Multiple sequence alignment - TraesCS5D01G105100

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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 TraesCS5D01G105100 chr5D 100.000 5316 0 0 1 5316 118999775 119005090 0.000000e+00 9817.0
1 TraesCS5D01G105100 chr5D 95.232 776 34 3 1 775 45126539 45127312 0.000000e+00 1225.0
2 TraesCS5D01G105100 chr5D 88.889 81 8 1 4525 4604 119004220 119004300 1.220000e-16 99.0
3 TraesCS5D01G105100 chr5D 88.889 81 8 1 4446 4526 119004299 119004378 1.220000e-16 99.0
4 TraesCS5D01G105100 chr5B 95.343 4488 129 33 851 5316 131314590 131319019 0.000000e+00 7057.0
5 TraesCS5D01G105100 chr5B 87.654 81 9 1 4525 4604 131318168 131318248 5.670000e-15 93.5
6 TraesCS5D01G105100 chr5A 96.528 4205 110 11 1141 5316 129107342 129111539 0.000000e+00 6924.0
7 TraesCS5D01G105100 chr5A 91.923 260 11 5 851 1109 129107091 129107341 6.550000e-94 355.0
8 TraesCS5D01G105100 chr5A 88.889 81 8 1 4525 4604 129110669 129110749 1.220000e-16 99.0
9 TraesCS5D01G105100 chr5A 89.024 82 6 3 4446 4526 129110748 129110827 1.220000e-16 99.0
10 TraesCS5D01G105100 chr7D 97.287 774 21 0 2 775 378894111 378894884 0.000000e+00 1314.0
11 TraesCS5D01G105100 chr7D 95.747 776 32 1 1 775 392751015 392750240 0.000000e+00 1249.0
12 TraesCS5D01G105100 chr7D 95.244 757 33 3 21 775 575615402 575616157 0.000000e+00 1195.0
13 TraesCS5D01G105100 chr7D 94.201 776 44 1 1 775 98631850 98632625 0.000000e+00 1182.0
14 TraesCS5D01G105100 chr6A 94.974 776 38 1 1 775 518824950 518825725 0.000000e+00 1216.0
15 TraesCS5D01G105100 chr4B 94.588 776 40 2 1 775 60323376 60324150 0.000000e+00 1199.0
16 TraesCS5D01G105100 chr4B 94.201 776 42 3 1 775 474468611 474467838 0.000000e+00 1181.0
17 TraesCS5D01G105100 chr2D 93.830 778 43 4 1 775 190439347 190438572 0.000000e+00 1166.0
18 TraesCS5D01G105100 chr2B 76.793 237 43 6 1464 1694 573826640 573826870 7.230000e-24 122.0


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 TraesCS5D01G105100 chr5D 118999775 119005090 5315 False 3338.333333 9817 92.592667 1 5316 3 chr5D.!!$F2 5315
1 TraesCS5D01G105100 chr5D 45126539 45127312 773 False 1225.000000 1225 95.232000 1 775 1 chr5D.!!$F1 774
2 TraesCS5D01G105100 chr5B 131314590 131319019 4429 False 3575.250000 7057 91.498500 851 5316 2 chr5B.!!$F1 4465
3 TraesCS5D01G105100 chr5A 129107091 129111539 4448 False 1869.250000 6924 91.591000 851 5316 4 chr5A.!!$F1 4465
4 TraesCS5D01G105100 chr7D 378894111 378894884 773 False 1314.000000 1314 97.287000 2 775 1 chr7D.!!$F2 773
