Multiple sequence alignment - TraesCS5D01G219600

Loading Multiple Alignment...

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 TraesCS5D01G219600 chr5D 100.000 3032 0 0 1 3032 328724134 328727165 0.000000e+00 5600.0
1 TraesCS5D01G219600 chr5D 88.934 741 75 4 2225 2962 236228893 236228157 0.000000e+00 907.0
2 TraesCS5D01G219600 chr5B 93.114 1365 54 21 704 2050 382081082 382082424 0.000000e+00 1964.0
3 TraesCS5D01G219600 chr5B 84.768 604 62 22 6 601 382080246 382080827 2.030000e-161 579.0
4 TraesCS5D01G219600 chr5B 93.651 63 4 0 2059 2121 382082714 382082776 8.950000e-16 95.3
5 TraesCS5D01G219600 chr5A 91.279 1376 60 21 704 2050 427821217 427819873 0.000000e+00 1821.0
6 TraesCS5D01G219600 chr5A 93.532 603 20 10 1 601 427822038 427821453 0.000000e+00 880.0
7 TraesCS5D01G219600 chr5A 96.774 62 2 0 2060 2121 427819327 427819266 1.490000e-18 104.0
8 TraesCS5D01G219600 chr4D 90.315 888 77 8 2125 3007 465441325 465442208 0.000000e+00 1155.0
9 TraesCS5D01G219600 chr4D 86.092 870 113 6 2137 3002 504377501 504376636 0.000000e+00 929.0
10 TraesCS5D01G219600 chr4D 86.179 861 113 5 2146 3002 504406869 504406011 0.000000e+00 926.0
11 TraesCS5D01G219600 chrUn 87.973 898 91 9 2119 3002 112022909 112022015 0.000000e+00 1044.0
12 TraesCS5D01G219600 chr6A 87.603 847 99 5 2122 2965 85584110 85584953 0.000000e+00 977.0
13 TraesCS5D01G219600 chr2D 89.460 759 71 8 2121 2876 24526454 24527206 0.000000e+00 950.0
14 TraesCS5D01G219600 chr6D 89.125 754 71 9 2129 2878 286638716 286639462 0.000000e+00 928.0
15 TraesCS5D01G219600 chr7D 84.563 881 124 9 2127 3003 458523172 458522300 0.000000e+00 863.0
16 TraesCS5D01G219600 chr7D 81.797 423 58 10 2585 3003 59871071 59871478 1.350000e-88 337.0
17 TraesCS5D01G219600 chr3D 88.662 538 37 9 2473 3004 30764195 30764714 4.260000e-178 634.0
18 TraesCS5D01G219600 chr3D 90.948 232 19 2 2790 3020 359340616 359340386 8.160000e-81 311.0


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 TraesCS5D01G219600 chr5D 328724134 328727165 3031 False 5600.000000 5600 100.000000 1 3032 1 chr5D.!!$F1 3031
1 TraesCS5D01G219600 chr5D 236228157 236228893 736 True 907.000000 907 88.934000 2225 2962 1 chr5D.!!$R1 737
2 TraesCS5D01G219600 chr5B 382080246 382082776 2530 False 879.433333 1964 90.511000 6 2121 3 chr5B.!!$F1 2115
3 TraesCS5D01G219600 chr5A 427819266 427822038 2772 True 935.000000 1821 93.861667 1 2121 3 chr5A.!!$R1 2120
