Multiple sequence alignment - TraesCS1A01G280500

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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 TraesCS1A01G280500 chr1A 100.000 3659 0 0 1 3659 478259640 478255982 0.000000e+00 6758
1 TraesCS1A01G280500 chr1D 89.700 3097 166 73 651 3659 377572619 377569588 0.000000e+00 3810
2 TraesCS1A01G280500 chr1D 86.070 402 23 10 126 526 377573405 377573036 5.690000e-108 401
3 TraesCS1A01G280500 chr1D 89.881 168 11 2 483 650 377573032 377572871 1.030000e-50 211
4 TraesCS1A01G280500 chr1D 85.185 108 4 5 1 108 377573558 377573463 2.320000e-17 100
5 TraesCS1A01G280500 chr1B 88.333 3120 182 77 651 3659 504507607 504504559 0.000000e+00 3578
6 TraesCS1A01G280500 chr1B 89.377 273 8 8 130 389 504508922 504508658 1.270000e-84 324
7 TraesCS1A01G280500 chr1B 86.498 237 15 12 427 656 504507912 504507686 1.010000e-60 244
8 TraesCS1A01G280500 chr1B 89.720 107 8 1 1 107 504509086 504508983 2.290000e-27 134


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 TraesCS1A01G280500 chr1A 478255982 478259640 3658 True 6758.0 6758 100.000 1 3659 1 chr1A.!!$R1 3658
1 TraesCS1A01G280500 chr1D 377569588 377573558 3970 True 1130.5 3810 87.709 1 3659 4 chr1D.!!$R1 3658
2 TraesCS1A01G280500 chr1B 504504559 504509086 4527 True 1070.0 3578 88.482 1 3659 4 chr1B.!!$R1 3658

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
147 188 0.035534 TGCAGCTCGGCATTTTCCTA 60.036 50.0 0.00 0.0 39.25 2.94 F
235 276 0.037139 GTATACCGCACCACACCACA 60.037 55.0 0.00 0.0 0.00 4.17 F
1737 2913 0.036858 GCCAGGGTGAGTTCTCAGTC 60.037 60.0 2.53 0.0 0.00 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1201 2364 0.179089 CCAAGCTGTCCTCCTCATCG 60.179 60.0 0.00 0.0 0.00 3.84 R
2159 3337 0.744281 ACAACCAGAACGGCCAAAAG 59.256 50.0 2.24 0.0 39.03 2.27 R
2716 3910 0.174845 CTCCACCGCTTTACCATCGA 59.825 55.0 0.00 0.0 0.00 3.59 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
24 25 4.789075 CGGGCCAGTACCACGACG 62.789 72.222 4.39 0.00 0.00 5.12
38 39 1.226211 CGACGGCCAGTACAGTACG 60.226 63.158 2.24 0.93 0.00 3.67
39 40 1.515736 GACGGCCAGTACAGTACGC 60.516 63.158 2.24 3.77 0.00 4.42
74 75 3.674423 GCAAGTACGTACTACAGTACCG 58.326 50.000 27.59 10.33 46.01 4.02
136 177 2.813908 GTTACCGGGTGCAGCTCG 60.814 66.667 16.65 16.59 41.64 5.03
143 184 2.639327 GGGTGCAGCTCGGCATTTT 61.639 57.895 16.65 0.00 46.92 1.82
144 185 1.153958 GGTGCAGCTCGGCATTTTC 60.154 57.895 9.07 0.00 46.92 2.29
146 187 1.303561 TGCAGCTCGGCATTTTCCT 60.304 52.632 0.00 0.00 39.25 3.36
147 188 0.035534 TGCAGCTCGGCATTTTCCTA 60.036 50.000 0.00 0.00 39.25 2.94
148 189 1.312815 GCAGCTCGGCATTTTCCTAT 58.687 50.000 0.00 0.00 0.00 2.57
162 203 7.345943 GCATTTTCCTATAGTTTTCTACTCGC 58.654 38.462 0.00 0.00 38.33 5.03
206 247 2.117423 CCCACGCCCTTTCCCTTT 59.883 61.111 0.00 0.00 0.00 3.11
222 263 3.198417 TCCCTTTTTCCACTCCGTATACC 59.802 47.826 0.00 0.00 0.00 2.73
223 264 3.192466 CCTTTTTCCACTCCGTATACCG 58.808 50.000 0.00 0.00 0.00 4.02
224 265 2.298411 TTTTCCACTCCGTATACCGC 57.702 50.000 0.00 0.00 34.38 5.68
