Multiple sequence alignment - TraesCS3D01G220800

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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 TraesCS3D01G220800 chr3D 100.000 2845 0 0 1 2845 301422312 301419468 0.000000e+00 5254
1 TraesCS3D01G220800 chr3D 95.833 120 4 1 2116 2234 431450780 431450661 2.890000e-45 193
2 TraesCS3D01G220800 chr3B 92.061 2217 99 36 220 2405 419796603 419798773 0.000000e+00 3048
3 TraesCS3D01G220800 chr3B 91.236 445 29 2 2401 2845 419800584 419801018 5.250000e-167 597
4 TraesCS3D01G220800 chr3B 88.546 227 17 9 18 238 419795979 419796202 1.680000e-67 267
5 TraesCS3D01G220800 chr3A 93.901 1738 66 18 351 2084 434004779 434006480 0.000000e+00 2586
6 TraesCS3D01G220800 chr3A 90.981 632 40 2 2231 2845 434042968 434043599 0.000000e+00 835
7 TraesCS3D01G220800 chr3A 88.473 347 25 8 1 343 434004393 434004728 3.410000e-109 405
8 TraesCS3D01G220800 chr1A 99.107 112 1 0 2125 2236 489400810 489400699 4.810000e-48 202
9 TraesCS3D01G220800 chr2B 97.414 116 3 0 2118 2233 743316892 743317007 6.220000e-47 198
10 TraesCS3D01G220800 chr2B 93.939 132 5 3 2117 2246 743331817 743331687 2.240000e-46 196
11 TraesCS3D01G220800 chr6A 94.531 128 6 1 2115 2242 158087908 158088034 2.240000e-46 196
12 TraesCS3D01G220800 chr5D 98.198 111 2 0 2125 2235 463187905 463187795 8.040000e-46 195
13 TraesCS3D01G220800 chr7D 94.444 126 4 3 2110 2232 241737039 241737164 1.040000e-44 191
14 TraesCS3D01G220800 chr7B 93.023 129 5 4 2125 2249 693255331 693255203 4.840000e-43 185
15 TraesCS3D01G220800 chr6B 92.308 130 8 2 2125 2253 576017033 576017161 1.740000e-42 183


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 TraesCS3D01G220800 chr3D 301419468 301422312 2844 True 5254.0 5254 100.000000 1 2845 1 chr3D.!!$R1 2844
1 TraesCS3D01G220800 chr3B 419795979 419801018 5039 False 1304.0 3048 90.614333 18 2845 3 chr3B.!!$F1 2827
2 TraesCS3D01G220800 chr3A 434004393 434006480 2087 False 1495.5 2586 91.187000 1 2084 2 chr3A.!!$F2 2083
3 TraesCS3D01G220800 chr3A 434042968 434043599 631 False 835.0 835 90.981000 2231 2845 1 chr3A.!!$F1 614

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
865 1337 1.070134 GCTGTACACCTCCACACTCAA 59.93 52.381 0.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2704 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.0 13.34 13.34 0.0 4.55 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
50 51 4.078639 GCTCTGGGCATGTTTAGACTAT 57.921 45.455 0.00 0.00 41.35 2.12
70 75 2.695359 TGCTTCTCCACCGTGTATTTC 58.305 47.619 0.00 0.00 0.00 2.17
