Multiple sequence alignment - TraesCS6D01G153800

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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 TraesCS6D01G153800 chr6D 100.000 6702 0 0 1 6702 128101668 128094967 0.000000e+00 12377.0
1 TraesCS6D01G153800 chr6D 89.744 78 6 1 3482 3557 319255399 319255322 1.540000e-16 99.0
2 TraesCS6D01G153800 chr6D 89.130 46 5 0 264 309 370694450 370694405 2.610000e-04 58.4
3 TraesCS6D01G153800 chr6A 94.148 4050 126 52 1 3990 150226565 150230563 0.000000e+00 6063.0
4 TraesCS6D01G153800 chr6A 84.363 1311 118 51 5415 6684 150232953 150234217 0.000000e+00 1205.0
5 TraesCS6D01G153800 chr6A 96.232 690 22 3 3983 4668 150231260 150231949 0.000000e+00 1127.0
6 TraesCS6D01G153800 chr6A 91.262 309 21 5 5092 5395 150232592 150232899 3.740000e-112 416.0
7 TraesCS6D01G153800 chr6A 95.531 179 5 2 4681 4857 150232148 150232325 3.960000e-72 283.0
8 TraesCS6D01G153800 chr6A 89.130 46 5 0 264 309 511540397 511540352 2.610000e-04 58.4
9 TraesCS6D01G153800 chr6B 95.577 2826 99 12 1855 4668 226870766 226867955 0.000000e+00 4503.0
10 TraesCS6D01G153800 chr6B 87.122 1949 82 63 1 1858 226872767 226870897 0.000000e+00 2052.0
11 TraesCS6D01G153800 chr6B 96.929 814 22 2 4667 5478 226867873 226867061 0.000000e+00 1362.0
12 TraesCS6D01G153800 chr6B 95.333 750 21 7 5957 6702 226866416 226865677 0.000000e+00 1179.0
13 TraesCS6D01G153800 chr6B 90.203 541 19 5 5477 5992 226866957 226866426 0.000000e+00 675.0
14 TraesCS6D01G153800 chr1A 81.051 533 77 21 6167 6684 490878311 490878834 2.910000e-108 403.0
15 TraesCS6D01G153800 chr1A 80.392 102 16 3 3483 3581 96040639 96040539 2.590000e-09 75.0
16 TraesCS6D01G153800 chr4D 84.524 84 11 1 3489 3570 71072754 71072837 1.550000e-11 82.4
17 TraesCS6D01G153800 chr3D 92.857 56 3 1 3488 3542 105428602 105428547 5.570000e-11 80.5
18 TraesCS6D01G153800 chr3D 82.418 91 14 1 3488 3576 331672515 331672425 2.000000e-10 78.7
19 TraesCS6D01G153800 chr3D 95.455 44 2 0 2565 2608 46105654 46105611 3.350000e-08 71.3
20 TraesCS6D01G153800 chr7D 90.323 62 2 2 3489 3546 387221871 387221932 2.000000e-10 78.7
21 TraesCS6D01G153800 chr3A 89.831 59 6 0 3480 3538 109987776 109987834 7.210000e-10 76.8


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 TraesCS6D01G153800 chr6D 128094967 128101668 6701 True 12377.0 12377 100.0000 1 6702 1 chr6D.!!$R1 6701
