Multiple sequence alignment - TraesCS1B01G228800

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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 TraesCS1B01G228800 chr1B 100.000 3180 0 0 1 3180 410666234 410669413 0.000000e+00 5873
1 TraesCS1B01G228800 chr1D 89.968 2811 110 60 1 2691 303292058 303294816 0.000000e+00 3470
2 TraesCS1B01G228800 chr1D 82.821 390 42 15 2760 3143 303294842 303295212 3.060000e-85 326
3 TraesCS1B01G228800 chr1A 88.549 2646 129 55 17 2554 380888639 380891218 0.000000e+00 3048


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 TraesCS1B01G228800 chr1B 410666234 410669413 3179 False 5873 5873 100.0000 1 3180 1 chr1B.!!$F1 3179
1 TraesCS1B01G228800 chr1D 303292058 303295212 3154 False 1898 3470 86.3945 1 3143 2 chr1D.!!$F1 3142
2 TraesCS1B01G228800 chr1A 380888639 380891218 2579 False 3048 3048 88.5490 17 2554 1 chr1A.!!$F1 2537

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
852 927 0.025001 CGCCTCAAATAGCACGAACG 59.975 55.0 0.0 0.0 0.0 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2702 2883 0.044092 TCCCCCTCTAAGCATGGACA 59.956 55.0 0.0 0.0 0.0 4.02 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
47 51 6.423776 TGGCCTTTCTTTTCATTTTCATCT 57.576 33.333 3.32 0.00 0.00 2.90
132 146 1.625315 CTCTCCCTGTTGTCATGTGGA 59.375 52.381 0.00 0.00 0.00 4.02
404 429 1.619827 TGAGAACAACGACCCGGTTAT 59.380 47.619 0.00 0.00 0.00 1.89
405 430 2.824936 TGAGAACAACGACCCGGTTATA 59.175 45.455 0.00 0.00 0.00 0.98
406 431 3.119388 TGAGAACAACGACCCGGTTATAG 60.119 47.826 0.00 0.00 0.00 1.31
478 506 5.445939 CGTGTAGATCCAACAGCACAATAAC 60.446 44.000 0.00 0.00 0.00 1.89
479 507 4.629634 TGTAGATCCAACAGCACAATAACG 59.370 41.667 0.00 0.00 0.00 3.18
480 508 2.420022 AGATCCAACAGCACAATAACGC 59.580 45.455 0.00 0.00 0.00 4.84
624 666 2.027073 GCTGACGTTGCCATCACGA 61.027 57.895 0.00 0.00 0.00 4.35
625 667 1.361668 GCTGACGTTGCCATCACGAT 61.362 55.000 0.00 0.00 0.00 3.73
626 668 1.078709 CTGACGTTGCCATCACGATT 58.921 50.000 0.00 0.00 0.00 3.34
627 669 1.061131 CTGACGTTGCCATCACGATTC 59.939 52.381 0.00 0.00 0.00 2.52
628 670 1.075542 GACGTTGCCATCACGATTCA 58.924 50.000 0.00 0.00 0.00 2.57
629 671 0.796312 ACGTTGCCATCACGATTCAC 59.204 50.000 0.00 0.00 0.00 3.18
643 685 1.388065 ATTCACGGGAGAGAGCGAGG 61.388 60.000 0.00 0.00 0.00 4.63
711 760 2.171237 TGATAAGACGAGAGGGACGGTA 59.829 50.000 0.00 0.00 34.93 4.02
770 828 1.219124 GCCGCAACTCTCTCATCCA 59.781 57.895 0.00 0.00 0.00 3.41
811 883 1.925888 GCCATCCCATCCAACTCCT 59.074 57.895 0.00 0.00 0.00 3.69
