Multiple sequence alignment - TraesCS2D01G331400

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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 TraesCS2D01G331400 chr2D 100.000 2171 0 0 1 2171 423876876 423874706 0.000000e+00 4010.0
1 TraesCS2D01G331400 chr2A 89.864 957 37 20 1 910 564498965 564499908 0.000000e+00 1175.0
2 TraesCS2D01G331400 chr2A 91.199 659 34 10 1532 2171 564500611 564501264 0.000000e+00 874.0
3 TraesCS2D01G331400 chr2A 87.057 649 36 10 900 1526 564499874 564500496 0.000000e+00 689.0
4 TraesCS2D01G331400 chr2B 91.800 561 15 15 1 552 497859508 497858970 0.000000e+00 752.0
5 TraesCS2D01G331400 chr2B 89.507 467 27 7 920 1379 497856771 497856320 2.420000e-159 571.0
6 TraesCS2D01G331400 chr2B 86.685 368 29 11 1818 2171 497855545 497855184 7.270000e-105 390.0
7 TraesCS2D01G331400 chr2B 88.545 323 10 8 583 890 497857067 497856757 1.220000e-97 366.0
8 TraesCS2D01G331400 chr5D 87.805 82 5 3 1343 1424 539461303 539461227 8.250000e-15 91.6
9 TraesCS2D01G331400 chr4A 86.250 80 11 0 1321 1400 467684204 467684283 1.070000e-13 87.9
10 TraesCS2D01G331400 chr4D 87.143 70 9 0 1321 1390 108628677 108628608 1.790000e-11 80.5
11 TraesCS2D01G331400 chr4D 87.143 70 9 0 1321 1390 280179706 280179775 1.790000e-11 80.5
12 TraesCS2D01G331400 chr5B 93.878 49 3 0 1343 1391 607489211 607489163 8.310000e-10 75.0
13 TraesCS2D01G331400 chr6D 81.443 97 11 5 1325 1421 331573576 331573487 2.990000e-09 73.1


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 TraesCS2D01G331400 chr2D 423874706 423876876 2170 True 4010.000000 4010 100.000000 1 2171 1 chr2D.!!$R1 2170
1 TraesCS2D01G331400 chr2A 564498965 564501264 2299 False 912.666667 1175 89.373333 1 2171 3 chr2A.!!$F1 2170
2 TraesCS2D01G331400 chr2B 497855184 497859508 4324 True 519.750000 752 89.134250 1 2171 4 chr2B.!!$R1 2170

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
332 342 0.18135 CATGCCCTCCCAGTCCTAAC 59.819 60.0 0.0 0.0 0.0 2.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1291 3238 0.868602 CACAGCAGCAGCAACACAAC 60.869 55.0 3.17 0.0 45.49 3.32 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
253 259 9.936759 GAACAAAATTTTGATAATAACCCCTCA 57.063 29.630 32.20 0.00 40.55 3.86
271 277 1.948834 TCACATAAATGCGCATCCCAG 59.051 47.619 25.53 16.35 0.00 4.45
331 341 0.988145 CCATGCCCTCCCAGTCCTAA 60.988 60.000 0.00 0.00 0.00 2.69
332 342 0.181350 CATGCCCTCCCAGTCCTAAC 59.819 60.000 0.00 0.00 0.00 2.34
333 343 0.253160 ATGCCCTCCCAGTCCTAACA 60.253 55.000 0.00 0.00 0.00 2.41
334 344 1.198759 TGCCCTCCCAGTCCTAACAC 61.199 60.000 0.00 0.00 0.00 3.32
408 437 9.260002 CTCTTCCATCTTCTATCTTCTAAAAGC 57.740 37.037 0.00 0.00 32.18 3.51
453 482 4.756084 AAAGATGGACGAAAAGCAGAAG 57.244 40.909 0.00 0.00 0.00 2.85
578 2348 2.429930 GCTAGGCCACACCACACA 59.570 61.111 5.01 0.00 43.14 3.72
