Multiple sequence alignment - TraesCS1D01G411500

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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 TraesCS1D01G411500 chr1D 100.000 2555 0 0 1 2555 473034187 473031633 0.000000e+00 4719.0
1 TraesCS1D01G411500 chr1A 95.151 1093 43 4 884 1966 566687689 566686597 0.000000e+00 1716.0
2 TraesCS1D01G411500 chr1A 93.267 505 13 2 1 484 566688816 566688312 0.000000e+00 725.0
3 TraesCS1D01G411500 chr1A 90.315 413 35 3 477 888 566688121 566687713 1.040000e-148 536.0
4 TraesCS1D01G411500 chr1A 88.889 72 8 0 2063 2134 364939945 364939874 3.500000e-14 89.8
5 TraesCS1D01G411500 chr1B 95.612 866 22 4 736 1600 657505914 657505064 0.000000e+00 1375.0
6 TraesCS1D01G411500 chr1B 89.480 827 34 19 1 801 657506703 657505904 0.000000e+00 996.0
7 TraesCS1D01G411500 chr1B 92.920 452 32 0 1952 2403 657503203 657502752 0.000000e+00 658.0
8 TraesCS1D01G411500 chr1B 88.272 162 10 5 1583 1744 657505045 657504893 4.340000e-43 185.0
9 TraesCS1D01G411500 chr1B 81.295 139 19 4 1756 1892 519505746 519505613 3.480000e-19 106.0
10 TraesCS1D01G411500 chr1B 81.295 139 19 4 1756 1892 519518227 519518094 3.480000e-19 106.0
11 TraesCS1D01G411500 chr1B 94.872 39 0 2 1706 1742 358017754 358017792 2.750000e-05 60.2
12 TraesCS1D01G411500 chr1B 83.333 66 7 4 1680 1744 121481157 121481219 9.870000e-05 58.4
13 TraesCS1D01G411500 chr1B 83.333 66 7 4 1680 1744 121603850 121603912 9.870000e-05 58.4
14 TraesCS1D01G411500 chr7D 81.731 208 38 0 2053 2260 22860747 22860540 9.400000e-40 174.0
15 TraesCS1D01G411500 chr7D 93.805 113 6 1 2439 2551 257459027 257459138 4.370000e-38 169.0
16 TraesCS1D01G411500 chr7D 92.241 116 7 2 2439 2553 629889042 629889156 2.030000e-36 163.0
17 TraesCS1D01G411500 chr3D 94.595 111 6 0 2441 2551 437738174 437738284 3.380000e-39 172.0
18 TraesCS1D01G411500 chr6A 93.103 116 7 1 2436 2551 445697656 445697770 4.370000e-38 169.0
19 TraesCS1D01G411500 chr6A 77.273 154 23 7 1744 1892 607453954 607453808 2.110000e-11 80.5
20 TraesCS1D01G411500 chr3A 93.103 116 6 1 2438 2551 27031145 27031030 4.370000e-38 169.0
21 TraesCS1D01G411500 chr5B 92.982 114 6 2 2439 2551 633283960 633283848 5.660000e-37 165.0
22 TraesCS1D01G411500 chr5B 81.818 154 22 5 1744 1895 275306817 275306966 9.600000e-25 124.0
23 TraesCS1D01G411500 chr5B 80.921 152 19 5 1744 1892 328105742 328105886 7.470000e-21 111.0
24 TraesCS1D01G411500 chr4A 82.199 191 34 0 2067 2257 706659663 706659853 5.660000e-37 165.0
25 TraesCS1D01G411500 chr4A 79.167 144 17 7 1755 1892 9613148 9613012 1.260000e-13 87.9
