Multiple sequence alignment - TraesCS3B01G525300

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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 TraesCS3B01G525300 chr3B 100.000 4079 0 0 1 4079 766978120 766982198 0.000000e+00 7533
1 TraesCS3B01G525300 chr3D 90.391 3736 162 70 2 3646 576758959 576755330 0.000000e+00 4728
2 TraesCS3B01G525300 chr3D 85.936 967 77 33 3139 4079 576755333 576754400 0.000000e+00 977
3 TraesCS3B01G525300 chr3A 91.714 2112 80 20 1938 4031 712143245 712141211 0.000000e+00 2843
4 TraesCS3B01G525300 chr3A 90.168 1546 87 21 405 1904 712144770 712143244 0.000000e+00 1953
5 TraesCS3B01G525300 chr3A 89.562 297 19 7 2 297 712145132 712144847 2.320000e-97 366
6 TraesCS3B01G525300 chr6B 87.302 126 11 3 3366 3491 547757809 547757689 5.500000e-29 139
7 TraesCS3B01G525300 chr5A 87.302 126 11 3 3366 3491 580528086 580527966 5.500000e-29 139
8 TraesCS3B01G525300 chr5B 86.508 126 12 2 3366 3491 76147882 76148002 2.560000e-27 134
9 TraesCS3B01G525300 chr4B 86.508 126 12 2 3366 3491 172833990 172834110 2.560000e-27 134
10 TraesCS3B01G525300 chr2B 86.508 126 12 3 3366 3491 553063215 553063335 2.560000e-27 134
11 TraesCS3B01G525300 chr1A 86.508 126 12 2 3366 3491 4012438 4012558 2.560000e-27 134
12 TraesCS3B01G525300 chr1A 86.508 126 12 2 3366 3491 411508331 411508211 2.560000e-27 134


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 TraesCS3B01G525300 chr3B 766978120 766982198 4078 False 7533.000000 7533 100.000000 1 4079 1 chr3B.!!$F1 4078
1 TraesCS3B01G525300 chr3D 576754400 576758959 4559 True 2852.500000 4728 88.163500 2 4079 2 chr3D.!!$R1 4077
2 TraesCS3B01G525300 chr3A 712141211 712145132 3921 True 1720.666667 2843 90.481333 2 4031 3 chr3A.!!$R1 4029

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
317 338 0.039165 TGCAGAATCGATCCGATCCG 60.039 55.0 0.0 0.0 46.30 4.18 F
322 343 0.108615 AATCGATCCGATCCGCATCC 60.109 55.0 0.0 0.0 46.30 3.51 F
430 451 0.321298 CTCCACTGGGGGTACGTTTG 60.321 60.0 0.0 0.0 37.22 2.93 F
818 909 0.593128 CCTCCAACAAGCCAAGAACG 59.407 55.0 0.0 0.0 0.00 3.95 F
2435 2556 0.250770 GTCAACCCTCTTCCACACCC 60.251 60.0 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1757 1876 0.677414 AGAGGTCGGAGTTCTCGTCC 60.677 60.000 0.00 0.0 36.39 4.79 R
1914 2033 0.872021 GATCCATGTCGGTCTGCGAC 60.872 60.000 0.00 0.0 36.95 5.19 R
2000 2119 1.297745 CGCGAAGTCCGAGTAGAGC 60.298 63.158 0.00 0.0 41.76 4.09 R
2590 2711 1.606224 GGGCCATTGTTGCTGTCTTTG 60.606 52.381 4.39 0.0 0.00 2.77 R
3975 4610 0.253044 TAGCCATCAAGGTGTGGAGC 59.747 55.000 0.00 0.0 40.61 4.70 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
313 334 0.601046 GCCATGCAGAATCGATCCGA 60.601 55.000 0.00 0.00 41.13 4.55
