Multiple sequence alignment - TraesCS1D01G238400

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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 TraesCS1D01G238400 chr1D 100.000 2446 0 0 1 2446 327998282 327995837 0.000000e+00 4518
1 TraesCS1D01G238400 chr1A 87.435 2507 175 54 7 2446 407130474 407128041 0.000000e+00 2756
2 TraesCS1D01G238400 chr1B 87.990 1632 111 36 102 1713 442153217 442151651 0.000000e+00 1849
3 TraesCS1D01G238400 chr1B 81.272 283 34 12 1848 2115 442136443 442136165 6.850000e-51 211
4 TraesCS1D01G238400 chr1B 84.390 205 25 6 2243 2446 442112480 442112282 6.900000e-46 195
5 TraesCS1D01G238400 chr1B 94.937 79 4 0 2169 2247 442136162 442136084 9.180000e-25 124
6 TraesCS1D01G238400 chr5A 88.618 123 13 1 7 128 596022442 596022320 5.450000e-32 148
7 TraesCS1D01G238400 chr5A 80.105 191 31 6 1 187 25885967 25886154 4.240000e-28 135
8 TraesCS1D01G238400 chr2B 87.597 129 15 1 1 128 40324192 40324320 5.450000e-32 148
9 TraesCS1D01G238400 chr6D 82.222 180 21 9 1 176 67405868 67406040 7.050000e-31 145
10 TraesCS1D01G238400 chr6D 80.402 199 27 9 7 201 450365740 450365550 9.120000e-30 141
11 TraesCS1D01G238400 chr4D 84.459 148 22 1 7 153 72412427 72412280 7.050000e-31 145
12 TraesCS1D01G238400 chr4D 84.286 140 21 1 7 145 490864466 490864327 4.240000e-28 135
13 TraesCS1D01G238400 chr4B 80.978 184 28 4 7 186 28633190 28633010 3.280000e-29 139
14 TraesCS1D01G238400 chr3B 79.688 192 27 8 1 187 564719029 564719213 7.100000e-26 128


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 TraesCS1D01G238400 chr1D 327995837 327998282 2445 True 4518 4518 100.000 1 2446 1 chr1D.!!$R1 2445
1 TraesCS1D01G238400 chr1A 407128041 407130474 2433 True 2756 2756 87.435 7 2446 1 chr1A.!!$R1 2439
2 TraesCS1D01G238400 chr1B 442151651 442153217 1566 True 1849 1849 87.990 102 1713 1 chr1B.!!$R2 1611

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
36 38 0.597377 CAACAAGGTTTGCCGGCTTC 60.597 55.0 29.7 17.0 40.5 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1467 1489 0.107214 ATCTGTAACCGTGGGCATGG 60.107 55.0 0.0 0.0 43.15 3.66 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 32 5.240844 ACTGTCTATTACAACAAGGTTTGCC 59.759 40.000 0.00 0.00 37.74 4.52
36 38 0.597377 CAACAAGGTTTGCCGGCTTC 60.597 55.000 29.70 17.00 40.50 3.86
49 51 2.683933 GCTTCGGTGAGGGAGGGA 60.684 66.667 0.00 0.00 0.00 4.20
55 57 1.381327 GGTGAGGGAGGGACGATGA 60.381 63.158 0.00 0.00 0.00 2.92
