Multiple sequence alignment - TraesCS1D01G449400

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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 TraesCS1D01G449400 chr1D 100.000 3194 0 0 1 3194 491665809 491662616 0.000000e+00 5899
1 TraesCS1D01G449400 chr1D 83.160 1918 304 10 1 1915 491696378 491694477 0.000000e+00 1735
2 TraesCS1D01G449400 chr1D 83.128 1784 281 14 114 1891 491639173 491637404 0.000000e+00 1609
3 TraesCS1D01G449400 chr1D 81.867 1853 311 18 47 1891 491688236 491686401 0.000000e+00 1537
4 TraesCS1D01G449400 chr1D 84.264 197 31 0 1 197 491688353 491688157 3.250000e-45 193
5 TraesCS1D01G449400 chr2D 93.036 1321 25 12 1930 3194 537297839 537299148 0.000000e+00 1868
6 TraesCS1D01G449400 chr2D 96.292 971 21 5 2226 3194 587157898 587158855 0.000000e+00 1580
7 TraesCS1D01G449400 chr2D 92.218 1118 38 13 2115 3194 7874567 7875673 0.000000e+00 1537
8 TraesCS1D01G449400 chr2D 94.603 945 21 7 2268 3194 11054450 11055382 0.000000e+00 1435
9 TraesCS1D01G449400 chr2D 92.989 271 14 3 1931 2198 486489942 486490210 1.070000e-104 390
10 TraesCS1D01G449400 chr2D 95.851 241 9 1 2955 3194 621004831 621005071 3.860000e-104 388
11 TraesCS1D01G449400 chr2D 91.515 165 12 2 3030 3194 31852019 31852181 3.210000e-55 226
12 TraesCS1D01G449400 chr1A 83.689 1919 301 9 1 1915 589638472 589636562 0.000000e+00 1799
13 TraesCS1D01G449400 chr1A 82.461 1910 310 20 1 1902 589447184 589445292 0.000000e+00 1648
14 TraesCS1D01G449400 chr1A 84.091 1716 241 22 114 1811 589500513 589498812 0.000000e+00 1628
15 TraesCS1D01G449400 chr1A 81.771 1909 322 19 1 1902 589478851 589476962 0.000000e+00 1574
16 TraesCS1D01G449400 chr1A 82.512 1704 261 22 1 1695 589454185 589452510 0.000000e+00 1461
17 TraesCS1D01G449400 chr1B 83.722 1800 277 13 112 1902 683583314 683581522 0.000000e+00 1687
18 TraesCS1D01G449400 chr4D 96.995 965 24 3 2231 3194 505825226 505824266 0.000000e+00 1616
19 TraesCS1D01G449400 chr4D 96.274 832 24 3 2229 3060 1842326 1841502 0.000000e+00 1358
20 TraesCS1D01G449400 chr7D 94.654 954 19 7 2249 3194 529691501 529692430 0.000000e+00 1450
21 TraesCS1D01G449400 chr7D 96.353 850 22 8 2223 3070 592575551 592574709 0.000000e+00 1389
22 TraesCS1D01G449400 chr7D 93.943 875 24 5 2339 3194 622253968 622254832 0.000000e+00 1295
23 TraesCS1D01G449400 chr7D 94.298 719 14 8 2495 3194 511122299 511123009 0.000000e+00 1075
24 TraesCS1D01G449400 chr7D 92.982 741 15 6 2483 3194 1191778 1192510 0.000000e+00 1046
25 TraesCS1D01G449400 chr7D 93.818 275 10 2 1930 2198 529690890 529691163 1.070000e-109 407
26 TraesCS1D01G449400 chr7D 93.860 228 10 2 1926 2153 41257684 41257461 1.100000e-89 340
27 TraesCS1D01G449400 chr7D 92.083 240 15 3 1917 2153 593251804 593252042 5.110000e-88 335
