Multiple sequence alignment - TraesCS2D01G206800

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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 TraesCS2D01G206800 chr2D 100.000 2540 0 0 1 2540 160212606 160210067 0.000000e+00 4691.0
1 TraesCS2D01G206800 chr2D 76.696 339 53 17 1143 1459 377122188 377122522 5.620000e-37 165.0
2 TraesCS2D01G206800 chr2B 92.781 1690 111 8 673 2355 216965839 216964154 0.000000e+00 2435.0
3 TraesCS2D01G206800 chr2B 85.481 675 57 16 1 640 216966510 216965842 0.000000e+00 665.0
4 TraesCS2D01G206800 chr2B 79.310 377 68 7 1775 2149 42935490 42935858 3.240000e-64 255.0
5 TraesCS2D01G206800 chr2B 90.411 146 10 2 2399 2540 216964148 216964003 3.340000e-44 189.0
6 TraesCS2D01G206800 chr2B 76.786 336 52 17 1143 1456 448695069 448695400 5.620000e-37 165.0
7 TraesCS2D01G206800 chr2A 90.056 1418 78 25 469 1869 171608789 171610160 0.000000e+00 1779.0
8 TraesCS2D01G206800 chr2A 78.806 335 41 12 2012 2346 171610187 171610491 5.540000e-47 198.0
9 TraesCS2D01G206800 chr2A 76.833 341 49 21 1143 1459 511076399 511076733 5.620000e-37 165.0
10 TraesCS2D01G206800 chr5A 84.533 375 54 3 1774 2147 537026593 537026222 3.990000e-98 368.0
11 TraesCS2D01G206800 chr5A 94.545 55 1 1 2342 2394 686412854 686412908 1.620000e-12 84.2
12 TraesCS2D01G206800 chr5A 89.394 66 4 2 2345 2407 564603586 564603521 2.090000e-11 80.5
13 TraesCS2D01G206800 chr3B 81.818 407 70 3 1775 2180 526193683 526193280 3.130000e-89 339.0
14 TraesCS2D01G206800 chr3B 90.323 62 2 3 2347 2404 16259832 16259893 7.530000e-11 78.7
15 TraesCS2D01G206800 chr6A 81.720 372 64 2 1775 2146 603605206 603604839 8.830000e-80 307.0
16 TraesCS2D01G206800 chr7A 83.810 315 47 3 1777 2091 521564883 521564573 1.910000e-76 296.0
17 TraesCS2D01G206800 chr5D 79.301 372 74 2 1775 2146 371678046 371678414 9.020000e-65 257.0
18 TraesCS2D01G206800 chr5D 76.959 217 45 4 1775 1990 434424343 434424131 4.440000e-23 119.0
19 TraesCS2D01G206800 chr6B 77.070 314 63 8 1775 2086 633728594 633728288 3.360000e-39 172.0
20 TraesCS2D01G206800 chr5B 77.612 201 39 4 1775 1973 441573522 441573718 1.600000e-22 117.0
21 TraesCS2D01G206800 chr5B 91.525 59 2 3 2350 2406 466369715 466369658 7.530000e-11 78.7
22 TraesCS2D01G206800 chr7D 94.643 56 0 2 2342 2394 592857566 592857511 1.620000e-12 84.2
23 TraesCS2D01G206800 chr3D 93.103 58 1 3 2346 2400 603946212 603946269 5.820000e-12 82.4
24 TraesCS2D01G206800 chr4D 92.982 57 1 3 2346 2399 72678724 72678668 2.090000e-11 80.5
25 TraesCS2D01G206800 chr7B 89.231 65 2 4 2350 2410 273296552 273296615 2.710000e-10 76.8
26 TraesCS2D01G206800 chr4B 89.231 65 2 4 2350 2410 538057179 538057116 2.710000e-10 76.8
27 TraesCS2D01G206800 chr1D 90.741 54 5 0 300 353 481390974 481390921 3.510000e-09 73.1


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 TraesCS2D01G206800 chr2D 160210067 160212606 2539 True 4691.000000 4691 100.000000 1 2540 1 chr2D.!!$R1 2539
1 TraesCS2D01G206800 chr2B 216964003 216966510 2507 True 1096.333333 2435 89.557667 1 2540 3 chr2B.!!$R1 2539
2 TraesCS2D01G206800 chr2A 171608789 171610491 1702 False 988.500000 1779 84.431000 469 2346 2 chr2A.!!$F2 1877

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