57 59 1.753078 TGAGGGAGGGACGATGACG 60.753 63.158 0.00 0.00 45.75 4.35
96 98 1.454653 GTTTCCGTGCTTGTAGTCGTC 59.545 52.381 0.00 0.00 0.00 4.20
98 100 1.208358 CCGTGCTTGTAGTCGTCGA 59.792 57.895 0.00 0.00 0.00 4.20
110 112 2.559440 AGTCGTCGATAGGTGGTCTAC 58.441 52.381 0.00 0.00 0.00 2.59
128 130 9.570488 GTGGTCTACGGATATAGATGTAATTTC 57.430 37.037 0.00 0.00 33.78 2.17
154 156 9.939802 CTACTACTTATGGTGTTCTTTTTACCT 57.060 33.333 0.00 0.00 35.51 3.08
156 158 9.636789 ACTACTTATGGTGTTCTTTTTACCTTT 57.363 29.630 0.00 0.00 35.51 3.11
163 165 7.493367 TGGTGTTCTTTTTACCTTTGTAATGG 58.507 34.615 0.00 0.00 36.84 3.16
177 179 8.109634 ACCTTTGTAATGGTTGATGAATAGAGT 58.890 33.333 0.00 0.00 33.06 3.24
179 181 9.166173 CTTTGTAATGGTTGATGAATAGAGTGA 57.834 33.333 0.00 0.00 0.00 3.41
192 194 6.198687 TGAATAGAGTGAAAGTTTTGCAACG 58.801 36.000 0.00 0.00 38.03 4.10
263 265 4.335647 CTGTGGTCGGGCAGCCTT 62.336 66.667 12.43 0.00 0.00 4.35
280 282 1.404986 CCTTTGGGAACACGATAGCGA 60.405 52.381 7.69 0.00 42.67 4.93
477 480 1.101049 ACGTGGCAGAACAAAGGTGG 61.101 55.000 0.00 0.00 0.00 4.61
484 487 2.034685 GCAGAACAAAGGTGGAAAGTCC 59.965 50.000 0.00 0.00 36.96 3.85
509 512 2.363788 TTCGACATGGACGGAAGAAG 57.636 50.000 12.97 0.00 0.00 2.85
582 585 3.822192 CAGCGGCTGCATGCACAT 61.822 61.111 18.46 0.00 46.23 3.21
603 606 2.473760 ATCCTCTCGAGTCCGCACG 61.474 63.158 13.13 0.00 35.37 5.34
719 730 7.322461 CGAACATGATAGATCTCTTACTTGTCG 59.678 40.741 0.00 0.00 0.00 4.35
791 802 1.589716 CCTTTCTGCCTGCTTTCGGG 61.590 60.000 0.00 0.00 41.86 5.14
805 816 3.005791 GCTTTCGGGATTGGGGAATAATG 59.994 47.826 0.00 0.00 0.00 1.90
811 822 7.092748 TCGGGATTGGGGAATAATGTATAAA 57.907 36.000 0.00 0.00 0.00 1.40
862 873 7.051623 AGTAATTCACATGCGGGAAAGTATAA 58.948 34.615 0.00 0.00 0.00 0.98
883 894 2.465097 GATCGATCGAGGGAGGCACG 62.465 65.000 23.84 0.00 0.00 5.34
934 948 4.217334 CGCTGTCTGTCCATCTATCTACAT 59.783 45.833 0.00 0.00 0.00 2.29
935 949 5.412904 CGCTGTCTGTCCATCTATCTACATA 59.587 44.000 0.00 0.00 0.00 2.29
936 950 6.403092 CGCTGTCTGTCCATCTATCTACATAG 60.403 46.154 0.00 0.00 34.24 2.23
937 951 6.432783 GCTGTCTGTCCATCTATCTACATAGT 59.567 42.308 0.00 0.00 34.54 2.12
938 952 7.608376 GCTGTCTGTCCATCTATCTACATAGTA 59.392 40.741 0.00 0.00 34.54 1.82
939 953 8.850007 TGTCTGTCCATCTATCTACATAGTAC 57.150 38.462 0.00 0.00 34.54 2.73
991 1005 3.923461 GGATCAATCCAAGATCGATCGAC 59.077 47.826 22.06 14.23 46.38 4.20
