Multiple sequence alignment - TraesCS1B01G025000

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 TraesCS1B01G025000 chr1B 100.000 2243 0 0 1 2243 12344656 12342414 0.000000e+00 4143.0
1 TraesCS1B01G025000 chr1B 88.949 1674 128 20 605 2243 13635056 13636707 0.000000e+00 2013.0
2 TraesCS1B01G025000 chr1B 89.707 1059 92 6 601 1645 13631944 13632999 0.000000e+00 1336.0
3 TraesCS1B01G025000 chr1B 94.509 601 28 4 1 600 13669888 13670484 0.000000e+00 922.0
4 TraesCS1B01G025000 chr1B 93.182 572 33 6 1 569 13634409 13634977 0.000000e+00 835.0
5 TraesCS1B01G025000 chr1B 94.063 539 31 1 1 538 13607566 13608104 0.000000e+00 817.0
6 TraesCS1B01G025000 chr1B 96.154 104 4 0 605 708 13670561 13670664 1.070000e-38 171.0
7 TraesCS1B01G025000 chr1B 91.736 121 8 2 1526 1645 13670661 13670780 1.380000e-37 167.0
8 TraesCS1B01G025000 chr1B 90.164 122 12 0 743 864 12500277 12500398 2.310000e-35 159.0
9 TraesCS1B01G025000 chr1B 90.164 122 12 0 743 864 12570468 12570589 2.310000e-35 159.0
10 TraesCS1B01G025000 chr1B 92.647 68 3 1 535 602 13631808 13631873 1.830000e-16 97.1
11 TraesCS1B01G025000 chrUn 88.590 1674 134 20 605 2243 325806622 325804971 0.000000e+00 1980.0
12 TraesCS1B01G025000 chrUn 89.619 1156 92 10 605 1753 2458355 2457221 0.000000e+00 1445.0
13 TraesCS1B01G025000 chrUn 88.070 1207 87 23 1072 2243 2461675 2460491 0.000000e+00 1378.0
14 TraesCS1B01G025000 chrUn 90.253 831 67 3 601 1419 297889760 297890588 0.000000e+00 1074.0
15 TraesCS1B01G025000 chrUn 93.357 572 32 6 1 569 2459002 2458434 0.000000e+00 841.0
16 TraesCS1B01G025000 chrUn 93.750 384 18 6 189 569 325807081 325806701 2.500000e-159 571.0
17 TraesCS1B01G025000 chrUn 93.989 366 20 2 1879 2243 2456786 2456422 9.050000e-154 553.0
18 TraesCS1B01G025000 chrUn 93.767 369 21 2 1876 2243 297885776 297886143 9.050000e-154 553.0
19 TraesCS1B01G025000 chrUn 92.647 68 3 1 535 602 297889624 297889689 1.830000e-16 97.1
20 TraesCS1B01G025000 chrUn 93.023 43 3 0 838 880 2436874 2436832 1.860000e-06 63.9
21 TraesCS1B01G025000 chr1D 89.368 348 28 5 605 952 9485713 9486051 1.590000e-116 429.0


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 TraesCS1B01G025000 chr1B 12342414 12344656 2242 True 4143.000 4143 100.000000 1 2243 1 chr1B.!!$R1 2242
