Multiple sequence alignment - TraesCS3B01G557700

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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 TraesCS3B01G557700 chr3B 100.000 2966 0 0 1 2966 792266121 792269086 0.000000e+00 5478
1 TraesCS3B01G557700 chr3B 95.932 1352 51 4 744 2091 792355749 792357100 0.000000e+00 2189
2 TraesCS3B01G557700 chr3B 92.989 1412 62 11 687 2091 793383910 793382529 0.000000e+00 2025
3 TraesCS3B01G557700 chr3B 95.359 1099 41 8 687 1780 792442441 792443534 0.000000e+00 1738
4 TraesCS3B01G557700 chr3B 85.634 1427 171 25 687 2091 793369365 793367951 0.000000e+00 1469
5 TraesCS3B01G557700 chr3B 94.708 926 39 6 1168 2091 793475046 793474129 0.000000e+00 1430
6 TraesCS3B01G557700 chr3B 84.926 1413 181 25 700 2091 792387098 792388499 0.000000e+00 1400
7 TraesCS3B01G557700 chr3B 95.942 690 24 3 2 689 163157057 163157744 0.000000e+00 1116
8 TraesCS3B01G557700 chr3B 95.210 689 29 4 2 687 185388070 185387383 0.000000e+00 1086
9 TraesCS3B01G557700 chr3B 93.829 632 20 6 2091 2714 793474060 793473440 0.000000e+00 933
10 TraesCS3B01G557700 chr3B 93.671 632 21 6 2091 2714 793382460 793381840 0.000000e+00 928
11 TraesCS3B01G557700 chr3B 93.513 632 22 6 2091 2714 792357169 792357789 0.000000e+00 922
12 TraesCS3B01G557700 chr3B 94.071 253 13 1 2714 2966 65200185 65200435 1.670000e-102 383
13 TraesCS3B01G557700 chr3B 79.778 450 61 15 2091 2527 793367846 793367414 1.730000e-77 300
14 TraesCS3B01G557700 chrUn 94.759 1412 62 10 687 2091 155025250 155023844 0.000000e+00 2187
15 TraesCS3B01G557700 chrUn 84.926 1413 181 23 700 2091 154993253 154991852 0.000000e+00 1400
16 TraesCS3B01G557700 chrUn 93.671 632 21 6 2091 2714 155023775 155023155 0.000000e+00 928
17 TraesCS3B01G557700 chrUn 99.668 301 1 0 2414 2714 155105503 155105203 4.320000e-153 551
18 TraesCS3B01G557700 chr3D 94.657 1385 70 3 708 2091 591124206 591125587 0.000000e+00 2145
19 TraesCS3B01G557700 chr3D 89.386 603 33 10 2085 2676 591125648 591126230 0.000000e+00 730
20 TraesCS3B01G557700 chr3D 80.132 453 57 17 2091 2527 591179327 591179762 1.030000e-79 307
21 TraesCS3B01G557700 chr3A 94.191 1291 66 5 718 2001 721508999 721510287 0.000000e+00 1960
22 TraesCS3B01G557700 chr3A 85.614 1418 167 22 700 2091 721565505 721566911 0.000000e+00 1454
23 TraesCS3B01G557700 chr3A 88.679 265 18 3 2085 2343 721510468 721510726 2.220000e-81 313
24 TraesCS3B01G557700 chr3A 80.000 450 60 15 2091 2527 721567016 721567448 3.710000e-79 305
25 TraesCS3B01G557700 chr3A 89.000 100 3 1 2343 2442 721510750 721510841 1.870000e-22 117
