Multiple sequence alignment - TraesCS3D01G080300

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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 TraesCS3D01G080300 chr3D 100.000 5824 0 0 1 5824 40012355 40006532 0.000000e+00 10756.0
1 TraesCS3D01G080300 chr3D 88.225 2191 238 15 2714 4902 25397179 25395007 0.000000e+00 2599.0
2 TraesCS3D01G080300 chr3D 86.016 615 66 12 951 1548 25398696 25398085 4.920000e-180 641.0
3 TraesCS3D01G080300 chr3D 89.286 140 13 2 148 287 589759275 589759138 2.160000e-39 174.0
4 TraesCS3D01G080300 chr3D 93.333 90 5 1 2135 2224 420315597 420315685 1.320000e-26 132.0
5 TraesCS3D01G080300 chr3A 96.470 3711 91 9 2119 5824 51472767 51469092 0.000000e+00 6091.0
6 TraesCS3D01G080300 chr3A 96.328 1961 51 9 1 1955 51474705 51472760 0.000000e+00 3203.0
7 TraesCS3D01G080300 chr3A 98.131 107 1 1 2012 2118 719934330 719934225 9.970000e-43 185.0
8 TraesCS3D01G080300 chr3A 92.308 117 8 1 1956 2072 685775548 685775433 1.300000e-36 165.0
9 TraesCS3D01G080300 chr3A 86.957 138 16 2 150 287 719641060 719640925 2.810000e-33 154.0
10 TraesCS3D01G080300 chr3A 89.855 69 2 4 5058 5121 51469761 51469693 3.740000e-12 84.2
11 TraesCS3D01G080300 chr3B 96.486 3700 90 12 2135 5824 63411204 63407535 0.000000e+00 6076.0
12 TraesCS3D01G080300 chr3B 96.516 1952 55 9 1 1949 63413145 63411204 0.000000e+00 3216.0
13 TraesCS3D01G080300 chr3B 90.419 167 12 3 4848 5010 63400134 63399968 3.530000e-52 217.0
14 TraesCS3D01G080300 chr3B 95.000 40 2 0 2124 2163 228488084 228488045 4.870000e-06 63.9
15 TraesCS3D01G080300 chr3B 97.143 35 1 0 2296 2330 63411092 63411058 6.300000e-05 60.2
16 TraesCS3D01G080300 chr7D 87.077 2306 265 21 2714 5017 37801891 37804165 0.000000e+00 2577.0
17 TraesCS3D01G080300 chr7D 82.857 770 92 21 932 1665 37800360 37801125 0.000000e+00 654.0
18 TraesCS3D01G080300 chr7D 93.333 165 8 2 1956 2118 116693913 116693750 2.100000e-59 241.0
19 TraesCS3D01G080300 chr7D 91.279 172 6 4 1956 2118 352097300 352097129 5.870000e-55 226.0
20 TraesCS3D01G080300 chr7D 86.145 166 12 2 1953 2118 59938440 59938594 1.000000e-37 169.0
21 TraesCS3D01G080300 chr7D 93.069 101 6 1 2124 2224 66526371 66526272 4.700000e-31 147.0
22 TraesCS3D01G080300 chr7D 80.714 140 17 7 2162 2298 37801374 37801506 3.710000e-17 100.0
23 TraesCS3D01G080300 chr4A 87.853 2198 243 15 2714 4902 687180957 687178775 0.000000e+00 2558.0
24 TraesCS3D01G080300 chr4A 85.895 631 70 12 933 1548 687182451 687181825 0.000000e+00 654.0
25 TraesCS3D01G080300 chr4A 88.372 172 9 1 1956 2116 92743853 92743682 4.600000e-46 196.0
26 TraesCS3D01G080300 chr4A 84.000 100 8 6 2200 2298 687181443 687181351 8.040000e-14 89.8
27 TraesCS3D01G080300 chr7A 86.858 2298 264 21 2729 5017 37113835 37116103 0.000000e+00 2536.0
28 TraesCS3D01G080300 chr7A 85.950 605 68 9 954 1545 37112297 37112897 1.070000e-176 630.0
29 TraesCS3D01G080300 chr2D 93.939 165 9 1 1955 2119 613442769 613442932 1.250000e-61 248.0
