Multiple sequence alignment - TraesCS3D01G182000

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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 TraesCS3D01G182000 chr3D 100.000 3242 0 0 1 3242 165584658 165587899 0.000000e+00 5987
1 TraesCS3D01G182000 chr3B 94.351 2797 103 8 1 2789 240801399 240804148 0.000000e+00 4239
2 TraesCS3D01G182000 chr3B 93.256 430 17 3 2822 3240 240804146 240804574 9.880000e-175 623
3 TraesCS3D01G182000 chr7D 88.592 1832 151 20 1063 2859 83163812 83162004 0.000000e+00 2172
4 TraesCS3D01G182000 chr7D 81.156 398 32 15 2855 3242 83101056 83100692 2.460000e-71 279


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 TraesCS3D01G182000 chr3D 165584658 165587899 3241 False 5987 5987 100.0000 1 3242 1 chr3D.!!$F1 3241
1 TraesCS3D01G182000 chr3B 240801399 240804574 3175 False 2431 4239 93.8035 1 3240 2 chr3B.!!$F1 3239
2 TraesCS3D01G182000 chr7D 83162004 83163812 1808 True 2172 2172 88.5920 1063 2859 1 chr7D.!!$R2 1796

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
370 372 0.035630 CCCCCAAAGAGTGAGAGCAG 60.036 60.000 0.00 0.00 0.00 4.24 F
1028 1030 0.388134 GTTCGCCTTCGAGCTGTGTA 60.388 55.000 0.00 0.00 46.34 2.90 F
1125 1127 1.224592 GATGTTGCCCGAGGGTCAT 59.775 57.895 10.26 11.64 37.65 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1243 1245 0.029267 AGGAGGAGGAGGCCATTGAT 60.029 55.000 5.01 0.0 0.00 2.57 R
1925 1935 0.678048 AAAGCGATGCTCCCTTGGTC 60.678 55.000 0.00 0.0 38.25 4.02 R
2348 2365 1.908619 TGGAGCTGCTACTGAATTGGA 59.091 47.619 13.97 0.0 0.00 3.53 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
94 95 0.251297 TGCACCCCTCTTTGGACATG 60.251 55.000 0.00 0.00 38.35 3.21
218 220 8.846943 ACACATTGTTAGTTACTGATGAATCA 57.153 30.769 0.00 0.00 35.16 2.57
219 221 9.453572 ACACATTGTTAGTTACTGATGAATCAT 57.546 29.630 0.00 0.00 36.02 2.45
233 235 9.896645 ACTGATGAATCATTGTTAGTTACTGAT 57.103 29.630 0.00 0.00 36.02 2.90
293 295 1.700955 AATATCCTACTCGGGCACGT 58.299 50.000 8.89 0.00 41.85 4.49
319 321 0.250945 TGCTATTCGCACAAACCCCA 60.251 50.000 0.00 0.00 45.47 4.96
324 326 4.341502 CGCACAAACCCCAAGGCG 62.342 66.667 0.00 0.00 38.45 5.52
341 343 1.066152 GGCGATTGCATCCTTTCCTTC 59.934 52.381 7.38 0.00 45.35 3.46
352 354 1.524008 CTTTCCTTCCAACCCGCACC 61.524 60.000 0.00 0.00 0.00 5.01
370 372 0.035630 CCCCCAAAGAGTGAGAGCAG 60.036 60.000 0.00 0.00 0.00 4.24
380 382 1.537397 TGAGAGCAGTTGCCCTCCT 60.537 57.895 12.27 0.40 44.09 3.69
