Multiple sequence alignment - TraesCS6A01G165700

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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 TraesCS6A01G165700 chr6A 100.000 4400 0 0 1 4400 166979019 166983418 0.000000e+00 8126.0
1 TraesCS6A01G165700 chr6D 96.032 2596 56 12 1830 4400 129484957 129487530 0.000000e+00 4180.0
2 TraesCS6A01G165700 chr6D 92.229 1660 91 18 6 1653 129483161 129484794 0.000000e+00 2316.0
3 TraesCS6A01G165700 chr6D 91.724 145 11 1 1641 1784 129484835 129484979 2.680000e-47 200.0
4 TraesCS6A01G165700 chr6D 90.278 72 4 3 1782 1851 4632421 4632491 1.690000e-14 91.6
5 TraesCS6A01G165700 chr6B 92.800 1500 83 16 6 1493 227638343 227639829 0.000000e+00 2148.0
6 TraesCS6A01G165700 chr6B 95.747 1058 39 6 1831 2885 227640074 227641128 0.000000e+00 1700.0
7 TraesCS6A01G165700 chr6B 91.510 907 41 15 3003 3889 227641251 227642141 0.000000e+00 1216.0
8 TraesCS6A01G165700 chr6B 90.577 520 30 5 3900 4400 227642262 227642781 0.000000e+00 671.0
9 TraesCS6A01G165700 chr2B 98.214 56 0 1 1782 1836 140766062 140766117 3.620000e-16 97.1
10 TraesCS6A01G165700 chr2B 96.491 57 2 0 1784 1840 273742096 273742040 1.300000e-15 95.3
11 TraesCS6A01G165700 chr5A 96.491 57 2 0 1781 1837 425456521 425456577 1.300000e-15 95.3
12 TraesCS6A01G165700 chr2A 92.424 66 2 3 1782 1845 593496837 593496901 1.690000e-14 91.6
13 TraesCS6A01G165700 chr2A 94.737 57 2 1 1785 1841 317953211 317953156 2.180000e-13 87.9
14 TraesCS6A01G165700 chr5B 96.296 54 2 0 1781 1834 243411147 243411200 6.060000e-14 89.8
15 TraesCS6A01G165700 chr2D 93.443 61 2 2 1786 1845 449516262 449516203 6.060000e-14 89.8
16 TraesCS6A01G165700 chr4A 89.041 73 4 4 1784 1855 475420570 475420501 2.180000e-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 TraesCS6A01G165700 chr6A 166979019 166983418 4399 False 8126.00 8126 100.000000 1 4400 1 chr6A.!!$F1 4399
1 TraesCS6A01G165700 chr6D 129483161 129487530 4369 False 2232.00 4180 93.328333 6 4400 3 chr6D.!!$F2 4394
2 TraesCS6A01G165700 chr6B 227638343 227642781 4438 False 1433.75 2148 92.658500 6 4400 4 chr6B.!!$F1 4394

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
727 753 0.461163 GGCATGATGCTGCATTGCAA 60.461 50.000 29.75 0.00 46.61 4.08 F
1380 1407 1.144057 GGTCCATCTGGCAGGTACG 59.856 63.158 15.73 0.74 34.44 3.67 F
1794 1880 0.811281 CTTGTTTTCCCGGATCCTGC 59.189 55.000 10.75 0.00 0.00 4.85 F
1795 1881 0.958382 TTGTTTTCCCGGATCCTGCG 60.958 55.000 10.75 0.00 0.00 5.18 F
1880 1966 1.479323 AGCATGATTGTGTTGATGCCC 59.521 47.619 0.00 0.00 41.81 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1776 1862 0.958382 CGCAGGATCCGGGAAAACAA 60.958 55.000 14.13 0.00 0.00 2.83 R
