Multiple sequence alignment - TraesCS7B01G293600

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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 TraesCS7B01G293600 chr7B 100.000 3283 0 0 1 3283 530382419 530385701 0.000000e+00 6063
1 TraesCS7B01G293600 chr7B 88.406 138 16 0 2331 2468 530384886 530384749 2.030000e-37 167
2 TraesCS7B01G293600 chr7A 91.540 2364 127 41 3 2332 567586323 567588647 0.000000e+00 3190
3 TraesCS7B01G293600 chr7A 92.935 821 42 13 2467 3283 567588646 567589454 0.000000e+00 1181
4 TraesCS7B01G293600 chr7D 96.151 1299 37 3 1035 2332 501099771 501101057 0.000000e+00 2109
5 TraesCS7B01G293600 chr7D 90.476 1218 53 31 3 1189 501098281 501099466 0.000000e+00 1548
6 TraesCS7B01G293600 chr7D 93.187 822 33 7 2467 3283 501101056 501101859 0.000000e+00 1186
7 TraesCS7B01G293600 chr6A 90.647 139 11 2 2331 2468 159936484 159936347 2.010000e-42 183
8 TraesCS7B01G293600 chr6A 85.211 142 19 2 2328 2468 159936344 159936484 9.490000e-31 145
9 TraesCS7B01G293600 chr6D 97.436 78 2 0 2324 2401 16703146 16703069 2.060000e-27 134
10 TraesCS7B01G293600 chr2D 93.407 91 2 4 2313 2402 278358795 278358708 7.390000e-27 132
11 TraesCS7B01G293600 chr2D 96.203 79 2 1 2323 2401 296173669 296173746 9.560000e-26 128
12 TraesCS7B01G293600 chr2D 95.775 71 3 0 2402 2472 201441635 201441565 7.440000e-22 115
13 TraesCS7B01G293600 chr3A 96.250 80 1 2 2322 2401 583696416 583696339 2.660000e-26 130
14 TraesCS7B01G293600 chr3D 95.181 83 1 3 2322 2401 336539168 336539250 9.560000e-26 128
15 TraesCS7B01G293600 chr3D 89.535 86 8 1 2399 2484 435299705 435299789 1.250000e-19 108
16 TraesCS7B01G293600 chrUn 94.595 74 4 0 2402 2475 110002971 110002898 7.440000e-22 115
17 TraesCS7B01G293600 chr1D 94.595 74 4 0 2399 2472 298577041 298577114 7.440000e-22 115
18 TraesCS7B01G293600 chr1D 80.556 144 22 5 2328 2471 112467923 112467786 4.480000e-19 106
19 TraesCS7B01G293600 chr1B 93.506 77 3 1 2402 2478 16924799 16924725 2.680000e-21 113


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 TraesCS7B01G293600 chr7B 530382419 530385701 3282 False 6063.000000 6063 100.000000 1 3283 1 chr7B.!!$F1 3282
1 TraesCS7B01G293600 chr7A 567586323 567589454 3131 False 2185.500000 3190 92.237500 3 3283 2 chr7A.!!$F1 3280
2 TraesCS7B01G293600 chr7D 501098281 501101859 3578 False 1614.333333 2109 93.271333 3 3283 3 chr7D.!!$F1 3280

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
353 375 0.179065 AGCCCGGCCTCGTTTTATAC 60.179 55.0 5.55 0.0 33.95 1.47 F
354 376 0.462403 GCCCGGCCTCGTTTTATACA 60.462 55.0 0.00 0.0 33.95 2.29 F
