Multiple sequence alignment - TraesCS5B01G564500

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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 TraesCS5B01G564500 chr5B 100.000 2963 0 0 1 2963 709914969 709917931 0.000000e+00 5472.0
1 TraesCS5B01G564500 chr5B 83.831 1305 162 25 1650 2929 710077411 710076131 0.000000e+00 1195.0
2 TraesCS5B01G564500 chr5B 89.817 491 50 0 967 1457 710078034 710077544 5.390000e-177 630.0
3 TraesCS5B01G564500 chr5B 99.145 234 2 0 957 1190 710023874 710024107 3.530000e-114 422.0
4 TraesCS5B01G564500 chr5B 87.744 359 28 11 471 815 710023344 710023700 3.560000e-109 405.0
5 TraesCS5B01G564500 chr5B 81.579 418 42 15 1 408 710022923 710023315 2.220000e-81 313.0
6 TraesCS5B01G564500 chr5B 77.447 235 42 9 1256 1486 448314184 448314411 2.400000e-26 130.0
7 TraesCS5B01G564500 chr4A 87.451 1267 105 20 385 1624 605543321 605542082 0.000000e+00 1410.0
8 TraesCS5B01G564500 chr4A 85.280 1216 128 21 899 2090 605425094 605423906 0.000000e+00 1206.0
9 TraesCS5B01G564500 chr4A 83.990 812 101 13 1 794 605428515 605427715 0.000000e+00 752.0
10 TraesCS5B01G564500 chr4A 77.665 788 141 21 2126 2900 605423903 605423138 5.830000e-122 448.0
11 TraesCS5B01G564500 chr5D 85.486 1254 154 18 845 2083 556925782 556924542 0.000000e+00 1282.0
12 TraesCS5B01G564500 chr5D 92.373 472 30 5 112 580 556926960 556926492 0.000000e+00 667.0
13 TraesCS5B01G564500 chr5D 81.328 723 106 23 1164 1868 556922055 556921344 7.170000e-156 560.0
14 TraesCS5B01G564500 chr5D 85.373 335 47 2 2589 2922 556923961 556923628 2.190000e-91 346.0
15 TraesCS5B01G564500 chr5D 77.882 425 71 15 2119 2542 556924470 556924068 2.950000e-60 243.0
16 TraesCS5B01G564500 chr5D 86.387 191 26 0 2656 2846 556914389 556914199 2.990000e-50 209.0
17 TraesCS5B01G564500 chr5D 77.447 235 42 9 1256 1486 375585819 375586046 2.400000e-26 130.0
18 TraesCS5B01G564500 chr5D 83.838 99 12 3 2723 2819 559680053 559679957 1.130000e-14 91.6
19 TraesCS5B01G564500 chr6A 77.895 570 97 16 952 1499 611309493 611308931 7.920000e-86 327.0
20 TraesCS5B01G564500 chr6A 83.432 169 28 0 2642 2810 611307806 611307638 1.100000e-34 158.0
21 TraesCS5B01G564500 chr6D 86.111 144 20 0 2675 2818 464729165 464729022 3.950000e-34 156.0
22 TraesCS5B01G564500 chr5A 76.395 233 44 9 1256 1484 476767743 476767968 6.710000e-22 115.0
23 TraesCS5B01G564500 chr7B 81.731 104 19 0 2715 2818 720117920 720117817 1.460000e-13 87.9


