Multiple sequence alignment - TraesCS4D01G279500

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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 TraesCS4D01G279500 chr4D 100.000 4505 0 0 1 4505 450687366 450682862 0.000000e+00 8320.0
1 TraesCS4D01G279500 chr4D 96.337 546 15 4 1 545 113173406 113172865 0.000000e+00 893.0
2 TraesCS4D01G279500 chr4D 74.271 2161 378 119 1190 3275 4518153 4520210 0.000000e+00 747.0
3 TraesCS4D01G279500 chr4D 75.551 1542 271 80 1887 3370 4525965 4527458 0.000000e+00 662.0
4 TraesCS4D01G279500 chr4D 77.437 1108 200 37 2279 3353 4628326 4629416 2.300000e-172 616.0
5 TraesCS4D01G279500 chr4D 79.576 896 153 21 2479 3353 4650653 4651539 8.280000e-172 614.0
6 TraesCS4D01G279500 chr4D 76.820 522 95 21 2597 3104 4273483 4272974 2.070000e-68 270.0
7 TraesCS4D01G279500 chr4D 76.308 325 57 15 1199 1517 4351409 4351099 6.030000e-34 156.0
8 TraesCS4D01G279500 chr4D 75.143 350 68 14 1194 1534 4247132 4247471 3.630000e-31 147.0
9 TraesCS4D01G279500 chr4D 74.303 323 63 16 1194 1505 4332770 4332457 7.920000e-23 119.0
10 TraesCS4D01G279500 chr4D 94.872 78 0 4 1791 1866 450685501 450685576 7.920000e-23 119.0
11 TraesCS4D01G279500 chr4A 93.631 2512 97 17 1964 4443 16049035 16051515 0.000000e+00 3694.0
12 TraesCS4D01G279500 chr4A 94.365 1260 49 11 548 1802 16047307 16048549 0.000000e+00 1914.0
13 TraesCS4D01G279500 chr4A 72.689 952 193 45 2180 3106 599124632 599123723 5.780000e-64 255.0
14 TraesCS4D01G279500 chr4A 95.604 91 4 0 1890 1980 16048933 16049023 3.630000e-31 147.0
15 TraesCS4D01G279500 chr4B 96.145 1738 57 7 2710 4441 564076320 564074587 0.000000e+00 2830.0
16 TraesCS4D01G279500 chr4B 92.314 1236 46 18 586 1814 564078382 564077189 0.000000e+00 1711.0
17 TraesCS4D01G279500 chr4B 96.394 832 16 7 1880 2711 564077190 564076373 0.000000e+00 1358.0
18 TraesCS4D01G279500 chr4B 73.709 852 158 49 2279 3103 7354935 7355747 5.740000e-69 272.0
19 TraesCS4D01G279500 chr4B 73.598 856 161 45 2279 3106 7171956 7172774 7.430000e-68 268.0
20 TraesCS4D01G279500 chr4B 73.629 857 159 47 2279 3106 7310022 7310840 7.430000e-68 268.0
21 TraesCS4D01G279500 chr4B 72.908 956 188 49 2180 3106 7264437 7265350 9.610000e-67 265.0
22 TraesCS4D01G279500 chr4B 74.432 352 67 17 1194 1534 4332990 4332651 3.660000e-26 130.0
23 TraesCS4D01G279500 chr4B 96.104 77 2 1 4429 4505 564074574 564074499 1.700000e-24 124.0
24 TraesCS4D01G279500 chr4B 97.500 40 1 0 545 584 564080874 564080835 8.090000e-08 69.4
25 TraesCS4D01G279500 chr1D 97.982 545 9 2 1 545 110576776 110577318 0.000000e+00 944.0
26 TraesCS4D01G279500 chr2A 97.253 546 10 5 1 545 726548470 726547929 0.000000e+00 920.0
27 TraesCS4D01G279500 chr7B 96.886 546 16 1 1 545 333356137 333355592 0.000000e+00 913.0
