Multiple sequence alignment - TraesCS6D01G386000

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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 TraesCS6D01G386000 chr6D 100.000 2922 0 0 1 2922 463684600 463681679 0.000000e+00 5397.0
1 TraesCS6D01G386000 chr6D 97.685 216 5 0 595 810 463710822 463710607 3.560000e-99 372.0
2 TraesCS6D01G386000 chr5D 94.110 815 21 6 1 815 123457132 123457919 0.000000e+00 1214.0
3 TraesCS6D01G386000 chr5D 95.833 216 9 0 595 810 123452886 123453101 1.670000e-92 350.0
4 TraesCS6D01G386000 chr7A 91.677 817 56 5 1 817 521493163 521492359 0.000000e+00 1122.0
5 TraesCS6D01G386000 chr7A 76.799 806 150 33 1 783 94434437 94435228 4.500000e-113 418.0
6 TraesCS6D01G386000 chr7A 94.712 208 11 0 595 802 521496083 521495876 1.010000e-84 324.0
7 TraesCS6D01G386000 chr6B 89.319 852 61 10 2093 2922 707128187 707129030 0.000000e+00 1042.0
8 TraesCS6D01G386000 chr6B 87.081 596 52 7 2345 2920 707116272 707116862 0.000000e+00 651.0
9 TraesCS6D01G386000 chr6B 88.889 414 42 3 1633 2043 707115778 707116190 9.340000e-140 507.0
10 TraesCS6D01G386000 chr6B 84.733 524 46 14 851 1353 707114853 707115363 7.270000e-136 494.0
11 TraesCS6D01G386000 chr6A 84.624 865 68 23 1602 2439 610308556 610307730 0.000000e+00 800.0
12 TraesCS6D01G386000 chr6A 86.111 576 37 20 992 1545 610309228 610308674 5.430000e-162 580.0
13 TraesCS6D01G386000 chr6A 84.884 344 50 2 1 343 555393911 555394253 2.160000e-91 346.0
14 TraesCS6D01G386000 chr6A 84.911 338 51 0 1 338 36724715 36725052 2.790000e-90 342.0
15 TraesCS6D01G386000 chr4B 85.588 340 48 1 1 339 30752430 30752769 3.580000e-94 355.0
16 TraesCS6D01G386000 chr4B 79.714 419 76 9 395 809 451796610 451797023 7.920000e-76 294.0
17 TraesCS6D01G386000 chrUn 84.257 343 54 0 1 343 132153478 132153136 4.670000e-88 335.0
18 TraesCS6D01G386000 chr4D 84.257 343 54 0 1 343 192255591 192255933 4.670000e-88 335.0
19 TraesCS6D01G386000 chr2B 83.965 343 55 0 1 343 3333603 3333945 2.170000e-86 329.0
20 TraesCS6D01G386000 chr2B 93.333 45 3 0 2261 2305 184593028 184592984 1.880000e-07 67.6


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 TraesCS6D01G386000 chr6D 463681679 463684600 2921 True 5397.000000 5397 100.0000 1 2922 1 chr6D.!!$R1 2921
1 TraesCS6D01G386000 chr5D 123457132 123457919 787 False 1214.000000 1214 94.1100 1 815 1 chr5D.!!$F2 814
2 TraesCS6D01G386000 chr7A 521492359 521496083 3724 True 723.000000 1122 93.1945 1 817 2 chr7A.!!$R1 816
3 TraesCS6D01G386000 chr7A 94434437 94435228 791 False 418.000000 418 76.7990 1 783 1 chr7A.!!$F1 782
4 TraesCS6D01G386000 chr6B 707128187 707129030 843 False 1042.000000 1042 89.3190 2093 2922 1 chr6B.!!$F1 829
5 TraesCS6D01G386000 chr6B 707114853 707116862 2009 False 550.666667 651 86.9010 851 2920 3 chr6B.!!$F2 2069
