Multiple sequence alignment - TraesCS6B01G154600

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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 TraesCS6B01G154600 chr6B 100.000 3362 0 0 1 3362 158076990 158073629 0.000000e+00 6209.0
1 TraesCS6B01G154600 chr6B 86.831 1982 239 20 252 2218 158149791 158147817 0.000000e+00 2194.0
2 TraesCS6B01G154600 chr6B 86.569 1988 247 18 246 2219 159402072 159404053 0.000000e+00 2174.0
3 TraesCS6B01G154600 chr6B 81.406 2404 373 48 177 2558 159377926 159380277 0.000000e+00 1895.0
4 TraesCS6B01G154600 chr6D 95.646 2779 85 8 1 2767 83047110 83044356 0.000000e+00 4429.0
5 TraesCS6B01G154600 chr6D 83.998 2331 311 47 248 2559 83057922 83055635 0.000000e+00 2182.0
6 TraesCS6B01G154600 chr6D 86.657 1986 245 18 247 2218 83124727 83122748 0.000000e+00 2182.0
7 TraesCS6B01G154600 chr6D 86.633 1990 242 20 246 2219 83540604 83542585 0.000000e+00 2180.0
8 TraesCS6B01G154600 chr6D 90.119 253 12 6 3002 3248 83044015 83043770 1.950000e-82 316.0
9 TraesCS6B01G154600 chr6D 87.245 196 8 1 2792 2970 83044205 83044010 1.220000e-49 207.0
10 TraesCS6B01G154600 chr6D 88.889 72 4 1 2860 2927 83017909 83017838 5.980000e-13 86.1
11 TraesCS6B01G154600 chr6A 86.860 1933 233 18 268 2185 100185064 100183138 0.000000e+00 2143.0
12 TraesCS6B01G154600 chr6A 86.210 1987 256 16 246 2219 100760978 100762959 0.000000e+00 2135.0
13 TraesCS6B01G154600 chr6A 86.709 1896 232 18 304 2185 100803097 100804986 0.000000e+00 2087.0
14 TraesCS6B01G154600 chr6A 81.456 2432 374 45 160 2567 100738176 100740554 0.000000e+00 1921.0
15 TraesCS6B01G154600 chr1D 90.123 81 8 0 2444 2524 363114753 363114833 4.590000e-19 106.0
16 TraesCS6B01G154600 chr3B 96.774 31 1 0 3207 3237 813271319 813271349 6.000000e-03 52.8


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 TraesCS6B01G154600 chr6B 158073629 158076990 3361 True 6209.000000 6209 100.000000 1 3362 1 chr6B.!!$R1 3361
1 TraesCS6B01G154600 chr6B 158147817 158149791 1974 True 2194.000000 2194 86.831000 252 2218 1 chr6B.!!$R2 1966
2 TraesCS6B01G154600 chr6B 159402072 159404053 1981 False 2174.000000 2174 86.569000 246 2219 1 chr6B.!!$F2 1973
3 TraesCS6B01G154600 chr6B 159377926 159380277 2351 False 1895.000000 1895 81.406000 177 2558 1 chr6B.!!$F1 2381
4 TraesCS6B01G154600 chr6D 83055635 83057922 2287 True 2182.000000 2182 83.998000 248 2559 1 chr6D.!!$R2 2311
5 TraesCS6B01G154600 chr6D 83122748 83124727 1979 True 2182.000000 2182 86.657000 247 2218 1 chr6D.!!$R3 1971
6 TraesCS6B01G154600 chr6D 83540604 83542585 1981 False 2180.000000 2180 86.633000 246 2219 1 chr6D.!!$F1 1973
7 TraesCS6B01G154600 chr6D 83043770 83047110 3340 True 1650.666667 4429 91.003333 1 3248 3 chr6D.!!$R4 3247
8 TraesCS6B01G154600 chr6A 100183138 100185064 1926 True 2143.000000 2143 86.860000 268 2185 1 chr6A.!!$R1 1917