1 TraesCS1B01G025000 chr1B 13631808 13636707 4899 False 1070.275 2013 91.121250 1 2243 4 chr1B.!!$F4 2242
2 TraesCS1B01G025000 chr1B 13607566 13608104 538 False 817.000 817 94.063000 1 538 1 chr1B.!!$F3 537
3 TraesCS1B01G025000 chr1B 13669888 13670780 892 False 420.000 922 94.133000 1 1645 3 chr1B.!!$F5 1644
4 TraesCS1B01G025000 chrUn 325804971 325807081 2110 True 1275.500 1980 91.170000 189 2243 2 chrUn.!!$R3 2054
5 TraesCS1B01G025000 chrUn 2456422 2461675 5253 True 1054.250 1445 91.258750 1 2243 4 chrUn.!!$R2 2242
6 TraesCS1B01G025000 chrUn 297885776 297890588 4812 False 574.700 1074 92.222333 535 2243 3 chrUn.!!$F1 1708

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
77 4091 0.24445 CATTCCGGCTGTGCAATTGT 59.756 50.0 7.4 0.0 0.0 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1513 5633 0.17668 GGAGCATGTCGTGTCATCCT 59.823 55.0 0.0 0.0 0.0 3.24 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
77 4091 0.244450 CATTCCGGCTGTGCAATTGT 59.756 50.000 7.40 0.00 0.00 2.71
85 4099 1.662876 GCTGTGCAATTGTACACCGTG 60.663 52.381 23.30 15.32 35.76 4.94
141 4155 1.317613 TTGTACCCAAGCTGTGCAAG 58.682 50.000 2.69 0.00 34.14 4.01
243 4257 2.472909 GGTGCCGCTCCACTATTGC 61.473 63.158 6.60 0.00 36.03 3.56
280 4294 0.882474 AGTCCTTGTTCGACCTCTCG 59.118 55.000 0.00 0.00 41.65 4.04
343 4358 1.299976 GGTGGACCTGCCTAACCTG 59.700 63.158 0.00 0.00 37.63 4.00
401 4416 5.097742 TCACTATTTTGATCGTGTGGGAT 57.902 39.130 0.00 0.00 0.00 3.85
431 4446 8.134895 TGGAATGAGTGAAAAACATGTAACTTC 58.865 33.333 0.00 3.21 0.00 3.01
452 4467 1.182667 GTTACCTTTCCACCATGCCC 58.817 55.000 0.00 0.00 0.00 5.36
533 4548 7.408756 AAAGCATTTGAGTTCTATAATGGCA 57.591 32.000 0.00 0.00 36.60 4.92
538 4553 7.591165 CATTTGAGTTCTATAATGGCATGAGG 58.409 38.462 0.00 0.00 0.00 3.86
553 4568 7.473735 TGGCATGAGGACAATTATTTTTACA 57.526 32.000 0.00 0.00 0.00 2.41
555 4570 9.194972 TGGCATGAGGACAATTATTTTTACATA 57.805 29.630 0.00 0.00 0.00 2.29
602 4617 9.604626 CTTCTTTGTTATTGTCTTGATTCTCAC 57.395 33.333 0.00 0.00 0.00 3.51
629 4716 2.027192 AGTCGTGGCATTGTAAGGATGT 60.027 45.455 0.00 0.00 0.00 3.06
692 4779 6.538021 GCACAAAATTGGGATATGTTGCAATA 59.462 34.615 0.59 0.00 31.80 1.90
772 4859 1.205820 CACGCGATGCATGCCTATG 59.794 57.895 15.93 3.49 37.36 2.23
789 4876 3.893200 CCTATGGTATTGTAGGACACCGA 59.107 47.826 0.00 0.00 39.91 4.69