433 435 3.948473 TCTCTCAGGACCGATCAAGTTAG 59.052 47.826 0.00 0.00 0.00 2.34
556 558 2.436173 GCATGGAAACCCTAGCTCTAGT 59.564 50.000 0.00 0.00 0.00 2.57
562 564 4.936411 GGAAACCCTAGCTCTAGTGTTTTC 59.064 45.833 15.23 11.35 41.49 2.29
617 619 7.749666 AGCATTGATGAGTAGTATAATGGGTT 58.250 34.615 0.00 0.00 0.00 4.11
774 776 4.768448 TGTTGATTGCTTCTCCATTGTGAT 59.232 37.500 0.00 0.00 0.00 3.06
783 785 4.487714 TCTCCATTGTGATAGGGTTCAC 57.512 45.455 0.00 0.00 45.05 3.18
799 801 4.088648 GGTTCACGTGAATTTAATGAGCG 58.911 43.478 31.81 0.00 36.33 5.03
801 803 4.577687 TCACGTGAATTTAATGAGCGTC 57.422 40.909 17.62 0.00 0.00 5.19
873 875 3.741476 GCTGCGTGCCCAAGGAAG 61.741 66.667 0.00 0.00 35.15 3.46
886 888 4.143333 GGAAGCGCCGCCACTCTA 62.143 66.667 4.98 0.00 0.00 2.43
887 889 2.107141 GAAGCGCCGCCACTCTAT 59.893 61.111 4.98 0.00 0.00 1.98
888 890 2.202932 AAGCGCCGCCACTCTATG 60.203 61.111 4.98 0.00 0.00 2.23
900 902 3.861276 CACTCTATGGTGGTAACGTCA 57.139 47.619 0.00 0.00 42.51 4.35
901 903 3.770666 CACTCTATGGTGGTAACGTCAG 58.229 50.000 0.00 0.00 42.51 3.51
902 904 3.442625 CACTCTATGGTGGTAACGTCAGA 59.557 47.826 0.00 0.00 42.51 3.27
903 905 4.098044 CACTCTATGGTGGTAACGTCAGAT 59.902 45.833 0.00 0.00 42.51 2.90
904 906 4.098044 ACTCTATGGTGGTAACGTCAGATG 59.902 45.833 0.00 0.00 42.51 2.90
905 907 4.274978 TCTATGGTGGTAACGTCAGATGA 58.725 43.478 0.00 0.00 42.51 2.92
906 908 4.893524 TCTATGGTGGTAACGTCAGATGAT 59.106 41.667 0.00 0.00 42.51 2.45
907 909 3.245518 TGGTGGTAACGTCAGATGATG 57.754 47.619 0.00 0.45 42.51 3.07
908 910 2.565391 TGGTGGTAACGTCAGATGATGT 59.435 45.455 1.79 1.79 45.48 3.06
909 911 3.187700 GGTGGTAACGTCAGATGATGTC 58.812 50.000 8.09 0.00 42.97 3.06
931 933 3.831642 TGGTGGTACCCTACAACTCTA 57.168 47.619 10.07 0.00 37.50 2.43
936 938 4.708421 GTGGTACCCTACAACTCTACATGA 59.292 45.833 10.07 0.00 29.78 3.07
966 968 0.452987 TGCATGCCGATTTGCTTCTC 59.547 50.000 16.68 0.00 39.60 2.87
975 977 2.293170 GATTTGCTTCTCCTGGTAGCC 58.707 52.381 12.97 0.00 34.03 3.93
980 982 1.229496 TTCTCCTGGTAGCCTGGCA 60.229 57.895 22.65 3.92 41.59 4.92
1028 1030 0.388134 GTTCGCCTTCGAGCTGTGTA 60.388 55.000 0.00 0.00 46.34 2.90
1045 1047 3.630769 TGTGTACAAAAATTGGCGGTACA 59.369 39.130 0.00 0.00 41.23 2.90
1046 1048 4.278669 TGTGTACAAAAATTGGCGGTACAT 59.721 37.500 0.00 0.00 44.05 2.29
1125 1127 1.224592 GATGTTGCCCGAGGGTCAT 59.775 57.895 10.26 11.64 37.65 3.06
