Multiple sequence alignment - TraesCS7A01G401100

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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 TraesCS7A01G401100 chr7A 100.000 2807 0 0 616 3422 580661861 580664667 0.000000e+00 5184
1 TraesCS7A01G401100 chr7A 100.000 169 0 0 1 169 580661246 580661414 2.560000e-81 313
2 TraesCS7A01G401100 chr7D 95.150 2825 109 13 616 3422 509920104 509922918 0.000000e+00 4433
3 TraesCS7A01G401100 chr7B 94.533 2817 127 12 616 3422 538218552 538221351 0.000000e+00 4324


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 TraesCS7A01G401100 chr7A 580661246 580664667 3421 False 2748.5 5184 100.000 1 3422 2 chr7A.!!$F1 3421
1 TraesCS7A01G401100 chr7D 509920104 509922918 2814 False 4433.0 4433 95.150 616 3422 1 chr7D.!!$F1 2806
2 TraesCS7A01G401100 chr7B 538218552 538221351 2799 False 4324.0 4324 94.533 616 3422 1 chr7B.!!$F1 2806

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
125 126 0.034477 TTACTAGCCCAGCTTTGCCC 60.034 55.000 0.00 0.0 40.44 5.36 F
148 149 0.179018 ACTCTCGCCACTGCCTTTTT 60.179 50.000 0.00 0.0 0.00 1.94 F
1219 1220 0.178891 TCTGGAGCTTGGGAAGAGGT 60.179 55.000 0.00 0.0 0.00 3.85 F
1380 1381 1.269174 TGGACAACCATGATTGTTGCG 59.731 47.619 6.95 0.0 45.42 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1029 1030 0.108207 CCAGATCCCTCACAGGCATC 59.892 60.000 0.0 0.0 32.73 3.91 R
1567 1568 1.331756 CTGCGAGCAAGCCGATAAAAT 59.668 47.619 0.0 0.0 36.02 1.82 R
2418 2419 0.035725 TCACATCTTGCAGGCCTCAG 60.036 55.000 0.0 0.0 0.00 3.35 R
2469 2470 0.391130 TGCCTGGCATAACTCACGAC 60.391 55.000 19.3 0.0 31.71 4.34 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
21 22 4.820894 GCCAAATCGTATAGGGTCCTAT 57.179 45.455 13.42 13.42 41.58 2.57
22 23 5.161943 GCCAAATCGTATAGGGTCCTATT 57.838 43.478 14.03 0.00 39.65 1.73
23 24 5.557866 GCCAAATCGTATAGGGTCCTATTT 58.442 41.667 14.03 2.51 39.65 1.40
24 25 6.704310 GCCAAATCGTATAGGGTCCTATTTA 58.296 40.000 14.03 2.43 39.65 1.40
25 26 6.817140 GCCAAATCGTATAGGGTCCTATTTAG 59.183 42.308 14.03 7.13 39.65 1.85
26 27 7.526693 GCCAAATCGTATAGGGTCCTATTTAGT 60.527 40.741 14.03 0.00 39.65 2.24
27 28 8.373220 CCAAATCGTATAGGGTCCTATTTAGTT 58.627 37.037 14.03 4.50 39.65 2.24
28 29 9.774413 CAAATCGTATAGGGTCCTATTTAGTTT 57.226 33.333 14.03 8.72 39.65 2.66
46 47 3.861002 TTTTTAGCAACTGGGCCCT 57.139 47.368 25.70 3.19 0.00 5.19
