Multiple sequence alignment - TraesCS1D01G057600

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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 TraesCS1D01G057600 chr1D 100.000 2569 0 0 1 2569 37896572 37899140 0.000000e+00 4745.0
1 TraesCS1D01G057600 chr1D 85.714 140 14 4 1835 1968 555100 555239 2.660000e-30 143.0
2 TraesCS1D01G057600 chr1B 90.649 1294 65 21 522 1780 57712064 57713336 0.000000e+00 1668.0
3 TraesCS1D01G057600 chr1A 91.696 1120 48 11 537 1635 36839647 36840742 0.000000e+00 1511.0
4 TraesCS1D01G057600 chr1A 81.607 560 72 12 1889 2446 478358931 478359461 3.930000e-118 435.0
5 TraesCS1D01G057600 chr1A 96.078 102 3 1 1675 1775 36840740 36840841 5.690000e-37 165.0
6 TraesCS1D01G057600 chr4D 92.211 719 43 3 1822 2536 258257897 258257188 0.000000e+00 1005.0
7 TraesCS1D01G057600 chr6D 89.757 576 49 7 1856 2430 57828770 57828204 0.000000e+00 728.0
8 TraesCS1D01G057600 chr5D 91.885 419 18 5 75 493 564795236 564794834 2.870000e-159 571.0
9 TraesCS1D01G057600 chr5D 91.489 94 8 0 88 181 250078441 250078534 2.070000e-26 130.0
10 TraesCS1D01G057600 chr5D 92.000 75 5 1 3 77 564806090 564806017 1.260000e-18 104.0
11 TraesCS1D01G057600 chrUn 89.011 455 39 7 1841 2290 77769038 77769486 1.040000e-153 553.0
12 TraesCS1D01G057600 chrUn 92.135 178 6 6 2287 2461 77771197 77771369 7.100000e-61 244.0
13 TraesCS1D01G057600 chr4A 94.444 360 18 1 162 521 483955623 483955266 1.040000e-153 553.0
14 TraesCS1D01G057600 chr4A 81.640 561 70 15 1889 2446 558647983 558647453 3.930000e-118 435.0
15 TraesCS1D01G057600 chr4A 93.500 200 12 1 4 203 483955814 483955616 1.930000e-76 296.0
16 TraesCS1D01G057600 chr4A 92.593 81 5 1 2458 2538 531049929 531050008 5.810000e-22 115.0
17 TraesCS1D01G057600 chr4B 93.056 360 22 2 162 521 489018622 489018978 8.140000e-145 523.0
18 TraesCS1D01G057600 chr4B 93.500 200 12 1 4 203 489018431 489018629 1.930000e-76 296.0
19 TraesCS1D01G057600 chr4B 86.429 140 13 4 1835 1968 135221204 135221343 5.730000e-32 148.0
20 TraesCS1D01G057600 chr4B 96.491 57 2 0 1777 1833 97944760 97944816 7.570000e-16 95.3
21 TraesCS1D01G057600 chr6B 94.249 313 16 1 162 474 49395841 49396151 6.430000e-131 477.0
22 TraesCS1D01G057600 chr6B 93.500 200 12 1 4 203 49395650 49395848 1.930000e-76 296.0
23 TraesCS1D01G057600 chr6B 98.246 57 1 0 1777 1833 114507249 114507193 1.630000e-17 100.0
24 TraesCS1D01G057600 chr6A 81.342 611 77 15 1843 2446 551860473 551859893 1.800000e-126 462.0
25 TraesCS1D01G057600 chr6A 98.246 57 1 0 1779 1835 74633343 74633287 1.630000e-17 100.0
26 TraesCS1D01G057600 chr2A 81.786 560 71 12 1889 2446 753013927 753014457 8.440000e-120 440.0
