Multiple sequence alignment - TraesCS5D01G480000

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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 TraesCS5D01G480000 chr5D 100.000 2390 0 0 1 2390 517757465 517759854 0.000000e+00 4414
1 TraesCS5D01G480000 chr5A 90.903 1561 79 30 1 1521 645130990 645132527 0.000000e+00 2037
2 TraesCS5D01G480000 chr5A 82.811 925 75 36 1530 2390 645132571 645133475 0.000000e+00 750
3 TraesCS5D01G480000 chr5B 90.191 1570 74 36 1 1521 650342774 650344312 0.000000e+00 1973
4 TraesCS5D01G480000 chr5B 82.088 910 73 26 1528 2390 650344356 650345222 0.000000e+00 695
5 TraesCS5D01G480000 chr6B 82.122 688 53 16 1731 2390 7599094 7598449 2.100000e-145 525


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 TraesCS5D01G480000 chr5D 517757465 517759854 2389 False 4414.0 4414 100.0000 1 2390 1 chr5D.!!$F1 2389
1 TraesCS5D01G480000 chr5A 645130990 645133475 2485 False 1393.5 2037 86.8570 1 2390 2 chr5A.!!$F1 2389
2 TraesCS5D01G480000 chr5B 650342774 650345222 2448 False 1334.0 1973 86.1395 1 2390 2 chr5B.!!$F1 2389
3 TraesCS5D01G480000 chr6B 7598449 7599094 645 True 525.0 525 82.1220 1731 2390 1 chr6B.!!$R1 659

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
353 374 0.24899 CAGAGCAGAGATCCGTCAGC 60.249 60.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2292 2470 0.251916 TCAAGAAACGGCGATCCCAT 59.748 50.0 16.62 0.0 0.0 4.0 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
28 29 5.641209 ACTCTACAAGCTAAAAGTGCTCATG 59.359 40.000 0.00 0.00 40.22 3.07
37 38 8.284945 AGCTAAAAGTGCTCATGAATCATAAA 57.715 30.769 0.00 0.00 35.67 1.40
38 39 8.910944 AGCTAAAAGTGCTCATGAATCATAAAT 58.089 29.630 0.00 0.00 35.67 1.40
77 79 7.138692 AGTGCATGTCAAACTAGAAATTCTC 57.861 36.000 0.00 0.00 0.00 2.87
82 84 7.627300 GCATGTCAAACTAGAAATTCTCCCTTC 60.627 40.741 0.00 0.00 0.00 3.46
85 87 7.998964 TGTCAAACTAGAAATTCTCCCTTCTTT 59.001 33.333 0.00 0.00 33.89 2.52
109 119 2.353579 ACGACTTTGCACACCAACTAAC 59.646 45.455 0.00 0.00 31.97 2.34
110 120 2.353269 CGACTTTGCACACCAACTAACA 59.647 45.455 0.00 0.00 31.97 2.41
117 127 1.812571 CACACCAACTAACATCCCAGC 59.187 52.381 0.00 0.00 0.00 4.85
123 138 5.066505 CACCAACTAACATCCCAGCTAATTC 59.933 44.000 0.00 0.00 0.00 2.17
