Multiple sequence alignment - TraesCS3A01G263400

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 TraesCS3A01G263400 chr3A 100.000 5123 0 0 1 5123 487430890 487436012 0.000000e+00 9461.0
1 TraesCS3A01G263400 chr3D 93.541 4490 176 46 136 4576 365328422 365332846 0.000000e+00 6580.0
2 TraesCS3A01G263400 chr3D 88.194 144 11 3 4782 4922 365334261 365334401 3.170000e-37 167.0
3 TraesCS3A01G263400 chr3D 86.400 125 17 0 4999 5123 365334435 365334559 2.490000e-28 137.0
4 TraesCS3A01G263400 chr3D 76.647 167 21 14 4756 4913 11928435 11928278 5.500000e-10 76.8
5 TraesCS3A01G263400 chr3B 94.390 2745 83 22 1546 4246 475827862 475830579 0.000000e+00 4150.0
6 TraesCS3A01G263400 chr3B 91.948 770 31 10 759 1508 475826975 475827733 0.000000e+00 1050.0
7 TraesCS3A01G263400 chr3B 83.775 906 70 25 4244 5093 475832859 475833743 0.000000e+00 787.0
8 TraesCS3A01G263400 chr3B 94.000 50 1 2 4865 4913 17146790 17146742 1.980000e-09 75.0
9 TraesCS3A01G263400 chr1B 90.698 43 3 1 4852 4894 638883987 638883946 7.170000e-04 56.5


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 TraesCS3A01G263400 chr3A 487430890 487436012 5122 False 9461.000000 9461 100.000000 1 5123 1 chr3A.!!$F1 5122
1 TraesCS3A01G263400 chr3D 365328422 365334559 6137 False 2294.666667 6580 89.378333 136 5123 3 chr3D.!!$F1 4987
2 TraesCS3A01G263400 chr3B 475826975 475833743 6768 False 1995.666667 4150 90.037667 759 5093 3 chr3B.!!$F1 4334

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
682 696 0.251564 AACAATGTGGGCCGGATCAA 60.252 50.000 5.05 0.00 0.00 2.57 F
1377 1419 0.033366 AAACATGTTTCAAGCCGCCC 59.967 50.000 18.13 0.00 0.00 6.13 F
1765 1898 0.107703 TTCTGTAGATGGCGCCCAAG 60.108 55.000 26.77 12.09 36.95 3.61 F
2385 2547 1.964933 GGGGTCGCTAAGAGAATAGCT 59.035 52.381 4.96 0.00 44.89 3.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1765 1898 1.063183 CCTCCTCCATCTGGATTCCC 58.937 60.000 0.00 0.00 44.46 3.97 R
2944 3106 2.407090 TCATCAAGTGCTGACTCAACG 58.593 47.619 0.00 0.00 36.69 4.10 R
3198 3362 3.988976 TGCCAAATAGAAGTCAGAGCT 57.011 42.857 0.00 0.00 0.00 4.09 R
4227 4406 1.428869 AAGTGAAGGCCTCAGACACT 58.571 50.000 21.08 21.08 42.40 3.55 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
209 212 9.777843 GAGATAAAAGTTATTTGCAAAAACGTG 57.222 29.630 17.19 0.00 0.00 4.49
