Multiple sequence alignment - TraesCS2A01G504100

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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 TraesCS2A01G504100 chr2A 100.000 2411 0 0 1 2411 733148865 733151275 0.000000e+00 4453.0
1 TraesCS2A01G504100 chr2A 85.855 813 67 25 1016 1801 733161473 733162264 0.000000e+00 821.0
2 TraesCS2A01G504100 chr2A 100.000 111 0 0 2657 2767 733151521 733151631 3.610000e-49 206.0
3 TraesCS2A01G504100 chr2A 97.143 35 1 0 2733 2767 733164299 733164333 2.980000e-05 60.2
4 TraesCS2A01G504100 chr2B 87.808 2067 109 46 15 2005 728299240 728301239 0.000000e+00 2289.0
5 TraesCS2A01G504100 chr2B 87.532 385 33 10 2027 2409 728307311 728307682 5.470000e-117 431.0
6 TraesCS2A01G504100 chr2D 90.169 1780 77 32 15 1740 598930077 598931812 0.000000e+00 2228.0
7 TraesCS2A01G504100 chr2D 83.362 583 45 26 1837 2409 598932568 598933108 2.480000e-135 492.0
8 TraesCS2A01G504100 chr2D 96.471 85 3 0 2680 2764 598933189 598933273 1.030000e-29 141.0


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 TraesCS2A01G504100 chr2A 733148865 733151631 2766 False 2329.500000 4453 100.000000 1 2767 2 chr2A.!!$F1 2766
1 TraesCS2A01G504100 chr2A 733161473 733164333 2860 False 440.600000 821 91.499000 1016 2767 2 chr2A.!!$F2 1751
2 TraesCS2A01G504100 chr2B 728299240 728301239 1999 False 2289.000000 2289 87.808000 15 2005 1 chr2B.!!$F1 1990
3 TraesCS2A01G504100 chr2D 598930077 598933273 3196 False 953.666667 2228 90.000667 15 2764 3 chr2D.!!$F1 2749

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
712 769 0.108329 GAGGGTTCGAGCGAATTCCA 60.108 55.0 21.13 0.0 36.45 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 4601 0.114168 AGCCTCCGCTATCTCAGGAT 59.886 55.0 0.0 0.0 46.08 3.24 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
74 75 2.744202 CCAAGCTAGCAAGTAGGTGTTG 59.256 50.000 18.83 8.90 39.52 3.33
127 128 4.063529 ACGGAAGTGTGGCATGTG 57.936 55.556 0.00 0.00 46.97 3.21
128 129 1.600636 ACGGAAGTGTGGCATGTGG 60.601 57.895 0.00 0.00 46.97 4.17
129 130 2.334946 CGGAAGTGTGGCATGTGGG 61.335 63.158 0.00 0.00 0.00 4.61
130 131 2.639327 GGAAGTGTGGCATGTGGGC 61.639 63.158 0.00 0.00 43.73 5.36
233 245 0.439985 CACGTCACCTTTCATGAGCG 59.560 55.000 0.00 0.00 0.00 5.03
325 337 2.428890 TGATCAACAAACACCACAACCC 59.571 45.455 0.00 0.00 0.00 4.11
326 338 2.223803 TCAACAAACACCACAACCCT 57.776 45.000 0.00 0.00 0.00 4.34
327 339 2.096248 TCAACAAACACCACAACCCTC 58.904 47.619 0.00 0.00 0.00 4.30
328 340 2.099405 CAACAAACACCACAACCCTCT 58.901 47.619 0.00 0.00 0.00 3.69
