Multiple sequence alignment - TraesCS1A01G417400

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 TraesCS1A01G417400 chr1A 100.000 6658 0 0 1 6658 575362382 575369039 0.000000e+00 12296
1 TraesCS1A01G417400 chr1D 95.262 5867 169 35 1 5811 479048836 479054649 0.000000e+00 9193
2 TraesCS1A01G417400 chr1D 87.059 765 51 24 5880 6606 479054649 479055403 0.000000e+00 821
3 TraesCS1A01G417400 chr1B 95.811 4679 132 33 1 4631 667223720 667228382 0.000000e+00 7496
4 TraesCS1A01G417400 chr1B 91.358 1863 122 24 4629 6462 667228486 667230338 0.000000e+00 2512
5 TraesCS1A01G417400 chr1B 93.732 351 21 1 2981 3330 121768910 121769260 5.910000e-145 525
6 TraesCS1A01G417400 chr1B 88.546 227 24 1 2015 2241 121768279 121768503 2.370000e-69 274
7 TraesCS1A01G417400 chr3B 90.078 514 46 5 646 1158 34547527 34547018 0.000000e+00 662
8 TraesCS1A01G417400 chr3B 89.844 512 45 7 643 1152 35541541 35542047 0.000000e+00 651
9 TraesCS1A01G417400 chr3B 89.494 514 49 5 643 1155 35725582 35726091 0.000000e+00 645
10 TraesCS1A01G417400 chr3B 89.300 514 50 5 643 1155 35513552 35514061 2.020000e-179 640
11 TraesCS1A01G417400 chr3B 89.300 514 50 5 643 1155 35797272 35797781 2.020000e-179 640
12 TraesCS1A01G417400 chr3B 91.477 176 15 0 1833 2008 34492878 34492703 6.670000e-60 243
13 TraesCS1A01G417400 chrUn 89.494 514 49 5 646 1158 286898238 286897729 0.000000e+00 645
14 TraesCS1A01G417400 chrUn 89.494 514 49 5 643 1155 378043938 378044447 0.000000e+00 645
15 TraesCS1A01G417400 chrUn 90.960 177 16 0 1832 2008 202812069 202811893 8.630000e-59 239
16 TraesCS1A01G417400 chrUn 90.960 177 16 0 1832 2008 241051651 241051475 8.630000e-59 239
17 TraesCS1A01G417400 chr4B 94.587 351 18 1 2981 3330 409740397 409740747 5.870000e-150 542
18 TraesCS1A01G417400 chr4B 90.421 261 25 0 2015 2275 409740137 409740397 1.780000e-90 344
19 TraesCS1A01G417400 chr5A 86.282 277 33 4 1837 2109 693879032 693878757 5.050000e-76 296
20 TraesCS1A01G417400 chr3A 92.090 177 14 0 1832 2008 745025020 745025196 3.990000e-62 250
21 TraesCS1A01G417400 chr3A 92.090 177 14 0 1832 2008 745092058 745092234 3.990000e-62 250
22 TraesCS1A01G417400 chr7A 91.160 181 15 1 1832 2011 81680972 81680792 1.850000e-60 244


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 TraesCS1A01G417400 chr1A 575362382 575369039 6657 False 12296.0 12296 100.0000 1 6658 1 chr1A.!!$F1 6657
1 TraesCS1A01G417400 chr1D 479048836 479055403 6567 False 5007.0 9193 91.1605 1 6606 2 chr1D.!!$F1 6605
2 TraesCS1A01G417400 chr1B 667223720 667230338 6618 False 5004.0 7496 93.5845 1 6462 2 chr1B.!!$F2 6461
3 TraesCS1A01G417400 chr1B 121768279 121769260 981 False 399.5 525 91.1390 2015 3330 2 chr1B.!!$F1 1315
4 TraesCS1A01G417400 chr3B 34547018 34547527 509 True 662.0 662 90.0780 646 1158 1 chr3B.!!$R2 512
