Multiple sequence alignment - TraesCS2D01G311800

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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 TraesCS2D01G311800 chr2D 100.000 3242 0 0 1 3242 401115423 401112182 0.000000e+00 5987.0
1 TraesCS2D01G311800 chr2B 94.693 3147 117 28 1 3104 475128959 475125820 0.000000e+00 4841.0
2 TraesCS2D01G311800 chr2A 94.371 3162 130 23 1 3127 537684962 537681814 0.000000e+00 4809.0
3 TraesCS2D01G311800 chr4D 78.082 146 26 5 349 489 260716163 260716307 1.600000e-13 87.9
4 TraesCS2D01G311800 chrUn 89.474 57 6 0 144 200 32053808 32053752 4.490000e-09 73.1
5 TraesCS2D01G311800 chr6A 87.755 49 6 0 152 200 489363965 489364013 1.260000e-04 58.4
6 TraesCS2D01G311800 chr1B 92.500 40 2 1 169 207 652281905 652281944 4.520000e-04 56.5


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 TraesCS2D01G311800 chr2D 401112182 401115423 3241 True 5987 5987 100.000 1 3242 1 chr2D.!!$R1 3241
1 TraesCS2D01G311800 chr2B 475125820 475128959 3139 True 4841 4841 94.693 1 3104 1 chr2B.!!$R1 3103
2 TraesCS2D01G311800 chr2A 537681814 537684962 3148 True 4809 4809 94.371 1 3127 1 chr2A.!!$R1 3126

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
695 719 0.902531 GACTCCGAGGAACAATGGGA 59.097 55.0 0.00 0.0 0.0 4.37 F
1890 1926 0.814010 AACGCGTGCAGTTCTTCCTT 60.814 50.0 14.98 0.0 0.0 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2183 0.815213 TGCAGAGTCGGCCATATTGC 60.815 55.0 12.91 6.42 0.00 3.56 R
3128 3181 0.320946 TTGTTGGGTAGCACCGTAGC 60.321 55.0 0.00 0.00 39.83 3.58 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
19 20 1.247567 AGACAAACATTTGAGGGGCG 58.752 50.000 11.24 0.00 40.55 6.13
87 88 7.443879 TGATCACTCTAGTTGTAGATGCTCTAG 59.556 40.741 0.00 0.00 34.63 2.43
95 96 2.954989 TGTAGATGCTCTAGGACTGCTG 59.045 50.000 0.00 0.00 28.01 4.41
115 116 3.792401 TGGCAGTAGGAAATGTCGTATG 58.208 45.455 0.00 0.00 0.00 2.39
244 245 7.895759 TCTTCTCTTTTCCCATTAAATTGTGG 58.104 34.615 0.00 0.00 35.22 4.17
329 332 7.276658 TCCTATTTCTGTAACAAAGTGTGTGA 58.723 34.615 0.00 0.00 40.60 3.58
415 419 9.050601 CATAATCACTAAAGGATGAAGGACTTC 57.949 37.037 5.14 5.14 39.91 3.01
475 479 7.707774 TGCAATGATTTAATGCATCTCAATG 57.292 32.000 0.00 6.01 44.52 2.82
494 498 9.494271 TCTCAATGTCTAAACATATGATAAGGC 57.506 33.333 10.38 5.27 45.48 4.35
513 517 9.813080 GATAAGGCGCAATAAAAATAAGACTAG 57.187 33.333 10.83 0.00 0.00 2.57
600 621 1.194896 GAGAATTCGTCGTCGCCTCG 61.195 60.000 0.00 0.00 36.96 4.63
