Multiple sequence alignment - TraesCS2D01G576400

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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 TraesCS2D01G576400 chr2D 100.000 3134 0 0 1 3134 639822858 639819725 0.000000e+00 5788.0
1 TraesCS2D01G576400 chr2D 84.260 2141 208 60 37 2121 639747701 639745634 0.000000e+00 1967.0
2 TraesCS2D01G576400 chr2D 86.072 1558 144 30 614 2122 639732800 639734333 0.000000e+00 1607.0
3 TraesCS2D01G576400 chr2D 86.503 326 25 7 2114 2431 639745608 639745294 1.080000e-89 340.0
4 TraesCS2D01G576400 chr2D 79.304 546 56 29 203 738 639891690 639891192 2.330000e-86 329.0
5 TraesCS2D01G576400 chr2D 81.667 420 50 15 158 572 639732193 639732590 1.080000e-84 324.0
6 TraesCS2D01G576400 chr2D 81.818 407 46 15 806 1204 639872410 639872024 1.810000e-82 316.0
7 TraesCS2D01G576400 chr2D 80.208 288 37 12 2820 3105 639744038 639743769 6.860000e-47 198.0
8 TraesCS2D01G576400 chr2D 85.882 170 23 1 1693 1861 639890196 639890027 2.480000e-41 180.0
9 TraesCS2D01G576400 chr2D 89.024 82 5 1 2111 2188 639734355 639734436 7.150000e-17 99.0
10 TraesCS2D01G576400 chr2D 91.429 70 1 1 359 423 639872787 639872718 1.200000e-14 91.6
11 TraesCS2D01G576400 chr2D 97.917 48 1 0 47 94 639732110 639732157 2.000000e-12 84.2
12 TraesCS2D01G576400 chr2B 86.228 1917 145 39 577 2424 798957265 798959131 0.000000e+00 1967.0
13 TraesCS2D01G576400 chr2B 82.410 2166 192 85 37 2122 799028270 799030326 0.000000e+00 1714.0
14 TraesCS2D01G576400 chr2B 85.217 1292 117 31 892 2122 799047711 799046433 0.000000e+00 1260.0
15 TraesCS2D01G576400 chr2B 82.999 1047 107 32 2109 3132 799046413 799045415 0.000000e+00 881.0
16 TraesCS2D01G576400 chr2B 90.015 671 50 7 997 1661 799107610 799106951 0.000000e+00 852.0
17 TraesCS2D01G576400 chr2B 84.409 635 49 25 37 639 799048522 799047906 2.100000e-161 579.0
18 TraesCS2D01G576400 chr2B 79.682 881 65 46 37 872 799108586 799107775 5.950000e-147 531.0
19 TraesCS2D01G576400 chr2B 89.588 413 43 0 1710 2122 799106634 799106222 2.770000e-145 525.0
20 TraesCS2D01G576400 chr2B 79.612 721 108 25 2427 3123 799030722 799031427 6.080000e-132 481.0
21 TraesCS2D01G576400 chr2B 83.422 187 16 3 693 864 799047891 799047705 3.240000e-35 159.0
22 TraesCS2D01G576400 chr2B 86.486 148 17 2 2987 3134 799105517 799105373 3.240000e-35 159.0
23 TraesCS2D01G576400 chr2B 86.364 88 5 1 2108 2188 799106203 799106116 4.310000e-14 89.8
24 TraesCS2D01G576400 chr2B 100.000 41 0 0 1226 1266 749661561 749661601 3.350000e-10 76.8
25 TraesCS2D01G576400 chr2A 87.710 1546 124 33 916 2421 765442342 765440823 0.000000e+00 1742.0
