Multiple sequence alignment - TraesCS5D01G184900

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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 TraesCS5D01G184900 chr5D 100.000 5000 0 0 1 5000 287308848 287303849 0.000000e+00 9234.0
1 TraesCS5D01G184900 chr5D 82.796 465 79 1 1 464 311368374 311368838 1.000000e-111 414.0
2 TraesCS5D01G184900 chr5D 89.130 46 4 1 4755 4799 513467234 513467279 6.990000e-04 56.5
3 TraesCS5D01G184900 chr5A 95.980 4005 112 17 828 4797 379134957 379130967 0.000000e+00 6458.0
4 TraesCS5D01G184900 chr5A 95.169 207 8 1 4794 5000 379130844 379130640 4.830000e-85 326.0
5 TraesCS5D01G184900 chr5B 96.306 3655 99 18 920 4542 326086956 326083306 0.000000e+00 5969.0
6 TraesCS5D01G184900 chr5B 81.667 660 105 14 102 752 525807671 525808323 7.370000e-148 534.0
7 TraesCS5D01G184900 chr5B 82.123 179 18 6 4822 5000 326082973 326082809 1.880000e-29 141.0
8 TraesCS5D01G184900 chr5B 90.426 94 9 0 4681 4774 326083256 326083163 1.890000e-24 124.0
9 TraesCS5D01G184900 chr7A 94.577 756 38 3 1 755 186094277 186095030 0.000000e+00 1166.0
10 TraesCS5D01G184900 chr7A 94.872 39 1 1 4759 4797 20386266 20386229 5.410000e-05 60.2
11 TraesCS5D01G184900 chr7A 94.737 38 2 0 4762 4799 680601280 680601317 5.410000e-05 60.2
12 TraesCS5D01G184900 chr2A 86.859 761 90 9 1 755 143271209 143271965 0.000000e+00 843.0
13 TraesCS5D01G184900 chr4B 82.614 765 113 15 1 753 460796037 460795281 0.000000e+00 658.0
14 TraesCS5D01G184900 chr1D 82.507 766 114 16 3 755 22317093 22317851 0.000000e+00 654.0
15 TraesCS5D01G184900 chr7D 81.520 487 89 1 1 486 579081979 579082465 2.800000e-107 399.0
16 TraesCS5D01G184900 chr6A 81.974 466 81 3 1 464 503601384 503601848 4.690000e-105 392.0
17 TraesCS5D01G184900 chr6A 80.860 465 88 1 1 464 61739645 61739181 1.020000e-96 364.0
18 TraesCS5D01G184900 chr3D 91.837 49 0 4 4751 4799 328381355 328381311 1.160000e-06 65.8
19 TraesCS5D01G184900 chr3A 93.182 44 1 2 4755 4798 33532488 33532447 4.180000e-06 63.9
20 TraesCS5D01G184900 chr3A 90.909 44 4 0 4757 4800 490617815 490617858 5.410000e-05 60.2
21 TraesCS5D01G184900 chr6D 94.872 39 2 0 4761 4799 280290093 280290131 1.500000e-05 62.1
22 TraesCS5D01G184900 chr2D 94.872 39 2 0 4761 4799 513852074 513852036 1.500000e-05 62.1


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 TraesCS5D01G184900 chr5D 287303849 287308848 4999 True 9234 9234 100.000000 1 5000 1 chr5D.!!$R1 4999
1 TraesCS5D01G184900 chr5A 379130640 379134957 4317 True 3392 6458 95.574500 828 5000 2 chr5A.!!$R1 4172
2 TraesCS5D01G184900 chr5B 326082809 326086956 4147 True 2078 5969 89.618333 920 5000 3 chr5B.!!$R1 4080
3 TraesCS5D01G184900 chr5B 525807671 525808323 652 False 534 534 81.667000 102 752 1 chr5B.!!$F1 650
4 TraesCS5D01G184900 chr7A 186094277 186095030 753 False 1166 1166 94.577000 1 755 1 chr7A.!!$F1 754
5 TraesCS5D01G184900 chr2A 143271209 143271965 756 False 843 843 86.859000 1 755 1 chr2A.!!$F1 754
