Multiple sequence alignment - TraesCS5B01G414700

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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 TraesCS5B01G414700 chr5B 100.000 3278 0 0 1 3278 588935560 588932283 0.000000e+00 6054
1 TraesCS5B01G414700 chr5B 100.000 153 0 0 2633 2785 588932777 588932625 1.930000e-72 283
2 TraesCS5B01G414700 chr5B 100.000 153 0 0 2784 2936 588932928 588932776 1.930000e-72 283
3 TraesCS5B01G414700 chr5D 96.643 1698 45 4 1088 2785 480601821 480600136 0.000000e+00 2809
4 TraesCS5B01G414700 chr5D 95.960 495 13 3 2784 3278 480600283 480599796 0.000000e+00 797
5 TraesCS5B01G414700 chr5A 95.965 1710 50 5 1088 2785 599780462 599778760 0.000000e+00 2758
6 TraesCS5B01G414700 chr5A 98.876 623 6 1 467 1088 143353037 143352415 0.000000e+00 1110
7 TraesCS5B01G414700 chr5A 95.565 496 16 3 2784 3278 599778907 599778417 0.000000e+00 789
8 TraesCS5B01G414700 chr2A 93.870 1664 85 7 1088 2747 1874386 1876036 0.000000e+00 2492
9 TraesCS5B01G414700 chr2A 80.054 747 118 20 1094 1826 2884280 2885009 2.900000e-145 525
10 TraesCS5B01G414700 chr2A 88.636 440 26 11 2784 3202 1875923 1876359 6.270000e-142 514
11 TraesCS5B01G414700 chr2A 95.305 213 9 1 3067 3278 1906001 1906213 1.460000e-88 337
12 TraesCS5B01G414700 chr2A 81.915 376 39 15 2906 3278 2990735 2991084 1.150000e-74 291
13 TraesCS5B01G414700 chr2A 73.896 521 87 29 2784 3275 2489975 2489475 2.620000e-36 163
14 TraesCS5B01G414700 chr2A 86.861 137 13 5 2906 3041 2383137 2383269 7.330000e-32 148
15 TraesCS5B01G414700 chr2D 96.408 1364 49 0 1088 2451 1994574 1995937 0.000000e+00 2248
16 TraesCS5B01G414700 chr2D 82.443 1441 204 28 1088 2500 22568082 22566663 0.000000e+00 1214
17 TraesCS5B01G414700 chr2D 92.348 379 19 6 2908 3278 1996238 1996614 6.230000e-147 531
18 TraesCS5B01G414700 chr2D 92.164 268 15 4 2484 2748 1995936 1996200 1.110000e-99 374
19 TraesCS5B01G414700 chr2D 74.742 388 58 29 2906 3275 2537527 2537162 1.590000e-28 137
20 TraesCS5B01G414700 chr2B 98.634 1098 9 4 1 1096 399344715 399343622 0.000000e+00 1940
21 TraesCS5B01G414700 chr2B 82.818 1228 191 11 1236 2447 8997792 8999015 0.000000e+00 1081
22 TraesCS5B01G414700 chr2B 87.195 492 33 12 2784 3247 473498 473987 1.730000e-147 532
23 TraesCS5B01G414700 chr2B 86.508 378 36 9 2906 3278 8569757 8570124 5.090000e-108 401
24 TraesCS5B01G414700 chr2B 92.336 274 15 2 1088 1361 472111 472378 5.130000e-103 385
25 TraesCS5B01G414700 chr2B 90.377 239 16 4 2513 2748 473379 473613 1.140000e-79 307
26 TraesCS5B01G414700 chr2B 86.641 262 23 9 3023 3278 9104146 9103891 2.490000e-71 279
27 TraesCS5B01G414700 chr2B 84.151 265 33 2 1088 1352 8568134 8568389 7.020000e-62 248
28 TraesCS5B01G414700 chr2B 75.395 443 74 19 2784 3199 9122282 9121848 7.230000e-42 182
