Multiple sequence alignment - TraesCS1D01G040600

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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 TraesCS1D01G040600 chr1D 100.000 2518 0 0 1 2518 19874451 19871934 0.000000e+00 4650.0
1 TraesCS1D01G040600 chr1D 83.784 111 17 1 2409 2518 412220657 412220767 1.230000e-18 104.0
2 TraesCS1D01G040600 chr1A 87.364 1654 169 17 1 1639 21280435 21278807 0.000000e+00 1860.0
3 TraesCS1D01G040600 chr1A 87.400 873 69 15 1679 2518 21278801 21277937 0.000000e+00 965.0
4 TraesCS1D01G040600 chr1B 87.800 1082 98 14 482 1535 31855528 31854453 0.000000e+00 1236.0
5 TraesCS1D01G040600 chr1B 81.081 111 19 2 2409 2518 555936752 555936861 1.240000e-13 87.9
6 TraesCS1D01G040600 chr7B 90.654 107 9 1 2408 2513 220277159 220277053 9.390000e-30 141.0
7 TraesCS1D01G040600 chr2D 87.850 107 12 1 2408 2513 645305628 645305734 9.460000e-25 124.0
8 TraesCS1D01G040600 chr2A 82.883 111 15 4 2409 2517 16860181 16860073 2.060000e-16 97.1


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 TraesCS1D01G040600 chr1D 19871934 19874451 2517 True 4650.0 4650 100.000 1 2518 1 chr1D.!!$R1 2517
1 TraesCS1D01G040600 chr1A 21277937 21280435 2498 True 1412.5 1860 87.382 1 2518 2 chr1A.!!$R1 2517
2 TraesCS1D01G040600 chr1B 31854453 31855528 1075 True 1236.0 1236 87.800 482 1535 1 chr1B.!!$R1 1053

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
835 843 0.107116 TGAGACGGAGACCTAGAGGC 60.107 60.0 0.0 0.0 39.32 4.7 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1668 1708 0.040058 TAACGGGTGAGGCCAGACTA 59.96 55.0 5.01 0.0 39.65 2.59 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
23 24 4.792521 ATAGTAATTCTAGCCCGAGCAG 57.207 45.455 0.00 0.00 43.56 4.24
72 76 3.449746 TCACCAACATTAAGGAAGGGG 57.550 47.619 0.00 0.00 0.00 4.79
90 94 9.218525 AGGAAGGGGACATATATATGATAACAG 57.781 37.037 26.05 1.57 37.15 3.16
171 176 5.258216 TCCTCTACTTCACTAAGACCAGT 57.742 43.478 0.00 0.00 36.50 4.00
178 183 6.936968 ACTTCACTAAGACCAGTATTTCCT 57.063 37.500 0.00 0.00 36.50 3.36
179 184 9.186837 CTACTTCACTAAGACCAGTATTTCCTA 57.813 37.037 0.00 0.00 36.50 2.94
221 226 7.038302 TGCTTAGGTTCCGAATATATCCTTGAT 60.038 37.037 0.00 0.00 0.00 2.57
222 227 7.278868 GCTTAGGTTCCGAATATATCCTTGATG 59.721 40.741 0.00 0.00 0.00 3.07
287 292 2.925706 TAGGCAGGCGACAACCCA 60.926 61.111 0.00 0.00 0.00 4.51
291 296 2.438434 CAGGCGACAACCCATCCC 60.438 66.667 0.00 0.00 0.00 3.85
292 297 3.728373 AGGCGACAACCCATCCCC 61.728 66.667 0.00 0.00 0.00 4.81
293 298 4.815108 GGCGACAACCCATCCCCC 62.815 72.222 0.00 0.00 0.00 5.40
318 324 2.234296 CCCCCTCCATATGCCCCTC 61.234 68.421 0.00 0.00 0.00 4.30
319 325 2.234296 CCCCTCCATATGCCCCTCC 61.234 68.421 0.00 0.00 0.00 4.30
320 326 2.596851 CCCTCCATATGCCCCTCCG 61.597 68.421 0.00 0.00 0.00 4.63
337 343 2.764128 GGCGAGGGGATGAGGTGA 60.764 66.667 0.00 0.00 0.00 4.02
339 345 1.144936 GCGAGGGGATGAGGTGAAG 59.855 63.158 0.00 0.00 0.00 3.02