1699 2237 0.108615 CGCTGGATGAGGACGAGTTT 60.109 55.0 0.00 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 2177 0.030235 CGACGCTCCGGAATATGTCA 59.970 55.0 19.05 0.0 0.00 3.58 R
1942 2480 0.529337 CATCAGTGGGCAGCTCGTAG 60.529 60.0 0.00 0.0 0.00 3.51 R
3141 3691 0.109086 GCAGCAGAGAAGCTCACGTA 60.109 55.0 0.00 0.0 44.54 3.57 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
54 55 3.316308 AGCAACTGTCCTAAAAGCAACAG 59.684 43.478 0.00 0.00 43.69 3.16
206 208 0.958876 GGGCGTTACCTTTCCACCAG 60.959 60.000 0.00 0.00 39.10 4.00
207 209 1.583495 GGCGTTACCTTTCCACCAGC 61.583 60.000 0.00 0.00 34.51 4.85
208 210 0.887387 GCGTTACCTTTCCACCAGCA 60.887 55.000 0.00 0.00 0.00 4.41
296 301 0.322975 CTTGTGGACTGTGGAGGGAG 59.677 60.000 0.00 0.00 0.00 4.30
301 306 1.388531 GACTGTGGAGGGAGGGAGA 59.611 63.158 0.00 0.00 0.00 3.71
353 375 0.179065 AGCCCGGCCTCGTTTTATAC 60.179 55.000 5.55 0.00 33.95 1.47
354 376 0.462403 GCCCGGCCTCGTTTTATACA 60.462 55.000 0.00 0.00 33.95 2.29
405 428 0.659417 GCCAATCAATCAGCGCATCG 60.659 55.000 11.47 0.00 0.00 3.84
437 460 2.125512 CTGTCACCCGCTACAGCC 60.126 66.667 0.00 0.00 36.96 4.85
448 476 4.753662 TACAGCCCCCTCGCTCGT 62.754 66.667 0.00 0.00 36.82 4.18
537 565 1.022735 GTCTCGTGCTCCTCGGAATA 58.977 55.000 0.00 0.00 0.00 1.75
572 611 1.847798 CGAGGTGGTGGATTTGGGGA 61.848 60.000 0.00 0.00 0.00 4.81
611 650 3.947841 GCTCGTGTTTGGCGTGCA 61.948 61.111 6.83 0.00 44.75 4.57
745 793 0.533755 GTGACAGTGCCAGCTGAACT 60.534 55.000 17.39 15.49 39.62 3.01
801 853 3.128349 TGCTAAAAGACGACCAACAGTC 58.872 45.455 0.00 0.00 42.54 3.51
841 893 4.205792 ACGTAAAAGCGTATTATGACGAGC 59.794 41.667 0.00 0.00 45.82 5.03
1621 2159 2.106844 GCCCTTTGATTTCGGCGAT 58.893 52.632 11.76 0.00 0.00 4.58
1699 2237 0.108615 CGCTGGATGAGGACGAGTTT 60.109 55.000 0.00 0.00 0.00 2.66
1711 2249 1.597854 CGAGTTTGAGGTGCTGCCA 60.598 57.895 0.00 0.00 40.61 4.92
1912 2450 2.284773 TGCATTGGGCCATGGCTT 60.285 55.556 34.70 15.48 43.89 4.35
2011 2549 2.954753 GCGTTCTGCTGGTGGTTCG 61.955 63.158 0.00 0.00 41.73 3.95
2284 2823 7.653311 GCTTCAATAACACAGAAAACCAATTCT 59.347 33.333 0.00 0.00 40.23 2.40
2317 2856 8.304138 CGATGCTTGTTTTATTCGTATTGTTTC 58.696 33.333 0.00 0.00 0.00 2.78
2336 2875 7.214467 TGTTTCTGACAAATCAATTACTCCC 57.786 36.000 0.00 0.00 34.69 4.30
2337 2876 7.004086 TGTTTCTGACAAATCAATTACTCCCT 58.996 34.615 0.00 0.00 34.69 4.20
2338 2877 7.174946 TGTTTCTGACAAATCAATTACTCCCTC 59.825 37.037 0.00 0.00 34.69 4.30
2339 2878 5.745227 TCTGACAAATCAATTACTCCCTCC 58.255 41.667 0.00 0.00 33.30 4.30
2340 2879 4.513442 TGACAAATCAATTACTCCCTCCG 58.487 43.478 0.00 0.00 0.00 4.63
