Multiple sequence alignment - TraesCS4A01G148000

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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 TraesCS4A01G148000 chr4A 100.000 2315 0 0 1 2315 275124718 275122404 0.000000e+00 4276.0
1 TraesCS4A01G148000 chr4A 93.923 1695 101 1 1 1693 275116511 275114817 0.000000e+00 2558.0
2 TraesCS4A01G148000 chr4A 92.040 1696 130 3 1 1696 275158671 275156981 0.000000e+00 2379.0
3 TraesCS4A01G148000 chr4A 89.078 1648 128 29 2 1636 414598688 414600296 0.000000e+00 1999.0
4 TraesCS4A01G148000 chr4A 87.485 1646 140 33 5 1632 281034772 281033175 0.000000e+00 1838.0
5 TraesCS4A01G148000 chr4A 93.227 502 17 4 1817 2315 275114825 275114338 0.000000e+00 723.0
6 TraesCS4A01G148000 chr4A 94.159 428 18 7 1893 2315 275144370 275143945 0.000000e+00 645.0
7 TraesCS4A01G148000 chr4A 98.413 126 2 0 1693 1818 665176831 665176956 2.990000e-54 222.0
8 TraesCS4A01G148000 chr4A 89.888 89 9 0 1817 1905 275156991 275156903 5.230000e-22 115.0
9 TraesCS4A01G148000 chr4A 88.660 97 4 6 1544 1636 184667712 184667805 6.760000e-21 111.0
10 TraesCS4A01G148000 chr4A 98.182 55 1 0 1827 1881 408766173 408766227 1.890000e-16 97.1
11 TraesCS4A01G148000 chr4A 86.905 84 10 1 1817 1899 408774469 408774552 2.450000e-15 93.5
12 TraesCS4A01G148000 chr4A 91.176 68 5 1 1487 1554 355482228 355482162 8.810000e-15 91.6
13 TraesCS4A01G148000 chr6A 91.730 919 71 5 725 1642 133590278 133589364 0.000000e+00 1271.0
14 TraesCS4A01G148000 chr6A 91.621 919 71 6 725 1642 133582337 133581424 0.000000e+00 1266.0
15 TraesCS4A01G148000 chr6A 86.621 583 60 16 2 575 235111550 235112123 1.510000e-176 628.0
16 TraesCS4A01G148000 chr6A 86.278 583 62 17 2 575 235102083 235102656 3.270000e-173 617.0
17 TraesCS4A01G148000 chr6A 86.278 583 61 17 2 575 235093448 235094020 1.180000e-172 616.0
18 TraesCS4A01G148000 chr6A 92.718 206 12 3 1438 1642 413238994 413238791 6.260000e-76 294.0
19 TraesCS4A01G148000 chr6A 92.965 199 11 3 1438 1635 413230746 413230550 1.050000e-73 287.0
20 TraesCS4A01G148000 chr6A 91.111 45 4 0 1817 1861 258388224 258388268 6.910000e-06 62.1
21 TraesCS4A01G148000 chr5A 88.998 918 91 4 559 1466 273242926 273243843 0.000000e+00 1127.0
22 TraesCS4A01G148000 chr5A 83.046 637 86 20 2 630 239338131 239338753 2.010000e-155 558.0
23 TraesCS4A01G148000 chr5A 96.203 79 2 1 1438 1516 291466236 291466159 6.710000e-26 128.0