168 189 5.828299 ACTAACACAAGCTTAAGCAACAA 57.172 34.783 28.39 6.90 45.16 2.83
169 190 5.578776 ACTAACACAAGCTTAAGCAACAAC 58.421 37.500 28.39 0.00 45.16 3.32
229 250 0.451783 GGGTTGCAGAATTAGCCACG 59.548 55.000 0.00 0.00 0.00 4.94
276 297 0.398696 ATAACCAATCGCCGGGCATA 59.601 50.000 20.71 6.68 0.00 3.14
353 374 0.248990 CAGAGCAGAGATCCGTCAGC 60.249 60.000 0.00 0.00 0.00 4.26
359 380 1.882167 GAGATCCGTCAGCAGCAGC 60.882 63.158 0.00 0.00 42.56 5.25
392 413 4.712051 AAACGGAACCTAGGGTTTAAGT 57.288 40.909 14.81 2.64 46.95 2.24
395 416 2.289819 CGGAACCTAGGGTTTAAGTGCA 60.290 50.000 14.81 0.00 46.95 4.57
400 421 1.004277 CTAGGGTTTAAGTGCAGGGCA 59.996 52.381 0.00 0.00 35.60 5.36
445 469 4.754667 GGCGGTCTTGGGGACGAC 62.755 72.222 0.00 0.00 45.35 4.34
751 795 2.099062 GCGCCAAGATTCGTGCAG 59.901 61.111 0.00 0.00 35.57 4.41
758 804 0.250513 AAGATTCGTGCAGGAGTCCC 59.749 55.000 23.28 5.59 0.00 4.46
788 842 3.237741 CCCCTCGGCTCAGATCCC 61.238 72.222 0.00 0.00 0.00 3.85
789 843 3.610669 CCCTCGGCTCAGATCCCG 61.611 72.222 2.05 2.05 45.64 5.14
795 849 2.430610 GGCTCAGATCCCGCTCACT 61.431 63.158 0.00 0.00 0.00 3.41
799 853 3.842923 AGATCCCGCTCACTGCCG 61.843 66.667 0.00 0.00 38.78 5.69
810 864 3.484806 ACTGCCGTGTGGGTCCAA 61.485 61.111 0.00 0.00 38.44 3.53
816 870 2.418356 GTGTGGGTCCAACGTCGA 59.582 61.111 0.00 0.00 0.00 4.20
857 911 3.080647 GGCTATCCGTTCCCAAGTG 57.919 57.895 0.00 0.00 0.00 3.16
858 912 0.539986 GGCTATCCGTTCCCAAGTGA 59.460 55.000 0.00 0.00 0.00 3.41
859 913 1.065709 GGCTATCCGTTCCCAAGTGAA 60.066 52.381 0.00 0.00 0.00 3.18
860 914 2.280628 GCTATCCGTTCCCAAGTGAAG 58.719 52.381 0.00 0.00 0.00 3.02
861 915 2.354805 GCTATCCGTTCCCAAGTGAAGT 60.355 50.000 0.00 0.00 0.00 3.01
862 916 2.474410 ATCCGTTCCCAAGTGAAGTC 57.526 50.000 0.00 0.00 0.00 3.01
864 918 0.949105 CCGTTCCCAAGTGAAGTCGG 60.949 60.000 0.00 0.00 30.67 4.79
867 921 2.546373 CGTTCCCAAGTGAAGTCGGTAA 60.546 50.000 0.00 0.00 0.00 2.85
868 922 3.671716 GTTCCCAAGTGAAGTCGGTAAT 58.328 45.455 0.00 0.00 0.00 1.89
869 923 3.604875 TCCCAAGTGAAGTCGGTAATC 57.395 47.619 0.00 0.00 0.00 1.75
870 924 2.901192 TCCCAAGTGAAGTCGGTAATCA 59.099 45.455 0.00 0.00 0.00 2.57
871 925 3.517901 TCCCAAGTGAAGTCGGTAATCAT 59.482 43.478 0.00 0.00 0.00 2.45
873 927 4.503910 CCAAGTGAAGTCGGTAATCATCA 58.496 43.478 0.00 0.00 0.00 3.07
