 TGAATGTCTATCTATACTTTGGTAAGC 57.017 33.333 0.00 0.00 34.60 3.09
2206 2422 9.130312 GAATGTCTATCTATACTTTGGTAAGCG 57.870 37.037 0.00 0.00 34.60 4.68
2207 2423 7.578310 TGTCTATCTATACTTTGGTAAGCGT 57.422 36.000 0.00 0.00 34.60 5.07
2208 2424 7.423199 TGTCTATCTATACTTTGGTAAGCGTG 58.577 38.462 0.00 0.00 34.60 5.34
2209 2425 6.362820 GTCTATCTATACTTTGGTAAGCGTGC 59.637 42.308 0.00 0.00 34.60 5.34
2210 2426 4.459390 TCTATACTTTGGTAAGCGTGCA 57.541 40.909 0.00 0.00 34.60 4.57
2211 2427 4.823157 TCTATACTTTGGTAAGCGTGCAA 58.177 39.130 0.00 0.00 34.60 4.08
2212 2428 5.239351 TCTATACTTTGGTAAGCGTGCAAA 58.761 37.500 0.00 0.00 34.60 3.68
2213 2429 2.774439 ACTTTGGTAAGCGTGCAAAG 57.226 45.000 0.00 0.00 38.42 2.77
2214 2430 2.294074 ACTTTGGTAAGCGTGCAAAGA 58.706 42.857 2.54 0.00 36.63 2.52
2215 2431 2.290641 ACTTTGGTAAGCGTGCAAAGAG 59.709 45.455 2.54 3.86 36.63 2.85
2216 2432 0.591170 TTGGTAAGCGTGCAAAGAGC 59.409 50.000 0.00 0.00 45.96 4.09
2229 2445 4.442350 GCAAAGAGCATCAAACAACAAC 57.558 40.909 0.00 0.00 44.79 3.32
2230 2446 3.245990 GCAAAGAGCATCAAACAACAACC 59.754 43.478 0.00 0.00 44.79 3.77
2231 2447 4.431809 CAAAGAGCATCAAACAACAACCA 58.568 39.130 0.00 0.00 37.82 3.67
2232 2448 4.942761 AAGAGCATCAAACAACAACCAT 57.057 36.364 0.00 0.00 37.82 3.55
2233 2449 4.247267 AGAGCATCAAACAACAACCATG 57.753 40.909 0.00 0.00 37.82 3.66
2234 2450 3.638160 AGAGCATCAAACAACAACCATGT 59.362 39.130 0.00 0.00 38.76 3.21
2235 2451 3.981211 AGCATCAAACAACAACCATGTC 58.019 40.909 0.00 0.00 39.40 3.06
2236 2452 3.638160 AGCATCAAACAACAACCATGTCT 59.362 39.130 0.00 0.00 39.40 3.41
2237 2453 3.737266 GCATCAAACAACAACCATGTCTG 59.263 43.478 0.00 0.00 39.40 3.51
2238 2454 4.737352 GCATCAAACAACAACCATGTCTGT 60.737 41.667 0.00 0.00 39.40 3.41
2239 2455 4.630894 TCAAACAACAACCATGTCTGTC 57.369 40.909 0.00 0.00 39.40 3.51
2240 2456 3.064682 TCAAACAACAACCATGTCTGTCG 59.935 43.478 0.00 0.00 39.40 4.35
2241 2457 2.613026 ACAACAACCATGTCTGTCGA 57.387 45.000 0.00 0.00 39.40 4.20
2242 2458 2.483876 ACAACAACCATGTCTGTCGAG 58.516 47.619 0.00 0.00 39.40 4.04
2243 2459 2.102420 ACAACAACCATGTCTGTCGAGA 59.898 45.455 0.00 0.00 39.40 4.04
2244 2460 3.130633 CAACAACCATGTCTGTCGAGAA 58.869 45.455 0.00 0.00 39.40 2.87
2245 2461 3.685139 ACAACCATGTCTGTCGAGAAT 57.315 42.857 0.00 0.00 33.41 2.40
2246 2462 3.329386 ACAACCATGTCTGTCGAGAATG 58.671 45.455 0.00 0.00 33.41 2.67
