Multiple sequence alignment - TraesCS2A01G216200

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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 TraesCS2A01G216200 chr2A 100.000 3951 0 0 1 3951 203225820 203229770 0.000000e+00 7297.0
1 TraesCS2A01G216200 chr2A 95.294 765 35 1 1 764 630136435 630137199 0.000000e+00 1212.0
2 TraesCS2A01G216200 chr2A 94.661 768 40 1 1 767 51444299 51445066 0.000000e+00 1190.0
3 TraesCS2A01G216200 chr2D 95.509 2093 59 11 768 2837 189284626 189286706 0.000000e+00 3312.0
4 TraesCS2A01G216200 chr2D 90.341 528 47 4 3423 3949 392529781 392529257 0.000000e+00 689.0
5 TraesCS2A01G216200 chr2D 88.652 564 22 12 2877 3421 189286797 189287337 0.000000e+00 649.0
6 TraesCS2A01G216200 chr2B 93.596 2108 93 19 766 2837 245297553 245299654 0.000000e+00 3107.0
7 TraesCS2A01G216200 chr2B 83.218 721 104 15 1158 1868 245129126 245129839 0.000000e+00 645.0
8 TraesCS2A01G216200 chr2B 79.122 752 120 21 2083 2811 245130051 245130788 5.940000e-133 484.0
9 TraesCS2A01G216200 chr2B 86.973 261 6 7 2882 3142 245299826 245300058 6.510000e-68 268.0
10 TraesCS2A01G216200 chr2B 87.006 177 11 5 3246 3421 245302045 245302210 5.210000e-44 189.0
11 TraesCS2A01G216200 chr2B 97.727 44 1 0 3156 3199 245300203 245300246 4.230000e-10 76.8
12 TraesCS2A01G216200 chr5A 94.942 771 38 1 1 770 492727246 492726476 0.000000e+00 1206.0
13 TraesCS2A01G216200 chr5A 81.633 245 41 4 2571 2813 546263467 546263709 2.410000e-47 200.0
14 TraesCS2A01G216200 chr1A 95.052 768 37 1 1 767 574891596 574890829 0.000000e+00 1206.0
15 TraesCS2A01G216200 chr1A 81.325 166 27 4 2583 2746 578207172 578207009 8.910000e-27 132.0
16 TraesCS2A01G216200 chr7A 94.922 768 38 1 1 767 666960879 666961646 0.000000e+00 1201.0
17 TraesCS2A01G216200 chr7A 94.553 771 41 1 1 770 697064937 697064167 0.000000e+00 1190.0
18 TraesCS2A01G216200 chr7A 91.358 486 40 2 3467 3951 225004512 225004028 0.000000e+00 664.0
19 TraesCS2A01G216200 chr3B 94.812 771 36 2 1 767 784876137 784875367 0.000000e+00 1199.0
20 TraesCS2A01G216200 chr3B 90.170 529 44 8 3423 3949 553063169 553063691 0.000000e+00 682.0
21 TraesCS2A01G216200 chrUn 94.798 769 37 3 1 767 370481589 370480822 0.000000e+00 1195.0
22 TraesCS2A01G216200 chr6B 94.661 768 40 1 1 767 647488608 647487841 0.000000e+00 1190.0
23 TraesCS2A01G216200 chr6B 80.189 212 39 2 2222 2430 623741034 623741245 5.290000e-34 156.0
24 TraesCS2A01G216200 chr7B 79.038 1331 225 37 1158 2461 520416560 520417863 0.000000e+00 863.0
25 TraesCS2A01G216200 chr7B 81.522 184 33 1 2568 2750 520417617 520417800 2.460000e-32 150.0
26 TraesCS2A01G216200 chr1D 90.566 530 43 7 3423 3950 447465081 447464557 0.000000e+00 695.0
