Multiple sequence alignment - TraesCS3B01G372200

Loading Multiple Alignment...

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 TraesCS3B01G372200 chr3B 100.000 3236 0 0 1 3236 584910772 584914007 0.000000e+00 5976.0
1 TraesCS3B01G372200 chr3D 93.533 2443 108 22 1 2404 446063182 446065613 0.000000e+00 3591.0
2 TraesCS3B01G372200 chr3D 90.102 293 18 5 2400 2691 446065728 446066010 1.420000e-98 370.0
3 TraesCS3B01G372200 chr3D 93.985 133 8 0 2695 2827 446066424 446066556 5.470000e-48 202.0
4 TraesCS3B01G372200 chr3A 91.295 2447 128 27 1 2404 587876454 587878858 0.000000e+00 3260.0
5 TraesCS3B01G372200 chr3A 90.382 759 45 14 2400 3153 587878970 587879705 0.000000e+00 972.0
6 TraesCS3B01G372200 chr7B 77.714 175 26 10 2399 2573 581793788 581793949 9.560000e-16 95.3
7 TraesCS3B01G372200 chr7B 97.368 38 1 0 2400 2437 211399736 211399699 7.490000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS3B01G372200 chr3B 584910772 584914007 3235 False 5976.000000 5976 100.0000 1 3236 1 chr3B.!!$F1 3235
1 TraesCS3B01G372200 chr3D 446063182 446066556 3374 False 1387.666667 3591 92.5400 1 2827 3 chr3D.!!$F1 2826
2 TraesCS3B01G372200 chr3A 587876454 587879705 3251 False 2116.000000 3260 90.8385 1 3153 2 chr3A.!!$F1 3152

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
544 574 0.546507 TGGGAGCCATGTGTAGGTGA 60.547 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2305 1.003118 TCGTTTGGCACTAATCTGGCT 59.997 47.619 0.0 0.0 37.6 4.75 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
47 48 1.863267 GCCAGATCAGAATCCTCACG 58.137 55.000 0.00 0.00 31.78 4.35
48 49 1.539929 GCCAGATCAGAATCCTCACGG 60.540 57.143 0.00 0.00 31.78 4.94
138 139 2.029623 GGCAGCATCCATCAGTTGATT 58.970 47.619 0.00 0.00 31.21 2.57
150 151 1.788308 CAGTTGATTTTTGCAGCACCG 59.212 47.619 0.00 0.00 0.00 4.94
186 187 1.674221 GCAGCGACCTCTCTGTCAAAT 60.674 52.381 0.00 0.00 34.88 2.32
454 460 2.577785 GCGGCGAGTTCGTAGCATC 61.578 63.158 12.98 0.00 41.04 3.91
482 488 6.879188 GTTTAGAACGAGAAGGATTGAGAG 57.121 41.667 0.00 0.00 0.00 3.20
487 493 3.287222 ACGAGAAGGATTGAGAGAGAGG 58.713 50.000 0.00 0.00 0.00 3.69
489 495 2.965147 GAGAAGGATTGAGAGAGAGGGG 59.035 54.545 0.00 0.00 0.00 4.79
544 574 0.546507 TGGGAGCCATGTGTAGGTGA 60.547 55.000 0.00 0.00 0.00 4.02
604 634 3.918294 ATCCATCCAAAAGGGCAAATG 57.082 42.857 0.00 0.00 36.21 2.32
874 907 2.628106 CAATTCCCATCGAGCGCG 59.372 61.111 2.41 2.41 39.35 6.86
875 908 2.173669 CAATTCCCATCGAGCGCGT 61.174 57.895 10.30 0.00 38.98 6.01
902 935 1.600413 CGCCAGTTCACTTGCCTTTTC 60.600 52.381 0.00 0.00 31.59 2.29
903 936 1.408702 GCCAGTTCACTTGCCTTTTCA 59.591 47.619 0.00 0.00 0.00 2.69
905 938 2.223805 CCAGTTCACTTGCCTTTTCACC 60.224 50.000 0.00 0.00 0.00 4.02
906 939 2.426738 CAGTTCACTTGCCTTTTCACCA 59.573 45.455 0.00 0.00 0.00 4.17
907 940 3.068590 CAGTTCACTTGCCTTTTCACCAT 59.931 43.478 0.00 0.00 0.00 3.55
915 952 6.482973 CACTTGCCTTTTCACCATAACAAAAT 59.517 34.615 0.00 0.00 0.00 1.82
941 978 5.934402 AGAGTTCCACGTCCATAAATAGT 57.066 39.130 0.00 0.00 0.00 2.12
