Multiple sequence alignment - TraesCS5A01G253700

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 TraesCS5A01G253700 chr5A 100.000 2495 0 0 1 2495 469889748 469887254 0.000000e+00 4608
1 TraesCS5A01G253700 chr5D 86.982 2558 174 78 1 2495 367785071 367782610 0.000000e+00 2732
2 TraesCS5A01G253700 chr5B 86.924 2019 130 61 1 1955 435599209 435597261 0.000000e+00 2143
3 TraesCS5A01G253700 chr5B 87.898 471 31 11 2040 2495 435597133 435596674 4.730000e-147 531


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 TraesCS5A01G253700 chr5A 469887254 469889748 2494 True 4608 4608 100.000 1 2495 1 chr5A.!!$R1 2494
1 TraesCS5A01G253700 chr5D 367782610 367785071 2461 True 2732 2732 86.982 1 2495 1 chr5D.!!$R1 2494
2 TraesCS5A01G253700 chr5B 435596674 435599209 2535 True 1337 2143 87.411 1 2495 2 chr5B.!!$R1 2494

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
468 536 0.10852 CCGACGATTTTCTTCCGGGA 60.109 55.0 0.0 0.0 33.94 5.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1839 1931 0.172803 GCATCCAAGAGGCAAGCAAG 59.827 55.0 0.0 0.0 39.28 4.01 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
86 87 1.269998 GTACCAGGAGATCGATTCCCG 59.730 57.143 17.64 10.96 35.20 5.14
87 88 1.005630 CCAGGAGATCGATTCCCGC 60.006 63.158 17.64 1.44 38.37 6.13
202 228 1.139853 GAGCTGATCCGAACCATTCCT 59.860 52.381 0.00 0.00 0.00 3.36
225 251 5.601662 TGCAGAATCGGAAGGAAATACTAG 58.398 41.667 0.00 0.00 0.00 2.57
226 252 5.128827 TGCAGAATCGGAAGGAAATACTAGT 59.871 40.000 0.00 0.00 0.00 2.57
227 253 6.322969 TGCAGAATCGGAAGGAAATACTAGTA 59.677 38.462 4.77 4.77 0.00 1.82
230 256 7.863375 CAGAATCGGAAGGAAATACTAGTACTG 59.137 40.741 4.31 0.00 0.00 2.74
240 266 7.606839 AGGAAATACTAGTACTGCTTCCAAAAC 59.393 37.037 23.61 8.18 34.55 2.43
252 278 3.740832 GCTTCCAAAACAAAAGATTCGGG 59.259 43.478 0.00 0.00 0.00 5.14
253 279 4.306600 CTTCCAAAACAAAAGATTCGGGG 58.693 43.478 0.00 0.00 0.00 5.73
254 280 3.567397 TCCAAAACAAAAGATTCGGGGA 58.433 40.909 0.00 0.00 0.00 4.81
255 281 3.961408 TCCAAAACAAAAGATTCGGGGAA 59.039 39.130 0.00 0.00 0.00 3.97
288 340 4.978580 GTGTCTTTTCAACTGAAATGAGGC 59.021 41.667 16.71 9.99 43.89 4.70
304 356 2.139118 GAGGCTGCGATAATGTCTTCC 58.861 52.381 0.00 0.00 0.00 3.46
329 381 3.103911 GCACGTCACGGTTCGGAG 61.104 66.667 0.35 1.83 0.00 4.63
396 451 2.479560 CCGAATTGAATTCCCTTTCGCC 60.480 50.000 20.33 0.00 38.21 5.54
