Multiple sequence alignment - TraesCS5A01G248100

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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 TraesCS5A01G248100 chr5A 100.000 3194 0 0 1 3194 461940041 461936848 0.000000e+00 5899.0
1 TraesCS5A01G248100 chr5A 92.659 722 35 8 2488 3194 461931993 461931275 0.000000e+00 1024.0
2 TraesCS5A01G248100 chr5A 93.238 562 36 2 2633 3194 461930629 461930070 0.000000e+00 826.0
3 TraesCS5A01G248100 chr5A 94.456 487 15 5 2016 2495 461932642 461932161 0.000000e+00 739.0
4 TraesCS5A01G248100 chr5D 90.585 2496 147 42 1 2462 361405961 361403520 0.000000e+00 3227.0
5 TraesCS5A01G248100 chr5D 87.500 536 40 12 2460 2975 361401747 361401219 7.630000e-166 593.0
6 TraesCS5A01G248100 chr5B 87.236 2507 156 86 497 2939 426995464 426993058 0.000000e+00 2706.0
7 TraesCS5A01G248100 chr3A 83.149 1086 113 30 1155 2207 716988181 716989229 0.000000e+00 928.0
8 TraesCS5A01G248100 chr3D 79.646 1356 163 57 897 2207 587608115 587609402 0.000000e+00 870.0
9 TraesCS5A01G248100 chr3D 100.000 28 0 0 1834 1861 19881319 19881346 6.000000e-03 52.8
10 TraesCS5A01G248100 chr3B 81.401 785 88 20 1440 2207 784926604 784927347 3.550000e-164 588.0
11 TraesCS5A01G248100 chr3B 80.113 533 54 28 948 1450 784925629 784926139 1.820000e-92 350.0
12 TraesCS5A01G248100 chr6A 77.391 690 106 35 1295 1953 96452612 96451942 6.510000e-97 364.0
13 TraesCS5A01G248100 chr4A 93.600 125 4 4 2084 2204 2701376 2701500 1.960000e-42 183.0
14 TraesCS5A01G248100 chr4A 100.000 29 0 0 300 328 550492184 550492156 2.000000e-03 54.7
15 TraesCS5A01G248100 chr2A 92.000 125 6 3 2084 2204 614570545 614570669 4.240000e-39 172.0
16 TraesCS5A01G248100 chr4B 83.660 153 21 4 1369 1519 592673653 592673503 1.190000e-29 141.0


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 TraesCS5A01G248100 chr5A 461936848 461940041 3193 True 5899 5899 100.0000 1 3194 1 chr5A.!!$R1 3193
1 TraesCS5A01G248100 chr5A 461930070 461932642 2572 True 863 1024 93.4510 2016 3194 3 chr5A.!!$R2 1178
2 TraesCS5A01G248100 chr5D 361401219 361405961 4742 True 1910 3227 89.0425 1 2975 2 chr5D.!!$R1 2974
3 TraesCS5A01G248100 chr5B 426993058 426995464 2406 True 2706 2706 87.2360 497 2939 1 chr5B.!!$R1 2442
4 TraesCS5A01G248100 chr3A 716988181 716989229 1048 False 928 928 83.1490 1155 2207 1 chr3A.!!$F1 1052
