Multiple sequence alignment - TraesCS3D01G143900

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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 TraesCS3D01G143900 chr3D 100.000 2704 0 0 1 2704 107072758 107070055 0 4994
1 TraesCS3D01G143900 chr3B 90.443 2731 145 53 1 2704 157922907 157920266 0 3491
2 TraesCS3D01G143900 chr3A 88.210 2782 188 47 1 2704 549618727 549621446 0 3192


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 TraesCS3D01G143900 chr3D 107070055 107072758 2703 True 4994 4994 100.000 1 2704 1 chr3D.!!$R1 2703
1 TraesCS3D01G143900 chr3B 157920266 157922907 2641 True 3491 3491 90.443 1 2704 1 chr3B.!!$R1 2703
2 TraesCS3D01G143900 chr3A 549618727 549621446 2719 False 3192 3192 88.210 1 2704 1 chr3A.!!$F1 2703

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
631 649 0.028902 GGACAGTGCGTGTTGAAACC 59.971 55.0 0.0 0.0 40.56 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1713 1803 0.321122 CTGAAGAACTTGGGCGAGCT 60.321 55.0 0.0 0.0 0.0 4.09 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
49 50 9.920946 AGGTGAGGCATTAGAGAAAAATAAATA 57.079 29.630 0.00 0.00 0.00 1.40
147 156 1.302949 GGGCATTGCTGTAGGTGGA 59.697 57.895 8.82 0.00 0.00 4.02
324 335 3.610677 GTGTTTTGACACCAAACCTTTCG 59.389 43.478 0.00 0.00 41.54 3.46
325 336 3.256136 TGTTTTGACACCAAACCTTTCGT 59.744 39.130 1.31 0.00 41.54 3.85
417 428 1.731700 CGATACCGCCTTCGAGGAA 59.268 57.895 0.00 0.00 37.67 3.36
442 453 1.671742 GCCGTGGAGAAGAAGGACA 59.328 57.895 0.00 0.00 0.00 4.02
505 516 0.875040 CAGCATGTAGGCAGCGAGAG 60.875 60.000 0.00 0.00 35.83 3.20
521 532 0.901124 AGAGAGCAGACAAGGCGATT 59.099 50.000 0.00 0.00 36.08 3.34
525 536 0.679002 AGCAGACAAGGCGATTGCAT 60.679 50.000 7.38 0.00 43.15 3.96
546 562 0.832030 GATTGTCATCGTCGTCGTCG 59.168 55.000 5.50 5.50 38.33 5.12
565 581 1.477295 CGGTCTAAGACTCCAGGAACC 59.523 57.143 0.00 0.00 32.47 3.62
597 615 2.930826 TGTCCCTTGGAGAACTTGTC 57.069 50.000 0.00 0.00 29.39 3.18
616 634 2.948979 GTCTGTGTTGAAACCATGGACA 59.051 45.455 21.47 9.15 0.00 4.02
617 635 3.003689 GTCTGTGTTGAAACCATGGACAG 59.996 47.826 21.47 18.89 0.00 3.51
618 636 2.951642 CTGTGTTGAAACCATGGACAGT 59.048 45.455 21.47 0.00 0.00 3.55
619 637 2.687425 TGTGTTGAAACCATGGACAGTG 59.313 45.455 21.47 0.00 0.00 3.66
620 638 1.680735 TGTTGAAACCATGGACAGTGC 59.319 47.619 21.47 4.98 0.00 4.40
621 639 0.950836 TTGAAACCATGGACAGTGCG 59.049 50.000 21.47 0.00 0.00 5.34