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 TraesCS5B01G564500 chr5B 709914969 709917931 2962 False 5472.0 5472 100.000000 1 2963 1 chr5B.!!$F2 2962
1 TraesCS5B01G564500 chr5B 710076131 710078034 1903 True 912.5 1195 86.824000 967 2929 2 chr5B.!!$R1 1962
2 TraesCS5B01G564500 chr5B 710022923 710024107 1184 False 380.0 422 89.489333 1 1190 3 chr5B.!!$F3 1189
3 TraesCS5B01G564500 chr4A 605542082 605543321 1239 True 1410.0 1410 87.451000 385 1624 1 chr4A.!!$R1 1239
4 TraesCS5B01G564500 chr4A 605423138 605428515 5377 True 802.0 1206 82.311667 1 2900 3 chr4A.!!$R2 2899
5 TraesCS5B01G564500 chr5D 556921344 556926960 5616 True 619.6 1282 84.488400 112 2922 5 chr5D.!!$R3 2810
6 TraesCS5B01G564500 chr6A 611307638 611309493 1855 True 242.5 327 80.663500 952 2810 2 chr6A.!!$R1 1858

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
28 29 0.678048 ATGCTCCTTCAACTTCGCCC 60.678 55.0 0.0 0.0 0.0 6.13 F
1501 4737 0.600782 GGCTTTGTGGTGTGGCAATG 60.601 55.0 0.0 0.0 0.0 2.82 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 4757 0.037590 CCGATTCAGAACCACCCCAA 59.962 55.0 0.00 0.00 0.00 4.12 R
2567 5958 0.040958 CGCACCTTGCAAGTCTTCAC 60.041 55.0 24.35 7.28 45.36 3.18 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
28 29 0.678048 ATGCTCCTTCAACTTCGCCC 60.678 55.000 0.00 0.00 0.00 6.13
30 31 0.889186 GCTCCTTCAACTTCGCCCAA 60.889 55.000 0.00 0.00 0.00 4.12
38 43 2.500098 TCAACTTCGCCCAATAGCTAGT 59.500 45.455 0.00 0.00 0.00 2.57
42 47 3.055385 ACTTCGCCCAATAGCTAGTTTGA 60.055 43.478 8.38 0.00 0.00 2.69
63 71 1.737793 GCCTAACGTCAACCTCAATGG 59.262 52.381 0.00 0.00 42.93 3.16
83 91 0.940833 TGTGTGGTGCATGTGTTACG 59.059 50.000 0.00 0.00 0.00 3.18
110 118 9.420118 TGGCTATTATCTTAAAAATGATGTGGT 57.580 29.630 0.00 0.00 0.00 4.16
122 130 8.761575 AAAAATGATGTGGTTTAATGTAGCTG 57.238 30.769 0.00 0.00 0.00 4.24
128 136 4.693566 TGTGGTTTAATGTAGCTGCAGTAC 59.306 41.667 16.64 15.87 0.00 2.73
156 164 8.866970 AAAACGAGTCCAAAATAGGGTTAATA 57.133 30.769 0.00 0.00 0.00 0.98
195 203 3.073650 AGCAGGACCTTCAACTTGATTCT 59.926 43.478 0.00 0.00 0.00 2.40
199 2551 6.105333 CAGGACCTTCAACTTGATTCTCTAG 58.895 44.000 0.00 0.00 0.00 2.43
266 2620 5.831997 TCTTTAGTTTTTGCTCTTTGCTCC 58.168 37.500 0.00 0.00 43.37 4.70
301 2655 4.576463 ACGTATCCCTCAAATTCAATGCTC 59.424 41.667 0.00 0.00 0.00 4.26
337 2691 4.455877 GCTACTTTGGCACTGTACAAGAAT 59.544 41.667 0.00 0.00 0.00 2.40