27 TraesCS2A01G216200 chr1D 91.368 475 40 1 3466 3939 402303415 402302941 0.000000e+00 649.0
28 TraesCS2A01G216200 chr1D 79.508 244 43 7 2565 2804 481452613 481452373 2.440000e-37 167.0
29 TraesCS2A01G216200 chr1D 78.027 223 43 5 2597 2815 481500524 481500304 6.890000e-28 135.0
30 TraesCS2A01G216200 chr3A 89.811 530 50 4 3423 3951 588657166 588656640 0.000000e+00 676.0
31 TraesCS2A01G216200 chr3D 91.718 483 39 1 3461 3942 582500742 582501224 0.000000e+00 669.0
32 TraesCS2A01G216200 chr3D 90.650 492 40 4 3462 3951 567669790 567669303 0.000000e+00 649.0
33 TraesCS2A01G216200 chr6D 90.835 491 41 4 3462 3951 158819824 158820311 0.000000e+00 654.0
34 TraesCS2A01G216200 chr6D 80.751 213 36 4 2222 2430 414001421 414001632 1.140000e-35 161.0
35 TraesCS2A01G216200 chr1B 79.412 238 43 6 2570 2804 670160196 670160430 3.160000e-36 163.0
36 TraesCS2A01G216200 chr1B 78.571 224 44 4 2583 2804 670149475 670149696 1.140000e-30 145.0
37 TraesCS2A01G216200 chr6A 80.751 213 36 4 2222 2430 558982059 558982270 1.140000e-35 161.0


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 TraesCS2A01G216200 chr2A 203225820 203229770 3950 False 7297.0 7297 100.0000 1 3951 1 chr2A.!!$F2 3950
1 TraesCS2A01G216200 chr2A 630136435 630137199 764 False 1212.0 1212 95.2940 1 764 1 chr2A.!!$F3 763
2 TraesCS2A01G216200 chr2A 51444299 51445066 767 False 1190.0 1190 94.6610 1 767 1 chr2A.!!$F1 766
3 TraesCS2A01G216200 chr2D 189284626 189287337 2711 False 1980.5 3312 92.0805 768 3421 2 chr2D.!!$F1 2653
4 TraesCS2A01G216200 chr2D 392529257 392529781 524 True 689.0 689 90.3410 3423 3949 1 chr2D.!!$R1 526
5 TraesCS2A01G216200 chr2B 245297553 245302210 4657 False 910.2 3107 91.3255 766 3421 4 chr2B.!!$F2 2655
6 TraesCS2A01G216200 chr2B 245129126 245130788 1662 False 564.5 645 81.1700 1158 2811 2 chr2B.!!$F1 1653
7 TraesCS2A01G216200 chr5A 492726476 492727246 770 True 1206.0 1206 94.9420 1 770 1 chr5A.!!$R1 769
8 TraesCS2A01G216200 chr1A 574890829 574891596 767 True 1206.0 1206 95.0520 1 767 1 chr1A.!!$R1 766
9 TraesCS2A01G216200 chr7A 666960879 666961646 767 False 1201.0 1201 94.9220 1 767 1 chr7A.!!$F1 766
10 TraesCS2A01G216200 chr7A 697064167 697064937 770 True 1190.0 1190 94.5530 1 770 1 chr7A.!!$R2 769
11 TraesCS2A01G216200 chr3B 784875367 784876137 770 True 1199.0 1199 94.8120 1 767 1 chr3B.!!$R1 766
12 TraesCS2A01G216200 chr3B 553063169 553063691 522 False 682.0 682 90.1700 3423 3949 1 chr3B.!!$F1 526
13 TraesCS2A01G216200 chrUn 370480822 370481589 767 True 1195.0 1195 94.7980 1 767 1 chrUn.!!$R1 766
14 TraesCS2A01G216200 chr6B 647487841 647488608 767 True 1190.0 1190 94.6610 1 767 1 chr6B.!!$R1 766
