Multiple sequence alignment - TraesCS1B01G429300

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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 TraesCS1B01G429300 chr1B 100.000 2963 0 0 1 2963 654032276 654029314 0.000000e+00 5472
1 TraesCS1B01G429300 chr1D 89.511 2107 118 45 27 2071 470734495 470732430 0.000000e+00 2571
2 TraesCS1B01G429300 chr1D 89.773 528 34 8 2187 2699 470732214 470731692 0.000000e+00 658
3 TraesCS1B01G429300 chr1D 92.251 271 15 2 2693 2963 470731619 470731355 2.160000e-101 379
4 TraesCS1B01G429300 chr1A 89.617 2013 117 45 101 2071 564397741 564395779 0.000000e+00 2475
5 TraesCS1B01G429300 chr1A 90.652 460 35 5 2240 2699 564395635 564395184 3.270000e-169 604
6 TraesCS1B01G429300 chr1A 86.047 258 16 11 2694 2951 564395110 564394873 2.930000e-65 259
7 TraesCS1B01G429300 chr2D 86.015 951 128 3 1036 1982 25024784 25025733 0.000000e+00 1014
8 TraesCS1B01G429300 chr2A 83.299 958 113 15 1036 1983 27499919 27500839 0.000000e+00 839
9 TraesCS1B01G429300 chr2A 87.823 271 27 3 2693 2963 83249868 83250132 2.220000e-81 313
10 TraesCS1B01G429300 chr3B 90.037 271 21 3 2693 2963 16303230 16302966 2.190000e-91 346
11 TraesCS1B01G429300 chr7B 92.233 206 14 1 2758 2963 176807247 176807044 1.040000e-74 291


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 TraesCS1B01G429300 chr1B 654029314 654032276 2962 True 5472.000000 5472 100.000000 1 2963 1 chr1B.!!$R1 2962
1 TraesCS1B01G429300 chr1D 470731355 470734495 3140 True 1202.666667 2571 90.511667 27 2963 3 chr1D.!!$R1 2936
2 TraesCS1B01G429300 chr1A 564394873 564397741 2868 True 1112.666667 2475 88.772000 101 2951 3 chr1A.!!$R1 2850
3 TraesCS1B01G429300 chr2D 25024784 25025733 949 False 1014.000000 1014 86.015000 1036 1982 1 chr2D.!!$F1 946
4 TraesCS1B01G429300 chr2A 27499919 27500839 920 False 839.000000 839 83.299000 1036 1983 1 chr2A.!!$F1 947

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
852 899 0.033503 GTCGTTTGGGGAATGGGGAT 60.034 55.0 0.0 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2821 3131 0.679505 TGGACCTGTCGAAGTTCTGG 59.32 55.0 0.56 1.02 0.0 3.86 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
23 24 6.069684 ACTGCAGAAAGAGTGAAGAAAATG 57.930 37.500 23.35 0.00 0.00 2.32
24 25 5.591877 ACTGCAGAAAGAGTGAAGAAAATGT 59.408 36.000 23.35 0.00 0.00 2.71
25 26 6.096001 ACTGCAGAAAGAGTGAAGAAAATGTT 59.904 34.615 23.35 0.00 0.00 2.71
64 65 3.103911 AGCGCTCGAAAACGACCG 61.104 61.111 2.64 0.00 0.00 4.79
65 66 3.101428 GCGCTCGAAAACGACCGA 61.101 61.111 0.00 0.00 0.00 4.69
88 89 2.776072 GCGCGTGTTATCGTTGCT 59.224 55.556 8.43 0.00 33.90 3.91
115 130 1.315257 CCTTGTCAAGCCGGGGAATG 61.315 60.000 2.18 0.00 0.00 2.67
