Multiple sequence alignment - TraesCS2B01G518800

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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 TraesCS2B01G518800 chr2B 100.000 2288 0 0 1 2288 713704745 713702458 0.000000e+00 4226.0
1 TraesCS2B01G518800 chr3A 91.566 1731 137 5 1 1727 418765663 418763938 0.000000e+00 2379.0
2 TraesCS2B01G518800 chr4A 91.302 1736 141 7 1 1732 327748377 327746648 0.000000e+00 2361.0
3 TraesCS2B01G518800 chr4D 91.244 1736 134 9 1 1730 116524560 116522837 0.000000e+00 2348.0
4 TraesCS2B01G518800 chr4D 91.071 1736 135 11 1 1728 493971112 493969389 0.000000e+00 2329.0
5 TraesCS2B01G518800 chr4D 90.793 1727 148 8 1 1723 421048639 421046920 0.000000e+00 2298.0
6 TraesCS2B01G518800 chr5A 90.746 1729 151 6 4 1729 604232060 604230338 0.000000e+00 2298.0
7 TraesCS2B01G518800 chr7D 90.542 1734 153 7 1 1730 432740546 432738820 0.000000e+00 2283.0
8 TraesCS2B01G518800 chr5B 90.504 1727 154 6 1 1723 410846055 410847775 0.000000e+00 2272.0
9 TraesCS2B01G518800 chr1A 90.265 1736 154 9 1 1728 31810747 31812475 0.000000e+00 2255.0
10 TraesCS2B01G518800 chr1A 94.444 36 2 0 2105 2140 15429108 15429073 3.180000e-04 56.5
11 TraesCS2B01G518800 chr2A 83.621 580 61 18 1727 2288 723835556 723834993 4.360000e-142 514.0
12 TraesCS2B01G518800 chr2D 84.038 213 26 2 1727 1931 50156923 50157135 4.990000e-47 198.0
13 TraesCS2B01G518800 chr2D 89.928 139 6 2 1778 1908 589512202 589512064 3.020000e-39 172.0


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 TraesCS2B01G518800 chr2B 713702458 713704745 2287 True 4226 4226 100.000 1 2288 1 chr2B.!!$R1 2287
1 TraesCS2B01G518800 chr3A 418763938 418765663 1725 True 2379 2379 91.566 1 1727 1 chr3A.!!$R1 1726
2 TraesCS2B01G518800 chr4A 327746648 327748377 1729 True 2361 2361 91.302 1 1732 1 chr4A.!!$R1 1731
3 TraesCS2B01G518800 chr4D 116522837 116524560 1723 True 2348 2348 91.244 1 1730 1 chr4D.!!$R1 1729
4 TraesCS2B01G518800 chr4D 493969389 493971112 1723 True 2329 2329 91.071 1 1728 1 chr4D.!!$R3 1727
5 TraesCS2B01G518800 chr4D 421046920 421048639 1719 True 2298 2298 90.793 1 1723 1 chr4D.!!$R2 1722
6 TraesCS2B01G518800 chr5A 604230338 604232060 1722 True 2298 2298 90.746 4 1729 1 chr5A.!!$R1 1725
7 TraesCS2B01G518800 chr7D 432738820 432740546 1726 True 2283 2283 90.542 1 1730 1 chr7D.!!$R1 1729
