Multiple sequence alignment - TraesCS6A01G409500

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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 TraesCS6A01G409500 chr6A 100.000 2246 0 0 1 2246 613357360 613355115 0.000000e+00 4148.0
1 TraesCS6A01G409500 chr6D 87.273 935 65 30 1265 2186 467091683 467090790 0.000000e+00 1018.0
2 TraesCS6A01G409500 chr6D 85.010 507 60 10 222 717 467092986 467092485 3.330000e-138 501.0
3 TraesCS6A01G409500 chr6D 87.955 357 15 9 841 1186 467092358 467092019 1.620000e-106 396.0
4 TraesCS6A01G409500 chr6D 94.083 169 8 2 55 223 467093122 467092956 2.860000e-64 255.0
5 TraesCS6A01G409500 chr6D 100.000 39 0 0 1 39 467093145 467093107 3.090000e-09 73.1
6 TraesCS6A01G409500 chr6B 86.250 960 50 30 823 1744 712269085 712268170 0.000000e+00 966.0
7 TraesCS6A01G409500 chr6B 83.857 446 45 14 1803 2246 712267865 712267445 1.250000e-107 399.0
8 TraesCS6A01G409500 chr6B 80.556 396 59 14 222 604 712269862 712269472 2.820000e-74 289.0
9 TraesCS6A01G409500 chr6B 87.179 195 11 6 55 236 712270006 712269813 2.260000e-50 209.0
10 TraesCS6A01G409500 chr6B 100.000 39 0 0 1 39 712270029 712269991 3.090000e-09 73.1
11 TraesCS6A01G409500 chr5D 80.563 710 70 33 1014 1713 398001054 398001705 3.350000e-133 484.0
12 TraesCS6A01G409500 chr4A 84.980 253 19 7 1462 1713 683941314 683941548 2.880000e-59 239.0
13 TraesCS6A01G409500 chr3B 84.980 253 19 7 1462 1713 754276957 754277191 2.880000e-59 239.0
14 TraesCS6A01G409500 chr3B 84.190 253 21 9 1462 1713 742415435 742415201 6.240000e-56 228.0
15 TraesCS6A01G409500 chr7B 87.054 224 11 7 1462 1683 640061312 640061519 1.040000e-58 237.0
16 TraesCS6A01G409500 chr2A 84.646 254 18 8 1462 1713 546306977 546306743 1.340000e-57 233.0
17 TraesCS6A01G409500 chr1A 84.064 251 21 7 1464 1713 504761066 504761298 8.070000e-55 224.0


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 TraesCS6A01G409500 chr6A 613355115 613357360 2245 True 4148.00 4148 100.0000 1 2246 1 chr6A.!!$R1 2245
1 TraesCS6A01G409500 chr6D 467090790 467093145 2355 True 448.62 1018 90.8642 1 2186 5 chr6D.!!$R1 2185
2 TraesCS6A01G409500 chr6B 712267445 712270029 2584 True 387.22 966 87.5684 1 2246 5 chr6B.!!$R1 2245
3 TraesCS6A01G409500 chr5D 398001054 398001705 651 False 484.00 484 80.5630 1014 1713 1 chr5D.!!$F1 699

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
703 779 0.454285 CACATTAAAGCCGTGTGCCG 60.454 55.0 0.0 0.0 42.71 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2135 2942 0.036105 AGAGCCGCACAATGTCATCA 60.036 50.0 0.0 0.0 0.0 3.07 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
39 40 5.188751 TGTTTCTGAATTTGGGTGGAAACTT 59.811 36.000 14.45 0.00 41.39 2.66
40 41 5.529581 TTCTGAATTTGGGTGGAAACTTC 57.470 39.130 0.00 0.00 0.00 3.01
41 42 4.803452 TCTGAATTTGGGTGGAAACTTCT 58.197 39.130 0.00 0.00 0.00 2.85
42 43 5.208121 TCTGAATTTGGGTGGAAACTTCTT 58.792 37.500 0.00 0.00 0.00 2.52
43 44 5.660864 TCTGAATTTGGGTGGAAACTTCTTT 59.339 36.000 0.00 0.00 0.00 2.52
