Multiple sequence alignment - TraesCS2D01G455400

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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 TraesCS2D01G455400 chr2D 100.000 4378 0 0 1 4378 563782444 563786821 0.000000e+00 8085.0
1 TraesCS2D01G455400 chr2D 91.384 708 60 1 1 707 13140297 13139590 0.000000e+00 968.0
2 TraesCS2D01G455400 chr2A 94.150 3624 129 37 780 4378 703865517 703869082 0.000000e+00 5441.0
3 TraesCS2D01G455400 chr2A 88.857 700 74 3 12 707 669501688 669500989 0.000000e+00 857.0
4 TraesCS2D01G455400 chr2B 93.208 3357 130 34 720 4035 674026560 674029859 0.000000e+00 4846.0
5 TraesCS2D01G455400 chr2B 88.761 347 12 11 4032 4378 674029903 674030222 2.450000e-107 399.0
6 TraesCS2D01G455400 chr7D 93.362 708 46 1 1 707 14413797 14414504 0.000000e+00 1046.0
7 TraesCS2D01G455400 chr7D 90.765 693 62 2 1 691 614816526 614815834 0.000000e+00 924.0
8 TraesCS2D01G455400 chr5D 91.298 701 54 5 12 708 32754952 32755649 0.000000e+00 950.0
9 TraesCS2D01G455400 chr5D 89.552 670 65 4 1 667 311466846 311466179 0.000000e+00 845.0
10 TraesCS2D01G455400 chrUn 89.740 692 70 1 1 691 81311754 81311063 0.000000e+00 883.0
11 TraesCS2D01G455400 chr6D 89.014 710 76 2 1 708 380504015 380504724 0.000000e+00 878.0
12 TraesCS2D01G455400 chr6D 89.660 677 69 1 12 687 55425465 55426141 0.000000e+00 861.0
13 TraesCS2D01G455400 chr3B 83.000 100 16 1 1834 1932 454138210 454138309 6.030000e-14 89.8
14 TraesCS2D01G455400 chr3B 83.000 100 16 1 1834 1932 454345481 454345580 6.030000e-14 89.8
15 TraesCS2D01G455400 chr3B 83.158 95 15 1 1839 1932 197090878 197090972 7.800000e-13 86.1
16 TraesCS2D01G455400 chr7B 83.158 95 15 1 1839 1932 728163289 728163383 7.800000e-13 86.1
17 TraesCS2D01G455400 chr5B 83.158 95 15 1 1839 1932 104905359 104905265 7.800000e-13 86.1
18 TraesCS2D01G455400 chr7A 81.633 98 17 1 1839 1935 578925597 578925500 3.630000e-11 80.5
19 TraesCS2D01G455400 chr7A 81.633 98 17 1 1839 1935 578929297 578929200 3.630000e-11 80.5


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 TraesCS2D01G455400 chr2D 563782444 563786821 4377 False 8085.0 8085 100.0000 1 4378 1 chr2D.!!$F1 4377
1 TraesCS2D01G455400 chr2D 13139590 13140297 707 True 968.0 968 91.3840 1 707 1 chr2D.!!$R1 706
2 TraesCS2D01G455400 chr2A 703865517 703869082 3565 False 5441.0 5441 94.1500 780 4378 1 chr2A.!!$F1 3598
3 TraesCS2D01G455400 chr2A 669500989 669501688 699 True 857.0 857 88.8570 12 707 1 chr2A.!!$R1 695
