Multiple sequence alignment - TraesCS5D01G434400

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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 TraesCS5D01G434400 chr5D 100.000 8479 0 0 1 8479 489895890 489904368 0.000000e+00 15621.0
1 TraesCS5D01G434400 chr5D 87.736 106 11 1 1284 1389 339100579 339100476 1.160000e-23 122.0
2 TraesCS5D01G434400 chr5A 95.713 7185 235 42 1341 8478 611555866 611563024 0.000000e+00 11494.0
3 TraesCS5D01G434400 chr5A 85.052 970 69 33 382 1305 611554934 611555873 0.000000e+00 918.0
4 TraesCS5D01G434400 chr5A 84.474 380 9 13 3 371 611554279 611554619 6.350000e-86 329.0
5 TraesCS5D01G434400 chr5B 97.905 3915 70 7 930 4838 604056010 604059918 0.000000e+00 6765.0
6 TraesCS5D01G434400 chr5B 96.023 3772 96 34 4741 8478 604059922 604063673 0.000000e+00 6085.0
7 TraesCS5D01G434400 chr5B 93.321 554 20 5 382 933 604055446 604055984 0.000000e+00 802.0
8 TraesCS5D01G434400 chr5B 87.013 231 18 8 1 219 604054650 604054880 5.080000e-62 250.0
9 TraesCS5D01G434400 chr3D 75.872 344 53 19 2606 2934 604716672 604717000 1.910000e-31 148.0
10 TraesCS5D01G434400 chr3D 89.216 102 9 2 1288 1389 22679057 22679156 8.940000e-25 126.0
11 TraesCS5D01G434400 chr3D 89.216 102 9 2 1291 1392 22767898 22767799 8.940000e-25 126.0
12 TraesCS5D01G434400 chr3D 86.667 75 10 0 2580 2654 604723975 604724049 5.450000e-12 84.2
13 TraesCS5D01G434400 chrUn 84.962 133 19 1 2581 2712 335984390 335984258 5.340000e-27 134.0
14 TraesCS5D01G434400 chrUn 84.962 133 19 1 2581 2712 360215308 360215176 5.340000e-27 134.0
15 TraesCS5D01G434400 chrUn 84.962 133 19 1 2581 2712 470692099 470691967 5.340000e-27 134.0
16 TraesCS5D01G434400 chr6B 94.118 85 5 0 1291 1375 642350236 642350320 6.910000e-26 130.0
17 TraesCS5D01G434400 chr6B 93.103 87 6 0 1291 1377 447890611 447890697 2.480000e-25 128.0
18 TraesCS5D01G434400 chr6D 92.308 91 5 1 1290 1380 296699491 296699579 2.480000e-25 128.0
19 TraesCS5D01G434400 chr7B 90.722 97 6 2 1291 1386 107127483 107127389 8.940000e-25 126.0
20 TraesCS5D01G434400 chr2A 91.209 91 6 1 1289 1379 361381705 361381617 1.160000e-23 122.0


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 TraesCS5D01G434400 chr5D 489895890 489904368 8478 False 15621.0 15621 100.0000 1 8479 1 chr5D.!!$F1 8478
1 TraesCS5D01G434400 chr5A 611554279 611563024 8745 False 4247.0 11494 88.4130 3 8478 3 chr5A.!!$F1 8475
