Multiple sequence alignment - TraesCS2A01G100200

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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 TraesCS2A01G100200 chr2A 100.000 2324 0 0 1 2324 53284160 53286483 0.000000e+00 4292.0
1 TraesCS2A01G100200 chr2D 94.709 1153 32 5 1 1129 42740853 42739706 0.000000e+00 1764.0
2 TraesCS2A01G100200 chr2D 95.460 859 17 7 340 1181 52018994 52019847 0.000000e+00 1351.0
3 TraesCS2A01G100200 chr2D 95.425 459 9 4 1127 1581 42737937 42737487 0.000000e+00 721.0
4 TraesCS2A01G100200 chr2D 94.189 413 8 3 1208 1606 52019846 52020256 1.180000e-172 616.0
5 TraesCS2A01G100200 chr2D 97.661 342 8 0 1 342 52018572 52018913 2.570000e-164 588.0
6 TraesCS2A01G100200 chr2D 91.036 357 8 4 1964 2300 42734133 42733781 5.850000e-126 460.0
7 TraesCS2A01G100200 chr2D 96.296 189 4 1 1603 1791 52022447 52022632 8.070000e-80 307.0
8 TraesCS2A01G100200 chr2D 96.262 107 4 0 1685 1791 42734248 42734142 2.370000e-40 176.0
9 TraesCS2A01G100200 chr2D 93.750 80 4 1 1573 1652 42734324 42734246 4.060000e-23 119.0
10 TraesCS2A01G100200 chr4A 95.495 111 4 1 1853 1962 199406639 199406529 2.370000e-40 176.0
11 TraesCS2A01G100200 chr4A 91.071 112 6 3 1789 1898 86297651 86297760 5.170000e-32 148.0
12 TraesCS2A01G100200 chr4B 94.595 111 5 1 1853 1962 583773816 583773706 1.100000e-38 171.0
13 TraesCS2A01G100200 chr4B 88.806 134 11 4 1853 1983 106858476 106858608 6.650000e-36 161.0
14 TraesCS2A01G100200 chr4B 85.714 154 14 8 1853 2002 334107950 334108099 3.090000e-34 156.0
15 TraesCS2A01G100200 chr3A 94.595 111 5 1 1853 1962 607110060 607110170 1.100000e-38 171.0
16 TraesCS2A01G100200 chrUn 93.805 113 6 1 1853 1964 95642685 95642797 3.970000e-38 169.0
17 TraesCS2A01G100200 chr2B 92.308 117 8 1 1853 1968 34111164 34111048 5.140000e-37 165.0
18 TraesCS2A01G100200 chr2B 86.735 98 10 3 1789 1886 184655509 184655603 3.160000e-19 106.0
19 TraesCS2A01G100200 chr1D 89.844 128 11 2 1853 1978 7179578 7179705 1.850000e-36 163.0
20 TraesCS2A01G100200 chr5B 89.683 126 11 2 1853 1977 660144600 660144724 2.390000e-35 159.0
21 TraesCS2A01G100200 chr5B 95.890 73 2 1 1786 1858 42698142 42698071 1.460000e-22 117.0
22 TraesCS2A01G100200 chr1A 89.320 103 9 2 1788 1888 95826135 95826033 6.740000e-26 128.0
23 TraesCS2A01G100200 chr6B 93.023 86 3 3 1806 1888 11284613 11284698 3.140000e-24 122.0
24 TraesCS2A01G100200 chr6A 95.833 72 1 2 1787 1858 594338418 594338349 5.250000e-22 115.0
25 TraesCS2A01G100200 chr6A 90.698 86 5 3 1773 1858 601207356 601207274 6.790000e-21 111.0