315 336 1.998315 CCATGCAGAATCGATCCGATC 59.002 52.381 0.00 0.00 46.30 3.69
316 337 1.998315 CATGCAGAATCGATCCGATCC 59.002 52.381 0.00 0.00 46.30 3.36
317 338 0.039165 TGCAGAATCGATCCGATCCG 60.039 55.000 0.00 0.00 46.30 4.18
318 339 1.347817 GCAGAATCGATCCGATCCGC 61.348 60.000 0.00 0.00 46.30 5.54
319 340 0.039165 CAGAATCGATCCGATCCGCA 60.039 55.000 0.00 0.00 46.30 5.69
320 341 0.891373 AGAATCGATCCGATCCGCAT 59.109 50.000 0.00 0.00 46.30 4.73
321 342 1.135257 AGAATCGATCCGATCCGCATC 60.135 52.381 0.00 0.00 46.30 3.91
322 343 0.108615 AATCGATCCGATCCGCATCC 60.109 55.000 0.00 0.00 46.30 3.51
323 344 2.271607 ATCGATCCGATCCGCATCCG 62.272 60.000 2.69 0.00 43.45 4.18
335 356 2.202987 CATCCGGTGCTCAGCTCC 60.203 66.667 7.77 7.77 38.64 4.70
338 359 4.020617 CCGGTGCTCAGCTCCCAA 62.021 66.667 12.25 0.00 38.79 4.12
366 387 4.511527 CACTCTAATGCAAGTCCACTCAT 58.488 43.478 0.00 0.00 0.00 2.90
383 404 4.074970 ACTCATCAGTGAAACAACCCATC 58.925 43.478 0.00 0.00 41.43 3.51
390 411 4.457603 CAGTGAAACAACCCATCGGAATTA 59.542 41.667 0.00 0.00 41.43 1.40
393 414 4.698304 TGAAACAACCCATCGGAATTAGAC 59.302 41.667 0.00 0.00 0.00 2.59
394 415 3.992943 ACAACCCATCGGAATTAGACA 57.007 42.857 0.00 0.00 0.00 3.41
395 416 4.295141 ACAACCCATCGGAATTAGACAA 57.705 40.909 0.00 0.00 0.00 3.18
396 417 4.855340 ACAACCCATCGGAATTAGACAAT 58.145 39.130 0.00 0.00 0.00 2.71
397 418 5.261216 ACAACCCATCGGAATTAGACAATT 58.739 37.500 0.00 0.00 37.06 2.32
398 419 6.419791 ACAACCCATCGGAATTAGACAATTA 58.580 36.000 0.00 0.00 34.44 1.40
399 420 6.542370 ACAACCCATCGGAATTAGACAATTAG 59.458 38.462 0.00 0.00 34.44 1.73
401 422 7.369551 ACCCATCGGAATTAGACAATTAGTA 57.630 36.000 0.00 0.00 34.44 1.82
402 423 7.215085 ACCCATCGGAATTAGACAATTAGTAC 58.785 38.462 0.00 0.00 34.44 2.73
403 424 7.070821 ACCCATCGGAATTAGACAATTAGTACT 59.929 37.037 0.00 0.00 34.44 2.73
418 439 2.520069 AGTACTGTGTCTCCTCCACTG 58.480 52.381 0.00 0.00 37.66 3.66
430 451 0.321298 CTCCACTGGGGGTACGTTTG 60.321 60.000 0.00 0.00 37.22 2.93
615 659 5.426833 TCTTCCTACGGGTTCTACTACTACT 59.573 44.000 0.00 0.00 0.00 2.57
730 786 2.022520 CCCGCGCCCTTTAAATCTC 58.977 57.895 0.00 0.00 0.00 2.75
749 805 2.456840 CCCTCCCTCCCACTCCTT 59.543 66.667 0.00 0.00 0.00 3.36
768 824 2.111878 CTCCATCCATCCCCACGC 59.888 66.667 0.00 0.00 0.00 5.34
769 825 2.366837 TCCATCCATCCCCACGCT 60.367 61.111 0.00 0.00 0.00 5.07
770 826 2.111878 CCATCCATCCCCACGCTC 59.888 66.667 0.00 0.00 0.00 5.03
818 909 0.593128 CCTCCAACAAGCCAAGAACG 59.407 55.000 0.00 0.00 0.00 3.95
819 910 1.593196 CTCCAACAAGCCAAGAACGA 58.407 50.000 0.00 0.00 0.00 3.85
869 964 3.740115 TGTTCTCCCTTGCAAGTTACTC 58.260 45.455 24.35 10.82 0.00 2.59
1360 1467 2.282446 GGATGGAGTCCCTCGGGA 59.718 66.667 6.74 0.00 41.50 5.14
1506 1622 1.203994 ACCGACTACCTCCATTTGACG 59.796 52.381 0.00 0.00 0.00 4.35
