Multiple sequence alignment - TraesCS1B01G024900

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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 TraesCS1B01G024900 chr1B 100.000 3074 0 0 1 3074 12092427 12095500 0.000000e+00 5677
1 TraesCS1B01G024900 chr1B 100.000 1576 0 0 1311 2886 12071865 12073440 0.000000e+00 2911
2 TraesCS1B01G024900 chr1B 99.847 1309 2 0 1 1309 12069989 12071297 0.000000e+00 2407
3 TraesCS1B01G024900 chr1D 92.163 1378 103 4 1006 2381 8854346 8855720 0.000000e+00 1941
4 TraesCS1B01G024900 chr1D 88.976 254 26 2 2162 2414 8883306 8883558 2.300000e-81 313
5 TraesCS1B01G024900 chr1D 88.583 254 27 2 2162 2414 8857593 8857845 1.070000e-79 307
6 TraesCS1B01G024900 chr1D 88.189 254 28 2 2162 2414 8870448 8870700 4.980000e-78 302
7 TraesCS1B01G024900 chr1D 86.957 138 18 0 2516 2653 8870988 8871125 4.100000e-34 156
8 TraesCS1B01G024900 chr1D 86.957 138 18 0 2516 2653 8883846 8883983 4.100000e-34 156
9 TraesCS1B01G024900 chr1D 86.232 138 19 0 2516 2653 8858133 8858270 1.910000e-32 150
10 TraesCS1B01G024900 chr1A 91.008 1379 120 3 1006 2381 10150934 10152311 0.000000e+00 1857
11 TraesCS1B01G024900 chr1A 87.640 267 31 1 2652 2918 144119475 144119211 2.980000e-80 309
12 TraesCS1B01G024900 chr1A 87.079 178 13 5 374 541 10150858 10151035 3.130000e-45 193
13 TraesCS1B01G024900 chr4D 79.080 1348 215 43 1049 2379 30557898 30556601 0.000000e+00 865
14 TraesCS1B01G024900 chr4D 78.293 1336 229 38 1049 2370 30513931 30515219 0.000000e+00 804
15 TraesCS1B01G024900 chr4D 77.761 1322 229 42 1049 2357 30523639 30524908 0.000000e+00 752
16 TraesCS1B01G024900 chr4D 78.627 903 146 27 1049 1940 30518470 30519336 3.460000e-154 555
17 TraesCS1B01G024900 chr4A 78.865 1339 220 41 1049 2372 572506839 572505549 0.000000e+00 846
18 TraesCS1B01G024900 chr4A 78.170 1388 222 51 1014 2364 24855068 24853725 0.000000e+00 809
19 TraesCS1B01G024900 chr4A 78.317 1319 217 41 1049 2346 572302365 572303635 0.000000e+00 787
20 TraesCS1B01G024900 chrUn 100.000 184 0 0 2891 3074 391378366 391378549 1.060000e-89 340
21 TraesCS1B01G024900 chrUn 100.000 184 0 0 2891 3074 391464953 391465136 1.060000e-89 340
22 TraesCS1B01G024900 chrUn 90.984 244 22 0 2672 2915 362111623 362111380 2.290000e-86 329
23 TraesCS1B01G024900 chrUn 86.047 258 27 6 1199 1453 339715586 339715837 5.050000e-68 268
24 TraesCS1B01G024900 chrUn 86.047 258 27 6 1199 1453 397315560 397315811 5.050000e-68 268
25 TraesCS1B01G024900 chr2A 89.963 269 19 7 2654 2918 2339164 2338900 1.060000e-89 340
26 TraesCS1B01G024900 chr6B 91.057 246 22 0 2672 2917 116204047 116204292 1.770000e-87 333
27 TraesCS1B01G024900 chr7A 91.915 235 19 0 2672 2906 303797773 303797539 2.290000e-86 329
28 TraesCS1B01G024900 chr3D 90.688 247 23 0 2672 2918 409642644 409642398 2.290000e-86 329
29 TraesCS1B01G024900 chr7D 91.489 235 20 0 2672 2906 440077780 440078014 1.060000e-84 324