5 TraesCS5D01G105100 chr7D 392750240 392751015 775 True 1249.000000 1249 95.747000 1 775 1 chr7D.!!$R1 774
6 TraesCS5D01G105100 chr7D 575615402 575616157 755 False 1195.000000 1195 95.244000 21 775 1 chr7D.!!$F3 754
7 TraesCS5D01G105100 chr7D 98631850 98632625 775 False 1182.000000 1182 94.201000 1 775 1 chr7D.!!$F1 774
8 TraesCS5D01G105100 chr6A 518824950 518825725 775 False 1216.000000 1216 94.974000 1 775 1 chr6A.!!$F1 774
9 TraesCS5D01G105100 chr4B 60323376 60324150 774 False 1199.000000 1199 94.588000 1 775 1 chr4B.!!$F1 774
10 TraesCS5D01G105100 chr4B 474467838 474468611 773 True 1181.000000 1181 94.201000 1 775 1 chr4B.!!$R1 774
11 TraesCS5D01G105100 chr2D 190438572 190439347 775 True 1166.000000 1166 93.830000 1 775 1 chr2D.!!$R1 774

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
775 779 0.040692 GAGTTTCGCGGTTTTGGGTC 60.041 55.000 6.13 0.0 0.00 4.46 F
930 935 0.259065 GTTCCCCTCCCTCCATTTCC 59.741 60.000 0.00 0.0 0.00 3.13 F
2259 2308 0.322816 GGGCTGAGGCTTGTCAATGA 60.323 55.000 5.84 0.0 38.73 2.57 F
3234 3300 0.322816 ATTCGTTGGCAGGTCAGCAT 60.323 50.000 0.00 0.0 35.83 3.79 F
3891 3958 3.220110 CAACCATGGATTCTATGCAGCT 58.780 45.455 21.47 0.0 32.88 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2290 2339 1.227704 TTTCACGCGGAAAGGCTCA 60.228 52.632 12.47 0.0 40.51 4.26 R
2770 2826 1.291877 GAGTGTCGCCAACTTCGCAT 61.292 55.000 0.00 0.0 0.00 4.73 R
3872 3939 3.117776 TGAAGCTGCATAGAATCCATGGT 60.118 43.478 12.58 0.0 0.00 3.55 R
4261 4328 2.679082 GGACTATGCAGACCCCTTCTA 58.321 52.381 0.00 0.0 31.12 2.10 R
4720 4788 4.401925 AGCTAAGCAGACAACTTTTCCAT 58.598 39.130 0.00 0.0 0.00 3.41 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
584 588 3.727146 GGTGTCTTGACGCCGTTT 58.273 55.556 16.21 0.00 0.00 3.60
775 779 0.040692 GAGTTTCGCGGTTTTGGGTC 60.041 55.000 6.13 0.00 0.00 4.46
776 780 1.369568 GTTTCGCGGTTTTGGGTCG 60.370 57.895 6.13 0.00 0.00 4.79
777 781 3.183776 TTTCGCGGTTTTGGGTCGC 62.184 57.895 6.13 0.00 45.15 5.19
782 786 3.579066 CGGTTTTGGGTCGCAATTT 57.421 47.368 2.81 0.00 0.00 1.82
783 787 1.135867 CGGTTTTGGGTCGCAATTTG 58.864 50.000 2.81 0.00 0.00 2.32
784 788 0.865111 GGTTTTGGGTCGCAATTTGC 59.135 50.000 11.42 11.42 40.69 3.68
796 800 3.449322 GCAATTTGCGTACTCTCGAAA 57.551 42.857 5.49 0.00 31.71 3.46
797 801 3.805823 GCAATTTGCGTACTCTCGAAAA 58.194 40.909 5.49 0.00 41.60 2.29
798 802 4.215965 GCAATTTGCGTACTCTCGAAAAA 58.784 39.130 5.49 0.00 40.89 1.94
819 823 3.733443 AACAATCACAAGTCTTTGGCC 57.267 42.857 0.00 0.00 38.66 5.36
820 824 1.608590 ACAATCACAAGTCTTTGGCCG 59.391 47.619 0.00 0.00 38.66 6.13