964 1003 3.188786 GATCGTCCCACTGCACGC 61.189 66.667 0.00 0.00 35.93 5.34
1021 1067 4.803426 GGTGCTCCAGCTCGACGG 62.803 72.222 0.00 0.00 42.66 4.79
1320 1366 1.450312 CGGAATTCTTGAGGGCGCT 60.450 57.895 7.64 1.38 0.00 5.92
1323 1369 2.315038 GAATTCTTGAGGGCGCTGCG 62.315 60.000 19.17 19.17 0.00 5.18
1423 1469 0.100682 CCGTGGAGAATCATCGTCGT 59.899 55.000 0.00 0.00 36.25 4.34
1427 1473 0.029567 GGAGAATCATCGTCGTCGCT 59.970 55.000 0.00 0.00 36.25 4.93
1428 1474 1.116436 GAGAATCATCGTCGTCGCTG 58.884 55.000 0.00 0.00 34.99 5.18
1429 1475 0.867753 AGAATCATCGTCGTCGCTGC 60.868 55.000 1.05 0.00 33.91 5.25
1473 1519 1.068588 CCTGACTTTGATCCGGCGATA 59.931 52.381 9.30 0.00 0.00 2.92
1556 1602 2.124695 GAATGAGGCCACGACCCC 60.125 66.667 5.01 0.00 0.00 4.95
1655 1701 2.797515 GTGTCGACGAGTTCCACAG 58.202 57.895 11.62 0.00 0.00 3.66
1983 2029 2.659016 CAGCAGCTCGACCTTGGA 59.341 61.111 0.00 0.00 0.00 3.53
2052 2098 3.449227 CTAGCCGGGTGCGAGACA 61.449 66.667 18.40 0.00 44.67 3.41
2188 2234 1.079819 ATGTTCGAGGAGTGCACGG 60.080 57.895 12.01 0.00 0.00 4.94
2190 2236 1.444553 GTTCGAGGAGTGCACGGAG 60.445 63.158 12.01 2.92 0.00 4.63
2238 2284 1.666011 GGTCTGTTGCCTCTGACGA 59.334 57.895 0.00 0.00 37.23 4.20
2259 2305 4.569943 GACCACAGCTAAGAGTTTCATGA 58.430 43.478 0.00 0.00 0.00 3.07
2272 2318 3.944015 AGTTTCATGAGCCAGATTAGTGC 59.056 43.478 0.00 0.00 0.00 4.40
2275 2321 2.239402 TCATGAGCCAGATTAGTGCCAA 59.761 45.455 0.00 0.00 0.00 4.52
2309 2355 0.107116 TAGGCGGACTGAGAGACTCC 60.107 60.000 0.00 0.00 0.00 3.85
2355 2401 1.084289 CTTACTTTACCGTGCTGCCC 58.916 55.000 0.00 0.00 0.00 5.36
2384 2432 4.619160 GCTGCCTTTAATTTTCTCCTGGTG 60.619 45.833 0.00 0.00 0.00 4.17
2389 2437 5.105997 CCTTTAATTTTCTCCTGGTGAGCAG 60.106 44.000 4.35 4.35 41.18 4.24
2425 2593 0.402504 TTGCTTGGTGTAATCCGGGT 59.597 50.000 0.00 0.00 0.00 5.28
2439 2607 2.719739 TCCGGGTTGTGTTGTTGTAAA 58.280 42.857 0.00 0.00 0.00 2.01
2440 2608 3.288964 TCCGGGTTGTGTTGTTGTAAAT 58.711 40.909 0.00 0.00 0.00 1.40
2441 2609 3.700038 TCCGGGTTGTGTTGTTGTAAATT 59.300 39.130 0.00 0.00 0.00 1.82
2442 2610 3.799420 CCGGGTTGTGTTGTTGTAAATTG 59.201 43.478 0.00 0.00 0.00 2.32
2443 2611 4.425520 CGGGTTGTGTTGTTGTAAATTGT 58.574 39.130 0.00 0.00 0.00 2.71
2444 2612 5.450137 CCGGGTTGTGTTGTTGTAAATTGTA 60.450 40.000 0.00 0.00 0.00 2.41
2445 2613 6.034591 CGGGTTGTGTTGTTGTAAATTGTAA 58.965 36.000 0.00 0.00 0.00 2.41
2474 2642 8.734386 CAACATCTTATATCCTGCCTATTTTCC 58.266 37.037 0.00 0.00 0.00 3.13
2483 2651 6.530019 TCCTGCCTATTTTCCTTTCATTTC 57.470 37.500 0.00 0.00 0.00 2.17
2490 2658 7.334421 GCCTATTTTCCTTTCATTTCCTTTTCC 59.666 37.037 0.00 0.00 0.00 3.13
2491 2659 8.597167 CCTATTTTCCTTTCATTTCCTTTTCCT 58.403 33.333 0.00 0.00 0.00 3.36
2511 2679 7.546778 TTCCTTTTATTTTCTTTTGTGTGGC 57.453 32.000 0.00 0.00 0.00 5.01
2529 2697 2.556189 TGGCGTTGTATTTGTCTGCAAT 59.444 40.909 0.00 0.00 34.18 3.56
2546 2714 8.458052 TGTCTGCAATGACGTCATTAATTTAAT 58.542 29.630 36.18 15.31 44.10 1.40
2573 2741 1.740025 CCGCAGGCCTTCTTTCTAAAG 59.260 52.381 0.00 0.00 46.14 1.85
