Multiple sequence alignment - TraesCS6D01G289700

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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 TraesCS6D01G289700 chr6D 100.000 3104 0 0 1 3104 400647270 400650373 0.000000e+00 5733.0
1 TraesCS6D01G289700 chr6A 89.131 2383 120 42 1 2290 546595245 546597581 0.000000e+00 2837.0
2 TraesCS6D01G289700 chr6A 80.671 626 54 30 2419 3015 546597867 546598454 1.030000e-114 424.0
3 TraesCS6D01G289700 chr6A 91.139 79 3 1 3009 3087 546598561 546598635 1.520000e-18 104.0
4 TraesCS6D01G289700 chr6B 89.462 2268 127 54 82 2285 599684634 599686853 0.000000e+00 2761.0
5 TraesCS6D01G289700 chr6B 83.791 401 27 19 2397 2763 599687028 599687424 2.290000e-91 346.0
6 TraesCS6D01G289700 chr7A 80.251 876 143 18 1121 1987 155646519 155645665 1.570000e-177 632.0
7 TraesCS6D01G289700 chr7B 79.954 878 142 22 1121 1987 115560973 115560119 1.580000e-172 616.0
8 TraesCS6D01G289700 chr7B 95.455 44 2 0 1796 1839 619072056 619072099 1.540000e-08 71.3


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 TraesCS6D01G289700 chr6D 400647270 400650373 3103 False 5733.000000 5733 100.000000 1 3104 1 chr6D.!!$F1 3103
1 TraesCS6D01G289700 chr6A 546595245 546598635 3390 False 1121.666667 2837 86.980333 1 3087 3 chr6A.!!$F1 3086
2 TraesCS6D01G289700 chr6B 599684634 599687424 2790 False 1553.500000 2761 86.626500 82 2763 2 chr6B.!!$F1 2681
3 TraesCS6D01G289700 chr7A 155645665 155646519 854 True 632.000000 632 80.251000 1121 1987 1 chr7A.!!$R1 866
4 TraesCS6D01G289700 chr7B 115560119 115560973 854 True 616.000000 616 79.954000 1121 1987 1 chr7B.!!$R1 866

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
382 398 0.171231 TCGATCTGCTTCGTGGTCTG 59.829 55.0 0.0 0.0 40.03 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2324 2450 0.033504 AATCAGCGTGACCGTGTCTT 59.966 50.0 5.77 0.0 36.15 3.01 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
25 26 6.528537 TTATGCTTTGGATATTTGTGTGCT 57.471 33.333 0.00 0.00 0.00 4.40
32 33 2.094675 GATATTTGTGTGCTGCCCACT 58.905 47.619 15.94 0.00 44.92 4.00
34 35 2.091102 ATTTGTGTGCTGCCCACTGC 62.091 55.000 15.94 0.00 44.92 4.40
39 40 2.668212 TGCTGCCCACTGCGTAAC 60.668 61.111 0.00 0.00 45.60 2.50
53 54 2.357009 TGCGTAACCGACCTTCTAGATC 59.643 50.000 0.00 0.00 35.63 2.75
54 55 2.617774 GCGTAACCGACCTTCTAGATCT 59.382 50.000 0.00 0.00 35.63 2.75
60 61 3.634448 ACCGACCTTCTAGATCTGTCATG 59.366 47.826 5.18 0.93 0.00 3.07
77 78 2.019249 CATGATCATGGCACTTTCGGT 58.981 47.619 25.37 0.00 35.24 4.69
