Multiple sequence alignment - TraesCS3A01G361200

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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 TraesCS3A01G361200 chr3A 100.000 2222 0 0 1 2222 608816341 608818562 0.000000e+00 4104
1 TraesCS3A01G361200 chr3B 85.432 2327 149 84 1 2222 619060175 619062416 0.000000e+00 2244
2 TraesCS3A01G361200 chr3D 87.209 1587 106 41 257 1779 465528515 465530068 0.000000e+00 1716
3 TraesCS3A01G361200 chr3D 88.521 453 20 8 1767 2205 465530094 465530528 9.090000e-144 520
4 TraesCS3A01G361200 chr3D 93.392 227 12 2 3 226 465527850 465528076 1.270000e-87 333
5 TraesCS3A01G361200 chr4D 93.590 78 5 0 1130 1207 360467937 360468014 1.390000e-22 117
6 TraesCS3A01G361200 chr4A 84.483 116 14 4 1130 1244 104391402 104391290 6.490000e-21 111


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 TraesCS3A01G361200 chr3A 608816341 608818562 2221 False 4104.000000 4104 100.000000 1 2222 1 chr3A.!!$F1 2221
1 TraesCS3A01G361200 chr3B 619060175 619062416 2241 False 2244.000000 2244 85.432000 1 2222 1 chr3B.!!$F1 2221
2 TraesCS3A01G361200 chr3D 465527850 465530528 2678 False 856.333333 1716 89.707333 3 2205 3 chr3D.!!$F1 2202

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
291 718 0.110373 GGTTGAATGTTCGTCACGGC 60.11 55.0 0.0 0.0 0.0 5.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 1754 0.175531 GAGAGAGGGAGCTTGTCTGC 59.824 60.0 0.0 0.0 0.0 4.26 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
17 18 3.876300 CTCGAGCTTTTGACCCGG 58.124 61.111 0.00 0.00 0.00 5.73
119 126 2.613223 GGCTACTTTGTGTCTGGAGACC 60.613 54.545 4.34 0.00 44.15 3.85
143 150 4.686972 TCTCTAGGTTTGAATGCTCATCG 58.313 43.478 0.00 0.00 0.00 3.84
226 235 3.715628 ATGGTCAAATTTAGCGATGGC 57.284 42.857 0.00 0.00 40.37 4.40
240 665 2.203337 TGGCTCACCACTGTTGCC 60.203 61.111 0.00 0.00 42.67 4.52
246 671 1.066257 CACCACTGTTGCCTTGTGC 59.934 57.895 0.00 0.00 41.77 4.57
255 680 4.730487 GCCTTGTGCATGGAGAGT 57.270 55.556 8.11 0.00 40.77 3.24
256 681 2.952714 GCCTTGTGCATGGAGAGTT 58.047 52.632 8.11 0.00 40.77 3.01
257 682 0.524862 GCCTTGTGCATGGAGAGTTG 59.475 55.000 8.11 0.00 40.77 3.16
258 683 1.171308 CCTTGTGCATGGAGAGTTGG 58.829 55.000 0.00 0.00 0.00 3.77
259 684 1.271543 CCTTGTGCATGGAGAGTTGGA 60.272 52.381 0.00 0.00 0.00 3.53
