Multiple sequence alignment - TraesCS5D01G147000

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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 TraesCS5D01G147000 chr5D 100.000 2352 0 0 1 2352 233487956 233490307 0.000000e+00 4344.0
1 TraesCS5D01G147000 chr5B 88.854 1588 105 32 177 1741 271577412 271575874 0.000000e+00 1886.0
2 TraesCS5D01G147000 chr5B 88.448 277 31 1 2076 2352 271310889 271310614 1.350000e-87 333.0
3 TraesCS5D01G147000 chr5B 86.905 168 12 3 3 160 271577640 271577473 1.860000e-41 180.0
4 TraesCS5D01G147000 chr5A 95.545 651 26 3 914 1561 321713110 321713760 0.000000e+00 1038.0
5 TraesCS5D01G147000 chr5A 87.066 835 62 25 1 810 321712299 321713112 0.000000e+00 902.0
6 TraesCS5D01G147000 chr5A 89.646 367 31 5 1660 2025 321713796 321714156 5.920000e-126 460.0
7 TraesCS5D01G147000 chr5A 95.683 278 10 2 2076 2352 321715278 321715554 1.660000e-121 446.0
8 TraesCS5D01G147000 chr1D 81.871 855 114 24 935 1757 324623027 324622182 0.000000e+00 682.0
9 TraesCS5D01G147000 chr1B 82.538 733 104 17 935 1658 436930413 436929696 7.140000e-175 623.0
10 TraesCS5D01G147000 chr1A 83.158 665 93 14 936 1587 420382084 420382742 7.240000e-165 590.0
11 TraesCS5D01G147000 chr3D 76.374 182 32 9 1124 1302 323246251 323246424 1.160000e-13 87.9
12 TraesCS5D01G147000 chr2D 81.522 92 16 1 2082 2173 555951204 555951114 9.010000e-10 75.0
13 TraesCS5D01G147000 chr2A 82.500 80 13 1 2082 2161 695449907 695449829 4.190000e-08 69.4


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 TraesCS5D01G147000 chr5D 233487956 233490307 2351 False 4344.0 4344 100.0000 1 2352 1 chr5D.!!$F1 2351
1 TraesCS5D01G147000 chr5B 271575874 271577640 1766 True 1033.0 1886 87.8795 3 1741 2 chr5B.!!$R2 1738
2 TraesCS5D01G147000 chr5A 321712299 321715554 3255 False 711.5 1038 91.9850 1 2352 4 chr5A.!!$F1 2351
3 TraesCS5D01G147000 chr1D 324622182 324623027 845 True 682.0 682 81.8710 935 1757 1 chr1D.!!$R1 822
4 TraesCS5D01G147000 chr1B 436929696 436930413 717 True 623.0 623 82.5380 935 1658 1 chr1B.!!$R1 723
5 TraesCS5D01G147000 chr1A 420382084 420382742 658 False 590.0 590 83.1580 936 1587 1 chr1A.!!$F1 651

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
337 414 0.03601 CTTCAGCCGAACCCACATCT 60.036 55.0 0.0 0.0 0.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2320 3572 0.107703 ACCAGCCATGTGTATGACGG 60.108 55.0 0.0 0.0 36.36 4.79 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
32 33 2.973945 AGTGGAAAATGACGGCTAGAC 58.026 47.619 0.00 0.00 0.00 2.59
52 60 3.838271 TGGAGGTGAGCGGCGATC 61.838 66.667 19.57 19.57 0.00 3.69
115 123 4.700692 GGGATGGTGAAGACCTAGTTTTTC 59.299 45.833 0.00 0.00 43.58 2.29
126 137 2.506231 CCTAGTTTTTCCCCCTCTCTCC 59.494 54.545 0.00 0.00 0.00 3.71
143 154 4.479056 TCTCTCCAGACCATAAGACCTAGT 59.521 45.833 0.00 0.00 0.00 2.57
200 260 5.046529 GCAATATCGATCTCACAGTTGACT 58.953 41.667 0.00 0.00 0.00 3.41
215 275 3.149196 GTTGACTCCAATCTTTCTGGCA 58.851 45.455 0.00 0.00 34.39 4.92
223 283 5.128205 TCCAATCTTTCTGGCACATCATAG 58.872 41.667 0.00 0.00 38.20 2.23
256 316 2.174639 TGCCCTCCGATTTCCATGTATT 59.825 45.455 0.00 0.00 0.00 1.89
260 320 4.127171 CCTCCGATTTCCATGTATTTCGT 58.873 43.478 0.00 0.00 0.00 3.85
261 321 4.024893 CCTCCGATTTCCATGTATTTCGTG 60.025 45.833 0.00 0.00 0.00 4.35
