Multiple sequence alignment - TraesCS5B01G492900

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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 TraesCS5B01G492900 chr5B 100.000 1753 0 0 644 2396 661131157 661129405 0.000000e+00 3238.0
1 TraesCS5B01G492900 chr5B 100.000 357 0 0 1 357 661131800 661131444 0.000000e+00 660.0
2 TraesCS5B01G492900 chr5D 93.431 1644 76 10 776 2396 526109887 526108253 0.000000e+00 2409.0
3 TraesCS5B01G492900 chr5D 93.197 294 18 1 2 293 526110726 526110433 4.730000e-117 431.0
4 TraesCS5B01G492900 chr5A 91.588 1581 74 14 833 2396 653134030 653132492 0.000000e+00 2128.0
5 TraesCS5B01G492900 chr1A 89.011 91 10 0 681 771 486748831 486748741 1.950000e-21 113.0
6 TraesCS5B01G492900 chr1A 78.667 150 28 4 1962 2108 320336591 320336443 1.960000e-16 97.1
7 TraesCS5B01G492900 chr1A 76.351 148 25 10 1979 2123 51704527 51704667 1.190000e-08 71.3
8 TraesCS5B01G492900 chr7B 90.361 83 6 2 1899 1979 303164603 303164521 9.060000e-20 108.0
9 TraesCS5B01G492900 chr7B 100.000 28 0 0 2079 2106 16252740 16252767 4.000000e-03 52.8
10 TraesCS5B01G492900 chr3D 85.714 98 14 0 679 776 607227083 607226986 1.170000e-18 104.0
11 TraesCS5B01G492900 chr3D 100.000 28 0 0 2079 2106 233290222 233290195 4.000000e-03 52.8
12 TraesCS5B01G492900 chr7D 92.188 64 5 0 2046 2109 609236799 609236862 9.120000e-15 91.6
13 TraesCS5B01G492900 chr7D 89.062 64 7 0 2046 2109 608875983 608875920 1.970000e-11 80.5
14 TraesCS5B01G492900 chr1B 93.333 60 4 0 2046 2105 647533844 647533903 3.280000e-14 89.8
15 TraesCS5B01G492900 chr2D 89.706 68 7 0 1913 1980 630017182 630017249 1.180000e-13 87.9
16 TraesCS5B01G492900 chr2B 90.164 61 6 0 1913 1973 772985000 772985060 1.970000e-11 80.5
17 TraesCS5B01G492900 chr3A 87.143 70 7 2 78 146 235347114 235347046 7.100000e-11 78.7
18 TraesCS5B01G492900 chr6B 84.722 72 8 2 681 750 66994347 66994417 4.270000e-08 69.4


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 TraesCS5B01G492900 chr5B 661129405 661131800 2395 True 1949 3238 100.000 1 2396 2 chr5B.!!$R1 2395
1 TraesCS5B01G492900 chr5D 526108253 526110726 2473 True 1420 2409 93.314 2 2396 2 chr5D.!!$R1 2394
2 TraesCS5B01G492900 chr5A 653132492 653134030 1538 True 2128 2128 91.588 833 2396 1 chr5A.!!$R1 1563

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
662 702 0.596082 ATGTAGCAAAACCGGTGTGC 59.404 50.0 27.98 27.98 38.59 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1496 1577 0.322187 GTCCGGTGGGCTAAACACAT 60.322 55.0 0.0 0.0 40.54 3.21 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
75 76 1.745087 TCTTGATTTGATCGGGCTTGC 59.255 47.619 0.00 0.00 0.00 4.01
