Multiple sequence alignment - TraesCS5A01G090600

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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 TraesCS5A01G090600 chr5A 100.000 2501 0 0 1 2501 122998896 122996396 0.000000e+00 4619.0
1 TraesCS5A01G090600 chr5A 92.593 54 4 0 1729 1782 122958311 122958258 7.420000e-11 78.7
2 TraesCS5A01G090600 chr5D 93.416 1215 56 10 602 1809 115975810 115974613 0.000000e+00 1779.0
3 TraesCS5A01G090600 chr5D 91.437 327 25 2 1 326 115978051 115977727 1.760000e-121 446.0
4 TraesCS5A01G090600 chr5B 92.841 908 48 10 702 1601 127538379 127537481 0.000000e+00 1301.0
5 TraesCS5A01G090600 chr5B 89.355 667 64 7 1840 2501 262054724 262054060 0.000000e+00 832.0
6 TraesCS5A01G090600 chr5B 81.350 622 72 22 1 600 127546664 127546065 1.350000e-127 466.0
7 TraesCS5A01G090600 chr5B 93.103 116 6 1 603 716 127540641 127540526 4.280000e-38 169.0
8 TraesCS5A01G090600 chr1D 92.090 670 48 5 1836 2501 417776273 417775605 0.000000e+00 939.0
9 TraesCS5A01G090600 chr4A 88.789 669 64 8 1840 2501 379467062 379467726 0.000000e+00 809.0
10 TraesCS5A01G090600 chr4A 87.338 616 68 7 1893 2501 69274526 69275138 0.000000e+00 697.0
11 TraesCS5A01G090600 chr7B 88.606 667 70 6 1840 2501 126028535 126029200 0.000000e+00 806.0
12 TraesCS5A01G090600 chr7A 90.822 523 42 4 1983 2501 10976254 10976774 0.000000e+00 695.0
13 TraesCS5A01G090600 chr3B 89.369 555 56 3 1840 2392 803196876 803197429 0.000000e+00 695.0
14 TraesCS5A01G090600 chr2D 89.493 552 48 8 1951 2498 346152704 346153249 0.000000e+00 689.0
15 TraesCS5A01G090600 chr7D 88.139 548 55 8 1953 2493 221354134 221353590 0.000000e+00 643.0


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 TraesCS5A01G090600 chr5A 122996396 122998896 2500 True 4619.0 4619 100.0000 1 2501 1 chr5A.!!$R2 2500
1 TraesCS5A01G090600 chr5D 115974613 115978051 3438 True 1112.5 1779 92.4265 1 1809 2 chr5D.!!$R1 1808
2 TraesCS5A01G090600 chr5B 262054060 262054724 664 True 832.0 832 89.3550 1840 2501 1 chr5B.!!$R2 661
3 TraesCS5A01G090600 chr5B 127537481 127540641 3160 True 735.0 1301 92.9720 603 1601 2 chr5B.!!$R3 998
4 TraesCS5A01G090600 chr5B 127546065 127546664 599 True 466.0 466 81.3500 1 600 1 chr5B.!!$R1 599
5 TraesCS5A01G090600 chr1D 417775605 417776273 668 True 939.0 939 92.0900 1836 2501 1 chr1D.!!$R1 665