1509 1625 2.618053 GACTACCTCCATTTGACGGTG 58.382 52.381 0.00 0.00 0.00 4.94
1627 1743 1.270907 ACAAACCCAGCCACACAAAA 58.729 45.000 0.00 0.00 0.00 2.44
1642 1758 6.347321 GCCACACAAAATTAATTAAGCACCAC 60.347 38.462 0.01 0.00 0.00 4.16
1659 1775 4.214119 GCACCACGCATCATCATTAACTAT 59.786 41.667 0.00 0.00 41.79 2.12
1660 1776 5.408299 GCACCACGCATCATCATTAACTATA 59.592 40.000 0.00 0.00 41.79 1.31
1661 1777 6.401474 GCACCACGCATCATCATTAACTATAG 60.401 42.308 0.00 0.00 41.79 1.31
1662 1778 5.639506 ACCACGCATCATCATTAACTATAGC 59.360 40.000 0.00 0.00 0.00 2.97
1666 1782 6.754209 ACGCATCATCATTAACTATAGCTAGC 59.246 38.462 6.62 6.62 0.00 3.42
1667 1783 6.753744 CGCATCATCATTAACTATAGCTAGCA 59.246 38.462 18.83 3.19 0.00 3.49
1669 1785 8.386606 GCATCATCATTAACTATAGCTAGCAAC 58.613 37.037 18.83 0.00 0.00 4.17
1670 1786 9.428097 CATCATCATTAACTATAGCTAGCAACA 57.572 33.333 18.83 1.36 0.00 3.33
1687 1806 7.149031 GCTAGCAACAAAATTAACAAGTAACCG 60.149 37.037 10.63 0.00 0.00 4.44
1736 1855 0.682209 CACCAAATGCAGGGAGAGGG 60.682 60.000 8.67 0.00 0.00 4.30
1839 1958 3.934962 GAGCCAGGATCGCCCTCC 61.935 72.222 0.00 0.00 45.60 4.30
1870 1989 5.464965 CCAAAGATGGTACGTGAATACAC 57.535 43.478 0.00 0.00 42.18 2.90
1871 1990 4.932799 CCAAAGATGGTACGTGAATACACA 59.067 41.667 0.00 0.00 43.02 3.72
1914 2033 4.718858 CATTTGTCACAACCAAATGCAG 57.281 40.909 11.53 0.00 46.93 4.41
1915 2034 3.883830 TTTGTCACAACCAAATGCAGT 57.116 38.095 0.00 0.00 0.00 4.40
1916 2035 3.435105 TTGTCACAACCAAATGCAGTC 57.565 42.857 0.00 0.00 0.00 3.51
1917 2036 1.333308 TGTCACAACCAAATGCAGTCG 59.667 47.619 0.00 0.00 0.00 4.18
1934 2053 1.946156 CGCAGACCGACATGGATCG 60.946 63.158 0.00 0.00 42.00 3.69
2000 2119 2.584608 GTGAGGTGGATCCGGGTG 59.415 66.667 7.39 0.00 41.99 4.61
2222 2341 1.766496 ACCAAGAACTTCGACCCTGAA 59.234 47.619 0.00 0.00 0.00 3.02
2272 2391 4.792068 TGATTAATCATTTTCTCGCCCCT 58.208 39.130 14.23 0.00 0.00 4.79
2277 2396 9.178758 GATTAATCATTTTCTCGCCCCTTATAT 57.821 33.333 10.68 0.00 0.00 0.86
2281 2400 9.614792 AATCATTTTCTCGCCCCTTATATATAC 57.385 33.333 0.00 0.00 0.00 1.47
2282 2401 8.141298 TCATTTTCTCGCCCCTTATATATACA 57.859 34.615 0.00 0.00 0.00 2.29
2349 2470 9.309516 GTGTGTGGTTTCGATTAATCTAATCTA 57.690 33.333 13.45 3.80 41.80 1.98
2350 2471 9.878667 TGTGTGGTTTCGATTAATCTAATCTAA 57.121 29.630 13.45 0.00 41.80 2.10
2435 2556 0.250770 GTCAACCCTCTTCCACACCC 60.251 60.000 0.00 0.00 0.00 4.61
2590 2711 0.250513 AGGTCTTCGGCAACATCCTC 59.749 55.000 0.00 0.00 0.00 3.71
2629 2750 1.418334 CCATCCTCCTCTACCCAGTG 58.582 60.000 0.00 0.00 0.00 3.66
2665 2786 3.362706 AGCAAAGCAGTTCCATCATCAT 58.637 40.909 0.00 0.00 0.00 2.45
2667 2788 3.129813 GCAAAGCAGTTCCATCATCATCA 59.870 43.478 0.00 0.00 0.00 3.07
