Multiple sequence alignment - TraesCS2D01G394400

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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 TraesCS2D01G394400 chr2D 100.000 3149 0 0 1 3149 505842815 505839667 0.000000e+00 5816.0
1 TraesCS2D01G394400 chr2B 89.526 2530 142 59 661 3149 593018506 593016059 0.000000e+00 3090.0
2 TraesCS2D01G394400 chr2B 93.638 613 22 5 43 652 593021759 593021161 0.000000e+00 900.0
3 TraesCS2D01G394400 chr2A 89.478 2224 74 47 2 2151 650261315 650259178 0.000000e+00 2663.0
4 TraesCS2D01G394400 chr2A 87.397 365 13 20 2167 2518 650259122 650258778 3.810000e-104 388.0
5 TraesCS2D01G394400 chr2A 88.278 273 25 6 2552 2820 650258776 650258507 1.410000e-83 320.0
6 TraesCS2D01G394400 chr2A 84.064 251 22 8 2913 3149 650258495 650258249 3.160000e-55 226.0
7 TraesCS2D01G394400 chr6D 82.353 102 18 0 1252 1353 340212627 340212728 4.330000e-14 89.8
8 TraesCS2D01G394400 chr6A 82.353 102 18 0 1252 1353 480310602 480310703 4.330000e-14 89.8


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 TraesCS2D01G394400 chr2D 505839667 505842815 3148 True 5816.00 5816 100.00000 1 3149 1 chr2D.!!$R1 3148
1 TraesCS2D01G394400 chr2B 593016059 593021759 5700 True 1995.00 3090 91.58200 43 3149 2 chr2B.!!$R1 3106
2 TraesCS2D01G394400 chr2A 650258249 650261315 3066 True 899.25 2663 87.30425 2 3149 4 chr2A.!!$R1 3147

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
541 561 0.326595 TCACTGGCCGGCTTAATGAA 59.673 50.0 28.56 3.23 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2218 4995 0.182537 TGAACAAGGGACACCAGGTG 59.817 55.0 18.93 18.93 40.13 4.0 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
35 36 2.900122 ACAACGATCGGCTTTGATTG 57.100 45.000 20.98 14.58 36.09 2.67
85 86 0.899019 TAGCATCGGGTACACTTGCA 59.101 50.000 18.56 5.66 35.79 4.08
281 293 4.060038 TCGGAGCACAAAATCTATCCTC 57.940 45.455 0.00 0.00 0.00 3.71
408 426 2.158928 GGGCATACATAACACGTACCCA 60.159 50.000 0.00 0.00 34.82 4.51
469 487 6.842163 CCACTGTTTGGTGTATTCTGTATTC 58.158 40.000 0.00 0.00 41.10 1.75
471 489 7.361201 CCACTGTTTGGTGTATTCTGTATTCTG 60.361 40.741 0.00 0.00 41.10 3.02
472 490 7.173218 CACTGTTTGGTGTATTCTGTATTCTGT 59.827 37.037 0.00 0.00 33.04 3.41
473 491 8.372459 ACTGTTTGGTGTATTCTGTATTCTGTA 58.628 33.333 0.00 0.00 0.00 2.74
541 561 0.326595 TCACTGGCCGGCTTAATGAA 59.673 50.000 28.56 3.23 0.00 2.57