26 TraesCS2D01G576400 chr2A 83.932 1475 130 52 775 2188 765373507 765374935 0.000000e+00 1312.0
27 TraesCS2D01G576400 chr2A 90.482 872 65 5 1266 2122 765393353 765392485 0.000000e+00 1134.0
28 TraesCS2D01G576400 chr2A 90.011 891 32 6 37 886 765443212 765442338 0.000000e+00 1099.0
29 TraesCS2D01G576400 chr2A 84.131 857 63 26 37 840 765394585 765393749 0.000000e+00 761.0
30 TraesCS2D01G576400 chr2A 81.053 855 132 19 1289 2118 765516097 765515248 0.000000e+00 654.0
31 TraesCS2D01G576400 chr2A 80.532 827 101 25 1339 2112 765278135 765278954 5.830000e-162 580.0
32 TraesCS2D01G576400 chr2A 92.615 325 23 1 902 1225 765393749 765393425 1.700000e-127 466.0
33 TraesCS2D01G576400 chr2A 82.653 490 59 13 2428 2897 765375214 765375697 8.090000e-111 411.0
34 TraesCS2D01G576400 chr2A 88.991 327 28 3 2109 2431 765392465 765392143 6.300000e-107 398.0
35 TraesCS2D01G576400 chr2A 77.934 639 65 26 151 737 765372898 765373512 2.330000e-86 329.0
36 TraesCS2D01G576400 chr2A 77.668 506 62 28 358 823 765548531 765548037 8.620000e-66 261.0
37 TraesCS2D01G576400 chr2A 80.548 365 47 12 2773 3134 765428676 765428333 3.100000e-65 259.0
38 TraesCS2D01G576400 chr2A 83.974 156 14 6 424 572 765517267 765517116 4.210000e-29 139.0
39 TraesCS2D01G576400 chr4B 97.674 43 1 0 1224 1266 139763249 139763291 1.210000e-09 75.0
40 TraesCS2D01G576400 chr7D 86.885 61 5 3 1207 1266 447070946 447070888 7.260000e-07 65.8


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 TraesCS2D01G576400 chr2D 639819725 639822858 3133 True 5788.00 5788 100.000000 1 3134 1 chr2D.!!$R1 3133
1 TraesCS2D01G576400 chr2D 639743769 639747701 3932 True 835.00 1967 83.657000 37 3105 3 chr2D.!!$R2 3068
2 TraesCS2D01G576400 chr2D 639732110 639734436 2326 False 528.55 1607 88.670000 47 2188 4 chr2D.!!$F1 2141
3 TraesCS2D01G576400 chr2D 639890027 639891690 1663 True 254.50 329 82.593000 203 1861 2 chr2D.!!$R4 1658
4 TraesCS2D01G576400 chr2D 639872024 639872787 763 True 203.80 316 86.623500 359 1204 2 chr2D.!!$R3 845
5 TraesCS2D01G576400 chr2B 798957265 798959131 1866 False 1967.00 1967 86.228000 577 2424 1 chr2B.!!$F2 1847
6 TraesCS2D01G576400 chr2B 799028270 799031427 3157 False 1097.50 1714 81.011000 37 3123 2 chr2B.!!$F3 3086
7 TraesCS2D01G576400 chr2B 799045415 799048522 3107 True 719.75 1260 84.011750 37 3132 4 chr2B.!!$R1 3095
8 TraesCS2D01G576400 chr2B 799105373 799108586 3213 True 431.36 852 86.427000 37 3134 5 chr2B.!!$R2 3097
9 TraesCS2D01G576400 chr2A 765440823 765443212 2389 True 1420.50 1742 88.860500 37 2421 2 chr2A.!!$R4 2384