30 TraesCS3D01G080300 chr2D 97.849 93 2 0 1956 2048 185386107 185386199 1.680000e-35 161.0
31 TraesCS3D01G080300 chr2B 88.889 189 8 3 1943 2119 305319071 305318884 2.730000e-53 220.0
32 TraesCS3D01G080300 chr2B 87.097 155 8 3 1965 2118 249532369 249532226 1.300000e-36 165.0
33 TraesCS3D01G080300 chr2B 87.097 155 8 3 1965 2118 291612852 291612709 1.300000e-36 165.0
34 TraesCS3D01G080300 chr1A 90.323 155 13 2 1965 2119 302943202 302943354 9.900000e-48 202.0
35 TraesCS3D01G080300 chr6A 87.730 163 10 1 1956 2118 609256203 609256051 1.290000e-41 182.0
36 TraesCS3D01G080300 chr5B 94.059 101 5 1 2124 2224 639280699 639280798 1.010000e-32 152.0
37 TraesCS3D01G080300 chr5B 83.537 164 6 2 1956 2119 617706273 617706415 3.660000e-27 134.0
38 TraesCS3D01G080300 chr7B 91.089 101 7 2 2124 2224 681240159 681240257 1.020000e-27 135.0
39 TraesCS3D01G080300 chr5D 98.630 73 1 0 2046 2118 329780531 329780603 4.740000e-26 130.0
40 TraesCS3D01G080300 chr5D 92.222 90 6 1 2133 2222 161443765 161443677 6.130000e-25 126.0
41 TraesCS3D01G080300 chr5D 91.304 92 7 1 2133 2224 20302688 20302598 2.200000e-24 124.0


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 TraesCS3D01G080300 chr3D 40006532 40012355 5823 True 10756.000000 10756 100.000000 1 5824 1 chr3D.!!$R1 5823
1 TraesCS3D01G080300 chr3D 25395007 25398696 3689 True 1620.000000 2599 87.120500 951 4902 2 chr3D.!!$R3 3951
2 TraesCS3D01G080300 chr3A 51469092 51474705 5613 True 3126.066667 6091 94.217667 1 5824 3 chr3A.!!$R4 5823
3 TraesCS3D01G080300 chr3B 63407535 63413145 5610 True 3117.400000 6076 96.715000 1 5824 3 chr3B.!!$R3 5823
4 TraesCS3D01G080300 chr7D 37800360 37804165 3805 False 1110.333333 2577 83.549333 932 5017 3 chr7D.!!$F2 4085
5 TraesCS3D01G080300 chr4A 687178775 687182451 3676 True 1100.600000 2558 85.916000 933 4902 3 chr4A.!!$R2 3969
6 TraesCS3D01G080300 chr7A 37112297 37116103 3806 False 1583.000000 2536 86.404000 954 5017 2 chr7A.!!$F1 4063

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
612 619 1.960417 TGTTTTCCACATCGAGCACA 58.040 45.000 0.00 0.00 0.00 4.57 F
2056 2124 1.067582 CCTAGGCGTCCGCTTTAGG 59.932 63.158 20.05 20.05 39.74 2.69 F
2097 2165 0.608035 CCCCAGTGCCTTAAAGCGAA 60.608 55.000 0.00 0.00 34.65 4.70 F
2098 2166 0.804989 CCCAGTGCCTTAAAGCGAAG 59.195 55.000 0.00 0.00 34.65 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2148 0.169009 GCTTCGCTTTAAGGCACTGG 59.831 55.000 10.44 0.0 40.86 4.00 R
4728 4932 1.343142 GGTTGGCTTGTTGGGGTTAAG 59.657 52.381 0.00 0.0 0.00 1.85 R
4817 5021 8.902040 GATAAAGAAAATGCTTTGTCTACAGG 57.098 34.615 5.50 0.0 40.60 4.00 R
4979 5186 9.822185 GAAATTCCATTTACCAAATAAGATGCT 57.178 29.630 0.00 0.0 31.47 3.79 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
274 275 2.818274 GCTCTAACCAACCGGCCG 60.818 66.667 21.04 21.04 34.57 6.13
438 443 9.603189 AAATACTATATCTGTACTGGTAAGCCT 57.397 33.333 0.00 0.00 35.27 4.58
612 619 1.960417 TGTTTTCCACATCGAGCACA 58.040 45.000 0.00 0.00 0.00 4.57
