Multiple sequence alignment - TraesCS1D01G114900

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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 TraesCS1D01G114900 chr1D 100.000 2459 0 0 1 2459 110734844 110732386 0.000000e+00 4542.0
1 TraesCS1D01G114900 chr1A 93.728 861 46 5 23 878 116696783 116695926 0.000000e+00 1284.0
2 TraesCS1D01G114900 chr1A 87.696 382 15 16 1658 2014 116695930 116695556 1.360000e-112 416.0
3 TraesCS1D01G114900 chr1A 96.491 57 0 2 1833 1888 116695644 116695589 2.600000e-15 93.5
4 TraesCS1D01G114900 chr1A 92.857 56 2 1 2404 2459 116694541 116694488 2.030000e-11 80.5
5 TraesCS1D01G114900 chr1B 93.677 854 51 3 25 878 168973372 168972522 0.000000e+00 1275.0
6 TraesCS1D01G114900 chr1B 88.764 267 29 1 2042 2308 168989084 168988819 2.360000e-85 326.0
7 TraesCS1D01G114900 chr1B 92.308 156 3 3 1886 2032 168972426 168972271 1.920000e-51 213.0
8 TraesCS1D01G114900 chr1B 90.123 162 6 3 1643 1804 168972537 168972386 4.150000e-48 202.0
9 TraesCS1D01G114900 chr1B 93.694 111 5 2 2277 2386 168971024 168970915 5.440000e-37 165.0
10 TraesCS1D01G114900 chr1B 93.694 111 5 2 2277 2386 168988813 168988704 5.440000e-37 165.0
11 TraesCS1D01G114900 chr1B 96.000 50 0 1 2410 2459 168970849 168970802 2.030000e-11 80.5
12 TraesCS1D01G114900 chr1B 96.000 50 0 1 2410 2459 168988638 168988591 2.030000e-11 80.5
13 TraesCS1D01G114900 chr7B 92.894 577 33 3 870 1439 711754235 711754810 0.000000e+00 832.0
14 TraesCS1D01G114900 chr7B 90.686 204 19 0 1425 1628 711754836 711755039 3.120000e-69 272.0
15 TraesCS1D01G114900 chr7D 95.532 470 19 2 870 1339 56295613 56295146 0.000000e+00 750.0
16 TraesCS1D01G114900 chr7D 92.833 293 19 1 1332 1624 56294880 56294590 8.130000e-115 424.0
17 TraesCS1D01G114900 chr2A 92.135 267 21 0 973 1239 17317693 17317959 6.420000e-101 377.0
18 TraesCS1D01G114900 chr2A 89.091 110 9 2 1516 1625 21142363 21142257 1.530000e-27 134.0
19 TraesCS1D01G114900 chr2A 90.476 84 6 2 855 937 17317606 17317688 2.590000e-20 110.0
20 TraesCS1D01G114900 chr3A 78.968 252 48 4 514 764 59425805 59425558 1.510000e-37 167.0
21 TraesCS1D01G114900 chr7A 91.176 102 9 0 1508 1609 518656525 518656424 3.300000e-29 139.0
22 TraesCS1D01G114900 chr4D 88.679 106 11 1 1523 1628 113163867 113163971 7.140000e-26 128.0
23 TraesCS1D01G114900 chr4B 91.209 91 8 0 1523 1613 173365506 173365596 9.230000e-25 124.0


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 TraesCS1D01G114900 chr1D 110732386 110734844 2458 True 4542.0 4542 100.0000 1 2459 1 chr1D.!!$R1 2458
1 TraesCS1D01G114900 chr1A 116694488 116696783 2295 True 468.5 1284 92.6930 23 2459 4 chr1A.!!$R1 2436
2 TraesCS1D01G114900 chr1B 168970802 168973372 2570 True 387.1 1275 93.1604 25 2459 5 chr1B.!!$R1 2434
3 TraesCS1D01G114900 chr7B 711754235 711755039 804 False 552.0 832 91.7900 870 1628 2 chr7B.!!$F1 758
4 TraesCS1D01G114900 chr7D 56294590 56295613 1023 True 587.0 750 94.1825 870 1624 2 chr7D.!!$R1 754