550 570 2.096496 CCGGCTTAATGAAGACAAGCTG 59.904 50.000 0.00 7.27 46.56 4.24
551 571 2.476854 CGGCTTAATGAAGACAAGCTGC 60.477 50.000 0.00 0.00 41.29 5.25
552 572 2.476854 GGCTTAATGAAGACAAGCTGCG 60.477 50.000 0.00 0.00 40.85 5.18
553 573 2.778659 CTTAATGAAGACAAGCTGCGC 58.221 47.619 0.00 0.00 34.25 6.09
554 574 2.099141 TAATGAAGACAAGCTGCGCT 57.901 45.000 9.73 0.00 42.56 5.92
555 575 0.520404 AATGAAGACAAGCTGCGCTG 59.480 50.000 9.73 10.04 39.62 5.18
556 576 1.919956 ATGAAGACAAGCTGCGCTGC 61.920 55.000 29.38 29.38 39.62 5.25
557 577 3.642008 GAAGACAAGCTGCGCTGCG 62.642 63.158 29.77 19.17 39.62 5.18
652 672 1.142778 GAGATCTGCTTCACGGCGTC 61.143 60.000 10.85 0.00 34.52 5.19
670 3336 4.375235 GCGTCGAAATTATTAGCTTAGCG 58.625 43.478 0.00 0.00 0.00 4.26
672 3347 5.663294 GCGTCGAAATTATTAGCTTAGCGAG 60.663 44.000 0.00 0.00 0.00 5.03
713 3388 3.102052 TCGTGTCTTTAAGCGAAAGGT 57.898 42.857 12.47 0.00 44.18 3.50
965 3663 3.779850 CTGTGGTGTGGGCAGCTGT 62.780 63.158 16.64 0.00 43.05 4.40
983 3681 3.371063 GAGTGACCGGGAGCGACA 61.371 66.667 6.32 0.00 0.00 4.35
984 3682 3.628280 GAGTGACCGGGAGCGACAC 62.628 68.421 6.32 6.25 0.00 3.67
1503 4225 2.044946 ATCCAAGAAGGCCACGGC 60.045 61.111 5.01 0.00 37.29 5.68
1560 4282 0.967380 CATCCTTGCAGGTCCCAACC 60.967 60.000 0.00 0.00 46.87 3.77
1635 4357 3.357079 CACTTCACGCCACAGCCC 61.357 66.667 0.00 0.00 34.57 5.19
1772 4497 2.861006 GAAGCACCGGAAAGCGAC 59.139 61.111 9.46 5.34 35.48 5.19
2185 4959 7.472334 ACAATGTAGATTGCTTCCAAGAAAT 57.528 32.000 12.27 0.00 42.54 2.17
2191 4968 2.448926 TGCTTCCAAGAAATCGTCGA 57.551 45.000 0.00 0.00 0.00 4.20
2192 4969 2.337583 TGCTTCCAAGAAATCGTCGAG 58.662 47.619 0.00 0.00 0.00 4.04
2193 4970 2.029380 TGCTTCCAAGAAATCGTCGAGA 60.029 45.455 0.00 0.00 0.00 4.04
2194 4971 2.345942 GCTTCCAAGAAATCGTCGAGAC 59.654 50.000 0.00 0.00 0.00 3.36
2218 4995 2.128035 CTCGGCTGATAACACGAATCC 58.872 52.381 0.00 0.00 34.70 3.01
2239 5016 1.073923 ACCTGGTGTCCCTTGTTCATC 59.926 52.381 0.00 0.00 0.00 2.92
2240 5017 1.614317 CCTGGTGTCCCTTGTTCATCC 60.614 57.143 0.00 0.00 0.00 3.51
2241 5018 1.073763 CTGGTGTCCCTTGTTCATCCA 59.926 52.381 0.00 0.00 0.00 3.41
2242 5019 1.073763 TGGTGTCCCTTGTTCATCCAG 59.926 52.381 0.00 0.00 0.00 3.86
2243 5020 1.614317 GGTGTCCCTTGTTCATCCAGG 60.614 57.143 0.00 0.00 0.00 4.45
2244 5021 0.698238 TGTCCCTTGTTCATCCAGGG 59.302 55.000 0.00 0.00 41.03 4.45