26 TraesCS1D01G411500 chr4A 77.941 136 22 6 1761 1893 476341651 476341521 7.580000e-11 78.7
27 TraesCS1D01G411500 chr4A 97.059 34 0 1 1711 1743 53013333 53013300 3.550000e-04 56.5
28 TraesCS1D01G411500 chr2D 92.308 117 7 2 2436 2551 575579484 575579599 5.660000e-37 165.0
29 TraesCS1D01G411500 chr4D 92.920 113 6 2 2438 2549 39214037 39213926 2.030000e-36 163.0
30 TraesCS1D01G411500 chr4D 79.412 136 20 6 1761 1893 100227831 100227961 3.500000e-14 89.8
31 TraesCS1D01G411500 chr5D 92.105 114 9 0 2438 2551 242955396 242955509 7.320000e-36 161.0
32 TraesCS1D01G411500 chr5D 80.612 196 38 0 2063 2258 463240477 463240672 4.400000e-33 152.0
33 TraesCS1D01G411500 chr6D 100.000 33 0 0 1711 1743 464610857 464610889 7.630000e-06 62.1
34 TraesCS1D01G411500 chr2A 92.500 40 3 0 1704 1743 633531684 633531645 9.870000e-05 58.4
35 TraesCS1D01G411500 chr3B 94.595 37 1 1 1707 1743 159567602 159567567 3.550000e-04 56.5
36 TraesCS1D01G411500 chr2B 94.444 36 1 1 1704 1739 18111194 18111228 1.000000e-03 54.7


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 TraesCS1D01G411500 chr1D 473031633 473034187 2554 True 4719.000000 4719 100.000 1 2555 1 chr1D.!!$R1 2554
1 TraesCS1D01G411500 chr1A 566686597 566688816 2219 True 992.333333 1716 92.911 1 1966 3 chr1A.!!$R2 1965
2 TraesCS1D01G411500 chr1B 657502752 657506703 3951 True 803.500000 1375 91.571 1 2403 4 chr1B.!!$R3 2402

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
44 45 0.179129 GCCATTGCGCTGCACTTATT 60.179 50.0 9.73 0.0 38.71 1.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2012 3852 0.390603 TTGCAATGGTCTACGACGGG 60.391 55.0 0.0 0.0 32.65 5.28 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
44 45 0.179129 GCCATTGCGCTGCACTTATT 60.179 50.000 9.73 0.00 38.71 1.40
162 163 6.529220 CCTTGAGGGAACAAGAATATAGAGG 58.471 44.000 9.55 0.00 46.85 3.69
414 435 4.603989 TTTCCCAACGTACATCACACTA 57.396 40.909 0.00 0.00 0.00 2.74
498 722 1.066303 GCGTGTTGGGTTTGATTGTCA 59.934 47.619 0.00 0.00 0.00 3.58
509 733 5.168569 GGTTTGATTGTCAGAGTGATCGTA 58.831 41.667 0.00 0.00 0.00 3.43
530 754 4.535526 ACTTTTATGGGGTTGCATGTTC 57.464 40.909 0.00 0.00 0.00 3.18
535 759 0.184692 TGGGGTTGCATGTTCTGTGA 59.815 50.000 0.00 0.00 0.00 3.58
541 765 3.433615 GGTTGCATGTTCTGTGAGTAGTC 59.566 47.826 0.00 0.00 0.00 2.59
554 778 1.816835 GAGTAGTCCACGTGTGATGGA 59.183 52.381 15.65 0.42 44.20 3.41
708 932 6.129194 GGTTTGATCGTTCCAGAAAATTTTCG 60.129 38.462 21.98 16.89 41.92 3.46
712 936 6.425721 TGATCGTTCCAGAAAATTTTCGTACT 59.574 34.615 21.98 5.10 41.92 2.73