1179 1181 3.371285 GGTATGTTCGCTTTCTCAACCTC 59.629 47.826 0.00 0.00 0.00 3.85
1243 1245 3.213206 ACCACTGCATTCTTGACTCAA 57.787 42.857 0.00 0.00 0.00 3.02
1248 1250 5.105877 CCACTGCATTCTTGACTCAATCAAT 60.106 40.000 0.00 0.00 46.37 2.57
1266 1274 2.041265 GGCCTCCTCCTCCTCCAA 59.959 66.667 0.00 0.00 0.00 3.53
1378 1386 3.056250 GGTGACACAGTCTGAGATCACAT 60.056 47.826 24.19 0.00 38.54 3.21
1499 1507 3.931907 ATCACAGTTGGCCTATGCTAA 57.068 42.857 3.32 0.00 35.37 3.09
1522 1530 2.309755 TCCCAAGACAAGCAATGGATCT 59.690 45.455 0.00 0.00 34.82 2.75
1614 1622 2.040145 TCCTGCATCTCATGGTTCACAA 59.960 45.455 0.00 0.00 0.00 3.33
1915 1925 6.931281 GCCTACTATCATTGCTGAAACTATCA 59.069 38.462 0.00 0.00 34.37 2.15
1925 1935 7.615582 TTGCTGAAACTATCATCTACAAAGG 57.384 36.000 0.00 0.00 37.44 3.11
1965 1975 2.027561 TGTGCAATACCACCTCAGTACC 60.028 50.000 0.00 0.00 34.85 3.34
1967 1977 1.935933 CAATACCACCTCAGTACCGC 58.064 55.000 0.00 0.00 0.00 5.68
1971 1981 1.079127 CCACCTCAGTACCGCCAAG 60.079 63.158 0.00 0.00 0.00 3.61
1977 1987 1.375523 CAGTACCGCCAAGTGGTCC 60.376 63.158 2.50 0.00 43.59 4.46
1996 2006 2.296752 TCCGAACCAGTTGACGAATGTA 59.703 45.455 0.00 0.00 0.00 2.29
2152 2162 7.492524 TCATCGTATCATCTTGTTTAGAAGCT 58.507 34.615 0.00 0.00 36.22 3.74
2154 2164 8.910666 CATCGTATCATCTTGTTTAGAAGCTAG 58.089 37.037 0.00 0.00 36.22 3.42
2407 2424 8.322828 TGTGGTACTTATTATAGTTGCCTTTCA 58.677 33.333 0.00 0.00 0.00 2.69
2486 2511 5.128171 TGCAACTAAGTATTCGTGTATCCCT 59.872 40.000 0.00 0.00 0.00 4.20
2542 2568 9.542462 TGCAATTTGACCAAGATACTACTATAC 57.458 33.333 0.00 0.00 0.00 1.47
2571 2597 9.467258 CAATTTGAGTTGTAATCATGTGAAAGT 57.533 29.630 0.00 0.00 0.00 2.66
2601 2627 5.640147 TCTCTGGGTGTTATTTGGAACATT 58.360 37.500 0.00 0.00 41.21 2.71
2605 2631 4.039730 TGGGTGTTATTTGGAACATTGTGG 59.960 41.667 0.00 0.00 41.21 4.17
2619 2645 5.181690 ACATTGTGGTATTGTTGTCACAC 57.818 39.130 0.00 0.00 39.46 3.82
2673 2699 4.396357 ACTTGTGTGGGGGATAAATTCA 57.604 40.909 0.00 0.00 0.00 2.57
2685 2711 7.663905 TGGGGGATAAATTCATGTAACTTATCG 59.336 37.037 10.29 0.00 32.25 2.92
2795 2867 7.519032 TTCTGTTGGTTAATTTTCCTACTGG 57.481 36.000 14.17 8.64 32.74 4.00
2796 2868 6.007703 TCTGTTGGTTAATTTTCCTACTGGG 58.992 40.000 14.17 0.00 32.74 4.45
2797 2869 4.525100 TGTTGGTTAATTTTCCTACTGGGC 59.475 41.667 11.74 0.00 32.42 5.36
2798 2870 4.668138 TGGTTAATTTTCCTACTGGGCT 57.332 40.909 0.00 0.00 34.39 5.19
2799 2871 4.340617 TGGTTAATTTTCCTACTGGGCTG 58.659 43.478 0.00 0.00 34.39 4.85