88 89 2.644992 CTTGCGGAACACCTTGGC 59.355 61.111 0.00 0.00 0.00 4.52
95 96 1.632589 GGAACACCTTGGCATTCCTT 58.367 50.000 9.11 0.00 38.08 3.36
106 107 2.433604 TGGCATTCCTTTGCTTTCACAA 59.566 40.909 0.00 0.00 42.38 3.33
118 119 1.112315 TTTCACAATGCCCAAGCCGT 61.112 50.000 0.00 0.00 38.69 5.68
125 126 2.125106 GCCCAAGCCGTCTCGATT 60.125 61.111 0.00 0.00 0.00 3.34
128 129 0.870307 CCCAAGCCGTCTCGATTACG 60.870 60.000 12.16 12.16 40.01 3.18
159 160 1.227973 CCTCGCTTATCCTTGCCCC 60.228 63.158 0.00 0.00 0.00 5.80
164 165 1.477558 CGCTTATCCTTGCCCCTGAAT 60.478 52.381 0.00 0.00 0.00 2.57
192 193 1.228245 GCTCTCAGCCACCAACCAA 60.228 57.895 0.00 0.00 34.48 3.67
214 215 5.695851 ATGAATTTGTCTGTCACTTCCAC 57.304 39.130 0.00 0.00 0.00 4.02
215 216 4.522114 TGAATTTGTCTGTCACTTCCACA 58.478 39.130 0.00 0.00 0.00 4.17
223 224 5.700832 TGTCTGTCACTTCCACAATATTGAC 59.299 40.000 22.16 7.62 35.08 3.18
238 239 7.846107 CACAATATTGACGTTAATCTGCAGTAC 59.154 37.037 22.16 7.22 0.00 2.73
246 247 7.116662 TGACGTTAATCTGCAGTACGTTAAATT 59.883 33.333 26.43 15.38 44.44 1.82
268 271 2.050691 CGTGTGCCACAAAAATGCTAC 58.949 47.619 0.00 0.00 33.40 3.58
287 290 4.809426 GCTACATACACGGACTAAAGCAAT 59.191 41.667 0.00 0.00 0.00 3.56
293 296 3.074412 CACGGACTAAAGCAATGGAACT 58.926 45.455 0.00 0.00 0.00 3.01
294 297 3.502211 CACGGACTAAAGCAATGGAACTT 59.498 43.478 0.00 0.00 0.00 2.66
295 298 4.023193 CACGGACTAAAGCAATGGAACTTT 60.023 41.667 0.00 0.00 0.00 2.66
296 299 5.180492 CACGGACTAAAGCAATGGAACTTTA 59.820 40.000 0.00 0.00 0.00 1.85
297 300 5.180680 ACGGACTAAAGCAATGGAACTTTAC 59.819 40.000 0.00 0.00 0.00 2.01
298 301 5.180492 CGGACTAAAGCAATGGAACTTTACA 59.820 40.000 0.00 0.00 0.00 2.41
299 302 6.612306 GGACTAAAGCAATGGAACTTTACAG 58.388 40.000 0.00 0.00 0.00 2.74
300 303 6.430000 GGACTAAAGCAATGGAACTTTACAGA 59.570 38.462 0.00 0.00 0.00 3.41
301 304 7.121315 GGACTAAAGCAATGGAACTTTACAGAT 59.879 37.037 0.00 0.00 0.00 2.90
302 305 8.045176 ACTAAAGCAATGGAACTTTACAGATC 57.955 34.615 0.00 0.00 0.00 2.75
303 306 6.899393 AAAGCAATGGAACTTTACAGATCA 57.101 33.333 0.00 0.00 0.00 2.92
304 307 6.506500 AAGCAATGGAACTTTACAGATCAG 57.493 37.500 0.00 0.00 0.00 2.90
305 308 4.397417 AGCAATGGAACTTTACAGATCAGC 59.603 41.667 0.00 0.00 0.00 4.26
306 309 4.397417 GCAATGGAACTTTACAGATCAGCT 59.603 41.667 0.00 0.00 0.00 4.24
319 322 4.822685 AGATCAGCTGACATGTCTCTTT 57.177 40.909 25.55 12.27 0.00 2.52
320 323 5.163281 AGATCAGCTGACATGTCTCTTTT 57.837 39.130 25.55 11.97 0.00 2.27
321 324 5.558818 AGATCAGCTGACATGTCTCTTTTT 58.441 37.500 25.55 7.84 0.00 1.94
322 325 6.705302 AGATCAGCTGACATGTCTCTTTTTA 58.295 36.000 25.55 3.59 0.00 1.52