6 TraesCS5A01G090600 chr4A 379467062 379467726 664 False 809.0 809 88.7890 1840 2501 1 chr4A.!!$F2 661
7 TraesCS5A01G090600 chr4A 69274526 69275138 612 False 697.0 697 87.3380 1893 2501 1 chr4A.!!$F1 608
8 TraesCS5A01G090600 chr7B 126028535 126029200 665 False 806.0 806 88.6060 1840 2501 1 chr7B.!!$F1 661
9 TraesCS5A01G090600 chr7A 10976254 10976774 520 False 695.0 695 90.8220 1983 2501 1 chr7A.!!$F1 518
10 TraesCS5A01G090600 chr3B 803196876 803197429 553 False 695.0 695 89.3690 1840 2392 1 chr3B.!!$F1 552
11 TraesCS5A01G090600 chr2D 346152704 346153249 545 False 689.0 689 89.4930 1951 2498 1 chr2D.!!$F1 547
12 TraesCS5A01G090600 chr7D 221353590 221354134 544 True 643.0 643 88.1390 1953 2493 1 chr7D.!!$R1 540

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
362 380 0.381801 GCATATGACGTGCCCCTTTG 59.618 55.0 6.97 0.0 36.61 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1834 5695 0.179073 CAGCTAGACCCGTCCCAATG 60.179 60.0 0.0 0.0 0.0 2.82 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
118 119 4.572985 TTTTTGAGATGTGCTTCTGGTG 57.427 40.909 0.00 0.00 0.00 4.17
119 120 3.490439 TTTGAGATGTGCTTCTGGTGA 57.510 42.857 0.00 0.00 0.00 4.02
142 143 4.919677 TGCACATGTTGTACTTATGACG 57.080 40.909 0.00 0.00 0.00 4.35
143 144 4.561105 TGCACATGTTGTACTTATGACGA 58.439 39.130 0.00 0.00 0.00 4.20
144 145 4.991687 TGCACATGTTGTACTTATGACGAA 59.008 37.500 0.00 0.00 0.00 3.85
217 235 2.022764 CACGGGTTGTGCATCTCATA 57.977 50.000 0.00 0.00 42.70 2.15
218 236 2.355197 CACGGGTTGTGCATCTCATAA 58.645 47.619 0.00 0.00 42.70 1.90
260 278 4.647611 TCACGGAACCAAATATGTGACTT 58.352 39.130 0.00 0.00 31.93 3.01
261 279 5.795972 TCACGGAACCAAATATGTGACTTA 58.204 37.500 0.00 0.00 31.93 2.24
265 283 5.446741 CGGAACCAAATATGTGACTTAACGG 60.447 44.000 0.00 0.00 0.00 4.44
301 319 1.142667 TCCTGGAAGCACACACAATGA 59.857 47.619 0.00 0.00 0.00 2.57
307 325 3.989817 GGAAGCACACACAATGATTTTCC 59.010 43.478 0.00 0.00 31.90 3.13
338 356 3.272766 GCACAACTTTGCTTCCCAC 57.727 52.632 0.00 0.00 39.59 4.61
357 375 0.940126 CAGAAGCATATGACGTGCCC 59.060 55.000 6.97 0.00 43.50 5.36
362 380 0.381801 GCATATGACGTGCCCCTTTG 59.618 55.000 6.97 0.00 36.61 2.77
418 436 5.576128 TGGTTTTCTTTATTACTCCCCCTG 58.424 41.667 0.00 0.00 0.00 4.45
419 437 5.075344 TGGTTTTCTTTATTACTCCCCCTGT 59.925 40.000 0.00 0.00 0.00 4.00
420 438 6.014647 GGTTTTCTTTATTACTCCCCCTGTT 58.985 40.000 0.00 0.00 0.00 3.16