8 TraesCS2B01G518800 chr5B 410846055 410847775 1720 False 2272 2272 90.504 1 1723 1 chr5B.!!$F1 1722
9 TraesCS2B01G518800 chr1A 31810747 31812475 1728 False 2255 2255 90.265 1 1728 1 chr1A.!!$F1 1727
10 TraesCS2B01G518800 chr2A 723834993 723835556 563 True 514 514 83.621 1727 2288 1 chr2A.!!$R1 561

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
756 770 0.174389 TGCAGATCGAGGAGAGCAAC 59.826 55.0 0.0 0.0 37.82 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 1792 0.179108 GCTCCGGTACTTAGCACTGG 60.179 60.0 4.07 4.07 42.85 4.0 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
39 40 2.037641 GGCTGGCCTTCATTTTCTTGTT 59.962 45.455 3.32 0.00 0.00 2.83
42 43 4.301628 CTGGCCTTCATTTTCTTGTTCAC 58.698 43.478 3.32 0.00 0.00 3.18
50 51 0.745128 TTTCTTGTTCACCGCCGTGT 60.745 50.000 5.09 0.00 41.09 4.49
53 54 4.920112 TGTTCACCGCCGTGTGGG 62.920 66.667 5.09 0.00 41.09 4.61
54 55 4.922026 GTTCACCGCCGTGTGGGT 62.922 66.667 5.09 0.00 41.09 4.51
55 56 3.232483 TTCACCGCCGTGTGGGTA 61.232 61.111 5.09 0.00 41.09 3.69
63 64 4.446413 CGTGTGGGTAGGCGGGTC 62.446 72.222 0.00 0.00 0.00 4.46
64 65 3.315949 GTGTGGGTAGGCGGGTCA 61.316 66.667 0.00 0.00 0.00 4.02
99 100 1.002087 GGTGGAGTTGTGGTCGATCTT 59.998 52.381 0.00 0.00 0.00 2.40
112 113 0.731417 CGATCTTCCAGGTACGACGT 59.269 55.000 5.52 5.52 0.00 4.34
171 172 1.460497 CCTCCTCCTTAGGCTCCCC 60.460 68.421 0.00 0.00 43.31 4.81
172 173 1.314867 CTCCTCCTTAGGCTCCCCA 59.685 63.158 0.00 0.00 43.31 4.96
240 243 1.067582 GACGGTCATTAGGAGCCCG 59.932 63.158 2.62 0.00 40.99 6.13
247 250 2.961062 GTCATTAGGAGCCCGGTAGTTA 59.039 50.000 0.00 0.00 0.00 2.24
277 280 5.843019 TGGACCACTTCTTCCTCTATTTT 57.157 39.130 0.00 0.00 32.55 1.82
340 343 4.722700 ACTGCCATCGCGCCCTTT 62.723 61.111 0.00 0.00 38.08 3.11
375 378 6.016777 GGAATCAACATCTTCAACTCTTGTGT 60.017 38.462 0.00 0.00 0.00 3.72
388 391 2.766263 CTCTTGTGTAGTGGCCCTCATA 59.234 50.000 0.00 0.00 0.00 2.15
444 447 0.737715 GAGCCGAAGTTCGAGCACAT 60.738 55.000 28.36 15.68 43.74 3.21
474 477 0.179067 TTCTCGAACTTGGTGCGGTT 60.179 50.000 0.00 0.00 34.96 4.44
508 511 1.553690 CGAGGAAGAAGGCCCTCCAA 61.554 60.000 0.00 0.00 44.66 3.53
602 611 3.529734 TGATAGTGAGAGAAGAGAGGGGT 59.470 47.826 0.00 0.00 0.00 4.95
603 612 4.727332 TGATAGTGAGAGAAGAGAGGGGTA 59.273 45.833 0.00 0.00 0.00 3.69
