Multiple sequence alignment - TraesCS5A01G216600

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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 TraesCS5A01G216600 chr5A 100.000 2579 0 0 1 2579 433379596 433377018 0.000000e+00 4763
1 TraesCS5A01G216600 chr5D 89.715 1439 94 26 733 2158 332459827 332458430 0.000000e+00 1788
2 TraesCS5A01G216600 chr5D 97.472 712 16 2 1 710 495898467 495897756 0.000000e+00 1214
3 TraesCS5A01G216600 chr5D 95.227 419 18 1 2161 2579 332457778 332457362 0.000000e+00 662
4 TraesCS5A01G216600 chr5D 94.322 317 18 0 1088 1404 331842146 331841830 1.070000e-133 486
5 TraesCS5A01G216600 chr5B 89.846 1428 93 24 733 2158 388481961 388480584 0.000000e+00 1786
6 TraesCS5A01G216600 chr5B 93.114 334 21 2 1071 1404 530609449 530609780 2.980000e-134 488
7 TraesCS5A01G216600 chr5B 93.827 324 20 0 1081 1404 535715422 535715099 2.980000e-134 488
8 TraesCS5A01G216600 chr2A 99.437 710 4 0 1 710 750618880 750618171 0.000000e+00 1290
9 TraesCS5A01G216600 chr6B 99.295 709 4 1 1 708 169059384 169058676 0.000000e+00 1280
10 TraesCS5A01G216600 chr6B 84.016 732 81 19 2 711 129682231 129681514 0.000000e+00 671
11 TraesCS5A01G216600 chr3D 97.335 713 17 2 1 711 174423479 174422767 0.000000e+00 1210
12 TraesCS5A01G216600 chr3D 97.195 713 17 2 1 710 558088014 558087302 0.000000e+00 1203
13 TraesCS5A01G216600 chr1D 94.904 314 16 0 1092 1405 445366814 445366501 2.310000e-135 492
14 TraesCS5A01G216600 chr1D 94.888 313 16 0 1092 1404 446476176 446476488 8.290000e-135 490
15 TraesCS5A01G216600 chr1A 94.888 313 16 0 1092 1404 541343823 541344135 8.290000e-135 490
16 TraesCS5A01G216600 chr4A 93.558 326 20 1 1080 1404 66148198 66147873 3.860000e-133 484


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 TraesCS5A01G216600 chr5A 433377018 433379596 2578 True 4763 4763 100.000 1 2579 1 chr5A.!!$R1 2578
1 TraesCS5A01G216600 chr5D 332457362 332459827 2465 True 1225 1788 92.471 733 2579 2 chr5D.!!$R3 1846
2 TraesCS5A01G216600 chr5D 495897756 495898467 711 True 1214 1214 97.472 1 710 1 chr5D.!!$R2 709
3 TraesCS5A01G216600 chr5B 388480584 388481961 1377 True 1786 1786 89.846 733 2158 1 chr5B.!!$R1 1425
4 TraesCS5A01G216600 chr2A 750618171 750618880 709 True 1290 1290 99.437 1 710 1 chr2A.!!$R1 709
5 TraesCS5A01G216600 chr6B 169058676 169059384 708 True 1280 1280 99.295 1 708 1 chr6B.!!$R2 707