5 TraesCS1A01G417400 chr3B 35541541 35542047 506 False 651.0 651 89.8440 643 1152 1 chr3B.!!$F2 509
6 TraesCS1A01G417400 chr3B 35725582 35726091 509 False 645.0 645 89.4940 643 1155 1 chr3B.!!$F3 512
7 TraesCS1A01G417400 chr3B 35513552 35514061 509 False 640.0 640 89.3000 643 1155 1 chr3B.!!$F1 512
8 TraesCS1A01G417400 chr3B 35797272 35797781 509 False 640.0 640 89.3000 643 1155 1 chr3B.!!$F4 512
9 TraesCS1A01G417400 chrUn 286897729 286898238 509 True 645.0 645 89.4940 646 1158 1 chrUn.!!$R3 512
10 TraesCS1A01G417400 chrUn 378043938 378044447 509 False 645.0 645 89.4940 643 1155 1 chrUn.!!$F1 512
11 TraesCS1A01G417400 chr4B 409740137 409740747 610 False 443.0 542 92.5040 2015 3330 2 chr4B.!!$F1 1315

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
792 854 1.337260 ACTCCTGCTGTTGTTAGAGCG 60.337 52.381 0.00 0.00 43.30 5.03 F
1373 1437 0.969894 AGAGTGAACCAGTCCTTCCG 59.030 55.000 0.00 0.00 34.63 4.30 F
2048 2122 0.456312 AACGAGCGTCGGATTCAGAC 60.456 55.000 6.85 6.85 45.59 3.51 F
2793 3242 0.974010 CAGGGTGGGAGCATGCAAAT 60.974 55.000 21.98 0.00 0.00 2.32 F
4449 4904 2.108250 AGTTGCCAGGGTTCAGTTATGT 59.892 45.455 0.00 0.00 0.00 2.29 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2025 2099 0.731514 GAATCCGACGCTCGTTGACA 60.732 55.000 10.95 0.0 38.40 3.58 R
2793 3242 1.202915 TCATCAGCTGCAAAACCCTGA 60.203 47.619 9.47 0.0 38.54 3.86 R
3936 4388 1.066787 GGTGGTGCTAACAGAGGAGAC 60.067 57.143 0.00 0.0 0.00 3.36 R
4714 5275 0.032615 ACTTTGGTGGGCAGGTTTCA 60.033 50.000 0.00 0.0 0.00 2.69 R
5966 6570 1.065998 TGCTGTTATGTTACCGGGTCC 60.066 52.381 6.32 0.0 0.00 4.46 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
113 142 5.664294 TCATGTTTTAGGCTTACTCGGTA 57.336 39.130 0.00 0.00 0.00 4.02
179 208 3.442273 CCGGTTGCCACTGTATGTTTTAT 59.558 43.478 0.00 0.00 0.00 1.40
196 225 7.459795 TGTTTTATTGGTGTGCAATCATAGA 57.540 32.000 0.00 0.00 0.00 1.98
197 226 7.537715 TGTTTTATTGGTGTGCAATCATAGAG 58.462 34.615 0.00 0.00 0.00 2.43
381 424 7.023575 GTCAAATAGCCTTCTGTGTTGTAATG 58.976 38.462 0.00 0.00 0.00 1.90
384 427 8.511321 CAAATAGCCTTCTGTGTTGTAATGTTA 58.489 33.333 0.00 0.00 0.00 2.41
509 553 5.534654 AGAAATGTAAGCTTGTTGGTGCTAA 59.465 36.000 9.86 0.00 38.75 3.09
792 854 1.337260 ACTCCTGCTGTTGTTAGAGCG 60.337 52.381 0.00 0.00 43.30 5.03
959 1022 7.120432 GTCAGGGCAATGGATAAAATCTAGATC 59.880 40.741 5.51 0.00 0.00 2.75
1373 1437 0.969894 AGAGTGAACCAGTCCTTCCG 59.030 55.000 0.00 0.00 34.63 4.30
1776 1840 7.538575 AGCATGGTGTAAATAGAATTGTTGTC 58.461 34.615 0.00 0.00 0.00 3.18
1924 1988 1.822186 GGACCACTGCCACGTTGTT 60.822 57.895 0.00 0.00 0.00 2.83
1984 2048 6.209192 AGTGCTGTTACCATTGATGATTTGAA 59.791 34.615 0.00 0.00 0.00 2.69
2002 2066 9.684448 TGATTTGAATTGCAATTAACGTTCTTA 57.316 25.926 24.15 5.25 36.15 2.10