119 134 1.253100 GTCAAGCCGGGGAATGAAAA 58.747 50.000 2.18 0.00 0.00 2.29
121 136 0.246360 CAAGCCGGGGAATGAAAACC 59.754 55.000 2.18 0.00 0.00 3.27
123 138 2.882132 CCGGGGAATGAAAACCGC 59.118 61.111 0.00 0.00 44.70 5.68
128 143 2.180769 GAATGAAAACCGCCCGGC 59.819 61.111 6.63 0.00 39.32 6.13
210 230 1.007336 CCGACCCAAAAGACTCGTCG 61.007 60.000 0.00 0.00 44.41 5.12
219 239 2.799814 AAGACTCGTCGAGCTCCCGA 62.800 60.000 22.00 18.70 36.06 5.14
243 263 1.375853 TTTCCAAGATGGCCATCGCG 61.376 55.000 34.48 28.48 42.48 5.87
274 297 4.016629 TGGTGACGACGACGACGG 62.017 66.667 22.36 6.21 44.46 4.79
618 656 3.755628 GTGGAGGCCGTCGTGCTA 61.756 66.667 0.00 0.00 0.00 3.49
697 735 3.357166 GCGCTAGCTATGTACTCTGTT 57.643 47.619 13.93 0.00 41.01 3.16
698 736 4.485024 GCGCTAGCTATGTACTCTGTTA 57.515 45.455 13.93 0.00 41.01 2.41
699 737 4.220572 GCGCTAGCTATGTACTCTGTTAC 58.779 47.826 13.93 0.00 41.01 2.50
700 738 4.023878 GCGCTAGCTATGTACTCTGTTACT 60.024 45.833 13.93 0.00 41.01 2.24
701 739 5.444983 CGCTAGCTATGTACTCTGTTACTG 58.555 45.833 13.93 0.00 0.00 2.74
702 740 5.007823 CGCTAGCTATGTACTCTGTTACTGT 59.992 44.000 13.93 0.00 0.00 3.55
703 741 6.458478 CGCTAGCTATGTACTCTGTTACTGTT 60.458 42.308 13.93 0.00 0.00 3.16
713 751 8.658609 TGTACTCTGTTACTGTTTGTTTGTTAC 58.341 33.333 0.00 0.00 0.00 2.50
779 826 6.075310 CGATCGACTACTCTGCTGTAAATTTC 60.075 42.308 10.26 0.00 0.00 2.17
782 829 4.504858 ACTACTCTGCTGTAAATTTCCCG 58.495 43.478 0.00 0.00 0.00 5.14
785 832 1.173043 CTGCTGTAAATTTCCCGCCA 58.827 50.000 0.00 0.00 0.00 5.69
795 842 2.002505 TTTCCCGCCATGAGGAAAAA 57.997 45.000 17.22 10.70 46.55 1.94
831 878 4.643334 TCCCAATCTGCTCAAGATGATTTG 59.357 41.667 0.00 0.00 45.37 2.32
845 892 0.594110 GATTTGCGTCGTTTGGGGAA 59.406 50.000 0.00 0.00 0.00 3.97
846 893 1.201414 GATTTGCGTCGTTTGGGGAAT 59.799 47.619 0.00 0.00 0.00 3.01
847 894 0.312416 TTTGCGTCGTTTGGGGAATG 59.688 50.000 0.00 0.00 0.00 2.67
848 895 1.519751 TTGCGTCGTTTGGGGAATGG 61.520 55.000 0.00 0.00 0.00 3.16
849 896 2.696759 GCGTCGTTTGGGGAATGGG 61.697 63.158 0.00 0.00 0.00 4.00
851 898 1.381076 GTCGTTTGGGGAATGGGGA 59.619 57.895 0.00 0.00 0.00 4.81
852 899 0.033503 GTCGTTTGGGGAATGGGGAT 60.034 55.000 0.00 0.00 0.00 3.85
872 927 4.569162 GGATGATGGTGTGATGCAATTTTG 59.431 41.667 0.00 0.00 0.00 2.44
873 928 4.603989 TGATGGTGTGATGCAATTTTGT 57.396 36.364 0.00 0.00 0.00 2.83
874 929 5.718724 TGATGGTGTGATGCAATTTTGTA 57.281 34.783 0.00 0.00 0.00 2.41
875 930 5.468592 TGATGGTGTGATGCAATTTTGTAC 58.531 37.500 0.00 0.00 0.00 2.90
876 931 5.243507 TGATGGTGTGATGCAATTTTGTACT 59.756 36.000 0.00 0.00 0.00 2.73
877 932 4.869215 TGGTGTGATGCAATTTTGTACTG 58.131 39.130 0.00 0.00 0.00 2.74
878 933 4.340666 TGGTGTGATGCAATTTTGTACTGT 59.659 37.500 0.00 0.00 0.00 3.55
