Multiple sequence alignment - TraesCS5D01G146100

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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 TraesCS5D01G146100 chr5D 100.000 3740 0 0 1 3740 232851032 232847293 0.000000e+00 6907
1 TraesCS5D01G146100 chr5A 93.131 2504 116 16 1 2476 322477350 322479825 0.000000e+00 3620
2 TraesCS5D01G146100 chr5A 92.406 1251 55 13 2504 3740 322479822 322481046 0.000000e+00 1748
3 TraesCS5D01G146100 chr5A 76.654 257 57 3 62 317 703521349 703521603 5.040000e-29 139
4 TraesCS5D01G146100 chr5A 76.654 257 57 3 62 317 703570585 703570839 5.040000e-29 139
5 TraesCS5D01G146100 chr5B 94.816 1736 70 7 750 2476 272166289 272168013 0.000000e+00 2689
6 TraesCS5D01G146100 chr5B 89.608 1020 66 17 2517 3529 272168020 272169006 0.000000e+00 1260
7 TraesCS5D01G146100 chr5B 97.653 213 4 1 3528 3740 272169100 272169311 7.630000e-97 364
8 TraesCS5D01G146100 chr4D 82.518 961 157 7 1478 2437 101506147 101505197 0.000000e+00 833
9 TraesCS5D01G146100 chr4A 81.818 979 161 12 1463 2437 473765656 473766621 0.000000e+00 806
10 TraesCS5D01G146100 chr4A 77.043 257 56 3 62 317 506359188 506359442 1.080000e-30 145
11 TraesCS5D01G146100 chr3A 77.043 257 55 4 62 317 525334557 525334304 1.080000e-30 145
12 TraesCS5D01G146100 chr3A 77.011 261 48 9 62 317 93165685 93165938 5.040000e-29 139
13 TraesCS5D01G146100 chr1A 77.043 257 56 3 62 317 466562770 466562516 1.080000e-30 145
14 TraesCS5D01G146100 chr7A 76.654 257 56 4 62 317 187555703 187555450 5.040000e-29 139
15 TraesCS5D01G146100 chr6A 76.654 257 57 3 62 317 113476081 113475827 5.040000e-29 139


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 TraesCS5D01G146100 chr5D 232847293 232851032 3739 True 6907.000000 6907 100.000000 1 3740 1 chr5D.!!$R1 3739
1 TraesCS5D01G146100 chr5A 322477350 322481046 3696 False 2684.000000 3620 92.768500 1 3740 2 chr5A.!!$F3 3739
2 TraesCS5D01G146100 chr5B 272166289 272169311 3022 False 1437.666667 2689 94.025667 750 3740 3 chr5B.!!$F1 2990
3 TraesCS5D01G146100 chr4D 101505197 101506147 950 True 833.000000 833 82.518000 1478 2437 1 chr4D.!!$R1 959
4 TraesCS5D01G146100 chr4A 473765656 473766621 965 False 806.000000 806 81.818000 1463 2437 1 chr4A.!!$F1 974

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
744 765 0.591170 AATCCAAACGTCACGGCAAG 59.409 50.0 0.35 0.0 0.0 4.01 F
2489 2526 0.187117 TGTCCAATTGCCCAGGTTGA 59.813 50.0 0.00 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2502 2539 0.038166 GCAACCCCTGACTGATGGAA 59.962 55.0 0.0 0.0 0.00 3.53 R
3628 3778 0.249031 GTTTGCTTCTGCCACACACC 60.249 55.0 0.0 0.0 38.71 4.16 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
