Multiple sequence alignment - TraesCS3A01G305900

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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 TraesCS3A01G305900 chr3A 100.000 3569 0 0 1 3569 542201642 542205210 0.000000e+00 6591.0
1 TraesCS3A01G305900 chr3A 82.158 695 116 7 1132 1822 113342383 113341693 1.100000e-164 590.0
2 TraesCS3A01G305900 chr3D 92.035 2649 140 35 5 2616 409023129 409020515 0.000000e+00 3657.0
3 TraesCS3A01G305900 chr3D 81.988 694 117 7 1133 1822 95246491 95245802 1.850000e-162 582.0
4 TraesCS3A01G305900 chr3D 88.740 373 27 7 3199 3569 409019807 409019448 3.270000e-120 442.0
5 TraesCS3A01G305900 chr3D 96.774 217 7 0 2832 3048 409020507 409020291 2.620000e-96 363.0
6 TraesCS3A01G305900 chr3D 88.710 124 6 2 3082 3203 409020313 409020196 1.030000e-30 145.0
7 TraesCS3A01G305900 chr3B 92.297 2233 78 31 514 2682 534966117 534963915 0.000000e+00 3085.0
8 TraesCS3A01G305900 chr3B 91.204 739 48 6 2833 3569 534963762 534963039 0.000000e+00 989.0
9 TraesCS3A01G305900 chr3B 88.362 464 43 7 1 459 534966612 534966155 6.740000e-152 547.0
10 TraesCS3A01G305900 chr3B 81.034 696 122 9 1132 1822 146183121 146182431 2.420000e-151 545.0
11 TraesCS3A01G305900 chr3B 95.763 118 4 1 2720 2836 534963913 534963796 4.700000e-44 189.0
12 TraesCS3A01G305900 chr3B 78.309 272 57 2 1486 1756 729415080 729415350 1.320000e-39 174.0
13 TraesCS3A01G305900 chr1B 79.508 1586 265 51 966 2529 576205384 576206931 0.000000e+00 1074.0
14 TraesCS3A01G305900 chr1A 79.282 1588 277 47 966 2529 521628990 521630549 0.000000e+00 1062.0
15 TraesCS3A01G305900 chr1D 80.296 1421 242 33 1128 2529 426586983 426588384 0.000000e+00 1038.0
16 TraesCS3A01G305900 chrUn 95.918 49 2 0 2682 2730 177183722 177183770 2.950000e-11 80.5
17 TraesCS3A01G305900 chrUn 95.918 49 2 0 2682 2730 401481464 401481416 2.950000e-11 80.5
18 TraesCS3A01G305900 chrUn 91.228 57 4 1 2682 2737 88217898 88217842 3.820000e-10 76.8
19 TraesCS3A01G305900 chr6D 95.918 49 2 0 2681 2729 14657946 14657994 2.950000e-11 80.5
20 TraesCS3A01G305900 chr4A 97.826 46 1 0 2682 2727 590947032 590946987 2.950000e-11 80.5
21 TraesCS3A01G305900 chr2B 95.918 49 2 0 2682 2730 3726757 3726709 2.950000e-11 80.5
22 TraesCS3A01G305900 chr2B 95.918 49 2 0 2682 2730 3813358 3813310 2.950000e-11 80.5
23 TraesCS3A01G305900 chr2B 92.683 41 2 1 285 325 477332677 477332716 1.380000e-04 58.4
24 TraesCS3A01G305900 chr4D 100.000 41 0 0 2682 2722 491706731 491706691 3.820000e-10 76.8
25 TraesCS3A01G305900 chr7D 86.364 66 7 2 2671 2734 620925920 620925985 1.780000e-08 71.3


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 TraesCS3A01G305900 chr3A 542201642 542205210 3568 False 6591.00 6591 100.00000 1 3569 1 chr3A.!!$F1 3568
1 TraesCS3A01G305900 chr3A 113341693 113342383 690 True 590.00 590 82.15800 1132 1822 1 chr3A.!!$R1 690
2 TraesCS3A01G305900 chr3D 409019448 409023129 3681 True 1151.75 3657 91.56475 5 3569 4 chr3D.!!$R2 3564
