Multiple sequence alignment - TraesCS3A01G168300

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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 TraesCS3A01G168300 chr3A 100.000 2755 0 0 1 2755 175807608 175810362 0.000000e+00 5088
1 TraesCS3A01G168300 chr3D 91.531 1842 79 28 962 2755 156206419 156208231 0.000000e+00 2466
2 TraesCS3A01G168300 chr3D 92.385 893 61 5 5 891 569062744 569061853 0.000000e+00 1266
3 TraesCS3A01G168300 chr3B 91.618 1539 83 22 963 2481 225449841 225448329 0.000000e+00 2085
4 TraesCS3A01G168300 chr3B 90.291 206 13 2 2550 2755 225445671 225445473 2.100000e-66 263
5 TraesCS3A01G168300 chr3B 96.053 76 3 0 2491 2566 225448272 225448197 1.040000e-24 124
6 TraesCS3A01G168300 chr6B 98.531 885 12 1 1 884 248358750 248359634 0.000000e+00 1561
7 TraesCS3A01G168300 chr6B 92.551 886 53 9 5 885 230768522 230769399 0.000000e+00 1258
8 TraesCS3A01G168300 chr2D 92.849 895 53 8 5 891 80626300 80625409 0.000000e+00 1288
9 TraesCS3A01G168300 chr6D 92.572 902 53 9 4 894 60457098 60456200 0.000000e+00 1282
10 TraesCS3A01G168300 chr7D 92.978 883 48 9 5 882 177572252 177571379 0.000000e+00 1275
11 TraesCS3A01G168300 chr1B 92.672 887 53 9 5 884 302038425 302037544 0.000000e+00 1267
12 TraesCS3A01G168300 chr5B 91.982 898 62 8 5 894 230013153 230014048 0.000000e+00 1251
13 TraesCS3A01G168300 chr2B 91.898 901 62 5 5 895 32183576 32182677 0.000000e+00 1249


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 TraesCS3A01G168300 chr3A 175807608 175810362 2754 False 5088 5088 100.000 1 2755 1 chr3A.!!$F1 2754
1 TraesCS3A01G168300 chr3D 156206419 156208231 1812 False 2466 2466 91.531 962 2755 1 chr3D.!!$F1 1793
2 TraesCS3A01G168300 chr3D 569061853 569062744 891 True 1266 1266 92.385 5 891 1 chr3D.!!$R1 886
3 TraesCS3A01G168300 chr3B 225445473 225449841 4368 True 824 2085 92.654 963 2755 3 chr3B.!!$R1 1792
4 TraesCS3A01G168300 chr6B 248358750 248359634 884 False 1561 1561 98.531 1 884 1 chr6B.!!$F2 883
5 TraesCS3A01G168300 chr6B 230768522 230769399 877 False 1258 1258 92.551 5 885 1 chr6B.!!$F1 880
6 TraesCS3A01G168300 chr2D 80625409 80626300 891 True 1288 1288 92.849 5 891 1 chr2D.!!$R1 886
7 TraesCS3A01G168300 chr6D 60456200 60457098 898 True 1282 1282 92.572 4 894 1 chr6D.!!$R1 890
8 TraesCS3A01G168300 chr7D 177571379 177572252 873 True 1275 1275 92.978 5 882 1 chr7D.!!$R1 877
9 TraesCS3A01G168300 chr1B 302037544 302038425 881 True 1267 1267 92.672 5 884 1 chr1B.!!$R1 879