28 TraesCS4D01G279500 chr7B 95.971 546 18 4 1 545 558983425 558982883 0.000000e+00 883.0
29 TraesCS4D01G279500 chr5B 96.514 545 13 3 1 545 703099794 703099256 0.000000e+00 896.0
30 TraesCS4D01G279500 chr5B 97.059 34 0 1 4397 4429 516899256 516899289 6.300000e-04 56.5
31 TraesCS4D01G279500 chr1B 95.978 547 17 4 1 546 667561893 667562435 0.000000e+00 883.0
32 TraesCS4D01G279500 chr3D 95.971 546 16 4 1 546 459316747 459317286 0.000000e+00 881.0
33 TraesCS4D01G279500 chr2B 95.963 545 15 3 1 545 319361768 319362305 0.000000e+00 878.0
34 TraesCS4D01G279500 chrUn 77.510 1205 210 45 2181 3353 47314630 47315805 0.000000e+00 667.0
35 TraesCS4D01G279500 chrUn 78.159 1108 195 34 2277 3353 47289306 47288215 0.000000e+00 662.0
36 TraesCS4D01G279500 chr6A 75.689 617 117 25 2478 3073 593025490 593024886 1.230000e-70 278.0
37 TraesCS4D01G279500 chr7D 82.581 155 24 3 1194 1345 629888193 629888039 2.830000e-27 134.0
38 TraesCS4D01G279500 chr7A 75.309 324 55 16 1201 1517 726273102 726272797 1.020000e-26 132.0
39 TraesCS4D01G279500 chr7A 75.000 324 56 16 1201 1517 726343807 726343502 4.730000e-25 126.0
40 TraesCS4D01G279500 chr7A 74.923 323 57 15 1201 1517 726363302 726362998 4.730000e-25 126.0
41 TraesCS4D01G279500 chr2D 100.000 28 0 0 4402 4429 317860156 317860183 8.000000e-03 52.8
42 TraesCS4D01G279500 chr2D 100.000 28 0 0 4402 4429 606381720 606381747 8.000000e-03 52.8


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 TraesCS4D01G279500 chr4D 450682862 450687366 4504 True 8320.000000 8320 100.000000 1 4505 1 chr4D.!!$R5 4504
1 TraesCS4D01G279500 chr4D 113172865 113173406 541 True 893.000000 893 96.337000 1 545 1 chr4D.!!$R4 544
2 TraesCS4D01G279500 chr4D 4518153 4520210 2057 False 747.000000 747 74.271000 1190 3275 1 chr4D.!!$F2 2085
3 TraesCS4D01G279500 chr4D 4525965 4527458 1493 False 662.000000 662 75.551000 1887 3370 1 chr4D.!!$F3 1483
4 TraesCS4D01G279500 chr4D 4628326 4629416 1090 False 616.000000 616 77.437000 2279 3353 1 chr4D.!!$F4 1074
5 TraesCS4D01G279500 chr4D 4650653 4651539 886 False 614.000000 614 79.576000 2479 3353 1 chr4D.!!$F5 874
6 TraesCS4D01G279500 chr4D 4272974 4273483 509 True 270.000000 270 76.820000 2597 3104 1 chr4D.!!$R1 507
7 TraesCS4D01G279500 chr4A 16047307 16051515 4208 False 1918.333333 3694 94.533333 548 4443 3 chr4A.!!$F1 3895
8 TraesCS4D01G279500 chr4A 599123723 599124632 909 True 255.000000 255 72.689000 2180 3106 1 chr4A.!!$R1 926
9 TraesCS4D01G279500 chr4B 564074499 564080874 6375 True 1218.480000 2830 95.691400 545 4505 5 chr4B.!!$R2 3960
10 TraesCS4D01G279500 chr4B 7354935 7355747 812 False 272.000000 272 73.709000 2279 3103 1 chr4B.!!$F4 824
11 TraesCS4D01G279500 chr4B 7171956 7172774 818 False 268.000000 268 73.598000 2279 3106 1 chr4B.!!$F1 827