3 TraesCS3A01G305900 chr3D 95245802 95246491 689 True 582.00 582 81.98800 1133 1822 1 chr3D.!!$R1 689
4 TraesCS3A01G305900 chr3B 534963039 534966612 3573 True 1202.50 3085 91.90650 1 3569 4 chr3B.!!$R2 3568
5 TraesCS3A01G305900 chr3B 146182431 146183121 690 True 545.00 545 81.03400 1132 1822 1 chr3B.!!$R1 690
6 TraesCS3A01G305900 chr1B 576205384 576206931 1547 False 1074.00 1074 79.50800 966 2529 1 chr1B.!!$F1 1563
7 TraesCS3A01G305900 chr1A 521628990 521630549 1559 False 1062.00 1062 79.28200 966 2529 1 chr1A.!!$F1 1563
8 TraesCS3A01G305900 chr1D 426586983 426588384 1401 False 1038.00 1038 80.29600 1128 2529 1 chr1D.!!$F1 1401

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
500 521 0.323629 TTTCATCTCCACGTGACCCC 59.676 55.0 19.3 0.0 0.0 4.95 F
1079 1185 0.105709 CCTTCCTCCTCCTCCTCCTC 60.106 65.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2385 2539 0.739462 CCGCGCAGATTGTTAGTGGA 60.739 55.0 8.75 0.0 34.65 4.02 R
2706 2861 0.178912 ACCCAAGTACTCCCTCCGTT 60.179 55.0 0.00 0.0 0.00 4.44 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
44 47 9.467258 CTTGCTTTTATGAATTCTTCTGACAAA 57.533 29.630 7.05 0.00 0.00 2.83
234 239 4.786507 TCAATCAGAATTGCAACAACTCG 58.213 39.130 0.00 0.00 41.76 4.18
260 265 1.106148 CGTTGTTAACACCGCAAACG 58.894 50.000 12.71 12.48 39.67 3.60
264 269 1.117234 GTTAACACCGCAAACGCTTG 58.883 50.000 0.00 0.00 38.22 4.01
403 408 2.296792 GGGGCAAAAGCACAAACAAAT 58.703 42.857 0.00 0.00 0.00 2.32
405 410 3.205338 GGGCAAAAGCACAAACAAATCT 58.795 40.909 0.00 0.00 0.00 2.40
444 452 7.309770 ACAACTCTTATTTGGAGAGAGAAGT 57.690 36.000 8.03 2.32 42.57 3.01
463 483 3.084786 AGTTAGTGAGCAAATTGAGCCC 58.915 45.455 0.00 0.00 0.00 5.19
488 509 7.551974 CCTGAGAGTATGTTGTCAATTTCATCT 59.448 37.037 0.00 0.00 0.00 2.90
493 514 4.747540 TGTTGTCAATTTCATCTCCACG 57.252 40.909 0.00 0.00 0.00 4.94
496 517 4.001618 TGTCAATTTCATCTCCACGTGA 57.998 40.909 19.30 2.03 0.00 4.35
497 518 3.745975 TGTCAATTTCATCTCCACGTGAC 59.254 43.478 19.30 2.47 35.75 3.67
498 519 3.125316 GTCAATTTCATCTCCACGTGACC 59.875 47.826 19.30 0.00 0.00 4.02
499 520 2.403252 ATTTCATCTCCACGTGACCC 57.597 50.000 19.30 0.00 0.00 4.46
500 521 0.323629 TTTCATCTCCACGTGACCCC 59.676 55.000 19.30 0.00 0.00 4.95
501 522 1.884075 TTCATCTCCACGTGACCCCG 61.884 60.000 19.30 0.00 0.00 5.73
502 523 3.771160 ATCTCCACGTGACCCCGC 61.771 66.667 19.30 0.00 0.00 6.13
504 525 4.308458 CTCCACGTGACCCCGCAA 62.308 66.667 19.30 0.00 0.00 4.85
505 526 3.818121 CTCCACGTGACCCCGCAAA 62.818 63.158 19.30 0.00 0.00 3.68
506 527 2.902846 CCACGTGACCCCGCAAAA 60.903 61.111 19.30 0.00 0.00 2.44
507 528 2.482333 CCACGTGACCCCGCAAAAA 61.482 57.895 19.30 0.00 0.00 1.94
779 856 8.364129 AGCCCATAATAAAAATACAAAATGCG 57.636 30.769 0.00 0.00 0.00 4.73
818 896 4.684134 TGCCCTCCCAAGCCAAGC 62.684 66.667 0.00 0.00 0.00 4.01
820 898 4.033776 CCCTCCCAAGCCAAGCGA 62.034 66.667 0.00 0.00 0.00 4.93
821 899 2.034066 CCTCCCAAGCCAAGCGAA 59.966 61.111 0.00 0.00 0.00 4.70