1065 1081 7.361542 CGATCTATCAATCCCAAAACATCATCC 60.362 40.741 0.00 0.00 0.00 3.51
1094 1112 2.256117 AGAACACACCACTGGCTAAC 57.744 50.000 0.00 0.00 0.00 2.34
1107 1125 3.257127 ACTGGCTAACTCTTCAGTGAGTC 59.743 47.826 0.00 0.00 45.49 3.36
1110 1128 3.494232 GCTAACTCTTCAGTGAGTCGTC 58.506 50.000 0.00 0.00 45.49 4.20
1147 1169 7.622893 ATCTCAGCTCTAATTTTCTTTCACC 57.377 36.000 0.00 0.00 0.00 4.02
1153 1175 6.314896 AGCTCTAATTTTCTTTCACCTGATCG 59.685 38.462 0.00 0.00 0.00 3.69
1160 1182 4.736126 TCTTTCACCTGATCGATTGCTA 57.264 40.909 0.00 0.00 0.00 3.49
1320 1342 2.967397 GGCTAAAAACGCCCACCC 59.033 61.111 0.00 0.00 41.73 4.61
1381 1403 1.422402 ACCCTGGCGTTTTTCTCCTTA 59.578 47.619 0.00 0.00 0.00 2.69
1453 1475 0.836606 TGCTGCGATTGAAGGGGATA 59.163 50.000 0.00 0.00 0.00 2.59
1457 1479 3.070018 CTGCGATTGAAGGGGATACATC 58.930 50.000 0.00 0.00 39.74 3.06
1458 1480 2.437651 TGCGATTGAAGGGGATACATCA 59.562 45.455 0.00 0.00 39.74 3.07
1459 1481 3.072915 TGCGATTGAAGGGGATACATCAT 59.927 43.478 0.00 0.00 39.74 2.45
1460 1482 4.285775 TGCGATTGAAGGGGATACATCATA 59.714 41.667 0.00 0.00 39.74 2.15
1465 1487 4.910195 TGAAGGGGATACATCATACATGC 58.090 43.478 0.00 0.00 39.74 4.06
1466 1488 4.350520 TGAAGGGGATACATCATACATGCA 59.649 41.667 0.00 0.00 39.74 3.96
1467 1489 4.292186 AGGGGATACATCATACATGCAC 57.708 45.455 0.00 0.00 39.74 4.57
1492 1522 1.209504 CCCACGGTTACAGATCACCAT 59.790 52.381 0.00 0.00 31.84 3.55
1523 1553 2.743752 CGGCTCTACGTCGTCGGAA 61.744 63.158 0.00 0.00 41.85 4.30
1550 1580 9.851686 ATCTTACATAATTAATCCAGTCTTGCA 57.148 29.630 0.00 0.00 0.00 4.08
1611 1652 3.308530 TGCGTAGATATCTTGCATCGTG 58.691 45.455 21.72 3.25 33.28 4.35
1639 1680 4.452455 GGCCCTGTATCTTTTGTATCATCG 59.548 45.833 0.00 0.00 0.00 3.84
1684 1733 4.097437 ACTTATATTCGAGGTCGTCTTGCA 59.903 41.667 0.00 0.00 40.80 4.08
1689 1738 2.066262 TCGAGGTCGTCTTGCAATTTC 58.934 47.619 0.00 0.00 40.80 2.17
1692 1741 2.478894 GAGGTCGTCTTGCAATTTCGAA 59.521 45.455 17.52 0.00 32.56 3.71
1727 1784 4.374843 TGTGCAATGGTCATGCTTAATC 57.625 40.909 0.00 0.00 44.14 1.75
1732 1789 2.036958 TGGTCATGCTTAATCGGGTG 57.963 50.000 0.00 0.00 0.00 4.61
1734 1791 2.172505 TGGTCATGCTTAATCGGGTGAT 59.827 45.455 0.00 0.00 35.98 3.06
1742 1799 4.520874 TGCTTAATCGGGTGATGAACAAAA 59.479 37.500 0.00 0.00 34.24 2.44
1750 1807 8.894768 ATCGGGTGATGAACAAAATTTTAAAA 57.105 26.923 2.44 2.51 32.21 1.52
1753 1810 7.585936 CGGGTGATGAACAAAATTTTAAAAAGC 59.414 33.333 4.44 0.00 0.00 3.51