2247 2463 2.015736 ACCATGTCTGTCGAGAATGC 57.984 50.000 0.00 0.00 0.00 3.56
2248 2464 1.552337 ACCATGTCTGTCGAGAATGCT 59.448 47.619 0.00 0.00 0.00 3.79
2249 2465 2.200067 CCATGTCTGTCGAGAATGCTC 58.800 52.381 0.00 0.00 37.81 4.26
2250 2466 2.159128 CCATGTCTGTCGAGAATGCTCT 60.159 50.000 0.00 0.00 39.06 4.09
2251 2467 2.643933 TGTCTGTCGAGAATGCTCTG 57.356 50.000 0.00 0.00 39.06 3.35
2252 2468 1.203287 TGTCTGTCGAGAATGCTCTGG 59.797 52.381 0.00 0.00 39.06 3.86
2253 2469 1.203523 GTCTGTCGAGAATGCTCTGGT 59.796 52.381 0.00 0.00 39.06 4.00
2254 2470 1.203287 TCTGTCGAGAATGCTCTGGTG 59.797 52.381 0.00 0.00 39.06 4.17
2255 2471 0.390340 TGTCGAGAATGCTCTGGTGC 60.390 55.000 0.00 0.00 39.06 5.01
2264 2480 2.672961 TGCTCTGGTGCATAGTGTAC 57.327 50.000 0.00 0.00 38.12 2.90
2265 2481 1.899142 TGCTCTGGTGCATAGTGTACA 59.101 47.619 0.00 0.00 38.12 2.90
2266 2482 2.501316 TGCTCTGGTGCATAGTGTACAT 59.499 45.455 0.00 0.00 38.12 2.29
2267 2483 3.704061 TGCTCTGGTGCATAGTGTACATA 59.296 43.478 0.00 0.00 38.12 2.29
2268 2484 4.202151 TGCTCTGGTGCATAGTGTACATAG 60.202 45.833 0.00 0.00 38.12 2.23
2269 2485 4.202161 GCTCTGGTGCATAGTGTACATAGT 60.202 45.833 0.00 0.00 34.53 2.12
2270 2486 5.682471 GCTCTGGTGCATAGTGTACATAGTT 60.682 44.000 0.00 0.00 34.53 2.24
2271 2487 5.660460 TCTGGTGCATAGTGTACATAGTTG 58.340 41.667 0.00 0.00 34.53 3.16
2272 2488 4.188462 TGGTGCATAGTGTACATAGTTGC 58.812 43.478 0.00 7.40 34.53 4.17
2273 2489 3.560068 GGTGCATAGTGTACATAGTTGCC 59.440 47.826 15.75 9.78 34.53 4.52
2274 2490 3.245284 GTGCATAGTGTACATAGTTGCCG 59.755 47.826 15.75 0.00 33.03 5.69
2275 2491 3.131400 TGCATAGTGTACATAGTTGCCGA 59.869 43.478 15.75 1.80 0.00 5.54
2276 2492 3.489785 GCATAGTGTACATAGTTGCCGAC 59.510 47.826 0.00 0.00 0.00 4.79
2277 2493 4.736759 GCATAGTGTACATAGTTGCCGACT 60.737 45.833 0.00 0.00 42.55 4.18
2283 2499 3.418684 ACATAGTTGCCGACTTCCTTT 57.581 42.857 0.00 0.00 39.86 3.11
2374 2590 2.084546 GTGTTAGGCTTGCAGTTAGGG 58.915 52.381 0.00 0.00 0.00 3.53
2400 2616 3.967332 AAATGAGATTGGGCCAACAAG 57.033 42.857 23.59 0.00 33.23 3.16
2513 2736 9.220767 AGATAGTAATCAAGTTCAACCTTTGTC 57.779 33.333 0.00 0.00 34.28 3.18
2515 2738 4.568152 AATCAAGTTCAACCTTTGTCGG 57.432 40.909 0.00 0.00 0.00 4.79
2516 2739 2.294074 TCAAGTTCAACCTTTGTCGGG 58.706 47.619 0.00 0.00 0.00 5.14
2517 2740 2.092861 TCAAGTTCAACCTTTGTCGGGA 60.093 45.455 0.00 0.00 0.00 5.14