26 TraesCS2A01G100200 chr1B 94.667 75 2 2 1785 1858 674058051 674057978 5.250000e-22 115.0
27 TraesCS2A01G100200 chr1B 84.906 106 9 7 1789 1888 670821433 670821537 1.470000e-17 100.0
28 TraesCS2A01G100200 chr5D 82.243 107 13 5 1790 1891 117342505 117342400 1.140000e-13 87.9


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 TraesCS2A01G100200 chr2A 53284160 53286483 2323 False 4292.0 4292 100.0000 1 2324 1 chr2A.!!$F1 2323
1 TraesCS2A01G100200 chr2D 52018572 52022632 4060 False 715.5 1351 95.9015 1 1791 4 chr2D.!!$F1 1790
2 TraesCS2A01G100200 chr2D 42733781 42740853 7072 True 648.0 1764 94.2364 1 2300 5 chr2D.!!$R1 2299

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
547 632 0.682209 GCAAGGGTGGATCAGTGCAT 60.682 55.0 0.0 0.0 32.29 3.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 9087 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.0 13.64 4.95 46.06 4.2 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
56 57 7.075121 TGTGTGTGATTTCTTAATTTGTAGCG 58.925 34.615 0.00 0.00 0.00 4.26
86 87 9.911788 AAGGATAATCTGAAGCTTCTTAAATCA 57.088 29.630 26.09 4.93 0.00 2.57
266 268 5.179368 TCTGAAAAATGTCCTAACAGAAGCG 59.821 40.000 0.00 0.00 39.20 4.68
328 330 9.371136 TGTTCTGTAAATTACATAGAGCTGAAG 57.629 33.333 6.27 0.00 38.15 3.02
378 463 5.594725 TGCTTATGTAACACCAAAAGGTTGA 59.405 36.000 0.00 0.00 36.83 3.18
379 464 6.266558 TGCTTATGTAACACCAAAAGGTTGAT 59.733 34.615 0.00 0.00 36.83 2.57
380 465 7.151976 GCTTATGTAACACCAAAAGGTTGATT 58.848 34.615 0.00 0.00 36.83 2.57
381 466 7.328493 GCTTATGTAACACCAAAAGGTTGATTC 59.672 37.037 0.00 0.00 36.83 2.52
382 467 5.176407 TGTAACACCAAAAGGTTGATTCG 57.824 39.130 0.00 0.00 36.83 3.34
425 510 6.588719 TCCCTTAGGTTGATTTGTTCATTG 57.411 37.500 0.00 0.00 33.34 2.82
492 577 7.069085 CCCTTTCAGATGGATGATTGTTTGTAT 59.931 37.037 0.00 0.00 0.00 2.29
547 632 0.682209 GCAAGGGTGGATCAGTGCAT 60.682 55.000 0.00 0.00 32.29 3.96
550 635 1.524621 GGGTGGATCAGTGCATCGG 60.525 63.158 0.00 0.00 0.00 4.18
555 640 2.228822 GTGGATCAGTGCATCGGTTTTT 59.771 45.455 0.00 0.00 0.00 1.94
622 707 3.458487 ACCCCTAATAACAGTTGCCCTAG 59.542 47.826 0.00 0.00 0.00 3.02
856 941 4.674281 AGTAGCTGTAGCCTACATTTCC 57.326 45.455 4.77 0.00 43.38 3.13
1153 3039 3.027412 ACGGCAGTCATATCTTCTGAGT 58.973 45.455 0.00 0.00 0.00 3.41
1181 3095 4.085357 TGCTTGGTTTGTACAGACAGAT 57.915 40.909 17.42 0.00 36.76 2.90
1182 3096 4.460263 TGCTTGGTTTGTACAGACAGATT 58.540 39.130 17.42 0.00 36.76 2.40
1183 3097 5.616270 TGCTTGGTTTGTACAGACAGATTA 58.384 37.500 17.42 0.00 36.76 1.75
