Multiple sequence alignment - TraesCS3D01G275000

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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 TraesCS3D01G275000 chr3D 100.000 6692 0 0 1 6692 381625317 381632008 0.00000 12358.0
1 TraesCS3D01G275000 chr3A 94.676 6105 205 45 5 6041 504797750 504803802 0.00000 9363.0
2 TraesCS3D01G275000 chr3A 89.568 834 65 13 2 822 504790309 504791133 0.00000 1038.0
3 TraesCS3D01G275000 chr3A 89.568 834 65 13 2 822 504792789 504793613 0.00000 1038.0
4 TraesCS3D01G275000 chr3A 89.448 834 66 13 2 822 504795269 504796093 0.00000 1033.0
5 TraesCS3D01G275000 chr3A 91.590 654 48 3 6040 6689 504803884 504804534 0.00000 896.0
6 TraesCS3D01G275000 chr3B 91.234 3867 189 44 1 3800 497087395 497091178 0.00000 5125.0
7 TraesCS3D01G275000 chr3B 95.128 2299 63 19 3760 6028 497091323 497093602 0.00000 3579.0
8 TraesCS3D01G275000 chr3B 92.745 510 28 5 6187 6692 497094787 497095291 0.00000 728.0
9 TraesCS3D01G275000 chr6B 78.182 110 15 6 3259 3364 65094379 65094483 0.00002 62.1


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 TraesCS3D01G275000 chr3D 381625317 381632008 6691 False 12358.0 12358 100.000000 1 6692 1 chr3D.!!$F1 6691
1 TraesCS3D01G275000 chr3A 504790309 504804534 14225 False 2673.6 9363 90.970000 2 6689 5 chr3A.!!$F1 6687
2 TraesCS3D01G275000 chr3B 497087395 497095291 7896 False 3144.0 5125 93.035667 1 6692 3 chr3B.!!$F1 6691

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
379 2862 0.030603 GAGGGAGGGGAGAAGGATGT 60.031 60.000 0.00 0.0 0.00 3.06 F
1296 8772 0.315251 CTGAGACGGTGAGCTGTTCA 59.685 55.000 0.00 0.0 33.67 3.18 F
1727 9203 1.009829 CAGGCGCAGTTGAGGTAATC 58.990 55.000 10.83 0.0 0.00 1.75 F
1848 9338 1.518325 TTGTGTGATAGGTGGCGTTG 58.482 50.000 0.00 0.0 0.00 4.10 F
3374 10893 1.807886 CGGGCGCTAGTTCTACAGT 59.192 57.895 7.64 0.0 0.00 3.55 F
4293 11999 0.109342 ATCCGGACATCAGGCCAATC 59.891 55.000 6.12 0.0 0.00 2.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1670 9146 0.460635 GGCGGCCAACGTATACTTGA 60.461 55.000 15.62 0.0 46.52 3.02 R
2107 9600 0.746659 GTCCAAAGCAAGTGCCAAGT 59.253 50.000 0.00 0.0 43.38 3.16 R
3415 10935 1.972872 CCAAAAGCTCTCACACCAGT 58.027 50.000 0.00 0.0 0.00 4.00 R
3629 11149 2.229792 CACACACACCCAATTAGCTGT 58.770 47.619 0.00 0.0 0.00 4.40 R
4545 12273 0.109781 GTGCACCATGCTGTTAACCG 60.110 55.000 5.22 0.0 45.31 4.44 R
