Multiple sequence alignment - TraesCS5D01G543700

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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 TraesCS5D01G543700 chr5D 100.000 3690 0 0 887 4576 553758451 553762140 0.000000e+00 6815.0
1 TraesCS5D01G543700 chr5D 100.000 474 0 0 1 474 553757565 553758038 0.000000e+00 876.0
2 TraesCS5D01G543700 chr5D 87.838 370 37 5 3762 4129 553865858 553866221 1.180000e-115 427.0
3 TraesCS5D01G543700 chr5D 95.588 68 3 0 2570 2637 553759987 553760054 4.840000e-20 110.0
4 TraesCS5D01G543700 chr5D 95.588 68 3 0 2423 2490 553760134 553760201 4.840000e-20 110.0
5 TraesCS5D01G543700 chr5D 93.617 47 2 1 948 994 553758451 553758496 8.210000e-08 69.4
6 TraesCS5D01G543700 chr5D 93.617 47 2 1 887 932 553758512 553758558 8.210000e-08 69.4
7 TraesCS5D01G543700 chr5B 96.303 1569 41 7 934 2493 697095638 697094078 0.000000e+00 2560.0
8 TraesCS5D01G543700 chr5B 95.167 1138 50 5 2570 3707 697094148 697093016 0.000000e+00 1792.0
9 TraesCS5D01G543700 chr5B 86.398 1588 179 19 989 2563 697030672 697029109 0.000000e+00 1701.0
10 TraesCS5D01G543700 chr5B 91.183 862 58 6 3718 4576 697085210 697084364 0.000000e+00 1155.0
11 TraesCS5D01G543700 chr5B 82.511 669 92 17 3119 3774 697029159 697028503 8.590000e-157 564.0
12 TraesCS5D01G543700 chr5B 93.304 224 15 0 3 226 697111814 697111591 9.490000e-87 331.0
13 TraesCS5D01G543700 chr5B 85.990 207 25 3 4 210 697033175 697032973 7.710000e-53 219.0
14 TraesCS5D01G543700 chr5B 91.549 71 6 0 2570 2640 697029252 697029182 1.050000e-16 99.0
15 TraesCS5D01G543700 chr4A 90.945 751 56 4 3828 4576 614863396 614862656 0.000000e+00 1000.0
16 TraesCS5D01G543700 chr4A 95.372 605 15 2 2178 2769 614864023 614863419 0.000000e+00 950.0
17 TraesCS5D01G543700 chr4A 96.163 443 17 0 1356 1798 614864471 614864029 0.000000e+00 725.0
18 TraesCS5D01G543700 chr4A 96.203 395 14 1 933 1327 614864859 614864466 0.000000e+00 645.0
19 TraesCS5D01G543700 chr4A 85.786 401 47 6 3 398 614865321 614864926 2.550000e-112 416.0
20 TraesCS5D01G543700 chr4A 94.366 71 4 0 2423 2493 614863618 614863548 4.840000e-20 110.0
21 TraesCS5D01G543700 chr6A 73.011 1508 306 65 1015 2481 33404264 33405711 1.950000e-118 436.0
22 TraesCS5D01G543700 chr6A 75.517 919 146 42 3252 4129 45414376 45413496 1.200000e-100 377.0
23 TraesCS5D01G543700 chr6A 84.211 361 42 10 3769 4125 33532294 33532643 2.040000e-88 337.0
24 TraesCS5D01G543700 chr6A 76.449 535 94 25 999 1526 30455108 30455617 1.260000e-65 261.0
25 TraesCS5D01G543700 chr6A 84.874 119 15 3 3100 3216 47447498 47447381 2.890000e-22 117.0
26 TraesCS5D01G543700 chr6A 84.874 119 15 3 3100 3216 47459227 47459110 2.890000e-22 117.0
27 TraesCS5D01G543700 chr6A 86.667 60 6 1 2433 2490 33015574 33015515 1.060000e-06 65.8
28 TraesCS5D01G543700 chr6A 84.483 58 8 1 1470 1526 28258067 28258010 6.400000e-04 56.5
29 TraesCS5D01G543700 chr6B 76.220 799 123 37 3252 4013 78446571 78445803 1.210000e-95 361.0