5 TraesCS5A01G248100 chr3D 587608115 587609402 1287 False 870 870 79.6460 897 2207 1 chr3D.!!$F2 1310
6 TraesCS5A01G248100 chr3B 784925629 784927347 1718 False 469 588 80.7570 948 2207 2 chr3B.!!$F1 1259
7 TraesCS5A01G248100 chr6A 96451942 96452612 670 True 364 364 77.3910 1295 1953 1 chr6A.!!$R1 658

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
556 572 0.037046 GCCCCCATGCACTTCAAAAG 60.037 55.0 0.0 0.0 0.0 2.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2289 2909 0.397941 TCCACCACCAAGCAGAGAAG 59.602 55.0 0.0 0.0 0.0 2.85 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
41 45 9.036980 AGAAGTACCAGTAGACACATTTCTAAT 57.963 33.333 0.00 0.00 29.70 1.73
112 116 0.740737 GCACCCACAGCCATAATCAC 59.259 55.000 0.00 0.00 0.00 3.06
118 122 2.684881 CCACAGCCATAATCACAGAACC 59.315 50.000 0.00 0.00 0.00 3.62
167 171 7.799784 AGTTTTTGTTTAAGAATCATGCATGC 58.200 30.769 22.25 11.82 0.00 4.06
259 264 6.658188 AGATGATTAGGTTCCTACTAGTGC 57.342 41.667 5.39 0.00 0.00 4.40
260 265 6.136857 AGATGATTAGGTTCCTACTAGTGCA 58.863 40.000 5.39 0.00 0.00 4.57
269 274 0.460284 CTACTAGTGCAACCAGCCCG 60.460 60.000 5.39 0.00 44.83 6.13
278 283 3.645268 AACCAGCCCGCCAGGATTC 62.645 63.158 0.00 0.00 41.02 2.52
297 302 6.670077 GATTCTAATCCCAGACTTGACAAC 57.330 41.667 0.00 0.00 0.00 3.32
298 303 5.560722 TTCTAATCCCAGACTTGACAACA 57.439 39.130 0.00 0.00 0.00 3.33
302 307 0.947244 CCCAGACTTGACAACAGTGC 59.053 55.000 0.00 0.00 0.00 4.40
305 310 1.524355 CAGACTTGACAACAGTGCTCG 59.476 52.381 0.00 0.00 0.00 5.03
337 342 9.480053 TTTCTGGATTTATTTCAAGCTTCTTTG 57.520 29.630 0.00 0.00 0.00 2.77
339 344 8.299570 TCTGGATTTATTTCAAGCTTCTTTGTC 58.700 33.333 0.00 0.00 0.00 3.18
340 345 7.083858 TGGATTTATTTCAAGCTTCTTTGTCG 58.916 34.615 0.00 0.00 0.00 4.35
341 346 7.040755 TGGATTTATTTCAAGCTTCTTTGTCGA 60.041 33.333 0.00 0.00 0.00 4.20
342 347 7.970614 GGATTTATTTCAAGCTTCTTTGTCGAT 59.029 33.333 0.00 0.00 0.00 3.59
343 348 9.346725 GATTTATTTCAAGCTTCTTTGTCGATT 57.653 29.630 0.00 0.00 0.00 3.34
344 349 9.696917 ATTTATTTCAAGCTTCTTTGTCGATTT 57.303 25.926 0.00 0.00 0.00 2.17
345 350 9.528018 TTTATTTCAAGCTTCTTTGTCGATTTT 57.472 25.926 0.00 0.00 0.00 1.82
366 374 6.833342 TTTTTCTAGCGAGAGTAAACGTTT 57.167 33.333 18.90 18.90 31.77 3.60
367 375 6.443876 TTTTCTAGCGAGAGTAAACGTTTC 57.556 37.500 18.42 9.41 31.77 2.78