27 TraesCS1D01G057600 chr2A 85.034 147 16 5 1846 1986 566615640 566615494 7.410000e-31 145.0
28 TraesCS1D01G057600 chr5A 81.250 560 74 13 1889 2446 493824236 493823706 8.500000e-115 424.0
29 TraesCS1D01G057600 chr5A 80.714 560 77 12 1889 2446 704840365 704840895 8.560000e-110 407.0
30 TraesCS1D01G057600 chr5A 81.122 196 32 5 14 206 491291961 491292154 4.430000e-33 152.0
31 TraesCS1D01G057600 chr7B 86.471 170 17 3 1844 2007 740571059 740571228 5.650000e-42 182.0
32 TraesCS1D01G057600 chr7B 92.754 69 3 2 1778 1846 399869535 399869469 5.850000e-17 99.0
33 TraesCS1D01G057600 chr7B 98.182 55 0 1 1779 1833 694079332 694079279 7.570000e-16 95.3
34 TraesCS1D01G057600 chr7B 95.000 60 2 1 1779 1838 696932165 696932107 2.720000e-15 93.5
35 TraesCS1D01G057600 chr5B 85.417 144 13 6 1838 1973 441444305 441444448 2.660000e-30 143.0
36 TraesCS1D01G057600 chr5B 98.182 55 1 0 1779 1833 457403167 457403221 2.100000e-16 97.1
37 TraesCS1D01G057600 chr3A 85.315 143 14 6 1838 1973 465840931 465840789 9.580000e-30 141.0
38 TraesCS1D01G057600 chr2B 94.915 59 3 0 1775 1833 406885037 406885095 2.720000e-15 93.5
39 TraesCS1D01G057600 chr3D 94.915 59 1 2 1777 1835 202383268 202383212 9.790000e-15 91.6


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 TraesCS1D01G057600 chr1D 37896572 37899140 2568 False 4745.0 4745 100.0000 1 2569 1 chr1D.!!$F2 2568
1 TraesCS1D01G057600 chr1B 57712064 57713336 1272 False 1668.0 1668 90.6490 522 1780 1 chr1B.!!$F1 1258
2 TraesCS1D01G057600 chr1A 36839647 36840841 1194 False 838.0 1511 93.8870 537 1775 2 chr1A.!!$F2 1238
3 TraesCS1D01G057600 chr1A 478358931 478359461 530 False 435.0 435 81.6070 1889 2446 1 chr1A.!!$F1 557
4 TraesCS1D01G057600 chr4D 258257188 258257897 709 True 1005.0 1005 92.2110 1822 2536 1 chr4D.!!$R1 714
5 TraesCS1D01G057600 chr6D 57828204 57828770 566 True 728.0 728 89.7570 1856 2430 1 chr6D.!!$R1 574
6 TraesCS1D01G057600 chrUn 77769038 77771369 2331 False 398.5 553 90.5730 1841 2461 2 chrUn.!!$F1 620
7 TraesCS1D01G057600 chr4A 558647453 558647983 530 True 435.0 435 81.6400 1889 2446 1 chr4A.!!$R1 557
8 TraesCS1D01G057600 chr4A 483955266 483955814 548 True 424.5 553 93.9720 4 521 2 chr4A.!!$R2 517
9 TraesCS1D01G057600 chr4B 489018431 489018978 547 False 409.5 523 93.2780 4 521 2 chr4B.!!$F3 517
10 TraesCS1D01G057600 chr6B 49395650 49396151 501 False 386.5 477 93.8745 4 474 2 chr6B.!!$F1 470
11 TraesCS1D01G057600 chr6A 551859893 551860473 580 True 462.0 462 81.3420 1843 2446 1 chr6A.!!$R2 603
12 TraesCS1D01G057600 chr2A 753013927 753014457 530 False 440.0 440 81.7860 1889 2446 1 chr2A.!!$F1 557
