Multiple sequence alignment - TraesCS3D01G295600

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 TraesCS3D01G295600 chr3D 100.000 2887 0 0 1 2887 408317774 408320660 0.000000e+00 5332.0
1 TraesCS3D01G295600 chr3D 98.113 106 2 0 2352 2457 614251196 614251091 4.910000e-43 185.0
2 TraesCS3D01G295600 chr3D 97.196 107 3 0 2352 2458 210622527 210622421 6.350000e-42 182.0
3 TraesCS3D01G295600 chr3D 95.614 114 4 1 2349 2461 443434258 443434371 6.350000e-42 182.0
4 TraesCS3D01G295600 chr3D 86.154 65 6 2 446 508 408318142 408318205 1.860000e-07 67.6
5 TraesCS3D01G295600 chr3B 90.285 1441 55 21 905 2295 534194448 534195853 0.000000e+00 1807.0
6 TraesCS3D01G295600 chr3B 91.046 927 31 9 1 909 534193524 534194416 0.000000e+00 1205.0
7 TraesCS3D01G295600 chr3B 84.714 700 57 19 1500 2183 534247423 534248088 0.000000e+00 654.0
8 TraesCS3D01G295600 chr3B 88.432 389 17 5 2517 2877 534195927 534196315 7.340000e-121 444.0
9 TraesCS3D01G295600 chr3B 79.866 149 18 7 2455 2591 534248253 534248401 6.580000e-17 99.0
10 TraesCS3D01G295600 chr3A 94.432 862 32 7 1285 2133 543176174 543175316 0.000000e+00 1312.0
11 TraesCS3D01G295600 chr3A 89.755 898 61 16 439 1323 543177051 543176172 0.000000e+00 1120.0
12 TraesCS3D01G295600 chr3A 81.724 580 53 27 1491 2060 543022382 543021846 4.420000e-118 435.0
13 TraesCS3D01G295600 chr3A 90.449 178 12 2 1 173 543177618 543177441 2.240000e-56 230.0
14 TraesCS3D01G295600 chr3A 92.157 153 11 1 2162 2313 543175318 543175166 6.270000e-52 215.0
15 TraesCS3D01G295600 chr3A 85.202 223 12 5 2453 2654 543175166 543174944 2.920000e-50 209.0
16 TraesCS3D01G295600 chr3A 89.583 144 15 0 1007 1150 543022863 543022720 1.770000e-42 183.0
17 TraesCS3D01G295600 chr3A 92.188 128 9 1 2056 2183 543016206 543016080 2.290000e-41 180.0
18 TraesCS3D01G295600 chr3A 93.333 105 7 0 177 281 543177410 543177306 3.850000e-34 156.0
19 TraesCS3D01G295600 chr3A 81.579 152 13 4 2455 2591 543015923 543015772 8.460000e-21 111.0
20 TraesCS3D01G295600 chr3A 93.243 74 4 1 369 442 543177152 543177080 1.090000e-19 108.0
21 TraesCS3D01G295600 chr3A 91.549 71 6 0 296 366 543177315 543177245 6.580000e-17 99.0
22 TraesCS3D01G295600 chr3A 90.909 55 5 0 2403 2457 12251913 12251967 1.110000e-09 75.0
23 TraesCS3D01G295600 chr1A 78.621 290 58 4 1591 1878 291669920 291669633 3.800000e-44 189.0
24 TraesCS3D01G295600 chr6B 97.222 108 3 0 2352 2459 30348350 30348243 1.770000e-42 183.0
25 TraesCS3D01G295600 chr6B 97.222 108 3 0 2349 2456 585798964 585799071 1.770000e-42 183.0
26 TraesCS3D01G295600 chr6A 96.396 111 4 0 2349 2459 381084238 381084348 1.770000e-42 183.0
27 TraesCS3D01G295600 chr4B 98.095 105 2 0 2352 2456 450453576 450453472 1.770000e-42 183.0
28 TraesCS3D01G295600 chr2D 94.872 117 6 0 2352 2468 502931393 502931277 1.770000e-42 183.0
29 TraesCS3D01G295600 chr2D 92.857 126 6 3 2349 2472 536091046 536091170 2.290000e-41 180.0
30 TraesCS3D01G295600 chr5D 85.135 148 20 1 1768 1915 371036592 371036447 1.790000e-32 150.0
31 TraesCS3D01G295600 chr5D 86.765 136 16 2 1781 1915 371288620 371288486 1.790000e-32 150.0
