Multiple sequence alignment - TraesCS5A01G016400

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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 TraesCS5A01G016400 chr5A 100.000 2612 0 0 1 2612 12193562 12190951 0.000000e+00 4824
1 TraesCS5A01G016400 chr5A 100.000 100 0 0 2831 2930 12190732 12190633 4.990000e-43 185
2 TraesCS5A01G016400 chr5B 94.616 2433 105 10 1 2432 13775479 13773072 0.000000e+00 3744
3 TraesCS5A01G016400 chr1D 88.874 2247 221 11 2 2239 6713943 6711717 0.000000e+00 2737
4 TraesCS5A01G016400 chr1D 90.795 1912 163 7 103 2005 407671788 407669881 0.000000e+00 2543
5 TraesCS5A01G016400 chr1D 78.138 494 56 24 2041 2529 407669777 407669331 1.730000e-67 267
6 TraesCS5A01G016400 chr1D 82.639 144 23 2 2266 2409 6916015 6916156 3.070000e-25 126
7 TraesCS5A01G016400 chr1A 88.844 2250 218 13 1 2239 8143836 8141609 0.000000e+00 2734
8 TraesCS5A01G016400 chr1A 86.223 2330 259 32 103 2417 7835439 7837721 0.000000e+00 2468
9 TraesCS5A01G016400 chr5D 91.823 1920 97 28 695 2596 18085120 18086997 0.000000e+00 2621
10 TraesCS5A01G016400 chr4B 87.622 2246 236 13 1 2239 36635194 36632984 0.000000e+00 2569
11 TraesCS5A01G016400 chr1B 86.999 2246 249 18 1 2239 8855249 8853040 0.000000e+00 2490
12 TraesCS5A01G016400 chr1B 83.333 162 23 4 2372 2529 8853021 8852860 2.350000e-31 147
13 TraesCS5A01G016400 chr2D 88.065 1902 200 17 81 1970 469984778 469986664 0.000000e+00 2230
14 TraesCS5A01G016400 chr2A 87.500 736 87 4 81 815 611296898 611297629 0.000000e+00 845


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 TraesCS5A01G016400 chr5A 12190633 12193562 2929 True 2504.5 4824 100.0000 1 2930 2 chr5A.!!$R1 2929
1 TraesCS5A01G016400 chr5B 13773072 13775479 2407 True 3744.0 3744 94.6160 1 2432 1 chr5B.!!$R1 2431
2 TraesCS5A01G016400 chr1D 6711717 6713943 2226 True 2737.0 2737 88.8740 2 2239 1 chr1D.!!$R1 2237
3 TraesCS5A01G016400 chr1D 407669331 407671788 2457 True 1405.0 2543 84.4665 103 2529 2 chr1D.!!$R2 2426
4 TraesCS5A01G016400 chr1A 8141609 8143836 2227 True 2734.0 2734 88.8440 1 2239 1 chr1A.!!$R1 2238
5 TraesCS5A01G016400 chr1A 7835439 7837721 2282 False 2468.0 2468 86.2230 103 2417 1 chr1A.!!$F1 2314
6 TraesCS5A01G016400 chr5D 18085120 18086997 1877 False 2621.0 2621 91.8230 695 2596 1 chr5D.!!$F1 1901
7 TraesCS5A01G016400 chr4B 36632984 36635194 2210 True 2569.0 2569 87.6220 1 2239 1 chr4B.!!$R1 2238
8 TraesCS5A01G016400 chr1B 8852860 8855249 2389 True 1318.5 2490 85.1660 1 2529 2 chr1B.!!$R1 2528
