Multiple sequence alignment - TraesCS4D01G130500

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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 TraesCS4D01G130500 chr4D 100.000 2861 0 0 1 2861 116524567 116521707 0.000000e+00 5284.0
1 TraesCS4D01G130500 chr4D 93.280 1741 110 5 1 1736 493971119 493969381 0.000000e+00 2560.0
2 TraesCS4D01G130500 chr4D 93.076 1733 99 11 1 1724 48683938 48682218 0.000000e+00 2516.0
3 TraesCS4D01G130500 chr4D 92.841 1732 114 6 1 1725 421048646 421046918 0.000000e+00 2503.0
4 TraesCS4D01G130500 chr3A 93.941 1733 99 2 1 1727 418765670 418763938 0.000000e+00 2614.0
5 TraesCS4D01G130500 chr1A 93.010 1731 116 5 1 1727 327011928 327010199 0.000000e+00 2521.0
6 TraesCS4D01G130500 chr5A 92.845 1733 116 4 1 1727 604232070 604230340 0.000000e+00 2507.0
7 TraesCS4D01G130500 chr5A 93.103 58 3 1 2365 2422 275104656 275104600 1.830000e-12 84.2
8 TraesCS4D01G130500 chr5A 84.884 86 6 5 1740 1824 122822816 122822737 2.360000e-11 80.5
9 TraesCS4D01G130500 chr5A 83.908 87 7 5 1738 1824 630003048 630002969 3.060000e-10 76.8
10 TraesCS4D01G130500 chr7D 92.754 1739 115 7 1 1732 432740553 432738819 0.000000e+00 2503.0
11 TraesCS4D01G130500 chr7D 78.883 412 41 31 2349 2723 32374989 32375391 1.320000e-58 237.0
12 TraesCS4D01G130500 chr5B 92.294 1739 126 3 2 1733 375712254 375710517 0.000000e+00 2462.0
13 TraesCS4D01G130500 chr5B 78.771 358 46 16 2346 2675 314290035 314290390 2.230000e-51 213.0
14 TraesCS4D01G130500 chr5B 89.552 67 5 2 2365 2430 225532026 225531961 1.830000e-12 84.2
15 TraesCS4D01G130500 chr5B 90.909 55 1 3 1770 1824 414451675 414451625 1.420000e-08 71.3
16 TraesCS4D01G130500 chr5B 83.562 73 7 4 1760 1831 98855841 98855773 2.380000e-06 63.9
17 TraesCS4D01G130500 chr4A 92.383 1733 125 5 1 1727 327748384 327746653 0.000000e+00 2462.0
18 TraesCS4D01G130500 chr4A 89.146 949 76 18 1882 2815 459758790 459759726 0.000000e+00 1157.0
19 TraesCS4D01G130500 chr4B 84.077 672 79 16 2128 2778 178377354 178376690 8.700000e-175 623.0
20 TraesCS4D01G130500 chr4B 85.161 310 30 11 1836 2131 178378851 178378544 1.290000e-78 303.0
21 TraesCS4D01G130500 chr4B 97.647 85 2 0 2777 2861 178376576 178376492 2.300000e-31 147.0
22 TraesCS4D01G130500 chr7B 80.588 340 46 13 2352 2673 587428505 587428168 7.920000e-61 244.0
23 TraesCS4D01G130500 chr7B 80.294 340 47 14 2352 2673 587239120 587238783 3.680000e-59 239.0
24 TraesCS4D01G130500 chr7B 80.352 341 46 12 2352 2673 587552329 587551991 3.680000e-59 239.0
25 TraesCS4D01G130500 chr7B 83.333 90 6 6 1733 1820 652704422 652704504 1.100000e-09 75.0
26 TraesCS4D01G130500 chr6A 79.444 360 39 16 2352 2690 383475807 383476152 3.710000e-54 222.0
27 TraesCS4D01G130500 chr6B 77.839 361 43 20 2352 2690 417236978 417237323 3.760000e-44 189.0