6 TraesCS6D01G386000 chr6A 610307730 610309228 1498 True 690.000000 800 85.3675 992 2439 2 chr6A.!!$R1 1447

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
868 3853 0.106819 CTCCTTGGCCATGCTAAGCT 60.107 55.0 6.09 0.0 44.01 3.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2078 5257 0.100325 CGACCACAAGCTGCAACAAA 59.9 50.0 1.02 0.0 0.0 2.83 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
35 2956 4.681978 GGGCGAGCTGGTTGTCGT 62.682 66.667 0.00 0.00 38.48 4.34
312 3233 2.186903 GTGGCGACGGATGTCCAT 59.813 61.111 0.00 0.00 42.37 3.41
501 3482 4.011517 GAGGGGAACGGCGTGGAA 62.012 66.667 15.70 0.00 0.00 3.53
616 3597 7.017254 ACCATGTTTAGAGAGAAGTTTAGGGAA 59.983 37.037 0.00 0.00 0.00 3.97
757 3742 2.548904 GGACTAGAGCACGATCGTGTAT 59.451 50.000 39.58 31.01 46.90 2.29
771 3756 6.094186 ACGATCGTGTATGCATGAGTCTATAT 59.906 38.462 22.06 0.00 43.11 0.86
856 3841 9.639601 GAAAATCAAAAGGTTTATACTCCTTGG 57.360 33.333 7.99 5.20 42.38 3.61
857 3842 6.775594 ATCAAAAGGTTTATACTCCTTGGC 57.224 37.500 7.99 0.00 42.38 4.52
858 3843 5.014202 TCAAAAGGTTTATACTCCTTGGCC 58.986 41.667 0.00 0.00 42.38 5.36
859 3844 4.668138 AAAGGTTTATACTCCTTGGCCA 57.332 40.909 0.00 0.00 42.38 5.36
860 3845 4.881157 AAGGTTTATACTCCTTGGCCAT 57.119 40.909 6.09 0.00 41.75 4.40
861 3846 4.170468 AGGTTTATACTCCTTGGCCATG 57.830 45.455 6.09 9.47 0.00 3.66
862 3847 2.623416 GGTTTATACTCCTTGGCCATGC 59.377 50.000 6.09 0.00 0.00 4.06
863 3848 3.555966 GTTTATACTCCTTGGCCATGCT 58.444 45.455 6.09 0.00 0.00 3.79
864 3849 4.445735 GGTTTATACTCCTTGGCCATGCTA 60.446 45.833 6.09 0.00 0.00 3.49
865 3850 5.130350 GTTTATACTCCTTGGCCATGCTAA 58.870 41.667 6.09 0.00 0.00 3.09
866 3851 3.498774 ATACTCCTTGGCCATGCTAAG 57.501 47.619 6.09 9.14 44.75 2.18
867 3852 0.394899 ACTCCTTGGCCATGCTAAGC 60.395 55.000 6.09 0.00 44.01 3.09
868 3853 0.106819 CTCCTTGGCCATGCTAAGCT 60.107 55.000 6.09 0.00 44.01 3.74
869 3854 0.107017 TCCTTGGCCATGCTAAGCTC 60.107 55.000 6.09 0.00 44.01 4.09
888 3873 1.160137 CAAAGCTAGCCAGTGTGACC 58.840 55.000 12.13 0.00 0.00 4.02
892 3877 1.964448 CTAGCCAGTGTGACCGACA 59.036 57.895 0.00 0.00 0.00 4.35
909 3894 0.746563 ACACGTGGGGCCGATAAATG 60.747 55.000 21.57 0.00 0.00 2.32
911 3896 1.525995 CGTGGGGCCGATAAATGCT 60.526 57.895 0.00 0.00 0.00 3.79
938 3923 3.382832 CCCGAGTCGAGCCCAGTT 61.383 66.667 15.64 0.00 0.00 3.16
939 3924 2.125912 CCGAGTCGAGCCCAGTTG 60.126 66.667 15.64 0.00 0.00 3.16
943 3928 0.109039 GAGTCGAGCCCAGTTGAGTC 60.109 60.000 0.00 0.00 0.00 3.36
946 3931 1.153939 CGAGCCCAGTTGAGTCGAG 60.154 63.158 0.00 0.00 32.32 4.04
977 3963 2.430367 GTTCTGGAACCCACCGCT 59.570 61.111 2.35 0.00 35.36 5.52
978 3964 1.671379 GTTCTGGAACCCACCGCTC 60.671 63.158 2.35 0.00 35.36 5.03
979 3965 2.890766 TTCTGGAACCCACCGCTCC 61.891 63.158 0.00 0.00 0.00 4.70
980 3966 3.636231 CTGGAACCCACCGCTCCA 61.636 66.667 0.00 0.00 36.89 3.86
