Multiple sequence alignment - TraesCS3A01G407200

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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 TraesCS3A01G407200 chr3A 100.000 2900 0 0 1 2900 652022899 652025798 0.000000e+00 5356.0
1 TraesCS3A01G407200 chr3B 91.844 2440 119 38 500 2898 680427562 680425162 0.000000e+00 3330.0
2 TraesCS3A01G407200 chr3B 91.466 457 18 14 1 441 680428007 680427556 2.470000e-170 608.0
3 TraesCS3A01G407200 chr3D 90.816 2145 108 44 819 2900 516876664 516878782 0.000000e+00 2787.0
4 TraesCS3A01G407200 chr6D 95.122 41 1 1 1319 1358 132775241 132775281 2.410000e-06 63.9


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 TraesCS3A01G407200 chr3A 652022899 652025798 2899 False 5356 5356 100.000 1 2900 1 chr3A.!!$F1 2899
1 TraesCS3A01G407200 chr3B 680425162 680428007 2845 True 1969 3330 91.655 1 2898 2 chr3B.!!$R1 2897
2 TraesCS3A01G407200 chr3D 516876664 516878782 2118 False 2787 2787 90.816 819 2900 1 chr3D.!!$F1 2081

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
478 494 0.106419 AAAAGGACCGAAACCAGGCA 60.106 50.0 0.0 0.0 0.0 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2122 2225 0.036732 GTGCAGTGGACCTGAATCCA 59.963 55.0 2.86 0.0 46.92 3.41 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
204 211 8.836413 TCTGAAAGGTGTGTAAACATTTCTTAG 58.164 33.333 12.01 4.42 46.05 2.18
313 326 7.985634 ATGTGACAGTTTGTTATTTCACAAC 57.014 32.000 6.34 0.00 35.00 3.32
321 334 8.751335 CAGTTTGTTATTTCACAACACAATACC 58.249 33.333 0.00 0.00 36.36 2.73
324 337 9.953697 TTTGTTATTTCACAACACAATACCTAC 57.046 29.630 0.00 0.00 36.36 3.18
325 338 8.101654 TGTTATTTCACAACACAATACCTACC 57.898 34.615 0.00 0.00 31.11 3.18
398 411 8.837099 AATATCTCATTTTCCCCACAAATACA 57.163 30.769 0.00 0.00 0.00 2.29
399 412 9.438163 AATATCTCATTTTCCCCACAAATACAT 57.562 29.630 0.00 0.00 0.00 2.29
400 413 7.738437 ATCTCATTTTCCCCACAAATACATT 57.262 32.000 0.00 0.00 0.00 2.71
401 414 8.837099 ATCTCATTTTCCCCACAAATACATTA 57.163 30.769 0.00 0.00 0.00 1.90
469 485 9.729281 AAACTGATAACTAAATAAAAGGACCGA 57.271 29.630 0.00 0.00 0.00 4.69
470 486 9.729281 AACTGATAACTAAATAAAAGGACCGAA 57.271 29.630 0.00 0.00 0.00 4.30
471 487 9.729281 ACTGATAACTAAATAAAAGGACCGAAA 57.271 29.630 0.00 0.00 0.00 3.46
472 488 9.983804 CTGATAACTAAATAAAAGGACCGAAAC 57.016 33.333 0.00 0.00 0.00 2.78
473 489 8.949177 TGATAACTAAATAAAAGGACCGAAACC 58.051 33.333 0.00 0.00 0.00 3.27