812 884 0.179006 GCCATCCCATCCAACTCCTC 60.179 60.000 0.00 0.00 0.00 3.71
813 885 1.516110 CCATCCCATCCAACTCCTCT 58.484 55.000 0.00 0.00 0.00 3.69
849 924 2.164663 CGCGCCTCAAATAGCACGA 61.165 57.895 0.00 0.00 36.70 4.35
850 925 1.692148 CGCGCCTCAAATAGCACGAA 61.692 55.000 0.00 0.00 36.70 3.85
851 926 0.247695 GCGCCTCAAATAGCACGAAC 60.248 55.000 0.00 0.00 0.00 3.95
852 927 0.025001 CGCCTCAAATAGCACGAACG 59.975 55.000 0.00 0.00 0.00 3.95
853 928 0.373716 GCCTCAAATAGCACGAACGG 59.626 55.000 0.00 0.00 0.00 4.44
1071 1155 3.197790 CCGCGCAAGGAGATGGTG 61.198 66.667 8.75 0.00 38.28 4.17
1072 1156 3.197790 CGCGCAAGGAGATGGTGG 61.198 66.667 8.75 0.00 38.28 4.61
1134 1221 2.435805 CCTCTTCATGGATTTCTCCCGA 59.564 50.000 0.00 0.00 41.29 5.14
1182 1269 2.680339 GTGCTGCTTGATTACCTTCTCC 59.320 50.000 0.00 0.00 0.00 3.71
1229 1316 5.938125 AGGCGATTAACTAACACACATCTTT 59.062 36.000 0.00 0.00 0.00 2.52
1311 1398 2.058595 GGCACGCCTCTTCTCCCTA 61.059 63.158 0.00 0.00 0.00 3.53
1552 1639 0.664166 CGCGCTTGCTTGATTGGTTT 60.664 50.000 5.56 0.00 36.08 3.27
1588 1675 2.858745 TCGATCGATCTACATGGTGGA 58.141 47.619 22.43 6.78 0.00 4.02
1750 1850 2.347490 GAGACCTTCAAGGCGGCA 59.653 61.111 13.08 0.00 39.63 5.69
1980 2089 2.854032 CAGGGTGGTGGAGGTGGT 60.854 66.667 0.00 0.00 0.00 4.16
2104 2216 4.811364 GCCTCTGCCTCCCAAGCC 62.811 72.222 0.00 0.00 0.00 4.35
2105 2217 4.479993 CCTCTGCCTCCCAAGCCG 62.480 72.222 0.00 0.00 0.00 5.52
2106 2218 4.479993 CTCTGCCTCCCAAGCCGG 62.480 72.222 0.00 0.00 0.00 6.13
2210 2323 2.212652 CGCCGGATCATGAAATCAGAA 58.787 47.619 5.05 0.00 0.00 3.02
2284 2401 2.231478 CTCTTTTCTCCCGTGCTAGTGA 59.769 50.000 0.00 0.00 0.00 3.41
2285 2402 2.631062 TCTTTTCTCCCGTGCTAGTGAA 59.369 45.455 0.00 0.00 0.00 3.18
2339 2466 9.733556 TTTTGCTGGTGATCTAGTAAATCTTTA 57.266 29.630 0.00 0.00 36.87 1.85
2340 2467 8.718102 TTGCTGGTGATCTAGTAAATCTTTAC 57.282 34.615 4.95 4.95 42.50 2.01
2399 2537 0.179200 GCAACGCGTTGATTAGGTGG 60.179 55.000 45.98 23.13 42.93 4.61
2442 2580 2.905880 TAGGCCTACGGAGCGCTC 60.906 66.667 29.38 29.38 0.00 5.03
2525 2681 1.914764 GACGAGGGGTGGTTGGGTA 60.915 63.158 0.00 0.00 0.00 3.69
2554 2710 3.053896 GGAAGTGGCGGGAAACGG 61.054 66.667 0.00 0.00 44.51 4.44
2583 2764 1.206072 GATCCCGATCGGACGTACG 59.794 63.158 35.42 15.74 46.09 3.67
2666 2847 1.241165 CATTCTGCTGCACTGGACAA 58.759 50.000 0.00 0.00 0.00 3.18
2671 2852 1.159713 TGCTGCACTGGACAAAGACG 61.160 55.000 0.00 0.00 0.00 4.18
2675 2856 1.227823 CACTGGACAAAGACGGGCA 60.228 57.895 0.00 0.00 0.00 5.36
2676 2857 1.071471 ACTGGACAAAGACGGGCAG 59.929 57.895 0.00 0.00 0.00 4.85
