Multiple sequence alignment - TraesCS3B01G258500

Loading Multiple Alignment...

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 TraesCS3B01G258500 chr3B 100.000 1984 0 0 1 1984 416153262 416151279 0.000000e+00 3664.0
1 TraesCS3B01G258500 chr3B 100.000 1729 0 0 2448 4176 416150815 416149087 0.000000e+00 3193.0
2 TraesCS3B01G258500 chr3B 92.788 416 28 2 1409 1823 763774074 763773660 5.970000e-168 601.0
3 TraesCS3B01G258500 chr3B 81.395 344 35 14 3008 3325 763773445 763773105 1.930000e-63 254.0
4 TraesCS3B01G258500 chr3B 77.696 408 50 24 757 1152 763774639 763774261 1.180000e-50 211.0
5 TraesCS3B01G258500 chr3B 87.611 113 8 4 1206 1312 763774249 763774137 4.380000e-25 126.0
6 TraesCS3B01G258500 chr3D 93.305 1882 92 13 1 1862 305578657 305580524 0.000000e+00 2747.0
7 TraesCS3B01G258500 chr3D 94.508 874 32 8 2487 3349 305580805 305581673 0.000000e+00 1334.0
8 TraesCS3B01G258500 chr3D 93.269 416 26 2 1409 1823 573690589 573691003 2.760000e-171 612.0
9 TraesCS3B01G258500 chr3D 81.977 344 38 13 3029 3348 573691242 573691585 1.910000e-68 270.0
10 TraesCS3B01G258500 chr3D 90.303 165 15 1 988 1152 573690236 573690399 9.090000e-52 215.0
11 TraesCS3B01G258500 chr3D 91.589 107 9 0 1206 1312 573690411 573690517 9.350000e-32 148.0
12 TraesCS3B01G258500 chr3D 86.111 72 7 2 1915 1984 305580551 305580621 1.610000e-09 75.0
13 TraesCS3B01G258500 chr3A 92.431 1876 76 24 1 1862 423618074 423619897 0.000000e+00 2617.0
14 TraesCS3B01G258500 chr3A 94.299 877 34 9 2489 3349 423620441 423621317 0.000000e+00 1328.0
15 TraesCS3B01G258500 chr3A 85.965 627 51 29 1206 1823 708322584 708323182 1.640000e-178 636.0
16 TraesCS3B01G258500 chr3A 77.757 544 51 35 2837 3348 708325376 708325881 1.910000e-68 270.0
17 TraesCS3B01G258500 chr3A 81.765 340 32 18 3038 3348 708323427 708323765 1.490000e-64 257.0
18 TraesCS3B01G258500 chr3A 88.554 166 16 1 972 1134 708322389 708322554 9.160000e-47 198.0
19 TraesCS3B01G258500 chr3A 95.402 87 3 1 2837 2923 708323264 708323349 2.020000e-28 137.0
20 TraesCS3B01G258500 chr3A 86.957 69 3 1 1922 1984 423619931 423619999 5.790000e-09 73.1
21 TraesCS3B01G258500 chr4A 95.209 814 39 0 3363 4176 288658228 288659041 0.000000e+00 1288.0
22 TraesCS3B01G258500 chr4A 85.000 80 8 4 3355 3432 373639212 373639289 1.240000e-10 78.7
23 TraesCS3B01G258500 chr7B 94.595 814 44 0 3363 4176 154414533 154413720 0.000000e+00 1260.0
24 TraesCS3B01G258500 chr7B 92.308 65 3 1 3363 3425 127748820 127748884 1.600000e-14 91.6
25 TraesCS3B01G258500 chr5B 90.552 815 71 3 3363 4176 618740076 618740885 0.000000e+00 1074.0
26 TraesCS3B01G258500 chr5A 87.105 791 101 1 3387 4176 206713072 206712282 0.000000e+00 894.0
27 TraesCS3B01G258500 chr2B 91.304 69 3 2 3360 3425 390079836 390079768 1.600000e-14 91.6
28 TraesCS3B01G258500 chr4B 89.855 69 5 2 3363 3430 521568485 521568552 2.070000e-13 87.9
