Multiple sequence alignment - TraesCS1B01G178700

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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 TraesCS1B01G178700 chr1B 100.000 2561 0 0 1 2561 324008782 324011342 0.000000e+00 4730.0
1 TraesCS1B01G178700 chr1B 86.305 387 36 4 1977 2348 64930611 64930995 3.070000e-109 405.0
2 TraesCS1B01G178700 chr1B 86.239 109 15 0 2354 2462 289296258 289296150 4.480000e-23 119.0
3 TraesCS1B01G178700 chr1D 93.257 1839 76 13 1 1814 224369307 224371122 0.000000e+00 2665.0
4 TraesCS1B01G178700 chr1D 88.630 387 29 2 1977 2348 233888832 233889218 8.350000e-125 457.0
5 TraesCS1B01G178700 chr1D 81.967 122 20 2 1804 1923 422070316 422070195 4.510000e-18 102.0
6 TraesCS1B01G178700 chr1A 96.296 972 31 3 709 1679 290955718 290956685 0.000000e+00 1591.0
7 TraesCS1B01G178700 chr1A 91.531 307 20 5 224 529 290954930 290955231 3.940000e-113 418.0
8 TraesCS1B01G178700 chr1A 87.288 118 9 2 1682 1798 290956777 290956889 2.070000e-26 130.0
9 TraesCS1B01G178700 chr3B 83.508 667 65 20 1939 2561 565260663 565259998 4.750000e-162 580.0
10 TraesCS1B01G178700 chr3B 78.680 394 53 15 1809 2184 386411822 386411442 1.530000e-57 233.0
11 TraesCS1B01G178700 chr5B 83.866 626 48 26 1977 2558 670464461 670465077 4.820000e-152 547.0
12 TraesCS1B01G178700 chr5B 83.227 626 52 26 1977 2558 670435505 670436121 2.260000e-145 525.0
13 TraesCS1B01G178700 chr5B 85.484 186 15 4 1977 2150 485727501 485727316 1.570000e-42 183.0
14 TraesCS1B01G178700 chr5D 83.466 629 51 27 1977 2561 305238617 305239236 1.040000e-148 536.0
15 TraesCS1B01G178700 chr7B 82.485 668 61 24 1939 2561 616780241 616779585 3.750000e-148 534.0
16 TraesCS1B01G178700 chrUn 83.227 626 52 26 1977 2558 175731381 175731997 2.260000e-145 525.0
17 TraesCS1B01G178700 chrUn 83.067 626 53 26 1977 2558 175702139 175702755 1.050000e-143 520.0
18 TraesCS1B01G178700 chr7D 82.353 629 59 21 1977 2561 412013454 412014074 1.370000e-137 499.0
19 TraesCS1B01G178700 chr7D 89.062 384 30 1 1977 2348 453146316 453145933 1.390000e-127 466.0
20 TraesCS1B01G178700 chr7D 84.615 195 22 3 2349 2543 50133950 50134136 1.210000e-43 187.0
21 TraesCS1B01G178700 chr7D 100.000 29 0 0 1802 1830 66875362 66875390 1.000000e-03 54.7
22 TraesCS1B01G178700 chr7D 96.875 32 1 0 1804 1835 611339661 611339630 1.000000e-03 54.7
23 TraesCS1B01G178700 chr2D 89.406 387 26 2 1977 2348 316140281 316140667 8.290000e-130 473.0
24 TraesCS1B01G178700 chr7A 88.630 387 28 3 1977 2348 88269773 88270158 8.350000e-125 457.0
25 TraesCS1B01G178700 chr5A 86.269 386 37 4 1978 2348 607597758 607598142 3.070000e-109 405.0
