Multiple sequence alignment - TraesCS5A01G185900

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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 TraesCS5A01G185900 chr5A 100.000 4453 0 0 1 4453 386174850 386170398 0.000000e+00 8224.0
1 TraesCS5A01G185900 chr5A 100.000 76 0 0 4717 4792 386170134 386170059 1.800000e-29 141.0
2 TraesCS5A01G185900 chr5A 94.444 72 3 1 4722 4792 285358234 285358163 5.070000e-20 110.0
3 TraesCS5A01G185900 chr5D 96.516 2641 73 9 3 2633 293368575 293365944 0.000000e+00 4349.0
4 TraesCS5A01G185900 chr5D 95.641 1583 47 10 2632 4207 293365784 293364217 0.000000e+00 2521.0
5 TraesCS5A01G185900 chr5D 92.369 249 13 2 4207 4449 293204187 293203939 2.740000e-92 350.0
6 TraesCS5A01G185900 chr5D 95.890 73 2 1 4717 4788 353793918 353793846 3.030000e-22 117.0
7 TraesCS5A01G185900 chr5B 95.839 2235 72 8 464 2686 334787337 334785112 0.000000e+00 3592.0
8 TraesCS5A01G185900 chr5B 95.798 1523 46 8 2688 4207 334784948 334783441 0.000000e+00 2442.0
9 TraesCS5A01G185900 chr5B 88.312 462 34 9 3 449 334788151 334787695 1.960000e-148 536.0
10 TraesCS5A01G185900 chr5B 92.276 246 16 1 4207 4449 334781007 334780762 3.550000e-91 346.0
11 TraesCS5A01G185900 chr3A 94.805 77 3 1 4717 4792 12707997 12708073 8.420000e-23 119.0
12 TraesCS5A01G185900 chr3A 94.340 53 3 0 1238 1290 700753276 700753328 1.110000e-11 82.4
13 TraesCS5A01G185900 chr4D 94.737 76 3 1 4718 4792 72249171 72249096 3.030000e-22 117.0
14 TraesCS5A01G185900 chr7A 95.833 72 2 1 4722 4792 576235971 576235900 1.090000e-21 115.0
15 TraesCS5A01G185900 chr7D 74.308 253 55 9 3159 3405 602748706 602748458 1.100000e-16 99.0
16 TraesCS5A01G185900 chr2D 83.158 95 16 0 3191 3285 9626455 9626361 2.380000e-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 TraesCS5A01G185900 chr5A 386170059 386174850 4791 True 4182.5 8224 100.00000 1 4792 2 chr5A.!!$R2 4791
1 TraesCS5A01G185900 chr5D 293364217 293368575 4358 True 3435.0 4349 96.07850 3 4207 2 chr5D.!!$R3 4204
2 TraesCS5A01G185900 chr5B 334780762 334788151 7389 True 1729.0 3592 93.05625 3 4449 4 chr5B.!!$R1 4446

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
635 996 0.250124 AGCGAACGTTTGTCCATGGA 60.250 50.000 11.44 11.44 0.00 3.41 F
1496 1859 0.951040 GACACCTTCAGGAACCTGCG 60.951 60.000 15.20 8.94 43.31 5.18 F
1557 1920 1.600013 TCCATTGTTTCGGTTGTGTCG 59.400 47.619 0.00 0.00 0.00 4.35 F
3380 4080 1.448540 GAGCACTGGGTCGGATGTG 60.449 63.158 0.00 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1696 2059 0.835941 ACCTCCTCTGGCAAGCATAG 59.164 55.0 0.00 0.0 0.00 2.23 R
3380 4080 1.146358 GGACGATGCCGAAGCTGTAC 61.146 60.0 0.00 0.0 40.80 2.90 R
3529 4229 0.463204 CTCGTCCATCTCAGCACCAT 59.537 55.0 0.00 0.0 0.00 3.55 R
4736 7875 0.036448 AGGAGGACGTCTTCTCGTGA 59.964 55.0 24.68 0.0 44.21 4.35 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