29 TraesCS3B01G258500 chr4D 90.769 65 4 1 3363 3425 305191989 305191925 7.440000e-13 86.1
30 TraesCS3B01G258500 chr6B 87.755 49 5 1 3590 3637 646235447 646235399 5.830000e-04 56.5


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 TraesCS3B01G258500 chr3B 416149087 416153262 4175 True 3428.500000 3664 100.0000 1 4176 2 chr3B.!!$R1 4175
1 TraesCS3B01G258500 chr3B 763773105 763774639 1534 True 298.000000 601 84.8725 757 3325 4 chr3B.!!$R2 2568
2 TraesCS3B01G258500 chr3D 305578657 305581673 3016 False 1385.333333 2747 91.3080 1 3349 3 chr3D.!!$F1 3348
3 TraesCS3B01G258500 chr3D 573690236 573691585 1349 False 311.250000 612 89.2845 988 3348 4 chr3D.!!$F2 2360
4 TraesCS3B01G258500 chr3A 423618074 423621317 3243 False 1339.366667 2617 91.2290 1 3349 3 chr3A.!!$F1 3348
5 TraesCS3B01G258500 chr3A 708322389 708325881 3492 False 299.600000 636 85.8886 972 3348 5 chr3A.!!$F2 2376
6 TraesCS3B01G258500 chr4A 288658228 288659041 813 False 1288.000000 1288 95.2090 3363 4176 1 chr4A.!!$F1 813
7 TraesCS3B01G258500 chr7B 154413720 154414533 813 True 1260.000000 1260 94.5950 3363 4176 1 chr7B.!!$R1 813
8 TraesCS3B01G258500 chr5B 618740076 618740885 809 False 1074.000000 1074 90.5520 3363 4176 1 chr5B.!!$F1 813
9 TraesCS3B01G258500 chr5A 206712282 206713072 790 True 894.000000 894 87.1050 3387 4176 1 chr5A.!!$R1 789

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
92 93 0.387202 AACGATGGATCTGGCGAGAG 59.613 55.0 4.31 0.0 0.00 3.20 F
1889 1971 0.391130 GCCGTGATGTGTGGCTTCTA 60.391 55.0 0.00 0.0 45.40 2.10 F
1897 1979 0.250513 GTGTGGCTTCTACCTCCAGG 59.749 60.0 0.00 0.0 42.17 4.45 F
1913 1995 0.901580 CAGGGGCTGCATCCAACTTT 60.902 55.0 9.17 0.0 0.00 2.66 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1895 1977 0.178924 AAAAGTTGGATGCAGCCCCT 60.179 50.000 20.33 11.71 0.0 4.79 R
3049 3182 1.588403 CTGCAGCATCGTCTCCTCG 60.588 63.158 0.00 0.00 0.0 4.63 R
3115 3248 2.047560 AAGAGGCGGCGGTTGTAC 60.048 61.111 9.78 0.00 0.0 2.90 R
3686 5964 2.904434 GGTGGGAGACAAGTAGGAAGAA 59.096 50.000 0.00 0.00 0.0 2.52 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
73 74 2.228480 GGGTGGAGGGCAACTACCA 61.228 63.158 14.89 0.00 38.82 3.25
92 93 0.387202 AACGATGGATCTGGCGAGAG 59.613 55.000 4.31 0.00 0.00 3.20
117 118 3.117888 TCCTTAATAAGCTCTTGGGGCAG 60.118 47.826 0.00 0.00 0.00 4.85
118 119 3.372025 CCTTAATAAGCTCTTGGGGCAGT 60.372 47.826 0.00 0.00 0.00 4.40
127 128 1.839994 TCTTGGGGCAGTAGAATCCAG 59.160 52.381 0.00 0.00 0.00 3.86
203 207 1.551452 GAGGTGGTGAGCTAGTGTCT 58.449 55.000 0.00 0.00 0.00 3.41
240 244 1.905894 TCATTGGACATGGGTCTTCGA 59.094 47.619 0.00 0.00 43.77 3.71
243 247 0.896479 TGGACATGGGTCTTCGACGA 60.896 55.000 0.00 0.00 43.77 4.20
316 322 2.299013 TGAAGTGAAGCTACGACACCAT 59.701 45.455 0.00 0.00 35.47 3.55