28 TraesCS4D01G130500 chr6D 84.699 183 21 6 2510 2690 269122000 269122177 2.930000e-40 176.0
29 TraesCS4D01G130500 chr7A 77.627 295 30 22 2351 2615 64475117 64474829 2.300000e-31 147.0
30 TraesCS4D01G130500 chr7A 87.097 62 5 3 2353 2413 422486349 422486408 1.840000e-07 67.6
31 TraesCS4D01G130500 chr7A 90.698 43 4 0 2375 2417 628984749 628984707 1.110000e-04 58.4
32 TraesCS4D01G130500 chr2D 74.425 348 54 24 2354 2670 3990185 3989842 1.800000e-22 117.0
33 TraesCS4D01G130500 chr1B 75.877 228 27 20 2353 2555 286319163 286318939 1.090000e-14 91.6
34 TraesCS4D01G130500 chr5D 87.671 73 6 3 2353 2425 306203925 306203994 6.570000e-12 82.4
35 TraesCS4D01G130500 chr3D 88.525 61 6 1 2377 2436 394612129 394612069 3.950000e-09 73.1
36 TraesCS4D01G130500 chr2B 82.105 95 8 7 1731 1824 281526034 281525948 3.950000e-09 73.1
37 TraesCS4D01G130500 chr2B 82.222 90 7 7 1735 1824 149242561 149242481 5.110000e-08 69.4
38 TraesCS4D01G130500 chr2B 84.211 76 5 5 1749 1824 304219263 304219195 1.840000e-07 67.6
39 TraesCS4D01G130500 chr3B 82.667 75 7 5 1750 1824 546259432 546259500 8.560000e-06 62.1


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 TraesCS4D01G130500 chr4D 116521707 116524567 2860 True 5284.000000 5284 100.000000 1 2861 1 chr4D.!!$R2 2860
1 TraesCS4D01G130500 chr4D 493969381 493971119 1738 True 2560.000000 2560 93.280000 1 1736 1 chr4D.!!$R4 1735
2 TraesCS4D01G130500 chr4D 48682218 48683938 1720 True 2516.000000 2516 93.076000 1 1724 1 chr4D.!!$R1 1723
3 TraesCS4D01G130500 chr4D 421046918 421048646 1728 True 2503.000000 2503 92.841000 1 1725 1 chr4D.!!$R3 1724
4 TraesCS4D01G130500 chr3A 418763938 418765670 1732 True 2614.000000 2614 93.941000 1 1727 1 chr3A.!!$R1 1726
5 TraesCS4D01G130500 chr1A 327010199 327011928 1729 True 2521.000000 2521 93.010000 1 1727 1 chr1A.!!$R1 1726
6 TraesCS4D01G130500 chr5A 604230340 604232070 1730 True 2507.000000 2507 92.845000 1 1727 1 chr5A.!!$R3 1726
7 TraesCS4D01G130500 chr7D 432738819 432740553 1734 True 2503.000000 2503 92.754000 1 1732 1 chr7D.!!$R1 1731
8 TraesCS4D01G130500 chr5B 375710517 375712254 1737 True 2462.000000 2462 92.294000 2 1733 1 chr5B.!!$R3 1731
9 TraesCS4D01G130500 chr4A 327746653 327748384 1731 True 2462.000000 2462 92.383000 1 1727 1 chr4A.!!$R1 1726
10 TraesCS4D01G130500 chr4A 459758790 459759726 936 False 1157.000000 1157 89.146000 1882 2815 1 chr4A.!!$F1 933
11 TraesCS4D01G130500 chr4B 178376492 178378851 2359 True 357.666667 623 88.961667 1836 2861 3 chr4B.!!$R1 1025

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
573 581 0.106015 TCATGGCGATGGAGAGGAGA 60.106 55.0 8.98 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1950 1985 0.106918 ACTTGGGTTTGAACTCGCCA 60.107 50.0 0.0 0.0 29.87 5.69 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