981 3967 2.933287 TGGAACCCACCGCTCCAT 60.933 61.111 0.00 0.00 34.26 3.41
982 3968 2.355115 GGAACCCACCGCTCCATT 59.645 61.111 0.00 0.00 0.00 3.16
983 3969 1.749258 GGAACCCACCGCTCCATTC 60.749 63.158 0.00 0.00 0.00 2.67
986 3972 3.781307 CCCACCGCTCCATTCCGA 61.781 66.667 0.00 0.00 0.00 4.55
987 3973 2.202932 CCACCGCTCCATTCCGAG 60.203 66.667 0.00 0.00 0.00 4.63
998 3996 1.097547 CATTCCGAGCCCACCATCAC 61.098 60.000 0.00 0.00 0.00 3.06
1010 4008 1.683025 CCATCACCATGGCCAAGCA 60.683 57.895 10.96 0.00 43.55 3.91
1016 4014 2.103538 CATGGCCAAGCATCACGC 59.896 61.111 10.96 0.00 42.91 5.34
1197 4211 0.621571 CCTCCCTCCCTCAATCACCA 60.622 60.000 0.00 0.00 0.00 4.17
1230 4244 1.141053 TGATCGATGACCTCCTCGAGA 59.859 52.381 15.71 0.00 45.96 4.04
1278 4292 1.378778 AAGCTCCTCGCCTACGACT 60.379 57.895 0.00 0.00 45.12 4.18
1520 4613 0.454452 GGTTGAAATTCAGTCCGCGC 60.454 55.000 0.00 0.00 0.00 6.86
1542 4635 0.455815 GCGATTTTGGGCTCCGATTT 59.544 50.000 0.00 0.00 0.00 2.17
1545 4638 2.094752 CGATTTTGGGCTCCGATTTGTT 60.095 45.455 0.00 0.00 0.00 2.83
1546 4639 3.511699 GATTTTGGGCTCCGATTTGTTC 58.488 45.455 0.00 0.00 0.00 3.18
1561 4654 3.306917 TTGTTCGAATTCTAGTCCGCA 57.693 42.857 0.00 0.00 0.00 5.69
1563 4656 2.230508 TGTTCGAATTCTAGTCCGCACT 59.769 45.455 0.00 0.00 36.55 4.40
1565 4658 2.089201 TCGAATTCTAGTCCGCACTGA 58.911 47.619 3.52 0.00 33.62 3.41
1567 4660 2.186076 GAATTCTAGTCCGCACTGACG 58.814 52.381 0.00 0.00 40.26 4.35
1576 4669 3.657537 CGCACTGACGGAAAACATC 57.342 52.632 0.00 0.00 0.00 3.06
1577 4670 0.179250 CGCACTGACGGAAAACATCG 60.179 55.000 0.00 0.00 0.00 3.84
1579 4672 0.165944 CACTGACGGAAAACATCGGC 59.834 55.000 0.00 0.00 34.54 5.54
1580 4673 1.289109 ACTGACGGAAAACATCGGCG 61.289 55.000 0.00 0.00 37.18 6.46
1581 4674 2.097728 GACGGAAAACATCGGCGC 59.902 61.111 0.00 0.00 31.85 6.53
1582 4675 2.358247 ACGGAAAACATCGGCGCT 60.358 55.556 7.64 0.00 31.85 5.92
1584 4677 1.511887 CGGAAAACATCGGCGCTTG 60.512 57.895 7.64 4.93 0.00 4.01
1585 4678 1.579429 GGAAAACATCGGCGCTTGT 59.421 52.632 7.64 5.67 0.00 3.16
1587 4680 1.601914 GGAAAACATCGGCGCTTGTTT 60.602 47.619 24.98 24.98 45.39 2.83
1588 4681 2.217429 AAAACATCGGCGCTTGTTTT 57.783 40.000 30.26 30.26 46.04 2.43
1589 4682 1.766069 AAACATCGGCGCTTGTTTTC 58.234 45.000 24.98 0.08 41.90 2.29
1590 4683 0.039527 AACATCGGCGCTTGTTTTCC 60.040 50.000 18.18 0.00 32.28 3.13
1594 4687 1.207593 CGGCGCTTGTTTTCCTCTG 59.792 57.895 7.64 0.00 0.00 3.35
1596 4689 0.238553 GGCGCTTGTTTTCCTCTGTC 59.761 55.000 7.64 0.00 0.00 3.51
1597 4690 0.944386 GCGCTTGTTTTCCTCTGTCA 59.056 50.000 0.00 0.00 0.00 3.58
1599 4692 2.030805 GCGCTTGTTTTCCTCTGTCAAT 60.031 45.455 0.00 0.00 0.00 2.57
1604 4758 5.450412 GCTTGTTTTCCTCTGTCAATTGTCA 60.450 40.000 5.13 5.21 0.00 3.58
1849 5015 4.467084 TTCTCCGTGGCCGCCATC 62.467 66.667 16.96 8.57 35.28 3.51