30 TraesCS5D01G543700 chr6B 83.611 360 46 9 3769 4125 60659467 60659816 4.410000e-85 326.0
31 TraesCS5D01G543700 chr6B 83.056 360 48 9 3769 4125 60625250 60625599 9.560000e-82 315.0
32 TraesCS5D01G543700 chr6B 77.679 448 81 13 2045 2481 59828330 59827891 5.880000e-64 255.0
33 TraesCS5D01G543700 chr6B 83.105 219 32 4 999 1213 45551861 45552078 1.300000e-45 195.0
34 TraesCS5D01G543700 chr6B 79.058 191 30 10 3860 4045 78592634 78592819 6.220000e-24 122.0
35 TraesCS5D01G543700 chr6B 75.124 201 41 5 2290 2481 78447240 78447040 8.160000e-13 86.1
36 TraesCS5D01G543700 chr6B 84.483 58 8 1 1470 1526 49052494 49052437 6.400000e-04 56.5
37 TraesCS5D01G543700 chr6D 84.821 224 28 4 3780 4003 29098043 29097826 2.140000e-53 220.0
38 TraesCS5D01G543700 chr6D 86.207 58 8 0 1469 1526 26516694 26516751 3.820000e-06 63.9
39 TraesCS5D01G543700 chr6D 84.483 58 8 1 1470 1526 26816327 26816270 6.400000e-04 56.5
40 TraesCS5D01G543700 chr6D 84.483 58 8 1 1470 1526 26860075 26860018 6.400000e-04 56.5
41 TraesCS5D01G543700 chr6D 84.483 58 8 1 1470 1526 26896415 26896358 6.400000e-04 56.5
42 TraesCS5D01G543700 chrUn 83.105 219 31 5 999 1213 95016320 95016536 1.300000e-45 195.0


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 TraesCS5D01G543700 chr5D 553757565 553762140 4575 False 1341.633333 6815 96.401667 1 4576 6 chr5D.!!$F2 4575
1 TraesCS5D01G543700 chr5B 697093016 697095638 2622 True 2176.000000 2560 95.735000 934 3707 2 chr5B.!!$R4 2773
2 TraesCS5D01G543700 chr5B 697084364 697085210 846 True 1155.000000 1155 91.183000 3718 4576 1 chr5B.!!$R1 858
3 TraesCS5D01G543700 chr5B 697028503 697033175 4672 True 645.750000 1701 86.612000 4 3774 4 chr5B.!!$R3 3770
4 TraesCS5D01G543700 chr4A 614862656 614865321 2665 True 641.000000 1000 93.139167 3 4576 6 chr4A.!!$R1 4573
5 TraesCS5D01G543700 chr6A 33404264 33405711 1447 False 436.000000 436 73.011000 1015 2481 1 chr6A.!!$F2 1466
6 TraesCS5D01G543700 chr6A 45413496 45414376 880 True 377.000000 377 75.517000 3252 4129 1 chr6A.!!$R3 877
7 TraesCS5D01G543700 chr6A 30455108 30455617 509 False 261.000000 261 76.449000 999 1526 1 chr6A.!!$F1 527
8 TraesCS5D01G543700 chr6B 78445803 78447240 1437 True 223.550000 361 75.672000 2290 4013 2 chr6B.!!$R3 1723

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
35 36 0.247736 CAGGCCTTTAGCGTCAGTCT 59.752 55.0 0.0 0.0 45.17 3.24 F
211 212 0.310543 GGCAAATCACAGTCGCAACA 59.689 50.0 0.0 0.0 0.00 3.33 F
224 225 0.595588 CGCAACAAATGTAGCACCCA 59.404 50.0 0.0 0.0 0.00 4.51 F
1756 3875 0.391661 CTTGATACCTGTGCCTGCGT 60.392 55.0 0.0 0.0 0.00 5.24 F
1757 3876 0.673333 TTGATACCTGTGCCTGCGTG 60.673 55.0 0.0 0.0 0.00 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 3875 0.107214 CCGCTCCCTAAATCCAAGCA 60.107 55.000 0.00 0.0 33.21 3.91 R
1757 3876 1.448119 GCCGCTCCCTAAATCCAAGC 61.448 60.000 0.00 0.0 0.00 4.01 R