211 214 9.777843 GATAAAAGTTATTTGCAAAAACGTGAG 57.222 29.630 17.19 0.00 0.00 3.51
276 288 5.964958 AGGGAAAATGTAGACATGTGTTG 57.035 39.130 1.15 0.00 36.56 3.33
277 289 5.630121 AGGGAAAATGTAGACATGTGTTGA 58.370 37.500 1.15 0.00 36.56 3.18
278 290 6.068010 AGGGAAAATGTAGACATGTGTTGAA 58.932 36.000 1.15 0.00 36.56 2.69
310 323 6.717997 GGAAAGAGGGAAAAGTGGTTGTATAA 59.282 38.462 0.00 0.00 0.00 0.98
418 432 9.515020 ACCATGTATTTAAAAATAGTCAATGCG 57.485 29.630 0.00 0.00 31.94 4.73
478 492 9.419297 TGTACATTTTGTAGAAGTAGACATGTC 57.581 33.333 18.47 18.47 32.84 3.06
530 544 4.616953 CGGTGAAAAACTGGCATAAAACT 58.383 39.130 0.00 0.00 0.00 2.66
531 545 4.679654 CGGTGAAAAACTGGCATAAAACTC 59.320 41.667 0.00 0.00 0.00 3.01
532 546 5.596845 GGTGAAAAACTGGCATAAAACTCA 58.403 37.500 0.00 0.00 0.00 3.41
575 589 7.069826 AGACAAAGGAAAACCAAGAAATCATGA 59.930 33.333 0.00 0.00 0.00 3.07
679 693 0.894835 GAAAACAATGTGGGCCGGAT 59.105 50.000 5.05 0.00 0.00 4.18
682 696 0.251564 AACAATGTGGGCCGGATCAA 60.252 50.000 5.05 0.00 0.00 2.57
726 740 2.691409 GCTGTCAGCCCATTACTACA 57.309 50.000 14.27 0.00 34.48 2.74
727 741 2.985896 GCTGTCAGCCCATTACTACAA 58.014 47.619 14.27 0.00 34.48 2.41
728 742 3.343617 GCTGTCAGCCCATTACTACAAA 58.656 45.455 14.27 0.00 34.48 2.83
730 744 3.343617 TGTCAGCCCATTACTACAAAGC 58.656 45.455 0.00 0.00 0.00 3.51
731 745 2.351726 GTCAGCCCATTACTACAAAGCG 59.648 50.000 0.00 0.00 0.00 4.68
756 771 0.813821 GCAGCCTGGCCTTTAAGAAG 59.186 55.000 16.57 0.00 0.00 2.85
819 846 3.856508 CGCTCACCGTCAAATCGT 58.143 55.556 0.00 0.00 0.00 3.73
822 849 0.731514 GCTCACCGTCAAATCGTCGA 60.732 55.000 0.00 0.00 0.00 4.20
823 850 1.693467 CTCACCGTCAAATCGTCGAA 58.307 50.000 0.00 0.00 0.00 3.71
1269 1311 3.086600 CCTCTGCTCCCTGTCCCC 61.087 72.222 0.00 0.00 0.00 4.81
1270 1312 3.086600 CTCTGCTCCCTGTCCCCC 61.087 72.222 0.00 0.00 0.00 5.40
1299 1341 1.648467 GGCGGCTGTGTTTGATCCTC 61.648 60.000 0.00 0.00 0.00 3.71
1300 1342 0.674895 GCGGCTGTGTTTGATCCTCT 60.675 55.000 0.00 0.00 0.00 3.69
1316 1358 2.563179 TCCTCTTTCACTAGCTCACCAC 59.437 50.000 0.00 0.00 0.00 4.16
1318 1360 1.961394 TCTTTCACTAGCTCACCACGT 59.039 47.619 0.00 0.00 0.00 4.49
1331 1373 1.280746 CCACGTGCTTGCTTCAGTG 59.719 57.895 10.91 0.00 0.00 3.66
1377 1419 0.033366 AAACATGTTTCAAGCCGCCC 59.967 50.000 18.13 0.00 0.00 6.13