26 TraesCS3B01G557700 chr6B 95.948 691 25 3 4 691 616665784 616666474 0.000000e+00 1118
27 TraesCS3B01G557700 chr6B 95.948 691 23 5 1 688 632245177 632244489 0.000000e+00 1116
28 TraesCS3B01G557700 chr6B 94.949 693 29 5 1 691 265017354 265018042 0.000000e+00 1081
29 TraesCS3B01G557700 chr4A 95.652 690 19 6 1 688 712454769 712454089 0.000000e+00 1098
30 TraesCS3B01G557700 chr4A 94.783 690 31 4 1 688 615685446 615686132 0.000000e+00 1070
31 TraesCS3B01G557700 chr4A 93.725 255 15 1 2712 2966 743631591 743631338 6.000000e-102 381
32 TraesCS3B01G557700 chr1D 95.245 694 29 4 1 690 247866932 247866239 0.000000e+00 1096
33 TraesCS3B01G557700 chr2B 95.362 690 29 3 4 691 197575500 197574812 0.000000e+00 1094
34 TraesCS3B01G557700 chr2B 93.701 254 14 2 2714 2966 723438030 723437778 2.160000e-101 379
35 TraesCS3B01G557700 chr2B 92.135 267 18 3 2701 2966 390921014 390921278 1.000000e-99 374
36 TraesCS3B01G557700 chr5B 93.701 254 14 2 2714 2966 427215682 427215934 2.160000e-101 379
37 TraesCS3B01G557700 chr5B 92.453 265 15 4 2704 2966 59719588 59719327 1.000000e-99 374
38 TraesCS3B01G557700 chr5B 92.996 257 16 2 2711 2966 341523163 341523418 1.000000e-99 374
39 TraesCS3B01G557700 chr5B 92.996 257 16 2 2711 2966 571108047 571108302 1.000000e-99 374
40 TraesCS3B01G557700 chr4B 93.701 254 14 2 2714 2966 423041676 423041928 2.160000e-101 379


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 TraesCS3B01G557700 chr3B 792266121 792269086 2965 False 5478.000000 5478 100.000000 1 2966 1 chr3B.!!$F3 2965
1 TraesCS3B01G557700 chr3B 792442441 792443534 1093 False 1738.000000 1738 95.359000 687 1780 1 chr3B.!!$F5 1093
2 TraesCS3B01G557700 chr3B 792355749 792357789 2040 False 1555.500000 2189 94.722500 744 2714 2 chr3B.!!$F6 1970
3 TraesCS3B01G557700 chr3B 793381840 793383910 2070 True 1476.500000 2025 93.330000 687 2714 2 chr3B.!!$R3 2027
4 TraesCS3B01G557700 chr3B 792387098 792388499 1401 False 1400.000000 1400 84.926000 700 2091 1 chr3B.!!$F4 1391
5 TraesCS3B01G557700 chr3B 793473440 793475046 1606 True 1181.500000 1430 94.268500 1168 2714 2 chr3B.!!$R4 1546
6 TraesCS3B01G557700 chr3B 163157057 163157744 687 False 1116.000000 1116 95.942000 2 689 1 chr3B.!!$F2 687
7 TraesCS3B01G557700 chr3B 185387383 185388070 687 True 1086.000000 1086 95.210000 2 687 1 chr3B.!!$R1 685
8 TraesCS3B01G557700 chr3B 793367414 793369365 1951 True 884.500000 1469 82.706000 687 2527 2 chr3B.!!$R2 1840
9 TraesCS3B01G557700 chrUn 155023155 155025250 2095 True 1557.500000 2187 94.215000 687 2714 2 chrUn.!!$R3 2027