341 347 1.615392 GTTGCTTCAATGGTTGAGCCT 59.385 47.619 9.79 0.00 41.38 4.58
351 357 3.228188 TGGTTGAGCCTGTCTTGATTT 57.772 42.857 0.00 0.00 38.35 2.17
353 359 3.149196 GGTTGAGCCTGTCTTGATTTCA 58.851 45.455 0.00 0.00 0.00 2.69
359 365 6.061441 TGAGCCTGTCTTGATTTCACTAAAA 58.939 36.000 0.00 0.00 0.00 1.52
373 379 5.217978 TCACTAAAATTGAGTGTACCGGT 57.782 39.130 13.98 13.98 43.95 5.28
397 403 1.261238 GGGTGGCTGTGTAGAGCTCT 61.261 60.000 22.17 22.17 39.11 4.09
430 436 2.403252 ACCGCTTCCAGTTATTCCTG 57.597 50.000 0.00 0.00 0.00 3.86
480 486 1.374252 GGCTTCGACTCGGCTTCAA 60.374 57.895 0.00 0.00 0.00 2.69
507 513 1.409241 CCATCCCTGACATGAGTTGGG 60.409 57.143 0.00 5.61 40.80 4.12
549 556 3.782443 CCCTGGTGGTAGCGTCCC 61.782 72.222 0.00 0.00 0.00 4.46
562 569 4.832608 GTCCCCGGTGATGGCGAC 62.833 72.222 0.00 0.00 0.00 5.19
593 600 1.912371 GCTGACGCCTCGAAAAAGGG 61.912 60.000 0.00 0.00 36.88 3.95
608 615 0.680921 AAGGGCCACATCACATTCGG 60.681 55.000 6.18 0.00 0.00 4.30
626 633 1.668151 GCAACTCGTGTCCAGGGTC 60.668 63.158 0.00 0.00 0.00 4.46
632 639 2.143925 CTCGTGTCCAGGGTCTTTTTC 58.856 52.381 0.00 0.00 0.00 2.29
637 644 4.070009 GTGTCCAGGGTCTTTTTCGTAAT 58.930 43.478 0.00 0.00 0.00 1.89
641 648 5.009310 GTCCAGGGTCTTTTTCGTAATGTTT 59.991 40.000 0.00 0.00 0.00 2.83
642 649 5.009210 TCCAGGGTCTTTTTCGTAATGTTTG 59.991 40.000 0.00 0.00 0.00 2.93
665 672 3.255642 TGGGCTCAGTTGTAATTTTGCTC 59.744 43.478 0.00 0.00 0.00 4.26
713 721 2.172717 ACCTGTACTGGACTGCAAAGTT 59.827 45.455 24.19 0.00 0.00 2.66
1191 1225 2.742372 CCGGCGGAGACCAACAAG 60.742 66.667 24.41 0.00 0.00 3.16
1192 1226 2.742372 CGGCGGAGACCAACAAGG 60.742 66.667 0.00 0.00 45.67 3.61
1193 1227 3.056328 GGCGGAGACCAACAAGGC 61.056 66.667 0.00 0.00 43.14 4.35
1194 1228 3.423154 GCGGAGACCAACAAGGCG 61.423 66.667 0.00 0.00 43.14 5.52
1363 1431 3.279434 GGCCTGTTTCCGTTGAGATTAT 58.721 45.455 0.00 0.00 0.00 1.28
1364 1432 3.694566 GGCCTGTTTCCGTTGAGATTATT 59.305 43.478 0.00 0.00 0.00 1.40
1365 1433 4.879545 GGCCTGTTTCCGTTGAGATTATTA 59.120 41.667 0.00 0.00 0.00 0.98
1366 1434 5.355910 GGCCTGTTTCCGTTGAGATTATTAA 59.644 40.000 0.00 0.00 0.00 1.40
1367 1435 6.458342 GGCCTGTTTCCGTTGAGATTATTAAG 60.458 42.308 0.00 0.00 0.00 1.85
1368 1436 6.093633 GCCTGTTTCCGTTGAGATTATTAAGT 59.906 38.462 0.00 0.00 0.00 2.24
1843 1925 4.143179 GGTCCGTTTCTACTCAATCAAACG 60.143 45.833 8.45 8.45 46.75 3.60
1845 1927 3.185594 CCGTTTCTACTCAATCAAACGCA 59.814 43.478 9.66 0.00 46.16 5.24
1848 1930 5.333035 CGTTTCTACTCAATCAAACGCAAGA 60.333 40.000 3.17 0.00 43.08 3.02
1862 1944 7.147312 TCAAACGCAAGATTCATTCATTTTCT 58.853 30.769 0.00 0.00 43.62 2.52
1864 1946 6.258230 ACGCAAGATTCATTCATTTTCTGA 57.742 33.333 0.00 0.00 43.62 3.27
1865 1947 6.680810 ACGCAAGATTCATTCATTTTCTGAA 58.319 32.000 0.00 0.00 44.57 3.02
1867 1949 8.461222 ACGCAAGATTCATTCATTTTCTGAATA 58.539 29.630 0.48 0.00 46.40 1.75