424 442 9.657728 TTTTCTTTATTACTCCCCCTGTTAAAA 57.342 29.630 0.00 0.00 0.00 1.52
426 444 7.177184 TCTTTATTACTCCCCCTGTTAAAACC 58.823 38.462 0.00 0.00 0.00 3.27
428 446 5.546035 ATTACTCCCCCTGTTAAAACCAT 57.454 39.130 0.00 0.00 0.00 3.55
429 447 3.451402 ACTCCCCCTGTTAAAACCATC 57.549 47.619 0.00 0.00 0.00 3.51
430 448 2.993863 ACTCCCCCTGTTAAAACCATCT 59.006 45.455 0.00 0.00 0.00 2.90
431 449 4.180723 ACTCCCCCTGTTAAAACCATCTA 58.819 43.478 0.00 0.00 0.00 1.98
520 542 7.888250 AAACTGAAATCCAGAAGAAGTTTCT 57.112 32.000 0.00 0.00 45.78 2.52
652 2341 3.871006 TCTGGTAAGCTATGCAATGTTCG 59.129 43.478 0.00 0.00 0.00 3.95
759 4610 3.181440 TGGGAAGAAGATTGAACAGCTGT 60.181 43.478 15.25 15.25 0.00 4.40
769 4620 5.879223 AGATTGAACAGCTGTGGAAAGATAG 59.121 40.000 22.49 0.00 0.00 2.08
770 4621 3.338249 TGAACAGCTGTGGAAAGATAGC 58.662 45.455 22.49 0.89 36.45 2.97
771 4622 3.244526 TGAACAGCTGTGGAAAGATAGCA 60.245 43.478 22.49 3.46 38.59 3.49
772 4623 2.983229 ACAGCTGTGGAAAGATAGCAG 58.017 47.619 20.97 0.00 38.59 4.24
774 4625 1.020437 GCTGTGGAAAGATAGCAGCC 58.980 55.000 0.00 0.00 44.61 4.85
775 4626 1.407989 GCTGTGGAAAGATAGCAGCCT 60.408 52.381 0.00 0.00 44.61 4.58
776 4627 2.286872 CTGTGGAAAGATAGCAGCCTG 58.713 52.381 0.00 0.00 0.00 4.85
777 4628 1.908619 TGTGGAAAGATAGCAGCCTGA 59.091 47.619 0.00 0.00 0.00 3.86
779 4630 2.093235 GTGGAAAGATAGCAGCCTGAGT 60.093 50.000 0.00 0.00 0.00 3.41
818 4673 1.275291 TGTGATCTCCGGTCCAAGTTC 59.725 52.381 0.00 0.00 0.00 3.01
887 4746 9.778741 TTCCTTTGCACCTACTCTATATAAATG 57.221 33.333 0.00 0.00 0.00 2.32
922 4782 3.675775 GCTCTCACTCATCACCAGTCTTC 60.676 52.174 0.00 0.00 0.00 2.87
1015 4875 3.254024 AAGATGGTCGCCGGCTGTT 62.254 57.895 26.68 7.07 0.00 3.16
1067 4927 2.514824 GGAGCGGATGTGGAAGGC 60.515 66.667 0.00 0.00 0.00 4.35
1270 5130 1.519455 CGGGTGATCAAGACGGAGC 60.519 63.158 0.00 0.00 0.00 4.70
1533 5393 7.427606 CAGCACGAGAAACATCAGAAATAAATC 59.572 37.037 0.00 0.00 0.00 2.17
1542 5402 7.893124 ACATCAGAAATAAATCAATCTGCCT 57.107 32.000 0.00 0.00 39.27 4.75
1625 5485 7.502696 AGTATATACCGGTGTTATTTGCTTCA 58.497 34.615 19.93 0.00 0.00 3.02
1727 5587 7.462571 AATCCCTGTTTTAAGCTCGTATTTT 57.537 32.000 0.00 0.00 0.00 1.82
1806 5667 7.654022 ATTTCTTGACAAAGGGTGTTCTTTA 57.346 32.000 0.00 0.00 41.96 1.85
1809 5670 8.754991 TTCTTGACAAAGGGTGTTCTTTATTA 57.245 30.769 0.00 0.00 41.96 0.98
