Multiple sequence alignment - TraesCS5A01G418700

Loading Multiple Alignment...

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 TraesCS5A01G418700 chr5A 100.000 2435 0 0 1 2435 606530686 606533120 0.000000e+00 4497.0
1 TraesCS5A01G418700 chr5A 86.047 1075 101 26 646 1707 606541859 606542897 0.000000e+00 1109.0
2 TraesCS5A01G418700 chr5A 85.688 1083 100 26 671 1743 606538029 606539066 0.000000e+00 1090.0
3 TraesCS5A01G418700 chr5A 89.209 139 9 4 1600 1737 606624473 606624606 4.160000e-38 169.0
4 TraesCS5A01G418700 chr5A 87.857 140 17 0 574 713 606469036 606469175 5.390000e-37 165.0
5 TraesCS5A01G418700 chr5A 85.586 111 10 5 639 743 606684220 606684330 7.120000e-21 111.0
6 TraesCS5A01G418700 chr5D 85.512 1974 180 41 494 2434 485301839 485303739 0.000000e+00 1964.0
7 TraesCS5A01G418700 chr5D 81.347 1796 202 74 644 2412 485350504 485352193 0.000000e+00 1338.0
8 TraesCS5A01G418700 chr5D 85.214 1028 103 23 671 1695 485354356 485355337 0.000000e+00 1011.0
9 TraesCS5A01G418700 chr5D 91.221 729 53 3 830 1558 485274623 485275340 0.000000e+00 981.0
10 TraesCS5A01G418700 chr5D 82.578 1125 95 46 635 1743 485375130 485376169 0.000000e+00 898.0
11 TraesCS5A01G418700 chr5D 83.480 793 95 22 777 1561 485918034 485918798 0.000000e+00 706.0
12 TraesCS5A01G418700 chr5D 88.535 471 45 6 7 472 485272793 485273259 1.630000e-156 562.0
13 TraesCS5A01G418700 chr5D 89.836 305 24 5 535 834 485273473 485273775 3.800000e-103 385.0
14 TraesCS5A01G418700 chr5D 84.109 258 28 10 1759 2008 485357612 485357864 1.130000e-58 237.0
15 TraesCS5A01G418700 chr5D 93.478 92 4 2 1624 1714 485611504 485611594 4.220000e-28 135.0
16 TraesCS5A01G418700 chr5D 93.243 74 4 1 671 743 485917953 485918026 9.210000e-20 108.0
17 TraesCS5A01G418700 chr5D 84.821 112 9 6 639 743 485765874 485765984 3.310000e-19 106.0
18 TraesCS5A01G418700 chr5D 91.892 74 5 1 671 743 485737995 485738068 4.280000e-18 102.0
19 TraesCS5A01G418700 chr5D 97.297 37 1 0 483 519 485273438 485273474 2.020000e-06 63.9
20 TraesCS5A01G418700 chr5B 87.602 1347 104 28 396 1728 596908350 596909647 0.000000e+00 1504.0
21 TraesCS5A01G418700 chr5B 84.274 1081 120 29 671 1745 596918231 596919267 0.000000e+00 1009.0
22 TraesCS5A01G418700 chr5B 84.442 977 87 32 671 1636 596933259 596934181 0.000000e+00 902.0
23 TraesCS5A01G418700 chr5B 83.617 824 90 26 777 1580 596972363 596973161 0.000000e+00 732.0
24 TraesCS5A01G418700 chr5B 85.935 647 64 16 1163 1799 596914283 596914912 0.000000e+00 665.0
25 TraesCS5A01G418700 chr5B 84.375 640 64 29 1741 2352 596909820 596910451 1.610000e-166 595.0
26 TraesCS5A01G418700 chr5B 94.595 74 3 1 671 743 596972282 596972355 1.980000e-21 113.0


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 TraesCS5A01G418700 chr5A 606530686 606533120 2434 False 4497.000 4497 100.000000 1 2435 1 chr5A.!!$F2 2434