10 TraesCS2D01G576400 chr2A 765392143 765394585 2442 True 689.75 1134 89.054750 37 2431 4 chr2A.!!$R3 2394
11 TraesCS2D01G576400 chr2A 765372898 765375697 2799 False 684.00 1312 81.506333 151 2897 3 chr2A.!!$F2 2746
12 TraesCS2D01G576400 chr2A 765278135 765278954 819 False 580.00 580 80.532000 1339 2112 1 chr2A.!!$F1 773
13 TraesCS2D01G576400 chr2A 765515248 765517267 2019 True 396.50 654 82.513500 424 2118 2 chr2A.!!$R5 1694

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
472 512 0.250295 TCCACTGCAGGTCCTTTTCG 60.250 55.0 19.93 0.00 0.00 3.46 F
1707 3103 0.099436 GCGTTGATGATCAAGGTGGC 59.901 55.0 23.62 14.39 42.39 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2079 3536 0.110486 GGCTGTCCAGGAAGTTCCAA 59.890 55.0 23.87 6.14 39.61 3.53 R
2553 4421 0.037975 ACCATTCGTGTACGGTCCAC 60.038 55.0 4.44 0.00 40.29 4.02 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
23 24 2.691409 AGTGACCACACCATATTCCG 57.309 50.000 2.78 0.00 46.99 4.30
24 25 1.014352 GTGACCACACCATATTCCGC 58.986 55.000 0.00 0.00 40.74 5.54
25 26 0.908910 TGACCACACCATATTCCGCT 59.091 50.000 0.00 0.00 0.00 5.52
26 27 1.134521 TGACCACACCATATTCCGCTC 60.135 52.381 0.00 0.00 0.00 5.03
27 28 0.908910 ACCACACCATATTCCGCTCA 59.091 50.000 0.00 0.00 0.00 4.26
28 29 1.280710 ACCACACCATATTCCGCTCAA 59.719 47.619 0.00 0.00 0.00 3.02
29 30 2.092429 ACCACACCATATTCCGCTCAAT 60.092 45.455 0.00 0.00 0.00 2.57
30 31 2.291465 CCACACCATATTCCGCTCAATG 59.709 50.000 0.00 0.00 0.00 2.82
31 32 2.291465 CACACCATATTCCGCTCAATGG 59.709 50.000 0.00 0.00 43.73 3.16
32 33 2.172505 ACACCATATTCCGCTCAATGGA 59.827 45.455 7.18 0.00 41.20 3.41
33 34 3.181440 ACACCATATTCCGCTCAATGGAT 60.181 43.478 7.18 0.00 41.20 3.41
34 35 3.438087 CACCATATTCCGCTCAATGGATC 59.562 47.826 7.18 0.00 41.20 3.36
35 36 2.674852 CCATATTCCGCTCAATGGATCG 59.325 50.000 0.00 0.00 41.20 3.69
207 219 2.087009 GCGAGACCTGCACGTACAC 61.087 63.158 0.00 0.00 32.93 2.90
252 264 3.636300 CCACCACAAAATTGACCAGAGAA 59.364 43.478 0.00 0.00 0.00 2.87
278 290 6.259638 CAATCTTGTCTCTCTAACCGTAGTC 58.740 44.000 0.00 0.00 0.00 2.59
472 512 0.250295 TCCACTGCAGGTCCTTTTCG 60.250 55.000 19.93 0.00 0.00 3.46
507 547 6.673978 TCTCTTCTATCTTCTTCCATTCCCAA 59.326 38.462 0.00 0.00 0.00 4.12
508 548 6.653989 TCTTCTATCTTCTTCCATTCCCAAC 58.346 40.000 0.00 0.00 0.00 3.77
509 549 5.373812 TCTATCTTCTTCCATTCCCAACC 57.626 43.478 0.00 0.00 0.00 3.77
512 552 4.844349 TCTTCTTCCATTCCCAACCTAG 57.156 45.455 0.00 0.00 0.00 3.02
599 698 2.026915 AGGACATGATTGCAGTGCACTA 60.027 45.455 21.20 4.24 38.71 2.74
654 1316 7.435068 GCTATATAGCCATCTAGAGCTAGAC 57.565 44.000 22.02 0.00 44.36 2.59