1 TraesCS6D01G153800 chr6A 150226565 150234217 7652 False 1818.8 6063 92.3072 1 6684 5 chr6A.!!$F1 6683
2 TraesCS6D01G153800 chr6B 226865677 226872767 7090 True 1954.2 4503 93.0328 1 6702 5 chr6B.!!$R1 6701
3 TraesCS6D01G153800 chr1A 490878311 490878834 523 False 403.0 403 81.0510 6167 6684 1 chr1A.!!$F1 517

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
970 1021 1.168714 GCCGTCAAGAGCAGGAAAAT 58.831 50.000 0.0 0.0 0.00 1.82 F
1241 1320 0.111639 GTATCTCCCTCTCCTCGCCT 59.888 60.000 0.0 0.0 0.00 5.52 F
2712 2982 1.134220 GGATCCGTGAAGGTAATGCCA 60.134 52.381 0.0 0.0 41.99 4.92 F
3570 3851 0.544697 TATTTTGGGACGGAGGGAGC 59.455 55.000 0.0 0.0 0.00 4.70 F
5421 6749 0.521291 AACACGATGGGATTGCGTTG 59.479 50.000 0.0 0.0 35.90 4.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2891 3161 0.240945 CGCGAAGACCCTGCATTTTT 59.759 50.000 0.00 0.0 0.00 1.94 R
2954 3224 8.540388 GGCTGATAGGTTGATTTATATACCTCA 58.460 37.037 0.00 0.0 41.16 3.86 R
3915 4196 0.585357 CACATAGCCAAGATCAGCGC 59.415 55.000 0.00 0.0 0.00 5.92 R
5485 6953 0.973496 TATGGGTCGCCACACTGCTA 60.973 55.000 0.00 0.0 0.00 3.49 R
6258 7825 2.667536 CAGCTGGCAAGTCGCAGT 60.668 61.111 5.57 0.0 45.17 4.40 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
98 99 2.285743 ACCCTCTCCCAGGCCTTC 60.286 66.667 0.00 0.00 41.80 3.46
812 855 5.737349 GCCTTGGTCTCTTCTTTCCTTTTTG 60.737 44.000 0.00 0.00 0.00 2.44
970 1021 1.168714 GCCGTCAAGAGCAGGAAAAT 58.831 50.000 0.00 0.00 0.00 1.82
973 1024 3.378427 GCCGTCAAGAGCAGGAAAATAAT 59.622 43.478 0.00 0.00 0.00 1.28
974 1025 4.574828 GCCGTCAAGAGCAGGAAAATAATA 59.425 41.667 0.00 0.00 0.00 0.98
975 1026 5.277538 GCCGTCAAGAGCAGGAAAATAATAG 60.278 44.000 0.00 0.00 0.00 1.73
976 1027 5.817816 CCGTCAAGAGCAGGAAAATAATAGT 59.182 40.000 0.00 0.00 0.00 2.12
1071 1128 6.741358 GCCACGATTTTCACTAGTATTTCAAC 59.259 38.462 0.00 0.00 0.00 3.18
1166 1241 1.893315 CAGTTCCCCTATTCCTCCCA 58.107 55.000 0.00 0.00 0.00 4.37
1167 1242 2.422746 CAGTTCCCCTATTCCTCCCAT 58.577 52.381 0.00 0.00 0.00 4.00
1170 1245 0.196118 TCCCCTATTCCTCCCATCCC 59.804 60.000 0.00 0.00 0.00 3.85
1173 1248 0.197145 CCTATTCCTCCCATCCCCCT 59.803 60.000 0.00 0.00 0.00 4.79
1175 1250 2.047865 CCTATTCCTCCCATCCCCCTAT 59.952 54.545 0.00 0.00 0.00 2.57
1176 1251 2.864639 ATTCCTCCCATCCCCCTATT 57.135 50.000 0.00 0.00 0.00 1.73
1177 1252 2.133858 TTCCTCCCATCCCCCTATTC 57.866 55.000 0.00 0.00 0.00 1.75
1178 1253 0.196118 TCCTCCCATCCCCCTATTCC 59.804 60.000 0.00 0.00 0.00 3.01