29 TraesCS5B01G414700 chr2B 77.818 275 40 10 2784 3041 8999223 8999493 2.040000e-32 150
30 TraesCS5B01G414700 chr2B 88.596 114 4 3 1088 1201 8997507 8997611 2.650000e-26 130
31 TraesCS5B01G414700 chr1A 98.634 1098 9 3 1 1092 299644926 299643829 0.000000e+00 1940
32 TraesCS5B01G414700 chr3A 98.713 1088 13 1 1 1087 686143727 686142640 0.000000e+00 1930
33 TraesCS5B01G414700 chr3B 98.620 1087 10 1 1 1087 177084722 177085803 0.000000e+00 1919
34 TraesCS5B01G414700 chr7B 98.260 1092 14 1 1 1087 551950340 551949249 0.000000e+00 1906
35 TraesCS5B01G414700 chr4B 98.257 1090 11 4 1 1087 117048357 117047273 0.000000e+00 1901
36 TraesCS5B01G414700 chr4B 83.767 1152 173 9 1146 2292 634316471 634317613 0.000000e+00 1079
37 TraesCS5B01G414700 chr6A 97.704 1089 20 1 1 1089 59572479 59571396 0.000000e+00 1868
38 TraesCS5B01G414700 chrUn 98.704 926 8 2 1 925 430960626 430959704 0.000000e+00 1640
39 TraesCS5B01G414700 chrUn 83.020 1384 203 15 1088 2447 15916102 15914727 0.000000e+00 1225
40 TraesCS5B01G414700 chrUn 98.824 680 6 2 1 679 468026745 468026067 0.000000e+00 1210
41 TraesCS5B01G414700 chrUn 81.941 1401 202 28 1088 2452 15478555 15477170 0.000000e+00 1138
42 TraesCS5B01G414700 chrUn 82.563 1319 202 14 1088 2389 15553547 15554854 0.000000e+00 1136


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 TraesCS5B01G414700 chr5B 588932283 588935560 3277 True 2206.666667 6054 100.000000 1 3278 3 chr5B.!!$R1 3277
1 TraesCS5B01G414700 chr5D 480599796 480601821 2025 True 1803.000000 2809 96.301500 1088 3278 2 chr5D.!!$R1 2190
2 TraesCS5B01G414700 chr5A 599778417 599780462 2045 True 1773.500000 2758 95.765000 1088 3278 2 chr5A.!!$R2 2190
3 TraesCS5B01G414700 chr5A 143352415 143353037 622 True 1110.000000 1110 98.876000 467 1088 1 chr5A.!!$R1 621
4 TraesCS5B01G414700 chr2A 1874386 1876359 1973 False 1503.000000 2492 91.253000 1088 3202 2 chr2A.!!$F5 2114
5 TraesCS5B01G414700 chr2A 2884280 2885009 729 False 525.000000 525 80.054000 1094 1826 1 chr2A.!!$F3 732
6 TraesCS5B01G414700 chr2D 22566663 22568082 1419 True 1214.000000 1214 82.443000 1088 2500 1 chr2D.!!$R2 1412
7 TraesCS5B01G414700 chr2D 1994574 1996614 2040 False 1051.000000 2248 93.640000 1088 3278 3 chr2D.!!$F1 2190
8 TraesCS5B01G414700 chr2B 399343622 399344715 1093 True 1940.000000 1940 98.634000 1 1096 1 chr2B.!!$R3 1095
9 TraesCS5B01G414700 chr2B 8997507 8999493 1986 False 453.666667 1081 83.077333 1088 3041 3 chr2B.!!$F3 1953
10 TraesCS5B01G414700 chr2B 472111 473987 1876 False 408.000000 532 89.969333 1088 3247 3 chr2B.!!$F1 2159
11 TraesCS5B01G414700 chr2B 8568134 8570124 1990 False 324.500000 401 85.329500 1088 3278 2 chr2B.!!$F2 2190
12 TraesCS5B01G414700 chr1A 299643829 299644926 1097 True 1940.000000 1940 98.634000 1 1092 1 chr1A.!!$R1 1091