879 934 5.532779 TGGTGTGATGCAATTTTGTACTGTA 59.467 36.000 0.00 0.00 0.00 2.74
880 935 6.208402 TGGTGTGATGCAATTTTGTACTGTAT 59.792 34.615 0.00 0.00 0.00 2.29
881 936 6.527722 GGTGTGATGCAATTTTGTACTGTATG 59.472 38.462 0.00 0.00 0.00 2.39
882 937 7.083858 GTGTGATGCAATTTTGTACTGTATGT 58.916 34.615 0.00 0.00 0.00 2.29
883 938 7.594758 GTGTGATGCAATTTTGTACTGTATGTT 59.405 33.333 0.00 0.00 0.00 2.71
884 939 7.807433 TGTGATGCAATTTTGTACTGTATGTTC 59.193 33.333 0.00 0.00 0.00 3.18
898 953 4.075682 TGTATGTTCATTTTTGGAGCCGA 58.924 39.130 0.00 0.00 0.00 5.54
899 954 4.704540 TGTATGTTCATTTTTGGAGCCGAT 59.295 37.500 0.00 0.00 0.00 4.18
912 967 3.689161 TGGAGCCGATGAGTTGTTTATTG 59.311 43.478 0.00 0.00 0.00 1.90
913 968 3.689649 GGAGCCGATGAGTTGTTTATTGT 59.310 43.478 0.00 0.00 0.00 2.71
916 971 6.128117 GGAGCCGATGAGTTGTTTATTGTAAA 60.128 38.462 0.00 0.00 0.00 2.01
937 993 1.612469 CTGTCGCTGTCTCGTGCAAG 61.612 60.000 0.00 0.00 0.00 4.01
938 994 2.734723 TCGCTGTCTCGTGCAAGC 60.735 61.111 0.00 0.00 0.00 4.01
939 995 3.037833 CGCTGTCTCGTGCAAGCA 61.038 61.111 6.62 0.00 0.00 3.91
941 997 2.246739 GCTGTCTCGTGCAAGCACA 61.247 57.895 23.23 10.66 46.47 4.57
942 998 1.858041 CTGTCTCGTGCAAGCACAG 59.142 57.895 23.23 18.23 46.47 3.66
943 999 2.167808 CTGTCTCGTGCAAGCACAGC 62.168 60.000 23.23 14.85 46.47 4.40
944 1000 2.108771 TCTCGTGCAAGCACAGCA 59.891 55.556 23.23 7.08 46.47 4.41
991 1056 0.106967 GGGATTGGGAGTGAAGGAGC 60.107 60.000 0.00 0.00 0.00 4.70
992 1057 0.915364 GGATTGGGAGTGAAGGAGCT 59.085 55.000 0.00 0.00 0.00 4.09
993 1058 1.407989 GGATTGGGAGTGAAGGAGCTG 60.408 57.143 0.00 0.00 0.00 4.24
1005 1078 2.202987 GAGCTGGAGGTCATGGCG 60.203 66.667 0.00 0.00 41.81 5.69
1832 1917 3.015332 GCCAGGAGGAGGAGGAGGA 62.015 68.421 0.00 0.00 36.89 3.71
1833 1918 1.232792 CCAGGAGGAGGAGGAGGAG 59.767 68.421 0.00 0.00 36.89 3.69
1834 1919 1.232792 CAGGAGGAGGAGGAGGAGG 59.767 68.421 0.00 0.00 0.00 4.30
1835 1920 2.123033 GGAGGAGGAGGAGGAGGC 60.123 72.222 0.00 0.00 0.00 4.70
1885 1970 0.745845 GCAGATGTTCTCGGCCATGT 60.746 55.000 2.24 0.00 38.94 3.21
2030 2126 9.988815 ATCTCATGGTCATGTATTACTAGTTTC 57.011 33.333 0.00 0.00 39.72 2.78
2031 2127 8.421784 TCTCATGGTCATGTATTACTAGTTTCC 58.578 37.037 0.00 0.00 39.72 3.13
2060 2156 7.439356 TGGACAAAATTCGATCTCTATGTCATC 59.561 37.037 14.37 3.93 38.09 2.92
2063 2159 9.039870 ACAAAATTCGATCTCTATGTCATCTTC 57.960 33.333 0.00 0.00 0.00 2.87
2071 2167 7.538334 CGATCTCTATGTCATCTTCTTAAGCAG 59.462 40.741 0.00 0.00 0.00 4.24
2073 2169 5.605534 TCTATGTCATCTTCTTAAGCAGCC 58.394 41.667 0.00 0.00 0.00 4.85
2074 2170 2.621338 TGTCATCTTCTTAAGCAGCCG 58.379 47.619 0.00 0.00 0.00 5.52
2075 2171 1.936547 GTCATCTTCTTAAGCAGCCGG 59.063 52.381 0.00 0.00 0.00 6.13