1179 1254 0.197145 CCTCCCATCCCCCTATTCCT 59.803 60.000 0.00 0.00 0.00 3.36
1207 1286 0.990374 CATCCTCCCTGATGATCCCC 59.010 60.000 0.00 0.00 43.94 4.81
1241 1320 0.111639 GTATCTCCCTCTCCTCGCCT 59.888 60.000 0.00 0.00 0.00 5.52
1243 1322 2.366153 ATCTCCCTCTCCTCGCCTCC 62.366 65.000 0.00 0.00 0.00 4.30
1244 1323 4.507916 TCCCTCTCCTCGCCTCCG 62.508 72.222 0.00 0.00 0.00 4.63
1247 1326 3.591835 CTCTCCTCGCCTCCGCTC 61.592 72.222 0.00 0.00 0.00 5.03
1248 1327 4.116585 TCTCCTCGCCTCCGCTCT 62.117 66.667 0.00 0.00 0.00 4.09
1264 1351 2.197324 CTCCTCCCCTCTCTCCGG 59.803 72.222 0.00 0.00 0.00 5.14
1526 1642 5.120830 GCATCTTCTTGTTCAGTCGTGTTAT 59.879 40.000 0.00 0.00 0.00 1.89
1769 1891 3.129109 CGACGCTCAGATACAGGTAGTA 58.871 50.000 0.00 0.00 37.06 1.82
1770 1892 3.558829 CGACGCTCAGATACAGGTAGTAA 59.441 47.826 0.00 0.00 36.05 2.24
1771 1893 4.552378 CGACGCTCAGATACAGGTAGTAAC 60.552 50.000 0.00 0.00 36.05 2.50
1772 1894 3.311871 ACGCTCAGATACAGGTAGTAACG 59.688 47.826 0.00 0.00 36.05 3.18
1773 1895 3.303857 CGCTCAGATACAGGTAGTAACGG 60.304 52.174 0.00 0.00 36.05 4.44
1774 1896 3.550436 GCTCAGATACAGGTAGTAACGGC 60.550 52.174 0.00 0.00 36.05 5.68
1775 1897 3.623703 TCAGATACAGGTAGTAACGGCA 58.376 45.455 0.00 0.00 36.05 5.69
1779 1901 2.174363 ACAGGTAGTAACGGCAAACC 57.826 50.000 0.00 0.00 0.00 3.27
1848 1970 4.167268 CGTCCTAGTTAGCAGTTTCTGAC 58.833 47.826 0.66 0.00 32.44 3.51
1913 2169 2.266554 CTGAGCTCGAGATTTGTGTCC 58.733 52.381 18.75 0.00 0.00 4.02
2047 2316 6.043411 GGTGAGTAGTAATGGTTGTCTGATC 58.957 44.000 0.00 0.00 0.00 2.92
2063 2332 2.786027 CTGATCGTTCGTGCTCTATGTG 59.214 50.000 0.00 0.00 0.00 3.21
2195 2464 2.225017 GGGTGGGTTGGATCTTTCTTGA 60.225 50.000 0.00 0.00 0.00 3.02
2712 2982 1.134220 GGATCCGTGAAGGTAATGCCA 60.134 52.381 0.00 0.00 41.99 4.92
2828 3098 3.258228 AGCTTGGTTGTTTTGGTTTTCG 58.742 40.909 0.00 0.00 0.00 3.46
2928 3198 1.892209 CGTGGGAGTTAACTTGGCTT 58.108 50.000 10.02 0.00 0.00 4.35
2954 3224 7.214381 TCGCTATTGCTTTACATAACATACCT 58.786 34.615 0.00 0.00 36.97 3.08
3009 3279 8.041323 TCTGGTTAAGTAGCCTAAGAATTCTTG 58.959 37.037 27.37 17.46 37.40 3.02
3085 3364 7.882791 TCTTTGTAAGAAGATTCAACTGCCATA 59.117 33.333 0.00 0.00 33.83 2.74
3115 3394 4.359434 TGTTTGTTATACTGCACCAGGA 57.641 40.909 0.00 0.00 35.51 3.86
3243 3522 5.957842 TTGCCATGAAGTTTCGAGTATTT 57.042 34.783 0.00 0.00 0.00 1.40