2341 2880 4.019681 TGACAAATCAATTACTCCCTCCGT 60.020 41.667 0.00 0.00 0.00 4.69
2342 2881 4.514401 ACAAATCAATTACTCCCTCCGTC 58.486 43.478 0.00 0.00 0.00 4.79
2343 2882 3.840124 AATCAATTACTCCCTCCGTCC 57.160 47.619 0.00 0.00 0.00 4.79
2344 2883 1.492764 TCAATTACTCCCTCCGTCCC 58.507 55.000 0.00 0.00 0.00 4.46
2345 2884 1.200519 CAATTACTCCCTCCGTCCCA 58.799 55.000 0.00 0.00 0.00 4.37
2346 2885 1.768870 CAATTACTCCCTCCGTCCCAT 59.231 52.381 0.00 0.00 0.00 4.00
2347 2886 2.969950 CAATTACTCCCTCCGTCCCATA 59.030 50.000 0.00 0.00 0.00 2.74
2348 2887 2.852714 TTACTCCCTCCGTCCCATAA 57.147 50.000 0.00 0.00 0.00 1.90
2349 2888 3.339713 TTACTCCCTCCGTCCCATAAT 57.660 47.619 0.00 0.00 0.00 1.28
2350 2889 4.474303 TTACTCCCTCCGTCCCATAATA 57.526 45.455 0.00 0.00 0.00 0.98
2351 2890 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2352 2891 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2353 2892 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2354 2893 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2355 2894 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2356 2895 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2357 2896 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
2358 2897 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
2359 2898 4.813027 TCCGTCCCATAATATAAGAACGC 58.187 43.478 0.00 0.00 0.00 4.84
2360 2899 4.525487 TCCGTCCCATAATATAAGAACGCT 59.475 41.667 0.00 0.00 0.00 5.07
2361 2900 5.011329 TCCGTCCCATAATATAAGAACGCTT 59.989 40.000 0.00 0.00 38.15 4.68
2362 2901 5.699458 CCGTCCCATAATATAAGAACGCTTT 59.301 40.000 0.00 0.00 35.56 3.51
2363 2902 6.204108 CCGTCCCATAATATAAGAACGCTTTT 59.796 38.462 0.00 0.00 35.56 2.27
2364 2903 7.069569 CGTCCCATAATATAAGAACGCTTTTG 58.930 38.462 0.00 0.00 35.56 2.44
2365 2904 7.042321 CGTCCCATAATATAAGAACGCTTTTGA 60.042 37.037 0.00 0.00 35.56 2.69
2366 2905 8.068380 GTCCCATAATATAAGAACGCTTTTGAC 58.932 37.037 0.00 0.00 35.56 3.18
2367 2906 7.771361 TCCCATAATATAAGAACGCTTTTGACA 59.229 33.333 0.00 0.00 35.56 3.58
2368 2907 7.855904 CCCATAATATAAGAACGCTTTTGACAC 59.144 37.037 0.00 0.00 35.56 3.67
2369 2908 8.612619 CCATAATATAAGAACGCTTTTGACACT 58.387 33.333 0.00 0.00 35.56 3.55
2372 2911 8.542497 AATATAAGAACGCTTTTGACACTACA 57.458 30.769 0.00 0.00 35.56 2.74
2373 2912 4.531659 AAGAACGCTTTTGACACTACAC 57.468 40.909 0.00 0.00 0.00 2.90
2374 2913 3.793559 AGAACGCTTTTGACACTACACT 58.206 40.909 0.00 0.00 0.00 3.55
2375 2914 4.940463 AGAACGCTTTTGACACTACACTA 58.060 39.130 0.00 0.00 0.00 2.74
2376 2915 4.982916 AGAACGCTTTTGACACTACACTAG 59.017 41.667 0.00 0.00 0.00 2.57