329 341 2.052782 ACAAACACCACAACCCTCTC 57.947 50.000 0.00 0.00 0.00 3.20
330 342 0.944386 CAAACACCACAACCCTCTCG 59.056 55.000 0.00 0.00 0.00 4.04
338 350 1.878522 CAACCCTCTCGAATCCGCG 60.879 63.158 0.00 0.00 35.37 6.46
387 415 1.341913 ATGCATGCATGGGCCAATGT 61.342 50.000 31.74 4.69 40.13 2.71
388 416 0.686769 TGCATGCATGGGCCAATGTA 60.687 50.000 27.34 17.93 40.13 2.29
467 497 6.280855 AGTGTAAATTAATCCAAACTGCCC 57.719 37.500 0.00 0.00 0.00 5.36
507 537 8.783093 CGGATAATTGGATATGCTTTTCTTGTA 58.217 33.333 0.00 0.00 0.00 2.41
559 592 5.119694 GTTTCTAACTGGCTCTATCCCAAG 58.880 45.833 0.00 0.00 30.66 3.61
560 593 4.265856 TCTAACTGGCTCTATCCCAAGA 57.734 45.455 0.00 0.00 30.66 3.02
561 594 4.820775 TCTAACTGGCTCTATCCCAAGAT 58.179 43.478 0.00 0.00 36.44 2.40
562 595 5.965486 TCTAACTGGCTCTATCCCAAGATA 58.035 41.667 0.00 0.00 33.67 1.98
600 645 7.542477 CCGCTAGTAGATAACAAATCGATCAAT 59.458 37.037 0.00 0.00 0.00 2.57
624 673 0.179004 TGGGATTTATTCCGCGGCAT 60.179 50.000 23.51 19.54 46.52 4.40
625 674 0.240945 GGGATTTATTCCGCGGCATG 59.759 55.000 23.51 0.00 46.52 4.06
626 675 0.240945 GGATTTATTCCGCGGCATGG 59.759 55.000 23.51 0.00 33.93 3.66
628 677 1.812571 GATTTATTCCGCGGCATGGAT 59.187 47.619 23.51 13.69 34.91 3.41
650 707 2.791347 TTATAGGGTTTCGCTTGCCA 57.209 45.000 0.00 0.00 0.00 4.92
712 769 0.108329 GAGGGTTCGAGCGAATTCCA 60.108 55.000 21.13 0.00 36.45 3.53
799 856 0.321653 CCCCAAAGTCTCCGGTCTTG 60.322 60.000 0.00 0.00 0.00 3.02
800 857 0.321653 CCCAAAGTCTCCGGTCTTGG 60.322 60.000 0.00 8.41 0.00 3.61
801 858 0.321653 CCAAAGTCTCCGGTCTTGGG 60.322 60.000 0.00 8.46 0.00 4.12
802 859 0.685097 CAAAGTCTCCGGTCTTGGGA 59.315 55.000 0.00 0.00 0.00 4.37
853 912 0.192566 ATATTCCACCCGCCTCCCTA 59.807 55.000 0.00 0.00 0.00 3.53
932 992 2.650813 GATCGGCGATCCAACTGCCT 62.651 60.000 33.76 5.24 46.67 4.75
948 1008 4.781934 ACTGCCTCACCAGGTTTATTATC 58.218 43.478 0.00 0.00 42.74 1.75
949 1009 4.475016 ACTGCCTCACCAGGTTTATTATCT 59.525 41.667 0.00 0.00 42.74 1.98
950 1010 5.036117 TGCCTCACCAGGTTTATTATCTC 57.964 43.478 0.00 0.00 42.74 2.75
951 1011 4.721776 TGCCTCACCAGGTTTATTATCTCT 59.278 41.667 0.00 0.00 42.74 3.10
952 1012 5.903010 TGCCTCACCAGGTTTATTATCTCTA 59.097 40.000 0.00 0.00 42.74 2.43
953 1013 6.558775 TGCCTCACCAGGTTTATTATCTCTAT 59.441 38.462 0.00 0.00 42.74 1.98
1024 1085 3.157949 CCGCCCTCTCCTTCCTCC 61.158 72.222 0.00 0.00 0.00 4.30
1227 1291 0.248458 GGCAGGACAACAACAACGTG 60.248 55.000 0.00 0.00 0.00 4.49
1669 1768 4.041740 AGCATATTGTGAAAGCAGCATG 57.958 40.909 0.00 0.00 40.87 4.06
1709 1812 3.731867 GCATGCCGTTCTTTTCCATGTAG 60.732 47.826 6.36 0.00 36.54 2.74