269 329 7.712797 ATTTCCATGTATTTCGTGGTAATTCC 58.287 34.615 6.08 0.00 44.88 3.01
270 330 5.432885 CCATGTATTTCGTGGTAATTCCC 57.567 43.478 0.00 0.00 45.46 3.97
271 331 4.884744 CCATGTATTTCGTGGTAATTCCCA 59.115 41.667 0.00 0.00 45.46 4.37
272 332 5.534654 CCATGTATTTCGTGGTAATTCCCAT 59.465 40.000 0.00 0.00 45.46 4.00
273 333 6.437928 CATGTATTTCGTGGTAATTCCCATG 58.562 40.000 2.88 2.88 41.96 3.66
274 334 4.884744 TGTATTTCGTGGTAATTCCCATGG 59.115 41.667 4.14 4.14 41.12 3.66
275 335 3.722908 TTTCGTGGTAATTCCCATGGA 57.277 42.857 15.22 0.00 41.12 3.41
276 336 3.943671 TTCGTGGTAATTCCCATGGAT 57.056 42.857 15.22 0.00 41.12 3.41
277 337 5.375283 TTTCGTGGTAATTCCCATGGATA 57.625 39.130 15.22 0.00 41.12 2.59
278 338 4.617253 TCGTGGTAATTCCCATGGATAG 57.383 45.455 15.22 0.00 41.12 2.08
279 339 3.971305 TCGTGGTAATTCCCATGGATAGT 59.029 43.478 15.22 1.98 41.12 2.12
280 340 4.065088 CGTGGTAATTCCCATGGATAGTG 58.935 47.826 15.22 0.00 37.77 2.74
281 341 3.821033 GTGGTAATTCCCATGGATAGTGC 59.179 47.826 15.22 3.14 36.74 4.40
282 342 3.181434 TGGTAATTCCCATGGATAGTGCC 60.181 47.826 15.22 12.95 34.77 5.01
283 343 3.181434 GGTAATTCCCATGGATAGTGCCA 60.181 47.826 15.22 0.00 43.23 4.92
337 414 0.036010 CTTCAGCCGAACCCACATCT 60.036 55.000 0.00 0.00 0.00 2.90
341 418 0.981183 AGCCGAACCCACATCTACAA 59.019 50.000 0.00 0.00 0.00 2.41
345 422 1.338674 CGAACCCACATCTACAAGCCA 60.339 52.381 0.00 0.00 0.00 4.75
349 426 1.645034 CCACATCTACAAGCCACTCG 58.355 55.000 0.00 0.00 0.00 4.18
390 467 4.329545 GAGCTGGCACCACGGGAA 62.330 66.667 0.00 0.00 0.00 3.97
466 543 2.360165 GCAGGCATTTCAGATGTTAGGG 59.640 50.000 0.00 0.00 0.00 3.53
470 547 4.475016 AGGCATTTCAGATGTTAGGGTACT 59.525 41.667 0.00 0.00 0.00 2.73
471 548 4.576463 GGCATTTCAGATGTTAGGGTACTG 59.424 45.833 0.00 0.00 0.00 2.74
472 549 5.186198 GCATTTCAGATGTTAGGGTACTGT 58.814 41.667 0.00 0.00 0.00 3.55
501 578 2.009042 GCTGCTAAGGTACCAGCTGTG 61.009 57.143 23.45 15.44 46.28 3.66
632 709 8.020819 TCGATTGATGACAACTTATTTTGTTCC 58.979 33.333 0.00 0.00 39.88 3.62
661 740 7.838498 AGTTTTTATTAGAATCGGATCGAACG 58.162 34.615 6.55 6.55 39.99 3.95
663 742 2.129823 TTAGAATCGGATCGAACGCC 57.870 50.000 7.87 0.58 39.99 5.68
695 774 4.116747 TGCAAACAAACCTTGTAGTTGG 57.883 40.909 6.24 0.00 44.59 3.77
715 794 0.831288 CATGCCCAAGGACAAACCCA 60.831 55.000 0.00 0.00 40.05 4.51
766 846 5.186603 AGCTCTTGACAATGTACTCTCATCA 59.813 40.000 0.00 0.00 0.00 3.07
770 850 5.003692 TGACAATGTACTCTCATCAGCTC 57.996 43.478 0.00 0.00 0.00 4.09
783 863 3.507233 TCATCAGCTCCAATGTGTTTTCC 59.493 43.478 0.00 0.00 0.00 3.13
791 871 2.988493 CCAATGTGTTTTCCTTGCATCG 59.012 45.455 0.00 0.00 0.00 3.84
793 873 1.028130 TGTGTTTTCCTTGCATCGCA 58.972 45.000 0.00 0.00 36.47 5.10
795 875 0.313672 TGTTTTCCTTGCATCGCACC 59.686 50.000 0.00 0.00 38.71 5.01
837 917 6.872920 AGTCAATTCTGAGGATTCACTCTAC 58.127 40.000 0.00 0.00 38.32 2.59
841 921 3.698289 TCTGAGGATTCACTCTACCGTT 58.302 45.455 0.00 0.00 38.32 4.44
850 930 4.106029 TCACTCTACCGTTGTGAATAGC 57.894 45.455 0.00 0.00 37.71 2.97
853 933 4.091509 CACTCTACCGTTGTGAATAGCAAC 59.908 45.833 0.00 0.00 41.81 4.17
860 940 3.743911 CGTTGTGAATAGCAACTGTACCA 59.256 43.478 6.61 0.00 42.73 3.25
872 952 1.633774 CTGTACCAGGACAGGTCACT 58.366 55.000 1.76 0.00 42.68 3.41
873 953 2.803956 CTGTACCAGGACAGGTCACTA 58.196 52.381 1.76 0.00 42.68 2.74