796 4883 3.478857 TTGTAGGACACCGACAAACAT 57.521 42.857 12.50 0.00 43.88 2.71
813 4900 4.365899 AACATGTGCAATGCATGACTAG 57.634 40.909 19.39 1.48 44.60 2.57
833 4920 9.990360 TGACTAGTATATTTTCACTTGTTGTCA 57.010 29.630 0.00 0.00 32.17 3.58
927 5014 3.667360 ACCAACACGACCTAAATACCAC 58.333 45.455 0.00 0.00 0.00 4.16
928 5015 2.669434 CCAACACGACCTAAATACCACG 59.331 50.000 0.00 0.00 0.00 4.94
933 5020 1.737696 CGACCTAAATACCACGCAGCA 60.738 52.381 0.00 0.00 0.00 4.41
952 5039 4.021368 CAGCACCTACAAGTACAACTAGGT 60.021 45.833 8.78 8.78 35.62 3.08
954 5041 5.956563 AGCACCTACAAGTACAACTAGGTAT 59.043 40.000 12.59 5.21 33.59 2.73
988 5075 4.946784 ATTGTTAAACAGACTCATCGGC 57.053 40.909 0.00 0.00 0.00 5.54
995 5082 4.148825 GACTCATCGGCTGGGCGT 62.149 66.667 15.54 1.73 0.00 5.68
998 5085 1.069765 CTCATCGGCTGGGCGTTAT 59.930 57.895 15.54 1.08 0.00 1.89
1006 5093 0.886490 GCTGGGCGTTATGATGGGAG 60.886 60.000 0.00 0.00 0.00 4.30
1009 5096 0.250338 GGGCGTTATGATGGGAGGAC 60.250 60.000 0.00 0.00 0.00 3.85
1036 5123 2.348998 CAGGTGCTGGTGAGGGTC 59.651 66.667 0.00 0.00 0.00 4.46
1046 5133 1.590147 GTGAGGGTCGTGACGGAAT 59.410 57.895 4.70 0.00 0.00 3.01
1113 5200 1.942586 GCGGTTGTACGGATCAAAGGT 60.943 52.381 0.00 0.00 0.00 3.50
1126 5213 2.684943 TCAAAGGTGATAGGCCCGATA 58.315 47.619 0.00 0.00 0.00 2.92
1134 5221 3.056749 GTGATAGGCCCGATATCTCGTTT 60.057 47.826 0.00 0.00 43.49 3.60
1216 5303 1.372087 CTCCAATGAAGCTGGCGTCC 61.372 60.000 6.11 0.00 33.63 4.79
1257 5344 0.527385 GCTAGCTCAACCTCGCTCAG 60.527 60.000 7.70 0.00 37.68 3.35
1309 5396 2.352388 ACGTAGTTGTGTTGCACTTGT 58.648 42.857 0.00 0.00 37.78 3.16
1310 5397 2.095213 ACGTAGTTGTGTTGCACTTGTG 59.905 45.455 0.00 0.00 37.78 3.33
1311 5398 2.450160 GTAGTTGTGTTGCACTTGTGC 58.550 47.619 17.73 17.73 35.11 4.57
1312 5399 0.173255 AGTTGTGTTGCACTTGTGCC 59.827 50.000 21.01 8.80 35.11 5.01
1313 5400 0.805711 GTTGTGTTGCACTTGTGCCC 60.806 55.000 21.01 12.89 35.11 5.36
1314 5401 1.253593 TTGTGTTGCACTTGTGCCCA 61.254 50.000 21.01 15.04 35.11 5.36
1315 5402 1.226945 GTGTTGCACTTGTGCCCAC 60.227 57.895 21.01 21.06 0.00 4.61
1316 5403 1.379710 TGTTGCACTTGTGCCCACT 60.380 52.632 21.01 0.00 0.00 4.00
1317 5404 0.106967 TGTTGCACTTGTGCCCACTA 60.107 50.000 21.01 1.26 0.00 2.74