695 719 0.902531 GACTCCGAGGAACAATGGGA 59.097 55.000 0.00 0.00 0.00 4.37
831 855 4.891037 GCCAGCCAGAGCCCATCC 62.891 72.222 0.00 0.00 41.25 3.51
832 856 4.559063 CCAGCCAGAGCCCATCCG 62.559 72.222 0.00 0.00 41.25 4.18
1470 1506 4.838486 CTCGACGTGCTCCTCGCC 62.838 72.222 0.00 0.00 38.05 5.54
1890 1926 0.814010 AACGCGTGCAGTTCTTCCTT 60.814 50.000 14.98 0.00 0.00 3.36
2004 2040 1.145945 TCATCTAGGAGGATGGCGTCT 59.854 52.381 6.67 0.00 42.22 4.18
2147 2183 4.240888 CCGCATTATCAGTACCATGAGAG 58.759 47.826 0.00 0.00 31.44 3.20
2240 2276 3.672808 ACAATGAAGAAGAGAGCCAGTG 58.327 45.455 0.00 0.00 0.00 3.66
2245 2281 3.056250 TGAAGAAGAGAGCCAGTGATGAC 60.056 47.826 0.00 0.00 0.00 3.06
2259 2295 5.934043 CCAGTGATGACAGACTGAATAACAA 59.066 40.000 10.08 0.00 41.90 2.83
2261 2297 5.641209 AGTGATGACAGACTGAATAACAAGC 59.359 40.000 10.08 0.37 0.00 4.01
2288 2324 5.070847 AGGCATTGGTGATTCAAAGAGTTTT 59.929 36.000 0.00 0.00 0.00 2.43
2588 2624 1.312815 GTTCTTTGCCAGACTGTGCT 58.687 50.000 14.46 0.00 0.00 4.40
2649 2685 8.443953 AAAAGTAGTCTTATCATCATCTTGCC 57.556 34.615 0.00 0.00 33.09 4.52
2650 2686 6.992664 AGTAGTCTTATCATCATCTTGCCT 57.007 37.500 0.00 0.00 0.00 4.75
2654 2690 7.129457 AGTCTTATCATCATCTTGCCTTGTA 57.871 36.000 0.00 0.00 0.00 2.41
2686 2722 2.015736 ATCTGCAGAACTAACTGGCG 57.984 50.000 22.50 0.00 38.22 5.69
2708 2744 4.679197 CGTGACCCATGTTTTACAATGTTG 59.321 41.667 0.00 0.00 0.00 3.33
2709 2745 4.447389 GTGACCCATGTTTTACAATGTTGC 59.553 41.667 0.00 0.00 0.00 4.17
2710 2746 3.993736 GACCCATGTTTTACAATGTTGCC 59.006 43.478 0.00 0.00 0.00 4.52
2713 2749 3.432933 CCATGTTTTACAATGTTGCCTGC 59.567 43.478 0.00 0.00 0.00 4.85
2716 2763 2.437200 TTTACAATGTTGCCTGCTGC 57.563 45.000 0.00 0.00 41.77 5.25
2761 2812 6.365970 AAAGATGTCATGAACCTGTAGTCT 57.634 37.500 0.00 0.00 0.00 3.24
2763 2814 4.774726 AGATGTCATGAACCTGTAGTCTGT 59.225 41.667 0.00 0.00 0.00 3.41
2771 2822 4.039852 TGAACCTGTAGTCTGTTGTATGCA 59.960 41.667 0.00 0.00 0.00 3.96
2797 2848 0.248843 GCTCTCTCAGGTTCAGGTGG 59.751 60.000 0.00 0.00 0.00 4.61
2824 2875 1.256376 CGTGCTAGTGCGATCAATCAC 59.744 52.381 2.64 0.00 43.34 3.06
2881 2932 3.596214 GAACAGGGAAGTGATTCGCTAA 58.404 45.455 7.17 0.00 41.49 3.09
2919 2970 4.307432 TCCTTCTCTGATTGTTGACGTTC 58.693 43.478 0.00 0.00 0.00 3.95
3108 3161 3.340034 CAAGCATGATGTTTTGGGCATT 58.660 40.909 0.00 0.00 0.00 3.56
3111 3164 3.514706 AGCATGATGTTTTGGGCATTACA 59.485 39.130 0.00 0.00 0.00 2.41
3113 3166 3.951775 TGATGTTTTGGGCATTACACC 57.048 42.857 0.00 0.00 0.00 4.16
