Multiple sequence alignment - TraesCS5A01G161000

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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 TraesCS5A01G161000 chr5A 100.000 3276 0 0 1 3276 342358088 342354813 0.000000e+00 6050
1 TraesCS5A01G161000 chr5D 93.382 2886 107 39 5 2861 257696295 257693465 0.000000e+00 4194
2 TraesCS5A01G161000 chr5D 88.889 171 11 5 3107 3276 257693326 257693163 1.540000e-48 204
3 TraesCS5A01G161000 chr5B 92.512 2898 116 37 4 2862 292004126 292001291 0.000000e+00 4056


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 TraesCS5A01G161000 chr5A 342354813 342358088 3275 True 6050 6050 100.0000 1 3276 1 chr5A.!!$R1 3275
1 TraesCS5A01G161000 chr5D 257693163 257696295 3132 True 2199 4194 91.1355 5 3276 2 chr5D.!!$R1 3271
2 TraesCS5A01G161000 chr5B 292001291 292004126 2835 True 4056 4056 92.5120 4 2862 1 chr5B.!!$R1 2858

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
418 435 1.088340 CCATCACAAGCGAGCAGAGG 61.088 60.0 0.0 0.0 0.0 3.69 F
1032 1102 0.436531 CGCTCTTTGTTGACTCGCTC 59.563 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1878 1951 0.319555 GTGCACGAAGACAGCTGGTA 60.320 55.0 19.93 0.0 0.0 3.25 R
3021 3106 0.396435 TGGCAATGTCGTGTCTTCCT 59.604 50.0 0.00 0.0 0.0 3.36 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
92 93 1.194772 CCGGTGAGAAAAACGAAGAGC 59.805 52.381 0.00 0.00 0.00 4.09
145 146 5.811613 TGCCAAAAGAACAAAGATCAAAGTG 59.188 36.000 0.00 0.00 0.00 3.16
149 150 7.221452 CCAAAAGAACAAAGATCAAAGTGAGTG 59.779 37.037 0.00 0.00 0.00 3.51
161 162 3.402628 AAGTGAGTGTACGGCTCAAAT 57.597 42.857 17.79 9.70 43.57 2.32
169 170 3.991773 GTGTACGGCTCAAATACAGTGAA 59.008 43.478 0.00 0.00 29.67 3.18
175 176 4.517285 GGCTCAAATACAGTGAATGAGGA 58.483 43.478 15.57 0.53 38.32 3.71
178 190 6.096001 GGCTCAAATACAGTGAATGAGGATTT 59.904 38.462 15.57 0.00 38.32 2.17
205 218 9.729281 TTTTTACGGGAAATGAGGGTATATATC 57.271 33.333 0.00 0.00 0.00 1.63
206 219 8.674925 TTTACGGGAAATGAGGGTATATATCT 57.325 34.615 0.00 0.00 0.00 1.98
207 220 8.674925 TTACGGGAAATGAGGGTATATATCTT 57.325 34.615 0.00 0.00 0.00 2.40
208 221 7.569599 ACGGGAAATGAGGGTATATATCTTT 57.430 36.000 0.00 0.00 0.00 2.52
209 222 7.985589 ACGGGAAATGAGGGTATATATCTTTT 58.014 34.615 0.00 0.00 0.00 2.27
210 223 8.445588 ACGGGAAATGAGGGTATATATCTTTTT 58.554 33.333 0.00 0.00 0.00 1.94
361 378 2.044551 GCAGGAGGGAAAGCTGGG 60.045 66.667 0.00 0.00 0.00 4.45
418 435 1.088340 CCATCACAAGCGAGCAGAGG 61.088 60.000 0.00 0.00 0.00 3.69
419 436 1.449246 ATCACAAGCGAGCAGAGGC 60.449 57.895 0.00 0.00 41.61 4.70
420 437 2.176314 ATCACAAGCGAGCAGAGGCA 62.176 55.000 0.00 0.00 44.61 4.75
421 438 2.047465 ACAAGCGAGCAGAGGCAG 60.047 61.111 0.00 0.00 44.61 4.85
422 439 2.818714 CAAGCGAGCAGAGGCAGG 60.819 66.667 0.00 0.00 44.61 4.85
423 440 4.093291 AAGCGAGCAGAGGCAGGG 62.093 66.667 0.00 0.00 44.61 4.45
538 579 3.726486 GCGAAAACCAAAAGCAAACCAAC 60.726 43.478 0.00 0.00 0.00 3.77
543 590 2.099098 ACCAAAAGCAAACCAACTCTCG 59.901 45.455 0.00 0.00 0.00 4.04
561 608 2.778717 CCTCCCCTCCCCCAATCC 60.779 72.222 0.00 0.00 0.00 3.01
634 693 1.470458 GCAATAAAGAAGCTGCTGCCC 60.470 52.381 12.44 4.75 40.80 5.36
