Multiple sequence alignment - TraesCS1A01G106400

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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 TraesCS1A01G106400 chr1A 100.000 2949 0 0 1 2949 104223899 104220951 0.000000e+00 5446
1 TraesCS1A01G106400 chr1D 92.861 2101 77 31 1 2071 101277463 101279520 0.000000e+00 2981
2 TraesCS1A01G106400 chr1D 88.308 804 83 8 2145 2943 101279522 101280319 0.000000e+00 953
3 TraesCS1A01G106400 chr1B 92.244 1934 78 35 1 1907 150524637 150522749 0.000000e+00 2675
4 TraesCS1A01G106400 chr1B 88.866 476 46 5 2474 2944 150374743 150374270 1.970000e-161 579
5 TraesCS1A01G106400 chr1B 83.617 470 49 10 1931 2397 150522070 150521626 1.630000e-112 416


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 TraesCS1A01G106400 chr1A 104220951 104223899 2948 True 5446.0 5446 100.0000 1 2949 1 chr1A.!!$R1 2948
1 TraesCS1A01G106400 chr1D 101277463 101280319 2856 False 1967.0 2981 90.5845 1 2943 2 chr1D.!!$F1 2942
2 TraesCS1A01G106400 chr1B 150521626 150524637 3011 True 1545.5 2675 87.9305 1 2397 2 chr1B.!!$R2 2396

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
635 667 0.601057 GGTTGGTTGGTGGTGTATGC 59.399 55.0 0.0 0.0 0.0 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2546 3257 0.04087 TTGTGGTTGTAATGTGCGCG 60.041 50.0 0.0 0.0 0.0 6.86 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
38 39 1.765161 CGATACATGTGCCGGCAGTG 61.765 60.000 33.73 31.54 0.00 3.66
52 60 1.860484 GCAGTGGCACAAGAAGCTCC 61.860 60.000 21.41 0.00 44.16 4.70
64 72 2.262471 GAAGCTCCATGTTGCCAGCG 62.262 60.000 3.92 0.00 36.95 5.18
76 84 1.672356 GCCAGCGGATGACAGTTGT 60.672 57.895 0.00 0.00 0.00 3.32
118 129 1.586578 GAACATTCTAATCGTCGCGCA 59.413 47.619 8.75 0.00 0.00 6.09
265 276 5.497474 AGTCCAATTAGTTAAATCGGCACT 58.503 37.500 0.00 0.00 0.00 4.40
366 388 2.983296 AGGGAGGAGGGAGATGTATTG 58.017 52.381 0.00 0.00 0.00 1.90
376 398 6.352016 AGGGAGATGTATTGCATGTAGTAG 57.648 41.667 0.00 0.00 38.06 2.57
427 455 2.103042 GCACATGACGCAGGAGACC 61.103 63.158 0.00 0.00 0.00 3.85
428 456 1.593787 CACATGACGCAGGAGACCT 59.406 57.895 0.00 0.00 0.00 3.85
432 460 1.734465 CATGACGCAGGAGACCTTTTC 59.266 52.381 0.00 0.00 0.00 2.29
469 497 4.106925 GCTGAGGTGGCAGGGAGG 62.107 72.222 0.00 0.00 36.41 4.30
635 667 0.601057 GGTTGGTTGGTGGTGTATGC 59.399 55.000 0.00 0.00 0.00 3.14
636 668 1.323412 GTTGGTTGGTGGTGTATGCA 58.677 50.000 0.00 0.00 0.00 3.96
637 669 1.892474 GTTGGTTGGTGGTGTATGCAT 59.108 47.619 3.79 3.79 0.00 3.96
638 670 1.543607 TGGTTGGTGGTGTATGCATG 58.456 50.000 10.16 0.00 0.00 4.06
745 778 2.025981 AGTTAGGAGGAACATGCATGCA 60.026 45.455 26.53 25.04 0.00 3.96
746 779 2.954318 GTTAGGAGGAACATGCATGCAT 59.046 45.455 27.46 27.46 37.08 3.96
819 852 4.275689 CCTACTCTCTCACTAGCATCACAG 59.724 50.000 0.00 0.00 0.00 3.66
827 860 8.314021 TCTCTCACTAGCATCACAGAAATAAAA 58.686 33.333 0.00 0.00 0.00 1.52
