Multiple sequence alignment - TraesCS7A01G199700

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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 TraesCS7A01G199700 chr7A 100.000 2249 0 0 1 2249 162514425 162512177 0.000000e+00 4154
1 TraesCS7A01G199700 chr7D 88.874 1510 95 27 690 2179 161187551 161186095 0.000000e+00 1790
2 TraesCS7A01G199700 chr7D 85.575 513 49 16 1 499 161188235 161187734 4.280000e-142 514
3 TraesCS7A01G199700 chr7B 90.402 896 40 20 520 1396 123312131 123311263 0.000000e+00 1136
4 TraesCS7A01G199700 chr7B 84.091 836 84 26 1426 2249 123311262 123310464 0.000000e+00 761
5 TraesCS7A01G199700 chr7B 84.651 215 20 5 287 500 123312391 123312189 3.790000e-48 202


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 TraesCS7A01G199700 chr7A 162512177 162514425 2248 True 4154.000000 4154 100.000000 1 2249 1 chr7A.!!$R1 2248
1 TraesCS7A01G199700 chr7D 161186095 161188235 2140 True 1152.000000 1790 87.224500 1 2179 2 chr7D.!!$R1 2178
2 TraesCS7A01G199700 chr7B 123310464 123312391 1927 True 699.666667 1136 86.381333 287 2249 3 chr7B.!!$R1 1962

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
962 1026 0.03831 AGCCCCCTACAAGCTTGTTC 59.962 55.0 35.2 17.37 42.35 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2032 1.379527 GAGGTGCCCAATTACTTCCG 58.62 55.0 0.0 0.0 0.0 4.3 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
30 34 4.695455 AGCAGCTTAACAATTATCACACGT 59.305 37.500 0.00 0.00 0.00 4.49
33 37 6.183360 GCAGCTTAACAATTATCACACGTACT 60.183 38.462 0.00 0.00 0.00 2.73
34 38 7.391786 CAGCTTAACAATTATCACACGTACTC 58.608 38.462 0.00 0.00 0.00 2.59
35 39 6.534079 AGCTTAACAATTATCACACGTACTCC 59.466 38.462 0.00 0.00 0.00 3.85
36 40 6.534079 GCTTAACAATTATCACACGTACTCCT 59.466 38.462 0.00 0.00 0.00 3.69
37 41 7.703621 GCTTAACAATTATCACACGTACTCCTA 59.296 37.037 0.00 0.00 0.00 2.94
38 42 8.915871 TTAACAATTATCACACGTACTCCTAC 57.084 34.615 0.00 0.00 0.00 3.18
39 43 6.770746 ACAATTATCACACGTACTCCTACT 57.229 37.500 0.00 0.00 0.00 2.57
40 44 7.870509 ACAATTATCACACGTACTCCTACTA 57.129 36.000 0.00 0.00 0.00 1.82
41 45 8.461249 ACAATTATCACACGTACTCCTACTAT 57.539 34.615 0.00 0.00 0.00 2.12
52 56 6.771749 ACGTACTCCTACTATGTAAGATGCTT 59.228 38.462 0.00 0.00 0.00 3.91
62 66 6.879458 ACTATGTAAGATGCTTCGAAAAAGGT 59.121 34.615 0.00 0.00 0.00 3.50
69 73 0.586319 CTTCGAAAAAGGTGCGAGCA 59.414 50.000 0.00 0.00 35.31 4.26
114 118 6.238184 GGTTTTGAGCAGTTTCTTGGAAATTG 60.238 38.462 9.94 9.94 0.00 2.32