673 687 1.002430 GGAAGAGTGACAGTCATGCCA 59.998 52.381 6.51 0.00 0.00 4.92
682 696 5.048504 AGTGACAGTCATGCCATTTTAACTG 60.049 40.000 6.51 5.61 39.90 3.16
708 722 5.012239 TGCTCTTCAATAAGCCATGAACTT 58.988 37.500 0.00 0.00 37.73 2.66
736 750 2.821969 GTGCCTGACTCCATGAATTGTT 59.178 45.455 0.00 0.00 0.00 2.83
756 770 0.174389 TGCAGATCGAGGAGAGCAAC 59.826 55.000 0.00 0.00 37.82 4.17
787 801 2.606519 AGGTGCTCCCAGCCGTTA 60.607 61.111 0.00 0.00 41.51 3.18
855 869 3.470888 CCCACCGCCGAGGAAGAT 61.471 66.667 3.89 0.00 45.00 2.40
991 1005 1.140052 TCCTTGCACCGAAACTTGAGA 59.860 47.619 0.00 0.00 0.00 3.27
996 1010 2.289382 TGCACCGAAACTTGAGAGCATA 60.289 45.455 0.00 0.00 0.00 3.14
1068 1082 1.966451 GCAGAGGAACAACACCGGG 60.966 63.158 6.32 0.00 0.00 5.73
1106 1120 2.017049 GGTGAAGCTAATGAACGGCAT 58.983 47.619 0.00 0.00 39.43 4.40
1182 1196 1.463444 GGCTACATGGTGACGTTCAAC 59.537 52.381 0.00 0.00 33.88 3.18
1196 1210 1.192146 TTCAACCTCCTCACTCCCGG 61.192 60.000 0.00 0.00 0.00 5.73
1412 1427 9.990360 TGAACTATGTTGTTAAGTAGTTGATGA 57.010 29.630 1.77 0.00 37.47 2.92
1417 1432 7.364522 TGTTGTTAAGTAGTTGATGATCTGC 57.635 36.000 0.00 0.00 0.00 4.26
1441 1457 3.109044 TCTCTGCTCTGCTTATGATGC 57.891 47.619 0.00 0.00 0.00 3.91
1445 1461 1.134729 TGCTCTGCTTATGATGCGTGA 60.135 47.619 0.00 0.00 0.00 4.35
1453 1469 3.425359 GCTTATGATGCGTGATACATGGC 60.425 47.826 0.00 0.00 0.00 4.40
1510 1526 3.283751 CAAAGAGGTTACCACACACCAA 58.716 45.455 3.51 0.00 35.25 3.67
1534 1551 3.444703 TTGCATACAACCAAACACCAC 57.555 42.857 0.00 0.00 0.00 4.16
1537 1554 1.606668 CATACAACCAAACACCACGCT 59.393 47.619 0.00 0.00 0.00 5.07
1596 1613 3.955145 CAGTGTGGTTCTGCCCATA 57.045 52.632 0.00 0.00 36.74 2.74
1621 1638 0.403271 AAGAGGGCATGCAGACAACT 59.597 50.000 21.36 6.98 0.00 3.16
1652 1669 2.646930 CAGATGGTGCATTTGAGGCTA 58.353 47.619 0.00 0.00 28.98 3.93
1744 1765 4.175337 TAGGGGCCGTGCTCATGC 62.175 66.667 9.43 0.00 40.20 4.06
1751 1772 3.896133 CGTGCTCATGCCCATGCC 61.896 66.667 3.41 0.00 38.65 4.40
1761 1782 3.866582 CCCATGCCCTCCGAGGAC 61.867 72.222 16.69 4.67 37.67 3.85
1765 1786 3.991924 ATGCCCTCCGAGGACTGCT 62.992 63.158 16.69 0.00 37.67 4.24
1766 1787 3.844090 GCCCTCCGAGGACTGCTC 61.844 72.222 16.69 0.00 37.67 4.26
1767 1788 2.043450 CCCTCCGAGGACTGCTCT 60.043 66.667 16.69 0.00 37.67 4.09