1868 1950 8.740369 CGCAAGATTCATTCATTTTCTGAATAC 58.260 33.333 0.48 0.00 46.54 1.89
1875 1957 4.944962 TCATTTTCTGAATACAGCCGTG 57.055 40.909 0.00 0.00 43.17 4.94
1876 1958 4.574892 TCATTTTCTGAATACAGCCGTGA 58.425 39.130 0.00 0.00 43.17 4.35
1877 1959 5.185454 TCATTTTCTGAATACAGCCGTGAT 58.815 37.500 0.00 0.00 43.17 3.06
1879 1961 3.610040 TTCTGAATACAGCCGTGATGT 57.390 42.857 0.72 0.72 43.17 3.06
1880 1962 2.892374 TCTGAATACAGCCGTGATGTG 58.108 47.619 5.25 0.00 43.17 3.21
1881 1963 2.233676 TCTGAATACAGCCGTGATGTGT 59.766 45.455 5.25 0.00 43.17 3.72
1882 1964 2.345876 TGAATACAGCCGTGATGTGTG 58.654 47.619 5.25 0.00 33.09 3.82
1883 1965 1.665679 GAATACAGCCGTGATGTGTGG 59.334 52.381 5.25 0.00 33.09 4.17
1887 1969 2.870372 GCCGTGATGTGTGGCTTC 59.130 61.111 0.00 0.00 45.40 3.86
1888 1970 1.672356 GCCGTGATGTGTGGCTTCT 60.672 57.895 0.00 0.00 45.40 2.85
1889 1971 0.391130 GCCGTGATGTGTGGCTTCTA 60.391 55.000 0.00 0.00 45.40 2.10
1890 1972 1.359848 CCGTGATGTGTGGCTTCTAC 58.640 55.000 0.00 0.00 0.00 2.59
1891 1973 1.359848 CGTGATGTGTGGCTTCTACC 58.640 55.000 0.00 0.00 0.00 3.18
1892 1974 1.066858 CGTGATGTGTGGCTTCTACCT 60.067 52.381 0.00 0.00 0.00 3.08
1893 1975 2.622436 GTGATGTGTGGCTTCTACCTC 58.378 52.381 0.00 0.00 0.00 3.85
1894 1976 1.555075 TGATGTGTGGCTTCTACCTCC 59.445 52.381 0.00 0.00 0.00 4.30
1895 1977 1.555075 GATGTGTGGCTTCTACCTCCA 59.445 52.381 0.00 0.00 0.00 3.86
1896 1978 0.976641 TGTGTGGCTTCTACCTCCAG 59.023 55.000 0.00 0.00 0.00 3.86
1897 1979 0.250513 GTGTGGCTTCTACCTCCAGG 59.749 60.000 0.00 0.00 42.17 4.45
1898 1980 0.909610 TGTGGCTTCTACCTCCAGGG 60.910 60.000 0.00 0.00 40.27 4.45
1899 1981 1.306997 TGGCTTCTACCTCCAGGGG 60.307 63.158 0.00 0.00 40.27 4.79
1900 1982 2.747443 GGCTTCTACCTCCAGGGGC 61.747 68.421 0.00 0.00 40.27 5.80
1901 1983 1.690985 GCTTCTACCTCCAGGGGCT 60.691 63.158 0.00 0.00 40.27 5.19
1902 1984 1.977293 GCTTCTACCTCCAGGGGCTG 61.977 65.000 0.00 0.00 40.27 4.85
1903 1985 1.977293 CTTCTACCTCCAGGGGCTGC 61.977 65.000 0.00 0.00 40.27 5.25
1904 1986 2.688666 CTACCTCCAGGGGCTGCA 60.689 66.667 0.50 0.00 40.27 4.41
1905 1987 2.042762 TACCTCCAGGGGCTGCAT 59.957 61.111 0.50 0.00 40.27 3.96
1906 1988 2.049627 CTACCTCCAGGGGCTGCATC 62.050 65.000 0.50 0.00 40.27 3.91
1907 1989 4.201122 CCTCCAGGGGCTGCATCC 62.201 72.222 0.50 0.00 0.00 3.51
1908 1990 3.414193 CTCCAGGGGCTGCATCCA 61.414 66.667 9.17 0.00 0.00 3.41
1909 1991 2.940467 TCCAGGGGCTGCATCCAA 60.940 61.111 9.17 0.00 0.00 3.53
1910 1992 2.757099 CCAGGGGCTGCATCCAAC 60.757 66.667 9.17 0.46 0.00 3.77
1911 1993 2.357836 CAGGGGCTGCATCCAACT 59.642 61.111 9.17 3.02 0.00 3.16
1912 1994 1.304713 CAGGGGCTGCATCCAACTT 60.305 57.895 9.17 0.00 0.00 2.66
1913 1995 0.901580 CAGGGGCTGCATCCAACTTT 60.902 55.000 9.17 0.00 0.00 2.66
2516 2629 9.653287 CCAAGATATGTTTGACTCTTTGTACTA 57.347 33.333 0.00 0.00 0.00 1.82
