Multiple sequence alignment - TraesCS5D01G282500

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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 TraesCS5D01G282500 chr5D 100.000 3340 0 0 1 3340 384018464 384015125 0.000000e+00 6168.0
1 TraesCS5D01G282500 chr5D 82.016 506 81 7 12 514 384154965 384155463 3.980000e-114 422.0
2 TraesCS5D01G282500 chr5D 81.670 491 76 10 12 496 373216633 373217115 2.410000e-106 396.0
3 TraesCS5D01G282500 chr5D 84.637 358 48 7 59 414 404882144 404882496 1.910000e-92 350.0
4 TraesCS5D01G282500 chr5D 73.729 354 64 25 1660 2001 75997826 75997490 9.800000e-21 111.0
5 TraesCS5D01G282500 chr5A 96.117 2266 78 6 1 2259 484438026 484435764 0.000000e+00 3688.0
6 TraesCS5D01G282500 chr5A 90.542 793 52 14 2551 3339 484434252 484433479 0.000000e+00 1027.0
7 TraesCS5D01G282500 chr5A 83.501 497 67 11 15 504 509125373 509124885 1.830000e-122 449.0
8 TraesCS5D01G282500 chr5A 82.105 475 78 5 44 514 484843698 484844169 1.870000e-107 399.0
9 TraesCS5D01G282500 chr5A 85.294 102 15 0 1657 1758 18857776 18857877 4.560000e-19 106.0
10 TraesCS5D01G282500 chr5A 75.500 200 39 8 1660 1854 71453624 71453430 4.590000e-14 89.8
11 TraesCS5D01G282500 chr5B 91.138 2460 153 36 1 2432 460494190 460491768 0.000000e+00 3275.0
12 TraesCS5D01G282500 chr5B 85.567 873 67 27 2484 3340 460477475 460476646 0.000000e+00 859.0
13 TraesCS5D01G282500 chr5B 81.504 492 77 10 12 497 443291249 443291732 3.120000e-105 392.0
14 TraesCS5D01G282500 chr5B 81.212 495 85 6 12 504 460943758 460944246 3.120000e-105 392.0
15 TraesCS5D01G282500 chr5B 72.159 352 73 21 1660 2001 84657302 84656966 2.140000e-12 84.2
16 TraesCS5D01G282500 chr3A 75.000 288 58 12 1600 1879 656135245 656135526 1.630000e-23 121.0
17 TraesCS5D01G282500 chr3A 87.255 102 13 0 1657 1758 121479961 121480062 2.110000e-22 117.0
18 TraesCS5D01G282500 chr3D 74.729 277 59 9 1600 1869 520824649 520824921 2.720000e-21 113.0
19 TraesCS5D01G282500 chr4A 75.610 205 44 4 1660 1861 547979761 547979560 2.740000e-16 97.1
20 TraesCS5D01G282500 chr4B 75.635 197 42 4 1660 1853 72902080 72901887 3.550000e-15 93.5
21 TraesCS5D01G282500 chr4D 74.634 205 46 4 1660 1861 49369393 49369192 5.940000e-13 86.1
22 TraesCS5D01G282500 chr6B 78.030 132 23 3 1729 1854 204124439 204124308 9.940000e-11 78.7


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 TraesCS5D01G282500 chr5D 384015125 384018464 3339 True 6168.0 6168 100.0000 1 3340 1 chr5D.!!$R2 3339
1 TraesCS5D01G282500 chr5A 484433479 484438026 4547 True 2357.5 3688 93.3295 1 3339 2 chr5A.!!$R3 3338
2 TraesCS5D01G282500 chr5B 460491768 460494190 2422 True 3275.0 3275 91.1380 1 2432 1 chr5B.!!$R3 2431
3 TraesCS5D01G282500 chr5B 460476646 460477475 829 True 859.0 859 85.5670 2484 3340 1 chr5B.!!$R2 856

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
544 545 1.139256 TGTACGGTCAGAAGCAAACCA 59.861 47.619 0.0 0.0 32.35 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2426 2484 0.033601 TTGTTGGCCGCCTTATGGAT 60.034 50.0 11.61 0.0 34.57 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
