Multiple sequence alignment - TraesCS5D01G241700

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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 TraesCS5D01G241700 chr5D 100.000 3341 0 0 1 3341 350674928 350678268 0.000000e+00 6170.0
1 TraesCS5D01G241700 chr5D 76.415 1272 247 45 1077 2320 406198247 406199493 3.640000e-179 638.0
2 TraesCS5D01G241700 chr5D 84.158 101 14 2 1261 1360 350703974 350704073 2.740000e-16 97.1
3 TraesCS5D01G241700 chr5B 94.986 2852 118 15 4 2852 411620591 411623420 0.000000e+00 4451.0
4 TraesCS5D01G241700 chr5B 76.457 1270 250 40 1077 2320 486896141 486897387 0.000000e+00 643.0
5 TraesCS5D01G241700 chr5B 92.105 418 26 4 2904 3316 411623418 411623833 1.730000e-162 582.0
6 TraesCS5D01G241700 chr5B 84.158 101 14 2 1261 1360 411757713 411757812 2.740000e-16 97.1
7 TraesCS5D01G241700 chr5B 88.312 77 8 1 11 86 710505181 710505105 1.280000e-14 91.6
8 TraesCS5D01G241700 chr5A 95.706 1607 50 10 886 2473 451137973 451139579 0.000000e+00 2567.0
9 TraesCS5D01G241700 chr5A 88.697 752 37 14 167 873 451137168 451137916 0.000000e+00 874.0
10 TraesCS5D01G241700 chr1A 80.759 369 51 11 2781 3142 518805796 518805441 1.530000e-68 270.0
11 TraesCS5D01G241700 chr1A 86.364 110 14 1 3144 3253 518804890 518804782 5.860000e-23 119.0
12 TraesCS5D01G241700 chr1A 87.838 74 7 2 2470 2541 449841679 449841606 5.940000e-13 86.1
13 TraesCS5D01G241700 chr1B 85.492 193 25 1 2951 3140 571705713 571705521 7.310000e-47 198.0
14 TraesCS5D01G241700 chr1B 93.333 45 3 0 3190 3234 321688220 321688176 2.150000e-07 67.6
15 TraesCS5D01G241700 chr1D 79.787 282 34 12 3050 3311 422862779 422862501 2.050000e-42 183.0
16 TraesCS5D01G241700 chr7D 82.635 167 19 6 2962 3118 63965167 63965333 4.490000e-29 139.0
17 TraesCS5D01G241700 chr2D 86.538 104 11 3 1258 1360 190369895 190369996 9.800000e-21 111.0
18 TraesCS5D01G241700 chr2D 76.923 130 24 6 2481 2608 95919218 95919093 5.980000e-08 69.4
19 TraesCS5D01G241700 chr2A 85.577 104 12 3 1258 1360 204930110 204930211 4.560000e-19 106.0
20 TraesCS5D01G241700 chr2B 84.615 104 13 3 1258 1360 247517936 247518037 2.120000e-17 100.0
21 TraesCS5D01G241700 chr7A 80.769 104 16 4 2781 2881 67638049 67638151 9.940000e-11 78.7


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 TraesCS5D01G241700 chr5D 350674928 350678268 3340 False 6170.0 6170 100.0000 1 3341 1 chr5D.!!$F1 3340
