Multiple sequence alignment - TraesCS2A01G574500

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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 TraesCS2A01G574500 chr2A 100.000 2507 0 0 1 2507 769484090 769486596 0.000000e+00 4630
1 TraesCS2A01G574500 chr2D 88.397 1741 101 31 820 2507 644282454 644284146 0.000000e+00 2002
2 TraesCS2A01G574500 chr2D 91.837 98 8 0 1741 1838 98693501 98693598 1.210000e-28 137
3 TraesCS2A01G574500 chr7A 99.512 819 4 0 1 819 499445983 499446801 0.000000e+00 1491
4 TraesCS2A01G574500 chr7A 99.145 819 6 1 1 819 575584697 575583880 0.000000e+00 1472
5 TraesCS2A01G574500 chr4B 99.156 829 5 2 1 827 173328461 173329289 0.000000e+00 1491
6 TraesCS2A01G574500 chr4B 99.036 830 6 2 1 829 604498955 604499783 0.000000e+00 1487
7 TraesCS2A01G574500 chr4B 76.375 309 55 13 1027 1329 629953758 629954054 1.550000e-32 150
8 TraesCS2A01G574500 chr3A 99.033 827 8 0 1 827 61242441 61241615 0.000000e+00 1483
9 TraesCS2A01G574500 chr3A 91.000 100 9 0 1740 1839 269394314 269394413 4.350000e-28 135
10 TraesCS2A01G574500 chr4A 98.912 827 8 1 1 826 344006879 344007705 0.000000e+00 1476
11 TraesCS2A01G574500 chr4A 99.145 819 7 0 1 819 593673207 593672389 0.000000e+00 1474
12 TraesCS2A01G574500 chr5B 98.791 827 7 3 1 825 295200998 295200173 0.000000e+00 1469
13 TraesCS2A01G574500 chr1B 98.906 823 5 3 1 823 33064755 33065573 0.000000e+00 1467
14 TraesCS2A01G574500 chr1B 89.720 107 11 0 1737 1843 252715214 252715320 1.210000e-28 137
15 TraesCS2A01G574500 chr1B 87.500 112 12 2 1728 1838 486243239 486243129 7.280000e-26 128
16 TraesCS2A01G574500 chr5D 75.510 441 88 18 1029 1459 450637933 450638363 5.470000e-47 198
17 TraesCS2A01G574500 chr4D 76.299 308 51 12 1027 1329 490138723 490139013 7.230000e-31 145
18 TraesCS2A01G574500 chrUn 92.857 98 7 0 1741 1838 21636770 21636673 2.600000e-30 143
19 TraesCS2A01G574500 chr6D 92.079 101 7 1 1741 1840 808301 808201 9.350000e-30 141
20 TraesCS2A01G574500 chr6B 90.385 104 8 2 1741 1844 710143909 710143808 4.350000e-28 135
21 TraesCS2A01G574500 chr5A 75.896 307 50 13 1027 1327 671484108 671484396 4.350000e-28 135
22 TraesCS2A01G574500 chr7B 88.889 108 10 2 1741 1846 237489312 237489419 5.630000e-27 132
23 TraesCS2A01G574500 chr1D 83.333 120 15 2 2059 2173 471437507 471437388 3.410000e-19 106


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 TraesCS2A01G574500 chr2A 769484090 769486596 2506 False 4630 4630 100.000 1 2507 1 chr2A.!!$F1 2506
1 TraesCS2A01G574500 chr2D 644282454 644284146 1692 False 2002 2002 88.397 820 2507 1 chr2D.!!$F2 1687
2 TraesCS2A01G574500 chr7A 499445983 499446801 818 False 1491 1491 99.512 1 819 1 chr7A.!!$F1 818
3 TraesCS2A01G574500 chr7A 575583880 575584697 817 True 1472 1472 99.145 1 819 1 chr7A.!!$R1 818