9 TraesCS5A01G016400 chr2D 469984778 469986664 1886 False 2230.0 2230 88.0650 81 1970 1 chr2D.!!$F1 1889
10 TraesCS5A01G016400 chr2A 611296898 611297629 731 False 845.0 845 87.5000 81 815 1 chr2A.!!$F1 734

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
728 729 0.398696 TCTTTACCTTCGCCTTGCCA 59.601 50.0 0.0 0.0 0.0 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2479 2782 0.108138 ACCCTCGTTATGCTGCAGTC 60.108 55.0 16.64 8.39 0.0 3.51 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
23 24 1.377202 GGGATTGTCCTCAAGCGCA 60.377 57.895 11.47 0.00 46.84 6.09
241 242 3.242867 AGACATCTCTGGTCAGGTCAAA 58.757 45.455 0.00 0.00 37.74 2.69
271 272 1.172812 GGTCACAAGCCAACCAGTCC 61.173 60.000 0.00 0.00 33.11 3.85
362 363 1.647346 CAATGGCATTGCACATCCAC 58.353 50.000 25.69 0.00 32.92 4.02
436 437 2.035632 GAGGATCGAACAGGAGGATGT 58.964 52.381 0.00 0.00 33.96 3.06
576 577 1.001293 TGTTGCTACCACTCAGAGCAG 59.999 52.381 0.00 0.00 46.29 4.24
668 669 3.515104 CTGGCATGGGGAATTGTTTAGTT 59.485 43.478 0.00 0.00 0.00 2.24
728 729 0.398696 TCTTTACCTTCGCCTTGCCA 59.601 50.000 0.00 0.00 0.00 4.92
785 786 3.011818 AGAAAACCAAACGTCGGAGTTT 58.988 40.909 10.75 9.63 44.27 2.66
1011 1014 8.768397 TCTGTATACAAGGGAATGTTAAGTGAT 58.232 33.333 7.06 0.00 34.75 3.06
1440 1449 3.064545 GCCGAATTCTGACTTCATTCAGG 59.935 47.826 3.52 7.19 42.95 3.86
1443 1452 2.496899 TTCTGACTTCATTCAGGGGC 57.503 50.000 0.46 0.00 42.95 5.80
1545 1554 6.070881 TGGTTTTGTTGGAAATCATATCTGGG 60.071 38.462 0.00 0.00 0.00 4.45
1579 1588 4.568359 CCTCACCTGAAGAATCATACAACG 59.432 45.833 0.00 0.00 34.37 4.10
1758 1773 5.991328 TCCAAGATAATGAGTTTGATCGC 57.009 39.130 0.00 0.00 0.00 4.58
1989 2012 6.769608 AGCTTGCAGTTTTTAATTAGTTGC 57.230 33.333 0.00 0.00 0.00 4.17
2005 2031 4.650972 AGTTGCCTCTTATTTGGGTGTA 57.349 40.909 0.00 0.00 0.00 2.90
2114 2222 4.401925 CAGGATGGGAACTTCAGAACTTT 58.598 43.478 0.00 0.00 36.27 2.66
2117 2225 6.660949 CAGGATGGGAACTTCAGAACTTTTAT 59.339 38.462 0.00 0.00 36.27 1.40
2210 2348 8.617809 GTTTTCAAACTGTACCTGATCAAACTA 58.382 33.333 0.00 0.00 36.03 2.24
2255 2393 6.058827 GAGTAGGTATTCTCGAACTGTACC 57.941 45.833 7.51 7.51 36.02 3.34
2256 2394 5.753716 AGTAGGTATTCTCGAACTGTACCT 58.246 41.667 17.34 17.34 45.21 3.08
2257 2395 6.893583 AGTAGGTATTCTCGAACTGTACCTA 58.106 40.000 15.92 15.92 42.38 3.08
2259 2397 5.753716 AGGTATTCTCGAACTGTACCTACT 58.246 41.667 13.66 0.00 42.38 2.57