821 825 1.068333 CAATCACAAGTCTTTGGCCGG 60.068 52.381 0.00 0.00 38.66 6.13
822 826 0.609131 ATCACAAGTCTTTGGCCGGG 60.609 55.000 2.18 0.00 38.66 5.73
823 827 2.115266 ACAAGTCTTTGGCCGGGG 59.885 61.111 2.18 0.00 38.66 5.73
824 828 2.676471 CAAGTCTTTGGCCGGGGG 60.676 66.667 2.18 0.00 0.00 5.40
825 829 3.182996 AAGTCTTTGGCCGGGGGT 61.183 61.111 2.18 0.00 0.00 4.95
826 830 2.774633 AAGTCTTTGGCCGGGGGTT 61.775 57.895 2.18 0.00 0.00 4.11
827 831 2.203582 GTCTTTGGCCGGGGGTTT 60.204 61.111 2.18 0.00 0.00 3.27
828 832 2.203567 TCTTTGGCCGGGGGTTTG 60.204 61.111 2.18 0.00 0.00 2.93
829 833 3.310307 CTTTGGCCGGGGGTTTGG 61.310 66.667 2.18 0.00 0.00 3.28
830 834 3.819016 CTTTGGCCGGGGGTTTGGA 62.819 63.158 2.18 0.00 0.00 3.53
831 835 3.167374 TTTGGCCGGGGGTTTGGAT 62.167 57.895 2.18 0.00 0.00 3.41
832 836 2.681273 TTTGGCCGGGGGTTTGGATT 62.681 55.000 2.18 0.00 0.00 3.01
833 837 1.801302 TTGGCCGGGGGTTTGGATTA 61.801 55.000 2.18 0.00 0.00 1.75
834 838 1.231928 GGCCGGGGGTTTGGATTAT 59.768 57.895 2.18 0.00 0.00 1.28
835 839 0.397957 GGCCGGGGGTTTGGATTATT 60.398 55.000 2.18 0.00 0.00 1.40
836 840 1.491668 GCCGGGGGTTTGGATTATTT 58.508 50.000 2.18 0.00 0.00 1.40
837 841 1.138069 GCCGGGGGTTTGGATTATTTG 59.862 52.381 2.18 0.00 0.00 2.32
838 842 1.138069 CCGGGGGTTTGGATTATTTGC 59.862 52.381 0.00 0.00 0.00 3.68
839 843 1.138069 CGGGGGTTTGGATTATTTGCC 59.862 52.381 0.00 0.00 0.00 4.52
840 844 1.488812 GGGGGTTTGGATTATTTGCCC 59.511 52.381 0.00 0.00 0.00 5.36
841 845 1.488812 GGGGTTTGGATTATTTGCCCC 59.511 52.381 0.00 0.00 46.19 5.80
842 846 1.138069 GGGTTTGGATTATTTGCCCCG 59.862 52.381 0.00 0.00 0.00 5.73
843 847 1.828595 GGTTTGGATTATTTGCCCCGT 59.171 47.619 0.00 0.00 0.00 5.28
844 848 2.235155 GGTTTGGATTATTTGCCCCGTT 59.765 45.455 0.00 0.00 0.00 4.44
845 849 3.517602 GTTTGGATTATTTGCCCCGTTC 58.482 45.455 0.00 0.00 0.00 3.95
846 850 2.818751 TGGATTATTTGCCCCGTTCT 57.181 45.000 0.00 0.00 0.00 3.01
847 851 3.935818 TGGATTATTTGCCCCGTTCTA 57.064 42.857 0.00 0.00 0.00 2.10
848 852 3.547746 TGGATTATTTGCCCCGTTCTAC 58.452 45.455 0.00 0.00 0.00 2.59
849 853 3.201266 TGGATTATTTGCCCCGTTCTACT 59.799 43.478 0.00 0.00 0.00 2.57
879 884 4.084118 CGAGAAAACCAAAGAAGCTGAGAG 60.084 45.833 0.00 0.00 0.00 3.20
880 885 5.041191 AGAAAACCAAAGAAGCTGAGAGA 57.959 39.130 0.00 0.00 0.00 3.10
881 886 4.819088 AGAAAACCAAAGAAGCTGAGAGAC 59.181 41.667 0.00 0.00 0.00 3.36
909 914 0.609957 CATCCCAGCTTGTTCCTGCA 60.610 55.000 0.00 0.00 0.00 4.41
914 919 0.595095 CAGCTTGTTCCTGCAGGTTC 59.405 55.000 31.58 23.83 36.34 3.62
915 920 0.538287 AGCTTGTTCCTGCAGGTTCC 60.538 55.000 31.58 19.93 36.34 3.62