2197 4318 2.268076 ACGAAAGGGTGTGCATGGC 61.268 57.895 0.00 0.0 0.00 4.40 R
3548 5735 1.164411 TGTGCAAAATACCAGCTCCG 58.836 50.000 0.00 0.0 0.00 4.63 R
3712 5914 5.144100 AGAGAAAGTCTTTGACTCCTCTCA 58.856 41.667 25.08 0.0 44.77 3.27 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
32 33 0.460987 CTCCAGGCCTTTAGCGTCAG 60.461 60.000 0.00 0.00 45.17 3.51
35 36 0.247736 CAGGCCTTTAGCGTCAGTCT 59.752 55.000 0.00 0.00 45.17 3.24
39 40 2.622436 GCCTTTAGCGTCAGTCTGATT 58.378 47.619 5.68 0.00 0.00 2.57
49 50 4.319766 GCGTCAGTCTGATTGTTTGATGTT 60.320 41.667 5.68 0.00 0.00 2.71
64 65 8.260270 TGTTTGATGTTCACTTCTATCAGATG 57.740 34.615 0.00 0.00 31.85 2.90
65 66 8.096414 TGTTTGATGTTCACTTCTATCAGATGA 58.904 33.333 0.00 0.00 31.85 2.92
66 67 9.107177 GTTTGATGTTCACTTCTATCAGATGAT 57.893 33.333 0.31 0.31 38.51 2.45
160 161 4.593956 AGAGTTTATTCCCTGGAAGCTTG 58.406 43.478 2.10 0.00 37.56 4.01
184 185 5.036117 ACGGGAACATAATAGAGTTGCAT 57.964 39.130 0.00 0.00 37.75 3.96
211 212 0.310543 GGCAAATCACAGTCGCAACA 59.689 50.000 0.00 0.00 0.00 3.33
224 225 0.595588 CGCAACAAATGTAGCACCCA 59.404 50.000 0.00 0.00 0.00 4.51
237 239 2.711542 AGCACCCATGTTTAGCTACAC 58.288 47.619 2.95 2.95 33.06 2.90
241 243 3.935203 CACCCATGTTTAGCTACACAGAG 59.065 47.826 17.17 12.06 0.00 3.35
242 244 3.838317 ACCCATGTTTAGCTACACAGAGA 59.162 43.478 17.17 0.00 0.00 3.10
244 246 5.221843 ACCCATGTTTAGCTACACAGAGAAA 60.222 40.000 17.17 0.00 0.00 2.52
248 250 4.101898 TGTTTAGCTACACAGAGAAACCCA 59.898 41.667 8.66 0.00 31.63 4.51
250 252 6.014070 TGTTTAGCTACACAGAGAAACCCATA 60.014 38.462 8.66 0.00 31.63 2.74
251 253 6.614694 TTAGCTACACAGAGAAACCCATAA 57.385 37.500 0.00 0.00 0.00 1.90
261 263 9.177608 CACAGAGAAACCCATAAATAGATGAAA 57.822 33.333 0.00 0.00 0.00 2.69
323 2373 6.428385 AACTCTCATATTCCTCGCAAAAAG 57.572 37.500 0.00 0.00 0.00 2.27
324 2374 5.491982 ACTCTCATATTCCTCGCAAAAAGT 58.508 37.500 0.00 0.00 0.00 2.66
329 2379 8.956426 TCTCATATTCCTCGCAAAAAGTAAAAT 58.044 29.630 0.00 0.00 0.00 1.82
357 2407 2.561858 AGGGACGGAGAGTTAAAGTGTC 59.438 50.000 0.00 0.00 0.00 3.67
446 2496 8.491045 TTTTGAGACAATTTAGGGGATTTTCT 57.509 30.769 0.00 0.00 0.00 2.52
447 2497 8.491045 TTTGAGACAATTTAGGGGATTTTCTT 57.509 30.769 0.00 0.00 0.00 2.52
448 2498 8.491045 TTGAGACAATTTAGGGGATTTTCTTT 57.509 30.769 0.00 0.00 0.00 2.52
449 2499 8.491045 TGAGACAATTTAGGGGATTTTCTTTT 57.509 30.769 0.00 0.00 0.00 2.27
450 2500 8.367156 TGAGACAATTTAGGGGATTTTCTTTTG 58.633 33.333 0.00 0.00 0.00 2.44
452 2502 8.588472 AGACAATTTAGGGGATTTTCTTTTGAG 58.412 33.333 0.00 0.00 0.00 3.02
453 2503 8.491045 ACAATTTAGGGGATTTTCTTTTGAGA 57.509 30.769 0.00 0.00 0.00 3.27
454 2504 8.367911 ACAATTTAGGGGATTTTCTTTTGAGAC 58.632 33.333 0.00 0.00 0.00 3.36
455 2505 8.367156 CAATTTAGGGGATTTTCTTTTGAGACA 58.633 33.333 0.00 0.00 0.00 3.41
456 2506 7.906199 TTTAGGGGATTTTCTTTTGAGACAA 57.094 32.000 0.00 0.00 0.00 3.18
457 2507 8.491045 TTTAGGGGATTTTCTTTTGAGACAAT 57.509 30.769 0.00 0.00 0.00 2.71
