Multiple sequence alignment - TraesCS7B01G234900

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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 TraesCS7B01G234900 chr7B 100.000 2327 0 0 1 2327 439258025 439260351 0.000000e+00 4298.0
1 TraesCS7B01G234900 chr7D 89.520 2252 127 41 13 2220 421857365 421855179 0.000000e+00 2750.0
2 TraesCS7B01G234900 chr7D 100.000 29 0 0 2015 2043 25188544 25188516 1.000000e-03 54.7
3 TraesCS7B01G234900 chr7A 90.448 1026 56 16 345 1347 511405219 511406225 0.000000e+00 1314.0
4 TraesCS7B01G234900 chr7A 83.214 560 61 20 1714 2265 511406663 511407197 1.250000e-132 483.0
5 TraesCS7B01G234900 chr7A 95.390 282 12 1 1435 1715 511406225 511406506 4.560000e-122 448.0
6 TraesCS7B01G234900 chr7A 100.000 29 0 0 2015 2043 26029312 26029284 1.000000e-03 54.7
7 TraesCS7B01G234900 chr5B 100.000 30 0 0 1933 1962 554809782 554809811 3.230000e-04 56.5


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 TraesCS7B01G234900 chr7B 439258025 439260351 2326 False 4298.000000 4298 100.000 1 2327 1 chr7B.!!$F1 2326
1 TraesCS7B01G234900 chr7D 421855179 421857365 2186 True 2750.000000 2750 89.520 13 2220 1 chr7D.!!$R2 2207
2 TraesCS7B01G234900 chr7A 511405219 511407197 1978 False 748.333333 1314 89.684 345 2265 3 chr7A.!!$F1 1920

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
707 716 0.689623 CATGTATGCCCTCTCCCTCC 59.31 60.0 0.0 0.0 0.0 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 1991 0.539986 GGTGATCCAACGGCCTAGAA 59.46 55.0 0.0 0.0 0.0 2.1 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
40 41 9.245481 CCCACTACAACCAAGGTTAAATAATTA 57.755 33.333 3.82 0.00 36.46 1.40
103 104 1.604147 GCACCACACAAATAGGCCCC 61.604 60.000 0.00 0.00 0.00 5.80
160 161 4.623932 AGTTGTGCTTTCTATGACAGGA 57.376 40.909 0.00 0.00 0.00 3.86
176 177 3.012518 ACAGGAAGTGTCAATATGCTGC 58.987 45.455 0.00 0.00 31.90 5.25
196 197 5.760253 GCTGCTGCTCCTAATTAACTGATTA 59.240 40.000 8.53 0.00 36.03 1.75
228 229 3.446442 ACCAGAACCATGCAATTCTCT 57.554 42.857 7.96 0.00 32.77 3.10
239 240 3.693807 TGCAATTCTCTGGCTCAATCTT 58.306 40.909 0.00 0.00 0.00 2.40
241 242 4.082408 TGCAATTCTCTGGCTCAATCTTTG 60.082 41.667 0.00 0.00 0.00 2.77
242 243 4.082354 GCAATTCTCTGGCTCAATCTTTGT 60.082 41.667 0.00 0.00 0.00 2.83
255 256 5.181009 TCAATCTTTGTGAGGTGCTCATAG 58.819 41.667 0.00 0.00 42.73 2.23
256 257 5.046376 TCAATCTTTGTGAGGTGCTCATAGA 60.046 40.000 0.00 0.00 42.73 1.98
272 273 6.019779 CTCATAGAGGTAGAGCATTGGTAC 57.980 45.833 0.00 0.00 0.00 3.34
275 276 2.427453 AGAGGTAGAGCATTGGTACGTG 59.573 50.000 0.00 0.00 0.00 4.49
278 279 1.659098 GTAGAGCATTGGTACGTGTGC 59.341 52.381 0.00 6.82 37.84 4.57
299 300 3.260740 CGTTTATAGGGGTGCGTGTAAA 58.739 45.455 0.00 0.00 0.00 2.01
316 317 5.231357 CGTGTAAATGTGTATGTATGAGCGT 59.769 40.000 0.00 0.00 0.00 5.07
318 319 5.751509 TGTAAATGTGTATGTATGAGCGTCC 59.248 40.000 0.00 0.00 0.00 4.79