916 921 1.527433 GCTTGTTCCTGCAGGTTCCC 61.527 60.000 31.58 17.58 36.34 3.97
917 922 0.895559 CTTGTTCCTGCAGGTTCCCC 60.896 60.000 31.58 15.92 36.34 4.81
930 935 0.259065 GTTCCCCTCCCTCCATTTCC 59.741 60.000 0.00 0.00 0.00 3.13
937 942 2.319762 CCCTCCATTTCCTGCCCCT 61.320 63.158 0.00 0.00 0.00 4.79
947 952 2.586792 CTGCCCCTTTCCTCCTCG 59.413 66.667 0.00 0.00 0.00 4.63
950 961 2.893398 CCCCTTTCCTCCTCGTCG 59.107 66.667 0.00 0.00 0.00 5.12
961 972 3.004171 CCTCCTCGTCGTCTATATCAGG 58.996 54.545 0.00 0.00 0.00 3.86
1120 1131 1.208293 GAGTCTCCGCCTCTGGATTTT 59.792 52.381 0.00 0.00 37.41 1.82
1171 1182 5.963586 GTCAACTTACCTTGTTTATATGCGC 59.036 40.000 0.00 0.00 0.00 6.09
1270 1281 2.087646 GTTTGGCTTCAGAGGGATCAC 58.912 52.381 0.00 0.00 0.00 3.06
1423 1458 5.272402 TCTGATGACTGTGAAGGAAGGATA 58.728 41.667 0.00 0.00 0.00 2.59
1442 1477 5.179533 GGATACTTCAGAGAAACTGTTCCC 58.820 45.833 0.00 0.00 45.86 3.97
1585 1622 9.847224 TTTTCCCTCCTTAATATCATCTGTAAC 57.153 33.333 0.00 0.00 0.00 2.50
1986 2035 4.274950 TGAAAACCTCGAAAATGACCAGAC 59.725 41.667 0.00 0.00 0.00 3.51
2094 2143 2.026822 GCTGGACTCCTGAGGAATTCAA 60.027 50.000 1.41 0.00 34.81 2.69
2259 2308 0.322816 GGGCTGAGGCTTGTCAATGA 60.323 55.000 5.84 0.00 38.73 2.57
2290 2339 3.913163 AGAGGGTTCTTGAAGGAATCACT 59.087 43.478 0.00 0.00 37.92 3.41
2330 2380 2.367202 CGCAGGGTGGAGGGTATGT 61.367 63.158 0.00 0.00 0.00 2.29
2423 2473 1.485838 CTGAGACCGATCATGTGCGC 61.486 60.000 0.00 0.00 0.00 6.09
2663 2717 4.142838 TGCATGATGCTTTCGTAGAACAAG 60.143 41.667 19.19 0.00 45.31 3.16
2674 2728 3.558418 TCGTAGAACAAGGTTGCTGAAAC 59.442 43.478 0.00 0.00 38.12 2.78
2734 2790 1.271379 ACTTTCCCCAAGATGTCACCG 60.271 52.381 0.00 0.00 36.21 4.94
2770 2826 3.497227 CCATCATAGGACATGCCATGACA 60.497 47.826 12.53 0.00 37.16 3.58
2795 2851 2.165319 AGTTGGCGACACTCTTTACC 57.835 50.000 7.78 0.00 42.67 2.85
2816 2872 4.082245 ACCTGCATGAAATTAAGGAAACCG 60.082 41.667 0.00 0.00 32.03 4.44
2822 2878 5.054390 TGAAATTAAGGAAACCGACATGC 57.946 39.130 0.00 0.00 0.00 4.06
2873 2929 3.323403 TGTTGGGGTGAAATTTGGTGATC 59.677 43.478 0.00 0.00 0.00 2.92
2899 2955 7.657761 CGTTACAAGCCCTTAGATAAGATTCAT 59.342 37.037 1.08 0.00 35.33 2.57
3119 3175 3.054655 GGGTGCTTCTGGGTTGAGTAATA 60.055 47.826 0.00 0.00 0.00 0.98
3234 3300 0.322816 ATTCGTTGGCAGGTCAGCAT 60.323 50.000 0.00 0.00 35.83 3.79
3872 3939 6.551736 GGTAGTTTAACGTCTACGGATACAA 58.448 40.000 7.50 0.00 44.95 2.41
3891 3958 3.220110 CAACCATGGATTCTATGCAGCT 58.780 45.455 21.47 0.00 32.88 4.24
4261 4328 1.752694 GCGACTCTCCAGAGCCTCT 60.753 63.158 3.33 0.00 45.79 3.69
