Multiple sequence alignment - TraesCS5D01G365200

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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 TraesCS5D01G365200 chr5D 100.000 2330 0 0 1 2330 442502934 442500605 0.000000e+00 4303.0
1 TraesCS5D01G365200 chr5D 100.000 37 0 0 1943 1979 3965408 3965372 4.150000e-08 69.4
2 TraesCS5D01G365200 chr5A 91.039 770 44 13 1 755 558690658 558689899 0.000000e+00 1016.0
3 TraesCS5D01G365200 chr5A 92.123 292 16 4 454 742 558689834 558689547 2.790000e-109 405.0
4 TraesCS5D01G365200 chr5A 88.947 190 12 8 825 1006 558689526 558689338 2.330000e-55 226.0
5 TraesCS5D01G365200 chr5A 92.806 139 10 0 1135 1273 558688936 558688798 3.930000e-48 202.0
6 TraesCS5D01G365200 chr5A 90.909 88 6 2 739 825 569803202 569803288 1.460000e-22 117.0
7 TraesCS5D01G365200 chr5B 93.639 676 20 5 1 669 538723324 538722665 0.000000e+00 989.0
8 TraesCS5D01G365200 chr5B 91.228 684 31 11 667 1339 538722551 538721886 0.000000e+00 904.0
9 TraesCS5D01G365200 chr5B 92.114 317 15 5 1603 1912 316763550 316763863 2.750000e-119 438.0
10 TraesCS5D01G365200 chr5B 90.127 314 21 5 1606 1912 613263350 613263040 1.300000e-107 399.0
11 TraesCS5D01G365200 chr5B 88.889 297 18 7 1362 1657 538721192 538720910 3.680000e-93 351.0
12 TraesCS5D01G365200 chr5B 89.209 278 18 3 1990 2255 538720546 538720269 1.030000e-88 337.0
13 TraesCS5D01G365200 chr6B 91.055 559 31 9 1362 1912 157015905 157015358 0.000000e+00 737.0
14 TraesCS5D01G365200 chr6B 90.966 476 26 7 1445 1912 357513918 357514384 1.970000e-175 625.0
15 TraesCS5D01G365200 chr4B 91.483 317 17 5 1603 1912 48006582 48006269 5.950000e-116 427.0
16 TraesCS5D01G365200 chr4B 91.815 281 16 3 1606 1879 515891976 515891696 3.630000e-103 385.0
17 TraesCS5D01G365200 chr4B 88.043 92 10 1 744 834 322674033 322674124 8.800000e-20 108.0
18 TraesCS5D01G365200 chr7B 91.167 317 18 5 1603 1912 120369629 120369316 2.770000e-114 422.0
19 TraesCS5D01G365200 chr7B 88.372 86 8 2 744 829 713284362 713284279 4.100000e-18 102.0
20 TraesCS5D01G365200 chrUn 90.536 317 18 7 1603 1912 37015586 37015897 2.160000e-110 409.0
21 TraesCS5D01G365200 chr1B 90.221 317 21 5 1603 1912 634032846 634033159 2.790000e-109 405.0
22 TraesCS5D01G365200 chr2D 79.695 197 31 7 547 740 626676742 626676932 1.450000e-27 134.0
23 TraesCS5D01G365200 chr2D 86.813 91 10 1 744 834 547882293 547882381 1.470000e-17 100.0
24 TraesCS5D01G365200 chr3D 89.583 96 6 3 755 849 556145718 556145810 4.070000e-23 119.0
25 TraesCS5D01G365200 chr3A 89.583 96 6 3 755 849 693161955 693162047 4.070000e-23 119.0
26 TraesCS5D01G365200 chr3A 88.506 87 9 1 744 829 358268356 358268442 1.140000e-18 104.0
27 TraesCS5D01G365200 chr4A 88.043 92 10 1 744 834 342448628 342448719 8.800000e-20 108.0
28 TraesCS5D01G365200 chr4D 86.957 92 11 1 744 834 179860424 179860333 4.100000e-18 102.0


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 TraesCS5D01G365200 chr5D 442500605 442502934 2329 True 4303.00 4303 100.00000 1 2330 1 chr5D.!!$R2 2329