320 321 1.746787 TGTGTATGTATGAGCGTCCGT 59.253 47.619 0.00 0.00 0.00 4.69
323 324 2.944349 TGTATGTATGAGCGTCCGTGTA 59.056 45.455 0.00 0.00 0.00 2.90
325 326 3.728076 ATGTATGAGCGTCCGTGTATT 57.272 42.857 0.00 0.00 0.00 1.89
329 330 3.795623 ATGAGCGTCCGTGTATTTACT 57.204 42.857 0.00 0.00 0.00 2.24
333 334 4.082841 TGAGCGTCCGTGTATTTACTGTAA 60.083 41.667 0.00 0.00 0.00 2.41
334 335 4.418392 AGCGTCCGTGTATTTACTGTAAG 58.582 43.478 0.00 0.00 42.29 2.34
343 348 7.705325 CCGTGTATTTACTGTAAGAAGCACTAT 59.295 37.037 16.53 4.69 37.43 2.12
356 361 4.472833 AGAAGCACTATTCCAAGATCCACT 59.527 41.667 0.00 0.00 0.00 4.00
418 423 6.322456 TCAGACTATCCGAATCAGAGTCATTT 59.678 38.462 0.00 0.00 39.20 2.32
420 425 6.983307 AGACTATCCGAATCAGAGTCATTTTG 59.017 38.462 0.00 0.00 39.20 2.44
492 497 5.012893 ACATCTCACTCACTGTCACATCTA 58.987 41.667 0.00 0.00 0.00 1.98
493 498 5.105957 ACATCTCACTCACTGTCACATCTAC 60.106 44.000 0.00 0.00 0.00 2.59
647 652 4.143030 GGATTTATCTGAATGCACGATCGG 60.143 45.833 20.98 9.59 0.00 4.18
684 693 1.078637 GCGACCCCCACTACCTTTC 60.079 63.158 0.00 0.00 0.00 2.62
707 716 0.689623 CATGTATGCCCTCTCCCTCC 59.310 60.000 0.00 0.00 0.00 4.30
861 888 1.252904 ACCGGCCCGCGTGTATATAT 61.253 55.000 4.92 0.00 0.00 0.86
862 889 0.740149 CCGGCCCGCGTGTATATATA 59.260 55.000 4.92 0.00 0.00 0.86
873 900 5.927689 CGCGTGTATATATAAGGGTTTCCAA 59.072 40.000 0.00 0.00 34.83 3.53
880 907 8.947115 GTATATATAAGGGTTTCCAAGTGCATC 58.053 37.037 0.00 0.00 34.83 3.91
907 942 1.065854 CCATCACTCGCTTCCTTCCTT 60.066 52.381 0.00 0.00 0.00 3.36
908 943 2.275318 CATCACTCGCTTCCTTCCTTC 58.725 52.381 0.00 0.00 0.00 3.46
909 944 1.338107 TCACTCGCTTCCTTCCTTCA 58.662 50.000 0.00 0.00 0.00 3.02
995 1030 8.926715 AATTTGTCAAGTAAGGTTTTCTGTTC 57.073 30.769 0.00 0.00 0.00 3.18
1015 1050 1.373570 GTTCATGGCTTCTTCGAGGG 58.626 55.000 0.00 0.00 0.00 4.30
1086 1121 1.660560 AAGCGGCAAGGATGATGCAC 61.661 55.000 1.45 0.00 45.60 4.57
1365 1403 2.498077 TCTGCGTGAGGGAGAGATG 58.502 57.895 0.00 0.00 38.30 2.90
1366 1404 1.039785 TCTGCGTGAGGGAGAGATGG 61.040 60.000 0.00 0.00 38.30 3.51
1367 1405 1.305297 TGCGTGAGGGAGAGATGGT 60.305 57.895 0.00 0.00 0.00 3.55
1368 1406 1.323271 TGCGTGAGGGAGAGATGGTC 61.323 60.000 0.00 0.00 0.00 4.02
1369 1407 1.323271 GCGTGAGGGAGAGATGGTCA 61.323 60.000 0.00 0.00 0.00 4.02
1371 1409 1.759445 CGTGAGGGAGAGATGGTCAAT 59.241 52.381 0.00 0.00 0.00 2.57
1372 1410 2.482664 CGTGAGGGAGAGATGGTCAATG 60.483 54.545 0.00 0.00 0.00 2.82
1373 1411 2.768527 GTGAGGGAGAGATGGTCAATGA 59.231 50.000 0.00 0.00 0.00 2.57
1374 1412 3.198635 GTGAGGGAGAGATGGTCAATGAA 59.801 47.826 0.00 0.00 0.00 2.57
1375 1413 4.042884 TGAGGGAGAGATGGTCAATGAAT 58.957 43.478 0.00 0.00 0.00 2.57
1376 1414 4.141551 TGAGGGAGAGATGGTCAATGAATG 60.142 45.833 0.00 0.00 0.00 2.67
1377 1415 4.042884 AGGGAGAGATGGTCAATGAATGA 58.957 43.478 0.00 0.00 35.05 2.57