2 TraesCS5D01G434400 chr5B 604054650 604063673 9023 False 3475.5 6765 93.5655 1 8478 4 chr5B.!!$F1 8477

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
754 1195 0.178924 ACAGGGGCTTGGCTTGAAAT 60.179 50.000 6.33 0.0 0.00 2.17 F
1090 1563 1.103987 TGGCGCAACCTGTTTAAGCA 61.104 50.000 10.83 0.0 40.22 3.91 F
1115 1588 1.142870 CCCTGTTGTTCTGACCAAGGA 59.857 52.381 0.00 0.0 0.00 3.36 F
2788 3276 0.036164 TTGCTCCACGTGGCATACTT 59.964 50.000 30.25 0.0 38.30 2.24 F
3236 3726 0.690762 ACTAGGGGCGTTGTGACAAT 59.309 50.000 0.00 0.0 0.00 2.71 F
3249 3739 5.390885 CGTTGTGACAATGACCCATTTAGAG 60.391 44.000 11.98 0.0 31.05 2.43 F
3738 4228 6.949352 AACATAATAGCTCCATCACCAAAG 57.051 37.500 0.00 0.0 0.00 2.77 F
4206 4698 1.072159 CGATGATCTGGAAGCCCCC 59.928 63.158 0.00 0.0 0.00 5.40 F
5861 6461 0.954452 CAGCACCAAAACCAGAGACC 59.046 55.000 0.00 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2712 3200 4.686972 TGATGTGCAGCAGATAGAAGTAC 58.313 43.478 4.72 0.0 0.00 2.73 R
2788 3276 3.826524 TCAAGCACCATACAAGGACAAA 58.173 40.909 0.00 0.0 0.00 2.83 R
2830 3318 4.797868 TCACAGTTTTGCAGTTGAAAATCG 59.202 37.500 0.00 0.0 0.00 3.34 R
3738 4228 0.249447 GTTTGCCAGACTGTTTGCCC 60.249 55.000 0.93 0.0 0.00 5.36 R
4165 4656 6.764085 TCGTCAAACTCAGTTAAATCCTGAAA 59.236 34.615 0.00 0.0 38.42 2.69 R
4206 4698 7.384660 TCAAATTTTGAATTCTTTGATGGGACG 59.615 33.333 9.36 0.0 36.59 4.79 R
5467 6065 3.877508 ACTGGAAACACAAGTAGCAGAAC 59.122 43.478 0.00 0.0 35.60 3.01 R
6130 6730 1.284982 CGTTGAAGCGGACTGGACAG 61.285 60.000 0.00 0.0 0.00 3.51 R
7720 8329 0.404040 CCACCAGGGCTTCAACCTTA 59.596 55.000 0.00 0.0 35.78 2.69 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
32 38 1.552578 AATTTAAACCCCTCGCCCAC 58.447 50.000 0.00 0.00 0.00 4.61
115 121 2.344500 CGTAAGCCACCCACGGAA 59.656 61.111 0.00 0.00 32.19 4.30
116 122 1.740296 CGTAAGCCACCCACGGAAG 60.740 63.158 0.00 0.00 32.19 3.46
117 123 1.675219 GTAAGCCACCCACGGAAGA 59.325 57.895 0.00 0.00 0.00 2.87
118 124 0.252197 GTAAGCCACCCACGGAAGAT 59.748 55.000 0.00 0.00 0.00 2.40
119 125 1.483415 GTAAGCCACCCACGGAAGATA 59.517 52.381 0.00 0.00 0.00 1.98
120 126 0.252197 AAGCCACCCACGGAAGATAC 59.748 55.000 0.00 0.00 0.00 2.24
122 128 1.906105 GCCACCCACGGAAGATACCA 61.906 60.000 0.00 0.00 0.00 3.25
124 130 0.459585 CACCCACGGAAGATACCACG 60.460 60.000 0.00 0.00 0.00 4.94
125 131 0.901580 ACCCACGGAAGATACCACGT 60.902 55.000 0.00 0.00 40.60 4.49
126 132 1.105457 CCCACGGAAGATACCACGTA 58.895 55.000 0.00 0.00 37.85 3.57