712 1393 0.602106 GTGTGCTCTGCTCTGCTTGA 60.602 55.000 0.00 0.00 0.00 3.02
844 1556 4.143030 GCATACAACATAGATGCACGATCC 60.143 45.833 0.00 0.00 44.35 3.36
873 1585 3.923017 GTGAACAAGCTAGCACCATTT 57.077 42.857 18.83 0.00 0.00 2.32
891 1603 3.593442 TTTTTGCCCCTCTCTGAAGAA 57.407 42.857 0.00 0.00 0.00 2.52
947 1725 0.814457 AGTTGAAAAGGTTGTGCGCA 59.186 45.000 5.66 5.66 0.00 6.09
959 1737 3.052036 GTTGTGCGCATGATTTCAGTTT 58.948 40.909 15.91 0.00 0.00 2.66
960 1738 2.932498 TGTGCGCATGATTTCAGTTTC 58.068 42.857 15.91 0.00 0.00 2.78
1309 2219 7.696453 GGTGGTGATTCAAGTTGAATATTAACG 59.304 37.037 27.01 0.00 46.20 3.18
1408 2321 2.030451 GTCGTCGGAGTGGTACTTCTTT 60.030 50.000 0.00 0.00 0.00 2.52
1420 2333 6.013293 AGTGGTACTTCTTTAGCTTCAAGGAT 60.013 38.462 0.00 0.00 0.00 3.24
1513 2426 2.579787 CCCGTGACATCGTCGAGC 60.580 66.667 0.00 0.00 34.95 5.03
1707 3103 0.099436 GCGTTGATGATCAAGGTGGC 59.901 55.000 23.62 14.39 42.39 5.01
1773 3170 4.796231 CCGAACCAGAGGCCGTCG 62.796 72.222 0.00 0.96 0.00 5.12
1824 3224 3.747266 CTCGGGGGCTACTACGAG 58.253 66.667 0.00 0.00 45.34 4.18
2237 3820 6.035368 ACAGATAGTAGATGATGTCCATGC 57.965 41.667 0.00 0.00 35.17 4.06
2292 3897 4.737578 AGACTACTCTGTTCCACTTACCA 58.262 43.478 0.00 0.00 0.00 3.25
2296 3901 4.338379 ACTCTGTTCCACTTACCAAGTC 57.662 45.455 0.00 0.00 40.46 3.01
2314 3920 5.181245 CCAAGTCCATGTGTTTTACTGTAGG 59.819 44.000 0.00 0.00 0.00 3.18
2451 4318 6.860023 CCACTCTGTTTCACTCAATGAATTTC 59.140 38.462 0.00 0.00 46.80 2.17
2462 4329 6.581542 CACTCAATGAATTTCTTGAACAGCTC 59.418 38.462 10.45 0.00 31.40 4.09
2475 4342 5.603170 TGAACAGCTCATCATCATCACTA 57.397 39.130 0.00 0.00 0.00 2.74
2483 4350 6.097412 AGCTCATCATCATCACTAAGTGTACA 59.903 38.462 0.00 0.00 34.79 2.90
2543 4411 4.025229 GCCATACGCGTGAGATAATTTTGA 60.025 41.667 24.59 0.00 0.00 2.69
2553 4421 7.375280 GCGTGAGATAATTTTGATTGATCTGTG 59.625 37.037 0.00 0.00 0.00 3.66
2557 4425 8.812513 AGATAATTTTGATTGATCTGTGTGGA 57.187 30.769 0.00 0.00 0.00 4.02
2569 4437 3.502237 GTGTGGACCGTACACGAAT 57.498 52.632 9.38 0.00 41.64 3.34
2615 4484 3.431207 CCACGGGGATTAGTTAACATCGT 60.431 47.826 0.00 4.11 35.59 3.73
2647 4516 7.559845 GCGATAGTGAGTTGATTAATTGAGTC 58.440 38.462 0.00 0.00 39.35 3.36
2664 4534 2.167487 GAGTCTCCCTGTCAACCATCTC 59.833 54.545 0.00 0.00 0.00 2.75
2678 4548 8.539544 TGTCAACCATCTCTTCTGATGTAATTA 58.460 33.333 0.00 0.00 41.47 1.40
2716 4591 9.520204 CATGGGATTGTTTGAGTCATAATTAAC 57.480 33.333 0.00 0.00 0.00 2.01
2811 4695 3.452627 CAGGGACTTGCACTACCTAGATT 59.547 47.826 0.00 0.00 34.60 2.40
