Multiple sequence alignment - TraesCS5A01G326800

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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 TraesCS5A01G326800 chr5A 100.000 2810 0 0 1 2810 536897631 536894822 0.000000e+00 5190.0
1 TraesCS5A01G326800 chr5A 80.526 570 68 22 1034 1598 536904549 536904018 5.640000e-107 398.0
2 TraesCS5A01G326800 chr5A 81.752 137 21 4 1419 1554 23915290 23915157 8.230000e-21 111.0
3 TraesCS5A01G326800 chr5A 81.752 137 21 4 1419 1554 24189072 24189205 8.230000e-21 111.0
4 TraesCS5A01G326800 chr5D 92.551 2846 146 36 1 2810 423465257 423462442 0.000000e+00 4021.0
5 TraesCS5A01G326800 chr5D 80.339 590 80 22 1015 1598 423469429 423468870 5.600000e-112 414.0
6 TraesCS5A01G326800 chr5D 79.137 139 21 8 1419 1554 35305532 35305665 3.860000e-14 89.8
7 TraesCS5A01G326800 chr5D 100.000 33 0 0 2454 2486 423462762 423462730 8.400000e-06 62.1
8 TraesCS5A01G326800 chrUn 81.022 137 22 4 1419 1554 293019317 293019184 3.830000e-19 106.0
9 TraesCS5A01G326800 chrUn 81.022 137 22 4 1419 1554 326320500 326320367 3.830000e-19 106.0
10 TraesCS5A01G326800 chrUn 80.292 137 23 4 1419 1554 313467609 313467742 1.780000e-17 100.0


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 TraesCS5A01G326800 chr5A 536894822 536897631 2809 True 5190.00 5190 100.0000 1 2810 1 chr5A.!!$R2 2809
1 TraesCS5A01G326800 chr5A 536904018 536904549 531 True 398.00 398 80.5260 1034 1598 1 chr5A.!!$R3 564
2 TraesCS5A01G326800 chr5D 423462442 423465257 2815 True 2041.55 4021 96.2755 1 2810 2 chr5D.!!$R2 2809
3 TraesCS5A01G326800 chr5D 423468870 423469429 559 True 414.00 414 80.3390 1015 1598 1 chr5D.!!$R1 583

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
993 1013 0.03213 GTCGAGCTCACACACCTTCA 59.968 55.0 15.4 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2701 2750 0.53087 GTCTCTGGCAATAGGACCGC 60.531 60.0 0.0 0.0 0.0 5.68 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
34 35 4.451150 GCTCCGCCATGGTCGACA 62.451 66.667 24.22 12.63 39.52 4.35
72 73 0.394565 GTATCTCCAGCCGATGCCTT 59.605 55.000 0.00 0.00 38.69 4.35
74 75 1.053264 ATCTCCAGCCGATGCCTTCT 61.053 55.000 0.00 0.00 38.69 2.85
85 86 1.806542 GATGCCTTCTTCGAAGCAACA 59.193 47.619 20.56 14.87 38.99 3.33
126 127 1.458220 CGCGATGATGTTGCAAAGCG 61.458 55.000 0.00 0.49 39.75 4.68
154 155 3.998672 TGGCCGACCACCTTCGTC 61.999 66.667 0.00 0.00 42.67 4.20