27 28 9.213799 GAGACTTTCTTCTTGAATGTAAGTCAT 57.786 33.333 20.87 13.06 42.30 3.06
48 49 5.244402 TCATTGTTCATCCTGCAAAGATGTT 59.756 36.000 20.26 5.21 41.56 2.71
95 96 5.649782 AATCCAAGTATCTTGGCTTGTTG 57.350 39.130 19.89 0.06 40.13 3.33
191 192 1.299541 GACACCGCCATGATAACCTG 58.700 55.000 0.00 0.00 0.00 4.00
265 266 4.454678 ACATGCCATATCATTGAGAACGT 58.545 39.130 0.00 0.00 0.00 3.99
305 306 2.184533 ACATTGGATACCACACGAGGA 58.815 47.619 0.00 0.00 30.78 3.71
406 407 1.531739 GGGCTCTCGGCTATCAGGAG 61.532 65.000 0.00 0.00 41.46 3.69
407 408 1.288752 GCTCTCGGCTATCAGGAGC 59.711 63.158 0.00 0.00 41.65 4.70
512 513 5.608449 CCATGATCTCAAACTCTAGATGCA 58.392 41.667 0.00 0.00 32.60 3.96
544 545 1.139256 TGTACGGTCAGAAGCAAACCA 59.861 47.619 0.00 0.00 32.35 3.67
585 589 1.334869 CAGTGTGTTGTTCCAAGAGCC 59.665 52.381 0.00 0.00 0.00 4.70
617 622 2.888834 AATGCCGTTTCTTGTTGCTT 57.111 40.000 0.00 0.00 0.00 3.91
730 735 2.803155 TTCTGGTGGGCGTCTCATGC 62.803 60.000 0.00 0.00 0.00 4.06
747 752 3.192001 TCATGCATTCAGGAAGAACTTGC 59.808 43.478 0.00 0.00 40.82 4.01
748 753 2.867624 TGCATTCAGGAAGAACTTGCT 58.132 42.857 2.88 2.88 40.96 3.91
851 861 1.541310 CCTTGTGACTGCCCGACCTA 61.541 60.000 0.00 0.00 0.00 3.08
931 941 4.437794 CCCAAATCACACACATCGAATGAG 60.438 45.833 7.02 2.00 0.00 2.90
1029 1042 0.891373 CTCAGTTCTCTCGAAGGCCA 59.109 55.000 5.01 0.00 0.00 5.36
1031 1044 1.273606 TCAGTTCTCTCGAAGGCCAAG 59.726 52.381 5.01 0.00 0.00 3.61
1429 1445 8.840833 TGTACATGTTTGATACTAGCTTTGAA 57.159 30.769 2.30 0.00 0.00 2.69
1430 1446 8.717821 TGTACATGTTTGATACTAGCTTTGAAC 58.282 33.333 2.30 0.00 0.00 3.18
1441 1459 9.980780 GATACTAGCTTTGAACTTTTGATTCTC 57.019 33.333 0.00 0.00 0.00 2.87
1566 1584 3.569701 GGTGACAATGCCTGAAAAAGAGA 59.430 43.478 0.00 0.00 0.00 3.10
1567 1585 4.219288 GGTGACAATGCCTGAAAAAGAGAT 59.781 41.667 0.00 0.00 0.00 2.75
1712 1730 2.450476 GGGCTGAACCACATCAAGAAT 58.550 47.619 0.00 0.00 42.05 2.40
2256 2274 0.753262 GAGCTACCCGGTCATGTGAT 59.247 55.000 0.00 0.00 39.89 3.06
2265 2318 2.032550 CCGGTCATGTGATTCATTCTGC 59.967 50.000 0.00 0.00 34.09 4.26
2267 2320 3.018856 GGTCATGTGATTCATTCTGCCA 58.981 45.455 0.00 0.00 34.09 4.92
2271 2324 2.715046 TGTGATTCATTCTGCCAGGTC 58.285 47.619 0.00 0.00 0.00 3.85
2276 2329 3.998913 TTCATTCTGCCAGGTCATGTA 57.001 42.857 0.00 0.00 0.00 2.29
2277 2330 3.266510 TCATTCTGCCAGGTCATGTAC 57.733 47.619 0.00 0.00 0.00 2.90
2279 2332 0.973632 TTCTGCCAGGTCATGTACGT 59.026 50.000 0.00 0.00 0.00 3.57
2280 2333 1.842052 TCTGCCAGGTCATGTACGTA 58.158 50.000 0.00 0.00 0.00 3.57
2281 2334 1.749063 TCTGCCAGGTCATGTACGTAG 59.251 52.381 0.00 0.00 0.00 3.51
2283 2336 2.686405 CTGCCAGGTCATGTACGTAGTA 59.314 50.000 0.00 0.00 45.11 1.82
2301 2354 8.167605 ACGTAGTAATAAGTAGACTCATGCAT 57.832 34.615 0.00 0.00 41.94 3.96
2302 2355 8.076781 ACGTAGTAATAAGTAGACTCATGCATG 58.923 37.037 21.07 21.07 41.94 4.06
2303 2356 7.539022 CGTAGTAATAAGTAGACTCATGCATGG 59.461 40.741 25.97 18.30 0.00 3.66
