Multiple sequence alignment - TraesCS1D01G398100

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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 TraesCS1D01G398100 chr1D 100.000 3068 0 0 1 3068 465351683 465348616 0.000000e+00 5666.0
1 TraesCS1D01G398100 chr1D 99.346 153 0 1 2095 2247 465349448 465349297 3.010000e-70 276.0
2 TraesCS1D01G398100 chr1D 99.346 153 0 1 2236 2387 465349589 465349437 3.010000e-70 276.0
3 TraesCS1D01G398100 chr1A 90.957 2267 96 35 1 2227 557874346 557872149 0.000000e+00 2950.0
4 TraesCS1D01G398100 chr1A 83.943 629 39 23 2435 3015 557865431 557864817 2.080000e-151 545.0
5 TraesCS1D01G398100 chr1B 90.445 2292 116 40 1 2248 642123929 642121697 0.000000e+00 2924.0
6 TraesCS1D01G398100 chr1B 85.561 838 55 27 2236 3015 642121870 642121041 0.000000e+00 817.0
7 TraesCS1D01G398100 chr4B 88.889 261 27 2 1424 1683 429345171 429344912 1.370000e-83 320.0
8 TraesCS1D01G398100 chr4B 86.517 89 6 2 2893 2981 82372323 82372405 3.260000e-15 93.5
9 TraesCS1D01G398100 chr4B 98.000 50 0 1 3019 3068 82372405 82372453 5.450000e-13 86.1
10 TraesCS1D01G398100 chr6D 80.902 377 40 19 1128 1497 460161834 460161483 5.040000e-68 268.0
11 TraesCS1D01G398100 chr2A 88.725 204 15 6 1942 2142 348213862 348214060 3.060000e-60 243.0
12 TraesCS1D01G398100 chr2A 93.333 75 4 1 1825 1898 348213791 348213865 3.230000e-20 110.0
13 TraesCS1D01G398100 chr2B 82.530 166 21 4 1332 1496 775136865 775136707 4.130000e-29 139.0
14 TraesCS1D01G398100 chr5B 97.619 42 1 0 3019 3060 472121798 472121757 4.240000e-09 73.1


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 TraesCS1D01G398100 chr1D 465348616 465351683 3067 True 2072.666667 5666 99.564 1 3068 3 chr1D.!!$R1 3067
1 TraesCS1D01G398100 chr1A 557872149 557874346 2197 True 2950.000000 2950 90.957 1 2227 1 chr1A.!!$R2 2226
2 TraesCS1D01G398100 chr1A 557864817 557865431 614 True 545.000000 545 83.943 2435 3015 1 chr1A.!!$R1 580
3 TraesCS1D01G398100 chr1B 642121041 642123929 2888 True 1870.500000 2924 88.003 1 3015 2 chr1B.!!$R1 3014

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
169 178 0.107831 GTCACCAACCAGCACCAGTA 59.892 55.0 0.0 0.0 0.0 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 2193 0.173708 CTAACGGAGTGGAGTGGAGC 59.826 60.0 0.0 0.0 45.0 4.7 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
87 88 3.332919 CTCCTCCAATAATGCAGATCGG 58.667 50.000 0.00 0.00 0.00 4.18
115 116 1.489481 TCTACATCCACTGAGGCAGG 58.511 55.000 0.00 0.00 35.51 4.85
161 170 1.881973 CATCACCAAGTCACCAACCAG 59.118 52.381 0.00 0.00 0.00 4.00
164 173 0.751643 ACCAAGTCACCAACCAGCAC 60.752 55.000 0.00 0.00 0.00 4.40
168 177 1.152963 GTCACCAACCAGCACCAGT 60.153 57.895 0.00 0.00 0.00 4.00
169 178 0.107831 GTCACCAACCAGCACCAGTA 59.892 55.000 0.00 0.00 0.00 2.74
214 223 1.024046 CATGATTGCACGGTTCCGGA 61.024 55.000 15.66 0.00 0.00 5.14
217 226 1.359459 GATTGCACGGTTCCGGAGAC 61.359 60.000 15.66 6.24 0.00 3.36