24 TraesCS4A01G148000 chr3A 88.840 914 99 3 559 1471 380624448 380625359 0.000000e+00 1120.0
25 TraesCS4A01G148000 chr3A 89.872 859 84 3 615 1471 553232572 553233429 0.000000e+00 1101.0
26 TraesCS4A01G148000 chr3A 83.022 642 82 22 2 630 699349227 699349854 7.230000e-155 556.0
27 TraesCS4A01G148000 chr3A 88.701 354 26 12 1969 2315 368914455 368914801 9.890000e-114 420.0
28 TraesCS4A01G148000 chr3A 89.412 340 26 7 1981 2315 368922629 368922963 9.890000e-114 420.0
29 TraesCS4A01G148000 chr3A 90.030 331 24 7 1990 2315 371178149 371178475 9.890000e-114 420.0
30 TraesCS4A01G148000 chr3A 99.187 123 1 0 1694 1816 708952473 708952351 2.990000e-54 222.0
31 TraesCS4A01G148000 chr7A 84.399 641 81 15 2 629 226749716 226750350 1.520000e-171 612.0
32 TraesCS4A01G148000 chr7A 83.070 632 90 15 5 631 268874928 268874309 2.010000e-155 558.0
33 TraesCS4A01G148000 chr7A 89.851 335 26 7 1986 2315 350834067 350833736 7.650000e-115 424.0
34 TraesCS4A01G148000 chr7A 95.588 136 5 1 1681 1816 90372023 90371889 1.390000e-52 217.0
35 TraesCS4A01G148000 chr7A 92.308 65 5 0 1817 1881 527121432 527121496 2.450000e-15 93.5
36 TraesCS4A01G148000 chr2A 85.082 610 71 17 2 600 216060355 216060955 2.540000e-169 604.0
37 TraesCS4A01G148000 chr2A 83.412 639 89 14 2 631 216068530 216069160 5.550000e-161 577.0
38 TraesCS4A01G148000 chr2A 90.988 344 25 6 1974 2315 507810883 507810544 2.100000e-125 459.0
39 TraesCS4A01G148000 chr2A 89.535 344 29 7 1974 2315 476534211 476533873 1.640000e-116 429.0
40 TraesCS4A01G148000 chr2A 89.941 338 26 6 1981 2315 538600345 538600013 1.640000e-116 429.0
41 TraesCS4A01G148000 chr2B 99.200 125 1 0 1693 1817 492706896 492707020 2.310000e-55 226.0
42 TraesCS4A01G148000 chr1A 99.194 124 1 0 1693 1816 204838155 204838032 8.320000e-55 224.0
43 TraesCS4A01G148000 chr1A 89.024 82 6 3 1873 1951 503089233 503089152 5.260000e-17 99.0
44 TraesCS4A01G148000 chr5D 98.400 125 2 0 1694 1818 519818287 519818163 1.080000e-53 220.0
45 TraesCS4A01G148000 chr1B 98.400 125 2 0 1694 1818 15344007 15343883 1.080000e-53 220.0
46 TraesCS4A01G148000 chr6B 94.891 137 5 2 1700 1836 523883278 523883412 1.800000e-51 213.0
47 TraesCS4A01G148000 chr7B 90.968 155 6 3 1667 1816 2932987 2932836 3.900000e-48 202.0