2076 2172 1.831106 TCATCTTCTTAAGCAGCCGGA 59.169 47.619 5.05 0.00 0.00 5.14
2078 2174 3.641436 TCATCTTCTTAAGCAGCCGGATA 59.359 43.478 5.05 0.00 0.00 2.59
2083 2179 4.415881 TCTTAAGCAGCCGGATATGAAA 57.584 40.909 5.05 0.00 0.00 2.69
2084 2180 4.973168 TCTTAAGCAGCCGGATATGAAAT 58.027 39.130 5.05 0.00 0.00 2.17
2087 2183 3.498774 AGCAGCCGGATATGAAATCTT 57.501 42.857 5.05 0.00 0.00 2.40
2089 2185 4.210331 AGCAGCCGGATATGAAATCTTTT 58.790 39.130 5.05 0.00 0.00 2.27
2091 2187 5.827797 AGCAGCCGGATATGAAATCTTTTAA 59.172 36.000 5.05 0.00 0.00 1.52
2092 2188 6.491403 AGCAGCCGGATATGAAATCTTTTAAT 59.509 34.615 5.05 0.00 0.00 1.40
2093 2189 6.803807 GCAGCCGGATATGAAATCTTTTAATC 59.196 38.462 5.05 0.00 0.00 1.75
2094 2190 7.017645 CAGCCGGATATGAAATCTTTTAATCG 58.982 38.462 5.05 0.00 0.00 3.34
2095 2191 6.934645 AGCCGGATATGAAATCTTTTAATCGA 59.065 34.615 5.05 0.00 0.00 3.59
2096 2192 7.607991 AGCCGGATATGAAATCTTTTAATCGAT 59.392 33.333 5.05 0.00 0.00 3.59
2097 2193 7.693951 GCCGGATATGAAATCTTTTAATCGATG 59.306 37.037 5.05 0.00 0.00 3.84
2171 2376 6.201806 CCGTTTTACATTTGCATCTCCAAAAA 59.798 34.615 0.00 0.00 38.12 1.94
2201 2417 3.163594 GTTGCGAAAATTGAGACGATGG 58.836 45.455 0.00 0.00 0.00 3.51
2256 2472 2.165641 TGTGGTACTAATCTGACAGCCG 59.834 50.000 0.00 0.00 0.00 5.52
2266 2482 0.809241 CTGACAGCCGAGGAGCAATC 60.809 60.000 0.00 0.00 34.23 2.67
2319 2550 2.341257 CTCAATTCCAGGTGTCTGTCG 58.659 52.381 0.00 0.00 39.31 4.35
2322 2553 2.185310 ATTCCAGGTGTCTGTCGGGC 62.185 60.000 0.00 0.00 39.31 6.13
2335 2566 4.418401 CGGGCATTTGCACCGTGG 62.418 66.667 18.40 0.00 42.67 4.94
2356 2587 7.067615 CCGTGGAAGATAGCATATATCTACACT 59.932 40.741 19.41 1.19 38.50 3.55
2369 2600 2.376109 TCTACACTAGAGCCTTTCCCG 58.624 52.381 0.00 0.00 0.00 5.14
2412 2643 5.187967 GTCTCCTTATCTCTTTCACTCCCAA 59.812 44.000 0.00 0.00 0.00 4.12
2416 2647 7.470192 TCCTTATCTCTTTCACTCCCAAAAAT 58.530 34.615 0.00 0.00 0.00 1.82
2417 2648 7.611855 TCCTTATCTCTTTCACTCCCAAAAATC 59.388 37.037 0.00 0.00 0.00 2.17
2418 2649 7.613411 CCTTATCTCTTTCACTCCCAAAAATCT 59.387 37.037 0.00 0.00 0.00 2.40
2626 2857 2.621929 GGGCTCTCAAGGTCTCACTCTA 60.622 54.545 0.00 0.00 0.00 2.43
2637 2868 5.714863 AGGTCTCACTCTATCCATCTTGAT 58.285 41.667 0.00 0.00 0.00 2.57
2710 3020 4.892934 AGATGTAGAAGTCATCTCTGGGTC 59.107 45.833 3.06 0.00 45.78 4.46
2718 3028 0.738975 CATCTCTGGGTCGAAGCGTA 59.261 55.000 0.00 0.00 0.00 4.42
2748 3058 9.037737 CAATAGAAATTCCATTGCTTTGGTATG 57.962 33.333 1.55 0.00 38.01 2.39
2749 3059 6.610075 AGAAATTCCATTGCTTTGGTATGT 57.390 33.333 5.56 0.00 38.01 2.29
2750 3060 7.716799 AGAAATTCCATTGCTTTGGTATGTA 57.283 32.000 5.56 0.00 38.01 2.29
2751 3061 8.310122 AGAAATTCCATTGCTTTGGTATGTAT 57.690 30.769 5.56 0.00 38.01 2.29