1450 1492 7.974675 TCTGAAATTACTCATGATTTCGGAAC 58.025 34.615 20.94 3.24 45.86 3.62
1482 1524 6.456447 TGTTTTGTATAGTTGTACTGCGTC 57.544 37.500 0.00 0.00 0.00 5.19
1585 1718 0.389817 TGAGCCACGATCTTGTTCCG 60.390 55.000 0.00 0.00 0.00 4.30
1606 1739 3.707793 GAAGGTGATAGGTTCTGTAGCG 58.292 50.000 0.00 0.00 0.00 4.26
1607 1740 2.736347 AGGTGATAGGTTCTGTAGCGT 58.264 47.619 0.00 0.00 0.00 5.07
1608 1741 3.894759 AGGTGATAGGTTCTGTAGCGTA 58.105 45.455 0.00 0.00 0.00 4.42
1609 1742 4.471548 AGGTGATAGGTTCTGTAGCGTAT 58.528 43.478 0.00 0.00 0.00 3.06
1620 1753 6.439599 GTTCTGTAGCGTATGTATGTCATCT 58.560 40.000 0.00 0.00 37.91 2.90
1635 1768 3.008923 TGTCATCTGAGGGTTGCAACATA 59.991 43.478 29.55 12.10 0.00 2.29
1640 1773 4.922206 TCTGAGGGTTGCAACATATTTCT 58.078 39.130 29.55 15.89 0.00 2.52
1717 1850 3.064207 TGCGATGTCTGTTGGTCTTTAC 58.936 45.455 0.00 0.00 0.00 2.01
1747 1880 6.043243 TCACCTTTTGTCTCCTACTTCTCATT 59.957 38.462 0.00 0.00 0.00 2.57
1765 1898 0.107703 TTCTGTAGATGGCGCCCAAG 60.108 55.000 26.77 12.09 36.95 3.61
1824 1959 6.884472 TCTGAATTGACCTTCCCTTGTATA 57.116 37.500 0.00 0.00 0.00 1.47
1832 1967 2.505819 CCTTCCCTTGTATACAGGCTGT 59.494 50.000 25.34 25.34 0.00 4.40
1960 2095 6.545298 GGAAAGATGGCATCTATCAAAAGACT 59.455 38.462 29.02 7.75 39.08 3.24
2064 2218 5.048991 TGTTACTTGCAGCTAGCCTAAAAAC 60.049 40.000 12.13 11.18 44.83 2.43
2096 2250 5.244626 ACATTAGCAGGCACTTTGAATCTTT 59.755 36.000 0.00 0.00 34.60 2.52
2138 2300 3.428413 TTTCCTTAAGTGGTAGTGCCC 57.572 47.619 0.97 0.00 36.04 5.36
2172 2334 4.953940 TTTTGAGACCAATTCAAAGGGG 57.046 40.909 1.37 0.00 43.22 4.79
2333 2495 5.654209 AGTTCTCTTTGCTTCACCTTTTTCT 59.346 36.000 0.00 0.00 0.00 2.52
2385 2547 1.964933 GGGGTCGCTAAGAGAATAGCT 59.035 52.381 4.96 0.00 44.89 3.32
2502 2664 5.448904 CGACCATGTCATTGAACAATATGCA 60.449 40.000 0.00 0.00 31.81 3.96
2526 2688 7.468357 GCAAGAATAAGAGGTTTCTGATGGATG 60.468 40.741 0.00 0.00 32.65 3.51
2528 2690 7.637511 AGAATAAGAGGTTTCTGATGGATGTT 58.362 34.615 0.00 0.00 32.79 2.71
2952 3116 8.818057 ACTGTATTAATCTAATTGCGTTGAGTC 58.182 33.333 0.00 0.00 0.00 3.36
3038 3202 5.809001 TCTGCAAGACATCCATCTTTACTT 58.191 37.500 0.00 0.00 38.67 2.24
3083 3247 6.560711 TGATCATGCATGAACAGAAAATCAG 58.439 36.000 31.79 0.00 40.69 2.90