1318 5405 1.247567 GTTGCACTTGTGCCCACTAT 58.752 50.000 21.01 0.00 0.00 2.12
1319 5406 1.068333 GTTGCACTTGTGCCCACTATG 60.068 52.381 21.01 0.00 0.00 2.23
1320 5407 0.399833 TGCACTTGTGCCCACTATGA 59.600 50.000 21.01 0.00 0.00 2.15
1321 5408 1.202867 TGCACTTGTGCCCACTATGAA 60.203 47.619 21.01 0.00 0.00 2.57
1371 5485 5.874831 TGGTAGCGCTTTAAATAATGTGTG 58.125 37.500 18.68 0.00 0.00 3.82
1392 5506 7.714813 TGTGTGATCATCCGTATTGATTAATGT 59.285 33.333 0.00 0.00 34.03 2.71
1443 5563 0.970640 TCCATTGTTCCCTCGTCGAA 59.029 50.000 0.00 0.00 0.00 3.71
1447 5567 3.581755 CATTGTTCCCTCGTCGAAAGTA 58.418 45.455 0.00 0.00 0.00 2.24
1449 5569 5.345702 CATTGTTCCCTCGTCGAAAGTATA 58.654 41.667 0.00 0.00 0.00 1.47
1454 5574 2.424601 CCCTCGTCGAAAGTATACACCA 59.575 50.000 5.50 0.00 0.00 4.17
1457 5577 4.201980 CCTCGTCGAAAGTATACACCATCA 60.202 45.833 5.50 0.00 0.00 3.07
1500 5620 9.533253 ACTAAATTCAAAACAAAAGAGGTCATG 57.467 29.630 0.00 0.00 0.00 3.07
1543 5663 0.548031 ACATGCTCCAATCGTCCCAT 59.452 50.000 0.00 0.00 0.00 4.00
1554 5674 1.717194 TCGTCCCATAGAAAACGCAC 58.283 50.000 0.00 0.00 35.22 5.34
1573 5693 6.321717 ACGCACTGATGTTAATTATGGTTTG 58.678 36.000 0.00 0.00 0.00 2.93
1639 5759 3.609853 AGCTTGATTTTATGCGAGTGGA 58.390 40.909 0.00 0.00 0.00 4.02
1645 5765 0.254747 TTTATGCGAGTGGAAGGGGG 59.745 55.000 0.00 0.00 0.00 5.40
1652 5772 1.152546 AGTGGAAGGGGGTTGTTGC 60.153 57.895 0.00 0.00 0.00 4.17
1661 5781 2.566724 AGGGGGTTGTTGCACATAATTG 59.433 45.455 0.00 0.00 0.00 2.32
1690 5810 8.907222 ATTTGCAATTTTTGAAATGTAGGACT 57.093 26.923 0.00 0.00 0.00 3.85
1713 5833 9.170584 GACTATTTTTGCACTTTCTTTACTGAC 57.829 33.333 0.00 0.00 0.00 3.51
1718 5838 3.944650 TGCACTTTCTTTACTGACTGCAA 59.055 39.130 0.00 0.00 30.70 4.08
1719 5839 4.035558 TGCACTTTCTTTACTGACTGCAAG 59.964 41.667 0.00 0.00 42.29 4.01
1723 5843 7.250569 CACTTTCTTTACTGACTGCAAGAAAA 58.749 34.615 15.23 5.93 42.08 2.29
1738 5858 5.466058 TGCAAGAAAATAAATGTTGCAGTGG 59.534 36.000 6.95 0.00 46.39 4.00
1760 5903 2.285950 CGTTATTAATGCAACGGTCGGG 60.286 50.000 13.37 0.00 42.82 5.14
1766 5909 3.799755 GCAACGGTCGGGCACATC 61.800 66.667 0.00 0.00 0.00 3.06
1775 5918 3.366476 CGGTCGGGCACATCAAAATTTAA 60.366 43.478 0.00 0.00 0.00 1.52
1781 5924 7.382759 GTCGGGCACATCAAAATTTAAGTTTTA 59.617 33.333 8.20 0.00 30.56 1.52
1804 5947 0.183731 GGATCGGGAAGGCCAAAGAT 59.816 55.000 5.01 1.84 35.15 2.40