2304 2357 7.603180 AGTAATAAGTAGACTCATGCATGGA 57.397 36.000 25.97 12.05 0.00 3.41
2305 2358 7.665690 AGTAATAAGTAGACTCATGCATGGAG 58.334 38.462 25.97 21.69 38.36 3.86
2306 2359 2.906691 AGTAGACTCATGCATGGAGC 57.093 50.000 25.97 14.77 45.96 4.70
2320 2373 3.191162 GCATGGAGCATTTGTGAAGTGTA 59.809 43.478 0.00 0.00 44.79 2.90
2325 2380 5.239306 TGGAGCATTTGTGAAGTGTAAGAAG 59.761 40.000 0.00 0.00 0.00 2.85
2327 2382 6.150140 GGAGCATTTGTGAAGTGTAAGAAGAT 59.850 38.462 0.00 0.00 0.00 2.40
2331 2389 6.706055 TTTGTGAAGTGTAAGAAGATAGCG 57.294 37.500 0.00 0.00 0.00 4.26
2336 2394 7.067129 TGTGAAGTGTAAGAAGATAGCGAGTAT 59.933 37.037 0.00 0.00 0.00 2.12
2337 2395 8.557864 GTGAAGTGTAAGAAGATAGCGAGTATA 58.442 37.037 0.00 0.00 0.00 1.47
2338 2396 9.117183 TGAAGTGTAAGAAGATAGCGAGTATAA 57.883 33.333 0.00 0.00 0.00 0.98
2339 2397 9.947669 GAAGTGTAAGAAGATAGCGAGTATAAA 57.052 33.333 0.00 0.00 0.00 1.40
2399 2457 4.552166 AGCGACCATATTGTATTTGCAC 57.448 40.909 0.00 0.00 0.00 4.57
2402 2460 4.499040 GCGACCATATTGTATTTGCACAAC 59.501 41.667 0.00 0.00 41.02 3.32
2414 2472 1.065600 GCACAACGGCAAGCTTGAA 59.934 52.632 30.39 0.00 0.00 2.69
2432 2490 5.066893 GCTTGAACAGCTCAAATCATCCATA 59.933 40.000 0.00 0.00 46.27 2.74
2433 2491 6.405065 GCTTGAACAGCTCAAATCATCCATAA 60.405 38.462 0.00 0.00 46.27 1.90
2434 2492 6.688637 TGAACAGCTCAAATCATCCATAAG 57.311 37.500 0.00 0.00 0.00 1.73
2435 2493 5.591472 TGAACAGCTCAAATCATCCATAAGG 59.409 40.000 0.00 0.00 0.00 2.69
2436 2494 3.887716 ACAGCTCAAATCATCCATAAGGC 59.112 43.478 0.00 0.00 33.74 4.35
2437 2495 3.058432 CAGCTCAAATCATCCATAAGGCG 60.058 47.826 0.00 0.00 33.74 5.52
2438 2496 2.227388 GCTCAAATCATCCATAAGGCGG 59.773 50.000 0.00 0.00 33.74 6.13
2439 2497 2.227388 CTCAAATCATCCATAAGGCGGC 59.773 50.000 0.00 0.00 33.74 6.53
2440 2498 1.270550 CAAATCATCCATAAGGCGGCC 59.729 52.381 12.11 12.11 33.74 6.13
2441 2499 0.478072 AATCATCCATAAGGCGGCCA 59.522 50.000 23.09 0.60 33.74 5.36
2443 2501 0.465460 TCATCCATAAGGCGGCCAAC 60.465 55.000 23.09 0.00 33.74 3.77
2444 2502 0.751277 CATCCATAAGGCGGCCAACA 60.751 55.000 23.09 5.68 33.74 3.33
2445 2503 0.033601 ATCCATAAGGCGGCCAACAA 60.034 50.000 23.09 3.28 33.74 2.83
2447 2505 1.213182 TCCATAAGGCGGCCAACAATA 59.787 47.619 23.09 6.39 33.74 1.90
2448 2506 2.158534 TCCATAAGGCGGCCAACAATAT 60.159 45.455 23.09 8.42 33.74 1.28
2450 2508 3.440173 CCATAAGGCGGCCAACAATATAG 59.560 47.826 23.09 1.43 0.00 1.31
2451 2509 2.729028 AAGGCGGCCAACAATATAGT 57.271 45.000 23.09 0.00 0.00 2.12
2453 2511 3.121738 AGGCGGCCAACAATATAGTAC 57.878 47.619 23.09 0.00 0.00 2.73
2455 2513 2.476821 GCGGCCAACAATATAGTACGT 58.523 47.619 2.24 0.00 0.00 3.57
2457 2515 3.426525 GCGGCCAACAATATAGTACGTAC 59.573 47.826 18.10 18.10 0.00 3.67
2458 2516 4.794003 GCGGCCAACAATATAGTACGTACT 60.794 45.833 29.62 29.62 40.24 2.73
2459 2517 5.284079 CGGCCAACAATATAGTACGTACTT 58.716 41.667 31.58 20.72 37.73 2.24
2461 2519 6.510536 GGCCAACAATATAGTACGTACTTCT 58.489 40.000 31.58 21.17 37.73 2.85