831 864 9.890629 TCACTAGCATCACAGAAATAAAATAGT 57.109 29.630 0.00 0.00 0.00 2.12
953 987 4.412199 TCTGACACCTAATTCCCCCAATAG 59.588 45.833 0.00 0.00 0.00 1.73
1075 1110 3.583806 CTGCATTATCTCCCTCATCGAC 58.416 50.000 0.00 0.00 0.00 4.20
1105 1140 1.003759 CTAGCCACTCTACGTACGCAG 60.004 57.143 16.72 12.80 0.00 5.18
1125 1160 0.735632 CGCACTTGCCTCTCTGTCTC 60.736 60.000 0.00 0.00 37.91 3.36
1126 1161 0.390998 GCACTTGCCTCTCTGTCTCC 60.391 60.000 0.00 0.00 34.31 3.71
1130 1165 0.616111 TTGCCTCTCTGTCTCCCTCC 60.616 60.000 0.00 0.00 0.00 4.30
1131 1166 1.760480 GCCTCTCTGTCTCCCTCCC 60.760 68.421 0.00 0.00 0.00 4.30
1136 1171 0.628522 CTCTGTCTCCCTCCCTCTCA 59.371 60.000 0.00 0.00 0.00 3.27
1140 1175 1.342474 TGTCTCCCTCCCTCTCACATC 60.342 57.143 0.00 0.00 0.00 3.06
1146 1187 0.179936 CTCCCTCTCACATCCCAAGC 59.820 60.000 0.00 0.00 0.00 4.01
1161 1202 3.685214 AAGCAGTAGCCGTCGCGAG 62.685 63.158 10.24 0.00 43.56 5.03
1551 1592 9.994432 CACACCAAAGACTCTTGATTATTTATC 57.006 33.333 0.00 0.00 0.00 1.75
1740 1788 4.529716 AATTATACGGGTGGGAATGGTT 57.470 40.909 0.00 0.00 0.00 3.67
1761 1809 8.690680 TGGTTATTGGTTTATTCGTTAATTGC 57.309 30.769 0.00 0.00 0.00 3.56
1818 1871 9.764870 GTGATGATGTAAATATGTATGCATGAC 57.235 33.333 10.16 4.48 36.58 3.06
1898 1953 8.736751 ATTTTGGTTGCTAGTATTTGTTTACG 57.263 30.769 0.00 0.00 0.00 3.18
1919 1974 5.734720 ACGAATCACTATGACAGGACAATT 58.265 37.500 0.00 0.00 0.00 2.32
1920 1975 6.873997 ACGAATCACTATGACAGGACAATTA 58.126 36.000 0.00 0.00 0.00 1.40
1921 1976 7.500992 ACGAATCACTATGACAGGACAATTAT 58.499 34.615 0.00 0.00 0.00 1.28
1922 1977 7.987458 ACGAATCACTATGACAGGACAATTATT 59.013 33.333 0.00 0.00 0.00 1.40
1923 1978 8.491152 CGAATCACTATGACAGGACAATTATTC 58.509 37.037 0.00 0.00 0.00 1.75
1925 1980 8.668510 ATCACTATGACAGGACAATTATTCAC 57.331 34.615 0.00 0.00 0.00 3.18
1926 1981 7.851228 TCACTATGACAGGACAATTATTCACT 58.149 34.615 0.00 0.00 0.00 3.41
1947 2657 6.704050 TCACTCTTATGTGATGTTTGTTTCGA 59.296 34.615 0.00 0.00 41.43 3.71
2006 2716 6.821665 TCAATTACCTGAGAATAGAAAACGGG 59.178 38.462 0.00 0.00 0.00 5.28
2047 2757 2.492088 GTGGTTTGATGGTTAAGAGGGC 59.508 50.000 0.00 0.00 0.00 5.19
2055 2765 0.107993 GGTTAAGAGGGCGGTGGTAC 60.108 60.000 0.00 0.00 0.00 3.34
2056 2766 0.107993 GTTAAGAGGGCGGTGGTACC 60.108 60.000 4.43 4.43 34.05 3.34
2072 2782 0.726366 TACCCCTAACCTCCCATGGT 59.274 55.000 11.73 0.00 43.11 3.55
2079 2789 0.037734 AACCTCCCATGGTTCGAACC 59.962 55.000 35.49 35.49 46.37 3.62
2096 2806 1.715785 ACCCCATGGTTGAGGTTTTG 58.284 50.000 11.73 0.00 44.75 2.44
2104 2814 1.602377 GGTTGAGGTTTTGGTGTCTCG 59.398 52.381 0.00 0.00 0.00 4.04
2105 2815 2.285977 GTTGAGGTTTTGGTGTCTCGT 58.714 47.619 0.00 0.00 0.00 4.18
2106 2816 2.681344 GTTGAGGTTTTGGTGTCTCGTT 59.319 45.455 0.00 0.00 0.00 3.85
2107 2817 2.993937 TGAGGTTTTGGTGTCTCGTTT 58.006 42.857 0.00 0.00 0.00 3.60