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
144 145 0.608856 TGATGTCGTGGGCAAGCATT 60.609 50.0 0.0 0.0 0.0 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1525 1851 0.615544 CAGGGGCATCCAACAACCAT 60.616 55.0 0.0 0.0 38.24 3.55 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
61 62 8.461222 GTTGTCATGGATTCATTCATTGTAAGA 58.539 33.333 0.00 0.00 0.00 2.10
132 133 0.926155 CGGTGAAGAGCATGATGTCG 59.074 55.000 0.00 0.00 0.00 4.35
138 139 1.450134 GAGCATGATGTCGTGGGCA 60.450 57.895 0.00 0.00 33.60 5.36
144 145 0.608856 TGATGTCGTGGGCAAGCATT 60.609 50.000 0.00 0.00 0.00 3.56
416 417 6.693113 TCTCTCACAGTCAAAAATATCGATCG 59.307 38.462 9.36 9.36 0.00 3.69
417 418 6.330278 TCTCACAGTCAAAAATATCGATCGT 58.670 36.000 15.94 5.23 0.00 3.73
470 471 2.268107 ACGGAGTAAAATGGGGTGGTA 58.732 47.619 0.00 0.00 41.94 3.25
484 485 1.002684 GGTGGTAGATACGACGCTGAG 60.003 57.143 0.00 0.00 36.02 3.35
503 504 4.626081 GGCGTGTCAGCAGTGGGT 62.626 66.667 0.00 0.00 39.27 4.51
533 534 1.295423 GTAGAGTGCGGCCTGGAAA 59.705 57.895 0.00 0.00 0.00 3.13
628 629 2.259818 CACCTCACGCTCGAAGCT 59.740 61.111 0.00 0.00 39.60 3.74
635 636 2.433145 CGCTCGAAGCTTGGCTCA 60.433 61.111 2.10 0.00 38.25 4.26
683 684 3.440228 GGAGAAGTAACTCATCGTCTGC 58.560 50.000 0.00 0.00 38.51 4.26
684 685 3.440228 GAGAAGTAACTCATCGTCTGCC 58.560 50.000 0.00 0.00 36.95 4.85
824 829 1.808343 GTACAAAGTTTGGTAGGGCGG 59.192 52.381 19.45 0.00 34.12 6.13
845 851 3.257375 GGGACCAAAGATAACACAAACCC 59.743 47.826 0.00 0.00 0.00 4.11
859 865 4.832266 ACACAAACCCATAGCTTTTGATGA 59.168 37.500 13.40 0.00 34.84 2.92
930 936 6.676950 AGAAACGATATGTTGCATGACAAAA 58.323 32.000 0.00 0.00 40.84 2.44
947 953 4.651778 ACAAAATAGCTGCTACTGTGGAA 58.348 39.130 12.26 0.00 0.00 3.53
948 954 5.070001 ACAAAATAGCTGCTACTGTGGAAA 58.930 37.500 12.26 0.00 0.00 3.13
949 955 5.534654 ACAAAATAGCTGCTACTGTGGAAAA 59.465 36.000 12.26 0.00 0.00 2.29
1158 1168 5.475719 TCTACTGATGGTTCTTTTGGTACG 58.524 41.667 0.00 0.00 0.00 3.67
1172 1182 0.872881 GGTACGTGCGATAATGGCGT 60.873 55.000 0.00 0.00 39.23 5.68
1214 1224 0.864455 GATAGCAGCGGAAGACATGC 59.136 55.000 0.00 0.00 38.97 4.06
1215 1225 0.533755 ATAGCAGCGGAAGACATGCC 60.534 55.000 0.00 0.00 39.51 4.40
1243 1253 0.820871 TTGTTGGTTTGTGCCTCACC 59.179 50.000 0.00 0.00 32.73 4.02
1269 1279 2.481952 AGATGCGTTTGAAGCTGAACTC 59.518 45.455 0.00 0.00 35.28 3.01
1371 1657 9.660180 GTTGTGAAGATACTAAAAGAGAAGGAT 57.340 33.333 0.00 0.00 0.00 3.24
1452 1778 7.122715 AGAGAGAGAGAGCTTGTCCTTTTATA 58.877 38.462 0.00 0.00 0.00 0.98
1485 1811 3.523157 TCCCAGAATAAGGTTGCAGATCA 59.477 43.478 0.00 0.00 0.00 2.92
1525 1851 1.503542 GGAGCGTCGAACCGAGTTA 59.496 57.895 0.00 0.00 36.23 2.24
1580 1906 5.209818 CCTTCTGGCTACCGATTGTAATA 57.790 43.478 0.00 0.00 0.00 0.98
1621 1947 5.945144 AGCTCCCTTTATCAATGCAAAAT 57.055 34.783 0.00 0.00 0.00 1.82
1624 1950 8.026396 AGCTCCCTTTATCAATGCAAAATAAT 57.974 30.769 0.00 0.00 0.00 1.28