32 TraesCS3D01G295600 chr5B 84.459 148 23 0 1768 1915 441053533 441053386 2.320000e-31 147.0
33 TraesCS3D01G295600 chr5A 84.459 148 21 1 1768 1915 474333729 474333584 8.340000e-31 145.0
34 TraesCS3D01G295600 chr5A 83.784 148 22 1 1768 1915 474089529 474089384 3.880000e-29 139.0


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 TraesCS3D01G295600 chr3D 408317774 408320660 2886 False 2699.800 5332 93.0770 1 2887 2 chr3D.!!$F2 2886
1 TraesCS3D01G295600 chr3B 534193524 534196315 2791 False 1152.000 1807 89.9210 1 2877 3 chr3B.!!$F1 2876
2 TraesCS3D01G295600 chr3B 534247423 534248401 978 False 376.500 654 82.2900 1500 2591 2 chr3B.!!$F2 1091
3 TraesCS3D01G295600 chr3A 543174944 543177618 2674 True 431.125 1312 91.2650 1 2654 8 chr3A.!!$R3 2653
4 TraesCS3D01G295600 chr3A 543021846 543022863 1017 True 309.000 435 85.6535 1007 2060 2 chr3A.!!$R2 1053

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
910 1134 1.227527 CAGTCACCCAACACAGCGA 60.228 57.895 0.0 0.0 0.0 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2443 2941 0.103208 CTGCATGTACTCCCTCCGTC 59.897 60.0 0.0 0.0 0.0 4.79 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
277 328 3.012518 GGACACTGCTGATGCTGTTATT 58.987 45.455 0.00 0.00 46.76 1.40
289 340 5.769662 TGATGCTGTTATTTTGGTTGAGACT 59.230 36.000 0.00 0.00 0.00 3.24
375 426 7.857734 CTTAGAGAGCAGATAGATATTCCGA 57.142 40.000 0.00 0.00 0.00 4.55
376 427 8.275015 CTTAGAGAGCAGATAGATATTCCGAA 57.725 38.462 0.00 0.00 0.00 4.30
626 799 8.195436 ACTTCTCTGAAATCGGATATTTACGAA 58.805 33.333 0.00 0.00 42.88 3.85
649 822 6.910536 ATTTACGATCCAAACTAAGCTCTG 57.089 37.500 0.00 0.00 0.00 3.35
653 826 2.080286 TCCAAACTAAGCTCTGCGAC 57.920 50.000 0.00 0.00 0.00 5.19
818 1000 8.947055 TTGATCTGATTCAGAATCACGATTTA 57.053 30.769 24.29 18.28 44.04 1.40
819 1001 9.551734 TTGATCTGATTCAGAATCACGATTTAT 57.448 29.630 24.29 13.11 44.04 1.40
820 1002 8.985805 TGATCTGATTCAGAATCACGATTTATG 58.014 33.333 24.29 14.38 44.04 1.90
821 1003 9.201127 GATCTGATTCAGAATCACGATTTATGA 57.799 33.333 24.29 17.63 44.04 2.15
822 1004 8.357796 TCTGATTCAGAATCACGATTTATGAC 57.642 34.615 20.18 0.00 42.69 3.06
823 1005 8.200120 TCTGATTCAGAATCACGATTTATGACT 58.800 33.333 20.18 4.34 42.69 3.41
824 1006 9.468532 CTGATTCAGAATCACGATTTATGACTA 57.531 33.333 20.18 0.00 42.69 2.59
825 1007 9.249457 TGATTCAGAATCACGATTTATGACTAC 57.751 33.333 20.18 0.00 42.69 2.73
874 1062 2.047560 GGTACACACTCCACGGCC 60.048 66.667 0.00 0.00 0.00 6.13
910 1134 1.227527 CAGTCACCCAACACAGCGA 60.228 57.895 0.00 0.00 0.00 4.93
915 1139 3.052082 CCCAACACAGCGAGCAGG 61.052 66.667 0.00 0.00 0.00 4.85
1408 1847 0.179215 GTTTGAAGAGCACGCCGATG 60.179 55.000 0.00 0.00 0.00 3.84
1808 2263 1.014352 AATCGTACGAAATGCAGGCC 58.986 50.000 23.56 0.00 0.00 5.19
1922 2377 8.088981 TCGTGCTAACTTAGAGATTCTTTCTTT 58.911 33.333 0.00 0.00 33.74 2.52
1932 2387 9.627123 TTAGAGATTCTTTCTTTGGTCAGAAAA 57.373 29.630 0.00 0.00 41.28 2.29
1982 2437 2.732412 ATCGATAACCTGGATGCTCG 57.268 50.000 0.00 2.55 0.00 5.03
2054 2516 8.394121 GTTTTTAACATCTCAAGCTGGATCTAG 58.606 37.037 0.86 0.86 0.00 2.43
2074 2536 6.291377 TCTAGAAGTTTCTGATTTGCAGTGT 58.709 36.000 4.67 0.00 45.14 3.55