1808 5951 1.203001 TCGGGAAGGCCAAAGATTGTT 60.203 47.619 5.01 0.00 35.15 2.83
1809 5952 2.040545 TCGGGAAGGCCAAAGATTGTTA 59.959 45.455 5.01 0.00 35.15 2.41
1811 5954 3.431415 GGGAAGGCCAAAGATTGTTAGT 58.569 45.455 5.01 0.00 35.15 2.24
1820 5963 5.446473 GCCAAAGATTGTTAGTCGATGTCAG 60.446 44.000 0.00 0.00 0.00 3.51
1825 5968 3.165058 TGTTAGTCGATGTCAGCCATC 57.835 47.619 0.00 0.00 45.50 3.51
1844 5987 0.379669 CATTCTGTGAAGATGGGCGC 59.620 55.000 0.00 0.00 0.00 6.53
1855 5998 1.486310 AGATGGGCGCTCAATAGACAA 59.514 47.619 17.15 0.00 0.00 3.18
1863 6006 4.752101 GGCGCTCAATAGACAACAAGATAT 59.248 41.667 7.64 0.00 0.00 1.63
1865 6008 6.591834 GGCGCTCAATAGACAACAAGATATAT 59.408 38.462 7.64 0.00 0.00 0.86
1912 6341 4.193865 GCTGGCGTAGTAATTTCCCTTTA 58.806 43.478 0.00 0.00 0.00 1.85
1913 6342 4.272748 GCTGGCGTAGTAATTTCCCTTTAG 59.727 45.833 0.00 0.00 0.00 1.85
1914 6343 4.773013 TGGCGTAGTAATTTCCCTTTAGG 58.227 43.478 0.00 0.00 0.00 2.69
1947 6376 4.363999 CTTTCTCTCGCCGATCTTGTTAT 58.636 43.478 0.00 0.00 0.00 1.89
1951 6380 4.038042 TCTCTCGCCGATCTTGTTATCAAT 59.962 41.667 0.00 0.00 32.82 2.57
2066 6495 2.095314 TGTCACAAGCAAACACACACAG 60.095 45.455 0.00 0.00 0.00 3.66
2138 6568 8.743714 TCCTTCTACATGTAGATGCTATGTATG 58.256 37.037 31.03 18.50 41.37 2.39
2149 6579 2.146005 CTATGTATGCACGTGCGCCG 62.146 60.000 33.22 15.25 45.83 6.46
2201 6631 9.935241 AGCATGACTATGATATGTAAACTAAGG 57.065 33.333 0.00 0.00 36.36 2.69
2204 6634 9.712305 ATGACTATGATATGTAAACTAAGGCAC 57.288 33.333 0.00 0.00 0.00 5.01
2205 6635 8.700973 TGACTATGATATGTAAACTAAGGCACA 58.299 33.333 0.00 0.00 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 4055 9.623000 AGCCGGAATGTAACTATTAATTTACTT 57.377 29.630 5.05 3.38 0.00 2.24
77 4091 3.719924 ACACGAGAAAATTCACGGTGTA 58.280 40.909 15.44 0.00 43.85 2.90
85 4099 8.476925 GGACAATGTTTAAACACGAGAAAATTC 58.523 33.333 22.78 8.74 42.51 2.17
141 4155 2.539346 CTGTCATGCACAGCTAAAGC 57.461 50.000 10.89 0.00 46.30 3.51
243 4257 6.515272 AGGACTGTGCCAAATTATAAACAG 57.485 37.500 9.99 9.99 40.61 3.16
280 4294 1.369625 CAAACGTGGTAGCCAGATCC 58.630 55.000 0.00 0.00 32.34 3.36
343 4358 2.507484 TCCATGGCATGCTATTGCTAC 58.493 47.619 22.02 0.00 42.38 3.58
401 4416 6.638610 ACATGTTTTTCACTCATTCCAAACA 58.361 32.000 0.00 0.00 38.22 2.83