874 928 5.118990 CCAAGTGAAGTCGGTAATCATCAT 58.881 41.667 0.00 0.00 0.00 2.45
875 929 5.235186 CCAAGTGAAGTCGGTAATCATCATC 59.765 44.000 0.00 0.00 0.00 2.92
876 930 4.611943 AGTGAAGTCGGTAATCATCATCG 58.388 43.478 0.00 0.00 0.00 3.84
877 931 4.098044 AGTGAAGTCGGTAATCATCATCGT 59.902 41.667 0.00 0.00 0.00 3.73
878 932 4.441415 GTGAAGTCGGTAATCATCATCGTC 59.559 45.833 0.00 0.00 0.00 4.20
879 933 3.644884 AGTCGGTAATCATCATCGTCC 57.355 47.619 0.00 0.00 0.00 4.79
880 934 3.223435 AGTCGGTAATCATCATCGTCCT 58.777 45.455 0.00 0.00 0.00 3.85
881 935 4.395625 AGTCGGTAATCATCATCGTCCTA 58.604 43.478 0.00 0.00 0.00 2.94
882 936 4.825634 AGTCGGTAATCATCATCGTCCTAA 59.174 41.667 0.00 0.00 0.00 2.69
886 940 7.811236 GTCGGTAATCATCATCGTCCTAATAAA 59.189 37.037 0.00 0.00 0.00 1.40
894 948 5.925509 TCATCGTCCTAATAAAAAGGAGGG 58.074 41.667 10.87 0.00 45.13 4.30
897 951 4.784300 TCGTCCTAATAAAAAGGAGGGGAA 59.216 41.667 10.87 0.00 45.13 3.97
901 955 6.158169 GTCCTAATAAAAAGGAGGGGAAGAGA 59.842 42.308 0.00 0.00 43.81 3.10
1397 1457 1.827399 AACGACGCCTGATCCTTGGT 61.827 55.000 0.00 0.00 0.00 3.67
1399 1459 2.045926 ACGCCTGATCCTTGGTGC 60.046 61.111 9.15 0.00 37.35 5.01
1402 1462 2.276740 CCTGATCCTTGGTGCCCC 59.723 66.667 0.00 0.00 0.00 5.80
1404 1464 2.933287 TGATCCTTGGTGCCCCGT 60.933 61.111 0.00 0.00 0.00 5.28
1407 1469 2.764637 GATCCTTGGTGCCCCGTGTT 62.765 60.000 0.00 0.00 0.00 3.32
1521 1585 7.448161 GGTGGTTCCATATTGATGATGAACATA 59.552 37.037 0.00 0.00 36.61 2.29
1522 1586 8.509690 GTGGTTCCATATTGATGATGAACATAG 58.490 37.037 0.00 0.00 39.56 2.23
1531 1632 3.391506 TGATGAACATAGCTCGGATGG 57.608 47.619 0.00 0.00 0.00 3.51
1551 1652 8.673711 CGGATGGAACTTGAATTTGATACTTTA 58.326 33.333 0.00 0.00 0.00 1.85
1577 1680 3.898123 AGTAGGTATATCTGTGCTGTGGG 59.102 47.826 0.00 0.00 0.00 4.61
1586 1689 0.822944 TGTGCTGTGGGTGTCAATGG 60.823 55.000 0.00 0.00 0.00 3.16
1591 1694 1.072173 CTGTGGGTGTCAATGGTCTGA 59.928 52.381 0.00 0.00 0.00 3.27
1602 1705 2.689983 CAATGGTCTGATAAACAGGGGC 59.310 50.000 0.00 0.00 45.76 5.80
1613 1716 3.121030 CAGGGGCGTTCGCTTGAG 61.121 66.667 16.40 2.21 36.43 3.02
1618 1721 0.521735 GGGCGTTCGCTTGAGATTTT 59.478 50.000 16.40 0.00 0.00 1.82
1667 1797 9.964354 ATACATTAAGCAGCTGGAATATATTGA 57.036 29.630 17.12 0.00 0.00 2.57
1691 1821 2.476854 GGATTCGTGCTGCTTGATGTTC 60.477 50.000 0.00 0.00 0.00 3.18