26 TraesCS1B01G178700 chr5A 85.976 164 11 2 1977 2128 139934053 139933890 5.670000e-37 165.0
27 TraesCS1B01G178700 chr5A 82.386 176 28 3 2365 2539 673083122 673083295 1.590000e-32 150.0
28 TraesCS1B01G178700 chr2B 84.579 214 31 2 2349 2561 251376937 251377149 7.180000e-51 211.0
29 TraesCS1B01G178700 chr2A 84.397 141 22 0 2421 2561 753593045 753592905 3.440000e-29 139.0
30 TraesCS1B01G178700 chr3A 93.023 43 3 0 1809 1851 699416236 699416278 2.130000e-06 63.9


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 TraesCS1B01G178700 chr1B 324008782 324011342 2560 False 4730 4730 100.000 1 2561 1 chr1B.!!$F2 2560
1 TraesCS1B01G178700 chr1D 224369307 224371122 1815 False 2665 2665 93.257 1 1814 1 chr1D.!!$F1 1813
2 TraesCS1B01G178700 chr1A 290954930 290956889 1959 False 713 1591 91.705 224 1798 3 chr1A.!!$F1 1574
3 TraesCS1B01G178700 chr3B 565259998 565260663 665 True 580 580 83.508 1939 2561 1 chr3B.!!$R2 622
4 TraesCS1B01G178700 chr5B 670464461 670465077 616 False 547 547 83.866 1977 2558 1 chr5B.!!$F2 581
5 TraesCS1B01G178700 chr5B 670435505 670436121 616 False 525 525 83.227 1977 2558 1 chr5B.!!$F1 581
6 TraesCS1B01G178700 chr5D 305238617 305239236 619 False 536 536 83.466 1977 2561 1 chr5D.!!$F1 584
7 TraesCS1B01G178700 chr7B 616779585 616780241 656 True 534 534 82.485 1939 2561 1 chr7B.!!$R1 622
8 TraesCS1B01G178700 chrUn 175731381 175731997 616 False 525 525 83.227 1977 2558 1 chrUn.!!$F2 581
9 TraesCS1B01G178700 chrUn 175702139 175702755 616 False 520 520 83.067 1977 2558 1 chrUn.!!$F1 581
10 TraesCS1B01G178700 chr7D 412013454 412014074 620 False 499 499 82.353 1977 2561 1 chr7D.!!$F3 584

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
90 91 0.036294 AACGAGGGCAAGGACTAAGC 60.036 55.0 0.0 0.0 0.0 3.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1827 2275 0.105224 TATGGGTCGGCATTACACGG 59.895 55.0 0.0 0.0 0.0 4.94 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
40 41 4.098914 AGTGAAGATGCAAACCCTTACA 57.901 40.909 0.00 0.00 0.00 2.41
67 68 2.674754 GGCCTTCCAATGACGGGA 59.325 61.111 0.00 0.00 30.66 5.14
83 84 2.033194 GGACGAAACGAGGGCAAGG 61.033 63.158 0.00 0.00 0.00 3.61
90 91 0.036294 AACGAGGGCAAGGACTAAGC 60.036 55.000 0.00 0.00 0.00 3.09
96 97 0.462759 GGCAAGGACTAAGCGAGCAT 60.463 55.000 0.00 0.00 0.00 3.79
97 98 0.933796 GCAAGGACTAAGCGAGCATC 59.066 55.000 0.00 0.00 0.00 3.91
102 103 1.137086 GGACTAAGCGAGCATCCTTCA 59.863 52.381 0.00 0.00 30.23 3.02
114 115 3.022406 GCATCCTTCAAGATGGCTTTCT 58.978 45.455 3.89 0.00 43.26 2.52
120 121 1.002366 CAAGATGGCTTTCTCGACGG 58.998 55.000 0.00 0.00 30.14 4.79
155 156 3.921677 TGGAATACCAAGAGTTGTCGTC 58.078 45.455 0.00 0.00 43.91 4.20