43 44 4.400884 TCACCAAAATTGTTATGGGATCCG 59.599 41.667 5.45 0.00 38.58 4.18
46 47 5.105513 ACCAAAATTGTTATGGGATCCGTTC 60.106 40.000 5.45 0.00 38.58 3.95
53 54 6.928348 TGTTATGGGATCCGTTCATATACT 57.072 37.500 5.45 0.00 0.00 2.12
54 55 6.697395 TGTTATGGGATCCGTTCATATACTG 58.303 40.000 5.45 0.00 0.00 2.74
96 97 9.101655 GTTTGATTCAAATGAATTTCATAGGGG 57.898 33.333 14.54 3.44 44.14 4.79
99 100 8.259411 TGATTCAAATGAATTTCATAGGGGTTG 58.741 33.333 12.15 11.95 44.14 3.77
103 104 8.435982 TCAAATGAATTTCATAGGGGTTGTTTT 58.564 29.630 12.15 0.00 35.76 2.43
224 225 9.282569 GATTTCATAGAAAATCTAGCATCCACT 57.717 33.333 0.00 0.00 40.77 4.00
319 320 7.037438 CGAATGGGAATGACATTTCAATCTTT 58.963 34.615 8.73 0.34 38.57 2.52
329 330 9.829507 ATGACATTTCAATCTTTTGTTTTACCA 57.170 25.926 0.00 0.00 34.61 3.25
330 331 9.829507 TGACATTTCAATCTTTTGTTTTACCAT 57.170 25.926 0.00 0.00 34.32 3.55
332 333 9.271828 ACATTTCAATCTTTTGTTTTACCATCC 57.728 29.630 0.00 0.00 34.32 3.51
334 335 6.985653 TCAATCTTTTGTTTTACCATCCCA 57.014 33.333 0.00 0.00 34.32 4.37
335 336 7.366847 TCAATCTTTTGTTTTACCATCCCAA 57.633 32.000 0.00 0.00 34.32 4.12
336 337 7.441017 TCAATCTTTTGTTTTACCATCCCAAG 58.559 34.615 0.00 0.00 34.32 3.61
372 375 6.864165 GCTCTCGGTAGGAATCTAAACATAAG 59.136 42.308 0.00 0.00 0.00 1.73
437 444 4.010253 TCTCACTCTACTCCCTCTCCTA 57.990 50.000 0.00 0.00 0.00 2.94
504 525 5.897377 AATTCCTGTATTTTGAACTCCCG 57.103 39.130 0.00 0.00 0.00 5.14
513 534 8.746052 TGTATTTTGAACTCCCGAATTCATAT 57.254 30.769 6.22 0.00 34.87 1.78
514 535 9.839817 TGTATTTTGAACTCCCGAATTCATATA 57.160 29.630 6.22 0.00 34.87 0.86
525 546 9.599866 CTCCCGAATTCATATAACATATAGCAA 57.400 33.333 6.22 0.00 0.00 3.91
546 567 8.959705 AGCAACTAAATATTACTACCTCCAAC 57.040 34.615 0.00 0.00 0.00 3.77
560 581 7.752638 ACTACCTCCAACCTAAAATAAGTGTT 58.247 34.615 0.00 0.00 0.00 3.32
561 582 8.883302 ACTACCTCCAACCTAAAATAAGTGTTA 58.117 33.333 0.00 0.00 0.00 2.41
566 587 8.611654 TCCAACCTAAAATAAGTGTTACAGTC 57.388 34.615 0.00 0.00 0.00 3.51
571 592 9.841295 ACCTAAAATAAGTGTTACAGTCTTGAA 57.159 29.630 0.00 0.00 0.00 2.69
589 610 9.660180 AGTCTTGAACTAGAACTATTTTGGATC 57.340 33.333 0.00 0.00 36.07 3.36
601 622 5.661759 ACTATTTTGGATCGAAGGGAGTAGT 59.338 40.000 0.00 0.00 0.00 2.73
602 623 6.837568 ACTATTTTGGATCGAAGGGAGTAGTA 59.162 38.462 0.00 0.00 0.00 1.82
603 624 6.555463 ATTTTGGATCGAAGGGAGTAGTAA 57.445 37.500 0.00 0.00 0.00 2.24
604 625 5.593679 TTTGGATCGAAGGGAGTAGTAAG 57.406 43.478 0.00 0.00 0.00 2.34
605 626 4.246712 TGGATCGAAGGGAGTAGTAAGT 57.753 45.455 0.00 0.00 0.00 2.24
606 627 4.607239 TGGATCGAAGGGAGTAGTAAGTT 58.393 43.478 0.00 0.00 0.00 2.66