248 258 7.858052 ATAATTCAGTCTTTTTGAAAGTGCG 57.142 32.000 0.87 0.00 38.01 5.34
291 301 2.825861 AAAGCACCCATCAGCAAAAG 57.174 45.000 0.00 0.00 0.00 2.27
350 361 1.140452 CCCACTGACCCATCATCTCTG 59.860 57.143 0.00 0.00 33.22 3.35
353 364 2.765135 CACTGACCCATCATCTCTGTCT 59.235 50.000 0.00 0.00 33.22 3.41
366 380 2.359848 TCTCTGTCTTTTCAACCGTCGA 59.640 45.455 0.00 0.00 0.00 4.20
367 381 3.005472 TCTCTGTCTTTTCAACCGTCGAT 59.995 43.478 0.00 0.00 0.00 3.59
369 383 3.005472 TCTGTCTTTTCAACCGTCGATCT 59.995 43.478 0.00 0.00 0.00 2.75
370 384 3.057019 TGTCTTTTCAACCGTCGATCTG 58.943 45.455 0.00 0.00 0.00 2.90
371 385 2.066262 TCTTTTCAACCGTCGATCTGC 58.934 47.619 0.00 0.00 0.00 4.26
374 388 1.710013 TTCAACCGTCGATCTGCTTC 58.290 50.000 0.00 0.00 0.00 3.86
378 394 1.874019 CCGTCGATCTGCTTCGTGG 60.874 63.158 0.00 4.78 40.03 4.94
382 398 0.171231 TCGATCTGCTTCGTGGTCTG 59.829 55.000 0.00 0.00 40.03 3.51
498 514 1.376037 GTTTCGTCTGCCTCCTGGG 60.376 63.158 0.00 0.00 38.36 4.45
513 529 1.586154 CTGGGCGGTGCAAAGTTAGG 61.586 60.000 0.00 0.00 0.00 2.69
591 608 1.303799 AAGCTTGCATGACCTCAGCG 61.304 55.000 0.00 0.00 0.00 5.18
592 609 2.758089 GCTTGCATGACCTCAGCGG 61.758 63.158 3.33 0.00 39.35 5.52
601 618 4.598894 CCTCAGCGGCGGATCCTG 62.599 72.222 9.78 7.52 0.00 3.86
607 624 1.448540 GCGGCGGATCCTGGATATG 60.449 63.158 9.66 6.23 0.00 1.78
649 666 1.074872 GAAGCTGCTTCAATTGCCGC 61.075 55.000 31.59 6.83 39.95 6.53
785 829 2.425668 ACTTGACCCAACGAAACCTTTG 59.574 45.455 0.00 0.00 0.00 2.77
818 862 2.096417 CACCAACTCGGACATTTCGTTC 60.096 50.000 0.00 0.00 38.63 3.95
833 877 1.281656 GTTCGTTGGAACCCAAGCG 59.718 57.895 0.00 6.54 44.82 4.68
834 878 1.894756 TTCGTTGGAACCCAAGCGG 60.895 57.895 15.24 4.07 44.82 5.52
835 879 2.281208 CGTTGGAACCCAAGCGGA 60.281 61.111 0.00 0.00 44.82 5.54
859 903 2.703798 CGGACGTTTCCCGCCTCTA 61.704 63.158 0.86 0.00 40.54 2.43
860 904 1.821258 GGACGTTTCCCGCCTCTAT 59.179 57.895 0.00 0.00 41.42 1.98
861 905 0.177373 GGACGTTTCCCGCCTCTATT 59.823 55.000 0.00 0.00 41.42 1.73
955 999 0.300193 GCTTCTCTTGCTTCGATCGC 59.700 55.000 11.09 0.00 0.00 4.58
977 1021 3.574826 CCTGCTCATCTCATCTCATCTGA 59.425 47.826 0.00 0.00 0.00 3.27
1746 1832 4.003788 CGGTTCCACCTGGACGCT 62.004 66.667 0.00 0.00 45.39 5.07
1923 2015 3.083997 GTGGACCTGGAGGCGGAT 61.084 66.667 0.00 0.00 39.32 4.18
2136 2240 4.210093 TGACGGTCACGCCACGTT 62.210 61.111 6.76 0.00 46.04 3.99
2151 2255 1.803519 CGTTCGTCTCTGCAGGCTC 60.804 63.158 15.13 3.47 0.00 4.70
2179 2292 1.448985 TTGCTAGTTCGATTGGCCAC 58.551 50.000 3.88 0.00 0.00 5.01