44 45 6.156083 TCTGAATTTGGGTGGAAACTTCTTTT 59.844 34.615 0.00 0.00 0.00 2.27
45 46 6.716284 TGAATTTGGGTGGAAACTTCTTTTT 58.284 32.000 0.00 0.00 0.00 1.94
65 66 5.683876 TTTTTGAGACAAATTTGGGTGGA 57.316 34.783 21.74 2.82 0.00 4.02
66 67 5.683876 TTTTGAGACAAATTTGGGTGGAA 57.316 34.783 21.74 8.43 0.00 3.53
67 68 5.683876 TTTGAGACAAATTTGGGTGGAAA 57.316 34.783 21.74 10.73 0.00 3.13
68 69 4.664150 TGAGACAAATTTGGGTGGAAAC 57.336 40.909 21.74 5.55 0.00 2.78
69 70 4.285863 TGAGACAAATTTGGGTGGAAACT 58.714 39.130 21.74 7.79 0.00 2.66
133 142 2.622011 TTTAGCTGGGCCGCAAACG 61.622 57.895 19.61 0.00 39.67 3.60
149 158 2.203209 CGGGCTTGTAGATGGGCC 60.203 66.667 0.00 0.00 43.42 5.80
178 187 0.458889 CCAACATGCCTGAATTGCCG 60.459 55.000 0.00 0.00 0.00 5.69
200 209 4.744631 CGCAAATTCAACCAGCTTAACTTT 59.255 37.500 0.00 0.00 0.00 2.66
201 210 5.918011 CGCAAATTCAACCAGCTTAACTTTA 59.082 36.000 0.00 0.00 0.00 1.85
202 211 6.586082 CGCAAATTCAACCAGCTTAACTTTAT 59.414 34.615 0.00 0.00 0.00 1.40
203 212 7.410728 CGCAAATTCAACCAGCTTAACTTTATG 60.411 37.037 0.00 0.00 0.00 1.90
204 213 7.148590 GCAAATTCAACCAGCTTAACTTTATGG 60.149 37.037 0.00 0.00 37.07 2.74
205 214 7.775053 AATTCAACCAGCTTAACTTTATGGA 57.225 32.000 0.00 0.00 34.99 3.41
206 215 6.569179 TTCAACCAGCTTAACTTTATGGAC 57.431 37.500 0.00 0.00 34.99 4.02
207 216 5.876357 TCAACCAGCTTAACTTTATGGACT 58.124 37.500 0.00 0.00 34.99 3.85
208 217 7.011499 TCAACCAGCTTAACTTTATGGACTA 57.989 36.000 0.00 0.00 34.99 2.59
209 218 7.630082 TCAACCAGCTTAACTTTATGGACTAT 58.370 34.615 0.00 0.00 34.99 2.12
210 219 8.107095 TCAACCAGCTTAACTTTATGGACTATT 58.893 33.333 0.00 0.00 34.99 1.73
211 220 7.865706 ACCAGCTTAACTTTATGGACTATTG 57.134 36.000 0.00 0.00 34.99 1.90
212 221 7.402862 ACCAGCTTAACTTTATGGACTATTGT 58.597 34.615 0.00 0.00 34.99 2.71
213 222 7.553044 ACCAGCTTAACTTTATGGACTATTGTC 59.447 37.037 0.00 0.00 42.22 3.18
214 223 7.770897 CCAGCTTAACTTTATGGACTATTGTCT 59.229 37.037 7.24 0.00 42.54 3.41
215 224 9.817809 CAGCTTAACTTTATGGACTATTGTCTA 57.182 33.333 7.24 1.35 42.54 2.59
245 254 9.569122 AAAGCTTAACTTATGGACTGTTTCTTA 57.431 29.630 0.00 0.00 37.75 2.10
246 255 9.740710 AAGCTTAACTTATGGACTGTTTCTTAT 57.259 29.630 0.00 0.00 36.62 1.73
278 287 8.585189 AAAAGTTTAACTTACTGGAGTACTCG 57.415 34.615 16.56 6.52 37.47 4.18
282 291 6.899393 TTAACTTACTGGAGTACTCGGAAA 57.101 37.500 16.56 7.44 0.00 3.13
288 297 4.282496 ACTGGAGTACTCGGAAATCAGAT 58.718 43.478 23.21 10.57 0.00 2.90
291 301 6.551601 ACTGGAGTACTCGGAAATCAGATAAT 59.448 38.462 23.21 5.88 0.00 1.28
292 302 6.749139 TGGAGTACTCGGAAATCAGATAATG 58.251 40.000 16.56 0.00 0.00 1.90
297 307 2.711009 TCGGAAATCAGATAATGCCCCT 59.289 45.455 0.00 0.00 0.00 4.79
298 308 3.907474 TCGGAAATCAGATAATGCCCCTA 59.093 43.478 0.00 0.00 0.00 3.53
299 309 4.536090 TCGGAAATCAGATAATGCCCCTAT 59.464 41.667 0.00 0.00 0.00 2.57
300 310 4.637534 CGGAAATCAGATAATGCCCCTATG 59.362 45.833 0.00 0.00 0.00 2.23
301 311 4.400567 GGAAATCAGATAATGCCCCTATGC 59.599 45.833 0.00 0.00 0.00 3.14