1726 1859 5.268387 TGATTTAGGTGGGTGTATTTGCAT 58.732 37.500 0.00 0.00 0.00 3.96
1763 1896 4.154737 TGATGTTCTTGCTGTGTGCTTATC 59.845 41.667 0.00 0.00 43.37 1.75
1771 1904 2.430465 CTGTGTGCTTATCAGGCTGTT 58.570 47.619 15.27 9.00 0.00 3.16
1805 1952 6.914215 GCTGTTATGTTGGATGTGTATGAATG 59.086 38.462 0.00 0.00 0.00 2.67
1825 1972 8.929827 TGAATGTATGATTATTGCTTGTTTGG 57.070 30.769 0.00 0.00 0.00 3.28
1826 1973 7.492020 TGAATGTATGATTATTGCTTGTTTGGC 59.508 33.333 0.00 0.00 0.00 4.52
1828 1975 3.229276 TGATTATTGCTTGTTTGGCCG 57.771 42.857 0.00 0.00 0.00 6.13
1832 1997 4.585955 TTATTGCTTGTTTGGCCGTAAA 57.414 36.364 0.00 0.00 0.00 2.01
1834 1999 2.500509 TGCTTGTTTGGCCGTAAAAG 57.499 45.000 0.00 0.00 0.00 2.27
1845 2010 2.093658 GGCCGTAAAAGATGACTCCAGA 60.094 50.000 0.00 0.00 0.00 3.86
1862 2027 3.907474 TCCAGAGATGGGTCACTTTTGTA 59.093 43.478 0.00 0.00 0.00 2.41
1866 2031 6.484643 CCAGAGATGGGTCACTTTTGTATATG 59.515 42.308 0.00 0.00 0.00 1.78
1905 2079 6.875195 CCAATTTATGTTTCTTTGGCTGTGAT 59.125 34.615 0.00 0.00 31.29 3.06
1910 2084 5.947228 TGTTTCTTTGGCTGTGATTAGAG 57.053 39.130 0.00 0.00 0.00 2.43
1911 2085 4.216257 TGTTTCTTTGGCTGTGATTAGAGC 59.784 41.667 0.00 0.00 42.17 4.09
1912 2086 3.988976 TCTTTGGCTGTGATTAGAGCT 57.011 42.857 6.58 0.00 42.49 4.09
1913 2087 5.420725 TTCTTTGGCTGTGATTAGAGCTA 57.579 39.130 6.58 0.00 42.49 3.32
1914 2088 5.016051 TCTTTGGCTGTGATTAGAGCTAG 57.984 43.478 6.58 2.88 42.49 3.42
1984 2159 3.877559 TGCTAGTGCTGATTGTGCTATT 58.122 40.909 0.00 0.00 40.48 1.73
1985 2160 4.264253 TGCTAGTGCTGATTGTGCTATTT 58.736 39.130 0.00 0.00 40.48 1.40
1986 2161 4.333649 TGCTAGTGCTGATTGTGCTATTTC 59.666 41.667 0.00 0.00 40.48 2.17
1998 2173 4.071423 TGTGCTATTTCAACTTGCTGCTA 58.929 39.130 0.00 0.00 0.00 3.49
2008 2183 7.539712 TTCAACTTGCTGCTATGTAGTATTC 57.460 36.000 0.00 0.00 0.00 1.75
2028 2204 4.300189 TCGTGTTTTCATGGGTTTCTTG 57.700 40.909 0.00 0.00 37.42 3.02
2115 2291 4.046286 TGTGGGATGGCTGTTTCTTAAT 57.954 40.909 0.00 0.00 0.00 1.40
2125 2301 5.068987 TGGCTGTTTCTTAATTTTGCAGAGT 59.931 36.000 0.00 0.00 0.00 3.24
2164 2340 7.330900 ACTCACAATCATGAAATCTTGGATC 57.669 36.000 0.00 0.00 0.00 3.36
2166 2342 7.067129 ACTCACAATCATGAAATCTTGGATCTG 59.933 37.037 0.00 0.00 0.00 2.90