323 326 7.164122 AGATCAGCTGACATGTCTCTTTTTAA 58.836 34.615 25.55 2.85 0.00 1.52
324 327 7.828223 AGATCAGCTGACATGTCTCTTTTTAAT 59.172 33.333 25.55 9.61 0.00 1.40
325 328 7.369803 TCAGCTGACATGTCTCTTTTTAATC 57.630 36.000 25.55 0.00 0.00 1.75
326 329 6.091305 TCAGCTGACATGTCTCTTTTTAATCG 59.909 38.462 25.55 8.97 0.00 3.34
327 330 5.352569 AGCTGACATGTCTCTTTTTAATCGG 59.647 40.000 25.55 2.55 0.00 4.18
328 331 5.447818 GCTGACATGTCTCTTTTTAATCGGG 60.448 44.000 25.55 0.00 0.00 5.14
329 332 4.394920 TGACATGTCTCTTTTTAATCGGGC 59.605 41.667 25.55 0.00 0.00 6.13
330 333 4.589908 ACATGTCTCTTTTTAATCGGGCT 58.410 39.130 0.00 0.00 0.00 5.19
331 334 5.741011 ACATGTCTCTTTTTAATCGGGCTA 58.259 37.500 0.00 0.00 0.00 3.93
332 335 6.177610 ACATGTCTCTTTTTAATCGGGCTAA 58.822 36.000 0.00 0.00 0.00 3.09
333 336 6.657541 ACATGTCTCTTTTTAATCGGGCTAAA 59.342 34.615 0.00 0.00 0.00 1.85
334 337 7.339466 ACATGTCTCTTTTTAATCGGGCTAAAT 59.661 33.333 0.00 0.00 0.00 1.40
335 338 8.836413 CATGTCTCTTTTTAATCGGGCTAAATA 58.164 33.333 0.00 0.00 0.00 1.40
336 339 8.795842 TGTCTCTTTTTAATCGGGCTAAATAA 57.204 30.769 0.00 0.00 0.00 1.40
337 340 8.671028 TGTCTCTTTTTAATCGGGCTAAATAAC 58.329 33.333 0.00 0.00 0.00 1.89
338 341 8.127327 GTCTCTTTTTAATCGGGCTAAATAACC 58.873 37.037 0.00 0.00 0.00 2.85
339 342 7.830201 TCTCTTTTTAATCGGGCTAAATAACCA 59.170 33.333 0.00 0.00 0.00 3.67
340 343 8.528044 TCTTTTTAATCGGGCTAAATAACCAT 57.472 30.769 0.00 0.00 0.00 3.55
341 344 8.626526 TCTTTTTAATCGGGCTAAATAACCATC 58.373 33.333 0.00 0.00 0.00 3.51
342 345 8.528044 TTTTTAATCGGGCTAAATAACCATCT 57.472 30.769 0.00 0.00 0.00 2.90
343 346 7.739498 TTTAATCGGGCTAAATAACCATCTC 57.261 36.000 0.00 0.00 0.00 2.75
344 347 3.764237 TCGGGCTAAATAACCATCTCC 57.236 47.619 0.00 0.00 0.00 3.71
345 348 2.370849 TCGGGCTAAATAACCATCTCCC 59.629 50.000 0.00 0.00 0.00 4.30
346 349 2.552373 CGGGCTAAATAACCATCTCCCC 60.552 54.545 0.00 0.00 0.00 4.81
347 350 2.225041 GGGCTAAATAACCATCTCCCCC 60.225 54.545 0.00 0.00 0.00 5.40
348 351 2.552373 GGCTAAATAACCATCTCCCCCG 60.552 54.545 0.00 0.00 0.00 5.73
349 352 2.370849 GCTAAATAACCATCTCCCCCGA 59.629 50.000 0.00 0.00 0.00 5.14
350 353 3.181448 GCTAAATAACCATCTCCCCCGAA 60.181 47.826 0.00 0.00 0.00 4.30
351 354 4.506802 GCTAAATAACCATCTCCCCCGAAT 60.507 45.833 0.00 0.00 0.00 3.34
352 355 4.536295 AAATAACCATCTCCCCCGAATT 57.464 40.909 0.00 0.00 0.00 2.17
353 356 5.656549 AAATAACCATCTCCCCCGAATTA 57.343 39.130 0.00 0.00 0.00 1.40
354 357 5.656549 AATAACCATCTCCCCCGAATTAA 57.343 39.130 0.00 0.00 0.00 1.40
355 358 3.292492 AACCATCTCCCCCGAATTAAC 57.708 47.619 0.00 0.00 0.00 2.01
356 359 2.201830 ACCATCTCCCCCGAATTAACA 58.798 47.619 0.00 0.00 0.00 2.41