13 TraesCS1D01G057600 chr5A 493823706 493824236 530 True 424.0 424 81.2500 1889 2446 1 chr5A.!!$R1 557
14 TraesCS1D01G057600 chr5A 704840365 704840895 530 False 407.0 407 80.7140 1889 2446 1 chr5A.!!$F2 557

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
469 503 0.250901 ATAGATCCAACGCCCCATGC 60.251 55.0 0.0 0.0 0.0 4.06 F
1061 1098 0.456142 CTGCTCATCGTCGTTTCGGA 60.456 55.0 0.0 0.0 0.0 4.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1499 1576 0.526954 CATAGCGGCCGTAGTCGTTT 60.527 55.0 28.7 5.01 35.01 3.60 R
2538 4337 0.320771 GTCTCCGTGATGGCAGTTGT 60.321 55.0 0.0 0.00 37.80 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
21 22 4.852134 ACAACAACATGCATGCTTTCTA 57.148 36.364 26.53 0.00 0.00 2.10
24 25 6.225318 ACAACAACATGCATGCTTTCTAAAT 58.775 32.000 26.53 0.28 0.00 1.40
26 27 5.786311 ACAACATGCATGCTTTCTAAATGT 58.214 33.333 26.53 14.84 0.00 2.71
36 37 7.905493 GCATGCTTTCTAAATGTGTTACTAGTC 59.095 37.037 11.37 0.00 0.00 2.59
42 43 6.849502 TCTAAATGTGTTACTAGTCTCGTGG 58.150 40.000 0.00 0.00 0.00 4.94
68 69 3.745799 TCCTTTGTTTCGCCATGTCTTA 58.254 40.909 0.00 0.00 0.00 2.10
110 111 8.528044 TGAATAAAACCCTCACAGTTAGTTTT 57.472 30.769 0.00 0.00 41.87 2.43
167 168 2.227388 CTGTTGCCTGGTCTTGATGTTC 59.773 50.000 0.00 0.00 0.00 3.18
278 311 2.550830 AGTTGTAAGCACCCAGTCAG 57.449 50.000 0.00 0.00 0.00 3.51
281 314 0.685097 TGTAAGCACCCAGTCAGTCC 59.315 55.000 0.00 0.00 0.00 3.85
305 338 4.157289 ACATGTAGGTTACCAGACTGTACG 59.843 45.833 3.51 0.00 0.00 3.67
385 419 1.067354 CACATGCTTCTTTTGAGGGGC 60.067 52.381 0.00 0.00 0.00 5.80
407 441 2.738743 AGATGCCAATGTTACAAGGGG 58.261 47.619 8.82 3.28 0.00 4.79
450 484 4.726317 TGAATTGATCCAGTCCATTCCCTA 59.274 41.667 0.00 0.00 37.90 3.53
469 503 0.250901 ATAGATCCAACGCCCCATGC 60.251 55.000 0.00 0.00 0.00 4.06
493 527 1.860399 GCTGTAGCACCGTATCACTCG 60.860 57.143 0.00 0.00 41.59 4.18
497 531 1.389555 AGCACCGTATCACTCGATGA 58.610 50.000 0.00 0.00 43.13 2.92
523 557 2.979678 GAGCACAGGATATTTCCCCCTA 59.020 50.000 0.00 0.00 43.76 3.53
741 778 4.799564 TTTGATTGCCTTGGGACATTAC 57.200 40.909 0.00 0.00 39.30 1.89
762 799 2.471607 CGCACTAGCACGCACTTG 59.528 61.111 0.00 0.00 42.27 3.16
763 800 2.174349 GCACTAGCACGCACTTGC 59.826 61.111 0.00 0.00 43.34 4.01
966 1003 2.356330 CGAGGGAACTGAGGACTAGAGT 60.356 54.545 0.00 0.00 44.43 3.24
978 1015 3.117663 AGGACTAGAGTTAGAGGGAGCTG 60.118 52.174 0.00 0.00 0.00 4.24
979 1016 3.117813 GGACTAGAGTTAGAGGGAGCTGA 60.118 52.174 0.00 0.00 0.00 4.26
980 1017 4.447180 GGACTAGAGTTAGAGGGAGCTGAT 60.447 50.000 0.00 0.00 0.00 2.90
981 1018 4.725490 ACTAGAGTTAGAGGGAGCTGATC 58.275 47.826 0.00 0.00 0.00 2.92