3430 3596 5.308825 AGGCAATGCAATACCTAGTATGTC 58.691 41.667 7.79 0.00 31.73 3.06
3556 3722 3.573967 CCCCTCTAGTGCACATTTTTGTT 59.426 43.478 21.04 0.00 0.00 2.83
3875 4047 7.123247 ACCATTGTCATTTCTTCTTATTCTGGG 59.877 37.037 0.00 0.00 0.00 4.45
3891 4063 9.765795 CTTATTCTGGGAGTACCTAAAATGTAG 57.234 37.037 0.00 0.00 41.11 2.74
3899 4071 7.881751 GGGAGTACCTAAAATGTAGAACACTTT 59.118 37.037 0.00 0.00 32.02 2.66
4443 6904 8.304596 TGTTTTAGTTGTTAATTGTGAACACCA 58.695 29.630 2.46 0.00 36.55 4.17
4450 6911 8.660373 GTTGTTAATTGTGAACACCATTTTTCA 58.340 29.630 8.99 5.09 36.55 2.69
4459 6920 7.714377 TGTGAACACCATTTTTCATTTAGCATT 59.286 29.630 2.46 0.00 34.34 3.56
4493 6954 5.583061 TCGAGAGAACAAAAGTAAACTTGCA 59.417 36.000 0.00 0.00 34.68 4.08
4516 6977 2.672961 TGGATTCTGCTGTTCCTACG 57.327 50.000 13.44 0.00 0.00 3.51
4518 6979 1.480954 GGATTCTGCTGTTCCTACGGA 59.519 52.381 7.67 0.00 31.98 4.69
4549 7010 3.250762 TGAAGATTGGTGTTCTTGAAGCG 59.749 43.478 0.00 0.00 33.65 4.68
4551 7012 2.808543 AGATTGGTGTTCTTGAAGCGAC 59.191 45.455 0.00 0.00 0.00 5.19
4555 7016 1.205657 GTGTTCTTGAAGCGACACGA 58.794 50.000 13.19 0.00 33.88 4.35
4568 7029 2.400399 CGACACGAGCCAAGAAAGTTA 58.600 47.619 0.00 0.00 0.00 2.24
4576 7037 4.680708 CGAGCCAAGAAAGTTAGCCATCTA 60.681 45.833 0.00 0.00 0.00 1.98
4579 8214 4.455606 CCAAGAAAGTTAGCCATCTAGGG 58.544 47.826 0.00 0.00 38.09 3.53
4586 8221 2.109181 GCCATCTAGGGCGTGGAC 59.891 66.667 0.00 0.00 45.40 4.02
4710 8348 9.013229 ACTGTTCTAGATATGTGCAAATTTTCA 57.987 29.630 0.00 0.00 0.00 2.69
4722 8360 4.445052 TGCAAATTTTCATGAAGAAGCGTG 59.555 37.500 8.41 5.15 37.57 5.34
4724 8362 3.855689 ATTTTCATGAAGAAGCGTGGG 57.144 42.857 8.41 0.00 37.57 4.61
4725 8363 0.881118 TTTCATGAAGAAGCGTGGGC 59.119 50.000 8.41 0.00 37.57 5.36
4726 8364 1.298157 TTCATGAAGAAGCGTGGGCG 61.298 55.000 3.38 0.00 46.35 6.13
4758 8454 9.836864 AATTGAAGCTCCAAAAAGACTATTTTT 57.163 25.926 0.00 0.00 30.31 1.94
4780 8478 7.396540 TTTTTCTCAGGCCTCAAAGAATATC 57.603 36.000 18.03 0.00 0.00 1.63
4781 8479 5.698741 TTCTCAGGCCTCAAAGAATATCA 57.301 39.130 0.00 0.00 0.00 2.15
4938 8639 9.525409 TTAATCTAGTGTTCGGTTTATTAGAGC 57.475 33.333 0.00 0.00 0.00 4.09
4964 8665 7.187824 TCTACATCCAGAAGTAGCAAAATCT 57.812 36.000 5.40 0.00 38.05 2.40
4975 8676 0.620030 GCAAAATCTGGCCCCCAAAT 59.380 50.000 0.00 0.00 30.80 2.32
