Multiple sequence alignment - TraesCS7A01G394600

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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 TraesCS7A01G394600 chr7A 100.000 2094 0 0 559 2652 572876321 572874228 0.000000e+00 3868.0
1 TraesCS7A01G394600 chr7A 85.775 1181 99 35 762 1888 573069984 573068819 0.000000e+00 1186.0
2 TraesCS7A01G394600 chr7A 100.000 276 0 0 1 276 572876879 572876604 6.550000e-141 510.0
3 TraesCS7A01G394600 chr7B 84.970 1976 168 60 759 2652 533309730 533307802 0.000000e+00 1884.0
4 TraesCS7A01G394600 chr7B 88.037 978 78 22 944 1899 533373070 533372110 0.000000e+00 1122.0
5 TraesCS7A01G394600 chr7B 88.546 908 70 18 934 1832 533552691 533551809 0.000000e+00 1070.0
6 TraesCS7A01G394600 chr7B 97.917 48 1 0 559 606 533310928 533310881 1.690000e-12 84.2
7 TraesCS7A01G394600 chr7B 89.796 49 3 2 785 831 533373256 533373208 7.930000e-06 62.1
8 TraesCS7A01G394600 chr7B 76.190 147 18 10 770 900 533553245 533553100 7.930000e-06 62.1
9 TraesCS7A01G394600 chr7D 90.859 1258 74 15 616 1838 505143873 505142622 0.000000e+00 1648.0
10 TraesCS7A01G394600 chr7D 86.940 1049 85 36 837 1859 505329756 505328734 0.000000e+00 1131.0
11 TraesCS7A01G394600 chr7D 91.327 761 59 7 932 1688 505589848 505589091 0.000000e+00 1033.0
12 TraesCS7A01G394600 chr7D 84.888 536 40 20 1827 2338 505141950 505141432 1.100000e-138 503.0
13 TraesCS7A01G394600 chr7D 85.239 481 32 16 616 1062 505351887 505351412 2.410000e-125 459.0
14 TraesCS7A01G394600 chr7D 88.258 264 17 5 1 259 505144908 505144654 1.190000e-78 303.0
15 TraesCS7A01G394600 chr7D 86.641 262 23 6 1 259 505352777 505352525 2.010000e-71 279.0
16 TraesCS7A01G394600 chr7D 82.353 289 14 8 2381 2652 505141350 505141082 1.600000e-52 217.0
17 TraesCS7A01G394600 chr6D 74.940 419 73 26 1110 1512 134283808 134284210 2.110000e-36 163.0
18 TraesCS7A01G394600 chr6D 74.004 477 86 31 1056 1512 134688943 134689401 2.730000e-35 159.0
19 TraesCS7A01G394600 chr5A 97.849 93 0 1 2246 2336 444527002 444526910 2.730000e-35 159.0
20 TraesCS7A01G394600 chr5D 95.918 98 2 1 2243 2338 347450007 347450104 9.830000e-35 158.0
21 TraesCS7A01G394600 chr3D 96.809 94 3 0 2249 2342 26569367 26569460 9.830000e-35 158.0
22 TraesCS7A01G394600 chr3D 95.050 101 3 1 2249 2349 26588437 26588339 9.830000e-35 158.0
23 TraesCS7A01G394600 chr2D 95.960 99 1 3 2249 2347 188839510 188839605 9.830000e-35 158.0