1710 1813 3.134574 TGCCGTTCTTTTCCATGTAGT 57.865 42.857 0.00 0.00 0.00 2.73
1711 1814 4.274602 TGCCGTTCTTTTCCATGTAGTA 57.725 40.909 0.00 0.00 0.00 1.82
1760 1863 5.988310 AGACATGGAAATGAAAATGCTGA 57.012 34.783 0.00 0.00 0.00 4.26
1770 1873 5.712217 ATGAAAATGCTGATTTGATTGCG 57.288 34.783 0.00 0.00 31.83 4.85
1782 1885 5.593909 TGATTTGATTGCGGGACAAGATATT 59.406 36.000 0.00 0.00 42.87 1.28
1783 1886 4.898829 TTGATTGCGGGACAAGATATTG 57.101 40.909 0.00 0.00 42.87 1.90
1784 1887 4.149511 TGATTGCGGGACAAGATATTGA 57.850 40.909 7.16 0.00 42.87 2.57
1785 1888 4.129380 TGATTGCGGGACAAGATATTGAG 58.871 43.478 7.16 0.00 42.87 3.02
1787 1896 3.627395 TGCGGGACAAGATATTGAGTT 57.373 42.857 7.16 0.00 0.00 3.01
1792 1901 5.106317 GCGGGACAAGATATTGAGTTGAAAA 60.106 40.000 7.16 0.00 0.00 2.29
1796 1905 9.010029 GGGACAAGATATTGAGTTGAAAAACTA 57.990 33.333 7.16 0.00 32.22 2.24
1801 1916 9.574516 AAGATATTGAGTTGAAAAACTACACCT 57.425 29.630 0.00 0.00 32.22 4.00
1834 1967 3.737266 CGCCTACTCGTACACAAGAAAAA 59.263 43.478 0.00 0.00 0.00 1.94
1835 1968 4.143389 CGCCTACTCGTACACAAGAAAAAG 60.143 45.833 0.00 0.00 0.00 2.27
1880 2702 5.303078 TGATTTGCACCAAAAAGCCTAGTTA 59.697 36.000 0.00 0.00 36.90 2.24
1881 2703 4.846779 TTGCACCAAAAAGCCTAGTTAG 57.153 40.909 0.00 0.00 0.00 2.34
1882 2704 3.827722 TGCACCAAAAAGCCTAGTTAGT 58.172 40.909 0.00 0.00 0.00 2.24
1883 2705 3.568007 TGCACCAAAAAGCCTAGTTAGTG 59.432 43.478 0.00 0.00 0.00 2.74
1884 2706 3.057526 GCACCAAAAAGCCTAGTTAGTGG 60.058 47.826 0.00 0.00 0.00 4.00
1951 4475 3.950397 CCACCAGGTAGCACTATTTCAA 58.050 45.455 0.00 0.00 0.00 2.69
1959 4483 7.309133 CCAGGTAGCACTATTTCAATTTCAACA 60.309 37.037 0.00 0.00 0.00 3.33
1997 4556 1.069703 CGACATTGACAAGGCAGTGTG 60.070 52.381 8.90 0.00 38.60 3.82
2019 4578 2.642139 GCTACATGCACTGCACATTT 57.358 45.000 5.67 0.00 43.04 2.32
2020 4579 2.256174 GCTACATGCACTGCACATTTG 58.744 47.619 5.67 3.23 43.04 2.32
2021 4580 2.352030 GCTACATGCACTGCACATTTGT 60.352 45.455 5.67 9.39 43.04 2.83
2023 4582 3.287312 ACATGCACTGCACATTTGTAC 57.713 42.857 5.67 0.00 43.04 2.90
2025 4584 3.058016 ACATGCACTGCACATTTGTACTC 60.058 43.478 5.67 0.00 43.04 2.59
2027 4586 3.213506 TGCACTGCACATTTGTACTCTT 58.786 40.909 0.00 0.00 31.71 2.85
2028 4587 3.003585 TGCACTGCACATTTGTACTCTTG 59.996 43.478 0.00 0.00 31.71 3.02
2029 4588 3.003689 GCACTGCACATTTGTACTCTTGT 59.996 43.478 0.00 0.00 0.00 3.16
2030 4589 4.213270 GCACTGCACATTTGTACTCTTGTA 59.787 41.667 0.00 0.00 0.00 2.41
2031 4590 5.679906 CACTGCACATTTGTACTCTTGTAC 58.320 41.667 0.00 0.00 46.74 2.90