1823 1852 3.011818 GTCAATCACTCCATGTGCATGA 58.988 45.455 13.21 0.00 45.81 3.07
1834 1863 1.662517 TGTGCATGACAAGTGTTCGT 58.337 45.000 0.00 0.00 0.00 3.85
1835 1864 1.597195 TGTGCATGACAAGTGTTCGTC 59.403 47.619 0.00 0.00 0.00 4.20
1842 1871 2.033236 TGACAAGTGTTCGTCGAAATGC 60.033 45.455 9.70 3.11 34.78 3.56
1848 1877 2.902484 GTGTTCGTCGAAATGCATCAAC 59.098 45.455 9.70 0.00 0.00 3.18
1859 1893 6.073494 TCGAAATGCATCAACGAAAAGTAAGA 60.073 34.615 16.33 0.00 0.00 2.10
1909 1943 4.577283 GCTATGTCCGGCCAAAAATTAGTA 59.423 41.667 2.24 0.00 0.00 1.82
1910 1944 5.277828 GCTATGTCCGGCCAAAAATTAGTAG 60.278 44.000 2.24 0.00 0.00 2.57
1916 1950 6.372381 GTCCGGCCAAAAATTAGTAGAGTAAA 59.628 38.462 2.24 0.00 0.00 2.01
1943 1977 1.062587 CCATTAAGCTTTGCTCGGTCG 59.937 52.381 3.20 0.00 38.25 4.79
1948 1982 0.753262 AGCTTTGCTCGGTCGGATAT 59.247 50.000 0.00 0.00 30.62 1.63
1958 1992 4.082136 GCTCGGTCGGATATTCCTCTAAAT 60.082 45.833 0.00 0.00 33.30 1.40
1961 1995 6.917533 TCGGTCGGATATTCCTCTAAATTAC 58.082 40.000 0.00 0.00 33.30 1.89
1963 1997 7.014518 TCGGTCGGATATTCCTCTAAATTACAA 59.985 37.037 0.00 0.00 33.30 2.41
1964 1998 7.328737 CGGTCGGATATTCCTCTAAATTACAAG 59.671 40.741 0.00 0.00 33.30 3.16
1969 2003 9.674068 GGATATTCCTCTAAATTACAAGGGATC 57.326 37.037 0.00 0.00 32.53 3.36
1973 2007 5.427481 TCCTCTAAATTACAAGGGATCGGTT 59.573 40.000 0.00 0.00 0.00 4.44
1974 2008 6.612456 TCCTCTAAATTACAAGGGATCGGTTA 59.388 38.462 0.00 0.00 0.00 2.85
1975 2009 6.929606 CCTCTAAATTACAAGGGATCGGTTAG 59.070 42.308 0.00 0.00 0.00 2.34
1976 2010 7.418712 CCTCTAAATTACAAGGGATCGGTTAGT 60.419 40.741 0.00 0.00 0.00 2.24
2019 2053 3.915437 TTTTTGAGCGAGGACCAATTC 57.085 42.857 0.00 0.00 0.00 2.17
2022 2056 0.976641 TGAGCGAGGACCAATTCACT 59.023 50.000 0.00 0.00 0.00 3.41
2023 2057 2.176045 TGAGCGAGGACCAATTCACTA 58.824 47.619 0.00 0.00 0.00 2.74
2034 2068 7.458397 AGGACCAATTCACTATTGAGTTGTTA 58.542 34.615 14.46 0.00 44.22 2.41
2058 2092 0.167470 CAAACAGCACCAGCATCTCG 59.833 55.000 0.00 0.00 45.49 4.04
2072 2106 0.106469 ATCTCGTCCTCAGCAGCCTA 60.106 55.000 0.00 0.00 0.00 3.93
2073 2107 0.749818 TCTCGTCCTCAGCAGCCTAG 60.750 60.000 0.00 0.00 0.00 3.02
2088 2122 3.438434 CAGCCTAGGAGCAAAGAGTTTTC 59.562 47.826 14.75 0.00 34.23 2.29
2097 2131 4.580868 AGCAAAGAGTTTTCCCTAGCTAC 58.419 43.478 0.00 0.00 0.00 3.58