5023 8741 4.096532 TGACCGAACAGCACAACAAAAATA 59.903 37.500 0.00 0.00 0.00 1.40
5031 8749 8.491331 AACAGCACAACAAAAATAGTTTTCAT 57.509 26.923 0.00 0.00 34.64 2.57
5050 8768 0.333312 TTGCCGGATACCCCATTTGT 59.667 50.000 5.05 0.00 34.14 2.83
5081 8799 9.617523 CCTCATATCCATATTATTACATGCACA 57.382 33.333 0.00 0.00 0.00 4.57
5099 8817 8.133627 ACATGCACATGAAATCTAATCTAAAGC 58.866 33.333 17.19 0.00 41.20 3.51
5100 8818 7.870509 TGCACATGAAATCTAATCTAAAGCT 57.129 32.000 0.00 0.00 0.00 3.74
5102 8820 9.049523 TGCACATGAAATCTAATCTAAAGCTAG 57.950 33.333 0.00 0.00 0.00 3.42
5109 8827 3.965347 TCTAATCTAAAGCTAGGCCCGTT 59.035 43.478 0.00 0.00 0.00 4.44
5110 8828 3.646736 AATCTAAAGCTAGGCCCGTTT 57.353 42.857 0.00 0.00 0.00 3.60
5111 8829 2.396590 TCTAAAGCTAGGCCCGTTTG 57.603 50.000 0.00 0.00 0.00 2.93
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
192 194 6.198216 ACATGACTCACGTTTTTGCAAATAAC 59.802 34.615 13.65 17.15 0.00 1.89
240 252 9.224267 CTACATTTTCCCTATACATCAGGAATG 57.776 37.037 0.00 0.00 38.17 2.67
251 263 8.544622 TCAACACATGTCTACATTTTCCCTATA 58.455 33.333 0.00 0.00 33.61 1.31
286 298 7.754851 TTATACAACCACTTTTCCCTCTTTC 57.245 36.000 0.00 0.00 0.00 2.62
292 304 9.984190 TGTTTAAATTATACAACCACTTTTCCC 57.016 29.630 0.00 0.00 0.00 3.97
497 511 3.113322 GTTTTTCACCGGTTTTCTCTGC 58.887 45.455 2.97 0.00 0.00 4.26
500 514 3.702330 CCAGTTTTTCACCGGTTTTCTC 58.298 45.455 2.97 0.00 0.00 2.87
509 523 5.596845 TGAGTTTTATGCCAGTTTTTCACC 58.403 37.500 0.00 0.00 0.00 4.02
543 557 7.948034 TCTTGGTTTTCCTTTGTCTCTTAAA 57.052 32.000 0.00 0.00 41.38 1.52
545 559 7.948034 TTTCTTGGTTTTCCTTTGTCTCTTA 57.052 32.000 0.00 0.00 41.38 2.10
580 594 4.260497 GCGTTTTCTTCTGTCTAAACCGTT 60.260 41.667 0.00 0.00 0.00 4.44
581 595 3.246936 GCGTTTTCTTCTGTCTAAACCGT 59.753 43.478 0.00 0.00 0.00 4.83
582 596 3.660904 CGCGTTTTCTTCTGTCTAAACCG 60.661 47.826 0.00 0.00 0.00 4.44
584 598 4.703899 TCGCGTTTTCTTCTGTCTAAAC 57.296 40.909 5.77 0.00 0.00 2.01
585 599 5.721876 TTTCGCGTTTTCTTCTGTCTAAA 57.278 34.783 5.77 0.00 0.00 1.85
586 600 5.721876 TTTTCGCGTTTTCTTCTGTCTAA 57.278 34.783 5.77 0.00 0.00 2.10
587 601 5.495502 GTTTTTCGCGTTTTCTTCTGTCTA 58.504 37.500 5.77 0.00 0.00 2.59
588 602 4.340263 GTTTTTCGCGTTTTCTTCTGTCT 58.660 39.130 5.77 0.00 0.00 3.41
589 603 3.481028 GGTTTTTCGCGTTTTCTTCTGTC 59.519 43.478 5.77 0.00 0.00 3.51