758 828 1.952296 CTCCTATCCCATTTGTGCTGC 59.048 52.381 0.00 0.00 0.00 5.25
866 936 4.832608 CCAACCGGCTACCTCGCC 62.833 72.222 0.00 0.00 46.68 5.54
910 980 4.882396 GCCGCTCTCCTCTTCCGC 62.882 72.222 0.00 0.00 0.00 5.54
945 1015 2.047844 CAGGACCGAGCACCACTG 60.048 66.667 0.00 0.00 0.00 3.66
946 1016 3.314331 AGGACCGAGCACCACTGG 61.314 66.667 0.00 0.00 0.00 4.00
947 1017 3.311110 GGACCGAGCACCACTGGA 61.311 66.667 0.71 0.00 0.00 3.86
948 1018 2.048127 GACCGAGCACCACTGGAC 60.048 66.667 0.71 0.00 0.00 4.02
949 1019 2.524394 ACCGAGCACCACTGGACT 60.524 61.111 0.71 0.00 0.00 3.85
950 1020 2.100879 GACCGAGCACCACTGGACTT 62.101 60.000 0.71 0.00 0.00 3.01
951 1021 1.669115 CCGAGCACCACTGGACTTG 60.669 63.158 0.71 2.88 0.00 3.16
984 1054 2.097036 TCACTGTATCTGTACCCACGG 58.903 52.381 0.00 0.00 0.00 4.94
996 1066 3.345808 CCACGGGAGCACGTTGTG 61.346 66.667 0.00 0.00 46.25 3.33
1032 1102 0.436531 CGCTCTTTGTTGACTCGCTC 59.563 55.000 0.00 0.00 0.00 5.03
1092 1162 3.474570 GAGGAGCAGTGGCCGGAT 61.475 66.667 5.05 0.00 42.56 4.18
1563 1636 2.606519 TCCTTCCTCCACCCCGTG 60.607 66.667 0.00 0.00 0.00 4.94
1674 1747 5.934625 TGCTGTCTCAAGAATAAAAGACTCC 59.065 40.000 0.00 0.00 39.09 3.85
1878 1951 2.999331 AGCGGTTGCCACATTATTACT 58.001 42.857 0.00 0.00 44.31 2.24
1879 1952 4.145365 AGCGGTTGCCACATTATTACTA 57.855 40.909 0.00 0.00 44.31 1.82
1880 1953 3.875134 AGCGGTTGCCACATTATTACTAC 59.125 43.478 0.00 0.00 44.31 2.73
2245 2318 2.189499 GGCGATGATGCTTCCACCC 61.189 63.158 0.00 0.00 34.52 4.61
2374 2447 1.144057 CGTAATGAGAAGCCGGCCT 59.856 57.895 26.15 14.98 0.00 5.19
2482 2556 1.208052 TGATGGCTCTTGGAGTAGCAC 59.792 52.381 0.00 0.00 40.61 4.40
2493 2568 1.686052 GGAGTAGCACTCTCATGGAGG 59.314 57.143 13.60 6.00 44.46 4.30
2494 2569 2.660572 GAGTAGCACTCTCATGGAGGA 58.339 52.381 13.60 1.27 45.83 3.71
2495 2570 2.622942 GAGTAGCACTCTCATGGAGGAG 59.377 54.545 13.60 11.18 45.83 3.69
2496 2571 1.686052 GTAGCACTCTCATGGAGGAGG 59.314 57.143 13.60 6.04 45.83 4.30
2497 2572 0.690411 AGCACTCTCATGGAGGAGGG 60.690 60.000 13.60 11.02 45.83 4.30
2552 2627 4.168291 CTCCGGCTTGCTCCCTCC 62.168 72.222 0.00 0.00 0.00 4.30
2716 2791 1.990799 CCTTGATTGTGTGCTGCATG 58.009 50.000 5.27 0.00 0.00 4.06
2724 2802 2.042259 TGTGCTGCATGCTACTGCC 61.042 57.895 20.33 11.58 41.58 4.85
2837 2922 8.782339 TGTAGTAGGGCAAAATAGAAAACTAC 57.218 34.615 0.00 0.00 38.04 2.73
2862 2947 7.393515 ACGAAGAATATTTTTAGAGGGTGCTTT 59.606 33.333 5.95 0.00 0.00 3.51
2863 2948 8.244113 CGAAGAATATTTTTAGAGGGTGCTTTT 58.756 33.333 0.00 0.00 0.00 2.27
2864 2949 9.929180 GAAGAATATTTTTAGAGGGTGCTTTTT 57.071 29.630 0.00 0.00 0.00 1.94
2915 3000 8.593945 TTTGAAATATTTTAGAGGGTGCTCAT 57.406 30.769 1.43 0.00 0.00 2.90
2969 3054 2.164422 GAGAAAATAGGGCTGCACAACC 59.836 50.000 4.01 0.00 0.00 3.77
2976 3061 0.825840 GGGCTGCACAACCCTACAAA 60.826 55.000 0.50 0.00 43.36 2.83
2977 3062 0.313987 GGCTGCACAACCCTACAAAC 59.686 55.000 0.50 0.00 0.00 2.93
2992 3077 6.382859 ACCCTACAAACAAGGTTCTTCAAAAT 59.617 34.615 0.00 0.00 31.70 1.82
2998 3083 5.576447 ACAAGGTTCTTCAAAATCAACGT 57.424 34.783 0.00 0.00 0.00 3.99
3006 3091 6.494893 TCTTCAAAATCAACGTATCAAGGG 57.505 37.500 0.00 0.00 0.00 3.95