1025 1062 2.100087 GCTCCAGTAGAGTTGGTAGAGC 59.900 54.545 0.00 0.00 45.21 4.09
1061 1098 0.456142 CTGCTCATCGTCGTTTCGGA 60.456 55.000 0.00 0.00 0.00 4.55
1089 1126 1.328279 CAGGTTGGTTGTTTCCCCTC 58.672 55.000 0.00 0.00 0.00 4.30
1158 1203 8.621286 TCTTCTGTTTGGAGCTAAACTTTTAAG 58.379 33.333 12.20 9.98 40.36 1.85
1159 1204 7.272037 TCTGTTTGGAGCTAAACTTTTAAGG 57.728 36.000 12.20 0.00 40.36 2.69
1168 1215 7.176865 GGAGCTAAACTTTTAAGGTGGATCTTT 59.823 37.037 0.00 0.00 0.00 2.52
1229 1287 5.819991 AGAAAAGATTCAGAAGGTATGCCA 58.180 37.500 1.54 0.00 38.06 4.92
1268 1326 1.304713 ATTCAGGCCCTGCACAAGG 60.305 57.895 5.66 0.00 46.94 3.61
1517 1594 0.526954 CAAACGACTACGGCCGCTAT 60.527 55.000 28.58 10.81 44.46 2.97
1597 1674 3.126225 GCTGCTCTGCTCCTGCAC 61.126 66.667 0.00 0.00 45.31 4.57
1720 1799 3.785122 AACCACTGGTTCGGGCACC 62.785 63.158 7.72 0.00 43.05 5.01
1780 1860 6.838198 TTGTACTGTATGCCGAATGTTATC 57.162 37.500 0.00 0.00 0.00 1.75
1781 1861 6.156748 TGTACTGTATGCCGAATGTTATCT 57.843 37.500 0.00 0.00 0.00 1.98
1782 1862 6.213677 TGTACTGTATGCCGAATGTTATCTC 58.786 40.000 0.00 0.00 0.00 2.75
1783 1863 5.537300 ACTGTATGCCGAATGTTATCTCT 57.463 39.130 0.00 0.00 0.00 3.10
1784 1864 6.650427 ACTGTATGCCGAATGTTATCTCTA 57.350 37.500 0.00 0.00 0.00 2.43
1785 1865 6.448006 ACTGTATGCCGAATGTTATCTCTAC 58.552 40.000 0.00 0.00 0.00 2.59
1786 1866 6.265649 ACTGTATGCCGAATGTTATCTCTACT 59.734 38.462 0.00 0.00 0.00 2.57
1787 1867 6.678878 TGTATGCCGAATGTTATCTCTACTC 58.321 40.000 0.00 0.00 0.00 2.59
1788 1868 4.585955 TGCCGAATGTTATCTCTACTCC 57.414 45.455 0.00 0.00 0.00 3.85
1789 1869 4.215908 TGCCGAATGTTATCTCTACTCCT 58.784 43.478 0.00 0.00 0.00 3.69
1790 1870 5.382616 TGCCGAATGTTATCTCTACTCCTA 58.617 41.667 0.00 0.00 0.00 2.94
1791 1871 5.831525 TGCCGAATGTTATCTCTACTCCTAA 59.168 40.000 0.00 0.00 0.00 2.69
1792 1872 6.493802 TGCCGAATGTTATCTCTACTCCTAAT 59.506 38.462 0.00 0.00 0.00 1.73
1793 1873 6.809196 GCCGAATGTTATCTCTACTCCTAATG 59.191 42.308 0.00 0.00 0.00 1.90
1794 1874 7.524038 GCCGAATGTTATCTCTACTCCTAATGT 60.524 40.741 0.00 0.00 0.00 2.71
1795 1875 8.024285 CCGAATGTTATCTCTACTCCTAATGTC 58.976 40.741 0.00 0.00 0.00 3.06
1796 1876 8.788806 CGAATGTTATCTCTACTCCTAATGTCT 58.211 37.037 0.00 0.00 0.00 3.41
1797 1877 9.906660 GAATGTTATCTCTACTCCTAATGTCTG 57.093 37.037 0.00 0.00 0.00 3.51
1798 1878 9.647918 AATGTTATCTCTACTCCTAATGTCTGA 57.352 33.333 0.00 0.00 0.00 3.27
1799 1879 8.684386 TGTTATCTCTACTCCTAATGTCTGAG 57.316 38.462 0.00 0.00 0.00 3.35
1800 1880 8.275758 TGTTATCTCTACTCCTAATGTCTGAGT 58.724 37.037 0.00 0.00 41.88 3.41
1801 1881 9.127277 GTTATCTCTACTCCTAATGTCTGAGTT 57.873 37.037 0.00 0.00 39.84 3.01