1184 3098 6.058833 TGCTTGGTTTGTACAGACAGATTAA 58.941 36.000 17.42 4.65 36.76 1.40
1185 3099 6.714810 TGCTTGGTTTGTACAGACAGATTAAT 59.285 34.615 17.42 0.00 36.76 1.40
1186 3100 7.880713 TGCTTGGTTTGTACAGACAGATTAATA 59.119 33.333 17.42 0.00 36.76 0.98
1187 3101 8.726988 GCTTGGTTTGTACAGACAGATTAATAA 58.273 33.333 17.42 0.00 36.76 1.40
1300 3218 5.045942 TGCCCAGAACTGTATGAGTTTATGA 60.046 40.000 1.18 0.00 45.48 2.15
1326 3246 0.106569 CCCCTGCATGCCAATGACTA 60.107 55.000 16.68 0.00 35.67 2.59
1327 3247 1.479942 CCCCTGCATGCCAATGACTAT 60.480 52.381 16.68 0.00 35.67 2.12
1335 3255 5.008911 TGCATGCCAATGACTATGTTACATC 59.991 40.000 16.68 0.00 35.67 3.06
1565 3495 2.429930 GGCACCTGGCTGTACACA 59.570 61.111 0.00 0.00 44.01 3.72
1781 9076 6.371548 TGATTTTTATGACGTGGAAGAAGAGG 59.628 38.462 0.00 0.00 0.00 3.69
1791 9086 2.492484 TGGAAGAAGAGGAGCGAAGTAC 59.508 50.000 0.00 0.00 0.00 2.73
1792 9087 2.756207 GGAAGAAGAGGAGCGAAGTACT 59.244 50.000 0.00 0.00 0.00 2.73
1793 9088 3.181494 GGAAGAAGAGGAGCGAAGTACTC 60.181 52.174 0.00 0.00 0.00 2.59
1798 9093 2.117257 GGAGCGAAGTACTCCCTCC 58.883 63.158 16.15 16.15 46.81 4.30
1799 9094 1.726533 GGAGCGAAGTACTCCCTCCG 61.727 65.000 16.15 8.27 46.81 4.63
1800 9095 1.001145 AGCGAAGTACTCCCTCCGT 60.001 57.895 0.00 0.00 0.00 4.69
1801 9096 1.031029 AGCGAAGTACTCCCTCCGTC 61.031 60.000 0.00 0.00 0.00 4.79
1802 9097 2.002509 GCGAAGTACTCCCTCCGTCC 62.003 65.000 0.00 0.00 0.00 4.79
1803 9098 1.712977 CGAAGTACTCCCTCCGTCCG 61.713 65.000 0.00 0.00 0.00 4.79
1804 9099 1.379576 AAGTACTCCCTCCGTCCGG 60.380 63.158 0.00 0.00 0.00 5.14
1805 9100 1.856539 AAGTACTCCCTCCGTCCGGA 61.857 60.000 0.00 0.00 42.90 5.14
1806 9101 1.379044 GTACTCCCTCCGTCCGGAA 60.379 63.158 5.23 0.00 44.66 4.30
1807 9102 0.967380 GTACTCCCTCCGTCCGGAAA 60.967 60.000 5.23 0.00 44.66 3.13
1808 9103 0.032813 TACTCCCTCCGTCCGGAAAT 60.033 55.000 5.23 0.00 44.66 2.17
1809 9104 0.032813 ACTCCCTCCGTCCGGAAATA 60.033 55.000 5.23 0.00 44.66 1.40
1810 9105 0.388294 CTCCCTCCGTCCGGAAATAC 59.612 60.000 5.23 0.00 44.66 1.89
1811 9106 0.032813 TCCCTCCGTCCGGAAATACT 60.033 55.000 5.23 0.00 44.66 2.12
1812 9107 0.828677 CCCTCCGTCCGGAAATACTT 59.171 55.000 5.23 0.00 44.66 2.24
1813 9108 1.472728 CCCTCCGTCCGGAAATACTTG 60.473 57.143 5.23 0.00 44.66 3.16
1814 9109 1.206371 CCTCCGTCCGGAAATACTTGT 59.794 52.381 5.23 0.00 44.66 3.16
1815 9110 2.537401 CTCCGTCCGGAAATACTTGTC 58.463 52.381 5.23 0.00 44.66 3.18
1816 9111 1.894466 TCCGTCCGGAAATACTTGTCA 59.106 47.619 5.23 0.00 42.05 3.58
1817 9112 2.498481 TCCGTCCGGAAATACTTGTCAT 59.502 45.455 5.23 0.00 42.05 3.06