152 153 1.153647 CGTCGCTGATTGCCAGGTA 60.154 57.895 0.00 0.00 43.13 3.08
237 239 1.550869 CCAAGTGCTGGGGGATTTCTT 60.551 52.381 0.00 0.00 42.17 2.52
451 464 6.908825 TCGAGAAATTGTTTCATGTTAAGGG 58.091 36.000 5.36 0.00 42.10 3.95
487 843 6.037786 TGGGTGTAAATGTAGTCTGAAGAG 57.962 41.667 0.00 0.00 0.00 2.85
490 846 6.981559 GGGTGTAAATGTAGTCTGAAGAGATC 59.018 42.308 0.00 0.00 0.00 2.75
569 930 6.596497 TCTTTATAAGGCGTCGGAAAATTCTT 59.404 34.615 0.00 0.00 0.00 2.52
605 966 6.148645 AGGTTTTAACAAAAGTTGGTTGCAAG 59.851 34.615 0.00 0.00 34.12 4.01
635 996 0.250124 AGCGAACGTTTGTCCATGGA 60.250 50.000 11.44 11.44 0.00 3.41
682 1043 3.279434 GAAGTACTCCCAAATGGCGAAT 58.721 45.455 0.00 0.00 0.00 3.34
751 1113 7.763172 TTGTTTGTAGTTTTTGTATGGCTTG 57.237 32.000 0.00 0.00 0.00 4.01
776 1138 2.202440 GCTCAGCTGCATTGCACG 60.202 61.111 9.47 5.54 33.79 5.34
783 1145 1.651240 GCTGCATTGCACGATCAGGT 61.651 55.000 7.38 0.00 33.79 4.00
791 1153 5.465390 GCATTGCACGATCAGGTTATTAGTA 59.535 40.000 3.15 0.00 0.00 1.82
792 1154 6.147821 GCATTGCACGATCAGGTTATTAGTAT 59.852 38.462 3.15 0.00 0.00 2.12
793 1155 7.307989 GCATTGCACGATCAGGTTATTAGTATT 60.308 37.037 3.15 0.00 0.00 1.89
794 1156 9.203421 CATTGCACGATCAGGTTATTAGTATTA 57.797 33.333 0.00 0.00 0.00 0.98
795 1157 8.583810 TTGCACGATCAGGTTATTAGTATTAC 57.416 34.615 0.00 0.00 0.00 1.89
796 1158 7.948357 TGCACGATCAGGTTATTAGTATTACT 58.052 34.615 1.30 1.30 0.00 2.24
842 1204 1.856629 CCAAATGGACCAGCTGGAAT 58.143 50.000 39.19 24.18 38.94 3.01
931 1294 2.497138 GGCTCCATTGCAAAAGCTTTT 58.503 42.857 18.74 18.74 35.12 2.27
1059 1422 4.985538 TCTGCTCCTTACTGTTTTCCATT 58.014 39.130 0.00 0.00 0.00 3.16
1091 1454 2.451490 TGCTACCTCACTCTCCTTCAG 58.549 52.381 0.00 0.00 0.00 3.02
1152 1515 1.526917 GGATATTGCCTGCGCTGGT 60.527 57.895 30.72 16.30 35.36 4.00
1327 1690 1.074084 TCCAAATTAGGCCGGTCAACA 59.926 47.619 9.71 0.00 0.00 3.33
1410 1773 1.072965 GGGAGCTATGGTGGGAATCTG 59.927 57.143 0.00 0.00 0.00 2.90
1428 1791 1.547372 CTGGGACTTTTCAATGGCAGG 59.453 52.381 0.00 0.00 0.00 4.85
1496 1859 0.951040 GACACCTTCAGGAACCTGCG 60.951 60.000 15.20 8.94 43.31 5.18
1557 1920 1.600013 TCCATTGTTTCGGTTGTGTCG 59.400 47.619 0.00 0.00 0.00 4.35
1674 2037 5.925506 TCAGTGAAACCTCATACCGAATA 57.074 39.130 0.00 0.00 37.80 1.75
1812 2175 2.753452 CCTAGCAGGTAAGAGTTCGTCA 59.247 50.000 0.00 0.00 0.00 4.35
1878 2250 4.347000 TCACAAGGAAAAGTACAGGCTACT 59.653 41.667 0.00 0.00 0.00 2.57
1953 2325 1.986378 CTTCTACGGAAGCAACGAGTG 59.014 52.381 0.00 0.00 41.80 3.51
1986 2358 2.698855 ATCAAACCTCCGATGGTGAG 57.301 50.000 0.19 0.00 40.73 3.51
2181 2553 4.193826 TGTTGCGATAAAGAAGCTCTCT 57.806 40.909 0.00 0.00 35.13 3.10
2408 2780 5.569355 TGAGGAATTATCTGGTTTCTTGCA 58.431 37.500 0.00 0.00 0.00 4.08
2419 2791 7.765695 TCTGGTTTCTTGCAGAATTTCTTAT 57.234 32.000 0.00 0.00 33.67 1.73