2075 2537 7.441836 TCTAGAAGTTTCTGATTTGCAGTGTA 58.558 34.615 4.67 0.00 45.14 2.90
2156 2618 7.746475 CGAAAGTAAATCTCAATGAGTGGAAAC 59.254 37.037 10.36 4.20 0.00 2.78
2157 2619 8.463930 AAAGTAAATCTCAATGAGTGGAAACA 57.536 30.769 10.36 0.00 38.70 2.83
2185 2647 5.581479 CGAGTCTAACTGCTGAGAAGTACTA 59.419 44.000 0.00 0.00 0.00 1.82
2186 2648 6.259167 CGAGTCTAACTGCTGAGAAGTACTAT 59.741 42.308 0.00 0.00 0.00 2.12
2189 2651 9.062524 AGTCTAACTGCTGAGAAGTACTATATG 57.937 37.037 0.00 0.00 0.00 1.78
2191 2653 8.218488 TCTAACTGCTGAGAAGTACTATATGGA 58.782 37.037 0.00 0.00 0.00 3.41
2192 2654 6.892658 ACTGCTGAGAAGTACTATATGGAG 57.107 41.667 0.00 0.00 0.00 3.86
2193 2655 6.606069 ACTGCTGAGAAGTACTATATGGAGA 58.394 40.000 0.00 0.00 0.00 3.71
2198 2661 9.069082 GCTGAGAAGTACTATATGGAGAAGTAA 57.931 37.037 0.00 0.00 0.00 2.24
2228 2725 1.035139 CTATGGTTGGAGGCCATTGC 58.965 55.000 5.01 0.00 43.65 3.56
2296 2794 7.857389 CCGAAGTATGAATATTCCAAACACATG 59.143 37.037 12.90 0.00 0.00 3.21
2321 2819 9.582431 TGTTTAACTTATTTCATACTCTCTCCG 57.418 33.333 0.00 0.00 0.00 4.63
2322 2820 9.583765 GTTTAACTTATTTCATACTCTCTCCGT 57.416 33.333 0.00 0.00 0.00 4.69
2323 2821 9.798994 TTTAACTTATTTCATACTCTCTCCGTC 57.201 33.333 0.00 0.00 0.00 4.79
2324 2822 7.648039 AACTTATTTCATACTCTCTCCGTCT 57.352 36.000 0.00 0.00 0.00 4.18
2325 2823 7.648039 ACTTATTTCATACTCTCTCCGTCTT 57.352 36.000 0.00 0.00 0.00 3.01
2326 2824 8.749026 ACTTATTTCATACTCTCTCCGTCTTA 57.251 34.615 0.00 0.00 0.00 2.10
2327 2825 9.186837 ACTTATTTCATACTCTCTCCGTCTTAA 57.813 33.333 0.00 0.00 0.00 1.85
2331 2829 9.892130 ATTTCATACTCTCTCCGTCTTAAAATT 57.108 29.630 0.00 0.00 0.00 1.82
2332 2830 8.928270 TTCATACTCTCTCCGTCTTAAAATTC 57.072 34.615 0.00 0.00 0.00 2.17
2333 2831 8.294954 TCATACTCTCTCCGTCTTAAAATTCT 57.705 34.615 0.00 0.00 0.00 2.40
2334 2832 8.750298 TCATACTCTCTCCGTCTTAAAATTCTT 58.250 33.333 0.00 0.00 0.00 2.52
2335 2833 8.812329 CATACTCTCTCCGTCTTAAAATTCTTG 58.188 37.037 0.00 0.00 0.00 3.02
2336 2834 6.760291 ACTCTCTCCGTCTTAAAATTCTTGT 58.240 36.000 0.00 0.00 0.00 3.16
2337 2835 6.869388 ACTCTCTCCGTCTTAAAATTCTTGTC 59.131 38.462 0.00 0.00 0.00 3.18
2338 2836 6.994221 TCTCTCCGTCTTAAAATTCTTGTCT 58.006 36.000 0.00 0.00 0.00 3.41
2339 2837 7.442656 TCTCTCCGTCTTAAAATTCTTGTCTT 58.557 34.615 0.00 0.00 0.00 3.01
2340 2838 8.582437 TCTCTCCGTCTTAAAATTCTTGTCTTA 58.418 33.333 0.00 0.00 0.00 2.10
2341 2839 8.530269 TCTCCGTCTTAAAATTCTTGTCTTAC 57.470 34.615 0.00 0.00 0.00 2.34
2342 2840 8.145767 TCTCCGTCTTAAAATTCTTGTCTTACA 58.854 33.333 0.00 0.00 0.00 2.41
2343 2841 8.842358 TCCGTCTTAAAATTCTTGTCTTACAT 57.158 30.769 0.00 0.00 0.00 2.29
2344 2842 9.280174 TCCGTCTTAAAATTCTTGTCTTACATT 57.720 29.630 0.00 0.00 0.00 2.71
2345 2843 9.893305 CCGTCTTAAAATTCTTGTCTTACATTT 57.107 29.630 0.00 0.00 0.00 2.32
2376 2874 9.661563 ATTGTCTTACATTTGTCTAAATACGGA 57.338 29.630 0.00 0.00 34.81 4.69
2377 2875 9.661563 TTGTCTTACATTTGTCTAAATACGGAT 57.338 29.630 0.00 0.00 34.81 4.18
2378 2876 9.093970 TGTCTTACATTTGTCTAAATACGGATG 57.906 33.333 0.00 0.00 34.81 3.51
2379 2877 9.095065 GTCTTACATTTGTCTAAATACGGATGT 57.905 33.333 0.00 0.00 34.81 3.06