6 TraesCS5D01G184900 chr4B 460795281 460796037 756 True 658 658 82.614000 1 753 1 chr4B.!!$R1 752
7 TraesCS5D01G184900 chr1D 22317093 22317851 758 False 654 654 82.507000 3 755 1 chr1D.!!$F1 752

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
773 797 0.108585 ATTACCCTGCGGCACATAGG 59.891 55.000 0.00 0.0 0.00 2.57 F
1845 1886 0.110678 TGATCTATCTCGGCGTCCCT 59.889 55.000 6.85 0.0 0.00 4.20 F
2274 2315 1.076485 GCAGGGGCAGGTTCATCAT 60.076 57.895 0.00 0.0 40.72 2.45 F
3651 3692 0.938008 GAACAGCTATTAGGCGCACC 59.062 55.000 10.83 0.0 37.29 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 1928 0.323302 TTGCATCCGAGCCACAGTAA 59.677 50.000 0.00 0.0 0.0 2.24 R
3651 3692 0.458669 GAAGAATGCACATGGGGCTG 59.541 55.000 12.08 0.0 0.0 4.85 R
3663 3704 2.098117 GCCGTTGGAATGAGGAAGAATG 59.902 50.000 0.00 0.0 0.0 2.67 R
4610 4670 1.202915 ACATGGCTGTGTTCATCCACA 60.203 47.619 0.00 0.0 41.7 4.17 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
193 194 1.076024 ACAATGATCACAGGGTTGCCT 59.924 47.619 0.00 0.00 0.00 4.75
326 329 1.241165 CAGGCTGACTTCATGTTGCA 58.759 50.000 9.42 0.00 32.71 4.08
588 602 1.601663 CGCCGCCAGATCAAACAAAAA 60.602 47.619 0.00 0.00 0.00 1.94
590 604 2.801342 GCCGCCAGATCAAACAAAAACA 60.801 45.455 0.00 0.00 0.00 2.83
596 610 5.462068 GCCAGATCAAACAAAAACACTAACC 59.538 40.000 0.00 0.00 0.00 2.85
658 676 0.978146 AGACTGCCCCGTTATCAGCT 60.978 55.000 0.00 0.00 0.00 4.24
768 792 3.509659 GGAATTACCCTGCGGCAC 58.490 61.111 0.00 0.00 0.00 5.01
769 793 1.377987 GGAATTACCCTGCGGCACA 60.378 57.895 0.00 0.00 0.00 4.57
770 794 0.751643 GGAATTACCCTGCGGCACAT 60.752 55.000 0.00 0.00 0.00 3.21
771 795 1.476110 GGAATTACCCTGCGGCACATA 60.476 52.381 0.00 0.00 0.00 2.29
772 796 1.873591 GAATTACCCTGCGGCACATAG 59.126 52.381 0.00 0.00 0.00 2.23
773 797 0.108585 ATTACCCTGCGGCACATAGG 59.891 55.000 0.00 0.00 0.00 2.57
774 798 1.268992 TTACCCTGCGGCACATAGGT 61.269 55.000 0.00 6.53 38.18 3.08
785 809 2.684001 CACATAGGTGCTCCCGTAAA 57.316 50.000 0.00 0.00 38.37 2.01
786 810 2.980568 CACATAGGTGCTCCCGTAAAA 58.019 47.619 0.00 0.00 38.37 1.52
787 811 2.936498 CACATAGGTGCTCCCGTAAAAG 59.064 50.000 0.00 0.00 38.37 2.27
788 812 2.570302 ACATAGGTGCTCCCGTAAAAGT 59.430 45.455 0.00 0.00 38.74 2.66
789 813 2.754946 TAGGTGCTCCCGTAAAAGTG 57.245 50.000 0.00 0.00 38.74 3.16
790 814 0.763035 AGGTGCTCCCGTAAAAGTGT 59.237 50.000 0.00 0.00 38.74 3.55
791 815 1.142262 AGGTGCTCCCGTAAAAGTGTT 59.858 47.619 0.00 0.00 38.74 3.32
792 816 1.534163 GGTGCTCCCGTAAAAGTGTTC 59.466 52.381 0.00 0.00 0.00 3.18
793 817 2.490991 GTGCTCCCGTAAAAGTGTTCT 58.509 47.619 0.00 0.00 0.00 3.01
794 818 2.479275 GTGCTCCCGTAAAAGTGTTCTC 59.521 50.000 0.00 0.00 0.00 2.87
795 819 2.074576 GCTCCCGTAAAAGTGTTCTCC 58.925 52.381 0.00 0.00 0.00 3.71
796 820 2.334838 CTCCCGTAAAAGTGTTCTCCG 58.665 52.381 0.00 0.00 0.00 4.63
797 821 0.794473 CCCGTAAAAGTGTTCTCCGC 59.206 55.000 0.00 0.00 0.00 5.54
798 822 0.437295 CCGTAAAAGTGTTCTCCGCG 59.563 55.000 0.00 0.00 0.00 6.46