622 640 0.179032 TGAAACCATGGACAGTGCGT 60.179 50.000 21.47 0.00 0.00 5.24
623 641 0.238289 GAAACCATGGACAGTGCGTG 59.762 55.000 21.47 7.30 0.00 5.34
624 642 0.465460 AAACCATGGACAGTGCGTGT 60.465 50.000 21.47 0.00 44.49 4.49
625 643 0.465460 AACCATGGACAGTGCGTGTT 60.465 50.000 21.47 5.21 40.56 3.32
626 644 1.165907 ACCATGGACAGTGCGTGTTG 61.166 55.000 21.47 1.82 40.56 3.33
627 645 0.884259 CCATGGACAGTGCGTGTTGA 60.884 55.000 5.56 0.00 40.56 3.18
628 646 0.943673 CATGGACAGTGCGTGTTGAA 59.056 50.000 6.11 0.00 40.56 2.69
629 647 1.333308 CATGGACAGTGCGTGTTGAAA 59.667 47.619 6.11 0.00 40.56 2.69
630 648 0.730265 TGGACAGTGCGTGTTGAAAC 59.270 50.000 0.00 0.00 40.56 2.78
631 649 0.028902 GGACAGTGCGTGTTGAAACC 59.971 55.000 0.00 0.00 40.56 3.27
632 650 0.730265 GACAGTGCGTGTTGAAACCA 59.270 50.000 0.00 0.00 40.56 3.67
633 651 1.333619 GACAGTGCGTGTTGAAACCAT 59.666 47.619 0.00 0.00 40.56 3.55
634 652 1.065401 ACAGTGCGTGTTGAAACCATG 59.935 47.619 0.00 0.00 34.94 3.66
635 653 0.667993 AGTGCGTGTTGAAACCATGG 59.332 50.000 11.19 11.19 0.00 3.66
636 654 0.665835 GTGCGTGTTGAAACCATGGA 59.334 50.000 21.47 0.00 0.00 3.41
637 655 0.665835 TGCGTGTTGAAACCATGGAC 59.334 50.000 21.47 6.11 0.00 4.02
638 656 0.665835 GCGTGTTGAAACCATGGACA 59.334 50.000 21.47 9.15 0.00 4.02
642 660 1.680735 TGTTGAAACCATGGACAGTGC 59.319 47.619 21.47 4.98 0.00 4.40
705 723 4.464008 TGAACTCTTGAGTCATGGCTTTT 58.536 39.130 0.00 0.00 0.00 2.27
731 749 1.900351 TCTGAACTGGGCAGATCCG 59.100 57.895 0.00 0.00 37.46 4.18
764 785 1.073199 GTCCTTGGGTGGTGACTGG 59.927 63.158 0.00 0.00 0.00 4.00
772 793 1.577328 GGTGGTGACTGGTGAATGCG 61.577 60.000 0.00 0.00 0.00 4.73
773 794 0.884704 GTGGTGACTGGTGAATGCGT 60.885 55.000 0.00 0.00 0.00 5.24
781 802 1.083806 TGGTGAATGCGTCTCGATGC 61.084 55.000 4.21 4.21 43.39 3.91
866 905 2.606519 TCCAGCTAACACCGGCCT 60.607 61.111 0.00 0.00 0.00 5.19
1010 1076 2.911509 AAGTGCAATGGCCACGCA 60.912 55.556 24.21 24.21 40.13 5.24
1188 1266 1.134965 CACTTCATCGACAGGGAGTCC 60.135 57.143 0.00 0.00 44.66 3.85
1240 1318 3.591254 GACGAGTGGTCCACCTGGC 62.591 68.421 18.80 9.78 39.90 4.85
1352 1437 2.277084 GGTAGGCAATACCGTGAACAG 58.723 52.381 1.94 0.00 44.61 3.16
1353 1438 1.664151 GTAGGCAATACCGTGAACAGC 59.336 52.381 0.00 0.00 46.52 4.40
1354 1439 0.324943 AGGCAATACCGTGAACAGCT 59.675 50.000 0.00 0.00 46.52 4.24