10 TraesCS3B01G557700 chrUn 154991852 154993253 1401 True 1400.000000 1400 84.926000 700 2091 1 chrUn.!!$R1 1391
11 TraesCS3B01G557700 chr3D 591124206 591126230 2024 False 1437.500000 2145 92.021500 708 2676 2 chr3D.!!$F2 1968
12 TraesCS3B01G557700 chr3A 721565505 721567448 1943 False 879.500000 1454 82.807000 700 2527 2 chr3A.!!$F2 1827
13 TraesCS3B01G557700 chr3A 721508999 721510841 1842 False 796.666667 1960 90.623333 718 2442 3 chr3A.!!$F1 1724
14 TraesCS3B01G557700 chr6B 616665784 616666474 690 False 1118.000000 1118 95.948000 4 691 1 chr6B.!!$F2 687
15 TraesCS3B01G557700 chr6B 632244489 632245177 688 True 1116.000000 1116 95.948000 1 688 1 chr6B.!!$R1 687
16 TraesCS3B01G557700 chr6B 265017354 265018042 688 False 1081.000000 1081 94.949000 1 691 1 chr6B.!!$F1 690
17 TraesCS3B01G557700 chr4A 712454089 712454769 680 True 1098.000000 1098 95.652000 1 688 1 chr4A.!!$R1 687
18 TraesCS3B01G557700 chr4A 615685446 615686132 686 False 1070.000000 1070 94.783000 1 688 1 chr4A.!!$F1 687
19 TraesCS3B01G557700 chr1D 247866239 247866932 693 True 1096.000000 1096 95.245000 1 690 1 chr1D.!!$R1 689
20 TraesCS3B01G557700 chr2B 197574812 197575500 688 True 1094.000000 1094 95.362000 4 691 1 chr2B.!!$R1 687

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
160 163 1.593209 GAATCGCCGCCGGTATGAA 60.593 57.895 4.45 0.0 34.56 2.57 F
1072 1126 0.375454 CACCAACGACGAGCAAACAA 59.625 50.000 0.00 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1585 1686 0.389948 GGTTCGACGTCTCTGGCAAT 60.390 55.0 14.7 0.0 0.0 3.56 R
2918 3217 0.102120 AAGCGCGAGAGGAAGAGATG 59.898 55.0 12.1 0.0 0.0 2.90 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
56 58 6.511767 CGATGAGAAATCTATTGTTTTCCCCG 60.512 42.308 6.97 3.67 34.25 5.73
143 146 2.494073 GGGGTGTTTATTTGCAATCCGA 59.506 45.455 0.00 0.00 0.00 4.55
160 163 1.593209 GAATCGCCGCCGGTATGAA 60.593 57.895 4.45 0.00 34.56 2.57
529 538 8.099537 AGTTAGATATGATCTGCGGATGAATTT 58.900 33.333 14.17 1.75 40.51 1.82
633 643 3.699038 TCAAAACACAGGGACTTTTCTGG 59.301 43.478 0.00 0.00 34.60 3.86
710 731 2.125952 CGATCGAGGCTGCACACA 60.126 61.111 10.26 0.00 0.00 3.72
715 736 2.401583 TCGAGGCTGCACACAAATAT 57.598 45.000 0.50 0.00 0.00 1.28
716 737 2.279741 TCGAGGCTGCACACAAATATC 58.720 47.619 0.50 0.00 0.00 1.63
732 753 8.777413 ACACAAATATCATCGAATCGAATCAAT 58.223 29.630 10.12 3.77 39.99 2.57
733 754 9.259015 CACAAATATCATCGAATCGAATCAATC 57.741 33.333 10.12 0.00 39.99 2.67
734 755 8.992073 ACAAATATCATCGAATCGAATCAATCA 58.008 29.630 10.12 0.00 39.99 2.57