256 269 0.105964 TTGTGTGGAGAGGGTGTTCG 59.894 55.0 0.00 0.00 0.0 3.95 F
744 782 0.109272 TTGGAAGAGACAGCTACGCG 60.109 55.0 3.53 3.53 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1497 1556 0.693049 AGGGAATGAGAGCACCGTTT 59.307 50.0 0.0 0.0 0.00 3.60 R
2286 2350 0.881796 GGTGCCTGCTTACCAAGAAC 59.118 55.0 0.0 0.0 36.94 3.01 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
38 39 8.854614 TTTGGTTCTTTCAAAAGATGGAAAAA 57.145 26.923 6.05 2.16 43.92 1.94
125 126 9.846248 GATCTTAGCTTCAAAACATACAACAAT 57.154 29.630 0.00 0.00 0.00 2.71
131 132 8.603181 AGCTTCAAAACATACAACAATTTTGAC 58.397 29.630 9.79 2.02 45.74 3.18
155 156 3.726291 ATTTGTACACAACCCAGTTGC 57.274 42.857 7.36 0.00 46.20 4.17
173 174 1.340017 TGCAGATCAACTGGTAAGCCC 60.340 52.381 0.00 0.00 45.82 5.19
174 175 1.656652 CAGATCAACTGGTAAGCCCG 58.343 55.000 0.00 0.00 42.39 6.13
178 179 3.253838 AACTGGTAAGCCCGCCCA 61.254 61.111 0.00 0.00 35.15 5.36
197 198 2.158696 CCATCCTTCATTCAGGAGGTCC 60.159 54.545 1.07 0.00 46.60 4.46
200 201 1.589414 CTTCATTCAGGAGGTCCCCT 58.411 55.000 0.00 0.00 36.90 4.79
218 219 0.962356 CTGATTGAGCCACCACCCAC 60.962 60.000 0.00 0.00 0.00 4.61
219 220 1.074775 GATTGAGCCACCACCCACA 59.925 57.895 0.00 0.00 0.00 4.17
225 226 2.113139 CCACCACCCACACACCTC 59.887 66.667 0.00 0.00 0.00 3.85
228 229 1.692749 ACCACCCACACACCTCTGT 60.693 57.895 0.00 0.00 0.00 3.41
250 263 5.476599 TGTCATAATTTTTGTGTGGAGAGGG 59.523 40.000 0.00 0.00 0.00 4.30
256 269 0.105964 TTGTGTGGAGAGGGTGTTCG 59.894 55.000 0.00 0.00 0.00 3.95
263 276 1.550976 GGAGAGGGTGTTCGACAAGAT 59.449 52.381 0.00 0.00 0.00 2.40
275 288 2.299013 TCGACAAGATGCTGGTTACAGT 59.701 45.455 0.00 0.00 46.62 3.55
277 290 2.744202 GACAAGATGCTGGTTACAGTGG 59.256 50.000 0.00 0.00 46.62 4.00
280 293 1.066858 AGATGCTGGTTACAGTGGACG 60.067 52.381 0.00 0.00 46.62 4.79
296 309 3.057019 TGGACGATTCTGAAAACTGACG 58.943 45.455 0.00 0.00 0.00 4.35
305 318 1.864711 TGAAAACTGACGTAGCAGCAC 59.135 47.619 4.28 0.00 39.51 4.40
311 324 1.004918 GACGTAGCAGCACCCTTGT 60.005 57.895 0.00 0.00 0.00 3.16
326 339 2.513065 CTTGTGCCGTGATTCGTGCC 62.513 60.000 0.00 0.00 37.94 5.01
327 340 3.047280 GTGCCGTGATTCGTGCCA 61.047 61.111 0.00 0.00 37.94 4.92
334 347 2.061773 CGTGATTCGTGCCAGGATATC 58.938 52.381 0.00 0.00 34.52 1.63
338 351 2.218953 TTCGTGCCAGGATATCGAAC 57.781 50.000 0.00 0.00 36.00 3.95
350 363 4.804139 AGGATATCGAACGACAATCAACAC 59.196 41.667 17.04 5.92 0.00 3.32
360 373 1.133982 ACAATCAACACGTTTGCTGCA 59.866 42.857 0.00 0.00 0.00 4.41
367 380 4.996113 CGTTTGCTGCAAGAACGT 57.004 50.000 23.99 0.00 40.71 3.99
379 392 3.098636 GCAAGAACGTTATCATTTCCGC 58.901 45.455 0.00 0.00 0.00 5.54
387 400 4.565564 ACGTTATCATTTCCGCAGTCTAAC 59.434 41.667 0.00 0.00 0.00 2.34
392 405 3.192001 TCATTTCCGCAGTCTAACGTACT 59.808 43.478 0.00 0.00 0.00 2.73
393 406 2.624316 TTCCGCAGTCTAACGTACTG 57.376 50.000 11.77 11.77 45.80 2.74
394 407 0.806868 TCCGCAGTCTAACGTACTGG 59.193 55.000 16.55 8.22 43.71 4.00
395 408 3.324170 CGCAGTCTAACGTACTGGG 57.676 57.895 16.54 16.54 46.92 4.45
397 410 2.563471 GCAGTCTAACGTACTGGGAG 57.437 55.000 16.55 0.00 43.71 4.30
398 411 1.817447 GCAGTCTAACGTACTGGGAGT 59.183 52.381 16.55 0.00 43.71 3.85