9 TraesCS6B01G154600 chr6A 100760978 100762959 1981 False 2135.000000 2135 86.210000 246 2219 1 chr6A.!!$F2 1973
10 TraesCS6B01G154600 chr6A 100803097 100804986 1889 False 2087.000000 2087 86.709000 304 2185 1 chr6A.!!$F3 1881
11 TraesCS6B01G154600 chr6A 100738176 100740554 2378 False 1921.000000 1921 81.456000 160 2567 1 chr6A.!!$F1 2407

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
166 167 1.759445 ACTAGTGCTGTATCTGGCAGG 59.241 52.381 15.73 0.0 39.22 4.85 F
1239 1250 0.179111 TCGACTTCATAAGCCTGCCG 60.179 55.000 0.00 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1920 1932 1.812235 AATTGAGTGCGATGAGTGCA 58.188 45.0 0.0 0.0 40.70 4.57 R
3132 3296 0.034670 AGCCCTTGCCTTGTCTCATC 60.035 55.0 0.0 0.0 38.69 2.92 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
29 30 5.224888 GCATATGCAATTCACCAATACCAG 58.775 41.667 22.84 0.00 41.59 4.00
55 56 2.041620 TCCTTGACCCATTCCCTCAAAG 59.958 50.000 0.00 0.00 0.00 2.77
75 76 5.959618 AAGAAAAACTAATCCTTGACCCG 57.040 39.130 0.00 0.00 0.00 5.28
87 88 5.346181 TCCTTGACCCGAATTTTGTTTTT 57.654 34.783 0.00 0.00 0.00 1.94
105 106 5.065090 TGTTTTTATCATGATGACCAGAGCG 59.935 40.000 18.72 0.00 0.00 5.03
155 156 5.991328 TCTTTCACAAGAAACTAGTGCTG 57.009 39.130 0.00 0.00 38.76 4.41
166 167 1.759445 ACTAGTGCTGTATCTGGCAGG 59.241 52.381 15.73 0.00 39.22 4.85
276 277 5.468540 ACCTTTCTTTGGTTTGGCTATTC 57.531 39.130 0.00 0.00 33.34 1.75
949 960 7.448161 TCTTCCAGATGAGCTTTTCAATGTTAA 59.552 33.333 0.00 0.00 39.77 2.01
1164 1175 0.441533 CAGCTCTAAGCAACTGCACG 59.558 55.000 4.22 0.00 45.56 5.34
1188 1199 7.825396 CGAATCTCGTGACAATTGACCTCAAT 61.825 42.308 13.59 0.00 40.47 2.57
1222 1233 3.250040 CAGTGGAAAACTTACCAAGGTCG 59.750 47.826 0.00 0.00 36.83 4.79
1239 1250 0.179111 TCGACTTCATAAGCCTGCCG 60.179 55.000 0.00 0.00 0.00 5.69
1294 1305 0.240945 CACCGGCACAATTCCAGAAC 59.759 55.000 0.00 0.00 0.00 3.01
1311 1322 2.695666 AGAACGCATATACTCCTGCAGT 59.304 45.455 13.81 0.00 38.30 4.40
1461 1472 6.831353 CACTTCAGATCCTTAGGAGTTCTAGA 59.169 42.308 7.19 4.03 34.05 2.43
1920 1932 4.030913 TGGAGGAGATCGGTCAGTTAAAT 58.969 43.478 0.00 0.00 0.00 1.40
1922 1934 3.798202 AGGAGATCGGTCAGTTAAATGC 58.202 45.455 0.00 0.00 0.00 3.56
2186 2199 4.641396 TCAAAACTGTGTGGTCCTATGAG 58.359 43.478 0.00 0.00 0.00 2.90
2219 2232 3.710926 CTCAGCAGGAGCAGGTCT 58.289 61.111 0.00 0.00 45.49 3.85
2220 2233 1.218585 CTCAGCAGGAGCAGGTCTG 59.781 63.158 0.00 0.00 45.49 3.51
2222 2235 1.079266 CAGCAGGAGCAGGTCTGAC 60.079 63.158 0.00 0.00 45.49 3.51
2241 2254 3.971305 TGACCTCCACTTCCTACAGAAAA 59.029 43.478 0.00 0.00 32.88 2.29
2242 2255 4.202326 TGACCTCCACTTCCTACAGAAAAC 60.202 45.833 0.00 0.00 32.88 2.43
2243 2256 3.714798 ACCTCCACTTCCTACAGAAAACA 59.285 43.478 0.00 0.00 32.88 2.83
2244 2257 4.202367 ACCTCCACTTCCTACAGAAAACAG 60.202 45.833 0.00 0.00 32.88 3.16