2045 4604 5.471257 ACTCTTGTACAGTTCTTTCGATCC 58.529 41.667 0.00 0.00 0.00 3.36
2047 4606 5.470368 TCTTGTACAGTTCTTTCGATCCTG 58.530 41.667 0.00 0.00 0.00 3.86
2048 4607 5.243060 TCTTGTACAGTTCTTTCGATCCTGA 59.757 40.000 0.00 0.00 0.00 3.86
2049 4608 5.060662 TGTACAGTTCTTTCGATCCTGAG 57.939 43.478 0.00 0.00 0.00 3.35
2050 4609 4.765339 TGTACAGTTCTTTCGATCCTGAGA 59.235 41.667 0.00 0.00 0.00 3.27
2051 4610 5.419155 TGTACAGTTCTTTCGATCCTGAGAT 59.581 40.000 0.00 0.00 34.57 2.75
2052 4611 6.602009 TGTACAGTTCTTTCGATCCTGAGATA 59.398 38.462 0.00 0.00 30.90 1.98
2053 4612 6.142818 ACAGTTCTTTCGATCCTGAGATAG 57.857 41.667 0.00 0.00 30.90 2.08
2054 4613 4.981674 CAGTTCTTTCGATCCTGAGATAGC 59.018 45.833 0.00 0.00 30.90 2.97
2055 4614 3.906014 TCTTTCGATCCTGAGATAGCG 57.094 47.619 0.00 0.00 30.90 4.26
2057 4616 2.271944 TTCGATCCTGAGATAGCGGA 57.728 50.000 0.00 0.00 30.90 5.54
2075 4634 2.210961 GGAGGCTTTTATCCTACGCAC 58.789 52.381 0.00 0.00 33.24 5.34
2088 4647 2.408050 CTACGCACTGCTGTCTCTTTT 58.592 47.619 0.00 0.00 0.00 2.27
2147 4707 3.009363 TCTGATTGTCTTTCCCTGATGCA 59.991 43.478 0.00 0.00 0.00 3.96
2157 4717 3.008835 TCCCTGATGCAAAGGATCAAG 57.991 47.619 18.12 3.67 36.91 3.02
2163 4723 4.005650 TGATGCAAAGGATCAAGTCTGAC 58.994 43.478 0.00 0.00 33.30 3.51
2164 4724 2.416747 TGCAAAGGATCAAGTCTGACG 58.583 47.619 1.52 0.00 33.30 4.35
2176 4736 4.873259 TCAAGTCTGACGTCATCAAACAAA 59.127 37.500 20.40 0.00 36.69 2.83
2200 4760 1.269051 CCCTTGTGTTTGCGTCTTTCC 60.269 52.381 0.00 0.00 0.00 3.13
2210 4770 1.265635 TGCGTCTTTCCCATTCAAACG 59.734 47.619 0.00 0.00 0.00 3.60
2239 4799 1.818060 GGCAATGTGATGTTGTGGCTA 59.182 47.619 0.00 0.00 0.00 3.93
2272 4832 5.334182 GCCAAGTCTTGTAAAACTCTAGTGC 60.334 44.000 11.61 0.00 0.00 4.40
2295 4855 5.666185 GCGCTTTGTATTTCACATTTTGCTC 60.666 40.000 0.00 0.00 36.90 4.26
2296 4856 5.164061 CGCTTTGTATTTCACATTTTGCTCC 60.164 40.000 0.00 0.00 36.90 4.70
2308 4868 2.572191 TTTGCTCCGTAGTGTATCCG 57.428 50.000 0.00 0.00 0.00 4.18
2309 4869 0.742505 TTGCTCCGTAGTGTATCCGG 59.257 55.000 0.00 0.00 43.03 5.14
2310 4870 1.007618 GCTCCGTAGTGTATCCGGC 60.008 63.158 0.00 0.00 41.46 6.13
2311 4871 1.731433 GCTCCGTAGTGTATCCGGCA 61.731 60.000 0.00 0.00 41.46 5.69
2312 4872 0.311165 CTCCGTAGTGTATCCGGCAG 59.689 60.000 0.00 0.00 41.46 4.85
2313 4873 0.107066 TCCGTAGTGTATCCGGCAGA 60.107 55.000 0.00 0.00 41.46 4.26
2314 4874 0.030369 CCGTAGTGTATCCGGCAGAC 59.970 60.000 0.00 0.00 34.62 3.51
2315 4875 1.022735 CGTAGTGTATCCGGCAGACT 58.977 55.000 9.98 9.98 0.00 3.24
2316 4876 1.404391 CGTAGTGTATCCGGCAGACTT 59.596 52.381 10.29 0.00 0.00 3.01