6 TraesCS5A01G216600 chr6B 129681514 129682231 717 True 671 671 84.016 2 711 1 chr6B.!!$R1 709
7 TraesCS5A01G216600 chr3D 174422767 174423479 712 True 1210 1210 97.335 1 711 1 chr3D.!!$R1 710
8 TraesCS5A01G216600 chr3D 558087302 558088014 712 True 1203 1203 97.195 1 710 1 chr3D.!!$R2 709

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
791 827 0.229753 CGCGCTATTTTCTGCTACCG 59.77 55.0 5.56 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1787 0.321122 GCACAGTTCCAGTAGCAGCT 60.321 55.0 0.0 0.0 0.0 4.24 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
35 36 8.879759 AGACGTTCACGAATTCAATAAATGTAT 58.120 29.630 6.30 0.82 43.02 2.29
235 239 5.047731 TCGGGAATGCAAAAATATGTTCACA 60.048 36.000 0.00 0.00 0.00 3.58
711 747 2.300152 AGCACTCTTGTGAATTCTCGGA 59.700 45.455 7.05 5.17 46.55 4.55
712 748 3.067106 GCACTCTTGTGAATTCTCGGAA 58.933 45.455 7.05 0.00 46.55 4.30
713 749 3.124297 GCACTCTTGTGAATTCTCGGAAG 59.876 47.826 7.05 4.42 46.55 3.46
714 750 4.560128 CACTCTTGTGAATTCTCGGAAGA 58.440 43.478 7.05 8.23 46.55 2.87
715 751 5.174395 CACTCTTGTGAATTCTCGGAAGAT 58.826 41.667 7.05 0.00 46.55 2.40
716 752 6.333416 CACTCTTGTGAATTCTCGGAAGATA 58.667 40.000 7.05 0.00 46.55 1.98
717 753 6.983307 CACTCTTGTGAATTCTCGGAAGATAT 59.017 38.462 7.05 0.00 46.55 1.63
718 754 8.138074 CACTCTTGTGAATTCTCGGAAGATATA 58.862 37.037 7.05 0.00 46.55 0.86
719 755 8.865090 ACTCTTGTGAATTCTCGGAAGATATAT 58.135 33.333 7.05 0.00 40.84 0.86
720 756 9.352784 CTCTTGTGAATTCTCGGAAGATATATC 57.647 37.037 7.05 4.42 40.84 1.63
721 757 8.307483 TCTTGTGAATTCTCGGAAGATATATCC 58.693 37.037 9.18 0.00 40.84 2.59
748 784 4.479993 CCCCTTCCCTGCTCGCTG 62.480 72.222 0.00 0.00 0.00 5.18
754 790 1.308069 TTCCCTGCTCGCTGAAATGC 61.308 55.000 0.00 0.00 0.00 3.56
784 820 4.421058 GAAAAATTCCCGCGCTATTTTCT 58.579 39.130 18.02 11.68 35.17 2.52
791 827 0.229753 CGCGCTATTTTCTGCTACCG 59.770 55.000 5.56 0.00 0.00 4.02
830 867 4.951963 CCGATCCGCGCTTCCTCC 62.952 72.222 5.56 0.00 39.11 4.30
832 869 4.951963 GATCCGCGCTTCCTCCGG 62.952 72.222 5.56 0.00 43.21 5.14
856 893 1.355720 ACCAATAGCAGCCAACCTCTT 59.644 47.619 0.00 0.00 0.00 2.85
871 908 0.745845 CTCTTCCCATCCAACGGCTG 60.746 60.000 0.00 0.00 0.00 4.85
970 1009 4.156556 CAGCCAGCAAACGCCATATATAAT 59.843 41.667 0.00 0.00 0.00 1.28
979 1018 3.711704 ACGCCATATATAATCCCCTCCAG 59.288 47.826 0.00 0.00 0.00 3.86