24 TraesCS7A01G394600 chr3B 95.000 100 3 2 2249 2347 44401500 44401598 3.530000e-34 156.0
25 TraesCS7A01G394600 chr3A 89.231 130 6 6 2249 2377 36673737 36673615 3.530000e-34 156.0


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 TraesCS7A01G394600 chr7A 572874228 572876879 2651 True 2189.00 3868 100.0000 1 2652 2 chr7A.!!$R2 2651
1 TraesCS7A01G394600 chr7A 573068819 573069984 1165 True 1186.00 1186 85.7750 762 1888 1 chr7A.!!$R1 1126
2 TraesCS7A01G394600 chr7B 533307802 533310928 3126 True 984.10 1884 91.4435 559 2652 2 chr7B.!!$R1 2093
3 TraesCS7A01G394600 chr7B 533372110 533373256 1146 True 592.05 1122 88.9165 785 1899 2 chr7B.!!$R2 1114
4 TraesCS7A01G394600 chr7B 533551809 533553245 1436 True 566.05 1070 82.3680 770 1832 2 chr7B.!!$R3 1062
5 TraesCS7A01G394600 chr7D 505328734 505329756 1022 True 1131.00 1131 86.9400 837 1859 1 chr7D.!!$R1 1022
6 TraesCS7A01G394600 chr7D 505589091 505589848 757 True 1033.00 1033 91.3270 932 1688 1 chr7D.!!$R2 756
7 TraesCS7A01G394600 chr7D 505141082 505144908 3826 True 667.75 1648 86.5895 1 2652 4 chr7D.!!$R3 2651
8 TraesCS7A01G394600 chr7D 505351412 505352777 1365 True 369.00 459 85.9400 1 1062 2 chr7D.!!$R4 1061

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
906 2336 0.32336 AAAGCAAGGGAGCGGCAATA 60.323 50.0 1.45 0.0 40.15 1.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 5057 0.108804 CGTACAATCTGGTCGGCACT 60.109 55.0 0.0 0.0 0.0 4.4 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
38 39 1.115467 ACCAGAAGCGGATCCAGTAG 58.885 55.000 13.41 0.00 0.00 2.57
41 42 2.366916 CCAGAAGCGGATCCAGTAGAAT 59.633 50.000 13.41 0.00 0.00 2.40
42 43 3.181461 CCAGAAGCGGATCCAGTAGAATT 60.181 47.826 13.41 0.00 0.00 2.17
72 73 5.309323 TGGCTTCATCTTTCGTTAATTGG 57.691 39.130 0.00 0.00 0.00 3.16
73 74 5.007034 TGGCTTCATCTTTCGTTAATTGGA 58.993 37.500 0.00 0.00 0.00 3.53
74 75 5.475220 TGGCTTCATCTTTCGTTAATTGGAA 59.525 36.000 0.00 0.00 0.00 3.53
75 76 6.015856 TGGCTTCATCTTTCGTTAATTGGAAA 60.016 34.615 0.00 0.00 0.00 3.13
76 77 7.035612 GGCTTCATCTTTCGTTAATTGGAAAT 58.964 34.615 0.00 0.00 32.25 2.17
77 78 7.545615 GGCTTCATCTTTCGTTAATTGGAAATT 59.454 33.333 0.00 0.00 32.25 1.82
78 79 8.375465 GCTTCATCTTTCGTTAATTGGAAATTG 58.625 33.333 0.00 0.00 32.25 2.32
79 80 8.755696 TTCATCTTTCGTTAATTGGAAATTGG 57.244 30.769 0.00 0.00 32.25 3.16
92 93 4.970711 TGGAAATTGGAATGCATGTGTTT 58.029 34.783 0.00 0.00 0.00 2.83