458 2508 8.491045 TTAGGGGATTTTCTTTTGAGACAATT 57.509 30.769 0.00 0.00 0.00 2.32
460 2510 8.491045 AGGGGATTTTCTTTTGAGACAATTTA 57.509 30.769 0.00 0.00 0.00 1.40
461 2511 8.588472 AGGGGATTTTCTTTTGAGACAATTTAG 58.412 33.333 0.00 0.00 0.00 1.85
462 2512 7.819415 GGGGATTTTCTTTTGAGACAATTTAGG 59.181 37.037 0.00 0.00 0.00 2.69
463 2513 7.819415 GGGATTTTCTTTTGAGACAATTTAGGG 59.181 37.037 0.00 0.00 0.00 3.53
464 2514 7.819415 GGATTTTCTTTTGAGACAATTTAGGGG 59.181 37.037 0.00 0.00 0.00 4.79
465 2515 6.664428 TTTCTTTTGAGACAATTTAGGGGG 57.336 37.500 0.00 0.00 0.00 5.40
466 2516 5.592587 TCTTTTGAGACAATTTAGGGGGA 57.407 39.130 0.00 0.00 0.00 4.81
467 2517 5.959512 TCTTTTGAGACAATTTAGGGGGAA 58.040 37.500 0.00 0.00 0.00 3.97
468 2518 6.377912 TCTTTTGAGACAATTTAGGGGGAAA 58.622 36.000 0.00 0.00 0.00 3.13
469 2519 6.841755 TCTTTTGAGACAATTTAGGGGGAAAA 59.158 34.615 0.00 0.00 0.00 2.29
470 2520 7.512402 TCTTTTGAGACAATTTAGGGGGAAAAT 59.488 33.333 0.00 0.00 0.00 1.82
471 2521 6.850752 TTGAGACAATTTAGGGGGAAAATC 57.149 37.500 0.00 0.00 0.00 2.17
472 2522 5.269189 TGAGACAATTTAGGGGGAAAATCC 58.731 41.667 0.00 0.00 35.23 3.01
473 2523 5.222442 TGAGACAATTTAGGGGGAAAATCCA 60.222 40.000 0.00 0.00 38.64 3.41
909 2959 3.569210 CCCTCAGCCCACCACACA 61.569 66.667 0.00 0.00 0.00 3.72
910 2960 2.281761 CCTCAGCCCACCACACAC 60.282 66.667 0.00 0.00 0.00 3.82
911 2961 2.510411 CTCAGCCCACCACACACA 59.490 61.111 0.00 0.00 0.00 3.72
912 2962 1.893808 CTCAGCCCACCACACACAC 60.894 63.158 0.00 0.00 0.00 3.82
913 2963 2.906897 CAGCCCACCACACACACC 60.907 66.667 0.00 0.00 0.00 4.16
914 2964 4.204028 AGCCCACCACACACACCC 62.204 66.667 0.00 0.00 0.00 4.61
916 2966 4.947147 CCCACCACACACACCCCG 62.947 72.222 0.00 0.00 0.00 5.73
917 2967 3.867783 CCACCACACACACCCCGA 61.868 66.667 0.00 0.00 0.00 5.14
918 2968 2.190843 CACCACACACACCCCGAA 59.809 61.111 0.00 0.00 0.00 4.30
919 2969 1.891919 CACCACACACACCCCGAAG 60.892 63.158 0.00 0.00 0.00 3.79
920 2970 2.978010 CCACACACACCCCGAAGC 60.978 66.667 0.00 0.00 0.00 3.86
921 2971 2.978010 CACACACACCCCGAAGCC 60.978 66.667 0.00 0.00 0.00 4.35
922 2972 4.619227 ACACACACCCCGAAGCCG 62.619 66.667 0.00 0.00 0.00 5.52
927 2977 4.776322 CACCCCGAAGCCGCATGA 62.776 66.667 0.00 0.00 0.00 3.07
928 2978 4.473520 ACCCCGAAGCCGCATGAG 62.474 66.667 0.00 0.00 0.00 2.90
929 2979 4.473520 CCCCGAAGCCGCATGAGT 62.474 66.667 0.00 0.00 0.00 3.41
930 2980 2.499205 CCCGAAGCCGCATGAGTA 59.501 61.111 0.00 0.00 0.00 2.59
931 2981 1.592669 CCCGAAGCCGCATGAGTAG 60.593 63.158 0.00 0.00 0.00 2.57
977 3027 4.596585 CCCACCACACACACCCCC 62.597 72.222 0.00 0.00 0.00 5.40
978 3028 3.814906 CCACCACACACACCCCCA 61.815 66.667 0.00 0.00 0.00 4.96
1083 3178 4.924187 ATCCTCCTCCGCCTCCCG 62.924 72.222 0.00 0.00 0.00 5.14
1161 3256 0.967887 CCTCCGACTCAGCCTTCTCA 60.968 60.000 0.00 0.00 0.00 3.27
1545 3643 1.274069 ACTGATGGTGAGGAGGGACAT 60.274 52.381 0.00 0.00 0.00 3.06