1818 9113 2.864343 CCGTCCGGAAATACTTGTCATC 59.136 50.000 5.23 0.00 37.50 2.92
1819 9114 3.517602 CGTCCGGAAATACTTGTCATCA 58.482 45.455 5.23 0.00 0.00 3.07
1820 9115 3.930229 CGTCCGGAAATACTTGTCATCAA 59.070 43.478 5.23 0.00 0.00 2.57
1821 9116 4.390603 CGTCCGGAAATACTTGTCATCAAA 59.609 41.667 5.23 0.00 32.87 2.69
1822 9117 5.106869 CGTCCGGAAATACTTGTCATCAAAA 60.107 40.000 5.23 0.00 32.87 2.44
1823 9118 6.403200 CGTCCGGAAATACTTGTCATCAAAAT 60.403 38.462 5.23 0.00 32.87 1.82
1824 9119 6.747280 GTCCGGAAATACTTGTCATCAAAATG 59.253 38.462 5.23 0.00 32.87 2.32
1825 9120 6.035843 CCGGAAATACTTGTCATCAAAATGG 58.964 40.000 0.00 0.00 33.42 3.16
1826 9121 6.127758 CCGGAAATACTTGTCATCAAAATGGA 60.128 38.462 0.00 0.00 33.42 3.41
1827 9122 7.416664 CCGGAAATACTTGTCATCAAAATGGAT 60.417 37.037 0.00 0.00 33.42 3.41
1828 9123 8.620416 CGGAAATACTTGTCATCAAAATGGATA 58.380 33.333 0.00 0.00 33.42 2.59
1835 9130 9.439500 ACTTGTCATCAAAATGGATAAAAATGG 57.561 29.630 0.00 0.00 33.42 3.16
1836 9131 9.656040 CTTGTCATCAAAATGGATAAAAATGGA 57.344 29.630 0.00 0.00 33.42 3.41
1882 9177 8.869109 ACTTGTCATCAAAATGGATAAAAAGGA 58.131 29.630 0.00 0.00 33.42 3.36
1883 9178 9.880157 CTTGTCATCAAAATGGATAAAAAGGAT 57.120 29.630 0.00 0.00 33.42 3.24
1884 9179 9.656040 TTGTCATCAAAATGGATAAAAAGGATG 57.344 29.630 0.00 0.00 33.42 3.51
1885 9180 8.814931 TGTCATCAAAATGGATAAAAAGGATGT 58.185 29.630 0.00 0.00 33.29 3.06
1953 9248 5.621197 TGATGACAAGTATTTTTGGACGG 57.379 39.130 0.00 0.00 32.32 4.79
1954 9249 5.309638 TGATGACAAGTATTTTTGGACGGA 58.690 37.500 0.00 0.00 32.32 4.69
1955 9250 5.411361 TGATGACAAGTATTTTTGGACGGAG 59.589 40.000 0.00 0.00 32.32 4.63
1956 9251 4.069304 TGACAAGTATTTTTGGACGGAGG 58.931 43.478 0.00 0.00 32.32 4.30
1957 9252 3.418047 ACAAGTATTTTTGGACGGAGGG 58.582 45.455 0.00 0.00 32.32 4.30
1958 9253 3.073356 ACAAGTATTTTTGGACGGAGGGA 59.927 43.478 0.00 0.00 32.32 4.20
1959 9254 3.629142 AGTATTTTTGGACGGAGGGAG 57.371 47.619 0.00 0.00 0.00 4.30
1960 9255 2.910977 AGTATTTTTGGACGGAGGGAGT 59.089 45.455 0.00 0.00 0.00 3.85
1961 9256 4.098894 AGTATTTTTGGACGGAGGGAGTA 58.901 43.478 0.00 0.00 0.00 2.59
1962 9257 4.720273 AGTATTTTTGGACGGAGGGAGTAT 59.280 41.667 0.00 0.00 0.00 2.12
1988 9283 7.655521 AGATTGACATTGGATCATTCATGTT 57.344 32.000 0.00 0.00 31.70 2.71
1989 9284 7.489160 AGATTGACATTGGATCATTCATGTTG 58.511 34.615 0.00 0.00 31.70 3.33
1990 9285 6.593268 TTGACATTGGATCATTCATGTTGT 57.407 33.333 0.00 0.00 0.00 3.32
2066 9372 8.415950 TTGCTATGGAATTTCTGGTTTTCTTA 57.584 30.769 0.00 0.00 0.00 2.10
2152 9458 3.609853 CATCAGTCGGAGGAAATTTGGA 58.390 45.455 0.00 0.00 0.00 3.53