3009 3094 6.494893 TCAAAATCAACGTATCAAGGGAAG 57.505 37.500 0.00 0.00 0.00 3.46
3010 3095 6.234920 TCAAAATCAACGTATCAAGGGAAGA 58.765 36.000 0.00 0.00 0.00 2.87
3011 3096 6.148811 TCAAAATCAACGTATCAAGGGAAGAC 59.851 38.462 0.00 0.00 0.00 3.01
3012 3097 4.819105 ATCAACGTATCAAGGGAAGACA 57.181 40.909 0.00 0.00 0.00 3.41
3013 3098 3.921677 TCAACGTATCAAGGGAAGACAC 58.078 45.455 0.00 0.00 0.00 3.67
3014 3099 2.649331 ACGTATCAAGGGAAGACACG 57.351 50.000 0.00 0.00 0.00 4.49
3015 3100 2.165167 ACGTATCAAGGGAAGACACGA 58.835 47.619 0.78 0.00 0.00 4.35
3016 3101 2.094854 ACGTATCAAGGGAAGACACGAC 60.095 50.000 0.78 0.00 0.00 4.34
3017 3102 2.094906 CGTATCAAGGGAAGACACGACA 60.095 50.000 0.00 0.00 0.00 4.35
3018 3103 3.428999 CGTATCAAGGGAAGACACGACAT 60.429 47.826 0.00 0.00 0.00 3.06
3019 3104 3.703001 ATCAAGGGAAGACACGACATT 57.297 42.857 0.00 0.00 0.00 2.71
3020 3105 2.766313 TCAAGGGAAGACACGACATTG 58.234 47.619 0.00 0.00 0.00 2.82
3021 3106 2.367241 TCAAGGGAAGACACGACATTGA 59.633 45.455 0.00 0.00 0.00 2.57
3022 3107 2.738846 CAAGGGAAGACACGACATTGAG 59.261 50.000 0.00 0.00 0.00 3.02
3023 3108 1.276421 AGGGAAGACACGACATTGAGG 59.724 52.381 0.00 0.00 0.00 3.86
3024 3109 1.275291 GGGAAGACACGACATTGAGGA 59.725 52.381 0.00 0.00 0.00 3.71
3025 3110 2.289444 GGGAAGACACGACATTGAGGAA 60.289 50.000 0.00 0.00 0.00 3.36
3026 3111 2.996621 GGAAGACACGACATTGAGGAAG 59.003 50.000 0.00 0.00 0.00 3.46
3027 3112 3.306088 GGAAGACACGACATTGAGGAAGA 60.306 47.826 0.00 0.00 0.00 2.87
3028 3113 3.305398 AGACACGACATTGAGGAAGAC 57.695 47.619 0.00 0.00 0.00 3.01
3029 3114 2.628178 AGACACGACATTGAGGAAGACA 59.372 45.455 0.00 0.00 0.00 3.41
3030 3115 2.731976 GACACGACATTGAGGAAGACAC 59.268 50.000 0.00 0.00 0.00 3.67
3031 3116 1.721389 CACGACATTGAGGAAGACACG 59.279 52.381 0.00 0.00 0.00 4.49
3032 3117 1.611977 ACGACATTGAGGAAGACACGA 59.388 47.619 0.00 0.00 0.00 4.35
3055 3140 4.106179 ACATTGCCATATCTTCACCCCATA 59.894 41.667 0.00 0.00 0.00 2.74
3061 3146 4.226846 CCATATCTTCACCCCATAGAGCAT 59.773 45.833 0.00 0.00 0.00 3.79
3064 3149 3.653164 TCTTCACCCCATAGAGCATGTA 58.347 45.455 0.00 0.00 32.21 2.29
3066 3151 4.660303 TCTTCACCCCATAGAGCATGTATT 59.340 41.667 0.00 0.00 32.21 1.89
3075 3160 6.148480 CCCATAGAGCATGTATTAGCAAACTC 59.852 42.308 0.00 0.00 32.21 3.01
3076 3161 6.148480 CCATAGAGCATGTATTAGCAAACTCC 59.852 42.308 0.00 0.00 32.21 3.85
3077 3162 5.102953 AGAGCATGTATTAGCAAACTCCA 57.897 39.130 0.00 0.00 0.00 3.86
3078 3163 5.500234 AGAGCATGTATTAGCAAACTCCAA 58.500 37.500 0.00 0.00 0.00 3.53
3079 3164 5.945784 AGAGCATGTATTAGCAAACTCCAAA 59.054 36.000 0.00 0.00 0.00 3.28
3080 3165 6.434028 AGAGCATGTATTAGCAAACTCCAAAA 59.566 34.615 0.00 0.00 0.00 2.44
3081 3166 6.389906 AGCATGTATTAGCAAACTCCAAAAC 58.610 36.000 0.00 0.00 0.00 2.43
3082 3167 5.286082 GCATGTATTAGCAAACTCCAAAACG 59.714 40.000 0.00 0.00 0.00 3.60
3083 3168 6.607689 CATGTATTAGCAAACTCCAAAACGA 58.392 36.000 0.00 0.00 0.00 3.85
3084 3169 5.992729 TGTATTAGCAAACTCCAAAACGAC 58.007 37.500 0.00 0.00 0.00 4.34
3085 3170 3.595709 TTAGCAAACTCCAAAACGACG 57.404 42.857 0.00 0.00 0.00 5.12
3086 3171 1.658994 AGCAAACTCCAAAACGACGA 58.341 45.000 0.00 0.00 0.00 4.20