127 133 1.477700 CCCACGGAAGATACCACGTAA 59.522 52.381 0.00 0.00 37.85 3.18
128 134 2.101917 CCCACGGAAGATACCACGTAAT 59.898 50.000 0.00 0.00 37.85 1.89
129 135 3.378339 CCACGGAAGATACCACGTAATC 58.622 50.000 0.00 0.00 37.85 1.75
130 136 3.378339 CACGGAAGATACCACGTAATCC 58.622 50.000 0.00 0.00 37.85 3.01
132 138 3.067742 ACGGAAGATACCACGTAATCCAG 59.932 47.826 0.00 0.00 37.85 3.86
133 139 3.391049 GGAAGATACCACGTAATCCAGC 58.609 50.000 0.00 0.00 0.00 4.85
134 140 3.181469 GGAAGATACCACGTAATCCAGCA 60.181 47.826 0.00 0.00 0.00 4.41
136 142 2.102588 AGATACCACGTAATCCAGCACC 59.897 50.000 0.00 0.00 0.00 5.01
138 144 1.298340 CCACGTAATCCAGCACCCA 59.702 57.895 0.00 0.00 0.00 4.51
184 202 5.508320 GCACGAAAAGGAAAGAAAATACCCA 60.508 40.000 0.00 0.00 0.00 4.51
546 968 3.322466 CGGACCACCTGCTTCCCT 61.322 66.667 0.00 0.00 0.00 4.20
565 987 4.042435 TCCCTTTTCGGTAAATTCTGACCT 59.958 41.667 3.45 0.00 33.21 3.85
612 1034 2.656422 CGCCAATTTCACGATGAACAAC 59.344 45.455 0.00 0.00 35.89 3.32
628 1052 1.764134 ACAACGGGTGTTTACTGGAGA 59.236 47.619 0.00 0.00 37.01 3.71
632 1056 2.173519 CGGGTGTTTACTGGAGACCTA 58.826 52.381 0.00 0.00 31.50 3.08
636 1060 5.668471 GGGTGTTTACTGGAGACCTATAAC 58.332 45.833 0.00 0.00 31.50 1.89
637 1061 5.424573 GGGTGTTTACTGGAGACCTATAACT 59.575 44.000 0.00 0.00 31.50 2.24
638 1062 6.608808 GGGTGTTTACTGGAGACCTATAACTA 59.391 42.308 0.00 0.00 31.50 2.24
639 1063 7.124750 GGGTGTTTACTGGAGACCTATAACTAA 59.875 40.741 0.00 0.00 31.50 2.24
681 1115 4.739716 GGTTAAAGTCGTAGTTTGTGTCGA 59.260 41.667 0.00 0.00 0.00 4.20
682 1116 5.403466 GGTTAAAGTCGTAGTTTGTGTCGAT 59.597 40.000 0.00 0.00 34.93 3.59
683 1117 6.582295 GGTTAAAGTCGTAGTTTGTGTCGATA 59.418 38.462 0.00 0.00 34.93 2.92
684 1118 7.274250 GGTTAAAGTCGTAGTTTGTGTCGATAT 59.726 37.037 0.00 0.00 34.93 1.63
685 1119 9.277565 GTTAAAGTCGTAGTTTGTGTCGATATA 57.722 33.333 0.00 0.00 34.93 0.86
716 1150 0.754217 ATGTGGGATGTGCATGGCTC 60.754 55.000 0.00 0.00 0.00 4.70
725 1159 2.894387 GCATGGCTCTGCGTCCTC 60.894 66.667 0.00 0.00 31.49 3.71
754 1195 0.178924 ACAGGGGCTTGGCTTGAAAT 60.179 50.000 6.33 0.00 0.00 2.17
828 1269 6.263392 TGTTTGTAAGCTACACTTAAATGGCA 59.737 34.615 0.00 0.00 42.50 4.92
861 1302 1.913762 CGGAGGGGAGTGTGGTCTT 60.914 63.158 0.00 0.00 0.00 3.01
999 1472 7.230510 TGCACTTACAAATCTGATACCTGTTTT 59.769 33.333 5.59 0.00 0.00 2.43
1090 1563 1.103987 TGGCGCAACCTGTTTAAGCA 61.104 50.000 10.83 0.00 40.22 3.91