822 900 2.042831 CCTCCCAAGCCAAGCGAAG 61.043 63.158 0.00 0.00 0.00 3.79
897 994 5.915196 AGCAAAGCAAACGAGAAATAGTTTC 59.085 36.000 0.00 0.00 38.37 2.78
955 1052 3.330720 CCACCTCCACCTCCACCC 61.331 72.222 0.00 0.00 0.00 4.61
1076 1182 1.074850 CCCCTTCCTCCTCCTCCTC 60.075 68.421 0.00 0.00 0.00 3.71
1077 1183 1.074850 CCCTTCCTCCTCCTCCTCC 60.075 68.421 0.00 0.00 0.00 4.30
1078 1184 1.598856 CCCTTCCTCCTCCTCCTCCT 61.599 65.000 0.00 0.00 0.00 3.69
1079 1185 0.105709 CCTTCCTCCTCCTCCTCCTC 60.106 65.000 0.00 0.00 0.00 3.71
1080 1186 0.105709 CTTCCTCCTCCTCCTCCTCC 60.106 65.000 0.00 0.00 0.00 4.30
1081 1187 0.556380 TTCCTCCTCCTCCTCCTCCT 60.556 60.000 0.00 0.00 0.00 3.69
1082 1188 0.996762 TCCTCCTCCTCCTCCTCCTC 60.997 65.000 0.00 0.00 0.00 3.71
1083 1189 1.150536 CTCCTCCTCCTCCTCCTCG 59.849 68.421 0.00 0.00 0.00 4.63
1084 1190 2.197324 CCTCCTCCTCCTCCTCGG 59.803 72.222 0.00 0.00 0.00 4.63
1085 1191 2.520741 CTCCTCCTCCTCCTCGGC 60.521 72.222 0.00 0.00 0.00 5.54
1086 1192 4.507916 TCCTCCTCCTCCTCGGCG 62.508 72.222 0.00 0.00 0.00 6.46
1810 1946 0.392595 GGGAGAATTCCGGTGTCCAC 60.393 60.000 0.00 0.00 45.04 4.02
1851 1987 2.555199 ACTAGCCTGATCATGCGTTTC 58.445 47.619 16.01 0.00 0.00 2.78
2005 2159 1.847328 TATGCTCGACTTGGGTCTCA 58.153 50.000 0.00 0.00 40.10 3.27
2052 2206 1.055040 CTCCACCTCCATCTCCATCC 58.945 60.000 0.00 0.00 0.00 3.51
2292 2446 6.423001 GTGAACCTATGTCGGACATTATAACC 59.577 42.308 26.94 13.39 39.88 2.85
2379 2533 2.035783 GGCACAAGGGAAGGGGTC 59.964 66.667 0.00 0.00 0.00 4.46
2385 2539 1.072143 AAGGGAAGGGGTCAAGGGT 60.072 57.895 0.00 0.00 0.00 4.34
2409 2563 2.205074 CTAACAATCTGCGCGGAGATT 58.795 47.619 39.51 39.51 42.34 2.40
2682 2837 8.950208 TGTGTCGAAAATGGTATTATGTGATA 57.050 30.769 0.00 0.00 0.00 2.15
2683 2838 8.822855 TGTGTCGAAAATGGTATTATGTGATAC 58.177 33.333 0.00 0.00 32.84 2.24
2684 2839 8.822855 GTGTCGAAAATGGTATTATGTGATACA 58.177 33.333 0.00 0.00 34.82 2.29
2685 2840 9.384764 TGTCGAAAATGGTATTATGTGATACAA 57.615 29.630 0.00 0.00 34.82 2.41
2692 2847 7.873719 TGGTATTATGTGATACAAAGTTGGG 57.126 36.000 0.00 0.00 34.82 4.12
2693 2848 7.406916 TGGTATTATGTGATACAAAGTTGGGT 58.593 34.615 0.00 0.00 34.82 4.51
2694 2849 7.554835 TGGTATTATGTGATACAAAGTTGGGTC 59.445 37.037 0.00 0.00 34.82 4.46
2695 2850 7.554835 GGTATTATGTGATACAAAGTTGGGTCA 59.445 37.037 0.00 0.00 34.82 4.02
2696 2851 9.120538 GTATTATGTGATACAAAGTTGGGTCAT 57.879 33.333 0.00 0.00 33.63 3.06
2697 2852 7.624360 TTATGTGATACAAAGTTGGGTCATC 57.376 36.000 0.00 0.00 31.60 2.92
2698 2853 5.241403 TGTGATACAAAGTTGGGTCATCT 57.759 39.130 0.00 0.00 31.60 2.90
2699 2854 6.367374 TGTGATACAAAGTTGGGTCATCTA 57.633 37.500 0.00 0.00 31.60 1.98
2700 2855 6.957631 TGTGATACAAAGTTGGGTCATCTAT 58.042 36.000 0.00 0.00 31.60 1.98
2701 2856 7.402054 TGTGATACAAAGTTGGGTCATCTATT 58.598 34.615 0.00 0.00 31.60 1.73
2702 2857 7.888021 TGTGATACAAAGTTGGGTCATCTATTT 59.112 33.333 0.00 0.00 31.60 1.40
2703 2858 8.739972 GTGATACAAAGTTGGGTCATCTATTTT 58.260 33.333 0.00 0.00 31.60 1.82