2720 2808 1.681486 TACCGGATGCCGCATCTTCA 61.681 55.000 28.09 11.89 46.86 3.02 R
2769 2857 3.131850 TCAGAGACAGCACTGACCA 57.868 52.632 4.31 0.00 36.92 4.02 R
3143 3283 3.495001 GGTTTCACTCAACACTACAGAGC 59.505 47.826 0.00 0.00 32.71 4.09 R
3808 3972 1.071071 CCCTTCGACAAGTGGTTGGTA 59.929 52.381 0.00 0.00 38.07 3.25 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
23 24 0.466922 AGCCCGCCGTGTACTATACT 60.467 55.000 0.00 0.00 0.00 2.12
24 25 1.202806 AGCCCGCCGTGTACTATACTA 60.203 52.381 0.00 0.00 0.00 1.82
25 26 1.068954 GCCCGCCGTGTACTATACTAC 60.069 57.143 0.00 0.00 0.00 2.73
26 27 1.537202 CCCGCCGTGTACTATACTACC 59.463 57.143 0.00 0.00 0.00 3.18
27 28 2.498167 CCGCCGTGTACTATACTACCT 58.502 52.381 0.00 0.00 0.00 3.08
29 30 3.316308 CCGCCGTGTACTATACTACCTTT 59.684 47.826 0.00 0.00 0.00 3.11
31 32 4.274459 CGCCGTGTACTATACTACCTTTCT 59.726 45.833 0.00 0.00 0.00 2.52
33 34 5.278218 GCCGTGTACTATACTACCTTTCTCC 60.278 48.000 0.00 0.00 0.00 3.71
34 35 5.049818 CCGTGTACTATACTACCTTTCTCCG 60.050 48.000 0.00 0.00 0.00 4.63
35 36 5.049818 CGTGTACTATACTACCTTTCTCCGG 60.050 48.000 0.00 0.00 0.00 5.14
36 37 5.825151 GTGTACTATACTACCTTTCTCCGGT 59.175 44.000 0.00 0.00 38.55 5.28
37 38 6.319911 GTGTACTATACTACCTTTCTCCGGTT 59.680 42.308 0.00 0.00 35.98 4.44
38 39 6.543831 TGTACTATACTACCTTTCTCCGGTTC 59.456 42.308 0.00 0.00 35.98 3.62
39 40 4.892345 ACTATACTACCTTTCTCCGGTTCC 59.108 45.833 0.00 0.00 35.98 3.62
40 41 1.273759 ACTACCTTTCTCCGGTTCCC 58.726 55.000 0.00 0.00 35.98 3.97
41 42 1.203275 ACTACCTTTCTCCGGTTCCCT 60.203 52.381 0.00 0.00 35.98 4.20
86 87 6.544564 ACCAAAAAGAACTCGTTCCAAATCTA 59.455 34.615 6.20 0.00 40.33 1.98
218 241 2.277072 CTCGCCTCCTCCTCCTCA 59.723 66.667 0.00 0.00 0.00 3.86
219 242 2.043852 TCGCCTCCTCCTCCTCAC 60.044 66.667 0.00 0.00 0.00 3.51
221 244 1.684049 CGCCTCCTCCTCCTCACTT 60.684 63.158 0.00 0.00 0.00 3.16
273 298 2.023788 GCCTCCACCTCTCTCTCTCTG 61.024 61.905 0.00 0.00 0.00 3.35
274 299 1.563879 CCTCCACCTCTCTCTCTCTGA 59.436 57.143 0.00 0.00 0.00 3.27
278 303 2.239654 CCACCTCTCTCTCTCTGACTCT 59.760 54.545 0.00 0.00 0.00 3.24
279 304 3.535561 CACCTCTCTCTCTCTGACTCTC 58.464 54.545 0.00 0.00 0.00 3.20
280 305 3.198635 CACCTCTCTCTCTCTGACTCTCT 59.801 52.174 0.00 0.00 0.00 3.10
281 306 3.452627 ACCTCTCTCTCTCTGACTCTCTC 59.547 52.174 0.00 0.00 0.00 3.20
282 307 3.708631 CCTCTCTCTCTCTGACTCTCTCT 59.291 52.174 0.00 0.00 0.00 3.10
283 308 4.202202 CCTCTCTCTCTCTGACTCTCTCTC 60.202 54.167 0.00 0.00 0.00 3.20
284 309 3.706594 TCTCTCTCTCTGACTCTCTCTCC 59.293 52.174 0.00 0.00 0.00 3.71
285 310 3.708631 CTCTCTCTCTGACTCTCTCTCCT 59.291 52.174 0.00 0.00 0.00 3.69
