Multiple sequence alignment - TraesCS5B01G052100

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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 TraesCS5B01G052100 chr5B 100.000 5483 0 0 1 5483 57432838 57438320 0.000000e+00 10126
1 TraesCS5B01G052100 chr5B 95.909 220 9 0 4943 5162 57440469 57440250 1.880000e-94 357
2 TraesCS5B01G052100 chr5D 93.613 4979 227 54 8 4943 54679389 54684319 0.000000e+00 7348
3 TraesCS5B01G052100 chr5D 93.392 227 15 0 4944 5170 54723224 54723450 2.450000e-88 337
4 TraesCS5B01G052100 chr5D 92.952 227 16 0 4944 5170 54732148 54731922 1.140000e-86 331
5 TraesCS5B01G052100 chr5D 96.190 105 4 0 4262 4366 54683595 54683699 7.300000e-39 172
6 TraesCS5B01G052100 chr5A 91.820 4034 239 48 386 4362 42618468 42622467 0.000000e+00 5537
7 TraesCS5B01G052100 chr5A 93.333 660 35 6 4289 4943 42622436 42623091 0.000000e+00 966
8 TraesCS5B01G052100 chr5A 86.772 378 33 11 8 384 42617846 42618207 6.610000e-109 405
9 TraesCS5B01G052100 chr1A 94.465 542 19 4 4943 5483 508186233 508185702 0.000000e+00 824
10 TraesCS5B01G052100 chr1A 95.475 221 10 0 4942 5162 508183462 508183682 2.430000e-93 353
11 TraesCS5B01G052100 chr2A 91.392 546 23 5 4944 5483 670307562 670307035 0.000000e+00 726
12 TraesCS5B01G052100 chr2A 94.064 219 13 0 4944 5162 670305076 670305294 3.170000e-87 333
13 TraesCS5B01G052100 chr7D 95.541 314 8 5 5170 5483 470197640 470197947 1.060000e-136 497
14 TraesCS5B01G052100 chr3A 87.792 385 26 9 1140 1510 631787683 631788060 1.090000e-116 431
15 TraesCS5B01G052100 chr3A 92.140 229 14 4 4944 5170 66168859 66169085 2.460000e-83 320
16 TraesCS5B01G052100 chr7A 89.439 303 20 8 5187 5483 528361977 528361681 6.710000e-99 372
17 TraesCS5B01G052100 chr1D 95.133 226 11 0 4944 5169 394276894 394276669 1.880000e-94 357
18 TraesCS5B01G052100 chr7B 86.769 325 12 19 5170 5483 494215531 494215835 3.170000e-87 333
19 TraesCS5B01G052100 chr6A 91.139 237 20 1 4933 5169 209785322 209785557 2.460000e-83 320
20 TraesCS5B01G052100 chr6B 87.368 285 22 7 1140 1411 669953799 669954082 1.150000e-81 315


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 TraesCS5B01G052100 chr5B 57432838 57438320 5482 False 10126.000000 10126 100.000000 1 5483 1 chr5B.!!$F1 5482
1 TraesCS5B01G052100 chr5D 54679389 54684319 4930 False 3760.000000 7348 94.901500 8 4943 2 chr5D.!!$F2 4935
2 TraesCS5B01G052100 chr5A 42617846 42623091 5245 False 2302.666667 5537 90.641667 8 4943 3 chr5A.!!$F1 4935