411 468 1.860641 TCGCCCTCACCTTTCTGATA 58.139 50.000 0.00 0.00 0.00 2.15
432 500 2.892305 GATCTGTCGGAGCCAATCG 58.108 57.895 0.00 0.00 0.00 3.34
468 536 0.108520 CCGACGATTTTCTTCCGGGA 60.109 55.000 0.00 0.00 33.94 5.14
501 569 0.521450 CGTGACAGTGAGATCGGTCG 60.521 60.000 0.00 0.00 35.82 4.79
507 575 1.297745 GTGAGATCGGTCGCTCGAC 60.298 63.158 13.45 13.45 42.21 4.20
508 576 2.052941 GAGATCGGTCGCTCGACG 60.053 66.667 15.07 10.93 45.41 5.12
516 584 2.142239 GTCGCTCGACGTTGTACCG 61.142 63.158 6.67 4.63 44.19 4.02
524 592 1.205064 ACGTTGTACCGTCTCGTCG 59.795 57.895 0.00 0.00 35.95 5.12
559 627 2.073056 TGCACGTGCTACTACAAATGG 58.927 47.619 37.59 0.00 42.66 3.16
571 639 1.677633 CAAATGGGTCCACCGGGTC 60.678 63.158 6.32 0.00 44.64 4.46
625 693 0.746063 ACCATGCACGCATTATTGGG 59.254 50.000 12.65 8.56 41.36 4.12
680 748 3.186047 CCCACGATCGAACCGCAC 61.186 66.667 24.34 0.00 0.00 5.34
681 749 3.186047 CCACGATCGAACCGCACC 61.186 66.667 24.34 0.00 0.00 5.01
682 750 3.541831 CACGATCGAACCGCACCG 61.542 66.667 24.34 0.00 0.00 4.94
685 753 3.849953 GATCGAACCGCACCGCAC 61.850 66.667 0.00 0.00 0.00 5.34
719 787 4.505970 CCCCCTCCTCCCCCTCTG 62.506 77.778 0.00 0.00 0.00 3.35
720 788 4.505970 CCCCTCCTCCCCCTCTGG 62.506 77.778 0.00 0.00 0.00 3.86
876 944 4.862823 CCGACTCCCCCTCCCTCC 62.863 77.778 0.00 0.00 0.00 4.30
877 945 4.862823 CGACTCCCCCTCCCTCCC 62.863 77.778 0.00 0.00 0.00 4.30
878 946 3.369388 GACTCCCCCTCCCTCCCT 61.369 72.222 0.00 0.00 0.00 4.20
879 947 3.369388 ACTCCCCCTCCCTCCCTC 61.369 72.222 0.00 0.00 0.00 4.30
902 970 0.182775 GTATCCATCCCACCACACCC 59.817 60.000 0.00 0.00 0.00 4.61
903 971 0.253394 TATCCATCCCACCACACCCA 60.253 55.000 0.00 0.00 0.00 4.51
908 976 4.947147 CCCACCACACCCACACCG 62.947 72.222 0.00 0.00 0.00 4.94
911 979 4.868116 ACCACACCCACACCGCAC 62.868 66.667 0.00 0.00 0.00 5.34
964 1038 1.883021 CAAATTGCAGACGGGTCCC 59.117 57.895 0.00 0.00 0.00 4.46
979 1053 2.607750 CCCCGGATCGATCCCCAT 60.608 66.667 33.51 0.00 44.24 4.00
980 1054 2.224159 CCCCGGATCGATCCCCATT 61.224 63.158 33.51 0.00 44.24 3.16
981 1055 1.296715 CCCGGATCGATCCCCATTC 59.703 63.158 33.51 12.21 44.24 2.67
982 1056 1.296715 CCGGATCGATCCCCATTCC 59.703 63.158 33.51 13.38 44.24 3.01
1302 1382 4.927782 TGCCGCGTCTGCCTTGTT 62.928 61.111 4.92 0.00 38.08 2.83
1305 1385 4.430423 CGCGTCTGCCTTGTTCGC 62.430 66.667 0.00 0.00 42.78 4.70
