Multiple sequence alignment - TraesCS7A01G230000

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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 TraesCS7A01G230000 chr7A 100.000 2964 0 0 1 2964 200511353 200508390 0.000000e+00 5474.0
1 TraesCS7A01G230000 chr7B 90.405 1678 76 33 470 2128 337025083 337023472 0.000000e+00 2128.0
2 TraesCS7A01G230000 chr7B 88.586 403 36 6 2566 2964 337022458 337022062 5.750000e-132 481.0
3 TraesCS7A01G230000 chr7B 91.908 346 14 5 1 332 337025784 337025439 3.460000e-129 472.0
4 TraesCS7A01G230000 chr7B 93.103 145 7 2 331 472 337025413 337025269 2.990000e-50 209.0
5 TraesCS7A01G230000 chr7D 93.234 1271 37 15 861 2128 191796882 191795658 0.000000e+00 1825.0
6 TraesCS7A01G230000 chr7D 93.834 519 18 8 331 844 191797380 191796871 0.000000e+00 769.0
7 TraesCS7A01G230000 chr7D 94.220 346 6 1 1 332 191797751 191797406 1.580000e-142 516.0
8 TraesCS7A01G230000 chr6B 81.250 288 40 12 1267 1553 542500247 542500521 1.380000e-53 220.0
9 TraesCS7A01G230000 chr6B 89.091 55 2 2 2261 2315 119526801 119526851 6.860000e-07 65.8
10 TraesCS7A01G230000 chr6B 90.000 50 1 2 2265 2314 659564183 659564228 8.870000e-06 62.1
11 TraesCS7A01G230000 chr6B 92.857 42 3 0 2276 2317 712247174 712247133 8.870000e-06 62.1
12 TraesCS7A01G230000 chr6A 81.250 288 40 11 1267 1553 502148327 502148601 1.380000e-53 220.0
13 TraesCS7A01G230000 chr6A 91.406 128 11 0 2357 2484 609592985 609593112 3.040000e-40 176.0
14 TraesCS7A01G230000 chr6A 97.436 39 1 0 2276 2314 242184210 242184172 1.910000e-07 67.6
15 TraesCS7A01G230000 chr2A 90.977 133 12 0 2354 2486 16527118 16526986 2.350000e-41 180.0
16 TraesCS7A01G230000 chr2A 86.207 58 4 2 2255 2312 766004657 766004710 3.190000e-05 60.2
17 TraesCS7A01G230000 chr5B 90.977 133 10 2 2353 2484 693967518 693967649 8.440000e-41 178.0
18 TraesCS7A01G230000 chr5B 91.837 49 4 0 2267 2315 693967481 693967529 5.300000e-08 69.4
19 TraesCS7A01G230000 chr5B 100.000 29 0 0 1504 1532 650338850 650338822 1.000000e-03 54.7
20 TraesCS7A01G230000 chr3A 91.473 129 11 0 2357 2485 313548669 313548797 8.440000e-41 178.0
21 TraesCS7A01G230000 chr3A 91.473 129 11 0 2357 2485 600920982 600920854 8.440000e-41 178.0
22 TraesCS7A01G230000 chr3A 93.277 119 8 0 2366 2484 534181980 534181862 3.040000e-40 176.0
23 TraesCS7A01G230000 chr3A 90.000 50 1 2 2265 2314 732488067 732488112 8.870000e-06 62.1
24 TraesCS7A01G230000 chr2B 91.406 128 11 0 2357 2484 442788083 442788210 3.040000e-40 176.0
25 TraesCS7A01G230000 chr5D 90.769 130 12 0 2357 2486 53583204 53583075 1.090000e-39 174.0
26 TraesCS7A01G230000 chr5A 91.870 123 10 0 2366 2488 605231261 605231139 3.930000e-39 172.0
27 TraesCS7A01G230000 chr5A 97.059 34 1 0 1499 1532 645127447 645127414 1.150000e-04 58.4
28 TraesCS7A01G230000 chr3B 97.500 40 1 0 2276 2315 409877159 409877120 5.300000e-08 69.4
29 TraesCS7A01G230000 chr2D 90.196 51 3 2 2267 2315 532176547 532176597 6.860000e-07 65.8
30 TraesCS7A01G230000 chr2D 100.000 30 0 0 1028 1057 290888187 290888216 4.130000e-04 56.5
31 TraesCS7A01G230000 chr1D 100.000 28 0 0 2543 2570 327931721 327931694 5.000000e-03 52.8


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 TraesCS7A01G230000 chr7A 200508390 200511353 2963 True 5474.000000 5474 100.000000 1 2964 1 chr7A.!!$R1 2963