71 76 2.301870 TGCTTCTCCACCGTGTATTTCT 59.698 45.455 0.00 0.00 0.00 2.52
75 80 5.617087 GCTTCTCCACCGTGTATTTCTTTTC 60.617 44.000 0.00 0.00 0.00 2.29
76 81 5.223449 TCTCCACCGTGTATTTCTTTTCT 57.777 39.130 0.00 0.00 0.00 2.52
80 85 6.731164 TCCACCGTGTATTTCTTTTCTTTTC 58.269 36.000 0.00 0.00 0.00 2.29
81 86 6.544564 TCCACCGTGTATTTCTTTTCTTTTCT 59.455 34.615 0.00 0.00 0.00 2.52
83 88 7.704899 CCACCGTGTATTTCTTTTCTTTTCTTT 59.295 33.333 0.00 0.00 0.00 2.52
84 89 8.743099 CACCGTGTATTTCTTTTCTTTTCTTTC 58.257 33.333 0.00 0.00 0.00 2.62
100 105 6.478512 TTTCTTTCTGCTATTTGGGTTTGT 57.521 33.333 0.00 0.00 0.00 2.83
101 106 6.478512 TTCTTTCTGCTATTTGGGTTTGTT 57.521 33.333 0.00 0.00 0.00 2.83
108 113 8.466617 TCTGCTATTTGGGTTTGTTTACTTAA 57.533 30.769 0.00 0.00 0.00 1.85
109 114 8.354426 TCTGCTATTTGGGTTTGTTTACTTAAC 58.646 33.333 0.00 0.00 37.26 2.01
111 116 8.697292 TGCTATTTGGGTTTGTTTACTTAACTT 58.303 29.630 0.00 0.00 37.64 2.66
115 120 6.058827 TGGGTTTGTTTACTTAACTTACGC 57.941 37.500 0.00 0.00 37.64 4.42
136 141 5.472137 ACGCTAGAATGCTGGTTTCTTTAAA 59.528 36.000 0.00 0.00 35.19 1.52
258 680 4.464008 AGAACTTCCACAAAGATGCTTCA 58.536 39.130 2.07 0.00 38.44 3.02
368 833 6.204688 CGGAAACTATTTGCCATTAGCTGATA 59.795 38.462 0.00 0.00 44.23 2.15
369 834 7.255104 CGGAAACTATTTGCCATTAGCTGATAA 60.255 37.037 0.00 0.00 44.23 1.75
376 841 5.443185 TGCCATTAGCTGATAAATTGCTC 57.557 39.130 0.00 0.00 44.23 4.26
401 868 3.365364 CCCGACAAACAAAATCTCTGCTC 60.365 47.826 0.00 0.00 0.00 4.26
439 906 3.377172 CAGGATTTCCAACGACAATACCC 59.623 47.826 0.00 0.00 38.89 3.69
450 917 5.978934 ACGACAATACCCAATAAATCGAC 57.021 39.130 0.00 0.00 32.83 4.20
606 1078 3.885297 ACATCATTCCGACCCATCATTTC 59.115 43.478 0.00 0.00 0.00 2.17
699 1171 5.008712 CCGTAGCTTATCATATATGCCGAGA 59.991 44.000 7.92 0.00 0.00 4.04
865 1337 1.070134 GCTGTACACCTCCACACTCAA 59.930 52.381 0.00 0.00 0.00 3.02
893 1365 6.980397 GGCACCTTCCATGAAATGTTTATTAG 59.020 38.462 0.00 0.00 44.81 1.73
894 1366 6.980397 GCACCTTCCATGAAATGTTTATTAGG 59.020 38.462 0.00 0.00 44.81 2.69
895 1367 7.147915 GCACCTTCCATGAAATGTTTATTAGGA 60.148 37.037 0.00 0.00 44.81 2.94
896 1368 8.408601 CACCTTCCATGAAATGTTTATTAGGAG 58.591 37.037 0.00 0.00 44.81 3.69
897 1369 8.116026 ACCTTCCATGAAATGTTTATTAGGAGT 58.884 33.333 0.00 0.00 44.81 3.85
898 1370 9.627123 CCTTCCATGAAATGTTTATTAGGAGTA 57.373 33.333 0.00 0.00 44.81 2.59
920 1392 8.412608 AGTAGAAACATGTTTAGACGATCATG 57.587 34.615 23.33 0.00 42.00 3.07
1028 1500 2.135664 AGTTCTTCCGTGTCACGAAG 57.864 50.000 26.53 23.42 46.05 3.79
1062 1534 0.896940 AGCCTACGAGACCGACCAAA 60.897 55.000 0.00 0.00 39.50 3.28