85 86 3.418068 GTCGTCGTCGTCCTCGGT 61.418 66.667 1.33 0.00 38.33 4.69
114 115 1.139058 GGTCAATCTGCCAGGTACGAT 59.861 52.381 0.00 0.00 0.00 3.73
156 157 0.535335 TGGCATCTACACCGGTTCTC 59.465 55.000 2.97 0.00 0.00 2.87
159 160 0.464452 CATCTACACCGGTTCTCCCC 59.536 60.000 2.97 0.00 0.00 4.81
243 244 2.908015 GGCGGTCATTAGGAGCCA 59.092 61.111 0.00 0.00 46.48 4.75
310 311 1.487976 GGAGACAGCCTGATTCATGGA 59.512 52.381 0.00 0.00 0.00 3.41
356 358 2.590092 CCCTTCGCTGGGTTAGGG 59.410 66.667 15.90 15.90 42.25 3.53
361 363 1.209504 CTTCGCTGGGTTAGGGATCAA 59.790 52.381 0.00 0.00 46.32 2.57
376 378 4.527038 AGGGATCAACGTCTTCAACTCTTA 59.473 41.667 0.00 0.00 0.00 2.10
494 496 4.954118 TCACCAGCCGACCACCCT 62.954 66.667 0.00 0.00 0.00 4.34
573 581 0.106015 TCATGGCGATGGAGAGGAGA 60.106 55.000 8.98 0.00 0.00 3.71
614 625 1.008084 AGAGGGGGTGGGTAAGTAGTC 59.992 57.143 0.00 0.00 0.00 2.59
713 727 4.264253 TCAATAAGCCATGAACTCTGTGG 58.736 43.478 0.00 0.00 36.09 4.17
797 811 2.954611 GGCCGTTGACAAGAAGGC 59.045 61.111 16.66 16.66 46.51 4.35
866 880 1.202200 CGAGGAAGAATCGAAGACGCT 60.202 52.381 0.00 0.00 42.51 5.07
870 884 3.192844 AGGAAGAATCGAAGACGCTAACA 59.807 43.478 0.00 0.00 42.51 2.41
937 951 1.677820 GCAACTACGGCCACTACCATT 60.678 52.381 2.24 0.00 0.00 3.16
984 998 0.620556 AGGTCATCCTTGCACCGAAT 59.379 50.000 0.00 0.00 42.12 3.34
1064 1079 1.673920 GTTCAAGCCGAGGAACAACAA 59.326 47.619 0.00 0.00 42.23 2.83
1162 1177 3.461061 GCCGTTCATCAGATCAAGATCA 58.539 45.455 12.21 0.00 40.22 2.92
1417 1438 8.709386 ATGTTGTTAAGTAGTTGATGCTCTAG 57.291 34.615 0.00 0.00 0.00 2.43
1470 1491 1.360192 GGTTGTGCTGAAGTGTGCC 59.640 57.895 0.00 0.00 0.00 5.01
1659 1683 1.345089 TGCATTTGAGGCTGCATTTGT 59.655 42.857 0.50 0.00 43.11 2.83
1727 1752 4.639171 GGCAACCAAACACGCCCG 62.639 66.667 0.00 0.00 38.67 6.13
1733 1758 1.301087 CCAAACACGCCCGTAGTGA 60.301 57.895 8.75 0.00 41.83 3.41
1736 1761 1.127951 CAAACACGCCCGTAGTGATTC 59.872 52.381 8.75 0.00 41.83 2.52
1737 1762 0.734942 AACACGCCCGTAGTGATTCG 60.735 55.000 8.75 0.00 41.83 3.34
1738 1763 1.153901 CACGCCCGTAGTGATTCGT 60.154 57.895 0.00 0.00 41.83 3.85
1739 1764 1.138047 CACGCCCGTAGTGATTCGTC 61.138 60.000 0.00 0.00 41.83 4.20
1740 1765 1.937846 CGCCCGTAGTGATTCGTCG 60.938 63.158 0.00 0.00 0.00 5.12
1741 1766 1.588139 GCCCGTAGTGATTCGTCGG 60.588 63.158 0.00 0.00 40.72 4.79
1742 1767 1.996786 GCCCGTAGTGATTCGTCGGA 61.997 60.000 3.45 0.00 43.22 4.55
1743 1768 0.666913 CCCGTAGTGATTCGTCGGAT 59.333 55.000 3.45 0.00 43.22 4.18
1744 1769 1.334779 CCCGTAGTGATTCGTCGGATC 60.335 57.143 6.57 6.57 43.22 3.36
1745 1770 1.659491 CCGTAGTGATTCGTCGGATCG 60.659 57.143 8.97 0.00 43.22 3.69
1746 1771 1.396644 GTAGTGATTCGTCGGATCGC 58.603 55.000 17.68 17.68 0.00 4.58