2191 9497 8.855110 TCAAGCAGAGGAATAGTAATAGAAGAG 58.145 37.037 0.00 0.00 0.00 2.85
2230 9536 7.985752 ACTTAAAAGAATGGACTAATAGGGTCG 59.014 37.037 0.00 0.00 34.82 4.79
2300 9615 7.013083 GTCTCTACCTGTCCGATCTTACAATTA 59.987 40.741 0.00 0.00 0.00 1.40
2301 9616 7.558807 TCTCTACCTGTCCGATCTTACAATTAA 59.441 37.037 0.00 0.00 0.00 1.40
2302 9617 8.070034 TCTACCTGTCCGATCTTACAATTAAA 57.930 34.615 0.00 0.00 0.00 1.52
2303 9618 8.195436 TCTACCTGTCCGATCTTACAATTAAAG 58.805 37.037 0.00 0.00 0.00 1.85
2304 9619 6.708285 ACCTGTCCGATCTTACAATTAAAGT 58.292 36.000 0.00 0.00 0.00 2.66
2305 9620 7.166167 ACCTGTCCGATCTTACAATTAAAGTT 58.834 34.615 0.00 0.00 0.00 2.66
2306 9621 8.316214 ACCTGTCCGATCTTACAATTAAAGTTA 58.684 33.333 0.00 0.00 0.00 2.24
2307 9622 8.818057 CCTGTCCGATCTTACAATTAAAGTTAG 58.182 37.037 0.00 0.00 0.00 2.34
2308 9623 8.712285 TGTCCGATCTTACAATTAAAGTTAGG 57.288 34.615 0.00 3.08 0.00 2.69
2309 9624 8.533657 TGTCCGATCTTACAATTAAAGTTAGGA 58.466 33.333 7.79 7.79 30.00 2.94
2310 9625 9.543783 GTCCGATCTTACAATTAAAGTTAGGAT 57.456 33.333 12.05 0.00 33.13 3.24
2311 9626 9.760077 TCCGATCTTACAATTAAAGTTAGGATC 57.240 33.333 7.79 0.00 28.49 3.36
2312 9627 9.765795 CCGATCTTACAATTAAAGTTAGGATCT 57.234 33.333 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 57 7.622893 AAGAAGCTTCAGATTATCCTTTGTC 57.377 36.000 27.57 0.00 0.00 3.18
328 330 7.929941 AGAATGTCTTCTACCATTTTTCTCC 57.070 36.000 0.00 0.00 40.00 3.71
378 463 2.038557 ACAAGCTGAACTGGTACCGAAT 59.961 45.455 7.57 0.00 27.21 3.34
379 464 1.414919 ACAAGCTGAACTGGTACCGAA 59.585 47.619 7.57 0.00 27.21 4.30
380 465 1.045407 ACAAGCTGAACTGGTACCGA 58.955 50.000 7.57 0.00 27.21 4.69
381 466 1.148310 CACAAGCTGAACTGGTACCG 58.852 55.000 7.57 4.79 28.41 4.02
382 467 2.256117 ACACAAGCTGAACTGGTACC 57.744 50.000 4.43 4.43 28.41 3.34
425 510 4.570772 TGCTCATAAATTTACCAGCGTCTC 59.429 41.667 18.65 1.69 0.00 3.36
492 577 7.120285 TGGAAAAATTGTGACAAAAAGAATGCA 59.880 29.630 0.62 0.00 0.00 3.96
555 640 0.743688 ACGCCTTTGCAATGACACAA 59.256 45.000 13.58 0.00 37.32 3.33
889 974 1.452145 TTGGGCAGGAAGAACGTTGC 61.452 55.000 5.00 1.40 0.00 4.17
1153 3039 4.081972 TCTGTACAAACCAAGCAAAGCAAA 60.082 37.500 0.00 0.00 0.00 3.68
1197 3111 2.772287 AGGTGAAGTTCAGCAAGTAGC 58.228 47.619 30.80 7.84 46.52 3.58
1198 3112 4.130118 ACAAGGTGAAGTTCAGCAAGTAG 58.870 43.478 30.80 19.04 46.52 2.57
1199 3113 4.150897 ACAAGGTGAAGTTCAGCAAGTA 57.849 40.909 30.80 0.00 46.52 2.24
1200 3114 3.004752 ACAAGGTGAAGTTCAGCAAGT 57.995 42.857 30.80 25.03 46.52 3.16