1130 1602 1.654023 GGTTCACCAAGGGCATACGC 61.654 60.000 0.00 0.00 35.64 4.42
1140 1612 1.113517 GGGCATACGCTCCTACTGGA 61.114 60.000 0.00 0.00 40.95 3.86
1643 2121 5.064707 GGCGAATGATGTGTTAGTGTTACAT 59.935 40.000 0.00 0.00 37.72 2.29
1644 2122 5.959527 GCGAATGATGTGTTAGTGTTACATG 59.040 40.000 0.00 0.00 35.35 3.21
1645 2123 5.959527 CGAATGATGTGTTAGTGTTACATGC 59.040 40.000 0.00 0.00 35.35 4.06
1646 2124 6.183360 CGAATGATGTGTTAGTGTTACATGCT 60.183 38.462 0.00 0.00 35.35 3.79
1649 2127 5.762711 TGATGTGTTAGTGTTACATGCTTGT 59.237 36.000 10.40 10.40 39.98 3.16
1650 2128 6.931840 TGATGTGTTAGTGTTACATGCTTGTA 59.068 34.615 8.29 8.29 37.28 2.41
1737 2216 9.342308 TGTAAATTCTCCATAATTCCATGACTC 57.658 33.333 0.00 0.00 0.00 3.36
1826 2305 2.202987 GGGTCAGCTGATCAGGCG 60.203 66.667 27.65 11.99 34.52 5.52
1911 2390 1.409412 GCGGACGCACATATCTACAG 58.591 55.000 12.31 0.00 41.49 2.74
1949 2435 2.811317 CGCCTCCGCACTCTTGAC 60.811 66.667 0.00 0.00 34.03 3.18
1950 2436 2.659610 GCCTCCGCACTCTTGACT 59.340 61.111 0.00 0.00 34.03 3.41
2064 2554 0.171007 CCAACAAGGCCAGCATAACG 59.829 55.000 5.01 0.00 0.00 3.18
2084 2574 9.098355 CATAACGCACATAGGTAGCAATATTAT 57.902 33.333 0.00 0.00 0.00 1.28
2123 2613 8.610248 TCAGTCTCAAATTGGATTAAACGTAA 57.390 30.769 0.00 0.00 0.00 3.18
2136 2626 5.659440 TTAAACGTAATACTCCCTCCGTT 57.341 39.130 0.00 0.00 39.88 4.44
2137 2627 3.790152 AACGTAATACTCCCTCCGTTC 57.210 47.619 0.00 0.00 33.76 3.95
2138 2628 1.672881 ACGTAATACTCCCTCCGTTCG 59.327 52.381 0.00 0.00 0.00 3.95
2139 2629 1.002033 CGTAATACTCCCTCCGTTCGG 60.002 57.143 4.74 4.74 0.00 4.30
2142 2632 2.083628 ATACTCCCTCCGTTCGGAAT 57.916 50.000 14.79 2.14 33.41 3.01
2145 2635 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2146 2636 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2153 2643 2.597305 CCGTTCGGAATTACTTGTCTCG 59.403 50.000 5.19 0.00 0.00 4.04
2154 2644 2.597305 CGTTCGGAATTACTTGTCTCGG 59.403 50.000 0.00 0.00 0.00 4.63
2155 2645 3.671433 CGTTCGGAATTACTTGTCTCGGA 60.671 47.826 0.00 0.00 0.00 4.55
2156 2646 4.240096 GTTCGGAATTACTTGTCTCGGAA 58.760 43.478 0.00 0.00 0.00 4.30
2157 2647 4.524316 TCGGAATTACTTGTCTCGGAAA 57.476 40.909 0.00 0.00 0.00 3.13
2159 2649 6.211587 TCGGAATTACTTGTCTCGGAAATA 57.788 37.500 0.00 0.00 0.00 1.40
2160 2650 6.270815 TCGGAATTACTTGTCTCGGAAATAG 58.729 40.000 0.00 0.00 0.00 1.73
2161 2651 6.095860 TCGGAATTACTTGTCTCGGAAATAGA 59.904 38.462 0.00 0.00 0.00 1.98
2162 2652 6.924060 CGGAATTACTTGTCTCGGAAATAGAT 59.076 38.462 0.00 0.00 0.00 1.98