990 1029 4.106925 CCTCCAGCAGCCTCCCAC 62.107 72.222 0.00 0.00 0.00 4.61
1011 1050 2.609350 CAATCCAAACCAATTCGGCTG 58.391 47.619 0.00 0.00 39.03 4.85
1048 1088 2.437085 AATCCCCAATTCCTTCGTCC 57.563 50.000 0.00 0.00 0.00 4.79
1104 1144 4.814294 GAAGATGTCCGGGCGCGT 62.814 66.667 22.32 2.64 0.00 6.01
1408 1448 1.227556 CTTCGGCGGTTAGGGGATG 60.228 63.158 7.21 0.00 0.00 3.51
1442 1482 0.818296 AGTGTGTCTATCAGGTCGCC 59.182 55.000 0.00 0.00 0.00 5.54
1478 1518 5.688176 GCTCGTGCTTGTGGTTTAATTTAAA 59.312 36.000 1.41 0.00 36.03 1.52
1479 1519 6.199342 GCTCGTGCTTGTGGTTTAATTTAAAA 59.801 34.615 1.41 0.00 36.03 1.52
1523 1563 4.792068 ACCTGGATTTGTTTCTCTGTTCA 58.208 39.130 0.00 0.00 0.00 3.18
1535 1576 6.366061 TGTTTCTCTGTTCAATATCGTCAGTG 59.634 38.462 0.00 0.00 0.00 3.66
1537 1578 3.179048 TCTGTTCAATATCGTCAGTGCG 58.821 45.455 1.21 1.21 0.00 5.34
1544 1585 0.599060 TATCGTCAGTGCGGTCACAA 59.401 50.000 7.03 0.00 45.49 3.33
1557 1598 2.549754 CGGTCACAACTTCTGATTTGCT 59.450 45.455 0.71 0.00 0.00 3.91
1597 1638 5.795441 GAAATTCTTTTCATTCGGTTCTCCG 59.205 40.000 0.00 0.00 46.85 4.63
1619 1660 4.148696 CGAAGCTAACTTGGCAAATTTGTG 59.851 41.667 19.03 9.77 35.82 3.33
1623 1664 4.324402 GCTAACTTGGCAAATTTGTGATCG 59.676 41.667 19.03 7.39 0.00 3.69
1709 1754 1.867233 CAGTGTGGTTTTCTCGTGAGG 59.133 52.381 0.00 0.00 0.00 3.86
1720 1765 2.234143 TCTCGTGAGGATGCTCATAGG 58.766 52.381 20.59 12.51 35.65 2.57
1721 1766 1.959985 CTCGTGAGGATGCTCATAGGT 59.040 52.381 20.59 0.00 35.65 3.08
1722 1767 1.957177 TCGTGAGGATGCTCATAGGTC 59.043 52.381 20.59 5.98 35.65 3.85
1723 1768 1.683385 CGTGAGGATGCTCATAGGTCA 59.317 52.381 20.59 0.00 35.65 4.02
1724 1769 2.298446 CGTGAGGATGCTCATAGGTCAT 59.702 50.000 20.59 0.00 35.65 3.06
1725 1770 3.507622 CGTGAGGATGCTCATAGGTCATA 59.492 47.826 20.59 0.00 35.65 2.15
1726 1771 4.380339 CGTGAGGATGCTCATAGGTCATAG 60.380 50.000 20.59 0.72 35.65 2.23
1727 1772 3.513119 TGAGGATGCTCATAGGTCATAGC 59.487 47.826 13.58 0.00 35.51 2.97
1728 1773 3.768757 GAGGATGCTCATAGGTCATAGCT 59.231 47.826 9.69 0.00 35.95 3.32
1729 1774 3.514706 AGGATGCTCATAGGTCATAGCTG 59.485 47.826 0.00 0.00 35.95 4.24
1730 1775 2.827800 TGCTCATAGGTCATAGCTGC 57.172 50.000 0.00 0.00 35.95 5.25
1731 1776 2.041701 TGCTCATAGGTCATAGCTGCA 58.958 47.619 1.02 0.00 35.95 4.41
1732 1777 2.636403 TGCTCATAGGTCATAGCTGCAT 59.364 45.455 1.02 0.00 35.95 3.96