4 TraesCS5D01G219600 chr4D 465441325 465442208 883 False 1155.000000 1155 90.315000 2125 3007 1 chr4D.!!$F1 882
5 TraesCS5D01G219600 chr4D 504376636 504377501 865 True 929.000000 929 86.092000 2137 3002 1 chr4D.!!$R1 865
6 TraesCS5D01G219600 chr4D 504406011 504406869 858 True 926.000000 926 86.179000 2146 3002 1 chr4D.!!$R2 856
7 TraesCS5D01G219600 chrUn 112022015 112022909 894 True 1044.000000 1044 87.973000 2119 3002 1 chrUn.!!$R1 883
8 TraesCS5D01G219600 chr6A 85584110 85584953 843 False 977.000000 977 87.603000 2122 2965 1 chr6A.!!$F1 843
9 TraesCS5D01G219600 chr2D 24526454 24527206 752 False 950.000000 950 89.460000 2121 2876 1 chr2D.!!$F1 755
10 TraesCS5D01G219600 chr6D 286638716 286639462 746 False 928.000000 928 89.125000 2129 2878 1 chr6D.!!$F1 749
11 TraesCS5D01G219600 chr7D 458522300 458523172 872 True 863.000000 863 84.563000 2127 3003 1 chr7D.!!$R1 876
12 TraesCS5D01G219600 chr3D 30764195 30764714 519 False 634.000000 634 88.662000 2473 3004 1 chr3D.!!$F1 531

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
849 1036 0.179148 CTTTCCGCCGCCAATTAACC 60.179 55.0 0.0 0.0 0.0 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2124 2873 0.10412 CGATGTGGGCGTTATCAGGA 59.896 55.0 0.0 0.0 0.0 3.86 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
139 140 0.318784 GGTCATCCGACGTGATAGCC 60.319 60.000 0.00 0.00 43.61 3.93
160 161 2.674852 CGTGCTGTCATCATAAGCTTGT 59.325 45.455 9.86 0.00 37.82 3.16
251 252 5.125100 TCTTTGCTTGTGATTGGTGAATC 57.875 39.130 0.00 0.00 38.85 2.52
271 272 1.201965 CGTGAATTGCTTCTTCGCTCC 60.202 52.381 0.00 0.00 32.29 4.70
309 314 8.286097 GCTGCTTGATAGTTTAATAAGATGACC 58.714 37.037 0.00 0.00 0.00 4.02
334 339 1.765314 AGACTTCAGAAGTGGCTGTGT 59.235 47.619 21.00 0.00 43.03 3.72
434 447 2.744202 AGCTGACTGAAAATAACCTGCG 59.256 45.455 0.00 0.00 0.00 5.18
556 573 3.695060 AGAGTTGGTGTATCGGTACAGAG 59.305 47.826 9.25 0.00 41.29 3.35
601 619 7.335924 TGAGGGTTTAGTCATACAAAATGCTAC 59.664 37.037 0.00 0.00 0.00 3.58
603 621 7.553044 AGGGTTTAGTCATACAAAATGCTACTC 59.447 37.037 0.00 0.00 0.00 2.59
604 622 7.201705 GGGTTTAGTCATACAAAATGCTACTCC 60.202 40.741 0.00 0.00 0.00 3.85
605 623 7.201705 GGTTTAGTCATACAAAATGCTACTCCC 60.202 40.741 0.00 0.00 0.00 4.30
606 624 5.700402 AGTCATACAAAATGCTACTCCCT 57.300 39.130 0.00 0.00 0.00 4.20
608 626 4.816925 GTCATACAAAATGCTACTCCCTCC 59.183 45.833 0.00 0.00 0.00 4.30