3118 3171 3.964031 TGTTTTGGGCATTACACCTCTTT 59.036 39.130 0.00 0.00 0.00 2.52
3119 3172 4.202202 TGTTTTGGGCATTACACCTCTTTG 60.202 41.667 0.00 0.00 0.00 2.77
3120 3173 3.517296 TTGGGCATTACACCTCTTTGA 57.483 42.857 0.00 0.00 0.00 2.69
3123 3176 3.826157 TGGGCATTACACCTCTTTGAAAG 59.174 43.478 0.00 0.00 0.00 2.62
3124 3177 4.079253 GGGCATTACACCTCTTTGAAAGA 58.921 43.478 7.49 7.49 35.87 2.52
3126 3179 5.461526 GGCATTACACCTCTTTGAAAGAAC 58.538 41.667 9.15 0.00 37.02 3.01
3127 3180 5.241728 GGCATTACACCTCTTTGAAAGAACT 59.758 40.000 9.15 0.00 37.02 3.01
3128 3181 6.145535 GCATTACACCTCTTTGAAAGAACTG 58.854 40.000 9.15 9.06 37.02 3.16
3129 3182 5.751243 TTACACCTCTTTGAAAGAACTGC 57.249 39.130 9.15 0.00 37.02 4.40
3130 3183 3.891049 ACACCTCTTTGAAAGAACTGCT 58.109 40.909 9.15 0.00 37.02 4.24
3131 3184 5.036117 ACACCTCTTTGAAAGAACTGCTA 57.964 39.130 9.15 0.00 37.02 3.49
3132 3185 4.816925 ACACCTCTTTGAAAGAACTGCTAC 59.183 41.667 9.15 0.00 37.02 3.58
3133 3186 4.058817 ACCTCTTTGAAAGAACTGCTACG 58.941 43.478 9.15 0.00 37.02 3.51
3134 3187 3.433615 CCTCTTTGAAAGAACTGCTACGG 59.566 47.826 9.15 0.50 37.02 4.02
3135 3188 4.058817 CTCTTTGAAAGAACTGCTACGGT 58.941 43.478 9.15 0.00 37.02 4.83
3136 3189 3.807622 TCTTTGAAAGAACTGCTACGGTG 59.192 43.478 4.94 0.00 33.83 4.94
3137 3190 1.508632 TGAAAGAACTGCTACGGTGC 58.491 50.000 0.00 0.00 0.00 5.01
3138 3191 1.070134 TGAAAGAACTGCTACGGTGCT 59.930 47.619 3.74 0.00 27.95 4.40
3139 3192 2.297880 TGAAAGAACTGCTACGGTGCTA 59.702 45.455 3.74 0.00 26.67 3.49
3140 3193 2.365408 AAGAACTGCTACGGTGCTAC 57.635 50.000 3.74 0.00 26.67 3.58
3141 3194 0.531200 AGAACTGCTACGGTGCTACC 59.469 55.000 3.74 0.00 34.05 3.18
3142 3195 0.459759 GAACTGCTACGGTGCTACCC 60.460 60.000 3.74 0.00 33.75 3.69
3143 3196 1.189524 AACTGCTACGGTGCTACCCA 61.190 55.000 3.74 0.00 33.75 4.51
3144 3197 1.189524 ACTGCTACGGTGCTACCCAA 61.190 55.000 3.74 0.00 33.75 4.12
3145 3198 0.739813 CTGCTACGGTGCTACCCAAC 60.740 60.000 3.74 0.00 33.75 3.77
3146 3199 1.294138 GCTACGGTGCTACCCAACA 59.706 57.895 0.00 0.00 33.75 3.33
3147 3200 0.320946 GCTACGGTGCTACCCAACAA 60.321 55.000 0.00 0.00 33.75 2.83
3148 3201 1.878948 GCTACGGTGCTACCCAACAAA 60.879 52.381 0.00 0.00 33.75 2.83
3149 3202 2.706890 CTACGGTGCTACCCAACAAAT 58.293 47.619 0.00 0.00 33.75 2.32
3150 3203 1.989706 ACGGTGCTACCCAACAAATT 58.010 45.000 0.00 0.00 33.75 1.82
3151 3204 3.143211 ACGGTGCTACCCAACAAATTA 57.857 42.857 0.00 0.00 33.75 1.40
3152 3205 2.815503 ACGGTGCTACCCAACAAATTAC 59.184 45.455 0.00 0.00 33.75 1.89