260 685 2.082231 CTTGTGCATGGAGAGTTGGAG 58.918 52.381 0.00 0.00 0.00 3.86
261 686 1.351076 TGTGCATGGAGAGTTGGAGA 58.649 50.000 0.00 0.00 0.00 3.71
284 711 1.726791 CACTCGAGGGTTGAATGTTCG 59.273 52.381 18.41 0.00 0.00 3.95
287 714 1.341852 TCGAGGGTTGAATGTTCGTCA 59.658 47.619 0.00 0.00 33.35 4.35
291 718 0.110373 GGTTGAATGTTCGTCACGGC 60.110 55.000 0.00 0.00 0.00 5.68
293 720 1.561717 TTGAATGTTCGTCACGGCCG 61.562 55.000 26.86 26.86 0.00 6.13
301 728 3.712881 GTCACGGCCGCTGTTCAC 61.713 66.667 28.58 12.85 0.00 3.18
302 729 3.923864 TCACGGCCGCTGTTCACT 61.924 61.111 28.58 0.00 0.00 3.41
306 733 1.082104 CGGCCGCTGTTCACTTTTC 60.082 57.895 14.67 0.00 0.00 2.29
307 734 1.781025 CGGCCGCTGTTCACTTTTCA 61.781 55.000 14.67 0.00 0.00 2.69
311 738 2.154462 CCGCTGTTCACTTTTCATCCT 58.846 47.619 0.00 0.00 0.00 3.24
316 743 4.555511 GCTGTTCACTTTTCATCCTCACAC 60.556 45.833 0.00 0.00 0.00 3.82
317 744 3.559655 TGTTCACTTTTCATCCTCACACG 59.440 43.478 0.00 0.00 0.00 4.49
332 759 2.141781 CACGGTGTGCTTACTCGTG 58.858 57.895 0.00 14.67 43.58 4.35
370 797 0.957395 ACTGATGGTTTCCTGCTGCG 60.957 55.000 0.00 0.00 0.00 5.18
376 803 3.294493 TTTCCTGCTGCGGTTGCC 61.294 61.111 7.82 0.00 41.78 4.52
394 821 3.609853 TGCCACTGTTCCATCATAACTC 58.390 45.455 0.00 0.00 0.00 3.01
436 863 7.707893 GTGCATGGATTTTATTAGCTTGTCAAT 59.292 33.333 0.00 0.00 0.00 2.57
479 906 0.733729 AGTCTAACGCTACGGCTGAG 59.266 55.000 0.00 0.00 36.09 3.35
490 917 1.922570 ACGGCTGAGCGTATTAACTG 58.077 50.000 0.00 0.00 0.00 3.16
516 943 2.158475 TGACCTTGGCCATTTCTCAACT 60.158 45.455 6.09 0.00 0.00 3.16
570 997 6.710744 TGTTTGCTAGTAGAGAAAAGGGAAAG 59.289 38.462 0.00 0.00 32.93 2.62
574 1001 3.883135 AGTAGAGAAAAGGGAAAGGGGA 58.117 45.455 0.00 0.00 0.00 4.81
621 1050 4.512914 GGCCCCATCCCTGACAGC 62.513 72.222 0.00 0.00 0.00 4.40
627 1056 4.101448 ATCCCTGACAGCCACGCC 62.101 66.667 0.00 0.00 0.00 5.68
682 1111 4.846137 CCGAGAACAAGATAAAAAGCAACG 59.154 41.667 0.00 0.00 0.00 4.10
716 1161 5.810074 GGAGATTAGAAGTGAGCTTTGTCTC 59.190 44.000 0.00 0.00 34.61 3.36
723 1168 1.070309 GTGAGCTTTGTCTCAACAGCG 60.070 52.381 0.00 0.00 43.89 5.18
744 1189 3.592059 GAAAACCCTGCATACACGTAGA 58.408 45.455 0.00 0.00 0.00 2.59
875 1320 1.134438 AGTTTCCCACCTCACTCCCC 61.134 60.000 0.00 0.00 0.00 4.81
904 1350 2.161855 CAGAGCTCACTGTCTCACTCT 58.838 52.381 17.77 0.00 34.93 3.24