2781 3091 2.125753 CTGCTGGGCTCTGACGAC 60.126 66.667 0.00 0.00 0.00 4.34
2802 3112 0.320683 GTGATTGGCCTTTTGCACCC 60.321 55.000 3.32 0.00 43.89 4.61
2821 3131 1.502163 CGCAGATCATTTCGGGGCTC 61.502 60.000 0.00 0.00 0.00 4.70
2851 3161 0.889186 ACAGGTCCAATGTTGCGTCC 60.889 55.000 0.00 0.00 0.00 4.79
2886 3196 2.565841 GGATAAGGTGTGGATGCTGTC 58.434 52.381 0.00 0.00 0.00 3.51
2897 3207 2.474561 ATGCTGTCTGGTGCATTCG 58.525 52.632 0.00 0.00 46.29 3.34
2916 3226 4.647424 TCGTTTTCCATGCTCTGTTTTT 57.353 36.364 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.591877 ACATTTTCTTCACTCTTTCTGCAGT 59.408 36.000 14.67 0.00 0.00 4.40
1 2 6.069684 ACATTTTCTTCACTCTTTCTGCAG 57.930 37.500 7.63 7.63 0.00 4.41
2 3 6.267817 CAACATTTTCTTCACTCTTTCTGCA 58.732 36.000 0.00 0.00 0.00 4.41
3 4 5.689068 CCAACATTTTCTTCACTCTTTCTGC 59.311 40.000 0.00 0.00 0.00 4.26
4 5 5.689068 GCCAACATTTTCTTCACTCTTTCTG 59.311 40.000 0.00 0.00 0.00 3.02
5 6 5.506317 CGCCAACATTTTCTTCACTCTTTCT 60.506 40.000 0.00 0.00 0.00 2.52
6 7 4.676924 CGCCAACATTTTCTTCACTCTTTC 59.323 41.667 0.00 0.00 0.00 2.62
7 8 4.097892 ACGCCAACATTTTCTTCACTCTTT 59.902 37.500 0.00 0.00 0.00 2.52
8 9 3.632145 ACGCCAACATTTTCTTCACTCTT 59.368 39.130 0.00 0.00 0.00 2.85
9 10 3.214328 ACGCCAACATTTTCTTCACTCT 58.786 40.909 0.00 0.00 0.00 3.24
10 11 3.555518 GACGCCAACATTTTCTTCACTC 58.444 45.455 0.00 0.00 0.00 3.51
11 12 2.032030 CGACGCCAACATTTTCTTCACT 60.032 45.455 0.00 0.00 0.00 3.41
12 13 2.307049 CGACGCCAACATTTTCTTCAC 58.693 47.619 0.00 0.00 0.00 3.18
13 14 1.265635 CCGACGCCAACATTTTCTTCA 59.734 47.619 0.00 0.00 0.00 3.02
14 15 1.963747 CCGACGCCAACATTTTCTTC 58.036 50.000 0.00 0.00 0.00 2.87
15 16 0.039527 GCCGACGCCAACATTTTCTT 60.040 50.000 0.00 0.00 0.00 2.52
16 17 1.169661 TGCCGACGCCAACATTTTCT 61.170 50.000 0.00 0.00 0.00 2.52
17 18 0.109319 ATGCCGACGCCAACATTTTC 60.109 50.000 0.00 0.00 0.00 2.29
18 19 0.109319 GATGCCGACGCCAACATTTT 60.109 50.000 0.00 0.00 0.00 1.82
19 20 1.506262 GATGCCGACGCCAACATTT 59.494 52.632 0.00 0.00 0.00 2.32
20 21 2.749865 CGATGCCGACGCCAACATT 61.750 57.895 0.00 0.00 38.22 2.71
21 22 3.195002 CGATGCCGACGCCAACAT 61.195 61.111 0.00 0.00 38.22 2.71
88 89 1.270305 CGGCTTGACAAGGAAGACAGA 60.270 52.381 16.80 0.00 0.00 3.41
193 213 1.699343 CTCGACGAGTCTTTTGGGTC 58.301 55.000 16.83 0.00 0.00 4.46
210 230 1.183549 TGGAAAGTAGTCGGGAGCTC 58.816 55.000 4.71 4.71 0.00 4.09
219 239 3.682718 CGATGGCCATCTTGGAAAGTAGT 60.683 47.826 36.51 4.68 46.34 2.73
220 240 2.874701 CGATGGCCATCTTGGAAAGTAG 59.125 50.000 36.51 17.61 46.34 2.57
221 241 2.917933 CGATGGCCATCTTGGAAAGTA 58.082 47.619 36.51 0.00 46.34 2.24
679 717 6.380095 ACAGTAACAGAGTACATAGCTAGC 57.620 41.667 6.62 6.62 0.00 3.42