120 124 4.619160 GCAGTTTCTTGGAAATTGGCTAGG 60.619 45.833 14.17 0.00 0.00 3.02
121 125 4.082026 CAGTTTCTTGGAAATTGGCTAGGG 60.082 45.833 7.36 0.00 0.00 3.53
122 126 3.825908 TTCTTGGAAATTGGCTAGGGT 57.174 42.857 0.00 0.00 0.00 4.34
126 130 0.629058 GGAAATTGGCTAGGGTGGGA 59.371 55.000 0.00 0.00 0.00 4.37
127 131 1.217942 GGAAATTGGCTAGGGTGGGAT 59.782 52.381 0.00 0.00 0.00 3.85
128 132 2.587522 GAAATTGGCTAGGGTGGGATC 58.412 52.381 0.00 0.00 0.00 3.36
148 152 4.041740 TCGACTCCGGATAAACATTGAG 57.958 45.455 3.57 0.00 36.24 3.02
153 157 6.292381 CGACTCCGGATAAACATTGAGAATTC 60.292 42.308 3.57 0.00 0.00 2.17
166 170 3.415212 TGAGAATTCAGGCCAAGTTCAG 58.585 45.455 5.01 0.00 0.00 3.02
205 209 1.067142 TGACCGTATCAGTTGACAGGC 60.067 52.381 0.00 0.00 31.91 4.85
230 234 4.759893 GGAGACGACCCCAGTACT 57.240 61.111 0.00 0.00 0.00 2.73
236 240 1.471684 GACGACCCCAGTACTACACAG 59.528 57.143 0.00 0.00 0.00 3.66
251 255 1.135199 ACACAGTGTCGACGACAAACT 60.135 47.619 30.68 21.51 44.49 2.66
265 269 6.948777 CGACGACAAACTAAATTAAGCTTCTC 59.051 38.462 0.00 0.00 0.00 2.87
285 289 5.657474 TCTCCCTAAATTAAGTACGCACAG 58.343 41.667 0.00 0.00 0.00 3.66
322 326 0.984995 GTCAAACTAGACCCCTGCCT 59.015 55.000 0.00 0.00 32.36 4.75
381 385 5.766174 AGTAAACCACATTTCCACGTATGTT 59.234 36.000 0.00 0.00 32.88 2.71
399 403 6.757010 CGTATGTTAACATATATGGAGCTCCC 59.243 42.308 29.95 12.55 40.53 4.30
400 404 5.499004 TGTTAACATATATGGAGCTCCCC 57.501 43.478 29.95 7.49 34.29 4.81
401 405 5.162637 TGTTAACATATATGGAGCTCCCCT 58.837 41.667 29.95 19.09 34.29 4.79
404 408 7.293771 TGTTAACATATATGGAGCTCCCCTAAA 59.706 37.037 29.95 11.51 34.29 1.85
405 409 6.780198 AACATATATGGAGCTCCCCTAAAA 57.220 37.500 29.95 10.69 34.29 1.52
406 410 6.780198 ACATATATGGAGCTCCCCTAAAAA 57.220 37.500 29.95 9.88 34.29 1.94
444 457 7.721399 ACAGATGAATTTGTACAGAAGGAAGTT 59.279 33.333 0.00 0.00 0.00 2.66
500 516 1.129811 GGCAACAGGTACATTGTACGC 59.870 52.381 18.23 15.17 0.00 4.42
511 568 2.887783 ACATTGTACGCATTTGTTCCCA 59.112 40.909 0.00 0.00 0.00 4.37
516 573 0.896923 ACGCATTTGTTCCCATGCAT 59.103 45.000 0.00 0.00 45.23 3.96
517 574 1.135024 ACGCATTTGTTCCCATGCATC 60.135 47.619 0.00 0.00 45.23 3.91
518 575 1.135053 CGCATTTGTTCCCATGCATCA 60.135 47.619 0.00 0.00 45.23 3.07
535 592 0.969149 TCATGCTCTGGTCAAGACGT 59.031 50.000 0.00 0.00 0.00 4.34
672 734 3.604065 TCGACGATGGAATTCTACGAG 57.396 47.619 19.51 14.40 0.00 4.18
680 742 2.158813 TGGAATTCTACGAGGGAATGCC 60.159 50.000 15.00 15.00 44.95 4.40