4 TraesCS2D01G455400 chr2B 674026560 674030222 3662 False 2622.5 4846 90.9845 720 4378 2 chr2B.!!$F1 3658
5 TraesCS2D01G455400 chr7D 14413797 14414504 707 False 1046.0 1046 93.3620 1 707 1 chr7D.!!$F1 706
6 TraesCS2D01G455400 chr7D 614815834 614816526 692 True 924.0 924 90.7650 1 691 1 chr7D.!!$R1 690
7 TraesCS2D01G455400 chr5D 32754952 32755649 697 False 950.0 950 91.2980 12 708 1 chr5D.!!$F1 696
8 TraesCS2D01G455400 chr5D 311466179 311466846 667 True 845.0 845 89.5520 1 667 1 chr5D.!!$R1 666
9 TraesCS2D01G455400 chrUn 81311063 81311754 691 True 883.0 883 89.7400 1 691 1 chrUn.!!$R1 690
10 TraesCS2D01G455400 chr6D 380504015 380504724 709 False 878.0 878 89.0140 1 708 1 chr6D.!!$F2 707
11 TraesCS2D01G455400 chr6D 55425465 55426141 676 False 861.0 861 89.6600 12 687 1 chr6D.!!$F1 675

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
718 724 0.896226 AGCGAGAGGTGTAAAGACCC 59.104 55.000 0.00 0.00 42.35 4.46 F
1239 1258 1.153086 GAGCGCCCAAGGTGATGAT 60.153 57.895 2.29 0.00 34.74 2.45 F
1815 1860 0.399833 TTGGACCACATAGCAGTGCA 59.600 50.000 19.20 3.62 38.18 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1536 1564 0.394899 GAACTGCTCCATCCCAAGGG 60.395 60.000 0.0 0.0 0.0 3.95 R
2799 2848 2.040947 TGCATTCCCAACATAGTGGTCA 59.959 45.455 0.0 0.0 36.9 4.02 R
3499 3548 3.917629 TGAAGTTGGTAAAGTATGGGGGA 59.082 43.478 0.0 0.0 0.0 4.81 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
124 128 1.448540 CAACGATCCTCAGGCGCTT 60.449 57.895 7.64 0.00 0.00 4.68
309 313 0.990374 AGCTTCCTCTGCTCCACATT 59.010 50.000 0.00 0.00 35.67 2.71
330 334 1.120530 GCCCTCCTTCGTTGGATCTA 58.879 55.000 0.00 0.00 35.30 1.98
492 496 3.451556 CTCCGGTCGCCATGAGCAT 62.452 63.158 0.00 0.00 45.52 3.79
572 576 2.198426 CAAGTTGCTGGGGTGGGT 59.802 61.111 0.00 0.00 0.00 4.51
714 720 2.181426 CGAGAGCGAGAGGTGTAAAG 57.819 55.000 0.00 0.00 45.11 1.85
715 721 1.738350 CGAGAGCGAGAGGTGTAAAGA 59.262 52.381 0.00 0.00 45.11 2.52
716 722 2.476519 CGAGAGCGAGAGGTGTAAAGAC 60.477 54.545 0.00 0.00 45.11 3.01
717 723 1.819903 AGAGCGAGAGGTGTAAAGACC 59.180 52.381 0.00 0.00 45.11 3.85
718 724 0.896226 AGCGAGAGGTGTAAAGACCC 59.104 55.000 0.00 0.00 42.35 4.46
843 849 3.742369 AGCAAACGCATCTTCCAAATTTG 59.258 39.130 11.40 11.40 0.00 2.32
844 850 3.494251 GCAAACGCATCTTCCAAATTTGT 59.506 39.130 16.73 0.00 0.00 2.83
876 883 1.487142 TCTTTCACGAAACCACCTGGA 59.513 47.619 0.00 0.00 38.94 3.86
955 962 1.674817 CCGTGTACCAGTGTCCATTCC 60.675 57.143 0.00 0.00 0.00 3.01