2229 2349 8.458052 TGTACATACTACTGCCATTGATTTTTG 58.542 33.333 0.00 0.00 0.00 2.44
2290 2416 5.978934 TTTTTCCGTGTCAAACTCTCTAC 57.021 39.130 0.00 0.00 0.00 2.59
2291 2417 4.931661 TTTCCGTGTCAAACTCTCTACT 57.068 40.909 0.00 0.00 0.00 2.57
2292 2418 4.500603 TTCCGTGTCAAACTCTCTACTC 57.499 45.455 0.00 0.00 0.00 2.59
2294 2420 3.752222 TCCGTGTCAAACTCTCTACTCTC 59.248 47.826 0.00 0.00 0.00 3.20
2296 2422 4.216687 CCGTGTCAAACTCTCTACTCTCTT 59.783 45.833 0.00 0.00 0.00 2.85
2297 2423 5.278561 CCGTGTCAAACTCTCTACTCTCTTT 60.279 44.000 0.00 0.00 0.00 2.52
2298 2424 6.210078 CGTGTCAAACTCTCTACTCTCTTTT 58.790 40.000 0.00 0.00 0.00 2.27
2300 2426 6.422400 GTGTCAAACTCTCTACTCTCTTTTGG 59.578 42.308 0.00 0.00 0.00 3.28
2301 2427 6.098409 TGTCAAACTCTCTACTCTCTTTTGGT 59.902 38.462 0.00 0.00 0.00 3.67
2302 2428 6.987404 GTCAAACTCTCTACTCTCTTTTGGTT 59.013 38.462 0.00 0.00 0.00 3.67
2303 2429 8.142551 GTCAAACTCTCTACTCTCTTTTGGTTA 58.857 37.037 0.00 0.00 0.00 2.85
2304 2430 8.142551 TCAAACTCTCTACTCTCTTTTGGTTAC 58.857 37.037 0.00 0.00 0.00 2.50
2305 2431 7.842887 AACTCTCTACTCTCTTTTGGTTACT 57.157 36.000 0.00 0.00 0.00 2.24
2306 2432 7.222000 ACTCTCTACTCTCTTTTGGTTACTG 57.778 40.000 0.00 0.00 0.00 2.74
2308 2434 6.075984 TCTCTACTCTCTTTTGGTTACTGGT 58.924 40.000 0.00 0.00 0.00 4.00
2309 2435 6.208994 TCTCTACTCTCTTTTGGTTACTGGTC 59.791 42.308 0.00 0.00 0.00 4.02
2310 2436 3.991367 ACTCTCTTTTGGTTACTGGTCG 58.009 45.455 0.00 0.00 0.00 4.79
2312 2438 4.141779 ACTCTCTTTTGGTTACTGGTCGTT 60.142 41.667 0.00 0.00 0.00 3.85
2313 2439 4.124238 TCTCTTTTGGTTACTGGTCGTTG 58.876 43.478 0.00 0.00 0.00 4.10
2314 2440 3.207778 TCTTTTGGTTACTGGTCGTTGG 58.792 45.455 0.00 0.00 0.00 3.77
2318 2444 2.290464 TGGTTACTGGTCGTTGGTTTG 58.710 47.619 0.00 0.00 0.00 2.93
2319 2445 1.002142 GGTTACTGGTCGTTGGTTTGC 60.002 52.381 0.00 0.00 0.00 3.68
2320 2446 1.002142 GTTACTGGTCGTTGGTTTGCC 60.002 52.381 0.00 0.00 0.00 4.52
2321 2447 0.881159 TACTGGTCGTTGGTTTGCCG 60.881 55.000 0.00 0.00 37.67 5.69
2322 2448 3.536498 CTGGTCGTTGGTTTGCCGC 62.536 63.158 0.00 0.00 37.67 6.53
2323 2449 4.337060 GGTCGTTGGTTTGCCGCC 62.337 66.667 0.00 0.00 37.67 6.13
2324 2450 3.587933 GTCGTTGGTTTGCCGCCA 61.588 61.111 0.00 0.00 37.67 5.69
2326 2452 2.354539 CGTTGGTTTGCCGCCAAG 60.355 61.111 4.29 0.00 45.50 3.61
2327 2453 2.840066 CGTTGGTTTGCCGCCAAGA 61.840 57.895 4.29 0.00 45.50 3.02
2328 2454 1.299850 GTTGGTTTGCCGCCAAGAC 60.300 57.895 4.29 0.00 45.50 3.01
2329 2455 1.754621 TTGGTTTGCCGCCAAGACA 60.755 52.632 0.37 0.00 40.69 3.41
2330 2456 2.010582 TTGGTTTGCCGCCAAGACAC 62.011 55.000 0.37 0.00 40.69 3.67