2245 2258 4.202367 CCTCCACTTCCTACAGAAAACAGT 60.202 45.833 0.00 0.00 32.88 3.55
2246 2259 5.367945 TCCACTTCCTACAGAAAACAGTT 57.632 39.130 0.00 0.00 32.88 3.16
2247 2260 5.365619 TCCACTTCCTACAGAAAACAGTTC 58.634 41.667 0.00 0.00 32.88 3.01
2248 2261 5.104693 TCCACTTCCTACAGAAAACAGTTCA 60.105 40.000 0.00 0.00 32.88 3.18
2249 2262 5.237344 CCACTTCCTACAGAAAACAGTTCAG 59.763 44.000 0.00 0.00 32.88 3.02
2250 2263 6.049149 CACTTCCTACAGAAAACAGTTCAGA 58.951 40.000 0.00 0.00 32.88 3.27
2251 2264 6.708054 CACTTCCTACAGAAAACAGTTCAGAT 59.292 38.462 0.00 0.00 32.88 2.90
2252 2265 6.708054 ACTTCCTACAGAAAACAGTTCAGATG 59.292 38.462 0.00 0.00 32.88 2.90
2253 2266 6.174720 TCCTACAGAAAACAGTTCAGATGT 57.825 37.500 0.00 0.00 0.00 3.06
2254 2267 7.297936 TCCTACAGAAAACAGTTCAGATGTA 57.702 36.000 0.00 0.00 0.00 2.29
2255 2268 7.732025 TCCTACAGAAAACAGTTCAGATGTAA 58.268 34.615 0.00 0.00 0.00 2.41
2256 2269 7.872993 TCCTACAGAAAACAGTTCAGATGTAAG 59.127 37.037 0.00 0.00 0.00 2.34
2257 2270 6.867662 ACAGAAAACAGTTCAGATGTAAGG 57.132 37.500 0.00 0.00 0.00 2.69
2258 2271 6.357367 ACAGAAAACAGTTCAGATGTAAGGT 58.643 36.000 0.00 0.00 0.00 3.50
2259 2272 6.483640 ACAGAAAACAGTTCAGATGTAAGGTC 59.516 38.462 0.00 0.00 0.00 3.85
2260 2273 6.483307 CAGAAAACAGTTCAGATGTAAGGTCA 59.517 38.462 0.00 0.00 0.00 4.02
2261 2274 7.012327 CAGAAAACAGTTCAGATGTAAGGTCAA 59.988 37.037 0.00 0.00 0.00 3.18
2330 2343 2.239400 TGGAGTCGGAGTGCTATATGG 58.761 52.381 5.91 0.00 0.00 2.74
2343 2356 5.824624 AGTGCTATATGGTCAGATGGTTTTG 59.175 40.000 0.00 0.00 0.00 2.44
2361 2374 6.321181 TGGTTTTGGCTAGATATTTTGGCTAG 59.679 38.462 0.00 0.00 35.78 3.42
2382 2397 4.603131 AGACCATGGCAATTGTTATCACT 58.397 39.130 13.04 0.00 0.00 3.41
2407 2423 6.883756 TGCCATGAACTGTGACATAATCTAAA 59.116 34.615 0.00 0.00 0.00 1.85
2427 2443 7.679783 TCTAAAGTGGTTCTCAATTCAGATGA 58.320 34.615 0.00 0.00 31.92 2.92
2428 2444 6.814506 AAAGTGGTTCTCAATTCAGATGAG 57.185 37.500 0.00 0.00 44.53 2.90
2429 2445 5.495926 AGTGGTTCTCAATTCAGATGAGT 57.504 39.130 3.72 0.00 43.77 3.41
2439 2456 6.997655 TCAATTCAGATGAGTAAGTCAGTGT 58.002 36.000 0.00 0.00 39.07 3.55
2448 2465 3.235200 AGTAAGTCAGTGTCTCCAGCTT 58.765 45.455 0.00 0.00 0.00 3.74
2614 2635 4.081198 AGGAGTGATAGAGTGCTTTTCCTG 60.081 45.833 0.00 0.00 31.66 3.86
2652 2673 0.656785 TAACACGCAAAACCGACACC 59.343 50.000 0.00 0.00 0.00 4.16
2670 2691 3.518381 CGACACCGGAACCATACAA 57.482 52.632 9.46 0.00 0.00 2.41
2737 2758 8.515414 GTTGAGATTTAACCAATTAAGCAGACT 58.485 33.333 0.00 0.00 31.90 3.24
2812 2959 3.127533 GCCGCTGCTCCGTGATTT 61.128 61.111 0.00 0.00 33.53 2.17
2815 2962 0.179111 CCGCTGCTCCGTGATTTCTA 60.179 55.000 0.00 0.00 0.00 2.10
2818 2965 2.346803 GCTGCTCCGTGATTTCTACAA 58.653 47.619 0.00 0.00 0.00 2.41
2987 3151 4.162690 GGTCTCCAGCGGCGGAAT 62.163 66.667 9.78 0.00 33.65 3.01
2988 3152 2.792947 GGTCTCCAGCGGCGGAATA 61.793 63.158 9.78 4.08 33.65 1.75