28 TraesCS1D01G449400 chr7D 91.556 225 10 6 1930 2153 163212372 163212156 5.180000e-78 302
29 TraesCS1D01G449400 chr7D 96.970 132 3 1 3064 3194 15686352 15686221 1.490000e-53 220
30 TraesCS1D01G449400 chr7D 96.970 132 3 1 3064 3194 16668345 16668476 1.490000e-53 220
31 TraesCS1D01G449400 chr7D 96.970 132 3 1 3064 3194 17876406 17876275 1.490000e-53 220
32 TraesCS1D01G449400 chr7D 90.909 165 13 2 3030 3194 23262953 23262791 1.490000e-53 220
33 TraesCS1D01G449400 chr7D 96.970 132 3 1 3064 3194 55144478 55144347 1.490000e-53 220
34 TraesCS1D01G449400 chr7D 90.909 165 13 2 3030 3194 100749915 100750077 1.490000e-53 220
35 TraesCS1D01G449400 chr7D 90.303 165 14 2 3030 3194 19223032 19223194 6.940000e-52 215
36 TraesCS1D01G449400 chr7D 96.183 131 5 0 3064 3194 185772298 185772168 6.940000e-52 215
37 TraesCS1D01G449400 chr7D 90.909 165 7 7 3037 3194 546439812 546439975 6.940000e-52 215
38 TraesCS1D01G449400 chr7D 87.978 183 16 3 3017 3194 109539296 109539115 8.980000e-51 211
39 TraesCS1D01G449400 chr5D 91.597 1083 28 23 2104 3150 398642496 398643551 0.000000e+00 1437
40 TraesCS1D01G449400 chr5D 75.841 1813 392 34 116 1902 434474780 434476572 0.000000e+00 880
41 TraesCS1D01G449400 chr5D 95.089 224 6 1 1930 2153 560310903 560311121 6.560000e-92 348
42 TraesCS1D01G449400 chrUn 93.203 971 45 14 2112 3070 132052022 132052983 0.000000e+00 1408
43 TraesCS1D01G449400 chrUn 94.783 230 6 2 1925 2154 108306744 108306967 1.410000e-93 353
44 TraesCS1D01G449400 chr6D 96.411 836 25 3 2235 3070 36738775 36739605 0.000000e+00 1373
45 TraesCS1D01G449400 chr3B 91.816 892 54 10 2180 3060 768204742 768205625 0.000000e+00 1225
46 TraesCS1D01G449400 chr3B 88.506 87 5 4 2113 2197 28553970 28554053 2.030000e-17 100
47 TraesCS1D01G449400 chr3B 88.506 87 5 4 2113 2197 601004382 601004465 2.030000e-17 100
48 TraesCS1D01G449400 chr3B 88.506 87 5 4 2113 2197 645973691 645973774 2.030000e-17 100
49 TraesCS1D01G449400 chr5B 91.000 900 65 9 2180 3070 317946001 317946893 0.000000e+00 1199
50 TraesCS1D01G449400 chr3D 94.515 237 7 2 1930 2166 567706669 567706439 8.420000e-96 361
51 TraesCS1D01G449400 chr3D 90.830 229 11 6 1927 2153 614102881 614103101 6.700000e-77 298
52 TraesCS1D01G449400 chr2A 90.476 84 6 2 2115 2197 19371039 19371121 3.370000e-20 110
53 TraesCS1D01G449400 chr2A 90.476 84 7 1 2115 2197 19837966 19837883 3.370000e-20 110
54 TraesCS1D01G449400 chr2A 90.476 84 6 2 2115 2197 19838010 19837928 3.370000e-20 110


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 TraesCS1D01G449400 chr1D 491662616 491665809 3193 True 5899.0 5899 100.0000 1 3194 1 chr1D.!!$R2 3193
1 TraesCS1D01G449400 chr1D 491694477 491696378 1901 True 1735.0 1735 83.1600 1 1915 1 chr1D.!!$R3 1914
2 TraesCS1D01G449400 chr1D 491637404 491639173 1769 True 1609.0 1609 83.1280 114 1891 1 chr1D.!!$R1 1777