30 TraesCS1B01G024900 chr2D 88.060 268 26 5 2642 2906 421011747 421012011 2.300000e-81 313


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 TraesCS1B01G024900 chr1B 12092427 12095500 3073 False 5677.000000 5677 100.000000 1 3074 1 chr1B.!!$F1 3073
1 TraesCS1B01G024900 chr1B 12069989 12073440 3451 False 2659.000000 2911 99.923500 1 2886 2 chr1B.!!$F2 2885
2 TraesCS1B01G024900 chr1D 8854346 8858270 3924 False 799.333333 1941 88.992667 1006 2653 3 chr1D.!!$F1 1647
3 TraesCS1B01G024900 chr1D 8883306 8883983 677 False 234.500000 313 87.966500 2162 2653 2 chr1D.!!$F3 491
4 TraesCS1B01G024900 chr1D 8870448 8871125 677 False 229.000000 302 87.573000 2162 2653 2 chr1D.!!$F2 491
5 TraesCS1B01G024900 chr1A 10150858 10152311 1453 False 1025.000000 1857 89.043500 374 2381 2 chr1A.!!$F1 2007
6 TraesCS1B01G024900 chr4D 30556601 30557898 1297 True 865.000000 865 79.080000 1049 2379 1 chr4D.!!$R1 1330
7 TraesCS1B01G024900 chr4D 30523639 30524908 1269 False 752.000000 752 77.761000 1049 2357 1 chr4D.!!$F1 1308
8 TraesCS1B01G024900 chr4D 30513931 30519336 5405 False 679.500000 804 78.460000 1049 2370 2 chr4D.!!$F2 1321
9 TraesCS1B01G024900 chr4A 572505549 572506839 1290 True 846.000000 846 78.865000 1049 2372 1 chr4A.!!$R2 1323
10 TraesCS1B01G024900 chr4A 24853725 24855068 1343 True 809.000000 809 78.170000 1014 2364 1 chr4A.!!$R1 1350
11 TraesCS1B01G024900 chr4A 572302365 572303635 1270 False 787.000000 787 78.317000 1049 2346 1 chr4A.!!$F1 1297

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
730 741 0.790866 GCGATCGCTGAAGCAAACAC 60.791 55.0 31.94 0.0 42.21 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2886 8182 6.253758 TGATCGTAATGGGAGTATCATAGGT 58.746 40.0 0.0 0.0 36.25 3.08 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
730 741 0.790866 GCGATCGCTGAAGCAAACAC 60.791 55.000 31.94 0.00 42.21 3.32
799 810 2.671619 ATGTTGGGCGGTCGTTGG 60.672 61.111 0.00 0.00 0.00 3.77
2886 8182 4.592778 TCCTAGTTGGCATGCATGATACTA 59.407 41.667 30.64 25.87 35.26 1.82
2887 8183 4.692625 CCTAGTTGGCATGCATGATACTAC 59.307 45.833 30.64 22.16 0.00 2.73
2888 8184 3.480470 AGTTGGCATGCATGATACTACC 58.520 45.455 30.64 19.65 0.00 3.18
2889 8185 3.137176 AGTTGGCATGCATGATACTACCT 59.863 43.478 30.64 11.98 0.00 3.08
2890 8186 4.347876 AGTTGGCATGCATGATACTACCTA 59.652 41.667 30.64 13.97 0.00 3.08
2891 8187 5.013495 AGTTGGCATGCATGATACTACCTAT 59.987 40.000 30.64 7.77 0.00 2.57
2892 8188 4.835678 TGGCATGCATGATACTACCTATG 58.164 43.478 30.64 0.23 0.00 2.23
2893 8189 4.531732 TGGCATGCATGATACTACCTATGA 59.468 41.667 30.64 1.93 0.00 2.15
2894 8190 5.190330 TGGCATGCATGATACTACCTATGAT 59.810 40.000 30.64 0.00 0.00 2.45
2895 8191 6.383726 TGGCATGCATGATACTACCTATGATA 59.616 38.462 30.64 0.87 0.00 2.15
2896 8192 6.703607 GGCATGCATGATACTACCTATGATAC 59.296 42.308 30.64 5.71 0.00 2.24
2897 8193 7.418368 GGCATGCATGATACTACCTATGATACT 60.418 40.741 30.64 0.00 0.00 2.12
2898 8194 7.651304 GCATGCATGATACTACCTATGATACTC 59.349 40.741 30.64 1.38 0.00 2.59