744 2657 2.770164 ACATAGTTGTCCAGCTCCAC 57.230 50.000 0.00 0.00 0.00 4.02
745 2658 1.279271 ACATAGTTGTCCAGCTCCACC 59.721 52.381 0.00 0.00 0.00 4.61
746 2659 1.556911 CATAGTTGTCCAGCTCCACCT 59.443 52.381 0.00 0.00 0.00 4.00
747 2660 1.267121 TAGTTGTCCAGCTCCACCTC 58.733 55.000 0.00 0.00 0.00 3.85
748 2661 1.003233 GTTGTCCAGCTCCACCTCC 60.003 63.158 0.00 0.00 0.00 4.30
749 2662 1.461268 TTGTCCAGCTCCACCTCCA 60.461 57.895 0.00 0.00 0.00 3.86
750 2663 1.483595 TTGTCCAGCTCCACCTCCAG 61.484 60.000 0.00 0.00 0.00 3.86
772 2685 3.432933 GCAGTTTTGCTCTCTCTCTCTTG 59.567 47.826 0.00 0.00 46.95 3.02
780 2693 3.848726 CTCTCTCTCTCTTGGAGCAAAC 58.151 50.000 0.00 0.00 41.60 2.93
785 2698 4.588951 TCTCTCTCTTGGAGCAAACTGTAA 59.411 41.667 0.00 0.00 41.60 2.41
855 2783 1.164041 CGTTCCAAAACCCTCACGCT 61.164 55.000 0.00 0.00 31.27 5.07
856 2784 1.874739 CGTTCCAAAACCCTCACGCTA 60.875 52.381 0.00 0.00 31.27 4.26
908 2836 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
909 2837 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
910 2838 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
911 2839 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
912 2840 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
913 2841 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
914 2842 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
915 2843 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
916 2844 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
917 2845 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
918 2846 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
919 2847 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
920 2848 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
921 2849 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
922 2850 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
923 2851 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
924 2852 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
925 2853 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
926 2854 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
927 2855 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
928 2856 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
929 2857 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
930 2858 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
931 2859 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
968 2896 4.412060 AGAGGAAGAAAAGAGAGGAGGA 57.588 45.455 0.00 0.00 0.00 3.71
972 2907 3.450817 GGAAGAAAAGAGAGGAGGAGGAG 59.549 52.174 0.00 0.00 0.00 3.69
973 2908 3.114643 AGAAAAGAGAGGAGGAGGAGG 57.885 52.381 0.00 0.00 0.00 4.30
974 2909 2.115427 GAAAAGAGAGGAGGAGGAGGG 58.885 57.143 0.00 0.00 0.00 4.30
975 2910 0.341609 AAAGAGAGGAGGAGGAGGGG 59.658 60.000 0.00 0.00 0.00 4.79