47 48 2.982339 TTTTTAGCAACTGGGCCCTA 57.018 45.000 25.70 8.68 0.00 3.53
48 49 3.466395 TTTTTAGCAACTGGGCCCTAT 57.534 42.857 25.70 8.15 0.00 2.57
49 50 3.466395 TTTTAGCAACTGGGCCCTATT 57.534 42.857 25.70 14.61 0.00 1.73
50 51 3.466395 TTTAGCAACTGGGCCCTATTT 57.534 42.857 25.70 10.45 0.00 1.40
51 52 4.594675 TTTAGCAACTGGGCCCTATTTA 57.405 40.909 25.70 0.00 0.00 1.40
52 53 2.736670 AGCAACTGGGCCCTATTTAG 57.263 50.000 25.70 14.42 0.00 1.85
53 54 1.215423 AGCAACTGGGCCCTATTTAGG 59.785 52.381 25.70 7.15 43.25 2.69
54 55 1.063942 GCAACTGGGCCCTATTTAGGT 60.064 52.381 25.70 7.16 42.03 3.08
55 56 2.654863 CAACTGGGCCCTATTTAGGTG 58.345 52.381 25.70 16.91 42.03 4.00
56 57 0.551396 ACTGGGCCCTATTTAGGTGC 59.449 55.000 25.70 5.89 42.03 5.01
60 61 3.307379 GCCCTATTTAGGTGCCTCG 57.693 57.895 3.05 0.00 42.03 4.63
61 62 0.885150 GCCCTATTTAGGTGCCTCGC 60.885 60.000 3.05 0.00 42.03 5.03
62 63 0.759346 CCCTATTTAGGTGCCTCGCT 59.241 55.000 3.05 0.00 42.03 4.93
63 64 1.541233 CCCTATTTAGGTGCCTCGCTG 60.541 57.143 3.05 0.00 42.03 5.18
64 65 1.541233 CCTATTTAGGTGCCTCGCTGG 60.541 57.143 0.00 0.00 38.69 4.85
65 66 1.412710 CTATTTAGGTGCCTCGCTGGA 59.587 52.381 0.00 0.00 38.35 3.86
66 67 0.179000 ATTTAGGTGCCTCGCTGGAG 59.821 55.000 0.00 0.00 40.14 3.86
74 75 2.977178 CTCGCTGGAGGTGCTCTT 59.023 61.111 0.00 0.00 36.61 2.85
75 76 1.447489 CTCGCTGGAGGTGCTCTTG 60.447 63.158 0.00 0.00 36.61 3.02
76 77 2.435586 CGCTGGAGGTGCTCTTGG 60.436 66.667 0.00 0.00 0.00 3.61
77 78 2.045536 GCTGGAGGTGCTCTTGGG 60.046 66.667 0.00 0.00 0.00 4.12
78 79 2.045536 CTGGAGGTGCTCTTGGGC 60.046 66.667 0.00 0.00 0.00 5.36
79 80 2.530151 TGGAGGTGCTCTTGGGCT 60.530 61.111 0.00 0.00 0.00 5.19
80 81 1.229496 TGGAGGTGCTCTTGGGCTA 60.229 57.895 0.00 0.00 0.00 3.93
81 82 1.267574 TGGAGGTGCTCTTGGGCTAG 61.268 60.000 0.00 0.00 0.00 3.42
82 83 0.978146 GGAGGTGCTCTTGGGCTAGA 60.978 60.000 0.00 0.00 0.00 2.43
83 84 0.176910 GAGGTGCTCTTGGGCTAGAC 59.823 60.000 0.00 0.00 0.00 2.59
84 85 1.153549 GGTGCTCTTGGGCTAGACG 60.154 63.158 0.00 0.00 0.00 4.18
85 86 1.153549 GTGCTCTTGGGCTAGACGG 60.154 63.158 0.00 0.00 0.00 4.79
86 87 2.359169 TGCTCTTGGGCTAGACGGG 61.359 63.158 0.00 0.00 0.00 5.28
87 88 2.501610 CTCTTGGGCTAGACGGGC 59.498 66.667 0.00 0.00 0.00 6.13
108 109 4.111967 GCCTTGGGCCTTGCTTTA 57.888 55.556 4.53 0.00 44.06 1.85
109 110 1.591703 GCCTTGGGCCTTGCTTTAC 59.408 57.895 4.53 0.00 44.06 2.01
