Multiple sequence alignment - TraesCS2D01G328200

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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 TraesCS2D01G328200 chr2D 100.000 2852 0 0 1 2852 421479391 421482242 0.000000e+00 5267.0
1 TraesCS2D01G328200 chr2B 90.602 1511 74 22 525 1981 493987164 493988660 0.000000e+00 1941.0
2 TraesCS2D01G328200 chr2B 86.158 419 33 3 2122 2540 493988730 493989123 2.030000e-116 429.0
3 TraesCS2D01G328200 chr2B 95.736 258 11 0 2595 2852 493989235 493989492 1.580000e-112 416.0
4 TraesCS2D01G328200 chr2B 97.059 68 2 0 2535 2602 493989148 493989215 6.460000e-22 115.0
5 TraesCS2D01G328200 chr2B 88.608 79 7 2 2028 2106 493988659 493988735 8.410000e-16 95.3
6 TraesCS2D01G328200 chr2A 90.102 1475 78 28 561 1981 567734722 567736182 0.000000e+00 1853.0
7 TraesCS2D01G328200 chr2A 91.171 521 36 3 2028 2540 567736181 567736699 0.000000e+00 699.0
8 TraesCS2D01G328200 chr2A 96.923 260 7 1 2276 2535 546743003 546742745 4.360000e-118 435.0
9 TraesCS2D01G328200 chr2A 93.471 291 15 2 1362 1652 546771201 546770915 2.030000e-116 429.0
10 TraesCS2D01G328200 chr2A 96.124 258 10 0 2595 2852 567736811 567737068 3.400000e-114 422.0
11 TraesCS2D01G328200 chr2A 95.495 111 5 0 2742 2852 546742739 546742629 8.120000e-41 178.0
12 TraesCS2D01G328200 chr2A 89.130 92 10 0 1860 1951 546743100 546743009 6.460000e-22 115.0
13 TraesCS2D01G328200 chr2A 97.059 68 2 0 2535 2602 567736724 567736791 6.460000e-22 115.0
14 TraesCS2D01G328200 chr5D 91.667 528 39 3 1 524 379390823 379391349 0.000000e+00 726.0
15 TraesCS2D01G328200 chr5D 87.324 497 50 8 36 526 37377381 37376892 8.930000e-155 556.0
16 TraesCS2D01G328200 chr6D 90.189 530 45 3 3 525 412058759 412058230 0.000000e+00 684.0
17 TraesCS2D01G328200 chr6D 89.773 528 49 3 1 524 437780901 437781427 0.000000e+00 671.0
18 TraesCS2D01G328200 chr3D 89.199 537 53 3 1 534 441424916 441425450 0.000000e+00 665.0
19 TraesCS2D01G328200 chr1D 88.469 529 58 2 1 526 10584860 10585388 1.110000e-178 636.0
20 TraesCS2D01G328200 chr5B 88.046 527 54 7 3 524 289561195 289561717 1.450000e-172 616.0
21 TraesCS2D01G328200 chr4B 87.879 528 58 4 4 527 393151224 393150699 1.450000e-172 616.0
22 TraesCS2D01G328200 chr6B 86.286 525 61 8 1 516 345632359 345631837 6.900000e-156 560.0
23 TraesCS2D01G328200 chr3B 86.331 417 32 3 2124 2540 9687690 9688081 5.640000e-117 431.0
24 TraesCS2D01G328200 chr3B 95.882 170 7 0 2595 2764 9688193 9688362 2.800000e-70 276.0
25 TraesCS2D01G328200 chr3B 87.500 136 14 3 1849 1981 9687483 9687618 1.370000e-33 154.0
26 TraesCS2D01G328200 chr3B 97.059 68 2 0 2535 2602 9688106 9688173 6.460000e-22 115.0


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 TraesCS2D01G328200 chr2D 421479391 421482242 2851 False 5267.00 5267 100.0000 1 2852 1 chr2D.!!$F1 2851