2598 2766 9.759473 AGAAGAAATTATCCTGGATCTTTGAAA 57.241 29.630 13.54 0.80 0.00 2.69
2605 2773 6.838401 ATCCTGGATCTTTGAAATCTAGGT 57.162 37.500 2.57 1.81 46.52 3.08
2708 3287 6.785076 TGGGAGATGGTTGTTTTCATACTAA 58.215 36.000 0.00 0.00 0.00 2.24
2717 3297 9.093970 TGGTTGTTTTCATACTAATATCAGTCG 57.906 33.333 0.00 0.00 0.00 4.18
2770 3350 7.502226 TCAGTTAAATGTTGACAGAGGACAAAT 59.498 33.333 2.43 0.00 30.82 2.32
2802 3382 3.923273 ACCCAGGAAAAGAAAGGGAAT 57.077 42.857 2.29 0.00 42.25 3.01
2835 3415 5.220815 GCTTCTGCAGTAAAATCATCTCCTG 60.221 44.000 14.67 0.00 39.41 3.86
2837 3417 5.423015 TCTGCAGTAAAATCATCTCCTGAC 58.577 41.667 14.67 0.00 36.48 3.51
2838 3418 4.183865 TGCAGTAAAATCATCTCCTGACG 58.816 43.478 0.00 0.00 36.48 4.35
2913 3493 5.627735 GCAGAACCAGAAATGAGGAGACATA 60.628 44.000 0.00 0.00 0.00 2.29
2947 3527 5.587289 TGCTTGAGGTGTTAAAACATGTTC 58.413 37.500 12.39 0.00 41.59 3.18
2957 3537 9.685828 GGTGTTAAAACATGTTCATAGCTTAAA 57.314 29.630 12.39 1.55 41.59 1.52
2984 3564 7.500992 TCTTGCTTCTTTATCCTGATTCGTAT 58.499 34.615 0.00 0.00 0.00 3.06
3001 3581 3.768757 TCGTATTTTCCTTCCCGGTCTAA 59.231 43.478 0.00 0.00 0.00 2.10
3013 3593 8.496088 TCCTTCCCGGTCTAAAAATGATTATTA 58.504 33.333 0.00 0.00 0.00 0.98
3057 3637 7.202526 TCCTCTCACATGAACAAAATGTTTTC 58.797 34.615 0.00 0.00 41.28 2.29
3065 3645 7.601886 ACATGAACAAAATGTTTTCTCACAACA 59.398 29.630 0.00 0.00 41.28 3.33
3066 3646 7.953158 TGAACAAAATGTTTTCTCACAACAA 57.047 28.000 0.00 0.00 41.28 2.83
3089 3669 9.723601 ACAAAAGTAATGGAATGCACAAATTAT 57.276 25.926 0.00 0.00 0.00 1.28
3110 3690 9.630098 AATTATTGTGCAAAGATTCTTACTGTG 57.370 29.630 0.00 0.00 0.00 3.66
3135 3719 4.360951 ACCACGGAGAAACCTTTAATCA 57.639 40.909 0.00 0.00 36.31 2.57
3140 3724 6.373216 CCACGGAGAAACCTTTAATCACAATA 59.627 38.462 0.00 0.00 36.31 1.90
3159 3743 5.699458 ACAATAGACTTTGTGAACTTACCCG 59.301 40.000 3.26 0.00 38.37 5.28
3160 3744 2.490991 AGACTTTGTGAACTTACCCGC 58.509 47.619 0.00 0.00 0.00 6.13
3161 3745 2.158871 AGACTTTGTGAACTTACCCGCA 60.159 45.455 0.00 0.00 0.00 5.69
3162 3746 2.614983 GACTTTGTGAACTTACCCGCAA 59.385 45.455 0.00 0.00 0.00 4.85
3163 3747 3.018149 ACTTTGTGAACTTACCCGCAAA 58.982 40.909 0.00 0.00 39.52 3.68
3164 3748 3.444388 ACTTTGTGAACTTACCCGCAAAA 59.556 39.130 0.00 0.00 40.71 2.44
3165 3749 4.082136 ACTTTGTGAACTTACCCGCAAAAA 60.082 37.500 0.00 0.00 40.71 1.94
3166 3750 3.701532 TGTGAACTTACCCGCAAAAAG 57.298 42.857 0.00 0.00 0.00 2.27
3167 3751 3.280295 TGTGAACTTACCCGCAAAAAGA 58.720 40.909 0.00 0.00 0.00 2.52
3168 3752 3.695060 TGTGAACTTACCCGCAAAAAGAA 59.305 39.130 0.00 0.00 0.00 2.52
3169 3753 4.158025 TGTGAACTTACCCGCAAAAAGAAA 59.842 37.500 0.00 0.00 0.00 2.52
3170 3754 5.103687 GTGAACTTACCCGCAAAAAGAAAA 58.896 37.500 0.00 0.00 0.00 2.29
3171 3755 5.231357 GTGAACTTACCCGCAAAAAGAAAAG 59.769 40.000 0.00 0.00 0.00 2.27
3172 3756 5.125739 TGAACTTACCCGCAAAAAGAAAAGA 59.874 36.000 0.00 0.00 0.00 2.52
3173 3757 4.928601 ACTTACCCGCAAAAAGAAAAGAC 58.071 39.130 0.00 0.00 0.00 3.01