3153 3206 2.814919 CGGTGCTACCCAACAAATTACA 59.185 45.455 0.00 0.00 33.75 2.41
3154 3207 3.442273 CGGTGCTACCCAACAAATTACAT 59.558 43.478 0.00 0.00 33.75 2.29
3155 3208 4.674101 CGGTGCTACCCAACAAATTACATG 60.674 45.833 0.00 0.00 33.75 3.21
3156 3209 4.381505 GGTGCTACCCAACAAATTACATGG 60.382 45.833 0.00 0.00 30.04 3.66
3157 3210 3.194542 TGCTACCCAACAAATTACATGGC 59.805 43.478 0.00 0.00 0.00 4.40
3158 3211 3.194542 GCTACCCAACAAATTACATGGCA 59.805 43.478 0.00 0.00 0.00 4.92
3159 3212 4.141959 GCTACCCAACAAATTACATGGCAT 60.142 41.667 0.00 0.00 0.00 4.40
3160 3213 4.205065 ACCCAACAAATTACATGGCATG 57.795 40.909 25.31 25.31 0.00 4.06
3161 3214 3.837146 ACCCAACAAATTACATGGCATGA 59.163 39.130 32.74 12.95 0.00 3.07
3162 3215 4.183101 CCCAACAAATTACATGGCATGAC 58.817 43.478 32.74 0.00 0.00 3.06
3163 3216 3.858812 CCAACAAATTACATGGCATGACG 59.141 43.478 32.74 15.48 0.00 4.35
3164 3217 4.380339 CCAACAAATTACATGGCATGACGA 60.380 41.667 32.74 17.60 0.00 4.20
3165 3218 5.342433 CAACAAATTACATGGCATGACGAT 58.658 37.500 32.74 18.92 0.00 3.73
3166 3219 5.173774 ACAAATTACATGGCATGACGATC 57.826 39.130 32.74 0.00 0.00 3.69
3167 3220 4.036734 ACAAATTACATGGCATGACGATCC 59.963 41.667 32.74 0.00 0.00 3.36
3168 3221 3.777106 ATTACATGGCATGACGATCCT 57.223 42.857 32.74 11.81 0.00 3.24
3169 3222 3.558931 TTACATGGCATGACGATCCTT 57.441 42.857 32.74 11.07 0.00 3.36
3170 3223 2.425143 ACATGGCATGACGATCCTTT 57.575 45.000 32.74 5.02 0.00 3.11
3171 3224 2.726821 ACATGGCATGACGATCCTTTT 58.273 42.857 32.74 4.23 0.00 2.27
3172 3225 2.424601 ACATGGCATGACGATCCTTTTG 59.575 45.455 32.74 4.33 0.00 2.44
3173 3226 2.198827 TGGCATGACGATCCTTTTGT 57.801 45.000 0.00 0.00 0.00 2.83
3174 3227 3.342377 TGGCATGACGATCCTTTTGTA 57.658 42.857 0.00 0.00 0.00 2.41
3175 3228 3.270027 TGGCATGACGATCCTTTTGTAG 58.730 45.455 0.00 0.00 0.00 2.74
3176 3229 3.055458 TGGCATGACGATCCTTTTGTAGA 60.055 43.478 0.00 0.00 0.00 2.59
3177 3230 3.938963 GGCATGACGATCCTTTTGTAGAA 59.061 43.478 0.00 0.00 0.00 2.10
3178 3231 4.034510 GGCATGACGATCCTTTTGTAGAAG 59.965 45.833 0.00 0.00 0.00 2.85
3179 3232 4.494855 GCATGACGATCCTTTTGTAGAAGC 60.495 45.833 0.00 0.00 0.00 3.86
3180 3233 3.596214 TGACGATCCTTTTGTAGAAGCC 58.404 45.455 0.00 0.00 0.00 4.35
3181 3234 3.007506 TGACGATCCTTTTGTAGAAGCCA 59.992 43.478 0.00 0.00 0.00 4.75
3182 3235 4.000988 GACGATCCTTTTGTAGAAGCCAA 58.999 43.478 0.00 0.00 0.00 4.52
3183 3236 4.003648 ACGATCCTTTTGTAGAAGCCAAG 58.996 43.478 0.00 0.00 0.00 3.61
3184 3237 4.253685 CGATCCTTTTGTAGAAGCCAAGA 58.746 43.478 0.00 0.00 0.00 3.02