609 627 4.473196 TCATACAAAATGCTACTCCCTCCA 59.527 41.667 0.00 0.00 0.00 3.86
611 629 6.328934 TCATACAAAATGCTACTCCCTCCATA 59.671 38.462 0.00 0.00 0.00 2.74
625 742 3.624777 CCTCCATAAAACTGATGCCACT 58.375 45.455 0.00 0.00 0.00 4.00
630 747 1.523758 AAAACTGATGCCACTCGGAC 58.476 50.000 0.00 0.00 0.00 4.79
640 757 1.289066 CACTCGGACAGCGAAAGGA 59.711 57.895 0.00 0.00 0.00 3.36
649 766 4.698575 GGACAGCGAAAGGAAGATCTTAT 58.301 43.478 8.25 0.00 0.00 1.73
676 795 7.872113 AGGATACAAATTTCTCCAGTCAATC 57.128 36.000 11.59 0.00 41.41 2.67
701 820 0.462225 GACCTAGCTTTTCCGAGCCC 60.462 60.000 0.00 0.00 43.74 5.19
702 821 0.910088 ACCTAGCTTTTCCGAGCCCT 60.910 55.000 0.00 0.00 43.74 5.19
760 932 1.455959 CCCACCCGGTCAACCAAAA 60.456 57.895 0.00 0.00 35.14 2.44
761 933 1.460273 CCCACCCGGTCAACCAAAAG 61.460 60.000 0.00 0.00 35.14 2.27
763 935 1.830847 ACCCGGTCAACCAAAAGCC 60.831 57.895 0.00 0.00 35.14 4.35
765 937 2.570284 CCGGTCAACCAAAAGCCCC 61.570 63.158 0.00 0.00 35.14 5.80
766 938 1.530655 CGGTCAACCAAAAGCCCCT 60.531 57.895 0.00 0.00 35.14 4.79
768 940 0.469144 GGTCAACCAAAAGCCCCTCA 60.469 55.000 0.00 0.00 35.64 3.86
769 941 1.632589 GTCAACCAAAAGCCCCTCAT 58.367 50.000 0.00 0.00 0.00 2.90
772 944 0.611896 AACCAAAAGCCCCTCATCGG 60.612 55.000 0.00 0.00 0.00 4.18
793 980 2.275812 CGCGCGACCGAATCAAAC 60.276 61.111 28.94 0.00 36.29 2.93
794 981 2.857448 GCGCGACCGAATCAAACA 59.143 55.556 12.10 0.00 36.29 2.83
795 982 1.205568 GCGCGACCGAATCAAACAA 59.794 52.632 12.10 0.00 36.29 2.83
796 983 0.384974 GCGCGACCGAATCAAACAAA 60.385 50.000 12.10 0.00 36.29 2.83
797 984 1.314581 CGCGACCGAATCAAACAAAC 58.685 50.000 0.00 0.00 36.29 2.93
798 985 1.314581 GCGACCGAATCAAACAAACG 58.685 50.000 0.00 0.00 0.00 3.60
799 986 1.314581 CGACCGAATCAAACAAACGC 58.685 50.000 0.00 0.00 0.00 4.84
800 987 1.333347 CGACCGAATCAAACAAACGCA 60.333 47.619 0.00 0.00 0.00 5.24
808 995 4.576106 ATCAAACAAACGCAACACAAAC 57.424 36.364 0.00 0.00 0.00 2.93
809 996 3.643763 TCAAACAAACGCAACACAAACT 58.356 36.364 0.00 0.00 0.00 2.66
815 1002 2.319136 ACGCAACACAAACTACTCCA 57.681 45.000 0.00 0.00 0.00 3.86
819 1006 3.548014 CGCAACACAAACTACTCCAAAGG 60.548 47.826 0.00 0.00 0.00 3.11
845 1032 4.114997 CGCTTTCCGCCGCCAATT 62.115 61.111 0.00 0.00 34.21 2.32
847 1034 1.509004 GCTTTCCGCCGCCAATTAA 59.491 52.632 0.00 0.00 0.00 1.40
848 1035 0.800683 GCTTTCCGCCGCCAATTAAC 60.801 55.000 0.00 0.00 0.00 2.01
849 1036 0.179148 CTTTCCGCCGCCAATTAACC 60.179 55.000 0.00 0.00 0.00 2.85