15 TraesCS2A01G216200 chr7B 520416560 520417863 1303 False 506.5 863 80.2800 1158 2750 2 chr7B.!!$F1 1592
16 TraesCS2A01G216200 chr1D 447464557 447465081 524 True 695.0 695 90.5660 3423 3950 1 chr1D.!!$R2 527
17 TraesCS2A01G216200 chr3A 588656640 588657166 526 True 676.0 676 89.8110 3423 3951 1 chr3A.!!$R1 528

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
174 179 0.248377 CGGTGGTTACGACGGAGATC 60.248 60.0 0.00 0.00 0.0 2.75 F
1145 1153 0.385473 CAGTTTTGTAACAGCGGCCG 60.385 55.0 24.05 24.05 36.7 6.13 F
1908 1926 0.337773 AGATGAGAGTGCTGAGGGGA 59.662 55.0 0.00 0.00 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1790 1805 0.244178 GCTATAGTAGGTGAGGCCGC 59.756 60.0 0.0 0.0 43.70 6.53 R
2728 2862 0.950071 GCCCGTTGCGTTGGTAGTAA 60.950 55.0 0.0 0.0 0.00 2.24 R
3443 5608 0.255318 GACTAGAGGTCTGGACGGGA 59.745 60.0 0.0 0.0 41.46 5.14 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
24 25 6.728200 CCATGGCACTATGTATAACAAACAG 58.272 40.000 0.00 0.00 0.00 3.16
174 179 0.248377 CGGTGGTTACGACGGAGATC 60.248 60.000 0.00 0.00 0.00 2.75
180 185 4.275443 GTGGTTACGACGGAGATCTAGAAT 59.725 45.833 0.00 0.00 0.00 2.40
224 229 9.935682 CCTACATATGCAAACTAAGTGTTATTG 57.064 33.333 1.58 0.00 38.03 1.90
232 237 6.590357 CAAACTAAGTGTTATTGTGACCTCG 58.410 40.000 0.00 0.00 38.03 4.63
462 467 1.719378 AGGGAAGAACAGAGGAGAGGA 59.281 52.381 0.00 0.00 0.00 3.71
464 469 2.907042 GGGAAGAACAGAGGAGAGGAAA 59.093 50.000 0.00 0.00 0.00 3.13
475 480 1.993301 GGAGAGGAAAAGGGGAAAGGA 59.007 52.381 0.00 0.00 0.00 3.36
478 483 1.006043 GAGGAAAAGGGGAAAGGAGGG 59.994 57.143 0.00 0.00 0.00 4.30
538 543 2.228822 GACCTTTAGTACCGGTTCGTGA 59.771 50.000 15.04 0.00 0.00 4.35
542 547 1.603456 TAGTACCGGTTCGTGACACA 58.397 50.000 15.04 0.00 0.00 3.72
568 573 2.185387 GTACTAAAGGTGCTGGAGGGA 58.815 52.381 0.00 0.00 0.00 4.20
603 608 0.835941 ATCCTGCCACCACTCTCATC 59.164 55.000 0.00 0.00 0.00 2.92
665 670 5.921408 GCCACGAATCGATACTAAAGATCTT 59.079 40.000 10.55 0.88 0.00 2.40
669 674 8.286800 CACGAATCGATACTAAAGATCTTCTCT 58.713 37.037 10.55 0.00 34.96 3.10
686 691 1.144057 CTCGCCTAGCCGTTGGAAT 59.856 57.895 0.00 0.00 0.00 3.01
688 693 1.144057 CGCCTAGCCGTTGGAATCT 59.856 57.895 0.00 0.00 0.00 2.40
705 710 4.274459 GGAATCTGCACTAATGGACACATC 59.726 45.833 0.00 0.00 35.94 3.06
801 806 7.717568 TCGACTGACCCAAATTTAAAATTCAA 58.282 30.769 0.00 0.00 0.00 2.69
817 822 0.468226 TCAAGCGGCTTGGGTATAGG 59.532 55.000 34.84 13.37 41.33 2.57
874 879 3.560636 GCCATTTAAGCCTCTCCACTA 57.439 47.619 0.00 0.00 0.00 2.74
923 928 0.678395 CTGACGATCCTCCATCCTGG 59.322 60.000 0.00 0.00 39.43 4.45
955 961 3.302434 CGCCGGCTATAAATACATGTACG 59.698 47.826 26.68 4.56 0.00 3.67
966 972 0.673644 ACATGTACGCCTTGTGCTCC 60.674 55.000 0.00 0.00 38.05 4.70