3 TraesCS1D01G449400 chr1D 491686401 491688353 1952 True 865.0 1537 83.0655 1 1891 2 chr1D.!!$R4 1890
4 TraesCS1D01G449400 chr2D 537297839 537299148 1309 False 1868.0 1868 93.0360 1930 3194 1 chr2D.!!$F5 1264
5 TraesCS1D01G449400 chr2D 587157898 587158855 957 False 1580.0 1580 96.2920 2226 3194 1 chr2D.!!$F6 968
6 TraesCS1D01G449400 chr2D 7874567 7875673 1106 False 1537.0 1537 92.2180 2115 3194 1 chr2D.!!$F1 1079
7 TraesCS1D01G449400 chr2D 11054450 11055382 932 False 1435.0 1435 94.6030 2268 3194 1 chr2D.!!$F2 926
8 TraesCS1D01G449400 chr1A 589636562 589638472 1910 True 1799.0 1799 83.6890 1 1915 1 chr1A.!!$R5 1914
9 TraesCS1D01G449400 chr1A 589445292 589447184 1892 True 1648.0 1648 82.4610 1 1902 1 chr1A.!!$R1 1901
10 TraesCS1D01G449400 chr1A 589498812 589500513 1701 True 1628.0 1628 84.0910 114 1811 1 chr1A.!!$R4 1697
11 TraesCS1D01G449400 chr1A 589476962 589478851 1889 True 1574.0 1574 81.7710 1 1902 1 chr1A.!!$R3 1901
12 TraesCS1D01G449400 chr1A 589452510 589454185 1675 True 1461.0 1461 82.5120 1 1695 1 chr1A.!!$R2 1694
13 TraesCS1D01G449400 chr1B 683581522 683583314 1792 True 1687.0 1687 83.7220 112 1902 1 chr1B.!!$R1 1790
14 TraesCS1D01G449400 chr4D 505824266 505825226 960 True 1616.0 1616 96.9950 2231 3194 1 chr4D.!!$R2 963
15 TraesCS1D01G449400 chr4D 1841502 1842326 824 True 1358.0 1358 96.2740 2229 3060 1 chr4D.!!$R1 831
16 TraesCS1D01G449400 chr7D 592574709 592575551 842 True 1389.0 1389 96.3530 2223 3070 1 chr7D.!!$R9 847
17 TraesCS1D01G449400 chr7D 622253968 622254832 864 False 1295.0 1295 93.9430 2339 3194 1 chr7D.!!$F8 855
18 TraesCS1D01G449400 chr7D 511122299 511123009 710 False 1075.0 1075 94.2980 2495 3194 1 chr7D.!!$F5 699
19 TraesCS1D01G449400 chr7D 1191778 1192510 732 False 1046.0 1046 92.9820 2483 3194 1 chr7D.!!$F1 711
20 TraesCS1D01G449400 chr7D 529690890 529692430 1540 False 928.5 1450 94.2360 1930 3194 2 chr7D.!!$F9 1264
21 TraesCS1D01G449400 chr5D 398642496 398643551 1055 False 1437.0 1437 91.5970 2104 3150 1 chr5D.!!$F1 1046
22 TraesCS1D01G449400 chr5D 434474780 434476572 1792 False 880.0 880 75.8410 116 1902 1 chr5D.!!$F2 1786
23 TraesCS1D01G449400 chrUn 132052022 132052983 961 False 1408.0 1408 93.2030 2112 3070 1 chrUn.!!$F2 958
24 TraesCS1D01G449400 chr6D 36738775 36739605 830 False 1373.0 1373 96.4110 2235 3070 1 chr6D.!!$F1 835
25 TraesCS1D01G449400 chr3B 768204742 768205625 883 False 1225.0 1225 91.8160 2180 3060 1 chr3B.!!$F4 880
26 TraesCS1D01G449400 chr5B 317946001 317946893 892 False 1199.0 1199 91.0000 2180 3070 1 chr5B.!!$F1 890

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
85 86 0.251634 TGTGGAGATTGGCGCACATA 59.748 50.0 10.83 0.0 0.00 2.29 F