1502 1590 0.831307 GCCTGGATTTAGGGACGAGT 59.169 55.000 0.00 0.00 38.32 4.18
1504 1592 1.139058 CCTGGATTTAGGGACGAGTGG 59.861 57.143 0.00 0.00 34.06 4.00
1507 1595 1.413077 GGATTTAGGGACGAGTGGAGG 59.587 57.143 0.00 0.00 0.00 4.30
1688 1780 2.890474 CGTGCCATCGCTGTACCC 60.890 66.667 0.00 0.00 35.36 3.69
1761 1853 3.195610 TGATGAGAAATCTGTGTACGGCT 59.804 43.478 0.00 0.00 0.00 5.52
1831 1923 2.027192 TGTCTTATGAACACCAGAGGGC 60.027 50.000 0.00 0.00 37.90 5.19
1834 1926 1.622607 TATGAACACCAGAGGGCCGG 61.623 60.000 0.00 0.00 37.90 6.13
1835 1927 3.637273 GAACACCAGAGGGCCGGT 61.637 66.667 1.90 0.00 37.90 5.28
1839 1931 3.637273 ACCAGAGGGCCGGTGTTC 61.637 66.667 1.90 0.00 37.90 3.18
1842 1934 1.672356 CAGAGGGCCGGTGTTCTTG 60.672 63.158 1.90 0.00 0.00 3.02
1864 1956 1.348008 TGCCTCTTGGATGCCCCTAG 61.348 60.000 0.00 0.00 38.85 3.02
1868 1960 0.548031 TCTTGGATGCCCCTAGCTTG 59.452 55.000 0.00 0.00 44.23 4.01
1884 1976 6.222389 CCTAGCTTGTCTCTCCAGATATTTG 58.778 44.000 0.00 0.00 0.00 2.32
1898 1990 7.918076 TCCAGATATTTGTGGAGAAAGTTACT 58.082 34.615 0.00 0.00 40.23 2.24
1899 1991 9.042450 TCCAGATATTTGTGGAGAAAGTTACTA 57.958 33.333 0.00 0.00 40.23 1.82
1942 2034 3.936453 TCTTTCCATGTATGCCGTTGTAC 59.064 43.478 0.00 0.00 0.00 2.90
1945 2037 4.316205 TCCATGTATGCCGTTGTACTAG 57.684 45.455 0.00 0.00 0.00 2.57
1947 2039 3.492656 CCATGTATGCCGTTGTACTAGCT 60.493 47.826 0.00 0.00 0.00 3.32
1949 2041 4.987408 TGTATGCCGTTGTACTAGCTAA 57.013 40.909 0.00 0.00 0.00 3.09
1951 2043 5.526115 TGTATGCCGTTGTACTAGCTAATC 58.474 41.667 0.00 0.00 0.00 1.75
1952 2044 4.939052 ATGCCGTTGTACTAGCTAATCT 57.061 40.909 0.00 0.00 0.00 2.40
1953 2045 4.303086 TGCCGTTGTACTAGCTAATCTC 57.697 45.455 0.00 0.00 0.00 2.75
1954 2046 3.697542 TGCCGTTGTACTAGCTAATCTCA 59.302 43.478 0.00 0.00 0.00 3.27
1955 2047 4.158949 TGCCGTTGTACTAGCTAATCTCAA 59.841 41.667 0.00 0.00 0.00 3.02
1956 2048 4.503370 GCCGTTGTACTAGCTAATCTCAAC 59.497 45.833 14.91 14.91 0.00 3.18
1958 2050 6.097356 CCGTTGTACTAGCTAATCTCAACAA 58.903 40.000 20.21 7.49 35.10 2.83
1959 2051 6.253727 CCGTTGTACTAGCTAATCTCAACAAG 59.746 42.308 20.21 12.60 35.10 3.16
1960 2052 6.807230 CGTTGTACTAGCTAATCTCAACAAGT 59.193 38.462 20.21 7.34 35.10 3.16
1965 2072 7.659652 ACTAGCTAATCTCAACAAGTGTTTC 57.340 36.000 0.00 0.00 35.83 2.78
1967 2074 6.551385 AGCTAATCTCAACAAGTGTTTCTG 57.449 37.500 0.00 0.00 35.83 3.02