2100 2134 6.013639 AGCAAAGAGTTTTCCCTAGCTACTAA 60.014 38.462 0.00 0.00 0.00 2.24
2110 2144 5.890049 TCCCTAGCTACTAATACTCCCTTC 58.110 45.833 0.00 0.00 0.00 3.46
2144 2181 8.958119 ATATAAAAGCGTTTAGATCACCAAGA 57.042 30.769 10.55 0.00 32.76 3.02
2145 2182 5.358298 AAAAGCGTTTAGATCACCAAGAC 57.642 39.130 0.00 0.00 0.00 3.01
2146 2183 3.963428 AGCGTTTAGATCACCAAGACT 57.037 42.857 0.00 0.00 0.00 3.24
2147 2184 3.851098 AGCGTTTAGATCACCAAGACTC 58.149 45.455 0.00 0.00 0.00 3.36
2148 2185 2.930682 GCGTTTAGATCACCAAGACTCC 59.069 50.000 0.00 0.00 0.00 3.85
2169 2206 6.485830 TCCAAGAGGGAGTACTATCAAATG 57.514 41.667 0.00 0.00 42.15 2.32
2170 2207 5.366768 TCCAAGAGGGAGTACTATCAAATGG 59.633 44.000 0.00 1.60 42.15 3.16
2197 2234 4.059511 CTCAAAGCTGGAGAGATATGCAG 58.940 47.826 9.50 0.00 41.22 4.41
2200 2237 1.693062 AGCTGGAGAGATATGCAGTGG 59.307 52.381 0.00 0.00 40.47 4.00
2207 2244 5.302059 TGGAGAGATATGCAGTGGTACTAAC 59.698 44.000 0.00 0.00 0.00 2.34
2214 2251 7.657761 AGATATGCAGTGGTACTAACAATTAGC 59.342 37.037 0.00 0.00 36.71 3.09
2228 2265 0.758734 ATTAGCAGCAGCACCGGATA 59.241 50.000 9.46 0.00 45.49 2.59
2243 2280 2.033299 CCGGATATGCGCATGACTTTTT 59.967 45.455 32.48 7.17 0.00 1.94
2267 2305 1.474478 CTCACTCGCTATCACTGGTGT 59.526 52.381 0.53 0.00 0.00 4.16
2282 2320 1.065636 TGGTGTGGTTGGACGTAAACA 60.066 47.619 13.77 0.59 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 3.699894 CCAGCCACTCGACCTGCT 61.700 66.667 0.00 0.00 33.52 4.24
50 51 3.151710 CGATGACCCGCCTACCCA 61.152 66.667 0.00 0.00 0.00 4.51
53 54 0.318784 GATGACGATGACCCGCCTAC 60.319 60.000 0.00 0.00 0.00 3.18
54 55 1.792118 CGATGACGATGACCCGCCTA 61.792 60.000 0.00 0.00 42.66 3.93
55 56 2.815308 GATGACGATGACCCGCCT 59.185 61.111 0.00 0.00 0.00 5.52
61 62 0.317103 CCGAGGACGATGACGATGAC 60.317 60.000 0.00 0.00 42.66 3.06
62 63 0.746923 ACCGAGGACGATGACGATGA 60.747 55.000 0.00 0.00 42.66 2.92
63 64 0.592500 CACCGAGGACGATGACGATG 60.593 60.000 0.00 0.00 42.66 3.84
64 65 1.725557 CCACCGAGGACGATGACGAT 61.726 60.000 0.00 0.00 42.66 3.73
87 88 1.822990 GTACCTGGAAGATCGACCACA 59.177 52.381 0.00 0.00 34.07 4.17
89 90 1.100510 CGTACCTGGAAGATCGACCA 58.899 55.000 0.00 12.05 34.07 4.02
99 100 3.991999 CAGGACGTCGTACCTGGA 58.008 61.111 24.55 0.00 46.76 3.86
112 113 4.704103 AGAGTGCCGGAGCCAGGA 62.704 66.667 5.05 0.00 38.69 3.86