474 490 8.866970 ATAACTAAATAAAAGGACCGAAACCA 57.133 30.769 0.00 0.00 0.00 3.67
475 491 6.812879 ACTAAATAAAAGGACCGAAACCAG 57.187 37.500 0.00 0.00 0.00 4.00
476 492 5.708697 ACTAAATAAAAGGACCGAAACCAGG 59.291 40.000 0.00 0.00 0.00 4.45
477 493 1.900245 TAAAAGGACCGAAACCAGGC 58.100 50.000 0.00 0.00 0.00 4.85
478 494 0.106419 AAAAGGACCGAAACCAGGCA 60.106 50.000 0.00 0.00 0.00 4.75
479 495 0.537371 AAAGGACCGAAACCAGGCAG 60.537 55.000 0.00 0.00 0.00 4.85
480 496 3.056328 GGACCGAAACCAGGCAGC 61.056 66.667 0.00 0.00 0.00 5.25
481 497 2.281484 GACCGAAACCAGGCAGCA 60.281 61.111 0.00 0.00 0.00 4.41
482 498 1.896660 GACCGAAACCAGGCAGCAA 60.897 57.895 0.00 0.00 0.00 3.91
483 499 1.856265 GACCGAAACCAGGCAGCAAG 61.856 60.000 0.00 0.00 0.00 4.01
484 500 2.256461 CGAAACCAGGCAGCAAGC 59.744 61.111 0.00 0.00 44.65 4.01
493 509 2.500582 GCAGCAAGCGTTCGAAGC 60.501 61.111 0.00 4.71 0.00 3.86
494 510 2.202096 CAGCAAGCGTTCGAAGCG 60.202 61.111 0.00 6.94 40.04 4.68
495 511 2.661866 AGCAAGCGTTCGAAGCGT 60.662 55.556 17.20 10.65 40.04 5.07
496 512 2.497628 GCAAGCGTTCGAAGCGTG 60.498 61.111 21.56 21.56 44.69 5.34
497 513 2.928361 CAAGCGTTCGAAGCGTGT 59.072 55.556 19.31 8.40 38.83 4.49
498 514 1.275657 CAAGCGTTCGAAGCGTGTT 59.724 52.632 19.31 12.21 38.83 3.32
499 515 0.315869 CAAGCGTTCGAAGCGTGTTT 60.316 50.000 19.31 11.12 38.83 2.83
500 516 0.375803 AAGCGTTCGAAGCGTGTTTT 59.624 45.000 17.20 4.47 40.04 2.43
501 517 0.375803 AGCGTTCGAAGCGTGTTTTT 59.624 45.000 17.20 0.00 40.04 1.94
528 544 6.481313 TCTCTGAGATTTGAGTTTCTGTGTTG 59.519 38.462 2.58 0.00 0.00 3.33
537 553 3.067106 AGTTTCTGTGTTGTATGCTCCG 58.933 45.455 0.00 0.00 0.00 4.63
541 557 2.151202 CTGTGTTGTATGCTCCGGTTT 58.849 47.619 0.00 0.00 0.00 3.27
542 558 2.552315 CTGTGTTGTATGCTCCGGTTTT 59.448 45.455 0.00 0.00 0.00 2.43
543 559 2.292016 TGTGTTGTATGCTCCGGTTTTG 59.708 45.455 0.00 0.00 0.00 2.44
544 560 2.550606 GTGTTGTATGCTCCGGTTTTGA 59.449 45.455 0.00 0.00 0.00 2.69
679 697 0.389817 TCACCTGAGACATTTCGCCG 60.390 55.000 0.00 0.00 0.00 6.46
687 705 1.059942 GACATTTCGCCGGCAAAAAG 58.940 50.000 28.98 20.62 0.00 2.27
693 711 0.676736 TCGCCGGCAAAAAGGAAATT 59.323 45.000 28.98 0.00 0.00 1.82
694 712 1.067693 CGCCGGCAAAAAGGAAATTC 58.932 50.000 28.98 0.00 0.00 2.17
711 730 6.992123 AGGAAATTCTTTTTACCCTGCAAAAG 59.008 34.615 0.73 0.73 40.12 2.27
754 776 4.276926 GTGTACCCCTACCTAGTGATTACG 59.723 50.000 0.00 0.00 0.00 3.18