1733 1778 3.072038 TGCTCATAGGTCATAGCTGCATT 59.928 43.478 1.02 0.00 35.95 3.56
1734 1779 4.070716 GCTCATAGGTCATAGCTGCATTT 58.929 43.478 1.02 0.00 32.18 2.32
1735 1780 4.518211 GCTCATAGGTCATAGCTGCATTTT 59.482 41.667 1.02 0.00 32.18 1.82
1736 1781 5.009410 GCTCATAGGTCATAGCTGCATTTTT 59.991 40.000 1.02 0.00 32.18 1.94
1737 1782 6.624352 TCATAGGTCATAGCTGCATTTTTC 57.376 37.500 1.02 0.00 0.00 2.29
1738 1783 6.359804 TCATAGGTCATAGCTGCATTTTTCT 58.640 36.000 1.02 0.00 0.00 2.52
1739 1784 4.978083 AGGTCATAGCTGCATTTTTCTG 57.022 40.909 1.02 0.00 0.00 3.02
1740 1785 4.592942 AGGTCATAGCTGCATTTTTCTGA 58.407 39.130 1.02 0.00 0.00 3.27
1741 1786 5.012239 AGGTCATAGCTGCATTTTTCTGAA 58.988 37.500 1.02 0.00 0.00 3.02
1742 1787 5.477984 AGGTCATAGCTGCATTTTTCTGAAA 59.522 36.000 1.02 0.00 0.00 2.69
1743 1788 5.803967 GGTCATAGCTGCATTTTTCTGAAAG 59.196 40.000 1.02 0.00 0.00 2.62
1760 1805 2.175878 AAGCTGCTACTGGAACTGTG 57.824 50.000 0.90 0.00 41.61 3.66
1813 1863 3.777106 AGGCAACATCTCTGAGACAAA 57.223 42.857 10.00 0.00 41.41 2.83
1814 1864 4.090761 AGGCAACATCTCTGAGACAAAA 57.909 40.909 10.00 0.00 41.41 2.44
1857 1907 5.179182 GGTGGTGGCATGAAAAGTTATTTTG 59.821 40.000 0.00 0.00 38.74 2.44
1860 1910 5.988561 GGTGGCATGAAAAGTTATTTTGTCA 59.011 36.000 0.00 0.00 38.74 3.58
1865 1915 7.224557 GGCATGAAAAGTTATTTTGTCACAAGT 59.775 33.333 0.00 0.00 38.74 3.16
2050 2101 7.526608 GCAACATAAGATTTGCACACTACTTA 58.473 34.615 1.51 0.00 46.13 2.24
2096 2147 7.946207 TGGTATTTCAGCATTAACAACTTCAA 58.054 30.769 0.00 0.00 0.00 2.69
2158 2209 5.471257 GGAACTGTTGGAGTACAAGACTAG 58.529 45.833 0.00 0.00 40.38 2.57
2159 2210 5.470047 AACTGTTGGAGTACAAGACTAGG 57.530 43.478 0.00 0.00 40.38 3.02
2163 2863 3.383698 TGGAGTACAAGACTAGGGAGG 57.616 52.381 0.00 0.00 39.06 4.30
2166 2866 2.427812 GAGTACAAGACTAGGGAGGTGC 59.572 54.545 0.00 0.00 39.06 5.01
2190 2890 5.449553 GGGTGATTCCTTGTCCATAATCTT 58.550 41.667 0.00 0.00 36.25 2.40
2191 2891 5.893824 GGGTGATTCCTTGTCCATAATCTTT 59.106 40.000 0.00 0.00 36.25 2.52
2192 2892 6.039829 GGGTGATTCCTTGTCCATAATCTTTC 59.960 42.308 0.00 0.00 36.25 2.62
2289 2989 2.807967 CAACGCTGGACTTTGATGAAGA 59.192 45.455 0.00 0.00 38.77 2.87
2307 3007 1.696336 AGACAACTCTGTGCCACATCT 59.304 47.619 0.00 0.00 35.30 2.90
2322 3022 3.246226 CCACATCTAATGTACAAGCGAGC 59.754 47.826 0.00 0.00 42.70 5.03