2384 2882 9.607988 ACATTTGTCTAAATACGGATGTATCAA 57.392 29.630 0.00 0.00 40.42 2.57
2386 2884 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
2387 2885 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
2388 2886 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
2389 2887 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
2390 2888 7.113124 GTCTAAATACGGATGTATCAAGTCACG 59.887 40.741 0.00 0.00 40.42 4.35
2391 2889 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
2392 2890 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
2393 2891 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
2394 2892 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
2395 2893 5.472148 ACGGATGTATCAAGTCACGTTTTA 58.528 37.500 0.00 0.00 0.00 1.52
2396 2894 5.575606 ACGGATGTATCAAGTCACGTTTTAG 59.424 40.000 0.00 0.00 0.00 1.85
2397 2895 5.575606 CGGATGTATCAAGTCACGTTTTAGT 59.424 40.000 0.00 0.00 0.00 2.24
2398 2896 6.748658 CGGATGTATCAAGTCACGTTTTAGTA 59.251 38.462 0.00 0.00 0.00 1.82
2399 2897 7.434307 CGGATGTATCAAGTCACGTTTTAGTAT 59.566 37.037 0.00 0.00 0.00 2.12
2400 2898 9.095065 GGATGTATCAAGTCACGTTTTAGTATT 57.905 33.333 0.00 0.00 0.00 1.89
2410 2908 9.962783 AGTCACGTTTTAGTATTAGATACATCC 57.037 33.333 0.00 0.00 38.21 3.51
2411 2909 8.899776 GTCACGTTTTAGTATTAGATACATCCG 58.100 37.037 0.00 0.00 38.21 4.18
2412 2910 8.623903 TCACGTTTTAGTATTAGATACATCCGT 58.376 33.333 0.00 0.00 38.21 4.69
2413 2911 9.882996 CACGTTTTAGTATTAGATACATCCGTA 57.117 33.333 0.00 0.00 38.21 4.02
2415 2913 9.059485 CGTTTTAGTATTAGATACATCCGTAGC 57.941 37.037 1.42 0.00 38.21 3.58
2420 2918 8.721019 AGTATTAGATACATCCGTAGCTAGAC 57.279 38.462 0.00 0.00 44.93 2.59
2421 2919 8.319881 AGTATTAGATACATCCGTAGCTAGACA 58.680 37.037 0.00 0.00 44.93 3.41
2422 2920 7.997773 ATTAGATACATCCGTAGCTAGACAA 57.002 36.000 0.00 0.00 44.93 3.18
2423 2921 7.812690 TTAGATACATCCGTAGCTAGACAAA 57.187 36.000 0.00 0.00 44.93 2.83
2424 2922 6.902771 AGATACATCCGTAGCTAGACAAAT 57.097 37.500 0.00 0.00 42.47 2.32
2425 2923 6.915349 AGATACATCCGTAGCTAGACAAATC 58.085 40.000 0.00 0.00 42.47 2.17
2426 2924 6.717540 AGATACATCCGTAGCTAGACAAATCT 59.282 38.462 0.00 0.00 42.47 2.40
2427 2925 7.883833 AGATACATCCGTAGCTAGACAAATCTA 59.116 37.037 0.00 0.00 42.47 1.98
2428 2926 6.710597 ACATCCGTAGCTAGACAAATCTAA 57.289 37.500 0.00 0.00 36.98 2.10
2429 2927 6.740110 ACATCCGTAGCTAGACAAATCTAAG 58.260 40.000 0.00 0.00 36.98 2.18
2430 2928 6.546403 ACATCCGTAGCTAGACAAATCTAAGA 59.454 38.462 0.00 0.00 36.98 2.10
2431 2929 6.374565 TCCGTAGCTAGACAAATCTAAGAC 57.625 41.667 0.00 0.00 36.98 3.01
2432 2930 5.884232 TCCGTAGCTAGACAAATCTAAGACA 59.116 40.000 0.00 0.00 36.98 3.41
2433 2931 6.376299 TCCGTAGCTAGACAAATCTAAGACAA 59.624 38.462 0.00 0.00 36.98 3.18
2434 2932 6.693545 CCGTAGCTAGACAAATCTAAGACAAG 59.306 42.308 0.00 0.00 36.98 3.16
2435 2933 7.415318 CCGTAGCTAGACAAATCTAAGACAAGA 60.415 40.741 0.00 0.00 36.98 3.02
2436 2934 7.968956 CGTAGCTAGACAAATCTAAGACAAGAA 59.031 37.037 0.00 0.00 36.98 2.52
2437 2935 9.810545 GTAGCTAGACAAATCTAAGACAAGAAT 57.189 33.333 0.00 0.00 36.98 2.40
2439 2937 9.732130 AGCTAGACAAATCTAAGACAAGAATTT 57.268 29.630 0.00 0.00 36.98 1.82