799 823 0.179258 CGTAAAAGTGTTCTCCGCGC 60.179 55.000 0.00 0.00 0.00 6.86
800 824 0.863144 GTAAAAGTGTTCTCCGCGCA 59.137 50.000 8.75 0.00 0.00 6.09
801 825 1.463444 GTAAAAGTGTTCTCCGCGCAT 59.537 47.619 8.75 0.00 0.00 4.73
802 826 0.238289 AAAAGTGTTCTCCGCGCATG 59.762 50.000 8.75 0.00 0.00 4.06
803 827 1.577328 AAAGTGTTCTCCGCGCATGG 61.577 55.000 8.75 0.38 0.00 3.66
804 828 2.731691 AAGTGTTCTCCGCGCATGGT 62.732 55.000 8.75 0.00 0.00 3.55
805 829 1.447140 GTGTTCTCCGCGCATGGTA 60.447 57.895 8.75 0.00 0.00 3.25
806 830 1.017177 GTGTTCTCCGCGCATGGTAA 61.017 55.000 8.75 0.00 0.00 2.85
807 831 0.739462 TGTTCTCCGCGCATGGTAAG 60.739 55.000 8.75 0.00 0.00 2.34
808 832 1.153449 TTCTCCGCGCATGGTAAGG 60.153 57.895 8.75 0.00 0.00 2.69
809 833 1.895020 TTCTCCGCGCATGGTAAGGT 61.895 55.000 8.75 0.00 0.00 3.50
810 834 2.125310 TCCGCGCATGGTAAGGTG 60.125 61.111 8.75 0.00 0.00 4.00
811 835 3.202001 CCGCGCATGGTAAGGTGG 61.202 66.667 8.75 0.00 0.00 4.61
812 836 2.125310 CGCGCATGGTAAGGTGGA 60.125 61.111 8.75 0.00 0.00 4.02
813 837 1.743623 CGCGCATGGTAAGGTGGAA 60.744 57.895 8.75 0.00 0.00 3.53
814 838 1.705337 CGCGCATGGTAAGGTGGAAG 61.705 60.000 8.75 0.00 0.00 3.46
815 839 0.676782 GCGCATGGTAAGGTGGAAGT 60.677 55.000 0.30 0.00 0.00 3.01
816 840 1.086696 CGCATGGTAAGGTGGAAGTG 58.913 55.000 0.00 0.00 0.00 3.16
817 841 0.811281 GCATGGTAAGGTGGAAGTGC 59.189 55.000 0.00 0.00 0.00 4.40
818 842 1.463674 CATGGTAAGGTGGAAGTGCC 58.536 55.000 0.00 0.00 37.10 5.01
819 843 1.004745 CATGGTAAGGTGGAAGTGCCT 59.995 52.381 0.00 0.00 37.63 4.75
820 844 0.690762 TGGTAAGGTGGAAGTGCCTC 59.309 55.000 0.00 0.00 37.63 4.70
821 845 0.690762 GGTAAGGTGGAAGTGCCTCA 59.309 55.000 0.00 0.00 37.63 3.86
822 846 1.073284 GGTAAGGTGGAAGTGCCTCAA 59.927 52.381 0.00 0.00 37.63 3.02
823 847 2.152016 GTAAGGTGGAAGTGCCTCAAC 58.848 52.381 0.00 0.00 37.63 3.18
824 848 0.846693 AAGGTGGAAGTGCCTCAACT 59.153 50.000 0.00 0.00 37.63 3.16
825 849 0.398318 AGGTGGAAGTGCCTCAACTC 59.602 55.000 0.00 0.00 37.63 3.01
826 850 0.606673 GGTGGAAGTGCCTCAACTCC 60.607 60.000 0.00 0.00 37.63 3.85
827 851 0.108585 GTGGAAGTGCCTCAACTCCA 59.891 55.000 0.00 0.00 37.63 3.86
828 852 0.843309 TGGAAGTGCCTCAACTCCAA 59.157 50.000 0.00 0.00 37.63 3.53
829 853 1.214175 TGGAAGTGCCTCAACTCCAAA 59.786 47.619 0.00 0.00 37.63 3.28
830 854 1.882623 GGAAGTGCCTCAACTCCAAAG 59.117 52.381 0.00 0.00 0.00 2.77
831 855 2.487265 GGAAGTGCCTCAACTCCAAAGA 60.487 50.000 0.00 0.00 0.00 2.52
832 856 3.214328 GAAGTGCCTCAACTCCAAAGAA 58.786 45.455 0.00 0.00 0.00 2.52
833 857 3.297134 AGTGCCTCAACTCCAAAGAAA 57.703 42.857 0.00 0.00 0.00 2.52
834 858 3.631250 AGTGCCTCAACTCCAAAGAAAA 58.369 40.909 0.00 0.00 0.00 2.29
835 859 3.633986 AGTGCCTCAACTCCAAAGAAAAG 59.366 43.478 0.00 0.00 0.00 2.27
836 860 3.381590 GTGCCTCAACTCCAAAGAAAAGT 59.618 43.478 0.00 0.00 0.00 2.66
837 861 3.381272 TGCCTCAACTCCAAAGAAAAGTG 59.619 43.478 0.00 0.00 0.00 3.16
838 862 3.632145 GCCTCAACTCCAAAGAAAAGTGA 59.368 43.478 0.00 0.00 0.00 3.41
