Multiple sequence alignment - TraesCS4B01G108800

Loading Multiple Alignment...

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 TraesCS4B01G108800 chr4B 100.000 2417 0 0 1 2417 119382022 119384438 0.000000e+00 4464
1 TraesCS4B01G108800 chr3B 98.271 1446 24 1 1 1445 767246184 767244739 0.000000e+00 2531
2 TraesCS4B01G108800 chrUn 97.503 1442 32 2 1 1441 119076006 119077444 0.000000e+00 2460
3 TraesCS4B01G108800 chr5B 97.297 1443 38 1 1 1442 273863672 273865114 0.000000e+00 2447
4 TraesCS4B01G108800 chr7D 97.163 1445 39 2 1 1444 590147552 590148995 0.000000e+00 2440
5 TraesCS4B01G108800 chr7D 95.433 1445 60 5 1 1442 449520127 449521568 0.000000e+00 2298
6 TraesCS4B01G108800 chr6A 96.325 1442 51 2 1 1441 592596618 592595178 0.000000e+00 2368
7 TraesCS4B01G108800 chr2D 90.490 1409 105 12 1 1404 71467994 71469378 0.000000e+00 1832
8 TraesCS4B01G108800 chr7A 97.036 911 27 0 532 1442 648084239 648083329 0.000000e+00 1533
9 TraesCS4B01G108800 chr6B 93.936 874 51 2 571 1444 569880899 569881770 0.000000e+00 1319
10 TraesCS4B01G108800 chr3A 89.867 977 96 3 365 1341 346706516 346707489 0.000000e+00 1253
11 TraesCS4B01G108800 chr4D 87.535 706 84 4 1 704 401868170 401868873 0.000000e+00 813
12 TraesCS4B01G108800 chr1A 81.856 959 130 20 1451 2387 486055313 486056249 0.000000e+00 767
13 TraesCS4B01G108800 chr4A 85.027 748 91 12 1476 2209 671805557 671804817 0.000000e+00 741
14 TraesCS4B01G108800 chr4A 81.899 337 60 1 1 336 492521363 492521699 1.410000e-72 283


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 TraesCS4B01G108800 chr4B 119382022 119384438 2416 False 4464 4464 100.000 1 2417 1 chr4B.!!$F1 2416
1 TraesCS4B01G108800 chr3B 767244739 767246184 1445 True 2531 2531 98.271 1 1445 1 chr3B.!!$R1 1444
2 TraesCS4B01G108800 chrUn 119076006 119077444 1438 False 2460 2460 97.503 1 1441 1 chrUn.!!$F1 1440
3 TraesCS4B01G108800 chr5B 273863672 273865114 1442 False 2447 2447 97.297 1 1442 1 chr5B.!!$F1 1441
4 TraesCS4B01G108800 chr7D 590147552 590148995 1443 False 2440 2440 97.163 1 1444 1 chr7D.!!$F2 1443
5 TraesCS4B01G108800 chr7D 449520127 449521568 1441 False 2298 2298 95.433 1 1442 1 chr7D.!!$F1 1441
6 TraesCS4B01G108800 chr6A 592595178 592596618 1440 True 2368 2368 96.325 1 1441 1 chr6A.!!$R1 1440