2336 2462 3.041940 CCGCCAAGACACGGTCAC 61.042 66.667 6.78 0.00 44.46 3.67
2338 2464 3.712881 GCCAAGACACGGTCACGC 61.713 66.667 6.78 1.99 46.04 5.34
2339 2465 2.029073 CCAAGACACGGTCACGCT 59.971 61.111 6.78 0.00 46.04 5.07
2340 2466 2.310233 CCAAGACACGGTCACGCTG 61.310 63.158 6.78 0.00 46.04 5.18
2343 2469 0.033504 AAGACACGGTCACGCTGATT 59.966 50.000 6.78 0.00 46.04 2.57
2396 2561 2.566833 ATGGTAGTTGCTGCTGTTGA 57.433 45.000 0.00 0.00 0.00 3.18
2407 2597 0.249447 TGCTGTTGATCGGGCTATCG 60.249 55.000 0.00 0.00 0.00 2.92
2429 2793 1.617947 AACAGCGACTCAGGATCCCC 61.618 60.000 8.55 0.00 0.00 4.81
2468 2832 2.284190 CGGGAGAGAGAATTTTGAGGC 58.716 52.381 0.00 0.00 0.00 4.70
2489 2853 3.243401 GCATCGCCGGGAAAAATTCTATT 60.243 43.478 2.18 0.00 0.00 1.73
2490 2854 4.290155 CATCGCCGGGAAAAATTCTATTG 58.710 43.478 2.18 0.00 0.00 1.90
2494 2858 4.503910 GCCGGGAAAAATTCTATTGCTTT 58.496 39.130 2.18 0.00 0.00 3.51
2496 2860 5.163864 GCCGGGAAAAATTCTATTGCTTTTG 60.164 40.000 2.18 0.00 0.00 2.44
2497 2861 5.931724 CCGGGAAAAATTCTATTGCTTTTGT 59.068 36.000 0.00 0.00 0.00 2.83
2498 2862 6.426633 CCGGGAAAAATTCTATTGCTTTTGTT 59.573 34.615 0.00 0.00 0.00 2.83
2499 2863 7.600752 CCGGGAAAAATTCTATTGCTTTTGTTA 59.399 33.333 0.00 0.00 0.00 2.41
2500 2864 8.983724 CGGGAAAAATTCTATTGCTTTTGTTAA 58.016 29.630 0.00 0.00 0.00 2.01
2520 2884 6.655848 TGTTAATATAGTTTGTTTGGTCGCCT 59.344 34.615 0.00 0.00 0.00 5.52
2551 2915 3.432252 GGTCCATGCACGCATTAGTATAC 59.568 47.826 0.72 0.00 33.90 1.47
2554 2918 3.398406 CATGCACGCATTAGTATACCCA 58.602 45.455 0.72 0.00 33.90 4.51
2569 2933 5.726793 AGTATACCCACATGACTTCCTTTCT 59.273 40.000 0.00 0.00 0.00 2.52
2645 3009 6.243900 ACCAGACAGACATCAATGAGAAAAT 58.756 36.000 0.00 0.00 0.00 1.82
2767 3167 8.454106 GTCACAGTGAATATAGTGAAGCAAATT 58.546 33.333 4.32 0.00 42.03 1.82
2770 3170 9.013229 ACAGTGAATATAGTGAAGCAAATTTGA 57.987 29.630 22.31 0.00 0.00 2.69
2787 3187 9.369904 GCAAATTTGATGTTATAGATGTTGGTT 57.630 29.630 22.31 0.00 0.00 3.67
2908 3308 6.652205 ATTACTTTGGAATGGAGGGAGTAA 57.348 37.500 0.00 0.00 34.02 2.24
3005 3407 8.937634 AATAAATAAAGCTCTTGATTTGCCAG 57.062 30.769 12.90 0.00 35.13 4.85
3006 3408 4.996788 ATAAAGCTCTTGATTTGCCAGG 57.003 40.909 0.00 0.00 33.52 4.45
3007 3409 1.553706 AAGCTCTTGATTTGCCAGGG 58.446 50.000 0.00 0.00 0.00 4.45
3050 3566 1.205417 CAAATGGGCCAATTCGAAGCT 59.795 47.619 11.89 0.00 0.00 3.74
3051 3567 1.560505 AATGGGCCAATTCGAAGCTT 58.439 45.000 11.89 0.00 0.00 3.74
3052 3568 2.435372 ATGGGCCAATTCGAAGCTTA 57.565 45.000 11.89 0.00 0.00 3.09