2702 3397 4.861210 ACATAACAGATAGCACTCTACGC 58.139 43.478 0.00 0.00 0.00 4.42
2716 3411 2.229302 CTCTACGCCTCTACCTATTGGC 59.771 54.545 0.00 0.00 41.76 4.52
2754 3449 4.946157 ACCATTTGCCAACAACAATTTTCA 59.054 33.333 0.00 0.00 34.87 2.69
2763 3458 4.961438 ACAACAATTTTCATCCCAAGCT 57.039 36.364 0.00 0.00 0.00 3.74
2764 3459 6.222389 CAACAACAATTTTCATCCCAAGCTA 58.778 36.000 0.00 0.00 0.00 3.32
2946 3643 1.831580 AAGCTACGACGGTAAGGACT 58.168 50.000 0.00 0.00 0.00 3.85
2973 3670 8.621286 CATTAGTCCATTACCAACAATTACTCC 58.379 37.037 0.00 0.00 0.00 3.85
3065 3765 8.699749 GCTTATTTTCAGGTCAACATTGTAAAC 58.300 33.333 0.00 0.00 0.00 2.01
3068 3768 7.639113 TTTTCAGGTCAACATTGTAAACTCT 57.361 32.000 0.00 0.00 0.00 3.24
3228 3928 4.961622 GCAACATCATGCTCGACG 57.038 55.556 0.00 0.00 43.06 5.12
3380 4080 1.448540 GAGCACTGGGTCGGATGTG 60.449 63.158 0.00 0.00 0.00 3.21
3422 4122 4.394712 GAGGTGGTGTCTGGCCGG 62.395 72.222 4.71 4.71 0.00 6.13
3529 4229 1.633774 GTGGACAAGAGACTGAGGGA 58.366 55.000 0.00 0.00 0.00 4.20
3535 4235 0.908198 AAGAGACTGAGGGATGGTGC 59.092 55.000 0.00 0.00 0.00 5.01
3712 4412 1.251251 GAGCCTGTTCTTGCCATGTT 58.749 50.000 0.00 0.00 0.00 2.71
3713 4413 0.963962 AGCCTGTTCTTGCCATGTTG 59.036 50.000 0.00 0.00 0.00 3.33
3714 4414 0.037975 GCCTGTTCTTGCCATGTTGG 60.038 55.000 0.00 0.00 41.55 3.77
3715 4415 1.619654 CCTGTTCTTGCCATGTTGGA 58.380 50.000 0.00 0.00 40.96 3.53
3716 4416 1.270550 CCTGTTCTTGCCATGTTGGAC 59.729 52.381 0.00 0.00 40.96 4.02
3717 4417 2.233271 CTGTTCTTGCCATGTTGGACT 58.767 47.619 0.00 0.00 40.96 3.85
3718 4418 2.624838 CTGTTCTTGCCATGTTGGACTT 59.375 45.455 0.00 0.00 40.96 3.01
3789 4489 1.816835 CTGCAGTTGGTTCTGATGCAT 59.183 47.619 5.25 0.00 45.08 3.96
3811 4511 2.736347 ACCGAGTAACTGATGCTACCT 58.264 47.619 0.00 0.00 0.00 3.08
3822 4522 1.341156 ATGCTACCTCCAGACTGGGC 61.341 60.000 21.56 16.01 38.32 5.36
3952 4652 5.357878 TGATTGAATTCACATAGCTTCCCAC 59.642 40.000 7.89 0.00 0.00 4.61
4018 4718 7.972832 ATGTGACTAGAATGTTTTCCGTTTA 57.027 32.000 0.00 0.00 31.84 2.01
4021 4721 7.041644 TGTGACTAGAATGTTTTCCGTTTAAGG 60.042 37.037 0.00 0.00 31.84 2.69
4033 4733 1.839424 GTTTAAGGCTGCAGGATGGT 58.161 50.000 17.12 0.00 35.86 3.55
4109 4811 8.103305 TCAGAGTCAAGCTAGGTTGAAATAATT 58.897 33.333 32.72 17.02 38.17 1.40
4226 7362 8.067751 TCTAGACTAAGATTACTGCATGTTGT 57.932 34.615 0.00 0.00 0.00 3.32
4267 7406 8.135529 GCTCTACTCTCTCCTCTTCTTTTAATC 58.864 40.741 0.00 0.00 0.00 1.75
4275 7414 8.758633 TCTCCTCTTCTTTTAATCTGTAAACG 57.241 34.615 0.00 0.00 0.00 3.60
4287 7426 9.846248 TTTAATCTGTAAACGTTACTCCTACTC 57.154 33.333 0.00 0.00 0.00 2.59
4315 7454 4.100479 CAGTGGCCCTGCATTTCA 57.900 55.556 0.00 0.00 33.59 2.69
4444 7583 9.517609 TCTTCAGTTAGATATTTCTCTTAACGC 57.482 33.333 0.00 0.00 33.17 4.84
4449 7588 4.683832 AGATATTTCTCTTAACGCGCACT 58.316 39.130 5.73 0.00 0.00 4.40
4450 7589 5.109903 AGATATTTCTCTTAACGCGCACTT 58.890 37.500 5.73 0.00 0.00 3.16
