Multiple sequence alignment - TraesCS5D01G306400

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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 TraesCS5D01G306400 chr5D 100.000 4754 0 0 1 4754 402949923 402954676 0.000000e+00 8780.0
1 TraesCS5D01G306400 chr5A 96.212 3881 103 20 901 4754 510544708 510540845 0.000000e+00 6312.0
2 TraesCS5D01G306400 chr5A 90.843 830 67 3 1902 2731 666233153 666232333 0.000000e+00 1103.0
3 TraesCS5D01G306400 chr5A 84.542 938 94 33 1 915 510545636 510544727 0.000000e+00 881.0
4 TraesCS5D01G306400 chr5A 90.200 500 49 0 3129 3628 666230673 666230174 0.000000e+00 652.0
5 TraesCS5D01G306400 chr5A 84.787 447 40 10 3351 3793 510540942 510540520 1.580000e-114 424.0
6 TraesCS5D01G306400 chr5A 79.257 646 57 29 987 1584 666234853 666234237 3.470000e-101 379.0
7 TraesCS5D01G306400 chr5A 93.088 217 15 0 2731 2947 666232224 666232008 7.680000e-83 318.0
8 TraesCS5D01G306400 chr5A 94.969 159 8 0 1583 1741 666234138 666233980 2.840000e-62 250.0
9 TraesCS5D01G306400 chr5A 87.805 123 15 0 1781 1903 666233429 666233307 1.380000e-30 145.0
10 TraesCS5D01G306400 chr5B 94.427 3499 100 47 323 3772 482287595 482291047 0.000000e+00 5293.0
11 TraesCS5D01G306400 chr5B 89.370 969 58 18 3810 4754 482291045 482291992 0.000000e+00 1177.0
12 TraesCS5D01G306400 chr5B 84.116 447 40 9 3351 3793 482291895 482292314 2.060000e-108 403.0
13 TraesCS5D01G306400 chr4D 90.811 838 64 6 1902 2736 485387299 485386472 0.000000e+00 1109.0
14 TraesCS5D01G306400 chr4D 89.600 500 49 2 3129 3628 485384725 485384229 2.410000e-177 632.0
15 TraesCS5D01G306400 chr4D 80.404 643 52 29 987 1584 485389010 485388397 5.690000e-114 422.0
16 TraesCS5D01G306400 chr4D 94.860 214 11 0 2731 2944 485386370 485386157 7.620000e-88 335.0
17 TraesCS5D01G306400 chr4D 94.969 159 8 0 1583 1741 485388295 485388137 2.840000e-62 250.0
18 TraesCS5D01G306400 chr4D 87.288 118 15 0 1786 1903 485387544 485387427 8.300000e-28 135.0
19 TraesCS5D01G306400 chr4D 82.482 137 23 1 4027 4162 507904608 507904744 8.360000e-23 119.0
20 TraesCS5D01G306400 chr4D 95.745 47 2 0 1737 1783 485388001 485387955 5.100000e-10 76.8
21 TraesCS5D01G306400 chr4B 90.482 830 70 3 1902 2731 618593729 618592909 0.000000e+00 1086.0
22 TraesCS5D01G306400 chr4B 89.600 500 49 2 3129 3628 618591087 618590591 2.410000e-177 632.0
23 TraesCS5D01G306400 chr4B 80.625 640 53 27 987 1584 618595451 618594841 3.400000e-116 429.0