12 TraesCS4D01G279500 chr4B 7310022 7310840 818 False 268.000000 268 73.629000 2279 3106 1 chr4B.!!$F3 827
13 TraesCS4D01G279500 chr4B 7264437 7265350 913 False 265.000000 265 72.908000 2180 3106 1 chr4B.!!$F2 926
14 TraesCS4D01G279500 chr1D 110576776 110577318 542 False 944.000000 944 97.982000 1 545 1 chr1D.!!$F1 544
15 TraesCS4D01G279500 chr2A 726547929 726548470 541 True 920.000000 920 97.253000 1 545 1 chr2A.!!$R1 544
16 TraesCS4D01G279500 chr7B 333355592 333356137 545 True 913.000000 913 96.886000 1 545 1 chr7B.!!$R1 544
17 TraesCS4D01G279500 chr7B 558982883 558983425 542 True 883.000000 883 95.971000 1 545 1 chr7B.!!$R2 544
18 TraesCS4D01G279500 chr5B 703099256 703099794 538 True 896.000000 896 96.514000 1 545 1 chr5B.!!$R1 544
19 TraesCS4D01G279500 chr1B 667561893 667562435 542 False 883.000000 883 95.978000 1 546 1 chr1B.!!$F1 545
20 TraesCS4D01G279500 chr3D 459316747 459317286 539 False 881.000000 881 95.971000 1 546 1 chr3D.!!$F1 545
21 TraesCS4D01G279500 chr2B 319361768 319362305 537 False 878.000000 878 95.963000 1 545 1 chr2B.!!$F1 544
22 TraesCS4D01G279500 chrUn 47314630 47315805 1175 False 667.000000 667 77.510000 2181 3353 1 chrUn.!!$F1 1172
23 TraesCS4D01G279500 chrUn 47288215 47289306 1091 True 662.000000 662 78.159000 2277 3353 1 chrUn.!!$R1 1076
24 TraesCS4D01G279500 chr6A 593024886 593025490 604 True 278.000000 278 75.689000 2478 3073 1 chr6A.!!$R1 595

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
912 3390 0.034960 CTCCTCTCCTGTCCTCGTGA 60.035 60.0 0.00 0.0 0.00 4.35 F
1164 3644 0.037697 TGACGATGGGTTTCGACTGG 60.038 55.0 0.31 0.0 41.62 4.00 F
1167 3647 0.174845 CGATGGGTTTCGACTGGCTA 59.825 55.0 0.00 0.0 41.62 3.93 F
1260 3746 0.394762 GATGGATGAGGGCAGTGCAA 60.395 55.0 18.61 0.0 0.00 4.08 F
2163 5036 0.467844 TGTATGTCATGGGCATGGGC 60.468 55.0 12.02 0.0 39.24 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1880 4713 0.109597 CCGACAATTCTGTTGCAGGC 60.110 55.000 0.0 0.0 35.82 4.85 R
2248 5128 3.007940 CCGAGCCATAACATAGGGATGAA 59.992 47.826 0.0 0.0 36.48 2.57 R
2473 5369 4.573900 AGCAACATCAGGAAACTAGAGTG 58.426 43.478 0.0 0.0 40.21 3.51 R
3219 6252 3.157087 ACGAGCAAATGGGACTTTCAAT 58.843 40.909 0.0 0.0 0.00 2.57 R
3625 6661 0.729690 GAAGCAAGAATCGTCCTGGC 59.270 55.000 0.0 0.0 0.00 4.85 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
610 3071 3.495352 ATAGCGAGCCGGCCGTAAC 62.495 63.158 29.37 13.39 0.00 2.50
683 3144 6.367421 GCGTCTCACTCTCTAATACATACTG 58.633 44.000 0.00 0.00 0.00 2.74
684 3145 6.566942 GCGTCTCACTCTCTAATACATACTGG 60.567 46.154 0.00 0.00 0.00 4.00
693 3167 9.632807 CTCTCTAATACATACTGGAGTATTTGC 57.367 37.037 0.00 0.00 40.38 3.68
852 3330 2.294791 CCAGCCACTAGAGTAATCGAGG 59.705 54.545 5.31 0.00 0.00 4.63
911 3389 0.322997 ACTCCTCTCCTGTCCTCGTG 60.323 60.000 0.00 0.00 0.00 4.35
