Multiple sequence alignment - TraesCS5D01G414100

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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 TraesCS5D01G414100 chr5D 100.000 2540 0 0 1 2540 476724226 476726765 0.000000e+00 4691.0
1 TraesCS5D01G414100 chr5D 88.150 962 75 15 761 1694 476708289 476709239 0.000000e+00 1109.0
2 TraesCS5D01G414100 chr5D 88.575 919 73 16 761 1669 476749581 476750477 0.000000e+00 1086.0
3 TraesCS5D01G414100 chr5D 85.117 981 86 32 761 1723 476784830 476785768 0.000000e+00 948.0
4 TraesCS5D01G414100 chr5D 92.683 41 2 1 1853 1893 525304023 525304062 9.810000e-05 58.4
5 TraesCS5D01G414100 chr5B 92.864 1121 62 6 480 1594 584142072 584143180 0.000000e+00 1611.0
6 TraesCS5D01G414100 chr5B 86.814 948 77 23 766 1678 584126562 584127496 0.000000e+00 1014.0
7 TraesCS5D01G414100 chr5B 86.311 957 87 18 656 1587 584245400 584246337 0.000000e+00 1002.0
8 TraesCS5D01G414100 chr5B 84.918 915 79 29 761 1662 584291802 584292670 0.000000e+00 870.0
9 TraesCS5D01G414100 chr5B 87.440 629 62 13 1746 2359 584143216 584143842 0.000000e+00 708.0
10 TraesCS5D01G414100 chr5B 85.488 441 28 9 38 471 584141676 584142087 6.490000e-116 427.0
11 TraesCS5D01G414100 chr5B 92.079 101 8 0 2355 2455 584167589 584167689 2.630000e-30 143.0
12 TraesCS5D01G414100 chr5A 90.890 966 60 15 761 1723 596044258 596045198 0.000000e+00 1271.0
13 TraesCS5D01G414100 chr5A 83.755 1145 107 36 761 1844 596032339 596033465 0.000000e+00 1011.0
14 TraesCS5D01G414100 chr5A 86.266 932 87 17 761 1669 596054650 596055563 0.000000e+00 974.0
15 TraesCS5D01G414100 chr5A 85.484 930 83 20 761 1664 596086543 596087446 0.000000e+00 922.0
16 TraesCS5D01G414100 chr5A 92.479 359 23 4 2183 2539 596047153 596047509 6.270000e-141 510.0
17 TraesCS5D01G414100 chr5A 80.880 591 87 14 1910 2498 596056468 596057034 2.320000e-120 442.0
18 TraesCS5D01G414100 chr5A 89.003 291 20 6 480 762 596043937 596044223 1.450000e-92 350.0
19 TraesCS5D01G414100 chr5A 93.194 191 13 0 2009 2199 596045451 596045641 5.350000e-72 281.0
20 TraesCS5D01G414100 chr5A 96.078 153 5 1 29 181 596043267 596043418 5.430000e-62 248.0
21 TraesCS5D01G414100 chr5A 81.940 299 28 7 177 468 596043672 596043951 1.970000e-56 230.0
22 TraesCS5D01G414100 chr5A 94.495 109 6 0 1967 2075 596045339 596045447 4.350000e-38 169.0
23 TraesCS5D01G414100 chr5A 90.517 116 10 1 1777 1891 596045209 596045324 4.380000e-33 152.0