3174 3758 4.643334 ACTTACCCGCAAAAAGAAAAGACT 59.357 37.500 0.00 0.00 0.00 3.24
3175 3759 5.126545 ACTTACCCGCAAAAAGAAAAGACTT 59.873 36.000 0.00 0.00 0.00 3.01
3176 3760 4.465632 ACCCGCAAAAAGAAAAGACTTT 57.534 36.364 0.00 0.00 41.09 2.66
3177 3761 4.180817 ACCCGCAAAAAGAAAAGACTTTG 58.819 39.130 0.06 0.00 39.57 2.77
3178 3762 4.180817 CCCGCAAAAAGAAAAGACTTTGT 58.819 39.130 0.06 0.00 39.57 2.83
3179 3763 4.032786 CCCGCAAAAAGAAAAGACTTTGTG 59.967 41.667 0.06 0.00 43.76 3.33
3180 3764 4.862018 CCGCAAAAAGAAAAGACTTTGTGA 59.138 37.500 13.35 0.00 43.68 3.58
3181 3765 5.347364 CCGCAAAAAGAAAAGACTTTGTGAA 59.653 36.000 13.35 0.00 43.68 3.18
3182 3766 6.233500 CGCAAAAAGAAAAGACTTTGTGAAC 58.766 36.000 13.35 0.00 43.68 3.18
3183 3767 6.128956 CGCAAAAAGAAAAGACTTTGTGAACA 60.129 34.615 13.35 0.00 43.68 3.18
3184 3768 7.229530 GCAAAAAGAAAAGACTTTGTGAACAG 58.770 34.615 13.35 0.00 43.68 3.16
3185 3769 6.951256 AAAAGAAAAGACTTTGTGAACAGC 57.049 33.333 0.06 0.00 39.57 4.40
3186 3770 5.904362 AAGAAAAGACTTTGTGAACAGCT 57.096 34.783 0.06 0.00 0.00 4.24
3187 3771 5.904362 AGAAAAGACTTTGTGAACAGCTT 57.096 34.783 0.06 0.00 0.00 3.74
3188 3772 6.272822 AGAAAAGACTTTGTGAACAGCTTT 57.727 33.333 0.06 0.00 0.00 3.51
3189 3773 7.391148 AGAAAAGACTTTGTGAACAGCTTTA 57.609 32.000 0.06 0.00 0.00 1.85
3190 3774 7.475840 AGAAAAGACTTTGTGAACAGCTTTAG 58.524 34.615 0.06 0.00 0.00 1.85
3191 3775 7.336931 AGAAAAGACTTTGTGAACAGCTTTAGA 59.663 33.333 0.06 0.00 0.00 2.10
3192 3776 6.610741 AAGACTTTGTGAACAGCTTTAGAG 57.389 37.500 0.00 0.00 0.00 2.43
3193 3777 5.059833 AGACTTTGTGAACAGCTTTAGAGG 58.940 41.667 0.00 0.00 0.00 3.69
3194 3778 5.036117 ACTTTGTGAACAGCTTTAGAGGA 57.964 39.130 0.00 0.00 0.00 3.71
3195 3779 5.437060 ACTTTGTGAACAGCTTTAGAGGAA 58.563 37.500 0.00 0.00 0.00 3.36
3196 3780 5.297029 ACTTTGTGAACAGCTTTAGAGGAAC 59.703 40.000 0.00 0.00 0.00 3.62
3197 3781 3.390135 TGTGAACAGCTTTAGAGGAACG 58.610 45.455 0.00 0.00 0.00 3.95
3198 3782 2.737252 GTGAACAGCTTTAGAGGAACGG 59.263 50.000 0.00 0.00 0.00 4.44
3199 3783 1.732809 GAACAGCTTTAGAGGAACGGC 59.267 52.381 0.00 0.00 0.00 5.68
3200 3784 0.685097 ACAGCTTTAGAGGAACGGCA 59.315 50.000 0.00 0.00 0.00 5.69
3201 3785 1.079503 CAGCTTTAGAGGAACGGCAC 58.920 55.000 0.00 0.00 0.00 5.01
3202 3786 0.685097 AGCTTTAGAGGAACGGCACA 59.315 50.000 0.00 0.00 0.00 4.57
3203 3787 1.071699 AGCTTTAGAGGAACGGCACAA 59.928 47.619 0.00 0.00 0.00 3.33
3204 3788 1.464997 GCTTTAGAGGAACGGCACAAG 59.535 52.381 0.00 0.00 0.00 3.16
3205 3789 2.767505 CTTTAGAGGAACGGCACAAGT 58.232 47.619 0.00 0.00 0.00 3.16
3206 3790 2.922740 TTAGAGGAACGGCACAAGTT 57.077 45.000 0.00 0.00 34.07 2.66
3207 3791 2.450609 TAGAGGAACGGCACAAGTTC 57.549 50.000 0.89 0.89 45.16 3.01
3208 3792 0.759346 AGAGGAACGGCACAAGTTCT 59.241 50.000 8.66 0.00 45.20 3.01
3209 3793 1.149148 GAGGAACGGCACAAGTTCTC 58.851 55.000 8.66 2.30 45.20 2.87
3210 3794 0.600255 AGGAACGGCACAAGTTCTCG 60.600 55.000 8.66 0.00 45.20 4.04
3211 3795 0.599204 GGAACGGCACAAGTTCTCGA 60.599 55.000 8.66 0.00 45.20 4.04