839 863 4.097892 GCCTCAACTCCAAAGAAAAGTGAA 59.902 41.667 0.00 0.00 0.00 3.18
840 864 5.394115 GCCTCAACTCCAAAGAAAAGTGAAA 60.394 40.000 0.00 0.00 0.00 2.69
841 865 6.268566 CCTCAACTCCAAAGAAAAGTGAAAG 58.731 40.000 0.00 0.00 0.00 2.62
909 933 2.816520 GTGGATACGCGGCGGTTT 60.817 61.111 27.37 10.54 42.51 3.27
910 934 2.816083 TGGATACGCGGCGGTTTG 60.816 61.111 27.37 0.00 42.51 2.93
951 975 4.439968 GGAGAATAGGATTTTCGTTCCGT 58.560 43.478 0.00 0.00 38.36 4.69
961 985 2.642139 TTCGTTCCGTTCTTCGCTAT 57.358 45.000 0.00 0.00 38.35 2.97
1014 1042 0.398696 TCTCTAGGGTTTTTGCGGCA 59.601 50.000 0.00 0.00 0.00 5.69
1096 1124 2.021068 ATGGAGATGACGGAGGTGCG 62.021 60.000 0.00 0.00 0.00 5.34
1617 1658 0.519999 CAAGAAATCGTGCAGCTCGC 60.520 55.000 12.05 0.00 42.89 5.03
1845 1886 0.110678 TGATCTATCTCGGCGTCCCT 59.889 55.000 6.85 0.00 0.00 4.20
1881 1922 5.474578 TGCAGACACATATAGAAGGGATC 57.525 43.478 0.00 0.00 0.00 3.36
1887 1928 4.654262 ACACATATAGAAGGGATCCAACGT 59.346 41.667 15.23 0.00 0.00 3.99
1916 1957 2.398498 CTCGGATGCAAAGGTCGATAG 58.602 52.381 0.00 0.00 0.00 2.08
2013 2054 1.133976 GCTAGCATCAGGATGTGGGTT 60.134 52.381 10.63 0.00 40.80 4.11
2031 2072 4.349636 TGGGTTGATAGGAACAAGAAGTCA 59.650 41.667 0.00 0.00 0.00 3.41
2253 2294 9.186323 CTTGTAGTATGTGATGTCTAGTTATGC 57.814 37.037 0.00 0.00 0.00 3.14
2256 2297 6.753180 AGTATGTGATGTCTAGTTATGCCTG 58.247 40.000 0.00 0.00 0.00 4.85
2273 2314 2.356278 GCAGGGGCAGGTTCATCA 59.644 61.111 0.00 0.00 40.72 3.07
2274 2315 1.076485 GCAGGGGCAGGTTCATCAT 60.076 57.895 0.00 0.00 40.72 2.45
2277 2318 1.479323 CAGGGGCAGGTTCATCATTTG 59.521 52.381 0.00 0.00 0.00 2.32
2350 2391 3.509967 TCGATTCAAGACAACAGGCTCTA 59.490 43.478 0.00 0.00 0.00 2.43
2568 2609 6.017605 GTGAAATTATCCTGTGTAGATGCTGG 60.018 42.308 0.00 0.00 0.00 4.85
2578 2619 4.225042 TGTGTAGATGCTGGGATGTAGTTT 59.775 41.667 0.00 0.00 0.00 2.66
2585 2626 3.287222 GCTGGGATGTAGTTTATTGCCA 58.713 45.455 0.00 0.00 0.00 4.92
2637 2678 4.712122 TGTATTTTCCTGCCCGATTTTC 57.288 40.909 0.00 0.00 0.00 2.29
2776 2817 4.340381 GGAGTGAGAAAAATCCCATGGATG 59.660 45.833 15.22 0.00 42.27 3.51
3156 3197 5.279406 GCTCAACCTATATGCAGATGAGAGT 60.279 44.000 11.97 0.00 34.13 3.24
3247 3288 5.469421 CCTGATGAGGCTGTTCTATTTGATC 59.531 44.000 0.00 0.00 30.52 2.92
3302 3343 3.002042 CAGAAGGATGCTAGTCAAATGCG 59.998 47.826 0.00 0.00 0.00 4.73
3317 3358 3.281727 AATGCGGACTGTATGGAATGT 57.718 42.857 0.00 0.00 0.00 2.71
3324 3365 3.279434 GACTGTATGGAATGTTGGGTCC 58.721 50.000 0.00 0.00 0.00 4.46
3510 3551 5.126061 TGATTCATTCTCACTCGATCTGTCA 59.874 40.000 0.00 0.00 0.00 3.58
3651 3692 0.938008 GAACAGCTATTAGGCGCACC 59.062 55.000 10.83 0.00 37.29 5.01
3707 3748 6.992305 GCAGTGTGCAAAGAGATTTGACTCT 61.992 44.000 4.96 0.00 44.73 3.24
3851 3892 8.338986 GTTTCTTTTCTAGTTCTTCTCCAGTTG 58.661 37.037 0.00 0.00 0.00 3.16
3922 3963 3.766051 GCCTTGGATCATTTTCACCTTCT 59.234 43.478 0.00 0.00 0.00 2.85
4031 4072 4.330894 CACGAGTTGACATGCATTGTATCT 59.669 41.667 0.00 0.00 39.18 1.98