5707 13448 0.532573 CTAACTCGCTCTTCAGCCCA 59.467 55.000 0.00 0.0 43.56 5.36 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
19 20 2.442236 TGGAGGAGGCAATGGATTTC 57.558 50.000 0.00 0.00 0.00 2.17
39 40 1.396996 CCACCATTGTTGCGCTACTAC 59.603 52.381 22.01 9.20 0.00 2.73
49 50 1.067060 TGCGCTACTACCAGCATGTAG 59.933 52.381 9.73 10.20 41.88 2.74
61 62 1.796151 CATGTAGTTGCACTGCCCG 59.204 57.895 0.00 0.00 29.18 6.13
77 78 4.247380 CGCCCTGATCTGGAGCCC 62.247 72.222 19.59 4.73 0.00 5.19
121 124 4.927782 TGCTTTGACGCCCACGCT 62.928 61.111 0.00 0.00 45.53 5.07
131 134 2.750350 CCCACGCTTCCTCCAACT 59.250 61.111 0.00 0.00 0.00 3.16
136 139 1.371183 CGCTTCCTCCAACTGGTCA 59.629 57.895 0.00 0.00 36.34 4.02
140 143 1.912043 CTTCCTCCAACTGGTCATCCT 59.088 52.381 0.00 0.00 36.34 3.24
171 174 1.174712 ATGGGCATAAGCACCATCGC 61.175 55.000 7.01 0.00 46.13 4.58
197 200 1.208052 CCTCCCTTGAGAGCGATTCAA 59.792 52.381 0.00 0.00 41.42 2.69
270 273 4.408821 AGATTGAAGGCGGCGGCA 62.409 61.111 34.87 15.33 42.47 5.69
303 306 0.461339 CGCGGTTAGGGTTAGCACAT 60.461 55.000 0.00 0.00 0.00 3.21
305 308 1.663695 CGGTTAGGGTTAGCACATGG 58.336 55.000 0.00 0.00 0.00 3.66
379 2862 0.030603 GAGGGAGGGGAGAAGGATGT 60.031 60.000 0.00 0.00 0.00 3.06
392 2875 7.420214 GGGGAGAAGGATGTGAATTATAAGACA 60.420 40.741 0.00 0.00 0.00 3.41
481 2965 6.347888 CGTAAGAACAAACATAAACGGATGGT 60.348 38.462 0.00 0.00 43.02 3.55
576 5539 7.980099 AGTATAGGTCGATTTTGTAGGTCTTTG 59.020 37.037 0.00 0.00 0.00 2.77
583 5546 8.008279 GTCGATTTTGTAGGTCTTTGTTTAGAC 58.992 37.037 0.00 0.00 43.05 2.59
599 5562 5.869344 TGTTTAGACGATCATTCCAAGTCTG 59.131 40.000 6.66 0.00 41.60 3.51
637 5600 4.637977 GGTCCTGGAAGCAAAAATCTAGAG 59.362 45.833 0.00 0.00 0.00 2.43
835 8296 3.434319 CAAATCTGCGCCGGCACT 61.434 61.111 28.98 1.85 46.21 4.40
1052 8513 1.219124 GTGAGGCGCAGGAGAATCA 59.781 57.895 10.83 0.00 36.25 2.57
1296 8772 0.315251 CTGAGACGGTGAGCTGTTCA 59.685 55.000 0.00 0.00 33.67 3.18
1370 8846 7.259290 TGAGGTTCACTTTGTTAATGAGTTC 57.741 36.000 0.00 0.00 0.00 3.01
1436 8912 3.378339 CGAGCGTTTAAACTATCCCGAT 58.622 45.455 16.01 0.46 0.00 4.18
1444 8920 6.075205 CGTTTAAACTATCCCGATGTTACTCG 60.075 42.308 16.01 0.00 38.37 4.18
1551 9027 3.314635 CCTAGCTTGCATTTTGCCTCTAG 59.685 47.826 0.00 5.28 44.23 2.43
1670 9146 2.823152 GCTTGGGAAAGGAGGATTTGGT 60.823 50.000 0.00 0.00 0.00 3.67
1703 9179 1.062525 CCGCCGCATTTCAGCTAAC 59.937 57.895 0.00 0.00 0.00 2.34
1727 9203 1.009829 CAGGCGCAGTTGAGGTAATC 58.990 55.000 10.83 0.00 0.00 1.75