1 TraesCS7A01G230000 chr7B 337022062 337025784 3722 True 822.500000 2128 91.000500 1 2964 4 chr7B.!!$R1 2963
2 TraesCS7A01G230000 chr7D 191795658 191797751 2093 True 1036.666667 1825 93.762667 1 2128 3 chr7D.!!$R1 2127

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
73 74 0.034896 GCAACCTGAGTCGGAAAGGA 59.965 55.0 0.0 0.0 34.97 3.36 F
260 275 0.381801 CAATTCAGTGCGGTATGGCC 59.618 55.0 0.0 0.0 0.00 5.36 F
273 288 0.466543 TATGGCCGATACACACACCC 59.533 55.0 0.0 0.0 0.00 4.61 F
848 1091 0.748005 GCGGCTGTCTCTCTCTCTCT 60.748 60.0 0.0 0.0 0.00 3.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1639 1893 0.164432 CGCCTGCATGCATGTATACG 59.836 55.0 26.79 22.67 0.00 3.06 R
1640 1894 0.518636 CCGCCTGCATGCATGTATAC 59.481 55.0 26.79 16.01 0.00 1.47 R
1641 1895 1.236616 GCCGCCTGCATGCATGTATA 61.237 55.0 26.79 13.26 40.77 1.47 R
2571 3265 0.033405 TGTACTCTCTCCTTCCGGGG 60.033 60.0 0.00 0.00 35.33 5.73 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
73 74 0.034896 GCAACCTGAGTCGGAAAGGA 59.965 55.000 0.00 0.00 34.97 3.36
122 123 6.090783 GTGCATGTTGATATGGCAATCATAG 58.909 40.000 11.37 5.59 41.20 2.23
229 244 2.125461 TAGCGCACTCGATCAATCTG 57.875 50.000 11.47 0.00 38.10 2.90
260 275 0.381801 CAATTCAGTGCGGTATGGCC 59.618 55.000 0.00 0.00 0.00 5.36
273 288 0.466543 TATGGCCGATACACACACCC 59.533 55.000 0.00 0.00 0.00 4.61
400 442 2.004733 GTTCCGCTAATTAACCGCTGT 58.995 47.619 0.90 0.00 0.00 4.40
408 450 1.026718 ATTAACCGCTGTGGCTGAGC 61.027 55.000 7.27 0.00 43.94 4.26
478 711 3.683365 ACTGTGTCAGTGTCATATGCA 57.317 42.857 0.00 0.00 43.63 3.96
606 842 2.565841 CCCCTTCTTCCTTAATCGCTG 58.434 52.381 0.00 0.00 0.00 5.18
668 904 1.219393 CTCTCCCCAGTCTTTCGCC 59.781 63.158 0.00 0.00 0.00 5.54
826 1069 2.778309 AAGCTGTCACTCTCTGCGGC 62.778 60.000 0.00 0.00 35.48 6.53
827 1070 2.125753 CTGTCACTCTCTGCGGCC 60.126 66.667 0.00 0.00 0.00 6.13
828 1071 2.601666 TGTCACTCTCTGCGGCCT 60.602 61.111 0.00 0.00 0.00 5.19
829 1072 2.125753 GTCACTCTCTGCGGCCTG 60.126 66.667 0.00 0.00 0.00 4.85
830 1073 4.074526 TCACTCTCTGCGGCCTGC 62.075 66.667 11.92 11.92 46.70 4.85
842 1085 3.768922 GCCTGCGGCTGTCTCTCT 61.769 66.667 11.61 0.00 46.69 3.10
843 1086 2.493973 CCTGCGGCTGTCTCTCTC 59.506 66.667 0.00 0.00 0.00 3.20
844 1087 2.051518 CCTGCGGCTGTCTCTCTCT 61.052 63.158 0.00 0.00 0.00 3.10
845 1088 1.433064 CTGCGGCTGTCTCTCTCTC 59.567 63.158 0.00 0.00 0.00 3.20
846 1089 1.001517 TGCGGCTGTCTCTCTCTCT 60.002 57.895 0.00 0.00 0.00 3.10
847 1090 1.029408 TGCGGCTGTCTCTCTCTCTC 61.029 60.000 0.00 0.00 0.00 3.20
848 1091 0.748005 GCGGCTGTCTCTCTCTCTCT 60.748 60.000 0.00 0.00 0.00 3.10
849 1092 1.299541 CGGCTGTCTCTCTCTCTCTC 58.700 60.000 0.00 0.00 0.00 3.20
850 1093 1.134401 CGGCTGTCTCTCTCTCTCTCT 60.134 57.143 0.00 0.00 0.00 3.10
851 1094 2.565841 GGCTGTCTCTCTCTCTCTCTC 58.434 57.143 0.00 0.00 0.00 3.20
852 1095 2.171448 GGCTGTCTCTCTCTCTCTCTCT 59.829 54.545 0.00 0.00 0.00 3.10
853 1096 3.462021 GCTGTCTCTCTCTCTCTCTCTC 58.538 54.545 0.00 0.00 0.00 3.20
854 1097 3.133721 GCTGTCTCTCTCTCTCTCTCTCT 59.866 52.174 0.00 0.00 0.00 3.10
855 1098 4.739137 GCTGTCTCTCTCTCTCTCTCTCTC 60.739 54.167 0.00 0.00 0.00 3.20