1201 1220 2.951101 CGGTACCCGCTTCCCTTGT 61.951 63.158 6.25 0.00 41.17 3.16
1208 1227 2.668550 GCTTCCCTTGTTCGCCGT 60.669 61.111 0.00 0.00 0.00 5.68
1237 1256 1.817099 GAGAGCGCCCAAGGTGATG 60.817 63.158 2.29 0.00 34.74 3.07
1238 1257 2.244117 GAGAGCGCCCAAGGTGATGA 62.244 60.000 2.29 0.00 34.74 2.92
1239 1258 1.153086 GAGCGCCCAAGGTGATGAT 60.153 57.895 2.29 0.00 34.74 2.45
1427 1453 4.039730 GCTATCCTGTGTCCAGTGATGTAT 59.960 45.833 0.00 0.00 36.95 2.29
1536 1564 3.882888 TGTGTGTGGTCTTGGAGAATTTC 59.117 43.478 0.00 0.00 0.00 2.17
1612 1657 0.669619 CATCAGTTGGTGCACTGCAA 59.330 50.000 17.98 10.63 43.51 4.08
1617 1662 2.095567 CAGTTGGTGCACTGCAATCTAC 60.096 50.000 17.98 8.39 41.47 2.59
1618 1663 2.154462 GTTGGTGCACTGCAATCTACT 58.846 47.619 17.98 0.00 41.47 2.57
1619 1664 3.007940 AGTTGGTGCACTGCAATCTACTA 59.992 43.478 17.98 0.00 41.47 1.82
1620 1665 3.912496 TGGTGCACTGCAATCTACTAT 57.088 42.857 17.98 0.00 41.47 2.12
1621 1666 4.220693 TGGTGCACTGCAATCTACTATT 57.779 40.909 17.98 0.00 41.47 1.73
1622 1667 4.588899 TGGTGCACTGCAATCTACTATTT 58.411 39.130 17.98 0.00 41.47 1.40
1623 1668 5.739959 TGGTGCACTGCAATCTACTATTTA 58.260 37.500 17.98 0.00 41.47 1.40
1624 1669 6.356556 TGGTGCACTGCAATCTACTATTTAT 58.643 36.000 17.98 0.00 41.47 1.40
1625 1670 7.505258 TGGTGCACTGCAATCTACTATTTATA 58.495 34.615 17.98 0.00 41.47 0.98
1651 1696 7.055667 TCTTTAACTTCTGAGTCACTGTCAT 57.944 36.000 0.00 0.00 34.21 3.06
1653 1698 8.638873 TCTTTAACTTCTGAGTCACTGTCATTA 58.361 33.333 0.00 0.00 34.21 1.90
1691 1736 8.768397 AGTATCTACTGTATTTTGGGATGACAA 58.232 33.333 0.00 0.00 34.72 3.18
1698 1743 8.739972 ACTGTATTTTGGGATGACAATAACTTC 58.260 33.333 0.00 0.00 0.00 3.01
1719 1764 7.680730 ACTTCTAGATAGCTTTTGGAACTTCA 58.319 34.615 0.00 0.00 0.00 3.02
1766 1811 7.439157 TCTCTTGGACAGTGATGTTATTTTG 57.561 36.000 0.00 0.00 0.00 2.44
1772 1817 6.072508 TGGACAGTGATGTTATTTTGCTTCTC 60.073 38.462 0.00 0.00 0.00 2.87
1774 1819 7.275888 ACAGTGATGTTATTTTGCTTCTCAA 57.724 32.000 0.00 0.00 0.00 3.02
1775 1820 7.889469 ACAGTGATGTTATTTTGCTTCTCAAT 58.111 30.769 0.00 0.00 34.12 2.57
1778 1823 9.846248 AGTGATGTTATTTTGCTTCTCAATAAC 57.154 29.630 6.95 6.95 41.08 1.89
1784 1829 5.705609 TTTTGCTTCTCAATAACTGGGAC 57.294 39.130 0.00 0.00 32.76 4.46
1791 1836 1.135199 TCAATAACTGGGACGACGCTC 60.135 52.381 3.44 0.00 0.00 5.03
1802 1847 1.925185 GACGACGCTCTAATTTGGACC 59.075 52.381 0.00 0.00 0.00 4.46
1803 1848 1.274167 ACGACGCTCTAATTTGGACCA 59.726 47.619 0.00 0.00 0.00 4.02