431 4446 0.808755 GCATGGTGGAAAGGTAACGG 59.191 55.000 0.00 0.00 46.39 4.44
560 4575 1.428912 AGAAGGGGCAACAATGAGGAA 59.571 47.619 0.00 0.00 39.74 3.36
561 4576 1.075601 AGAAGGGGCAACAATGAGGA 58.924 50.000 0.00 0.00 39.74 3.71
602 4617 2.315925 ACAATGCCACGACTATCCAG 57.684 50.000 0.00 0.00 0.00 3.86
629 4716 1.894466 CCATTCCCACTGAACATGCAA 59.106 47.619 0.00 0.00 35.31 4.08
692 4779 3.127548 GTGTCGACATGCCAATCTTCAAT 59.872 43.478 23.12 0.00 0.00 2.57
757 4844 1.742761 ATACCATAGGCATGCATCGC 58.257 50.000 21.36 4.26 0.00 4.58
772 4859 3.598019 TTGTCGGTGTCCTACAATACC 57.402 47.619 2.50 0.00 34.90 2.73
789 4876 3.061322 GTCATGCATTGCACATGTTTGT 58.939 40.909 14.66 0.00 43.04 2.83
796 4883 7.806409 AAATATACTAGTCATGCATTGCACA 57.194 32.000 14.66 0.17 43.04 4.57
833 4920 2.754552 ACAAGCATGACCAACGCATAAT 59.245 40.909 0.00 0.00 0.00 1.28
927 5014 1.459592 GTTGTACTTGTAGGTGCTGCG 59.540 52.381 0.00 0.00 0.00 5.18
928 5015 2.767505 AGTTGTACTTGTAGGTGCTGC 58.232 47.619 0.00 0.00 0.00 5.25
933 5020 9.539194 AACTAATACCTAGTTGTACTTGTAGGT 57.461 33.333 18.62 18.62 46.96 3.08
954 5041 8.347035 GTCTGTTTAACAATTGCTGGTAACTAA 58.653 33.333 5.05 0.00 36.92 2.24
959 5046 6.058833 TGAGTCTGTTTAACAATTGCTGGTA 58.941 36.000 5.05 0.00 0.00 3.25
988 5075 0.250467 CCTCCCATCATAACGCCCAG 60.250 60.000 0.00 0.00 0.00 4.45
995 5082 1.964223 GCTCGAGTCCTCCCATCATAA 59.036 52.381 15.13 0.00 0.00 1.90
998 5085 1.758514 GGCTCGAGTCCTCCCATCA 60.759 63.158 15.13 0.00 0.00 3.07
1006 5093 3.386237 ACCTGCTGGCTCGAGTCC 61.386 66.667 15.72 16.01 36.63 3.85
1031 5118 1.605058 CCAGATTCCGTCACGACCCT 61.605 60.000 0.00 0.00 0.00 4.34
1036 5123 1.630148 GTCTTCCAGATTCCGTCACG 58.370 55.000 0.00 0.00 0.00 4.35
1083 5170 1.068417 TACAACCGCGTTCTGCACT 59.932 52.632 4.92 0.00 46.97 4.40
1113 5200 2.509166 ACGAGATATCGGGCCTATCA 57.491 50.000 15.07 0.00 37.45 2.15
1126 5213 1.157870 CCGCCGGCAATAAACGAGAT 61.158 55.000 28.98 0.00 0.00 2.75
1134 5221 2.502093 CCTGTACCGCCGGCAATA 59.498 61.111 28.98 15.25 0.00 1.90
1216 5303 0.393077 ACGACAGGGGTCTTCACAAG 59.607 55.000 0.00 0.00 42.05 3.16
1303 5390 3.084039 ACATTCATAGTGGGCACAAGTG 58.916 45.455 0.00 0.00 0.00 3.16
1307 5394 1.462616 GCACATTCATAGTGGGCACA 58.537 50.000 0.00 0.00 45.21 4.57
1310 5397 2.158755 ACCTAGCACATTCATAGTGGGC 60.159 50.000 0.00 0.00 46.22 5.36