171 172 2.097056 GTCGTCGCAAGTAGTCCAAAAC 60.097 50.000 0.00 0.00 39.48 2.43
173 174 2.285756 CGTCGCAAGTAGTCCAAAACAA 59.714 45.455 0.00 0.00 39.48 2.83
320 321 2.414138 GGAATGCAATGCAAGCAAAGAC 59.586 45.455 13.45 11.28 46.27 3.01
358 359 4.423732 GGGACTCGCAAAATTACGTAGTA 58.576 43.478 0.00 0.00 45.11 1.82
359 360 4.501921 GGGACTCGCAAAATTACGTAGTAG 59.498 45.833 0.00 0.00 46.93 2.57
360 361 5.098211 GGACTCGCAAAATTACGTAGTAGT 58.902 41.667 0.00 0.00 46.93 2.73
570 911 7.905493 CCATTAACGCTCTTCAAGTCTTTATTC 59.095 37.037 0.00 0.00 0.00 1.75
651 1004 3.372554 GACGTGCTACCTCTGCCCC 62.373 68.421 0.00 0.00 0.00 5.80
675 1030 3.508840 CCCATTGAAGTCCGCGGC 61.509 66.667 23.51 16.31 0.00 6.53
681 1036 1.248785 TTGAAGTCCGCGGCTAGAGT 61.249 55.000 23.51 2.44 0.00 3.24
803 1158 1.251527 GGAACCGAGGAGACAGAGCA 61.252 60.000 0.00 0.00 0.00 4.26
804 1159 0.172352 GAACCGAGGAGACAGAGCAG 59.828 60.000 0.00 0.00 0.00 4.24
805 1160 1.254284 AACCGAGGAGACAGAGCAGG 61.254 60.000 0.00 0.00 0.00 4.85
814 1169 4.486503 CAGAGCAGGAGGGCAGGC 62.487 72.222 0.00 0.00 35.83 4.85
951 1306 4.200283 CCGGTCTCTGCCTCTCGC 62.200 72.222 0.00 0.00 38.31 5.03
1212 1567 4.124943 TCCTCCCCGTCCTCCTCG 62.125 72.222 0.00 0.00 0.00 4.63
1263 1618 3.057666 TGTTCACGCAAGGTACGTATACA 60.058 43.478 0.00 0.00 42.96 2.29
1265 1620 1.850441 CACGCAAGGTACGTATACAGC 59.150 52.381 0.00 0.74 42.96 4.40
1303 1658 1.150081 GTGCCATCCTCCCCTGATG 59.850 63.158 0.00 0.00 39.44 3.07
1458 1816 1.432270 GGAGGAAGAATGCGGCTTCG 61.432 60.000 0.00 0.00 42.01 3.79
1562 1920 0.517316 GCCTGTGTCACGGATTGAAC 59.483 55.000 13.67 0.00 35.39 3.18
1601 1959 0.105039 CTAGCGGCTACAAGGAAGGG 59.895 60.000 5.42 0.00 0.00 3.95
1699 2147 6.777213 TGGCTTGTAGTTTTACCTTTTTGA 57.223 33.333 0.00 0.00 0.00 2.69
1716 2164 5.549742 TTTTGAGATTGGAAAGTGGCATT 57.450 34.783 0.00 0.00 0.00 3.56
1718 2166 6.662865 TTTGAGATTGGAAAGTGGCATTAA 57.337 33.333 0.00 0.00 0.00 1.40
1731 2179 2.680339 TGGCATTAATTCGTTGATGCGA 59.320 40.909 10.46 5.49 44.33 5.10
1814 2262 5.817296 TCATCTAACGCAATGTTTAGAGCAT 59.183 36.000 10.64 0.00 42.09 3.79
1815 2263 5.718649 TCTAACGCAATGTTTAGAGCATC 57.281 39.130 3.38 0.00 42.09 3.91
1816 2264 5.419542 TCTAACGCAATGTTTAGAGCATCT 58.580 37.500 3.38 0.00 45.30 2.90
1817 2265 4.606457 AACGCAATGTTTAGAGCATCTC 57.394 40.909 0.00 0.00 38.49 2.75
1818 2266 4.256920 AACGCAATGTTTAGAGCATCTCT 58.743 39.130 1.71 1.71 38.49 3.10
1819 2267 5.419542 AACGCAATGTTTAGAGCATCTCTA 58.580 37.500 0.00 0.00 38.49 2.43
1820 2268 5.521735 AACGCAATGTTTAGAGCATCTCTAG 59.478 40.000 4.07 0.00 38.49 2.43
1821 2269 7.881246 AACGCAATGTTTAGAGCATCTCTAGC 61.881 42.308 4.07 3.13 38.49 3.42