3 TraesCS5B01G052100 chr1A 508185702 508186233 531 True 824.000000 824 94.465000 4943 5483 1 chr1A.!!$R1 540
4 TraesCS5B01G052100 chr2A 670307035 670307562 527 True 726.000000 726 91.392000 4944 5483 1 chr2A.!!$R1 539

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
763 1028 0.109272 TTCATCGTCTCACGGACAGC 60.109 55.000 0.00 0.00 44.70 4.40 F
1689 1984 0.739561 CCACTACCTCGCTGTCCTAC 59.260 60.000 0.00 0.00 0.00 3.18 F
2462 2772 0.253044 TTGATTCTTCCCGGCTGGAG 59.747 55.000 15.09 3.01 46.24 3.86 F
4003 4323 1.071385 GTCAGGGGCATCGAGAATGAT 59.929 52.381 0.00 0.00 37.59 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1887 2189 0.436531 CAAGAGAAAGTGACGCGAGC 59.563 55.000 15.93 4.68 0.00 5.03 R
3589 3907 1.423584 TGAAGAGCCTGACACTGGAA 58.576 50.000 0.00 0.00 0.00 3.53 R
4216 4536 1.485066 AGAGTTGACGAAACCACCACT 59.515 47.619 0.00 0.00 39.85 4.00 R
5368 5748 0.539051 ATGGAGAGAGAAAGCACCGG 59.461 55.000 0.00 0.00 0.00 5.28 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
70 71 4.142038 ACACTTTTGAAGTATGTGTCCCC 58.858 43.478 0.00 0.00 40.46 4.81
82 83 1.002624 TGTCCCCCTCGATGCAAAC 60.003 57.895 0.00 0.00 0.00 2.93
85 86 1.750399 CCCCCTCGATGCAAACCTG 60.750 63.158 0.00 0.00 0.00 4.00
90 91 0.321564 CTCGATGCAAACCTGTCCCA 60.322 55.000 0.00 0.00 0.00 4.37
93 94 1.545582 CGATGCAAACCTGTCCCAAAT 59.454 47.619 0.00 0.00 0.00 2.32
196 198 0.478072 TGCAGACCCAAATGGACACT 59.522 50.000 0.00 0.00 37.39 3.55
197 199 1.702401 TGCAGACCCAAATGGACACTA 59.298 47.619 0.00 0.00 37.39 2.74
299 304 3.869272 CGCTTGCGGCCTCATGAC 61.869 66.667 12.50 3.47 37.74 3.06
384 389 6.955963 GCTAATTCTTGATCACAACACTTACG 59.044 38.462 0.00 0.00 32.27 3.18
464 728 8.082242 ACTAAAATAATTTTGAGCACCTGACAC 58.918 33.333 0.00 0.00 34.19 3.67
486 750 2.418609 CCGGCCCATTCAAAAGAAATCC 60.419 50.000 0.00 0.00 0.00 3.01
499 763 2.991250 AGAAATCCCCACGACATTCAG 58.009 47.619 0.00 0.00 0.00 3.02
507 771 1.672356 ACGACATTCAGCAGCCCAC 60.672 57.895 0.00 0.00 0.00 4.61
514 778 2.361610 CAGCAGCCCACGGGAAAT 60.362 61.111 6.21 0.00 37.50 2.17
520 784 1.755395 GCCCACGGGAAATAACCCC 60.755 63.158 6.21 0.00 46.62 4.95
581 846 1.327303 TTTCCTCCAAGCAATGCGTT 58.673 45.000 0.00 0.00 0.00 4.84
582 847 2.192664 TTCCTCCAAGCAATGCGTTA 57.807 45.000 0.00 0.00 0.00 3.18
602 867 6.316890 GCGTTATCATAAACCTTTTCCTACCA 59.683 38.462 0.00 0.00 0.00 3.25
666 931 2.803956 AGTCATTCCCTACGTCTGACA 58.196 47.619 8.73 0.00 38.90 3.58