1635 3748 2.589720 CTTCCATCCAAGCATGCCATA 58.410 47.619 15.66 0.00 0.00 2.74
1692 3805 6.454795 GGATTTCATTTACTGGTTGCTCAAA 58.545 36.000 0.00 0.00 0.00 2.69
1756 3875 0.391661 CTTGATACCTGTGCCTGCGT 60.392 55.000 0.00 0.00 0.00 5.24
1757 3876 0.673333 TTGATACCTGTGCCTGCGTG 60.673 55.000 0.00 0.00 0.00 5.34
2288 4417 6.815142 GCTGCTTGATGACCTTTCAAAATATT 59.185 34.615 0.00 0.00 34.61 1.28
2330 4460 2.093500 TCTATTCTGATGCTTGCACGGT 60.093 45.455 0.00 0.00 0.00 4.83
2818 4966 4.946784 ACAACAGTGTGAAGTTGAAGAC 57.053 40.909 11.72 0.00 46.01 3.01
2843 4991 4.402155 ACTCCATGAAAACTTGCTTGAACA 59.598 37.500 0.00 0.00 0.00 3.18
2866 5014 6.204882 ACAAACTGAAATGTCAAGTAGGTAGC 59.795 38.462 0.00 0.00 31.88 3.58
2884 5032 7.321717 AGGTAGCTCAATATGTACATTGGAT 57.678 36.000 14.77 0.00 36.69 3.41
2910 5058 8.656849 TGCTTAAAGCTAGTTCTATTTCTTTCG 58.343 33.333 0.00 0.00 42.97 3.46
2931 5082 9.907576 CTTTCGTTCAATATTGTTATCTCTGAC 57.092 33.333 14.97 1.98 0.00 3.51
3091 5249 7.033530 TCAAGCCAAATTTACTCGAAAAAGA 57.966 32.000 0.00 0.00 0.00 2.52
3331 5490 5.847111 AGGTAATAGTTCGAGTGTGCATA 57.153 39.130 0.00 0.00 0.00 3.14
3342 5501 8.677300 AGTTCGAGTGTGCATATTCATTTTTAT 58.323 29.630 6.76 0.00 0.00 1.40
3400 5565 4.638421 TGTCAGTAGGTCTGGTTTTGTTTG 59.362 41.667 0.00 0.00 43.76 2.93
3408 5573 3.305897 GTCTGGTTTTGTTTGCCTTTTCG 59.694 43.478 0.00 0.00 0.00 3.46
3518 5705 7.661127 TGGCTTTTCATTGATCATTTGAAAG 57.339 32.000 22.92 18.33 39.67 2.62
3548 5735 1.717194 CAGAAACATGCATTGGTGGC 58.283 50.000 0.00 0.00 0.00 5.01
3712 5914 7.094205 CCTTTTACTGCCATTTCTCAAGTACAT 60.094 37.037 0.00 0.00 0.00 2.29
4041 6244 0.035915 GTGCAGGTTCTTCTCCCTCC 60.036 60.000 0.00 0.00 0.00 4.30
4172 6375 2.388890 GATGGCCAGGCACGCTCTAT 62.389 60.000 15.19 0.00 0.00 1.98
4174 6377 2.501128 GCCAGGCACGCTCTATGA 59.499 61.111 6.55 0.00 0.00 2.15
4176 6379 0.533755 GCCAGGCACGCTCTATGAAT 60.534 55.000 6.55 0.00 0.00 2.57
4184 6387 1.451936 GCTCTATGAATGGGCCCGT 59.548 57.895 19.37 15.91 0.00 5.28
4185 6388 0.685097 GCTCTATGAATGGGCCCGTA 59.315 55.000 19.47 1.96 0.00 4.02
4226 6429 3.957435 ATGGCTCTCGTCGGGACCA 62.957 63.158 15.71 15.71 0.00 4.02
4356 6562 2.548067 GGGTGGATGACTTATCGCGATT 60.548 50.000 28.81 9.60 36.62 3.34
4360 6566 5.335426 GGTGGATGACTTATCGCGATTACTA 60.335 44.000 28.81 5.97 36.62 1.82
4391 6597 2.039137 GGAGTCGACCCTTCCCCT 59.961 66.667 13.01 0.00 0.00 4.79
4487 6693 1.080230 CCGAGAGTGACACCAGCAG 60.080 63.158 0.84 0.00 0.00 4.24
4561 6767 2.435586 CAGCGGTCTCCTTGCCTG 60.436 66.667 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.203287 GCCTGGAGATTTTTGCTCACC 59.797 52.381 0.00 0.00 34.07 4.02
1 2 1.203287 GGCCTGGAGATTTTTGCTCAC 59.797 52.381 0.00 0.00 34.07 3.51
16 17 0.247736 AGACTGACGCTAAAGGCCTG 59.752 55.000 5.69 0.00 37.74 4.85
32 33 6.963796 AGAAGTGAACATCAAACAATCAGAC 58.036 36.000 0.00 0.00 0.00 3.51
35 36 8.620116 TGATAGAAGTGAACATCAAACAATCA 57.380 30.769 0.00 0.00 0.00 2.57