856 1099 4.614475 TGTCTCTCTCTCTCTCTCTCTCT 58.386 47.826 0.00 0.00 0.00 3.10
859 1102 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
863 1106 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
872 1117 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
873 1118 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
954 1199 1.069838 CGACTAGAGATACGCACGCAT 60.070 52.381 0.00 0.00 0.00 4.73
1260 1511 1.151810 AGGAGGAACCCTTGAGCCA 60.152 57.895 0.00 0.00 40.05 4.75
1419 1670 2.046507 CACCTGGCTCTGCAGACC 60.047 66.667 13.74 18.80 0.00 3.85
1560 1814 4.938832 GCACACAACACAGGTAATACCATA 59.061 41.667 12.54 0.00 41.95 2.74
1561 1815 5.163794 GCACACAACACAGGTAATACCATAC 60.164 44.000 12.54 0.00 41.95 2.39
1562 1816 5.062934 CACACAACACAGGTAATACCATACG 59.937 44.000 12.54 0.00 41.95 3.06
1563 1817 5.172934 CACAACACAGGTAATACCATACGT 58.827 41.667 12.54 0.00 41.95 3.57
1577 1831 3.119029 ACCATACGTACGTACCATGCTTT 60.119 43.478 28.99 9.08 33.01 3.51
1634 1888 4.429561 CGTCGTACGTGTCTCCAC 57.570 61.111 16.05 2.96 36.74 4.02
1970 2230 4.892934 ACCTCCTCAGAGTCTGACAATATC 59.107 45.833 19.10 0.00 38.58 1.63
1971 2231 4.280677 CCTCCTCAGAGTCTGACAATATCC 59.719 50.000 19.10 0.00 38.58 2.59
1972 2232 5.136068 TCCTCAGAGTCTGACAATATCCT 57.864 43.478 19.10 0.00 35.39 3.24
2108 2377 5.583457 TGATGCACTGACAATATTCTCACTG 59.417 40.000 0.00 0.00 0.00 3.66
2128 2397 5.807011 CACTGGCTTATTTTGGTTTATGCTC 59.193 40.000 0.00 0.00 0.00 4.26
2146 2587 3.181491 TGCTCTTTAAGTTGTTGTGCACC 60.181 43.478 15.69 0.00 0.00 5.01
2172 2613 5.582689 ATGGTAAGCTAAATGCAACCTTC 57.417 39.130 0.00 0.00 44.98 3.46
2180 2621 5.358160 AGCTAAATGCAACCTTCCTAATGTC 59.642 40.000 0.00 0.00 45.94 3.06
2204 2645 3.244215 CCCTTCTAGACTTGTGTTCAGCA 60.244 47.826 0.00 0.00 0.00 4.41
2235 2677 3.316283 ACACCAACGCATTTAAGCAATG 58.684 40.909 0.00 0.00 44.79 2.82
2237 2679 2.298729 ACCAACGCATTTAAGCAATGGT 59.701 40.909 6.77 6.77 43.89 3.55
2244 2686 8.901748 CAACGCATTTAAGCAATGGTAATATAC 58.098 33.333 0.00 0.00 42.51 1.47
2246 2688 8.792633 ACGCATTTAAGCAATGGTAATATACAT 58.207 29.630 0.00 0.00 42.51 2.29
2293 2742 7.546250 ACTCGATCCATCTGTTCCTAAATAT 57.454 36.000 0.00 0.00 0.00 1.28
2294 2743 8.651589 ACTCGATCCATCTGTTCCTAAATATA 57.348 34.615 0.00 0.00 0.00 0.86
2295 2744 9.090103 ACTCGATCCATCTGTTCCTAAATATAA 57.910 33.333 0.00 0.00 0.00 0.98
2296 2745 9.579768 CTCGATCCATCTGTTCCTAAATATAAG 57.420 37.037 0.00 0.00 0.00 1.73
2298 2873 9.360093 CGATCCATCTGTTCCTAAATATAAGTC 57.640 37.037 0.00 0.00 0.00 3.01
2318 2893 9.930693 ATAAGTCTTTTAAGAGATTTCACGACT 57.069 29.630 6.98 0.00 35.32 4.18
2319 2894 8.664211 AAGTCTTTTAAGAGATTTCACGACTT 57.336 30.769 0.00 0.00 35.32 3.01
2320 2895 8.077836 AGTCTTTTAAGAGATTTCACGACTTG 57.922 34.615 0.00 0.00 35.32 3.16
2321 2896 7.926555 AGTCTTTTAAGAGATTTCACGACTTGA 59.073 33.333 0.00 0.00 35.32 3.02
2322 2897 8.713271 GTCTTTTAAGAGATTTCACGACTTGAT 58.287 33.333 0.00 0.00 35.32 2.57
2324 2899 6.968131 TTAAGAGATTTCACGACTTGATGG 57.032 37.500 0.00 0.00 32.84 3.51
2325 2900 4.808414 AGAGATTTCACGACTTGATGGA 57.192 40.909 0.00 0.00 32.84 3.41
2326 2901 5.152623 AGAGATTTCACGACTTGATGGAA 57.847 39.130 0.00 0.00 32.84 3.53
2327 2902 5.738909 AGAGATTTCACGACTTGATGGAAT 58.261 37.500 0.00 0.00 32.84 3.01