7 TraesCS4B01G108800 chr2D 71467994 71469378 1384 False 1832 1832 90.490 1 1404 1 chr2D.!!$F1 1403
8 TraesCS4B01G108800 chr7A 648083329 648084239 910 True 1533 1533 97.036 532 1442 1 chr7A.!!$R1 910
9 TraesCS4B01G108800 chr6B 569880899 569881770 871 False 1319 1319 93.936 571 1444 1 chr6B.!!$F1 873
10 TraesCS4B01G108800 chr3A 346706516 346707489 973 False 1253 1253 89.867 365 1341 1 chr3A.!!$F1 976
11 TraesCS4B01G108800 chr4D 401868170 401868873 703 False 813 813 87.535 1 704 1 chr4D.!!$F1 703
12 TraesCS4B01G108800 chr1A 486055313 486056249 936 False 767 767 81.856 1451 2387 1 chr1A.!!$F1 936
13 TraesCS4B01G108800 chr4A 671804817 671805557 740 True 741 741 85.027 1476 2209 1 chr4A.!!$R1 733

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
542 546 0.235926 GTTCTTGCCTCGAAGCACAC 59.764 55.0 8.54 2.39 43.97 3.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 1913 0.257039 ATTGGCAAGCTCCGGAAGAT 59.743 50.0 5.23 0.0 0.0 2.4 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
264 266 4.062293 CAACGTTCTGGAAAGTGGATGTA 58.938 43.478 0.00 0.00 33.49 2.29
322 324 5.670792 AATGTCAGATTTCATTGCATGGT 57.329 34.783 0.00 0.00 33.74 3.55
465 469 2.263895 TATGGACCTTACAGTGCCCT 57.736 50.000 0.00 0.00 0.00 5.19
476 480 0.609957 CAGTGCCCTGCAAAGATCCA 60.610 55.000 0.00 0.00 41.47 3.41
542 546 0.235926 GTTCTTGCCTCGAAGCACAC 59.764 55.000 8.54 2.39 43.97 3.82
626 632 3.228188 TGAGTGCCCAAGATCAAAAGT 57.772 42.857 0.00 0.00 0.00 2.66
928 935 1.346395 AGCTACGTGTTGGTTCATGGA 59.654 47.619 0.00 0.00 0.00 3.41
1000 1007 2.435805 CGGGATCTTCTTGAGGGATCAA 59.564 50.000 0.00 0.00 37.99 2.57
1148 1155 0.666913 ATTGGATGCAGCAAGATCGC 59.333 50.000 3.51 0.00 0.00 4.58
1469 1478 4.697514 TCACAAGAGAAGTTCAAGTCCAG 58.302 43.478 5.50 0.00 0.00 3.86
1474 1483 2.746362 GAGAAGTTCAAGTCCAGGCATG 59.254 50.000 5.50 0.00 0.00 4.06
1510 1519 4.431524 CCCCTACTCCTGCCCCCA 62.432 72.222 0.00 0.00 0.00 4.96
1524 1533 1.443407 CCCCAGCTACATCACCTCG 59.557 63.158 0.00 0.00 0.00 4.63
1531 1540 3.316588 CAGCTACATCACCTCGTCTACAT 59.683 47.826 0.00 0.00 0.00 2.29
1533 1542 5.182190 CAGCTACATCACCTCGTCTACATAT 59.818 44.000 0.00 0.00 0.00 1.78
1536 1545 8.265764 AGCTACATCACCTCGTCTACATATATA 58.734 37.037 0.00 0.00 0.00 0.86
1547 1556 9.589111 CTCGTCTACATATATACTCTGCTTCTA 57.411 37.037 0.00 0.00 0.00 2.10