991 997 2.678324 GGCTATCCTCTGATACGCAAC 58.322 52.381 0.00 0.00 33.20 4.17
1144 1152 0.663269 GCAGTTTTGTAACAGCGGCC 60.663 55.000 0.00 0.00 37.10 6.13
1145 1153 0.385473 CAGTTTTGTAACAGCGGCCG 60.385 55.000 24.05 24.05 36.70 6.13
1146 1154 1.081708 GTTTTGTAACAGCGGCCGG 60.082 57.895 29.38 14.21 34.31 6.13
1147 1155 2.910345 TTTTGTAACAGCGGCCGGC 61.910 57.895 29.38 21.18 44.05 6.13
1472 1484 1.163554 GAGGTCTTCAAGCAGGCAAG 58.836 55.000 0.00 0.00 0.00 4.01
1659 1674 3.495629 CGGTGATGAGTCCCATGATTGAT 60.496 47.826 0.00 0.00 35.17 2.57
1717 1732 2.135139 TCTACCCGTACTACGCGTATG 58.865 52.381 20.91 15.73 40.91 2.39
1790 1805 4.778415 CGTGGGCGACAGTCGGAG 62.778 72.222 24.13 0.00 40.84 4.63
1897 1912 5.186797 AGGAACCACACTAAGAAGATGAGAG 59.813 44.000 0.00 0.00 0.00 3.20
1902 1920 4.863689 CACACTAAGAAGATGAGAGTGCTG 59.136 45.833 0.00 0.00 40.97 4.41
1906 1924 2.109774 AGAAGATGAGAGTGCTGAGGG 58.890 52.381 0.00 0.00 0.00 4.30
1907 1925 1.138661 GAAGATGAGAGTGCTGAGGGG 59.861 57.143 0.00 0.00 0.00 4.79
1908 1926 0.337773 AGATGAGAGTGCTGAGGGGA 59.662 55.000 0.00 0.00 0.00 4.81
2813 2947 0.108585 TCAGGCACCAAGTGAGTTCC 59.891 55.000 0.00 0.00 35.23 3.62
2832 2966 6.407202 AGTTCCTGACGCTCAAAACTTATAT 58.593 36.000 8.38 0.00 32.05 0.86
2833 2967 7.553334 AGTTCCTGACGCTCAAAACTTATATA 58.447 34.615 8.38 0.00 32.05 0.86
2834 2968 7.491696 AGTTCCTGACGCTCAAAACTTATATAC 59.508 37.037 8.38 0.00 32.05 1.47
2835 2969 7.108841 TCCTGACGCTCAAAACTTATATACT 57.891 36.000 0.00 0.00 0.00 2.12
2836 2970 8.229253 TCCTGACGCTCAAAACTTATATACTA 57.771 34.615 0.00 0.00 0.00 1.82
2837 2971 8.133627 TCCTGACGCTCAAAACTTATATACTAC 58.866 37.037 0.00 0.00 0.00 2.73
2838 2972 8.136165 CCTGACGCTCAAAACTTATATACTACT 58.864 37.037 0.00 0.00 0.00 2.57
2839 2973 9.171701 CTGACGCTCAAAACTTATATACTACTC 57.828 37.037 0.00 0.00 0.00 2.59
2840 2974 8.133627 TGACGCTCAAAACTTATATACTACTCC 58.866 37.037 0.00 0.00 0.00 3.85
2841 2975 8.004087 ACGCTCAAAACTTATATACTACTCCA 57.996 34.615 0.00 0.00 0.00 3.86
2842 2976 8.136165 ACGCTCAAAACTTATATACTACTCCAG 58.864 37.037 0.00 0.00 0.00 3.86
2843 2977 8.136165 CGCTCAAAACTTATATACTACTCCAGT 58.864 37.037 0.00 0.00 41.62 4.00
2874 3008 5.451908 ACTAACATGACGTTTCTGCAAATG 58.548 37.500 0.00 0.00 39.14 2.32
2875 3009 4.566545 AACATGACGTTTCTGCAAATGA 57.433 36.364 0.00 0.00 32.35 2.57
2877 3011 3.565482 ACATGACGTTTCTGCAAATGAGT 59.435 39.130 0.00 0.00 33.32 3.41
2878 3012 4.036734 ACATGACGTTTCTGCAAATGAGTT 59.963 37.500 0.00 0.00 33.32 3.01
2879 3013 4.209452 TGACGTTTCTGCAAATGAGTTC 57.791 40.909 0.00 0.00 33.32 3.01
2880 3014 3.625313 TGACGTTTCTGCAAATGAGTTCA 59.375 39.130 0.00 0.00 33.32 3.18
2975 3254 0.319211 TGAACCGACAACTGGTAGCG 60.319 55.000 0.00 0.00 39.29 4.26