2377 2916 4.317671 ACGCTTTTGACACTACACTAGT 57.682 40.909 0.00 0.00 40.28 2.57
2390 2929 6.579491 ACTACACTAGTGTCAAAAACGTTC 57.421 37.500 31.11 0.00 43.74 3.95
2391 2930 6.335777 ACTACACTAGTGTCAAAAACGTTCT 58.664 36.000 31.11 5.44 43.74 3.01
2392 2931 6.815142 ACTACACTAGTGTCAAAAACGTTCTT 59.185 34.615 31.11 4.99 43.74 2.52
2393 2932 7.975616 ACTACACTAGTGTCAAAAACGTTCTTA 59.024 33.333 31.11 8.36 43.74 2.10
2394 2933 7.781548 ACACTAGTGTCAAAAACGTTCTTAT 57.218 32.000 22.95 0.00 40.24 1.73
2395 2934 8.876275 ACACTAGTGTCAAAAACGTTCTTATA 57.124 30.769 22.95 0.00 40.24 0.98
2396 2935 9.485206 ACACTAGTGTCAAAAACGTTCTTATAT 57.515 29.630 22.95 0.00 40.24 0.86
2459 2998 7.486802 AAAACGTTCTTATATTATGGGACGG 57.513 36.000 0.00 1.76 0.00 4.79
2460 2999 6.409524 AACGTTCTTATATTATGGGACGGA 57.590 37.500 0.00 0.00 0.00 4.69
2461 3000 6.022163 ACGTTCTTATATTATGGGACGGAG 57.978 41.667 13.18 0.00 0.00 4.63
2462 3001 5.047519 ACGTTCTTATATTATGGGACGGAGG 60.048 44.000 13.18 0.00 0.00 4.30
2463 3002 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
2464 3003 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2465 3004 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2514 3053 7.072177 TCCTTTTCTTATTGCATCAGTTACG 57.928 36.000 0.00 0.00 0.00 3.18
2521 3060 0.463654 TGCATCAGTTACGGGCATCC 60.464 55.000 0.00 0.00 0.00 3.51
2533 3072 2.301296 ACGGGCATCCTGATATCAGAAG 59.699 50.000 30.40 20.16 46.59 2.85
2612 3151 2.171448 ACCTCAGTGTTGCTCTTCTGTT 59.829 45.455 0.00 0.00 0.00 3.16
2801 3340 6.215845 ACTATTTGGTTTGAAGTGTTGATGC 58.784 36.000 0.00 0.00 0.00 3.91
2806 3345 4.081752 TGGTTTGAAGTGTTGATGCAACTT 60.082 37.500 11.11 0.36 43.85 2.66
2937 3476 2.884012 TGTATTGGTTGTGGCAGAACTG 59.116 45.455 24.34 0.00 0.00 3.16
2955 3494 8.877808 CAGAACTGCTTCAGTAATATATGTCA 57.122 34.615 0.00 0.00 44.62 3.58
2965 3504 8.091385 TCAGTAATATATGTCATGCTTTGCTG 57.909 34.615 11.70 11.70 0.00 4.41
3131 3681 8.540388 TGGGAGTATATATCATTTCTGTAAGGC 58.460 37.037 0.00 0.00 0.00 4.35
3132 3682 7.707035 GGGAGTATATATCATTTCTGTAAGGCG 59.293 40.741 0.00 0.00 0.00 5.52
3133 3683 8.467598 GGAGTATATATCATTTCTGTAAGGCGA 58.532 37.037 0.00 0.00 0.00 5.54
3134 3684 9.509855 GAGTATATATCATTTCTGTAAGGCGAG 57.490 37.037 0.00 0.00 0.00 5.03
3135 3685 8.470805 AGTATATATCATTTCTGTAAGGCGAGG 58.529 37.037 0.00 0.00 0.00 4.63
3136 3686 2.024176 TCATTTCTGTAAGGCGAGGC 57.976 50.000 0.00 0.00 0.00 4.70
3137 3687 1.555075 TCATTTCTGTAAGGCGAGGCT 59.445 47.619 0.00 0.00 0.00 4.58
3138 3688 2.764010 TCATTTCTGTAAGGCGAGGCTA 59.236 45.455 0.00 0.00 0.00 3.93
3139 3689 2.667473 TTTCTGTAAGGCGAGGCTAC 57.333 50.000 0.00 0.22 0.00 3.58