13 TraesCS5B01G414700 chr3A 686142640 686143727 1087 True 1930.000000 1930 98.713000 1 1087 1 chr3A.!!$R1 1086
14 TraesCS5B01G414700 chr3B 177084722 177085803 1081 False 1919.000000 1919 98.620000 1 1087 1 chr3B.!!$F1 1086
15 TraesCS5B01G414700 chr7B 551949249 551950340 1091 True 1906.000000 1906 98.260000 1 1087 1 chr7B.!!$R1 1086
16 TraesCS5B01G414700 chr4B 117047273 117048357 1084 True 1901.000000 1901 98.257000 1 1087 1 chr4B.!!$R1 1086
17 TraesCS5B01G414700 chr4B 634316471 634317613 1142 False 1079.000000 1079 83.767000 1146 2292 1 chr4B.!!$F1 1146
18 TraesCS5B01G414700 chr6A 59571396 59572479 1083 True 1868.000000 1868 97.704000 1 1089 1 chr6A.!!$R1 1088
19 TraesCS5B01G414700 chrUn 430959704 430960626 922 True 1640.000000 1640 98.704000 1 925 1 chrUn.!!$R3 924
20 TraesCS5B01G414700 chrUn 15914727 15916102 1375 True 1225.000000 1225 83.020000 1088 2447 1 chrUn.!!$R2 1359
21 TraesCS5B01G414700 chrUn 468026067 468026745 678 True 1210.000000 1210 98.824000 1 679 1 chrUn.!!$R4 678
22 TraesCS5B01G414700 chrUn 15477170 15478555 1385 True 1138.000000 1138 81.941000 1088 2452 1 chrUn.!!$R1 1364
23 TraesCS5B01G414700 chrUn 15553547 15554854 1307 False 1136.000000 1136 82.563000 1088 2389 1 chrUn.!!$F1 1301

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
381 382 1.527034 GCATGAAGCCAGTGAACTCA 58.473 50.0 0.0 0.0 37.23 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2376 2607 0.250338 GGAACTCCAAGGCGTTGTCT 60.25 55.0 17.23 0.0 35.64 3.41 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
179 180 3.333680 TCCTCATAAGCCAAAACCCTCTT 59.666 43.478 0.00 0.0 0.00 2.85
381 382 1.527034 GCATGAAGCCAGTGAACTCA 58.473 50.000 0.00 0.0 37.23 3.41
424 425 2.342279 CCGGACAGCGAGGAACAA 59.658 61.111 0.00 0.0 0.00 2.83
1305 1482 8.533569 AATTGGAGATACGGGATTGTAAAAAT 57.466 30.769 0.00 0.0 0.00 1.82
1353 1539 1.812235 TGCGACAAACAGCATCAGAT 58.188 45.000 0.00 0.0 38.59 2.90
1417 1609 2.679716 GGGTGCTGCTCTTCCCAT 59.320 61.111 14.26 0.0 39.68 4.00
1646 1849 5.104485 AGCTTACGAAATTAGAAGGGATGGT 60.104 40.000 0.00 0.0 0.00 3.55
1993 2196 0.923729 TGGGTATGGGCATGAAGGGT 60.924 55.000 0.00 0.0 0.00 4.34
2000 2203 1.304381 GGCATGAAGGGTTGGAGCA 60.304 57.895 0.00 0.0 0.00 4.26
2034 2237 0.998145 AAGAGGATGCCCTTCAGCTT 59.002 50.000 0.00 0.0 44.53 3.74
2376 2607 6.070366 TGCATTTATTCCCATCCAATGTTCAA 60.070 34.615 0.00 0.0 0.00 2.69
2510 2816 5.687166 TCCTTCCTGTACAAATTATCCGT 57.313 39.130 0.00 0.0 0.00 4.69
2540 2873 0.603569 ACTTCACTCCTGCTGTACCG 59.396 55.000 0.00 0.0 0.00 4.02
2676 3012 3.443681 AGATTTATTTGTCAACGCCCCTG 59.556 43.478 0.00 0.0 0.00 4.45
2749 3142 7.830739 TCTGCAAGTCTCTTTTCTTTTCTTTT 58.169 30.769 0.00 0.0 33.76 2.27
2750 3143 7.970614 TCTGCAAGTCTCTTTTCTTTTCTTTTC 59.029 33.333 0.00 0.0 33.76 2.29