2237 2415 3.701040 GCATTGTGGGGATCAGTATGTTT 59.299 43.478 0.00 0.00 37.40 2.83
2263 2441 1.848652 TGTAGTGTGGGTCTAGGAGC 58.151 55.000 0.00 0.00 0.00 4.70
2276 2454 1.751351 CTAGGAGCCGATGAACTGTCA 59.249 52.381 0.00 0.00 38.41 3.58
2278 2456 2.388735 AGGAGCCGATGAACTGTCATA 58.611 47.619 0.00 0.00 44.83 2.15
2284 2462 6.260050 GGAGCCGATGAACTGTCATAAATTAA 59.740 38.462 0.00 0.00 44.83 1.40
2292 2470 8.334263 TGAACTGTCATAAATTAAGTGCATCA 57.666 30.769 0.00 0.00 0.00 3.07
2300 2478 5.443185 AAATTAAGTGCATCATGGGATCG 57.557 39.130 0.00 0.00 0.00 3.69
2302 2480 0.820891 AAGTGCATCATGGGATCGCC 60.821 55.000 7.38 0.12 31.03 5.54
2317 2495 2.679355 TCGCCGTTTCTTGATTTGTG 57.321 45.000 0.00 0.00 0.00 3.33
2355 2533 3.760684 AGCCTGTGGACAATCTTGAATTC 59.239 43.478 0.00 0.00 0.00 2.17
2357 2535 3.127548 CCTGTGGACAATCTTGAATTCGG 59.872 47.826 0.04 0.00 0.00 4.30
2382 2560 7.824779 GGAGACTACATCTGAATTGGTACTTTT 59.175 37.037 0.00 0.00 38.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 6.576313 CGCTGTTATTTATGATTCATGAGCAC 59.424 38.462 9.46 1.18 0.00 4.40
28 29 9.651718 CTTTACTTCCGCTGTTATTTATGATTC 57.348 33.333 0.00 0.00 0.00 2.52
37 38 3.670625 TGCACTTTACTTCCGCTGTTAT 58.329 40.909 0.00 0.00 0.00 1.89
38 39 3.114668 TGCACTTTACTTCCGCTGTTA 57.885 42.857 0.00 0.00 0.00 2.41
77 79 1.266989 GCAAAGTCGTGGAAAGAAGGG 59.733 52.381 0.00 0.00 0.00 3.95
82 84 1.268539 GGTGTGCAAAGTCGTGGAAAG 60.269 52.381 0.00 0.00 0.00 2.62
85 87 0.393132 TTGGTGTGCAAAGTCGTGGA 60.393 50.000 0.00 0.00 0.00 4.02
109 119 5.649782 ACTTTGTTGAATTAGCTGGGATG 57.350 39.130 0.00 0.00 0.00 3.51
110 120 6.152831 GGTAACTTTGTTGAATTAGCTGGGAT 59.847 38.462 0.00 0.00 0.00 3.85
168 189 3.832527 ACATTTAGCTTCCTTGTGTGGT 58.167 40.909 0.00 0.00 0.00 4.16
169 190 4.853924 AACATTTAGCTTCCTTGTGTGG 57.146 40.909 0.00 0.00 0.00 4.17
229 250 6.743575 ATTGCCGATAGTATGCTTATTTCC 57.256 37.500 0.00 0.00 0.00 3.13
266 287 2.666190 CTGGATGTATGCCCGGCG 60.666 66.667 4.58 0.00 0.00 6.46
276 297 2.180276 GTACAGGTGAGGACTGGATGT 58.820 52.381 0.00 0.00 40.23 3.06
353 374 3.720818 CGTTTAATTAATCGCTGCTGCTG 59.279 43.478 14.03 0.77 36.97 4.41
359 380 5.479716 AGGTTCCGTTTAATTAATCGCTG 57.520 39.130 18.84 9.68 0.00 5.18
410 431 1.470112 GCCGAGAACTTCAGGTAGCTC 60.470 57.143 0.00 0.00 0.00 4.09