2704 2859 8.739039 TGATACAAAGTTGGGTCATCTATTTTG 58.261 33.333 0.00 0.00 0.00 2.44
2705 2860 6.345096 ACAAAGTTGGGTCATCTATTTTGG 57.655 37.500 0.00 0.00 0.00 3.28
2706 2861 6.074648 ACAAAGTTGGGTCATCTATTTTGGA 58.925 36.000 0.00 0.00 0.00 3.53
2707 2862 6.553100 ACAAAGTTGGGTCATCTATTTTGGAA 59.447 34.615 0.00 0.00 0.00 3.53
2708 2863 6.590234 AAGTTGGGTCATCTATTTTGGAAC 57.410 37.500 0.00 0.00 0.00 3.62
2709 2864 4.700213 AGTTGGGTCATCTATTTTGGAACG 59.300 41.667 0.00 0.00 0.00 3.95
2710 2865 3.616219 TGGGTCATCTATTTTGGAACGG 58.384 45.455 0.00 0.00 0.00 4.44
2711 2866 3.264706 TGGGTCATCTATTTTGGAACGGA 59.735 43.478 0.00 0.00 0.00 4.69
2712 2867 3.877508 GGGTCATCTATTTTGGAACGGAG 59.122 47.826 0.00 0.00 0.00 4.63
2713 2868 3.877508 GGTCATCTATTTTGGAACGGAGG 59.122 47.826 0.00 0.00 0.00 4.30
2714 2869 3.877508 GTCATCTATTTTGGAACGGAGGG 59.122 47.826 0.00 0.00 0.00 4.30
2715 2870 3.778075 TCATCTATTTTGGAACGGAGGGA 59.222 43.478 0.00 0.00 0.00 4.20
2716 2871 3.906720 TCTATTTTGGAACGGAGGGAG 57.093 47.619 0.00 0.00 0.00 4.30
2717 2872 3.178865 TCTATTTTGGAACGGAGGGAGT 58.821 45.455 0.00 0.00 0.00 3.85
2718 2873 4.355549 TCTATTTTGGAACGGAGGGAGTA 58.644 43.478 0.00 0.00 0.00 2.59
2726 2881 0.706433 ACGGAGGGAGTACTTGGGTA 59.294 55.000 0.00 0.00 0.00 3.69
2737 2892 6.373495 GGGAGTACTTGGGTATGTAGTTTTTG 59.627 42.308 0.00 0.00 0.00 2.44
2738 2893 6.128090 GGAGTACTTGGGTATGTAGTTTTTGC 60.128 42.308 0.00 0.00 0.00 3.68
2998 3191 7.541091 TCAACGATTGAAATCTCTACTACACAC 59.459 37.037 0.00 0.00 36.59 3.82
3057 3250 7.175073 TCGTAGTTCTAATCAGATGTACGAG 57.825 40.000 6.26 0.00 41.83 4.18
3058 3251 6.760298 TCGTAGTTCTAATCAGATGTACGAGT 59.240 38.462 6.26 0.00 41.83 4.18
3060 3253 8.003224 CGTAGTTCTAATCAGATGTACGAGTAC 58.997 40.741 6.46 6.46 41.21 2.73
3126 3319 3.380320 ACCTAGTTTGTGGCTGTTGAAAC 59.620 43.478 0.00 0.00 0.00 2.78
3161 3354 9.995003 ATTGTTTCATTTGTTCCTTAAGCATAA 57.005 25.926 0.00 0.00 0.00 1.90
3162 3355 9.474920 TTGTTTCATTTGTTCCTTAAGCATAAG 57.525 29.630 1.64 1.64 38.61 1.73
3163 3356 7.598493 TGTTTCATTTGTTCCTTAAGCATAAGC 59.402 33.333 3.13 0.00 37.74 3.09
3164 3357 6.832520 TCATTTGTTCCTTAAGCATAAGCA 57.167 33.333 3.13 0.00 45.49 3.91
3165 3358 6.620678 TCATTTGTTCCTTAAGCATAAGCAC 58.379 36.000 3.13 3.35 45.49 4.40
3166 3359 6.208402 TCATTTGTTCCTTAAGCATAAGCACA 59.792 34.615 3.13 5.70 45.49 4.57
3208 3796 2.746362 CAGAGTGGTTCTGCATTTCTCC 59.254 50.000 0.00 0.00 46.30 3.71
3209 3797 2.373169 AGAGTGGTTCTGCATTTCTCCA 59.627 45.455 0.00 0.00 33.93 3.86
3222 3811 4.737352 GCATTTCTCCAACAAAGCTTGTCA 60.737 41.667 0.00 0.00 44.59 3.58
3261 3851 4.590647 TCCTTTTTCCAATGCATTACCACA 59.409 37.500 12.53 0.00 0.00 4.17
3291 3881 7.490962 TCGTGGATGTATATTTTTCATCACC 57.509 36.000 0.00 0.00 39.47 4.02
3324 3915 1.005215 AGAATCAGAGGGGTTGCTTGG 59.995 52.381 0.00 0.00 0.00 3.61
3325 3916 0.779997 AATCAGAGGGGTTGCTTGGT 59.220 50.000 0.00 0.00 0.00 3.67
3326 3917 0.779997 ATCAGAGGGGTTGCTTGGTT 59.220 50.000 0.00 0.00 0.00 3.67