1755 1812 7.860373 GGTGATGAACAAAATTTTAAAAAGCCC 59.140 33.333 4.44 0.00 0.00 5.19
1766 1823 2.364972 AAAAAGCCCGCTATAGCCAT 57.635 45.000 19.00 0.00 37.91 4.40
1768 1825 0.764890 AAAGCCCGCTATAGCCATGA 59.235 50.000 19.00 0.00 37.91 3.07
1776 1833 5.292765 CCCGCTATAGCCATGATATAACAG 58.707 45.833 19.00 0.11 37.91 3.16
1805 1862 0.170339 GGTGCCGCTAAATGGTGTTC 59.830 55.000 0.00 0.00 0.00 3.18
1858 1916 9.878599 AATAACAAACTATATCGCTATTGTTGC 57.121 29.630 10.87 0.00 40.18 4.17
1874 1932 0.867746 TTGCGCTGTAGCTGTTTGAG 59.132 50.000 9.73 0.00 39.32 3.02
1900 1958 1.064758 TGTCGCTATTTGGAATGGCCT 60.065 47.619 3.32 0.00 37.63 5.19
1903 1961 1.113788 GCTATTTGGAATGGCCTGCA 58.886 50.000 3.32 0.00 37.63 4.41
1908 1966 0.680618 TTGGAATGGCCTGCAGTTTG 59.319 50.000 13.81 0.00 37.63 2.93
1914 1972 2.356665 TGGCCTGCAGTTTGAAACTA 57.643 45.000 10.63 0.00 40.46 2.24
1915 1973 2.875296 TGGCCTGCAGTTTGAAACTAT 58.125 42.857 10.63 0.00 40.46 2.12
1916 1974 3.230134 TGGCCTGCAGTTTGAAACTATT 58.770 40.909 10.63 0.00 40.46 1.73
1917 1975 3.640967 TGGCCTGCAGTTTGAAACTATTT 59.359 39.130 10.63 0.00 40.46 1.40
1918 1976 4.100808 TGGCCTGCAGTTTGAAACTATTTT 59.899 37.500 10.63 0.00 40.46 1.82
1919 1977 4.448732 GGCCTGCAGTTTGAAACTATTTTG 59.551 41.667 10.63 0.05 40.46 2.44
1920 1978 5.288804 GCCTGCAGTTTGAAACTATTTTGA 58.711 37.500 10.63 0.00 40.46 2.69
1921 1979 5.175673 GCCTGCAGTTTGAAACTATTTTGAC 59.824 40.000 10.63 0.00 40.46 3.18
1922 1980 5.399301 CCTGCAGTTTGAAACTATTTTGACG 59.601 40.000 10.63 0.00 40.46 4.35
1947 2005 7.465111 CGAATGGATGTTGAACTCTCATTACAG 60.465 40.741 0.00 0.00 28.33 2.74
1948 2006 6.114187 TGGATGTTGAACTCTCATTACAGT 57.886 37.500 0.00 0.00 28.33 3.55
1949 2007 6.166279 TGGATGTTGAACTCTCATTACAGTC 58.834 40.000 0.00 0.00 28.33 3.51
1965 2023 9.534565 TCATTACAGTCTTAAGAAGTATGCATC 57.465 33.333 6.78 0.00 0.00 3.91
1972 2030 7.448777 AGTCTTAAGAAGTATGCATCGGAGATA 59.551 37.037 6.78 0.00 45.12 1.98
2008 2066 8.461222 TGCGAAAGATGAACTATTTTCAATGAT 58.539 29.630 0.00 0.00 31.56 2.45
2058 2117 4.404715 AGGCAGATCCATTTTGAAATCAGG 59.595 41.667 0.00 0.00 37.29 3.86
2061 2120 6.168389 GCAGATCCATTTTGAAATCAGGTTT 58.832 36.000 0.00 0.00 0.00 3.27
2064 2123 5.482163 TCCATTTTGAAATCAGGTTTCCC 57.518 39.130 3.59 0.00 44.53 3.97
2079 2142 5.830457 CAGGTTTCCCTTTTCTTCTCTCTTT 59.170 40.000 0.00 0.00 39.89 2.52
2094 2157 9.449719 TCTTCTCTCTTTTTAAAACTGACTTGT 57.550 29.630 0.00 0.00 0.00 3.16
2127 2190 3.133721 TGCTTGGTTTTACTTGGCAATGT 59.866 39.130 0.00 3.98 0.00 2.71