445 469 3.417275 ATGGAGCTCTTCGCCGACG 62.417 63.158 14.64 0.00 40.39 5.12
659 697 0.172352 CTCGAAGCTTCTTCCGCTCT 59.828 55.000 23.50 0.00 36.56 4.09
661 699 0.318762 AACTCGAAGCTTCTTCCGCT 59.681 50.000 23.50 1.28 39.94 5.52
795 849 4.920112 CGTTGGACCCACACGGCA 62.920 66.667 12.59 0.00 33.26 5.69
799 853 1.952635 GTCGACGTTGGACCCACAC 60.953 63.158 0.00 0.00 0.00 3.82
852 906 5.051441 CGATGATGATTACCGACTTCACTTG 60.051 44.000 0.00 0.00 0.00 3.16
857 911 3.982058 GGACGATGATGATTACCGACTTC 59.018 47.826 0.00 0.00 0.00 3.01
858 912 3.637229 AGGACGATGATGATTACCGACTT 59.363 43.478 0.00 0.00 0.00 3.01
859 913 3.223435 AGGACGATGATGATTACCGACT 58.777 45.455 0.00 0.00 0.00 4.18
860 914 3.644884 AGGACGATGATGATTACCGAC 57.355 47.619 0.00 0.00 0.00 4.79
861 915 5.977489 ATTAGGACGATGATGATTACCGA 57.023 39.130 0.00 0.00 0.00 4.69
862 916 8.528917 TTTTATTAGGACGATGATGATTACCG 57.471 34.615 0.00 0.00 0.00 4.02
867 921 7.880195 CCTCCTTTTTATTAGGACGATGATGAT 59.120 37.037 0.00 0.00 36.88 2.45
868 922 7.217200 CCTCCTTTTTATTAGGACGATGATGA 58.783 38.462 0.00 0.00 36.88 2.92
869 923 6.428159 CCCTCCTTTTTATTAGGACGATGATG 59.572 42.308 0.00 0.00 36.88 3.07
870 924 6.465894 CCCCTCCTTTTTATTAGGACGATGAT 60.466 42.308 0.00 0.00 36.88 2.45
871 925 5.163237 CCCCTCCTTTTTATTAGGACGATGA 60.163 44.000 0.00 0.00 36.88 2.92
873 927 4.973211 TCCCCTCCTTTTTATTAGGACGAT 59.027 41.667 0.00 0.00 36.88 3.73
874 928 4.364470 TCCCCTCCTTTTTATTAGGACGA 58.636 43.478 0.00 0.00 36.88 4.20
875 929 4.765813 TCCCCTCCTTTTTATTAGGACG 57.234 45.455 0.00 0.00 36.88 4.79
876 930 6.158169 TCTCTTCCCCTCCTTTTTATTAGGAC 59.842 42.308 0.00 0.00 36.88 3.85
877 931 6.277036 TCTCTTCCCCTCCTTTTTATTAGGA 58.723 40.000 0.00 0.00 39.46 2.94
878 932 6.576778 TCTCTTCCCCTCCTTTTTATTAGG 57.423 41.667 0.00 0.00 0.00 2.69
879 933 7.057264 CCTTCTCTTCCCCTCCTTTTTATTAG 58.943 42.308 0.00 0.00 0.00 1.73
880 934 6.738563 TCCTTCTCTTCCCCTCCTTTTTATTA 59.261 38.462 0.00 0.00 0.00 0.98
881 935 5.555941 TCCTTCTCTTCCCCTCCTTTTTATT 59.444 40.000 0.00 0.00 0.00 1.40
882 936 5.108752 TCCTTCTCTTCCCCTCCTTTTTAT 58.891 41.667 0.00 0.00 0.00 1.40
886 940 2.743131 TCCTTCTCTTCCCCTCCTTT 57.257 50.000 0.00 0.00 0.00 3.11
894 948 2.239150 GGGGGTAGTTTCCTTCTCTTCC 59.761 54.545 0.00 0.00 0.00 3.46
897 951 2.735259 TGGGGGTAGTTTCCTTCTCT 57.265 50.000 0.00 0.00 0.00 3.10