2462 2520 7.520453 CGGCCAACAATATAGTACGTACTTCTA 60.520 40.741 31.58 22.45 37.73 2.10
2463 2521 7.806960 GGCCAACAATATAGTACGTACTTCTAG 59.193 40.741 31.58 19.59 37.73 2.43
2464 2522 8.348507 GCCAACAATATAGTACGTACTTCTAGT 58.651 37.037 31.58 19.41 37.73 2.57
2478 2536 7.642060 GTACTTCTAGTACGTAACATGAACG 57.358 40.000 19.02 19.02 41.27 3.95
2522 3770 5.476945 ACAGAATGACAAACTTGGATTACCC 59.523 40.000 0.00 0.00 39.69 3.69
2533 3781 1.354031 TGGATTACCCAAAGCAGCTCA 59.646 47.619 0.00 0.00 43.29 4.26
2535 3783 3.201930 TGGATTACCCAAAGCAGCTCATA 59.798 43.478 0.00 0.00 43.29 2.15
2541 3789 4.599041 ACCCAAAGCAGCTCATACATTAA 58.401 39.130 0.00 0.00 0.00 1.40
2543 3791 4.883585 CCCAAAGCAGCTCATACATTAAGA 59.116 41.667 0.00 0.00 0.00 2.10
2544 3792 5.357878 CCCAAAGCAGCTCATACATTAAGAA 59.642 40.000 0.00 0.00 0.00 2.52
2545 3793 6.127647 CCCAAAGCAGCTCATACATTAAGAAA 60.128 38.462 0.00 0.00 0.00 2.52
2546 3794 6.749118 CCAAAGCAGCTCATACATTAAGAAAC 59.251 38.462 0.00 0.00 0.00 2.78
2548 3796 7.636150 AAGCAGCTCATACATTAAGAAACAT 57.364 32.000 0.00 0.00 0.00 2.71
2582 3843 2.903784 ACCAGTGTTGCCAGAGTACATA 59.096 45.455 0.00 0.00 0.00 2.29
2583 3844 3.055819 ACCAGTGTTGCCAGAGTACATAG 60.056 47.826 0.00 0.00 0.00 2.23
2596 3857 7.439655 GCCAGAGTACATAGGTGAAAAAGATAG 59.560 40.741 0.00 0.00 0.00 2.08
2600 3861 7.203910 AGTACATAGGTGAAAAAGATAGCTCG 58.796 38.462 0.00 0.00 0.00 5.03
2613 3874 3.395669 GCTCGCGGCTTCGTAATT 58.604 55.556 6.13 0.00 38.06 1.40
2631 3892 7.351981 TCGTAATTAGTAGCGCTCGTAAATAA 58.648 34.615 16.34 6.75 0.00 1.40
2632 3893 8.017373 TCGTAATTAGTAGCGCTCGTAAATAAT 58.983 33.333 16.34 9.13 0.00 1.28
2633 3894 9.265938 CGTAATTAGTAGCGCTCGTAAATAATA 57.734 33.333 16.34 0.00 0.00 0.98
2636 3897 9.850628 AATTAGTAGCGCTCGTAAATAATATCA 57.149 29.630 16.34 0.00 0.00 2.15
2637 3898 9.850628 ATTAGTAGCGCTCGTAAATAATATCAA 57.149 29.630 16.34 0.00 0.00 2.57
2638 3899 9.850628 TTAGTAGCGCTCGTAAATAATATCAAT 57.149 29.630 16.34 0.00 0.00 2.57
2670 3932 8.997621 ACAATTACAACGTATAACTGTCTGAT 57.002 30.769 0.00 0.00 0.00 2.90
2671 3933 9.084164 ACAATTACAACGTATAACTGTCTGATC 57.916 33.333 0.00 0.00 0.00 2.92
2672 3934 9.083080 CAATTACAACGTATAACTGTCTGATCA 57.917 33.333 0.00 0.00 0.00 2.92
2673 3935 8.858003 ATTACAACGTATAACTGTCTGATCAG 57.142 34.615 17.07 17.07 40.80 2.90
2674 3936 6.510879 ACAACGTATAACTGTCTGATCAGA 57.489 37.500 21.67 21.67 38.63 3.27
2709 3971 1.270550 CAAAACTTGCAGGGCCTAGTG 59.729 52.381 5.28 0.00 0.00 2.74
2722 3984 1.270839 GCCTAGTGGTGCTTGTTCAGA 60.271 52.381 0.00 0.00 35.27 3.27
2750 4012 4.617959 TCTTCAGTAGTTTCCTCAACACG 58.382 43.478 0.00 0.00 37.93 4.49
2756 4018 3.536956 AGTTTCCTCAACACGTCTTCA 57.463 42.857 0.00 0.00 37.93 3.02
2860 4122 2.349590 GCCAAATGAAAATGGTGAGGC 58.650 47.619 0.00 0.00 39.00 4.70
2873 4135 1.065126 GGTGAGGCCTTTCTGTGCTAT 60.065 52.381 6.77 0.00 0.00 2.97
2874 4136 2.170607 GGTGAGGCCTTTCTGTGCTATA 59.829 50.000 6.77 0.00 0.00 1.31
2876 4138 4.455606 GTGAGGCCTTTCTGTGCTATAAT 58.544 43.478 6.77 0.00 0.00 1.28