10 TraesCS3A01G168300 chr5B 230013153 230014048 895 False 1251 1251 91.982 5 894 1 chr5B.!!$F1 889
11 TraesCS3A01G168300 chr2B 32182677 32183576 899 True 1249 1249 91.898 5 895 1 chr2B.!!$R1 890

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
950 977 0.526662 ATCTTCTCCACACGGACGAC 59.473 55.0 0.0 0.0 35.91 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2104 2158 0.512952 CAACGCTGCTTCGCTAAGTT 59.487 50.0 0.0 0.0 34.99 2.66 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
452 463 9.899226 ATAATTTATAGCGCAAGATCCTTTTTC 57.101 29.630 11.47 0.00 43.02 2.29
898 925 9.653287 TCTTTTGCTAGTGTATATATATGTGCC 57.347 33.333 5.44 0.00 0.00 5.01
899 926 8.786826 TTTTGCTAGTGTATATATATGTGCCC 57.213 34.615 5.44 0.00 0.00 5.36
900 927 7.489239 TTGCTAGTGTATATATATGTGCCCA 57.511 36.000 5.44 0.00 0.00 5.36
901 928 7.489239 TGCTAGTGTATATATATGTGCCCAA 57.511 36.000 5.44 0.00 0.00 4.12
902 929 8.089625 TGCTAGTGTATATATATGTGCCCAAT 57.910 34.615 5.44 0.00 0.00 3.16
903 930 7.986889 TGCTAGTGTATATATATGTGCCCAATG 59.013 37.037 5.44 0.00 0.00 2.82
904 931 7.041780 GCTAGTGTATATATATGTGCCCAATGC 60.042 40.741 5.44 0.00 41.77 3.56
914 941 3.772619 GCCCAATGCAGCATCAATT 57.227 47.368 8.77 0.00 40.77 2.32
915 942 2.894763 GCCCAATGCAGCATCAATTA 57.105 45.000 8.77 0.00 40.77 1.40
916 943 3.396260 GCCCAATGCAGCATCAATTAT 57.604 42.857 8.77 0.00 40.77 1.28
917 944 3.735591 GCCCAATGCAGCATCAATTATT 58.264 40.909 8.77 0.00 40.77 1.40
918 945 4.885413 GCCCAATGCAGCATCAATTATTA 58.115 39.130 8.77 0.00 40.77 0.98
919 946 5.484715 GCCCAATGCAGCATCAATTATTAT 58.515 37.500 8.77 0.00 40.77 1.28
920 947 5.579511 GCCCAATGCAGCATCAATTATTATC 59.420 40.000 8.77 0.00 40.77 1.75
921 948 5.803461 CCCAATGCAGCATCAATTATTATCG 59.197 40.000 8.77 0.00 0.00 2.92
922 949 6.349528 CCCAATGCAGCATCAATTATTATCGA 60.350 38.462 8.77 0.00 0.00 3.59
923 950 7.255569 CCAATGCAGCATCAATTATTATCGAT 58.744 34.615 8.77 2.16 0.00 3.59
924 951 7.220108 CCAATGCAGCATCAATTATTATCGATG 59.780 37.037 8.77 0.00 38.61 3.84
932 959 8.975410 CATCAATTATTATCGATGCACCAAAT 57.025 30.769 8.54 0.96 0.00 2.32
933 960 9.069078 CATCAATTATTATCGATGCACCAAATC 57.931 33.333 8.54 0.00 0.00 2.17
934 961 8.394971 TCAATTATTATCGATGCACCAAATCT 57.605 30.769 8.54 0.00 0.00 2.40
935 962 8.849168 TCAATTATTATCGATGCACCAAATCTT 58.151 29.630 8.54 0.00 0.00 2.40
936 963 9.121517 CAATTATTATCGATGCACCAAATCTTC 57.878 33.333 8.54 0.00 0.00 2.87
937 964 8.627208 ATTATTATCGATGCACCAAATCTTCT 57.373 30.769 8.54 0.00 0.00 2.85