1862 5028 4.907034 CCATCGACGTCGCCCTCG 62.907 72.222 32.19 17.02 39.60 4.63
1929 5095 2.801631 CCCCCACCTGATCGCTCTC 61.802 68.421 0.00 0.00 0.00 3.20
1972 5147 3.885901 GCCTCCTGTTTTTATCCTCATCC 59.114 47.826 0.00 0.00 0.00 3.51
1994 5169 6.649155 TCCATCAGTAGCTTGTTAATTAGCA 58.351 36.000 12.52 0.00 39.85 3.49
1996 5171 7.442364 TCCATCAGTAGCTTGTTAATTAGCATC 59.558 37.037 2.62 0.00 39.85 3.91
1997 5172 7.227314 CCATCAGTAGCTTGTTAATTAGCATCA 59.773 37.037 2.62 0.00 39.85 3.07
1999 5174 6.538742 TCAGTAGCTTGTTAATTAGCATCACC 59.461 38.462 2.62 0.00 39.85 4.02
2000 5175 6.316140 CAGTAGCTTGTTAATTAGCATCACCA 59.684 38.462 2.62 0.00 39.85 4.17
2001 5176 5.824904 AGCTTGTTAATTAGCATCACCAG 57.175 39.130 2.62 0.00 39.85 4.00
2002 5177 5.256474 AGCTTGTTAATTAGCATCACCAGT 58.744 37.500 2.62 0.00 39.85 4.00
2003 5178 6.414732 AGCTTGTTAATTAGCATCACCAGTA 58.585 36.000 2.62 0.00 39.85 2.74
2004 5179 6.540189 AGCTTGTTAATTAGCATCACCAGTAG 59.460 38.462 2.62 0.00 39.85 2.57
2005 5180 6.238484 GCTTGTTAATTAGCATCACCAGTAGG 60.238 42.308 2.62 0.00 37.35 3.18
2006 5181 8.544009 GCTTGTTAATTAGCATCACCAGTAGGT 61.544 40.741 2.62 0.00 42.26 3.08
2054 5233 8.507524 AATTACTGCACTTAAAAGGTAGATCC 57.492 34.615 0.00 0.00 0.00 3.36
2058 5237 5.357257 TGCACTTAAAAGGTAGATCCGATC 58.643 41.667 0.00 0.00 41.99 3.69
2066 5245 6.546428 AAAGGTAGATCCGATCAGAAAGAA 57.454 37.500 11.01 0.00 41.99 2.52
2068 5247 5.450453 AGGTAGATCCGATCAGAAAGAAGA 58.550 41.667 11.01 0.00 41.99 2.87
2078 5257 7.044798 CCGATCAGAAAGAAGAGGTAATTTCT 58.955 38.462 0.00 0.00 41.45 2.52
2086 5265 6.959639 AGAAGAGGTAATTTCTTTGTTGCA 57.040 33.333 0.00 0.00 35.14 4.08
2087 5266 6.974965 AGAAGAGGTAATTTCTTTGTTGCAG 58.025 36.000 0.00 0.00 35.14 4.41
2089 5268 4.829492 AGAGGTAATTTCTTTGTTGCAGCT 59.171 37.500 1.17 0.00 0.00 4.24
2091 5270 5.291971 AGGTAATTTCTTTGTTGCAGCTTG 58.708 37.500 1.17 0.00 0.00 4.01
2092 5271 5.049828 GGTAATTTCTTTGTTGCAGCTTGT 58.950 37.500 1.17 0.00 0.00 3.16
2093 5272 5.050837 GGTAATTTCTTTGTTGCAGCTTGTG 60.051 40.000 1.17 0.00 0.00 3.33
2096 5275 1.405105 TCTTTGTTGCAGCTTGTGGTC 59.595 47.619 1.17 0.00 0.00 4.02
2098 5277 2.050985 GTTGCAGCTTGTGGTCGC 60.051 61.111 0.00 0.00 0.00 5.19
2099 5278 2.203195 TTGCAGCTTGTGGTCGCT 60.203 55.556 0.00 0.00 36.83 4.93
2100 5279 1.070615 TTGCAGCTTGTGGTCGCTA 59.929 52.632 0.00 0.00 34.58 4.26
2101 5280 1.227999 TTGCAGCTTGTGGTCGCTAC 61.228 55.000 0.00 0.00 34.58 3.58
2102 5281 1.667830 GCAGCTTGTGGTCGCTACA 60.668 57.895 0.00 0.00 34.58 2.74
2103 5282 1.021390 GCAGCTTGTGGTCGCTACAT 61.021 55.000 0.00 0.00 34.58 2.29
2159 5340 6.686630 TGGTATTGCTTCAACGATCATTTTT 58.313 32.000 0.00 0.00 0.00 1.94
2243 5447 3.000082 GCAATAAGCGGCAATCTTACC 58.000 47.619 1.45 0.00 0.00 2.85
2252 5456 3.790789 GCGGCAATCTTACCAAAATACCG 60.791 47.826 0.00 0.00 39.84 4.02