125 126 0.036577 GTGCAGATGCCAGTGAGAGT 60.037 55.000 1.72 0.00 41.18 3.24
127 128 1.297689 GGTGCAGATGCCAGTGAGA 59.702 57.895 1.72 0.00 41.18 3.27
240 243 6.046290 AGTGGTCCAAGTACAATAACTACC 57.954 41.667 0.00 0.00 0.00 3.18
247 250 4.351111 AGGAAGAAGTGGTCCAAGTACAAT 59.649 41.667 0.00 0.00 36.28 2.71
295 298 2.142356 TTCGTTGGGCCATGAATCAT 57.858 45.000 7.26 0.00 0.00 2.45
340 343 0.770499 TGTTGATTCCTGACCCAGCA 59.230 50.000 0.00 0.00 0.00 4.41
375 378 1.879575 AGTGCTTATGAGGGCCACTA 58.120 50.000 6.18 0.00 0.00 2.74
388 391 5.690464 AGAAGGAATCTGATGTAGTGCTT 57.310 39.130 0.00 0.00 36.88 3.91
444 447 2.248248 AGTTCGAGAACACCATGGAGA 58.752 47.619 21.47 3.00 43.47 3.71
474 477 1.452651 CTCGGGTAGTCGGCTGGTA 60.453 63.158 0.00 0.00 0.00 3.25
485 488 1.688187 GGGCCTTCTTCCTCGGGTA 60.688 63.158 0.84 0.00 0.00 3.69
508 511 1.007607 CCTTCCCTTGGGGTATTGGT 58.992 55.000 5.78 0.00 44.74 3.67
602 611 2.463752 CTGCCCACCACTACTTACCTA 58.536 52.381 0.00 0.00 0.00 3.08
603 612 1.276622 CTGCCCACCACTACTTACCT 58.723 55.000 0.00 0.00 0.00 3.08
673 687 7.490402 GCTTATTGAAGAGCATGCAGTTAAAAT 59.510 33.333 21.98 15.98 38.73 1.82
682 696 3.317149 TCATGGCTTATTGAAGAGCATGC 59.683 43.478 10.51 10.51 40.63 4.06
708 722 0.254462 TGGAGTCAGGCACAACACAA 59.746 50.000 0.00 0.00 0.00 3.33
736 750 0.897621 TTGCTCTCCTCGATCTGCAA 59.102 50.000 0.00 0.00 37.96 4.08
756 770 3.461773 ACCTCCGTGCCCATCTCG 61.462 66.667 0.00 0.00 0.00 4.04
780 794 0.466555 TGCCCTTGTTGTTAACGGCT 60.467 50.000 17.31 0.00 36.67 5.52
787 801 2.429927 GCTCCTTGCCCTTGTTGTT 58.570 52.632 0.00 0.00 35.15 2.83
855 869 3.154584 AACCGTTGGCGTCTTCGGA 62.155 57.895 24.51 0.00 44.86 4.55
908 922 1.651987 GCCATAGTTGTAGCGCTTGA 58.348 50.000 18.68 0.00 0.00 3.02
916 930 4.034410 TCATGGTAGTGGCCATAGTTGTA 58.966 43.478 9.72 0.00 46.71 2.41
996 1010 2.535317 AAGTCCAGGGGCATGGGT 60.535 61.111 7.99 0.00 41.01 4.51
1052 1066 1.450211 CACCCGGTGTTGTTCCTCT 59.550 57.895 9.64 0.00 0.00 3.69
1068 1082 2.665603 GTCACCCTCCAGGAGCAC 59.334 66.667 11.57 0.86 39.89 4.40
1106 1120 1.616327 CCCTGATCCTGGGTCACCA 60.616 63.158 5.31 0.00 46.94 4.17
1115 1129 0.988678 GGTAGCCCAACCCTGATCCT 60.989 60.000 0.00 0.00 33.02 3.24
1182 1196 3.775654 GTGCCGGGAGTGAGGAGG 61.776 72.222 2.18 0.00 0.00 4.30