1559 1568 5.477510 ACTCTGCTTCTACTGATTTCTGTG 58.522 41.667 0.86 0.00 0.00 3.66
1562 1571 3.244526 TGCTTCTACTGATTTCTGTGGCA 60.245 43.478 0.86 0.00 0.00 4.92
1564 1573 4.573900 CTTCTACTGATTTCTGTGGCACT 58.426 43.478 19.83 0.00 0.00 4.40
1617 1626 8.756927 TGACTTATGCATCCCAAATTGAAATTA 58.243 29.630 0.19 0.00 0.00 1.40
1625 1634 7.147742 GCATCCCAAATTGAAATTAGGAGGTAA 60.148 37.037 15.28 0.00 36.20 2.85
1634 1643 5.180492 TGAAATTAGGAGGTAACAAAGCACG 59.820 40.000 0.00 0.00 41.41 5.34
1637 1646 1.583495 GGAGGTAACAAAGCACGCCC 61.583 60.000 0.00 0.00 41.41 6.13
1705 1714 6.734104 ATCTGCTAAGTGATTTGAACACTC 57.266 37.500 0.00 0.00 46.01 3.51
1719 1728 9.515020 GATTTGAACACTCTGTCAAAAACATAA 57.485 29.630 3.22 0.00 37.23 1.90
1722 1731 9.868277 TTGAACACTCTGTCAAAAACATAAATT 57.132 25.926 0.00 0.00 37.23 1.82
1748 1757 3.885901 TCCGACACAATTTGGTCAAATCA 59.114 39.130 9.08 0.00 39.88 2.57
1763 1772 8.918202 TGGTCAAATCAACTATTATATGGACC 57.082 34.615 0.00 0.00 0.00 4.46
1782 1791 5.300792 TGGACCTACACAAAATTTGAGGAAC 59.699 40.000 13.19 7.85 0.00 3.62
1787 1796 7.230712 ACCTACACAAAATTTGAGGAACCTAAG 59.769 37.037 13.19 0.00 0.00 2.18
1789 1798 9.280174 CTACACAAAATTTGAGGAACCTAAGTA 57.720 33.333 13.19 0.00 0.00 2.24
1822 1833 2.302157 ACCAAAGAGGCCAGTACACTAC 59.698 50.000 5.01 0.00 43.14 2.73
1826 1837 2.605257 AGAGGCCAGTACACTACACAA 58.395 47.619 5.01 0.00 0.00 3.33
1836 1847 6.460537 CCAGTACACTACACAACTACTTGTCA 60.461 42.308 0.00 0.00 38.66 3.58
1837 1848 7.145985 CAGTACACTACACAACTACTTGTCAT 58.854 38.462 0.00 0.00 38.66 3.06
1838 1849 7.114953 CAGTACACTACACAACTACTTGTCATG 59.885 40.741 0.00 0.00 38.66 3.07
1862 1873 6.938596 TGATGATGAATATGAAAGCCTACCAG 59.061 38.462 0.00 0.00 0.00 4.00
1868 1879 2.185004 TGAAAGCCTACCAGCAAGAC 57.815 50.000 0.00 0.00 34.23 3.01
1878 1889 2.233271 ACCAGCAAGACACAAATGAGG 58.767 47.619 0.00 0.00 0.00 3.86
1890 1901 2.887152 ACAAATGAGGAAGGAGCACAAC 59.113 45.455 0.00 0.00 0.00 3.32
1902 1913 4.973168 AGGAGCACAACTATTCAAGTCAA 58.027 39.130 0.00 0.00 37.50 3.18
1904 1915 5.645497 AGGAGCACAACTATTCAAGTCAATC 59.355 40.000 0.00 0.00 37.50 2.67
1909 1930 6.537566 CACAACTATTCAAGTCAATCTTCCG 58.462 40.000 0.00 0.00 37.50 4.30
1928 1949 2.141517 CGGAGCTTGCCAATATGAGAG 58.858 52.381 0.00 0.00 0.00 3.20
1930 1951 2.569059 GAGCTTGCCAATATGAGAGCA 58.431 47.619 0.00 0.00 32.78 4.26