1828 2276 0.678950 GAGCATCTCTAGCAGACCCC 59.321 60.000 0.00 0.00 32.26 4.95
1829 2277 1.112315 AGCATCTCTAGCAGACCCCG 61.112 60.000 0.00 0.00 32.26 5.73
1830 2278 1.395826 GCATCTCTAGCAGACCCCGT 61.396 60.000 0.00 0.00 32.26 5.28
1831 2279 0.387202 CATCTCTAGCAGACCCCGTG 59.613 60.000 0.00 0.00 32.26 4.94
1832 2280 0.033011 ATCTCTAGCAGACCCCGTGT 60.033 55.000 0.00 0.00 32.26 4.49
1833 2281 0.622136 TCTCTAGCAGACCCCGTGTA 59.378 55.000 0.00 0.00 0.00 2.90
1834 2282 1.005097 TCTCTAGCAGACCCCGTGTAA 59.995 52.381 0.00 0.00 0.00 2.41
1835 2283 2.032620 CTCTAGCAGACCCCGTGTAAT 58.967 52.381 0.00 0.00 0.00 1.89
1836 2284 1.754803 TCTAGCAGACCCCGTGTAATG 59.245 52.381 0.00 0.00 0.00 1.90
1837 2285 0.177141 TAGCAGACCCCGTGTAATGC 59.823 55.000 0.00 0.00 39.11 3.56
1838 2286 2.112815 GCAGACCCCGTGTAATGCC 61.113 63.158 0.00 0.00 34.98 4.40
1839 2287 1.813753 CAGACCCCGTGTAATGCCG 60.814 63.158 0.00 0.00 0.00 5.69
1840 2288 1.985662 AGACCCCGTGTAATGCCGA 60.986 57.895 0.00 0.00 0.00 5.54
1841 2289 1.812507 GACCCCGTGTAATGCCGAC 60.813 63.158 0.00 0.00 0.00 4.79
1842 2290 2.512974 CCCCGTGTAATGCCGACC 60.513 66.667 0.00 0.00 0.00 4.79
1843 2291 2.512974 CCCGTGTAATGCCGACCC 60.513 66.667 0.00 0.00 0.00 4.46
1844 2292 2.266372 CCGTGTAATGCCGACCCA 59.734 61.111 0.00 0.00 0.00 4.51
1845 2293 1.153249 CCGTGTAATGCCGACCCAT 60.153 57.895 0.00 0.00 0.00 4.00
1846 2294 0.105224 CCGTGTAATGCCGACCCATA 59.895 55.000 0.00 0.00 0.00 2.74
1847 2295 1.473610 CCGTGTAATGCCGACCCATAA 60.474 52.381 0.00 0.00 0.00 1.90
1848 2296 2.281517 CGTGTAATGCCGACCCATAAA 58.718 47.619 0.00 0.00 0.00 1.40
1849 2297 2.678836 CGTGTAATGCCGACCCATAAAA 59.321 45.455 0.00 0.00 0.00 1.52
1850 2298 3.314080 CGTGTAATGCCGACCCATAAAAT 59.686 43.478 0.00 0.00 0.00 1.82
1851 2299 4.512198 CGTGTAATGCCGACCCATAAAATA 59.488 41.667 0.00 0.00 0.00 1.40
1852 2300 5.559417 CGTGTAATGCCGACCCATAAAATAC 60.559 44.000 0.00 0.00 0.00 1.89
1853 2301 4.512198 TGTAATGCCGACCCATAAAATACG 59.488 41.667 0.00 0.00 0.00 3.06
1854 2302 2.695127 TGCCGACCCATAAAATACGT 57.305 45.000 0.00 0.00 0.00 3.57
1855 2303 3.815856 TGCCGACCCATAAAATACGTA 57.184 42.857 0.00 0.00 0.00 3.57
1856 2304 4.339872 TGCCGACCCATAAAATACGTAT 57.660 40.909 1.14 1.14 0.00 3.06
1857 2305 4.706035 TGCCGACCCATAAAATACGTATT 58.294 39.130 15.07 15.07 0.00 1.89
1858 2306 4.751098 TGCCGACCCATAAAATACGTATTC 59.249 41.667 20.57 5.52 0.00 1.75
1859 2307 4.751098 GCCGACCCATAAAATACGTATTCA 59.249 41.667 20.57 12.25 0.00 2.57
1860 2308 5.410439 GCCGACCCATAAAATACGTATTCAT 59.590 40.000 20.57 14.75 0.00 2.57
1861 2309 6.072893 GCCGACCCATAAAATACGTATTCATT 60.073 38.462 20.57 14.42 0.00 2.57