2288 5493 2.795224 GGCTATGGCAAATAGCGACGG 61.795 57.143 18.93 0.00 45.83 4.79
2365 5571 2.693591 TCTATCGGATCTGTGTTGGGTC 59.306 50.000 0.42 0.00 0.00 4.46
2402 5608 4.561105 CCTTGAAGGTAGAAGACACACTC 58.439 47.826 2.25 0.00 0.00 3.51
2431 5637 6.549433 AATTCAGATGCAAACCCATAATGT 57.451 33.333 0.00 0.00 0.00 2.71
2478 5684 7.066142 ACCACCATTAGGCATTATTCATGTTA 58.934 34.615 0.00 0.00 39.06 2.41
2607 5813 5.232202 ACTTACAATATCGCGTTCACATGAG 59.768 40.000 5.77 0.00 0.00 2.90
2645 5851 0.754957 CAAAGTTCAGTGGGGTGCCA 60.755 55.000 0.00 0.00 0.00 4.92
2660 5866 6.761242 GTGGGGTGCCAAAATTATTTAATCTC 59.239 38.462 0.00 0.00 0.00 2.75
2800 6026 1.139058 CCTCCCCCGTCAACTTCATAG 59.861 57.143 0.00 0.00 0.00 2.23
2839 6065 1.993370 GTAGTAGCGCCACTTGAACAG 59.007 52.381 15.04 0.00 0.00 3.16
2866 6092 0.109342 GGCCACTGATACCCTCCATG 59.891 60.000 0.00 0.00 0.00 3.66
2902 6128 1.539065 CGCTGAAGGCCATCGTATCTT 60.539 52.381 5.01 0.00 37.74 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 2956 3.556625 CGTCGACGGCATTTTCCA 58.443 55.556 29.70 0.00 35.37 3.53
64 2985 4.702081 GACGACACCGCGCTCACT 62.702 66.667 5.56 0.00 39.95 3.41
616 3597 5.789643 ATAAATCAGTGTGGTGTGCTTTT 57.210 34.783 0.00 0.00 0.00 2.27
684 3668 2.124151 GCGGCACCCCATGATCTT 60.124 61.111 0.00 0.00 0.00 2.40
757 3742 5.249420 ACGCTCTCTATATAGACTCATGCA 58.751 41.667 8.44 0.00 0.00 3.96
771 3756 1.699656 GCCGACGTGTACGCTCTCTA 61.700 60.000 4.67 0.00 44.43 2.43
830 3815 9.639601 CCAAGGAGTATAAACCTTTTGATTTTC 57.360 33.333 8.44 0.00 43.54 2.29
831 3816 8.094548 GCCAAGGAGTATAAACCTTTTGATTTT 58.905 33.333 8.44 0.00 43.54 1.82
832 3817 7.310423 GGCCAAGGAGTATAAACCTTTTGATTT 60.310 37.037 0.00 0.00 43.54 2.17
833 3818 6.154534 GGCCAAGGAGTATAAACCTTTTGATT 59.845 38.462 0.00 0.00 43.54 2.57
834 3819 5.656859 GGCCAAGGAGTATAAACCTTTTGAT 59.343 40.000 0.00 0.00 43.54 2.57
835 3820 5.014202 GGCCAAGGAGTATAAACCTTTTGA 58.986 41.667 0.00 0.00 43.54 2.69
836 3821 4.770010 TGGCCAAGGAGTATAAACCTTTTG 59.230 41.667 0.61 5.54 43.54 2.44
837 3822 5.005628 TGGCCAAGGAGTATAAACCTTTT 57.994 39.130 0.61 0.00 43.54 2.27
838 3823 4.668138 TGGCCAAGGAGTATAAACCTTT 57.332 40.909 0.61 0.00 43.54 3.11
839 3824 4.536765 CATGGCCAAGGAGTATAAACCTT 58.463 43.478 10.96 6.04 45.87 3.50
840 3825 3.688414 GCATGGCCAAGGAGTATAAACCT 60.688 47.826 10.96 0.00 38.23 3.50
841 3826 2.623416 GCATGGCCAAGGAGTATAAACC 59.377 50.000 10.96 0.00 0.00 3.27
842 3827 3.555966 AGCATGGCCAAGGAGTATAAAC 58.444 45.455 10.96 0.00 0.00 2.01
843 3828 3.951563 AGCATGGCCAAGGAGTATAAA 57.048 42.857 10.96 0.00 0.00 1.40
844 3829 4.746702 GCTTAGCATGGCCAAGGAGTATAA 60.747 45.833 10.96 1.75 0.00 0.98
845 3830 3.244561 GCTTAGCATGGCCAAGGAGTATA 60.245 47.826 10.96 0.00 0.00 1.47
846 3831 2.487986 GCTTAGCATGGCCAAGGAGTAT 60.488 50.000 10.96 0.00 0.00 2.12
847 3832 1.134098 GCTTAGCATGGCCAAGGAGTA 60.134 52.381 10.96 0.00 0.00 2.59