1747 1772 0.309922 TAGTGATTCGTCGGATCGCC 59.690 55.000 20.90 8.81 0.00 5.54
1748 1773 1.065928 GTGATTCGTCGGATCGCCT 59.934 57.895 15.02 0.00 0.00 5.52
1749 1774 0.935366 GTGATTCGTCGGATCGCCTC 60.935 60.000 15.02 0.00 0.00 4.70
1750 1775 1.371881 GATTCGTCGGATCGCCTCC 60.372 63.158 0.00 0.00 41.07 4.30
1751 1776 1.797211 GATTCGTCGGATCGCCTCCT 61.797 60.000 0.00 0.00 42.47 3.69
1752 1777 0.536687 ATTCGTCGGATCGCCTCCTA 60.537 55.000 0.00 0.00 42.47 2.94
1753 1778 0.536687 TTCGTCGGATCGCCTCCTAT 60.537 55.000 0.00 0.00 42.47 2.57
1754 1779 0.322648 TCGTCGGATCGCCTCCTATA 59.677 55.000 0.00 0.00 42.47 1.31
1755 1780 1.065636 TCGTCGGATCGCCTCCTATAT 60.066 52.381 0.00 0.00 42.47 0.86
1756 1781 2.169144 TCGTCGGATCGCCTCCTATATA 59.831 50.000 0.00 0.00 42.47 0.86
1757 1782 2.544686 CGTCGGATCGCCTCCTATATAG 59.455 54.545 2.46 2.46 42.47 1.31
1758 1783 2.879646 GTCGGATCGCCTCCTATATAGG 59.120 54.545 21.21 21.21 42.47 2.57
1759 1784 2.508716 TCGGATCGCCTCCTATATAGGT 59.491 50.000 25.06 7.75 44.02 3.08
1760 1785 3.713248 TCGGATCGCCTCCTATATAGGTA 59.287 47.826 25.06 12.98 44.02 3.08
1761 1786 4.066490 CGGATCGCCTCCTATATAGGTAG 58.934 52.174 25.06 19.81 44.02 3.18
1762 1787 4.400120 GGATCGCCTCCTATATAGGTAGG 58.600 52.174 27.09 27.09 44.02 3.18
1763 1788 3.947612 TCGCCTCCTATATAGGTAGGG 57.052 52.381 29.53 26.00 44.02 3.53
1764 1789 2.091994 TCGCCTCCTATATAGGTAGGGC 60.092 54.545 30.60 30.60 44.02 5.19
1765 1790 2.308690 GCCTCCTATATAGGTAGGGCG 58.691 57.143 29.53 16.40 44.02 6.13
1766 1791 2.946785 CCTCCTATATAGGTAGGGCGG 58.053 57.143 25.06 14.12 44.02 6.13
1767 1792 2.512896 CCTCCTATATAGGTAGGGCGGA 59.487 54.545 25.06 5.91 44.02 5.54
1768 1793 3.553904 CTCCTATATAGGTAGGGCGGAC 58.446 54.545 25.06 0.00 44.02 4.79
1769 1794 2.921612 TCCTATATAGGTAGGGCGGACA 59.078 50.000 25.06 2.44 44.02 4.02
1770 1795 3.053842 TCCTATATAGGTAGGGCGGACAG 60.054 52.174 25.06 0.00 44.02 3.51
1771 1796 2.994957 ATATAGGTAGGGCGGACAGT 57.005 50.000 0.00 0.00 0.00 3.55
1772 1797 4.080129 CCTATATAGGTAGGGCGGACAGTA 60.080 50.000 19.30 0.00 38.05 2.74
1773 1798 2.761786 ATAGGTAGGGCGGACAGTAA 57.238 50.000 0.00 0.00 0.00 2.24
1774 1799 1.767759 TAGGTAGGGCGGACAGTAAC 58.232 55.000 0.00 0.00 0.00 2.50
1775 1800 0.251922 AGGTAGGGCGGACAGTAACA 60.252 55.000 0.00 0.00 0.00 2.41
1776 1801 0.175073 GGTAGGGCGGACAGTAACAG 59.825 60.000 0.00 0.00 0.00 3.16
1777 1802 1.180029 GTAGGGCGGACAGTAACAGA 58.820 55.000 0.00 0.00 0.00 3.41
1778 1803 1.134560 GTAGGGCGGACAGTAACAGAG 59.865 57.143 0.00 0.00 0.00 3.35
1779 1804 1.218316 GGGCGGACAGTAACAGAGG 59.782 63.158 0.00 0.00 0.00 3.69
1780 1805 1.255667 GGGCGGACAGTAACAGAGGA 61.256 60.000 0.00 0.00 0.00 3.71
1781 1806 0.173708 GGCGGACAGTAACAGAGGAG 59.826 60.000 0.00 0.00 0.00 3.69