662 702 0.596082 ATGTAGCAAAACCGGTGTGC 59.404 50.000 27.98 27.98 38.59 4.57
663 703 1.284715 GTAGCAAAACCGGTGTGCC 59.715 57.895 30.21 17.74 39.13 5.01
707 747 5.520288 CGTTGTACAATGCTAGATGCTTAGT 59.480 40.000 14.61 0.00 43.37 2.24
708 748 6.508563 CGTTGTACAATGCTAGATGCTTAGTG 60.509 42.308 14.61 0.00 43.37 2.74
713 753 5.363868 ACAATGCTAGATGCTTAGTGAGGTA 59.636 40.000 0.00 0.00 43.37 3.08
723 763 8.594550 AGATGCTTAGTGAGGTACTTAGAAAAA 58.405 33.333 0.00 0.00 41.55 1.94
750 790 5.376854 TCTGATTTTTCTAAAGCACCAGC 57.623 39.130 0.00 0.00 34.92 4.85
763 803 1.004927 GCACCAGCGCTTATTTCTACG 60.005 52.381 7.50 0.00 0.00 3.51
764 804 1.593006 CACCAGCGCTTATTTCTACGG 59.407 52.381 7.50 4.89 0.00 4.02
771 811 4.038162 AGCGCTTATTTCTACGGAAGAGAT 59.962 41.667 2.64 0.00 35.05 2.75
773 813 4.149046 CGCTTATTTCTACGGAAGAGATGC 59.851 45.833 4.06 0.45 35.05 3.91
803 869 7.765695 AAAAAGGCTGATTCATTTCTCTACA 57.234 32.000 0.00 0.00 0.00 2.74
805 871 4.775236 AGGCTGATTCATTTCTCTACACC 58.225 43.478 0.00 0.00 0.00 4.16
806 872 4.472833 AGGCTGATTCATTTCTCTACACCT 59.527 41.667 0.00 0.00 0.00 4.00
825 893 3.099141 CCTCCCCTAAACATGTTGCATT 58.901 45.455 12.82 0.00 0.00 3.56
826 894 3.515104 CCTCCCCTAAACATGTTGCATTT 59.485 43.478 12.82 0.00 0.00 2.32
856 926 2.124011 AAACGCATTGCACAGAGTTG 57.876 45.000 9.69 0.00 0.00 3.16
876 946 1.933853 GTTGTTCTTGAGTCGCACAGT 59.066 47.619 0.00 0.00 0.00 3.55
884 954 3.106407 GTCGCACAGTCTCCACGC 61.106 66.667 0.00 0.00 0.00 5.34
897 967 4.953868 CACGCCGTGACCCGACAA 62.954 66.667 12.85 0.00 39.56 3.18
1400 1470 4.363990 CGCGCTCCTGTGAGTGGT 62.364 66.667 5.56 0.00 46.92 4.16
1465 1543 9.759259 GCTTTGCAAAACATTTCCTAATTATTC 57.241 29.630 13.84 0.00 0.00 1.75
1529 1610 1.001633 ACCGGACTAAACTGCGTCAAT 59.998 47.619 9.46 0.00 31.88 2.57
1533 1614 4.331717 CCGGACTAAACTGCGTCAATATTT 59.668 41.667 0.00 0.00 31.88 1.40
1626 1707 6.694877 AGGACTAAGGACTTGTTTTGAAAC 57.305 37.500 0.00 0.00 39.33 2.78
1713 1794 2.443887 TGCGTGGTACTTACAAGGTC 57.556 50.000 0.00 0.00 0.00 3.85
1749 1830 8.807667 AAAGAAAACAGATGATTGTGATTGTC 57.192 30.769 0.00 0.00 0.00 3.18
1756 1837 9.896645 AACAGATGATTGTGATTGTCTATAAGT 57.103 29.630 0.00 0.00 0.00 2.24
1796 1877 7.996644 AGTGGACCAATTGAAGAAGTTAACTTA 59.003 33.333 20.58 5.55 36.11 2.24
1866 1947 9.273016 GAGAAATCCGATAAACATAGAAATCCA 57.727 33.333 0.00 0.00 0.00 3.41
1891 1972 1.746220 CGGCCAAACATTCGGGATTTA 59.254 47.619 2.24 0.00 0.00 1.40
1892 1973 2.360801 CGGCCAAACATTCGGGATTTAT 59.639 45.455 2.24 0.00 0.00 1.40
1893 1974 3.550030 CGGCCAAACATTCGGGATTTATC 60.550 47.826 2.24 0.00 0.00 1.75
1894 1975 3.383185 GGCCAAACATTCGGGATTTATCA 59.617 43.478 0.00 0.00 0.00 2.15