2752 3145 8.306761 TGCAAGTCTCTTTTCTTTTCTTTTCTT 58.693 29.630 0.00 0.0 0.00 2.52
2775 3168 9.743057 TCTTTATTTGTTTTGGTTCTATGTGTG 57.257 29.630 0.00 0.0 0.00 3.82
2776 3169 7.938563 TTATTTGTTTTGGTTCTATGTGTGC 57.061 32.000 0.00 0.0 0.00 4.57
2778 3171 4.566545 TGTTTTGGTTCTATGTGTGCAG 57.433 40.909 0.00 0.0 0.00 4.41
2779 3172 3.317711 TGTTTTGGTTCTATGTGTGCAGG 59.682 43.478 0.00 0.0 0.00 4.85
2781 3174 2.183478 TGGTTCTATGTGTGCAGGTG 57.817 50.000 0.00 0.0 0.00 4.00
2782 3175 1.419762 TGGTTCTATGTGTGCAGGTGT 59.580 47.619 0.00 0.0 0.00 4.16
2783 3176 2.158682 TGGTTCTATGTGTGCAGGTGTT 60.159 45.455 0.00 0.0 0.00 3.32
2784 3177 2.484264 GGTTCTATGTGTGCAGGTGTTC 59.516 50.000 0.00 0.0 0.00 3.18
2785 3178 3.138304 GTTCTATGTGTGCAGGTGTTCA 58.862 45.455 0.00 0.0 0.00 3.18
2786 3179 3.483808 TCTATGTGTGCAGGTGTTCAA 57.516 42.857 0.00 0.0 0.00 2.69
2787 3180 3.138304 TCTATGTGTGCAGGTGTTCAAC 58.862 45.455 0.00 0.0 0.00 3.18
2788 3181 0.662619 ATGTGTGCAGGTGTTCAACG 59.337 50.000 0.00 0.0 0.00 4.10
2789 3182 0.391793 TGTGTGCAGGTGTTCAACGA 60.392 50.000 0.00 0.0 0.00 3.85
2790 3183 0.944386 GTGTGCAGGTGTTCAACGAT 59.056 50.000 0.00 0.0 0.00 3.73
2791 3184 2.139917 GTGTGCAGGTGTTCAACGATA 58.860 47.619 0.00 0.0 0.00 2.92
2792 3185 2.157668 GTGTGCAGGTGTTCAACGATAG 59.842 50.000 0.00 0.0 46.19 2.08
2822 3215 9.722056 AAATATCTCAGATTTATTTGTCAACGC 57.278 29.630 0.00 0.0 0.00 4.84
2823 3216 5.545658 TCTCAGATTTATTTGTCAACGCC 57.454 39.130 0.00 0.0 0.00 5.68
2824 3217 4.394920 TCTCAGATTTATTTGTCAACGCCC 59.605 41.667 0.00 0.0 0.00 6.13
2825 3218 3.442273 TCAGATTTATTTGTCAACGCCCC 59.558 43.478 0.00 0.0 0.00 5.80
2826 3219 3.443681 CAGATTTATTTGTCAACGCCCCT 59.556 43.478 0.00 0.0 0.00 4.79
2827 3220 3.443681 AGATTTATTTGTCAACGCCCCTG 59.556 43.478 0.00 0.0 0.00 4.45
2828 3221 2.570415 TTATTTGTCAACGCCCCTGA 57.430 45.000 0.00 0.0 0.00 3.86
2829 3222 2.799126 TATTTGTCAACGCCCCTGAT 57.201 45.000 0.00 0.0 0.00 2.90
2830 3223 1.463674 ATTTGTCAACGCCCCTGATC 58.536 50.000 0.00 0.0 0.00 2.92
2831 3224 0.400213 TTTGTCAACGCCCCTGATCT 59.600 50.000 0.00 0.0 0.00 2.75
2832 3225 0.400213 TTGTCAACGCCCCTGATCTT 59.600 50.000 0.00 0.0 0.00 2.40
2833 3226 0.400213 TGTCAACGCCCCTGATCTTT 59.600 50.000 0.00 0.0 0.00 2.52
2834 3227 1.087501 GTCAACGCCCCTGATCTTTC 58.912 55.000 0.00 0.0 0.00 2.62
2835 3228 0.035439 TCAACGCCCCTGATCTTTCC 60.035 55.000 0.00 0.0 0.00 3.13
2836 3229 0.322456 CAACGCCCCTGATCTTTCCA 60.322 55.000 0.00 0.0 0.00 3.53
2837 3230 0.322546 AACGCCCCTGATCTTTCCAC 60.323 55.000 0.00 0.0 0.00 4.02
2838 3231 1.299648 CGCCCCTGATCTTTCCACA 59.700 57.895 0.00 0.0 0.00 4.17
2839 3232 0.322456 CGCCCCTGATCTTTCCACAA 60.322 55.000 0.00 0.0 0.00 3.33
2840 3233 1.467920 GCCCCTGATCTTTCCACAAG 58.532 55.000 0.00 0.0 0.00 3.16
2841 3234 1.957113 GCCCCTGATCTTTCCACAAGG 60.957 57.143 0.00 0.0 0.00 3.61