2884 3013 1.066858 TGAGCCTCAACGACAAGATCC 60.067 52.381 0.00 0.00 0.00 3.36
2904 3033 0.246635 TAGACTTCTGCGACAAGGCC 59.753 55.000 0.00 0.00 27.62 5.19
2943 3072 2.104331 CTAGCGCCCTACACCACG 59.896 66.667 2.29 0.00 0.00 4.94
3049 3178 3.117738 AGCCCCAGGACAGAGAATATTTG 60.118 47.826 0.00 0.00 0.00 2.32
3146 3284 7.012989 GTGTACATAAATGTAGGAAATGTCCCC 59.987 40.741 0.00 0.00 43.32 4.81
3186 3324 0.673985 AAAAAGGCGGCCTGAAGAAC 59.326 50.000 24.63 0.00 32.13 3.01
3187 3325 0.467290 AAAAGGCGGCCTGAAGAACA 60.467 50.000 24.63 0.00 32.13 3.18
3209 3349 3.630769 ACGCAGCATAGCAACTAGTAGTA 59.369 43.478 2.50 0.00 0.00 1.82
3213 3359 5.524284 CAGCATAGCAACTAGTAGTAGTGG 58.476 45.833 11.04 9.28 39.60 4.00
3214 3360 4.585162 AGCATAGCAACTAGTAGTAGTGGG 59.415 45.833 11.04 7.92 39.60 4.61
3215 3361 4.583489 GCATAGCAACTAGTAGTAGTGGGA 59.417 45.833 11.04 0.00 39.60 4.37
3216 3362 5.507650 GCATAGCAACTAGTAGTAGTGGGAC 60.508 48.000 11.04 1.99 39.60 4.46
3231 3377 1.509923 GGACGGAGGTACCTCAACG 59.490 63.158 36.73 32.24 44.40 4.10
3263 3413 2.763448 AGTAGAGCAGCCTGACCTTTAG 59.237 50.000 0.00 0.00 0.00 1.85
3265 3415 0.251634 GAGCAGCCTGACCTTTAGCT 59.748 55.000 0.00 0.00 35.52 3.32
3279 3429 2.160721 TTAGCTCTGGGTGTAGAGGG 57.839 55.000 0.00 0.00 43.49 4.30
3352 3503 1.829533 ACAAGCCCACCAGCTGTTG 60.830 57.895 13.81 8.92 44.11 3.33
3353 3504 1.829533 CAAGCCCACCAGCTGTTGT 60.830 57.895 13.81 0.70 44.11 3.32
3354 3505 1.076044 AAGCCCACCAGCTGTTGTT 60.076 52.632 13.81 0.00 44.11 2.83
3355 3506 1.109323 AAGCCCACCAGCTGTTGTTC 61.109 55.000 13.81 2.44 44.11 3.18
3450 3601 4.763073 TCAGTCAATAATGGCAGAGAGTG 58.237 43.478 0.00 0.00 31.99 3.51
3490 3641 9.553064 ACCTTCAGTATCAAATGATATTGTCTC 57.447 33.333 19.23 3.26 42.12 3.36
3491 3642 9.551734 CCTTCAGTATCAAATGATATTGTCTCA 57.448 33.333 19.23 4.32 42.12 3.27
3523 4157 4.822685 AGCACTTGTCTCATCTCAGAAT 57.177 40.909 0.00 0.00 0.00 2.40
3540 4175 6.321181 TCTCAGAATTACCTGCACAAGTTTTT 59.679 34.615 0.00 0.00 34.28 1.94
3594 4229 8.969260 TCAAAATGATATGCTCTGAACTATGT 57.031 30.769 0.00 0.00 0.00 2.29
3595 4230 8.833493 TCAAAATGATATGCTCTGAACTATGTG 58.167 33.333 0.00 0.00 0.00 3.21
3632 4267 5.743026 TTCTTGTCGTTTAATCAAGCACA 57.257 34.783 0.00 0.00 38.56 4.57
3739 4374 1.212935 AGTGGTTCAACTTCTGCAGGT 59.787 47.619 15.13 1.12 0.00 4.00
3762 4397 9.683870 AGGTTATACGAATAATTGGTACCAAAA 57.316 29.630 30.31 21.23 39.55 2.44
3794 4429 7.307160 GGCAGGAATAAAAGTGTAAAGTTTTGC 60.307 37.037 8.48 3.37 0.00 3.68
3876 4511 5.897377 ACACTCCTGCATTTTATACCAAC 57.103 39.130 0.00 0.00 0.00 3.77
3933 4568 7.311092 TCATAGGTAACAAAGGAGAAACAGA 57.689 36.000 0.00 0.00 41.41 3.41
4019 4656 4.274147 TGCAGTCTTTTCCACACCTTTTA 58.726 39.130 0.00 0.00 0.00 1.52