2108 2818 4.139859 TGAGGTTTTGGTGTCTCGTTTA 57.860 40.909 0.00 0.00 0.00 2.01
2109 2819 4.710324 TGAGGTTTTGGTGTCTCGTTTAT 58.290 39.130 0.00 0.00 0.00 1.40
2110 2820 5.127491 TGAGGTTTTGGTGTCTCGTTTATT 58.873 37.500 0.00 0.00 0.00 1.40
2111 2821 5.237779 TGAGGTTTTGGTGTCTCGTTTATTC 59.762 40.000 0.00 0.00 0.00 1.75
2112 2822 5.374071 AGGTTTTGGTGTCTCGTTTATTCT 58.626 37.500 0.00 0.00 0.00 2.40
2113 2823 5.826208 AGGTTTTGGTGTCTCGTTTATTCTT 59.174 36.000 0.00 0.00 0.00 2.52
2114 2824 6.320418 AGGTTTTGGTGTCTCGTTTATTCTTT 59.680 34.615 0.00 0.00 0.00 2.52
2115 2825 6.635641 GGTTTTGGTGTCTCGTTTATTCTTTC 59.364 38.462 0.00 0.00 0.00 2.62
2116 2826 6.928979 TTTGGTGTCTCGTTTATTCTTTCA 57.071 33.333 0.00 0.00 0.00 2.69
2117 2827 6.928979 TTGGTGTCTCGTTTATTCTTTCAA 57.071 33.333 0.00 0.00 0.00 2.69
2127 2837 7.617225 TCGTTTATTCTTTCAATAGGAGGTGA 58.383 34.615 0.00 0.00 0.00 4.02
2133 2843 6.688073 TCTTTCAATAGGAGGTGACTTTCT 57.312 37.500 0.00 0.00 44.43 2.52
2134 2844 7.792364 TCTTTCAATAGGAGGTGACTTTCTA 57.208 36.000 0.00 0.00 44.43 2.10
2140 2850 8.206867 TCAATAGGAGGTGACTTTCTATCAATG 58.793 37.037 0.00 0.00 44.43 2.82
2142 2852 4.785376 AGGAGGTGACTTTCTATCAATGGT 59.215 41.667 0.00 0.00 44.43 3.55
2143 2853 4.878397 GGAGGTGACTTTCTATCAATGGTG 59.122 45.833 0.00 0.00 44.43 4.17
2167 2877 3.309436 AATGCGACGTGGCTAGCCA 62.309 57.895 32.88 32.88 45.02 4.75
2208 2918 3.049912 GGATGTGCTTTTCGTTTTGTCC 58.950 45.455 0.00 0.00 0.00 4.02
2210 2920 1.738350 TGTGCTTTTCGTTTTGTCCGA 59.262 42.857 0.00 0.00 0.00 4.55
2359 3069 3.282021 GGTGATGGCTGCTAGATTTCAA 58.718 45.455 0.00 0.00 0.00 2.69
2400 3111 0.555769 TTCCCAAGGCAGTTGTTCCT 59.444 50.000 0.00 0.00 33.87 3.36
2410 3121 2.226674 GCAGTTGTTCCTTAGGTGCTTC 59.773 50.000 0.00 0.00 0.00 3.86
2411 3122 3.476552 CAGTTGTTCCTTAGGTGCTTCA 58.523 45.455 0.00 0.00 0.00 3.02
2446 3157 6.783892 TTTATTTTTCAGGAGCATGCAAAC 57.216 33.333 21.98 9.36 0.00 2.93
2455 3166 1.111116 AGCATGCAAACTGTGTGCCT 61.111 50.000 21.98 7.72 41.49 4.75
2464 3175 4.787598 CAAACTGTGTGCCTTAGCTTTAG 58.212 43.478 0.00 0.00 40.80 1.85
2515 3226 2.039084 AGACAAACTCCCATCACACCTC 59.961 50.000 0.00 0.00 0.00 3.85
2517 3228 1.001974 CAAACTCCCATCACACCTCGA 59.998 52.381 0.00 0.00 0.00 4.04
2533 3244 3.447944 ACCTCGATGAGAAGTAAACTCCC 59.552 47.826 0.00 0.00 33.95 4.30
2539 3250 3.173965 TGAGAAGTAAACTCCCCTCCAG 58.826 50.000 0.00 0.00 33.95 3.86
2542 3253 2.046280 AGTAAACTCCCCTCCAGCTT 57.954 50.000 0.00 0.00 0.00 3.74
2546 3257 0.402121 AACTCCCCTCCAGCTTGAAC 59.598 55.000 0.00 0.00 0.00 3.18
2549 3260 3.121030 CCCTCCAGCTTGAACGCG 61.121 66.667 3.53 3.53 34.40 6.01
2566 3277 1.404477 GCGCACATTACAACCACAAC 58.596 50.000 0.30 0.00 0.00 3.32
2567 3278 1.268794 GCGCACATTACAACCACAACA 60.269 47.619 0.30 0.00 0.00 3.33
2579 3290 5.129634 ACAACCACAACACACAAGATCATA 58.870 37.500 0.00 0.00 0.00 2.15
2595 3306 6.460103 AGATCATATCCTAAACTGGCCATT 57.540 37.500 5.51 0.00 0.00 3.16