3327 3918 1.440618 TCAGAGGGGTTGCTTGGTTA 58.559 50.000 0.00 0.00 0.00 2.85
3328 3919 1.351017 TCAGAGGGGTTGCTTGGTTAG 59.649 52.381 0.00 0.00 0.00 2.34
3372 3963 7.295340 ACACCTTTATTTTCACCTAAAGACCT 58.705 34.615 4.14 0.00 37.19 3.85
3380 3971 0.685097 ACCTAAAGACCTGCGCTTCA 59.315 50.000 9.73 0.00 0.00 3.02
3385 3976 0.035317 AAGACCTGCGCTTCACATGA 59.965 50.000 9.73 0.00 0.00 3.07
3406 3997 9.369904 ACATGATTTTGTGCTTTCATATTTACC 57.630 29.630 0.00 0.00 0.00 2.85
3410 4001 9.294030 GATTTTGTGCTTTCATATTTACCTCTG 57.706 33.333 0.00 0.00 0.00 3.35
3429 4020 1.002792 AAGAGGAGAGGGGCTGGAG 59.997 63.158 0.00 0.00 0.00 3.86
3445 4036 3.381272 GCTGGAGCCACATTTAAATAGCA 59.619 43.478 15.44 1.21 34.31 3.49
3450 4041 7.059788 TGGAGCCACATTTAAATAGCAATAGA 58.940 34.615 15.44 0.00 0.00 1.98
3464 4055 5.138125 AGCAATAGATTTTTGTGGTGTGG 57.862 39.130 0.00 0.00 0.00 4.17
3483 4074 1.129326 GTACGTGTGTGTCTGTCTGC 58.871 55.000 0.00 0.00 0.00 4.26
3500 4091 1.331756 CTGCGATCACAATAACTGGCC 59.668 52.381 0.00 0.00 0.00 5.36
3521 4112 1.466558 GCTAAAAGGTCTGCTGCACTC 59.533 52.381 0.00 0.00 0.00 3.51
3523 4114 1.602311 AAAAGGTCTGCTGCACTCTG 58.398 50.000 0.00 0.00 0.00 3.35
3544 4135 4.942852 TGTCCACTTAATTTGGTGCAAAG 58.057 39.130 0.00 0.00 36.76 2.77
3546 4137 5.127845 TGTCCACTTAATTTGGTGCAAAGAA 59.872 36.000 0.00 0.00 36.76 2.52
3550 4141 7.772757 TCCACTTAATTTGGTGCAAAGAAAAAT 59.227 29.630 0.00 0.00 36.76 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 106 7.548075 TCTTGTTCTTTATATGGTTTCGTCCTC 59.452 37.037 0.00 0.00 0.00 3.71
105 108 7.605410 TCTTGTTCTTTATATGGTTTCGTCC 57.395 36.000 0.00 0.00 0.00 4.79
120 124 3.378339 CCGACGTGTACTTCTTGTTCTT 58.622 45.455 0.00 0.00 0.00 2.52
260 265 9.846248 ATAAGTTGTATTTCTGAACATTCAAGC 57.154 29.630 0.00 0.00 36.64 4.01
359 364 9.974980 CCCGCAAAACCTTATATTAACATTATT 57.025 29.630 0.00 0.00 0.00 1.40
360 365 8.581578 CCCCGCAAAACCTTATATTAACATTAT 58.418 33.333 0.00 0.00 0.00 1.28
364 369 4.098196 GCCCCGCAAAACCTTATATTAACA 59.902 41.667 0.00 0.00 0.00 2.41
380 385 2.725312 TTTGTGCTTTTGCCCCGCA 61.725 52.632 0.00 0.00 46.87 5.69
381 386 2.107953 TTTGTGCTTTTGCCCCGC 59.892 55.556 0.00 0.00 46.87 6.13
444 452 3.084039 CAGGGCTCAATTTGCTCACTAA 58.916 45.455 3.30 0.00 32.41 2.24
463 483 8.489990 AGATGAAATTGACAACATACTCTCAG 57.510 34.615 0.00 0.00 0.00 3.35
488 509 2.888464 TTTTTGCGGGGTCACGTGGA 62.888 55.000 17.00 0.00 35.98 4.02
508 529 9.426837 CACAATTTACATGTGGAGATGATTTTT 57.573 29.630 9.11 0.00 43.45 1.94
509 530 8.805175 TCACAATTTACATGTGGAGATGATTTT 58.195 29.630 9.11 0.00 46.37 1.82
510 531 8.352137 TCACAATTTACATGTGGAGATGATTT 57.648 30.769 9.11 0.00 46.37 2.17
511 532 7.943079 TCACAATTTACATGTGGAGATGATT 57.057 32.000 9.11 0.00 46.37 2.57
512 533 7.943079 TTCACAATTTACATGTGGAGATGAT 57.057 32.000 9.11 0.00 46.37 2.45
513 534 7.611079 TCATTCACAATTTACATGTGGAGATGA 59.389 33.333 9.11 10.38 46.37 2.92
514 535 7.699391 GTCATTCACAATTTACATGTGGAGATG 59.301 37.037 9.11 3.91 46.37 2.90