909 1355 2.091541 CTCACTGTCTCACTCTCCTCC 58.908 57.143 0.00 0.00 0.00 4.30
912 1358 2.830923 CACTGTCTCACTCTCCTCCATT 59.169 50.000 0.00 0.00 0.00 3.16
916 1362 2.693074 GTCTCACTCTCCTCCATTCTCC 59.307 54.545 0.00 0.00 0.00 3.71
925 1371 4.016666 TCTCCTCCATTCTCCTCTCTTCTT 60.017 45.833 0.00 0.00 0.00 2.52
927 1373 3.068024 CCTCCATTCTCCTCTCTTCTTCG 59.932 52.174 0.00 0.00 0.00 3.79
928 1374 3.699038 CTCCATTCTCCTCTCTTCTTCGT 59.301 47.826 0.00 0.00 0.00 3.85
929 1375 3.697045 TCCATTCTCCTCTCTTCTTCGTC 59.303 47.826 0.00 0.00 0.00 4.20
930 1376 3.181480 CCATTCTCCTCTCTTCTTCGTCC 60.181 52.174 0.00 0.00 0.00 4.79
931 1377 2.881111 TCTCCTCTCTTCTTCGTCCA 57.119 50.000 0.00 0.00 0.00 4.02
932 1378 3.156288 TCTCCTCTCTTCTTCGTCCAA 57.844 47.619 0.00 0.00 0.00 3.53
933 1379 3.085533 TCTCCTCTCTTCTTCGTCCAAG 58.914 50.000 0.00 0.00 0.00 3.61
934 1380 2.823154 CTCCTCTCTTCTTCGTCCAAGT 59.177 50.000 0.00 0.00 33.27 3.16
935 1381 2.558795 TCCTCTCTTCTTCGTCCAAGTG 59.441 50.000 0.00 0.00 33.27 3.16
937 1383 3.366883 CCTCTCTTCTTCGTCCAAGTGAG 60.367 52.174 11.65 11.65 38.86 3.51
938 1384 2.029828 TCTCTTCTTCGTCCAAGTGAGC 60.030 50.000 0.00 0.00 35.58 4.26
939 1385 1.964223 TCTTCTTCGTCCAAGTGAGCT 59.036 47.619 0.00 0.00 33.27 4.09
940 1386 3.154710 TCTTCTTCGTCCAAGTGAGCTA 58.845 45.455 0.00 0.00 33.27 3.32
941 1387 3.191581 TCTTCTTCGTCCAAGTGAGCTAG 59.808 47.826 0.00 0.00 33.27 3.42
942 1388 1.202582 TCTTCGTCCAAGTGAGCTAGC 59.797 52.381 6.62 6.62 33.27 3.42
943 1389 1.203523 CTTCGTCCAAGTGAGCTAGCT 59.796 52.381 19.45 19.45 0.00 3.32
944 1390 0.811915 TCGTCCAAGTGAGCTAGCTC 59.188 55.000 33.47 33.47 43.01 4.09
945 1391 0.814457 CGTCCAAGTGAGCTAGCTCT 59.186 55.000 37.42 21.28 43.12 4.09
953 1415 0.753479 TGAGCTAGCTCTCCCTTCGG 60.753 60.000 37.42 0.00 43.12 4.30
1279 1754 3.117657 TCCATCGAGGAGTAGCAGG 57.882 57.895 0.00 0.00 43.07 4.85
1299 1780 0.455410 CAGACAAGCTCCCTCTCTCG 59.545 60.000 0.00 0.00 0.00 4.04
1300 1781 0.039035 AGACAAGCTCCCTCTCTCGT 59.961 55.000 0.00 0.00 0.00 4.18
1312 1793 1.135333 CTCTCTCGTTAGCCCAAGGAC 59.865 57.143 0.00 0.00 0.00 3.85
1313 1794 0.179134 CTCTCGTTAGCCCAAGGACG 60.179 60.000 0.00 0.00 36.89 4.79
1314 1795 0.609957 TCTCGTTAGCCCAAGGACGA 60.610 55.000 0.00 0.00 41.62 4.20
1315 1796 0.245539 CTCGTTAGCCCAAGGACGAA 59.754 55.000 0.00 0.00 42.99 3.85