756 778 3.830121 ACCCCTACCTAGTGATTACGAG 58.170 50.000 0.00 0.00 0.00 4.18
763 785 5.821516 ACCTAGTGATTACGAGACTTCTG 57.178 43.478 0.00 0.00 31.96 3.02
790 812 8.261492 ACTCTGTTATCAGTTTCAGCAATAAG 57.739 34.615 0.83 0.00 41.91 1.73
797 819 6.271488 TCAGTTTCAGCAATAAGATTTGGG 57.729 37.500 0.00 0.00 0.00 4.12
799 821 5.047092 CAGTTTCAGCAATAAGATTTGGGGT 60.047 40.000 0.00 0.00 0.00 4.95
810 832 4.293662 AGATTTGGGGTGAGAACTCTTC 57.706 45.455 3.51 0.00 0.00 2.87
846 868 0.596082 GATGGAACCCAACAACACCG 59.404 55.000 0.00 0.00 36.95 4.94
854 876 2.909965 AACAACACCGCGGCCAAT 60.910 55.556 28.58 6.23 0.00 3.16
858 880 4.652131 ACACCGCGGCCAATCCAA 62.652 61.111 28.58 0.00 34.01 3.53
870 892 1.474320 CCAATCCAAACGGATCGCCTA 60.474 52.381 0.00 0.00 42.81 3.93
871 893 2.285083 CAATCCAAACGGATCGCCTAA 58.715 47.619 0.00 0.00 42.81 2.69
872 894 1.949465 ATCCAAACGGATCGCCTAAC 58.051 50.000 0.00 0.00 39.16 2.34
883 905 4.573162 GCCTAACGAACGAGCAGT 57.427 55.556 0.14 0.00 0.00 4.40
1367 1401 4.135153 CCCGGTCCGTCAGCAGAG 62.135 72.222 11.06 0.00 0.00 3.35
1433 1468 3.446799 CTCTGCTTAGCTTAGCTGACTG 58.553 50.000 24.72 15.33 42.05 3.51
1437 1472 1.139853 CTTAGCTTAGCTGACTGGGGG 59.860 57.143 17.97 0.00 40.10 5.40
1584 1619 0.683504 TCTACGAGGCCAAGGTCTCC 60.684 60.000 14.68 0.00 43.36 3.71
1628 1663 0.179100 GTTGCTCATCGGCTCTGCTA 60.179 55.000 0.00 0.00 0.00 3.49
1655 1694 1.434379 CGTTGTCGCGTGTTCGTTC 60.434 57.895 5.77 0.00 39.49 3.95
1706 1745 3.743017 TTCCTGGCCATGCTCCCC 61.743 66.667 5.51 0.00 0.00 4.81
1730 1769 2.672996 CGCCCCAAAGTCAGGGTG 60.673 66.667 0.00 0.00 46.88 4.61
1793 1845 7.453393 TGAACTCTCACTGAATTTACCAGAAT 58.547 34.615 0.00 0.00 35.69 2.40
1909 1982 1.529309 GAGGAATGAGGAGCCACCC 59.471 63.158 0.00 0.00 40.05 4.61
1927 2000 2.678934 TCCGGCAGCTACCTCGTT 60.679 61.111 0.42 0.00 0.00 3.85
1928 2001 2.202756 CCGGCAGCTACCTCGTTC 60.203 66.667 0.42 0.00 0.00 3.95
1929 2002 2.571757 CGGCAGCTACCTCGTTCA 59.428 61.111 0.42 0.00 0.00 3.18
1944 2017 1.846782 CGTTCAATCTCTCGCCTTACG 59.153 52.381 0.00 0.00 45.62 3.18
1966 2039 4.531332 GCTCTGTTTTCAGCTTTGTACTG 58.469 43.478 0.00 0.00 46.59 2.74
1972 2046 2.751166 TCAGCTTTGTACTGAGGAGC 57.249 50.000 0.00 0.00 39.21 4.70
1975 2049 1.071605 GCTTTGTACTGAGGAGCACG 58.928 55.000 0.00 0.00 33.68 5.34
1977 2051 2.600731 CTTTGTACTGAGGAGCACGAG 58.399 52.381 0.00 0.00 0.00 4.18
1978 2052 1.905637 TTGTACTGAGGAGCACGAGA 58.094 50.000 0.00 0.00 0.00 4.04