2815 4699 5.128991 GGGACTTGCACTACCTAGATTTAGT 59.871 44.000 0.00 0.00 0.00 2.24
2816 4700 6.323225 GGGACTTGCACTACCTAGATTTAGTA 59.677 42.308 0.00 0.00 0.00 1.82
2817 4701 7.201835 GGACTTGCACTACCTAGATTTAGTAC 58.798 42.308 0.00 0.00 0.00 2.73
2818 4702 7.147949 GGACTTGCACTACCTAGATTTAGTACA 60.148 40.741 0.00 0.00 0.00 2.90
2855 5491 1.403679 TGTTGCTTGTGGCTGTTGTAC 59.596 47.619 0.00 0.00 42.39 2.90
2891 5527 4.584327 AAATGTTCTTTTCTGAACGGGG 57.416 40.909 0.00 0.00 46.59 5.73
2902 5538 2.076863 CTGAACGGGGTCAATCTGTTC 58.923 52.381 8.38 8.38 45.67 3.18
2904 5540 0.953960 AACGGGGTCAATCTGTTCGC 60.954 55.000 0.00 0.00 0.00 4.70
2909 5545 1.327764 GGGTCAATCTGTTCGCGAATC 59.672 52.381 26.23 18.17 0.00 2.52
2911 5547 2.271800 GTCAATCTGTTCGCGAATCCT 58.728 47.619 26.23 7.56 0.00 3.24
2915 5551 2.288961 TCTGTTCGCGAATCCTTACC 57.711 50.000 26.23 10.62 0.00 2.85
2917 5553 2.028839 TCTGTTCGCGAATCCTTACCAA 60.029 45.455 26.23 4.78 0.00 3.67
2950 5590 8.319881 GGAATACCTACTAAACAGAAAGGAAGT 58.680 37.037 0.00 0.00 0.00 3.01
2953 5593 5.221864 ACCTACTAAACAGAAAGGAAGTGGG 60.222 44.000 0.00 0.00 40.34 4.61
2964 5613 2.568979 AGGAAGTGGGCCTGGTAATAA 58.431 47.619 4.53 0.00 33.59 1.40
2980 5629 5.587043 TGGTAATAACGAATTCCGCTTCATT 59.413 36.000 0.00 0.00 43.32 2.57
3041 5691 4.635833 ACGGGAAATAAAACAAACGTGT 57.364 36.364 0.00 0.00 40.75 4.49
3062 5712 8.098912 ACGTGTAGGTATTCCTTTGAAACTTAT 58.901 33.333 0.00 0.00 42.12 1.73
3097 5748 4.814234 TCTATCGTGTGGCAATGGTATTTC 59.186 41.667 0.00 0.00 0.00 2.17
3099 5750 1.735018 CGTGTGGCAATGGTATTTCGA 59.265 47.619 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.570772 CGGAATATGGTGTGGTCACTTTAG 59.429 45.833 2.66 0.00 43.41 1.85
1 2 4.509616 CGGAATATGGTGTGGTCACTTTA 58.490 43.478 2.66 0.00 43.41 1.85
2 3 3.343617 CGGAATATGGTGTGGTCACTTT 58.656 45.455 2.66 0.00 43.41 2.66
3 4 2.939640 GCGGAATATGGTGTGGTCACTT 60.940 50.000 2.66 0.00 43.41 3.16
5 6 1.014352 GCGGAATATGGTGTGGTCAC 58.986 55.000 0.00 0.00 43.19 3.67
8 9 0.908910 TGAGCGGAATATGGTGTGGT 59.091 50.000 0.00 0.00 0.00 4.16
9 10 2.036958 TTGAGCGGAATATGGTGTGG 57.963 50.000 0.00 0.00 0.00 4.17
10 11 2.291465 CCATTGAGCGGAATATGGTGTG 59.709 50.000 0.00 0.00 34.23 3.82
11 12 2.172505 TCCATTGAGCGGAATATGGTGT 59.827 45.455 0.00 0.00 38.88 4.16
12 13 2.849942 TCCATTGAGCGGAATATGGTG 58.150 47.619 0.00 0.00 38.88 4.17
13 14 3.679389 GATCCATTGAGCGGAATATGGT 58.321 45.455 0.00 0.00 38.88 3.55
14 15 2.674852 CGATCCATTGAGCGGAATATGG 59.325 50.000 0.00 0.00 46.19 2.74
23 24 2.386249 GAGTACGTCGATCCATTGAGC 58.614 52.381 0.00 0.00 0.00 4.26
24 25 2.602456 CGGAGTACGTCGATCCATTGAG 60.602 54.545 12.50 0.00 37.93 3.02