1934 1955 3.003482 GCTTGCCAATATGAGAGCAGAAG 59.997 47.826 0.00 0.00 36.44 2.85
1937 1958 2.158696 GCCAATATGAGAGCAGAAGGGT 60.159 50.000 0.00 0.00 0.00 4.34
1939 1960 4.636249 CCAATATGAGAGCAGAAGGGTAC 58.364 47.826 0.00 0.00 0.00 3.34
1987 2008 2.713863 TGCATCATGTGGCAGATACA 57.286 45.000 9.44 0.00 34.58 2.29
1993 2014 5.622914 GCATCATGTGGCAGATACAAAAGTT 60.623 40.000 0.00 0.00 0.00 2.66
1996 2017 4.481930 TGTGGCAGATACAAAAGTTTCG 57.518 40.909 0.00 0.00 0.00 3.46
2008 2029 4.566360 ACAAAAGTTTCGCAAAGATTGTGG 59.434 37.500 4.05 0.00 41.37 4.17
2012 2033 2.704725 TTCGCAAAGATTGTGGCTTC 57.295 45.000 4.05 0.00 41.37 3.86
2023 2044 0.961019 TGTGGCTTCAATGTTGCTCC 59.039 50.000 0.00 0.00 0.00 4.70
2028 2049 1.200948 GCTTCAATGTTGCTCCACCTC 59.799 52.381 0.00 0.00 0.00 3.85
2092 2114 6.840705 ACTGAATGTAAATTGGGGCATATCTT 59.159 34.615 0.00 0.00 0.00 2.40
2096 2118 5.714863 TGTAAATTGGGGCATATCTTGGAT 58.285 37.500 0.00 0.00 0.00 3.41
2107 2129 5.474532 GGCATATCTTGGATAATGAAGTGCA 59.525 40.000 0.00 0.00 0.00 4.57
2116 2138 4.450419 GGATAATGAAGTGCAGAATCTCCG 59.550 45.833 0.00 0.00 0.00 4.63
2119 2141 0.250513 GAAGTGCAGAATCTCCGGGT 59.749 55.000 0.00 0.00 0.00 5.28
2131 2153 3.173668 TCTCCGGGTTATTCACATTCG 57.826 47.619 0.00 0.00 0.00 3.34
2134 2156 4.049186 CTCCGGGTTATTCACATTCGTAG 58.951 47.826 0.00 0.00 0.00 3.51
2139 2161 4.684703 GGGTTATTCACATTCGTAGATCCG 59.315 45.833 0.00 0.00 35.04 4.18
2173 2198 4.695606 AGGTACTTGAGGAAGGAATACCA 58.304 43.478 0.00 0.00 33.57 3.25
2226 2257 1.603456 TTTTCAGACGCAGATTGGCA 58.397 45.000 0.00 0.00 0.00 4.92
2232 2263 2.098607 CAGACGCAGATTGGCAATCATT 59.901 45.455 34.54 17.65 40.42 2.57
2233 2264 2.756760 AGACGCAGATTGGCAATCATTT 59.243 40.909 34.54 19.45 40.42 2.32
2234 2265 2.855963 GACGCAGATTGGCAATCATTTG 59.144 45.455 34.54 26.16 40.42 2.32
2236 2267 2.601314 CGCAGATTGGCAATCATTTGTG 59.399 45.455 34.54 26.78 40.42 3.33
2240 2271 5.475719 CAGATTGGCAATCATTTGTGTTCT 58.524 37.500 34.54 13.73 40.42 3.01
2243 2274 5.471556 TTGGCAATCATTTGTGTTCTGAT 57.528 34.783 0.00 0.00 35.17 2.90
2332 2363 9.353999 GAAGAACACGCTAATTCCAAATAATTT 57.646 29.630 0.00 0.00 31.63 1.82
2383 2414 5.923684 GCTAAATGGCTACTACAGAGATGAC 59.076 44.000 0.00 0.00 0.00 3.06
2387 2418 4.290093 TGGCTACTACAGAGATGACCAAT 58.710 43.478 0.00 0.00 0.00 3.16