4029 4668 9.793252 CTTTTCCACACCTTTTATCTGATAATG 57.207 33.333 10.68 8.61 0.00 1.90
4056 4695 8.630917 TGTATACAGTCTGCTTAATAGAAGTCC 58.369 37.037 0.08 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.146342 GTTCACCATCACCAGACAGTG 58.854 52.381 0.00 0.00 39.20 3.66
10 11 0.321475 TCGCATGCTGTTCACCATCA 60.321 50.000 17.13 0.00 0.00 3.07
27 28 1.342555 CATGCTTTGTGCCATGTTCG 58.657 50.000 0.00 0.00 42.00 3.95
66 67 3.561213 CATGAGGCTGTCTGCGCG 61.561 66.667 0.00 0.00 44.05 6.86
247 249 3.231736 AGGTGTGTTCCTCGCGGT 61.232 61.111 6.13 0.00 31.32 5.68
248 250 2.738521 CAGGTGTGTTCCTCGCGG 60.739 66.667 6.13 0.00 35.37 6.46
249 251 3.414700 GCAGGTGTGTTCCTCGCG 61.415 66.667 0.00 0.00 35.37 5.87
318 339 2.202987 GGAGCTGAGCACCGGATG 60.203 66.667 9.46 3.68 28.62 3.51
319 340 3.474570 GGGAGCTGAGCACCGGAT 61.475 66.667 14.63 0.00 40.13 4.18
321 342 3.965539 CTTGGGAGCTGAGCACCGG 62.966 68.421 14.63 0.00 40.13 5.28
322 343 2.435586 CTTGGGAGCTGAGCACCG 60.436 66.667 14.63 0.00 40.13 4.94
323 344 2.749441 GCTTGGGAGCTGAGCACC 60.749 66.667 12.75 12.75 45.65 5.01
334 355 1.386533 CATTAGAGTGCCTGCTTGGG 58.613 55.000 0.00 0.00 36.00 4.12
335 356 0.737219 GCATTAGAGTGCCTGCTTGG 59.263 55.000 0.00 0.00 39.18 3.61
338 359 1.004044 ACTTGCATTAGAGTGCCTGCT 59.996 47.619 0.00 0.00 44.43 4.24
345 366 4.223700 TGATGAGTGGACTTGCATTAGAGT 59.776 41.667 0.00 0.00 0.00 3.24
366 387 1.418264 TCCGATGGGTTGTTTCACTGA 59.582 47.619 0.00 0.00 33.83 3.41
376 397 6.659824 ACTAATTGTCTAATTCCGATGGGTT 58.340 36.000 0.00 0.00 37.64 4.11
383 404 7.974501 AGACACAGTACTAATTGTCTAATTCCG 59.025 37.037 23.07 0.00 45.41 4.30
393 414 5.186021 AGTGGAGGAGACACAGTACTAATTG 59.814 44.000 0.00 0.00 41.21 2.32
394 415 5.186021 CAGTGGAGGAGACACAGTACTAATT 59.814 44.000 0.00 0.00 41.21 1.40
395 416 4.707448 CAGTGGAGGAGACACAGTACTAAT 59.293 45.833 0.00 0.00 41.21 1.73
396 417 4.079970 CAGTGGAGGAGACACAGTACTAA 58.920 47.826 0.00 0.00 41.21 2.24
397 418 3.561528 CCAGTGGAGGAGACACAGTACTA 60.562 52.174 1.68 0.00 41.21 1.82
398 419 2.520069 CAGTGGAGGAGACACAGTACT 58.480 52.381 0.00 0.00 41.21 2.73
399 420 1.546476 CCAGTGGAGGAGACACAGTAC 59.454 57.143 1.68 0.00 41.21 2.73
401 422 0.833834 CCCAGTGGAGGAGACACAGT 60.834 60.000 11.95 0.00 41.21 3.55
402 423 1.548357 CCCCAGTGGAGGAGACACAG 61.548 65.000 11.95 0.00 41.21 3.66
403 424 1.536418 CCCCAGTGGAGGAGACACA 60.536 63.158 11.95 0.00 41.21 3.72
418 439 2.743538 GCCGTCAAACGTACCCCC 60.744 66.667 0.00 0.00 40.58 5.40
495 539 2.791501 TTTTACAGCCCGGTCGCCTC 62.792 60.000 0.00 0.00 0.00 4.70
496 540 2.400269 TTTTTACAGCCCGGTCGCCT 62.400 55.000 0.00 0.00 0.00 5.52
576 620 0.733223 GAAGACCGACTGCTCCGTTC 60.733 60.000 0.00 0.00 0.00 3.95
580 624 0.456628 GTAGGAAGACCGACTGCTCC 59.543 60.000 0.00 0.00 41.83 4.70