850 1037 0.609681 TTTCCGCCGCCAATTAACCT 60.610 50.000 0.00 0.00 0.00 3.50
853 1040 1.714899 CCGCCGCCAATTAACCTCTG 61.715 60.000 0.00 0.00 0.00 3.35
854 1041 1.433471 GCCGCCAATTAACCTCTGC 59.567 57.895 0.00 0.00 0.00 4.26
855 1042 2.004808 GCCGCCAATTAACCTCTGCC 62.005 60.000 0.00 0.00 0.00 4.85
856 1043 0.394352 CCGCCAATTAACCTCTGCCT 60.394 55.000 0.00 0.00 0.00 4.75
941 1129 2.791613 TATATAGCCCGCTCCGCCCA 62.792 60.000 0.00 0.00 0.00 5.36
983 1176 1.070758 ACGCACAGGATTGTCTCTGTT 59.929 47.619 0.00 0.00 41.71 3.16
1316 1512 4.803426 GAGCCCGCTCACCGTCAG 62.803 72.222 11.81 0.00 42.31 3.51
1434 1630 1.979155 CAGGAGCAGGACGGTGAGA 60.979 63.158 0.00 0.00 0.00 3.27
1435 1631 1.680651 AGGAGCAGGACGGTGAGAG 60.681 63.158 0.00 0.00 0.00 3.20
2052 2251 2.749839 GCGTGGGCTGGCATTACA 60.750 61.111 2.88 0.00 35.83 2.41
2053 2252 2.120909 GCGTGGGCTGGCATTACAT 61.121 57.895 2.88 0.00 35.83 2.29
2054 2253 1.729276 CGTGGGCTGGCATTACATG 59.271 57.895 2.88 0.00 0.00 3.21
2075 2824 0.517316 CCTTAGCGTTTGTGACAGGC 59.483 55.000 0.00 0.00 0.00 4.85
2121 2870 2.185004 TTCTCCTCCCTTTCGCTTTG 57.815 50.000 0.00 0.00 0.00 2.77
2122 2871 0.324943 TCTCCTCCCTTTCGCTTTGG 59.675 55.000 0.00 0.00 0.00 3.28
2123 2872 0.678048 CTCCTCCCTTTCGCTTTGGG 60.678 60.000 0.00 0.00 42.20 4.12
2124 2873 1.074951 CCTCCCTTTCGCTTTGGGT 59.925 57.895 0.00 0.00 41.58 4.51
2125 2874 0.960861 CCTCCCTTTCGCTTTGGGTC 60.961 60.000 0.00 0.00 41.58 4.46
2141 2890 0.180406 GGTCCTGATAACGCCCACAT 59.820 55.000 0.00 0.00 0.00 3.21
2144 2893 0.880278 CCTGATAACGCCCACATCGG 60.880 60.000 0.00 0.00 0.00 4.18
2176 2930 1.346395 GACATCCGCCCATACACCATA 59.654 52.381 0.00 0.00 0.00 2.74
2191 2945 2.696989 CCATATGTGGTGTGAGCAGA 57.303 50.000 0.00 0.00 40.83 4.26
2205 2959 1.746991 GCAGAAGGCAGCCTACACC 60.747 63.158 16.56 4.63 43.97 4.16
2223 2977 2.258013 CGGTTGTGTGTGGGCGAAT 61.258 57.895 0.00 0.00 0.00 3.34
2233 2987 6.350103 TGTGTGTGGGCGAATATTAGAATTA 58.650 36.000 0.00 0.00 0.00 1.40
2240 2994 5.944007 GGGCGAATATTAGAATTACCCACAT 59.056 40.000 0.00 0.00 36.20 3.21
2274 3034 1.651987 ACTTTGTGTCACACGTCCAG 58.348 50.000 4.80 0.00 37.14 3.86
2285 3045 1.271656 ACACGTCCAGCAAGTACTACC 59.728 52.381 0.00 0.00 0.00 3.18
2292 3053 2.119495 CAGCAAGTACTACCCATCCCT 58.881 52.381 0.00 0.00 0.00 4.20
2298 3059 3.136896 AGTACTACCCATCCCTACCTCA 58.863 50.000 0.00 0.00 0.00 3.86
2513 3277 4.391830 CGTGTGTGATTAACTACTTGCCAT 59.608 41.667 0.00 0.00 0.00 4.40