2317 4877 2.159282 CGTAGTGTATCCGGCAGACTTT 60.159 50.000 10.29 0.00 0.00 2.66
2318 4878 2.386661 AGTGTATCCGGCAGACTTTG 57.613 50.000 0.00 0.00 0.00 2.77
2319 4879 1.623811 AGTGTATCCGGCAGACTTTGT 59.376 47.619 0.00 0.00 0.00 2.83
2320 4880 2.829720 AGTGTATCCGGCAGACTTTGTA 59.170 45.455 0.00 0.00 0.00 2.41
2321 4881 3.451178 AGTGTATCCGGCAGACTTTGTAT 59.549 43.478 0.00 0.00 0.00 2.29
2322 4882 3.555956 GTGTATCCGGCAGACTTTGTATG 59.444 47.826 0.00 0.00 0.00 2.39
2323 4883 3.449377 TGTATCCGGCAGACTTTGTATGA 59.551 43.478 0.00 0.00 0.00 2.15
2324 4884 2.380084 TCCGGCAGACTTTGTATGAC 57.620 50.000 0.00 0.00 28.24 3.06
2325 4885 1.066430 TCCGGCAGACTTTGTATGACC 60.066 52.381 0.00 0.00 27.44 4.02
2357 4917 8.131100 ACTTAATCAATAAATGCCGACATTCTG 58.869 33.333 0.00 0.00 45.90 3.02
2362 4922 7.028962 TCAATAAATGCCGACATTCTGAAAAG 58.971 34.615 0.00 0.00 45.90 2.27
2364 4924 4.691860 AATGCCGACATTCTGAAAAGAG 57.308 40.909 0.00 0.00 43.08 2.85
2365 4925 2.426522 TGCCGACATTCTGAAAAGAGG 58.573 47.619 0.00 0.00 0.00 3.69
2366 4926 2.038426 TGCCGACATTCTGAAAAGAGGA 59.962 45.455 0.00 0.00 0.00 3.71
2368 4928 3.664107 CCGACATTCTGAAAAGAGGACA 58.336 45.455 0.00 0.00 0.00 4.02
2369 4929 3.681897 CCGACATTCTGAAAAGAGGACAG 59.318 47.826 0.00 0.00 0.00 3.51
2370 4930 4.310769 CGACATTCTGAAAAGAGGACAGT 58.689 43.478 0.00 0.00 33.93 3.55
2388 4948 1.537202 AGTTGTCGCAATTTCAGGAGC 59.463 47.619 0.00 0.00 0.00 4.70
2392 4952 2.938451 TGTCGCAATTTCAGGAGCTATG 59.062 45.455 0.00 0.00 0.00 2.23
2393 4953 1.942657 TCGCAATTTCAGGAGCTATGC 59.057 47.619 0.00 0.00 0.00 3.14
2409 4969 2.685850 ATGCACCGAAAGTACCCTAC 57.314 50.000 0.00 0.00 0.00 3.18
2695 5255 5.543714 ACGTGGAAACAATATGTGTACTCA 58.456 37.500 0.00 0.00 46.06 3.41
2707 5267 9.988350 CAATATGTGTACTCACCTTGATAAAAC 57.012 33.333 12.55 0.00 43.26 2.43
2735 5295 4.747108 AGATGTACGAATTAGCATGCTGAC 59.253 41.667 30.42 16.01 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 4.722700 ATGGCACTCGTGGTGGGC 62.723 66.667 11.68 3.80 45.44 5.36
3 4 0.606401 AGAAATGGCACTCGTGGTGG 60.606 55.000 11.68 0.00 45.44 4.61
5 6 0.687354 AGAGAAATGGCACTCGTGGT 59.313 50.000 0.00 0.00 38.08 4.16
6 7 2.672961 TAGAGAAATGGCACTCGTGG 57.327 50.000 0.00 0.00 38.08 4.94
7 8 3.525537 ACATAGAGAAATGGCACTCGTG 58.474 45.455 0.00 0.11 38.08 4.35
8 9 3.895232 ACATAGAGAAATGGCACTCGT 57.105 42.857 0.00 0.00 38.08 4.18
9 10 5.551760 AAAACATAGAGAAATGGCACTCG 57.448 39.130 0.00 0.00 38.08 4.18
35 36 1.470996 GGATGCCAACAACCTTGCCA 61.471 55.000 0.00 0.00 35.88 4.92
74 75 2.953640 TCGTGTAAACATTGAACCGC 57.046 45.000 0.00 0.00 0.00 5.68