2989 3153 1.367840 GTCTCCAGCGGCGGAATAT 59.632 57.895 9.78 0.00 33.65 1.28
2990 3154 0.667792 GTCTCCAGCGGCGGAATATC 60.668 60.000 9.78 0.00 33.65 1.63
2991 3155 1.112916 TCTCCAGCGGCGGAATATCA 61.113 55.000 9.78 0.00 33.65 2.15
2992 3156 0.249868 CTCCAGCGGCGGAATATCAA 60.250 55.000 9.78 0.00 33.65 2.57
2993 3157 0.531974 TCCAGCGGCGGAATATCAAC 60.532 55.000 9.78 0.00 29.93 3.18
2994 3158 1.507141 CCAGCGGCGGAATATCAACC 61.507 60.000 9.78 0.00 0.00 3.77
2995 3159 1.227853 AGCGGCGGAATATCAACCC 60.228 57.895 9.78 0.00 0.00 4.11
2996 3160 2.258726 GCGGCGGAATATCAACCCC 61.259 63.158 9.78 0.00 0.00 4.95
2997 3161 1.599797 CGGCGGAATATCAACCCCC 60.600 63.158 0.00 0.00 0.00 5.40
2998 3162 1.599797 GGCGGAATATCAACCCCCG 60.600 63.158 0.00 0.00 42.74 5.73
2999 3163 4.058797 CGGAATATCAACCCCCGC 57.941 61.111 0.00 0.00 33.47 6.13
3000 3164 1.959226 CGGAATATCAACCCCCGCG 60.959 63.158 0.00 0.00 33.47 6.46
3001 3165 1.599797 GGAATATCAACCCCCGCGG 60.600 63.158 21.04 21.04 37.81 6.46
3017 3181 3.320014 GGCCCCGCCTACCTATCC 61.320 72.222 0.00 0.00 46.69 2.59
3043 3207 1.099879 GGCGAGCAGATTTCATGGCT 61.100 55.000 0.00 0.00 39.75 4.75
3051 3215 2.652893 GATTTCATGGCTGCGGCGAC 62.653 60.000 12.98 2.02 39.81 5.19
3066 3230 1.501741 CGACCAGTTTTCATGGCGG 59.498 57.895 0.00 0.00 41.87 6.13
3082 3246 3.047877 GGCGGCGTTACTTGCTGT 61.048 61.111 9.37 0.00 40.87 4.40
3116 3280 0.396974 TGTGAGGCAAGGGCTGTTTT 60.397 50.000 0.00 0.00 38.98 2.43
3179 3344 2.624557 GGAGAGAAAGGAGTCTGGGCTA 60.625 54.545 0.00 0.00 0.00 3.93
3236 3406 1.398390 GACACCAAACATCGATCCAGC 59.602 52.381 0.00 0.00 0.00 4.85
3248 3418 4.406648 TCGATCCAGCACTCAACATTAT 57.593 40.909 0.00 0.00 0.00 1.28
3249 3419 4.769688 TCGATCCAGCACTCAACATTATT 58.230 39.130 0.00 0.00 0.00 1.40
3250 3420 5.185454 TCGATCCAGCACTCAACATTATTT 58.815 37.500 0.00 0.00 0.00 1.40
3251 3421 5.647658 TCGATCCAGCACTCAACATTATTTT 59.352 36.000 0.00 0.00 0.00 1.82
3252 3422 6.150976 TCGATCCAGCACTCAACATTATTTTT 59.849 34.615 0.00 0.00 0.00 1.94
3276 3446 9.678941 TTTTCTACATCAGTACATATAGAAGCG 57.321 33.333 0.00 0.00 32.03 4.68
3277 3447 6.843208 TCTACATCAGTACATATAGAAGCGC 58.157 40.000 0.00 0.00 0.00 5.92
3278 3448 5.713792 ACATCAGTACATATAGAAGCGCT 57.286 39.130 2.64 2.64 0.00 5.92
3279 3449 5.704888 ACATCAGTACATATAGAAGCGCTC 58.295 41.667 12.06 4.30 0.00 5.03
3280 3450 5.241728 ACATCAGTACATATAGAAGCGCTCA 59.758 40.000 12.06 0.00 0.00 4.26
3281 3451 5.966742 TCAGTACATATAGAAGCGCTCAT 57.033 39.130 12.06 7.40 0.00 2.90
3282 3452 5.703876 TCAGTACATATAGAAGCGCTCATG 58.296 41.667 12.06 11.91 0.00 3.07
3283 3453 5.241728 TCAGTACATATAGAAGCGCTCATGT 59.758 40.000 12.06 16.87 36.72 3.21
3284 3454 6.430000 TCAGTACATATAGAAGCGCTCATGTA 59.570 38.462 12.06 15.89 35.33 2.29
3285 3455 6.524933 CAGTACATATAGAAGCGCTCATGTAC 59.475 42.308 28.88 28.88 45.20 2.90
3286 3456 5.453567 ACATATAGAAGCGCTCATGTACA 57.546 39.130 12.06 0.00 33.18 2.90