2877 4139 5.454755 GGTGAGGCCTTTCTGTGCTATAATA 60.455 44.000 6.77 0.00 0.00 0.98
2878 4140 6.055588 GTGAGGCCTTTCTGTGCTATAATAA 58.944 40.000 6.77 0.00 0.00 1.40
2879 4141 6.203723 GTGAGGCCTTTCTGTGCTATAATAAG 59.796 42.308 6.77 0.00 0.00 1.73
2881 4143 6.292150 AGGCCTTTCTGTGCTATAATAAGTC 58.708 40.000 0.00 0.00 0.00 3.01
2882 4144 6.100424 AGGCCTTTCTGTGCTATAATAAGTCT 59.900 38.462 0.00 0.00 0.00 3.24
2925 4187 4.758165 ACACTCGGGTAAAACCAACATTAG 59.242 41.667 0.00 0.00 41.02 1.73
2952 4216 7.278875 ACAACCCAAACATTGTAAAACATCAT 58.721 30.769 0.00 0.00 37.27 2.45
2958 4222 7.958567 CCAAACATTGTAAAACATCATGATTGC 59.041 33.333 5.16 0.00 32.47 3.56
2966 4230 5.679734 AAACATCATGATTGCGATACTCC 57.320 39.130 5.16 0.00 0.00 3.85
3150 4414 1.745489 CCAGGCCAGCTAAACGACC 60.745 63.158 5.01 0.00 0.00 4.79
3151 4415 1.003839 CAGGCCAGCTAAACGACCA 60.004 57.895 5.01 0.00 0.00 4.02
3156 4420 1.747206 GCCAGCTAAACGACCATCCAT 60.747 52.381 0.00 0.00 0.00 3.41
3239 4503 5.756347 TCGTTACAATATATGCAACCCTGAC 59.244 40.000 0.00 0.00 32.55 3.51
3261 4525 4.468510 ACTGCAATCCAAACATCATCCATT 59.531 37.500 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 5.534278 TGTAACATCTTTGCAGGATGAACAA 59.466 36.000 27.17 16.12 42.02 2.83
95 96 4.997395 TCTTTCTGCAACACCTGAAGATAC 59.003 41.667 0.00 0.00 39.67 2.24
191 192 6.429385 AGAAACCAATGATCTTCACTGTCTTC 59.571 38.462 0.00 0.00 0.00 2.87
265 266 0.317160 AAGGCATTCGAGTGACGTCA 59.683 50.000 15.76 15.76 43.13 4.35
293 294 3.683885 AGGATGTCCTCGTGTGGTA 57.316 52.632 0.00 0.00 44.77 3.25
305 306 2.357836 CAGCTGGCCCAAGGATGT 59.642 61.111 5.57 0.00 0.00 3.06
383 384 1.369321 GATAGCCGAGAGCCCCTTG 59.631 63.158 0.00 0.00 45.47 3.61
406 407 2.164422 GGAACCTTTGGCTCAACATAGC 59.836 50.000 0.00 0.00 41.99 2.97
512 513 3.994392 CTGACCGTACATAGCAACTTGTT 59.006 43.478 0.00 0.00 0.00 2.83
528 529 2.336554 CAATGGTTTGCTTCTGACCG 57.663 50.000 0.00 0.00 36.22 4.79
544 545 3.896888 TGGTCTTTCTGAACATTGGCAAT 59.103 39.130 6.96 6.96 37.49 3.56
585 589 6.319399 AGAAACGGCATTAAGGAAAAATACG 58.681 36.000 0.00 0.00 0.00 3.06
637 642 4.889409 CAGGGAATAAAGGCTAGAATGCAA 59.111 41.667 0.00 0.00 34.04 4.08
730 735 6.876257 AGTAACTAGCAAGTTCTTCCTGAATG 59.124 38.462 0.00 0.00 42.42 2.67
747 752 8.593492 TGCATGCATTGAGTAATAGTAACTAG 57.407 34.615 18.46 0.00 0.00 2.57
748 753 8.204160 ACTGCATGCATTGAGTAATAGTAACTA 58.796 33.333 22.97 0.00 0.00 2.24
931 941 5.044558 TGTTTTTGGCATTTAGTCCGTTTC 58.955 37.500 0.00 0.00 0.00 2.78
1029 1042 1.379576 GGCCATTGCTGGAGCTCTT 60.380 57.895 14.64 0.00 46.37 2.85
1031 1044 2.044650 TGGCCATTGCTGGAGCTC 60.045 61.111 0.00 4.71 46.37 4.09
1052 1068 2.124778 GCAGGAGAAGCAGGGAGC 60.125 66.667 0.00 0.00 46.19 4.70
1353 1369 2.587522 GGGGCAAAGTTCTCTGTTCTT 58.412 47.619 0.00 0.00 0.00 2.52
1422 1438 5.108385 TCCGAGAATCAAAAGTTCAAAGC 57.892 39.130 0.00 0.00 33.17 3.51
1423 1439 6.902341 TGATCCGAGAATCAAAAGTTCAAAG 58.098 36.000 0.00 0.00 32.80 2.77
1424 1440 6.875948 TGATCCGAGAATCAAAAGTTCAAA 57.124 33.333 0.00 0.00 32.80 2.69