3262 3541 9.771534 GAGTATTTTGATATTTGCTAGGTCTCT 57.228 33.333 0.00 0.00 0.00 3.10
3274 3553 3.133003 GCTAGGTCTCTGCACTATCCAAA 59.867 47.826 0.00 0.00 0.00 3.28
3315 3594 8.450578 TTTGATCTGTGTAGTTCAGTTTGATT 57.549 30.769 0.00 0.00 34.91 2.57
3343 3622 7.735326 AGTGACCATACTAGAATTAGTTGGT 57.265 36.000 15.19 15.19 44.62 3.67
3500 3779 3.873910 ACAAAATCATACTCCCTCCGTG 58.126 45.455 0.00 0.00 0.00 4.94
3570 3851 0.544697 TATTTTGGGACGGAGGGAGC 59.455 55.000 0.00 0.00 0.00 4.70
3796 4077 2.170607 AGTCCACTACCGCAAATGCTAT 59.829 45.455 3.63 0.00 39.32 2.97
3802 4083 5.238432 CCACTACCGCAAATGCTATGAATTA 59.762 40.000 3.63 0.00 39.32 1.40
3915 4196 1.466167 CTTCTCAAATGTGGTGAGCCG 59.534 52.381 0.00 0.00 41.94 5.52
3966 4247 2.038863 TCCTCCAGTCTTAAAGGGCA 57.961 50.000 0.00 0.00 0.00 5.36
3998 4983 2.566833 AGCACCTACAAAGCATGACA 57.433 45.000 0.00 0.00 0.00 3.58
4046 5031 8.193953 AGAAAGAAGGGAAATTAGAATTTGCA 57.806 30.769 17.53 0.00 45.15 4.08
4145 5130 7.882791 TCTGTGTTTCCTTCTTTCTTGCATATA 59.117 33.333 0.00 0.00 0.00 0.86
4243 5228 5.376854 TGCTATTTTTGTGAGCCTTTCTC 57.623 39.130 0.00 0.00 42.23 2.87
4244 5229 4.083324 TGCTATTTTTGTGAGCCTTTCTCG 60.083 41.667 0.00 0.00 44.86 4.04
4281 5266 1.293179 CCTGTCGACCACTGATGCA 59.707 57.895 14.12 0.00 0.00 3.96
4284 5269 2.079158 CTGTCGACCACTGATGCAAAT 58.921 47.619 14.12 0.00 0.00 2.32
4287 5273 3.000041 GTCGACCACTGATGCAAATGTA 59.000 45.455 3.51 0.00 0.00 2.29
4292 5278 6.542005 TCGACCACTGATGCAAATGTAATTAT 59.458 34.615 0.00 0.00 33.67 1.28
4936 6113 5.104817 CCTTCACCCAAGCAAAAATATGGAT 60.105 40.000 0.00 0.00 34.82 3.41
5004 6181 5.972107 ATAGTCATTAGCCAAATGCATCC 57.028 39.130 0.00 0.00 44.03 3.51
5012 6189 3.550820 AGCCAAATGCATCCGTGTTATA 58.449 40.909 0.00 0.00 44.83 0.98
5168 6496 2.376109 CATGCCTTGAAAGCAGAGGAT 58.624 47.619 0.00 0.00 44.90 3.24
5323 6651 2.632377 CACCACTGCAACTATACCAGG 58.368 52.381 0.00 0.00 0.00 4.45
5406 6734 1.692411 AGGCAAGGACCAAGAAACAC 58.308 50.000 0.00 0.00 0.00 3.32
5421 6749 0.521291 AACACGATGGGATTGCGTTG 59.479 50.000 0.00 0.00 35.90 4.10
5485 6953 7.763071 GTCTGACCGTTGTTTACTAGGAAATAT 59.237 37.037 2.78 0.00 0.00 1.28
5558 7026 6.184789 GTTTAAGAGAACCATATGGGGTGAA 58.815 40.000 25.55 7.49 41.32 3.18
5623 7099 6.681777 ACTAGAACTGATTTGTGGCATTTTC 58.318 36.000 0.00 0.00 0.00 2.29
5625 7101 2.676076 ACTGATTTGTGGCATTTTCGC 58.324 42.857 0.00 0.00 0.00 4.70
5635 7111 1.138671 CATTTTCGCCGGCCGATTT 59.861 52.632 30.73 0.00 46.81 2.17