3087 3172 2.218603 AGCAAACTCCAAAACGACGAT 58.781 42.857 0.00 0.00 0.00 3.73
3088 3173 3.395639 AGCAAACTCCAAAACGACGATA 58.604 40.909 0.00 0.00 0.00 2.92
3089 3174 4.000988 AGCAAACTCCAAAACGACGATAT 58.999 39.130 0.00 0.00 0.00 1.63
3090 3175 4.454504 AGCAAACTCCAAAACGACGATATT 59.545 37.500 0.00 0.00 0.00 1.28
3091 3176 4.553429 GCAAACTCCAAAACGACGATATTG 59.447 41.667 0.00 3.54 0.00 1.90
3092 3177 4.336532 AACTCCAAAACGACGATATTGC 57.663 40.909 0.00 0.00 0.00 3.56
3093 3178 2.676342 ACTCCAAAACGACGATATTGCC 59.324 45.455 0.00 0.00 0.00 4.52
3094 3179 2.675844 CTCCAAAACGACGATATTGCCA 59.324 45.455 0.00 0.00 0.00 4.92
3095 3180 3.275143 TCCAAAACGACGATATTGCCAT 58.725 40.909 0.00 0.00 0.00 4.40
3096 3181 4.443621 TCCAAAACGACGATATTGCCATA 58.556 39.130 0.00 0.00 0.00 2.74
3097 3182 5.060506 TCCAAAACGACGATATTGCCATAT 58.939 37.500 0.00 0.00 0.00 1.78
3098 3183 5.178623 TCCAAAACGACGATATTGCCATATC 59.821 40.000 0.00 7.57 38.57 1.63
3099 3184 5.179368 CCAAAACGACGATATTGCCATATCT 59.821 40.000 14.08 3.70 39.46 1.98
3100 3185 6.293407 CCAAAACGACGATATTGCCATATCTT 60.293 38.462 14.08 6.40 39.46 2.40
3101 3186 6.861065 AAACGACGATATTGCCATATCTTT 57.139 33.333 14.08 6.58 39.46 2.52
3102 3187 6.467723 AACGACGATATTGCCATATCTTTC 57.532 37.500 14.08 9.85 39.46 2.62
3103 3188 5.538118 ACGACGATATTGCCATATCTTTCA 58.462 37.500 14.08 0.00 39.46 2.69
3104 3189 5.405571 ACGACGATATTGCCATATCTTTCAC 59.594 40.000 14.08 2.96 39.46 3.18
3105 3190 5.163953 CGACGATATTGCCATATCTTTCACC 60.164 44.000 14.08 0.00 39.46 4.02
3123 3208 4.026744 TCACCCCAAAACAATGTCTTCAA 58.973 39.130 0.00 0.00 0.00 2.69
3137 3222 0.657368 CTTCAACAAAGACGCCGTGC 60.657 55.000 0.00 0.00 37.12 5.34
3152 3237 0.387112 CGTGCGTAAACACCGTCCTA 60.387 55.000 0.00 0.00 37.25 2.94
3158 3243 2.352030 CGTAAACACCGTCCTAGCAAGA 60.352 50.000 0.00 0.00 0.00 3.02
3185 3270 2.368439 CATCAAATGTCGGACCATGGT 58.632 47.619 19.89 19.89 0.00 3.55
3194 3279 0.601057 CGGACCATGGTTTTTCACCC 59.399 55.000 20.85 12.60 46.68 4.61
3195 3280 1.821666 CGGACCATGGTTTTTCACCCT 60.822 52.381 20.85 0.00 46.68 4.34
3196 3281 2.325484 GGACCATGGTTTTTCACCCTT 58.675 47.619 20.85 0.00 46.68 3.95
3197 3282 2.037121 GGACCATGGTTTTTCACCCTTG 59.963 50.000 20.85 0.00 46.68 3.61
3203 3288 2.685897 TGGTTTTTCACCCTTGAGTTCG 59.314 45.455 0.00 0.00 46.68 3.95
3211 3296 1.003718 CCTTGAGTTCGACACCCCC 60.004 63.158 0.00 0.00 0.00 5.40
3257 3342 1.912763 TTGGCATGGAGGGGCAAAC 60.913 57.895 0.00 0.00 46.14 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.662686 CCCTCCTCCCAATCCTATCC 58.337 60.000 0.00 0.00 0.00 2.59
1 2 0.988063 GCCCTCCTCCCAATCCTATC 59.012 60.000 0.00 0.00 0.00 2.08
2 3 0.838122 CGCCCTCCTCCCAATCCTAT 60.838 60.000 0.00 0.00 0.00 2.57
9 10 2.465725 TTTTTACGCCCTCCTCCCA 58.534 52.632 0.00 0.00 0.00 4.37
28 29 4.065789 GGAGTCCTTCACAAATTTCTCGT 58.934 43.478 0.41 0.00 0.00 4.18
42 43 1.831652 CGCACCTCCAAGGAGTCCTT 61.832 60.000 19.27 19.27 45.88 3.36
43 44 2.286523 CGCACCTCCAAGGAGTCCT 61.287 63.158 5.62 5.62 37.67 3.85
92 93 0.754217 TTCCCGTCTACCCTCCATCG 60.754 60.000 0.00 0.00 0.00 3.84
124 125 7.756722 ACACTCACTTTGATCTTTGTTCTTTTG 59.243 33.333 0.00 0.00 0.00 2.44