2800 2872 4.043561 TGGTTAATTTTCCTACTGGGCTGA 59.956 41.667 0.00 0.00 34.39 4.26
2801 2873 5.014202 GGTTAATTTTCCTACTGGGCTGAA 58.986 41.667 0.00 0.00 34.39 3.02
2802 2874 5.125578 GGTTAATTTTCCTACTGGGCTGAAG 59.874 44.000 0.00 0.00 34.39 3.02
2803 2875 2.879103 TTTTCCTACTGGGCTGAAGG 57.121 50.000 0.00 0.00 34.39 3.46
2804 2876 1.742308 TTTCCTACTGGGCTGAAGGT 58.258 50.000 0.00 0.00 34.39 3.50
2805 2877 2.634639 TTCCTACTGGGCTGAAGGTA 57.365 50.000 0.00 0.00 34.39 3.08
2806 2878 2.868964 TCCTACTGGGCTGAAGGTAT 57.131 50.000 0.00 0.00 34.39 2.73
2807 2879 3.130734 TCCTACTGGGCTGAAGGTATT 57.869 47.619 0.00 0.00 34.39 1.89
2808 2880 2.771943 TCCTACTGGGCTGAAGGTATTG 59.228 50.000 0.00 0.00 34.39 1.90
2809 2881 2.505819 CCTACTGGGCTGAAGGTATTGT 59.494 50.000 0.00 0.00 0.00 2.71
2810 2882 3.709653 CCTACTGGGCTGAAGGTATTGTA 59.290 47.826 0.00 0.00 0.00 2.41
2811 2883 3.914426 ACTGGGCTGAAGGTATTGTAG 57.086 47.619 0.00 0.00 0.00 2.74
2812 2884 2.092914 ACTGGGCTGAAGGTATTGTAGC 60.093 50.000 0.00 0.00 0.00 3.58
2813 2885 2.171448 CTGGGCTGAAGGTATTGTAGCT 59.829 50.000 0.00 0.00 38.32 3.32
2814 2886 2.092968 TGGGCTGAAGGTATTGTAGCTG 60.093 50.000 0.00 0.00 36.50 4.24
2815 2887 1.943340 GGCTGAAGGTATTGTAGCTGC 59.057 52.381 0.00 0.00 36.50 5.25
2816 2888 2.420687 GGCTGAAGGTATTGTAGCTGCT 60.421 50.000 7.57 7.57 36.50 4.24
2817 2889 2.611292 GCTGAAGGTATTGTAGCTGCTG 59.389 50.000 13.43 0.00 36.50 4.41
2818 2890 3.679917 GCTGAAGGTATTGTAGCTGCTGA 60.680 47.826 13.43 0.00 36.50 4.26
2819 2891 3.861840 TGAAGGTATTGTAGCTGCTGAC 58.138 45.455 13.43 7.31 36.50 3.51
2820 2892 2.990066 AGGTATTGTAGCTGCTGACC 57.010 50.000 13.43 11.21 34.78 4.02
2876 2949 8.450578 TGCTTGATAACTTTGGTATAGATTGG 57.549 34.615 0.00 0.00 0.00 3.16
2888 2961 7.803487 TGGTATAGATTGGATGATGTCTCAT 57.197 36.000 0.00 0.00 44.93 2.90
2910 2983 6.430925 TCATCTGACACCTCCTTTTGTATTTG 59.569 38.462 0.00 0.00 0.00 2.32
2919 3002 5.466393 CCTCCTTTTGTATTTGTTTTGCAGG 59.534 40.000 0.00 0.00 0.00 4.85
2935 3018 2.229543 TGCAGGCTTAAAGTGATGCAAG 59.770 45.455 0.00 0.00 40.43 4.01
2991 3074 8.134895 GGTTTTACACAGATGAATGAACAAGAA 58.865 33.333 0.00 0.00 0.00 2.52
3002 3085 5.471456 TGAATGAACAAGAAAGGAGAGCTTC 59.529 40.000 0.00 0.00 0.00 3.86
3003 3086 4.422073 TGAACAAGAAAGGAGAGCTTCA 57.578 40.909 0.00 0.00 0.00 3.02
3061 3144 0.536460 AACAACTCATTCCCGCGGTT 60.536 50.000 26.12 6.76 0.00 4.44
3068 3151 0.105964 CATTCCCGCGGTTCCTATCA 59.894 55.000 26.12 0.00 0.00 2.15