2518 2741 2.685897 CAAGTTCAACCTTTGTCGGGAA 59.314 45.455 0.00 0.00 0.00 3.97
2519 2742 3.007473 AGTTCAACCTTTGTCGGGAAA 57.993 42.857 0.00 0.00 0.00 3.13
2530 2753 3.622166 TGTCGGGAAAGGAAAGGATAC 57.378 47.619 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 0.949105 CAAAGAGCCAAGCGTACGGT 60.949 55.000 15.34 15.34 0.00 4.83
34 35 0.669318 TCAAAGAGCCAAGCGTACGG 60.669 55.000 18.39 0.63 0.00 4.02
153 154 6.259829 TGAACAATTATCATGTGGTACCATCG 59.740 38.462 19.72 9.79 0.00 3.84
268 349 9.599866 CCACCTTTTTAAAAGAAAAGAAGTCAT 57.400 29.630 17.91 0.00 45.20 3.06
275 356 7.223971 GGCACTACCACCTTTTTAAAAGAAAAG 59.776 37.037 17.91 10.11 40.67 2.27
286 367 0.112412 CAGGGGCACTACCACCTTTT 59.888 55.000 0.00 0.00 46.79 2.27
353 457 3.309954 AGCTGAAACACGAGAAGAAACAC 59.690 43.478 0.00 0.00 0.00 3.32
429 533 4.085009 TGTCATGGCATCCAACACAATTA 58.915 39.130 0.00 0.00 36.95 1.40
433 537 1.536940 CTGTCATGGCATCCAACACA 58.463 50.000 0.00 0.00 36.95 3.72
434 538 0.171903 GCTGTCATGGCATCCAACAC 59.828 55.000 0.00 0.00 36.95 3.32
435 539 0.966875 GGCTGTCATGGCATCCAACA 60.967 55.000 15.22 1.78 36.95 3.33
438 542 1.378911 GTGGCTGTCATGGCATCCA 60.379 57.895 18.65 18.65 44.18 3.41
439 543 0.754217 ATGTGGCTGTCATGGCATCC 60.754 55.000 13.32 13.32 44.18 3.51
440 544 0.666913 GATGTGGCTGTCATGGCATC 59.333 55.000 0.00 0.00 44.18 3.91
452 556 2.012673 CAGCTCTTGTTAGGATGTGGC 58.987 52.381 0.00 0.00 0.00 5.01
467 571 6.758886 GCCTGGTGTGAATATATATACAGCTC 59.241 42.308 20.51 11.22 40.91 4.09
499 603 1.070445 CATGGACGATCAGGGGAGC 59.930 63.158 0.00 0.00 0.00 4.70
500 604 0.760567 TCCATGGACGATCAGGGGAG 60.761 60.000 11.44 0.00 38.93 4.30
506 610 2.677902 GCTGAAACTCCATGGACGATCA 60.678 50.000 11.44 13.54 0.00 2.92
619 723 1.381851 CTTCTGCTGGGAGGCCTTT 59.618 57.895 6.77 0.00 0.00 3.11
667 771 3.742640 GCATACAACTGAGACCCCTGATC 60.743 52.174 0.00 0.00 0.00 2.92
736 840 4.473520 ACGATCAAGCCCGCCCAG 62.474 66.667 0.00 0.00 0.00 4.45
775 879 1.019278 CGGTTTCAGGCGTGCAGTAT 61.019 55.000 0.35 0.00 0.00 2.12
982 1086 4.511527 ACCATAATGAGACTGCAACTCAG 58.488 43.478 21.82 13.60 45.49 3.35
985 1089 5.045578 AGGTAACCATAATGAGACTGCAACT 60.046 40.000 0.00 0.00 37.17 3.16
991 1095 3.780294 TGGCAGGTAACCATAATGAGACT 59.220 43.478 0.00 0.00 30.29 3.24
997 1101 4.862641 AGACTTGGCAGGTAACCATAAT 57.137 40.909 0.82 0.00 36.96 1.28