785 792 9.995957 GAGCAAAGACTTCTTTCCTAATAAATC 57.004 33.333 1.04 0.00 43.72 2.17
806 813 8.414629 AAATCATAGGGAGGAATATCAAAAGC 57.585 34.615 0.00 0.00 0.00 3.51
814 821 6.044682 GGAGGAATATCAAAAGCAAATGGTG 58.955 40.000 0.00 0.00 0.00 4.17
947 954 6.781138 TGCAATGTTTTCCGTCACTATAATC 58.219 36.000 0.00 0.00 0.00 1.75
950 957 8.774586 GCAATGTTTTCCGTCACTATAATCTAT 58.225 33.333 0.00 0.00 0.00 1.98
1413 1437 3.701532 TTTTTCTTACACTGGGCAACG 57.298 42.857 0.00 0.00 37.60 4.10
1953 2021 2.951642 CAGGAGGAGCAGTTTGTTTCAA 59.048 45.455 0.00 0.00 0.00 2.69
1955 2023 3.823304 AGGAGGAGCAGTTTGTTTCAATC 59.177 43.478 0.00 0.00 0.00 2.67
1957 2025 5.003804 GGAGGAGCAGTTTGTTTCAATCTA 58.996 41.667 0.00 0.00 0.00 1.98
1958 2026 5.649831 GGAGGAGCAGTTTGTTTCAATCTAT 59.350 40.000 0.00 0.00 0.00 1.98
1959 2027 6.404074 GGAGGAGCAGTTTGTTTCAATCTATG 60.404 42.308 0.00 0.00 0.00 2.23
1960 2028 6.006449 AGGAGCAGTTTGTTTCAATCTATGT 58.994 36.000 0.00 0.00 0.00 2.29
1961 2029 6.491403 AGGAGCAGTTTGTTTCAATCTATGTT 59.509 34.615 0.00 0.00 0.00 2.71
1962 2030 7.014615 AGGAGCAGTTTGTTTCAATCTATGTTT 59.985 33.333 0.00 0.00 0.00 2.83
1963 2031 7.653311 GGAGCAGTTTGTTTCAATCTATGTTTT 59.347 33.333 0.00 0.00 0.00 2.43
1964 2032 8.947055 AGCAGTTTGTTTCAATCTATGTTTTT 57.053 26.923 0.00 0.00 0.00 1.94
1970 2038 8.514136 TTGTTTCAATCTATGTTTTTAAGGCG 57.486 30.769 0.00 0.00 0.00 5.52
1971 2039 7.653647 TGTTTCAATCTATGTTTTTAAGGCGT 58.346 30.769 0.00 0.00 0.00 5.68
1972 2040 7.806014 TGTTTCAATCTATGTTTTTAAGGCGTC 59.194 33.333 0.00 0.00 0.00 5.19
1973 2041 6.431198 TCAATCTATGTTTTTAAGGCGTCC 57.569 37.500 0.00 0.00 0.00 4.79
1974 2042 5.064198 TCAATCTATGTTTTTAAGGCGTCCG 59.936 40.000 0.00 0.00 0.00 4.79
1975 2043 3.929094 TCTATGTTTTTAAGGCGTCCGT 58.071 40.909 0.00 0.00 0.00 4.69
1976 2044 5.070770 TCTATGTTTTTAAGGCGTCCGTA 57.929 39.130 0.00 0.00 0.00 4.02
1977 2045 5.477510 TCTATGTTTTTAAGGCGTCCGTAA 58.522 37.500 0.00 0.00 0.00 3.18
1978 2046 4.673534 ATGTTTTTAAGGCGTCCGTAAG 57.326 40.909 4.97 0.00 30.10 2.34
1998 2066 4.327885 GAAGCCTATGCGTCGAGG 57.672 61.111 0.00 0.00 44.33 4.63
2054 2122 2.497770 GCCTAGGCGTCCGCTTTA 59.502 61.111 20.16 4.28 41.60 1.85
2055 2123 1.591863 GCCTAGGCGTCCGCTTTAG 60.592 63.158 20.16 12.65 41.60 1.85
2056 2124 1.067582 CCTAGGCGTCCGCTTTAGG 59.932 63.158 20.05 20.05 39.74 2.69
2057 2125 1.591863 CTAGGCGTCCGCTTTAGGC 60.592 63.158 11.82 0.00 41.60 3.93
2094 2162 4.018409 CCCCCAGTGCCTTAAAGC 57.982 61.111 0.00 0.00 0.00 3.51
2095 2163 2.046285 CCCCCAGTGCCTTAAAGCG 61.046 63.158 0.00 0.00 34.65 4.68
2096 2164 1.002624 CCCCAGTGCCTTAAAGCGA 60.003 57.895 0.00 0.00 34.65 4.93
2097 2165 0.608035 CCCCAGTGCCTTAAAGCGAA 60.608 55.000 0.00 0.00 34.65 4.70
2098 2166 0.804989 CCCAGTGCCTTAAAGCGAAG 59.195 55.000 0.00 0.00 34.65 3.79
2113 2181 1.587991 CGAAGCGTCGCCTTAAAAAC 58.412 50.000 14.86 0.00 41.08 2.43
2114 2182 1.070443 CGAAGCGTCGCCTTAAAAACA 60.070 47.619 14.86 0.00 41.08 2.83
2115 2183 2.412325 CGAAGCGTCGCCTTAAAAACAT 60.412 45.455 14.86 0.00 41.08 2.71