772 795 1.734655 TCTCCAATATGGGCCTCCTC 58.265 55.000 4.53 0.00 38.32 3.71
840 888 2.843545 GGTGGCCAACCTTCCTGA 59.156 61.111 10.67 0.00 46.55 3.86
841 889 1.603739 GGTGGCCAACCTTCCTGAC 60.604 63.158 10.67 0.00 46.55 3.51
842 890 1.603739 GTGGCCAACCTTCCTGACC 60.604 63.158 7.24 0.00 36.63 4.02
843 891 2.035783 GGCCAACCTTCCTGACCC 59.964 66.667 0.00 0.00 0.00 4.46
844 892 2.035783 GCCAACCTTCCTGACCCC 59.964 66.667 0.00 0.00 0.00 4.95
845 893 2.351276 CCAACCTTCCTGACCCCG 59.649 66.667 0.00 0.00 0.00 5.73
846 894 2.359975 CAACCTTCCTGACCCCGC 60.360 66.667 0.00 0.00 0.00 6.13
847 895 3.647771 AACCTTCCTGACCCCGCC 61.648 66.667 0.00 0.00 0.00 6.13
848 896 4.974438 ACCTTCCTGACCCCGCCA 62.974 66.667 0.00 0.00 0.00 5.69
849 897 3.646715 CCTTCCTGACCCCGCCAA 61.647 66.667 0.00 0.00 0.00 4.52
850 898 2.359975 CTTCCTGACCCCGCCAAC 60.360 66.667 0.00 0.00 0.00 3.77
851 899 2.852075 TTCCTGACCCCGCCAACT 60.852 61.111 0.00 0.00 0.00 3.16
852 900 3.190738 TTCCTGACCCCGCCAACTG 62.191 63.158 0.00 0.00 0.00 3.16
1004 1053 3.294214 GAACTCCCAAGAATGCCATGAT 58.706 45.455 0.00 0.00 0.00 2.45
1072 1126 0.375454 CACCAACGACGAGCAAACAA 59.625 50.000 0.00 0.00 0.00 2.83
1089 1143 3.844577 ACAAAGCACTACGTCGTCTAT 57.155 42.857 0.00 0.00 0.00 1.98
1262 1316 1.209261 TCCGCTCATTGTATTCCAGCA 59.791 47.619 0.00 0.00 0.00 4.41
1585 1686 7.228108 CCTGCTATATCAATTGCTCAGAAGAAA 59.772 37.037 0.00 0.00 35.24 2.52
1627 1728 6.269307 ACCTGGTAATATCACCGTAATTAGCT 59.731 38.462 0.00 0.00 41.88 3.32
1644 1745 1.893062 CTGGCACCTCATCGAGTCA 59.107 57.895 0.00 0.00 0.00 3.41
1687 1788 1.225855 GCATCGACGGCAATTCCATA 58.774 50.000 6.06 0.00 34.01 2.74
1910 2011 2.226962 AAGTCCGGTACTTCTAGCCA 57.773 50.000 11.94 0.00 45.64 4.75
2211 2463 8.147058 TGTAGTTTACTTATTGTTTGTCCGGTA 58.853 33.333 0.00 0.00 0.00 4.02
2246 2499 2.765352 CCTGAAGGAGGCGGGATAT 58.235 57.895 0.00 0.00 34.01 1.63
2714 3013 5.814705 AGAAGCTGAAAATCTCCGTGATAAG 59.185 40.000 0.00 0.00 34.45 1.73
2715 3014 5.344743 AGCTGAAAATCTCCGTGATAAGA 57.655 39.130 0.00 0.00 34.45 2.10
2716 3015 5.355596 AGCTGAAAATCTCCGTGATAAGAG 58.644 41.667 0.00 0.00 34.45 2.85
2717 3016 4.025313 GCTGAAAATCTCCGTGATAAGAGC 60.025 45.833 0.00 0.00 34.45 4.09
2718 3017 5.084818 TGAAAATCTCCGTGATAAGAGCA 57.915 39.130 0.00 0.00 34.45 4.26
2719 3018 5.674525 TGAAAATCTCCGTGATAAGAGCAT 58.325 37.500 0.00 0.00 34.45 3.79
2720 3019 5.755375 TGAAAATCTCCGTGATAAGAGCATC 59.245 40.000 0.00 0.00 34.45 3.91
2721 3020 5.543507 AAATCTCCGTGATAAGAGCATCT 57.456 39.130 0.00 0.00 40.63 2.90