1 TraesCS5D01G241700 chr5D 406198247 406199493 1246 False 638.0 638 76.4150 1077 2320 1 chr5D.!!$F3 1243
2 TraesCS5D01G241700 chr5B 411620591 411623833 3242 False 2516.5 4451 93.5455 4 3316 2 chr5B.!!$F3 3312
3 TraesCS5D01G241700 chr5B 486896141 486897387 1246 False 643.0 643 76.4570 1077 2320 1 chr5B.!!$F2 1243
4 TraesCS5D01G241700 chr5A 451137168 451139579 2411 False 1720.5 2567 92.2015 167 2473 2 chr5A.!!$F1 2306

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
880 925 0.029567 CCGGATCAGTGTCGAGCTAC 59.97 60.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2867 2985 0.396811 AAGGTGGAGTCCTCGTTTGG 59.603 55.0 11.33 0.0 36.74 3.28 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
41 42 3.765894 TTGTGGTGGTGGCGGTCAG 62.766 63.158 0.00 0.00 0.00 3.51
44 45 3.936203 GGTGGTGGCGGTCAGTGA 61.936 66.667 0.00 0.00 0.00 3.41
46 47 4.293648 TGGTGGCGGTCAGTGACG 62.294 66.667 16.89 12.90 32.65 4.35
60 61 3.007323 GACGGCTAGGGTTGGGGT 61.007 66.667 0.00 0.00 0.00 4.95
413 448 4.113815 CCAGCATCCGAGGGGCAA 62.114 66.667 8.83 0.00 0.00 4.52
590 630 0.098200 CTCCGTTAGATCGACGCACA 59.902 55.000 16.15 4.81 39.09 4.57
612 652 1.135972 CGCTCACCTCCGAATTTTGTG 60.136 52.381 0.00 0.00 0.00 3.33
658 698 2.249337 GCACGATCGCAGATCTCTATG 58.751 52.381 16.60 2.69 45.12 2.23
769 809 1.079888 GCCAAGTTTTCCATGCCCG 60.080 57.895 0.00 0.00 0.00 6.13
843 888 4.517952 TTGTTAATTCACAGCACCATGG 57.482 40.909 11.19 11.19 0.00 3.66
880 925 0.029567 CCGGATCAGTGTCGAGCTAC 59.970 60.000 0.00 0.00 0.00 3.58
901 990 0.040692 CATACGCATGTGCATGGAGC 60.041 55.000 11.06 0.00 45.96 4.70
947 1040 1.004440 AGAAGCCTTCACGCTCACC 60.004 57.895 7.29 0.00 38.44 4.02
955 1048 4.758251 CACGCTCACCGCATCCCA 62.758 66.667 0.00 0.00 41.76 4.37
1101 1200 4.722700 GGCTTCGGCTTCCAGGCA 62.723 66.667 0.00 0.00 41.44 4.75
1377 1482 1.737735 CATGCTCTGCGTCGACCAA 60.738 57.895 10.58 0.00 0.00 3.67
1959 2067 1.392710 GGGTCATCATCGACTCCGGT 61.393 60.000 0.00 0.00 36.12 5.28
2310 2418 1.452833 GCTGTCCTTCATCCCTGCC 60.453 63.158 0.00 0.00 0.00 4.85
2445 2562 1.152860 TTTGGTGCTTGGCGAGGAA 60.153 52.632 3.44 0.00 0.00 3.36
2496 2613 2.746362 TCTTTCTAAGTCTCGGTCGACC 59.254 50.000 25.28 25.28 34.46 4.79
2616 2733 7.500992 TCTTGTATGTTATCTCATTGAGACCC 58.499 38.462 18.35 9.71 41.76 4.46
2665 2782 7.607991 ACGAGATTTTGATTGACTTATGGTTCT 59.392 33.333 0.00 0.00 0.00 3.01
2673 2790 4.530710 TGACTTATGGTTCTAGCGTTGT 57.469 40.909 0.00 0.00 0.00 3.32