607 628 5.021458 TGGATCGAAGGGAGTAGTAAGTTT 58.979 41.667 0.00 0.00 0.00 2.66
608 629 5.482878 TGGATCGAAGGGAGTAGTAAGTTTT 59.517 40.000 0.00 0.00 0.00 2.43
609 630 6.664816 TGGATCGAAGGGAGTAGTAAGTTTTA 59.335 38.462 0.00 0.00 0.00 1.52
610 631 7.178983 TGGATCGAAGGGAGTAGTAAGTTTTAA 59.821 37.037 0.00 0.00 0.00 1.52
611 632 7.490725 GGATCGAAGGGAGTAGTAAGTTTTAAC 59.509 40.741 0.00 0.00 0.00 2.01
612 633 7.288810 TCGAAGGGAGTAGTAAGTTTTAACA 57.711 36.000 0.00 0.00 0.00 2.41
613 634 7.725251 TCGAAGGGAGTAGTAAGTTTTAACAA 58.275 34.615 0.00 0.00 0.00 2.83
614 635 8.370182 TCGAAGGGAGTAGTAAGTTTTAACAAT 58.630 33.333 0.00 0.00 0.00 2.71
615 636 8.996271 CGAAGGGAGTAGTAAGTTTTAACAATT 58.004 33.333 0.00 0.00 0.00 2.32
641 662 0.966370 GTAGGAGGTCGTGACTGGCT 60.966 60.000 0.00 0.00 0.00 4.75
691 712 0.612174 TGGAACCGAGACCTCTCCTG 60.612 60.000 0.00 0.00 39.79 3.86
703 724 1.614903 CCTCTCCTGCATGCAACAAAA 59.385 47.619 22.88 5.61 0.00 2.44
705 726 2.295349 CTCTCCTGCATGCAACAAAACT 59.705 45.455 22.88 0.00 0.00 2.66
711 732 3.593096 TGCATGCAACAAAACTGAACAA 58.407 36.364 20.30 0.00 0.00 2.83
720 741 2.430332 CAAAACTGAACAAAGCCCCTCA 59.570 45.455 0.00 0.00 0.00 3.86
736 757 3.877508 CCCCTCAGAATAATCCAAACGTC 59.122 47.826 0.00 0.00 0.00 4.34
743 764 1.880271 TAATCCAAACGTCACGGCAA 58.120 45.000 0.35 0.00 0.00 4.52
744 765 0.591170 AATCCAAACGTCACGGCAAG 59.409 50.000 0.35 0.00 0.00 4.01
1008 1035 2.358258 TCTCAATCCCCAAACCCTCTT 58.642 47.619 0.00 0.00 0.00 2.85
1051 1079 1.079127 CGTCTCAAATCCCGTGGCT 60.079 57.895 0.00 0.00 0.00 4.75
1125 1153 4.617593 TCTTACTCTCTCGGGGGTAAAAT 58.382 43.478 0.00 0.00 0.00 1.82
1131 1160 6.728411 ACTCTCTCGGGGGTAAAATAAAAAT 58.272 36.000 0.00 0.00 0.00 1.82
1327 1357 0.391263 GTTAAGAGGCGGAGGTGGTG 60.391 60.000 0.00 0.00 0.00 4.17
1432 1463 0.322008 CTCCTGGCTTTCTCACCACC 60.322 60.000 0.00 0.00 0.00 4.61
1471 1502 1.809207 GTGGTGCCCATGGATTTCG 59.191 57.895 15.22 0.00 35.28 3.46
1584 1615 2.262572 CAAAATTGCAGGAGTACGCC 57.737 50.000 7.70 7.70 0.00 5.68
1722 1753 2.986728 AGGTTTGTCCCAGTACTTCCAT 59.013 45.455 0.00 0.00 36.75 3.41
1877 1908 2.187946 GCTGGCCTATGACGCTGT 59.812 61.111 3.32 0.00 0.00 4.40
1926 1957 2.789203 GAACATCGTCGCGTCAGGC 61.789 63.158 5.77 0.00 38.69 4.85
2193 2230 1.916697 GCTCGCAAGCTTGGAAGGTC 61.917 60.000 27.10 8.86 45.55 3.85
2429 2466 6.424812 GCATAGTTTGTTTTGGATTTTCTGCT 59.575 34.615 0.00 0.00 0.00 4.24
2484 2521 2.976589 GGAATTTGTCCAATTGCCCAG 58.023 47.619 0.00 0.00 46.97 4.45
2485 2522 2.355007 GGAATTTGTCCAATTGCCCAGG 60.355 50.000 0.00 0.00 46.97 4.45
2486 2523 2.028561 ATTTGTCCAATTGCCCAGGT 57.971 45.000 0.00 0.00 0.00 4.00