1355 1440 0.447801 GGCAATACCGTGAACAGCTG 59.552 55.000 13.48 13.48 0.00 4.24
1356 1441 1.438651 GCAATACCGTGAACAGCTGA 58.561 50.000 23.35 0.00 0.00 4.26
1357 1442 1.804151 GCAATACCGTGAACAGCTGAA 59.196 47.619 23.35 2.14 0.00 3.02
1359 1444 2.805671 CAATACCGTGAACAGCTGAACA 59.194 45.455 23.35 16.46 0.00 3.18
1360 1445 1.860676 TACCGTGAACAGCTGAACAC 58.139 50.000 23.35 24.89 0.00 3.32
1361 1446 0.814010 ACCGTGAACAGCTGAACACC 60.814 55.000 27.61 17.20 0.00 4.16
1362 1447 1.564622 CGTGAACAGCTGAACACCG 59.435 57.895 27.61 21.83 0.00 4.94
1363 1448 0.874175 CGTGAACAGCTGAACACCGA 60.874 55.000 27.61 5.83 0.00 4.69
1364 1449 0.861837 GTGAACAGCTGAACACCGAG 59.138 55.000 23.35 0.00 0.00 4.63
1365 1450 0.464036 TGAACAGCTGAACACCGAGT 59.536 50.000 23.35 0.00 0.00 4.18
1366 1451 1.140816 GAACAGCTGAACACCGAGTC 58.859 55.000 23.35 0.00 0.00 3.36
1367 1452 0.464036 AACAGCTGAACACCGAGTCA 59.536 50.000 23.35 0.00 0.00 3.41
1368 1453 0.681733 ACAGCTGAACACCGAGTCAT 59.318 50.000 23.35 0.00 0.00 3.06
1369 1454 1.073964 CAGCTGAACACCGAGTCATG 58.926 55.000 8.42 0.00 0.00 3.07
1370 1455 0.671781 AGCTGAACACCGAGTCATGC 60.672 55.000 0.00 0.00 0.00 4.06
1400 1485 1.024271 TGCTGCTCTGTTTTGACCAC 58.976 50.000 0.00 0.00 0.00 4.16
1550 1640 0.834687 ACAACCCCTTCACTAGGCGA 60.835 55.000 0.00 0.00 43.27 5.54
1685 1775 1.153469 CCTCAGGCTCTTCTTCGGC 60.153 63.158 0.00 0.00 0.00 5.54
1693 1783 1.606737 GCTCTTCTTCGGCTCACAAGT 60.607 52.381 0.00 0.00 0.00 3.16
1694 1784 2.760374 CTCTTCTTCGGCTCACAAGTT 58.240 47.619 0.00 0.00 0.00 2.66
1705 1795 2.545946 GCTCACAAGTTCCACTCTGAAC 59.454 50.000 0.00 0.00 43.95 3.18
1706 1796 3.797039 CTCACAAGTTCCACTCTGAACA 58.203 45.455 6.67 0.00 45.62 3.18
1707 1797 3.531538 TCACAAGTTCCACTCTGAACAC 58.468 45.455 6.67 0.00 45.62 3.32
1708 1798 3.197766 TCACAAGTTCCACTCTGAACACT 59.802 43.478 6.67 0.00 45.62 3.55
1709 1799 3.557595 CACAAGTTCCACTCTGAACACTC 59.442 47.826 6.67 0.00 45.62 3.51
1712 1802 2.139118 GTTCCACTCTGAACACTCTGC 58.861 52.381 0.00 0.00 43.27 4.26
1713 1803 1.413118 TCCACTCTGAACACTCTGCA 58.587 50.000 0.00 0.00 0.00 4.41
1714 1804 1.342496 TCCACTCTGAACACTCTGCAG 59.658 52.381 7.63 7.63 0.00 4.41
1715 1805 1.146637 CACTCTGAACACTCTGCAGC 58.853 55.000 9.47 0.00 0.00 5.25
1716 1806 1.047002 ACTCTGAACACTCTGCAGCT 58.953 50.000 9.47 0.00 0.00 4.24
1717 1807 1.000731 ACTCTGAACACTCTGCAGCTC 59.999 52.381 9.47 0.92 0.00 4.09