976 2911 1.598856 AAGAGAGGAGGAGGAGGGGG 61.599 65.000 0.00 0.00 0.00 5.40
1010 2945 1.372087 GCGGGAAGGATGTGCTTCAG 61.372 60.000 14.79 9.64 0.00 3.02
1012 2947 1.034292 GGGAAGGATGTGCTTCAGGC 61.034 60.000 14.79 0.00 42.22 4.85
1014 2949 1.377536 GAAGGATGTGCTTCAGGCTC 58.622 55.000 9.08 0.00 42.39 4.70
1020 2955 0.181114 TGTGCTTCAGGCTCAACAGT 59.819 50.000 0.00 0.00 40.78 3.55
1226 3173 1.303309 GCCCTACTCATGTGCATGTC 58.697 55.000 11.38 0.00 39.72 3.06
1243 3190 5.527214 TGCATGTCTGTATGTATAGCAAACC 59.473 40.000 0.00 0.00 0.00 3.27
1291 3238 4.883026 CGAGGGTACGGACTGTTG 57.117 61.111 0.00 0.00 0.00 3.33
1310 3260 0.868602 GTTGTGTTGCTGCTGCTGTG 60.869 55.000 17.00 0.00 40.48 3.66
1311 3261 2.007113 TTGTGTTGCTGCTGCTGTGG 62.007 55.000 17.00 0.00 40.48 4.17
1313 3263 4.353437 GTTGCTGCTGCTGTGGCC 62.353 66.667 17.00 0.00 40.48 5.36
1318 3268 4.687215 TGCTGCTGTGGCCGTCTC 62.687 66.667 0.00 0.00 37.74 3.36
1329 3279 1.393487 GGCCGTCTCCTACTCCTTCC 61.393 65.000 0.00 0.00 0.00 3.46
1337 3287 0.753262 CCTACTCCTTCCGGTCCATG 59.247 60.000 0.00 0.00 0.00 3.66
1338 3288 0.105039 CTACTCCTTCCGGTCCATGC 59.895 60.000 0.00 0.00 0.00 4.06
1345 3295 1.334869 CTTCCGGTCCATGCTAATTGC 59.665 52.381 0.00 0.00 43.25 3.56
1354 3304 2.223876 CCATGCTAATTGCCGCTCAAAT 60.224 45.455 0.00 0.00 42.00 2.32
1403 3362 8.276325 CGTCTAGATACATTTATTTCAGCAACC 58.724 37.037 0.00 0.00 0.00 3.77
1404 3363 9.109393 GTCTAGATACATTTATTTCAGCAACCA 57.891 33.333 0.00 0.00 0.00 3.67
1405 3364 9.679661 TCTAGATACATTTATTTCAGCAACCAA 57.320 29.630 0.00 0.00 0.00 3.67
1406 3365 9.722056 CTAGATACATTTATTTCAGCAACCAAC 57.278 33.333 0.00 0.00 0.00 3.77
1407 3366 8.121305 AGATACATTTATTTCAGCAACCAACA 57.879 30.769 0.00 0.00 0.00 3.33
1449 3408 2.290367 CTCGGTTTCTTGTGTTGCATCA 59.710 45.455 0.00 0.00 0.00 3.07
1493 3452 3.517500 GGAATGGTTTGGCCTATTTCCAA 59.482 43.478 3.32 0.00 41.47 3.53
1507 3629 7.417456 GGCCTATTTCCAAACCTTATAAACCTG 60.417 40.741 0.00 0.00 0.00 4.00
1718 4100 9.586435 AAAAGAGGAAAACAAGTCAATTACAAG 57.414 29.630 0.00 0.00 0.00 3.16
1719 4101 8.519799 AAGAGGAAAACAAGTCAATTACAAGA 57.480 30.769 0.00 0.00 0.00 3.02
1720 4102 8.159344 AGAGGAAAACAAGTCAATTACAAGAG 57.841 34.615 0.00 0.00 0.00 2.85
1722 4104 8.519799 AGGAAAACAAGTCAATTACAAGAGAA 57.480 30.769 0.00 0.00 0.00 2.87
1723 4105 8.406297 AGGAAAACAAGTCAATTACAAGAGAAC 58.594 33.333 0.00 0.00 0.00 3.01
1855 4251 6.381801 CAACAAGCTTCATCCGATTAAACTT 58.618 36.000 0.00 0.00 0.00 2.66
1859 4255 7.390718 ACAAGCTTCATCCGATTAAACTTAACT 59.609 33.333 0.00 0.00 0.00 2.24
1860 4256 7.308782 AGCTTCATCCGATTAAACTTAACTG 57.691 36.000 0.00 0.00 0.00 3.16
1862 4258 7.278868 AGCTTCATCCGATTAAACTTAACTGAG 59.721 37.037 0.00 0.00 0.00 3.35
1863 4259 7.064728 GCTTCATCCGATTAAACTTAACTGAGT 59.935 37.037 0.00 0.00 0.00 3.41