2260 2398 6.186234 AGGTATTCTCGAACTGTACCTACTT 58.814 40.000 13.66 0.00 42.38 2.24
2261 2399 6.095160 AGGTATTCTCGAACTGTACCTACTTG 59.905 42.308 13.66 0.00 42.38 3.16
2262 2400 4.778534 TTCTCGAACTGTACCTACTTGG 57.221 45.455 0.00 0.00 42.93 3.61
2263 2401 4.025040 TCTCGAACTGTACCTACTTGGA 57.975 45.455 0.00 0.00 39.71 3.53
2264 2402 3.755378 TCTCGAACTGTACCTACTTGGAC 59.245 47.826 0.00 0.00 39.71 4.02
2265 2403 3.489355 TCGAACTGTACCTACTTGGACA 58.511 45.455 0.00 0.00 39.71 4.02
2266 2404 3.890756 TCGAACTGTACCTACTTGGACAA 59.109 43.478 0.00 0.00 39.71 3.18
2267 2405 4.022589 TCGAACTGTACCTACTTGGACAAG 60.023 45.833 10.34 10.34 43.79 3.16
2268 2406 4.022589 CGAACTGTACCTACTTGGACAAGA 60.023 45.833 18.15 2.27 40.79 3.02
2269 2407 5.336531 CGAACTGTACCTACTTGGACAAGAT 60.337 44.000 18.15 5.87 40.79 2.40
2270 2408 5.407407 ACTGTACCTACTTGGACAAGATG 57.593 43.478 18.15 9.75 40.79 2.90
2271 2409 4.838986 ACTGTACCTACTTGGACAAGATGT 59.161 41.667 18.15 12.96 40.79 3.06
2272 2410 5.307196 ACTGTACCTACTTGGACAAGATGTT 59.693 40.000 18.15 0.00 40.79 2.71
2273 2411 6.495872 ACTGTACCTACTTGGACAAGATGTTA 59.504 38.462 18.15 0.30 40.79 2.41
2274 2412 6.931838 TGTACCTACTTGGACAAGATGTTAG 58.068 40.000 18.15 9.14 40.79 2.34
2275 2413 6.722590 TGTACCTACTTGGACAAGATGTTAGA 59.277 38.462 18.15 0.67 40.79 2.10
2276 2414 6.038997 ACCTACTTGGACAAGATGTTAGAC 57.961 41.667 18.15 0.00 40.79 2.59
2277 2415 5.780793 ACCTACTTGGACAAGATGTTAGACT 59.219 40.000 18.15 0.00 40.79 3.24
2310 2448 3.648067 GGGTGGATATGATCAAGAGACCA 59.352 47.826 0.00 3.03 0.00 4.02
2315 2453 5.842874 TGGATATGATCAAGAGACCACATCT 59.157 40.000 0.00 0.00 41.91 2.90
2324 2462 5.600069 TCAAGAGACCACATCTGCTGTATAT 59.400 40.000 0.00 0.00 38.00 0.86
2328 2466 5.994250 AGACCACATCTGCTGTATATTTGT 58.006 37.500 0.00 0.00 35.81 2.83
2330 2468 5.744171 ACCACATCTGCTGTATATTTGTCA 58.256 37.500 0.00 0.00 35.91 3.58
2332 2470 5.237996 CCACATCTGCTGTATATTTGTCAGG 59.762 44.000 0.00 0.00 35.91 3.86
2341 2479 9.237187 TGCTGTATATTTGTCAGGTATTTTCAA 57.763 29.630 0.00 0.00 0.00 2.69
2438 2739 2.281484 GGTGCCAGCTGAACCGAA 60.281 61.111 17.39 0.00 0.00 4.30
2463 2766 3.367910 CCTTCGGAGACTCTGAAAAGAGG 60.368 52.174 23.71 18.26 40.86 3.69
2471 2774 2.107204 ACTCTGAAAAGAGGGCACATGT 59.893 45.455 7.60 0.00 40.08 3.21
2474 2777 3.569701 TCTGAAAAGAGGGCACATGTTTC 59.430 43.478 0.00 0.00 0.00 2.78
2476 2779 2.683211 AAAGAGGGCACATGTTTCCT 57.317 45.000 14.66 14.66 0.00 3.36
2477 2780 1.915141 AAGAGGGCACATGTTTCCTG 58.085 50.000 18.48 0.00 0.00 3.86