1378 1416 4.664064 AGGGAGAGATGGTCAATGAATGAT 59.336 41.667 0.00 0.00 40.97 2.45
1379 1417 4.760715 GGGAGAGATGGTCAATGAATGATG 59.239 45.833 0.00 0.00 40.97 3.07
1380 1418 5.455755 GGGAGAGATGGTCAATGAATGATGA 60.456 44.000 0.00 0.00 40.97 2.92
1381 1419 5.469421 GGAGAGATGGTCAATGAATGATGAC 59.531 44.000 0.00 0.00 44.07 3.06
1382 1420 5.055144 AGAGATGGTCAATGAATGATGACG 58.945 41.667 0.00 0.00 45.39 4.35
1383 1421 4.774124 AGATGGTCAATGAATGATGACGT 58.226 39.130 0.00 0.00 45.39 4.34
1384 1422 4.813161 AGATGGTCAATGAATGATGACGTC 59.187 41.667 9.11 9.11 45.39 4.34
1385 1423 3.936564 TGGTCAATGAATGATGACGTCA 58.063 40.909 22.48 22.48 45.39 4.35
1386 1424 3.684305 TGGTCAATGAATGATGACGTCAC 59.316 43.478 22.71 15.11 45.39 3.67
1387 1425 3.242091 GGTCAATGAATGATGACGTCACG 60.242 47.826 22.71 0.00 45.39 4.35
1388 1426 3.367932 GTCAATGAATGATGACGTCACGT 59.632 43.478 22.71 0.09 41.16 4.49
1389 1427 3.612423 TCAATGAATGATGACGTCACGTC 59.388 43.478 23.75 23.75 44.12 4.34
1390 1428 4.618227 TCAATGAATGATGACGTCACGTCT 60.618 41.667 29.47 15.94 44.15 4.18
1391 1429 6.077868 TCAATGAATGATGACGTCACGTCTT 61.078 40.000 29.47 23.84 44.15 3.01
1415 1453 0.943673 CATGCATGTTATCCGGCGAA 59.056 50.000 18.91 0.00 0.00 4.70
1416 1454 1.333308 CATGCATGTTATCCGGCGAAA 59.667 47.619 18.91 0.00 0.00 3.46
1417 1455 1.013596 TGCATGTTATCCGGCGAAAG 58.986 50.000 9.30 0.00 0.00 2.62
1418 1456 1.014352 GCATGTTATCCGGCGAAAGT 58.986 50.000 9.30 0.00 0.00 2.66
1419 1457 1.268032 GCATGTTATCCGGCGAAAGTG 60.268 52.381 9.30 3.39 0.00 3.16
1476 1516 2.778659 CAACGCCACTAGTAGTACGTC 58.221 52.381 23.21 5.87 38.63 4.34
1480 1520 1.596727 GCCACTAGTAGTACGTCCGAG 59.403 57.143 1.57 0.00 0.00 4.63
1742 1964 4.719026 AGGACCGTCTATACATCAGGTA 57.281 45.455 0.00 0.00 36.16 3.08
1786 2011 1.227263 CTAGGCCGTTGGATCACCG 60.227 63.158 0.00 0.00 39.42 4.94
1816 2041 2.158900 CCACTATCCTCCCACACATGTC 60.159 54.545 0.00 0.00 0.00 3.06
1828 2053 3.415212 CACACATGTCCATCTTCAAGGT 58.585 45.455 0.00 0.00 0.00 3.50
1890 2115 2.602676 CCCCGTTCCATCCACCTGT 61.603 63.158 0.00 0.00 0.00 4.00
1894 2119 1.002659 CCGTTCCATCCACCTGTTACA 59.997 52.381 0.00 0.00 0.00 2.41
1897 2122 1.344065 TCCATCCACCTGTTACACGT 58.656 50.000 0.00 0.00 0.00 4.49
1901 2126 1.300311 CCACCTGTTACACGTCGCA 60.300 57.895 0.00 0.00 0.00 5.10
1903 2128 0.438445 CACCTGTTACACGTCGCATG 59.562 55.000 0.00 0.00 0.00 4.06
1904 2129 0.669318 ACCTGTTACACGTCGCATGG 60.669 55.000 0.00 0.00 0.00 3.66
1905 2130 1.419922 CTGTTACACGTCGCATGGC 59.580 57.895 0.00 0.00 0.00 4.40
1906 2131 1.005512 TGTTACACGTCGCATGGCT 60.006 52.632 0.00 0.00 0.00 4.75
1907 2132 1.288419 TGTTACACGTCGCATGGCTG 61.288 55.000 0.00 0.00 0.00 4.85
1908 2133 1.739929 TTACACGTCGCATGGCTGG 60.740 57.895 0.00 0.00 0.00 4.85
1975 2200 2.551071 CCTCAACCTCAACCTCCTTCAC 60.551 54.545 0.00 0.00 0.00 3.18
1984 2209 3.136443 TCAACCTCCTTCACTGTCATTGT 59.864 43.478 0.00 0.00 0.00 2.71