4037 4078 3.455543 TGACATGCATTGTATCTCCTCCA 59.544 43.478 0.00 0.00 39.18 3.86
4083 4124 3.844211 ACTATGCCAGTACCTCCTGAAAA 59.156 43.478 0.00 0.00 34.98 2.29
4157 4202 5.650543 CCATTTTACTGGCAAGTGGAATAC 58.349 41.667 3.21 0.00 37.19 1.89
4216 4261 6.640907 GTCTGCAGATTATTTTGGTTTCGTTT 59.359 34.615 21.47 0.00 0.00 3.60
4253 4298 3.802685 GCCACGTGGTAGTATCATTTCTC 59.197 47.826 33.92 9.75 37.57 2.87
4260 4305 8.189460 ACGTGGTAGTATCATTTCTCTTACTTC 58.811 37.037 0.00 0.00 0.00 3.01
4274 4319 9.477484 TTTCTCTTACTTCTCAACATTCTGTAC 57.523 33.333 0.00 0.00 0.00 2.90
4397 4443 3.056891 CACCCGGAAACAATAGTTGCAAT 60.057 43.478 0.73 0.00 38.17 3.56
4478 4526 4.797800 TGAGAGATGATGCATAGCTACC 57.202 45.455 0.00 0.00 0.00 3.18
4479 4527 4.414677 TGAGAGATGATGCATAGCTACCT 58.585 43.478 0.00 0.00 0.00 3.08
4480 4528 4.462132 TGAGAGATGATGCATAGCTACCTC 59.538 45.833 0.00 3.52 0.00 3.85
4549 4609 2.207501 CTGCATCTGGGCTGGAGGTT 62.208 60.000 0.00 0.00 34.04 3.50
4553 4613 0.842635 ATCTGGGCTGGAGGTTGATC 59.157 55.000 0.00 0.00 0.00 2.92
4554 4614 0.547471 TCTGGGCTGGAGGTTGATCA 60.547 55.000 0.00 0.00 0.00 2.92
4555 4615 0.549950 CTGGGCTGGAGGTTGATCAT 59.450 55.000 0.00 0.00 0.00 2.45
4556 4616 1.770658 CTGGGCTGGAGGTTGATCATA 59.229 52.381 0.00 0.00 0.00 2.15
4557 4617 1.770658 TGGGCTGGAGGTTGATCATAG 59.229 52.381 0.00 0.00 0.00 2.23
4563 4623 4.262808 GCTGGAGGTTGATCATAGTAGCAT 60.263 45.833 0.00 0.00 0.00 3.79
4610 4670 6.435164 ACAGGCTACAGGGATCATAAATTTT 58.565 36.000 0.00 0.00 0.00 1.82
4631 4691 2.291209 TGGATGAACACAGCCATGTT 57.709 45.000 3.04 2.94 43.74 2.71
4638 4698 2.687700 ACACAGCCATGTTTTTGCAA 57.312 40.000 0.00 0.00 37.65 4.08
4647 4707 4.209080 GCCATGTTTTTGCAAGTCTGTTAC 59.791 41.667 0.00 0.00 0.00 2.50
4659 4719 5.690857 GCAAGTCTGTTACGTTCTAAGAAGT 59.309 40.000 0.00 0.00 0.00 3.01
4663 4723 6.425114 AGTCTGTTACGTTCTAAGAAGTACGA 59.575 38.462 10.80 0.00 46.03 3.43
4781 4850 3.995636 AGCTCATAAAGTACTCCCTCCA 58.004 45.455 0.00 0.00 0.00 3.86
4817 5012 2.795329 ACAAGGGTCTTGGTATTGCAG 58.205 47.619 11.65 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 194 2.361104 GGGCCATGGCACTTTCGA 60.361 61.111 36.56 0.00 42.14 3.71
213 216 3.077359 GGATTGGGAAAGAGTGACACTG 58.923 50.000 14.14 0.00 0.00 3.66
326 329 4.503991 CCTTCAGCAACTACTGGTTCTTCT 60.504 45.833 0.00 0.00 38.26 2.85
416 419 1.723220 AGATGACGTCGTCTTCGAGA 58.277 50.000 30.25 8.98 46.96 4.04
466 469 1.065564 AGGCAAGCTTGAGGATCTCAC 60.066 52.381 30.39 8.43 40.46 3.51
588 602 0.186630 GGGTTTGGTGGGGTTAGTGT 59.813 55.000 0.00 0.00 0.00 3.55
590 604 0.481128 CTGGGTTTGGTGGGGTTAGT 59.519 55.000 0.00 0.00 0.00 2.24
658 676 1.820056 CTAGTGCTCTCCCGCTCGA 60.820 63.158 0.00 0.00 0.00 4.04
766 790 2.684001 TTTACGGGAGCACCTATGTG 57.316 50.000 0.00 0.00 45.65 3.21
767 791 2.570302 ACTTTTACGGGAGCACCTATGT 59.430 45.455 0.00 0.00 36.97 2.29
768 792 2.936498 CACTTTTACGGGAGCACCTATG 59.064 50.000 0.00 0.00 36.97 2.23
769 793 2.570302 ACACTTTTACGGGAGCACCTAT 59.430 45.455 0.00 0.00 36.97 2.57