1311 5398 3.470709 CACCTAGCACATTCATAGTGGG 58.529 50.000 0.00 0.00 37.46 4.61
1312 5399 2.874701 GCACCTAGCACATTCATAGTGG 59.125 50.000 0.00 0.00 44.79 4.00
1425 5545 1.732259 CTTTCGACGAGGGAACAATGG 59.268 52.381 0.00 0.00 0.00 3.16
1437 5557 7.593644 TCATATTGATGGTGTATACTTTCGACG 59.406 37.037 4.17 0.00 33.49 5.12
1443 5563 9.988815 GAAGTCTCATATTGATGGTGTATACTT 57.011 33.333 4.17 0.00 33.49 2.24
1447 5567 9.334947 CTTTGAAGTCTCATATTGATGGTGTAT 57.665 33.333 0.00 0.00 33.49 2.29
1449 5569 7.335422 GTCTTTGAAGTCTCATATTGATGGTGT 59.665 37.037 0.00 0.00 33.49 4.16
1481 5601 4.709397 ACCACATGACCTCTTTTGTTTTGA 59.291 37.500 0.00 0.00 0.00 2.69
1484 5604 3.636764 GGACCACATGACCTCTTTTGTTT 59.363 43.478 0.00 0.00 0.00 2.83
1487 5607 2.554032 GTGGACCACATGACCTCTTTTG 59.446 50.000 20.14 0.00 34.08 2.44
1488 5608 2.174639 TGTGGACCACATGACCTCTTTT 59.825 45.455 23.72 0.00 39.62 2.27
1489 5609 1.774254 TGTGGACCACATGACCTCTTT 59.226 47.619 23.72 0.00 39.62 2.52
1490 5610 1.434188 TGTGGACCACATGACCTCTT 58.566 50.000 23.72 0.00 39.62 2.85
1491 5611 1.072331 GTTGTGGACCACATGACCTCT 59.928 52.381 27.61 0.00 44.16 3.69
1492 5612 1.523758 GTTGTGGACCACATGACCTC 58.476 55.000 27.61 10.51 44.16 3.85
1513 5633 0.176680 GGAGCATGTCGTGTCATCCT 59.823 55.000 0.00 0.00 0.00 3.24
1517 5637 1.725641 GATTGGAGCATGTCGTGTCA 58.274 50.000 0.00 0.00 0.00 3.58
1543 5663 8.394877 CCATAATTAACATCAGTGCGTTTTCTA 58.605 33.333 3.50 0.00 0.00 2.10
1554 5674 9.734620 CATACACCAAACCATAATTAACATCAG 57.265 33.333 0.00 0.00 0.00 2.90
1573 5693 6.885922 ACCTCTTAACTAATCACCATACACC 58.114 40.000 0.00 0.00 0.00 4.16
1602 5722 5.612725 TCAAGCTCACATACACCATATGA 57.387 39.130 3.65 0.00 0.00 2.15
1687 5807 9.170584 GTCAGTAAAGAAAGTGCAAAAATAGTC 57.829 33.333 0.00 0.00 0.00 2.59
1690 5810 7.647715 GCAGTCAGTAAAGAAAGTGCAAAAATA 59.352 33.333 0.00 0.00 0.00 1.40
1718 5838 4.236935 CGCCACTGCAACATTTATTTTCT 58.763 39.130 0.00 0.00 37.32 2.52
1719 5839 3.987220 ACGCCACTGCAACATTTATTTTC 59.013 39.130 0.00 0.00 37.32 2.29
1723 5843 4.981806 ATAACGCCACTGCAACATTTAT 57.018 36.364 0.00 0.00 37.32 1.40
1736 5856 2.085320 ACCGTTGCATTAATAACGCCA 58.915 42.857 15.07 0.00 45.91 5.69
1738 5858 2.359598 CGACCGTTGCATTAATAACGC 58.640 47.619 15.07 4.08 45.91 4.84