1425 1441 6.183360 CGATGATCCGAGAATCAAAAGTTCAA 60.183 38.462 0.00 0.00 39.04 2.69
1427 1443 5.292101 ACGATGATCCGAGAATCAAAAGTTC 59.708 40.000 0.00 0.00 39.04 3.01
1428 1444 5.178797 ACGATGATCCGAGAATCAAAAGTT 58.821 37.500 0.00 0.00 39.04 2.66
1429 1445 4.759782 ACGATGATCCGAGAATCAAAAGT 58.240 39.130 0.00 0.00 39.04 2.66
1430 1446 5.291858 TCAACGATGATCCGAGAATCAAAAG 59.708 40.000 0.00 0.00 39.04 2.27
1441 1459 3.000041 TCCAACTTTCAACGATGATCCG 59.000 45.455 0.00 0.00 34.96 4.18
1566 1584 5.980116 GCAGAGTACTGTTATCATCGTCAAT 59.020 40.000 0.00 0.00 45.04 2.57
1567 1585 5.340803 GCAGAGTACTGTTATCATCGTCAA 58.659 41.667 0.00 0.00 45.04 3.18
1712 1730 3.241530 AGCGACACCAGCTTCCCA 61.242 61.111 0.00 0.00 43.24 4.37
2246 2264 3.018856 TGGCAGAATGAATCACATGACC 58.981 45.455 0.00 0.00 39.69 4.02
2256 2274 2.885135 ACATGACCTGGCAGAATGAA 57.115 45.000 17.94 0.00 39.69 2.57
2265 2318 7.035840 ACTTATTACTACGTACATGACCTGG 57.964 40.000 0.00 0.00 0.00 4.45
2267 2320 9.050601 GTCTACTTATTACTACGTACATGACCT 57.949 37.037 0.00 0.00 0.00 3.85
2276 2329 7.563888 TGCATGAGTCTACTTATTACTACGT 57.436 36.000 0.00 0.00 0.00 3.57
2277 2330 7.539022 CCATGCATGAGTCTACTTATTACTACG 59.461 40.741 28.31 0.04 0.00 3.51
2279 2332 8.706322 TCCATGCATGAGTCTACTTATTACTA 57.294 34.615 28.31 0.00 0.00 1.82
2280 2333 7.603180 TCCATGCATGAGTCTACTTATTACT 57.397 36.000 28.31 0.00 0.00 2.24
2281 2334 6.367422 GCTCCATGCATGAGTCTACTTATTAC 59.633 42.308 28.31 3.08 42.31 1.89
2282 2335 6.459066 GCTCCATGCATGAGTCTACTTATTA 58.541 40.000 28.31 0.00 42.31 0.98
2283 2336 5.303971 GCTCCATGCATGAGTCTACTTATT 58.696 41.667 28.31 0.00 42.31 1.40
2284 2337 4.892433 GCTCCATGCATGAGTCTACTTAT 58.108 43.478 28.31 0.00 42.31 1.73
2301 2354 4.713553 TCTTACACTTCACAAATGCTCCA 58.286 39.130 0.00 0.00 0.00 3.86
2302 2355 5.470098 TCTTCTTACACTTCACAAATGCTCC 59.530 40.000 0.00 0.00 0.00 4.70
2303 2356 6.545504 TCTTCTTACACTTCACAAATGCTC 57.454 37.500 0.00 0.00 0.00 4.26
2304 2357 7.148340 GCTATCTTCTTACACTTCACAAATGCT 60.148 37.037 0.00 0.00 0.00 3.79
2305 2358 6.963805 GCTATCTTCTTACACTTCACAAATGC 59.036 38.462 0.00 0.00 0.00 3.56
2306 2359 7.063426 TCGCTATCTTCTTACACTTCACAAATG 59.937 37.037 0.00 0.00 0.00 2.32
2307 2360 7.097192 TCGCTATCTTCTTACACTTCACAAAT 58.903 34.615 0.00 0.00 0.00 2.32
2308 2361 6.452242 TCGCTATCTTCTTACACTTCACAAA 58.548 36.000 0.00 0.00 0.00 2.83
2359 2417 7.436970 TGGTCGCTTACATATATTTACACACTG 59.563 37.037 0.00 0.00 0.00 3.66
2373 2431 6.262049 TGCAAATACAATATGGTCGCTTACAT 59.738 34.615 0.00 0.00 0.00 2.29
2374 2432 5.586643 TGCAAATACAATATGGTCGCTTACA 59.413 36.000 0.00 0.00 0.00 2.41
2376 2434 5.586643 TGTGCAAATACAATATGGTCGCTTA 59.413 36.000 0.00 0.00 0.00 3.09
2377 2435 4.397730 TGTGCAAATACAATATGGTCGCTT 59.602 37.500 0.00 0.00 0.00 4.68
2378 2436 3.944650 TGTGCAAATACAATATGGTCGCT 59.055 39.130 0.00 0.00 0.00 4.93
2379 2437 4.285807 TGTGCAAATACAATATGGTCGC 57.714 40.909 0.00 0.00 0.00 5.19
2380 2438 4.728131 CGTTGTGCAAATACAATATGGTCG 59.272 41.667 0.00 0.00 42.02 4.79
2396 2454 1.065600 TTCAAGCTTGCCGTTGTGC 59.934 52.632 21.99 0.00 0.00 4.57