4 TraesCS2A01G574500 chr4B 173328461 173329289 828 False 1491 1491 99.156 1 827 1 chr4B.!!$F1 826
5 TraesCS2A01G574500 chr4B 604498955 604499783 828 False 1487 1487 99.036 1 829 1 chr4B.!!$F2 828
6 TraesCS2A01G574500 chr3A 61241615 61242441 826 True 1483 1483 99.033 1 827 1 chr3A.!!$R1 826
7 TraesCS2A01G574500 chr4A 344006879 344007705 826 False 1476 1476 98.912 1 826 1 chr4A.!!$F1 825
8 TraesCS2A01G574500 chr4A 593672389 593673207 818 True 1474 1474 99.145 1 819 1 chr4A.!!$R1 818
9 TraesCS2A01G574500 chr5B 295200173 295200998 825 True 1469 1469 98.791 1 825 1 chr5B.!!$R1 824
10 TraesCS2A01G574500 chr1B 33064755 33065573 818 False 1467 1467 98.906 1 823 1 chr1B.!!$F1 822

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
932 935 0.386352 TCGTCTCCTACAAACACGCG 60.386 55.0 3.53 3.53 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2353 2407 0.034477 GCCGAGGAAAAAGGGGATCA 60.034 55.0 0.0 0.0 0.0 2.92 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
471 472 7.870445 ACATGTTTGCGACCAAATTAATACTTT 59.130 29.630 0.00 0.00 42.44 2.66
848 851 6.895607 AAAAGTTTGTTTTAATGTCGGTGG 57.104 33.333 0.00 0.00 0.00 4.61
854 857 3.003897 TGTTTTAATGTCGGTGGTGAAGC 59.996 43.478 0.00 0.00 0.00 3.86
861 864 2.835605 CGGTGGTGAAGCGTACAAT 58.164 52.632 0.00 0.00 44.71 2.71
872 875 5.394322 GTGAAGCGTACAATGTACAAACAAC 59.606 40.000 21.63 10.93 39.58 3.32
884 887 0.817634 CAAACAACTGGAGTCGGCCA 60.818 55.000 2.24 0.00 36.30 5.36
932 935 0.386352 TCGTCTCCTACAAACACGCG 60.386 55.000 3.53 3.53 0.00 6.01
972 975 1.521681 CCCAACCTCGAAGATCGGC 60.522 63.158 0.00 0.00 40.88 5.54
987 990 0.753479 TCGGCAGAGGAGAGATCCAC 60.753 60.000 0.00 0.00 0.00 4.02
1005 1008 2.422127 CCACCCAACAATTACGATGTCC 59.578 50.000 0.00 0.00 0.00 4.02
1006 1009 3.078097 CACCCAACAATTACGATGTCCA 58.922 45.455 0.00 0.00 0.00 4.02
1056 1059 4.477975 CTCCACTCGTCGGACGGC 62.478 72.222 28.07 0.00 42.81 5.68
1185 1191 4.489771 GTCACCGGCCCCATCCTG 62.490 72.222 0.00 0.00 0.00 3.86
1217 1223 0.319297 GAGTACGTCAACCGGCACTT 60.319 55.000 0.00 0.00 42.24 3.16
1218 1224 0.599204 AGTACGTCAACCGGCACTTG 60.599 55.000 0.00 0.00 42.24 3.16
1219 1225 1.301087 TACGTCAACCGGCACTTGG 60.301 57.895 0.00 0.00 42.24 3.61
1220 1226 1.746322 TACGTCAACCGGCACTTGGA 61.746 55.000 0.00 0.00 42.24 3.53
1284 1290 3.854669 CCCCTGAGGCGCTTCGAT 61.855 66.667 15.28 0.00 0.00 3.59
1329 1335 0.171455 ACACGCTCTTCGACCTCATC 59.829 55.000 0.00 0.00 41.67 2.92
1374 1380 3.775654 GGGCTCCTGGACCTCACG 61.776 72.222 12.89 0.00 40.87 4.35
1442 1448 1.742900 CGCACGCACTTCTACATCCG 61.743 60.000 0.00 0.00 0.00 4.18
1446 1452 0.370273 CGCACTTCTACATCCGCAAC 59.630 55.000 0.00 0.00 0.00 4.17
1461 1467 1.153901 CAACGACTACACCGCCGAT 60.154 57.895 0.00 0.00 0.00 4.18
1465 1471 1.807886 GACTACACCGCCGATGAGT 59.192 57.895 0.00 0.00 0.00 3.41