670 935 1.100510 TTCCCTACGTCTGACATCCG 58.899 55.000 8.73 0.00 0.00 4.18
677 942 2.755876 TCTGACATCCGCTCCGCT 60.756 61.111 0.00 0.00 0.00 5.52
745 1010 1.048160 CAACAACCCCTGGCAACCTT 61.048 55.000 0.00 0.00 0.00 3.50
752 1017 1.026718 CCCTGGCAACCTTCATCGTC 61.027 60.000 0.00 0.00 0.00 4.20
763 1028 0.109272 TTCATCGTCTCACGGACAGC 60.109 55.000 0.00 0.00 44.70 4.40
764 1029 1.517257 CATCGTCTCACGGACAGCC 60.517 63.158 0.00 0.00 44.70 4.85
834 1099 4.287067 GTGGGAGCAGGAGATATTTCCATA 59.713 45.833 14.40 0.00 39.84 2.74
847 1112 4.918129 CCATACCGTACGCGCGCT 62.918 66.667 32.58 19.60 36.67 5.92
876 1141 2.544694 CGCAGAAATATCTCTCGTGGCT 60.545 50.000 0.00 0.00 32.03 4.75
900 1173 3.330998 CCTATTAACCCCATTCCCTCTCC 59.669 52.174 0.00 0.00 0.00 3.71
918 1191 2.760385 CCCCCTCTCCACTCGTCC 60.760 72.222 0.00 0.00 0.00 4.79
919 1192 2.760385 CCCCTCTCCACTCGTCCC 60.760 72.222 0.00 0.00 0.00 4.46
921 1194 2.360980 CCTCTCCACTCGTCCCCT 59.639 66.667 0.00 0.00 0.00 4.79
1397 1682 1.682087 GCTGTTCCCCATCCAGGTAAC 60.682 57.143 0.00 0.00 34.66 2.50
1458 1744 7.876068 TCTTCAATTGGAACGTGATTACTACTT 59.124 33.333 5.42 0.00 0.00 2.24
1462 1748 5.068234 TGGAACGTGATTACTACTTCCTG 57.932 43.478 0.00 0.00 31.96 3.86
1464 1750 4.863131 GGAACGTGATTACTACTTCCTGTG 59.137 45.833 0.00 0.00 0.00 3.66
1465 1751 4.451629 ACGTGATTACTACTTCCTGTGG 57.548 45.455 0.00 0.00 0.00 4.17
1471 1757 0.879765 ACTACTTCCTGTGGTCGTCG 59.120 55.000 0.00 0.00 35.35 5.12
1492 1778 2.508526 GTGGATTGTTTGCTCTCTGGT 58.491 47.619 0.00 0.00 0.00 4.00
1498 1784 1.270839 TGTTTGCTCTCTGGTGCTACC 60.271 52.381 0.00 0.00 39.22 3.18
1512 1798 2.016318 TGCTACCGCTTGATTGATTGG 58.984 47.619 0.00 0.00 36.97 3.16
1519 1805 2.416296 CGCTTGATTGATTGGTGCACAT 60.416 45.455 20.43 3.94 0.00 3.21
1580 1866 6.587206 TGATGGAATGTTGTAATTTCTGCA 57.413 33.333 0.00 0.00 0.00 4.41
1584 1870 4.622740 GGAATGTTGTAATTTCTGCACAGC 59.377 41.667 0.00 0.00 0.00 4.40
1684 1979 1.270678 GGTTTTCCACTACCTCGCTGT 60.271 52.381 0.00 0.00 40.31 4.40
1689 1984 0.739561 CCACTACCTCGCTGTCCTAC 59.260 60.000 0.00 0.00 0.00 3.18
1735 2030 4.186856 TCGTTCTGAATGCACAGATGTA 57.813 40.909 7.76 0.00 44.67 2.29
1739 2034 6.816140 TCGTTCTGAATGCACAGATGTATTAA 59.184 34.615 7.76 0.00 44.67 1.40
1742 2037 7.500720 TCTGAATGCACAGATGTATTAATGG 57.499 36.000 3.01 0.00 40.77 3.16
1889 2191 7.555965 TCACTCTGTATTATTATGTGTGTGCT 58.444 34.615 0.00 0.00 0.00 4.40
1892 2194 5.462068 TCTGTATTATTATGTGTGTGCTCGC 59.538 40.000 0.00 0.00 0.00 5.03