110 111 0.900182 GCCTTGGGCCTTGCTTTACT 60.900 55.000 4.53 0.00 44.06 2.24
111 112 1.615919 GCCTTGGGCCTTGCTTTACTA 60.616 52.381 4.53 0.00 44.06 1.82
112 113 2.369394 CCTTGGGCCTTGCTTTACTAG 58.631 52.381 4.53 0.00 0.00 2.57
123 124 1.133216 GCTTTACTAGCCCAGCTTTGC 59.867 52.381 0.00 0.00 44.48 3.68
124 125 1.745653 CTTTACTAGCCCAGCTTTGCC 59.254 52.381 0.00 0.00 40.44 4.52
125 126 0.034477 TTACTAGCCCAGCTTTGCCC 60.034 55.000 0.00 0.00 40.44 5.36
126 127 0.914417 TACTAGCCCAGCTTTGCCCT 60.914 55.000 0.00 0.00 40.44 5.19
127 128 1.000396 CTAGCCCAGCTTTGCCCTT 60.000 57.895 0.00 0.00 40.44 3.95
128 129 1.000896 TAGCCCAGCTTTGCCCTTC 60.001 57.895 0.00 0.00 40.44 3.46
129 130 1.788518 TAGCCCAGCTTTGCCCTTCA 61.789 55.000 0.00 0.00 40.44 3.02
130 131 2.935740 GCCCAGCTTTGCCCTTCAC 61.936 63.158 0.00 0.00 0.00 3.18
131 132 1.228675 CCCAGCTTTGCCCTTCACT 60.229 57.895 0.00 0.00 0.00 3.41
132 133 1.246737 CCCAGCTTTGCCCTTCACTC 61.247 60.000 0.00 0.00 0.00 3.51
133 134 0.251077 CCAGCTTTGCCCTTCACTCT 60.251 55.000 0.00 0.00 0.00 3.24
134 135 1.163554 CAGCTTTGCCCTTCACTCTC 58.836 55.000 0.00 0.00 0.00 3.20
135 136 0.321122 AGCTTTGCCCTTCACTCTCG 60.321 55.000 0.00 0.00 0.00 4.04
136 137 1.916697 GCTTTGCCCTTCACTCTCGC 61.917 60.000 0.00 0.00 0.00 5.03
137 138 1.301677 CTTTGCCCTTCACTCTCGCC 61.302 60.000 0.00 0.00 0.00 5.54
138 139 2.050836 TTTGCCCTTCACTCTCGCCA 62.051 55.000 0.00 0.00 0.00 5.69
139 140 2.435059 GCCCTTCACTCTCGCCAC 60.435 66.667 0.00 0.00 0.00 5.01
140 141 2.948720 GCCCTTCACTCTCGCCACT 61.949 63.158 0.00 0.00 0.00 4.00
141 142 1.079543 CCCTTCACTCTCGCCACTG 60.080 63.158 0.00 0.00 0.00 3.66
142 143 1.739562 CCTTCACTCTCGCCACTGC 60.740 63.158 0.00 0.00 0.00 4.40
143 144 1.739562 CTTCACTCTCGCCACTGCC 60.740 63.158 0.00 0.00 0.00 4.85
144 145 2.164865 CTTCACTCTCGCCACTGCCT 62.165 60.000 0.00 0.00 0.00 4.75
145 146 1.758440 TTCACTCTCGCCACTGCCTT 61.758 55.000 0.00 0.00 0.00 4.35
146 147 1.302033 CACTCTCGCCACTGCCTTT 60.302 57.895 0.00 0.00 0.00 3.11
147 148 0.886490 CACTCTCGCCACTGCCTTTT 60.886 55.000 0.00 0.00 0.00 2.27
148 149 0.179018 ACTCTCGCCACTGCCTTTTT 60.179 50.000 0.00 0.00 0.00 1.94
870 871 0.772124 TCACCTTCCCCTTCCTGCTT 60.772 55.000 0.00 0.00 0.00 3.91
924 925 3.221222 GACGCTGTCCTAGGGCAT 58.779 61.111 18.38 1.04 42.75 4.40
926 927 2.590007 CGCTGTCCTAGGGCATGC 60.590 66.667 18.38 20.13 32.19 4.06
927 928 2.591753 GCTGTCCTAGGGCATGCA 59.408 61.111 24.24 10.34 0.00 3.96