3130 3213 2.010497 TGTAGCGCACAAACAAACTGA 58.990 42.857 11.47 0.00 32.95 3.41
3208 3291 8.879227 TGATCATGAGGTGTATTATTGGACATA 58.121 33.333 0.09 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 9.716556 TTAGCCTTAAAATGTATTAATTGGGGA 57.283 29.630 0.00 0.00 0.00 4.81
49 50 4.270008 ACCAACATCCACTGCTAATTACC 58.730 43.478 0.00 0.00 0.00 2.85
50 51 5.648092 AGAACCAACATCCACTGCTAATTAC 59.352 40.000 0.00 0.00 0.00 1.89
60 61 1.000274 GGTGCAAGAACCAACATCCAC 60.000 52.381 0.00 0.00 40.22 4.02
62 63 0.603065 GGGTGCAAGAACCAACATCC 59.397 55.000 0.00 0.00 42.47 3.51
94 95 2.742589 CGGAAGTTGAAGAGTAAAGGGC 59.257 50.000 0.00 0.00 0.00 5.19
275 277 0.959553 CACGTGCCCGAGTAGGATAT 59.040 55.000 0.82 0.00 45.00 1.63
281 283 4.367023 GCCACACGTGCCCGAGTA 62.367 66.667 17.22 0.00 35.67 2.59
305 307 2.494530 GCCTTGGGGTTTGTGCGAA 61.495 57.895 0.00 0.00 34.45 4.70
307 309 4.341502 CGCCTTGGGGTTTGTGCG 62.342 66.667 0.00 0.00 35.81 5.34
319 321 1.106285 GGAAAGGATGCAATCGCCTT 58.894 50.000 7.46 7.46 46.86 4.35
324 326 3.118992 GGTTGGAAGGAAAGGATGCAATC 60.119 47.826 0.00 0.00 44.55 2.67
341 343 4.924187 TTTGGGGGTGCGGGTTGG 62.924 66.667 0.00 0.00 0.00 3.77
352 354 0.689623 ACTGCTCTCACTCTTTGGGG 59.310 55.000 0.00 0.00 0.00 4.96
370 372 2.371259 GGGGAGAGAGGAGGGCAAC 61.371 68.421 0.00 0.00 0.00 4.17
380 382 1.866997 TGGGAGGGAAGGGGAGAGA 60.867 63.158 0.00 0.00 0.00 3.10
451 453 9.860393 AATACCTCTGGGAATATAAAGGAGTAT 57.140 33.333 0.00 0.00 36.25 2.12
535 537 2.436173 ACTAGAGCTAGGGTTTCCATGC 59.564 50.000 9.18 0.00 37.49 4.06
598 600 7.990886 TGTTTCCAACCCATTATACTACTCATC 59.009 37.037 0.00 0.00 0.00 2.92
617 619 7.002250 TGCATCCAAGAAAATTATGTTTCCA 57.998 32.000 0.00 0.00 38.10 3.53
631 633 7.047891 CCTACAAACTAACTATGCATCCAAGA 58.952 38.462 0.19 0.00 0.00 3.02
632 634 6.823689 ACCTACAAACTAACTATGCATCCAAG 59.176 38.462 0.19 0.00 0.00 3.61
646 648 6.005198 CCACATAACCCAAACCTACAAACTA 58.995 40.000 0.00 0.00 0.00 2.24
648 650 4.828387 TCCACATAACCCAAACCTACAAAC 59.172 41.667 0.00 0.00 0.00 2.93
774 776 5.353123 GCTCATTAAATTCACGTGAACCCTA 59.647 40.000 31.87 19.56 36.80 3.53
783 785 4.584029 ACTGACGCTCATTAAATTCACG 57.416 40.909 0.00 0.00 0.00 4.35
792 794 5.162075 GTTCACTAAGTACTGACGCTCATT 58.838 41.667 0.00 0.00 0.00 2.57
799 801 4.863491 TGTTCGGTTCACTAAGTACTGAC 58.137 43.478 0.00 0.00 33.29 3.51
801 803 5.045215 TGTTGTTCGGTTCACTAAGTACTG 58.955 41.667 0.00 0.00 0.00 2.74