2478 2781 0.773644 AGAGGGCACATGTTTCCTGT 59.226 50.000 18.48 13.09 0.00 4.00
2479 2782 0.883833 GAGGGCACATGTTTCCTGTG 59.116 55.000 18.48 0.00 45.39 3.66
2480 2783 0.478072 AGGGCACATGTTTCCTGTGA 59.522 50.000 14.14 0.00 45.44 3.58
2482 2785 1.609208 GGCACATGTTTCCTGTGACT 58.391 50.000 7.57 0.00 46.92 3.41
2483 2786 1.267806 GGCACATGTTTCCTGTGACTG 59.732 52.381 7.57 0.00 46.92 3.51
2484 2787 1.335324 GCACATGTTTCCTGTGACTGC 60.335 52.381 7.57 0.00 45.44 4.40
2485 2788 1.948834 CACATGTTTCCTGTGACTGCA 59.051 47.619 0.00 0.00 45.44 4.41
2486 2789 2.031420 CACATGTTTCCTGTGACTGCAG 60.031 50.000 13.48 13.48 45.44 4.41
2487 2790 1.068748 CATGTTTCCTGTGACTGCAGC 60.069 52.381 15.27 7.45 35.28 5.25
2488 2791 0.107263 TGTTTCCTGTGACTGCAGCA 60.107 50.000 15.27 10.30 35.28 4.41
2489 2792 1.242076 GTTTCCTGTGACTGCAGCAT 58.758 50.000 15.27 0.00 35.28 3.79
2490 2793 2.224499 TGTTTCCTGTGACTGCAGCATA 60.224 45.455 15.27 10.27 35.28 3.14
2491 2794 2.813754 GTTTCCTGTGACTGCAGCATAA 59.186 45.455 15.27 5.17 35.28 1.90
2492 2795 2.099141 TCCTGTGACTGCAGCATAAC 57.901 50.000 15.27 7.66 35.28 1.89
2493 2796 0.723414 CCTGTGACTGCAGCATAACG 59.277 55.000 15.27 0.00 35.28 3.18
2496 2799 1.002366 GTGACTGCAGCATAACGAGG 58.998 55.000 15.27 0.00 0.00 4.63
2497 2800 0.108186 TGACTGCAGCATAACGAGGG 60.108 55.000 15.27 0.00 0.00 4.30
2498 2801 0.108138 GACTGCAGCATAACGAGGGT 60.108 55.000 15.27 0.00 0.00 4.34
2530 2837 4.082571 AGGTAACAATCTTCATGCAGCAAC 60.083 41.667 0.00 0.00 41.41 4.17
2533 2840 5.710513 AACAATCTTCATGCAGCAACTTA 57.289 34.783 0.00 0.00 0.00 2.24
2566 2900 1.546323 CCTGGCTGAAATGACACCAGT 60.546 52.381 6.60 0.00 45.26 4.00
2575 2909 6.560003 TGAAATGACACCAGTAGGATATGT 57.440 37.500 0.00 0.00 38.69 2.29
2585 2919 8.639761 ACACCAGTAGGATATGTTCTATGTTAC 58.360 37.037 0.00 0.00 38.69 2.50
2586 2920 8.088981 CACCAGTAGGATATGTTCTATGTTACC 58.911 40.741 0.00 0.00 38.69 2.85
2596 2930 4.040706 TGTTCTATGTTACCCCGAAGTGTT 59.959 41.667 0.00 0.00 0.00 3.32
2597 2931 4.895668 TCTATGTTACCCCGAAGTGTTT 57.104 40.909 0.00 0.00 0.00 2.83
2598 2932 5.231702 TCTATGTTACCCCGAAGTGTTTT 57.768 39.130 0.00 0.00 0.00 2.43
2599 2933 6.357579 TCTATGTTACCCCGAAGTGTTTTA 57.642 37.500 0.00 0.00 0.00 1.52
2600 2934 6.767456 TCTATGTTACCCCGAAGTGTTTTAA 58.233 36.000 0.00 0.00 0.00 1.52
2601 2935 7.396418 TCTATGTTACCCCGAAGTGTTTTAAT 58.604 34.615 0.00 0.00 0.00 1.40
2602 2936 8.538701 TCTATGTTACCCCGAAGTGTTTTAATA 58.461 33.333 0.00 0.00 0.00 0.98