3185 3238 4.695455 CGATCCTTTTGTAGAAGCCAAGAA 59.305 41.667 0.00 0.00 0.00 2.52
3186 3239 5.390991 CGATCCTTTTGTAGAAGCCAAGAAC 60.391 44.000 0.00 0.00 0.00 3.01
3187 3240 4.142038 TCCTTTTGTAGAAGCCAAGAACC 58.858 43.478 0.00 0.00 0.00 3.62
3188 3241 3.058224 CCTTTTGTAGAAGCCAAGAACCG 60.058 47.826 0.00 0.00 0.00 4.44
3189 3242 2.922740 TTGTAGAAGCCAAGAACCGT 57.077 45.000 0.00 0.00 0.00 4.83
3190 3243 4.339872 TTTGTAGAAGCCAAGAACCGTA 57.660 40.909 0.00 0.00 0.00 4.02
3191 3244 3.587797 TGTAGAAGCCAAGAACCGTAG 57.412 47.619 0.00 0.00 0.00 3.51
3192 3245 3.159472 TGTAGAAGCCAAGAACCGTAGA 58.841 45.455 0.00 0.00 0.00 2.59
3193 3246 3.575256 TGTAGAAGCCAAGAACCGTAGAA 59.425 43.478 0.00 0.00 0.00 2.10
3194 3247 3.983044 AGAAGCCAAGAACCGTAGAAT 57.017 42.857 0.00 0.00 0.00 2.40
3195 3248 3.600388 AGAAGCCAAGAACCGTAGAATG 58.400 45.455 0.00 0.00 0.00 2.67
3196 3249 2.403252 AGCCAAGAACCGTAGAATGG 57.597 50.000 0.00 0.00 0.00 3.16
3197 3250 1.628846 AGCCAAGAACCGTAGAATGGT 59.371 47.619 0.00 0.00 39.71 3.55
3198 3251 2.835764 AGCCAAGAACCGTAGAATGGTA 59.164 45.455 0.00 0.00 36.21 3.25
3199 3252 3.262405 AGCCAAGAACCGTAGAATGGTAA 59.738 43.478 0.00 0.00 36.21 2.85
3200 3253 4.080526 AGCCAAGAACCGTAGAATGGTAAT 60.081 41.667 0.00 0.00 36.21 1.89
3201 3254 4.272748 GCCAAGAACCGTAGAATGGTAATC 59.727 45.833 0.00 0.00 36.21 1.75
3202 3255 5.424757 CCAAGAACCGTAGAATGGTAATCA 58.575 41.667 0.00 0.00 36.21 2.57
3203 3256 6.055588 CCAAGAACCGTAGAATGGTAATCAT 58.944 40.000 0.00 0.00 36.21 2.45
3204 3257 7.214381 CCAAGAACCGTAGAATGGTAATCATA 58.786 38.462 0.00 0.00 36.21 2.15
3205 3258 7.878127 CCAAGAACCGTAGAATGGTAATCATAT 59.122 37.037 0.00 0.00 36.21 1.78
3206 3259 9.923143 CAAGAACCGTAGAATGGTAATCATATA 57.077 33.333 0.00 0.00 36.21 0.86
3209 3262 9.871238 GAACCGTAGAATGGTAATCATATATGT 57.129 33.333 12.42 0.00 36.21 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 2.544267 GCATACGACATTTCCTACTGCC 59.456 50.000 0.00 0.00 0.00 4.85
263 266 7.279090 CCGGTCACAACAAAAGTATCATACATA 59.721 37.037 0.00 0.00 0.00 2.29
278 281 2.414994 TGGTTAAACCGGTCACAACA 57.585 45.000 20.85 9.99 42.58 3.33
279 282 2.422832 TGTTGGTTAAACCGGTCACAAC 59.577 45.455 22.23 22.23 42.58 3.32
392 396 7.264294 AGAAGTCCTTCATCCTTTAGTGATT 57.736 36.000 9.54 0.00 41.84 2.57
402 406 4.142609 TGCATGTAGAAGTCCTTCATCC 57.857 45.455 9.54 0.00 41.84 3.51
406 410 5.819379 TCATCAATGCATGTAGAAGTCCTTC 59.181 40.000 0.00 0.00 39.78 3.46
475 479 6.539649 TTGCGCCTTATCATATGTTTAGAC 57.460 37.500 4.18 0.00 0.00 2.59