2116 2184 3.181528 CGAAGCGTCGCCTTAAAAACATA 60.182 43.478 14.86 0.00 41.08 2.29
2117 2185 4.331962 GAAGCGTCGCCTTAAAAACATAG 58.668 43.478 14.86 0.00 0.00 2.23
2118 2186 2.676342 AGCGTCGCCTTAAAAACATAGG 59.324 45.455 14.86 0.00 0.00 2.57
2119 2187 2.417586 GCGTCGCCTTAAAAACATAGGT 59.582 45.455 5.75 0.00 0.00 3.08
2120 2188 3.120095 GCGTCGCCTTAAAAACATAGGTT 60.120 43.478 5.75 0.00 39.43 3.50
2122 2190 5.084055 CGTCGCCTTAAAAACATAGGTTTC 58.916 41.667 5.89 0.00 46.20 2.78
2123 2191 5.334260 CGTCGCCTTAAAAACATAGGTTTCA 60.334 40.000 5.89 0.00 46.20 2.69
2164 2232 6.540189 AGTTAGCATATAAAGTTGTCTGCCTG 59.460 38.462 0.00 0.00 0.00 4.85
2255 2324 9.860898 AAATGTCTAGAATTTAAATCTTGCCAC 57.139 29.630 0.10 0.00 0.00 5.01
2268 2337 1.895131 CTTGCCACTGCCTTGGTTTAT 59.105 47.619 2.82 0.00 39.09 1.40
2269 2338 2.889170 TGCCACTGCCTTGGTTTATA 57.111 45.000 2.82 0.00 39.09 0.98
2273 2342 4.080015 TGCCACTGCCTTGGTTTATATAGT 60.080 41.667 2.82 0.00 39.09 2.12
2330 2399 6.324512 TGCCTTGGTTTATAGCATCATTCATT 59.675 34.615 0.00 0.00 0.00 2.57
2366 2435 5.230182 TGCTTACATATAGGCATCTTCACG 58.770 41.667 0.00 0.00 38.40 4.35
2390 2459 2.227194 CTTCGTTACTGCCCCTTTGTT 58.773 47.619 0.00 0.00 0.00 2.83
2711 2899 7.867403 GGTTTTCATTGTTTGTACTGTCATGAT 59.133 33.333 0.00 0.00 0.00 2.45
2807 3002 4.523083 TGGATGAAACTAGGGATTTTCCG 58.477 43.478 0.00 0.00 37.43 4.30
3353 3555 1.613630 ATGTGGAGGAGAAGGCGGT 60.614 57.895 0.00 0.00 0.00 5.68
4538 4742 1.884579 CTCCCCTGCATGCATGTTATC 59.115 52.381 26.79 11.44 0.00 1.75
4728 4932 2.685850 TAAACCTAGAAGGAAGCGGC 57.314 50.000 0.00 0.00 37.67 6.53
4817 5021 0.595095 CCACCTGTGAAGCTGCTTTC 59.405 55.000 17.10 12.97 0.00 2.62
4979 5186 3.133901 TCGCCATTCTTGCTGGATAAGTA 59.866 43.478 0.00 0.00 35.70 2.24
4991 5198 7.734924 TGCTGGATAAGTAGCATCTTATTTG 57.265 36.000 12.41 8.44 44.36 2.32
5078 5285 9.219603 TCAAACATCTATGCCTAGTATTATTGC 57.780 33.333 0.00 0.00 0.00 3.56
5079 5286 8.454106 CAAACATCTATGCCTAGTATTATTGCC 58.546 37.037 0.00 0.00 0.00 4.52
5095 5302 1.305201 TGCCTTCCACGAACAAGAAC 58.695 50.000 0.00 0.00 0.00 3.01
5129 5338 1.970640 ACTTTTGGTTGCCTTCCATCC 59.029 47.619 0.00 0.00 34.75 3.51
5134 5343 0.685458 GGTTGCCTTCCATCCATGCT 60.685 55.000 0.00 0.00 34.13 3.79
5146 5355 7.667219 CCTTCCATCCATGCTTAGTATTATTGT 59.333 37.037 0.00 0.00 0.00 2.71
5205 5414 2.215907 TTGGTTGCCGAATTGTTGTG 57.784 45.000 0.00 0.00 0.00 3.33
5213 5422 3.243234 TGCCGAATTGTTGTGTAGGTTTG 60.243 43.478 0.00 0.00 0.00 2.93
5237 5448 0.911769 CCACCCTGACTCTAATGCCA 59.088 55.000 0.00 0.00 0.00 4.92
5251 5462 3.333029 AATGCCATTTAACTTGCACCC 57.667 42.857 0.00 0.00 36.41 4.61
5252 5463 2.008242 TGCCATTTAACTTGCACCCT 57.992 45.000 0.00 0.00 0.00 4.34
5253 5464 1.617850 TGCCATTTAACTTGCACCCTG 59.382 47.619 0.00 0.00 0.00 4.45
5254 5465 1.892474 GCCATTTAACTTGCACCCTGA 59.108 47.619 0.00 0.00 0.00 3.86
5255 5466 2.298729 GCCATTTAACTTGCACCCTGAA 59.701 45.455 0.00 0.00 0.00 3.02
5256 5467 3.860754 GCCATTTAACTTGCACCCTGAAC 60.861 47.826 0.00 0.00 0.00 3.18