848 3833 0.394899 GCTTAGCATGGCCAAGGAGT 60.395 55.000 10.96 0.00 0.00 3.85
849 3834 0.106819 AGCTTAGCATGGCCAAGGAG 60.107 55.000 10.96 5.01 0.00 3.69
850 3835 0.107017 GAGCTTAGCATGGCCAAGGA 60.107 55.000 10.96 0.00 0.00 3.36
851 3836 0.394762 TGAGCTTAGCATGGCCAAGG 60.395 55.000 10.96 6.44 0.00 3.61
852 3837 1.466856 TTGAGCTTAGCATGGCCAAG 58.533 50.000 10.96 6.55 0.00 3.61
853 3838 1.820519 CTTTGAGCTTAGCATGGCCAA 59.179 47.619 10.96 0.00 0.00 4.52
854 3839 1.466856 CTTTGAGCTTAGCATGGCCA 58.533 50.000 8.56 8.56 0.00 5.36
855 3840 0.101939 GCTTTGAGCTTAGCATGGCC 59.898 55.000 7.07 0.00 38.45 5.36
856 3841 3.637297 GCTTTGAGCTTAGCATGGC 57.363 52.632 7.07 0.00 38.45 4.40
866 3851 0.801251 CACACTGGCTAGCTTTGAGC 59.199 55.000 15.72 0.00 42.84 4.26
867 3852 2.072298 GTCACACTGGCTAGCTTTGAG 58.928 52.381 15.72 8.21 0.00 3.02
868 3853 1.270839 GGTCACACTGGCTAGCTTTGA 60.271 52.381 15.72 7.35 0.00 2.69
869 3854 1.160137 GGTCACACTGGCTAGCTTTG 58.840 55.000 15.72 11.48 0.00 2.77
875 3860 4.184439 TGTCGGTCACACTGGCTA 57.816 55.556 0.00 0.00 28.59 3.93
882 3867 3.918977 CCCCACGTGTCGGTCACA 61.919 66.667 15.65 0.00 46.44 3.58
888 3873 2.839043 TTTATCGGCCCCACGTGTCG 62.839 60.000 15.65 12.39 34.94 4.35
892 3877 1.822186 GCATTTATCGGCCCCACGT 60.822 57.895 0.00 0.00 34.94 4.49
893 3878 1.507141 GAGCATTTATCGGCCCCACG 61.507 60.000 0.00 0.00 0.00 4.94
925 3910 1.867919 CGACTCAACTGGGCTCGACT 61.868 60.000 0.00 0.00 0.00 4.18
931 3916 0.172352 CTCTCTCGACTCAACTGGGC 59.828 60.000 0.00 0.00 0.00 5.36
938 3923 2.049185 GGCTGGCTCTCTCGACTCA 61.049 63.158 0.00 0.00 0.00 3.41
939 3924 2.781158 GGGCTGGCTCTCTCGACTC 61.781 68.421 0.00 0.00 0.00 3.36
943 3928 3.847602 CCTGGGCTGGCTCTCTCG 61.848 72.222 0.00 0.00 0.00 4.04
946 3931 2.270527 GAACCTGGGCTGGCTCTC 59.729 66.667 0.00 0.00 0.00 3.20
977 3963 1.983119 GATGGTGGGCTCGGAATGGA 61.983 60.000 0.00 0.00 0.00 3.41
978 3964 1.526917 GATGGTGGGCTCGGAATGG 60.527 63.158 0.00 0.00 0.00 3.16
979 3965 1.097547 GTGATGGTGGGCTCGGAATG 61.098 60.000 0.00 0.00 0.00 2.67
980 3966 1.224592 GTGATGGTGGGCTCGGAAT 59.775 57.895 0.00 0.00 0.00 3.01
981 3967 2.668632 GTGATGGTGGGCTCGGAA 59.331 61.111 0.00 0.00 0.00 4.30
982 3968 3.399181 GGTGATGGTGGGCTCGGA 61.399 66.667 0.00 0.00 0.00 4.55
983 3969 3.047807 ATGGTGATGGTGGGCTCGG 62.048 63.158 0.00 0.00 0.00 4.63
986 3972 2.685366 CCATGGTGATGGTGGGCT 59.315 61.111 2.57 0.00 43.98 5.19
998 3996 2.802792 CGTGATGCTTGGCCATGG 59.197 61.111 19.47 7.63 0.00 3.66
1135 4142 4.521062 CTTGGCGAGGGAGGCGAG 62.521 72.222 0.00 0.00 40.98 5.03
1230 4244 2.659610 GTGAGCAGCGGGAAGAGT 59.340 61.111 0.00 0.00 0.00 3.24
1269 4283 1.012889 CGTCGTCGTAGTCGTAGGC 60.013 63.158 0.00 0.00 40.43 3.93
1374 4466 4.083862 GACGGTGGTGGAGGAGGC 62.084 72.222 0.00 0.00 0.00 4.70
1520 4613 3.518068 GGAGCCCAAAATCGCGGG 61.518 66.667 6.13 0.00 46.15 6.13