2446 2944 9.322776 CAAATCTAAGACAAGAATTTTGAGACG 57.677 33.333 7.18 0.00 31.51 4.18
2447 2945 7.602517 ATCTAAGACAAGAATTTTGAGACGG 57.397 36.000 7.18 0.00 0.00 4.79
2448 2946 6.755206 TCTAAGACAAGAATTTTGAGACGGA 58.245 36.000 7.18 0.00 0.00 4.69
2449 2947 5.931441 AAGACAAGAATTTTGAGACGGAG 57.069 39.130 7.18 0.00 0.00 4.63
2450 2948 4.319177 AGACAAGAATTTTGAGACGGAGG 58.681 43.478 7.18 0.00 0.00 4.30
2451 2949 3.412386 ACAAGAATTTTGAGACGGAGGG 58.588 45.455 7.18 0.00 0.00 4.30
2459 2957 1.763968 TGAGACGGAGGGAGTACATG 58.236 55.000 0.00 0.00 0.00 3.21
2518 3027 7.983166 AAGATAGTAAACATACCACCACCTA 57.017 36.000 0.00 0.00 0.00 3.08
2607 3136 6.176183 CCATAGATGCTCCCTACCTTTTATG 58.824 44.000 0.00 0.00 0.00 1.90
2668 3202 3.703556 CAGAGGGATCACAGTACTGTCAT 59.296 47.826 25.63 19.47 42.83 3.06
2670 3204 3.957497 GAGGGATCACAGTACTGTCATCT 59.043 47.826 31.00 17.86 40.34 2.90
2710 3249 1.831736 AGTGCCGCTGGAGTAATTAGT 59.168 47.619 0.00 0.00 0.00 2.24
2724 3263 9.362151 TGGAGTAATTAGTTGGAAGTTTTTCAT 57.638 29.630 0.00 0.00 34.90 2.57
2775 3325 0.379669 CCTCAAATGCTCGTGCCATC 59.620 55.000 7.05 0.00 38.71 3.51
2814 3364 1.883084 GCCAACGAGCTCGGTATGG 60.883 63.158 34.67 34.67 44.95 2.74
2831 3381 1.722034 TGGTGAGTTTCTCTGCCTCT 58.278 50.000 10.30 0.00 31.44 3.69
2833 3383 2.224378 TGGTGAGTTTCTCTGCCTCTTG 60.224 50.000 10.30 0.00 31.44 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
120 126 3.764885 ACACAAAACAAGAGTGCAGAC 57.235 42.857 0.00 0.00 36.76 3.51
326 377 3.314913 TGTTCGAATCAAGAGCAGCAAAA 59.685 39.130 0.00 0.00 0.00 2.44
375 426 3.320826 GGTCCATTTTTGCAGTACCAGTT 59.679 43.478 0.00 0.00 0.00 3.16
376 427 2.890945 GGTCCATTTTTGCAGTACCAGT 59.109 45.455 0.00 0.00 0.00 4.00
413 554 4.855340 TCTGAACAAACCAGTCTTTCCTT 58.145 39.130 0.00 0.00 33.57 3.36
626 799 5.294552 GCAGAGCTTAGTTTGGATCGTAAAT 59.705 40.000 0.00 0.00 0.00 1.40
649 822 6.266323 TCTAGTGACAAAATCATAGAGTCGC 58.734 40.000 0.00 0.00 40.28 5.19
720 893 6.207025 AGCTCTGATGATAAGATTGCAAATCC 59.793 38.462 1.71 0.00 0.00 3.01
728 901 6.649973 CGGATCAAAGCTCTGATGATAAGATT 59.350 38.462 7.41 0.00 36.15 2.40
818 1000 4.611943 GTCATGCTGTATCACGTAGTCAT 58.388 43.478 0.00 0.00 41.61 3.06
819 1001 3.486875 CGTCATGCTGTATCACGTAGTCA 60.487 47.826 0.00 0.00 41.61 3.41
820 1002 3.036633 CGTCATGCTGTATCACGTAGTC 58.963 50.000 0.00 0.00 41.61 2.59
822 1004 2.783832 CACGTCATGCTGTATCACGTAG 59.216 50.000 7.52 0.00 41.58 3.51
823 1005 2.792749 CACGTCATGCTGTATCACGTA 58.207 47.619 7.52 0.00 41.58 3.57
824 1006 1.629013 CACGTCATGCTGTATCACGT 58.371 50.000 1.54 1.54 44.21 4.49
895 1083 2.280797 GCTCGCTGTGTTGGGTGA 60.281 61.111 0.00 0.00 0.00 4.02
915 1139 4.814294 CCGGTAGCCTGACGGTGC 62.814 72.222 0.00 0.00 42.53 5.01
920 1144 0.735287 GAACGAACCGGTAGCCTGAC 60.735 60.000 8.00 0.00 0.00 3.51
923 1147 0.611714 AATGAACGAACCGGTAGCCT 59.388 50.000 8.00 0.00 0.00 4.58
1239 1606 4.641645 CACGGCCAGGGCTTGTCA 62.642 66.667 12.03 0.00 41.60 3.58
1626 2070 2.125350 GCGAGCCTCCTCTTGGTG 60.125 66.667 0.00 0.00 35.90 4.17
1695 2139 2.926242 GGAACAGGGGTGGTCCGA 60.926 66.667 0.00 0.00 35.77 4.55