1802 1882 7.581213 ATCTCTACTCCTAATGTCTGAGTTG 57.419 40.000 0.00 0.00 39.84 3.16
1803 1883 5.888724 TCTCTACTCCTAATGTCTGAGTTGG 59.111 44.000 0.00 0.00 39.84 3.77
1804 1884 5.580998 TCTACTCCTAATGTCTGAGTTGGT 58.419 41.667 0.00 0.00 39.84 3.67
1805 1885 6.017192 TCTACTCCTAATGTCTGAGTTGGTT 58.983 40.000 0.00 0.00 39.84 3.67
1806 1886 4.899502 ACTCCTAATGTCTGAGTTGGTTG 58.100 43.478 0.00 0.00 35.93 3.77
1807 1887 4.593206 ACTCCTAATGTCTGAGTTGGTTGA 59.407 41.667 0.00 0.00 35.93 3.18
1808 1888 5.071788 ACTCCTAATGTCTGAGTTGGTTGAA 59.928 40.000 0.00 0.00 35.93 2.69
1809 1889 6.126863 TCCTAATGTCTGAGTTGGTTGAAT 57.873 37.500 0.00 0.00 0.00 2.57
1810 1890 7.038302 ACTCCTAATGTCTGAGTTGGTTGAATA 60.038 37.037 0.00 0.00 35.93 1.75
1811 1891 7.331026 TCCTAATGTCTGAGTTGGTTGAATAG 58.669 38.462 0.00 0.00 0.00 1.73
1812 1892 7.038302 TCCTAATGTCTGAGTTGGTTGAATAGT 60.038 37.037 0.00 0.00 0.00 2.12
1813 1893 8.258007 CCTAATGTCTGAGTTGGTTGAATAGTA 58.742 37.037 0.00 0.00 0.00 1.82
1814 1894 9.823647 CTAATGTCTGAGTTGGTTGAATAGTAT 57.176 33.333 0.00 0.00 0.00 2.12
1816 1896 8.723942 ATGTCTGAGTTGGTTGAATAGTATTC 57.276 34.615 14.86 14.86 0.00 1.75
1817 1897 7.676004 TGTCTGAGTTGGTTGAATAGTATTCA 58.324 34.615 19.51 19.51 0.00 2.57
1818 1898 7.602644 TGTCTGAGTTGGTTGAATAGTATTCAC 59.397 37.037 22.44 16.98 0.00 3.18
1819 1899 6.811665 TCTGAGTTGGTTGAATAGTATTCACG 59.188 38.462 22.44 8.27 0.00 4.35
1820 1900 5.872617 TGAGTTGGTTGAATAGTATTCACGG 59.127 40.000 22.44 0.00 0.00 4.94
1824 1904 7.879160 AGTTGGTTGAATAGTATTCACGGTTTA 59.121 33.333 22.44 6.80 0.00 2.01
1898 1982 2.900716 TCAGACACATCACAAACGGA 57.099 45.000 0.00 0.00 0.00 4.69
1978 2062 7.637709 AAAATCCTAACTTTTCAAACGCATC 57.362 32.000 0.00 0.00 0.00 3.91
2029 2113 3.585289 TGATTAGGCAGTTGGTAGGTGAA 59.415 43.478 0.00 0.00 0.00 3.18
2053 2137 0.474273 TCCCTTCGTACCCCCAAACT 60.474 55.000 0.00 0.00 0.00 2.66
2100 2184 0.252761 TCCTCAAGATTCCGCATGCA 59.747 50.000 19.57 0.00 0.00 3.96
2101 2185 1.097232 CCTCAAGATTCCGCATGCAA 58.903 50.000 19.57 5.62 0.00 4.08
2102 2186 1.473677 CCTCAAGATTCCGCATGCAAA 59.526 47.619 19.57 11.72 0.00 3.68
2487 4286 3.428180 CGACAATGAGACAGACAGGTAGG 60.428 52.174 0.00 0.00 0.00 3.18
2488 4287 3.764434 GACAATGAGACAGACAGGTAGGA 59.236 47.826 0.00 0.00 0.00 2.94
2553 4352 3.634568 TTTTTACAACTGCCATCACGG 57.365 42.857 0.00 0.00 38.11 4.94
2554 4353 2.552599 TTTACAACTGCCATCACGGA 57.447 45.000 0.00 0.00 36.56 4.69
2555 4354 2.093306 TTACAACTGCCATCACGGAG 57.907 50.000 0.00 0.00 36.56 4.63
2556 4355 1.262417 TACAACTGCCATCACGGAGA 58.738 50.000 0.00 0.00 36.56 3.71