1991 2216 3.006110 CCTTCACTGTCATTGTTTGCCAT 59.994 43.478 0.00 0.00 0.00 4.40
1995 2220 1.200716 CTGTCATTGTTTGCCATCGCT 59.799 47.619 0.00 0.00 35.36 4.93
2009 2234 4.899239 CGCTGCGACCATCCCTCC 62.899 72.222 18.66 0.00 0.00 4.30
2061 2293 2.735772 ATCTTCCTGGGACGCGCAT 61.736 57.895 5.73 0.00 0.00 4.73
2066 2298 2.202919 CTGGGACGCGCATCATCA 60.203 61.111 5.73 1.97 0.00 3.07
2095 2327 3.330701 TCTTGGATTAGGTCTTGGCTTGT 59.669 43.478 0.00 0.00 0.00 3.16
2116 2348 3.670523 GTCCTCGAGCAAAGCAAAAATTC 59.329 43.478 6.99 0.00 0.00 2.17
2128 2360 0.165944 AAAAATTCAGCGACGCTCGG 59.834 50.000 21.67 10.37 40.84 4.63
2170 2404 5.762825 ACAGGCATACAATGATTAGCAAG 57.237 39.130 0.00 0.00 0.00 4.01
2183 2417 2.357327 TAGCAAGCGCGAAGAAACTA 57.643 45.000 12.10 0.00 45.49 2.24
2198 2432 3.565902 AGAAACTAGCAGGCACAAAAGAC 59.434 43.478 0.00 0.00 0.00 3.01
2223 2457 5.651387 TCATGAAAGATCGACTCACTCTT 57.349 39.130 0.00 0.00 0.00 2.85
2225 2459 6.459066 TCATGAAAGATCGACTCACTCTTTT 58.541 36.000 11.22 0.00 38.87 2.27
2255 2489 8.996988 TTTACAGTATGCTCGTTTTGTTTAAG 57.003 30.769 0.00 0.00 42.53 1.85
2265 2499 5.055812 TCGTTTTGTTTAAGTGACCGGTAT 58.944 37.500 7.34 0.00 0.00 2.73
2266 2500 6.219473 TCGTTTTGTTTAAGTGACCGGTATA 58.781 36.000 7.34 0.00 0.00 1.47
2267 2501 6.873076 TCGTTTTGTTTAAGTGACCGGTATAT 59.127 34.615 7.34 0.00 0.00 0.86
2268 2502 7.063308 TCGTTTTGTTTAAGTGACCGGTATATC 59.937 37.037 7.34 0.00 0.00 1.63
2269 2503 7.466805 GTTTTGTTTAAGTGACCGGTATATCC 58.533 38.462 7.34 0.00 0.00 2.59
2283 2517 5.181690 GGTATATCCGGTTTGTACGTACA 57.818 43.478 24.10 24.10 0.00 2.90
2284 2518 5.772521 GGTATATCCGGTTTGTACGTACAT 58.227 41.667 27.82 14.20 35.89 2.29
2285 2519 6.908825 GGTATATCCGGTTTGTACGTACATA 58.091 40.000 27.82 20.67 35.89 2.29
2286 2520 6.801862 GGTATATCCGGTTTGTACGTACATAC 59.198 42.308 29.87 29.87 37.40 2.39
2298 2532 2.674954 CGTACATACGTGTTTGGGTGA 58.325 47.619 0.00 0.00 44.13 4.02
2299 2533 3.255725 CGTACATACGTGTTTGGGTGAT 58.744 45.455 0.00 0.00 44.13 3.06
2300 2534 4.422840 CGTACATACGTGTTTGGGTGATA 58.577 43.478 0.00 0.00 44.13 2.15
2301 2535 4.863689 CGTACATACGTGTTTGGGTGATAA 59.136 41.667 0.00 0.00 44.13 1.75
2302 2536 5.521010 CGTACATACGTGTTTGGGTGATAAT 59.479 40.000 0.00 0.00 44.13 1.28
2303 2537 5.811399 ACATACGTGTTTGGGTGATAATG 57.189 39.130 0.00 0.00 34.01 1.90
2304 2538 4.638421 ACATACGTGTTTGGGTGATAATGG 59.362 41.667 0.00 0.00 34.01 3.16
2305 2539 1.816224 ACGTGTTTGGGTGATAATGGC 59.184 47.619 0.00 0.00 0.00 4.40
2306 2540 1.815613 CGTGTTTGGGTGATAATGGCA 59.184 47.619 0.00 0.00 0.00 4.92
2307 2541 2.415357 CGTGTTTGGGTGATAATGGCAC 60.415 50.000 0.00 0.00 35.56 5.01
2308 2542 1.815613 TGTTTGGGTGATAATGGCACG 59.184 47.619 0.00 0.00 37.13 5.34
2309 2543 1.816224 GTTTGGGTGATAATGGCACGT 59.184 47.619 0.00 0.00 37.13 4.49
2310 2544 1.745232 TTGGGTGATAATGGCACGTC 58.255 50.000 0.00 0.00 37.13 4.34