5257 5468 3.573967 CCATTTAACTTGCACCCTGAACT 59.426 43.478 0.00 0.00 0.00 3.01
5258 5469 4.321230 CCATTTAACTTGCACCCTGAACTC 60.321 45.833 0.00 0.00 0.00 3.01
5259 5470 2.561478 TAACTTGCACCCTGAACTCC 57.439 50.000 0.00 0.00 0.00 3.85
5260 5471 0.846693 AACTTGCACCCTGAACTCCT 59.153 50.000 0.00 0.00 0.00 3.69
5261 5472 1.729586 ACTTGCACCCTGAACTCCTA 58.270 50.000 0.00 0.00 0.00 2.94
5262 5473 1.625818 ACTTGCACCCTGAACTCCTAG 59.374 52.381 0.00 0.00 0.00 3.02
5263 5474 1.902508 CTTGCACCCTGAACTCCTAGA 59.097 52.381 0.00 0.00 0.00 2.43
5264 5475 2.024176 TGCACCCTGAACTCCTAGAA 57.976 50.000 0.00 0.00 0.00 2.10
5315 5526 1.595058 TTCCTCTCCTCTCCCCTCCC 61.595 65.000 0.00 0.00 0.00 4.30
5316 5527 2.612251 CTCTCCTCTCCCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
5317 5528 2.018086 CTCTCCTCTCCCCTCCCCT 61.018 68.421 0.00 0.00 0.00 4.79
5318 5529 2.285180 CTCCTCTCCCCTCCCCTG 59.715 72.222 0.00 0.00 0.00 4.45
5334 5545 1.679139 CCTGCCTGTGTCTTTGTTCA 58.321 50.000 0.00 0.00 0.00 3.18
5382 5593 4.407296 CCTTTGCTACTCTCCATAGTCCTT 59.593 45.833 0.00 0.00 0.00 3.36
5410 5621 1.476891 TCAAGCTAGCCACCTACTTCG 59.523 52.381 12.13 0.00 0.00 3.79
5413 5624 1.064166 AGCTAGCCACCTACTTCGGTA 60.064 52.381 12.13 0.00 34.94 4.02
5430 5641 1.074889 GGTAGGTGTGGAATGGTGGTT 59.925 52.381 0.00 0.00 0.00 3.67
5441 5652 2.985847 GGTGGTTGCTGGCCAGAC 60.986 66.667 37.21 25.15 36.57 3.51
5501 5715 4.262938 GCAAAGGTGGAGGTCTTACTACTT 60.263 45.833 0.00 0.00 0.00 2.24
5548 5762 7.363968 GGTGCTAGGTTGAGTTCTTACTATCTT 60.364 40.741 0.00 0.00 33.84 2.40
5646 5860 9.844257 TTTCATACATTTGATTTGGTTTTCCTT 57.156 25.926 0.00 0.00 41.38 3.36
5662 5876 7.076362 GGTTTTCCTTGAATTCGAAGTACTTC 58.924 38.462 23.25 23.25 36.94 3.01
5671 5885 4.978083 TTCGAAGTACTTCCTAGCGATT 57.022 40.909 26.12 0.00 36.27 3.34
5705 5919 6.571731 CGTCTGAACTAATCTTCCACTGGTAA 60.572 42.308 0.00 0.00 0.00 2.85
5736 5950 4.452455 GGTGCTAATACCCATCGATGAAAG 59.548 45.833 26.86 16.27 34.56 2.62
5747 5961 5.121811 CCATCGATGAAAGGAATTCTGACT 58.878 41.667 26.86 0.00 38.92 3.41
5764 5978 2.357637 TGACTGTTGCTGTTTGGCTAAC 59.642 45.455 4.82 4.82 37.26 2.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
274 275 7.637709 AAATAAAATTCAAGAACCGAGCAAC 57.362 32.000 0.00 0.00 0.00 4.17
416 421 6.265649 CACAGGCTTACCAGTACAGATATAGT 59.734 42.308 0.00 0.00 39.06 2.12
623 630 1.364269 TAACCATTGGGAACGGGACT 58.636 50.000 7.78 0.00 38.05 3.85
675 682 5.873712 ACCATCGCAGATCTATGATGATTTC 59.126 40.000 26.38 0.00 45.12 2.17
691 698 4.681074 TCCAATCAAGTATACCATCGCA 57.319 40.909 0.00 0.00 0.00 5.10
785 792 7.587037 TTTGCTTTTGATATTCCTCCCTATG 57.413 36.000 0.00 0.00 0.00 2.23
806 813 1.229428 ACGACAGACTGCACCATTTG 58.771 50.000 1.25 0.00 0.00 2.32
814 821 1.083401 CGCACAAACGACAGACTGC 60.083 57.895 1.25 0.00 34.06 4.40
867 874 7.865385 GCACCAGTTTAACATGAGATTTTACAA 59.135 33.333 0.00 0.00 0.00 2.41
922 929 4.685169 ATAGTGACGGAAAACATTGCAG 57.315 40.909 0.00 0.00 0.00 4.41
1402 1426 0.670546 CACTCCTACGTTGCCCAGTG 60.671 60.000 0.00 0.34 0.00 3.66