1115 1588 1.142870 CCCTGTTGTTCTGACCAAGGA 59.857 52.381 0.00 0.00 0.00 3.36
1179 1652 1.677552 GCGAAAGGGAAGGACCTCA 59.322 57.895 0.00 0.00 40.87 3.86
1318 1791 6.553852 TCCCTCCGTAAAGAAATATAAGAGCT 59.446 38.462 0.00 0.00 0.00 4.09
1337 1810 8.710835 AAGAGCTTTTAGATCACTACTTTAGC 57.289 34.615 0.00 0.00 31.99 3.09
1391 1865 7.048512 CAGGGGGAGTACTAGTTATTTTTCTG 58.951 42.308 0.00 0.00 0.00 3.02
1393 1867 7.239143 AGGGGGAGTACTAGTTATTTTTCTGTT 59.761 37.037 0.00 0.00 0.00 3.16
1528 2003 7.707624 TGCATTAATCCAAGTCATTTCTCTT 57.292 32.000 0.00 0.00 0.00 2.85
1934 2414 4.332543 TGACGAATTCCATCAAGTGTATGC 59.667 41.667 0.00 0.00 0.00 3.14
2114 2601 5.632244 TCAATTTGACATCTGATGTGGTG 57.368 39.130 26.71 15.75 45.03 4.17
2174 2661 2.003301 GACCTCTTTCGATTCACCTGC 58.997 52.381 0.00 0.00 0.00 4.85
2178 2665 1.148310 CTTTCGATTCACCTGCACGT 58.852 50.000 0.00 0.00 0.00 4.49
2388 2876 4.751767 TGGTTTGAATTTCAGTTGCCTT 57.248 36.364 0.00 0.00 0.00 4.35
2621 3109 4.709397 TCAAGTCAACAATGAAAACCCTGT 59.291 37.500 0.00 0.00 37.30 4.00
2760 3248 7.323049 TCTCTTTCCTTCTCATAGTTCTACG 57.677 40.000 0.00 0.00 0.00 3.51
2788 3276 0.036164 TTGCTCCACGTGGCATACTT 59.964 50.000 30.25 0.00 38.30 2.24
2830 3318 7.306457 GCTTGAATTTTCTCTTTTCAGTTGAGC 60.306 37.037 0.00 0.00 31.54 4.26
3130 3618 3.203716 GTTGATACCCAATCGACCCTTC 58.796 50.000 0.00 0.00 41.52 3.46
3134 3622 4.905456 TGATACCCAATCGACCCTTCTAAT 59.095 41.667 0.00 0.00 37.42 1.73
3222 3712 5.409826 GTCATCCTGTTTGACTGAAACTAGG 59.590 44.000 0.00 0.00 43.90 3.02
3236 3726 0.690762 ACTAGGGGCGTTGTGACAAT 59.309 50.000 0.00 0.00 0.00 2.71
3249 3739 5.390885 CGTTGTGACAATGACCCATTTAGAG 60.391 44.000 11.98 0.00 31.05 2.43
3305 3795 7.733773 TTAGTGAGGATTGAGGAACATTCTA 57.266 36.000 0.00 0.00 0.00 2.10
3738 4228 6.949352 AACATAATAGCTCCATCACCAAAG 57.051 37.500 0.00 0.00 0.00 2.77
3919 4409 9.671279 TGAATAAAGACAAGCTGATGAAAGATA 57.329 29.630 0.00 0.00 0.00 1.98
4091 4581 7.029563 GCTGTTTTTGAGGTATGGTAGAAATG 58.970 38.462 0.00 0.00 0.00 2.32
4206 4698 1.072159 CGATGATCTGGAAGCCCCC 59.928 63.158 0.00 0.00 0.00 5.40
4520 5012 1.982938 ACCGTCCTGAGGGTACTGC 60.983 63.158 9.67 0.00 46.62 4.40
4853 5446 6.715280 TCACTTGAGGAGCTTCTTTCATATT 58.285 36.000 0.00 0.00 0.00 1.28
4921 5514 1.668419 GTGTGCACCAAGTTCAGACT 58.332 50.000 15.69 0.00 37.87 3.24
5467 6065 6.273825 ACTATTTGGAGTATCTGCTAACGTG 58.726 40.000 0.00 0.00 33.73 4.49