1029 1030 1.446792 ACGCAGGCTGTTCGATCAG 60.447 57.895 19.10 17.42 38.35 2.90
1090 1091 2.902343 GCTATGTGCGAAGGGGCC 60.902 66.667 0.00 0.00 0.00 5.80
1128 1129 1.077429 GGTGTTCTGGAGGATGGCC 60.077 63.158 0.00 0.00 0.00 5.36
1219 1220 0.178891 TCTGGAGCTTGGGAAGAGGT 60.179 55.000 0.00 0.00 0.00 3.85
1323 1324 4.344865 TTGGAGCGGGCCAAGTCC 62.345 66.667 4.39 7.37 42.75 3.85
1380 1381 1.269174 TGGACAACCATGATTGTTGCG 59.731 47.619 6.95 0.00 45.42 4.85
1567 1568 6.745190 GCCTGATGAGATTACCATGGTCAATA 60.745 42.308 23.76 0.00 0.00 1.90
1656 1657 1.798813 CACCGGCTTTCACTTAGTGTC 59.201 52.381 12.41 0.96 34.79 3.67
1689 1690 6.403527 GCACAAATCTAGTTGACATGTATGCA 60.404 38.462 0.00 0.00 32.59 3.96
1812 1813 1.596260 CGTGCTGATGAGGCAATACAG 59.404 52.381 0.00 0.00 41.54 2.74
1821 1822 2.829720 TGAGGCAATACAGTACTTCCGT 59.170 45.455 0.00 0.00 0.00 4.69
1914 1915 3.644861 CCTGGTTAAAGAAGGCCGT 57.355 52.632 0.00 0.00 0.00 5.68
1917 1918 2.500229 CTGGTTAAAGAAGGCCGTGAA 58.500 47.619 0.00 0.00 0.00 3.18
2022 2023 4.272991 GCAGGTCATTTAGATGAAGCAGAG 59.727 45.833 0.00 0.00 43.58 3.35
2091 2092 4.310769 GTGCTCTCTTCTTTGCTTGTAGA 58.689 43.478 0.00 0.00 0.00 2.59
2092 2093 4.151512 GTGCTCTCTTCTTTGCTTGTAGAC 59.848 45.833 0.00 0.00 0.00 2.59
2097 2098 4.645535 TCTTCTTTGCTTGTAGACTGCAT 58.354 39.130 0.00 0.00 36.55 3.96
2310 2311 6.484364 AATGGGGTGGTTCATGAATTTATC 57.516 37.500 12.12 1.59 0.00 1.75
2364 2365 4.936411 GCTATCTATGACTGCTTGCATGAT 59.064 41.667 3.33 0.00 0.00 2.45
2370 2371 3.876341 TGACTGCTTGCATGATATCACA 58.124 40.909 7.78 0.00 0.00 3.58
2408 2409 5.464057 ACACTGCAAACATGATTGACATTTG 59.536 36.000 18.88 15.48 37.07 2.32
2418 2419 2.222007 TTGACATTTGTGCAACTGGC 57.778 45.000 7.10 4.57 45.13 4.85
2444 2445 3.004106 GGCCTGCAAGATGTGATATGTTC 59.996 47.826 0.00 0.00 34.07 3.18
2465 2466 4.155449 TCGATTATTTTGCGCAACTCAAC 58.845 39.130 24.99 11.78 0.00 3.18
2469 2470 1.850377 TTTTGCGCAACTCAACCATG 58.150 45.000 24.99 0.00 0.00 3.66
2551 2552 2.033372 TGGGCCATTACATCAGCATTG 58.967 47.619 0.00 0.00 0.00 2.82
2556 2557 2.223876 CCATTACATCAGCATTGTGGCC 60.224 50.000 0.00 0.00 0.00 5.36
2576 2577 3.000727 CCCTTTTACAGCTTACCAGTCG 58.999 50.000 0.00 0.00 0.00 4.18
2588 2594 5.705441 AGCTTACCAGTCGATGAAAAATTCA 59.295 36.000 0.00 0.00 45.01 2.57
2621 2627 4.034975 GCTCAAGGCAGTATCTCAATTCAC 59.965 45.833 0.00 0.00 41.35 3.18
2639 2645 2.103042 CAAGGTACTGCTGCGCCTC 61.103 63.158 4.18 0.00 40.86 4.70