2163 2653 7.096023 CGGAATTACTTGTCTCGGAAATAGATG 60.096 40.741 0.00 0.00 0.00 2.90
2164 2654 7.711339 GGAATTACTTGTCTCGGAAATAGATGT 59.289 37.037 0.00 0.00 0.00 3.06
2165 2655 9.745880 GAATTACTTGTCTCGGAAATAGATGTA 57.254 33.333 0.00 0.00 0.00 2.29
2167 2657 9.915629 ATTACTTGTCTCGGAAATAGATGTATC 57.084 33.333 0.00 0.00 0.00 2.24
2169 2659 8.693120 ACTTGTCTCGGAAATAGATGTATCTA 57.307 34.615 4.22 4.22 43.00 1.98
2170 2660 8.788806 ACTTGTCTCGGAAATAGATGTATCTAG 58.211 37.037 7.57 0.00 42.20 2.43
2172 2662 8.919777 TGTCTCGGAAATAGATGTATCTAGAA 57.080 34.615 0.00 0.00 42.20 2.10
2173 2663 8.784994 TGTCTCGGAAATAGATGTATCTAGAAC 58.215 37.037 0.00 0.00 42.20 3.01
2202 2692 9.698309 AAATACGTCTAGATACATCCATTTCTG 57.302 33.333 0.00 0.00 0.00 3.02
2204 2694 6.507900 ACGTCTAGATACATCCATTTCTGTG 58.492 40.000 0.00 0.00 0.00 3.66
2205 2695 6.321435 ACGTCTAGATACATCCATTTCTGTGA 59.679 38.462 0.00 0.00 0.00 3.58
2206 2696 6.638873 CGTCTAGATACATCCATTTCTGTGAC 59.361 42.308 0.00 0.00 0.00 3.67
2207 2697 7.492524 GTCTAGATACATCCATTTCTGTGACA 58.507 38.462 0.00 0.00 0.00 3.58
2208 2698 7.981789 GTCTAGATACATCCATTTCTGTGACAA 59.018 37.037 0.00 0.00 0.00 3.18
2209 2699 8.200120 TCTAGATACATCCATTTCTGTGACAAG 58.800 37.037 0.00 0.00 0.00 3.16
2211 2701 7.851228 AGATACATCCATTTCTGTGACAAGTA 58.149 34.615 0.00 0.00 0.00 2.24
2212 2702 8.321353 AGATACATCCATTTCTGTGACAAGTAA 58.679 33.333 0.00 0.00 0.00 2.24
2213 2703 9.113838 GATACATCCATTTCTGTGACAAGTAAT 57.886 33.333 0.00 0.00 0.00 1.89
2214 2704 7.765695 ACATCCATTTCTGTGACAAGTAATT 57.234 32.000 0.00 0.00 0.00 1.40
2215 2705 7.820648 ACATCCATTTCTGTGACAAGTAATTC 58.179 34.615 0.00 0.00 0.00 2.17
2216 2706 6.817765 TCCATTTCTGTGACAAGTAATTCC 57.182 37.500 0.00 0.00 0.00 3.01
2217 2707 5.411361 TCCATTTCTGTGACAAGTAATTCCG 59.589 40.000 0.00 0.00 0.00 4.30
2218 2708 5.411361 CCATTTCTGTGACAAGTAATTCCGA 59.589 40.000 0.00 0.00 0.00 4.55
2219 2709 6.072728 CCATTTCTGTGACAAGTAATTCCGAA 60.073 38.462 0.00 0.00 0.00 4.30
2220 2710 5.917541 TTCTGTGACAAGTAATTCCGAAC 57.082 39.130 0.00 0.00 0.00 3.95
2221 2711 3.985279 TCTGTGACAAGTAATTCCGAACG 59.015 43.478 0.00 0.00 0.00 3.95
2222 2712 3.061322 TGTGACAAGTAATTCCGAACGG 58.939 45.455 6.94 6.94 0.00 4.44
2223 2713 3.243805 TGTGACAAGTAATTCCGAACGGA 60.244 43.478 12.04 12.04 43.52 4.69
2224 2714 3.367025 GTGACAAGTAATTCCGAACGGAG 59.633 47.826 15.34 5.60 46.06 4.63
2225 2715 2.928116 GACAAGTAATTCCGAACGGAGG 59.072 50.000 15.34 4.52 46.06 4.30
2254 2744 9.401873 GTACATTACAAGACCAAACATAAAACC 57.598 33.333 0.00 0.00 0.00 3.27
2255 2745 7.142680 ACATTACAAGACCAAACATAAAACCG 58.857 34.615 0.00 0.00 0.00 4.44