303 328 2.123854 CCCTCCCGTGGATCTCGA 60.124 66.667 11.16 0.00 0.00 4.04
306 331 0.538516 CCTCCCGTGGATCTCGATCT 60.539 60.000 11.16 0.00 37.92 2.75
326 351 1.700042 GGATTGTGCCGATCCCTCCT 61.700 60.000 9.31 0.00 38.23 3.69
511 536 1.350351 CTGGATTCCTGGCCTGGATAG 59.650 57.143 29.96 20.63 35.83 2.08
522 547 5.165961 TGGCCTGGATAGTTATTAGATGC 57.834 43.478 3.32 0.00 0.00 3.91
586 611 1.194781 AGGTGTCTGCCCTGTCGAAT 61.195 55.000 0.00 0.00 0.00 3.34
611 636 7.118496 ACCTCGAGTGATTATCTTTCAGATT 57.882 36.000 12.31 0.00 36.20 2.40
614 639 7.493971 CCTCGAGTGATTATCTTTCAGATTTGT 59.506 37.037 12.31 0.00 36.20 2.83
631 656 3.498927 TTGTCTCGATTAGGTCCGTTC 57.501 47.619 0.00 0.00 0.00 3.95
633 658 1.019673 TCTCGATTAGGTCCGTTCCG 58.980 55.000 0.00 0.00 0.00 4.30
665 691 3.485394 TGCTGCTTTTAGTTGATGTGGA 58.515 40.909 0.00 0.00 0.00 4.02
685 711 3.987220 GGATTTGTGTAATGTGGTTGTGC 59.013 43.478 0.00 0.00 0.00 4.57
727 753 0.461163 GGCATGATGCTGCATTGCAA 60.461 50.000 29.75 0.00 46.61 4.08
782 808 7.012607 AGTGGGCTATGCTTTATATCCAAAAT 58.987 34.615 0.00 0.00 30.60 1.82
822 848 7.117379 GCTTGCTTCATTTTATTCTTGCTTTCT 59.883 33.333 0.00 0.00 0.00 2.52
910 936 8.250332 GGAATATGCTGACTTGGACAATTTTTA 58.750 33.333 0.00 0.00 0.00 1.52
1097 1124 9.196552 GAAATTAGGAACACCATTTTTCTCAAG 57.803 33.333 0.00 0.00 0.00 3.02
1272 1299 2.274437 CGGACAACATGTGATGAGAGG 58.726 52.381 0.00 0.00 0.00 3.69
1380 1407 1.144057 GGTCCATCTGGCAGGTACG 59.856 63.158 15.73 0.74 34.44 3.67
1392 1419 2.481568 GGCAGGTACGAACTTTGTAACC 59.518 50.000 1.09 1.63 29.56 2.85
1466 1493 6.285224 TCTTCGTCTTTGAATTAGTGTTGGA 58.715 36.000 0.00 0.00 0.00 3.53
1468 1495 5.361427 TCGTCTTTGAATTAGTGTTGGACA 58.639 37.500 0.00 0.00 0.00 4.02
1498 1525 9.092338 TCCATAAACCGGTGTATATATGTACTT 57.908 33.333 17.14 0.65 0.00 2.24
1503 1530 9.918630 AAACCGGTGTATATATGTACTTCATAC 57.081 33.333 8.52 0.99 41.13 2.39
1513 1540 9.770097 ATATATGTACTTCATACCATATGCAGC 57.230 33.333 0.00 0.00 41.13 5.25
1520 1547 4.835678 TCATACCATATGCAGCGAATCAT 58.164 39.130 0.00 0.00 0.00 2.45
1523 1550 2.810274 ACCATATGCAGCGAATCATCAC 59.190 45.455 0.00 0.00 0.00 3.06
1525 1552 3.501062 CCATATGCAGCGAATCATCACTT 59.499 43.478 0.00 0.00 0.00 3.16
1534 1561 6.320171 CAGCGAATCATCACTTCAGATTTTT 58.680 36.000 0.00 0.00 32.51 1.94
1559 1586 4.141274 TCCAATCCACCAGACTTCAGAAAA 60.141 41.667 0.00 0.00 0.00 2.29
1560 1587 4.768968 CCAATCCACCAGACTTCAGAAAAT 59.231 41.667 0.00 0.00 0.00 1.82
1561 1588 5.945784 CCAATCCACCAGACTTCAGAAAATA 59.054 40.000 0.00 0.00 0.00 1.40
1567 1594 7.944554 TCCACCAGACTTCAGAAAATATTCTTT 59.055 33.333 0.00 0.00 43.43 2.52
1653 1681 5.831997 ACTTTGGTGACATTTAGCTTTGTC 58.168 37.500 14.05 14.05 42.32 3.18