2157 2220 7.733402 AAACAATAATACTACGTGGTTGTGT 57.267 32.000 10.71 0.00 0.00 3.72
2158 2221 6.715344 ACAATAATACTACGTGGTTGTGTG 57.285 37.500 10.71 5.48 0.00 3.82
2204 2276 3.388350 GGTTGACCCTCCTTCTCGATAAT 59.612 47.826 0.00 0.00 0.00 1.28
2209 2281 5.839063 TGACCCTCCTTCTCGATAATAATGT 59.161 40.000 0.00 0.00 0.00 2.71
2214 2286 6.483307 CCTCCTTCTCGATAATAATGTGCAAA 59.517 38.462 0.00 0.00 0.00 3.68
2247 2319 4.142816 GCAATAGTTATGCTCAATAGGGCG 60.143 45.833 0.00 0.00 40.64 6.13
2313 2385 6.677781 TTTAGGTGATAGAAATTTCCTGCG 57.322 37.500 14.61 0.00 0.00 5.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.506114 ACCTTGTTGTAATAGACAGTTGAGAA 58.494 34.615 0.00 0.00 39.88 2.87
1 2 7.062749 ACCTTGTTGTAATAGACAGTTGAGA 57.937 36.000 0.00 0.00 39.88 3.27
2 3 7.730364 AACCTTGTTGTAATAGACAGTTGAG 57.270 36.000 0.00 0.00 39.88 3.02
3 4 7.468084 GCAAACCTTGTTGTAATAGACAGTTGA 60.468 37.037 0.00 0.00 39.88 3.18
4 5 6.636850 GCAAACCTTGTTGTAATAGACAGTTG 59.363 38.462 0.00 0.00 39.88 3.16
5 6 6.238925 GGCAAACCTTGTTGTAATAGACAGTT 60.239 38.462 0.00 0.00 39.88 3.16
14 15 0.386113 GCCGGCAAACCTTGTTGTAA 59.614 50.000 24.80 0.00 0.00 2.41
17 18 0.597377 GAAGCCGGCAAACCTTGTTG 60.597 55.000 31.54 0.00 0.00 3.33
30 32 4.148825 CCTCCCTCACCGAAGCCG 62.149 72.222 0.00 0.00 0.00 5.52
36 38 2.442272 ATCGTCCCTCCCTCACCG 60.442 66.667 0.00 0.00 0.00 4.94
96 98 5.668471 TCTATATCCGTAGACCACCTATCG 58.332 45.833 0.00 0.00 0.00 2.92
98 100 6.971340 ACATCTATATCCGTAGACCACCTAT 58.029 40.000 0.00 0.00 33.78 2.57
128 130 9.939802 AGGTAAAAAGAACACCATAAGTAGTAG 57.060 33.333 0.00 0.00 34.62 2.57
131 133 9.893305 CAAAGGTAAAAAGAACACCATAAGTAG 57.107 33.333 0.00 0.00 34.62 2.57
137 139 8.147704 CCATTACAAAGGTAAAAAGAACACCAT 58.852 33.333 0.00 0.00 42.43 3.55
139 141 7.494211 ACCATTACAAAGGTAAAAAGAACACC 58.506 34.615 0.00 0.00 42.43 4.16
149 151 9.967451 TCTATTCATCAACCATTACAAAGGTAA 57.033 29.630 0.00 0.00 43.25 2.85
154 156 9.513906 TTCACTCTATTCATCAACCATTACAAA 57.486 29.630 0.00 0.00 0.00 2.83
156 158 9.166173 CTTTCACTCTATTCATCAACCATTACA 57.834 33.333 0.00 0.00 0.00 2.41
163 165 7.862372 TGCAAAACTTTCACTCTATTCATCAAC 59.138 33.333 0.00 0.00 0.00 3.18
177 179 5.907197 TTTTTGTCGTTGCAAAACTTTCA 57.093 30.435 0.00 0.00 44.77 2.69
201 203 5.368145 ACCCATTTTGCTTCTTCTTTTTCC 58.632 37.500 0.00 0.00 0.00 3.13
204 206 5.125356 CCAACCCATTTTGCTTCTTCTTTT 58.875 37.500 0.00 0.00 0.00 2.27
205 207 4.444733 CCCAACCCATTTTGCTTCTTCTTT 60.445 41.667 0.00 0.00 0.00 2.52