734 959 1.089112 CGGCACACACATGACATGAT 58.911 50.000 22.19 6.78 0.00 2.45
778 1003 2.655090 TGCCTCTTGTGATTGTCCAA 57.345 45.000 0.00 0.00 0.00 3.53
881 1162 4.035208 CGTGACCACCAATTAATTAGCTCC 59.965 45.833 0.00 0.00 0.00 4.70
882 1163 4.947388 GTGACCACCAATTAATTAGCTCCA 59.053 41.667 0.00 0.00 0.00 3.86
933 1246 7.840342 AAATAAAGACTAGACTCATGCACAG 57.160 36.000 0.00 0.00 0.00 3.66
999 1312 1.675483 GCTCATCAAACACCACACACA 59.325 47.619 0.00 0.00 0.00 3.72
1324 1637 1.859398 GCAAACTGCATCGACGACA 59.141 52.632 0.00 0.00 44.26 4.35
1347 1660 1.952296 CATAGAGTGGCCAAGGCATTC 59.048 52.381 7.24 8.29 43.15 2.67
1420 1733 0.108424 CTTCAGCTCGGAGTTCAGGG 60.108 60.000 6.90 0.00 0.00 4.45
1755 2131 1.353022 AGGCAGGGTCCGTTCATAAAA 59.647 47.619 0.00 0.00 0.00 1.52
1813 2189 3.012518 AGACATGCTCTATTGTGTTGGC 58.987 45.455 0.00 0.00 0.00 4.52
1828 2204 4.244862 GTGTTGGCCCACTTATTTCATTG 58.755 43.478 8.65 0.00 32.50 2.82
1892 2272 8.533657 TCTTATATTTGTGAACGGAGGAAGTAA 58.466 33.333 0.00 0.00 0.00 2.24
1921 2301 7.063898 GCCAAGAAATTAAAAGAGGAATGAAGC 59.936 37.037 0.00 0.00 0.00 3.86
1971 3811 6.594159 CGACCAATATAAAGAGGTCTTGTTGT 59.406 38.462 8.60 0.00 46.45 3.32
1988 3828 4.047822 TGTTGTAGAAAAATTGCGCAAGG 58.952 39.130 28.62 0.00 38.28 3.61
2007 3847 3.605634 AGGGAAGTTTTGTTGCAAAACC 58.394 40.909 24.79 14.93 40.10 3.27
2012 3852 5.518847 GGAAGTTTTGTTGCAAAACCTAGAC 59.481 40.000 24.79 15.31 40.10 2.59
2017 3857 1.534163 GTTGCAAAACCTAGACCCGTC 59.466 52.381 0.00 0.00 0.00 4.79
2055 3895 9.135843 CAACCAGCATATATTTCATAAGCATTG 57.864 33.333 0.00 0.00 0.00 2.82
2072 3912 3.248363 GCATTGTTTTGCAAGGGAAGTTC 59.752 43.478 0.00 0.00 42.31 3.01
2084 3924 2.099098 AGGGAAGTTCTGTTGCAAAACG 59.901 45.455 0.00 0.00 0.00 3.60
2091 3931 2.215196 TCTGTTGCAAAACGTAGACCC 58.785 47.619 0.00 0.00 0.00 4.46
2113 3953 2.839975 TCGTAGACCATTGCAACAACA 58.160 42.857 0.00 0.00 0.00 3.33
2135 3975 7.941795 ACACATACGTTTCATAAGTATAGGC 57.058 36.000 0.00 0.00 30.75 3.93
2145 3985 4.350816 TCATAAGTATAGGCCCAGTTGCAT 59.649 41.667 0.00 0.00 0.00 3.96
2159 3999 3.303495 CAGTTGCATAACCTAGTTCGACG 59.697 47.826 0.00 0.00 37.52 5.12
2166 4006 5.278169 GCATAACCTAGTTCGACGAAGGATA 60.278 44.000 18.64 12.37 32.60 2.59
2168 4008 3.883669 ACCTAGTTCGACGAAGGATAGT 58.116 45.455 18.64 7.53 32.60 2.12
2216 4056 2.125912 CAGAGAAGGTGGCGGACG 60.126 66.667 0.00 0.00 0.00 4.79
2234 4074 2.740055 CGGCTGCTATGATCCGCC 60.740 66.667 0.00 0.00 35.20 6.13
2254 4094 3.011818 CCGGGTAATGGTAAGTGTTTCC 58.988 50.000 0.00 0.00 0.00 3.13