1659 1687 3.745975 TGACATTTAGCTTTGTCACCTCG 59.254 43.478 17.77 0.00 45.35 4.63
1673 1758 3.245519 GTCACCTCGTTTCAGAACAGAAC 59.754 47.826 0.00 0.00 35.44 3.01
1680 1765 4.340097 TCGTTTCAGAACAGAACCAGTAGA 59.660 41.667 0.00 0.00 35.44 2.59
1681 1766 5.010719 TCGTTTCAGAACAGAACCAGTAGAT 59.989 40.000 0.00 0.00 35.44 1.98
1706 1791 5.603596 TCTGAAATGCAGCAATTCAACTTT 58.396 33.333 23.21 7.39 44.52 2.66
1776 1862 8.641498 AGAATTTCTGTTTCCATAATGTGACT 57.359 30.769 0.00 0.00 0.00 3.41
1777 1863 9.082313 AGAATTTCTGTTTCCATAATGTGACTT 57.918 29.630 0.00 0.00 0.00 3.01
1778 1864 9.132521 GAATTTCTGTTTCCATAATGTGACTTG 57.867 33.333 0.00 0.00 0.00 3.16
1779 1865 7.581213 TTTCTGTTTCCATAATGTGACTTGT 57.419 32.000 0.00 0.00 0.00 3.16
1780 1866 7.581213 TTCTGTTTCCATAATGTGACTTGTT 57.419 32.000 0.00 0.00 0.00 2.83
1781 1867 7.581213 TCTGTTTCCATAATGTGACTTGTTT 57.419 32.000 0.00 0.00 0.00 2.83
1782 1868 8.006298 TCTGTTTCCATAATGTGACTTGTTTT 57.994 30.769 0.00 0.00 0.00 2.43
1783 1869 8.134895 TCTGTTTCCATAATGTGACTTGTTTTC 58.865 33.333 0.00 0.00 0.00 2.29
1784 1870 7.206687 TGTTTCCATAATGTGACTTGTTTTCC 58.793 34.615 0.00 0.00 0.00 3.13
1785 1871 5.975693 TCCATAATGTGACTTGTTTTCCC 57.024 39.130 0.00 0.00 0.00 3.97
1786 1872 4.457603 TCCATAATGTGACTTGTTTTCCCG 59.542 41.667 0.00 0.00 0.00 5.14
1787 1873 4.380444 CCATAATGTGACTTGTTTTCCCGG 60.380 45.833 0.00 0.00 0.00 5.73
1788 1874 2.649531 ATGTGACTTGTTTTCCCGGA 57.350 45.000 0.73 0.00 0.00 5.14
1789 1875 2.649531 TGTGACTTGTTTTCCCGGAT 57.350 45.000 0.73 0.00 0.00 4.18
1790 1876 2.500229 TGTGACTTGTTTTCCCGGATC 58.500 47.619 0.73 0.00 0.00 3.36
1791 1877 1.810755 GTGACTTGTTTTCCCGGATCC 59.189 52.381 0.73 0.00 0.00 3.36
1792 1878 1.702957 TGACTTGTTTTCCCGGATCCT 59.297 47.619 10.75 0.00 0.00 3.24
1793 1879 2.084546 GACTTGTTTTCCCGGATCCTG 58.915 52.381 10.75 2.58 0.00 3.86
1794 1880 0.811281 CTTGTTTTCCCGGATCCTGC 59.189 55.000 10.75 0.00 0.00 4.85
1795 1881 0.958382 TTGTTTTCCCGGATCCTGCG 60.958 55.000 10.75 0.00 0.00 5.18
1796 1882 2.437716 TTTTCCCGGATCCTGCGC 60.438 61.111 10.75 0.00 0.00 6.09
1797 1883 3.261039 TTTTCCCGGATCCTGCGCA 62.261 57.895 10.98 10.98 0.00 6.09
1798 1884 2.756321 TTTTCCCGGATCCTGCGCAA 62.756 55.000 13.05 0.00 0.00 4.85
1799 1885 3.680620 TTCCCGGATCCTGCGCAAG 62.681 63.158 13.05 5.31 43.44 4.01
1819 1905 4.814294 GGAGCTACGTGCACCGGG 62.814 72.222 12.15 0.00 42.21 5.73
1830 1916 2.917227 CACCGGGCTGCCCTTTTT 60.917 61.111 33.39 13.23 42.67 1.94
1879 1965 2.927477 CAAGCATGATTGTGTTGATGCC 59.073 45.455 15.52 0.00 41.81 4.40
1880 1966 1.479323 AGCATGATTGTGTTGATGCCC 59.521 47.619 0.00 0.00 41.81 5.36
2135 2223 7.018635 ACCTTGCATTTTTGTCAATTTTCAG 57.981 32.000 0.00 0.00 0.00 3.02