207 209 2.634453 CCCAACCCATTTTGCTTCTTCT 59.366 45.455 0.00 0.00 0.00 2.85
208 210 2.368548 ACCCAACCCATTTTGCTTCTTC 59.631 45.455 0.00 0.00 0.00 2.87
209 211 2.104622 CACCCAACCCATTTTGCTTCTT 59.895 45.455 0.00 0.00 0.00 2.52
210 212 1.693606 CACCCAACCCATTTTGCTTCT 59.306 47.619 0.00 0.00 0.00 2.85
211 213 1.691434 TCACCCAACCCATTTTGCTTC 59.309 47.619 0.00 0.00 0.00 3.86
263 265 0.459585 GCTCGCTATCGTGTTCCCAA 60.460 55.000 0.00 0.00 36.96 4.12
280 282 1.594293 CACCGACCAAACACTCGCT 60.594 57.895 0.00 0.00 0.00 4.93
390 392 4.201783 GCCTTTTAATGTAAGCGTGATCGT 60.202 41.667 0.00 0.00 39.49 3.73
477 480 5.601662 TCCATGTCGAATATCTGGACTTTC 58.398 41.667 0.00 0.00 31.19 2.62
484 487 3.643159 TCCGTCCATGTCGAATATCTG 57.357 47.619 8.71 0.00 0.00 2.90
488 491 3.446161 ACTTCTTCCGTCCATGTCGAATA 59.554 43.478 8.71 0.00 0.00 1.75
509 512 2.504244 CGGCTCTGACGTTCCGAC 60.504 66.667 7.92 0.00 44.23 4.79
535 538 4.164204 GGCAGAGGAGGGAATAGAATAGT 58.836 47.826 0.00 0.00 0.00 2.12
582 585 2.775856 GCGGACTCGAGAGGATGCA 61.776 63.158 21.68 0.00 39.00 3.96
603 606 2.503375 CGTAGCGTCACCGACCAC 60.503 66.667 0.00 0.00 35.63 4.16
719 730 4.468643 CTGACCTAGCGAATAACGAGATC 58.531 47.826 0.00 0.00 45.77 2.75
791 802 7.989416 TCGGTTTATACATTATTCCCCAATC 57.011 36.000 0.00 0.00 0.00 2.67
805 816 9.944663 TTCTAATGCATTCATTTCGGTTTATAC 57.055 29.630 16.86 0.00 42.51 1.47
811 822 8.450578 TCTATTTCTAATGCATTCATTTCGGT 57.549 30.769 16.86 0.00 42.51 4.69
828 839 6.260936 CCCGCATGTGAATTACTTCTATTTCT 59.739 38.462 8.11 0.00 32.29 2.52
883 894 1.167851 ATATATGTGCACGCATGGCC 58.832 50.000 13.13 0.00 0.00 5.36
934 948 5.220796 CGAGCTGTGTATGCAACTAGTACTA 60.221 44.000 1.89 1.89 0.00 1.82
935 949 4.438880 CGAGCTGTGTATGCAACTAGTACT 60.439 45.833 0.00 0.00 0.00 2.73
936 950 3.791887 CGAGCTGTGTATGCAACTAGTAC 59.208 47.826 0.00 0.00 0.00 2.73
937 951 3.692593 TCGAGCTGTGTATGCAACTAGTA 59.307 43.478 0.00 0.00 0.00 1.82
938 952 2.492088 TCGAGCTGTGTATGCAACTAGT 59.508 45.455 0.00 0.00 0.00 2.57
939 953 3.150848 TCGAGCTGTGTATGCAACTAG 57.849 47.619 0.00 0.00 0.00 2.57
991 1005 0.039437 CCGTTCTCCATATCGACGGG 60.039 60.000 5.39 0.00 46.93 5.28
1065 1081 1.156736 GGTGTGTTCTTCGACATGGG 58.843 55.000 0.00 0.00 0.00 4.00
1094 1112 4.166187 TCATTGACGACTCACTGAAGAG 57.834 45.455 0.00 0.00 34.15 2.85
1107 1125 7.066163 AGAGCTGAGATAGATAGATCATTGACG 59.934 40.741 0.00 0.00 29.71 4.35
1147 1169 4.185467 AGCCTATGTAGCAATCGATCAG 57.815 45.455 0.00 0.00 0.00 2.90