2842 3235 1.467920 CCCTGATCTTTCCACAAGGC 58.532 55.000 0.00 0.0 33.74 4.35
2843 3236 1.089920 CCTGATCTTTCCACAAGGCG 58.910 55.000 0.00 0.0 33.74 5.52
2844 3237 1.339055 CCTGATCTTTCCACAAGGCGA 60.339 52.381 0.00 0.0 33.74 5.54
2845 3238 2.005451 CTGATCTTTCCACAAGGCGAG 58.995 52.381 0.00 0.0 33.74 5.03
2846 3239 1.623311 TGATCTTTCCACAAGGCGAGA 59.377 47.619 0.00 0.0 32.53 4.04
2847 3240 2.038426 TGATCTTTCCACAAGGCGAGAA 59.962 45.455 0.00 0.0 32.01 2.87
2848 3241 2.631160 TCTTTCCACAAGGCGAGAAA 57.369 45.000 0.00 0.0 33.74 2.52
2857 3250 0.942252 AAGGCGAGAAAACCAACGTC 59.058 50.000 0.00 0.0 0.00 4.34
2861 3263 2.129607 GCGAGAAAACCAACGTCACTA 58.870 47.619 0.00 0.0 0.00 2.74
2863 3265 2.155155 CGAGAAAACCAACGTCACTAGC 59.845 50.000 0.00 0.0 0.00 3.42
2864 3266 3.128349 GAGAAAACCAACGTCACTAGCA 58.872 45.455 0.00 0.0 0.00 3.49
2865 3267 3.131396 AGAAAACCAACGTCACTAGCAG 58.869 45.455 0.00 0.0 0.00 4.24
2866 3268 1.226746 AAACCAACGTCACTAGCAGC 58.773 50.000 0.00 0.0 0.00 5.25
2867 3269 0.393077 AACCAACGTCACTAGCAGCT 59.607 50.000 0.00 0.0 0.00 4.24
2869 3271 1.616865 ACCAACGTCACTAGCAGCTAA 59.383 47.619 3.09 0.0 0.00 3.09
2870 3272 2.233922 ACCAACGTCACTAGCAGCTAAT 59.766 45.455 3.09 0.0 0.00 1.73
2875 3277 5.326200 ACGTCACTAGCAGCTAATACTTT 57.674 39.130 3.09 0.0 0.00 2.66
2876 3278 5.341617 ACGTCACTAGCAGCTAATACTTTC 58.658 41.667 3.09 0.0 0.00 2.62
2877 3279 5.125739 ACGTCACTAGCAGCTAATACTTTCT 59.874 40.000 3.09 0.0 0.00 2.52
2878 3280 5.457148 CGTCACTAGCAGCTAATACTTTCTG 59.543 44.000 3.09 0.0 0.00 3.02
2884 3286 4.902964 GCAGCTAATACTTTCTGCAAGTC 58.097 43.478 8.04 0.0 42.62 3.01
2885 3287 4.633565 GCAGCTAATACTTTCTGCAAGTCT 59.366 41.667 8.04 0.0 42.62 3.24
2886 3288 5.220567 GCAGCTAATACTTTCTGCAAGTCTC 60.221 44.000 8.04 0.0 42.62 3.36
2887 3289 6.105333 CAGCTAATACTTTCTGCAAGTCTCT 58.895 40.000 0.00 0.0 42.62 3.10
2888 3290 6.593382 CAGCTAATACTTTCTGCAAGTCTCTT 59.407 38.462 0.00 0.0 42.62 2.85
2889 3291 7.118971 CAGCTAATACTTTCTGCAAGTCTCTTT 59.881 37.037 0.00 0.0 42.62 2.52
2890 3292 7.663493 AGCTAATACTTTCTGCAAGTCTCTTTT 59.337 33.333 0.00 0.0 42.62 2.27
2891 3293 7.960195 GCTAATACTTTCTGCAAGTCTCTTTTC 59.040 37.037 0.00 0.0 42.62 2.29
2892 3294 9.213799 CTAATACTTTCTGCAAGTCTCTTTTCT 57.786 33.333 0.00 0.0 42.62 2.52
2893 3295 8.457238 AATACTTTCTGCAAGTCTCTTTTCTT 57.543 30.769 0.00 0.0 42.62 2.52
2894 3296 6.765915 ACTTTCTGCAAGTCTCTTTTCTTT 57.234 33.333 0.00 0.0 42.62 2.52
2895 3297 7.163001 ACTTTCTGCAAGTCTCTTTTCTTTT 57.837 32.000 0.00 0.0 42.62 2.27
2896 3298 7.254137 ACTTTCTGCAAGTCTCTTTTCTTTTC 58.746 34.615 0.00 0.0 42.62 2.29
2897 3299 7.121907 ACTTTCTGCAAGTCTCTTTTCTTTTCT 59.878 33.333 0.00 0.0 42.62 2.52
2898 3300 7.396540 TTCTGCAAGTCTCTTTTCTTTTCTT 57.603 32.000 0.00 0.0 33.76 2.52
2899 3301 7.396540 TCTGCAAGTCTCTTTTCTTTTCTTT 57.603 32.000 0.00 0.0 33.76 2.52