874 954 2.492484 CTGTACCAGGACAGGTCACTAC 59.508 54.545 1.76 0.00 42.68 2.73
881 961 3.960755 CAGGACAGGTCACTACATGGATA 59.039 47.826 0.00 0.00 41.69 2.59
883 963 3.961408 GGACAGGTCACTACATGGATAGT 59.039 47.826 0.00 0.00 41.69 2.12
899 979 5.758924 TGGATAGTTTCGTATGTCTCATCG 58.241 41.667 0.00 0.00 0.00 3.84
913 993 1.339291 CTCATCGGCATGCTACTCTGA 59.661 52.381 18.92 12.17 0.00 3.27
996 1076 5.299148 TGAATCAAGGCAAGGATTTTTGTG 58.701 37.500 0.00 0.00 34.06 3.33
1043 1123 0.532640 CAAAGGTTGCCCCAGTTTGC 60.533 55.000 0.00 0.00 34.66 3.68
1121 1206 2.371841 TCCCAGATTATCGTGGAATGGG 59.628 50.000 8.22 8.22 46.01 4.00
1228 1314 3.620488 TCCAATAGGAATTGTGGAGCAC 58.380 45.455 0.00 0.00 42.23 4.40
1334 1420 4.287067 AGAGAAATCTTGCCACTGGTTCTA 59.713 41.667 0.00 0.00 0.00 2.10
1406 1508 6.043327 CACTGAAAATGAAAGTGTGTCGTA 57.957 37.500 0.00 0.00 37.20 3.43
1414 1516 3.062909 TGAAAGTGTGTCGTAGTTGCAAC 59.937 43.478 22.17 22.17 0.00 4.17
1476 1578 2.496871 GACCCATGCAATTGATGGTGAA 59.503 45.455 23.69 0.00 39.08 3.18
1576 1685 5.544176 TCTCAGTAATATCCCCTCAATCCAC 59.456 44.000 0.00 0.00 0.00 4.02
1592 1701 1.542472 TCCACATGTGATTTGCAGCAG 59.458 47.619 27.46 6.26 0.00 4.24
1602 1711 3.069872 TGATTTGCAGCAGTTTGTGGATT 59.930 39.130 0.00 0.00 0.00 3.01
1603 1712 2.798976 TTGCAGCAGTTTGTGGATTC 57.201 45.000 0.00 0.00 0.00 2.52
1604 1713 0.592637 TGCAGCAGTTTGTGGATTCG 59.407 50.000 0.00 0.00 0.00 3.34
1609 1718 2.485426 AGCAGTTTGTGGATTCGATGTG 59.515 45.455 0.00 0.00 0.00 3.21
1767 1896 0.955428 TCTTGCCACTCGGATGTTGC 60.955 55.000 0.00 0.00 0.00 4.17
1771 1900 0.391130 GCCACTCGGATGTTGCAGTA 60.391 55.000 0.00 0.00 0.00 2.74
1772 1901 1.943968 GCCACTCGGATGTTGCAGTAA 60.944 52.381 0.00 0.00 0.00 2.24
1776 1905 3.935203 CACTCGGATGTTGCAGTAAGAAT 59.065 43.478 0.00 0.00 0.00 2.40
1783 1912 5.523188 GGATGTTGCAGTAAGAATCAGAGAG 59.477 44.000 0.00 0.00 0.00 3.20
1785 1914 5.233225 TGTTGCAGTAAGAATCAGAGAGTG 58.767 41.667 0.00 0.00 0.00 3.51
1800 1929 7.606858 TCAGAGAGTGATTGATTGATTTCAC 57.393 36.000 0.00 0.00 38.97 3.18
1801 1930 6.312180 TCAGAGAGTGATTGATTGATTTCACG 59.688 38.462 0.00 0.00 42.51 4.35
1802 1931 5.583854 AGAGAGTGATTGATTGATTTCACGG 59.416 40.000 0.00 0.00 42.51 4.94
1819 1948 4.637771 GGTGTGCTTTCGCCCTAT 57.362 55.556 0.00 0.00 34.43 2.57
1839 1968 6.546034 CCCTATGGTATTTTCCATTTCGTTCT 59.454 38.462 3.55 0.00 44.75 3.01
1871 2000 1.299468 GACTATGCCCGAGTCAGCG 60.299 63.158 5.20 0.00 42.47 5.18
1879 2008 0.386100 CCCGAGTCAGCGTATCATCG 60.386 60.000 0.00 0.00 0.00 3.84
1884 2013 2.976509 GAGTCAGCGTATCATCGTCATG 59.023 50.000 0.00 0.00 0.00 3.07
1934 2063 5.609423 AGCAGCCATTACAAAATTCAAACA 58.391 33.333 0.00 0.00 0.00 2.83
1966 2095 2.819608 TGGGAGTGCATAGTTCAAAAGC 59.180 45.455 0.00 0.00 0.00 3.51
2004 2134 6.492007 GTGGATCCACATATGCTTCATAAG 57.508 41.667 35.21 0.00 45.53 1.73
2005 2135 6.233434 GTGGATCCACATATGCTTCATAAGA 58.767 40.000 35.21 0.00 45.53 2.10
2006 2136 6.148480 GTGGATCCACATATGCTTCATAAGAC 59.852 42.308 35.21 5.34 45.53 3.01
2007 2137 5.645497 GGATCCACATATGCTTCATAAGACC 59.355 44.000 6.95 0.00 29.74 3.85
2008 2138 5.628797 TCCACATATGCTTCATAAGACCA 57.371 39.130 1.58 0.00 29.74 4.02
2009 2139 6.000246 TCCACATATGCTTCATAAGACCAA 58.000 37.500 1.58 0.00 29.74 3.67
2010 2140 6.604171 TCCACATATGCTTCATAAGACCAAT 58.396 36.000 1.58 0.00 29.74 3.16