2603 2937 7.999450 ATGTTACCCCGAAGTGTTTTAATAA 57.001 32.000 0.00 0.00 0.00 1.40
2604 2938 7.437793 TGTTACCCCGAAGTGTTTTAATAAG 57.562 36.000 0.00 0.00 0.00 1.73
2605 2939 6.430616 TGTTACCCCGAAGTGTTTTAATAAGG 59.569 38.462 0.00 0.00 0.00 2.69
2606 2940 4.989277 ACCCCGAAGTGTTTTAATAAGGT 58.011 39.130 0.00 0.00 0.00 3.50
2607 2941 4.763279 ACCCCGAAGTGTTTTAATAAGGTG 59.237 41.667 0.00 0.00 0.00 4.00
2608 2942 5.005094 CCCCGAAGTGTTTTAATAAGGTGA 58.995 41.667 0.00 0.00 0.00 4.02
2609 2943 5.474189 CCCCGAAGTGTTTTAATAAGGTGAA 59.526 40.000 0.00 0.00 0.00 3.18
2610 2944 6.152154 CCCCGAAGTGTTTTAATAAGGTGAAT 59.848 38.462 0.00 0.00 0.00 2.57
2611 2945 7.337436 CCCCGAAGTGTTTTAATAAGGTGAATA 59.663 37.037 0.00 0.00 0.00 1.75
2861 3195 9.461312 TTTGCTTCCATAAGTAATATGTTGAGT 57.539 29.630 0.00 0.00 39.90 3.41
2862 3196 8.437360 TGCTTCCATAAGTAATATGTTGAGTG 57.563 34.615 0.00 0.00 39.90 3.51
2863 3197 7.012327 TGCTTCCATAAGTAATATGTTGAGTGC 59.988 37.037 0.00 0.00 39.90 4.40
2864 3198 7.012327 GCTTCCATAAGTAATATGTTGAGTGCA 59.988 37.037 0.00 0.00 39.90 4.57
2865 3199 8.437360 TTCCATAAGTAATATGTTGAGTGCAG 57.563 34.615 0.00 0.00 39.90 4.41
2866 3200 7.791029 TCCATAAGTAATATGTTGAGTGCAGA 58.209 34.615 0.00 0.00 39.90 4.26
2867 3201 8.264347 TCCATAAGTAATATGTTGAGTGCAGAA 58.736 33.333 0.00 0.00 39.90 3.02
2868 3202 8.892723 CCATAAGTAATATGTTGAGTGCAGAAA 58.107 33.333 0.00 0.00 39.90 2.52
2872 3206 9.846248 AAGTAATATGTTGAGTGCAGAAAATTC 57.154 29.630 0.00 0.00 0.00 2.17
2873 3207 9.236006 AGTAATATGTTGAGTGCAGAAAATTCT 57.764 29.630 0.00 0.00 38.25 2.40
2901 3235 9.809096 ATTTTTGTAAACATATTGTGTGTCACA 57.191 25.926 0.18 0.18 43.02 3.58
2915 3249 7.736447 TGTGTGTCACAATATTCATGTACAA 57.264 32.000 7.38 0.00 41.69 2.41
2916 3250 7.580600 TGTGTGTCACAATATTCATGTACAAC 58.419 34.615 7.38 0.00 41.69 3.32
2917 3251 7.227512 TGTGTGTCACAATATTCATGTACAACA 59.772 33.333 7.38 0.00 41.69 3.33
2918 3252 8.236586 GTGTGTCACAATATTCATGTACAACAT 58.763 33.333 7.38 0.00 35.19 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
241 242 4.406456 TGGCTTGTGACCAAATATTCAGT 58.594 39.130 0.00 0.00 33.12 3.41
313 314 1.553690 AAGGTCCGCATGTAGCAGGT 61.554 55.000 0.00 0.00 46.13 4.00
362 363 1.137872 GCTCTCCATACAGTCACAGGG 59.862 57.143 0.00 0.00 0.00 4.45
436 437 5.106869 GCAATGTAACGGTGTGTTTCTGATA 60.107 40.000 0.00 0.00 42.09 2.15
576 577 2.606725 CCGAGACATGCTTCTTCACATC 59.393 50.000 0.00 0.00 0.00 3.06
785 786 7.461182 AACCAATAATACTTGCAGCAGTAAA 57.539 32.000 2.47 0.00 32.90 2.01