750 812 6.037412 TTGACTTTTCATCAAACGGGACGG 62.037 45.833 0.00 0.00 43.49 4.79
898 961 1.134560 CCAAGCTACTACCACCTCGTC 59.865 57.143 0.00 0.00 0.00 4.20
962 1026 0.038310 AGCCCCCTACAAGCTTGTTC 59.962 55.000 35.20 17.37 42.35 3.18
963 1027 0.038310 GCCCCCTACAAGCTTGTTCT 59.962 55.000 35.20 15.02 42.35 3.01
994 1074 0.537371 AAGGAAGCCAAGGTTGACGG 60.537 55.000 0.00 0.00 0.00 4.79
1033 1113 4.933064 GGACGATGAGGCTCGCCG 62.933 72.222 21.36 21.36 42.35 6.46
1227 1310 4.912395 TGCACCACCAACAGCCCC 62.912 66.667 0.00 0.00 0.00 5.80
1302 1387 4.716977 ACGACCACCCCCTCCCTC 62.717 72.222 0.00 0.00 0.00 4.30
1306 1391 4.825679 CCACCCCCTCCCTCCCTC 62.826 77.778 0.00 0.00 0.00 4.30
1322 1407 0.820871 CCTCCTCTCTCGGGTTCAAG 59.179 60.000 0.00 0.00 0.00 3.02
1371 1456 3.907260 ATGGCGGGCTCACAGTGTG 62.907 63.158 17.53 17.53 34.45 3.82
1396 1481 4.201960 GCATGTTCTTTTTCCCTAGCTAGC 60.202 45.833 15.74 6.62 0.00 3.42
1434 1519 2.740826 CGGCGGTCGACATGGTTT 60.741 61.111 18.91 0.00 42.43 3.27
1440 1525 1.130373 CGGTCGACATGGTTTGATTGG 59.870 52.381 18.91 0.00 0.00 3.16
1503 1588 3.809990 CGTGGTTTTCGCTTTCGC 58.190 55.556 0.00 0.00 35.26 4.70
1530 1615 6.695713 GGGTGTTGATTTGTACAGAAGAAAAC 59.304 38.462 0.00 0.00 0.00 2.43
1555 1645 7.943447 ACATACTCGTATACTTGGTAGGATCTT 59.057 37.037 13.88 0.00 0.00 2.40
1558 1648 8.075761 ACTCGTATACTTGGTAGGATCTTTTT 57.924 34.615 0.56 0.00 0.00 1.94
1560 1650 7.844009 TCGTATACTTGGTAGGATCTTTTTGT 58.156 34.615 0.56 0.00 0.00 2.83
1561 1651 8.316214 TCGTATACTTGGTAGGATCTTTTTGTT 58.684 33.333 0.56 0.00 0.00 2.83
1703 1800 7.599245 AGCACAGTTATGTACTCTAACTCAAAC 59.401 37.037 14.64 8.09 37.33 2.93
1732 1830 8.807667 AAAAGAAAGTTATGTGCTCTGATTTG 57.192 30.769 0.00 0.00 0.00 2.32
1737 1835 4.702131 AGTTATGTGCTCTGATTTGGGTTC 59.298 41.667 0.00 0.00 0.00 3.62
1760 1858 3.789224 GTGGATCAACAAAAACGTGTCAC 59.211 43.478 0.00 0.00 0.00 3.67
1763 1861 3.479505 TCAACAAAAACGTGTCACCTG 57.520 42.857 0.00 0.00 0.00 4.00
1764 1862 2.814919 TCAACAAAAACGTGTCACCTGT 59.185 40.909 0.00 0.00 0.00 4.00
1765 1863 3.253677 TCAACAAAAACGTGTCACCTGTT 59.746 39.130 0.00 0.00 0.00 3.16
1766 1864 3.481112 ACAAAAACGTGTCACCTGTTC 57.519 42.857 0.00 0.00 0.00 3.18
1767 1865 2.814919 ACAAAAACGTGTCACCTGTTCA 59.185 40.909 0.00 0.00 0.00 3.18
1768 1866 3.168193 CAAAAACGTGTCACCTGTTCAC 58.832 45.455 0.00 0.00 0.00 3.18
1769 1867 1.375551 AAACGTGTCACCTGTTCACC 58.624 50.000 0.00 0.00 0.00 4.02
1773 1871 0.935196 GTGTCACCTGTTCACCGTTC 59.065 55.000 0.00 0.00 0.00 3.95