515 536 7.613022 AGTCATTCACAATTTACATGTGGAGAT 59.387 33.333 9.11 0.00 46.37 2.75
516 537 6.942005 AGTCATTCACAATTTACATGTGGAGA 59.058 34.615 9.11 0.00 46.37 3.71
517 538 7.149569 AGTCATTCACAATTTACATGTGGAG 57.850 36.000 9.11 0.00 46.37 3.86
518 539 6.150976 GGAGTCATTCACAATTTACATGTGGA 59.849 38.462 9.11 0.00 46.37 4.02
519 540 6.072008 TGGAGTCATTCACAATTTACATGTGG 60.072 38.462 9.11 0.00 46.37 4.17
521 542 6.716628 ACTGGAGTCATTCACAATTTACATGT 59.283 34.615 2.69 2.69 0.00 3.21
522 543 7.025365 CACTGGAGTCATTCACAATTTACATG 58.975 38.462 0.00 0.00 0.00 3.21
523 544 6.942005 TCACTGGAGTCATTCACAATTTACAT 59.058 34.615 0.00 0.00 0.00 2.29
524 545 6.295249 TCACTGGAGTCATTCACAATTTACA 58.705 36.000 0.00 0.00 0.00 2.41
525 546 6.801539 TCACTGGAGTCATTCACAATTTAC 57.198 37.500 0.00 0.00 0.00 2.01
572 593 1.780919 AGCTCCAGGGGTACTTTTGTT 59.219 47.619 0.00 0.00 0.00 2.83
573 594 1.446016 AGCTCCAGGGGTACTTTTGT 58.554 50.000 0.00 0.00 0.00 2.83
576 597 2.349445 AGAAAGCTCCAGGGGTACTTT 58.651 47.619 0.00 0.00 33.93 2.66
577 598 2.046280 AGAAAGCTCCAGGGGTACTT 57.954 50.000 0.00 0.00 0.00 2.24
579 600 1.065345 GGAAGAAAGCTCCAGGGGTAC 60.065 57.143 0.00 0.00 0.00 3.34
693 752 2.639065 TGTGCCATATTTCGAGGGTTC 58.361 47.619 0.00 0.00 0.00 3.62
696 755 3.734902 GCTTTTGTGCCATATTTCGAGGG 60.735 47.826 0.00 0.00 0.00 4.30
755 828 8.359060 TCGCATTTTGTATTTTTATTATGGGC 57.641 30.769 0.00 0.00 0.00 5.36
818 896 4.033776 TTGGGCTGGGGCTCTTCG 62.034 66.667 0.00 0.00 40.19 3.79
819 897 2.361737 GTTGGGCTGGGGCTCTTC 60.362 66.667 0.00 0.00 40.19 2.87
820 898 3.984732 GGTTGGGCTGGGGCTCTT 61.985 66.667 0.00 0.00 40.19 2.85
822 900 4.066139 ATGGTTGGGCTGGGGCTC 62.066 66.667 0.00 0.00 39.89 4.70
897 994 2.125512 AGCTTAACGGCTCTGCGG 60.126 61.111 0.00 0.00 38.24 5.69
955 1052 2.897350 GCGAGGCGAAGGGGATTG 60.897 66.667 0.00 0.00 0.00 2.67
1810 1946 1.003718 GGTCCTTGGAGAACCACCG 60.004 63.158 0.00 0.00 46.80 4.94
1851 1987 1.110442 TGCTTGGGTTTGTGTCAAGG 58.890 50.000 0.00 0.00 38.52 3.61
1901 2037 0.841289 TCCTTTCTTGAACCACCGGT 59.159 50.000 0.00 0.00 37.65 5.28
2005 2159 1.353091 GGTTGAGGAAGAGGGTCAGT 58.647 55.000 0.00 0.00 0.00 3.41
2052 2206 3.077359 GTCTCCATCAACTTCTTGTGGG 58.923 50.000 0.00 0.00 33.10 4.61
2172 2326 2.658373 TGTCGAACGCATTAAGGCTA 57.342 45.000 10.75 0.00 0.00 3.93
2292 2446 4.142315 ACATTTGCGATCTCCTCCAATTTG 60.142 41.667 0.00 0.00 0.00 2.32
2358 2512 2.356667 CCTTCCCTTGTGCCCTCC 59.643 66.667 0.00 0.00 0.00 4.30
2379 2533 2.749621 GCAGATTGTTAGTGGACCCTTG 59.250 50.000 0.00 0.00 0.00 3.61
2385 2539 0.739462 CCGCGCAGATTGTTAGTGGA 60.739 55.000 8.75 0.00 34.65 4.02
2409 2563 1.850345 AGGGAGGGTGTGAGTTCAAAA 59.150 47.619 0.00 0.00 0.00 2.44
2457 2611 4.772624 TCATCATACTCTTCCTTATCCCCG 59.227 45.833 0.00 0.00 0.00 5.73
2659 2814 8.950208 TGTATCACATAATACCATTTTCGACA 57.050 30.769 0.00 0.00 32.21 4.35
2677 2832 7.865706 AATAGATGACCCAACTTTGTATCAC 57.134 36.000 0.00 0.00 0.00 3.06
2682 2837 6.074648 TCCAAAATAGATGACCCAACTTTGT 58.925 36.000 0.00 0.00 0.00 2.83