2547 2668 4.164988 ACTCCAATTGATTACTCAGGAGGG 59.835 45.833 16.47 4.63 41.99 4.30
2637 2760 3.507622 GCTTTCAATGCTCTTACCCAAGT 59.492 43.478 0.00 0.00 33.20 3.16
2639 2762 4.365514 TTCAATGCTCTTACCCAAGTGA 57.634 40.909 0.00 0.00 33.20 3.41
2641 2764 4.072131 TCAATGCTCTTACCCAAGTGAAC 58.928 43.478 0.00 0.00 33.20 3.18
2643 2766 1.689813 TGCTCTTACCCAAGTGAACGA 59.310 47.619 0.00 0.00 33.20 3.85
2696 2820 6.256321 CAGCCCATAATTACAAAACATGCTTC 59.744 38.462 0.00 0.00 0.00 3.86
2715 2841 5.047164 TGCTTCCCGTATAGTACAAAGTTGA 60.047 40.000 0.00 0.00 0.00 3.18
2721 2847 5.810587 CCGTATAGTACAAAGTTGATGCACT 59.189 40.000 0.00 0.00 0.00 4.40
2995 3122 4.745125 GCATATTCTGAAGCTAAGCGTGTA 59.255 41.667 0.00 0.00 0.00 2.90
3017 3146 5.725325 AAGCCGAGGATTAGATACTAACC 57.275 43.478 0.00 0.00 0.00 2.85
3049 3182 3.499929 TATACGCAGGCAGCTCGGC 62.500 63.158 0.00 2.19 42.61 5.54
3115 3248 4.463879 CTGGAGAGGCCCTGCGTG 62.464 72.222 0.00 0.00 35.80 5.34
3250 5510 1.293179 GGGTCCCATTTGTTGCAGC 59.707 57.895 1.78 0.00 0.00 5.25
3334 5611 3.428045 CGCCCAATTTGTCCATTTCTCTC 60.428 47.826 0.00 0.00 0.00 3.20
3349 5626 2.693069 TCTCTCTTGCAGCTAAACAGC 58.307 47.619 0.00 0.00 0.00 4.40
3350 5627 1.392853 CTCTCTTGCAGCTAAACAGCG 59.607 52.381 0.00 0.00 40.27 5.18
3351 5628 0.179205 CTCTTGCAGCTAAACAGCGC 60.179 55.000 0.00 0.00 40.27 5.92
3352 5629 0.603707 TCTTGCAGCTAAACAGCGCT 60.604 50.000 2.64 2.64 40.27 5.92
3353 5630 0.453950 CTTGCAGCTAAACAGCGCTG 60.454 55.000 34.89 34.89 40.27 5.18
3355 5632 0.320334 TGCAGCTAAACAGCGCTGTA 60.320 50.000 40.76 26.34 44.13 2.74
3356 5633 0.095417 GCAGCTAAACAGCGCTGTAC 59.905 55.000 40.76 28.57 44.13 2.90
3357 5634 1.428448 CAGCTAAACAGCGCTGTACA 58.572 50.000 40.76 28.93 44.13 2.90
3358 5635 1.798223 CAGCTAAACAGCGCTGTACAA 59.202 47.619 40.76 26.84 44.13 2.41
3359 5636 1.798813 AGCTAAACAGCGCTGTACAAC 59.201 47.619 40.76 28.90 44.13 3.32
3360 5637 1.529438 GCTAAACAGCGCTGTACAACA 59.471 47.619 40.76 22.59 44.13 3.33
3361 5638 2.661979 GCTAAACAGCGCTGTACAACAC 60.662 50.000 40.76 24.16 44.13 3.32
3481 5759 0.833834 ACCCACTCCACTCCACTCTG 60.834 60.000 0.00 0.00 0.00 3.35
3580 5858 0.036010 CCATGGTTCCTTGAGCGTCT 60.036 55.000 2.57 0.00 0.00 4.18
3583 5861 1.919240 TGGTTCCTTGAGCGTCTCTA 58.081 50.000 8.07 0.87 0.00 2.43
3657 5935 4.217118 GCAGATCAACATGACAAAGGAGTT 59.783 41.667 0.00 0.00 0.00 3.01
3686 5964 4.914983 TCTTCTGTTGGCTTTGATGATCT 58.085 39.130 0.00 0.00 0.00 2.75
3831 6109 2.420129 GCAAGTGATCCACCGTATCCTT 60.420 50.000 0.00 0.00 34.49 3.36
3896 6174 3.386078 GCCATGTCTGAGTCTTCTATCCA 59.614 47.826 0.00 0.00 0.00 3.41
3938 6216 7.328277 TGTACTGCCAACCACATAAATATTC 57.672 36.000 0.00 0.00 0.00 1.75
3951 6229 8.773645 CCACATAAATATTCTGCAAGATAACGA 58.226 33.333 0.00 0.00 46.36 3.85
3970 6248 0.251341 ACGCCCAGCTCTTCCAAATT 60.251 50.000 0.00 0.00 0.00 1.82