2646 2652 4.933563 TGCTGCGCCTCACAAGCA 62.934 61.111 13.18 13.18 39.25 3.91
2648 2654 3.033184 CTGCGCCTCACAAGCAAA 58.967 55.556 4.18 0.00 40.63 3.68
2649 2655 1.359833 CTGCGCCTCACAAGCAAAA 59.640 52.632 4.18 0.00 40.63 2.44
2650 2656 0.038892 CTGCGCCTCACAAGCAAAAT 60.039 50.000 4.18 0.00 40.63 1.82
2651 2657 1.199789 CTGCGCCTCACAAGCAAAATA 59.800 47.619 4.18 0.00 40.63 1.40
2652 2658 1.611006 TGCGCCTCACAAGCAAAATAA 59.389 42.857 4.18 0.00 38.01 1.40
2653 2659 2.035193 TGCGCCTCACAAGCAAAATAAA 59.965 40.909 4.18 0.00 38.01 1.40
2654 2660 3.056304 GCGCCTCACAAGCAAAATAAAA 58.944 40.909 0.00 0.00 0.00 1.52
2655 2661 3.679502 GCGCCTCACAAGCAAAATAAAAT 59.320 39.130 0.00 0.00 0.00 1.82
2660 2666 8.442384 CGCCTCACAAGCAAAATAAAATAAAAT 58.558 29.630 0.00 0.00 0.00 1.82
2695 2702 5.009610 GTCAAAAGTTGGATTGGTGCTTAGA 59.990 40.000 0.00 0.00 0.00 2.10
2698 2705 3.624777 AGTTGGATTGGTGCTTAGATGG 58.375 45.455 0.00 0.00 0.00 3.51
2702 2709 3.026694 GGATTGGTGCTTAGATGGCTTT 58.973 45.455 0.00 0.00 0.00 3.51
2904 2918 9.421806 TCGTGAAAAATATTCTTTGCAAATGAT 57.578 25.926 13.23 11.81 29.54 2.45
2932 2946 5.418840 GTCAAATACATCACCAATTGGACCT 59.581 40.000 31.22 11.20 38.94 3.85
2940 2954 4.662278 TCACCAATTGGACCTCCTAAAAG 58.338 43.478 31.22 0.00 38.94 2.27
2980 2997 8.325046 AGATGACTCTTATAAACCAAAAGAGCT 58.675 33.333 10.42 0.00 46.61 4.09
3007 3024 9.979270 CTGTAAGAATTCAGTAATTTGTAGCAG 57.021 33.333 8.44 0.00 35.41 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.820894 ATAGGACCCTATACGATTTGGC 57.179 45.455 6.79 0.00 37.47 4.52
1 2 7.904205 ACTAAATAGGACCCTATACGATTTGG 58.096 38.462 8.86 6.15 38.20 3.28
2 3 9.774413 AAACTAAATAGGACCCTATACGATTTG 57.226 33.333 8.86 4.27 38.20 2.32
28 29 2.982339 TAGGGCCCAGTTGCTAAAAA 57.018 45.000 27.56 0.00 0.00 1.94
29 30 3.466395 AATAGGGCCCAGTTGCTAAAA 57.534 42.857 27.56 0.00 0.00 1.52
30 31 3.466395 AAATAGGGCCCAGTTGCTAAA 57.534 42.857 27.56 0.00 0.00 1.85
31 32 3.117663 CCTAAATAGGGCCCAGTTGCTAA 60.118 47.826 27.56 0.00 39.86 3.09
32 33 2.441750 CCTAAATAGGGCCCAGTTGCTA 59.558 50.000 27.56 6.59 39.86 3.49
33 34 1.215423 CCTAAATAGGGCCCAGTTGCT 59.785 52.381 27.56 3.89 39.86 3.91
34 35 1.692411 CCTAAATAGGGCCCAGTTGC 58.308 55.000 27.56 0.00 39.86 4.17
44 45 3.864758 TCCAGCGAGGCACCTAAATAGG 61.865 54.545 4.91 4.91 42.79 2.57
45 46 1.412710 TCCAGCGAGGCACCTAAATAG 59.587 52.381 0.00 0.00 37.29 1.73