2683 2838 6.588719 TCCAAAATAGATGACCCAACTTTG 57.411 37.500 0.00 0.00 0.00 2.77
2684 2839 6.294508 CGTTCCAAAATAGATGACCCAACTTT 60.295 38.462 0.00 0.00 0.00 2.66
2685 2840 5.183140 CGTTCCAAAATAGATGACCCAACTT 59.817 40.000 0.00 0.00 0.00 2.66
2686 2841 4.700213 CGTTCCAAAATAGATGACCCAACT 59.300 41.667 0.00 0.00 0.00 3.16
2687 2842 4.142469 CCGTTCCAAAATAGATGACCCAAC 60.142 45.833 0.00 0.00 0.00 3.77
2688 2843 4.013728 CCGTTCCAAAATAGATGACCCAA 58.986 43.478 0.00 0.00 0.00 4.12
2689 2844 3.264706 TCCGTTCCAAAATAGATGACCCA 59.735 43.478 0.00 0.00 0.00 4.51
2690 2845 3.877508 CTCCGTTCCAAAATAGATGACCC 59.122 47.826 0.00 0.00 0.00 4.46
2691 2846 3.877508 CCTCCGTTCCAAAATAGATGACC 59.122 47.826 0.00 0.00 0.00 4.02
2692 2847 3.877508 CCCTCCGTTCCAAAATAGATGAC 59.122 47.826 0.00 0.00 0.00 3.06
2693 2848 3.778075 TCCCTCCGTTCCAAAATAGATGA 59.222 43.478 0.00 0.00 0.00 2.92
2694 2849 4.130118 CTCCCTCCGTTCCAAAATAGATG 58.870 47.826 0.00 0.00 0.00 2.90
2695 2850 3.780850 ACTCCCTCCGTTCCAAAATAGAT 59.219 43.478 0.00 0.00 0.00 1.98
2696 2851 3.178865 ACTCCCTCCGTTCCAAAATAGA 58.821 45.455 0.00 0.00 0.00 1.98
2697 2852 3.629142 ACTCCCTCCGTTCCAAAATAG 57.371 47.619 0.00 0.00 0.00 1.73
2698 2853 4.098894 AGTACTCCCTCCGTTCCAAAATA 58.901 43.478 0.00 0.00 0.00 1.40
2699 2854 2.910977 AGTACTCCCTCCGTTCCAAAAT 59.089 45.455 0.00 0.00 0.00 1.82
2700 2855 2.332117 AGTACTCCCTCCGTTCCAAAA 58.668 47.619 0.00 0.00 0.00 2.44
2701 2856 2.019807 AGTACTCCCTCCGTTCCAAA 57.980 50.000 0.00 0.00 0.00 3.28
2702 2857 1.621814 CAAGTACTCCCTCCGTTCCAA 59.378 52.381 0.00 0.00 0.00 3.53
2703 2858 1.263356 CAAGTACTCCCTCCGTTCCA 58.737 55.000 0.00 0.00 0.00 3.53
2704 2859 0.535797 CCAAGTACTCCCTCCGTTCC 59.464 60.000 0.00 0.00 0.00 3.62
2705 2860 0.535797 CCCAAGTACTCCCTCCGTTC 59.464 60.000 0.00 0.00 0.00 3.95
2706 2861 0.178912 ACCCAAGTACTCCCTCCGTT 60.179 55.000 0.00 0.00 0.00 4.44
2707 2862 0.706433 TACCCAAGTACTCCCTCCGT 59.294 55.000 0.00 0.00 0.00 4.69
2708 2863 1.687123 CATACCCAAGTACTCCCTCCG 59.313 57.143 0.00 0.00 0.00 4.63
2709 2864 2.760581 ACATACCCAAGTACTCCCTCC 58.239 52.381 0.00 0.00 0.00 4.30
2710 2865 4.544683 ACTACATACCCAAGTACTCCCTC 58.455 47.826 0.00 0.00 0.00 4.30
2711 2866 4.621797 ACTACATACCCAAGTACTCCCT 57.378 45.455 0.00 0.00 0.00 4.20
2712 2867 5.688814 AAACTACATACCCAAGTACTCCC 57.311 43.478 0.00 0.00 0.00 4.30
2713 2868 6.128090 GCAAAAACTACATACCCAAGTACTCC 60.128 42.308 0.00 0.00 0.00 3.85
2714 2869 6.428771 TGCAAAAACTACATACCCAAGTACTC 59.571 38.462 0.00 0.00 0.00 2.59
2715 2870 6.300703 TGCAAAAACTACATACCCAAGTACT 58.699 36.000 0.00 0.00 0.00 2.73
2716 2871 6.563222 TGCAAAAACTACATACCCAAGTAC 57.437 37.500 0.00 0.00 0.00 2.73
2717 2872 7.172342 AGATGCAAAAACTACATACCCAAGTA 58.828 34.615 0.00 0.00 0.00 2.24
2718 2873 6.010219 AGATGCAAAAACTACATACCCAAGT 58.990 36.000 0.00 0.00 0.00 3.16
2726 2881 7.812191 TGCGATTTTAAGATGCAAAAACTACAT 59.188 29.630 0.00 0.00 31.69 2.29