1227 1331 2.240493 ACAGAACCACGAGAACTTGG 57.760 50.000 0.00 0.00 40.62 3.61
1258 1362 7.397476 CAGGATGTAAATATAGAGGGCAGTAGA 59.603 40.741 0.00 0.00 0.00 2.59
1316 1444 8.363761 ACTTGATTAAGTAGGTAGCTGTTACT 57.636 34.615 4.27 0.00 45.07 2.24
1323 1451 8.228464 GTCACAAAACTTGATTAAGTAGGTAGC 58.772 37.037 2.94 0.00 46.14 3.58
1327 1455 7.957484 CGATGTCACAAAACTTGATTAAGTAGG 59.043 37.037 2.94 0.00 46.14 3.18
1366 1495 9.418045 CGGTAATGTTCCTCACAATTTATTTTT 57.582 29.630 0.00 0.00 39.50 1.94
1367 1496 7.544217 GCGGTAATGTTCCTCACAATTTATTTT 59.456 33.333 0.00 0.00 39.50 1.82
1371 1500 5.004448 TGCGGTAATGTTCCTCACAATTTA 58.996 37.500 0.00 0.00 39.50 1.40
1452 1581 1.656652 CTGAGAATAGCCCCAACACG 58.343 55.000 0.00 0.00 0.00 4.49
1476 1605 4.948847 TGGTTCATAATCTGACCATCTCG 58.051 43.478 0.00 0.00 33.11 4.04
1488 1617 4.474651 TGTCAGGGAGTCATGGTTCATAAT 59.525 41.667 0.00 0.00 0.00 1.28
1652 1781 9.713740 CTATTGCAGAACTTGAATATCTTTGAC 57.286 33.333 0.00 0.00 0.00 3.18
1691 1820 3.945285 CAGATTAAACCCACGGTAAGCAT 59.055 43.478 0.00 0.00 33.12 3.79
1720 1849 2.235650 CACTGATCAGGAGCTGGAGAAA 59.764 50.000 26.08 0.00 31.51 2.52
1793 1922 9.662947 TCTAACAGCTTCCTTACTTAATAAACC 57.337 33.333 0.00 0.00 0.00 3.27
1855 1984 7.237055 TGGACCTATTCAGATTCAGATGATGAT 59.763 37.037 0.00 0.00 37.89 2.45
1856 1985 6.556116 TGGACCTATTCAGATTCAGATGATGA 59.444 38.462 0.00 0.00 35.62 2.92
1857 1986 6.649973 GTGGACCTATTCAGATTCAGATGATG 59.350 42.308 0.00 0.00 0.00 3.07
1863 1992 4.760530 TGGTGGACCTATTCAGATTCAG 57.239 45.455 0.00 0.00 36.82 3.02
1991 2120 4.099419 GGATGGAACCATTTCGGCTAAAAT 59.901 41.667 7.79 0.00 39.03 1.82
2035 2164 7.420184 AATAAGCAGTGTTGGTTTTAAATGC 57.580 32.000 0.00 0.00 42.03 3.56
2048 2177 6.475402 GCAACAACAAACTAAATAAGCAGTGT 59.525 34.615 0.00 0.00 0.00 3.55
2081 2210 1.335324 GCTACATTCCAATCGGCATGC 60.335 52.381 9.90 9.90 39.34 4.06
2084 2213 0.254462 TGGCTACATTCCAATCGGCA 59.746 50.000 0.00 0.00 0.00 5.69
2116 2247 3.455910 TCTGAAGCTGTACAATATGCCCT 59.544 43.478 0.00 0.00 0.00 5.19
2129 2260 5.277538 GGTTGTAACTGAAACTCTGAAGCTG 60.278 44.000 0.00 0.00 0.00 4.24
2179 2395 9.982651 GCTTACCAAAGTATAGATAGACATTCA 57.017 33.333 0.00 0.00 34.99 2.57
2180 2396 9.130312 CGCTTACCAAAGTATAGATAGACATTC 57.870 37.037 0.00 0.00 34.99 2.67
2181 2397 8.639761 ACGCTTACCAAAGTATAGATAGACATT 58.360 33.333 0.00 0.00 34.99 2.71