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 TraesCS4A01G148000 chr4A 275122404 275124718 2314 True 4276.0 4276 100.000 1 2315 1 chr4A.!!$R1 2314
1 TraesCS4A01G148000 chr4A 414598688 414600296 1608 False 1999.0 1999 89.078 2 1636 1 chr4A.!!$F4 1634
2 TraesCS4A01G148000 chr4A 281033175 281034772 1597 True 1838.0 1838 87.485 5 1632 1 chr4A.!!$R3 1627
3 TraesCS4A01G148000 chr4A 275114338 275116511 2173 True 1640.5 2558 93.575 1 2315 2 chr4A.!!$R5 2314
4 TraesCS4A01G148000 chr4A 275156903 275158671 1768 True 1247.0 2379 90.964 1 1905 2 chr4A.!!$R6 1904
5 TraesCS4A01G148000 chr6A 133589364 133590278 914 True 1271.0 1271 91.730 725 1642 1 chr6A.!!$R2 917
6 TraesCS4A01G148000 chr6A 133581424 133582337 913 True 1266.0 1266 91.621 725 1642 1 chr6A.!!$R1 917
7 TraesCS4A01G148000 chr6A 235111550 235112123 573 False 628.0 628 86.621 2 575 1 chr6A.!!$F3 573
8 TraesCS4A01G148000 chr6A 235102083 235102656 573 False 617.0 617 86.278 2 575 1 chr6A.!!$F2 573
9 TraesCS4A01G148000 chr6A 235093448 235094020 572 False 616.0 616 86.278 2 575 1 chr6A.!!$F1 573
10 TraesCS4A01G148000 chr5A 273242926 273243843 917 False 1127.0 1127 88.998 559 1466 1 chr5A.!!$F2 907
11 TraesCS4A01G148000 chr5A 239338131 239338753 622 False 558.0 558 83.046 2 630 1 chr5A.!!$F1 628
12 TraesCS4A01G148000 chr3A 380624448 380625359 911 False 1120.0 1120 88.840 559 1471 1 chr3A.!!$F4 912
13 TraesCS4A01G148000 chr3A 553232572 553233429 857 False 1101.0 1101 89.872 615 1471 1 chr3A.!!$F5 856
14 TraesCS4A01G148000 chr3A 699349227 699349854 627 False 556.0 556 83.022 2 630 1 chr3A.!!$F6 628
15 TraesCS4A01G148000 chr7A 226749716 226750350 634 False 612.0 612 84.399 2 629 1 chr7A.!!$F1 627
16 TraesCS4A01G148000 chr7A 268874309 268874928 619 True 558.0 558 83.070 5 631 1 chr7A.!!$R2 626
17 TraesCS4A01G148000 chr2A 216060355 216060955 600 False 604.0 604 85.082 2 600 1 chr2A.!!$F1 598
18 TraesCS4A01G148000 chr2A 216068530 216069160 630 False 577.0 577 83.412 2 631 1 chr2A.!!$F2 629

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
920 961 0.608035 GGCGTTCCCTGATTTGGACA 60.608 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1766 1822 0.037326 GCCATTCGACCACTGACTGA 60.037 55.0 0.0 0.0 0.0 3.41 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
295 330 1.076850 ATGCAATCGTCCATGGGCA 60.077 52.632 18.31 15.11 35.54 5.36
332 370 5.321516 GTTATACTTTCGAAGCGTGCAAAT 58.678 37.500 11.14 1.82 0.00 2.32