399 412 3.012518 GCAGTCTAACGTACTGGGAGTA 58.987 50.000 16.55 0.00 43.71 2.59
400 413 3.181502 GCAGTCTAACGTACTGGGAGTAC 60.182 52.174 16.55 4.13 45.71 2.73
424 458 6.814644 ACAATATTTGAATGCACATGGTTCAG 59.185 34.615 0.00 0.00 33.82 3.02
461 495 9.719355 GTGATAAAATACCCTGTCCAAAAATTT 57.281 29.630 0.00 0.00 0.00 1.82
598 635 6.790232 AATGGAAAGTTGGAACTCTTGAAA 57.210 33.333 0.00 0.00 38.57 2.69
599 636 6.983906 ATGGAAAGTTGGAACTCTTGAAAT 57.016 33.333 0.00 0.00 38.57 2.17
641 678 8.532819 AGTTCGATAATACTCAGAGTCCTTTTT 58.467 33.333 6.27 0.00 0.00 1.94
671 708 7.255173 GCGAGTTCTCCTAGATAATACTCACAA 60.255 40.741 0.00 0.00 31.24 3.33
742 780 2.724977 TGTTGGAAGAGACAGCTACG 57.275 50.000 0.00 0.00 0.00 3.51
744 782 0.109272 TTGGAAGAGACAGCTACGCG 60.109 55.000 3.53 3.53 0.00 6.01
848 887 6.894339 TCCTTGTTCTTGTTCCTATTTTCC 57.106 37.500 0.00 0.00 0.00 3.13
857 896 8.533569 TCTTGTTCCTATTTTCCTTCTTGTTT 57.466 30.769 0.00 0.00 0.00 2.83
946 989 2.029290 TCACTGGGCGAGTTCTTCTTAC 60.029 50.000 0.00 0.00 29.75 2.34
988 1031 1.079127 ACCCGACATTTCCGCTCAG 60.079 57.895 0.00 0.00 0.00 3.35
1088 1147 4.996434 GCCGATGCCTCCGATGGG 62.996 72.222 0.00 0.00 0.00 4.00
1089 1148 4.320456 CCGATGCCTCCGATGGGG 62.320 72.222 0.00 0.00 37.02 4.96
1358 1417 2.819595 CCACGCGGTGAAGATGGG 60.820 66.667 12.47 0.00 35.23 4.00
1553 1613 6.322201 CCCAAACCTTAAGCTGACATGATTAT 59.678 38.462 0.00 0.00 0.00 1.28
1634 1694 5.928601 CGGAGTACGTTCAAGAGAATTAC 57.071 43.478 0.00 0.00 35.92 1.89
1671 1731 0.905337 ACTCCTCCTCCTTGGTTCGG 60.905 60.000 0.00 0.00 37.07 4.30
1707 1767 4.863131 AGAGTTATAAGAAACGCGAACCTG 59.137 41.667 15.93 0.00 34.75 4.00
1773 1833 1.720694 GCGAAGGTCTCTCTCCCTCG 61.721 65.000 0.00 0.00 0.00 4.63
1836 1896 1.301423 TTTCGAGAAACCCGGTGTTG 58.699 50.000 8.79 0.00 37.23 3.33
1842 1902 0.108019 GAAACCCGGTGTTGAGGTCT 59.892 55.000 8.79 0.00 37.23 3.85
1860 1920 0.321671 CTGCCTTCCGGAACAAGAGA 59.678 55.000 14.35 0.00 0.00 3.10
1870 1930 2.682836 GGAACAAGAGACAGAGAGCAC 58.317 52.381 0.00 0.00 0.00 4.40
1871 1931 2.611722 GGAACAAGAGACAGAGAGCACC 60.612 54.545 0.00 0.00 0.00 5.01
1883 1943 0.685097 AGAGCACCGCCAACTTTCTA 59.315 50.000 0.00 0.00 0.00 2.10
1893 1953 4.690280 CCGCCAACTTTCTAAAAATGCATT 59.310 37.500 5.99 5.99 0.00 3.56
1913 1973 3.044235 TGACAACTGCGAGATCAACAT 57.956 42.857 0.00 0.00 0.00 2.71
1914 1974 4.186856 TGACAACTGCGAGATCAACATA 57.813 40.909 0.00 0.00 0.00 2.29
1949 2009 6.204359 CAACTTATGCATTATCTTGTGGAGC 58.796 40.000 3.54 0.00 0.00 4.70
1954 2014 3.379057 TGCATTATCTTGTGGAGCACATG 59.621 43.478 0.00 0.00 44.16 3.21
1991 2052 7.867403 CTGGAAATCAGTAAGCTTTGCTTTTAA 59.133 33.333 3.20 0.00 41.13 1.52
2107 2168 8.153550 ACAAAACTATGTTTGGCCAAAATGATA 58.846 29.630 31.92 23.49 41.82 2.15
2111 2172 5.999205 ATGTTTGGCCAAAATGATAGACA 57.001 34.783 31.92 22.98 31.33 3.41
2163 2224 8.028938 TCTTAGAAAATAAAAGCTGTGATTGCC 58.971 33.333 0.00 0.00 0.00 4.52
2190 2251 4.906618 ACAAGATTTGATACCCGTTCAGT 58.093 39.130 0.00 0.00 0.00 3.41
2193 2254 4.504858 AGATTTGATACCCGTTCAGTCAC 58.495 43.478 0.00 0.00 0.00 3.67
2201 2262 2.022129 CGTTCAGTCACTGTCCGCC 61.022 63.158 4.28 0.00 32.61 6.13
2230 2294 1.227639 GCTGACGTATAGAGGCTCGA 58.772 55.000 9.22 3.87 0.00 4.04