2388 2419 5.454966 TGGCTACTACAGAGATGACCAATA 58.545 41.667 0.00 0.00 0.00 1.90
2389 2420 5.536538 TGGCTACTACAGAGATGACCAATAG 59.463 44.000 0.00 0.00 0.00 1.73
2390 2421 5.770663 GGCTACTACAGAGATGACCAATAGA 59.229 44.000 0.00 0.00 0.00 1.98
2391 2422 6.265649 GGCTACTACAGAGATGACCAATAGAA 59.734 42.308 0.00 0.00 0.00 2.10
2392 2423 7.142680 GCTACTACAGAGATGACCAATAGAAC 58.857 42.308 0.00 0.00 0.00 3.01
2393 2424 7.013846 GCTACTACAGAGATGACCAATAGAACT 59.986 40.741 0.00 0.00 0.00 3.01
2394 2425 9.562408 CTACTACAGAGATGACCAATAGAACTA 57.438 37.037 0.00 0.00 0.00 2.24
2395 2426 8.824756 ACTACAGAGATGACCAATAGAACTAA 57.175 34.615 0.00 0.00 0.00 2.24
2396 2427 9.256228 ACTACAGAGATGACCAATAGAACTAAA 57.744 33.333 0.00 0.00 0.00 1.85
2397 2428 9.522804 CTACAGAGATGACCAATAGAACTAAAC 57.477 37.037 0.00 0.00 0.00 2.01
2398 2429 7.036220 ACAGAGATGACCAATAGAACTAAACG 58.964 38.462 0.00 0.00 0.00 3.60
2399 2430 7.036220 CAGAGATGACCAATAGAACTAAACGT 58.964 38.462 0.00 0.00 0.00 3.99
2400 2431 7.221067 CAGAGATGACCAATAGAACTAAACGTC 59.779 40.741 0.00 0.00 0.00 4.34
2401 2432 7.122948 AGAGATGACCAATAGAACTAAACGTCT 59.877 37.037 0.00 0.00 0.00 4.18
2402 2433 8.289939 AGATGACCAATAGAACTAAACGTCTA 57.710 34.615 0.00 0.00 0.00 2.59
2403 2434 8.189460 AGATGACCAATAGAACTAAACGTCTAC 58.811 37.037 0.00 0.00 0.00 2.59
2404 2435 7.458409 TGACCAATAGAACTAAACGTCTACT 57.542 36.000 0.00 0.00 0.00 2.57
2405 2436 8.565896 TGACCAATAGAACTAAACGTCTACTA 57.434 34.615 0.00 0.00 0.00 1.82
2406 2437 9.182214 TGACCAATAGAACTAAACGTCTACTAT 57.818 33.333 0.00 0.00 0.00 2.12
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.774234 ACACCAGCCATTATACTCTGCT 59.226 45.455 0.00 0.00 0.00 4.24
264 266 7.419172 GGCAAGGGTATAGAAAGTATTCTCTGT 60.419 40.741 0.00 0.00 44.75 3.41
322 324 5.732331 AAGATTCCATTCTTGGTGGGATA 57.268 39.130 0.00 0.00 44.06 2.59
465 469 7.905265 TCCAAATAAAAATCTGGATCTTTGCA 58.095 30.769 0.00 0.00 32.97 4.08
542 546 3.851403 CGGGCAATATGTTTTCACTTTCG 59.149 43.478 0.00 0.00 0.00 3.46
626 632 0.395036 CCCCAATTGTCGCCATACCA 60.395 55.000 4.43 0.00 0.00 3.25
928 935 2.170012 TACCCCTGTATCGGCTTCTT 57.830 50.000 0.00 0.00 0.00 2.52
1000 1007 0.399949 TCTCGGATTACTGCCCCCAT 60.400 55.000 0.00 0.00 0.00 4.00
1445 1454 4.162320 TGGACTTGAACTTCTCTTGTGAGT 59.838 41.667 0.00 0.00 40.98 3.41