2515 3279 6.091577 CGTGTGTGATTAACTACTTGCCATAA 59.908 38.462 0.00 0.00 0.00 1.90
2561 3326 3.069300 TGTGTTTACCTAGTTGCCACGTA 59.931 43.478 0.00 0.00 0.00 3.57
2621 3393 7.446931 ACAATTGTCATGTGTGTTTATCTGGTA 59.553 33.333 4.92 0.00 0.00 3.25
2623 3395 6.109156 TGTCATGTGTGTTTATCTGGTAGT 57.891 37.500 0.00 0.00 0.00 2.73
2655 3427 0.387367 ACTGCAGTTGTCGTCTAGCG 60.387 55.000 15.25 0.83 43.01 4.26
2674 3446 3.057019 GCGACGAATCATAGTTGCCATA 58.943 45.455 0.00 0.00 40.82 2.74
2730 3503 1.240256 TTGCCATCCAACAACGTACC 58.760 50.000 0.00 0.00 0.00 3.34
2910 3685 3.055819 ACGTGGCACTCAGATTCTAACAT 60.056 43.478 16.72 0.00 0.00 2.71
2915 3692 7.517417 CGTGGCACTCAGATTCTAACATATTTC 60.517 40.741 16.72 0.00 0.00 2.17
2918 3699 8.897752 GGCACTCAGATTCTAACATATTTCTTT 58.102 33.333 0.00 0.00 0.00 2.52
2981 3763 1.074319 GCGATGTGCAAACATGCCAG 61.074 55.000 0.00 0.00 45.45 4.85
2984 3766 1.270274 GATGTGCAAACATGCCAGACA 59.730 47.619 0.00 0.00 0.00 3.41
3007 3789 4.340617 TGTGGGAGTTATCATTTGGGTTC 58.659 43.478 0.00 0.00 0.00 3.62
3008 3790 4.044065 TGTGGGAGTTATCATTTGGGTTCT 59.956 41.667 0.00 0.00 0.00 3.01
3009 3791 5.251932 TGTGGGAGTTATCATTTGGGTTCTA 59.748 40.000 0.00 0.00 0.00 2.10
3010 3792 6.069088 TGTGGGAGTTATCATTTGGGTTCTAT 60.069 38.462 0.00 0.00 0.00 1.98
3011 3793 6.833933 GTGGGAGTTATCATTTGGGTTCTATT 59.166 38.462 0.00 0.00 0.00 1.73
3012 3794 7.342026 GTGGGAGTTATCATTTGGGTTCTATTT 59.658 37.037 0.00 0.00 0.00 1.40
3013 3795 8.561769 TGGGAGTTATCATTTGGGTTCTATTTA 58.438 33.333 0.00 0.00 0.00 1.40
3014 3796 8.847196 GGGAGTTATCATTTGGGTTCTATTTAC 58.153 37.037 0.00 0.00 0.00 2.01
3015 3797 9.628500 GGAGTTATCATTTGGGTTCTATTTACT 57.372 33.333 0.00 0.00 0.00 2.24
3019 3801 7.573968 ATCATTTGGGTTCTATTTACTCTGC 57.426 36.000 0.00 0.00 0.00 4.26
3020 3802 6.480763 TCATTTGGGTTCTATTTACTCTGCA 58.519 36.000 0.00 0.00 0.00 4.41
3021 3803 7.118723 TCATTTGGGTTCTATTTACTCTGCAT 58.881 34.615 0.00 0.00 0.00 3.96
3022 3804 7.283127 TCATTTGGGTTCTATTTACTCTGCATC 59.717 37.037 0.00 0.00 0.00 3.91
3023 3805 5.957771 TGGGTTCTATTTACTCTGCATCT 57.042 39.130 0.00 0.00 0.00 2.90
3024 3806 6.313519 TGGGTTCTATTTACTCTGCATCTT 57.686 37.500 0.00 0.00 0.00 2.40
3025 3807 7.432148 TGGGTTCTATTTACTCTGCATCTTA 57.568 36.000 0.00 0.00 0.00 2.10
3026 3808 7.500992 TGGGTTCTATTTACTCTGCATCTTAG 58.499 38.462 0.00 0.00 0.00 2.18
3027 3809 7.125811 TGGGTTCTATTTACTCTGCATCTTAGT 59.874 37.037 0.00 0.00 0.00 2.24