1804 1849 1.659098 CGACGCTCTAATTTGGACCAC 59.341 52.381 0.00 0.00 0.00 4.16
1805 1850 2.695359 GACGCTCTAATTTGGACCACA 58.305 47.619 0.00 0.00 0.00 4.17
1809 1854 3.248602 CGCTCTAATTTGGACCACATAGC 59.751 47.826 0.00 0.00 0.00 2.97
1810 1855 4.199310 GCTCTAATTTGGACCACATAGCA 58.801 43.478 8.42 0.00 0.00 3.49
1811 1856 4.274459 GCTCTAATTTGGACCACATAGCAG 59.726 45.833 8.42 1.39 0.00 4.24
1812 1857 5.431765 CTCTAATTTGGACCACATAGCAGT 58.568 41.667 0.00 0.00 0.00 4.40
1813 1858 5.185454 TCTAATTTGGACCACATAGCAGTG 58.815 41.667 0.00 0.00 39.21 3.66
1814 1859 1.533625 TTTGGACCACATAGCAGTGC 58.466 50.000 7.13 7.13 38.18 4.40
1815 1860 0.399833 TTGGACCACATAGCAGTGCA 59.600 50.000 19.20 3.62 38.18 4.57
1816 1861 0.620030 TGGACCACATAGCAGTGCAT 59.380 50.000 19.20 6.05 38.18 3.96
1817 1862 1.303309 GGACCACATAGCAGTGCATC 58.697 55.000 19.20 2.83 38.18 3.91
1818 1863 1.134280 GGACCACATAGCAGTGCATCT 60.134 52.381 19.20 0.00 38.18 2.90
1819 1864 2.636830 GACCACATAGCAGTGCATCTT 58.363 47.619 19.20 0.00 38.18 2.40
1820 1865 3.432186 GGACCACATAGCAGTGCATCTTA 60.432 47.826 19.20 0.44 38.18 2.10
1821 1866 3.535561 ACCACATAGCAGTGCATCTTAC 58.464 45.455 19.20 0.00 38.18 2.34
1822 1867 3.055167 ACCACATAGCAGTGCATCTTACA 60.055 43.478 19.20 0.00 38.18 2.41
1823 1868 3.310774 CCACATAGCAGTGCATCTTACAC 59.689 47.826 19.20 0.00 38.18 2.90
1824 1869 3.934579 CACATAGCAGTGCATCTTACACA 59.065 43.478 19.20 0.00 40.59 3.72
1825 1870 3.935203 ACATAGCAGTGCATCTTACACAC 59.065 43.478 19.20 0.00 40.59 3.82
1826 1871 2.549064 AGCAGTGCATCTTACACACA 57.451 45.000 19.20 0.00 40.59 3.72
1827 1872 2.146342 AGCAGTGCATCTTACACACAC 58.854 47.619 19.20 0.00 40.59 3.82
1828 1873 1.872952 GCAGTGCATCTTACACACACA 59.127 47.619 11.09 0.00 40.59 3.72
1829 1874 2.349817 GCAGTGCATCTTACACACACAC 60.350 50.000 11.09 0.00 40.59 3.82
1830 1875 3.133691 CAGTGCATCTTACACACACACT 58.866 45.455 0.00 0.00 40.59 3.55
1831 1876 4.306600 CAGTGCATCTTACACACACACTA 58.693 43.478 0.00 0.00 40.59 2.74
1832 1877 4.150627 CAGTGCATCTTACACACACACTAC 59.849 45.833 0.00 0.00 40.59 2.73
1837 1882 5.107453 GCATCTTACACACACACTACAAGTC 60.107 44.000 0.00 0.00 0.00 3.01
1884 1929 5.871524 AGTGCATCTTACACACTATCACTTG 59.128 40.000 0.00 0.00 42.65 3.16
1889 1934 7.308589 GCATCTTACACACTATCACTTGGTTTT 60.309 37.037 0.00 0.00 0.00 2.43
1895 1940 4.037923 ACACTATCACTTGGTTTTGCTTGG 59.962 41.667 0.00 0.00 0.00 3.61
1912 1957 1.305718 GGCATGGCCCCCAACTAAA 60.306 57.895 8.35 0.00 44.06 1.85