770 794 1.972795 ACACTTTTACGGGAGCACCTA 59.027 47.619 0.00 0.00 36.97 3.08
771 795 0.763035 ACACTTTTACGGGAGCACCT 59.237 50.000 0.00 0.00 36.97 4.00
772 796 1.534163 GAACACTTTTACGGGAGCACC 59.466 52.381 0.00 0.00 0.00 5.01
773 797 2.479275 GAGAACACTTTTACGGGAGCAC 59.521 50.000 0.00 0.00 0.00 4.40
774 798 2.549349 GGAGAACACTTTTACGGGAGCA 60.549 50.000 0.00 0.00 0.00 4.26
775 799 2.074576 GGAGAACACTTTTACGGGAGC 58.925 52.381 0.00 0.00 0.00 4.70
776 800 2.334838 CGGAGAACACTTTTACGGGAG 58.665 52.381 0.00 0.00 0.00 4.30
777 801 1.606224 GCGGAGAACACTTTTACGGGA 60.606 52.381 0.00 0.00 0.00 5.14
778 802 0.794473 GCGGAGAACACTTTTACGGG 59.206 55.000 0.00 0.00 0.00 5.28
779 803 0.437295 CGCGGAGAACACTTTTACGG 59.563 55.000 0.00 0.00 0.00 4.02
780 804 0.179258 GCGCGGAGAACACTTTTACG 60.179 55.000 8.83 0.00 0.00 3.18
781 805 0.863144 TGCGCGGAGAACACTTTTAC 59.137 50.000 8.83 0.00 0.00 2.01
782 806 1.463056 CATGCGCGGAGAACACTTTTA 59.537 47.619 8.83 0.00 0.00 1.52
783 807 0.238289 CATGCGCGGAGAACACTTTT 59.762 50.000 8.83 0.00 0.00 2.27
784 808 1.577328 CCATGCGCGGAGAACACTTT 61.577 55.000 8.83 0.00 0.00 2.66
785 809 2.034879 CCATGCGCGGAGAACACTT 61.035 57.895 8.83 0.00 0.00 3.16
786 810 1.884075 TACCATGCGCGGAGAACACT 61.884 55.000 8.83 0.00 0.00 3.55
787 811 1.017177 TTACCATGCGCGGAGAACAC 61.017 55.000 8.83 0.00 0.00 3.32
788 812 0.739462 CTTACCATGCGCGGAGAACA 60.739 55.000 8.83 0.00 0.00 3.18
789 813 1.429148 CCTTACCATGCGCGGAGAAC 61.429 60.000 8.83 0.00 0.00 3.01
790 814 1.153449 CCTTACCATGCGCGGAGAA 60.153 57.895 8.83 0.00 0.00 2.87
791 815 2.355986 ACCTTACCATGCGCGGAGA 61.356 57.895 8.83 0.00 0.00 3.71
792 816 2.173669 CACCTTACCATGCGCGGAG 61.174 63.158 8.83 0.00 0.00 4.63
793 817 2.125310 CACCTTACCATGCGCGGA 60.125 61.111 8.83 5.00 0.00 5.54
794 818 3.202001 CCACCTTACCATGCGCGG 61.202 66.667 8.83 0.14 0.00 6.46
795 819 1.705337 CTTCCACCTTACCATGCGCG 61.705 60.000 0.00 0.00 0.00 6.86
796 820 0.676782 ACTTCCACCTTACCATGCGC 60.677 55.000 0.00 0.00 0.00 6.09
797 821 1.086696 CACTTCCACCTTACCATGCG 58.913 55.000 0.00 0.00 0.00 4.73
798 822 0.811281 GCACTTCCACCTTACCATGC 59.189 55.000 0.00 0.00 0.00 4.06
799 823 1.004745 AGGCACTTCCACCTTACCATG 59.995 52.381 0.00 0.00 37.29 3.66
800 824 1.282157 GAGGCACTTCCACCTTACCAT 59.718 52.381 0.00 0.00 41.55 3.55
801 825 0.690762 GAGGCACTTCCACCTTACCA 59.309 55.000 0.00 0.00 41.55 3.25
802 826 0.690762 TGAGGCACTTCCACCTTACC 59.309 55.000 0.00 0.00 41.55 2.85
803 827 2.152016 GTTGAGGCACTTCCACCTTAC 58.848 52.381 0.00 0.00 41.55 2.34
804 828 2.038557 GAGTTGAGGCACTTCCACCTTA 59.961 50.000 0.00 0.00 41.55 2.69
805 829 0.846693 AGTTGAGGCACTTCCACCTT 59.153 50.000 0.00 0.00 41.55 3.50
806 830 0.398318 GAGTTGAGGCACTTCCACCT 59.602 55.000 0.00 0.00 41.55 4.00
807 831 0.606673 GGAGTTGAGGCACTTCCACC 60.607 60.000 0.00 0.00 41.55 4.61
808 832 0.108585 TGGAGTTGAGGCACTTCCAC 59.891 55.000 0.00 0.00 41.55 4.02
809 833 0.843309 TTGGAGTTGAGGCACTTCCA 59.157 50.000 0.00 0.00 41.55 3.53