1992 2066 5.339008 AGCACGAGAAAGGATGTACATAA 57.661 39.130 8.71 0.00 0.00 1.90
1995 2069 5.232414 GCACGAGAAAGGATGTACATAAGTC 59.768 44.000 8.71 4.44 0.00 3.01
2006 2080 8.267894 AGGATGTACATAAGTCTACATTTTGCT 58.732 33.333 8.71 0.00 33.78 3.91
2007 2081 8.552034 GGATGTACATAAGTCTACATTTTGCTC 58.448 37.037 8.71 0.00 33.78 4.26
2008 2082 9.098355 GATGTACATAAGTCTACATTTTGCTCA 57.902 33.333 8.71 0.00 33.78 4.26
2009 2083 8.479313 TGTACATAAGTCTACATTTTGCTCAG 57.521 34.615 0.00 0.00 0.00 3.35
2010 2084 8.094548 TGTACATAAGTCTACATTTTGCTCAGT 58.905 33.333 0.00 0.00 0.00 3.41
2011 2085 7.986085 ACATAAGTCTACATTTTGCTCAGTT 57.014 32.000 0.00 0.00 0.00 3.16
2012 2086 8.396272 ACATAAGTCTACATTTTGCTCAGTTT 57.604 30.769 0.00 0.00 0.00 2.66
2038 2129 7.602265 TCACAAGAGAATCATCAATCGTGTAAA 59.398 33.333 0.00 0.00 37.82 2.01
2039 2130 7.901889 CACAAGAGAATCATCAATCGTGTAAAG 59.098 37.037 0.00 0.00 37.82 1.85
2049 2140 6.325919 TCAATCGTGTAAAGCCTTTCAAAT 57.674 33.333 0.00 0.00 0.00 2.32
2055 2146 7.970384 TCGTGTAAAGCCTTTCAAATATACAG 58.030 34.615 0.00 0.00 0.00 2.74
2090 2184 6.962686 TCAAATCATATATGCAAGCTCACAC 58.037 36.000 7.92 0.00 0.00 3.82
2105 2200 0.731514 CACACGCGTTCCGATACAGT 60.732 55.000 10.22 0.00 41.02 3.55
2116 2219 1.393603 CGATACAGTCAGAGGCCTCA 58.606 55.000 33.90 12.52 0.00 3.86
2117 2220 1.336440 CGATACAGTCAGAGGCCTCAG 59.664 57.143 33.90 26.54 0.00 3.35
2125 2228 3.719121 GAGGCCTCAGCTTCTGGA 58.281 61.111 28.43 0.00 41.71 3.86
2145 2248 3.271014 CAGGTCCACTGCACATGC 58.729 61.111 0.00 0.00 40.97 4.06
2156 2259 3.662153 CACATGCACAGCACGGCA 61.662 61.111 0.00 0.00 43.04 5.69
2157 2260 3.663176 ACATGCACAGCACGGCAC 61.663 61.111 0.00 0.00 43.04 5.01
2185 2288 1.169661 ACGGCCAAAATGTTCAGCGA 61.170 50.000 2.24 0.00 0.00 4.93
2188 2291 1.337110 GCCAAAATGTTCAGCGACGC 61.337 55.000 13.03 13.03 0.00 5.19
2260 2363 2.178912 TGGAAGGGAACATGACGAAC 57.821 50.000 0.00 0.00 0.00 3.95
2850 2953 0.172803 CCTTCTTGCTCAGCCATTGC 59.827 55.000 0.00 0.00 37.95 3.56
2851 2954 0.172803 CTTCTTGCTCAGCCATTGCC 59.827 55.000 0.00 0.00 38.69 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
306 319 7.255660 GGAAAATGGTAGGTATTGTGTTGTGAA 60.256 37.037 0.00 0.00 0.00 3.18
313 326 6.210584 AGGTTTGGAAAATGGTAGGTATTGTG 59.789 38.462 0.00 0.00 0.00 3.33
321 334 7.044798 TGTCAAAAAGGTTTGGAAAATGGTAG 58.955 34.615 0.00 0.00 43.70 3.18
324 337 6.150140 TGTTGTCAAAAAGGTTTGGAAAATGG 59.850 34.615 0.00 0.00 43.70 3.16