3053 3569 2.208132 TGGGCCAATTCGAAGCTTAA 57.792 45.000 2.13 0.00 0.00 1.85
3060 3576 7.068839 TGGGCCAATTCGAAGCTTAATTAATTA 59.931 33.333 2.13 3.71 0.00 1.40
3094 3610 2.796227 GCACTTGCTGCGGTTTTAC 58.204 52.632 0.00 0.00 35.72 2.01
3095 3611 0.310854 GCACTTGCTGCGGTTTTACT 59.689 50.000 0.00 0.00 35.72 2.24
3096 3612 1.663161 GCACTTGCTGCGGTTTTACTC 60.663 52.381 0.00 0.00 35.72 2.59
3097 3613 1.069227 CACTTGCTGCGGTTTTACTCC 60.069 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 5.679382 GCAGCACACAAATATCCAAAGCATA 60.679 40.000 0.00 0.00 0.00 3.14
25 26 3.617735 TCGGTTACGCAGTGGGCA 61.618 61.111 7.17 0.00 45.73 5.36
32 33 1.825090 TCTAGAAGGTCGGTTACGCA 58.175 50.000 0.00 0.00 40.69 5.24
34 35 3.626670 ACAGATCTAGAAGGTCGGTTACG 59.373 47.826 0.00 0.00 42.74 3.18
39 40 3.885901 TCATGACAGATCTAGAAGGTCGG 59.114 47.826 13.69 10.09 0.00 4.79
53 54 3.242641 CGAAAGTGCCATGATCATGACAG 60.243 47.826 32.71 19.06 41.20 3.51
54 55 2.679336 CGAAAGTGCCATGATCATGACA 59.321 45.455 32.71 26.31 41.20 3.58
60 61 0.652592 CGACCGAAAGTGCCATGATC 59.347 55.000 0.00 0.00 0.00 2.92
77 78 1.812571 GCTTTGAAGCCCTTGATTCGA 59.187 47.619 4.38 0.00 46.20 3.71
248 258 0.718343 GCATGACACGAGCAACTCTC 59.282 55.000 0.00 0.00 38.47 3.20
336 347 4.836825 TGAAAAGACAGAGATGATGGGTC 58.163 43.478 0.00 0.00 0.00 4.46
350 361 2.159827 GCAGATCGACGGTTGAAAAGAC 60.160 50.000 1.47 0.00 0.00 3.01
353 364 2.163818 AGCAGATCGACGGTTGAAAA 57.836 45.000 1.47 0.00 0.00 2.29
366 380 0.534412 CTCCAGACCACGAAGCAGAT 59.466 55.000 0.00 0.00 0.00 2.90
367 381 1.967535 CTCCAGACCACGAAGCAGA 59.032 57.895 0.00 0.00 0.00 4.26
369 383 2.343758 GCTCCAGACCACGAAGCA 59.656 61.111 0.00 0.00 33.21 3.91
370 384 1.739562 CTGCTCCAGACCACGAAGC 60.740 63.158 0.00 0.00 32.44 3.86
371 385 1.079543 CCTGCTCCAGACCACGAAG 60.080 63.158 0.00 0.00 32.44 3.79
374 388 1.079543 CTTCCTGCTCCAGACCACG 60.080 63.158 0.00 0.00 32.44 4.94
378 394 0.827368 CTACCCTTCCTGCTCCAGAC 59.173 60.000 0.00 0.00 32.44 3.51
382 398 0.617820 TGACCTACCCTTCCTGCTCC 60.618 60.000 0.00 0.00 0.00 4.70
498 514 1.519408 TCTTCCTAACTTTGCACCGC 58.481 50.000 0.00 0.00 0.00 5.68
536 552 2.093658 TCTCGTGTGGAGATTAAAGGGC 60.094 50.000 0.00 0.00 46.80 5.19
537 553 3.887621 TCTCGTGTGGAGATTAAAGGG 57.112 47.619 0.00 0.00 46.80 3.95
591 608 1.813513 CAACATATCCAGGATCCGCC 58.186 55.000 4.75 0.00 0.00 6.13
592 609 1.160137 GCAACATATCCAGGATCCGC 58.840 55.000 4.75 0.00 0.00 5.54
601 618 2.560504 TGATCCACACGCAACATATCC 58.439 47.619 0.00 0.00 0.00 2.59
607 624 2.076100 TCAGATTGATCCACACGCAAC 58.924 47.619 0.00 0.00 0.00 4.17