2899 8195 7.646548 TGCATGATACTACCTATGATACTCC 57.353 40.000 0.00 0.00 0.00 3.85
2900 8196 6.607600 TGCATGATACTACCTATGATACTCCC 59.392 42.308 0.00 0.00 0.00 4.30
2901 8197 6.607600 GCATGATACTACCTATGATACTCCCA 59.392 42.308 0.00 0.00 0.00 4.37
2902 8198 7.288852 GCATGATACTACCTATGATACTCCCAT 59.711 40.741 0.00 0.00 0.00 4.00
2903 8199 9.206690 CATGATACTACCTATGATACTCCCATT 57.793 37.037 0.00 0.00 0.00 3.16
2905 8201 9.696572 TGATACTACCTATGATACTCCCATTAC 57.303 37.037 0.00 0.00 0.00 1.89
2906 8202 8.749026 ATACTACCTATGATACTCCCATTACG 57.251 38.462 0.00 0.00 0.00 3.18
2907 8203 6.787170 ACTACCTATGATACTCCCATTACGA 58.213 40.000 0.00 0.00 0.00 3.43
2908 8204 7.411808 ACTACCTATGATACTCCCATTACGAT 58.588 38.462 0.00 0.00 0.00 3.73
2909 8205 6.777213 ACCTATGATACTCCCATTACGATC 57.223 41.667 0.00 0.00 0.00 3.69
2910 8206 6.253758 ACCTATGATACTCCCATTACGATCA 58.746 40.000 0.00 0.00 0.00 2.92
2911 8207 6.724441 ACCTATGATACTCCCATTACGATCAA 59.276 38.462 0.00 0.00 0.00 2.57
2912 8208 7.036220 CCTATGATACTCCCATTACGATCAAC 58.964 42.308 0.00 0.00 0.00 3.18
2913 8209 5.209818 TGATACTCCCATTACGATCAACC 57.790 43.478 0.00 0.00 0.00 3.77
2914 8210 4.899457 TGATACTCCCATTACGATCAACCT 59.101 41.667 0.00 0.00 0.00 3.50
2915 8211 5.365605 TGATACTCCCATTACGATCAACCTT 59.634 40.000 0.00 0.00 0.00 3.50
2916 8212 6.551975 TGATACTCCCATTACGATCAACCTTA 59.448 38.462 0.00 0.00 0.00 2.69
2917 8213 5.888982 ACTCCCATTACGATCAACCTTAT 57.111 39.130 0.00 0.00 0.00 1.73
2918 8214 5.855045 ACTCCCATTACGATCAACCTTATC 58.145 41.667 0.00 0.00 0.00 1.75
2923 8219 2.517598 CGATCAACCTTATCGCCCG 58.482 57.895 0.00 0.00 39.70 6.13
2924 8220 0.031585 CGATCAACCTTATCGCCCGA 59.968 55.000 0.00 0.00 39.70 5.14
2925 8221 1.784525 GATCAACCTTATCGCCCGAG 58.215 55.000 0.00 0.00 0.00 4.63
2926 8222 0.249911 ATCAACCTTATCGCCCGAGC 60.250 55.000 0.00 0.00 0.00 5.03
2927 8223 1.153449 CAACCTTATCGCCCGAGCA 60.153 57.895 0.00 0.00 39.83 4.26
2928 8224 0.532862 CAACCTTATCGCCCGAGCAT 60.533 55.000 0.00 0.00 39.83 3.79
2929 8225 0.532862 AACCTTATCGCCCGAGCATG 60.533 55.000 0.00 0.00 39.83 4.06
2930 8226 1.669115 CCTTATCGCCCGAGCATGG 60.669 63.158 0.00 0.00 39.83 3.66
2938 8234 2.501128 CCGAGCATGGGACGATGT 59.499 61.111 0.00 0.00 35.02 3.06
2939 8235 1.739667 CCGAGCATGGGACGATGTA 59.260 57.895 0.00 0.00 35.02 2.29
2940 8236 0.318441 CCGAGCATGGGACGATGTAT 59.682 55.000 0.00 0.00 35.02 2.29
2941 8237 1.670087 CCGAGCATGGGACGATGTATC 60.670 57.143 0.00 0.00 35.02 2.24
2953 8249 3.917329 CGATGTATCGGAGCTTAAGGA 57.083 47.619 4.29 0.00 45.93 3.36
2954 8250 3.827625 CGATGTATCGGAGCTTAAGGAG 58.172 50.000 4.29 0.00 45.93 3.69
2955 8251 3.502595 CGATGTATCGGAGCTTAAGGAGA 59.497 47.826 4.29 0.00 45.93 3.71
2956 8252 4.378978 CGATGTATCGGAGCTTAAGGAGAG 60.379 50.000 4.29 0.00 45.93 3.20
2957 8253 3.223435 TGTATCGGAGCTTAAGGAGAGG 58.777 50.000 4.29 0.00 0.00 3.69
2958 8254 2.757894 ATCGGAGCTTAAGGAGAGGA 57.242 50.000 4.29 0.00 0.00 3.71