1409 1433 2.236690 CGTTACGACACTCCTACGTTG 58.763 52.381 0.00 0.00 40.61 4.10
1413 1437 3.737305 GTGTACGTTACGACACTCCTAC 58.263 50.000 22.81 11.05 42.21 3.18
1953 2021 4.510571 ACGGACGCCTTAAAAACATAGAT 58.489 39.130 0.00 0.00 0.00 1.98
1955 2023 5.220529 CCTTACGGACGCCTTAAAAACATAG 60.221 44.000 0.00 0.00 0.00 2.23
1957 2025 3.437741 CCTTACGGACGCCTTAAAAACAT 59.562 43.478 0.00 0.00 0.00 2.71
1958 2026 2.807392 CCTTACGGACGCCTTAAAAACA 59.193 45.455 0.00 0.00 0.00 2.83
1959 2027 2.413239 GCCTTACGGACGCCTTAAAAAC 60.413 50.000 0.00 0.00 0.00 2.43
1960 2028 1.805943 GCCTTACGGACGCCTTAAAAA 59.194 47.619 0.00 0.00 0.00 1.94
1961 2029 1.441738 GCCTTACGGACGCCTTAAAA 58.558 50.000 0.00 0.00 0.00 1.52
1962 2030 0.737019 CGCCTTACGGACGCCTTAAA 60.737 55.000 0.00 0.00 38.44 1.52
1963 2031 1.153784 CGCCTTACGGACGCCTTAA 60.154 57.895 0.00 0.00 38.44 1.85
1964 2032 1.594194 TTCGCCTTACGGACGCCTTA 61.594 55.000 0.00 0.00 43.89 2.69
1965 2033 2.830704 CTTCGCCTTACGGACGCCTT 62.831 60.000 0.00 0.00 43.89 4.35
1966 2034 3.352338 CTTCGCCTTACGGACGCCT 62.352 63.158 0.00 0.00 43.89 5.52
1967 2035 2.884207 CTTCGCCTTACGGACGCC 60.884 66.667 0.00 0.00 43.89 5.68
1968 2036 3.551915 GCTTCGCCTTACGGACGC 61.552 66.667 0.00 0.00 43.89 5.19
1969 2037 2.884207 GGCTTCGCCTTACGGACG 60.884 66.667 0.00 0.00 46.69 4.79
1981 2049 4.327885 CCTCGACGCATAGGCTTC 57.672 61.111 0.00 0.00 38.10 3.86
2003 2071 1.603236 TATTTGCAAAGCGCTGGGGG 61.603 55.000 12.58 1.49 43.06 5.40
2004 2072 0.461135 ATATTTGCAAAGCGCTGGGG 59.539 50.000 12.58 4.50 43.06 4.96
2005 2073 1.563111 CATATTTGCAAAGCGCTGGG 58.437 50.000 12.58 7.58 43.06 4.45
2037 2105 1.591863 CTAAAGCGGACGCCTAGGC 60.592 63.158 24.75 24.75 43.17 3.93
2038 2106 1.067582 CCTAAAGCGGACGCCTAGG 59.932 63.158 20.88 20.88 43.17 3.02
2039 2107 1.591863 GCCTAAAGCGGACGCCTAG 60.592 63.158 13.63 13.52 43.17 3.02
2040 2108 2.497770 GCCTAAAGCGGACGCCTA 59.502 61.111 13.63 4.63 43.17 3.93
2077 2145 2.046285 CGCTTTAAGGCACTGGGGG 61.046 63.158 10.44 0.00 40.86 5.40
2078 2146 0.608035 TTCGCTTTAAGGCACTGGGG 60.608 55.000 10.44 0.00 40.86 4.96
2079 2147 0.804989 CTTCGCTTTAAGGCACTGGG 59.195 55.000 10.44 0.00 40.86 4.45
2080 2148 0.169009 GCTTCGCTTTAAGGCACTGG 59.831 55.000 10.44 0.00 40.86 4.00
2081 2149 0.179215 CGCTTCGCTTTAAGGCACTG 60.179 55.000 10.44 0.00 40.86 3.66
2083 2151 0.179222 GACGCTTCGCTTTAAGGCAC 60.179 55.000 10.44 0.00 0.00 5.01
2084 2152 1.623081 CGACGCTTCGCTTTAAGGCA 61.623 55.000 10.44 0.00 38.71 4.75
2085 2153 1.058903 CGACGCTTCGCTTTAAGGC 59.941 57.895 0.00 0.00 38.71 4.35
2095 2163 2.673976 TGTTTTTAAGGCGACGCTTC 57.326 45.000 20.77 3.61 0.00 3.86
2096 2164 3.126343 CCTATGTTTTTAAGGCGACGCTT 59.874 43.478 20.77 9.77 0.00 4.68
2097 2165 2.676342 CCTATGTTTTTAAGGCGACGCT 59.324 45.455 20.77 2.90 0.00 5.07
2098 2166 2.417586 ACCTATGTTTTTAAGGCGACGC 59.582 45.455 12.43 12.43 33.42 5.19
2099 2167 4.673534 AACCTATGTTTTTAAGGCGACG 57.326 40.909 0.00 0.00 33.42 5.12