649 666 3.669290 CGATCGAGCCTTGACTAGCTATG 60.669 52.174 10.26 0.00 40.11 2.23
785 829 1.067060 GAGTTGGTGTGTGCTTTTCCC 59.933 52.381 0.00 0.00 0.00 3.97
818 862 2.281208 TCCGCTTGGGTTCCAACG 60.281 61.111 11.69 11.69 38.75 4.10
819 863 2.613506 CGTCCGCTTGGGTTCCAAC 61.614 63.158 0.00 0.00 38.75 3.77
820 864 2.281208 CGTCCGCTTGGGTTCCAA 60.281 61.111 0.00 0.00 41.69 3.53
821 865 4.323477 CCGTCCGCTTGGGTTCCA 62.323 66.667 0.00 0.00 37.00 3.53
955 999 3.574826 TCAGATGAGATGAGATGAGCAGG 59.425 47.826 0.00 0.00 0.00 4.85
977 1021 7.201679 CCATTGCTAATCGATGAAGTCTTTCTT 60.202 37.037 0.00 0.00 38.60 2.52
1182 1253 0.104487 GGTAGTCCTTTAGCCTCGCC 59.896 60.000 0.00 0.00 0.00 5.54
1191 1262 2.031495 AGTGGCTCAGGTAGTCCTTT 57.969 50.000 0.00 0.00 43.07 3.11
1524 1610 3.912907 GTCGCCCGGTCGATGGAT 61.913 66.667 12.16 0.00 40.84 3.41
1770 1856 2.680352 GGGCTGGAGGACGTCTCA 60.680 66.667 16.46 10.57 44.19 3.27
1923 2015 2.606213 TGGATCCCCTGCACGTCA 60.606 61.111 9.90 0.00 0.00 4.35
2136 2240 3.282271 CAGAGCCTGCAGAGACGA 58.718 61.111 17.39 0.00 0.00 4.20
2151 2255 0.647410 CGAACTAGCAATCGTGGCAG 59.353 55.000 0.00 0.00 34.48 4.85
2155 2259 2.285834 GCCAATCGAACTAGCAATCGTG 60.286 50.000 11.46 5.42 39.91 4.35
2156 2260 1.933853 GCCAATCGAACTAGCAATCGT 59.066 47.619 11.46 0.08 39.91 3.73
2179 2292 9.401058 ACAGAAGAATCTACCCAAAAATATCAG 57.599 33.333 0.00 0.00 33.50 2.90
2274 2400 5.365403 AAGAGAGTAGAGAGTTTGACACG 57.635 43.478 0.00 0.00 0.00 4.49
2286 2412 5.048224 CGACCAGTAACCAAAAGAGAGTAGA 60.048 44.000 0.00 0.00 0.00 2.59
2290 2416 3.991367 ACGACCAGTAACCAAAAGAGAG 58.009 45.455 0.00 0.00 0.00 3.20
2291 2417 4.124238 CAACGACCAGTAACCAAAAGAGA 58.876 43.478 0.00 0.00 0.00 3.10
2292 2418 3.250040 CCAACGACCAGTAACCAAAAGAG 59.750 47.826 0.00 0.00 0.00 2.85
2294 2420 2.946990 ACCAACGACCAGTAACCAAAAG 59.053 45.455 0.00 0.00 0.00 2.27
2296 2422 2.713863 ACCAACGACCAGTAACCAAA 57.286 45.000 0.00 0.00 0.00 3.28
2297 2423 2.683867 CAAACCAACGACCAGTAACCAA 59.316 45.455 0.00 0.00 0.00 3.67
2298 2424 2.290464 CAAACCAACGACCAGTAACCA 58.710 47.619 0.00 0.00 0.00 3.67
2300 2426 1.002142 GGCAAACCAACGACCAGTAAC 60.002 52.381 0.00 0.00 35.26 2.50
2301 2427 1.310904 GGCAAACCAACGACCAGTAA 58.689 50.000 0.00 0.00 35.26 2.24
2302 2428 0.881159 CGGCAAACCAACGACCAGTA 60.881 55.000 0.00 0.00 34.57 2.74
2303 2429 2.184167 CGGCAAACCAACGACCAGT 61.184 57.895 0.00 0.00 34.57 4.00
2304 2430 2.637025 CGGCAAACCAACGACCAG 59.363 61.111 0.00 0.00 34.57 4.00
2305 2431 3.587933 GCGGCAAACCAACGACCA 61.588 61.111 0.00 0.00 34.57 4.02