3140 3690 1.848652 TTCTGTAAGGCGAGGCTACT 58.151 50.000 0.00 0.00 0.00 2.57
3141 3691 1.848652 TCTGTAAGGCGAGGCTACTT 58.151 50.000 0.00 0.00 0.00 2.24
3142 3692 3.008835 TCTGTAAGGCGAGGCTACTTA 57.991 47.619 0.00 0.00 0.00 2.24
3143 3693 2.686915 TCTGTAAGGCGAGGCTACTTAC 59.313 50.000 20.52 20.52 44.12 2.34
3144 3694 1.402968 TGTAAGGCGAGGCTACTTACG 59.597 52.381 21.24 9.18 45.82 3.18
3188 3738 8.426569 TGTAAGTACTGTGGTCCTTTAACTAT 57.573 34.615 0.00 0.00 0.00 2.12
3204 3754 9.661563 CCTTTAACTATCACACAATACCAACTA 57.338 33.333 0.00 0.00 0.00 2.24
3242 3792 3.706086 ACCAAACAAGCCATCAAAGTTCT 59.294 39.130 0.00 0.00 0.00 3.01
3248 3798 4.278419 ACAAGCCATCAAAGTTCTGTTACC 59.722 41.667 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.077359 GCTAGTTTGTCATGGACTGCTT 58.923 45.455 0.00 0.00 33.15 3.91
1 2 2.038952 TGCTAGTTTGTCATGGACTGCT 59.961 45.455 0.00 0.00 33.15 4.24
12 13 3.941483 GCTGGATGTATGTGCTAGTTTGT 59.059 43.478 0.00 0.00 0.00 2.83
14 15 4.220693 TGCTGGATGTATGTGCTAGTTT 57.779 40.909 0.00 0.00 0.00 2.66
54 55 0.681175 AGTTGCAGTGGAAAATGGGC 59.319 50.000 0.00 0.00 0.00 5.36
203 205 1.515020 CCGGAGAGACTTCTGCTGG 59.485 63.158 0.00 0.00 39.43 4.85
206 208 0.387565 GATCCCGGAGAGACTTCTGC 59.612 60.000 0.73 0.00 38.32 4.26
207 209 1.036707 GGATCCCGGAGAGACTTCTG 58.963 60.000 0.73 0.00 32.53 3.02
208 210 0.466555 CGGATCCCGGAGAGACTTCT 60.467 60.000 0.73 0.00 44.15 2.85
235 237 1.373497 CTGGTCGCGTCTGCTCTTT 60.373 57.895 5.77 0.00 39.65 2.52
339 361 1.859080 CTCGCTGTATAAAACGAGGCC 59.141 52.381 7.69 0.00 46.20 5.19
405 428 0.670854 GACAGCGAGAGGTTTGGACC 60.671 60.000 0.00 0.00 46.92 4.46
572 611 4.699522 GGCACGGGCGAAACTCCT 62.700 66.667 2.17 0.00 42.47 3.69
826 878 0.995234 TCGCGCTCGTCATAATACGC 60.995 55.000 5.56 0.00 42.56 4.42
918 979 3.615709 GTTGGTGGGCAACTGGGC 61.616 66.667 0.00 0.00 42.44 5.36
919 980 2.917227 GGTTGGTGGGCAACTGGG 60.917 66.667 0.00 0.00 33.41 4.45
920 981 2.123511 TGGTTGGTGGGCAACTGG 60.124 61.111 0.00 0.00 33.41 4.00
921 982 1.152777 TCTGGTTGGTGGGCAACTG 60.153 57.895 0.00 0.00 33.41 3.16
922 983 1.151450 CTCTGGTTGGTGGGCAACT 59.849 57.895 0.00 0.00 33.41 3.16
923 984 1.150536 TCTCTGGTTGGTGGGCAAC 59.849 57.895 0.00 0.00 0.00 4.17
1019 1080 3.082055 GGAGGAGGGGAACGGGAC 61.082 72.222 0.00 0.00 0.00 4.46
1625 2163 2.021068 ATGTCATCGAGCTCCGGGTG 62.021 60.000 8.47 1.45 39.14 4.61
1626 2164 0.467474 TATGTCATCGAGCTCCGGGT 60.467 55.000 8.47 0.00 39.14 5.28
1639 2177 0.030235 CGACGCTCCGGAATATGTCA 59.970 55.000 19.05 0.00 0.00 3.58
1690 2228 1.569479 GCAGCACCTCAAACTCGTCC 61.569 60.000 0.00 0.00 0.00 4.79