1718 1808 0.038801 TCTGAACACTCTGCAGCTCG 60.039 55.000 9.47 2.20 0.00 5.03
1719 1809 1.624865 CTGAACACTCTGCAGCTCGC 61.625 60.000 9.47 1.70 42.89 5.03
1720 1810 2.358003 AACACTCTGCAGCTCGCC 60.358 61.111 9.47 0.00 41.33 5.54
1721 1811 3.890936 AACACTCTGCAGCTCGCCC 62.891 63.158 9.47 0.00 41.33 6.13
1722 1812 4.383861 CACTCTGCAGCTCGCCCA 62.384 66.667 9.47 0.00 41.33 5.36
1723 1813 3.630013 ACTCTGCAGCTCGCCCAA 61.630 61.111 9.47 0.00 41.33 4.12
1724 1814 2.818714 CTCTGCAGCTCGCCCAAG 60.819 66.667 9.47 0.00 41.33 3.61
1725 1815 3.602513 CTCTGCAGCTCGCCCAAGT 62.603 63.158 9.47 0.00 41.33 3.16
1726 1816 2.670934 CTGCAGCTCGCCCAAGTT 60.671 61.111 0.00 0.00 41.33 2.66
1727 1817 2.669569 TGCAGCTCGCCCAAGTTC 60.670 61.111 5.82 0.00 41.33 3.01
1728 1818 2.359230 GCAGCTCGCCCAAGTTCT 60.359 61.111 0.00 0.00 32.94 3.01
1729 1819 1.968540 GCAGCTCGCCCAAGTTCTT 60.969 57.895 0.00 0.00 32.94 2.52
1730 1820 1.916697 GCAGCTCGCCCAAGTTCTTC 61.917 60.000 0.00 0.00 32.94 2.87
1731 1821 0.603707 CAGCTCGCCCAAGTTCTTCA 60.604 55.000 0.00 0.00 0.00 3.02
1732 1822 0.321122 AGCTCGCCCAAGTTCTTCAG 60.321 55.000 0.00 0.00 0.00 3.02
1733 1823 0.603975 GCTCGCCCAAGTTCTTCAGT 60.604 55.000 0.00 0.00 0.00 3.41
1734 1824 1.337823 GCTCGCCCAAGTTCTTCAGTA 60.338 52.381 0.00 0.00 0.00 2.74
1735 1825 2.678190 GCTCGCCCAAGTTCTTCAGTAT 60.678 50.000 0.00 0.00 0.00 2.12
1736 1826 3.190874 CTCGCCCAAGTTCTTCAGTATC 58.809 50.000 0.00 0.00 0.00 2.24
1737 1827 2.832129 TCGCCCAAGTTCTTCAGTATCT 59.168 45.455 0.00 0.00 0.00 1.98
1767 1857 2.579207 TTGCCTGCTGTACGAGATAC 57.421 50.000 0.00 0.00 0.00 2.24
1768 1858 1.470051 TGCCTGCTGTACGAGATACA 58.530 50.000 0.00 0.00 41.71 2.29
1770 1860 2.034685 TGCCTGCTGTACGAGATACATC 59.965 50.000 0.00 0.00 43.01 3.06
1775 1865 5.645929 CCTGCTGTACGAGATACATCTATCT 59.354 44.000 0.00 0.00 43.01 1.98
1781 1871 7.712797 TGTACGAGATACATCTATCTGCAAAA 58.287 34.615 0.00 0.00 39.47 2.44
1782 1872 7.862873 TGTACGAGATACATCTATCTGCAAAAG 59.137 37.037 0.00 0.00 39.47 2.27
1802 1892 7.355778 CAAAAGCTTTCTCTTCTATCAAACGT 58.644 34.615 13.10 0.00 0.00 3.99
1816 1909 7.970384 TCTATCAAACGTTTACAATGTGATCC 58.030 34.615 14.20 0.00 0.00 3.36
1822 1915 4.223032 ACGTTTACAATGTGATCCTCCTCT 59.777 41.667 0.00 0.00 0.00 3.69
1827 1920 3.072184 ACAATGTGATCCTCCTCTATGGC 59.928 47.826 0.00 0.00 35.26 4.40
1836 1929 1.007964 CCTCTATGGCGCGTCTCTG 60.008 63.158 13.81 1.21 0.00 3.35