106 107 5.401972 TGCATGTGTTTTCTTTATCTTTGCG 59.598 36.000 0.00 0.00 0.00 4.85
108 109 6.398935 GCATGTGTTTTCTTTATCTTTGCGAC 60.399 38.462 0.00 0.00 0.00 5.19
113 114 8.068380 GTGTTTTCTTTATCTTTGCGACTAGTT 58.932 33.333 0.00 0.00 0.00 2.24
129 130 4.007659 ACTAGTTTATTGGCCGGTTTCTG 58.992 43.478 1.90 0.00 0.00 3.02
131 132 0.523966 TTTATTGGCCGGTTTCTGCG 59.476 50.000 1.90 0.00 0.00 5.18
140 141 2.290641 GCCGGTTTCTGCGATGAAATAT 59.709 45.455 1.90 0.00 38.09 1.28
145 146 5.559035 CGGTTTCTGCGATGAAATATTCTCC 60.559 44.000 6.55 2.61 38.09 3.71
158 159 0.831307 ATTCTCCGGTTCCTAGGTGC 59.169 55.000 9.08 2.68 0.00 5.01
170 171 4.955811 TCCTAGGTGCATATACACTTGG 57.044 45.455 9.08 0.62 40.52 3.61
268 636 7.390996 TGTTATACCTAAAATGTTTTGCGAGGA 59.609 33.333 10.84 0.00 31.17 3.71
272 640 5.983118 ACCTAAAATGTTTTGCGAGGAAAAG 59.017 36.000 10.84 0.00 31.17 2.27
275 643 7.384932 CCTAAAATGTTTTGCGAGGAAAAGAAT 59.615 33.333 2.80 0.00 29.06 2.40
603 974 8.880991 TGGCTAACCTTTTTACACCAATATAA 57.119 30.769 0.00 0.00 36.63 0.98
604 975 8.741841 TGGCTAACCTTTTTACACCAATATAAC 58.258 33.333 0.00 0.00 36.63 1.89
609 980 8.575649 ACCTTTTTACACCAATATAACAGAGG 57.424 34.615 0.00 0.00 0.00 3.69
612 983 9.238368 CTTTTTACACCAATATAACAGAGGGAA 57.762 33.333 0.00 0.00 0.00 3.97
614 985 8.746052 TTTACACCAATATAACAGAGGGAATG 57.254 34.615 0.00 0.00 0.00 2.67
650 1218 0.795698 TTGTCGCGATCACACCATTG 59.204 50.000 14.06 0.00 0.00 2.82
668 1236 5.649831 ACCATTGGCTCTCTAAGTGAAAATC 59.350 40.000 1.54 0.00 0.00 2.17
680 1248 5.975693 AAGTGAAAATCTTATTTGCCGGA 57.024 34.783 5.05 0.00 0.00 5.14
703 1944 5.607119 TTTCGAAGAACAAACTAGGATGC 57.393 39.130 0.00 0.00 45.90 3.91
715 1956 2.873472 ACTAGGATGCGTCTAACTCTCG 59.127 50.000 5.77 0.00 0.00 4.04
716 1957 1.752683 AGGATGCGTCTAACTCTCGT 58.247 50.000 5.77 0.00 0.00 4.18
726 2120 6.313164 TGCGTCTAACTCTCGTATATAGATGG 59.687 42.308 0.00 0.00 32.68 3.51
833 2235 9.143631 CTTTGGCAATAAATAAAGAAAGGAGTG 57.856 33.333 0.00 0.00 33.18 3.51
866 2292 0.457851 ACTGAGAATCGAGAAGGGCG 59.542 55.000 0.00 0.00 38.61 6.13
901 2331 1.903404 ACCAAAAGCAAGGGAGCGG 60.903 57.895 0.00 0.00 40.15 5.52
904 2334 1.832167 AAAAGCAAGGGAGCGGCAA 60.832 52.632 1.45 0.00 40.15 4.52
905 2335 1.187567 AAAAGCAAGGGAGCGGCAAT 61.188 50.000 1.45 0.00 40.15 3.56
906 2336 0.323360 AAAGCAAGGGAGCGGCAATA 60.323 50.000 1.45 0.00 40.15 1.90
909 2339 0.746659 GCAAGGGAGCGGCAATAAAT 59.253 50.000 1.45 0.00 0.00 1.40
911 2341 2.360801 GCAAGGGAGCGGCAATAAATAA 59.639 45.455 1.45 0.00 0.00 1.40