225 226 0.970937 TGTTCCTAGAGTCCGGCTGG 60.971 60.000 4.71 4.71 0.00 4.85
235 236 3.803082 CCGGCTGGCGTGACAATG 61.803 66.667 22.22 1.05 0.00 2.82
251 252 1.407979 CAATGATGCAAAGAGGGGCTC 59.592 52.381 0.00 0.00 0.00 4.70
314 315 7.010830 CACTGGTAGTAGATTGTGATGTTGATG 59.989 40.741 0.00 0.00 0.00 3.07
316 317 7.394016 TGGTAGTAGATTGTGATGTTGATGTT 58.606 34.615 0.00 0.00 0.00 2.71
317 318 7.334171 TGGTAGTAGATTGTGATGTTGATGTTG 59.666 37.037 0.00 0.00 0.00 3.33
324 325 3.314913 TGTGATGTTGATGTTGTGACCAC 59.685 43.478 0.00 0.00 0.00 4.16
367 368 2.351060 GCAATGCCGATGATATGGTGTG 60.351 50.000 0.00 0.00 0.00 3.82
381 382 2.435422 TGGTGTGCCATGATGTTACAG 58.565 47.619 0.00 0.00 40.46 2.74
384 385 3.599343 GTGTGCCATGATGTTACAGAGA 58.401 45.455 0.00 0.00 0.00 3.10
385 386 3.620374 GTGTGCCATGATGTTACAGAGAG 59.380 47.826 0.00 0.00 0.00 3.20
386 387 3.515104 TGTGCCATGATGTTACAGAGAGA 59.485 43.478 0.00 0.00 0.00 3.10
387 388 3.868077 GTGCCATGATGTTACAGAGAGAC 59.132 47.826 0.00 0.00 0.00 3.36
388 389 3.118629 TGCCATGATGTTACAGAGAGACC 60.119 47.826 0.00 0.00 0.00 3.85
390 391 3.381590 CCATGATGTTACAGAGAGACCGA 59.618 47.826 0.00 0.00 0.00 4.69
391 392 4.038522 CCATGATGTTACAGAGAGACCGAT 59.961 45.833 0.00 0.00 0.00 4.18
392 393 5.452496 CCATGATGTTACAGAGAGACCGATT 60.452 44.000 0.00 0.00 0.00 3.34
394 395 6.378710 TGATGTTACAGAGAGACCGATTAG 57.621 41.667 0.00 0.00 0.00 1.73
395 396 6.120220 TGATGTTACAGAGAGACCGATTAGA 58.880 40.000 0.00 0.00 0.00 2.10
398 402 2.938838 ACAGAGAGACCGATTAGAGGG 58.061 52.381 0.00 0.00 0.00 4.30
418 422 2.356278 GAGGGGTTCATGGCAGCA 59.644 61.111 0.00 0.00 0.00 4.41
432 436 1.003580 GGCAGCAGGGCAATAGCTATA 59.996 52.381 6.68 0.00 42.77 1.31
433 437 2.553028 GGCAGCAGGGCAATAGCTATAA 60.553 50.000 6.68 0.00 42.77 0.98
434 438 3.149196 GCAGCAGGGCAATAGCTATAAA 58.851 45.455 6.68 0.00 41.70 1.40
436 440 4.219288 GCAGCAGGGCAATAGCTATAAATT 59.781 41.667 6.68 0.00 41.70 1.82
437 441 5.706916 CAGCAGGGCAATAGCTATAAATTG 58.293 41.667 6.68 4.58 41.70 2.32
438 442 5.242393 CAGCAGGGCAATAGCTATAAATTGT 59.758 40.000 6.68 0.00 41.70 2.71
439 443 5.474876 AGCAGGGCAATAGCTATAAATTGTC 59.525 40.000 6.68 4.79 41.70 3.18
440 444 5.617751 GCAGGGCAATAGCTATAAATTGTCG 60.618 44.000 6.68 0.00 38.34 4.35
441 445 5.470098 CAGGGCAATAGCTATAAATTGTCGT 59.530 40.000 6.68 3.82 38.34 4.34
481 485 2.738521 CCACGCAACTCTGTCGGG 60.739 66.667 0.00 0.00 0.00 5.14