1 TraesCS5A01G418700 chr5A 606538029 606542897 4868 False 1099.500 1109 85.867500 646 1743 2 chr5A.!!$F5 1097
2 TraesCS5A01G418700 chr5D 485301839 485303739 1900 False 1964.000 1964 85.512000 494 2434 1 chr5D.!!$F1 1940
3 TraesCS5A01G418700 chr5D 485375130 485376169 1039 False 898.000 898 82.578000 635 1743 1 chr5D.!!$F2 1108
4 TraesCS5A01G418700 chr5D 485350504 485357864 7360 False 862.000 1338 83.556667 644 2412 3 chr5D.!!$F7 1768
5 TraesCS5A01G418700 chr5D 485272793 485275340 2547 False 497.975 981 91.722250 7 1558 4 chr5D.!!$F6 1551
6 TraesCS5A01G418700 chr5D 485917953 485918798 845 False 407.000 706 88.361500 671 1561 2 chr5D.!!$F8 890
7 TraesCS5A01G418700 chr5B 596908350 596919267 10917 False 943.250 1504 85.546500 396 2352 4 chr5B.!!$F2 1956
8 TraesCS5A01G418700 chr5B 596933259 596934181 922 False 902.000 902 84.442000 671 1636 1 chr5B.!!$F1 965
9 TraesCS5A01G418700 chr5B 596972282 596973161 879 False 422.500 732 89.106000 671 1580 2 chr5B.!!$F3 909

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
721 4055 0.105246 CAGCTCCCCTCCTCACCTAT 60.105 60.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2094 18264 1.081509 GCATTTGCGCTTTCGGTGA 60.082 52.632 9.73 0.0 35.95 4.02 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
135 136 9.865321 ATTGCTGGTATTGATGCATATATTTTC 57.135 29.630 0.00 0.00 35.27 2.29
137 138 7.450944 TGCTGGTATTGATGCATATATTTTCCA 59.549 33.333 0.00 2.48 0.00 3.53
169 171 7.394359 TGGAATTTTCGAATTTCCATCTTCTCT 59.606 33.333 26.90 0.00 42.72 3.10
236 239 6.369629 TCAGGAACTTAAGATTTTCCAACCA 58.630 36.000 19.92 3.96 41.24 3.67
252 255 8.649973 TTTCCAACCAATAAATTGTGTTGTAC 57.350 30.769 21.90 0.00 41.72 2.90
253 256 7.589958 TCCAACCAATAAATTGTGTTGTACT 57.410 32.000 21.90 1.19 41.72 2.73
255 258 9.303116 TCCAACCAATAAATTGTGTTGTACTAT 57.697 29.630 21.90 0.00 41.72 2.12
256 259 9.921637 CCAACCAATAAATTGTGTTGTACTATT 57.078 29.630 21.90 0.00 41.72 1.73
274 277 9.865321 TGTACTATTGACCTTGTCTGTATAAAC 57.135 33.333 0.00 0.00 33.15 2.01
278 281 9.653287 CTATTGACCTTGTCTGTATAAACTTCA 57.347 33.333 0.00 0.00 33.15 3.02
279 282 7.962964 TTGACCTTGTCTGTATAAACTTCAG 57.037 36.000 0.00 0.00 33.15 3.02
281 284 5.865085 ACCTTGTCTGTATAAACTTCAGCA 58.135 37.500 0.00 0.00 0.00 4.41
283 286 5.163953 CCTTGTCTGTATAAACTTCAGCACG 60.164 44.000 0.00 0.00 0.00 5.34
284 287 4.242475 TGTCTGTATAAACTTCAGCACGG 58.758 43.478 0.00 0.00 0.00 4.94
314 320 5.639506 ACCTTGTGTGATCTATTCAAAGTCG 59.360 40.000 0.00 0.00 35.70 4.18
338 344 1.880027 CAAAGGCCTTGTGTGTAGGTC 59.120 52.381 21.33 0.00 37.67 3.85
350 356 2.043248 TAGGTCGCCTCTCCCACC 60.043 66.667 1.46 0.00 34.61 4.61
363 369 4.051922 CTCTCCCACCGAAAGAATAATCG 58.948 47.826 0.00 0.00 38.74 3.34
364 370 3.702548 TCTCCCACCGAAAGAATAATCGA 59.297 43.478 0.00 0.00 41.43 3.59
365 371 4.344102 TCTCCCACCGAAAGAATAATCGAT 59.656 41.667 0.00 0.00 41.43 3.59