24 TraesCS5D01G414100 chr5A 93.023 43 3 0 1850 1892 641586557 641586599 2.110000e-06 63.9
25 TraesCS5D01G414100 chr4A 91.667 48 4 0 1844 1891 577472459 577472506 1.630000e-07 67.6
26 TraesCS5D01G414100 chr2A 93.182 44 2 1 1849 1891 596353266 596353223 2.110000e-06 63.9
27 TraesCS5D01G414100 chr6B 94.872 39 2 0 1855 1893 657091708 657091746 7.590000e-06 62.1
28 TraesCS5D01G414100 chr3A 88.000 50 4 2 1853 1900 66275386 66275435 9.810000e-05 58.4
29 TraesCS5D01G414100 chr7D 100.000 30 0 0 1 30 486383865 486383894 3.530000e-04 56.5
30 TraesCS5D01G414100 chr6A 100.000 30 0 0 1 30 541691633 541691662 3.530000e-04 56.5
31 TraesCS5D01G414100 chr2D 86.538 52 5 2 1853 1902 636888501 636888450 3.530000e-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 TraesCS5D01G414100 chr5D 476724226 476726765 2539 False 4691.000000 4691 100.000000 1 2540 1 chr5D.!!$F2 2539
1 TraesCS5D01G414100 chr5D 476708289 476709239 950 False 1109.000000 1109 88.150000 761 1694 1 chr5D.!!$F1 933
2 TraesCS5D01G414100 chr5D 476749581 476750477 896 False 1086.000000 1086 88.575000 761 1669 1 chr5D.!!$F3 908
3 TraesCS5D01G414100 chr5D 476784830 476785768 938 False 948.000000 948 85.117000 761 1723 1 chr5D.!!$F4 962
4 TraesCS5D01G414100 chr5B 584126562 584127496 934 False 1014.000000 1014 86.814000 766 1678 1 chr5B.!!$F1 912
5 TraesCS5D01G414100 chr5B 584245400 584246337 937 False 1002.000000 1002 86.311000 656 1587 1 chr5B.!!$F3 931
6 TraesCS5D01G414100 chr5B 584141676 584143842 2166 False 915.333333 1611 88.597333 38 2359 3 chr5B.!!$F5 2321
7 TraesCS5D01G414100 chr5B 584291802 584292670 868 False 870.000000 870 84.918000 761 1662 1 chr5B.!!$F4 901
8 TraesCS5D01G414100 chr5A 596032339 596033465 1126 False 1011.000000 1011 83.755000 761 1844 1 chr5A.!!$F1 1083
9 TraesCS5D01G414100 chr5A 596086543 596087446 903 False 922.000000 922 85.484000 761 1664 1 chr5A.!!$F2 903
10 TraesCS5D01G414100 chr5A 596054650 596057034 2384 False 708.000000 974 83.573000 761 2498 2 chr5A.!!$F5 1737
11 TraesCS5D01G414100 chr5A 596043267 596047509 4242 False 401.375000 1271 91.074500 29 2539 8 chr5A.!!$F4 2510

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
680 956 0.305313 GTTGTGCAACTTAACCGCGA 59.695 50.0 8.23 0.0 38.25 5.87 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 2892 0.24445 AACCGATTACGCCGAAGACA 59.756 50.0 0.0 0.0 38.29 3.41 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