2377 2898 4.789012 TGCTGAAAGAAAATGGACCATC 57.211 40.909 7.63 0.00 34.07 3.51
2433 4768 2.234300 TCCTTCCACGACAAGTTCAC 57.766 50.000 0.00 0.00 0.00 3.18
2528 4863 2.490903 GACCTCTGGTACTCGCAAGTAA 59.509 50.000 0.00 0.00 39.66 2.24
2552 4887 7.667043 AAGTAAGAATATTGTTGAACGAGCA 57.333 32.000 8.05 0.00 0.00 4.26
2562 4897 2.542020 TGAACGAGCAAGGATCACAA 57.458 45.000 0.00 0.00 0.00 3.33
2623 4958 1.403679 TGGTCGGTGCACAAAAGAAAG 59.596 47.619 20.43 0.00 0.00 2.62
2638 4973 0.608035 GAAAGGGATGTGGCCGACAA 60.608 55.000 11.29 0.00 38.36 3.18
2647 4982 0.534203 GTGGCCGACAACTTTGAGGA 60.534 55.000 0.00 0.00 33.65 3.71
2664 4999 1.070105 GACCCCACACAACGCACTA 59.930 57.895 0.00 0.00 0.00 2.74
2678 5013 0.324943 GCACTAAGGGAAGGCAGTCA 59.675 55.000 0.00 0.00 0.00 3.41
2710 5045 4.702612 TCGCCATAGGAAGATACAGATCTC 59.297 45.833 0.00 0.00 41.87 2.75
2751 5086 1.250840 AAGGGCCTTGTCGGAATTGC 61.251 55.000 20.19 0.00 33.16 3.56
2805 5140 3.512724 CCCATTTCATTGAGAGGTTGCTT 59.487 43.478 0.00 0.00 0.00 3.91
2818 5154 4.460731 AGAGGTTGCTTGAATCTTAAAGGC 59.539 41.667 0.00 0.00 0.00 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 1.529244 GCAGGGGTGTTCTTGTGCT 60.529 57.895 0.00 0.00 0.00 4.40
50 51 2.301870 AGAAATACACGGTGGAGAAGCA 59.698 45.455 13.48 0.00 0.00 3.91
70 75 7.928167 ACCCAAATAGCAGAAAGAAAAGAAAAG 59.072 33.333 0.00 0.00 0.00 2.27
71 76 7.791029 ACCCAAATAGCAGAAAGAAAAGAAAA 58.209 30.769 0.00 0.00 0.00 2.29
75 80 6.986231 ACAAACCCAAATAGCAGAAAGAAAAG 59.014 34.615 0.00 0.00 0.00 2.27
76 81 6.883744 ACAAACCCAAATAGCAGAAAGAAAA 58.116 32.000 0.00 0.00 0.00 2.29
80 85 7.433680 AGTAAACAAACCCAAATAGCAGAAAG 58.566 34.615 0.00 0.00 0.00 2.62
81 86 7.354751 AGTAAACAAACCCAAATAGCAGAAA 57.645 32.000 0.00 0.00 0.00 2.52
83 88 6.969993 AAGTAAACAAACCCAAATAGCAGA 57.030 33.333 0.00 0.00 0.00 4.26
84 89 8.357402 AGTTAAGTAAACAAACCCAAATAGCAG 58.643 33.333 0.00 0.00 40.83 4.24
89 94 7.648908 GCGTAAGTTAAGTAAACAAACCCAAAT 59.351 33.333 0.00 0.00 40.83 2.32
100 105 7.277098 CCAGCATTCTAGCGTAAGTTAAGTAAA 59.723 37.037 0.00 0.00 40.15 2.01
101 106 6.755141 CCAGCATTCTAGCGTAAGTTAAGTAA 59.245 38.462 0.00 0.00 40.15 2.24
108 113 3.611766 AACCAGCATTCTAGCGTAAGT 57.388 42.857 0.00 0.00 40.15 2.24
109 114 4.184629 AGAAACCAGCATTCTAGCGTAAG 58.815 43.478 0.00 0.00 40.15 2.34
111 116 3.887621 AGAAACCAGCATTCTAGCGTA 57.112 42.857 0.00 0.00 40.15 4.42
112 117 2.770164 AGAAACCAGCATTCTAGCGT 57.230 45.000 0.00 0.00 40.15 5.07
113 118 5.545658 TTAAAGAAACCAGCATTCTAGCG 57.454 39.130 0.00 0.00 36.14 4.26
114 119 7.593825 TCTTTTAAAGAAACCAGCATTCTAGC 58.406 34.615 4.77 0.00 36.14 3.42