1011 1014 5.996669 TCACTGCTATAGTAATCGTCGAA 57.003 39.130 0.00 0.00 37.60 3.71
1440 1449 1.098050 CAAGATAACCTGCAGTGCCC 58.902 55.000 13.72 0.00 0.00 5.36
1443 1452 1.098050 GGGCAAGATAACCTGCAGTG 58.902 55.000 13.81 6.81 0.00 3.66
1579 1588 2.174319 GGTTACCGCTGCTGCTAGC 61.174 63.158 8.10 8.10 42.82 3.42
1989 2012 5.008316 GGCGTTAATACACCCAAATAAGAGG 59.992 44.000 0.00 0.00 0.00 3.69
1999 2025 8.671028 CCATATAAAATAGGCGTTAATACACCC 58.329 37.037 0.00 0.00 0.00 4.61
2038 2144 8.978874 TTTCTATCTCTGCCATATTTTGCTAA 57.021 30.769 0.00 0.00 0.00 3.09
2114 2222 4.599041 ACCTATTCCTGCACTGCAAATAA 58.401 39.130 4.99 0.37 38.41 1.40
2117 2225 2.584835 ACCTATTCCTGCACTGCAAA 57.415 45.000 4.99 0.00 38.41 3.68
2154 2276 8.798859 ATTTAACCCATAGCTAGCATCTTATG 57.201 34.615 18.83 15.01 0.00 1.90
2246 2384 5.464030 TCTTGTCCAAGTAGGTACAGTTC 57.536 43.478 6.90 0.00 39.38 3.01
2250 2388 5.818678 AACATCTTGTCCAAGTAGGTACA 57.181 39.130 6.90 0.00 39.38 2.90
2252 2390 6.952358 AGTCTAACATCTTGTCCAAGTAGGTA 59.048 38.462 6.90 3.78 39.38 3.08
2253 2391 5.780793 AGTCTAACATCTTGTCCAAGTAGGT 59.219 40.000 6.90 2.89 39.38 3.08
2255 2393 7.378966 TCAAGTCTAACATCTTGTCCAAGTAG 58.621 38.462 6.90 2.42 40.97 2.57
2256 2394 7.297936 TCAAGTCTAACATCTTGTCCAAGTA 57.702 36.000 6.90 0.00 40.97 2.24
2257 2395 6.174720 TCAAGTCTAACATCTTGTCCAAGT 57.825 37.500 6.90 0.00 40.97 3.16
2258 2396 7.496529 TTTCAAGTCTAACATCTTGTCCAAG 57.503 36.000 0.47 0.47 40.97 3.61
2259 2397 6.017109 GCTTTCAAGTCTAACATCTTGTCCAA 60.017 38.462 0.00 0.00 40.97 3.53
2260 2398 5.470098 GCTTTCAAGTCTAACATCTTGTCCA 59.530 40.000 0.00 0.00 40.97 4.02
2261 2399 5.703130 AGCTTTCAAGTCTAACATCTTGTCC 59.297 40.000 0.00 0.00 40.97 4.02
2262 2400 6.203723 ACAGCTTTCAAGTCTAACATCTTGTC 59.796 38.462 0.00 0.00 40.97 3.18
2263 2401 6.017605 CACAGCTTTCAAGTCTAACATCTTGT 60.018 38.462 0.00 0.00 40.97 3.16
2264 2402 6.369005 CACAGCTTTCAAGTCTAACATCTTG 58.631 40.000 0.00 0.00 41.36 3.02
2265 2403 5.471456 CCACAGCTTTCAAGTCTAACATCTT 59.529 40.000 0.00 0.00 0.00 2.40
2266 2404 4.999950 CCACAGCTTTCAAGTCTAACATCT 59.000 41.667 0.00 0.00 0.00 2.90
2267 2405 4.154918 CCCACAGCTTTCAAGTCTAACATC 59.845 45.833 0.00 0.00 0.00 3.06
2268 2406 4.074970 CCCACAGCTTTCAAGTCTAACAT 58.925 43.478 0.00 0.00 0.00 2.71
2269 2407 3.118038 ACCCACAGCTTTCAAGTCTAACA 60.118 43.478 0.00 0.00 0.00 2.41
2270 2408 3.251004 CACCCACAGCTTTCAAGTCTAAC 59.749 47.826 0.00 0.00 0.00 2.34
2271 2409 3.476552 CACCCACAGCTTTCAAGTCTAA 58.523 45.455 0.00 0.00 0.00 2.10