3212 3796 0.784778 GAACGGCACAAGTTCTCGAG 59.215 55.000 5.93 5.93 43.24 4.04
3213 3797 1.222115 AACGGCACAAGTTCTCGAGC 61.222 55.000 7.81 0.00 0.00 5.03
3214 3798 1.664649 CGGCACAAGTTCTCGAGCA 60.665 57.895 7.81 0.00 0.00 4.26
3215 3799 1.621301 CGGCACAAGTTCTCGAGCAG 61.621 60.000 7.81 0.00 0.00 4.24
3216 3800 1.294659 GGCACAAGTTCTCGAGCAGG 61.295 60.000 7.81 0.00 0.00 4.85
3217 3801 0.319900 GCACAAGTTCTCGAGCAGGA 60.320 55.000 7.81 0.00 0.00 3.86
3218 3802 1.674221 GCACAAGTTCTCGAGCAGGAT 60.674 52.381 7.81 0.00 0.00 3.24
3219 3803 1.998315 CACAAGTTCTCGAGCAGGATG 59.002 52.381 7.81 5.60 40.87 3.51
3220 3804 1.066573 ACAAGTTCTCGAGCAGGATGG 60.067 52.381 7.81 0.00 35.86 3.51
3231 3815 2.185004 GCAGGATGGTTACACACAGT 57.815 50.000 0.00 0.00 35.86 3.55
3232 3816 2.504367 GCAGGATGGTTACACACAGTT 58.496 47.619 0.00 0.00 35.86 3.16
3233 3817 2.884639 GCAGGATGGTTACACACAGTTT 59.115 45.455 0.00 0.00 35.86 2.66
3234 3818 4.069304 GCAGGATGGTTACACACAGTTTA 58.931 43.478 0.00 0.00 35.86 2.01
3235 3819 4.083484 GCAGGATGGTTACACACAGTTTAC 60.083 45.833 0.00 0.00 35.86 2.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
47 48 1.209747 AGAGGGCGGTTCATTTACTCC 59.790 52.381 0.00 0.00 0.00 3.85
48 49 2.693267 AGAGGGCGGTTCATTTACTC 57.307 50.000 0.00 0.00 0.00 2.59
138 139 2.712539 CGTGACGGTGCTGCAAAA 59.287 55.556 2.77 0.00 0.00 2.44
186 187 0.673333 CAGACACCGGTGCTGCAATA 60.673 55.000 34.26 0.00 31.71 1.90
235 236 4.452733 GGCGTCTGCTAGCCGGTT 62.453 66.667 13.29 0.00 44.22 4.44
327 333 1.375908 CCGCTCCTACTGCTGCAAA 60.376 57.895 3.02 0.00 0.00 3.68
487 493 0.398098 TCCCTAGTTCGTCATCCCCC 60.398 60.000 0.00 0.00 0.00 5.40
489 495 2.040178 ACATCCCTAGTTCGTCATCCC 58.960 52.381 0.00 0.00 0.00 3.85
544 574 3.198635 TCTCTTTCATCGCTTCCCATCTT 59.801 43.478 0.00 0.00 0.00 2.40
616 646 0.831307 AGGATCAACCGCTTAGGGAC 59.169 55.000 0.00 0.00 46.96 4.46
617 647 1.209504 CAAGGATCAACCGCTTAGGGA 59.790 52.381 0.00 0.00 46.96 4.20
618 648 1.668419 CAAGGATCAACCGCTTAGGG 58.332 55.000 0.00 0.00 46.96 3.53
902 935 7.382218 GTGGAACTCTTTGATTTTGTTATGGTG 59.618 37.037 0.00 0.00 0.00 4.17
903 936 7.433680 GTGGAACTCTTTGATTTTGTTATGGT 58.566 34.615 0.00 0.00 0.00 3.55
905 938 7.138736 ACGTGGAACTCTTTGATTTTGTTATG 58.861 34.615 0.00 0.00 31.75 1.90
906 939 7.272037 ACGTGGAACTCTTTGATTTTGTTAT 57.728 32.000 0.00 0.00 31.75 1.89
907 940 6.238538 GGACGTGGAACTCTTTGATTTTGTTA 60.239 38.462 0.00 0.00 31.75 2.41
915 952 4.610605 TTATGGACGTGGAACTCTTTGA 57.389 40.909 0.00 0.00 31.75 2.69
967 1006 4.521062 AGATGTCAGAGCCGCCGC 62.521 66.667 0.00 0.00 0.00 6.53
1152 1198 1.364901 CAACGTCGTGTAGGGGTGT 59.635 57.895 0.00 0.00 0.00 4.16
1323 1369 1.597700 CTGTGCTCGACGTTGACGAC 61.598 60.000 10.87 3.13 43.02 4.34
1327 1373 2.729491 CGCTGTGCTCGACGTTGA 60.729 61.111 5.16 5.16 0.00 3.18
1473 1519 2.915659 TCGCGGAACAGGGACAGT 60.916 61.111 6.13 0.00 0.00 3.55
1632 1678 4.617486 AACTCGTCGACACGCGCA 62.617 61.111 17.16 0.00 46.28 6.09
1655 1701 1.209261 CCTTCTTCTCCTCCAGCTTCC 59.791 57.143 0.00 0.00 0.00 3.46
