Multiple sequence alignment - TraesCS5D01G504000

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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 TraesCS5D01G504000 chr5D 100.000 2667 0 0 1 2667 530492759 530490093 0.000000e+00 4926.0
1 TraesCS5D01G504000 chr5D 84.957 698 76 12 999 1679 530442351 530441666 0.000000e+00 680.0
2 TraesCS5D01G504000 chr5D 84.370 659 85 9 902 1553 530439069 530438422 4.850000e-177 630.0
3 TraesCS5D01G504000 chr5D 80.435 184 35 1 49 231 9338676 9338493 3.580000e-29 139.0
4 TraesCS5D01G504000 chr4A 94.206 1605 81 7 99 1702 641575789 641577382 0.000000e+00 2438.0
5 TraesCS5D01G504000 chr4A 90.376 665 47 9 1702 2359 698370696 698370042 0.000000e+00 857.0
6 TraesCS5D01G504000 chr4A 81.620 778 109 22 903 1655 641579362 641580130 4.880000e-172 614.0
7 TraesCS5D01G504000 chr4A 79.726 804 108 32 913 1698 641588520 641589286 5.060000e-147 531.0
8 TraesCS5D01G504000 chr5B 94.247 956 49 4 750 1702 669690820 669689868 0.000000e+00 1456.0
9 TraesCS5D01G504000 chr5B 84.954 545 74 5 1016 1553 669688185 669687642 1.810000e-151 545.0
10 TraesCS5D01G504000 chr5B 90.345 145 10 4 1701 1843 91047735 91047877 1.260000e-43 187.0
11 TraesCS5D01G504000 chr5B 100.000 35 0 0 569 603 116662609 116662575 6.160000e-07 65.8
12 TraesCS5D01G504000 chr5B 97.222 36 1 0 975 1010 100839628 100839663 7.970000e-06 62.1
13 TraesCS5D01G504000 chr1D 89.896 960 77 8 1720 2667 112475453 112474502 0.000000e+00 1218.0
14 TraesCS5D01G504000 chr1D 89.803 912 76 12 1703 2606 426600437 426601339 0.000000e+00 1153.0
15 TraesCS5D01G504000 chr1D 82.674 733 99 17 810 1531 321319192 321319907 2.250000e-175 625.0
16 TraesCS5D01G504000 chr3B 90.305 918 77 5 1701 2614 664115999 664116908 0.000000e+00 1192.0
17 TraesCS5D01G504000 chr6A 90.481 914 68 11 1702 2606 51726050 51726953 0.000000e+00 1188.0
18 TraesCS5D01G504000 chr3D 90.471 913 68 9 1702 2606 68868837 68867936 0.000000e+00 1186.0
19 TraesCS5D01G504000 chr7A 90.252 913 73 8 1702 2606 632036801 632035897 0.000000e+00 1179.0
20 TraesCS5D01G504000 chr7A 86.667 135 16 2 84 217 329465895 329466028 5.950000e-32 148.0
21 TraesCS5D01G504000 chr2D 89.783 920 72 10 1701 2606 98682375 98681464 0.000000e+00 1158.0
22 TraesCS5D01G504000 chr2D 82.603 799 106 19 912 1686 131388443 131389232 0.000000e+00 675.0
23 TraesCS5D01G504000 chr6D 89.845 906 79 5 1718 2617 418283893 418282995 0.000000e+00 1151.0