341 347 1.418334 CGAGGGGATGAGGTGAAGAT 58.582 55.000 0.00 0.00 0.00 2.40
342 348 1.342819 CGAGGGGATGAGGTGAAGATC 59.657 57.143 0.00 0.00 0.00 2.75
343 349 1.696884 GAGGGGATGAGGTGAAGATCC 59.303 57.143 0.00 0.00 35.78 3.36
346 352 2.926778 GGATGAGGTGAAGATCCCAG 57.073 55.000 0.00 0.00 31.01 4.45
359 365 2.107204 AGATCCCAGTGCTTCTGTTTGT 59.893 45.455 8.23 0.00 42.19 2.83
364 370 2.291741 CCAGTGCTTCTGTTTGTTCTCC 59.708 50.000 8.23 0.00 42.19 3.71
369 375 2.221981 GCTTCTGTTTGTTCTCCGAGTG 59.778 50.000 0.00 0.00 0.00 3.51
382 388 4.148825 GAGTGGCGGTGGCGAGAT 62.149 66.667 0.00 0.00 41.24 2.75
385 391 4.451150 TGGCGGTGGCGAGATGAC 62.451 66.667 0.00 0.00 41.24 3.06
386 392 4.451150 GGCGGTGGCGAGATGACA 62.451 66.667 0.00 0.00 41.24 3.58
387 393 2.434185 GCGGTGGCGAGATGACAA 60.434 61.111 0.00 0.00 37.33 3.18
420 426 5.365605 TCGGTGTGGAATAAGGTATCTTCAT 59.634 40.000 0.00 0.00 34.59 2.57
423 429 6.931840 GGTGTGGAATAAGGTATCTTCATCTC 59.068 42.308 0.00 0.00 34.59 2.75
429 435 4.846779 AAGGTATCTTCATCTCGCTCTC 57.153 45.455 0.00 0.00 0.00 3.20
430 436 3.826524 AGGTATCTTCATCTCGCTCTCA 58.173 45.455 0.00 0.00 0.00 3.27
445 451 0.465705 TCTCATTCCGATGGTGCCTC 59.534 55.000 0.00 0.00 33.93 4.70
447 453 0.911769 TCATTCCGATGGTGCCTCTT 59.088 50.000 0.00 0.00 33.93 2.85
448 454 1.281867 TCATTCCGATGGTGCCTCTTT 59.718 47.619 0.00 0.00 33.93 2.52
449 455 1.402968 CATTCCGATGGTGCCTCTTTG 59.597 52.381 0.00 0.00 0.00 2.77
450 456 0.400213 TTCCGATGGTGCCTCTTTGT 59.600 50.000 0.00 0.00 0.00 2.83
451 457 1.271856 TCCGATGGTGCCTCTTTGTA 58.728 50.000 0.00 0.00 0.00 2.41
452 458 1.837439 TCCGATGGTGCCTCTTTGTAT 59.163 47.619 0.00 0.00 0.00 2.29
453 459 2.238646 TCCGATGGTGCCTCTTTGTATT 59.761 45.455 0.00 0.00 0.00 1.89
454 460 2.355756 CCGATGGTGCCTCTTTGTATTG 59.644 50.000 0.00 0.00 0.00 1.90
457 463 2.422597 TGGTGCCTCTTTGTATTGTCG 58.577 47.619 0.00 0.00 0.00 4.35
490 496 3.041946 GAGGATGGTGTGTCCCTAGATT 58.958 50.000 0.00 0.00 36.36 2.40
517 523 5.924475 TCTCTGTGTCCGAATTTTTCTTC 57.076 39.130 0.00 0.00 0.00 2.87
533 539 3.111853 TCTTCTGCATGTTTGTCTCGT 57.888 42.857 0.00 0.00 0.00 4.18
535 541 4.627058 TCTTCTGCATGTTTGTCTCGTTA 58.373 39.130 0.00 0.00 0.00 3.18
541 547 3.550275 GCATGTTTGTCTCGTTATCGCTA 59.450 43.478 0.00 0.00 36.96 4.26
544 550 4.989044 TGTTTGTCTCGTTATCGCTATCA 58.011 39.130 0.00 0.00 36.96 2.15
594 600 2.865079 TGGTCCTCCATCTCGAGTATC 58.135 52.381 13.13 0.00 39.03 2.24
610 616 5.896922 GAGTATCGACTGATGAATGTTGG 57.103 43.478 0.00 0.00 35.45 3.77
628 634 2.515523 CCAGCCTTGGCCTCGATG 60.516 66.667 3.32 0.00 37.73 3.84
660 666 6.115446 TGTGAGATTTGTGTTCTTTGACTCT 58.885 36.000 0.00 0.00 0.00 3.24
662 668 5.008019 TGAGATTTGTGTTCTTTGACTCTGC 59.992 40.000 0.00 0.00 0.00 4.26
669 675 0.905357 TCTTTGACTCTGCCTAGCCC 59.095 55.000 0.00 0.00 0.00 5.19
700 706 2.811431 CGTTCTACAGGCACATTCCAAA 59.189 45.455 0.00 0.00 0.00 3.28
705 711 6.024552 TCTACAGGCACATTCCAAAATTTC 57.975 37.500 0.00 0.00 0.00 2.17