327 341 0.830023 TCCCAGTGTCACATCCGTCA 60.830 55.000 5.62 0.00 0.00 4.35
382 396 3.142838 TCCGGTAGGTGCGGCTAC 61.143 66.667 0.00 0.00 39.05 3.58
386 400 2.794028 GGTAGGTGCGGCTACCCTC 61.794 68.421 15.05 9.92 41.83 4.30
387 401 2.056223 GTAGGTGCGGCTACCCTCA 61.056 63.158 15.05 2.48 41.83 3.86
388 402 1.075525 TAGGTGCGGCTACCCTCAT 60.076 57.895 15.05 3.29 41.83 2.90
389 403 1.399744 TAGGTGCGGCTACCCTCATG 61.400 60.000 15.05 0.00 41.83 3.07
390 404 2.203070 GTGCGGCTACCCTCATGG 60.203 66.667 0.00 0.00 41.37 3.66
402 416 0.471191 CCTCATGGCTCATGCACCTA 59.529 55.000 9.54 0.00 41.18 3.08
498 513 2.984155 GCTCCCCGGATCGATCGA 60.984 66.667 21.86 21.86 0.00 3.59
729 757 2.690778 GCTGTTAAGTGCCCGCCTG 61.691 63.158 0.00 0.00 0.00 4.85
730 758 2.671619 TGTTAAGTGCCCGCCTGC 60.672 61.111 0.00 0.00 0.00 4.85
731 759 3.799755 GTTAAGTGCCCGCCTGCG 61.800 66.667 4.20 4.20 39.44 5.18
816 879 0.601311 GCTCGCCACCTCCATATCAC 60.601 60.000 0.00 0.00 0.00 3.06
818 881 1.071471 CGCCACCTCCATATCACCC 59.929 63.158 0.00 0.00 0.00 4.61
819 882 1.071471 GCCACCTCCATATCACCCG 59.929 63.158 0.00 0.00 0.00 5.28
820 883 1.407656 GCCACCTCCATATCACCCGA 61.408 60.000 0.00 0.00 0.00 5.14
821 884 0.681733 CCACCTCCATATCACCCGAG 59.318 60.000 0.00 0.00 0.00 4.63
822 885 1.704641 CACCTCCATATCACCCGAGA 58.295 55.000 0.00 0.00 0.00 4.04
825 888 0.242286 CTCCATATCACCCGAGAGCG 59.758 60.000 0.00 0.00 37.24 5.03
826 889 0.179001 TCCATATCACCCGAGAGCGA 60.179 55.000 0.00 0.00 40.82 4.93
828 891 0.387878 CATATCACCCGAGAGCGAGC 60.388 60.000 0.00 0.00 40.82 5.03
829 892 1.857318 ATATCACCCGAGAGCGAGCG 61.857 60.000 0.00 0.00 40.82 5.03
830 893 2.935627 TATCACCCGAGAGCGAGCGA 62.936 60.000 0.00 0.00 40.82 4.93
845 908 2.052690 GCGAGCTACCTCCACCTCA 61.053 63.158 0.00 0.00 34.49 3.86
874 937 3.051479 GTAACAACCCACCCCGCG 61.051 66.667 0.00 0.00 0.00 6.46
1133 1196 1.006337 CCACGCCCAACAACAATGG 60.006 57.895 0.00 0.00 37.71 3.16
1535 1601 1.407989 GGAGATGGAGGCCACAGAAAG 60.408 57.143 5.01 0.00 35.80 2.62
2142 2208 4.135153 CCGCTCCACTCCACTCCG 62.135 72.222 0.00 0.00 0.00 4.63
2143 2209 3.374402 CGCTCCACTCCACTCCGT 61.374 66.667 0.00 0.00 0.00 4.69
2146 2212 0.173708 GCTCCACTCCACTCCGTTAG 59.826 60.000 0.00 0.00 0.00 2.34
2168 2234 1.269309 CCGAAGCTCGAGTAGAATGGG 60.269 57.143 15.13 3.17 43.74 4.00
2169 2235 1.269309 CGAAGCTCGAGTAGAATGGGG 60.269 57.143 15.13 0.00 43.74 4.96
2216 2294 0.749049 TCATCAGCGGACTGGATCTG 59.251 55.000 0.00 0.00 44.59 2.90
2217 2295 0.749049 CATCAGCGGACTGGATCTGA 59.251 55.000 0.00 0.00 44.59 3.27
2218 2296 1.343789 CATCAGCGGACTGGATCTGAT 59.656 52.381 0.00 0.00 44.44 2.90
2219 2297 1.489481 TCAGCGGACTGGATCTGATT 58.511 50.000 0.00 0.00 44.59 2.57
2220 2298 2.666317 TCAGCGGACTGGATCTGATTA 58.334 47.619 0.00 0.00 44.59 1.75
2221 2299 2.625314 TCAGCGGACTGGATCTGATTAG 59.375 50.000 0.00 0.00 44.59 1.73
2222 2300 1.967066 AGCGGACTGGATCTGATTAGG 59.033 52.381 0.00 0.00 35.44 2.69