1796 1894 2.407090 GCATGCCTGGAAGTGTTTTTC 58.593 47.619 6.36 0.00 0.00 2.29
1799 1897 4.301628 CATGCCTGGAAGTGTTTTTCTTC 58.698 43.478 0.00 0.00 40.10 2.87
1809 1907 7.280205 TGGAAGTGTTTTTCTTCTTACAGAGAC 59.720 37.037 0.00 0.00 40.50 3.36
1860 1958 3.172575 ATTCGCGTGCGTCACTCG 61.173 61.111 14.47 13.58 42.77 4.18
1894 1992 2.866156 GCCAAAAGGCAGAACTTTTCAC 59.134 45.455 0.84 0.00 45.96 3.18
1934 2032 1.568025 GTGGCGTCAACCGTTTCTC 59.432 57.895 0.00 0.00 39.32 2.87
2138 2240 3.370231 GGCGGCCGGTGTTTCAAT 61.370 61.111 29.38 0.00 0.00 2.57
2144 2246 2.413634 CGGCCGGTGTTTCAATTTAGAC 60.414 50.000 20.10 0.00 0.00 2.59
2180 2282 3.705072 ACTCTTCAAACCCCCTCTATACG 59.295 47.826 0.00 0.00 0.00 3.06
2181 2283 3.705072 CTCTTCAAACCCCCTCTATACGT 59.295 47.826 0.00 0.00 0.00 3.57
2182 2284 3.703052 TCTTCAAACCCCCTCTATACGTC 59.297 47.826 0.00 0.00 0.00 4.34
2183 2285 3.393426 TCAAACCCCCTCTATACGTCT 57.607 47.619 0.00 0.00 0.00 4.18
2185 2287 2.083628 AACCCCCTCTATACGTCTGG 57.916 55.000 0.00 0.00 0.00 3.86
2186 2288 1.229131 ACCCCCTCTATACGTCTGGA 58.771 55.000 0.00 0.00 0.00 3.86
2187 2289 1.133544 ACCCCCTCTATACGTCTGGAC 60.134 57.143 0.00 0.00 0.00 4.02
2205 2307 4.062656 GGATGGCGCGGGCAAAAA 62.063 61.111 26.61 8.75 42.43 1.94
2226 2332 6.901081 AAAATCCGACTCAAAGGAATTTCT 57.099 33.333 0.00 0.00 35.40 2.52
2232 2338 5.645497 CCGACTCAAAGGAATTTCTGAGAAT 59.355 40.000 16.67 1.00 38.91 2.40
2235 2341 7.095060 CGACTCAAAGGAATTTCTGAGAATTCA 60.095 37.037 16.67 0.00 44.19 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.163864 CGTGTGATAATTGTTAAGCTGCTCA 60.164 40.000 1.00 0.00 0.00 4.26
19 23 9.565090 TTACATAGTAGGAGTACGTGTGATAAT 57.435 33.333 0.00 0.00 35.66 1.28
30 34 7.222161 TCGAAGCATCTTACATAGTAGGAGTA 58.778 38.462 0.00 0.00 0.00 2.59
33 37 6.954487 TTCGAAGCATCTTACATAGTAGGA 57.046 37.500 0.00 0.00 0.00 2.94
34 38 8.420374 TTTTTCGAAGCATCTTACATAGTAGG 57.580 34.615 0.00 0.00 0.00 3.18
35 39 8.543774 CCTTTTTCGAAGCATCTTACATAGTAG 58.456 37.037 0.00 0.00 0.00 2.57
36 40 8.038944 ACCTTTTTCGAAGCATCTTACATAGTA 58.961 33.333 0.00 0.00 0.00 1.82
37 41 6.879458 ACCTTTTTCGAAGCATCTTACATAGT 59.121 34.615 0.00 0.00 0.00 2.12
38 42 7.182761 CACCTTTTTCGAAGCATCTTACATAG 58.817 38.462 0.00 0.00 0.00 2.23
39 43 6.403200 GCACCTTTTTCGAAGCATCTTACATA 60.403 38.462 0.00 0.00 0.00 2.29
40 44 5.619981 GCACCTTTTTCGAAGCATCTTACAT 60.620 40.000 0.00 0.00 0.00 2.29
41 45 4.320202 GCACCTTTTTCGAAGCATCTTACA 60.320 41.667 0.00 0.00 0.00 2.41
52 56 0.516877 CATGCTCGCACCTTTTTCGA 59.483 50.000 0.00 0.00 0.00 3.71