1466 1472 0.172803 GACTACACCGCCGATGAGTT 59.827 55.000 0.00 0.00 0.00 3.01
1470 1476 2.100631 CACCGCCGATGAGTTGGAC 61.101 63.158 0.00 0.00 0.00 4.02
1525 1531 5.355596 AGTAGCTGCAATCTTGATCACTAC 58.644 41.667 4.12 0.51 0.00 2.73
1529 1535 4.208047 GCTGCAATCTTGATCACTACTACG 59.792 45.833 0.00 0.00 0.00 3.51
1537 1543 4.268767 TGATCACTACTACGCACGTTAG 57.731 45.455 0.00 0.52 0.00 2.34
1549 1555 1.337387 GCACGTTAGGTAGGCTAGGAG 59.663 57.143 0.00 0.00 0.00 3.69
1563 1569 5.348833 AGGCTAGGAGACATATCAATCCAT 58.651 41.667 0.00 0.00 34.08 3.41
1579 1585 3.558931 TCCATCAATACATCCACGCTT 57.441 42.857 0.00 0.00 0.00 4.68
1580 1586 3.205338 TCCATCAATACATCCACGCTTG 58.795 45.455 0.00 0.00 0.00 4.01
1581 1587 2.287188 CCATCAATACATCCACGCTTGC 60.287 50.000 0.00 0.00 0.00 4.01
1582 1588 2.401583 TCAATACATCCACGCTTGCT 57.598 45.000 0.00 0.00 0.00 3.91
1583 1589 2.710377 TCAATACATCCACGCTTGCTT 58.290 42.857 0.00 0.00 0.00 3.91
1584 1590 2.419673 TCAATACATCCACGCTTGCTTG 59.580 45.455 0.00 0.00 0.00 4.01
1617 1628 9.553064 AATATGTTTTGGCTTGTGTTAATTTGA 57.447 25.926 0.00 0.00 0.00 2.69
1677 1689 6.417191 TGATGTTATGCCGTAAAGAAGAAC 57.583 37.500 0.00 0.00 0.00 3.01
1720 1732 7.618019 TGGTCTAATATCTGTCCTTGCTAAT 57.382 36.000 0.00 0.00 0.00 1.73
1762 1774 5.532779 GCTACTCCTTCCATCCCAAAATAAG 59.467 44.000 0.00 0.00 0.00 1.73
1764 1776 6.652205 ACTCCTTCCATCCCAAAATAAGTA 57.348 37.500 0.00 0.00 0.00 2.24
1840 1852 2.359981 TGGGACAGAGGGAGTATACG 57.640 55.000 0.00 0.00 0.00 3.06
1845 1857 4.277921 GGGACAGAGGGAGTATACGTTAAG 59.722 50.000 0.00 0.00 0.00 1.85
1846 1858 4.277921 GGACAGAGGGAGTATACGTTAAGG 59.722 50.000 0.00 0.00 0.00 2.69
1847 1859 4.213513 ACAGAGGGAGTATACGTTAAGGG 58.786 47.826 0.00 0.00 0.00 3.95
1848 1860 4.079558 ACAGAGGGAGTATACGTTAAGGGA 60.080 45.833 0.00 0.00 0.00 4.20
1849 1861 4.891756 CAGAGGGAGTATACGTTAAGGGAA 59.108 45.833 0.00 0.00 0.00 3.97
1850 1862 5.009811 CAGAGGGAGTATACGTTAAGGGAAG 59.990 48.000 0.00 0.00 0.00 3.46
1851 1863 4.876580 AGGGAGTATACGTTAAGGGAAGT 58.123 43.478 0.00 0.00 0.00 3.01
1852 1864 4.648307 AGGGAGTATACGTTAAGGGAAGTG 59.352 45.833 0.00 0.00 0.00 3.16
1853 1865 4.646492 GGGAGTATACGTTAAGGGAAGTGA 59.354 45.833 0.00 0.00 0.00 3.41
1854 1866 5.303845 GGGAGTATACGTTAAGGGAAGTGAT 59.696 44.000 0.00 0.00 0.00 3.06
1855 1867 6.183360 GGGAGTATACGTTAAGGGAAGTGATT 60.183 42.308 0.00 0.00 0.00 2.57
1856 1868 6.922407 GGAGTATACGTTAAGGGAAGTGATTC 59.078 42.308 0.00 0.00 0.00 2.52
1857 1869 6.814043 AGTATACGTTAAGGGAAGTGATTCC 58.186 40.000 0.00 0.00 40.38 3.01
1868 1880 2.474410 AGTGATTCCCTTCAACCGAC 57.526 50.000 0.00 0.00 0.00 4.79
1883 1895 0.109086 CCGACTGATCTTGTGCGAGT 60.109 55.000 0.00 0.00 0.00 4.18
1886 1898 2.408050 GACTGATCTTGTGCGAGTGTT 58.592 47.619 0.00 0.00 0.00 3.32
1887 1899 2.802816 GACTGATCTTGTGCGAGTGTTT 59.197 45.455 0.00 0.00 0.00 2.83