2900 3302 7.830739 TCTGCAAGTCTCTTTTCTTTTCTTTT 58.169 30.769 0.00 0.0 33.76 2.27
2901 3303 7.970614 TCTGCAAGTCTCTTTTCTTTTCTTTTC 59.029 33.333 0.00 0.0 33.76 2.29
2902 3304 7.830739 TGCAAGTCTCTTTTCTTTTCTTTTCT 58.169 30.769 0.00 0.0 0.00 2.52
2903 3305 8.306761 TGCAAGTCTCTTTTCTTTTCTTTTCTT 58.693 29.630 0.00 0.0 0.00 2.52
2904 3306 9.144747 GCAAGTCTCTTTTCTTTTCTTTTCTTT 57.855 29.630 0.00 0.0 0.00 2.52
3002 3413 6.038271 GGGTTATTGTTATTCATCAAGACGCT 59.962 38.462 0.00 0.0 0.00 5.07
3042 3453 7.733402 AATTTGGGTTTCACAATCAGAATTG 57.267 32.000 0.00 0.0 46.42 2.32
3125 3538 7.891183 ATTATCATCCACTCTACGTTATTGC 57.109 36.000 0.00 0.0 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
179 180 4.058124 GGTTGCTGATCGTGCTTATGATA 58.942 43.478 11.02 0.00 0.00 2.15
381 382 8.251721 GTGATCTTTGATGGTACTAACTACACT 58.748 37.037 0.00 0.00 0.00 3.55
424 425 1.094785 GCTGCATCGGGTTATGTTGT 58.905 50.000 0.00 0.00 0.00 3.32
520 531 0.758685 CCTTGATCTCCTCTCCCGCT 60.759 60.000 0.00 0.00 0.00 5.52
670 681 3.396822 ATCTCCTACCCAGCCGCCT 62.397 63.158 0.00 0.00 0.00 5.52
1305 1482 3.201266 CCCCCACTACCAGCTGTTTTATA 59.799 47.826 13.81 0.00 0.00 0.98
1417 1609 4.911390 TGTAGTGAGTCACAGAGATGAGA 58.089 43.478 24.73 0.00 36.74 3.27
1646 1849 3.441500 TTGAGAGAGGCTCTAGTGTCA 57.558 47.619 18.75 14.59 41.35 3.58
1993 2196 0.473755 TCCTTGCTGAAGTGCTCCAA 59.526 50.000 0.00 0.00 0.00 3.53
2000 2203 1.271271 CCTCTTGCTCCTTGCTGAAGT 60.271 52.381 0.00 0.00 43.37 3.01
2034 2237 1.719378 AGTTTCTGGAGGGAGGAGAGA 59.281 52.381 0.00 0.00 0.00 3.10
2376 2607 0.250338 GGAACTCCAAGGCGTTGTCT 60.250 55.000 17.23 0.00 35.64 3.41
2510 2816 4.563580 GCAGGAGTGAAGTTCCATACTCAA 60.564 45.833 18.44 0.00 40.91 3.02
2676 3012 2.386661 TCTCGCCTTGTGGAAAGATC 57.613 50.000 0.00 0.00 34.57 2.75
2749 3142 9.743057 CACACATAGAACCAAAACAAATAAAGA 57.257 29.630 0.00 0.00 0.00 2.52
2750 3143 8.487176 GCACACATAGAACCAAAACAAATAAAG 58.513 33.333 0.00 0.00 0.00 1.85
2752 3145 7.492524 TGCACACATAGAACCAAAACAAATAA 58.507 30.769 0.00 0.00 0.00 1.40
2754 3147 5.911752 TGCACACATAGAACCAAAACAAAT 58.088 33.333 0.00 0.00 0.00 2.32
2755 3148 5.330455 TGCACACATAGAACCAAAACAAA 57.670 34.783 0.00 0.00 0.00 2.83
2757 3150 3.317711 CCTGCACACATAGAACCAAAACA 59.682 43.478 0.00 0.00 0.00 2.83
2758 3151 3.317993 ACCTGCACACATAGAACCAAAAC 59.682 43.478 0.00 0.00 0.00 2.43
2759 3152 3.317711 CACCTGCACACATAGAACCAAAA 59.682 43.478 0.00 0.00 0.00 2.44
2760 3153 2.884012 CACCTGCACACATAGAACCAAA 59.116 45.455 0.00 0.00 0.00 3.28
2761 3154 2.158682 ACACCTGCACACATAGAACCAA 60.159 45.455 0.00 0.00 0.00 3.67
2772 3165 2.224185 ACTATCGTTGAACACCTGCACA 60.224 45.455 0.00 0.00 0.00 4.57
2774 3167 2.036604 TCACTATCGTTGAACACCTGCA 59.963 45.455 0.00 0.00 0.00 4.41
2775 3168 2.683968 TCACTATCGTTGAACACCTGC 58.316 47.619 0.00 0.00 0.00 4.85