2306 2370 0.605319 TTCTTGGTAAGCAGGCACCG 60.605 55.000 0.00 0.00 37.66 4.94
2309 2373 3.712907 GGTAAGCAGGCACCGGGA 61.713 66.667 6.32 0.00 0.00 5.14
2346 2410 2.472695 ATTGCTCCACTGCGAGTTAA 57.527 45.000 0.00 0.00 35.36 2.01
2348 2412 1.795768 TGCTCCACTGCGAGTTAAAG 58.204 50.000 0.00 0.00 35.36 1.85
2349 2413 1.070134 TGCTCCACTGCGAGTTAAAGT 59.930 47.619 0.00 0.00 35.36 2.66
2355 2419 5.464168 TCCACTGCGAGTTAAAGTTAGTAC 58.536 41.667 0.00 0.00 0.00 2.73
2357 2421 5.693104 CCACTGCGAGTTAAAGTTAGTACAA 59.307 40.000 0.00 0.00 0.00 2.41
2358 2422 6.367969 CCACTGCGAGTTAAAGTTAGTACAAT 59.632 38.462 0.00 0.00 0.00 2.71
2359 2423 7.095355 CCACTGCGAGTTAAAGTTAGTACAATT 60.095 37.037 0.00 0.00 0.00 2.32
2360 2424 7.740346 CACTGCGAGTTAAAGTTAGTACAATTG 59.260 37.037 3.24 3.24 0.00 2.32
2361 2425 7.095355 ACTGCGAGTTAAAGTTAGTACAATTGG 60.095 37.037 10.83 0.00 0.00 3.16
2362 2426 6.148150 TGCGAGTTAAAGTTAGTACAATTGGG 59.852 38.462 10.83 0.00 0.00 4.12
2363 2427 6.148315 GCGAGTTAAAGTTAGTACAATTGGGT 59.852 38.462 10.83 0.00 0.00 4.51
2364 2428 7.622880 GCGAGTTAAAGTTAGTACAATTGGGTC 60.623 40.741 10.83 0.00 0.00 4.46
2365 2429 7.385752 CGAGTTAAAGTTAGTACAATTGGGTCA 59.614 37.037 10.83 0.00 0.00 4.02
2366 2430 9.227777 GAGTTAAAGTTAGTACAATTGGGTCAT 57.772 33.333 10.83 0.00 0.00 3.06
2367 2431 9.227777 AGTTAAAGTTAGTACAATTGGGTCATC 57.772 33.333 10.83 0.00 0.00 2.92
2368 2432 9.227777 GTTAAAGTTAGTACAATTGGGTCATCT 57.772 33.333 10.83 0.00 0.00 2.90
2371 2435 9.975218 AAAGTTAGTACAATTGGGTCATCTATT 57.025 29.630 10.83 0.00 0.00 1.73
2372 2436 9.975218 AAGTTAGTACAATTGGGTCATCTATTT 57.025 29.630 10.83 0.00 0.00 1.40
2373 2437 9.975218 AGTTAGTACAATTGGGTCATCTATTTT 57.025 29.630 10.83 0.00 0.00 1.82
2375 2439 7.645058 AGTACAATTGGGTCATCTATTTTGG 57.355 36.000 10.83 0.00 0.00 3.28
2376 2440 7.410174 AGTACAATTGGGTCATCTATTTTGGA 58.590 34.615 10.83 0.00 0.00 3.53
2377 2441 7.893302 AGTACAATTGGGTCATCTATTTTGGAA 59.107 33.333 10.83 0.00 0.00 3.53
2378 2442 6.935167 ACAATTGGGTCATCTATTTTGGAAC 58.065 36.000 10.83 0.00 0.00 3.62
2379 2443 5.835113 ATTGGGTCATCTATTTTGGAACG 57.165 39.130 0.00 0.00 0.00 3.95
2380 2444 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2381 2445 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2382 2446 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2383 2447 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2384 2448 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2385 2449 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2386 2450 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2387 2451 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2388 2452 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2389 2453 2.845363 TTTTGGAACGGAGGGAGTAC 57.155 50.000 0.00 0.00 0.00 2.73
2390 2454 1.719529 TTTGGAACGGAGGGAGTACA 58.280 50.000 0.00 0.00 0.00 2.90
2391 2455 1.946984 TTGGAACGGAGGGAGTACAT 58.053 50.000 0.00 0.00 0.00 2.29
2392 2456 1.481871 TGGAACGGAGGGAGTACATC 58.518 55.000 0.00 0.00 0.00 3.06
2393 2457 1.006758 TGGAACGGAGGGAGTACATCT 59.993 52.381 0.00 0.00 0.00 2.90
2394 2458 2.242965 TGGAACGGAGGGAGTACATCTA 59.757 50.000 0.00 0.00 0.00 1.98
2395 2459 2.885894 GGAACGGAGGGAGTACATCTAG 59.114 54.545 0.00 0.00 0.00 2.43