2272 2410 2.224523 CCACCCACAGCTTTCAAGTCTA 60.225 50.000 0.00 0.00 0.00 2.59
2273 2411 1.477558 CCACCCACAGCTTTCAAGTCT 60.478 52.381 0.00 0.00 0.00 3.24
2274 2412 0.954452 CCACCCACAGCTTTCAAGTC 59.046 55.000 0.00 0.00 0.00 3.01
2275 2413 0.550914 TCCACCCACAGCTTTCAAGT 59.449 50.000 0.00 0.00 0.00 3.16
2276 2414 1.915141 ATCCACCCACAGCTTTCAAG 58.085 50.000 0.00 0.00 0.00 3.02
2277 2415 3.010027 TCATATCCACCCACAGCTTTCAA 59.990 43.478 0.00 0.00 0.00 2.69
2310 2448 5.994250 ACCTGACAAATATACAGCAGATGT 58.006 37.500 0.00 0.00 46.45 3.06
2315 2453 8.800370 TGAAAATACCTGACAAATATACAGCA 57.200 30.769 0.00 0.00 0.00 4.41
2328 2466 8.300286 TCGCACATAATTTTTGAAAATACCTGA 58.700 29.630 2.41 0.00 37.62 3.86
2330 2468 9.651913 AATCGCACATAATTTTTGAAAATACCT 57.348 25.926 2.41 0.00 37.62 3.08
2344 2482 9.283768 TGAAGGATTATACAAATCGCACATAAT 57.716 29.630 0.00 0.00 0.00 1.28
2346 2484 8.846943 ATGAAGGATTATACAAATCGCACATA 57.153 30.769 0.00 0.00 0.00 2.29
2347 2485 7.750229 ATGAAGGATTATACAAATCGCACAT 57.250 32.000 0.00 0.00 0.00 3.21
2380 2681 4.091549 ACACTGAAATCCAAGATGCCATT 58.908 39.130 0.00 0.00 0.00 3.16
2438 2739 7.238137 CTCTTTTCAGAGTCTCCGAAGGTGT 62.238 48.000 0.00 0.00 45.09 4.16
2463 2766 1.267806 CAGTCACAGGAAACATGTGCC 59.732 52.381 0.00 4.29 46.11 5.01
2471 2774 2.813754 GTTATGCTGCAGTCACAGGAAA 59.186 45.455 16.64 0.00 41.62 3.13
2474 2777 0.723414 CGTTATGCTGCAGTCACAGG 59.277 55.000 16.64 6.54 38.16 4.00
2476 2779 1.672737 CCTCGTTATGCTGCAGTCACA 60.673 52.381 16.64 5.17 0.00 3.58
2477 2780 1.002366 CCTCGTTATGCTGCAGTCAC 58.998 55.000 16.64 6.15 0.00 3.67
2478 2781 0.108186 CCCTCGTTATGCTGCAGTCA 60.108 55.000 16.64 14.12 0.00 3.41
2479 2782 0.108138 ACCCTCGTTATGCTGCAGTC 60.108 55.000 16.64 8.39 0.00 3.51
2480 2783 0.324943 AACCCTCGTTATGCTGCAGT 59.675 50.000 16.64 0.00 0.00 4.40
2481 2784 1.933853 GTAACCCTCGTTATGCTGCAG 59.066 52.381 10.11 10.11 36.84 4.41
2482 2785 1.276705 TGTAACCCTCGTTATGCTGCA 59.723 47.619 4.13 4.13 36.84 4.41
2483 2786 2.018542 TGTAACCCTCGTTATGCTGC 57.981 50.000 0.00 0.00 36.84 5.25
2484 2787 3.749088 TGTTTGTAACCCTCGTTATGCTG 59.251 43.478 0.00 0.00 36.84 4.41
2485 2788 4.010667 TGTTTGTAACCCTCGTTATGCT 57.989 40.909 0.00 0.00 36.84 3.79
2486 2789 4.379082 CCTTGTTTGTAACCCTCGTTATGC 60.379 45.833 0.00 0.00 36.84 3.14
2487 2790 4.758165 ACCTTGTTTGTAACCCTCGTTATG 59.242 41.667 0.00 0.00 36.84 1.90
2488 2791 4.976864 ACCTTGTTTGTAACCCTCGTTAT 58.023 39.130 0.00 0.00 36.84 1.89