388 396 3.671262 TCGACAACGAAGAAGGCAA 57.329 47.368 0.00 0.00 45.74 4.52
389 397 1.214367 TCGACAACGAAGAAGGCAAC 58.786 50.000 0.00 0.00 45.74 4.17
402 410 3.555518 GAAGGCAACGTCAATCTCAAAC 58.444 45.455 0.00 0.00 45.22 2.93
431 440 5.715070 ACCATATCTCGAAAGTGCTATAGC 58.285 41.667 18.18 18.18 42.50 2.97
449 458 2.111878 AGCAGGGTGAGTGTGTGC 59.888 61.111 0.00 0.00 0.00 4.57
450 459 3.349006 GCAGGGTGAGTGTGTGCG 61.349 66.667 0.00 0.00 0.00 5.34
451 460 3.349006 CAGGGTGAGTGTGTGCGC 61.349 66.667 0.00 0.00 0.00 6.09
452 461 4.969196 AGGGTGAGTGTGTGCGCG 62.969 66.667 0.00 0.00 0.00 6.86
471 480 0.179073 GCGTGTCTGTGGGCATCTAT 60.179 55.000 0.00 0.00 0.00 1.98
476 485 4.501400 CGTGTCTGTGGGCATCTATGATTA 60.501 45.833 0.00 0.00 0.00 1.75
478 487 6.572314 CGTGTCTGTGGGCATCTATGATTATA 60.572 42.308 0.00 0.00 0.00 0.98
479 488 6.591834 GTGTCTGTGGGCATCTATGATTATAC 59.408 42.308 0.00 0.00 0.00 1.47
482 491 5.491070 TGTGGGCATCTATGATTATACTGC 58.509 41.667 0.00 0.00 0.00 4.40
487 496 8.496916 TGGGCATCTATGATTATACTGCATTAT 58.503 33.333 1.87 1.87 29.85 1.28
488 497 9.347240 GGGCATCTATGATTATACTGCATTATT 57.653 33.333 1.51 0.00 29.85 1.40
556 572 0.037046 GCCCCCATGCACTTCAAAAG 60.037 55.000 0.00 0.00 0.00 2.27
571 587 3.843999 TCAAAAGGTTGTTGCACACTTC 58.156 40.909 0.00 0.00 36.07 3.01
649 666 7.115378 GCACCATTCAAGATGTAAAAGACAAAG 59.885 37.037 0.00 0.00 42.78 2.77
653 670 6.560253 TCAAGATGTAAAAGACAAAGGAGC 57.440 37.500 0.00 0.00 42.78 4.70
671 688 3.735746 GGAGCATTCAAAACAAAACTCGG 59.264 43.478 0.00 0.00 0.00 4.63
672 689 4.359706 GAGCATTCAAAACAAAACTCGGT 58.640 39.130 0.00 0.00 0.00 4.69
682 699 6.394025 AAACAAAACTCGGTAAAATAGGCA 57.606 33.333 0.00 0.00 0.00 4.75
683 700 5.622770 ACAAAACTCGGTAAAATAGGCAG 57.377 39.130 0.00 0.00 0.00 4.85
684 701 5.067954 ACAAAACTCGGTAAAATAGGCAGT 58.932 37.500 0.00 0.00 0.00 4.40
761 778 0.463833 CGGTGGACCTAGCAATTCCC 60.464 60.000 0.00 0.00 0.00 3.97
786 810 3.941188 CCCGCTCCACACACACCT 61.941 66.667 0.00 0.00 0.00 4.00
796 820 2.948979 CCACACACACCTACAACAACAT 59.051 45.455 0.00 0.00 0.00 2.71
799 832 4.024893 CACACACACCTACAACAACATCTC 60.025 45.833 0.00 0.00 0.00 2.75
803 836 3.008049 ACACCTACAACAACATCTCCTCC 59.992 47.826 0.00 0.00 0.00 4.30
805 838 3.008049 ACCTACAACAACATCTCCTCCAC 59.992 47.826 0.00 0.00 0.00 4.02