2399 4239 1.001378 GCTGCAAACGGTCAGACAAAT 60.001 47.619 2.17 0.00 32.26 2.32
2403 4243 2.477375 GCAAACGGTCAGACAAATACGA 59.523 45.455 2.17 0.00 0.00 3.43
2404 4244 3.663493 GCAAACGGTCAGACAAATACGAC 60.663 47.826 2.17 0.00 0.00 4.34
2405 4245 2.358939 ACGGTCAGACAAATACGACC 57.641 50.000 2.17 0.00 43.73 4.79
2406 4246 1.067354 ACGGTCAGACAAATACGACCC 60.067 52.381 2.17 0.00 44.20 4.46
2407 4247 1.067425 CGGTCAGACAAATACGACCCA 60.067 52.381 2.17 0.00 44.20 4.51
2408 4248 2.418197 CGGTCAGACAAATACGACCCAT 60.418 50.000 2.17 0.00 44.20 4.00
2409 4249 3.181484 CGGTCAGACAAATACGACCCATA 60.181 47.826 2.17 0.00 44.20 2.74
2410 4250 4.678574 CGGTCAGACAAATACGACCCATAA 60.679 45.833 2.17 0.00 44.20 1.90
2411 4251 5.180271 GGTCAGACAAATACGACCCATAAA 58.820 41.667 2.17 0.00 41.77 1.40
2412 4252 5.293569 GGTCAGACAAATACGACCCATAAAG 59.706 44.000 2.17 0.00 41.77 1.85
2413 4253 5.873164 GTCAGACAAATACGACCCATAAAGT 59.127 40.000 0.00 0.00 0.00 2.66
2414 4254 6.370718 GTCAGACAAATACGACCCATAAAGTT 59.629 38.462 0.00 0.00 0.00 2.66
2415 4255 6.370442 TCAGACAAATACGACCCATAAAGTTG 59.630 38.462 0.00 0.00 0.00 3.16
2416 4256 6.148811 CAGACAAATACGACCCATAAAGTTGT 59.851 38.462 0.00 0.00 35.92 3.32
2417 4257 6.148811 AGACAAATACGACCCATAAAGTTGTG 59.851 38.462 0.00 0.00 33.79 3.33
2418 4258 5.998981 ACAAATACGACCCATAAAGTTGTGA 59.001 36.000 0.00 0.00 33.79 3.58
2419 4259 6.657541 ACAAATACGACCCATAAAGTTGTGAT 59.342 34.615 0.00 0.00 33.79 3.06
2420 4260 6.677781 AATACGACCCATAAAGTTGTGATG 57.322 37.500 0.00 0.00 33.79 3.07
2421 4261 4.015872 ACGACCCATAAAGTTGTGATGT 57.984 40.909 0.00 0.00 30.46 3.06
2422 4262 4.394729 ACGACCCATAAAGTTGTGATGTT 58.605 39.130 0.00 0.00 30.46 2.71
2423 4263 5.553123 ACGACCCATAAAGTTGTGATGTTA 58.447 37.500 0.00 0.00 30.46 2.41
2424 4264 6.177610 ACGACCCATAAAGTTGTGATGTTAT 58.822 36.000 0.00 0.00 30.46 1.89
2425 4265 6.093495 ACGACCCATAAAGTTGTGATGTTATG 59.907 38.462 0.00 0.00 34.92 1.90
2426 4266 6.207691 ACCCATAAAGTTGTGATGTTATGC 57.792 37.500 0.00 0.00 34.17 3.14
2427 4267 5.163663 ACCCATAAAGTTGTGATGTTATGCG 60.164 40.000 0.00 0.00 34.17 4.73
2428 4268 5.273170 CCATAAAGTTGTGATGTTATGCGG 58.727 41.667 0.00 0.00 34.17 5.69
2429 4269 2.919666 AAGTTGTGATGTTATGCGGC 57.080 45.000 0.00 0.00 0.00 6.53
2430 4270 0.726827 AGTTGTGATGTTATGCGGCG 59.273 50.000 0.51 0.51 0.00 6.46
2431 4271 0.248054 GTTGTGATGTTATGCGGCGG 60.248 55.000 9.78 0.00 0.00 6.13
2432 4272 1.372838 TTGTGATGTTATGCGGCGGG 61.373 55.000 9.78 0.00 0.00 6.13
2433 4273 2.203139 TGATGTTATGCGGCGGGG 60.203 61.111 9.78 0.00 0.00 5.73
