Multiple sequence alignment - TraesCS5A01G281900

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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 TraesCS5A01G281900 chr5A 100.000 2421 0 0 1 2421 491213934 491216354 0.000000e+00 4471.0
1 TraesCS5A01G281900 chr5D 90.898 2461 154 43 1 2421 388042786 388045216 0.000000e+00 3240.0
2 TraesCS5A01G281900 chr5D 91.228 285 21 3 1645 1926 500855668 500855951 3.780000e-103 385.0
3 TraesCS5A01G281900 chr5D 84.412 340 43 5 2088 2421 477177320 477177655 2.320000e-85 326.0
4 TraesCS5A01G281900 chr5B 86.424 987 76 27 1 946 466643273 466644242 0.000000e+00 1027.0
5 TraesCS5A01G281900 chr5B 94.498 418 23 0 967 1384 466644382 466644799 0.000000e+00 645.0
6 TraesCS5A01G281900 chr5B 92.481 266 17 3 1381 1643 466645143 466645408 6.320000e-101 377.0
7 TraesCS5A01G281900 chr5B 78.068 383 61 19 404 768 298488434 298488057 1.130000e-53 220.0
8 TraesCS5A01G281900 chr5B 90.798 163 10 4 1919 2079 466645392 466645551 1.890000e-51 213.0
9 TraesCS5A01G281900 chr5B 76.056 426 77 17 416 823 584065742 584065324 5.280000e-47 198.0
10 TraesCS5A01G281900 chr7D 92.527 281 19 1 1645 1923 616195093 616195373 3.750000e-108 401.0
11 TraesCS5A01G281900 chr7D 80.000 265 49 4 496 757 530898280 530898017 2.460000e-45 193.0
12 TraesCS5A01G281900 chr1B 91.697 277 20 2 1645 1919 57690110 57689835 4.880000e-102 381.0
13 TraesCS5A01G281900 chr1B 85.755 351 39 7 2078 2421 480829315 480829661 6.360000e-96 361.0
14 TraesCS5A01G281900 chr1B 85.100 349 33 9 2079 2421 681000242 680999907 2.980000e-89 339.0
15 TraesCS5A01G281900 chr1B 83.871 186 28 2 1176 1360 16480526 16480342 2.470000e-40 176.0
16 TraesCS5A01G281900 chr1B 82.796 186 30 2 1176 1360 16652499 16652315 5.350000e-37 165.0
17 TraesCS5A01G281900 chr1B 84.270 89 14 0 1187 1275 16457121 16457033 1.190000e-13 87.9
18 TraesCS5A01G281900 chr3D 93.050 259 16 1 1648 1904 539555370 539555112 6.320000e-101 377.0
19 TraesCS5A01G281900 chr3D 93.571 140 8 1 2167 2305 181802930 181803069 8.770000e-50 207.0
20 TraesCS5A01G281900 chr3D 97.143 35 1 0 334 368 33170437 33170403 2.600000e-05 60.2
21 TraesCS5A01G281900 chr2A 89.892 277 25 2 1645 1919 65033862 65033587 1.060000e-93 353.0
22 TraesCS5A01G281900 chr3A 85.100 349 41 7 2079 2421 150797240 150796897 1.780000e-91 346.0
23 TraesCS5A01G281900 chr7B 85.971 278 18 4 1645 1920 465585926 465586184 6.590000e-71 278.0
24 TraesCS5A01G281900 chr7B 89.256 121 13 0 2206 2326 605358988 605359108 4.170000e-33 152.0
25 TraesCS5A01G281900 chr7B 94.737 38 2 0 327 364 639499287 639499250 2.600000e-05 60.2