2011 2075 7.099666 GCAATTAACGTTCTTAACAATTGCA 57.900 32.000 32.07 3.84 46.52 4.08
2012 2076 7.559845 GCAATTAACGTTCTTAACAATTGCAA 58.440 30.769 32.07 0.00 46.52 4.08
2013 2077 8.220434 GCAATTAACGTTCTTAACAATTGCAAT 58.780 29.630 32.07 5.99 46.52 3.56
2048 2122 0.456312 AACGAGCGTCGGATTCAGAC 60.456 55.000 6.85 6.85 45.59 3.51
2058 2132 1.762957 CGGATTCAGACCCCACTATGT 59.237 52.381 0.00 0.00 0.00 2.29
2089 2163 4.568072 TGCTTGCCTGGACTATTTTCTA 57.432 40.909 0.00 0.00 0.00 2.10
2118 2192 7.475015 TGCAGCATTTTATGTTCTGATAGTTC 58.525 34.615 0.00 0.00 0.00 3.01
2132 2206 8.713271 GTTCTGATAGTTCTTTGACCTTACTTG 58.287 37.037 0.00 0.00 0.00 3.16
2137 2211 4.580580 AGTTCTTTGACCTTACTTGGCTTG 59.419 41.667 0.00 0.00 0.00 4.01
2140 2214 5.197451 TCTTTGACCTTACTTGGCTTGAAA 58.803 37.500 0.00 0.00 0.00 2.69
2301 2748 8.303876 TGTTTTGGAGTAATTTATTCTTCTGGC 58.696 33.333 0.00 0.00 0.00 4.85
2348 2796 7.472543 TCTGCTGTTCTTTCTACAAAAACTTC 58.527 34.615 0.00 0.00 0.00 3.01
2793 3242 0.974010 CAGGGTGGGAGCATGCAAAT 60.974 55.000 21.98 0.00 0.00 2.32
2866 3315 6.183360 GGGGAGAATAGCATCAAAGAGAAAAC 60.183 42.308 0.00 0.00 0.00 2.43
2877 3326 4.678743 AGAAAACCCGGGCCTGGC 62.679 66.667 26.87 11.05 0.00 4.85
2901 3350 6.683883 CAAAACAGCTAATACTACTTCGACG 58.316 40.000 0.00 0.00 0.00 5.12
2978 3427 4.019321 TGTCCAAGTAAAGCCTGCTTCTAT 60.019 41.667 4.63 0.00 34.84 1.98
3099 3548 2.610438 ATGGCATTCCACCAGAAAGT 57.390 45.000 0.00 0.00 46.92 2.66
3330 3780 2.183679 AGAATCTCTGCGAAACCTCCT 58.816 47.619 0.00 0.00 0.00 3.69
3868 4320 5.463154 TGGAAAAGAAAATTTCTGGGGAGA 58.537 37.500 9.21 0.00 40.59 3.71
4234 4688 5.368256 AATGAAAGCTACTCTTGCACTTG 57.632 39.130 0.00 0.00 42.95 3.16
4258 4712 7.174413 TGTTTGATGTTATCCTTTGGATCTCA 58.826 34.615 1.98 4.61 42.11 3.27
4265 4719 2.348472 TCCTTTGGATCTCAACCCTGT 58.652 47.619 0.00 0.00 34.67 4.00
4322 4776 7.762615 CACAAGCACATTCCATCTTGAAAATAT 59.237 33.333 7.69 0.00 39.22 1.28
4371 4825 7.149307 TGTGCTATATTAATACGCTACTGCAA 58.851 34.615 15.58 0.00 39.64 4.08
4408 4863 8.902540 TGATCTTTATTCAGTTACACACAGTT 57.097 30.769 0.00 0.00 0.00 3.16
4449 4904 2.108250 AGTTGCCAGGGTTCAGTTATGT 59.892 45.455 0.00 0.00 0.00 2.29
4707 5268 4.921515 TGTGACTGCGAGTATTGTTTAGAC 59.078 41.667 0.00 0.00 0.00 2.59
4708 5269 4.921515 GTGACTGCGAGTATTGTTTAGACA 59.078 41.667 0.00 0.00 0.00 3.41
4714 5275 4.495422 CGAGTATTGTTTAGACAGTGGCT 58.505 43.478 2.72 2.72 37.04 4.75
4731 5292 1.398958 GCTGAAACCTGCCCACCAAA 61.399 55.000 0.00 0.00 0.00 3.28
4810 5376 9.362151 ACTCTAATTTTGGTCTTTGTTTGGATA 57.638 29.630 0.00 0.00 0.00 2.59
4877 5443 6.029346 AGTTCATTTTCCTTGCCAACATAG 57.971 37.500 0.00 0.00 0.00 2.23
4902 5468 5.239306 CCGATGCCAAACATAATCTGTACAT 59.761 40.000 0.00 0.00 39.84 2.29