371 377 7.307219 CCCACCGAAAGAATAATCGATCTTTAC 60.307 40.741 10.83 5.59 43.86 2.01
389 395 6.683715 TCTTTACGAGATACACATGTGTCAA 58.316 36.000 33.72 18.93 43.74 3.18
394 400 6.863275 ACGAGATACACATGTGTCAAATCTA 58.137 36.000 33.72 15.88 43.74 1.98
408 414 7.180229 TGTGTCAAATCTAGGGTTTGATCTCTA 59.820 37.037 19.91 8.71 44.56 2.43
412 418 7.619698 TCAAATCTAGGGTTTGATCTCTAGTGA 59.380 37.037 15.67 0.00 39.81 3.41
427 433 1.227943 GTGAGCTGAGGGTGCAACA 60.228 57.895 3.06 0.00 39.98 3.33
430 436 1.845809 GAGCTGAGGGTGCAACAACG 61.846 60.000 3.06 0.00 39.98 4.10
443 449 4.002982 TGCAACAACGCTTCTAATCATCT 58.997 39.130 0.00 0.00 0.00 2.90
455 461 9.639601 CGCTTCTAATCATCTAACCACATATTA 57.360 33.333 0.00 0.00 0.00 0.98
532 715 1.639298 GCGAATGAGACAGTGGTGCC 61.639 60.000 0.00 0.00 0.00 5.01
721 4055 0.105246 CAGCTCCCCTCCTCACCTAT 60.105 60.000 0.00 0.00 0.00 2.57
743 4077 9.764363 CCTATACACAGAAAATTGTAGCTATCA 57.236 33.333 0.00 0.00 31.83 2.15
749 4083 7.225538 CACAGAAAATTGTAGCTATCACCTAGG 59.774 40.741 7.41 7.41 0.00 3.02
784 4120 0.660488 CCACACAACACAAAGCGCTA 59.340 50.000 12.05 0.00 0.00 4.26
806 4142 1.535462 CCTTTTTGGATTGACGACGCT 59.465 47.619 0.00 0.00 38.35 5.07
817 4161 2.128128 CGACGCTCGCACAAACAC 60.128 61.111 0.00 0.00 31.14 3.32
858 5054 6.134535 ACCAACCTAATGTCCTAATCACAA 57.865 37.500 0.00 0.00 0.00 3.33
863 5059 6.235664 ACCTAATGTCCTAATCACAACGTTT 58.764 36.000 0.00 0.00 0.00 3.60
865 5061 7.332678 ACCTAATGTCCTAATCACAACGTTTAC 59.667 37.037 0.00 0.00 0.00 2.01
867 5063 4.317488 TGTCCTAATCACAACGTTTACCC 58.683 43.478 0.00 0.00 0.00 3.69
871 5067 0.321830 ATCACAACGTTTACCCGGGG 60.322 55.000 27.92 12.73 0.00 5.73
872 5068 1.071128 CACAACGTTTACCCGGGGA 59.929 57.895 27.92 16.00 0.00 4.81
951 5148 3.208383 CAACCAGCACACCGCACA 61.208 61.111 0.00 0.00 46.13 4.57
952 5149 3.209097 AACCAGCACACCGCACAC 61.209 61.111 0.00 0.00 46.13 3.82
1215 5473 2.363276 ATGCCGTCCGTCACCCTA 60.363 61.111 0.00 0.00 0.00 3.53
1221 5479 2.677524 TCCGTCACCCTACCCACG 60.678 66.667 0.00 0.00 0.00 4.94
1348 5606 1.227527 CCGATGCCCGCTATTGTCA 60.228 57.895 0.00 0.00 36.84 3.58
1350 5608 1.229428 CGATGCCCGCTATTGTCATT 58.771 50.000 0.00 0.00 0.00 2.57
1388 10845 3.110178 CTTGCCGTTCGTCCCGAC 61.110 66.667 0.00 0.00 34.89 4.79
1447 15322 4.710695 CGTAGGCACGTCCACGCA 62.711 66.667 0.00 0.00 43.31 5.24
1448 15325 2.356553 GTAGGCACGTCCACGCAA 60.357 61.111 0.00 0.00 44.43 4.85
1469 15346 4.314440 TGCTGTCGCCCTGTCCAC 62.314 66.667 0.00 0.00 34.43 4.02
1470 15347 4.314440 GCTGTCGCCCTGTCCACA 62.314 66.667 0.00 0.00 0.00 4.17
1471 15348 2.665000 CTGTCGCCCTGTCCACAT 59.335 61.111 0.00 0.00 0.00 3.21
1472 15349 1.448540 CTGTCGCCCTGTCCACATC 60.449 63.158 0.00 0.00 0.00 3.06
1473 15350 1.892819 CTGTCGCCCTGTCCACATCT 61.893 60.000 0.00 0.00 0.00 2.90
1474 15351 0.613572 TGTCGCCCTGTCCACATCTA 60.614 55.000 0.00 0.00 0.00 1.98