3028 3810 7.988028 GGGTTCTATTTACTCTGCATCTTAGTT 59.012 37.037 0.00 0.00 0.00 2.24
3029 3811 9.384764 GGTTCTATTTACTCTGCATCTTAGTTT 57.615 33.333 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
139 140 2.674852 ACAAGCTTATGATGACAGCACG 59.325 45.455 0.00 0.00 0.00 5.34
251 252 1.201965 GGAGCGAAGAAGCAATTCACG 60.202 52.381 0.00 0.00 40.15 4.35
271 272 1.469703 TCAAGCAGCATTTCCACGATG 59.530 47.619 0.00 0.00 0.00 3.84
309 314 1.996191 GCCACTTCTGAAGTCTAAGCG 59.004 52.381 19.65 8.02 40.46 4.68
353 366 1.310904 GTTTAGACGCCCACCAAACA 58.689 50.000 0.00 0.00 0.00 2.83
374 387 0.036388 GACCCTGCCGATCTGTCAAA 60.036 55.000 0.00 0.00 0.00 2.69
413 426 2.744202 CGCAGGTTATTTTCAGTCAGCT 59.256 45.455 0.00 0.00 0.00 4.24
416 429 2.499197 TGCGCAGGTTATTTTCAGTCA 58.501 42.857 5.66 0.00 0.00 3.41
434 447 0.593128 ACCAAGCGTTCTTCACATGC 59.407 50.000 0.00 0.00 0.00 4.06
475 488 0.957395 CCGAGCCAAGTGCAATGTCT 60.957 55.000 0.00 0.00 44.83 3.41
556 573 3.375699 TCACCCTCCTAGAGACAAATCC 58.624 50.000 0.00 0.00 0.00 3.01
601 619 3.217626 GGCATCAGTTTTATGGAGGGAG 58.782 50.000 0.00 0.00 0.00 4.30
603 621 2.689983 GTGGCATCAGTTTTATGGAGGG 59.310 50.000 0.00 0.00 0.00 4.30
604 622 3.624777 AGTGGCATCAGTTTTATGGAGG 58.375 45.455 0.00 0.00 0.00 4.30
605 623 3.310774 CGAGTGGCATCAGTTTTATGGAG 59.689 47.826 0.00 0.00 0.00 3.86
606 624 3.270027 CGAGTGGCATCAGTTTTATGGA 58.730 45.455 0.00 0.00 0.00 3.41
608 626 3.063997 GTCCGAGTGGCATCAGTTTTATG 59.936 47.826 0.00 0.00 34.14 1.90
609 627 3.270877 GTCCGAGTGGCATCAGTTTTAT 58.729 45.455 0.00 0.00 34.14 1.40
611 629 1.202758 TGTCCGAGTGGCATCAGTTTT 60.203 47.619 0.00 0.00 34.14 2.43
625 742 0.895530 ATCTTCCTTTCGCTGTCCGA 59.104 50.000 0.00 0.00 45.77 4.55
630 747 5.236047 CCTTGATAAGATCTTCCTTTCGCTG 59.764 44.000 12.24 0.87 0.00 5.18
649 766 6.778821 TGACTGGAGAAATTTGTATCCTTGA 58.221 36.000 12.52 0.00 32.79 3.02
676 795 0.744771 GGAAAAGCTAGGTCGCCAGG 60.745 60.000 0.00 0.00 0.00 4.45
701 820 2.507992 CCAGCTTCTCGCGTCCAG 60.508 66.667 5.77 1.02 45.59 3.86
702 821 4.742201 GCCAGCTTCTCGCGTCCA 62.742 66.667 5.77 0.00 45.59 4.02
742 914 1.455959 TTTTGGTTGACCGGGTGGG 60.456 57.895 3.30 0.00 40.75 4.61
748 920 1.524008 GAGGGGCTTTTGGTTGACCG 61.524 60.000 0.00 0.00 39.43 4.79
793 980 3.181505 TGGAGTAGTTTGTGTTGCGTTTG 60.182 43.478 0.00 0.00 0.00 2.93
794 981 3.011119 TGGAGTAGTTTGTGTTGCGTTT 58.989 40.909 0.00 0.00 0.00 3.60