131 132 4.750098 CCGTACACTCACTTTGATCTTTGT 59.250 41.667 0.00 0.00 0.00 2.83
145 146 3.612860 CACTGTATTTGAGCCGTACACTC 59.387 47.826 6.05 6.05 34.62 3.51
149 150 4.868171 TCATTCACTGTATTTGAGCCGTAC 59.132 41.667 0.00 0.00 0.00 3.67
184 197 7.569599 AAAGATATATACCCTCATTTCCCGT 57.430 36.000 0.00 0.00 0.00 5.28
208 221 7.284074 TCTCCAAAGATATATACCCGCAAAAA 58.716 34.615 0.00 0.00 0.00 1.94
209 222 6.833041 TCTCCAAAGATATATACCCGCAAAA 58.167 36.000 0.00 0.00 0.00 2.44
210 223 6.428083 TCTCCAAAGATATATACCCGCAAA 57.572 37.500 0.00 0.00 0.00 3.68
211 224 5.568825 GCTCTCCAAAGATATATACCCGCAA 60.569 44.000 0.00 0.00 0.00 4.85
212 225 4.081642 GCTCTCCAAAGATATATACCCGCA 60.082 45.833 0.00 0.00 0.00 5.69
213 226 4.081642 TGCTCTCCAAAGATATATACCCGC 60.082 45.833 0.00 0.00 0.00 6.13
214 227 5.661056 TGCTCTCCAAAGATATATACCCG 57.339 43.478 0.00 0.00 0.00 5.28
215 228 6.951971 ACATGCTCTCCAAAGATATATACCC 58.048 40.000 0.00 0.00 0.00 3.69
216 229 7.615403 TGACATGCTCTCCAAAGATATATACC 58.385 38.462 0.00 0.00 0.00 2.73
217 230 9.096160 CATGACATGCTCTCCAAAGATATATAC 57.904 37.037 1.71 0.00 0.00 1.47
296 313 2.872858 GGCATATTCTCCGTGAAAGGAC 59.127 50.000 0.00 0.00 38.29 3.85
377 394 3.378399 GACCTTGCCTCCTCGCTCC 62.378 68.421 0.00 0.00 0.00 4.70
378 395 2.185608 GACCTTGCCTCCTCGCTC 59.814 66.667 0.00 0.00 0.00 5.03
418 435 0.877743 GCTGTCTTTTCTCACCCTGC 59.122 55.000 0.00 0.00 0.00 4.85
419 436 1.876156 GTGCTGTCTTTTCTCACCCTG 59.124 52.381 0.00 0.00 0.00 4.45
420 437 1.771255 AGTGCTGTCTTTTCTCACCCT 59.229 47.619 0.00 0.00 0.00 4.34
421 438 1.876156 CAGTGCTGTCTTTTCTCACCC 59.124 52.381 0.00 0.00 0.00 4.61
422 439 1.265365 GCAGTGCTGTCTTTTCTCACC 59.735 52.381 8.18 0.00 0.00 4.02
423 440 2.216898 AGCAGTGCTGTCTTTTCTCAC 58.783 47.619 18.98 0.00 37.57 3.51
424 441 2.487934 GAGCAGTGCTGTCTTTTCTCA 58.512 47.619 25.35 0.00 39.88 3.27
425 442 1.458827 CGAGCAGTGCTGTCTTTTCTC 59.541 52.381 25.35 3.55 39.88 2.87
466 489 1.691823 GGGTTCCCCAGGAAGGAAG 59.308 63.158 0.00 0.00 43.99 3.46
467 490 3.931707 GGGTTCCCCAGGAAGGAA 58.068 61.111 0.00 0.00 42.88 3.36
543 590 3.502875 GATTGGGGGAGGGGAGGC 61.503 72.222 0.00 0.00 0.00 4.70
561 608 3.465403 CGGGCAGAGGGAGACAGG 61.465 72.222 0.00 0.00 0.00 4.00
607 666 0.455815 GCTTCTTTATTGCGGGGGTG 59.544 55.000 0.00 0.00 0.00 4.61
675 735 1.522900 AGAGAGAGAGAGAGGGGGAG 58.477 60.000 0.00 0.00 0.00 4.30
676 736 1.850345 GAAGAGAGAGAGAGAGGGGGA 59.150 57.143 0.00 0.00 0.00 4.81
677 737 1.476833 CGAAGAGAGAGAGAGAGGGGG 60.477 61.905 0.00 0.00 0.00 5.40
678 738 1.211949 ACGAAGAGAGAGAGAGAGGGG 59.788 57.143 0.00 0.00 0.00 4.79
679 739 2.170607 AGACGAAGAGAGAGAGAGAGGG 59.829 54.545 0.00 0.00 0.00 4.30
680 740 3.543680 AGACGAAGAGAGAGAGAGAGG 57.456 52.381 0.00 0.00 0.00 3.69
681 741 3.871594 GGAAGACGAAGAGAGAGAGAGAG 59.128 52.174 0.00 0.00 0.00 3.20
825 895 4.760047 CTGCGGCTACGGCTGGTT 62.760 66.667 0.00 0.00 44.48 3.67
935 1005 2.919971 GACAAGTCCAGTGGTGCTC 58.080 57.895 9.54 0.00 0.00 4.26
946 1016 0.389037 GACGTAACGGGGGACAAGTC 60.389 60.000 0.00 0.00 0.00 3.01
947 1017 1.114722 TGACGTAACGGGGGACAAGT 61.115 55.000 0.00 0.00 0.00 3.16