148 150 5.105595 TGACCATGTGATCTTGTCAGAGTAG 60.106 44.000 0.00 0.00 37.56 2.57
189 449 3.307242 CGATTTTTACCTTGGAGCTCTCG 59.693 47.826 14.64 6.44 0.00 4.04
233 493 3.325135 CCTTCCGGTAAAGAGCATCCTAT 59.675 47.826 0.00 0.00 33.66 2.57
234 494 4.310769 CTTCCGGTAAAGAGCATCCTATG 58.689 47.826 0.00 0.00 33.66 2.23
235 495 2.632996 TCCGGTAAAGAGCATCCTATGG 59.367 50.000 0.00 0.00 33.66 2.74
236 496 2.417719 CGGTAAAGAGCATCCTATGGC 58.582 52.381 0.00 0.00 33.66 4.40
237 497 2.784347 GGTAAAGAGCATCCTATGGCC 58.216 52.381 0.00 0.00 33.66 5.36
238 498 2.373502 GGTAAAGAGCATCCTATGGCCT 59.626 50.000 3.32 0.00 33.66 5.19
240 500 3.778954 AAAGAGCATCCTATGGCCTAC 57.221 47.619 3.32 0.00 33.66 3.18
254 520 1.844497 GGCCTACCTAACCTCACCATT 59.156 52.381 0.00 0.00 0.00 3.16
255 521 2.158798 GGCCTACCTAACCTCACCATTC 60.159 54.545 0.00 0.00 0.00 2.67
314 580 0.761187 TCTTCTGGCACAAGAGCACT 59.239 50.000 0.68 0.00 38.70 4.40
332 598 3.359033 CACTTCATCACCAATCCCATGT 58.641 45.455 0.00 0.00 0.00 3.21
366 632 2.134789 ATGTGAGGCTAAGCTTTGGG 57.865 50.000 3.20 0.00 0.00 4.12
400 666 6.380846 TGCAAGAAATTGGGCTGATTAATACT 59.619 34.615 0.00 0.00 0.00 2.12
412 678 6.944862 GGCTGATTAATACTGGGAGAATGATT 59.055 38.462 0.00 0.00 0.00 2.57
451 718 5.048434 AGGCTCTTGAGCTTATGTGAAAAAC 60.048 40.000 20.12 1.49 34.73 2.43
454 721 6.697019 GCTCTTGAGCTTATGTGAAAAACAAA 59.303 34.615 14.65 0.00 43.61 2.83
458 725 7.985634 TGAGCTTATGTGAAAAACAAAACTC 57.014 32.000 0.00 0.00 43.61 3.01
459 726 7.771183 TGAGCTTATGTGAAAAACAAAACTCT 58.229 30.769 0.00 0.00 43.61 3.24
460 727 8.898761 TGAGCTTATGTGAAAAACAAAACTCTA 58.101 29.630 0.00 0.00 43.61 2.43
461 728 9.899226 GAGCTTATGTGAAAAACAAAACTCTAT 57.101 29.630 0.00 0.00 43.61 1.98
567 839 6.605471 TTCTTCACAAGGATGCTAAGTCTA 57.395 37.500 0.00 0.00 0.00 2.59
604 876 4.917415 GTCCGTTGGATTGTTTTCTGAATG 59.083 41.667 0.00 0.00 32.73 2.67
605 877 4.582656 TCCGTTGGATTGTTTTCTGAATGT 59.417 37.500 0.00 0.00 0.00 2.71
606 878 5.068460 TCCGTTGGATTGTTTTCTGAATGTT 59.932 36.000 0.00 0.00 0.00 2.71
607 879 5.752955 CCGTTGGATTGTTTTCTGAATGTTT 59.247 36.000 0.00 0.00 0.00 2.83
635 908 0.378257 ATGATGAACGCATTGCCGTC 59.622 50.000 2.41 1.23 41.16 4.79
648 921 0.793861 TGCCGTCTTTGATTGTACGC 59.206 50.000 0.00 0.00 34.13 4.42
651 927 1.795872 CCGTCTTTGATTGTACGCACA 59.204 47.619 0.00 0.00 34.13 4.57
680 956 0.305313 GTTGTGCAACTTAACCGCGA 59.695 50.000 8.23 0.00 38.25 5.87
704 980 0.332632 AGGATTTTGCTAGCTGGCCA 59.667 50.000 20.33 4.71 0.00 5.36