225 266 1.184431 TTTCCACTCCGTATACCGCA 58.816 50.000 0.00 0.00 34.38 5.69
226 267 0.457035 TTCCACTCCGTATACCGCAC 59.543 55.000 0.00 0.00 34.38 5.34
227 268 1.066918 CCACTCCGTATACCGCACC 59.933 63.158 0.00 0.00 34.38 5.01
228 269 1.669049 CCACTCCGTATACCGCACCA 61.669 60.000 0.00 0.00 34.38 4.17
229 270 0.526954 CACTCCGTATACCGCACCAC 60.527 60.000 0.00 0.00 34.38 4.16
230 271 0.966875 ACTCCGTATACCGCACCACA 60.967 55.000 0.00 0.00 34.38 4.17
231 272 0.526954 CTCCGTATACCGCACCACAC 60.527 60.000 0.00 0.00 34.38 3.82
232 273 1.519898 CCGTATACCGCACCACACC 60.520 63.158 0.00 0.00 34.38 4.16
233 274 1.215912 CGTATACCGCACCACACCA 59.784 57.895 0.00 0.00 0.00 4.17
234 275 1.079875 CGTATACCGCACCACACCAC 61.080 60.000 0.00 0.00 0.00 4.16
235 276 0.037139 GTATACCGCACCACACCACA 60.037 55.000 0.00 0.00 0.00 4.17
236 277 0.248012 TATACCGCACCACACCACAG 59.752 55.000 0.00 0.00 0.00 3.66
313 364 4.202315 ACACAACTTAAATTCCCAAAGCCC 60.202 41.667 0.00 0.00 0.00 5.19
315 366 4.040339 ACAACTTAAATTCCCAAAGCCCAG 59.960 41.667 0.00 0.00 0.00 4.45
323 374 0.842635 CCCAAAGCCCAGCTAGAGAT 59.157 55.000 0.00 0.00 38.25 2.75
389 453 1.079405 CGCTTCTTTACTCCCGCCA 60.079 57.895 0.00 0.00 0.00 5.69
390 454 0.672401 CGCTTCTTTACTCCCGCCAA 60.672 55.000 0.00 0.00 0.00 4.52
391 455 0.803117 GCTTCTTTACTCCCGCCAAC 59.197 55.000 0.00 0.00 0.00 3.77
392 456 1.610886 GCTTCTTTACTCCCGCCAACT 60.611 52.381 0.00 0.00 0.00 3.16
393 457 2.347731 CTTCTTTACTCCCGCCAACTC 58.652 52.381 0.00 0.00 0.00 3.01
394 458 0.245539 TCTTTACTCCCGCCAACTCG 59.754 55.000 0.00 0.00 0.00 4.18
395 459 1.359459 CTTTACTCCCGCCAACTCGC 61.359 60.000 0.00 0.00 0.00 5.03
396 460 2.791501 TTTACTCCCGCCAACTCGCC 62.792 60.000 0.00 0.00 0.00 5.54
404 468 0.738389 CGCCAACTCGCCCAATTTAT 59.262 50.000 0.00 0.00 0.00 1.40
407 471 2.165437 GCCAACTCGCCCAATTTATTGA 59.835 45.455 4.07 0.00 40.14 2.57
415 479 4.524714 TCGCCCAATTTATTGACCTGAAAA 59.475 37.500 4.07 0.00 40.14 2.29
418 482 5.167845 CCCAATTTATTGACCTGAAAACCG 58.832 41.667 4.07 0.00 40.14 4.44
452 1237 3.259425 GAGCAGTTGCACTTGCGGG 62.259 63.158 14.05 0.00 45.83 6.13
453 1238 3.595758 GCAGTTGCACTTGCGGGT 61.596 61.111 5.92 0.00 45.83 5.28
454 1239 3.119193 CAGTTGCACTTGCGGGTT 58.881 55.556 0.00 0.00 45.83 4.11
455 1240 1.299316 CAGTTGCACTTGCGGGTTG 60.299 57.895 0.00 0.00 45.83 3.77
456 1241 2.658268 GTTGCACTTGCGGGTTGC 60.658 61.111 0.00 0.00 45.83 4.17
504 1337 4.385825 CACTGCACTCTGGTTTAGGTTTA 58.614 43.478 0.00 0.00 0.00 2.01
530 1363 3.430218 CAGTGCCTAACGAAGACAGAAAG 59.570 47.826 0.00 0.00 0.00 2.62
531 1364 3.321111 AGTGCCTAACGAAGACAGAAAGA 59.679 43.478 0.00 0.00 0.00 2.52
532 1365 4.056050 GTGCCTAACGAAGACAGAAAGAA 58.944 43.478 0.00 0.00 0.00 2.52
533 1366 4.510340 GTGCCTAACGAAGACAGAAAGAAA 59.490 41.667 0.00 0.00 0.00 2.52
543 1376 6.142958 CGAAGACAGAAAGAAAATTTGCCTTC 59.857 38.462 0.00 0.00 0.00 3.46
591 1424 2.740447 GTGGGTTCAGCTACCGTTTAAG 59.260 50.000 0.00 0.00 39.18 1.85
594 1427 3.434641 GGGTTCAGCTACCGTTTAAGAAC 59.565 47.826 0.00 0.02 39.18 3.01
641 1474 3.641648 ACATGGCGCACATAATAAATGC 58.358 40.909 10.83 0.00 37.84 3.56