680 718 8.244802 ACAAACAGTAACAGAGTACATAGCTAG 58.755 37.037 0.00 0.00 0.00 3.42
682 720 6.994221 ACAAACAGTAACAGAGTACATAGCT 58.006 36.000 0.00 0.00 0.00 3.32
683 721 7.653767 AACAAACAGTAACAGAGTACATAGC 57.346 36.000 0.00 0.00 0.00 2.97
684 722 9.042008 ACAAACAAACAGTAACAGAGTACATAG 57.958 33.333 0.00 0.00 0.00 2.23
686 724 7.859325 ACAAACAAACAGTAACAGAGTACAT 57.141 32.000 0.00 0.00 0.00 2.29
687 725 7.675962 AACAAACAAACAGTAACAGAGTACA 57.324 32.000 0.00 0.00 0.00 2.90
688 726 8.876790 AGTAACAAACAAACAGTAACAGAGTAC 58.123 33.333 0.00 0.00 0.00 2.73
689 727 9.439500 AAGTAACAAACAAACAGTAACAGAGTA 57.561 29.630 0.00 0.00 0.00 2.59
690 728 7.916914 AGTAACAAACAAACAGTAACAGAGT 57.083 32.000 0.00 0.00 0.00 3.24
691 729 7.218204 GCAAGTAACAAACAAACAGTAACAGAG 59.782 37.037 0.00 0.00 0.00 3.35
693 731 7.027161 AGCAAGTAACAAACAAACAGTAACAG 58.973 34.615 0.00 0.00 0.00 3.16
694 732 6.915349 AGCAAGTAACAAACAAACAGTAACA 58.085 32.000 0.00 0.00 0.00 2.41
697 735 6.237996 CGAGAGCAAGTAACAAACAAACAGTA 60.238 38.462 0.00 0.00 0.00 2.74
698 736 5.447279 CGAGAGCAAGTAACAAACAAACAGT 60.447 40.000 0.00 0.00 0.00 3.55
699 737 4.963953 CGAGAGCAAGTAACAAACAAACAG 59.036 41.667 0.00 0.00 0.00 3.16
700 738 4.201871 CCGAGAGCAAGTAACAAACAAACA 60.202 41.667 0.00 0.00 0.00 2.83
701 739 4.201881 ACCGAGAGCAAGTAACAAACAAAC 60.202 41.667 0.00 0.00 0.00 2.93
702 740 3.942748 ACCGAGAGCAAGTAACAAACAAA 59.057 39.130 0.00 0.00 0.00 2.83
703 741 3.537580 ACCGAGAGCAAGTAACAAACAA 58.462 40.909 0.00 0.00 0.00 2.83
713 751 1.884235 ACCAAAGAACCGAGAGCAAG 58.116 50.000 0.00 0.00 0.00 4.01
779 826 0.897863 TGGTTTTTCCTCATGGCGGG 60.898 55.000 0.00 0.00 37.07 6.13
785 832 6.070596 GGAATTTCTCCATGGTTTTTCCTCAT 60.071 38.462 12.58 0.00 44.67 2.90
803 850 5.359009 TCATCTTGAGCAGATTGGGAATTTC 59.641 40.000 0.00 0.00 40.67 2.17
831 878 2.696759 CCCATTCCCCAAACGACGC 61.697 63.158 0.00 0.00 0.00 5.19
845 892 1.479942 GCATCACACCATCATCCCCAT 60.480 52.381 0.00 0.00 0.00 4.00
846 893 0.106569 GCATCACACCATCATCCCCA 60.107 55.000 0.00 0.00 0.00 4.96
847 894 0.106569 TGCATCACACCATCATCCCC 60.107 55.000 0.00 0.00 0.00 4.81
848 895 1.766494 TTGCATCACACCATCATCCC 58.234 50.000 0.00 0.00 0.00 3.85
849 896 4.395959 AAATTGCATCACACCATCATCC 57.604 40.909 0.00 0.00 0.00 3.51
851 898 5.155278 ACAAAATTGCATCACACCATCAT 57.845 34.783 0.00 0.00 0.00 2.45
852 899 4.603989 ACAAAATTGCATCACACCATCA 57.396 36.364 0.00 0.00 0.00 3.07
872 927 6.322491 GGCTCCAAAAATGAACATACAGTAC 58.678 40.000 0.00 0.00 0.00 2.73
873 928 5.123186 CGGCTCCAAAAATGAACATACAGTA 59.877 40.000 0.00 0.00 0.00 2.74
874 929 4.082787 CGGCTCCAAAAATGAACATACAGT 60.083 41.667 0.00 0.00 0.00 3.55
875 930 4.155826 TCGGCTCCAAAAATGAACATACAG 59.844 41.667 0.00 0.00 0.00 2.74