482 486 2.738521 CACGCAACTCTGTCGGGG 60.739 66.667 0.00 0.00 0.00 5.73
486 490 1.596934 GCAACTCTGTCGGGGATGA 59.403 57.895 0.00 0.00 0.00 2.92
538 542 3.663644 CAACATGTGCCTTGTTGCA 57.336 47.368 15.70 0.00 45.10 4.08
559 563 2.319136 AGCTAACACGACACAACCAA 57.681 45.000 0.00 0.00 0.00 3.67
560 564 2.210116 AGCTAACACGACACAACCAAG 58.790 47.619 0.00 0.00 0.00 3.61
565 569 1.594293 ACGACACAACCAAGCGAGG 60.594 57.895 0.00 0.00 0.00 4.63
566 570 2.317609 CGACACAACCAAGCGAGGG 61.318 63.158 2.52 0.00 0.00 4.30
573 577 1.526575 AACCAAGCGAGGGCAACATG 61.527 55.000 2.52 0.00 43.41 3.21
574 578 2.180017 CAAGCGAGGGCAACATGC 59.820 61.111 0.00 0.00 44.08 4.06
646 651 0.512952 GATCAGTTTGCTGTTCGCGT 59.487 50.000 5.77 0.00 43.05 6.01
664 669 2.905075 CGTGCAGATCCAATGGTTCTA 58.095 47.619 12.13 0.00 31.34 2.10
670 675 3.135348 CAGATCCAATGGTTCTAGAGGCA 59.865 47.826 12.13 0.00 31.34 4.75
678 683 1.539280 GGTTCTAGAGGCAGCCGATTC 60.539 57.143 5.55 0.00 0.00 2.52
708 713 3.292936 AGCCGGCCGATACGTAGG 61.293 66.667 30.73 8.26 0.00 3.18
717 722 3.950395 GGCCGATACGTAGGGTCTATTAT 59.050 47.826 14.77 0.00 0.00 1.28
718 723 4.400567 GGCCGATACGTAGGGTCTATTATT 59.599 45.833 14.77 0.00 0.00 1.40
719 724 5.590259 GGCCGATACGTAGGGTCTATTATTA 59.410 44.000 14.77 0.00 0.00 0.98
720 725 6.458888 GGCCGATACGTAGGGTCTATTATTAC 60.459 46.154 14.77 0.00 0.00 1.89
721 726 6.709643 CCGATACGTAGGGTCTATTATTACG 58.290 44.000 0.08 1.33 41.88 3.18
987 1007 1.363807 CACAGGTCGAGCTCACACA 59.636 57.895 15.54 0.00 0.00 3.72
993 1013 0.032130 GTCGAGCTCACACACCTTCA 59.968 55.000 15.40 0.00 0.00 3.02
994 1014 0.032130 TCGAGCTCACACACCTTCAC 59.968 55.000 15.40 0.00 0.00 3.18
1011 1037 1.000506 TCACGCACAACCTAGAACTCC 59.999 52.381 0.00 0.00 0.00 3.85
1167 1202 0.388520 CACCATCGTGCTCTTCGTCA 60.389 55.000 0.00 0.00 32.04 4.35
1193 1228 2.678836 CGTCTCCTACGTCATCTTCAGT 59.321 50.000 0.00 0.00 46.72 3.41
1196 1231 2.164422 CTCCTACGTCATCTTCAGTGCA 59.836 50.000 0.00 0.00 0.00 4.57
1250 1285 2.342279 CGCCAACAAGGACTCGGA 59.658 61.111 0.00 0.00 41.22 4.55
1391 1432 1.048160 GCAAGGAGGAGGAGGAGGAG 61.048 65.000 0.00 0.00 0.00 3.69
1392 1433 0.633921 CAAGGAGGAGGAGGAGGAGA 59.366 60.000 0.00 0.00 0.00 3.71
1393 1434 1.007721 CAAGGAGGAGGAGGAGGAGAA 59.992 57.143 0.00 0.00 0.00 2.87
1394 1435 0.933700 AGGAGGAGGAGGAGGAGAAG 59.066 60.000 0.00 0.00 0.00 2.85