2959 8255 2.526888 TCGGAGCTTAAGGAGAGGAA 57.473 50.000 4.29 0.00 0.00 3.36
2960 8256 2.816411 TCGGAGCTTAAGGAGAGGAAA 58.184 47.619 4.29 0.00 0.00 3.13
2961 8257 3.170717 TCGGAGCTTAAGGAGAGGAAAA 58.829 45.455 4.29 0.00 0.00 2.29
2962 8258 3.581332 TCGGAGCTTAAGGAGAGGAAAAA 59.419 43.478 4.29 0.00 0.00 1.94
2963 8259 3.935828 CGGAGCTTAAGGAGAGGAAAAAG 59.064 47.826 4.29 0.00 0.00 2.27
2964 8260 4.265893 GGAGCTTAAGGAGAGGAAAAAGG 58.734 47.826 4.29 0.00 0.00 3.11
2965 8261 4.263550 GGAGCTTAAGGAGAGGAAAAAGGT 60.264 45.833 4.29 0.00 0.00 3.50
2966 8262 5.317808 GAGCTTAAGGAGAGGAAAAAGGTT 58.682 41.667 4.29 0.00 0.00 3.50
2967 8263 5.073428 AGCTTAAGGAGAGGAAAAAGGTTG 58.927 41.667 4.29 0.00 0.00 3.77
2968 8264 4.827835 GCTTAAGGAGAGGAAAAAGGTTGT 59.172 41.667 4.29 0.00 0.00 3.32
2969 8265 5.048643 GCTTAAGGAGAGGAAAAAGGTTGTC 60.049 44.000 4.29 0.00 0.00 3.18
2970 8266 3.127425 AGGAGAGGAAAAAGGTTGTCG 57.873 47.619 0.00 0.00 0.00 4.35
2971 8267 2.152016 GGAGAGGAAAAAGGTTGTCGG 58.848 52.381 0.00 0.00 0.00 4.79
2972 8268 2.486727 GGAGAGGAAAAAGGTTGTCGGT 60.487 50.000 0.00 0.00 0.00 4.69
2973 8269 3.211865 GAGAGGAAAAAGGTTGTCGGTT 58.788 45.455 0.00 0.00 0.00 4.44
2974 8270 3.211865 AGAGGAAAAAGGTTGTCGGTTC 58.788 45.455 0.00 0.00 0.00 3.62
2975 8271 2.946990 GAGGAAAAAGGTTGTCGGTTCA 59.053 45.455 0.00 0.00 0.00 3.18
2976 8272 2.949644 AGGAAAAAGGTTGTCGGTTCAG 59.050 45.455 0.00 0.00 0.00 3.02
2977 8273 2.034179 GGAAAAAGGTTGTCGGTTCAGG 59.966 50.000 0.00 0.00 0.00 3.86
2978 8274 1.029681 AAAAGGTTGTCGGTTCAGGC 58.970 50.000 0.00 0.00 0.00 4.85
2979 8275 0.822121 AAAGGTTGTCGGTTCAGGCC 60.822 55.000 0.00 0.00 0.00 5.19
2980 8276 1.990160 AAGGTTGTCGGTTCAGGCCA 61.990 55.000 5.01 0.00 0.00 5.36
2981 8277 1.966451 GGTTGTCGGTTCAGGCCAG 60.966 63.158 5.01 0.00 0.00 4.85
2982 8278 1.966451 GTTGTCGGTTCAGGCCAGG 60.966 63.158 5.01 0.00 0.00 4.45
2983 8279 3.190738 TTGTCGGTTCAGGCCAGGG 62.191 63.158 5.01 0.00 0.00 4.45
2984 8280 4.410400 GTCGGTTCAGGCCAGGGG 62.410 72.222 5.01 0.00 0.00 4.79
2985 8281 4.649705 TCGGTTCAGGCCAGGGGA 62.650 66.667 5.01 0.00 0.00 4.81
2986 8282 4.101448 CGGTTCAGGCCAGGGGAG 62.101 72.222 5.01 0.00 0.00 4.30
2987 8283 4.432741 GGTTCAGGCCAGGGGAGC 62.433 72.222 5.01 0.00 0.00 4.70
2988 8284 3.334054 GTTCAGGCCAGGGGAGCT 61.334 66.667 5.01 0.00 0.00 4.09
2989 8285 2.532715 TTCAGGCCAGGGGAGCTT 60.533 61.111 5.01 0.00 0.00 3.74
2990 8286 1.229820 TTCAGGCCAGGGGAGCTTA 60.230 57.895 5.01 0.00 0.00 3.09
2991 8287 0.624500 TTCAGGCCAGGGGAGCTTAT 60.625 55.000 5.01 0.00 0.00 1.73
2992 8288 0.624500 TCAGGCCAGGGGAGCTTATT 60.625 55.000 5.01 0.00 0.00 1.40
2993 8289 0.466922 CAGGCCAGGGGAGCTTATTG 60.467 60.000 5.01 0.00 0.00 1.90
2994 8290 1.152673 GGCCAGGGGAGCTTATTGG 60.153 63.158 0.00 0.00 0.00 3.16
2995 8291 1.615262 GCCAGGGGAGCTTATTGGT 59.385 57.895 8.62 0.00 0.00 3.67
2996 8292 0.033109 GCCAGGGGAGCTTATTGGTT 60.033 55.000 8.62 0.00 0.00 3.67
2997 8293 1.214424 GCCAGGGGAGCTTATTGGTTA 59.786 52.381 8.62 0.00 0.00 2.85