5714 7190 7.878127 TGTTAACCCTTTTGATTGTGTTGAAAA 59.122 29.630 2.48 0.00 0.00 2.29
5797 7309 2.224548 GGAGTACTGTTTCCAACTGGCT 60.225 50.000 0.00 0.00 34.98 4.75
5811 7323 4.942761 AACTGGCTTGTTGAAATGATGT 57.057 36.364 0.00 0.00 0.00 3.06
5812 7324 4.942761 ACTGGCTTGTTGAAATGATGTT 57.057 36.364 0.00 0.00 0.00 2.71
5813 7325 4.624015 ACTGGCTTGTTGAAATGATGTTG 58.376 39.130 0.00 0.00 0.00 3.33
5814 7326 4.099881 ACTGGCTTGTTGAAATGATGTTGT 59.900 37.500 0.00 0.00 0.00 3.32
5815 7327 4.370049 TGGCTTGTTGAAATGATGTTGTG 58.630 39.130 0.00 0.00 0.00 3.33
5816 7328 4.141981 TGGCTTGTTGAAATGATGTTGTGT 60.142 37.500 0.00 0.00 0.00 3.72
5817 7329 4.810491 GGCTTGTTGAAATGATGTTGTGTT 59.190 37.500 0.00 0.00 0.00 3.32
5818 7330 5.294060 GGCTTGTTGAAATGATGTTGTGTTT 59.706 36.000 0.00 0.00 0.00 2.83
5819 7331 6.186785 GCTTGTTGAAATGATGTTGTGTTTG 58.813 36.000 0.00 0.00 0.00 2.93
5820 7332 5.715429 TGTTGAAATGATGTTGTGTTTGC 57.285 34.783 0.00 0.00 0.00 3.68
5821 7333 4.569966 TGTTGAAATGATGTTGTGTTTGCC 59.430 37.500 0.00 0.00 0.00 4.52
5882 7394 3.558674 CCCAAAGGTAGGTGCAGAG 57.441 57.895 0.00 0.00 0.00 3.35
5890 7404 5.763876 AAGGTAGGTGCAGAGAAATTAGT 57.236 39.130 0.00 0.00 0.00 2.24
5976 7537 2.068519 TCACGAGATGTTGCACATGAC 58.931 47.619 0.00 0.00 39.27 3.06
6059 7620 3.453868 TGGAGATGAGGAAAGTCCATCA 58.546 45.455 0.00 0.00 39.61 3.07
6066 7627 3.269178 GAGGAAAGTCCATCAAGCTGAG 58.731 50.000 0.00 0.00 39.61 3.35
6159 7722 1.027357 GGAGGTGCTGCATTACATGG 58.973 55.000 5.27 0.00 0.00 3.66
6160 7723 1.027357 GAGGTGCTGCATTACATGGG 58.973 55.000 5.27 0.00 0.00 4.00
6534 8106 2.949714 ATCGTCTTGCTTGTTTGTCG 57.050 45.000 0.00 0.00 0.00 4.35
6624 8199 2.747855 CTTCCTGGCTTCCCACGC 60.748 66.667 0.00 0.00 35.79 5.34
6644 8219 1.553690 GCTCCTGCTGGGTCACCTAA 61.554 60.000 10.07 0.00 37.76 2.69
6684 8259 2.183478 TTGCGCAAATGAGAAGAGGA 57.817 45.000 22.78 0.00 0.00 3.71
6685 8260 1.730501 TGCGCAAATGAGAAGAGGAG 58.269 50.000 8.16 0.00 0.00 3.69
6686 8261 0.376502 GCGCAAATGAGAAGAGGAGC 59.623 55.000 0.30 0.00 0.00 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
98 99 4.200283 GGCTCGGTCGCTCTCTGG 62.200 72.222 0.00 0.00 0.00 3.86
812 855 6.260936 AGAACCCGATGTCATATCATCAAAAC 59.739 38.462 7.32 0.00 42.82 2.43
990 1041 2.261671 CACCTTCTCCCACGACCG 59.738 66.667 0.00 0.00 0.00 4.79
1166 1241 1.203622 GGATGGGAGGAATAGGGGGAT 60.204 57.143 0.00 0.00 0.00 3.85