1412 1427 2.967201 AGCAGAGCAGAGATAAGCAGAT 59.033 45.455 0.00 0.00 0.00 2.90
1417 1432 5.349270 GCATCATAAGCAGAGCAGAGATAAG 59.651 44.000 0.00 0.00 0.00 1.73
1453 1469 2.610694 CCAGCACACTTCGGCACAG 61.611 63.158 0.00 0.00 0.00 3.66
1534 1551 1.600023 TAGTGGACAAACCCAAAGCG 58.400 50.000 0.00 0.00 38.06 4.68
1537 1554 3.068873 GCATGTTAGTGGACAAACCCAAA 59.931 43.478 0.00 0.00 38.06 3.28
1596 1613 2.362120 GCATGCCCTCTTGCCTGT 60.362 61.111 6.36 0.00 37.39 4.00
1621 1638 3.641437 GCACCATCTGCAAGTTGTTTA 57.359 42.857 4.48 0.00 46.29 2.01
1652 1669 2.426024 CTCAGCTTGGCTATGCAAATGT 59.574 45.455 10.56 0.00 36.40 2.71
1744 1765 3.866582 GTCCTCGGAGGGCATGGG 61.867 72.222 23.39 0.00 40.51 4.00
1745 1766 2.765807 AGTCCTCGGAGGGCATGG 60.766 66.667 29.01 1.70 44.17 3.66
1746 1767 2.503061 CAGTCCTCGGAGGGCATG 59.497 66.667 29.01 19.47 44.17 4.06
1748 1769 4.704103 AGCAGTCCTCGGAGGGCA 62.704 66.667 29.01 6.37 44.17 5.36
1751 1772 1.662438 GACAGAGCAGTCCTCGGAGG 61.662 65.000 18.25 18.25 45.54 4.30
1767 1788 0.892755 CGGTACTTAGCACTGGGACA 59.107 55.000 0.00 0.00 0.00 4.02
1771 1792 0.179108 GCTCCGGTACTTAGCACTGG 60.179 60.000 4.07 4.07 42.85 4.00
1772 1793 0.530744 TGCTCCGGTACTTAGCACTG 59.469 55.000 10.52 0.00 38.50 3.66
1773 1794 1.409427 GATGCTCCGGTACTTAGCACT 59.591 52.381 16.21 6.79 44.23 4.40
1776 1797 0.666913 TCGATGCTCCGGTACTTAGC 59.333 55.000 0.00 2.63 34.89 3.09
1813 1834 2.031769 ACGAACACTTGTCATGCACATG 60.032 45.455 4.18 4.18 40.09 3.21
1823 1852 1.937223 TGCATTTCGACGAACACTTGT 59.063 42.857 10.38 0.00 0.00 3.16
1834 1863 4.481930 ACTTTTCGTTGATGCATTTCGA 57.518 36.364 14.44 14.44 0.00 3.71
1835 1864 6.077197 TCTTACTTTTCGTTGATGCATTTCG 58.923 36.000 0.00 6.71 0.00 3.46
1842 1871 9.210426 CGGAATAAATCTTACTTTTCGTTGATG 57.790 33.333 0.00 0.00 0.00 3.07
1859 1893 9.204570 CGATCCTCTAAATACAACGGAATAAAT 57.795 33.333 0.00 0.00 0.00 1.40
1916 1950 6.942576 ACCGAGCAAAGCTTAATGGAATATAT 59.057 34.615 0.00 0.00 39.88 0.86
1921 1955 2.747446 GACCGAGCAAAGCTTAATGGAA 59.253 45.455 0.00 0.00 39.88 3.53
1925 1959 1.066430 TCCGACCGAGCAAAGCTTAAT 60.066 47.619 0.00 0.00 39.88 1.40
1926 1960 0.319083 TCCGACCGAGCAAAGCTTAA 59.681 50.000 0.00 0.00 39.88 1.85
1943 1977 9.674068 GATCCCTTGTAATTTAGAGGAATATCC 57.326 37.037 7.15 0.00 36.58 2.59
1948 1982 5.427481 ACCGATCCCTTGTAATTTAGAGGAA 59.573 40.000 7.15 0.00 0.00 3.36