26 TraesCS5A01G281900 chr6D 78.588 425 72 19 405 820 106699853 106699439 1.850000e-66 263.0
27 TraesCS5A01G281900 chr6D 77.562 361 64 12 412 756 105425879 105425520 4.080000e-48 202.0
28 TraesCS5A01G281900 chr6D 80.709 254 36 11 405 652 78360826 78360580 4.110000e-43 185.0
29 TraesCS5A01G281900 chr1D 86.066 244 32 1 1645 1886 437830735 437830978 6.640000e-66 261.0
30 TraesCS5A01G281900 chr1D 82.162 185 33 0 1176 1360 11201922 11201738 2.490000e-35 159.0
31 TraesCS5A01G281900 chr1D 82.734 139 19 4 227 361 475925206 475925069 4.230000e-23 119.0
32 TraesCS5A01G281900 chr1D 87.234 94 12 0 1178 1271 10955130 10955037 9.150000e-20 108.0
33 TraesCS5A01G281900 chr6B 90.576 191 16 1 1645 1833 237385130 237384940 4.000000e-63 252.0
34 TraesCS5A01G281900 chr2D 75.124 402 76 21 405 793 593213124 593212734 1.490000e-37 167.0
35 TraesCS5A01G281900 chr2D 82.394 142 21 4 226 364 601173687 601173827 1.180000e-23 121.0
36 TraesCS5A01G281900 chr1A 82.486 177 29 2 1176 1351 22631973 22632148 1.160000e-33 154.0
37 TraesCS5A01G281900 chr1A 86.585 82 11 0 1191 1272 22661601 22661682 9.220000e-15 91.6
38 TraesCS5A01G281900 chr4D 75.920 299 58 12 501 793 96628247 96628537 9.020000e-30 141.0
39 TraesCS5A01G281900 chr4D 83.740 123 13 5 253 370 397159892 397160012 2.540000e-20 110.0
40 TraesCS5A01G281900 chr7A 80.795 151 23 6 218 363 677688817 677688668 1.970000e-21 113.0
41 TraesCS5A01G281900 chr3B 79.730 148 26 4 220 364 526689957 526689811 1.180000e-18 104.0


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 TraesCS5A01G281900 chr5A 491213934 491216354 2420 False 4471.0 4471 100.00000 1 2421 1 chr5A.!!$F1 2420
1 TraesCS5A01G281900 chr5D 388042786 388045216 2430 False 3240.0 3240 90.89800 1 2421 1 chr5D.!!$F1 2420
2 TraesCS5A01G281900 chr5B 466643273 466645551 2278 False 565.5 1027 91.05025 1 2079 4 chr5B.!!$F1 2078

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
40 41 0.094558 CGCATGTACATTCAACGCGT 59.905 50.0 22.41 5.58 37.99 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1681 2195 0.03213 GAGAGAGCGGTGTTGTGACA 59.968 55.0 0.0 0.0 0.0 3.58 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
40 41 0.094558 CGCATGTACATTCAACGCGT 59.905 50.000 22.41 5.58 37.99 6.01
81 82 2.125350 CTGAGGAGGCAAGGACGC 60.125 66.667 0.00 0.00 0.00 5.19
90 91 0.861837 GGCAAGGACGCGATATGAAG 59.138 55.000 15.93 0.00 0.00 3.02
97 98 2.316792 GACGCGATATGAAGCACGTAT 58.683 47.619 15.93 0.00 33.31 3.06
115 116 6.604012 CACGTATGGTTGTTACTTTATGCAA 58.396 36.000 0.00 0.00 0.00 4.08