529 542 7.391275 CCGGTTTAAAGGTCCTGTCTTATTTTA 59.609 37.037 0.00 0.00 0.00 1.52
600 621 0.528470 CTAGCAGGGTATAGGAGCGC 59.472 60.000 0.00 0.00 0.00 5.92
695 719 2.030562 CGCCACGTTCCACTTCCT 59.969 61.111 0.00 0.00 0.00 3.36
746 770 2.446435 GTATTTTGGGCTTCCTGCAGA 58.554 47.619 17.39 0.00 45.15 4.26
977 1001 1.911766 GCGGATCGGGGAGGGATTA 60.912 63.158 2.13 0.00 0.00 1.75
1470 1506 0.322546 GCTTCTGGTTGTAGGTGGGG 60.323 60.000 0.00 0.00 0.00 4.96
1890 1926 3.066900 GTGAGAGCTCCTTCTGCGTATTA 59.933 47.826 10.93 0.00 35.28 0.98
2004 2040 3.361786 TCTCGATGTGGAATCTGGTACA 58.638 45.455 0.00 0.00 0.00 2.90
2094 2130 2.103042 GCGGTGATGGTGTCTGCTC 61.103 63.158 0.00 0.00 0.00 4.26
2147 2183 0.815213 TGCAGAGTCGGCCATATTGC 60.815 55.000 12.91 6.42 0.00 3.56
2181 2217 1.363443 CTCCTCATCGCTCTGCTCC 59.637 63.158 0.00 0.00 0.00 4.70
2240 2276 4.937620 TGGCTTGTTATTCAGTCTGTCATC 59.062 41.667 0.00 0.00 0.00 2.92
2245 2281 3.119708 GCCTTGGCTTGTTATTCAGTCTG 60.120 47.826 4.11 0.00 0.00 3.51
2288 2324 9.179909 CAATGTAACCCTAACACATACCAATAA 57.820 33.333 0.00 0.00 32.70 1.40
2566 2602 2.542411 GCACAGTCTGGCAAAGAACAAG 60.542 50.000 4.53 0.00 36.40 3.16
2568 2604 1.024271 GCACAGTCTGGCAAAGAACA 58.976 50.000 4.53 0.00 36.40 3.18
2569 2605 1.265365 GAGCACAGTCTGGCAAAGAAC 59.735 52.381 13.61 0.00 36.40 3.01
2597 2633 4.946157 ACATATAATAATCCAGGCTGCTGC 59.054 41.667 9.56 7.10 38.76 5.25
2631 2667 7.443575 ACATACAAGGCAAGATGATGATAAGAC 59.556 37.037 0.00 0.00 0.00 3.01
2648 2684 9.888878 CTGCAGATAAATATTTCACATACAAGG 57.111 33.333 8.42 0.00 0.00 3.61
2684 2720 3.241701 CATTGTAAAACATGGGTCACGC 58.758 45.455 0.00 0.00 0.00 5.34
2686 2722 4.447389 GCAACATTGTAAAACATGGGTCAC 59.553 41.667 0.00 0.00 0.00 3.67
2738 2785 6.169094 CAGACTACAGGTTCATGACATCTTT 58.831 40.000 0.00 0.00 0.00 2.52
2739 2786 5.247110 ACAGACTACAGGTTCATGACATCTT 59.753 40.000 0.00 0.00 0.00 2.40
2771 2822 2.968574 TGAACCTGAGAGAGCAAGACTT 59.031 45.455 0.00 0.00 0.00 3.01
2797 2848 2.720758 CGCACTAGCACGTCAGCAC 61.721 63.158 0.36 0.00 42.27 4.40
2824 2875 8.573885 AGAACTTCCCCTTTTTACGATAAAAAG 58.426 33.333 22.48 22.48 43.32 2.27
2881 2932 6.206243 CAGAGAAGGAAACATCAACAATCAGT 59.794 38.462 0.00 0.00 0.00 3.41
2919 2970 4.842091 GCCGCGCCAAATGCAGAG 62.842 66.667 0.00 0.00 41.33 3.35
3007 3060 4.142160 ACAACTGTTGGCTTTTCTTCTTCC 60.142 41.667 23.15 0.00 34.12 3.46
3095 3148 3.778265 AGAGGTGTAATGCCCAAAACAT 58.222 40.909 0.00 0.00 0.00 2.71
3108 3161 5.036117 AGCAGTTCTTTCAAAGAGGTGTA 57.964 39.130 0.00 0.00 39.03 2.90