1862 2310 7.520937 GCCGACCCATAAAATACGTATTCATTT 60.521 37.037 20.57 13.76 0.00 2.32
1863 2311 8.013378 CCGACCCATAAAATACGTATTCATTTC 58.987 37.037 20.57 10.09 0.00 2.17
1864 2312 8.552865 CGACCCATAAAATACGTATTCATTTCA 58.447 33.333 20.57 4.08 0.00 2.69
1865 2313 9.659830 GACCCATAAAATACGTATTCATTTCAC 57.340 33.333 20.57 6.66 0.00 3.18
1866 2314 8.339714 ACCCATAAAATACGTATTCATTTCACG 58.660 33.333 20.57 7.69 41.32 4.35
1867 2315 8.552865 CCCATAAAATACGTATTCATTTCACGA 58.447 33.333 20.57 0.00 38.96 4.35
1868 2316 9.923786 CCATAAAATACGTATTCATTTCACGAA 57.076 29.630 20.57 0.00 38.96 3.85
1885 2333 2.279851 AAAAACGGCTTTGCGGGC 60.280 55.556 2.48 0.00 33.14 6.13
1886 2334 3.800685 AAAAACGGCTTTGCGGGCC 62.801 57.895 0.00 0.00 45.57 5.80
1921 2369 4.992511 GCACACCCCGCAACCGTA 62.993 66.667 0.00 0.00 0.00 4.02
1922 2370 2.280933 CACACCCCGCAACCGTAA 60.281 61.111 0.00 0.00 0.00 3.18
1923 2371 1.892862 CACACCCCGCAACCGTAAA 60.893 57.895 0.00 0.00 0.00 2.01
1924 2372 1.153005 ACACCCCGCAACCGTAAAA 60.153 52.632 0.00 0.00 0.00 1.52
1925 2373 0.750911 ACACCCCGCAACCGTAAAAA 60.751 50.000 0.00 0.00 0.00 1.94
1951 2399 8.764524 AAGATATCCGCAGTAAATCAGTAATC 57.235 34.615 0.00 0.00 0.00 1.75
1952 2400 7.324178 AGATATCCGCAGTAAATCAGTAATCC 58.676 38.462 0.00 0.00 0.00 3.01
2044 2492 7.051623 TCTTTGTTAGAGTAGCAAGACCAAAA 58.948 34.615 0.00 0.00 30.60 2.44
2076 2536 7.234355 AGAACCACAAGAAGATATCCAACTTT 58.766 34.615 0.00 0.00 0.00 2.66
2077 2537 6.824305 ACCACAAGAAGATATCCAACTTTG 57.176 37.500 0.00 0.99 0.00 2.77
2132 2592 2.684374 TCCATGCCTTCATTGTTGATCG 59.316 45.455 0.00 0.00 0.00 3.69
2213 2676 5.068591 GCTTCCCCTCTAGTTTCTTCTCTAG 59.931 48.000 0.00 0.00 36.10 2.43
2234 2697 1.353103 GCACATGTAGCCGCATCAC 59.647 57.895 0.00 0.00 0.00 3.06
2242 2705 1.796190 TAGCCGCATCACTAGCCTCG 61.796 60.000 0.00 0.00 0.00 4.63
2282 2746 9.463443 GTGCACAAACATCTATTAAGTTTCTTT 57.537 29.630 13.17 0.00 33.54 2.52
2316 2780 4.960938 TCGATGTATTCTTCTCCCCAATG 58.039 43.478 0.00 0.00 0.00 2.82
2352 2845 3.448686 CATCTTCCTACACACATCCGAC 58.551 50.000 0.00 0.00 0.00 4.79
2366 2859 3.323979 ACATCCGACTAGGTTGACAAAGT 59.676 43.478 0.00 0.00 41.23 2.66
2376 2869 5.424121 AGGTTGACAAAGTCGAATGAAAG 57.576 39.130 0.00 0.00 34.95 2.62
2385 2878 4.474226 AGTCGAATGAAAGCAAGAACAC 57.526 40.909 0.00 0.00 0.00 3.32
2419 2912 7.254852 GTTTTCGCATTTGAAGAATACCCATA 58.745 34.615 0.00 0.00 0.00 2.74
2440 2933 2.613506 GGGTGTTGTGGCGTGCTAC 61.614 63.158 0.93 0.93 0.00 3.58
2540 3033 4.003788 CGAGCCTGGGTGACGGTT 62.004 66.667 1.59 0.00 0.00 4.44
2551 3044 2.047179 GACGGTTGGCTGAGTCCC 60.047 66.667 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