948 1018 0.668401 GTGACGTAACGGGGGACAAG 60.668 60.000 0.00 0.00 0.00 3.16
949 1019 1.114722 AGTGACGTAACGGGGGACAA 61.115 55.000 0.00 0.00 0.00 3.18
950 1020 1.531365 AGTGACGTAACGGGGGACA 60.531 57.895 0.00 0.00 0.00 4.02
951 1021 1.080298 CAGTGACGTAACGGGGGAC 60.080 63.158 0.00 0.00 0.00 4.46
984 1054 2.672996 ATGGCCACAACGTGCTCC 60.673 61.111 8.16 0.00 31.34 4.70
1032 1102 2.759973 TGCTCCTCCGGGCAGTAG 60.760 66.667 0.00 0.00 34.22 2.57
1101 1171 2.029844 GTCGTCAAGAGCCACCAGC 61.030 63.158 0.00 0.00 44.25 4.85
1386 1459 2.050350 CCGCGTCTCCTCCACCTTA 61.050 63.158 4.92 0.00 0.00 2.69
1542 1615 0.983378 CGGGGTGGAGGAAGGAGAAT 60.983 60.000 0.00 0.00 0.00 2.40
1717 1790 3.390521 TACCGTGGCCAGCTCCAG 61.391 66.667 5.11 0.00 36.67 3.86
1878 1951 0.319555 GTGCACGAAGACAGCTGGTA 60.320 55.000 19.93 0.00 0.00 3.25
1879 1952 1.595382 GTGCACGAAGACAGCTGGT 60.595 57.895 19.93 2.28 0.00 4.00
1880 1953 1.595109 TGTGCACGAAGACAGCTGG 60.595 57.895 19.93 1.54 0.00 4.85
1999 2072 2.516930 CCGCCGAAGCCCATGAAT 60.517 61.111 0.00 0.00 34.57 2.57
2155 2228 3.775654 GAGACTGACCCCGGCCAG 61.776 72.222 2.24 13.09 36.53 4.85
2393 2466 1.058979 GCCGCATTGCAAAATTACACG 59.941 47.619 1.71 0.00 0.00 4.49
2446 2520 3.418995 CCATCAATGGCTAATCTCCCTG 58.581 50.000 0.00 0.00 41.75 4.45
2482 2556 0.471591 CCTCCCCTCCTCCATGAGAG 60.472 65.000 0.00 0.00 42.83 3.20
2493 2568 0.691413 CCTACCTTGTCCCTCCCCTC 60.691 65.000 0.00 0.00 0.00 4.30
2494 2569 1.396594 CCTACCTTGTCCCTCCCCT 59.603 63.158 0.00 0.00 0.00 4.79
2495 2570 2.376165 GCCTACCTTGTCCCTCCCC 61.376 68.421 0.00 0.00 0.00 4.81
2496 2571 2.732619 CGCCTACCTTGTCCCTCCC 61.733 68.421 0.00 0.00 0.00 4.30
2497 2572 2.732619 CCGCCTACCTTGTCCCTCC 61.733 68.421 0.00 0.00 0.00 4.30
2552 2627 2.971428 ATTCATGGCGCCGTCGTAGG 62.971 60.000 20.90 7.47 38.14 3.18
2724 2802 6.400568 ACATTCCATCAGTTTTAATGCCAAG 58.599 36.000 0.00 0.00 32.10 3.61
2817 2897 7.388437 TCTTCGTAGTTTTCTATTTTGCCCTA 58.612 34.615 0.00 0.00 34.69 3.53
2818 2898 6.235664 TCTTCGTAGTTTTCTATTTTGCCCT 58.764 36.000 0.00 0.00 34.69 5.19
2819 2899 6.490566 TCTTCGTAGTTTTCTATTTTGCCC 57.509 37.500 0.00 0.00 34.69 5.36
2837 2922 6.927294 AGCACCCTCTAAAAATATTCTTCG 57.073 37.500 0.00 0.00 0.00 3.79
2888 2973 8.865090 TGAGCACCCTCTAAAATATTTCAAAAA 58.135 29.630 0.10 0.00 38.93 1.94
2889 2974 8.415950 TGAGCACCCTCTAAAATATTTCAAAA 57.584 30.769 0.10 0.00 38.93 2.44
2890 2975 8.593945 ATGAGCACCCTCTAAAATATTTCAAA 57.406 30.769 0.10 0.00 38.93 2.69
2891 2976 9.866655 ATATGAGCACCCTCTAAAATATTTCAA 57.133 29.630 0.10 0.00 38.93 2.69
2892 2977 9.866655 AATATGAGCACCCTCTAAAATATTTCA 57.133 29.630 0.10 0.00 38.93 2.69
2894 2979 9.866655 TCAATATGAGCACCCTCTAAAATATTT 57.133 29.630 0.00 0.00 38.93 1.40
2895 2980 9.866655 TTCAATATGAGCACCCTCTAAAATATT 57.133 29.630 0.00 0.00 38.93 1.28
2896 2981 9.866655 TTTCAATATGAGCACCCTCTAAAATAT 57.133 29.630 0.00 0.00 38.93 1.28
2897 2982 9.342308 CTTTCAATATGAGCACCCTCTAAAATA 57.658 33.333 0.00 0.00 38.93 1.40
2898 2983 8.055181 TCTTTCAATATGAGCACCCTCTAAAAT 58.945 33.333 0.00 0.00 38.93 1.82
2939 3024 2.354805 GCCCTATTTTCTCGTCTGTGGT 60.355 50.000 0.00 0.00 0.00 4.16