39 40 8.096414 TCATCTGATAGAAGTGAACATCAAACA 58.904 33.333 0.00 0.00 0.00 2.83
64 65 6.349973 TGAACGTTTCAAGCTATCATCATC 57.650 37.500 0.46 0.00 36.59 2.92
65 66 6.741992 TTGAACGTTTCAAGCTATCATCAT 57.258 33.333 0.46 0.00 44.21 2.45
81 82 0.322187 GGTGCCCATAGGTTGAACGT 60.322 55.000 0.00 0.00 34.57 3.99
102 103 0.871722 TTTTGATCTCCGTGGTTGCG 59.128 50.000 0.00 0.00 0.00 4.85
160 161 3.808174 GCAACTCTATTATGTTCCCGTCC 59.192 47.826 0.00 0.00 0.00 4.79
184 185 3.555547 CGACTGTGATTTGCCGAATGATA 59.444 43.478 0.00 0.00 0.00 2.15
211 212 4.344104 AGCTAAACATGGGTGCTACATTT 58.656 39.130 0.00 0.00 31.71 2.32
224 225 5.221843 TGGGTTTCTCTGTGTAGCTAAACAT 60.222 40.000 17.16 0.00 33.53 2.71
340 2390 3.504906 TGATCGACACTTTAACTCTCCGT 59.495 43.478 0.00 0.00 0.00 4.69
344 2394 7.787725 AAAAGTTGATCGACACTTTAACTCT 57.212 32.000 15.59 0.00 33.27 3.24
420 2470 8.933653 AGAAAATCCCCTAAATTGTCTCAAAAA 58.066 29.630 0.00 0.00 26.48 1.94
421 2471 8.491045 AGAAAATCCCCTAAATTGTCTCAAAA 57.509 30.769 0.00 0.00 26.48 2.44
422 2472 8.491045 AAGAAAATCCCCTAAATTGTCTCAAA 57.509 30.769 0.00 0.00 30.93 2.69
425 2475 8.585018 TCAAAAGAAAATCCCCTAAATTGTCTC 58.415 33.333 0.00 0.00 30.93 3.36
426 2476 8.491045 TCAAAAGAAAATCCCCTAAATTGTCT 57.509 30.769 0.00 0.00 33.07 3.41
428 2478 8.367911 GTCTCAAAAGAAAATCCCCTAAATTGT 58.632 33.333 0.00 0.00 31.93 2.71
430 2480 8.491045 TGTCTCAAAAGAAAATCCCCTAAATT 57.509 30.769 0.00 0.00 31.93 1.82
431 2481 8.491045 TTGTCTCAAAAGAAAATCCCCTAAAT 57.509 30.769 0.00 0.00 31.93 1.40
432 2482 7.906199 TTGTCTCAAAAGAAAATCCCCTAAA 57.094 32.000 0.00 0.00 31.93 1.85
433 2483 8.491045 AATTGTCTCAAAAGAAAATCCCCTAA 57.509 30.769 0.00 0.00 38.32 2.69
434 2484 8.491045 AAATTGTCTCAAAAGAAAATCCCCTA 57.509 30.769 0.00 0.00 38.32 3.53
435 2485 7.379059 AAATTGTCTCAAAAGAAAATCCCCT 57.621 32.000 0.00 0.00 38.32 4.79
436 2486 7.819415 CCTAAATTGTCTCAAAAGAAAATCCCC 59.181 37.037 0.00 0.00 38.32 4.81
437 2487 7.819415 CCCTAAATTGTCTCAAAAGAAAATCCC 59.181 37.037 0.00 0.00 38.32 3.85
438 2488 7.819415 CCCCTAAATTGTCTCAAAAGAAAATCC 59.181 37.037 0.00 0.00 38.32 3.01
439 2489 7.819415 CCCCCTAAATTGTCTCAAAAGAAAATC 59.181 37.037 0.00 0.00 38.32 2.17
440 2490 7.512402 TCCCCCTAAATTGTCTCAAAAGAAAAT 59.488 33.333 0.00 0.00 40.56 1.82
441 2491 6.841755 TCCCCCTAAATTGTCTCAAAAGAAAA 59.158 34.615 0.00 0.00 33.21 2.29
442 2492 6.377912 TCCCCCTAAATTGTCTCAAAAGAAA 58.622 36.000 0.00 0.00 31.93 2.52
443 2493 5.959512 TCCCCCTAAATTGTCTCAAAAGAA 58.040 37.500 0.00 0.00 31.93 2.52
444 2494 5.592587 TCCCCCTAAATTGTCTCAAAAGA 57.407 39.130 0.00 0.00 0.00 2.52
445 2495 6.664428 TTTCCCCCTAAATTGTCTCAAAAG 57.336 37.500 0.00 0.00 0.00 2.27
446 2496 7.256511 GGATTTTCCCCCTAAATTGTCTCAAAA 60.257 37.037 0.00 0.00 0.00 2.44
447 2497 6.212589 GGATTTTCCCCCTAAATTGTCTCAAA 59.787 38.462 0.00 0.00 0.00 2.69
448 2498 5.719563 GGATTTTCCCCCTAAATTGTCTCAA 59.280 40.000 0.00 0.00 0.00 3.02