1483 15371 3.223435 CTGTCCACATCTACGATAGGGT 58.777 50.000 0.00 0.00 43.77 4.34
1540 15428 3.491639 TGGACACGACGTACATTTTCTTG 59.508 43.478 0.00 0.00 31.56 3.02
1578 15466 7.170828 GGTGTTTTATATGCGATGTATCACAGA 59.829 37.037 0.00 0.00 0.00 3.41
1579 15467 8.712363 GTGTTTTATATGCGATGTATCACAGAT 58.288 33.333 0.00 0.00 0.00 2.90
1583 15471 9.487790 TTTATATGCGATGTATCACAGATTTCA 57.512 29.630 0.00 0.00 0.00 2.69
1584 15472 5.663795 ATGCGATGTATCACAGATTTCAC 57.336 39.130 0.00 0.00 0.00 3.18
1585 15473 4.502962 TGCGATGTATCACAGATTTCACA 58.497 39.130 0.00 0.00 0.00 3.58
1586 15474 4.567959 TGCGATGTATCACAGATTTCACAG 59.432 41.667 0.00 0.00 0.00 3.66
1598 15486 9.154847 TCACAGATTTCACAGTATCAGTAATTG 57.845 33.333 0.00 0.00 0.00 2.32
1607 15497 7.023575 CACAGTATCAGTAATTGTTGCCTTTC 58.976 38.462 0.00 0.00 0.00 2.62
1611 15501 8.860088 AGTATCAGTAATTGTTGCCTTTCTTTT 58.140 29.630 0.00 0.00 0.00 2.27
1614 15504 7.136119 TCAGTAATTGTTGCCTTTCTTTTACG 58.864 34.615 0.00 0.00 0.00 3.18
1615 15505 6.915843 CAGTAATTGTTGCCTTTCTTTTACGT 59.084 34.615 0.00 0.00 0.00 3.57
1616 15506 7.112984 CAGTAATTGTTGCCTTTCTTTTACGTC 59.887 37.037 0.00 0.00 0.00 4.34
1618 15508 2.619646 TGTTGCCTTTCTTTTACGTCCC 59.380 45.455 0.00 0.00 0.00 4.46
1619 15509 2.619646 GTTGCCTTTCTTTTACGTCCCA 59.380 45.455 0.00 0.00 0.00 4.37
1620 15510 2.500229 TGCCTTTCTTTTACGTCCCAG 58.500 47.619 0.00 0.00 0.00 4.45
1653 15551 7.717436 TGTATTGGTAGTGTTTGAATGTTGAGA 59.283 33.333 0.00 0.00 0.00 3.27
1654 15552 7.581213 ATTGGTAGTGTTTGAATGTTGAGAA 57.419 32.000 0.00 0.00 0.00 2.87
1765 17913 7.984422 AATGAGTGATTGTACAATTGTCTCA 57.016 32.000 30.15 30.15 36.97 3.27
1773 17921 5.139435 TGTACAATTGTCTCAGTCCTCTG 57.861 43.478 15.85 0.00 42.54 3.35
1781 17929 2.663566 TCAGTCCTCTGAGGTGCTG 58.336 57.895 28.29 28.29 44.58 4.41
1782 17930 1.079266 CAGTCCTCTGAGGTGCTGC 60.079 63.158 25.52 13.65 43.76 5.25
1802 17950 6.484643 TGCTGCAAAATATAAGAGAGGTCATC 59.515 38.462 0.00 0.00 0.00 2.92
1871 18021 6.808212 CCTGCACCAAAAGTAATAGTGAATTG 59.192 38.462 0.00 0.00 0.00 2.32
1873 18023 5.576774 GCACCAAAAGTAATAGTGAATTGCC 59.423 40.000 0.00 0.00 31.01 4.52
1875 18025 5.777732 ACCAAAAGTAATAGTGAATTGCCCA 59.222 36.000 0.00 0.00 31.01 5.36
1882 18032 9.791801 AAGTAATAGTGAATTGCCCAAAAATTT 57.208 25.926 0.00 0.00 31.01 1.82
1895 18045 6.976925 TGCCCAAAAATTTAAAAGTGCAATTG 59.023 30.769 0.00 0.00 0.00 2.32
1959 18118 6.084326 AGTAGTGCAATTACAACAAAAGGG 57.916 37.500 11.07 0.00 30.47 3.95
1961 18120 5.806654 AGTGCAATTACAACAAAAGGGAT 57.193 34.783 0.00 0.00 0.00 3.85
1970 18129 5.371115 ACAACAAAAGGGATGATAACACG 57.629 39.130 0.00 0.00 0.00 4.49
2009 18168 8.871629 TGCATAAGGGAGAGTAATTACAAAAA 57.128 30.769 17.65 0.00 0.00 1.94
2054 18217 7.790861 AAGTACAATTATACAAAAGTTGCGC 57.209 32.000 0.00 0.00 0.00 6.09
2055 18218 6.319399 AGTACAATTATACAAAAGTTGCGCC 58.681 36.000 4.18 0.00 0.00 6.53