1808 2263 1.296867 GCCATCGTTGTCGCAATCG 60.297 57.895 0.00 3.07 36.96 3.34
1831 2286 1.738350 CCAAGTGCTCAGCTTGATCAG 59.262 52.381 0.00 0.00 44.29 2.90
1922 2377 6.549364 ACATGTATTTCCAAGTTTTCTGACCA 59.451 34.615 0.00 0.00 0.00 4.02
1932 2387 6.916360 ACCAAATCACATGTATTTCCAAGT 57.084 33.333 0.00 0.00 0.00 3.16
1982 2437 3.870723 TTACACGCAGATGTTGACAAC 57.129 42.857 11.54 11.54 33.85 3.32
2054 2516 6.521133 CGATTACACTGCAAATCAGAAACTTC 59.479 38.462 9.02 0.00 45.72 3.01
2074 2536 8.664798 CAGGAATCAACAACTGAAATACGATTA 58.335 33.333 0.00 0.00 37.67 1.75
2075 2537 7.362056 CCAGGAATCAACAACTGAAATACGATT 60.362 37.037 0.00 0.00 37.67 3.34
2144 2606 2.368875 ACTCGAGGTGTTTCCACTCATT 59.631 45.455 18.41 0.00 41.53 2.57
2149 2611 3.005578 AGTTAGACTCGAGGTGTTTCCAC 59.994 47.826 18.41 4.83 41.06 4.02
2151 2613 3.576648 CAGTTAGACTCGAGGTGTTTCC 58.423 50.000 18.41 0.00 0.00 3.13
2156 2618 1.813178 TCAGCAGTTAGACTCGAGGTG 59.187 52.381 18.41 3.58 0.00 4.00
2157 2619 2.088423 CTCAGCAGTTAGACTCGAGGT 58.912 52.381 18.41 6.06 0.00 3.85
2159 2621 3.438781 ACTTCTCAGCAGTTAGACTCGAG 59.561 47.826 11.84 11.84 0.00 4.04
2189 2651 7.829706 ACCATAGGTTCAGAAAATTACTTCTCC 59.170 37.037 0.00 0.00 29.44 3.71
2191 2653 9.014297 CAACCATAGGTTCAGAAAATTACTTCT 57.986 33.333 0.00 0.00 43.05 2.85
2192 2654 8.244113 CCAACCATAGGTTCAGAAAATTACTTC 58.756 37.037 0.00 0.00 43.05 3.01
2193 2655 7.947890 TCCAACCATAGGTTCAGAAAATTACTT 59.052 33.333 0.00 0.00 43.05 2.24
2198 2661 5.264395 CCTCCAACCATAGGTTCAGAAAAT 58.736 41.667 0.00 0.00 43.05 1.82
2228 2725 7.039784 TGTGAATTTGTTTTCAGGATAAGGAGG 60.040 37.037 0.00 0.00 36.34 4.30
2296 2794 9.583765 ACGGAGAGAGTATGAAATAAGTTAAAC 57.416 33.333 0.00 0.00 0.00 2.01
2298 2796 9.186837 AGACGGAGAGAGTATGAAATAAGTTAA 57.813 33.333 0.00 0.00 0.00 2.01
2301 2799 7.648039 AAGACGGAGAGAGTATGAAATAAGT 57.352 36.000 0.00 0.00 0.00 2.24
2312 2810 6.760291 ACAAGAATTTTAAGACGGAGAGAGT 58.240 36.000 0.00 0.00 0.00 3.24
2313 2811 7.093992 AGACAAGAATTTTAAGACGGAGAGAG 58.906 38.462 0.00 0.00 0.00 3.20
2314 2812 6.994221 AGACAAGAATTTTAAGACGGAGAGA 58.006 36.000 0.00 0.00 0.00 3.10
2315 2813 7.659652 AAGACAAGAATTTTAAGACGGAGAG 57.340 36.000 0.00 0.00 0.00 3.20
2316 2814 8.145767 TGTAAGACAAGAATTTTAAGACGGAGA 58.854 33.333 0.00 0.00 0.00 3.71
2317 2815 8.306680 TGTAAGACAAGAATTTTAAGACGGAG 57.693 34.615 0.00 0.00 0.00 4.63
2318 2816 8.842358 ATGTAAGACAAGAATTTTAAGACGGA 57.158 30.769 0.00 0.00 0.00 4.69
2319 2817 9.893305 AAATGTAAGACAAGAATTTTAAGACGG 57.107 29.630 0.00 0.00 0.00 4.79
2350 2848 9.661563 TCCGTATTTAGACAAATGTAAGACAAT 57.338 29.630 0.00 0.00 35.88 2.71
2351 2849 9.661563 ATCCGTATTTAGACAAATGTAAGACAA 57.338 29.630 0.00 0.00 35.88 3.18
2352 2850 9.093970 CATCCGTATTTAGACAAATGTAAGACA 57.906 33.333 0.00 0.00 35.88 3.41
2353 2851 9.095065 ACATCCGTATTTAGACAAATGTAAGAC 57.905 33.333 0.00 0.00 35.88 3.01
2358 2856 9.607988 TTGATACATCCGTATTTAGACAAATGT 57.392 29.630 0.00 0.00 38.48 2.71
2360 2858 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
2361 2859 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
2362 2860 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