2396 2460 3.434739 GGAACGGAGGGAGTACATCTAGA 60.435 52.174 0.00 0.00 0.00 2.43
2397 2461 3.211718 ACGGAGGGAGTACATCTAGAC 57.788 52.381 0.00 0.00 0.00 2.59
2403 2467 6.127793 GGAGGGAGTACATCTAGACTTACAA 58.872 44.000 12.84 0.00 0.00 2.41
2408 2472 6.752815 GGAGTACATCTAGACTTACAAACTGC 59.247 42.308 12.84 4.86 0.00 4.40
2416 2480 8.067751 TCTAGACTTACAAACTGCATCATAGT 57.932 34.615 0.00 0.00 0.00 2.12
2419 2483 8.396272 AGACTTACAAACTGCATCATAGTTTT 57.604 30.769 0.00 0.00 43.71 2.43
2422 2486 8.076178 ACTTACAAACTGCATCATAGTTTTGTC 58.924 33.333 1.03 0.00 43.71 3.18
2476 2540 6.600822 AGAGTTCATCGAATTTTCCACATGAT 59.399 34.615 0.00 0.00 0.00 2.45
2519 2587 9.638239 ATTGTTACAAATTCGCTGATTTAACAT 57.362 25.926 0.66 2.15 32.15 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 9.636965 CGAAATTTTTCCATCTTTTGAAAGAAC 57.363 29.630 9.96 0.00 39.80 3.01
18 19 9.593134 TCGAAATTTTTCCATCTTTTGAAAGAA 57.407 25.926 9.96 0.00 39.80 2.52
21 22 9.980780 GTTTCGAAATTTTTCCATCTTTTGAAA 57.019 25.926 14.69 0.00 38.07 2.69
81 82 9.014533 GCTAAGATCTTTTGAATCCGATTTTTC 57.985 33.333 14.36 0.00 0.00 2.29
88 89 6.668541 TGAAGCTAAGATCTTTTGAATCCG 57.331 37.500 14.36 0.00 0.00 4.18
99 100 9.846248 ATTGTTGTATGTTTTGAAGCTAAGATC 57.154 29.630 0.00 0.00 0.00 2.75
125 126 6.377429 TGGGTTGTGTACAAATACAGTCAAAA 59.623 34.615 0.00 0.00 42.06 2.44
131 132 5.757886 CAACTGGGTTGTGTACAAATACAG 58.242 41.667 16.34 16.34 42.06 2.74
139 140 1.961793 TCTGCAACTGGGTTGTGTAC 58.038 50.000 11.27 0.00 44.40 2.90
141 142 1.133823 TGATCTGCAACTGGGTTGTGT 60.134 47.619 11.27 0.00 44.40 3.72
155 156 1.656652 CGGGCTTACCAGTTGATCTG 58.343 55.000 0.00 0.00 43.27 2.90
173 174 0.181114 TCCTGAATGAAGGATGGGCG 59.819 55.000 0.00 0.00 41.60 6.13
174 175 1.478288 CCTCCTGAATGAAGGATGGGC 60.478 57.143 0.00 0.00 45.41 5.36
178 179 2.131023 GGGACCTCCTGAATGAAGGAT 58.869 52.381 0.00 0.00 45.41 3.24
197 198 1.379044 GGTGGTGGCTCAATCAGGG 60.379 63.158 0.00 0.00 0.00 4.45
200 201 1.074775 GTGGGTGGTGGCTCAATCA 59.925 57.895 0.00 0.00 0.00 2.57
218 219 6.638063 CACACAAAAATTATGACAGAGGTGTG 59.362 38.462 0.00 0.00 43.98 3.82
219 220 6.239008 CCACACAAAAATTATGACAGAGGTGT 60.239 38.462 0.00 0.00 40.71 4.16
225 226 6.349611 CCCTCTCCACACAAAAATTATGACAG 60.350 42.308 0.00 0.00 0.00 3.51
228 229 5.476599 CACCCTCTCCACACAAAAATTATGA 59.523 40.000 0.00 0.00 0.00 2.15
250 263 1.512926 ACCAGCATCTTGTCGAACAC 58.487 50.000 0.00 0.00 0.00 3.32
256 269 2.744202 CCACTGTAACCAGCATCTTGTC 59.256 50.000 0.00 0.00 42.81 3.18
263 276 0.973632 ATCGTCCACTGTAACCAGCA 59.026 50.000 0.00 0.00 42.81 4.41
275 288 3.057019 CGTCAGTTTTCAGAATCGTCCA 58.943 45.455 0.00 0.00 0.00 4.02
277 290 4.201504 GCTACGTCAGTTTTCAGAATCGTC 60.202 45.833 0.00 0.00 0.00 4.20
280 293 4.434857 GCTGCTACGTCAGTTTTCAGAATC 60.435 45.833 6.18 0.00 36.49 2.52
305 318 3.177600 CGAATCACGGCACAAGGG 58.822 61.111 0.00 0.00 38.46 3.95
316 329 1.960689 TCGATATCCTGGCACGAATCA 59.039 47.619 0.00 0.00 0.00 2.57
326 339 4.803613 TGTTGATTGTCGTTCGATATCCTG 59.196 41.667 13.42 0.00 0.00 3.86
327 340 4.804139 GTGTTGATTGTCGTTCGATATCCT 59.196 41.667 13.42 0.00 0.00 3.24
334 347 2.638628 AACGTGTTGATTGTCGTTCG 57.361 45.000 0.00 0.00 41.53 3.95
338 351 2.036217 CAGCAAACGTGTTGATTGTCG 58.964 47.619 12.62 0.00 38.17 4.35