1806 9296 6.992715 GTGTAACAGTGGAGATAATATTGGCT 59.007 38.462 0.00 0.00 36.32 4.75
1848 9338 1.518325 TTGTGTGATAGGTGGCGTTG 58.482 50.000 0.00 0.00 0.00 4.10
2106 9599 7.075009 AGGGGATTACTTCATTATGGTAATGGT 59.925 37.037 10.18 4.22 36.62 3.55
2107 9600 8.387813 GGGGATTACTTCATTATGGTAATGGTA 58.612 37.037 10.18 3.46 36.62 3.25
2108 9601 9.227777 GGGATTACTTCATTATGGTAATGGTAC 57.772 37.037 10.18 0.00 36.62 3.34
2112 9605 9.621629 TTACTTCATTATGGTAATGGTACTTGG 57.378 33.333 9.18 0.00 0.00 3.61
2456 9950 5.853936 TCCCCTTCGTCTCATATATTTGTG 58.146 41.667 0.00 0.00 0.00 3.33
2739 10245 1.935873 CATGTTGAGTATGACCAGCGG 59.064 52.381 0.00 0.00 0.00 5.52
2968 10479 8.582433 TTCCGTTTGTAATTTTTCCTCATTTC 57.418 30.769 0.00 0.00 0.00 2.17
2970 10481 6.088883 CCGTTTGTAATTTTTCCTCATTTCCG 59.911 38.462 0.00 0.00 0.00 4.30
2985 10496 3.899052 TTTCCGGTTCCGATATCTTGT 57.101 42.857 13.08 0.00 0.00 3.16
3021 10532 6.192863 GCTTTTATGTTCTTCTTAACATCGCG 59.807 38.462 0.00 0.00 44.79 5.87
3374 10893 1.807886 CGGGCGCTAGTTCTACAGT 59.192 57.895 7.64 0.00 0.00 3.55
3629 11149 2.803670 GTTGCGCGTGCTCTCGTA 60.804 61.111 23.16 0.00 43.34 3.43
3646 11166 2.300723 TCGTACAGCTAATTGGGTGTGT 59.699 45.455 29.86 12.03 45.66 3.72
3719 11239 3.386402 GCTCTGACTAGGAAATACAGCCT 59.614 47.826 0.00 0.00 38.31 4.58
3821 11526 0.883833 GGCTTGCTTGCACACATAGT 59.116 50.000 0.00 0.00 34.04 2.12
3849 11555 9.516546 AGATCATTCATACGTTATACTGGTCTA 57.483 33.333 0.00 0.00 0.00 2.59
3915 11621 2.857748 TCGTTATGCTAGTGTTCATGCG 59.142 45.455 0.00 0.00 0.00 4.73
4278 11984 1.420138 AGTATAGTGGGCCCAAATCCG 59.580 52.381 30.64 0.00 0.00 4.18
4281 11987 1.917336 TAGTGGGCCCAAATCCGGAC 61.917 60.000 30.64 11.94 0.00 4.79
4293 11999 0.109342 ATCCGGACATCAGGCCAATC 59.891 55.000 6.12 0.00 0.00 2.67
4302 12008 1.896220 TCAGGCCAATCAACACAGAC 58.104 50.000 5.01 0.00 0.00 3.51
4328 12034 6.655425 GGTGCTCAGAAGGTAGTCTTATTTTT 59.345 38.462 0.00 0.00 35.50 1.94
4465 12171 4.077822 AGATGAGCAACCAAAGAAGAAGG 58.922 43.478 0.00 0.00 0.00 3.46
4537 12265 3.243068 GCGGCCTATGAAACAAAGGTATG 60.243 47.826 0.00 0.00 32.67 2.39
4545 12273 6.575162 ATGAAACAAAGGTATGTTGACTCC 57.425 37.500 0.00 0.00 42.49 3.85
4692 12421 3.700538 TGACAAAGGGAATGAAGATGGG 58.299 45.455 0.00 0.00 0.00 4.00
4813 12542 8.402472 CACATTTCCTTCACAAAGTTAGTAACA 58.598 33.333 15.28 0.00 0.00 2.41
5091 12823 7.496920 TCATTTTGACTATCTGGCTTGTCTATG 59.503 37.037 0.00 0.00 0.00 2.23