2223 2301 1.606737 GCGGACTGGATCTGATTAGGC 60.607 57.143 0.00 0.00 35.44 3.93
2224 2302 1.336332 CGGACTGGATCTGATTAGGCG 60.336 57.143 0.00 0.00 35.44 5.52
2225 2303 1.001406 GGACTGGATCTGATTAGGCGG 59.999 57.143 0.00 0.00 0.00 6.13
2226 2304 0.394565 ACTGGATCTGATTAGGCGGC 59.605 55.000 0.00 0.00 0.00 6.53
2227 2305 0.668706 CTGGATCTGATTAGGCGGCG 60.669 60.000 0.51 0.51 0.00 6.46
2228 2306 2.029844 GGATCTGATTAGGCGGCGC 61.030 63.158 26.17 26.17 0.00 6.53
2270 2348 4.500116 GTCGGCCTCACTCCGCTC 62.500 72.222 0.00 0.00 46.05 5.03
2273 2351 4.459089 GGCCTCACTCCGCTCCAC 62.459 72.222 0.00 0.00 0.00 4.02
2274 2352 3.386237 GCCTCACTCCGCTCCACT 61.386 66.667 0.00 0.00 0.00 4.00
2275 2353 2.888863 CCTCACTCCGCTCCACTC 59.111 66.667 0.00 0.00 0.00 3.51
2276 2354 2.716017 CCTCACTCCGCTCCACTCC 61.716 68.421 0.00 0.00 0.00 3.85
2277 2355 1.979155 CTCACTCCGCTCCACTCCA 60.979 63.158 0.00 0.00 0.00 3.86
2278 2356 2.219325 CTCACTCCGCTCCACTCCAC 62.219 65.000 0.00 0.00 0.00 4.02
2279 2357 2.118513 ACTCCGCTCCACTCCACT 59.881 61.111 0.00 0.00 0.00 4.00
2280 2358 1.979693 ACTCCGCTCCACTCCACTC 60.980 63.158 0.00 0.00 0.00 3.51
2281 2359 2.680352 TCCGCTCCACTCCACTCC 60.680 66.667 0.00 0.00 0.00 3.85
2282 2360 4.135153 CCGCTCCACTCCACTCCG 62.135 72.222 0.00 0.00 0.00 4.63
2283 2361 3.374402 CGCTCCACTCCACTCCGT 61.374 66.667 0.00 0.00 0.00 4.69
2284 2362 2.932234 CGCTCCACTCCACTCCGTT 61.932 63.158 0.00 0.00 0.00 4.44
2285 2363 1.592400 CGCTCCACTCCACTCCGTTA 61.592 60.000 0.00 0.00 0.00 3.18
2286 2364 0.173708 GCTCCACTCCACTCCGTTAG 59.826 60.000 0.00 0.00 0.00 2.34
2287 2365 1.835494 CTCCACTCCACTCCGTTAGA 58.165 55.000 0.00 0.00 0.00 2.10
2288 2366 1.473278 CTCCACTCCACTCCGTTAGAC 59.527 57.143 0.00 0.00 0.00 2.59
2289 2367 0.531200 CCACTCCACTCCGTTAGACC 59.469 60.000 0.00 0.00 0.00 3.85
2290 2368 0.170561 CACTCCACTCCGTTAGACCG 59.829 60.000 0.00 0.00 0.00 4.79
2291 2369 0.037303 ACTCCACTCCGTTAGACCGA 59.963 55.000 0.00 0.00 0.00 4.69
2292 2370 1.171308 CTCCACTCCGTTAGACCGAA 58.829 55.000 0.00 0.00 0.00 4.30
2293 2371 1.132643 CTCCACTCCGTTAGACCGAAG 59.867 57.143 0.00 0.00 0.00 3.79
2294 2372 0.458025 CCACTCCGTTAGACCGAAGC 60.458 60.000 0.00 0.00 0.00 3.86
2295 2373 0.526662 CACTCCGTTAGACCGAAGCT 59.473 55.000 0.00 0.00 0.00 3.74
2296 2374 0.810016 ACTCCGTTAGACCGAAGCTC 59.190 55.000 0.00 0.00 0.00 4.09
2297 2375 0.248134 CTCCGTTAGACCGAAGCTCG 60.248 60.000 0.00 0.00 40.07 5.03
2298 2376 0.674581 TCCGTTAGACCGAAGCTCGA 60.675 55.000 7.07 0.00 43.74 4.04
2299 2377 0.248134 CCGTTAGACCGAAGCTCGAG 60.248 60.000 8.45 8.45 43.74 4.04
2300 2378 0.447011 CGTTAGACCGAAGCTCGAGT 59.553 55.000 15.13 0.00 43.74 4.18
2301 2379 1.662629 CGTTAGACCGAAGCTCGAGTA 59.337 52.381 15.13 0.00 43.74 2.59
2302 2380 2.285718 CGTTAGACCGAAGCTCGAGTAG 60.286 54.545 15.13 3.11 43.74 2.57
2303 2381 2.935201 GTTAGACCGAAGCTCGAGTAGA 59.065 50.000 15.13 0.00 43.74 2.59
2304 2382 2.110901 AGACCGAAGCTCGAGTAGAA 57.889 50.000 15.13 0.00 43.74 2.10