2253 5030 1.866483 TTCATCCAGGGCCAGCACAT 61.866 55.000 6.18 0.00 0.00 3.21
2272 5049 6.417635 AGCACATACTTTTTCGTTTGAATGTG 59.582 34.615 7.55 7.55 39.16 3.21
2316 5093 2.410575 ACCAGTACCACCACCACTTTA 58.589 47.619 0.00 0.00 0.00 1.85
2340 5117 3.121544 GCTTTCTAGCATGGGTACGTAC 58.878 50.000 17.56 17.56 46.95 3.67
2371 5148 0.781787 CGATTTTGCGACACGTCTGA 59.218 50.000 0.00 0.00 0.00 3.27
2543 5328 1.345715 GGGACGGTGGAATCAGGGAT 61.346 60.000 0.00 0.00 0.00 3.85
2544 5329 1.420430 GGACGGTGGAATCAGGGATA 58.580 55.000 0.00 0.00 0.00 2.59
2591 5376 2.125310 TGCGCGGAGTTATGGGTG 60.125 61.111 8.83 0.00 0.00 4.61
2592 5377 2.125269 GCGCGGAGTTATGGGTGT 60.125 61.111 8.83 0.00 0.00 4.16
2593 5378 2.461110 GCGCGGAGTTATGGGTGTG 61.461 63.158 8.83 0.00 0.00 3.82
2594 5379 1.813753 CGCGGAGTTATGGGTGTGG 60.814 63.158 0.00 0.00 0.00 4.17
2595 5380 1.298667 GCGGAGTTATGGGTGTGGT 59.701 57.895 0.00 0.00 0.00 4.16
2598 5383 0.988832 GGAGTTATGGGTGTGGTGGA 59.011 55.000 0.00 0.00 0.00 4.02
2604 5389 3.175710 GGGTGTGGTGGAGGTGGT 61.176 66.667 0.00 0.00 0.00 4.16
2668 5461 1.134367 TGGATGTTAACGCGAGAGGAG 59.866 52.381 15.93 0.00 0.00 3.69
2731 5524 2.026356 TCTTTCTCCATCCGGAAATGCA 60.026 45.455 9.01 0.00 42.21 3.96
2734 5527 2.801483 TCTCCATCCGGAAATGCAAAA 58.199 42.857 9.01 0.00 42.21 2.44
2735 5528 2.754552 TCTCCATCCGGAAATGCAAAAG 59.245 45.455 9.01 0.00 42.21 2.27
2740 5533 4.493547 CATCCGGAAATGCAAAAGCTTTA 58.506 39.130 13.10 0.00 0.00 1.85
2741 5534 4.592485 TCCGGAAATGCAAAAGCTTTAA 57.408 36.364 13.10 1.70 0.00 1.52
2748 5541 6.293407 GGAAATGCAAAAGCTTTAAAACTCCC 60.293 38.462 13.10 6.23 0.00 4.30
2791 5584 1.804372 CGCTCCTCGGAGGAATTTCAG 60.804 57.143 25.95 14.90 45.28 3.02
2799 5592 2.094700 CGGAGGAATTTCAGACGTCTCA 60.095 50.000 16.96 0.00 0.00 3.27
2800 5593 3.429547 CGGAGGAATTTCAGACGTCTCAT 60.430 47.826 16.96 5.32 0.00 2.90
2822 5615 3.033764 GTTGACGGCTTGACGCGA 61.034 61.111 15.93 0.00 40.44 5.87
2823 5616 2.048597 TTGACGGCTTGACGCGAT 60.049 55.556 15.93 0.00 40.44 4.58
2825 5618 2.506217 GACGGCTTGACGCGATGA 60.506 61.111 15.93 0.00 40.44 2.92
2826 5619 2.048597 ACGGCTTGACGCGATGAA 60.049 55.556 15.93 0.46 40.44 2.57
2828 5621 1.059369 CGGCTTGACGCGATGAAAG 59.941 57.895 15.93 11.56 40.44 2.62
2830 5623 0.371645 GGCTTGACGCGATGAAAGAG 59.628 55.000 15.93 1.48 40.44 2.85
2831 5624 1.071605 GCTTGACGCGATGAAAGAGT 58.928 50.000 15.93 0.00 0.00 3.24