2188 2234 2.668280 GCCCGTTCTCGTTGCACTC 61.668 63.158 0.00 0.00 34.59 3.51
2190 2236 2.665185 AGCCCGTTCTCGTTGCAC 60.665 61.111 0.00 0.00 36.08 4.57
2238 2284 4.573900 CTCATGAAACTCTTAGCTGTGGT 58.426 43.478 0.00 0.00 0.00 4.16
2259 2305 1.003118 TCGTTTGGCACTAATCTGGCT 59.997 47.619 0.00 0.00 37.60 4.75
2309 2355 1.741706 TGTAGCCTACGAGAACGAAGG 59.258 52.381 0.00 0.00 42.66 3.46
2355 2401 5.302357 AGAAAATTAAAGGCAGCTTCTCG 57.698 39.130 0.00 0.00 0.00 4.04
2384 2432 6.578919 GCAAACAACAAACTAAGATACTGCTC 59.421 38.462 0.00 0.00 0.00 4.26
2389 2437 7.167468 CACCAAGCAAACAACAAACTAAGATAC 59.833 37.037 0.00 0.00 0.00 2.24
2425 2593 8.383619 GTTGCATTACAATTTACAACAACACAA 58.616 29.630 0.00 0.00 41.27 3.33
2439 2607 8.517878 GCAGGATATAAGATGTTGCATTACAAT 58.482 33.333 0.00 0.00 41.27 2.71
2440 2608 7.040478 GGCAGGATATAAGATGTTGCATTACAA 60.040 37.037 0.00 0.00 35.33 2.41
2441 2609 6.430925 GGCAGGATATAAGATGTTGCATTACA 59.569 38.462 0.00 0.00 0.00 2.41
2442 2610 6.656693 AGGCAGGATATAAGATGTTGCATTAC 59.343 38.462 0.00 0.00 0.00 1.89
2443 2611 6.782986 AGGCAGGATATAAGATGTTGCATTA 58.217 36.000 0.00 0.00 0.00 1.90
2444 2612 5.638133 AGGCAGGATATAAGATGTTGCATT 58.362 37.500 0.00 0.00 0.00 3.56
2445 2613 5.252586 AGGCAGGATATAAGATGTTGCAT 57.747 39.130 0.00 0.00 0.00 3.96
2457 2625 8.788238 AAATGAAAGGAAAATAGGCAGGATAT 57.212 30.769 0.00 0.00 0.00 1.63
2483 2651 9.986833 CACACAAAAGAAAATAAAAGGAAAAGG 57.013 29.630 0.00 0.00 0.00 3.11
2490 2658 6.582437 ACGCCACACAAAAGAAAATAAAAG 57.418 33.333 0.00 0.00 0.00 2.27
2491 2659 6.369065 ACAACGCCACACAAAAGAAAATAAAA 59.631 30.769 0.00 0.00 0.00 1.52
2492 2660 5.869888 ACAACGCCACACAAAAGAAAATAAA 59.130 32.000 0.00 0.00 0.00 1.40
2495 2663 3.855858 ACAACGCCACACAAAAGAAAAT 58.144 36.364 0.00 0.00 0.00 1.82
2499 2667 4.142359 ACAAATACAACGCCACACAAAAGA 60.142 37.500 0.00 0.00 0.00 2.52
2504 2672 2.289274 CAGACAAATACAACGCCACACA 59.711 45.455 0.00 0.00 0.00 3.72
2511 2679 3.840209 CGTCATTGCAGACAAATACAACG 59.160 43.478 6.87 0.00 39.77 4.10
2594 2762 9.793259 AACAGACAGAAAAATACCTAGATTTCA 57.207 29.630 0.00 0.00 34.91 2.69
2598 2766 9.965902 ATCAAACAGACAGAAAAATACCTAGAT 57.034 29.630 0.00 0.00 0.00 1.98
2605 2773 7.437862 GGCAAACATCAAACAGACAGAAAAATA 59.562 33.333 0.00 0.00 0.00 1.40
2708 3287 9.817809 ATGTATTTACTCACAAACGACTGATAT 57.182 29.630 0.00 0.00 0.00 1.63
2747 3327 7.648142 TGATTTGTCCTCTGTCAACATTTAAC 58.352 34.615 0.00 0.00 0.00 2.01
2770 3350 5.783360 TCTTTTCCTGGGTAGTATCAACTGA 59.217 40.000 0.00 0.00 36.36 3.41
2802 3382 4.135293 TGCAGAAGCTAGCAGGGA 57.865 55.556 18.83 1.06 42.74 4.20
2835 3415 5.402867 GCTAGATGAACAGGTAAATAGCGTC 59.597 44.000 0.00 0.00 0.00 5.19
2837 3417 5.289595 TGCTAGATGAACAGGTAAATAGCG 58.710 41.667 0.00 0.00 37.74 4.26
2838 3418 6.931281 TCATGCTAGATGAACAGGTAAATAGC 59.069 38.462 0.00 0.00 35.96 2.97
2913 3493 5.171339 ACACCTCAAGCAATATCAGACTT 57.829 39.130 0.00 0.00 0.00 3.01
2920 3500 7.895759 ACATGTTTTAACACCTCAAGCAATAT 58.104 30.769 0.00 0.00 42.51 1.28
2957 3537 6.825721 ACGAATCAGGATAAAGAAGCAAGAAT 59.174 34.615 0.00 0.00 0.00 2.40