2487 2524 1.799933 TTTGTCCAATTGCCCAGGTT 58.200 45.000 0.00 0.00 0.00 3.50
2488 2525 1.047002 TTGTCCAATTGCCCAGGTTG 58.953 50.000 0.00 0.00 0.00 3.77
2489 2526 0.187117 TGTCCAATTGCCCAGGTTGA 59.813 50.000 0.00 0.00 0.00 3.18
2490 2527 1.337118 GTCCAATTGCCCAGGTTGAA 58.663 50.000 0.00 0.00 0.00 2.69
2491 2528 1.273327 GTCCAATTGCCCAGGTTGAAG 59.727 52.381 0.00 0.00 0.00 3.02
2492 2529 0.609662 CCAATTGCCCAGGTTGAAGG 59.390 55.000 0.00 0.00 0.00 3.46
2493 2530 1.341080 CAATTGCCCAGGTTGAAGGT 58.659 50.000 0.00 0.00 0.00 3.50
2494 2531 1.001181 CAATTGCCCAGGTTGAAGGTG 59.999 52.381 0.00 0.00 0.00 4.00
2495 2532 0.542702 ATTGCCCAGGTTGAAGGTGG 60.543 55.000 0.00 0.00 0.00 4.61
2496 2533 2.991540 GCCCAGGTTGAAGGTGGC 60.992 66.667 0.00 0.00 0.00 5.01
2497 2534 2.520458 CCCAGGTTGAAGGTGGCA 59.480 61.111 0.00 0.00 0.00 4.92
2498 2535 1.152567 CCCAGGTTGAAGGTGGCAA 60.153 57.895 0.00 0.00 0.00 4.52
2499 2536 1.181098 CCCAGGTTGAAGGTGGCAAG 61.181 60.000 0.00 0.00 0.00 4.01
2500 2537 0.468029 CCAGGTTGAAGGTGGCAAGT 60.468 55.000 0.00 0.00 0.00 3.16
2501 2538 0.670162 CAGGTTGAAGGTGGCAAGTG 59.330 55.000 0.00 0.00 0.00 3.16
2502 2539 0.258774 AGGTTGAAGGTGGCAAGTGT 59.741 50.000 0.00 0.00 0.00 3.55
2503 2540 1.111277 GGTTGAAGGTGGCAAGTGTT 58.889 50.000 0.00 0.00 0.00 3.32
2504 2541 1.067060 GGTTGAAGGTGGCAAGTGTTC 59.933 52.381 0.00 0.00 0.00 3.18
2505 2542 1.067060 GTTGAAGGTGGCAAGTGTTCC 59.933 52.381 0.00 0.00 0.00 3.62
2506 2543 0.257328 TGAAGGTGGCAAGTGTTCCA 59.743 50.000 0.00 0.00 0.00 3.53
2549 2586 0.392327 GAAGTCAGGGCTCAGCTTCC 60.392 60.000 0.00 0.00 31.97 3.46
2558 2595 2.032528 TCAGCTTCCGCCCTTGTG 59.967 61.111 0.00 0.00 36.60 3.33
2643 2683 6.827762 TGATGTTCATAGTTGCCATGTTCATA 59.172 34.615 0.00 0.00 0.00 2.15
2707 2747 8.896744 TGAATGTATCAAGTCAGATTTGGAATC 58.103 33.333 5.86 0.00 34.30 2.52
2716 2756 5.713861 AGTCAGATTTGGAATCCCTCAAAAG 59.286 40.000 0.00 0.00 36.60 2.27
2717 2757 5.478332 GTCAGATTTGGAATCCCTCAAAAGT 59.522 40.000 0.00 0.00 36.60 2.66
2722 2762 9.104713 AGATTTGGAATCCCTCAAAAGTAAAAT 57.895 29.630 0.00 0.00 36.60 1.82
2792 2832 0.650512 AACACTCACTGCAAACGACG 59.349 50.000 0.00 0.00 0.00 5.12
2801 2841 2.419324 ACTGCAAACGACGTGGTTTTTA 59.581 40.909 23.72 15.07 38.01 1.52
2811 2851 8.496872 AACGACGTGGTTTTTATTGAAATTAG 57.503 30.769 10.40 0.00 0.00 1.73
2844 2884 5.491635 GGATCAGTTCCATTTTAGCACTC 57.508 43.478 0.00 0.00 44.74 3.51
2936 2976 6.809869 AGCCTGATAACTTATTTTTCATGGC 58.190 36.000 0.00 0.00 38.39 4.40
2978 3018 4.798907 GTCTGTATGTGGTGTGAACTATCG 59.201 45.833 0.00 0.00 0.00 2.92
2991 3031 4.023878 GTGAACTATCGGCTATCTTCTCGT 60.024 45.833 0.00 0.00 0.00 4.18