1331 1812 3.315418 GACGAACCTCCTGTGTAAAGAC 58.685 50.000 0.00 0.00 0.00 3.01
1335 1816 4.458295 CGAACCTCCTGTGTAAAGACTAGA 59.542 45.833 0.00 0.00 0.00 2.43
1336 1817 5.125739 CGAACCTCCTGTGTAAAGACTAGAT 59.874 44.000 0.00 0.00 0.00 1.98
1337 1818 6.350277 CGAACCTCCTGTGTAAAGACTAGATT 60.350 42.308 0.00 0.00 0.00 2.40
1339 1820 7.317722 ACCTCCTGTGTAAAGACTAGATTTT 57.682 36.000 0.00 0.00 0.00 1.82
1340 1821 7.387643 ACCTCCTGTGTAAAGACTAGATTTTC 58.612 38.462 0.00 0.00 0.00 2.29
1341 1822 7.235812 ACCTCCTGTGTAAAGACTAGATTTTCT 59.764 37.037 0.00 0.00 0.00 2.52
1344 1825 9.490379 TCCTGTGTAAAGACTAGATTTTCTTTC 57.510 33.333 8.81 3.92 40.47 2.62
1369 1862 3.990959 TTTTTCTTGCCCTTGGTTGTT 57.009 38.095 0.00 0.00 0.00 2.83
1371 1864 4.664150 TTTTCTTGCCCTTGGTTGTTAG 57.336 40.909 0.00 0.00 0.00 2.34
1377 1870 4.650972 TGCCCTTGGTTGTTAGTAAGAT 57.349 40.909 0.00 0.00 0.00 2.40
1386 1879 6.327934 TGGTTGTTAGTAAGATTAGAGCGAC 58.672 40.000 0.00 0.00 0.00 5.19
1418 1911 0.796491 CGCCGCGCATTTTGTTGTAT 60.796 50.000 8.75 0.00 0.00 2.29
1420 1913 1.058979 GCCGCGCATTTTGTTGTATTG 59.941 47.619 8.75 0.00 0.00 1.90
1449 1949 5.803237 ATCTGATGTCATGTGAGCATCTA 57.197 39.130 17.89 11.36 39.58 1.98
1457 1957 6.685657 TGTCATGTGAGCATCTATCTGATAC 58.314 40.000 0.00 0.00 34.92 2.24
1458 1958 6.492772 TGTCATGTGAGCATCTATCTGATACT 59.507 38.462 0.00 0.00 34.92 2.12
1459 1959 7.667219 TGTCATGTGAGCATCTATCTGATACTA 59.333 37.037 0.00 0.00 34.92 1.82
1460 1960 7.967854 GTCATGTGAGCATCTATCTGATACTAC 59.032 40.741 0.00 0.00 34.92 2.73
1461 1961 7.887495 TCATGTGAGCATCTATCTGATACTACT 59.113 37.037 0.00 0.00 34.92 2.57
1462 1962 9.171877 CATGTGAGCATCTATCTGATACTACTA 57.828 37.037 0.00 0.00 34.92 1.82
1496 1996 5.411361 AGAATTGTTGATCGTCGAAATTGGA 59.589 36.000 0.00 0.00 0.00 3.53
1518 2018 3.393941 AGGAGGCTATTGGATTCCTGAAG 59.606 47.826 3.95 0.00 36.92 3.02
1522 2022 3.879892 GGCTATTGGATTCCTGAAGTGTC 59.120 47.826 3.95 0.00 0.00 3.67
1523 2023 4.384647 GGCTATTGGATTCCTGAAGTGTCT 60.385 45.833 3.95 0.00 0.00 3.41
1540 2040 3.075005 TACTGTGCGCTCCCCCTC 61.075 66.667 9.73 0.00 0.00 4.30
1563 2063 1.080434 GACTCCTCGATATGCGGGC 60.080 63.158 0.00 0.00 39.82 6.13
1567 2067 2.335011 CTCGATATGCGGGCGTGA 59.665 61.111 0.00 0.00 41.33 4.35
1618 2118 4.522789 ACGAATCTTAACATTTGGGCAACT 59.477 37.500 0.00 0.00 0.00 3.16