913 2343 4.610945 CAAGGGAGCGGCAATAAATAAAG 58.389 43.478 1.45 0.00 0.00 1.85
915 2345 4.532834 AGGGAGCGGCAATAAATAAAGAA 58.467 39.130 1.45 0.00 0.00 2.52
916 2346 4.953579 AGGGAGCGGCAATAAATAAAGAAA 59.046 37.500 1.45 0.00 0.00 2.52
917 2347 5.067805 AGGGAGCGGCAATAAATAAAGAAAG 59.932 40.000 1.45 0.00 0.00 2.62
918 2348 5.281727 GGAGCGGCAATAAATAAAGAAAGG 58.718 41.667 1.45 0.00 0.00 3.11
920 2350 6.136541 AGCGGCAATAAATAAAGAAAGGAG 57.863 37.500 1.45 0.00 0.00 3.69
921 2351 5.652452 AGCGGCAATAAATAAAGAAAGGAGT 59.348 36.000 1.45 0.00 0.00 3.85
922 2352 5.743872 GCGGCAATAAATAAAGAAAGGAGTG 59.256 40.000 0.00 0.00 0.00 3.51
1522 3349 1.592400 TTGGGGAGTACTCTGCGACG 61.592 60.000 21.88 0.00 32.69 5.12
1567 3394 3.958860 AAGAAGGCTGCCGTGGCT 61.959 61.111 12.97 5.84 45.04 4.75
1690 3522 7.013655 CCGAGTGATAAAATGGAAGGAAATCAT 59.986 37.037 0.00 0.00 0.00 2.45
1985 4551 2.319472 GCGCATGTCTTCTTTTTGTCC 58.681 47.619 0.30 0.00 0.00 4.02
1991 4557 2.685897 TGTCTTCTTTTTGTCCCCGTTG 59.314 45.455 0.00 0.00 0.00 4.10
1992 4558 2.686405 GTCTTCTTTTTGTCCCCGTTGT 59.314 45.455 0.00 0.00 0.00 3.32
1993 4559 2.685897 TCTTCTTTTTGTCCCCGTTGTG 59.314 45.455 0.00 0.00 0.00 3.33
1994 4560 2.131776 TCTTTTTGTCCCCGTTGTGT 57.868 45.000 0.00 0.00 0.00 3.72
1995 4561 2.018515 TCTTTTTGTCCCCGTTGTGTC 58.981 47.619 0.00 0.00 0.00 3.67
2042 4622 7.584396 ATTTAGGGGAGGAGACTTTAGAAAA 57.416 36.000 0.00 0.00 44.43 2.29
2043 4623 7.584396 TTTAGGGGAGGAGACTTTAGAAAAT 57.416 36.000 0.00 0.00 44.43 1.82
2049 4629 6.892456 GGGAGGAGACTTTAGAAAATGGAAAT 59.108 38.462 0.00 0.00 44.43 2.17
2050 4630 8.053355 GGGAGGAGACTTTAGAAAATGGAAATA 58.947 37.037 0.00 0.00 44.43 1.40
2079 4659 4.416533 GAGCATCTCTCGTGGCAG 57.583 61.111 0.00 0.00 31.20 4.85
2084 4664 2.432146 AGCATCTCTCGTGGCAGAATTA 59.568 45.455 0.00 0.00 0.00 1.40
2085 4665 2.799412 GCATCTCTCGTGGCAGAATTAG 59.201 50.000 0.00 0.00 0.00 1.73
2091 4671 1.086696 CGTGGCAGAATTAGTGGTGG 58.913 55.000 0.00 0.00 0.00 4.61
2110 4690 2.555325 TGGGTACGGATTAGCTATGTCG 59.445 50.000 0.00 1.42 0.00 4.35
2146 4729 3.228453 ACTTCAACTGACGGAGAAGGTA 58.772 45.455 18.63 0.00 41.25 3.08
2147 4730 3.005578 ACTTCAACTGACGGAGAAGGTAC 59.994 47.826 18.63 0.00 41.25 3.34
2149 4732 2.557056 TCAACTGACGGAGAAGGTACTG 59.443 50.000 0.00 0.00 40.86 2.74
2150 4733 1.546961 ACTGACGGAGAAGGTACTGG 58.453 55.000 0.00 0.00 40.86 4.00
2151 4734 1.203025 ACTGACGGAGAAGGTACTGGT 60.203 52.381 0.00 0.00 40.86 4.00