3111 3164 4.058817 CGTAGCAGTTCTTTCAAAGAGGT 58.941 43.478 0.00 0.00 39.03 3.85
3113 3166 4.058817 ACCGTAGCAGTTCTTTCAAAGAG 58.941 43.478 0.00 0.00 39.03 2.85
3118 3171 1.070134 AGCACCGTAGCAGTTCTTTCA 59.930 47.619 0.00 0.00 36.85 2.69
3119 3172 1.797025 AGCACCGTAGCAGTTCTTTC 58.203 50.000 0.00 0.00 36.85 2.62
3120 3173 2.612221 GGTAGCACCGTAGCAGTTCTTT 60.612 50.000 0.00 0.00 36.85 2.52
3123 3176 0.459759 GGGTAGCACCGTAGCAGTTC 60.460 60.000 0.00 0.00 39.83 3.01
3124 3177 1.189524 TGGGTAGCACCGTAGCAGTT 61.190 55.000 0.00 0.00 39.83 3.16
3126 3179 0.739813 GTTGGGTAGCACCGTAGCAG 60.740 60.000 0.00 0.00 39.83 4.24
3127 3180 1.294138 GTTGGGTAGCACCGTAGCA 59.706 57.895 0.00 0.00 39.83 3.49
3128 3181 0.320946 TTGTTGGGTAGCACCGTAGC 60.321 55.000 0.00 0.00 39.83 3.58
3129 3182 2.172851 TTTGTTGGGTAGCACCGTAG 57.827 50.000 0.00 0.00 39.83 3.51
3130 3183 2.863132 ATTTGTTGGGTAGCACCGTA 57.137 45.000 0.00 0.00 39.83 4.02
3131 3184 1.989706 AATTTGTTGGGTAGCACCGT 58.010 45.000 0.00 0.00 39.83 4.83
3132 3185 2.814919 TGTAATTTGTTGGGTAGCACCG 59.185 45.455 0.00 0.00 39.83 4.94
3133 3186 4.381505 CCATGTAATTTGTTGGGTAGCACC 60.382 45.833 0.00 0.00 37.60 5.01
3134 3187 4.743493 CCATGTAATTTGTTGGGTAGCAC 58.257 43.478 0.00 0.00 0.00 4.40
3135 3188 3.194542 GCCATGTAATTTGTTGGGTAGCA 59.805 43.478 0.00 0.00 0.00 3.49
3136 3189 3.194542 TGCCATGTAATTTGTTGGGTAGC 59.805 43.478 0.00 0.00 0.00 3.58
3137 3190 5.126869 TCATGCCATGTAATTTGTTGGGTAG 59.873 40.000 4.31 0.00 0.00 3.18
3138 3191 5.019470 TCATGCCATGTAATTTGTTGGGTA 58.981 37.500 4.31 0.00 0.00 3.69
3139 3192 3.837146 TCATGCCATGTAATTTGTTGGGT 59.163 39.130 4.31 0.00 0.00 4.51
3140 3193 4.183101 GTCATGCCATGTAATTTGTTGGG 58.817 43.478 4.31 0.00 0.00 4.12
3141 3194 3.858812 CGTCATGCCATGTAATTTGTTGG 59.141 43.478 4.31 0.00 0.00 3.77
3142 3195 4.731720 TCGTCATGCCATGTAATTTGTTG 58.268 39.130 4.31 0.00 0.00 3.33
3143 3196 5.450412 GGATCGTCATGCCATGTAATTTGTT 60.450 40.000 4.31 0.00 0.00 2.83
3144 3197 4.036734 GGATCGTCATGCCATGTAATTTGT 59.963 41.667 4.31 0.00 0.00 2.83
3145 3198 4.276678 AGGATCGTCATGCCATGTAATTTG 59.723 41.667 4.31 0.00 0.00 2.32
3146 3199 4.464008 AGGATCGTCATGCCATGTAATTT 58.536 39.130 4.31 0.00 0.00 1.82
3147 3200 4.090761 AGGATCGTCATGCCATGTAATT 57.909 40.909 4.31 0.00 0.00 1.40
3148 3201 3.777106 AGGATCGTCATGCCATGTAAT 57.223 42.857 4.31 0.00 0.00 1.89
3149 3202 3.558931 AAGGATCGTCATGCCATGTAA 57.441 42.857 4.31 0.00 0.00 2.41
3150 3203 3.558931 AAAGGATCGTCATGCCATGTA 57.441 42.857 4.31 0.00 0.00 2.29