2627 3338 1.303317 AACCAACACCGGCCATCTC 60.303 57.895 0.00 0.00 0.00 2.75
2643 3354 3.571401 CCATCTCCAAAGAGCAACAACTT 59.429 43.478 0.00 0.00 40.22 2.66
2654 3366 7.573968 AAGAGCAACAACTTCAAAGAACTAT 57.426 32.000 0.00 0.00 0.00 2.12
2655 3367 7.195839 AGAGCAACAACTTCAAAGAACTATC 57.804 36.000 0.00 0.00 0.00 2.08
2684 3396 1.077265 CACCAGCCACCCCTTGAAT 59.923 57.895 0.00 0.00 0.00 2.57
2701 3413 2.304761 TGAATGGCCTAAAAGAGTCGGT 59.695 45.455 3.32 0.00 0.00 4.69
2703 3415 3.821421 ATGGCCTAAAAGAGTCGGTAG 57.179 47.619 3.32 0.00 0.00 3.18
2704 3416 2.532843 TGGCCTAAAAGAGTCGGTAGT 58.467 47.619 3.32 0.00 0.00 2.73
2705 3417 2.232941 TGGCCTAAAAGAGTCGGTAGTG 59.767 50.000 3.32 0.00 0.00 2.74
2706 3418 2.233186 GGCCTAAAAGAGTCGGTAGTGT 59.767 50.000 0.00 0.00 0.00 3.55
2708 3420 3.305881 GCCTAAAAGAGTCGGTAGTGTGT 60.306 47.826 0.00 0.00 0.00 3.72
2709 3421 4.235360 CCTAAAAGAGTCGGTAGTGTGTG 58.765 47.826 0.00 0.00 0.00 3.82
2711 3423 1.700955 AAGAGTCGGTAGTGTGTGGT 58.299 50.000 0.00 0.00 0.00 4.16
2712 3424 0.959553 AGAGTCGGTAGTGTGTGGTG 59.040 55.000 0.00 0.00 0.00 4.17
2715 3427 1.152504 TCGGTAGTGTGTGGTGGGA 60.153 57.895 0.00 0.00 0.00 4.37
2716 3428 1.005394 CGGTAGTGTGTGGTGGGAC 60.005 63.158 0.00 0.00 0.00 4.46
2717 3429 1.469335 CGGTAGTGTGTGGTGGGACT 61.469 60.000 0.00 0.00 0.00 3.85
2745 3458 6.692486 ACAACTACGAGAAAGTCATCATCTT 58.308 36.000 0.00 0.00 0.00 2.40
2756 3469 1.839994 TCATCATCTTGGACTCACCCC 59.160 52.381 0.00 0.00 38.00 4.95
2757 3470 0.833287 ATCATCTTGGACTCACCCCG 59.167 55.000 0.00 0.00 38.00 5.73
2758 3471 0.544357 TCATCTTGGACTCACCCCGT 60.544 55.000 0.00 0.00 38.00 5.28
2761 3474 0.178955 TCTTGGACTCACCCCGTACA 60.179 55.000 0.00 0.00 38.00 2.90
2762 3475 0.902531 CTTGGACTCACCCCGTACAT 59.097 55.000 0.00 0.00 38.00 2.29
2763 3476 2.104967 CTTGGACTCACCCCGTACATA 58.895 52.381 0.00 0.00 38.00 2.29
2765 3478 0.388294 GGACTCACCCCGTACATAGC 59.612 60.000 0.00 0.00 0.00 2.97
2783 3499 1.457831 CTAGCGCCCCTAGACCCTT 60.458 63.158 2.29 0.00 45.30 3.95
2790 3506 0.824759 CCCCTAGACCCTTGAGAACG 59.175 60.000 0.00 0.00 0.00 3.95
2791 3507 0.824759 CCCTAGACCCTTGAGAACGG 59.175 60.000 0.00 0.00 0.00 4.44
2799 3515 2.027469 ACCCTTGAGAACGGTCCATAAC 60.027 50.000 0.00 0.00 0.00 1.89
2802 3518 2.380084 TGAGAACGGTCCATAACAGC 57.620 50.000 0.00 0.00 0.00 4.40
2807 3523 2.813179 CGGTCCATAACAGCAGCGC 61.813 63.158 0.00 0.00 0.00 5.92
2825 3541 1.423845 CGCACCATAGGAACGCAAC 59.576 57.895 0.00 0.00 0.00 4.17
2826 3542 1.019278 CGCACCATAGGAACGCAACT 61.019 55.000 0.00 0.00 0.00 3.16
2846 3562 3.274288 CTTAGAACCTCCAAGCCATGTC 58.726 50.000 0.00 0.00 0.00 3.06
2872 3588 2.672961 TACGATGCTCCAAACAGAGG 57.327 50.000 0.00 0.00 34.26 3.69
2873 3589 0.036010 ACGATGCTCCAAACAGAGGG 60.036 55.000 0.00 0.00 34.26 4.30
2875 3591 1.134280 CGATGCTCCAAACAGAGGGAT 60.134 52.381 0.00 0.00 34.26 3.85