1925 2227 7.330262 TCTCTTGTGACAATAGTTATGCATGA 58.670 34.615 10.16 0.00 0.00 3.07
1983 2287 6.150140 GTCAATCAAATCATCCCTGTATAGGC 59.850 42.308 0.00 0.00 43.16 3.93
1991 2295 3.593442 TCCCTGTATAGGCCCAATTTG 57.407 47.619 0.00 0.00 43.16 2.32
1998 2302 6.777580 CCTGTATAGGCCCAATTTGTTATCTT 59.222 38.462 0.00 0.00 37.25 2.40
2003 2307 5.003160 AGGCCCAATTTGTTATCTTTTTGC 58.997 37.500 0.00 0.00 0.00 3.68
2004 2308 5.003160 GGCCCAATTTGTTATCTTTTTGCT 58.997 37.500 0.00 0.00 0.00 3.91
2273 2583 3.364964 CGCAGCTAACAAGTAAGTTTGGG 60.365 47.826 0.00 0.00 33.07 4.12
2325 2635 2.355818 CCTCTACCCCTTTTAGTGCCAC 60.356 54.545 0.00 0.00 0.00 5.01
2462 2772 0.253044 TTGATTCTTCCCGGCTGGAG 59.747 55.000 15.09 3.01 46.24 3.86
2485 2795 3.969976 ACACTCTGTGTATATGGAGGCAT 59.030 43.478 1.12 0.00 45.56 4.40
2593 2903 3.496130 AGACGTGCTCTGAATTTGTCAAG 59.504 43.478 0.00 0.00 35.22 3.02
2654 2964 2.029918 GTCAGTGGGTTTTGATGAAGCC 60.030 50.000 0.00 0.00 45.23 4.35
2793 3103 4.082245 TCGATCTTGTGAGTGATGCTTACA 60.082 41.667 0.00 0.00 41.19 2.41
2809 3119 5.743467 TGCTTACACATGTTTTACTGAACG 58.257 37.500 0.00 0.00 32.18 3.95
2880 3190 8.885722 CCTTATTTGTCATGCATTTGCTATTTT 58.114 29.630 0.00 0.00 42.66 1.82
2893 3204 8.392612 GCATTTGCTATTTTGACTTGCATTTAT 58.607 29.630 0.00 0.00 38.21 1.40
2933 3244 9.601971 GTAACTTCAATTTTGTTATGTTCGCTA 57.398 29.630 0.00 0.00 0.00 4.26
3345 3660 5.068215 AGCTAGCAGAAGGGATTAGTCTA 57.932 43.478 18.83 0.00 0.00 2.59
3430 3745 6.465084 AGGATGTTTTCTCTGTAGTACCAAC 58.535 40.000 0.00 0.00 0.00 3.77
3589 3907 4.464951 TGTCATACACTATGGGTCGAAGTT 59.535 41.667 0.00 0.00 36.81 2.66
3665 3983 1.073125 TCAAGGATTTCGTGAAGGGCA 59.927 47.619 0.00 0.00 31.17 5.36
3741 4059 7.382218 CCAAATGTTGATCTGGTTAGTGTTTTC 59.618 37.037 0.00 0.00 0.00 2.29
3758 4076 5.593095 GTGTTTTCCTGTCCTTTCCTTTACT 59.407 40.000 0.00 0.00 0.00 2.24
4003 4323 1.071385 GTCAGGGGCATCGAGAATGAT 59.929 52.381 0.00 0.00 37.59 2.45
4043 4363 3.623510 GGAGGTGAGATTTTCCGTCATTC 59.376 47.826 0.00 0.00 0.00 2.67
4144 4464 4.780815 TGAAGGTTCTGACTTGACAATGT 58.219 39.130 0.00 0.00 0.00 2.71
4154 4474 5.680619 TGACTTGACAATGTCTAGTGGTTT 58.319 37.500 29.14 9.42 45.33 3.27
4164 4484 6.877611 ATGTCTAGTGGTTTTGATTCGTTT 57.122 33.333 0.00 0.00 0.00 3.60
4227 4547 3.670377 GGCCGCAGTGGTGGTTTC 61.670 66.667 0.89 0.00 46.76 2.78
4229 4549 2.590575 CCGCAGTGGTGGTTTCGT 60.591 61.111 0.00 0.00 39.94 3.85
4239 4559 2.093394 TGGTGGTTTCGTCAACTCTTCA 60.093 45.455 1.24 0.00 35.46 3.02