2998 8294 2.357777 GCCAGGGGAGCTTATTGGTTAA 60.358 50.000 8.62 0.00 0.00 2.01
2999 8295 3.691311 GCCAGGGGAGCTTATTGGTTAAT 60.691 47.826 8.62 0.00 0.00 1.40
3000 8296 4.447180 GCCAGGGGAGCTTATTGGTTAATA 60.447 45.833 8.62 0.00 0.00 0.98
3001 8297 5.752030 GCCAGGGGAGCTTATTGGTTAATAT 60.752 44.000 8.62 0.00 0.00 1.28
3002 8298 6.314917 CCAGGGGAGCTTATTGGTTAATATT 58.685 40.000 0.00 0.00 0.00 1.28
3003 8299 6.782494 CCAGGGGAGCTTATTGGTTAATATTT 59.218 38.462 0.00 0.00 0.00 1.40
3004 8300 7.947890 CCAGGGGAGCTTATTGGTTAATATTTA 59.052 37.037 0.00 0.00 0.00 1.40
3005 8301 9.533831 CAGGGGAGCTTATTGGTTAATATTTAT 57.466 33.333 0.00 0.00 0.00 1.40
3006 8302 9.533831 AGGGGAGCTTATTGGTTAATATTTATG 57.466 33.333 0.00 0.00 0.00 1.90
3007 8303 8.749354 GGGGAGCTTATTGGTTAATATTTATGG 58.251 37.037 0.00 0.00 0.00 2.74
3008 8304 8.251026 GGGAGCTTATTGGTTAATATTTATGGC 58.749 37.037 0.00 0.00 0.00 4.40
3009 8305 9.025041 GGAGCTTATTGGTTAATATTTATGGCT 57.975 33.333 0.00 0.00 0.00 4.75
3017 8313 8.862325 TGGTTAATATTTATGGCTACATGAGG 57.138 34.615 0.00 0.00 37.97 3.86
3018 8314 8.664992 TGGTTAATATTTATGGCTACATGAGGA 58.335 33.333 0.00 0.00 37.97 3.71
3019 8315 9.515226 GGTTAATATTTATGGCTACATGAGGAA 57.485 33.333 0.00 0.00 37.97 3.36
3026 8322 8.621532 TTTATGGCTACATGAGGAATATGAAC 57.378 34.615 0.00 0.00 37.97 3.18
3027 8323 5.628797 TGGCTACATGAGGAATATGAACA 57.371 39.130 0.00 0.00 0.00 3.18
3028 8324 6.000246 TGGCTACATGAGGAATATGAACAA 58.000 37.500 0.00 0.00 0.00 2.83
3029 8325 5.822519 TGGCTACATGAGGAATATGAACAAC 59.177 40.000 0.00 0.00 0.00 3.32
3030 8326 5.822519 GGCTACATGAGGAATATGAACAACA 59.177 40.000 0.00 0.00 0.00 3.33
3031 8327 6.318648 GGCTACATGAGGAATATGAACAACAA 59.681 38.462 0.00 0.00 0.00 2.83
3032 8328 7.013655 GGCTACATGAGGAATATGAACAACAAT 59.986 37.037 0.00 0.00 0.00 2.71
3033 8329 8.072567 GCTACATGAGGAATATGAACAACAATC 58.927 37.037 0.00 0.00 0.00 2.67
3034 8330 7.019774 ACATGAGGAATATGAACAACAATCG 57.980 36.000 0.00 0.00 0.00 3.34
3035 8331 6.599244 ACATGAGGAATATGAACAACAATCGT 59.401 34.615 0.00 0.00 0.00 3.73
3036 8332 7.121168 ACATGAGGAATATGAACAACAATCGTT 59.879 33.333 0.00 0.00 35.01 3.85
3051 8347 6.095432 ACAATCGTTGGATTTGAATTCCAA 57.905 33.333 15.40 15.40 40.90 3.53
3059 8355 7.831691 TTGGATTTGAATTCCAACAACTAGA 57.168 32.000 15.40 0.00 38.46 2.43
3060 8356 7.831691 TGGATTTGAATTCCAACAACTAGAA 57.168 32.000 6.35 0.00 33.85 2.10
3069 8365 2.030540 CCAACAACTAGAAGTCGACCGA 60.031 50.000 13.01 0.00 0.00 4.69
3070 8366 3.235195 CAACAACTAGAAGTCGACCGAG 58.765 50.000 13.01 6.18 0.00 4.63
3072 8368 1.199327 CAACTAGAAGTCGACCGAGCA 59.801 52.381 13.01 0.00 0.00 4.26
3073 8369 1.752683 ACTAGAAGTCGACCGAGCAT 58.247 50.000 13.01 0.00 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
799 810 1.067915 GCCCATCTCTACGAGCATCTC 60.068 57.143 0.00 0.00 0.00 2.75
2886 8182 6.253758 TGATCGTAATGGGAGTATCATAGGT 58.746 40.000 0.00 0.00 36.25 3.08
2887 8183 6.775594 TGATCGTAATGGGAGTATCATAGG 57.224 41.667 0.00 0.00 36.25 2.57