581 625 0.099082 CGTAGGAAGACCGACTGCTC 59.901 60.000 0.00 0.00 39.17 4.26
730 786 4.825679 GGAGTGGGAGGGAGGGGG 62.826 77.778 0.00 0.00 0.00 5.40
749 805 1.766059 CGTGGGGATGGATGGAGGA 60.766 63.158 0.00 0.00 0.00 3.71
768 824 2.520741 GGCGGAGAGAGAGGGGAG 60.521 72.222 0.00 0.00 0.00 4.30
769 825 4.507916 CGGCGGAGAGAGAGGGGA 62.508 72.222 0.00 0.00 0.00 4.81
818 909 0.804933 AATTACCGGCGAGCGAGTTC 60.805 55.000 9.30 0.00 0.00 3.01
819 910 0.457035 TAATTACCGGCGAGCGAGTT 59.543 50.000 9.30 0.00 0.00 3.01
904 999 1.648720 CCAAGTGTCCACGCAGTTG 59.351 57.895 6.65 6.65 41.61 3.16
978 1076 2.197875 GCCTCCCCGGACTAGCTA 59.802 66.667 0.73 0.00 33.16 3.32
979 1077 4.075793 TGCCTCCCCGGACTAGCT 62.076 66.667 0.73 0.00 33.16 3.32
980 1078 3.541713 CTGCCTCCCCGGACTAGC 61.542 72.222 0.73 0.40 33.16 3.42
981 1079 3.541713 GCTGCCTCCCCGGACTAG 61.542 72.222 0.73 0.00 33.16 2.57
1122 1229 1.367840 GTCGTGGAAGCTGAGGTGT 59.632 57.895 0.00 0.00 0.00 4.16
1627 1743 5.299028 TGATGATGCGTGGTGCTTAATTAAT 59.701 36.000 0.00 0.00 46.63 1.40
1642 1758 6.753744 TGCTAGCTATAGTTAATGATGATGCG 59.246 38.462 17.23 0.00 0.00 4.73
1659 1775 9.887406 GTTACTTGTTAATTTTGTTGCTAGCTA 57.113 29.630 17.23 5.31 0.00 3.32
1660 1776 7.865889 GGTTACTTGTTAATTTTGTTGCTAGCT 59.134 33.333 17.23 0.00 0.00 3.32
1661 1777 7.149031 CGGTTACTTGTTAATTTTGTTGCTAGC 60.149 37.037 8.10 8.10 0.00 3.42
1662 1778 7.149031 GCGGTTACTTGTTAATTTTGTTGCTAG 60.149 37.037 0.00 0.00 0.00 3.42
1666 1782 6.561350 GCTGCGGTTACTTGTTAATTTTGTTG 60.561 38.462 0.00 0.00 0.00 3.33
1667 1783 5.460748 GCTGCGGTTACTTGTTAATTTTGTT 59.539 36.000 0.00 0.00 0.00 2.83
1669 1785 4.979197 TGCTGCGGTTACTTGTTAATTTTG 59.021 37.500 0.00 0.00 0.00 2.44
1670 1786 5.189659 TGCTGCGGTTACTTGTTAATTTT 57.810 34.783 0.00 0.00 0.00 1.82
1679 1798 0.974383 AGGTACTGCTGCGGTTACTT 59.026 50.000 20.58 9.31 37.18 2.24
1702 1821 5.732247 GCATTTGGTGTTTATGGGACGATAC 60.732 44.000 0.00 0.00 0.00 2.24
1736 1855 1.448540 CGAGCAGGTGACCACATCC 60.449 63.158 3.63 0.00 0.00 3.51
1757 1876 0.677414 AGAGGTCGGAGTTCTCGTCC 60.677 60.000 0.00 0.00 36.39 4.79
1760 1879 1.455248 AGAAGAGGTCGGAGTTCTCG 58.545 55.000 0.00 0.00 34.28 4.04
1870 1989 6.096695 TGATTGATTTGCTTGTGTGATCATG 58.903 36.000 0.00 0.00 0.00 3.07
1871 1990 6.275494 TGATTGATTTGCTTGTGTGATCAT 57.725 33.333 0.00 0.00 0.00 2.45
1912 2031 1.807165 CCATGTCGGTCTGCGACTG 60.807 63.158 0.00 10.17 40.02 3.51
1913 2032 1.323271 ATCCATGTCGGTCTGCGACT 61.323 55.000 0.00 0.00 37.29 4.18
1914 2033 0.872021 GATCCATGTCGGTCTGCGAC 60.872 60.000 0.00 0.00 36.95 5.19
1915 2034 1.437573 GATCCATGTCGGTCTGCGA 59.562 57.895 0.00 0.00 35.57 5.10
1916 2035 1.946156 CGATCCATGTCGGTCTGCG 60.946 63.158 0.00 0.00 37.94 5.18
1917 2036 2.240500 GCGATCCATGTCGGTCTGC 61.241 63.158 7.71 0.00 41.72 4.26