886 888 3.197766 ACATCATCTGACGTTACCACCAT 59.802 43.478 0.00 0.00 0.00 3.55
887 889 2.565391 ACATCATCTGACGTTACCACCA 59.435 45.455 0.00 0.00 0.00 4.17
888 890 3.187700 GACATCATCTGACGTTACCACC 58.812 50.000 0.00 0.00 0.00 4.61
889 891 3.845178 TGACATCATCTGACGTTACCAC 58.155 45.455 0.00 0.00 0.00 4.16
890 892 4.432712 CATGACATCATCTGACGTTACCA 58.567 43.478 0.00 0.00 33.61 3.25
891 893 3.804325 CCATGACATCATCTGACGTTACC 59.196 47.826 0.00 0.00 33.61 2.85
892 894 4.268644 CACCATGACATCATCTGACGTTAC 59.731 45.833 0.00 0.00 33.61 2.50
893 895 4.432712 CACCATGACATCATCTGACGTTA 58.567 43.478 0.00 0.00 33.61 3.18
894 896 3.264947 CACCATGACATCATCTGACGTT 58.735 45.455 0.00 0.00 33.61 3.99
895 897 2.419159 CCACCATGACATCATCTGACGT 60.419 50.000 0.00 0.00 33.61 4.34
896 898 2.207590 CCACCATGACATCATCTGACG 58.792 52.381 0.00 0.00 33.61 4.35
897 899 3.272574 ACCACCATGACATCATCTGAC 57.727 47.619 0.00 0.00 33.61 3.51
898 900 3.134623 GGTACCACCATGACATCATCTGA 59.865 47.826 7.15 0.00 38.42 3.27
899 901 3.470709 GGTACCACCATGACATCATCTG 58.529 50.000 7.15 0.00 38.42 2.90
900 902 3.845781 GGTACCACCATGACATCATCT 57.154 47.619 7.15 0.00 38.42 2.90
931 933 0.037046 TGCAGTGATGACGCTCATGT 60.037 50.000 0.00 0.00 37.20 3.21
936 938 2.110967 GGCATGCAGTGATGACGCT 61.111 57.895 21.36 0.00 37.34 5.07
966 968 2.543067 GAAGGTGCCAGGCTACCAGG 62.543 65.000 26.03 0.00 39.46 4.45
975 977 1.687612 ACCATCCAGAAGGTGCCAG 59.312 57.895 0.00 0.00 36.60 4.85
980 982 2.338809 TCAAGTCACCATCCAGAAGGT 58.661 47.619 0.00 0.00 39.10 3.50
1028 1030 3.572255 AGTGATGTACCGCCAATTTTTGT 59.428 39.130 0.00 0.00 0.00 2.83
1045 1047 1.095228 CCGCGTGGGCAAATAGTGAT 61.095 55.000 7.26 0.00 39.92 3.06
1046 1048 1.743623 CCGCGTGGGCAAATAGTGA 60.744 57.895 7.26 0.00 39.92 3.41
1125 1127 4.590553 TGGCCAGGGTGGAGACCA 62.591 66.667 0.00 0.00 45.25 4.02
1160 1162 2.069273 CGAGGTTGAGAAAGCGAACAT 58.931 47.619 0.00 0.00 0.00 2.71
1179 1181 3.584868 GACCAAGGTCCCCGTGTCG 62.585 68.421 8.06 0.00 39.08 4.35
1243 1245 0.029267 AGGAGGAGGAGGCCATTGAT 60.029 55.000 5.01 0.00 0.00 2.57
1248 1250 2.415962 TTTGGAGGAGGAGGAGGCCA 62.416 60.000 5.01 0.00 0.00 5.36
1266 1274 3.069318 GCGGAGTCCTCGTCCCTT 61.069 66.667 7.77 0.00 0.00 3.95
1361 1369 3.126514 GCCAAATGTGATCTCAGACTGTG 59.873 47.826 1.59 0.00 0.00 3.66
1378 1386 3.648067 AGATAGCAGTAGCATAGGCCAAA 59.352 43.478 5.01 0.00 45.49 3.28
1499 1507 1.425066 TCCATTGCTTGTCTTGGGAGT 59.575 47.619 0.00 0.00 0.00 3.85