1958 1992 6.855763 TTTCTACTAACCGATCCCTTGTAA 57.144 37.500 0.00 0.00 0.00 2.41
1961 1995 4.511826 GCATTTCTACTAACCGATCCCTTG 59.488 45.833 0.00 0.00 0.00 3.61
1963 1997 3.071167 GGCATTTCTACTAACCGATCCCT 59.929 47.826 0.00 0.00 0.00 4.20
1964 1998 3.400255 GGCATTTCTACTAACCGATCCC 58.600 50.000 0.00 0.00 0.00 3.85
1969 2003 3.808174 GCTTAGGGCATTTCTACTAACCG 59.192 47.826 0.00 0.00 41.35 4.44
2003 2037 0.976641 AGTGAATTGGTCCTCGCTCA 59.023 50.000 0.00 0.00 0.00 4.26
2034 2068 2.758736 TGCTGGTGCTGTTTGTTTTT 57.241 40.000 0.00 0.00 40.48 1.94
2045 2079 1.520342 GAGGACGAGATGCTGGTGC 60.520 63.158 0.00 0.00 40.20 5.01
2047 2081 1.954362 GCTGAGGACGAGATGCTGGT 61.954 60.000 0.00 0.00 0.00 4.00
2058 2092 2.026945 GCTCCTAGGCTGCTGAGGAC 62.027 65.000 15.97 10.92 34.36 3.85
2072 2106 3.560239 GCTAGGGAAAACTCTTTGCTCCT 60.560 47.826 0.00 0.00 33.62 3.69
2073 2107 2.750166 GCTAGGGAAAACTCTTTGCTCC 59.250 50.000 0.00 0.00 33.62 4.70
2088 2122 5.642165 TGAAGGGAGTATTAGTAGCTAGGG 58.358 45.833 0.00 0.00 0.00 3.53
2125 2162 4.246458 GAGTCTTGGTGATCTAAACGCTT 58.754 43.478 0.00 0.00 0.00 4.68
2128 2165 4.188247 TGGAGTCTTGGTGATCTAAACG 57.812 45.455 0.00 0.00 0.00 3.60
2146 2183 5.366768 CCATTTGATAGTACTCCCTCTTGGA 59.633 44.000 0.00 0.00 42.41 3.53
2147 2184 5.366768 TCCATTTGATAGTACTCCCTCTTGG 59.633 44.000 0.00 2.06 0.00 3.61
2148 2185 6.485830 TCCATTTGATAGTACTCCCTCTTG 57.514 41.667 0.00 0.00 0.00 3.02
2161 2198 5.595542 CCAGCTTTGAGGATTCCATTTGATA 59.404 40.000 5.29 0.00 0.00 2.15
2169 2206 2.503356 TCTCTCCAGCTTTGAGGATTCC 59.497 50.000 9.56 0.00 32.53 3.01
2170 2207 3.902881 TCTCTCCAGCTTTGAGGATTC 57.097 47.619 9.56 0.00 32.53 2.52
2197 2234 4.201822 GCTGCTGCTAATTGTTAGTACCAC 60.202 45.833 8.53 0.00 35.66 4.16
2200 2237 4.201822 GGTGCTGCTGCTAATTGTTAGTAC 60.202 45.833 17.00 1.76 40.48 2.73
2207 2244 1.026182 TCCGGTGCTGCTGCTAATTG 61.026 55.000 17.00 2.25 40.48 2.32
2214 2251 2.601398 CGCATATCCGGTGCTGCTG 61.601 63.158 13.06 7.74 40.37 4.41
2243 2280 1.095600 AGTGATAGCGAGTGAGCGAA 58.904 50.000 0.00 0.00 43.00 4.70
2246 2283 0.457851 ACCAGTGATAGCGAGTGAGC 59.542 55.000 0.00 0.00 37.41 4.26
2267 2305 1.485480 TGAGGTGTTTACGTCCAACCA 59.515 47.619 10.97 0.00 40.16 3.67


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

AutoCloner maintained by Alex Coulton.