2726 2843 8.070769 TGTTTTAAAACCAACACAAAAGCTTTC 58.929 29.630 24.55 0.00 38.11 2.62
2733 2850 5.170748 CCAACACAAAAGCTTTCCCATATC 58.829 41.667 13.10 0.00 0.00 1.63
2797 2914 3.511146 AGTAGGTTACCGAAATGACCGAA 59.489 43.478 0.00 0.00 37.26 4.30
2806 2923 0.320073 AAATGACCGAAAGCGACCGA 60.320 50.000 0.00 0.00 40.82 4.69
2843 2961 2.533266 TCTTGCGGCATAAGGATCTC 57.467 50.000 2.28 0.00 0.00 2.75
2852 2970 5.008613 GCGGCATAAGGATCTCAAATGTTTA 59.991 40.000 0.00 0.00 0.00 2.01
2853 2971 6.662616 CGGCATAAGGATCTCAAATGTTTAG 58.337 40.000 0.00 0.00 0.00 1.85
2854 2972 6.442112 GGCATAAGGATCTCAAATGTTTAGC 58.558 40.000 0.00 0.00 0.00 3.09
2855 2973 6.138761 GCATAAGGATCTCAAATGTTTAGCG 58.861 40.000 0.00 0.00 0.00 4.26
2856 2974 4.622701 AAGGATCTCAAATGTTTAGCGC 57.377 40.909 0.00 0.00 0.00 5.92
2857 2975 2.945668 AGGATCTCAAATGTTTAGCGCC 59.054 45.455 2.29 0.00 0.00 6.53
2858 2976 2.033424 GGATCTCAAATGTTTAGCGCCC 59.967 50.000 2.29 0.00 0.00 6.13
2859 2977 1.083489 TCTCAAATGTTTAGCGCCCG 58.917 50.000 2.29 0.00 0.00 6.13
2860 2978 0.523335 CTCAAATGTTTAGCGCCCGC 60.523 55.000 2.29 4.20 42.33 6.13
2872 2990 3.449227 GCCCGCTAAGCCCCAAAC 61.449 66.667 0.00 0.00 0.00 2.93
2873 2991 3.131478 CCCGCTAAGCCCCAAACG 61.131 66.667 0.00 0.00 0.00 3.60
2874 2992 2.046700 CCGCTAAGCCCCAAACGA 60.047 61.111 0.00 0.00 0.00 3.85
2875 2993 2.106683 CCGCTAAGCCCCAAACGAG 61.107 63.158 0.00 0.00 0.00 4.18
2876 2994 2.106683 CGCTAAGCCCCAAACGAGG 61.107 63.158 0.00 0.00 0.00 4.63
2877 2995 1.298667 GCTAAGCCCCAAACGAGGA 59.701 57.895 0.00 0.00 0.00 3.71
2878 2996 1.025113 GCTAAGCCCCAAACGAGGAC 61.025 60.000 0.00 0.00 0.00 3.85
2879 2997 0.613777 CTAAGCCCCAAACGAGGACT 59.386 55.000 0.00 0.00 0.00 3.85
2880 2998 0.611714 TAAGCCCCAAACGAGGACTC 59.388 55.000 0.00 0.00 0.00 3.36
2881 2999 2.046217 GCCCCAAACGAGGACTCC 60.046 66.667 0.00 0.00 0.00 3.85
2882 3000 2.890766 GCCCCAAACGAGGACTCCA 61.891 63.158 0.00 0.00 0.00 3.86
2883 3001 1.003718 CCCCAAACGAGGACTCCAC 60.004 63.158 0.00 0.00 0.00 4.02
2884 3002 1.003718 CCCAAACGAGGACTCCACC 60.004 63.158 0.00 0.00 0.00 4.61
2885 3003 1.481056 CCCAAACGAGGACTCCACCT 61.481 60.000 0.00 0.00 43.64 4.00
2886 3004 0.396811 CCAAACGAGGACTCCACCTT 59.603 55.000 0.00 0.00 40.73 3.50
2887 3005 1.621814 CCAAACGAGGACTCCACCTTA 59.378 52.381 0.00 0.00 40.73 2.69
2888 3006 2.038033 CCAAACGAGGACTCCACCTTAA 59.962 50.000 0.00 0.00 40.73 1.85