134 135 4.201666 TGCAATGACAAAGCAAAAACGAAC 60.202 37.500 3.01 0.00 34.97 3.95
169 170 5.422666 TCAGTTAAGAATAATGCATGCGG 57.577 39.130 14.09 0.00 0.00 5.69
212 213 3.610040 ACTTTCTGTGTCATCGCCATA 57.390 42.857 0.00 0.00 0.00 2.74
225 233 3.650070 TCGCCATAAGTATGCTCTCTG 57.350 47.619 0.00 0.00 32.40 3.35
226 234 2.959030 TCGCCATAAGTATGCTCTCTGT 59.041 45.455 0.00 0.00 32.40 3.41
227 235 3.384789 TCGCCATAAGTATGCTCTCTGTT 59.615 43.478 0.00 0.00 32.40 3.16
228 236 3.738282 CGCCATAAGTATGCTCTCTGTTC 59.262 47.826 0.00 0.00 32.40 3.18
229 237 4.697514 GCCATAAGTATGCTCTCTGTTCA 58.302 43.478 0.00 0.00 32.40 3.18
230 238 4.509600 GCCATAAGTATGCTCTCTGTTCAC 59.490 45.833 0.00 0.00 32.40 3.18
231 239 4.742167 CCATAAGTATGCTCTCTGTTCACG 59.258 45.833 0.00 0.00 32.40 4.35
239 247 8.414003 AGTATGCTCTCTGTTCACGAATATAAA 58.586 33.333 0.00 0.00 0.00 1.40
364 404 2.185004 ATTTGTGAACGGAGGGAGTG 57.815 50.000 0.00 0.00 0.00 3.51
406 446 3.450817 TGGTCATATACTCATATGCGGGG 59.549 47.826 0.00 0.00 42.57 5.73
413 453 7.344612 TCATATACTCATATGCGGGGAAAGTAT 59.655 37.037 12.81 12.81 42.57 2.12
414 454 4.706842 ACTCATATGCGGGGAAAGTATT 57.293 40.909 0.00 0.00 0.00 1.89
463 505 3.571571 TGATACCAACTTTGAGACGACG 58.428 45.455 0.00 0.00 0.00 5.12
464 506 1.774639 TACCAACTTTGAGACGACGC 58.225 50.000 0.00 0.00 0.00 5.19
544 587 5.180810 AGAACCCCTAAAAAGTCAGATCC 57.819 43.478 0.00 0.00 0.00 3.36
599 642 7.264373 AGACAAACCTAGAATGAAAAGTGTG 57.736 36.000 0.00 0.00 0.00 3.82
636 679 5.124457 AGCATAATTGACACTGTTCACATCC 59.876 40.000 0.00 0.00 0.00 3.51
839 882 2.232208 CTCCCATCATATGCGTGCTAGA 59.768 50.000 0.00 0.00 0.00 2.43
877 920 1.078759 GCTGGTCAACGACTCGATGG 61.079 60.000 5.20 0.00 30.83 3.51
906 949 8.778358 GGGACAGATACTTAATTTCACATCATC 58.222 37.037 0.00 0.00 0.00 2.92
908 951 9.249457 GACAGATACTTAATTTCACATCATCGA 57.751 33.333 0.00 0.00 0.00 3.59
937 980 1.406898 CTGATCCAGCTCGCTCAGTTA 59.593 52.381 4.24 0.00 32.35 2.24
946 1091 4.973051 CAGCTCGCTCAGTTATTAGTACTG 59.027 45.833 5.39 0.00 43.41 2.74
957 1102 6.089551 CAGTTATTAGTACTGGCATCGCATAC 59.910 42.308 5.39 0.00 39.42 2.39
958 1103 4.873746 ATTAGTACTGGCATCGCATACT 57.126 40.909 5.39 0.00 31.58 2.12
959 1104 5.977489 ATTAGTACTGGCATCGCATACTA 57.023 39.130 5.39 0.00 30.17 1.82
960 1105 3.924918 AGTACTGGCATCGCATACTAG 57.075 47.619 0.00 0.00 0.00 2.57
961 1106 3.223435 AGTACTGGCATCGCATACTAGT 58.777 45.455 0.00 0.00 0.00 2.57
962 1107 4.395625 AGTACTGGCATCGCATACTAGTA 58.604 43.478 4.77 4.77 0.00 1.82
963 1108 3.924918 ACTGGCATCGCATACTAGTAG 57.075 47.619 8.85 0.00 0.00 2.57