1864 4260 9.582431 CTTCATCCGATTAAACTTAACTGAGTA 57.418 33.333 0.00 0.00 0.00 2.59
1865 4261 8.922058 TCATCCGATTAAACTTAACTGAGTAC 57.078 34.615 0.00 0.00 0.00 2.73
1891 4287 3.438087 GGATGGTTCATGTTCAGTGAGTG 59.562 47.826 0.00 0.00 0.00 3.51
1930 4326 6.820656 CACAAGCTCAAGTGTCCTTATAGAAT 59.179 38.462 5.91 0.00 0.00 2.40
1971 4367 3.181513 GCACACATCTGCAACTACTCATG 60.182 47.826 0.00 0.00 37.11 3.07
2003 4401 9.174166 ACAGTGTTCAATAACTTTAAAGTCTGT 57.826 29.630 20.78 20.12 38.57 3.41
2013 4411 4.887655 ACTTTAAAGTCTGTGGACCCAAAG 59.112 41.667 15.22 0.00 43.05 2.77
2107 4510 3.517602 TCGTGAATCCTAAATGACACGG 58.482 45.455 15.30 0.77 46.68 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
92 97 2.376855 TCCCAAACATGACACCACCATA 59.623 45.455 0.00 0.00 0.00 2.74
117 122 1.080569 CAAATGCTCCGGCCAACAC 60.081 57.895 2.24 0.00 37.74 3.32
253 259 1.949525 GACTGGGATGCGCATTTATGT 59.050 47.619 26.12 19.99 0.00 2.29
331 341 3.214328 GTGTCCTCCATTGACAAAGTGT 58.786 45.455 0.00 0.00 43.82 3.55
332 342 2.554032 GGTGTCCTCCATTGACAAAGTG 59.446 50.000 0.00 0.00 43.82 3.16
333 343 2.489073 GGGTGTCCTCCATTGACAAAGT 60.489 50.000 0.00 0.00 43.82 2.66
334 344 2.162681 GGGTGTCCTCCATTGACAAAG 58.837 52.381 0.00 0.00 43.82 2.77
408 437 3.859386 GCTGCGGAATATTTGTCTTTTGG 59.141 43.478 0.00 0.00 0.00 3.28
573 2343 1.135139 ACGGAATCTCGATCCTGTGTG 59.865 52.381 2.23 0.00 34.66 3.82
574 2344 1.135139 CACGGAATCTCGATCCTGTGT 59.865 52.381 14.79 0.72 37.04 3.72
575 2345 1.845266 CACGGAATCTCGATCCTGTG 58.155 55.000 11.40 11.40 36.18 3.66
576 2346 0.103208 GCACGGAATCTCGATCCTGT 59.897 55.000 2.23 0.00 34.66 4.00
577 2347 0.103026 TGCACGGAATCTCGATCCTG 59.897 55.000 2.23 1.56 34.66 3.86
578 2348 1.043816 ATGCACGGAATCTCGATCCT 58.956 50.000 2.23 0.00 34.66 3.24
678 2591 1.822186 GGCTTCAACGGTGGTGTGT 60.822 57.895 0.00 0.00 0.00 3.72
744 2657 1.163554 GAGAGCAAAACTGCTGGAGG 58.836 55.000 3.98 0.00 46.36 4.30
745 2658 2.075338 GAGAGAGCAAAACTGCTGGAG 58.925 52.381 3.98 0.00 46.36 3.86
746 2659 1.696336 AGAGAGAGCAAAACTGCTGGA 59.304 47.619 3.98 0.00 46.36 3.86
747 2660 2.075338 GAGAGAGAGCAAAACTGCTGG 58.925 52.381 3.98 0.00 46.36 4.85
748 2661 2.995258 GAGAGAGAGAGCAAAACTGCTG 59.005 50.000 3.98 0.00 46.36 4.41
750 2663 3.317603 AGAGAGAGAGAGCAAAACTGC 57.682 47.619 0.00 0.00 0.00 4.40
767 2680 3.476552 TGGTTACAGTTTGCTCCAAGAG 58.523 45.455 0.00 0.00 0.00 2.85
768 2681 3.569194 TGGTTACAGTTTGCTCCAAGA 57.431 42.857 0.00 0.00 0.00 3.02
769 2682 4.853924 AATGGTTACAGTTTGCTCCAAG 57.146 40.909 0.00 0.00 0.00 3.61
772 2685 5.241728 AGAGAAAATGGTTACAGTTTGCTCC 59.758 40.000 12.85 0.00 44.04 4.70
780 2693 8.462016 CCCTTTTATCAGAGAAAATGGTTACAG 58.538 37.037 13.65 0.00 30.94 2.74
785 2698 4.399303 CGCCCTTTTATCAGAGAAAATGGT 59.601 41.667 19.74 0.00 35.30 3.55
908 2836 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