381 2742 7.873195 TGGATGGTCTAGCTAGCTCTATATAA 58.127 38.462 23.26 0.00 0.00 0.98
383 2744 8.626526 GGATGGTCTAGCTAGCTCTATATAAAC 58.373 40.741 23.26 8.58 0.00 2.01
600 2993 5.985530 GCATGGCCTCTTACATTATTTTTCC 59.014 40.000 3.32 0.00 0.00 3.13
866 3989 4.946478 ATTACTGATCTAGTGTGGGCTC 57.054 45.455 7.74 0.00 40.65 4.70
875 3998 1.153168 GTGTGGGCTCTGTGTGTGT 60.153 57.895 0.00 0.00 0.00 3.72
880 4003 1.166531 GGGCTCTGTGTGTGTTCACC 61.167 60.000 0.37 0.00 43.26 4.02
922 4092 8.023706 GCTAAGCTTTAGTTGCTCTGTTATTTT 58.976 33.333 3.20 0.00 40.22 1.82
1183 4401 0.896019 GCTAGCCTATCTGGGAGCGA 60.896 60.000 2.29 0.00 36.00 4.93
1362 4595 5.696822 CATCTGTTGAATCTTGTTGTCCAG 58.303 41.667 0.00 0.00 0.00 3.86
1366 4599 3.855255 TGAATCTTGTTGTCCAGGTGA 57.145 42.857 0.00 0.00 0.00 4.02
1367 4600 4.163441 TGAATCTTGTTGTCCAGGTGAA 57.837 40.909 0.00 0.00 0.00 3.18
1398 4631 9.492730 ACCCTGTATATCTTTTGGAAATCATTT 57.507 29.630 0.00 0.00 0.00 2.32
1413 4649 1.133513 TCATTTGATGGCGGCCCTAAT 60.134 47.619 17.97 7.77 0.00 1.73
1481 4717 5.983333 ATCAAGTATGGGGAGAGAACATT 57.017 39.130 0.00 0.00 0.00 2.71
1499 4735 1.260538 TTGGCTTTGTGGTGTGGCAA 61.261 50.000 0.00 0.00 41.48 4.52
1501 4737 0.600782 GGCTTTGTGGTGTGGCAATG 60.601 55.000 0.00 0.00 0.00 2.82
1503 4739 1.339610 GCTTTGTGGTGTGGCAATGTA 59.660 47.619 0.00 0.00 0.00 2.29
1524 4760 6.991938 TGTAAGAAACATGAGGGAAATTTGG 58.008 36.000 0.00 0.00 31.43 3.28
1529 4768 1.832998 CATGAGGGAAATTTGGGGTGG 59.167 52.381 0.00 0.00 0.00 4.61
1535 4774 2.604139 GGAAATTTGGGGTGGTTCTGA 58.396 47.619 0.00 0.00 0.00 3.27
1536 4775 2.969262 GGAAATTTGGGGTGGTTCTGAA 59.031 45.455 0.00 0.00 0.00 3.02
1566 4826 2.418746 GCGCCTTGATACCTCTTCTGAA 60.419 50.000 0.00 0.00 0.00 3.02
1567 4827 3.452474 CGCCTTGATACCTCTTCTGAAG 58.548 50.000 11.18 11.18 0.00 3.02
1568 4828 3.131223 CGCCTTGATACCTCTTCTGAAGA 59.869 47.826 18.40 18.40 35.87 2.87
1637 4897 2.381725 ACTAGCCTTTCGTACAAGCC 57.618 50.000 0.00 0.00 0.00 4.35
1670 4932 7.844493 ACCGTTGGGATATAGATAGTTTACA 57.156 36.000 0.00 0.00 36.97 2.41
1671 4933 7.893658 ACCGTTGGGATATAGATAGTTTACAG 58.106 38.462 0.00 0.00 36.97 2.74
1787 5049 1.065998 GGGTTGCACCATACTTCGGTA 60.066 52.381 7.49 0.00 41.02 4.02
1801 5063 8.520351 CCATACTTCGGTACATCTCACATATTA 58.480 37.037 0.00 0.00 32.78 0.98
1818 5080 2.863132 TTACCTTTCTGGCCGCTTTA 57.137 45.000 0.00 0.00 40.22 1.85
1893 5161 4.137116 TGACACTGTAATCACCTATGGC 57.863 45.455 0.00 0.00 0.00 4.40
1896 5164 4.295201 ACACTGTAATCACCTATGGCCTA 58.705 43.478 3.32 0.00 0.00 3.93