2877 3593 0.329261 TGCTCCAAACAGAGGGATGG 59.671 55.000 0.00 0.00 34.26 3.51
2880 3596 1.002134 CCAAACAGAGGGATGGCGT 60.002 57.895 0.00 0.00 0.00 5.68
2882 3598 1.079127 AAACAGAGGGATGGCGTCG 60.079 57.895 0.00 0.00 0.00 5.12
2886 3602 2.833582 GAGGGATGGCGTCGAGGA 60.834 66.667 9.75 0.00 0.00 3.71
2887 3603 2.123251 AGGGATGGCGTCGAGGAT 60.123 61.111 9.75 0.00 0.00 3.24
2904 3620 0.882042 GATGCCGCCATCGTCATTCT 60.882 55.000 0.00 0.00 38.59 2.40
2915 3631 1.822371 TCGTCATTCTGGATCCGAACA 59.178 47.619 17.47 7.92 0.00 3.18
2918 3634 4.098807 TCGTCATTCTGGATCCGAACATAA 59.901 41.667 17.47 2.83 0.00 1.90
2927 3643 3.312697 GGATCCGAACATAAGCTTTCACC 59.687 47.826 3.20 0.00 0.00 4.02
2928 3644 3.695830 TCCGAACATAAGCTTTCACCT 57.304 42.857 3.20 0.00 0.00 4.00
2943 3659 3.374042 TCACCTGGAGAAAACAAACCA 57.626 42.857 0.00 0.00 0.00 3.67
2944 3660 3.702792 TCACCTGGAGAAAACAAACCAA 58.297 40.909 0.00 0.00 31.85 3.67
2945 3661 3.699038 TCACCTGGAGAAAACAAACCAAG 59.301 43.478 0.00 0.00 31.85 3.61
2946 3662 3.447229 CACCTGGAGAAAACAAACCAAGT 59.553 43.478 0.00 0.00 31.85 3.16
2947 3663 3.447229 ACCTGGAGAAAACAAACCAAGTG 59.553 43.478 0.00 0.00 31.85 3.16
2948 3664 3.699038 CCTGGAGAAAACAAACCAAGTGA 59.301 43.478 0.00 0.00 31.85 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.671796 TATCGGTAGGCCATGACGTG 59.328 55.000 5.01 0.00 34.09 4.49
38 39 1.068055 CAACATGGAGCTTCTTGTGCC 60.068 52.381 13.97 0.00 0.00 5.01
64 72 4.224715 TCGATATCGACAACTGTCATCC 57.775 45.455 23.48 0.17 44.99 3.51
78 86 2.041966 CCGCTAACACGTGTCGATATC 58.958 52.381 23.61 5.68 0.00 1.63
106 114 1.064952 TCTTGATCTGCGCGACGATTA 59.935 47.619 12.10 4.19 0.00 1.75
118 129 2.834549 ACGACACCCTTGATCTTGATCT 59.165 45.455 11.31 0.00 0.00 2.75
366 388 9.653067 CTAAGCACGATATATACTACTACATGC 57.347 37.037 0.00 0.00 0.00 4.06
376 398 9.355215 ACATAGTTTGCTAAGCACGATATATAC 57.645 33.333 0.00 0.00 38.71 1.47
427 455 3.117589 GCATGCAGCACAGGAAAAG 57.882 52.632 14.21 0.00 44.79 2.27
467 495 0.762842 TGCACCACACCACTCTACCT 60.763 55.000 0.00 0.00 0.00 3.08
469 497 1.270839 ACATGCACCACACCACTCTAC 60.271 52.381 0.00 0.00 0.00 2.59
635 667 0.612229 ACAGGCAGACACCTCTCATG 59.388 55.000 0.00 0.00 38.26 3.07
636 668 0.612229 CACAGGCAGACACCTCTCAT 59.388 55.000 0.00 0.00 38.26 2.90
637 669 0.760567 ACACAGGCAGACACCTCTCA 60.761 55.000 0.00 0.00 38.26 3.27
638 670 0.394565 AACACAGGCAGACACCTCTC 59.605 55.000 0.00 0.00 38.26 3.20
745 778 1.210204 TTGCTTGAGGGAGAGGGCAT 61.210 55.000 0.00 0.00 0.00 4.40
746 779 1.210204 ATTGCTTGAGGGAGAGGGCA 61.210 55.000 0.00 0.00 0.00 5.36
747 780 0.839946 TATTGCTTGAGGGAGAGGGC 59.160 55.000 0.00 0.00 0.00 5.19
748 781 1.141858 GGTATTGCTTGAGGGAGAGGG 59.858 57.143 0.00 0.00 0.00 4.30
790 823 0.324830 AGTGAGAGAGTAGGGGTGGC 60.325 60.000 0.00 0.00 0.00 5.01
953 987 0.253327 CTAGGTTGGAAGGGGTGAGC 59.747 60.000 0.00 0.00 0.00 4.26