2942 3027 2.678190 GCAGCCCTATTTTCTCGTCTGT 60.678 50.000 0.00 0.00 0.00 3.41
2969 3054 7.488322 TGATTTTGAAGAACCTTGTTTGTAGG 58.512 34.615 0.00 0.00 38.79 3.18
2976 3061 5.576447 ACGTTGATTTTGAAGAACCTTGT 57.424 34.783 0.00 0.00 0.00 3.16
2977 3062 7.359595 TGATACGTTGATTTTGAAGAACCTTG 58.640 34.615 0.00 0.00 0.00 3.61
2992 3077 3.613193 CGTGTCTTCCCTTGATACGTTGA 60.613 47.826 0.00 0.00 41.69 3.18
2998 3083 4.221924 TCAATGTCGTGTCTTCCCTTGATA 59.778 41.667 0.00 0.00 0.00 2.15
3006 3091 3.675698 GTCTTCCTCAATGTCGTGTCTTC 59.324 47.826 0.00 0.00 0.00 2.87
3009 3094 2.731976 GTGTCTTCCTCAATGTCGTGTC 59.268 50.000 0.00 0.00 0.00 3.67
3010 3095 2.755650 GTGTCTTCCTCAATGTCGTGT 58.244 47.619 0.00 0.00 0.00 4.49
3011 3096 1.721389 CGTGTCTTCCTCAATGTCGTG 59.279 52.381 0.00 0.00 0.00 4.35
3012 3097 1.611977 TCGTGTCTTCCTCAATGTCGT 59.388 47.619 0.00 0.00 0.00 4.34
3013 3098 1.986378 GTCGTGTCTTCCTCAATGTCG 59.014 52.381 0.00 0.00 0.00 4.35
3014 3099 3.026630 TGTCGTGTCTTCCTCAATGTC 57.973 47.619 0.00 0.00 0.00 3.06
3015 3100 3.685139 ATGTCGTGTCTTCCTCAATGT 57.315 42.857 0.00 0.00 0.00 2.71
3016 3101 3.425359 GCAATGTCGTGTCTTCCTCAATG 60.425 47.826 0.00 0.00 0.00 2.82
3017 3102 2.744202 GCAATGTCGTGTCTTCCTCAAT 59.256 45.455 0.00 0.00 0.00 2.57
3018 3103 2.143122 GCAATGTCGTGTCTTCCTCAA 58.857 47.619 0.00 0.00 0.00 3.02
3019 3104 1.608025 GGCAATGTCGTGTCTTCCTCA 60.608 52.381 0.00 0.00 0.00 3.86
3020 3105 1.079503 GGCAATGTCGTGTCTTCCTC 58.920 55.000 0.00 0.00 0.00 3.71
3021 3106 0.396435 TGGCAATGTCGTGTCTTCCT 59.604 50.000 0.00 0.00 0.00 3.36
3022 3107 1.453155 ATGGCAATGTCGTGTCTTCC 58.547 50.000 0.00 0.00 0.00 3.46
3023 3108 4.122776 AGATATGGCAATGTCGTGTCTTC 58.877 43.478 0.31 0.00 0.00 2.87
3024 3109 4.142609 AGATATGGCAATGTCGTGTCTT 57.857 40.909 0.31 0.00 0.00 3.01
3025 3110 3.827008 AGATATGGCAATGTCGTGTCT 57.173 42.857 0.31 0.31 0.00 3.41
3026 3111 3.871006 TGAAGATATGGCAATGTCGTGTC 59.129 43.478 0.00 0.00 0.00 3.67
3027 3112 3.623060 GTGAAGATATGGCAATGTCGTGT 59.377 43.478 0.00 0.00 0.00 4.49
3028 3113 3.002656 GGTGAAGATATGGCAATGTCGTG 59.997 47.826 0.00 0.00 0.00 4.35
3029 3114 3.206150 GGTGAAGATATGGCAATGTCGT 58.794 45.455 0.00 0.00 0.00 4.34
3030 3115 2.549754 GGGTGAAGATATGGCAATGTCG 59.450 50.000 0.00 0.00 0.00 4.35
3031 3116 2.887152 GGGGTGAAGATATGGCAATGTC 59.113 50.000 0.00 0.00 0.00 3.06
3032 3117 2.244510 TGGGGTGAAGATATGGCAATGT 59.755 45.455 0.00 0.00 0.00 2.71
3055 3140 5.102953 TGGAGTTTGCTAATACATGCTCT 57.897 39.130 0.00 0.00 0.00 4.09
3061 3146 5.333492 CGTCGTTTTGGAGTTTGCTAATACA 60.333 40.000 0.00 0.00 0.00 2.29
3064 3149 3.810941 TCGTCGTTTTGGAGTTTGCTAAT 59.189 39.130 0.00 0.00 0.00 1.73
3066 3151 2.823984 TCGTCGTTTTGGAGTTTGCTA 58.176 42.857 0.00 0.00 0.00 3.49
3075 3160 3.691049 ATGGCAATATCGTCGTTTTGG 57.309 42.857 0.00 0.00 0.00 3.28
3076 3161 6.228273 AGATATGGCAATATCGTCGTTTTG 57.772 37.500 14.26 0.00 46.40 2.44
3077 3162 6.861065 AAGATATGGCAATATCGTCGTTTT 57.139 33.333 14.26 1.18 46.40 2.43
3078 3163 6.481976 TGAAAGATATGGCAATATCGTCGTTT 59.518 34.615 14.26 9.78 46.40 3.60
3079 3164 5.989168 TGAAAGATATGGCAATATCGTCGTT 59.011 36.000 14.26 8.27 46.40 3.85