1948 1993 8.959548 TGATTGTTCACATGAATGCTTACTATT 58.040 29.630 0.00 0.00 36.33 1.73
2010 2055 5.869579 AGGAATACTTGAGAGAAGCAACAA 58.130 37.500 0.00 0.00 0.00 2.83
2061 2106 6.981722 ACAATCAAGGCTACCTTAAGTTTTG 58.018 36.000 0.97 2.48 42.67 2.44
2072 2117 6.215495 ACCTTAAGTTTTGTTTTAGCTGCA 57.785 33.333 1.02 0.00 0.00 4.41
2092 2137 3.181528 GCATGTTTCATCATTTGTTGCCG 60.182 43.478 0.00 0.00 0.00 5.69
2400 2449 9.427821 ACTCTTGAACCATCTAGTCATTATAGT 57.572 33.333 0.00 0.00 31.39 2.12
2513 2562 4.846940 AGAGGTTCTTGACTTCTGGGTATT 59.153 41.667 0.00 0.00 42.52 1.89
2799 2848 2.158623 TGGTGACCTTCAGATTGCTTGT 60.159 45.455 2.11 0.00 0.00 3.16
3434 3483 3.881688 GAGAACAGTGGAGCATGCATAAT 59.118 43.478 21.98 0.00 39.99 1.28
3621 3670 9.465199 TCCTTGAATGATCATGTTTATCTTTCA 57.535 29.630 9.46 14.90 41.74 2.69
3798 3847 4.250464 CGACCCTCAAATGCAGTTACTTA 58.750 43.478 0.00 0.00 0.00 2.24
4025 4079 2.311688 CTGCCCATACTGGACCGGTC 62.312 65.000 27.04 27.04 40.96 4.79
4191 4294 0.398696 TTGTGTATGGGCCGAACTGT 59.601 50.000 0.00 0.00 0.00 3.55
4273 4378 4.699522 GACCTCGCCGCACCCTTT 62.700 66.667 0.00 0.00 0.00 3.11
4276 4381 2.815647 CTCGCCGCACCCTTTCTC 60.816 66.667 0.00 0.00 0.00 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
101 105 1.450312 CCTGAGGATCGTTGTGGGC 60.450 63.158 0.00 0.00 38.61 5.36
105 109 2.125512 GCGCCTGAGGATCGTTGT 60.126 61.111 0.65 0.00 38.61 3.32
309 313 1.956629 GATCCAACGAAGGAGGGCGA 61.957 60.000 6.73 0.00 41.90 5.54
477 481 3.333189 CGATGCTCATGGCGACCG 61.333 66.667 0.00 0.00 45.43 4.79
572 576 2.682136 TAGCTGCACCCACGCCTA 60.682 61.111 1.02 0.00 0.00 3.93
622 627 0.811616 CCACAGATCTAACCCAGCGC 60.812 60.000 0.00 0.00 0.00 5.92
708 714 8.999905 AAATAGTTTGGTTTAGGGTCTTTACA 57.000 30.769 0.00 0.00 0.00 2.41
709 715 9.293404 AGAAATAGTTTGGTTTAGGGTCTTTAC 57.707 33.333 0.00 0.00 0.00 2.01
710 716 9.871175 AAGAAATAGTTTGGTTTAGGGTCTTTA 57.129 29.630 0.00 0.00 0.00 1.85
712 718 8.777578 AAAGAAATAGTTTGGTTTAGGGTCTT 57.222 30.769 0.00 0.00 0.00 3.01
713 719 8.777578 AAAAGAAATAGTTTGGTTTAGGGTCT 57.222 30.769 0.00 0.00 0.00 3.85
874 881 3.001330 CGATGTAGTTTGAAAGCGGATCC 59.999 47.826 0.00 0.00 0.00 3.36
876 883 2.936498 CCGATGTAGTTTGAAAGCGGAT 59.064 45.455 0.00 0.00 39.85 4.18
916 923 4.129737 CGAGCCGGAGCCTCGAAA 62.130 66.667 21.13 0.00 40.08 3.46
1208 1227 2.172372 GCGCTCTCCTCGTCGTCTA 61.172 63.158 0.00 0.00 0.00 2.59
1237 1256 0.249657 GGCGGACTGACCAGATCATC 60.250 60.000 3.76 0.00 36.48 2.92
1238 1257 0.689080 AGGCGGACTGACCAGATCAT 60.689 55.000 3.76 0.00 36.48 2.45