302 312 3.659183 ATCAGATAATGCCCCTATGCC 57.341 47.619 0.00 0.00 0.00 4.40
303 313 1.635487 TCAGATAATGCCCCTATGCCC 59.365 52.381 0.00 0.00 0.00 5.36
335 345 5.725551 ATTTAGACATCCCCATACACCAA 57.274 39.130 0.00 0.00 0.00 3.67
354 368 2.749076 CAAACATTTGGAGCCATCTCGA 59.251 45.455 0.00 0.00 40.26 4.04
364 378 2.728839 GAGCCATCTCGAAAGCTATTCG 59.271 50.000 18.78 18.78 42.74 3.34
391 411 2.028925 CTTGCAAAACCCCCACGC 59.971 61.111 0.00 0.00 0.00 5.34
396 416 2.840572 AAAACCCCCACGCCCAAC 60.841 61.111 0.00 0.00 0.00 3.77
451 478 4.736896 GGTCGCCGCCGAAGACTT 62.737 66.667 10.66 0.00 46.34 3.01
452 479 2.180017 GTCGCCGCCGAAGACTTA 59.820 61.111 0.00 0.00 46.34 2.24
455 482 1.026182 TCGCCGCCGAAGACTTAGTA 61.026 55.000 0.00 0.00 41.17 1.82
488 515 1.217882 ACTTTCTCTTCAACCGTGCG 58.782 50.000 0.00 0.00 0.00 5.34
629 674 1.172812 GGTGCGAGGTTTTTGCTCCT 61.173 55.000 0.00 0.00 43.58 3.69
637 682 4.659115 GAGGTTTTTGCTCCTAAAGGGTA 58.341 43.478 0.00 0.00 33.83 3.69
653 698 1.202891 GGGTAAGGCACAACTGTCCTT 60.203 52.381 14.13 14.13 38.33 3.36
659 704 1.604278 GGCACAACTGTCCTTCACTTC 59.396 52.381 0.00 0.00 0.00 3.01
665 710 1.891060 CTGTCCTTCACTTCACGCGC 61.891 60.000 5.73 0.00 0.00 6.86
675 720 1.413767 CTTCACGCGCGCTCTAATGT 61.414 55.000 32.58 15.70 0.00 2.71
703 779 0.454285 CACATTAAAGCCGTGTGCCG 60.454 55.000 0.00 0.00 42.71 5.69
718 794 2.032071 CCGAACCACACACCCTCC 59.968 66.667 0.00 0.00 0.00 4.30
784 968 5.760253 GGTTAGTATGGTCTTCATGGATGTG 59.240 44.000 0.00 0.00 37.30 3.21
793 977 6.119536 GGTCTTCATGGATGTGTATTTGGTA 58.880 40.000 0.00 0.00 0.00 3.25
797 981 5.444176 TCATGGATGTGTATTTGGTATGCA 58.556 37.500 0.00 0.00 0.00 3.96
798 982 5.532032 TCATGGATGTGTATTTGGTATGCAG 59.468 40.000 0.00 0.00 0.00 4.41
815 999 7.446931 TGGTATGCAGTTAATGTGAGAAAAGAA 59.553 33.333 0.00 0.00 0.00 2.52
817 1001 6.072112 TGCAGTTAATGTGAGAAAAGAACC 57.928 37.500 0.00 0.00 0.00 3.62
818 1002 5.827797 TGCAGTTAATGTGAGAAAAGAACCT 59.172 36.000 0.00 0.00 0.00 3.50
819 1003 6.017109 TGCAGTTAATGTGAGAAAAGAACCTC 60.017 38.462 0.00 0.00 0.00 3.85
820 1004 6.205658 GCAGTTAATGTGAGAAAAGAACCTCT 59.794 38.462 0.00 0.00 0.00 3.69
824 1031 8.621286 GTTAATGTGAGAAAAGAACCTCTGAAA 58.379 33.333 0.00 0.00 0.00 2.69
827 1034 7.088589 TGTGAGAAAAGAACCTCTGAAAAAG 57.911 36.000 0.00 0.00 0.00 2.27
886 1099 2.032860 ATCCCGTGGATCTCGCCAAG 62.033 60.000 0.05 0.00 38.09 3.61
1116 1350 1.059058 CGACGACGACGAGGAAGAG 59.941 63.158 15.32 0.00 42.66 2.85
1119 1353 2.490685 GACGACGAGGAAGAGGCC 59.509 66.667 0.00 0.00 0.00 5.19
1126 1360 1.079057 GAGGAAGAGGCCAACGACC 60.079 63.158 5.01 7.81 0.00 4.79
1127 1361 2.434359 GGAAGAGGCCAACGACCG 60.434 66.667 5.01 0.00 0.00 4.79
1129 1363 4.699522 AAGAGGCCAACGACCGCC 62.700 66.667 5.01 0.00 46.09 6.13
1258 1498 4.316823 TGTGACCCGCTCCCTCCT 62.317 66.667 0.00 0.00 0.00 3.69
1280 1777 1.591594 ATCCATCGCTTGCGTACGG 60.592 57.895 18.39 12.88 0.00 4.02
1322 1830 3.411446 CGTCCTCTGCTCTAGATCTGAT 58.589 50.000 5.18 0.00 34.21 2.90