46 47 1.412710 CTCCAGCGAGGCACCTAAATA 59.587 52.381 0.00 0.00 37.29 1.40
47 48 0.179000 CTCCAGCGAGGCACCTAAAT 59.821 55.000 0.00 0.00 37.29 1.40
48 49 1.596934 CTCCAGCGAGGCACCTAAA 59.403 57.895 0.00 0.00 37.29 1.85
49 50 3.298958 CTCCAGCGAGGCACCTAA 58.701 61.111 0.00 0.00 37.29 2.69
57 58 1.447489 CAAGAGCACCTCCAGCGAG 60.447 63.158 0.00 0.00 37.01 5.03
58 59 2.659016 CAAGAGCACCTCCAGCGA 59.341 61.111 0.00 0.00 37.01 4.93
59 60 2.435586 CCAAGAGCACCTCCAGCG 60.436 66.667 0.00 0.00 37.01 5.18
60 61 2.045536 CCCAAGAGCACCTCCAGC 60.046 66.667 0.00 0.00 0.00 4.85
61 62 1.267574 TAGCCCAAGAGCACCTCCAG 61.268 60.000 0.00 0.00 34.23 3.86
62 63 1.229496 TAGCCCAAGAGCACCTCCA 60.229 57.895 0.00 0.00 34.23 3.86
63 64 0.978146 TCTAGCCCAAGAGCACCTCC 60.978 60.000 0.00 0.00 34.23 4.30
64 65 0.176910 GTCTAGCCCAAGAGCACCTC 59.823 60.000 0.00 0.00 34.23 3.85
65 66 1.608717 CGTCTAGCCCAAGAGCACCT 61.609 60.000 0.00 0.00 34.23 4.00
66 67 1.153549 CGTCTAGCCCAAGAGCACC 60.154 63.158 0.00 0.00 34.23 5.01
67 68 1.153549 CCGTCTAGCCCAAGAGCAC 60.154 63.158 0.00 0.00 34.23 4.40
68 69 2.359169 CCCGTCTAGCCCAAGAGCA 61.359 63.158 0.00 0.00 34.23 4.26
69 70 2.501610 CCCGTCTAGCCCAAGAGC 59.498 66.667 0.00 0.00 0.00 4.09
70 71 2.501610 GCCCGTCTAGCCCAAGAG 59.498 66.667 0.00 0.00 0.00 2.85
71 72 3.081409 GGCCCGTCTAGCCCAAGA 61.081 66.667 0.00 0.00 45.16 3.02
92 93 2.369394 CTAGTAAAGCAAGGCCCAAGG 58.631 52.381 0.00 0.00 0.00 3.61
104 105 1.745653 GGCAAAGCTGGGCTAGTAAAG 59.254 52.381 9.44 0.00 38.25 1.85
105 106 1.615919 GGGCAAAGCTGGGCTAGTAAA 60.616 52.381 11.27 0.00 38.25 2.01
106 107 0.034477 GGGCAAAGCTGGGCTAGTAA 60.034 55.000 11.27 0.00 38.25 2.24
107 108 0.914417 AGGGCAAAGCTGGGCTAGTA 60.914 55.000 11.27 0.00 38.25 1.82
108 109 1.793820 AAGGGCAAAGCTGGGCTAGT 61.794 55.000 11.27 0.00 38.25 2.57
109 110 1.000396 AAGGGCAAAGCTGGGCTAG 60.000 57.895 11.27 0.00 38.25 3.42
110 111 1.000896 GAAGGGCAAAGCTGGGCTA 60.001 57.895 11.27 0.00 38.25 3.93
111 112 2.283460 GAAGGGCAAAGCTGGGCT 60.283 61.111 11.27 0.00 42.56 5.19
112 113 2.601367 TGAAGGGCAAAGCTGGGC 60.601 61.111 3.84 3.84 0.00 5.36
113 114 1.228675 AGTGAAGGGCAAAGCTGGG 60.229 57.895 0.00 0.00 0.00 4.45
114 115 0.251077 AGAGTGAAGGGCAAAGCTGG 60.251 55.000 0.00 0.00 0.00 4.85
115 116 1.163554 GAGAGTGAAGGGCAAAGCTG 58.836 55.000 0.00 0.00 0.00 4.24
116 117 0.321122 CGAGAGTGAAGGGCAAAGCT 60.321 55.000 0.00 0.00 0.00 3.74