2678 2859 2.397413 CTGGACAAAGACGGGCAGGT 62.397 60.000 0.00 0.00 0.00 4.00
2681 2862 0.534203 GACAAAGACGGGCAGGTTCA 60.534 55.000 0.00 0.00 0.00 3.18
2682 2863 0.818040 ACAAAGACGGGCAGGTTCAC 60.818 55.000 0.00 0.00 0.00 3.18
2683 2864 1.597027 AAAGACGGGCAGGTTCACG 60.597 57.895 0.00 0.00 0.00 4.35
2684 2865 4.681978 AGACGGGCAGGTTCACGC 62.682 66.667 0.00 0.00 0.00 5.34
2707 2888 4.386951 CGGCCGTGACCATGTCCA 62.387 66.667 19.50 0.00 0.00 4.02
2708 2889 2.272146 GGCCGTGACCATGTCCAT 59.728 61.111 0.00 0.00 0.00 3.41
2709 2890 2.114670 GGCCGTGACCATGTCCATG 61.115 63.158 0.14 0.14 38.51 3.66
2710 2891 2.764314 GCCGTGACCATGTCCATGC 61.764 63.158 1.64 0.00 37.49 4.06
2711 2892 1.078214 CCGTGACCATGTCCATGCT 60.078 57.895 1.64 0.00 37.49 3.79
2712 2893 0.677731 CCGTGACCATGTCCATGCTT 60.678 55.000 1.64 0.00 37.49 3.91
2713 2894 1.406751 CCGTGACCATGTCCATGCTTA 60.407 52.381 1.64 0.00 37.49 3.09
2714 2895 1.935873 CGTGACCATGTCCATGCTTAG 59.064 52.381 1.64 0.00 37.49 2.18
2715 2896 2.418609 CGTGACCATGTCCATGCTTAGA 60.419 50.000 1.64 0.00 37.49 2.10
2716 2897 3.201290 GTGACCATGTCCATGCTTAGAG 58.799 50.000 1.64 0.00 37.49 2.43
2717 2898 2.171237 TGACCATGTCCATGCTTAGAGG 59.829 50.000 1.64 0.00 37.49 3.69
2718 2899 1.492176 ACCATGTCCATGCTTAGAGGG 59.508 52.381 1.64 0.00 37.49 4.30
2719 2900 1.202855 CCATGTCCATGCTTAGAGGGG 60.203 57.143 1.64 0.00 37.49 4.79
2720 2901 1.143813 ATGTCCATGCTTAGAGGGGG 58.856 55.000 0.00 0.00 0.00 5.40
2721 2902 0.044092 TGTCCATGCTTAGAGGGGGA 59.956 55.000 0.00 0.00 0.00 4.81
2722 2903 0.761802 GTCCATGCTTAGAGGGGGAG 59.238 60.000 0.00 0.00 0.00 4.30
2723 2904 0.343372 TCCATGCTTAGAGGGGGAGT 59.657 55.000 0.00 0.00 0.00 3.85
2727 2908 3.095347 GCTTAGAGGGGGAGTGCCG 62.095 68.421 0.00 0.00 33.83 5.69
2736 2917 1.377202 GGGAGTGCCGCAGAAATGA 60.377 57.895 0.00 0.00 33.83 2.57
2743 2924 0.449388 GCCGCAGAAATGAAGGTGAG 59.551 55.000 0.00 0.00 0.00 3.51
2747 2928 0.095935 CAGAAATGAAGGTGAGCGCG 59.904 55.000 0.00 0.00 0.00 6.86
2750 2931 2.187599 AAATGAAGGTGAGCGCGTGC 62.188 55.000 14.39 14.39 43.24 5.34
2803 2984 1.079543 CTCACTCCGGCTTGGACTG 60.080 63.158 0.00 0.00 43.74 3.51
2820 3001 0.532862 CTGACCACACTGGAACGCTT 60.533 55.000 0.00 0.00 40.96 4.68
2831 3012 1.758280 TGGAACGCTTATCCGGTACAT 59.242 47.619 0.00 0.00 32.98 2.29
2835 3016 1.340248 ACGCTTATCCGGTACATCTGG 59.660 52.381 0.00 0.00 43.70 3.86
2841 3022 0.907704 TCCGGTACATCTGGCCTTGT 60.908 55.000 3.32 8.06 42.13 3.16
2843 3024 1.369091 CGGTACATCTGGCCTTGTGC 61.369 60.000 3.32 8.85 40.16 4.57
2851 3032 2.034066 GGCCTTGTGCTGCTACCA 59.966 61.111 0.00 0.00 40.92 3.25