136 141 5.221541 GGGGTCGACAGATCTCATATTTCTT 60.222 44.000 18.91 0.00 0.00 2.52
143 148 1.216678 AGAGGGGTCGACAGATCTCAT 59.783 52.381 18.91 5.64 27.67 2.90
144 149 0.626382 AGAGGGGTCGACAGATCTCA 59.374 55.000 18.91 0.00 27.67 3.27
258 680 0.546122 TAATGAAGCGATGGGGCAGT 59.454 50.000 0.00 0.00 34.64 4.40
344 766 5.835113 TCAGCTAATGGCAAATAGTTTCC 57.165 39.130 11.03 0.00 44.79 3.13
368 833 1.339929 GTTTGTCGGGGTGAGCAATTT 59.660 47.619 0.00 0.00 0.00 1.82
369 834 0.958822 GTTTGTCGGGGTGAGCAATT 59.041 50.000 0.00 0.00 0.00 2.32
376 841 2.884639 AGAGATTTTGTTTGTCGGGGTG 59.115 45.455 0.00 0.00 0.00 4.61
401 868 2.023673 TCCTGTTGTGTGCTTCCTTTG 58.976 47.619 0.00 0.00 0.00 2.77
465 932 7.432252 GCACAAGCATGTACTGTAAAATAATCC 59.568 37.037 0.00 0.00 37.82 3.01
699 1171 0.822164 GCTCAGGATTTGCATTGGCT 59.178 50.000 0.00 0.00 41.91 4.75
807 1279 1.865865 TTTCTTGTCTCGGCTCACAC 58.134 50.000 0.00 0.00 0.00 3.82
815 1287 4.310769 AGATGAGGTGTTTTCTTGTCTCG 58.689 43.478 0.00 0.00 0.00 4.04
865 1337 0.039618 ATTTCATGGAAGGTGCCGGT 59.960 50.000 1.90 0.00 0.00 5.28
893 1365 7.033791 TGATCGTCTAAACATGTTTCTACTCC 58.966 38.462 26.46 15.49 34.23 3.85
894 1366 8.535592 CATGATCGTCTAAACATGTTTCTACTC 58.464 37.037 26.46 18.00 36.42 2.59
895 1367 8.035394 ACATGATCGTCTAAACATGTTTCTACT 58.965 33.333 26.46 11.19 46.98 2.57
896 1368 8.186178 ACATGATCGTCTAAACATGTTTCTAC 57.814 34.615 26.46 21.98 46.98 2.59
920 1392 2.219355 CGTCACGTGCGAACATAAAAC 58.781 47.619 22.18 6.58 0.00 2.43
1028 1500 0.611896 AGGCTGGGTTTGGTGTATGC 60.612 55.000 0.00 0.00 0.00 3.14
1140 1612 2.982130 CTGGTACTTGCTCCGGCT 59.018 61.111 0.00 0.00 39.59 5.52
1643 2121 9.750125 CAACTGATCTTACATATACTACAAGCA 57.250 33.333 0.00 0.00 0.00 3.91
1644 2122 9.197694 CCAACTGATCTTACATATACTACAAGC 57.802 37.037 0.00 0.00 0.00 4.01
1737 2216 4.332543 TCGCATATAACCTCACAAGCAAAG 59.667 41.667 0.00 0.00 0.00 2.77
1826 2305 6.024049 GCATCTTTTACTGCACACTGTAATC 58.976 40.000 0.00 0.00 39.18 1.75
1911 2390 3.103738 GCACATGACATGCGAGAAAATC 58.896 45.455 15.49 0.00 32.45 2.17
1944 2430 1.132262 GCAGGAGAGTCGAGAGTCAAG 59.868 57.143 10.20 0.00 33.26 3.02
1945 2431 1.169577 GCAGGAGAGTCGAGAGTCAA 58.830 55.000 10.20 0.00 33.26 3.18
1946 2432 1.021920 CGCAGGAGAGTCGAGAGTCA 61.022 60.000 10.20 0.00 33.26 3.41
1947 2433 1.022451 ACGCAGGAGAGTCGAGAGTC 61.022 60.000 0.00 0.00 0.00 3.36
1948 2434 1.003112 ACGCAGGAGAGTCGAGAGT 60.003 57.895 0.00 0.00 0.00 3.24
1949 2435 1.719117 GACGCAGGAGAGTCGAGAG 59.281 63.158 0.00 0.00 34.91 3.20
1950 2436 3.892122 GACGCAGGAGAGTCGAGA 58.108 61.111 0.00 0.00 34.91 4.04