24 TraesCS5D01G504000 chr6D 88.100 916 85 11 1702 2606 114160406 114159504 0.000000e+00 1066.0
25 TraesCS5D01G504000 chr6D 81.429 70 11 2 316 385 57788323 57788256 3.710000e-04 56.5
26 TraesCS5D01G504000 chr6B 88.913 911 84 10 1702 2604 637883323 637882422 0.000000e+00 1107.0
27 TraesCS5D01G504000 chr2A 88.229 892 90 6 1702 2586 732268905 732269788 0.000000e+00 1051.0
28 TraesCS5D01G504000 chr2A 79.938 643 98 18 903 1518 138156053 138156691 6.770000e-121 444.0
29 TraesCS5D01G504000 chr4D 87.664 916 84 13 1702 2606 63230184 63229287 0.000000e+00 1038.0
30 TraesCS5D01G504000 chr2B 82.730 967 110 29 750 1686 185793675 185794614 0.000000e+00 808.0
31 TraesCS5D01G504000 chr2B 87.857 280 22 5 1695 1971 656523683 656523953 4.280000e-83 318.0
32 TraesCS5D01G504000 chr7B 83.594 128 21 0 85 212 362529121 362529248 1.300000e-23 121.0
33 TraesCS5D01G504000 chr7B 78.333 180 30 6 8 186 22509148 22509319 1.010000e-19 108.0
34 TraesCS5D01G504000 chr4B 77.340 203 36 6 10 211 60703775 60703968 7.800000e-21 111.0
35 TraesCS5D01G504000 chr7D 86.154 65 7 2 116 180 558983453 558983515 4.760000e-08 69.4


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS5D01G504000 chr5D 530490093 530492759 2666 True 4926.0 4926 100.0000 1 2667 1 chr5D.!!$R2 2666
1 TraesCS5D01G504000 chr5D 530438422 530442351 3929 True 655.0 680 84.6635 902 1679 2 chr5D.!!$R3 777
2 TraesCS5D01G504000 chr4A 641575789 641580130 4341 False 1526.0 2438 87.9130 99 1702 2 chr4A.!!$F2 1603
3 TraesCS5D01G504000 chr4A 698370042 698370696 654 True 857.0 857 90.3760 1702 2359 1 chr4A.!!$R1 657
4 TraesCS5D01G504000 chr4A 641588520 641589286 766 False 531.0 531 79.7260 913 1698 1 chr4A.!!$F1 785
5 TraesCS5D01G504000 chr5B 669687642 669690820 3178 True 1000.5 1456 89.6005 750 1702 2 chr5B.!!$R2 952
6 TraesCS5D01G504000 chr1D 112474502 112475453 951 True 1218.0 1218 89.8960 1720 2667 1 chr1D.!!$R1 947
7 TraesCS5D01G504000 chr1D 426600437 426601339 902 False 1153.0 1153 89.8030 1703 2606 1 chr1D.!!$F2 903
8 TraesCS5D01G504000 chr1D 321319192 321319907 715 False 625.0 625 82.6740 810 1531 1 chr1D.!!$F1 721
9 TraesCS5D01G504000 chr3B 664115999 664116908 909 False 1192.0 1192 90.3050 1701 2614 1 chr3B.!!$F1 913
10 TraesCS5D01G504000 chr6A 51726050 51726953 903 False 1188.0 1188 90.4810 1702 2606 1 chr6A.!!$F1 904