363 402 0.655733 CGTTCGGTGCAAAGTCAAGT 59.344 50.000 0.00 0.00 0.00 3.16
432 471 1.542987 GCTCTAGGGTCGACGGTAGAT 60.543 57.143 20.01 2.98 0.00 1.98
613 654 4.697756 CCAAGCCCTTCGCGGTCA 62.698 66.667 6.13 0.00 44.76 4.02
650 691 2.029623 GGTCTTCGGTGATAGTAGGCA 58.970 52.381 0.00 0.00 0.00 4.75
700 741 2.055838 GCGTAACACGTGTCTTCATCA 58.944 47.619 23.61 0.00 44.73 3.07
750 791 3.944055 ACTTGACGTATCTGAGTGCTT 57.056 42.857 0.00 0.00 0.00 3.91
855 896 3.106672 GACAGTTCCACATCGATCGTAC 58.893 50.000 15.94 3.64 0.00 3.67
920 961 0.608035 GGCGTTCCCTGATTTGGACA 60.608 55.000 0.00 0.00 0.00 4.02
966 1007 2.591715 GTGGTGCACGAAGGCAGT 60.592 61.111 11.45 0.00 45.96 4.40
971 1012 1.300931 TGCACGAAGGCAGTGAGAC 60.301 57.895 11.06 0.00 41.83 3.36
1201 1243 1.333636 AAGGCGGACATGGAGGAGAG 61.334 60.000 0.00 0.00 0.00 3.20
1312 1354 0.397254 CGATGGGGAGGTAGTGGAGT 60.397 60.000 0.00 0.00 0.00 3.85
1313 1355 1.133575 CGATGGGGAGGTAGTGGAGTA 60.134 57.143 0.00 0.00 0.00 2.59
1345 1388 1.376812 GAACCTACGGCCTGGTTGG 60.377 63.158 23.37 16.69 45.48 3.77
1358 1401 1.826487 GGTTGGTGCTGGTTCGGTT 60.826 57.895 0.00 0.00 0.00 4.44
1360 1403 1.826054 TTGGTGCTGGTTCGGTTGG 60.826 57.895 0.00 0.00 0.00 3.77
1435 1488 0.030705 AGCCTAGGCATGGAAGGAGA 60.031 55.000 34.70 0.00 44.88 3.71
1710 1766 4.475135 GGAAGCGGCTCCCCTGAC 62.475 72.222 1.45 0.00 0.00 3.51
1711 1767 4.821589 GAAGCGGCTCCCCTGACG 62.822 72.222 1.45 0.00 42.16 4.35
1754 1810 2.362889 CCATGTGGGCCTGTTCCC 60.363 66.667 4.53 0.00 46.73 3.97
1755 1811 2.362889 CATGTGGGCCTGTTCCCC 60.363 66.667 4.53 0.00 45.97 4.81
1756 1812 4.047125 ATGTGGGCCTGTTCCCCG 62.047 66.667 4.53 0.00 45.95 5.73
1758 1814 3.728373 GTGGGCCTGTTCCCCGAT 61.728 66.667 4.53 0.00 45.95 4.18
1759 1815 3.727258 TGGGCCTGTTCCCCGATG 61.727 66.667 4.53 0.00 45.95 3.84
1760 1816 4.506255 GGGCCTGTTCCCCGATGG 62.506 72.222 0.84 0.00 40.51 3.51
1776 1832 0.914644 ATGGGTCCATCAGTCAGTGG 59.085 55.000 0.00 0.00 36.82 4.00
1777 1833 0.473694 TGGGTCCATCAGTCAGTGGT 60.474 55.000 0.00 0.00 36.84 4.16
1778 1834 0.250513 GGGTCCATCAGTCAGTGGTC 59.749 60.000 0.00 0.00 36.84 4.02
1779 1835 0.108615 GGTCCATCAGTCAGTGGTCG 60.109 60.000 0.00 0.00 36.84 4.79
1780 1836 0.888619 GTCCATCAGTCAGTGGTCGA 59.111 55.000 0.00 0.00 36.84 4.20
1781 1837 1.272490 GTCCATCAGTCAGTGGTCGAA 59.728 52.381 0.00 0.00 36.84 3.71