1677 2003 8.078596 GGGTACGTACTTGGTGTTAGATTATAG 58.921 40.741 24.07 0.00 0.00 1.31
1678 2004 8.078596 GGTACGTACTTGGTGTTAGATTATAGG 58.921 40.741 24.07 0.00 0.00 2.57
1679 2005 7.886629 ACGTACTTGGTGTTAGATTATAGGA 57.113 36.000 0.00 0.00 0.00 2.94
1680 2006 7.938715 ACGTACTTGGTGTTAGATTATAGGAG 58.061 38.462 0.00 0.00 0.00 3.69
1681 2007 7.559170 ACGTACTTGGTGTTAGATTATAGGAGT 59.441 37.037 0.00 0.00 0.00 3.85
1682 2008 9.060347 CGTACTTGGTGTTAGATTATAGGAGTA 57.940 37.037 0.00 0.00 0.00 2.59
1705 2031 6.944234 ACTTCTATATAAACAAAGCTGCCC 57.056 37.500 0.00 0.00 0.00 5.36
1784 2249 4.753107 ACGTTTCTGTCATGGTAAAATCGT 59.247 37.500 0.00 0.00 0.00 3.73
1785 2250 5.107220 ACGTTTCTGTCATGGTAAAATCGTC 60.107 40.000 0.00 0.00 0.00 4.20
1786 2251 5.107259 CGTTTCTGTCATGGTAAAATCGTCA 60.107 40.000 0.00 0.00 0.00 4.35
1787 2252 6.402118 CGTTTCTGTCATGGTAAAATCGTCAT 60.402 38.462 0.00 0.00 0.00 3.06
1788 2253 7.201487 CGTTTCTGTCATGGTAAAATCGTCATA 60.201 37.037 0.00 0.00 0.00 2.15
1789 2254 7.770801 TTCTGTCATGGTAAAATCGTCATAG 57.229 36.000 0.00 0.00 0.00 2.23
1790 2255 6.873997 TCTGTCATGGTAAAATCGTCATAGT 58.126 36.000 0.00 0.00 0.00 2.12
1791 2256 8.002984 TCTGTCATGGTAAAATCGTCATAGTA 57.997 34.615 0.00 0.00 0.00 1.82
1792 2257 8.471609 TCTGTCATGGTAAAATCGTCATAGTAA 58.528 33.333 0.00 0.00 0.00 2.24
1793 2258 9.093970 CTGTCATGGTAAAATCGTCATAGTAAA 57.906 33.333 0.00 0.00 0.00 2.01
1794 2259 9.607988 TGTCATGGTAAAATCGTCATAGTAAAT 57.392 29.630 0.00 0.00 0.00 1.40
1800 2265 9.807386 GGTAAAATCGTCATAGTAAATACATGC 57.193 33.333 0.00 0.00 0.00 4.06
1801 2266 9.807386 GTAAAATCGTCATAGTAAATACATGCC 57.193 33.333 0.00 0.00 0.00 4.40
1802 2267 8.445275 AAAATCGTCATAGTAAATACATGCCA 57.555 30.769 0.00 0.00 0.00 4.92
1803 2268 7.421530 AATCGTCATAGTAAATACATGCCAC 57.578 36.000 0.00 0.00 0.00 5.01
1804 2269 6.156748 TCGTCATAGTAAATACATGCCACT 57.843 37.500 0.00 0.00 0.00 4.00
1805 2270 6.578944 TCGTCATAGTAAATACATGCCACTT 58.421 36.000 0.00 0.00 0.00 3.16
1806 2271 7.045416 TCGTCATAGTAAATACATGCCACTTT 58.955 34.615 0.00 0.00 0.00 2.66
1807 2272 7.551262 TCGTCATAGTAAATACATGCCACTTTT 59.449 33.333 0.00 0.00 0.00 2.27
1808 2273 8.822855 CGTCATAGTAAATACATGCCACTTTTA 58.177 33.333 0.00 0.00 0.00 1.52
1811 2276 9.811655 CATAGTAAATACATGCCACTTTTATCG 57.188 33.333 0.00 0.00 0.00 2.92
1812 2277 6.725246 AGTAAATACATGCCACTTTTATCGC 58.275 36.000 0.00 0.00 0.00 4.58
1813 2278 5.574891 AAATACATGCCACTTTTATCGCA 57.425 34.783 0.00 0.00 35.35 5.10
1814 2279 5.574891 AATACATGCCACTTTTATCGCAA 57.425 34.783 0.00 0.00 34.38 4.85
1815 2280 3.932545 ACATGCCACTTTTATCGCAAA 57.067 38.095 0.00 0.00 34.38 3.68
1816 2281 4.250116 ACATGCCACTTTTATCGCAAAA 57.750 36.364 0.00 0.00 34.38 2.44
1817 2282 4.626042 ACATGCCACTTTTATCGCAAAAA 58.374 34.783 0.00 0.00 34.38 1.94
1862 2327 6.870971 TTTTCTTTCCACTAGTAAATGCGT 57.129 33.333 0.00 0.00 0.00 5.24
1863 2328 7.966246 TTTTCTTTCCACTAGTAAATGCGTA 57.034 32.000 0.00 0.00 0.00 4.42