1446 1455 4.697514 TGGACTTGAACTTCTCTTGTGAG 58.302 43.478 0.00 0.00 41.51 3.51
1447 1456 4.443457 CCTGGACTTGAACTTCTCTTGTGA 60.443 45.833 0.00 0.00 0.00 3.58
1448 1457 3.812053 CCTGGACTTGAACTTCTCTTGTG 59.188 47.826 0.00 0.00 0.00 3.33
1449 1458 3.745797 GCCTGGACTTGAACTTCTCTTGT 60.746 47.826 0.00 0.00 0.00 3.16
1459 1468 2.229792 GACAACATGCCTGGACTTGAA 58.770 47.619 0.00 0.00 0.00 2.69
1461 1470 0.518636 CGACAACATGCCTGGACTTG 59.481 55.000 0.00 0.25 0.00 3.16
1462 1471 0.606401 CCGACAACATGCCTGGACTT 60.606 55.000 0.00 0.00 0.00 3.01
1469 1478 3.044059 GCTGAGCCGACAACATGCC 62.044 63.158 0.00 0.00 0.00 4.40
1474 1483 0.305922 GCATATGCTGAGCCGACAAC 59.694 55.000 20.64 0.00 38.21 3.32
1509 1518 2.683362 TGTAGACGAGGTGATGTAGCTG 59.317 50.000 0.00 0.00 37.23 4.24
1510 1519 3.000684 TGTAGACGAGGTGATGTAGCT 57.999 47.619 0.00 0.00 40.52 3.32
1533 1542 8.409371 CACAGAAATCAGTAGAAGCAGAGTATA 58.591 37.037 0.00 0.00 0.00 1.47
1536 1545 5.477510 CACAGAAATCAGTAGAAGCAGAGT 58.522 41.667 0.00 0.00 0.00 3.24
1547 1556 4.623932 TCTTAGTGCCACAGAAATCAGT 57.376 40.909 0.00 0.00 0.00 3.41
1556 1565 5.227569 TCTTCTGAAATCTTAGTGCCACA 57.772 39.130 0.00 0.00 0.00 4.17
1559 1568 6.428159 TGACTTTCTTCTGAAATCTTAGTGCC 59.572 38.462 0.00 0.00 40.85 5.01
1562 1571 9.784531 TGATTGACTTTCTTCTGAAATCTTAGT 57.215 29.630 0.00 0.00 40.85 2.24
1564 1573 9.784531 ACTGATTGACTTTCTTCTGAAATCTTA 57.215 29.630 0.00 0.00 40.85 2.10
1595 1604 8.316497 TCCTAATTTCAATTTGGGATGCATAA 57.684 30.769 0.00 0.00 40.31 1.90
1603 1612 7.475137 TGTTACCTCCTAATTTCAATTTGGG 57.525 36.000 11.39 2.77 40.31 4.12
1617 1626 0.605589 GGCGTGCTTTGTTACCTCCT 60.606 55.000 0.00 0.00 0.00 3.69
1634 1643 2.268600 AAAAATGCATGCCCGGGC 59.731 55.556 39.40 39.40 42.35 6.13
1691 1700 6.806249 TGTTTTTGACAGAGTGTTCAAATCAC 59.194 34.615 0.00 0.00 32.14 3.06
1703 1712 9.708222 CGGAGATAATTTATGTTTTTGACAGAG 57.292 33.333 0.00 0.00 42.62 3.35
1705 1714 9.490663 GTCGGAGATAATTTATGTTTTTGACAG 57.509 33.333 0.00 0.00 39.89 3.51
1719 1728 5.943416 TGACCAAATTGTGTCGGAGATAATT 59.057 36.000 4.39 4.39 40.67 1.40
1722 1731 4.545208 TGACCAAATTGTGTCGGAGATA 57.455 40.909 9.05 0.00 40.67 1.98
1725 1734 3.980646 TTTGACCAAATTGTGTCGGAG 57.019 42.857 9.05 0.00 34.18 4.63
1728 1737 5.280945 AGTTGATTTGACCAAATTGTGTCG 58.719 37.500 9.09 0.00 40.77 4.35