24 TraesCS5D01G306400 chr4B 94.860 214 11 0 2731 2944 618592800 618592587 7.620000e-88 335.0
25 TraesCS5D01G306400 chr4B 94.969 159 8 0 1583 1741 618594730 618594572 2.840000e-62 250.0
26 TraesCS5D01G306400 chr4B 88.983 118 13 0 1786 1903 618593983 618593866 3.830000e-31 147.0
27 TraesCS5D01G306400 chr4B 84.328 134 21 0 4031 4164 655752125 655751992 1.070000e-26 132.0
28 TraesCS5D01G306400 chr1D 87.050 556 72 0 2014 2569 382921534 382922089 3.120000e-176 628.0
29 TraesCS5D01G306400 chr1D 85.598 493 61 8 3129 3619 382908086 382908570 4.240000e-140 508.0
30 TraesCS5D01G306400 chr1D 82.724 492 82 1 3129 3620 382926100 382926588 7.310000e-118 435.0
31 TraesCS5D01G306400 chr1D 93.636 110 7 0 2619 2728 382922262 382922371 1.060000e-36 165.0
32 TraesCS5D01G306400 chr1D 84.277 159 25 0 1583 1741 382893757 382893915 6.370000e-34 156.0
33 TraesCS5D01G306400 chr1D 90.909 110 10 0 2619 2728 383164115 383164224 1.070000e-31 148.0
34 TraesCS5D01G306400 chr1D 91.026 78 5 2 2943 3019 382922825 382922901 2.340000e-18 104.0
35 TraesCS5D01G306400 chr1A 85.548 602 85 2 1969 2569 482796963 482797563 3.120000e-176 628.0
36 TraesCS5D01G306400 chr1A 85.548 602 85 2 1969 2569 482803364 482803964 3.120000e-176 628.0
37 TraesCS5D01G306400 chr1A 85.548 602 85 2 1969 2569 482810044 482810644 3.120000e-176 628.0
38 TraesCS5D01G306400 chr1A 85.772 492 60 8 3129 3618 482812908 482813391 3.280000e-141 512.0
39 TraesCS5D01G306400 chr1A 85.535 159 23 0 1583 1741 482795217 482795375 2.940000e-37 167.0
40 TraesCS5D01G306400 chr1A 85.535 159 23 0 1583 1741 482799529 482799687 2.940000e-37 167.0
41 TraesCS5D01G306400 chr1A 80.000 190 32 3 2761 2944 539879577 539879766 8.300000e-28 135.0
42 TraesCS5D01G306400 chr1B 82.046 479 83 2 3129 3607 513164137 513164612 5.730000e-109 405.0
43 TraesCS5D01G306400 chr1B 86.164 159 22 0 1583 1741 512983354 512983512 6.330000e-39 172.0
44 TraesCS5D01G306400 chr1B 93.636 110 7 0 2619 2728 513162001 513162110 1.060000e-36 165.0
45 TraesCS5D01G306400 chr1B 90.909 110 10 0 2619 2728 513471350 513471459 1.070000e-31 148.0
46 TraesCS5D01G306400 chr3D 95.652 46 2 0 1858 1903 459464738 459464783 1.830000e-09 75.0
47 TraesCS5D01G306400 chr3B 87.692 65 7 1 4033 4096 506619381 506619445 1.830000e-09 75.0
48 TraesCS5D01G306400 chr3A 91.837 49 4 0 1858 1906 601559352 601559304 8.540000e-08 69.4