360 373 4.000988 ACTGCGGAAATGATAACGTTCTT 58.999 39.130 2.82 0.00 0.00 2.52
366 379 4.565564 ACGTTAGACTGCGGAAATGATAAC 59.434 41.667 0.00 0.00 0.00 1.89
367 380 4.751060 ACGTTAGACTGCGGAAATGATAA 58.249 39.130 0.00 0.00 0.00 1.75
379 392 4.612932 GTACTCCCAGTACGTTAGACTG 57.387 50.000 9.54 9.54 41.27 3.51
392 405 5.948758 TGTGCATTCAAATATTGTACTCCCA 59.051 36.000 0.00 0.00 0.00 4.37
393 406 6.449635 TGTGCATTCAAATATTGTACTCCC 57.550 37.500 0.00 0.00 0.00 4.30
394 407 6.919662 CCATGTGCATTCAAATATTGTACTCC 59.080 38.462 0.00 0.00 0.00 3.85
395 408 7.483307 ACCATGTGCATTCAAATATTGTACTC 58.517 34.615 0.00 0.00 0.00 2.59
396 409 7.408756 ACCATGTGCATTCAAATATTGTACT 57.591 32.000 0.00 0.00 0.00 2.73
397 410 7.758980 TGAACCATGTGCATTCAAATATTGTAC 59.241 33.333 0.00 0.00 29.56 2.90
398 411 7.834803 TGAACCATGTGCATTCAAATATTGTA 58.165 30.769 0.00 0.00 29.56 2.41
399 412 6.699366 TGAACCATGTGCATTCAAATATTGT 58.301 32.000 0.00 0.00 29.56 2.71
400 413 7.036829 TCTGAACCATGTGCATTCAAATATTG 58.963 34.615 1.67 0.00 32.19 1.90
407 441 5.008980 TGTATTCTGAACCATGTGCATTCA 58.991 37.500 0.00 0.00 0.00 2.57
412 446 5.643777 ACTAGTTGTATTCTGAACCATGTGC 59.356 40.000 0.00 0.00 0.00 4.57
447 481 9.807649 CTATTATCTTGGAAATTTTTGGACAGG 57.192 33.333 0.00 0.00 0.00 4.00
461 495 8.573885 CAGACGTGGTATTACTATTATCTTGGA 58.426 37.037 0.00 0.00 0.00 3.53
482 516 3.854809 GCACTAAAGCTACTTCTCAGACG 59.145 47.826 0.00 0.00 0.00 4.18
575 610 6.790232 TTTCAAGAGTTCCAACTTTCCATT 57.210 33.333 0.00 0.00 39.88 3.16
598 635 6.590234 TCGAACTGATGCCATGTAGTATAT 57.410 37.500 0.00 0.00 0.00 0.86
599 636 6.590234 ATCGAACTGATGCCATGTAGTATA 57.410 37.500 0.00 0.00 35.45 1.47
641 678 8.921353 AGTATTATCTAGGAGAACTCGCTAAA 57.079 34.615 0.00 0.00 0.00 1.85
644 681 6.428771 GTGAGTATTATCTAGGAGAACTCGCT 59.571 42.308 14.18 0.00 39.01 4.93
645 682 6.205076 TGTGAGTATTATCTAGGAGAACTCGC 59.795 42.308 14.41 14.41 41.21 5.03
646 683 7.731882 TGTGAGTATTATCTAGGAGAACTCG 57.268 40.000 0.00 0.00 35.71 4.18
648 685 9.084533 GGATTGTGAGTATTATCTAGGAGAACT 57.915 37.037 0.00 0.00 0.00 3.01
649 686 8.024285 CGGATTGTGAGTATTATCTAGGAGAAC 58.976 40.741 0.00 0.00 0.00 3.01
650 687 7.724506 ACGGATTGTGAGTATTATCTAGGAGAA 59.275 37.037 0.00 0.00 0.00 2.87
651 688 7.232188 ACGGATTGTGAGTATTATCTAGGAGA 58.768 38.462 0.00 0.00 0.00 3.71
652 689 7.455641 ACGGATTGTGAGTATTATCTAGGAG 57.544 40.000 0.00 0.00 0.00 3.69
653 690 7.610692 CCTACGGATTGTGAGTATTATCTAGGA 59.389 40.741 0.00 0.00 0.00 2.94
654 691 7.393796 ACCTACGGATTGTGAGTATTATCTAGG 59.606 40.741 0.00 0.00 0.00 3.02
655 692 8.338072 ACCTACGGATTGTGAGTATTATCTAG 57.662 38.462 0.00 0.00 0.00 2.43
656 693 7.940688 TGACCTACGGATTGTGAGTATTATCTA 59.059 37.037 0.00 0.00 0.00 1.98
663 700 5.670792 AATTGACCTACGGATTGTGAGTA 57.329 39.130 0.00 0.00 0.00 2.59
671 708 4.881850 CAGCCTTTAAATTGACCTACGGAT 59.118 41.667 0.00 0.00 0.00 4.18
685 722 6.990349 CGATTCTTCCTATAACCAGCCTTTAA 59.010 38.462 0.00 0.00 0.00 1.52
759 797 3.749665 AGCAGATAGAGGATGTCTTGC 57.250 47.619 0.00 0.00 36.64 4.01
946 989 2.957006 ACGAGTTAGTGGGCAGTATAGG 59.043 50.000 0.00 0.00 0.00 2.57
982 1025 1.021390 ATTTTCCGGTGAGCTGAGCG 61.021 55.000 18.09 18.09 36.60 5.03