5752 6352 3.804036 CTCCATTAACTACCATTGCCGA 58.196 45.455 0.00 0.00 0.00 5.54
5861 6461 0.954452 CAGCACCAAAACCAGAGACC 59.046 55.000 0.00 0.00 0.00 3.85
5900 6500 2.615869 CCAGCTAGCACTTCACTCTTC 58.384 52.381 18.83 0.00 0.00 2.87
5913 6513 1.214589 CTCTTCGGTACCGTGGGTG 59.785 63.158 32.16 19.00 36.19 4.61
5941 6541 3.623453 GCTGAATCCAAGTCTAAAGCCCT 60.623 47.826 0.00 0.00 0.00 5.19
5970 6570 1.760613 CCAGCAAGGCATCATCCAATT 59.239 47.619 0.00 0.00 0.00 2.32
6130 6730 6.392625 TTCTACACCATCTACTACATCTGC 57.607 41.667 0.00 0.00 0.00 4.26
6286 6886 2.350522 CACGATCTTTGGTAGCAAGCT 58.649 47.619 7.51 0.00 0.00 3.74
6417 7020 1.000163 GCACTGTCTCTTTCGGAGTGA 60.000 52.381 0.00 0.00 42.40 3.41
6597 7203 0.905357 AGGGGTTTCGTCATCTGGAG 59.095 55.000 0.00 0.00 0.00 3.86
6959 7565 0.106318 AATCAGCATCTTCAGGGGGC 60.106 55.000 0.00 0.00 0.00 5.80
7064 7670 4.826733 AGCATGAATTTGTCTACACCACAA 59.173 37.500 0.00 0.00 31.76 3.33
7495 8101 2.159517 GGTAGCCTCGCTGTTCAATTTG 60.160 50.000 0.00 0.00 40.10 2.32
7538 8144 0.965363 ATGGTGCAATGTCCGGGAAC 60.965 55.000 0.00 0.00 0.00 3.62
7640 8249 6.894654 CACAGGACATATATCTATCTGGAGGT 59.105 42.308 0.00 0.00 0.00 3.85
7652 8261 0.798776 CTGGAGGTTGTCATGCGAAC 59.201 55.000 0.00 0.00 0.00 3.95
7658 8267 1.069227 GGTTGTCATGCGAACCTCAAC 60.069 52.381 15.09 0.00 38.91 3.18
7720 8329 1.978455 TTGCTTGGTGGGTCAGTCGT 61.978 55.000 0.00 0.00 0.00 4.34
7725 8334 0.470456 TGGTGGGTCAGTCGTAAGGT 60.470 55.000 0.00 0.00 38.47 3.50
7844 8457 4.451096 TGTCTGAGTTTCTTATTTGCGTCC 59.549 41.667 0.00 0.00 0.00 4.79
7846 8459 3.655486 TGAGTTTCTTATTTGCGTCCGA 58.345 40.909 0.00 0.00 0.00 4.55
7862 8475 3.436015 CGTCCGATCCGATATAGTTGTCT 59.564 47.826 0.00 0.00 0.00 3.41
7892 8509 9.436957 CAGAGAAAGTGTACTGGTGTATTATTT 57.563 33.333 0.00 0.00 0.00 1.40
7932 8555 7.964666 ACTGGCTTAGAACTCTAGTTTAGAT 57.035 36.000 0.00 0.00 38.56 1.98
7972 8595 1.071471 CTGCCGTCTGGTCTGGTTT 59.929 57.895 0.00 0.00 37.67 3.27
7978 8601 3.670625 CCGTCTGGTCTGGTTTATTTCA 58.329 45.455 0.00 0.00 0.00 2.69
7980 8603 5.424757 CCGTCTGGTCTGGTTTATTTCATA 58.575 41.667 0.00 0.00 0.00 2.15
8091 8719 2.143122 TGTTTTGGAAGCACTAGAGCG 58.857 47.619 6.51 0.00 40.15 5.03
8153 8781 3.439293 CAATGTGCCGTGTTTGTTTACA 58.561 40.909 0.00 0.00 0.00 2.41
8155 8783 1.202200 TGTGCCGTGTTTGTTTACAGC 60.202 47.619 0.00 0.00 0.00 4.40
8280 8918 3.496160 CCGTTCTCCAGGAAAAAGGAAGA 60.496 47.826 1.20 0.00 35.51 2.87