1 TraesCS5D01G365200 chr5A 558688798 558690658 1860 True 462.25 1016 91.22875 1 1273 4 chr5A.!!$R1 1272
2 TraesCS5D01G365200 chr5B 538720269 538723324 3055 True 645.25 989 90.74125 1 2255 4 chr5B.!!$R2 2254
3 TraesCS5D01G365200 chr6B 157015358 157015905 547 True 737.00 737 91.05500 1362 1912 1 chr6B.!!$R1 550


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
225 238 0.680618 TTAGGGCGAACAGAAACCGA 59.319 50.0 0.0 0.0 0.0 4.69 F
1192 2010 0.814457 TATTGGTGCGTTCATTGGGC 59.186 50.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1278 2101 0.035630 GAGCTGGCCTCACATCAAGT 60.036 55.0 3.32 0.0 40.45 3.16 R
2044 3632 0.108756 GACACCGTGTCTAGCCTTCC 60.109 60.0 22.08 0.0 43.73 3.46 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
225 238 0.680618 TTAGGGCGAACAGAAACCGA 59.319 50.000 0.00 0.00 0.00 4.69
314 327 6.306356 GCAATGATGTGCATAATCGTAAATCC 59.694 38.462 7.31 0.00 44.29 3.01
404 417 9.934190 ATTGATTTTCAAGTTTTTGTGCAATAC 57.066 25.926 0.00 0.00 40.05 1.89
405 418 8.715191 TGATTTTCAAGTTTTTGTGCAATACT 57.285 26.923 0.00 0.00 35.73 2.12
486 499 6.552445 AGCCATCTTAAGTTGTCAGTAGAT 57.448 37.500 11.63 0.00 0.00 1.98
488 501 6.820656 AGCCATCTTAAGTTGTCAGTAGATTG 59.179 38.462 11.63 0.00 0.00 2.67
585 607 6.747414 TGAAGCTCCATACAACACCTATAT 57.253 37.500 0.00 0.00 0.00 0.86
586 608 7.849322 TGAAGCTCCATACAACACCTATATA 57.151 36.000 0.00 0.00 0.00 0.86
742 1246 9.817365 CAACATTCTTACAAGACTACAGAAATG 57.183 33.333 0.00 0.00 34.13 2.32
749 1253 4.042187 ACAAGACTACAGAAATGCTCCCTT 59.958 41.667 0.00 0.00 0.00 3.95
751 1255 3.118956 AGACTACAGAAATGCTCCCTTCG 60.119 47.826 0.00 0.00 0.00 3.79
784 1288 5.751243 AGTGTCGTGCTTTTAGTTCAAAT 57.249 34.783 0.00 0.00 0.00 2.32
785 1289 6.131544 AGTGTCGTGCTTTTAGTTCAAATT 57.868 33.333 0.00 0.00 0.00 1.82
786 1290 6.560711 AGTGTCGTGCTTTTAGTTCAAATTT 58.439 32.000 0.00 0.00 0.00 1.82
787 1291 6.472163 AGTGTCGTGCTTTTAGTTCAAATTTG 59.528 34.615 12.15 12.15 0.00 2.32
788 1292 6.470877 GTGTCGTGCTTTTAGTTCAAATTTGA 59.529 34.615 16.91 16.91 34.92 2.69
789 1293 7.008810 GTGTCGTGCTTTTAGTTCAAATTTGAA 59.991 33.333 26.01 26.01 44.31 2.69
813 1317 9.113876 GAACTAAAACCATGACACTTATTTTCG 57.886 33.333 0.00 0.00 0.00 3.46
817 1321 6.627395 AACCATGACACTTATTTTCGAACA 57.373 33.333 0.00 0.00 0.00 3.18
850 1354 6.757010 AGTAGTAAATAAGACTCACATTGCCG 59.243 38.462 0.00 0.00 0.00 5.69
863 1367 4.457257 TCACATTGCCGATTTATGTGTCAA 59.543 37.500 12.52 0.00 45.76 3.18
864 1368 5.125257 TCACATTGCCGATTTATGTGTCAAT 59.875 36.000 12.52 0.00 45.76 2.57
1020 1532 5.066505 GGACATGATGGTGGAATCTGTTAAC 59.933 44.000 0.00 0.00 0.00 2.01
1107 1620 3.891422 AATGCATTGGGTGTGTATTGG 57.109 42.857 12.09 0.00 31.96 3.16
1108 1621 2.593925 TGCATTGGGTGTGTATTGGA 57.406 45.000 0.00 0.00 0.00 3.53
1109 1622 2.445427 TGCATTGGGTGTGTATTGGAG 58.555 47.619 0.00 0.00 0.00 3.86
1119 1632 7.107542 TGGGTGTGTATTGGAGTAGTTATTTC 58.892 38.462 0.00 0.00 0.00 2.17