1895 1976 4.359706 GCCAAACATTCGGGATTTATCAC 58.640 43.478 0.00 0.00 0.00 3.06
1896 1977 4.736464 GCCAAACATTCGGGATTTATCACC 60.736 45.833 0.00 0.00 0.00 4.02
1897 1978 4.202111 CCAAACATTCGGGATTTATCACCC 60.202 45.833 0.00 0.00 42.43 4.61
1917 1998 2.287308 CCTGGCAAATCGAACGTTTTCA 60.287 45.455 0.46 0.00 0.00 2.69
1977 2058 1.002468 GCAAGCATGTCAACTTCGTGT 60.002 47.619 0.00 0.00 0.00 4.49
2004 2085 8.729805 TCAGTTTAATTTTGCCAGAAAATTGT 57.270 26.923 13.43 0.00 39.40 2.71
2005 2086 9.171877 TCAGTTTAATTTTGCCAGAAAATTGTT 57.828 25.926 13.43 0.00 39.40 2.83
2017 2098 5.636965 CCAGAAAATTGTTGTGTGTGTCAAA 59.363 36.000 0.00 0.00 0.00 2.69
2039 2120 1.730501 ACTTGTCATCCATGCGTCAG 58.269 50.000 0.00 0.00 0.00 3.51
2052 2133 3.535280 TGCGTCAGTAGAATTGCCATA 57.465 42.857 0.00 0.00 0.00 2.74
2053 2134 3.867857 TGCGTCAGTAGAATTGCCATAA 58.132 40.909 0.00 0.00 0.00 1.90
2108 2189 6.238621 CGAACATTCGGGATTTATCATTTCCA 60.239 38.462 6.11 0.00 46.30 3.53
2111 2192 8.884124 ACATTCGGGATTTATCATTTCCATAT 57.116 30.769 0.00 0.00 0.00 1.78
2214 2295 7.312154 TGTTAACTTGATGTGTTGAATATGGC 58.688 34.615 7.22 0.00 0.00 4.40
2233 2314 4.269183 TGGCGATCCAACAAATATTGAGT 58.731 39.130 0.00 0.00 39.99 3.41
2239 2320 6.852853 CGATCCAACAAATATTGAGTGCATAC 59.147 38.462 0.00 0.00 0.00 2.39
2282 2365 5.667539 TTCACCTGGACATTGAACAAAAA 57.332 34.783 0.00 0.00 0.00 1.94
2331 2418 5.905903 CAACTTTTTGCACGTTTGTTTACA 58.094 33.333 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 5.476945 AGGAAATTAAAGATTGGAAGCGTGT 59.523 36.000 0.00 0.00 0.00 4.49
75 76 0.609131 AGGAATGCCAAGGTGTTCCG 60.609 55.000 14.61 0.00 43.75 4.30
88 89 3.434299 GGCATTGTGAAAGCAAAGGAATG 59.566 43.478 0.00 0.00 31.63 2.67
95 96 1.540797 GCTTGGGCATTGTGAAAGCAA 60.541 47.619 11.81 0.00 42.19 3.91
106 107 2.257409 AATCGAGACGGCTTGGGCAT 62.257 55.000 5.45 0.00 40.87 4.40
144 145 0.107214 TTCAGGGGCAAGGATAAGCG 60.107 55.000 0.00 0.00 0.00 4.68
159 160 3.295093 TGAGAGCTAGGACAGGATTCAG 58.705 50.000 0.00 0.00 0.00 3.02
164 165 0.396417 GGCTGAGAGCTAGGACAGGA 60.396 60.000 0.00 0.00 41.99 3.86
192 193 5.132502 TGTGGAAGTGACAGACAAATTCAT 58.867 37.500 0.00 0.00 31.89 2.57
214 215 7.057402 CGTACTGCAGATTAACGTCAATATTG 58.943 38.462 23.35 9.29 0.00 1.90
215 216 6.755141 ACGTACTGCAGATTAACGTCAATATT 59.245 34.615 23.35 4.18 42.62 1.28
223 224 7.159818 CGAAATTTAACGTACTGCAGATTAACG 59.840 37.037 23.35 23.47 39.37 3.18
268 271 4.188462 TCCATTGCTTTAGTCCGTGTATG 58.812 43.478 0.00 0.00 0.00 2.39
287 290 4.040339 TGTCAGCTGATCTGTAAAGTTCCA 59.960 41.667 21.47 5.17 43.32 3.53
293 296 5.186603 AGAGACATGTCAGCTGATCTGTAAA 59.813 40.000 27.02 7.26 43.32 2.01