1 TraesCS2D01G328200 chr2B 493987164 493989492 2328 False 599.26 1941 91.6326 525 2852 5 chr2B.!!$F1 2327
2 TraesCS2D01G328200 chr2A 567734722 567737068 2346 False 772.25 1853 93.6140 561 2852 4 chr2A.!!$F1 2291
3 TraesCS2D01G328200 chr5D 379390823 379391349 526 False 726.00 726 91.6670 1 524 1 chr5D.!!$F1 523
4 TraesCS2D01G328200 chr6D 412058230 412058759 529 True 684.00 684 90.1890 3 525 1 chr6D.!!$R1 522
5 TraesCS2D01G328200 chr6D 437780901 437781427 526 False 671.00 671 89.7730 1 524 1 chr6D.!!$F1 523
6 TraesCS2D01G328200 chr3D 441424916 441425450 534 False 665.00 665 89.1990 1 534 1 chr3D.!!$F1 533
7 TraesCS2D01G328200 chr1D 10584860 10585388 528 False 636.00 636 88.4690 1 526 1 chr1D.!!$F1 525
8 TraesCS2D01G328200 chr5B 289561195 289561717 522 False 616.00 616 88.0460 3 524 1 chr5B.!!$F1 521
9 TraesCS2D01G328200 chr4B 393150699 393151224 525 True 616.00 616 87.8790 4 527 1 chr4B.!!$R1 523
10 TraesCS2D01G328200 chr6B 345631837 345632359 522 True 560.00 560 86.2860 1 516 1 chr6B.!!$R1 515
11 TraesCS2D01G328200 chr3B 9687483 9688362 879 False 244.00 431 91.6930 1849 2764 4 chr3B.!!$F1 915

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
896 916 0.380378 CACCGACGCCATAAATTGGG 59.62 55.0 0.0 0.0 46.55 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2236 2354 0.172803 CTCCTAGGGAACGTTCACCG 59.827 60.0 26.45 17.36 44.03 4.94 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
112 116 3.448686 ACTTCTCGTTGATAGGCAATCG 58.551 45.455 0.00 0.00 39.03 3.34
114 118 2.809446 TCTCGTTGATAGGCAATCGTG 58.191 47.619 0.00 0.00 39.03 4.35
173 177 4.893524 ACTAAAGTTGCCTTTTTAGCACCT 59.106 37.500 9.53 0.00 41.18 4.00
190 194 6.648879 AGCACCTAAAGTTGCTCAAAATAA 57.351 33.333 0.00 0.00 30.14 1.40
254 259 1.002366 CTCATCGCGAGAAACCCAAG 58.998 55.000 16.66 0.00 45.45 3.61
255 260 1.404181 CTCATCGCGAGAAACCCAAGA 60.404 52.381 16.66 0.32 45.45 3.02
275 281 8.742777 CCCAAGAGTGAAAATGAATCTGAATTA 58.257 33.333 0.00 0.00 0.00 1.40
351 361 2.546368 TGCACGTACATGTTTCTTGACC 59.454 45.455 2.30 0.00 0.00 4.02
589 603 5.452636 GCCTCCTGTTGTTTCCACAAATTTA 60.453 40.000 0.00 0.00 44.72 1.40
595 609 7.010091 CCTGTTGTTTCCACAAATTTAAGTGTC 59.990 37.037 7.61 0.00 44.72 3.67
674 692 6.653526 TCACCTTGATGATTTGATTTGTGT 57.346 33.333 0.00 0.00 0.00 3.72
675 693 6.680810 TCACCTTGATGATTTGATTTGTGTC 58.319 36.000 0.00 0.00 0.00 3.67
829 849 0.950555 TCTCACATGCAGACGGTTGC 60.951 55.000 6.47 6.47 44.33 4.17
896 916 0.380378 CACCGACGCCATAAATTGGG 59.620 55.000 0.00 0.00 46.55 4.12
905 925 2.681422 CCATAAATTGGGGCCTGACAT 58.319 47.619 0.84 0.00 42.33 3.06
1034 1060 2.342650 GCTCTCGCCATGGCCAAAA 61.343 57.895 30.79 12.87 37.98 2.44
1628 1681 1.481056 CCAAGACCCTCCACGACCTT 61.481 60.000 0.00 0.00 0.00 3.50