2737 2892 3.956233 TGAGCATGCGATTTTAAGATGC 58.044 40.909 13.01 0.00 39.80 3.91
2738 2893 5.338822 CGATTGAGCATGCGATTTTAAGATG 59.661 40.000 13.01 0.00 0.00 2.90
2750 2906 5.178996 ACAAGATAGAATCGATTGAGCATGC 59.821 40.000 16.96 10.51 0.00 4.06
2921 3114 4.811024 TCAAACTGCATCGGATTACAGATC 59.189 41.667 19.47 0.00 34.25 2.75
3027 3220 8.635877 ACATCTGATTAGAACTACGAACAATC 57.364 34.615 0.00 0.00 36.32 2.67
3090 3283 7.063074 CCACAAACTAGGTTGATTAGAACTACG 59.937 40.741 27.07 0.00 32.59 3.51
3150 3343 7.043192 GCAAATATTGTGTGCTTATGCTTAAGG 60.043 37.037 18.14 3.81 40.48 2.69
3162 3355 3.618594 TCTCTCGAGCAAATATTGTGTGC 59.381 43.478 7.81 2.91 38.59 4.57
3163 3356 5.005203 GTCTCTCTCGAGCAAATATTGTGTG 59.995 44.000 7.81 0.00 37.19 3.82
3164 3357 5.105752 GTCTCTCTCGAGCAAATATTGTGT 58.894 41.667 7.81 0.00 37.19 3.72
3165 3358 5.105063 TGTCTCTCTCGAGCAAATATTGTG 58.895 41.667 7.81 0.00 37.19 3.33
3166 3359 5.126222 TCTGTCTCTCTCGAGCAAATATTGT 59.874 40.000 7.81 0.00 37.19 2.71
3193 3386 4.301628 CTTTGTTGGAGAAATGCAGAACC 58.698 43.478 0.00 0.00 0.00 3.62
3195 3388 3.638160 AGCTTTGTTGGAGAAATGCAGAA 59.362 39.130 0.00 0.00 0.00 3.02
3208 3796 8.572828 TGTTGTATAATTGACAAGCTTTGTTG 57.427 30.769 0.00 0.00 45.52 3.33
3209 3797 8.413229 ACTGTTGTATAATTGACAAGCTTTGTT 58.587 29.630 0.00 0.00 45.52 2.83
3222 3811 7.507616 TGGAAAAAGGACCACTGTTGTATAATT 59.492 33.333 0.00 0.00 0.00 1.40
3291 3881 5.534654 CCCTCTGATTCTCCACTCTACTTAG 59.465 48.000 0.00 0.00 0.00 2.18
3324 3915 9.363763 GTGTTTCTACCCTTAATGAGTACTAAC 57.636 37.037 0.00 0.00 0.00 2.34
3325 3916 8.534496 GGTGTTTCTACCCTTAATGAGTACTAA 58.466 37.037 0.00 0.00 34.56 2.24
3326 3917 7.897565 AGGTGTTTCTACCCTTAATGAGTACTA 59.102 37.037 0.00 0.00 41.83 1.82
3327 3918 6.729569 AGGTGTTTCTACCCTTAATGAGTACT 59.270 38.462 0.00 0.00 41.83 2.73
3328 3919 6.944096 AGGTGTTTCTACCCTTAATGAGTAC 58.056 40.000 0.00 0.00 41.83 2.73
3380 3971 9.369904 GGTAAATATGAAAGCACAAAATCATGT 57.630 29.630 0.00 0.00 34.54 3.21
3385 3976 9.023962 TCAGAGGTAAATATGAAAGCACAAAAT 57.976 29.630 0.00 0.00 0.00 1.82
3406 3997 0.032217 AGCCCCTCTCCTCTTCAGAG 60.032 60.000 0.00 0.00 41.71 3.35
3410 4001 1.002274 TCCAGCCCCTCTCCTCTTC 59.998 63.158 0.00 0.00 0.00 2.87
3438 4029 7.818930 CCACACCACAAAAATCTATTGCTATTT 59.181 33.333 0.00 0.00 0.00 1.40
3445 4036 5.766174 ACGTACCACACCACAAAAATCTATT 59.234 36.000 0.00 0.00 0.00 1.73
3450 4041 3.018149 ACACGTACCACACCACAAAAAT 58.982 40.909 0.00 0.00 0.00 1.82
3455 4046 0.460459 CACACACGTACCACACCACA 60.460 55.000 0.00 0.00 0.00 4.17
3464 4055 1.129326 GCAGACAGACACACACGTAC 58.871 55.000 0.00 0.00 0.00 3.67
3483 4074 0.304705 GCGGCCAGTTATTGTGATCG 59.695 55.000 2.24 0.00 0.00 3.69
3500 4091 0.166814 GTGCAGCAGACCTTTTAGCG 59.833 55.000 0.00 0.00 0.00 4.26
3521 4112 4.582701 TTGCACCAAATTAAGTGGACAG 57.417 40.909 13.56 5.60 39.62 3.51
3523 4114 5.195001 TCTTTGCACCAAATTAAGTGGAC 57.805 39.130 13.56 6.82 39.62 4.02


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

AutoCloner maintained by Alex Coulton.