2100 2168 6.004408 TGAAACCTATGTTTTTAAGGCGAC 57.996 37.500 0.00 0.00 44.57 5.19
2101 2169 6.636562 TTGAAACCTATGTTTTTAAGGCGA 57.363 33.333 0.00 0.00 44.57 5.54
2102 2170 6.866248 ACATTGAAACCTATGTTTTTAAGGCG 59.134 34.615 0.00 0.00 44.57 5.52
2103 2171 8.495148 CAACATTGAAACCTATGTTTTTAAGGC 58.505 33.333 0.00 0.00 44.57 4.35
2104 2172 9.541143 ACAACATTGAAACCTATGTTTTTAAGG 57.459 29.630 0.00 2.36 44.57 2.69
2106 2174 9.319143 CCACAACATTGAAACCTATGTTTTTAA 57.681 29.630 0.00 0.00 44.57 1.52
2107 2175 8.478877 ACCACAACATTGAAACCTATGTTTTTA 58.521 29.630 0.00 0.00 44.57 1.52
2108 2176 7.334858 ACCACAACATTGAAACCTATGTTTTT 58.665 30.769 0.00 0.00 44.57 1.94
2109 2177 6.883744 ACCACAACATTGAAACCTATGTTTT 58.116 32.000 0.00 0.00 44.57 2.43
2111 2179 6.478512 AACCACAACATTGAAACCTATGTT 57.521 33.333 0.00 0.00 43.70 2.71
2112 2180 6.208599 CCTAACCACAACATTGAAACCTATGT 59.791 38.462 0.00 0.00 36.58 2.29
2113 2181 6.620678 CCTAACCACAACATTGAAACCTATG 58.379 40.000 0.00 0.00 0.00 2.23
2114 2182 5.185056 GCCTAACCACAACATTGAAACCTAT 59.815 40.000 0.00 0.00 0.00 2.57
2115 2183 4.521256 GCCTAACCACAACATTGAAACCTA 59.479 41.667 0.00 0.00 0.00 3.08
2116 2184 3.320826 GCCTAACCACAACATTGAAACCT 59.679 43.478 0.00 0.00 0.00 3.50
2117 2185 3.068873 TGCCTAACCACAACATTGAAACC 59.931 43.478 0.00 0.00 0.00 3.27
2118 2186 4.202111 ACTGCCTAACCACAACATTGAAAC 60.202 41.667 0.00 0.00 0.00 2.78
2119 2187 3.957497 ACTGCCTAACCACAACATTGAAA 59.043 39.130 0.00 0.00 0.00 2.69
2120 2188 3.561143 ACTGCCTAACCACAACATTGAA 58.439 40.909 0.00 0.00 0.00 2.69
2121 2189 3.222173 ACTGCCTAACCACAACATTGA 57.778 42.857 0.00 0.00 0.00 2.57
2122 2190 4.615912 GCTAACTGCCTAACCACAACATTG 60.616 45.833 0.00 0.00 35.15 2.82
2123 2191 3.506067 GCTAACTGCCTAACCACAACATT 59.494 43.478 0.00 0.00 35.15 2.71
2164 2232 6.808704 CAGCTAAAAACTCCAGAAAATAAGGC 59.191 38.462 0.00 0.00 0.00 4.35
2366 2435 0.320697 AGGGGCAGTAACGAAGTGTC 59.679 55.000 0.00 0.00 45.00 3.67
2807 3002 1.483415 ACATCATGGCCAAATTCCAGC 59.517 47.619 10.96 0.00 36.98 4.85
4728 4932 1.343142 GGTTGGCTTGTTGGGGTTAAG 59.657 52.381 0.00 0.00 0.00 1.85
4817 5021 8.902040 GATAAAGAAAATGCTTTGTCTACAGG 57.098 34.615 5.50 0.00 40.60 4.00
4979 5186 9.822185 GAAATTCCATTTACCAAATAAGATGCT 57.178 29.630 0.00 0.00 31.47 3.79
4988 5195 7.847711 TCCTTGAGAAATTCCATTTACCAAA 57.152 32.000 0.00 0.00 31.47 3.28
4991 5198 7.410120 ACATCCTTGAGAAATTCCATTTACC 57.590 36.000 0.00 0.00 31.47 2.85
5078 5285 5.334879 CCTTAATGTTCTTGTTCGTGGAAGG 60.335 44.000 0.00 0.00 0.00 3.46
5079 5286 5.468746 TCCTTAATGTTCTTGTTCGTGGAAG 59.531 40.000 0.00 0.00 0.00 3.46
5095 5302 7.415653 GGCAACCAAAAGTAGATCTCCTTAATG 60.416 40.741 0.00 2.76 0.00 1.90
5129 5338 9.276590 TCATGGAAGACAATAATACTAAGCATG 57.723 33.333 0.00 0.00 0.00 4.06
5205 5414 2.158579 TCAGGGTGGAAACCAAACCTAC 60.159 50.000 12.64 0.00 39.93 3.18
5213 5422 3.610911 CATTAGAGTCAGGGTGGAAACC 58.389 50.000 0.00 0.00 0.00 3.27
5237 5448 3.826729 GGAGTTCAGGGTGCAAGTTAAAT 59.173 43.478 0.00 0.00 0.00 1.40