2984 3564 5.386924 TCATTTTTAGACCGGGAAGGAAAA 58.613 37.500 6.32 6.92 45.00 2.29
3017 3597 9.219603 CATGTGAGAGGAAGATAAACTAACAAA 57.780 33.333 0.00 0.00 0.00 2.83
3039 3619 7.601886 TGTTGTGAGAAAACATTTTGTTCATGT 59.398 29.630 0.00 0.00 40.14 3.21
3040 3620 7.961855 TGTTGTGAGAAAACATTTTGTTCATG 58.038 30.769 0.00 0.00 40.14 3.07
3057 3637 6.144402 GTGCATTCCATTACTTTTGTTGTGAG 59.856 38.462 0.00 0.00 0.00 3.51
3066 3646 9.723601 ACAATAATTTGTGCATTCCATTACTTT 57.276 25.926 0.00 0.00 44.36 2.66
3089 3669 5.129634 TCCACAGTAAGAATCTTTGCACAA 58.870 37.500 0.00 0.00 0.00 3.33
3092 3672 5.880332 GGTATCCACAGTAAGAATCTTTGCA 59.120 40.000 0.00 0.00 0.00 4.08
3093 3673 5.880332 TGGTATCCACAGTAAGAATCTTTGC 59.120 40.000 0.00 0.00 0.00 3.68
3109 3689 1.946984 AGGTTTCTCCGTGGTATCCA 58.053 50.000 0.00 0.00 41.99 3.41
3110 3690 3.345508 AAAGGTTTCTCCGTGGTATCC 57.654 47.619 0.00 0.00 41.99 2.59
3118 3702 7.549488 AGTCTATTGTGATTAAAGGTTTCTCCG 59.451 37.037 0.00 0.00 41.99 4.63
3135 3719 5.699458 CGGGTAAGTTCACAAAGTCTATTGT 59.301 40.000 0.00 0.00 44.08 2.71
3140 3724 2.158871 TGCGGGTAAGTTCACAAAGTCT 60.159 45.455 0.00 0.00 0.00 3.24
3153 3737 5.585820 AAGTCTTTTCTTTTTGCGGGTAA 57.414 34.783 0.00 0.00 0.00 2.85
3154 3738 5.105675 ACAAAGTCTTTTCTTTTTGCGGGTA 60.106 36.000 0.00 0.00 35.77 3.69
3155 3739 4.180817 CAAAGTCTTTTCTTTTTGCGGGT 58.819 39.130 0.00 0.00 35.77 5.28
3156 3740 4.032786 CACAAAGTCTTTTCTTTTTGCGGG 59.967 41.667 0.00 0.00 35.77 6.13
3157 3741 4.862018 TCACAAAGTCTTTTCTTTTTGCGG 59.138 37.500 0.00 0.00 36.01 5.69
3158 3742 6.128956 TGTTCACAAAGTCTTTTCTTTTTGCG 60.129 34.615 0.00 0.00 36.01 4.85
3159 3743 7.116061 TGTTCACAAAGTCTTTTCTTTTTGC 57.884 32.000 0.00 0.00 36.01 3.68
3160 3744 7.116805 AGCTGTTCACAAAGTCTTTTCTTTTTG 59.883 33.333 0.00 0.00 36.82 2.44
3161 3745 7.154656 AGCTGTTCACAAAGTCTTTTCTTTTT 58.845 30.769 0.00 0.00 35.77 1.94
3162 3746 6.691508 AGCTGTTCACAAAGTCTTTTCTTTT 58.308 32.000 0.00 0.00 35.77 2.27
3163 3747 6.272822 AGCTGTTCACAAAGTCTTTTCTTT 57.727 33.333 0.00 0.00 38.04 2.52
3164 3748 5.904362 AGCTGTTCACAAAGTCTTTTCTT 57.096 34.783 0.00 0.00 0.00 2.52
3165 3749 5.904362 AAGCTGTTCACAAAGTCTTTTCT 57.096 34.783 0.00 0.00 0.00 2.52
3166 3750 7.472543 TCTAAAGCTGTTCACAAAGTCTTTTC 58.527 34.615 0.00 0.00 0.00 2.29
3167 3751 7.391148 TCTAAAGCTGTTCACAAAGTCTTTT 57.609 32.000 0.00 0.00 0.00 2.27
3168 3752 6.038714 CCTCTAAAGCTGTTCACAAAGTCTTT 59.961 38.462 0.00 0.00 0.00 2.52
3169 3753 5.529060 CCTCTAAAGCTGTTCACAAAGTCTT 59.471 40.000 0.00 0.00 0.00 3.01
3170 3754 5.059833 CCTCTAAAGCTGTTCACAAAGTCT 58.940 41.667 0.00 0.00 0.00 3.24
3171 3755 5.057149 TCCTCTAAAGCTGTTCACAAAGTC 58.943 41.667 0.00 0.00 0.00 3.01
3172 3756 5.036117 TCCTCTAAAGCTGTTCACAAAGT 57.964 39.130 0.00 0.00 0.00 2.66
3173 3757 5.559035 CGTTCCTCTAAAGCTGTTCACAAAG 60.559 44.000 0.00 0.00 0.00 2.77
3174 3758 4.272504 CGTTCCTCTAAAGCTGTTCACAAA 59.727 41.667 0.00 0.00 0.00 2.83
3175 3759 3.807622 CGTTCCTCTAAAGCTGTTCACAA 59.192 43.478 0.00 0.00 0.00 3.33