2306 2432 4.337060 GGCGGCAAACCAACGACC 62.337 66.667 3.07 0.00 34.57 4.79
2308 2434 2.829003 TTGGCGGCAAACCAACGA 60.829 55.556 23.43 0.00 42.23 3.85
2309 2435 2.354539 CTTGGCGGCAAACCAACG 60.355 61.111 25.45 8.90 42.23 4.10
2310 2436 1.299850 GTCTTGGCGGCAAACCAAC 60.300 57.895 25.45 16.19 42.23 3.77
2312 2438 2.124109 TGTCTTGGCGGCAAACCA 60.124 55.556 25.45 20.16 34.57 3.67
2313 2439 2.335011 GTGTCTTGGCGGCAAACC 59.665 61.111 25.45 17.89 0.00 3.27
2314 2440 2.051345 CGTGTCTTGGCGGCAAAC 60.051 61.111 25.45 23.06 0.00 2.93
2320 2446 3.403057 CGTGACCGTGTCTTGGCG 61.403 66.667 5.77 0.00 33.15 5.69
2321 2447 3.712881 GCGTGACCGTGTCTTGGC 61.713 66.667 5.77 3.38 36.15 4.52
2322 2448 2.029073 AGCGTGACCGTGTCTTGG 59.971 61.111 5.77 0.00 36.15 3.61
2323 2449 0.667487 ATCAGCGTGACCGTGTCTTG 60.667 55.000 5.77 0.55 36.15 3.02
2324 2450 0.033504 AATCAGCGTGACCGTGTCTT 59.966 50.000 5.77 0.00 36.15 3.01
2326 2452 1.852895 GATAATCAGCGTGACCGTGTC 59.147 52.381 0.00 0.00 36.15 3.67
2327 2453 1.203758 TGATAATCAGCGTGACCGTGT 59.796 47.619 0.00 0.00 36.15 4.49
2328 2454 1.588404 GTGATAATCAGCGTGACCGTG 59.412 52.381 0.00 0.00 36.15 4.94
2329 2455 1.203758 TGTGATAATCAGCGTGACCGT 59.796 47.619 0.00 0.00 36.15 4.83
2330 2456 1.588404 GTGTGATAATCAGCGTGACCG 59.412 52.381 0.00 0.00 37.07 4.79
2332 2458 6.589830 AAATAGTGTGATAATCAGCGTGAC 57.410 37.500 0.00 0.00 0.00 3.67
2333 2459 7.119116 ACAAAAATAGTGTGATAATCAGCGTGA 59.881 33.333 0.00 0.00 0.00 4.35
2335 2461 7.377766 ACAAAAATAGTGTGATAATCAGCGT 57.622 32.000 0.00 0.00 0.00 5.07
2336 2462 9.210426 GTTACAAAAATAGTGTGATAATCAGCG 57.790 33.333 0.00 0.00 0.00 5.18
2337 2463 9.503427 GGTTACAAAAATAGTGTGATAATCAGC 57.497 33.333 0.00 0.00 0.00 4.26
2343 2469 9.431887 GACAGAGGTTACAAAAATAGTGTGATA 57.568 33.333 0.00 0.00 0.00 2.15
2396 2561 1.069765 CTGTTGCCGATAGCCCGAT 59.930 57.895 0.00 0.00 42.71 4.18
2407 2597 1.078848 ATCCTGAGTCGCTGTTGCC 60.079 57.895 0.00 0.00 35.36 4.52
2429 2793 4.508128 ATAGGACACACGCCCGCG 62.508 66.667 7.69 7.69 46.03 6.46
2438 2802 1.143277 TCTCTCTCCCGGATAGGACAC 59.857 57.143 0.73 0.00 45.00 3.67
2468 2832 4.290155 CAATAGAATTTTTCCCGGCGATG 58.710 43.478 9.30 0.00 0.00 3.84
2494 2858 7.175293 AGGCGACCAAACAAACTATATTAACAA 59.825 33.333 0.00 0.00 0.00 2.83
2496 2860 6.964934 CAGGCGACCAAACAAACTATATTAAC 59.035 38.462 0.00 0.00 0.00 2.01
2497 2861 6.655848 ACAGGCGACCAAACAAACTATATTAA 59.344 34.615 0.00 0.00 0.00 1.40
2498 2862 6.174760 ACAGGCGACCAAACAAACTATATTA 58.825 36.000 0.00 0.00 0.00 0.98
2499 2863 5.007682 ACAGGCGACCAAACAAACTATATT 58.992 37.500 0.00 0.00 0.00 1.28