2011 2141 6.487668 TCCACATATGCTTCATAAGACCAATG 59.512 38.462 1.58 0.00 29.74 2.82
2012 2142 6.487668 CCACATATGCTTCATAAGACCAATGA 59.512 38.462 1.58 0.00 29.74 2.57
2013 2143 7.308408 CCACATATGCTTCATAAGACCAATGAG 60.308 40.741 1.58 0.00 34.93 2.90
2014 2144 7.228108 CACATATGCTTCATAAGACCAATGAGT 59.772 37.037 1.58 0.00 34.93 3.41
2015 2145 8.432013 ACATATGCTTCATAAGACCAATGAGTA 58.568 33.333 1.58 0.00 34.93 2.59
2016 2146 8.933807 CATATGCTTCATAAGACCAATGAGTAG 58.066 37.037 0.00 0.00 34.93 2.57
2017 2147 6.299805 TGCTTCATAAGACCAATGAGTAGT 57.700 37.500 0.00 0.00 34.93 2.73
2018 2148 6.711277 TGCTTCATAAGACCAATGAGTAGTT 58.289 36.000 0.00 0.00 34.93 2.24
2019 2149 6.595326 TGCTTCATAAGACCAATGAGTAGTTG 59.405 38.462 0.00 0.00 34.93 3.16
2020 2150 6.457528 GCTTCATAAGACCAATGAGTAGTTGC 60.458 42.308 0.00 0.00 34.93 4.17
2021 2151 6.048732 TCATAAGACCAATGAGTAGTTGCA 57.951 37.500 0.00 0.00 0.00 4.08
2022 2152 5.874810 TCATAAGACCAATGAGTAGTTGCAC 59.125 40.000 0.00 0.00 0.00 4.57
2023 2153 2.688507 AGACCAATGAGTAGTTGCACG 58.311 47.619 0.00 0.00 0.00 5.34
2024 2154 2.037251 AGACCAATGAGTAGTTGCACGT 59.963 45.455 0.00 0.00 0.00 4.49
2025 2155 2.806244 GACCAATGAGTAGTTGCACGTT 59.194 45.455 0.00 0.00 0.00 3.99
2026 2156 3.211045 ACCAATGAGTAGTTGCACGTTT 58.789 40.909 0.00 0.00 0.00 3.60
2027 2157 4.382291 ACCAATGAGTAGTTGCACGTTTA 58.618 39.130 0.00 0.00 0.00 2.01
2028 2158 4.817464 ACCAATGAGTAGTTGCACGTTTAA 59.183 37.500 0.00 0.00 0.00 1.52
2029 2159 5.049680 ACCAATGAGTAGTTGCACGTTTAAG 60.050 40.000 0.00 0.00 0.00 1.85
2030 2160 5.178623 CCAATGAGTAGTTGCACGTTTAAGA 59.821 40.000 0.00 0.00 0.00 2.10
2031 2161 5.840940 ATGAGTAGTTGCACGTTTAAGAC 57.159 39.130 0.00 0.00 0.00 3.01
2032 2162 4.053295 TGAGTAGTTGCACGTTTAAGACC 58.947 43.478 0.00 0.00 0.00 3.85
2033 2163 4.053295 GAGTAGTTGCACGTTTAAGACCA 58.947 43.478 0.00 0.00 0.00 4.02
2034 2164 4.444536 AGTAGTTGCACGTTTAAGACCAA 58.555 39.130 0.00 0.00 0.00 3.67
2035 2165 5.061179 AGTAGTTGCACGTTTAAGACCAAT 58.939 37.500 0.00 0.00 0.00 3.16
2036 2166 4.223320 AGTTGCACGTTTAAGACCAATG 57.777 40.909 0.00 0.00 0.00 2.82
2037 2167 3.880490 AGTTGCACGTTTAAGACCAATGA 59.120 39.130 0.00 0.00 0.00 2.57
2038 2168 4.024048 AGTTGCACGTTTAAGACCAATGAG 60.024 41.667 0.00 0.00 0.00 2.90
2039 2169 3.472652 TGCACGTTTAAGACCAATGAGT 58.527 40.909 0.00 0.00 0.00 3.41
2040 2170 4.633175 TGCACGTTTAAGACCAATGAGTA 58.367 39.130 0.00 0.00 0.00 2.59
2041 2171 4.688879 TGCACGTTTAAGACCAATGAGTAG 59.311 41.667 0.00 0.00 0.00 2.57
2042 2172 4.689345 GCACGTTTAAGACCAATGAGTAGT 59.311 41.667 0.00 0.00 0.00 2.73
2043 2173 5.178809 GCACGTTTAAGACCAATGAGTAGTT 59.821 40.000 0.00 0.00 0.00 2.24
2044 2174 6.590357 CACGTTTAAGACCAATGAGTAGTTG 58.410 40.000 0.00 0.00 0.00 3.16
2045 2175 5.178809 ACGTTTAAGACCAATGAGTAGTTGC 59.821 40.000 0.00 0.00 0.00 4.17
2046 2176 5.178623 CGTTTAAGACCAATGAGTAGTTGCA 59.821 40.000 0.00 0.00 0.00 4.08
2047 2177 6.371389 GTTTAAGACCAATGAGTAGTTGCAC 58.629 40.000 0.00 0.00 0.00 4.57
2048 2178 2.688507 AGACCAATGAGTAGTTGCACG 58.311 47.619 0.00 0.00 0.00 5.34
2049 2179 2.037251 AGACCAATGAGTAGTTGCACGT 59.963 45.455 0.00 0.00 0.00 4.49
2050 2180 2.806244 GACCAATGAGTAGTTGCACGTT 59.194 45.455 0.00 0.00 0.00 3.99
2111 3362 0.249398 ACAACTATCCTGCCCGACAC 59.751 55.000 0.00 0.00 0.00 3.67