2853 3034 1.302832 GCCTTGTGCTGCTACCAGT 60.303 57.895 0.00 0.00 41.26 4.00
2857 3038 3.257933 GTGCTGCTACCAGTGCAC 58.742 61.111 9.40 9.40 46.66 4.57
2867 3048 2.034532 CAGTGCACCAGCCATCCA 59.965 61.111 14.63 0.00 41.13 3.41
2874 3055 1.483415 GCACCAGCCATCCAAAATCAT 59.517 47.619 0.00 0.00 33.58 2.45
2876 3057 3.527533 CACCAGCCATCCAAAATCATTG 58.472 45.455 0.00 0.00 0.00 2.82
2879 3060 4.964262 ACCAGCCATCCAAAATCATTGTAT 59.036 37.500 0.00 0.00 0.00 2.29
2881 3062 5.294356 CAGCCATCCAAAATCATTGTATGG 58.706 41.667 8.04 8.04 36.35 2.74
2915 3096 7.656707 AATTCTGAAATAATTTGGTGTGTGC 57.343 32.000 0.00 0.00 0.00 4.57
2919 3100 5.851720 TGAAATAATTTGGTGTGTGCACAT 58.148 33.333 24.69 6.69 46.95 3.21
2927 3108 4.961435 TGGTGTGTGCACATAACATATG 57.039 40.909 28.02 0.00 46.95 1.78
2930 3111 4.635765 GGTGTGTGCACATAACATATGTCT 59.364 41.667 24.87 2.50 46.95 3.41
2932 3113 6.238103 GGTGTGTGCACATAACATATGTCTAC 60.238 42.308 24.87 7.03 46.95 2.59
2941 3122 7.171508 CACATAACATATGTCTACCATGTCACC 59.828 40.741 9.23 0.00 34.86 4.02
2943 3124 5.282055 ACATATGTCTACCATGTCACCAG 57.718 43.478 1.41 0.00 34.86 4.00
2947 3128 4.908601 TGTCTACCATGTCACCAGAAAT 57.091 40.909 0.00 0.00 0.00 2.17
2948 3129 6.560003 ATGTCTACCATGTCACCAGAAATA 57.440 37.500 0.00 0.00 30.69 1.40
2950 3131 6.957631 TGTCTACCATGTCACCAGAAATAAT 58.042 36.000 0.00 0.00 0.00 1.28
2951 3132 8.084985 TGTCTACCATGTCACCAGAAATAATA 57.915 34.615 0.00 0.00 0.00 0.98
2953 3134 9.561069 GTCTACCATGTCACCAGAAATAATAAT 57.439 33.333 0.00 0.00 0.00 1.28
2975 3158 5.947228 TTGAATTACAGCTGGAGAAACAG 57.053 39.130 19.93 0.00 41.41 3.16
2976 3159 5.227569 TGAATTACAGCTGGAGAAACAGA 57.772 39.130 19.93 0.00 40.97 3.41
2977 3160 5.620206 TGAATTACAGCTGGAGAAACAGAA 58.380 37.500 19.93 0.00 40.97 3.02
2993 3176 6.532657 AGAAACAGAAACAACAAATTCAGCAG 59.467 34.615 0.00 0.00 0.00 4.24
3021 3206 5.856156 CATGCTAATGGGCCAAATTTATGA 58.144 37.500 11.89 0.00 0.00 2.15
3026 3211 3.127791 TGGGCCAAATTTATGACCCAT 57.872 42.857 2.13 0.00 42.38 4.00
3098 3283 8.241497 TGTTGTTTCTAGAGTTGTAGGTCTAA 57.759 34.615 0.00 0.00 0.00 2.10
3124 3309 9.787532 ATTTGTATCTGAATATTTGGTGAAACG 57.212 29.630 0.00 0.00 38.12 3.60
3125 3310 8.554835 TTGTATCTGAATATTTGGTGAAACGA 57.445 30.769 0.00 0.00 38.12 3.85
3143 3328 6.197655 TGAAACGATAGATGTACGTTATGTGC 59.802 38.462 0.00 0.00 46.74 4.57
3144 3329 4.216731 ACGATAGATGTACGTTATGTGCG 58.783 43.478 0.00 0.00 36.91 5.34
3145 3330 4.024641 ACGATAGATGTACGTTATGTGCGA 60.025 41.667 0.00 0.00 36.91 5.10