2066 18236 7.484035 ACAAAAGTTGCGCCAAAATATAAAA 57.516 28.000 4.18 0.00 0.00 1.52
2069 18239 8.838961 CAAAAGTTGCGCCAAAATATAAAAATG 58.161 29.630 4.18 0.00 0.00 2.32
2112 18282 0.662970 TTCACCGAAAGCGCAAATGC 60.663 50.000 11.47 0.00 35.83 3.56
2117 18287 0.933973 CGAAAGCGCAAATGCACACA 60.934 50.000 11.47 0.00 42.21 3.72
2151 18321 7.692908 TTGCTTACAAAAACTAGATTTGCAC 57.307 32.000 18.97 10.65 40.58 4.57
2153 18323 6.040391 TGCTTACAAAAACTAGATTTGCACCT 59.960 34.615 18.97 8.00 40.58 4.00
2154 18324 6.923508 GCTTACAAAAACTAGATTTGCACCTT 59.076 34.615 18.97 7.75 40.58 3.50
2162 18332 7.817418 AACTAGATTTGCACCTTAAAACTGA 57.183 32.000 0.00 0.00 0.00 3.41
2164 18334 7.875971 ACTAGATTTGCACCTTAAAACTGAAG 58.124 34.615 0.00 0.00 0.00 3.02
2168 18338 5.452078 TTGCACCTTAAAACTGAAGATGG 57.548 39.130 0.00 0.00 0.00 3.51
2186 18356 8.058235 TGAAGATGGACAATTTATTCCCATACA 58.942 33.333 0.00 0.00 37.71 2.29
2194 18364 8.603242 ACAATTTATTCCCATACACGATAGAC 57.397 34.615 0.00 0.00 41.38 2.59
2210 18380 7.010367 ACACGATAGACGAAAACAACTACAAAA 59.990 33.333 0.00 0.00 45.77 2.44
2213 18383 8.433126 CGATAGACGAAAACAACTACAAAAGAT 58.567 33.333 0.00 0.00 45.77 2.40
2216 18386 8.882415 AGACGAAAACAACTACAAAAGATAGA 57.118 30.769 0.00 0.00 0.00 1.98
2250 18420 7.602753 AGGTGCCAAAGATAAATTAGTGAAAC 58.397 34.615 0.00 0.00 0.00 2.78
2252 18422 6.811665 GTGCCAAAGATAAATTAGTGAAACCC 59.188 38.462 0.00 0.00 37.80 4.11
2315 18485 7.947282 TCTTTTGTAGGGGAAACAAACATTAG 58.053 34.615 1.13 0.00 44.26 1.73
2337 18507 4.776308 AGTAGTACTTCCTCGGTTCCAAAT 59.224 41.667 0.00 0.00 0.00 2.32
2346 18516 4.941263 TCCTCGGTTCCAAATTACTTGATG 59.059 41.667 0.00 0.00 37.17 3.07
2353 18523 6.072673 GGTTCCAAATTACTTGATGTTCTCGT 60.073 38.462 0.00 0.00 37.17 4.18
2357 18527 9.058174 TCCAAATTACTTGATGTTCTCGTTTTA 57.942 29.630 0.00 0.00 37.17 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.708563 TGTTTGTTTTGTAGGCTGAGC 57.291 42.857 0.00 0.00 0.00 4.26
2 3 3.131400 GGGTTGTTTGTTTTGTAGGCTGA 59.869 43.478 0.00 0.00 0.00 4.26
3 4 3.118956 TGGGTTGTTTGTTTTGTAGGCTG 60.119 43.478 0.00 0.00 0.00 4.85
4 5 3.100671 TGGGTTGTTTGTTTTGTAGGCT 58.899 40.909 0.00 0.00 0.00 4.58
119 120 7.490840 CACAAGGTGGAAAATATATGCATCAA 58.509 34.615 0.19 0.00 0.00 2.57
137 138 5.069781 TGGAAATTCGAAAATTCCACAAGGT 59.930 36.000 30.15 0.00 33.93 3.50
244 247 5.989777 ACAGACAAGGTCAATAGTACAACAC 59.010 40.000 0.00 0.00 34.60 3.32
252 255 9.653287 TGAAGTTTATACAGACAAGGTCAATAG 57.347 33.333 0.00 0.00 34.60 1.73
253 256 9.653287 CTGAAGTTTATACAGACAAGGTCAATA 57.347 33.333 0.00 0.00 34.60 1.90
255 258 6.426937 GCTGAAGTTTATACAGACAAGGTCAA 59.573 38.462 0.00 0.00 34.60 3.18
256 259 5.932303 GCTGAAGTTTATACAGACAAGGTCA 59.068 40.000 0.00 0.00 34.60 4.02
283 286 7.047891 TGAATAGATCACACAAGGTCAATACC 58.952 38.462 0.00 0.00 38.52 2.73
284 287 8.492673 TTGAATAGATCACACAAGGTCAATAC 57.507 34.615 0.00 0.00 37.92 1.89