2311 2545 0.615850 TGGGTGATAATGGCACGTCA 59.384 50.000 0.00 0.00 37.13 4.35
2312 2546 1.211703 TGGGTGATAATGGCACGTCAT 59.788 47.619 0.00 0.00 37.13 3.06
2313 2547 2.297701 GGGTGATAATGGCACGTCATT 58.702 47.619 7.53 7.53 40.15 2.57
2314 2548 2.033299 GGGTGATAATGGCACGTCATTG 59.967 50.000 11.59 0.00 37.82 2.82
2315 2549 2.541588 GGTGATAATGGCACGTCATTGC 60.542 50.000 11.59 0.16 42.18 3.56
2316 2550 1.330213 TGATAATGGCACGTCATTGCG 59.670 47.619 11.59 0.07 44.00 4.85
2317 2551 1.330521 GATAATGGCACGTCATTGCGT 59.669 47.619 11.59 1.20 46.88 5.24
2318 2552 0.724549 TAATGGCACGTCATTGCGTC 59.275 50.000 11.59 0.00 43.83 5.19
2319 2553 1.922135 AATGGCACGTCATTGCGTCC 61.922 55.000 1.96 8.31 43.83 4.79
2320 2554 3.047280 GGCACGTCATTGCGTCCA 61.047 61.111 3.67 0.00 43.83 4.02
2321 2555 2.398554 GGCACGTCATTGCGTCCAT 61.399 57.895 3.67 0.00 43.83 3.41
2322 2556 1.226101 GCACGTCATTGCGTCCATG 60.226 57.895 3.67 0.00 43.83 3.66
2323 2557 1.226101 CACGTCATTGCGTCCATGC 60.226 57.895 3.67 0.00 43.83 4.06
2324 2558 1.670730 ACGTCATTGCGTCCATGCA 60.671 52.632 0.00 0.00 41.71 3.96
2325 2559 1.026182 ACGTCATTGCGTCCATGCAT 61.026 50.000 0.00 0.00 45.78 3.96
2326 2560 0.590481 CGTCATTGCGTCCATGCATG 60.590 55.000 20.19 20.19 45.78 4.06
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.039879 ACCTTGGTTGTAGTGGGATCAC 59.960 50.000 0.00 0.00 43.93 3.06
10 11 2.344592 ACCTTGGTTGTAGTGGGATCA 58.655 47.619 0.00 0.00 0.00 2.92
11 12 3.434940 AACCTTGGTTGTAGTGGGATC 57.565 47.619 4.00 0.00 0.00 3.36
41 42 8.336801 ACTGTTGTAACTTTCTCTCAGTTTTT 57.663 30.769 0.00 0.00 35.95 1.94
48 49 7.516312 CGGTAACAACTGTTGTAACTTTCTCTC 60.516 40.741 24.93 6.31 44.59 3.20
103 104 8.299570 GCCTGTAATAAATCCATAAATCCAGTG 58.700 37.037 0.00 0.00 0.00 3.66
160 161 2.681848 GAGCAGCAGCATATTGACACTT 59.318 45.455 3.17 0.00 45.49 3.16
166 167 6.206243 AGTTAATTAGGAGCAGCAGCATATTG 59.794 38.462 3.17 0.00 45.49 1.90
176 177 8.200792 AGAGTGTAATCAGTTAATTAGGAGCAG 58.799 37.037 0.00 0.00 0.00 4.24
228 229 2.507484 CACCTCACAAAGATTGAGCCA 58.493 47.619 0.00 0.00 39.43 4.75
239 240 2.540383 ACCTCTATGAGCACCTCACAA 58.460 47.619 0.00 0.00 43.63 3.33
241 242 3.556999 TCTACCTCTATGAGCACCTCAC 58.443 50.000 0.00 0.00 43.63 3.51
242 243 3.826524 CTCTACCTCTATGAGCACCTCA 58.173 50.000 0.00 0.00 44.99 3.86
255 256 2.165845 ACACGTACCAATGCTCTACCTC 59.834 50.000 0.00 0.00 0.00 3.85
256 257 2.094182 CACACGTACCAATGCTCTACCT 60.094 50.000 0.00 0.00 0.00 3.08
275 276 0.741927 ACGCACCCCTATAAACGCAC 60.742 55.000 0.00 0.00 0.00 5.34
278 279 2.582728 TACACGCACCCCTATAAACG 57.417 50.000 0.00 0.00 0.00 3.60
281 282 4.193090 CACATTTACACGCACCCCTATAA 58.807 43.478 0.00 0.00 0.00 0.98
287 288 2.745281 ACATACACATTTACACGCACCC 59.255 45.455 0.00 0.00 0.00 4.61
299 300 2.361119 ACGGACGCTCATACATACACAT 59.639 45.455 0.00 0.00 0.00 3.21
316 317 5.865552 GTGCTTCTTACAGTAAATACACGGA 59.134 40.000 0.00 0.00 0.00 4.69