2722 3021 5.132897 AATCTCCGTGATAAGAGCATCTC 57.867 43.478 0.00 0.00 38.59 2.75
2723 3022 4.021544 AATCTCCGTGATAAGAGCATCTCC 60.022 45.833 0.00 0.00 38.59 3.71
2724 3023 6.449974 AATCTCCGTGATAAGAGCATCTCCA 61.450 44.000 0.00 0.00 38.59 3.86
2725 3024 7.870270 AATCTCCGTGATAAGAGCATCTCCAA 61.870 42.308 0.00 0.00 38.59 3.53
2726 3025 9.770926 AATCTCCGTGATAAGAGCATCTCCAAC 62.771 44.444 0.00 0.00 38.59 3.77
2731 3030 2.892425 GAGCATCTCCAACGGCCG 60.892 66.667 26.86 26.86 0.00 6.13
2740 3039 4.622456 CAACGGCCGCGCAAAACT 62.622 61.111 28.58 0.00 0.00 2.66
2741 3040 2.973600 AACGGCCGCGCAAAACTA 60.974 55.556 28.58 0.00 0.00 2.24
2742 3041 2.961669 AACGGCCGCGCAAAACTAG 61.962 57.895 28.58 0.00 0.00 2.57
2743 3042 4.811761 CGGCCGCGCAAAACTAGC 62.812 66.667 14.67 0.00 0.00 3.42
2760 3059 2.349648 CGTCGCGCCGCAAAATAG 60.350 61.111 10.75 0.00 0.00 1.73
2761 3060 2.022762 GTCGCGCCGCAAAATAGG 59.977 61.111 10.75 0.00 0.00 2.57
2772 3071 3.881630 GCAAAATAGGCGTTTTTAGCG 57.118 42.857 1.70 0.00 35.00 4.26
2836 3135 4.079748 CGCGCGCTAAAACGGGTT 62.080 61.111 30.48 0.00 46.53 4.11
2837 3136 2.501008 GCGCGCTAAAACGGGTTG 60.501 61.111 26.67 0.00 46.53 3.77
2838 3137 2.174835 CGCGCTAAAACGGGTTGG 59.825 61.111 5.56 0.00 40.69 3.77
2839 3138 2.319096 CGCGCTAAAACGGGTTGGA 61.319 57.895 5.56 0.00 40.69 3.53
2840 3139 1.208358 GCGCTAAAACGGGTTGGAC 59.792 57.895 0.00 0.00 0.00 4.02
2841 3140 1.494189 CGCTAAAACGGGTTGGACG 59.506 57.895 0.00 0.00 37.36 4.79
2842 3141 1.208358 GCTAAAACGGGTTGGACGC 59.792 57.895 0.00 0.00 34.00 5.19
2858 3157 4.645921 GCGCGGGCAAAAGCACTT 62.646 61.111 20.76 0.00 39.62 3.16
2859 3158 2.950673 CGCGGGCAAAAGCACTTA 59.049 55.556 0.00 0.00 0.00 2.24
2860 3159 1.442017 CGCGGGCAAAAGCACTTAC 60.442 57.895 0.00 0.00 0.00 2.34
2861 3160 1.657556 GCGGGCAAAAGCACTTACA 59.342 52.632 0.00 0.00 0.00 2.41
2862 3161 0.663269 GCGGGCAAAAGCACTTACAC 60.663 55.000 0.00 0.00 0.00 2.90
2863 3162 0.385473 CGGGCAAAAGCACTTACACG 60.385 55.000 0.00 0.00 0.00 4.49
2864 3163 0.663269 GGGCAAAAGCACTTACACGC 60.663 55.000 0.00 0.00 0.00 5.34
2865 3164 0.996727 GGCAAAAGCACTTACACGCG 60.997 55.000 3.53 3.53 0.00 6.01
2866 3165 1.596841 GCAAAAGCACTTACACGCGC 61.597 55.000 5.73 0.00 0.00 6.86
2867 3166 1.083015 AAAAGCACTTACACGCGCG 60.083 52.632 30.96 30.96 0.00 6.86
2868 3167 2.438385 AAAAGCACTTACACGCGCGG 62.438 55.000 35.22 24.36 0.00 6.46
2886 3185 3.269347 CGTATTTCGGGCGCCCAG 61.269 66.667 42.78 33.39 35.37 4.45
2887 3186 2.124860 GTATTTCGGGCGCCCAGT 60.125 61.111 42.78 26.81 35.37 4.00
2888 3187 1.144496 GTATTTCGGGCGCCCAGTA 59.856 57.895 42.78 27.39 35.37 2.74