2557 4356 0.320771 ACAACTGCCATCACGGAGAC 60.321 55.000 0.00 0.00 36.56 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 7.031372 AGTAACACATTTAGAAAGCATGCATG 58.969 34.615 22.70 22.70 0.00 4.06
8 9 7.161773 AGTAACACATTTAGAAAGCATGCAT 57.838 32.000 21.98 4.57 0.00 3.96
9 10 6.573664 AGTAACACATTTAGAAAGCATGCA 57.426 33.333 21.98 0.00 0.00 3.96
10 11 7.752695 ACTAGTAACACATTTAGAAAGCATGC 58.247 34.615 10.51 10.51 0.00 4.06
21 22 5.717078 TCCACGAGACTAGTAACACATTT 57.283 39.130 0.00 0.00 0.00 2.32
24 25 5.008331 AGATTCCACGAGACTAGTAACACA 58.992 41.667 0.00 0.00 0.00 3.72
26 27 4.639310 GGAGATTCCACGAGACTAGTAACA 59.361 45.833 0.00 0.00 36.28 2.41
36 37 3.123621 CGAAACAAAGGAGATTCCACGAG 59.876 47.826 0.00 0.00 39.61 4.18
42 43 3.191371 ACATGGCGAAACAAAGGAGATTC 59.809 43.478 0.00 0.00 0.00 2.52
96 97 9.490379 AATCCTACAAGTAAAACTAACTGTGAG 57.510 33.333 0.00 0.00 0.00 3.51
110 111 9.515226 AGTGAAGCAAATAAAATCCTACAAGTA 57.485 29.630 0.00 0.00 0.00 2.24
146 147 1.901591 ACATCAAGACCAGGCAACAG 58.098 50.000 0.00 0.00 41.41 3.16
167 168 3.128415 TCGTTTTGCCACATACATCCATG 59.872 43.478 0.00 0.00 0.00 3.66
258 291 2.969950 ACTGACTGGGTGCTTACAACTA 59.030 45.455 0.00 0.00 32.44 2.24
278 311 3.514309 AGTCTGGTAACCTACATGTGGAC 59.486 47.826 11.31 0.75 0.00 4.02
281 314 4.537135 ACAGTCTGGTAACCTACATGTG 57.463 45.455 9.11 0.00 0.00 3.21
364 398 1.067354 CCCCTCAAAAGAAGCATGTGC 60.067 52.381 0.00 0.00 42.49 4.57
385 419 3.119029 CCCCTTGTAACATTGGCATCTTG 60.119 47.826 0.00 0.00 0.00 3.02
393 427 2.094078 CACATGCCCCCTTGTAACATTG 60.094 50.000 0.00 0.00 0.00 2.82
397 431 2.500392 TACACATGCCCCCTTGTAAC 57.500 50.000 0.00 0.00 0.00 2.50
403 437 3.268334 TCAACTATTTACACATGCCCCCT 59.732 43.478 0.00 0.00 0.00 4.79
407 441 6.494893 TTCAGTCAACTATTTACACATGCC 57.505 37.500 0.00 0.00 0.00 4.40
450 484 0.250901 GCATGGGGCGTTGGATCTAT 60.251 55.000 0.00 0.00 0.00 1.98
493 527 2.653234 ATCCTGTGCTCCCATTCATC 57.347 50.000 0.00 0.00 0.00 2.92
497 531 3.437052 GGGAAATATCCTGTGCTCCCATT 60.437 47.826 0.00 0.00 45.77 3.16
523 557 0.386476 TCGACCGCACTGTGTTAAGT 59.614 50.000 9.86 2.04 0.00 2.24
600 634 1.993948 GGAAAGTAGAGGCCGGGGT 60.994 63.158 2.18 0.00 0.00 4.95
966 1003 2.488167 CCTCTCGATCAGCTCCCTCTAA 60.488 54.545 0.00 0.00 0.00 2.10
978 1015 4.993029 TTTCCTCTTCTTCCTCTCGATC 57.007 45.455 0.00 0.00 0.00 3.69
979 1016 5.396213 CCATTTTCCTCTTCTTCCTCTCGAT 60.396 44.000 0.00 0.00 0.00 3.59
980 1017 4.081420 CCATTTTCCTCTTCTTCCTCTCGA 60.081 45.833 0.00 0.00 0.00 4.04
981 1018 4.187694 CCATTTTCCTCTTCTTCCTCTCG 58.812 47.826 0.00 0.00 0.00 4.04
1025 1062 4.249661 GAGCAGTAGAAGAACAAGGGAAG 58.750 47.826 0.00 0.00 0.00 3.46
1075 1112 0.481128 GGGAAGAGGGGAAACAACCA 59.519 55.000 0.00 0.00 0.00 3.67