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 TraesCS5D01G306400 chr5D 402949923 402954676 4753 False 8780.000000 8780 100.000000 1 4754 1 chr5D.!!$F1 4753
1 TraesCS5D01G306400 chr5A 510540520 510545636 5116 True 2539.000000 6312 88.513667 1 4754 3 chr5A.!!$R1 4753
2 TraesCS5D01G306400 chr5A 666230174 666234853 4679 True 474.500000 1103 89.360333 987 3628 6 chr5A.!!$R2 2641
3 TraesCS5D01G306400 chr5B 482287595 482292314 4719 False 2291.000000 5293 89.304333 323 4754 3 chr5B.!!$F1 4431
4 TraesCS5D01G306400 chr4D 485384229 485389010 4781 True 422.828571 1109 90.525286 987 3628 7 chr4D.!!$R1 2641
5 TraesCS5D01G306400 chr4B 618590591 618595451 4860 True 479.833333 1086 89.919833 987 3628 6 chr4B.!!$R2 2641
6 TraesCS5D01G306400 chr1D 382921534 382926588 5054 False 333.000000 628 88.609000 2014 3620 4 chr1D.!!$F4 1606
7 TraesCS5D01G306400 chr1A 482810044 482813391 3347 False 570.000000 628 85.660000 1969 3618 2 chr1A.!!$F3 1649
8 TraesCS5D01G306400 chr1A 482795217 482803964 8747 False 397.500000 628 85.541500 1583 2569 4 chr1A.!!$F2 986
9 TraesCS5D01G306400 chr1B 513162001 513164612 2611 False 285.000000 405 87.841000 2619 3607 2 chr1B.!!$F3 988

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
672 728 0.377554 CGTAGGTCGCAGTAGGTGAG 59.622 60.0 0.00 0.0 36.51 3.51 F
2107 3870 0.392863 CCGTTGCTGGGTGATCATCA 60.393 55.0 8.54 5.0 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2646 4532 1.208052 ACGATGATGAAGAGGTGGTGG 59.792 52.381 0.0 0.0 0.0 4.61 R
4097 14856 1.953686 CTTTTCTTTCGCCTCCAACCA 59.046 47.619 0.0 0.0 0.0 3.67 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
68 69 3.869065 TGACCACGAATCTTTGATACCC 58.131 45.455 0.00 0.00 0.00 3.69
78 79 4.837093 TCTTTGATACCCCACGAGAAAT 57.163 40.909 0.00 0.00 0.00 2.17
86 87 1.867233 CCCCACGAGAAATCGCATTAG 59.133 52.381 0.00 0.00 36.44 1.73
87 88 2.483013 CCCCACGAGAAATCGCATTAGA 60.483 50.000 0.00 0.00 36.44 2.10
156 158 5.514914 GTGCGAGTCAAAAGTTCATTCAAAA 59.485 36.000 0.00 0.00 0.00 2.44
191 193 2.801077 AACCTCCGGGTATTTTCTGG 57.199 50.000 0.00 0.00 46.67 3.86
196 198 3.538591 CTCCGGGTATTTTCTGGTTACC 58.461 50.000 0.00 0.00 35.63 2.85
197 199 3.183801 TCCGGGTATTTTCTGGTTACCT 58.816 45.455 0.00 0.00 36.45 3.08
201 203 3.054875 GGGTATTTTCTGGTTACCTCGGT 60.055 47.826 2.07 0.00 36.45 4.69
210 212 2.633967 TGGTTACCTCGGTAGCTGAAAA 59.366 45.455 2.07 0.00 33.31 2.29
247 254 6.752351 ACGAGCTTTTCTTTTCTTTTCTTTCC 59.248 34.615 0.00 0.00 0.00 3.13