2178 4761 3.494850 CCAAACGGCAGGTGGATAT 57.505 52.632 3.20 0.00 34.05 1.63
2179 4762 1.024271 CCAAACGGCAGGTGGATATG 58.976 55.000 3.20 0.00 34.05 1.78
2180 4763 0.381801 CAAACGGCAGGTGGATATGC 59.618 55.000 0.00 0.00 41.80 3.14
2188 4771 0.106708 AGGTGGATATGCGCATCGTT 59.893 50.000 29.11 13.35 0.00 3.85
2213 4796 2.047844 CGCACAGGCTGCTACACT 60.048 61.111 15.89 0.00 44.64 3.55
2216 4799 1.079503 GCACAGGCTGCTACACTAAC 58.920 55.000 15.89 0.00 43.33 2.34
2235 4818 9.815936 ACACTAACAAATAAACTTTATACGCAC 57.184 29.630 0.00 0.00 0.00 5.34
2236 4819 9.269415 CACTAACAAATAAACTTTATACGCACC 57.731 33.333 0.00 0.00 0.00 5.01
2237 4820 9.223099 ACTAACAAATAAACTTTATACGCACCT 57.777 29.630 0.00 0.00 0.00 4.00
2245 4828 7.958053 AAACTTTATACGCACCTATATCACC 57.042 36.000 0.00 0.00 0.00 4.02
2331 4914 3.743521 TCAAATCCCACTCTTGACACAG 58.256 45.455 0.00 0.00 0.00 3.66
2334 4923 3.864789 ATCCCACTCTTGACACAGTTT 57.135 42.857 0.00 0.00 0.00 2.66
2375 4964 7.920160 ATTTGCTTCACCTTTTCTTTTTGAA 57.080 28.000 0.00 0.00 0.00 2.69
2376 4965 7.920160 TTTGCTTCACCTTTTCTTTTTGAAT 57.080 28.000 0.00 0.00 34.24 2.57
2377 4966 6.907206 TGCTTCACCTTTTCTTTTTGAATG 57.093 33.333 0.00 0.00 34.24 2.67
2378 4967 6.405538 TGCTTCACCTTTTCTTTTTGAATGT 58.594 32.000 0.00 0.00 34.24 2.71
2379 4968 7.551585 TGCTTCACCTTTTCTTTTTGAATGTA 58.448 30.769 0.00 0.00 34.24 2.29
2418 5049 0.591170 AATTTTGGTCTGTGCCGTCG 59.409 50.000 0.00 0.00 0.00 5.12
2421 5052 2.596553 TTTGGTCTGTGCCGTCGGTT 62.597 55.000 13.94 0.00 0.00 4.44
2422 5053 3.041940 GGTCTGTGCCGTCGGTTG 61.042 66.667 13.94 1.06 0.00 3.77
2423 5054 3.712881 GTCTGTGCCGTCGGTTGC 61.713 66.667 13.94 4.11 0.00 4.17
2424 5055 4.980805 TCTGTGCCGTCGGTTGCC 62.981 66.667 13.94 0.00 0.00 4.52
2441 5072 1.811266 CCGAGTGCCGACCAGATTG 60.811 63.158 0.00 0.00 41.76 2.67
2449 5080 1.403780 GCCGACCAGATTGTACGACTT 60.404 52.381 0.00 0.00 0.00 3.01
2451 5082 2.527100 CGACCAGATTGTACGACTTCC 58.473 52.381 0.00 0.00 0.00 3.46
2459 5090 0.803117 TGTACGACTTCCGCTGAGAG 59.197 55.000 0.00 0.00 43.32 3.20
2502 5134 2.583593 GAGCATCTCACCGACGCC 60.584 66.667 0.00 0.00 0.00 5.68
2586 5241 0.036022 GCAACAGCTCCTGGTCTTCT 59.964 55.000 0.00 0.00 35.51 2.85
2597 5252 3.196469 TCCTGGTCTTCTCAACATGCTAG 59.804 47.826 0.00 0.00 0.00 3.42
2598 5253 2.935201 CTGGTCTTCTCAACATGCTAGC 59.065 50.000 8.10 8.10 0.00 3.42