716 722 3.839778 TCCAAAATTTCCCTTCTTCCGT 58.160 40.909 0.00 0.00 0.00 4.69
725 731 2.508439 TTCTTCCGTGCGGCGATC 60.508 61.111 12.98 0.57 44.77 3.69
727 733 1.659622 TTCTTCCGTGCGGCGATCTA 61.660 55.000 12.98 0.00 44.77 1.98
729 735 2.607668 CTTCCGTGCGGCGATCTACA 62.608 60.000 12.98 0.00 44.77 2.74
730 736 2.011741 TTCCGTGCGGCGATCTACAT 62.012 55.000 12.98 0.00 44.77 2.29
731 737 1.167781 TCCGTGCGGCGATCTACATA 61.168 55.000 12.98 0.00 44.77 2.29
759 767 1.001268 GCTATCGTCGGCATCTTCTGA 60.001 52.381 0.00 0.00 0.00 3.27
769 777 6.033341 GTCGGCATCTTCTGATCTACATATC 58.967 44.000 0.00 0.00 0.00 1.63
812 820 4.016444 TCTGAGTTTCAACAGGTTTGCTT 58.984 39.130 0.00 0.00 35.20 3.91
815 823 1.852280 GTTTCAACAGGTTTGCTTCGC 59.148 47.619 0.00 0.00 0.00 4.70
829 837 1.303398 TTCGCTGAGACGGAGACCT 60.303 57.895 0.00 0.00 0.00 3.85
835 843 0.107116 TGAGACGGAGACCTAGAGGC 60.107 60.000 0.00 0.00 39.32 4.70
842 850 1.305381 AGACCTAGAGGCGGCAACT 60.305 57.895 13.08 12.72 39.32 3.16
845 853 1.742768 CCTAGAGGCGGCAACTAGG 59.257 63.158 31.19 31.19 44.37 3.02
894 902 4.631234 TGGAGGAGGAATAATACTGTGGT 58.369 43.478 0.00 0.00 0.00 4.16
948 957 2.183679 TGCAAGGGTGTTTTTGAAGGT 58.816 42.857 0.00 0.00 0.00 3.50
968 982 9.764363 TGAAGGTTACATGCTACTCAATAATAG 57.236 33.333 0.00 0.00 0.00 1.73
1101 1122 1.490490 TGGGCAAGAGACTGTTGTTCT 59.510 47.619 13.37 0.00 0.00 3.01
1119 1140 4.671590 TGGCCGTCCTCCTCGTCA 62.672 66.667 0.00 0.00 0.00 4.35
1248 1273 3.782244 GAGCTGGCGTGCGACAAG 61.782 66.667 0.68 0.00 38.13 3.16
1444 1470 2.809601 CCGGCGACCTCACTTTCG 60.810 66.667 9.30 0.00 38.31 3.46
1446 1472 2.087009 CGGCGACCTCACTTTCGTC 61.087 63.158 0.00 0.00 37.56 4.20
1536 1569 6.932356 TCTGAATAAATGGACAAGATCTGC 57.068 37.500 0.00 0.00 0.00 4.26
1544 1577 3.300388 TGGACAAGATCTGCCTAGTAGG 58.700 50.000 12.27 12.27 38.80 3.18
1547 1580 4.202172 GGACAAGATCTGCCTAGTAGGTTC 60.202 50.000 17.69 9.60 37.80 3.62
1549 1582 4.965532 ACAAGATCTGCCTAGTAGGTTCAT 59.034 41.667 17.69 6.82 37.80 2.57
1552 1585 2.466846 TCTGCCTAGTAGGTTCATGCA 58.533 47.619 17.69 7.15 37.80 3.96
1609 1649 2.960819 ACTCGATCTTTTAGCTGCGTT 58.039 42.857 0.00 0.00 0.00 4.84
1640 1680 4.133796 GATGCAAAGGCCGGGCAC 62.134 66.667 31.59 16.51 40.83 5.01
1653 1693 4.643387 GGCACCACGTTGGGCTCT 62.643 66.667 14.14 0.00 43.37 4.09
1654 1694 3.357079 GCACCACGTTGGGCTCTG 61.357 66.667 6.62 0.00 43.37 3.35
1655 1695 2.425592 CACCACGTTGGGCTCTGA 59.574 61.111 8.57 0.00 43.37 3.27
1656 1696 1.961277 CACCACGTTGGGCTCTGAC 60.961 63.158 8.57 0.00 43.37 3.51
1657 1697 2.738521 CCACGTTGGGCTCTGACG 60.739 66.667 10.80 10.80 42.13 4.35
1658 1698 2.338620 CACGTTGGGCTCTGACGA 59.661 61.111 17.78 0.00 39.85 4.20
1659 1699 1.079819 CACGTTGGGCTCTGACGAT 60.080 57.895 17.78 2.25 39.85 3.73
1660 1700 0.670546 CACGTTGGGCTCTGACGATT 60.671 55.000 17.78 0.00 39.85 3.34
1661 1701 0.034896 ACGTTGGGCTCTGACGATTT 59.965 50.000 17.78 0.00 39.85 2.17
1662 1702 0.443869 CGTTGGGCTCTGACGATTTG 59.556 55.000 7.19 0.00 38.99 2.32