1766 5909 9.783256 CCCGATCCTACTAAAACTTAAATTTTG 57.217 33.333 4.94 0.29 33.80 2.44
1775 5918 3.134262 GCCTTCCCGATCCTACTAAAACT 59.866 47.826 0.00 0.00 0.00 2.66
1781 5924 0.326238 TTGGCCTTCCCGATCCTACT 60.326 55.000 3.32 0.00 35.87 2.57
1790 5933 3.431415 ACTAACAATCTTTGGCCTTCCC 58.569 45.455 3.32 0.00 34.12 3.97
1804 5947 3.521560 GATGGCTGACATCGACTAACAA 58.478 45.455 7.91 0.00 45.87 2.83
1820 5963 3.984508 CCATCTTCACAGAATGATGGC 57.015 47.619 17.25 0.00 46.00 4.40
1825 5968 0.379669 GCGCCCATCTTCACAGAATG 59.620 55.000 0.00 0.00 46.00 2.67
1829 5972 0.674581 TTGAGCGCCCATCTTCACAG 60.675 55.000 2.29 0.00 0.00 3.66
1865 6008 8.673711 GCCATATTGCCTAATTCGAATATGTTA 58.326 33.333 11.83 0.00 37.19 2.41
1874 6017 2.095059 GCCAGCCATATTGCCTAATTCG 60.095 50.000 0.00 0.00 0.00 3.34
1875 6018 2.095059 CGCCAGCCATATTGCCTAATTC 60.095 50.000 0.00 0.00 0.00 2.17
1876 6019 1.888512 CGCCAGCCATATTGCCTAATT 59.111 47.619 0.00 0.00 0.00 1.40
1877 6020 1.202927 ACGCCAGCCATATTGCCTAAT 60.203 47.619 0.00 0.00 0.00 1.73
1912 6341 3.999663 CGAGAGAAAGCAAAGATGAACCT 59.000 43.478 0.00 0.00 0.00 3.50
1913 6342 3.425492 GCGAGAGAAAGCAAAGATGAACC 60.425 47.826 0.00 0.00 0.00 3.62
1914 6343 3.425492 GGCGAGAGAAAGCAAAGATGAAC 60.425 47.826 0.00 0.00 34.54 3.18
1947 6376 5.567037 TTTTGAGGGTTGAGAGAGATTGA 57.433 39.130 0.00 0.00 0.00 2.57
1951 6380 5.832539 ATCTTTTTGAGGGTTGAGAGAGA 57.167 39.130 0.00 0.00 0.00 3.10
2011 6440 8.249638 TGAAATTTGAAAAGTTGTCTCACATCA 58.750 29.630 0.00 0.00 0.00 3.07
2027 6456 5.298026 TGTGACACCTTCGATGAAATTTGAA 59.702 36.000 2.45 0.00 0.00 2.69
2090 6520 6.042093 AGGAGTGTACATGTAATACCATGAGG 59.958 42.308 7.25 0.00 43.99 3.86
2095 6525 7.616542 TGTAGAAGGAGTGTACATGTAATACCA 59.383 37.037 7.25 0.00 31.29 3.25
2110 6540 6.780031 ACATAGCATCTACATGTAGAAGGAGT 59.220 38.462 33.30 23.67 44.44 3.85
2175 6605 9.935241 CCTTAGTTTACATATCATAGTCATGCT 57.065 33.333 0.00 0.00 31.73 3.79
2179 6609 8.700973 TGTGCCTTAGTTTACATATCATAGTCA 58.299 33.333 0.00 0.00 0.00 3.41
2201 6631 2.358898 ACACCTCTGATGTGTTTTGTGC 59.641 45.455 12.15 0.00 44.19 4.57
2204 6634 5.049405 GGTAAGACACCTCTGATGTGTTTTG 60.049 44.000 22.93 0.73 46.43 2.44
2205 6635 5.063880 GGTAAGACACCTCTGATGTGTTTT 58.936 41.667 19.99 19.99 46.43 2.43


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

AutoCloner maintained by Alex Coulton.