1141 1959 2.113139 AAGACGGGCCCAGTGTTG 59.887 61.111 24.92 6.57 0.00 3.33
1192 2010 0.814457 TATTGGTGCGTTCATTGGGC 59.186 50.000 0.00 0.00 0.00 5.36
1248 2066 4.023193 CCTTTGCTGTTCCAGACGTTTTAT 60.023 41.667 0.00 0.00 32.44 1.40
1307 2130 1.451028 GGCCAGCTCCACATCTGTC 60.451 63.158 0.00 0.00 0.00 3.51
1339 2162 3.967987 ACCCATATCCTGACCTGAAGTAC 59.032 47.826 0.00 0.00 0.00 2.73
1340 2163 3.325135 CCCATATCCTGACCTGAAGTACC 59.675 52.174 0.00 0.00 0.00 3.34
1342 2165 5.394738 CCATATCCTGACCTGAAGTACCTA 58.605 45.833 0.00 0.00 0.00 3.08
1343 2166 5.839063 CCATATCCTGACCTGAAGTACCTAA 59.161 44.000 0.00 0.00 0.00 2.69
1345 2168 7.016661 CCATATCCTGACCTGAAGTACCTAAAT 59.983 40.741 0.00 0.00 0.00 1.40
1346 2169 5.934402 TCCTGACCTGAAGTACCTAAATC 57.066 43.478 0.00 0.00 0.00 2.17
1348 2171 5.422331 TCCTGACCTGAAGTACCTAAATCTG 59.578 44.000 0.00 0.00 0.00 2.90
1349 2172 5.187967 CCTGACCTGAAGTACCTAAATCTGT 59.812 44.000 0.00 0.00 0.00 3.41
1350 2173 6.380274 CCTGACCTGAAGTACCTAAATCTGTA 59.620 42.308 0.00 0.00 0.00 2.74
1351 2174 7.166691 TGACCTGAAGTACCTAAATCTGTAC 57.833 40.000 0.00 0.00 38.06 2.90
1352 2175 6.154021 TGACCTGAAGTACCTAAATCTGTACC 59.846 42.308 0.00 0.00 38.45 3.34
1353 2176 5.424573 ACCTGAAGTACCTAAATCTGTACCC 59.575 44.000 0.00 0.00 38.45 3.69
1354 2177 5.424252 CCTGAAGTACCTAAATCTGTACCCA 59.576 44.000 0.00 0.00 38.45 4.51
1356 2179 7.289317 CCTGAAGTACCTAAATCTGTACCCATA 59.711 40.741 0.00 0.00 38.45 2.74
1359 2182 9.708092 GAAGTACCTAAATCTGTACCCATATTC 57.292 37.037 0.00 0.00 38.45 1.75
1521 3016 2.208132 ATCGGGCACTCGATCTCTAT 57.792 50.000 0.00 0.00 45.43 1.98
1523 3018 0.242286 CGGGCACTCGATCTCTATGG 59.758 60.000 0.00 0.00 0.00 2.74
1524 3019 1.333177 GGGCACTCGATCTCTATGGT 58.667 55.000 0.00 0.00 0.00 3.55
1544 3039 3.440522 GGTGCCAAAAGAACCTACAGATC 59.559 47.826 0.00 0.00 41.79 2.75
1546 3041 2.678336 GCCAAAAGAACCTACAGATCGG 59.322 50.000 0.00 0.00 0.00 4.18
1548 3043 4.622220 GCCAAAAGAACCTACAGATCGGTA 60.622 45.833 5.57 5.57 32.07 4.02
1558 3053 6.746120 ACCTACAGATCGGTACATCATTTAC 58.254 40.000 1.18 0.00 0.00 2.01
1570 3065 5.627182 ACATCATTTACTGAGGATCTGCT 57.373 39.130 0.00 0.00 37.89 4.24
1576 3071 5.426689 TTTACTGAGGATCTGCTTCACAT 57.573 39.130 0.00 0.00 37.61 3.21
1586 3081 4.662468 TCTGCTTCACATAGAGGATCAC 57.338 45.455 0.00 0.00 37.82 3.06
1638 3133 9.148879 ACTCTCATGTAGTATAAGTATTGCCTT 57.851 33.333 2.24 0.00 0.00 4.35
1643 3138 8.765219 CATGTAGTATAAGTATTGCCTTGTCAC 58.235 37.037 0.00 0.00 0.00 3.67
1657 3152 3.380004 CCTTGTCACTGTGGTAAGCAAAA 59.620 43.478 8.11 0.00 0.00 2.44
1666 3220 9.290988 TCACTGTGGTAAGCAAAATAATTCTTA 57.709 29.630 8.11 0.00 0.00 2.10
1672 3226 9.168451 TGGTAAGCAAAATAATTCTTATCGACA 57.832 29.630 0.00 0.00 0.00 4.35
1692 3246 6.768861 TCGACAAGGATTTCTAAAGGTCAAAA 59.231 34.615 0.00 0.00 0.00 2.44
1841 3401 1.962807 CAATCTCAAAGGCCACCACAA 59.037 47.619 5.01 0.00 0.00 3.33
1887 3447 1.584175 CTAATGCAGCAGGAGAGCAG 58.416 55.000 0.00 0.00 42.14 4.24
1888 3448 0.463295 TAATGCAGCAGGAGAGCAGC 60.463 55.000 0.00 0.00 45.86 5.25