3287 3457 5.223382 ACATATAGAAGCGCTCATGTACAC 58.777 41.667 12.06 0.00 33.18 2.90
3288 3458 3.801114 ATAGAAGCGCTCATGTACACA 57.199 42.857 12.06 0.00 0.00 3.72
3289 3459 2.680312 AGAAGCGCTCATGTACACAT 57.320 45.000 12.06 0.00 36.96 3.21
3290 3460 2.977914 AGAAGCGCTCATGTACACATT 58.022 42.857 12.06 0.00 33.61 2.71
3291 3461 4.123497 AGAAGCGCTCATGTACACATTA 57.877 40.909 12.06 0.00 33.61 1.90
3292 3462 4.697514 AGAAGCGCTCATGTACACATTAT 58.302 39.130 12.06 0.00 33.61 1.28
3293 3463 5.118990 AGAAGCGCTCATGTACACATTATT 58.881 37.500 12.06 0.00 33.61 1.40
3294 3464 5.586243 AGAAGCGCTCATGTACACATTATTT 59.414 36.000 12.06 0.00 33.61 1.40
3295 3465 5.818136 AGCGCTCATGTACACATTATTTT 57.182 34.783 2.64 0.00 33.61 1.82
3296 3466 6.194796 AGCGCTCATGTACACATTATTTTT 57.805 33.333 2.64 0.00 33.61 1.94
3346 3516 9.614792 AAAACTGTGTCTAAGAAAATACTGTCT 57.385 29.630 0.00 0.00 0.00 3.41
3347 3517 8.819643 AACTGTGTCTAAGAAAATACTGTCTC 57.180 34.615 0.00 0.00 0.00 3.36
3348 3518 7.952671 ACTGTGTCTAAGAAAATACTGTCTCA 58.047 34.615 0.00 0.00 0.00 3.27
3349 3519 8.421784 ACTGTGTCTAAGAAAATACTGTCTCAA 58.578 33.333 0.00 0.00 0.00 3.02
3350 3520 9.261180 CTGTGTCTAAGAAAATACTGTCTCAAA 57.739 33.333 0.00 0.00 0.00 2.69
3351 3521 9.607988 TGTGTCTAAGAAAATACTGTCTCAAAA 57.392 29.630 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.045213 TCAAGGATTAGCTGGTATTGGTGAA 60.045 40.000 0.00 0.00 0.00 3.18
29 30 2.175715 AGGGAATGGGTCAAGGATTAGC 59.824 50.000 0.00 0.00 0.00 3.09
55 56 5.952526 TTCGGGTCAAGGATTAGTTTTTC 57.047 39.130 0.00 0.00 0.00 2.29
87 88 2.597455 TCCGCTCTGGTCATCATGATA 58.403 47.619 8.15 0.00 39.52 2.15
105 106 4.099573 TCTGGTCTCCGTTTCATTAGATCC 59.900 45.833 0.00 0.00 0.00 3.36
166 167 0.813821 CCAGAGGCTTAAGCTTTGGC 59.186 55.000 25.88 10.89 41.70 4.52
276 277 0.107945 GCCAAGGAGACCAGTAGCAG 60.108 60.000 0.00 0.00 0.00 4.24
577 587 5.255687 TGACATCAATAACAAGGATGCTGT 58.744 37.500 0.00 0.00 41.58 4.40
1047 1058 5.239306 TGGAATATTGCCGATGAACTCATTC 59.761 40.000 4.35 0.00 36.57 2.67
1164 1175 4.245660 TGAGGTCAATTGTCACGAGATTC 58.754 43.478 5.13 0.00 0.00 2.52
1173 1184 4.458989 TGGTTGCTATTGAGGTCAATTGTC 59.541 41.667 10.39 0.00 43.48 3.18
1222 1233 2.024176 TTCGGCAGGCTTATGAAGTC 57.976 50.000 0.00 0.00 0.00 3.01
1251 1262 9.818796 GTGAAGTCATTGAAAAGAAGATCTAAC 57.181 33.333 0.00 0.00 0.00 2.34
1294 1305 2.989840 GCTTACTGCAGGAGTATATGCG 59.010 50.000 19.93 0.00 45.54 4.73
1311 1322 1.902508 AGCCTTAGTGCAGTCAGCTTA 59.097 47.619 0.00 0.00 45.94 3.09
1461 1472 5.388654 CCAATATAAAGGATGGTGAGGCTT 58.611 41.667 0.00 0.00 0.00 4.35
1898 1910 2.820728 TAACTGACCGATCTCCTCCA 57.179 50.000 0.00 0.00 0.00 3.86
1920 1932 1.812235 AATTGAGTGCGATGAGTGCA 58.188 45.000 0.00 0.00 40.70 4.57
1922 1934 4.093998 AGCTTAAATTGAGTGCGATGAGTG 59.906 41.667 0.00 0.00 0.00 3.51