62 66 0.735978 CGTCTGTTACCATGCTCGCA 60.736 55.000 0.00 0.00 0.00 5.10
69 73 0.398696 TTGCCACCGTCTGTTACCAT 59.601 50.000 0.00 0.00 0.00 3.55
81 85 0.032540 CTGCTCAAAACCTTGCCACC 59.967 55.000 0.00 0.00 32.14 4.61
114 118 1.457831 AGTCGATCCCACCCTAGCC 60.458 63.158 0.00 0.00 0.00 3.93
120 124 0.538977 TATCCGGAGTCGATCCCACC 60.539 60.000 11.34 0.00 46.50 4.61
121 125 1.325355 TTATCCGGAGTCGATCCCAC 58.675 55.000 11.34 0.00 46.50 4.61
122 126 1.684983 GTTTATCCGGAGTCGATCCCA 59.315 52.381 11.34 0.00 46.50 4.37
126 130 4.341235 TCTCAATGTTTATCCGGAGTCGAT 59.659 41.667 11.34 0.00 39.00 3.59
127 131 3.697542 TCTCAATGTTTATCCGGAGTCGA 59.302 43.478 11.34 0.00 39.00 4.20
128 132 4.041740 TCTCAATGTTTATCCGGAGTCG 57.958 45.455 11.34 0.00 0.00 4.18
148 152 2.489722 GTCCTGAACTTGGCCTGAATTC 59.510 50.000 3.32 0.00 0.00 2.17
153 157 1.672356 CCGTCCTGAACTTGGCCTG 60.672 63.158 3.32 0.00 0.00 4.85
166 170 4.684242 GGTCAAAACATTTGAATTCCGTCC 59.316 41.667 7.07 0.08 0.00 4.79
205 209 1.354506 GGGTCGTCTCCGATACGTG 59.645 63.158 0.00 0.00 46.30 4.49
224 228 2.477754 TCGTCGACACTGTGTAGTACTG 59.522 50.000 14.31 8.69 34.74 2.74
227 231 2.482864 TGTCGTCGACACTGTGTAGTA 58.517 47.619 23.70 0.00 37.67 1.82
230 234 2.097954 AGTTTGTCGTCGACACTGTGTA 59.902 45.455 26.95 9.29 42.60 2.90
236 240 5.782200 GCTTAATTTAGTTTGTCGTCGACAC 59.218 40.000 26.95 16.64 42.60 3.67
265 269 4.569564 GGACTGTGCGTACTTAATTTAGGG 59.430 45.833 4.97 0.00 0.00 3.53
285 289 0.320697 ACCTAGCGTTCAACAGGGAC 59.679 55.000 0.00 0.00 32.12 4.46
322 326 2.861472 TTGGGGGCCAAGGCACTA 60.861 61.111 13.85 0.00 45.29 2.74
381 385 7.881912 TTTTAGGGGAGCTCCATATATGTTA 57.118 36.000 33.29 10.63 37.91 2.41
416 420 8.547967 TTCCTTCTGTACAAATTCATCTGTAC 57.452 34.615 10.07 10.07 45.33 2.90
421 425 8.352942 ACAAACTTCCTTCTGTACAAATTCATC 58.647 33.333 0.00 0.00 0.00 2.92
475 488 1.200716 CAATGTACCTGTTGCCTGCAG 59.799 52.381 6.78 6.78 0.00 4.41
481 494 1.801771 TGCGTACAATGTACCTGTTGC 59.198 47.619 16.89 13.96 0.00 4.17
500 516 2.869801 GCATGATGCATGGGAACAAATG 59.130 45.455 13.36 0.00 44.26 2.32
516 573 0.969149 ACGTCTTGACCAGAGCATGA 59.031 50.000 0.00 0.00 29.34 3.07
517 574 1.073964 CACGTCTTGACCAGAGCATG 58.926 55.000 0.00 0.00 29.34 4.06
518 575 0.671781 GCACGTCTTGACCAGAGCAT 60.672 55.000 0.00 0.00 29.34 3.79
621 682 1.565067 TCCGTTCTTCTTCCTACCCC 58.435 55.000 0.00 0.00 0.00 4.95
726 788 4.320202 CGTCCCGTTTGATGAAAAGTCAAT 60.320 41.667 0.00 0.00 37.30 2.57