2434 4274 2.978010 GATGTTATGCGGCGGGGG 60.978 66.667 9.78 0.00 0.00 5.40
2435 4275 3.767630 GATGTTATGCGGCGGGGGT 62.768 63.158 9.78 0.00 0.00 4.95
2436 4276 4.787286 TGTTATGCGGCGGGGGTG 62.787 66.667 9.78 0.00 0.00 4.61
2443 4283 4.832608 CGGCGGGGGTGCTAAGAC 62.833 72.222 0.00 0.00 34.52 3.01
2444 4284 3.400054 GGCGGGGGTGCTAAGACT 61.400 66.667 0.00 0.00 34.52 3.24
2445 4285 2.062177 GGCGGGGGTGCTAAGACTA 61.062 63.158 0.00 0.00 34.52 2.59
2446 4286 1.143401 GCGGGGGTGCTAAGACTAC 59.857 63.158 0.00 0.00 0.00 2.73
2447 4287 1.821258 CGGGGGTGCTAAGACTACC 59.179 63.158 0.00 0.00 0.00 3.18
2452 4292 2.674796 GGTGCTAAGACTACCCACAG 57.325 55.000 0.00 0.00 0.00 3.66
2453 4293 1.900486 GGTGCTAAGACTACCCACAGT 59.100 52.381 0.00 0.00 0.00 3.55
2454 4294 3.094572 GGTGCTAAGACTACCCACAGTA 58.905 50.000 0.00 0.00 0.00 2.74
2466 4306 6.636562 CTACCCACAGTAGGAGTAACATAG 57.363 45.833 0.00 0.00 44.19 2.23
2467 4307 5.202746 ACCCACAGTAGGAGTAACATAGA 57.797 43.478 0.00 0.00 0.00 1.98
2468 4308 5.778542 ACCCACAGTAGGAGTAACATAGAT 58.221 41.667 0.00 0.00 0.00 1.98
2469 4309 6.919158 ACCCACAGTAGGAGTAACATAGATA 58.081 40.000 0.00 0.00 0.00 1.98
2470 4310 7.005296 ACCCACAGTAGGAGTAACATAGATAG 58.995 42.308 0.00 0.00 0.00 2.08
2471 4311 7.005296 CCCACAGTAGGAGTAACATAGATAGT 58.995 42.308 0.00 0.00 0.00 2.12
2472 4312 8.162085 CCCACAGTAGGAGTAACATAGATAGTA 58.838 40.741 0.00 0.00 0.00 1.82
2473 4313 9.570468 CCACAGTAGGAGTAACATAGATAGTAA 57.430 37.037 0.00 0.00 0.00 2.24
2480 4320 9.642343 AGGAGTAACATAGATAGTAACATCACA 57.358 33.333 0.00 0.00 0.00 3.58
2481 4321 9.680315 GGAGTAACATAGATAGTAACATCACAC 57.320 37.037 0.00 0.00 0.00 3.82
2520 4360 9.961265 AATAGATGATGTGTCAAGCAATAAATG 57.039 29.630 0.00 0.00 38.01 2.32
2521 4361 7.634671 AGATGATGTGTCAAGCAATAAATGA 57.365 32.000 0.00 0.00 38.01 2.57
2522 4362 8.058667 AGATGATGTGTCAAGCAATAAATGAA 57.941 30.769 0.00 0.00 38.01 2.57
2523 4363 8.525316 AGATGATGTGTCAAGCAATAAATGAAA 58.475 29.630 0.00 0.00 38.01 2.69
2524 4364 9.142515 GATGATGTGTCAAGCAATAAATGAAAA 57.857 29.630 0.00 0.00 38.01 2.29
2525 4365 8.883954 TGATGTGTCAAGCAATAAATGAAAAA 57.116 26.923 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
44 45 0.326595 ACACACAGGGACAACACACA 59.673 50.000 0.00 0.00 0.00 3.72
162 163 5.988561 TCAGCAAACACCAACCAATTAATTC 59.011 36.000 0.00 0.00 0.00 2.17
498 722 4.715297 ACCCCATAAAAGTACGATCACTCT 59.285 41.667 0.00 0.00 0.00 3.24
509 733 4.021192 CAGAACATGCAACCCCATAAAAGT 60.021 41.667 0.00 0.00 0.00 2.66
530 754 1.607148 TCACACGTGGACTACTCACAG 59.393 52.381 21.57 0.00 35.03 3.66