1864 2329 6.956299 TTCTTTCCACTAGTAAATGCGTAC 57.044 37.500 0.00 0.00 0.00 3.67
1865 2330 6.028146 TCTTTCCACTAGTAAATGCGTACA 57.972 37.500 0.00 0.00 0.00 2.90
1866 2331 6.636705 TCTTTCCACTAGTAAATGCGTACAT 58.363 36.000 0.00 0.00 38.49 2.29
1881 2346 6.867799 TGCGTACATTTTTAGATGCAAATG 57.132 33.333 5.24 5.24 43.31 2.32
1882 2347 5.288232 TGCGTACATTTTTAGATGCAAATGC 59.712 36.000 6.48 0.00 42.01 3.56
1883 2348 8.317563 ATGCGTACATTTTTAGATGCAAATGCA 61.318 33.333 10.94 10.94 44.82 3.96
1896 2361 4.577687 GCAAATGCATGTTTCTGTCATG 57.422 40.909 0.00 0.00 43.58 3.07
1897 2362 3.369756 GCAAATGCATGTTTCTGTCATGG 59.630 43.478 0.00 0.00 41.77 3.66
1898 2363 4.562082 CAAATGCATGTTTCTGTCATGGT 58.438 39.130 0.00 0.00 41.77 3.55
1899 2364 5.712004 CAAATGCATGTTTCTGTCATGGTA 58.288 37.500 0.00 0.00 41.77 3.25
1900 2365 5.981088 AATGCATGTTTCTGTCATGGTAA 57.019 34.783 0.00 0.00 41.77 2.85
1901 2366 5.981088 ATGCATGTTTCTGTCATGGTAAA 57.019 34.783 0.00 0.00 41.77 2.01
1902 2367 5.781210 TGCATGTTTCTGTCATGGTAAAA 57.219 34.783 7.78 0.00 41.77 1.52
1903 2368 6.343716 TGCATGTTTCTGTCATGGTAAAAT 57.656 33.333 7.78 0.00 41.77 1.82
1904 2369 6.389091 TGCATGTTTCTGTCATGGTAAAATC 58.611 36.000 7.78 0.00 41.77 2.17
1905 2370 6.015603 TGCATGTTTCTGTCATGGTAAAATCA 60.016 34.615 7.78 0.00 41.77 2.57
2045 3000 7.846107 GCAACAGTCATGTCACTATTTAATACG 59.154 37.037 0.00 0.00 39.29 3.06
2146 3101 9.561270 CTAGACACATTTATAGATACATCCGTG 57.439 37.037 0.00 0.00 0.00 4.94
2151 3106 8.703336 CACATTTATAGATACATCCGTGTCAAG 58.297 37.037 0.00 0.00 39.77 3.02
2152 3107 8.421784 ACATTTATAGATACATCCGTGTCAAGT 58.578 33.333 0.00 0.00 39.77 3.16
2174 3178 7.171630 AGTAATTTGAGACGGAGATTGTACT 57.828 36.000 0.00 0.00 0.00 2.73
2181 3185 5.708697 TGAGACGGAGATTGTACTAAGTCAA 59.291 40.000 0.00 0.00 32.69 3.18
2187 3191 6.331061 GGAGATTGTACTAAGTCAACGACAT 58.669 40.000 0.00 0.00 34.60 3.06
2211 3222 9.381027 CATTTATTGCATACTAAACACATACCG 57.619 33.333 0.00 0.00 0.00 4.02
2217 3228 5.448089 GCATACTAAACACATACCGTTTGGG 60.448 44.000 0.00 0.00 38.66 4.12
2267 3625 3.963129 TGATTATGCCCCTTTTCGTCTT 58.037 40.909 0.00 0.00 0.00 3.01
2269 3627 4.770010 TGATTATGCCCCTTTTCGTCTTTT 59.230 37.500 0.00 0.00 0.00 2.27
2270 3628 5.245075 TGATTATGCCCCTTTTCGTCTTTTT 59.755 36.000 0.00 0.00 0.00 1.94
2271 3629 6.434652 TGATTATGCCCCTTTTCGTCTTTTTA 59.565 34.615 0.00 0.00 0.00 1.52
2272 3630 6.844097 TTATGCCCCTTTTCGTCTTTTTAT 57.156 33.333 0.00 0.00 0.00 1.40
2273 3631 5.738619 ATGCCCCTTTTCGTCTTTTTATT 57.261 34.783 0.00 0.00 0.00 1.40
2274 3632 4.877282 TGCCCCTTTTCGTCTTTTTATTG 58.123 39.130 0.00 0.00 0.00 1.90
2276 3634 4.262292 GCCCCTTTTCGTCTTTTTATTGGT 60.262 41.667 0.00 0.00 0.00 3.67
2277 3635 5.047872 GCCCCTTTTCGTCTTTTTATTGGTA 60.048 40.000 0.00 0.00 0.00 3.25
2278 3636 6.350696 GCCCCTTTTCGTCTTTTTATTGGTAT 60.351 38.462 0.00 0.00 0.00 2.73
2279 3637 7.148035 GCCCCTTTTCGTCTTTTTATTGGTATA 60.148 37.037 0.00 0.00 0.00 1.47