1323 1831 3.189080 CGTCCTCTGCTCTAGATCTGATG 59.811 52.174 5.18 2.44 34.21 3.07
1324 1832 4.397420 GTCCTCTGCTCTAGATCTGATGA 58.603 47.826 5.18 4.50 34.21 2.92
1384 1902 1.966762 CCGATTTTGTTGCTGGCCT 59.033 52.632 3.32 0.00 0.00 5.19
1513 2046 2.159747 GCCGTCGTGTGGTAATTTCTTC 60.160 50.000 0.00 0.00 0.00 2.87
1533 2066 0.028902 CGTAGCGGATCGATGTGTCA 59.971 55.000 0.54 0.00 0.00 3.58
1541 2074 3.583806 GGATCGATGTGTCAGATGGATC 58.416 50.000 20.31 20.31 35.45 3.36
1586 2122 0.961019 GTTGAATTGCTGCCCTGTGA 59.039 50.000 0.00 0.00 0.00 3.58
1587 2123 1.340889 GTTGAATTGCTGCCCTGTGAA 59.659 47.619 0.00 0.00 0.00 3.18
1588 2124 1.927487 TGAATTGCTGCCCTGTGAAT 58.073 45.000 0.00 0.00 0.00 2.57
1589 2125 1.546923 TGAATTGCTGCCCTGTGAATG 59.453 47.619 0.00 0.00 0.00 2.67
1590 2126 1.820519 GAATTGCTGCCCTGTGAATGA 59.179 47.619 0.00 0.00 0.00 2.57
1633 2173 0.163788 CGGATCGATTTGCGGCATAC 59.836 55.000 2.28 0.00 41.33 2.39
1695 2235 6.344500 CCACAGCATATAATAGATCCCTGAC 58.656 44.000 0.00 0.00 0.00 3.51
1740 2280 5.851720 TGCTTGCAAATGGTTTCTTTGATA 58.148 33.333 0.00 0.00 35.99 2.15
1744 2284 8.291740 GCTTGCAAATGGTTTCTTTGATATTTT 58.708 29.630 0.00 0.00 35.99 1.82
1762 2302 8.239314 TGATATTTTTCTCACAAGTCTTGATGC 58.761 33.333 19.53 0.00 0.00 3.91
1763 2303 4.836125 TTTTCTCACAAGTCTTGATGCC 57.164 40.909 19.53 0.00 0.00 4.40
1764 2304 3.777106 TTCTCACAAGTCTTGATGCCT 57.223 42.857 19.53 0.00 0.00 4.75
1770 2310 2.037772 ACAAGTCTTGATGCCTCGTCTT 59.962 45.455 19.53 0.00 0.00 3.01
1810 2606 4.908601 TGGATGGATTGTGTCAGTTAGT 57.091 40.909 0.00 0.00 0.00 2.24
1811 2607 4.578871 TGGATGGATTGTGTCAGTTAGTG 58.421 43.478 0.00 0.00 0.00 2.74
1822 2618 8.896320 TTGTGTCAGTTAGTGTATTGTTGTAT 57.104 30.769 0.00 0.00 0.00 2.29
1837 2633 3.752747 TGTTGTATGCCATCAGTTCTGTG 59.247 43.478 0.00 0.00 0.00 3.66
1857 2653 1.344458 GCTGTGTGACTGTCGAGATG 58.656 55.000 2.98 0.00 0.00 2.90
1898 2694 5.300034 TGATTGGGCTAAGCTTGTTCATATG 59.700 40.000 9.86 0.00 0.00 1.78
1921 2717 2.562738 GCAATTGGTAGGGTTTTGCTCT 59.437 45.455 7.72 0.00 39.56 4.09
1958 2754 0.672401 TGCCAAAGATCCGTTCGACC 60.672 55.000 0.00 0.00 0.00 4.79
1969 2765 2.357034 TTCGACCGTGCTTGCCTC 60.357 61.111 0.00 0.00 0.00 4.70
1970 2767 3.158537 TTCGACCGTGCTTGCCTCA 62.159 57.895 0.00 0.00 0.00 3.86
2040 2847 3.673746 ATATGTCGTGTGAAATTGCCG 57.326 42.857 0.00 0.00 0.00 5.69
2042 2849 1.018148 TGTCGTGTGAAATTGCCGTT 58.982 45.000 0.00 0.00 0.00 4.44
2043 2850 1.402259 TGTCGTGTGAAATTGCCGTTT 59.598 42.857 0.00 0.00 0.00 3.60
2070 2877 4.801330 TTGATGTCCTGTGATTCTACGT 57.199 40.909 0.00 0.00 0.00 3.57
2076 2883 1.402325 CCTGTGATTCTACGTCGTGCA 60.402 52.381 8.47 0.00 0.00 4.57
2077 2884 1.914051 CTGTGATTCTACGTCGTGCAG 59.086 52.381 8.47 0.00 0.00 4.41
2078 2885 1.268625 TGTGATTCTACGTCGTGCAGT 59.731 47.619 8.47 0.00 0.00 4.40
2079 2886 1.649171 GTGATTCTACGTCGTGCAGTG 59.351 52.381 8.47 0.00 0.00 3.66
2080 2887 1.538075 TGATTCTACGTCGTGCAGTGA 59.462 47.619 8.47 0.00 0.00 3.41