1782 1807 0.889306 GCGGACAGTAACAGAGGAGT 59.111 55.000 0.00 0.00 0.00 3.85
1783 1808 2.089980 GCGGACAGTAACAGAGGAGTA 58.910 52.381 0.00 0.00 0.00 2.59
1784 1809 2.688958 GCGGACAGTAACAGAGGAGTAT 59.311 50.000 0.00 0.00 0.00 2.12
1785 1810 3.243134 GCGGACAGTAACAGAGGAGTATC 60.243 52.174 0.00 0.00 0.00 2.24
1786 1811 3.945921 CGGACAGTAACAGAGGAGTATCA 59.054 47.826 0.00 0.00 36.25 2.15
1787 1812 4.580995 CGGACAGTAACAGAGGAGTATCAT 59.419 45.833 0.00 0.00 36.25 2.45
1788 1813 5.067936 CGGACAGTAACAGAGGAGTATCATT 59.932 44.000 0.00 0.00 36.25 2.57
1789 1814 6.508777 GGACAGTAACAGAGGAGTATCATTC 58.491 44.000 0.00 0.00 36.25 2.67
1790 1815 6.322712 GGACAGTAACAGAGGAGTATCATTCT 59.677 42.308 0.00 0.00 36.25 2.40
1791 1816 7.106439 ACAGTAACAGAGGAGTATCATTCTG 57.894 40.000 8.24 8.24 46.97 3.02
1799 1824 8.458573 CAGAGGAGTATCATTCTGTTACTAGT 57.541 38.462 0.00 0.00 40.96 2.57
1800 1825 9.562408 CAGAGGAGTATCATTCTGTTACTAGTA 57.438 37.037 0.00 0.00 40.96 1.82
1803 1828 9.696572 AGGAGTATCATTCTGTTACTAGTAACA 57.303 33.333 34.88 34.88 44.51 2.41
1817 1842 9.363763 GTTACTAGTAACAAAATAGTCCAGTCC 57.636 37.037 31.74 6.55 43.55 3.85
1818 1843 7.793948 ACTAGTAACAAAATAGTCCAGTCCT 57.206 36.000 0.00 0.00 0.00 3.85
1819 1844 8.890410 ACTAGTAACAAAATAGTCCAGTCCTA 57.110 34.615 0.00 0.00 0.00 2.94
1820 1845 9.490083 ACTAGTAACAAAATAGTCCAGTCCTAT 57.510 33.333 0.00 0.00 0.00 2.57
1947 1982 6.834168 AGGCTAGAGAATAGATAAGCTGTC 57.166 41.667 0.00 0.00 0.00 3.51
1968 2003 0.593128 CTGGCGAGTTCAAACCCAAG 59.407 55.000 0.00 0.00 0.00 3.61
2002 2037 6.182627 TCTTCCTTGAGATGTGCATTAACAT 58.817 36.000 0.00 0.00 43.47 2.71
2023 2062 7.687941 ACATCAAATGTATTTTCGTCTCCTT 57.312 32.000 0.00 0.00 42.78 3.36
2024 2063 8.786826 ACATCAAATGTATTTTCGTCTCCTTA 57.213 30.769 0.00 0.00 42.78 2.69
2066 2105 3.031736 TCCCTCATTGCTCCTACAGTAC 58.968 50.000 0.00 0.00 0.00 2.73
2093 2132 6.202762 TGCATAGCATAAGTATCTTTCCAACG 59.797 38.462 0.00 0.00 31.71 4.10
2123 2162 2.359975 GGGGTTGCTTGGACCTCG 60.360 66.667 0.00 0.00 37.34 4.63
2253 3485 6.446318 TCTTCTTATTTGGTCAAACACATGC 58.554 36.000 0.00 0.00 32.51 4.06
2273 3505 3.067461 TGCATTTTTCTGGTAAGCAACGT 59.933 39.130 0.00 0.00 0.00 3.99
2277 3509 6.607689 CATTTTTCTGGTAAGCAACGTATCA 58.392 36.000 0.00 0.00 0.00 2.15
2347 3581 4.852134 TTTCAATGGCATAAGCGCATAT 57.148 36.364 11.47 4.24 43.41 1.78
2373 3607 4.838423 TCCGAATATCTAATTCTGAGCCCA 59.162 41.667 0.00 0.00 0.00 5.36
2375 3609 5.174395 CGAATATCTAATTCTGAGCCCAGG 58.826 45.833 0.00 0.00 40.76 4.45
2390 3624 4.142045 AGGCTCATCTGCACCTGA 57.858 55.556 0.00 0.00 34.04 3.86
2409 3643 8.699749 GCACCTGATGAACAGTAAATTAAAAAC 58.300 33.333 0.00 0.00 44.40 2.43
2410 3644 9.743057 CACCTGATGAACAGTAAATTAAAAACA 57.257 29.630 0.00 0.00 44.40 2.83
2615 3871 0.606130 TTGACACAGGCATCACGCAT 60.606 50.000 0.00 0.00 45.17 4.73