25 26 1.332686 CGGAGTACGTCGATCCATTGA 59.667 52.381 12.50 0.00 37.93 2.57
26 27 1.755161 CGGAGTACGTCGATCCATTG 58.245 55.000 12.50 0.00 37.93 2.82
27 28 0.030369 GCGGAGTACGTCGATCCATT 59.970 55.000 13.53 0.00 46.52 3.16
28 29 1.653115 GCGGAGTACGTCGATCCAT 59.347 57.895 13.53 0.00 46.52 3.41
29 30 2.816360 CGCGGAGTACGTCGATCCA 61.816 63.158 13.53 0.00 46.52 3.41
30 31 2.052414 CGCGGAGTACGTCGATCC 60.052 66.667 13.53 2.50 46.52 3.36
31 32 1.061570 AACGCGGAGTACGTCGATC 59.938 57.895 12.47 0.00 44.30 3.69
32 33 1.226211 CAACGCGGAGTACGTCGAT 60.226 57.895 12.47 3.90 44.30 3.59
33 34 2.174107 CAACGCGGAGTACGTCGA 59.826 61.111 12.47 0.00 44.30 4.20
34 35 1.862147 CTCAACGCGGAGTACGTCG 60.862 63.158 12.47 9.53 44.30 5.12
35 36 1.208614 ACTCAACGCGGAGTACGTC 59.791 57.895 15.16 0.00 45.95 4.34
199 211 3.305964 CTGAACTACAGGTGTGTACGTG 58.694 50.000 0.00 0.00 45.62 4.49
252 264 3.833070 ACGGTTAGAGAGACAAGATTGGT 59.167 43.478 0.00 0.00 0.00 3.67
472 512 9.366216 GAAGAAGATAGAAGAGAAAAGAGGAAC 57.634 37.037 0.00 0.00 0.00 3.62
507 547 2.019249 TGCGCGTAGTGTAATCTAGGT 58.981 47.619 8.43 0.00 41.96 3.08
508 548 2.768833 TGCGCGTAGTGTAATCTAGG 57.231 50.000 8.43 0.00 41.96 3.02
509 549 6.033619 GGATTTATGCGCGTAGTGTAATCTAG 59.966 42.308 22.02 0.00 41.96 2.43
512 552 4.446385 TGGATTTATGCGCGTAGTGTAATC 59.554 41.667 17.66 17.66 41.96 1.75
599 698 9.875708 ACCAAATCTGTCTCTCTATCTACTATT 57.124 33.333 0.00 0.00 0.00 1.73
689 1357 1.735920 CAGAGCAGAGCACACGGAC 60.736 63.158 0.00 0.00 0.00 4.79
712 1393 0.392706 TGACCACAGACGCTTGACAT 59.607 50.000 0.00 0.00 0.00 3.06
844 1556 1.645034 AGCTTGTTCACCGATCGATG 58.355 50.000 18.66 10.77 0.00 3.84
856 1568 3.392882 GCAAAAATGGTGCTAGCTTGTT 58.607 40.909 17.23 0.00 39.00 2.83
873 1585 1.774254 TGTTCTTCAGAGAGGGGCAAA 59.226 47.619 0.00 0.00 32.44 3.68
947 1725 7.439157 TTGATGTCTTCGAAACTGAAATCAT 57.561 32.000 15.63 4.23 28.28 2.45
959 1737 3.876274 AAGCTAGCTTGATGTCTTCGA 57.124 42.857 28.83 0.00 34.60 3.71
1113 1966 0.391130 CGAGGTCGATCTTTTGGGCA 60.391 55.000 0.00 0.00 43.02 5.36
1227 2084 6.697641 AGTATTTTGGAACAGAGGGAGTAA 57.302 37.500 0.00 0.00 42.39 2.24
1228 2085 6.043938 ACAAGTATTTTGGAACAGAGGGAGTA 59.956 38.462 0.00 0.00 42.39 2.59
1309 2219 3.072184 ACCTCTCTGCACCATCCATTATC 59.928 47.826 0.00 0.00 0.00 1.75
1408 2321 3.430374 GGTACTTGCGATCCTTGAAGCTA 60.430 47.826 0.00 0.00 0.00 3.32
1707 3103 1.453379 CCAGCCTTCCTCCTGCATG 60.453 63.158 0.00 0.00 0.00 4.06
1773 3170 1.779569 CGTATGCCGGGAAGATGTAC 58.220 55.000 0.00 0.00 0.00 2.90
2079 3536 0.110486 GGCTGTCCAGGAAGTTCCAA 59.890 55.000 23.87 6.14 39.61 3.53