11 TraesCS5D01G504000 chr3D 68867936 68868837 901 True 1186.0 1186 90.4710 1702 2606 1 chr3D.!!$R1 904
12 TraesCS5D01G504000 chr7A 632035897 632036801 904 True 1179.0 1179 90.2520 1702 2606 1 chr7A.!!$R1 904
13 TraesCS5D01G504000 chr2D 98681464 98682375 911 True 1158.0 1158 89.7830 1701 2606 1 chr2D.!!$R1 905
14 TraesCS5D01G504000 chr2D 131388443 131389232 789 False 675.0 675 82.6030 912 1686 1 chr2D.!!$F1 774
15 TraesCS5D01G504000 chr6D 418282995 418283893 898 True 1151.0 1151 89.8450 1718 2617 1 chr6D.!!$R3 899
16 TraesCS5D01G504000 chr6D 114159504 114160406 902 True 1066.0 1066 88.1000 1702 2606 1 chr6D.!!$R2 904
17 TraesCS5D01G504000 chr6B 637882422 637883323 901 True 1107.0 1107 88.9130 1702 2604 1 chr6B.!!$R1 902
18 TraesCS5D01G504000 chr2A 732268905 732269788 883 False 1051.0 1051 88.2290 1702 2586 1 chr2A.!!$F2 884
19 TraesCS5D01G504000 chr2A 138156053 138156691 638 False 444.0 444 79.9380 903 1518 1 chr2A.!!$F1 615
20 TraesCS5D01G504000 chr4D 63229287 63230184 897 True 1038.0 1038 87.6640 1702 2606 1 chr4D.!!$R1 904
21 TraesCS5D01G504000 chr2B 185793675 185794614 939 False 808.0 808 82.7300 750 1686 1 chr2B.!!$F1 936

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
88 89 0.033503 ACGGTTGGATTTGGGGGATC 60.034 55.0 0.00 0.00 0.00 3.36 F
89 90 0.755327 CGGTTGGATTTGGGGGATCC 60.755 60.0 1.92 1.92 42.78 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1012 1055 0.536460 TGCTGATGCATCGCCATGAT 60.536 50.0 28.26 0.0 45.31 2.45 R
1991 2769 0.832135 AGGTGGTGACGATGACAGGT 60.832 55.0 0.00 0.0 0.00 4.00 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
21 22 4.909696 TGGTGTAACAACCACATTTCTG 57.090 40.909 0.00 0.00 45.43 3.02
22 23 3.067461 TGGTGTAACAACCACATTTCTGC 59.933 43.478 0.00 0.00 45.43 4.26
23 24 3.552068 GGTGTAACAACCACATTTCTGCC 60.552 47.826 0.00 0.00 39.98 4.85
24 25 2.625790 TGTAACAACCACATTTCTGCCC 59.374 45.455 0.00 0.00 0.00 5.36
25 26 1.047801 AACAACCACATTTCTGCCCC 58.952 50.000 0.00 0.00 0.00 5.80
26 27 0.105760 ACAACCACATTTCTGCCCCA 60.106 50.000 0.00 0.00 0.00 4.96
27 28 0.318120 CAACCACATTTCTGCCCCAC 59.682 55.000 0.00 0.00 0.00 4.61
28 29 0.105760 AACCACATTTCTGCCCCACA 60.106 50.000 0.00 0.00 0.00 4.17
29 30 0.114954 ACCACATTTCTGCCCCACAT 59.885 50.000 0.00 0.00 0.00 3.21
30 31 0.533491 CCACATTTCTGCCCCACATG 59.467 55.000 0.00 0.00 0.00 3.21
31 32 1.259609 CACATTTCTGCCCCACATGT 58.740 50.000 0.00 0.00 0.00 3.21