4451 7590 5.581085 AGATATTTCTCTTAACGCGCACTTT 59.419 36.000 5.73 0.00 0.00 2.66
4452 7591 3.955771 TTTCTCTTAACGCGCACTTTT 57.044 38.095 5.73 0.00 0.00 2.27
4735 7874 0.938713 CGTGTAGAGAGGTAGGAGCG 59.061 60.000 0.00 0.00 0.00 5.03
4736 7875 1.743091 CGTGTAGAGAGGTAGGAGCGT 60.743 57.143 0.00 0.00 0.00 5.07
4737 7876 1.941975 GTGTAGAGAGGTAGGAGCGTC 59.058 57.143 0.00 0.00 0.00 5.19
4738 7877 1.558294 TGTAGAGAGGTAGGAGCGTCA 59.442 52.381 0.00 0.00 0.00 4.35
4739 7878 1.941975 GTAGAGAGGTAGGAGCGTCAC 59.058 57.143 0.00 0.00 0.00 3.67
4740 7879 0.745128 AGAGAGGTAGGAGCGTCACG 60.745 60.000 0.00 0.00 0.00 4.35
4741 7880 0.743701 GAGAGGTAGGAGCGTCACGA 60.744 60.000 0.00 0.00 0.00 4.35
4742 7881 0.745128 AGAGGTAGGAGCGTCACGAG 60.745 60.000 0.00 0.00 0.00 4.18
4743 7882 0.743701 GAGGTAGGAGCGTCACGAGA 60.744 60.000 0.00 0.00 0.00 4.04
4744 7883 0.322277 AGGTAGGAGCGTCACGAGAA 60.322 55.000 0.00 0.00 0.00 2.87
4745 7884 0.099082 GGTAGGAGCGTCACGAGAAG 59.901 60.000 0.00 0.00 0.00 2.85
4746 7885 1.085091 GTAGGAGCGTCACGAGAAGA 58.915 55.000 0.00 0.00 0.00 2.87
4747 7886 1.085091 TAGGAGCGTCACGAGAAGAC 58.915 55.000 0.00 0.00 0.00 3.01
4753 7892 3.679831 GTCACGAGAAGACGTCCTC 57.320 57.895 13.01 9.31 44.76 3.71
4754 7893 0.168568 GTCACGAGAAGACGTCCTCC 59.831 60.000 13.01 1.35 44.76 4.30
4755 7894 0.036448 TCACGAGAAGACGTCCTCCT 59.964 55.000 13.01 6.81 44.76 3.69
4756 7895 0.169230 CACGAGAAGACGTCCTCCTG 59.831 60.000 13.01 8.87 44.76 3.86
4757 7896 0.250814 ACGAGAAGACGTCCTCCTGT 60.251 55.000 13.01 7.48 43.02 4.00
4758 7897 0.448593 CGAGAAGACGTCCTCCTGTC 59.551 60.000 13.01 1.91 35.33 3.51
4759 7898 0.812549 GAGAAGACGTCCTCCTGTCC 59.187 60.000 13.01 0.00 35.71 4.02
4760 7899 0.406361 AGAAGACGTCCTCCTGTCCT 59.594 55.000 13.01 0.00 35.71 3.85
4761 7900 0.528470 GAAGACGTCCTCCTGTCCTG 59.472 60.000 13.01 0.00 35.71 3.86
4762 7901 0.178958 AAGACGTCCTCCTGTCCTGT 60.179 55.000 13.01 0.00 35.71 4.00
4763 7902 0.896019 AGACGTCCTCCTGTCCTGTG 60.896 60.000 13.01 0.00 35.71 3.66
4764 7903 1.878656 GACGTCCTCCTGTCCTGTGG 61.879 65.000 3.51 0.00 0.00 4.17
4765 7904 2.650116 CGTCCTCCTGTCCTGTGGG 61.650 68.421 0.00 0.00 0.00 4.61
4766 7905 1.229209 GTCCTCCTGTCCTGTGGGA 60.229 63.158 0.00 0.00 39.70 4.37
4767 7906 1.079256 TCCTCCTGTCCTGTGGGAG 59.921 63.158 0.00 0.00 43.12 4.30
4768 7907 2.664081 CCTCCTGTCCTGTGGGAGC 61.664 68.421 0.00 0.00 43.66 4.70
4769 7908 1.915266 CTCCTGTCCTGTGGGAGCA 60.915 63.158 0.00 0.00 43.12 4.26
4770 7909 2.177594 CTCCTGTCCTGTGGGAGCAC 62.178 65.000 0.00 0.00 43.12 4.40
4771 7910 2.519622 CCTGTCCTGTGGGAGCACA 61.520 63.158 0.00 0.00 43.12 4.57
4772 7911 1.451504 CTGTCCTGTGGGAGCACAA 59.548 57.895 0.00 0.00 43.12 3.33
4773 7912 0.604780 CTGTCCTGTGGGAGCACAAG 60.605 60.000 0.00 0.00 43.12 3.16
4774 7913 1.053835 TGTCCTGTGGGAGCACAAGA 61.054 55.000 0.00 0.00 43.12 3.02