1029 1444 4.157958 GTCTCGTACGACGCGGCT 62.158 66.667 15.28 0.00 42.21 5.52
1326 1741 4.379243 CTCGTCAAGGCCGCCACT 62.379 66.667 13.15 0.00 0.00 4.00
1422 1837 1.392710 CGGCCGAGGATAGGTTCACT 61.393 60.000 24.07 0.00 31.21 3.41
1723 2853 5.455056 TGTGGAGTTAGTTTCTCAGAGTC 57.545 43.478 0.00 0.00 34.04 3.36
1724 2854 4.893524 TGTGGAGTTAGTTTCTCAGAGTCA 59.106 41.667 0.00 0.00 34.04 3.41
1728 2858 5.708230 GGAGTTAGTTTCTCAGAGTCAGAGA 59.292 44.000 10.96 10.96 40.20 3.10
1729 2859 6.349033 GGAGTTAGTTTCTCAGAGTCAGAGAC 60.349 46.154 14.30 5.64 41.53 3.36
1730 2860 6.303839 AGTTAGTTTCTCAGAGTCAGAGACT 58.696 40.000 14.30 12.11 46.42 3.24
1739 2869 2.969821 AGTCAGAGACTCAGAGTGGT 57.030 50.000 8.15 0.00 38.71 4.16
1741 2871 3.950397 AGTCAGAGACTCAGAGTGGTAG 58.050 50.000 8.15 0.00 38.71 3.18
1742 2872 3.585289 AGTCAGAGACTCAGAGTGGTAGA 59.415 47.826 8.15 0.00 38.71 2.59
1743 2873 4.042311 AGTCAGAGACTCAGAGTGGTAGAA 59.958 45.833 8.15 0.00 38.71 2.10
1750 2885 5.941647 AGACTCAGAGTGGTAGAAGTAGAAC 59.058 44.000 8.15 0.00 0.00 3.01
1757 2892 5.803552 AGTGGTAGAAGTAGAACTAGTCGT 58.196 41.667 0.00 0.00 0.00 4.34
1769 2904 0.723414 CTAGTCGTGTCTTCGGCGTA 59.277 55.000 6.85 0.00 40.52 4.42
1770 2905 1.129251 CTAGTCGTGTCTTCGGCGTAA 59.871 52.381 6.85 0.00 40.52 3.18
1771 2906 0.524862 AGTCGTGTCTTCGGCGTAAT 59.475 50.000 6.85 0.00 40.52 1.89
1772 2907 0.912528 GTCGTGTCTTCGGCGTAATC 59.087 55.000 6.85 0.00 0.00 1.75
1773 2908 0.521867 TCGTGTCTTCGGCGTAATCG 60.522 55.000 6.85 6.23 40.37 3.34
1774 2909 1.469126 CGTGTCTTCGGCGTAATCGG 61.469 60.000 6.85 0.00 37.56 4.18
1775 2910 0.457337 GTGTCTTCGGCGTAATCGGT 60.457 55.000 6.85 0.00 37.56 4.69
1777 2912 1.472082 TGTCTTCGGCGTAATCGGTTA 59.528 47.619 6.85 0.00 37.56 2.85
1778 2913 2.114825 GTCTTCGGCGTAATCGGTTAG 58.885 52.381 6.85 0.00 37.56 2.34
1844 2990 8.965819 TGTCAATGTAATGTAAATATTGCACCT 58.034 29.630 0.00 0.00 35.89 4.00
1891 3038 8.895845 CGTCTCAAAATAAGTGTCTGAATTTTG 58.104 33.333 14.12 14.12 44.73 2.44
1893 3040 9.734620 TCTCAAAATAAGTGTCTGAATTTTGTG 57.265 29.630 17.39 15.85 44.18 3.33
1894 3041 9.520204 CTCAAAATAAGTGTCTGAATTTTGTGT 57.480 29.630 17.39 0.00 44.18 3.72
1903 3050 7.706179 AGTGTCTGAATTTTGTGTATTTTGTGG 59.294 33.333 0.00 0.00 0.00 4.17
1904 3051 7.704472 GTGTCTGAATTTTGTGTATTTTGTGGA 59.296 33.333 0.00 0.00 0.00 4.02
1906 3053 7.920682 GTCTGAATTTTGTGTATTTTGTGGAGT 59.079 33.333 0.00 0.00 0.00 3.85