964 1109 3.223435 ACTGGCATCGCATACTAGTAGT 58.777 45.455 8.85 8.14 0.00 2.73
965 1110 3.004839 ACTGGCATCGCATACTAGTAGTG 59.995 47.826 13.29 8.07 0.00 2.74
1009 1171 2.492088 CGGGGATCGATCACATAGCTAA 59.508 50.000 28.03 0.00 42.43 3.09
1111 1273 2.238646 GGGGTTAGTGTGATCATGGTGA 59.761 50.000 0.00 0.00 0.00 4.02
1156 1318 2.724377 CGGCTATGAGCTGCTCGA 59.276 61.111 23.35 13.56 41.20 4.04
1163 1325 0.461693 ATGAGCTGCTCGAAGAAGGC 60.462 55.000 23.35 0.00 34.09 4.35
1331 1493 1.359848 GTCCGCATCTTCGTTGACAT 58.640 50.000 0.00 0.00 0.00 3.06
1437 1947 1.153353 AATTTCATATACGCCCGCCG 58.847 50.000 0.00 0.00 44.21 6.46
1463 1973 2.953648 TGGATCAATGCATGGATGTCAC 59.046 45.455 21.60 6.62 0.00 3.67
1464 1974 2.031420 GGATCAATGCATGGATGTCACG 60.031 50.000 21.60 0.00 0.00 4.35
1467 1977 0.034186 AATGCATGGATGTCACGGGT 60.034 50.000 0.00 0.00 0.00 5.28
1470 1980 0.171007 GCATGGATGTCACGGGTTTG 59.829 55.000 0.00 0.00 0.00 2.93
1492 2003 2.093288 TGTGCTAGCTCTTGGATCCTTG 60.093 50.000 17.23 5.76 0.00 3.61
1504 2015 7.320384 TCTTGGATCCTTGATATTGCATCTA 57.680 36.000 14.23 0.00 0.00 1.98
1602 2116 3.491619 CCAGGATGTCGGTCTATGTTGAG 60.492 52.174 0.00 0.00 0.00 3.02
1676 2190 1.282875 GCTCAAAGCACCAACGACC 59.717 57.895 0.00 0.00 41.89 4.79
1681 2195 0.534203 AAAGCACCAACGACCGACAT 60.534 50.000 0.00 0.00 0.00 3.06
1700 2214 0.032130 TGTCACAACACCGCTCTCTC 59.968 55.000 0.00 0.00 0.00 3.20
1703 2217 1.004277 CACAACACCGCTCTCTCGTC 61.004 60.000 0.00 0.00 0.00 4.20
1708 2222 1.375652 ACCGCTCTCTCGTCGAAGA 60.376 57.895 0.03 0.03 0.00 2.87
1760 2276 4.692625 AGAGCTTGTATTTGTGCAGTGTAG 59.307 41.667 0.00 0.00 0.00 2.74
1762 2278 3.189287 GCTTGTATTTGTGCAGTGTAGCT 59.811 43.478 0.00 0.00 34.99 3.32
1768 2284 1.165907 TGTGCAGTGTAGCTGTTGGC 61.166 55.000 0.00 0.00 46.64 4.52
1801 2317 0.747852 TCATGAGTTGGCCGCGTATA 59.252 50.000 4.92 0.00 0.00 1.47
1821 2337 2.202518 CGTAGCACCCCACGTACG 60.203 66.667 15.01 15.01 33.56 3.67
1822 2338 2.182537 GTAGCACCCCACGTACGG 59.817 66.667 21.06 8.46 0.00 4.02
1834 2350 1.287815 CGTACGGCAGTCTGGTTCA 59.712 57.895 7.57 0.00 0.00 3.18
1835 2351 1.007336 CGTACGGCAGTCTGGTTCAC 61.007 60.000 7.57 0.00 0.00 3.18
1996 2523 1.820519 GGCAAACTCAGATGGATGCAA 59.179 47.619 0.00 0.00 35.57 4.08
2012 2539 4.499019 GGATGCAAAAAGAAGACGGTTCAA 60.499 41.667 0.00 0.00 0.00 2.69
2017 2544 5.051039 GCAAAAAGAAGACGGTTCAATTTCC 60.051 40.000 3.00 0.00 0.00 3.13
2053 2581 9.396022 TGCCTCTAATTTCTTGTTATTCTAAGG 57.604 33.333 0.00 0.00 0.00 2.69
2070 2598 0.758734 AGGAAGTTTTTGCAAGGGCC 59.241 50.000 0.00 0.00 40.13 5.80