1075 1110 1.133199 AGAGTGGCTAGAGGAGATGGG 60.133 57.143 0.00 0.00 0.00 4.00
1105 1140 2.358003 ACAGAGAGGCAAGTGCGC 60.358 61.111 0.00 0.00 43.26 6.09
1125 1160 0.621571 TTGGGATGTGAGAGGGAGGG 60.622 60.000 0.00 0.00 0.00 4.30
1126 1161 0.835941 CTTGGGATGTGAGAGGGAGG 59.164 60.000 0.00 0.00 0.00 4.30
1130 1165 0.617413 ACTGCTTGGGATGTGAGAGG 59.383 55.000 0.00 0.00 0.00 3.69
1131 1166 2.741228 GCTACTGCTTGGGATGTGAGAG 60.741 54.545 0.00 0.00 36.03 3.20
1136 1171 1.221840 CGGCTACTGCTTGGGATGT 59.778 57.895 0.00 0.00 39.59 3.06
1140 1175 2.509336 CGACGGCTACTGCTTGGG 60.509 66.667 0.00 0.00 39.59 4.12
1161 1202 2.091112 CATGGCGGATCTCGATCGC 61.091 63.158 11.09 12.09 42.43 4.58
1350 1391 2.806019 CGCTTCCATCTTCCTCCTGATG 60.806 54.545 0.00 0.00 39.60 3.07
1551 1592 7.118825 TCGACACGACCTATATAGTAGAAATGG 59.881 40.741 8.92 0.00 0.00 3.16
1561 1605 3.999046 TCTGCTCGACACGACCTATATA 58.001 45.455 0.00 0.00 0.00 0.86
1562 1606 2.847441 TCTGCTCGACACGACCTATAT 58.153 47.619 0.00 0.00 0.00 0.86
1563 1607 2.320745 TCTGCTCGACACGACCTATA 57.679 50.000 0.00 0.00 0.00 1.31
1564 1608 1.132643 GTTCTGCTCGACACGACCTAT 59.867 52.381 0.00 0.00 0.00 2.57
1661 1705 7.114106 GCCGAAAGAGAAAGAAAGAAAGAAATG 59.886 37.037 0.00 0.00 0.00 2.32
1740 1788 8.731605 TCACAGCAATTAACGAATAAACCAATA 58.268 29.630 0.00 0.00 0.00 1.90
1850 1903 7.615582 ATTTCCATTGTAGCATCATATACCG 57.384 36.000 0.00 0.00 0.00 4.02
1898 1953 9.330063 TGAATAATTGTCCTGTCATAGTGATTC 57.670 33.333 0.00 0.00 0.00 2.52
1923 1978 6.887368 TCGAAACAAACATCACATAAGAGTG 58.113 36.000 0.00 0.00 40.85 3.51
1925 1980 8.955061 ATTTCGAAACAAACATCACATAAGAG 57.045 30.769 13.81 0.00 0.00 2.85
2002 2712 2.005370 TGGTTCTCTGACTAACCCGT 57.995 50.000 12.36 0.00 43.78 5.28
2006 2716 5.471257 CCACTAGTTGGTTCTCTGACTAAC 58.529 45.833 0.00 0.00 41.10 2.34
2055 2765 4.520063 ACCATGGGAGGTTAGGGG 57.480 61.111 18.09 0.00 39.34 4.79
2079 2789 1.344114 CACCAAAACCTCAACCATGGG 59.656 52.381 18.09 0.00 32.21 4.00
2091 2801 7.190871 TGAAAGAATAAACGAGACACCAAAAC 58.809 34.615 0.00 0.00 0.00 2.43
2096 2806 7.548075 TCCTATTGAAAGAATAAACGAGACACC 59.452 37.037 0.00 0.00 0.00 4.16
2104 2814 8.794335 AGTCACCTCCTATTGAAAGAATAAAC 57.206 34.615 0.00 0.00 0.00 2.01
2105 2815 9.807921 AAAGTCACCTCCTATTGAAAGAATAAA 57.192 29.630 0.00 0.00 0.00 1.40
2106 2816 9.449719 GAAAGTCACCTCCTATTGAAAGAATAA 57.550 33.333 0.00 0.00 0.00 1.40
2107 2817 8.826765 AGAAAGTCACCTCCTATTGAAAGAATA 58.173 33.333 0.00 0.00 0.00 1.75
2108 2818 7.694093 AGAAAGTCACCTCCTATTGAAAGAAT 58.306 34.615 0.00 0.00 0.00 2.40
2109 2819 7.079451 AGAAAGTCACCTCCTATTGAAAGAA 57.921 36.000 0.00 0.00 0.00 2.52
2110 2820 6.688073 AGAAAGTCACCTCCTATTGAAAGA 57.312 37.500 0.00 0.00 0.00 2.52
2111 2821 8.260818 TGATAGAAAGTCACCTCCTATTGAAAG 58.739 37.037 0.00 0.00 0.00 2.62
2112 2822 8.146053 TGATAGAAAGTCACCTCCTATTGAAA 57.854 34.615 0.00 0.00 0.00 2.69