912 3390 0.034960 CTCCTCTCCTGTCCTCGTGA 60.035 60.000 0.00 0.00 0.00 4.35
913 3391 0.322636 TCCTCTCCTGTCCTCGTGAC 60.323 60.000 1.64 1.64 44.72 3.67
914 3392 1.316706 CCTCTCCTGTCCTCGTGACC 61.317 65.000 5.60 0.00 43.78 4.02
915 3393 0.322997 CTCTCCTGTCCTCGTGACCT 60.323 60.000 5.60 0.00 43.78 3.85
916 3394 0.322636 TCTCCTGTCCTCGTGACCTC 60.323 60.000 5.60 0.00 43.78 3.85
917 3395 1.649390 CTCCTGTCCTCGTGACCTCG 61.649 65.000 5.60 0.00 43.78 4.63
918 3396 1.972223 CCTGTCCTCGTGACCTCGT 60.972 63.158 5.60 0.00 43.78 4.18
973 3452 4.719369 GACCCGAACGTGCTCGCT 62.719 66.667 8.29 0.00 41.18 4.93
1070 3550 4.003788 CGCCACGGTGAGTCCCTT 62.004 66.667 10.28 0.00 0.00 3.95
1161 3641 0.437295 CGTTGACGATGGGTTTCGAC 59.563 55.000 0.00 0.00 41.62 4.20
1162 3642 1.792006 GTTGACGATGGGTTTCGACT 58.208 50.000 0.31 0.00 41.62 4.18
1163 3643 1.459592 GTTGACGATGGGTTTCGACTG 59.540 52.381 0.31 0.00 41.62 3.51
1164 3644 0.037697 TGACGATGGGTTTCGACTGG 60.038 55.000 0.31 0.00 41.62 4.00
1167 3647 0.174845 CGATGGGTTTCGACTGGCTA 59.825 55.000 0.00 0.00 41.62 3.93
1183 3663 1.337118 GCTAGCTATCTGGCTGACCT 58.663 55.000 7.70 0.00 42.71 3.85
1184 3664 1.691434 GCTAGCTATCTGGCTGACCTT 59.309 52.381 7.70 0.00 42.71 3.50
1185 3665 2.103941 GCTAGCTATCTGGCTGACCTTT 59.896 50.000 7.70 0.00 42.71 3.11
1186 3666 2.706339 AGCTATCTGGCTGACCTTTG 57.294 50.000 0.00 0.00 41.43 2.77
1247 3733 1.523258 GCAGCTGCAGTCGATGGAT 60.523 57.895 33.36 0.00 41.59 3.41
1260 3746 0.394762 GATGGATGAGGGCAGTGCAA 60.395 55.000 18.61 0.00 0.00 4.08
1301 3787 4.583871 AGGTCATCAACATCTTCCTCAAC 58.416 43.478 0.00 0.00 0.00 3.18
1543 4043 3.828875 AGCCCTTCTTTTCTATCCTCG 57.171 47.619 0.00 0.00 0.00 4.63
1545 4045 2.474816 CCCTTCTTTTCTATCCTCGCG 58.525 52.381 0.00 0.00 0.00 5.87
1559 4059 2.350498 TCCTCGCGCTATTTTTAACTGC 59.650 45.455 5.56 0.00 0.00 4.40
1781 4312 3.625764 TGGAGGTTTTTCAAGTCTGTTCG 59.374 43.478 0.00 0.00 0.00 3.95
1784 4315 3.632145 AGGTTTTTCAAGTCTGTTCGCAT 59.368 39.130 0.00 0.00 0.00 4.73
1785 4316 4.097892 AGGTTTTTCAAGTCTGTTCGCATT 59.902 37.500 0.00 0.00 0.00 3.56
1786 4317 4.803613 GGTTTTTCAAGTCTGTTCGCATTT 59.196 37.500 0.00 0.00 0.00 2.32
1815 4346 4.463515 TCGTATATGTCAGCGTAGTGTC 57.536 45.455 0.00 0.00 0.00 3.67
1816 4347 3.060070 TCGTATATGTCAGCGTAGTGTCG 60.060 47.826 0.00 0.00 0.00 4.35
1817 4348 3.302935 CGTATATGTCAGCGTAGTGTCGT 60.303 47.826 0.00 0.00 0.00 4.34
1819 4350 2.433868 ATGTCAGCGTAGTGTCGTTT 57.566 45.000 0.00 0.00 0.00 3.60
1821 4352 1.202325 TGTCAGCGTAGTGTCGTTTGT 60.202 47.619 0.00 0.00 0.00 2.83
1822 4353 2.033174 TGTCAGCGTAGTGTCGTTTGTA 59.967 45.455 0.00 0.00 0.00 2.41
1823 4354 2.403037 GTCAGCGTAGTGTCGTTTGTAC 59.597 50.000 0.00 0.00 0.00 2.90
1833 4364 5.646467 GTGTCGTTTGTACACATAGTTGT 57.354 39.130 0.00 0.00 45.26 3.32