2776 3169 5.666969 TTTTCACTATCGTTGAACACCTG 57.333 39.130 0.00 0.00 0.00 4.00
2778 3171 8.197988 AGATATTTTCACTATCGTTGAACACC 57.802 34.615 0.00 0.00 32.07 4.16
2779 3172 8.869897 TGAGATATTTTCACTATCGTTGAACAC 58.130 33.333 0.00 0.00 32.07 3.32
2781 3174 9.302345 TCTGAGATATTTTCACTATCGTTGAAC 57.698 33.333 0.00 0.00 32.07 3.18
2796 3189 9.722056 GCGTTGACAAATAAATCTGAGATATTT 57.278 29.630 0.00 0.00 31.25 1.40
2797 3190 8.345565 GGCGTTGACAAATAAATCTGAGATATT 58.654 33.333 0.00 0.00 0.00 1.28
2798 3191 7.041098 GGGCGTTGACAAATAAATCTGAGATAT 60.041 37.037 0.00 0.00 0.00 1.63
2799 3192 6.260050 GGGCGTTGACAAATAAATCTGAGATA 59.740 38.462 0.00 0.00 0.00 1.98
2800 3193 5.066505 GGGCGTTGACAAATAAATCTGAGAT 59.933 40.000 0.00 0.00 0.00 2.75
2801 3194 4.394920 GGGCGTTGACAAATAAATCTGAGA 59.605 41.667 0.00 0.00 0.00 3.27
2802 3195 4.438744 GGGGCGTTGACAAATAAATCTGAG 60.439 45.833 0.00 0.00 0.00 3.35
2803 3196 3.442273 GGGGCGTTGACAAATAAATCTGA 59.558 43.478 0.00 0.00 0.00 3.27
2804 3197 3.443681 AGGGGCGTTGACAAATAAATCTG 59.556 43.478 0.00 0.00 0.00 2.90
2805 3198 3.443681 CAGGGGCGTTGACAAATAAATCT 59.556 43.478 0.00 0.00 0.00 2.40
2806 3199 3.442273 TCAGGGGCGTTGACAAATAAATC 59.558 43.478 0.00 0.00 0.00 2.17
2807 3200 3.426615 TCAGGGGCGTTGACAAATAAAT 58.573 40.909 0.00 0.00 0.00 1.40
2808 3201 2.865079 TCAGGGGCGTTGACAAATAAA 58.135 42.857 0.00 0.00 0.00 1.40
2809 3202 2.570415 TCAGGGGCGTTGACAAATAA 57.430 45.000 0.00 0.00 0.00 1.40
2810 3203 2.238646 AGATCAGGGGCGTTGACAAATA 59.761 45.455 0.00 0.00 0.00 1.40
2811 3204 1.004745 AGATCAGGGGCGTTGACAAAT 59.995 47.619 0.00 0.00 0.00 2.32
2812 3205 0.400213 AGATCAGGGGCGTTGACAAA 59.600 50.000 0.00 0.00 0.00 2.83
2813 3206 0.400213 AAGATCAGGGGCGTTGACAA 59.600 50.000 0.00 0.00 0.00 3.18
2814 3207 0.400213 AAAGATCAGGGGCGTTGACA 59.600 50.000 0.00 0.00 0.00 3.58
2815 3208 1.087501 GAAAGATCAGGGGCGTTGAC 58.912 55.000 0.00 0.00 0.00 3.18
2816 3209 0.035439 GGAAAGATCAGGGGCGTTGA 60.035 55.000 0.00 0.00 0.00 3.18
2817 3210 0.322456 TGGAAAGATCAGGGGCGTTG 60.322 55.000 0.00 0.00 0.00 4.10
2818 3211 0.322546 GTGGAAAGATCAGGGGCGTT 60.323 55.000 0.00 0.00 0.00 4.84
2819 3212 1.299976 GTGGAAAGATCAGGGGCGT 59.700 57.895 0.00 0.00 0.00 5.68
2820 3213 0.322456 TTGTGGAAAGATCAGGGGCG 60.322 55.000 0.00 0.00 0.00 6.13
2821 3214 1.467920 CTTGTGGAAAGATCAGGGGC 58.532 55.000 0.00 0.00 0.00 5.80
2822 3215 1.957113 GCCTTGTGGAAAGATCAGGGG 60.957 57.143 0.00 0.00 34.57 4.79
2823 3216 1.467920 GCCTTGTGGAAAGATCAGGG 58.532 55.000 0.00 0.00 34.57 4.45
2824 3217 1.089920 CGCCTTGTGGAAAGATCAGG 58.910 55.000 0.00 0.00 34.57 3.86
2825 3218 2.005451 CTCGCCTTGTGGAAAGATCAG 58.995 52.381 0.00 0.00 34.57 2.90
2826 3219 1.623311 TCTCGCCTTGTGGAAAGATCA 59.377 47.619 0.00 0.00 34.57 2.92
2827 3220 2.386661 TCTCGCCTTGTGGAAAGATC 57.613 50.000 0.00 0.00 34.57 2.75