2363 2861 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
2364 2862 7.113124 CGTGACTTGATACATCCGTATTTAGAC 59.887 40.741 0.00 0.00 38.48 2.59
2365 2863 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
2366 2864 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
2367 2865 6.798482 ACGTGACTTGATACATCCGTATTTA 58.202 36.000 0.00 0.00 38.48 1.40
2368 2866 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
2369 2867 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
2370 2868 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
2371 2869 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
2372 2870 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
2373 2871 4.921470 AAAACGTGACTTGATACATCCG 57.079 40.909 0.00 0.00 0.00 4.18
2374 2872 6.963049 ACTAAAACGTGACTTGATACATCC 57.037 37.500 0.00 0.00 0.00 3.51
2384 2882 9.962783 GGATGTATCTAATACTAAAACGTGACT 57.037 33.333 0.00 0.00 36.70 3.41
2385 2883 8.899776 CGGATGTATCTAATACTAAAACGTGAC 58.100 37.037 0.00 0.00 36.70 3.67
2386 2884 8.623903 ACGGATGTATCTAATACTAAAACGTGA 58.376 33.333 0.00 0.00 36.70 4.35
2387 2885 8.792831 ACGGATGTATCTAATACTAAAACGTG 57.207 34.615 0.00 0.00 36.70 4.49
2389 2887 9.059485 GCTACGGATGTATCTAATACTAAAACG 57.941 37.037 0.00 0.00 36.70 3.60
2394 2892 9.814899 GTCTAGCTACGGATGTATCTAATACTA 57.185 37.037 0.00 0.00 36.70 1.82
2395 2893 8.319881 TGTCTAGCTACGGATGTATCTAATACT 58.680 37.037 0.00 0.00 36.70 2.12
2396 2894 8.489990 TGTCTAGCTACGGATGTATCTAATAC 57.510 38.462 0.00 0.00 31.01 1.89
2397 2895 9.511272 TTTGTCTAGCTACGGATGTATCTAATA 57.489 33.333 0.00 0.00 31.01 0.98
2398 2896 7.997773 TTGTCTAGCTACGGATGTATCTAAT 57.002 36.000 0.00 0.00 31.01 1.73
2399 2897 7.812690 TTTGTCTAGCTACGGATGTATCTAA 57.187 36.000 0.00 0.00 31.01 2.10
2400 2898 7.883833 AGATTTGTCTAGCTACGGATGTATCTA 59.116 37.037 0.00 0.00 30.17 1.98
2401 2899 6.717540 AGATTTGTCTAGCTACGGATGTATCT 59.282 38.462 0.00 0.00 32.17 1.98
2402 2900 6.915349 AGATTTGTCTAGCTACGGATGTATC 58.085 40.000 0.00 0.00 0.00 2.24
2403 2901 6.902771 AGATTTGTCTAGCTACGGATGTAT 57.097 37.500 0.00 0.00 0.00 2.29
2404 2902 7.718314 TCTTAGATTTGTCTAGCTACGGATGTA 59.282 37.037 0.00 0.00 0.00 2.29
2405 2903 6.546403 TCTTAGATTTGTCTAGCTACGGATGT 59.454 38.462 0.00 0.00 0.00 3.06
2406 2904 6.858993 GTCTTAGATTTGTCTAGCTACGGATG 59.141 42.308 0.00 0.00 0.00 3.51
2407 2905 6.546403 TGTCTTAGATTTGTCTAGCTACGGAT 59.454 38.462 0.00 0.00 0.00 4.18
2408 2906 5.884232 TGTCTTAGATTTGTCTAGCTACGGA 59.116 40.000 0.00 0.00 0.00 4.69
2409 2907 6.132791 TGTCTTAGATTTGTCTAGCTACGG 57.867 41.667 0.00 0.00 0.00 4.02
2410 2908 7.473366 TCTTGTCTTAGATTTGTCTAGCTACG 58.527 38.462 0.00 0.00 0.00 3.51
2411 2909 9.810545 ATTCTTGTCTTAGATTTGTCTAGCTAC 57.189 33.333 0.00 0.00 0.00 3.58
2413 2911 9.732130 AAATTCTTGTCTTAGATTTGTCTAGCT 57.268 29.630 0.00 0.00 0.00 3.32
2420 2918 9.322776 CGTCTCAAAATTCTTGTCTTAGATTTG 57.677 33.333 0.00 0.00 30.65 2.32
2421 2919 8.507249 CCGTCTCAAAATTCTTGTCTTAGATTT 58.493 33.333 0.00 0.00 0.00 2.17
2422 2920 7.878127 TCCGTCTCAAAATTCTTGTCTTAGATT 59.122 33.333 0.00 0.00 0.00 2.40
2423 2921 7.386851 TCCGTCTCAAAATTCTTGTCTTAGAT 58.613 34.615 0.00 0.00 0.00 1.98