2331 4050 9.315525 GATGGATTAGTAGTGTTAGAGGAAAAC 57.684 37.037 0.00 0.00 0.00 2.43
2332 4051 7.318141 TGGATTAGTAGTGTTAGAGGAAAACG 58.682 38.462 0.00 0.00 0.00 3.60
2333 4052 6.255237 GGATTAGTAGTGTTAGAGGAAAACGC 59.745 42.308 0.00 0.00 37.56 4.84
2386 4105 9.338622 GGAAACGTACCTATACCTAACTAACTA 57.661 37.037 0.00 0.00 0.00 2.24
2389 4108 9.907229 AACGTACCTATACCTAACTAACTAACT 57.093 33.333 0.00 0.00 0.00 2.24
2390 4109 9.331282 ACGTACCTATACCTAACTAACTAACTG 57.669 37.037 0.00 0.00 0.00 3.16
2391 4110 9.331282 CGTACCTATACCTAACTAACTAACTGT 57.669 37.037 0.00 0.00 0.00 3.55
2442 4225 4.405358 TCAGGTAGACATGCATGTATCACA 59.595 41.667 31.45 11.76 41.95 3.58
2443 4226 4.509230 CAGGTAGACATGCATGTATCACAC 59.491 45.833 31.45 21.98 41.95 3.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.856629 ACTCCCTCCGTTCCGAATTA 58.143 50.000 0.00 0.00 0.00 1.40
1 2 1.479730 GTACTCCCTCCGTTCCGAATT 59.520 52.381 0.00 0.00 0.00 2.17
2 3 1.109609 GTACTCCCTCCGTTCCGAAT 58.890 55.000 0.00 0.00 0.00 3.34
3 4 1.308069 CGTACTCCCTCCGTTCCGAA 61.308 60.000 0.00 0.00 0.00 4.30
4 5 1.746615 CGTACTCCCTCCGTTCCGA 60.747 63.158 0.00 0.00 0.00 4.55
5 6 1.308069 TTCGTACTCCCTCCGTTCCG 61.308 60.000 0.00 0.00 0.00 4.30
6 7 0.455005 CTTCGTACTCCCTCCGTTCC 59.545 60.000 0.00 0.00 0.00 3.62
7 8 1.172175 ACTTCGTACTCCCTCCGTTC 58.828 55.000 0.00 0.00 0.00 3.95
8 9 2.496899 TACTTCGTACTCCCTCCGTT 57.503 50.000 0.00 0.00 0.00 4.44
9 10 2.496899 TTACTTCGTACTCCCTCCGT 57.503 50.000 0.00 0.00 0.00 4.69
10 11 4.336433 TGTATTTACTTCGTACTCCCTCCG 59.664 45.833 0.00 0.00 0.00 4.63
11 12 5.841957 TGTATTTACTTCGTACTCCCTCC 57.158 43.478 0.00 0.00 0.00 4.30
12 13 6.803642 ACATGTATTTACTTCGTACTCCCTC 58.196 40.000 0.00 0.00 0.00 4.30
13 14 6.786967 ACATGTATTTACTTCGTACTCCCT 57.213 37.500 0.00 0.00 0.00 4.20
14 15 6.815142 ACAACATGTATTTACTTCGTACTCCC 59.185 38.462 0.00 0.00 0.00 4.30
15 16 7.543172 TGACAACATGTATTTACTTCGTACTCC 59.457 37.037 0.00 0.00 0.00 3.85
16 17 8.456904 TGACAACATGTATTTACTTCGTACTC 57.543 34.615 0.00 0.00 0.00 2.59
17 18 8.869897 CATGACAACATGTATTTACTTCGTACT 58.130 33.333 0.00 0.00 46.01 2.73
38 39 8.627403 ACATCTTACAATGAATGAATCCATGAC 58.373 33.333 0.00 0.00 32.36 3.06
61 62 5.047021 CGAGGATAGGGTAATCACATCACAT 60.047 44.000 0.00 0.00 0.00 3.21
132 133 1.004679 CACCCAAATGCTTGCCCAC 60.005 57.895 0.00 0.00 0.00 4.61
138 139 1.077663 ACTCCCATCACCCAAATGCTT 59.922 47.619 0.00 0.00 0.00 3.91
144 145 1.628340 CAGTACACTCCCATCACCCAA 59.372 52.381 0.00 0.00 0.00 4.12
325 326 0.247736 CCCTTGACGGACTTCCTCAG 59.752 60.000 0.00 0.00 33.16 3.35
430 431 9.439500 ACTCCGTAAGCATTAGTTTATTTTGTA 57.561 29.630 0.00 0.00 0.00 2.41
458 459 2.101917 CGTCGTATCTACCACCCCATTT 59.898 50.000 0.00 0.00 0.00 2.32
461 462 1.386525 GCGTCGTATCTACCACCCCA 61.387 60.000 0.00 0.00 0.00 4.96
467 468 0.592148 CCCTCAGCGTCGTATCTACC 59.408 60.000 0.00 0.00 0.00 3.18
470 471 2.491022 GCCCCTCAGCGTCGTATCT 61.491 63.158 0.00 0.00 0.00 1.98