2993 3272 0.250513 CGAAGACCAAAGGCTAGGCT 59.749 55.000 14.10 14.10 0.00 4.58
2994 3273 1.743996 GAAGACCAAAGGCTAGGCTG 58.256 55.000 20.99 10.10 0.00 4.85
2995 3274 0.329596 AAGACCAAAGGCTAGGCTGG 59.670 55.000 20.99 20.14 34.95 4.85
2996 3275 1.750780 GACCAAAGGCTAGGCTGGC 60.751 63.158 20.99 15.25 31.74 4.85
2997 3276 2.203549 GACCAAAGGCTAGGCTGGCT 62.204 60.000 20.99 14.17 45.04 4.75
2998 3277 1.452833 CCAAAGGCTAGGCTGGCTC 60.453 63.158 20.99 12.48 42.20 4.70
2999 3278 1.452833 CAAAGGCTAGGCTGGCTCC 60.453 63.158 20.99 6.91 42.20 4.70
3000 3279 1.617839 AAAGGCTAGGCTGGCTCCT 60.618 57.895 20.99 9.27 42.20 3.69
3001 3280 0.326618 AAAGGCTAGGCTGGCTCCTA 60.327 55.000 20.99 6.07 42.20 2.94
3002 3281 0.104725 AAGGCTAGGCTGGCTCCTAT 60.105 55.000 20.99 0.00 42.20 2.57
3003 3282 0.544120 AGGCTAGGCTGGCTCCTATC 60.544 60.000 22.53 4.62 38.54 2.08
3004 3283 0.544120 GGCTAGGCTGGCTCCTATCT 60.544 60.000 22.53 0.00 38.01 1.98
3005 3284 1.272760 GGCTAGGCTGGCTCCTATCTA 60.273 57.143 22.53 0.00 38.01 1.98
3006 3285 2.625617 GGCTAGGCTGGCTCCTATCTAT 60.626 54.545 22.53 0.00 38.01 1.98
3009 3288 4.098807 GCTAGGCTGGCTCCTATCTATTAC 59.901 50.000 16.33 0.00 38.01 1.89
3061 3340 6.570672 ACTACTTCGTATCAAAGTGTCTCA 57.429 37.500 0.00 0.00 37.52 3.27
3062 3341 6.978338 ACTACTTCGTATCAAAGTGTCTCAA 58.022 36.000 0.00 0.00 37.52 3.02
3063 3342 7.431249 ACTACTTCGTATCAAAGTGTCTCAAA 58.569 34.615 0.00 0.00 37.52 2.69
3064 3343 6.771188 ACTTCGTATCAAAGTGTCTCAAAG 57.229 37.500 0.00 0.00 35.68 2.77
3072 3354 9.657121 GTATCAAAGTGTCTCAAAGAAAGAAAG 57.343 33.333 0.00 0.00 0.00 2.62
3078 3360 7.539436 AGTGTCTCAAAGAAAGAAAGAAAACC 58.461 34.615 0.00 0.00 0.00 3.27
3142 3424 2.172717 ACTAGGCGAATAAACCCATGCT 59.827 45.455 0.00 0.00 0.00 3.79
3327 5492 6.038356 GCCTCCACAACATTCATTCTATTTG 58.962 40.000 0.00 0.00 0.00 2.32
3369 5534 9.515020 TTCAAATTTATAGAGGCAATTTAAGCG 57.485 29.630 0.00 0.00 30.60 4.68
3414 5579 8.597227 CATTGAATAAACACGATAACTAACGGA 58.403 33.333 0.00 0.00 0.00 4.69
3415 5580 7.510428 TGAATAAACACGATAACTAACGGAC 57.490 36.000 0.00 0.00 0.00 4.79
3416 5581 7.315142 TGAATAAACACGATAACTAACGGACT 58.685 34.615 0.00 0.00 0.00 3.85
3417 5582 8.458052 TGAATAAACACGATAACTAACGGACTA 58.542 33.333 0.00 0.00 0.00 2.59
3418 5583 8.847444 AATAAACACGATAACTAACGGACTAG 57.153 34.615 0.00 0.00 0.00 2.57
3419 5584 4.284378 ACACGATAACTAACGGACTAGC 57.716 45.455 0.00 0.00 0.00 3.42
3420 5585 3.944015 ACACGATAACTAACGGACTAGCT 59.056 43.478 0.00 0.00 0.00 3.32
3421 5586 4.201891 ACACGATAACTAACGGACTAGCTG 60.202 45.833 0.00 0.00 0.00 4.24
3429 5594 2.760385 GGACTAGCTGCCCGTCCT 60.760 66.667 23.10 0.00 42.99 3.85
3441 5606 2.362632 CGTCCTCCTCCCCTTCGT 60.363 66.667 0.00 0.00 0.00 3.85