1167 1242 0.196118 GGATGGGAGGAATAGGGGGA 59.804 60.000 0.00 0.00 0.00 4.81
1170 1245 0.103930 TGGGGATGGGAGGAATAGGG 60.104 60.000 0.00 0.00 0.00 3.53
1173 1248 1.518525 AGGATGGGGATGGGAGGAATA 59.481 52.381 0.00 0.00 0.00 1.75
1175 1250 0.401979 GAGGATGGGGATGGGAGGAA 60.402 60.000 0.00 0.00 0.00 3.36
1176 1251 1.240129 GAGGATGGGGATGGGAGGA 59.760 63.158 0.00 0.00 0.00 3.71
1177 1252 1.849823 GGAGGATGGGGATGGGAGG 60.850 68.421 0.00 0.00 0.00 4.30
1178 1253 1.849823 GGGAGGATGGGGATGGGAG 60.850 68.421 0.00 0.00 0.00 4.30
1179 1254 2.293934 GGGAGGATGGGGATGGGA 59.706 66.667 0.00 0.00 0.00 4.37
1207 1286 0.592148 GATACGACTAGTGGAGCGGG 59.408 60.000 12.28 0.00 0.00 6.13
1241 1320 3.024356 AGAGGGGAGGAGAGCGGA 61.024 66.667 0.00 0.00 0.00 5.54
1243 1322 1.528309 GAGAGAGGGGAGGAGAGCG 60.528 68.421 0.00 0.00 0.00 5.03
1244 1323 1.152546 GGAGAGAGGGGAGGAGAGC 60.153 68.421 0.00 0.00 0.00 4.09
1245 1324 1.150536 CGGAGAGAGGGGAGGAGAG 59.849 68.421 0.00 0.00 0.00 3.20
1246 1325 2.387772 CCGGAGAGAGGGGAGGAGA 61.388 68.421 0.00 0.00 0.00 3.71
1247 1326 2.197324 CCGGAGAGAGGGGAGGAG 59.803 72.222 0.00 0.00 0.00 3.69
1248 1327 2.617538 ACCGGAGAGAGGGGAGGA 60.618 66.667 9.46 0.00 0.00 3.71
1541 1657 4.504097 CACTTTGCAAAACTGCTTAGGTTC 59.496 41.667 13.84 0.00 35.49 3.62
1542 1658 4.159506 TCACTTTGCAAAACTGCTTAGGTT 59.840 37.500 13.84 0.00 35.49 3.50
1544 1660 4.044426 GTCACTTTGCAAAACTGCTTAGG 58.956 43.478 13.84 0.54 35.49 2.69
1546 1662 3.488384 CCGTCACTTTGCAAAACTGCTTA 60.488 43.478 13.84 0.00 35.49 3.09
1547 1663 2.529151 CGTCACTTTGCAAAACTGCTT 58.471 42.857 13.84 0.00 35.49 3.91
1550 1666 2.097466 ACTCCGTCACTTTGCAAAACTG 59.903 45.455 13.84 11.23 0.00 3.16
1551 1667 2.365582 ACTCCGTCACTTTGCAAAACT 58.634 42.857 13.84 0.00 0.00 2.66
1552 1668 2.844122 ACTCCGTCACTTTGCAAAAC 57.156 45.000 13.84 7.83 0.00 2.43
1553 1669 3.859411 AAACTCCGTCACTTTGCAAAA 57.141 38.095 13.84 0.00 0.00 2.44
1563 1685 3.725819 CGGCACAAAACTCCGTCA 58.274 55.556 0.00 0.00 38.47 4.35
1772 1894 4.026226 CAAGGTTTGCGGTTTGCC 57.974 55.556 0.00 0.00 45.60 4.52
1848 1970 2.983136 CGCAGGATATCAAGTAGAAGCG 59.017 50.000 4.83 4.36 35.42 4.68
1913 2169 2.667536 ACAAGCAGCGCACCTGAG 60.668 61.111 11.47 4.43 44.64 3.35
2047 2316 1.201812 GCAACACATAGAGCACGAACG 60.202 52.381 0.00 0.00 0.00 3.95
2063 2332 4.088421 GCATGCAGCATGAGCAAC 57.912 55.556 35.16 15.73 46.27 4.17
2712 2982 6.460261 CCACTACACTGAGATGAATACACGAT 60.460 42.308 0.00 0.00 0.00 3.73