2113 2823 7.733773 TGATAGAAAGTCACCTCCTATTGAA 57.266 36.000 0.00 0.00 0.00 2.69
2114 2824 7.733773 TTGATAGAAAGTCACCTCCTATTGA 57.266 36.000 0.00 0.00 0.00 2.57
2115 2825 7.443575 CCATTGATAGAAAGTCACCTCCTATTG 59.556 40.741 0.00 0.00 0.00 1.90
2116 2826 7.127955 ACCATTGATAGAAAGTCACCTCCTATT 59.872 37.037 0.00 0.00 0.00 1.73
2117 2827 6.617371 ACCATTGATAGAAAGTCACCTCCTAT 59.383 38.462 0.00 0.00 0.00 2.57
2140 2850 0.650512 CACGTCGCATTGGTATCACC 59.349 55.000 0.00 0.00 39.22 4.02
2142 2852 1.087202 GCCACGTCGCATTGGTATCA 61.087 55.000 0.00 0.00 35.09 2.15
2143 2853 0.810031 AGCCACGTCGCATTGGTATC 60.810 55.000 8.15 0.00 35.09 2.24
2167 2877 2.665000 CCCCTCGTGTGCATCAGT 59.335 61.111 0.00 0.00 0.00 3.41
2169 2879 2.927856 ACCCCCTCGTGTGCATCA 60.928 61.111 0.00 0.00 0.00 3.07
2208 2918 2.672714 TGTTGTTCAATCCGAGAGTCG 58.327 47.619 0.00 0.00 40.07 4.18
2210 2920 3.804036 TGTTGTTGTTCAATCCGAGAGT 58.196 40.909 0.00 0.00 38.38 3.24
2278 2988 1.477685 ATCCACGTTGTCCCCGTCTT 61.478 55.000 0.00 0.00 36.17 3.01
2281 2991 2.660802 GATCCACGTTGTCCCCGT 59.339 61.111 0.00 0.00 39.52 5.28
2311 3021 2.227703 TCCTCCTCCAATCTACCCTCT 58.772 52.381 0.00 0.00 0.00 3.69
2426 3137 4.202284 ACAGTTTGCATGCTCCTGAAAAAT 60.202 37.500 27.15 13.62 0.00 1.82
2431 3142 1.241165 CACAGTTTGCATGCTCCTGA 58.759 50.000 27.15 4.89 0.00 3.86
2432 3143 0.956633 ACACAGTTTGCATGCTCCTG 59.043 50.000 20.33 21.39 0.00 3.86
2434 3145 0.665369 GCACACAGTTTGCATGCTCC 60.665 55.000 20.33 6.48 39.93 4.70
2435 3146 0.665369 GGCACACAGTTTGCATGCTC 60.665 55.000 20.33 9.44 42.12 4.26
2446 3157 4.180057 CTCTCTAAAGCTAAGGCACACAG 58.820 47.826 0.00 0.00 41.70 3.66
2493 3204 3.248024 AGGTGTGATGGGAGTTTGTCTA 58.752 45.455 0.00 0.00 0.00 2.59
2507 3218 4.523173 AGTTTACTTCTCATCGAGGTGTGA 59.477 41.667 0.00 0.00 33.54 3.58
2515 3226 3.181474 GGAGGGGAGTTTACTTCTCATCG 60.181 52.174 0.00 0.00 34.04 3.84
2517 3228 3.777522 CTGGAGGGGAGTTTACTTCTCAT 59.222 47.826 0.00 0.00 34.04 2.90
2533 3244 3.793144 GCGCGTTCAAGCTGGAGG 61.793 66.667 8.43 0.00 34.40 4.30
2539 3250 0.110419 TGTAATGTGCGCGTTCAAGC 60.110 50.000 8.24 0.00 0.00 4.01
2542 3253 0.236187 GGTTGTAATGTGCGCGTTCA 59.764 50.000 8.24 7.97 0.00 3.18
2546 3257 0.040870 TTGTGGTTGTAATGTGCGCG 60.041 50.000 0.00 0.00 0.00 6.86
2549 3260 3.112580 GTGTGTTGTGGTTGTAATGTGC 58.887 45.455 0.00 0.00 0.00 4.57
2566 3277 6.017605 GCCAGTTTAGGATATGATCTTGTGTG 60.018 42.308 0.00 0.00 0.00 3.82
2567 3278 6.058183 GCCAGTTTAGGATATGATCTTGTGT 58.942 40.000 0.00 0.00 0.00 3.72
2595 3306 1.810151 GTTGGTTGAGATGCGGCTTTA 59.190 47.619 0.00 0.00 0.00 1.85
2627 3338 4.997565 TCTTTGAAGTTGTTGCTCTTTGG 58.002 39.130 0.00 0.00 0.00 3.28
2643 3354 3.596214 GTCGGCAAGGATAGTTCTTTGA 58.404 45.455 2.45 0.00 40.42 2.69
2684 3396 2.232941 CACTACCGACTCTTTTAGGCCA 59.767 50.000 5.01 0.00 0.00 5.36
2701 3413 1.133294 TCTGAGTCCCACCACACACTA 60.133 52.381 0.00 0.00 0.00 2.74