2489 2792 4.420522 ACCTTGTTTGTAACCCTCGTTA 57.579 40.909 0.00 0.00 33.17 3.18
2490 2793 3.286329 ACCTTGTTTGTAACCCTCGTT 57.714 42.857 0.00 0.00 35.90 3.85
2491 2794 4.129380 GTTACCTTGTTTGTAACCCTCGT 58.871 43.478 0.00 0.00 41.27 4.18
2492 2795 4.128643 TGTTACCTTGTTTGTAACCCTCG 58.871 43.478 9.94 0.00 44.69 4.63
2493 2796 6.489022 AGATTGTTACCTTGTTTGTAACCCTC 59.511 38.462 9.94 7.21 44.69 4.30
2496 2799 7.708998 TGAAGATTGTTACCTTGTTTGTAACC 58.291 34.615 9.94 0.00 44.69 2.85
2497 2800 9.180678 CATGAAGATTGTTACCTTGTTTGTAAC 57.819 33.333 6.40 6.40 45.23 2.50
2498 2801 7.865385 GCATGAAGATTGTTACCTTGTTTGTAA 59.135 33.333 0.00 0.00 0.00 2.41
2530 2837 3.054802 AGCCAGGATTCCAACTCACTAAG 60.055 47.826 5.29 0.00 0.00 2.18
2533 2840 1.004044 CAGCCAGGATTCCAACTCACT 59.996 52.381 5.29 0.00 0.00 3.41
2566 2900 6.554784 TCGGGGTAACATAGAACATATCCTA 58.445 40.000 0.00 0.00 39.74 2.94
2575 2909 4.895668 AACACTTCGGGGTAACATAGAA 57.104 40.909 0.00 0.00 39.74 2.10
2585 2919 5.005094 TCACCTTATTAAAACACTTCGGGG 58.995 41.667 0.00 0.00 0.00 5.73
2586 2920 6.563222 TTCACCTTATTAAAACACTTCGGG 57.437 37.500 0.00 0.00 0.00 5.14
2835 3169 9.461312 ACTCAACATATTACTTATGGAAGCAAA 57.539 29.630 0.00 0.00 41.80 3.68
2836 3170 8.892723 CACTCAACATATTACTTATGGAAGCAA 58.107 33.333 0.00 0.00 41.80 3.91
2837 3171 7.012327 GCACTCAACATATTACTTATGGAAGCA 59.988 37.037 0.00 0.00 41.80 3.91
2838 3172 7.012327 TGCACTCAACATATTACTTATGGAAGC 59.988 37.037 0.00 0.00 41.80 3.86
2839 3173 8.437360 TGCACTCAACATATTACTTATGGAAG 57.563 34.615 0.00 0.00 41.80 3.46
2840 3174 8.264347 TCTGCACTCAACATATTACTTATGGAA 58.736 33.333 0.00 0.00 41.80 3.53
2841 3175 7.791029 TCTGCACTCAACATATTACTTATGGA 58.209 34.615 0.00 0.00 41.80 3.41
2842 3176 8.437360 TTCTGCACTCAACATATTACTTATGG 57.563 34.615 0.00 0.00 41.80 2.74
2846 3180 9.846248 GAATTTTCTGCACTCAACATATTACTT 57.154 29.630 0.00 0.00 0.00 2.24
2847 3181 9.236006 AGAATTTTCTGCACTCAACATATTACT 57.764 29.630 0.00 0.00 35.89 2.24
2848 3182 9.282247 CAGAATTTTCTGCACTCAACATATTAC 57.718 33.333 7.34 0.00 46.97 1.89
2875 3209 9.809096 TGTGACACACAATATGTTTACAAAAAT 57.191 25.926 3.56 0.00 41.69 1.82
2891 3225 7.227512 TGTTGTACATGAATATTGTGACACACA 59.772 33.333 8.05 2.86 43.02 3.72
2892 3226 7.580600 TGTTGTACATGAATATTGTGACACAC 58.419 34.615 8.05 0.00 34.56 3.82
2893 3227 7.736447 TGTTGTACATGAATATTGTGACACA 57.264 32.000 3.56 3.56 0.00 3.72


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

AutoCloner maintained by Alex Coulton.