3146 3331 5.086727 CGATAGATGTACGTTATGTGCGAT 58.913 41.667 0.00 0.00 34.88 4.58
3147 3332 5.567915 CGATAGATGTACGTTATGTGCGATT 59.432 40.000 0.00 0.00 34.88 3.34
3148 3333 6.087687 CGATAGATGTACGTTATGTGCGATTT 59.912 38.462 0.00 0.00 34.88 2.17
3149 3334 5.389642 AGATGTACGTTATGTGCGATTTG 57.610 39.130 0.00 0.00 35.72 2.32
3150 3335 4.868171 AGATGTACGTTATGTGCGATTTGT 59.132 37.500 0.00 0.00 35.72 2.83
3151 3336 4.314948 TGTACGTTATGTGCGATTTGTG 57.685 40.909 0.00 0.00 35.72 3.33
3152 3337 2.241259 ACGTTATGTGCGATTTGTGC 57.759 45.000 0.00 0.00 0.00 4.57
3153 3338 1.533299 ACGTTATGTGCGATTTGTGCA 59.467 42.857 0.00 0.00 40.70 4.57
3158 3343 4.041617 TGCGATTTGTGCACTCGT 57.958 50.000 22.86 8.21 37.44 4.18
3159 3344 3.202923 TGCGATTTGTGCACTCGTA 57.797 47.368 22.86 17.99 37.44 3.43
3160 3345 1.067693 TGCGATTTGTGCACTCGTAG 58.932 50.000 22.86 11.83 37.44 3.51
3161 3346 0.247301 GCGATTTGTGCACTCGTAGC 60.247 55.000 22.86 16.73 34.96 3.58
3162 3347 1.067693 CGATTTGTGCACTCGTAGCA 58.932 50.000 19.41 0.00 40.19 3.49
3169 3354 2.293677 TGCACTCGTAGCACCATAAG 57.706 50.000 0.00 0.00 37.02 1.73
3170 3355 1.134818 TGCACTCGTAGCACCATAAGG 60.135 52.381 0.00 0.00 37.02 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 81 1.433534 GTTTGACGGAGGCTTCTCTG 58.566 55.000 0.00 0.00 46.63 3.35
132 146 1.532868 GAAAGAGACGTTGCACTGCAT 59.467 47.619 4.10 0.00 38.76 3.96
339 364 1.536943 GCTGTTCCTCGGTCCTCTGT 61.537 60.000 0.00 0.00 0.00 3.41
428 455 1.069823 GAGTCAGATGGCCATCGACAT 59.930 52.381 40.26 32.29 42.48 3.06
479 507 2.785713 TGTTTTAACCGCTTTCCTGC 57.214 45.000 0.00 0.00 0.00 4.85
480 508 4.447389 CCAAATGTTTTAACCGCTTTCCTG 59.553 41.667 0.00 0.00 0.00 3.86
513 544 1.731324 ATCCCCCGTCCAAAACCCAA 61.731 55.000 0.00 0.00 0.00 4.12
564 595 2.845317 TACGTGCACCACCCACCT 60.845 61.111 12.15 0.00 0.00 4.00
624 666 1.388065 CCTCGCTCTCTCCCGTGAAT 61.388 60.000 0.00 0.00 0.00 2.57
625 667 2.046864 CCTCGCTCTCTCCCGTGAA 61.047 63.158 0.00 0.00 0.00 3.18
626 668 2.438614 CCTCGCTCTCTCCCGTGA 60.439 66.667 0.00 0.00 0.00 4.35
627 669 3.522731 CCCTCGCTCTCTCCCGTG 61.523 72.222 0.00 0.00 0.00 4.94
628 670 2.783122 TTTCCCTCGCTCTCTCCCGT 62.783 60.000 0.00 0.00 0.00 5.28
629 671 1.605058 TTTTCCCTCGCTCTCTCCCG 61.605 60.000 0.00 0.00 0.00 5.14
630 672 0.176910 CTTTTCCCTCGCTCTCTCCC 59.823 60.000 0.00 0.00 0.00 4.30
643 685 1.620822 TTTGCTGGCTCCTCTTTTCC 58.379 50.000 0.00 0.00 0.00 3.13
711 760 1.209128 CAACGCGACTCAACTGTTCT 58.791 50.000 15.93 0.00 0.00 3.01
995 1079 2.111878 CCAGATCACCCATCCGGC 59.888 66.667 0.00 0.00 33.26 6.13
1091 1175 4.816984 GATGCTGCTGCTGCCCCT 62.817 66.667 25.44 12.39 40.48 4.79