1902 1914 1.675641 GTTTGCGGCCTCCATGTCT 60.676 57.895 0.00 0.00 0.00 3.41
1951 1963 3.326747 AGGTAATCTCACGTTCTGCAAC 58.673 45.455 0.00 0.00 0.00 4.17
1972 1984 5.675684 ACTGGTCCATTGTTTTTGAAAGT 57.324 34.783 0.00 0.00 0.00 2.66
1974 1986 4.764172 TGGTCCATTGTTTTTGAAAGTGG 58.236 39.130 0.00 0.00 0.00 4.00
1979 1991 6.035975 GTCCATTGTTTTTGAAAGTGGTTCTG 59.964 38.462 0.00 0.00 37.13 3.02
1998 2010 2.808543 CTGCAACTAGTCCCTTGTTGAC 59.191 50.000 18.29 11.71 45.12 3.18
2117 2138 3.409026 ACAAGACCTTGCAAGTAGAGG 57.591 47.619 24.35 12.65 44.03 3.69
2118 2139 2.972713 ACAAGACCTTGCAAGTAGAGGA 59.027 45.455 24.35 0.00 44.03 3.71
2119 2140 3.391296 ACAAGACCTTGCAAGTAGAGGAA 59.609 43.478 24.35 0.00 44.03 3.36
2120 2141 3.971245 AGACCTTGCAAGTAGAGGAAG 57.029 47.619 24.35 9.35 34.61 3.46
2121 2142 3.511477 AGACCTTGCAAGTAGAGGAAGA 58.489 45.455 24.35 0.00 36.66 2.87
2122 2143 4.100373 AGACCTTGCAAGTAGAGGAAGAT 58.900 43.478 24.35 0.00 36.66 2.40
2123 2144 4.081198 AGACCTTGCAAGTAGAGGAAGATG 60.081 45.833 24.35 7.46 36.66 2.90
2124 2145 3.584848 ACCTTGCAAGTAGAGGAAGATGT 59.415 43.478 24.35 8.08 36.66 3.06
2125 2146 4.042187 ACCTTGCAAGTAGAGGAAGATGTT 59.958 41.667 24.35 0.00 36.66 2.71
2126 2147 5.006386 CCTTGCAAGTAGAGGAAGATGTTT 58.994 41.667 24.35 0.00 36.66 2.83
2127 2148 5.106396 CCTTGCAAGTAGAGGAAGATGTTTG 60.106 44.000 24.35 0.00 36.66 2.93
2128 2149 4.326826 TGCAAGTAGAGGAAGATGTTTGG 58.673 43.478 0.00 0.00 0.00 3.28
2129 2150 3.127721 GCAAGTAGAGGAAGATGTTTGGC 59.872 47.826 0.00 0.00 0.00 4.52
2130 2151 4.583871 CAAGTAGAGGAAGATGTTTGGCT 58.416 43.478 0.00 0.00 0.00 4.75
2131 2152 4.213564 AGTAGAGGAAGATGTTTGGCTG 57.786 45.455 0.00 0.00 0.00 4.85
2132 2153 2.503895 AGAGGAAGATGTTTGGCTGG 57.496 50.000 0.00 0.00 0.00 4.85
2133 2154 1.707427 AGAGGAAGATGTTTGGCTGGT 59.293 47.619 0.00 0.00 0.00 4.00
2134 2155 2.087646 GAGGAAGATGTTTGGCTGGTC 58.912 52.381 0.00 0.00 0.00 4.02
2135 2156 0.804989 GGAAGATGTTTGGCTGGTCG 59.195 55.000 0.00 0.00 0.00 4.79
2136 2157 1.610624 GGAAGATGTTTGGCTGGTCGA 60.611 52.381 0.00 0.00 0.00 4.20
2137 2158 2.359900 GAAGATGTTTGGCTGGTCGAT 58.640 47.619 0.00 0.00 0.00 3.59
2138 2159 2.496899 AGATGTTTGGCTGGTCGATT 57.503 45.000 0.00 0.00 0.00 3.34
2149 2170 2.069273 CTGGTCGATTGTGTCAGAACC 58.931 52.381 0.00 0.00 0.00 3.62
2157 2178 0.037326 TGTGTCAGAACCGATGGCTC 60.037 55.000 0.00 0.00 0.00 4.70
2200 2221 2.118132 GCATGTAGCAACCCCCATG 58.882 57.895 0.00 0.00 44.79 3.66
2216 2237 3.305676 CCCCATGTGTTAATGCGTTTTCA 60.306 43.478 0.00 0.00 0.00 2.69
2222 2243 6.952935 TGTGTTAATGCGTTTTCAAGTTTT 57.047 29.167 0.00 0.00 0.00 2.43
2223 2244 6.983910 TGTGTTAATGCGTTTTCAAGTTTTC 58.016 32.000 0.00 0.00 0.00 2.29
2224 2245 6.809196 TGTGTTAATGCGTTTTCAAGTTTTCT 59.191 30.769 0.00 0.00 0.00 2.52
2225 2246 7.008810 TGTGTTAATGCGTTTTCAAGTTTTCTC 59.991 33.333 0.00 0.00 0.00 2.87