490 491 3.569210 CCCCACCCACTGCTGACA 61.569 66.667 0.00 0.00 0.00 3.58
533 534 3.077556 ACCGGATCCTCGCAGCTT 61.078 61.111 9.46 0.00 0.00 3.74
628 629 0.538057 CTGCTGGTTCCTTGAGCCAA 60.538 55.000 1.32 0.00 42.06 4.52
635 636 0.538287 GCAACCTCTGCTGGTTCCTT 60.538 55.000 6.42 0.00 46.37 3.36
736 737 2.159517 GGTGATCCAACGATGTTTGAGC 60.160 50.000 0.00 0.00 0.00 4.26
824 829 3.892588 TGGGTTTGTGTTATCTTTGGTCC 59.107 43.478 0.00 0.00 0.00 4.46
878 884 4.646040 TGCCAGTTCCTCCAAATTATCATG 59.354 41.667 0.00 0.00 0.00 3.07
930 936 4.286297 TGTTTTCCACAGTAGCAGCTAT 57.714 40.909 5.14 0.00 0.00 2.97
1113 1123 2.677875 GCCAGCCAACCTTCAGGG 60.678 66.667 0.00 0.00 40.27 4.45
1158 1168 0.878523 TGCCTACGCCATTATCGCAC 60.879 55.000 0.00 0.00 0.00 5.34
1172 1182 7.839680 TCTCTAGTAATCATTGATGTGCCTA 57.160 36.000 0.00 0.00 0.00 3.93
1214 1224 2.168313 ACAAACCAACAAGCAGAAAGGG 59.832 45.455 0.00 0.00 0.00 3.95
1215 1225 3.189285 CACAAACCAACAAGCAGAAAGG 58.811 45.455 0.00 0.00 0.00 3.11
1269 1279 1.202580 CGGACTCCTCTAATTGCCAGG 60.203 57.143 0.00 0.00 0.00 4.45
1371 1657 4.972568 TGGCCCAGGTATGACTTATTCTTA 59.027 41.667 0.00 0.00 0.00 2.10
1403 1689 7.071321 TCTCTCCTAACATCTCCTTAATTTCCC 59.929 40.741 0.00 0.00 0.00 3.97
1452 1778 9.305555 CAACCTTATTCTGGGAATGATCAATAT 57.694 33.333 0.00 0.00 0.00 1.28
1461 1787 4.591321 TCTGCAACCTTATTCTGGGAAT 57.409 40.909 0.00 0.00 0.00 3.01
1476 1802 5.500234 ACAAATAGGCTAGTTGATCTGCAA 58.500 37.500 33.65 0.00 37.22 4.08
1485 1811 4.184629 CGCTCTTGACAAATAGGCTAGTT 58.815 43.478 0.58 0.58 29.44 2.24
1525 1851 0.615544 CAGGGGCATCCAACAACCAT 60.616 55.000 0.00 0.00 38.24 3.55
1533 1859 1.695239 AGAGCATCAGGGGCATCCA 60.695 57.895 0.00 0.00 37.82 3.41
1580 1906 9.214962 AGGGAGCTTTATTTAGTTACTGATAGT 57.785 33.333 0.00 0.00 0.00 2.12
1640 1966 9.768662 CACCAAGTACGTACCCTTATTATTATT 57.231 33.333 21.80 2.55 0.00 1.40
1641 1967 8.927411 ACACCAAGTACGTACCCTTATTATTAT 58.073 33.333 21.80 0.00 0.00 1.28
1642 1968 8.305046 ACACCAAGTACGTACCCTTATTATTA 57.695 34.615 21.80 0.00 0.00 0.98
1643 1969 7.186570 ACACCAAGTACGTACCCTTATTATT 57.813 36.000 21.80 4.51 0.00 1.40
1644 1970 6.796785 ACACCAAGTACGTACCCTTATTAT 57.203 37.500 21.80 0.00 0.00 1.28
1645 1971 6.603940 AACACCAAGTACGTACCCTTATTA 57.396 37.500 21.80 0.00 0.00 0.98
1646 1972 5.488262 AACACCAAGTACGTACCCTTATT 57.512 39.130 21.80 6.71 0.00 1.40
1647 1973 5.951747 TCTAACACCAAGTACGTACCCTTAT 59.048 40.000 21.80 0.00 0.00 1.73
1648 1974 5.321102 TCTAACACCAAGTACGTACCCTTA 58.679 41.667 21.80 7.81 0.00 2.69
1649 1975 4.151883 TCTAACACCAAGTACGTACCCTT 58.848 43.478 21.80 8.20 0.00 3.95
1650 1976 3.766545 TCTAACACCAAGTACGTACCCT 58.233 45.455 21.80 7.09 0.00 4.34
1651 1977 4.725790 ATCTAACACCAAGTACGTACCC 57.274 45.455 21.80 0.00 0.00 3.69
1652 1978 8.078596 CCTATAATCTAACACCAAGTACGTACC 58.921 40.741 21.80 4.66 0.00 3.34
1653 1979 8.840321 TCCTATAATCTAACACCAAGTACGTAC 58.160 37.037 18.10 18.10 0.00 3.67