1844 4375 5.646467 ACACATAGTTGTACAAACGACAC 57.354 39.130 10.51 0.00 41.80 3.67
1845 4376 5.353938 ACACATAGTTGTACAAACGACACT 58.646 37.500 10.51 5.35 41.80 3.55
1846 4377 6.506147 ACACATAGTTGTACAAACGACACTA 58.494 36.000 10.51 7.56 41.80 2.74
1847 4378 6.418819 ACACATAGTTGTACAAACGACACTAC 59.581 38.462 10.51 0.00 41.80 2.73
1848 4379 5.626543 ACATAGTTGTACAAACGACACTACG 59.373 40.000 10.51 2.37 41.80 3.51
1849 4380 2.791004 AGTTGTACAAACGACACTACGC 59.209 45.455 10.51 0.00 41.80 4.42
1850 4381 2.780065 TGTACAAACGACACTACGCT 57.220 45.000 0.00 0.00 36.70 5.07
1851 4382 2.387185 TGTACAAACGACACTACGCTG 58.613 47.619 0.00 0.00 36.70 5.18
1852 4383 2.033174 TGTACAAACGACACTACGCTGA 59.967 45.455 0.00 0.00 36.70 4.26
1854 4385 1.202325 ACAAACGACACTACGCTGACA 60.202 47.619 0.00 0.00 36.70 3.58
1855 4386 2.058798 CAAACGACACTACGCTGACAT 58.941 47.619 0.00 0.00 36.70 3.06
1857 4388 3.777465 AACGACACTACGCTGACATAT 57.223 42.857 0.00 0.00 36.70 1.78
1858 4389 4.888038 AACGACACTACGCTGACATATA 57.112 40.909 0.00 0.00 36.70 0.86
1860 4391 3.216031 CGACACTACGCTGACATATACG 58.784 50.000 0.00 0.00 0.00 3.06
1861 4392 3.060070 CGACACTACGCTGACATATACGA 60.060 47.826 0.00 0.00 0.00 3.43
1862 4393 4.551410 CGACACTACGCTGACATATACGAA 60.551 45.833 0.00 0.00 0.00 3.85
1864 4395 6.549912 ACACTACGCTGACATATACGAATA 57.450 37.500 0.00 0.00 0.00 1.75
1866 4397 6.204301 ACACTACGCTGACATATACGAATAGT 59.796 38.462 0.00 0.00 0.00 2.12
1867 4398 7.076362 CACTACGCTGACATATACGAATAGTT 58.924 38.462 0.00 0.00 0.00 2.24
1868 4399 8.225777 CACTACGCTGACATATACGAATAGTTA 58.774 37.037 0.00 0.00 0.00 2.24
1972 4805 9.431887 GGTCTTGTGAACATTTCTAGTATTACA 57.568 33.333 0.00 0.00 0.00 2.41
2021 4882 7.526608 CGTTATTCTAGGTCAGCAATGAAAAA 58.473 34.615 0.00 0.00 0.00 1.94
2083 4948 5.521735 GCTAGTCTACATCACACAATTGGAG 59.478 44.000 10.83 4.49 0.00 3.86
2162 5035 2.297698 ATGTATGTCATGGGCATGGG 57.702 50.000 12.02 0.00 39.24 4.00
2163 5036 0.467844 TGTATGTCATGGGCATGGGC 60.468 55.000 12.02 0.00 39.24 5.36
2164 5037 0.467844 GTATGTCATGGGCATGGGCA 60.468 55.000 12.02 0.00 43.71 5.36
2165 5038 0.483770 TATGTCATGGGCATGGGCAT 59.516 50.000 12.02 1.89 43.71 4.40
2166 5039 1.118965 ATGTCATGGGCATGGGCATG 61.119 55.000 0.00 0.00 43.71 4.06
2204 5083 8.447833 CGTGTTGTTTAGCCATAATTAGAAGAA 58.552 33.333 0.00 0.00 0.00 2.52
2246 5126 6.260050 AGCGATGTAACGGAAATGTCAATATT 59.740 34.615 0.00 0.00 0.00 1.28
2247 5127 7.439955 AGCGATGTAACGGAAATGTCAATATTA 59.560 33.333 0.00 0.00 0.00 0.98
2248 5128 8.227791 GCGATGTAACGGAAATGTCAATATTAT 58.772 33.333 0.00 0.00 0.00 1.28
2412 5300 6.770286 AGGAAATGGCTCCTTGAGAATATA 57.230 37.500 0.00 0.00 43.76 0.86
2456 5349 5.392703 CCATATGTATCAGCATGCCATGTTC 60.393 44.000 15.66 1.75 34.76 3.18
2460 5353 2.951457 TCAGCATGCCATGTTCAATG 57.049 45.000 15.66 2.45 34.76 2.82