2889 3007 3.307480 CCAAACGAGGACTCCACCTTAAT 60.307 47.826 0.00 0.00 40.73 1.40
2890 3008 4.324267 CAAACGAGGACTCCACCTTAATT 58.676 43.478 0.00 0.00 40.73 1.40
2891 3009 3.889520 ACGAGGACTCCACCTTAATTC 57.110 47.619 0.00 0.00 40.73 2.17
2892 3010 3.442076 ACGAGGACTCCACCTTAATTCT 58.558 45.455 0.00 0.00 40.73 2.40
2893 3011 4.607239 ACGAGGACTCCACCTTAATTCTA 58.393 43.478 0.00 0.00 40.73 2.10
2894 3012 4.401837 ACGAGGACTCCACCTTAATTCTAC 59.598 45.833 0.00 0.00 40.73 2.59
2895 3013 4.645588 CGAGGACTCCACCTTAATTCTACT 59.354 45.833 0.00 0.00 40.73 2.57
2896 3014 5.221087 CGAGGACTCCACCTTAATTCTACTC 60.221 48.000 0.00 0.00 40.73 2.59
2897 3015 4.645588 AGGACTCCACCTTAATTCTACTCG 59.354 45.833 0.00 0.00 36.86 4.18
2898 3016 4.361420 GACTCCACCTTAATTCTACTCGC 58.639 47.826 0.00 0.00 0.00 5.03
2899 3017 4.024670 ACTCCACCTTAATTCTACTCGCT 58.975 43.478 0.00 0.00 0.00 4.93
2900 3018 4.466726 ACTCCACCTTAATTCTACTCGCTT 59.533 41.667 0.00 0.00 0.00 4.68
2901 3019 5.655532 ACTCCACCTTAATTCTACTCGCTTA 59.344 40.000 0.00 0.00 0.00 3.09
2902 3020 6.324254 ACTCCACCTTAATTCTACTCGCTTAT 59.676 38.462 0.00 0.00 0.00 1.73
2903 3021 7.120923 TCCACCTTAATTCTACTCGCTTATT 57.879 36.000 0.00 0.00 0.00 1.40
2904 3022 7.562135 TCCACCTTAATTCTACTCGCTTATTT 58.438 34.615 0.00 0.00 0.00 1.40
2905 3023 8.044908 TCCACCTTAATTCTACTCGCTTATTTT 58.955 33.333 0.00 0.00 0.00 1.82
2912 3030 4.755411 TCTACTCGCTTATTTTGGGACAG 58.245 43.478 0.00 0.00 42.39 3.51
2919 3037 3.625313 GCTTATTTTGGGACAGAGAGAGC 59.375 47.826 0.00 0.00 42.39 4.09
2969 3089 7.660208 ACGTCATGTTCCTAAAGACTTGTATTT 59.340 33.333 0.00 0.00 0.00 1.40
2972 3092 8.999431 TCATGTTCCTAAAGACTTGTATTTCAC 58.001 33.333 0.00 0.00 0.00 3.18
3003 3123 6.352051 CCAAATCTCCCATGAAGCCAAAATAA 60.352 38.462 0.00 0.00 0.00 1.40
3016 3136 4.706962 AGCCAAAATAACCATGGAGAAGAC 59.293 41.667 21.47 0.00 36.27 3.01
3089 3212 5.469479 ACCGAGTTAAAATTGCTCCAATTG 58.531 37.500 0.00 0.00 42.32 2.32
3093 3216 6.570378 CGAGTTAAAATTGCTCCAATTGTCCT 60.570 38.462 4.43 0.00 42.32 3.85
3095 3218 7.602753 AGTTAAAATTGCTCCAATTGTCCTAC 58.397 34.615 4.43 0.36 42.32 3.18
3102 3225 4.263462 TGCTCCAATTGTCCTACTTGATGT 60.263 41.667 4.43 0.00 0.00 3.06
3117 3240 1.208052 TGATGTGAGCTAGACCAAGCC 59.792 52.381 0.00 0.00 43.86 4.35
3122 3245 2.680339 GTGAGCTAGACCAAGCCAATTC 59.320 50.000 0.00 0.00 43.86 2.17
3126 3249 3.009473 AGCTAGACCAAGCCAATTCTTGA 59.991 43.478 8.15 0.00 44.61 3.02