1840 1933 2.004808 CTATGGCGCGTCTCTGGTCA 62.005 60.000 13.81 0.00 0.00 4.02
1851 1944 0.933097 CTCTGGTCATCCATTTCGCG 59.067 55.000 0.00 0.00 43.43 5.87
1852 1945 0.534873 TCTGGTCATCCATTTCGCGA 59.465 50.000 3.71 3.71 43.43 5.87
1878 1971 0.517755 TCGTCGAGCACTCTGAAGAC 59.482 55.000 0.00 0.00 0.00 3.01
1879 1972 0.791238 CGTCGAGCACTCTGAAGACG 60.791 60.000 10.09 10.09 43.79 4.18
1948 2041 3.644966 AACACCTTGTTCTTCACCTCA 57.355 42.857 0.00 0.00 35.27 3.86
1950 2043 3.279434 ACACCTTGTTCTTCACCTCAAC 58.721 45.455 0.00 0.00 0.00 3.18
1987 2080 3.689002 CTTCCTCAAGCCGGCCTCC 62.689 68.421 26.15 0.00 0.00 4.30
2075 2168 3.798511 TGTGGTTGCCGGTGGTCA 61.799 61.111 1.90 0.00 0.00 4.02
2158 2251 3.485431 CAGGAGTTGAGCAGCGCG 61.485 66.667 0.00 0.00 0.00 6.86
2184 2277 4.101448 GCACAGGTCGGCTCCCAT 62.101 66.667 0.00 0.00 0.00 4.00
2227 2320 2.034687 GCCTCCTTGAGCAAGCCA 59.965 61.111 4.72 0.00 37.11 4.75
2230 2323 2.034687 TCCTTGAGCAAGCCAGCC 59.965 61.111 4.72 0.00 37.11 4.85
2305 2398 3.005155 TGTGCTCCAGTATCATCTGATCG 59.995 47.826 0.00 0.00 37.61 3.69
2602 2695 0.032540 CGACCATGGATCTGATCGCA 59.967 55.000 21.47 10.58 0.00 5.10
2623 2716 4.530857 GCATGGACCTCCCGACCG 62.531 72.222 0.00 0.00 37.93 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
49 50 6.037172 GCATTTCTTAGTTGATGTCGGTATGT 59.963 38.462 0.00 0.00 0.00 2.29
324 335 1.142748 CTCCTCCATCTGCCACGAC 59.857 63.158 0.00 0.00 0.00 4.34
325 336 1.000359 TCTCCTCCATCTGCCACGA 60.000 57.895 0.00 0.00 0.00 4.35
417 428 3.241530 TTCTCCACGGCCAGCAGT 61.242 61.111 2.24 0.00 0.00 4.40
505 516 1.300971 TGCAATCGCCTTGTCTGCTC 61.301 55.000 0.00 0.00 37.18 4.26
521 532 2.345876 ACGACGATGACAATCAATGCA 58.654 42.857 0.00 0.00 32.61 3.96
525 536 2.247637 GACGACGACGATGACAATCAA 58.752 47.619 15.32 0.00 42.66 2.57
529 540 1.154357 CCGACGACGACGATGACAA 60.154 57.895 20.63 0.00 42.66 3.18
546 562 2.498078 CTGGTTCCTGGAGTCTTAGACC 59.502 54.545 8.96 4.81 32.18 3.85
565 581 4.584325 TCCAAGGGACAAATTCAGTTTCTG 59.416 41.667 0.00 0.00 0.00 3.02
597 615 2.951642 ACTGTCCATGGTTTCAACACAG 59.048 45.455 20.33 20.33 35.61 3.66
616 634 0.667993 CCATGGTTTCAACACGCACT 59.332 50.000 2.57 0.00 0.00 4.40
617 635 0.665835 TCCATGGTTTCAACACGCAC 59.334 50.000 12.58 0.00 0.00 5.34
618 636 0.665835 GTCCATGGTTTCAACACGCA 59.334 50.000 12.58 0.00 0.00 5.24
619 637 0.665835 TGTCCATGGTTTCAACACGC 59.334 50.000 12.58 0.00 0.00 5.34