2757 5752 5.148651 ACCTACTTGTTCACTTAATCGCT 57.851 39.130 0.00 0.00 0.00 4.93
2775 5770 7.606858 AATCGCTAATCATGTGATTGATAGG 57.393 36.000 16.40 4.03 43.90 2.57
3590 6626 7.839680 TCTCTGAATATGTAGGTAGCATTCA 57.160 36.000 0.00 0.00 35.10 2.57
3656 6692 1.424493 CTTGCTTCGCGATCACCCTC 61.424 60.000 10.88 0.00 0.00 4.30
3657 6693 2.956964 GCTTCGCGATCACCCTCG 60.957 66.667 10.88 0.00 41.54 4.63
3689 6729 5.478233 TGTTGTCTTGTGTGTTGATGTAC 57.522 39.130 0.00 0.00 0.00 2.90
3717 6757 6.472808 GTCTGTTAACTCTTTATACCTCAGCG 59.527 42.308 7.22 0.00 0.00 5.18
3743 6783 0.107017 ATGGCCCATAGACTGTGTGC 60.107 55.000 0.00 0.00 0.00 4.57
3792 6832 6.103330 GGTGACTTGGTTTTGTTGTATGTTT 58.897 36.000 0.00 0.00 0.00 2.83
4153 7195 2.376808 AGAATGCCTCTGAAGTGACG 57.623 50.000 0.00 0.00 31.12 4.35
4196 7238 5.538433 GGAGGTGTCAGAGCTAATAGAGATT 59.462 44.000 0.00 0.00 30.42 2.40
4263 7305 6.402658 GCAGTTCTGAAGCTATAAGAAACACC 60.403 42.308 3.84 0.00 32.03 4.16
4337 7381 1.203025 ACTCGGAGGTACCAGACAGTT 60.203 52.381 15.94 0.00 38.90 3.16
4487 7555 2.104963 GGCTTACACCCAAGATCCCTAG 59.895 54.545 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
533 543 7.483307 GGTCATTACCGTTGACTAGTACAATA 58.517 38.462 0.00 0.00 42.48 1.90
610 3071 0.179161 TTTTTGTTGCACGTGGTCCG 60.179 50.000 18.88 0.00 44.03 4.79
656 3117 0.382515 ATTAGAGAGTGAGACGCGCC 59.617 55.000 5.73 0.00 0.00 6.53
658 3119 3.946308 TGTATTAGAGAGTGAGACGCG 57.054 47.619 3.53 3.53 0.00 6.01
659 3120 6.367421 CAGTATGTATTAGAGAGTGAGACGC 58.633 44.000 0.00 0.00 0.00 5.19
660 3121 6.706716 TCCAGTATGTATTAGAGAGTGAGACG 59.293 42.308 0.00 0.00 0.00 4.18
661 3122 7.717875 ACTCCAGTATGTATTAGAGAGTGAGAC 59.282 40.741 0.00 0.00 32.37 3.36
662 3123 7.807198 ACTCCAGTATGTATTAGAGAGTGAGA 58.193 38.462 0.00 0.00 32.37 3.27
663 3124 9.733556 ATACTCCAGTATGTATTAGAGAGTGAG 57.266 37.037 0.00 0.00 39.57 3.51
668 3129 8.297426 CGCAAATACTCCAGTATGTATTAGAGA 58.703 37.037 0.00 0.00 40.78 3.10
683 3144 2.543777 TAGCCCATCGCAAATACTCC 57.456 50.000 0.00 0.00 41.38 3.85
684 3145 2.160417 GCATAGCCCATCGCAAATACTC 59.840 50.000 0.00 0.00 41.38 2.59
693 3167 2.620115 ACTTTCAATGCATAGCCCATCG 59.380 45.455 0.00 0.00 0.00 3.84
911 3389 4.131088 GGCGGAGTGGACGAGGTC 62.131 72.222 0.00 0.00 0.00 3.85
1070 3550 1.329256 GCGGCTATAGAAGTGAGGGA 58.671 55.000 3.21 0.00 0.00 4.20
1161 3641 1.000731 GTCAGCCAGATAGCTAGCCAG 59.999 57.143 12.13 0.00 42.61 4.85
1162 3642 1.043816 GTCAGCCAGATAGCTAGCCA 58.956 55.000 12.13 0.00 42.61 4.75
1163 3643 0.320050 GGTCAGCCAGATAGCTAGCC 59.680 60.000 12.13 0.00 42.61 3.93
1164 3644 1.337118 AGGTCAGCCAGATAGCTAGC 58.663 55.000 6.62 6.62 42.61 3.42
1167 3647 1.407989 GCAAAGGTCAGCCAGATAGCT 60.408 52.381 0.00 0.00 46.45 3.32