1917 2084 0.030235 GGTTTGAGAACACCGGCAAC 59.970 55.0 0.00 0.0 37.51 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2020 2187 0.175073 GATAGTTGGTCGCGGGTCTT 59.825 55.0 6.13 0.0 0.00 3.01 R
2820 3401 6.039616 GCACTTGTTGTTTTCCTGACAATAA 58.960 36.0 0.00 0.0 39.03 1.40 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
21 22 4.002906 TGTGTCAACCCTTAGTAGCTTG 57.997 45.455 0.00 0.00 0.00 4.01
41 42 4.011966 TGAACATGCTTGATGTCAGTCT 57.988 40.909 6.60 0.00 45.12 3.24
81 82 2.046023 CCTGTGGAGATTGGCGCA 60.046 61.111 10.83 0.00 0.00 6.09
83 84 1.672030 CTGTGGAGATTGGCGCACA 60.672 57.895 10.83 1.22 0.00 4.57
85 86 0.251634 TGTGGAGATTGGCGCACATA 59.748 50.000 10.83 0.00 0.00 2.29
89 90 1.331756 GGAGATTGGCGCACATACAAG 59.668 52.381 10.83 0.00 0.00 3.16
201 346 2.356638 TGGAAACAACAGCTTGACTGGA 60.357 45.455 0.00 0.00 43.56 3.86
250 395 7.651808 TGGTTTGATGAATTTGAAGTCTCTTC 58.348 34.615 2.95 2.95 0.00 2.87
260 405 9.225436 GAATTTGAAGTCTCTTCACTTATCCTT 57.775 33.333 11.05 0.00 36.71 3.36
299 444 4.481368 TTATTGACTCGCATTGGGTACT 57.519 40.909 0.24 0.00 0.00 2.73
300 445 2.093306 TTGACTCGCATTGGGTACTG 57.907 50.000 0.24 0.00 0.00 2.74
345 490 4.335315 TCGTTATCATCTTGTCATTTGGGC 59.665 41.667 0.00 0.00 0.00 5.36
360 505 0.853586 TGGGCCCCCAGTTTCCTAAT 60.854 55.000 22.27 0.00 41.89 1.73
431 576 5.883583 AGCCTAGTTGGTAGGATCCCAGG 62.884 56.522 8.55 3.78 44.94 4.45
499 644 0.796927 GAACCAACTAAGTGGCGAGC 59.203 55.000 0.00 0.00 43.00 5.03
532 677 4.081752 GTCTGGAGTTCATGTCAGTGATCT 60.082 45.833 0.00 0.00 32.36 2.75
533 678 4.529769 TCTGGAGTTCATGTCAGTGATCTT 59.470 41.667 0.00 0.00 30.42 2.40
560 705 7.609146 TCTTTCAATGCAGTCAAATCTACTGAT 59.391 33.333 7.39 0.00 45.89 2.90
609 754 8.830580 AGAACAATTGAGTTATTGGACATATCG 58.169 33.333 13.59 0.00 39.33 2.92
636 781 5.784578 ACTCTTTAAATGGGTTTGTGTCC 57.215 39.130 0.00 0.00 0.00 4.02
678 826 4.880886 GCAGGTTGCAATTTTGTTTTCT 57.119 36.364 0.59 0.00 44.26 2.52
724 872 4.325204 CCATGTCAATTTGTCAAATGCGAG 59.675 41.667 11.54 3.40 0.00 5.03
754 902 6.349363 GCGGGTCTTAGATCTTTCAAACAATT 60.349 38.462 0.00 0.00 0.00 2.32
788 936 1.963515 ACTTCCTGATTGTGGCCAAAC 59.036 47.619 7.24 0.00 33.44 2.93
879 1027 3.056536 TGGAAATCACGACTCTTCTCCTG 60.057 47.826 0.00 0.00 0.00 3.86
919 1067 4.184649 AGTGGATTTCCTTTGTTCCTGT 57.815 40.909 0.00 0.00 36.82 4.00
926 1074 7.288852 TGGATTTCCTTTGTTCCTGTGAAAATA 59.711 33.333 0.00 0.00 36.82 1.40
933 1081 7.039784 CCTTTGTTCCTGTGAAAATATCCAAGA 60.040 37.037 0.00 0.00 30.79 3.02
951 1099 5.928839 TCCAAGACTTCTTTTTCTCGATCTG 59.071 40.000 0.00 0.00 33.11 2.90
955 1103 6.155827 AGACTTCTTTTTCTCGATCTGACTG 58.844 40.000 0.00 0.00 0.00 3.51
975 1123 6.376864 TGACTGAAAACAAATTCACTGGAGAA 59.623 34.615 0.00 0.00 35.55 2.87
1045 1193 8.441312 ACGGTTAAGATCAAACAACTTTTCTA 57.559 30.769 11.65 0.00 0.00 2.10