1810 5671 8.161699 TCTTGACAAAGGGTGTTCTTTATTAC 57.838 34.615 0.00 0.00 41.96 1.89
1811 5672 7.996644 TCTTGACAAAGGGTGTTCTTTATTACT 59.003 33.333 0.00 0.00 41.96 2.24
1812 5673 7.739498 TGACAAAGGGTGTTCTTTATTACTC 57.261 36.000 0.00 0.00 41.96 2.59
1813 5674 6.713450 TGACAAAGGGTGTTCTTTATTACTCC 59.287 38.462 0.00 0.00 41.96 3.85
1814 5675 6.008331 ACAAAGGGTGTTCTTTATTACTCCC 58.992 40.000 0.00 0.00 44.62 4.30
1815 5676 4.857130 AGGGTGTTCTTTATTACTCCCC 57.143 45.455 8.34 0.00 45.13 4.81
1816 5677 4.445564 AGGGTGTTCTTTATTACTCCCCT 58.554 43.478 8.34 0.00 45.13 4.79
1817 5678 4.856182 AGGGTGTTCTTTATTACTCCCCTT 59.144 41.667 8.34 0.00 45.13 3.95
1818 5679 4.948004 GGGTGTTCTTTATTACTCCCCTTG 59.052 45.833 0.00 0.00 40.55 3.61
1819 5680 5.516062 GGGTGTTCTTTATTACTCCCCTTGT 60.516 44.000 0.00 0.00 40.55 3.16
1820 5681 6.008331 GGTGTTCTTTATTACTCCCCTTGTT 58.992 40.000 0.00 0.00 0.00 2.83
1821 5682 6.150641 GGTGTTCTTTATTACTCCCCTTGTTC 59.849 42.308 0.00 0.00 0.00 3.18
1822 5683 6.713450 GTGTTCTTTATTACTCCCCTTGTTCA 59.287 38.462 0.00 0.00 0.00 3.18
1823 5684 7.393515 GTGTTCTTTATTACTCCCCTTGTTCAT 59.606 37.037 0.00 0.00 0.00 2.57
1824 5685 7.947890 TGTTCTTTATTACTCCCCTTGTTCATT 59.052 33.333 0.00 0.00 0.00 2.57
1825 5686 8.803235 GTTCTTTATTACTCCCCTTGTTCATTT 58.197 33.333 0.00 0.00 0.00 2.32
1835 5696 8.778059 ACTCCCCTTGTTCATTTATATAAGACA 58.222 33.333 0.00 0.00 0.00 3.41
1836 5697 9.799106 CTCCCCTTGTTCATTTATATAAGACAT 57.201 33.333 0.00 0.00 0.00 3.06
1878 5739 1.019673 CGGGTACTAGCTAGCGTTCA 58.980 55.000 20.91 0.00 0.00 3.18
1899 5760 0.466555 TAGCGGCCGGCCAAATAAAT 60.467 50.000 42.78 22.10 45.17 1.40
1911 5772 5.163602 CGGCCAAATAAATTAAGTGCCTGTA 60.164 40.000 2.24 0.00 35.51 2.74
1923 5785 0.844661 TGCCTGTACCTTGGTCCCAT 60.845 55.000 0.00 0.00 0.00 4.00
2027 5891 3.190744 GTGTGGTCTCTTCTCACGTGATA 59.809 47.826 20.40 9.48 34.43 2.15
2033 5897 4.036262 GTCTCTTCTCACGTGATAGATGCT 59.964 45.833 20.40 0.00 0.00 3.79
2141 6008 0.843872 CGCGCGTCGAAATTCAGATA 59.156 50.000 24.19 0.00 41.67 1.98
2171 6039 2.355481 GAAACCCTCGCGACGTGT 60.355 61.111 3.71 0.00 0.00 4.49
2211 6079 1.665679 CATGGGGATGTTTCGACGAAG 59.334 52.381 10.61 0.00 0.00 3.79
2246 6114 8.518430 TGCCAACTAAATATCAATGTATGTGT 57.482 30.769 0.00 0.00 0.00 3.72
2302 6333 1.073763 TGTGTGCCAAATAGTCCTGCT 59.926 47.619 0.00 0.00 0.00 4.24
2310 6341 6.318900 GTGCCAAATAGTCCTGCTAACTAAAT 59.681 38.462 0.00 0.00 33.19 1.40