5045 5642 5.368145 ACTTGTGCTAACTTTGACTGATCA 58.632 37.500 0.00 0.00 0.00 2.92
5255 5859 0.736325 GCTCGGCTTGTGTGACGTAT 60.736 55.000 0.00 0.00 0.00 3.06
5363 5967 4.968719 TCTCCTGGCTCTAATAACCAATCA 59.031 41.667 0.00 0.00 31.81 2.57
5365 5969 6.101734 TCTCCTGGCTCTAATAACCAATCAAT 59.898 38.462 0.00 0.00 31.81 2.57
5496 6100 0.698238 TGGTACAGCAGCCATTCCTT 59.302 50.000 0.00 0.00 0.00 3.36
5591 6195 6.482641 CCAGTTCCTCTCTATCATCAAATGTG 59.517 42.308 0.00 0.00 0.00 3.21
5642 6246 1.276622 ATGCCGTCTTTACAGACCCT 58.723 50.000 3.46 0.00 46.19 4.34
5649 6253 3.139077 GTCTTTACAGACCCTGGTGTTG 58.861 50.000 0.00 0.00 43.50 3.33
5651 6255 0.250124 TTACAGACCCTGGTGTTGCG 60.250 55.000 0.00 0.00 35.51 4.85
5691 6295 6.618379 GCACTTTTTGTTGGAAAAGAGTTGTG 60.618 38.462 14.83 6.22 45.20 3.33
5717 6321 7.821846 GGTTCATGGCAAGGTTTGAAATATTTA 59.178 33.333 0.00 0.00 30.51 1.40
5720 6324 9.956640 TCATGGCAAGGTTTGAAATATTTATTT 57.043 25.926 0.00 0.00 38.51 1.40
5811 6415 9.565213 CTGTTGAATAGTTTGAAGGAAATCATC 57.435 33.333 0.00 0.00 0.00 2.92
5856 6460 3.131709 GCAGAATAGCTGGCAGGATTA 57.868 47.619 17.64 0.00 45.03 1.75
5870 6474 7.308229 GCTGGCAGGATTAAAGTATGACATAAG 60.308 40.741 17.64 0.00 0.00 1.73
5871 6475 6.486657 TGGCAGGATTAAAGTATGACATAAGC 59.513 38.462 0.00 0.00 0.00 3.09
5873 6477 7.229506 GGCAGGATTAAAGTATGACATAAGCTT 59.770 37.037 3.48 3.48 0.00 3.74
5888 6492 7.227314 TGACATAAGCTTGTGATTTAGCATAGG 59.773 37.037 27.54 0.00 39.85 2.57
5890 6494 7.443575 ACATAAGCTTGTGATTTAGCATAGGAG 59.556 37.037 27.54 0.00 39.85 3.69
5917 6521 0.675837 CTCAGGTGATGTGCAGGGTG 60.676 60.000 0.00 0.00 0.00 4.61
5956 6560 3.500343 CCAAGTGGTTCCCTCAGATTTT 58.500 45.455 0.00 0.00 0.00 1.82
5966 6570 8.856103 TGGTTCCCTCAGATTTTTAGTTTTTAG 58.144 33.333 0.00 0.00 0.00 1.85
5985 6589 1.208776 AGGACCCGGTAACATAACAGC 59.791 52.381 0.00 0.00 0.00 4.40
5997 6601 8.495949 CGGTAACATAACAGCAATATTTCTAGG 58.504 37.037 0.00 0.00 0.00 3.02
6001 6605 7.512992 ACATAACAGCAATATTTCTAGGAGCT 58.487 34.615 0.00 0.00 0.00 4.09
6073 6679 4.998788 TGGAGTCTAATTCAGATCGTGTG 58.001 43.478 0.00 0.00 35.17 3.82
6075 6681 4.800993 GGAGTCTAATTCAGATCGTGTGTG 59.199 45.833 0.00 0.00 35.17 3.82
6077 6683 4.081972 AGTCTAATTCAGATCGTGTGTGCT 60.082 41.667 0.00 0.00 35.17 4.40
6093 6699 8.279800 TCGTGTGTGCTATATAAATATGCAAAC 58.720 33.333 14.39 14.39 36.56 2.93
6152 6766 4.097892 CGGTTCCAGCTGCCTTTATTTATT 59.902 41.667 8.66 0.00 0.00 1.40
6181 6796 6.071320 AGGAAAATATGTTCTCCCTAATGCC 58.929 40.000 5.61 0.00 0.00 4.40
6211 6826 3.008813 AGTTGCCTATCAGCTATCATGGG 59.991 47.826 0.00 0.00 34.29 4.00
6231 6846 4.039488 TGGGACGTTAGTGTACATTGTTCT 59.961 41.667 0.00 0.00 0.00 3.01
6232 6847 4.387862 GGGACGTTAGTGTACATTGTTCTG 59.612 45.833 0.00 0.00 0.00 3.02
6262 6877 4.330250 ACAGTAAAGCTCAGTAGGTACGA 58.670 43.478 0.00 0.00 31.75 3.43