1908 3055 9.743057 CTGAATTTTGTGTATTTTGTGGAGTAA 57.257 29.630 0.00 0.00 0.00 2.24
1935 3090 1.250328 CTGGCCTGAACTTCATTGCA 58.750 50.000 3.32 0.00 0.00 4.08
1937 3092 0.109597 GGCCTGAACTTCATTGCACG 60.110 55.000 12.84 0.00 0.00 5.34
1962 3117 7.362229 CGTGCCCTCATTTTTAGGTTTGTATTA 60.362 37.037 0.00 0.00 31.70 0.98
1985 3140 5.947228 TTCAGCAGTAATCTTCCAAGTTG 57.053 39.130 0.00 0.00 0.00 3.16
2048 3203 8.680903 CAAGAATGCAAACATAGGAGAAACTAT 58.319 33.333 0.00 0.00 34.62 2.12
2137 3363 4.697828 TGATGTGCCGTTATTTGTGTATGT 59.302 37.500 0.00 0.00 0.00 2.29
2283 5038 0.759346 ACCAGGCTCGTGAACTCTTT 59.241 50.000 0.00 0.00 0.00 2.52
2327 5087 5.065914 AGCAGACTTAAGCACAAGATGAAA 58.934 37.500 1.29 0.00 0.00 2.69
2349 5109 3.914426 TTCTTCTAGCCCATCCTTCAC 57.086 47.619 0.00 0.00 0.00 3.18
2354 5114 0.824109 TAGCCCATCCTTCACGACAG 59.176 55.000 0.00 0.00 0.00 3.51
2443 5203 2.600769 AAGCCACCGAGGAGACGT 60.601 61.111 0.00 0.00 41.22 4.34
2444 5204 2.207924 AAGCCACCGAGGAGACGTT 61.208 57.895 0.00 0.00 41.22 3.99
2502 5262 5.710099 GGAATGGTGGAACTCAATTAACTCA 59.290 40.000 0.00 0.00 36.74 3.41
2503 5263 6.208599 GGAATGGTGGAACTCAATTAACTCAA 59.791 38.462 0.00 0.00 36.74 3.02
2533 5293 5.535030 AGGAGGGTCATTTTTGTTTACAGTC 59.465 40.000 0.00 0.00 0.00 3.51
2539 5299 6.039382 GGTCATTTTTGTTTACAGTCACTCCT 59.961 38.462 0.00 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 2.827322 TCCTTTCGGAATTACTCGTCCA 59.173 45.455 0.00 0.00 36.03 4.02
3 4 3.445857 CCTCCTTTCGGAATTACTCGTC 58.554 50.000 0.00 0.00 39.29 4.20
5 6 2.429610 TCCCTCCTTTCGGAATTACTCG 59.570 50.000 0.00 0.00 39.29 4.18
6 7 3.451540 ACTCCCTCCTTTCGGAATTACTC 59.548 47.826 0.00 0.00 39.29 2.59
7 8 3.451890 ACTCCCTCCTTTCGGAATTACT 58.548 45.455 0.00 0.00 39.29 2.24
8 9 3.908643 ACTCCCTCCTTTCGGAATTAC 57.091 47.619 0.00 0.00 39.29 1.89
9 10 4.617593 AGTACTCCCTCCTTTCGGAATTA 58.382 43.478 0.00 0.00 39.29 1.40
10 11 3.451890 AGTACTCCCTCCTTTCGGAATT 58.548 45.455 0.00 0.00 39.29 2.17
11 12 3.117552 AGTACTCCCTCCTTTCGGAAT 57.882 47.619 0.00 0.00 39.29 3.01
12 13 2.617840 AGTACTCCCTCCTTTCGGAA 57.382 50.000 0.00 0.00 39.29 4.30
13 14 2.579860 AGTAGTACTCCCTCCTTTCGGA 59.420 50.000 0.00 0.00 37.82 4.55
14 15 2.950975 GAGTAGTACTCCCTCCTTTCGG 59.049 54.545 18.10 0.00 39.28 4.30
15 16 3.618351 TGAGTAGTACTCCCTCCTTTCG 58.382 50.000 24.32 0.00 44.44 3.46
16 17 4.403113 CCTTGAGTAGTACTCCCTCCTTTC 59.597 50.000 24.32 1.22 44.44 2.62
17 18 4.045590 TCCTTGAGTAGTACTCCCTCCTTT 59.954 45.833 24.32 0.00 44.44 3.11