2182 2398 8.082852 CACGCTTACCAAAGTATAGATAGACAT 58.917 37.037 0.00 0.00 34.99 3.06
2183 2399 7.423199 CACGCTTACCAAAGTATAGATAGACA 58.577 38.462 0.00 0.00 34.99 3.41
2184 2400 6.362820 GCACGCTTACCAAAGTATAGATAGAC 59.637 42.308 0.00 0.00 34.99 2.59
2185 2401 6.040054 TGCACGCTTACCAAAGTATAGATAGA 59.960 38.462 0.00 0.00 34.99 1.98
2186 2402 6.213677 TGCACGCTTACCAAAGTATAGATAG 58.786 40.000 0.00 0.00 34.99 2.08
2187 2403 6.151663 TGCACGCTTACCAAAGTATAGATA 57.848 37.500 0.00 0.00 34.99 1.98
2188 2404 5.018539 TGCACGCTTACCAAAGTATAGAT 57.981 39.130 0.00 0.00 34.99 1.98
2189 2405 4.459390 TGCACGCTTACCAAAGTATAGA 57.541 40.909 0.00 0.00 34.99 1.98
2190 2406 5.350365 TCTTTGCACGCTTACCAAAGTATAG 59.650 40.000 10.87 0.00 43.49 1.31
2191 2407 5.239351 TCTTTGCACGCTTACCAAAGTATA 58.761 37.500 10.87 0.00 43.49 1.47
2192 2408 4.069304 TCTTTGCACGCTTACCAAAGTAT 58.931 39.130 10.87 0.00 43.49 2.12
2193 2409 3.468770 TCTTTGCACGCTTACCAAAGTA 58.531 40.909 10.87 0.00 43.49 2.24
2194 2410 2.290641 CTCTTTGCACGCTTACCAAAGT 59.709 45.455 10.87 0.00 43.49 2.66
2195 2411 2.918131 GCTCTTTGCACGCTTACCAAAG 60.918 50.000 6.11 6.11 44.07 2.77
2196 2412 1.001815 GCTCTTTGCACGCTTACCAAA 60.002 47.619 0.00 0.00 42.31 3.28
2197 2413 0.591170 GCTCTTTGCACGCTTACCAA 59.409 50.000 0.00 0.00 42.31 3.67
2198 2414 2.244000 GCTCTTTGCACGCTTACCA 58.756 52.632 0.00 0.00 42.31 3.25
2208 2424 3.245990 GGTTGTTGTTTGATGCTCTTTGC 59.754 43.478 0.00 0.00 43.25 3.68
2209 2425 4.431809 TGGTTGTTGTTTGATGCTCTTTG 58.568 39.130 0.00 0.00 0.00 2.77
2210 2426 4.734398 TGGTTGTTGTTTGATGCTCTTT 57.266 36.364 0.00 0.00 0.00 2.52
2211 2427 4.099881 ACATGGTTGTTGTTTGATGCTCTT 59.900 37.500 0.00 0.00 29.55 2.85
2212 2428 3.638160 ACATGGTTGTTGTTTGATGCTCT 59.362 39.130 0.00 0.00 29.55 4.09
2213 2429 3.981211 ACATGGTTGTTGTTTGATGCTC 58.019 40.909 0.00 0.00 29.55 4.26
2214 2430 3.638160 AGACATGGTTGTTGTTTGATGCT 59.362 39.130 0.00 0.00 35.79 3.79
2215 2431 3.737266 CAGACATGGTTGTTGTTTGATGC 59.263 43.478 0.00 0.00 35.79 3.91
2216 2432 4.935702 ACAGACATGGTTGTTGTTTGATG 58.064 39.130 0.00 0.00 35.79 3.07
2217 2433 4.261155 CGACAGACATGGTTGTTGTTTGAT 60.261 41.667 0.00 0.00 35.79 2.57
2218 2434 3.064682 CGACAGACATGGTTGTTGTTTGA 59.935 43.478 0.00 0.00 35.79 2.69
2219 2435 3.064682 TCGACAGACATGGTTGTTGTTTG 59.935 43.478 14.94 0.00 35.79 2.93
2220 2436 3.275143 TCGACAGACATGGTTGTTGTTT 58.725 40.909 14.94 0.00 35.79 2.83