4775 7914 0.603975 GTCCTGTGGGAGCACAAGAC 60.604 60.000 0.00 0.00 43.12 3.01
4776 7915 1.669115 CCTGTGGGAGCACAAGACG 60.669 63.158 0.00 0.00 34.35 4.18
4777 7916 1.367471 CTGTGGGAGCACAAGACGA 59.633 57.895 0.00 0.00 34.35 4.20
4778 7917 0.036952 CTGTGGGAGCACAAGACGAT 60.037 55.000 0.00 0.00 34.35 3.73
4779 7918 0.320683 TGTGGGAGCACAAGACGATG 60.321 55.000 0.00 0.00 31.35 3.84
4780 7919 0.037326 GTGGGAGCACAAGACGATGA 60.037 55.000 0.00 0.00 0.00 2.92
4781 7920 0.247460 TGGGAGCACAAGACGATGAG 59.753 55.000 0.00 0.00 0.00 2.90
4782 7921 0.532573 GGGAGCACAAGACGATGAGA 59.467 55.000 0.00 0.00 0.00 3.27
4783 7922 1.634702 GGAGCACAAGACGATGAGAC 58.365 55.000 0.00 0.00 0.00 3.36
4784 7923 1.634702 GAGCACAAGACGATGAGACC 58.365 55.000 0.00 0.00 0.00 3.85
4785 7924 0.969149 AGCACAAGACGATGAGACCA 59.031 50.000 0.00 0.00 0.00 4.02
4786 7925 1.067283 AGCACAAGACGATGAGACCAG 60.067 52.381 0.00 0.00 0.00 4.00
4787 7926 1.067565 GCACAAGACGATGAGACCAGA 60.068 52.381 0.00 0.00 0.00 3.86
4788 7927 2.873609 CACAAGACGATGAGACCAGAG 58.126 52.381 0.00 0.00 0.00 3.35
4789 7928 2.489722 CACAAGACGATGAGACCAGAGA 59.510 50.000 0.00 0.00 0.00 3.10
4790 7929 3.130164 CACAAGACGATGAGACCAGAGAT 59.870 47.826 0.00 0.00 0.00 2.75
4791 7930 3.380004 ACAAGACGATGAGACCAGAGATC 59.620 47.826 0.00 0.00 0.00 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 2.694760 GGCCCTCGCTTGCTTCTTG 61.695 63.158 0.00 0.00 34.44 3.02
78 79 2.285818 ACCATAACCAGGCCGGGA 60.286 61.111 30.18 7.46 40.22 5.14
152 153 1.005394 CGGTGGTTGACCTTAGCGT 60.005 57.895 1.34 0.00 43.55 5.07
169 170 0.958091 TGAAGTTCATGGTTTGGCCG 59.042 50.000 0.08 0.00 41.21 6.13
237 239 8.132362 ACGAACTTGTTTAACAGCAATAAATCA 58.868 29.630 0.00 0.00 0.00 2.57
396 409 0.251297 CCATGTTGAGCAAGGTCCCA 60.251 55.000 0.00 0.00 31.67 4.37
451 464 7.398829 ACATTTACACCCAAATTTTATTCCCC 58.601 34.615 0.00 0.00 0.00 4.81
569 930 9.883142 ACTTTTGTTAAAACCTGATGAATGAAA 57.117 25.926 0.00 0.00 0.00 2.69
585 946 7.656137 TGTTAACTTGCAACCAACTTTTGTTAA 59.344 29.630 7.22 3.02 41.35 2.01
605 966 0.584876 ACGTTCGCTGGCTTGTTAAC 59.415 50.000 0.00 0.00 0.00 2.01
635 996 5.128992 CATTAGTGCTTAACCCCGTTTTT 57.871 39.130 0.00 0.00 0.00 1.94
660 1021 1.065709 TCGCCATTTGGGAGTACTTCC 60.066 52.381 13.97 13.97 46.00 3.46
682 1043 2.038557 GCAGTGTAGAGGTGGGAGAAAA 59.961 50.000 0.00 0.00 0.00 2.29
740 1102 1.342819 GCACCCAAACAAGCCATACAA 59.657 47.619 0.00 0.00 0.00 2.41
742 1104 1.202348 GAGCACCCAAACAAGCCATAC 59.798 52.381 0.00 0.00 0.00 2.39
751 1113 2.195567 TGCAGCTGAGCACCCAAAC 61.196 57.895 20.43 0.00 40.11 2.93
791 1153 7.492352 AGAAACTGCAAAGACGTAAAGTAAT 57.508 32.000 0.00 0.00 0.00 1.89
792 1154 6.913873 AGAAACTGCAAAGACGTAAAGTAA 57.086 33.333 0.00 0.00 0.00 2.24
793 1155 8.330302 GTTTAGAAACTGCAAAGACGTAAAGTA 58.670 33.333 0.00 0.00 36.03 2.24
794 1156 6.913873 TTAGAAACTGCAAAGACGTAAAGT 57.086 33.333 0.00 0.00 0.00 2.66