1663 1703 1.808411 GTTGGGCTCTGACGATTTGA 58.192 50.000 0.00 0.00 0.00 2.69
1664 1704 2.151202 GTTGGGCTCTGACGATTTGAA 58.849 47.619 0.00 0.00 0.00 2.69
1665 1705 2.552315 GTTGGGCTCTGACGATTTGAAA 59.448 45.455 0.00 0.00 0.00 2.69
1666 1706 2.857483 TGGGCTCTGACGATTTGAAAA 58.143 42.857 0.00 0.00 0.00 2.29
1667 1707 3.420893 TGGGCTCTGACGATTTGAAAAT 58.579 40.909 0.00 0.00 0.00 1.82
1668 1708 3.826157 TGGGCTCTGACGATTTGAAAATT 59.174 39.130 0.00 0.00 0.00 1.82
1669 1709 5.007034 TGGGCTCTGACGATTTGAAAATTA 58.993 37.500 0.00 0.00 0.00 1.40
1670 1710 5.123820 TGGGCTCTGACGATTTGAAAATTAG 59.876 40.000 0.00 0.00 0.00 1.73
1671 1711 5.123979 GGGCTCTGACGATTTGAAAATTAGT 59.876 40.000 0.00 0.00 0.00 2.24
1672 1712 6.251549 GGCTCTGACGATTTGAAAATTAGTC 58.748 40.000 13.68 13.68 37.12 2.59
1673 1713 6.092807 GGCTCTGACGATTTGAAAATTAGTCT 59.907 38.462 17.92 0.00 37.30 3.24
1674 1714 6.958193 GCTCTGACGATTTGAAAATTAGTCTG 59.042 38.462 17.92 17.27 37.30 3.51
1675 1715 7.364522 TCTGACGATTTGAAAATTAGTCTGG 57.635 36.000 19.43 14.43 37.30 3.86
1676 1716 5.938322 TGACGATTTGAAAATTAGTCTGGC 58.062 37.500 17.92 0.00 37.30 4.85
1677 1717 5.106317 TGACGATTTGAAAATTAGTCTGGCC 60.106 40.000 17.92 0.00 37.30 5.36
1685 1725 0.617820 ATTAGTCTGGCCTCACCCGT 60.618 55.000 3.32 0.00 37.83 5.28
1686 1726 0.834687 TTAGTCTGGCCTCACCCGTT 60.835 55.000 3.32 0.00 37.83 4.44
1704 1744 7.767198 TCACCCGTTATCTAAGAAAACTTATGG 59.233 37.037 0.00 0.00 0.00 2.74
1718 1758 6.926630 AAACTTATGGCAACTTCCCAATTA 57.073 33.333 0.00 0.00 35.67 1.40
1737 1777 1.241315 ATCCGGCTTCAAAACCACCG 61.241 55.000 0.00 0.00 43.44 4.94
1752 1792 1.343465 CCACCGTGGTTCTGTCTAACT 59.657 52.381 9.64 0.00 31.35 2.24
1753 1793 2.224209 CCACCGTGGTTCTGTCTAACTT 60.224 50.000 9.64 0.00 31.35 2.66
1761 1801 3.819337 GGTTCTGTCTAACTTTGTTCCCC 59.181 47.826 0.00 0.00 0.00 4.81
1766 1806 4.913784 TGTCTAACTTTGTTCCCCATACC 58.086 43.478 0.00 0.00 0.00 2.73
1779 1819 5.152306 TCCCCATACCTACACACTTATCT 57.848 43.478 0.00 0.00 0.00 1.98
1804 1844 8.492673 TCAAAGTTGTAAGCTAATACCATCAG 57.507 34.615 0.00 0.00 0.00 2.90
1807 1847 9.515226 AAAGTTGTAAGCTAATACCATCAGAAA 57.485 29.630 0.00 0.00 0.00 2.52
1812 1852 5.248380 AGCTAATACCATCAGAAATCCCC 57.752 43.478 0.00 0.00 0.00 4.81
1824 1864 6.693315 TCAGAAATCCCCGTTTAATTGATC 57.307 37.500 0.00 0.00 0.00 2.92
1830 1870 4.594970 TCCCCGTTTAATTGATCATGTGT 58.405 39.130 0.00 0.00 0.00 3.72
1834 1874 4.794762 CCGTTTAATTGATCATGTGTGCAG 59.205 41.667 0.00 0.00 0.00 4.41
1850 1890 1.617740 GCAGTGCGCATCCTTTTAAC 58.382 50.000 15.91 0.00 41.79 2.01
1878 1918 9.541143 GAAAAGTATTCCTGTTTTTCATCCAAA 57.459 29.630 4.26 0.00 38.65 3.28
1917 1957 1.739466 TGCGTCCTTTTCATGCAGATC 59.261 47.619 0.00 0.00 31.94 2.75
1988 2028 9.513906 TCACATAGAATTTATGTTGAGTTGGAA 57.486 29.630 9.28 0.00 36.13 3.53
1989 2029 9.778993 CACATAGAATTTATGTTGAGTTGGAAG 57.221 33.333 9.28 0.00 36.13 3.46