18 19 3.596956 TCCTTGAGTAGTACTCCCTCCTT 59.403 47.826 24.32 0.00 44.44 3.36
19 20 3.053470 GTCCTTGAGTAGTACTCCCTCCT 60.053 52.174 24.32 0.00 44.44 3.69
20 21 3.289836 GTCCTTGAGTAGTACTCCCTCC 58.710 54.545 24.32 7.79 44.44 4.30
21 22 3.965694 TGTCCTTGAGTAGTACTCCCTC 58.034 50.000 24.32 7.10 44.44 4.30
22 23 4.611564 ATGTCCTTGAGTAGTACTCCCT 57.388 45.455 24.32 0.00 44.44 4.20
23 24 5.692928 TCTATGTCCTTGAGTAGTACTCCC 58.307 45.833 24.32 5.08 44.44 4.30
24 25 6.358991 ACTCTATGTCCTTGAGTAGTACTCC 58.641 44.000 24.32 11.21 44.44 3.85
25 26 7.868906 AACTCTATGTCCTTGAGTAGTACTC 57.131 40.000 21.35 21.35 45.26 2.59
26 27 9.924010 AATAACTCTATGTCCTTGAGTAGTACT 57.076 33.333 1.37 1.37 38.74 2.73
29 30 9.256228 TCAAATAACTCTATGTCCTTGAGTAGT 57.744 33.333 0.00 0.00 38.74 2.73
32 33 9.793259 TTTTCAAATAACTCTATGTCCTTGAGT 57.207 29.630 0.00 0.00 40.98 3.41
148 150 5.659048 ATCGTTATAGCAACTTAGCAAGC 57.341 39.130 0.00 0.00 36.85 4.01
189 449 3.056821 GGTTGACCCACCATTCTTTAAGC 60.057 47.826 0.00 0.00 36.73 3.09
215 475 2.872038 GCCATAGGATGCTCTTTACCGG 60.872 54.545 0.00 0.00 0.00 5.28
217 477 2.373502 AGGCCATAGGATGCTCTTTACC 59.626 50.000 5.01 0.00 0.00 2.85
233 493 0.117541 TGGTGAGGTTAGGTAGGCCA 59.882 55.000 5.01 0.00 37.19 5.36
234 494 1.508256 ATGGTGAGGTTAGGTAGGCC 58.492 55.000 0.00 0.00 0.00 5.19
235 495 2.772515 AGAATGGTGAGGTTAGGTAGGC 59.227 50.000 0.00 0.00 0.00 3.93
236 496 6.749036 ATAAGAATGGTGAGGTTAGGTAGG 57.251 41.667 0.00 0.00 0.00 3.18
237 497 8.925338 AGTAATAAGAATGGTGAGGTTAGGTAG 58.075 37.037 0.00 0.00 0.00 3.18
238 498 8.849543 AGTAATAAGAATGGTGAGGTTAGGTA 57.150 34.615 0.00 0.00 0.00 3.08
240 500 7.012421 GCAAGTAATAAGAATGGTGAGGTTAGG 59.988 40.741 0.00 0.00 0.00 2.69
314 580 2.496871 GCAACATGGGATTGGTGATGAA 59.503 45.455 0.00 0.00 36.36 2.57
366 632 2.352323 CCAATTTCTTGCACCCGGTTAC 60.352 50.000 0.00 0.00 0.00 2.50
400 666 6.968263 TTACACACAAAAATCATTCTCCCA 57.032 33.333 0.00 0.00 0.00 4.37
412 678 5.592282 TCAAGAGCCTGAATTACACACAAAA 59.408 36.000 0.00 0.00 0.00 2.44
416 682 4.935885 CTCAAGAGCCTGAATTACACAC 57.064 45.455 0.00 0.00 0.00 3.82
543 810 6.059787 AGACTTAGCATCCTTGTGAAGAAT 57.940 37.500 0.00 0.00 0.00 2.40
567 839 0.608582 ACGGACAGCTCGTTACCTCT 60.609 55.000 0.00 0.00 37.61 3.69
610 882 3.679025 GGCAATGCGTTCATCATGAAAAA 59.321 39.130 0.29 0.00 38.22 1.94
620 893 0.040514 CAAAGACGGCAATGCGTTCA 60.041 50.000 0.00 0.00 0.00 3.18