318 319 6.946229 AGTGCTTCTTACAGTAAATACACG 57.054 37.500 0.00 0.00 0.00 4.49
320 321 9.595823 GGAATAGTGCTTCTTACAGTAAATACA 57.404 33.333 0.00 0.00 0.00 2.29
323 324 9.167311 CTTGGAATAGTGCTTCTTACAGTAAAT 57.833 33.333 0.00 0.00 0.00 1.40
325 326 7.903145 TCTTGGAATAGTGCTTCTTACAGTAA 58.097 34.615 0.00 0.00 0.00 2.24
329 330 6.070251 TGGATCTTGGAATAGTGCTTCTTACA 60.070 38.462 0.00 0.00 0.00 2.41
333 334 4.472833 AGTGGATCTTGGAATAGTGCTTCT 59.527 41.667 0.00 0.00 0.00 2.85
334 335 4.574013 CAGTGGATCTTGGAATAGTGCTTC 59.426 45.833 0.00 0.00 0.00 3.86
343 348 2.501723 GACTAGCCAGTGGATCTTGGAA 59.498 50.000 15.20 0.00 34.21 3.53
356 361 1.136828 ACACCACCTTTGACTAGCCA 58.863 50.000 0.00 0.00 0.00 4.75
418 423 2.304470 TGAGCCAGCAATACAGGTACAA 59.696 45.455 0.00 0.00 0.00 2.41
420 425 2.280628 GTGAGCCAGCAATACAGGTAC 58.719 52.381 0.00 0.00 0.00 3.34
513 518 2.603021 TGTTTGCTTATGGAGGCCAAA 58.397 42.857 5.01 0.00 36.95 3.28
647 652 1.429148 CTTCGGCATAGCAACGACCC 61.429 60.000 0.00 0.00 36.24 4.46
657 662 3.857038 GGGGGTCGCTTCGGCATA 61.857 66.667 0.00 0.00 41.88 3.14
707 716 5.470845 AAAATGCGACGATCTTTTAGAGG 57.529 39.130 0.00 0.00 0.00 3.69
861 888 2.378547 AGGATGCACTTGGAAACCCTTA 59.621 45.455 0.00 0.00 0.00 2.69
862 889 1.147817 AGGATGCACTTGGAAACCCTT 59.852 47.619 0.00 0.00 0.00 3.95
873 900 1.076485 GATGGGCCAAGGATGCACT 60.076 57.895 11.89 0.00 31.89 4.40
880 907 2.825836 GCGAGTGATGGGCCAAGG 60.826 66.667 11.89 0.00 0.00 3.61
885 912 1.078143 AAGGAAGCGAGTGATGGGC 60.078 57.895 0.00 0.00 0.00 5.36
995 1030 1.002366 CCTCGAAGAAGCCATGAACG 58.998 55.000 0.00 0.00 34.09 3.95
1015 1050 1.724582 AAGAACAACAGCACGGCCAC 61.725 55.000 2.24 0.00 0.00 5.01
1027 1062 2.354510 CGAGAGTGCAAACCAAGAACAA 59.645 45.455 0.00 0.00 0.00 2.83
1086 1121 0.670162 CCAGCACAACCTCACCTTTG 59.330 55.000 0.00 0.00 0.00 2.77
1102 1137 1.447643 CGCCTCCTCCATTACCCAG 59.552 63.158 0.00 0.00 0.00 4.45
1362 1400 4.571984 TGACGTCATCATTCATTGACCATC 59.428 41.667 15.76 0.00 39.23 3.51
1364 1402 3.684305 GTGACGTCATCATTCATTGACCA 59.316 43.478 23.12 0.00 40.28 4.02
1365 1403 3.242091 CGTGACGTCATCATTCATTGACC 60.242 47.826 23.12 2.62 40.28 4.02
1366 1404 3.367932 ACGTGACGTCATCATTCATTGAC 59.632 43.478 23.12 2.84 40.28 3.18
1367 1405 3.584834 ACGTGACGTCATCATTCATTGA 58.415 40.909 23.12 0.00 40.28 2.57
1368 1406 3.997319 ACGTGACGTCATCATTCATTG 57.003 42.857 23.12 5.95 40.28 2.82
1386 1424 0.166597 AACATGCATGCACGAAGACG 59.833 50.000 25.37 8.02 45.75 4.18
1387 1425 3.546815 GGATAACATGCATGCACGAAGAC 60.547 47.826 25.37 13.23 0.00 3.01
1388 1426 2.613595 GGATAACATGCATGCACGAAGA 59.386 45.455 25.37 8.10 0.00 2.87
1389 1427 2.600556 CGGATAACATGCATGCACGAAG 60.601 50.000 25.37 15.54 0.00 3.79
1390 1428 1.330213 CGGATAACATGCATGCACGAA 59.670 47.619 25.37 9.38 0.00 3.85
1391 1429 0.936600 CGGATAACATGCATGCACGA 59.063 50.000 25.37 8.89 0.00 4.35