667 1751 9.385902 CAATAATAACAATAAATCGGAGCACAG 57.614 33.333 0.00 0.00 0.00 3.66
674 1758 6.374333 ACAATAAATCGGAGCACAGTTTGTAT 59.626 34.615 0.00 0.00 0.00 2.29
760 1846 7.897575 ATCGGAATATACTTCAGAAATGAGC 57.102 36.000 0.00 0.00 0.00 4.26
762 1848 6.042093 TCGGAATATACTTCAGAAATGAGCCT 59.958 38.462 0.00 0.00 0.00 4.58
763 1849 7.232737 TCGGAATATACTTCAGAAATGAGCCTA 59.767 37.037 0.00 0.00 0.00 3.93
764 1850 7.329717 CGGAATATACTTCAGAAATGAGCCTAC 59.670 40.741 0.00 0.00 0.00 3.18
765 1851 7.604545 GGAATATACTTCAGAAATGAGCCTACC 59.395 40.741 0.00 0.00 0.00 3.18
766 1852 3.252974 ACTTCAGAAATGAGCCTACCG 57.747 47.619 0.00 0.00 0.00 4.02
767 1853 2.093447 ACTTCAGAAATGAGCCTACCGG 60.093 50.000 0.00 0.00 0.00 5.28
867 1978 8.628630 AAAAGAAAAGAGACCTCCTTAATGAG 57.371 34.615 1.03 1.03 0.00 2.90
988 2103 1.451936 CATCGACATTCCCCTCCCC 59.548 63.158 0.00 0.00 0.00 4.81
989 2104 1.056700 CATCGACATTCCCCTCCCCT 61.057 60.000 0.00 0.00 0.00 4.79
990 2105 0.764752 ATCGACATTCCCCTCCCCTC 60.765 60.000 0.00 0.00 0.00 4.30
993 2108 2.778717 CATTCCCCTCCCCTCCCC 60.779 72.222 0.00 0.00 0.00 4.81
994 2109 2.973034 ATTCCCCTCCCCTCCCCT 60.973 66.667 0.00 0.00 0.00 4.79
995 2110 3.054557 ATTCCCCTCCCCTCCCCTC 62.055 68.421 0.00 0.00 0.00 4.30
998 2113 4.179599 CCCTCCCCTCCCCTCCTC 62.180 77.778 0.00 0.00 0.00 3.71
999 2114 4.179599 CCTCCCCTCCCCTCCTCC 62.180 77.778 0.00 0.00 0.00 4.30
1000 2115 4.548513 CTCCCCTCCCCTCCTCCG 62.549 77.778 0.00 0.00 0.00 4.63
1035 2164 1.661341 CTGATAAGCACAGCACTCCC 58.339 55.000 0.00 0.00 0.00 4.30
1048 2177 0.918983 CACTCCCCTGCCTTCCATTA 59.081 55.000 0.00 0.00 0.00 1.90
1086 2249 1.002366 CGATTCTTCAAGGTGGAGCG 58.998 55.000 0.00 0.00 0.00 5.03
1147 2310 0.613853 TCCCCGACGAGTTCTTGGAT 60.614 55.000 0.00 0.00 0.00 3.41
1267 2430 3.041940 CTCGGCGGCGACAAACTT 61.042 61.111 31.46 0.00 0.00 2.66
1311 2487 1.795170 TTCTTGCTCCTTTGCGTGGC 61.795 55.000 0.00 0.00 35.36 5.01
1354 2530 1.135972 CGGTTCCTGATTGTTCGCTTG 60.136 52.381 0.00 0.00 0.00 4.01
1355 2531 2.151202 GGTTCCTGATTGTTCGCTTGA 58.849 47.619 0.00 0.00 0.00 3.02
1405 2581 3.414700 CCCAAGTCGACGCTGTGC 61.415 66.667 10.46 0.00 0.00 4.57
1737 2913 0.036858 GCCAGGGTGAGTTCTCAGTC 60.037 60.000 2.53 0.00 0.00 3.51
1803 2981 7.693952 TCTTCTTTAACATCTGTGTTTGTGTC 58.306 34.615 0.00 0.00 46.07 3.67
1810 2988 4.142622 ACATCTGTGTTTGTGTCTGTGTTG 60.143 41.667 0.00 0.00 34.01 3.33
2143 3321 1.000506 GGAAGAAGTCTGGTGCGTGTA 59.999 52.381 0.00 0.00 0.00 2.90
2159 3337 2.666619 CGTGTACCACTCGTAACACCTC 60.667 54.545 0.00 0.00 31.05 3.85
2188 3366 2.486592 CGTTCTGGTTGTTGATTACCCC 59.513 50.000 0.00 0.00 33.34 4.95
2226 3404 4.178956 TGGTGGCTAAATATTCTTCCCC 57.821 45.455 0.00 0.00 0.00 4.81
2318 3496 2.202453 GAACCTCGACGACCTCGC 60.202 66.667 0.00 0.00 42.62 5.03
2355 3533 2.785258 GGCGGCATCGTTCTTGAC 59.215 61.111 3.07 0.00 38.89 3.18
2372 3550 3.998913 TGACCATGGTAAGCATCTCAA 57.001 42.857 19.80 0.00 0.00 3.02
2373 3551 4.299586 TGACCATGGTAAGCATCTCAAA 57.700 40.909 19.80 0.00 0.00 2.69
2375 3553 3.356290 ACCATGGTAAGCATCTCAAACC 58.644 45.455 18.10 0.00 0.00 3.27