620 638 1.946768 ACTGTCCATGGTTTCAACACG 59.053 47.619 12.58 5.27 0.00 4.49
621 639 2.543653 GCACTGTCCATGGTTTCAACAC 60.544 50.000 12.58 0.61 0.00 3.32
622 640 1.680735 GCACTGTCCATGGTTTCAACA 59.319 47.619 12.58 7.35 0.00 3.33
623 641 1.334960 CGCACTGTCCATGGTTTCAAC 60.335 52.381 12.58 2.23 0.00 3.18
624 642 0.950836 CGCACTGTCCATGGTTTCAA 59.049 50.000 12.58 0.00 0.00 2.69
625 643 0.107643 TCGCACTGTCCATGGTTTCA 59.892 50.000 12.58 9.00 0.00 2.69
626 644 1.398390 GATCGCACTGTCCATGGTTTC 59.602 52.381 12.58 4.59 0.00 2.78
627 645 1.453155 GATCGCACTGTCCATGGTTT 58.547 50.000 12.58 0.00 0.00 3.27
628 646 0.740868 CGATCGCACTGTCCATGGTT 60.741 55.000 12.58 0.00 0.00 3.67
629 647 1.153568 CGATCGCACTGTCCATGGT 60.154 57.895 12.58 0.00 0.00 3.55
630 648 1.153568 ACGATCGCACTGTCCATGG 60.154 57.895 16.60 4.97 0.00 3.66
631 649 2.001357 CACGATCGCACTGTCCATG 58.999 57.895 16.60 0.00 0.00 3.66
632 650 1.811266 GCACGATCGCACTGTCCAT 60.811 57.895 16.60 0.00 0.00 3.41
633 651 2.432456 GCACGATCGCACTGTCCA 60.432 61.111 16.60 0.00 0.00 4.02
634 652 2.125912 AGCACGATCGCACTGTCC 60.126 61.111 16.60 0.00 0.00 4.02
635 653 2.500442 CGAGCACGATCGCACTGTC 61.500 63.158 16.60 4.32 42.66 3.51
636 654 2.504899 CGAGCACGATCGCACTGT 60.505 61.111 16.60 0.00 42.66 3.55
637 655 2.500442 GACGAGCACGATCGCACTG 61.500 63.158 16.60 7.48 46.60 3.66
638 656 2.202492 GACGAGCACGATCGCACT 60.202 61.111 16.60 12.92 46.60 4.40
675 693 0.795085 CTCAAGAGTTCAAGGCGCAG 59.205 55.000 10.83 0.00 0.00 5.18
676 694 0.106708 ACTCAAGAGTTCAAGGCGCA 59.893 50.000 10.83 0.00 38.83 6.09
677 695 0.793250 GACTCAAGAGTTCAAGGCGC 59.207 55.000 0.00 0.00 42.66 6.53
678 696 2.154854 TGACTCAAGAGTTCAAGGCG 57.845 50.000 3.96 0.00 42.66 5.52
705 723 6.753913 ATCTGCCCAGTTCAGATCTTATTA 57.246 37.500 0.00 0.00 45.31 0.98
731 749 4.990426 CCCAAGGACAACACATTTTCATTC 59.010 41.667 0.00 0.00 0.00 2.67
764 785 1.139816 TCGCATCGAGACGCATTCAC 61.140 55.000 5.07 0.00 0.00 3.18
772 793 1.922903 CACAGCATCGCATCGAGAC 59.077 57.895 0.00 0.00 39.91 3.36
773 794 1.879884 GCACAGCATCGCATCGAGA 60.880 57.895 0.00 0.00 39.91 4.04
781 802 2.177531 GCAACAGGCACAGCATCG 59.822 61.111 0.00 0.00 43.97 3.84
866 905 0.772124 AGCAGGAGGGGGACAAGAAA 60.772 55.000 0.00 0.00 0.00 2.52
1240 1318 4.315122 CTCGTCGCCGATCCTCCG 62.315 72.222 0.00 0.00 43.27 4.63
1338 1416 2.805671 TGTTCAGCTGTTCACGGTATTG 59.194 45.455 14.67 0.00 0.00 1.90