1782 1838 2.093973 GTCCATCAGTCAGTGGTCGAAT 60.094 50.000 0.00 0.00 36.84 3.34
1783 1839 2.094026 TCCATCAGTCAGTGGTCGAATG 60.094 50.000 0.00 0.00 36.84 2.67
1784 1840 2.274437 CATCAGTCAGTGGTCGAATGG 58.726 52.381 0.00 0.00 0.00 3.16
1785 1841 0.037326 TCAGTCAGTGGTCGAATGGC 60.037 55.000 0.00 0.00 0.00 4.40
1786 1842 0.320683 CAGTCAGTGGTCGAATGGCA 60.321 55.000 0.00 0.00 0.00 4.92
1787 1843 0.320771 AGTCAGTGGTCGAATGGCAC 60.321 55.000 0.00 0.00 0.00 5.01
1788 1844 1.003839 TCAGTGGTCGAATGGCACC 60.004 57.895 0.00 0.00 0.00 5.01
1789 1845 2.040544 CAGTGGTCGAATGGCACCC 61.041 63.158 0.00 0.00 0.00 4.61
1790 1846 2.224159 AGTGGTCGAATGGCACCCT 61.224 57.895 0.00 0.00 0.00 4.34
1791 1847 2.040544 GTGGTCGAATGGCACCCTG 61.041 63.158 0.00 0.00 0.00 4.45
1792 1848 3.134127 GGTCGAATGGCACCCTGC 61.134 66.667 0.00 0.00 44.08 4.85
1809 1865 2.107141 CCGAACGGCAGAGGATCC 59.893 66.667 2.48 2.48 33.66 3.36
1810 1866 2.427245 CCGAACGGCAGAGGATCCT 61.427 63.158 16.13 16.13 33.66 3.24
1811 1867 1.066587 CGAACGGCAGAGGATCCTC 59.933 63.158 31.27 31.27 43.03 3.71
1812 1868 1.066587 GAACGGCAGAGGATCCTCG 59.933 63.158 31.51 26.20 46.90 4.63
1813 1869 1.668101 GAACGGCAGAGGATCCTCGT 61.668 60.000 31.51 24.57 46.90 4.18
1814 1870 1.668101 AACGGCAGAGGATCCTCGTC 61.668 60.000 31.51 25.76 46.90 4.20
1815 1871 2.851071 CGGCAGAGGATCCTCGTCC 61.851 68.421 31.51 30.77 46.90 4.79
1816 1872 2.503382 GGCAGAGGATCCTCGTCCC 61.503 68.421 31.51 27.06 46.90 4.46
1817 1873 1.456705 GCAGAGGATCCTCGTCCCT 60.457 63.158 31.51 14.67 46.90 4.20
1818 1874 1.743321 GCAGAGGATCCTCGTCCCTG 61.743 65.000 31.51 24.83 46.90 4.45
1819 1875 1.112315 CAGAGGATCCTCGTCCCTGG 61.112 65.000 31.51 14.81 46.90 4.45
1820 1876 1.230497 GAGGATCCTCGTCCCTGGA 59.770 63.158 25.78 0.00 39.17 3.86
1821 1877 0.825840 GAGGATCCTCGTCCCTGGAG 60.826 65.000 25.78 0.00 39.17 3.86
1868 1924 3.551407 GAGGGGATCGGGTGAGGC 61.551 72.222 0.00 0.00 0.00 4.70
1905 1961 2.610859 GGAGTGGGCCTTGGGAGA 60.611 66.667 4.53 0.00 0.00 3.71
1988 2047 1.334384 GGGCCTGGACTCTCTTCTCC 61.334 65.000 0.84 0.00 0.00 3.71
2035 2094 8.131731 CCTTTAACAAAAAGCATATAGAGGAGC 58.868 37.037 0.00 0.00 0.00 4.70
2102 2161 7.575343 CGGTTAAATTTCCCGGACTCATAAAAA 60.575 37.037 17.27 0.00 38.09 1.94
2225 2284 3.146066 TGGAGAGTCCAAAAATGTTCGG 58.854 45.455 0.00 0.00 45.00 4.30
2226 2285 3.181449 TGGAGAGTCCAAAAATGTTCGGA 60.181 43.478 0.00 0.00 45.00 4.55