2219 2232 2.992847 TCTGTAGGAAGTGGAGGTCA 57.007 50.000 0.00 0.00 0.00 4.02
2220 2233 4.202326 TGTTTTCTGTAGGAAGTGGAGGTC 60.202 45.833 0.00 0.00 35.16 3.85
2222 2235 4.202367 ACTGTTTTCTGTAGGAAGTGGAGG 60.202 45.833 0.00 0.00 35.16 4.30
2241 2254 5.680619 TGTTTGACCTTACATCTGAACTGT 58.319 37.500 0.00 0.00 0.00 3.55
2242 2255 5.760253 ACTGTTTGACCTTACATCTGAACTG 59.240 40.000 0.00 0.00 0.00 3.16
2243 2256 5.930135 ACTGTTTGACCTTACATCTGAACT 58.070 37.500 0.00 0.00 0.00 3.01
2244 2257 6.260050 TGAACTGTTTGACCTTACATCTGAAC 59.740 38.462 0.00 0.00 0.00 3.18
2245 2258 6.353323 TGAACTGTTTGACCTTACATCTGAA 58.647 36.000 0.00 0.00 0.00 3.02
2246 2259 5.924356 TGAACTGTTTGACCTTACATCTGA 58.076 37.500 0.00 0.00 0.00 3.27
2247 2260 5.991606 TCTGAACTGTTTGACCTTACATCTG 59.008 40.000 0.00 0.00 0.00 2.90
2248 2261 6.174720 TCTGAACTGTTTGACCTTACATCT 57.825 37.500 0.00 0.00 0.00 2.90
2249 2262 6.428159 ACATCTGAACTGTTTGACCTTACATC 59.572 38.462 0.00 0.00 0.00 3.06
2250 2263 6.299141 ACATCTGAACTGTTTGACCTTACAT 58.701 36.000 0.00 0.00 0.00 2.29
2251 2264 5.680619 ACATCTGAACTGTTTGACCTTACA 58.319 37.500 0.00 0.00 0.00 2.41
2252 2265 7.095187 CCTTACATCTGAACTGTTTGACCTTAC 60.095 40.741 0.00 0.00 0.00 2.34
2253 2266 6.934645 CCTTACATCTGAACTGTTTGACCTTA 59.065 38.462 0.00 0.00 0.00 2.69
2254 2267 5.765182 CCTTACATCTGAACTGTTTGACCTT 59.235 40.000 0.00 0.00 0.00 3.50
2255 2268 5.163195 ACCTTACATCTGAACTGTTTGACCT 60.163 40.000 0.00 0.00 0.00 3.85
2256 2269 5.063880 ACCTTACATCTGAACTGTTTGACC 58.936 41.667 0.00 0.00 0.00 4.02
2257 2270 5.758296 TGACCTTACATCTGAACTGTTTGAC 59.242 40.000 0.00 0.00 0.00 3.18
2258 2271 5.924356 TGACCTTACATCTGAACTGTTTGA 58.076 37.500 0.00 0.00 0.00 2.69
2259 2272 6.808008 ATGACCTTACATCTGAACTGTTTG 57.192 37.500 0.00 0.00 0.00 2.93
2330 2343 7.573968 AAATATCTAGCCAAAACCATCTGAC 57.426 36.000 0.00 0.00 0.00 3.51
2343 2356 5.228945 TGGTCTAGCCAAAATATCTAGCC 57.771 43.478 3.71 0.00 45.94 3.93
2361 2374 4.675510 CAGTGATAACAATTGCCATGGTC 58.324 43.478 14.67 6.41 0.00 4.02
2382 2397 4.847198 AGATTATGTCACAGTTCATGGCA 58.153 39.130 0.00 0.00 35.83 4.92
2407 2423 5.495926 ACTCATCTGAATTGAGAACCACT 57.504 39.130 13.66 0.00 42.63 4.00
2424 2440 3.194542 GCTGGAGACACTGACTTACTCAT 59.805 47.826 0.00 0.00 35.60 2.90
2425 2441 2.558795 GCTGGAGACACTGACTTACTCA 59.441 50.000 0.00 0.00 35.60 3.41
2427 2443 2.883026 AGCTGGAGACACTGACTTACT 58.117 47.619 0.00 0.00 35.60 2.24
2428 2444 3.005897 TGAAGCTGGAGACACTGACTTAC 59.994 47.826 0.00 0.00 35.60 2.34
2429 2445 3.230976 TGAAGCTGGAGACACTGACTTA 58.769 45.455 0.00 0.00 35.60 2.24
2439 2456 1.904537 TGATCTTGCTGAAGCTGGAGA 59.095 47.619 3.61 5.19 42.66 3.71
2448 2465 2.356432 CCAGGGATGTTGATCTTGCTGA 60.356 50.000 0.00 0.00 0.00 4.26
2479 2496 8.750416 CAGATTGAACGTCAATAACTAGAGATG 58.250 37.037 11.52 0.00 46.20 2.90
2578 2599 7.279090 ACTCTATCACTCCTCGAATATGTATCG 59.721 40.741 0.00 0.00 41.53 2.92