4347 4414 8.806429 TGAATAGTGTGGATAACAATTGTGAT 57.194 30.769 12.82 10.44 41.57 3.06
4557 4625 4.216257 ACAATGTGTGGAGCTTGTATTGTC 59.784 41.667 0.00 0.00 33.46 3.18
4574 4642 7.359595 TGTATTGTCATTTGTTAGCAACAGAC 58.640 34.615 13.21 13.21 43.27 3.51
4720 4788 5.480073 AGTGAGGTGCTTTTATTAAATGCCA 59.520 36.000 18.84 10.28 39.88 4.92
4872 4941 9.216117 GTACAACAGTAATTTCTAGTGTGGAAT 57.784 33.333 8.99 0.00 32.01 3.01
5006 5075 3.901222 TCACTCCACACTGTTGATCCTTA 59.099 43.478 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 2.125552 CGTCAAGGCCTCATCGCA 60.126 61.111 5.23 0.00 0.00 5.10
759 763 3.023950 CGACCCAAAACCGCGAAA 58.976 55.556 8.23 0.00 0.00 3.46
776 780 3.449322 TTTCGAGAGTACGCAAATTGC 57.551 42.857 8.09 8.09 40.69 3.56
796 800 4.875536 GGCCAAAGACTTGTGATTGTTTTT 59.124 37.500 0.00 0.00 0.00 1.94
797 801 4.441792 GGCCAAAGACTTGTGATTGTTTT 58.558 39.130 0.00 0.00 0.00 2.43
798 802 3.490761 CGGCCAAAGACTTGTGATTGTTT 60.491 43.478 2.24 0.00 0.00 2.83
799 803 2.034558 CGGCCAAAGACTTGTGATTGTT 59.965 45.455 2.24 0.00 0.00 2.83
800 804 1.608590 CGGCCAAAGACTTGTGATTGT 59.391 47.619 2.24 0.00 0.00 2.71
801 805 1.068333 CCGGCCAAAGACTTGTGATTG 60.068 52.381 2.24 0.00 0.00 2.67
802 806 1.247567 CCGGCCAAAGACTTGTGATT 58.752 50.000 2.24 0.00 0.00 2.57
803 807 0.609131 CCCGGCCAAAGACTTGTGAT 60.609 55.000 2.24 0.00 0.00 3.06
804 808 1.228124 CCCGGCCAAAGACTTGTGA 60.228 57.895 2.24 0.00 0.00 3.58
805 809 2.268076 CCCCGGCCAAAGACTTGTG 61.268 63.158 2.24 0.00 0.00 3.33
806 810 2.115266 CCCCGGCCAAAGACTTGT 59.885 61.111 2.24 0.00 0.00 3.16
807 811 2.676471 CCCCCGGCCAAAGACTTG 60.676 66.667 2.24 0.00 0.00 3.16
808 812 2.306715 AAACCCCCGGCCAAAGACTT 62.307 55.000 2.24 0.00 0.00 3.01
809 813 2.774633 AAACCCCCGGCCAAAGACT 61.775 57.895 2.24 0.00 0.00 3.24
810 814 2.203582 AAACCCCCGGCCAAAGAC 60.204 61.111 2.24 0.00 0.00 3.01
811 815 2.203567 CAAACCCCCGGCCAAAGA 60.204 61.111 2.24 0.00 0.00 2.52
812 816 3.310307 CCAAACCCCCGGCCAAAG 61.310 66.667 2.24 0.00 0.00 2.77
813 817 2.681273 AATCCAAACCCCCGGCCAAA 62.681 55.000 2.24 0.00 0.00 3.28
814 818 1.801302 TAATCCAAACCCCCGGCCAA 61.801 55.000 2.24 0.00 0.00 4.52
815 819 1.585651 ATAATCCAAACCCCCGGCCA 61.586 55.000 2.24 0.00 0.00 5.36
816 820 0.397957 AATAATCCAAACCCCCGGCC 60.398 55.000 0.00 0.00 0.00 6.13
817 821 1.138069 CAAATAATCCAAACCCCCGGC 59.862 52.381 0.00 0.00 0.00 6.13
818 822 1.138069 GCAAATAATCCAAACCCCCGG 59.862 52.381 0.00 0.00 0.00 5.73
819 823 1.138069 GGCAAATAATCCAAACCCCCG 59.862 52.381 0.00 0.00 0.00 5.73
820 824 1.488812 GGGCAAATAATCCAAACCCCC 59.511 52.381 0.00 0.00 0.00 5.40