5204 12936 0.609957 CTTCCATGGCAACTGCTGGA 60.610 55.000 6.96 8.24 41.70 3.86
5296 13031 4.093850 GGTGTTTGTTTACTTCGACACTGT 59.906 41.667 0.00 0.00 37.93 3.55
5615 13356 2.200792 TGTTGTGACAAATTGTGCCG 57.799 45.000 2.20 0.00 31.49 5.69
5616 13357 0.852136 GTTGTGACAAATTGTGCCGC 59.148 50.000 2.20 0.00 0.00 6.53
5667 13408 5.337578 AGAATCTCTACCTTGCTTCAGTC 57.662 43.478 0.00 0.00 0.00 3.51
5707 13448 6.238103 CGTATCGTAGAAATCTTTTGCCATGT 60.238 38.462 0.00 0.00 43.58 3.21
5766 13507 3.877508 AGCTCAGTGGTAGTTTTGTGTTC 59.122 43.478 0.00 0.00 0.00 3.18
5822 13564 2.880268 TGTGAAGATGTTTCTGCCTGTG 59.120 45.455 0.00 0.00 30.72 3.66
5908 13651 2.089349 GCGGACGACTCTTGACTGC 61.089 63.158 0.00 0.00 0.00 4.40
5932 13675 6.697892 GCAGTGTAAGGTGATACTTAGATGTC 59.302 42.308 0.00 0.00 33.87 3.06
5933 13676 6.913132 CAGTGTAAGGTGATACTTAGATGTCG 59.087 42.308 0.00 0.00 33.87 4.35
5954 13697 6.134061 GTCGAAACACCTGACTTAAATGTTC 58.866 40.000 0.00 0.00 32.46 3.18
5972 13715 1.188219 TCTGTGCTCCTGTCTGGTCC 61.188 60.000 0.00 0.00 37.07 4.46
6052 13959 5.514204 CCCGTACTAAATAATATTCTCGCCG 59.486 44.000 0.00 0.00 0.00 6.46
6068 13975 0.736053 GCCGAAACTGACACACCAAA 59.264 50.000 0.00 0.00 0.00 3.28
6071 13978 2.878406 CCGAAACTGACACACCAAATCT 59.122 45.455 0.00 0.00 0.00 2.40
6117 14024 4.732784 TGAAATAAAAACCGAGCTGCATC 58.267 39.130 1.02 0.00 0.00 3.91
6118 14025 3.405170 AATAAAAACCGAGCTGCATCG 57.595 42.857 1.02 8.37 42.36 3.84
6132 14039 1.503542 CATCGTCAGGGCAACAAGC 59.496 57.895 0.00 0.00 44.65 4.01
6166 14073 3.571571 TCTCAAGACCAAATCGTACACG 58.428 45.455 0.00 0.00 41.45 4.49
6202 14975 4.635699 AAGTGGTAAAGGAGTACAAGGG 57.364 45.455 0.00 0.00 0.00 3.95
6210 14983 0.393132 GGAGTACAAGGGAAGCTGCC 60.393 60.000 0.16 0.16 0.00 4.85
6213 14986 0.960861 GTACAAGGGAAGCTGCCACC 60.961 60.000 14.44 0.00 0.00 4.61
6426 15202 0.100682 GCATACGTGGAGAGCGAAGA 59.899 55.000 0.00 0.00 0.00 2.87
6428 15204 2.876091 CATACGTGGAGAGCGAAGAAA 58.124 47.619 0.00 0.00 0.00 2.52
6436 15212 3.070446 TGGAGAGCGAAGAAAGTAAACCA 59.930 43.478 0.00 0.00 0.00 3.67
6465 15244 6.156519 GCAATGTATGATTGTGATGATGCAT 58.843 36.000 0.00 0.00 34.66 3.96
6486 15265 3.283303 GCATTTGCAAGGCCGGTA 58.717 55.556 12.66 0.00 41.59 4.02
6489 15268 0.458370 CATTTGCAAGGCCGGTAAGC 60.458 55.000 1.90 3.10 0.00 3.09
6492 15271 1.241315 TTGCAAGGCCGGTAAGCTTC 61.241 55.000 0.00 0.00 0.00 3.86