2424 2922 6.755206 TCCGTCTCAAAATTCTTGTCTTAGA 58.245 36.000 0.00 0.00 0.00 2.10
2425 2923 6.091441 CCTCCGTCTCAAAATTCTTGTCTTAG 59.909 42.308 0.00 0.00 0.00 2.18
2426 2924 5.932303 CCTCCGTCTCAAAATTCTTGTCTTA 59.068 40.000 0.00 0.00 0.00 2.10
2427 2925 4.757149 CCTCCGTCTCAAAATTCTTGTCTT 59.243 41.667 0.00 0.00 0.00 3.01
2428 2926 4.319177 CCTCCGTCTCAAAATTCTTGTCT 58.681 43.478 0.00 0.00 0.00 3.41
2429 2927 3.437049 CCCTCCGTCTCAAAATTCTTGTC 59.563 47.826 0.00 0.00 0.00 3.18
2430 2928 3.072476 TCCCTCCGTCTCAAAATTCTTGT 59.928 43.478 0.00 0.00 0.00 3.16
2431 2929 3.674997 TCCCTCCGTCTCAAAATTCTTG 58.325 45.455 0.00 0.00 0.00 3.02
2432 2930 3.328050 ACTCCCTCCGTCTCAAAATTCTT 59.672 43.478 0.00 0.00 0.00 2.52
2433 2931 2.907042 ACTCCCTCCGTCTCAAAATTCT 59.093 45.455 0.00 0.00 0.00 2.40
2434 2932 3.336138 ACTCCCTCCGTCTCAAAATTC 57.664 47.619 0.00 0.00 0.00 2.17
2435 2933 3.581332 TGTACTCCCTCCGTCTCAAAATT 59.419 43.478 0.00 0.00 0.00 1.82
2436 2934 3.170717 TGTACTCCCTCCGTCTCAAAAT 58.829 45.455 0.00 0.00 0.00 1.82
2437 2935 2.600790 TGTACTCCCTCCGTCTCAAAA 58.399 47.619 0.00 0.00 0.00 2.44
2438 2936 2.297698 TGTACTCCCTCCGTCTCAAA 57.702 50.000 0.00 0.00 0.00 2.69
2439 2937 2.100197 CATGTACTCCCTCCGTCTCAA 58.900 52.381 0.00 0.00 0.00 3.02
2440 2938 1.763968 CATGTACTCCCTCCGTCTCA 58.236 55.000 0.00 0.00 0.00 3.27
2441 2939 0.386113 GCATGTACTCCCTCCGTCTC 59.614 60.000 0.00 0.00 0.00 3.36
2442 2940 0.324368 TGCATGTACTCCCTCCGTCT 60.324 55.000 0.00 0.00 0.00 4.18
2443 2941 0.103208 CTGCATGTACTCCCTCCGTC 59.897 60.000 0.00 0.00 0.00 4.79
2444 2942 0.324368 TCTGCATGTACTCCCTCCGT 60.324 55.000 0.00 0.00 0.00 4.69
2445 2943 0.387202 CTCTGCATGTACTCCCTCCG 59.613 60.000 0.00 0.00 0.00 4.63
2446 2944 0.105778 GCTCTGCATGTACTCCCTCC 59.894 60.000 0.00 0.00 0.00 4.30
2447 2945 0.826715 TGCTCTGCATGTACTCCCTC 59.173 55.000 0.00 0.00 31.71 4.30
2448 2946 1.279496 TTGCTCTGCATGTACTCCCT 58.721 50.000 0.00 0.00 38.76 4.20
2449 2947 2.158842 AGATTGCTCTGCATGTACTCCC 60.159 50.000 0.00 0.00 38.76 4.30
2450 2948 3.191078 AGATTGCTCTGCATGTACTCC 57.809 47.619 0.00 0.00 38.76 3.85
2451 2949 4.686972 TGTAGATTGCTCTGCATGTACTC 58.313 43.478 0.00 0.00 38.94 2.59
2459 2957 4.573607 TCACATCATTGTAGATTGCTCTGC 59.426 41.667 0.00 0.00 33.76 4.26
2591 3115 3.492829 CCGTCTCATAAAAGGTAGGGAGC 60.493 52.174 0.00 0.00 0.00 4.70
2668 3202 2.504175 GGTAGCTATGGGGTGTTCAAGA 59.496 50.000 0.00 0.00 0.00 3.02
2670 3204 2.238646 CTGGTAGCTATGGGGTGTTCAA 59.761 50.000 0.00 0.00 0.00 2.69
2710 3249 4.810491 GCTGCTTCAATGAAAAACTTCCAA 59.190 37.500 0.00 0.00 0.00 3.53
2724 3263 5.240183 GCTTGAATATCTATGGCTGCTTCAA 59.760 40.000 0.00 4.59 32.18 2.69
2775 3325 4.686554 GGCTCTAGATAATAAGTTGGCACG 59.313 45.833 0.00 0.00 0.00 5.34
2810 3360 3.445008 AGAGGCAGAGAAACTCACCATA 58.555 45.455 11.41 0.00 33.30 2.74
2814 3364 2.805099 CACAAGAGGCAGAGAAACTCAC 59.195 50.000 0.00 0.00 33.76 3.51
2831 3381 5.499313 TCATGTTGGCTCAATAGATCACAA 58.501 37.500 0.00 0.00 0.00 3.33
2833 3383 5.761726 TGATCATGTTGGCTCAATAGATCAC 59.238 40.000 16.41 0.00 35.29 3.06


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

AutoCloner maintained by Alex Coulton.