1640 1693 1.268899 CACGACCTTGACGACTACCTT 59.731 52.381 0.00 0.00 34.70 3.50
1653 1706 5.558818 ACGACTACCTTCTCAAGAACTAGA 58.441 41.667 0.00 0.00 0.00 2.43
1654 1707 5.644636 ACGACTACCTTCTCAAGAACTAGAG 59.355 44.000 0.00 0.00 0.00 2.43
1655 1708 5.644636 CGACTACCTTCTCAAGAACTAGAGT 59.355 44.000 0.00 0.00 33.63 3.24
1656 1709 6.817641 CGACTACCTTCTCAAGAACTAGAGTA 59.182 42.308 0.00 0.00 33.63 2.59
1657 1710 7.010738 CGACTACCTTCTCAAGAACTAGAGTAG 59.989 44.444 0.00 0.00 33.63 2.57
1660 1713 6.014012 ACCTTCTCAAGAACTAGAGTAGCTT 58.986 40.000 0.00 0.00 33.63 3.74
1661 1714 6.495526 ACCTTCTCAAGAACTAGAGTAGCTTT 59.504 38.462 0.00 0.00 33.63 3.51
1662 1715 7.015779 ACCTTCTCAAGAACTAGAGTAGCTTTT 59.984 37.037 0.00 0.00 33.63 2.27
1663 1716 8.524487 CCTTCTCAAGAACTAGAGTAGCTTTTA 58.476 37.037 0.00 0.00 33.63 1.52
1664 1717 9.349145 CTTCTCAAGAACTAGAGTAGCTTTTAC 57.651 37.037 0.00 0.00 33.63 2.01
1720 1791 1.072806 CGTCCATCCATCCATCCATGT 59.927 52.381 0.00 0.00 0.00 3.21
1721 1792 2.787994 GTCCATCCATCCATCCATGTC 58.212 52.381 0.00 0.00 0.00 3.06
1729 1800 3.389002 CCATCCATCCATGTCTACTGTCA 59.611 47.826 0.00 0.00 0.00 3.58
1735 1806 5.221244 CCATCCATGTCTACTGTCATCGTTA 60.221 44.000 0.00 0.00 0.00 3.18
1737 1808 4.948004 TCCATGTCTACTGTCATCGTTACT 59.052 41.667 0.00 0.00 0.00 2.24
1740 1811 4.482386 TGTCTACTGTCATCGTTACTTGC 58.518 43.478 0.00 0.00 0.00 4.01
1748 1819 1.394917 CATCGTTACTTGCTGTCTGCC 59.605 52.381 0.00 0.00 42.00 4.85
1753 1824 0.105964 TACTTGCTGTCTGCCGTGTT 59.894 50.000 0.00 0.00 42.00 3.32
1757 1828 2.358737 CTGTCTGCCGTGTTCCCC 60.359 66.667 0.00 0.00 0.00 4.81
1760 1831 2.933287 TCTGCCGTGTTCCCCCAT 60.933 61.111 0.00 0.00 0.00 4.00
1762 1833 2.933287 TGCCGTGTTCCCCCATCT 60.933 61.111 0.00 0.00 0.00 2.90
1777 1848 3.215151 CCCATCTAGCTTACTCTCACGA 58.785 50.000 0.00 0.00 0.00 4.35
1794 1865 0.503961 CGAAAACGACCGTGTGTACC 59.496 55.000 0.00 0.00 0.00 3.34
1795 1866 1.569708 GAAAACGACCGTGTGTACCA 58.430 50.000 0.00 0.00 0.00 3.25
1840 1914 1.361668 GGACGGACGCGTGAGTAGTA 61.362 60.000 20.70 0.00 0.00 1.82
1842 1916 0.671781 ACGGACGCGTGAGTAGTAGT 60.672 55.000 20.70 1.31 0.00 2.73
1843 1917 0.247576 CGGACGCGTGAGTAGTAGTG 60.248 60.000 20.70 0.00 0.00 2.74
1844 1918 0.098376 GGACGCGTGAGTAGTAGTGG 59.902 60.000 20.70 0.00 0.00 4.00
1846 1920 0.801251 ACGCGTGAGTAGTAGTGGAC 59.199 55.000 12.93 0.00 0.00 4.02
1905 1988 5.119588 CGTACGAATGGTGTTAGATTTGTGT 59.880 40.000 10.44 0.00 30.38 3.72
1908 1991 5.049680 ACGAATGGTGTTAGATTTGTGTGAC 60.050 40.000 0.00 0.00 0.00 3.67
1930 2013 2.358957 TGGTTTGATTCGATCTGCAGG 58.641 47.619 15.13 0.00 0.00 4.85
1938 2021 6.271488 TGATTCGATCTGCAGGAAAAATTT 57.729 33.333 15.13 0.00 0.00 1.82
1951 2034 6.090763 GCAGGAAAAATTTAGTATGTTGTGGC 59.909 38.462 0.00 0.00 0.00 5.01
1959 2042 5.554822 TTAGTATGTTGTGGCGGAATTTC 57.445 39.130 0.00 0.00 0.00 2.17