4272 4592 0.885879 GGTTTGGTGATTCCGGGTTC 59.114 55.000 0.00 0.00 39.52 3.62
4356 4682 2.290287 CCGATCAGGTGGTGGTGGA 61.290 63.158 0.00 0.00 34.51 4.02
4516 4887 3.055240 CCCATAGCCCAGCAAATTTTTGA 60.055 43.478 7.21 0.00 40.55 2.69
4572 4943 5.586243 CGGCTTGATGGTTCTTATATATGGG 59.414 44.000 0.00 0.00 0.00 4.00
4576 4947 7.885399 GCTTGATGGTTCTTATATATGGGAAGT 59.115 37.037 0.00 0.00 0.00 3.01
4581 4952 7.313731 TGGTTCTTATATATGGGAAGTCCTCT 58.686 38.462 0.00 0.00 36.20 3.69
4587 4958 4.762289 ATATGGGAAGTCCTCTTGTCAC 57.238 45.455 0.00 0.00 36.20 3.67
4656 5028 4.492570 CGAATTTCTAGCGTGGACAACATC 60.493 45.833 0.00 0.00 0.00 3.06
4657 5029 1.990799 TTCTAGCGTGGACAACATCG 58.009 50.000 0.00 0.00 0.00 3.84
4676 5048 2.575805 GGCTTATATTGCCTGGAGCT 57.424 50.000 10.95 0.00 46.38 4.09
4873 5246 6.423182 CCTTTTGTGGACCTTATCTAATGGA 58.577 40.000 0.00 0.00 0.00 3.41
4881 5254 5.130477 GGACCTTATCTAATGGACCAGAACA 59.870 44.000 0.00 0.00 36.10 3.18
4882 5255 6.352737 GGACCTTATCTAATGGACCAGAACAA 60.353 42.308 0.00 0.00 36.10 2.83
4904 5277 8.261492 ACAATAGTCTCTAGAAGCAAATGTTG 57.739 34.615 0.00 0.00 0.00 3.33
5002 5375 4.935808 CAGGTGATGGTTTAGTCCTTGTAC 59.064 45.833 0.00 0.00 0.00 2.90
5011 5384 6.183360 TGGTTTAGTCCTTGTACTTGCAAAAG 60.183 38.462 0.00 0.73 0.00 2.27
5012 5385 3.990318 AGTCCTTGTACTTGCAAAAGC 57.010 42.857 0.00 0.00 0.00 3.51
5014 5387 3.891366 AGTCCTTGTACTTGCAAAAGCAT 59.109 39.130 0.00 0.00 0.00 3.79
5058 5437 4.321899 GCAATGGAGGTGCAAATTTAGTCA 60.322 41.667 0.00 0.00 41.80 3.41
5076 5455 3.119291 GTCATAGACCAATCACAGCTCG 58.881 50.000 0.00 0.00 0.00 5.03
5141 5521 1.384191 CACTTAGCCCCCTGCCTTT 59.616 57.895 0.00 0.00 42.71 3.11
5229 5609 1.541147 CTCGCTGATCATCTCCTCTCC 59.459 57.143 0.00 0.00 0.00 3.71
5323 5703 0.250513 GGGAGTAGCCACTTGAGGTG 59.749 60.000 0.00 0.00 44.96 4.00
5324 5704 0.391793 GGAGTAGCCACTTGAGGTGC 60.392 60.000 0.00 0.00 44.08 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 9.007901 TCAAAAGTGTTCATGGTTTTTGAAAAT 57.992 25.926 14.97 0.00 41.84 1.82
70 71 1.026718 GGGACAGGTTTGCATCGAGG 61.027 60.000 0.00 0.00 0.00 4.63
90 91 5.069781 TCGACCCATTTTCACTCCAAAATTT 59.930 36.000 0.00 0.00 34.37 1.82
93 94 3.556999 TCGACCCATTTTCACTCCAAAA 58.443 40.909 0.00 0.00 0.00 2.44
196 198 1.700739 ACGGACCCATTTTGTCTGGTA 59.299 47.619 4.45 0.00 42.26 3.25
197 199 0.476771 ACGGACCCATTTTGTCTGGT 59.523 50.000 4.45 0.00 42.26 4.00
296 301 3.141398 GTTCCTGAGCTTCACAATGTCA 58.859 45.455 0.00 0.00 0.00 3.58