3988 6266 8.801882 TCCAAATTCCTTTATACGACTGAAAT 57.198 30.769 0.00 0.00 0.00 2.17
4040 6318 1.006086 CGATGCCGCTGTGTATTTCA 58.994 50.000 0.00 0.00 0.00 2.69
4168 6446 3.117738 ACATTTCTCCTGGGATGTCCATC 60.118 47.826 0.86 0.00 46.01 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
73 74 0.387202 CTCTCGCCAGATCCATCGTT 59.613 55.000 0.00 0.00 0.00 3.85
109 110 1.281867 CACTGGATTCTACTGCCCCAA 59.718 52.381 0.00 0.00 0.00 4.12
117 118 4.020128 ACCTCCAACTTCACTGGATTCTAC 60.020 45.833 0.00 0.00 42.12 2.59
118 119 4.168101 ACCTCCAACTTCACTGGATTCTA 58.832 43.478 0.00 0.00 42.12 2.10
127 128 4.200092 AGAGAAACAACCTCCAACTTCAC 58.800 43.478 0.00 0.00 0.00 3.18
203 207 7.069455 TGTCCAATGATCGATCTAAGGAAGTTA 59.931 37.037 25.02 12.73 0.00 2.24
240 244 1.368950 CATGCTCCGGATCCATCGT 59.631 57.895 13.41 0.00 0.00 3.73
243 247 0.687354 GGTACATGCTCCGGATCCAT 59.313 55.000 13.41 8.37 0.00 3.41
284 290 2.654987 CTTCACTTCAAAAAGCCGCTC 58.345 47.619 0.00 0.00 35.81 5.03
291 297 4.034742 GGTGTCGTAGCTTCACTTCAAAAA 59.965 41.667 0.00 0.00 33.30 1.94
316 322 4.156556 GCTCAACCATTGAAGCAACATAGA 59.843 41.667 7.62 0.00 39.58 1.98
341 347 8.902806 ACACTCAATTTTAGTGAAATCAAGACA 58.097 29.630 19.72 0.00 45.89 3.41
351 357 5.217978 ACCGGTACACTCAATTTTAGTGA 57.782 39.130 19.72 5.63 45.89 3.41
353 359 4.022068 TCGACCGGTACACTCAATTTTAGT 60.022 41.667 7.34 0.00 0.00 2.24
359 365 1.203994 CCTTCGACCGGTACACTCAAT 59.796 52.381 7.34 0.00 0.00 2.57
373 379 0.541063 TCTACACAGCCACCCTTCGA 60.541 55.000 0.00 0.00 0.00 3.71
397 403 1.748879 GCGGTTTAGCCTGATGCCA 60.749 57.895 0.00 0.00 42.71 4.92
430 436 1.133025 CCTTTTGACATCATGGTCGGC 59.867 52.381 0.00 0.00 40.72 5.54
469 475 4.503991 GGATGGAAGATATTGAAGCCGAGT 60.504 45.833 0.00 0.00 0.00 4.18
480 486 5.161135 ACTCATGTCAGGGATGGAAGATAT 58.839 41.667 0.00 0.00 0.00 1.63
507 513 0.878961 AACCTTGTCGTCGCTTCACC 60.879 55.000 0.00 0.00 0.00 4.02
549 556 2.819595 CAAGGTCGCCATCACCGG 60.820 66.667 0.00 0.00 39.13 5.28
562 569 1.369091 GCGTCAGCCACATACCAAGG 61.369 60.000 0.00 0.00 37.42 3.61
593 600 0.456653 GTTGCCGAATGTGATGTGGC 60.457 55.000 0.00 0.00 45.91 5.01
608 615 1.668151 GACCCTGGACACGAGTTGC 60.668 63.158 0.00 0.00 0.00 4.17
626 633 4.616953 AGCCCACAAACATTACGAAAAAG 58.383 39.130 0.00 0.00 0.00 2.27
632 639 2.151202 ACTGAGCCCACAAACATTACG 58.849 47.619 0.00 0.00 0.00 3.18
637 644 2.719531 TACAACTGAGCCCACAAACA 57.280 45.000 0.00 0.00 0.00 2.83
641 648 3.243704 GCAAAATTACAACTGAGCCCACA 60.244 43.478 0.00 0.00 0.00 4.17
642 649 3.005791 AGCAAAATTACAACTGAGCCCAC 59.994 43.478 0.00 0.00 0.00 4.61
665 672 2.637872 TGTCACCAGGACCCTTAGAAAG 59.362 50.000 0.00 0.00 46.38 2.62
748 757 3.522553 CAGGTTGTTCTTCTACCGATCC 58.477 50.000 0.00 0.00 44.46 3.36
1174 1208 2.742372 CTTGTTGGTCTCCGCCGG 60.742 66.667 0.00 0.00 0.00 6.13
1180 1214 3.423154 CGGCGCCTTGTTGGTCTC 61.423 66.667 26.68 0.00 38.35 3.36