651 927 6.699642 GGTTAAGTTGCACAACACACAAATAT 59.300 34.615 15.40 0.00 43.47 1.28
680 956 2.173569 CCAGCTAGCAAAATCCTACCCT 59.826 50.000 18.83 0.00 0.00 4.34
688 964 1.760192 CTCTGGCCAGCTAGCAAAAT 58.240 50.000 28.91 0.00 0.00 1.82
704 980 3.673594 CGATCAAGTTAACGGTGAGCTCT 60.674 47.826 20.77 7.20 0.00 4.09
816 1129 0.108520 TTGTCGTGTAGCCGGGAATC 60.109 55.000 2.18 0.00 0.00 2.52
818 1131 1.005867 GTTGTCGTGTAGCCGGGAA 60.006 57.895 2.18 0.00 0.00 3.97
1214 1629 0.105039 CACGAAGTAGATCTGCCCCC 59.895 60.000 5.18 0.00 41.61 5.40
1416 1831 0.382636 CGAACGTCGCCAAAGTGAAC 60.383 55.000 0.00 0.00 33.38 3.18
1690 2121 5.359194 ACTAACTCCACATATCCACAAGG 57.641 43.478 0.00 0.00 0.00 3.61
1723 2853 4.331968 ACTTCTACCACTCTGAGTCTCTG 58.668 47.826 7.49 0.50 0.00 3.35
1724 2854 4.650972 ACTTCTACCACTCTGAGTCTCT 57.349 45.455 7.49 0.00 0.00 3.10
1728 2858 5.883180 AGTTCTACTTCTACCACTCTGAGT 58.117 41.667 4.06 4.06 0.00 3.41
1729 2859 7.107542 ACTAGTTCTACTTCTACCACTCTGAG 58.892 42.308 2.45 2.45 0.00 3.35
1730 2860 7.018487 ACTAGTTCTACTTCTACCACTCTGA 57.982 40.000 0.00 0.00 0.00 3.27
1731 2861 6.036300 CGACTAGTTCTACTTCTACCACTCTG 59.964 46.154 0.00 0.00 0.00 3.35
1732 2862 6.108015 CGACTAGTTCTACTTCTACCACTCT 58.892 44.000 0.00 0.00 0.00 3.24
1734 2864 5.642919 CACGACTAGTTCTACTTCTACCACT 59.357 44.000 0.00 0.00 0.00 4.00
1736 2866 5.555017 ACACGACTAGTTCTACTTCTACCA 58.445 41.667 0.00 0.00 0.00 3.25
1737 2867 5.874261 AGACACGACTAGTTCTACTTCTACC 59.126 44.000 0.00 0.00 0.00 3.18
1738 2868 6.966435 AGACACGACTAGTTCTACTTCTAC 57.034 41.667 0.00 0.00 0.00 2.59
1739 2869 6.309980 CGAAGACACGACTAGTTCTACTTCTA 59.690 42.308 18.69 0.00 35.09 2.10
1740 2870 5.120519 CGAAGACACGACTAGTTCTACTTCT 59.879 44.000 18.69 7.53 35.09 2.85
1741 2871 5.315195 CGAAGACACGACTAGTTCTACTTC 58.685 45.833 0.00 8.40 35.09 3.01
1742 2872 4.153835 CCGAAGACACGACTAGTTCTACTT 59.846 45.833 0.00 0.16 35.09 2.24
1743 2873 3.683822 CCGAAGACACGACTAGTTCTACT 59.316 47.826 0.00 0.00 35.09 2.57
1750 2885 0.723414 TACGCCGAAGACACGACTAG 59.277 55.000 0.00 0.00 35.09 2.57
1757 2892 0.244450 AACCGATTACGCCGAAGACA 59.756 50.000 0.00 0.00 38.29 3.41
1769 2904 3.192001 TGCTTCTGACGTACTAACCGATT 59.808 43.478 0.00 0.00 0.00 3.34
1770 2905 2.751259 TGCTTCTGACGTACTAACCGAT 59.249 45.455 0.00 0.00 0.00 4.18
1771 2906 2.095567 GTGCTTCTGACGTACTAACCGA 60.096 50.000 0.00 0.00 0.00 4.69
1772 2907 2.095364 AGTGCTTCTGACGTACTAACCG 60.095 50.000 3.16 0.00 0.00 4.44