2227 2286 3.818773 GGAGAGTCCAAAAATGTTCGGAA 59.181 43.478 0.00 0.00 36.28 4.30
2228 2287 4.459337 GGAGAGTCCAAAAATGTTCGGAAT 59.541 41.667 0.00 0.00 36.28 3.01
2229 2288 5.048013 GGAGAGTCCAAAAATGTTCGGAATT 60.048 40.000 0.00 0.00 36.28 2.17
2230 2289 6.405278 AGAGTCCAAAAATGTTCGGAATTT 57.595 33.333 0.00 0.00 0.00 1.82
2231 2290 6.816136 AGAGTCCAAAAATGTTCGGAATTTT 58.184 32.000 0.00 0.00 38.54 1.82
2242 2301 6.358118 TGTTCGGAATTTTATTGGAGATCG 57.642 37.500 0.00 0.00 0.00 3.69
2256 2315 2.548920 GGAGATCGGGAAAGCGATGAAT 60.549 50.000 0.00 0.00 0.00 2.57
2270 2329 3.670055 GCGATGAATGAAAAATATGGGCG 59.330 43.478 0.00 0.00 0.00 6.13
2309 2368 1.614903 TGAAGCAGGAAAAGGCATGTG 59.385 47.619 0.00 0.00 0.00 3.21
2310 2369 1.615392 GAAGCAGGAAAAGGCATGTGT 59.385 47.619 0.00 0.00 0.00 3.72
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
295 330 2.957006 AGTATAACCGCCGAGAATGACT 59.043 45.455 0.00 0.00 0.00 3.41
332 370 1.111116 ACCGAACGAGAACTGTCCCA 61.111 55.000 0.00 0.00 0.00 4.37
363 402 1.059692 CGTCGCGAGAACGTCTACTTA 59.940 52.381 10.24 0.00 45.01 2.24
650 691 4.202245 AGTTCGGCTACAACATGTGTAT 57.798 40.909 0.00 0.00 41.93 2.29
700 741 1.317613 TCGTGTGTACCACTACCGTT 58.682 50.000 11.21 0.00 42.20 4.44
721 762 3.127203 CAGATACGTCAAGTTCGACTCCT 59.873 47.826 0.00 0.00 33.54 3.69
723 764 4.142859 ACTCAGATACGTCAAGTTCGACTC 60.143 45.833 0.00 0.00 33.54 3.36
750 791 2.985282 AAGTACCACGACGCCCGA 60.985 61.111 4.79 0.00 41.76 5.14
855 896 3.861840 ACATCTACGAAACATGGACCTG 58.138 45.455 0.00 0.00 0.00 4.00
920 961 2.296471 CCCTTGTGTCGTTGACTAGACT 59.704 50.000 0.00 0.00 38.16 3.24
966 1007 1.350684 TGCATGCCACTTAAGGTCTCA 59.649 47.619 16.68 0.00 0.00 3.27
971 1012 0.456653 GCGTTGCATGCCACTTAAGG 60.457 55.000 18.68 10.88 0.00 2.69
1135 1177 4.385405 GCCTCTGCTCGCAGGTGT 62.385 66.667 17.93 0.00 43.75 4.16
1201 1243 2.123982 CCTGCCCATGCCCTTCTC 60.124 66.667 0.00 0.00 36.33 2.87
1226 1268 4.308458 TTCGTCCCTGCACCACCG 62.308 66.667 0.00 0.00 0.00 4.94
1289 1331 1.001760 ACTACCTCCCCATCGCTGT 59.998 57.895 0.00 0.00 0.00 4.40
1298 1340 0.105607 CCCCTACTCCACTACCTCCC 60.106 65.000 0.00 0.00 0.00 4.30
1345 1388 4.025401 CGCCAACCGAACCAGCAC 62.025 66.667 0.00 0.00 40.02 4.40
1435 1488 1.512735 GCCCCCTTCCTCTGTATCTT 58.487 55.000 0.00 0.00 0.00 2.40
1646 1702 2.196749 CTTGTCTTCCATCGATCCACG 58.803 52.381 0.00 0.00 44.09 4.94