988 1031 1.322538 ATGGCCATTTTCCGGTGAGC 61.323 55.000 14.09 0.00 0.00 4.26
1025 1075 4.962836 CCATCGGAGGCATGCCCC 62.963 72.222 33.14 29.06 36.58 5.80
1078 1137 4.320456 CATCGGCCCCATCGGAGG 62.320 72.222 0.00 0.00 0.00 4.30
1079 1138 4.320456 CCATCGGCCCCATCGGAG 62.320 72.222 0.00 0.00 0.00 4.63
1082 1141 4.626081 GACCCATCGGCCCCATCG 62.626 72.222 0.00 0.00 0.00 3.84
1083 1142 4.271016 GGACCCATCGGCCCCATC 62.271 72.222 0.00 0.00 0.00 3.51
1358 1417 3.031417 ATCACCAGGTACGCCAGCC 62.031 63.158 0.00 0.00 37.19 4.85
1497 1556 0.693049 AGGGAATGAGAGCACCGTTT 59.307 50.000 0.00 0.00 0.00 3.60
1553 1613 8.185505 GGTCGTAATAAAACAATTTCCAGCATA 58.814 33.333 0.00 0.00 0.00 3.14
1575 1635 1.037493 TTCAGTATCCATCCGGGTCG 58.963 55.000 0.00 0.00 38.11 4.79
1707 1767 8.669394 AATTTAAATTTGAGAATTCCGTCGTC 57.331 30.769 7.64 0.00 34.44 4.20
1734 1794 1.404047 CGTGGGGTCCAATTCATTTGC 60.404 52.381 0.00 0.00 34.18 3.68
1745 1805 4.754667 GACCTTCGCGTGGGGTCC 62.755 72.222 25.30 14.28 42.45 4.46
1761 1821 2.370349 GACAATCACGAGGGAGAGAGA 58.630 52.381 0.00 0.00 0.00 3.10
1773 1833 1.482593 ACCCTCATCCTCGACAATCAC 59.517 52.381 0.00 0.00 0.00 3.06
1860 1920 2.031163 GTTGGCGGTGCTCTCTGT 59.969 61.111 0.00 0.00 0.00 3.41
1870 1930 3.648009 TGCATTTTTAGAAAGTTGGCGG 58.352 40.909 0.00 0.00 0.00 6.13
1871 1931 5.404968 TCAATGCATTTTTAGAAAGTTGGCG 59.595 36.000 9.83 0.00 0.00 5.69
1883 1943 3.715495 TCGCAGTTGTCAATGCATTTTT 58.285 36.364 9.83 0.00 42.68 1.94
1893 1953 2.524569 TGTTGATCTCGCAGTTGTCA 57.475 45.000 0.00 0.00 0.00 3.58
1954 2014 2.554032 CTGATTTCCAGTGTGAACCCAC 59.446 50.000 0.00 0.00 38.10 4.61
2003 2064 9.836864 TCAAACATAGATATTGTTCATAGTGCT 57.163 29.630 0.00 0.00 36.32 4.40
2075 2136 4.057432 GCCAAACATAGTTTTGTGCACAT 58.943 39.130 22.39 8.28 35.09 3.21
2163 2224 5.818136 ACGGGTATCAAATCTTGTCATTG 57.182 39.130 0.00 0.00 0.00 2.82
2230 2294 3.767673 TCTACAACCACGGAGAGCTAATT 59.232 43.478 0.00 0.00 0.00 1.40
2286 2350 0.881796 GGTGCCTGCTTACCAAGAAC 59.118 55.000 0.00 0.00 36.94 3.01
2306 2370 7.817962 AGCAATATTCAACATACTATACGTCCC 59.182 37.037 0.00 0.00 0.00 4.46
2309 2373 8.364894 TGGAGCAATATTCAACATACTATACGT 58.635 33.333 0.00 0.00 0.00 3.57
2314 2378 6.483307 GCAGTGGAGCAATATTCAACATACTA 59.517 38.462 0.00 0.00 0.00 1.82
2346 2410 9.975218 AAATAGATGACCCAATTGTACTAACTT 57.025 29.630 4.43 0.00 0.00 2.66
2349 2413 9.184523 CCAAAATAGATGACCCAATTGTACTAA 57.815 33.333 4.43 0.00 0.00 2.24
2355 2419 6.035843 CGTTCCAAAATAGATGACCCAATTG 58.964 40.000 0.00 0.00 0.00 2.32
2357 2421 4.644685 CCGTTCCAAAATAGATGACCCAAT 59.355 41.667 0.00 0.00 0.00 3.16
2358 2422 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2359 2423 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2360 2424 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2361 2425 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2362 2426 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2363 2427 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2364 2428 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2365 2429 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2366 2430 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2367 2431 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2368 2432 3.839490 TGTACTCCCTCCGTTCCAAAATA 59.161 43.478 0.00 0.00 0.00 1.40