1395 1436 0.930726 GGAGGAGGAGGAGGAGAAGA 59.069 60.000 0.00 0.00 0.00 2.87
1396 1437 1.289530 GGAGGAGGAGGAGGAGAAGAA 59.710 57.143 0.00 0.00 0.00 2.52
1397 1438 2.666317 GAGGAGGAGGAGGAGAAGAAG 58.334 57.143 0.00 0.00 0.00 2.85
1398 1439 1.290732 AGGAGGAGGAGGAGAAGAAGG 59.709 57.143 0.00 0.00 0.00 3.46
1399 1440 1.289530 GGAGGAGGAGGAGAAGAAGGA 59.710 57.143 0.00 0.00 0.00 3.36
1400 1441 2.384828 GAGGAGGAGGAGAAGAAGGAC 58.615 57.143 0.00 0.00 0.00 3.85
1401 1442 1.007842 AGGAGGAGGAGAAGAAGGACC 59.992 57.143 0.00 0.00 0.00 4.46
1629 1676 4.966787 ACGGCGGTGGCATTGGTT 62.967 61.111 13.24 0.00 42.47 3.67
1678 1725 4.478195 GGTGTGACCGATCGACAG 57.522 61.111 18.66 1.96 0.00 3.51
1714 1761 2.781595 GATGGCGGTCACGGTTCACT 62.782 60.000 0.00 0.00 41.36 3.41
1721 1768 2.615447 CGGTCACGGTTCACTATAGCTA 59.385 50.000 0.00 0.00 36.18 3.32
1746 1793 6.551385 AGTTTAGCTGAACTTTGATGTCTG 57.449 37.500 17.56 0.00 36.49 3.51
1760 1807 3.066621 TGATGTCTGAAACAGGTTGTTGC 59.933 43.478 0.00 0.00 40.14 4.17
1768 1815 3.508744 AACAGGTTGTTGCTTTCAGTG 57.491 42.857 0.00 0.00 39.45 3.66
1803 1851 8.381387 GCTTATAATAACTAATAAGACAGCGCC 58.619 37.037 2.29 0.00 37.72 6.53
1839 1887 2.796593 GTTGCTTGAAATTCAGTGGTGC 59.203 45.455 0.00 0.00 0.00 5.01
1843 1891 3.119849 GCTTGAAATTCAGTGGTGCGTAT 60.120 43.478 0.00 0.00 0.00 3.06
1857 1905 4.189231 GGTGCGTATGTAGATTTTCCAGT 58.811 43.478 0.00 0.00 0.00 4.00
1877 1925 2.098770 GTGAAGAAGATGAGGGCAATGC 59.901 50.000 0.00 0.00 0.00 3.56
2000 2048 1.002087 ACGAGGGTTCTACAGCAAAGG 59.998 52.381 0.00 0.00 0.00 3.11
2090 2138 7.138736 CGAAAATAAGGATTGCGGTTTCATAT 58.861 34.615 0.00 0.00 0.00 1.78
2117 2165 0.031721 GCGGTAGGGTTCCACTATCG 59.968 60.000 1.89 1.89 45.30 2.92
2120 2168 2.951642 CGGTAGGGTTCCACTATCGTAA 59.048 50.000 0.00 0.00 39.52 3.18
2243 2291 9.408648 AGGGGTACATTTGTAATCTTTATCTTG 57.591 33.333 0.00 0.00 31.52 3.02
2253 2301 3.136641 TCTTTATCTTGGAGGAGGGCT 57.863 47.619 0.00 0.00 0.00 5.19
2281 2329 8.926710 CCGCACTATCTTATTTCGATCTTATTT 58.073 33.333 0.00 0.00 0.00 1.40
2366 2414 2.926200 CTCTCAAGCAACTATGGTGTCG 59.074 50.000 0.00 0.00 37.35 4.35
2368 2416 3.067106 CTCAAGCAACTATGGTGTCGTT 58.933 45.455 0.00 0.00 37.35 3.85
2388 2436 1.028330 AGCAGTCCATGGCAATGTCG 61.028 55.000 6.96 0.00 31.27 4.35
2391 2439 0.324614 AGTCCATGGCAATGTCGTCA 59.675 50.000 6.96 0.00 31.27 4.35
2406 2454 3.985279 TGTCGTCAGGTCGAAAATTGTAG 59.015 43.478 0.00 0.00 41.47 2.74