1890 3450 2.820479 GCAGCAGGAGAGCAGCAG 60.820 66.667 0.00 0.00 45.12 4.24
1912 3472 3.618507 GCACTGACCAGTCTAGCTTGAAT 60.619 47.826 0.00 0.00 40.20 2.57
1913 3473 4.180057 CACTGACCAGTCTAGCTTGAATC 58.820 47.826 0.00 0.00 40.20 2.52
1914 3474 4.081752 CACTGACCAGTCTAGCTTGAATCT 60.082 45.833 0.00 0.00 40.20 2.40
1915 3475 4.081752 ACTGACCAGTCTAGCTTGAATCTG 60.082 45.833 0.00 4.26 36.92 2.90
1916 3476 3.834813 TGACCAGTCTAGCTTGAATCTGT 59.165 43.478 12.47 6.17 0.00 3.41
1917 3477 4.180057 GACCAGTCTAGCTTGAATCTGTG 58.820 47.826 12.47 8.08 0.00 3.66
1918 3478 2.935201 CCAGTCTAGCTTGAATCTGTGC 59.065 50.000 12.47 0.00 0.00 4.57
1919 3479 3.369261 CCAGTCTAGCTTGAATCTGTGCT 60.369 47.826 12.47 0.00 39.30 4.40
1920 3480 3.617706 CAGTCTAGCTTGAATCTGTGCTG 59.382 47.826 0.00 0.00 37.02 4.41
1921 3481 3.260380 AGTCTAGCTTGAATCTGTGCTGT 59.740 43.478 0.00 0.00 37.02 4.40
1922 3482 4.464244 AGTCTAGCTTGAATCTGTGCTGTA 59.536 41.667 0.00 0.00 37.02 2.74
1923 3483 4.564769 GTCTAGCTTGAATCTGTGCTGTAC 59.435 45.833 0.00 0.00 37.02 2.90
1924 3484 3.407424 AGCTTGAATCTGTGCTGTACA 57.593 42.857 0.00 0.00 37.78 2.90
1925 3485 3.947868 AGCTTGAATCTGTGCTGTACAT 58.052 40.909 0.00 0.00 38.92 2.29
1930 3490 4.498241 TGAATCTGTGCTGTACATCACTC 58.502 43.478 25.48 16.89 38.92 3.51
1938 3498 5.067805 TGTGCTGTACATCACTCCTATGTAG 59.932 44.000 25.48 0.00 39.76 2.74
1945 3505 3.596940 TCACTCCTATGTAGTCCCTCC 57.403 52.381 0.00 0.00 0.00 4.30
1957 3517 4.472108 TGTAGTCCCTCCGTTCCATAATTT 59.528 41.667 0.00 0.00 0.00 1.82
1960 3520 6.069705 AGTCCCTCCGTTCCATAATTTTTA 57.930 37.500 0.00 0.00 0.00 1.52
1962 3522 6.771267 AGTCCCTCCGTTCCATAATTTTTATC 59.229 38.462 0.00 0.00 0.00 1.75
2001 3589 5.298347 AGGTTCTGCTCTGTTACAGTTTAC 58.702 41.667 12.41 1.60 35.37 2.01
2021 3609 3.460825 ACACTGGGGGATTAGAGCTAAA 58.539 45.455 0.00 0.00 0.00 1.85
2044 3632 1.546476 ACTAACGGTGCCTCTCTGAAG 59.454 52.381 0.00 0.00 0.00 3.02
2075 3663 3.340727 CGGTGTCGTTGAGGGTATC 57.659 57.895 0.00 0.00 0.00 2.24
2090 3678 3.197983 AGGGTATCTTTCTGTTTCCCTCG 59.802 47.826 0.00 0.00 39.44 4.63
2127 3715 0.681564 TTTCAACCACACGGCCAACT 60.682 50.000 2.24 0.00 34.57 3.16
2137 3725 2.218603 CACGGCCAACTTACAGTTTCT 58.781 47.619 2.24 0.00 36.03 2.52
2156 3745 7.955864 CAGTTTCTTATTTAGCACTTACGGTTC 59.044 37.037 0.00 0.00 0.00 3.62
2167 3756 2.229784 ACTTACGGTTCGGGAAGTACAG 59.770 50.000 6.26 0.00 36.13 2.74
2168 3757 1.176527 TACGGTTCGGGAAGTACAGG 58.823 55.000 0.00 0.00 0.00 4.00
2171 3760 0.035739 GGTTCGGGAAGTACAGGCAA 59.964 55.000 0.00 0.00 0.00 4.52
2234 3833 3.281727 TGGAGTACCAAGCAATCCATC 57.718 47.619 0.00 0.00 43.91 3.51
2235 3834 2.846206 TGGAGTACCAAGCAATCCATCT 59.154 45.455 0.00 0.00 43.91 2.90
2236 3835 3.209410 GGAGTACCAAGCAATCCATCTG 58.791 50.000 0.00 0.00 35.97 2.90
2237 3836 3.370953 GGAGTACCAAGCAATCCATCTGT 60.371 47.826 0.00 0.00 35.97 3.41
2238 3837 4.141711 GGAGTACCAAGCAATCCATCTGTA 60.142 45.833 0.00 0.00 35.97 2.74