6493 15272 2.750888 GCAAGGCCGGTAAGCTTCG 61.751 63.158 0.00 0.40 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 1.067635 AGCGCAACAATGGTGGAAATC 60.068 47.619 11.47 0.00 0.00 2.17
19 20 1.396996 GTAGTAGCGCAACAATGGTGG 59.603 52.381 11.47 0.00 0.00 4.61
61 62 3.883549 GGGGCTCCAGATCAGGGC 61.884 72.222 0.00 6.68 0.00 5.19
121 124 2.044793 AGGATGACCAGTTGGAGGAA 57.955 50.000 4.92 0.00 38.94 3.36
131 134 1.559065 GGGAACGGGAAGGATGACCA 61.559 60.000 0.00 0.00 38.94 4.02
136 139 1.645402 CCATGGGGAACGGGAAGGAT 61.645 60.000 2.85 0.00 35.59 3.24
171 174 2.022240 GCTCTCAAGGGAGGTAGGCG 62.022 65.000 0.00 0.00 41.69 5.52
274 277 0.880278 CCTAACCGCGCTGCACATAT 60.880 55.000 5.56 0.00 0.00 1.78
275 278 1.520564 CCTAACCGCGCTGCACATA 60.521 57.895 5.56 0.00 0.00 2.29
303 306 3.241530 ACCTCTCCACGCTTGCCA 61.242 61.111 0.00 0.00 0.00 4.92
305 308 2.743928 CCACCTCTCCACGCTTGC 60.744 66.667 0.00 0.00 0.00 4.01
342 2825 0.530288 TCAGCATGGATCGTTGTCGA 59.470 50.000 0.00 0.00 43.57 4.20
347 2830 0.467384 CTCCCTCAGCATGGATCGTT 59.533 55.000 0.00 0.00 36.16 3.85
348 2831 1.406065 CCTCCCTCAGCATGGATCGT 61.406 60.000 0.00 0.00 36.16 3.73
356 2839 1.306482 CTTCTCCCCTCCCTCAGCA 60.306 63.158 0.00 0.00 0.00 4.41
358 2841 0.267356 ATCCTTCTCCCCTCCCTCAG 59.733 60.000 0.00 0.00 0.00 3.35
359 2842 0.030705 CATCCTTCTCCCCTCCCTCA 60.031 60.000 0.00 0.00 0.00 3.86
392 2875 1.174712 GGCTAATCCCACATGCGCAT 61.175 55.000 19.28 19.28 0.00 4.73
429 2912 1.085893 TCGACACCGCACGAAGTATA 58.914 50.000 0.00 0.00 35.17 1.47
481 2965 0.901580 GACTACGTCCAACCCTCCCA 60.902 60.000 0.00 0.00 0.00 4.37
576 5539 5.869888 ACAGACTTGGAATGATCGTCTAAAC 59.130 40.000 0.00 0.00 33.53 2.01
583 5546 3.329386 ACACACAGACTTGGAATGATCG 58.671 45.455 0.00 0.00 0.00 3.69
599 5562 1.344763 AGGACCTCACAAGCTACACAC 59.655 52.381 0.00 0.00 0.00 3.82
637 5600 1.804326 ACGTGACGGCGTAATGAGC 60.804 57.895 23.02 5.37 43.83 4.26
1145 8621 3.087666 GCCCTCTCTTCCTCCGCAG 62.088 68.421 0.00 0.00 0.00 5.18
1146 8622 3.077556 GCCCTCTCTTCCTCCGCA 61.078 66.667 0.00 0.00 0.00 5.69
1147 8623 4.214327 CGCCCTCTCTTCCTCCGC 62.214 72.222 0.00 0.00 0.00 5.54
1218 8694 0.617535 TGTCCTGGTCATCCATCGGT 60.618 55.000 0.00 0.00 43.43 4.69
1296 8772 7.291411 ACATAGGAGAAGCGAAACATAGTAT 57.709 36.000 0.00 0.00 0.00 2.12
1455 8931 6.486657 ACCATGCGAGCTAAAACACATATATT 59.513 34.615 0.00 0.00 0.00 1.28
1574 9050 3.926616 ACCAGACACAGATTAAACGAGG 58.073 45.455 0.00 0.00 0.00 4.63
1670 9146 0.460635 GGCGGCCAACGTATACTTGA 60.461 55.000 15.62 0.00 46.52 3.02