2383 3561 5.410439 GGTAAGCATCTCAAACCGAACTAAA 59.590 40.000 0.00 0.00 0.00 1.85
2385 3563 7.279313 GGTAAGCATCTCAAACCGAACTAAATA 59.721 37.037 0.00 0.00 0.00 1.40
2386 3564 6.663944 AGCATCTCAAACCGAACTAAATAC 57.336 37.500 0.00 0.00 0.00 1.89
2387 3565 5.291128 AGCATCTCAAACCGAACTAAATACG 59.709 40.000 0.00 0.00 0.00 3.06
2395 3573 4.619931 CCGAACTAAATACGGCGTTATC 57.380 45.455 21.24 5.64 40.19 1.75
2396 3574 4.293415 CCGAACTAAATACGGCGTTATCT 58.707 43.478 21.24 3.13 40.19 1.98
2397 3575 4.147653 CCGAACTAAATACGGCGTTATCTG 59.852 45.833 21.24 9.15 40.19 2.90
2398 3576 4.147653 CGAACTAAATACGGCGTTATCTGG 59.852 45.833 21.24 7.43 0.00 3.86
2402 3580 5.979517 ACTAAATACGGCGTTATCTGGTAAC 59.020 40.000 21.24 0.62 39.44 2.50
2432 3610 0.242286 TCTGACAGCGAGCTCTGTTC 59.758 55.000 12.85 3.51 46.40 3.18
2433 3611 0.735632 CTGACAGCGAGCTCTGTTCC 60.736 60.000 12.85 0.36 46.40 3.62
2532 3710 3.426568 GCGCTCTGCCACAGTTCC 61.427 66.667 0.00 0.00 37.76 3.62
2548 3726 0.104672 TTCCTGAACCCAGTCTCCCA 60.105 55.000 0.00 0.00 38.74 4.37
2561 3739 1.077716 CTCCCACCGGAACAATCCC 60.078 63.158 9.46 0.00 43.37 3.85
2711 3905 0.755686 TGACACATTGGTTTTGGGGC 59.244 50.000 0.00 0.00 0.00 5.80
2744 3938 0.467384 AAGCGGTGGAGATGGATGAG 59.533 55.000 0.00 0.00 0.00 2.90
2823 4027 1.471964 GCGAGAGAGATGTGTTAGCG 58.528 55.000 0.00 0.00 0.00 4.26
2834 4038 2.139917 TGTGTTAGCGGTTTGTAGCAG 58.860 47.619 0.00 0.00 35.48 4.24
2906 4118 6.551227 AGAAATAAAAGGCCCATGTTATCTCC 59.449 38.462 0.00 0.00 0.00 3.71
2923 4135 4.530857 CCCGTCTCCGTCCATGGC 62.531 72.222 6.96 0.96 0.00 4.40
2924 4136 3.461773 CCGTCTCCGTCCATGGCT 61.462 66.667 6.96 0.00 0.00 4.75
2925 4137 2.202797 CGTCTCCGTCCATGGCTG 60.203 66.667 6.96 0.88 0.00 4.85
2926 4138 2.187946 GTCTCCGTCCATGGCTGG 59.812 66.667 6.96 11.42 44.64 4.85
2927 4139 3.785859 TCTCCGTCCATGGCTGGC 61.786 66.667 6.96 0.00 42.80 4.85
2928 4140 3.790437 CTCCGTCCATGGCTGGCT 61.790 66.667 6.96 0.00 42.80 4.75
2929 4141 3.329889 TCCGTCCATGGCTGGCTT 61.330 61.111 6.96 0.00 42.80 4.35
2930 4142 2.361610 CCGTCCATGGCTGGCTTT 60.362 61.111 6.96 0.00 42.80 3.51
2993 4205 1.064825 GTTTCCCTCTCTGTTCCCCA 58.935 55.000 0.00 0.00 0.00 4.96
2994 4206 1.064825 TTTCCCTCTCTGTTCCCCAC 58.935 55.000 0.00 0.00 0.00 4.61
2995 4207 0.840722 TTCCCTCTCTGTTCCCCACC 60.841 60.000 0.00 0.00 0.00 4.61
3000 4212 0.840722 TCTCTGTTCCCCACCCCTTC 60.841 60.000 0.00 0.00 0.00 3.46
3011 4223 1.075659 ACCCCTTCTGCAGCCTTTC 59.924 57.895 9.47 0.00 0.00 2.62
3055 4271 1.518903 GGCTCCATGAATAAGGGCGC 61.519 60.000 0.00 0.00 0.00 6.53
3061 4277 1.261619 CATGAATAAGGGCGCTCGTTC 59.738 52.381 7.64 11.61 0.00 3.95
3062 4278 0.804544 TGAATAAGGGCGCTCGTTCG 60.805 55.000 7.64 0.00 0.00 3.95
3065 4281 1.082117 ATAAGGGCGCTCGTTCGTTG 61.082 55.000 7.64 0.00 0.00 4.10
3066 4282 2.424705 TAAGGGCGCTCGTTCGTTGT 62.425 55.000 7.64 0.00 0.00 3.32
3067 4283 4.072088 GGGCGCTCGTTCGTTGTG 62.072 66.667 7.64 0.00 0.00 3.33
3068 4284 3.335534 GGCGCTCGTTCGTTGTGT 61.336 61.111 7.64 0.00 0.00 3.72
3069 4285 2.128128 GCGCTCGTTCGTTGTGTG 60.128 61.111 0.00 0.00 0.00 3.82