338 344 2.125512 CTTTCGGTGGGAGAGGCG 60.126 66.667 0.00 0.00 0.00 5.52
350 356 8.490291 TCTCGTAAAGATCGATTATTCTTTCG 57.510 34.615 13.53 15.23 40.42 3.46
363 369 6.972901 TGACACATGTGTATCTCGTAAAGATC 59.027 38.462 30.63 13.56 43.90 2.75
364 370 6.863275 TGACACATGTGTATCTCGTAAAGAT 58.137 36.000 30.63 3.37 45.05 2.40
365 371 6.262193 TGACACATGTGTATCTCGTAAAGA 57.738 37.500 30.63 0.00 45.05 2.52
371 377 6.419116 CCTAGATTTGACACATGTGTATCTCG 59.581 42.308 31.75 27.04 45.05 4.04
376 382 5.755409 ACCCTAGATTTGACACATGTGTA 57.245 39.130 30.63 16.59 45.05 2.90
389 395 6.041523 GCTCACTAGAGATCAAACCCTAGATT 59.958 42.308 0.00 0.00 44.98 2.40
394 400 3.450457 CAGCTCACTAGAGATCAAACCCT 59.550 47.826 0.00 0.00 44.98 4.34
408 414 1.072159 GTTGCACCCTCAGCTCACT 59.928 57.895 0.00 0.00 0.00 3.41
412 418 1.893808 CGTTGTTGCACCCTCAGCT 60.894 57.895 0.00 0.00 0.00 4.24
427 433 5.730550 TGTGGTTAGATGATTAGAAGCGTT 58.269 37.500 0.00 0.00 0.00 4.84
459 465 8.291191 TGTGCCATAGTTGATCAAATAATCAA 57.709 30.769 18.53 0.00 42.01 2.57
462 468 8.916062 TCAATGTGCCATAGTTGATCAAATAAT 58.084 29.630 18.53 4.94 0.00 1.28
464 470 7.878547 TCAATGTGCCATAGTTGATCAAATA 57.121 32.000 17.14 17.14 0.00 1.40
465 471 6.778834 TCAATGTGCCATAGTTGATCAAAT 57.221 33.333 13.58 13.58 0.00 2.32
466 472 6.778834 ATCAATGTGCCATAGTTGATCAAA 57.221 33.333 10.35 0.00 36.81 2.69
467 473 9.743581 ATATATCAATGTGCCATAGTTGATCAA 57.256 29.630 3.38 3.38 40.59 2.57
478 484 9.129532 TGACAAAATGTATATATCAATGTGCCA 57.870 29.630 0.00 0.00 0.00 4.92
532 715 1.470098 CCAAGCTCCAAGGTGAAATCG 59.530 52.381 0.00 0.00 0.00 3.34
541 725 4.785301 TGGATATTTCTCCAAGCTCCAAG 58.215 43.478 0.00 0.00 42.36 3.61
604 792 1.676967 GAAGGTGCCCTTGCTCTGG 60.677 63.158 10.77 0.00 44.82 3.86
721 4055 7.620880 AGGTGATAGCTACAATTTTCTGTGTA 58.379 34.615 0.00 0.00 0.00 2.90
743 4077 0.483770 GAGGTAGCTAGGGCCTAGGT 59.516 60.000 38.59 38.59 45.17 3.08
749 4083 1.455217 TGGTCGAGGTAGCTAGGGC 60.455 63.158 0.00 0.00 39.06 5.19
784 4120 1.877443 CGTCGTCAATCCAAAAAGGGT 59.123 47.619 0.00 0.00 38.24 4.34
806 4142 2.802247 CAGATTGAGAGTGTTTGTGCGA 59.198 45.455 0.00 0.00 0.00 5.10
817 4161 1.815003 GGTTGTTGGCCAGATTGAGAG 59.185 52.381 5.11 0.00 0.00 3.20
858 5054 4.980339 ATTTATATCCCCGGGTAAACGT 57.020 40.909 21.85 2.49 0.00 3.99
863 5059 2.987437 TGGCAATTTATATCCCCGGGTA 59.013 45.455 21.85 2.85 0.00 3.69
865 5061 2.446435 CTGGCAATTTATATCCCCGGG 58.554 52.381 15.80 15.80 0.00 5.73
867 5063 1.818674 GCCTGGCAATTTATATCCCCG 59.181 52.381 15.17 0.00 0.00 5.73
871 5067 5.473039 GGTCAATGCCTGGCAATTTATATC 58.527 41.667 27.24 10.37 43.62 1.63
872 5068 4.284234 GGGTCAATGCCTGGCAATTTATAT 59.716 41.667 27.24 3.81 43.62 0.86
940 5136 4.054455 CGTACGTGTGCGGTGTGC 62.054 66.667 7.22 0.00 46.70 4.57
974 5179 2.944349 AGAGCTAGCGGTTGTACTAGTC 59.056 50.000 9.55 0.00 38.50 2.59