2832 5625 1.461127 GCTTGACGCGATGAAAGAGTT 59.539 47.619 15.93 0.00 0.00 3.01
2833 5626 2.096218 GCTTGACGCGATGAAAGAGTTT 60.096 45.455 15.93 0.00 0.00 2.66
2834 5627 3.607078 GCTTGACGCGATGAAAGAGTTTT 60.607 43.478 15.93 0.00 0.00 2.43
2835 5628 3.788434 TGACGCGATGAAAGAGTTTTC 57.212 42.857 15.93 0.00 42.45 2.29
2848 5641 8.731275 TGAAAGAGTTTTCATGTGTAGAAAGA 57.269 30.769 0.00 0.00 45.77 2.52
2849 5642 9.173021 TGAAAGAGTTTTCATGTGTAGAAAGAA 57.827 29.630 0.00 0.00 45.77 2.52
2851 5644 9.956720 AAAGAGTTTTCATGTGTAGAAAGAATG 57.043 29.630 0.00 0.00 36.45 2.67
2852 5645 7.588512 AGAGTTTTCATGTGTAGAAAGAATGC 58.411 34.615 0.00 0.00 36.45 3.56
2853 5646 6.681777 AGTTTTCATGTGTAGAAAGAATGCC 58.318 36.000 0.00 0.00 36.45 4.40
2858 5651 3.674997 TGTGTAGAAAGAATGCCAGGAC 58.325 45.455 0.00 0.00 0.00 3.85
2865 5658 1.831580 AGAATGCCAGGACTTTCAGC 58.168 50.000 0.00 0.00 0.00 4.26
2866 5659 1.353694 AGAATGCCAGGACTTTCAGCT 59.646 47.619 0.00 0.00 0.00 4.24
2870 5663 1.322442 GCCAGGACTTTCAGCTGTTT 58.678 50.000 14.67 0.00 0.00 2.83
2874 5667 4.616835 GCCAGGACTTTCAGCTGTTTAATG 60.617 45.833 14.67 5.84 0.00 1.90
2891 5710 1.153188 TGTGCACCCACACTCACAG 60.153 57.895 15.69 0.00 46.51 3.66
2893 5712 1.146041 TGCACCCACACTCACAGTC 59.854 57.895 0.00 0.00 0.00 3.51
2894 5713 1.146041 GCACCCACACTCACAGTCA 59.854 57.895 0.00 0.00 0.00 3.41
2895 5714 1.160329 GCACCCACACTCACAGTCAC 61.160 60.000 0.00 0.00 0.00 3.67
2896 5715 0.177836 CACCCACACTCACAGTCACA 59.822 55.000 0.00 0.00 0.00 3.58
2897 5716 0.465705 ACCCACACTCACAGTCACAG 59.534 55.000 0.00 0.00 0.00 3.66
2898 5717 0.752658 CCCACACTCACAGTCACAGA 59.247 55.000 0.00 0.00 0.00 3.41
2899 5718 1.269988 CCCACACTCACAGTCACAGAG 60.270 57.143 0.00 0.00 35.56 3.35
2900 5719 1.495878 CACACTCACAGTCACAGAGC 58.504 55.000 0.00 0.00 32.71 4.09
2901 5720 1.068281 CACACTCACAGTCACAGAGCT 59.932 52.381 0.00 0.00 32.71 4.09
2902 5721 1.068281 ACACTCACAGTCACAGAGCTG 59.932 52.381 0.00 0.00 38.58 4.24
2920 5739 2.012673 CTGTGATGGTCAGCTAAAGCC 58.987 52.381 0.00 0.00 43.38 4.35
2926 5745 0.673644 GGTCAGCTAAAGCCAGCGAA 60.674 55.000 0.00 0.00 46.52 4.70
2975 5798 1.541233 CCTTATCTGCATGGGGACGAC 60.541 57.143 0.00 0.00 0.00 4.34
2988 5811 1.226746 GGACGACTGGTTCTTGTTGG 58.773 55.000 0.00 0.00 0.00 3.77
3001 5824 4.074627 TCTTGTTGGTTTATCACGTGGA 57.925 40.909 17.00 2.69 0.00 4.02
3003 5826 5.067273 TCTTGTTGGTTTATCACGTGGAAT 58.933 37.500 17.00 5.26 0.00 3.01