2828 3221 2.859165 TTCTCGCCTTGTGGAAAGAT 57.141 45.000 0.00 0.00 34.57 2.40
2829 3222 2.616842 GTTTTCTCGCCTTGTGGAAAGA 59.383 45.455 0.00 0.00 34.57 2.52
2830 3223 2.287608 GGTTTTCTCGCCTTGTGGAAAG 60.288 50.000 0.00 0.00 34.57 2.62
2831 3224 1.679153 GGTTTTCTCGCCTTGTGGAAA 59.321 47.619 0.00 0.00 34.57 3.13
2832 3225 1.314730 GGTTTTCTCGCCTTGTGGAA 58.685 50.000 0.00 0.00 34.57 3.53
2833 3226 0.181587 TGGTTTTCTCGCCTTGTGGA 59.818 50.000 0.00 0.00 34.57 4.02
2834 3227 1.028905 TTGGTTTTCTCGCCTTGTGG 58.971 50.000 0.00 0.00 0.00 4.17
2835 3228 1.596954 CGTTGGTTTTCTCGCCTTGTG 60.597 52.381 0.00 0.00 0.00 3.33
2836 3229 0.661020 CGTTGGTTTTCTCGCCTTGT 59.339 50.000 0.00 0.00 0.00 3.16
2837 3230 0.661020 ACGTTGGTTTTCTCGCCTTG 59.339 50.000 0.00 0.00 0.00 3.61
2838 3231 0.942252 GACGTTGGTTTTCTCGCCTT 59.058 50.000 0.00 0.00 0.00 4.35
2839 3232 0.179067 TGACGTTGGTTTTCTCGCCT 60.179 50.000 0.00 0.00 0.00 5.52
2840 3233 0.041576 GTGACGTTGGTTTTCTCGCC 60.042 55.000 0.00 0.00 0.00 5.54
2841 3234 0.935196 AGTGACGTTGGTTTTCTCGC 59.065 50.000 0.00 0.00 0.00 5.03
2842 3235 2.155155 GCTAGTGACGTTGGTTTTCTCG 59.845 50.000 0.00 0.00 0.00 4.04
2843 3236 3.128349 TGCTAGTGACGTTGGTTTTCTC 58.872 45.455 0.00 0.00 0.00 2.87
2844 3237 3.131396 CTGCTAGTGACGTTGGTTTTCT 58.869 45.455 0.00 0.00 0.00 2.52
2845 3238 2.349532 GCTGCTAGTGACGTTGGTTTTC 60.350 50.000 0.00 0.00 0.00 2.29
2846 3239 1.602377 GCTGCTAGTGACGTTGGTTTT 59.398 47.619 0.00 0.00 0.00 2.43
2847 3240 1.202651 AGCTGCTAGTGACGTTGGTTT 60.203 47.619 0.00 0.00 0.00 3.27
2848 3241 0.393077 AGCTGCTAGTGACGTTGGTT 59.607 50.000 0.00 0.00 0.00 3.67
2857 3250 5.649602 GCAGAAAGTATTAGCTGCTAGTG 57.350 43.478 14.15 0.00 46.57 2.74
2875 3277 7.396540 AAAGAAAAGAAAAGAGACTTGCAGA 57.603 32.000 0.00 0.00 0.00 4.26
2876 3278 7.972832 AGAAAAGAAAAGAAAAGAGACTTGCAG 59.027 33.333 0.00 0.00 0.00 4.41
2877 3279 7.830739 AGAAAAGAAAAGAAAAGAGACTTGCA 58.169 30.769 0.00 0.00 0.00 4.08
2878 3280 8.694975 AAGAAAAGAAAAGAAAAGAGACTTGC 57.305 30.769 0.00 0.00 0.00 4.01
2900 3302 9.743057 CACACATAGAACCAAAACAAATAAAGA 57.257 29.630 0.00 0.00 0.00 2.52
2901 3303 8.487176 GCACACATAGAACCAAAACAAATAAAG 58.513 33.333 0.00 0.00 0.00 1.85
2902 3304 7.981789 TGCACACATAGAACCAAAACAAATAAA 59.018 29.630 0.00 0.00 0.00 1.40
2903 3305 7.492524 TGCACACATAGAACCAAAACAAATAA 58.507 30.769 0.00 0.00 0.00 1.40
2904 3306 7.043961 TGCACACATAGAACCAAAACAAATA 57.956 32.000 0.00 0.00 0.00 1.40
3002 3413 6.717289 ACCCAAATTATGCAAGTAGACTACA 58.283 36.000 14.95 0.00 0.00 2.74
3104 3515 4.100963 TGGCAATAACGTAGAGTGGATGAT 59.899 41.667 0.00 0.00 0.00 2.45
3125 3538 2.445427 TGCATCAACACCTGGTATTGG 58.555 47.619 17.19 4.09 0.00 3.16


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

AutoCloner maintained by Alex Coulton.