3442 5607 2.416432 CGTCCTCCTCCCCTTCGTC 61.416 68.421 0.00 0.00 0.00 4.20
3443 5608 1.000612 GTCCTCCTCCCCTTCGTCT 59.999 63.158 0.00 0.00 0.00 4.18
3447 5612 3.148279 CCTCCCCTTCGTCTCCCG 61.148 72.222 0.00 0.00 38.13 5.14
3448 5613 2.362632 CTCCCCTTCGTCTCCCGT 60.363 66.667 0.00 0.00 37.94 5.28
3450 5615 3.459063 CCCCTTCGTCTCCCGTCC 61.459 72.222 0.00 0.00 37.94 4.79
3451 5616 2.678934 CCCTTCGTCTCCCGTCCA 60.679 66.667 0.00 0.00 37.94 4.02
3452 5617 2.711922 CCCTTCGTCTCCCGTCCAG 61.712 68.421 0.00 0.00 37.94 3.86
3453 5618 1.677966 CCTTCGTCTCCCGTCCAGA 60.678 63.158 0.00 0.00 37.94 3.86
3459 5624 0.255318 GTCTCCCGTCCAGACCTCTA 59.745 60.000 0.00 0.00 35.19 2.43
3703 5868 2.203294 GTCGGTGGGTGTTGCCTT 60.203 61.111 0.00 0.00 37.43 4.35
3815 5980 2.664436 CGGGTGTCGTTTTCCTCGC 61.664 63.158 0.00 0.00 0.00 5.03
3894 6061 0.617820 AGGAGGCTACCATTGACGGT 60.618 55.000 0.00 0.00 43.46 4.83
3899 6066 1.079405 CTACCATTGACGGTGGCGT 60.079 57.895 0.00 0.00 40.39 5.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
24 25 6.542852 TCGTATAATTATCTTACCCGTACGC 58.457 40.000 10.49 0.00 34.22 4.42
145 150 2.048023 TAACCACCGTCGATCGCCT 61.048 57.895 11.09 0.00 38.35 5.52
174 179 6.092259 GGTGTGGTTTACTTAGTGCATTCTAG 59.908 42.308 0.00 0.00 0.00 2.43
180 185 3.849563 AGGTGTGGTTTACTTAGTGCA 57.150 42.857 0.00 0.00 0.00 4.57
224 229 7.189693 TGATTTATATGCAAATCGAGGTCAC 57.810 36.000 0.00 0.00 44.42 3.67
326 331 7.984422 TTGTTCTTTCATCTCTCATTGCTAA 57.016 32.000 0.00 0.00 0.00 3.09
462 467 2.110188 GTTCTCCCTCCTTTCCCCTTTT 59.890 50.000 0.00 0.00 0.00 2.27
464 469 1.373536 GTTCTCCCTCCTTTCCCCTT 58.626 55.000 0.00 0.00 0.00 3.95
475 480 0.472734 ACCAGCACTCTGTTCTCCCT 60.473 55.000 0.00 0.00 38.66 4.20
478 483 0.681733 TCCACCAGCACTCTGTTCTC 59.318 55.000 0.00 0.00 38.66 2.87
538 543 3.469739 CACCTTTAGTACCGGTTTGTGT 58.530 45.455 15.04 0.00 0.00 3.72
542 547 2.551504 CCAGCACCTTTAGTACCGGTTT 60.552 50.000 15.04 4.12 0.00 3.27
568 573 2.840651 CAGGATGTTGTTAGAGAGGGGT 59.159 50.000 0.00 0.00 0.00 4.95
578 583 0.185901 AGTGGTGGCAGGATGTTGTT 59.814 50.000 0.00 0.00 39.31 2.83
603 608 1.358725 CGTGCCATGAACCGGTACTG 61.359 60.000 8.00 5.69 37.03 2.74
649 654 5.179742 GGCGAGAGAAGATCTTTAGTATCGA 59.820 44.000 23.49 0.00 38.84 3.59
665 670 2.415608 CCAACGGCTAGGCGAGAGA 61.416 63.158 40.86 0.00 0.00 3.10
669 674 1.143183 GATTCCAACGGCTAGGCGA 59.857 57.895 40.86 21.49 0.00 5.54
686 691 3.261643 ACTGATGTGTCCATTAGTGCAGA 59.738 43.478 0.00 0.00 43.88 4.26
688 693 3.701205 ACTGATGTGTCCATTAGTGCA 57.299 42.857 0.01 0.00 43.88 4.57
705 710 1.588674 TTGTAACAGAACCGGCACTG 58.411 50.000 21.66 21.66 39.65 3.66
801 806 1.797320 TTACCTATACCCAAGCCGCT 58.203 50.000 0.00 0.00 0.00 5.52