2399 2457 3.168628 CTGTTCAAGCTTGCCGTTG 57.831 52.632 21.99 6.73 0.00 4.10
2409 2467 5.578005 ATGGATGATTTGAGCTGTTCAAG 57.422 39.130 7.01 0.00 46.01 3.02
2414 2472 3.887716 GCCTTATGGATGATTTGAGCTGT 59.112 43.478 0.00 0.00 34.57 4.40
2419 2477 2.229792 GCCGCCTTATGGATGATTTGA 58.770 47.619 0.00 0.00 34.57 2.69
2424 2482 0.465460 GTTGGCCGCCTTATGGATGA 60.465 55.000 11.61 0.00 34.57 2.92
2426 2484 0.033601 TTGTTGGCCGCCTTATGGAT 60.034 50.000 11.61 0.00 34.57 3.41
2432 2490 2.729028 ACTATATTGTTGGCCGCCTT 57.271 45.000 11.61 0.00 0.00 4.35
2433 2491 2.547218 CGTACTATATTGTTGGCCGCCT 60.547 50.000 11.61 0.00 0.00 5.52
2434 2492 1.796459 CGTACTATATTGTTGGCCGCC 59.204 52.381 1.04 1.04 0.00 6.13
2435 2493 2.476821 ACGTACTATATTGTTGGCCGC 58.523 47.619 0.00 0.00 0.00 6.53
2436 2494 4.863491 AGTACGTACTATATTGTTGGCCG 58.137 43.478 26.36 0.00 34.13 6.13
2437 2495 6.510536 AGAAGTACGTACTATATTGTTGGCC 58.489 40.000 27.59 0.00 34.99 5.36
2438 2496 8.348507 ACTAGAAGTACGTACTATATTGTTGGC 58.651 37.037 27.59 7.94 34.99 4.52
2455 2513 6.092670 AGCGTTCATGTTACGTACTAGAAGTA 59.907 38.462 19.01 0.00 40.92 2.24
2457 2515 5.330295 AGCGTTCATGTTACGTACTAGAAG 58.670 41.667 19.01 0.00 40.92 2.85
2458 2516 5.300969 AGCGTTCATGTTACGTACTAGAA 57.699 39.130 19.01 0.00 40.92 2.10
2459 2517 4.952262 AGCGTTCATGTTACGTACTAGA 57.048 40.909 19.01 0.00 40.92 2.43
2461 2519 7.970061 AGATTTAAGCGTTCATGTTACGTACTA 59.030 33.333 19.01 9.34 40.92 1.82
2462 2520 6.810182 AGATTTAAGCGTTCATGTTACGTACT 59.190 34.615 19.01 9.74 40.92 2.73
2463 2521 6.986118 AGATTTAAGCGTTCATGTTACGTAC 58.014 36.000 19.01 8.13 40.92 3.67
2464 2522 7.585286 AAGATTTAAGCGTTCATGTTACGTA 57.415 32.000 19.01 0.00 40.92 3.57
2465 2523 6.476243 AAGATTTAAGCGTTCATGTTACGT 57.524 33.333 19.01 0.00 40.92 3.57
2466 2524 7.775729 AAAAGATTTAAGCGTTCATGTTACG 57.224 32.000 15.47 15.47 41.71 3.18
2494 3742 5.261209 TCCAAGTTTGTCATTCTGTTTGG 57.739 39.130 0.00 0.00 36.13 3.28
2495 3743 7.382218 GGTAATCCAAGTTTGTCATTCTGTTTG 59.618 37.037 0.00 0.00 0.00 2.93
2496 3744 7.433680 GGTAATCCAAGTTTGTCATTCTGTTT 58.566 34.615 0.00 0.00 0.00 2.83
2497 3745 6.015434 GGGTAATCCAAGTTTGTCATTCTGTT 60.015 38.462 0.00 0.00 35.00 3.16
2499 3747 5.476599 TGGGTAATCCAAGTTTGTCATTCTG 59.523 40.000 0.00 0.00 43.84 3.02
2522 3770 7.307694 TGTTTCTTAATGTATGAGCTGCTTTG 58.692 34.615 2.53 0.00 0.00 2.77
2541 3789 7.175641 CACTGGTAGAAAAGGATGAATGTTTCT 59.824 37.037 0.00 0.00 41.79 2.52
2543 3791 6.777580 ACACTGGTAGAAAAGGATGAATGTTT 59.222 34.615 0.00 0.00 0.00 2.83
2544 3792 6.306987 ACACTGGTAGAAAAGGATGAATGTT 58.693 36.000 0.00 0.00 0.00 2.71
2545 3793 5.880901 ACACTGGTAGAAAAGGATGAATGT 58.119 37.500 0.00 0.00 0.00 2.71
2546 3794 6.615088 CAACACTGGTAGAAAAGGATGAATG 58.385 40.000 0.00 0.00 0.00 2.67
2548 3796 4.518970 GCAACACTGGTAGAAAAGGATGAA 59.481 41.667 0.00 0.00 0.00 2.57
2563 3824 3.055819 ACCTATGTACTCTGGCAACACTG 60.056 47.826 0.00 0.00 46.17 3.66
2582 3843 2.271800 CGCGAGCTATCTTTTTCACCT 58.728 47.619 0.00 0.00 0.00 4.00