40 41 0.104725 TTGGAAGGCCCCCACAATTT 60.105 50.000 13.59 0.00 32.58 1.82
67 68 1.301479 GTCCTTGCCCTCGTTTCGT 60.301 57.895 0.00 0.00 0.00 3.85
83 84 2.586258 TGAAGGATGCTCGCTTAGTC 57.414 50.000 0.00 0.00 0.00 2.59
90 91 0.942962 GCCATCTTGAAGGATGCTCG 59.057 55.000 0.00 0.00 41.04 5.03
96 97 2.567169 TCGAGAAAGCCATCTTGAAGGA 59.433 45.455 4.24 0.00 37.00 3.36
97 98 2.675348 GTCGAGAAAGCCATCTTGAAGG 59.325 50.000 7.65 0.00 40.64 3.46
102 103 0.608640 ACCGTCGAGAAAGCCATCTT 59.391 50.000 0.00 0.00 0.00 2.40
120 121 7.819415 TCTTGGTATTCCATAATGATCATCGAC 59.181 37.037 9.06 0.00 43.91 4.20
134 135 3.613193 CGACGACAACTCTTGGTATTCCA 60.613 47.826 0.00 0.00 42.66 3.53
155 156 4.545823 TTCTTGTTTTGGACTACTTGCG 57.454 40.909 0.00 0.00 0.00 4.85
194 195 3.377346 TCAGTGCTGAAGAGTGAGTTC 57.623 47.619 0.00 0.00 36.53 3.01
203 204 3.589988 ACGGAGTAATTCAGTGCTGAAG 58.410 45.455 17.93 7.04 46.82 3.02
205 206 4.014406 TCTACGGAGTAATTCAGTGCTGA 58.986 43.478 0.00 0.00 45.13 4.26
320 321 5.501715 CGAGTCCCGTCATAAATTGATTTG 58.498 41.667 0.00 0.00 36.54 2.32
651 1004 1.044790 GGACTTCAATGGGCCCATGG 61.045 60.000 38.06 34.55 36.68 3.66
805 1160 3.424105 AATCCCTGGCCTGCCCTC 61.424 66.667 3.32 0.00 34.56 4.30
963 1318 3.569250 GCTCCCAAAGCGAATACAAAA 57.431 42.857 0.00 0.00 42.21 2.44
1203 1558 3.075641 GGGTGGGACGAGGAGGAC 61.076 72.222 0.00 0.00 0.00 3.85
1230 1585 1.995991 CGTGAACATAAGGTCCGCG 59.004 57.895 0.00 0.00 0.00 6.46
1273 1628 3.881952 ATGGCACGCAGAGAACGCA 62.882 57.895 0.00 0.00 0.00 5.24
1303 1658 4.343581 TGCTCGCGCAGGATTATC 57.656 55.556 8.75 0.00 42.25 1.75
1562 1920 1.202348 GCACGATTTTTCCTCCTTGGG 59.798 52.381 0.00 0.00 36.20 4.12
1601 1959 3.244457 CCGGTACTTCCATATCCCTTTCC 60.244 52.174 0.00 0.00 35.57 3.13
1685 2043 8.817100 CACTTTCCAATCTCAAAAAGGTAAAAC 58.183 33.333 0.00 0.00 33.92 2.43
1690 2138 4.202253 GCCACTTTCCAATCTCAAAAAGGT 60.202 41.667 0.00 0.00 33.92 3.50
1699 2147 5.418840 ACGAATTAATGCCACTTTCCAATCT 59.581 36.000 0.00 0.00 0.00 2.40
1716 2164 6.700081 AGCTAAACTATCGCATCAACGAATTA 59.300 34.615 0.00 0.00 46.59 1.40
1718 2166 5.050490 AGCTAAACTATCGCATCAACGAAT 58.950 37.500 0.00 0.00 46.59 3.34
1731 2179 9.138596 TGTTTACTTTTGGGAAAGCTAAACTAT 57.861 29.630 21.06 2.06 44.92 2.12
1774 2222 7.679638 GCGTTAGATGATTTCCTGCAGTAATTT 60.680 37.037 13.81 4.34 0.00 1.82
1780 2228 2.938451 TGCGTTAGATGATTTCCTGCAG 59.062 45.455 6.78 6.78 0.00 4.41
1814 2262 0.622136 TACACGGGGTCTGCTAGAGA 59.378 55.000 0.00 0.00 0.00 3.10
1815 2263 1.471119 TTACACGGGGTCTGCTAGAG 58.529 55.000 0.00 0.00 0.00 2.43
1816 2264 1.754803 CATTACACGGGGTCTGCTAGA 59.245 52.381 0.00 0.00 0.00 2.43