807 840 2.851195 ACAACAACATCTCCTCCACAC 58.149 47.619 0.00 0.00 0.00 3.82
808 841 2.172505 ACAACAACATCTCCTCCACACA 59.827 45.455 0.00 0.00 0.00 3.72
809 842 2.549754 CAACAACATCTCCTCCACACAC 59.450 50.000 0.00 0.00 0.00 3.82
810 843 1.768275 ACAACATCTCCTCCACACACA 59.232 47.619 0.00 0.00 0.00 3.72
811 844 2.146342 CAACATCTCCTCCACACACAC 58.854 52.381 0.00 0.00 0.00 3.82
812 845 1.423584 ACATCTCCTCCACACACACA 58.576 50.000 0.00 0.00 0.00 3.72
813 846 1.768275 ACATCTCCTCCACACACACAA 59.232 47.619 0.00 0.00 0.00 3.33
814 847 2.172505 ACATCTCCTCCACACACACAAA 59.827 45.455 0.00 0.00 0.00 2.83
815 848 3.213506 CATCTCCTCCACACACACAAAA 58.786 45.455 0.00 0.00 0.00 2.44
855 888 4.873129 CGGCCGTCATCCACCTCG 62.873 72.222 19.50 0.00 0.00 4.63
856 889 3.458163 GGCCGTCATCCACCTCGA 61.458 66.667 0.00 0.00 0.00 4.04
859 892 2.494918 CGTCATCCACCTCGACCC 59.505 66.667 0.00 0.00 0.00 4.46
860 893 2.494918 GTCATCCACCTCGACCCG 59.505 66.667 0.00 0.00 0.00 5.28
862 895 4.530857 CATCCACCTCGACCCGCC 62.531 72.222 0.00 0.00 0.00 6.13
865 898 4.452733 CCACCTCGACCCGCCTTC 62.453 72.222 0.00 0.00 0.00 3.46
927 963 0.320771 CCTCCCAGTTCACAACTCCG 60.321 60.000 0.00 0.00 40.46 4.63
930 966 1.275291 TCCCAGTTCACAACTCCGATC 59.725 52.381 0.00 0.00 40.46 3.69
946 983 1.499049 GATCGTCCCATAAAGCGTCC 58.501 55.000 0.00 0.00 0.00 4.79
961 1001 2.058595 GTCCAGCTTCCCTCCGCTA 61.059 63.158 0.00 0.00 34.58 4.26
986 1026 4.079850 AGCGCCACTCAGCAGAGG 62.080 66.667 11.18 0.00 46.44 3.69
990 1030 2.433838 CCACTCAGCAGAGGCACG 60.434 66.667 11.18 0.00 46.44 5.34
1125 1165 2.186125 GGCGGGCAGTACTACACC 59.814 66.667 0.00 0.00 0.00 4.16
1675 2258 2.826738 AGGAGAGCGAGGACGAGC 60.827 66.667 0.00 0.00 42.66 5.03
1695 2278 1.258676 GGATCATACGGGAGGAGACC 58.741 60.000 0.00 0.00 0.00 3.85
2201 2809 2.542205 GGCAACGTGTTTAGTTTGACCC 60.542 50.000 0.00 0.00 0.00 4.46
2254 2869 0.323725 GCTTGCTGGGAATGGGAAGA 60.324 55.000 0.00 0.00 33.70 2.87
2289 2909 2.255881 CCGTTTGTCCCGGTGGAAC 61.256 63.158 0.00 0.00 44.07 3.62
2445 3107 9.347240 AGATATTCCTGTCAATTTTATCTGGTG 57.653 33.333 0.00 0.00 0.00 4.17
2446 3108 6.780457 ATTCCTGTCAATTTTATCTGGTGG 57.220 37.500 0.00 0.00 0.00 4.61
2447 3109 5.255397 TCCTGTCAATTTTATCTGGTGGT 57.745 39.130 0.00 0.00 0.00 4.16
2573 5193 2.616842 GTGACATGAACAAGAACCGGTT 59.383 45.455 22.50 22.50 0.00 4.44