876 931 4.075682 TCGGCTCCAAAAATGAACATACA 58.924 39.130 0.00 0.00 0.00 2.29
877 932 4.695217 TCGGCTCCAAAAATGAACATAC 57.305 40.909 0.00 0.00 0.00 2.39
878 933 4.946772 TCATCGGCTCCAAAAATGAACATA 59.053 37.500 0.00 0.00 0.00 2.29
879 934 3.763360 TCATCGGCTCCAAAAATGAACAT 59.237 39.130 0.00 0.00 0.00 2.71
880 935 3.153130 TCATCGGCTCCAAAAATGAACA 58.847 40.909 0.00 0.00 0.00 3.18
881 936 3.191371 ACTCATCGGCTCCAAAAATGAAC 59.809 43.478 0.00 0.00 0.00 3.18
882 937 3.420893 ACTCATCGGCTCCAAAAATGAA 58.579 40.909 0.00 0.00 0.00 2.57
883 938 3.071874 ACTCATCGGCTCCAAAAATGA 57.928 42.857 0.00 0.00 0.00 2.57
884 939 3.057315 ACAACTCATCGGCTCCAAAAATG 60.057 43.478 0.00 0.00 0.00 2.32
898 953 7.962918 GCGACAGATTTACAATAAACAACTCAT 59.037 33.333 0.00 0.00 0.00 2.90
899 954 7.172532 AGCGACAGATTTACAATAAACAACTCA 59.827 33.333 0.00 0.00 0.00 3.41
912 967 2.594654 CACGAGACAGCGACAGATTTAC 59.405 50.000 0.00 0.00 34.83 2.01
913 968 2.863739 CACGAGACAGCGACAGATTTA 58.136 47.619 0.00 0.00 34.83 1.40
916 971 1.153939 GCACGAGACAGCGACAGAT 60.154 57.895 0.00 0.00 34.83 2.90
969 1034 0.257039 CCTTCACTCCCAATCCCCAG 59.743 60.000 0.00 0.00 0.00 4.45
991 1056 1.227764 CCATCGCCATGACCTCCAG 60.228 63.158 0.00 0.00 30.57 3.86
992 1057 1.688884 TCCATCGCCATGACCTCCA 60.689 57.895 0.00 0.00 30.57 3.86
993 1058 1.070445 CTCCATCGCCATGACCTCC 59.930 63.158 0.00 0.00 30.57 4.30
1005 1078 2.107953 GCTGTCGCCTCCTCCATC 59.892 66.667 0.00 0.00 0.00 3.51
1920 2005 1.583967 CTCGACGACGGTGATCAGC 60.584 63.158 15.01 15.01 40.21 4.26
2023 2119 4.156008 CGAATTTTGTCCAGGGGAAACTAG 59.844 45.833 0.00 0.00 31.38 2.57
2030 2126 2.945668 GAGATCGAATTTTGTCCAGGGG 59.054 50.000 0.00 0.00 0.00 4.79
2031 2127 3.878778 AGAGATCGAATTTTGTCCAGGG 58.121 45.455 0.00 0.00 0.00 4.45
2060 2156 3.995199 TCATATCCGGCTGCTTAAGAAG 58.005 45.455 6.67 6.34 0.00 2.85
2063 2159 4.999950 AGATTTCATATCCGGCTGCTTAAG 59.000 41.667 0.00 0.00 0.00 1.85
2071 2167 7.129109 TCGATTAAAAGATTTCATATCCGGC 57.871 36.000 0.00 0.00 0.00 6.13
2141 2237 3.444703 TGCAAATGTAAAACGGCAGTT 57.555 38.095 0.00 0.00 43.50 3.16
2142 2238 3.255642 AGATGCAAATGTAAAACGGCAGT 59.744 39.130 0.00 0.00 34.43 4.40
2171 2376 3.105203 CAATTTTCGCAACGTGTGAGTT 58.895 40.909 0.00 0.00 38.23 3.01
2173 2378 2.966708 CTCAATTTTCGCAACGTGTGAG 59.033 45.455 0.00 0.00 38.23 3.51
2174 2379 2.609916 TCTCAATTTTCGCAACGTGTGA 59.390 40.909 0.00 0.00 34.72 3.58
2175 2380 2.713976 GTCTCAATTTTCGCAACGTGTG 59.286 45.455 0.00 0.00 0.00 3.82
2176 2381 2.598907 CGTCTCAATTTTCGCAACGTGT 60.599 45.455 0.00 0.00 0.00 4.49
2179 2384 2.570468 TCGTCTCAATTTTCGCAACG 57.430 45.000 0.00 0.00 0.00 4.10
2181 2386 2.811431 ACCATCGTCTCAATTTTCGCAA 59.189 40.909 0.00 0.00 0.00 4.85