259 266 7.764695 TTCTTTTCTTTCCGAATTCAAAACC 57.235 32.000 6.22 0.00 0.00 3.27
263 270 8.865590 TTTTCTTTCCGAATTCAAAACCTTAG 57.134 30.769 6.22 0.00 0.00 2.18
268 275 6.470557 TCCGAATTCAAAACCTTAGTAACG 57.529 37.500 6.22 0.00 0.00 3.18
269 276 6.222389 TCCGAATTCAAAACCTTAGTAACGA 58.778 36.000 6.22 0.00 0.00 3.85
272 279 7.225397 CGAATTCAAAACCTTAGTAACGACTC 58.775 38.462 6.22 0.00 37.10 3.36
321 337 7.262048 TCTAACAACTTGAACCATTGTTTTCC 58.738 34.615 6.87 0.00 42.43 3.13
339 355 4.967084 TTCCTTTTGCTACACCTACTGA 57.033 40.909 0.00 0.00 0.00 3.41
375 392 5.804692 TCTGCAAACTAAAAGTTTCACGA 57.195 34.783 2.13 0.00 44.47 4.35
410 427 9.014297 ACGGATTTCTTTCATTTTGAGTAAGAT 57.986 29.630 0.00 0.00 27.31 2.40
439 456 2.022129 AGCGCTGCTGTCGTTGTAC 61.022 57.895 10.39 0.00 37.57 2.90
441 458 1.626654 GCGCTGCTGTCGTTGTACAT 61.627 55.000 0.00 0.00 0.00 2.29
459 476 2.765699 ACATATGCGCCAAAAAGGGAAT 59.234 40.909 4.18 0.00 38.09 3.01
563 605 0.455972 TAGTACGTAAACCGCGTGCC 60.456 55.000 4.92 0.00 43.93 5.01
584 630 2.751436 ATCTGCATGCGGCCGTTT 60.751 55.556 28.70 11.97 43.89 3.60
589 635 4.817063 CATGCGGCCGTTTGAGCG 62.817 66.667 28.70 4.70 0.00 5.03
636 682 4.672409 GACCTTTTGTTTGTTCTGACCAG 58.328 43.478 0.00 0.00 0.00 4.00
671 727 2.474561 CGTAGGTCGCAGTAGGTGA 58.525 57.895 0.00 0.00 0.00 4.02
672 728 0.377554 CGTAGGTCGCAGTAGGTGAG 59.622 60.000 0.00 0.00 36.51 3.51
673 729 0.739561 GTAGGTCGCAGTAGGTGAGG 59.260 60.000 0.00 0.00 36.51 3.86
674 730 0.395311 TAGGTCGCAGTAGGTGAGGG 60.395 60.000 0.00 0.00 36.51 4.30
785 841 3.351885 AGTCCCTCTCTCCCGGCT 61.352 66.667 0.00 0.00 0.00 5.52
786 842 2.007568 AGTCCCTCTCTCCCGGCTA 61.008 63.158 0.00 0.00 0.00 3.93
787 843 1.829096 GTCCCTCTCTCCCGGCTAC 60.829 68.421 0.00 0.00 0.00 3.58
799 855 3.094572 TCCCGGCTACCTGCTATATTAC 58.905 50.000 0.00 0.00 42.39 1.89
821 877 2.736721 GACGAGCAGCATTGAACTGTTA 59.263 45.455 0.00 0.00 37.47 2.41
870 929 1.070445 CATCAGCATCTCCTCCTCCAC 59.930 57.143 0.00 0.00 0.00 4.02
935 1031 1.751927 CTGGCTGCCCATCTTGGAC 60.752 63.158 17.53 0.00 40.96 4.02
937 1033 3.512516 GCTGCCCATCTTGGACGC 61.513 66.667 0.00 0.00 40.96 5.19
1383 1524 2.094182 GTCGACAAGGATCAAGCAGGTA 60.094 50.000 11.55 0.00 0.00 3.08
1418 1559 1.225376 AAAATCGCGTCCGTCAAGCA 61.225 50.000 5.77 0.00 35.54 3.91
1791 3390 4.162690 GCGGAGGTCGGGCAGATT 62.163 66.667 0.00 0.00 39.69 2.40
2107 3870 0.392863 CCGTTGCTGGGTGATCATCA 60.393 55.000 8.54 5.00 0.00 3.07