2226 2247 7.008810 GTGTTAATGCGTTTTCAAGTTTTCTCA 59.991 33.333 0.00 0.00 0.00 3.27
2227 2248 7.219917 TGTTAATGCGTTTTCAAGTTTTCTCAG 59.780 33.333 0.00 0.00 0.00 3.35
2231 2252 5.163663 TGCGTTTTCAAGTTTTCTCAGACAT 60.164 36.000 0.00 0.00 0.00 3.06
2253 2274 8.862325 ACATGATATTGTTTTGACAGAGGTAA 57.138 30.769 0.00 0.00 0.00 2.85
2266 2287 2.890311 CAGAGGTAAATGTTTGGTGCCA 59.110 45.455 0.00 0.00 0.00 4.92
2270 2291 2.224161 GGTAAATGTTTGGTGCCAGCAA 60.224 45.455 4.99 4.99 33.27 3.91
2287 2324 3.296709 AAGCCGGCTACCTCACACG 62.297 63.158 33.07 0.00 0.00 4.49
2323 2377 2.756760 ACCACCGCTTTATCTACTCGAA 59.243 45.455 0.00 0.00 0.00 3.71
2326 2380 4.809426 CCACCGCTTTATCTACTCGAAAAT 59.191 41.667 0.00 0.00 0.00 1.82
2327 2381 5.276868 CCACCGCTTTATCTACTCGAAAATG 60.277 44.000 0.00 0.00 0.00 2.32
2353 2407 0.344790 ACCATCATCTCCCACCTCCT 59.655 55.000 0.00 0.00 0.00 3.69
2387 2442 2.378634 CGGCCTCTTCCCTTCCCAT 61.379 63.158 0.00 0.00 0.00 4.00
2425 2480 0.918983 GTCTCCCATCAATCCACCCA 59.081 55.000 0.00 0.00 0.00 4.51
2427 2482 0.106519 CTCCCATCAATCCACCCACC 60.107 60.000 0.00 0.00 0.00 4.61
2429 2484 1.696686 CCATCAATCCACCCACCCA 59.303 57.895 0.00 0.00 0.00 4.51
2458 2513 1.133809 AGCTCCCTACCAAGGTGCAA 61.134 55.000 1.07 0.00 41.89 4.08
2484 2539 1.069636 GCTTTGCGTTGTGAGAAGAGG 60.070 52.381 0.00 0.00 0.00 3.69
2494 2549 0.325671 TGAGAAGAGGGCCCTAGGTG 60.326 60.000 28.78 0.05 0.00 4.00
2497 2552 0.910088 GAAGAGGGCCCTAGGTGTGT 60.910 60.000 28.78 0.00 0.00 3.72
2498 2553 1.201429 AAGAGGGCCCTAGGTGTGTG 61.201 60.000 28.78 0.00 0.00 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
848 851 5.085636 TGTTTGTACATTGTACGCTTCAC 57.914 39.130 19.28 12.25 0.00 3.18
854 857 5.235616 ACTCCAGTTGTTTGTACATTGTACG 59.764 40.000 19.28 5.22 33.44 3.67
861 864 2.828877 CCGACTCCAGTTGTTTGTACA 58.171 47.619 0.00 0.00 0.00 2.90
884 887 4.675029 CGGTTCAGAACGGGCCGT 62.675 66.667 28.83 28.83 43.97 5.68
888 891 1.080025 GGAGTCGGTTCAGAACGGG 60.080 63.158 18.13 8.46 33.09 5.28
915 918 1.623973 GCCGCGTGTTTGTAGGAGAC 61.624 60.000 4.92 0.00 0.00 3.36
916 919 1.373748 GCCGCGTGTTTGTAGGAGA 60.374 57.895 4.92 0.00 0.00 3.71
917 920 2.726691 CGCCGCGTGTTTGTAGGAG 61.727 63.158 4.92 0.00 0.00 3.69
972 975 1.484240 GTTGGGTGGATCTCTCCTCTG 59.516 57.143 0.00 0.00 42.59 3.35
987 990 2.095213 CGTGGACATCGTAATTGTTGGG 59.905 50.000 0.00 0.00 0.00 4.12
1005 1008 5.068234 TCCTGTTCTTATTAGTGGACGTG 57.932 43.478 0.00 0.00 0.00 4.49
1006 1009 5.479375 TCTTCCTGTTCTTATTAGTGGACGT 59.521 40.000 0.00 0.00 0.00 4.34
1103 1106 1.153107 TCCAGCATGCCCTTGATCG 60.153 57.895 15.66 0.00 31.97 3.69
1104 1107 0.822532 CCTCCAGCATGCCCTTGATC 60.823 60.000 15.66 0.00 31.97 2.92
1217 1223 2.257371 CGCCGTCTTCTTCGTCCA 59.743 61.111 0.00 0.00 0.00 4.02
1218 1224 3.179939 GCGCCGTCTTCTTCGTCC 61.180 66.667 0.00 0.00 0.00 4.79