1694 1750 4.821589 CGTCAGGGGAGCCGCTTC 62.822 72.222 3.01 0.00 37.10 3.86
1757 1813 0.914644 CCACTGACTGATGGACCCAT 59.085 55.000 0.32 0.32 38.34 4.00
1758 1814 0.473694 ACCACTGACTGATGGACCCA 60.474 55.000 0.00 0.00 39.46 4.51
1759 1815 0.250513 GACCACTGACTGATGGACCC 59.749 60.000 0.00 0.00 39.46 4.46
1760 1816 0.108615 CGACCACTGACTGATGGACC 60.109 60.000 0.00 0.00 39.46 4.46
1761 1817 0.888619 TCGACCACTGACTGATGGAC 59.111 55.000 0.00 0.00 39.46 4.02
1762 1818 1.627864 TTCGACCACTGACTGATGGA 58.372 50.000 0.00 0.00 39.46 3.41
1763 1819 2.274437 CATTCGACCACTGACTGATGG 58.726 52.381 0.00 0.00 42.13 3.51
1764 1820 2.274437 CCATTCGACCACTGACTGATG 58.726 52.381 0.00 0.00 0.00 3.07
1765 1821 1.406069 GCCATTCGACCACTGACTGAT 60.406 52.381 0.00 0.00 0.00 2.90
1766 1822 0.037326 GCCATTCGACCACTGACTGA 60.037 55.000 0.00 0.00 0.00 3.41
1767 1823 0.320683 TGCCATTCGACCACTGACTG 60.321 55.000 0.00 0.00 0.00 3.51
1768 1824 0.320771 GTGCCATTCGACCACTGACT 60.321 55.000 0.00 0.00 0.00 3.41
1769 1825 1.298859 GGTGCCATTCGACCACTGAC 61.299 60.000 0.00 0.00 31.97 3.51
1770 1826 1.003839 GGTGCCATTCGACCACTGA 60.004 57.895 0.00 0.00 31.97 3.41
1771 1827 2.040544 GGGTGCCATTCGACCACTG 61.041 63.158 0.00 0.00 33.48 3.66
1772 1828 2.224159 AGGGTGCCATTCGACCACT 61.224 57.895 0.00 0.00 33.48 4.00
1773 1829 2.040544 CAGGGTGCCATTCGACCAC 61.041 63.158 0.00 0.00 33.48 4.16
1774 1830 2.350895 CAGGGTGCCATTCGACCA 59.649 61.111 0.00 0.00 33.48 4.02
1775 1831 3.134127 GCAGGGTGCCATTCGACC 61.134 66.667 0.00 0.00 37.42 4.79
1792 1848 2.107141 GGATCCTCTGCCGTTCGG 59.893 66.667 3.84 6.90 0.00 4.30
1793 1849 1.066587 GAGGATCCTCTGCCGTTCG 59.933 63.158 31.11 0.00 39.80 3.95
1794 1850 1.066587 CGAGGATCCTCTGCCGTTC 59.933 63.158 33.70 11.23 40.69 3.95
1795 1851 1.668101 GACGAGGATCCTCTGCCGTT 61.668 60.000 33.70 15.24 40.69 4.44
1796 1852 2.043852 ACGAGGATCCTCTGCCGT 60.044 61.111 33.70 25.82 40.69 5.68
1797 1853 2.725008 GACGAGGATCCTCTGCCG 59.275 66.667 33.70 25.21 40.69 5.69
1798 1854 2.503382 GGGACGAGGATCCTCTGCC 61.503 68.421 33.70 30.91 40.69 4.85
1799 1855 1.456705 AGGGACGAGGATCCTCTGC 60.457 63.158 33.70 25.24 40.69 4.26
1800 1856 1.112315 CCAGGGACGAGGATCCTCTG 61.112 65.000 33.70 28.14 40.69 3.35
1801 1857 1.231641 CCAGGGACGAGGATCCTCT 59.768 63.158 33.70 22.77 40.69 3.69
1802 1858 0.825840 CTCCAGGGACGAGGATCCTC 60.826 65.000 29.15 29.15 38.95 3.71