2305 2383 2.645802 AGACCGAAGCTCGAGTAGAAT 58.354 47.619 15.13 0.00 43.74 2.40
2306 2384 2.356382 AGACCGAAGCTCGAGTAGAATG 59.644 50.000 15.13 1.56 43.74 2.67
2307 2385 1.405821 ACCGAAGCTCGAGTAGAATGG 59.594 52.381 15.13 11.07 43.74 3.16
2308 2386 1.269309 CCGAAGCTCGAGTAGAATGGG 60.269 57.143 15.13 3.17 43.74 4.00
2309 2387 1.269309 CGAAGCTCGAGTAGAATGGGG 60.269 57.143 15.13 0.00 43.74 4.96
2310 2388 0.466124 AAGCTCGAGTAGAATGGGGC 59.534 55.000 15.13 0.00 0.00 5.80
2311 2389 1.069935 GCTCGAGTAGAATGGGGCC 59.930 63.158 15.13 0.00 0.00 5.80
2312 2390 1.749033 CTCGAGTAGAATGGGGCCC 59.251 63.158 18.17 18.17 0.00 5.80
2313 2391 1.759459 CTCGAGTAGAATGGGGCCCC 61.759 65.000 36.14 36.14 0.00 5.80
2363 2441 1.606737 GCGGACTGGATCTGATTAGGC 60.607 57.143 0.00 0.00 35.44 3.93
2397 2479 4.263209 CGGCCGCTGTTGCAACAA 62.263 61.111 30.62 15.96 38.66 2.83
2418 2511 4.126520 ACCTTGGGTGGTTGATTACATT 57.873 40.909 0.00 0.00 36.89 2.71
2429 2522 9.003658 GGTGGTTGATTACATTAGATAATGGAG 57.996 37.037 15.17 0.00 45.54 3.86
2430 2523 9.003658 GTGGTTGATTACATTAGATAATGGAGG 57.996 37.037 15.17 0.00 45.54 4.30
2431 2524 8.723365 TGGTTGATTACATTAGATAATGGAGGT 58.277 33.333 15.17 2.12 45.54 3.85
2432 2525 9.220767 GGTTGATTACATTAGATAATGGAGGTC 57.779 37.037 15.17 9.99 45.54 3.85
2433 2526 9.778741 GTTGATTACATTAGATAATGGAGGTCA 57.221 33.333 15.17 11.90 45.54 4.02
2484 2582 5.841237 ACTAGTACTAGTGTAGGGTCCGATA 59.159 44.000 30.33 0.00 44.11 2.92
2529 2642 3.898123 AGTGGTGCCGACTATATTCATCT 59.102 43.478 0.00 0.00 0.00 2.90
2564 2682 1.746615 CTGCCTGTCCCACGAATGG 60.747 63.158 0.00 0.00 46.81 3.16
2662 2803 9.825972 CAGTTTTATGTGGTTTTACAGTAGATG 57.174 33.333 0.00 0.00 33.44 2.90
2674 2815 9.509855 GTTTTACAGTAGATGTCAGTAGATGAG 57.490 37.037 0.00 0.00 42.70 2.90
2684 2825 2.954989 TCAGTAGATGAGGCTGTGCTAG 59.045 50.000 0.00 0.00 32.77 3.42
2722 2864 0.874390 AAGCATTGCACCACAGTACG 59.126 50.000 11.91 0.00 0.00 3.67
2723 2865 0.250295 AGCATTGCACCACAGTACGT 60.250 50.000 11.91 0.00 0.00 3.57
2724 2866 1.001520 AGCATTGCACCACAGTACGTA 59.998 47.619 11.91 0.00 0.00 3.57
2725 2867 1.127951 GCATTGCACCACAGTACGTAC 59.872 52.381 18.10 18.10 0.00 3.67
2726 2868 2.409012 CATTGCACCACAGTACGTACA 58.591 47.619 26.55 3.82 0.00 2.90
2788 2930 1.025113 TAGGAGCGTCACCTCTCACG 61.025 60.000 0.00 0.00 38.76 4.35
2927 3080 1.291184 CGACTGCAACTGCGAATCCA 61.291 55.000 0.00 0.00 45.83 3.41
2999 3168 2.590007 GCAGTGGATAGGGCTGCG 60.590 66.667 0.00 0.00 44.64 5.18
3028 3198 4.782116 CACGCACGCACGATGCAG 62.782 66.667 14.58 10.69 45.36 4.41
3031 3201 4.806481 GCACGCACGATGCAGCAG 62.806 66.667 1.53 0.00 45.36 4.24
3032 3202 4.806481 CACGCACGATGCAGCAGC 62.806 66.667 1.53 0.00 45.36 5.25
3043 3213 2.877396 GCAGCAGCAGTGTTGAAAC 58.123 52.632 11.60 0.00 37.06 2.78
3044 3214 0.595825 GCAGCAGCAGTGTTGAAACC 60.596 55.000 11.60 0.00 37.06 3.27
3045 3215 0.740149 CAGCAGCAGTGTTGAAACCA 59.260 50.000 11.60 0.00 37.06 3.67