3087 4303 5.361427 TGTGTGTGACGAGAAATAAAGGAA 58.639 37.500 0.00 0.00 0.00 3.36
3088 4304 5.465390 TGTGTGTGACGAGAAATAAAGGAAG 59.535 40.000 0.00 0.00 0.00 3.46
3089 4305 4.994852 TGTGTGACGAGAAATAAAGGAAGG 59.005 41.667 0.00 0.00 0.00 3.46
3090 4306 5.221561 TGTGTGACGAGAAATAAAGGAAGGA 60.222 40.000 0.00 0.00 0.00 3.36
3091 4307 5.875359 GTGTGACGAGAAATAAAGGAAGGAT 59.125 40.000 0.00 0.00 0.00 3.24
3190 4406 3.487544 GCAAAGTTAGGCTCGGCTTTATG 60.488 47.826 9.48 3.19 30.98 1.90
3200 4416 9.817809 TTAGGCTCGGCTTTATGATAATAATAG 57.182 33.333 0.00 0.00 0.00 1.73
3201 4417 8.079211 AGGCTCGGCTTTATGATAATAATAGA 57.921 34.615 0.00 0.00 0.00 1.98
3202 4418 8.540388 AGGCTCGGCTTTATGATAATAATAGAA 58.460 33.333 0.00 0.00 0.00 2.10
3246 4462 0.305922 CTCGGAATGAATGGAAGCGC 59.694 55.000 0.00 0.00 0.00 5.92
3284 4500 4.354071 TTTGGTAATGATGCGTGTCATG 57.646 40.909 5.62 0.00 38.76 3.07
3294 4510 4.567959 TGATGCGTGTCATGTCTTAATCAG 59.432 41.667 0.00 0.00 35.05 2.90
3324 4540 0.671472 CGCTTGTGTGCATCTGAGGA 60.671 55.000 0.00 0.00 0.00 3.71
3528 4745 1.862911 TCTGGCCTCCTCTCCTAATCT 59.137 52.381 3.32 0.00 0.00 2.40
3576 4793 0.601311 GTCTATCCAGCGTGGGCATC 60.601 60.000 4.52 0.00 43.41 3.91
3653 4882 0.947244 CATTAATGGCCCTCAGACGC 59.053 55.000 7.62 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 1.153628 CAGGCGTACTGTACTGGCC 60.154 63.158 21.92 21.92 42.42 5.36
39 40 4.717629 TTGCGCGAGACGGACAGG 62.718 66.667 12.10 0.00 44.09 4.00
45 46 3.737494 AGTACGTACTTGCGCGAGACG 62.737 57.143 30.72 30.72 37.91 4.18
136 177 7.518529 GCGAGTAGAAAACTATAGGAAAATGCC 60.519 40.741 4.43 0.00 39.07 4.40
143 184 3.004106 GGCGCGAGTAGAAAACTATAGGA 59.996 47.826 12.10 0.00 39.07 2.94
144 185 3.306818 GGCGCGAGTAGAAAACTATAGG 58.693 50.000 12.10 0.00 39.07 2.57
146 187 2.287188 CGGGCGCGAGTAGAAAACTATA 60.287 50.000 19.65 0.00 39.07 1.31
147 188 1.535437 CGGGCGCGAGTAGAAAACTAT 60.535 52.381 19.65 0.00 39.07 2.12
148 189 0.179156 CGGGCGCGAGTAGAAAACTA 60.179 55.000 19.65 0.00 39.07 2.24
162 203 3.829044 TGATGTCGGGTACGGGCG 61.829 66.667 0.00 0.00 41.39 6.13
206 247 1.135024 GTGCGGTATACGGAGTGGAAA 60.135 52.381 14.13 0.00 45.97 3.13
222 263 3.952675 GTGCTGTGGTGTGGTGCG 61.953 66.667 0.00 0.00 0.00 5.34
223 264 2.828095 TGTGCTGTGGTGTGGTGC 60.828 61.111 0.00 0.00 0.00 5.01
224 265 2.480610 GGTGTGCTGTGGTGTGGTG 61.481 63.158 0.00 0.00 0.00 4.17
225 266 2.124320 GGTGTGCTGTGGTGTGGT 60.124 61.111 0.00 0.00 0.00 4.16
226 267 2.906897 GGGTGTGCTGTGGTGTGG 60.907 66.667 0.00 0.00 0.00 4.17
227 268 3.279116 CGGGTGTGCTGTGGTGTG 61.279 66.667 0.00 0.00 0.00 3.82
231 272 4.954970 AAGGCGGGTGTGCTGTGG 62.955 66.667 0.00 0.00 34.52 4.17
232 273 1.169661 TTAAAGGCGGGTGTGCTGTG 61.170 55.000 0.00 0.00 34.52 3.66
233 274 0.466555 TTTAAAGGCGGGTGTGCTGT 60.467 50.000 0.00 0.00 34.52 4.40
234 275 0.240945 CTTTAAAGGCGGGTGTGCTG 59.759 55.000 7.37 0.00 34.52 4.41
235 276 1.524008 GCTTTAAAGGCGGGTGTGCT 61.524 55.000 16.78 0.00 34.52 4.40
236 277 1.080772 GCTTTAAAGGCGGGTGTGC 60.081 57.895 16.78 0.00 0.00 4.57
313 364 5.084818 TCCTCTCGAGATATCTCTAGCTG 57.915 47.826 26.29 19.43 40.75 4.24