2000 2119 1.297745 CGCGAAGTCCGAGTAGAGC 60.298 63.158 0.00 0.00 41.76 4.09
2222 2341 1.911357 TGTTCCATGATGTCAGCCTCT 59.089 47.619 0.00 0.00 0.00 3.69
2277 2396 8.334632 CGTCAACATCTGCATTTGTATTGTATA 58.665 33.333 2.44 0.00 0.00 1.47
2278 2397 7.188834 CGTCAACATCTGCATTTGTATTGTAT 58.811 34.615 2.44 0.00 0.00 2.29
2279 2398 6.541969 CGTCAACATCTGCATTTGTATTGTA 58.458 36.000 2.44 0.00 0.00 2.41
2280 2399 5.393124 CGTCAACATCTGCATTTGTATTGT 58.607 37.500 2.44 0.00 0.00 2.71
2281 2400 4.263677 GCGTCAACATCTGCATTTGTATTG 59.736 41.667 2.44 0.00 0.00 1.90
2282 2401 4.082841 TGCGTCAACATCTGCATTTGTATT 60.083 37.500 2.44 0.00 31.31 1.89
2349 2470 7.276438 GCAAAGACAAAGAACAAGAACAAGATT 59.724 33.333 0.00 0.00 0.00 2.40
2350 2471 6.753744 GCAAAGACAAAGAACAAGAACAAGAT 59.246 34.615 0.00 0.00 0.00 2.40
2351 2472 6.092748 GCAAAGACAAAGAACAAGAACAAGA 58.907 36.000 0.00 0.00 0.00 3.02
2352 2473 5.863397 TGCAAAGACAAAGAACAAGAACAAG 59.137 36.000 0.00 0.00 0.00 3.16
2353 2474 5.777802 TGCAAAGACAAAGAACAAGAACAA 58.222 33.333 0.00 0.00 0.00 2.83
2354 2475 5.384063 TGCAAAGACAAAGAACAAGAACA 57.616 34.783 0.00 0.00 0.00 3.18
2355 2476 4.800471 CCTGCAAAGACAAAGAACAAGAAC 59.200 41.667 0.00 0.00 0.00 3.01
2356 2477 4.704540 TCCTGCAAAGACAAAGAACAAGAA 59.295 37.500 0.00 0.00 0.00 2.52
2357 2478 4.269183 TCCTGCAAAGACAAAGAACAAGA 58.731 39.130 0.00 0.00 0.00 3.02
2358 2479 4.498682 CCTCCTGCAAAGACAAAGAACAAG 60.499 45.833 0.00 0.00 0.00 3.16
2359 2480 3.381272 CCTCCTGCAAAGACAAAGAACAA 59.619 43.478 0.00 0.00 0.00 2.83
2360 2481 2.951642 CCTCCTGCAAAGACAAAGAACA 59.048 45.455 0.00 0.00 0.00 3.18
2361 2482 2.952310 ACCTCCTGCAAAGACAAAGAAC 59.048 45.455 0.00 0.00 0.00 3.01
2362 2483 3.297134 ACCTCCTGCAAAGACAAAGAA 57.703 42.857 0.00 0.00 0.00 2.52
2435 2556 2.516923 GAACTCGAGGTACGTGACATG 58.483 52.381 18.41 0.00 43.13 3.21
2590 2711 1.606224 GGGCCATTGTTGCTGTCTTTG 60.606 52.381 4.39 0.00 0.00 2.77
2629 2750 5.762045 TGCTTTGCTTACTTTGATCTGTTC 58.238 37.500 0.00 0.00 0.00 3.18
2688 2809 2.160205 CGTACAACCAGAGGACAGAGA 58.840 52.381 0.00 0.00 0.00 3.10
2856 2985 4.680237 TTGAGGCTCACCGCGTGG 62.680 66.667 18.55 14.93 42.76 4.94
2859 2988 4.717629 TCGTTGAGGCTCACCGCG 62.718 66.667 26.94 23.92 42.76 6.46
2884 3013 1.634702 GCCTTGTCGCAGAAGTCTAG 58.365 55.000 0.00 0.00 39.69 2.43
2904 3033 4.812476 TGCTTCATCCCGACGCCG 62.812 66.667 0.00 0.00 38.10 6.46
2943 3072 2.257676 GCTTTCCACTGCTGCTGC 59.742 61.111 8.89 8.89 40.20 5.25
3141 3279 4.508662 CAGATCTTGTCTTTACAGGGGAC 58.491 47.826 0.00 0.00 36.83 4.46
3146 3284 3.849911 TCGGCAGATCTTGTCTTTACAG 58.150 45.455 0.00 0.00 36.83 2.74
3186 3324 1.645034 ACTAGTTGCTATGCTGCGTG 58.355 50.000 4.25 0.00 35.36 5.34
3187 3325 2.427453 ACTACTAGTTGCTATGCTGCGT 59.573 45.455 0.00 0.00 35.36 5.24