901 955 2.645797 TCGATTTGGGGGTAGTTTCCTT 59.354 45.455 0.00 0.00 0.00 3.36
928 983 3.626924 GGCTCGGTGGTGTCTGGT 61.627 66.667 0.00 0.00 0.00 4.00
1521 1585 3.356529 AATTCAAGTTCCATCCGAGCT 57.643 42.857 0.00 0.00 32.59 4.09
1522 1586 3.440173 TCAAATTCAAGTTCCATCCGAGC 59.560 43.478 0.00 0.00 0.00 5.03
1551 1652 7.256332 CCCACAGCACAGATATACCTACTAATT 60.256 40.741 0.00 0.00 0.00 1.40
1568 1669 0.823356 ACCATTGACACCCACAGCAC 60.823 55.000 0.00 0.00 0.00 4.40
1577 1680 4.396166 CCCTGTTTATCAGACCATTGACAC 59.604 45.833 0.00 0.00 46.27 3.67
1586 1689 2.007608 GAACGCCCCTGTTTATCAGAC 58.992 52.381 0.00 0.00 46.27 3.51
1591 1694 0.322187 AAGCGAACGCCCCTGTTTAT 60.322 50.000 15.44 0.00 43.17 1.40
1602 1705 6.193410 CACATATCAAAAATCTCAAGCGAACG 59.807 38.462 0.00 0.00 0.00 3.95
1613 1716 9.089601 TGAACAATCATGCACATATCAAAAATC 57.910 29.630 0.00 0.00 0.00 2.17
1618 1721 7.576861 ATCTGAACAATCATGCACATATCAA 57.423 32.000 0.00 0.00 34.37 2.57
1665 1795 0.610174 AAGCAGCACGAATCCTCTCA 59.390 50.000 0.00 0.00 0.00 3.27
1667 1797 0.610174 TCAAGCAGCACGAATCCTCT 59.390 50.000 0.00 0.00 0.00 3.69
1691 1821 7.067008 CACCCACCTAAATCAGTAGTAATTTGG 59.933 40.741 0.00 0.00 0.00 3.28
1726 1859 6.210796 CAAGAACATCAGAGCAACATCAAAA 58.789 36.000 0.00 0.00 0.00 2.44
1763 1896 0.457035 AGCAAACACACAACAGCCTG 59.543 50.000 0.00 0.00 0.00 4.85
1771 1904 3.696548 TCCAACATAACAGCAAACACACA 59.303 39.130 0.00 0.00 0.00 3.72
1805 1952 4.739716 CGGCCAAACAAGCAATAATCATAC 59.260 41.667 2.24 0.00 0.00 2.39
1825 1972 3.119101 TCTCTGGAGTCATCTTTTACGGC 60.119 47.826 0.00 0.00 0.00 5.68
1826 1973 4.720649 TCTCTGGAGTCATCTTTTACGG 57.279 45.455 0.00 0.00 0.00 4.02
1828 1975 5.104735 ACCCATCTCTGGAGTCATCTTTTAC 60.105 44.000 0.00 0.00 46.37 2.01
1832 1997 3.037549 GACCCATCTCTGGAGTCATCTT 58.962 50.000 0.00 0.00 46.37 2.40
1834 1999 2.102252 GTGACCCATCTCTGGAGTCATC 59.898 54.545 14.68 8.40 45.86 2.92
1845 2010 9.920946 AATAACATATACAAAAGTGACCCATCT 57.079 29.630 0.00 0.00 0.00 2.90
1873 2038 7.602265 GCCAAAGAAACATAAATTGGTACATGT 59.398 33.333 2.69 2.69 41.98 3.21
1885 2050 7.362056 GCTCTAATCACAGCCAAAGAAACATAA 60.362 37.037 0.00 0.00 0.00 1.90
1894 2068 4.467795 ACTCTAGCTCTAATCACAGCCAAA 59.532 41.667 0.00 0.00 36.17 3.28
1905 2079 8.512956 CACTAACAAACTACACTCTAGCTCTAA 58.487 37.037 0.00 0.00 0.00 2.10