3176 3760 3.390135 CGTTCCTCTAAAGCTGTTCACA 58.610 45.455 0.00 0.00 0.00 3.58
3177 3761 2.737252 CCGTTCCTCTAAAGCTGTTCAC 59.263 50.000 0.00 0.00 0.00 3.18
3178 3762 2.870435 GCCGTTCCTCTAAAGCTGTTCA 60.870 50.000 0.00 0.00 0.00 3.18
3179 3763 1.732809 GCCGTTCCTCTAAAGCTGTTC 59.267 52.381 0.00 0.00 0.00 3.18
3180 3764 1.071699 TGCCGTTCCTCTAAAGCTGTT 59.928 47.619 0.00 0.00 0.00 3.16
3181 3765 0.685097 TGCCGTTCCTCTAAAGCTGT 59.315 50.000 0.00 0.00 0.00 4.40
3182 3766 1.079503 GTGCCGTTCCTCTAAAGCTG 58.920 55.000 0.00 0.00 0.00 4.24
3183 3767 0.685097 TGTGCCGTTCCTCTAAAGCT 59.315 50.000 0.00 0.00 0.00 3.74
3184 3768 1.464997 CTTGTGCCGTTCCTCTAAAGC 59.535 52.381 0.00 0.00 0.00 3.51
3185 3769 2.767505 ACTTGTGCCGTTCCTCTAAAG 58.232 47.619 0.00 0.00 0.00 1.85
3186 3770 2.922740 ACTTGTGCCGTTCCTCTAAA 57.077 45.000 0.00 0.00 0.00 1.85
3187 3771 2.367567 AGAACTTGTGCCGTTCCTCTAA 59.632 45.455 0.00 0.00 41.19 2.10
3188 3772 1.968493 AGAACTTGTGCCGTTCCTCTA 59.032 47.619 0.00 0.00 41.19 2.43
3189 3773 0.759346 AGAACTTGTGCCGTTCCTCT 59.241 50.000 0.00 0.00 41.19 3.69
3190 3774 1.149148 GAGAACTTGTGCCGTTCCTC 58.851 55.000 0.00 0.00 41.19 3.71
3191 3775 0.600255 CGAGAACTTGTGCCGTTCCT 60.600 55.000 0.00 0.00 41.19 3.36
3192 3776 0.599204 TCGAGAACTTGTGCCGTTCC 60.599 55.000 0.00 0.00 41.19 3.62
3193 3777 0.784778 CTCGAGAACTTGTGCCGTTC 59.215 55.000 6.58 0.00 40.72 3.95
3194 3778 1.222115 GCTCGAGAACTTGTGCCGTT 61.222 55.000 18.75 0.00 0.00 4.44
3195 3779 1.664965 GCTCGAGAACTTGTGCCGT 60.665 57.895 18.75 0.00 0.00 5.68
3196 3780 1.621301 CTGCTCGAGAACTTGTGCCG 61.621 60.000 18.75 4.16 33.71 5.69
3197 3781 1.294659 CCTGCTCGAGAACTTGTGCC 61.295 60.000 18.75 0.00 33.71 5.01
3198 3782 0.319900 TCCTGCTCGAGAACTTGTGC 60.320 55.000 18.75 0.00 34.87 4.57
3199 3783 1.998315 CATCCTGCTCGAGAACTTGTG 59.002 52.381 18.75 3.22 0.00 3.33
3200 3784 1.066573 CCATCCTGCTCGAGAACTTGT 60.067 52.381 18.75 0.00 0.00 3.16
3201 3785 1.066573 ACCATCCTGCTCGAGAACTTG 60.067 52.381 18.75 6.24 0.00 3.16
3202 3786 1.270907 ACCATCCTGCTCGAGAACTT 58.729 50.000 18.75 0.00 0.00 2.66
3203 3787 1.270907 AACCATCCTGCTCGAGAACT 58.729 50.000 18.75 0.00 0.00 3.01
3204 3788 2.094182 TGTAACCATCCTGCTCGAGAAC 60.094 50.000 18.75 0.00 0.00 3.01
3205 3789 2.094182 GTGTAACCATCCTGCTCGAGAA 60.094 50.000 18.75 4.16 0.00 2.87
3206 3790 1.476891 GTGTAACCATCCTGCTCGAGA 59.523 52.381 18.75 0.02 0.00 4.04
3207 3791 1.204704 TGTGTAACCATCCTGCTCGAG 59.795 52.381 8.45 8.45 34.36 4.04
3208 3792 1.067142 GTGTGTAACCATCCTGCTCGA 60.067 52.381 0.00 0.00 34.36 4.04
3209 3793 1.337728 TGTGTGTAACCATCCTGCTCG 60.338 52.381 0.00 0.00 34.36 5.03
3210 3794 2.289694 ACTGTGTGTAACCATCCTGCTC 60.290 50.000 0.00 0.00 34.36 4.26
3211 3795 1.699634 ACTGTGTGTAACCATCCTGCT 59.300 47.619 0.00 0.00 34.36 4.24
3212 3796 2.185004 ACTGTGTGTAACCATCCTGC 57.815 50.000 0.00 0.00 34.36 4.85
3213 3797 5.607119 GTAAACTGTGTGTAACCATCCTG 57.393 43.478 0.00 0.00 34.36 3.86


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

AutoCloner maintained by Alex Coulton.