2121 2649 3.555139 GCAGATCTTTTCTCTCACATCCG 59.445 47.826 0.00 0.00 29.93 4.18
2128 2656 0.904649 TCTCTCACATCCGCCATGTT 59.095 50.000 0.00 0.00 43.89 2.71
2137 2670 1.262417 TCCGCCATGTTCTAGACACA 58.738 50.000 9.28 9.28 42.04 3.72
2141 2674 2.413837 GCCATGTTCTAGACACACGTT 58.586 47.619 9.11 0.00 42.04 3.99
2150 2683 0.951558 AGACACACGTTTTGATGGGC 59.048 50.000 0.89 0.00 0.00 5.36
2155 2688 1.530419 ACGTTTTGATGGGCCAGCA 60.530 52.632 22.63 22.63 0.00 4.41
2158 2691 0.319813 GTTTTGATGGGCCAGCACAC 60.320 55.000 26.48 20.00 29.15 3.82
2173 2706 1.884235 CACACCGCTTTTCTCCTTCT 58.116 50.000 0.00 0.00 0.00 2.85
2281 2815 3.380995 TCTGACCATGCAGAGCGT 58.619 55.556 0.00 0.00 39.84 5.07
2284 2818 1.364626 CTGACCATGCAGAGCGTTCC 61.365 60.000 0.00 0.00 38.14 3.62
2285 2819 2.434884 ACCATGCAGAGCGTTCCG 60.435 61.111 0.00 0.00 0.00 4.30
2292 2826 1.880894 CAGAGCGTTCCGTACTCCA 59.119 57.895 0.00 0.00 0.00 3.86
2311 2845 2.821969 CCAATTCTTGCAACTAGGCACT 59.178 45.455 0.00 0.00 44.86 4.40
2324 2858 5.262588 ACTAGGCACTTGTTTCAAAAAGG 57.737 39.130 0.00 0.00 42.67 3.11
2325 2859 2.905075 AGGCACTTGTTTCAAAAAGGC 58.095 42.857 0.00 0.00 27.25 4.35
2326 2860 2.235898 AGGCACTTGTTTCAAAAAGGCA 59.764 40.909 0.00 0.00 27.25 4.75
2327 2861 3.118298 AGGCACTTGTTTCAAAAAGGCAT 60.118 39.130 0.00 0.00 27.25 4.40
2328 2862 4.100808 AGGCACTTGTTTCAAAAAGGCATA 59.899 37.500 0.00 0.00 27.25 3.14
2329 2863 4.996758 GGCACTTGTTTCAAAAAGGCATAT 59.003 37.500 0.00 0.00 0.00 1.78
2330 2864 5.469760 GGCACTTGTTTCAAAAAGGCATATT 59.530 36.000 0.00 0.00 0.00 1.28
2331 2865 6.365050 GCACTTGTTTCAAAAAGGCATATTG 58.635 36.000 0.00 0.00 0.00 1.90
2332 2866 6.365050 CACTTGTTTCAAAAAGGCATATTGC 58.635 36.000 0.00 0.00 44.08 3.56
2355 2889 0.531974 AACCACACATTCTCACGCGT 60.532 50.000 5.58 5.58 0.00 6.01
2357 2891 1.221466 CCACACATTCTCACGCGTGT 61.221 55.000 35.74 16.67 43.12 4.49
2371 2905 1.078426 CGTGTTGACCCTCCCATCC 60.078 63.158 0.00 0.00 0.00 3.51
2373 2907 1.928567 TGTTGACCCTCCCATCCCC 60.929 63.158 0.00 0.00 0.00 4.81
2374 2908 1.928567 GTTGACCCTCCCATCCCCA 60.929 63.158 0.00 0.00 0.00 4.96
2376 2910 1.506028 TTGACCCTCCCATCCCCAAC 61.506 60.000 0.00 0.00 0.00 3.77
2381 2915 0.030092 CCTCCCATCCCCAACCTCTA 60.030 60.000 0.00 0.00 0.00 2.43
2409 2945 1.755783 GCCCTGCCTCTTTCCATGG 60.756 63.158 4.97 4.97 0.00 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
66 67 1.735376 TATCGCGTCCTTGCCTCCTC 61.735 60.000 5.77 0.00 0.00 3.71
81 82 3.802139 ACAACCATACGTGCTTCATATCG 59.198 43.478 0.00 0.00 0.00 2.92
90 91 5.025826 GCATAAAGTAACAACCATACGTGC 58.974 41.667 0.00 0.00 0.00 5.34