2630 5256 6.721571 ATTCACACGGTTGAGTTATTGTAG 57.278 37.500 0.00 0.00 0.00 2.74
2631 5257 5.204409 TCACACGGTTGAGTTATTGTAGT 57.796 39.130 0.00 0.00 0.00 2.73
2632 5258 6.330004 TCACACGGTTGAGTTATTGTAGTA 57.670 37.500 0.00 0.00 0.00 1.82
2781 6625 9.342308 ACGTTGGATATTTTGATGTTGATATCT 57.658 29.630 3.98 0.00 33.85 1.98
2808 6652 5.240844 CCATCTGCATATGAGCAAGAATTCA 59.759 40.000 13.31 0.00 45.13 2.57
2812 6656 6.320418 TCTGCATATGAGCAAGAATTCAACAT 59.680 34.615 6.97 7.87 45.13 2.71
2817 6661 8.804743 CATATGAGCAAGAATTCAACATGTTTC 58.195 33.333 8.77 4.01 0.00 2.78
2822 6666 5.332506 GCAAGAATTCAACATGTTTCGGTTG 60.333 40.000 8.77 9.13 44.35 3.77
2825 6677 0.671251 TCAACATGTTTCGGTTGGGC 59.329 50.000 8.77 0.00 43.44 5.36
2882 6738 2.030893 CGACATGTGGTGTTTGCTTCAT 60.031 45.455 1.15 0.00 42.36 2.57
2895 6751 2.585330 TGCTTCATGAACAAGGCAAGA 58.415 42.857 15.44 0.00 0.00 3.02
2900 6756 5.107220 GCTTCATGAACAAGGCAAGAAAATG 60.107 40.000 3.38 0.00 0.00 2.32
2925 6781 2.815503 TGCATGAACCATTGAGTGTCTG 59.184 45.455 0.00 0.00 0.00 3.51
2926 6782 3.076621 GCATGAACCATTGAGTGTCTGA 58.923 45.455 0.00 0.00 0.00 3.27
2933 6789 4.074970 ACCATTGAGTGTCTGAATGAACC 58.925 43.478 9.71 0.00 37.27 3.62
3049 6905 0.946221 CGGATCATTCTGGTAGCCGC 60.946 60.000 0.00 0.00 0.00 6.53
3053 6909 0.744414 TCATTCTGGTAGCCGCAAGC 60.744 55.000 0.00 0.00 44.25 4.01
3068 6924 1.583404 GCAAGCGCAATAAATGAACCG 59.417 47.619 11.47 0.00 38.36 4.44
3083 6939 2.101582 TGAACCGAAAACCCCAAATGTG 59.898 45.455 0.00 0.00 0.00 3.21
3107 6963 5.866092 GGAGAATCTGGAAAATTTGTGAAGC 59.134 40.000 0.00 0.00 33.73 3.86
3122 6978 4.885413 TGTGAAGCCATCTTTTTGGAATG 58.115 39.130 0.00 0.00 39.25 2.67
3142 6998 1.070786 TGGTTGTCGCCTCCACTTC 59.929 57.895 0.00 0.00 0.00 3.01
3149 7005 2.741092 GCCTCCACTTCGTCACCA 59.259 61.111 0.00 0.00 0.00 4.17
3161 7017 3.157949 TCACCACTCACCACCGCA 61.158 61.111 0.00 0.00 0.00 5.69
3173 7029 2.487762 CACCACCGCATTTCAGTTACAT 59.512 45.455 0.00 0.00 0.00 2.29
3174 7030 3.687212 CACCACCGCATTTCAGTTACATA 59.313 43.478 0.00 0.00 0.00 2.29
3180 7036 4.971830 CCGCATTTCAGTTACATATTGCAG 59.028 41.667 0.00 0.00 0.00 4.41
3183 7039 6.527722 CGCATTTCAGTTACATATTGCAGTTT 59.472 34.615 0.00 0.00 0.00 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
94 98 2.019249 CTGTGATTATGGCTGTGGGTG 58.981 52.381 0.00 0.00 0.00 4.61