2888 8184 7.036220 GGTTGATCGTAATGGGAGTATCATAG 58.964 42.308 0.00 0.00 36.25 2.23
2889 8185 6.724441 AGGTTGATCGTAATGGGAGTATCATA 59.276 38.462 0.00 0.00 36.25 2.15
2890 8186 5.544176 AGGTTGATCGTAATGGGAGTATCAT 59.456 40.000 0.00 0.00 36.25 2.45
2891 8187 4.899457 AGGTTGATCGTAATGGGAGTATCA 59.101 41.667 0.00 0.00 36.25 2.15
2892 8188 5.470047 AGGTTGATCGTAATGGGAGTATC 57.530 43.478 0.00 0.00 0.00 2.24
2893 8189 5.888982 AAGGTTGATCGTAATGGGAGTAT 57.111 39.130 0.00 0.00 0.00 2.12
2894 8190 6.294342 CGATAAGGTTGATCGTAATGGGAGTA 60.294 42.308 0.00 0.00 41.00 2.59
2895 8191 5.509163 CGATAAGGTTGATCGTAATGGGAGT 60.509 44.000 0.00 0.00 41.00 3.85
2896 8192 4.923871 CGATAAGGTTGATCGTAATGGGAG 59.076 45.833 0.00 0.00 41.00 4.30
2897 8193 4.798263 GCGATAAGGTTGATCGTAATGGGA 60.798 45.833 6.86 0.00 46.25 4.37
2898 8194 3.432252 GCGATAAGGTTGATCGTAATGGG 59.568 47.826 6.86 0.00 46.25 4.00
2899 8195 3.432252 GGCGATAAGGTTGATCGTAATGG 59.568 47.826 6.86 0.00 46.25 3.16
2900 8196 3.432252 GGGCGATAAGGTTGATCGTAATG 59.568 47.826 6.86 0.00 46.25 1.90
2901 8197 3.660865 GGGCGATAAGGTTGATCGTAAT 58.339 45.455 6.86 0.00 46.25 1.89
2902 8198 2.544277 CGGGCGATAAGGTTGATCGTAA 60.544 50.000 6.86 0.00 46.25 3.18
2903 8199 1.001048 CGGGCGATAAGGTTGATCGTA 60.001 52.381 6.86 0.00 46.25 3.43
2904 8200 0.249322 CGGGCGATAAGGTTGATCGT 60.249 55.000 6.86 0.00 46.25 3.73
2906 8202 1.784525 CTCGGGCGATAAGGTTGATC 58.215 55.000 0.00 0.00 0.00 2.92
2907 8203 0.249911 GCTCGGGCGATAAGGTTGAT 60.250 55.000 0.00 0.00 0.00 2.57
2908 8204 1.143183 GCTCGGGCGATAAGGTTGA 59.857 57.895 0.00 0.00 0.00 3.18
2909 8205 0.532862 ATGCTCGGGCGATAAGGTTG 60.533 55.000 1.14 0.00 42.25 3.77
2910 8206 0.532862 CATGCTCGGGCGATAAGGTT 60.533 55.000 1.14 0.00 42.25 3.50
2911 8207 1.069765 CATGCTCGGGCGATAAGGT 59.930 57.895 1.14 0.00 42.25 3.50
2912 8208 1.669115 CCATGCTCGGGCGATAAGG 60.669 63.158 1.14 0.00 42.25 2.69
2913 8209 1.669115 CCCATGCTCGGGCGATAAG 60.669 63.158 1.14 0.00 40.07 1.73
2914 8210 2.137528 TCCCATGCTCGGGCGATAA 61.138 57.895 1.14 0.00 46.92 1.75
2915 8211 2.523168 TCCCATGCTCGGGCGATA 60.523 61.111 1.14 0.00 46.92 2.92
2916 8212 4.241555 GTCCCATGCTCGGGCGAT 62.242 66.667 1.14 0.00 46.92 4.58
2919 8215 4.241555 ATCGTCCCATGCTCGGGC 62.242 66.667 0.00 0.00 46.92 6.13
2921 8217 0.318441 ATACATCGTCCCATGCTCGG 59.682 55.000 0.00 0.00 0.00 4.63
2922 8218 1.702886 GATACATCGTCCCATGCTCG 58.297 55.000 0.00 0.00 0.00 5.03
2923 8219 1.702886 CGATACATCGTCCCATGCTC 58.297 55.000 3.45 0.00 44.74 4.26
2924 8220 3.894257 CGATACATCGTCCCATGCT 57.106 52.632 3.45 0.00 44.74 3.79
2934 8230 4.082463 CCTCTCCTTAAGCTCCGATACATC 60.082 50.000 0.00 0.00 0.00 3.06
2935 8231 3.829601 CCTCTCCTTAAGCTCCGATACAT 59.170 47.826 0.00 0.00 0.00 2.29
2936 8232 3.117625 TCCTCTCCTTAAGCTCCGATACA 60.118 47.826 0.00 0.00 0.00 2.29
2937 8233 3.488363 TCCTCTCCTTAAGCTCCGATAC 58.512 50.000 0.00 0.00 0.00 2.24
2938 8234 3.878237 TCCTCTCCTTAAGCTCCGATA 57.122 47.619 0.00 0.00 0.00 2.92