1659 2161 5.429615 GTCGACCGTTTTCTTTCTTTACTG 58.570 41.667 3.51 0.00 0.00 2.74
1673 2175 3.073798 TCTTTACTGCTGGAAATCACCCA 59.926 43.478 0.95 0.00 0.00 4.51
1709 2211 3.294038 AGGATTCTCAGCTCCATTTGG 57.706 47.619 0.00 0.00 33.75 3.28
1710 2212 2.091994 AGGATTCTCAGCTCCATTTGGG 60.092 50.000 0.00 0.00 33.75 4.12
1725 2227 7.852971 TCCATTTGGGAAAATAACTAGTACG 57.147 36.000 0.00 0.00 44.80 3.67
1751 2256 6.265196 TCAAAACCAGTGATAACATTTCAGCT 59.735 34.615 0.00 0.00 0.00 4.24
1806 2349 2.607187 CTACTCCACGTAGCAACCTTG 58.393 52.381 0.00 0.00 39.22 3.61
1807 2350 0.034896 ACTCCACGTAGCAACCTTGG 59.965 55.000 0.00 0.00 0.00 3.61
1808 2351 0.034896 CTCCACGTAGCAACCTTGGT 59.965 55.000 0.00 0.00 42.29 3.67
1809 2352 1.274167 CTCCACGTAGCAACCTTGGTA 59.726 52.381 0.00 0.00 39.88 3.25
1824 2375 2.188062 TGGTAGGCAGGTTTTTACCG 57.812 50.000 0.00 0.00 38.69 4.02
1855 2406 0.310543 TGGTAAAACTTGCAGCAGCG 59.689 50.000 0.00 0.00 46.23 5.18
1914 2465 3.320626 GTTGCAATCTTTTTGAGGGAGC 58.679 45.455 0.59 0.00 0.00 4.70
2052 2613 2.959707 TGTTGCACGTAAAAATCCCCTT 59.040 40.909 0.00 0.00 0.00 3.95
2088 2652 4.778143 CCTTCCCTTGGACCGCCG 62.778 72.222 0.00 0.00 36.79 6.46
2117 2681 1.205460 TACTTGGGAGCTGGAACCCC 61.205 60.000 5.78 3.12 45.01 4.95
2150 2714 1.749634 AGCTACCGAATCACTACGCTT 59.250 47.619 0.00 0.00 0.00 4.68
2158 2722 1.100510 ATCACTACGCTTCGCCTACA 58.899 50.000 0.00 0.00 0.00 2.74
2192 2770 3.092301 CAGCATCCGATCCTATCCTACA 58.908 50.000 0.00 0.00 0.00 2.74
2212 2790 1.016130 CGACGCTTCATGGCTTCAGT 61.016 55.000 0.00 0.00 31.96 3.41
2213 2791 0.723981 GACGCTTCATGGCTTCAGTC 59.276 55.000 0.00 0.00 31.96 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 1.225426 GATGATGTGGGAGCTGGCA 59.775 57.895 0.00 0.00 0.00 4.92
43 47 3.186345 CAGGGCTTGCAGATGATGT 57.814 52.632 0.00 0.00 0.00 3.06
119 126 5.033589 ATGAGCATTCAAACCTAGAGAGG 57.966 43.478 0.00 0.00 42.11 3.69
143 150 3.660111 GCGGTGAACAGTGGGTGC 61.660 66.667 0.00 0.00 0.00 5.01
146 153 0.951040 GAAGAGCGGTGAACAGTGGG 60.951 60.000 0.00 0.00 0.00 4.61
202 211 3.129852 TCGCTAAATTTGACCATTGCG 57.870 42.857 0.00 0.00 42.89 4.85
226 235 0.664761 CACAAGGCAACAGTGGTGAG 59.335 55.000 13.73 0.36 40.08 3.51
228 237 1.066257 GCACAAGGCAACAGTGGTG 59.934 57.895 2.98 2.98 42.85 4.17