1962 2052 4.522789 AGTATGTTGTGGCGGAATTTCTTT 59.477 37.500 0.00 0.00 0.00 2.52
1972 2062 4.500716 GGCGGAATTTCTTTCTTCAAACCA 60.501 41.667 0.00 0.00 34.56 3.67
1980 2070 4.642429 TCTTTCTTCAAACCAGGCTACTC 58.358 43.478 0.00 0.00 0.00 2.59
1981 2071 3.418684 TTCTTCAAACCAGGCTACTCC 57.581 47.619 0.00 0.00 0.00 3.85
1982 2072 1.628846 TCTTCAAACCAGGCTACTCCC 59.371 52.381 0.00 0.00 34.51 4.30
1983 2073 0.696501 TTCAAACCAGGCTACTCCCC 59.303 55.000 0.00 0.00 34.51 4.81
1984 2074 0.178873 TCAAACCAGGCTACTCCCCT 60.179 55.000 0.00 0.00 34.51 4.79
1985 2075 0.698818 CAAACCAGGCTACTCCCCTT 59.301 55.000 0.00 0.00 34.51 3.95
1986 2076 0.992695 AAACCAGGCTACTCCCCTTC 59.007 55.000 0.00 0.00 34.51 3.46
1987 2077 0.119358 AACCAGGCTACTCCCCTTCT 59.881 55.000 0.00 0.00 34.51 2.85
1988 2078 0.325765 ACCAGGCTACTCCCCTTCTC 60.326 60.000 0.00 0.00 34.51 2.87
1989 2079 1.051556 CCAGGCTACTCCCCTTCTCC 61.052 65.000 0.00 0.00 34.51 3.71
1990 2080 0.031616 CAGGCTACTCCCCTTCTCCT 60.032 60.000 0.00 0.00 34.51 3.69
1991 2081 0.719623 AGGCTACTCCCCTTCTCCTT 59.280 55.000 0.00 0.00 34.51 3.36
1992 2082 1.938069 AGGCTACTCCCCTTCTCCTTA 59.062 52.381 0.00 0.00 34.51 2.69
1993 2083 2.318207 AGGCTACTCCCCTTCTCCTTAA 59.682 50.000 0.00 0.00 34.51 1.85
1994 2084 3.050954 AGGCTACTCCCCTTCTCCTTAAT 60.051 47.826 0.00 0.00 34.51 1.40
1995 2085 4.172241 AGGCTACTCCCCTTCTCCTTAATA 59.828 45.833 0.00 0.00 34.51 0.98
1996 2086 4.906060 GGCTACTCCCCTTCTCCTTAATAA 59.094 45.833 0.00 0.00 0.00 1.40
1997 2087 5.548446 GGCTACTCCCCTTCTCCTTAATAAT 59.452 44.000 0.00 0.00 0.00 1.28
1998 2088 6.044520 GGCTACTCCCCTTCTCCTTAATAATT 59.955 42.308 0.00 0.00 0.00 1.40
1999 2089 7.421499 GGCTACTCCCCTTCTCCTTAATAATTT 60.421 40.741 0.00 0.00 0.00 1.82
2000 2090 7.999545 GCTACTCCCCTTCTCCTTAATAATTTT 59.000 37.037 0.00 0.00 0.00 1.82
2001 2091 9.562408 CTACTCCCCTTCTCCTTAATAATTTTC 57.438 37.037 0.00 0.00 0.00 2.29
2002 2092 7.939781 ACTCCCCTTCTCCTTAATAATTTTCA 58.060 34.615 0.00 0.00 0.00 2.69
2003 2093 8.569596 ACTCCCCTTCTCCTTAATAATTTTCAT 58.430 33.333 0.00 0.00 0.00 2.57
2065 2163 0.881796 GGCGGGGAAGAGAAAACAAG 59.118 55.000 0.00 0.00 0.00 3.16
2080 2178 0.605589 ACAAGGAGTTTGGGCGCTAC 60.606 55.000 7.64 0.66 41.25 3.58
2081 2179 0.605319 CAAGGAGTTTGGGCGCTACA 60.605 55.000 7.64 3.94 32.95 2.74
2084 2182 1.305930 GGAGTTTGGGCGCTACAAGG 61.306 60.000 7.64 0.00 0.00 3.61
2107 2205 2.350738 CCACCGCATGGGAAAAAGT 58.649 52.632 12.02 0.00 45.95 2.66
2108 2206 1.540267 CCACCGCATGGGAAAAAGTA 58.460 50.000 12.02 0.00 45.95 2.24
2109 2207 1.472480 CCACCGCATGGGAAAAAGTAG 59.528 52.381 12.02 0.00 45.95 2.57
2110 2208 2.432444 CACCGCATGGGAAAAAGTAGA 58.568 47.619 12.02 0.00 40.75 2.59
2111 2209 2.161609 CACCGCATGGGAAAAAGTAGAC 59.838 50.000 12.02 0.00 40.75 2.59
2112 2210 2.039879 ACCGCATGGGAAAAAGTAGACT 59.960 45.455 12.02 0.00 40.75 3.24