727 789 3.002862 CGTCCCGTTTGATGAAAAGTCAA 59.997 43.478 0.00 0.00 37.30 3.18
898 961 4.340263 TGTCGTCGAGATGTAATTCTTCG 58.660 43.478 0.00 0.00 0.00 3.79
962 1026 3.264450 TGGCTTCCTTCTTCTCCCTTTAG 59.736 47.826 0.00 0.00 0.00 1.85
963 1027 3.256704 TGGCTTCCTTCTTCTCCCTTTA 58.743 45.455 0.00 0.00 0.00 1.85
1054 1134 3.123620 GACCGCCAGAAGCAGCAG 61.124 66.667 0.00 0.00 44.04 4.24
1056 1136 4.400961 AGGACCGCCAGAAGCAGC 62.401 66.667 0.00 0.00 44.04 5.25
1059 1139 4.821589 CCGAGGACCGCCAGAAGC 62.822 72.222 0.00 0.00 36.29 3.86
1304 1389 0.174617 GCTTGAACCCGAGAGAGGAG 59.825 60.000 0.00 0.00 0.00 3.69
1305 1390 0.251832 AGCTTGAACCCGAGAGAGGA 60.252 55.000 0.00 0.00 0.00 3.71
1306 1391 0.610687 AAGCTTGAACCCGAGAGAGG 59.389 55.000 0.00 0.00 0.00 3.69
1322 1407 1.864029 GCTGGTCCGTCAAAAACAAGC 60.864 52.381 0.00 0.00 0.00 4.01
1353 1438 3.640407 ACACTGTGAGCCCGCCAT 61.640 61.111 15.86 0.00 0.00 4.40
1371 1456 2.732282 GCTAGGGAAAAAGAACATGCGC 60.732 50.000 0.00 0.00 0.00 6.09
1396 1481 3.979739 GCTAGTCGGCCGGCCTAG 61.980 72.222 41.01 33.66 33.00 3.02
1422 1507 3.252215 TCAACCAATCAAACCATGTCGAC 59.748 43.478 9.11 9.11 0.00 4.20
1423 1508 3.481453 TCAACCAATCAAACCATGTCGA 58.519 40.909 0.00 0.00 0.00 4.20
1434 1519 4.500545 CCAACCAACGAATTCAACCAATCA 60.501 41.667 6.22 0.00 0.00 2.57
1440 1525 4.678622 AGAAACCAACCAACGAATTCAAC 58.321 39.130 6.22 0.00 0.00 3.18
1498 1583 0.312416 CAAATCAACACCCGGCGAAA 59.688 50.000 9.30 0.00 0.00 3.46
1499 1584 0.820074 ACAAATCAACACCCGGCGAA 60.820 50.000 9.30 0.00 0.00 4.70
1500 1585 0.035036 TACAAATCAACACCCGGCGA 59.965 50.000 9.30 0.00 0.00 5.54
1501 1586 0.167251 GTACAAATCAACACCCGGCG 59.833 55.000 0.00 0.00 0.00 6.46
1502 1587 1.199097 CTGTACAAATCAACACCCGGC 59.801 52.381 0.00 0.00 0.00 6.13
1503 1588 2.773487 TCTGTACAAATCAACACCCGG 58.227 47.619 0.00 0.00 0.00 5.73
1530 1615 7.925043 AGATCCTACCAAGTATACGAGTATG 57.075 40.000 6.04 0.00 0.00 2.39
1560 1650 7.095271 GCAGCTTGCCTATGTTTTATTCAAAAA 60.095 33.333 0.00 0.00 37.42 1.94
1561 1651 6.368516 GCAGCTTGCCTATGTTTTATTCAAAA 59.631 34.615 0.00 0.00 37.42 2.44
1645 1735 9.715121 AAGATTTGACAAATTATCACAAAGCAT 57.285 25.926 14.46 0.00 38.65 3.79
1657 1747 8.715191 TGTGCTTTGTTAAGATTTGACAAATT 57.285 26.923 14.46 3.69 41.02 1.82
1659 1749 7.319646 ACTGTGCTTTGTTAAGATTTGACAAA 58.680 30.769 2.48 2.48 39.99 2.83
1672 1762 7.931948 AGTTAGAGTACATAACTGTGCTTTGTT 59.068 33.333 17.81 0.00 46.71 2.83
1710 1807 5.416952 CCCAAATCAGAGCACATAACTTTCT 59.583 40.000 0.00 0.00 0.00 2.52