229 238 3.525221 GCACAAGGCAACAGTGGT 58.475 55.556 0.00 0.00 42.85 4.16
240 665 2.082231 CTCCAACTCTCCATGCACAAG 58.918 52.381 0.00 0.00 0.00 3.16
254 679 0.528470 CCCTCGAGTGAGTCTCCAAC 59.472 60.000 12.31 0.00 40.85 3.77
255 680 0.112606 ACCCTCGAGTGAGTCTCCAA 59.887 55.000 12.31 0.00 40.85 3.53
256 681 0.112606 AACCCTCGAGTGAGTCTCCA 59.887 55.000 12.31 0.00 40.85 3.86
257 682 0.528470 CAACCCTCGAGTGAGTCTCC 59.472 60.000 12.31 0.00 40.85 3.71
258 683 1.535833 TCAACCCTCGAGTGAGTCTC 58.464 55.000 12.31 0.00 40.85 3.36
259 684 1.996798 TTCAACCCTCGAGTGAGTCT 58.003 50.000 12.31 0.00 40.85 3.24
260 685 2.028930 ACATTCAACCCTCGAGTGAGTC 60.029 50.000 12.31 0.00 40.85 3.36
261 686 1.971357 ACATTCAACCCTCGAGTGAGT 59.029 47.619 12.31 2.69 40.85 3.41
284 711 3.712881 GTGAACAGCGGCCGTGAC 61.713 66.667 28.70 20.04 0.00 3.67
287 714 1.782028 GAAAAGTGAACAGCGGCCGT 61.782 55.000 28.70 11.01 0.00 5.68
291 718 2.154462 AGGATGAAAAGTGAACAGCGG 58.846 47.619 0.00 0.00 0.00 5.52
293 720 3.565482 TGTGAGGATGAAAAGTGAACAGC 59.435 43.478 0.00 0.00 0.00 4.40
301 728 2.494059 ACACCGTGTGAGGATGAAAAG 58.506 47.619 2.57 0.00 36.96 2.27
302 729 2.631160 ACACCGTGTGAGGATGAAAA 57.369 45.000 2.57 0.00 36.96 2.29
316 743 0.596600 ACACACGAGTAAGCACACCG 60.597 55.000 0.00 0.00 0.00 4.94
317 744 0.859232 CACACACGAGTAAGCACACC 59.141 55.000 0.00 0.00 0.00 4.16
332 759 5.527951 TCAGTAAATTTGACCATTGCACAC 58.472 37.500 0.00 0.00 0.00 3.82
394 821 2.439409 TGCACAGAACCATCCAATCAG 58.561 47.619 0.00 0.00 0.00 2.90
442 869 7.589221 CGTTAGACTCGGTTCCATTATAGTAAC 59.411 40.741 0.00 0.00 0.00 2.50
458 885 0.589229 CAGCCGTAGCGTTAGACTCG 60.589 60.000 0.00 0.00 46.67 4.18
479 906 1.664151 GGTCAGTGCCAGTTAATACGC 59.336 52.381 0.00 0.00 0.00 4.42
490 917 1.187567 AAATGGCCAAGGTCAGTGCC 61.188 55.000 10.96 0.00 44.27 5.01
516 943 1.961394 ACTTGGAGTGACAGCGAAGTA 59.039 47.619 4.60 0.00 0.00 2.24
634 1063 3.024043 CGTGCAACACCGCAAAGC 61.024 61.111 0.00 0.00 45.14 3.51
635 1064 1.369209 CTCGTGCAACACCGCAAAG 60.369 57.895 0.00 0.00 45.14 2.77
636 1065 2.712539 CTCGTGCAACACCGCAAA 59.287 55.556 0.00 0.00 45.14 3.68
637 1066 3.276091 CCTCGTGCAACACCGCAA 61.276 61.111 0.00 0.00 45.14 4.85
682 1111 8.458843 GCTCACTTCTAATCTCCTACTCATATC 58.541 40.741 0.00 0.00 0.00 1.63
723 1168 3.592059 TCTACGTGTATGCAGGGTTTTC 58.408 45.455 8.37 0.00 35.03 2.29