2113 2211 2.420022 CCGCATGGGAAAAAGTAGACTG 59.580 50.000 12.02 0.00 38.47 3.51
2114 2212 3.074412 CGCATGGGAAAAAGTAGACTGT 58.926 45.455 3.11 0.00 0.00 3.55
2115 2213 3.125316 CGCATGGGAAAAAGTAGACTGTC 59.875 47.826 3.11 0.00 0.00 3.51
2116 2214 4.072131 GCATGGGAAAAAGTAGACTGTCA 58.928 43.478 10.88 0.00 0.00 3.58
2117 2215 4.702131 GCATGGGAAAAAGTAGACTGTCAT 59.298 41.667 10.88 0.00 0.00 3.06
2118 2216 5.163713 GCATGGGAAAAAGTAGACTGTCATC 60.164 44.000 10.88 2.54 0.00 2.92
2119 2217 5.560722 TGGGAAAAAGTAGACTGTCATCA 57.439 39.130 10.88 0.00 0.00 3.07
2120 2218 5.935945 TGGGAAAAAGTAGACTGTCATCAA 58.064 37.500 10.88 0.00 0.00 2.57
2161 2279 3.766545 AGCAGTACCAACCACATGAAAT 58.233 40.909 0.00 0.00 0.00 2.17
2186 2304 3.533606 ACAGACAAAGATGATCTCCCG 57.466 47.619 0.00 0.00 0.00 5.14
2188 2306 4.023980 ACAGACAAAGATGATCTCCCGTA 58.976 43.478 0.00 0.00 0.00 4.02
2193 2311 5.745227 ACAAAGATGATCTCCCGTACAAAT 58.255 37.500 0.00 0.00 0.00 2.32
2199 2317 5.614324 TGATCTCCCGTACAAATCAAGAT 57.386 39.130 0.00 0.00 0.00 2.40
2211 2329 4.997395 ACAAATCAAGATGCGACAACTACT 59.003 37.500 0.00 0.00 0.00 2.57
2236 2354 6.913673 TCAAAAGCACAACGAAAATACTAACC 59.086 34.615 0.00 0.00 0.00 2.85
2297 2415 3.080300 TCGATGGCATTTTTAGGTGGT 57.920 42.857 0.00 0.00 0.00 4.16
2303 2421 3.288092 GGCATTTTTAGGTGGTAGGAGG 58.712 50.000 0.00 0.00 0.00 4.30
2365 2483 0.740149 CAGAAAATGCCATGCGCCTA 59.260 50.000 4.18 0.00 36.24 3.93
2401 2519 2.693069 CGTCTCTGAAGAAACTGCCAT 58.307 47.619 0.00 0.00 31.93 4.40
2429 2547 0.988832 TTCGTAAATGCCACCCCTCT 59.011 50.000 0.00 0.00 0.00 3.69
2430 2548 0.988832 TCGTAAATGCCACCCCTCTT 59.011 50.000 0.00 0.00 0.00 2.85
2437 2555 1.299976 GCCACCCCTCTTGACGAAT 59.700 57.895 0.00 0.00 0.00 3.34
2456 2574 0.392461 TGTTCGCTGGCTATTGGGTC 60.392 55.000 0.00 0.00 0.00 4.46
2457 2575 1.095807 GTTCGCTGGCTATTGGGTCC 61.096 60.000 0.00 0.00 0.00 4.46
2458 2576 1.558167 TTCGCTGGCTATTGGGTCCA 61.558 55.000 0.00 0.00 0.00 4.02
2459 2577 1.077787 CGCTGGCTATTGGGTCCAA 60.078 57.895 4.78 4.78 40.47 3.53
2460 2578 0.679640 CGCTGGCTATTGGGTCCAAA 60.680 55.000 6.52 0.00 39.55 3.28
2471 2594 2.035632 TGGGTCCAAACACAAATGTCC 58.964 47.619 0.00 0.00 38.45 4.02
2583 2736 8.684386 TCAATACAACATGAAAGAACAAGGTA 57.316 30.769 0.00 0.00 0.00 3.08
2658 2838 4.202010 GCAAAACTCCACACATAACACTGT 60.202 41.667 0.00 0.00 0.00 3.55
2670 2850 4.270084 ACATAACACTGTCACAACGAGTTG 59.730 41.667 13.76 13.76 45.58 3.16
2678 2858 1.140052 TCACAACGAGTTGGGACACAT 59.860 47.619 16.05 0.00 46.97 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 7.778382 ACTAAATTCACATATAAGTTGTCCCCC 59.222 37.037 0.00 0.00 0.00 5.40
112 116 5.306394 ACTTCTTCTTAGTTTGCCTACCAC 58.694 41.667 0.00 0.00 0.00 4.16
114 118 5.334957 GCAACTTCTTCTTAGTTTGCCTACC 60.335 44.000 0.00 0.00 33.73 3.18