2239 3838 4.770795 AGTACCAAGCAATCCATCTGTAC 58.229 43.478 0.00 0.00 0.00 2.90
2240 3839 4.471386 AGTACCAAGCAATCCATCTGTACT 59.529 41.667 0.00 0.00 34.44 2.73
2241 3840 4.307032 ACCAAGCAATCCATCTGTACTT 57.693 40.909 0.00 0.00 0.00 2.24
2242 3841 4.012374 ACCAAGCAATCCATCTGTACTTG 58.988 43.478 0.00 0.00 34.30 3.16
2243 3842 4.012374 CCAAGCAATCCATCTGTACTTGT 58.988 43.478 0.00 0.00 33.00 3.16
2244 3843 4.460382 CCAAGCAATCCATCTGTACTTGTT 59.540 41.667 0.00 0.00 33.00 2.83
2245 3844 5.647658 CCAAGCAATCCATCTGTACTTGTTA 59.352 40.000 0.00 0.00 33.00 2.41
2246 3845 6.319658 CCAAGCAATCCATCTGTACTTGTTAT 59.680 38.462 0.00 0.00 33.00 1.89
2247 3846 7.498900 CCAAGCAATCCATCTGTACTTGTTATA 59.501 37.037 0.00 0.00 33.00 0.98
2248 3847 9.060347 CAAGCAATCCATCTGTACTTGTTATAT 57.940 33.333 0.00 0.00 0.00 0.86
2249 3848 9.632638 AAGCAATCCATCTGTACTTGTTATATT 57.367 29.630 0.00 0.00 0.00 1.28
2250 3849 9.632638 AGCAATCCATCTGTACTTGTTATATTT 57.367 29.630 0.00 0.00 0.00 1.40
2251 3850 9.884465 GCAATCCATCTGTACTTGTTATATTTC 57.116 33.333 0.00 0.00 0.00 2.17
2275 3874 8.893219 TCTAATATGATTCTTGCAGTACCAAG 57.107 34.615 5.72 5.72 42.73 3.61
2278 3877 0.804989 ATTCTTGCAGTACCAAGCGC 59.195 50.000 0.00 0.00 41.47 5.92
2287 3886 1.450134 TACCAAGCGCTGCCATCTG 60.450 57.895 12.58 3.61 0.00 2.90
2323 3922 8.621532 ATTTCTAAACTAGCATGTTGACTTCA 57.378 30.769 0.00 0.00 0.00 3.02
2324 3923 8.445275 TTTCTAAACTAGCATGTTGACTTCAA 57.555 30.769 0.00 0.00 0.00 2.69
2325 3924 7.658179 TCTAAACTAGCATGTTGACTTCAAG 57.342 36.000 0.00 0.00 36.39 3.02
2326 3925 5.695851 AAACTAGCATGTTGACTTCAAGG 57.304 39.130 0.00 0.00 36.39 3.61
2327 3926 4.623932 ACTAGCATGTTGACTTCAAGGA 57.376 40.909 0.00 0.00 36.39 3.36
2328 3927 5.171339 ACTAGCATGTTGACTTCAAGGAT 57.829 39.130 0.00 0.00 36.39 3.24
2329 3928 4.940046 ACTAGCATGTTGACTTCAAGGATG 59.060 41.667 0.00 0.06 36.39 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
225 238 3.010584 ACTGATATCCAAGTGGGCTGTTT 59.989 43.478 0.00 0.00 36.21 2.83
314 327 1.069204 AGTGCAGCCTACCATCATACG 59.931 52.381 0.00 0.00 0.00 3.06
486 499 6.419791 CCATCTACCCTATAAACACCAACAA 58.580 40.000 0.00 0.00 0.00 2.83
488 501 4.820173 GCCATCTACCCTATAAACACCAAC 59.180 45.833 0.00 0.00 0.00 3.77
698 836 9.415544 AGAATGTTGATGTTTTAATCAAGCTTC 57.584 29.630 0.00 6.58 44.96 3.86
734 1238 1.339151 GGACGAAGGGAGCATTTCTGT 60.339 52.381 0.00 0.00 0.00 3.41
742 1246 2.413310 TATTTTGGGACGAAGGGAGC 57.587 50.000 0.00 0.00 0.00 4.70
749 1253 3.061322 CACGACACTTATTTTGGGACGA 58.939 45.455 0.00 0.00 0.00 4.20
751 1255 2.812011 AGCACGACACTTATTTTGGGAC 59.188 45.455 0.00 0.00 0.00 4.46
786 1290 9.959749 GAAAATAAGTGTCATGGTTTTAGTTCA 57.040 29.630 0.00 0.00 0.00 3.18
787 1291 9.113876 CGAAAATAAGTGTCATGGTTTTAGTTC 57.886 33.333 0.00 0.00 0.00 3.01
788 1292 8.842280 TCGAAAATAAGTGTCATGGTTTTAGTT 58.158 29.630 0.00 0.00 0.00 2.24
789 1293 8.385898 TCGAAAATAAGTGTCATGGTTTTAGT 57.614 30.769 0.00 0.00 0.00 2.24
790 1294 9.113876 GTTCGAAAATAAGTGTCATGGTTTTAG 57.886 33.333 0.00 0.00 0.00 1.85