2889 3188 1.144496 TATTTCGGGCGCCCAGTAC 59.856 57.895 42.78 18.06 35.37 2.73
2890 3189 1.615165 TATTTCGGGCGCCCAGTACA 61.615 55.000 42.78 23.03 35.37 2.90
2891 3190 2.869503 ATTTCGGGCGCCCAGTACAG 62.870 60.000 42.78 26.41 35.37 2.74
2926 3225 3.326210 CGCTCGCGCCATCTCTTC 61.326 66.667 0.00 0.00 0.00 2.87
2927 3226 2.964389 GCTCGCGCCATCTCTTCC 60.964 66.667 0.00 0.00 0.00 3.46
2928 3227 2.811101 CTCGCGCCATCTCTTCCT 59.189 61.111 0.00 0.00 0.00 3.36
2929 3228 1.299773 CTCGCGCCATCTCTTCCTC 60.300 63.158 0.00 0.00 0.00 3.71
2930 3229 1.733402 CTCGCGCCATCTCTTCCTCT 61.733 60.000 0.00 0.00 0.00 3.69
2931 3230 1.299773 CGCGCCATCTCTTCCTCTC 60.300 63.158 0.00 0.00 0.00 3.20
2932 3231 1.299773 GCGCCATCTCTTCCTCTCG 60.300 63.158 0.00 0.00 0.00 4.04
2933 3232 1.299773 CGCCATCTCTTCCTCTCGC 60.300 63.158 0.00 0.00 0.00 5.03
2934 3233 1.299773 GCCATCTCTTCCTCTCGCG 60.300 63.158 0.00 0.00 0.00 5.87
2935 3234 1.299773 CCATCTCTTCCTCTCGCGC 60.300 63.158 0.00 0.00 0.00 6.86
2936 3235 1.732917 CATCTCTTCCTCTCGCGCT 59.267 57.895 5.56 0.00 0.00 5.92
2937 3236 0.102120 CATCTCTTCCTCTCGCGCTT 59.898 55.000 5.56 0.00 0.00 4.68
2938 3237 0.383949 ATCTCTTCCTCTCGCGCTTC 59.616 55.000 5.56 0.00 0.00 3.86
2939 3238 1.226831 CTCTTCCTCTCGCGCTTCC 60.227 63.158 5.56 0.00 0.00 3.46
2940 3239 1.938657 CTCTTCCTCTCGCGCTTCCA 61.939 60.000 5.56 0.00 0.00 3.53
2941 3240 1.079819 CTTCCTCTCGCGCTTCCAA 60.080 57.895 5.56 0.00 0.00 3.53
2942 3241 1.355066 CTTCCTCTCGCGCTTCCAAC 61.355 60.000 5.56 0.00 0.00 3.77
2943 3242 2.781595 TTCCTCTCGCGCTTCCAACC 62.782 60.000 5.56 0.00 0.00 3.77
2944 3243 2.815647 CTCTCGCGCTTCCAACCC 60.816 66.667 5.56 0.00 0.00 4.11
2945 3244 4.388499 TCTCGCGCTTCCAACCCC 62.388 66.667 5.56 0.00 0.00 4.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
56 58 4.458989 TGCATACCTCTGAAAAATGTCACC 59.541 41.667 0.00 0.00 0.00 4.02
113 115 6.249951 TGCAAATAAACACCCCACTATAACT 58.750 36.000 0.00 0.00 0.00 2.24
143 146 0.745128 TTTTCATACCGGCGGCGATT 60.745 50.000 34.49 21.14 0.00 3.34
504 513 7.840342 AATTCATCCGCAGATCATATCTAAC 57.160 36.000 0.00 0.00 37.58 2.34
633 643 1.083489 TCGTCCGTCATGGCATTTTC 58.917 50.000 0.00 0.00 37.80 2.29
698 708 3.303593 CGATGATATTTGTGTGCAGCCTC 60.304 47.826 0.00 0.00 0.00 4.70
715 736 6.507023 TCTCTTGATTGATTCGATTCGATGA 58.493 36.000 9.96 4.04 35.23 2.92
716 737 6.760161 TCTCTTGATTGATTCGATTCGATG 57.240 37.500 9.96 2.06 35.23 3.84
772 795 0.179100 ACCATTGCAGGATCGACGAG 60.179 55.000 3.01 0.00 0.00 4.18
1004 1053 2.676121 CATTGGTGGAGCCGGCAA 60.676 61.111 31.54 13.75 41.21 4.52