795 1157 6.631636 GGTTTAGAAACTGCAAAGACGTAAAG 59.368 38.462 5.20 0.00 38.89 1.85
796 1158 6.316890 AGGTTTAGAAACTGCAAAGACGTAAA 59.683 34.615 5.20 0.00 38.89 2.01
806 1168 2.356665 TGGCAGGTTTAGAAACTGCA 57.643 45.000 26.32 13.49 41.00 4.41
842 1204 2.036992 CCACCCAAAGCTTGCAACAATA 59.963 45.455 0.00 0.00 0.00 1.90
931 1294 4.274950 GGAGAATTGAACAGAACGAAACCA 59.725 41.667 0.00 0.00 0.00 3.67
1048 1411 5.473066 AAAGGGACATGAATGGAAAACAG 57.527 39.130 0.00 0.00 0.00 3.16
1059 1422 2.642311 TGAGGTAGCAAAAGGGACATGA 59.358 45.455 0.00 0.00 0.00 3.07
1091 1454 1.657822 GGGATCGGAGAAGTTGAAGC 58.342 55.000 0.00 0.00 43.58 3.86
1128 1491 0.952497 CGCAGGCAATATCCGCATCT 60.952 55.000 0.09 0.00 0.00 2.90
1152 1515 1.377202 GGCGTGGAAGAAGGCATCA 60.377 57.895 0.00 0.00 32.60 3.07
1275 1638 0.476338 TGTTAAAGCTGGCCACCTCA 59.524 50.000 0.00 0.00 0.00 3.86
1327 1690 1.591594 CATCGGCGCTGTAATCCGT 60.592 57.895 17.37 0.00 43.35 4.69
1410 1773 1.923356 TCCTGCCATTGAAAAGTCCC 58.077 50.000 0.00 0.00 0.00 4.46
1428 1791 2.223711 ACCGGTTGCATTCTTGTTGTTC 60.224 45.455 0.00 0.00 0.00 3.18
1496 1859 1.337821 GTTGTCATCGTCGTCCACTC 58.662 55.000 0.00 0.00 0.00 3.51
1557 1920 6.590677 GTGTAAGTTTCTTATCAGGTGAGGTC 59.409 42.308 0.00 0.00 0.00 3.85
1674 2037 9.897744 CATAGTTTCATGTCAATACTTGTGTTT 57.102 29.630 0.00 0.00 33.58 2.83
1696 2059 0.835941 ACCTCCTCTGGCAAGCATAG 59.164 55.000 0.00 0.00 0.00 2.23
1953 2325 4.948847 AGGTTTGATTTGCTTTCTTCCAC 58.051 39.130 0.00 0.00 0.00 4.02
1986 2358 8.246180 TCAGCCTTATCATTTTCATCTTCAAAC 58.754 33.333 0.00 0.00 0.00 2.93
2181 2553 5.494724 CTCCCTTGAACAGATGATTCAGAA 58.505 41.667 0.00 0.00 37.38 3.02
2385 2757 5.569355 TGCAAGAAACCAGATAATTCCTCA 58.431 37.500 0.00 0.00 0.00 3.86
2442 2814 9.737427 TCTTCTACGAACTGATCAATTAATCTC 57.263 33.333 0.00 0.00 0.00 2.75
2702 3397 4.590647 TCTCAAGATGCCAATAGGTAGAGG 59.409 45.833 0.00 0.00 37.19 3.69
2716 3411 4.381292 GCAAATGGTTCCCTTCTCAAGATG 60.381 45.833 0.00 0.00 0.00 2.90
2754 3449 5.248705 GCCTAACCTAACTATAGCTTGGGAT 59.751 44.000 17.95 11.90 30.61 3.85
2764 3459 8.430431 GGTTTTCATCTAGCCTAACCTAACTAT 58.570 37.037 0.00 0.00 33.84 2.12
2844 3541 3.889538 GAGGTTAAAGCTGTTGGTTCCTT 59.110 43.478 0.00 0.00 32.90 3.36
2845 3542 3.487372 GAGGTTAAAGCTGTTGGTTCCT 58.513 45.455 0.00 0.00 32.90 3.36
2846 3543 2.225727 CGAGGTTAAAGCTGTTGGTTCC 59.774 50.000 0.00 0.00 32.90 3.62
2847 3544 3.135994 TCGAGGTTAAAGCTGTTGGTTC 58.864 45.455 0.00 0.00 32.90 3.62
2848 3545 3.202829 TCGAGGTTAAAGCTGTTGGTT 57.797 42.857 0.00 0.00 35.14 3.67
2849 3546 2.922740 TCGAGGTTAAAGCTGTTGGT 57.077 45.000 0.00 0.00 0.00 3.67
2850 3547 3.621715 GGTATCGAGGTTAAAGCTGTTGG 59.378 47.826 0.00 0.00 0.00 3.77
2851 3548 4.250464 TGGTATCGAGGTTAAAGCTGTTG 58.750 43.478 0.00 0.00 0.00 3.33
2852 3549 4.546829 TGGTATCGAGGTTAAAGCTGTT 57.453 40.909 0.00 0.00 0.00 3.16