2614 2635 0.846693 ATGTATCCAACCCTGAGCCC 59.153 55.000 0.00 0.00 0.00 5.19
2652 2673 1.073177 GTTGTATGGTTCCGGTGTCG 58.927 55.000 0.00 0.00 0.00 4.35
2670 2691 2.934886 AACTGCAAATTGCCAATGGT 57.065 40.000 15.98 3.97 44.23 3.55
2776 2797 8.616076 GCAGCGGCTTAATTATAATCTATGATT 58.384 33.333 0.00 0.00 36.96 2.57
2797 2944 0.924090 GTAGAAATCACGGAGCAGCG 59.076 55.000 0.00 0.00 0.00 5.18
2818 2965 9.197694 CGAGGTAAATGAATCGAAATAATCTCT 57.802 33.333 0.00 0.00 37.35 3.10
2970 3134 2.100879 ATATTCCGCCGCTGGAGACC 62.101 60.000 4.52 0.00 39.72 3.85
2971 3135 0.667792 GATATTCCGCCGCTGGAGAC 60.668 60.000 4.52 0.00 39.72 3.36
2972 3136 1.112916 TGATATTCCGCCGCTGGAGA 61.113 55.000 4.52 0.00 39.72 3.71
2973 3137 0.249868 TTGATATTCCGCCGCTGGAG 60.250 55.000 4.52 0.00 39.72 3.86
2974 3138 0.531974 GTTGATATTCCGCCGCTGGA 60.532 55.000 0.00 0.52 35.83 3.86
2975 3139 1.507141 GGTTGATATTCCGCCGCTGG 61.507 60.000 0.00 0.00 0.00 4.85
2976 3140 1.507141 GGGTTGATATTCCGCCGCTG 61.507 60.000 0.00 0.00 0.00 5.18
2977 3141 1.227853 GGGTTGATATTCCGCCGCT 60.228 57.895 0.00 0.00 0.00 5.52
2978 3142 2.258726 GGGGTTGATATTCCGCCGC 61.259 63.158 0.00 0.00 0.00 6.53
2979 3143 1.599797 GGGGGTTGATATTCCGCCG 60.600 63.158 10.93 0.00 44.57 6.46
2980 3144 4.494515 GGGGGTTGATATTCCGCC 57.505 61.111 10.93 10.93 46.54 6.13
2981 3145 4.058797 CGGGGGTTGATATTCCGC 57.941 61.111 0.00 0.00 34.17 5.54
2982 3146 1.959226 CGCGGGGGTTGATATTCCG 60.959 63.158 0.00 0.00 43.13 4.30
2983 3147 1.599797 CCGCGGGGGTTGATATTCC 60.600 63.158 20.10 0.00 0.00 3.01
2984 3148 2.258726 GCCGCGGGGGTTGATATTC 61.259 63.158 29.38 0.41 38.44 1.75
2985 3149 2.203294 GCCGCGGGGGTTGATATT 60.203 61.111 29.38 0.00 38.44 1.28
2986 3150 4.265056 GGCCGCGGGGGTTGATAT 62.265 66.667 29.38 0.00 38.44 1.63
3001 3165 2.203803 AGGATAGGTAGGCGGGGC 60.204 66.667 0.00 0.00 0.00 5.80
3017 3181 2.859273 AAATCTGCTCGCCACCGGAG 62.859 60.000 9.46 0.00 34.56 4.63
3043 3207 1.599518 ATGAAAACTGGTCGCCGCA 60.600 52.632 0.00 0.00 0.00 5.69
3051 3215 2.179018 CGCCGCCATGAAAACTGG 59.821 61.111 0.00 0.00 36.81 4.00
3066 3230 1.956620 GAGACAGCAAGTAACGCCGC 61.957 60.000 0.00 0.00 0.00 6.53
3097 3261 0.396974 AAAACAGCCCTTGCCTCACA 60.397 50.000 0.00 0.00 38.69 3.58
3116 3280 8.749841 TTGTCTCATCAAAAACGAAAAGAAAA 57.250 26.923 0.00 0.00 0.00 2.29
3120 3284 5.173854 GCCTTGTCTCATCAAAAACGAAAAG 59.826 40.000 0.00 0.00 0.00 2.27
3124 3288 3.210227 TGCCTTGTCTCATCAAAAACGA 58.790 40.909 0.00 0.00 0.00 3.85
3125 3289 3.624326 TGCCTTGTCTCATCAAAAACG 57.376 42.857 0.00 0.00 0.00 3.60
3126 3290 4.301628 CCTTGCCTTGTCTCATCAAAAAC 58.698 43.478 0.00 0.00 0.00 2.43
3128 3292 2.892852 CCCTTGCCTTGTCTCATCAAAA 59.107 45.455 0.00 0.00 0.00 2.44
3129 3293 2.517959 CCCTTGCCTTGTCTCATCAAA 58.482 47.619 0.00 0.00 0.00 2.69
3130 3294 1.887956 GCCCTTGCCTTGTCTCATCAA 60.888 52.381 0.00 0.00 0.00 2.57