449 2499 5.222442 TGGATTTTCCCCCTAAATTGTCTCA 60.222 40.000 0.00 0.00 35.03 3.27
450 2500 5.269189 TGGATTTTCCCCCTAAATTGTCTC 58.731 41.667 0.00 0.00 35.03 3.36
892 2942 3.569210 TGTGTGGTGGGCTGAGGG 61.569 66.667 0.00 0.00 0.00 4.30
893 2943 2.281761 GTGTGTGGTGGGCTGAGG 60.282 66.667 0.00 0.00 0.00 3.86
894 2944 1.893808 GTGTGTGTGGTGGGCTGAG 60.894 63.158 0.00 0.00 0.00 3.35
895 2945 2.191908 GTGTGTGTGGTGGGCTGA 59.808 61.111 0.00 0.00 0.00 4.26
896 2946 2.906897 GGTGTGTGTGGTGGGCTG 60.907 66.667 0.00 0.00 0.00 4.85
897 2947 4.204028 GGGTGTGTGTGGTGGGCT 62.204 66.667 0.00 0.00 0.00 5.19
899 2949 4.947147 CGGGGTGTGTGTGGTGGG 62.947 72.222 0.00 0.00 0.00 4.61
900 2950 3.408099 TTCGGGGTGTGTGTGGTGG 62.408 63.158 0.00 0.00 0.00 4.61
901 2951 1.891919 CTTCGGGGTGTGTGTGGTG 60.892 63.158 0.00 0.00 0.00 4.17
902 2952 2.508928 CTTCGGGGTGTGTGTGGT 59.491 61.111 0.00 0.00 0.00 4.16
903 2953 2.978010 GCTTCGGGGTGTGTGTGG 60.978 66.667 0.00 0.00 0.00 4.17
904 2954 2.978010 GGCTTCGGGGTGTGTGTG 60.978 66.667 0.00 0.00 0.00 3.82
905 2955 4.619227 CGGCTTCGGGGTGTGTGT 62.619 66.667 0.00 0.00 0.00 3.72
910 2960 4.776322 TCATGCGGCTTCGGGGTG 62.776 66.667 0.00 0.00 0.00 4.61
911 2961 4.473520 CTCATGCGGCTTCGGGGT 62.474 66.667 0.00 0.00 0.00 4.95
912 2962 2.978452 CTACTCATGCGGCTTCGGGG 62.978 65.000 0.00 0.00 0.00 5.73
913 2963 1.592669 CTACTCATGCGGCTTCGGG 60.593 63.158 0.00 0.00 0.00 5.14
914 2964 0.384309 TACTACTCATGCGGCTTCGG 59.616 55.000 0.00 0.00 0.00 4.30
915 2965 1.600663 CCTACTACTCATGCGGCTTCG 60.601 57.143 0.00 0.00 0.00 3.79
916 2966 1.269831 CCCTACTACTCATGCGGCTTC 60.270 57.143 0.00 0.00 0.00 3.86
917 2967 0.753262 CCCTACTACTCATGCGGCTT 59.247 55.000 0.00 0.00 0.00 4.35
918 2968 1.749334 GCCCTACTACTCATGCGGCT 61.749 60.000 0.00 0.00 32.09 5.52
919 2969 1.301009 GCCCTACTACTCATGCGGC 60.301 63.158 0.00 0.00 0.00 6.53
920 2970 0.464036 TTGCCCTACTACTCATGCGG 59.536 55.000 0.00 0.00 0.00 5.69
921 2971 1.409064 TCTTGCCCTACTACTCATGCG 59.591 52.381 0.00 0.00 0.00 4.73
922 2972 2.799917 CGTCTTGCCCTACTACTCATGC 60.800 54.545 0.00 0.00 0.00 4.06
923 2973 2.688446 TCGTCTTGCCCTACTACTCATG 59.312 50.000 0.00 0.00 0.00 3.07
924 2974 2.952978 CTCGTCTTGCCCTACTACTCAT 59.047 50.000 0.00 0.00 0.00 2.90
925 2975 2.366533 CTCGTCTTGCCCTACTACTCA 58.633 52.381 0.00 0.00 0.00 3.41
926 2976 1.065851 GCTCGTCTTGCCCTACTACTC 59.934 57.143 0.00 0.00 0.00 2.59
927 2977 1.104630 GCTCGTCTTGCCCTACTACT 58.895 55.000 0.00 0.00 0.00 2.57
928 2978 0.102663 GGCTCGTCTTGCCCTACTAC 59.897 60.000 0.00 0.00 44.32 2.73
929 2979 2.501492 GGCTCGTCTTGCCCTACTA 58.499 57.895 0.00 0.00 44.32 1.82
930 2980 3.300013 GGCTCGTCTTGCCCTACT 58.700 61.111 0.00 0.00 44.32 2.57
977 3027 2.507102 CCTACTCGTGCGGCTGTG 60.507 66.667 0.00 0.00 0.00 3.66
978 3028 3.760035 CCCTACTCGTGCGGCTGT 61.760 66.667 0.00 0.00 0.00 4.40
1150 3245 4.742201 GCGGCGTGAGAAGGCTGA 62.742 66.667 9.37 0.00 37.75 4.26