810 834 1.882623 CTTTGGAGTTGAGGCACTTCC 59.117 52.381 0.00 0.00 41.55 3.46
811 835 2.851195 TCTTTGGAGTTGAGGCACTTC 58.149 47.619 0.00 0.00 41.55 3.01
812 836 3.297134 TTCTTTGGAGTTGAGGCACTT 57.703 42.857 0.00 0.00 41.55 3.16
814 838 3.381590 ACTTTTCTTTGGAGTTGAGGCAC 59.618 43.478 0.00 0.00 0.00 5.01
815 839 3.381272 CACTTTTCTTTGGAGTTGAGGCA 59.619 43.478 0.00 0.00 0.00 4.75
816 840 3.632145 TCACTTTTCTTTGGAGTTGAGGC 59.368 43.478 0.00 0.00 0.00 4.70
817 841 5.835113 TTCACTTTTCTTTGGAGTTGAGG 57.165 39.130 0.00 0.00 0.00 3.86
818 842 7.088589 TCTTTCACTTTTCTTTGGAGTTGAG 57.911 36.000 0.00 0.00 0.00 3.02
819 843 7.461182 TTCTTTCACTTTTCTTTGGAGTTGA 57.539 32.000 0.00 0.00 0.00 3.18
820 844 8.532977 TTTTCTTTCACTTTTCTTTGGAGTTG 57.467 30.769 0.00 0.00 0.00 3.16
847 871 1.406180 GTGGTGCCGGTGTTTTAGTTT 59.594 47.619 1.90 0.00 0.00 2.66
851 875 0.955178 CATGTGGTGCCGGTGTTTTA 59.045 50.000 1.90 0.00 0.00 1.52
909 933 1.077787 CCAGTTGCGGGGAATAGCA 60.078 57.895 0.00 0.00 42.15 3.49
910 934 2.481471 GCCAGTTGCGGGGAATAGC 61.481 63.158 0.00 0.00 0.00 2.97
951 975 1.551430 TGGGGACGAAATAGCGAAGAA 59.449 47.619 0.00 0.00 34.83 2.52
961 985 1.280998 GGAGAAGGAATGGGGACGAAA 59.719 52.381 0.00 0.00 0.00 3.46
1014 1042 3.470888 CCGGAGCTGGGATTCGGT 61.471 66.667 0.00 0.00 36.38 4.69
1881 1922 1.289109 CCGAGCCACAGTAACGTTGG 61.289 60.000 11.99 4.76 0.00 3.77
1887 1928 0.323302 TTGCATCCGAGCCACAGTAA 59.677 50.000 0.00 0.00 0.00 2.24
1916 1957 1.432270 GACATACTGCGAGGCAAGGC 61.432 60.000 0.00 0.00 38.41 4.35
2013 2054 5.808366 ACACTGACTTCTTGTTCCTATCA 57.192 39.130 0.00 0.00 0.00 2.15
2031 2072 2.241176 TGAGTCCTGGTGGAAAAACACT 59.759 45.455 0.00 0.00 45.18 3.55
2219 2260 6.409704 ACATCACATACTACAAGATGTTGCT 58.590 36.000 1.83 0.00 44.86 3.91
2230 2271 7.810282 CAGGCATAACTAGACATCACATACTAC 59.190 40.741 0.00 0.00 0.00 2.73
2256 2297 0.685458 AATGATGAACCTGCCCCTGC 60.685 55.000 0.00 0.00 38.26 4.85
2269 2310 9.903682 AAAGAGTAGAATGTCAAACAAATGATG 57.096 29.630 0.00 0.00 0.00 3.07
2271 2312 9.950680 GAAAAGAGTAGAATGTCAAACAAATGA 57.049 29.630 0.00 0.00 0.00 2.57
2272 2313 9.956720 AGAAAAGAGTAGAATGTCAAACAAATG 57.043 29.630 0.00 0.00 0.00 2.32
2273 2314 9.956720 CAGAAAAGAGTAGAATGTCAAACAAAT 57.043 29.630 0.00 0.00 0.00 2.32
2274 2315 7.915397 GCAGAAAAGAGTAGAATGTCAAACAAA 59.085 33.333 0.00 0.00 0.00 2.83
2277 2318 6.959361 TGCAGAAAAGAGTAGAATGTCAAAC 58.041 36.000 0.00 0.00 0.00 2.93
2296 2337 1.374947 GTGCAAGGGGTACTGCAGA 59.625 57.895 23.35 0.48 35.12 4.26
2350 2391 3.361786 GGTTATAACCCATGCAACAGGT 58.638 45.455 22.15 0.00 43.43 4.00
2545 2586 5.471456 CCCAGCATCTACACAGGATAATTTC 59.529 44.000 0.00 0.00 0.00 2.17
2551 2592 2.180946 TCCCAGCATCTACACAGGAT 57.819 50.000 0.00 0.00 0.00 3.24
2568 2609 5.295787 TCGTCAATGGCAATAAACTACATCC 59.704 40.000 0.00 0.00 0.00 3.51
2578 2619 4.457257 TGACACATTTCGTCAATGGCAATA 59.543 37.500 12.64 0.00 46.06 1.90
2585 2626 7.490725 TGAAAAACAATGACACATTTCGTCAAT 59.509 29.630 0.00 0.00 45.91 2.57