232 237 1.270625 TGGGTTTCTCGCGATGAGTTT 60.271 47.619 10.36 0.00 45.46 2.66
275 281 9.436957 AGTCATAACTTTTGATTCAAGTATCGT 57.563 29.630 0.00 0.00 33.12 3.73
351 361 4.860907 ACGCTACCTACTTTACACAAATCG 59.139 41.667 0.00 0.00 0.00 3.34
447 458 4.127171 ACACGACAAAAAGCTCACACTAT 58.873 39.130 0.00 0.00 0.00 2.12
530 544 4.042684 TGATGCCCACAGCCATATGTATTA 59.957 41.667 1.24 0.00 42.71 0.98
589 603 6.080648 TGAACACGTTATAGAGTGACACTT 57.919 37.500 10.01 2.76 40.56 3.16
595 609 3.430374 CCCCCTGAACACGTTATAGAGTG 60.430 52.174 7.77 7.77 43.46 3.51
675 693 6.980051 TGATCAATCAAGTCAGTGATCTTG 57.020 37.500 20.46 20.46 44.59 3.02
792 812 2.045926 CTGGCTGTACAGGGGTGC 60.046 66.667 23.95 10.13 34.84 5.01
829 849 3.345714 GTGATAATTCAGAGCAAACGCG 58.654 45.455 3.53 3.53 30.85 6.01
896 916 0.109342 CCATCTACCCATGTCAGGCC 59.891 60.000 0.00 0.00 0.00 5.19
905 925 0.758734 CGGCAAGATCCATCTACCCA 59.241 55.000 0.00 0.00 35.76 4.51
1034 1060 0.253044 AGTGACTGTGGTGCTTGTGT 59.747 50.000 0.00 0.00 0.00 3.72
1097 1123 1.520564 CGATCGACCGGGATGCAAA 60.521 57.895 10.26 0.00 0.00 3.68
1366 1418 0.255890 CACCATCGGAACCCCTGAAT 59.744 55.000 0.00 0.00 0.00 2.57
1466 1519 3.999663 CCCTGAAGTTCTTGTAGAAGCTG 59.000 47.826 4.17 0.00 34.42 4.24
1617 1670 1.135746 GTAGTCGTCAAGGTCGTGGAG 60.136 57.143 0.00 0.00 0.00 3.86
1628 1681 4.142790 AGTTCTTGAGAAGGTAGTCGTCA 58.857 43.478 0.00 0.00 34.27 4.35
1640 1693 8.638629 AGTAAAAGCTACTCTAGTTCTTGAGA 57.361 34.615 15.59 0.00 34.65 3.27
1657 1710 1.927838 GACGAGGCAGCTAGTAAAAGC 59.072 52.381 0.00 0.00 43.11 3.51
1660 1713 0.179145 GCGACGAGGCAGCTAGTAAA 60.179 55.000 0.00 0.00 0.00 2.01
1661 1714 1.030488 AGCGACGAGGCAGCTAGTAA 61.030 55.000 0.00 0.00 39.74 2.24
1662 1715 1.451567 AGCGACGAGGCAGCTAGTA 60.452 57.895 0.00 0.00 39.74 1.82
1663 1716 2.752238 AGCGACGAGGCAGCTAGT 60.752 61.111 0.00 0.00 39.74 2.57
1664 1717 2.278466 CAGCGACGAGGCAGCTAG 60.278 66.667 0.00 0.00 39.48 3.42
1695 1753 0.759060 ATGGATGGATGGACGGACGA 60.759 55.000 0.00 0.00 0.00 4.20
1720 1791 4.217767 ACAGCAAGTAACGATGACAGTAGA 59.782 41.667 0.00 0.00 0.00 2.59
1721 1792 4.486090 ACAGCAAGTAACGATGACAGTAG 58.514 43.478 0.00 0.00 0.00 2.57
1740 1811 2.358737 GGGGAACACGGCAGACAG 60.359 66.667 0.00 0.00 0.00 3.51
1748 1819 0.541863 AAGCTAGATGGGGGAACACG 59.458 55.000 0.00 0.00 35.32 4.49
1753 1824 2.518407 TGAGAGTAAGCTAGATGGGGGA 59.482 50.000 0.00 0.00 0.00 4.81
1757 1828 4.902443 TTCGTGAGAGTAAGCTAGATGG 57.098 45.455 0.00 0.00 43.69 3.51
1760 1831 4.453478 TCGTTTTCGTGAGAGTAAGCTAGA 59.547 41.667 0.00 0.00 43.69 2.43
1762 1833 4.470462 GTCGTTTTCGTGAGAGTAAGCTA 58.530 43.478 0.00 0.00 43.69 3.32
1777 1848 3.756739 TGGTACACACGGTCGTTTT 57.243 47.368 0.00 0.00 0.00 2.43
1794 1865 0.374758 GGCAGATGCACACGTACATG 59.625 55.000 7.19 0.00 44.36 3.21