32 33 1.067425 CACATTTCTGCCCCACATGTG 60.067 52.381 19.31 19.31 38.98 3.21
44 45 2.378038 CCACATGTGGGTTAGATTGGG 58.622 52.381 33.56 6.51 46.81 4.12
45 46 2.378038 CACATGTGGGTTAGATTGGGG 58.622 52.381 18.51 0.00 0.00 4.96
46 47 1.287739 ACATGTGGGTTAGATTGGGGG 59.712 52.381 0.00 0.00 0.00 5.40
76 77 2.411628 TGGATTGTCCATACGGTTGG 57.588 50.000 0.00 0.00 42.67 3.77
77 78 1.909986 TGGATTGTCCATACGGTTGGA 59.090 47.619 4.61 4.61 42.67 3.53
83 84 2.428544 TCCATACGGTTGGATTTGGG 57.571 50.000 4.61 0.00 40.90 4.12
84 85 1.064314 TCCATACGGTTGGATTTGGGG 60.064 52.381 4.61 0.00 40.90 4.96
85 86 1.398692 CATACGGTTGGATTTGGGGG 58.601 55.000 0.00 0.00 0.00 5.40
86 87 1.064314 CATACGGTTGGATTTGGGGGA 60.064 52.381 0.00 0.00 0.00 4.81
87 88 1.300927 TACGGTTGGATTTGGGGGAT 58.699 50.000 0.00 0.00 0.00 3.85
88 89 0.033503 ACGGTTGGATTTGGGGGATC 60.034 55.000 0.00 0.00 0.00 3.36
89 90 0.755327 CGGTTGGATTTGGGGGATCC 60.755 60.000 1.92 1.92 42.78 3.36
118 119 1.135402 GCCCATTTGATGTCCGAACAC 60.135 52.381 0.00 0.00 38.48 3.32
126 127 3.408851 GTCCGAACACGCCCGAAC 61.409 66.667 0.00 0.00 0.00 3.95
144 145 4.504461 CCGAACGTATGAAGGAGAAATGAG 59.496 45.833 0.00 0.00 0.00 2.90
147 148 4.688021 ACGTATGAAGGAGAAATGAGCTC 58.312 43.478 6.82 6.82 0.00 4.09
171 172 2.771943 ACCTTGGAGGCGATCTTAATCA 59.228 45.455 0.00 0.00 39.63 2.57
172 173 3.392616 ACCTTGGAGGCGATCTTAATCAT 59.607 43.478 0.00 0.00 39.63 2.45
199 200 8.278729 TGTTTGATTCATCTACATGCATTGTA 57.721 30.769 0.00 2.67 39.87 2.41
226 227 0.790814 GCAACGCACAGGAGTTCTAC 59.209 55.000 0.00 0.00 34.64 2.59
262 263 3.641906 AGTATAAAGATGTCGGGGAGGTG 59.358 47.826 0.00 0.00 0.00 4.00
268 269 3.254617 GTCGGGGAGGTGGGGTTT 61.255 66.667 0.00 0.00 0.00 3.27
606 607 5.192496 CAAAGCAAGCACGAAAAATCAAAG 58.808 37.500 0.00 0.00 0.00 2.77
646 647 6.521151 AGAGATGAGGCAAAAATAAACCAG 57.479 37.500 0.00 0.00 0.00 4.00
649 650 7.121315 AGAGATGAGGCAAAAATAAACCAGTAC 59.879 37.037 0.00 0.00 0.00 2.73
653 654 2.912345 GCAAAAATAAACCAGTACGCCG 59.088 45.455 0.00 0.00 0.00 6.46
661 662 1.751927 CCAGTACGCCGACCTACCT 60.752 63.158 0.00 0.00 0.00 3.08
688 689 5.566469 TCCCGAAAGATTACATCCAAAACT 58.434 37.500 0.00 0.00 0.00 2.66
709 710 6.385649 ACTGTACGTTTTGATTGGTTGAAT 57.614 33.333 0.00 0.00 0.00 2.57
711 712 5.444983 TGTACGTTTTGATTGGTTGAATCG 58.555 37.500 0.00 0.00 43.22 3.34
714 715 4.515944 ACGTTTTGATTGGTTGAATCGGTA 59.484 37.500 0.00 0.00 43.22 4.02