2323 6354 9.325198 CCTGCTAACTAAATATCAATGTGTGTA 57.675 33.333 0.00 0.00 0.00 2.90
2393 6427 4.980573 AGTCCTGCCAACTAAACACAATA 58.019 39.130 0.00 0.00 0.00 1.90
2433 6467 3.120385 TCGCGCCAACTGAGCATG 61.120 61.111 0.00 0.00 0.00 4.06
2445 6480 3.743521 ACTGAGCATGTGTGTGTGTAAT 58.256 40.909 0.00 0.00 0.00 1.89
2453 6488 5.872617 GCATGTGTGTGTGTAATTAGTCCTA 59.127 40.000 0.00 0.00 0.00 2.94
2454 6489 6.538742 GCATGTGTGTGTGTAATTAGTCCTAT 59.461 38.462 0.00 0.00 0.00 2.57
2475 6510 9.056005 TCCTATCAACTAAATATCAATGTGTGC 57.944 33.333 0.00 0.00 0.00 4.57
2478 6513 4.552166 ACTAAATATCAATGTGTGCGCC 57.448 40.909 4.18 0.00 0.00 6.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 3.490439 TTCACCAGAAGCACATCTCAA 57.510 42.857 0.00 0.00 0.00 3.02
101 102 3.340928 CATTCACCAGAAGCACATCTCA 58.659 45.455 0.00 0.00 37.14 3.27
118 119 5.959527 CGTCATAAGTACAACATGTGCATTC 59.040 40.000 0.00 0.00 35.34 2.67
119 120 5.641636 TCGTCATAAGTACAACATGTGCATT 59.358 36.000 0.00 0.00 35.34 3.56
200 218 2.905075 TCTTATGAGATGCACAACCCG 58.095 47.619 0.00 0.00 0.00 5.28
210 228 7.338703 AAGCACATCATGTGTTTCTTATGAGAT 59.661 33.333 19.13 0.00 46.41 2.75
280 298 1.955778 CATTGTGTGTGCTTCCAGGAA 59.044 47.619 0.71 0.71 0.00 3.36
335 353 1.328680 GCACGTCATATGCTTCTGTGG 59.671 52.381 0.00 0.00 40.08 4.17
338 356 0.940126 GGGCACGTCATATGCTTCTG 59.060 55.000 0.00 0.00 42.93 3.02
389 407 9.470399 GGGGAGTAATAAAGAAAACCATCTAAA 57.530 33.333 0.00 0.00 0.00 1.85
390 408 8.057011 GGGGGAGTAATAAAGAAAACCATCTAA 58.943 37.037 0.00 0.00 0.00 2.10
391 409 7.407918 AGGGGGAGTAATAAAGAAAACCATCTA 59.592 37.037 0.00 0.00 0.00 1.98
393 411 6.321435 CAGGGGGAGTAATAAAGAAAACCATC 59.679 42.308 0.00 0.00 0.00 3.51
395 413 5.075344 ACAGGGGGAGTAATAAAGAAAACCA 59.925 40.000 0.00 0.00 0.00 3.67
396 414 5.577100 ACAGGGGGAGTAATAAAGAAAACC 58.423 41.667 0.00 0.00 0.00 3.27
397 415 8.640063 TTAACAGGGGGAGTAATAAAGAAAAC 57.360 34.615 0.00 0.00 0.00 2.43
398 416 9.657728 TTTTAACAGGGGGAGTAATAAAGAAAA 57.342 29.630 0.00 0.00 0.00 2.29
399 417 9.081204 GTTTTAACAGGGGGAGTAATAAAGAAA 57.919 33.333 0.00 0.00 0.00 2.52
400 418 7.670979 GGTTTTAACAGGGGGAGTAATAAAGAA 59.329 37.037 0.00 0.00 0.00 2.52
401 419 7.177184 GGTTTTAACAGGGGGAGTAATAAAGA 58.823 38.462 0.00 0.00 0.00 2.52
402 420 6.949463 TGGTTTTAACAGGGGGAGTAATAAAG 59.051 38.462 0.00 0.00 0.00 1.85