3012 5835 3.812156 ATCACGTGGAATTGGTCGATA 57.188 42.857 17.00 0.00 0.00 2.92
3019 5842 2.159156 TGGAATTGGTCGATACGGACAG 60.159 50.000 0.00 0.00 38.70 3.51
3021 5844 0.750850 ATTGGTCGATACGGACAGGG 59.249 55.000 0.00 0.00 38.70 4.45
3022 5845 0.323633 TTGGTCGATACGGACAGGGA 60.324 55.000 0.00 0.00 38.70 4.20
3023 5846 0.750546 TGGTCGATACGGACAGGGAG 60.751 60.000 0.00 0.00 38.70 4.30
3024 5847 0.465097 GGTCGATACGGACAGGGAGA 60.465 60.000 0.00 0.00 38.70 3.71
3036 5859 3.161866 GACAGGGAGAGAGAGAACAAGT 58.838 50.000 0.00 0.00 0.00 3.16
3059 5892 2.819595 CAACTGGCACGGGATCGG 60.820 66.667 0.00 0.00 40.47 4.18
3065 5898 2.413765 GCACGGGATCGGAGAGAC 59.586 66.667 0.00 0.00 43.63 3.36
3067 5900 2.516460 ACGGGATCGGAGAGACGG 60.516 66.667 0.00 0.00 43.63 4.79
3068 5901 2.516460 CGGGATCGGAGAGACGGT 60.516 66.667 0.00 0.00 43.63 4.83
3095 5937 3.451894 CCATCCAGTTTGGGCCGC 61.452 66.667 0.00 0.00 38.32 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.074259 TCGTTGTAGTAGGTTCTGTAGCA 58.926 43.478 0.00 0.00 0.00 3.49
19 20 2.672961 TCTCAATCAAAGCCGATCGT 57.327 45.000 15.09 0.00 0.00 3.73
35 36 4.819088 GCCAAGGAGGTGATTTCTTATCTC 59.181 45.833 0.00 0.00 40.61 2.75
82 83 2.689471 CCCATCGAATCTTCCAATTGCA 59.311 45.455 0.00 0.00 0.00 4.08
83 84 2.689983 ACCCATCGAATCTTCCAATTGC 59.310 45.455 0.00 0.00 0.00 3.56
408 426 4.580551 GCGCGCACGTAGGGGTAT 62.581 66.667 29.10 0.00 42.83 2.73
553 573 2.406401 GCCATTGTAGCTGCGCAG 59.594 61.111 32.83 32.83 0.00 5.18
554 574 3.133464 GGCCATTGTAGCTGCGCA 61.133 61.111 10.98 10.98 0.00 6.09
555 575 4.241999 CGGCCATTGTAGCTGCGC 62.242 66.667 2.24 0.00 0.00 6.09
556 576 3.576356 CCGGCCATTGTAGCTGCG 61.576 66.667 2.24 0.00 35.17 5.18
557 577 2.438434 ACCGGCCATTGTAGCTGC 60.438 61.111 0.00 0.00 35.17 5.25
558 578 1.078497 TGACCGGCCATTGTAGCTG 60.078 57.895 0.00 0.00 36.32 4.24
559 579 1.221840 CTGACCGGCCATTGTAGCT 59.778 57.895 0.00 0.00 0.00 3.32
560 580 2.472909 GCTGACCGGCCATTGTAGC 61.473 63.158 0.00 1.49 0.00 3.58
561 581 0.392998 AAGCTGACCGGCCATTGTAG 60.393 55.000 0.00 0.00 0.00 2.74
562 582 0.037590 AAAGCTGACCGGCCATTGTA 59.962 50.000 0.00 0.00 0.00 2.41
670 3336 2.093288 TGATGGTCAGTTGGATCAGCTC 60.093 50.000 0.00 0.00 43.49 4.09
672 3347 2.408271 TGATGGTCAGTTGGATCAGC 57.592 50.000 0.00 0.00 43.39 4.26
674 3349 3.055167 ACGATTGATGGTCAGTTGGATCA 60.055 43.478 0.00 0.00 41.89 2.92