3033 3073 7.596494 CAGTCTGTTGATGATTTGGTGTTATT 58.404 34.615 0.00 0.00 0.00 1.40
3037 3077 7.448161 TCTGTTGATGATTTGGTGTTATTGTCT 59.552 33.333 0.00 0.00 0.00 3.41
3152 3194 3.201930 TCAACAATGCTGGAATAGGGCTA 59.798 43.478 0.00 0.00 0.00 3.93
3166 3208 2.191400 AGGGCTATTGCTGACTGAAGA 58.809 47.619 0.00 0.00 39.59 2.87
3175 3217 7.226325 GCTATTGCTGACTGAAGATTTAGATGT 59.774 37.037 0.00 0.00 36.03 3.06
3200 3242 4.339814 TGACGGTTTAAACAAGAGGCATTT 59.660 37.500 19.57 0.00 0.00 2.32
3346 3395 1.575447 ATTCCCAGGCCCTCTTGTCC 61.575 60.000 0.00 0.00 0.00 4.02
3379 3428 1.547675 GGAAGTGGGCTTGAACATCCA 60.548 52.381 0.00 0.00 34.91 3.41
3480 3535 9.076596 GTTTATTCTTGTGTTGGAAGATTATGC 57.923 33.333 0.00 0.00 29.60 3.14
3482 3537 5.885230 TCTTGTGTTGGAAGATTATGCAG 57.115 39.130 0.00 0.00 0.00 4.41
3628 3778 2.880268 TCAGTGGATGTGTTTGCTGAAG 59.120 45.455 0.00 0.00 31.14 3.02
3656 3806 1.961277 AGAAGCAAACCGGAGTGCG 60.961 57.895 22.40 0.00 45.62 5.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.524306 TGGTGAACCCATTTCCATGAC 58.476 47.619 0.00 0.00 38.72 3.06
6 7 2.988636 TGGTGAACCCATTTCCATGA 57.011 45.000 0.00 0.00 38.72 3.07
10 11 4.713553 ACAATTTTGGTGAACCCATTTCC 58.286 39.130 0.00 0.00 44.74 3.13
25 26 6.790232 ATGAACGGATCCCATAACAATTTT 57.210 33.333 6.06 0.00 0.00 1.82
256 257 8.984891 TTTGAGTTTATTTGGTTGCATCATAG 57.015 30.769 0.00 0.00 0.00 2.23
260 261 8.437742 CAAGATTTGAGTTTATTTGGTTGCATC 58.562 33.333 0.00 0.00 0.00 3.91
263 264 7.713764 ACAAGATTTGAGTTTATTTGGTTGC 57.286 32.000 0.00 0.00 0.00 4.17
266 267 8.934023 TCCTACAAGATTTGAGTTTATTTGGT 57.066 30.769 0.00 0.00 0.00 3.67
272 273 9.667107 ATTCGAATCCTACAAGATTTGAGTTTA 57.333 29.630 4.39 0.00 43.99 2.01
319 320 6.985653 TTGATTCTTGGGATGGTAAAACAA 57.014 33.333 0.00 0.00 0.00 2.83
326 327 3.879321 GCCTCTTTGATTCTTGGGATGGT 60.879 47.826 0.00 0.00 0.00 3.55
327 328 2.692041 GCCTCTTTGATTCTTGGGATGG 59.308 50.000 0.00 0.00 0.00 3.51
328 329 3.629087 AGCCTCTTTGATTCTTGGGATG 58.371 45.455 0.00 0.00 0.00 3.51
329 330 3.526841 AGAGCCTCTTTGATTCTTGGGAT 59.473 43.478 0.00 0.00 0.00 3.85
330 331 2.915604 AGAGCCTCTTTGATTCTTGGGA 59.084 45.455 0.00 0.00 0.00 4.37
331 332 3.277715 GAGAGCCTCTTTGATTCTTGGG 58.722 50.000 0.00 0.00 0.00 4.12
332 333 2.935201 CGAGAGCCTCTTTGATTCTTGG 59.065 50.000 0.00 0.00 0.00 3.61
334 335 2.569404 ACCGAGAGCCTCTTTGATTCTT 59.431 45.455 0.00 0.00 0.00 2.52
335 336 2.183679 ACCGAGAGCCTCTTTGATTCT 58.816 47.619 0.00 0.00 0.00 2.40
336 337 2.682155 ACCGAGAGCCTCTTTGATTC 57.318 50.000 0.00 0.00 0.00 2.52
380 383 9.109393 AGCGCATGAGACTTCTTAAAAATAATA 57.891 29.630 11.47 0.00 0.00 0.98