3046 3216 1.134753 CAGCAGCAGTGTTGAAACCAA 59.865 47.619 11.60 0.00 37.06 3.67
3047 3217 1.134946 AGCAGCAGTGTTGAAACCAAC 59.865 47.619 11.60 0.00 43.10 3.77
3048 3218 1.802508 GCAGCAGTGTTGAAACCAACC 60.803 52.381 11.60 0.00 42.35 3.77
3049 3219 0.738389 AGCAGTGTTGAAACCAACCG 59.262 50.000 5.93 0.00 42.35 4.44
3050 3220 0.248866 GCAGTGTTGAAACCAACCGG 60.249 55.000 0.00 0.00 42.35 5.28
3059 3229 4.497984 ACCAACCGGTGCAGTGCA 62.498 61.111 15.37 15.37 46.79 4.57
3060 3230 3.663176 CCAACCGGTGCAGTGCAG 61.663 66.667 20.42 9.88 40.08 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.882927 CAATCAACGGTGTCGGGTGT 60.883 55.000 0.00 0.00 41.39 4.16
87 88 1.542030 AGTGGATGTAGATCGATCGGC 59.458 52.381 19.33 15.78 0.00 5.54
98 99 0.909133 TGCCTGCCTCAGTGGATGTA 60.909 55.000 0.00 0.00 38.35 2.29
123 132 4.154347 GCGAGGGAGAGTGGCTGG 62.154 72.222 0.00 0.00 0.00 4.85
126 135 3.453070 GATGGCGAGGGAGAGTGGC 62.453 68.421 0.00 0.00 0.00 5.01
127 136 2.060383 TGATGGCGAGGGAGAGTGG 61.060 63.158 0.00 0.00 0.00 4.00
128 137 1.142748 GTGATGGCGAGGGAGAGTG 59.857 63.158 0.00 0.00 0.00 3.51
129 138 2.060980 GGTGATGGCGAGGGAGAGT 61.061 63.158 0.00 0.00 0.00 3.24
164 173 4.765449 TGCTGCCGCTGCTACTGG 62.765 66.667 21.13 0.00 38.71 4.00
327 341 1.001503 CAGAGAGCTGGGAGAGGGT 59.998 63.158 0.00 0.00 38.51 4.34
382 396 1.826921 GGTGCATGAGCCATGAGGG 60.827 63.158 16.46 0.00 43.81 4.30
386 400 0.179026 AGCTAGGTGCATGAGCCATG 60.179 55.000 12.31 9.94 45.94 3.66
387 401 0.108207 GAGCTAGGTGCATGAGCCAT 59.892 55.000 0.00 0.00 45.94 4.40
388 402 0.979709 AGAGCTAGGTGCATGAGCCA 60.980 55.000 0.00 0.00 45.94 4.75
389 403 0.249826 GAGAGCTAGGTGCATGAGCC 60.250 60.000 0.00 0.00 45.94 4.70
390 404 0.752054 AGAGAGCTAGGTGCATGAGC 59.248 55.000 0.00 8.88 45.94 4.26
515 530 4.995058 AGGCGGTGGGGAAGGGAA 62.995 66.667 0.00 0.00 0.00 3.97
554 569 1.446099 CAAAGCGAGTAGGCAGCGA 60.446 57.895 0.00 0.00 35.78 4.93
636 660 3.273084 TGAAAACGAGCGGCGCAA 61.273 55.556 35.02 5.56 46.04 4.85
668 692 0.674269 CGGTGCCGGGTTAAAAGCTA 60.674 55.000 2.18 0.00 35.56 3.32
669 693 1.969589 CGGTGCCGGGTTAAAAGCT 60.970 57.895 2.18 0.00 35.56 3.74
670 694 2.564458 CGGTGCCGGGTTAAAAGC 59.436 61.111 2.18 0.00 35.56 3.51
799 862 1.407656 GGGTGATATGGAGGTGGCGA 61.408 60.000 0.00 0.00 0.00 5.54
818 881 2.052590 GTAGCTCGCTCGCTCTCG 60.053 66.667 0.00 0.00 41.30 4.04
819 882 2.113131 GAGGTAGCTCGCTCGCTCTC 62.113 65.000 6.12 0.00 41.30 3.20
820 883 2.124487 AGGTAGCTCGCTCGCTCT 60.124 61.111 0.00 0.00 41.30 4.09
821 884 2.330041 GAGGTAGCTCGCTCGCTC 59.670 66.667 6.12 0.00 41.30 5.03
822 885 3.213402 GGAGGTAGCTCGCTCGCT 61.213 66.667 15.43 2.17 43.83 4.93
825 888 1.730451 GAGGTGGAGGTAGCTCGCTC 61.730 65.000 15.43 9.23 35.73 5.03
826 889 1.755008 GAGGTGGAGGTAGCTCGCT 60.755 63.158 15.43 0.00 35.73 4.93
828 891 1.810532 GTGAGGTGGAGGTAGCTCG 59.189 63.158 15.43 0.00 45.65 5.03