1522 1530 1.221840 GAAGATCCCAGCTCGCCAA 59.778 57.895 0.00 0.00 0.00 4.52
1614 1622 2.040412 GGGTGGGTCAATCTGAAGAACT 59.960 50.000 0.00 0.00 0.00 3.01
1802 1812 0.110869 CGGGGTAAACCTTCCCACAA 59.889 55.000 0.00 0.00 45.06 3.33
1805 1815 0.178879 TACCGGGGTAAACCTTCCCA 60.179 55.000 6.32 0.00 45.06 4.37
1902 1912 6.818644 GTCCTTTGTAGATGATAGTTTCAGCA 59.181 38.462 1.71 0.00 43.37 4.41
1915 1925 2.239907 GCTCCCTTGGTCCTTTGTAGAT 59.760 50.000 0.00 0.00 0.00 1.98
1925 1935 0.678048 AAAGCGATGCTCCCTTGGTC 60.678 55.000 0.00 0.00 38.25 4.02
1965 1975 3.047877 GGTTCGGACCACTTGGCG 61.048 66.667 8.43 0.00 45.77 5.69
1977 1987 2.092211 GCTACATTCGTCAACTGGTTCG 59.908 50.000 0.00 0.00 0.00 3.95
1996 2006 2.968574 CGGGGCTATATCCATAGATGCT 59.031 50.000 0.00 0.00 36.96 3.79
2152 2162 8.494433 AGGACAAAATGAGAACATATTAGCCTA 58.506 33.333 0.00 0.00 35.50 3.93
2154 2164 7.573968 AGGACAAAATGAGAACATATTAGCC 57.426 36.000 0.00 0.00 35.50 3.93
2240 2250 4.755629 GGCGAAACTTTCTCTTAACCTTCT 59.244 41.667 0.12 0.00 0.00 2.85
2348 2365 1.908619 TGGAGCTGCTACTGAATTGGA 59.091 47.619 13.97 0.00 0.00 3.53
2542 2568 7.369607 TCACATGATTACAACTCAAATTGTGG 58.630 34.615 0.00 0.00 42.74 4.17
2571 2597 6.836527 TCCAAATAACACCCAGAGAAAGAAAA 59.163 34.615 0.00 0.00 0.00 2.29
2601 2627 2.907634 ACGTGTGACAACAATACCACA 58.092 42.857 0.00 0.00 38.27 4.17
2619 2645 9.477484 AAGCACCTAGTGAGAAATATAAATACG 57.523 33.333 0.00 0.00 35.23 3.06
2673 2699 6.636705 TGGTTTCTAGCACGATAAGTTACAT 58.363 36.000 0.00 0.00 0.00 2.29
2685 2711 7.611213 AACAATACTACATGGTTTCTAGCAC 57.389 36.000 0.00 0.00 34.03 4.40
2786 2858 2.634639 TACCTTCAGCCCAGTAGGAA 57.365 50.000 0.00 0.00 38.24 3.36
2787 2859 2.771943 CAATACCTTCAGCCCAGTAGGA 59.228 50.000 0.00 0.00 38.24 2.94
2788 2860 2.505819 ACAATACCTTCAGCCCAGTAGG 59.494 50.000 0.00 0.00 39.47 3.18
2789 2861 3.914426 ACAATACCTTCAGCCCAGTAG 57.086 47.619 0.00 0.00 0.00 2.57
2790 2862 3.134081 GCTACAATACCTTCAGCCCAGTA 59.866 47.826 0.00 0.00 0.00 2.74
2791 2863 2.092914 GCTACAATACCTTCAGCCCAGT 60.093 50.000 0.00 0.00 0.00 4.00
2792 2864 2.171448 AGCTACAATACCTTCAGCCCAG 59.829 50.000 0.00 0.00 32.58 4.45
2793 2865 2.092968 CAGCTACAATACCTTCAGCCCA 60.093 50.000 0.00 0.00 32.58 5.36
2794 2866 2.565841 CAGCTACAATACCTTCAGCCC 58.434 52.381 0.00 0.00 32.58 5.19
2795 2867 1.943340 GCAGCTACAATACCTTCAGCC 59.057 52.381 0.00 0.00 32.58 4.85
2796 2868 2.611292 CAGCAGCTACAATACCTTCAGC 59.389 50.000 0.00 0.00 0.00 4.26