1089 1126 3.071457 AGCAAAATCAAAAGGGTGGGAAG 59.929 43.478 0.00 0.00 0.00 3.46
1158 1203 1.541588 GACCACAGCAAAAGATCCACC 59.458 52.381 0.00 0.00 0.00 4.61
1159 1204 2.508526 AGACCACAGCAAAAGATCCAC 58.491 47.619 0.00 0.00 0.00 4.02
1168 1215 3.476552 CTCCTACAAAAGACCACAGCAA 58.523 45.455 0.00 0.00 0.00 3.91
1268 1326 8.603242 TCATTTAGTTCTCAAACAAGTCTACC 57.397 34.615 0.00 0.00 37.88 3.18
1398 1475 5.741388 ATTTGGCGAGATGAGAACAATAC 57.259 39.130 0.00 0.00 0.00 1.89
1499 1576 0.526954 CATAGCGGCCGTAGTCGTTT 60.527 55.000 28.70 5.01 35.01 3.60
1517 1594 2.915659 AACGCTGGAGTCGGGTCA 60.916 61.111 0.00 0.00 0.00 4.02
1720 1799 6.796705 ATCAGTTACAAACTTAGGAAACCG 57.203 37.500 0.00 0.00 40.46 4.44
1756 1836 7.217200 AGATAACATTCGGCATACAGTACAAT 58.783 34.615 0.00 0.00 0.00 2.71
1780 1860 5.654650 ACCAACTCAGACATTAGGAGTAGAG 59.345 44.000 0.00 0.00 40.80 2.43
1781 1861 5.580998 ACCAACTCAGACATTAGGAGTAGA 58.419 41.667 0.00 0.00 40.80 2.59
1782 1862 5.923733 ACCAACTCAGACATTAGGAGTAG 57.076 43.478 0.00 0.00 40.80 2.57
1783 1863 5.778241 TCAACCAACTCAGACATTAGGAGTA 59.222 40.000 0.00 0.00 40.80 2.59
1784 1864 4.593206 TCAACCAACTCAGACATTAGGAGT 59.407 41.667 0.00 0.00 43.35 3.85
1785 1865 5.152623 TCAACCAACTCAGACATTAGGAG 57.847 43.478 0.00 0.00 34.85 3.69
1786 1866 5.560722 TTCAACCAACTCAGACATTAGGA 57.439 39.130 0.00 0.00 0.00 2.94
1787 1867 7.106239 ACTATTCAACCAACTCAGACATTAGG 58.894 38.462 0.00 0.00 0.00 2.69
1788 1868 9.823647 ATACTATTCAACCAACTCAGACATTAG 57.176 33.333 0.00 0.00 0.00 1.73
1790 1870 9.167311 GAATACTATTCAACCAACTCAGACATT 57.833 33.333 4.18 0.00 0.00 2.71
1791 1871 8.321353 TGAATACTATTCAACCAACTCAGACAT 58.679 33.333 8.76 0.00 0.00 3.06
1792 1872 7.602644 GTGAATACTATTCAACCAACTCAGACA 59.397 37.037 12.23 0.00 0.00 3.41
1793 1873 7.201444 CGTGAATACTATTCAACCAACTCAGAC 60.201 40.741 12.23 0.00 0.00 3.51
1794 1874 6.811665 CGTGAATACTATTCAACCAACTCAGA 59.188 38.462 12.23 0.00 0.00 3.27
1795 1875 6.036083 CCGTGAATACTATTCAACCAACTCAG 59.964 42.308 12.23 0.00 0.00 3.35
1796 1876 5.872617 CCGTGAATACTATTCAACCAACTCA 59.127 40.000 12.23 0.00 0.00 3.41
1797 1877 5.873164 ACCGTGAATACTATTCAACCAACTC 59.127 40.000 12.23 0.00 0.00 3.01
1798 1878 5.801380 ACCGTGAATACTATTCAACCAACT 58.199 37.500 12.23 0.00 0.00 3.16
1799 1879 6.490566 AACCGTGAATACTATTCAACCAAC 57.509 37.500 12.23 0.94 0.00 3.77
1800 1880 8.795842 ATAAACCGTGAATACTATTCAACCAA 57.204 30.769 12.23 0.00 0.00 3.67
1801 1881 8.795842 AATAAACCGTGAATACTATTCAACCA 57.204 30.769 12.23 0.00 0.00 3.67
1804 1884 9.976255 CGAAAATAAACCGTGAATACTATTCAA 57.024 29.630 12.23 0.00 0.00 2.69