1817 2265 1.806623 GCATTACACGGGGTCTGCTAG 60.807 57.143 9.81 0.00 36.11 3.42
1818 2266 0.177141 GCATTACACGGGGTCTGCTA 59.823 55.000 9.81 0.00 36.11 3.49
1819 2267 1.078426 GCATTACACGGGGTCTGCT 60.078 57.895 9.81 0.00 36.11 4.24
1820 2268 2.112815 GGCATTACACGGGGTCTGC 61.113 63.158 8.84 8.84 37.49 4.26
1821 2269 1.813753 CGGCATTACACGGGGTCTG 60.814 63.158 0.00 0.00 0.00 3.51
1822 2270 1.985662 TCGGCATTACACGGGGTCT 60.986 57.895 0.00 0.00 0.00 3.85
1823 2271 1.812507 GTCGGCATTACACGGGGTC 60.813 63.158 0.00 0.00 0.00 4.46
1824 2272 2.266689 GTCGGCATTACACGGGGT 59.733 61.111 0.00 0.00 0.00 4.95
1825 2273 2.512974 GGTCGGCATTACACGGGG 60.513 66.667 0.00 0.00 0.00 5.73
1826 2274 2.512974 GGGTCGGCATTACACGGG 60.513 66.667 0.00 0.00 0.00 5.28
1827 2275 0.105224 TATGGGTCGGCATTACACGG 59.895 55.000 0.00 0.00 0.00 4.94
1828 2276 1.942677 TTATGGGTCGGCATTACACG 58.057 50.000 0.00 0.00 0.00 4.49
1829 2277 4.911514 ATTTTATGGGTCGGCATTACAC 57.088 40.909 0.00 0.00 0.00 2.90
1830 2278 4.512198 CGTATTTTATGGGTCGGCATTACA 59.488 41.667 0.00 0.00 0.00 2.41
1831 2279 4.512571 ACGTATTTTATGGGTCGGCATTAC 59.487 41.667 0.00 0.00 0.00 1.89
1832 2280 4.706035 ACGTATTTTATGGGTCGGCATTA 58.294 39.130 0.00 0.00 0.00 1.90
1833 2281 3.547746 ACGTATTTTATGGGTCGGCATT 58.452 40.909 0.00 0.00 0.00 3.56
1834 2282 3.202829 ACGTATTTTATGGGTCGGCAT 57.797 42.857 0.00 0.00 0.00 4.40
1835 2283 2.695127 ACGTATTTTATGGGTCGGCA 57.305 45.000 0.00 0.00 0.00 5.69
1836 2284 4.751098 TGAATACGTATTTTATGGGTCGGC 59.249 41.667 21.18 5.44 0.00 5.54
1837 2285 7.429636 AATGAATACGTATTTTATGGGTCGG 57.570 36.000 21.18 0.00 0.00 4.79
1838 2286 8.552865 TGAAATGAATACGTATTTTATGGGTCG 58.447 33.333 21.18 0.00 0.00 4.79
1839 2287 9.659830 GTGAAATGAATACGTATTTTATGGGTC 57.340 33.333 21.18 15.40 0.00 4.46
1840 2288 8.339714 CGTGAAATGAATACGTATTTTATGGGT 58.660 33.333 21.18 8.93 33.48 4.51
1841 2289 8.552865 TCGTGAAATGAATACGTATTTTATGGG 58.447 33.333 21.18 8.13 38.80 4.00
1842 2290 9.923786 TTCGTGAAATGAATACGTATTTTATGG 57.076 29.630 21.18 7.47 36.82 2.74
1868 2316 2.279851 GCCCGCAAAGCCGTTTTT 60.280 55.556 0.00 0.00 0.00 1.94
1869 2317 4.293648 GGCCCGCAAAGCCGTTTT 62.294 61.111 0.00 0.00 41.41 2.43
1904 2352 4.992511 TACGGTTGCGGGGTGTGC 62.993 66.667 0.00 0.00 0.00 4.57
1905 2353 1.445716 TTTTACGGTTGCGGGGTGTG 61.446 55.000 0.00 0.00 0.00 3.82
1906 2354 0.750911 TTTTTACGGTTGCGGGGTGT 60.751 50.000 0.00 0.00 0.00 4.16
1907 2355 2.031360 TTTTTACGGTTGCGGGGTG 58.969 52.632 0.00 0.00 0.00 4.61
1908 2356 4.575180 TTTTTACGGTTGCGGGGT 57.425 50.000 0.00 0.00 0.00 4.95
1923 2371 7.865706 ACTGATTTACTGCGGATATCTTTTT 57.134 32.000 0.00 0.00 0.00 1.94