829 892 1.810532 CGTGAGGTGGAGGTAGCTC 59.189 63.158 13.67 13.67 43.61 4.09
830 893 2.352032 GCGTGAGGTGGAGGTAGCT 61.352 63.158 0.00 0.00 0.00 3.32
833 896 3.066190 CGGCGTGAGGTGGAGGTA 61.066 66.667 0.00 0.00 0.00 3.08
834 897 4.988716 TCGGCGTGAGGTGGAGGT 62.989 66.667 6.85 0.00 0.00 3.85
845 908 0.936297 GTTGTTACGTCTGTCGGCGT 60.936 55.000 6.85 0.00 44.69 5.68
1068 1131 2.758089 GGTGCTGAAGATGCCGCAG 61.758 63.158 0.00 0.00 32.38 5.18
1071 1134 2.758089 GCAGGTGCTGAAGATGCCG 61.758 63.158 0.00 0.00 38.21 5.69
1146 1209 4.344865 CCACCCTTCACCCCACCG 62.345 72.222 0.00 0.00 0.00 4.94
1323 1389 0.740164 TCGACGAGGACGAGGAAGAG 60.740 60.000 0.00 0.00 42.66 2.85
1535 1601 2.251371 GCGGCACCGTCTTTGAAC 59.749 61.111 11.27 0.00 42.09 3.18
2072 2138 2.421424 GGGTTGCTACTTGCTTCATCAG 59.579 50.000 0.00 0.00 43.37 2.90
2073 2139 2.436417 GGGTTGCTACTTGCTTCATCA 58.564 47.619 0.00 0.00 43.37 3.07
2076 2142 1.234615 GCGGGTTGCTACTTGCTTCA 61.235 55.000 0.00 0.00 43.37 3.02
2079 2145 2.359975 GGCGGGTTGCTACTTGCT 60.360 61.111 12.78 0.00 45.43 3.91
2080 2146 3.799755 CGGCGGGTTGCTACTTGC 61.800 66.667 0.00 2.74 45.43 4.01
2081 2147 3.124921 CCGGCGGGTTGCTACTTG 61.125 66.667 20.56 0.00 45.43 3.16
2127 2193 0.173708 CTAACGGAGTGGAGTGGAGC 59.826 60.000 0.00 0.00 45.00 4.70
2142 2208 2.935201 TCTACTCGAGCTTCGGTCTAAC 59.065 50.000 13.61 0.00 40.88 2.34
2143 2209 3.257469 TCTACTCGAGCTTCGGTCTAA 57.743 47.619 13.61 0.00 40.88 2.10
2146 2212 2.541999 CCATTCTACTCGAGCTTCGGTC 60.542 54.545 13.61 0.00 40.88 4.79
2198 2276 0.749049 TCAGATCCAGTCCGCTGATG 59.251 55.000 0.00 0.00 45.28 3.07
2256 2334 4.459089 GTGGAGCGGAGTGAGGCC 62.459 72.222 0.00 0.00 0.00 5.19
2257 2335 3.363844 GAGTGGAGCGGAGTGAGGC 62.364 68.421 0.00 0.00 0.00 4.70
2258 2336 2.716017 GGAGTGGAGCGGAGTGAGG 61.716 68.421 0.00 0.00 0.00 3.86
2259 2337 1.979155 TGGAGTGGAGCGGAGTGAG 60.979 63.158 0.00 0.00 0.00 3.51
2260 2338 2.117423 TGGAGTGGAGCGGAGTGA 59.883 61.111 0.00 0.00 0.00 3.41
2261 2339 2.219325 GAGTGGAGTGGAGCGGAGTG 62.219 65.000 0.00 0.00 0.00 3.51
2262 2340 1.979693 GAGTGGAGTGGAGCGGAGT 60.980 63.158 0.00 0.00 0.00 3.85
2263 2341 2.716017 GGAGTGGAGTGGAGCGGAG 61.716 68.421 0.00 0.00 0.00 4.63
2264 2342 2.680352 GGAGTGGAGTGGAGCGGA 60.680 66.667 0.00 0.00 0.00 5.54
2265 2343 4.135153 CGGAGTGGAGTGGAGCGG 62.135 72.222 0.00 0.00 0.00 5.52
2266 2344 1.592400 TAACGGAGTGGAGTGGAGCG 61.592 60.000 0.00 0.00 45.00 5.03
2267 2345 0.173708 CTAACGGAGTGGAGTGGAGC 59.826 60.000 0.00 0.00 45.00 4.70
2268 2346 1.473278 GTCTAACGGAGTGGAGTGGAG 59.527 57.143 0.00 0.00 45.00 3.86
2269 2347 1.542492 GTCTAACGGAGTGGAGTGGA 58.458 55.000 0.00 0.00 45.00 4.02
2270 2348 0.531200 GGTCTAACGGAGTGGAGTGG 59.469 60.000 0.00 0.00 45.00 4.00
2271 2349 0.170561 CGGTCTAACGGAGTGGAGTG 59.829 60.000 0.00 0.00 45.00 3.51
2272 2350 0.037303 TCGGTCTAACGGAGTGGAGT 59.963 55.000 0.00 0.00 45.00 3.85
2273 2351 1.132643 CTTCGGTCTAACGGAGTGGAG 59.867 57.143 0.00 0.00 45.00 3.86