1089 1143 7.168219 AGAAAGGATTGTGCAAGACATAGTTA 58.832 34.615 0.00 0.00 33.40 2.24
1262 1316 0.991355 TGACCACACACCCTTCCCTT 60.991 55.000 0.00 0.00 0.00 3.95
1585 1686 0.389948 GGTTCGACGTCTCTGGCAAT 60.390 55.000 14.70 0.00 0.00 3.56
1627 1728 1.184970 TGTGACTCGATGAGGTGCCA 61.185 55.000 0.00 0.00 33.35 4.92
1644 1745 2.200081 ACCATGAGTAGCTTCCCATGT 58.800 47.619 12.65 0.62 35.79 3.21
1687 1788 3.904339 AGAGTGACCCACAAAGTATCTGT 59.096 43.478 0.00 0.00 36.74 3.41
2287 2541 4.814234 TCAAAGGTGTTGTATCACACTCAC 59.186 41.667 4.10 5.69 45.56 3.51
2288 2542 5.029807 TCAAAGGTGTTGTATCACACTCA 57.970 39.130 4.10 0.00 45.56 3.41
2289 2543 6.560253 AATCAAAGGTGTTGTATCACACTC 57.440 37.500 4.10 0.00 45.56 3.51
2290 2544 6.959639 AAATCAAAGGTGTTGTATCACACT 57.040 33.333 4.10 0.00 45.56 3.55
2315 2585 0.732571 GTATGGCACAACACCATCGG 59.267 55.000 0.00 0.00 44.85 4.18
2686 2985 2.675348 CGGAGATTTTCAGCTTCTGGAC 59.325 50.000 0.00 0.00 31.51 4.02
2714 3013 2.892425 CGGCCGTTGGAGATGCTC 60.892 66.667 19.50 0.00 0.00 4.26
2723 3022 3.243274 TAGTTTTGCGCGGCCGTTG 62.243 57.895 28.70 20.73 36.67 4.10
2724 3023 2.961669 CTAGTTTTGCGCGGCCGTT 61.962 57.895 28.70 5.01 36.67 4.44
2725 3024 3.419759 CTAGTTTTGCGCGGCCGT 61.420 61.111 28.70 6.42 36.67 5.68
2726 3025 4.811761 GCTAGTTTTGCGCGGCCG 62.812 66.667 24.05 24.05 37.57 6.13
2727 3026 4.811761 CGCTAGTTTTGCGCGGCC 62.812 66.667 8.83 0.00 46.72 6.13
2743 3042 2.349648 CTATTTTGCGGCGCGACG 60.350 61.111 33.75 33.75 0.00 5.12
2744 3043 2.022762 CCTATTTTGCGGCGCGAC 59.977 61.111 28.09 5.80 0.00 5.19
2745 3044 3.871574 GCCTATTTTGCGGCGCGA 61.872 61.111 28.09 24.12 36.45 5.87
2752 3051 3.881630 CGCTAAAAACGCCTATTTTGC 57.118 42.857 0.00 0.00 32.12 3.68
2819 3118 4.079748 AACCCGTTTTAGCGCGCG 62.080 61.111 28.44 28.44 0.00 6.86
2820 3119 2.501008 CAACCCGTTTTAGCGCGC 60.501 61.111 26.66 26.66 0.00 6.86
2821 3120 2.174835 CCAACCCGTTTTAGCGCG 59.825 61.111 0.00 0.00 0.00 6.86
2822 3121 1.208358 GTCCAACCCGTTTTAGCGC 59.792 57.895 0.00 0.00 0.00 5.92
2823 3122 1.494189 CGTCCAACCCGTTTTAGCG 59.506 57.895 0.00 0.00 0.00 4.26
2824 3123 1.208358 GCGTCCAACCCGTTTTAGC 59.792 57.895 0.00 0.00 0.00 3.09
2825 3124 1.494189 CGCGTCCAACCCGTTTTAG 59.506 57.895 0.00 0.00 0.00 1.85
2826 3125 2.606030 GCGCGTCCAACCCGTTTTA 61.606 57.895 8.43 0.00 0.00 1.52
2827 3126 3.956317 GCGCGTCCAACCCGTTTT 61.956 61.111 8.43 0.00 0.00 2.43
2841 3140 3.262142 TAAGTGCTTTTGCCCGCGC 62.262 57.895 0.00 0.00 46.87 6.86
2842 3141 1.442017 GTAAGTGCTTTTGCCCGCG 60.442 57.895 0.00 0.00 46.87 6.46
2843 3142 0.663269 GTGTAAGTGCTTTTGCCCGC 60.663 55.000 0.00 0.00 46.87 6.13