1795 1866 0.250234 AGGCAGATGCACACGTACAT 59.750 50.000 7.19 0.00 44.36 2.29
1818 1892 4.778415 CTCACGCGTCCGTCCCAG 62.778 72.222 9.86 0.00 46.39 4.45
1827 1901 0.801251 GTCCACTACTACTCACGCGT 59.199 55.000 5.58 5.58 0.00 6.01
1860 1943 5.630896 CGTATACGTGACCATAAAGTTGG 57.369 43.478 17.16 0.00 37.40 3.77
1905 1988 3.436704 GCAGATCGAATCAAACCAAGTCA 59.563 43.478 0.00 0.00 0.00 3.41
1908 1991 3.181503 CCTGCAGATCGAATCAAACCAAG 60.182 47.826 17.39 0.00 0.00 3.61
1930 2013 6.383415 TCCGCCACAACATACTAAATTTTTC 58.617 36.000 0.00 0.00 0.00 2.29
1938 2021 4.839121 AGAAATTCCGCCACAACATACTA 58.161 39.130 0.00 0.00 0.00 1.82
1951 2034 5.222631 CCTGGTTTGAAGAAAGAAATTCCG 58.777 41.667 0.00 0.00 38.94 4.30
1959 2042 3.753797 GGAGTAGCCTGGTTTGAAGAAAG 59.246 47.826 0.00 0.00 0.00 2.62
1962 2052 1.628846 GGGAGTAGCCTGGTTTGAAGA 59.371 52.381 0.00 0.00 36.66 2.87
1972 2062 0.719623 AAGGAGAAGGGGAGTAGCCT 59.280 55.000 0.00 0.00 36.66 4.58
1995 2085 9.974980 ATGTTTTGTACTTCCGTTATGAAAATT 57.025 25.926 0.00 0.00 0.00 1.82
1996 2086 9.974980 AATGTTTTGTACTTCCGTTATGAAAAT 57.025 25.926 0.00 0.00 0.00 1.82
1997 2087 9.239002 CAATGTTTTGTACTTCCGTTATGAAAA 57.761 29.630 0.00 0.00 0.00 2.29
1998 2088 8.622157 TCAATGTTTTGTACTTCCGTTATGAAA 58.378 29.630 0.00 0.00 34.32 2.69
1999 2089 8.155821 TCAATGTTTTGTACTTCCGTTATGAA 57.844 30.769 0.00 0.00 34.32 2.57
2000 2090 7.442969 ACTCAATGTTTTGTACTTCCGTTATGA 59.557 33.333 0.00 0.00 34.32 2.15
2001 2091 7.581476 ACTCAATGTTTTGTACTTCCGTTATG 58.419 34.615 0.00 0.00 34.32 1.90
2002 2092 7.739498 ACTCAATGTTTTGTACTTCCGTTAT 57.261 32.000 0.00 0.00 34.32 1.89
2003 2093 7.280428 TGAACTCAATGTTTTGTACTTCCGTTA 59.720 33.333 0.00 0.00 39.30 3.18
2004 2094 6.094325 TGAACTCAATGTTTTGTACTTCCGTT 59.906 34.615 0.00 0.00 39.30 4.44
2005 2095 5.587043 TGAACTCAATGTTTTGTACTTCCGT 59.413 36.000 0.00 0.00 39.30 4.69
2006 2096 6.055231 TGAACTCAATGTTTTGTACTTCCG 57.945 37.500 0.00 0.00 39.30 4.30
2007 2097 7.703328 TCTTGAACTCAATGTTTTGTACTTCC 58.297 34.615 0.00 0.00 39.30 3.46
2008 2098 8.612619 TCTCTTGAACTCAATGTTTTGTACTTC 58.387 33.333 0.00 0.00 39.30 3.01
2009 2099 8.506168 TCTCTTGAACTCAATGTTTTGTACTT 57.494 30.769 0.00 0.00 39.30 2.24
2010 2100 7.987458 TCTCTCTTGAACTCAATGTTTTGTACT 59.013 33.333 0.00 0.00 39.30 2.73
2011 2101 8.142994 TCTCTCTTGAACTCAATGTTTTGTAC 57.857 34.615 0.00 0.00 39.30 2.90
2012 2102 8.204160 TCTCTCTCTTGAACTCAATGTTTTGTA 58.796 33.333 0.00 0.00 39.30 2.41
2013 2103 7.050377 TCTCTCTCTTGAACTCAATGTTTTGT 58.950 34.615 0.00 0.00 39.30 2.83
2014 2104 7.488187 TCTCTCTCTTGAACTCAATGTTTTG 57.512 36.000 0.00 0.00 39.30 2.44
2015 2105 9.784531 TTATCTCTCTCTTGAACTCAATGTTTT 57.215 29.630 0.00 0.00 39.30 2.43
2016 2106 9.213799 GTTATCTCTCTCTTGAACTCAATGTTT 57.786 33.333 0.00 0.00 39.30 2.83
2017 2107 8.370940 TGTTATCTCTCTCTTGAACTCAATGTT 58.629 33.333 0.00 0.00 42.38 2.71