2349 3049 1.605710 CATTGATGAGCGGGGACATTC 59.394 52.381 0.00 0.00 0.00 2.67
2351 3051 0.107703 TGATGAGCGGGGACATTCAC 60.108 55.000 0.00 0.00 0.00 3.18
2352 3052 0.179000 GATGAGCGGGGACATTCACT 59.821 55.000 0.00 0.00 0.00 3.41
2372 3072 3.769844 ACTGTTCTCCCGACATGAGTAAT 59.230 43.478 0.00 0.00 0.00 1.89
2394 3094 4.457466 TCGAAAAGGAAGCAAAACTAGGT 58.543 39.130 0.00 0.00 0.00 3.08
2432 3132 8.960591 CAATTCCTTCAAGATAGGTGTTACAAT 58.039 33.333 0.00 0.00 34.29 2.71
2458 3158 2.834450 CGAGAATTGTTGCACGAATTCG 59.166 45.455 25.64 25.64 41.50 3.34
2483 3183 5.308237 AGAGGTTGACTAAATCCAGACAGTT 59.692 40.000 0.00 0.00 0.00 3.16
2489 3189 5.153950 ACTAAATCCAGACAGTTGACCTC 57.846 43.478 0.00 0.00 0.00 3.85
2527 3227 1.209019 AGCCTCTGAGTTGCGATGATT 59.791 47.619 3.66 0.00 0.00 2.57
2542 3242 3.632145 CGATGATTACCCCTCCCAAAAAG 59.368 47.826 0.00 0.00 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 8.724153 CACATACATTTATTGAATTCGTGAACG 58.276 33.333 0.04 0.00 41.45 3.95
711 747 4.589374 GGGGCATAGTAGCGGATATATCTT 59.411 45.833 12.42 2.16 34.64 2.40
712 748 4.140900 AGGGGCATAGTAGCGGATATATCT 60.141 45.833 12.42 0.00 34.64 1.98
713 749 4.153411 AGGGGCATAGTAGCGGATATATC 58.847 47.826 3.96 3.96 34.64 1.63
714 750 4.200447 AGGGGCATAGTAGCGGATATAT 57.800 45.455 0.00 0.00 34.64 0.86
715 751 3.682592 AGGGGCATAGTAGCGGATATA 57.317 47.619 0.00 0.00 34.64 0.86
716 752 2.552093 AGGGGCATAGTAGCGGATAT 57.448 50.000 0.00 0.00 34.64 1.63
717 753 2.176889 GAAGGGGCATAGTAGCGGATA 58.823 52.381 0.00 0.00 34.64 2.59
718 754 0.977395 GAAGGGGCATAGTAGCGGAT 59.023 55.000 0.00 0.00 34.64 4.18
719 755 1.119574 GGAAGGGGCATAGTAGCGGA 61.120 60.000 0.00 0.00 34.64 5.54
720 756 1.371558 GGAAGGGGCATAGTAGCGG 59.628 63.158 0.00 0.00 34.64 5.52
721 757 1.122019 AGGGAAGGGGCATAGTAGCG 61.122 60.000 0.00 0.00 34.64 4.26
722 758 0.398318 CAGGGAAGGGGCATAGTAGC 59.602 60.000 0.00 0.00 0.00 3.58
723 759 0.398318 GCAGGGAAGGGGCATAGTAG 59.602 60.000 0.00 0.00 0.00 2.57
724 760 0.030092 AGCAGGGAAGGGGCATAGTA 60.030 55.000 0.00 0.00 0.00 1.82
725 761 1.308216 AGCAGGGAAGGGGCATAGT 60.308 57.895 0.00 0.00 0.00 2.12
726 762 1.453669 GAGCAGGGAAGGGGCATAG 59.546 63.158 0.00 0.00 0.00 2.23
727 763 2.443394 CGAGCAGGGAAGGGGCATA 61.443 63.158 0.00 0.00 0.00 3.14
728 764 3.801997 CGAGCAGGGAAGGGGCAT 61.802 66.667 0.00 0.00 0.00 4.40
731 767 4.479993 CAGCGAGCAGGGAAGGGG 62.480 72.222 0.00 0.00 0.00 4.79