2274 2352 1.171308 CTTCGGTCTAACGGAGTGGA 58.829 55.000 0.00 0.00 45.00 4.02
2275 2353 0.458025 GCTTCGGTCTAACGGAGTGG 60.458 60.000 0.00 0.00 45.00 4.00
2276 2354 0.526662 AGCTTCGGTCTAACGGAGTG 59.473 55.000 0.00 0.00 45.00 3.51
2277 2355 2.869999 CGAGCTTCGGTCTAACGGAGT 61.870 57.143 0.00 0.00 41.52 3.85
2278 2356 0.248134 CGAGCTTCGGTCTAACGGAG 60.248 60.000 0.00 0.00 42.37 4.63
2279 2357 0.674581 TCGAGCTTCGGTCTAACGGA 60.675 55.000 5.87 0.00 40.88 4.69
2280 2358 0.248134 CTCGAGCTTCGGTCTAACGG 60.248 60.000 0.00 0.00 40.88 4.44
2281 2359 0.447011 ACTCGAGCTTCGGTCTAACG 59.553 55.000 13.61 0.00 40.88 3.18
2282 2360 2.935201 TCTACTCGAGCTTCGGTCTAAC 59.065 50.000 13.61 0.00 40.88 2.34
2283 2361 3.257469 TCTACTCGAGCTTCGGTCTAA 57.743 47.619 13.61 0.00 40.88 2.10
2284 2362 2.975732 TCTACTCGAGCTTCGGTCTA 57.024 50.000 13.61 0.00 40.88 2.59
2285 2363 2.110901 TTCTACTCGAGCTTCGGTCT 57.889 50.000 13.61 0.00 40.88 3.85
2286 2364 2.541999 CCATTCTACTCGAGCTTCGGTC 60.542 54.545 13.61 0.00 40.88 4.79
2287 2365 1.405821 CCATTCTACTCGAGCTTCGGT 59.594 52.381 13.61 0.00 40.88 4.69
2288 2366 1.269309 CCCATTCTACTCGAGCTTCGG 60.269 57.143 13.61 5.80 40.88 4.30
2289 2367 1.269309 CCCCATTCTACTCGAGCTTCG 60.269 57.143 13.61 0.00 42.10 3.79
2290 2368 1.539280 GCCCCATTCTACTCGAGCTTC 60.539 57.143 13.61 0.00 0.00 3.86
2291 2369 0.466124 GCCCCATTCTACTCGAGCTT 59.534 55.000 13.61 0.00 0.00 3.74
2292 2370 1.403687 GGCCCCATTCTACTCGAGCT 61.404 60.000 13.61 2.35 0.00 4.09
2293 2371 1.069935 GGCCCCATTCTACTCGAGC 59.930 63.158 13.61 0.00 0.00 5.03
2294 2372 1.749033 GGGCCCCATTCTACTCGAG 59.251 63.158 12.23 11.84 0.00 4.04
2295 2373 1.764854 GGGGCCCCATTCTACTCGA 60.765 63.158 37.61 0.00 35.81 4.04
2296 2374 2.070039 TGGGGCCCCATTCTACTCG 61.070 63.158 41.29 0.00 41.89 4.18
2297 2375 4.083155 TGGGGCCCCATTCTACTC 57.917 61.111 41.29 11.10 41.89 2.59
2321 2399 4.867599 GATCCGCCGTCCCGTCAC 62.868 72.222 0.00 0.00 0.00 3.67
2323 2401 3.843117 GATGATCCGCCGTCCCGTC 62.843 68.421 0.00 0.00 0.00 4.79
2324 2402 3.912907 GATGATCCGCCGTCCCGT 61.913 66.667 0.00 0.00 0.00 5.28
2325 2403 3.848347 CTGATGATCCGCCGTCCCG 62.848 68.421 0.00 0.00 0.00 5.14
2326 2404 2.029666 CTGATGATCCGCCGTCCC 59.970 66.667 0.00 0.00 0.00 4.46
2327 2405 2.663188 GCTGATGATCCGCCGTCC 60.663 66.667 0.00 0.00 0.00 4.79
2328 2406 3.032609 CGCTGATGATCCGCCGTC 61.033 66.667 3.24 0.00 0.00 4.79
2329 2407 4.592192 CCGCTGATGATCCGCCGT 62.592 66.667 3.24 0.00 0.00 5.68
2330 2408 4.284860 TCCGCTGATGATCCGCCG 62.285 66.667 3.24 0.00 0.00 6.46
2331 2409 2.663188 GTCCGCTGATGATCCGCC 60.663 66.667 3.24 0.00 0.00 6.13
2332 2410 1.953138 CAGTCCGCTGATGATCCGC 60.953 63.158 0.00 0.00 45.28 5.54
2333 2411 1.300465 CCAGTCCGCTGATGATCCG 60.300 63.158 0.00 0.00 45.28 4.18
2334 2412 0.683973 ATCCAGTCCGCTGATGATCC 59.316 55.000 0.00 0.00 45.28 3.36
2335 2413 1.617850 AGATCCAGTCCGCTGATGATC 59.382 52.381 0.00 6.98 45.28 2.92