2426 2474 8.862325 TTGTAGGAGCATAAAAAGAATGAAGA 57.138 30.769 0.00 0.00 0.00 2.87
2484 2532 4.082026 GCAAACTATCCATGCAAGTTTCCT 60.082 41.667 9.90 0.00 40.52 3.36
2507 2555 4.755411 TGAGTAAGGAAGCAAACTATCCG 58.245 43.478 0.00 0.00 38.31 4.18
2523 2571 2.341846 TCCGTGCAAGTTTCCTTCTT 57.658 45.000 0.00 0.00 0.00 2.52
2542 2590 3.265737 TCTTAGCCAAGCAACTTCCCATA 59.734 43.478 0.00 0.00 0.00 2.74
2570 2618 6.724893 AGCAGGGTTAACATGTAAGTTTTT 57.275 33.333 8.10 0.00 33.07 1.94
2572 2620 5.924254 GCAGGGTTAACATGTAAGTTTTTCC 59.076 40.000 8.10 0.00 33.07 3.13
2574 2622 7.685884 GCAGGGTTAACATGTAAGTTTTTCCTT 60.686 37.037 8.10 0.00 33.07 3.36
2575 2623 8.852135 CAGGGTTAACATGTAAGTTTTTCCTTA 58.148 33.333 8.10 0.00 33.07 2.69
2576 2624 9.596308 AGGGTTAACATGTAAGTTTTTCCTTAT 57.404 29.630 8.10 0.00 33.07 1.73
2577 2625 9.850628 GGGTTAACATGTAAGTTTTTCCTTATC 57.149 33.333 8.10 0.00 33.07 1.75
2578 2626 9.550811 GGTTAACATGTAAGTTTTTCCTTATCG 57.449 33.333 8.10 0.00 33.07 2.92
2581 2629 7.972832 ACATGTAAGTTTTTCCTTATCGACA 57.027 32.000 0.00 0.00 30.13 4.35
2582 2630 8.561738 ACATGTAAGTTTTTCCTTATCGACAT 57.438 30.769 0.00 0.00 30.13 3.06
2645 2694 1.000060 TGCGTAAAGTTCTACCTGCGT 60.000 47.619 0.00 0.00 0.00 5.24
2674 2723 0.955919 GCCAGAAAAGACCACCTCCG 60.956 60.000 0.00 0.00 0.00 4.63
2721 2770 0.105039 CGGTCCTATTGCCAGAGACC 59.895 60.000 0.00 0.00 42.94 3.85
2769 2818 0.107703 GTGGCAGATCGATGGAACCA 60.108 55.000 0.54 1.96 0.00 3.67
2770 2819 0.107703 TGGCAGATCGATGGAACCAC 60.108 55.000 0.54 0.00 0.00 4.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
159 160 2.524034 CATCGGCTAGAGATACATGCG 58.476 52.381 0.00 0.00 0.00 4.73
210 211 3.905678 CGCCAGCCGGACTCTAGG 61.906 72.222 5.05 0.78 0.00 3.02
225 226 2.512885 CTCTTTGCATCATTGTCACGC 58.487 47.619 0.00 0.00 0.00 5.34
235 236 1.078143 ACGAGCCCCTCTTTGCATC 60.078 57.895 0.00 0.00 0.00 3.91
316 317 0.533978 CCACCGATGTTGTGGTCACA 60.534 55.000 0.00 0.00 46.62 3.58
317 318 2.244000 CCACCGATGTTGTGGTCAC 58.756 57.895 1.27 0.00 46.62 3.67
350 351 0.534877 GGCACACCATATCATCGGCA 60.535 55.000 0.00 0.00 35.26 5.69
367 368 3.462021 GGTCTCTCTGTAACATCATGGC 58.538 50.000 0.00 0.00 0.00 4.40
378 379 2.423660 CCCCTCTAATCGGTCTCTCTGT 60.424 54.545 0.00 0.00 0.00 3.41
381 382 1.623163 CCCCCTCTAATCGGTCTCTC 58.377 60.000 0.00 0.00 0.00 3.20