748 784 1.492720 TTTTTCCGCCGTTGCATTTC 58.507 45.000 0.00 0.00 37.32 2.17
830 867 0.676466 TGGCTGCTATTGGTTGACCG 60.676 55.000 0.00 0.00 39.43 4.79
832 869 1.202348 GGTTGGCTGCTATTGGTTGAC 59.798 52.381 0.00 0.00 0.00 3.18
856 893 1.299648 CTTCAGCCGTTGGATGGGA 59.700 57.895 0.72 0.00 39.86 4.37
947 986 1.308047 TATATGGCGTTTGCTGGCTG 58.692 50.000 0.00 0.00 42.25 4.85
949 988 4.438744 GGATTATATATGGCGTTTGCTGGC 60.439 45.833 0.00 0.00 42.25 4.85
955 994 4.538490 TGGAGGGGATTATATATGGCGTTT 59.462 41.667 0.00 0.00 0.00 3.60
956 995 4.108570 TGGAGGGGATTATATATGGCGTT 58.891 43.478 0.00 0.00 0.00 4.84
957 996 3.711704 CTGGAGGGGATTATATATGGCGT 59.288 47.826 0.00 0.00 0.00 5.68
958 997 3.495100 GCTGGAGGGGATTATATATGGCG 60.495 52.174 0.00 0.00 0.00 5.69
959 998 3.459598 TGCTGGAGGGGATTATATATGGC 59.540 47.826 0.00 0.00 0.00 4.40
960 999 4.445448 GCTGCTGGAGGGGATTATATATGG 60.445 50.000 0.00 0.00 0.00 2.74
961 1000 4.445448 GGCTGCTGGAGGGGATTATATATG 60.445 50.000 0.00 0.00 0.00 1.78
962 1001 3.718956 GGCTGCTGGAGGGGATTATATAT 59.281 47.826 0.00 0.00 0.00 0.86
979 1018 2.440980 GGATTGGTGGGAGGCTGC 60.441 66.667 0.00 0.00 0.00 5.25
987 1026 2.353605 CCGAATTGGTTTGGATTGGTGG 60.354 50.000 0.00 0.00 40.82 4.61
990 1029 1.550072 AGCCGAATTGGTTTGGATTGG 59.450 47.619 0.00 0.00 40.82 3.16
1011 1050 2.514458 TTTTTCTCTGGGAGGGATGC 57.486 50.000 0.00 0.00 0.00 3.91
1048 1088 4.244802 GCGTCTCGCGAGGAGGAG 62.245 72.222 33.98 20.85 44.55 3.69
1066 1106 2.508887 CTCTCGGCTCTGCTGTGC 60.509 66.667 8.93 8.93 36.18 4.57
1078 1118 0.665835 CGGACATCTTCTCCCTCTCG 59.334 60.000 0.00 0.00 0.00 4.04
1084 1124 2.107141 CGCCCGGACATCTTCTCC 59.893 66.667 0.73 0.00 0.00 3.71
1339 1379 1.808390 GTACACGACGTCCATGGCC 60.808 63.158 10.58 0.00 0.00 5.36
1408 1448 0.322008 ACACTGAAGCCAAGCTAGCC 60.322 55.000 12.13 0.00 38.25 3.93
1457 1497 6.789877 GCATTTTAAATTAAACCACAAGCACG 59.210 34.615 0.00 0.00 0.00 5.34
1478 1518 7.123247 AGGTAGCATTTTCTCATAACAAGCATT 59.877 33.333 0.00 0.00 0.00 3.56
1479 1519 6.604795 AGGTAGCATTTTCTCATAACAAGCAT 59.395 34.615 0.00 0.00 0.00 3.79
1493 1533 6.494835 AGAGAAACAAATCCAGGTAGCATTTT 59.505 34.615 0.00 0.00 0.00 1.82
1523 1563 1.203758 TGTGACCGCACTGACGATATT 59.796 47.619 0.00 0.00 45.36 1.28
1535 1576 2.918131 GCAAATCAGAAGTTGTGACCGC 60.918 50.000 4.61 4.80 33.10 5.68