791 1295 8.622157 TGTTCGAAAATAAGTGTCATGGTTTTA 58.378 29.630 0.00 0.00 0.00 1.52
792 1296 7.484975 TGTTCGAAAATAAGTGTCATGGTTTT 58.515 30.769 0.00 0.00 0.00 2.43
793 1297 7.012894 TCTGTTCGAAAATAAGTGTCATGGTTT 59.987 33.333 0.00 0.00 0.00 3.27
813 1317 8.407832 GTCTTATTTACTACTCTCCCTCTGTTC 58.592 40.741 0.00 0.00 0.00 3.18
817 1321 7.776500 GTGAGTCTTATTTACTACTCTCCCTCT 59.224 40.741 0.00 0.00 39.27 3.69
850 1354 5.524646 CCCATGCCAAATTGACACATAAATC 59.475 40.000 0.00 0.00 0.00 2.17
863 1367 0.043032 ACCATGACCCCATGCCAAAT 59.957 50.000 0.00 0.00 46.73 2.32
864 1368 0.903924 CACCATGACCCCATGCCAAA 60.904 55.000 0.00 0.00 46.73 3.28
1020 1532 1.795872 TGAACACACTTAATCGCCACG 59.204 47.619 0.00 0.00 0.00 4.94
1131 1644 1.021968 AAACGTCTTCAACACTGGGC 58.978 50.000 0.00 0.00 0.00 5.36
1141 1959 8.333186 ACTGTTCATACAAGTAAAAACGTCTTC 58.667 33.333 0.00 0.00 32.92 2.87
1204 2022 3.655211 AAGCCTGGCTGAGTGGGG 61.655 66.667 24.16 0.00 39.62 4.96
1248 2066 8.573035 GTTGTACCAAGGAATACATTTTTCTGA 58.427 33.333 0.00 0.00 31.55 3.27
1274 2097 2.625737 CTGGCCTCACATCAAGTACAG 58.374 52.381 3.32 0.00 0.00 2.74
1278 2101 0.035630 GAGCTGGCCTCACATCAAGT 60.036 55.000 3.32 0.00 40.45 3.16
1285 2108 1.451028 GATGTGGAGCTGGCCTCAC 60.451 63.158 3.32 5.61 42.62 3.51
1307 2130 6.498651 AGGTCAGGATATGGGTACAGATTTAG 59.501 42.308 0.00 0.00 0.00 1.85
1339 2162 7.944554 ACCAATGAATATGGGTACAGATTTAGG 59.055 37.037 0.00 0.00 38.93 2.69
1340 2163 8.786898 CACCAATGAATATGGGTACAGATTTAG 58.213 37.037 0.00 0.00 38.64 1.85
1342 2165 6.040842 GCACCAATGAATATGGGTACAGATTT 59.959 38.462 0.00 0.00 38.64 2.17
1343 2166 5.536161 GCACCAATGAATATGGGTACAGATT 59.464 40.000 0.00 0.00 38.64 2.40
1345 2168 4.165950 AGCACCAATGAATATGGGTACAGA 59.834 41.667 0.00 0.00 38.64 3.41
1346 2169 4.276678 CAGCACCAATGAATATGGGTACAG 59.723 45.833 0.00 0.00 38.64 2.74
1348 2171 3.004734 GCAGCACCAATGAATATGGGTAC 59.995 47.826 0.00 0.00 38.64 3.34
1349 2172 3.221771 GCAGCACCAATGAATATGGGTA 58.778 45.455 0.00 0.00 38.64 3.69
1350 2173 2.034124 GCAGCACCAATGAATATGGGT 58.966 47.619 0.00 0.00 41.56 4.51
1351 2174 2.033372 TGCAGCACCAATGAATATGGG 58.967 47.619 0.00 0.00 42.48 4.00
1352 2175 3.804786 TTGCAGCACCAATGAATATGG 57.195 42.857 0.00 0.00 43.84 2.74
1353 2176 5.466819 CCTATTGCAGCACCAATGAATATG 58.533 41.667 0.00 0.00 36.21 1.78
1354 2177 4.021719 GCCTATTGCAGCACCAATGAATAT 60.022 41.667 0.00 0.00 40.77 1.28
1356 2179 2.101917 GCCTATTGCAGCACCAATGAAT 59.898 45.455 0.00 0.00 40.77 2.57
1359 2182 1.108776 AGCCTATTGCAGCACCAATG 58.891 50.000 0.00 3.32 44.83 2.82
1485 2979 1.998315 CGATTGTGTGAGAGCTTCCTG 59.002 52.381 0.00 0.00 0.00 3.86
1521 3016 2.173782 TCTGTAGGTTCTTTTGGCACCA 59.826 45.455 0.00 0.00 32.43 4.17
1523 3018 3.125316 CGATCTGTAGGTTCTTTTGGCAC 59.875 47.826 0.00 0.00 0.00 5.01
1524 3019 3.334691 CGATCTGTAGGTTCTTTTGGCA 58.665 45.455 0.00 0.00 0.00 4.92
1544 3039 5.923114 CAGATCCTCAGTAAATGATGTACCG 59.077 44.000 0.00 0.00 37.28 4.02
1546 3041 6.520272 AGCAGATCCTCAGTAAATGATGTAC 58.480 40.000 0.00 0.00 37.28 2.90