2161 2249 2.971330 CCTGGCTGGAACTGATATCTCT 59.029 50.000 4.05 0.00 38.35 3.10
2720 2808 5.767168 AGCTAAAGATGCAACTTCTTTGACT 59.233 36.000 19.42 14.34 42.03 3.41
2769 2857 8.186821 GCATTGAGCAAGTAAAAGACAGATTAT 58.813 33.333 0.00 0.00 44.79 1.28
2878 2966 3.988517 GCTACTCACTTGTTCTGTACCAC 59.011 47.826 0.00 0.00 0.00 4.16
2885 3010 8.198109 ACTCACTTGTTCTGTACCACATATATC 58.802 37.037 0.00 0.00 0.00 1.63
2886 3011 7.497595 TCACTTGTTCTGTACCACATATATCC 58.502 38.462 0.00 0.00 0.00 2.59
2925 3050 4.228824 ACCTGGGTCTTCTACTTACAACA 58.771 43.478 0.00 0.00 0.00 3.33
2957 3097 5.869579 AGATTTCCTACAGAGTGCTTTCAA 58.130 37.500 0.00 0.00 0.00 2.69
3058 3198 3.129462 TGTTTTCCGCATCACTTTTGTCA 59.871 39.130 0.00 0.00 0.00 3.58
3143 3283 4.751600 TGTTTCTGTAATCTGTGCTCTGTG 59.248 41.667 0.00 0.00 0.00 3.66
3144 3284 2.964740 TCTGTAATCTGTGCTCTGTGC 58.035 47.619 0.00 0.00 43.25 4.57
3145 3285 2.564504 TCTGTAATCTGTGCTCTGTGCT 59.435 45.455 3.20 0.00 43.37 4.40
3146 3286 2.928757 CTGTAATCTGTGCTCTGTGCTC 59.071 50.000 3.20 0.19 43.37 4.26
3147 3287 2.564504 TGTAATCTGTGCTCTGTGCTCT 59.435 45.455 3.20 0.00 43.37 4.09
3148 3288 2.096220 AATCTGTGCTCTGTGCTCTG 57.904 50.000 3.20 4.15 43.37 3.35
3149 3289 0.975135 ATCTGTGCTCTGTGCTCTGT 59.025 50.000 3.20 0.00 43.37 3.41
3555 3713 6.180472 GGATTAAACAAGTGGGAGAATGAGA 58.820 40.000 0.00 0.00 0.00 3.27
3769 3928 3.980646 AATTGTCAGCTGCACGTTAAA 57.019 38.095 9.47 0.00 0.00 1.52
3780 3939 5.987347 AGCTGCACGTTAAAACTTACTCTTA 59.013 36.000 1.02 0.00 0.00 2.10
3828 3992 0.179029 ACCAACCACTTGTCGAAGGG 60.179 55.000 0.00 0.00 32.95 3.95
3917 4191 4.742417 CTGTGTATATGCCTAGCTAGCTG 58.258 47.826 27.68 16.13 0.00 4.24
3924 4198 4.306967 CTAGCTAGCTGGCCGGCC 62.307 72.222 39.40 39.40 0.00 6.13
3938 4212 2.124570 GGCCAGGTGACGATGCAT 60.125 61.111 0.00 0.00 0.00 3.96
3940 4214 1.746615 GCCAGGTGACGATGCATGT 60.747 57.895 2.46 2.18 0.00 3.21
4031 4305 3.767806 CAGAGGGAGCTGAGCGCA 61.768 66.667 11.47 0.00 42.61 6.09
4112 4386 4.181010 ACCTGCGGCAGCCTATGG 62.181 66.667 24.27 13.01 44.33 2.74
4129 4403 2.508887 GAGCGTCTGCAGCCTCAG 60.509 66.667 9.47 0.00 46.23 3.35
4166 4445 3.622612 TCATCACATCACATAGCAAACGG 59.377 43.478 0.00 0.00 0.00 4.44
4202 4486 0.797249 ACTGACTAAGCGCGCGTAAG 60.797 55.000 32.35 25.72 43.44 2.34
4214 4498 1.954437 CGCGTAAGTCACTCGTGTAA 58.046 50.000 0.00 0.00 41.68 2.41
4216 4500 2.663879 CGCGTAAGTCACTCGTGTAAGT 60.664 50.000 0.00 0.00 41.68 2.24
4218 4502 3.851105 GCGTAAGTCACTCGTGTAAGTGT 60.851 47.826 4.15 0.00 42.19 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.174712 TATAGTACACGGCGGGCTCC 61.175 60.000 10.14 0.00 0.00 4.70