938 965 5.991328 TTATCGATGCACCAAATCTTCTC 57.009 39.130 8.54 0.00 0.00 2.87
939 966 2.632377 TCGATGCACCAAATCTTCTCC 58.368 47.619 0.00 0.00 0.00 3.71
940 967 2.027285 TCGATGCACCAAATCTTCTCCA 60.027 45.455 0.00 0.00 0.00 3.86
941 968 2.096496 CGATGCACCAAATCTTCTCCAC 59.904 50.000 0.00 0.00 0.00 4.02
942 969 2.655090 TGCACCAAATCTTCTCCACA 57.345 45.000 0.00 0.00 0.00 4.17
943 970 2.229792 TGCACCAAATCTTCTCCACAC 58.770 47.619 0.00 0.00 0.00 3.82
944 971 1.197721 GCACCAAATCTTCTCCACACG 59.802 52.381 0.00 0.00 0.00 4.49
945 972 1.806542 CACCAAATCTTCTCCACACGG 59.193 52.381 0.00 0.00 0.00 4.94
946 973 1.697432 ACCAAATCTTCTCCACACGGA 59.303 47.619 0.00 0.00 39.79 4.69
947 974 2.076863 CCAAATCTTCTCCACACGGAC 58.923 52.381 0.00 0.00 35.91 4.79
948 975 1.726791 CAAATCTTCTCCACACGGACG 59.273 52.381 0.00 0.00 35.91 4.79
949 976 1.254026 AATCTTCTCCACACGGACGA 58.746 50.000 0.00 0.00 35.91 4.20
950 977 0.526662 ATCTTCTCCACACGGACGAC 59.473 55.000 0.00 0.00 35.91 4.34
951 978 1.080705 CTTCTCCACACGGACGACC 60.081 63.158 0.00 0.00 35.91 4.79
952 979 2.488087 CTTCTCCACACGGACGACCC 62.488 65.000 0.00 0.00 35.91 4.46
1011 1038 1.973281 CCACACGATGCAGCCCTTT 60.973 57.895 0.00 0.00 0.00 3.11
1024 1051 2.978010 CCTTTTCGCGGCACACCT 60.978 61.111 6.13 0.00 0.00 4.00
1056 1083 0.625849 CCCTCAAGCAGGTACCCAAT 59.374 55.000 8.74 0.00 41.51 3.16
1065 1092 1.004745 CAGGTACCCAATCCACAGCTT 59.995 52.381 8.74 0.00 0.00 3.74
1069 1096 3.442625 GGTACCCAATCCACAGCTTTAAC 59.557 47.826 0.00 0.00 0.00 2.01
1525 1570 3.737172 CGGGCCCAAGTGCGAAAG 61.737 66.667 24.92 0.00 0.00 2.62
1527 1572 2.282180 GGCCCAAGTGCGAAAGGA 60.282 61.111 0.00 0.00 0.00 3.36
1570 1621 1.000607 GATCCAGCATTACTACGGCGA 60.001 52.381 16.62 0.00 0.00 5.54
1636 1687 2.750350 CAAGGCCTCGTGGTCCTT 59.250 61.111 19.85 19.85 44.73 3.36
1649 1700 0.106967 GGTCCTTGGATGGAGAAGGC 60.107 60.000 0.00 0.00 38.97 4.35
1651 1702 0.253347 TCCTTGGATGGAGAAGGCCT 60.253 55.000 0.00 0.00 38.97 5.19
1657 1708 1.753368 GATGGAGAAGGCCTCGAGGG 61.753 65.000 32.06 14.53 42.89 4.30
1703 1754 1.941668 GCGGTGAAGGAGTTCTTGGAG 60.942 57.143 0.00 0.00 35.50 3.86
1799 1853 2.420022 GAGTGTGTTCGCCAAAGCATAT 59.580 45.455 0.00 0.00 39.83 1.78
1824 1878 4.870426 TCAAAGTTCAGAGAACACAGTGAC 59.130 41.667 7.81 0.87 0.00 3.67
1834 1888 3.509967 AGAACACAGTGACGATGGATGTA 59.490 43.478 7.81 0.00 0.00 2.29
1977 2031 0.248289 ATTTTGCTCCAGTGCCATGC 59.752 50.000 0.00 0.00 0.00 4.06