1211 1251 0.519077 CTTGGCTTTCGTCTTGCTCC 59.481 55.000 0.00 0.00 0.00 4.70
1365 1433 9.935682 CGTGACAGCATGAATTATAATTAACTT 57.064 29.630 10.68 0.00 39.69 2.66
1366 1434 9.325198 TCGTGACAGCATGAATTATAATTAACT 57.675 29.630 10.68 3.84 39.69 2.24
1367 1435 9.370126 GTCGTGACAGCATGAATTATAATTAAC 57.630 33.333 10.68 0.79 41.45 2.01
1368 1436 8.272866 CGTCGTGACAGCATGAATTATAATTAA 58.727 33.333 10.68 4.15 41.45 1.40
1631 1707 4.477975 GAGCCCGACACGACGAGG 62.478 72.222 0.00 0.00 35.09 4.63
1827 1903 6.426633 TGAATCTTGCGTTTGATTGAGTAGAA 59.573 34.615 0.00 0.00 33.60 2.10
1862 1944 2.345876 CACACATCACGGCTGTATTCA 58.654 47.619 0.00 0.00 0.00 2.57
1864 1946 1.737838 CCACACATCACGGCTGTATT 58.262 50.000 0.00 0.00 0.00 1.89
1865 1947 0.744414 GCCACACATCACGGCTGTAT 60.744 55.000 0.00 0.00 42.78 2.29
1867 1949 2.669569 GCCACACATCACGGCTGT 60.670 61.111 0.00 0.00 42.78 4.40
1870 1952 0.391130 TAGAAGCCACACATCACGGC 60.391 55.000 0.00 0.00 46.62 5.68
1871 1953 1.359848 GTAGAAGCCACACATCACGG 58.640 55.000 0.00 0.00 0.00 4.94
1872 1954 1.066858 AGGTAGAAGCCACACATCACG 60.067 52.381 0.00 0.00 0.00 4.35
1875 1957 1.555075 TGGAGGTAGAAGCCACACATC 59.445 52.381 0.00 0.00 0.00 3.06
1876 1958 1.556911 CTGGAGGTAGAAGCCACACAT 59.443 52.381 0.00 0.00 0.00 3.21
1877 1959 0.976641 CTGGAGGTAGAAGCCACACA 59.023 55.000 0.00 0.00 0.00 3.72
1879 1961 0.909610 CCCTGGAGGTAGAAGCCACA 60.910 60.000 0.00 0.00 0.00 4.17
1880 1962 1.627297 CCCCTGGAGGTAGAAGCCAC 61.627 65.000 0.00 0.00 0.00 5.01
1881 1963 1.306997 CCCCTGGAGGTAGAAGCCA 60.307 63.158 0.00 0.00 0.00 4.75
1882 1964 2.747443 GCCCCTGGAGGTAGAAGCC 61.747 68.421 0.00 0.00 0.00 4.35
1883 1965 1.690985 AGCCCCTGGAGGTAGAAGC 60.691 63.158 0.00 0.00 0.00 3.86
1884 1966 1.977293 GCAGCCCCTGGAGGTAGAAG 61.977 65.000 0.00 0.00 31.21 2.85
1886 1968 2.365635 GCAGCCCCTGGAGGTAGA 60.366 66.667 0.00 0.00 31.21 2.59
1887 1969 2.049627 GATGCAGCCCCTGGAGGTAG 62.050 65.000 0.00 0.00 34.87 3.18
1888 1970 2.042762 ATGCAGCCCCTGGAGGTA 59.957 61.111 0.00 0.00 34.87 3.08
1889 1971 3.415087 GATGCAGCCCCTGGAGGT 61.415 66.667 0.00 0.00 34.87 3.85
1890 1972 4.201122 GGATGCAGCCCCTGGAGG 62.201 72.222 10.76 0.00 34.87 4.30
1891 1973 2.987596 TTGGATGCAGCCCCTGGAG 61.988 63.158 20.33 0.00 34.87 3.86
1892 1974 2.940467 TTGGATGCAGCCCCTGGA 60.940 61.111 20.33 0.00 36.05 3.86
1893 1975 2.757099 GTTGGATGCAGCCCCTGG 60.757 66.667 20.33 0.00 31.21 4.45
1894 1976 0.901580 AAAGTTGGATGCAGCCCCTG 60.902 55.000 20.33 0.00 34.12 4.45
1895 1977 0.178924 AAAAGTTGGATGCAGCCCCT 60.179 50.000 20.33 11.71 0.00 4.79
1896 1978 0.686789 AAAAAGTTGGATGCAGCCCC 59.313 50.000 20.33 9.26 0.00 5.80
1929 2011 3.083293 TGAACCCATCACACATCACATG 58.917 45.455 0.00 0.00 31.50 3.21
2479 2570 6.995686 TCAAACATATCTTGGTGTAGTGTTGT 59.004 34.615 0.00 0.00 0.00 3.32
2480 2571 7.173218 AGTCAAACATATCTTGGTGTAGTGTTG 59.827 37.037 0.00 0.00 0.00 3.33