2600 5255 3.769300 TGGTCTTCTCAACATGCTAGCTA 59.231 43.478 17.23 2.58 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 1.403814 TCTACTGGATCCGCTTCTGG 58.596 55.000 7.39 0.00 0.00 3.86
42 43 5.841810 ACGAAAGATGAAGCCAATCAAAAA 58.158 33.333 0.00 0.00 32.06 1.94
72 73 6.790285 AGAAAACACATGCATTCCAATTTC 57.210 33.333 0.00 5.16 0.00 2.17
73 74 7.571080 AAAGAAAACACATGCATTCCAATTT 57.429 28.000 0.00 0.00 0.00 1.82
74 75 8.851541 ATAAAGAAAACACATGCATTCCAATT 57.148 26.923 0.00 0.00 0.00 2.32
75 76 8.316214 AGATAAAGAAAACACATGCATTCCAAT 58.684 29.630 0.00 0.00 0.00 3.16
76 77 7.669427 AGATAAAGAAAACACATGCATTCCAA 58.331 30.769 0.00 0.00 0.00 3.53
77 78 7.230849 AGATAAAGAAAACACATGCATTCCA 57.769 32.000 0.00 0.00 0.00 3.53
78 79 8.437742 CAAAGATAAAGAAAACACATGCATTCC 58.562 33.333 0.00 0.00 0.00 3.01
79 80 7.953710 GCAAAGATAAAGAAAACACATGCATTC 59.046 33.333 0.00 0.00 0.00 2.67
106 107 4.094442 CAGAAACCGGCCAATAAACTAGTC 59.906 45.833 0.00 0.00 0.00 2.59
108 109 3.181500 GCAGAAACCGGCCAATAAACTAG 60.181 47.826 0.00 0.00 0.00 2.57
113 114 0.321741 TCGCAGAAACCGGCCAATAA 60.322 50.000 0.00 0.00 0.00 1.40
129 130 3.186613 GGAACCGGAGAATATTTCATCGC 59.813 47.826 9.46 0.00 0.00 4.58
131 132 6.166982 CCTAGGAACCGGAGAATATTTCATC 58.833 44.000 9.46 0.00 0.00 2.92
140 141 0.543410 TGCACCTAGGAACCGGAGAA 60.543 55.000 17.98 0.00 0.00 2.87
145 146 3.321111 AGTGTATATGCACCTAGGAACCG 59.679 47.826 17.98 1.67 40.04 4.44
241 247 8.024285 CCTCGCAAAACATTTTAGGTATAACAA 58.976 33.333 0.00 0.00 0.00 2.83
612 983 8.635124 CGCGACAAACTTTTCATATAAAAACAT 58.365 29.630 0.00 0.00 0.00 2.71
614 985 8.206516 TCGCGACAAACTTTTCATATAAAAAC 57.793 30.769 3.71 0.00 0.00 2.43
634 1202 2.106074 GCCAATGGTGTGATCGCGA 61.106 57.895 13.09 13.09 0.00 5.87
650 1218 7.912773 GCAAATAAGATTTTCACTTAGAGAGCC 59.087 37.037 0.00 0.00 34.13 4.70
668 1236 4.875544 TCTTCGAAATCCGGCAAATAAG 57.124 40.909 0.00 0.00 39.14 1.73
680 1248 5.163854 CGCATCCTAGTTTGTTCTTCGAAAT 60.164 40.000 0.00 0.00 0.00 2.17
703 1944 7.040494 TCCCATCTATATACGAGAGTTAGACG 58.960 42.308 0.00 0.00 46.40 4.18
743 2137 9.021807 GCCTGAGTATAACTGTATAAGGATACA 57.978 37.037 0.00 0.00 44.60 2.29
833 2235 1.003580 TCTCAGTTTCTCATGGTGGGC 59.996 52.381 0.00 0.00 0.00 5.36
866 2292 4.829064 TTGGTGTTATTGTGAGCTTGTC 57.171 40.909 0.00 0.00 0.00 3.18
901 2331 6.042777 GGGCACTCCTTTCTTTATTTATTGC 58.957 40.000 0.00 0.00 0.00 3.56
904 2334 5.893824 CCAGGGCACTCCTTTCTTTATTTAT 59.106 40.000 0.00 0.00 45.47 1.40
905 2335 5.014755 TCCAGGGCACTCCTTTCTTTATTTA 59.985 40.000 0.00 0.00 45.47 1.40