117 118 1.916697 GCGAGAGTGAAGGGCAAAGC 61.917 60.000 0.00 0.00 0.00 3.51
118 119 1.301677 GGCGAGAGTGAAGGGCAAAG 61.302 60.000 0.00 0.00 0.00 2.77
119 120 1.302511 GGCGAGAGTGAAGGGCAAA 60.303 57.895 0.00 0.00 0.00 3.68
120 121 2.347490 GGCGAGAGTGAAGGGCAA 59.653 61.111 0.00 0.00 0.00 4.52
121 122 2.922503 TGGCGAGAGTGAAGGGCA 60.923 61.111 0.00 0.00 0.00 5.36
122 123 2.435059 GTGGCGAGAGTGAAGGGC 60.435 66.667 0.00 0.00 0.00 5.19
123 124 1.079543 CAGTGGCGAGAGTGAAGGG 60.080 63.158 0.00 0.00 0.00 3.95
124 125 1.739562 GCAGTGGCGAGAGTGAAGG 60.740 63.158 0.00 0.00 0.00 3.46
125 126 1.739562 GGCAGTGGCGAGAGTGAAG 60.740 63.158 0.00 0.00 42.47 3.02
126 127 1.758440 AAGGCAGTGGCGAGAGTGAA 61.758 55.000 11.51 0.00 42.47 3.18
127 128 1.758440 AAAGGCAGTGGCGAGAGTGA 61.758 55.000 11.51 0.00 42.47 3.41
128 129 0.886490 AAAAGGCAGTGGCGAGAGTG 60.886 55.000 11.51 0.00 42.47 3.51
129 130 0.179018 AAAAAGGCAGTGGCGAGAGT 60.179 50.000 11.51 0.00 42.47 3.24
130 131 2.633860 AAAAAGGCAGTGGCGAGAG 58.366 52.632 11.51 0.00 42.47 3.20
131 132 4.898607 AAAAAGGCAGTGGCGAGA 57.101 50.000 11.51 0.00 42.47 4.04
622 623 2.477176 CGACGAGGCTGGAGGAGAG 61.477 68.421 2.65 0.00 0.00 3.20
625 626 3.062466 CACGACGAGGCTGGAGGA 61.062 66.667 2.65 0.00 0.00 3.71
646 647 4.047059 GTCGTCGGAGTGGGCGAA 62.047 66.667 0.00 0.00 35.08 4.70
924 925 1.377202 GAACCCGAGCCTGAATGCA 60.377 57.895 0.00 0.00 0.00 3.96
926 927 1.026718 GTGGAACCCGAGCCTGAATG 61.027 60.000 0.00 0.00 0.00 2.67
927 928 1.299976 GTGGAACCCGAGCCTGAAT 59.700 57.895 0.00 0.00 0.00 2.57
1029 1030 0.108207 CCAGATCCCTCACAGGCATC 59.892 60.000 0.00 0.00 32.73 3.91
1090 1091 2.378634 CCAAGGCCTCCCCAGGTAG 61.379 68.421 5.23 0.00 42.74 3.18
1128 1129 4.899239 GCCAGCGTCCCATCCTCG 62.899 72.222 0.00 0.00 0.00 4.63
1219 1220 1.490490 GCTCTCCACATACCCATGGAA 59.510 52.381 15.22 0.30 44.42 3.53
1227 1228 3.118629 TCACTCCATTGCTCTCCACATAC 60.119 47.826 0.00 0.00 0.00 2.39
1323 1324 2.196749 CCATCAATCCTCTCGAACACG 58.803 52.381 0.00 0.00 0.00 4.49
1380 1381 3.560068 CCATCAGCCCGAACTTTGTATAC 59.440 47.826 0.00 0.00 0.00 1.47
1567 1568 1.331756 CTGCGAGCAAGCCGATAAAAT 59.668 47.619 0.00 0.00 36.02 1.82
1596 1597 4.785914 TGAACCCACATACCCATTTCTAGA 59.214 41.667 0.00 0.00 0.00 2.43
1656 1657 5.120830 GTCAACTAGATTTGTGCCTAGTGTG 59.879 44.000 0.00 0.00 43.26 3.82
1689 1690 3.403038 CTTCTCGATGTTCCCACACTTT 58.597 45.455 0.00 0.00 35.03 2.66