8294 8932 2.579873 AGGAAGAAATCGGCATCCATG 58.420 47.619 0.00 0.00 32.47 3.66
8438 9084 1.650528 CTCTTCTTCCCTCCCTGTGT 58.349 55.000 0.00 0.00 0.00 3.72
8439 9085 1.277557 CTCTTCTTCCCTCCCTGTGTG 59.722 57.143 0.00 0.00 0.00 3.82
8478 9124 2.943033 CCTTTTGGACTTTGTCGACAGT 59.057 45.455 19.11 14.26 44.07 3.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 109 1.153229 GGTATCTTCCGTGGGTGGC 60.153 63.158 0.00 0.00 0.00 5.01
112 118 3.181469 TGCTGGATTACGTGGTATCTTCC 60.181 47.826 0.00 0.00 0.00 3.46
113 119 3.802685 GTGCTGGATTACGTGGTATCTTC 59.197 47.826 0.00 0.00 0.00 2.87
114 120 3.431766 GGTGCTGGATTACGTGGTATCTT 60.432 47.826 0.00 0.00 0.00 2.40
115 121 2.102588 GGTGCTGGATTACGTGGTATCT 59.897 50.000 0.00 0.00 0.00 1.98
116 122 2.480845 GGTGCTGGATTACGTGGTATC 58.519 52.381 0.00 0.00 0.00 2.24
117 123 1.140252 GGGTGCTGGATTACGTGGTAT 59.860 52.381 0.00 0.00 0.00 2.73
118 124 0.538118 GGGTGCTGGATTACGTGGTA 59.462 55.000 0.00 0.00 0.00 3.25
119 125 1.298667 GGGTGCTGGATTACGTGGT 59.701 57.895 0.00 0.00 0.00 4.16
120 126 0.744414 CTGGGTGCTGGATTACGTGG 60.744 60.000 0.00 0.00 0.00 4.94
122 128 1.078426 GCTGGGTGCTGGATTACGT 60.078 57.895 0.00 0.00 38.95 3.57
124 130 1.453928 GGGCTGGGTGCTGGATTAC 60.454 63.158 0.00 0.00 42.39 1.89
125 131 1.928046 TGGGCTGGGTGCTGGATTA 60.928 57.895 0.00 0.00 42.39 1.75
126 132 3.267233 TGGGCTGGGTGCTGGATT 61.267 61.111 0.00 0.00 42.39 3.01
127 133 4.052518 GTGGGCTGGGTGCTGGAT 62.053 66.667 0.00 0.00 42.39 3.41
387 809 2.273776 GGAAGGAGGGGAAGCTGC 59.726 66.667 0.00 0.00 0.00 5.25
417 839 1.531149 CGAGCAAACACGAATCTTGGT 59.469 47.619 0.00 0.00 33.70 3.67
420 842 0.163788 CGCGAGCAAACACGAATCTT 59.836 50.000 0.00 0.00 30.81 2.40
448 870 2.515523 CGCAGCCAATCTCAGGGG 60.516 66.667 0.00 0.00 0.00 4.79
546 968 4.449743 CGTCAGGTCAGAATTTACCGAAAA 59.550 41.667 0.00 0.00 40.88 2.29
565 987 1.016627 GCCAGCAATAGCATTCGTCA 58.983 50.000 0.00 0.00 45.49 4.35
612 1034 0.974383 AGGTCTCCAGTAAACACCCG 59.026 55.000 0.00 0.00 0.00 5.28
628 1052 8.919777 AGCAAGTTGAAACTTTAGTTATAGGT 57.080 30.769 7.16 0.00 46.52 3.08
636 1060 8.871686 AACCATAAAGCAAGTTGAAACTTTAG 57.128 30.769 7.16 3.79 46.52 1.85
638 1062 9.660180 TTTAACCATAAAGCAAGTTGAAACTTT 57.340 25.926 7.16 9.31 46.52 2.66
639 1063 9.313118 CTTTAACCATAAAGCAAGTTGAAACTT 57.687 29.630 7.16 2.56 42.66 2.66
684 1118 9.391227 TGCACATCCCACATCCATATATATATA 57.609 33.333 4.90 4.92 0.00 0.86
685 1119 8.278988 TGCACATCCCACATCCATATATATAT 57.721 34.615 0.00 0.00 0.00 0.86