3 4 0.039708 GTATAGTACACGGCGGGCTC 60.040 60.000 10.14 1.76 0.00 4.70
4 5 0.466922 AGTATAGTACACGGCGGGCT 60.467 55.000 10.14 0.66 0.00 5.19
218 241 3.979497 CGGGGAAGGGGGCAAAGT 61.979 66.667 0.00 0.00 0.00 2.66
273 298 0.185175 GGGAGGGAGGAGAGAGAGTC 59.815 65.000 0.00 0.00 0.00 3.36
274 299 1.641552 CGGGAGGGAGGAGAGAGAGT 61.642 65.000 0.00 0.00 0.00 3.24
278 303 2.684104 CACGGGAGGGAGGAGAGA 59.316 66.667 0.00 0.00 32.31 3.10
279 304 2.305314 ATCCACGGGAGGGAGGAGAG 62.305 65.000 0.00 0.00 37.96 3.20
280 305 2.299727 GATCCACGGGAGGGAGGAGA 62.300 65.000 0.00 0.00 37.96 3.71
281 306 1.834822 GATCCACGGGAGGGAGGAG 60.835 68.421 0.00 0.00 37.96 3.69
282 307 2.282446 GATCCACGGGAGGGAGGA 59.718 66.667 0.00 0.00 37.96 3.71
283 308 1.834822 GAGATCCACGGGAGGGAGG 60.835 68.421 0.00 0.00 37.96 4.30
284 309 2.196925 CGAGATCCACGGGAGGGAG 61.197 68.421 0.00 0.00 37.96 4.30
285 310 2.008006 ATCGAGATCCACGGGAGGGA 62.008 60.000 9.43 0.00 39.14 4.20
303 328 0.109342 GGGATCGGCACAATCCAGAT 59.891 55.000 11.86 0.00 36.22 2.90
306 331 1.526887 GAGGGATCGGCACAATCCA 59.473 57.895 11.86 0.00 36.22 3.41
340 365 2.283529 GCCAAGAGACCACGGGAGA 61.284 63.158 0.00 0.00 0.00 3.71
423 448 0.992802 CTCTTAAGAAGCACGACGGC 59.007 55.000 6.63 0.00 0.00 5.68
511 536 1.484356 ACGGCGTCGCATCTAATAAC 58.516 50.000 20.50 0.00 40.63 1.89
605 630 4.202020 CGGACCTAATCGAGACAAATCTGA 60.202 45.833 0.00 0.00 34.34 3.27
611 636 2.165030 GGAACGGACCTAATCGAGACAA 59.835 50.000 0.00 0.00 0.00 3.18
633 658 1.589716 AAAGCAGCATCTCCGCCAAC 61.590 55.000 0.00 0.00 0.00 3.77
665 691 4.261994 GGAGCACAACCACATTACACAAAT 60.262 41.667 0.00 0.00 0.00 2.32
685 711 5.527951 CCATCAGACATTGAGATTCAAGGAG 59.472 44.000 10.05 0.18 40.25 3.69
726 752 5.211201 CAACTATGGAAGGAATTCCCCATT 58.789 41.667 29.46 16.44 38.48 3.16
727 753 4.232820 ACAACTATGGAAGGAATTCCCCAT 59.767 41.667 28.13 28.13 40.01 4.00
782 808 2.944129 AGCAAGCCCACTAGTTTGAAA 58.056 42.857 8.83 0.00 0.00 2.69
822 848 1.810151 GAATGGTTTCCAGCGCTAACA 59.190 47.619 20.03 10.67 36.75 2.41
910 936 2.706339 TGCCTGCACCAACAAAATTT 57.294 40.000 0.00 0.00 0.00 1.82
985 1012 9.334947 CACTGATACCATATTCAAGAATGTCTT 57.665 33.333 5.59 0.00 37.14 3.01
1097 1124 0.922243 TTTGGTACCTCCCCATCCCC 60.922 60.000 14.36 0.00 34.77 4.81
1272 1299 1.269621 GGAGGCAATGCATCAATGAGC 60.270 52.381 21.52 0.00 41.39 4.26
1380 1407 6.396450 AGAGTAAGATCGGGTTACAAAGTTC 58.604 40.000 6.23 0.00 33.52 3.01
1392 1419 5.465051 CACACCATGATAGAGTAAGATCGG 58.535 45.833 0.00 0.00 0.00 4.18
1440 1467 7.444183 TCCAACACTAATTCAAAGACGAAGAAT 59.556 33.333 0.00 0.00 33.68 2.40
1466 1493 1.913419 ACACCGGTTTATGGATCCTGT 59.087 47.619 14.23 2.29 0.00 4.00