2797 3067 0.737219 CAACCAAGCTATGCTCCAGC 59.263 55.000 0.00 0.00 38.25 4.85
2891 3161 0.240945 CGCGAAGACCCTGCATTTTT 59.759 50.000 0.00 0.00 0.00 1.94
2954 3224 8.540388 GGCTGATAGGTTGATTTATATACCTCA 58.460 37.037 0.00 0.00 41.16 3.86
3147 3426 8.623903 GTCATGAATTAGTTTGCCATGAGATTA 58.376 33.333 0.00 0.00 42.63 1.75
3243 3522 5.104776 AGTGCAGAGACCTAGCAAATATCAA 60.105 40.000 0.00 0.00 40.35 2.57
3343 3622 9.483916 CCCTTGTACGTAATGATATGTTTGATA 57.516 33.333 0.00 0.00 33.36 2.15
3500 3779 6.868339 ACTAAATCAGCAACACTTATTTTGGC 59.132 34.615 0.00 0.00 34.69 4.52
3570 3851 3.218453 ACTGTCAGGAGTCTCGGATATG 58.782 50.000 4.53 0.00 0.00 1.78
3583 3864 1.802960 GCAACATGTCAGACTGTCAGG 59.197 52.381 10.88 11.86 0.00 3.86
3796 4077 7.531857 TTGGCTACAGAAAACCAATAATTCA 57.468 32.000 0.00 0.00 37.26 2.57
3802 4083 5.806654 ACATTTGGCTACAGAAAACCAAT 57.193 34.783 0.00 0.00 41.59 3.16
3915 4196 0.585357 CACATAGCCAAGATCAGCGC 59.415 55.000 0.00 0.00 0.00 5.92
3917 4198 1.872313 GCTCACATAGCCAAGATCAGC 59.128 52.381 0.00 0.00 46.25 4.26
3966 4247 4.415596 TGTAGGTGCTTTGGAATCCAATT 58.584 39.130 16.30 0.96 43.55 2.32
4266 5251 1.806542 ACATTTGCATCAGTGGTCGAC 59.193 47.619 7.13 7.13 0.00 4.20
4281 5266 7.605449 ACAAGACAGCTGCAATAATTACATTT 58.395 30.769 15.27 0.00 0.00 2.32
4284 5269 6.573664 AACAAGACAGCTGCAATAATTACA 57.426 33.333 15.27 0.00 0.00 2.41
4287 5273 5.473039 GGAAACAAGACAGCTGCAATAATT 58.527 37.500 15.27 2.64 0.00 1.40
4292 5278 0.662619 CGGAAACAAGACAGCTGCAA 59.337 50.000 15.27 0.00 0.00 4.08
4574 5560 5.062809 GTGCTTCAGAACTATACAGACAAGC 59.937 44.000 0.00 0.00 35.38 4.01
4936 6113 3.753272 GCTGCTGACCAAATTTACTCAGA 59.247 43.478 20.81 10.11 33.30 3.27
5004 6181 4.052608 TGTGCGAATATGGGTATAACACG 58.947 43.478 0.00 0.00 0.00 4.49
5012 6189 4.578928 GGTTAGAATTGTGCGAATATGGGT 59.421 41.667 0.00 0.00 0.00 4.51
5108 6433 8.910666 CAACGTAATAATGAAAAGCAATTGTGA 58.089 29.630 7.40 0.00 0.00 3.58
5323 6651 4.390297 GGCTTCAGAAGACACTATGAACAC 59.610 45.833 14.86 0.00 36.21 3.32
5406 6734 2.408835 GCCAACGCAATCCCATCG 59.591 61.111 0.00 0.00 34.03 3.84
5485 6953 0.973496 TATGGGTCGCCACACTGCTA 60.973 55.000 0.00 0.00 0.00 3.49
5623 7099 4.160635 GTGTCAAATCGGCCGGCG 62.161 66.667 27.83 16.23 0.00 6.46
5625 7101 1.234615 ACAAGTGTCAAATCGGCCGG 61.235 55.000 27.83 9.38 0.00 6.13
5627 7103 3.907894 TTAACAAGTGTCAAATCGGCC 57.092 42.857 0.00 0.00 0.00 6.13