1973 2080 6.048073 TCTCAACAAGTGTTTCTGAAATCG 57.952 37.500 6.06 0.00 35.83 3.34
1976 2083 5.007626 TCAACAAGTGTTTCTGAAATCGGAG 59.992 40.000 6.06 0.52 35.83 4.63
1988 2095 1.534729 AATCGGAGCAAGAAACCACC 58.465 50.000 0.00 0.00 0.00 4.61
1989 2096 0.400213 ATCGGAGCAAGAAACCACCA 59.600 50.000 0.00 0.00 0.00 4.17
1990 2097 0.181587 TCGGAGCAAGAAACCACCAA 59.818 50.000 0.00 0.00 0.00 3.67
1992 2099 1.613437 CGGAGCAAGAAACCACCAATT 59.387 47.619 0.00 0.00 0.00 2.32
1995 2102 4.082245 CGGAGCAAGAAACCACCAATTATT 60.082 41.667 0.00 0.00 0.00 1.40
1996 2103 5.124776 CGGAGCAAGAAACCACCAATTATTA 59.875 40.000 0.00 0.00 0.00 0.98
1997 2104 6.349777 CGGAGCAAGAAACCACCAATTATTAA 60.350 38.462 0.00 0.00 0.00 1.40
1998 2105 7.382898 GGAGCAAGAAACCACCAATTATTAAA 58.617 34.615 0.00 0.00 0.00 1.52
1999 2106 7.875554 GGAGCAAGAAACCACCAATTATTAAAA 59.124 33.333 0.00 0.00 0.00 1.52
2002 2109 8.279800 GCAAGAAACCACCAATTATTAAAACAC 58.720 33.333 0.00 0.00 0.00 3.32
2004 2111 7.942990 AGAAACCACCAATTATTAAAACACGA 58.057 30.769 0.00 0.00 0.00 4.35
2005 2112 8.581578 AGAAACCACCAATTATTAAAACACGAT 58.418 29.630 0.00 0.00 0.00 3.73
2006 2113 9.843334 GAAACCACCAATTATTAAAACACGATA 57.157 29.630 0.00 0.00 0.00 2.92
2007 2114 9.849166 AAACCACCAATTATTAAAACACGATAG 57.151 29.630 0.00 0.00 46.19 2.08
2038 2148 7.488187 AACCTGATCAATGATCAATAAGACG 57.512 36.000 24.09 12.10 46.51 4.18
2057 2216 2.199236 CGGTGCTATTCGGGTACTTTC 58.801 52.381 0.00 0.00 0.00 2.62
2059 2218 3.195661 GGTGCTATTCGGGTACTTTCTG 58.804 50.000 0.00 0.00 0.00 3.02
2062 2221 3.195661 GCTATTCGGGTACTTTCTGGTG 58.804 50.000 0.00 0.00 0.00 4.17
2069 2228 2.550639 GGGTACTTTCTGGTGGCGTTTA 60.551 50.000 0.00 0.00 0.00 2.01
2075 2235 6.584185 ACTTTCTGGTGGCGTTTATTAAAT 57.416 33.333 0.00 0.00 0.00 1.40
2089 2249 9.554724 GCGTTTATTAAATCAGATCAAGAAACA 57.445 29.630 18.68 0.00 33.76 2.83
2149 2312 8.754991 TTAAACCAGATGAAGAAACCACTAAA 57.245 30.769 0.00 0.00 0.00 1.85
2150 2313 7.654022 AAACCAGATGAAGAAACCACTAAAA 57.346 32.000 0.00 0.00 0.00 1.52
2158 2323 6.205784 TGAAGAAACCACTAAAAAGCAATCG 58.794 36.000 0.00 0.00 0.00 3.34
2176 2345 6.725246 GCAATCGCTACTGGTGTTTATTAAT 58.275 36.000 0.00 0.00 34.30 1.40
2179 2348 5.045215 TCGCTACTGGTGTTTATTAATCCG 58.955 41.667 0.00 0.00 0.00 4.18
2193 2362 7.562454 TTATTAATCCGGATCAAGAAACCAC 57.438 36.000 19.43 0.00 0.00 4.16