112 116 6.675026 CATAATCATATGCCACAAGGTTCTG 58.325 40.000 0.00 0.00 37.19 3.02
144 148 7.441760 ACTGCATGCATGATTCTTAAACAAAAA 59.558 29.630 30.64 0.00 0.00 1.94
167 171 8.779354 AGTTTTATGAAGCTTCCTAACTACTG 57.221 34.615 23.42 0.00 0.00 2.74
235 240 7.295340 TGCACTAGTAGGAACCTAATCATCTA 58.705 38.462 4.09 0.77 0.00 1.98
259 264 3.944250 AATCCTGGCGGGCTGGTTG 62.944 63.158 23.43 2.65 34.39 3.77
260 265 3.645268 GAATCCTGGCGGGCTGGTT 62.645 63.158 23.43 17.33 34.39 3.67
275 280 6.126863 TGTTGTCAAGTCTGGGATTAGAAT 57.873 37.500 0.00 0.00 0.00 2.40
278 283 4.692625 CACTGTTGTCAAGTCTGGGATTAG 59.307 45.833 0.00 0.00 0.00 1.73
343 348 6.074142 GGAAACGTTTACTCTCGCTAGAAAAA 60.074 38.462 16.21 0.00 0.00 1.94
344 349 5.403466 GGAAACGTTTACTCTCGCTAGAAAA 59.597 40.000 16.21 0.00 0.00 2.29
345 350 4.919754 GGAAACGTTTACTCTCGCTAGAAA 59.080 41.667 16.21 0.00 0.00 2.52
384 392 2.290641 ACAGTTTGAGATTGACGTTGCC 59.709 45.455 0.00 0.00 0.00 4.52
388 396 4.795970 GTCAACAGTTTGAGATTGACGT 57.204 40.909 0.00 0.00 42.60 4.34
393 401 6.536582 CGAGATATGGTCAACAGTTTGAGATT 59.463 38.462 0.00 0.00 42.60 2.40
400 408 5.639506 CACTTTCGAGATATGGTCAACAGTT 59.360 40.000 0.00 0.00 0.00 3.16
402 410 4.033358 GCACTTTCGAGATATGGTCAACAG 59.967 45.833 0.00 0.00 0.00 3.16
431 440 2.256591 GCACACACTCACCCTGCTG 61.257 63.158 0.00 0.00 0.00 4.41
451 460 2.557059 TAGATGCCCACAGACACGCG 62.557 60.000 3.53 3.53 0.00 6.01
452 461 0.179073 ATAGATGCCCACAGACACGC 60.179 55.000 0.00 0.00 0.00 5.34
453 462 1.136891 TCATAGATGCCCACAGACACG 59.863 52.381 0.00 0.00 0.00 4.49
454 463 2.988010 TCATAGATGCCCACAGACAC 57.012 50.000 0.00 0.00 0.00 3.67
458 467 5.583854 GCAGTATAATCATAGATGCCCACAG 59.416 44.000 0.00 0.00 29.82 3.66
491 500 6.484977 CCTAAAGCAAAGCCCATGTTTAAAAA 59.515 34.615 0.00 0.00 0.00 1.94
493 502 5.305644 TCCTAAAGCAAAGCCCATGTTTAAA 59.694 36.000 0.00 0.00 0.00 1.52
494 503 4.835615 TCCTAAAGCAAAGCCCATGTTTAA 59.164 37.500 0.00 0.00 0.00 1.52
495 504 4.411927 TCCTAAAGCAAAGCCCATGTTTA 58.588 39.130 0.00 0.00 0.00 2.01
543 559 3.197265 GCAACAACCTTTTGAAGTGCAT 58.803 40.909 0.00 0.00 37.91 3.96
556 572 3.181487 ACAGAATGAAGTGTGCAACAACC 60.181 43.478 0.00 0.00 46.86 3.77
571 587 4.873817 TGCTTTGGTCAAATGACAGAATG 58.126 39.130 14.93 9.79 46.47 2.67
649 666 3.735746 CCGAGTTTTGTTTTGAATGCTCC 59.264 43.478 0.00 0.00 0.00 4.70
