Multiple sequence alignment - TraesCS1D01G313000

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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 TraesCS1D01G313000 chr1D 100.000 2381 0 0 1 2381 408556444 408558824 0.000000e+00 4397
1 TraesCS1D01G313000 chr1D 92.308 676 47 4 746 1421 408534586 408535256 0.000000e+00 955
2 TraesCS1D01G313000 chr1D 83.922 510 68 8 912 1421 408711833 408712328 2.140000e-130 475
3 TraesCS1D01G313000 chr1D 86.988 415 48 4 1007 1421 408631294 408631702 1.670000e-126 462
4 TraesCS1D01G313000 chr1D 76.851 743 112 37 500 1230 408769444 408770138 4.840000e-97 364
5 TraesCS1D01G313000 chr1D 96.347 219 3 1 1425 1638 408565946 408566164 2.910000e-94 355
6 TraesCS1D01G313000 chr1D 75.662 604 81 29 500 1084 408816573 408817129 8.500000e-60 241
7 TraesCS1D01G313000 chr1D 88.820 161 18 0 500 660 408534394 408534554 5.190000e-47 198
8 TraesCS1D01G313000 chr1B 92.927 919 49 7 503 1421 549890750 549891652 0.000000e+00 1323
9 TraesCS1D01G313000 chr1B 92.222 90 5 2 414 502 549890620 549890708 2.480000e-25 126
10 TraesCS1D01G313000 chr6D 90.947 950 66 8 1440 2381 466654700 466655637 0.000000e+00 1260
11 TraesCS1D01G313000 chr1A 90.919 925 62 3 500 1421 504631934 504632839 0.000000e+00 1223
12 TraesCS1D01G313000 chr1A 83.803 426 52 15 1 418 424210142 424209726 2.870000e-104 388
13 TraesCS1D01G313000 chr1A 86.441 354 33 12 1 351 424212247 424211906 8.040000e-100 374
14 TraesCS1D01G313000 chr6B 88.982 953 82 10 1440 2381 711883537 711884477 0.000000e+00 1157
15 TraesCS1D01G313000 chr6B 86.473 207 16 4 1440 1638 2218965 2218763 1.430000e-52 217
16 TraesCS1D01G313000 chr7D 88.959 951 76 9 1440 2381 7942679 7943609 0.000000e+00 1147
17 TraesCS1D01G313000 chr7D 89.255 940 70 13 1451 2381 495703817 495702900 0.000000e+00 1147
18 TraesCS1D01G313000 chr7D 93.373 166 6 5 1474 1637 434903959 434903797 8.500000e-60 241
19 TraesCS1D01G313000 chr2A 93.342 766 41 7 1622 2381 20813315 20814076 0.000000e+00 1123
20 TraesCS1D01G313000 chr2D 92.680 765 46 10 1622 2380 380940617 380941377 0.000000e+00 1094
21 TraesCS1D01G313000 chr5A 92.428 766 46 9 1622 2381 259097753 259096994 0.000000e+00 1083
22 TraesCS1D01G313000 chr4D 92.288 765 50 9 1622 2381 294020715 294019955 0.000000e+00 1077
23 TraesCS1D01G313000 chr4A 92.188 768 48 8 1622 2381 495101293 495102056 0.000000e+00 1075
24 TraesCS1D01G313000 chr3A 92.177 767 48 9 1622 2381 170221235 170221996 0.000000e+00 1074
25 TraesCS1D01G313000 chr2B 92.057 768 49 11 1622 2381 745729017 745729780 0.000000e+00 1070
26 TraesCS1D01G313000 chr5D 85.476 420 41 16 1 414 97369376 97368971 1.020000e-113 420
27 TraesCS1D01G313000 chr5D 85.238 420 42 16 1 414 97357660 97357255 4.740000e-112 414
28 TraesCS1D01G313000 chr5D 88.026 309 22 11 1 301 548080673 548080974 3.770000e-93 351
29 TraesCS1D01G313000 chr5B 82.955 440 46 23 1 431 698262949 698263368 1.040000e-98 370
30 TraesCS1D01G313000 chr5B 82.955 440 44 26 1 431 698265223 698265640 3.740000e-98 368
31 TraesCS1D01G313000 chr5B 82.955 440 44 26 1 431 698267510 698267927 3.740000e-98 368
32 TraesCS1D01G313000 chr5B 92.825 223 10 2 1421 1638 219063140 219062919 3.820000e-83 318
33 TraesCS1D01G313000 chr6A 88.816 304 27 6 1 301 17709902 17709603 1.340000e-97 366
34 TraesCS1D01G313000 chr7A 91.244 217 13 2 1432 1643 237732927 237733142 8.330000e-75 291