2079 2133 5.094429 TGTGATGTTTTGTTCTGTCATCG 57.906 39.130 0.00 0.00 38.06 3.84
2080 2134 3.908382 GTGATGTTTTGTTCTGTCATCGC 59.092 43.478 0.00 0.00 38.06 4.58
2081 2135 3.058293 TGATGTTTTGTTCTGTCATCGCC 60.058 43.478 0.00 0.00 38.06 5.54
2082 2136 2.293170 TGTTTTGTTCTGTCATCGCCA 58.707 42.857 0.00 0.00 0.00 5.69
2083 2137 2.884012 TGTTTTGTTCTGTCATCGCCAT 59.116 40.909 0.00 0.00 0.00 4.40
2139 2194 3.005261 AGCGTTGACTGGCTAGATAGATG 59.995 47.826 3.17 0.00 37.83 2.90
2143 2198 4.862902 TGACTGGCTAGATAGATGAAGC 57.137 45.455 3.17 0.00 0.00 3.86
2144 2199 4.218312 TGACTGGCTAGATAGATGAAGCA 58.782 43.478 3.17 0.00 36.68 3.91
2145 2200 4.837298 TGACTGGCTAGATAGATGAAGCAT 59.163 41.667 3.17 0.00 36.68 3.79
2146 2201 5.149973 ACTGGCTAGATAGATGAAGCATG 57.850 43.478 3.17 0.00 36.68 4.06
2147 2202 4.837298 ACTGGCTAGATAGATGAAGCATGA 59.163 41.667 3.17 0.00 36.68 3.07
2148 2203 5.306419 ACTGGCTAGATAGATGAAGCATGAA 59.694 40.000 3.17 0.00 36.68 2.57
2149 2204 5.791666 TGGCTAGATAGATGAAGCATGAAG 58.208 41.667 0.00 0.00 36.68 3.02
2150 2205 5.177326 GGCTAGATAGATGAAGCATGAAGG 58.823 45.833 0.00 0.00 36.68 3.46
2151 2206 5.279910 GGCTAGATAGATGAAGCATGAAGGT 60.280 44.000 0.00 0.00 36.68 3.50
2152 2207 6.071108 GGCTAGATAGATGAAGCATGAAGGTA 60.071 42.308 0.00 0.00 36.68 3.08
2153 2208 7.364585 GGCTAGATAGATGAAGCATGAAGGTAT 60.365 40.741 0.00 0.00 36.68 2.73
2154 2209 8.690884 GCTAGATAGATGAAGCATGAAGGTATA 58.309 37.037 0.00 0.00 35.05 1.47
2159 2214 7.603180 AGATGAAGCATGAAGGTATAGTACA 57.397 36.000 0.00 0.00 0.00 2.90
2185 2240 6.942576 ACTTAAGTGAGGTTATGTTTGCTGAT 59.057 34.615 7.48 0.00 0.00 2.90
2190 2245 5.126061 GTGAGGTTATGTTTGCTGATCCAAT 59.874 40.000 0.00 0.00 0.00 3.16
2204 2259 5.066893 GCTGATCCAATTGCATTTAGTCAGA 59.933 40.000 21.45 6.74 34.10 3.27
2218 2273 6.959639 TTTAGTCAGAACTTTGCCAAGAAT 57.040 33.333 4.25 0.00 36.92 2.40
2224 2279 8.866140 AGTCAGAACTTTGCCAAGAATACCTTG 61.866 40.741 4.25 0.00 41.49 3.61
2237 2292 5.675538 AGAATACCTTGAGATTTCTTCCCG 58.324 41.667 0.00 0.00 0.00 5.14
2238 2293 2.115343 ACCTTGAGATTTCTTCCCGC 57.885 50.000 0.00 0.00 0.00 6.13
2239 2294 1.009829 CCTTGAGATTTCTTCCCGCG 58.990 55.000 0.00 0.00 0.00 6.46
2309 2369 9.512588 AGAAATGTTCAAAATCTGTCAGACTAT 57.487 29.630 4.21 0.00 0.00 2.12
2310 2370 9.552114 GAAATGTTCAAAATCTGTCAGACTATG 57.448 33.333 4.21 4.61 0.00 2.23
2311 2371 8.853077 AATGTTCAAAATCTGTCAGACTATGA 57.147 30.769 4.21 6.91 34.79 2.15