3128 3251 5.104360 AGCTAGACCAAGCCAATTCTTGATA 60.104 40.000 8.15 0.00 44.61 2.15
3196 3319 9.593134 TTGCAAAGTTGACATAAACTACAATTT 57.407 25.926 0.00 0.00 39.48 1.82
3205 3328 3.866883 AAACTACAATTTGGCCATCCG 57.133 42.857 6.09 0.00 34.14 4.18
3206 3329 1.102978 ACTACAATTTGGCCATCCGC 58.897 50.000 6.09 0.00 34.14 5.54
3220 3343 0.464036 ATCCGCGATGTTGAAGCCTA 59.536 50.000 8.23 0.00 0.00 3.93
3226 3349 2.550978 CGATGTTGAAGCCTATCCGTT 58.449 47.619 0.00 0.00 0.00 4.44
3232 3355 1.626321 TGAAGCCTATCCGTTGTCCAA 59.374 47.619 0.00 0.00 0.00 3.53
3284 3407 2.348411 AATTATGCTTAGGCGGCACT 57.652 45.000 13.08 0.00 42.69 4.40
3301 3424 4.327087 CGGCACTAAAATCTTCCAAATTGC 59.673 41.667 0.00 0.00 0.00 3.56
3316 3439 5.242838 TCCAAATTGCCGGCTTATATTTAGG 59.757 40.000 29.70 23.93 0.00 2.69
3317 3440 5.469479 CAAATTGCCGGCTTATATTTAGGG 58.531 41.667 29.70 11.71 0.00 3.53
3318 3441 2.194201 TGCCGGCTTATATTTAGGGC 57.806 50.000 29.70 0.00 39.48 5.19
3319 3442 1.702957 TGCCGGCTTATATTTAGGGCT 59.297 47.619 29.70 0.00 39.73 5.19
3320 3443 2.907696 TGCCGGCTTATATTTAGGGCTA 59.092 45.455 29.70 0.00 39.73 3.93
3321 3444 3.521937 TGCCGGCTTATATTTAGGGCTAT 59.478 43.478 29.70 0.00 39.73 2.97
3322 3445 4.018779 TGCCGGCTTATATTTAGGGCTATT 60.019 41.667 29.70 0.00 39.73 1.73
3323 3446 4.948004 GCCGGCTTATATTTAGGGCTATTT 59.052 41.667 22.15 0.00 36.21 1.40
3324 3447 5.417894 GCCGGCTTATATTTAGGGCTATTTT 59.582 40.000 22.15 0.00 36.21 1.82
3325 3448 6.071560 GCCGGCTTATATTTAGGGCTATTTTT 60.072 38.462 22.15 0.00 36.21 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 3.284449 GACCGCCACCACCACAAC 61.284 66.667 0.00 0.00 0.00 3.32
41 42 2.267961 CCCAACCCTAGCCGTCAC 59.732 66.667 0.00 0.00 0.00 3.67
44 45 3.327404 CACCCCAACCCTAGCCGT 61.327 66.667 0.00 0.00 0.00 5.68
46 47 4.442454 GGCACCCCAACCCTAGCC 62.442 72.222 0.00 0.00 34.71 3.93
90 91 2.475371 ATCTGACCCTGCGCTTGCTT 62.475 55.000 9.73 0.00 40.12 3.91
413 448 2.083774 TCTGCGCGGATTTTGATTTCT 58.916 42.857 16.69 0.00 0.00 2.52
445 480 2.159667 TCTGAGCATTCAATCGCGTTTG 60.160 45.455 21.08 21.08 31.69 2.93
461 496 1.153005 GGGGAGCAGCCAATCTGAG 60.153 63.158 0.00 0.00 45.72 3.35
590 630 2.009774 CAAAATTCGGAGGTGAGCGAT 58.990 47.619 0.00 0.00 0.00 4.58
612 652 6.512415 GCATATGGAACTTCAATCAGTGTAGC 60.512 42.308 4.56 0.00 0.00 3.58
769 809 3.614092 TGGTCATGGAGCAGAGAATTTC 58.386 45.455 0.00 0.00 35.04 2.17