152 153 4.327087 CCAAAAGCGAGGTTGCATATTTTC 59.673 41.667 0.00 0.00 37.31 2.29
205 216 5.379732 TGAAAGGTGACGTGAAAAACTTT 57.620 34.783 0.00 0.00 0.00 2.66
233 245 2.286654 GCAAGATCTGATTGGCGCTTAC 60.287 50.000 7.64 0.00 0.00 2.34
325 337 0.855349 CATTTCCGCGGATTCGAGAG 59.145 55.000 31.56 11.06 38.46 3.20
326 338 0.458260 TCATTTCCGCGGATTCGAGA 59.542 50.000 31.56 19.14 38.46 4.04
327 339 1.193203 CATCATTTCCGCGGATTCGAG 59.807 52.381 31.56 17.11 39.00 4.04
328 340 1.217001 CATCATTTCCGCGGATTCGA 58.783 50.000 31.56 24.23 39.00 3.71
329 341 0.235665 CCATCATTTCCGCGGATTCG 59.764 55.000 31.56 19.65 39.81 3.34
330 342 1.002468 CACCATCATTTCCGCGGATTC 60.002 52.381 31.56 0.00 0.00 2.52
338 350 2.093500 GCCTTTTCCCACCATCATTTCC 60.093 50.000 0.00 0.00 0.00 3.13
439 469 7.151308 CAGTTTGGATTAATTTACACTTGCCA 58.849 34.615 0.00 0.00 0.00 4.92
507 537 2.540515 CGTCTCAGCCGTATGTTGATT 58.459 47.619 0.00 0.00 33.39 2.57
540 573 6.672266 TTATCTTGGGATAGAGCCAGTTAG 57.328 41.667 0.00 0.00 36.03 2.34
600 645 3.942748 GCCGCGGAATAAATCCCATAATA 59.057 43.478 33.48 0.00 46.39 0.98
603 648 1.072489 TGCCGCGGAATAAATCCCATA 59.928 47.619 33.48 0.00 46.39 2.74
613 658 1.909700 AATTATCCATGCCGCGGAAT 58.090 45.000 33.48 24.55 35.77 3.01
624 673 5.472137 GCAAGCGAAACCCTATAATTATCCA 59.528 40.000 0.00 0.00 0.00 3.41
625 674 5.106277 GGCAAGCGAAACCCTATAATTATCC 60.106 44.000 0.00 0.00 0.00 2.59
626 675 5.472137 TGGCAAGCGAAACCCTATAATTATC 59.528 40.000 0.00 0.00 0.00 1.75
628 677 4.577283 GTGGCAAGCGAAACCCTATAATTA 59.423 41.667 0.00 0.00 0.00 1.40
650 707 3.920196 ACGTCCGGTTGCTTCGGT 61.920 61.111 0.00 0.00 46.82 4.69
712 769 2.814336 GACAAGGGCGAAAATTCAGAGT 59.186 45.455 0.00 0.00 0.00 3.24
750 807 2.224402 GGAATTTCCTCCGGGATCTCTG 60.224 54.545 8.25 0.00 41.87 3.35
801 858 3.291101 TACGCGTGCAACCTCCCTC 62.291 63.158 24.59 0.00 0.00 4.30
802 859 3.296709 CTACGCGTGCAACCTCCCT 62.297 63.158 24.59 0.00 0.00 4.20
853 912 1.299468 GGCGTGAGAGCGATCGATT 60.299 57.895 21.57 5.67 38.18 3.34
932 992 7.455008 GGGAGATAGAGATAATAAACCTGGTGA 59.545 40.741 0.00 0.00 0.00 4.02
948 1008 2.992114 CGGGGCGGGGAGATAGAG 60.992 72.222 0.00 0.00 0.00 2.43
1024 1085 1.449246 CTGCTTTCGGCTGGAGGAG 60.449 63.158 0.00 0.00 42.39 3.69
1227 1291 0.396278 ACCCCTGGCCGTAGTAGTAC 60.396 60.000 0.00 0.00 0.00 2.73
1610 1709 8.980481 ATAATTAAACAAGTGGACATAGAGGG 57.020 34.615 0.00 0.00 0.00 4.30
1650 1749 4.989044 TCACATGCTGCTTTCACAATATG 58.011 39.130 0.00 0.00 0.00 1.78
1669 1768 1.153784 CATGCACGCCCCAAATCAC 60.154 57.895 0.00 0.00 0.00 3.06