2500 2864 4.585879 ACAGGCGACCAAACAAACTATAT 58.414 39.130 0.00 0.00 0.00 0.86
2501 2865 3.998341 GACAGGCGACCAAACAAACTATA 59.002 43.478 0.00 0.00 0.00 1.31
2520 2884 0.537143 GTGCATGGACCAAGTGGACA 60.537 55.000 13.23 3.23 38.94 4.02
2551 2915 3.423539 TGAGAAAGGAAGTCATGTGGG 57.576 47.619 0.00 0.00 0.00 4.61
2554 2918 5.634118 TGGAATTGAGAAAGGAAGTCATGT 58.366 37.500 0.00 0.00 0.00 3.21
2569 2933 5.120399 ACGTCAACTGTACTTTGGAATTGA 58.880 37.500 7.64 0.00 0.00 2.57
2645 3009 1.671850 CGGAGCGCAGACTTTTCCTAA 60.672 52.381 11.47 0.00 0.00 2.69
2676 3045 1.316706 ACCCAACCAAACCACACGTG 61.317 55.000 15.48 15.48 0.00 4.49
2677 3046 0.255318 TACCCAACCAAACCACACGT 59.745 50.000 0.00 0.00 0.00 4.49
2679 3048 2.061509 ACTACCCAACCAAACCACAC 57.938 50.000 0.00 0.00 0.00 3.82
2680 3049 2.025226 TCAACTACCCAACCAAACCACA 60.025 45.455 0.00 0.00 0.00 4.17
2739 3133 6.643388 TGCTTCACTATATTCACTGTGACAT 58.357 36.000 10.56 9.36 38.87 3.06
2740 3134 6.036577 TGCTTCACTATATTCACTGTGACA 57.963 37.500 10.56 1.70 38.87 3.58
2849 3249 9.974980 GAAGTTTTAATATTGTCCCAAGTCAAA 57.025 29.630 0.00 0.00 0.00 2.69
2850 3250 9.137459 TGAAGTTTTAATATTGTCCCAAGTCAA 57.863 29.630 0.00 0.00 0.00 3.18
2851 3251 8.698973 TGAAGTTTTAATATTGTCCCAAGTCA 57.301 30.769 0.00 0.00 0.00 3.41
2852 3252 9.626045 CTTGAAGTTTTAATATTGTCCCAAGTC 57.374 33.333 0.00 0.00 0.00 3.01
2853 3253 9.143155 ACTTGAAGTTTTAATATTGTCCCAAGT 57.857 29.630 0.00 0.00 35.81 3.16
2854 3254 9.626045 GACTTGAAGTTTTAATATTGTCCCAAG 57.374 33.333 0.00 0.00 34.18 3.61
2855 3255 9.362151 AGACTTGAAGTTTTAATATTGTCCCAA 57.638 29.630 0.00 0.00 0.00 4.12
2856 3256 8.934023 AGACTTGAAGTTTTAATATTGTCCCA 57.066 30.769 0.00 0.00 0.00 4.37
2869 3269 9.403583 TCCAAAGTAATTGTAGACTTGAAGTTT 57.596 29.630 0.00 0.00 36.05 2.66
2882 3282 5.222337 ACTCCCTCCATTCCAAAGTAATTGT 60.222 40.000 0.00 0.00 37.32 2.71
2908 3308 8.800332 GCTTAATTGATATGAATCATTCAGGGT 58.200 33.333 6.19 0.00 43.98 4.34
3026 3542 0.179103 CGAATTGGCCCATTTGGAGC 60.179 55.000 8.66 0.00 37.39 4.70
3050 3566 8.336806 CCTGTCGTGGCGTTTATAATTAATTAA 58.663 33.333 11.80 0.00 0.00 1.40
3051 3567 7.518689 GCCTGTCGTGGCGTTTATAATTAATTA 60.519 37.037 10.27 10.27 43.74 1.40
3052 3568 6.721321 CCTGTCGTGGCGTTTATAATTAATT 58.279 36.000 5.89 5.89 0.00 1.40
3053 3569 5.277634 GCCTGTCGTGGCGTTTATAATTAAT 60.278 40.000 0.00 0.00 43.74 1.40
3060 3576 3.884900 GCCTGTCGTGGCGTTTAT 58.115 55.556 1.71 0.00 43.74 1.40


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

AutoCloner maintained by Alex Coulton.