1711 2249 2.224137 CGTCACATCTGTCATATGCCCT 60.224 50.000 0.00 0.00 0.00 5.19
1721 2259 2.592993 CCCCCACCGTCACATCTGT 61.593 63.158 0.00 0.00 0.00 3.41
1942 2480 0.529337 CATCAGTGGGCAGCTCGTAG 60.529 60.000 0.00 0.00 0.00 3.51
2011 2549 1.174712 ATGTGCCCAACTGTGCTGTC 61.175 55.000 0.00 0.00 0.00 3.51
2030 2568 2.224450 CCCATGCTCACATCTGCATAGA 60.224 50.000 0.00 0.00 46.65 1.98
2284 2823 5.062183 CGAATAAAACAAGCATCGAGTGAGA 59.938 40.000 0.00 0.00 32.38 3.27
2317 2856 4.572389 CGGAGGGAGTAATTGATTTGTCAG 59.428 45.833 0.00 0.00 0.00 3.51
2330 2869 4.687262 ATATTATGGGACGGAGGGAGTA 57.313 45.455 0.00 0.00 0.00 2.59
2331 2870 3.562108 ATATTATGGGACGGAGGGAGT 57.438 47.619 0.00 0.00 0.00 3.85
2332 2871 5.269991 TCTTATATTATGGGACGGAGGGAG 58.730 45.833 0.00 0.00 0.00 4.30
2333 2872 5.279562 TCTTATATTATGGGACGGAGGGA 57.720 43.478 0.00 0.00 0.00 4.20
2334 2873 5.623824 CGTTCTTATATTATGGGACGGAGGG 60.624 48.000 0.00 0.00 0.00 4.30
2335 2874 5.408356 CGTTCTTATATTATGGGACGGAGG 58.592 45.833 0.00 0.00 0.00 4.30
2336 2875 4.863131 GCGTTCTTATATTATGGGACGGAG 59.137 45.833 11.52 0.00 0.00 4.63
2337 2876 4.525487 AGCGTTCTTATATTATGGGACGGA 59.475 41.667 11.52 0.00 0.00 4.69
2338 2877 4.817517 AGCGTTCTTATATTATGGGACGG 58.182 43.478 11.52 0.00 0.00 4.79
2339 2878 6.780706 AAAGCGTTCTTATATTATGGGACG 57.219 37.500 7.50 7.50 31.02 4.79
2340 2879 8.068380 GTCAAAAGCGTTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 31.02 4.46
2341 2880 7.771361 TGTCAAAAGCGTTCTTATATTATGGGA 59.229 33.333 0.00 0.00 31.02 4.37
2342 2881 7.855904 GTGTCAAAAGCGTTCTTATATTATGGG 59.144 37.037 0.00 0.00 31.02 4.00
2343 2882 8.612619 AGTGTCAAAAGCGTTCTTATATTATGG 58.387 33.333 0.00 0.00 31.02 2.74
2346 2885 9.642327 TGTAGTGTCAAAAGCGTTCTTATATTA 57.358 29.630 0.00 0.00 31.02 0.98
2347 2886 8.440833 GTGTAGTGTCAAAAGCGTTCTTATATT 58.559 33.333 0.00 0.00 31.02 1.28
2348 2887 7.817962 AGTGTAGTGTCAAAAGCGTTCTTATAT 59.182 33.333 0.00 0.00 31.02 0.86
2349 2888 7.149973 AGTGTAGTGTCAAAAGCGTTCTTATA 58.850 34.615 0.00 0.00 31.02 0.98
2350 2889 5.989777 AGTGTAGTGTCAAAAGCGTTCTTAT 59.010 36.000 0.00 0.00 31.02 1.73
2351 2890 5.353938 AGTGTAGTGTCAAAAGCGTTCTTA 58.646 37.500 0.00 0.00 31.02 2.10
2352 2891 4.189231 AGTGTAGTGTCAAAAGCGTTCTT 58.811 39.130 0.00 0.00 0.00 2.52
2353 2892 3.793559 AGTGTAGTGTCAAAAGCGTTCT 58.206 40.909 0.00 0.00 0.00 3.01
2354 2893 4.743644 ACTAGTGTAGTGTCAAAAGCGTTC 59.256 41.667 0.00 0.00 37.69 3.95
2355 2894 4.690122 ACTAGTGTAGTGTCAAAAGCGTT 58.310 39.130 0.00 0.00 37.69 4.84
2356 2895 4.317671 ACTAGTGTAGTGTCAAAAGCGT 57.682 40.909 0.00 0.00 37.69 5.07