1548 3043 5.627182 AGCAGATCCTCAGTAAATGATGT 57.373 39.130 0.00 0.00 37.28 3.06
1558 3053 4.262121 CCTCTATGTGAAGCAGATCCTCAG 60.262 50.000 0.00 0.00 0.00 3.35
1570 3065 6.266330 CCTATCAGTGTGATCCTCTATGTGAA 59.734 42.308 0.00 0.00 38.26 3.18
1576 3071 4.816048 ACCCTATCAGTGTGATCCTCTA 57.184 45.455 0.00 0.00 38.26 2.43
1638 3133 6.892658 ATTATTTTGCTTACCACAGTGACA 57.107 33.333 0.62 0.00 0.00 3.58
1643 3138 9.438291 CGATAAGAATTATTTTGCTTACCACAG 57.562 33.333 0.00 0.00 42.35 3.66
1666 3220 6.049955 TGACCTTTAGAAATCCTTGTCGAT 57.950 37.500 0.00 0.00 0.00 3.59
1887 3447 0.739112 GCTAGACTGGTCAGTGCTGC 60.739 60.000 8.49 5.85 42.66 5.25
1888 3448 0.894141 AGCTAGACTGGTCAGTGCTG 59.106 55.000 8.49 0.00 42.66 4.41
1889 3449 1.274728 CAAGCTAGACTGGTCAGTGCT 59.725 52.381 8.49 8.28 42.66 4.40
1890 3450 1.273606 TCAAGCTAGACTGGTCAGTGC 59.726 52.381 8.49 6.12 42.66 4.40
1916 3476 5.201243 ACTACATAGGAGTGATGTACAGCA 58.799 41.667 10.32 10.32 38.47 4.41
1917 3477 5.278561 GGACTACATAGGAGTGATGTACAGC 60.279 48.000 3.61 3.61 38.47 4.40
1918 3478 5.241949 GGGACTACATAGGAGTGATGTACAG 59.758 48.000 0.33 0.00 38.47 2.74
1919 3479 5.103643 AGGGACTACATAGGAGTGATGTACA 60.104 44.000 0.00 0.00 38.47 2.90
1920 3480 5.386924 AGGGACTACATAGGAGTGATGTAC 58.613 45.833 0.00 0.00 38.47 2.90
1921 3481 5.457778 GGAGGGACTACATAGGAGTGATGTA 60.458 48.000 0.00 0.00 40.63 2.29
1922 3482 4.475345 GAGGGACTACATAGGAGTGATGT 58.525 47.826 0.00 0.00 41.55 3.06
1923 3483 3.829601 GGAGGGACTACATAGGAGTGATG 59.170 52.174 0.00 0.00 40.63 3.07
1924 3484 3.498841 CGGAGGGACTACATAGGAGTGAT 60.499 52.174 0.00 0.00 41.36 3.06
1925 3485 2.158652 CGGAGGGACTACATAGGAGTGA 60.159 54.545 0.00 0.00 41.36 3.41
1930 3490 1.962100 GGAACGGAGGGACTACATAGG 59.038 57.143 0.00 0.00 41.36 2.57
1938 3498 6.293244 CGATAAAAATTATGGAACGGAGGGAC 60.293 42.308 0.00 0.00 0.00 4.46
1945 3505 8.455598 AAAACCACGATAAAAATTATGGAACG 57.544 30.769 0.00 0.00 0.00 3.95
1957 3517 7.571080 ACCTTTGAACTAAAACCACGATAAA 57.429 32.000 0.00 0.00 0.00 1.40
1960 3520 5.826208 AGAACCTTTGAACTAAAACCACGAT 59.174 36.000 0.00 0.00 0.00 3.73
1962 3522 5.270853 CAGAACCTTTGAACTAAAACCACG 58.729 41.667 0.00 0.00 0.00 4.94
1975 3535 4.130118 ACTGTAACAGAGCAGAACCTTTG 58.870 43.478 0.00 0.00 36.62 2.77
1976 3536 4.423625 ACTGTAACAGAGCAGAACCTTT 57.576 40.909 0.00 0.00 36.62 3.11
2001 3589 4.713792 ATTTAGCTCTAATCCCCCAGTG 57.286 45.455 0.00 0.00 0.00 3.66
2007 3595 7.384387 CACCGTTAGTTATTTAGCTCTAATCCC 59.616 40.741 0.00 0.00 0.00 3.85
2021 3609 3.362706 TCAGAGAGGCACCGTTAGTTAT 58.637 45.455 0.00 0.00 0.00 1.89
2044 3632 0.108756 GACACCGTGTCTAGCCTTCC 60.109 60.000 22.08 0.00 43.73 3.46
2063 3651 4.392138 GGAAACAGAAAGATACCCTCAACG 59.608 45.833 0.00 0.00 0.00 4.10
2069 3657 3.532542 CGAGGGAAACAGAAAGATACCC 58.467 50.000 0.00 0.00 36.47 3.69
2075 3663 1.002544 AGAGGCGAGGGAAACAGAAAG 59.997 52.381 0.00 0.00 0.00 2.62
2127 3715 8.928733 CCGTAAGTGCTAAATAAGAAACTGTAA 58.071 33.333 0.00 0.00 0.00 2.41