1239 1258 1.305297 AGGCGGACTGACCAGATCA 60.305 57.895 3.76 0.00 38.90 2.92
1427 1453 4.340097 TGGACTGACAACTCTCGTTTAGAA 59.660 41.667 0.00 0.00 32.46 2.10
1536 1564 0.394899 GAACTGCTCCATCCCAAGGG 60.395 60.000 0.00 0.00 0.00 3.95
1623 1668 9.646427 GACAGTGACTCAGAAGTTAAAGAATAT 57.354 33.333 0.00 0.00 35.28 1.28
1624 1669 8.638873 TGACAGTGACTCAGAAGTTAAAGAATA 58.361 33.333 0.00 0.00 35.28 1.75
1625 1670 7.500992 TGACAGTGACTCAGAAGTTAAAGAAT 58.499 34.615 0.00 0.00 35.28 2.40
1673 1718 8.960591 AGAAGTTATTGTCATCCCAAAATACAG 58.039 33.333 0.00 0.00 0.00 2.74
1674 1719 8.877864 AGAAGTTATTGTCATCCCAAAATACA 57.122 30.769 0.00 0.00 0.00 2.29
1677 1722 9.927081 ATCTAGAAGTTATTGTCATCCCAAAAT 57.073 29.630 0.00 0.00 0.00 1.82
1698 1743 9.436957 TTTAGTGAAGTTCCAAAAGCTATCTAG 57.563 33.333 0.00 0.00 0.00 2.43
1734 1779 6.536582 ACATCACTGTCCAAGAGAAAATATCG 59.463 38.462 0.00 0.00 0.00 2.92
1735 1780 7.856145 ACATCACTGTCCAAGAGAAAATATC 57.144 36.000 0.00 0.00 0.00 1.63
1766 1811 2.930682 GTCGTCCCAGTTATTGAGAAGC 59.069 50.000 0.00 0.00 0.00 3.86
1772 1817 1.135083 AGAGCGTCGTCCCAGTTATTG 60.135 52.381 0.00 0.00 0.00 1.90
1774 1819 2.048444 TAGAGCGTCGTCCCAGTTAT 57.952 50.000 0.00 0.00 0.00 1.89
1775 1820 1.825090 TTAGAGCGTCGTCCCAGTTA 58.175 50.000 0.00 0.00 0.00 2.24
1778 1823 1.927174 CAAATTAGAGCGTCGTCCCAG 59.073 52.381 0.00 0.00 0.00 4.45
1784 1829 1.659098 GTGGTCCAAATTAGAGCGTCG 59.341 52.381 0.00 0.00 34.46 5.12
1791 1836 4.201950 GCACTGCTATGTGGTCCAAATTAG 60.202 45.833 0.00 0.11 38.31 1.73
1802 1847 3.934579 TGTGTAAGATGCACTGCTATGTG 59.065 43.478 1.98 0.00 40.62 3.21
1803 1848 3.935203 GTGTGTAAGATGCACTGCTATGT 59.065 43.478 1.98 0.00 37.70 2.29
1804 1849 3.934579 TGTGTGTAAGATGCACTGCTATG 59.065 43.478 1.98 0.00 37.70 2.23
1805 1850 3.935203 GTGTGTGTAAGATGCACTGCTAT 59.065 43.478 1.98 0.00 37.70 2.97
1809 1854 3.133691 AGTGTGTGTGTAAGATGCACTG 58.866 45.455 0.00 0.00 37.70 3.66
1810 1855 3.475566 AGTGTGTGTGTAAGATGCACT 57.524 42.857 0.00 0.00 37.70 4.40
1811 1856 4.055360 TGTAGTGTGTGTGTAAGATGCAC 58.945 43.478 0.00 0.00 37.37 4.57
1812 1857 4.329462 TGTAGTGTGTGTGTAAGATGCA 57.671 40.909 0.00 0.00 0.00 3.96
1813 1858 4.750098 ACTTGTAGTGTGTGTGTAAGATGC 59.250 41.667 0.00 0.00 0.00 3.91
1814 1859 5.405571 GGACTTGTAGTGTGTGTGTAAGATG 59.594 44.000 0.00 0.00 0.00 2.90
1815 1860 5.069914 TGGACTTGTAGTGTGTGTGTAAGAT 59.930 40.000 0.00 0.00 0.00 2.40
1816 1861 4.403113 TGGACTTGTAGTGTGTGTGTAAGA 59.597 41.667 0.00 0.00 0.00 2.10