294 297 4.708909 AGAGACATGTCAGCTGATCTGTAA 59.291 41.667 27.02 8.71 43.32 2.41
295 298 4.276642 AGAGACATGTCAGCTGATCTGTA 58.723 43.478 27.02 10.72 43.32 2.74
296 299 3.098377 AGAGACATGTCAGCTGATCTGT 58.902 45.455 27.02 25.46 43.32 3.41
297 300 3.804786 AGAGACATGTCAGCTGATCTG 57.195 47.619 27.02 21.02 44.21 2.90
298 301 4.822685 AAAGAGACATGTCAGCTGATCT 57.177 40.909 27.02 18.21 0.00 2.75
299 302 5.876612 AAAAAGAGACATGTCAGCTGATC 57.123 39.130 27.02 13.34 0.00 2.92
300 303 7.201591 CGATTAAAAAGAGACATGTCAGCTGAT 60.202 37.037 27.02 2.86 0.00 2.90
301 304 6.091305 CGATTAAAAAGAGACATGTCAGCTGA 59.909 38.462 27.02 13.74 0.00 4.26
302 305 6.246449 CGATTAAAAAGAGACATGTCAGCTG 58.754 40.000 27.02 7.63 0.00 4.24
303 306 5.352569 CCGATTAAAAAGAGACATGTCAGCT 59.647 40.000 27.02 19.77 0.00 4.24
304 307 5.447818 CCCGATTAAAAAGAGACATGTCAGC 60.448 44.000 27.02 17.91 0.00 4.26
305 308 5.447818 GCCCGATTAAAAAGAGACATGTCAG 60.448 44.000 27.02 4.14 0.00 3.51
306 309 4.394920 GCCCGATTAAAAAGAGACATGTCA 59.605 41.667 27.02 4.65 0.00 3.58
307 310 4.636206 AGCCCGATTAAAAAGAGACATGTC 59.364 41.667 18.47 18.47 0.00 3.06
308 311 4.589908 AGCCCGATTAAAAAGAGACATGT 58.410 39.130 0.00 0.00 0.00 3.21
309 312 6.677781 TTAGCCCGATTAAAAAGAGACATG 57.322 37.500 0.00 0.00 0.00 3.21
310 313 7.881775 ATTTAGCCCGATTAAAAAGAGACAT 57.118 32.000 0.00 0.00 0.00 3.06
311 314 8.671028 GTTATTTAGCCCGATTAAAAAGAGACA 58.329 33.333 0.00 0.00 0.00 3.41
312 315 8.127327 GGTTATTTAGCCCGATTAAAAAGAGAC 58.873 37.037 0.00 0.00 0.00 3.36
313 316 7.830201 TGGTTATTTAGCCCGATTAAAAAGAGA 59.170 33.333 0.00 0.00 0.00 3.10
314 317 7.992008 TGGTTATTTAGCCCGATTAAAAAGAG 58.008 34.615 0.00 0.00 0.00 2.85
315 318 7.941431 TGGTTATTTAGCCCGATTAAAAAGA 57.059 32.000 0.00 0.00 0.00 2.52
316 319 8.630037 AGATGGTTATTTAGCCCGATTAAAAAG 58.370 33.333 0.00 0.00 0.00 2.27
317 320 8.528044 AGATGGTTATTTAGCCCGATTAAAAA 57.472 30.769 0.00 0.00 0.00 1.94
318 321 7.229907 GGAGATGGTTATTTAGCCCGATTAAAA 59.770 37.037 0.00 0.00 0.00 1.52
319 322 6.713450 GGAGATGGTTATTTAGCCCGATTAAA 59.287 38.462 0.00 0.00 0.00 1.52
320 323 6.235664 GGAGATGGTTATTTAGCCCGATTAA 58.764 40.000 0.00 0.00 0.00 1.40
321 324 5.280317 GGGAGATGGTTATTTAGCCCGATTA 60.280 44.000 0.00 0.00 0.00 1.75
322 325 4.506802 GGGAGATGGTTATTTAGCCCGATT 60.507 45.833 0.00 0.00 0.00 3.34
323 326 3.009143 GGGAGATGGTTATTTAGCCCGAT 59.991 47.826 0.00 0.00 0.00 4.18
324 327 2.370849 GGGAGATGGTTATTTAGCCCGA 59.629 50.000 0.00 0.00 0.00 5.14
325 328 2.552373 GGGGAGATGGTTATTTAGCCCG 60.552 54.545 0.00 0.00 35.15 6.13
326 329 2.225041 GGGGGAGATGGTTATTTAGCCC 60.225 54.545 0.00 0.00 0.00 5.19
327 330 2.552373 CGGGGGAGATGGTTATTTAGCC 60.552 54.545 0.00 0.00 0.00 3.93