325 338 7.138692 TGTTGTCAAAAAGGTTTGGAAAATG 57.861 32.000 0.00 0.00 43.70 2.32
443 459 9.729281 TCGGTCCTTTTATTTAGTTATCAGTTT 57.271 29.630 0.00 0.00 0.00 2.66
444 460 9.729281 TTCGGTCCTTTTATTTAGTTATCAGTT 57.271 29.630 0.00 0.00 0.00 3.16
446 462 9.983804 GTTTCGGTCCTTTTATTTAGTTATCAG 57.016 33.333 0.00 0.00 0.00 2.90
447 463 8.949177 GGTTTCGGTCCTTTTATTTAGTTATCA 58.051 33.333 0.00 0.00 0.00 2.15
448 464 8.949177 TGGTTTCGGTCCTTTTATTTAGTTATC 58.051 33.333 0.00 0.00 0.00 1.75
449 465 8.866970 TGGTTTCGGTCCTTTTATTTAGTTAT 57.133 30.769 0.00 0.00 0.00 1.89
450 466 7.391275 CCTGGTTTCGGTCCTTTTATTTAGTTA 59.609 37.037 0.00 0.00 0.00 2.24
451 467 6.208007 CCTGGTTTCGGTCCTTTTATTTAGTT 59.792 38.462 0.00 0.00 0.00 2.24
452 468 5.708697 CCTGGTTTCGGTCCTTTTATTTAGT 59.291 40.000 0.00 0.00 0.00 2.24
453 469 5.392703 GCCTGGTTTCGGTCCTTTTATTTAG 60.393 44.000 0.00 0.00 0.00 1.85
454 470 4.460034 GCCTGGTTTCGGTCCTTTTATTTA 59.540 41.667 0.00 0.00 0.00 1.40
455 471 3.257375 GCCTGGTTTCGGTCCTTTTATTT 59.743 43.478 0.00 0.00 0.00 1.40
456 472 2.823747 GCCTGGTTTCGGTCCTTTTATT 59.176 45.455 0.00 0.00 0.00 1.40
457 473 2.224917 TGCCTGGTTTCGGTCCTTTTAT 60.225 45.455 0.00 0.00 0.00 1.40
458 474 1.143277 TGCCTGGTTTCGGTCCTTTTA 59.857 47.619 0.00 0.00 0.00 1.52
459 475 0.106419 TGCCTGGTTTCGGTCCTTTT 60.106 50.000 0.00 0.00 0.00 2.27
460 476 0.537371 CTGCCTGGTTTCGGTCCTTT 60.537 55.000 0.00 0.00 0.00 3.11
461 477 1.073199 CTGCCTGGTTTCGGTCCTT 59.927 57.895 0.00 0.00 0.00 3.36
462 478 2.750350 CTGCCTGGTTTCGGTCCT 59.250 61.111 0.00 0.00 0.00 3.85
463 479 3.056328 GCTGCCTGGTTTCGGTCC 61.056 66.667 0.00 0.00 0.00 4.46
464 480 1.856265 CTTGCTGCCTGGTTTCGGTC 61.856 60.000 0.00 0.00 0.00 4.79
465 481 1.898574 CTTGCTGCCTGGTTTCGGT 60.899 57.895 0.00 0.00 0.00 4.69
466 482 2.956987 CTTGCTGCCTGGTTTCGG 59.043 61.111 0.00 0.00 0.00 4.30
467 483 2.256461 GCTTGCTGCCTGGTTTCG 59.744 61.111 0.00 0.00 35.15 3.46
468 484 2.075426 AACGCTTGCTGCCTGGTTTC 62.075 55.000 0.00 0.00 38.78 2.78
469 485 2.075426 GAACGCTTGCTGCCTGGTTT 62.075 55.000 0.00 0.00 38.78 3.27
470 486 2.519302 AACGCTTGCTGCCTGGTT 60.519 55.556 0.00 0.00 38.78 3.67
471 487 2.980233 GAACGCTTGCTGCCTGGT 60.980 61.111 0.00 0.00 38.78 4.00
472 488 4.093952 CGAACGCTTGCTGCCTGG 62.094 66.667 0.00 0.00 38.78 4.45
473 489 2.504461 CTTCGAACGCTTGCTGCCTG 62.504 60.000 0.00 0.00 38.78 4.85