535 759 1.919240 TCCATCACACGTGGACTACT 58.081 50.000 21.57 0.00 40.72 2.57
541 765 1.879380 ACACAAATCCATCACACGTGG 59.121 47.619 21.57 9.11 38.11 4.94
575 799 8.842358 TTGTCCAGATAGTTAACGAAAAATCT 57.158 30.769 0.00 2.91 0.00 2.40
624 848 6.436843 AACGGAGACAAAATATTTGCCTAG 57.563 37.500 0.39 1.28 0.00 3.02
675 899 2.070783 GAACGATCAAACCCAGCGTTA 58.929 47.619 0.00 0.00 44.07 3.18
676 900 0.872388 GAACGATCAAACCCAGCGTT 59.128 50.000 0.00 0.00 46.31 4.84
708 932 0.790207 CATGTGTGTGCCGACAGTAC 59.210 55.000 0.00 0.00 30.74 2.73
712 936 0.250252 ATGTCATGTGTGTGCCGACA 60.250 50.000 0.00 0.00 40.59 4.35
778 1003 5.128335 CGTACCTCTAGTATTTTTCAGGGGT 59.872 44.000 0.00 0.00 44.24 4.95
881 1162 3.960102 AGAGAAGCAGGGAACTAGAGATG 59.040 47.826 0.00 0.00 40.21 2.90
882 1163 4.264373 AGAGAAGCAGGGAACTAGAGAT 57.736 45.455 0.00 0.00 40.21 2.75
933 1246 4.566004 TCCTTATATAACCTGCATGCGTC 58.434 43.478 14.09 0.00 0.00 5.19
1114 1427 2.279741 TGTCTTGGCGCATGTAGATTC 58.720 47.619 10.83 0.00 0.00 2.52
1324 1637 1.565759 TGCCTTGGCCACTCTATGAAT 59.434 47.619 3.88 0.00 0.00 2.57
1369 1682 1.144057 CCTCGTCGCCAGGCTTAAT 59.856 57.895 10.54 0.00 0.00 1.40
1420 1733 3.195698 GTCTTCCCCGCATGTCGC 61.196 66.667 0.00 0.00 36.73 5.19
1797 2173 0.403655 TGGGCCAACACAATAGAGCA 59.596 50.000 2.13 0.00 0.00 4.26
1813 2189 3.763360 TGGACTGCAATGAAATAAGTGGG 59.237 43.478 0.00 0.00 0.00 4.61
1859 2235 8.050778 TCCGTTCACAAATATAAGATGCTTTT 57.949 30.769 0.00 0.00 0.00 2.27
1892 2272 8.596293 TCATTCCTCTTTTAATTTCTTGGCATT 58.404 29.630 0.00 0.00 0.00 3.56
1959 3799 5.625311 CGCAATTTTTCTACAACAAGACCTC 59.375 40.000 0.00 0.00 0.00 3.85
1971 3811 3.572255 ACTTCCCTTGCGCAATTTTTCTA 59.428 39.130 25.26 0.00 0.00 2.10
1988 3828 5.518847 GTCTAGGTTTTGCAACAAAACTTCC 59.481 40.000 26.20 15.50 39.41 3.46
2007 3847 1.964552 ATGGTCTACGACGGGTCTAG 58.035 55.000 0.00 0.00 32.65 2.43
2012 3852 0.390603 TTGCAATGGTCTACGACGGG 60.391 55.000 0.00 0.00 32.65 5.28
2017 3857 0.447801 GCTGGTTGCAATGGTCTACG 59.552 55.000 0.59 0.00 42.31 3.51
2041 3881 6.149807 CCCTTGCAAAACAATGCTTATGAAAT 59.850 34.615 0.00 0.00 46.54 2.17
2051 3891 4.508861 CAGAACTTCCCTTGCAAAACAATG 59.491 41.667 0.00 0.00 37.72 2.82
2055 3895 3.801114 ACAGAACTTCCCTTGCAAAAC 57.199 42.857 0.00 0.00 0.00 2.43
2072 3912 1.070175 CGGGTCTACGTTTTGCAACAG 60.070 52.381 0.00 0.00 32.54 3.16
2084 3924 1.673168 ATGGTCTACGACGGGTCTAC 58.327 55.000 0.00 0.00 32.65 2.59
2091 3931 1.424403 TGTTGCAATGGTCTACGACG 58.576 50.000 0.59 0.00 32.65 5.12
2100 3940 3.281341 ACGTATGTGTTGTTGCAATGG 57.719 42.857 0.59 0.00 0.00 3.16