795 982 2.634600 TGGAGTAGTTTGTGTTGCGTT 58.365 42.857 0.00 0.00 0.00 4.84
796 983 2.319136 TGGAGTAGTTTGTGTTGCGT 57.681 45.000 0.00 0.00 0.00 5.24
797 984 3.548014 CCTTTGGAGTAGTTTGTGTTGCG 60.548 47.826 0.00 0.00 0.00 4.85
798 985 3.795488 GCCTTTGGAGTAGTTTGTGTTGC 60.795 47.826 0.00 0.00 0.00 4.17
799 986 3.243401 GGCCTTTGGAGTAGTTTGTGTTG 60.243 47.826 0.00 0.00 0.00 3.33
800 987 2.956333 GGCCTTTGGAGTAGTTTGTGTT 59.044 45.455 0.00 0.00 0.00 3.32
808 995 1.078426 CACGGGGCCTTTGGAGTAG 60.078 63.158 0.84 0.00 0.00 2.57
809 996 3.074281 CACGGGGCCTTTGGAGTA 58.926 61.111 0.84 0.00 0.00 2.59
838 1025 1.017387 GAGGCAGAGGTTAATTGGCG 58.983 55.000 0.00 0.00 41.70 5.69
839 1026 2.019984 CAGAGGCAGAGGTTAATTGGC 58.980 52.381 0.00 0.00 37.63 4.52
840 1027 2.239654 TCCAGAGGCAGAGGTTAATTGG 59.760 50.000 0.00 0.00 0.00 3.16
841 1028 3.054802 ACTCCAGAGGCAGAGGTTAATTG 60.055 47.826 0.00 0.00 34.27 2.32
842 1029 3.185455 ACTCCAGAGGCAGAGGTTAATT 58.815 45.455 0.00 0.00 34.27 1.40
844 1031 2.180276 GACTCCAGAGGCAGAGGTTAA 58.820 52.381 0.00 0.00 36.17 2.01
845 1032 1.853963 GACTCCAGAGGCAGAGGTTA 58.146 55.000 0.00 0.00 36.17 2.85
847 1034 1.680651 CGACTCCAGAGGCAGAGGT 60.681 63.158 0.64 0.00 35.77 3.85
848 1035 1.662438 GACGACTCCAGAGGCAGAGG 61.662 65.000 0.64 0.00 35.77 3.69
849 1036 1.662438 GGACGACTCCAGAGGCAGAG 61.662 65.000 0.64 0.00 35.77 3.35
850 1037 1.679305 GGACGACTCCAGAGGCAGA 60.679 63.158 0.64 0.00 35.77 4.26
853 1040 2.750637 TCGGACGACTCCAGAGGC 60.751 66.667 0.00 0.00 36.12 4.70
854 1041 1.674651 TGTCGGACGACTCCAGAGG 60.675 63.158 23.18 0.00 44.80 3.69
855 1042 1.502640 GTGTCGGACGACTCCAGAG 59.497 63.158 23.18 0.00 44.80 3.35
856 1043 3.664495 GTGTCGGACGACTCCAGA 58.336 61.111 23.18 2.34 44.80 3.86
881 1069 3.125316 GTGATTAAGTTTGGAGGTGCGAG 59.875 47.826 0.00 0.00 0.00 5.03
983 1176 1.608336 ATCGGTCCCGTGGAGACAA 60.608 57.895 5.52 0.00 46.06 3.18
1231 1424 3.441290 CTGCTGCTGGCTCTTGGC 61.441 66.667 0.00 0.00 42.39 4.52
1232 1425 3.441290 GCTGCTGCTGGCTCTTGG 61.441 66.667 8.53 0.00 42.39 3.61
2050 2249 0.881118 CACAAACGCTAAGGGCATGT 59.119 50.000 0.00 0.00 41.91 3.21
2052 2251 1.165270 GTCACAAACGCTAAGGGCAT 58.835 50.000 0.00 0.00 41.91 4.40
2053 2252 0.179043 TGTCACAAACGCTAAGGGCA 60.179 50.000 0.00 0.00 41.91 5.36
2054 2253 0.517316 CTGTCACAAACGCTAAGGGC 59.483 55.000 0.00 0.00 37.64 5.19
2055 2254 1.156736 CCTGTCACAAACGCTAAGGG 58.843 55.000 0.00 0.00 0.00 3.95