904 1350 4.285863 GAAGAAGAGAGGAGAATGGAGGA 58.714 47.826 0.00 0.00 0.00 3.71
909 1355 3.445450 TGGACGAAGAAGAGAGGAGAATG 59.555 47.826 0.00 0.00 0.00 2.67
912 1358 2.881111 TGGACGAAGAAGAGAGGAGA 57.119 50.000 0.00 0.00 0.00 3.71
916 1362 3.832276 CTCACTTGGACGAAGAAGAGAG 58.168 50.000 14.40 0.00 38.51 3.20
925 1371 0.811915 GAGCTAGCTCACTTGGACGA 59.188 55.000 34.70 0.00 42.31 4.20
927 1373 1.136110 GGAGAGCTAGCTCACTTGGAC 59.864 57.143 38.86 20.00 44.99 4.02
928 1374 1.479709 GGAGAGCTAGCTCACTTGGA 58.520 55.000 38.86 0.00 44.99 3.53
929 1375 0.463620 GGGAGAGCTAGCTCACTTGG 59.536 60.000 38.86 0.00 44.99 3.61
930 1376 1.484038 AGGGAGAGCTAGCTCACTTG 58.516 55.000 38.86 0.00 46.18 3.16
933 1379 0.383949 CGAAGGGAGAGCTAGCTCAC 59.616 60.000 38.86 33.47 44.99 3.51
934 1380 2.800516 CGAAGGGAGAGCTAGCTCA 58.199 57.895 38.86 0.00 44.99 4.26
973 1435 2.802106 CTCTTCCCGCGAGTCCTC 59.198 66.667 8.23 0.00 0.00 3.71
1279 1754 0.175531 GAGAGAGGGAGCTTGTCTGC 59.824 60.000 0.00 0.00 0.00 4.26
1299 1780 0.323957 AGGTTCGTCCTTGGGCTAAC 59.676 55.000 0.71 0.71 45.67 2.34
1300 1781 2.768046 AGGTTCGTCCTTGGGCTAA 58.232 52.632 0.00 0.00 45.67 3.09
1312 1793 3.662247 AGTCTTTACACAGGAGGTTCG 57.338 47.619 0.00 0.00 0.00 3.95
1313 1794 5.979288 TCTAGTCTTTACACAGGAGGTTC 57.021 43.478 0.00 0.00 0.00 3.62
1314 1795 6.936968 AATCTAGTCTTTACACAGGAGGTT 57.063 37.500 0.00 0.00 0.00 3.50
1315 1796 6.936968 AAATCTAGTCTTTACACAGGAGGT 57.063 37.500 0.00 0.00 0.00 3.85
1350 1843 4.027437 ACTAACAACCAAGGGCAAGAAAA 58.973 39.130 0.00 0.00 0.00 2.29
1357 1850 6.412214 TCTAATCTTACTAACAACCAAGGGC 58.588 40.000 0.00 0.00 0.00 5.19
1360 1853 7.009357 GTCGCTCTAATCTTACTAACAACCAAG 59.991 40.741 0.00 0.00 0.00 3.61
1363 1856 5.454877 CGTCGCTCTAATCTTACTAACAACC 59.545 44.000 0.00 0.00 0.00 3.77
1367 1860 4.595116 TGCGTCGCTCTAATCTTACTAAC 58.405 43.478 19.50 0.00 0.00 2.34
1368 1861 4.334759 ACTGCGTCGCTCTAATCTTACTAA 59.665 41.667 19.50 0.00 0.00 2.24
1369 1862 3.875727 ACTGCGTCGCTCTAATCTTACTA 59.124 43.478 19.50 0.00 0.00 1.82
1371 1864 2.784380 CACTGCGTCGCTCTAATCTTAC 59.216 50.000 19.50 0.00 0.00 2.34
1377 1870 4.861883 GACACTGCGTCGCTCTAA 57.138 55.556 19.50 0.00 34.19 2.10
1418 1911 8.615211 GCTCACATGACATCAGATTAATAACAA 58.385 33.333 0.00 0.00 0.00 2.83
1420 1913 8.146479 TGCTCACATGACATCAGATTAATAAC 57.854 34.615 0.00 0.00 0.00 1.89