2175 3427 5.450137 CCATTTCTTCAAGGATGCTCATCAC 60.450 44.000 11.49 2.17 39.54 3.06
2229 3481 8.365399 TCGATGTACAGATCCAATAAATCAAC 57.635 34.615 0.33 0.00 0.00 3.18
2239 3491 6.737254 TCCAATAAATCAACGAACTCCTTC 57.263 37.500 0.00 0.00 0.00 3.46
2257 3509 0.690192 TCGGGGAAGCAAACTCATCA 59.310 50.000 0.00 0.00 0.00 3.07
2275 3527 0.250038 CATCCGGTGAATCCATCGCT 60.250 55.000 0.00 0.00 45.06 4.93
2311 3563 9.905171 ATGAGAAAAAGAATCTAAAAACAGCTC 57.095 29.630 0.00 0.00 0.00 4.09
2336 3588 2.779755 TTTCCGTCATACACATGGCT 57.220 45.000 0.00 0.00 34.43 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 95 3.833559 AGGTCTTCACCATCCCAAATT 57.166 42.857 0.00 0.00 46.68 1.82
115 123 0.563173 TATGGTCTGGAGAGAGGGGG 59.437 60.000 0.00 0.00 0.00 5.40
126 137 3.865745 CGCAAACTAGGTCTTATGGTCTG 59.134 47.826 0.00 0.00 0.00 3.51
162 201 4.450419 CGATATTGCAGAAGAGGTTCCATC 59.550 45.833 0.00 0.00 32.48 3.51
200 260 3.438216 TGATGTGCCAGAAAGATTGGA 57.562 42.857 0.00 0.00 37.96 3.53
215 275 3.813240 GCATTCCTGCCATCCTATGATGT 60.813 47.826 7.16 0.00 45.78 3.06
256 316 3.943671 ATCCATGGGAATTACCACGAA 57.056 42.857 12.95 0.00 44.72 3.85
260 320 3.181434 GGCACTATCCATGGGAATTACCA 60.181 47.826 13.08 13.08 46.24 3.25
261 321 3.181434 TGGCACTATCCATGGGAATTACC 60.181 47.826 13.02 0.00 34.34 2.85
263 323 3.181434 GGTGGCACTATCCATGGGAATTA 60.181 47.826 18.45 0.00 38.57 1.40
271 331 1.422781 CTCCATGGTGGCACTATCCAT 59.577 52.381 18.45 9.61 41.88 3.41
272 332 0.839277 CTCCATGGTGGCACTATCCA 59.161 55.000 18.45 7.36 37.47 3.41
273 333 0.839946 ACTCCATGGTGGCACTATCC 59.160 55.000 18.45 0.54 37.47 2.59
274 334 2.700897 ACTACTCCATGGTGGCACTATC 59.299 50.000 18.45 1.07 37.47 2.08
275 335 2.764269 ACTACTCCATGGTGGCACTAT 58.236 47.619 18.45 14.77 37.47 2.12
276 336 2.247699 ACTACTCCATGGTGGCACTA 57.752 50.000 18.45 12.70 37.47 2.74
277 337 1.362224 AACTACTCCATGGTGGCACT 58.638 50.000 18.45 0.00 37.47 4.40
278 338 2.200373 AAACTACTCCATGGTGGCAC 57.800 50.000 17.76 9.70 37.47 5.01
279 339 5.904984 ATATAAACTACTCCATGGTGGCA 57.095 39.130 17.76 4.71 37.47 4.92
280 340 8.685838 TTAAATATAAACTACTCCATGGTGGC 57.314 34.615 17.76 0.00 37.47 5.01
337 414 0.613260 AATGGCTCGAGTGGCTTGTA 59.387 50.000 15.13 0.00 0.00 2.41
341 418 1.965754 GAGGAATGGCTCGAGTGGCT 61.966 60.000 15.13 0.00 0.00 4.75
345 422 1.134280 CAATGGAGGAATGGCTCGAGT 60.134 52.381 15.13 0.00 0.00 4.18
349 426 2.726821 TGAACAATGGAGGAATGGCTC 58.273 47.619 0.00 0.00 0.00 4.70
412 489 3.898517 GATGCATCCACATCTGACATG 57.101 47.619 16.23 0.00 42.63 3.21
466 543 1.079503 GCAGCCTAGCACAACAGTAC 58.920 55.000 0.00 0.00 0.00 2.73
470 547 1.339055 CCTTAGCAGCCTAGCACAACA 60.339 52.381 0.00 0.00 36.85 3.33
471 548 1.339151 ACCTTAGCAGCCTAGCACAAC 60.339 52.381 0.00 0.00 36.85 3.32
472 549 0.984230 ACCTTAGCAGCCTAGCACAA 59.016 50.000 0.00 0.00 36.85 3.33
641 720 4.022589 AGGCGTTCGATCCGATTCTAATAA 60.023 41.667 8.96 0.00 35.23 1.40
643 722 2.296471 AGGCGTTCGATCCGATTCTAAT 59.704 45.455 8.96 0.00 35.23 1.73
695 774 1.293179 GGTTTGTCCTTGGGCATGC 59.707 57.895 9.90 9.90 0.00 4.06
737 817 7.123397 TGAGAGTACATTGTCAAGAGCTAGATT 59.877 37.037 0.00 0.00 0.00 2.40
738 818 6.605194 TGAGAGTACATTGTCAAGAGCTAGAT 59.395 38.462 0.00 0.00 0.00 1.98
740 820 6.201226 TGAGAGTACATTGTCAAGAGCTAG 57.799 41.667 0.00 0.00 0.00 3.42