299 304 5.426504 AGATAGTTCCTGAGCTTCACAATG 58.573 41.667 0.00 0.00 0.00 2.82
384 389 9.450807 AAAACATGCTCAAATTTATATAGCGTC 57.549 29.630 0.00 0.00 35.95 5.19
464 728 0.972883 TTTCTTTTGAATGGGCCGGG 59.027 50.000 2.18 0.00 38.37 5.73
486 750 2.401766 GGCTGCTGAATGTCGTGGG 61.402 63.158 0.00 0.00 0.00 4.61
499 763 1.663379 GGTTATTTCCCGTGGGCTGC 61.663 60.000 0.00 0.00 34.68 5.25
514 778 0.913205 TTATTGCTCGGCTGGGGTTA 59.087 50.000 0.00 0.00 0.00 2.85
520 784 3.425422 GGGCTTATTGCTCGGCTG 58.575 61.111 0.00 0.00 42.39 4.85
581 846 7.227910 GCGAATGGTAGGAAAAGGTTTATGATA 59.772 37.037 0.00 0.00 0.00 2.15
582 847 6.039382 GCGAATGGTAGGAAAAGGTTTATGAT 59.961 38.462 0.00 0.00 0.00 2.45
602 867 2.351276 GGGTGTCAGTGGGCGAAT 59.649 61.111 0.00 0.00 0.00 3.34
677 942 0.609957 TGAAGAGGTTACGCGGGAGA 60.610 55.000 12.47 0.00 0.00 3.71
775 1040 1.439644 GTCAGGAGGTCAGCGATCC 59.560 63.158 0.00 0.00 0.00 3.36
777 1042 2.060980 GGGTCAGGAGGTCAGCGAT 61.061 63.158 0.00 0.00 0.00 4.58
779 1044 3.775654 GGGGTCAGGAGGTCAGCG 61.776 72.222 0.00 0.00 0.00 5.18
781 1046 2.294078 GGTGGGGTCAGGAGGTCAG 61.294 68.421 0.00 0.00 0.00 3.51
847 1112 0.033504 GATATTTCTGCGGCTCCGGA 59.966 55.000 2.93 2.93 40.19 5.14
876 1141 2.445525 GAGGGAATGGGGTTAATAGGCA 59.554 50.000 0.00 0.00 0.00 4.75
915 1188 2.284151 GGAGGAGGAGGAGGGGAC 59.716 72.222 0.00 0.00 0.00 4.46
918 1191 2.612251 GGAGGAGGAGGAGGAGGG 59.388 72.222 0.00 0.00 0.00 4.30
919 1192 2.612251 GGGAGGAGGAGGAGGAGG 59.388 72.222 0.00 0.00 0.00 4.30
921 1194 2.204624 TGGGGAGGAGGAGGAGGA 60.205 66.667 0.00 0.00 0.00 3.71
1437 1722 6.594159 CAGGAAGTAGTAATCACGTTCCAATT 59.406 38.462 0.00 0.00 36.83 2.32
1458 1744 3.299977 CCACCGACGACCACAGGA 61.300 66.667 0.00 0.00 0.00 3.86
1462 1748 0.601841 AACAATCCACCGACGACCAC 60.602 55.000 0.00 0.00 0.00 4.16
1464 1750 0.515564 CAAACAATCCACCGACGACC 59.484 55.000 0.00 0.00 0.00 4.79
1465 1751 0.110373 GCAAACAATCCACCGACGAC 60.110 55.000 0.00 0.00 0.00 4.34
1471 1757 1.815003 CCAGAGAGCAAACAATCCACC 59.185 52.381 0.00 0.00 0.00 4.61
1498 1784 1.068402 TGTGCACCAATCAATCAAGCG 60.068 47.619 15.69 0.00 0.00 4.68
1580 1866 8.230472 AGCTATGCTCAAAATTAATTAGCTGT 57.770 30.769 17.91 11.44 36.05 4.40
1609 1895 1.320344 ACATCGGAGCAAGCCTCGTA 61.320 55.000 4.96 0.00 41.71 3.43
1611 1897 2.169789 CACATCGGAGCAAGCCTCG 61.170 63.158 0.00 0.00 41.71 4.63
1689 1984 1.016130 AAGATCACAGTTGCCTCGCG 61.016 55.000 0.00 0.00 0.00 5.87
1712 2007 4.005650 ACATCTGTGCATTCAGAACGAAT 58.994 39.130 10.71 0.00 45.65 3.34