1735 1838 8.750515 TCAGCATTTTCATTTCCATGTCTATA 57.249 30.769 0.00 0.00 0.00 1.31
1760 1863 5.593909 TCAATATCTTGTCCCGCAATCAAAT 59.406 36.000 0.00 0.00 36.36 2.32
1770 1873 7.886338 AGTTTTTCAACTCAATATCTTGTCCC 58.114 34.615 0.00 0.00 39.15 4.46
1782 1885 5.588648 CCAGAAGGTGTAGTTTTTCAACTCA 59.411 40.000 0.00 0.00 42.66 3.41
1783 1886 6.061231 CCAGAAGGTGTAGTTTTTCAACTC 57.939 41.667 0.00 0.00 42.66 3.01
1801 1916 1.605058 GAGTAGGCGAGGCACCAGAA 61.605 60.000 0.00 0.00 0.00 3.02
1812 1927 2.624316 TTCTTGTGTACGAGTAGGCG 57.376 50.000 0.00 0.00 37.29 5.52
1813 1928 4.748600 ACTTTTTCTTGTGTACGAGTAGGC 59.251 41.667 0.00 0.00 0.00 3.93
1834 1967 3.557228 AGACCGTCGAATAGTCCTACT 57.443 47.619 7.02 0.00 0.00 2.57
1835 1968 4.095483 TCAAAGACCGTCGAATAGTCCTAC 59.905 45.833 7.02 0.00 0.00 3.18
1881 2703 4.814294 CTACTCGTGCCCCGCCAC 62.814 72.222 0.00 0.00 36.19 5.01
1884 2706 4.208686 CTCCTACTCGTGCCCCGC 62.209 72.222 0.00 0.00 36.19 6.13
1887 2709 2.180159 TTTGCCTCCTACTCGTGCCC 62.180 60.000 0.00 0.00 0.00 5.36
1951 4475 1.538047 ATGGCTGCGTCTGTTGAAAT 58.462 45.000 0.00 0.00 0.00 2.17
1959 4483 1.290009 GGCAAAAATGGCTGCGTCT 59.710 52.632 0.00 0.00 39.55 4.18
2020 4579 6.527372 GGATCGAAAGAACTGTACAAGAGTAC 59.473 42.308 0.00 0.00 46.75 2.73
2036 4595 2.554462 TCCGCTATCTCAGGATCGAAAG 59.446 50.000 0.00 0.00 33.71 2.62
2037 4596 2.554462 CTCCGCTATCTCAGGATCGAAA 59.446 50.000 0.00 0.00 33.04 3.46
2040 4599 0.808125 CCTCCGCTATCTCAGGATCG 59.192 60.000 0.00 0.00 33.04 3.69
2041 4600 0.530288 GCCTCCGCTATCTCAGGATC 59.470 60.000 0.00 0.00 33.04 3.36
2042 4601 0.114168 AGCCTCCGCTATCTCAGGAT 59.886 55.000 0.00 0.00 46.08 3.24
2043 4602 1.539165 AGCCTCCGCTATCTCAGGA 59.461 57.895 0.00 0.00 46.08 3.86
2053 4612 1.499049 CGTAGGATAAAAGCCTCCGC 58.501 55.000 0.00 0.00 36.96 5.54
2054 4613 1.202486 TGCGTAGGATAAAAGCCTCCG 60.202 52.381 0.00 0.00 37.84 4.63
2055 4614 2.158943 AGTGCGTAGGATAAAAGCCTCC 60.159 50.000 0.00 0.00 36.96 4.30
2057 4616 2.906354 CAGTGCGTAGGATAAAAGCCT 58.094 47.619 0.00 0.00 39.56 4.58
2070 4629 0.940126 CAAAAGAGACAGCAGTGCGT 59.060 50.000 10.00 10.86 0.00 5.24
2075 4634 2.615447 TCTTGTGCAAAAGAGACAGCAG 59.385 45.455 15.62 0.00 37.72 4.24
2088 4647 0.257328 TCAACCCTTGGTCTTGTGCA 59.743 50.000 0.00 0.00 33.12 4.57
2147 4707 4.021104 TGATGACGTCAGACTTGATCCTTT 60.021 41.667 24.41 1.38 35.39 3.11
2157 4717 3.531982 CGTTTGTTTGATGACGTCAGAC 58.468 45.455 24.41 19.32 41.16 3.51
2163 4723 0.386731 GGGCCGTTTGTTTGATGACG 60.387 55.000 0.00 0.00 35.44 4.35
2164 4724 0.958822 AGGGCCGTTTGTTTGATGAC 59.041 50.000 0.00 0.00 0.00 3.06