906 2336 4.089361 CCAGGGCACTCCTTTCTTTATTT 58.911 43.478 0.00 0.00 45.47 1.40
909 2339 2.039879 GTCCAGGGCACTCCTTTCTTTA 59.960 50.000 0.00 0.00 45.47 1.85
911 2341 0.402121 GTCCAGGGCACTCCTTTCTT 59.598 55.000 0.00 0.00 45.47 2.52
913 2343 0.035915 GAGTCCAGGGCACTCCTTTC 60.036 60.000 0.00 0.00 45.47 2.62
915 2345 3.813150 GAGTCCAGGGCACTCCTT 58.187 61.111 0.00 0.00 45.47 3.36
918 2348 0.324830 AGTAGGAGTCCAGGGCACTC 60.325 60.000 12.86 0.00 39.78 3.51
920 2350 0.905337 ACAGTAGGAGTCCAGGGCAC 60.905 60.000 12.86 1.03 0.00 5.01
921 2351 0.614979 GACAGTAGGAGTCCAGGGCA 60.615 60.000 12.86 0.00 0.00 5.36
922 2352 2.203806 GACAGTAGGAGTCCAGGGC 58.796 63.158 12.86 0.00 0.00 5.19
1541 3368 1.078214 CAGCCTTCTTGCCGATCCA 60.078 57.895 0.00 0.00 0.00 3.41
1793 3639 3.574614 CAAATCAACCAAACGACATCCC 58.425 45.455 0.00 0.00 0.00 3.85
1899 4464 2.084546 GACCACTAGCCCAACACAATC 58.915 52.381 0.00 0.00 0.00 2.67
1934 4499 8.651588 GTCAACCGAATATTATCACATGATCTC 58.348 37.037 0.00 0.00 36.05 2.75
1985 4551 2.677003 GGCATCACGACACAACGGG 61.677 63.158 0.00 0.00 38.09 5.28
1991 4557 6.604735 AAATAATCTTAGGCATCACGACAC 57.395 37.500 0.00 0.00 0.00 3.67
1992 4558 6.597672 ACAAAATAATCTTAGGCATCACGACA 59.402 34.615 0.00 0.00 0.00 4.35
1993 4559 7.016361 ACAAAATAATCTTAGGCATCACGAC 57.984 36.000 0.00 0.00 0.00 4.34
1994 4560 8.902540 ATACAAAATAATCTTAGGCATCACGA 57.097 30.769 0.00 0.00 0.00 4.35
1995 4561 9.950680 AAATACAAAATAATCTTAGGCATCACG 57.049 29.630 0.00 0.00 0.00 4.35
2023 4589 4.227527 TCCATTTTCTAAAGTCTCCTCCCC 59.772 45.833 0.00 0.00 0.00 4.81
2042 4622 4.274459 GCTCGATGCTTCAACTATTTCCAT 59.726 41.667 0.08 0.00 38.95 3.41
2043 4623 3.623060 GCTCGATGCTTCAACTATTTCCA 59.377 43.478 0.08 0.00 38.95 3.53
2049 4629 3.382865 AGAGATGCTCGATGCTTCAACTA 59.617 43.478 18.11 0.00 45.09 2.24
2050 4630 2.168106 AGAGATGCTCGATGCTTCAACT 59.832 45.455 18.11 14.72 45.09 3.16
2074 4654 1.072266 ACCCACCACTAATTCTGCCA 58.928 50.000 0.00 0.00 0.00 4.92
2079 4659 3.832615 ATCCGTACCCACCACTAATTC 57.167 47.619 0.00 0.00 0.00 2.17
2084 4664 0.828677 GCTAATCCGTACCCACCACT 59.171 55.000 0.00 0.00 0.00 4.00
2085 4665 0.828677 AGCTAATCCGTACCCACCAC 59.171 55.000 0.00 0.00 0.00 4.16
2091 4671 4.494350 TTCGACATAGCTAATCCGTACC 57.506 45.455 0.00 0.00 0.00 3.34
2110 4690 6.205464 TCAGTTGAAGTCCACAAGATGATTTC 59.795 38.462 0.00 0.00 0.00 2.17
2174 4757 0.235665 CCACCAACGATGCGCATATC 59.764 55.000 25.40 12.38 0.00 1.63