843 888 0.106967 GGAGGAATCAAGGGTCTGGC 60.107 60.000 0.00 0.00 0.00 4.85
880 925 1.529865 CTCCATGCACATGCGTATGAG 59.470 52.381 20.86 13.48 45.83 2.90
901 990 5.281693 TCGTGTTATATATACCGTGTCCG 57.718 43.478 0.00 0.00 0.00 4.79
902 991 6.749118 GGATTCGTGTTATATATACCGTGTCC 59.251 42.308 0.00 4.81 0.00 4.02
947 1040 2.827051 CGGCTGTGATTGGGATGCG 61.827 63.158 0.00 0.00 0.00 4.73
955 1048 2.100631 GCACGCTACGGCTGTGATT 61.101 57.895 8.92 0.00 41.63 2.57
1377 1482 2.283388 TCGAAGTAGGGCGTGGGT 60.283 61.111 0.00 0.00 0.00 4.51
1617 1725 2.809601 CCGTTGAAGAGCGACCCG 60.810 66.667 0.00 0.00 0.00 5.28
2055 2163 1.299926 GCACGTGTTCAGGTCGTCT 60.300 57.895 18.38 0.00 35.62 4.18
2310 2418 1.066143 AGACTCATTAGGTTGCACGGG 60.066 52.381 0.00 0.00 0.00 5.28
2445 2562 4.516698 CAGATAATCAGCCCGCAGTTAAAT 59.483 41.667 0.00 0.00 0.00 1.40
2608 2725 2.829384 GGGTGTGGCTGGGTCTCAA 61.829 63.158 0.00 0.00 0.00 3.02
2616 2733 3.117888 AGGATACAAATAGGGTGTGGCTG 60.118 47.826 0.00 0.00 41.41 4.85
2775 2892 3.091545 TCGGTCATTTCGGTAACCTACT 58.908 45.455 0.00 0.00 0.00 2.57
2776 2893 3.508744 TCGGTCATTTCGGTAACCTAC 57.491 47.619 0.00 0.00 0.00 3.18
2823 2941 2.170397 TGAGATCCTTATGCCGCAAGAA 59.830 45.455 0.00 0.00 43.02 2.52
2843 2961 4.071374 GCGGGCGCTAAACATTTG 57.929 55.556 7.64 0.00 38.26 2.32
2855 2973 3.449227 GTTTGGGGCTTAGCGGGC 61.449 66.667 0.00 0.00 0.00 6.13
2856 2974 3.131478 CGTTTGGGGCTTAGCGGG 61.131 66.667 0.00 0.00 0.00 6.13
2857 2975 2.046700 TCGTTTGGGGCTTAGCGG 60.047 61.111 0.00 0.00 0.00 5.52
2858 2976 2.106683 CCTCGTTTGGGGCTTAGCG 61.107 63.158 0.00 0.00 0.00 4.26
2859 2977 1.025113 GTCCTCGTTTGGGGCTTAGC 61.025 60.000 0.00 0.00 0.00 3.09
2860 2978 0.613777 AGTCCTCGTTTGGGGCTTAG 59.386 55.000 0.00 0.00 34.87 2.18
2861 2979 0.611714 GAGTCCTCGTTTGGGGCTTA 59.388 55.000 0.00 0.00 39.10 3.09
2862 2980 1.375326 GAGTCCTCGTTTGGGGCTT 59.625 57.895 0.00 0.00 39.10 4.35
2863 2981 2.593956 GGAGTCCTCGTTTGGGGCT 61.594 63.158 0.41 0.00 42.03 5.19
2864 2982 2.046217 GGAGTCCTCGTTTGGGGC 60.046 66.667 0.41 0.00 0.00 5.80
2865 2983 1.003718 GTGGAGTCCTCGTTTGGGG 60.004 63.158 11.33 0.00 0.00 4.96
2866 2984 1.003718 GGTGGAGTCCTCGTTTGGG 60.004 63.158 11.33 0.00 0.00 4.12
2867 2985 0.396811 AAGGTGGAGTCCTCGTTTGG 59.603 55.000 11.33 0.00 36.74 3.28
2868 2986 3.396260 TTAAGGTGGAGTCCTCGTTTG 57.604 47.619 20.67 0.00 36.74 2.93
2869 2987 4.286291 AGAATTAAGGTGGAGTCCTCGTTT 59.714 41.667 20.67 12.64 36.74 3.60