2123 2613 2.083628 ATTCCGAACGGAGGGAGTAT 57.916 50.000 15.34 3.38 46.06 2.12
2125 2615 1.479730 GTAATTCCGAACGGAGGGAGT 59.520 52.381 15.34 4.12 46.06 3.85
2136 2626 4.524316 TTTCCGAGACAAGTAATTCCGA 57.476 40.909 0.00 0.00 0.00 4.55
2137 2627 6.270815 TCTATTTCCGAGACAAGTAATTCCG 58.729 40.000 0.00 0.00 0.00 4.30
2138 2628 7.711339 ACATCTATTTCCGAGACAAGTAATTCC 59.289 37.037 0.00 0.00 0.00 3.01
2139 2629 8.649973 ACATCTATTTCCGAGACAAGTAATTC 57.350 34.615 0.00 0.00 0.00 2.17
2142 2632 9.132923 AGATACATCTATTTCCGAGACAAGTAA 57.867 33.333 0.00 0.00 34.85 2.24
2145 2635 9.004717 TCTAGATACATCTATTTCCGAGACAAG 57.995 37.037 0.00 0.00 38.60 3.16
2146 2636 8.919777 TCTAGATACATCTATTTCCGAGACAA 57.080 34.615 0.00 0.00 38.60 3.18
2178 2668 8.300286 CACAGAAATGGATGTATCTAGACGTAT 58.700 37.037 0.00 0.00 0.00 3.06
2180 2670 6.321435 TCACAGAAATGGATGTATCTAGACGT 59.679 38.462 0.00 0.00 0.00 4.34
2181 2671 6.638873 GTCACAGAAATGGATGTATCTAGACG 59.361 42.308 0.00 0.00 0.00 4.18
2183 2673 7.660030 TGTCACAGAAATGGATGTATCTAGA 57.340 36.000 0.00 0.00 0.00 2.43
2184 2674 7.984050 ACTTGTCACAGAAATGGATGTATCTAG 59.016 37.037 0.00 0.00 0.00 2.43
2186 2676 6.715280 ACTTGTCACAGAAATGGATGTATCT 58.285 36.000 0.00 0.00 0.00 1.98
2187 2677 6.992063 ACTTGTCACAGAAATGGATGTATC 57.008 37.500 0.00 0.00 0.00 2.24
2188 2678 9.466497 AATTACTTGTCACAGAAATGGATGTAT 57.534 29.630 0.00 0.00 0.00 2.29
2189 2679 8.862325 AATTACTTGTCACAGAAATGGATGTA 57.138 30.769 0.00 0.00 0.00 2.29
2190 2680 7.094205 GGAATTACTTGTCACAGAAATGGATGT 60.094 37.037 0.00 0.00 0.00 3.06
2191 2681 7.253422 GGAATTACTTGTCACAGAAATGGATG 58.747 38.462 0.00 0.00 0.00 3.51
2193 2683 5.411361 CGGAATTACTTGTCACAGAAATGGA 59.589 40.000 0.00 0.00 0.00 3.41
2194 2684 5.411361 TCGGAATTACTTGTCACAGAAATGG 59.589 40.000 0.00 0.00 0.00 3.16
2195 2685 6.480524 TCGGAATTACTTGTCACAGAAATG 57.519 37.500 0.00 0.00 0.00 2.32
2196 2686 6.347402 CGTTCGGAATTACTTGTCACAGAAAT 60.347 38.462 0.00 0.00 0.00 2.17
2197 2687 5.050634 CGTTCGGAATTACTTGTCACAGAAA 60.051 40.000 0.00 0.00 0.00 2.52
2200 2690 3.122948 CCGTTCGGAATTACTTGTCACAG 59.877 47.826 5.19 0.00 0.00 3.66
2201 2691 3.061322 CCGTTCGGAATTACTTGTCACA 58.939 45.455 5.19 0.00 0.00 3.58
2202 2692 3.319755 TCCGTTCGGAATTACTTGTCAC 58.680 45.455 11.66 0.00 0.00 3.67
2204 2694 2.928116 CCTCCGTTCGGAATTACTTGTC 59.072 50.000 14.79 0.00 33.41 3.18
2205 2695 2.354403 CCCTCCGTTCGGAATTACTTGT 60.354 50.000 14.79 0.00 33.41 3.16
2206 2696 2.093869 TCCCTCCGTTCGGAATTACTTG 60.094 50.000 14.79 1.97 33.41 3.16