315 366 4.273480 GCATCCTCTCGAGATATCTCTAGC 59.727 50.000 26.29 12.87 40.75 3.42
323 374 5.384063 GAGAATTGCATCCTCTCGAGATA 57.616 43.478 17.03 7.87 0.00 1.98
389 453 3.443681 CAGGTCAATAAATTGGGCGAGTT 59.556 43.478 3.00 0.00 38.30 3.01
390 454 3.016736 CAGGTCAATAAATTGGGCGAGT 58.983 45.455 3.00 0.00 38.30 4.18
391 455 3.278574 TCAGGTCAATAAATTGGGCGAG 58.721 45.455 3.00 0.00 38.30 5.03
392 456 3.358111 TCAGGTCAATAAATTGGGCGA 57.642 42.857 3.00 0.00 38.30 5.54
393 457 4.448537 TTTCAGGTCAATAAATTGGGCG 57.551 40.909 3.00 0.00 38.30 6.13
394 458 4.935205 GGTTTTCAGGTCAATAAATTGGGC 59.065 41.667 3.00 0.00 38.30 5.36
395 459 5.047660 TCGGTTTTCAGGTCAATAAATTGGG 60.048 40.000 3.00 0.00 38.30 4.12
396 460 5.861787 GTCGGTTTTCAGGTCAATAAATTGG 59.138 40.000 3.00 0.00 38.30 3.16
404 468 1.539496 CGAGGTCGGTTTTCAGGTCAA 60.539 52.381 0.00 0.00 35.37 3.18
477 1262 1.414061 AACCAGAGTGCAGTGGAGCT 61.414 55.000 15.09 0.00 37.27 4.09
504 1337 1.272769 GTCTTCGTTAGGCACTGACCT 59.727 52.381 0.00 0.00 42.36 3.85
530 1363 0.608130 AGCGGGGAAGGCAAATTTTC 59.392 50.000 0.00 0.00 0.00 2.29
531 1364 1.931635 TAGCGGGGAAGGCAAATTTT 58.068 45.000 0.00 0.00 0.00 1.82
532 1365 2.159179 ATAGCGGGGAAGGCAAATTT 57.841 45.000 0.00 0.00 0.00 1.82
533 1366 2.031870 GAATAGCGGGGAAGGCAAATT 58.968 47.619 0.00 0.00 0.00 1.82
543 1376 2.654863 ACCAAAATCAGAATAGCGGGG 58.345 47.619 0.00 0.00 0.00 5.73
591 1424 1.073199 CCACCCACTCACCAGGTTC 59.927 63.158 0.00 0.00 0.00 3.62
594 1427 0.322816 CATTCCACCCACTCACCAGG 60.323 60.000 0.00 0.00 0.00 4.45
641 1474 9.385902 CTGTGCTCCGATTTATTGTTATTATTG 57.614 33.333 0.00 0.00 0.00 1.90
711 1796 4.859304 TTCTTCAGAATGCATTGTGCTT 57.141 36.364 27.14 0.00 45.31 3.91
760 1846 1.517242 CGTAGTACTAGCCCGGTAGG 58.483 60.000 1.87 0.00 39.47 3.18
762 1848 3.706055 CCGTAGTACTAGCCCGGTA 57.294 57.895 17.88 0.00 34.10 4.02
763 1849 1.609783 ACCGTAGTACTAGCCCGGT 59.390 57.895 23.32 23.32 46.31 5.28
764 1850 0.665298 GAACCGTAGTACTAGCCCGG 59.335 60.000 22.27 22.27 44.06 5.73
765 1851 1.064654 GTGAACCGTAGTACTAGCCCG 59.935 57.143 1.87 3.64 0.00 6.13
766 1852 2.094675 TGTGAACCGTAGTACTAGCCC 58.905 52.381 1.87 0.00 0.00 5.19
767 1853 2.476854 CGTGTGAACCGTAGTACTAGCC 60.477 54.545 1.87 0.00 0.00 3.93
769 1855 2.160219 TGCGTGTGAACCGTAGTACTAG 59.840 50.000 1.87 0.00 0.00 2.57
770 1856 2.095768 GTGCGTGTGAACCGTAGTACTA 60.096 50.000 0.00 0.00 0.00 1.82
771 1857 0.953727 TGCGTGTGAACCGTAGTACT 59.046 50.000 0.00 0.00 0.00 2.73
774 1885 1.300388 GGTGCGTGTGAACCGTAGT 60.300 57.895 0.00 0.00 32.81 2.73
880 1991 2.164338 GCGAGGTTTGTGGGGAAATAA 58.836 47.619 0.00 0.00 0.00 1.40
881 1992 1.614850 GGCGAGGTTTGTGGGGAAATA 60.615 52.381 0.00 0.00 0.00 1.40
882 1993 0.898326 GGCGAGGTTTGTGGGGAAAT 60.898 55.000 0.00 0.00 0.00 2.17
988 2103 4.075793 TGGGACGGAGGAGGGGAG 62.076 72.222 0.00 0.00 0.00 4.30
989 2104 4.393778 GTGGGACGGAGGAGGGGA 62.394 72.222 0.00 0.00 0.00 4.81
993 2108 0.905337 AAAGAGGTGGGACGGAGGAG 60.905 60.000 0.00 0.00 0.00 3.69
994 2109 0.903454 GAAAGAGGTGGGACGGAGGA 60.903 60.000 0.00 0.00 0.00 3.71