1962 5230 1.627864 TGATGTCACCTCGGACTTGA 58.372 50.000 0.00 0.00 38.61 3.02
2035 5321 3.323775 ACTAGGTGTCCAAGGAAAAGGA 58.676 45.455 0.00 0.00 0.00 3.36
2111 5397 2.963498 GACCGGCAGTCAAGTAAAAC 57.037 50.000 0.00 0.00 45.55 2.43
2157 5482 4.523813 CGAATGTATTTTGCGGGACATAC 58.476 43.478 0.00 0.00 32.31 2.39
2169 5494 2.882137 CGGGACATACCAAAAGTTGTGT 59.118 45.455 0.00 0.00 41.20 3.72
2246 5571 0.526524 GTCGTCCAGAGGATTGCTCG 60.527 60.000 0.00 0.00 32.73 5.03
2256 5581 0.531974 GGATTGCTCGGTATCGCCAA 60.532 55.000 4.24 4.24 36.97 4.52
2257 5582 0.861837 GATTGCTCGGTATCGCCAAG 59.138 55.000 7.26 0.00 36.97 3.61
2261 5586 0.876342 GCTCGGTATCGCCAAGAAGG 60.876 60.000 0.00 0.00 41.84 3.46
2316 5641 2.789409 ATCTTGGCCCACTTCTACAC 57.211 50.000 0.00 0.00 0.00 2.90
2322 5647 2.290260 TGGCCCACTTCTACACAAGATG 60.290 50.000 0.00 0.00 33.05 2.90
2328 5653 3.187227 CACTTCTACACAAGATGGTGCAC 59.813 47.826 8.80 8.80 42.55 4.57
2329 5654 2.078849 TCTACACAAGATGGTGCACG 57.921 50.000 11.45 0.00 42.55 5.34
2332 5657 0.106708 ACACAAGATGGTGCACGAGT 59.893 50.000 11.45 0.00 42.55 4.18
2334 5659 1.726791 CACAAGATGGTGCACGAGTAC 59.273 52.381 11.45 3.21 31.10 2.73
2370 5695 8.812513 ACTTTGATCATCAGTCCATTATCAAA 57.187 30.769 0.00 0.00 39.64 2.69
2371 5696 9.417561 ACTTTGATCATCAGTCCATTATCAAAT 57.582 29.630 0.00 0.00 40.54 2.32
2407 5732 5.074652 ACAGAGGTATGGCTGAGTAGGTATA 59.925 44.000 0.00 0.00 36.07 1.47
2433 5758 2.427320 GGCACTGCTGTGGACAGA 59.573 61.111 23.15 0.00 46.59 3.41
2454 5779 4.530161 AGAGAGTCTAGTGATGCTTTGGTT 59.470 41.667 0.00 0.00 0.00 3.67
2466 5794 1.433053 CTTTGGTTCGTGTGTGCCGA 61.433 55.000 0.00 0.00 0.00 5.54
2477 5805 1.148310 GTGTGCCGAATGATATCCCG 58.852 55.000 0.00 1.56 0.00 5.14
2502 5830 6.923508 GCTATATGGTTTATCTTTTGGCCAAC 59.076 38.462 20.35 4.23 0.00 3.77
2504 5832 2.297597 TGGTTTATCTTTTGGCCAACCG 59.702 45.455 20.35 12.39 39.70 4.44
2530 5858 3.313249 TGAAATGCTGCCAATCTACGATG 59.687 43.478 0.00 0.00 0.00 3.84
2542 5873 0.179094 CTACGATGGCGGCCAAAGTA 60.179 55.000 27.70 27.23 43.17 2.24
2549 5940 1.359459 GGCGGCCAAAGTAGTCTTCG 61.359 60.000 15.62 0.00 32.90 3.79
2567 5958 0.729116 CGGTCAGTAGCATGGCTTTG 59.271 55.000 0.00 0.00 40.44 2.77
2572 5963 3.076621 TCAGTAGCATGGCTTTGTGAAG 58.923 45.455 0.00 0.00 40.44 3.02
2578 5969 2.669364 CATGGCTTTGTGAAGACTTGC 58.331 47.619 0.00 0.00 41.75 4.01
2580 5971 2.098614 TGGCTTTGTGAAGACTTGCAA 58.901 42.857 0.00 0.00 41.75 4.08