403 421 6.861129 TGGTTTTAACAGGGGGAGTAATAAA 58.139 36.000 0.00 0.00 0.00 1.40
404 422 6.466009 TGGTTTTAACAGGGGGAGTAATAA 57.534 37.500 0.00 0.00 0.00 1.40
406 424 5.255443 AGATGGTTTTAACAGGGGGAGTAAT 59.745 40.000 0.00 0.00 0.00 1.89
407 425 4.604490 AGATGGTTTTAACAGGGGGAGTAA 59.396 41.667 0.00 0.00 0.00 2.24
408 426 4.180723 AGATGGTTTTAACAGGGGGAGTA 58.819 43.478 0.00 0.00 0.00 2.59
409 427 2.993863 AGATGGTTTTAACAGGGGGAGT 59.006 45.455 0.00 0.00 0.00 3.85
410 428 3.739401 AGATGGTTTTAACAGGGGGAG 57.261 47.619 0.00 0.00 0.00 4.30
411 429 5.602291 TTTAGATGGTTTTAACAGGGGGA 57.398 39.130 0.00 0.00 0.00 4.81
412 430 5.046878 GGTTTTAGATGGTTTTAACAGGGGG 60.047 44.000 0.00 0.00 0.00 5.40
413 431 5.540719 TGGTTTTAGATGGTTTTAACAGGGG 59.459 40.000 0.00 0.00 0.00 4.79
418 436 7.430441 TCTGCTTGGTTTTAGATGGTTTTAAC 58.570 34.615 0.00 0.00 0.00 2.01
419 437 7.589958 TCTGCTTGGTTTTAGATGGTTTTAA 57.410 32.000 0.00 0.00 0.00 1.52
420 438 7.589958 TTCTGCTTGGTTTTAGATGGTTTTA 57.410 32.000 0.00 0.00 0.00 1.52
424 442 6.458210 CAATTTCTGCTTGGTTTTAGATGGT 58.542 36.000 0.00 0.00 0.00 3.55
426 444 6.690530 TCCAATTTCTGCTTGGTTTTAGATG 58.309 36.000 1.98 0.00 43.07 2.90
428 446 6.323739 ACTTCCAATTTCTGCTTGGTTTTAGA 59.676 34.615 1.98 0.00 43.07 2.10
429 447 6.421801 CACTTCCAATTTCTGCTTGGTTTTAG 59.578 38.462 1.98 0.19 43.07 1.85
430 448 6.097554 TCACTTCCAATTTCTGCTTGGTTTTA 59.902 34.615 1.98 0.00 43.07 1.52
431 449 5.104982 TCACTTCCAATTTCTGCTTGGTTTT 60.105 36.000 1.98 0.00 43.07 2.43
498 520 6.652900 GCTAGAAACTTCTTCTGGATTTCAGT 59.347 38.462 0.00 0.00 40.19 3.41
499 521 6.652481 TGCTAGAAACTTCTTCTGGATTTCAG 59.348 38.462 0.00 0.00 40.41 3.02
548 570 2.925170 ACTTCCTGTGGAGCGCCT 60.925 61.111 8.34 0.00 31.21 5.52
549 571 2.527951 ATCACTTCCTGTGGAGCGCC 62.528 60.000 2.29 0.00 46.20 6.53
551 573 0.460987 GGATCACTTCCTGTGGAGCG 60.461 60.000 0.00 0.00 46.20 5.03
600 2287 1.671850 GCACGCTAGGAGCAACTAACA 60.672 52.381 0.00 0.00 42.58 2.41
682 2373 9.448438 AGCATACTATTCTTGTTGTTGATGTAA 57.552 29.630 0.00 0.00 0.00 2.41
759 4610 2.093288 CACTCAGGCTGCTATCTTTCCA 60.093 50.000 10.34 0.00 0.00 3.53
770 4621 0.391395 CTCTTGGAGCACTCAGGCTG 60.391 60.000 8.58 8.58 45.99 4.85
772 4623 0.390998 GACTCTTGGAGCACTCAGGC 60.391 60.000 0.00 0.00 32.04 4.85
773 4624 0.248843 GGACTCTTGGAGCACTCAGG 59.751 60.000 0.00 0.00 32.04 3.86