3151 3204 2.424601 CAAAAGGATCGTCATGCCATGT 59.575 45.455 4.31 0.00 0.00 3.21
3152 3205 2.424601 ACAAAAGGATCGTCATGCCATG 59.575 45.455 0.00 0.00 0.00 3.66
3153 3206 2.726821 ACAAAAGGATCGTCATGCCAT 58.273 42.857 0.00 0.00 0.00 4.40
3154 3207 2.198827 ACAAAAGGATCGTCATGCCA 57.801 45.000 0.00 0.00 0.00 4.92
3155 3208 3.531538 TCTACAAAAGGATCGTCATGCC 58.468 45.455 0.00 0.00 0.00 4.40
3156 3209 4.494855 GCTTCTACAAAAGGATCGTCATGC 60.495 45.833 0.00 0.00 0.00 4.06
3157 3210 4.034510 GGCTTCTACAAAAGGATCGTCATG 59.965 45.833 0.00 0.00 0.00 3.07
3158 3211 4.192317 GGCTTCTACAAAAGGATCGTCAT 58.808 43.478 0.00 0.00 0.00 3.06
3159 3212 3.007506 TGGCTTCTACAAAAGGATCGTCA 59.992 43.478 0.00 0.00 0.00 4.35
3160 3213 3.596214 TGGCTTCTACAAAAGGATCGTC 58.404 45.455 0.00 0.00 0.00 4.20
3161 3214 3.695830 TGGCTTCTACAAAAGGATCGT 57.304 42.857 0.00 0.00 0.00 3.73
3162 3215 4.253685 TCTTGGCTTCTACAAAAGGATCG 58.746 43.478 0.00 0.00 0.00 3.69
3163 3216 5.106118 GGTTCTTGGCTTCTACAAAAGGATC 60.106 44.000 0.00 0.00 0.00 3.36
3164 3217 4.767409 GGTTCTTGGCTTCTACAAAAGGAT 59.233 41.667 0.00 0.00 0.00 3.24
3165 3218 4.142038 GGTTCTTGGCTTCTACAAAAGGA 58.858 43.478 0.00 0.00 0.00 3.36
3166 3219 3.058224 CGGTTCTTGGCTTCTACAAAAGG 60.058 47.826 0.00 0.00 0.00 3.11
3167 3220 3.564225 ACGGTTCTTGGCTTCTACAAAAG 59.436 43.478 0.00 0.00 0.00 2.27
3168 3221 3.547746 ACGGTTCTTGGCTTCTACAAAA 58.452 40.909 0.00 0.00 0.00 2.44
3169 3222 3.202829 ACGGTTCTTGGCTTCTACAAA 57.797 42.857 0.00 0.00 0.00 2.83
3170 3223 2.922740 ACGGTTCTTGGCTTCTACAA 57.077 45.000 0.00 0.00 0.00 2.41
3171 3224 3.159472 TCTACGGTTCTTGGCTTCTACA 58.841 45.455 0.00 0.00 0.00 2.74
3172 3225 3.863142 TCTACGGTTCTTGGCTTCTAC 57.137 47.619 0.00 0.00 0.00 2.59
3173 3226 4.382685 CCATTCTACGGTTCTTGGCTTCTA 60.383 45.833 0.00 0.00 0.00 2.10
3174 3227 3.600388 CATTCTACGGTTCTTGGCTTCT 58.400 45.455 0.00 0.00 0.00 2.85
3175 3228 2.678336 CCATTCTACGGTTCTTGGCTTC 59.322 50.000 0.00 0.00 0.00 3.86
3176 3229 2.039879 ACCATTCTACGGTTCTTGGCTT 59.960 45.455 0.00 0.00 30.53 4.35
3177 3230 1.628846 ACCATTCTACGGTTCTTGGCT 59.371 47.619 0.00 0.00 30.53 4.75
3178 3231 2.109425 ACCATTCTACGGTTCTTGGC 57.891 50.000 0.00 0.00 30.53 4.52
3179 3232 5.424757 TGATTACCATTCTACGGTTCTTGG 58.575 41.667 0.00 0.00 37.99 3.61
3180 3233 8.833231 ATATGATTACCATTCTACGGTTCTTG 57.167 34.615 0.00 0.00 37.99 3.02
3183 3236 9.871238 ACATATATGATTACCATTCTACGGTTC 57.129 33.333 19.63 0.00 37.99 3.62


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

AutoCloner maintained by Alex Coulton.