2328 2903 5.583854 AGAGATTTCACGACTTGATGGAATG 59.416 40.000 0.00 0.00 32.84 2.67
2329 2904 3.829886 TTTCACGACTTGATGGAATGC 57.170 42.857 0.00 0.00 32.84 3.56
2331 2906 2.989909 TCACGACTTGATGGAATGCAT 58.010 42.857 0.00 0.00 0.00 3.96
2332 2907 2.679336 TCACGACTTGATGGAATGCATG 59.321 45.455 0.00 0.00 0.00 4.06
2333 2908 2.019249 ACGACTTGATGGAATGCATGG 58.981 47.619 0.00 0.00 0.00 3.66
2334 2909 2.019249 CGACTTGATGGAATGCATGGT 58.981 47.619 0.00 0.00 0.00 3.55
2335 2910 2.223409 CGACTTGATGGAATGCATGGTG 60.223 50.000 0.00 0.00 0.00 4.17
2336 2911 2.756760 GACTTGATGGAATGCATGGTGT 59.243 45.455 0.00 0.00 0.00 4.16
2337 2912 3.167485 ACTTGATGGAATGCATGGTGTT 58.833 40.909 0.00 0.00 0.00 3.32
2338 2913 3.194116 ACTTGATGGAATGCATGGTGTTC 59.806 43.478 0.00 0.00 0.00 3.18
2339 2914 2.101783 TGATGGAATGCATGGTGTTCC 58.898 47.619 0.00 4.28 41.37 3.62
2340 2915 3.761896 TGGAATGCATGGTGTTCCA 57.238 47.368 13.51 13.51 46.67 3.53
2355 2930 6.837312 TGGTGTTCCATCTCTAAAGAAAAGA 58.163 36.000 0.00 0.00 39.03 2.52
2356 2931 7.287061 TGGTGTTCCATCTCTAAAGAAAAGAA 58.713 34.615 0.00 0.00 39.03 2.52
2357 2932 7.445402 TGGTGTTCCATCTCTAAAGAAAAGAAG 59.555 37.037 0.00 0.00 39.03 2.85
2358 2933 7.661847 GGTGTTCCATCTCTAAAGAAAAGAAGA 59.338 37.037 0.00 0.00 34.49 2.87
2359 2934 9.225436 GTGTTCCATCTCTAAAGAAAAGAAGAT 57.775 33.333 0.00 0.00 34.49 2.40
2360 2935 9.799106 TGTTCCATCTCTAAAGAAAAGAAGATT 57.201 29.630 0.00 0.00 34.49 2.40
2372 2947 9.579932 AAAGAAAAGAAGATTTCACTATGGACT 57.420 29.630 2.99 0.00 40.89 3.85
2385 2960 8.706322 TTCACTATGGACTATATACAGAGCAA 57.294 34.615 0.00 0.00 0.00 3.91
2389 2964 9.935241 ACTATGGACTATATACAGAGCAAAATG 57.065 33.333 0.00 0.00 0.00 2.32
2425 3000 9.044150 ACACTCTAAAGTACGTCTATCTACATC 57.956 37.037 0.00 0.00 33.25 3.06
2489 3064 4.370094 AGGAATAGAGGGAGTAGTACCG 57.630 50.000 0.00 0.00 0.00 4.02
2497 3072 0.659957 GGAGTAGTACCGCCGTACAG 59.340 60.000 16.10 0.00 46.25 2.74
2571 3265 1.400846 TCCGTCTGAGCGACAAGTATC 59.599 52.381 0.00 0.00 42.98 2.24
2572 3266 1.534175 CCGTCTGAGCGACAAGTATCC 60.534 57.143 0.00 0.00 42.98 2.59
2578 3272 0.974010 AGCGACAAGTATCCCCGGAA 60.974 55.000 0.73 0.00 0.00 4.30
2596 3290 5.927954 CGGAAGGAGAGAGTACATAGTAC 57.072 47.826 0.00 0.00 0.00 2.73
2603 3494 7.493367 AGGAGAGAGTACATAGTACAATTTGC 58.507 38.462 9.68 0.00 0.00 3.68
2604 3495 7.124298 AGGAGAGAGTACATAGTACAATTTGCA 59.876 37.037 9.68 0.00 0.00 4.08
2615 3506 9.027129 CATAGTACAATTTGCAGAAATTCATGG 57.973 33.333 0.00 0.00 39.34 3.66
2645 3536 2.120909 GCAGGGGTACGCATGCATT 61.121 57.895 35.24 6.25 46.88 3.56
2649 3543 1.202651 AGGGGTACGCATGCATTCTAC 60.203 52.381 19.57 10.39 46.88 2.59
2668 3562 2.855180 ACGCATTTGCTTCAAGATTCG 58.145 42.857 0.51 0.00 39.32 3.34
2675 3569 2.071540 TGCTTCAAGATTCGTGAGCTG 58.928 47.619 17.50 8.91 0.00 4.24
2731 3625 4.160252 GGTCCATGCATGATAGTTTTTGGT 59.840 41.667 28.31 0.00 0.00 3.67
2742 3636 8.892723 CATGATAGTTTTTGGTAGAGTTGCATA 58.107 33.333 0.00 0.00 0.00 3.14
2744 3638 8.892723 TGATAGTTTTTGGTAGAGTTGCATATG 58.107 33.333 0.00 0.00 0.00 1.78
2745 3639 5.954335 AGTTTTTGGTAGAGTTGCATATGC 58.046 37.500 21.09 21.09 42.50 3.14
2755 3649 3.748623 GCATATGCATCACCCGCA 58.251 55.556 22.84 0.00 44.94 5.69