1219 1225 3.179939 GGCGCCGTCTTCTTCGTC 61.180 66.667 12.58 0.00 0.00 4.20
1220 1226 4.736896 GGGCGCCGTCTTCTTCGT 62.737 66.667 22.54 0.00 0.00 3.85
1224 1230 2.678934 TACAGGGCGCCGTCTTCT 60.679 61.111 20.79 7.62 0.00 2.85
1273 1279 2.172483 AACTGGTCATCGAAGCGCCT 62.172 55.000 2.29 0.00 0.00 5.52
1284 1290 0.751277 CCACCTGCACAAACTGGTCA 60.751 55.000 0.00 0.00 39.62 4.02
1329 1335 4.891727 AGATAGTTGGCCGCCGCG 62.892 66.667 5.59 5.59 35.02 6.46
1442 1448 3.475774 CGGCGGTGTAGTCGTTGC 61.476 66.667 0.00 0.00 34.13 4.17
1446 1452 1.298413 CTCATCGGCGGTGTAGTCG 60.298 63.158 20.91 1.19 41.09 4.18
1470 1476 0.394080 AGTTCTCCCTACGGACCTCG 60.394 60.000 0.00 0.00 45.88 4.63
1525 1531 0.737219 AGCCTACCTAACGTGCGTAG 59.263 55.000 0.00 9.05 0.00 3.51
1529 1535 1.337387 CTCCTAGCCTACCTAACGTGC 59.663 57.143 0.00 0.00 0.00 5.34
1537 1543 5.128008 GGATTGATATGTCTCCTAGCCTACC 59.872 48.000 0.00 0.00 0.00 3.18
1549 1555 8.671921 GTGGATGTATTGATGGATTGATATGTC 58.328 37.037 0.00 0.00 0.00 3.06
1563 1569 2.401583 AGCAAGCGTGGATGTATTGA 57.598 45.000 0.79 0.00 0.00 2.57
1579 1585 6.434028 AGCCAAAACATATTTAGTCTCAAGCA 59.566 34.615 0.00 0.00 0.00 3.91
1580 1586 6.856895 AGCCAAAACATATTTAGTCTCAAGC 58.143 36.000 0.00 0.00 0.00 4.01
1581 1587 8.299570 ACAAGCCAAAACATATTTAGTCTCAAG 58.700 33.333 0.00 0.00 0.00 3.02
1582 1588 8.081633 CACAAGCCAAAACATATTTAGTCTCAA 58.918 33.333 0.00 0.00 0.00 3.02
1583 1589 7.230510 ACACAAGCCAAAACATATTTAGTCTCA 59.769 33.333 0.00 0.00 0.00 3.27
1584 1590 7.593825 ACACAAGCCAAAACATATTTAGTCTC 58.406 34.615 0.00 0.00 0.00 3.36
1617 1628 7.870509 AATCGGCTTGCATCAACATATATAT 57.129 32.000 0.00 0.00 0.00 0.86
1677 1689 2.479656 CCAATTGGCGGAACAACATTTG 59.520 45.455 12.53 0.00 32.39 2.32
1720 1732 9.905713 AGGAGTAGCAAACAATATTAGAATTGA 57.094 29.630 3.73 0.00 38.84 2.57
1811 1823 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
1847 1859 2.742589 GTCGGTTGAAGGGAATCACTTC 59.257 50.000 17.79 17.79 43.52 3.01
1848 1860 2.372172 AGTCGGTTGAAGGGAATCACTT 59.628 45.455 0.00 0.00 0.00 3.16
1849 1861 1.978580 AGTCGGTTGAAGGGAATCACT 59.021 47.619 0.00 0.00 0.00 3.41
1850 1862 2.076863 CAGTCGGTTGAAGGGAATCAC 58.923 52.381 0.00 0.00 0.00 3.06
1851 1863 1.974957 TCAGTCGGTTGAAGGGAATCA 59.025 47.619 0.00 0.00 0.00 2.57
1852 1864 2.762535 TCAGTCGGTTGAAGGGAATC 57.237 50.000 0.00 0.00 0.00 2.52
1853 1865 2.840651 AGATCAGTCGGTTGAAGGGAAT 59.159 45.455 0.00 0.00 0.00 3.01
1854 1866 2.257207 AGATCAGTCGGTTGAAGGGAA 58.743 47.619 0.00 0.00 0.00 3.97
1855 1867 1.938585 AGATCAGTCGGTTGAAGGGA 58.061 50.000 0.00 0.00 0.00 4.20
1856 1868 2.289694 ACAAGATCAGTCGGTTGAAGGG 60.290 50.000 0.00 0.00 0.00 3.95
1857 1869 2.738846 CACAAGATCAGTCGGTTGAAGG 59.261 50.000 0.00 0.00 0.00 3.46
1858 1870 2.158449 GCACAAGATCAGTCGGTTGAAG 59.842 50.000 0.00 0.00 0.00 3.02