1153 1175 2.561419 TCGGGTAGCCTATGTAGCAATC 59.439 50.000 9.73 0.00 0.00 2.67
1160 1182 3.851955 CCGTCGGGTAGCCTATGT 58.148 61.111 9.73 0.00 0.00 2.29
1381 1403 3.552890 GGCAAGGCTGAAGAAAACGAATT 60.553 43.478 0.00 0.00 0.00 2.17
1467 1489 0.107214 ATCTGTAACCGTGGGCATGG 60.107 55.000 0.00 0.00 43.15 3.66
1550 1580 7.116376 CACAAATGACGTAGAACATCTAACAGT 59.884 37.037 0.00 0.00 29.58 3.55
1611 1652 3.421844 ACAAAAGATACAGGGCCTTGAC 58.578 45.455 23.57 12.05 0.00 3.18
1659 1708 5.624491 GCAAGACGACCTCGAATATAAGTAC 59.376 44.000 0.78 0.00 43.02 2.73
1684 1733 5.047092 ACATCAAAAGCTGGGATTCGAAATT 60.047 36.000 0.00 0.00 0.00 1.82
1689 1738 2.733227 GCACATCAAAAGCTGGGATTCG 60.733 50.000 0.00 0.00 0.00 3.34
1692 1741 1.927487 TGCACATCAAAAGCTGGGAT 58.073 45.000 0.00 0.00 0.00 3.85
1727 1784 7.585936 GCTTTTTAAAATTTTGTTCATCACCCG 59.414 33.333 13.76 0.00 0.00 5.28
1732 1789 6.577055 GCGGGCTTTTTAAAATTTTGTTCATC 59.423 34.615 13.76 0.00 0.00 2.92
1734 1791 5.586643 AGCGGGCTTTTTAAAATTTTGTTCA 59.413 32.000 13.76 0.00 0.00 3.18
1742 1799 4.647399 TGGCTATAGCGGGCTTTTTAAAAT 59.353 37.500 18.30 0.00 43.26 1.82
1750 1807 0.987294 ATCATGGCTATAGCGGGCTT 59.013 50.000 18.30 0.75 43.26 4.35
1753 1810 5.163405 ACTGTTATATCATGGCTATAGCGGG 60.163 44.000 18.30 10.15 43.26 6.13
1755 1812 7.545615 TCAAACTGTTATATCATGGCTATAGCG 59.454 37.037 18.30 5.25 43.26 4.26
1766 1823 5.359576 GCACCCCAATCAAACTGTTATATCA 59.640 40.000 0.00 0.00 0.00 2.15
1768 1825 4.649218 GGCACCCCAATCAAACTGTTATAT 59.351 41.667 0.00 0.00 0.00 0.86
1776 1833 0.963355 TAGCGGCACCCCAATCAAAC 60.963 55.000 1.45 0.00 0.00 2.93
1784 1841 2.044352 ACCATTTAGCGGCACCCC 60.044 61.111 1.45 0.00 0.00 4.95
1855 1913 3.058870 GCTCAAACAGCTACAGCGCAA 62.059 52.381 11.47 0.00 45.83 4.85
1874 1932 1.953559 TCCAAATAGCGACATCCTGC 58.046 50.000 0.00 0.00 0.00 4.85
1875 1933 3.251729 CCATTCCAAATAGCGACATCCTG 59.748 47.826 0.00 0.00 0.00 3.86
1876 1934 3.480470 CCATTCCAAATAGCGACATCCT 58.520 45.455 0.00 0.00 0.00 3.24
1877 1935 2.030805 GCCATTCCAAATAGCGACATCC 60.031 50.000 0.00 0.00 0.00 3.51
1900 1958 6.125327 TCGTCAAAATAGTTTCAAACTGCA 57.875 33.333 13.39 0.00 42.84 4.41
1903 1961 7.936584 TCCATTCGTCAAAATAGTTTCAAACT 58.063 30.769 8.15 8.15 45.40 2.66
1908 1966 8.020819 TCAACATCCATTCGTCAAAATAGTTTC 58.979 33.333 0.00 0.00 0.00 2.78
1914 1972 6.207417 AGAGTTCAACATCCATTCGTCAAAAT 59.793 34.615 0.00 0.00 0.00 1.82