2622 6016 3.505680 TCCTCCATCGGACAATTTTGTTG 59.494 43.478 0.00 0.00 42.43 3.33
2624 6018 4.475944 CTCCATCGGACAATTTTGTTGTC 58.524 43.478 11.41 11.41 45.89 3.18
2647 6044 6.370994 GTCGACTAAAGATGATATACCGGAGA 59.629 42.308 9.46 0.00 0.00 3.71
2669 6066 3.914984 CGGAGGAGTGCAGAAAAGA 57.085 52.632 0.00 0.00 0.00 2.52
2686 6083 0.175302 AGAGCAGCTGTTGGAGATCG 59.825 55.000 16.64 0.00 0.00 3.69
2692 6089 2.094286 CAGCTGTTGGAGATCGAAGAGT 60.094 50.000 5.25 0.00 43.63 3.24
2693 6090 2.564947 AGCTGTTGGAGATCGAAGAGTT 59.435 45.455 0.00 0.00 43.63 3.01
2824 6221 1.909302 ACTACAGACTTGGGGATGTGG 59.091 52.381 0.00 0.00 0.00 4.17
2827 6224 0.692476 CAGACTTGGGGATGTGGTGA 59.308 55.000 0.00 0.00 0.00 4.02
2851 6248 1.179174 CCCCATCGAGATGACGGCTA 61.179 60.000 14.12 0.00 41.20 3.93
2857 6257 1.136110 TCGAGATGACGGCTAATGCAA 59.864 47.619 0.00 0.00 41.91 4.08
2891 6291 1.272490 CCACTACGCCTTCTGACTTCA 59.728 52.381 0.00 0.00 0.00 3.02
2904 6304 5.661056 TCTGACTTCATCCTCAACGTTAT 57.339 39.130 0.00 0.00 0.00 1.89
2924 6325 2.235891 TGACGGCTGATCGGTATGTAT 58.764 47.619 0.00 0.00 0.00 2.29
2929 6330 6.993902 TGACGGCTGATCGGTATGTATATATA 59.006 38.462 0.00 0.00 0.00 0.86
2933 6419 7.148390 CGGCTGATCGGTATGTATATATAGGAG 60.148 44.444 2.89 0.00 0.00 3.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 5.109903 ACGTTAGGCTCAAACTAGCTATTG 58.890 41.667 0.00 0.00 42.37 1.90
30 31 4.401519 TGACGTTAGGCTCAAACTAGCTAT 59.598 41.667 0.00 0.00 42.37 2.97
38 43 2.103432 TGAGGTTGACGTTAGGCTCAAA 59.897 45.455 0.00 0.00 0.00 2.69
42 47 2.615493 CCATTGAGGTTGACGTTAGGCT 60.615 50.000 0.00 0.00 0.00 4.58
63 71 1.333702 CGTAACACATGCACCACACAC 60.334 52.381 0.00 0.00 0.00 3.82
65 73 0.941542 ACGTAACACATGCACCACAC 59.058 50.000 0.00 0.00 0.00 3.82
83 91 9.683069 CCACATCATTTTTAAGATAATAGCCAC 57.317 33.333 0.00 0.00 0.00 5.01
104 112 4.335416 ACTGCAGCTACATTAAACCACAT 58.665 39.130 15.27 0.00 0.00 3.21
156 164 5.701290 GTCCTGCTCTGTGTAACTGTTTAAT 59.299 40.000 0.00 0.00 38.04 1.40
170 178 2.149578 CAAGTTGAAGGTCCTGCTCTG 58.850 52.381 0.00 0.00 0.00 3.35
173 181 3.073650 AGAATCAAGTTGAAGGTCCTGCT 59.926 43.478 10.14 0.00 0.00 4.24
174 182 3.416156 AGAATCAAGTTGAAGGTCCTGC 58.584 45.455 10.14 0.00 0.00 4.85
195 203 5.487488 TGCTTTAGTTTTGAGGGATCCTAGA 59.513 40.000 12.58 0.00 31.76 2.43
199 2551 4.156739 CACTGCTTTAGTTTTGAGGGATCC 59.843 45.833 1.92 1.92 37.60 3.36
266 2620 2.936498 AGGGATACGTTTCTTGCAATCG 59.064 45.455 0.00 5.80 37.60 3.34