2637 2678 7.630242 TCTCCTTATGTGCCATAAAGAAAAG 57.370 36.000 8.40 0.18 0.00 2.27
2776 2817 3.569701 TCTTGAAACAATTGCTCCAGGAC 59.430 43.478 5.05 0.00 0.00 3.85
2968 3009 2.459644 CAGGGGCAAATTTCTGATGGA 58.540 47.619 0.00 0.00 0.00 3.41
3156 3197 1.060729 TCACCTCGGGAAATGAACCA 58.939 50.000 0.00 0.00 0.00 3.67
3247 3288 2.951642 TGGCTGAAAGAGGTTCTTTGTG 59.048 45.455 8.66 3.29 45.85 3.33
3302 3343 3.279434 GACCCAACATTCCATACAGTCC 58.721 50.000 0.00 0.00 0.00 3.85
3317 3358 2.028112 CACAGAGAGAATTCGGACCCAA 60.028 50.000 0.00 0.00 0.00 4.12
3324 3365 3.062763 ACAACTGCACAGAGAGAATTCG 58.937 45.455 4.31 0.00 0.00 3.34
3651 3692 0.458669 GAAGAATGCACATGGGGCTG 59.541 55.000 12.08 0.00 0.00 4.85
3663 3704 2.098117 GCCGTTGGAATGAGGAAGAATG 59.902 50.000 0.00 0.00 0.00 2.67
3664 3705 2.290896 TGCCGTTGGAATGAGGAAGAAT 60.291 45.455 0.00 0.00 0.00 2.40
3707 3748 4.483950 TCTCCTCTTTCTGTTCCTCTTCA 58.516 43.478 0.00 0.00 0.00 3.02
3876 3917 9.372369 GGCCTATATCAATCTGATTACAACTAC 57.628 37.037 1.98 0.00 38.26 2.73
4011 4052 5.121811 AGGAGATACAATGCATGTCAACTC 58.878 41.667 0.00 7.38 42.70 3.01
4017 4058 3.457380 ACTGGAGGAGATACAATGCATGT 59.543 43.478 0.00 3.37 46.36 3.21
4031 4072 2.327325 AAGCAGGTAAGACTGGAGGA 57.673 50.000 0.00 0.00 38.90 3.71
4037 4078 5.658634 TGACAGATGATAAGCAGGTAAGACT 59.341 40.000 0.00 0.00 0.00 3.24
4083 4124 2.233271 CTCCCACAATGCTTCAACAGT 58.767 47.619 0.00 0.00 0.00 3.55
4216 4261 3.684305 CACGTGGCATCTGTAATGAGAAA 59.316 43.478 7.95 0.00 0.00 2.52
4274 4319 5.163581 CCAAGCAAAATGTCCTATCTGAAGG 60.164 44.000 0.00 1.01 38.06 3.46
4397 4443 9.620259 AAACTTTTGCCATAAACATAGGAAAAA 57.380 25.926 0.00 0.00 37.55 1.94
4480 4528 4.037923 AGTTCCATGCTGTTTTTGTACAGG 59.962 41.667 0.00 0.00 44.50 4.00
4549 4609 9.720874 AGAGGGAATAATATGCTACTATGATCA 57.279 33.333 0.00 0.00 0.00 2.92
4553 4613 8.954950 CCAAGAGGGAATAATATGCTACTATG 57.045 38.462 0.00 0.00 40.01 2.23
4610 4670 1.202915 ACATGGCTGTGTTCATCCACA 60.203 47.619 0.00 0.00 41.70 4.17
4631 4691 6.535865 TCTTAGAACGTAACAGACTTGCAAAA 59.464 34.615 0.00 0.00 0.00 2.44
4638 4698 6.425114 TCGTACTTCTTAGAACGTAACAGACT 59.575 38.462 5.10 0.00 36.73 3.24
4647 4707 3.114693 AGCGTCGTACTTCTTAGAACG 57.885 47.619 0.00 0.00 36.71 3.95
4659 4719 2.297033 AGGGTAACAAGAAAGCGTCGTA 59.703 45.455 0.00 0.00 39.74 3.43
4663 4723 2.922740 TCAGGGTAACAAGAAAGCGT 57.077 45.000 0.00 0.00 39.74 5.07
4753 4822 8.738645 AGGGAGTACTTTATGAGCTAAAAATG 57.261 34.615 0.00 0.00 0.00 2.32
4781 4850 8.525729 AGACCCTTGTTCTTATATTATGGGAT 57.474 34.615 0.00 0.00 36.20 3.85
4875 5156 5.636903 ACTTGTTCCTAGCCATGATATGT 57.363 39.130 0.00 0.00 0.00 2.29
4901 5182 2.034687 GCAGCCAGAAGCCCAGAA 59.965 61.111 0.00 0.00 45.47 3.02
4964 5245 5.309638 TCAATCAATCCGTCCACAGTTTAA 58.690 37.500 0.00 0.00 0.00 1.52
4966 5247 3.750371 TCAATCAATCCGTCCACAGTTT 58.250 40.909 0.00 0.00 0.00 2.66
4974 5255 2.158755 ACTCCCCATCAATCAATCCGTC 60.159 50.000 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.