713 3388 3.636313 GATCCGCACCGTCCGTTCA 62.636 63.158 0.00 0.00 0.00 3.18
786 3465 1.139989 GCTGCGTCGCATGTATACAT 58.860 50.000 22.03 12.75 38.13 2.29
788 3467 0.504384 CAGCTGCGTCGCATGTATAC 59.496 55.000 22.03 6.40 38.13 1.47
789 3468 0.383949 TCAGCTGCGTCGCATGTATA 59.616 50.000 22.03 2.82 38.13 1.47
965 3663 3.371063 GTCGCTCCCGGTCACTCA 61.371 66.667 0.00 0.00 34.56 3.41
1560 4282 3.790437 ACCCTCCGATGCTGCTGG 61.790 66.667 0.00 0.19 0.00 4.85
2191 4968 2.033550 GTGTTATCAGCCGAGATCGTCT 59.966 50.000 1.09 0.00 37.74 4.18
2192 4969 2.386249 GTGTTATCAGCCGAGATCGTC 58.614 52.381 1.09 0.00 37.74 4.20
2193 4970 1.268589 CGTGTTATCAGCCGAGATCGT 60.269 52.381 1.09 0.00 37.74 3.73
2194 4971 1.002792 TCGTGTTATCAGCCGAGATCG 60.003 52.381 0.00 0.00 39.44 3.69
2195 4972 2.776312 TCGTGTTATCAGCCGAGATC 57.224 50.000 0.00 0.00 0.00 2.75
2218 4995 0.182537 TGAACAAGGGACACCAGGTG 59.817 55.000 18.93 18.93 40.13 4.00
2239 5016 0.323725 AAAGTATGTGCTGGCCCTGG 60.324 55.000 0.00 0.00 0.00 4.45
2240 5017 1.549203 AAAAGTATGTGCTGGCCCTG 58.451 50.000 0.00 0.00 0.00 4.45
2241 5018 2.171003 GAAAAAGTATGTGCTGGCCCT 58.829 47.619 0.00 0.00 0.00 5.19
2242 5019 1.135402 CGAAAAAGTATGTGCTGGCCC 60.135 52.381 0.00 0.00 0.00 5.80
2243 5020 1.539827 ACGAAAAAGTATGTGCTGGCC 59.460 47.619 0.00 0.00 0.00 5.36
2244 5021 2.989422 ACGAAAAAGTATGTGCTGGC 57.011 45.000 0.00 0.00 0.00 4.85
2253 5030 5.741510 CAGTGCACATTCAAACGAAAAAGTA 59.258 36.000 21.04 0.00 0.00 2.24
2373 5150 2.434359 CTCACGGGGGTTCTTCGC 60.434 66.667 0.00 0.00 0.00 4.70
2381 5165 1.153289 CATTCAGCTCTCACGGGGG 60.153 63.158 0.00 0.00 0.00 5.40
2543 5328 0.907704 TTCCAGGCTCCCGCTTTCTA 60.908 55.000 0.00 0.00 36.09 2.10
2544 5329 2.224159 TTCCAGGCTCCCGCTTTCT 61.224 57.895 0.00 0.00 36.09 2.52
2591 5376 2.113139 CACCACCACCTCCACCAC 59.887 66.667 0.00 0.00 0.00 4.16
2592 5377 3.174987 CCACCACCACCTCCACCA 61.175 66.667 0.00 0.00 0.00 4.17
2593 5378 3.175710 ACCACCACCACCTCCACC 61.176 66.667 0.00 0.00 0.00 4.61
2594 5379 2.113139 CACCACCACCACCTCCAC 59.887 66.667 0.00 0.00 0.00 4.02
2595 5380 3.174987 CCACCACCACCACCTCCA 61.175 66.667 0.00 0.00 0.00 3.86
2598 5383 3.498071 CACCCACCACCACCACCT 61.498 66.667 0.00 0.00 0.00 4.00
2648 5441 1.134367 CTCCTCTCGCGTTAACATCCA 59.866 52.381 5.77 0.00 0.00 3.41
2652 5445 1.214589 GGCTCCTCTCGCGTTAACA 59.785 57.895 5.77 0.00 0.00 2.41
2731 5524 4.344102 GGTGGAGGGAGTTTTAAAGCTTTT 59.656 41.667 18.47 0.00 0.00 2.27