2221 2437 2.872245 CTCGACAGACATGGTTGTTGTT 59.128 45.455 14.94 0.00 35.79 2.83
2222 2438 2.102420 TCTCGACAGACATGGTTGTTGT 59.898 45.455 14.94 4.82 35.79 3.32
2223 2439 2.754472 TCTCGACAGACATGGTTGTTG 58.246 47.619 11.08 11.08 35.79 3.33
2224 2440 3.469008 TTCTCGACAGACATGGTTGTT 57.531 42.857 0.00 0.00 35.79 2.83
2225 2441 3.329386 CATTCTCGACAGACATGGTTGT 58.671 45.455 4.27 4.27 39.32 3.32
2226 2442 2.094894 GCATTCTCGACAGACATGGTTG 59.905 50.000 0.00 0.00 0.00 3.77
2227 2443 2.027745 AGCATTCTCGACAGACATGGTT 60.028 45.455 0.00 0.00 30.35 3.67
2228 2444 1.552337 AGCATTCTCGACAGACATGGT 59.448 47.619 0.00 0.00 0.00 3.55
2229 2445 2.159128 AGAGCATTCTCGACAGACATGG 60.159 50.000 0.00 0.00 44.02 3.66
2230 2446 2.858941 CAGAGCATTCTCGACAGACATG 59.141 50.000 0.00 0.00 44.02 3.21
2231 2447 2.159128 CCAGAGCATTCTCGACAGACAT 60.159 50.000 0.00 0.00 44.02 3.06
2232 2448 1.203287 CCAGAGCATTCTCGACAGACA 59.797 52.381 0.00 0.00 44.02 3.41
2233 2449 1.203523 ACCAGAGCATTCTCGACAGAC 59.796 52.381 0.00 0.00 44.02 3.51
2234 2450 1.203287 CACCAGAGCATTCTCGACAGA 59.797 52.381 0.00 0.00 44.02 3.41
2235 2451 1.638133 CACCAGAGCATTCTCGACAG 58.362 55.000 0.00 0.00 44.02 3.51
2236 2452 0.390340 GCACCAGAGCATTCTCGACA 60.390 55.000 0.00 0.00 44.02 4.35
2237 2453 0.390340 TGCACCAGAGCATTCTCGAC 60.390 55.000 0.00 0.00 44.02 4.20
2238 2454 1.974543 TGCACCAGAGCATTCTCGA 59.025 52.632 0.00 0.00 44.02 4.04
2239 2455 4.604114 TGCACCAGAGCATTCTCG 57.396 55.556 0.00 0.00 44.02 4.04
2246 2462 2.672961 TGTACACTATGCACCAGAGC 57.327 50.000 4.22 0.00 0.00 4.09
2247 2463 5.521906 ACTATGTACACTATGCACCAGAG 57.478 43.478 0.00 0.00 0.00 3.35
2248 2464 5.660460 CAACTATGTACACTATGCACCAGA 58.340 41.667 0.00 0.00 0.00 3.86
2249 2465 4.271049 GCAACTATGTACACTATGCACCAG 59.729 45.833 15.75 0.00 32.80 4.00
2250 2466 4.188462 GCAACTATGTACACTATGCACCA 58.812 43.478 15.75 0.00 32.80 4.17
2251 2467 3.560068 GGCAACTATGTACACTATGCACC 59.440 47.826 19.87 6.10 34.14 5.01
2252 2468 3.245284 CGGCAACTATGTACACTATGCAC 59.755 47.826 19.87 11.87 34.14 4.57
2253 2469 3.131400 TCGGCAACTATGTACACTATGCA 59.869 43.478 19.87 0.00 34.14 3.96
2254 2470 3.489785 GTCGGCAACTATGTACACTATGC 59.510 47.826 13.44 13.44 0.00 3.14
2255 2471 4.933330 AGTCGGCAACTATGTACACTATG 58.067 43.478 0.00 0.00 36.07 2.23
2256 2472 5.451520 GGAAGTCGGCAACTATGTACACTAT 60.452 44.000 0.00 0.00 37.17 2.12