2081 2888 2.163613 TGATTCTACGTCGTGCAGTGAT 59.836 45.455 8.47 0.00 0.00 3.06
2082 2889 2.257974 TTCTACGTCGTGCAGTGATC 57.742 50.000 8.47 0.00 0.00 2.92
2083 2890 1.161843 TCTACGTCGTGCAGTGATCA 58.838 50.000 8.47 0.00 0.00 2.92
2084 2891 1.130561 TCTACGTCGTGCAGTGATCAG 59.869 52.381 8.47 0.00 0.00 2.90
2107 2914 1.442526 GATCAGATTGGGGTGCAGCG 61.443 60.000 10.24 0.00 0.00 5.18
2124 2931 1.912371 GCGTGGCTTTGTCTACCTGC 61.912 60.000 0.00 0.00 0.00 4.85
2128 2935 2.939103 GTGGCTTTGTCTACCTGCTATG 59.061 50.000 0.00 0.00 0.00 2.23
2135 2942 3.441101 TGTCTACCTGCTATGTGTTCCT 58.559 45.455 0.00 0.00 0.00 3.36
2155 2962 1.089920 GATGACATTGTGCGGCTCTT 58.910 50.000 0.00 0.00 0.00 2.85
2161 2968 0.179000 ATTGTGCGGCTCTTAGGAGG 59.821 55.000 3.79 0.00 39.80 4.30
2201 3008 2.620627 GGTTGCCACTAACCCTAATGCT 60.621 50.000 0.00 0.00 43.44 3.79
2221 3028 2.675767 AGCATATTTCGCAGCAATCG 57.324 45.000 0.00 0.00 0.00 3.34
2224 3031 2.715997 GCATATTTCGCAGCAATCGAAC 59.284 45.455 7.11 0.00 44.34 3.95
2226 3033 2.532531 ATTTCGCAGCAATCGAACTG 57.467 45.000 8.62 8.62 44.34 3.16
2236 3044 2.598589 CAATCGAACTGCAATTGTGGG 58.401 47.619 7.40 0.44 0.00 4.61
2239 3047 0.240945 CGAACTGCAATTGTGGGGAC 59.759 55.000 7.40 0.00 0.00 4.46
2241 3049 1.541588 GAACTGCAATTGTGGGGACTC 59.458 52.381 7.40 0.00 0.00 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
43 44 5.683876 TCCACCCAAATTTGTCTCAAAAA 57.316 34.783 16.73 0.00 0.00 1.94
44 45 5.683876 TTCCACCCAAATTTGTCTCAAAA 57.316 34.783 16.73 2.01 0.00 2.44
45 46 5.188751 AGTTTCCACCCAAATTTGTCTCAAA 59.811 36.000 16.73 6.48 0.00 2.69
46 47 4.714308 AGTTTCCACCCAAATTTGTCTCAA 59.286 37.500 16.73 0.88 0.00 3.02
47 48 4.099266 CAGTTTCCACCCAAATTTGTCTCA 59.901 41.667 16.73 0.00 0.00 3.27
48 49 4.340950 TCAGTTTCCACCCAAATTTGTCTC 59.659 41.667 16.73 0.00 0.00 3.36
49 50 4.285863 TCAGTTTCCACCCAAATTTGTCT 58.714 39.130 16.73 0.00 0.00 3.41
50 51 4.664150 TCAGTTTCCACCCAAATTTGTC 57.336 40.909 16.73 0.00 0.00 3.18
51 52 4.469586 AGTTCAGTTTCCACCCAAATTTGT 59.530 37.500 16.73 0.00 0.00 2.83
52 53 4.810491 CAGTTCAGTTTCCACCCAAATTTG 59.190 41.667 11.40 11.40 0.00 2.32
53 54 4.141733 CCAGTTCAGTTTCCACCCAAATTT 60.142 41.667 0.00 0.00 0.00 1.82
54 55 3.387699 CCAGTTCAGTTTCCACCCAAATT 59.612 43.478 0.00 0.00 0.00 1.82
55 56 2.965147 CCAGTTCAGTTTCCACCCAAAT 59.035 45.455 0.00 0.00 0.00 2.32
56 57 2.291930 ACCAGTTCAGTTTCCACCCAAA 60.292 45.455 0.00 0.00 0.00 3.28
57 58 1.286553 ACCAGTTCAGTTTCCACCCAA 59.713 47.619 0.00 0.00 0.00 4.12
58 59 0.923358 ACCAGTTCAGTTTCCACCCA 59.077 50.000 0.00 0.00 0.00 4.51
59 60 2.067365 AACCAGTTCAGTTTCCACCC 57.933 50.000 0.00 0.00 0.00 4.61
60 61 4.023193 CACATAACCAGTTCAGTTTCCACC 60.023 45.833 0.00 0.00 0.00 4.61
61 62 4.578928 ACACATAACCAGTTCAGTTTCCAC 59.421 41.667 0.00 0.00 0.00 4.02
62 63 4.787551 ACACATAACCAGTTCAGTTTCCA 58.212 39.130 0.00 0.00 0.00 3.53
63 64 5.519722 CAACACATAACCAGTTCAGTTTCC 58.480 41.667 0.00 0.00 0.00 3.13
64 65 4.976116 GCAACACATAACCAGTTCAGTTTC 59.024 41.667 0.00 0.00 0.00 2.78