2202 2371 6.338146 CGGATCAAGAAACCACTACTATTCA 58.662 40.000 0.00 0.00 0.00 2.57
2203 2372 6.816640 CGGATCAAGAAACCACTACTATTCAA 59.183 38.462 0.00 0.00 0.00 2.69
2204 2373 7.495934 CGGATCAAGAAACCACTACTATTCAAT 59.504 37.037 0.00 0.00 0.00 2.57
2205 2374 8.831550 GGATCAAGAAACCACTACTATTCAATC 58.168 37.037 0.00 0.00 0.00 2.67
2225 2399 9.947433 TTCAATCGGGTAATTTCTAGAGTTAAA 57.053 29.630 0.00 0.00 0.00 1.52
2246 2420 9.626045 GTTAAATAAACCAGATGAAGAAACCAG 57.374 33.333 0.00 0.00 31.38 4.00
2250 2424 2.107204 ACCAGATGAAGAAACCAGCACT 59.893 45.455 0.00 0.00 0.00 4.40
2253 2427 4.318332 CAGATGAAGAAACCAGCACTACA 58.682 43.478 0.00 0.00 0.00 2.74
2264 2438 3.244630 ACCAGCACTACAATTCGGGTAAA 60.245 43.478 0.00 0.00 0.00 2.01
2271 2445 5.006358 CACTACAATTCGGGTAAATTCTCCG 59.994 44.000 7.49 7.49 44.59 4.63
2326 2504 8.202137 GCACTAATCAGGAGTATAAAACCAGTA 58.798 37.037 0.00 0.00 0.00 2.74
2351 2530 4.466828 GTTGTTGGTTGAGTGATCGATTG 58.533 43.478 0.00 0.00 0.00 2.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
202 228 4.487714 AGTATTTCCTTCCGATTCTGCA 57.512 40.909 0.00 0.00 0.00 4.41
225 251 6.142320 CGAATCTTTTGTTTTGGAAGCAGTAC 59.858 38.462 0.00 0.00 0.00 2.73
226 252 6.205784 CGAATCTTTTGTTTTGGAAGCAGTA 58.794 36.000 0.00 0.00 0.00 2.74
227 253 5.043248 CGAATCTTTTGTTTTGGAAGCAGT 58.957 37.500 0.00 0.00 0.00 4.40
230 256 3.740832 CCCGAATCTTTTGTTTTGGAAGC 59.259 43.478 0.00 0.00 35.58 3.86
264 290 5.207768 CCTCATTTCAGTTGAAAAGACACG 58.792 41.667 10.96 2.18 45.81 4.49
265 291 4.978580 GCCTCATTTCAGTTGAAAAGACAC 59.021 41.667 10.96 2.62 45.81 3.67
266 292 4.889409 AGCCTCATTTCAGTTGAAAAGACA 59.111 37.500 10.96 0.00 45.81 3.41
288 340 3.046390 GACTCGGAAGACATTATCGCAG 58.954 50.000 0.00 0.00 35.39 5.18
304 356 2.365068 CCGTGACGTGCTTGACTCG 61.365 63.158 3.64 0.00 40.98 4.18
329 381 1.197721 CGATTCCTGCCATTTATCCGC 59.802 52.381 0.00 0.00 0.00 5.54
396 451 5.071519 ACAGATCCATATCAGAAAGGTGAGG 59.928 44.000 0.00 0.00 34.28 3.86
411 468 1.071385 GATTGGCTCCGACAGATCCAT 59.929 52.381 0.00 0.00 40.45 3.41
507 575 2.142239 GCGACGAGACGGTACAACG 61.142 63.158 0.00 0.00 40.31 4.10
508 576 1.799121 GGCGACGAGACGGTACAAC 60.799 63.158 0.00 0.00 0.00 3.32
546 614 2.640184 GGTGGACCCATTTGTAGTAGC 58.360 52.381 0.00 0.00 0.00 3.58
547 615 2.419574 CCGGTGGACCCATTTGTAGTAG 60.420 54.545 0.00 0.00 0.00 2.57
548 616 1.555992 CCGGTGGACCCATTTGTAGTA 59.444 52.381 0.00 0.00 0.00 1.82