2312 2372 8.853077 ATGTTCAAAATCTGTCAGACTATGAA 57.147 30.769 16.32 16.32 40.43 2.57
2313 2373 8.315391 TGTTCAAAATCTGTCAGACTATGAAG 57.685 34.615 18.93 3.81 40.43 3.02
2314 2374 7.388776 TGTTCAAAATCTGTCAGACTATGAAGG 59.611 37.037 18.93 2.30 40.43 3.46
2315 2375 7.009179 TCAAAATCTGTCAGACTATGAAGGT 57.991 36.000 4.21 0.00 40.43 3.50
2316 2376 8.134202 TCAAAATCTGTCAGACTATGAAGGTA 57.866 34.615 4.21 0.00 40.43 3.08
2317 2377 8.762645 TCAAAATCTGTCAGACTATGAAGGTAT 58.237 33.333 4.21 0.00 40.43 2.73
2318 2378 8.824781 CAAAATCTGTCAGACTATGAAGGTATG 58.175 37.037 4.21 0.00 40.43 2.39
2319 2379 7.904558 AATCTGTCAGACTATGAAGGTATGA 57.095 36.000 4.21 0.00 40.43 2.15
2320 2380 7.904558 ATCTGTCAGACTATGAAGGTATGAA 57.095 36.000 4.21 0.00 40.43 2.57
2352 2412 2.685100 ACCAGCTAGCTTTCAACGTAC 58.315 47.619 16.46 0.00 0.00 3.67
2392 2452 3.300765 AGCAGCAAACTGGCCTGC 61.301 61.111 9.95 8.17 44.63 4.85
2413 2473 5.192927 TGCCCATCTTACATCTTACAAAGG 58.807 41.667 0.00 0.00 0.00 3.11
2415 2475 5.885912 GCCCATCTTACATCTTACAAAGGAA 59.114 40.000 0.00 0.00 0.00 3.36
2416 2476 6.547510 GCCCATCTTACATCTTACAAAGGAAT 59.452 38.462 0.00 0.00 0.00 3.01
2437 2497 4.521130 TGACTATGGATTATCGGCTCAC 57.479 45.455 0.00 0.00 0.00 3.51
2443 2503 2.698274 TGGATTATCGGCTCACTGCTAA 59.302 45.455 0.00 0.00 42.39 3.09
2451 2511 4.320023 TCGGCTCACTGCTAATTTTAACA 58.680 39.130 0.00 0.00 42.39 2.41
2546 2653 1.672898 GCCCCAGCAAAGCAAATGA 59.327 52.632 0.00 0.00 39.53 2.57
2547 2654 0.035176 GCCCCAGCAAAGCAAATGAA 59.965 50.000 0.00 0.00 39.53 2.57
2556 2663 3.795877 CAAAGCAAATGAACAACACCCT 58.204 40.909 0.00 0.00 0.00 4.34
2639 5288 1.468565 CCACCAAGAAATGCAGATGCG 60.469 52.381 0.00 0.00 45.83 4.73
2677 5326 1.839994 TGAGGAGCCTCATTTCGGATT 59.160 47.619 15.01 0.00 46.80 3.01
2684 5333 4.019174 AGCCTCATTTCGGATTCACAAAT 58.981 39.130 0.00 0.00 0.00 2.32
2685 5334 5.192927 AGCCTCATTTCGGATTCACAAATA 58.807 37.500 0.00 0.00 0.00 1.40
2686 5335 5.066505 AGCCTCATTTCGGATTCACAAATAC 59.933 40.000 0.00 0.00 0.00 1.89
2704 5353 6.986817 ACAAATACTATCACTTTCCCTGATCG 59.013 38.462 0.00 0.00 30.76 3.69
2722 5371 0.179240 CGAATCTGCGACAGTTGCAC 60.179 55.000 11.83 1.26 37.44 4.57
2744 5393 2.037251 TGTCCAGGAAACTCTCTTTCGG 59.963 50.000 0.00 0.00 40.21 4.30
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
452 463 1.006102 GGATCACCGCCGGTATGAG 60.006 63.158 9.25 0.00 32.11 2.90
551 563 0.102120 CTGTTGTTTTTCCCTGCGCA 59.898 50.000 10.98 10.98 0.00 6.09
552 564 0.383949 TCTGTTGTTTTTCCCTGCGC 59.616 50.000 0.00 0.00 0.00 6.09