2797 2869 3.868077 GTCAGCAGCTACAATACCTTCAG 59.132 47.826 0.00 0.00 0.00 3.02
2798 2870 3.369471 GGTCAGCAGCTACAATACCTTCA 60.369 47.826 0.00 0.00 0.00 3.02
2799 2871 3.118592 AGGTCAGCAGCTACAATACCTTC 60.119 47.826 0.00 0.00 31.95 3.46
2800 2872 2.840651 AGGTCAGCAGCTACAATACCTT 59.159 45.455 0.00 0.00 31.95 3.50
2801 2873 2.472029 AGGTCAGCAGCTACAATACCT 58.528 47.619 0.00 0.59 0.00 3.08
2802 2874 2.990066 AGGTCAGCAGCTACAATACC 57.010 50.000 0.00 0.00 0.00 2.73
2803 2875 4.130286 AGAAGGTCAGCAGCTACAATAC 57.870 45.455 0.00 0.00 0.00 1.89
2804 2876 4.826274 AAGAAGGTCAGCAGCTACAATA 57.174 40.909 0.00 0.00 0.00 1.90
2805 2877 3.710209 AAGAAGGTCAGCAGCTACAAT 57.290 42.857 0.00 0.00 0.00 2.71
2806 2878 3.492102 AAAGAAGGTCAGCAGCTACAA 57.508 42.857 0.00 0.00 0.00 2.41
2807 2879 3.492102 AAAAGAAGGTCAGCAGCTACA 57.508 42.857 0.00 0.00 0.00 2.74
2808 2880 4.938226 ACATAAAAGAAGGTCAGCAGCTAC 59.062 41.667 0.00 0.00 0.00 3.58
2809 2881 5.046304 AGACATAAAAGAAGGTCAGCAGCTA 60.046 40.000 0.00 0.00 32.79 3.32
2810 2882 4.006319 GACATAAAAGAAGGTCAGCAGCT 58.994 43.478 0.00 0.00 0.00 4.24
2811 2883 4.006319 AGACATAAAAGAAGGTCAGCAGC 58.994 43.478 0.00 0.00 32.79 5.25
2812 2884 6.634805 TCTAGACATAAAAGAAGGTCAGCAG 58.365 40.000 0.00 0.00 32.79 4.24
2813 2885 6.605471 TCTAGACATAAAAGAAGGTCAGCA 57.395 37.500 0.00 0.00 32.79 4.41
2814 2886 6.018343 GCATCTAGACATAAAAGAAGGTCAGC 60.018 42.308 0.00 0.00 32.79 4.26
2815 2887 6.481644 GGCATCTAGACATAAAAGAAGGTCAG 59.518 42.308 0.00 0.00 32.79 3.51
2816 2888 6.156949 AGGCATCTAGACATAAAAGAAGGTCA 59.843 38.462 0.00 0.00 32.79 4.02
2817 2889 6.587273 AGGCATCTAGACATAAAAGAAGGTC 58.413 40.000 0.00 0.00 0.00 3.85
2818 2890 6.567602 AGGCATCTAGACATAAAAGAAGGT 57.432 37.500 0.00 0.00 0.00 3.50
2819 2891 9.566432 AATAAGGCATCTAGACATAAAAGAAGG 57.434 33.333 0.00 0.00 0.00 3.46
2888 2961 5.690865 ACAAATACAAAAGGAGGTGTCAGA 58.309 37.500 0.00 0.00 0.00 3.27
2910 2983 3.429881 GCATCACTTTAAGCCTGCAAAAC 59.570 43.478 8.46 0.00 0.00 2.43
2935 3018 7.039882 AGAATTGAAATCCATTGACATGCTTC 58.960 34.615 0.00 0.00 0.00 3.86
3096 3179 3.131396 GCGCTACATGGCTACAAGTATT 58.869 45.455 0.00 0.00 31.20 1.89
3191 3274 9.975218 ATAATTCCCTATGTCCAATAATACACC 57.025 33.333 0.00 0.00 0.00 4.16
3208 3291 8.691661 ATGCTTATTTGTCGTAATAATTCCCT 57.308 30.769 0.00 0.00 31.53 4.20


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

AutoCloner maintained by Alex Coulton.