671 688 6.864342 TGAGTGTCTCTACTGCCTATTTTAC 58.136 40.000 0.00 0.00 0.00 2.01
672 689 7.476540 TTGAGTGTCTCTACTGCCTATTTTA 57.523 36.000 0.00 0.00 0.00 1.52
682 699 3.388024 TGCTGGTTTTGAGTGTCTCTACT 59.612 43.478 0.00 0.00 0.00 2.57
683 700 3.495001 GTGCTGGTTTTGAGTGTCTCTAC 59.505 47.826 0.00 0.00 0.00 2.59
684 701 3.388024 AGTGCTGGTTTTGAGTGTCTCTA 59.612 43.478 0.00 0.00 0.00 2.43
761 778 4.410400 GTGGAGCGGGAAGGGTGG 62.410 72.222 0.00 0.00 0.00 4.61
786 810 3.389656 TGTGTGGAGGAGATGTTGTTGTA 59.610 43.478 0.00 0.00 0.00 2.41
796 820 3.358111 TTTTTGTGTGTGTGGAGGAGA 57.642 42.857 0.00 0.00 0.00 3.71
821 854 1.626654 CCGGCTTGTTGCTGTACTCG 61.627 60.000 0.00 0.00 46.27 4.18
822 855 1.912371 GCCGGCTTGTTGCTGTACTC 61.912 60.000 22.15 0.00 46.27 2.59
855 888 1.446272 CGTGAGAAGAAGGCGGGTC 60.446 63.158 0.00 0.00 0.00 4.46
856 889 0.896940 TACGTGAGAAGAAGGCGGGT 60.897 55.000 0.00 0.00 0.00 5.28
859 892 5.115171 CGTTTATATACGTGAGAAGAAGGCG 59.885 44.000 7.47 0.00 36.80 5.52
860 893 5.107951 GCGTTTATATACGTGAGAAGAAGGC 60.108 44.000 15.58 0.04 43.22 4.35
927 963 1.202486 TGGACGCTTTATGGGACGATC 60.202 52.381 0.00 0.00 0.00 3.69
930 966 1.429148 GCTGGACGCTTTATGGGACG 61.429 60.000 0.00 0.00 35.14 4.79
946 983 0.316841 GATCTAGCGGAGGGAAGCTG 59.683 60.000 0.00 0.00 44.32 4.24
961 1001 0.104487 CTGAGTGGCGCTGATGATCT 59.896 55.000 4.71 0.00 0.00 2.75
990 1030 2.031768 GGCCCCATCGATCTGCTC 59.968 66.667 0.00 0.00 0.00 4.26
1031 1071 0.975887 GATCAGGAGGAGGAGCCATC 59.024 60.000 0.00 0.00 40.02 3.51
1032 1072 0.831288 CGATCAGGAGGAGGAGCCAT 60.831 60.000 0.00 0.00 40.02 4.40
1125 1165 1.308069 CCATGGACGGGCTGAAGTTG 61.308 60.000 5.56 0.00 0.00 3.16
1146 1189 0.656259 TGAGGACGACGATGACGATC 59.344 55.000 0.00 0.00 42.66 3.69
1314 1386 1.609783 CATGGTGGGGAAGGTCTCC 59.390 63.158 0.00 0.00 44.54 3.71
1675 2258 0.882474 GTCTCCTCCCGTATGATCCG 59.118 60.000 0.00 0.00 0.00 4.18
2254 2869 1.066752 GGAAAGCAACGGCCGTTTT 59.933 52.632 39.64 30.59 42.56 2.43
2289 2909 0.397941 TCCACCACCAAGCAGAGAAG 59.602 55.000 0.00 0.00 0.00 2.85
2560 5180 4.070009 GGATTAGTCAACCGGTTCTTGTT 58.930 43.478 19.24 4.24 0.00 2.83
2573 5193 4.019792 ACATGTGTGCTTGGATTAGTCA 57.980 40.909 0.00 0.00 0.00 3.41
2630 5256 6.823689 TGCACCAAGAAGAAAAGATAGGATAC 59.176 38.462 0.00 0.00 0.00 2.24
2631 5257 6.957631 TGCACCAAGAAGAAAAGATAGGATA 58.042 36.000 0.00 0.00 0.00 2.59