686 1120 7.688918 TGCACATCCCACATCCATATATATA 57.311 36.000 0.00 0.00 0.00 0.86
703 1137 2.044832 GACGCAGAGCCATGCACATC 62.045 60.000 10.95 2.18 46.87 3.06
716 1150 1.261619 GTGTTGTTCTTGAGGACGCAG 59.738 52.381 0.00 0.00 0.00 5.18
725 1159 1.067516 CAAGCCCCTGTGTTGTTCTTG 59.932 52.381 0.00 0.00 0.00 3.02
861 1302 6.078664 ACCCAACCAAACATATAGTTCCAAA 58.921 36.000 0.00 0.00 40.26 3.28
999 1472 2.107031 AGCATCTTGGCCTGCATACATA 59.893 45.455 16.24 0.00 40.88 2.29
1090 1563 1.073923 GGTCAGAACAACAGGGGATGT 59.926 52.381 0.00 0.00 46.97 3.06
1115 1588 5.047188 CCCTGCGTAAAAATTTCAAACAGT 58.953 37.500 0.00 0.00 0.00 3.55
1179 1652 1.344065 TTGTCACCGGATGTACCAGT 58.656 50.000 9.46 0.00 38.90 4.00
1536 2013 8.267894 TCCAAAATAATGGAACAAGAAACCAAA 58.732 29.630 0.00 0.00 46.36 3.28
1537 2014 7.796054 TCCAAAATAATGGAACAAGAAACCAA 58.204 30.769 0.00 0.00 46.36 3.67
1538 2015 7.366847 TCCAAAATAATGGAACAAGAAACCA 57.633 32.000 0.00 0.00 46.36 3.67
2114 2601 9.387123 GAACTTTGATCAATCTAAACAACTGAC 57.613 33.333 9.40 0.00 0.00 3.51
2174 2661 4.851014 CACATTTGTGCACCTAATAACGTG 59.149 41.667 15.69 13.41 39.39 4.49
2604 3092 5.301805 AGGAAGTACAGGGTTTTCATTGTTG 59.698 40.000 0.00 0.00 0.00 3.33
2621 3109 5.513094 GCCATATAGCCATTCACAGGAAGTA 60.513 44.000 0.00 0.00 36.25 2.24
2712 3200 4.686972 TGATGTGCAGCAGATAGAAGTAC 58.313 43.478 4.72 0.00 0.00 2.73
2760 3248 4.102649 GCCACGTGGAGCAAAATATAAAC 58.897 43.478 38.30 11.03 37.39 2.01
2788 3276 3.826524 TCAAGCACCATACAAGGACAAA 58.173 40.909 0.00 0.00 0.00 2.83
2830 3318 4.797868 TCACAGTTTTGCAGTTGAAAATCG 59.202 37.500 0.00 0.00 0.00 3.34
3019 3507 7.076842 ACATGAACAAGAATATACAGTGCAC 57.923 36.000 9.40 9.40 0.00 4.57
3212 3702 1.156736 CACAACGCCCCTAGTTTCAG 58.843 55.000 0.00 0.00 0.00 3.02
3222 3712 1.579429 GGTCATTGTCACAACGCCC 59.421 57.895 0.00 0.00 0.00 6.13
3236 3726 6.928348 TGAGACTAAACTCTAAATGGGTCA 57.072 37.500 0.00 0.00 37.73 4.02
3305 3795 3.446161 CCAGACCATGCAAAATCTGATGT 59.554 43.478 20.28 0.00 40.92 3.06
3738 4228 0.249447 GTTTGCCAGACTGTTTGCCC 60.249 55.000 0.93 0.00 0.00 5.36
3919 4409 8.400947 CGTATTGGAATGAACTTTTGATGATCT 58.599 33.333 0.00 0.00 0.00 2.75
4165 4656 6.764085 TCGTCAAACTCAGTTAAATCCTGAAA 59.236 34.615 0.00 0.00 38.42 2.69
4206 4698 7.384660 TCAAATTTTGAATTCTTTGATGGGACG 59.615 33.333 9.36 0.00 36.59 4.79
4921 5514 9.562408 TCACTACAATCCAAAAGTATACAACAA 57.438 29.630 5.50 0.00 0.00 2.83