1134 1282 1.917872 TTGGGGACATACCAAAGTGC 58.082 50.000 0.00 0.00 44.52 4.40
1139 1287 2.277084 GGACATACCAAAGTGCGTAGG 58.723 52.381 0.00 0.00 38.79 3.18
1150 1298 5.336744 CAAAGTGCGTAGGAAACTTGAAAA 58.663 37.500 5.14 0.00 43.67 2.29
1155 1303 5.454554 GTGCGTAGGAAACTTGAAAACTTTC 59.545 40.000 0.00 0.00 43.67 2.62
1284 1438 2.164422 GGTGATAAAAGGGCAAGTGCTC 59.836 50.000 2.85 0.00 43.28 4.26
1392 1553 4.400529 CCTTGCCGGGCTAATAAATTTT 57.599 40.909 21.46 0.00 0.00 1.82
1447 1608 7.722949 ATCCCATATAATATTGGCAACCTTG 57.277 36.000 0.00 0.00 0.00 3.61
1543 1704 6.284459 ACATACCTGAGCTATCTAAACTTGC 58.716 40.000 0.00 0.00 0.00 4.01
1551 1712 6.538742 TGAGCTATCTAAACTTGCCATACAAC 59.461 38.462 0.00 0.00 33.68 3.32
1565 1726 4.458989 GCCATACAACAATCTGTCAGGAAA 59.541 41.667 0.00 0.00 0.00 3.13
1636 1797 4.398319 CTCCATGTACATTGGTAATCCCC 58.602 47.826 5.37 0.00 0.00 4.81
1637 1798 4.051478 TCCATGTACATTGGTAATCCCCT 58.949 43.478 5.37 0.00 0.00 4.79
1641 1802 5.367945 TGTACATTGGTAATCCCCTTCTC 57.632 43.478 0.00 0.00 0.00 2.87
1669 1836 7.106890 TGGACATCCAGTTCGAAATAAATGTA 58.893 34.615 18.93 7.53 42.01 2.29
1670 1837 7.773224 TGGACATCCAGTTCGAAATAAATGTAT 59.227 33.333 18.93 4.46 42.01 2.29
1673 1840 8.956426 ACATCCAGTTCGAAATAAATGTATTGT 58.044 29.630 17.99 4.58 30.04 2.71
1688 1855 6.582677 ATGTATTGTTCCTCCTAGAGATCG 57.417 41.667 0.00 0.00 0.00 3.69
1689 1856 4.278669 TGTATTGTTCCTCCTAGAGATCGC 59.721 45.833 0.00 0.00 0.00 4.58
1695 1862 1.698506 CTCCTAGAGATCGCCCAACT 58.301 55.000 0.00 0.00 0.00 3.16
1697 1864 2.817258 CTCCTAGAGATCGCCCAACTAG 59.183 54.545 0.00 0.00 0.00 2.57
1698 1865 1.889829 CCTAGAGATCGCCCAACTAGG 59.110 57.143 0.00 0.00 42.33 3.02
1774 1941 9.527157 TTCTAGGATTAATCATTGGTTTTGTGA 57.473 29.630 17.07 0.00 0.00 3.58
1776 1943 7.781324 AGGATTAATCATTGGTTTTGTGACT 57.219 32.000 17.07 0.00 0.00 3.41
1790 1957 3.512516 GACTGGCGCTTGGATGGC 61.513 66.667 7.64 0.00 0.00 4.40
1806 1973 1.293179 GGCATTTTGCGGGCTTCTT 59.707 52.632 0.00 0.00 46.21 2.52
1811 1978 2.969628 TTTTGCGGGCTTCTTTTCAA 57.030 40.000 0.00 0.00 0.00 2.69
1829 1996 6.627087 TTTCAAGAAGAGATGGAGGTATGT 57.373 37.500 0.00 0.00 0.00 2.29
1832 1999 6.409704 TCAAGAAGAGATGGAGGTATGTTTG 58.590 40.000 0.00 0.00 0.00 2.93
1842 2009 4.017126 GGAGGTATGTTTGCTTTAGGCTT 58.983 43.478 0.00 0.00 42.39 4.35
1844 2011 3.689649 AGGTATGTTTGCTTTAGGCTTCG 59.310 43.478 0.00 0.00 42.39 3.79
1845 2012 3.181500 GGTATGTTTGCTTTAGGCTTCGG 60.181 47.826 0.00 0.00 42.39 4.30
1852 2019 1.610886 GCTTTAGGCTTCGGGACAAGT 60.611 52.381 0.00 0.00 38.06 3.16
1854 2021 2.178912 TTAGGCTTCGGGACAAGTTG 57.821 50.000 0.00 0.00 0.00 3.16
1867 2034 4.142600 GGGACAAGTTGTATGACAGATTGC 60.143 45.833 8.88 0.00 32.17 3.56
1904 2071 1.698506 ACTTGGCGGAAATGGTTTGA 58.301 45.000 0.00 0.00 0.00 2.69