1542 4635 2.230508 AGTGCGGACTAGAATTCGAACA 59.769 45.455 8.23 0.00 33.91 3.18
1545 4638 2.089201 TCAGTGCGGACTAGAATTCGA 58.911 47.619 10.03 0.00 0.00 3.71
1546 4639 2.186076 GTCAGTGCGGACTAGAATTCG 58.814 52.381 10.03 0.00 34.92 3.34
1559 4652 0.165944 CCGATGTTTTCCGTCAGTGC 59.834 55.000 0.00 0.00 0.00 4.40
1561 4654 1.289109 CGCCGATGTTTTCCGTCAGT 61.289 55.000 0.00 0.00 0.00 3.41
1563 4656 2.673114 GCGCCGATGTTTTCCGTCA 61.673 57.895 0.00 0.00 0.00 4.35
1565 4658 1.964373 AAGCGCCGATGTTTTCCGT 60.964 52.632 2.29 0.00 0.00 4.69
1567 4660 0.039527 AACAAGCGCCGATGTTTTCC 60.040 50.000 15.55 0.00 36.39 3.13
1568 4661 1.766069 AAACAAGCGCCGATGTTTTC 58.234 45.000 23.05 0.00 44.91 2.29
1569 4662 3.957383 AAACAAGCGCCGATGTTTT 57.043 42.105 23.05 12.43 44.91 2.43
1571 4664 0.039527 GGAAAACAAGCGCCGATGTT 60.040 50.000 15.55 15.55 41.31 2.71
1572 4665 0.889186 AGGAAAACAAGCGCCGATGT 60.889 50.000 2.29 4.21 0.00 3.06
1573 4666 0.179189 GAGGAAAACAAGCGCCGATG 60.179 55.000 2.29 3.43 0.00 3.84
1574 4667 0.321653 AGAGGAAAACAAGCGCCGAT 60.322 50.000 2.29 0.00 0.00 4.18
1576 4669 1.207593 CAGAGGAAAACAAGCGCCG 59.792 57.895 2.29 0.00 0.00 6.46
1577 4670 0.238553 GACAGAGGAAAACAAGCGCC 59.761 55.000 2.29 0.00 0.00 6.53
1579 4672 3.904136 ATTGACAGAGGAAAACAAGCG 57.096 42.857 0.00 0.00 0.00 4.68
1580 4673 4.936891 ACAATTGACAGAGGAAAACAAGC 58.063 39.130 13.59 0.00 0.00 4.01
1581 4674 6.135290 TGACAATTGACAGAGGAAAACAAG 57.865 37.500 13.59 0.00 0.00 3.16
1582 4675 6.506147 CATGACAATTGACAGAGGAAAACAA 58.494 36.000 13.59 0.00 0.00 2.83
1584 4677 4.919754 GCATGACAATTGACAGAGGAAAAC 59.080 41.667 13.59 0.00 0.00 2.43
1585 4678 4.583907 TGCATGACAATTGACAGAGGAAAA 59.416 37.500 13.59 0.00 0.00 2.29
1587 4680 3.753815 TGCATGACAATTGACAGAGGAA 58.246 40.909 13.59 0.00 0.00 3.36
1588 4681 3.340928 CTGCATGACAATTGACAGAGGA 58.659 45.455 13.59 9.43 0.00 3.71
1589 4682 2.422479 CCTGCATGACAATTGACAGAGG 59.578 50.000 13.59 14.16 0.00 3.69
1590 4683 3.079578 ACCTGCATGACAATTGACAGAG 58.920 45.455 13.59 10.21 0.00 3.35
1594 4687 1.466360 GCGACCTGCATGACAATTGAC 60.466 52.381 13.59 6.72 45.45 3.18
1596 4689 3.317608 GCGACCTGCATGACAATTG 57.682 52.632 3.24 3.24 45.45 2.32
1972 5147 8.066595 GTGATGCTAATTAACAAGCTACTGATG 58.933 37.037 11.11 0.00 39.53 3.07
1999 5174 4.100529 CACCACGACGTAATAACCTACTG 58.899 47.826 0.00 0.00 0.00 2.74
2000 5175 4.009675 TCACCACGACGTAATAACCTACT 58.990 43.478 0.00 0.00 0.00 2.57
2001 5176 4.355543 TCACCACGACGTAATAACCTAC 57.644 45.455 0.00 0.00 0.00 3.18
2002 5177 5.581126 AATCACCACGACGTAATAACCTA 57.419 39.130 0.00 0.00 0.00 3.08
2003 5178 4.460948 AATCACCACGACGTAATAACCT 57.539 40.909 0.00 0.00 0.00 3.50
2004 5179 6.833342 ATTAATCACCACGACGTAATAACC 57.167 37.500 0.00 0.00 0.00 2.85
2044 5221 5.894393 TCTTCTTTCTGATCGGATCTACCTT 59.106 40.000 18.16 0.00 36.31 3.50