2012 2052 9.833182 GAAGAGTGATCAAAGAAATAAAAGGTC 57.167 33.333 0.00 0.00 0.00 3.85
2052 2095 9.720769 TTTTCATCGTACTAGATTTTCTTCCTT 57.279 29.630 0.00 0.00 0.00 3.36
2058 2101 6.531948 CGTACTAGATTTTCTTCCTTCACCAG 59.468 42.308 0.00 0.00 0.00 4.00
2061 2104 7.974504 ACTAGATTTTCTTCCTTCACCAGTTA 58.025 34.615 0.00 0.00 0.00 2.24
2062 2105 8.606830 ACTAGATTTTCTTCCTTCACCAGTTAT 58.393 33.333 0.00 0.00 0.00 1.89
2094 2137 4.967084 ATAATATTAGTCGCCACCCACA 57.033 40.909 1.02 0.00 0.00 4.17
2373 2428 0.991146 TGTGAGCTATGAAAGGGGCA 59.009 50.000 0.00 0.00 0.00 5.36
2396 2451 3.722908 TCTAGCCATCGTAGGAGCTAT 57.277 47.619 6.80 0.00 37.22 2.97
2402 2475 2.802816 CCATCGTAGGAGCTATTTGTGC 59.197 50.000 0.00 0.00 0.00 4.57
2416 2489 1.850377 TTGTGCGGACATTTTGCAAG 58.150 45.000 11.62 0.00 40.83 4.01
2435 2508 5.985530 TGCAAGATATTTCGATGAGATTCGT 59.014 36.000 0.00 0.00 40.03 3.85
2444 2517 6.812481 TTCGATGAGATTCGTTGTATGAAG 57.188 37.500 0.00 0.00 40.03 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.891580 CCTGCTCGGGCTAGAATTACTA 59.108 50.000 9.62 0.00 39.59 1.82
23 24 1.153784 CCATTCAACATGTGCCGCC 60.154 57.895 0.00 0.00 0.00 6.13
109 113 8.485976 TTGAAAAGTTATGTTTCCCTTGTTTG 57.514 30.769 0.00 0.00 34.67 2.93
144 149 8.294954 TGGTCTTAGTGAAGTAGAGGATAAAG 57.705 38.462 0.00 0.00 34.03 1.85
145 150 7.894364 ACTGGTCTTAGTGAAGTAGAGGATAAA 59.106 37.037 0.00 0.00 34.03 1.40
204 209 9.366216 CGTTAATTCATCAAGGATATATTCGGA 57.634 33.333 0.00 0.00 0.00 4.55
205 210 9.366216 TCGTTAATTCATCAAGGATATATTCGG 57.634 33.333 0.00 0.00 0.00 4.30
221 226 5.790593 AGCTTAAGTGGTCTCGTTAATTCA 58.209 37.500 4.02 0.00 0.00 2.57
222 227 7.758528 TCTTAGCTTAAGTGGTCTCGTTAATTC 59.241 37.037 4.02 0.00 37.10 2.17
229 234 4.859798 CACTTCTTAGCTTAAGTGGTCTCG 59.140 45.833 20.38 3.12 45.68 4.04
261 266 3.335711 GCCTGCCTAGGTGGGAAT 58.664 61.111 21.20 0.00 46.41 3.01
299 305 2.121506 GGGGCATATGGAGGGGGA 60.122 66.667 4.56 0.00 0.00 4.81
301 307 2.234296 GGAGGGGCATATGGAGGGG 61.234 68.421 4.56 0.00 0.00 4.79
319 325 4.227134 CACCTCATCCCCTCGCCG 62.227 72.222 0.00 0.00 0.00 6.46
320 326 2.317149 CTTCACCTCATCCCCTCGCC 62.317 65.000 0.00 0.00 0.00 5.54
324 330 1.813102 GGATCTTCACCTCATCCCCT 58.187 55.000 0.00 0.00 31.31 4.79
327 333 2.122768 ACTGGGATCTTCACCTCATCC 58.877 52.381 0.00 0.00 36.14 3.51
330 336 0.615331 GCACTGGGATCTTCACCTCA 59.385 55.000 0.00 0.00 0.00 3.86
344 350 6.075780 CTCGGAGAACAAACAGAAGCACTG 62.076 50.000 0.00 8.93 44.59 3.66
346 352 2.210116 TCGGAGAACAAACAGAAGCAC 58.790 47.619 0.00 0.00 0.00 4.40
369 375 3.950794 TTGTCATCTCGCCACCGCC 62.951 63.158 0.00 0.00 0.00 6.13
382 388 4.277239 CCGAAGGCGATGTTGTCA 57.723 55.556 0.00 0.00 46.14 3.58
420 426 0.670706 CCATCGGAATGAGAGCGAGA 59.329 55.000 0.00 0.00 34.61 4.04
423 429 1.493950 GCACCATCGGAATGAGAGCG 61.494 60.000 0.00 0.00 34.61 5.03
429 435 1.402968 CAAAGAGGCACCATCGGAATG 59.597 52.381 0.00 0.00 0.00 2.67
430 436 1.004745 ACAAAGAGGCACCATCGGAAT 59.995 47.619 0.00 0.00 0.00 3.01