1468 1495 7.402071 ACATATATACACCGGTTTATGGATCCT 59.598 37.037 21.07 0.89 0.00 3.24
1474 1501 9.917129 TGAAGTACATATATACACCGGTTTATG 57.083 33.333 21.07 16.37 0.00 1.90
1498 1525 4.270245 TGATTCGCTGCATATGGTATGA 57.730 40.909 4.56 0.00 0.00 2.15
1503 1530 3.072211 AGTGATGATTCGCTGCATATGG 58.928 45.455 4.56 0.00 41.15 2.74
1534 1561 3.394274 TCTGAAGTCTGGTGGATTGGAAA 59.606 43.478 0.00 0.00 0.00 3.13
1536 1563 2.619931 TCTGAAGTCTGGTGGATTGGA 58.380 47.619 0.00 0.00 0.00 3.53
1541 1568 7.020827 AGAATATTTTCTGAAGTCTGGTGGA 57.979 36.000 0.00 0.00 40.74 4.02
1592 1619 4.647611 ACATTGATCCGTTCAACCAGTAA 58.352 39.130 0.64 0.00 46.80 2.24
1593 1620 4.280436 ACATTGATCCGTTCAACCAGTA 57.720 40.909 0.64 0.00 46.80 2.74
1594 1621 3.140325 ACATTGATCCGTTCAACCAGT 57.860 42.857 0.64 0.00 46.80 4.00
1653 1681 2.544267 GGTTCTGTTCTGAAACGAGGTG 59.456 50.000 0.00 0.00 38.28 4.00
1655 1683 2.802816 CTGGTTCTGTTCTGAAACGAGG 59.197 50.000 0.00 0.00 38.28 4.63
1656 1684 3.458189 ACTGGTTCTGTTCTGAAACGAG 58.542 45.455 0.00 0.00 38.28 4.18
1657 1685 3.536956 ACTGGTTCTGTTCTGAAACGA 57.463 42.857 0.00 0.00 38.28 3.85
1658 1686 4.617959 TCTACTGGTTCTGTTCTGAAACG 58.382 43.478 0.00 0.00 38.28 3.60
1659 1687 7.442666 AGAAATCTACTGGTTCTGTTCTGAAAC 59.557 37.037 0.00 1.48 34.47 2.78
1673 1758 4.397103 TGCTGCATTTCAGAAATCTACTGG 59.603 41.667 5.32 0.00 45.72 4.00
1681 1766 5.603596 AGTTGAATTGCTGCATTTCAGAAA 58.396 33.333 28.12 17.68 44.21 2.52
1686 1771 5.236911 TGGAAAAGTTGAATTGCTGCATTTC 59.763 36.000 23.34 23.34 0.00 2.17
1764 1850 4.380444 CCGGGAAAACAAGTCACATTATGG 60.380 45.833 0.00 0.00 0.00 2.74
1773 1859 2.084546 CAGGATCCGGGAAAACAAGTC 58.915 52.381 5.98 0.00 0.00 3.01
1776 1862 0.958382 CGCAGGATCCGGGAAAACAA 60.958 55.000 14.13 0.00 0.00 2.83
1777 1863 1.376683 CGCAGGATCCGGGAAAACA 60.377 57.895 14.13 0.00 0.00 2.83
1778 1864 2.761195 GCGCAGGATCCGGGAAAAC 61.761 63.158 14.13 0.00 0.00 2.43
1779 1865 2.437716 GCGCAGGATCCGGGAAAA 60.438 61.111 14.13 0.00 0.00 2.29
1780 1866 3.261039 TTGCGCAGGATCCGGGAAA 62.261 57.895 11.31 11.25 0.00 3.13
1781 1867 3.680620 CTTGCGCAGGATCCGGGAA 62.681 63.158 15.39 10.11 0.00 3.97
1782 1868 4.161295 CTTGCGCAGGATCCGGGA 62.161 66.667 15.39 0.00 0.00 5.14
1787 1873 4.838152 TCCCGCTTGCGCAGGATC 62.838 66.667 25.12 5.31 37.80 3.36
1788 1874 4.845580 CTCCCGCTTGCGCAGGAT 62.846 66.667 25.12 0.00 41.70 3.24
1791 1877 4.819761 TAGCTCCCGCTTGCGCAG 62.820 66.667 11.31 6.32 46.47 5.18
1794 1880 4.796231 ACGTAGCTCCCGCTTGCG 62.796 66.667 8.14 8.14 46.47 4.85
1795 1881 3.188786 CACGTAGCTCCCGCTTGC 61.189 66.667 5.69 0.00 46.47 4.01
1796 1882 3.188786 GCACGTAGCTCCCGCTTG 61.189 66.667 5.69 0.00 46.47 4.01
1797 1883 3.691342 TGCACGTAGCTCCCGCTT 61.691 61.111 10.54 0.00 46.47 4.68