1392 1430 0.041047 CCGGATAACATGCATGCACG 60.041 55.000 25.37 19.13 0.00 5.34
1393 1431 0.318107 GCCGGATAACATGCATGCAC 60.318 55.000 25.37 9.03 0.00 4.57
1415 1453 1.081242 CGGGCACGTACGTACACTT 60.081 57.895 22.34 6.12 34.81 3.16
1416 1454 2.562912 CGGGCACGTACGTACACT 59.437 61.111 22.34 6.79 34.81 3.55
1417 1455 3.174573 GCGGGCACGTACGTACAC 61.175 66.667 22.34 16.41 43.45 2.90
1418 1456 4.757354 CGCGGGCACGTACGTACA 62.757 66.667 22.34 0.00 43.45 2.90
1419 1457 3.375500 TACGCGGGCACGTACGTAC 62.375 63.158 22.34 16.05 46.19 3.67
1460 1498 1.596727 CTCGGACGTACTACTAGTGGC 59.403 57.143 5.39 0.00 0.00 5.01
1476 1516 8.846607 GCATTTTACTACAACAAATTTACTCGG 58.153 33.333 0.00 0.00 0.00 4.63
1480 1520 9.739786 GCATGCATTTTACTACAACAAATTTAC 57.260 29.630 14.21 0.00 0.00 2.01
1557 1598 2.393768 CCGATGACAGCACACCTGC 61.394 63.158 0.00 0.00 45.78 4.85
1636 1700 9.784531 ATACTTGGAGAGTACAAAATATCATGG 57.215 33.333 0.00 0.00 43.38 3.66
1752 1977 4.082245 CGGCCTAGAAAATTGTTTGATGGT 60.082 41.667 0.00 0.00 0.00 3.55
1766 1991 0.539986 GGTGATCCAACGGCCTAGAA 59.460 55.000 0.00 0.00 0.00 2.10
1786 2011 1.136500 GGAGGATAGTGGTCGTTGGAC 59.864 57.143 0.00 0.00 42.66 4.02
1828 2053 5.072329 AGGAAGAAGATGAGAGTGGTTGAAA 59.928 40.000 0.00 0.00 0.00 2.69
1877 2102 1.695242 ACGTGTAACAGGTGGATGGAA 59.305 47.619 0.00 0.00 35.74 3.53
1890 2115 1.739929 CCAGCCATGCGACGTGTAA 60.740 57.895 0.00 0.00 0.00 2.41
1984 2209 3.430862 GGTCGCAGCGATGGCAAA 61.431 61.111 22.72 0.00 43.41 3.68
1991 2216 3.838271 GAGGGATGGTCGCAGCGA 61.838 66.667 15.11 15.11 0.00 4.93
1995 2220 2.989639 CTTGGAGGGATGGTCGCA 59.010 61.111 0.00 0.00 0.00 5.10
2095 2327 3.317711 TGAATTTTTGCTTTGCTCGAGGA 59.682 39.130 15.58 9.02 0.00 3.71
2116 2348 3.240203 TTTTTCCGAGCGTCGCTG 58.760 55.556 27.16 16.28 39.88 5.18
2135 2367 4.769488 TGTATGCCTGTTTGCCTGAATTTA 59.231 37.500 0.00 0.00 0.00 1.40
2136 2368 3.577848 TGTATGCCTGTTTGCCTGAATTT 59.422 39.130 0.00 0.00 0.00 1.82
2137 2369 3.164268 TGTATGCCTGTTTGCCTGAATT 58.836 40.909 0.00 0.00 0.00 2.17
2138 2370 2.806434 TGTATGCCTGTTTGCCTGAAT 58.194 42.857 0.00 0.00 0.00 2.57
2139 2371 2.284754 TGTATGCCTGTTTGCCTGAA 57.715 45.000 0.00 0.00 0.00 3.02
2140 2372 2.284754 TTGTATGCCTGTTTGCCTGA 57.715 45.000 0.00 0.00 0.00 3.86
2141 2373 2.492881 TCATTGTATGCCTGTTTGCCTG 59.507 45.455 0.00 0.00 0.00 4.85
2142 2374 2.806434 TCATTGTATGCCTGTTTGCCT 58.194 42.857 0.00 0.00 0.00 4.75
2143 2375 3.806625 ATCATTGTATGCCTGTTTGCC 57.193 42.857 0.00 0.00 0.00 4.52
2144 2376 4.741676 GCTAATCATTGTATGCCTGTTTGC 59.258 41.667 0.00 0.00 0.00 3.68
2145 2377 5.893687 TGCTAATCATTGTATGCCTGTTTG 58.106 37.500 0.00 0.00 0.00 2.93
2146 2378 6.528537 TTGCTAATCATTGTATGCCTGTTT 57.471 33.333 0.00 0.00 0.00 2.83
2147 2379 5.450965 GCTTGCTAATCATTGTATGCCTGTT 60.451 40.000 0.00 0.00 0.00 3.16
2158 2392 2.279741 TCTTCGCGCTTGCTAATCATT 58.720 42.857 5.56 0.00 36.08 2.57