398 402 3.346734 TGCCATGAACCCCTCCCC 61.347 66.667 0.00 0.00 0.00 4.81
402 406 2.357836 CTGCTGCCATGAACCCCT 59.642 61.111 0.00 0.00 0.00 4.79
405 409 3.455469 GCCCTGCTGCCATGAACC 61.455 66.667 0.00 0.00 0.00 3.62
418 422 5.470098 CACGACAATTTATAGCTATTGCCCT 59.530 40.000 12.39 0.00 40.80 5.19
432 436 2.322081 CCGACCGCCACGACAATTT 61.322 57.895 0.00 0.00 0.00 1.82
433 437 2.740826 CCGACCGCCACGACAATT 60.741 61.111 0.00 0.00 0.00 2.32
453 457 4.927782 TGCGTGGAGTGTGGCACC 62.928 66.667 16.26 6.59 34.49 5.01
455 459 2.899838 GTTGCGTGGAGTGTGGCA 60.900 61.111 0.00 0.00 0.00 4.92
466 470 2.283529 ATCCCCGACAGAGTTGCGT 61.284 57.895 0.00 0.00 0.00 5.24
481 485 5.163416 CCCCAAATTGTATTGGTCTTCATCC 60.163 44.000 5.44 0.00 46.94 3.51
482 486 5.656416 TCCCCAAATTGTATTGGTCTTCATC 59.344 40.000 5.44 0.00 46.94 2.92
486 490 6.272090 ACAAATCCCCAAATTGTATTGGTCTT 59.728 34.615 5.44 0.00 46.94 3.01
538 542 2.634600 TGGTTGTGTCGTGTTAGCTTT 58.365 42.857 0.00 0.00 0.00 3.51
573 577 1.636988 GCTCATTTGCAACATGAGGC 58.363 50.000 30.84 24.32 45.45 4.70
574 578 1.468565 CCGCTCATTTGCAACATGAGG 60.469 52.381 30.84 24.72 45.45 3.86
646 651 3.135348 CCTCTAGAACCATTGGATCTGCA 59.865 47.826 22.07 9.71 35.61 4.41
664 669 1.068753 CATCGAATCGGCTGCCTCT 59.931 57.895 17.92 0.00 0.00 3.69
670 675 0.176680 AAGCTCACATCGAATCGGCT 59.823 50.000 1.76 0.00 0.00 5.52
678 683 2.169789 CCGGCTGAAGCTCACATCG 61.170 63.158 1.74 0.00 41.70 3.84
708 713 6.576185 TCCTTTCCACACGTAATAATAGACC 58.424 40.000 0.00 0.00 0.00 3.85
717 722 3.555586 GGCTAACTCCTTTCCACACGTAA 60.556 47.826 0.00 0.00 0.00 3.18
718 723 2.028748 GGCTAACTCCTTTCCACACGTA 60.029 50.000 0.00 0.00 0.00 3.57
719 724 1.270678 GGCTAACTCCTTTCCACACGT 60.271 52.381 0.00 0.00 0.00 4.49
720 725 1.439679 GGCTAACTCCTTTCCACACG 58.560 55.000 0.00 0.00 0.00 4.49
721 726 1.822506 GGGCTAACTCCTTTCCACAC 58.177 55.000 0.00 0.00 0.00 3.82
722 727 0.323629 CGGGCTAACTCCTTTCCACA 59.676 55.000 0.00 0.00 0.00 4.17
987 1007 1.045407 TCTAGGTTGTGCGTGAAGGT 58.955 50.000 0.00 0.00 0.00 3.50
993 1013 1.000955 CTGGAGTTCTAGGTTGTGCGT 59.999 52.381 0.00 0.00 0.00 5.24
994 1014 1.000955 ACTGGAGTTCTAGGTTGTGCG 59.999 52.381 0.00 0.00 0.00 5.34
1011 1037 0.038892 GGTTGCTGCATGGTGAACTG 60.039 55.000 1.84 0.00 0.00 3.16
1185 1220 1.134965 GGCGTAGACTGCACTGAAGAT 60.135 52.381 0.00 0.00 0.00 2.40
1363 1404 2.037620 CTCCTCCTTGCCTCCGATGG 62.038 65.000 0.00 0.00 0.00 3.51