822 826 1.138069 CGGGGCAAATAATCCAAACCC 59.862 52.381 0.00 0.00 34.99 4.11
823 827 1.828595 ACGGGGCAAATAATCCAAACC 59.171 47.619 0.00 0.00 0.00 3.27
824 828 3.194755 AGAACGGGGCAAATAATCCAAAC 59.805 43.478 0.00 0.00 0.00 2.93
825 829 3.436243 AGAACGGGGCAAATAATCCAAA 58.564 40.909 0.00 0.00 0.00 3.28
826 830 3.094484 AGAACGGGGCAAATAATCCAA 57.906 42.857 0.00 0.00 0.00 3.53
827 831 2.818751 AGAACGGGGCAAATAATCCA 57.181 45.000 0.00 0.00 0.00 3.41
828 832 3.816994 AGTAGAACGGGGCAAATAATCC 58.183 45.455 0.00 0.00 0.00 3.01
829 833 5.449999 CCAAAGTAGAACGGGGCAAATAATC 60.450 44.000 0.00 0.00 0.00 1.75
830 834 4.401202 CCAAAGTAGAACGGGGCAAATAAT 59.599 41.667 0.00 0.00 0.00 1.28
831 835 3.759618 CCAAAGTAGAACGGGGCAAATAA 59.240 43.478 0.00 0.00 0.00 1.40
832 836 3.349022 CCAAAGTAGAACGGGGCAAATA 58.651 45.455 0.00 0.00 0.00 1.40
833 837 2.167662 CCAAAGTAGAACGGGGCAAAT 58.832 47.619 0.00 0.00 0.00 2.32
834 838 1.611519 CCAAAGTAGAACGGGGCAAA 58.388 50.000 0.00 0.00 0.00 3.68
835 839 0.891904 GCCAAAGTAGAACGGGGCAA 60.892 55.000 0.00 0.00 41.02 4.52
836 840 1.302993 GCCAAAGTAGAACGGGGCA 60.303 57.895 0.00 0.00 41.02 5.36
837 841 2.044555 GGCCAAAGTAGAACGGGGC 61.045 63.158 0.00 0.00 40.63 5.80
838 842 1.378119 GGGCCAAAGTAGAACGGGG 60.378 63.158 4.39 0.00 0.00 5.73
839 843 1.743995 CGGGCCAAAGTAGAACGGG 60.744 63.158 4.39 0.00 0.00 5.28
840 844 0.739813 CTCGGGCCAAAGTAGAACGG 60.740 60.000 4.39 0.00 0.00 4.44
841 845 0.245539 TCTCGGGCCAAAGTAGAACG 59.754 55.000 4.39 0.00 0.00 3.95
842 846 2.467566 TTCTCGGGCCAAAGTAGAAC 57.532 50.000 4.39 0.00 0.00 3.01
843 847 3.143728 GTTTTCTCGGGCCAAAGTAGAA 58.856 45.455 4.39 2.63 0.00 2.10
844 848 2.551504 GGTTTTCTCGGGCCAAAGTAGA 60.552 50.000 4.39 0.00 0.00 2.59
845 849 1.810755 GGTTTTCTCGGGCCAAAGTAG 59.189 52.381 4.39 0.00 0.00 2.57
846 850 1.143277 TGGTTTTCTCGGGCCAAAGTA 59.857 47.619 4.39 0.00 0.00 2.24
847 851 0.106419 TGGTTTTCTCGGGCCAAAGT 60.106 50.000 4.39 0.00 0.00 2.66
848 852 1.036707 TTGGTTTTCTCGGGCCAAAG 58.963 50.000 4.39 0.10 37.97 2.77
849 853 1.410882 CTTTGGTTTTCTCGGGCCAAA 59.589 47.619 4.39 4.97 45.36 3.28
890 895 0.609957 TGCAGGAACAAGCTGGGATG 60.610 55.000 0.00 0.00 32.89 3.51
891 896 0.323178 CTGCAGGAACAAGCTGGGAT 60.323 55.000 5.57 0.00 32.89 3.85
914 919 1.925888 CAGGAAATGGAGGGAGGGG 59.074 63.158 0.00 0.00 0.00 4.79
915 920 1.228510 GCAGGAAATGGAGGGAGGG 59.771 63.158 0.00 0.00 0.00 4.30
916 921 1.228510 GGCAGGAAATGGAGGGAGG 59.771 63.158 0.00 0.00 0.00 4.30
917 922 1.228510 GGGCAGGAAATGGAGGGAG 59.771 63.158 0.00 0.00 0.00 4.30
930 935 2.245438 GACGAGGAGGAAAGGGGCAG 62.245 65.000 0.00 0.00 0.00 4.85