874 879 2.270205 CGCCCTCACATTGGCTCT 59.730 61.111 0.00 0.00 45.71 4.09
890 895 3.625897 TCAGTGGAGGGTGGCACG 61.626 66.667 12.17 0.00 0.00 5.34
966 972 2.096248 GTATCAGAGGATAGCCGGGAG 58.904 57.143 2.18 0.00 36.69 4.30
991 997 2.740981 GAGTGAGTTCCATGCTGTTCTG 59.259 50.000 0.00 0.00 0.00 3.02
1144 1152 0.854062 TCTGTAAACAAACGTCGCCG 59.146 50.000 0.00 0.00 40.83 6.46
1145 1153 1.193874 CCTCTGTAAACAAACGTCGCC 59.806 52.381 0.00 0.00 0.00 5.54
1146 1154 1.398071 GCCTCTGTAAACAAACGTCGC 60.398 52.381 0.00 0.00 0.00 5.19
1147 1155 1.862201 TGCCTCTGTAAACAAACGTCG 59.138 47.619 0.00 0.00 0.00 5.12
1155 1163 0.741221 CCTCGCCTGCCTCTGTAAAC 60.741 60.000 0.00 0.00 0.00 2.01
1291 1303 1.428448 CTGTTCTTCATCGCGTCCAA 58.572 50.000 5.77 0.00 0.00 3.53
1659 1674 2.260869 GCCTGTCTGCGCCAAGAAA 61.261 57.895 4.18 0.00 0.00 2.52
1790 1805 0.244178 GCTATAGTAGGTGAGGCCGC 59.756 60.000 0.00 0.00 43.70 6.53
1897 1912 2.993853 CCTTCCTCCCCTCAGCAC 59.006 66.667 0.00 0.00 0.00 4.40
1902 1920 4.475135 GCACGCCTTCCTCCCCTC 62.475 72.222 0.00 0.00 0.00 4.30
2067 2088 2.106683 GTCGAATTCAGGGCGGTGG 61.107 63.158 6.22 0.00 0.00 4.61
2325 2382 2.260434 GTGTCGGGCTCGTAGCAA 59.740 61.111 5.57 0.00 44.75 3.91
2406 2463 2.805353 CCGGAGAAGTCGCACGTG 60.805 66.667 12.28 12.28 0.00 4.49
2728 2862 0.950071 GCCCGTTGCGTTGGTAGTAA 60.950 55.000 0.00 0.00 0.00 2.24
2813 2947 9.171701 GAGTAGTATATAAGTTTTGAGCGTCAG 57.828 37.037 0.00 0.00 0.00 3.51
2833 2967 9.393512 CATGTTAGTACTTAGTACTGGAGTAGT 57.606 37.037 29.05 22.03 46.99 2.73
2834 2968 9.610705 TCATGTTAGTACTTAGTACTGGAGTAG 57.389 37.037 29.05 16.63 46.99 2.57
2835 2969 9.388506 GTCATGTTAGTACTTAGTACTGGAGTA 57.611 37.037 29.05 10.86 46.99 2.59
2836 2970 7.065563 CGTCATGTTAGTACTTAGTACTGGAGT 59.934 40.741 29.05 13.59 46.99 3.85
2837 2971 7.065563 ACGTCATGTTAGTACTTAGTACTGGAG 59.934 40.741 29.05 16.48 46.99 3.86
2838 2972 6.881065 ACGTCATGTTAGTACTTAGTACTGGA 59.119 38.462 29.05 17.42 46.99 3.86
2839 2973 7.081526 ACGTCATGTTAGTACTTAGTACTGG 57.918 40.000 29.05 15.68 46.99 4.00
2840 2974 8.961294 AAACGTCATGTTAGTACTTAGTACTG 57.039 34.615 29.05 16.17 46.99 2.74
2842 2976 9.059485 CAGAAACGTCATGTTAGTACTTAGTAC 57.941 37.037 14.13 14.13 40.84 2.73
2843 2977 7.752239 GCAGAAACGTCATGTTAGTACTTAGTA 59.248 37.037 0.00 0.00 40.84 1.82
2844 2978 6.585322 GCAGAAACGTCATGTTAGTACTTAGT 59.415 38.462 0.00 0.00 40.84 2.24
2845 2979 6.584942 TGCAGAAACGTCATGTTAGTACTTAG 59.415 38.462 0.00 0.00 40.84 2.18
2846 2980 6.448852 TGCAGAAACGTCATGTTAGTACTTA 58.551 36.000 0.00 0.00 40.84 2.24
2847 2981 5.294356 TGCAGAAACGTCATGTTAGTACTT 58.706 37.500 0.00 0.00 40.84 2.24
2848 2982 4.878439 TGCAGAAACGTCATGTTAGTACT 58.122 39.130 0.00 0.00 40.84 2.73