2759 3653 0.111061 ATATGCATCACCCGCACCAT 59.889 50.000 0.19 0.00 43.35 3.55
2761 3655 2.124570 GCATCACCCGCACCATCT 60.125 61.111 0.00 0.00 0.00 2.90
2762 3656 2.182842 GCATCACCCGCACCATCTC 61.183 63.158 0.00 0.00 0.00 2.75
2777 3671 4.399303 CACCATCTCCCATACTTTCAAACC 59.601 45.833 0.00 0.00 0.00 3.27
2807 3701 8.234546 AGTTTGAATTAAGTTTCGTTCGCATAT 58.765 29.630 0.00 0.00 0.00 1.78
2849 3744 4.685165 GTGTGCATATTTGTGTTCATTGCA 59.315 37.500 0.00 0.00 36.37 4.08
2910 3805 5.784578 ACCCATTTAGTTTTTCTCCACAC 57.215 39.130 0.00 0.00 0.00 3.82
2916 3811 7.417342 CCATTTAGTTTTTCTCCACACAAAGGA 60.417 37.037 0.00 0.00 0.00 3.36
2952 3847 5.407407 TCTTTAGCCGGATATCCATCTTC 57.593 43.478 21.70 5.27 35.14 2.87
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
122 123 4.749598 TGCATGTGGATCATTCGTATACAC 59.250 41.667 3.32 0.00 34.09 2.90
229 244 5.230726 CCGCACTGAATTGATAGAAAATTGC 59.769 40.000 0.00 0.00 0.00 3.56
260 275 0.532573 AGCTCAGGGTGTGTGTATCG 59.467 55.000 0.00 0.00 0.00 2.92
408 450 3.033184 TGCCTTTGCAGAACGCTG 58.967 55.556 0.00 0.00 44.23 5.18
444 489 5.705441 ACTGACACAGTGTTTTCAGAAAGAA 59.295 36.000 27.51 0.00 43.63 2.52
461 506 2.337583 ACGTGCATATGACACTGACAC 58.662 47.619 20.51 11.12 35.84 3.67
517 753 3.724914 CTTTCGCGGGAGGAGGAGC 62.725 68.421 6.13 0.00 0.00 4.70
578 814 2.361737 GAAGAAGGGGGCAGCCAC 60.362 66.667 15.19 10.34 0.00 5.01
580 816 1.571773 TAAGGAAGAAGGGGGCAGCC 61.572 60.000 1.26 1.26 0.00 4.85
606 842 0.457337 CCTACACGTACCGAACTGGC 60.457 60.000 0.00 0.00 43.94 4.85
700 936 1.491505 GGATACTCGGCGCTTTGAGC 61.492 60.000 19.71 8.02 38.02 4.26
701 937 0.179111 TGGATACTCGGCGCTTTGAG 60.179 55.000 18.66 18.66 38.21 3.02
702 938 0.459585 GTGGATACTCGGCGCTTTGA 60.460 55.000 7.64 1.98 37.61 2.69
827 1070 1.031571 AGAGAGAGAGACAGCCGCAG 61.032 60.000 0.00 0.00 0.00 5.18
828 1071 1.001517 AGAGAGAGAGACAGCCGCA 60.002 57.895 0.00 0.00 0.00 5.69
829 1072 0.748005 AGAGAGAGAGAGACAGCCGC 60.748 60.000 0.00 0.00 0.00 6.53
830 1073 1.134401 AGAGAGAGAGAGAGACAGCCG 60.134 57.143 0.00 0.00 0.00 5.52
831 1074 2.171448 AGAGAGAGAGAGAGAGACAGCC 59.829 54.545 0.00 0.00 0.00 4.85
832 1075 3.133721 AGAGAGAGAGAGAGAGAGACAGC 59.866 52.174 0.00 0.00 0.00 4.40
833 1076 4.648762 AGAGAGAGAGAGAGAGAGAGACAG 59.351 50.000 0.00 0.00 0.00 3.51
834 1077 4.614475 AGAGAGAGAGAGAGAGAGAGACA 58.386 47.826 0.00 0.00 0.00 3.41
835 1078 4.892934 AGAGAGAGAGAGAGAGAGAGAGAC 59.107 50.000 0.00 0.00 0.00 3.36
836 1079 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
837 1080 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
838 1081 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
839 1082 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
840 1083 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
841 1084 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
842 1085 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
843 1086 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
844 1087 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
845 1088 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
846 1089 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
847 1090 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