2367 2906 6.335777 AGAACGTTTTTGACACTAGTGTAGT 58.664 36.000 27.98 15.35 45.05 2.73
2368 2907 6.823678 AGAACGTTTTTGACACTAGTGTAG 57.176 37.500 27.98 14.79 45.05 2.74
2369 2908 8.876275 ATAAGAACGTTTTTGACACTAGTGTA 57.124 30.769 27.98 11.50 45.05 2.90
2434 2973 7.769970 TCCGTCCCATAATATAAGAACGTTTTT 59.230 33.333 9.22 9.22 0.00 1.94
2435 2974 7.274447 TCCGTCCCATAATATAAGAACGTTTT 58.726 34.615 0.46 0.00 0.00 2.43
2436 2975 6.819284 TCCGTCCCATAATATAAGAACGTTT 58.181 36.000 0.46 0.00 0.00 3.60
2437 2976 6.409524 TCCGTCCCATAATATAAGAACGTT 57.590 37.500 0.00 0.00 0.00 3.99
2438 2977 5.047519 CCTCCGTCCCATAATATAAGAACGT 60.048 44.000 0.00 0.00 0.00 3.99
2439 2978 5.408356 CCTCCGTCCCATAATATAAGAACG 58.592 45.833 0.00 0.00 0.00 3.95
2440 2979 5.482878 TCCCTCCGTCCCATAATATAAGAAC 59.517 44.000 0.00 0.00 0.00 3.01
2441 2980 5.657446 TCCCTCCGTCCCATAATATAAGAA 58.343 41.667 0.00 0.00 0.00 2.52
2442 2981 5.222484 ACTCCCTCCGTCCCATAATATAAGA 60.222 44.000 0.00 0.00 0.00 2.10
2443 2982 5.024118 ACTCCCTCCGTCCCATAATATAAG 58.976 45.833 0.00 0.00 0.00 1.73
2444 2983 5.019657 ACTCCCTCCGTCCCATAATATAA 57.980 43.478 0.00 0.00 0.00 0.98
2445 2984 4.687262 ACTCCCTCCGTCCCATAATATA 57.313 45.455 0.00 0.00 0.00 0.86
2446 2985 3.562108 ACTCCCTCCGTCCCATAATAT 57.438 47.619 0.00 0.00 0.00 1.28
2447 2986 3.400322 ACTACTCCCTCCGTCCCATAATA 59.600 47.826 0.00 0.00 0.00 0.98
2448 2987 2.179424 ACTACTCCCTCCGTCCCATAAT 59.821 50.000 0.00 0.00 0.00 1.28
2449 2988 1.572415 ACTACTCCCTCCGTCCCATAA 59.428 52.381 0.00 0.00 0.00 1.90
2450 2989 1.229131 ACTACTCCCTCCGTCCCATA 58.771 55.000 0.00 0.00 0.00 2.74
2451 2990 1.229131 TACTACTCCCTCCGTCCCAT 58.771 55.000 0.00 0.00 0.00 4.00
2452 2991 1.229131 ATACTACTCCCTCCGTCCCA 58.771 55.000 0.00 0.00 0.00 4.37
2453 2992 2.378378 AATACTACTCCCTCCGTCCC 57.622 55.000 0.00 0.00 0.00 4.46
2454 2993 3.959449 AGAAAATACTACTCCCTCCGTCC 59.041 47.826 0.00 0.00 0.00 4.79
2455 2994 5.360429 AGAAGAAAATACTACTCCCTCCGTC 59.640 44.000 0.00 0.00 0.00 4.79
2456 2995 5.270794 AGAAGAAAATACTACTCCCTCCGT 58.729 41.667 0.00 0.00 0.00 4.69
2457 2996 5.855740 AGAAGAAAATACTACTCCCTCCG 57.144 43.478 0.00 0.00 0.00 4.63
2458 2997 7.201929 CCAGTAGAAGAAAATACTACTCCCTCC 60.202 44.444 0.00 0.00 42.92 4.30
2459 2998 7.560626 TCCAGTAGAAGAAAATACTACTCCCTC 59.439 40.741 0.00 0.00 42.92 4.30
2460 2999 7.420029 TCCAGTAGAAGAAAATACTACTCCCT 58.580 38.462 0.00 0.00 42.92 4.20
2461 3000 7.657023 TCCAGTAGAAGAAAATACTACTCCC 57.343 40.000 0.00 0.00 42.92 4.30
2491 3030 6.258160 CCGTAACTGATGCAATAAGAAAAGG 58.742 40.000 0.00 0.00 0.00 3.11
2514 3053 2.039480 TGCTTCTGATATCAGGATGCCC 59.961 50.000 28.30 11.93 43.91 5.36