591 605 2.462565 CGGTTTTTCGCGTTTTCTTCTG 59.537 45.455 5.77 0.00 0.00 3.02
592 606 2.540157 CCGGTTTTTCGCGTTTTCTTCT 60.540 45.455 5.77 0.00 0.00 2.85
593 607 1.776897 CCGGTTTTTCGCGTTTTCTTC 59.223 47.619 5.77 0.00 0.00 2.87
654 668 2.365293 GGCCCACATTGTTTTCTTCAGT 59.635 45.455 0.00 0.00 0.00 3.41
667 681 1.224592 GTCTTGATCCGGCCCACAT 59.775 57.895 0.00 0.00 0.00 3.21
712 726 2.351726 GTCGCTTTGTAGTAATGGGCTG 59.648 50.000 0.00 0.00 0.00 4.85
726 740 4.008933 AGGCTGCTCGGTCGCTTT 62.009 61.111 0.00 0.00 0.00 3.51
727 741 4.749310 CAGGCTGCTCGGTCGCTT 62.749 66.667 0.00 0.00 0.00 4.68
822 849 3.207778 TCCCTTTGTTCGACGATTTGTT 58.792 40.909 0.00 0.00 0.00 2.83
823 850 2.841215 TCCCTTTGTTCGACGATTTGT 58.159 42.857 0.00 0.00 0.00 2.83
915 957 0.106217 GAGGAGAGGGAGAGGGACAG 60.106 65.000 0.00 0.00 0.00 3.51
982 1024 1.326852 CATGTGATGCTTGCTCGAGTC 59.673 52.381 15.13 7.10 0.00 3.36
983 1025 1.366679 CATGTGATGCTTGCTCGAGT 58.633 50.000 15.13 0.00 0.00 4.18
984 1026 0.656259 CCATGTGATGCTTGCTCGAG 59.344 55.000 8.45 8.45 0.00 4.04
985 1027 1.371337 GCCATGTGATGCTTGCTCGA 61.371 55.000 0.00 0.00 0.00 4.04
986 1028 1.063649 GCCATGTGATGCTTGCTCG 59.936 57.895 0.00 0.00 0.00 5.03
1270 1312 4.060038 CAGCCGCCCCAAGCAAAG 62.060 66.667 0.00 0.00 44.04 2.77
1299 1341 2.061773 CACGTGGTGAGCTAGTGAAAG 58.938 52.381 7.95 0.00 35.23 2.62
1300 1342 1.872237 GCACGTGGTGAGCTAGTGAAA 60.872 52.381 18.88 0.00 35.23 2.69
1316 1358 0.236711 CCTTCACTGAAGCAAGCACG 59.763 55.000 12.69 0.00 38.24 5.34
1318 1360 2.430465 GATCCTTCACTGAAGCAAGCA 58.570 47.619 12.69 0.00 38.24 3.91
1331 1373 4.010349 ACTTTTGACCATTCGGATCCTTC 58.990 43.478 10.75 0.00 35.59 3.46
1377 1419 2.883574 AGTCTCGAGTCTCGACTACTG 58.116 52.381 24.53 15.17 44.82 2.74
1414 1456 7.325660 TGAGTAATTTCAGATCAGAAATGGC 57.674 36.000 22.33 17.82 44.96 4.40
1449 1491 3.556775 ACTATACAAAACAACACGCACGT 59.443 39.130 0.00 0.00 0.00 4.49
1450 1492 4.123276 ACTATACAAAACAACACGCACG 57.877 40.909 0.00 0.00 0.00 5.34
1482 1524 1.515088 CTAGACACGAGTGGCGCAG 60.515 63.158 10.83 4.02 45.19 5.18
1585 1718 3.130693 ACGCTACAGAACCTATCACCTTC 59.869 47.826 0.00 0.00 0.00 3.46
1606 1739 4.752101 GCAACCCTCAGATGACATACATAC 59.248 45.833 0.00 0.00 39.56 2.39
1607 1740 4.408596 TGCAACCCTCAGATGACATACATA 59.591 41.667 0.00 0.00 39.56 2.29