848 1091 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
849 1092 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
850 1093 5.136068 AGAGAGAGAGAGAGAGAGAGAGA 57.864 47.826 0.00 0.00 0.00 3.10
851 1094 4.023279 CGAGAGAGAGAGAGAGAGAGAGAG 60.023 54.167 0.00 0.00 0.00 3.20
852 1095 3.885901 CGAGAGAGAGAGAGAGAGAGAGA 59.114 52.174 0.00 0.00 0.00 3.10
853 1096 3.005261 CCGAGAGAGAGAGAGAGAGAGAG 59.995 56.522 0.00 0.00 0.00 3.20
854 1097 2.959030 CCGAGAGAGAGAGAGAGAGAGA 59.041 54.545 0.00 0.00 0.00 3.10
855 1098 2.546795 GCCGAGAGAGAGAGAGAGAGAG 60.547 59.091 0.00 0.00 0.00 3.20
856 1099 1.412710 GCCGAGAGAGAGAGAGAGAGA 59.587 57.143 0.00 0.00 0.00 3.10
859 1102 1.498865 GCGCCGAGAGAGAGAGAGAG 61.499 65.000 0.00 0.00 0.00 3.20
863 1106 4.605967 GCGCGCCGAGAGAGAGAG 62.606 72.222 23.24 0.00 0.00 3.20
873 1118 4.980903 AAGCAACAAAGCGCGCCG 62.981 61.111 30.33 19.49 40.15 6.46
912 1157 5.287752 TCGATCTGTACTATGTTTTTGCGAC 59.712 40.000 0.00 0.00 0.00 5.19
918 1163 8.734218 TCTCTAGTCGATCTGTACTATGTTTT 57.266 34.615 0.00 0.00 0.00 2.43
1230 1478 4.020617 CCTCCTCCGGCAACAGCA 62.021 66.667 0.00 0.00 0.00 4.41
1253 1504 1.078214 CGCTTCCCTGATGGCTCAA 60.078 57.895 0.00 0.00 0.00 3.02
1560 1814 3.728864 CGTAGAAAGCATGGTACGTACGT 60.729 47.826 25.98 25.98 34.84 3.57
1561 1815 2.780014 CGTAGAAAGCATGGTACGTACG 59.220 50.000 18.98 15.01 34.84 3.67
1577 1831 4.555313 GCATGTATACAAGGCGTACGTAGA 60.555 45.833 17.90 0.00 31.27 2.59
1629 1883 2.117137 GCATGTATACGTCACGTGGAG 58.883 52.381 14.62 12.44 41.39 3.86
1630 1884 1.473278 TGCATGTATACGTCACGTGGA 59.527 47.619 14.62 15.16 41.39 4.02
1631 1885 1.915952 TGCATGTATACGTCACGTGG 58.084 50.000 14.62 2.57 41.39 4.94
1632 1886 2.347568 GCATGCATGTATACGTCACGTG 60.348 50.000 26.79 9.94 41.39 4.49
1633 1887 1.858458 GCATGCATGTATACGTCACGT 59.142 47.619 26.79 8.49 44.35 4.49
1634 1888 1.857837 TGCATGCATGTATACGTCACG 59.142 47.619 26.79 0.00 0.00 4.35
1635 1889 2.221749 CCTGCATGCATGTATACGTCAC 59.778 50.000 26.79 8.24 0.00 3.67
1636 1890 2.482864 CCTGCATGCATGTATACGTCA 58.517 47.619 26.79 13.59 0.00 4.35
1637 1891 1.195448 GCCTGCATGCATGTATACGTC 59.805 52.381 26.79 9.65 0.00 4.34
1638 1892 1.229428 GCCTGCATGCATGTATACGT 58.771 50.000 26.79 0.00 0.00 3.57
1639 1893 0.164432 CGCCTGCATGCATGTATACG 59.836 55.000 26.79 22.67 0.00 3.06
1640 1894 0.518636 CCGCCTGCATGCATGTATAC 59.481 55.000 26.79 16.01 0.00 1.47
1641 1895 1.236616 GCCGCCTGCATGCATGTATA 61.237 55.000 26.79 13.26 40.77 1.47
1642 1896 2.558286 GCCGCCTGCATGCATGTAT 61.558 57.895 26.79 0.00 40.77 2.29
1970 2230 4.289245 ACCCATGGGATGAAAAACATAGG 58.711 43.478 38.07 4.79 39.56 2.57
1971 2231 5.937975 AACCCATGGGATGAAAAACATAG 57.062 39.130 38.07 5.50 39.56 2.23
1972 2232 6.155393 GGTTAACCCATGGGATGAAAAACATA 59.845 38.462 38.07 3.77 39.56 2.29
2006 2266 4.208253 CCGCAAAAAGAAAAACGCATAACT 59.792 37.500 0.00 0.00 0.00 2.24
2018 2279 6.797995 CGCTTAACTTATTACCGCAAAAAGAA 59.202 34.615 0.00 0.00 0.00 2.52
2019 2280 6.073112 ACGCTTAACTTATTACCGCAAAAAGA 60.073 34.615 0.00 0.00 0.00 2.52
2020 2281 6.032042 CACGCTTAACTTATTACCGCAAAAAG 59.968 38.462 0.00 0.00 0.00 2.27
2108 2377 8.996024 TTAAAGAGCATAAACCAAAATAAGCC 57.004 30.769 0.00 0.00 0.00 4.35
2128 2397 2.098443 ACCGGTGCACAACAACTTAAAG 59.902 45.455 20.43 0.00 31.87 1.85