97 98 6.641169 TGTCATTGCATAAAGTAACAACCA 57.359 33.333 0.00 0.00 0.00 3.67
115 116 5.347342 TCATGTTCGTTTTTGCTTTGTCAT 58.653 33.333 0.00 0.00 0.00 3.06
134 135 5.068234 TCTTAACTGAACGTACCCTCATG 57.932 43.478 0.00 0.00 0.00 3.07
169 170 5.796424 ATTATCCAAAGGTCCATGCATTC 57.204 39.130 0.00 0.00 0.00 2.67
181 182 8.331022 CGATGACACAGAAAGTATTATCCAAAG 58.669 37.037 0.00 0.00 0.00 2.77
212 213 4.521130 TTCGTGAACAGAGAGCATACTT 57.479 40.909 0.00 0.00 0.00 2.24
225 233 7.753132 TGTCCAAAGCATTTTATATTCGTGAAC 59.247 33.333 0.00 0.00 35.03 3.18
226 234 7.821652 TGTCCAAAGCATTTTATATTCGTGAA 58.178 30.769 0.00 0.00 35.03 3.18
227 235 7.384439 TGTCCAAAGCATTTTATATTCGTGA 57.616 32.000 0.00 0.00 35.03 4.35
228 236 8.633075 AATGTCCAAAGCATTTTATATTCGTG 57.367 30.769 0.00 0.00 35.03 4.35
229 237 9.301153 GAAATGTCCAAAGCATTTTATATTCGT 57.699 29.630 5.00 0.00 43.87 3.85
230 238 9.299963 TGAAATGTCCAAAGCATTTTATATTCG 57.700 29.630 5.00 0.00 43.87 3.34
239 247 7.899973 AGTCTATTTGAAATGTCCAAAGCATT 58.100 30.769 0.00 0.00 37.00 3.56
511 553 7.237055 ACTTTTTAGGGGTTCTAGTCACATACT 59.763 37.037 0.00 0.00 42.62 2.12
523 565 4.918588 TGGATCTGACTTTTTAGGGGTTC 58.081 43.478 0.00 0.00 0.00 3.62
606 649 7.596248 GTGAACAGTGTCAATTATGCTTTTGAT 59.404 33.333 0.00 0.00 34.60 2.57
839 882 1.207811 GCTGGCCCAAATTAATGCTGT 59.792 47.619 0.00 0.00 0.00 4.40
877 920 4.272748 GTGAAATTAAGTATCTGTCCCGCC 59.727 45.833 0.00 0.00 0.00 6.13
906 949 1.590238 GCTGGATCAGTTGACGATTCG 59.410 52.381 4.14 4.14 33.43 3.34
908 951 2.736719 CGAGCTGGATCAGTTGACGATT 60.737 50.000 0.00 0.00 33.43 3.34
937 980 4.873746 AGTATGCGATGCCAGTACTAAT 57.126 40.909 0.00 0.00 0.00 1.73
946 1091 3.644884 ACACTACTAGTATGCGATGCC 57.355 47.619 2.33 0.00 0.00 4.40
963 1108 9.017669 CGAACAACACTACTCCTATTTATACAC 57.982 37.037 0.00 0.00 0.00 2.90
964 1109 8.192774 CCGAACAACACTACTCCTATTTATACA 58.807 37.037 0.00 0.00 0.00 2.29
965 1110 7.650903 CCCGAACAACACTACTCCTATTTATAC 59.349 40.741 0.00 0.00 0.00 1.47
1009 1171 6.646653 CCAATCAACGTGCTATATGTGATAGT 59.353 38.462 0.00 0.00 0.00 2.12
1073 1235 0.610232 CCCAGCAGGACCCTTTTGAG 60.610 60.000 0.00 0.00 38.24 3.02
1132 1294 2.060383 AGCTCATAGCCGCAGTGGA 61.060 57.895 3.39 0.00 43.77 4.02
1185 1347 3.470888 CCTACCACCTCCGGCCAG 61.471 72.222 2.24 0.00 0.00 4.85
1204 1366 2.050836 TTGGCCTTCTCCACGCTCAA 62.051 55.000 3.32 0.00 35.50 3.02
1306 1468 3.918220 GAAGATGCGGACGCGCTG 61.918 66.667 5.73 5.39 45.51 5.18
1437 1947 4.159693 ACATCCATGCATTGATCCATATGC 59.840 41.667 10.22 14.30 45.66 3.14
1463 1973 0.320771 AGAGCTAGCACACAAACCCG 60.321 55.000 18.83 0.00 0.00 5.28