1844 1930 8.629158 ACAATCATGCTTGTTAGTAGAAAACAA 58.371 29.630 9.09 1.88 42.83 2.83
1879 1965 5.358160 AGTGAGAACTTCCAAGAAAAACAGG 59.642 40.000 0.00 0.00 0.00 4.00
1880 1966 6.442513 AGTGAGAACTTCCAAGAAAAACAG 57.557 37.500 0.00 0.00 0.00 3.16
2161 2249 5.716228 CCATAATAGGGGCTGCATTTCATTA 59.284 40.000 0.50 0.00 0.00 1.90
2720 2808 1.681486 TACCGGATGCCGCATCTTCA 61.681 55.000 28.09 11.89 46.86 3.02
2769 2857 3.131850 TCAGAGACAGCACTGACCA 57.868 52.632 4.31 0.00 36.92 4.02
2885 3010 5.221303 CCCAGGTAGCATTAATCACATTTGG 60.221 44.000 0.00 0.00 0.00 3.28
2886 3011 5.360714 ACCCAGGTAGCATTAATCACATTTG 59.639 40.000 0.00 0.00 0.00 2.32
3043 3183 3.745332 TGCTATGACAAAAGTGATGCG 57.255 42.857 0.00 0.00 0.00 4.73
3058 3198 3.576118 AGCTCGGATAACACTCATGCTAT 59.424 43.478 0.00 0.00 0.00 2.97
3143 3283 3.495001 GGTTTCACTCAACACTACAGAGC 59.505 47.826 0.00 0.00 32.71 4.09
3144 3284 4.950050 AGGTTTCACTCAACACTACAGAG 58.050 43.478 0.00 0.00 35.56 3.35
3145 3285 5.353394 AAGGTTTCACTCAACACTACAGA 57.647 39.130 0.00 0.00 0.00 3.41
3146 3286 6.436843 AAAAGGTTTCACTCAACACTACAG 57.563 37.500 0.00 0.00 0.00 2.74
3147 3287 8.514330 AATAAAAGGTTTCACTCAACACTACA 57.486 30.769 0.00 0.00 0.00 2.74
3191 3331 5.045286 AGACTGGAACCAAGCTTCAATAGAT 60.045 40.000 0.00 0.00 0.00 1.98
3555 3713 7.112122 TCCACTAATTTTGATACTCACTGCAT 58.888 34.615 0.00 0.00 0.00 3.96
3748 3907 3.980646 TTAACGTGCAGCTGACAATTT 57.019 38.095 20.43 12.87 0.00 1.82
3808 3972 1.071071 CCCTTCGACAAGTGGTTGGTA 59.929 52.381 0.00 0.00 38.07 3.25
3881 4045 7.308229 GGCATATACACAGCATAGAAGAAAAGG 60.308 40.741 0.00 0.00 0.00 3.11
3893 4057 3.056536 GCTAGCTAGGCATATACACAGCA 60.057 47.826 22.10 0.00 0.00 4.41
3924 4198 1.136891 TCCTACATGCATCGTCACCTG 59.863 52.381 0.00 0.00 0.00 4.00
3936 4210 5.829391 TGTTCCATCCATGAAATCCTACATG 59.171 40.000 0.00 0.00 42.12 3.21
3938 4212 5.439721 CTGTTCCATCCATGAAATCCTACA 58.560 41.667 0.00 0.00 0.00 2.74
3940 4214 4.464008 GCTGTTCCATCCATGAAATCCTA 58.536 43.478 0.00 0.00 0.00 2.94
4043 4317 4.883300 GCCGTCGCCGACTACTCG 62.883 72.222 16.07 1.02 39.83 4.18
4109 4383 3.382803 GAGGCTGCAGACGCTCCAT 62.383 63.158 20.43 0.00 39.64 3.41
4112 4386 2.508887 CTGAGGCTGCAGACGCTC 60.509 66.667 24.46 13.32 38.14 5.03
4166 4445 3.664107 TCAGTGCACCTGATAACTGTTC 58.336 45.455 14.63 0.00 45.34 3.18
4190 4474 2.049433 AGTGACTTACGCGCGCTT 60.049 55.556 32.58 23.63 0.00 4.68
4214 4498 1.447643 GTCAGACAGGTGCCACACT 59.552 57.895 0.00 0.00 34.40 3.55
4216 4500 1.681486 TTCGTCAGACAGGTGCCACA 61.681 55.000 0.41 0.00 0.00 4.17
4218 4502 1.367471 CTTCGTCAGACAGGTGCCA 59.633 57.895 0.41 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.