2113 3953 6.042322 TGGGCCTATACTTATGAAACGTATGT 59.958 38.462 4.53 0.00 0.00 2.29
2135 3975 2.936498 CGAACTAGGTTATGCAACTGGG 59.064 50.000 0.00 0.00 34.88 4.45
2145 3985 5.431765 ACTATCCTTCGTCGAACTAGGTTA 58.568 41.667 2.90 3.22 0.00 2.85
2159 3999 0.977395 AGGCCCGCATACTATCCTTC 59.023 55.000 0.00 0.00 0.00 3.46
2166 4006 1.139058 CTAAGTGAAGGCCCGCATACT 59.861 52.381 0.00 0.00 0.00 2.12
2168 4008 1.138266 GTCTAAGTGAAGGCCCGCATA 59.862 52.381 0.00 0.00 0.00 3.14
2234 4074 3.011818 GGGAAACACTTACCATTACCCG 58.988 50.000 0.00 0.00 35.28 5.28
2366 4206 7.282224 TGACCGTTTGCAGCTAATTAATATTCT 59.718 33.333 0.00 0.00 0.00 2.40
2399 4239 5.155278 ACATCACAACTTTATGGGTCGTA 57.845 39.130 0.00 0.00 0.00 3.43
2403 4243 5.163663 CGCATAACATCACAACTTTATGGGT 60.164 40.000 8.36 0.00 38.81 4.51
2404 4244 5.273170 CGCATAACATCACAACTTTATGGG 58.727 41.667 0.00 0.00 38.04 4.00
2405 4245 5.273170 CCGCATAACATCACAACTTTATGG 58.727 41.667 0.00 0.00 34.05 2.74
2406 4246 4.734854 GCCGCATAACATCACAACTTTATG 59.265 41.667 0.00 0.00 35.76 1.90
2407 4247 4.495679 CGCCGCATAACATCACAACTTTAT 60.496 41.667 0.00 0.00 0.00 1.40
2408 4248 3.181515 CGCCGCATAACATCACAACTTTA 60.182 43.478 0.00 0.00 0.00 1.85
2409 4249 2.414029 CGCCGCATAACATCACAACTTT 60.414 45.455 0.00 0.00 0.00 2.66
2410 4250 1.130373 CGCCGCATAACATCACAACTT 59.870 47.619 0.00 0.00 0.00 2.66
2411 4251 0.726827 CGCCGCATAACATCACAACT 59.273 50.000 0.00 0.00 0.00 3.16
2412 4252 0.248054 CCGCCGCATAACATCACAAC 60.248 55.000 0.00 0.00 0.00 3.32
2413 4253 1.372838 CCCGCCGCATAACATCACAA 61.373 55.000 0.00 0.00 0.00 3.33
2414 4254 1.817520 CCCGCCGCATAACATCACA 60.818 57.895 0.00 0.00 0.00 3.58
2415 4255 2.542907 CCCCGCCGCATAACATCAC 61.543 63.158 0.00 0.00 0.00 3.06
2416 4256 2.203139 CCCCGCCGCATAACATCA 60.203 61.111 0.00 0.00 0.00 3.07
2417 4257 2.978010 CCCCCGCCGCATAACATC 60.978 66.667 0.00 0.00 0.00 3.06
2418 4258 3.804329 ACCCCCGCCGCATAACAT 61.804 61.111 0.00 0.00 0.00 2.71
2419 4259 4.787286 CACCCCCGCCGCATAACA 62.787 66.667 0.00 0.00 0.00 2.41
2426 4266 4.832608 GTCTTAGCACCCCCGCCG 62.833 72.222 0.00 0.00 0.00 6.46
2427 4267 2.062177 TAGTCTTAGCACCCCCGCC 61.062 63.158 0.00 0.00 0.00 6.13
2428 4268 1.143401 GTAGTCTTAGCACCCCCGC 59.857 63.158 0.00 0.00 0.00 6.13
2429 4269 1.683418 GGGTAGTCTTAGCACCCCCG 61.683 65.000 5.54 0.00 45.34 5.73
2430 4270 2.219027 GGGTAGTCTTAGCACCCCC 58.781 63.158 5.54 0.00 45.34 5.40
2433 4273 1.900486 ACTGTGGGTAGTCTTAGCACC 59.100 52.381 0.00 0.00 0.00 5.01
2434 4274 3.130693 CCTACTGTGGGTAGTCTTAGCAC 59.869 52.174 1.43 0.00 44.66 4.40