2734 5527 2.552373 CGGTGGAGGGAGTTTTAAAGCT 60.552 50.000 4.01 4.01 0.00 3.74
2735 5528 1.810755 CGGTGGAGGGAGTTTTAAAGC 59.189 52.381 0.00 0.00 0.00 3.51
2740 5533 0.106419 TTTGCGGTGGAGGGAGTTTT 60.106 50.000 0.00 0.00 0.00 2.43
2741 5534 0.537371 CTTTGCGGTGGAGGGAGTTT 60.537 55.000 0.00 0.00 0.00 2.66
2748 5541 2.680913 CGGAAGCTTTGCGGTGGAG 61.681 63.158 0.00 0.00 41.03 3.86
2799 5592 0.865769 GTCAAGCCGTCAACGACAAT 59.134 50.000 3.71 0.00 43.02 2.71
2800 5593 1.484227 CGTCAAGCCGTCAACGACAA 61.484 55.000 3.71 0.00 43.02 3.18
2825 5618 9.956720 CATTCTTTCTACACATGAAAACTCTTT 57.043 29.630 0.00 0.00 33.70 2.52
2826 5619 8.078596 GCATTCTTTCTACACATGAAAACTCTT 58.921 33.333 0.00 0.00 33.70 2.85
2828 5621 6.803807 GGCATTCTTTCTACACATGAAAACTC 59.196 38.462 0.00 0.00 33.70 3.01
2830 5623 6.446318 TGGCATTCTTTCTACACATGAAAAC 58.554 36.000 0.00 0.00 33.70 2.43
2831 5624 6.294675 CCTGGCATTCTTTCTACACATGAAAA 60.295 38.462 0.00 0.00 33.70 2.29
2832 5625 5.183713 CCTGGCATTCTTTCTACACATGAAA 59.816 40.000 0.00 0.00 33.15 2.69
2833 5626 4.701651 CCTGGCATTCTTTCTACACATGAA 59.298 41.667 0.00 0.00 0.00 2.57
2834 5627 4.019411 TCCTGGCATTCTTTCTACACATGA 60.019 41.667 0.00 0.00 0.00 3.07
2835 5628 4.095483 GTCCTGGCATTCTTTCTACACATG 59.905 45.833 0.00 0.00 0.00 3.21
2836 5629 4.018960 AGTCCTGGCATTCTTTCTACACAT 60.019 41.667 0.00 0.00 0.00 3.21
2837 5630 3.327757 AGTCCTGGCATTCTTTCTACACA 59.672 43.478 0.00 0.00 0.00 3.72
2838 5631 3.944087 AGTCCTGGCATTCTTTCTACAC 58.056 45.455 0.00 0.00 0.00 2.90
2839 5632 4.640771 AAGTCCTGGCATTCTTTCTACA 57.359 40.909 0.00 0.00 0.00 2.74
2840 5633 5.003804 TGAAAGTCCTGGCATTCTTTCTAC 58.996 41.667 24.80 11.50 43.21 2.59
2841 5634 5.241403 TGAAAGTCCTGGCATTCTTTCTA 57.759 39.130 24.80 15.86 43.21 2.10
2842 5635 4.077822 CTGAAAGTCCTGGCATTCTTTCT 58.922 43.478 24.80 5.91 43.21 2.52
2843 5636 3.366781 GCTGAAAGTCCTGGCATTCTTTC 60.367 47.826 21.26 21.26 43.14 2.62
2844 5637 2.560105 GCTGAAAGTCCTGGCATTCTTT 59.440 45.455 10.05 10.05 35.30 2.52
2845 5638 2.165998 GCTGAAAGTCCTGGCATTCTT 58.834 47.619 0.00 0.00 35.30 2.52
2846 5639 1.353694 AGCTGAAAGTCCTGGCATTCT 59.646 47.619 0.00 0.00 35.30 2.40
2847 5640 1.471684 CAGCTGAAAGTCCTGGCATTC 59.528 52.381 8.42 0.00 35.30 2.67
2848 5641 1.202976 ACAGCTGAAAGTCCTGGCATT 60.203 47.619 23.35 0.00 35.30 3.56
2849 5642 0.403271 ACAGCTGAAAGTCCTGGCAT 59.597 50.000 23.35 0.00 35.30 4.40