995 2110 1.597461 GAAAGAGGTGGGACGGAGG 59.403 63.158 0.00 0.00 0.00 4.30
997 2112 2.280552 CGGAAAGAGGTGGGACGGA 61.281 63.158 0.00 0.00 0.00 4.69
998 2113 2.264794 CGGAAAGAGGTGGGACGG 59.735 66.667 0.00 0.00 0.00 4.79
999 2114 2.434359 GCGGAAAGAGGTGGGACG 60.434 66.667 0.00 0.00 0.00 4.79
1000 2115 1.376037 CAGCGGAAAGAGGTGGGAC 60.376 63.158 0.00 0.00 33.87 4.46
1035 2164 3.386543 CCGTCTAATGGAAGGCAGG 57.613 57.895 0.00 0.00 36.83 4.85
1086 2249 1.745489 GACCACTCCACCGCCATTC 60.745 63.158 0.00 0.00 0.00 2.67
1129 2292 0.460284 CATCCAAGAACTCGTCGGGG 60.460 60.000 0.00 0.00 0.00 5.73
1147 2310 1.166129 CCTCGGAGAAGAAGTCGTCA 58.834 55.000 6.58 0.00 34.09 4.35
1201 2364 0.179089 CCAAGCTGTCCTCCTCATCG 60.179 60.000 0.00 0.00 0.00 3.84
1291 2454 0.883833 CCACGCAAAGGAGCAAGAAT 59.116 50.000 0.00 0.00 0.00 2.40
1311 2487 2.382519 GCAGGTACTACGCATAACGAG 58.617 52.381 0.00 0.00 41.07 4.18
1354 2530 1.272147 ACCTCCTCCTGCCAAACAATC 60.272 52.381 0.00 0.00 0.00 2.67
1355 2531 0.779997 ACCTCCTCCTGCCAAACAAT 59.220 50.000 0.00 0.00 0.00 2.71
1414 2590 2.581354 CTCTCCTGGCCGGACTTG 59.419 66.667 15.09 0.28 36.69 3.16
1753 2929 1.464734 TCTTCAGGTAGGAGACGCAG 58.535 55.000 0.00 0.00 0.00 5.18
1803 2981 3.304257 GGAGATGAAACTGCACAACACAG 60.304 47.826 0.00 0.00 41.08 3.66
1810 2988 3.565482 TGTTTGAGGAGATGAAACTGCAC 59.435 43.478 0.00 0.00 32.01 4.57
1932 3110 2.514824 GCCGGGCTCAGGTCAATC 60.515 66.667 12.87 0.00 0.00 2.67
2143 3321 3.463944 CAAAAGAGGTGTTACGAGTGGT 58.536 45.455 0.00 0.00 0.00 4.16
2146 3324 2.490991 GCCAAAAGAGGTGTTACGAGT 58.509 47.619 0.00 0.00 0.00 4.18
2159 3337 0.744281 ACAACCAGAACGGCCAAAAG 59.256 50.000 2.24 0.00 39.03 2.27
2226 3404 0.934496 TGACGCGAAAGACACCAAAG 59.066 50.000 15.93 0.00 0.00 2.77
2289 3467 1.133216 TCGAGGTTCAGATTCAGAGCG 59.867 52.381 0.00 0.00 0.00 5.03
2355 3533 2.355756 CGGTTTGAGATGCTTACCATGG 59.644 50.000 11.19 11.19 33.29 3.66
2372 3550 2.368655 ACGCCGTATTTAGTTCGGTT 57.631 45.000 0.00 0.00 45.11 4.44
2373 3551 2.368655 AACGCCGTATTTAGTTCGGT 57.631 45.000 0.00 0.00 45.11 4.69
2375 3553 4.147653 CCAGATAACGCCGTATTTAGTTCG 59.852 45.833 0.00 0.00 0.00 3.95
2392 3570 6.046593 CAGATTAACTTGCCGTTACCAGATA 58.953 40.000 0.00 0.00 37.80 1.98
2393 3571 4.876107 CAGATTAACTTGCCGTTACCAGAT 59.124 41.667 0.00 0.00 37.80 2.90
2395 3573 4.092968 GTCAGATTAACTTGCCGTTACCAG 59.907 45.833 0.00 0.00 37.80 4.00
2396 3574 3.998341 GTCAGATTAACTTGCCGTTACCA 59.002 43.478 0.00 0.00 37.80 3.25
2397 3575 3.998341 TGTCAGATTAACTTGCCGTTACC 59.002 43.478 0.00 0.00 37.80 2.85
2398 3576 4.435651 GCTGTCAGATTAACTTGCCGTTAC 60.436 45.833 3.32 0.00 37.80 2.50
2402 3580 1.061131 CGCTGTCAGATTAACTTGCCG 59.939 52.381 3.32 0.00 0.00 5.69
2432 3610 3.694058 ATCAAGGCCTCTGCGCAGG 62.694 63.158 35.36 23.58 38.85 4.85
2433 3611 2.124819 ATCAAGGCCTCTGCGCAG 60.125 61.111 31.53 31.53 38.85 5.18
2532 3710 1.679898 GGTGGGAGACTGGGTTCAG 59.320 63.158 0.00 0.00 46.10 3.02
2561 3739 5.649395 TGAGATTAAATGGAGCCAAGAACAG 59.351 40.000 0.00 0.00 0.00 3.16
2651 3845 4.380655 CCTGCTAAAACTGACGCTACTACT 60.381 45.833 0.00 0.00 0.00 2.57