2618 3874 1.308069 ACACAGGCATCACGCATTCC 61.308 55.000 0.00 0.00 45.17 3.01
2635 3891 3.319137 TTCCGTCATCTTTCTCCACAG 57.681 47.619 0.00 0.00 0.00 3.66
2643 3903 6.580041 CGTCATCTTTCTCCACAGAAAATTTG 59.420 38.462 0.00 0.00 46.03 2.32
2644 3904 7.520453 CGTCATCTTTCTCCACAGAAAATTTGA 60.520 37.037 0.00 0.93 46.03 2.69
2709 3970 1.228124 CCCGAGAGCCAAAACACCA 60.228 57.895 0.00 0.00 0.00 4.17
2743 4004 8.051901 ACAATCATGATACCATATGCAATCAG 57.948 34.615 9.04 12.37 32.25 2.90
2762 4023 0.375106 GATTCCAAAAGAGCTCGCCG 59.625 55.000 8.37 0.00 0.00 6.46
2828 4204 6.814954 AGCTAGGTTGATGATAAGGAGAAA 57.185 37.500 0.00 0.00 0.00 2.52
2829 4205 7.200434 AGCTAGGTTGATGATAAGGAGAAAA 57.800 36.000 0.00 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
85 86 0.532573 GCAGATTGACCTCGACTCCA 59.467 55.000 0.00 0.00 0.00 3.86
159 160 2.073101 GTGGGGAGCCTAAGGAGGG 61.073 68.421 0.00 0.00 43.97 4.30
201 202 1.601419 GCAGTGTACTGGTAGGCGGA 61.601 60.000 13.41 0.00 43.94 5.54
205 206 1.153628 GCCGCAGTGTACTGGTAGG 60.154 63.158 13.41 4.70 43.94 3.18
208 209 2.030562 GTGCCGCAGTGTACTGGT 59.969 61.111 13.41 0.00 43.94 4.00
243 244 6.729569 AGGTGGTCCAAGTATAAGAACTACTT 59.270 38.462 0.00 0.00 39.42 2.24
296 297 0.106819 GCTGGTCCATGAATCAGGCT 60.107 55.000 0.00 0.00 0.00 4.58
310 311 0.532573 AGTCGACATCATTCGCTGGT 59.467 50.000 19.50 0.00 38.95 4.00
356 358 5.348724 TGCATAAGAGTTGAAGACGTTGATC 59.651 40.000 0.00 0.00 0.00 2.92
361 363 3.990469 CACTGCATAAGAGTTGAAGACGT 59.010 43.478 0.00 0.00 0.00 4.34
376 378 1.226542 CTCATGAGGGCCACTGCAT 59.773 57.895 15.38 0.35 40.13 3.96
494 496 0.983378 GCTGGAGGGCCTTCTTCCTA 60.983 60.000 14.33 0.00 32.74 2.94
532 534 3.365265 CAGCTCCAACGCCAACCC 61.365 66.667 0.00 0.00 0.00 4.11
573 581 6.154363 CCTCTCTTCTCTCACTATCAACCTTT 59.846 42.308 0.00 0.00 0.00 3.11
614 625 2.762535 ATTTACTCACCCTGACCACG 57.237 50.000 0.00 0.00 0.00 4.94
713 727 2.119801 ATTCATGGAGTCAGGCACAC 57.880 50.000 0.00 0.00 0.00 3.82
797 811 1.452108 GGATGAACCGCCTCCTTGG 60.452 63.158 0.00 0.00 39.35 3.61
866 880 0.319211 CTCGTGGTCGCCAACTGTTA 60.319 55.000 0.00 0.00 34.18 2.41
880 894 2.584418 CTCCTCCATGCGCTCGTG 60.584 66.667 9.73 4.92 0.00 4.35
915 929 1.213537 GTAGTGGCCGTAGTTGCGA 59.786 57.895 0.00 0.00 0.00 5.10
937 951 1.615424 GAGTTGGGCCACCCTCCTA 60.615 63.158 17.71 0.00 45.70 2.94
984 998 0.394762 GCATGGGGATGCACTCAAGA 60.395 55.000 2.14 0.00 46.25 3.02
1162 1177 2.688507 CTTGAACGTCACCATGTAGCT 58.311 47.619 0.00 0.00 0.00 3.32
1260 1275 2.357034 GCGGTGAAGGCTTCGTCA 60.357 61.111 21.42 2.82 0.00 4.35
1417 1438 4.375272 TCATAAGCAGAGCAGAGCATAAC 58.625 43.478 0.00 0.00 0.00 1.89
1470 1491 1.405121 GGCTAGTTGGTGAGGTTACCG 60.405 57.143 0.00 0.00 43.87 4.02