2175 4758 0.179059 TCCACCAACGATGCGCATAT 60.179 50.000 25.40 12.22 0.00 1.78
2176 4759 0.809636 CTCCACCAACGATGCGCATA 60.810 55.000 25.40 2.83 0.00 3.14
2177 4760 2.046411 TCCACCAACGATGCGCAT 60.046 55.556 25.66 25.66 0.00 4.73
2178 4761 2.741985 CTCCACCAACGATGCGCA 60.742 61.111 14.96 14.96 0.00 6.09
2179 4762 4.166011 GCTCCACCAACGATGCGC 62.166 66.667 0.00 0.00 0.00 6.09
2180 4763 3.853330 CGCTCCACCAACGATGCG 61.853 66.667 0.00 0.00 37.57 4.73
2235 4818 4.999950 GCCATCTTGACTTGGTGATATAGG 59.000 45.833 0.00 0.00 35.34 2.57
2236 4819 4.999950 GGCCATCTTGACTTGGTGATATAG 59.000 45.833 0.00 0.00 35.34 1.31
2237 4820 4.503123 CGGCCATCTTGACTTGGTGATATA 60.503 45.833 2.24 0.00 35.34 0.86
2238 4821 3.745480 CGGCCATCTTGACTTGGTGATAT 60.745 47.826 2.24 0.00 35.34 1.63
2240 4823 1.679944 CGGCCATCTTGACTTGGTGAT 60.680 52.381 2.24 0.00 35.34 3.06
2245 4828 1.466167 CAACTCGGCCATCTTGACTTG 59.534 52.381 2.24 0.00 0.00 3.16
2399 5030 0.591170 CGACGGCACAGACCAAAATT 59.409 50.000 0.00 0.00 0.00 1.82
2401 5032 1.890041 CCGACGGCACAGACCAAAA 60.890 57.895 0.00 0.00 0.00 2.44
2402 5033 2.280524 CCGACGGCACAGACCAAA 60.281 61.111 0.00 0.00 0.00 3.28
2422 5053 3.665675 AATCTGGTCGGCACTCGGC 62.666 63.158 0.00 0.00 43.79 5.54
2423 5054 1.811266 CAATCTGGTCGGCACTCGG 60.811 63.158 0.00 0.00 39.77 4.63
2424 5055 0.172578 TACAATCTGGTCGGCACTCG 59.827 55.000 0.00 0.00 40.90 4.18
2425 5056 1.641577 GTACAATCTGGTCGGCACTC 58.358 55.000 0.00 0.00 0.00 3.51
2426 5057 0.108804 CGTACAATCTGGTCGGCACT 60.109 55.000 0.00 0.00 0.00 4.40
2427 5058 0.108992 TCGTACAATCTGGTCGGCAC 60.109 55.000 0.00 0.00 0.00 5.01
2441 5072 1.085091 TCTCTCAGCGGAAGTCGTAC 58.915 55.000 0.00 0.00 41.72 3.67
2449 5080 2.808315 GCCGATTCTCTCAGCGGA 59.192 61.111 0.73 0.00 46.29 5.54
2459 5090 1.227263 TTCAGCCTAGCGCCGATTC 60.227 57.895 2.29 0.00 38.78 2.52
2466 5098 4.451150 TGCCCGTTCAGCCTAGCG 62.451 66.667 0.00 0.00 0.00 4.26
2502 5134 0.689623 AGCTCAGACTTCCAGTTGGG 59.310 55.000 0.00 0.00 35.41 4.12
2586 5241 3.264998 TGCATGTAGCTAGCATGTTGA 57.735 42.857 24.52 13.91 43.93 3.18
2597 5252 4.865925 TCAAAAAGAATGCATGCATGTAGC 59.134 37.500 32.79 21.10 45.96 3.58
2598 5253 6.954616 TTCAAAAAGAATGCATGCATGTAG 57.045 33.333 32.79 17.76 36.68 2.74
2600 5255 6.621316 TTTTCAAAAAGAATGCATGCATGT 57.379 29.167 32.79 21.80 36.68 3.21


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

AutoCloner maintained by Alex Coulton.