1803 1859 1.231641 CTCCAGGGACGAGGATCCT 59.768 63.158 16.13 16.13 38.95 3.24
1804 1860 3.863606 CTCCAGGGACGAGGATCC 58.136 66.667 2.48 2.48 36.86 3.36
1815 1871 2.285668 TCTCCCTTGGCCTCCAGG 60.286 66.667 3.32 6.77 33.81 4.45
1816 1872 1.306482 TCTCTCCCTTGGCCTCCAG 60.306 63.158 3.32 0.00 33.81 3.86
1817 1873 1.306482 CTCTCTCCCTTGGCCTCCA 60.306 63.158 3.32 0.00 0.00 3.86
1818 1874 0.399806 ATCTCTCTCCCTTGGCCTCC 60.400 60.000 3.32 0.00 0.00 4.30
1819 1875 0.758123 CATCTCTCTCCCTTGGCCTC 59.242 60.000 3.32 0.00 0.00 4.70
1820 1876 0.693767 CCATCTCTCTCCCTTGGCCT 60.694 60.000 3.32 0.00 0.00 5.19
1821 1877 1.704007 CCCATCTCTCTCCCTTGGCC 61.704 65.000 0.00 0.00 0.00 5.36
1822 1878 0.692419 TCCCATCTCTCTCCCTTGGC 60.692 60.000 0.00 0.00 0.00 4.52
1823 1879 1.977129 GATCCCATCTCTCTCCCTTGG 59.023 57.143 0.00 0.00 0.00 3.61
1905 1961 3.680196 TCCCTCTACTGGGCCGGT 61.680 66.667 23.80 23.80 46.67 5.28
2018 2077 6.426587 TCCTTTTGCTCCTCTATATGCTTTT 58.573 36.000 0.00 0.00 0.00 2.27
2035 2094 2.398754 ACCCCCTCCTTTTCCTTTTG 57.601 50.000 0.00 0.00 0.00 2.44
2218 2277 6.017109 CCGATCTCCAATAAAATTCCGAACAT 60.017 38.462 0.00 0.00 0.00 2.71
2219 2278 5.295787 CCGATCTCCAATAAAATTCCGAACA 59.704 40.000 0.00 0.00 0.00 3.18
2220 2279 5.277828 CCCGATCTCCAATAAAATTCCGAAC 60.278 44.000 0.00 0.00 0.00 3.95
2221 2280 4.819630 CCCGATCTCCAATAAAATTCCGAA 59.180 41.667 0.00 0.00 0.00 4.30
2222 2281 4.101898 TCCCGATCTCCAATAAAATTCCGA 59.898 41.667 0.00 0.00 0.00 4.55
2223 2282 4.385825 TCCCGATCTCCAATAAAATTCCG 58.614 43.478 0.00 0.00 0.00 4.30
2224 2283 6.709018 TTTCCCGATCTCCAATAAAATTCC 57.291 37.500 0.00 0.00 0.00 3.01
2225 2284 6.209361 GCTTTCCCGATCTCCAATAAAATTC 58.791 40.000 0.00 0.00 0.00 2.17
2226 2285 5.221048 CGCTTTCCCGATCTCCAATAAAATT 60.221 40.000 0.00 0.00 0.00 1.82
2227 2286 4.275936 CGCTTTCCCGATCTCCAATAAAAT 59.724 41.667 0.00 0.00 0.00 1.82
2228 2287 3.625764 CGCTTTCCCGATCTCCAATAAAA 59.374 43.478 0.00 0.00 0.00 1.52
2229 2288 3.118555 TCGCTTTCCCGATCTCCAATAAA 60.119 43.478 0.00 0.00 31.36 1.40
2230 2289 2.432874 TCGCTTTCCCGATCTCCAATAA 59.567 45.455 0.00 0.00 31.36 1.40
2231 2290 2.036387 TCGCTTTCCCGATCTCCAATA 58.964 47.619 0.00 0.00 31.36 1.90
2242 2301 6.421801 CCATATTTTTCATTCATCGCTTTCCC 59.578 38.462 0.00 0.00 0.00 3.97
2256 2315 4.322349 CCCAAACTTCGCCCATATTTTTCA 60.322 41.667 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.