1911 2078 2.607038 GCGGAAATGGTTTGAGAACACC 60.607 50.000 0.00 0.00 37.51 4.16
1915 2082 0.179004 ATGGTTTGAGAACACCGGCA 60.179 50.000 0.00 0.00 37.51 5.69
1916 2083 0.394488 TGGTTTGAGAACACCGGCAA 60.394 50.000 0.00 0.00 37.51 4.52
1917 2084 0.030235 GGTTTGAGAACACCGGCAAC 59.970 55.000 0.00 0.00 37.51 4.17
2009 2176 2.853235 CCAAAGGGGTCTTTAGTCGT 57.147 50.000 0.00 0.00 40.92 4.34
2020 2187 1.542915 CTTTAGTCGTGGTTCGGGAGA 59.457 52.381 0.00 0.00 40.32 3.71
2093 2285 2.743179 GGAGGGGCGGGACTAAAGG 61.743 68.421 0.00 0.00 0.00 3.11
2175 2367 1.375013 TCCTTTAGTCGCGGTTGGC 60.375 57.895 6.13 0.00 38.69 4.52
2177 2369 1.669760 CTTTAGTCGCGGTTGGCCA 60.670 57.895 0.00 0.00 38.94 5.36
2820 3401 9.170890 TGAGGGTTAATAGAATTGACATCCTAT 57.829 33.333 0.00 0.00 0.00 2.57
3015 3612 4.262678 GGGTGGTGATTAGAGATTAGAGGC 60.263 50.000 0.00 0.00 0.00 4.70
3020 3617 8.371699 GTGGTGATTAGAGATTAGAGGCTAAAT 58.628 37.037 0.00 0.00 0.00 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 3.878778 AGCATGTTCAAGCTACTAAGGG 58.121 45.455 0.62 0.00 39.78 3.95
12 13 5.491070 ACATCAAGCATGTTCAAGCTACTA 58.509 37.500 3.05 0.00 43.89 1.82
14 15 4.154737 TGACATCAAGCATGTTCAAGCTAC 59.845 41.667 3.05 0.00 46.53 3.58
21 22 3.999001 TGAGACTGACATCAAGCATGTTC 59.001 43.478 0.00 0.00 46.53 3.18
81 82 8.648693 AGGTCTAAGTAAGTCAAACTTGTATGT 58.351 33.333 2.65 0.00 39.11 2.29
83 84 9.490379 CAAGGTCTAAGTAAGTCAAACTTGTAT 57.510 33.333 2.65 0.00 39.11 2.29
85 86 6.766467 CCAAGGTCTAAGTAAGTCAAACTTGT 59.234 38.462 2.65 0.00 39.11 3.16
89 90 5.861727 TCCCAAGGTCTAAGTAAGTCAAAC 58.138 41.667 0.00 0.00 0.00 2.93
191 264 3.668447 TCTGAAATCACTCCAGTCAAGC 58.332 45.455 0.00 0.00 0.00 4.01
197 342 7.627298 AAATGATCTTCTGAAATCACTCCAG 57.373 36.000 13.58 0.00 34.88 3.86
201 346 7.313646 CAGCAAAATGATCTTCTGAAATCACT 58.686 34.615 13.58 4.85 34.88 3.41
207 352 6.040729 TCAAACCAGCAAAATGATCTTCTGAA 59.959 34.615 0.00 0.00 0.00 3.02
268 413 6.851222 ATGCGAGTCAATAATAACTTCCAG 57.149 37.500 0.00 0.00 0.00 3.86
299 444 3.888323 TGCTAAATCCAAGTTGAACAGCA 59.112 39.130 3.87 8.66 34.36 4.41
300 445 4.503741 TGCTAAATCCAAGTTGAACAGC 57.496 40.909 3.87 6.25 0.00 4.40
345 490 1.007118 AGCCAATTAGGAAACTGGGGG 59.993 52.381 0.00 0.00 43.88 5.40
360 505 2.665000 CTCTGCCCTCGAAGCCAA 59.335 61.111 4.76 0.00 0.00 4.52
409 554 1.294068 TGGGATCCTACCAACTAGGCT 59.706 52.381 12.58 0.00 42.03 4.58
431 576 5.358725 TCAGAAAAGGTAGTCCAAAACCAAC 59.641 40.000 0.00 0.00 38.30 3.77
499 644 5.186021 ACATGAACTCCAGACTAAGTGGTAG 59.814 44.000 0.00 0.00 36.37 3.18
507 652 4.407365 TCACTGACATGAACTCCAGACTA 58.593 43.478 0.00 0.00 0.00 2.59
509 654 3.667497 TCACTGACATGAACTCCAGAC 57.333 47.619 0.00 0.00 0.00 3.51
532 677 8.077991 CAGTAGATTTGACTGCATTGAAAGAAA 58.922 33.333 0.00 0.00 38.06 2.52
533 678 7.445096 TCAGTAGATTTGACTGCATTGAAAGAA 59.555 33.333 0.00 0.00 43.37 2.52