6263 6878 4.395542 ACAGTAAAGCTCAGTAGGTACGAG 59.604 45.833 0.00 0.00 31.75 4.18
6349 6971 5.163893 CGGAAATATTGTGTAAACGAGCTGT 60.164 40.000 0.00 0.00 0.00 4.40
6360 6982 6.311935 GTGTAAACGAGCTGTTGGTTGATATA 59.688 38.462 0.00 0.00 40.84 0.86
6396 7018 5.062308 GGTGTCGATTTTTGTAGCAGACTAG 59.938 44.000 0.00 0.00 0.00 2.57
6422 7044 2.380941 TGCTTGTGCATTGCTATGGAT 58.619 42.857 10.49 0.00 45.31 3.41
6427 7049 4.898829 TGTGCATTGCTATGGATGTTAC 57.101 40.909 10.49 0.00 34.44 2.50
6430 7052 6.118852 TGTGCATTGCTATGGATGTTACTAA 58.881 36.000 10.49 0.00 34.44 2.24
6431 7053 6.601217 TGTGCATTGCTATGGATGTTACTAAA 59.399 34.615 10.49 0.00 34.44 1.85
6452 7074 1.464608 CACTTGTGCCACCATAGTTCG 59.535 52.381 0.00 0.00 0.00 3.95
6533 7178 8.576442 CCAATCAACCATATGTAGGGTAATTTC 58.424 37.037 1.24 0.00 39.84 2.17
6569 7214 2.894126 AGAGATGAACTGAACGTCACCT 59.106 45.455 0.00 0.00 0.00 4.00
6573 7218 3.088194 TGAACTGAACGTCACCTACAC 57.912 47.619 0.00 0.00 0.00 2.90
6633 7280 3.825143 AAAAAGTGTTCATGCCTGCTT 57.175 38.095 0.00 0.00 0.00 3.91
6634 7281 3.825143 AAAAGTGTTCATGCCTGCTTT 57.175 38.095 0.00 0.00 0.00 3.51
6635 7282 3.825143 AAAGTGTTCATGCCTGCTTTT 57.175 38.095 0.00 0.00 0.00 2.27
6636 7283 4.935352 AAAGTGTTCATGCCTGCTTTTA 57.065 36.364 0.00 0.00 0.00 1.52
6637 7284 5.473066 AAAGTGTTCATGCCTGCTTTTAT 57.527 34.783 0.00 0.00 0.00 1.40
6638 7285 5.473066 AAGTGTTCATGCCTGCTTTTATT 57.527 34.783 0.00 0.00 0.00 1.40
6639 7286 6.588719 AAGTGTTCATGCCTGCTTTTATTA 57.411 33.333 0.00 0.00 0.00 0.98
6640 7287 6.780457 AGTGTTCATGCCTGCTTTTATTAT 57.220 33.333 0.00 0.00 0.00 1.28
6641 7288 7.174107 AGTGTTCATGCCTGCTTTTATTATT 57.826 32.000 0.00 0.00 0.00 1.40
6642 7289 8.292444 AGTGTTCATGCCTGCTTTTATTATTA 57.708 30.769 0.00 0.00 0.00 0.98
6643 7290 8.748412 AGTGTTCATGCCTGCTTTTATTATTAA 58.252 29.630 0.00 0.00 0.00 1.40
6644 7291 9.023967 GTGTTCATGCCTGCTTTTATTATTAAG 57.976 33.333 0.00 0.00 0.00 1.85
6645 7292 8.196771 TGTTCATGCCTGCTTTTATTATTAAGG 58.803 33.333 0.00 0.00 0.00 2.69
6646 7293 7.896383 TCATGCCTGCTTTTATTATTAAGGT 57.104 32.000 0.00 0.00 0.00 3.50
6647 7294 7.940850 TCATGCCTGCTTTTATTATTAAGGTC 58.059 34.615 0.00 0.00 0.00 3.85
6648 7295 6.709018 TGCCTGCTTTTATTATTAAGGTCC 57.291 37.500 0.00 0.00 0.00 4.46
6649 7296 6.431722 TGCCTGCTTTTATTATTAAGGTCCT 58.568 36.000 0.00 0.00 0.00 3.85
6650 7297 7.579105 TGCCTGCTTTTATTATTAAGGTCCTA 58.421 34.615 0.00 0.00 0.00 2.94
6651 7298 8.224720 TGCCTGCTTTTATTATTAAGGTCCTAT 58.775 33.333 0.00 0.00 0.00 2.57
6652 7299 9.078990 GCCTGCTTTTATTATTAAGGTCCTATT 57.921 33.333 0.00 0.00 0.00 1.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 142 1.273606 CTGACTGGACATTCTCACGGT 59.726 52.381 0.00 0.00 0.00 4.83
179 208 3.609853 GTCCTCTATGATTGCACACCAA 58.390 45.455 0.00 0.00 37.94 3.67