381 384 7.989826 AGCGCATGAGACTTCTTAAAAATAAT 58.010 30.769 11.47 0.00 0.00 1.28
384 391 5.886960 AGCGCATGAGACTTCTTAAAAAT 57.113 34.783 11.47 0.00 0.00 1.82
390 397 0.801251 GCAAGCGCATGAGACTTCTT 59.199 50.000 18.15 0.00 38.36 2.52
391 398 0.321034 TGCAAGCGCATGAGACTTCT 60.321 50.000 18.15 0.00 45.36 2.85
392 399 2.165380 TGCAAGCGCATGAGACTTC 58.835 52.632 18.15 0.00 45.36 3.01
412 419 4.349930 GGAGAGGGAGTAGAGTGAGATACT 59.650 50.000 0.00 0.00 44.02 2.12
413 420 4.349930 AGGAGAGGGAGTAGAGTGAGATAC 59.650 50.000 0.00 0.00 0.00 2.24
437 444 5.163322 TGTTGCACAAGAAATTGGAGGATTT 60.163 36.000 0.00 0.00 32.16 2.17
534 555 8.439964 ACACTTATTTTAGGTTGGAGGTAGTA 57.560 34.615 0.00 0.00 0.00 1.82
560 581 9.706691 CCAAAATAGTTCTAGTTCAAGACTGTA 57.293 33.333 0.00 0.00 39.48 2.74
561 582 8.429641 TCCAAAATAGTTCTAGTTCAAGACTGT 58.570 33.333 0.00 0.00 39.48 3.55
566 587 8.703604 TCGATCCAAAATAGTTCTAGTTCAAG 57.296 34.615 0.00 0.00 0.00 3.02
571 592 6.383147 TCCCTTCGATCCAAAATAGTTCTAGT 59.617 38.462 0.00 0.00 0.00 2.57
589 610 7.951530 TTGTTAAAACTTACTACTCCCTTCG 57.048 36.000 0.00 0.00 0.00 3.79
603 624 9.462606 CCTCCTACCATAGAAATTGTTAAAACT 57.537 33.333 0.00 0.00 0.00 2.66
604 625 9.239551 ACCTCCTACCATAGAAATTGTTAAAAC 57.760 33.333 0.00 0.00 0.00 2.43
605 626 9.457436 GACCTCCTACCATAGAAATTGTTAAAA 57.543 33.333 0.00 0.00 0.00 1.52
606 627 7.767198 CGACCTCCTACCATAGAAATTGTTAAA 59.233 37.037 0.00 0.00 0.00 1.52
607 628 7.093201 ACGACCTCCTACCATAGAAATTGTTAA 60.093 37.037 0.00 0.00 0.00 2.01
608 629 6.381994 ACGACCTCCTACCATAGAAATTGTTA 59.618 38.462 0.00 0.00 0.00 2.41
609 630 5.189145 ACGACCTCCTACCATAGAAATTGTT 59.811 40.000 0.00 0.00 0.00 2.83
610 631 4.715297 ACGACCTCCTACCATAGAAATTGT 59.285 41.667 0.00 0.00 0.00 2.71
611 632 5.050490 CACGACCTCCTACCATAGAAATTG 58.950 45.833 0.00 0.00 0.00 2.32
612 633 4.960469 TCACGACCTCCTACCATAGAAATT 59.040 41.667 0.00 0.00 0.00 1.82
613 634 4.341520 GTCACGACCTCCTACCATAGAAAT 59.658 45.833 0.00 0.00 0.00 2.17
614 635 3.698040 GTCACGACCTCCTACCATAGAAA 59.302 47.826 0.00 0.00 0.00 2.52
615 636 3.053842 AGTCACGACCTCCTACCATAGAA 60.054 47.826 0.00 0.00 0.00 2.10
616 637 2.508716 AGTCACGACCTCCTACCATAGA 59.491 50.000 0.00 0.00 0.00 1.98
617 638 2.619177 CAGTCACGACCTCCTACCATAG 59.381 54.545 0.00 0.00 0.00 2.23
618 639 2.651455 CAGTCACGACCTCCTACCATA 58.349 52.381 0.00 0.00 0.00 2.74
619 640 1.475403 CAGTCACGACCTCCTACCAT 58.525 55.000 0.00 0.00 0.00 3.55
620 641 0.611062 CCAGTCACGACCTCCTACCA 60.611 60.000 0.00 0.00 0.00 3.25
621 642 1.946475 GCCAGTCACGACCTCCTACC 61.946 65.000 0.00 0.00 0.00 3.18
622 643 0.966370 AGCCAGTCACGACCTCCTAC 60.966 60.000 0.00 0.00 0.00 3.18