1659 1683 3.032265 TCTCAACTCAGCCTGGCTATA 57.968 47.619 22.90 11.77 36.40 1.31
1727 1752 1.396644 GCGATCCGACGAATCACTAC 58.603 55.000 0.00 0.00 35.09 2.73
1733 1758 2.728817 GGAGGCGATCCGACGAAT 59.271 61.111 0.00 0.00 41.28 3.34
1741 1766 4.400120 CCCTACCTATATAGGAGGCGATC 58.600 52.174 31.53 0.00 46.63 3.69
1742 1767 3.436761 GCCCTACCTATATAGGAGGCGAT 60.437 52.174 31.53 13.14 46.63 4.58
1743 1768 2.091994 GCCCTACCTATATAGGAGGCGA 60.092 54.545 31.53 12.18 46.63 5.54
1744 1769 2.308690 GCCCTACCTATATAGGAGGCG 58.691 57.143 31.53 23.33 46.63 5.52
1745 1770 2.308690 CGCCCTACCTATATAGGAGGC 58.691 57.143 31.35 31.35 46.63 4.70
1746 1771 2.512896 TCCGCCCTACCTATATAGGAGG 59.487 54.545 31.53 28.06 46.63 4.30
1747 1772 3.053842 TGTCCGCCCTACCTATATAGGAG 60.054 52.174 31.53 22.51 46.63 3.69
1748 1773 2.921612 TGTCCGCCCTACCTATATAGGA 59.078 50.000 31.53 15.87 46.63 2.94
1750 1775 3.965694 ACTGTCCGCCCTACCTATATAG 58.034 50.000 2.46 2.46 0.00 1.31
1751 1776 5.222109 TGTTACTGTCCGCCCTACCTATATA 60.222 44.000 0.00 0.00 0.00 0.86
1752 1777 2.994957 ACTGTCCGCCCTACCTATAT 57.005 50.000 0.00 0.00 0.00 0.86
1753 1778 3.117550 TGTTACTGTCCGCCCTACCTATA 60.118 47.826 0.00 0.00 0.00 1.31
1754 1779 2.314246 GTTACTGTCCGCCCTACCTAT 58.686 52.381 0.00 0.00 0.00 2.57
1755 1780 1.005805 TGTTACTGTCCGCCCTACCTA 59.994 52.381 0.00 0.00 0.00 3.08
1756 1781 0.251922 TGTTACTGTCCGCCCTACCT 60.252 55.000 0.00 0.00 0.00 3.08
1757 1782 0.175073 CTGTTACTGTCCGCCCTACC 59.825 60.000 0.00 0.00 0.00 3.18
1758 1783 1.134560 CTCTGTTACTGTCCGCCCTAC 59.865 57.143 0.00 0.00 0.00 3.18
1759 1784 1.471119 CTCTGTTACTGTCCGCCCTA 58.529 55.000 0.00 0.00 0.00 3.53
1760 1785 1.258445 CCTCTGTTACTGTCCGCCCT 61.258 60.000 0.00 0.00 0.00 5.19
1761 1786 1.218316 CCTCTGTTACTGTCCGCCC 59.782 63.158 0.00 0.00 0.00 6.13
1762 1787 0.173708 CTCCTCTGTTACTGTCCGCC 59.826 60.000 0.00 0.00 0.00 6.13
1763 1788 0.889306 ACTCCTCTGTTACTGTCCGC 59.111 55.000 0.00 0.00 0.00 5.54
1764 1789 3.945921 TGATACTCCTCTGTTACTGTCCG 59.054 47.826 0.00 0.00 0.00 4.79
1765 1790 6.322712 AGAATGATACTCCTCTGTTACTGTCC 59.677 42.308 0.00 0.00 0.00 4.02
1766 1791 7.147983 ACAGAATGATACTCCTCTGTTACTGTC 60.148 40.741 0.00 0.00 44.71 3.51
1767 1792 6.665680 ACAGAATGATACTCCTCTGTTACTGT 59.334 38.462 0.00 0.00 44.71 3.55
1768 1793 7.106439 ACAGAATGATACTCCTCTGTTACTG 57.894 40.000 0.00 0.00 44.71 2.74
1791 1816 9.363763 GGACTGGACTATTTTGTTACTAGTAAC 57.636 37.037 30.62 30.62 44.16 2.50
1792 1817 9.317827 AGGACTGGACTATTTTGTTACTAGTAA 57.682 33.333 11.38 11.38 0.00 2.24
1793 1818 8.890410 AGGACTGGACTATTTTGTTACTAGTA 57.110 34.615 0.00 0.00 0.00 1.82
1794 1819 7.793948 AGGACTGGACTATTTTGTTACTAGT 57.206 36.000 0.00 0.00 0.00 2.57
1823 1848 9.965902 AAAATTTGATATGTTACTCTCTGTCCT 57.034 29.630 0.00 0.00 0.00 3.85