65 66 4.644685 AGCAACACATAACCAGTTCAGTTT 59.355 37.500 0.00 0.00 0.00 2.66
66 67 4.036734 CAGCAACACATAACCAGTTCAGTT 59.963 41.667 0.00 0.00 0.00 3.16
67 68 3.565482 CAGCAACACATAACCAGTTCAGT 59.435 43.478 0.00 0.00 0.00 3.41
68 69 3.058016 CCAGCAACACATAACCAGTTCAG 60.058 47.826 0.00 0.00 0.00 3.02
69 70 2.884012 CCAGCAACACATAACCAGTTCA 59.116 45.455 0.00 0.00 0.00 3.18
133 142 2.203209 CGGCCCATCTACAAGCCC 60.203 66.667 0.00 0.00 42.66 5.19
149 158 1.226101 GCATGTTGGTCGCATGACG 60.226 57.895 9.17 0.00 46.49 4.35
178 187 7.148590 CCATAAAGTTAAGCTGGTTGAATTTGC 60.149 37.037 16.45 0.00 0.00 3.68
217 226 8.914011 AGAAACAGTCCATAAGTTAAGCTTTTT 58.086 29.630 3.20 0.00 38.57 1.94
218 227 8.465273 AGAAACAGTCCATAAGTTAAGCTTTT 57.535 30.769 3.20 0.00 38.57 2.27
219 228 8.465273 AAGAAACAGTCCATAAGTTAAGCTTT 57.535 30.769 3.20 0.00 38.57 3.51
220 229 9.740710 ATAAGAAACAGTCCATAAGTTAAGCTT 57.259 29.630 3.48 3.48 41.05 3.74
252 261 8.697960 CGAGTACTCCAGTAAGTTAAACTTTTC 58.302 37.037 17.23 0.00 39.51 2.29
256 265 6.006449 TCCGAGTACTCCAGTAAGTTAAACT 58.994 40.000 17.23 0.00 31.52 2.66
257 266 6.259550 TCCGAGTACTCCAGTAAGTTAAAC 57.740 41.667 17.23 0.00 31.52 2.01
260 269 6.660521 TGATTTCCGAGTACTCCAGTAAGTTA 59.339 38.462 17.23 0.00 31.52 2.24
267 276 4.927978 ATCTGATTTCCGAGTACTCCAG 57.072 45.455 17.23 15.81 0.00 3.86
278 287 4.400567 GCATAGGGGCATTATCTGATTTCC 59.599 45.833 0.00 0.00 0.00 3.13
282 291 2.243221 GGGCATAGGGGCATTATCTGAT 59.757 50.000 0.00 0.00 45.66 2.90
288 297 3.600919 GGGGGCATAGGGGCATTA 58.399 61.111 0.00 0.00 45.66 1.90
312 322 5.725551 TGGTGTATGGGGATGTCTAAATT 57.274 39.130 0.00 0.00 0.00 1.82
314 324 5.222151 TGTTTGGTGTATGGGGATGTCTAAA 60.222 40.000 0.00 0.00 0.00 1.85
315 325 4.289934 TGTTTGGTGTATGGGGATGTCTAA 59.710 41.667 0.00 0.00 0.00 2.10
335 345 2.787473 TCGAGATGGCTCCAAATGTT 57.213 45.000 0.00 0.00 37.91 2.71
345 359 2.474816 ACGAATAGCTTTCGAGATGGC 58.525 47.619 26.61 0.00 43.97 4.40
354 368 6.373216 TGCAAGGTACATTTACGAATAGCTTT 59.627 34.615 0.00 0.00 0.00 3.51
364 378 4.561938 GGGGGTTTTGCAAGGTACATTTAC 60.562 45.833 0.00 0.00 0.00 2.01
396 416 2.753966 CCATCTTTCCACGCGGCAG 61.754 63.158 12.47 0.00 0.00 4.85
399 419 1.079127 AGACCATCTTTCCACGCGG 60.079 57.895 12.47 0.00 0.00 6.46
401 421 1.084370 CGGAGACCATCTTTCCACGC 61.084 60.000 0.00 0.00 0.00 5.34
402 422 0.460284 CCGGAGACCATCTTTCCACG 60.460 60.000 0.00 0.00 0.00 4.94
403 423 0.744771 GCCGGAGACCATCTTTCCAC 60.745 60.000 5.05 0.00 0.00 4.02
404 424 1.602237 GCCGGAGACCATCTTTCCA 59.398 57.895 5.05 0.00 0.00 3.53
405 425 1.521681 CGCCGGAGACCATCTTTCC 60.522 63.158 5.05 0.00 0.00 3.13
444 471 5.749620 TCGATTGCGATCTACTAAGTCTTC 58.250 41.667 12.19 0.00 42.51 2.87
467 494 2.031683 CGCACGGTTGAAGAGAAAGTTT 59.968 45.455 0.00 0.00 0.00 2.66
488 515 2.096248 TGTGTTTGGTGGTGGTTCTTC 58.904 47.619 0.00 0.00 0.00 2.87
629 674 3.497227 GGACAGTTGTGCCTTACCCTTTA 60.497 47.826 0.00 0.00 0.00 1.85
637 682 1.212935 AGTGAAGGACAGTTGTGCCTT 59.787 47.619 12.65 12.65 44.32 4.35