1093 1177 4.816984 AGGATGCTGCTGCTGCCC 62.817 66.667 25.44 20.16 40.48 5.36
1094 1178 3.210528 GAGGATGCTGCTGCTGCC 61.211 66.667 25.44 16.30 40.48 4.85
1134 1221 1.101331 GTCGGTTACCTCCATCTCGT 58.899 55.000 0.00 0.00 0.00 4.18
1182 1269 2.347697 TCACAACCGTCATCGAGAAG 57.652 50.000 0.00 0.00 39.71 2.85
1332 1419 2.466867 GTGTATCACCTTGTGCCCG 58.533 57.895 0.00 0.00 32.98 6.13
1486 1573 0.708370 CGGTCGATCTCGTTGTTGTG 59.292 55.000 0.00 0.00 40.80 3.33
1585 1672 2.621147 CCCACCATCATCACAACATCCA 60.621 50.000 0.00 0.00 0.00 3.41
1588 1675 2.905415 ACCCACCATCATCACAACAT 57.095 45.000 0.00 0.00 0.00 2.71
1724 1824 1.827399 TTGAAGGTCTCCGCCTCCAC 61.827 60.000 0.00 0.00 38.03 4.02
2210 2323 5.189736 TGATCTACTACAGCTTTTCCATGGT 59.810 40.000 12.58 0.00 0.00 3.55
2284 2401 1.071385 GCGATCATGGAGGGATCAGTT 59.929 52.381 0.00 0.00 40.93 3.16
2285 2402 0.683973 GCGATCATGGAGGGATCAGT 59.316 55.000 0.00 0.00 40.93 3.41
2339 2466 7.538678 GTCACGCAAGATTCAAATCAAATTAGT 59.461 33.333 5.59 0.00 43.62 2.24
2340 2467 7.538334 TGTCACGCAAGATTCAAATCAAATTAG 59.462 33.333 5.59 0.00 43.62 1.73
2341 2468 7.366513 TGTCACGCAAGATTCAAATCAAATTA 58.633 30.769 5.59 0.00 43.62 1.40
2342 2469 6.215121 TGTCACGCAAGATTCAAATCAAATT 58.785 32.000 5.59 0.00 43.62 1.82
2344 2471 5.180367 TGTCACGCAAGATTCAAATCAAA 57.820 34.783 5.59 0.00 43.62 2.69
2399 2537 2.620863 CGTGCGCGGTAACAAAATC 58.379 52.632 12.87 0.00 0.00 2.17
2480 2618 0.109132 CCTGCTTCAACCAATTCGCC 60.109 55.000 0.00 0.00 0.00 5.54
2666 2847 2.030562 CGTGAACCTGCCCGTCTT 59.969 61.111 0.00 0.00 0.00 3.01
2690 2871 3.680620 ATGGACATGGTCACGGCCG 62.681 63.158 26.86 26.86 33.68 6.13
2691 2872 2.114670 CATGGACATGGTCACGGCC 61.115 63.158 4.39 0.00 35.24 6.13
2692 2873 2.764314 GCATGGACATGGTCACGGC 61.764 63.158 13.63 0.00 39.16 5.68
2693 2874 1.078214 AGCATGGACATGGTCACGG 60.078 57.895 10.91 0.00 45.37 4.94
2694 2875 4.623814 AGCATGGACATGGTCACG 57.376 55.556 10.91 0.00 45.37 4.35
2699 2880 1.202855 CCCCTCTAAGCATGGACATGG 60.203 57.143 13.63 0.00 39.16 3.66
2700 2881 1.202855 CCCCCTCTAAGCATGGACATG 60.203 57.143 7.91 7.91 41.60 3.21
2701 2882 1.143813 CCCCCTCTAAGCATGGACAT 58.856 55.000 0.00 0.00 0.00 3.06
2702 2883 0.044092 TCCCCCTCTAAGCATGGACA 59.956 55.000 0.00 0.00 0.00 4.02
2703 2884 0.761802 CTCCCCCTCTAAGCATGGAC 59.238 60.000 0.00 0.00 0.00 4.02
2704 2885 0.343372 ACTCCCCCTCTAAGCATGGA 59.657 55.000 0.00 0.00 0.00 3.41
2705 2886 0.471617 CACTCCCCCTCTAAGCATGG 59.528 60.000 0.00 0.00 0.00 3.66
2706 2887 0.179034 GCACTCCCCCTCTAAGCATG 60.179 60.000 0.00 0.00 0.00 4.06