2703 3415 0.249911 GTCTGAGTCCCACCACACAC 60.250 60.000 0.00 0.00 0.00 3.82
2704 3416 0.689412 TGTCTGAGTCCCACCACACA 60.689 55.000 0.00 0.00 0.00 3.72
2705 3417 0.468226 TTGTCTGAGTCCCACCACAC 59.532 55.000 0.00 0.00 0.00 3.82
2706 3418 0.468226 GTTGTCTGAGTCCCACCACA 59.532 55.000 0.00 0.00 0.00 4.17
2708 3420 1.968493 GTAGTTGTCTGAGTCCCACCA 59.032 52.381 0.00 0.00 0.00 4.17
2709 3421 1.067776 CGTAGTTGTCTGAGTCCCACC 60.068 57.143 0.00 0.00 0.00 4.61
2711 3423 2.160205 CTCGTAGTTGTCTGAGTCCCA 58.840 52.381 0.00 0.00 0.00 4.37
2712 3424 2.434428 TCTCGTAGTTGTCTGAGTCCC 58.566 52.381 0.00 0.00 0.00 4.46
2715 3427 4.579340 TGACTTTCTCGTAGTTGTCTGAGT 59.421 41.667 0.00 0.00 0.00 3.41
2716 3428 5.109662 TGACTTTCTCGTAGTTGTCTGAG 57.890 43.478 0.00 0.00 0.00 3.35
2717 3429 5.240844 TGATGACTTTCTCGTAGTTGTCTGA 59.759 40.000 0.00 0.00 0.00 3.27
2745 3458 1.771565 CTATGTACGGGGTGAGTCCA 58.228 55.000 0.00 0.00 38.11 4.02
2756 3469 1.080705 GGGGCGCTAGCTATGTACG 60.081 63.158 13.93 0.00 44.37 3.67
2757 3470 1.473278 CTAGGGGCGCTAGCTATGTAC 59.527 57.143 23.36 0.00 44.37 2.90
2758 3471 1.353358 TCTAGGGGCGCTAGCTATGTA 59.647 52.381 28.29 11.60 44.37 2.29
2761 3474 0.612453 GGTCTAGGGGCGCTAGCTAT 60.612 60.000 28.29 0.00 44.37 2.97
2762 3475 1.228490 GGTCTAGGGGCGCTAGCTA 60.228 63.158 28.29 13.57 44.37 3.32
2763 3476 2.522193 GGTCTAGGGGCGCTAGCT 60.522 66.667 28.29 0.00 44.37 3.32
2765 3478 1.457831 AAGGGTCTAGGGGCGCTAG 60.458 63.158 27.48 27.48 0.00 3.42
2783 3499 1.621317 TGCTGTTATGGACCGTTCTCA 59.379 47.619 0.00 0.00 0.00 3.27
2790 3506 2.813179 CGCGCTGCTGTTATGGACC 61.813 63.158 5.56 0.00 0.00 4.46
2791 3507 2.703409 CGCGCTGCTGTTATGGAC 59.297 61.111 5.56 0.00 0.00 4.02
2799 3515 3.933498 CTATGGTGCGCGCTGCTG 61.933 66.667 33.29 13.32 46.63 4.41
2802 3518 2.511373 TTCCTATGGTGCGCGCTG 60.511 61.111 33.29 14.19 0.00 5.18
2807 3523 1.019278 AGTTGCGTTCCTATGGTGCG 61.019 55.000 0.00 0.00 0.00 5.34
2825 3541 3.054802 AGACATGGCTTGGAGGTTCTAAG 60.055 47.826 0.00 0.00 37.92 2.18
2826 3542 2.912956 AGACATGGCTTGGAGGTTCTAA 59.087 45.455 0.00 0.00 0.00 2.10
2846 3562 3.689161 TGTTTGGAGCATCGTATTTGGAG 59.311 43.478 0.00 0.00 34.37 3.86
2872 3588 2.663188 GCATCCTCGACGCCATCC 60.663 66.667 0.00 0.00 0.00 3.51
2873 3589 2.663188 GGCATCCTCGACGCCATC 60.663 66.667 5.72 0.00 40.93 3.51
2880 3596 4.284860 CGATGGCGGCATCCTCGA 62.285 66.667 37.14 5.85 32.41 4.04
2890 3606 1.143305 GATCCAGAATGACGATGGCG 58.857 55.000 0.00 0.00 39.69 5.69
2891 3607 1.517242 GGATCCAGAATGACGATGGC 58.483 55.000 6.95 0.00 39.69 4.40
2904 3620 3.938963 GTGAAAGCTTATGTTCGGATCCA 59.061 43.478 13.41 0.00 0.00 3.41
2915 3631 5.385198 TGTTTTCTCCAGGTGAAAGCTTAT 58.615 37.500 23.48 0.00 46.63 1.73
2927 3643 4.981806 TCACTTGGTTTGTTTTCTCCAG 57.018 40.909 0.00 0.00 0.00 3.86


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

AutoCloner maintained by Alex Coulton.