1608 1741 3.200605 TGCAACCCTCAGATGACATACAT 59.799 43.478 0.00 0.00 42.47 2.29
1609 1742 2.571202 TGCAACCCTCAGATGACATACA 59.429 45.455 0.00 0.00 0.00 2.29
1620 1753 4.155826 CGAAGAAATATGTTGCAACCCTCA 59.844 41.667 26.14 8.56 0.00 3.86
1635 1768 9.784531 AGATCATATCAACAATACCGAAGAAAT 57.215 29.630 0.00 0.00 0.00 2.17
1640 1773 6.015772 TCGGAGATCATATCAACAATACCGAA 60.016 38.462 0.00 0.00 40.96 4.30
1717 1850 5.859495 AGTAGGAGACAAAAGGTGAGAAAG 58.141 41.667 0.00 0.00 0.00 2.62
1747 1880 1.522092 CTTGGGCGCCATCTACAGA 59.478 57.895 30.85 6.56 31.53 3.41
1765 1898 1.063183 CCTCCTCCATCTGGATTCCC 58.937 60.000 0.00 0.00 44.46 3.97
1824 1959 3.957497 TGAACCAAATACAAACAGCCTGT 59.043 39.130 0.00 0.00 0.00 4.00
1832 1967 7.013846 CAGGGAACTACTTGAACCAAATACAAA 59.986 37.037 0.00 0.00 40.21 2.83
1960 2095 9.824216 ACCTGATATTACTAGCTTAAGATACCA 57.176 33.333 6.67 0.00 0.00 3.25
2064 2218 3.684788 AGTGCCTGCTAATGTTAGTTTCG 59.315 43.478 2.11 0.00 33.32 3.46
2138 2300 6.539649 TGGTCTCAAAATTCTACAGAAACG 57.460 37.500 0.00 0.00 37.61 3.60
2172 2334 6.625960 GCCAACTCTTCCAGAATATTTCAACC 60.626 42.308 0.00 0.00 0.00 3.77
2502 2664 7.637511 ACATCCATCAGAAACCTCTTATTCTT 58.362 34.615 0.00 0.00 33.73 2.52
2944 3106 2.407090 TCATCAAGTGCTGACTCAACG 58.593 47.619 0.00 0.00 36.69 4.10
2945 3107 5.174395 AGTATCATCAAGTGCTGACTCAAC 58.826 41.667 0.00 0.00 36.69 3.18
2952 3116 7.976175 TGACTAAGTTAGTATCATCAAGTGCTG 59.024 37.037 15.52 0.00 39.59 4.41
3038 3202 8.035984 TGATCATAACTGGTTGTTATAACACGA 58.964 33.333 17.85 9.53 46.69 4.35
3195 3359 4.697352 TGCCAAATAGAAGTCAGAGCTTTC 59.303 41.667 0.00 0.00 0.00 2.62
3198 3362 3.988976 TGCCAAATAGAAGTCAGAGCT 57.011 42.857 0.00 0.00 0.00 4.09
3776 3947 4.634199 ACATGAGAAAAAGGTGCAAATGG 58.366 39.130 0.00 0.00 0.00 3.16
3875 4047 9.269453 ACAAAGTGTTCTACATTTTAGGTACTC 57.731 33.333 0.00 0.00 36.14 2.59
3891 4063 5.168526 TCTGCAACATGTACAAAGTGTTC 57.831 39.130 9.79 6.77 34.09 3.18
3899 4071 5.048782 GGAGAACAAATCTGCAACATGTACA 60.049 40.000 0.00 0.00 45.25 2.90
3968 4143 5.220381 TCTCGTACAGAAATTGACTCACAC 58.780 41.667 0.00 0.00 0.00 3.82
4156 4331 3.543494 CGATCAACGAAACCATGCATTTC 59.457 43.478 0.00 0.00 45.77 2.17
4227 4406 1.428869 AAGTGAAGGCCTCAGACACT 58.571 50.000 21.08 21.08 42.40 3.55