1537 1578 4.083271 GGTAGCAAATCAGAAGTTGTGACC 60.083 45.833 4.61 0.00 33.42 4.02
1544 1585 4.385825 TCAAACGGTAGCAAATCAGAAGT 58.614 39.130 0.00 0.00 0.00 3.01
1557 1598 6.687081 AGAATTTCACAAACTCAAACGGTA 57.313 33.333 0.00 0.00 0.00 4.02
1592 1633 0.973632 TGCCAAGTTAGCTTCGGAGA 59.026 50.000 0.00 0.00 31.49 3.71
1595 1636 3.575965 AATTTGCCAAGTTAGCTTCGG 57.424 42.857 0.00 0.00 31.49 4.30
1597 1638 5.288804 TCACAAATTTGCCAAGTTAGCTTC 58.711 37.500 18.12 0.00 31.49 3.86
1619 1660 5.705441 TGCAAATGGTAGATAAATCCCGATC 59.295 40.000 0.00 0.00 0.00 3.69
1623 1664 8.829612 CAAAAATGCAAATGGTAGATAAATCCC 58.170 33.333 0.00 0.00 0.00 3.85
1683 1728 3.243068 ACGAGAAAACCACACTGCAATTC 60.243 43.478 0.00 0.00 0.00 2.17
1696 1741 2.688507 TGAGCATCCTCACGAGAAAAC 58.311 47.619 0.00 0.00 42.98 2.43
1709 1754 3.260740 GCAGCTATGACCTATGAGCATC 58.739 50.000 0.00 0.00 37.40 3.91
1720 1765 5.287992 GCTTTCAGAAAAATGCAGCTATGAC 59.712 40.000 0.00 0.00 31.55 3.06
1721 1766 5.184479 AGCTTTCAGAAAAATGCAGCTATGA 59.816 36.000 3.37 0.00 35.78 2.15
1722 1767 5.288712 CAGCTTTCAGAAAAATGCAGCTATG 59.711 40.000 4.75 0.00 35.78 2.23
1723 1768 5.408356 CAGCTTTCAGAAAAATGCAGCTAT 58.592 37.500 4.75 0.00 35.78 2.97
1724 1769 4.801891 CAGCTTTCAGAAAAATGCAGCTA 58.198 39.130 4.75 0.00 35.78 3.32
1725 1770 3.650139 CAGCTTTCAGAAAAATGCAGCT 58.350 40.909 8.01 4.13 37.15 4.24
1726 1771 2.157085 GCAGCTTTCAGAAAAATGCAGC 59.843 45.455 19.96 13.98 37.22 5.25
1727 1772 3.650139 AGCAGCTTTCAGAAAAATGCAG 58.350 40.909 23.99 11.92 38.61 4.41
1728 1773 3.738830 AGCAGCTTTCAGAAAAATGCA 57.261 38.095 23.99 0.00 38.61 3.96
1729 1774 4.620184 CAGTAGCAGCTTTCAGAAAAATGC 59.380 41.667 18.28 18.28 37.39 3.56
1730 1775 5.048504 TCCAGTAGCAGCTTTCAGAAAAATG 60.049 40.000 0.00 0.34 0.00 2.32
1731 1776 5.072741 TCCAGTAGCAGCTTTCAGAAAAAT 58.927 37.500 0.00 0.00 0.00 1.82
1732 1777 4.460263 TCCAGTAGCAGCTTTCAGAAAAA 58.540 39.130 0.00 0.00 0.00 1.94
1733 1778 4.085357 TCCAGTAGCAGCTTTCAGAAAA 57.915 40.909 0.00 0.00 0.00 2.29
1734 1779 3.769739 TCCAGTAGCAGCTTTCAGAAA 57.230 42.857 0.00 0.00 0.00 2.52
1735 1780 3.071602 AGTTCCAGTAGCAGCTTTCAGAA 59.928 43.478 0.00 0.00 0.00 3.02
1736 1781 2.634940 AGTTCCAGTAGCAGCTTTCAGA 59.365 45.455 0.00 0.00 0.00 3.27
1737 1782 2.740981 CAGTTCCAGTAGCAGCTTTCAG 59.259 50.000 0.00 0.00 0.00 3.02
1738 1783 2.104792 ACAGTTCCAGTAGCAGCTTTCA 59.895 45.455 0.00 0.00 0.00 2.69