1183 3663 1.078497 ATCGATCACGCCAGGCAAA 60.078 52.632 13.30 0.00 39.58 3.68
1184 3664 1.521457 GATCGATCACGCCAGGCAA 60.521 57.895 20.52 0.00 39.58 4.52
1185 3665 1.106944 TAGATCGATCACGCCAGGCA 61.107 55.000 26.47 0.00 39.58 4.75
1186 3666 0.387878 CTAGATCGATCACGCCAGGC 60.388 60.000 26.47 0.00 39.58 4.85
1188 3668 0.242286 CCCTAGATCGATCACGCCAG 59.758 60.000 26.47 14.09 39.58 4.85
1247 3733 2.203337 GTGGTTGCACTGCCCTCA 60.203 61.111 0.00 0.00 0.00 3.86
1301 3787 3.471244 GAGGATCCTGTCGGCGTCG 62.471 68.421 22.02 1.15 37.82 5.12
1543 4043 5.174943 ACAAACAAGCAGTTAAAAATAGCGC 59.825 36.000 0.00 0.00 40.26 5.92
1545 4045 8.817100 AGAAACAAACAAGCAGTTAAAAATAGC 58.183 29.630 0.00 0.00 40.26 2.97
1559 4059 4.612259 CGATGCAGAGGAGAAACAAACAAG 60.612 45.833 0.00 0.00 0.00 3.16
1785 4316 7.997107 ACGCTGACATATACGAATAGAAAAA 57.003 32.000 0.00 0.00 0.00 1.94
1786 4317 8.347771 ACTACGCTGACATATACGAATAGAAAA 58.652 33.333 0.00 0.00 0.00 2.29
1821 4352 6.506147 AGTGTCGTTTGTACAACTATGTGTA 58.494 36.000 8.07 0.00 40.84 2.90
1822 4353 5.353938 AGTGTCGTTTGTACAACTATGTGT 58.646 37.500 8.07 0.00 40.84 3.72
1823 4354 5.900339 AGTGTCGTTTGTACAACTATGTG 57.100 39.130 8.07 0.00 40.84 3.21
1827 4358 3.974401 GCGTAGTGTCGTTTGTACAACTA 59.026 43.478 8.07 3.22 0.00 2.24
1828 4359 2.791004 GCGTAGTGTCGTTTGTACAACT 59.209 45.455 8.07 4.27 0.00 3.16
1829 4360 2.791004 AGCGTAGTGTCGTTTGTACAAC 59.209 45.455 8.07 3.09 0.00 3.32
1831 4362 2.033174 TCAGCGTAGTGTCGTTTGTACA 59.967 45.455 0.00 0.00 0.00 2.90
1832 4363 2.403037 GTCAGCGTAGTGTCGTTTGTAC 59.597 50.000 0.00 0.00 0.00 2.90
1833 4364 2.033174 TGTCAGCGTAGTGTCGTTTGTA 59.967 45.455 0.00 0.00 0.00 2.41
1835 4366 1.483316 TGTCAGCGTAGTGTCGTTTG 58.517 50.000 0.00 0.00 0.00 2.93
1836 4367 2.433868 ATGTCAGCGTAGTGTCGTTT 57.566 45.000 0.00 0.00 0.00 3.60
1838 4369 3.302935 CGTATATGTCAGCGTAGTGTCGT 60.303 47.826 0.00 0.00 0.00 4.34
1840 4371 4.463515 TCGTATATGTCAGCGTAGTGTC 57.536 45.455 0.00 0.00 0.00 3.67
1842 4373 6.600350 ACTATTCGTATATGTCAGCGTAGTG 58.400 40.000 0.00 0.00 0.00 2.74
1846 4377 8.944029 ACTATAACTATTCGTATATGTCAGCGT 58.056 33.333 0.00 0.00 0.00 5.07
1847 4378 9.770503 AACTATAACTATTCGTATATGTCAGCG 57.229 33.333 0.00 0.00 0.00 5.18
1857 4388 8.036575 AGGCAAACACAACTATAACTATTCGTA 58.963 33.333 0.00 0.00 0.00 3.43
1858 4389 6.877322 AGGCAAACACAACTATAACTATTCGT 59.123 34.615 0.00 0.00 0.00 3.85
1860 4391 6.967199 GCAGGCAAACACAACTATAACTATTC 59.033 38.462 0.00 0.00 0.00 1.75
1861 4392 6.432783 TGCAGGCAAACACAACTATAACTATT 59.567 34.615 0.00 0.00 0.00 1.73
1862 4393 5.943416 TGCAGGCAAACACAACTATAACTAT 59.057 36.000 0.00 0.00 0.00 2.12
1864 4395 4.141287 TGCAGGCAAACACAACTATAACT 58.859 39.130 0.00 0.00 0.00 2.24
1866 4397 4.339530 TGTTGCAGGCAAACACAACTATAA 59.660 37.500 8.47 0.00 42.22 0.98
1867 4398 3.885901 TGTTGCAGGCAAACACAACTATA 59.114 39.130 8.47 0.00 42.22 1.31