937 942 4.711399 TGATATAGACGACGAGGAGGAAA 58.289 43.478 0.00 0.00 0.00 3.13
947 952 0.896226 GGGGGCCTGATATAGACGAC 59.104 60.000 0.84 0.00 0.00 4.34
967 978 0.462759 GAAGGAGGAGTCCATTGGCG 60.463 60.000 12.86 0.00 46.80 5.69
1120 1131 4.338118 GCGTTGATTTTATCCCAAGGATGA 59.662 41.667 6.38 0.00 43.06 2.92
1130 1141 4.156008 AGTTGACCAGGCGTTGATTTTATC 59.844 41.667 0.00 0.00 0.00 1.75
1171 1182 0.469070 CCTTCAGATCAGCCCAGGAG 59.531 60.000 0.00 0.00 0.00 3.69
1270 1281 0.543749 GGTCATGAACTCCTCCCCTG 59.456 60.000 2.64 0.00 0.00 4.45
1442 1477 2.424956 GGCCTTTCATTAGCTGTTCCTG 59.575 50.000 0.00 0.00 0.00 3.86
1455 1490 7.953005 TCACAAATGAATAATAGGCCTTTCA 57.047 32.000 12.58 15.91 33.06 2.69
1585 1622 6.088824 GCAGATGTGAGAAAGGTTGTAATTG 58.911 40.000 0.00 0.00 0.00 2.32
1986 2035 2.162608 TGACCAAACCTGACAACGTTTG 59.837 45.455 15.92 15.92 45.40 2.93
2094 2143 2.027192 CGGCCCCATACTATATGCTTGT 60.027 50.000 0.00 0.00 0.00 3.16
2259 2308 2.110899 TCAAGAACCCTCTCTCCAGAGT 59.889 50.000 3.50 0.00 44.49 3.24
2290 2339 1.227704 TTTCACGCGGAAAGGCTCA 60.228 52.632 12.47 0.00 40.51 4.26
2330 2380 7.466746 AAAGCTTAAATGTGAGGCAAATAGA 57.533 32.000 0.00 0.00 0.00 1.98
2423 2473 4.022068 TCAAATCCTACAAAAGCAGCAAGG 60.022 41.667 0.00 0.00 0.00 3.61
2663 2717 3.211045 TGTTAGTCCAGTTTCAGCAACC 58.789 45.455 0.00 0.00 35.77 3.77
2674 2728 4.377897 ACCGAAAGAACTTGTTAGTCCAG 58.622 43.478 0.00 0.00 31.99 3.86
2770 2826 1.291877 GAGTGTCGCCAACTTCGCAT 61.292 55.000 0.00 0.00 0.00 4.73
2795 2851 5.095490 GTCGGTTTCCTTAATTTCATGCAG 58.905 41.667 0.00 0.00 0.00 4.41
2816 2872 5.179742 TGGCATCAAAGAAAAATTGCATGTC 59.820 36.000 0.00 0.00 0.00 3.06
2822 2878 8.537049 TGAAGTATGGCATCAAAGAAAAATTG 57.463 30.769 1.65 0.00 0.00 2.32
2873 2929 6.984474 TGAATCTTATCTAAGGGCTTGTAACG 59.016 38.462 0.00 0.00 34.14 3.18
2899 2955 4.565652 GGATAAAGCACCTTCTCTGGTTGA 60.566 45.833 0.00 0.00 38.45 3.18
3119 3175 8.571461 TTCAGTATCTGCTGATTTTGAAGAAT 57.429 30.769 19.33 0.00 43.99 2.40
3234 3300 6.518537 GCAAGAAGTCTCCTTGAAACCTACTA 60.519 42.308 2.50 0.00 42.57 1.82
3872 3939 3.117776 TGAAGCTGCATAGAATCCATGGT 60.118 43.478 12.58 0.00 0.00 3.55
4261 4328 2.679082 GGACTATGCAGACCCCTTCTA 58.321 52.381 0.00 0.00 31.12 2.10
4347 4414 3.849574 TCCTTGATCCCCACATTGTTCTA 59.150 43.478 0.00 0.00 0.00 2.10
4720 4788 4.401925 AGCTAAGCAGACAACTTTTCCAT 58.598 39.130 0.00 0.00 0.00 3.41
4872 4941 8.740123 AATTTCATATTTGGGATGTGTACGTA 57.260 30.769 0.00 0.00 0.00 3.57
5006 5075 5.753721 AGTATCTTCTTGAAGCTCCTTGT 57.246 39.130 5.56 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.