1915 1973 5.530915 AGAGTTCAACATCCATTCGTCAAAA 59.469 36.000 0.00 0.00 0.00 2.44
1916 1974 5.063204 AGAGTTCAACATCCATTCGTCAAA 58.937 37.500 0.00 0.00 0.00 2.69
1917 1975 4.641396 AGAGTTCAACATCCATTCGTCAA 58.359 39.130 0.00 0.00 0.00 3.18
1918 1976 4.245660 GAGAGTTCAACATCCATTCGTCA 58.754 43.478 0.00 0.00 0.00 4.35
1919 1977 4.245660 TGAGAGTTCAACATCCATTCGTC 58.754 43.478 0.00 0.00 0.00 4.20
1920 1978 4.271696 TGAGAGTTCAACATCCATTCGT 57.728 40.909 0.00 0.00 0.00 3.85
1921 1979 5.808042 AATGAGAGTTCAACATCCATTCG 57.192 39.130 0.00 0.00 36.78 3.34
1922 1980 7.335422 ACTGTAATGAGAGTTCAACATCCATTC 59.665 37.037 5.06 0.96 36.78 2.67
1947 2005 5.833082 TCTCCGATGCATACTTCTTAAGAC 58.167 41.667 4.18 0.00 0.00 3.01
1948 2006 6.656632 ATCTCCGATGCATACTTCTTAAGA 57.343 37.500 0.00 0.00 0.00 2.10
1949 2007 7.821652 TCTATCTCCGATGCATACTTCTTAAG 58.178 38.462 0.00 0.00 0.00 1.85
1965 2023 5.657470 TTCGCATGAAATTTCTATCTCCG 57.343 39.130 18.64 12.02 0.00 4.63
1972 2030 6.917533 AGTTCATCTTTCGCATGAAATTTCT 58.082 32.000 18.64 2.40 42.90 2.52
2008 2066 8.616942 CACGGGTGAATTTGTAATGTTGATATA 58.383 33.333 0.00 0.00 0.00 0.86
2011 2069 5.475220 TCACGGGTGAATTTGTAATGTTGAT 59.525 36.000 0.00 0.00 36.53 2.57
2026 2084 2.359169 GGATCTGCCTCACGGGTGA 61.359 63.158 1.05 1.05 38.06 4.02
2031 2089 2.358957 TCAAAATGGATCTGCCTCACG 58.641 47.619 0.00 0.00 37.63 4.35
2061 2120 9.475620 AGTTTTAAAAAGAGAGAAGAAAAGGGA 57.524 29.630 1.31 0.00 0.00 4.20
2079 2142 6.045955 GGATGCCAAACAAGTCAGTTTTAAA 58.954 36.000 0.00 0.00 39.55 1.52
2112 2175 8.948631 TGTTTATTCAACATTGCCAAGTAAAA 57.051 26.923 0.00 0.00 40.71 1.52
2144 2207 2.448926 TGATCCACACAACCACGTAG 57.551 50.000 0.00 0.00 0.00 3.51
2145 2208 2.912690 TTGATCCACACAACCACGTA 57.087 45.000 0.00 0.00 0.00 3.57
2146 2209 1.879380 CATTGATCCACACAACCACGT 59.121 47.619 0.00 0.00 0.00 4.49
2147 2210 1.199789 CCATTGATCCACACAACCACG 59.800 52.381 0.00 0.00 0.00 4.94
2157 2220 1.758280 GCCTTTGCATCCATTGATCCA 59.242 47.619 0.00 0.00 37.47 3.41
2158 2221 1.069668 GGCCTTTGCATCCATTGATCC 59.930 52.381 0.00 0.00 40.13 3.36
2227 2299 4.618460 CGTCGCCCTATTGAGCATAACTAT 60.618 45.833 0.00 0.00 0.00 2.12
2232 2304 0.317160 CCGTCGCCCTATTGAGCATA 59.683 55.000 0.00 0.00 0.00 3.14
2240 2312 1.544825 CCATCCATCCGTCGCCCTAT 61.545 60.000 0.00 0.00 0.00 2.57
2247 2319 1.482593 AGAGTTCACCATCCATCCGTC 59.517 52.381 0.00 0.00 0.00 4.79


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

AutoCloner maintained by Alex Coulton.