2336 2414 1.343789 CAGATCCAGTCCGCTGATGAT 59.656 52.381 0.00 0.00 45.28 2.45
2337 2415 0.749049 CAGATCCAGTCCGCTGATGA 59.251 55.000 0.00 0.00 45.28 2.92
2338 2416 0.749049 TCAGATCCAGTCCGCTGATG 59.251 55.000 0.00 0.00 45.28 3.07
2339 2417 1.714541 ATCAGATCCAGTCCGCTGAT 58.285 50.000 0.00 0.00 45.28 2.90
2340 2418 1.489481 AATCAGATCCAGTCCGCTGA 58.511 50.000 0.00 0.00 45.28 4.26
2341 2419 2.288702 CCTAATCAGATCCAGTCCGCTG 60.289 54.545 0.00 0.00 42.22 5.18
2342 2420 1.967066 CCTAATCAGATCCAGTCCGCT 59.033 52.381 0.00 0.00 0.00 5.52
2383 2465 0.871163 CAAGGTTGTTGCAACAGCGG 60.871 55.000 31.57 22.33 40.51 5.52
2387 2469 0.534412 CACCCAAGGTTGTTGCAACA 59.466 50.000 27.96 27.96 31.02 3.33
2397 2479 3.825908 ATGTAATCAACCACCCAAGGT 57.174 42.857 0.00 0.00 45.91 3.50
2418 2511 4.223953 GGACACCTGACCTCCATTATCTA 58.776 47.826 0.00 0.00 0.00 1.98
2429 2522 3.278592 GACGGACGGACACCTGACC 62.279 68.421 0.00 0.00 0.00 4.02
2430 2523 2.257676 GACGGACGGACACCTGAC 59.742 66.667 0.00 0.00 0.00 3.51
2431 2524 2.203379 TGACGGACGGACACCTGA 60.203 61.111 0.00 0.00 0.00 3.86
2432 2525 2.258591 CTGACGGACGGACACCTG 59.741 66.667 0.00 0.00 0.00 4.00
2433 2526 2.203451 ACTGACGGACGGACACCT 60.203 61.111 0.00 0.00 0.00 4.00
2484 2582 9.327628 CACTACAAATCAAGATCATCTCATCTT 57.672 33.333 0.00 0.00 42.80 2.40
2529 2642 4.523558 CAGGCAGATCTCATCTCACTGATA 59.476 45.833 0.00 0.00 40.16 2.15
2564 2682 4.664150 ACGAGGAGATGAGGAGAAAATC 57.336 45.455 0.00 0.00 0.00 2.17
2567 2685 2.423892 CGAACGAGGAGATGAGGAGAAA 59.576 50.000 0.00 0.00 0.00 2.52
2568 2686 2.017782 CGAACGAGGAGATGAGGAGAA 58.982 52.381 0.00 0.00 0.00 2.87
2573 2691 1.066587 GGCCGAACGAGGAGATGAG 59.933 63.158 0.00 0.00 0.00 2.90
2574 2692 2.771639 CGGCCGAACGAGGAGATGA 61.772 63.158 24.07 0.00 35.47 2.92
2631 2767 7.286775 ACTGTAAAACCACATAAAACTGGACAT 59.713 33.333 0.00 0.00 0.00 3.06
2632 2768 6.603997 ACTGTAAAACCACATAAAACTGGACA 59.396 34.615 0.00 0.00 0.00 4.02
2638 2774 9.821662 GACATCTACTGTAAAACCACATAAAAC 57.178 33.333 0.00 0.00 38.54 2.43
2662 2803 1.480137 AGCACAGCCTCATCTACTGAC 59.520 52.381 0.00 0.00 35.38 3.51
2684 2825 0.884704 TGGCTTTTCTCAGACGTGGC 60.885 55.000 0.00 0.00 0.00 5.01
2726 2868 3.315749 GGAGATAAGCAGCAGTACGTACT 59.684 47.826 22.45 22.45 36.90 2.73
2788 2930 1.598701 GCCACAGAGTGCCATTTCCC 61.599 60.000 0.00 0.00 31.34 3.97
2820 2965 0.107654 AGCTCGATTACCCAGCAACC 60.108 55.000 0.00 0.00 35.46 3.77
2927 3080 2.510691 CTGTACGCGCGGGGAATT 60.511 61.111 35.22 14.64 0.00 2.17
3025 3195 0.595825 GGTTTCAACACTGCTGCTGC 60.596 55.000 8.89 8.89 40.20 5.25
3026 3196 0.740149 TGGTTTCAACACTGCTGCTG 59.260 50.000 4.89 4.89 0.00 4.41
3027 3197 1.473258 TTGGTTTCAACACTGCTGCT 58.527 45.000 0.00 0.00 0.00 4.24
3043 3213 3.663176 CTGCACTGCACCGGTTGG 61.663 66.667 2.97 0.00 42.84 3.77
3044 3214 4.332637 GCTGCACTGCACCGGTTG 62.333 66.667 2.97 0.75 33.79 3.77


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

AutoCloner maintained by Alex Coulton.