196 225 2.904434 AGTGGTTACTCATTTCGGTCCT 59.096 45.455 0.00 0.00 28.79 3.85
197 226 3.329929 AGTGGTTACTCATTTCGGTCC 57.670 47.619 0.00 0.00 28.79 4.46
381 424 5.804979 TGCGTACGGAAGGTAAAACTATAAC 59.195 40.000 18.39 0.00 31.61 1.89
384 427 4.176271 GTGCGTACGGAAGGTAAAACTAT 58.824 43.478 18.39 0.00 31.61 2.12
976 1039 1.157870 ACGATAAGCAAATCCGCGGG 61.158 55.000 27.83 10.44 36.85 6.13
1776 1840 3.181482 ACAGACTGACCTGCATATCTTCG 60.181 47.826 10.08 0.00 37.68 3.79
1924 1988 5.617528 TTCAAGGCTACGGTTATATTGGA 57.382 39.130 0.00 0.00 0.00 3.53
1984 2048 8.220434 GCAATTGTTAAGAACGTTAATTGCAAT 58.780 29.630 32.07 23.77 46.52 3.56
2002 2066 7.940850 ACACTACTCAGTTAATTGCAATTGTT 58.059 30.769 30.43 15.04 30.46 2.83
2008 2072 5.176774 CGTTGACACTACTCAGTTAATTGCA 59.823 40.000 0.00 0.00 30.46 4.08
2009 2073 5.404366 TCGTTGACACTACTCAGTTAATTGC 59.596 40.000 0.00 0.00 30.46 3.56
2011 2075 5.634020 GCTCGTTGACACTACTCAGTTAATT 59.366 40.000 0.00 0.00 30.46 1.40
2012 2076 5.162075 GCTCGTTGACACTACTCAGTTAAT 58.838 41.667 0.00 0.00 30.46 1.40
2013 2077 4.543692 GCTCGTTGACACTACTCAGTTAA 58.456 43.478 0.00 0.00 30.46 2.01
2025 2099 0.731514 GAATCCGACGCTCGTTGACA 60.732 55.000 10.95 0.00 38.40 3.58
2048 2122 3.190535 GCAAGTGTTACAACATAGTGGGG 59.809 47.826 0.00 0.00 41.59 4.96
2058 2132 1.680735 CCAGGCAAGCAAGTGTTACAA 59.319 47.619 0.00 0.00 0.00 2.41
2089 2163 7.578310 ATCAGAACATAAAATGCTGCAGTAT 57.422 32.000 16.64 14.28 0.00 2.12
2118 2192 5.514274 TTTCAAGCCAAGTAAGGTCAAAG 57.486 39.130 0.00 0.00 0.00 2.77
2249 2696 9.872721 ATGCTAGTTACATCATATTGAGATCTG 57.127 33.333 0.00 0.00 0.00 2.90
2348 2796 2.884663 TGCAAAAGCACGGTATAACG 57.115 45.000 9.04 9.04 40.31 3.18
2369 2817 2.863704 GCCACAAAAACATCACCTCAGC 60.864 50.000 0.00 0.00 0.00 4.26
2376 2824 3.957497 ACTACTTGGCCACAAAAACATCA 59.043 39.130 3.88 0.00 35.89 3.07
2658 3107 5.366186 GGGCTGATCAGGATCATATACATCT 59.634 44.000 23.89 0.00 45.74 2.90
2793 3242 1.202915 TCATCAGCTGCAAAACCCTGA 60.203 47.619 9.47 0.00 38.54 3.86
2877 3326 6.525628 TCGTCGAAGTAGTATTAGCTGTTTTG 59.474 38.462 0.00 0.00 0.00 2.44
2901 3350 2.687935 TCTTTGGTTTCCAGTTGCACTC 59.312 45.455 0.00 0.00 33.81 3.51
2978 3427 5.210430 TGGGTCGACCATTAGTATCCTTAA 58.790 41.667 34.40 0.00 46.80 1.85
3330 3780 2.555227 GGGAAGGGCAGAATTTGACAGA 60.555 50.000 0.00 0.00 36.08 3.41
3564 4014 3.126514 TCTCTAACCGCTGAAGTAACTCG 59.873 47.826 0.00 0.00 0.00 4.18
3868 4320 2.925966 TTTGGGGAAGATGAAGCCAT 57.074 45.000 0.00 0.00 35.29 4.40
3936 4388 1.066787 GGTGGTGCTAACAGAGGAGAC 60.067 57.143 0.00 0.00 0.00 3.36
4182 4634 6.652900 GGTAAGGATGCCAAAAATTAAGCAAA 59.347 34.615 0.00 0.00 38.99 3.68
4234 4688 7.630242 TGAGATCCAAAGGATAACATCAAAC 57.370 36.000 0.00 0.00 43.27 2.93
4265 4719 6.322456 CAGATGATCTAACCTCAACACCTAGA 59.678 42.308 0.00 0.00 0.00 2.43