741 821 6.378280 TGATGAGAGTACATTGTCAAGAGCTA 59.622 38.462 0.00 0.00 0.00 3.32
742 822 5.186603 TGATGAGAGTACATTGTCAAGAGCT 59.813 40.000 0.00 0.00 0.00 4.09
744 824 5.519566 GCTGATGAGAGTACATTGTCAAGAG 59.480 44.000 0.00 0.00 0.00 2.85
745 825 5.186603 AGCTGATGAGAGTACATTGTCAAGA 59.813 40.000 0.00 0.00 0.00 3.02
747 827 5.411831 AGCTGATGAGAGTACATTGTCAA 57.588 39.130 0.00 0.00 0.00 3.18
748 828 4.142071 GGAGCTGATGAGAGTACATTGTCA 60.142 45.833 0.00 0.00 0.00 3.58
749 829 4.142071 TGGAGCTGATGAGAGTACATTGTC 60.142 45.833 0.00 0.00 0.00 3.18
750 830 3.771479 TGGAGCTGATGAGAGTACATTGT 59.229 43.478 0.00 0.00 0.00 2.71
751 831 4.397481 TGGAGCTGATGAGAGTACATTG 57.603 45.455 0.00 0.00 0.00 2.82
752 832 5.104610 ACATTGGAGCTGATGAGAGTACATT 60.105 40.000 0.00 0.00 0.00 2.71
753 833 4.408270 ACATTGGAGCTGATGAGAGTACAT 59.592 41.667 0.00 0.00 0.00 2.29
766 846 2.036346 GCAAGGAAAACACATTGGAGCT 59.964 45.455 0.00 0.00 33.13 4.09
770 850 2.988493 CGATGCAAGGAAAACACATTGG 59.012 45.455 0.00 0.00 33.13 3.16
791 871 5.472478 ACTTAAACTAGTTTTAGCCTGGTGC 59.528 40.000 26.41 0.00 33.83 5.01
793 873 6.834107 TGACTTAAACTAGTTTTAGCCTGGT 58.166 36.000 26.41 13.00 33.83 4.00
795 875 9.827411 GAATTGACTTAAACTAGTTTTAGCCTG 57.173 33.333 26.41 10.71 33.83 4.85
860 940 2.623418 TCCATGTAGTGACCTGTCCT 57.377 50.000 0.00 0.00 0.00 3.85
872 952 7.576861 TGAGACATACGAAACTATCCATGTA 57.423 36.000 0.00 0.00 32.91 2.29
873 953 6.465439 TGAGACATACGAAACTATCCATGT 57.535 37.500 0.00 0.00 34.53 3.21
874 954 6.306596 CGATGAGACATACGAAACTATCCATG 59.693 42.308 0.00 0.00 0.00 3.66
881 961 2.165641 TGCCGATGAGACATACGAAACT 59.834 45.455 0.00 0.00 0.00 2.66
883 963 2.951457 TGCCGATGAGACATACGAAA 57.049 45.000 0.00 0.00 0.00 3.46
899 979 2.158986 ACATGACTCAGAGTAGCATGCC 60.159 50.000 23.25 0.00 39.82 4.40
913 993 8.997323 CACAAGAAGAAGAAAGATTACATGACT 58.003 33.333 0.00 0.00 0.00 3.41
996 1076 2.093764 CAGTCTCAGGAAGGACATCACC 60.094 54.545 0.00 0.00 35.18 4.02
1043 1123 2.119495 AGGTGGGATGCAAGTACCTAG 58.881 52.381 12.02 0.00 39.84 3.02
1144 1229 3.244805 CCACCTGCCTGTCATGATCATAT 60.245 47.826 8.15 0.00 0.00 1.78
1145 1230 2.105306 CCACCTGCCTGTCATGATCATA 59.895 50.000 8.15 0.00 0.00 2.15
1228 1314 3.003068 GGATCTCTGCATCGGTGAATTTG 59.997 47.826 0.00 0.00 0.00 2.32
1334 1420 6.535508 GCAGAGAGTTACTTCGATTTACCAAT 59.464 38.462 0.00 0.00 0.00 3.16
1406 1508 0.461135 CAAGGCCAACAGTTGCAACT 59.539 50.000 26.36 26.36 40.60 3.16
1414 1516 1.608590 CAACTACACCAAGGCCAACAG 59.391 52.381 5.01 0.00 0.00 3.16
1476 1578 9.109246 TCACTGATAATAGATCATGGAAGGATT 57.891 33.333 0.00 0.00 37.56 3.01
1549 1658 7.295672 TGGATTGAGGGGATATTACTGAGAATT 59.704 37.037 0.00 0.00 0.00 2.17
1550 1659 6.794493 TGGATTGAGGGGATATTACTGAGAAT 59.206 38.462 0.00 0.00 0.00 2.40
1576 1685 3.183574 CACAAACTGCTGCAAATCACATG 59.816 43.478 3.02 0.00 0.00 3.21
1592 1701 2.031245 TGTGCACATCGAATCCACAAAC 60.031 45.455 17.42 0.00 33.90 2.93
1602 1711 3.852939 GCAACTCAATTTGTGCACATCGA 60.853 43.478 22.39 13.30 0.00 3.59
1603 1712 2.406024 GCAACTCAATTTGTGCACATCG 59.594 45.455 22.39 9.54 0.00 3.84
1604 1713 2.733026 GGCAACTCAATTTGTGCACATC 59.267 45.455 22.39 0.00 0.00 3.06
1767 1896 8.819015 CAATCAATCACTCTCTGATTCTTACTG 58.181 37.037 0.00 0.00 45.08 2.74
1771 1900 9.463902 AAATCAATCAATCACTCTCTGATTCTT 57.536 29.630 0.00 0.00 45.08 2.52