1077 5299 4.980805 GTGTCGGCCAGGTTGCGA 62.981 66.667 2.24 0.00 0.00 5.10
1221 5479 4.626081 AGTGTCACCTGCGGCACC 62.626 66.667 0.00 0.00 32.75 5.01
1341 5599 3.605634 CGTCACCTTGGGAATGACAATA 58.394 45.455 8.81 0.00 42.37 1.90
1348 5606 1.675641 GCAGCGTCACCTTGGGAAT 60.676 57.895 0.00 0.00 0.00 3.01
1350 5608 4.329545 GGCAGCGTCACCTTGGGA 62.330 66.667 0.00 0.00 0.00 4.37
1388 10845 1.695893 CGGCATAGGCACGTTCACAG 61.696 60.000 0.15 0.00 43.71 3.66
1456 15333 0.179108 GTAGATGTGGACAGGGCGAC 60.179 60.000 0.00 0.00 0.00 5.19
1469 15346 0.959553 ACGGCACCCTATCGTAGATG 59.040 55.000 0.00 0.00 45.12 2.90
1470 15347 1.612463 GAACGGCACCCTATCGTAGAT 59.388 52.381 0.00 0.00 45.12 1.98
1471 15348 1.027357 GAACGGCACCCTATCGTAGA 58.973 55.000 0.00 0.00 45.75 2.59
1472 15349 0.317603 CGAACGGCACCCTATCGTAG 60.318 60.000 0.00 0.00 36.01 3.51
1473 15350 1.031571 ACGAACGGCACCCTATCGTA 61.032 55.000 8.71 0.00 39.43 3.43
1474 15351 2.345760 ACGAACGGCACCCTATCGT 61.346 57.895 0.00 5.68 37.55 3.73
1483 15371 1.299850 CACTCTCACACGAACGGCA 60.300 57.895 0.00 0.00 0.00 5.69
1540 15428 1.585297 AAAACACCAAGCTTGCATGC 58.415 45.000 21.43 16.37 0.00 4.06
1578 15466 7.394359 AGGCAACAATTACTGATACTGTGAAAT 59.606 33.333 0.00 0.00 41.41 2.17
1579 15467 6.714810 AGGCAACAATTACTGATACTGTGAAA 59.285 34.615 0.00 0.00 41.41 2.69
1581 15469 5.804639 AGGCAACAATTACTGATACTGTGA 58.195 37.500 0.00 0.00 41.41 3.58
1582 15470 6.500684 AAGGCAACAATTACTGATACTGTG 57.499 37.500 0.00 0.00 41.41 3.66
1583 15471 6.942576 AGAAAGGCAACAATTACTGATACTGT 59.057 34.615 0.00 0.00 41.41 3.55
1584 15472 7.383102 AGAAAGGCAACAATTACTGATACTG 57.617 36.000 0.00 0.00 41.41 2.74
1585 15473 8.409358 AAAGAAAGGCAACAATTACTGATACT 57.591 30.769 0.00 0.00 41.41 2.12
1598 15486 2.619646 TGGGACGTAAAAGAAAGGCAAC 59.380 45.455 0.00 0.00 0.00 4.17
1607 15497 9.193133 CAATACATATACTCTGGGACGTAAAAG 57.807 37.037 0.00 0.00 0.00 2.27
1611 15501 6.309357 ACCAATACATATACTCTGGGACGTA 58.691 40.000 0.00 0.00 0.00 3.57
1612 15502 5.145564 ACCAATACATATACTCTGGGACGT 58.854 41.667 0.00 0.00 0.00 4.34
1613 15503 5.723672 ACCAATACATATACTCTGGGACG 57.276 43.478 0.00 0.00 0.00 4.79
1614 15504 7.232941 ACACTACCAATACATATACTCTGGGAC 59.767 40.741 0.00 0.00 0.00 4.46
1615 15505 7.302948 ACACTACCAATACATATACTCTGGGA 58.697 38.462 0.00 0.00 0.00 4.37
1616 15506 7.540474 ACACTACCAATACATATACTCTGGG 57.460 40.000 0.00 0.00 0.00 4.45
1745 17893 5.934625 GGACTGAGACAATTGTACAATCACT 59.065 40.000 21.02 18.29 0.00 3.41
1746 17894 5.934625 AGGACTGAGACAATTGTACAATCAC 59.065 40.000 21.02 14.45 0.00 3.06
1747 17895 6.014242 AGAGGACTGAGACAATTGTACAATCA 60.014 38.462 21.02 13.95 0.00 2.57
1748 17896 6.312426 CAGAGGACTGAGACAATTGTACAATC 59.688 42.308 21.02 13.43 46.03 2.67
1749 17897 6.014242 TCAGAGGACTGAGACAATTGTACAAT 60.014 38.462 15.47 15.47 46.55 2.71
1750 17898 5.304357 TCAGAGGACTGAGACAATTGTACAA 59.696 40.000 11.95 11.41 46.55 2.41