1374 1415 1.290732 CTTCTCCTCCTCCTCCTCCTT 59.709 57.143 0.00 0.00 0.00 3.36
1391 1432 2.125633 GCGTCGGGGTCCTTCTTC 60.126 66.667 0.00 0.00 0.00 2.87
1392 1433 4.065281 CGCGTCGGGGTCCTTCTT 62.065 66.667 0.00 0.00 0.00 2.52
1670 1717 2.792890 CGATCCACACTCACTGTCGATC 60.793 54.545 0.00 0.00 41.64 3.69
1674 1721 0.737715 GCCGATCCACACTCACTGTC 60.738 60.000 0.00 0.00 0.00 3.51
1677 1724 0.900182 TCTGCCGATCCACACTCACT 60.900 55.000 0.00 0.00 0.00 3.41
1678 1725 0.176680 ATCTGCCGATCCACACTCAC 59.823 55.000 0.00 0.00 0.00 3.51
1721 1768 8.097038 TCAGACATCAAAGTTCAGCTAAACTAT 58.903 33.333 1.71 0.00 38.52 2.12
1746 1793 3.859386 CACTGAAAGCAACAACCTGTTTC 59.141 43.478 0.00 0.00 35.09 2.78
1760 1807 2.486472 AGCTGGGTGATCACTGAAAG 57.514 50.000 24.50 16.63 42.29 2.62
1839 1887 7.759886 TCTTCTTCACTGGAAAATCTACATACG 59.240 37.037 0.00 0.00 31.35 3.06
1843 1891 7.679783 TCATCTTCTTCACTGGAAAATCTACA 58.320 34.615 0.00 0.00 31.35 2.74
1857 1905 2.372264 GCATTGCCCTCATCTTCTTCA 58.628 47.619 0.00 0.00 0.00 3.02
1877 1925 2.822255 CCGGGTGTGCCATTACGG 60.822 66.667 0.00 0.00 36.17 4.02
1878 1926 2.104253 GTCCGGGTGTGCCATTACG 61.104 63.158 0.00 0.00 36.17 3.18
1879 1927 1.747745 GGTCCGGGTGTGCCATTAC 60.748 63.158 0.00 0.00 36.17 1.89
1880 1928 1.906105 GAGGTCCGGGTGTGCCATTA 61.906 60.000 0.00 0.00 36.17 1.90
1881 1929 3.256960 AGGTCCGGGTGTGCCATT 61.257 61.111 0.00 0.00 36.17 3.16
1882 1930 3.717294 GAGGTCCGGGTGTGCCAT 61.717 66.667 0.00 0.00 36.17 4.40
1925 1973 4.796231 CGTCCAAGGCGAGGTCCG 62.796 72.222 0.00 0.00 42.21 4.79
1984 2032 0.696501 TCCCCTTTGCTGTAGAACCC 59.303 55.000 0.00 0.00 0.00 4.11
1986 2034 3.440522 GTCAATCCCCTTTGCTGTAGAAC 59.559 47.826 0.00 0.00 0.00 3.01
2011 2059 4.089065 GCTCGATTGTTTTGCATCTTTCAC 59.911 41.667 0.00 0.00 0.00 3.18
2090 2138 3.322828 GTGGAACCCTACCGCTATAATGA 59.677 47.826 0.00 0.00 35.35 2.57
2173 2221 6.001460 TCTGGTGGTACATAACAAAGAAAGG 58.999 40.000 0.00 0.00 44.52 3.11
2183 2231 4.018779 CCCTCCTTTTCTGGTGGTACATAA 60.019 45.833 0.00 0.00 44.52 1.90
2210 2258 6.542370 AGATTACAAATGTACCCCTTCATTCG 59.458 38.462 0.00 0.00 33.86 3.34
2253 2301 3.446310 TCGAAATAAGATAGTGCGGCA 57.554 42.857 0.00 0.00 0.00 5.69
2281 2329 3.306225 GCAAATGGCTTGGACTTTCATCA 60.306 43.478 0.00 0.00 40.25 3.07
2286 2334 1.000274 GACGCAAATGGCTTGGACTTT 60.000 47.619 0.00 0.00 41.67 2.66
2366 2414 2.094675 ACATTGCCATGGACTGCTAAC 58.905 47.619 18.40 0.00 34.27 2.34