4322 4776 8.532819 ACAATACACAAAAACTTTCTTAACCCA 58.467 29.630 0.00 0.00 0.00 4.51
4513 4968 4.630644 ATCTGTTCTGTTGAGTGGATGT 57.369 40.909 0.00 0.00 0.00 3.06
4564 5019 5.733091 GCAGAAATGACAAACACACTAGCAA 60.733 40.000 0.00 0.00 0.00 3.91
4714 5275 0.032615 ACTTTGGTGGGCAGGTTTCA 60.033 50.000 0.00 0.00 0.00 2.69
4771 5337 6.880529 CCAAAATTAGAGTCATGGCCAAAAAT 59.119 34.615 10.96 0.00 0.00 1.82
4877 5443 2.358898 ACAGATTATGTTTGGCATCGGC 59.641 45.455 0.00 0.00 39.96 5.54
5045 5642 3.896888 TCAGCACAAAAGGGAACATGAAT 59.103 39.130 0.00 0.00 0.00 2.57
5255 5859 4.403137 GCAGATTGCCGCGTTGCA 62.403 61.111 4.92 5.48 37.42 4.08
5363 5967 7.668469 ACGGGAATTAAACTTTTCTGAGGTATT 59.332 33.333 0.00 0.00 0.00 1.89
5365 5969 6.536447 ACGGGAATTAAACTTTTCTGAGGTA 58.464 36.000 0.00 0.00 0.00 3.08
5496 6100 4.081365 TGCACTTGGAACGGATTCACTATA 60.081 41.667 0.00 0.00 36.46 1.31
5642 6246 2.034048 TACCTCACTGCGCAACACCA 62.034 55.000 13.05 0.00 0.00 4.17
5649 6253 2.817423 GCAGCATACCTCACTGCGC 61.817 63.158 0.00 0.00 46.38 6.09
5691 6295 3.467374 TTTCAAACCTTGCCATGAACC 57.533 42.857 0.00 0.00 31.96 3.62
5759 6363 3.678548 GGCAAGTAGTAGCAGTGTAACAC 59.321 47.826 0.00 0.00 41.43 3.32
5760 6364 3.576982 AGGCAAGTAGTAGCAGTGTAACA 59.423 43.478 0.00 0.00 41.43 2.41
5761 6365 4.189639 AGGCAAGTAGTAGCAGTGTAAC 57.810 45.455 0.00 0.00 0.00 2.50
5762 6366 4.159135 GGTAGGCAAGTAGTAGCAGTGTAA 59.841 45.833 0.00 0.00 0.00 2.41
5764 6368 2.496470 GGTAGGCAAGTAGTAGCAGTGT 59.504 50.000 0.00 0.00 0.00 3.55
5765 6369 2.761208 AGGTAGGCAAGTAGTAGCAGTG 59.239 50.000 0.00 0.00 0.00 3.66
5766 6370 2.761208 CAGGTAGGCAAGTAGTAGCAGT 59.239 50.000 0.00 0.00 0.00 4.40
5767 6371 2.761208 ACAGGTAGGCAAGTAGTAGCAG 59.239 50.000 0.00 0.00 0.00 4.24
5768 6372 2.816411 ACAGGTAGGCAAGTAGTAGCA 58.184 47.619 0.00 0.00 0.00 3.49
5769 6373 3.194968 TCAACAGGTAGGCAAGTAGTAGC 59.805 47.826 0.00 0.00 0.00 3.58
5770 6374 5.401531 TTCAACAGGTAGGCAAGTAGTAG 57.598 43.478 0.00 0.00 0.00 2.57
5771 6375 6.666546 ACTATTCAACAGGTAGGCAAGTAGTA 59.333 38.462 0.00 0.00 0.00 1.82
5772 6376 4.910458 ATTCAACAGGTAGGCAAGTAGT 57.090 40.909 0.00 0.00 0.00 2.73
5811 6415 5.961396 ACTAGTGGTATAAGCTGGTATCG 57.039 43.478 0.00 0.00 0.00 2.92
5850 6454 9.113838 CACAAGCTTATGTCATACTTTAATCCT 57.886 33.333 0.00 0.00 0.00 3.24
5870 6474 4.024218 CAGCTCCTATGCTAAATCACAAGC 60.024 45.833 0.00 0.00 41.98 4.01
5871 6475 4.514441 CCAGCTCCTATGCTAAATCACAAG 59.486 45.833 0.00 0.00 41.98 3.16
5873 6477 3.455910 ACCAGCTCCTATGCTAAATCACA 59.544 43.478 0.00 0.00 41.98 3.58
5917 6521 2.882927 GGTTCCCACCAGTTTTTCAC 57.117 50.000 0.00 0.00 43.61 3.18
5956 6560 5.559148 TGTTACCGGGTCCTAAAAACTAA 57.441 39.130 6.32 0.00 0.00 2.24
5966 6570 1.065998 TGCTGTTATGTTACCGGGTCC 60.066 52.381 6.32 0.00 0.00 4.46