1654 1980 8.978874 TCCTATAATCTAACACCAAGTACGTA 57.021 34.615 0.00 0.00 0.00 3.57
1655 1981 7.559170 ACTCCTATAATCTAACACCAAGTACGT 59.441 37.037 0.00 0.00 0.00 3.57
1656 1982 7.938715 ACTCCTATAATCTAACACCAAGTACG 58.061 38.462 0.00 0.00 0.00 3.67
1677 2003 8.766151 GCAGCTTTGTTTATATAGAAGTACTCC 58.234 37.037 0.00 0.00 0.00 3.85
1678 2004 8.766151 GGCAGCTTTGTTTATATAGAAGTACTC 58.234 37.037 0.00 0.00 0.00 2.59
1679 2005 7.715686 GGGCAGCTTTGTTTATATAGAAGTACT 59.284 37.037 0.00 0.00 0.00 2.73
1680 2006 7.497909 TGGGCAGCTTTGTTTATATAGAAGTAC 59.502 37.037 0.00 0.00 0.00 2.73
1681 2007 7.570132 TGGGCAGCTTTGTTTATATAGAAGTA 58.430 34.615 0.00 0.00 0.00 2.24
1682 2008 6.423182 TGGGCAGCTTTGTTTATATAGAAGT 58.577 36.000 0.00 0.00 0.00 3.01
1785 2250 9.811655 CGATAAAAGTGGCATGTATTTACTATG 57.188 33.333 0.00 0.00 0.00 2.23
1786 2251 8.504005 GCGATAAAAGTGGCATGTATTTACTAT 58.496 33.333 0.00 0.00 0.00 2.12
1787 2252 7.496263 TGCGATAAAAGTGGCATGTATTTACTA 59.504 33.333 0.00 0.00 0.00 1.82
1788 2253 6.317642 TGCGATAAAAGTGGCATGTATTTACT 59.682 34.615 0.00 0.00 0.00 2.24
1789 2254 6.491394 TGCGATAAAAGTGGCATGTATTTAC 58.509 36.000 0.00 0.00 0.00 2.01
1790 2255 6.685527 TGCGATAAAAGTGGCATGTATTTA 57.314 33.333 0.00 0.00 0.00 1.40
1791 2256 5.574891 TGCGATAAAAGTGGCATGTATTT 57.425 34.783 0.00 0.00 0.00 1.40
1792 2257 5.574891 TTGCGATAAAAGTGGCATGTATT 57.425 34.783 0.00 0.00 32.82 1.89
1793 2258 5.574891 TTTGCGATAAAAGTGGCATGTAT 57.425 34.783 0.00 0.00 32.82 2.29
1794 2259 5.378292 TTTTGCGATAAAAGTGGCATGTA 57.622 34.783 0.00 0.00 32.82 2.29
1795 2260 3.932545 TTTGCGATAAAAGTGGCATGT 57.067 38.095 0.00 0.00 32.82 3.21
1838 2303 7.266922 ACGCATTTACTAGTGGAAAGAAAAA 57.733 32.000 5.39 0.00 0.00 1.94
1839 2304 6.870971 ACGCATTTACTAGTGGAAAGAAAA 57.129 33.333 5.39 0.00 0.00 2.29
1840 2305 6.930164 TGTACGCATTTACTAGTGGAAAGAAA 59.070 34.615 5.39 0.00 0.00 2.52
1841 2306 6.457355 TGTACGCATTTACTAGTGGAAAGAA 58.543 36.000 5.39 0.00 0.00 2.52
1842 2307 6.028146 TGTACGCATTTACTAGTGGAAAGA 57.972 37.500 5.39 0.00 0.00 2.52
1843 2308 6.903883 ATGTACGCATTTACTAGTGGAAAG 57.096 37.500 5.39 0.00 29.54 2.62
1856 2321 7.464444 GCATTTGCATCTAAAAATGTACGCATT 60.464 33.333 8.03 0.00 42.92 3.56
1857 2322 6.019640 GCATTTGCATCTAAAAATGTACGCAT 60.020 34.615 8.03 0.00 42.92 4.73
1858 2323 5.288232 GCATTTGCATCTAAAAATGTACGCA 59.712 36.000 8.03 0.00 42.92 5.24
1859 2324 5.717251 GCATTTGCATCTAAAAATGTACGC 58.283 37.500 8.03 0.00 42.92 4.42
1875 2340 3.369756 CCATGACAGAAACATGCATTTGC 59.630 43.478 0.00 0.00 42.31 3.68
1876 2341 4.562082 ACCATGACAGAAACATGCATTTG 58.438 39.130 0.00 0.00 42.31 2.32
1877 2342 4.877378 ACCATGACAGAAACATGCATTT 57.123 36.364 0.00 0.00 42.31 2.32
1878 2343 5.981088 TTACCATGACAGAAACATGCATT 57.019 34.783 0.00 0.00 42.31 3.56
1879 2344 5.981088 TTTACCATGACAGAAACATGCAT 57.019 34.783 0.00 0.00 42.31 3.96
1880 2345 5.781210 TTTTACCATGACAGAAACATGCA 57.219 34.783 0.00 0.00 42.31 3.96