1859 1871 2.143122 GCACAAGATCAGTCGGTTGAA 58.857 47.619 0.00 0.00 0.00 2.69
1860 1872 1.795768 GCACAAGATCAGTCGGTTGA 58.204 50.000 0.00 0.00 0.00 3.18
1861 1873 0.439985 CGCACAAGATCAGTCGGTTG 59.560 55.000 0.00 0.00 0.00 3.77
1862 1874 0.317160 TCGCACAAGATCAGTCGGTT 59.683 50.000 0.00 0.00 0.00 4.44
1863 1875 0.109086 CTCGCACAAGATCAGTCGGT 60.109 55.000 0.00 0.00 0.00 4.69
1868 1880 2.663879 GCAAACACTCGCACAAGATCAG 60.664 50.000 0.00 0.00 0.00 2.90
1883 1895 1.971167 GACATGGAGGCCGCAAACA 60.971 57.895 9.31 0.00 0.00 2.83
1886 1898 2.046023 CAGACATGGAGGCCGCAA 60.046 61.111 9.31 0.00 0.00 4.85
1887 1899 3.315142 GACAGACATGGAGGCCGCA 62.315 63.158 9.31 0.00 0.00 5.69
1902 1914 1.066430 GTTTCACTAGCCCATCCGACA 60.066 52.381 0.00 0.00 0.00 4.35
1927 1939 2.738964 GCAGAACGTGAGATTACCTCCC 60.739 54.545 0.00 0.00 41.25 4.30
1942 1954 1.956477 ACAATGGACCAGTTGCAGAAC 59.044 47.619 0.00 0.00 0.00 3.01
1951 1963 4.810491 CCACTTTCAAAAACAATGGACCAG 59.190 41.667 0.00 0.00 0.00 4.00
1972 1984 1.729586 AGGGACTAGTTGCAGAACCA 58.270 50.000 0.00 0.00 36.02 3.67
1974 1986 3.127425 ACAAGGGACTAGTTGCAGAAC 57.873 47.619 0.00 0.00 38.49 3.01
1979 1991 2.152016 GGTCAACAAGGGACTAGTTGC 58.848 52.381 0.00 0.00 41.67 4.17
2028 2040 8.938906 GCAACATTGGTCATTTCTTTTATGAAT 58.061 29.630 0.00 0.00 34.06 2.57
2069 2089 7.306167 GCGGAAACATTTGCAACATAGATTATG 60.306 37.037 0.00 0.00 41.88 1.90
2070 2090 6.697019 GCGGAAACATTTGCAACATAGATTAT 59.303 34.615 0.00 0.00 0.00 1.28
2071 2091 6.033341 GCGGAAACATTTGCAACATAGATTA 58.967 36.000 0.00 0.00 0.00 1.75
2073 2093 4.082300 TGCGGAAACATTTGCAACATAGAT 60.082 37.500 0.00 0.00 33.80 1.98
2074 2094 3.254411 TGCGGAAACATTTGCAACATAGA 59.746 39.130 0.00 0.00 33.80 1.98
2088 2108 1.864029 GCAAGGTCTTGTTGCGGAAAC 60.864 52.381 11.71 0.00 40.87 2.78
2117 2138 1.808411 TCGACCAGCCAAACATCTTC 58.192 50.000 0.00 0.00 0.00 2.87
2118 2139 2.489329 CAATCGACCAGCCAAACATCTT 59.511 45.455 0.00 0.00 0.00 2.40
2119 2140 2.086869 CAATCGACCAGCCAAACATCT 58.913 47.619 0.00 0.00 0.00 2.90
2120 2141 1.812571 ACAATCGACCAGCCAAACATC 59.187 47.619 0.00 0.00 0.00 3.06
2121 2142 1.541147 CACAATCGACCAGCCAAACAT 59.459 47.619 0.00 0.00 0.00 2.71
2122 2143 0.950836 CACAATCGACCAGCCAAACA 59.049 50.000 0.00 0.00 0.00 2.83
2123 2144 0.951558 ACACAATCGACCAGCCAAAC 59.048 50.000 0.00 0.00 0.00 2.93
2124 2145 1.234821 GACACAATCGACCAGCCAAA 58.765 50.000 0.00 0.00 0.00 3.28
2125 2146 0.107643 TGACACAATCGACCAGCCAA 59.892 50.000 0.00 0.00 0.00 4.52
2126 2147 0.320683 CTGACACAATCGACCAGCCA 60.321 55.000 0.00 0.00 0.00 4.75
2127 2148 0.037326 TCTGACACAATCGACCAGCC 60.037 55.000 0.00 0.00 0.00 4.85
2128 2149 1.461127 GTTCTGACACAATCGACCAGC 59.539 52.381 0.00 0.00 0.00 4.85
2129 2150 2.069273 GGTTCTGACACAATCGACCAG 58.931 52.381 0.00 0.00 0.00 4.00