3131 3295 0.322816 GCCCTTGCCTTGTCTCATCA 60.323 55.000 0.00 0.00 0.00 3.07
3132 3296 0.034670 AGCCCTTGCCTTGTCTCATC 60.035 55.000 0.00 0.00 38.69 2.92
3133 3297 0.323178 CAGCCCTTGCCTTGTCTCAT 60.323 55.000 0.00 0.00 38.69 2.90
3137 3301 3.376918 GCCAGCCCTTGCCTTGTC 61.377 66.667 0.00 0.00 38.69 3.18
3154 3318 1.748493 CAGACTCCTTTCTCTCCCTCG 59.252 57.143 0.00 0.00 0.00 4.63
3250 3420 9.678941 CGCTTCTATATGTACTGATGTAGAAAA 57.321 33.333 11.20 0.00 36.30 2.29
3251 3421 7.808381 GCGCTTCTATATGTACTGATGTAGAAA 59.192 37.037 0.00 1.18 36.30 2.52
3252 3422 7.175119 AGCGCTTCTATATGTACTGATGTAGAA 59.825 37.037 2.64 10.19 35.09 2.10
3253 3423 6.655425 AGCGCTTCTATATGTACTGATGTAGA 59.345 38.462 2.64 0.00 0.00 2.59
3254 3424 6.847400 AGCGCTTCTATATGTACTGATGTAG 58.153 40.000 2.64 0.00 0.00 2.74
3255 3425 6.430000 TGAGCGCTTCTATATGTACTGATGTA 59.570 38.462 13.26 0.00 0.00 2.29
3256 3426 5.241728 TGAGCGCTTCTATATGTACTGATGT 59.758 40.000 13.26 0.00 0.00 3.06
3257 3427 5.703876 TGAGCGCTTCTATATGTACTGATG 58.296 41.667 13.26 0.00 0.00 3.07
3258 3428 5.966742 TGAGCGCTTCTATATGTACTGAT 57.033 39.130 13.26 0.00 0.00 2.90
3259 3429 5.241728 ACATGAGCGCTTCTATATGTACTGA 59.758 40.000 13.26 0.00 33.52 3.41
3260 3430 5.465051 ACATGAGCGCTTCTATATGTACTG 58.535 41.667 13.26 0.00 33.52 2.74
3261 3431 5.713792 ACATGAGCGCTTCTATATGTACT 57.286 39.130 13.26 0.00 33.52 2.73
3262 3432 6.305877 GTGTACATGAGCGCTTCTATATGTAC 59.694 42.308 30.16 30.16 45.06 2.90
3263 3433 6.016610 TGTGTACATGAGCGCTTCTATATGTA 60.017 38.462 13.26 17.46 35.55 2.29
3264 3434 5.221244 TGTGTACATGAGCGCTTCTATATGT 60.221 40.000 13.26 18.41 36.90 2.29
3265 3435 5.222631 TGTGTACATGAGCGCTTCTATATG 58.777 41.667 13.26 13.76 0.00 1.78
3266 3436 5.453567 TGTGTACATGAGCGCTTCTATAT 57.546 39.130 13.26 0.00 0.00 0.86
3267 3437 4.911514 TGTGTACATGAGCGCTTCTATA 57.088 40.909 13.26 0.00 0.00 1.31
3268 3438 3.801114 TGTGTACATGAGCGCTTCTAT 57.199 42.857 13.26 3.91 0.00 1.98
3269 3439 3.801114 ATGTGTACATGAGCGCTTCTA 57.199 42.857 13.26 1.08 34.83 2.10
3270 3440 2.680312 ATGTGTACATGAGCGCTTCT 57.320 45.000 13.26 0.00 34.83 2.85
3271 3441 5.409643 AATAATGTGTACATGAGCGCTTC 57.590 39.130 13.26 5.55 36.56 3.86
3272 3442 5.818136 AAATAATGTGTACATGAGCGCTT 57.182 34.783 13.26 0.00 36.56 4.68
3273 3443 5.818136 AAAATAATGTGTACATGAGCGCT 57.182 34.783 11.27 11.27 36.56 5.92
3320 3490 9.614792 AGACAGTATTTTCTTAGACACAGTTTT 57.385 29.630 0.00 0.00 0.00 2.43
3321 3491 9.262358 GAGACAGTATTTTCTTAGACACAGTTT 57.738 33.333 0.00 0.00 0.00 2.66
3322 3492 8.421784 TGAGACAGTATTTTCTTAGACACAGTT 58.578 33.333 0.00 0.00 0.00 3.16
3323 3493 7.952671 TGAGACAGTATTTTCTTAGACACAGT 58.047 34.615 0.00 0.00 0.00 3.55
3324 3494 8.818141 TTGAGACAGTATTTTCTTAGACACAG 57.182 34.615 0.00 0.00 0.00 3.66
3325 3495 9.607988 TTTTGAGACAGTATTTTCTTAGACACA 57.392 29.630 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.