328 331 2.370849 TCGGGGGAGATGGTTATTTAGC 59.629 50.000 0.00 0.00 0.00 3.09
329 332 4.699925 TTCGGGGGAGATGGTTATTTAG 57.300 45.455 0.00 0.00 0.00 1.85
330 333 5.656549 AATTCGGGGGAGATGGTTATTTA 57.343 39.130 0.00 0.00 0.00 1.40
331 334 4.536295 AATTCGGGGGAGATGGTTATTT 57.464 40.909 0.00 0.00 0.00 1.40
332 335 5.103855 TGTTAATTCGGGGGAGATGGTTATT 60.104 40.000 0.00 0.00 0.00 1.40
333 336 4.414182 TGTTAATTCGGGGGAGATGGTTAT 59.586 41.667 0.00 0.00 0.00 1.89
334 337 3.781407 TGTTAATTCGGGGGAGATGGTTA 59.219 43.478 0.00 0.00 0.00 2.85
335 338 2.578940 TGTTAATTCGGGGGAGATGGTT 59.421 45.455 0.00 0.00 0.00 3.67
336 339 2.201830 TGTTAATTCGGGGGAGATGGT 58.798 47.619 0.00 0.00 0.00 3.55
662 702 2.870435 GCCTTATGCCGTATAGGTGTGG 60.870 54.545 0.00 0.00 43.70 4.17
663 703 2.413837 GCCTTATGCCGTATAGGTGTG 58.586 52.381 0.00 0.00 43.70 3.82
672 712 0.037139 TGTACAACGCCTTATGCCGT 60.037 50.000 0.00 0.00 36.24 5.68
692 732 5.144100 AGTACCTCACTAAGCATCTAGCAT 58.856 41.667 0.00 0.00 40.28 3.79
698 738 8.773404 TTTTTCTAAGTACCTCACTAAGCATC 57.227 34.615 0.00 0.00 36.04 3.91
728 768 4.083324 CGCTGGTGCTTTAGAAAAATCAGA 60.083 41.667 0.00 0.00 36.97 3.27
730 770 3.611530 GCGCTGGTGCTTTAGAAAAATCA 60.612 43.478 0.00 0.00 36.97 2.57
732 772 2.558359 AGCGCTGGTGCTTTAGAAAAAT 59.442 40.909 10.39 0.00 44.46 1.82
733 773 1.953686 AGCGCTGGTGCTTTAGAAAAA 59.046 42.857 10.39 0.00 44.46 1.94
743 783 1.004927 CGTAGAAATAAGCGCTGGTGC 60.005 52.381 12.58 0.00 0.00 5.01
746 786 2.218953 TCCGTAGAAATAAGCGCTGG 57.781 50.000 12.58 4.11 0.00 4.85
747 787 3.444916 TCTTCCGTAGAAATAAGCGCTG 58.555 45.455 12.58 0.00 0.00 5.18
750 790 4.149046 GCATCTCTTCCGTAGAAATAAGCG 59.851 45.833 0.00 0.00 30.91 4.68
785 851 4.813697 GGAGGTGTAGAGAAATGAATCAGC 59.186 45.833 0.00 0.00 0.00 4.26
802 868 1.818674 GCAACATGTTTAGGGGAGGTG 59.181 52.381 8.77 0.00 0.00 4.00
803 869 1.427368 TGCAACATGTTTAGGGGAGGT 59.573 47.619 8.77 0.00 0.00 3.85
805 871 4.806640 AAATGCAACATGTTTAGGGGAG 57.193 40.909 8.77 0.00 0.00 4.30
806 872 5.540337 TGTAAAATGCAACATGTTTAGGGGA 59.460 36.000 8.77 0.00 0.00 4.81
825 893 4.276183 TGCAATGCGTTTAGACCTTGTAAA 59.724 37.500 0.00 0.00 0.00 2.01
826 894 3.815962 TGCAATGCGTTTAGACCTTGTAA 59.184 39.130 0.00 0.00 0.00 2.41
856 926 1.933853 ACTGTGCGACTCAAGAACAAC 59.066 47.619 0.00 0.00 0.00 3.32
884 954 0.944311 CTTGTCTTGTCGGGTCACGG 60.944 60.000 0.00 0.00 44.45 4.94
893 963 1.423395 CACCGAGCTCTTGTCTTGTC 58.577 55.000 12.85 0.00 0.00 3.18
894 964 0.034059 CCACCGAGCTCTTGTCTTGT 59.966 55.000 12.85 0.00 0.00 3.16
895 965 0.318441 TCCACCGAGCTCTTGTCTTG 59.682 55.000 12.85 0.00 0.00 3.02
896 966 1.270907 ATCCACCGAGCTCTTGTCTT 58.729 50.000 12.85 0.00 0.00 3.01