474 490 2.280797 TTCGAACGCTTGCTGCCT 60.281 55.556 0.00 0.00 38.78 4.75
475 491 2.174349 CTTCGAACGCTTGCTGCC 59.826 61.111 0.00 0.00 38.78 4.85
476 492 2.500582 GCTTCGAACGCTTGCTGC 60.501 61.111 10.97 0.00 38.57 5.25
477 493 2.202096 CGCTTCGAACGCTTGCTG 60.202 61.111 14.67 2.37 0.00 4.41
478 494 2.661866 ACGCTTCGAACGCTTGCT 60.662 55.556 16.42 0.00 0.00 3.91
479 495 2.497628 CACGCTTCGAACGCTTGC 60.498 61.111 16.42 7.90 0.00 4.01
480 496 0.315869 AAACACGCTTCGAACGCTTG 60.316 50.000 17.91 17.91 33.43 4.01
481 497 0.375803 AAAACACGCTTCGAACGCTT 59.624 45.000 16.42 6.45 0.00 4.68
482 498 0.375803 AAAAACACGCTTCGAACGCT 59.624 45.000 16.42 5.28 0.00 5.07
483 499 2.849521 AAAAACACGCTTCGAACGC 58.150 47.368 16.42 12.76 0.00 4.84
499 515 8.400947 CACAGAAACTCAAATCTCAGAGAAAAA 58.599 33.333 3.63 0.00 35.83 1.94
500 516 7.554118 ACACAGAAACTCAAATCTCAGAGAAAA 59.446 33.333 3.63 0.00 35.83 2.29
501 517 7.050377 ACACAGAAACTCAAATCTCAGAGAAA 58.950 34.615 3.63 0.00 35.83 2.52
502 518 6.586344 ACACAGAAACTCAAATCTCAGAGAA 58.414 36.000 3.63 0.00 35.83 2.87
503 519 6.166984 ACACAGAAACTCAAATCTCAGAGA 57.833 37.500 1.54 1.54 35.83 3.10
504 520 6.259608 ACAACACAGAAACTCAAATCTCAGAG 59.740 38.462 0.00 0.00 37.87 3.35
505 521 6.115446 ACAACACAGAAACTCAAATCTCAGA 58.885 36.000 0.00 0.00 0.00 3.27
506 522 6.369059 ACAACACAGAAACTCAAATCTCAG 57.631 37.500 0.00 0.00 0.00 3.35
507 523 7.520453 GCATACAACACAGAAACTCAAATCTCA 60.520 37.037 0.00 0.00 0.00 3.27
508 524 6.798959 GCATACAACACAGAAACTCAAATCTC 59.201 38.462 0.00 0.00 0.00 2.75
509 525 6.488006 AGCATACAACACAGAAACTCAAATCT 59.512 34.615 0.00 0.00 0.00 2.40
510 526 6.672147 AGCATACAACACAGAAACTCAAATC 58.328 36.000 0.00 0.00 0.00 2.17
514 530 4.065088 GGAGCATACAACACAGAAACTCA 58.935 43.478 0.00 0.00 0.00 3.41
515 531 3.123621 CGGAGCATACAACACAGAAACTC 59.876 47.826 0.00 0.00 0.00 3.01
521 537 1.808411 AACCGGAGCATACAACACAG 58.192 50.000 9.46 0.00 0.00 3.66
528 544 2.479560 GGCATTCAAAACCGGAGCATAC 60.480 50.000 9.46 0.00 0.00 2.39
537 553 2.549329 CCAAAGCAAGGCATTCAAAACC 59.451 45.455 0.00 0.00 0.00 3.27
541 557 1.422531 ACCCAAAGCAAGGCATTCAA 58.577 45.000 0.00 0.00 0.00 2.69
542 558 1.422531 AACCCAAAGCAAGGCATTCA 58.577 45.000 0.00 0.00 0.00 2.57
543 559 2.549064 AAACCCAAAGCAAGGCATTC 57.451 45.000 0.00 0.00 0.00 2.67
544 560 2.172293 TGAAAACCCAAAGCAAGGCATT 59.828 40.909 0.00 0.00 0.00 3.56
599 616 3.798515 AGGGGTGAGAGGTTAACACATA 58.201 45.455 8.10 0.00 36.42 2.29