909 2837 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
910 2838 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
911 2839 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
912 2840 5.538053 TGATCTCTCTCTCTCTCTCTCTCTC 59.462 48.000 0.00 0.00 0.00 3.20
913 2841 5.462240 TGATCTCTCTCTCTCTCTCTCTCT 58.538 45.833 0.00 0.00 0.00 3.10
914 2842 5.798125 TGATCTCTCTCTCTCTCTCTCTC 57.202 47.826 0.00 0.00 0.00 3.20
915 2843 5.071519 CCTTGATCTCTCTCTCTCTCTCTCT 59.928 48.000 0.00 0.00 0.00 3.10
916 2844 5.163258 ACCTTGATCTCTCTCTCTCTCTCTC 60.163 48.000 0.00 0.00 0.00 3.20
917 2845 4.723789 ACCTTGATCTCTCTCTCTCTCTCT 59.276 45.833 0.00 0.00 0.00 3.10
918 2846 5.041191 ACCTTGATCTCTCTCTCTCTCTC 57.959 47.826 0.00 0.00 0.00 3.20
919 2847 5.456921 AACCTTGATCTCTCTCTCTCTCT 57.543 43.478 0.00 0.00 0.00 3.10
920 2848 7.823745 ATAAACCTTGATCTCTCTCTCTCTC 57.176 40.000 0.00 0.00 0.00 3.20
925 2853 9.753674 CCTCTATATAAACCTTGATCTCTCTCT 57.246 37.037 0.00 0.00 0.00 3.10
926 2854 9.747898 TCCTCTATATAAACCTTGATCTCTCTC 57.252 37.037 0.00 0.00 0.00 3.20
984 2919 3.801997 ATCCTTCCCGCCTGCCTG 61.802 66.667 0.00 0.00 0.00 4.85
985 2920 3.801997 CATCCTTCCCGCCTGCCT 61.802 66.667 0.00 0.00 0.00 4.75
986 2921 4.115199 ACATCCTTCCCGCCTGCC 62.115 66.667 0.00 0.00 0.00 4.85
987 2922 2.825836 CACATCCTTCCCGCCTGC 60.826 66.667 0.00 0.00 0.00 4.85
988 2923 2.825836 GCACATCCTTCCCGCCTG 60.826 66.667 0.00 0.00 0.00 4.85
989 2924 2.543067 GAAGCACATCCTTCCCGCCT 62.543 60.000 0.00 0.00 36.15 5.52
990 2925 2.044946 AAGCACATCCTTCCCGCC 60.045 61.111 0.00 0.00 0.00 6.13
991 2926 1.372087 CTGAAGCACATCCTTCCCGC 61.372 60.000 0.00 0.00 40.34 6.13
992 2927 0.745845 CCTGAAGCACATCCTTCCCG 60.746 60.000 0.00 0.00 40.34 5.14
993 2928 1.034292 GCCTGAAGCACATCCTTCCC 61.034 60.000 0.00 0.00 40.34 3.97
1010 2945 1.208293 CCCTCTCCTTACTGTTGAGCC 59.792 57.143 0.00 0.00 0.00 4.70
1012 2947 2.234908 CCACCCTCTCCTTACTGTTGAG 59.765 54.545 0.00 0.00 0.00 3.02
1014 2949 1.279271 CCCACCCTCTCCTTACTGTTG 59.721 57.143 0.00 0.00 0.00 3.33
1020 2955 1.615424 GCACCCCACCCTCTCCTTA 60.615 63.158 0.00 0.00 0.00 2.69
1208 3143 2.093288 ACAGACATGCACATGAGTAGGG 60.093 50.000 17.19 3.53 41.20 3.53
1243 3190 2.722629 CAGAGCAACAAAATTCTGCACG 59.277 45.455 0.00 0.00 38.58 5.34
1291 3238 0.868602 CACAGCAGCAGCAACACAAC 60.869 55.000 3.17 0.00 45.49 3.32
1310 3260 1.393487 GGAAGGAGTAGGAGACGGCC 61.393 65.000 0.00 0.00 0.00 6.13
1311 3261 1.726533 CGGAAGGAGTAGGAGACGGC 61.727 65.000 0.00 0.00 0.00 5.68
1337 3287 3.149436 TCAATTTGAGCGGCAATTAGC 57.851 42.857 1.45 0.00 44.65 3.09
1338 3288 4.737054 ACTTCAATTTGAGCGGCAATTAG 58.263 39.130 1.45 0.00 36.15 1.73
1345 3295 6.758886 AGTTCTAGATACTTCAATTTGAGCGG 59.241 38.462 0.00 0.00 0.00 5.52
1354 3304 9.784680 GACGTATTTCAGTTCTAGATACTTCAA 57.215 33.333 0.00 0.00 0.00 2.69