2146 2587 4.261031 GGTTGCATTTAGCTTACCATACCG 60.261 45.833 0.00 0.00 43.60 4.02
2172 2613 3.930035 AGTCTAGAAGGGGGACATTAGG 58.070 50.000 0.00 0.00 32.27 2.69
2180 2621 2.637872 TGAACACAAGTCTAGAAGGGGG 59.362 50.000 0.00 0.00 0.00 5.40
2293 2742 9.760077 AAGTCGTGAAATCTCTTAAAAGACTTA 57.240 29.630 2.84 0.00 41.53 2.24
2294 2743 8.552034 CAAGTCGTGAAATCTCTTAAAAGACTT 58.448 33.333 0.00 0.00 43.31 3.01
2295 2744 7.926555 TCAAGTCGTGAAATCTCTTAAAAGACT 59.073 33.333 0.00 0.00 36.89 3.24
2296 2745 8.073355 TCAAGTCGTGAAATCTCTTAAAAGAC 57.927 34.615 0.00 0.00 31.51 3.01
2298 2873 7.959651 CCATCAAGTCGTGAAATCTCTTAAAAG 59.040 37.037 0.00 0.00 40.50 2.27
2303 2878 5.152623 TCCATCAAGTCGTGAAATCTCTT 57.847 39.130 0.00 0.00 40.50 2.85
2315 2890 2.756760 ACACCATGCATTCCATCAAGTC 59.243 45.455 0.00 0.00 29.71 3.01
2317 2892 3.429822 GGAACACCATGCATTCCATCAAG 60.430 47.826 10.52 0.00 41.40 3.02
2318 2893 2.496871 GGAACACCATGCATTCCATCAA 59.503 45.455 10.52 0.00 41.40 2.57
2319 2894 2.101783 GGAACACCATGCATTCCATCA 58.898 47.619 10.52 0.00 41.40 3.07
2320 2895 2.101783 TGGAACACCATGCATTCCATC 58.898 47.619 13.51 1.94 45.46 3.51
2321 2896 2.234896 TGGAACACCATGCATTCCAT 57.765 45.000 13.51 0.00 45.46 3.41
2346 2921 9.579932 AGTCCATAGTGAAATCTTCTTTTCTTT 57.420 29.630 0.00 0.00 36.71 2.52
2357 2932 9.796120 GCTCTGTATATAGTCCATAGTGAAATC 57.204 37.037 0.00 0.00 0.00 2.17
2358 2933 9.314133 TGCTCTGTATATAGTCCATAGTGAAAT 57.686 33.333 0.00 0.00 0.00 2.17
2359 2934 8.706322 TGCTCTGTATATAGTCCATAGTGAAA 57.294 34.615 0.00 0.00 0.00 2.69
2360 2935 8.706322 TTGCTCTGTATATAGTCCATAGTGAA 57.294 34.615 0.00 0.00 0.00 3.18
2361 2936 8.706322 TTTGCTCTGTATATAGTCCATAGTGA 57.294 34.615 0.00 0.00 0.00 3.41
2362 2937 9.935241 ATTTTGCTCTGTATATAGTCCATAGTG 57.065 33.333 0.00 0.00 0.00 2.74
2363 2938 9.935241 CATTTTGCTCTGTATATAGTCCATAGT 57.065 33.333 0.00 0.00 0.00 2.12
2366 2941 8.654997 ACTCATTTTGCTCTGTATATAGTCCAT 58.345 33.333 0.00 0.00 0.00 3.41
2367 2942 7.928167 CACTCATTTTGCTCTGTATATAGTCCA 59.072 37.037 0.00 0.00 0.00 4.02
2368 2943 8.144478 TCACTCATTTTGCTCTGTATATAGTCC 58.856 37.037 0.00 0.00 0.00 3.85
2369 2944 9.534565 TTCACTCATTTTGCTCTGTATATAGTC 57.465 33.333 0.00 0.00 0.00 2.59
2375 2950 9.013229 TGTAAATTCACTCATTTTGCTCTGTAT 57.987 29.630 0.00 0.00 0.00 2.29
2376 2951 8.289618 GTGTAAATTCACTCATTTTGCTCTGTA 58.710 33.333 0.00 0.00 35.68 2.74
2377 2952 7.013655 AGTGTAAATTCACTCATTTTGCTCTGT 59.986 33.333 0.00 0.00 44.07 3.41
2378 2953 7.365741 AGTGTAAATTCACTCATTTTGCTCTG 58.634 34.615 0.00 0.00 44.07 3.35
2379 2954 7.516198 AGTGTAAATTCACTCATTTTGCTCT 57.484 32.000 0.00 0.00 44.07 4.09
2397 2972 9.875691 TGTAGATAGACGTACTTTAGAGTGTAA 57.124 33.333 0.00 0.00 36.60 2.41
2462 3037 9.994017 GGTACTACTCCCTCTATTCCTAAATAT 57.006 37.037 0.00 0.00 0.00 1.28
2464 3039 6.947158 CGGTACTACTCCCTCTATTCCTAAAT 59.053 42.308 0.00 0.00 0.00 1.40
2465 3040 6.302269 CGGTACTACTCCCTCTATTCCTAAA 58.698 44.000 0.00 0.00 0.00 1.85
2466 3041 5.747248 GCGGTACTACTCCCTCTATTCCTAA 60.747 48.000 0.00 0.00 0.00 2.69
2467 3042 4.263243 GCGGTACTACTCCCTCTATTCCTA 60.263 50.000 0.00 0.00 0.00 2.94
2469 3044 2.819019 GCGGTACTACTCCCTCTATTCC 59.181 54.545 0.00 0.00 0.00 3.01