1201 3115 4.999950 AGATACAAGGTGAAGTTCAGCAAG 59.000 41.667 30.80 24.49 46.52 4.01
1202 3116 4.973168 AGATACAAGGTGAAGTTCAGCAA 58.027 39.130 30.80 16.63 46.52 3.91
1203 3117 4.563580 GGAGATACAAGGTGAAGTTCAGCA 60.564 45.833 30.80 14.91 46.52 4.41
1204 3118 3.935828 GGAGATACAAGGTGAAGTTCAGC 59.064 47.826 24.29 24.29 44.62 4.26
1205 3119 5.186797 AGAGGAGATACAAGGTGAAGTTCAG 59.813 44.000 5.62 0.00 0.00 3.02
1206 3120 5.047021 CAGAGGAGATACAAGGTGAAGTTCA 60.047 44.000 0.08 0.08 0.00 3.18
1207 3121 5.186021 TCAGAGGAGATACAAGGTGAAGTTC 59.814 44.000 0.00 0.00 0.00 3.01
1208 3122 5.087323 TCAGAGGAGATACAAGGTGAAGTT 58.913 41.667 0.00 0.00 0.00 2.66
1300 3218 2.363406 GCATGCAGGGGGAAAGCT 60.363 61.111 14.21 0.00 0.00 3.74
1326 3246 5.670485 TCAGGTAATTCGCAGATGTAACAT 58.330 37.500 0.00 0.00 35.04 2.71
1327 3247 5.079689 TCAGGTAATTCGCAGATGTAACA 57.920 39.130 0.00 0.00 35.04 2.41
1335 3255 6.712549 CATATATGCATCAGGTAATTCGCAG 58.287 40.000 0.19 0.00 32.10 5.18
1562 3492 9.455847 CTCTCCTTTTTCTTAAATTCTGTTGTG 57.544 33.333 0.00 0.00 0.00 3.33
1682 8977 6.505344 TGGGAGAACCTGCAATCCTATATTAT 59.495 38.462 0.00 0.00 41.11 1.28
1683 8978 5.849475 TGGGAGAACCTGCAATCCTATATTA 59.151 40.000 0.00 0.00 41.11 0.98
1791 9086 0.388294 GTATTTCCGGACGGAGGGAG 59.612 60.000 13.64 0.00 46.06 4.30
1792 9087 0.032813 AGTATTTCCGGACGGAGGGA 60.033 55.000 13.64 4.95 46.06 4.20
1793 9088 0.828677 AAGTATTTCCGGACGGAGGG 59.171 55.000 13.64 0.00 46.06 4.30
1794 9089 1.206371 ACAAGTATTTCCGGACGGAGG 59.794 52.381 13.64 0.00 46.06 4.30
1795 9090 2.094390 TGACAAGTATTTCCGGACGGAG 60.094 50.000 13.64 3.15 46.06 4.63
1796 9091 1.894466 TGACAAGTATTTCCGGACGGA 59.106 47.619 1.83 9.76 43.52 4.69
1798 9093 3.517602 TGATGACAAGTATTTCCGGACG 58.482 45.455 1.83 0.00 0.00 4.79
1799 9094 5.873179 TTTGATGACAAGTATTTCCGGAC 57.127 39.130 1.83 0.00 37.32 4.79
1800 9095 6.127758 CCATTTTGATGACAAGTATTTCCGGA 60.128 38.462 0.00 0.00 37.32 5.14
1801 9096 6.035843 CCATTTTGATGACAAGTATTTCCGG 58.964 40.000 0.00 0.00 37.32 5.14
1802 9097 6.851609 TCCATTTTGATGACAAGTATTTCCG 58.148 36.000 0.00 0.00 37.32 4.30
1809 9104 9.439500 CCATTTTTATCCATTTTGATGACAAGT 57.561 29.630 0.00 0.00 37.32 3.16
1810 9105 9.656040 TCCATTTTTATCCATTTTGATGACAAG 57.344 29.630 0.00 0.00 37.32 3.16
1856 9151 8.869109 TCCTTTTTATCCATTTTGATGACAAGT 58.131 29.630 0.00 0.00 37.32 3.16
1857 9152 9.880157 ATCCTTTTTATCCATTTTGATGACAAG 57.120 29.630 0.00 0.00 37.32 3.16
1858 9153 9.656040 CATCCTTTTTATCCATTTTGATGACAA 57.344 29.630 0.00 0.00 31.12 3.18
1859 9154 8.814931 ACATCCTTTTTATCCATTTTGATGACA 58.185 29.630 0.00 0.00 33.22 3.58