623 644 0.965866 CAGCCAGTCACGACCTCCTA 60.966 60.000 0.00 0.00 0.00 2.94
657 678 0.176910 TTCCACTGCAACGTCACTGA 59.823 50.000 0.00 0.00 0.00 3.41
665 686 1.228657 GGTCTCGGTTCCACTGCAAC 61.229 60.000 0.00 0.00 0.00 4.17
671 692 0.612453 AGGAGAGGTCTCGGTTCCAC 60.612 60.000 0.90 0.00 43.76 4.02
691 712 4.580528 CTTTGTTCAGTTTTGTTGCATGC 58.419 39.130 11.82 11.82 0.00 4.06
703 724 1.140312 TCTGAGGGGCTTTGTTCAGT 58.860 50.000 0.88 0.00 38.50 3.41
705 726 2.978156 ATTCTGAGGGGCTTTGTTCA 57.022 45.000 0.00 0.00 0.00 3.18
711 732 4.281657 GTTTGGATTATTCTGAGGGGCTT 58.718 43.478 0.00 0.00 0.00 4.35
720 741 2.676342 GCCGTGACGTTTGGATTATTCT 59.324 45.455 3.64 0.00 0.00 2.40
744 765 2.034221 GCTTGTCCAGGGTGTCCC 59.966 66.667 0.00 0.00 45.90 4.46
796 817 2.258591 GAAGCGCACTGTCTCCGA 59.741 61.111 11.47 0.00 0.00 4.55
854 881 2.464459 GCATACAGCTGTCACGGCC 61.464 63.158 25.56 3.39 41.15 6.13
1131 1160 6.591935 AGACAGGACTGTGAAAACAAGATTA 58.408 36.000 10.08 0.00 45.05 1.75
1233 1263 3.557207 GCGCATTTATTGAGCCCAG 57.443 52.632 0.30 0.00 44.48 4.45
1242 1272 3.123804 CTCTACAAGGACGCGCATTTAT 58.876 45.455 5.73 0.00 0.00 1.40
1317 1347 1.100510 TACGAGAATCACCACCTCCG 58.899 55.000 0.00 0.00 33.17 4.63
1327 1357 3.679326 GGCGCGCGTACGAGAATC 61.679 66.667 32.35 10.85 42.18 2.52
1373 1404 0.682855 AGAAGAGTCAGGAGGAGCCG 60.683 60.000 0.00 0.00 43.43 5.52
1376 1407 2.682856 CGAGAAGAAGAGTCAGGAGGAG 59.317 54.545 0.00 0.00 0.00 3.69
1432 1463 3.089874 TCCGCCAGGAATCCAGGG 61.090 66.667 12.86 9.13 45.12 4.45
1471 1502 2.610727 GGAGGAGGCAGACGCATAATAC 60.611 54.545 0.00 0.00 41.24 1.89
1755 1786 2.362503 ACCATCCTCTCCACGCGA 60.363 61.111 15.93 0.00 0.00 5.87
1926 1957 3.689161 TGAAATGTACAAGAATCGGGCTG 59.311 43.478 0.00 0.00 0.00 4.85
2429 2466 5.048782 GCATTGTTAGTGATGGTTGAACTCA 60.049 40.000 0.00 0.00 0.00 3.41
2476 2513 0.542702 CCACCTTCAACCTGGGCAAT 60.543 55.000 0.00 0.00 0.00 3.56
2477 2514 1.152567 CCACCTTCAACCTGGGCAA 60.153 57.895 0.00 0.00 0.00 4.52
2478 2515 2.520458 CCACCTTCAACCTGGGCA 59.480 61.111 0.00 0.00 0.00 5.36
2479 2516 2.991540 GCCACCTTCAACCTGGGC 60.992 66.667 0.00 0.00 0.00 5.36
2480 2517 1.152567 TTGCCACCTTCAACCTGGG 60.153 57.895 0.00 0.00 0.00 4.45
2481 2518 0.468029 ACTTGCCACCTTCAACCTGG 60.468 55.000 0.00 0.00 0.00 4.45
2482 2519 0.670162 CACTTGCCACCTTCAACCTG 59.330 55.000 0.00 0.00 0.00 4.00
2483 2520 0.258774 ACACTTGCCACCTTCAACCT 59.741 50.000 0.00 0.00 0.00 3.50
2484 2521 1.067060 GAACACTTGCCACCTTCAACC 59.933 52.381 0.00 0.00 0.00 3.77
2485 2522 1.067060 GGAACACTTGCCACCTTCAAC 59.933 52.381 0.00 0.00 0.00 3.18
2486 2523 1.341482 TGGAACACTTGCCACCTTCAA 60.341 47.619 0.00 0.00 0.00 2.69