600 617 2.632537 AGGGGTGAGAGGTTAACACAT 58.367 47.619 8.10 0.00 36.42 3.21
602 619 2.552373 CCAAGGGGTGAGAGGTTAACAC 60.552 54.545 8.10 0.96 0.00 3.32
603 620 1.702957 CCAAGGGGTGAGAGGTTAACA 59.297 52.381 8.10 0.00 0.00 2.41
604 621 1.982958 TCCAAGGGGTGAGAGGTTAAC 59.017 52.381 0.00 0.00 34.93 2.01
605 622 2.426431 TCCAAGGGGTGAGAGGTTAA 57.574 50.000 0.00 0.00 34.93 2.01
687 705 6.204688 CCTTTTGCAGGGTAAAAAGAATTTCC 59.795 38.462 7.68 0.00 43.13 3.13
693 711 5.941555 TTTCCTTTTGCAGGGTAAAAAGA 57.058 34.783 7.68 0.00 43.13 2.52
694 712 6.993786 TTTTTCCTTTTGCAGGGTAAAAAG 57.006 33.333 13.29 7.91 44.12 2.27
754 776 7.385778 ACTGATAACAGAGTACAGAAGTCTC 57.614 40.000 7.05 0.00 46.03 3.36
756 778 8.082852 TGAAACTGATAACAGAGTACAGAAGTC 58.917 37.037 7.05 0.00 46.03 3.01
763 785 7.602517 ATTGCTGAAACTGATAACAGAGTAC 57.397 36.000 7.05 0.00 46.03 2.73
790 812 4.293662 AGAAGAGTTCTCACCCCAAATC 57.706 45.455 2.64 0.00 34.07 2.17
797 819 2.818432 TGGTCGTAGAAGAGTTCTCACC 59.182 50.000 2.64 0.00 39.69 4.02
799 821 3.887110 TGTTGGTCGTAGAAGAGTTCTCA 59.113 43.478 2.64 0.00 39.69 3.27
810 832 3.118775 TCCATCTTCCATGTTGGTCGTAG 60.119 47.826 0.00 0.00 39.03 3.51
846 868 3.059386 TCCGTTTGGATTGGCCGC 61.059 61.111 0.00 0.00 40.17 6.53
854 876 2.826639 TCGTTAGGCGATCCGTTTGGA 61.827 52.381 0.00 0.00 45.68 3.53
870 892 1.498865 CTTGGCACTGCTCGTTCGTT 61.499 55.000 0.00 0.00 0.00 3.85
871 893 1.956170 CTTGGCACTGCTCGTTCGT 60.956 57.895 0.00 0.00 0.00 3.85
872 894 1.664649 TCTTGGCACTGCTCGTTCG 60.665 57.895 0.00 0.00 0.00 3.95
883 905 0.830648 CGAGGGGATAAGTCTTGGCA 59.169 55.000 0.00 0.00 0.00 4.92
995 1017 2.401766 GCTCCCGACCACATGCTTG 61.402 63.158 0.00 0.00 0.00 4.01
1367 1401 0.040958 GGAAATGCATCATCGTCGGC 60.041 55.000 0.00 0.00 0.00 5.54
1584 1619 1.144936 GAGTGGCGAGAGAATGGGG 59.855 63.158 0.00 0.00 0.00 4.96
1628 1663 1.390123 CACGCGACAACGATGAGAAAT 59.610 47.619 15.93 0.00 42.66 2.17
1655 1694 1.374758 GGACAGAACCTGCAGACGG 60.375 63.158 17.39 9.45 34.37 4.79
1706 1745 3.952628 GACTTTGGGGCGGAGGTCG 62.953 68.421 0.00 0.00 42.76 4.79
1793 1845 3.057104 TCGGCTCGAAAGTTATTCACAGA 60.057 43.478 0.00 0.00 31.06 3.41
1909 1982 2.615262 GAACGAGGTAGCTGCCGGAG 62.615 65.000 15.76 12.73 0.00 4.63
1920 1993 0.173708 GGCGAGAGATTGAACGAGGT 59.826 55.000 0.00 0.00 0.00 3.85
1927 2000 3.642901 GCGTAAGGCGAGAGATTGA 57.357 52.632 0.00 0.00 44.77 2.57
1944 2017 4.273480 TCAGTACAAAGCTGAAAACAGAGC 59.727 41.667 0.00 0.00 39.70 4.09