1464 1974 1.537202 CAAGAGCTAGCACACAAACCC 59.463 52.381 18.83 0.00 0.00 4.11
1467 1977 2.928801 TCCAAGAGCTAGCACACAAA 57.071 45.000 18.83 0.00 0.00 2.83
1470 1980 1.484240 AGGATCCAAGAGCTAGCACAC 59.516 52.381 18.83 7.96 0.00 3.82
1527 2039 1.979308 TCCAACTCCGTCCAACCAATA 59.021 47.619 0.00 0.00 0.00 1.90
1528 2040 0.768622 TCCAACTCCGTCCAACCAAT 59.231 50.000 0.00 0.00 0.00 3.16
1529 2041 0.768622 ATCCAACTCCGTCCAACCAA 59.231 50.000 0.00 0.00 0.00 3.67
1602 2116 8.617290 TTATACAAGAAGTTCCTGAAAAGTCC 57.383 34.615 8.49 0.00 0.00 3.85
1661 2175 1.278637 GTCGGTCGTTGGTGCTTTG 59.721 57.895 0.00 0.00 0.00 2.77
1676 2190 1.204062 GCGGTGTTGTGACATGTCG 59.796 57.895 20.54 8.06 38.23 4.35
1681 2195 0.032130 GAGAGAGCGGTGTTGTGACA 59.968 55.000 0.00 0.00 0.00 3.58
1700 2214 2.115595 CTGCTGCTAATCTCTTCGACG 58.884 52.381 0.00 0.00 0.00 5.12
1703 2217 1.592081 GTGCTGCTGCTAATCTCTTCG 59.408 52.381 17.00 0.00 40.48 3.79
1708 2222 1.817099 GGCGTGCTGCTGCTAATCT 60.817 57.895 17.00 0.00 45.43 2.40
1736 2252 3.885297 ACACTGCACAAATACAAGCTCTT 59.115 39.130 0.00 0.00 0.00 2.85
1760 2276 1.429423 GCGGTATTCTGCCAACAGC 59.571 57.895 0.00 0.00 44.10 4.40
1762 2278 0.739462 CTCGCGGTATTCTGCCAACA 60.739 55.000 6.13 0.00 42.47 3.33
1768 2284 2.223595 ACTCATGACTCGCGGTATTCTG 60.224 50.000 6.13 0.00 0.00 3.02
1821 2337 0.886490 CACCTGTGAACCAGACTGCC 60.886 60.000 0.00 0.00 44.49 4.85
1822 2338 0.886490 CCACCTGTGAACCAGACTGC 60.886 60.000 0.00 0.00 44.49 4.40
1834 2350 3.054361 ACAAGAAAGTTCAGTCCACCTGT 60.054 43.478 0.00 0.00 42.19 4.00
1835 2351 3.545703 ACAAGAAAGTTCAGTCCACCTG 58.454 45.455 0.00 0.00 42.97 4.00
1839 2355 6.094881 CCAAGTTTACAAGAAAGTTCAGTCCA 59.905 38.462 0.00 0.00 0.00 4.02
1844 2360 8.463607 CCTTAACCAAGTTTACAAGAAAGTTCA 58.536 33.333 0.00 0.00 0.00 3.18
1846 2362 7.262772 GCCTTAACCAAGTTTACAAGAAAGTT 58.737 34.615 0.00 0.00 0.00 2.66
1939 2458 3.234353 TCGGACCTCTATCTCATGCAAT 58.766 45.455 0.00 0.00 0.00 3.56
1950 2469 2.025155 CAAAGCTAGCTCGGACCTCTA 58.975 52.381 19.65 0.00 0.00 2.43
1979 2506 6.266103 TCTTCTTTTTGCATCCATCTGAGTTT 59.734 34.615 0.00 0.00 0.00 2.66
1981 2508 5.182760 GTCTTCTTTTTGCATCCATCTGAGT 59.817 40.000 0.00 0.00 0.00 3.41
1996 2523 7.576861 TTAGGAAATTGAACCGTCTTCTTTT 57.423 32.000 0.00 0.00 0.00 2.27
2053 2581 2.620251 AAGGCCCTTGCAAAAACTTC 57.380 45.000 0.00 0.00 40.13 3.01
2070 2598 5.707298 TGATCACTGGCTTTTCCTAGAAAAG 59.293 40.000 20.38 20.38 39.55 2.27
2086 2614 7.517361 AGAAAAGATCTGCCAGTTGATCACTG 61.517 42.308 14.68 14.68 44.18 3.66