2137 3725 4.081752 TCCCGAACCGTAAGTGCTAAATAA 60.082 41.667 0.00 0.00 0.00 1.40
2156 3745 1.482593 AGATCTTGCCTGTACTTCCCG 59.517 52.381 0.00 0.00 0.00 5.14
2167 3756 2.430465 TGAGCTCACAAAGATCTTGCC 58.570 47.619 13.74 3.05 41.17 4.52
2168 3757 4.874966 AGTATGAGCTCACAAAGATCTTGC 59.125 41.667 20.97 7.67 41.17 4.01
2171 3760 5.929058 TCAGTATGAGCTCACAAAGATCT 57.071 39.130 20.97 2.59 42.56 2.75
2216 3815 3.878778 ACAGATGGATTGCTTGGTACTC 58.121 45.455 0.00 0.00 0.00 2.59
2217 3816 4.471386 AGTACAGATGGATTGCTTGGTACT 59.529 41.667 0.00 0.00 36.36 2.73
2218 3817 4.770795 AGTACAGATGGATTGCTTGGTAC 58.229 43.478 0.00 0.00 0.00 3.34
2219 3818 5.185454 CAAGTACAGATGGATTGCTTGGTA 58.815 41.667 0.00 0.00 0.00 3.25
2220 3819 4.012374 CAAGTACAGATGGATTGCTTGGT 58.988 43.478 0.00 0.00 0.00 3.67
2221 3820 4.012374 ACAAGTACAGATGGATTGCTTGG 58.988 43.478 0.00 0.00 36.96 3.61
2222 3821 5.633830 AACAAGTACAGATGGATTGCTTG 57.366 39.130 0.00 0.00 38.14 4.01
2223 3822 9.632638 AATATAACAAGTACAGATGGATTGCTT 57.367 29.630 0.00 0.00 0.00 3.91
2224 3823 9.632638 AAATATAACAAGTACAGATGGATTGCT 57.367 29.630 0.00 0.00 0.00 3.91
2225 3824 9.884465 GAAATATAACAAGTACAGATGGATTGC 57.116 33.333 0.00 0.00 0.00 3.56
2247 3846 9.851686 TGGTACTGCAAGAATCATATTAGAAAT 57.148 29.630 0.00 0.00 37.43 2.17
2248 3847 9.679661 TTGGTACTGCAAGAATCATATTAGAAA 57.320 29.630 0.00 0.00 37.43 2.52
2249 3848 9.330063 CTTGGTACTGCAAGAATCATATTAGAA 57.670 33.333 6.11 0.00 37.43 2.10
2250 3849 7.442364 GCTTGGTACTGCAAGAATCATATTAGA 59.558 37.037 14.00 0.00 37.43 2.10
2251 3850 7.570140 CGCTTGGTACTGCAAGAATCATATTAG 60.570 40.741 14.00 0.00 37.43 1.73
2252 3851 6.202762 CGCTTGGTACTGCAAGAATCATATTA 59.797 38.462 14.00 0.00 37.43 0.98
2253 3852 5.008019 CGCTTGGTACTGCAAGAATCATATT 59.992 40.000 14.00 0.00 37.43 1.28
2254 3853 4.512944 CGCTTGGTACTGCAAGAATCATAT 59.487 41.667 14.00 0.00 37.43 1.78
2255 3854 3.871006 CGCTTGGTACTGCAAGAATCATA 59.129 43.478 14.00 0.00 37.43 2.15
2256 3855 2.679837 CGCTTGGTACTGCAAGAATCAT 59.320 45.455 14.00 0.00 37.43 2.45
2257 3856 2.076100 CGCTTGGTACTGCAAGAATCA 58.924 47.619 14.00 0.00 37.43 2.57
2258 3857 1.202076 GCGCTTGGTACTGCAAGAATC 60.202 52.381 14.00 1.32 37.43 2.52
2259 3858 0.804989 GCGCTTGGTACTGCAAGAAT 59.195 50.000 14.00 0.00 37.43 2.40
2260 3859 0.250295 AGCGCTTGGTACTGCAAGAA 60.250 50.000 2.64 0.00 37.43 2.52
2261 3860 0.950555 CAGCGCTTGGTACTGCAAGA 60.951 55.000 7.50 0.00 37.43 3.02
2262 3861 1.499056 CAGCGCTTGGTACTGCAAG 59.501 57.895 7.50 7.33 42.29 4.01
2263 3862 3.654201 CAGCGCTTGGTACTGCAA 58.346 55.556 7.50 0.00 0.00 4.08
2275 3874 1.021390 ACAAGTACAGATGGCAGCGC 61.021 55.000 0.00 0.00 0.00 5.92
2278 3877 8.668510 AGAAATATAACAAGTACAGATGGCAG 57.331 34.615 0.00 0.00 0.00 4.85
2306 3905 4.623932 TCCTTGAAGTCAACATGCTAGT 57.376 40.909 0.00 0.00 0.00 2.57
2307 3906 5.481200 CATCCTTGAAGTCAACATGCTAG 57.519 43.478 0.00 0.00 0.00 3.42



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

AutoCloner maintained by Alex Coulton.