2632 5258 5.819991 TGCACCAAGAAGAAAAGATAGGAT 58.180 37.500 0.00 0.00 0.00 3.24
2644 5270 2.633509 GCTGCCCTGCACCAAGAAG 61.634 63.158 0.00 0.00 33.79 2.85
2693 6535 3.857854 CGTCTGCTGATGCACCGC 61.858 66.667 0.00 0.00 45.31 5.68
2739 6581 2.552315 CAACGTTGGCACTTCATAGGTT 59.448 45.455 20.71 0.00 0.00 3.50
2781 6625 3.644738 TCTTGCTCATATGCAGATGGAGA 59.355 43.478 20.58 14.93 44.27 3.71
2808 6652 0.387565 GTGCCCAACCGAAACATGTT 59.612 50.000 4.92 4.92 0.00 2.71
2812 6656 2.122167 GGTGTGCCCAACCGAAACA 61.122 57.895 0.00 0.00 0.00 2.83
2867 6723 3.435105 TGTTCATGAAGCAAACACCAC 57.565 42.857 8.80 0.00 0.00 4.16
2882 6738 6.101332 GCATATCATTTTCTTGCCTTGTTCA 58.899 36.000 0.00 0.00 0.00 3.18
2895 6751 7.709182 CACTCAATGGTTCATGCATATCATTTT 59.291 33.333 5.39 0.00 31.79 1.82
2900 6756 5.530171 AGACACTCAATGGTTCATGCATATC 59.470 40.000 0.00 0.00 0.00 1.63
2925 6781 5.581126 TCATGCCTATGTTTGGTTCATTC 57.419 39.130 0.00 0.00 35.73 2.67
2926 6782 6.154877 TCAATCATGCCTATGTTTGGTTCATT 59.845 34.615 9.78 0.00 41.27 2.57
2933 6789 6.623486 TGTTTCTCAATCATGCCTATGTTTG 58.377 36.000 0.00 0.00 41.84 2.93
2979 6835 8.268850 ACATGTGAAATCACCAGAGTTTATAC 57.731 34.615 10.83 0.00 45.88 1.47
2981 6837 7.765695 AACATGTGAAATCACCAGAGTTTAT 57.234 32.000 10.83 0.00 45.88 1.40
3021 6877 1.811965 CAGAATGATCCGCACACCAAA 59.188 47.619 0.00 0.00 39.69 3.28
3049 6905 3.129852 TCGGTTCATTTATTGCGCTTG 57.870 42.857 9.73 0.00 0.00 4.01
3053 6909 3.610677 GGGTTTTCGGTTCATTTATTGCG 59.389 43.478 0.00 0.00 0.00 4.85
3068 6924 4.528206 AGATTCTCCACATTTGGGGTTTTC 59.472 41.667 0.00 0.00 45.01 2.29
3083 6939 5.866092 GCTTCACAAATTTTCCAGATTCTCC 59.134 40.000 0.00 0.00 0.00 3.71
3107 6963 4.202346 ACAACCACCATTCCAAAAAGATGG 60.202 41.667 0.00 0.00 42.12 3.51
3122 6978 2.668550 GTGGAGGCGACAACCACC 60.669 66.667 21.87 6.38 46.78 4.61
3142 6998 2.355837 CGGTGGTGAGTGGTGACG 60.356 66.667 0.00 0.00 0.00 4.35
3149 7005 0.108585 ACTGAAATGCGGTGGTGAGT 59.891 50.000 0.00 0.00 33.94 3.41
3161 7017 7.895759 ACCAAACTGCAATATGTAACTGAAAT 58.104 30.769 0.00 0.00 0.00 2.17
3173 7029 1.804151 GTGAGCGACCAAACTGCAATA 59.196 47.619 0.00 0.00 0.00 1.90
3174 7030 0.593128 GTGAGCGACCAAACTGCAAT 59.407 50.000 0.00 0.00 0.00 3.56


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

AutoCloner maintained by Alex Coulton.