301 2655 4.393371 GCCAAAGTAGCAGAAGAGTAAAGG 59.607 45.833 0.00 0.00 0.00 3.11
337 2691 6.418101 CATCCAGGTCTCTTTCTTTATTCCA 58.582 40.000 0.00 0.00 0.00 3.53
381 2742 5.509670 GCCAAAACTTAATTGAGCTCTGGTT 60.510 40.000 16.19 9.37 0.00 3.67
383 2744 4.022068 TGCCAAAACTTAATTGAGCTCTGG 60.022 41.667 16.19 10.86 0.00 3.86
600 2993 3.635373 TCCTATAACTAGAAGCACCACGG 59.365 47.826 0.00 0.00 0.00 4.94
837 3960 9.303116 CCCACACTAGATCAGTAATATAGAGTT 57.697 37.037 0.00 0.00 32.73 3.01
854 3977 0.681733 ACACACAGAGCCCACACTAG 59.318 55.000 0.00 0.00 0.00 2.57
866 3989 2.878406 CCTTAAGGGTGAACACACACAG 59.122 50.000 14.25 2.40 40.05 3.66
902 4072 7.040409 ACCTGGAAAATAACAGAGCAACTAAAG 60.040 37.037 0.00 0.00 36.86 1.85
982 4200 3.825014 CTCATTGATGCCCTTCCCTAATG 59.175 47.826 0.00 0.00 0.00 1.90
1183 4401 2.629051 GACATAAGCGGCTACCAAGTT 58.371 47.619 1.35 0.00 0.00 2.66
1366 4599 5.491078 TCCAAAAGATATACAGGGTGAGGTT 59.509 40.000 0.00 0.00 0.00 3.50
1367 4600 5.036916 TCCAAAAGATATACAGGGTGAGGT 58.963 41.667 0.00 0.00 0.00 3.85
1398 4631 0.322456 GCATATTAGGGCCGCCATCA 60.322 55.000 12.58 0.00 0.00 3.07
1434 4670 5.830991 AGTGCCAGTAACAAACAAAAGGATA 59.169 36.000 0.00 0.00 0.00 2.59
1481 4717 1.047596 ATTGCCACACCACAAAGCCA 61.048 50.000 0.00 0.00 0.00 4.75
1501 4737 6.398095 CCCAAATTTCCCTCATGTTTCTTAC 58.602 40.000 0.00 0.00 0.00 2.34
1503 4739 4.286808 CCCCAAATTTCCCTCATGTTTCTT 59.713 41.667 0.00 0.00 0.00 2.52
1512 4748 1.899814 GAACCACCCCAAATTTCCCTC 59.100 52.381 0.00 0.00 0.00 4.30
1518 4754 2.825532 CGATTCAGAACCACCCCAAATT 59.174 45.455 0.00 0.00 0.00 1.82
1519 4755 2.446435 CGATTCAGAACCACCCCAAAT 58.554 47.619 0.00 0.00 0.00 2.32
1521 4757 0.037590 CCGATTCAGAACCACCCCAA 59.962 55.000 0.00 0.00 0.00 4.12
1523 4759 0.326927 TTCCGATTCAGAACCACCCC 59.673 55.000 0.00 0.00 0.00 4.95
1524 4760 1.810755 GTTTCCGATTCAGAACCACCC 59.189 52.381 0.00 0.00 0.00 4.61
1529 4768 0.518559 GCGCGTTTCCGATTCAGAAC 60.519 55.000 8.43 0.00 35.63 3.01
1535 4774 1.024579 ATCAAGGCGCGTTTCCGATT 61.025 50.000 13.51 0.00 35.63 3.34
1536 4775 0.179094 TATCAAGGCGCGTTTCCGAT 60.179 50.000 13.51 14.76 35.63 4.18
1566 4826 3.507622 GCAAGGCATAGAAAACAAGGTCT 59.492 43.478 0.00 0.00 0.00 3.85
1567 4827 3.367395 GGCAAGGCATAGAAAACAAGGTC 60.367 47.826 0.00 0.00 0.00 3.85
1568 4828 2.562738 GGCAAGGCATAGAAAACAAGGT 59.437 45.455 0.00 0.00 0.00 3.50
1637 4897 0.108329 ATCCCAACGGTTAGCGTGAG 60.108 55.000 10.94 6.46 0.00 3.51