549 617 0.326927 CCGGTGGACCCATTTGTAGT 59.673 55.000 0.00 0.00 0.00 2.73
550 618 0.393808 CCCGGTGGACCCATTTGTAG 60.394 60.000 0.00 0.00 0.00 2.74
551 619 1.135068 ACCCGGTGGACCCATTTGTA 61.135 55.000 0.00 0.00 34.81 2.41
559 627 2.253403 GATCCAAGACCCGGTGGACC 62.253 65.000 13.37 0.15 46.53 4.46
684 752 4.344865 GGACACCCCACATGCGGT 62.345 66.667 0.00 0.00 34.14 5.68
713 781 1.190833 CCCGATCTCATCCCAGAGGG 61.191 65.000 0.00 0.00 46.11 4.30
715 783 1.670590 GCCCGATCTCATCCCAGAG 59.329 63.158 0.00 0.00 36.97 3.35
716 784 2.203082 CGCCCGATCTCATCCCAGA 61.203 63.158 0.00 0.00 0.00 3.86
717 785 2.341543 CGCCCGATCTCATCCCAG 59.658 66.667 0.00 0.00 0.00 4.45
718 786 2.443952 ACGCCCGATCTCATCCCA 60.444 61.111 0.00 0.00 0.00 4.37
719 787 2.340443 GACGCCCGATCTCATCCC 59.660 66.667 0.00 0.00 0.00 3.85
720 788 2.340443 GGACGCCCGATCTCATCC 59.660 66.667 0.00 0.00 0.00 3.51
834 902 2.677003 CGCATTTATAGCCGGCCCG 61.677 63.158 26.15 9.28 0.00 6.13
836 904 2.561373 GCGCATTTATAGCCGGCC 59.439 61.111 26.15 5.07 0.00 6.13
837 905 2.561373 GGCGCATTTATAGCCGGC 59.439 61.111 21.89 21.89 41.53 6.13
841 909 1.524008 GGGGTGGGCGCATTTATAGC 61.524 60.000 10.83 0.00 0.00 2.97
842 910 1.234615 CGGGGTGGGCGCATTTATAG 61.235 60.000 10.83 0.00 0.00 1.31
914 982 3.775654 GTGGTCTGGGCGAGGGAG 61.776 72.222 0.00 0.00 0.00 4.30
923 991 0.321653 CTTCTTTCGGGGTGGTCTGG 60.322 60.000 0.00 0.00 0.00 3.86
930 998 2.969300 TTTGCGCCTTCTTTCGGGGT 62.969 55.000 4.18 0.00 36.88 4.95
1502 1590 2.922955 TCTCTCTCTTCTCTTCCCTCCA 59.077 50.000 0.00 0.00 0.00 3.86
1504 1592 4.275936 CGAATCTCTCTCTTCTCTTCCCTC 59.724 50.000 0.00 0.00 0.00 4.30
1507 1595 3.243401 GGCGAATCTCTCTCTTCTCTTCC 60.243 52.174 0.00 0.00 0.00 3.46
1688 1780 6.904011 CGCTCTCTGCTGAAAAATATTTACAG 59.096 38.462 21.08 21.08 40.11 2.74
1805 1897 5.029807 TCTGGTGTTCATAAGACACACAA 57.970 39.130 9.29 4.24 42.26 3.33
1806 1898 4.503123 CCTCTGGTGTTCATAAGACACACA 60.503 45.833 9.29 4.65 42.26 3.72
1807 1899 3.997021 CCTCTGGTGTTCATAAGACACAC 59.003 47.826 9.29 6.82 40.16 3.82
1813 1905 1.743772 CGGCCCTCTGGTGTTCATAAG 60.744 57.143 0.00 0.00 0.00 1.73
1831 1923 1.856265 GAGGCAAGCAAGAACACCGG 61.856 60.000 0.00 0.00 0.00 5.28
1834 1926 1.000938 CCAAGAGGCAAGCAAGAACAC 60.001 52.381 0.00 0.00 0.00 3.32
1835 1927 1.133823 TCCAAGAGGCAAGCAAGAACA 60.134 47.619 0.00 0.00 33.74 3.18