2130 2151 1.604438 CGGTTCTGACACAATCGACCA 60.604 52.381 0.00 0.00 0.00 4.02
2131 2152 1.068474 CGGTTCTGACACAATCGACC 58.932 55.000 0.00 0.00 0.00 4.79
2132 2153 2.060326 TCGGTTCTGACACAATCGAC 57.940 50.000 0.00 0.00 0.00 4.20
2133 2154 2.606108 CATCGGTTCTGACACAATCGA 58.394 47.619 1.17 1.17 0.00 3.59
2134 2155 1.660607 CCATCGGTTCTGACACAATCG 59.339 52.381 0.00 0.00 0.00 3.34
2135 2156 1.398390 GCCATCGGTTCTGACACAATC 59.602 52.381 0.00 0.00 0.00 2.67
2136 2157 1.003580 AGCCATCGGTTCTGACACAAT 59.996 47.619 0.00 0.00 0.00 2.71
2137 2158 0.396435 AGCCATCGGTTCTGACACAA 59.604 50.000 0.00 0.00 0.00 3.33
2138 2159 0.037326 GAGCCATCGGTTCTGACACA 60.037 55.000 0.00 0.00 30.11 3.72
2177 2198 3.876198 GGTTGCTACATGCCGCCG 61.876 66.667 0.00 0.00 42.00 6.46
2184 2205 0.704076 ACACATGGGGGTTGCTACAT 59.296 50.000 0.00 0.00 0.00 2.29
2193 2214 1.181786 AACGCATTAACACATGGGGG 58.818 50.000 0.00 0.00 40.56 5.40
2194 2215 3.249917 GAAAACGCATTAACACATGGGG 58.750 45.455 0.00 0.00 40.56 4.96
2200 2221 7.008810 TGAGAAAACTTGAAAACGCATTAACAC 59.991 33.333 0.00 0.00 0.00 3.32
2222 2243 8.096414 TCTGTCAAAACAATATCATGTCTGAGA 58.904 33.333 0.00 0.00 34.24 3.27
2223 2244 8.260270 TCTGTCAAAACAATATCATGTCTGAG 57.740 34.615 0.00 0.00 34.24 3.35
2224 2245 7.335171 CCTCTGTCAAAACAATATCATGTCTGA 59.665 37.037 0.00 0.00 34.24 3.27
2225 2246 7.120285 ACCTCTGTCAAAACAATATCATGTCTG 59.880 37.037 0.00 0.00 34.24 3.51
2226 2247 7.170965 ACCTCTGTCAAAACAATATCATGTCT 58.829 34.615 0.00 0.00 34.24 3.41
2227 2248 7.383102 ACCTCTGTCAAAACAATATCATGTC 57.617 36.000 0.00 0.00 34.24 3.06
2231 2252 9.295825 ACATTTACCTCTGTCAAAACAATATCA 57.704 29.630 0.00 0.00 34.24 2.15
2242 2263 3.568007 GCACCAAACATTTACCTCTGTCA 59.432 43.478 0.00 0.00 0.00 3.58
2253 2274 0.249996 GCTTGCTGGCACCAAACATT 60.250 50.000 0.00 0.00 0.00 2.71
2266 2287 3.003173 TGAGGTAGCCGGCTTGCT 61.003 61.111 37.74 13.72 45.38 3.91
2270 2291 3.760035 CGTGTGAGGTAGCCGGCT 61.760 66.667 34.85 34.85 0.00 5.52
2296 2333 2.552231 GATAAAGCGGTGGTGGGGCT 62.552 60.000 0.00 0.00 39.01 5.19
2307 2344 5.050972 GGGTCATTTTCGAGTAGATAAAGCG 60.051 44.000 0.00 0.00 0.00 4.68
2323 2377 1.846439 AGATGATGGTCCGGGTCATTT 59.154 47.619 0.00 0.00 33.03 2.32
2326 2380 1.048724 GGAGATGATGGTCCGGGTCA 61.049 60.000 0.00 0.00 0.00 4.02
2327 2381 1.749033 GGAGATGATGGTCCGGGTC 59.251 63.158 0.00 0.00 0.00 4.46
2353 2407 0.034477 GCCGAGGAAAAAGGGGATCA 60.034 55.000 0.00 0.00 0.00 2.92
2387 2442 1.228245 GGGAGTCAGCTTGTTGCCA 60.228 57.895 0.00 0.00 44.23 4.92
2446 2501 1.228003 CGGTGGTTGCACCTTGGTA 60.228 57.895 0.00 0.00 42.87 3.25
2468 2523 1.301716 GCCCTCTTCTCACAACGCA 60.302 57.895 0.00 0.00 0.00 5.24
2484 2539 4.426313 GGGCACACACCTAGGGCC 62.426 72.222 14.81 15.28 43.86 5.80


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

AutoCloner maintained by Alex Coulton.