2904 3601 7.869937 GCTTAGTGCTCTGATGAATACTATTGA 59.130 37.037 0.00 0.00 38.95 2.57
2946 3643 9.391006 GAGTAATTGTTGGTAATGGACTAATGA 57.609 33.333 0.00 0.00 30.34 2.57
2987 3684 3.437049 GTCAAGTGTAACATCAGGGAAGC 59.563 47.826 0.00 0.00 41.43 3.86
3068 3768 9.841295 AGTGAAGTACTTAATTTCAGTTGGTTA 57.159 29.630 8.42 0.00 35.67 2.85
3098 3798 5.878116 CCTGTCAATGGAAGGTTATCGTTAA 59.122 40.000 0.00 0.00 0.00 2.01
3228 3928 2.159338 CCAGCTTGGTGTTGTATGATGC 60.159 50.000 0.00 0.00 31.35 3.91
3380 4080 1.146358 GGACGATGCCGAAGCTGTAC 61.146 60.000 0.00 0.00 40.80 2.90
3487 4187 5.701290 ACCACTTCAAGTATAGTGTTCTTGC 59.299 40.000 0.00 0.00 40.06 4.01
3529 4229 0.463204 CTCGTCCATCTCAGCACCAT 59.537 55.000 0.00 0.00 0.00 3.55
3535 4235 2.279120 GCCGCTCGTCCATCTCAG 60.279 66.667 0.00 0.00 0.00 3.35
3712 4412 3.482436 GTGTAACCATGTTCCAAGTCCA 58.518 45.455 0.00 0.00 0.00 4.02
3789 4489 4.275810 AGGTAGCATCAGTTACTCGGTTA 58.724 43.478 0.00 0.00 32.65 2.85
3811 4511 0.907486 CAATGAGAGCCCAGTCTGGA 59.093 55.000 21.23 0.00 40.96 3.86
3822 4522 5.624344 AAGCATCAACTTCACAATGAGAG 57.376 39.130 0.00 0.00 0.00 3.20
3994 4694 6.877611 AAACGGAAAACATTCTAGTCACAT 57.122 33.333 0.00 0.00 0.00 3.21
4018 4718 0.106819 GATCACCATCCTGCAGCCTT 60.107 55.000 8.66 0.00 0.00 4.35
4021 4721 1.022735 CAAGATCACCATCCTGCAGC 58.977 55.000 8.66 0.00 0.00 5.25
4033 4733 9.618890 CCTTTTCTAGGTGATTAATCAAGATCA 57.381 33.333 19.55 6.78 39.39 2.92
4067 4767 9.909644 CTTGACTCTGAAAATGATGAAATCTTT 57.090 29.630 0.00 0.00 45.81 2.52
4083 4783 4.955811 TTTCAACCTAGCTTGACTCTGA 57.044 40.909 0.00 0.00 29.62 3.27
4109 4811 9.545105 CAAGCATATGAAATTGGGCTTAATAAA 57.455 29.630 6.97 0.00 39.36 1.40
4216 7352 9.480538 GCATGAAATTTAAATTACAACATGCAG 57.519 29.630 33.88 20.39 42.52 4.41
4267 7406 4.094212 GCGAGTAGGAGTAACGTTTACAG 58.906 47.826 5.91 2.56 0.00 2.74
4275 7414 3.795623 TCCATTGCGAGTAGGAGTAAC 57.204 47.619 0.00 0.00 0.00 2.50
4279 7418 1.134699 TGCTTCCATTGCGAGTAGGAG 60.135 52.381 0.00 0.00 0.00 3.69
4281 7420 1.293924 CTGCTTCCATTGCGAGTAGG 58.706 55.000 0.00 0.00 0.00 3.18
4287 7426 2.180017 GCCACTGCTTCCATTGCG 59.820 61.111 0.00 0.00 33.53 4.85
4350 7489 6.616947 TGGGCGTCTTATCAAATTAACAAAG 58.383 36.000 0.00 0.00 0.00 2.77
4424 7563 6.198591 AGTGCGCGTTAAGAGAAATATCTAAC 59.801 38.462 8.43 0.00 35.54 2.34
4432 7571 3.955771 AAAAGTGCGCGTTAAGAGAAA 57.044 38.095 8.43 0.00 0.00 2.52
4716 7855 0.938713 CGCTCCTACCTCTCTACACG 59.061 60.000 0.00 0.00 0.00 4.49
4717 7856 1.941975 GACGCTCCTACCTCTCTACAC 59.058 57.143 0.00 0.00 0.00 2.90
4718 7857 1.558294 TGACGCTCCTACCTCTCTACA 59.442 52.381 0.00 0.00 0.00 2.74
4719 7858 1.941975 GTGACGCTCCTACCTCTCTAC 59.058 57.143 0.00 0.00 0.00 2.59
4720 7859 1.472904 CGTGACGCTCCTACCTCTCTA 60.473 57.143 0.00 0.00 0.00 2.43
4721 7860 0.745128 CGTGACGCTCCTACCTCTCT 60.745 60.000 0.00 0.00 0.00 3.10