4443 6904 5.882000 GCCCTGGAAATGCTAAATGAAAAAT 59.118 36.000 0.00 0.00 0.00 1.82
4450 6911 2.624838 CGATGCCCTGGAAATGCTAAAT 59.375 45.455 0.00 0.00 0.00 1.40
4459 6920 0.537188 GTTCTCTCGATGCCCTGGAA 59.463 55.000 0.00 0.00 0.00 3.53
4493 6954 3.947612 AGGAACAGCAGAATCCATGAT 57.052 42.857 0.00 0.00 35.62 2.45
4516 6977 5.006386 ACACCAATCTTCATTGTCTCTTCC 58.994 41.667 0.00 0.00 38.22 3.46
4518 6979 6.302269 AGAACACCAATCTTCATTGTCTCTT 58.698 36.000 0.00 0.00 38.22 2.85
4549 7010 2.157863 GCTAACTTTCTTGGCTCGTGTC 59.842 50.000 0.00 0.00 0.00 3.67
4551 7012 1.464997 GGCTAACTTTCTTGGCTCGTG 59.535 52.381 0.00 0.00 0.00 4.35
4555 7016 3.728385 AGATGGCTAACTTTCTTGGCT 57.272 42.857 0.00 0.00 0.00 4.75
4576 7037 1.152756 AGCAAAAAGTCCACGCCCT 60.153 52.632 0.00 0.00 0.00 5.19
4579 8214 1.285950 GGGAGCAAAAAGTCCACGC 59.714 57.895 0.00 0.00 34.14 5.34
4586 8221 0.667993 TTGAGCACGGGAGCAAAAAG 59.332 50.000 0.00 0.00 36.85 2.27
4680 8318 6.968131 TTGCACATATCTAGAACAGTCAAC 57.032 37.500 0.00 0.00 0.00 3.18
4710 8348 0.605319 TTTCGCCCACGCTTCTTCAT 60.605 50.000 0.00 0.00 39.84 2.57
4758 8454 6.065976 TGATATTCTTTGAGGCCTGAGAAA 57.934 37.500 12.00 5.43 32.47 2.52
4761 8457 6.544931 TGAAATGATATTCTTTGAGGCCTGAG 59.455 38.462 12.00 5.38 0.00 3.35
4938 8639 7.714377 AGATTTTGCTACTTCTGGATGTAGATG 59.286 37.037 20.49 0.00 39.84 2.90
4949 8650 2.621668 GGGGCCAGATTTTGCTACTTCT 60.622 50.000 4.39 0.00 0.00 2.85
4950 8651 1.751351 GGGGCCAGATTTTGCTACTTC 59.249 52.381 4.39 0.00 0.00 3.01
4990 8708 2.169146 GTTCGGTCAATACCCGCGG 61.169 63.158 21.04 21.04 45.09 6.46
4994 8712 1.084289 GTGCTGTTCGGTCAATACCC 58.916 55.000 0.00 0.00 43.54 3.69
4996 8714 2.546368 TGTTGTGCTGTTCGGTCAATAC 59.454 45.455 0.00 0.00 0.00 1.89
4997 8715 2.839975 TGTTGTGCTGTTCGGTCAATA 58.160 42.857 0.00 0.00 0.00 1.90
5005 8723 7.958674 TGAAAACTATTTTTGTTGTGCTGTTC 58.041 30.769 0.00 0.00 34.94 3.18
5006 8724 7.897575 TGAAAACTATTTTTGTTGTGCTGTT 57.102 28.000 0.00 0.00 34.94 3.16
5010 8728 6.632434 GGCAATGAAAACTATTTTTGTTGTGC 59.368 34.615 0.00 1.26 34.94 4.57
5023 8741 2.375146 GGGTATCCGGCAATGAAAACT 58.625 47.619 0.00 0.00 0.00 2.66
5031 8749 0.333312 ACAAATGGGGTATCCGGCAA 59.667 50.000 0.00 0.00 38.76 4.52
5081 8799 7.171653 GGGCCTAGCTTTAGATTAGATTTCAT 58.828 38.462 0.84 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.