1966 2039 1.205893 ACATCCTTTCTCGTGCTCCTC 59.794 52.381 0.00 0.00 0.00 3.71
1972 2046 6.565234 AGACTTATGTACATCCTTTCTCGTG 58.435 40.000 12.68 0.00 0.00 4.35
1992 2066 5.822519 TGTGAAACTGAGCAAAATGTAGACT 59.177 36.000 0.00 0.00 38.04 3.24
1995 2069 6.728200 TCTTGTGAAACTGAGCAAAATGTAG 58.272 36.000 0.00 0.00 38.04 2.74
2003 2077 4.707105 TGATTCTCTTGTGAAACTGAGCA 58.293 39.130 0.00 0.00 37.78 4.26
2004 2078 5.410746 TGATGATTCTCTTGTGAAACTGAGC 59.589 40.000 0.00 0.00 37.78 4.26
2006 2080 7.148523 CGATTGATGATTCTCTTGTGAAACTGA 60.149 37.037 0.00 0.00 38.04 3.41
2007 2081 6.959871 CGATTGATGATTCTCTTGTGAAACTG 59.040 38.462 0.00 0.00 38.04 3.16
2008 2082 6.652481 ACGATTGATGATTCTCTTGTGAAACT 59.348 34.615 0.00 0.00 38.04 2.66
2009 2083 6.740002 CACGATTGATGATTCTCTTGTGAAAC 59.260 38.462 0.00 0.00 37.35 2.78
2010 2084 6.427853 ACACGATTGATGATTCTCTTGTGAAA 59.572 34.615 0.00 0.00 0.00 2.69
2011 2085 5.934043 ACACGATTGATGATTCTCTTGTGAA 59.066 36.000 0.00 0.00 0.00 3.18
2012 2086 5.482006 ACACGATTGATGATTCTCTTGTGA 58.518 37.500 0.00 0.00 0.00 3.58
2038 2129 7.118723 TGTTGGATCTGTATATTTGAAAGGCT 58.881 34.615 0.00 0.00 0.00 4.58
2039 2130 7.333528 TGTTGGATCTGTATATTTGAAAGGC 57.666 36.000 0.00 0.00 0.00 4.35
2055 2146 9.917129 TGCATATATGATTTGATTTGTTGGATC 57.083 29.630 17.10 0.00 0.00 3.36
2105 2200 4.883465 AGAAGCTGAGGCCTCTGA 57.117 55.556 36.14 17.29 37.79 3.27
2116 2219 1.661463 TGGACCTGAATCCAGAAGCT 58.339 50.000 0.00 0.00 44.14 3.74
2122 2225 0.036732 GTGCAGTGGACCTGAATCCA 59.963 55.000 2.86 0.00 46.92 3.41
2125 2228 1.830279 CATGTGCAGTGGACCTGAAT 58.170 50.000 13.58 0.00 44.49 2.57
2164 2267 1.284297 GCTGAACATTTTGGCCGTGC 61.284 55.000 0.00 0.00 0.00 5.34
2165 2268 1.003262 CGCTGAACATTTTGGCCGTG 61.003 55.000 0.00 0.00 0.00 4.94
2166 2269 1.169661 TCGCTGAACATTTTGGCCGT 61.170 50.000 0.00 0.00 0.00 5.68
2167 2270 0.729140 GTCGCTGAACATTTTGGCCG 60.729 55.000 0.00 0.00 0.00 6.13
2168 2271 0.729140 CGTCGCTGAACATTTTGGCC 60.729 55.000 0.00 0.00 0.00 5.36
2185 2288 2.960170 GACCTCGTGTACCTGCGT 59.040 61.111 0.00 0.00 0.00 5.24
2188 2291 1.505353 GACCGACCTCGTGTACCTG 59.495 63.158 0.00 0.00 37.74 4.00
2260 2363 1.153939 CTTCGTCGTCAGCCTCCTG 60.154 63.158 0.00 0.00 40.54 3.86
2871 2976 5.241506 GTCTCATCAAACCCAACAATCTCAA 59.758 40.000 0.00 0.00 0.00 3.02


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

AutoCloner maintained by Alex Coulton.