1757 1766 5.640147 TCCTCAAATTTTGTGTAGGTCCAT 58.360 37.500 8.89 0.00 0.00 3.41
1762 1771 7.230712 ACTTAGGTTCCTCAAATTTTGTGTAGG 59.769 37.037 8.89 8.62 0.00 3.18
1763 1772 8.166422 ACTTAGGTTCCTCAAATTTTGTGTAG 57.834 34.615 8.89 0.00 0.00 2.74
1773 1782 9.933723 GTTGTAATACTACTTAGGTTCCTCAAA 57.066 33.333 0.00 0.00 0.00 2.69
1787 1796 6.760298 GGCCTCTTTGGTAGTTGTAATACTAC 59.240 42.308 0.00 5.57 46.26 2.73
1789 1798 5.249852 TGGCCTCTTTGGTAGTTGTAATACT 59.750 40.000 3.32 0.00 38.35 2.12
1836 1847 7.464273 TGGTAGGCTTTCATATTCATCATCAT 58.536 34.615 0.00 0.00 0.00 2.45
1837 1848 6.840527 TGGTAGGCTTTCATATTCATCATCA 58.159 36.000 0.00 0.00 0.00 3.07
1838 1849 6.128063 GCTGGTAGGCTTTCATATTCATCATC 60.128 42.308 0.00 0.00 0.00 2.92
1851 1862 1.142870 TGTGTCTTGCTGGTAGGCTTT 59.857 47.619 0.00 0.00 0.00 3.51
1862 1873 3.149196 TCCTTCCTCATTTGTGTCTTGC 58.851 45.455 0.00 0.00 0.00 4.01
1868 1879 2.507484 TGTGCTCCTTCCTCATTTGTG 58.493 47.619 0.00 0.00 0.00 3.33
1878 1889 4.997395 TGACTTGAATAGTTGTGCTCCTTC 59.003 41.667 0.00 0.00 37.17 3.46
1890 1901 4.509600 GCTCCGGAAGATTGACTTGAATAG 59.490 45.833 5.23 0.00 39.13 1.73
1902 1913 0.257039 ATTGGCAAGCTCCGGAAGAT 59.743 50.000 5.23 0.00 0.00 2.40
1904 1915 1.605710 CATATTGGCAAGCTCCGGAAG 59.394 52.381 5.23 0.46 0.00 3.46
1909 1930 1.878734 GCTCTCATATTGGCAAGCTCC 59.121 52.381 5.96 0.00 0.00 4.70
1928 1949 1.098050 CATGCCAAGTACCCTTCTGC 58.902 55.000 0.00 0.00 0.00 4.26
1930 1951 1.668826 TCCATGCCAAGTACCCTTCT 58.331 50.000 0.00 0.00 0.00 2.85
1934 1955 1.490490 TCTGATCCATGCCAAGTACCC 59.510 52.381 0.00 0.00 0.00 3.69
1937 1958 5.378230 AGATTTCTGATCCATGCCAAGTA 57.622 39.130 0.00 0.00 0.00 2.24
1939 1960 4.643334 TCAAGATTTCTGATCCATGCCAAG 59.357 41.667 0.00 0.00 0.00 3.61
1987 2008 3.555547 GCCACAATCTTTGCGAAACTTTT 59.444 39.130 0.00 0.00 0.00 2.27
1993 2014 1.952990 TGAAGCCACAATCTTTGCGAA 59.047 42.857 0.00 0.00 0.00 4.70
1996 2017 3.656559 ACATTGAAGCCACAATCTTTGC 58.343 40.909 3.47 0.00 38.25 3.68
2008 2029 1.200948 GAGGTGGAGCAACATTGAAGC 59.799 52.381 0.00 0.00 0.00 3.86
2012 2033 5.649782 ATTTTAGAGGTGGAGCAACATTG 57.350 39.130 0.00 0.00 0.00 2.82
2049 2071 9.719355 ACATTCAGTTTGTACTATTGTATGTGA 57.281 29.630 11.89 0.00 31.96 3.58
2060 2082 6.295067 GCCCCAATTTACATTCAGTTTGTACT 60.295 38.462 0.00 0.00 34.00 2.73