2870 2988 3.838903 AGAATTAAGGTGGAGTCCTCGTT 59.161 43.478 19.70 19.70 36.74 3.85
2871 2989 3.442076 AGAATTAAGGTGGAGTCCTCGT 58.558 45.455 11.33 5.61 36.74 4.18
2872 2990 4.645588 AGTAGAATTAAGGTGGAGTCCTCG 59.354 45.833 11.33 0.00 36.74 4.63
2873 2991 5.221087 CGAGTAGAATTAAGGTGGAGTCCTC 60.221 48.000 11.33 6.72 36.74 3.71
2874 2992 4.645588 CGAGTAGAATTAAGGTGGAGTCCT 59.354 45.833 11.33 0.00 39.84 3.85
2875 2993 4.737055 GCGAGTAGAATTAAGGTGGAGTCC 60.737 50.000 0.73 0.73 0.00 3.85
2876 2994 4.098196 AGCGAGTAGAATTAAGGTGGAGTC 59.902 45.833 0.00 0.00 0.00 3.36
2877 2995 4.024670 AGCGAGTAGAATTAAGGTGGAGT 58.975 43.478 0.00 0.00 0.00 3.85
2878 2996 4.657436 AGCGAGTAGAATTAAGGTGGAG 57.343 45.455 0.00 0.00 0.00 3.86
2879 2997 6.726490 ATAAGCGAGTAGAATTAAGGTGGA 57.274 37.500 0.00 0.00 0.00 4.02
2880 2998 7.787725 AAATAAGCGAGTAGAATTAAGGTGG 57.212 36.000 0.00 0.00 0.00 4.61
2881 2999 8.122952 CCAAAATAAGCGAGTAGAATTAAGGTG 58.877 37.037 0.00 0.00 0.00 4.00
2882 3000 7.282450 CCCAAAATAAGCGAGTAGAATTAAGGT 59.718 37.037 0.00 0.00 0.00 3.50
2883 3001 7.497909 TCCCAAAATAAGCGAGTAGAATTAAGG 59.502 37.037 0.00 0.00 0.00 2.69
2884 3002 8.336080 GTCCCAAAATAAGCGAGTAGAATTAAG 58.664 37.037 0.00 0.00 0.00 1.85
2885 3003 7.825270 TGTCCCAAAATAAGCGAGTAGAATTAA 59.175 33.333 0.00 0.00 0.00 1.40
2886 3004 7.332557 TGTCCCAAAATAAGCGAGTAGAATTA 58.667 34.615 0.00 0.00 0.00 1.40
2887 3005 6.177610 TGTCCCAAAATAAGCGAGTAGAATT 58.822 36.000 0.00 0.00 0.00 2.17
2888 3006 5.741011 TGTCCCAAAATAAGCGAGTAGAAT 58.259 37.500 0.00 0.00 0.00 2.40
2889 3007 5.046878 TCTGTCCCAAAATAAGCGAGTAGAA 60.047 40.000 0.00 0.00 0.00 2.10
2890 3008 4.464951 TCTGTCCCAAAATAAGCGAGTAGA 59.535 41.667 0.00 0.00 0.00 2.59
2891 3009 4.755411 TCTGTCCCAAAATAAGCGAGTAG 58.245 43.478 0.00 0.00 0.00 2.57
2892 3010 4.464951 TCTCTGTCCCAAAATAAGCGAGTA 59.535 41.667 0.00 0.00 0.00 2.59
2893 3011 3.260884 TCTCTGTCCCAAAATAAGCGAGT 59.739 43.478 0.00 0.00 0.00 4.18
2894 3012 3.861840 TCTCTGTCCCAAAATAAGCGAG 58.138 45.455 0.00 0.00 0.00 5.03
2895 3013 3.513912 TCTCTCTGTCCCAAAATAAGCGA 59.486 43.478 0.00 0.00 0.00 4.93
2896 3014 3.861840 TCTCTCTGTCCCAAAATAAGCG 58.138 45.455 0.00 0.00 0.00 4.68
2897 3015 3.625313 GCTCTCTCTGTCCCAAAATAAGC 59.375 47.826 0.00 0.00 0.00 3.09
2898 3016 4.633565 GTGCTCTCTCTGTCCCAAAATAAG 59.366 45.833 0.00 0.00 0.00 1.73
2899 3017 4.287067 AGTGCTCTCTCTGTCCCAAAATAA 59.713 41.667 0.00 0.00 0.00 1.40