2176 4736 3.591835 CGCAAACACAAGGGCCGT 61.592 61.111 0.00 0.00 0.00 5.68
2200 4760 1.334599 CCGACCAACACGTTTGAATGG 60.335 52.381 10.71 6.27 38.46 3.16
2210 4770 0.881118 ATCACATTGCCGACCAACAC 59.119 50.000 0.00 0.00 35.99 3.32
2239 4799 8.474831 AGTTTTACAAGACTTGGCTAAAACATT 58.525 29.630 31.14 20.60 40.65 2.71
2272 4832 5.164061 GGAGCAAAATGTGAAATACAAAGCG 60.164 40.000 0.00 0.00 43.77 4.68
2296 4856 1.022735 AGTCTGCCGGATACACTACG 58.977 55.000 5.05 0.00 0.00 3.51
2308 4868 7.048512 AGTAATAAGGTCATACAAAGTCTGCC 58.951 38.462 0.00 0.00 0.00 4.85
2309 4869 8.494016 AAGTAATAAGGTCATACAAAGTCTGC 57.506 34.615 0.00 0.00 0.00 4.26
2341 4901 5.123820 CCTCTTTTCAGAATGTCGGCATTTA 59.876 40.000 17.67 2.99 44.61 1.40
2348 4908 4.310769 ACTGTCCTCTTTTCAGAATGTCG 58.689 43.478 0.00 0.00 37.40 4.35
2352 4912 4.752101 CGACAACTGTCCTCTTTTCAGAAT 59.248 41.667 4.30 0.00 41.86 2.40
2357 4917 2.210116 TGCGACAACTGTCCTCTTTTC 58.790 47.619 4.30 0.00 41.86 2.29
2362 4922 2.548057 TGAAATTGCGACAACTGTCCTC 59.452 45.455 4.30 0.00 41.86 3.71
2364 4924 2.350772 CCTGAAATTGCGACAACTGTCC 60.351 50.000 4.30 0.00 41.86 4.02
2365 4925 2.548057 TCCTGAAATTGCGACAACTGTC 59.452 45.455 0.00 0.00 41.47 3.51
2366 4926 2.549754 CTCCTGAAATTGCGACAACTGT 59.450 45.455 0.00 0.00 0.00 3.55
2368 4928 1.537202 GCTCCTGAAATTGCGACAACT 59.463 47.619 0.00 0.00 0.00 3.16
2369 4929 1.537202 AGCTCCTGAAATTGCGACAAC 59.463 47.619 0.00 0.00 0.00 3.32
2370 4930 1.896220 AGCTCCTGAAATTGCGACAA 58.104 45.000 0.00 0.00 0.00 3.18
2388 4948 2.981859 AGGGTACTTTCGGTGCATAG 57.018 50.000 0.00 0.00 32.05 2.23
2392 4952 3.040409 CGTAGGGTACTTTCGGTGC 57.960 57.895 0.00 0.00 0.00 5.01
2667 5227 8.838365 AGTACACATATTGTTTCCACGTAAAAA 58.162 29.630 0.00 0.00 39.91 1.94
2668 5228 8.380743 AGTACACATATTGTTTCCACGTAAAA 57.619 30.769 0.00 0.00 39.91 1.52
2669 5229 7.656542 TGAGTACACATATTGTTTCCACGTAAA 59.343 33.333 0.00 0.00 39.91 2.01
2670 5230 7.116662 GTGAGTACACATATTGTTTCCACGTAA 59.883 37.037 0.00 0.00 45.32 3.18
2671 5231 6.587226 GTGAGTACACATATTGTTTCCACGTA 59.413 38.462 0.00 0.00 45.32 3.57
2672 5232 5.407387 GTGAGTACACATATTGTTTCCACGT 59.593 40.000 0.00 0.00 45.32 4.49
2673 5233 5.854157 GTGAGTACACATATTGTTTCCACG 58.146 41.667 0.00 0.00 45.32 4.94
2695 5255 8.308931 TCGTACATCTACTTGTTTTATCAAGGT 58.691 33.333 10.44 2.35 46.11 3.50
2707 5267 6.422100 AGCATGCTAATTCGTACATCTACTTG 59.578 38.462 21.21 0.00 0.00 3.16
2735 5295 8.697846 TTTAGAGTACATATTTTCTCGTGTGG 57.302 34.615 0.00 0.00 32.90 4.17


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

AutoCloner maintained by Alex Coulton.