1822 2124 3.501828 ACTGCTGAACAATATCACGCAAA 59.498 39.130 0.00 0.00 35.00 3.68
1887 2189 0.436531 CAAGAGAAAGTGACGCGAGC 59.563 55.000 15.93 4.68 0.00 5.03
1889 2191 1.066454 TCACAAGAGAAAGTGACGCGA 59.934 47.619 15.93 0.00 39.65 5.87
1983 2287 6.147656 GGTGAGCAAAAAGATAACAAATTGGG 59.852 38.462 0.00 0.00 0.00 4.12
1991 2295 8.915654 CAACATAAAGGTGAGCAAAAAGATAAC 58.084 33.333 0.00 0.00 36.95 1.89
1998 2302 5.843673 TGACAACATAAAGGTGAGCAAAA 57.156 34.783 0.00 0.00 36.95 2.44
2003 2307 7.439157 TTGAAGATGACAACATAAAGGTGAG 57.561 36.000 0.00 0.00 36.95 3.51
2004 2308 9.685276 ATATTGAAGATGACAACATAAAGGTGA 57.315 29.630 0.00 0.00 36.95 4.02
2084 2392 4.420522 AACATCCAAAACACAAGGCATT 57.579 36.364 0.00 0.00 0.00 3.56
2325 2635 4.133820 TGAGGTGACAATACAACACAAGG 58.866 43.478 0.00 0.00 36.42 3.61
2462 2772 3.384789 TGCCTCCATATACACAGAGTGTC 59.615 47.826 6.00 0.00 43.92 3.67
2485 2795 5.302568 ACTCTCATTTGTTGCTGAATTGGAA 59.697 36.000 0.00 0.00 0.00 3.53
2593 2903 2.933906 TCGAGAACAACAAACTGGACAC 59.066 45.455 0.00 0.00 0.00 3.67
2654 2964 5.897518 CACATTTTGCAAAATTGTCTCAACG 59.102 36.000 30.13 19.12 36.52 4.10
2793 3103 2.616376 TGCAGCGTTCAGTAAAACATGT 59.384 40.909 0.00 0.00 0.00 3.21
2809 3119 4.426416 TGCAATGAAATCATAGTTGCAGC 58.574 39.130 15.30 0.00 40.56 5.25
2933 3244 3.086282 ACAACAAAAGTCCGAACCAACT 58.914 40.909 0.00 0.00 0.00 3.16
3298 3613 2.432510 GGTCATCTTCACCCACCTAGAG 59.567 54.545 0.00 0.00 0.00 2.43
3345 3660 7.172875 GCATGATTCTCTGTAGCAATAGACAAT 59.827 37.037 0.00 0.00 0.00 2.71
3393 3708 4.525912 AAACATCCTTGCCTGAATCAAC 57.474 40.909 0.00 0.00 0.00 3.18
3445 3761 7.095060 TGCAGAAAGAAACTTAGATAGCACTTG 60.095 37.037 0.00 0.00 0.00 3.16
3589 3907 1.423584 TGAAGAGCCTGACACTGGAA 58.576 50.000 0.00 0.00 0.00 3.53
3665 3983 7.759489 TCAGTGGCAATCAAAGTATTAAAGT 57.241 32.000 0.00 0.00 0.00 2.66
3741 4059 6.096282 TGACAAAAAGTAAAGGAAAGGACAGG 59.904 38.462 0.00 0.00 0.00 4.00
3790 4108 6.441093 TGAGATAATGTTGCCAGCTTTAAG 57.559 37.500 0.00 0.00 0.00 1.85
3830 4148 2.059490 ACACAGCCAGTAAGGGGTTTA 58.941 47.619 0.00 0.00 36.26 2.01
4003 4323 3.486383 CTCCTTAAACTTGCCTCCAACA 58.514 45.455 0.00 0.00 0.00 3.33
4043 4363 1.983972 AAACTCGAGCAGCGACTTAG 58.016 50.000 13.61 0.00 45.59 2.18
4096 4416 3.084039 TGATCTTTGGAAGCTGCGAAAT 58.916 40.909 1.89 0.00 0.00 2.17
4144 4464 5.369833 TCCAAACGAATCAAAACCACTAGA 58.630 37.500 0.00 0.00 0.00 2.43
4154 4474 2.552155 CCTCCACCTCCAAACGAATCAA 60.552 50.000 0.00 0.00 0.00 2.57