2170 2404 1.710339 CCTGCTAGTTTCTTCGCGC 59.290 57.895 0.00 0.00 0.00 6.86
2183 2417 2.378038 TGAAAGTCTTTTGTGCCTGCT 58.622 42.857 0.00 0.00 0.00 4.24
2198 2432 6.098679 AGAGTGAGTCGATCTTTCATGAAAG 58.901 40.000 33.28 33.28 46.82 2.62
2229 2463 9.440784 CTTAAACAAAACGAGCATACTGTAAAA 57.559 29.630 0.00 0.00 0.00 1.52
2231 2465 8.065407 CACTTAAACAAAACGAGCATACTGTAA 58.935 33.333 0.00 0.00 0.00 2.41
2232 2466 7.438757 TCACTTAAACAAAACGAGCATACTGTA 59.561 33.333 0.00 0.00 0.00 2.74
2233 2467 6.259167 TCACTTAAACAAAACGAGCATACTGT 59.741 34.615 0.00 0.00 0.00 3.55
2236 2470 5.849604 GGTCACTTAAACAAAACGAGCATAC 59.150 40.000 0.00 0.00 0.00 2.39
2265 2499 4.843147 CGTATGTACGTACAAACCGGATA 58.157 43.478 30.46 14.58 44.13 2.59
2266 2500 3.694734 CGTATGTACGTACAAACCGGAT 58.305 45.455 30.46 15.58 44.13 4.18
2267 2501 3.129852 CGTATGTACGTACAAACCGGA 57.870 47.619 30.46 7.30 44.13 5.14
2279 2513 6.238266 CCATTATCACCCAAACACGTATGTAC 60.238 42.308 0.00 0.00 38.45 2.90
2280 2514 5.818336 CCATTATCACCCAAACACGTATGTA 59.182 40.000 0.00 0.00 38.45 2.29
2281 2515 4.638421 CCATTATCACCCAAACACGTATGT 59.362 41.667 0.00 0.00 42.46 2.29
2282 2516 4.497340 GCCATTATCACCCAAACACGTATG 60.497 45.833 0.00 0.00 0.00 2.39
2283 2517 3.630312 GCCATTATCACCCAAACACGTAT 59.370 43.478 0.00 0.00 0.00 3.06
2284 2518 3.011119 GCCATTATCACCCAAACACGTA 58.989 45.455 0.00 0.00 0.00 3.57
2285 2519 1.816224 GCCATTATCACCCAAACACGT 59.184 47.619 0.00 0.00 0.00 4.49
2286 2520 1.815613 TGCCATTATCACCCAAACACG 59.184 47.619 0.00 0.00 0.00 4.49
2287 2521 2.415357 CGTGCCATTATCACCCAAACAC 60.415 50.000 0.00 0.00 0.00 3.32
2288 2522 1.815613 CGTGCCATTATCACCCAAACA 59.184 47.619 0.00 0.00 0.00 2.83
2289 2523 1.816224 ACGTGCCATTATCACCCAAAC 59.184 47.619 0.00 0.00 0.00 2.93
2290 2524 2.088423 GACGTGCCATTATCACCCAAA 58.912 47.619 0.00 0.00 0.00 3.28
2291 2525 1.003696 TGACGTGCCATTATCACCCAA 59.996 47.619 0.00 0.00 0.00 4.12
2292 2526 0.615850 TGACGTGCCATTATCACCCA 59.384 50.000 0.00 0.00 0.00 4.51
2293 2527 1.967319 ATGACGTGCCATTATCACCC 58.033 50.000 0.00 0.00 0.00 4.61
2294 2528 2.541588 GCAATGACGTGCCATTATCACC 60.542 50.000 0.00 0.00 38.66 4.02
2295 2529 2.719798 GCAATGACGTGCCATTATCAC 58.280 47.619 0.00 0.00 38.66 3.06
2296 2530 1.330213 CGCAATGACGTGCCATTATCA 59.670 47.619 0.00 0.00 41.73 2.15
2297 2531 1.330521 ACGCAATGACGTGCCATTATC 59.669 47.619 0.00 0.00 46.28 1.75
2298 2532 1.378531 ACGCAATGACGTGCCATTAT 58.621 45.000 0.00 0.00 46.28 1.28
2299 2533 2.847725 ACGCAATGACGTGCCATTA 58.152 47.368 0.00 0.00 46.28 1.90
2300 2534 3.667087 ACGCAATGACGTGCCATT 58.333 50.000 0.00 0.00 46.28 3.16
2307 2541 0.590481 CATGCATGGACGCAATGACG 60.590 55.000 19.40 0.00 46.87 4.35
2308 2542 3.245443 CATGCATGGACGCAATGAC 57.755 52.632 19.40 0.00 46.87 3.06


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

AutoCloner maintained by Alex Coulton.