1348 1433 0.464036 TGACTCGGTGTTCAGCTGTT 59.536 50.000 14.67 0.00 0.00 3.16
1352 1437 1.790387 GCATGACTCGGTGTTCAGC 59.210 57.895 0.00 0.00 0.00 4.26
1353 1438 1.354337 CCGCATGACTCGGTGTTCAG 61.354 60.000 0.00 0.00 41.85 3.02
1354 1439 1.374125 CCGCATGACTCGGTGTTCA 60.374 57.895 0.00 0.00 41.85 3.18
1355 1440 1.078759 CTCCGCATGACTCGGTGTTC 61.079 60.000 9.63 0.00 46.49 3.18
1356 1441 1.079819 CTCCGCATGACTCGGTGTT 60.080 57.895 9.63 0.00 46.49 3.32
1357 1442 2.276116 ACTCCGCATGACTCGGTGT 61.276 57.895 10.82 10.82 45.40 4.16
1359 1444 1.215647 GAACTCCGCATGACTCGGT 59.784 57.895 9.63 0.00 46.49 4.69
1361 1446 4.094684 GGAACTCCGCATGACTCG 57.905 61.111 0.00 0.00 0.00 4.18
1373 1458 0.179045 AACAGAGCAGCAACGGAACT 60.179 50.000 0.00 0.00 0.00 3.01
1507 1597 4.841441 TGAAGGTGTTCATGGCCC 57.159 55.556 0.00 0.00 37.79 5.80
1550 1640 2.354305 GCGACGACGTCAAGGTGT 60.354 61.111 26.26 4.40 41.98 4.16
1693 1783 1.762370 TGCAGAGTGTTCAGAGTGGAA 59.238 47.619 0.00 0.00 0.00 3.53
1694 1784 1.342496 CTGCAGAGTGTTCAGAGTGGA 59.658 52.381 8.42 0.00 0.00 4.02
1712 1802 0.603707 TGAAGAACTTGGGCGAGCTG 60.604 55.000 0.00 0.00 0.00 4.24
1713 1803 0.321122 CTGAAGAACTTGGGCGAGCT 60.321 55.000 0.00 0.00 0.00 4.09
1714 1804 0.603975 ACTGAAGAACTTGGGCGAGC 60.604 55.000 0.00 0.00 0.00 5.03
1715 1805 2.743636 TACTGAAGAACTTGGGCGAG 57.256 50.000 0.00 0.00 0.00 5.03
1716 1806 2.832129 AGATACTGAAGAACTTGGGCGA 59.168 45.455 0.00 0.00 0.00 5.54
1717 1807 3.118956 AGAGATACTGAAGAACTTGGGCG 60.119 47.826 0.00 0.00 0.00 6.13
1718 1808 4.081420 TGAGAGATACTGAAGAACTTGGGC 60.081 45.833 0.00 0.00 0.00 5.36
1719 1809 5.186797 AGTGAGAGATACTGAAGAACTTGGG 59.813 44.000 0.00 0.00 0.00 4.12
1720 1810 6.152661 AGAGTGAGAGATACTGAAGAACTTGG 59.847 42.308 0.00 0.00 0.00 3.61
1721 1811 7.028962 CAGAGTGAGAGATACTGAAGAACTTG 58.971 42.308 0.00 0.00 0.00 3.16
1722 1812 6.719370 ACAGAGTGAGAGATACTGAAGAACTT 59.281 38.462 0.00 0.00 33.53 2.66
1723 1813 6.245408 ACAGAGTGAGAGATACTGAAGAACT 58.755 40.000 0.00 0.00 33.53 3.01
1724 1814 6.509418 ACAGAGTGAGAGATACTGAAGAAC 57.491 41.667 0.00 0.00 33.53 3.01
1725 1815 7.374272 CAAACAGAGTGAGAGATACTGAAGAA 58.626 38.462 0.00 0.00 33.53 2.52
1726 1816 6.571344 GCAAACAGAGTGAGAGATACTGAAGA 60.571 42.308 0.00 0.00 33.53 2.87
1727 1817 5.576384 GCAAACAGAGTGAGAGATACTGAAG 59.424 44.000 0.00 0.00 33.53 3.02
1728 1818 5.473931 GCAAACAGAGTGAGAGATACTGAA 58.526 41.667 0.00 0.00 33.53 3.02