1836 1928 1.609208 TCCAAGAGGCAAGCAAGAAC 58.391 50.000 0.00 0.00 33.74 3.01
1837 1929 2.165167 CATCCAAGAGGCAAGCAAGAA 58.835 47.619 0.00 0.00 33.74 2.52
1839 1931 0.172803 GCATCCAAGAGGCAAGCAAG 59.827 55.000 0.00 0.00 39.28 4.01
1842 1934 2.421399 GGGCATCCAAGAGGCAAGC 61.421 63.158 3.49 0.00 41.39 4.01
1864 1956 4.574013 CCACAAATATCTGGAGAGACAAGC 59.426 45.833 0.00 0.00 0.00 4.01
1909 2001 9.120538 GGCATACATGGAAAGAGTAAAATAAGA 57.879 33.333 0.00 0.00 0.00 2.10
1927 2019 5.524971 TTAGCTAGTACAACGGCATACAT 57.475 39.130 0.00 0.00 0.00 2.29
1930 2022 5.533528 TGAGATTAGCTAGTACAACGGCATA 59.466 40.000 0.00 0.00 0.00 3.14
1932 2024 3.697542 TGAGATTAGCTAGTACAACGGCA 59.302 43.478 0.00 0.00 0.00 5.69
1933 2025 4.303086 TGAGATTAGCTAGTACAACGGC 57.697 45.455 0.00 0.00 0.00 5.68
1942 2034 7.600375 TCAGAAACACTTGTTGAGATTAGCTAG 59.400 37.037 0.00 0.00 38.44 3.42
1945 2037 6.545504 TCAGAAACACTTGTTGAGATTAGC 57.454 37.500 0.00 0.00 38.44 3.09
1947 2039 8.282592 CGATTTCAGAAACACTTGTTGAGATTA 58.717 33.333 0.00 0.00 38.44 1.75
1949 2041 6.293626 CCGATTTCAGAAACACTTGTTGAGAT 60.294 38.462 0.00 0.00 38.44 2.75
1951 2043 5.007626 TCCGATTTCAGAAACACTTGTTGAG 59.992 40.000 0.00 0.00 38.44 3.02
1952 2044 4.878971 TCCGATTTCAGAAACACTTGTTGA 59.121 37.500 0.00 0.00 38.44 3.18
1953 2045 5.168526 TCCGATTTCAGAAACACTTGTTG 57.831 39.130 0.00 0.00 38.44 3.33
1954 2046 4.261197 GCTCCGATTTCAGAAACACTTGTT 60.261 41.667 0.00 0.00 40.50 2.83
1955 2047 3.251004 GCTCCGATTTCAGAAACACTTGT 59.749 43.478 0.00 0.00 0.00 3.16
1956 2048 3.250762 TGCTCCGATTTCAGAAACACTTG 59.749 43.478 0.00 0.00 0.00 3.16
1958 2050 3.126001 TGCTCCGATTTCAGAAACACT 57.874 42.857 0.00 0.00 0.00 3.55
1959 2051 3.498397 TCTTGCTCCGATTTCAGAAACAC 59.502 43.478 0.00 0.00 0.00 3.32
1960 2052 3.738982 TCTTGCTCCGATTTCAGAAACA 58.261 40.909 0.00 0.00 0.00 2.83
1965 2072 2.813754 TGGTTTCTTGCTCCGATTTCAG 59.186 45.455 0.00 0.00 0.00 3.02
1967 2074 2.095212 GGTGGTTTCTTGCTCCGATTTC 60.095 50.000 0.00 0.00 0.00 2.17
1973 2080 5.405935 AATAATTGGTGGTTTCTTGCTCC 57.594 39.130 0.00 0.00 0.00 4.70
1976 2083 8.279800 GTGTTTTAATAATTGGTGGTTTCTTGC 58.720 33.333 0.00 0.00 0.00 4.01
1997 2104 9.661563 TGATCAGGTTTAATAACTATCGTGTTT 57.338 29.630 0.00 0.00 34.59 2.83
1998 2105 9.661563 TTGATCAGGTTTAATAACTATCGTGTT 57.338 29.630 0.00 0.00 34.59 3.32
1999 2106 9.832445 ATTGATCAGGTTTAATAACTATCGTGT 57.168 29.630 0.00 0.00 34.59 4.49