896 923 2.894763 TAATTGATGCTGCATTGGGC 57.105 45.000 17.36 4.32 45.13 5.36
897 924 5.803461 CGATAATAATTGATGCTGCATTGGG 59.197 40.000 17.36 0.00 0.00 4.12
898 925 6.614160 TCGATAATAATTGATGCTGCATTGG 58.386 36.000 17.36 0.00 0.00 3.16
899 926 8.104222 CATCGATAATAATTGATGCTGCATTG 57.896 34.615 17.36 1.79 43.72 2.82
908 935 9.017509 AGATTTGGTGCATCGATAATAATTGAT 57.982 29.630 0.00 0.00 36.77 2.57
909 936 8.394971 AGATTTGGTGCATCGATAATAATTGA 57.605 30.769 0.00 0.00 0.00 2.57
910 937 9.121517 GAAGATTTGGTGCATCGATAATAATTG 57.878 33.333 0.00 0.00 0.00 2.32
911 938 9.071276 AGAAGATTTGGTGCATCGATAATAATT 57.929 29.630 0.00 0.00 0.00 1.40
912 939 8.627208 AGAAGATTTGGTGCATCGATAATAAT 57.373 30.769 0.00 0.00 0.00 1.28
913 940 7.173218 GGAGAAGATTTGGTGCATCGATAATAA 59.827 37.037 0.00 0.00 0.00 1.40
914 941 6.650807 GGAGAAGATTTGGTGCATCGATAATA 59.349 38.462 0.00 0.00 0.00 0.98
915 942 5.471456 GGAGAAGATTTGGTGCATCGATAAT 59.529 40.000 0.00 0.00 0.00 1.28
916 943 4.816385 GGAGAAGATTTGGTGCATCGATAA 59.184 41.667 0.00 0.00 0.00 1.75
917 944 4.141733 TGGAGAAGATTTGGTGCATCGATA 60.142 41.667 0.00 0.00 0.00 2.92
918 945 3.209410 GGAGAAGATTTGGTGCATCGAT 58.791 45.455 0.00 0.00 0.00 3.59
919 946 2.027285 TGGAGAAGATTTGGTGCATCGA 60.027 45.455 0.00 0.00 0.00 3.59
920 947 2.096496 GTGGAGAAGATTTGGTGCATCG 59.904 50.000 0.00 0.00 0.00 3.84
921 948 3.084039 TGTGGAGAAGATTTGGTGCATC 58.916 45.455 0.00 0.00 0.00 3.91
922 949 2.821969 GTGTGGAGAAGATTTGGTGCAT 59.178 45.455 0.00 0.00 0.00 3.96
923 950 2.229792 GTGTGGAGAAGATTTGGTGCA 58.770 47.619 0.00 0.00 0.00 4.57
924 951 1.197721 CGTGTGGAGAAGATTTGGTGC 59.802 52.381 0.00 0.00 0.00 5.01
925 952 1.806542 CCGTGTGGAGAAGATTTGGTG 59.193 52.381 0.00 0.00 37.49 4.17
926 953 1.697432 TCCGTGTGGAGAAGATTTGGT 59.303 47.619 0.00 0.00 40.17 3.67
927 954 2.472695 TCCGTGTGGAGAAGATTTGG 57.527 50.000 0.00 0.00 40.17 3.28
956 983 2.898840 AGGATGCAATGCGCCTCG 60.899 61.111 12.73 0.00 40.91 4.63
957 984 2.719979 CAGGATGCAATGCGCCTC 59.280 61.111 15.14 5.28 40.91 4.70
1024 1051 2.094757 TTGAGGGACGCGAAGAAGCA 62.095 55.000 15.93 0.00 36.85 3.91
1056 1083 1.073284 GTGAGGGGTTAAAGCTGTGGA 59.927 52.381 0.00 0.00 0.00 4.02
1088 1115 4.332543 TCAGAAGGGGGAGGCGGT 62.333 66.667 0.00 0.00 0.00 5.68
1199 1226 1.078497 GGATGCGGTCATGGTGTCA 60.078 57.895 0.00 0.00 31.96 3.58
1525 1570 0.906066 GTCCACCCTCCTCTTCTTCC 59.094 60.000 0.00 0.00 0.00 3.46
1527 1572 0.905337 CCGTCCACCCTCCTCTTCTT 60.905 60.000 0.00 0.00 0.00 2.52