1812 1813 6.563222 AGCTCTATCATTCTACGGAAGTAC 57.437 41.667 0.00 0.00 46.88 2.73
1821 1822 6.178607 TGCAATCCAAGCTCTATCATTCTA 57.821 37.500 0.00 0.00 0.00 2.10
2022 2023 3.278574 TGGCATGGTGTTTACTAGATGC 58.721 45.455 0.00 0.00 35.26 3.91
2091 2092 5.369699 ACCCAGAGTAATATTACCATGCAGT 59.630 40.000 19.74 14.85 34.19 4.40
2092 2093 5.702670 CACCCAGAGTAATATTACCATGCAG 59.297 44.000 19.74 14.37 34.19 4.41
2097 2098 6.126594 CCCTTTCACCCAGAGTAATATTACCA 60.127 42.308 19.74 0.00 34.19 3.25
2310 2311 3.649073 TGTATGTGACTTGTCCTTCACG 58.351 45.455 0.00 0.00 44.35 4.35
2364 2365 5.767665 AGTGTGCCTTATTTGTTGTGTGATA 59.232 36.000 0.00 0.00 0.00 2.15
2370 2371 2.692557 TGCAGTGTGCCTTATTTGTTGT 59.307 40.909 0.00 0.00 44.23 3.32
2418 2419 0.035725 TCACATCTTGCAGGCCTCAG 60.036 55.000 0.00 0.00 0.00 3.35
2444 2445 3.300590 GGTTGAGTTGCGCAAAATAATCG 59.699 43.478 26.87 0.00 0.00 3.34
2465 2466 1.935873 CTGGCATAACTCACGACATGG 59.064 52.381 0.00 0.00 0.00 3.66
2469 2470 0.391130 TGCCTGGCATAACTCACGAC 60.391 55.000 19.30 0.00 31.71 4.34
2551 2552 1.816835 GGTAAGCTGTAAAAGGGCCAC 59.183 52.381 6.18 0.00 0.00 5.01
2556 2557 3.921677 TCGACTGGTAAGCTGTAAAAGG 58.078 45.455 0.00 0.00 0.00 3.11
2576 2577 5.867716 AGCATCTGCACTTGAATTTTTCATC 59.132 36.000 4.79 0.00 45.16 2.92
2588 2594 2.564471 GCCTTGAGCATCTGCACTT 58.436 52.632 4.79 0.00 45.16 3.16
2660 2666 9.474920 CAATCCAACTTTTGACAAGCTTAATTA 57.525 29.630 0.00 0.00 0.00 1.40
2678 2685 2.099756 GCCATCTAAGCACCAATCCAAC 59.900 50.000 0.00 0.00 0.00 3.77
2702 2709 6.536447 AGGACTGGTACGGAAATAAGAAAAA 58.464 36.000 0.00 0.00 38.67 1.94
2798 2805 7.147266 TGAGTAGGGAAAGGAAAAGTTTAAGGA 60.147 37.037 0.00 0.00 0.00 3.36
2816 2823 5.860941 ATCAGATACAACTGTGAGTAGGG 57.139 43.478 0.00 0.00 38.79 3.53
2904 2918 8.465999 GTCCAATTGGTGATGTATTTGACATTA 58.534 33.333 23.76 0.00 41.75 1.90
2925 2939 2.444033 TCCCCTTTTAGGAGGTCCAA 57.556 50.000 0.00 0.00 37.67 3.53
2932 2946 3.603965 TTGCAACTTCCCCTTTTAGGA 57.396 42.857 0.00 0.00 37.67 2.94
2940 2954 2.893489 AGTCATCTTTTGCAACTTCCCC 59.107 45.455 0.00 0.00 0.00 4.81
2980 2997 9.719355 TGCTACAAATTACTGAATTCTTACAGA 57.281 29.630 7.05 0.00 34.01 3.41
3304 3323 1.795768 TCTTTCGACACATGGCTGAC 58.204 50.000 0.00 0.00 0.00 3.51
3359 3378 7.385205 CGGAACATATGATAGACAAAGTAAGGG 59.615 40.741 10.38 0.00 0.00 3.95


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

AutoCloner maintained by Alex Coulton.