897 967 1.066573 CAATCCACCGAGCTCTTGTCT 60.067 52.381 12.85 0.00 0.00 3.41
1368 1438 1.429825 CGCGATGAGGACGAAGAGT 59.570 57.895 0.00 0.00 0.00 3.24
1400 1470 2.604686 AGAAGGAGGGAGCACGCA 60.605 61.111 0.36 0.00 0.00 5.24
1447 1525 9.920946 TCCAGCTAGAATAATTAGGAAATGTTT 57.079 29.630 0.00 0.00 0.00 2.83
1496 1577 0.322187 GTCCGGTGGGCTAAACACAT 60.322 55.000 0.00 0.00 40.54 3.21
1626 1707 1.209128 AAACTGTCAGCGAGTTCACG 58.791 50.000 0.00 0.00 32.33 4.35
1796 1877 5.047590 ACATGACTGTGTGAATGATGCAAAT 60.048 36.000 0.00 0.00 33.22 2.32
1866 1947 1.474879 CCCGAATGTTTGGCCGTTATT 59.525 47.619 0.00 0.00 0.00 1.40
1891 1972 1.463674 GTTCGATTTGCCAGGGTGAT 58.536 50.000 0.00 0.00 0.00 3.06
1892 1973 0.953471 CGTTCGATTTGCCAGGGTGA 60.953 55.000 0.00 0.00 0.00 4.02
1893 1974 1.234615 ACGTTCGATTTGCCAGGGTG 61.235 55.000 0.00 0.00 0.00 4.61
1894 1975 0.536460 AACGTTCGATTTGCCAGGGT 60.536 50.000 0.00 0.00 0.00 4.34
1895 1976 0.596082 AAACGTTCGATTTGCCAGGG 59.404 50.000 0.00 0.00 0.00 4.45
1896 1977 2.287308 TGAAAACGTTCGATTTGCCAGG 60.287 45.455 0.00 0.00 36.46 4.45
1897 1978 2.993545 TGAAAACGTTCGATTTGCCAG 58.006 42.857 0.00 0.00 36.46 4.85
1917 1998 1.196808 CGCGTCACTAAACTTGCCATT 59.803 47.619 0.00 0.00 0.00 3.16
1966 2047 8.855279 CAAAATTAAACTGAAACACGAAGTTGA 58.145 29.630 0.00 0.00 41.61 3.18
2004 2085 6.502136 TGACAAGTTATTTGACACACACAA 57.498 33.333 0.00 0.00 39.21 3.33
2005 2086 6.238621 GGATGACAAGTTATTTGACACACACA 60.239 38.462 0.00 0.00 42.58 3.72
2017 2098 3.872696 TGACGCATGGATGACAAGTTAT 58.127 40.909 0.00 0.00 0.00 1.89
2053 2134 3.137533 CCATGGCAAACCGAATGTTTTT 58.862 40.909 0.00 0.00 44.80 1.94
2063 2144 3.056465 TCGGAATTTAACCATGGCAAACC 60.056 43.478 13.04 9.81 0.00 3.27
2064 2145 4.181309 TCGGAATTTAACCATGGCAAAC 57.819 40.909 13.04 1.90 0.00 2.93
2108 2189 7.402941 TGGTGTGTGCCTCCAGAATATATATAT 59.597 37.037 0.00 0.00 0.00 0.86
2111 2192 4.904853 TGGTGTGTGCCTCCAGAATATATA 59.095 41.667 0.00 0.00 0.00 0.86
2113 2194 3.111484 TGGTGTGTGCCTCCAGAATATA 58.889 45.455 0.00 0.00 0.00 0.86
2191 2272 6.372937 TCGCCATATTCAACACATCAAGTTAA 59.627 34.615 0.00 0.00 0.00 2.01
2214 2295 5.233957 TGCACTCAATATTTGTTGGATCG 57.766 39.130 0.00 0.00 0.00 3.69
2233 2314 6.839124 ACAAAAGGAAATCATGAGTATGCA 57.161 33.333 0.09 0.00 34.21 3.96
2239 2320 7.383300 GGTGAAAGAACAAAAGGAAATCATGAG 59.617 37.037 0.09 0.00 0.00 2.90
2282 2365 7.392673 GCAGATGATATGGTTGTTGATTATCCT 59.607 37.037 0.00 0.00 0.00 3.24
2321 2408 7.041984 CCTCTCTTACTGTTCCTGTAAACAAAC 60.042 40.741 0.00 0.00 38.60 2.93
2331 2418 1.079658 AGGCCCTCTCTTACTGTTCCT 59.920 52.381 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.