2646 4532 0.034337 TCAACGCCTTCTGGTACACC 59.966 55.000 0.00 0.00 35.27 4.16
3868 14626 8.637196 TCAGTACATACCCAGTTCTATAGATG 57.363 38.462 2.58 0.00 0.00 2.90
3891 14649 5.300792 TGGAAGTAGGTGTTGGTTGATTTTC 59.699 40.000 0.00 0.00 0.00 2.29
3911 14669 2.703536 TCACAAGCTGGGTCAAGAGTTA 59.296 45.455 0.00 0.00 0.00 2.24
3968 14727 5.457487 CCAATGCCCCCTTGTACAGATATTA 60.457 44.000 0.00 0.00 0.00 0.98
3969 14728 6.248433 CAATGCCCCCTTGTACAGATATTAT 58.752 40.000 0.00 0.00 0.00 1.28
3970 14729 5.922960 TGCCCCCTTGTACAGATATTATT 57.077 39.130 0.00 0.00 0.00 1.40
3971 14730 5.876357 TGCCCCCTTGTACAGATATTATTC 58.124 41.667 0.00 0.00 0.00 1.75
3972 14731 5.222048 TGCCCCCTTGTACAGATATTATTCC 60.222 44.000 0.00 0.00 0.00 3.01
3975 14734 6.045577 CCCCCTTGTACAGATATTATTCCCTT 59.954 42.308 0.00 0.00 0.00 3.95
3976 14735 7.168905 CCCCTTGTACAGATATTATTCCCTTC 58.831 42.308 0.00 0.00 0.00 3.46
3977 14736 7.017651 CCCCTTGTACAGATATTATTCCCTTCT 59.982 40.741 0.00 0.00 0.00 2.85
4041 14800 8.905103 ACAACTAACAAAAACACAATAGTCAC 57.095 30.769 0.00 0.00 0.00 3.67
4097 14856 6.777782 AGTTGATCTTGTGAGAGGAGAAATT 58.222 36.000 0.00 0.00 34.85 1.82
4166 14925 9.675464 TGACCGTTAAATCTTAATCTAATGGTT 57.325 29.630 6.14 0.00 41.55 3.67
4191 14950 7.759607 TGGAAAATTGAATTATCCCCCAAAAA 58.240 30.769 0.00 0.00 0.00 1.94
4213 14972 5.772393 AACCAAATGTATAGTCTGGTCCA 57.228 39.130 0.00 0.00 39.48 4.02
4218 14977 7.176690 ACCAAATGTATAGTCTGGTCCAAAAAG 59.823 37.037 0.00 0.00 35.44 2.27
4220 14981 5.174037 TGTATAGTCTGGTCCAAAAAGGG 57.826 43.478 0.00 0.00 38.24 3.95
4334 15099 1.474077 CCTCTTACAATGCAAGGTGCC 59.526 52.381 0.00 0.00 44.23 5.01
4342 15107 3.084039 CAATGCAAGGTGCCTAGAGAAA 58.916 45.455 0.00 0.00 44.23 2.52
4454 15219 1.019805 GCAGGGCAGACGAACCTTAC 61.020 60.000 0.00 0.00 30.66 2.34
4521 15306 3.756783 CCCCTCCCTCCTCCTCGT 61.757 72.222 0.00 0.00 0.00 4.18
4526 15311 2.037367 CCCTCCTCCTCGTCACCA 59.963 66.667 0.00 0.00 0.00 4.17
4542 15327 3.283684 CACCAAAAGGCGCCGTCA 61.284 61.111 23.20 0.00 0.00 4.35
4586 15371 1.921346 TGGCGGGGCTTCCTTCTAA 60.921 57.895 0.00 0.00 0.00 2.10
4717 15502 4.155733 TTCCGCGGCGTCATGGAT 62.156 61.111 23.51 0.00 0.00 3.41
4718 15503 2.787567 TTCCGCGGCGTCATGGATA 61.788 57.895 23.51 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 1.555992 TCCGTCCGGTAACCAAATCAT 59.444 47.619 0.00 0.00 36.47 2.45
23 24 1.667212 GGCGATAACCGAATTTTCCGT 59.333 47.619 0.00 0.00 41.76 4.69