2061 2083 5.867174 GCCCCAATTTACATTCAGTTTGTAC 59.133 40.000 0.00 0.00 29.60 2.90
2092 2114 5.371526 GGAGATTCTGCACTTCATTATCCA 58.628 41.667 0.00 0.00 0.00 3.41
2096 2118 3.432186 CCCGGAGATTCTGCACTTCATTA 60.432 47.826 0.73 0.00 0.00 1.90
2107 2129 5.368989 GAATGTGAATAACCCGGAGATTCT 58.631 41.667 0.73 0.00 32.01 2.40
2116 2138 4.684703 CGGATCTACGAATGTGAATAACCC 59.315 45.833 0.00 0.00 35.47 4.11
2142 2167 7.066781 TCCTTCCTCAAGTACCTTTGATTTTT 58.933 34.615 0.00 0.00 36.55 1.94
2152 2177 5.632034 ATGGTATTCCTTCCTCAAGTACC 57.368 43.478 0.00 0.00 32.73 3.34
2213 2244 2.855963 CAAATGATTGCCAATCTGCGTC 59.144 45.455 17.73 0.00 38.72 5.19
2214 2245 2.231964 ACAAATGATTGCCAATCTGCGT 59.768 40.909 17.73 7.55 40.34 5.24
2215 2246 2.601314 CACAAATGATTGCCAATCTGCG 59.399 45.455 17.73 6.99 40.34 5.18
2218 2249 5.244402 TCAGAACACAAATGATTGCCAATCT 59.756 36.000 17.73 1.79 40.34 2.40
2221 2252 4.933505 TCAGAACACAAATGATTGCCAA 57.066 36.364 0.00 0.00 40.34 4.52
2226 2257 8.853126 TCAAAGAGAATCAGAACACAAATGATT 58.147 29.630 0.00 0.00 44.26 2.57
2232 2263 8.204160 TCTACTTCAAAGAGAATCAGAACACAA 58.796 33.333 0.00 0.00 37.82 3.33
2233 2264 7.726216 TCTACTTCAAAGAGAATCAGAACACA 58.274 34.615 0.00 0.00 37.82 3.72
2234 2265 8.594881 TTCTACTTCAAAGAGAATCAGAACAC 57.405 34.615 0.00 0.00 37.82 3.32
2287 2318 8.977412 TGTTCTTCACTGTCCATAGTTCATATA 58.023 33.333 0.00 0.00 0.00 0.86
2288 2319 7.766278 GTGTTCTTCACTGTCCATAGTTCATAT 59.234 37.037 0.00 0.00 43.13 1.78
2289 2320 7.097192 GTGTTCTTCACTGTCCATAGTTCATA 58.903 38.462 0.00 0.00 43.13 2.15
2299 2330 2.433868 TAGCGTGTTCTTCACTGTCC 57.566 50.000 0.00 0.00 44.16 4.02
2300 2331 4.143094 GGAATTAGCGTGTTCTTCACTGTC 60.143 45.833 0.00 0.00 44.16 3.51
2302 2333 3.745975 TGGAATTAGCGTGTTCTTCACTG 59.254 43.478 0.00 0.00 44.16 3.66
2303 2334 4.002906 TGGAATTAGCGTGTTCTTCACT 57.997 40.909 0.00 0.00 44.16 3.41
2315 2346 8.934825 TCAACTGCAAAATTATTTGGAATTAGC 58.065 29.630 0.00 0.00 44.75 3.09
2342 2373 9.965824 GCCATTTAGCTCTATATTGCTTTAAAA 57.034 29.630 0.00 2.04 40.35 1.52
2345 2376 9.436957 GTAGCCATTTAGCTCTATATTGCTTTA 57.563 33.333 9.79 0.00 43.67 1.85
2351 2382 9.535170 TCTGTAGTAGCCATTTAGCTCTATATT 57.465 33.333 0.00 0.00 43.67 1.28
2365 2396 3.382083 TGGTCATCTCTGTAGTAGCCA 57.618 47.619 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.