2207 2697 2.167900 CTCCCTCCGTTCGGAATTACTT 59.832 50.000 14.79 0.00 33.41 2.24
2208 2698 1.755380 CTCCCTCCGTTCGGAATTACT 59.245 52.381 14.79 0.00 33.41 2.24
2209 2699 1.479730 ACTCCCTCCGTTCGGAATTAC 59.520 52.381 14.79 0.00 33.41 1.89
2211 2701 1.479730 GTACTCCCTCCGTTCGGAATT 59.520 52.381 14.79 0.00 33.41 2.17
2212 2702 1.109609 GTACTCCCTCCGTTCGGAAT 58.890 55.000 14.79 2.09 33.41 3.01
2213 2703 0.251297 TGTACTCCCTCCGTTCGGAA 60.251 55.000 14.79 0.04 33.41 4.30
2214 2704 0.033796 ATGTACTCCCTCCGTTCGGA 60.034 55.000 13.34 13.34 0.00 4.55
2215 2705 0.822164 AATGTACTCCCTCCGTTCGG 59.178 55.000 4.74 4.74 0.00 4.30
2216 2706 2.424601 TGTAATGTACTCCCTCCGTTCG 59.575 50.000 0.00 0.00 0.00 3.95
2217 2707 4.159135 TCTTGTAATGTACTCCCTCCGTTC 59.841 45.833 0.00 0.00 0.00 3.95
2218 2708 4.081807 GTCTTGTAATGTACTCCCTCCGTT 60.082 45.833 0.00 0.00 0.00 4.44
2219 2709 3.446516 GTCTTGTAATGTACTCCCTCCGT 59.553 47.826 0.00 0.00 0.00 4.69
2220 2710 3.181478 GGTCTTGTAATGTACTCCCTCCG 60.181 52.174 0.00 0.00 0.00 4.63
2221 2711 3.773119 TGGTCTTGTAATGTACTCCCTCC 59.227 47.826 0.00 0.00 0.00 4.30
2222 2712 5.416271 TTGGTCTTGTAATGTACTCCCTC 57.584 43.478 0.00 0.00 0.00 4.30
2223 2713 5.072600 TGTTTGGTCTTGTAATGTACTCCCT 59.927 40.000 0.00 0.00 0.00 4.20
2224 2714 5.310451 TGTTTGGTCTTGTAATGTACTCCC 58.690 41.667 0.00 0.00 0.00 4.30
2225 2715 8.556213 TTATGTTTGGTCTTGTAATGTACTCC 57.444 34.615 0.00 0.00 0.00 3.85
2422 4757 1.771073 TTGCCGCAGTGAACTTGTCG 61.771 55.000 0.00 0.00 0.00 4.35
2433 4768 0.318107 CAACTTTGGACTTGCCGCAG 60.318 55.000 0.00 0.00 40.66 5.18
2528 4863 7.667043 TGCTCGTTCAACAATATTCTTACTT 57.333 32.000 0.00 0.00 0.00 2.24
2552 4887 9.638176 AAAGCTTCAGATATAATTGTGATCCTT 57.362 29.630 0.00 0.00 0.00 3.36
2562 4897 8.938883 TGGGTTAGAGAAAGCTTCAGATATAAT 58.061 33.333 0.00 0.00 35.83 1.28
2623 4958 0.893727 AAAGTTGTCGGCCACATCCC 60.894 55.000 2.24 0.00 33.90 3.85
2638 4973 0.923358 TTGTGTGGGGTCCTCAAAGT 59.077 50.000 0.00 0.00 0.00 2.66
2647 4982 0.534203 CTTAGTGCGTTGTGTGGGGT 60.534 55.000 0.00 0.00 0.00 4.95
2664 4999 1.075601 TCCAATGACTGCCTTCCCTT 58.924 50.000 0.00 0.00 0.00 3.95
2678 5013 2.088104 TCCTATGGCGAGAGTCCAAT 57.912 50.000 0.00 0.00 39.90 3.16
2710 5045 2.351276 CCACCTCGGTTCCCCTTG 59.649 66.667 0.00 0.00 0.00 3.61
2751 5086 0.105658 TATTCCCAGGGTCCTCGGAG 60.106 60.000 5.01 0.00 34.91 4.63
2805 5140 4.329638 TCAATGGGGCCTTTAAGATTCA 57.670 40.909 0.84 0.00 0.00 2.57
2818 5154 7.056635 GGTACCATAGATGATATTCAATGGGG 58.943 42.308 7.15 0.00 36.87 4.96


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

AutoCloner maintained by Alex Coulton.