560 705 5.063017 TGGTAACTTGGGTATCAAACCAA 57.937 39.130 0.00 0.00 44.74 3.67
609 754 7.489160 ACACAAACCCATTTAAAGAGTTTCTC 58.511 34.615 9.04 0.00 0.00 2.87
636 781 2.095567 CAGTTGTGGAGCTCGGAAATTG 60.096 50.000 7.83 5.00 0.00 2.32
702 850 5.155643 TCTCGCATTTGACAAATTGACATG 58.844 37.500 10.77 1.93 0.00 3.21
704 852 4.827304 TCTCGCATTTGACAAATTGACA 57.173 36.364 10.77 0.00 0.00 3.58
724 872 4.876107 TGAAAGATCTAAGACCCGCAATTC 59.124 41.667 0.00 0.00 0.00 2.17
754 902 4.277476 TCAGGAAGTTCCTTTGAAAGCAA 58.723 39.130 22.36 0.00 46.91 3.91
788 936 1.804748 GGTTCCACCGTTTTAGCTCTG 59.195 52.381 0.00 0.00 0.00 3.35
879 1027 4.327087 CCACTTGAAAAACTGTTGTTGCTC 59.673 41.667 0.00 0.00 36.39 4.26
926 1074 6.593382 CAGATCGAGAAAAAGAAGTCTTGGAT 59.407 38.462 0.00 0.00 36.12 3.41
933 1081 6.090483 TCAGTCAGATCGAGAAAAAGAAGT 57.910 37.500 0.00 0.00 0.00 3.01
951 1099 6.377327 TCTCCAGTGAATTTGTTTTCAGTC 57.623 37.500 0.00 0.00 37.20 3.51
955 1103 8.360390 AGGTAATTCTCCAGTGAATTTGTTTTC 58.640 33.333 11.63 0.00 42.06 2.29
975 1123 5.456763 GGCTTCACTAATCCATCCAGGTAAT 60.457 44.000 0.00 0.00 39.02 1.89
1045 1193 6.153340 CCCATTATTTCAACTGGAATGTGACT 59.847 38.462 0.00 0.00 34.91 3.41
1121 1269 3.688694 TTCCTACGCACTTTGGTATGT 57.311 42.857 0.00 0.00 0.00 2.29
1150 1298 3.499918 GCAATAGCTGTGTCAGTGAAAGT 59.500 43.478 0.00 0.00 37.91 2.66
1180 1328 9.590451 TTCAAAGAAAGGATTATCAAATGATGC 57.410 29.630 6.17 0.00 36.05 3.91
1226 1374 5.397899 CCATTAGACATACCCATGGAACTGT 60.398 44.000 15.22 12.84 37.20 3.55
1362 1516 2.514824 CCGGCAAGGGAGCTTAGC 60.515 66.667 0.00 0.00 35.97 3.09
1447 1608 1.107114 TCAAGAGACTCCAGCGATCC 58.893 55.000 0.00 0.00 0.00 3.36
1543 1704 6.573664 TTTTCCTGACAGATTGTTGTATGG 57.426 37.500 3.32 0.00 0.00 2.74
1551 1712 5.065218 CGAGGGTATTTTTCCTGACAGATTG 59.935 44.000 3.32 0.00 32.74 2.67
1636 1797 3.594134 GAACTGGATGTCCACAGAGAAG 58.406 50.000 0.00 0.00 42.01 2.85
1637 1798 2.029020 CGAACTGGATGTCCACAGAGAA 60.029 50.000 0.00 0.00 42.01 2.87
1641 1802 2.455674 TTCGAACTGGATGTCCACAG 57.544 50.000 0.00 0.00 42.01 3.66
1662 1823 8.577296 CGATCTCTAGGAGGAACAATACATTTA 58.423 37.037 0.00 0.00 0.00 1.40
1663 1824 7.437748 CGATCTCTAGGAGGAACAATACATTT 58.562 38.462 0.00 0.00 0.00 2.32
1669 1836 2.630580 GGCGATCTCTAGGAGGAACAAT 59.369 50.000 0.00 0.00 0.00 2.71
1670 1837 2.032620 GGCGATCTCTAGGAGGAACAA 58.967 52.381 0.00 0.00 0.00 2.83
1673 1840 0.556258 TGGGCGATCTCTAGGAGGAA 59.444 55.000 0.00 0.00 0.00 3.36
1695 1862 2.239654 CCACCTTGCTGAATCTTCCCTA 59.760 50.000 0.00 0.00 0.00 3.53
1697 1864 1.467920 CCACCTTGCTGAATCTTCCC 58.532 55.000 0.00 0.00 0.00 3.97
1698 1865 0.813821 GCCACCTTGCTGAATCTTCC 59.186 55.000 0.00 0.00 0.00 3.46
1761 1928 1.769733 CGCCAGTCACAAAACCAATG 58.230 50.000 0.00 0.00 0.00 2.82