5467 6065 3.877508 ACTGGAAACACAAGTAGCAGAAC 59.122 43.478 0.00 0.00 35.60 3.01
5861 6461 1.808945 GGCTTTGTCTCTGTGGATGTG 59.191 52.381 0.00 0.00 0.00 3.21
5900 6500 2.182537 GTAGCACCCACGGTACCG 59.817 66.667 32.22 32.22 46.03 4.02
5913 6513 3.258971 AGACTTGGATTCAGCTGTAGC 57.741 47.619 14.67 6.86 42.49 3.58
6130 6730 1.284982 CGTTGAAGCGGACTGGACAG 61.285 60.000 0.00 0.00 0.00 3.51
6597 7203 3.274288 CTCCAAAAGATACAGTCCCAGC 58.726 50.000 0.00 0.00 0.00 4.85
6959 7565 1.052287 GTGCTCCAAATGAAAACGCG 58.948 50.000 3.53 3.53 0.00 6.01
6962 7568 4.293415 CTGACTGTGCTCCAAATGAAAAC 58.707 43.478 0.00 0.00 0.00 2.43
7064 7670 2.307496 TTGTCATCCCAAATGCAGGT 57.693 45.000 0.00 0.00 0.00 4.00
7310 7916 1.866853 CGCCAAACTGGAAAGCTCCC 61.867 60.000 0.00 0.00 40.96 4.30
7495 8101 4.620982 GAAAATAGCCACCATGTAATGCC 58.379 43.478 0.00 0.00 44.97 4.40
7538 8144 1.656652 GAGTTCCCATCCACATGACG 58.343 55.000 0.00 0.00 30.57 4.35
7640 8249 2.143122 GAGTTGAGGTTCGCATGACAA 58.857 47.619 0.00 0.00 0.00 3.18
7652 8261 2.918712 ACACTGACCTTGAGTTGAGG 57.081 50.000 0.00 0.00 40.24 3.86
7658 8267 3.129638 GGCTACTCTACACTGACCTTGAG 59.870 52.174 0.00 0.00 0.00 3.02
7720 8329 0.404040 CCACCAGGGCTTCAACCTTA 59.596 55.000 0.00 0.00 35.78 2.69
7844 8457 3.846896 GCGAAGACAACTATATCGGATCG 59.153 47.826 0.00 0.00 34.29 3.69
7846 8459 4.519350 TCTGCGAAGACAACTATATCGGAT 59.481 41.667 0.00 0.00 33.52 4.18
7862 8475 2.364324 ACCAGTACACTTTCTCTGCGAA 59.636 45.455 0.00 0.00 0.00 4.70
7892 8509 2.625790 GCCAGTTGGGTGTGAAACAATA 59.374 45.455 0.00 0.00 42.39 1.90
7893 8510 1.412343 GCCAGTTGGGTGTGAAACAAT 59.588 47.619 0.00 0.00 42.39 2.71
7896 8513 1.111277 AAGCCAGTTGGGTGTGAAAC 58.889 50.000 3.24 0.00 46.73 2.78
7932 8555 6.462347 GCAGGGAAAAGGAGACAAAATTACAA 60.462 38.462 0.00 0.00 0.00 2.41
7972 8595 8.596271 TCGGACGCAAATAAGAATATGAAATA 57.404 30.769 0.00 0.00 0.00 1.40
7980 8603 8.999431 ACAAATATATCGGACGCAAATAAGAAT 58.001 29.630 0.00 0.00 0.00 2.40
8091 8719 1.237285 AACATCCAGGAAGCACGCAC 61.237 55.000 0.00 0.00 0.00 5.34
8294 8932 2.731217 ACGTGACTGCAAATTCAAAGC 58.269 42.857 0.00 0.00 0.00 3.51
8296 8934 3.313803 TGCTACGTGACTGCAAATTCAAA 59.686 39.130 0.00 0.00 33.48 2.69
8438 9084 3.129502 CGTCGCCGTCTCTACCCA 61.130 66.667 0.00 0.00 0.00 4.51
8439 9085 4.549516 GCGTCGCCGTCTCTACCC 62.550 72.222 5.75 0.00 36.15 3.69


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

AutoCloner maintained by Alex Coulton.