740 741 2.741878 CGTGGATTGTATGTCCTCACCC 60.742 54.545 0.00 0.00 36.68 4.61
785 790 3.778718 CGGAATTTTATCTTGCGTCGTTG 59.221 43.478 0.00 0.00 33.47 4.10
789 794 5.856126 ATTTTATCTTGCGTCGTTGAAGA 57.144 34.783 0.00 0.22 0.00 2.87
790 795 4.640805 TTTATCTTGCGTCGTTGAAGAC 57.359 40.909 5.87 0.00 37.76 3.01
820 827 2.058913 GCGCTAGCTAGGTCTGATTC 57.941 55.000 22.10 2.01 41.01 2.52
1012 1055 3.441163 GGTAAGCACGATACGATGACAA 58.559 45.455 0.00 0.00 0.00 3.18
1077 1122 1.381327 CCTCCTGGCTACCGGAGAA 60.381 63.158 9.46 0.00 42.53 2.87
1128 1173 0.108662 TCATCAGAACGACATGCGCT 60.109 50.000 9.73 0.00 46.04 5.92
1137 1182 4.687215 ACATGCGCTGCTGTCGGT 62.687 61.111 9.73 0.00 0.00 4.69
1470 1556 1.208293 GAGGGGAGTGCGAAGAAGAAT 59.792 52.381 0.00 0.00 0.00 2.40
1813 2587 2.161410 CGATACAACACAACCCACATGG 59.839 50.000 0.00 0.00 41.37 3.66
1882 2659 1.069090 ACGACGACACATGCCAACT 59.931 52.632 0.00 0.00 0.00 3.16
1910 2687 1.891919 ACGTGCAAGCAACCGACAT 60.892 52.632 11.27 0.00 0.00 3.06
1917 2694 0.537188 AAGCAACCGACATCTCCGAT 59.463 50.000 0.00 0.00 0.00 4.18
1919 2696 0.931005 GCAACCGACATCTCCGATTC 59.069 55.000 0.00 0.00 0.00 2.52
1991 2769 1.015085 CCGCAAACGACCACCGAATA 61.015 55.000 0.00 0.00 43.93 1.75
2305 3521 1.050988 CCTCCATCACCCGATCCAGT 61.051 60.000 0.00 0.00 0.00 4.00
2306 3522 0.833287 CTCCATCACCCGATCCAGTT 59.167 55.000 0.00 0.00 0.00 3.16
2543 5852 3.809374 GATCCCACGATCCACCGCC 62.809 68.421 0.00 0.00 39.29 6.13
2563 5872 4.248842 CAGACACGCACCACCCCA 62.249 66.667 0.00 0.00 0.00 4.96
2621 5994 1.079819 CGGAGTCCAAGTGCATCGT 60.080 57.895 10.49 0.00 0.00 3.73
2630 6003 4.147322 GTGCATCGTCCGCAACCG 62.147 66.667 0.00 0.00 41.97 4.44
2654 6027 2.123854 AGCCATGGCCAGCAGATG 60.124 61.111 33.14 7.99 43.17 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 3.552068 GGCAGAAATGTGGTTGTTACACC 60.552 47.826 0.00 0.00 38.05 4.16
4 5 2.029380 GGGGCAGAAATGTGGTTGTTAC 60.029 50.000 0.00 0.00 0.00 2.50
6 7 1.047801 GGGGCAGAAATGTGGTTGTT 58.952 50.000 0.00 0.00 0.00 2.83
7 8 0.105760 TGGGGCAGAAATGTGGTTGT 60.106 50.000 0.00 0.00 0.00 3.32
8 9 0.318120 GTGGGGCAGAAATGTGGTTG 59.682 55.000 0.00 0.00 0.00 3.77
9 10 0.105760 TGTGGGGCAGAAATGTGGTT 60.106 50.000 0.00 0.00 0.00 3.67
10 11 0.114954 ATGTGGGGCAGAAATGTGGT 59.885 50.000 0.00 0.00 0.00 4.16
11 12 0.533491 CATGTGGGGCAGAAATGTGG 59.467 55.000 0.00 0.00 0.00 4.17