2707 2888 1.348775 GGCACTCCCCCTCTAAGCAT 61.349 60.000 0.00 0.00 0.00 3.79
2708 2889 1.995626 GGCACTCCCCCTCTAAGCA 60.996 63.158 0.00 0.00 0.00 3.91
2709 2890 2.911928 GGCACTCCCCCTCTAAGC 59.088 66.667 0.00 0.00 0.00 3.09
2710 2891 3.095347 GCGGCACTCCCCCTCTAAG 62.095 68.421 0.00 0.00 0.00 2.18
2711 2892 3.081409 GCGGCACTCCCCCTCTAA 61.081 66.667 0.00 0.00 0.00 2.10
2712 2893 4.392166 TGCGGCACTCCCCCTCTA 62.392 66.667 0.00 0.00 0.00 2.43
2716 2897 3.645268 ATTTCTGCGGCACTCCCCC 62.645 63.158 0.00 0.00 0.00 5.40
2717 2898 2.044946 ATTTCTGCGGCACTCCCC 60.045 61.111 0.00 0.00 0.00 4.81
2718 2899 0.960364 TTCATTTCTGCGGCACTCCC 60.960 55.000 0.00 0.00 0.00 4.30
2719 2900 0.449388 CTTCATTTCTGCGGCACTCC 59.551 55.000 0.00 0.00 0.00 3.85
2720 2901 0.449388 CCTTCATTTCTGCGGCACTC 59.551 55.000 0.00 0.00 0.00 3.51
2721 2902 0.250901 ACCTTCATTTCTGCGGCACT 60.251 50.000 0.00 0.00 0.00 4.40
2722 2903 0.109597 CACCTTCATTTCTGCGGCAC 60.110 55.000 0.00 0.00 0.00 5.01
2723 2904 0.250684 TCACCTTCATTTCTGCGGCA 60.251 50.000 1.29 1.29 0.00 5.69
2727 2908 0.179179 GCGCTCACCTTCATTTCTGC 60.179 55.000 0.00 0.00 0.00 4.26
2732 2913 2.680913 GCACGCGCTCACCTTCATT 61.681 57.895 5.73 0.00 34.30 2.57
2803 2984 2.000447 GATAAGCGTTCCAGTGTGGTC 59.000 52.381 0.00 0.00 39.03 4.02
2811 2992 1.184431 TGTACCGGATAAGCGTTCCA 58.816 50.000 9.46 0.00 32.45 3.53
2820 3001 1.691976 CAAGGCCAGATGTACCGGATA 59.308 52.381 9.46 0.00 0.00 2.59
2831 3012 1.003355 GTAGCAGCACAAGGCCAGA 60.003 57.895 5.01 0.00 46.50 3.86
2835 3016 1.302832 ACTGGTAGCAGCACAAGGC 60.303 57.895 21.58 0.00 45.30 4.35
2843 3024 4.291047 CTGGTGCACTGGTAGCAG 57.709 61.111 20.16 20.16 46.09 4.24
2851 3032 0.469705 TTTTGGATGGCTGGTGCACT 60.470 50.000 17.98 0.00 41.91 4.40
2853 3034 0.896923 GATTTTGGATGGCTGGTGCA 59.103 50.000 0.00 0.00 41.91 4.57
2857 3038 3.899052 ACAATGATTTTGGATGGCTGG 57.101 42.857 0.00 0.00 0.00 4.85
2892 3073 6.646240 GTGCACACACCAAATTATTTCAGAAT 59.354 34.615 13.17 0.00 41.21 2.40
2901 3082 5.774498 TGTTATGTGCACACACCAAATTA 57.226 34.783 24.37 4.93 46.86 1.40
2904 3085 5.242615 ACATATGTTATGTGCACACACCAAA 59.757 36.000 24.37 8.88 46.86 3.28
2905 3086 4.764308 ACATATGTTATGTGCACACACCAA 59.236 37.500 24.37 11.12 46.86 3.67
2906 3087 4.331108 ACATATGTTATGTGCACACACCA 58.669 39.130 24.37 18.27 46.86 4.17
2907 3088 4.635765 AGACATATGTTATGTGCACACACC 59.364 41.667 24.37 12.90 46.86 4.16
2908 3089 5.801350 AGACATATGTTATGTGCACACAC 57.199 39.130 24.37 21.53 45.05 3.82
2909 3090 5.815222 GGTAGACATATGTTATGTGCACACA 59.185 40.000 24.37 16.59 46.44 3.72