653 698 2.466520 TTAGAGCGCGCGTGAAGTGA 62.467 55.000 32.35 8.95 0.00 3.41
659 704 2.317689 CACATTAGAGCGCGCGTG 59.682 61.111 32.35 21.80 0.00 5.34
665 710 1.756375 GCGAGGCACACATTAGAGCG 61.756 60.000 0.00 0.00 0.00 5.03
718 794 6.634837 TGCGCAAAATTATATGTAAATCACCG 59.365 34.615 8.16 0.00 0.00 4.94
748 921 5.815581 ACCATACTAACCATGACACACATT 58.184 37.500 0.00 0.00 37.07 2.71
751 924 5.086104 AGACCATACTAACCATGACACAC 57.914 43.478 0.00 0.00 0.00 3.82
755 928 5.760253 CCATGAAGACCATACTAACCATGAC 59.240 44.000 0.00 0.00 33.31 3.06
760 944 5.760253 CACATCCATGAAGACCATACTAACC 59.240 44.000 0.00 0.00 33.31 2.85
784 968 8.208718 TCTCACATTAACTGCATACCAAATAC 57.791 34.615 0.00 0.00 0.00 1.89
793 977 6.491403 AGGTTCTTTTCTCACATTAACTGCAT 59.509 34.615 0.00 0.00 0.00 3.96
797 981 7.509546 TCAGAGGTTCTTTTCTCACATTAACT 58.490 34.615 0.00 0.00 32.76 2.24
798 982 7.730364 TCAGAGGTTCTTTTCTCACATTAAC 57.270 36.000 0.00 0.00 32.76 2.01
818 1002 3.879295 CACTTGTGCTCCTCTTTTTCAGA 59.121 43.478 0.00 0.00 0.00 3.27
819 1003 3.629398 ACACTTGTGCTCCTCTTTTTCAG 59.371 43.478 0.10 0.00 0.00 3.02
820 1004 3.620488 ACACTTGTGCTCCTCTTTTTCA 58.380 40.909 0.10 0.00 0.00 2.69
824 1031 4.520492 CCAAATACACTTGTGCTCCTCTTT 59.480 41.667 0.10 0.00 0.00 2.52
827 1034 2.749621 CCCAAATACACTTGTGCTCCTC 59.250 50.000 0.10 0.00 0.00 3.71
838 1045 1.621317 CCAACCCCAACCCAAATACAC 59.379 52.381 0.00 0.00 0.00 2.90
886 1099 3.103890 GGGGAGGGGAATGGGGAC 61.104 72.222 0.00 0.00 0.00 4.46
1119 1353 4.096003 ATGAGGGGGCGGTCGTTG 62.096 66.667 0.00 0.00 0.00 4.10
1258 1498 1.681486 TACGCAAGCGATGGATGGGA 61.681 55.000 22.30 0.00 42.83 4.37
1322 1830 0.733909 CGACGAGCAGCAGTTCATCA 60.734 55.000 0.00 0.00 0.00 3.07
1323 1831 1.994467 CGACGAGCAGCAGTTCATC 59.006 57.895 0.00 0.00 0.00 2.92
1324 1832 4.175599 CGACGAGCAGCAGTTCAT 57.824 55.556 0.00 0.00 0.00 2.57
1417 1935 2.802247 CACACACACACACACAGATAGG 59.198 50.000 0.00 0.00 0.00 2.57
1418 1936 3.245990 CACACACACACACACACAGATAG 59.754 47.826 0.00 0.00 0.00 2.08
1419 1937 3.194062 CACACACACACACACACAGATA 58.806 45.455 0.00 0.00 0.00 1.98
1420 1938 2.009051 CACACACACACACACACAGAT 58.991 47.619 0.00 0.00 0.00 2.90
1533 2066 7.998465 ATAGAGATTGATCCATGATCCATCT 57.002 36.000 16.28 16.28 46.88 2.90
1586 2122 2.550978 CGGAGCGTAGAACCATTCATT 58.449 47.619 0.00 0.00 0.00 2.57
1587 2123 2.225068 CGGAGCGTAGAACCATTCAT 57.775 50.000 0.00 0.00 0.00 2.57
1588 2124 3.733236 CGGAGCGTAGAACCATTCA 57.267 52.632 0.00 0.00 0.00 2.57
1615 2155 0.163788 CGTATGCCGCAAATCGATCC 59.836 55.000 0.00 0.00 41.67 3.36
1633 2173 0.740868 ATGAACAGGTCGACATGCCG 60.741 55.000 28.52 7.31 0.00 5.69
1637 2177 5.084818 TCATTACATGAACAGGTCGACAT 57.915 39.130 18.91 7.60 36.11 3.06
1695 2235 2.016961 CATCGGCCATTTCCACTCG 58.983 57.895 2.24 0.00 0.00 4.18
1740 2280 5.537674 AGGCATCAAGACTTGTGAGAAAAAT 59.462 36.000 14.75 0.00 20.59 1.82
1744 2284 3.668447 GAGGCATCAAGACTTGTGAGAA 58.332 45.455 14.75 0.00 33.72 2.87