2101 2629 3.431486 GGCGGATGTGAGAGAAAAGATCT 60.431 47.826 0.00 0.00 42.61 2.75
2121 2649 2.080286 ACGTGTGTCTAGAACATGGC 57.920 50.000 21.17 7.56 40.80 4.40
2128 2656 3.659786 CCCATCAAAACGTGTGTCTAGA 58.340 45.455 0.00 0.00 0.00 2.43
2137 2670 1.530419 TGCTGGCCCATCAAAACGT 60.530 52.632 0.00 0.00 0.00 3.99
2141 2674 1.907807 GGTGTGCTGGCCCATCAAA 60.908 57.895 0.00 0.00 0.00 2.69
2155 2688 2.495084 GAAGAAGGAGAAAAGCGGTGT 58.505 47.619 0.00 0.00 0.00 4.16
2158 2691 2.481289 AGGAAGAAGGAGAAAAGCGG 57.519 50.000 0.00 0.00 0.00 5.52
2164 2697 4.290942 GGTGGAGATAGGAAGAAGGAGAA 58.709 47.826 0.00 0.00 0.00 2.87
2173 2706 2.158813 GCCATTTCGGTGGAGATAGGAA 60.159 50.000 6.60 0.00 42.02 3.36
2292 2826 3.891366 ACAAGTGCCTAGTTGCAAGAATT 59.109 39.130 0.00 0.00 44.11 2.17
2311 2845 6.317140 TGTTGCAATATGCCTTTTTGAAACAA 59.683 30.769 0.59 0.00 42.87 2.83
2323 2857 2.288702 TGTGTGGTTGTTGCAATATGCC 60.289 45.455 0.59 6.39 44.23 4.40
2324 2858 3.023946 TGTGTGGTTGTTGCAATATGC 57.976 42.857 0.59 0.00 45.29 3.14
2325 2859 5.472148 AGAATGTGTGGTTGTTGCAATATG 58.528 37.500 0.59 0.00 0.00 1.78
2326 2860 5.243507 TGAGAATGTGTGGTTGTTGCAATAT 59.756 36.000 0.59 0.00 0.00 1.28
2327 2861 4.582240 TGAGAATGTGTGGTTGTTGCAATA 59.418 37.500 0.59 0.00 0.00 1.90
2328 2862 3.384146 TGAGAATGTGTGGTTGTTGCAAT 59.616 39.130 0.59 0.00 0.00 3.56
2329 2863 2.757314 TGAGAATGTGTGGTTGTTGCAA 59.243 40.909 0.00 0.00 0.00 4.08
2330 2864 2.098934 GTGAGAATGTGTGGTTGTTGCA 59.901 45.455 0.00 0.00 0.00 4.08
2331 2865 2.731217 GTGAGAATGTGTGGTTGTTGC 58.269 47.619 0.00 0.00 0.00 4.17
2332 2866 2.854424 GCGTGAGAATGTGTGGTTGTTG 60.854 50.000 0.00 0.00 0.00 3.33
2333 2867 1.333619 GCGTGAGAATGTGTGGTTGTT 59.666 47.619 0.00 0.00 0.00 2.83
2334 2868 0.944386 GCGTGAGAATGTGTGGTTGT 59.056 50.000 0.00 0.00 0.00 3.32
2335 2869 0.110688 CGCGTGAGAATGTGTGGTTG 60.111 55.000 0.00 0.00 0.00 3.77
2336 2870 0.531974 ACGCGTGAGAATGTGTGGTT 60.532 50.000 12.93 0.00 0.00 3.67
2342 2876 0.859232 GTCAACACGCGTGAGAATGT 59.141 50.000 42.94 19.18 32.89 2.71
2355 2889 1.928567 GGGGATGGGAGGGTCAACA 60.929 63.158 0.00 0.00 0.00 3.33
2357 2891 1.151474 TTGGGGATGGGAGGGTCAA 60.151 57.895 0.00 0.00 0.00 3.18
2371 2905 1.683917 CGTGGAGAGATAGAGGTTGGG 59.316 57.143 0.00 0.00 0.00 4.12
2373 2907 1.067821 GGCGTGGAGAGATAGAGGTTG 59.932 57.143 0.00 0.00 0.00 3.77
2374 2908 1.404843 GGCGTGGAGAGATAGAGGTT 58.595 55.000 0.00 0.00 0.00 3.50
2376 2910 0.178975 AGGGCGTGGAGAGATAGAGG 60.179 60.000 0.00 0.00 0.00 3.69
2381 2915 3.474570 GGCAGGGCGTGGAGAGAT 61.475 66.667 9.49 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.