1636 1687 1.001631 TCGAGGCCTTCTCCATCCA 59.998 57.895 6.77 0.00 39.30 3.41
1649 1700 2.494530 GGCTGCTCTACCCTCGAGG 61.495 68.421 25.36 25.36 43.78 4.63
1651 1702 0.687757 AATGGCTGCTCTACCCTCGA 60.688 55.000 0.00 0.00 0.00 4.04
1778 1832 0.593128 ATGCTTTGGCGAACACACTC 59.407 50.000 0.00 0.00 42.25 3.51
1799 1853 5.937540 TCACTGTGTTCTCTGAACTTTGAAA 59.062 36.000 7.79 0.00 0.00 2.69
1824 1878 5.801350 ACATTCAGTTTGTACATCCATCG 57.199 39.130 0.00 0.00 0.00 3.84
1977 2031 2.731572 AGCATGAAGATGAACCCAAGG 58.268 47.619 0.00 0.00 0.00 3.61
2033 2087 6.528014 TGTTTTTGCATATCTTGTTGCTTG 57.472 33.333 0.00 0.00 39.60 4.01
2068 2122 0.804364 TTGCATGGCGATGACAGAAC 59.196 50.000 13.46 0.00 0.00 3.01
2104 2158 0.512952 CAACGCTGCTTCGCTAAGTT 59.487 50.000 0.00 0.00 34.99 2.66
2119 2174 4.837896 TCATCTATCTAGCCAGTCAACG 57.162 45.455 0.00 0.00 0.00 4.10
2139 2194 9.595823 TTAAGTTGTACTATACCTTCATGCTTC 57.404 33.333 0.00 0.00 0.00 3.86
2145 2200 8.746530 CCTCACTTAAGTTGTACTATACCTTCA 58.253 37.037 5.07 0.00 0.00 3.02
2146 2201 8.747471 ACCTCACTTAAGTTGTACTATACCTTC 58.253 37.037 5.07 0.00 0.00 3.46
2147 2202 8.661752 ACCTCACTTAAGTTGTACTATACCTT 57.338 34.615 5.07 0.00 0.00 3.50
2148 2203 8.661752 AACCTCACTTAAGTTGTACTATACCT 57.338 34.615 5.07 0.00 0.00 3.08
2154 2209 9.052759 CAAACATAACCTCACTTAAGTTGTACT 57.947 33.333 5.07 0.00 0.00 2.73
2155 2210 7.801783 GCAAACATAACCTCACTTAAGTTGTAC 59.198 37.037 5.07 0.00 0.00 2.90
2159 2214 6.770785 TCAGCAAACATAACCTCACTTAAGTT 59.229 34.615 5.07 0.00 0.00 2.66
2185 2240 6.899393 AAGTTCTGACTAAATGCAATTGGA 57.101 33.333 7.72 4.46 33.10 3.53
2190 2245 4.340666 TGGCAAAGTTCTGACTAAATGCAA 59.659 37.500 0.00 1.67 39.71 4.08
2218 2273 2.418197 CGCGGGAAGAAATCTCAAGGTA 60.418 50.000 0.00 0.00 0.00 3.08
2224 2279 3.824414 TTTTTCGCGGGAAGAAATCTC 57.176 42.857 14.60 0.00 37.43 2.75
2309 2369 8.933653 TGGTAGTCATCATAATTCATACCTTCA 58.066 33.333 0.00 0.00 33.99 3.02
2310 2370 9.429359 CTGGTAGTCATCATAATTCATACCTTC 57.571 37.037 0.00 0.00 33.99 3.46
2311 2371 7.880195 GCTGGTAGTCATCATAATTCATACCTT 59.120 37.037 0.00 0.00 33.99 3.50
2312 2372 7.236432 AGCTGGTAGTCATCATAATTCATACCT 59.764 37.037 0.00 0.00 33.99 3.08
2313 2373 7.390027 AGCTGGTAGTCATCATAATTCATACC 58.610 38.462 0.00 0.00 33.56 2.73
2314 2374 9.579768 CTAGCTGGTAGTCATCATAATTCATAC 57.420 37.037 5.74 0.00 0.00 2.39
2315 2375 8.253810 GCTAGCTGGTAGTCATCATAATTCATA 58.746 37.037 7.70 0.00 0.00 2.15