2369 2433 2.640826 TGTACTCCCTCCGTTCCAAAAT 59.359 45.455 0.00 0.00 0.00 1.82
2370 2434 2.048601 TGTACTCCCTCCGTTCCAAAA 58.951 47.619 0.00 0.00 0.00 2.44
2371 2435 1.719529 TGTACTCCCTCCGTTCCAAA 58.280 50.000 0.00 0.00 0.00 3.28
2372 2436 1.829222 GATGTACTCCCTCCGTTCCAA 59.171 52.381 0.00 0.00 0.00 3.53
2373 2437 1.006758 AGATGTACTCCCTCCGTTCCA 59.993 52.381 0.00 0.00 0.00 3.53
2374 2438 1.777941 AGATGTACTCCCTCCGTTCC 58.222 55.000 0.00 0.00 0.00 3.62
2375 2439 3.565063 GTCTAGATGTACTCCCTCCGTTC 59.435 52.174 0.00 0.00 0.00 3.95
2376 2440 3.202595 AGTCTAGATGTACTCCCTCCGTT 59.797 47.826 0.00 0.00 0.00 4.44
2377 2441 2.778850 AGTCTAGATGTACTCCCTCCGT 59.221 50.000 0.00 0.00 0.00 4.69
2378 2442 3.495434 AGTCTAGATGTACTCCCTCCG 57.505 52.381 0.00 0.00 0.00 4.63
2379 2443 5.692928 TGTAAGTCTAGATGTACTCCCTCC 58.307 45.833 13.79 0.00 0.00 4.30
2380 2444 7.339976 AGTTTGTAAGTCTAGATGTACTCCCTC 59.660 40.741 13.79 4.50 0.00 4.30
2381 2445 7.122948 CAGTTTGTAAGTCTAGATGTACTCCCT 59.877 40.741 13.79 6.60 0.00 4.20
2382 2446 7.259161 CAGTTTGTAAGTCTAGATGTACTCCC 58.741 42.308 13.79 5.08 0.00 4.30
2383 2447 6.752815 GCAGTTTGTAAGTCTAGATGTACTCC 59.247 42.308 13.79 5.32 0.00 3.85
2384 2448 7.313646 TGCAGTTTGTAAGTCTAGATGTACTC 58.686 38.462 13.79 7.29 0.00 2.59
2385 2449 7.228314 TGCAGTTTGTAAGTCTAGATGTACT 57.772 36.000 13.79 0.00 0.00 2.73
2386 2450 7.759886 TGATGCAGTTTGTAAGTCTAGATGTAC 59.240 37.037 0.00 2.35 0.00 2.90
2387 2451 7.836842 TGATGCAGTTTGTAAGTCTAGATGTA 58.163 34.615 0.00 0.00 0.00 2.29
2388 2452 6.701340 TGATGCAGTTTGTAAGTCTAGATGT 58.299 36.000 0.00 0.00 0.00 3.06
2389 2453 7.783090 ATGATGCAGTTTGTAAGTCTAGATG 57.217 36.000 0.00 0.00 0.00 2.90
2390 2454 8.700051 ACTATGATGCAGTTTGTAAGTCTAGAT 58.300 33.333 0.00 0.00 0.00 1.98
2391 2455 8.067751 ACTATGATGCAGTTTGTAAGTCTAGA 57.932 34.615 0.00 0.00 0.00 2.43
2392 2456 8.709386 AACTATGATGCAGTTTGTAAGTCTAG 57.291 34.615 0.00 0.00 32.28 2.43
2393 2457 9.502091 AAAACTATGATGCAGTTTGTAAGTCTA 57.498 29.630 2.19 0.00 43.62 2.59
2394 2458 7.986085 AAACTATGATGCAGTTTGTAAGTCT 57.014 32.000 0.66 0.00 42.98 3.24
2395 2459 8.076178 ACAAAACTATGATGCAGTTTGTAAGTC 58.924 33.333 2.19 0.00 43.62 3.01
2396 2460 7.940850 ACAAAACTATGATGCAGTTTGTAAGT 58.059 30.769 2.19 0.00 43.62 2.24
2397 2461 7.269084 CGACAAAACTATGATGCAGTTTGTAAG 59.731 37.037 2.19 0.00 43.62 2.34
2403 2467 4.142816 GCTCGACAAAACTATGATGCAGTT 60.143 41.667 0.00 0.00 37.85 3.16
2408 2472 4.437239 AGGAGCTCGACAAAACTATGATG 58.563 43.478 7.83 0.00 0.00 3.07
2416 2480 3.055819 AGAAGCATAGGAGCTCGACAAAA 60.056 43.478 7.83 0.00 45.89 2.44
2419 2483 1.678627 GAGAAGCATAGGAGCTCGACA 59.321 52.381 7.83 0.00 45.89 4.35
2422 2486 1.602668 GCAGAGAAGCATAGGAGCTCG 60.603 57.143 7.83 0.00 45.89 5.03
2491 2559 6.393720 AAATCAGCGAATTTGTAACAATGC 57.606 33.333 0.00 0.00 0.00 3.56
2494 2562 8.910666 CATGTTAAATCAGCGAATTTGTAACAA 58.089 29.630 13.99 0.00 33.84 2.83
2504 2572 3.369756 GTCGACCATGTTAAATCAGCGAA 59.630 43.478 3.51 0.00 0.00 4.70
2519 2587 2.917227 TGCTCTGGCTGTCGACCA 60.917 61.111 14.12 2.71 39.59 4.02


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

AutoCloner maintained by Alex Coulton.