445 451 2.107950 TGCCTCCCGACAATACAAAG 57.892 50.000 0.00 0.00 0.00 2.77
447 453 2.752354 CAAATGCCTCCCGACAATACAA 59.248 45.455 0.00 0.00 0.00 2.41
448 454 2.364632 CAAATGCCTCCCGACAATACA 58.635 47.619 0.00 0.00 0.00 2.29
449 455 1.676006 CCAAATGCCTCCCGACAATAC 59.324 52.381 0.00 0.00 0.00 1.89
450 456 1.562008 TCCAAATGCCTCCCGACAATA 59.438 47.619 0.00 0.00 0.00 1.90
451 457 0.331278 TCCAAATGCCTCCCGACAAT 59.669 50.000 0.00 0.00 0.00 2.71
452 458 0.322456 CTCCAAATGCCTCCCGACAA 60.322 55.000 0.00 0.00 0.00 3.18
453 459 1.299648 CTCCAAATGCCTCCCGACA 59.700 57.895 0.00 0.00 0.00 4.35
454 460 1.452108 CCTCCAAATGCCTCCCGAC 60.452 63.158 0.00 0.00 0.00 4.79
457 463 0.468771 CCATCCTCCAAATGCCTCCC 60.469 60.000 0.00 0.00 0.00 4.30
467 473 0.415830 TAGGGACACACCATCCTCCA 59.584 55.000 0.00 0.00 41.20 3.86
468 474 1.123928 CTAGGGACACACCATCCTCC 58.876 60.000 0.00 0.00 41.20 4.30
490 496 3.380479 AATTCGGACACAGAGAAACGA 57.620 42.857 0.00 0.00 0.00 3.85
517 523 3.782250 GCGATAACGAGACAAACATGCAG 60.782 47.826 0.00 0.00 42.66 4.41
541 547 0.036105 TGTTGTCCGCTCTGCATGAT 60.036 50.000 0.00 0.00 0.00 2.45
544 550 2.029288 CGTGTTGTCCGCTCTGCAT 61.029 57.895 0.00 0.00 0.00 3.96
594 600 1.399440 CTGGCCAACATTCATCAGTCG 59.601 52.381 7.01 0.00 0.00 4.18
598 604 0.040058 AGGCTGGCCAACATTCATCA 59.960 50.000 7.01 0.00 38.92 3.07
627 633 1.425066 ACAAATCTCACAAGCTCCCCA 59.575 47.619 0.00 0.00 0.00 4.96
628 634 1.815003 CACAAATCTCACAAGCTCCCC 59.185 52.381 0.00 0.00 0.00 4.81
669 675 0.806102 CTGTAGAACGCCCCATGTCG 60.806 60.000 0.00 0.00 0.00 4.35
700 706 1.165270 CGCACGGAAGAAGGGAAATT 58.835 50.000 0.00 0.00 0.00 1.82
716 722 0.039165 CTGCTATGTAGATCGCCGCA 60.039 55.000 0.00 0.00 0.00 5.69
742 750 1.959985 AGATCAGAAGATGCCGACGAT 59.040 47.619 0.00 0.00 33.72 3.73
745 753 3.717400 TGTAGATCAGAAGATGCCGAC 57.283 47.619 0.00 0.00 33.72 4.79
759 767 2.724454 ACTAGCGGCCGATATGTAGAT 58.276 47.619 33.48 5.45 0.00 1.98
769 777 0.997196 GTTTGTAGAACTAGCGGCCG 59.003 55.000 24.05 24.05 0.00 6.13
812 820 0.462225 CTAGGTCTCCGTCTCAGCGA 60.462 60.000 0.00 0.00 0.00 4.93
815 823 1.961793 CCTCTAGGTCTCCGTCTCAG 58.038 60.000 0.00 0.00 0.00 3.35
829 837 1.066430 CAAACCTAGTTGCCGCCTCTA 60.066 52.381 0.00 0.00 0.00 2.43
968 982 2.677542 GGGGGAAGGGATAACATTCC 57.322 55.000 2.41 2.41 41.51 3.01
1070 1085 4.219507 AGTCTCTTGCCCATCTCGTATATG 59.780 45.833 0.00 0.00 0.00 1.78
1101 1122 3.379445 GACGAGGAGGACGGCCAA 61.379 66.667 11.69 0.00 36.29 4.52
1119 1140 5.376775 CGAATTCGAACACTTACGGGAAGT 61.377 45.833 23.29 0.00 45.31 3.01
1444 1470 1.772182 CATATTCCTCAGTCGGCGAC 58.228 55.000 31.33 31.33 0.00 5.19
1446 1472 1.278172 CGCATATTCCTCAGTCGGCG 61.278 60.000 0.00 0.00 37.17 6.46
1447 1473 0.946221 CCGCATATTCCTCAGTCGGC 60.946 60.000 0.00 0.00 0.00 5.54
1536 1569 5.529060 GGAAAGATTGCATGAACCTACTAGG 59.471 44.000 0.00 0.00 42.49 3.02
1544 1577 5.990996 TCCTTTTTGGAAAGATTGCATGAAC 59.009 36.000 0.00 0.00 44.03 3.18