1385 3344 7.721402 AGTTGTTGGTTGCTGAAATAAATGTA 58.279 30.769 0.00 0.00 0.00 2.29
1391 3350 8.465999 CCATATTAGTTGTTGGTTGCTGAAATA 58.534 33.333 0.00 0.00 0.00 1.40
1392 3351 7.178274 TCCATATTAGTTGTTGGTTGCTGAAAT 59.822 33.333 0.00 0.00 0.00 2.17
1403 3362 6.299141 AGCCCTGTATCCATATTAGTTGTTG 58.701 40.000 0.00 0.00 0.00 3.33
1404 3363 6.330250 AGAGCCCTGTATCCATATTAGTTGTT 59.670 38.462 0.00 0.00 0.00 2.83
1405 3364 5.846714 AGAGCCCTGTATCCATATTAGTTGT 59.153 40.000 0.00 0.00 0.00 3.32
1406 3365 6.365970 AGAGCCCTGTATCCATATTAGTTG 57.634 41.667 0.00 0.00 0.00 3.16
1407 3366 5.186021 CGAGAGCCCTGTATCCATATTAGTT 59.814 44.000 0.00 0.00 0.00 2.24
1449 3408 4.396166 CCAGCTCGTTCCTACAAAATGATT 59.604 41.667 0.00 0.00 0.00 2.57
1493 3452 7.569599 TTCTCCTCTTCAGGTTTATAAGGTT 57.430 36.000 0.00 0.00 41.28 3.50
1547 3915 9.553064 TTACAACCATAGGTCTTACGTTTTAAA 57.447 29.630 0.00 0.00 33.12 1.52
1549 3917 8.367156 AGTTACAACCATAGGTCTTACGTTTTA 58.633 33.333 0.00 0.00 33.12 1.52
1554 3922 5.957798 TGAGTTACAACCATAGGTCTTACG 58.042 41.667 0.00 0.00 33.12 3.18
1587 3955 1.063469 CTTTGCTTGTTTGTCGACCGT 59.937 47.619 14.12 0.00 0.00 4.83
1589 3957 2.844122 ACTTTGCTTGTTTGTCGACC 57.156 45.000 14.12 0.00 0.00 4.79
1674 4048 7.551617 TCCTCTTTTCCCTTAATAATGTTCGTC 59.448 37.037 0.00 0.00 0.00 4.20
1696 4074 8.154649 TCTCTTGTAATTGACTTGTTTTCCTC 57.845 34.615 0.00 0.00 0.00 3.71
1817 4213 3.248266 GCTTGTTGCTATTTGGCTGAAG 58.752 45.455 0.00 0.00 38.95 3.02
1855 4251 6.428083 TGAACCATCCAAAGTACTCAGTTA 57.572 37.500 0.00 0.00 0.00 2.24
1859 4255 5.241403 ACATGAACCATCCAAAGTACTCA 57.759 39.130 0.00 0.00 0.00 3.41
1860 4256 5.705441 TGAACATGAACCATCCAAAGTACTC 59.295 40.000 0.00 0.00 0.00 2.59
1862 4258 5.473504 ACTGAACATGAACCATCCAAAGTAC 59.526 40.000 0.00 0.00 0.00 2.73
1863 4259 5.473162 CACTGAACATGAACCATCCAAAGTA 59.527 40.000 0.00 0.00 0.00 2.24
1864 4260 4.279169 CACTGAACATGAACCATCCAAAGT 59.721 41.667 0.00 0.00 0.00 2.66
1865 4261 4.520111 TCACTGAACATGAACCATCCAAAG 59.480 41.667 0.00 0.00 0.00 2.77
1891 4287 5.284079 TGAGCTTGTGAAATTTGAGCTTTC 58.716 37.500 13.13 0.00 43.22 2.62
1930 4326 1.843368 CCTGACTAGGTAACCCGTGA 58.157 55.000 0.00 0.00 39.39 4.35
1978 4376 9.438291 CACAGACTTTAAAGTTATTGAACACTG 57.562 33.333 21.40 19.82 39.88 3.66
1979 4377 8.621286 CCACAGACTTTAAAGTTATTGAACACT 58.379 33.333 21.40 8.22 39.88 3.55
1999 4397 2.024846 TCAAAACCTTTGGGTCCACAGA 60.025 45.455 4.84 0.00 46.67 3.41
2003 4401 1.063266 AGCTCAAAACCTTTGGGTCCA 60.063 47.619 1.26 0.00 46.67 4.02
2013 4411 7.865385 TGTGTATGTTTAAATCAGCTCAAAACC 59.135 33.333 0.00 0.00 30.75 3.27
2053 4451 8.530311 TCCATTTGCATGTGTGATTAAATAAGT 58.470 29.630 0.00 0.00 0.00 2.24
2107 4510 2.273538 ATCCATCAGATGCTTCCAGC 57.726 50.000 4.68 0.00 42.82 4.85


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

AutoCloner maintained by Alex Coulton.