2182 2387 2.159430 CACCATCGTCTCAATTTTCGCA 59.841 45.455 0.00 0.00 0.00 5.10
2183 2388 2.774007 CACCATCGTCTCAATTTTCGC 58.226 47.619 0.00 0.00 0.00 4.70
2184 2389 2.159430 TGCACCATCGTCTCAATTTTCG 59.841 45.455 0.00 0.00 0.00 3.46
2185 2390 3.058293 TGTGCACCATCGTCTCAATTTTC 60.058 43.478 15.69 0.00 0.00 2.29
2201 2417 7.682611 ATCTGAATAGAAGATGCCATGTGCAC 61.683 42.308 10.75 10.75 44.64 4.57
2228 2444 5.104941 TGTCAGATTAGTACCACATCCCAAG 60.105 44.000 0.00 0.00 0.00 3.61
2229 2445 4.780554 TGTCAGATTAGTACCACATCCCAA 59.219 41.667 0.00 0.00 0.00 4.12
2256 2472 1.831580 AGGTTTGCAGATTGCTCCTC 58.168 50.000 2.48 0.00 45.31 3.71
2319 2550 2.490993 CTTCCACGGTGCAAATGCCC 62.491 60.000 1.68 3.15 41.18 5.36
2322 2553 2.223340 GCTATCTTCCACGGTGCAAATG 60.223 50.000 1.68 0.00 0.00 2.32
2356 2587 1.899437 CTGCACCGGGAAAGGCTCTA 61.899 60.000 6.32 0.00 33.69 2.43
2412 2643 5.336531 CCATTCTTGCTGCTGAAGAGATTTT 60.337 40.000 0.00 0.00 31.17 1.82
2416 2647 2.708051 CCATTCTTGCTGCTGAAGAGA 58.292 47.619 0.00 0.00 31.17 3.10
2417 2648 1.132643 GCCATTCTTGCTGCTGAAGAG 59.867 52.381 0.00 3.12 31.17 2.85
2418 2649 1.171308 GCCATTCTTGCTGCTGAAGA 58.829 50.000 0.00 0.00 0.00 2.87
2582 2813 3.672295 CTCACGGAAGGGCCTGAGC 62.672 68.421 6.92 0.00 36.12 4.26
2626 2857 3.495100 GCACGGAAGGTATCAAGATGGAT 60.495 47.826 0.00 0.00 0.00 3.41
2637 2868 6.316890 GGAAATTTATTACTGCACGGAAGGTA 59.683 38.462 0.00 0.00 0.00 3.08
2674 2905 6.314120 ACTTCTACATCTATCATCAGAGCCT 58.686 40.000 0.00 0.00 0.00 4.58
2710 3020 5.332656 GGAATTTCTATTGCTCTACGCTTCG 60.333 44.000 0.00 0.00 40.11 3.79
2727 3037 8.196771 TCATACATACCAAAGCAATGGAATTTC 58.803 33.333 14.09 0.00 43.54 2.17
2733 3043 5.535783 TCCATCATACATACCAAAGCAATGG 59.464 40.000 6.27 6.27 46.38 3.16
2748 3058 3.243301 CCAGCAGCAACATTCCATCATAC 60.243 47.826 0.00 0.00 0.00 2.39
2749 3059 2.953648 CCAGCAGCAACATTCCATCATA 59.046 45.455 0.00 0.00 0.00 2.15
2750 3060 1.754803 CCAGCAGCAACATTCCATCAT 59.245 47.619 0.00 0.00 0.00 2.45
2751 3061 1.179152 CCAGCAGCAACATTCCATCA 58.821 50.000 0.00 0.00 0.00 3.07
2781 3091 1.606224 GGTGCAAAAGGCCAATCACTG 60.606 52.381 5.01 0.00 43.89 3.66
2802 3112 1.502163 GAGCCCCGAAATGATCTGCG 61.502 60.000 0.00 0.00 0.00 5.18
2821 3131 0.679505 TGGACCTGTCGAAGTTCTGG 59.320 55.000 0.56 1.02 0.00 3.86
2886 3196 2.598589 CATGGAAAACGAATGCACCAG 58.401 47.619 0.00 0.00 0.00 4.00
2916 3226 7.094377 CCCTATGCAAGAGCTAAACTGTAAAAA 60.094 37.037 0.00 0.00 42.74 1.94
2919 3229 5.188948 TCCCTATGCAAGAGCTAAACTGTAA 59.811 40.000 0.00 0.00 42.74 2.41
2920 3230 4.714802 TCCCTATGCAAGAGCTAAACTGTA 59.285 41.667 0.00 0.00 42.74 2.74


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

AutoCloner maintained by Alex Coulton.