2056 2255 0.517316 GCCTGTCACAAACGCTAAGG 59.483 55.000 0.00 0.00 0.00 2.69
2121 2870 1.153229 GTGGGCGTTATCAGGACCC 60.153 63.158 0.00 0.00 34.65 4.46
2122 2871 0.180406 ATGTGGGCGTTATCAGGACC 59.820 55.000 0.00 0.00 36.36 4.46
2123 2872 1.583054 GATGTGGGCGTTATCAGGAC 58.417 55.000 0.00 0.00 0.00 3.85
2124 2873 0.104120 CGATGTGGGCGTTATCAGGA 59.896 55.000 0.00 0.00 0.00 3.86
2125 2874 0.880278 CCGATGTGGGCGTTATCAGG 60.880 60.000 0.00 0.00 0.00 3.86
2141 2890 3.220110 GGATGTCTAGTATGTCACCCGA 58.780 50.000 0.00 0.00 0.00 5.14
2144 2893 2.288273 GGCGGATGTCTAGTATGTCACC 60.288 54.545 0.00 0.00 0.00 4.02
2148 2897 2.082140 TGGGCGGATGTCTAGTATGT 57.918 50.000 0.00 0.00 0.00 2.29
2176 2930 0.607489 GCCTTCTGCTCACACCACAT 60.607 55.000 0.00 0.00 36.87 3.21
2182 2936 1.194121 TAGGCTGCCTTCTGCTCACA 61.194 55.000 28.55 1.54 42.00 3.58
2191 2945 2.526046 AACCGGTGTAGGCTGCCTT 61.526 57.895 28.55 11.17 34.61 4.35
2205 2959 0.951525 TATTCGCCCACACACAACCG 60.952 55.000 0.00 0.00 0.00 4.44
2240 2994 2.674563 AAAGTAGCTGCGCCCACACA 62.675 55.000 4.18 0.00 0.00 3.72
2274 3034 2.367894 GGTAGGGATGGGTAGTACTTGC 59.632 54.545 0.00 0.00 0.00 4.01
2285 3045 2.417516 CGCGTGAGGTAGGGATGG 59.582 66.667 0.00 0.00 0.00 3.51
2292 3053 3.607661 TGCCACACGCGTGAGGTA 61.608 61.111 41.97 38.52 46.80 3.08
2515 3279 9.023962 ACATATGACAACTATTGTTTGACCATT 57.976 29.630 10.38 0.00 45.52 3.16
2538 3303 3.071479 CGTGGCAACTAGGTAAACACAT 58.929 45.455 8.73 0.00 37.61 3.21
2621 3393 2.014554 CAGTTGCGCGTACGTGACT 61.015 57.895 31.45 22.61 42.83 3.41
2623 3395 3.399770 GCAGTTGCGCGTACGTGA 61.400 61.111 31.45 14.12 42.83 4.35
2655 3427 5.466728 ACACATATGGCAACTATGATTCGTC 59.533 40.000 13.57 0.00 32.17 4.20
2674 3446 3.071479 CGTGGCAACTAGGTAAACACAT 58.929 45.455 8.73 0.00 37.61 3.21
2730 3503 1.433053 TTTTCGCCCACACGACACTG 61.433 55.000 0.00 0.00 42.78 3.66
2910 3685 9.737427 TTGTTTTGCACGAATTCTAAAGAAATA 57.263 25.926 3.52 0.00 37.61 1.40
2915 3692 8.538856 TGATTTTGTTTTGCACGAATTCTAAAG 58.461 29.630 3.52 0.00 33.10 1.85
2918 3699 7.305705 CGTTGATTTTGTTTTGCACGAATTCTA 60.306 33.333 3.52 0.00 33.10 2.10
2921 3703 5.062809 ACGTTGATTTTGTTTTGCACGAATT 59.937 32.000 0.00 0.00 0.00 2.17
2981 3763 4.339247 CCCAAATGATAACTCCCACATGTC 59.661 45.833 0.00 0.00 0.00 3.06
2984 3766 4.608170 ACCCAAATGATAACTCCCACAT 57.392 40.909 0.00 0.00 0.00 3.21


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

AutoCloner maintained by Alex Coulton.