12 13 1.067425 CACATGTGGGGCAGAAATGTG 60.067 52.381 18.51 4.44 41.35 3.21
13 14 1.259609 CACATGTGGGGCAGAAATGT 58.740 50.000 18.51 0.00 31.79 2.71
14 15 0.533491 CCACATGTGGGGCAGAAATG 59.467 55.000 33.56 6.98 46.81 2.32
15 16 2.980541 CCACATGTGGGGCAGAAAT 58.019 52.632 33.56 0.00 46.81 2.17
16 17 4.517663 CCACATGTGGGGCAGAAA 57.482 55.556 33.56 0.00 46.81 2.52
25 26 2.378038 CCCCAATCTAACCCACATGTG 58.622 52.381 19.31 19.31 0.00 3.21
26 27 1.287739 CCCCCAATCTAACCCACATGT 59.712 52.381 0.00 0.00 0.00 3.21
27 28 2.071778 CCCCCAATCTAACCCACATG 57.928 55.000 0.00 0.00 0.00 3.21
58 59 2.702592 TCCAACCGTATGGACAATCC 57.297 50.000 8.33 0.00 44.52 3.01
65 66 1.398692 CCCCAAATCCAACCGTATGG 58.601 55.000 0.00 0.00 42.12 2.74
66 67 1.064314 TCCCCCAAATCCAACCGTATG 60.064 52.381 0.00 0.00 0.00 2.39
67 68 1.300927 TCCCCCAAATCCAACCGTAT 58.699 50.000 0.00 0.00 0.00 3.06
68 69 1.213430 GATCCCCCAAATCCAACCGTA 59.787 52.381 0.00 0.00 0.00 4.02
69 70 0.033503 GATCCCCCAAATCCAACCGT 60.034 55.000 0.00 0.00 0.00 4.83
70 71 0.755327 GGATCCCCCAAATCCAACCG 60.755 60.000 0.00 0.00 42.01 4.44
71 72 3.223946 GGATCCCCCAAATCCAACC 57.776 57.895 0.00 0.00 42.01 3.77
82 83 3.942439 GCACCTAGCGGGATCCCC 61.942 72.222 25.73 17.38 41.09 4.81
96 97 1.135402 GTTCGGACATCAAATGGGCAC 60.135 52.381 0.00 0.00 33.60 5.01
97 98 1.173043 GTTCGGACATCAAATGGGCA 58.827 50.000 0.00 0.00 33.60 5.36
118 119 0.870307 CTCCTTCATACGTTCGGGCG 60.870 60.000 0.00 0.00 37.94 6.13
126 127 4.054671 GGAGCTCATTTCTCCTTCATACG 58.945 47.826 17.19 0.00 45.13 3.06
147 148 1.961180 AAGATCGCCTCCAAGGTCGG 61.961 60.000 9.01 0.00 37.80 4.79
148 149 0.744874 TAAGATCGCCTCCAAGGTCG 59.255 55.000 0.00 0.00 37.80 4.79
171 172 9.093970 CAATGCATGTAGATGAATCAAACAAAT 57.906 29.630 0.00 0.00 31.64 2.32
172 173 8.089597 ACAATGCATGTAGATGAATCAAACAAA 58.910 29.630 0.00 0.00 41.63 2.83
189 190 4.414852 GTTGCTACAACCTACAATGCATG 58.585 43.478 0.00 0.00 0.00 4.06
199 200 0.884704 CCTGTGCGTTGCTACAACCT 60.885 55.000 4.96 0.00 0.00 3.50
236 237 5.539193 CCTCCCCGACATCTTTATACTACTT 59.461 44.000 0.00 0.00 0.00 2.24
237 238 5.078256 CCTCCCCGACATCTTTATACTACT 58.922 45.833 0.00 0.00 0.00 2.57
238 239 4.831710 ACCTCCCCGACATCTTTATACTAC 59.168 45.833 0.00 0.00 0.00 2.73
246 247 1.995626 CCCACCTCCCCGACATCTT 60.996 63.158 0.00 0.00 0.00 2.40
262 263 1.533033 CTCCCACCCAACAAACCCC 60.533 63.158 0.00 0.00 0.00 4.95