2054 5233 8.485976 AAGAAATTACCTCTTCTTTCTGATCG 57.514 34.615 0.00 0.00 38.45 3.69
2058 5237 9.455847 CAACAAAGAAATTACCTCTTCTTTCTG 57.544 33.333 6.79 4.86 44.65 3.02
2066 5245 4.829492 AGCTGCAACAAAGAAATTACCTCT 59.171 37.500 1.02 0.00 0.00 3.69
2068 5247 5.163416 ACAAGCTGCAACAAAGAAATTACCT 60.163 36.000 1.02 0.00 0.00 3.08
2078 5257 0.100325 CGACCACAAGCTGCAACAAA 59.900 50.000 1.02 0.00 0.00 2.83
2084 5263 1.021390 ATGTAGCGACCACAAGCTGC 61.021 55.000 0.00 0.00 44.32 5.25
2086 5265 2.185004 AAATGTAGCGACCACAAGCT 57.815 45.000 0.00 0.00 46.53 3.74
2087 5266 2.225491 TGAAAATGTAGCGACCACAAGC 59.775 45.455 0.00 0.00 0.00 4.01
2089 5268 2.550606 GGTGAAAATGTAGCGACCACAA 59.449 45.455 0.00 0.00 0.00 3.33
2091 5270 2.147958 TGGTGAAAATGTAGCGACCAC 58.852 47.619 0.00 0.00 0.00 4.16
2092 5271 2.552599 TGGTGAAAATGTAGCGACCA 57.447 45.000 0.00 0.00 0.00 4.02
2093 5272 4.083003 TGAAATGGTGAAAATGTAGCGACC 60.083 41.667 0.00 0.00 0.00 4.79
2096 5275 5.046910 ACTGAAATGGTGAAAATGTAGCG 57.953 39.130 0.00 0.00 0.00 4.26
2103 5282 9.691362 GCTAATTCTTAACTGAAATGGTGAAAA 57.309 29.630 0.00 0.00 0.00 2.29
2159 5340 4.394729 AGTTCTTTCGGGCTGTTATTCAA 58.605 39.130 0.00 0.00 0.00 2.69
2161 5342 3.374367 GGAGTTCTTTCGGGCTGTTATTC 59.626 47.826 0.00 0.00 0.00 1.75
2163 5346 2.304761 TGGAGTTCTTTCGGGCTGTTAT 59.695 45.455 0.00 0.00 0.00 1.89
2243 5447 9.337091 CCCGCTATTTTAATTATCGGTATTTTG 57.663 33.333 7.89 0.00 34.16 2.44
2252 5456 6.094881 TGCCATAGCCCGCTATTTTAATTATC 59.905 38.462 6.48 0.00 37.16 1.75
2288 5493 2.851008 GCATTTAGCTGATTTCGACGGC 60.851 50.000 0.00 0.00 41.15 5.68
2312 5517 3.490419 GCCACTCTAGTATTGTACCACGG 60.490 52.174 0.00 0.00 0.00 4.94
2365 5571 0.179073 CAAGGGATACACGGAGCCAG 60.179 60.000 0.00 0.00 39.74 4.85
2402 5608 4.155826 TGGGTTTGCATCTGAATTTAGACG 59.844 41.667 1.44 0.00 0.00 4.18
2431 5637 1.467920 TGTGTGTCATTTGTGGTGCA 58.532 45.000 0.00 0.00 0.00 4.57
2478 5684 3.964031 TGCGGGGGCTTATCATTTTTATT 59.036 39.130 0.00 0.00 0.00 1.40
2512 5718 5.009010 CAGTGCTATGGACTTGTCACTTTTT 59.991 40.000 3.08 0.00 33.08 1.94
2513 5719 4.516698 CAGTGCTATGGACTTGTCACTTTT 59.483 41.667 3.08 0.00 33.08 2.27
2514 5720 4.067896 CAGTGCTATGGACTTGTCACTTT 58.932 43.478 3.08 0.00 33.08 2.66
2517 5723 2.289694 ACCAGTGCTATGGACTTGTCAC 60.290 50.000 13.83 0.00 43.57 3.67
2691 5917 7.413438 GGCGGATTAGTAAAGAAGATATGCATG 60.413 40.741 10.16 0.00 0.00 4.06
2710 5936 0.765510 GAAGATAGGGTGGGCGGATT 59.234 55.000 0.00 0.00 0.00 3.01
2749 5975 1.060698 GCCTCGATCGCTAACAACAAC 59.939 52.381 11.09 0.00 0.00 3.32
2818 6044 1.337447 TGTTCAAGTGGCGCTACTACC 60.337 52.381 27.48 14.67 0.00 3.18
2893 6119 5.106869 GCGTAGAGTGAGATCAAGATACGAT 60.107 44.000 18.44 0.00 35.98 3.73
2902 6128 1.834188 TGTGGCGTAGAGTGAGATCA 58.166 50.000 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.