2939 8235 2.757894 TCCTCTCCTTAAGCTCCGAT 57.242 50.000 0.00 0.00 0.00 4.18
2940 8236 2.526888 TTCCTCTCCTTAAGCTCCGA 57.473 50.000 0.00 0.00 0.00 4.55
2941 8237 3.611766 TTTTCCTCTCCTTAAGCTCCG 57.388 47.619 0.00 0.00 0.00 4.63
2942 8238 4.263550 ACCTTTTTCCTCTCCTTAAGCTCC 60.264 45.833 0.00 0.00 0.00 4.70
2943 8239 4.912586 ACCTTTTTCCTCTCCTTAAGCTC 58.087 43.478 0.00 0.00 0.00 4.09
2944 8240 5.073428 CAACCTTTTTCCTCTCCTTAAGCT 58.927 41.667 0.00 0.00 0.00 3.74
2945 8241 4.827835 ACAACCTTTTTCCTCTCCTTAAGC 59.172 41.667 0.00 0.00 0.00 3.09
2946 8242 5.179555 CGACAACCTTTTTCCTCTCCTTAAG 59.820 44.000 0.00 0.00 0.00 1.85
2947 8243 5.061179 CGACAACCTTTTTCCTCTCCTTAA 58.939 41.667 0.00 0.00 0.00 1.85
2948 8244 4.504340 CCGACAACCTTTTTCCTCTCCTTA 60.504 45.833 0.00 0.00 0.00 2.69
2949 8245 3.477530 CGACAACCTTTTTCCTCTCCTT 58.522 45.455 0.00 0.00 0.00 3.36
2950 8246 2.224548 CCGACAACCTTTTTCCTCTCCT 60.225 50.000 0.00 0.00 0.00 3.69
2951 8247 2.152016 CCGACAACCTTTTTCCTCTCC 58.848 52.381 0.00 0.00 0.00 3.71
2952 8248 2.847441 ACCGACAACCTTTTTCCTCTC 58.153 47.619 0.00 0.00 0.00 3.20
2953 8249 3.211865 GAACCGACAACCTTTTTCCTCT 58.788 45.455 0.00 0.00 0.00 3.69
2954 8250 2.946990 TGAACCGACAACCTTTTTCCTC 59.053 45.455 0.00 0.00 0.00 3.71
2955 8251 2.949644 CTGAACCGACAACCTTTTTCCT 59.050 45.455 0.00 0.00 0.00 3.36
2956 8252 2.034179 CCTGAACCGACAACCTTTTTCC 59.966 50.000 0.00 0.00 0.00 3.13
2957 8253 2.543031 GCCTGAACCGACAACCTTTTTC 60.543 50.000 0.00 0.00 0.00 2.29
2958 8254 1.407618 GCCTGAACCGACAACCTTTTT 59.592 47.619 0.00 0.00 0.00 1.94
2959 8255 1.029681 GCCTGAACCGACAACCTTTT 58.970 50.000 0.00 0.00 0.00 2.27
2960 8256 0.822121 GGCCTGAACCGACAACCTTT 60.822 55.000 0.00 0.00 0.00 3.11
2961 8257 1.228154 GGCCTGAACCGACAACCTT 60.228 57.895 0.00 0.00 0.00 3.50
2962 8258 2.397413 CTGGCCTGAACCGACAACCT 62.397 60.000 3.32 0.00 0.00 3.50
2963 8259 1.966451 CTGGCCTGAACCGACAACC 60.966 63.158 3.32 0.00 0.00 3.77
2964 8260 1.966451 CCTGGCCTGAACCGACAAC 60.966 63.158 11.88 0.00 0.00 3.32
2965 8261 2.429930 CCTGGCCTGAACCGACAA 59.570 61.111 11.88 0.00 0.00 3.18
2966 8262 3.636231 CCCTGGCCTGAACCGACA 61.636 66.667 11.88 0.00 0.00 4.35
2967 8263 4.410400 CCCCTGGCCTGAACCGAC 62.410 72.222 11.88 0.00 0.00 4.79
2968 8264 4.649705 TCCCCTGGCCTGAACCGA 62.650 66.667 11.88 0.00 0.00 4.69
2969 8265 4.101448 CTCCCCTGGCCTGAACCG 62.101 72.222 11.88 0.00 0.00 4.44
2970 8266 4.432741 GCTCCCCTGGCCTGAACC 62.433 72.222 11.88 0.00 0.00 3.62
2971 8267 1.562672 TAAGCTCCCCTGGCCTGAAC 61.563 60.000 11.88 0.00 0.00 3.18
2972 8268 0.624500 ATAAGCTCCCCTGGCCTGAA 60.625 55.000 11.88 0.00 0.00 3.02
2973 8269 0.624500 AATAAGCTCCCCTGGCCTGA 60.625 55.000 11.88 0.00 0.00 3.86
2974 8270 0.466922 CAATAAGCTCCCCTGGCCTG 60.467 60.000 3.32 2.54 0.00 4.85
2975 8271 1.649271 CCAATAAGCTCCCCTGGCCT 61.649 60.000 3.32 0.00 0.00 5.19
2976 8272 1.152673 CCAATAAGCTCCCCTGGCC 60.153 63.158 0.00 0.00 0.00 5.36