1433 3528 0.178947 AGCAATTTTGAACCCCGGGA 60.179 50.000 26.32 0.00 0.00 5.14
1545 3643 4.202080 ACGTAGGCAATCGCTTCTGTAATA 60.202 41.667 0.00 0.00 38.60 0.98
1692 3805 5.982356 TCAAACTCAAGAATCTCATCCGAT 58.018 37.500 0.00 0.00 0.00 4.18
1756 3875 0.107214 CCGCTCCCTAAATCCAAGCA 60.107 55.000 0.00 0.00 33.21 3.91
1757 3876 1.448119 GCCGCTCCCTAAATCCAAGC 61.448 60.000 0.00 0.00 0.00 4.01
2197 4318 2.268076 ACGAAAGGGTGTGCATGGC 61.268 57.895 0.00 0.00 0.00 4.40
2288 4417 6.596309 AGAACACTAGAGAACATCATCACA 57.404 37.500 0.00 0.00 0.00 3.58
2600 4748 9.454859 AAAGTGAAATATAGTTTGCTAGCTCTT 57.545 29.630 17.23 1.66 0.00 2.85
2733 4881 7.035004 ACGCTTAAACGACCATTATACAGTTA 58.965 34.615 5.08 0.00 36.70 2.24
2798 4946 4.944962 TGTCTTCAACTTCACACTGTTG 57.055 40.909 0.00 0.00 43.28 3.33
2818 4966 4.935702 TCAAGCAAGTTTTCATGGAGTTG 58.064 39.130 0.00 0.74 0.00 3.16
2843 4991 6.534634 AGCTACCTACTTGACATTTCAGTTT 58.465 36.000 0.00 0.00 31.71 2.66
2866 5014 9.888878 CTTTAAGCATCCAATGTACATATTGAG 57.111 33.333 9.21 1.19 39.79 3.02
2884 5032 8.656849 CGAAAGAAATAGAACTAGCTTTAAGCA 58.343 33.333 19.63 4.48 45.56 3.91
2910 5058 8.072567 GCATGGTCAGAGATAACAATATTGAAC 58.927 37.037 22.16 9.47 0.00 3.18
3065 5223 7.647715 TCTTTTTCGAGTAAATTTGGCTTGAAG 59.352 33.333 18.42 12.25 35.03 3.02
3259 5417 7.759489 ATTTATTAAGCTCACTCCACACAAA 57.241 32.000 0.00 0.00 0.00 2.83
3261 5419 7.168219 AGAATTTATTAAGCTCACTCCACACA 58.832 34.615 0.00 0.00 0.00 3.72
3300 5458 5.011329 ACTCGAACTATTACCTTGTGTGGAA 59.989 40.000 0.00 0.00 0.00 3.53
3400 5565 7.527457 ACTTTGAGACAATATTACGAAAAGGC 58.473 34.615 16.52 0.00 0.00 4.35
3489 5665 7.498239 TCAAATGATCAATGAAAAGCCAAACAA 59.502 29.630 11.06 0.00 0.00 2.83
3518 5705 4.354725 GCATGTTTCTGCAAACGTAAAC 57.645 40.909 0.00 0.00 44.41 2.01
3548 5735 1.164411 TGTGCAAAATACCAGCTCCG 58.836 50.000 0.00 0.00 0.00 4.63
3558 5754 7.148540 GCAATCATCTTATGTGTTGTGCAAAAT 60.149 33.333 0.00 0.00 33.12 1.82
3712 5914 5.144100 AGAGAAAGTCTTTGACTCCTCTCA 58.856 41.667 25.08 0.00 44.77 3.27
4041 6244 2.600439 TCAGTCATCTGAGGGGCTG 58.400 57.895 7.24 7.24 44.58 4.85
4062 6265 5.544562 CCTAGAAAGGGTAAGGATCCTAAGG 59.455 48.000 16.55 5.62 33.72 2.69
4172 6375 2.994699 CACCTACGGGCCCATTCA 59.005 61.111 24.92 1.50 35.63 2.57
4174 6377 3.334891 TGCACCTACGGGCCCATT 61.335 61.111 24.92 10.82 35.63 3.16
4184 6387 1.897423 CCGTCACCATCTGCACCTA 59.103 57.895 0.00 0.00 0.00 3.08
4185 6388 2.665000 CCGTCACCATCTGCACCT 59.335 61.111 0.00 0.00 0.00 4.00
4191 6394 1.758514 ATCTCGGCCGTCACCATCT 60.759 57.895 27.15 0.00 0.00 2.90
4226 6429 3.699894 CACCAGGCGAGCTGGAGT 61.700 66.667 13.73 0.00 44.39 3.85
4245 6448 4.517703 CTCGTCGGCGTCGTCCTC 62.518 72.222 24.03 0.00 39.49 3.71
4324 6529 1.651770 TCATCCACCCCTAGGTCTTCT 59.348 52.381 8.29 0.00 46.45 2.85
4545 6751 4.400961 GCAGGCAAGGAGACCGCT 62.401 66.667 0.00 0.00 0.00 5.52


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

AutoCloner maintained by Alex Coulton.