2018 2108 7.901029 TGTTATCTCTCTCTTGAACTCAATGT 58.099 34.615 0.00 0.00 35.02 2.71
2019 2109 8.819015 CATGTTATCTCTCTCTTGAACTCAATG 58.181 37.037 0.00 0.00 35.02 2.82
2020 2110 7.986320 CCATGTTATCTCTCTCTTGAACTCAAT 59.014 37.037 0.00 0.00 35.02 2.57
2021 2111 7.326454 CCATGTTATCTCTCTCTTGAACTCAA 58.674 38.462 0.00 0.00 0.00 3.02
2022 2112 6.127225 CCCATGTTATCTCTCTCTTGAACTCA 60.127 42.308 0.00 0.00 0.00 3.41
2023 2113 6.279882 CCCATGTTATCTCTCTCTTGAACTC 58.720 44.000 0.00 0.00 0.00 3.01
2024 2114 5.396213 GCCCATGTTATCTCTCTCTTGAACT 60.396 44.000 0.00 0.00 0.00 3.01
2025 2115 4.813697 GCCCATGTTATCTCTCTCTTGAAC 59.186 45.833 0.00 0.00 0.00 3.18
2026 2116 4.442052 CGCCCATGTTATCTCTCTCTTGAA 60.442 45.833 0.00 0.00 0.00 2.69
2027 2117 3.068732 CGCCCATGTTATCTCTCTCTTGA 59.931 47.826 0.00 0.00 0.00 3.02
2065 2163 1.305930 CCTTGTAGCGCCCAAACTCC 61.306 60.000 2.29 0.00 0.00 3.85
2071 2169 1.302993 GGTTTCCTTGTAGCGCCCA 60.303 57.895 2.29 0.00 0.00 5.36
2080 2178 1.586028 CATGCGGTGGGTTTCCTTG 59.414 57.895 0.00 0.00 0.00 3.61
2081 2179 1.606313 CCATGCGGTGGGTTTCCTT 60.606 57.895 0.10 0.00 44.79 3.36
2099 2197 7.730364 TTCTTGATGACAGTCTACTTTTTCC 57.270 36.000 1.31 0.00 0.00 3.13
2161 2279 7.147724 ACGGGAGATCATCTTTGTCTGTAATAA 60.148 37.037 0.00 0.00 0.00 1.40
2181 2299 2.285220 CGCATCTTGATTTGTACGGGAG 59.715 50.000 0.00 0.00 0.00 4.30
2186 2304 5.283060 AGTTGTCGCATCTTGATTTGTAC 57.717 39.130 0.00 0.00 0.00 2.90
2188 2306 4.997395 AGTAGTTGTCGCATCTTGATTTGT 59.003 37.500 0.00 0.00 0.00 2.83
2193 2311 3.934457 TGAGTAGTTGTCGCATCTTGA 57.066 42.857 0.00 0.00 0.00 3.02
2199 2317 2.286833 GTGCTTTTGAGTAGTTGTCGCA 59.713 45.455 0.00 0.00 0.00 5.10
2211 2329 6.913673 GGTTAGTATTTTCGTTGTGCTTTTGA 59.086 34.615 0.00 0.00 0.00 2.69
2236 2354 0.172803 CTCCTAGGGAACGTTCACCG 59.827 60.000 26.45 17.36 44.03 4.94
2365 2483 5.647658 TCAGAGACGCATGGTAATTTTTCAT 59.352 36.000 0.00 0.00 0.00 2.57
2437 2555 0.392461 GACCCAATAGCCAGCGAACA 60.392 55.000 0.00 0.00 0.00 3.18
2456 2574 4.218200 TCTGCTATGGACATTTGTGTTTGG 59.782 41.667 0.00 0.00 0.00 3.28
2457 2575 5.156355 GTCTGCTATGGACATTTGTGTTTG 58.844 41.667 0.00 0.00 34.23 2.93
2458 2576 4.218417 GGTCTGCTATGGACATTTGTGTTT 59.782 41.667 0.00 0.00 35.61 2.83
2459 2577 3.758554 GGTCTGCTATGGACATTTGTGTT 59.241 43.478 0.00 0.00 35.61 3.32
2460 2578 3.244875 TGGTCTGCTATGGACATTTGTGT 60.245 43.478 0.00 0.00 35.61 3.72
2471 2594 2.157668 GTCGTGTTGTTGGTCTGCTATG 59.842 50.000 0.00 0.00 0.00 2.23
2583 2736 6.128282 CGTGCCACTTTTGAGATAGTGTTTAT 60.128 38.462 0.00 0.00 40.06 1.40
2658 2838 0.537653 TGTGTCCCAACTCGTTGTGA 59.462 50.000 8.77 0.25 38.85 3.58
2678 2858 1.195442 TGCGGTGTTGGGGACTGATA 61.195 55.000 0.00 0.00 0.00 2.15


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

AutoCloner maintained by Alex Coulton.