1930 9225 5.765677 TCCGTCCAAAAATACTTGTCATCAA 59.234 36.000 0.00 0.00 0.00 2.57
1931 9226 5.309638 TCCGTCCAAAAATACTTGTCATCA 58.690 37.500 0.00 0.00 0.00 3.07
1932 9227 5.163754 CCTCCGTCCAAAAATACTTGTCATC 60.164 44.000 0.00 0.00 0.00 2.92
1933 9228 4.700213 CCTCCGTCCAAAAATACTTGTCAT 59.300 41.667 0.00 0.00 0.00 3.06
1934 9229 4.069304 CCTCCGTCCAAAAATACTTGTCA 58.931 43.478 0.00 0.00 0.00 3.58
1935 9230 3.439129 CCCTCCGTCCAAAAATACTTGTC 59.561 47.826 0.00 0.00 0.00 3.18
1936 9231 3.073356 TCCCTCCGTCCAAAAATACTTGT 59.927 43.478 0.00 0.00 0.00 3.16
1937 9232 3.681593 TCCCTCCGTCCAAAAATACTTG 58.318 45.455 0.00 0.00 0.00 3.16
1938 9233 3.329814 ACTCCCTCCGTCCAAAAATACTT 59.670 43.478 0.00 0.00 0.00 2.24
1939 9234 2.910977 ACTCCCTCCGTCCAAAAATACT 59.089 45.455 0.00 0.00 0.00 2.12
1940 9235 3.345508 ACTCCCTCCGTCCAAAAATAC 57.654 47.619 0.00 0.00 0.00 1.89
1941 9236 6.612456 TCTTATACTCCCTCCGTCCAAAAATA 59.388 38.462 0.00 0.00 0.00 1.40
1942 9237 5.427481 TCTTATACTCCCTCCGTCCAAAAAT 59.573 40.000 0.00 0.00 0.00 1.82
1943 9238 4.778958 TCTTATACTCCCTCCGTCCAAAAA 59.221 41.667 0.00 0.00 0.00 1.94
1944 9239 4.355549 TCTTATACTCCCTCCGTCCAAAA 58.644 43.478 0.00 0.00 0.00 2.44
1945 9240 3.985127 TCTTATACTCCCTCCGTCCAAA 58.015 45.455 0.00 0.00 0.00 3.28
1946 9241 3.675348 TCTTATACTCCCTCCGTCCAA 57.325 47.619 0.00 0.00 0.00 3.53
1947 9242 3.895656 CAATCTTATACTCCCTCCGTCCA 59.104 47.826 0.00 0.00 0.00 4.02
1948 9243 4.022155 GTCAATCTTATACTCCCTCCGTCC 60.022 50.000 0.00 0.00 0.00 4.79
1949 9244 4.583489 TGTCAATCTTATACTCCCTCCGTC 59.417 45.833 0.00 0.00 0.00 4.79
1950 9245 4.543689 TGTCAATCTTATACTCCCTCCGT 58.456 43.478 0.00 0.00 0.00 4.69
1951 9246 5.730296 ATGTCAATCTTATACTCCCTCCG 57.270 43.478 0.00 0.00 0.00 4.63
1952 9247 6.043243 TCCAATGTCAATCTTATACTCCCTCC 59.957 42.308 0.00 0.00 0.00 4.30
1953 9248 7.067496 TCCAATGTCAATCTTATACTCCCTC 57.933 40.000 0.00 0.00 0.00 4.30
1954 9249 7.293299 TGATCCAATGTCAATCTTATACTCCCT 59.707 37.037 0.00 0.00 0.00 4.20
1955 9250 7.453393 TGATCCAATGTCAATCTTATACTCCC 58.547 38.462 0.00 0.00 0.00 4.30
1956 9251 9.512588 AATGATCCAATGTCAATCTTATACTCC 57.487 33.333 0.00 0.00 0.00 3.85
1961 9256 9.363401 ACATGAATGATCCAATGTCAATCTTAT 57.637 29.630 0.00 0.00 0.00 1.73
1962 9257 8.756486 ACATGAATGATCCAATGTCAATCTTA 57.244 30.769 0.00 0.00 0.00 2.10
2042 9348 6.916360 AAGAAAACCAGAAATTCCATAGCA 57.084 33.333 0.00 0.00 0.00 3.49
2166 9472 8.637986 ACTCTTCTATTACTATTCCTCTGCTTG 58.362 37.037 0.00 0.00 0.00 4.01


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

AutoCloner maintained by Alex Coulton.