1765 17913 1.123861 TTGCAGCACCTCAGAGGACT 61.124 55.000 24.45 16.29 37.67 3.85
1773 17921 5.238214 CCTCTCTTATATTTTGCAGCACCTC 59.762 44.000 0.00 0.00 0.00 3.85
1781 17929 8.093927 AGCTAGATGACCTCTCTTATATTTTGC 58.906 37.037 0.00 0.00 35.28 3.68
1782 17930 9.638239 GAGCTAGATGACCTCTCTTATATTTTG 57.362 37.037 0.00 0.00 35.28 2.44
1812 17960 7.396540 ACAAAATTCCTAATGGTTAGCTCAG 57.603 36.000 0.00 0.00 34.23 3.35
1871 18021 6.074409 GCAATTGCACTTTTAAATTTTTGGGC 60.074 34.615 25.36 0.00 41.59 5.36
1951 18110 6.834168 ATTTCGTGTTATCATCCCTTTTGT 57.166 33.333 0.00 0.00 0.00 2.83
1953 18112 7.415206 GCACTATTTCGTGTTATCATCCCTTTT 60.415 37.037 0.00 0.00 37.24 2.27
1959 18118 8.736742 CAATTTGCACTATTTCGTGTTATCATC 58.263 33.333 0.00 0.00 37.24 2.92
1961 18120 6.526325 GCAATTTGCACTATTTCGTGTTATCA 59.474 34.615 16.35 0.00 44.26 2.15
2041 18204 8.589335 TTTTATATTTTGGCGCAACTTTTGTA 57.411 26.923 10.83 0.00 0.00 2.41
2046 18209 7.897575 TCATTTTTATATTTTGGCGCAACTT 57.102 28.000 10.83 0.00 0.00 2.66
2048 18211 8.386606 TCAATCATTTTTATATTTTGGCGCAAC 58.613 29.630 10.83 0.00 0.00 4.17
2049 18212 8.484641 TCAATCATTTTTATATTTTGGCGCAA 57.515 26.923 10.83 0.00 0.00 4.85
2050 18213 8.386606 GTTCAATCATTTTTATATTTTGGCGCA 58.613 29.630 10.83 0.00 0.00 6.09
2051 18214 7.850492 GGTTCAATCATTTTTATATTTTGGCGC 59.150 33.333 0.00 0.00 0.00 6.53
2052 18215 8.877779 TGGTTCAATCATTTTTATATTTTGGCG 58.122 29.630 0.00 0.00 0.00 5.69
2094 18264 1.081509 GCATTTGCGCTTTCGGTGA 60.082 52.632 9.73 0.00 35.95 4.02
2145 18315 5.596361 TCCATCTTCAGTTTTAAGGTGCAAA 59.404 36.000 0.00 0.00 34.38 3.68
2162 18332 7.013274 CGTGTATGGGAATAAATTGTCCATCTT 59.987 37.037 9.25 0.00 38.87 2.40
2164 18334 6.485313 TCGTGTATGGGAATAAATTGTCCATC 59.515 38.462 9.25 4.92 38.87 3.51
2168 18338 8.709646 GTCTATCGTGTATGGGAATAAATTGTC 58.290 37.037 0.00 0.00 0.00 3.18
2179 18349 4.426416 TGTTTTCGTCTATCGTGTATGGG 58.574 43.478 0.00 0.00 40.80 4.00
2186 18356 7.436080 TCTTTTGTAGTTGTTTTCGTCTATCGT 59.564 33.333 0.00 0.00 40.80 3.73
2244 18414 6.502136 TTTTTGTTTCCAAATGGGTTTCAC 57.498 33.333 0.00 0.00 40.14 3.18
2246 18416 9.509855 GTTTATTTTTGTTTCCAAATGGGTTTC 57.490 29.630 0.00 0.00 40.14 2.78
2250 18420 7.989826 TGTGTTTATTTTTGTTTCCAAATGGG 58.010 30.769 0.00 0.00 40.14 4.00
2286 18456 8.307582 TGTTTGTTTCCCCTACAAAAGAAATA 57.692 30.769 0.00 0.00 44.42 1.40
2287 18457 7.189079 TGTTTGTTTCCCCTACAAAAGAAAT 57.811 32.000 0.00 0.00 44.42 2.17
2291 18461 7.722363 ACTAATGTTTGTTTCCCCTACAAAAG 58.278 34.615 0.00 0.00 44.42 2.27
2292 18462 7.663043 ACTAATGTTTGTTTCCCCTACAAAA 57.337 32.000 0.00 0.00 44.42 2.44
2302 18472 8.645487 CGAGGAAGTACTACTAATGTTTGTTTC 58.355 37.037 0.00 0.00 0.00 2.78
2306 18476 6.628185 ACCGAGGAAGTACTACTAATGTTTG 58.372 40.000 0.00 0.00 0.00 2.93
2315 18485 4.525912 TTTGGAACCGAGGAAGTACTAC 57.474 45.455 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.