46 47 4.451900 GGGTATCAAAGATTCGTGGTCAT 58.548 43.478 0.00 0.00 0.00 3.06
48 49 3.203716 GGGGTATCAAAGATTCGTGGTC 58.796 50.000 0.00 0.00 0.00 4.02
68 69 3.246226 CCTTCTAATGCGATTTCTCGTGG 59.754 47.826 0.00 0.00 46.71 4.94
78 79 3.436704 CAGAAAGTTGCCTTCTAATGCGA 59.563 43.478 0.00 0.00 0.00 5.10
116 117 7.199766 TGACTCGCACAAAATCACTTAAAATT 58.800 30.769 0.00 0.00 0.00 1.82
119 120 5.743026 TGACTCGCACAAAATCACTTAAA 57.257 34.783 0.00 0.00 0.00 1.52
133 135 4.891627 TTGAATGAACTTTTGACTCGCA 57.108 36.364 0.00 0.00 0.00 5.10
156 158 3.756963 GGAGGTTACCAAGCGATTTCTTT 59.243 43.478 3.51 0.00 0.00 2.52
191 193 4.933400 TGAATTTTCAGCTACCGAGGTAAC 59.067 41.667 3.37 0.00 32.50 2.50
229 231 9.646427 TTGAATTCGGAAAGAAAAGAAAAGAAA 57.354 25.926 0.04 0.00 42.91 2.52
247 254 7.113704 AGTCGTTACTAAGGTTTTGAATTCG 57.886 36.000 0.04 0.00 32.84 3.34
278 285 5.367352 TGTTAGAAACACACCCCTTCTAGAA 59.633 40.000 4.81 4.81 36.25 2.10
280 287 5.223449 TGTTAGAAACACACCCCTTCTAG 57.777 43.478 0.00 0.00 36.25 2.43
281 288 5.131475 AGTTGTTAGAAACACACCCCTTCTA 59.869 40.000 0.00 0.00 41.97 2.10
282 289 4.079958 AGTTGTTAGAAACACACCCCTTCT 60.080 41.667 0.00 0.00 41.97 2.85
283 290 4.204799 AGTTGTTAGAAACACACCCCTTC 58.795 43.478 0.00 0.00 41.97 3.46
284 291 4.245251 AGTTGTTAGAAACACACCCCTT 57.755 40.909 0.00 0.00 41.97 3.95
285 292 3.945640 AGTTGTTAGAAACACACCCCT 57.054 42.857 0.00 0.00 41.97 4.79
286 293 3.949113 TCAAGTTGTTAGAAACACACCCC 59.051 43.478 2.11 0.00 41.97 4.95
321 337 4.056050 ACGTTCAGTAGGTGTAGCAAAAG 58.944 43.478 0.00 0.00 0.00 2.27
375 392 0.881118 AAGAAATCCGTGCACGCAAT 59.119 45.000 33.17 23.98 38.18 3.56
410 427 2.169832 AGCAGCGCTGAAAACTCTTA 57.830 45.000 40.21 0.00 37.57 2.10
434 451 3.119316 CCCTTTTTGGCGCATATGTACAA 60.119 43.478 10.83 0.00 0.00 2.41
439 456 2.957491 TTCCCTTTTTGGCGCATATG 57.043 45.000 10.83 0.00 0.00 1.78
441 458 1.754226 GGATTCCCTTTTTGGCGCATA 59.246 47.619 10.83 0.00 0.00 3.14
459 476 2.184322 GCCTGCGACGAGAATGGA 59.816 61.111 0.00 0.00 0.00 3.41
478 514 6.676237 TTAGCATTTATTGAGCATGAACGA 57.324 33.333 0.00 0.00 0.00 3.85
545 587 1.734117 GGCACGCGGTTTACGTACT 60.734 57.895 12.47 0.00 42.96 2.73
662 718 0.252284 ACTCACCCCCTCACCTACTG 60.252 60.000 0.00 0.00 0.00 2.74
667 723 2.034221 GCAACTCACCCCCTCACC 59.966 66.667 0.00 0.00 0.00 4.02
668 724 2.034221 GGCAACTCACCCCCTCAC 59.966 66.667 0.00 0.00 0.00 3.51
742 798 1.421485 CGTGGCGCAAAGTCTCATC 59.579 57.895 10.83 0.00 0.00 2.92