1670 4932 1.215423 ACTTGGTTGAAAGGTCTGGCT 59.785 47.619 0.00 0.00 0.00 4.75
1671 4933 1.692411 ACTTGGTTGAAAGGTCTGGC 58.308 50.000 0.00 0.00 0.00 4.85
1787 5049 6.058183 GCCAGAAAGGTAATATGTGAGATGT 58.942 40.000 0.00 0.00 40.61 3.06
1801 5063 0.400594 ACTAAAGCGGCCAGAAAGGT 59.599 50.000 2.24 0.00 40.61 3.50
1818 5080 7.671302 TGTTTCTTATTACAGAGAAGAGCACT 58.329 34.615 0.00 0.00 33.77 4.40
1902 5170 1.416401 ACTTCAAGAGAGAAACCGCCA 59.584 47.619 0.00 0.00 0.00 5.69
1962 5230 4.013050 GAGTCTTTTCCTTTAGCCATGCT 58.987 43.478 0.00 0.00 43.41 3.79
2035 5321 2.036217 CCATGCAGTTTGACCACAACAT 59.964 45.455 0.00 0.00 35.63 2.71
2111 5397 0.461870 TTTCCTGATCACGGCCATCG 60.462 55.000 2.24 0.00 45.88 3.84
2157 5482 6.560253 AGCTTACTGATACACAACTTTTGG 57.440 37.500 0.00 0.00 34.12 3.28
2246 5571 0.539986 TCCACCTTCTTGGCGATACC 59.460 55.000 0.00 0.00 40.22 2.73
2256 5581 1.840635 GGGCTACTTGATCCACCTTCT 59.159 52.381 0.00 0.00 0.00 2.85
2257 5582 1.134068 GGGGCTACTTGATCCACCTTC 60.134 57.143 0.00 0.00 0.00 3.46
2261 5586 0.181350 CTGGGGGCTACTTGATCCAC 59.819 60.000 0.00 0.00 0.00 4.02
2304 5629 3.338249 CACCATCTTGTGTAGAAGTGGG 58.662 50.000 11.84 7.27 37.47 4.61
2310 5635 1.616374 TCGTGCACCATCTTGTGTAGA 59.384 47.619 12.15 0.00 38.52 2.59
2316 5641 1.359848 GGTACTCGTGCACCATCTTG 58.640 55.000 12.15 0.00 34.77 3.02
2322 5647 0.249398 AATCAGGGTACTCGTGCACC 59.751 55.000 12.15 0.00 0.00 5.01
2328 5653 3.611766 AAGTTGGAATCAGGGTACTCG 57.388 47.619 0.00 0.00 0.00 4.18
2329 5654 4.906618 TCAAAGTTGGAATCAGGGTACTC 58.093 43.478 0.00 0.00 0.00 2.59
2332 5657 5.512942 TGATCAAAGTTGGAATCAGGGTA 57.487 39.130 0.00 0.00 0.00 3.69
2334 5659 4.951715 TGATGATCAAAGTTGGAATCAGGG 59.048 41.667 0.00 0.00 0.00 4.45
2370 5695 9.062367 AGCCATACCTCTGTAATTATATGGAAT 57.938 33.333 18.53 8.04 40.98 3.01
2371 5696 8.321353 CAGCCATACCTCTGTAATTATATGGAA 58.679 37.037 18.53 0.00 40.98 3.53
2380 5705 4.835615 CCTACTCAGCCATACCTCTGTAAT 59.164 45.833 0.00 0.00 0.00 1.89
2382 5707 3.204606 ACCTACTCAGCCATACCTCTGTA 59.795 47.826 0.00 0.00 0.00 2.74
2392 5717 4.752621 TGGGTATATACCTACTCAGCCA 57.247 45.455 27.24 13.78 45.72 4.75
2407 5732 3.009115 AGCAGTGCCGGTGGGTAT 61.009 61.111 12.58 0.00 34.97 2.73
2433 5758 4.619394 CGAACCAAAGCATCACTAGACTCT 60.619 45.833 0.00 0.00 0.00 3.24
2454 5779 2.469826 GATATCATTCGGCACACACGA 58.530 47.619 0.00 0.00 38.78 4.35
2466 5794 8.938883 AGATAAACCATATAGCGGGATATCATT 58.061 33.333 4.83 0.00 33.24 2.57