2470 3045 2.819019 GGCGGTACTACTCCCTCTATTC 59.181 54.545 0.00 0.00 0.00 1.75
2471 3046 2.813354 CGGCGGTACTACTCCCTCTATT 60.813 54.545 0.00 0.00 0.00 1.73
2472 3047 1.271271 CGGCGGTACTACTCCCTCTAT 60.271 57.143 0.00 0.00 0.00 1.98
2473 3048 0.107456 CGGCGGTACTACTCCCTCTA 59.893 60.000 0.00 0.00 0.00 2.43
2474 3049 1.153005 CGGCGGTACTACTCCCTCT 60.153 63.158 0.00 0.00 0.00 3.69
2475 3050 0.179045 TACGGCGGTACTACTCCCTC 60.179 60.000 13.24 0.00 0.00 4.30
2476 3051 0.464554 GTACGGCGGTACTACTCCCT 60.465 60.000 23.14 0.00 44.53 4.20
2477 3052 2.025719 GTACGGCGGTACTACTCCC 58.974 63.158 23.14 0.00 44.53 4.30
2489 3064 2.028883 GCGACAAGTATTTCTGTACGGC 59.971 50.000 0.00 0.00 0.00 5.68
2539 3114 4.274705 CGCTCAGACGGATATATCTAGCAT 59.725 45.833 12.42 0.00 0.00 3.79
2542 3117 5.398176 GTCGCTCAGACGGATATATCTAG 57.602 47.826 12.42 9.38 40.43 2.43
2556 3131 0.249073 CGGGGATACTTGTCGCTCAG 60.249 60.000 0.00 0.00 0.00 3.35
2571 3265 0.033405 TGTACTCTCTCCTTCCGGGG 60.033 60.000 0.00 0.00 35.33 5.73
2572 3266 2.074729 ATGTACTCTCTCCTTCCGGG 57.925 55.000 0.00 0.00 0.00 5.73
2578 3272 7.124298 TGCAAATTGTACTATGTACTCTCTCCT 59.876 37.037 8.94 0.00 0.00 3.69
2591 3285 7.035004 GCCATGAATTTCTGCAAATTGTACTA 58.965 34.615 1.10 0.00 41.47 1.82
2592 3286 5.870978 GCCATGAATTTCTGCAAATTGTACT 59.129 36.000 1.10 0.00 41.47 2.73
2593 3287 5.220265 CGCCATGAATTTCTGCAAATTGTAC 60.220 40.000 1.10 0.00 41.47 2.90
2594 3288 4.863689 CGCCATGAATTTCTGCAAATTGTA 59.136 37.500 1.10 0.00 41.47 2.41
2595 3289 3.680937 CGCCATGAATTTCTGCAAATTGT 59.319 39.130 1.10 0.00 41.47 2.71
2596 3290 3.927758 TCGCCATGAATTTCTGCAAATTG 59.072 39.130 1.10 0.00 41.47 2.32
2603 3494 3.113322 CTGCATTCGCCATGAATTTCTG 58.887 45.455 0.00 0.00 45.06 3.02
2604 3495 2.100252 CCTGCATTCGCCATGAATTTCT 59.900 45.455 0.00 0.00 45.06 2.52
2612 3503 4.445710 TGCCCCTGCATTCGCCAT 62.446 61.111 0.00 0.00 44.23 4.40
2634 3525 3.354131 TGCGTAGAATGCATGCGTA 57.646 47.368 13.96 0.00 34.76 4.42
2668 3562 7.445945 AGGACTATTCATATAAACCAGCTCAC 58.554 38.462 0.00 0.00 0.00 3.51
2742 3636 1.825191 GATGGTGCGGGTGATGCAT 60.825 57.895 0.00 0.00 45.34 3.96
2744 3638 2.124570 AGATGGTGCGGGTGATGC 60.125 61.111 0.00 0.00 0.00 3.91
2745 3639 1.524621 GGAGATGGTGCGGGTGATG 60.525 63.158 0.00 0.00 0.00 3.07
2755 3649 4.600062 GGTTTGAAAGTATGGGAGATGGT 58.400 43.478 0.00 0.00 0.00 3.55
2759 3653 4.627284 TTCGGTTTGAAAGTATGGGAGA 57.373 40.909 0.00 0.00 32.37 3.71
2777 3671 7.471563 CGAACGAAACTTAATTCAAACTTTCG 58.528 34.615 8.38 8.38 39.75 3.46
2784 3678 8.875803 ACTATATGCGAACGAAACTTAATTCAA 58.124 29.630 0.00 0.00 0.00 2.69
2785 3679 8.415192 ACTATATGCGAACGAAACTTAATTCA 57.585 30.769 0.00 0.00 0.00 2.57
2786 3680 9.698617 AAACTATATGCGAACGAAACTTAATTC 57.301 29.630 0.00 0.00 0.00 2.17
2796 3690 6.469139 TTTGTTGAAACTATATGCGAACGA 57.531 33.333 0.00 0.00 0.00 3.85
2849 3744 6.321435 GGGCTAGGAAAACAGTAGCATAATTT 59.679 38.462 3.22 0.00 40.87 1.82
2872 3767 1.568597 TGGGTAGATTGAACATGGGGG 59.431 52.381 0.00 0.00 0.00 5.40
2924 3819 6.222038 TGGATATCCGGCTAAAGATACATC 57.778 41.667 17.04 0.00 39.43 3.06
2927 3822 6.472686 AGATGGATATCCGGCTAAAGATAC 57.527 41.667 17.04 0.00 39.43 2.24


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

AutoCloner maintained by Alex Coulton.