743 799 3.566261 CGTGGCGCAAAGTCTCAT 58.434 55.556 10.83 0.00 0.00 2.90
785 841 4.067192 TGCTCGTCGTAATATAGCAGGTA 58.933 43.478 0.36 0.00 38.22 3.08
786 842 2.882761 TGCTCGTCGTAATATAGCAGGT 59.117 45.455 0.36 0.00 38.22 4.00
787 843 3.554259 TGCTCGTCGTAATATAGCAGG 57.446 47.619 0.36 0.00 38.22 4.85
799 855 0.094216 CAGTTCAATGCTGCTCGTCG 59.906 55.000 0.00 0.00 0.00 5.12
841 900 2.035704 GGAGATGCTGATGAGATCACGT 59.964 50.000 0.00 0.00 35.06 4.49
855 914 1.524482 GTGGTGGAGGAGGAGATGC 59.476 63.158 0.00 0.00 0.00 3.91
870 929 4.880120 TGATTAGACTCACGTAGTAGGTGG 59.120 45.833 19.91 13.89 41.61 4.61
925 1021 1.466167 CAACAGAAGCGTCCAAGATGG 59.534 52.381 0.00 0.00 39.43 3.51
935 1031 2.978010 AACCGGCCAACAGAAGCG 60.978 61.111 0.00 0.00 0.00 4.68
937 1033 0.535102 AGTCAACCGGCCAACAGAAG 60.535 55.000 0.00 0.00 0.00 2.85
1169 1307 3.154952 CGTTGTCGTCGTCGTCGG 61.155 66.667 11.74 0.00 38.33 4.79
2646 4532 1.208052 ACGATGATGAAGAGGTGGTGG 59.792 52.381 0.00 0.00 0.00 4.61
3833 14591 7.328737 ACTGGGTATGTACTGAATTAACAGAC 58.671 38.462 0.00 1.23 40.63 3.51
3868 14626 5.300792 TGAAAATCAACCAACACCTACTTCC 59.699 40.000 0.00 0.00 0.00 3.46
3891 14649 1.972872 AACTCTTGACCCAGCTTGTG 58.027 50.000 0.00 0.00 0.00 3.33
4039 14798 7.132694 TGCAAATTCAGTCTACTTACATGTG 57.867 36.000 9.11 0.00 0.00 3.21
4041 14800 9.630098 AAATTGCAAATTCAGTCTACTTACATG 57.370 29.630 1.71 0.00 0.00 3.21
4050 14809 9.768662 AACTTATTCAAATTGCAAATTCAGTCT 57.231 25.926 1.71 0.00 0.00 3.24
4097 14856 1.953686 CTTTTCTTTCGCCTCCAACCA 59.046 47.619 0.00 0.00 0.00 3.67
4166 14925 6.959606 TTTGGGGGATAATTCAATTTTCCA 57.040 33.333 18.25 4.39 40.72 3.53
4191 14950 5.772393 TGGACCAGACTATACATTTGGTT 57.228 39.130 0.00 0.00 41.95 3.67
4193 14952 7.362920 CCTTTTTGGACCAGACTATACATTTGG 60.363 40.741 0.00 0.00 38.35 3.28
4334 15099 7.447374 AGAGATCGATGTGGTATTTCTCTAG 57.553 40.000 0.54 0.00 37.34 2.43
4342 15107 8.637196 TTAGTGAATAGAGATCGATGTGGTAT 57.363 34.615 0.54 0.00 0.00 2.73
4526 15311 2.978010 CTGACGGCGCCTTTTGGT 60.978 61.111 26.68 14.92 42.99 3.67
4626 15411 2.036098 TGAAGCACCATGCCCCTG 59.964 61.111 0.00 0.00 46.52 4.45
4634 15419 4.704833 GCCTCGCCTGAAGCACCA 62.705 66.667 0.00 0.00 44.04 4.17
4717 15502 0.541063 TGTCACTCTCGGCCACCTTA 60.541 55.000 2.24 0.00 0.00 2.69
4718 15503 1.407656 TTGTCACTCTCGGCCACCTT 61.408 55.000 2.24 0.00 0.00 3.50


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

AutoCloner maintained by Alex Coulton.