1729 1819 4.081972 GGCAAACAGAGTGAGAGATACTGA 60.082 45.833 0.00 0.00 33.53 3.41
1730 1820 4.081752 AGGCAAACAGAGTGAGAGATACTG 60.082 45.833 0.00 0.00 35.14 2.74
1731 1821 4.081752 CAGGCAAACAGAGTGAGAGATACT 60.082 45.833 0.00 0.00 0.00 2.12
1732 1822 4.180057 CAGGCAAACAGAGTGAGAGATAC 58.820 47.826 0.00 0.00 0.00 2.24
1733 1823 3.368843 GCAGGCAAACAGAGTGAGAGATA 60.369 47.826 0.00 0.00 0.00 1.98
1734 1824 2.614987 GCAGGCAAACAGAGTGAGAGAT 60.615 50.000 0.00 0.00 0.00 2.75
1735 1825 1.270518 GCAGGCAAACAGAGTGAGAGA 60.271 52.381 0.00 0.00 0.00 3.10
1736 1826 1.155042 GCAGGCAAACAGAGTGAGAG 58.845 55.000 0.00 0.00 0.00 3.20
1737 1827 0.761187 AGCAGGCAAACAGAGTGAGA 59.239 50.000 0.00 0.00 0.00 3.27
1781 1871 7.656137 TGTAAACGTTTGATAGAAGAGAAAGCT 59.344 33.333 23.46 0.00 0.00 3.74
1782 1872 7.793902 TGTAAACGTTTGATAGAAGAGAAAGC 58.206 34.615 23.46 0.00 0.00 3.51
1802 1892 6.688922 GCCATAGAGGAGGATCACATTGTAAA 60.689 42.308 0.00 0.00 41.22 2.01
1816 1909 1.169661 AGAGACGCGCCATAGAGGAG 61.170 60.000 5.73 0.00 41.22 3.69
1822 1915 1.391933 ATGACCAGAGACGCGCCATA 61.392 55.000 5.73 0.00 0.00 2.74
1827 1920 2.885113 TGGATGACCAGAGACGCG 59.115 61.111 3.53 3.53 41.77 6.01
1836 1929 2.479837 TGTATCGCGAAATGGATGACC 58.520 47.619 15.24 0.00 0.00 4.02
1840 1933 4.389664 CGATTTGTATCGCGAAATGGAT 57.610 40.909 15.24 5.02 46.15 3.41
1851 1944 3.483922 CAGAGTGCTCGACGATTTGTATC 59.516 47.826 0.00 0.00 34.09 2.24
1852 1945 3.128764 TCAGAGTGCTCGACGATTTGTAT 59.871 43.478 0.00 0.00 34.09 2.29
1878 1971 2.641439 GATGCCCAGAGCTGAGGACG 62.641 65.000 0.00 0.00 44.23 4.79
1879 1972 1.145819 GATGCCCAGAGCTGAGGAC 59.854 63.158 0.00 0.00 44.23 3.85
1920 2013 2.733956 AGAACAAGGTGTTTGCCTTCA 58.266 42.857 0.00 0.00 46.33 3.02
1927 2020 3.963129 TGAGGTGAAGAACAAGGTGTTT 58.037 40.909 0.00 0.00 41.28 2.83
1967 2060 2.185310 GAGGCCGGCTTGAGGAAGAA 62.185 60.000 28.56 0.00 0.00 2.52
1987 2080 1.517832 GGTGAGGGTGATGACGAGG 59.482 63.158 0.00 0.00 0.00 4.63
2093 2186 1.440145 GAAGCCACCATAGCGAAGGC 61.440 60.000 0.00 0.00 45.54 4.35
2206 2299 1.743252 CTTGCTCAAGGAGGCGTCC 60.743 63.158 17.88 17.88 44.33 4.79
2212 2305 2.045131 GGCTGGCTTGCTCAAGGAG 61.045 63.158 11.15 0.00 38.80 3.69
2350 2443 2.049802 TTCGTCGCCGTTCTGTCC 60.050 61.111 0.00 0.00 35.01 4.02
2646 2739 0.898326 TACCGTTCTCTCAGCCTGCA 60.898 55.000 0.00 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.