4164 4484 2.122729 CCTCCACCTCCACCTCCA 59.877 66.667 0.00 0.00 0.00 3.86
4216 4536 1.485066 AGAGTTGACGAAACCACCACT 59.515 47.619 0.00 0.00 39.85 4.00
4227 4547 2.064762 CCTCTGCTTGAAGAGTTGACG 58.935 52.381 0.00 0.00 41.89 4.35
4229 4549 2.224378 CCACCTCTGCTTGAAGAGTTGA 60.224 50.000 4.93 0.00 38.60 3.18
4239 4559 3.133365 AAACCCGCCACCTCTGCTT 62.133 57.895 0.00 0.00 0.00 3.91
4272 4592 2.357034 CCACCACCTGAACGACCG 60.357 66.667 0.00 0.00 0.00 4.79
4356 4682 1.548582 CCACCACTTGAGCCAAATCCT 60.549 52.381 0.00 0.00 0.00 3.24
4516 4887 1.678970 GGTTGCCTTCCGCTCCAAT 60.679 57.895 0.00 0.00 38.78 3.16
4549 4920 6.721318 TCCCATATATAAGAACCATCAAGCC 58.279 40.000 0.00 0.00 0.00 4.35
4581 4952 8.458573 ACATGTTAATTTACCTCTTGTGACAA 57.541 30.769 0.00 0.00 0.00 3.18
4587 4958 9.994432 GAATCAGACATGTTAATTTACCTCTTG 57.006 33.333 0.00 0.00 0.00 3.02
4749 5121 7.447238 GCATATATTTTACAAGGAACCCTGCTA 59.553 37.037 0.00 0.00 32.13 3.49
4873 5246 5.717178 TGCTTCTAGAGACTATTGTTCTGGT 59.283 40.000 0.00 0.00 0.00 4.00
4881 5254 8.535335 TCTCAACATTTGCTTCTAGAGACTATT 58.465 33.333 0.00 0.00 0.00 1.73
4882 5255 8.072321 TCTCAACATTTGCTTCTAGAGACTAT 57.928 34.615 0.00 0.00 0.00 2.12
4904 5277 6.979817 GTCATGGTATCTGATGCATAGATCTC 59.020 42.308 16.86 12.85 36.38 2.75
5011 5384 6.865205 GCAAGTTCAGGGATGAAATAATATGC 59.135 38.462 0.00 0.00 0.00 3.14
5012 5385 7.944061 TGCAAGTTCAGGGATGAAATAATATG 58.056 34.615 0.00 0.00 0.00 1.78
5014 5387 7.953005 TTGCAAGTTCAGGGATGAAATAATA 57.047 32.000 0.00 0.00 0.00 0.98
5058 5437 1.202580 GGCGAGCTGTGATTGGTCTAT 60.203 52.381 0.00 0.00 0.00 1.98
5076 5455 1.588082 CACTTGGCATCCAGTTGGC 59.412 57.895 0.00 0.00 42.20 4.52
5141 5521 1.173043 CTGCGGGTTGATAAGGCAAA 58.827 50.000 0.00 0.00 32.59 3.68
5323 5703 3.775654 CCACCCCTCCGTCTCTGC 61.776 72.222 0.00 0.00 0.00 4.26
5324 5704 1.913762 AACCACCCCTCCGTCTCTG 60.914 63.158 0.00 0.00 0.00 3.35
5367 5747 1.448717 GGAGAGAGAAAGCACCGGC 60.449 63.158 0.00 0.00 41.61 6.13
5368 5748 0.539051 ATGGAGAGAGAAAGCACCGG 59.461 55.000 0.00 0.00 0.00 5.28
5369 5749 1.205655 TCATGGAGAGAGAAAGCACCG 59.794 52.381 0.00 0.00 0.00 4.94
5370 5750 3.557228 ATCATGGAGAGAGAAAGCACC 57.443 47.619 0.00 0.00 0.00 5.01
5371 5751 4.260170 ACAATCATGGAGAGAGAAAGCAC 58.740 43.478 0.00 0.00 0.00 4.40
5438 5818 3.287222 TGAAGAACCAAAGTGGGAACAG 58.713 45.455 0.00 0.00 43.37 3.16


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

AutoCloner maintained by Alex Coulton.