1805 1885 9.153721 ACGAAAATAAACCGTGAATACTATTCA 57.846 29.630 7.31 7.31 35.02 2.57
1806 1886 9.628983 GACGAAAATAAACCGTGAATACTATTC 57.371 33.333 2.22 2.22 36.60 1.75
1807 1887 9.374838 AGACGAAAATAAACCGTGAATACTATT 57.625 29.630 0.00 0.00 36.60 1.73
1808 1888 8.937634 AGACGAAAATAAACCGTGAATACTAT 57.062 30.769 0.00 0.00 36.60 2.12
1809 1889 9.853555 TTAGACGAAAATAAACCGTGAATACTA 57.146 29.630 0.00 0.00 36.60 1.82
1810 1890 8.650714 GTTAGACGAAAATAAACCGTGAATACT 58.349 33.333 0.00 0.00 36.60 2.12
1811 1891 7.899841 GGTTAGACGAAAATAAACCGTGAATAC 59.100 37.037 0.00 0.00 36.60 1.89
1812 1892 7.818930 AGGTTAGACGAAAATAAACCGTGAATA 59.181 33.333 0.00 0.00 43.49 1.75
1813 1893 6.652062 AGGTTAGACGAAAATAAACCGTGAAT 59.348 34.615 0.00 0.00 43.49 2.57
1814 1894 5.990996 AGGTTAGACGAAAATAAACCGTGAA 59.009 36.000 0.00 0.00 43.49 3.18
1815 1895 5.540911 AGGTTAGACGAAAATAAACCGTGA 58.459 37.500 0.00 0.00 43.49 4.35
1816 1896 5.851047 AGGTTAGACGAAAATAAACCGTG 57.149 39.130 0.00 0.00 43.49 4.94
1817 1897 5.409520 GGAAGGTTAGACGAAAATAAACCGT 59.590 40.000 0.00 0.00 43.49 4.83
1818 1898 5.163824 GGGAAGGTTAGACGAAAATAAACCG 60.164 44.000 0.00 0.00 43.49 4.44
1819 1899 5.942236 AGGGAAGGTTAGACGAAAATAAACC 59.058 40.000 0.00 0.00 39.92 3.27
1820 1900 6.093219 GGAGGGAAGGTTAGACGAAAATAAAC 59.907 42.308 0.00 0.00 0.00 2.01
1824 1904 3.054582 GGGAGGGAAGGTTAGACGAAAAT 60.055 47.826 0.00 0.00 0.00 1.82
1834 1914 5.087923 AGTTTTTATTGGGAGGGAAGGTT 57.912 39.130 0.00 0.00 0.00 3.50
1898 1982 9.772973 TGCTTATAACGTGATATCATTACCTTT 57.227 29.630 9.02 0.00 0.00 3.11
1970 2054 4.094442 GGAAAGGTAAGAATCGATGCGTTT 59.906 41.667 0.00 0.00 0.00 3.60
1978 2062 6.422400 GCAGAGATTAGGAAAGGTAAGAATCG 59.578 42.308 0.00 0.00 0.00 3.34
2029 2113 1.332889 GGGGGTACGAAGGGACGATT 61.333 60.000 0.00 0.00 37.03 3.34
2053 2137 1.515954 GAGCCTGGGTTCGATCGAA 59.484 57.895 25.96 25.96 0.00 3.71
2151 2235 1.003051 GGGAGAGGGGCAGAGGTTA 59.997 63.158 0.00 0.00 0.00 2.85
2471 4270 3.808834 TCTTCCTACCTGTCTGTCTCA 57.191 47.619 0.00 0.00 0.00 3.27
2536 4335 1.621317 TCTCCGTGATGGCAGTTGTAA 59.379 47.619 0.00 0.00 37.80 2.41
2537 4336 1.067142 GTCTCCGTGATGGCAGTTGTA 60.067 52.381 0.00 0.00 37.80 2.41
2538 4337 0.320771 GTCTCCGTGATGGCAGTTGT 60.321 55.000 0.00 0.00 37.80 3.32
2539 4338 1.354337 CGTCTCCGTGATGGCAGTTG 61.354 60.000 0.00 0.00 37.80 3.16
2540 4339 1.079819 CGTCTCCGTGATGGCAGTT 60.080 57.895 0.00 0.00 37.80 3.16
2541 4340 2.573869 CGTCTCCGTGATGGCAGT 59.426 61.111 0.00 0.00 37.80 4.40
2542 4341 2.887568 GCGTCTCCGTGATGGCAG 60.888 66.667 0.00 0.00 37.80 4.85


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

AutoCloner maintained by Alex Coulton.