2849 2983 5.585500 TTGCAGAAACGTCATGTTAGTAC 57.415 39.130 0.00 0.00 40.84 2.73
2975 3254 1.680249 CCAGCCTAGCCTTTGGTCTTC 60.680 57.143 0.00 0.00 0.00 2.87
2993 3272 5.717178 CCAAGCTAGTAATAGATAGGAGCCA 59.283 44.000 0.38 0.00 0.00 4.75
2994 3273 5.952947 TCCAAGCTAGTAATAGATAGGAGCC 59.047 44.000 0.38 0.00 0.00 4.70
2995 3274 7.469537 TTCCAAGCTAGTAATAGATAGGAGC 57.530 40.000 0.38 0.00 0.00 4.70
3005 3284 9.905713 TTGAGTTCATTATTCCAAGCTAGTAAT 57.094 29.630 0.00 0.00 0.00 1.89
3006 3285 9.162764 GTTGAGTTCATTATTCCAAGCTAGTAA 57.837 33.333 0.00 0.00 0.00 2.24
3009 3288 6.709643 CGTTGAGTTCATTATTCCAAGCTAG 58.290 40.000 0.00 0.00 0.00 3.42
3061 3340 6.920817 ACGAAGTGGTTTTCTTTCTTTCTTT 58.079 32.000 0.00 0.00 42.51 2.52
3062 3341 6.510879 ACGAAGTGGTTTTCTTTCTTTCTT 57.489 33.333 0.00 0.00 42.51 2.52
3063 3342 7.497909 TGATACGAAGTGGTTTTCTTTCTTTCT 59.502 33.333 0.00 0.00 45.73 2.52
3064 3343 7.636326 TGATACGAAGTGGTTTTCTTTCTTTC 58.364 34.615 0.00 0.00 45.73 2.62
3072 3354 6.956047 ACTTCTTTGATACGAAGTGGTTTTC 58.044 36.000 4.08 0.00 45.78 2.29
3078 3360 9.130312 GGCTATATACTTCTTTGATACGAAGTG 57.870 37.037 13.24 0.18 46.62 3.16
3142 3424 8.306038 ACCATAATGGCGTTATATAAGACGTAA 58.694 33.333 11.45 0.00 42.67 3.18
3258 5255 1.178534 GCACAAGCCTGGCAACCTAA 61.179 55.000 22.65 0.00 33.58 2.69
3259 5256 1.603455 GCACAAGCCTGGCAACCTA 60.603 57.895 22.65 0.00 33.58 3.08
3263 5428 1.611474 TTTGTGCACAAGCCTGGCAA 61.611 50.000 29.50 11.95 39.57 4.52
3414 5579 2.760385 GGAGGACGGGCAGCTAGT 60.760 66.667 0.00 0.00 0.00 2.57
3415 5580 2.443016 AGGAGGACGGGCAGCTAG 60.443 66.667 0.00 0.00 0.00 3.42
3416 5581 2.442272 GAGGAGGACGGGCAGCTA 60.442 66.667 0.00 0.00 0.00 3.32
3429 5594 2.363361 GGGAGACGAAGGGGAGGA 59.637 66.667 0.00 0.00 0.00 3.71
3441 5606 0.547075 CTAGAGGTCTGGACGGGAGA 59.453 60.000 0.00 0.00 0.00 3.71
3442 5607 0.256464 ACTAGAGGTCTGGACGGGAG 59.744 60.000 0.00 0.00 0.00 4.30
3443 5608 0.255318 GACTAGAGGTCTGGACGGGA 59.745 60.000 0.00 0.00 41.46 5.14
3451 5616 1.227946 GGAGGCGGACTAGAGGTCT 59.772 63.158 0.00 0.00 43.97 3.85
3452 5617 1.829096 GGGAGGCGGACTAGAGGTC 60.829 68.421 0.00 0.00 43.79 3.85
3453 5618 2.279408 GGGAGGCGGACTAGAGGT 59.721 66.667 0.00 0.00 0.00 3.85
3551 5716 2.594303 CACAGCCACGCCTCCAAA 60.594 61.111 0.00 0.00 0.00 3.28
3638 5803 3.053826 ACAACCAAAGGTAGAGGAGGTT 58.946 45.455 0.00 0.00 39.76 3.50
3815 5980 4.760047 CCCCAACGTCGCCTCCAG 62.760 72.222 0.00 0.00 0.00 3.86
3866 6033 5.313506 TCAATGGTAGCCTCCTCTAGATCTA 59.686 44.000 1.69 1.69 0.00 1.98
3873 6040 1.115467 CGTCAATGGTAGCCTCCTCT 58.885 55.000 0.00 0.00 0.00 3.69


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

AutoCloner maintained by Alex Coulton.