1824 1849 9.994432 CAAAATTTGATATGTTACTCTCTGTCC 57.006 33.333 0.00 0.00 0.00 4.02
1865 1891 8.890718 GCATGATGCATTGTTCTATATATGTCT 58.109 33.333 13.36 0.00 44.26 3.41
1888 1923 4.543689 AGATTGGTCAATGAGGATTGCAT 58.456 39.130 0.43 0.00 39.16 3.96
1925 1960 5.636837 CGACAGCTTATCTATTCTCTAGCC 58.363 45.833 0.00 0.00 0.00 3.93
1947 1982 2.556287 GGTTTGAACTCGCCAGCG 59.444 61.111 5.50 5.50 41.35 5.18
1950 1985 0.106918 ACTTGGGTTTGAACTCGCCA 60.107 50.000 0.00 0.00 29.87 5.69
1958 1993 1.494721 AGAAGGAGCACTTGGGTTTGA 59.505 47.619 0.00 0.00 40.21 2.69
1968 2003 2.564947 TCTCAAGGAAGAGAAGGAGCAC 59.435 50.000 0.00 0.00 41.45 4.40
2012 2047 7.389330 TGCACATAGAAAATTAAGGAGACGAAA 59.611 33.333 0.00 0.00 0.00 3.46
2023 2062 6.461370 GGGACATGCATGCACATAGAAAATTA 60.461 38.462 25.37 0.00 0.00 1.40
2024 2063 5.353938 GGACATGCATGCACATAGAAAATT 58.646 37.500 25.37 0.00 0.00 1.82
2026 2065 3.130869 GGGACATGCATGCACATAGAAAA 59.869 43.478 25.37 0.00 0.00 2.29
2090 2129 0.684153 CCCCATCCATGGCTTTCGTT 60.684 55.000 6.96 0.00 46.70 3.85
2093 2132 0.826062 CAACCCCATCCATGGCTTTC 59.174 55.000 6.96 0.00 46.70 2.62
2253 3485 6.523201 GTGATACGTTGCTTACCAGAAAAATG 59.477 38.462 0.00 0.00 0.00 2.32
2273 3505 2.030185 GCTATTTCTCGGAGGCGTGATA 60.030 50.000 4.96 0.00 0.00 2.15
2277 3509 1.043673 AGGCTATTTCTCGGAGGCGT 61.044 55.000 4.96 0.00 40.51 5.68
2279 3511 2.333688 AAAGGCTATTTCTCGGAGGC 57.666 50.000 4.96 0.00 36.07 4.70
2347 3581 7.180229 TGGGCTCAGAATTAGATATTCGGATTA 59.820 37.037 0.00 0.00 33.22 1.75
2373 3607 0.180642 CATCAGGTGCAGATGAGCCT 59.819 55.000 8.38 0.00 44.34 4.58
2375 3609 3.774616 TCATCAGGTGCAGATGAGC 57.225 52.632 11.87 0.00 44.98 4.26
2435 3676 3.213506 CGCCCTCATACATTTTCCATGA 58.786 45.455 0.00 0.00 0.00 3.07
2448 3689 0.532115 GAAATTTGGCACGCCCTCAT 59.468 50.000 5.42 0.00 34.56 2.90
2453 3703 0.512518 GCTTTGAAATTTGGCACGCC 59.487 50.000 0.00 0.00 0.00 5.68
2511 3767 8.846607 GTGAAAAAGTTTACTGTTTGTACACTG 58.153 33.333 2.84 0.00 40.20 3.66
2516 3772 8.238631 GGTCTGTGAAAAAGTTTACTGTTTGTA 58.761 33.333 2.84 0.00 33.75 2.41
2561 3817 5.584253 TTGGATGTCTGAGTAGCTCTTAC 57.416 43.478 0.00 0.00 0.00 2.34
2615 3871 2.897326 TCTGTGGAGAAAGATGACGGAA 59.103 45.455 0.00 0.00 0.00 4.30
2618 3874 5.869753 ATTTTCTGTGGAGAAAGATGACG 57.130 39.130 0.00 0.00 46.53 4.35
2709 3970 7.565190 ATGGTATCATGATTGTATGGAGAGT 57.435 36.000 14.65 0.00 31.34 3.24
2743 4004 0.375106 CGGCGAGCTCTTTTGGAATC 59.625 55.000 12.85 0.00 0.00 2.52
2762 4023 8.947115 GGTGAGGCATATATAAGATTAAACACC 58.053 37.037 0.00 0.00 34.84 4.16
2828 4204 9.075678 AGAAATCAGTGATCAAAAGAACATCTT 57.924 29.630 5.98 0.00 38.59 2.40
2829 4205 8.632906 AGAAATCAGTGATCAAAAGAACATCT 57.367 30.769 5.98 0.00 0.00 2.90


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

AutoCloner maintained by Alex Coulton.