1639 1679 2.426023 GTCAGAGCCCAACGTGGT 59.574 61.111 0.00 0.00 35.17 4.16
1640 1680 2.507110 ATCGTCAGAGCCCAACGTGG 62.507 60.000 0.00 0.00 37.64 4.94
1641 1681 0.670546 AATCGTCAGAGCCCAACGTG 60.671 55.000 0.00 0.00 37.64 4.49
1643 1683 0.443869 CAAATCGTCAGAGCCCAACG 59.556 55.000 0.00 0.00 37.74 4.10
1644 1684 1.808411 TCAAATCGTCAGAGCCCAAC 58.192 50.000 0.00 0.00 0.00 3.77
1645 1685 2.559698 TTCAAATCGTCAGAGCCCAA 57.440 45.000 0.00 0.00 0.00 4.12
1646 1686 2.559698 TTTCAAATCGTCAGAGCCCA 57.440 45.000 0.00 0.00 0.00 5.36
1647 1687 4.440839 AATTTTCAAATCGTCAGAGCCC 57.559 40.909 0.00 0.00 0.00 5.19
1648 1688 6.092807 AGACTAATTTTCAAATCGTCAGAGCC 59.907 38.462 13.09 0.00 34.17 4.70
1649 1689 6.958193 CAGACTAATTTTCAAATCGTCAGAGC 59.042 38.462 13.09 0.00 34.17 4.09
1650 1690 7.459486 CCAGACTAATTTTCAAATCGTCAGAG 58.541 38.462 13.09 6.33 34.17 3.35
1651 1691 6.128282 GCCAGACTAATTTTCAAATCGTCAGA 60.128 38.462 13.09 0.00 34.17 3.27
1652 1692 6.024049 GCCAGACTAATTTTCAAATCGTCAG 58.976 40.000 13.09 7.91 34.17 3.51
1653 1693 5.106317 GGCCAGACTAATTTTCAAATCGTCA 60.106 40.000 0.00 0.00 34.17 4.35
1654 1694 5.123979 AGGCCAGACTAATTTTCAAATCGTC 59.876 40.000 5.01 6.57 33.00 4.20
1655 1695 5.010282 AGGCCAGACTAATTTTCAAATCGT 58.990 37.500 5.01 0.00 0.00 3.73
1656 1696 5.123820 TGAGGCCAGACTAATTTTCAAATCG 59.876 40.000 5.01 0.00 0.00 3.34
1657 1697 6.325596 GTGAGGCCAGACTAATTTTCAAATC 58.674 40.000 5.01 0.00 0.00 2.17
1658 1698 5.185828 GGTGAGGCCAGACTAATTTTCAAAT 59.814 40.000 5.01 0.00 37.17 2.32
1659 1699 4.522789 GGTGAGGCCAGACTAATTTTCAAA 59.477 41.667 5.01 0.00 37.17 2.69
1660 1700 4.079253 GGTGAGGCCAGACTAATTTTCAA 58.921 43.478 5.01 0.00 37.17 2.69
1661 1701 3.561313 GGGTGAGGCCAGACTAATTTTCA 60.561 47.826 5.01 0.00 39.65 2.69
1662 1702 3.017442 GGGTGAGGCCAGACTAATTTTC 58.983 50.000 5.01 0.00 39.65 2.29
1663 1703 2.618045 CGGGTGAGGCCAGACTAATTTT 60.618 50.000 5.01 0.00 39.65 1.82
1664 1704 1.065418 CGGGTGAGGCCAGACTAATTT 60.065 52.381 5.01 0.00 39.65 1.82
1665 1705 0.541863 CGGGTGAGGCCAGACTAATT 59.458 55.000 5.01 0.00 39.65 1.40
1666 1706 0.617820 ACGGGTGAGGCCAGACTAAT 60.618 55.000 5.01 0.00 39.65 1.73
1667 1707 0.834687 AACGGGTGAGGCCAGACTAA 60.835 55.000 5.01 0.00 39.65 2.24
1668 1708 0.040058 TAACGGGTGAGGCCAGACTA 59.960 55.000 5.01 0.00 39.65 2.59
1669 1709 0.617820 ATAACGGGTGAGGCCAGACT 60.618 55.000 5.01 0.00 39.65 3.24
1670 1710 0.179081 GATAACGGGTGAGGCCAGAC 60.179 60.000 5.01 0.00 39.65 3.51
1671 1711 0.325296 AGATAACGGGTGAGGCCAGA 60.325 55.000 5.01 0.00 39.65 3.86
1672 1712 1.410004 TAGATAACGGGTGAGGCCAG 58.590 55.000 5.01 0.00 39.65 4.85
1673 1713 1.760613 CTTAGATAACGGGTGAGGCCA 59.239 52.381 5.01 0.00 39.65 5.36
1674 1714 2.037144 TCTTAGATAACGGGTGAGGCC 58.963 52.381 0.00 0.00 0.00 5.19
1675 1715 3.814005 TTCTTAGATAACGGGTGAGGC 57.186 47.619 0.00 0.00 0.00 4.70
1676 1716 5.731591 AGTTTTCTTAGATAACGGGTGAGG 58.268 41.667 9.27 0.00 30.88 3.86
1677 1717 8.818057 CATAAGTTTTCTTAGATAACGGGTGAG 58.182 37.037 9.27 0.00 44.27 3.51