1752 2292 1.066573 CCAAGACGAGGCATCAAGACT 60.067 52.381 0.00 0.00 39.48 3.24
1758 2298 1.667724 CACAATCCAAGACGAGGCATC 59.332 52.381 0.00 0.00 0.00 3.91
1761 2301 0.321653 ACCACAATCCAAGACGAGGC 60.322 55.000 0.00 0.00 0.00 4.70
1762 2302 3.198068 CATACCACAATCCAAGACGAGG 58.802 50.000 0.00 0.00 0.00 4.63
1763 2303 3.861840 ACATACCACAATCCAAGACGAG 58.138 45.455 0.00 0.00 0.00 4.18
1764 2304 3.973206 ACATACCACAATCCAAGACGA 57.027 42.857 0.00 0.00 0.00 4.20
1770 2310 6.323482 CCATCCATTTAACATACCACAATCCA 59.677 38.462 0.00 0.00 0.00 3.41
1810 2606 6.093909 CAGAACTGATGGCATACAACAATACA 59.906 38.462 0.00 0.00 30.99 2.29
1811 2607 6.094048 ACAGAACTGATGGCATACAACAATAC 59.906 38.462 0.00 0.00 30.99 1.89
1822 2618 4.402851 GCCACAGAACTGATGGCA 57.597 55.556 26.78 0.00 46.83 4.92
1837 2633 0.244994 ATCTCGACAGTCACACAGCC 59.755 55.000 0.41 0.00 0.00 4.85
1857 2653 0.036388 TCACGAAAGCCATCAGGTCC 60.036 55.000 0.00 0.00 37.19 4.46
1898 2694 2.959516 GCAAAACCCTACCAATTGCTC 58.040 47.619 0.00 0.00 42.24 4.26
1921 2717 3.198417 TGGCATCTTCATCAGCAGTCTAA 59.802 43.478 0.00 0.00 0.00 2.10
1958 2754 0.311790 AAACACATGAGGCAAGCACG 59.688 50.000 0.00 0.00 0.00 5.34
1969 2765 9.401873 CAAGCATAATATCCACATAAACACATG 57.598 33.333 0.00 0.00 0.00 3.21
1970 2767 9.135189 ACAAGCATAATATCCACATAAACACAT 57.865 29.630 0.00 0.00 0.00 3.21
2020 2827 3.006940 ACGGCAATTTCACACGACATAT 58.993 40.909 0.00 0.00 0.00 1.78
2028 2835 6.042777 TCAATTAACAAACGGCAATTTCACA 58.957 32.000 0.00 0.00 0.00 3.58
2040 2847 8.299570 AGAATCACAGGACATCAATTAACAAAC 58.700 33.333 0.00 0.00 0.00 2.93
2042 2849 8.946085 GTAGAATCACAGGACATCAATTAACAA 58.054 33.333 0.00 0.00 0.00 2.83
2043 2850 7.277760 CGTAGAATCACAGGACATCAATTAACA 59.722 37.037 0.00 0.00 0.00 2.41
2070 2877 1.247567 TCACTCTGATCACTGCACGA 58.752 50.000 0.00 0.00 0.00 4.35
2080 2887 3.136077 CACCCCAATCTGATCACTCTGAT 59.864 47.826 0.00 0.00 40.34 2.90
2081 2888 2.502947 CACCCCAATCTGATCACTCTGA 59.497 50.000 0.00 0.00 34.34 3.27
2082 2889 2.915349 CACCCCAATCTGATCACTCTG 58.085 52.381 0.00 0.00 0.00 3.35
2083 2890 1.211457 GCACCCCAATCTGATCACTCT 59.789 52.381 0.00 0.00 0.00 3.24
2084 2891 1.065199 TGCACCCCAATCTGATCACTC 60.065 52.381 0.00 0.00 0.00 3.51
2107 2914 2.762535 TAGCAGGTAGACAAAGCCAC 57.237 50.000 0.00 0.00 0.00 5.01
2124 2931 5.448225 GCACAATGTCATCAGGAACACATAG 60.448 44.000 0.00 0.00 0.00 2.23
2128 2935 2.413239 CGCACAATGTCATCAGGAACAC 60.413 50.000 0.00 0.00 0.00 3.32
2135 2942 0.036105 AGAGCCGCACAATGTCATCA 60.036 50.000 0.00 0.00 0.00 3.07
2155 2962 2.929301 ACCAACCCTTGATTCCTCCTA 58.071 47.619 0.00 0.00 0.00 2.94
2161 2968 1.273327 CCAGCAACCAACCCTTGATTC 59.727 52.381 0.00 0.00 0.00 2.52
2196 3003 2.880268 TGCTGCGAAATATGCTAGCATT 59.120 40.909 33.74 18.33 39.65 3.56
2201 3008 3.389221 TCGATTGCTGCGAAATATGCTA 58.611 40.909 0.00 0.00 34.45 3.49
2221 3028 1.541588 GAGTCCCCACAATTGCAGTTC 59.458 52.381 5.05 0.00 0.00 3.01
2224 3031 2.787473 TAGAGTCCCCACAATTGCAG 57.213 50.000 5.05 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.