1707 9183 1.026718 ATTACCTCAACTGCGCCTGC 61.027 55.000 4.18 0.00 43.20 4.85
1727 9203 1.097547 GGTTGGTGGCCAGATCATCG 61.098 60.000 5.11 0.00 33.81 3.84
1806 9296 4.935352 AGCAGAAGTTTTATTTGCCACA 57.065 36.364 0.00 0.00 35.44 4.17
1820 9310 4.083110 CCACCTATCACACAAAAGCAGAAG 60.083 45.833 0.00 0.00 0.00 2.85
1848 9338 5.362556 TGCTGTTCTTATGCTCAAACTTC 57.637 39.130 0.00 0.00 0.00 3.01
2106 9599 1.953686 GTCCAAAGCAAGTGCCAAGTA 59.046 47.619 0.00 0.00 43.38 2.24
2107 9600 0.746659 GTCCAAAGCAAGTGCCAAGT 59.253 50.000 0.00 0.00 43.38 3.16
2108 9601 1.035139 AGTCCAAAGCAAGTGCCAAG 58.965 50.000 0.00 0.00 43.38 3.61
2109 9602 2.356665 TAGTCCAAAGCAAGTGCCAA 57.643 45.000 0.00 0.00 43.38 4.52
2110 9603 1.953686 GTTAGTCCAAAGCAAGTGCCA 59.046 47.619 0.00 0.00 43.38 4.92
2111 9604 1.953686 TGTTAGTCCAAAGCAAGTGCC 59.046 47.619 0.00 0.00 43.38 5.01
2112 9605 3.923017 ATGTTAGTCCAAAGCAAGTGC 57.077 42.857 0.00 0.00 42.49 4.40
2456 9950 4.496341 CCGTGGACATATCTGCAATTGTTC 60.496 45.833 7.40 0.00 0.00 3.18
2760 10266 8.078060 TGTCAGTTATCATAAAGGAGTCATCA 57.922 34.615 0.00 0.00 0.00 3.07
2968 10479 2.882927 TCACAAGATATCGGAACCGG 57.117 50.000 13.29 0.00 40.25 5.28
2970 10481 4.094442 GTGGTTTCACAAGATATCGGAACC 59.906 45.833 10.22 10.22 43.13 3.62
2985 10496 7.719633 AGAAGAACATAAAAGCTAGTGGTTTCA 59.280 33.333 0.00 0.00 42.26 2.69
3021 10532 8.837389 GGTACCAACTCAAATCTGGTATATTTC 58.163 37.037 7.15 0.00 45.14 2.17
3219 10733 4.501559 CGCAAATAATTGGCTCACTCATTG 59.498 41.667 0.00 0.00 37.02 2.82
3374 10893 3.474486 TTTCCTGTGCTGCAGCCGA 62.474 57.895 34.64 21.18 43.71 5.54
3415 10935 1.972872 CCAAAAGCTCTCACACCAGT 58.027 50.000 0.00 0.00 0.00 4.00
3629 11149 2.229792 CACACACACCCAATTAGCTGT 58.770 47.619 0.00 0.00 0.00 4.40
3849 11555 8.246180 CAGCCATGATAAAACAATAAGACAACT 58.754 33.333 0.00 0.00 0.00 3.16
3915 11621 0.767375 TGCCTATCCTCCCAAGATGC 59.233 55.000 0.00 0.00 0.00 3.91
4278 11984 1.474077 GTGTTGATTGGCCTGATGTCC 59.526 52.381 3.32 0.00 0.00 4.02
4281 11987 2.163010 GTCTGTGTTGATTGGCCTGATG 59.837 50.000 3.32 0.00 0.00 3.07
4302 12008 1.178276 AGACTACCTTCTGAGCACCG 58.822 55.000 0.00 0.00 0.00 4.94
4328 12034 8.885494 AGCAATGTTTTCAAATAGCAAACTAA 57.115 26.923 0.00 0.00 34.91 2.24
4537 12265 1.873698 TGCTGTTAACCGGAGTCAAC 58.126 50.000 9.46 6.87 0.00 3.18
4545 12273 0.109781 GTGCACCATGCTGTTAACCG 60.110 55.000 5.22 0.00 45.31 4.44
4692 12421 9.390795 CAAGATGATATGCAACTAATAAACAGC 57.609 33.333 0.00 0.00 0.00 4.40