2018 2128 5.237127 GCACCGTCTTATTGATCATTGATCA 59.763 40.000 22.47 22.47 45.78 2.92
2019 2129 5.468072 AGCACCGTCTTATTGATCATTGATC 59.532 40.000 17.97 17.97 39.31 2.92
2020 2130 5.371526 AGCACCGTCTTATTGATCATTGAT 58.628 37.500 0.00 0.00 0.00 2.57
2021 2131 4.769688 AGCACCGTCTTATTGATCATTGA 58.230 39.130 0.00 0.00 0.00 2.57
2022 2132 6.791887 ATAGCACCGTCTTATTGATCATTG 57.208 37.500 0.00 0.00 0.00 2.82
2023 2133 6.146184 CGAATAGCACCGTCTTATTGATCATT 59.854 38.462 0.00 0.00 0.00 2.57
2024 2134 5.635280 CGAATAGCACCGTCTTATTGATCAT 59.365 40.000 0.00 0.00 0.00 2.45
2025 2135 4.982295 CGAATAGCACCGTCTTATTGATCA 59.018 41.667 0.00 0.00 0.00 2.92
2032 2142 1.477553 ACCCGAATAGCACCGTCTTA 58.522 50.000 0.00 0.00 0.00 2.10
2035 2145 0.743097 AGTACCCGAATAGCACCGTC 59.257 55.000 0.00 0.00 0.00 4.79
2036 2146 1.188863 AAGTACCCGAATAGCACCGT 58.811 50.000 0.00 0.00 0.00 4.83
2038 2148 3.195661 CAGAAAGTACCCGAATAGCACC 58.804 50.000 0.00 0.00 0.00 5.01
2057 2216 5.811399 TCTGATTTAATAAACGCCACCAG 57.189 39.130 0.00 0.00 0.00 4.00
2059 2218 6.371809 TGATCTGATTTAATAAACGCCACC 57.628 37.500 0.00 0.00 0.00 4.61
2062 2221 9.010366 GTTTCTTGATCTGATTTAATAAACGCC 57.990 33.333 0.00 0.00 0.00 5.68
2075 2235 9.298250 AGTAGTACTAGTTGTTTCTTGATCTGA 57.702 33.333 1.87 0.00 0.00 3.27
2158 2323 5.362263 TCCGGATTAATAAACACCAGTAGC 58.638 41.667 0.00 0.00 0.00 3.58
2161 2326 5.996644 TGATCCGGATTAATAAACACCAGT 58.003 37.500 20.22 0.00 0.00 4.00
2176 2345 3.170717 AGTAGTGGTTTCTTGATCCGGA 58.829 45.455 6.61 6.61 0.00 5.14
2179 2348 8.738645 ATTGAATAGTAGTGGTTTCTTGATCC 57.261 34.615 0.00 0.00 0.00 3.36
2219 2388 9.362151 TGGTTTCTTCATCTGGTTTATTTAACT 57.638 29.630 0.00 0.00 36.93 2.24
2225 2399 5.183904 GTGCTGGTTTCTTCATCTGGTTTAT 59.816 40.000 0.00 0.00 0.00 1.40
2232 2406 4.623932 TGTAGTGCTGGTTTCTTCATCT 57.376 40.909 0.00 0.00 0.00 2.90
2236 2410 4.378459 CCGAATTGTAGTGCTGGTTTCTTC 60.378 45.833 0.00 0.00 0.00 2.87
2246 2420 5.220796 GGAGAATTTACCCGAATTGTAGTGC 60.221 44.000 0.00 0.00 29.75 4.40
2264 2438 0.984230 TGTTTGGAGCCTCGGAGAAT 59.016 50.000 6.58 0.00 34.09 2.40
2271 2445 1.285950 GCCGTTTGTTTGGAGCCTC 59.714 57.895 0.00 0.00 0.00 4.70
2326 2504 2.810400 CGATCACTCAACCAACAACCCT 60.810 50.000 0.00 0.00 0.00 4.34


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

AutoCloner maintained by Alex Coulton.