1774 1941 3.650298 ATGCCATCCAAGCGCCAGT 62.650 57.895 2.29 0.00 0.00 4.00
1776 1943 1.543065 AAAATGCCATCCAAGCGCCA 61.543 50.000 2.29 0.00 0.00 5.69
1790 1957 2.753296 TGAAAAGAAGCCCGCAAAATG 58.247 42.857 0.00 0.00 0.00 2.32
1806 1973 6.627087 ACATACCTCCATCTCTTCTTGAAA 57.373 37.500 0.00 0.00 0.00 2.69
1811 1978 4.472833 AGCAAACATACCTCCATCTCTTCT 59.527 41.667 0.00 0.00 0.00 2.85
1832 1999 1.087501 CTTGTCCCGAAGCCTAAAGC 58.912 55.000 0.00 0.00 44.25 3.51
1842 2009 2.894765 TCTGTCATACAACTTGTCCCGA 59.105 45.455 0.00 0.00 0.00 5.14
1844 2011 4.142600 GCAATCTGTCATACAACTTGTCCC 60.143 45.833 0.00 0.00 0.00 4.46
1845 2012 4.455533 TGCAATCTGTCATACAACTTGTCC 59.544 41.667 0.00 0.00 0.00 4.02
1867 2034 5.630680 GCCAAGTAACAACAGAAATGACATG 59.369 40.000 0.00 0.00 0.00 3.21
1911 2078 4.891727 ATAGCTCCGCCGTTGCCG 62.892 66.667 0.00 0.00 0.00 5.69
1915 2082 0.669077 CTAGTGATAGCTCCGCCGTT 59.331 55.000 0.00 0.00 0.00 4.44
1916 2083 0.465824 ACTAGTGATAGCTCCGCCGT 60.466 55.000 0.00 0.00 0.00 5.68
1917 2084 1.465387 CTACTAGTGATAGCTCCGCCG 59.535 57.143 5.39 0.00 0.00 6.46
1918 2085 2.780714 TCTACTAGTGATAGCTCCGCC 58.219 52.381 5.39 0.00 0.00 6.13
1919 2086 4.832590 TTTCTACTAGTGATAGCTCCGC 57.167 45.455 5.39 0.00 0.00 5.54
1920 2087 7.028926 TCTTTTTCTACTAGTGATAGCTCCG 57.971 40.000 5.39 0.00 0.00 4.63
1921 2088 7.430441 CCTCTTTTTCTACTAGTGATAGCTCC 58.570 42.308 5.39 0.00 0.00 4.70
1922 2089 6.921307 GCCTCTTTTTCTACTAGTGATAGCTC 59.079 42.308 5.39 0.00 0.00 4.09
1923 2090 6.609616 AGCCTCTTTTTCTACTAGTGATAGCT 59.390 38.462 5.39 0.00 0.00 3.32
1924 2091 6.811954 AGCCTCTTTTTCTACTAGTGATAGC 58.188 40.000 5.39 0.00 0.00 2.97
1925 2092 7.923878 GGAAGCCTCTTTTTCTACTAGTGATAG 59.076 40.741 5.39 0.00 0.00 2.08
1926 2093 7.399191 TGGAAGCCTCTTTTTCTACTAGTGATA 59.601 37.037 5.39 0.00 0.00 2.15
1927 2094 6.213600 TGGAAGCCTCTTTTTCTACTAGTGAT 59.786 38.462 5.39 0.00 0.00 3.06
1928 2095 5.542635 TGGAAGCCTCTTTTTCTACTAGTGA 59.457 40.000 5.39 0.00 0.00 3.41
1960 2127 6.206498 GTTCGATTATTTTGGGGACTAATGC 58.794 40.000 0.00 0.00 0.00 3.56
2009 2176 3.801620 GGGTCTTCTCCCGAACCA 58.198 61.111 0.00 0.00 38.17 3.67
2020 2187 0.175073 GATAGTTGGTCGCGGGTCTT 59.825 55.000 6.13 0.00 0.00 3.01
2479 3009 9.587772 TTTGAGGATTTTGAAAATGTTTAACGA 57.412 25.926 8.03 0.00 0.00 3.85
2565 3101 2.428890 GACCATTGTTTGACCACCACAA 59.571 45.455 0.00 0.00 34.97 3.33
2566 3102 2.028130 GACCATTGTTTGACCACCACA 58.972 47.619 0.00 0.00 0.00 4.17
2567 3103 2.028130 TGACCATTGTTTGACCACCAC 58.972 47.619 0.00 0.00 0.00 4.16
2569 3105 3.132111 AGTTTGACCATTGTTTGACCACC 59.868 43.478 0.00 0.00 0.00 4.61
2820 3401 6.039616 GCACTTGTTGTTTTCCTGACAATAA 58.960 36.000 0.00 0.00 39.03 1.40


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

AutoCloner maintained by Alex Coulton.