268 269 2.531685 CCTCCCTCCCACCCAACA 60.532 66.667 0.00 0.00 0.00 3.33
340 341 9.725019 AACTCTAGTATTGAATCACAATCACAA 57.275 29.630 0.00 0.00 44.77 3.33
571 572 1.682849 TGCTTTGGCAGGTACCGAT 59.317 52.632 6.18 0.00 44.28 4.18
594 595 6.486253 TCATCTCTCCACTTTGATTTTTCG 57.514 37.500 0.00 0.00 0.00 3.46
606 607 7.363181 CCTCATCTCTTATCATCATCTCTCCAC 60.363 44.444 0.00 0.00 0.00 4.02
646 647 1.332065 GAGTTAGGTAGGTCGGCGTAC 59.668 57.143 11.30 11.30 35.79 3.67
649 650 1.732308 GGAGTTAGGTAGGTCGGCG 59.268 63.158 0.00 0.00 0.00 6.46
653 654 3.359950 TCTTTCGGGAGTTAGGTAGGTC 58.640 50.000 0.00 0.00 0.00 3.85
661 662 5.943349 TGGATGTAATCTTTCGGGAGTTA 57.057 39.130 0.00 0.00 44.71 2.24
688 689 5.444983 CGATTCAACCAATCAAAACGTACA 58.555 37.500 0.00 0.00 41.13 2.90
711 712 2.433239 ACATACAATCCACGGGACTACC 59.567 50.000 0.00 0.00 32.98 3.18
714 715 1.485066 GGACATACAATCCACGGGACT 59.515 52.381 0.00 0.00 36.15 3.85
740 741 5.347093 CGTATTGAGAGAAATCGGATGGATG 59.653 44.000 0.00 0.00 34.93 3.51
766 771 6.077838 GTCTTCAACGACGCAAGATAAAATT 58.922 36.000 7.51 0.00 43.62 1.82
785 790 4.207429 GCTAGCGCTTTATAGTGTGTCTTC 59.793 45.833 18.68 0.00 34.31 2.87
789 794 3.802948 AGCTAGCGCTTTATAGTGTGT 57.197 42.857 18.68 0.00 46.47 3.72
790 795 4.230657 CCTAGCTAGCGCTTTATAGTGTG 58.769 47.826 18.68 0.94 46.47 3.82
876 894 5.048846 ACTATTTTACCAGCGATGGGAAT 57.951 39.130 25.79 21.00 30.69 3.01
1012 1055 0.536460 TGCTGATGCATCGCCATGAT 60.536 50.000 28.26 0.00 45.31 2.45
1035 1080 3.118592 GGATGAGGGTGAGGAGTAAACTG 60.119 52.174 0.00 0.00 0.00 3.16
1036 1081 3.108376 GGATGAGGGTGAGGAGTAAACT 58.892 50.000 0.00 0.00 0.00 2.66
1470 1556 1.825474 GTGTTCTCCTTCCTCATCGGA 59.175 52.381 0.00 0.00 41.06 4.55
1882 2659 2.203266 TTGCACGTGTGGCCATCA 60.203 55.556 18.38 6.28 0.00 3.07
1910 2687 1.007580 CTCGTCGTCAGAATCGGAGA 58.992 55.000 0.00 0.00 45.75 3.71
1917 2694 3.291809 TTATGTTGCTCGTCGTCAGAA 57.708 42.857 0.00 0.00 0.00 3.02
1919 2696 2.345641 CCTTTATGTTGCTCGTCGTCAG 59.654 50.000 0.00 0.00 0.00 3.51
1991 2769 0.832135 AGGTGGTGACGATGACAGGT 60.832 55.000 0.00 0.00 0.00 4.00
2305 3521 3.334583 CGGAGGAAAACCTCAGATCAA 57.665 47.619 16.44 0.00 38.48 2.57
2543 5852 2.972505 GGTGGTGCGTGTCTGGTG 60.973 66.667 0.00 0.00 0.00 4.17
2630 6003 4.783621 TGGCCATGGCTCGTCTGC 62.784 66.667 34.70 17.52 41.60 4.26


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

AutoCloner maintained by Alex Coulton.