1817 1862 4.689071 TGGACTTGTAGTGTGTGTGTAAG 58.311 43.478 0.00 0.00 0.00 2.34
1818 1863 4.403113 TCTGGACTTGTAGTGTGTGTGTAA 59.597 41.667 0.00 0.00 0.00 2.41
1819 1864 3.955551 TCTGGACTTGTAGTGTGTGTGTA 59.044 43.478 0.00 0.00 0.00 2.90
1820 1865 2.764010 TCTGGACTTGTAGTGTGTGTGT 59.236 45.455 0.00 0.00 0.00 3.72
1821 1866 3.123804 GTCTGGACTTGTAGTGTGTGTG 58.876 50.000 0.00 0.00 0.00 3.82
1822 1867 3.031736 AGTCTGGACTTGTAGTGTGTGT 58.968 45.455 0.00 0.00 38.83 3.72
1823 1868 3.735237 AGTCTGGACTTGTAGTGTGTG 57.265 47.619 0.00 0.00 38.83 3.82
1858 1903 7.170393 AGTGATAGTGTGTAAGATGCACTAA 57.830 36.000 7.56 0.00 45.20 2.24
1878 1923 1.189752 TGCCAAGCAAAACCAAGTGA 58.810 45.000 0.00 0.00 34.76 3.41
1884 1929 3.970721 GCCATGCCAAGCAAAACC 58.029 55.556 0.00 0.00 43.62 3.27
1895 1940 1.686587 GTATTTAGTTGGGGGCCATGC 59.313 52.381 4.39 0.00 31.53 4.06
1902 1947 7.122650 ACAATCAACATCTGTATTTAGTTGGGG 59.877 37.037 0.00 0.00 39.84 4.96
1910 1955 8.795513 TCATGTGAACAATCAACATCTGTATTT 58.204 29.630 0.00 0.00 37.30 1.40
1912 1957 7.926674 TCATGTGAACAATCAACATCTGTAT 57.073 32.000 0.00 0.00 37.30 2.29
1948 1993 6.422333 TGAATAGCCTCATGTTATTCACCAA 58.578 36.000 14.62 1.54 38.31 3.67
2061 2106 6.956299 AATGATGAAACATGCAGCTAAAAC 57.044 33.333 0.00 0.00 0.00 2.43
2072 2117 2.995258 GCGGCAACAAATGATGAAACAT 59.005 40.909 0.00 0.00 0.00 2.71
2352 2401 5.104900 AGTGAACTTGTTCTAACACCAGAGT 60.105 40.000 13.65 0.00 38.92 3.24
2400 2449 3.389656 TCTGTACGCATCCCCATCAAATA 59.610 43.478 0.00 0.00 0.00 1.40
2513 2562 5.246981 AGTCTTTTCCACATCATCTCCAA 57.753 39.130 0.00 0.00 0.00 3.53
2799 2848 2.040947 TGCATTCCCAACATAGTGGTCA 59.959 45.455 0.00 0.00 36.90 4.02
3499 3548 3.917629 TGAAGTTGGTAAAGTATGGGGGA 59.082 43.478 0.00 0.00 0.00 4.81
3547 3596 6.649141 GGTCAGCACATATCCGATTAATTACA 59.351 38.462 0.00 0.00 0.00 2.41
3730 3779 6.718388 TCAAAATATTGAGAAGCGCATAGTG 58.282 36.000 11.47 0.00 40.59 2.74
3798 3847 5.359009 CCAGCATCATGAGTTCAAAATAGGT 59.641 40.000 0.09 0.00 0.00 3.08
4156 4259 2.860971 AACAAGGCTGAGGGGGCT 60.861 61.111 0.00 0.00 44.08 5.19
4158 4261 1.604593 CACAACAAGGCTGAGGGGG 60.605 63.158 0.00 0.00 0.00 5.40
4159 4262 0.400213 TACACAACAAGGCTGAGGGG 59.600 55.000 0.00 0.00 0.00 4.79
4165 4268 0.611896 GGCCCATACACAACAAGGCT 60.612 55.000 0.00 0.00 40.32 4.58
4191 4294 0.250467 GGCAAGCTGGTCTCACTTGA 60.250 55.000 6.18 0.00 42.71 3.02


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

AutoCloner maintained by Alex Coulton.