1459 1959 7.976734 CGATCAACAATTCTTCCTCTTACTAGT 59.023 37.037 0.00 0.00 0.00 2.57
1460 1960 7.976734 ACGATCAACAATTCTTCCTCTTACTAG 59.023 37.037 0.00 0.00 0.00 2.57
1461 1961 7.837863 ACGATCAACAATTCTTCCTCTTACTA 58.162 34.615 0.00 0.00 0.00 1.82
1462 1962 6.702329 ACGATCAACAATTCTTCCTCTTACT 58.298 36.000 0.00 0.00 0.00 2.24
1476 1976 3.435327 CCTCCAATTTCGACGATCAACAA 59.565 43.478 0.00 0.00 0.00 2.83
1496 1996 3.066208 TCAGGAATCCAATAGCCTCCT 57.934 47.619 0.61 0.00 36.96 3.69
1518 2018 1.446272 GGGAGCGCACAGTAGACAC 60.446 63.158 11.47 0.00 0.00 3.67
1522 2022 3.077556 AGGGGGAGCGCACAGTAG 61.078 66.667 11.47 0.00 0.00 2.57
1523 2023 3.075005 GAGGGGGAGCGCACAGTA 61.075 66.667 11.47 0.00 0.00 2.74
1540 2040 1.781429 CGCATATCGAGGAGTCAAACG 59.219 52.381 0.00 0.00 41.67 3.60
1563 2063 0.525455 TCGCACTCCGATGAATCACG 60.525 55.000 0.00 0.00 41.89 4.35
1567 2067 1.751351 TCTCTTCGCACTCCGATGAAT 59.249 47.619 3.53 0.00 45.63 2.57
1709 2211 8.086851 TGGTTTTGACGTACTAGTTATTTTCC 57.913 34.615 0.00 0.00 0.00 3.13
1710 2212 8.768019 ACTGGTTTTGACGTACTAGTTATTTTC 58.232 33.333 0.00 0.00 32.99 2.29
1721 2223 5.910637 TGTTATCACTGGTTTTGACGTAC 57.089 39.130 0.00 0.00 0.00 3.67
1725 2227 6.363357 GCTGAAATGTTATCACTGGTTTTGAC 59.637 38.462 0.00 0.00 0.00 3.18
1751 2256 6.574465 GCCAAGGAGTATGTGAAAACTCTCTA 60.574 42.308 2.82 0.00 41.53 2.43
1806 2349 0.806868 GCGGTAAAAACCTGCCTACC 59.193 55.000 0.00 0.00 0.00 3.18
1807 2350 1.467342 CAGCGGTAAAAACCTGCCTAC 59.533 52.381 0.00 0.00 32.51 3.18
1808 2351 1.816074 CAGCGGTAAAAACCTGCCTA 58.184 50.000 0.00 0.00 32.51 3.93
1809 2352 1.524008 GCAGCGGTAAAAACCTGCCT 61.524 55.000 0.00 0.00 43.58 4.75
1824 2375 0.887387 TTTTACCACGACCAGGCAGC 60.887 55.000 0.00 0.00 0.00 5.25
1855 2406 3.323691 GGCTCCTAGATTCCTCTTCTTCC 59.676 52.174 0.00 0.00 32.66 3.46
2105 2669 2.045536 CTGCAGGGGTTCCAGCTC 60.046 66.667 5.57 0.00 44.74 4.09
2117 2681 1.066587 GTAGCTAGACGGGCTGCAG 59.933 63.158 10.11 10.11 41.00 4.41
2150 2714 2.416836 GCTGTACTGATTGTGTAGGCGA 60.417 50.000 3.61 0.00 0.00 5.54
2158 2722 2.636830 GGATGCTGCTGTACTGATTGT 58.363 47.619 3.61 0.00 0.00 2.71
2192 2770 1.005037 TGAAGCCATGAAGCGTCGT 60.005 52.632 0.00 0.00 43.20 4.34


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

AutoCloner maintained by Alex Coulton.