2521 3060 9.368674 CTTCTATAATGGTGCTTCTGATATCAG 57.631 37.037 24.32 24.32 45.08 2.90
2533 3072 7.617041 ACAAAAGAGTCTTCTATAATGGTGC 57.383 36.000 5.70 0.00 31.96 5.01
2565 3104 7.792374 TGATTAAAGCATACCAGATTGAGAC 57.208 36.000 0.00 0.00 0.00 3.36
2612 3151 9.739276 ATCACCACAAAGAAATTACATCTAAGA 57.261 29.630 0.00 0.00 0.00 2.10
2764 3303 6.830873 AACCAAATAGTACGACTAGTGACT 57.169 37.500 0.00 3.45 33.66 3.41
2801 3340 3.568007 TCAACTCCCAATCGGAAAAGTTG 59.432 43.478 6.70 6.70 41.40 3.16
2806 3345 3.088532 CCATTCAACTCCCAATCGGAAA 58.911 45.455 0.00 0.00 41.40 3.13
2937 3476 7.536622 GCAAAGCATGACATATATTACTGAAGC 59.463 37.037 0.00 0.00 0.00 3.86
2938 3477 8.781196 AGCAAAGCATGACATATATTACTGAAG 58.219 33.333 0.00 0.00 0.00 3.02
2939 3478 8.562052 CAGCAAAGCATGACATATATTACTGAA 58.438 33.333 0.00 0.00 0.00 3.02
2941 3480 8.013947 GTCAGCAAAGCATGACATATATTACTG 58.986 37.037 0.00 0.00 44.21 2.74
2942 3481 7.935755 AGTCAGCAAAGCATGACATATATTACT 59.064 33.333 17.38 0.00 46.63 2.24
2943 3482 8.013947 CAGTCAGCAAAGCATGACATATATTAC 58.986 37.037 17.38 0.00 46.63 1.89
2944 3483 7.308169 GCAGTCAGCAAAGCATGACATATATTA 60.308 37.037 17.38 0.00 46.63 0.98
2945 3484 6.514541 GCAGTCAGCAAAGCATGACATATATT 60.515 38.462 17.38 1.40 46.63 1.28
2946 3485 5.048921 GCAGTCAGCAAAGCATGACATATAT 60.049 40.000 17.38 0.00 46.63 0.86
2947 3486 4.274214 GCAGTCAGCAAAGCATGACATATA 59.726 41.667 17.38 0.00 46.63 0.86
2948 3487 3.066342 GCAGTCAGCAAAGCATGACATAT 59.934 43.478 17.38 2.39 46.63 1.78
2949 3488 2.421073 GCAGTCAGCAAAGCATGACATA 59.579 45.455 17.38 0.00 46.63 2.29
2950 3489 1.201647 GCAGTCAGCAAAGCATGACAT 59.798 47.619 17.38 0.00 46.63 3.06
2952 3491 3.396491 GCAGTCAGCAAAGCATGAC 57.604 52.632 0.00 11.16 44.97 3.06
2965 3504 3.628942 TGATGGCAGTAAATCATGCAGTC 59.371 43.478 0.00 0.00 44.37 3.51
3138 3688 1.889829 AGCAGAGAAGCTCACGTAAGT 59.110 47.619 0.00 0.00 46.06 2.24
3139 3689 2.257894 CAGCAGAGAAGCTCACGTAAG 58.742 52.381 0.00 0.00 44.54 2.34
3140 3690 1.670087 GCAGCAGAGAAGCTCACGTAA 60.670 52.381 0.00 0.00 44.54 3.18
3141 3691 0.109086 GCAGCAGAGAAGCTCACGTA 60.109 55.000 0.00 0.00 44.54 3.57
3142 3692 1.373999 GCAGCAGAGAAGCTCACGT 60.374 57.895 0.00 0.00 44.54 4.49
3143 3693 1.373873 TGCAGCAGAGAAGCTCACG 60.374 57.895 0.00 0.00 44.54 4.35
3144 3694 0.320596 AGTGCAGCAGAGAAGCTCAC 60.321 55.000 0.00 0.00 44.54 3.51
3204 3754 3.849563 TTGGTACTGCTAAACACCACT 57.150 42.857 0.00 0.00 40.69 4.00
3242 3792 2.242708 ACCAACCACTCCAAAGGTAACA 59.757 45.455 0.00 0.00 37.07 2.41


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

AutoCloner maintained by Alex Coulton.