2257 2473 4.142315 GGAAGTCGGCAACTATGTACACTA 60.142 45.833 0.00 0.00 37.17 2.74
2258 2474 3.368116 GGAAGTCGGCAACTATGTACACT 60.368 47.826 0.00 0.00 37.17 3.55
2259 2475 2.928116 GGAAGTCGGCAACTATGTACAC 59.072 50.000 0.00 0.00 37.17 2.90
2260 2476 2.829720 AGGAAGTCGGCAACTATGTACA 59.170 45.455 0.00 0.00 37.17 2.90
2261 2477 3.521947 AGGAAGTCGGCAACTATGTAC 57.478 47.619 0.00 0.00 37.17 2.90
2262 2478 4.546829 AAAGGAAGTCGGCAACTATGTA 57.453 40.909 0.00 0.00 37.17 2.29
2263 2479 3.418684 AAAGGAAGTCGGCAACTATGT 57.581 42.857 0.00 0.00 37.17 2.29
2264 2480 4.935808 ACTTAAAGGAAGTCGGCAACTATG 59.064 41.667 0.00 0.00 45.81 2.23
2265 2481 5.161943 ACTTAAAGGAAGTCGGCAACTAT 57.838 39.130 0.00 0.00 45.81 2.12
2266 2482 4.612264 ACTTAAAGGAAGTCGGCAACTA 57.388 40.909 0.00 0.00 45.81 2.24
2267 2483 3.487120 ACTTAAAGGAAGTCGGCAACT 57.513 42.857 0.00 0.00 45.81 3.16
2268 2484 5.391629 CCATTACTTAAAGGAAGTCGGCAAC 60.392 44.000 0.00 0.00 45.81 4.17
2269 2485 4.698304 CCATTACTTAAAGGAAGTCGGCAA 59.302 41.667 0.00 0.00 45.81 4.52
2270 2486 4.020039 TCCATTACTTAAAGGAAGTCGGCA 60.020 41.667 0.00 0.00 45.81 5.69
2271 2487 4.510571 TCCATTACTTAAAGGAAGTCGGC 58.489 43.478 0.00 0.00 45.81 5.54
2272 2488 6.663944 CTTCCATTACTTAAAGGAAGTCGG 57.336 41.667 18.71 0.38 45.81 4.79
2283 2499 9.667107 CACCAGAAATAAGTCTTCCATTACTTA 57.333 33.333 0.00 0.00 41.18 2.24
2294 2510 9.712305 GCATATATACACACCAGAAATAAGTCT 57.288 33.333 0.00 0.00 0.00 3.24
2354 2570 2.084546 CCCTAACTGCAAGCCTAACAC 58.915 52.381 0.00 0.00 37.60 3.32
2492 2708 5.449304 CCGACAAAGGTTGAACTTGATTAC 58.551 41.667 4.58 0.00 0.00 1.89
2497 2720 2.294074 TCCCGACAAAGGTTGAACTTG 58.706 47.619 0.00 0.00 0.00 3.16
2513 2736 2.289565 GCAGTATCCTTTCCTTTCCCG 58.710 52.381 0.00 0.00 0.00 5.14
2515 2738 3.691609 CACTGCAGTATCCTTTCCTTTCC 59.308 47.826 21.20 0.00 0.00 3.13
2516 2739 4.154918 CACACTGCAGTATCCTTTCCTTTC 59.845 45.833 21.20 0.00 0.00 2.62
2517 2740 4.074970 CACACTGCAGTATCCTTTCCTTT 58.925 43.478 21.20 0.00 0.00 3.11
2518 2741 3.073062 ACACACTGCAGTATCCTTTCCTT 59.927 43.478 21.20 0.00 0.00 3.36
2519 2742 2.639839 ACACACTGCAGTATCCTTTCCT 59.360 45.455 21.20 0.00 0.00 3.36
2530 2753 5.120363 GCTATGATATGATGACACACTGCAG 59.880 44.000 13.48 13.48 0.00 4.41
2533 2756 6.402226 GCATGCTATGATATGATGACACACTG 60.402 42.308 11.37 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.