2487 2524 0.257328 TGGAACACTTGCCACCTTCA 59.743 50.000 0.00 0.00 0.00 3.02
2488 2525 3.109847 TGGAACACTTGCCACCTTC 57.890 52.632 0.00 0.00 0.00 3.46
2501 2538 1.826385 CAACCCCTGACTGATGGAAC 58.174 55.000 0.00 0.00 0.00 3.62
2502 2539 0.038166 GCAACCCCTGACTGATGGAA 59.962 55.000 0.00 0.00 0.00 3.53
2503 2540 0.842030 AGCAACCCCTGACTGATGGA 60.842 55.000 0.00 0.00 0.00 3.41
2504 2541 0.911769 TAGCAACCCCTGACTGATGG 59.088 55.000 0.00 0.00 0.00 3.51
2505 2542 2.787473 TTAGCAACCCCTGACTGATG 57.213 50.000 0.00 0.00 0.00 3.07
2506 2543 4.475016 AGTAATTAGCAACCCCTGACTGAT 59.525 41.667 0.00 0.00 0.00 2.90
2558 2595 2.289631 CCAACCAAAAGAATGCCTTCCC 60.290 50.000 0.00 0.00 33.02 3.97
2567 2607 6.981559 CCTTCGAAATAAACCAACCAAAAGAA 59.018 34.615 0.00 0.00 0.00 2.52
2643 2683 2.235898 GAGATGAACAGAGCTCCTTGGT 59.764 50.000 10.93 0.60 0.00 3.67
2707 2747 7.544217 CGTCCCATTTTATTTTACTTTTGAGGG 59.456 37.037 0.00 0.00 0.00 4.30
2716 2756 8.920509 AAATACAGCGTCCCATTTTATTTTAC 57.079 30.769 0.00 0.00 0.00 2.01
2717 2757 8.740906 TGAAATACAGCGTCCCATTTTATTTTA 58.259 29.630 0.00 0.00 0.00 1.52
2722 2762 5.492895 TCTGAAATACAGCGTCCCATTTTA 58.507 37.500 0.00 0.00 45.38 1.52
2726 2766 2.158900 CCTCTGAAATACAGCGTCCCAT 60.159 50.000 0.00 0.00 45.38 4.00
2801 2841 9.753674 TGATCCCAAACTAGAACTAATTTCAAT 57.246 29.630 0.00 0.00 36.57 2.57
2844 2884 4.440112 GGTGTCTGAACAGGAAAACCAAAG 60.440 45.833 1.93 0.00 35.64 2.77
2978 3018 5.251601 AGAACTGTAACGAGAAGATAGCC 57.748 43.478 0.00 0.00 0.00 3.93
2991 3031 3.128349 GACTGCGGAACAAGAACTGTAA 58.872 45.455 0.00 0.00 37.23 2.41
3050 3090 6.430616 ACCCTAGTAAGCTTCGAGTATCATAC 59.569 42.308 0.00 0.00 33.17 2.39
3103 3145 8.468399 TGCTAATTTCTGAACAATGATAATGCA 58.532 29.630 0.00 0.00 0.00 3.96
3152 3194 7.280428 CAGACATCTAAATCTTCAGTCAGCAAT 59.720 37.037 0.00 0.00 0.00 3.56
3166 3208 7.972832 TGTTTAAACCGTCAGACATCTAAAT 57.027 32.000 15.59 0.00 0.00 1.40
3175 3217 3.135994 GCCTCTTGTTTAAACCGTCAGA 58.864 45.455 15.59 10.21 0.00 3.27
3224 3266 6.526566 AAGTGAAGAGTTGTGTAACGATTC 57.473 37.500 0.00 0.00 42.39 2.52
3256 3298 6.734502 TTCATAAATCAGTCCGGGTACATA 57.265 37.500 0.00 0.00 0.00 2.29
3309 3357 7.053316 TGGGAATGCATACTTTGATAAATGG 57.947 36.000 0.00 0.00 0.00 3.16
3346 3395 3.860754 GCCCACTTCCGAAGAAATTTTGG 60.861 47.826 15.23 10.12 0.00 3.28
3480 3535 1.472878 TCATCGGTTTCCTCGAGACTG 59.527 52.381 15.71 9.65 40.09 3.51
3482 3537 2.873133 ATCATCGGTTTCCTCGAGAC 57.127 50.000 15.71 3.83 40.09 3.36
3628 3778 0.249031 GTTTGCTTCTGCCACACACC 60.249 55.000 0.00 0.00 38.71 4.16


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

AutoCloner maintained by Alex Coulton.