6015 6619 5.593909 ACAACTGTTCATCAAATTGGACTCA 59.406 36.000 0.00 0.00 30.82 3.41
6023 6627 6.158598 GGCACATAACAACTGTTCATCAAAT 58.841 36.000 0.00 0.00 39.31 2.32
6170 6785 2.843701 CTGCTTACAGGCATTAGGGAG 58.156 52.381 0.00 0.00 41.63 4.30
6194 6809 2.828520 ACGTCCCATGATAGCTGATAGG 59.171 50.000 0.00 0.00 0.00 2.57
6211 6826 6.758593 TTCAGAACAATGTACACTAACGTC 57.241 37.500 0.00 0.00 0.00 4.34
6231 6846 6.509418 ACTGAGCTTTACTGTTTTGTTTCA 57.491 33.333 0.00 0.00 0.00 2.69
6232 6847 7.132863 CCTACTGAGCTTTACTGTTTTGTTTC 58.867 38.462 0.00 0.00 0.00 2.78
6245 6860 5.662674 AAATCTCGTACCTACTGAGCTTT 57.337 39.130 0.00 0.00 31.60 3.51
6305 6924 7.989416 TTCCGTAATATTCCTTGTTTTCTGT 57.011 32.000 0.00 0.00 0.00 3.41
6342 6964 6.223852 AGGTAATATATCAACCAACAGCTCG 58.776 40.000 15.90 0.00 35.64 5.03
6349 6971 7.777910 CACCCAAAGAGGTAATATATCAACCAA 59.222 37.037 15.90 0.00 38.39 3.67
6360 6982 4.569719 AATCGACACCCAAAGAGGTAAT 57.430 40.909 0.00 0.00 38.39 1.89
6418 7040 4.517453 GGCACAAGTGTTTAGTAACATCCA 59.483 41.667 1.79 0.00 45.41 3.41
6422 7044 3.628487 GGTGGCACAAGTGTTTAGTAACA 59.372 43.478 20.82 0.00 44.16 2.41
6427 7049 4.072131 ACTATGGTGGCACAAGTGTTTAG 58.928 43.478 20.82 8.89 44.16 1.85
6430 7052 2.656947 ACTATGGTGGCACAAGTGTT 57.343 45.000 20.82 0.00 44.16 3.32
6431 7053 2.504367 GAACTATGGTGGCACAAGTGT 58.496 47.619 20.82 8.37 44.16 3.55
6442 7064 4.765856 ACTCAACTACTCACGAACTATGGT 59.234 41.667 0.00 0.00 0.00 3.55
6557 7202 3.191581 AGATCTGTGTAGGTGACGTTCAG 59.808 47.826 0.00 0.00 0.00 3.02
6558 7203 3.154710 AGATCTGTGTAGGTGACGTTCA 58.845 45.455 0.00 0.00 0.00 3.18
6613 7260 3.825143 AAGCAGGCATGAACACTTTTT 57.175 38.095 0.62 0.00 0.00 1.94
6614 7261 3.825143 AAAGCAGGCATGAACACTTTT 57.175 38.095 0.62 0.00 0.00 2.27
6615 7262 3.825143 AAAAGCAGGCATGAACACTTT 57.175 38.095 0.62 0.00 0.00 2.66
6616 7263 5.473066 AATAAAAGCAGGCATGAACACTT 57.527 34.783 0.62 0.00 0.00 3.16
6617 7264 6.780457 ATAATAAAAGCAGGCATGAACACT 57.220 33.333 0.62 0.00 0.00 3.55
6618 7265 8.925161 TTAATAATAAAAGCAGGCATGAACAC 57.075 30.769 0.62 0.00 0.00 3.32
6619 7266 8.196771 CCTTAATAATAAAAGCAGGCATGAACA 58.803 33.333 0.62 0.00 0.00 3.18
6620 7267 8.197439 ACCTTAATAATAAAAGCAGGCATGAAC 58.803 33.333 0.62 0.00 0.00 3.18
6621 7268 8.305046 ACCTTAATAATAAAAGCAGGCATGAA 57.695 30.769 0.62 0.00 0.00 2.57
6622 7269 7.014230 GGACCTTAATAATAAAAGCAGGCATGA 59.986 37.037 0.62 0.00 0.00 3.07
6623 7270 7.014615 AGGACCTTAATAATAAAAGCAGGCATG 59.985 37.037 0.00 0.00 0.00 4.06
6624 7271 7.069344 AGGACCTTAATAATAAAAGCAGGCAT 58.931 34.615 0.00 0.00 0.00 4.40
6625 7272 6.431722 AGGACCTTAATAATAAAAGCAGGCA 58.568 36.000 0.00 0.00 0.00 4.75
6626 7273 6.961360 AGGACCTTAATAATAAAAGCAGGC 57.039 37.500 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.