4813 12542 3.057033 GCCATGAAAGAAACAGACTGCAT 60.057 43.478 1.25 0.00 0.00 3.96
5091 12823 3.190874 GCTGAGTATACAGTGTTCCTGC 58.809 50.000 0.00 0.00 45.68 4.85
5204 12936 6.462347 GGGACATAACAATCGCCCATTTATTT 60.462 38.462 0.00 0.00 35.63 1.40
5442 13178 3.087031 CAATGCAGTCTGATCCCAAGTT 58.913 45.455 3.32 0.00 0.00 2.66
5615 13356 1.881973 TCTCCTGCAATGACACAAAGC 59.118 47.619 0.00 0.00 0.00 3.51
5616 13357 4.572985 TTTCTCCTGCAATGACACAAAG 57.427 40.909 0.00 0.00 0.00 2.77
5707 13448 0.532573 CTAACTCGCTCTTCAGCCCA 59.467 55.000 0.00 0.00 43.56 5.36
5766 13507 0.664166 GCATTCACAACTTGCCCACG 60.664 55.000 0.00 0.00 0.00 4.94
5908 13651 6.913132 CGACATCTAAGTATCACCTTACACTG 59.087 42.308 0.00 0.00 0.00 3.66
5932 13675 6.136071 CAGAACATTTAAGTCAGGTGTTTCG 58.864 40.000 0.00 0.00 33.55 3.46
5933 13676 6.912591 CACAGAACATTTAAGTCAGGTGTTTC 59.087 38.462 0.00 0.00 33.55 2.78
5954 13697 1.190833 AGGACCAGACAGGAGCACAG 61.191 60.000 0.00 0.00 41.22 3.66
5972 13715 1.373497 GGCTCTCACACGACCACAG 60.373 63.158 0.00 0.00 0.00 3.66
6052 13959 7.084486 GGAAATAGATTTGGTGTGTCAGTTTC 58.916 38.462 0.00 0.00 0.00 2.78
6068 13975 2.171448 AGCTCGGCTTGTGGAAATAGAT 59.829 45.455 0.00 0.00 33.89 1.98
6071 13978 1.277842 TCAGCTCGGCTTGTGGAAATA 59.722 47.619 0.00 0.00 36.40 1.40
6132 14039 1.303074 TTGAGAAGCTGCAGCAGGG 60.303 57.895 38.24 3.04 45.16 4.45
6166 14073 2.289945 ACCACTTTCTCCTGTCATGCTC 60.290 50.000 0.00 0.00 0.00 4.26
6202 14975 1.022735 CAGATCATGGTGGCAGCTTC 58.977 55.000 18.53 9.37 0.00 3.86
6210 14983 3.442625 AGTTGAATGTGCAGATCATGGTG 59.557 43.478 0.00 0.00 0.00 4.17
6213 14986 4.957759 TCAGTTGAATGTGCAGATCATG 57.042 40.909 0.00 0.00 0.00 3.07
6268 15041 2.849964 CGGCTAGCATGGAGAGCGA 61.850 63.158 18.24 0.00 37.07 4.93
6269 15042 2.355445 TTCGGCTAGCATGGAGAGCG 62.355 60.000 18.24 8.23 37.07 5.03
6270 15043 0.599728 CTTCGGCTAGCATGGAGAGC 60.600 60.000 18.24 0.00 35.39 4.09
6313 15086 2.447887 GCGGCTGTGATGTCGTCTG 61.448 63.158 0.00 0.00 37.38 3.51
6426 15202 6.719370 TCATACATTGCCTTCTGGTTTACTTT 59.281 34.615 0.00 0.00 35.27 2.66
6428 15204 5.815581 TCATACATTGCCTTCTGGTTTACT 58.184 37.500 0.00 0.00 35.27 2.24
6436 15212 6.124340 TCATCACAATCATACATTGCCTTCT 58.876 36.000 0.00 0.00 32.55 2.85
6481 15260 2.018542 TTGATTCCGAAGCTTACCGG 57.981 50.000 18.07 18.07 46.57 5.28


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

AutoCloner maintained by Alex Coulton.