2911 3092 5.983540 TGGTAGACATATGTTATGTGCACA 58.016 37.500 24.08 24.08 31.52 4.57
2915 3096 7.171508 GGTGACATGGTAGACATATGTTATGTG 59.828 40.741 10.30 7.43 37.84 3.21
2919 3100 6.609616 TCTGGTGACATGGTAGACATATGTTA 59.390 38.462 10.30 2.05 41.51 2.41
2927 3108 8.958119 TTATTATTTCTGGTGACATGGTAGAC 57.042 34.615 0.00 0.00 41.51 2.59
2930 3111 9.913310 TCAATTATTATTTCTGGTGACATGGTA 57.087 29.630 0.00 0.00 41.51 3.25
2948 3129 9.023962 TGTTTCTCCAGCTGTAATTCAATTATT 57.976 29.630 13.81 0.00 0.00 1.40
2950 3131 7.882791 TCTGTTTCTCCAGCTGTAATTCAATTA 59.117 33.333 13.81 0.00 32.32 1.40
2951 3132 6.716628 TCTGTTTCTCCAGCTGTAATTCAATT 59.283 34.615 13.81 0.00 32.32 2.32
2953 3134 5.620206 TCTGTTTCTCCAGCTGTAATTCAA 58.380 37.500 13.81 0.00 32.32 2.69
2955 3136 6.017109 TGTTTCTGTTTCTCCAGCTGTAATTC 60.017 38.462 13.81 0.00 32.32 2.17
2966 3149 6.019559 GCTGAATTTGTTGTTTCTGTTTCTCC 60.020 38.462 0.00 0.00 0.00 3.71
2972 3155 5.329035 ACTGCTGAATTTGTTGTTTCTGT 57.671 34.783 0.00 0.00 0.00 3.41
2975 3158 6.039616 TGGTAACTGCTGAATTTGTTGTTTC 58.960 36.000 0.00 0.00 37.61 2.78
2976 3159 5.971763 TGGTAACTGCTGAATTTGTTGTTT 58.028 33.333 0.00 0.00 37.61 2.83
2977 3160 5.590530 TGGTAACTGCTGAATTTGTTGTT 57.409 34.783 0.00 0.00 37.61 2.83
3068 3253 9.185680 ACCTACAACTCTAGAAACAACAAAAAT 57.814 29.630 0.00 0.00 0.00 1.82
3069 3254 8.570068 ACCTACAACTCTAGAAACAACAAAAA 57.430 30.769 0.00 0.00 0.00 1.94
3070 3255 8.044908 AGACCTACAACTCTAGAAACAACAAAA 58.955 33.333 0.00 0.00 0.00 2.44
3071 3256 7.562135 AGACCTACAACTCTAGAAACAACAAA 58.438 34.615 0.00 0.00 0.00 2.83
3074 3259 9.708092 AATTAGACCTACAACTCTAGAAACAAC 57.292 33.333 0.00 0.00 0.00 3.32
3098 3283 9.787532 CGTTTCACCAAATATTCAGATACAAAT 57.212 29.630 0.00 0.00 0.00 2.32
3112 3297 6.103997 ACGTACATCTATCGTTTCACCAAAT 58.896 36.000 0.00 0.00 34.07 2.32
3118 3303 6.197655 GCACATAACGTACATCTATCGTTTCA 59.802 38.462 7.42 0.00 43.56 2.69
3124 3309 6.929587 AATCGCACATAACGTACATCTATC 57.070 37.500 0.00 0.00 0.00 2.08
3125 3310 6.700081 ACAAATCGCACATAACGTACATCTAT 59.300 34.615 0.00 0.00 0.00 1.98
3134 3319 2.239751 TGCACAAATCGCACATAACG 57.760 45.000 0.00 0.00 33.55 3.18
3143 3328 1.067693 TGCTACGAGTGCACAAATCG 58.932 50.000 21.04 21.18 42.04 3.34
3150 3335 1.134818 CCTTATGGTGCTACGAGTGCA 60.135 52.381 0.00 0.00 38.19 4.57
3151 3336 1.134788 ACCTTATGGTGCTACGAGTGC 60.135 52.381 0.00 0.00 46.51 4.40
3152 3337 2.961526 ACCTTATGGTGCTACGAGTG 57.038 50.000 0.00 0.00 46.51 3.51


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

AutoCloner maintained by Alex Coulton.