774 4625 0.972134 TGGACTCTTGGAGCACTCAG 59.028 55.000 0.00 0.00 32.04 3.35
775 4626 1.070758 GTTGGACTCTTGGAGCACTCA 59.929 52.381 0.00 0.00 32.04 3.41
776 4627 1.609320 GGTTGGACTCTTGGAGCACTC 60.609 57.143 0.00 0.00 32.04 3.51
777 4628 0.398318 GGTTGGACTCTTGGAGCACT 59.602 55.000 0.00 0.00 32.04 4.40
779 4630 1.067295 ATGGTTGGACTCTTGGAGCA 58.933 50.000 0.00 0.00 32.04 4.26
818 4673 9.991906 AAGGGATTCATAAAATAGCAATTGATG 57.008 29.630 10.34 2.13 0.00 3.07
959 4819 1.375140 ACTGGATCGCTGCACACTG 60.375 57.895 0.00 0.00 0.00 3.66
1015 4875 1.443702 CGCACTCGTCGGTGATGAA 60.444 57.895 15.29 0.00 39.34 2.57
1295 5155 2.435586 CCTGCGACTTGAGCTGGG 60.436 66.667 0.00 0.00 45.97 4.45
1447 5307 1.086634 GCCTCGACCATCTTGAGCAC 61.087 60.000 0.00 0.00 0.00 4.40
1576 5436 6.524734 TCACCATAATAGAGGCATGTACTTG 58.475 40.000 4.42 4.42 0.00 3.16
1577 5437 6.327626 ACTCACCATAATAGAGGCATGTACTT 59.672 38.462 0.00 0.00 33.76 2.24
1625 5485 5.853810 CGATTATTCTCACGAAGTCGATCAT 59.146 40.000 7.87 0.00 41.61 2.45
1644 5504 5.704515 CGTACTAAAGATCCTCCCTCGATTA 59.295 44.000 0.00 0.00 0.00 1.75
1678 5538 9.562408 TTAAACACTCATATACACCTCAAACAA 57.438 29.630 0.00 0.00 0.00 2.83
1727 5587 3.691049 GCTTGAAGCAACTTACACACA 57.309 42.857 13.09 0.00 41.89 3.72
1768 5628 7.575414 TGTCAAGAAATAAACCAAACTGCTA 57.425 32.000 0.00 0.00 0.00 3.49
1786 5647 8.166422 AGTAATAAAGAACACCCTTTGTCAAG 57.834 34.615 0.00 0.00 37.51 3.02
1809 5670 8.778059 TGTCTTATATAAATGAACAAGGGGAGT 58.222 33.333 0.00 0.00 0.00 3.85
1810 5671 9.799106 ATGTCTTATATAAATGAACAAGGGGAG 57.201 33.333 0.00 0.00 0.00 4.30
1817 5678 9.051679 CGTCCCAATGTCTTATATAAATGAACA 57.948 33.333 0.00 0.45 0.00 3.18
1818 5679 8.504005 CCGTCCCAATGTCTTATATAAATGAAC 58.496 37.037 0.00 0.00 0.00 3.18
1819 5680 7.663905 CCCGTCCCAATGTCTTATATAAATGAA 59.336 37.037 0.00 0.00 0.00 2.57
1820 5681 7.165485 CCCGTCCCAATGTCTTATATAAATGA 58.835 38.462 0.00 0.00 0.00 2.57
1821 5682 6.940298 ACCCGTCCCAATGTCTTATATAAATG 59.060 38.462 0.00 0.00 0.00 2.32
1822 5683 7.017254 AGACCCGTCCCAATGTCTTATATAAAT 59.983 37.037 0.00 0.00 34.53 1.40
1823 5684 6.328148 AGACCCGTCCCAATGTCTTATATAAA 59.672 38.462 0.00 0.00 34.53 1.40
1824 5685 5.842328 AGACCCGTCCCAATGTCTTATATAA 59.158 40.000 0.00 0.00 34.53 0.98
1825 5686 5.399991 AGACCCGTCCCAATGTCTTATATA 58.600 41.667 0.00 0.00 34.53 0.86
1826 5687 4.232091 AGACCCGTCCCAATGTCTTATAT 58.768 43.478 0.00 0.00 34.53 0.86