2850 5643 0.183492 AACAGCTGAAAGTCCTGGCA 59.817 50.000 23.35 0.00 35.30 4.92
2851 5644 1.322442 AAACAGCTGAAAGTCCTGGC 58.678 50.000 23.35 0.00 35.30 4.85
2852 5645 4.520492 ACATTAAACAGCTGAAAGTCCTGG 59.480 41.667 23.35 3.71 35.30 4.45
2853 5646 5.455392 CACATTAAACAGCTGAAAGTCCTG 58.545 41.667 23.35 10.78 35.30 3.86
2858 5651 3.983344 GGTGCACATTAAACAGCTGAAAG 59.017 43.478 23.35 3.89 0.00 2.62
2865 5658 2.622942 AGTGTGGGTGCACATTAAACAG 59.377 45.455 20.43 0.00 41.52 3.16
2866 5659 2.621055 GAGTGTGGGTGCACATTAAACA 59.379 45.455 20.43 11.67 41.52 2.83
2870 5663 1.141858 TGTGAGTGTGGGTGCACATTA 59.858 47.619 20.43 0.45 41.52 1.90
2874 5667 1.153168 ACTGTGAGTGTGGGTGCAC 60.153 57.895 8.80 8.80 39.51 4.57
2900 5719 2.012673 GGCTTTAGCTGACCATCACAG 58.987 52.381 0.00 0.00 41.70 3.66
2901 5720 1.350684 TGGCTTTAGCTGACCATCACA 59.649 47.619 0.00 0.00 41.70 3.58
2902 5721 2.012673 CTGGCTTTAGCTGACCATCAC 58.987 52.381 0.00 0.00 41.70 3.06
2920 5739 0.723414 ATGAATCGTGTGCTTCGCTG 59.277 50.000 0.00 0.00 0.00 5.18
2926 5745 1.028330 CCAGCCATGAATCGTGTGCT 61.028 55.000 11.05 11.05 30.94 4.40
2929 5748 0.541392 TAGCCAGCCATGAATCGTGT 59.459 50.000 1.46 0.00 0.00 4.49
2975 5798 4.274950 ACGTGATAAACCAACAAGAACCAG 59.725 41.667 0.00 0.00 0.00 4.00
2988 5811 3.680937 TCGACCAATTCCACGTGATAAAC 59.319 43.478 19.30 0.00 0.00 2.01
3001 5824 1.138266 CCCTGTCCGTATCGACCAATT 59.862 52.381 0.00 0.00 31.35 2.32
3003 5826 0.323633 TCCCTGTCCGTATCGACCAA 60.324 55.000 0.00 0.00 31.35 3.67
3012 5835 0.699399 TTCTCTCTCTCCCTGTCCGT 59.301 55.000 0.00 0.00 0.00 4.69
3019 5842 2.559231 ACGAACTTGTTCTCTCTCTCCC 59.441 50.000 11.11 0.00 0.00 4.30
3021 5844 3.253677 TGGACGAACTTGTTCTCTCTCTC 59.746 47.826 11.11 0.00 0.00 3.20
3022 5845 3.223435 TGGACGAACTTGTTCTCTCTCT 58.777 45.455 11.11 0.00 0.00 3.10
3023 5846 3.644884 TGGACGAACTTGTTCTCTCTC 57.355 47.619 11.11 1.91 0.00 3.20
3024 5847 3.385111 AGTTGGACGAACTTGTTCTCTCT 59.615 43.478 11.11 6.22 42.70 3.10
3036 5859 2.280524 CCGTGCCAGTTGGACGAA 60.281 61.111 9.90 0.00 39.41 3.85
3067 5900 1.520787 CTGGATGGACCGGCGTTAC 60.521 63.158 6.01 0.00 42.61 2.50
3068 5901 2.897207 CTGGATGGACCGGCGTTA 59.103 61.111 6.01 0.00 42.61 3.18
3103 5945 1.597027 GGTGGCGCTGGCGTTATAT 60.597 57.895 16.21 0.00 41.24 0.86


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

AutoCloner maintained by Alex Coulton.