5251 5462 5.393678 GCTACTTCTGGTTCTAGGAGTTCAG 60.394 48.000 2.62 0.00 37.66 3.02
5252 5463 4.463186 GCTACTTCTGGTTCTAGGAGTTCA 59.537 45.833 2.62 0.00 37.66 3.18
5253 5464 4.463186 TGCTACTTCTGGTTCTAGGAGTTC 59.537 45.833 2.62 0.00 37.66 3.01
5254 5465 4.221041 GTGCTACTTCTGGTTCTAGGAGTT 59.779 45.833 2.62 0.00 37.66 3.01
5255 5466 3.764972 GTGCTACTTCTGGTTCTAGGAGT 59.235 47.826 2.86 2.86 39.78 3.85
5256 5467 3.131400 GGTGCTACTTCTGGTTCTAGGAG 59.869 52.174 0.00 0.00 0.00 3.69
5257 5468 3.097614 GGTGCTACTTCTGGTTCTAGGA 58.902 50.000 0.00 0.00 0.00 2.94
5258 5469 2.832129 TGGTGCTACTTCTGGTTCTAGG 59.168 50.000 0.00 0.00 0.00 3.02
5259 5470 4.744795 ATGGTGCTACTTCTGGTTCTAG 57.255 45.455 0.00 0.00 0.00 2.43
5260 5471 5.012664 TGAAATGGTGCTACTTCTGGTTCTA 59.987 40.000 0.00 0.00 0.00 2.10
5261 5472 4.202461 TGAAATGGTGCTACTTCTGGTTCT 60.202 41.667 0.00 0.00 0.00 3.01
5262 5473 4.072131 TGAAATGGTGCTACTTCTGGTTC 58.928 43.478 0.00 0.00 0.00 3.62
5263 5474 4.098914 TGAAATGGTGCTACTTCTGGTT 57.901 40.909 0.00 0.00 0.00 3.67
5264 5475 3.788227 TGAAATGGTGCTACTTCTGGT 57.212 42.857 0.00 0.00 0.00 4.00
5315 5526 1.334869 GTGAACAAAGACACAGGCAGG 59.665 52.381 0.00 0.00 37.05 4.85
5316 5527 2.289002 GAGTGAACAAAGACACAGGCAG 59.711 50.000 0.00 0.00 39.18 4.85
5317 5528 2.288666 GAGTGAACAAAGACACAGGCA 58.711 47.619 0.00 0.00 39.18 4.75
5318 5529 1.604278 GGAGTGAACAAAGACACAGGC 59.396 52.381 0.00 0.00 39.18 4.85
5334 5545 0.548197 TTTGGGGTCGGTATGGGAGT 60.548 55.000 0.00 0.00 0.00 3.85
5382 5593 1.047801 TGGCTAGCTTGACAGTGACA 58.952 50.000 15.72 0.00 0.00 3.58
5410 5621 0.696501 ACCACCATTCCACACCTACC 59.303 55.000 0.00 0.00 0.00 3.18
5413 5624 0.827507 GCAACCACCATTCCACACCT 60.828 55.000 0.00 0.00 0.00 4.00
5430 5641 3.957586 CCACAGGTCTGGCCAGCA 61.958 66.667 28.91 14.20 40.61 4.41
5441 5652 1.675641 GGTTGCCAGTAGCCACAGG 60.676 63.158 0.00 0.00 42.71 4.00
5473 5684 3.268032 CCTCCACCTTTGCCCCCT 61.268 66.667 0.00 0.00 0.00 4.79
5501 5715 5.939883 CACCCAAGAGTCACAGAATTAATCA 59.060 40.000 0.00 0.00 0.00 2.57
5642 5856 5.740290 AGGAAGTACTTCGAATTCAAGGA 57.260 39.130 25.44 9.37 40.37 3.36
5646 5860 4.397103 TCGCTAGGAAGTACTTCGAATTCA 59.603 41.667 25.44 8.71 40.37 2.57
5662 5876 3.752222 AGACGTAGGATACAATCGCTAGG 59.248 47.826 0.00 0.00 43.24 3.02
5671 5885 7.013083 GGAAGATTAGTTCAGACGTAGGATACA 59.987 40.741 0.00 0.00 43.24 2.29
5717 5931 7.880195 AGAATTCCTTTCATCGATGGGTATTAG 59.120 37.037 24.61 12.29 36.75 1.73
5725 5939 5.583854 ACAGTCAGAATTCCTTTCATCGATG 59.416 40.000 19.61 19.61 36.75 3.84
5730 5944 5.048224 CAGCAACAGTCAGAATTCCTTTCAT 60.048 40.000 0.65 0.00 36.75 2.57
5736 5950 4.293415 CAAACAGCAACAGTCAGAATTCC 58.707 43.478 0.65 0.00 0.00 3.01
5747 5961 1.036707 GGGTTAGCCAAACAGCAACA 58.963 50.000 0.00 0.00 40.08 3.33
5783 5997 3.153919 GGTGAACCTGCAATGGTAAAGA 58.846 45.455 0.00 0.00 39.83 2.52
5784 5998 2.095263 CGGTGAACCTGCAATGGTAAAG 60.095 50.000 0.00 0.00 39.83 1.85
5792 6006 1.371183 CCTCTCGGTGAACCTGCAA 59.629 57.895 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.