1910 2084 5.471257 AGCACTAACAAACTACACTCTAGC 58.529 41.667 0.00 0.00 0.00 3.42
1911 2085 6.678878 TGAGCACTAACAAACTACACTCTAG 58.321 40.000 0.00 0.00 0.00 2.43
1912 2086 6.644248 TGAGCACTAACAAACTACACTCTA 57.356 37.500 0.00 0.00 0.00 2.43
1913 2087 5.531122 TGAGCACTAACAAACTACACTCT 57.469 39.130 0.00 0.00 0.00 3.24
1914 2088 5.389935 GCATGAGCACTAACAAACTACACTC 60.390 44.000 0.00 0.00 41.58 3.51
1984 2159 6.255670 CGAATACTACATAGCAGCAAGTTGAA 59.744 38.462 7.16 0.00 0.00 2.69
1985 2160 5.748630 CGAATACTACATAGCAGCAAGTTGA 59.251 40.000 7.16 0.00 0.00 3.18
1986 2161 5.520288 ACGAATACTACATAGCAGCAAGTTG 59.480 40.000 0.00 0.00 0.00 3.16
1998 2173 6.177610 ACCCATGAAAACACGAATACTACAT 58.822 36.000 0.00 0.00 0.00 2.29
2008 2183 4.290155 CTCAAGAAACCCATGAAAACACG 58.710 43.478 0.00 0.00 0.00 4.49
2028 2204 2.223923 ACTAGACAAGCCATCATCGCTC 60.224 50.000 0.00 0.00 34.84 5.03
2115 2291 5.185635 CCCCTCAAAATCATACTCTGCAAAA 59.814 40.000 0.00 0.00 0.00 2.44
2150 2326 4.166725 TGCTACCCAGATCCAAGATTTCAT 59.833 41.667 0.00 0.00 0.00 2.57
2164 2340 7.880195 AGTAAGATATGCTAATTTGCTACCCAG 59.120 37.037 12.99 0.00 0.00 4.45
2166 2342 7.661847 ACAGTAAGATATGCTAATTTGCTACCC 59.338 37.037 12.99 1.14 0.00 3.69
2237 2415 4.019681 CCTAGACCCACACTACAAATCCAA 60.020 45.833 0.00 0.00 0.00 3.53
2263 2441 6.907212 GCACTTAATTTATGACAGTTCATCGG 59.093 38.462 0.00 0.00 41.87 4.18
2264 2442 7.463544 TGCACTTAATTTATGACAGTTCATCG 58.536 34.615 0.00 0.00 41.87 3.84
2276 2454 6.349611 GCGATCCCATGATGCACTTAATTTAT 60.350 38.462 0.00 0.00 0.00 1.40
2278 2456 4.261741 GCGATCCCATGATGCACTTAATTT 60.262 41.667 0.00 0.00 0.00 1.82
2284 2462 1.228063 GGCGATCCCATGATGCACT 60.228 57.895 0.00 0.00 31.03 4.40
2292 2470 0.251916 TCAAGAAACGGCGATCCCAT 59.748 50.000 16.62 0.00 0.00 4.00
2300 2478 3.730715 CACTTCACAAATCAAGAAACGGC 59.269 43.478 0.00 0.00 0.00 5.68
2302 2480 5.568482 TCACACTTCACAAATCAAGAAACG 58.432 37.500 0.00 0.00 0.00 3.60
2317 2495 3.196685 ACAGGCTCCTAGAATCACACTTC 59.803 47.826 0.00 0.00 0.00 3.01
2355 2533 4.392921 ACCAATTCAGATGTAGTCTCCG 57.607 45.455 0.00 0.00 34.00 4.63
2357 2535 8.660373 CAAAAGTACCAATTCAGATGTAGTCTC 58.340 37.037 0.00 0.00 34.00 3.36


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

AutoCloner maintained by Alex Coulton.