2477 5805 6.648879 TGGCCAAAAGATAAACCATATAGC 57.351 37.500 0.61 0.00 0.00 2.97
2502 5830 3.830192 GGCAGCATTTCAGGGCGG 61.830 66.667 0.00 0.00 34.54 6.13
2504 5832 0.179092 GATTGGCAGCATTTCAGGGC 60.179 55.000 0.00 0.00 0.00 5.19
2530 5858 1.359459 CGAAGACTACTTTGGCCGCC 61.359 60.000 1.04 1.04 36.39 6.13
2542 5873 1.478510 CCATGCTACTGACCGAAGACT 59.521 52.381 0.00 0.00 0.00 3.24
2549 5940 1.470098 CACAAAGCCATGCTACTGACC 59.530 52.381 5.42 0.00 38.25 4.02
2567 5958 0.040958 CGCACCTTGCAAGTCTTCAC 60.041 55.000 24.35 7.28 45.36 3.18
2572 5963 1.237285 ACATCCGCACCTTGCAAGTC 61.237 55.000 24.35 12.18 45.36 3.01
2578 5969 2.746904 TGTCATTAACATCCGCACCTTG 59.253 45.455 0.00 0.00 31.20 3.61
2580 5971 2.779755 TGTCATTAACATCCGCACCT 57.220 45.000 0.00 0.00 31.20 4.00
2604 5998 3.058570 TCGACAACAAAATTGTCCGATGG 60.059 43.478 12.82 1.06 44.29 3.51
2622 6016 6.370994 TCTCCGGTATATCATCTTTAGTCGAC 59.629 42.308 7.70 7.70 0.00 4.20
2624 6018 6.403418 GGTCTCCGGTATATCATCTTTAGTCG 60.403 46.154 0.00 0.00 0.00 4.18
2647 6044 3.846405 TTCTGCACTCCTCCGGGGT 62.846 63.158 0.00 0.00 36.25 4.95
2663 6060 2.498167 TCTCCAACAGCTGCTCTTTTC 58.502 47.619 15.27 0.00 0.00 2.29
2665 6062 2.709213 GATCTCCAACAGCTGCTCTTT 58.291 47.619 15.27 0.00 0.00 2.52
2669 6066 0.610174 TTCGATCTCCAACAGCTGCT 59.390 50.000 15.27 0.00 0.00 4.24
2686 6083 3.707102 AGCAGACCTACCCATAACTCTTC 59.293 47.826 0.00 0.00 0.00 2.87
2692 6089 2.679082 GAGGAGCAGACCTACCCATAA 58.321 52.381 0.00 0.00 40.73 1.90
2693 6090 1.133136 GGAGGAGCAGACCTACCCATA 60.133 57.143 0.00 0.00 40.73 2.74
2748 6145 1.305633 TCCTCTGGCTAGCAGTGCT 60.306 57.895 23.44 23.44 43.41 4.40
2751 6148 1.382420 CCCTCCTCTGGCTAGCAGT 60.382 63.158 18.24 0.00 0.00 4.40
2824 6221 0.179000 ATCTCGATGGGGCAGTTCAC 59.821 55.000 0.00 0.00 0.00 3.18
2827 6224 0.179000 GTCATCTCGATGGGGCAGTT 59.821 55.000 7.03 0.00 39.24 3.16
2851 6248 1.133025 GCGCTGACCAATAGTTGCATT 59.867 47.619 0.00 0.00 0.00 3.56
2857 6257 1.134788 GTAGTGGCGCTGACCAATAGT 60.135 52.381 11.58 0.00 40.68 2.12
2904 6304 1.682740 TACATACCGATCAGCCGTCA 58.317 50.000 0.00 0.00 0.00 4.35
2924 6325 7.813148 GCGTGCAGAAAGAAATACTCCTATATA 59.187 37.037 0.00 0.00 0.00 0.86
2929 6330 3.003480 GCGTGCAGAAAGAAATACTCCT 58.997 45.455 0.00 0.00 0.00 3.69
2933 6419 2.495939 CGTGCGTGCAGAAAGAAATAC 58.504 47.619 0.00 0.00 0.00 1.89


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

AutoCloner maintained by Alex Coulton.