1868 4399 2.692557 TGTTGCAGGCAAACACAACTAT 59.307 40.909 8.47 0.00 42.22 2.12
1880 4713 0.109597 CCGACAATTCTGTTGCAGGC 60.110 55.000 0.00 0.00 35.82 4.85
1972 4805 6.151648 CGCCATTGGACCAATAATAGATTCAT 59.848 38.462 19.41 0.00 32.35 2.57
1980 4813 5.833131 AGAATAACGCCATTGGACCAATAAT 59.167 36.000 19.41 6.94 32.35 1.28
2021 4882 7.606456 ACCATAATTGTTTGTAGAACGACAGAT 59.394 33.333 0.00 0.00 0.00 2.90
2083 4948 6.484643 TGATGCATAGGAGACATTAGAAAAGC 59.515 38.462 0.00 0.00 0.00 3.51
2204 5083 9.764363 TTACATCGCTCATAACTAAATTCAGAT 57.236 29.630 0.00 0.00 0.00 2.90
2205 5084 9.031360 GTTACATCGCTCATAACTAAATTCAGA 57.969 33.333 0.00 0.00 0.00 3.27
2246 5126 5.104941 CCGAGCCATAACATAGGGATGAATA 60.105 44.000 0.00 0.00 36.48 1.75
2247 5127 4.323792 CCGAGCCATAACATAGGGATGAAT 60.324 45.833 0.00 0.00 36.48 2.57
2248 5128 3.007940 CCGAGCCATAACATAGGGATGAA 59.992 47.826 0.00 0.00 36.48 2.57
2368 5256 6.484288 TCCTATCATGGTTGTCAACAGATTT 58.516 36.000 17.29 2.15 0.00 2.17
2370 5258 5.698741 TCCTATCATGGTTGTCAACAGAT 57.301 39.130 17.29 16.89 0.00 2.90
2372 5260 6.405065 CCATTTCCTATCATGGTTGTCAACAG 60.405 42.308 17.29 6.84 36.01 3.16
2473 5369 4.573900 AGCAACATCAGGAAACTAGAGTG 58.426 43.478 0.00 0.00 40.21 3.51
2729 5698 8.985805 CGATTAAGTGAACAAGTAGGTTAGTTT 58.014 33.333 0.00 0.00 0.00 2.66
2757 5752 9.645128 AACCAAATCCTATCAATCACATGATTA 57.355 29.630 6.79 0.00 42.41 1.75
3219 6252 3.157087 ACGAGCAAATGGGACTTTCAAT 58.843 40.909 0.00 0.00 0.00 2.57
3483 6519 2.123854 ATAGGACTCGAGGCCGCA 60.124 61.111 31.50 23.31 35.37 5.69
3491 6527 8.407064 ACTTTGATTACTTCTACATAGGACTCG 58.593 37.037 0.00 0.00 0.00 4.18
3590 6626 2.807676 CTCCAAAGCCCAATACCTGTT 58.192 47.619 0.00 0.00 0.00 3.16
3625 6661 0.729690 GAAGCAAGAATCGTCCTGGC 59.270 55.000 0.00 0.00 0.00 4.85
3656 6692 5.624900 CACACAAGACAACAAATTACATCCG 59.375 40.000 0.00 0.00 0.00 4.18
3657 6693 6.503524 ACACACAAGACAACAAATTACATCC 58.496 36.000 0.00 0.00 0.00 3.51
3689 6729 7.837863 TGAGGTATAAAGAGTTAACAGACAGG 58.162 38.462 8.61 0.00 0.00 4.00
3792 6832 3.243501 GCATTTCACAAGACAGAGCCAAA 60.244 43.478 0.00 0.00 0.00 3.28
3850 6890 4.018490 TCAAGCCATACACTTACTCGGTA 58.982 43.478 0.00 0.00 0.00 4.02
3852 6892 3.520290 TCAAGCCATACACTTACTCGG 57.480 47.619 0.00 0.00 0.00 4.63
3995 7036 0.765510 GGTGCCCCTCCCTAACATAG 59.234 60.000 0.00 0.00 0.00 2.23
4026 7067 2.827755 TGCACCCTAGATGTTGTCCTA 58.172 47.619 0.00 0.00 0.00 2.94
4153 7195 2.491693 TCCGAGCAAAACATTTCCATCC 59.508 45.455 0.00 0.00 0.00 3.51
4225 7267 3.636764 TCAGAACTGCACACTCTTGTCTA 59.363 43.478 0.00 0.00 31.66 2.59
4337 7381 7.051623 TCTAGCAACTCAACTCCTTTGTTTTA 58.948 34.615 0.00 0.00 36.49 1.52


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

AutoCloner maintained by Alex Coulton.