1772 1901 9.111613 GAAATCAATCAATCACTCTCTGATTCT 57.888 33.333 0.00 0.00 45.08 2.40
1776 1905 6.312180 CGTGAAATCAATCAATCACTCTCTGA 59.688 38.462 0.00 0.00 39.94 3.27
1783 1912 4.082787 ACACCCGTGAAATCAATCAATCAC 60.083 41.667 0.96 0.00 38.98 3.06
1785 1914 4.414852 CACACCCGTGAAATCAATCAATC 58.585 43.478 0.96 0.00 46.80 2.67
1819 1948 7.989416 AGTTAGAACGAAATGGAAAATACCA 57.011 32.000 0.00 0.00 44.41 3.25
1839 1968 8.241497 TCGGGCATAGTCTAGAAAAATAGTTA 57.759 34.615 0.00 0.00 0.00 2.24
1852 1981 1.729470 CGCTGACTCGGGCATAGTCT 61.729 60.000 16.41 0.00 43.13 3.24
1855 1984 0.598562 ATACGCTGACTCGGGCATAG 59.401 55.000 0.00 0.00 0.00 2.23
1858 1987 1.391933 ATGATACGCTGACTCGGGCA 61.392 55.000 0.00 0.00 0.00 5.36
1860 1989 0.386100 CGATGATACGCTGACTCGGG 60.386 60.000 0.00 0.00 0.00 5.14
1862 1991 1.003866 TGACGATGATACGCTGACTCG 60.004 52.381 0.00 0.00 36.70 4.18
1899 2028 1.890876 TGGCTGCTTCGCTTTTCTTA 58.109 45.000 0.00 0.00 0.00 2.10
1901 2030 1.251251 AATGGCTGCTTCGCTTTTCT 58.749 45.000 0.00 0.00 0.00 2.52
1907 2036 2.346099 TTTTGTAATGGCTGCTTCGC 57.654 45.000 0.00 0.00 0.00 4.70
1909 2038 6.202570 TGTTTGAATTTTGTAATGGCTGCTTC 59.797 34.615 0.00 0.00 0.00 3.86
1942 2071 5.125417 GCTTTTGAACTATGCACTCCCAATA 59.875 40.000 0.00 0.00 0.00 1.90
1943 2072 4.082026 GCTTTTGAACTATGCACTCCCAAT 60.082 41.667 0.00 0.00 0.00 3.16
1945 2074 2.819608 GCTTTTGAACTATGCACTCCCA 59.180 45.455 0.00 0.00 0.00 4.37
1946 2075 3.084786 AGCTTTTGAACTATGCACTCCC 58.915 45.455 0.00 0.00 0.00 4.30
1947 2076 3.119708 CCAGCTTTTGAACTATGCACTCC 60.120 47.826 0.00 0.00 0.00 3.85
1966 2095 3.881688 GGATCCACACTGAAATCATCCAG 59.118 47.826 6.95 0.00 36.53 3.86
1998 2128 5.874810 GTGCAACTACTCATTGGTCTTATGA 59.125 40.000 0.00 0.00 0.00 2.15
2000 2130 4.870426 CGTGCAACTACTCATTGGTCTTAT 59.130 41.667 0.00 0.00 31.75 1.73
2001 2131 4.242475 CGTGCAACTACTCATTGGTCTTA 58.758 43.478 0.00 0.00 31.75 2.10
2002 2132 3.067106 CGTGCAACTACTCATTGGTCTT 58.933 45.455 0.00 0.00 31.75 3.01
2003 2133 2.037251 ACGTGCAACTACTCATTGGTCT 59.963 45.455 0.00 0.00 31.75 3.85
2004 2134 2.413837 ACGTGCAACTACTCATTGGTC 58.586 47.619 0.00 0.00 31.75 4.02
2005 2135 2.543777 ACGTGCAACTACTCATTGGT 57.456 45.000 0.00 0.00 31.75 3.67
2006 2136 3.896648 AAACGTGCAACTACTCATTGG 57.103 42.857 0.00 0.00 31.75 3.16
2007 2137 6.071463 GTCTTAAACGTGCAACTACTCATTG 58.929 40.000 0.00 0.00 31.75 2.82
2008 2138 5.178809 GGTCTTAAACGTGCAACTACTCATT 59.821 40.000 0.00 0.00 31.75 2.57
2009 2139 4.689345 GGTCTTAAACGTGCAACTACTCAT 59.311 41.667 0.00 0.00 31.75 2.90
2010 2140 4.053295 GGTCTTAAACGTGCAACTACTCA 58.947 43.478 0.00 0.00 31.75 3.41
2011 2141 4.053295 TGGTCTTAAACGTGCAACTACTC 58.947 43.478 0.00 0.00 31.75 2.59
2012 2142 4.062677 TGGTCTTAAACGTGCAACTACT 57.937 40.909 0.00 0.00 31.75 2.57
2013 2143 4.799419 TTGGTCTTAAACGTGCAACTAC 57.201 40.909 0.00 0.00 31.75 2.73
2014 2144 5.057819 TCATTGGTCTTAAACGTGCAACTA 58.942 37.500 0.00 0.00 31.75 2.24
2015 2145 3.880490 TCATTGGTCTTAAACGTGCAACT 59.120 39.130 0.00 0.00 31.75 3.16
2016 2146 4.217754 TCATTGGTCTTAAACGTGCAAC 57.782 40.909 0.00 0.00 0.00 4.17
2017 2147 3.880490 ACTCATTGGTCTTAAACGTGCAA 59.120 39.130 0.00 0.00 0.00 4.08
2018 2148 3.472652 ACTCATTGGTCTTAAACGTGCA 58.527 40.909 0.00 0.00 0.00 4.57
2019 2149 4.689345 ACTACTCATTGGTCTTAAACGTGC 59.311 41.667 0.00 0.00 0.00 5.34