2652 3846 3.858238 CCTGCTAAAACTGACGCTACTAC 59.142 47.826 0.00 0.00 0.00 2.73
2653 3847 3.508793 ACCTGCTAAAACTGACGCTACTA 59.491 43.478 0.00 0.00 0.00 1.82
2711 3905 2.856346 CGCTTTACCATCGACGGCG 61.856 63.158 2.87 2.87 39.35 6.46
2716 3910 0.174845 CTCCACCGCTTTACCATCGA 59.825 55.000 0.00 0.00 0.00 3.59
2721 3915 0.539986 TCCATCTCCACCGCTTTACC 59.460 55.000 0.00 0.00 0.00 2.85
2722 3916 2.158957 TCATCCATCTCCACCGCTTTAC 60.159 50.000 0.00 0.00 0.00 2.01
2723 3917 2.103094 CTCATCCATCTCCACCGCTTTA 59.897 50.000 0.00 0.00 0.00 1.85
2724 3918 0.911769 TCATCCATCTCCACCGCTTT 59.088 50.000 0.00 0.00 0.00 3.51
2744 3938 5.064441 ACTAACATGGATTTCTTGCTTGC 57.936 39.130 0.00 0.00 0.00 4.01
2823 4027 1.009829 CATCTCGCCTGCTACAAACC 58.990 55.000 0.00 0.00 0.00 3.27
2834 4038 3.496130 CACTCCAACATTATCATCTCGCC 59.504 47.826 0.00 0.00 0.00 5.54
2926 4138 1.560004 GGCAAAGCGGCAAAGAAAGC 61.560 55.000 1.45 0.00 40.76 3.51
2927 4139 2.520942 GGCAAAGCGGCAAAGAAAG 58.479 52.632 1.45 0.00 40.76 2.62
2928 4140 4.748409 GGCAAAGCGGCAAAGAAA 57.252 50.000 1.45 0.00 40.76 2.52
2993 4205 1.075659 GAAAGGCTGCAGAAGGGGT 59.924 57.895 20.43 0.00 0.00 4.95
2994 4206 2.042831 CGAAAGGCTGCAGAAGGGG 61.043 63.158 20.43 0.00 0.00 4.79
2995 4207 2.694760 GCGAAAGGCTGCAGAAGGG 61.695 63.158 20.43 1.56 39.11 3.95
3055 4271 0.226235 CGTCACACACAACGAACGAG 59.774 55.000 0.14 0.00 41.29 4.18
3061 4277 4.702247 TTATTTCTCGTCACACACAACG 57.298 40.909 0.00 0.00 40.17 4.10
3062 4278 5.235616 TCCTTTATTTCTCGTCACACACAAC 59.764 40.000 0.00 0.00 0.00 3.32
3065 4281 5.107065 CCTTCCTTTATTTCTCGTCACACAC 60.107 44.000 0.00 0.00 0.00 3.82
3066 4282 4.994852 CCTTCCTTTATTTCTCGTCACACA 59.005 41.667 0.00 0.00 0.00 3.72
3067 4283 5.235516 TCCTTCCTTTATTTCTCGTCACAC 58.764 41.667 0.00 0.00 0.00 3.82
3068 4284 5.477607 TCCTTCCTTTATTTCTCGTCACA 57.522 39.130 0.00 0.00 0.00 3.58
3069 4285 6.986904 AATCCTTCCTTTATTTCTCGTCAC 57.013 37.500 0.00 0.00 0.00 3.67
3127 4343 9.559958 AAGCAACGAATGAAATGAAATACTTAG 57.440 29.630 0.00 0.00 0.00 2.18
3128 4344 9.906660 AAAGCAACGAATGAAATGAAATACTTA 57.093 25.926 0.00 0.00 0.00 2.24
3129 4345 8.816640 AAAGCAACGAATGAAATGAAATACTT 57.183 26.923 0.00 0.00 0.00 2.24
3246 4462 3.381272 ACCAAATAAATGAGACCGCCATG 59.619 43.478 0.00 0.00 0.00 3.66
3284 4500 3.933332 CGGAGAAACACCCTGATTAAGAC 59.067 47.826 0.00 0.00 0.00 3.01
3294 4510 0.818040 ACACAAGCGGAGAAACACCC 60.818 55.000 0.00 0.00 0.00 4.61
3324 4540 4.451900 CGATTAAGATAAACCCTGGTGCT 58.548 43.478 0.00 0.00 0.00 4.40
3329 4545 4.134563 CACCCCGATTAAGATAAACCCTG 58.865 47.826 0.00 0.00 0.00 4.45
3528 4745 2.985282 CCGAGCAAGCCAGCCAAA 60.985 61.111 0.00 0.00 34.23 3.28
3557 4774 0.601311 GATGCCCACGCTGGATAGAC 60.601 60.000 5.71 0.00 40.96 2.59
3558 4775 1.748403 GATGCCCACGCTGGATAGA 59.252 57.895 5.71 0.00 40.96 1.98
3559 4776 1.665916 CGATGCCCACGCTGGATAG 60.666 63.158 5.71 0.00 40.96 2.08
3560 4777 2.421314 CGATGCCCACGCTGGATA 59.579 61.111 5.71 0.00 40.96 2.59


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

AutoCloner maintained by Alex Coulton.