1686 1726 9.174166 GGAAGTTGCCATAAGTTTTCTTAGATA 57.826 33.333 0.00 0.00 44.27 1.98
1704 1744 1.067060 GCCGGATAATTGGGAAGTTGC 59.933 52.381 5.05 0.00 0.00 4.17
1718 1758 1.241315 CGGTGGTTTTGAAGCCGGAT 61.241 55.000 5.05 0.00 38.86 4.18
1737 1777 4.275196 GGGAACAAAGTTAGACAGAACCAC 59.725 45.833 0.00 0.00 0.00 4.16
1743 1783 4.941873 GGTATGGGGAACAAAGTTAGACAG 59.058 45.833 0.00 0.00 0.00 3.51
1745 1785 5.175388 AGGTATGGGGAACAAAGTTAGAC 57.825 43.478 0.00 0.00 0.00 2.59
1752 1792 3.653836 AGTGTGTAGGTATGGGGAACAAA 59.346 43.478 0.00 0.00 0.00 2.83
1753 1793 3.253220 AGTGTGTAGGTATGGGGAACAA 58.747 45.455 0.00 0.00 0.00 2.83
1761 1801 8.873830 CAACTTTGAGATAAGTGTGTAGGTATG 58.126 37.037 0.00 0.00 38.33 2.39
1766 1806 8.436200 GCTTACAACTTTGAGATAAGTGTGTAG 58.564 37.037 0.00 0.00 38.33 2.74
1779 1819 8.318412 TCTGATGGTATTAGCTTACAACTTTGA 58.682 33.333 0.00 0.00 0.00 2.69
1799 1839 6.449635 TCAATTAAACGGGGATTTCTGATG 57.550 37.500 0.00 0.00 0.00 3.07
1804 1844 6.697019 CACATGATCAATTAAACGGGGATTTC 59.303 38.462 0.00 0.00 0.00 2.17
1807 1847 5.067674 CACACATGATCAATTAAACGGGGAT 59.932 40.000 0.00 0.00 0.00 3.85
1812 1852 5.284424 CACTGCACACATGATCAATTAAACG 59.716 40.000 0.00 0.00 0.00 3.60
1834 1874 0.800012 TCCGTTAAAAGGATGCGCAC 59.200 50.000 14.90 6.86 31.86 5.34
1850 1890 6.806739 GGATGAAAAACAGGAATACTTTTCCG 59.193 38.462 0.00 0.00 43.23 4.30
1878 1918 3.546020 CGCACGACATCAAACAAGAACTT 60.546 43.478 0.00 0.00 0.00 2.66
1964 2004 9.739276 TCTTCCAACTCAACATAAATTCTATGT 57.261 29.630 7.19 7.19 39.60 2.29
1969 2009 8.099364 TCACTCTTCCAACTCAACATAAATTC 57.901 34.615 0.00 0.00 0.00 2.17
1988 2028 9.579932 AAGACCTTTTATTTCTTTGATCACTCT 57.420 29.630 0.00 0.00 0.00 3.24
1989 2029 9.833182 GAAGACCTTTTATTTCTTTGATCACTC 57.167 33.333 0.00 0.00 29.54 3.51
2024 2067 9.756461 GGAAGAAAATCTAGTACGATGAAAAAC 57.244 33.333 0.00 0.00 0.00 2.43
2025 2068 9.720769 AGGAAGAAAATCTAGTACGATGAAAAA 57.279 29.630 0.00 0.00 0.00 1.94
2042 2085 5.833131 AGCAATAACTGGTGAAGGAAGAAAA 59.167 36.000 0.00 0.00 33.42 2.29
2046 2089 7.396540 AATAAGCAATAACTGGTGAAGGAAG 57.603 36.000 0.00 0.00 35.42 3.46
2294 2349 7.841282 TGTCCTGACCCAAAAATAATTACAA 57.159 32.000 0.00 0.00 0.00 2.41
2296 2351 7.123547 TCCATGTCCTGACCCAAAAATAATTAC 59.876 37.037 0.00 0.00 0.00 1.89
2299 2354 5.588845 TCCATGTCCTGACCCAAAAATAAT 58.411 37.500 0.00 0.00 0.00 1.28
2373 2428 1.957877 GCTCCTACGATGGCTAGAACT 59.042 52.381 0.00 0.00 0.00 3.01
2385 2440 1.202371 TCCGCACAAATAGCTCCTACG 60.202 52.381 0.00 0.00 0.00 3.51
2396 2451 2.159184 TCTTGCAAAATGTCCGCACAAA 60.159 40.909 0.00 0.00 35.64 2.83
2402 2475 5.568482 TCGAAATATCTTGCAAAATGTCCG 58.432 37.500 0.00 0.00 0.00 4.79
2416 2489 9.129209 TCATACAACGAATCTCATCGAAATATC 57.871 33.333 3.47 0.00 45.48 1.63
2435 2508 8.523915 ACTCCAAATATTCATGCTTCATACAA 57.476 30.769 0.00 0.00 0.00 2.41


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

AutoCloner maintained by Alex Coulton.