2020 2150 6.590357 CAACTACTCATTGGTCTTAAACGTG 58.410 40.000 0.00 0.00 0.00 4.49
2021 2151 5.178809 GCAACTACTCATTGGTCTTAAACGT 59.821 40.000 0.00 0.00 0.00 3.99
2022 2152 5.178623 TGCAACTACTCATTGGTCTTAAACG 59.821 40.000 0.00 0.00 0.00 3.60
2023 2153 6.371389 GTGCAACTACTCATTGGTCTTAAAC 58.629 40.000 0.00 0.00 0.00 2.01
2024 2154 5.178623 CGTGCAACTACTCATTGGTCTTAAA 59.821 40.000 0.00 0.00 31.75 1.52
2025 2155 4.688879 CGTGCAACTACTCATTGGTCTTAA 59.311 41.667 0.00 0.00 31.75 1.85
2026 2156 4.242475 CGTGCAACTACTCATTGGTCTTA 58.758 43.478 0.00 0.00 31.75 2.10
2027 2157 3.067106 CGTGCAACTACTCATTGGTCTT 58.933 45.455 0.00 0.00 31.75 3.01
2028 2158 2.037251 ACGTGCAACTACTCATTGGTCT 59.963 45.455 0.00 0.00 31.75 3.85
2029 2159 2.413837 ACGTGCAACTACTCATTGGTC 58.586 47.619 0.00 0.00 31.75 4.02
2030 2160 2.543777 ACGTGCAACTACTCATTGGT 57.456 45.000 0.00 0.00 31.75 3.67
2031 2161 3.896648 AAACGTGCAACTACTCATTGG 57.103 42.857 0.00 0.00 31.75 3.16
2032 2162 6.071463 GTCTTAAACGTGCAACTACTCATTG 58.929 40.000 0.00 0.00 31.75 2.82
2033 2163 5.178809 GGTCTTAAACGTGCAACTACTCATT 59.821 40.000 0.00 0.00 31.75 2.57
2034 2164 4.689345 GGTCTTAAACGTGCAACTACTCAT 59.311 41.667 0.00 0.00 31.75 2.90
2035 2165 4.053295 GGTCTTAAACGTGCAACTACTCA 58.947 43.478 0.00 0.00 31.75 3.41
2036 2166 4.053295 TGGTCTTAAACGTGCAACTACTC 58.947 43.478 0.00 0.00 31.75 2.59
2037 2167 4.062677 TGGTCTTAAACGTGCAACTACT 57.937 40.909 0.00 0.00 31.75 2.57
2038 2168 4.799419 TTGGTCTTAAACGTGCAACTAC 57.201 40.909 0.00 0.00 31.75 2.73
2039 2169 5.057819 TCATTGGTCTTAAACGTGCAACTA 58.942 37.500 0.00 0.00 31.75 2.24
2040 2170 3.880490 TCATTGGTCTTAAACGTGCAACT 59.120 39.130 0.00 0.00 31.75 3.16
2041 2171 4.217754 TCATTGGTCTTAAACGTGCAAC 57.782 40.909 0.00 0.00 0.00 4.17
2042 2172 3.880490 ACTCATTGGTCTTAAACGTGCAA 59.120 39.130 0.00 0.00 0.00 4.08
2043 2173 3.472652 ACTCATTGGTCTTAAACGTGCA 58.527 40.909 0.00 0.00 0.00 4.57
2044 2174 4.689345 ACTACTCATTGGTCTTAAACGTGC 59.311 41.667 0.00 0.00 0.00 5.34
2045 2175 6.590357 CAACTACTCATTGGTCTTAAACGTG 58.410 40.000 0.00 0.00 0.00 4.49
2046 2176 5.178809 GCAACTACTCATTGGTCTTAAACGT 59.821 40.000 0.00 0.00 0.00 3.99
2047 2177 5.178623 TGCAACTACTCATTGGTCTTAAACG 59.821 40.000 0.00 0.00 0.00 3.60
2048 2178 6.371389 GTGCAACTACTCATTGGTCTTAAAC 58.629 40.000 0.00 0.00 0.00 2.01
2049 2179 5.178623 CGTGCAACTACTCATTGGTCTTAAA 59.821 40.000 0.00 0.00 31.75 1.52
2050 2180 4.688879 CGTGCAACTACTCATTGGTCTTAA 59.311 41.667 0.00 0.00 31.75 1.85
2111 3362 4.131596 TGTTCTTAACTTCAAGGGTTCGG 58.868 43.478 0.00 0.00 0.00 4.30
2175 3427 2.099141 AGACGATGACATGTTGGTGG 57.901 50.000 0.00 0.00 0.00 4.61
2213 3465 6.653989 AGGAGTTCGTTGATTTATTGGATCT 58.346 36.000 0.00 0.00 0.00 2.75
2214 3466 6.927294 AGGAGTTCGTTGATTTATTGGATC 57.073 37.500 0.00 0.00 0.00 3.36
2239 3491 1.672881 GATGATGAGTTTGCTTCCCCG 59.327 52.381 0.00 0.00 0.00 5.73
2257 3509 0.469917 AAGCGATGGATTCACCGGAT 59.530 50.000 9.46 0.00 42.61 4.18
2275 3527 8.181904 AGATTCTTTTTCTCATTTGTAGGCAA 57.818 30.769 0.00 0.00 0.00 4.52
2311 3563 5.504010 GCCATGTGTATGACGGAAATGTTAG 60.504 44.000 0.00 0.00 36.36 2.34
2320 3572 0.107703 ACCAGCCATGTGTATGACGG 60.108 55.000 0.00 0.00 36.36 4.79


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

AutoCloner maintained by Alex Coulton.