2435 4275 3.010920 TCCTACTGTGGGTAGTCTTAGCA 59.989 47.826 10.18 0.00 44.66 3.49
2436 4276 3.629087 TCCTACTGTGGGTAGTCTTAGC 58.371 50.000 10.18 0.00 44.66 3.09
2437 4277 4.857679 ACTCCTACTGTGGGTAGTCTTAG 58.142 47.826 10.18 1.02 44.66 2.18
2438 4278 4.942363 ACTCCTACTGTGGGTAGTCTTA 57.058 45.455 10.18 0.00 44.66 2.10
2439 4279 3.829728 ACTCCTACTGTGGGTAGTCTT 57.170 47.619 10.18 0.00 44.66 3.01
2440 4280 4.043812 TGTTACTCCTACTGTGGGTAGTCT 59.956 45.833 10.18 0.00 44.66 3.24
2441 4281 4.338879 TGTTACTCCTACTGTGGGTAGTC 58.661 47.826 10.18 3.27 44.66 2.59
2442 4282 4.393239 TGTTACTCCTACTGTGGGTAGT 57.607 45.455 10.18 13.46 44.66 2.73
2443 4283 6.363065 TCTATGTTACTCCTACTGTGGGTAG 58.637 44.000 10.18 8.70 45.45 3.18
2444 4284 6.331577 TCTATGTTACTCCTACTGTGGGTA 57.668 41.667 10.18 0.00 0.00 3.69
2445 4285 5.202746 TCTATGTTACTCCTACTGTGGGT 57.797 43.478 10.18 0.00 0.00 4.51
2446 4286 7.005296 ACTATCTATGTTACTCCTACTGTGGG 58.995 42.308 3.43 3.43 0.00 4.61
2447 4287 9.570468 TTACTATCTATGTTACTCCTACTGTGG 57.430 37.037 0.00 0.00 0.00 4.17
2454 4294 9.642343 TGTGATGTTACTATCTATGTTACTCCT 57.358 33.333 0.00 0.00 0.00 3.69
2455 4295 9.680315 GTGTGATGTTACTATCTATGTTACTCC 57.320 37.037 0.00 0.00 0.00 3.85
2494 4334 9.961265 CATTTATTGCTTGACACATCATCTATT 57.039 29.630 0.00 0.00 33.85 1.73
2495 4335 9.346005 TCATTTATTGCTTGACACATCATCTAT 57.654 29.630 0.00 0.00 33.85 1.98
2496 4336 8.735692 TCATTTATTGCTTGACACATCATCTA 57.264 30.769 0.00 0.00 33.85 1.98
2497 4337 7.634671 TCATTTATTGCTTGACACATCATCT 57.365 32.000 0.00 0.00 33.85 2.90
2498 4338 8.692110 TTTCATTTATTGCTTGACACATCATC 57.308 30.769 0.00 0.00 33.85 2.92
2499 4339 9.491675 TTTTTCATTTATTGCTTGACACATCAT 57.508 25.926 0.00 0.00 33.85 2.45
2500 4340 8.883954 TTTTTCATTTATTGCTTGACACATCA 57.116 26.923 0.00 0.00 0.00 3.07
2522 4362 9.476202 GCTATGTTACCACTTTTCTTCATTTTT 57.524 29.630 0.00 0.00 0.00 1.94
2523 4363 8.860088 AGCTATGTTACCACTTTTCTTCATTTT 58.140 29.630 0.00 0.00 0.00 1.82
2524 4364 8.409358 AGCTATGTTACCACTTTTCTTCATTT 57.591 30.769 0.00 0.00 0.00 2.32
2525 4365 8.947115 GTAGCTATGTTACCACTTTTCTTCATT 58.053 33.333 0.00 0.00 0.00 2.57
2526 4366 8.322091 AGTAGCTATGTTACCACTTTTCTTCAT 58.678 33.333 0.00 0.00 0.00 2.57
2527 4367 7.602644 CAGTAGCTATGTTACCACTTTTCTTCA 59.397 37.037 0.00 0.00 0.00 3.02
2528 4368 7.603024 ACAGTAGCTATGTTACCACTTTTCTTC 59.397 37.037 0.00 0.00 0.00 2.87
2529 4369 7.450903 ACAGTAGCTATGTTACCACTTTTCTT 58.549 34.615 0.00 0.00 0.00 2.52
2530 4370 7.005709 ACAGTAGCTATGTTACCACTTTTCT 57.994 36.000 0.00 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.