2368 2416 1.743431 CGACATTGCCATGGACTGCTA 60.743 52.381 18.40 0.00 34.27 3.49
2388 2436 3.371285 GCTCCTACAATTTTCGACCTGAC 59.629 47.826 0.00 0.00 0.00 3.51
2391 2439 3.695830 TGCTCCTACAATTTTCGACCT 57.304 42.857 0.00 0.00 0.00 3.85
2430 2478 9.693739 TTACTCTCAAATATTTTGCCAGGAATA 57.306 29.630 0.00 0.00 0.00 1.75
2432 2480 7.362920 GCTTACTCTCAAATATTTTGCCAGGAA 60.363 37.037 0.00 0.00 0.00 3.36
2433 2481 6.095440 GCTTACTCTCAAATATTTTGCCAGGA 59.905 38.462 0.00 0.00 0.00 3.86
2448 2496 5.178797 GGATAGTTTGCTTGCTTACTCTCA 58.821 41.667 11.59 0.00 0.00 3.27
2451 2499 5.731686 GCATGGATAGTTTGCTTGCTTACTC 60.732 44.000 5.89 0.00 41.67 2.59
2453 2501 4.142403 TGCATGGATAGTTTGCTTGCTTAC 60.142 41.667 12.40 0.00 44.14 2.34
2484 2532 5.175859 CGGATAGTTTGCTTCCTTACTCAA 58.824 41.667 0.00 0.00 0.00 3.02
2487 2535 4.504858 CACGGATAGTTTGCTTCCTTACT 58.495 43.478 0.00 0.00 0.00 2.24
2493 2541 2.484264 ACTTGCACGGATAGTTTGCTTC 59.516 45.455 0.00 0.00 37.16 3.86
2523 2571 3.730215 TTATGGGAAGTTGCTTGGCTA 57.270 42.857 0.00 0.00 0.00 3.93
2574 2622 9.537192 CCACAATAGTTTTAAGGTATGTCGATA 57.463 33.333 0.00 0.00 0.00 2.92
2575 2623 8.044908 ACCACAATAGTTTTAAGGTATGTCGAT 58.955 33.333 0.00 0.00 0.00 3.59
2576 2624 7.388437 ACCACAATAGTTTTAAGGTATGTCGA 58.612 34.615 0.00 0.00 0.00 4.20
2577 2625 7.605410 ACCACAATAGTTTTAAGGTATGTCG 57.395 36.000 0.00 0.00 0.00 4.35
2578 2626 8.789762 ACAACCACAATAGTTTTAAGGTATGTC 58.210 33.333 0.00 0.00 0.00 3.06
2579 2627 8.700439 ACAACCACAATAGTTTTAAGGTATGT 57.300 30.769 0.00 0.00 0.00 2.29
2580 2628 9.405587 CAACAACCACAATAGTTTTAAGGTATG 57.594 33.333 0.00 0.00 0.00 2.39
2581 2629 9.357161 TCAACAACCACAATAGTTTTAAGGTAT 57.643 29.630 0.00 0.00 0.00 2.73
2582 2630 8.749026 TCAACAACCACAATAGTTTTAAGGTA 57.251 30.769 0.00 0.00 0.00 3.08
2634 2683 3.845178 CAATACACTCACGCAGGTAGAA 58.155 45.455 0.00 0.00 0.00 2.10
2635 2684 2.416836 GCAATACACTCACGCAGGTAGA 60.417 50.000 0.00 0.00 0.00 2.59
2645 2694 4.072131 GGTCTTTTCTGGCAATACACTCA 58.928 43.478 0.00 0.00 0.00 3.41
2701 2750 0.530870 GTCTCTGGCAATAGGACCGC 60.531 60.000 0.00 0.00 0.00 5.68
2715 2764 1.689273 GATATGGAACCTGCGGTCTCT 59.311 52.381 0.69 0.00 33.12 3.10
2721 2770 1.138859 TCCTGTGATATGGAACCTGCG 59.861 52.381 0.00 0.00 0.00 5.18
2788 2837 2.418628 CACTCGTTCCAACACAACAGTT 59.581 45.455 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.