1827 5688 3.649843 AGACCCGTCCCAATGTCTTATA 58.350 45.455 0.00 0.00 34.53 0.98
1828 5689 2.478292 AGACCCGTCCCAATGTCTTAT 58.522 47.619 0.00 0.00 34.53 1.73
1829 5690 1.946984 AGACCCGTCCCAATGTCTTA 58.053 50.000 0.00 0.00 34.53 2.10
1830 5691 1.831736 CTAGACCCGTCCCAATGTCTT 59.168 52.381 0.00 0.00 38.85 3.01
1831 5692 1.486211 CTAGACCCGTCCCAATGTCT 58.514 55.000 0.00 0.00 40.87 3.41
1832 5693 0.179081 GCTAGACCCGTCCCAATGTC 60.179 60.000 0.00 0.00 0.00 3.06
1833 5694 0.617820 AGCTAGACCCGTCCCAATGT 60.618 55.000 0.00 0.00 0.00 2.71
1834 5695 0.179073 CAGCTAGACCCGTCCCAATG 60.179 60.000 0.00 0.00 0.00 2.82
1835 5696 1.338136 CCAGCTAGACCCGTCCCAAT 61.338 60.000 0.00 0.00 0.00 3.16
1836 5697 1.987855 CCAGCTAGACCCGTCCCAA 60.988 63.158 0.00 0.00 0.00 4.12
1837 5698 2.363795 CCAGCTAGACCCGTCCCA 60.364 66.667 0.00 0.00 0.00 4.37
1838 5699 3.851128 GCCAGCTAGACCCGTCCC 61.851 72.222 0.00 0.00 0.00 4.46
1878 5739 2.260088 TTATTTGGCCGGCCGCTAGT 62.260 55.000 39.00 24.79 39.42 2.57
1899 5760 2.039348 GGACCAAGGTACAGGCACTTAA 59.961 50.000 0.00 0.00 34.60 1.85
1923 5785 1.466856 ATACGCGGTTGTCTAGTCCA 58.533 50.000 12.47 0.00 0.00 4.02
2027 5891 1.945354 GCAGTGGCATGCAAGCATCT 61.945 55.000 21.36 9.99 45.77 2.90
2171 6039 4.280436 TGCGGGATCTACTTTTGAAGAA 57.720 40.909 0.00 0.00 0.00 2.52
2211 6079 7.272978 TGATATTTAGTTGGCAGGAAGACTAC 58.727 38.462 0.00 0.00 0.00 2.73
2246 6114 4.516321 TGGCGCGACAATATAGTCTAGTTA 59.484 41.667 15.11 0.00 36.38 2.24
2257 6203 1.358725 GCTCAGTTGGCGCGACAATA 61.359 55.000 32.77 18.21 32.24 1.90
2310 6341 9.016438 TGTAGTCTAGTTGTACACACATTGATA 57.984 33.333 0.00 0.00 33.76 2.15
2323 6354 3.941483 GCATGGCAATGTAGTCTAGTTGT 59.059 43.478 2.31 0.00 36.08 3.32
2393 6427 6.565811 CGACAATGTAGTTTAGTTGCACACAT 60.566 38.462 0.00 0.00 0.00 3.21
2406 6440 0.515564 GTTGGCGCGACAATGTAGTT 59.484 50.000 32.77 0.00 32.24 2.24
2433 6467 7.817962 AGTTGATAGGACTAATTACACACACAC 59.182 37.037 0.00 0.00 0.00 3.82
2453 6488 6.201517 GCGCACACATTGATATTTAGTTGAT 58.798 36.000 0.30 0.00 0.00 2.57
2454 6489 5.448496 GGCGCACACATTGATATTTAGTTGA 60.448 40.000 10.83 0.00 0.00 3.18
2475 6510 3.235195 GCGATAATGTAGTCTAGTGGCG 58.765 50.000 0.00 0.00 0.00 5.69
2478 6513 3.235195 GGCGCGATAATGTAGTCTAGTG 58.765 50.000 12.10 0.00 0.00 2.74


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

AutoCloner maintained by Alex Coulton.