3080 3165 5.405571 GTGAAAGATATGGCAATATCGTCGT 59.594 40.000 14.26 0.00 46.40 4.34
3081 3166 5.163953 GGTGAAAGATATGGCAATATCGTCG 60.164 44.000 14.26 0.00 46.40 5.12
3082 3167 5.122396 GGGTGAAAGATATGGCAATATCGTC 59.878 44.000 14.26 15.11 46.40 4.20
3083 3168 5.003804 GGGTGAAAGATATGGCAATATCGT 58.996 41.667 14.26 9.29 46.40 3.73
3084 3169 4.396166 GGGGTGAAAGATATGGCAATATCG 59.604 45.833 14.26 0.00 46.40 2.92
3085 3170 5.324409 TGGGGTGAAAGATATGGCAATATC 58.676 41.667 12.58 12.58 43.49 1.63
3086 3171 5.337956 TGGGGTGAAAGATATGGCAATAT 57.662 39.130 0.00 0.00 0.00 1.28
3087 3172 4.805140 TGGGGTGAAAGATATGGCAATA 57.195 40.909 0.00 0.00 0.00 1.90
3088 3173 3.686227 TGGGGTGAAAGATATGGCAAT 57.314 42.857 0.00 0.00 0.00 3.56
3089 3174 3.464720 TTGGGGTGAAAGATATGGCAA 57.535 42.857 0.00 0.00 0.00 4.52
3090 3175 3.464720 TTTGGGGTGAAAGATATGGCA 57.535 42.857 0.00 0.00 0.00 4.92
3091 3176 3.513515 TGTTTTGGGGTGAAAGATATGGC 59.486 43.478 0.00 0.00 0.00 4.40
3092 3177 5.736951 TTGTTTTGGGGTGAAAGATATGG 57.263 39.130 0.00 0.00 0.00 2.74
3093 3178 6.700352 ACATTGTTTTGGGGTGAAAGATATG 58.300 36.000 0.00 0.00 0.00 1.78
3094 3179 6.725834 AGACATTGTTTTGGGGTGAAAGATAT 59.274 34.615 0.00 0.00 0.00 1.63
3095 3180 6.074648 AGACATTGTTTTGGGGTGAAAGATA 58.925 36.000 0.00 0.00 0.00 1.98
3096 3181 4.901250 AGACATTGTTTTGGGGTGAAAGAT 59.099 37.500 0.00 0.00 0.00 2.40
3097 3182 4.285863 AGACATTGTTTTGGGGTGAAAGA 58.714 39.130 0.00 0.00 0.00 2.52
3098 3183 4.670896 AGACATTGTTTTGGGGTGAAAG 57.329 40.909 0.00 0.00 0.00 2.62
3099 3184 4.467795 TGAAGACATTGTTTTGGGGTGAAA 59.532 37.500 0.00 0.00 0.00 2.69
3100 3185 4.026744 TGAAGACATTGTTTTGGGGTGAA 58.973 39.130 0.00 0.00 0.00 3.18
3101 3186 3.636679 TGAAGACATTGTTTTGGGGTGA 58.363 40.909 0.00 0.00 0.00 4.02
3102 3187 4.119136 GTTGAAGACATTGTTTTGGGGTG 58.881 43.478 0.00 0.00 0.00 4.61
3103 3188 3.772025 TGTTGAAGACATTGTTTTGGGGT 59.228 39.130 0.00 0.00 32.00 4.95
3104 3189 4.399004 TGTTGAAGACATTGTTTTGGGG 57.601 40.909 0.00 0.00 32.00 4.96
3105 3190 6.105333 TCTTTGTTGAAGACATTGTTTTGGG 58.895 36.000 0.00 0.00 39.44 4.12
3131 3216 3.285776 GACGGTGTTTACGCACGGC 62.286 63.158 0.00 3.05 41.47 5.68
3134 3219 1.343506 CTAGGACGGTGTTTACGCAC 58.656 55.000 0.00 0.00 38.56 5.34
3137 3222 1.990563 CTTGCTAGGACGGTGTTTACG 59.009 52.381 0.00 0.00 37.36 3.18
3152 3237 1.825090 TTTGATGGTCGCATCTTGCT 58.175 45.000 0.00 0.00 42.25 3.91
3169 3254 3.639094 TGAAAAACCATGGTCCGACATTT 59.361 39.130 20.07 11.04 0.00 2.32
3185 3270 3.375922 GTGTCGAACTCAAGGGTGAAAAA 59.624 43.478 0.00 0.00 31.88 1.94
3194 3279 4.695560 GGGGGTGTCGAACTCAAG 57.304 61.111 0.00 0.00 0.00 3.02
3211 3296 0.400213 TTGGCTTGGTGGTACTCAGG 59.600 55.000 0.00 0.00 0.00 3.86
3212 3297 2.154462 CTTTGGCTTGGTGGTACTCAG 58.846 52.381 0.00 0.00 0.00 3.35
3213 3298 1.493022 ACTTTGGCTTGGTGGTACTCA 59.507 47.619 0.00 0.00 0.00 3.41
3214 3299 2.271944 ACTTTGGCTTGGTGGTACTC 57.728 50.000 0.00 0.00 0.00 2.59
3215 3300 2.748209 AACTTTGGCTTGGTGGTACT 57.252 45.000 0.00 0.00 0.00 2.73
3216 3301 4.332828 AGATAACTTTGGCTTGGTGGTAC 58.667 43.478 0.00 0.00 0.00 3.34


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

AutoCloner maintained by Alex Coulton.