1773 2908 3.243336 CAGTGCTTCTGACGTACTAACC 58.757 50.000 4.69 0.00 46.27 2.85
1774 2909 3.898529 ACAGTGCTTCTGACGTACTAAC 58.101 45.455 14.40 0.00 46.27 2.34
1775 2910 5.892160 ATACAGTGCTTCTGACGTACTAA 57.108 39.130 14.40 0.00 46.27 2.24
1777 2912 5.892160 TTATACAGTGCTTCTGACGTACT 57.108 39.130 14.40 0.00 46.27 2.73
1778 2913 8.798748 ATATTTATACAGTGCTTCTGACGTAC 57.201 34.615 14.40 0.00 46.27 3.67
1891 3038 6.490566 AACCGATTACTCCACAAAATACAC 57.509 37.500 0.00 0.00 0.00 2.90
1893 3040 7.201582 CCAGTAACCGATTACTCCACAAAATAC 60.202 40.741 0.00 0.00 46.73 1.89
1894 3041 6.819649 CCAGTAACCGATTACTCCACAAAATA 59.180 38.462 0.00 0.00 46.73 1.40
1896 3043 4.998672 CCAGTAACCGATTACTCCACAAAA 59.001 41.667 0.00 0.00 46.73 2.44
1897 3044 4.571919 CCAGTAACCGATTACTCCACAAA 58.428 43.478 0.00 0.00 46.73 2.83
1900 3047 2.547826 GCCAGTAACCGATTACTCCAC 58.452 52.381 0.00 0.00 46.73 4.02
1903 3050 2.429610 TCAGGCCAGTAACCGATTACTC 59.570 50.000 5.01 0.00 46.73 2.59
1906 3053 2.835764 AGTTCAGGCCAGTAACCGATTA 59.164 45.455 5.01 0.00 0.00 1.75
1908 3055 1.276622 AGTTCAGGCCAGTAACCGAT 58.723 50.000 5.01 0.00 0.00 4.18
1909 3056 1.001633 GAAGTTCAGGCCAGTAACCGA 59.998 52.381 5.01 0.00 0.00 4.69
1935 3090 2.579410 ACCTAAAAATGAGGGCACGT 57.421 45.000 0.00 0.00 38.52 4.49
1937 3092 4.600692 ACAAACCTAAAAATGAGGGCAC 57.399 40.909 0.00 0.00 38.52 5.01
1962 3117 5.105997 GCAACTTGGAAGATTACTGCTGAAT 60.106 40.000 0.00 0.00 0.00 2.57
1985 3140 0.379669 CTCCGTGATCATTGGCTTGC 59.620 55.000 11.15 0.00 0.00 4.01
2013 3168 3.123050 GTTTGCATTCTTGTGTTCCACC 58.877 45.455 0.00 0.00 32.73 4.61
2016 3171 5.048083 TCCTATGTTTGCATTCTTGTGTTCC 60.048 40.000 0.00 0.00 36.58 3.62
2137 3363 8.883954 TTCACACAATTTCAAGCAAATTCATA 57.116 26.923 0.00 0.00 41.94 2.15
2327 5087 4.684485 CGTGAAGGATGGGCTAGAAGAAAT 60.684 45.833 0.00 0.00 0.00 2.17
2349 5109 8.240682 AGCATAGCTCTAGTATTTATTCTGTCG 58.759 37.037 0.00 0.00 30.62 4.35
2381 5141 7.665145 TGTAGTCATTCATGAAAAATCCTGTCA 59.335 33.333 13.09 6.09 38.75 3.58
2384 5144 8.048534 AGTGTAGTCATTCATGAAAAATCCTG 57.951 34.615 13.09 5.18 38.75 3.86
2443 5203 5.421693 CACAATCCCATAGAAAATGGTGGAA 59.578 40.000 3.49 0.00 37.48 3.53
2444 5204 4.955450 CACAATCCCATAGAAAATGGTGGA 59.045 41.667 3.49 0.00 37.48 4.02
2510 5270 5.300792 TGACTGTAAACAAAAATGACCCTCC 59.699 40.000 0.00 0.00 0.00 4.30
2512 5272 5.891551 AGTGACTGTAAACAAAAATGACCCT 59.108 36.000 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.