2844 3143 0.385473 CGTGTAAGTGCTTTTGCCCG 60.385 55.000 0.00 0.00 46.87 6.13
2845 3144 0.663269 GCGTGTAAGTGCTTTTGCCC 60.663 55.000 0.00 0.00 46.87 5.36
2846 3145 0.996727 CGCGTGTAAGTGCTTTTGCC 60.997 55.000 0.00 0.00 46.87 4.52
2847 3146 1.596841 GCGCGTGTAAGTGCTTTTGC 61.597 55.000 8.43 0.00 43.64 3.68
2848 3147 1.320382 CGCGCGTGTAAGTGCTTTTG 61.320 55.000 24.19 0.00 44.70 2.44
2849 3148 1.083015 CGCGCGTGTAAGTGCTTTT 60.083 52.632 24.19 0.00 44.70 2.27
2850 3149 2.549282 CGCGCGTGTAAGTGCTTT 59.451 55.556 24.19 0.00 44.70 3.51
2851 3150 3.411351 CCGCGCGTGTAAGTGCTT 61.411 61.111 29.95 0.00 44.70 3.91
2869 3168 2.632136 TACTGGGCGCCCGAAATACG 62.632 60.000 39.00 21.98 39.42 3.06
2870 3169 1.144496 TACTGGGCGCCCGAAATAC 59.856 57.895 39.00 15.47 39.42 1.89
2871 3170 1.144496 GTACTGGGCGCCCGAAATA 59.856 57.895 39.00 24.67 39.42 1.40
2872 3171 2.124860 GTACTGGGCGCCCGAAAT 60.125 61.111 39.00 25.73 39.42 2.17
2873 3172 3.599285 CTGTACTGGGCGCCCGAAA 62.599 63.158 39.00 24.16 39.42 3.46
2874 3173 4.077184 CTGTACTGGGCGCCCGAA 62.077 66.667 39.00 24.55 39.42 4.30
2911 3210 1.299773 GAGGAAGAGATGGCGCGAG 60.300 63.158 12.10 0.00 0.00 5.03
2912 3211 1.729470 GAGAGGAAGAGATGGCGCGA 61.729 60.000 12.10 0.00 0.00 5.87
2913 3212 1.299773 GAGAGGAAGAGATGGCGCG 60.300 63.158 0.00 0.00 0.00 6.86
2914 3213 1.299773 CGAGAGGAAGAGATGGCGC 60.300 63.158 0.00 0.00 0.00 6.53
2915 3214 1.299773 GCGAGAGGAAGAGATGGCG 60.300 63.158 0.00 0.00 0.00 5.69
2916 3215 1.299773 CGCGAGAGGAAGAGATGGC 60.300 63.158 0.00 0.00 0.00 4.40
2917 3216 1.299773 GCGCGAGAGGAAGAGATGG 60.300 63.158 12.10 0.00 0.00 3.51
2918 3217 0.102120 AAGCGCGAGAGGAAGAGATG 59.898 55.000 12.10 0.00 0.00 2.90
2919 3218 0.383949 GAAGCGCGAGAGGAAGAGAT 59.616 55.000 12.10 0.00 0.00 2.75
2920 3219 1.658686 GGAAGCGCGAGAGGAAGAGA 61.659 60.000 12.10 0.00 0.00 3.10
2921 3220 1.226831 GGAAGCGCGAGAGGAAGAG 60.227 63.158 12.10 0.00 0.00 2.85
2922 3221 1.532604 TTGGAAGCGCGAGAGGAAGA 61.533 55.000 12.10 0.00 0.00 2.87
2923 3222 1.079819 TTGGAAGCGCGAGAGGAAG 60.080 57.895 12.10 0.00 0.00 3.46
2924 3223 1.374252 GTTGGAAGCGCGAGAGGAA 60.374 57.895 12.10 0.00 0.00 3.36
2925 3224 2.261671 GTTGGAAGCGCGAGAGGA 59.738 61.111 12.10 0.00 0.00 3.71
2926 3225 2.815647 GGTTGGAAGCGCGAGAGG 60.816 66.667 12.10 0.00 0.00 3.69
2927 3226 2.815647 GGGTTGGAAGCGCGAGAG 60.816 66.667 12.10 0.00 0.00 3.20
2928 3227 4.388499 GGGGTTGGAAGCGCGAGA 62.388 66.667 12.10 0.00 0.00 4.04


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

AutoCloner maintained by Alex Coulton.