2481 2572 7.224297 AGTCAAACATATCTTGGTGTAGTGTT 58.776 34.615 0.00 0.00 0.00 3.32
2482 2573 6.769512 AGTCAAACATATCTTGGTGTAGTGT 58.230 36.000 0.00 0.00 0.00 3.55
2483 2574 7.099764 AGAGTCAAACATATCTTGGTGTAGTG 58.900 38.462 0.00 0.00 0.00 2.74
2484 2575 7.246171 AGAGTCAAACATATCTTGGTGTAGT 57.754 36.000 0.00 0.00 0.00 2.73
2485 2576 8.446273 CAAAGAGTCAAACATATCTTGGTGTAG 58.554 37.037 0.00 0.00 32.50 2.74
2486 2577 7.936847 ACAAAGAGTCAAACATATCTTGGTGTA 59.063 33.333 0.00 0.00 35.19 2.90
2487 2578 6.772716 ACAAAGAGTCAAACATATCTTGGTGT 59.227 34.615 0.00 0.00 35.19 4.16
2490 2603 8.553459 AGTACAAAGAGTCAAACATATCTTGG 57.447 34.615 0.00 0.00 32.50 3.61
2525 2642 4.712476 CCCTCCTGAGTAATCAATTGGAG 58.288 47.826 16.18 16.18 39.26 3.86
2547 2668 3.633525 TGAATACCCATCAATGCTTCTGC 59.366 43.478 0.00 0.00 40.20 4.26
2639 2762 2.936498 CTGTCAAGTTGAACAGGTCGTT 59.064 45.455 19.49 0.00 41.86 3.85
2641 2764 2.550978 ACTGTCAAGTTGAACAGGTCG 58.449 47.619 25.68 12.08 33.15 4.79
2643 2766 4.634443 GTGTTACTGTCAAGTTGAACAGGT 59.366 41.667 25.68 16.94 36.18 4.00
2696 2820 5.006358 GTGCATCAACTTTGTACTATACGGG 59.994 44.000 0.00 0.00 0.00 5.28
2715 2841 2.497273 GGATTTGGTGGCTTTAGTGCAT 59.503 45.455 0.00 0.00 34.04 3.96
2721 2847 2.291282 ACGGATGGATTTGGTGGCTTTA 60.291 45.455 0.00 0.00 0.00 1.85
2995 3122 5.145564 TGGTTAGTATCTAATCCTCGGCTT 58.854 41.667 0.00 0.00 0.00 4.35
3017 3146 2.678836 TGCGTATACCCGAAAACCATTG 59.321 45.455 0.00 0.00 0.00 2.82
3049 3182 1.588403 CTGCAGCATCGTCTCCTCG 60.588 63.158 0.00 0.00 0.00 4.63
3115 3248 2.047560 AAGAGGCGGCGGTTGTAC 60.048 61.111 9.78 0.00 0.00 2.90
3250 5510 3.848272 ATACACGGCCAAACAATCAAG 57.152 42.857 2.24 0.00 0.00 3.02
3384 5661 7.290248 TCTGCCTTCTATAAAGCTAAGGTACAT 59.710 37.037 11.44 0.00 40.55 2.29
3385 5662 6.610020 TCTGCCTTCTATAAAGCTAAGGTACA 59.390 38.462 11.44 2.79 40.55 2.90
3481 5759 4.201576 CGTTTTGTGAGTAGTCGCTTTTC 58.798 43.478 12.20 1.11 34.00 2.29
3583 5861 7.962918 GCACGAGTATTCAGAAATGTAAATGTT 59.037 33.333 0.00 0.00 0.00 2.71
3657 5935 5.630121 TCAAAGCCAACAGAAGAGGATTTA 58.370 37.500 0.00 0.00 38.83 1.40
3686 5964 2.904434 GGTGGGAGACAAGTAGGAAGAA 59.096 50.000 0.00 0.00 0.00 2.52
3831 6109 4.072131 GTGCTATTTTTGTGACCAGGAGA 58.928 43.478 0.00 0.00 0.00 3.71
3896 6174 5.067936 CAGTACAATATCGAGTCTGGACCTT 59.932 44.000 0.00 0.00 0.00 3.50
3938 6216 0.739462 TGGGCGTCGTTATCTTGCAG 60.739 55.000 0.00 0.00 0.00 4.41
3951 6229 0.251341 AATTTGGAAGAGCTGGGCGT 60.251 50.000 0.00 0.00 0.00 5.68
3970 6248 5.840243 TCCGATTTCAGTCGTATAAAGGA 57.160 39.130 0.00 0.00 39.89 3.36
3988 6266 1.075970 CTGTGAGGGAGGGATCCGA 60.076 63.158 5.45 0.00 0.00 4.55
4040 6318 1.601759 GGCAGTGGTGTGCTGACAT 60.602 57.895 0.00 0.00 43.45 3.06


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

AutoCloner maintained by Alex Coulton.