1881 2346 6.389091 TGATTTTACCATGACAGAAACATGC 58.611 36.000 0.00 0.00 42.31 4.06
1882 2347 8.464404 AGATGATTTTACCATGACAGAAACATG 58.536 33.333 0.00 0.00 42.99 3.21
1883 2348 8.585471 AGATGATTTTACCATGACAGAAACAT 57.415 30.769 0.00 0.00 0.00 2.71
1884 2349 8.408043 AAGATGATTTTACCATGACAGAAACA 57.592 30.769 0.00 0.00 0.00 2.83
1885 2350 9.994432 CTAAGATGATTTTACCATGACAGAAAC 57.006 33.333 0.00 0.00 0.00 2.78
1886 2351 9.739276 ACTAAGATGATTTTACCATGACAGAAA 57.261 29.630 0.00 0.00 0.00 2.52
1903 2368 9.546428 CCATGTGTCATGTATTTACTAAGATGA 57.454 33.333 8.57 0.00 0.00 2.92
1904 2369 8.285394 GCCATGTGTCATGTATTTACTAAGATG 58.715 37.037 8.57 0.00 0.00 2.90
1905 2370 8.213679 AGCCATGTGTCATGTATTTACTAAGAT 58.786 33.333 8.57 0.00 0.00 2.40
2074 3029 9.975218 AATCTAAGACAAGTAATTTGGTATGGT 57.025 29.630 0.00 0.00 41.25 3.55
2146 3101 6.369065 ACAATCTCCGTCTCAAATTACTTGAC 59.631 38.462 0.00 0.00 39.20 3.18
2151 3106 8.922058 TTAGTACAATCTCCGTCTCAAATTAC 57.078 34.615 0.00 0.00 0.00 1.89
2152 3107 8.746530 ACTTAGTACAATCTCCGTCTCAAATTA 58.253 33.333 0.00 0.00 0.00 1.40
2154 3109 7.093902 TGACTTAGTACAATCTCCGTCTCAAAT 60.094 37.037 0.00 0.00 0.00 2.32
2156 3111 5.708697 TGACTTAGTACAATCTCCGTCTCAA 59.291 40.000 0.00 0.00 0.00 3.02
2157 3112 5.250982 TGACTTAGTACAATCTCCGTCTCA 58.749 41.667 0.00 0.00 0.00 3.27
2162 3117 4.792189 GTCGTTGACTTAGTACAATCTCCG 59.208 45.833 0.00 0.00 0.00 4.63
2174 3178 8.487313 AGTATGCAATAAATGTCGTTGACTTA 57.513 30.769 0.00 0.00 33.15 2.24
2181 3185 8.035165 TGTGTTTAGTATGCAATAAATGTCGT 57.965 30.769 0.00 0.00 0.00 4.34
2187 3191 8.495361 ACGGTATGTGTTTAGTATGCAATAAA 57.505 30.769 0.00 0.00 0.00 1.40
2211 3222 6.095377 GTCATCAAATCAGATCAACCCAAAC 58.905 40.000 0.00 0.00 0.00 2.93
2217 3228 6.748333 TCTTGGTCATCAAATCAGATCAAC 57.252 37.500 0.00 0.00 34.56 3.18
2222 3580 9.465199 TCAAATAATCTTGGTCATCAAATCAGA 57.535 29.630 0.00 0.00 34.56 3.27
2386 4105 4.751098 TCGCCAAAAGATACGTTTACAGTT 59.249 37.500 0.00 0.00 0.00 3.16
2388 4107 4.634991 GTCGCCAAAAGATACGTTTACAG 58.365 43.478 0.00 0.00 0.00 2.74
2389 4108 3.121611 CGTCGCCAAAAGATACGTTTACA 59.878 43.478 0.00 0.00 0.00 2.41
2390 4109 3.121778 ACGTCGCCAAAAGATACGTTTAC 59.878 43.478 0.00 0.00 43.63 2.01
2391 4110 3.316283 ACGTCGCCAAAAGATACGTTTA 58.684 40.909 0.00 0.00 43.63 2.01
2392 4111 2.137523 ACGTCGCCAAAAGATACGTTT 58.862 42.857 0.00 0.00 43.63 3.60
2393 4112 1.787012 ACGTCGCCAAAAGATACGTT 58.213 45.000 0.00 0.00 43.63 3.99
2396 4115 4.916099 ACTTTACGTCGCCAAAAGATAC 57.084 40.909 13.29 0.00 34.90 2.24
2398 4117 5.172934 TGATACTTTACGTCGCCAAAAGAT 58.827 37.500 13.29 4.36 34.90 2.40
2400 4119 4.201685 CCTGATACTTTACGTCGCCAAAAG 60.202 45.833 6.27 6.27 36.51 2.27
2401 4120 3.680937 CCTGATACTTTACGTCGCCAAAA 59.319 43.478 0.00 0.00 0.00 2.44
2402 4121 3.255725 CCTGATACTTTACGTCGCCAAA 58.744 45.455 0.00 0.00 0.00 3.28


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

AutoCloner maintained by Alex Coulton.