2977 8273 0.033109 AACCAATAAGCTCCCCTGGC 60.033 55.000 0.00 0.00 0.00 4.85
2978 8274 3.662759 TTAACCAATAAGCTCCCCTGG 57.337 47.619 0.00 0.00 0.00 4.45
2979 8275 7.839680 AAATATTAACCAATAAGCTCCCCTG 57.160 36.000 0.00 0.00 30.50 4.45
2980 8276 9.533831 CATAAATATTAACCAATAAGCTCCCCT 57.466 33.333 0.00 0.00 30.50 4.79
2981 8277 8.749354 CCATAAATATTAACCAATAAGCTCCCC 58.251 37.037 0.00 0.00 30.50 4.81
2982 8278 8.251026 GCCATAAATATTAACCAATAAGCTCCC 58.749 37.037 0.00 0.00 30.50 4.30
2983 8279 9.025041 AGCCATAAATATTAACCAATAAGCTCC 57.975 33.333 0.00 0.00 30.50 4.70
2991 8287 9.295825 CCTCATGTAGCCATAAATATTAACCAA 57.704 33.333 0.00 0.00 0.00 3.67
2992 8288 8.664992 TCCTCATGTAGCCATAAATATTAACCA 58.335 33.333 0.00 0.00 0.00 3.67
2993 8289 9.515226 TTCCTCATGTAGCCATAAATATTAACC 57.485 33.333 0.00 0.00 0.00 2.85
3000 8296 9.236006 GTTCATATTCCTCATGTAGCCATAAAT 57.764 33.333 0.00 0.00 0.00 1.40
3001 8297 8.217111 TGTTCATATTCCTCATGTAGCCATAAA 58.783 33.333 0.00 0.00 0.00 1.40
3002 8298 7.744733 TGTTCATATTCCTCATGTAGCCATAA 58.255 34.615 0.00 0.00 0.00 1.90
3003 8299 7.315066 TGTTCATATTCCTCATGTAGCCATA 57.685 36.000 0.00 0.00 0.00 2.74
3004 8300 6.191657 TGTTCATATTCCTCATGTAGCCAT 57.808 37.500 0.00 0.00 0.00 4.40
3005 8301 5.628797 TGTTCATATTCCTCATGTAGCCA 57.371 39.130 0.00 0.00 0.00 4.75
3006 8302 5.822519 TGTTGTTCATATTCCTCATGTAGCC 59.177 40.000 0.00 0.00 0.00 3.93
3007 8303 6.925610 TGTTGTTCATATTCCTCATGTAGC 57.074 37.500 0.00 0.00 0.00 3.58
3008 8304 8.278408 CGATTGTTGTTCATATTCCTCATGTAG 58.722 37.037 0.00 0.00 0.00 2.74
3009 8305 7.768582 ACGATTGTTGTTCATATTCCTCATGTA 59.231 33.333 0.00 0.00 0.00 2.29
3010 8306 6.599244 ACGATTGTTGTTCATATTCCTCATGT 59.401 34.615 0.00 0.00 0.00 3.21
3011 8307 7.019774 ACGATTGTTGTTCATATTCCTCATG 57.980 36.000 0.00 0.00 0.00 3.07
3012 8308 7.630242 AACGATTGTTGTTCATATTCCTCAT 57.370 32.000 0.00 0.00 36.81 2.90
3027 8323 6.095432 TGGAATTCAAATCCAACGATTGTT 57.905 33.333 7.93 0.00 43.84 2.83
3028 8324 5.720371 TGGAATTCAAATCCAACGATTGT 57.280 34.783 7.93 0.00 43.84 2.71
3036 8332 7.505585 ACTTCTAGTTGTTGGAATTCAAATCCA 59.494 33.333 7.93 0.00 45.09 3.41
3037 8333 7.886338 ACTTCTAGTTGTTGGAATTCAAATCC 58.114 34.615 7.93 0.00 37.08 3.01
3038 8334 7.746475 CGACTTCTAGTTGTTGGAATTCAAATC 59.254 37.037 7.93 0.00 37.08 2.17
3039 8335 7.444183 TCGACTTCTAGTTGTTGGAATTCAAAT 59.556 33.333 7.93 0.00 37.08 2.32
3040 8336 6.764085 TCGACTTCTAGTTGTTGGAATTCAAA 59.236 34.615 7.93 0.00 37.08 2.69
3045 8341 4.566987 GGTCGACTTCTAGTTGTTGGAAT 58.433 43.478 16.46 0.00 31.48 3.01
3046 8342 3.551454 CGGTCGACTTCTAGTTGTTGGAA 60.551 47.826 16.46 0.00 31.48 3.53
3049 8345 3.235195 CTCGGTCGACTTCTAGTTGTTG 58.765 50.000 16.46 0.00 31.48 3.33
3051 8347 1.199558 GCTCGGTCGACTTCTAGTTGT 59.800 52.381 16.46 0.00 31.48 3.32
3052 8348 1.199327 TGCTCGGTCGACTTCTAGTTG 59.801 52.381 16.46 0.00 0.00 3.16
3054 8350 1.752683 ATGCTCGGTCGACTTCTAGT 58.247 50.000 16.46 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.