2292 3897 4.760204 GCCTACAGTAAAACACATGGACTT 59.240 41.667 0.00 0.00 0.00 3.01
2296 3901 3.190535 GTGGCCTACAGTAAAACACATGG 59.809 47.826 3.32 0.00 0.00 3.66
2314 3920 2.037251 TCAGTAAGTGGAACAGAGTGGC 59.963 50.000 0.00 0.00 41.80 5.01
2451 4318 4.876679 AGTGATGATGATGAGCTGTTCAAG 59.123 41.667 0.00 0.00 39.77 3.02
2543 4411 2.565391 TGTACGGTCCACACAGATCAAT 59.435 45.455 0.00 0.00 0.00 2.57
2553 4421 0.037975 ACCATTCGTGTACGGTCCAC 60.038 55.000 4.44 0.00 40.29 4.02
2557 4425 7.119553 ACATTTAATTAACCATTCGTGTACGGT 59.880 33.333 4.44 0.00 40.29 4.83
2569 4437 6.393990 GGCACATCACACATTTAATTAACCA 58.606 36.000 0.00 0.00 0.00 3.67
2615 4484 1.992667 CAACTCACTATCGCGCTTGAA 59.007 47.619 5.56 0.00 0.00 2.69
2647 4516 2.836981 AGAAGAGATGGTTGACAGGGAG 59.163 50.000 0.00 0.00 0.00 4.30
2664 4534 9.144085 GACGCGTAAATTTAATTACATCAGAAG 57.856 33.333 13.97 0.00 35.89 2.85
2678 4548 3.442273 ACAATCCCATGACGCGTAAATTT 59.558 39.130 13.97 0.00 0.00 1.82
2716 4591 2.770802 AGACCCATCCATCTGTCTCAAG 59.229 50.000 0.00 0.00 32.85 3.02
2766 4647 8.135529 CCTGTCAGTTTGTTGACTATATCGATA 58.864 37.037 7.75 7.75 46.00 2.92
2767 4648 6.980978 CCTGTCAGTTTGTTGACTATATCGAT 59.019 38.462 2.16 2.16 46.00 3.59
2768 4649 6.330278 CCTGTCAGTTTGTTGACTATATCGA 58.670 40.000 7.56 0.00 46.00 3.59
2785 4669 1.338200 GGTAGTGCAAGTCCCTGTCAG 60.338 57.143 0.00 0.00 0.00 3.51
2891 5527 2.271800 AGGATTCGCGAACAGATTGAC 58.728 47.619 26.00 8.11 0.00 3.18
2902 5538 2.198406 TCGATTTGGTAAGGATTCGCG 58.802 47.619 0.00 0.00 0.00 5.87
2904 5540 4.377021 TCCATCGATTTGGTAAGGATTCG 58.623 43.478 5.00 0.00 38.01 3.34
2909 5545 5.621193 AGGTATTCCATCGATTTGGTAAGG 58.379 41.667 5.00 0.00 38.01 2.69
2911 5547 7.369551 AGTAGGTATTCCATCGATTTGGTAA 57.630 36.000 5.00 0.00 38.01 2.85
2915 5551 8.657074 TGTTTAGTAGGTATTCCATCGATTTG 57.343 34.615 0.00 0.00 35.89 2.32
2917 5553 8.246430 TCTGTTTAGTAGGTATTCCATCGATT 57.754 34.615 0.00 0.00 35.89 3.34
2950 5590 3.547746 GAATTCGTTATTACCAGGCCCA 58.452 45.455 0.00 0.00 0.00 5.36
2953 5593 2.032290 GCGGAATTCGTTATTACCAGGC 60.032 50.000 0.00 0.00 41.72 4.85
2964 5613 4.693566 TGAAGTTAATGAAGCGGAATTCGT 59.306 37.500 0.00 0.00 41.72 3.85
3018 5668 6.316440 ACACGTTTGTTTTATTTCCCGTAT 57.684 33.333 0.00 0.00 28.43 3.06
3020 5670 4.635833 ACACGTTTGTTTTATTTCCCGT 57.364 36.364 0.00 0.00 28.43 5.28
3062 5712 4.503910 CACACGATAGAAACTCCCATCAA 58.496 43.478 0.00 0.00 41.38 2.57
3064 5714 3.458189 CCACACGATAGAAACTCCCATC 58.542 50.000 0.00 0.00 41.38 3.51
3097 5748 9.233232 GGATTTGTTATTAGTGGCTTATTTTCG 57.767 33.333 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.