2316 2376 7.038445 AGCTAGCTGGTAGTCATCATAATTCAT 60.038 37.037 18.57 0.00 0.00 2.57
2317 2377 6.268617 AGCTAGCTGGTAGTCATCATAATTCA 59.731 38.462 18.57 0.00 0.00 2.57
2318 2378 6.696411 AGCTAGCTGGTAGTCATCATAATTC 58.304 40.000 18.57 0.00 0.00 2.17
2319 2379 6.678568 AGCTAGCTGGTAGTCATCATAATT 57.321 37.500 18.57 0.00 0.00 1.40
2320 2380 6.678568 AAGCTAGCTGGTAGTCATCATAAT 57.321 37.500 20.16 0.00 0.00 1.28
2352 2412 7.118245 TGCTGACTAATAATTTGGATATCGCAG 59.882 37.037 0.00 0.00 0.00 5.18
2392 2452 7.775093 TCATTCCTTTGTAAGATGTAAGATGGG 59.225 37.037 0.00 0.00 0.00 4.00
2413 2473 5.578727 GTGAGCCGATAATCCATAGTCATTC 59.421 44.000 0.00 0.00 0.00 2.67
2415 2475 4.774726 AGTGAGCCGATAATCCATAGTCAT 59.225 41.667 0.00 0.00 0.00 3.06
2416 2476 4.021981 CAGTGAGCCGATAATCCATAGTCA 60.022 45.833 0.00 0.00 0.00 3.41
2437 2497 7.035612 GGGTCCTCAAATGTTAAAATTAGCAG 58.964 38.462 0.00 0.00 0.00 4.24
2443 2503 9.547279 AATTCTAGGGTCCTCAAATGTTAAAAT 57.453 29.630 0.00 0.00 0.00 1.82
2451 2511 4.228210 TCTGCAATTCTAGGGTCCTCAAAT 59.772 41.667 0.00 0.00 0.00 2.32
2482 2542 9.433153 AGAGTATCGTCTCATATACGTTTCATA 57.567 33.333 0.00 0.00 42.67 2.15
2483 2543 8.325421 AGAGTATCGTCTCATATACGTTTCAT 57.675 34.615 0.00 0.00 42.67 2.57
2485 2545 8.706936 TGTAGAGTATCGTCTCATATACGTTTC 58.293 37.037 0.00 0.00 42.67 2.78
2486 2546 8.599055 TGTAGAGTATCGTCTCATATACGTTT 57.401 34.615 0.00 0.00 42.67 3.60
2487 2547 7.871973 ACTGTAGAGTATCGTCTCATATACGTT 59.128 37.037 0.00 0.00 42.67 3.99
2488 2548 7.377398 ACTGTAGAGTATCGTCTCATATACGT 58.623 38.462 0.00 0.00 42.67 3.57
2546 2653 3.118920 GCCAAAAACAGTAGGGTGTTGTT 60.119 43.478 0.00 0.00 39.82 2.83
2547 2654 2.429250 GCCAAAAACAGTAGGGTGTTGT 59.571 45.455 0.00 0.00 39.82 3.32
2598 5247 9.423964 TGGTGGTTAAGTAGAAAGGTAAAATTT 57.576 29.630 0.00 0.00 0.00 1.82
2611 5260 5.705441 TCTGCATTTCTTGGTGGTTAAGTAG 59.295 40.000 0.00 0.00 0.00 2.57
2617 5266 2.028748 GCATCTGCATTTCTTGGTGGTT 60.029 45.455 0.00 0.00 41.59 3.67
2677 5326 7.252612 TCAGGGAAAGTGATAGTATTTGTGA 57.747 36.000 0.00 0.00 0.00 3.58
2684 5333 6.778069 AGATTCGATCAGGGAAAGTGATAGTA 59.222 38.462 0.00 0.00 34.69 1.82
2685 5334 5.600484 AGATTCGATCAGGGAAAGTGATAGT 59.400 40.000 0.00 0.00 34.69 2.12
2686 5335 5.925397 CAGATTCGATCAGGGAAAGTGATAG 59.075 44.000 0.00 0.00 34.69 2.08
2704 5353 3.664930 GTGCAACTGTCGCAGATTC 57.335 52.632 12.77 0.00 40.78 2.52
2722 5371 3.321497 CGAAAGAGAGTTTCCTGGACAG 58.679 50.000 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.