3209 3349 1.000107 GAGGTACCTCCGTCCCACT 60.000 63.158 28.87 0.00 41.99 4.00
3213 3359 0.962356 TCGTTGAGGTACCTCCGTCC 60.962 60.000 34.05 19.49 42.09 4.79
3214 3360 0.883833 TTCGTTGAGGTACCTCCGTC 59.116 55.000 34.05 23.09 42.09 4.79
3215 3361 0.600057 GTTCGTTGAGGTACCTCCGT 59.400 55.000 34.05 5.15 42.09 4.69
3216 3362 0.599558 TGTTCGTTGAGGTACCTCCG 59.400 55.000 34.05 29.62 42.09 4.63
3231 3377 3.249917 GCTGCTCTACTCTGAAGTGTTC 58.750 50.000 0.00 0.00 36.92 3.18
3263 3413 0.905337 ACACCCTCTACACCCAGAGC 60.905 60.000 0.00 0.00 40.70 4.09
3265 3415 0.485543 TCACACCCTCTACACCCAGA 59.514 55.000 0.00 0.00 0.00 3.86
3279 3429 2.229792 TGATTGCCTCCAAAGTCACAC 58.770 47.619 0.00 0.00 34.05 3.82
3352 3503 1.912110 CTGCTCTACGCTGTAACGAAC 59.088 52.381 0.00 0.00 40.11 3.95
3353 3504 1.808343 TCTGCTCTACGCTGTAACGAA 59.192 47.619 0.00 0.00 40.11 3.85
3354 3505 1.397343 CTCTGCTCTACGCTGTAACGA 59.603 52.381 0.00 0.00 40.11 3.85
3355 3506 1.130749 ACTCTGCTCTACGCTGTAACG 59.869 52.381 0.00 0.00 40.11 3.18
3450 3601 3.579151 ACTGAAGGTTCTACCCTGAAGTC 59.421 47.826 0.00 0.00 39.75 3.01
3490 3641 5.237127 TGAGACAAGTGCTTAACAGACAATG 59.763 40.000 0.00 0.00 0.00 2.82
3491 3642 5.368145 TGAGACAAGTGCTTAACAGACAAT 58.632 37.500 0.00 0.00 0.00 2.71
3493 3644 4.400529 TGAGACAAGTGCTTAACAGACA 57.599 40.909 0.00 0.00 0.00 3.41
3494 3645 5.233988 AGATGAGACAAGTGCTTAACAGAC 58.766 41.667 0.00 0.00 0.00 3.51
3497 4131 5.011023 TCTGAGATGAGACAAGTGCTTAACA 59.989 40.000 0.00 0.00 0.00 2.41
3540 4175 8.956426 CATAAAGATTAACAGAGCCTGGTTAAA 58.044 33.333 8.05 0.00 35.51 1.52
3545 4180 7.500227 TGATTCATAAAGATTAACAGAGCCTGG 59.500 37.037 7.06 0.00 35.51 4.45
3594 4229 5.636837 GACAAGAAACTTTACTGTTGCACA 58.363 37.500 0.00 0.00 0.00 4.57
3595 4230 4.728608 CGACAAGAAACTTTACTGTTGCAC 59.271 41.667 0.00 0.00 0.00 4.57
3632 4267 7.920682 CCAAAAGCTTCACTATTTGTAACAAGT 59.079 33.333 0.00 0.00 32.29 3.16
3762 4397 4.677182 ACACTTTTATTCCTGCCCATTCT 58.323 39.130 0.00 0.00 0.00 2.40
3794 4429 3.169099 TCTTTCTCTGTTCCCTCCTCAG 58.831 50.000 0.00 0.00 0.00 3.35
3842 4477 2.205074 CAGGAGTGTATTGCATCCGTC 58.795 52.381 0.00 0.00 36.91 4.79
3876 4511 6.516718 AGGGACAATAGTAGATCACAATTCG 58.483 40.000 0.00 0.00 0.00 3.34
3933 4568 8.017418 TCATAAATTGGAACTTTTGTCTTGGT 57.983 30.769 0.00 0.00 0.00 3.67
3975 4610 0.253044 TAGCCATCAAGGTGTGGAGC 59.747 55.000 0.00 0.00 40.61 4.70
4019 4656 8.187913 AGCAGACTGTATACACATTATCAGAT 57.812 34.615 0.08 0.00 33.14 2.90
4029 4668 9.453325 GACTTCTATTAAGCAGACTGTATACAC 57.547 37.037 0.08 0.00 0.00 2.90
4052 4691 2.320681 TAGTTGCCACTACCAGGACT 57.679 50.000 0.00 0.00 34.06 3.85


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

AutoCloner maintained by Alex Coulton.