5628 7104 5.798434 GGTATTTAACAAGTGTCAAATCGGC 59.202 40.000 0.00 0.00 0.00 5.54
5635 7111 5.468746 GTGAGCAGGTATTTAACAAGTGTCA 59.531 40.000 0.00 0.00 0.00 3.58
5797 7309 5.064452 GGCAAACACAACATCATTTCAACAA 59.936 36.000 0.00 0.00 0.00 2.83
5803 7315 3.132925 GCAGGCAAACACAACATCATTT 58.867 40.909 0.00 0.00 0.00 2.32
5806 7318 1.401761 AGCAGGCAAACACAACATCA 58.598 45.000 0.00 0.00 0.00 3.07
5807 7319 2.813754 TCTAGCAGGCAAACACAACATC 59.186 45.455 0.00 0.00 0.00 3.06
5808 7320 2.862541 TCTAGCAGGCAAACACAACAT 58.137 42.857 0.00 0.00 0.00 2.71
5811 7323 4.584325 AGAAATTCTAGCAGGCAAACACAA 59.416 37.500 0.00 0.00 0.00 3.33
5812 7324 4.144297 AGAAATTCTAGCAGGCAAACACA 58.856 39.130 0.00 0.00 0.00 3.72
5813 7325 4.773323 AGAAATTCTAGCAGGCAAACAC 57.227 40.909 0.00 0.00 0.00 3.32
5814 7326 5.643777 GTCTAGAAATTCTAGCAGGCAAACA 59.356 40.000 21.80 2.36 44.65 2.83
5815 7327 5.877564 AGTCTAGAAATTCTAGCAGGCAAAC 59.122 40.000 21.80 13.99 44.65 2.93
5816 7328 5.877012 CAGTCTAGAAATTCTAGCAGGCAAA 59.123 40.000 21.80 3.66 44.65 3.68
5817 7329 5.187772 TCAGTCTAGAAATTCTAGCAGGCAA 59.812 40.000 21.80 4.31 44.65 4.52
5818 7330 4.711846 TCAGTCTAGAAATTCTAGCAGGCA 59.288 41.667 21.80 4.96 44.65 4.75
5819 7331 5.163457 ACTCAGTCTAGAAATTCTAGCAGGC 60.163 44.000 21.80 12.87 44.65 4.85
5820 7332 6.321181 AGACTCAGTCTAGAAATTCTAGCAGG 59.679 42.308 21.80 13.99 44.65 4.85
5821 7333 7.333528 AGACTCAGTCTAGAAATTCTAGCAG 57.666 40.000 21.80 16.37 44.65 4.24
5864 7376 0.984230 TCTCTGCACCTACCTTTGGG 59.016 55.000 0.00 0.00 38.88 4.12
5890 7404 6.312918 GGCGATTGATTCTTCAAGTACAGTTA 59.687 38.462 0.00 0.00 44.75 2.24
5976 7537 4.323417 TGAGCTGTAACTAACCACAATGG 58.677 43.478 0.00 0.00 45.02 3.16
5994 7555 2.531912 CGATCAGTGTCGTGTTATGAGC 59.468 50.000 6.87 0.00 36.88 4.26
6027 7588 8.383175 ACTTTCCTCATCTCCAAGTTTGTAATA 58.617 33.333 0.00 0.00 0.00 0.98
6059 7620 1.684248 GGAATGTCCCATGCTCAGCTT 60.684 52.381 0.00 0.00 0.00 3.74
6145 7708 2.212812 TGTTCCCATGTAATGCAGCA 57.787 45.000 0.00 0.00 44.97 4.41
6159 7722 1.135721 GAATCCAGCAAGCCATGTTCC 59.864 52.381 0.00 0.00 0.00 3.62
6160 7723 1.820519 TGAATCCAGCAAGCCATGTTC 59.179 47.619 0.00 0.00 0.00 3.18
6258 7825 2.667536 CAGCTGGCAAGTCGCAGT 60.668 61.111 5.57 0.00 45.17 4.40
6534 8106 5.591643 TGAGACTTGAATACGCTTTCAAC 57.408 39.130 8.76 2.52 39.91 3.18


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

AutoCloner maintained by Alex Coulton.