4722 7861 0.743701 TCGTGACGCTCCTACCTCTC 60.744 60.000 0.00 0.00 0.00 3.20
4723 7862 0.745128 CTCGTGACGCTCCTACCTCT 60.745 60.000 0.00 0.00 0.00 3.69
4724 7863 0.743701 TCTCGTGACGCTCCTACCTC 60.744 60.000 0.00 0.00 0.00 3.85
4725 7864 0.322277 TTCTCGTGACGCTCCTACCT 60.322 55.000 0.00 0.00 0.00 3.08
4726 7865 0.099082 CTTCTCGTGACGCTCCTACC 59.901 60.000 0.00 0.00 0.00 3.18
4727 7866 1.085091 TCTTCTCGTGACGCTCCTAC 58.915 55.000 0.00 0.00 0.00 3.18
4728 7867 1.085091 GTCTTCTCGTGACGCTCCTA 58.915 55.000 0.00 0.00 0.00 2.94
4729 7868 1.877367 GTCTTCTCGTGACGCTCCT 59.123 57.895 0.00 0.00 0.00 3.69
4730 7869 4.461784 GTCTTCTCGTGACGCTCC 57.538 61.111 0.00 0.00 0.00 4.70
4735 7874 0.168568 GGAGGACGTCTTCTCGTGAC 59.831 60.000 24.68 5.72 44.21 3.67
4736 7875 0.036448 AGGAGGACGTCTTCTCGTGA 59.964 55.000 24.68 0.00 44.21 4.35
4737 7876 0.169230 CAGGAGGACGTCTTCTCGTG 59.831 60.000 24.68 22.96 44.21 4.35
4738 7877 0.250814 ACAGGAGGACGTCTTCTCGT 60.251 55.000 24.68 18.78 46.88 4.18
4739 7878 0.448593 GACAGGAGGACGTCTTCTCG 59.551 60.000 24.68 18.21 0.00 4.04
4740 7879 0.812549 GGACAGGAGGACGTCTTCTC 59.187 60.000 24.68 18.14 32.57 2.87
4741 7880 0.406361 AGGACAGGAGGACGTCTTCT 59.594 55.000 24.68 10.69 32.57 2.85
4742 7881 0.528470 CAGGACAGGAGGACGTCTTC 59.472 60.000 18.69 18.69 32.57 2.87
4743 7882 0.178958 ACAGGACAGGAGGACGTCTT 60.179 55.000 16.46 7.97 32.57 3.01
4744 7883 0.896019 CACAGGACAGGAGGACGTCT 60.896 60.000 16.46 0.90 32.57 4.18
4745 7884 1.587054 CACAGGACAGGAGGACGTC 59.413 63.158 7.13 7.13 0.00 4.34
4746 7885 1.908793 CCACAGGACAGGAGGACGT 60.909 63.158 0.00 0.00 0.00 4.34
4747 7886 2.650116 CCCACAGGACAGGAGGACG 61.650 68.421 0.00 0.00 33.47 4.79
4748 7887 1.229209 TCCCACAGGACAGGAGGAC 60.229 63.158 0.00 0.00 37.19 3.85
4749 7888 1.079256 CTCCCACAGGACAGGAGGA 59.921 63.158 0.00 0.00 42.98 3.71
4750 7889 2.664081 GCTCCCACAGGACAGGAGG 61.664 68.421 7.36 0.00 46.14 4.30
4752 7891 2.204034 TGCTCCCACAGGACAGGA 59.796 61.111 0.00 0.00 37.19 3.86
4753 7892 2.348998 GTGCTCCCACAGGACAGG 59.651 66.667 0.00 0.00 42.99 4.00
4761 7900 0.037326 TCATCGTCTTGTGCTCCCAC 60.037 55.000 0.00 0.00 42.40 4.61
4762 7901 0.247460 CTCATCGTCTTGTGCTCCCA 59.753 55.000 0.00 0.00 0.00 4.37
4763 7902 0.532573 TCTCATCGTCTTGTGCTCCC 59.467 55.000 0.00 0.00 0.00 4.30
4764 7903 1.634702 GTCTCATCGTCTTGTGCTCC 58.365 55.000 0.00 0.00 0.00 4.70
4765 7904 1.067565 TGGTCTCATCGTCTTGTGCTC 60.068 52.381 0.00 0.00 0.00 4.26
4766 7905 0.969149 TGGTCTCATCGTCTTGTGCT 59.031 50.000 0.00 0.00 0.00 4.40
4767 7906 1.067565 TCTGGTCTCATCGTCTTGTGC 60.068 52.381 0.00 0.00 0.00 4.57
4768 7907 2.489722 TCTCTGGTCTCATCGTCTTGTG 59.510 50.000 0.00 0.00 0.00 3.33
4769 7908 2.796557 TCTCTGGTCTCATCGTCTTGT 58.203 47.619 0.00 0.00 0.00 3.16
4770 7909 3.963665 GATCTCTGGTCTCATCGTCTTG 58.036 50.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.