2900 3018 3.840666 AGTGCTCTCTCTGTCCCAAAATA 59.159 43.478 0.00 0.00 0.00 1.40
2901 3019 2.641815 AGTGCTCTCTCTGTCCCAAAAT 59.358 45.455 0.00 0.00 0.00 1.82
2902 3020 2.050144 AGTGCTCTCTCTGTCCCAAAA 58.950 47.619 0.00 0.00 0.00 2.44
2903 3021 1.722034 AGTGCTCTCTCTGTCCCAAA 58.278 50.000 0.00 0.00 0.00 3.28
2904 3022 1.345741 CAAGTGCTCTCTCTGTCCCAA 59.654 52.381 0.00 0.00 0.00 4.12
2905 3023 0.972134 CAAGTGCTCTCTCTGTCCCA 59.028 55.000 0.00 0.00 0.00 4.37
2919 3037 2.710377 TGCCTGGTGTAATAGCAAGTG 58.290 47.619 0.00 0.00 36.15 3.16
2937 3055 4.391830 TCTTTAGGAACATGACGTCAATGC 59.608 41.667 24.13 16.44 0.00 3.56
2969 3089 4.227982 TCATGGGAGATTTGGAATGAGTGA 59.772 41.667 0.00 0.00 0.00 3.41
2972 3092 4.037684 GCTTCATGGGAGATTTGGAATGAG 59.962 45.833 0.00 0.00 0.00 2.90
3003 3123 2.040412 GGAAAGGTGTCTTCTCCATGGT 59.960 50.000 12.58 0.00 31.82 3.55
3016 3136 4.094887 CGAATGGTAATGTGAGGAAAGGTG 59.905 45.833 0.00 0.00 0.00 4.00
3089 3212 4.202070 GGTCTAGCTCACATCAAGTAGGAC 60.202 50.000 0.00 0.00 0.00 3.85
3093 3216 4.382040 GCTTGGTCTAGCTCACATCAAGTA 60.382 45.833 11.95 0.00 38.15 2.24
3095 3218 2.935201 GCTTGGTCTAGCTCACATCAAG 59.065 50.000 7.74 7.74 38.15 3.02
3102 3225 2.573462 AGAATTGGCTTGGTCTAGCTCA 59.427 45.455 0.00 0.00 40.99 4.26
3122 3245 9.993454 TCATCTAGAATTTGGTCTGATATCAAG 57.007 33.333 6.90 1.67 0.00 3.02
3126 3249 7.393216 GGCTCATCTAGAATTTGGTCTGATAT 58.607 38.462 0.00 0.00 0.00 1.63
3128 3251 5.619220 GGCTCATCTAGAATTTGGTCTGAT 58.381 41.667 0.00 0.00 0.00 2.90
3165 3288 2.693797 ATGTCAACTTTGCAAGCGAG 57.306 45.000 0.00 0.00 0.00 5.03
3169 3292 8.801715 ATTGTAGTTTATGTCAACTTTGCAAG 57.198 30.769 0.00 0.00 38.07 4.01
3196 3319 2.811542 TTCAACATCGCGGATGGCCA 62.812 55.000 8.56 8.56 43.60 5.36
3205 3328 0.861837 CGGATAGGCTTCAACATCGC 59.138 55.000 0.00 0.00 0.00 4.58
3206 3329 2.225068 ACGGATAGGCTTCAACATCG 57.775 50.000 0.00 0.00 0.00 3.84
3220 3343 2.233922 AGATCGAGTTTGGACAACGGAT 59.766 45.455 0.00 0.00 0.00 4.18
3267 3390 2.992124 TTAGTGCCGCCTAAGCATAA 57.008 45.000 0.00 0.00 43.29 1.90
3268 3391 2.992124 TTTAGTGCCGCCTAAGCATA 57.008 45.000 0.00 0.00 43.29 3.14
3284 3407 3.513515 AGCCGGCAATTTGGAAGATTTTA 59.486 39.130 31.54 0.00 0.00 1.52
3301 3424 7.462571 AAAAATAGCCCTAAATATAAGCCGG 57.537 36.000 0.00 0.00 0.00 6.13


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

AutoCloner maintained by Alex Coulton.