1714 1811 4.307032 ACCCAAATCAGAGCACATAACT 57.693 40.909 0.00 0.00 0.00 2.24
1715 1812 4.437390 CGAACCCAAATCAGAGCACATAAC 60.437 45.833 0.00 0.00 0.00 1.89
1726 1824 2.817258 GTTGATCCACGAACCCAAATCA 59.183 45.455 0.00 0.00 0.00 2.57
1732 1830 3.377439 GTTTTTGTTGATCCACGAACCC 58.623 45.455 0.00 0.00 0.00 4.11
1737 1835 3.033185 GACACGTTTTTGTTGATCCACG 58.967 45.455 0.00 0.00 0.00 4.94
1760 1858 1.227999 ATGCGTGAACGGTGAACAGG 61.228 55.000 4.84 0.00 40.23 4.00
1763 1861 1.440353 GCATGCGTGAACGGTGAAC 60.440 57.895 10.93 0.00 40.23 3.18
1764 1862 2.612567 GGCATGCGTGAACGGTGAA 61.613 57.895 12.44 0.00 40.23 3.18
1765 1863 3.047280 GGCATGCGTGAACGGTGA 61.047 61.111 12.44 0.00 40.23 4.02
1766 1864 3.049674 AGGCATGCGTGAACGGTG 61.050 61.111 12.95 0.00 40.23 4.94
1767 1865 3.049674 CAGGCATGCGTGAACGGT 61.050 61.111 31.46 0.00 40.23 4.83
1768 1866 3.803082 CCAGGCATGCGTGAACGG 61.803 66.667 35.33 18.97 40.23 4.44
1769 1867 2.244436 CTTCCAGGCATGCGTGAACG 62.244 60.000 35.33 21.60 43.27 3.95
1773 1871 1.518056 AACACTTCCAGGCATGCGTG 61.518 55.000 28.99 28.99 0.00 5.34
1796 1894 5.121454 GTGCAATGAAGGTCTCTGTAAGAAG 59.879 44.000 0.00 0.00 46.34 2.85
1799 1897 4.573900 AGTGCAATGAAGGTCTCTGTAAG 58.426 43.478 0.00 0.00 0.00 2.34
1894 1992 3.550992 GGCATACACGTGGCGTCG 61.551 66.667 21.57 4.47 38.32 5.12
1934 2032 1.379527 GAGGTGCCCAATTACTTCCG 58.620 55.000 0.00 0.00 0.00 4.30
1942 2042 4.115199 GGAGCCGAGGTGCCCAAT 62.115 66.667 0.00 0.00 0.00 3.16
2024 2124 2.107141 GGAGATCGAACTGGCCCG 59.893 66.667 0.00 0.00 0.00 6.13
2054 2154 2.401766 CGTGGAACTGAGGCCATGC 61.402 63.158 5.01 0.00 36.41 4.06
2094 2195 5.589050 CAGAAAGATGAGAATTGATGGCTGA 59.411 40.000 0.00 0.00 0.00 4.26
2188 2290 4.062656 TTTTTGCCCGCGCCATCC 62.063 61.111 0.00 0.00 0.00 3.51
2202 2304 7.014230 TCAGAAATTCCTTTGAGTCGGATTTTT 59.986 33.333 6.78 2.37 34.69 1.94
2203 2305 6.490040 TCAGAAATTCCTTTGAGTCGGATTTT 59.510 34.615 5.58 5.58 36.26 1.82
2204 2306 6.003950 TCAGAAATTCCTTTGAGTCGGATTT 58.996 36.000 0.00 0.00 0.00 2.17
2205 2307 5.560724 TCAGAAATTCCTTTGAGTCGGATT 58.439 37.500 0.00 0.00 0.00 3.01
2206 2308 5.046304 TCTCAGAAATTCCTTTGAGTCGGAT 60.046 40.000 9.55 0.00 38.50 4.18
2207 2309 4.283467 TCTCAGAAATTCCTTTGAGTCGGA 59.717 41.667 9.55 0.00 38.50 4.55
2208 2310 4.569943 TCTCAGAAATTCCTTTGAGTCGG 58.430 43.478 9.55 0.00 38.50 4.79
2209 2311 6.734104 ATTCTCAGAAATTCCTTTGAGTCG 57.266 37.500 9.55 0.00 38.50 4.18


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

AutoCloner maintained by Alex Coulton.