1924 2372 8.958119 TTACTGATTTACTGCGGATATCTTTT 57.042 30.769 0.00 0.00 0.00 2.27
1925 2373 9.209175 GATTACTGATTTACTGCGGATATCTTT 57.791 33.333 0.00 0.00 0.00 2.52
1926 2374 7.819900 GGATTACTGATTTACTGCGGATATCTT 59.180 37.037 0.00 0.00 0.00 2.40
1927 2375 7.324178 GGATTACTGATTTACTGCGGATATCT 58.676 38.462 0.00 0.00 0.00 1.98
1928 2376 6.253727 CGGATTACTGATTTACTGCGGATATC 59.746 42.308 0.00 0.00 0.00 1.63
1929 2377 6.100004 CGGATTACTGATTTACTGCGGATAT 58.900 40.000 0.00 0.00 0.00 1.63
1930 2378 5.466819 CGGATTACTGATTTACTGCGGATA 58.533 41.667 0.00 0.00 0.00 2.59
1931 2379 4.307432 CGGATTACTGATTTACTGCGGAT 58.693 43.478 0.00 0.00 0.00 4.18
1932 2380 3.713288 CGGATTACTGATTTACTGCGGA 58.287 45.455 0.00 0.00 0.00 5.54
1933 2381 2.221055 GCGGATTACTGATTTACTGCGG 59.779 50.000 0.00 0.00 0.00 5.69
1934 2382 2.863740 TGCGGATTACTGATTTACTGCG 59.136 45.455 0.00 0.00 33.13 5.18
1935 2383 5.424121 AATGCGGATTACTGATTTACTGC 57.576 39.130 0.00 0.00 0.00 4.40
1936 2384 7.015226 TGAAATGCGGATTACTGATTTACTG 57.985 36.000 1.39 0.00 0.00 2.74
1937 2385 7.624360 TTGAAATGCGGATTACTGATTTACT 57.376 32.000 1.39 0.00 0.00 2.24
1984 2432 6.655078 ATTATGTATCCAATGCCCTTGAAC 57.345 37.500 0.00 0.00 36.97 3.18
2044 2492 8.360390 GGATATCTTCTTGTGGTTCTTGTTTTT 58.640 33.333 2.05 0.00 0.00 1.94
2076 2536 3.197766 CCAACTAGTGGGAGCAGTTATCA 59.802 47.826 11.30 0.00 44.64 2.15
2077 2537 3.798202 CCAACTAGTGGGAGCAGTTATC 58.202 50.000 11.30 0.00 44.64 1.75
2107 2567 4.151121 TCAACAATGAAGGCATGGAGAAA 58.849 39.130 0.00 0.00 34.26 2.52
2132 2592 4.217118 AGAATGCAAGATCAATAATCCGCC 59.783 41.667 0.00 0.00 34.08 6.13
2213 2676 0.248215 GATGCGGCTACATGTGCAAC 60.248 55.000 9.11 4.48 41.22 4.17
2234 2697 1.202268 CGTTGGTAGAACCGAGGCTAG 60.202 57.143 0.00 0.00 42.58 3.42
2242 2705 1.145803 GTGCACTCGTTGGTAGAACC 58.854 55.000 10.32 0.00 39.22 3.62
2309 2773 0.614294 TGCTCATTTTGGCATTGGGG 59.386 50.000 0.00 0.00 33.23 4.96
2316 2780 3.492137 GGAAGATGGATGCTCATTTTGGC 60.492 47.826 0.00 0.00 0.00 4.52
2352 2845 6.539649 TTTCATTCGACTTTGTCAACCTAG 57.460 37.500 0.00 0.00 32.09 3.02
2366 2859 3.003275 GGTGTGTTCTTGCTTTCATTCGA 59.997 43.478 0.00 0.00 0.00 3.71
2376 2869 3.670377 GGCGGGGTGTGTTCTTGC 61.670 66.667 0.00 0.00 0.00 4.01
2430 2923 0.742990 GGCTAACATGTAGCACGCCA 60.743 55.000 21.15 0.00 42.06 5.69
2440 2933 1.300971 ACAGTGCTGCGGCTAACATG 61.301 55.000 20.27 12.03 39.59 3.21
2468 2961 0.456142 GCTCATACAGTGCGACGACA 60.456 55.000 0.00 0.00 0.00 4.35
2529 3022 3.164977 TCAGCCAACCGTCACCCA 61.165 61.111 0.00 0.00 0.00 4.51


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

AutoCloner maintained by Alex Coulton.