2583 3844 1.327764 CCGCGAGCTATCTTTTTCACC 59.672 52.381 8.23 0.00 0.00 4.02
2596 3857 0.503117 CTAATTACGAAGCCGCGAGC 59.497 55.000 8.23 9.98 44.25 5.03
2600 3861 1.450905 CGCTACTAATTACGAAGCCGC 59.549 52.381 0.00 0.00 39.95 6.53
2665 3927 4.783764 TTTAGCTTGTCGTCTGATCAGA 57.216 40.909 21.67 21.67 34.56 3.27
2666 3928 5.177511 TGTTTTTAGCTTGTCGTCTGATCAG 59.822 40.000 17.07 17.07 0.00 2.90
2668 3930 5.591643 TGTTTTTAGCTTGTCGTCTGATC 57.408 39.130 0.00 0.00 0.00 2.92
2670 3932 5.804692 TTTGTTTTTAGCTTGTCGTCTGA 57.195 34.783 0.00 0.00 0.00 3.27
2671 3933 6.027749 AGTTTTGTTTTTAGCTTGTCGTCTG 58.972 36.000 0.00 0.00 0.00 3.51
2672 3934 6.190954 AGTTTTGTTTTTAGCTTGTCGTCT 57.809 33.333 0.00 0.00 0.00 4.18
2673 3935 6.682943 CAAGTTTTGTTTTTAGCTTGTCGTC 58.317 36.000 0.00 0.00 31.57 4.20
2674 3936 5.061684 GCAAGTTTTGTTTTTAGCTTGTCGT 59.938 36.000 0.00 0.00 36.62 4.34
2675 3937 5.061560 TGCAAGTTTTGTTTTTAGCTTGTCG 59.938 36.000 0.00 0.00 36.62 4.35
2676 3938 6.401955 TGCAAGTTTTGTTTTTAGCTTGTC 57.598 33.333 0.00 0.00 36.62 3.18
2709 3971 5.048504 TGAAGAATTGATCTGAACAAGCACC 60.049 40.000 6.51 0.00 38.79 5.01
2722 3984 7.939039 TGTTGAGGAAACTACTGAAGAATTGAT 59.061 33.333 0.00 0.00 44.43 2.57
2774 4036 0.698238 AGCATGACTGGGCTTTACCA 59.302 50.000 0.00 0.00 42.05 3.25
2860 4122 9.469807 CTGTAGACTTATTATAGCACAGAAAGG 57.530 37.037 0.00 0.00 35.32 3.11
2873 4135 9.278978 CAGTGCTCTATCTCTGTAGACTTATTA 57.721 37.037 0.00 0.00 33.57 0.98
2874 4136 7.996066 TCAGTGCTCTATCTCTGTAGACTTATT 59.004 37.037 0.00 0.00 33.57 1.40
2876 4138 6.890293 TCAGTGCTCTATCTCTGTAGACTTA 58.110 40.000 0.00 0.00 33.57 2.24
2877 4139 5.750524 TCAGTGCTCTATCTCTGTAGACTT 58.249 41.667 0.00 0.00 33.57 3.01
2878 4140 5.366482 TCAGTGCTCTATCTCTGTAGACT 57.634 43.478 0.00 0.00 33.57 3.24
2879 4141 6.127869 TGTTTCAGTGCTCTATCTCTGTAGAC 60.128 42.308 0.00 0.00 33.57 2.59
2881 4143 6.033341 GTGTTTCAGTGCTCTATCTCTGTAG 58.967 44.000 0.00 0.00 0.00 2.74
2882 4144 5.712446 AGTGTTTCAGTGCTCTATCTCTGTA 59.288 40.000 0.00 0.00 0.00 2.74
2892 4154 0.249911 ACCCGAGTGTTTCAGTGCTC 60.250 55.000 0.00 0.00 0.00 4.26
2925 4187 6.969828 TGTTTTACAATGTTTGGGTTGTTC 57.030 33.333 0.00 0.00 39.18 3.18
2952 4216 1.069090 GCCCGGAGTATCGCAATCA 59.931 57.895 0.73 0.00 34.37 2.57
2958 4222 1.672854 TTCTGTGGCCCGGAGTATCG 61.673 60.000 0.73 0.00 34.37 2.92
2966 4230 0.888736 TTGTGTCATTCTGTGGCCCG 60.889 55.000 0.00 0.00 0.00 6.13
3034 4298 2.173569 ACTGTCTGCTTTCCTCTGGTTT 59.826 45.455 0.00 0.00 0.00 3.27
3150 4414 5.049612 CAGACCTTCGATCATTTGATGGATG 60.050 44.000 6.16 8.26 38.69 3.51
3151 4415 5.061853 CAGACCTTCGATCATTTGATGGAT 58.938 41.667 6.16 0.00 38.69 3.41
3156 4420 8.879759 GTTATTTACAGACCTTCGATCATTTGA 58.120 33.333 0.00 0.00 0.00 2.69
3191 4455 9.860898 CGATGATTTGTATAGTGAGGATATTGA 57.139 33.333 0.00 0.00 0.00 2.57
3239 4503 4.665833 ATGGATGATGTTTGGATTGCAG 57.334 40.909 0.00 0.00 0.00 4.41
3305 4570 9.489084 TGTACTGCGCTTATAATAAATCAGATT 57.511 29.630 9.73 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.