1739 1784 2.481952 CACAGTTCCAGTAGCAGCTTTC 59.518 50.000 0.00 0.00 0.00 2.62
1740 1785 2.498167 CACAGTTCCAGTAGCAGCTTT 58.502 47.619 0.00 0.00 0.00 3.51
1741 1786 1.879796 GCACAGTTCCAGTAGCAGCTT 60.880 52.381 0.00 0.00 0.00 3.74
1742 1787 0.321122 GCACAGTTCCAGTAGCAGCT 60.321 55.000 0.00 0.00 0.00 4.24
1743 1788 0.321122 AGCACAGTTCCAGTAGCAGC 60.321 55.000 0.00 0.00 0.00 5.25
1760 1805 1.992188 GCTTTCGTAGCGTCAGAGC 59.008 57.895 0.00 0.00 40.71 4.09
1813 1863 0.892814 GGAGCTTGCAGCAGGAAGTT 60.893 55.000 9.09 5.82 45.56 2.66
1814 1864 1.303155 GGAGCTTGCAGCAGGAAGT 60.303 57.895 9.09 0.00 45.56 3.01
1832 1882 0.673437 AACTTTTCATGCCACCACCG 59.327 50.000 0.00 0.00 0.00 4.94
1929 1980 1.740025 GGTCAAGTTCTGTATGCCAGC 59.260 52.381 0.00 0.00 41.25 4.85
2050 2101 7.823745 ACCAAAATACTGTGATTTCTTGACT 57.176 32.000 0.00 0.00 0.00 3.41
2158 2209 2.124695 GAATCACCCGCACCTCCC 60.125 66.667 0.00 0.00 0.00 4.30
2159 2210 2.124695 GGAATCACCCGCACCTCC 60.125 66.667 0.00 0.00 0.00 4.30
2163 2863 1.305930 GGACAAGGAATCACCCGCAC 61.306 60.000 0.00 0.00 40.05 5.34
2166 2866 3.275617 TTATGGACAAGGAATCACCCG 57.724 47.619 0.00 0.00 40.05 5.28
2272 2972 3.817647 AGTTGTCTTCATCAAAGTCCAGC 59.182 43.478 0.00 0.00 36.31 4.85
2289 2989 3.769739 TTAGATGTGGCACAGAGTTGT 57.230 42.857 26.04 10.04 41.80 3.32
2307 3007 1.742411 GCCCAGCTCGCTTGTACATTA 60.742 52.381 0.00 0.00 0.00 1.90
2322 3022 1.721664 CCGCTCATCAATGTGCCCAG 61.722 60.000 10.48 0.00 42.51 4.45
2349 3049 1.273606 ACTCATGTCGGGAGAACAGTG 59.726 52.381 0.00 0.00 42.89 3.66
2351 3051 3.868757 TTACTCATGTCGGGAGAACAG 57.131 47.619 0.00 0.00 42.89 3.16
2352 3052 3.181490 CGATTACTCATGTCGGGAGAACA 60.181 47.826 0.00 0.00 42.89 3.18
2372 3072 4.457466 ACCTAGTTTTGCTTCCTTTTCGA 58.543 39.130 0.00 0.00 0.00 3.71
2394 3094 6.384015 TCTTGAAGGAATTGCAGGAGATAGTA 59.616 38.462 0.00 0.00 0.00 1.82
2432 3132 0.790207 GTGCAACAATTCTCGCTCGA 59.210 50.000 0.00 0.00 36.32 4.04
2458 3158 5.046950 ACTGTCTGGATTTAGTCAACCTCTC 60.047 44.000 0.00 0.00 0.00 3.20
2489 3189 5.036908 GAGGCTACTCACATGTGATCATGG 61.037 50.000 28.00 18.13 43.19 3.66
2527 3227 1.089123 ATGGCTTTTTGGGAGGGGTA 58.911 50.000 0.00 0.00 0.00 3.69
2542 3242 8.914011 AGGTCCATTTATTTCTAAACTTATGGC 58.086 33.333 0.00 0.00 29.24 4.40


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

AutoCloner maintained by Alex Coulton.