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 TraesCS1D01G313000 chr1D 408556444 408558824 2380 False 4397.000000 4397 100.0000 1 2381 1 chr1D.!!$F1 2380
1 TraesCS1D01G313000 chr1D 408534394 408535256 862 False 576.500000 955 90.5640 500 1421 2 chr1D.!!$F7 921
2 TraesCS1D01G313000 chr1D 408769444 408770138 694 False 364.000000 364 76.8510 500 1230 1 chr1D.!!$F5 730
3 TraesCS1D01G313000 chr1D 408816573 408817129 556 False 241.000000 241 75.6620 500 1084 1 chr1D.!!$F6 584
4 TraesCS1D01G313000 chr1B 549890620 549891652 1032 False 724.500000 1323 92.5745 414 1421 2 chr1B.!!$F1 1007
5 TraesCS1D01G313000 chr6D 466654700 466655637 937 False 1260.000000 1260 90.9470 1440 2381 1 chr6D.!!$F1 941
6 TraesCS1D01G313000 chr1A 504631934 504632839 905 False 1223.000000 1223 90.9190 500 1421 1 chr1A.!!$F1 921
7 TraesCS1D01G313000 chr1A 424209726 424212247 2521 True 381.000000 388 85.1220 1 418 2 chr1A.!!$R1 417
8 TraesCS1D01G313000 chr6B 711883537 711884477 940 False 1157.000000 1157 88.9820 1440 2381 1 chr6B.!!$F1 941
9 TraesCS1D01G313000 chr7D 7942679 7943609 930 False 1147.000000 1147 88.9590 1440 2381 1 chr7D.!!$F1 941
10 TraesCS1D01G313000 chr7D 495702900 495703817 917 True 1147.000000 1147 89.2550 1451 2381 1 chr7D.!!$R2 930
11 TraesCS1D01G313000 chr2A 20813315 20814076 761 False 1123.000000 1123 93.3420 1622 2381 1 chr2A.!!$F1 759
12 TraesCS1D01G313000 chr2D 380940617 380941377 760 False 1094.000000 1094 92.6800 1622 2380 1 chr2D.!!$F1 758
13 TraesCS1D01G313000 chr5A 259096994 259097753 759 True 1083.000000 1083 92.4280 1622 2381 1 chr5A.!!$R1 759
14 TraesCS1D01G313000 chr4D 294019955 294020715 760 True 1077.000000 1077 92.2880 1622 2381 1 chr4D.!!$R1 759
15 TraesCS1D01G313000 chr4A 495101293 495102056 763 False 1075.000000 1075 92.1880 1622 2381 1 chr4A.!!$F1 759
16 TraesCS1D01G313000 chr3A 170221235 170221996 761 False 1074.000000 1074 92.1770 1622 2381 1 chr3A.!!$F1 759
17 TraesCS1D01G313000 chr2B 745729017 745729780 763 False 1070.000000 1070 92.0570 1622 2381 1 chr2B.!!$F1 759
18 TraesCS1D01G313000 chr5B 698262949 698267927 4978 False 368.666667 370 82.9550 1 431 3 chr5B.!!$F1 430

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
335 2868 0.602638 TGAGTTCCACCATCGTGTGC 60.603 55.0 0.0 0.0 38.41 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1434 5432 1.546923 TCTGTCTCTCGTCTCTCTCGT 59.453 52.381 0.0 0.0 0.0 4.18 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
63 64 1.995626 GCTAGGAAGGAGGGTGCCA 60.996 63.158 0.00 0.00 0.00 4.92
138 139 1.484038 AGTGGAGAGGAGATCAGCAC 58.516 55.000 0.00 0.00 0.00 4.40
217 2749 2.203625 GTGAGGGCTGGGGCAAAA 60.204 61.111 0.00 0.00 40.87 2.44
235 2767 6.817270 GCAAAAATGTAGCCATTGTGATAG 57.183 37.500 0.00 0.00 40.42 2.08
243 2775 2.025037 AGCCATTGTGATAGCCAAGGAA 60.025 45.455 0.00 0.00 0.00 3.36
246 2778 3.629398 CCATTGTGATAGCCAAGGAAGAC 59.371 47.826 0.00 0.00 0.00 3.01
252 2784 2.247699 TAGCCAAGGAAGACAGCCTA 57.752 50.000 0.00 0.00 33.76 3.93
254 2786 1.211457 AGCCAAGGAAGACAGCCTATG 59.789 52.381 0.00 0.00 33.76 2.23
278 2811 4.082125 CAAAGCCTATTTGTGTCCTTCCT 58.918 43.478 0.00 0.00 0.00 3.36
289 2822 1.338674 TGTCCTTCCTTGGTACATGCG 60.339 52.381 0.00 0.00 39.30 4.73
290 2823 0.981183 TCCTTCCTTGGTACATGCGT 59.019 50.000 0.00 0.00 39.30 5.24
291 2824 1.086696 CCTTCCTTGGTACATGCGTG 58.913 55.000 3.82 3.82 39.30 5.34
292 2825 1.610624 CCTTCCTTGGTACATGCGTGT 60.611 52.381 17.19 17.19 39.30 4.49
295 2828 1.619332 TCCTTGGTACATGCGTGTGTA 59.381 47.619 21.92 7.05 39.30 2.90
307 2840 2.128821 GCGTGTGTATGTGTGTGTGTA 58.871 47.619 0.00 0.00 0.00 2.90
314 2847 6.631238 GTGTGTATGTGTGTGTGTATGTTTTC 59.369 38.462 0.00 0.00 0.00 2.29
315 2848 6.540551 TGTGTATGTGTGTGTGTATGTTTTCT 59.459 34.615 0.00 0.00 0.00 2.52
317 2850 7.375808 GTGTATGTGTGTGTGTATGTTTTCTTG 59.624 37.037 0.00 0.00 0.00 3.02
318 2851 6.691754 ATGTGTGTGTGTATGTTTTCTTGA 57.308 33.333 0.00 0.00 0.00 3.02
322 2855 6.687105 GTGTGTGTGTATGTTTTCTTGAGTTC 59.313 38.462 0.00 0.00 0.00 3.01
324 2857 5.883115 TGTGTGTATGTTTTCTTGAGTTCCA 59.117 36.000 0.00 0.00 0.00 3.53
325 2858 6.183360 TGTGTGTATGTTTTCTTGAGTTCCAC 60.183 38.462 0.00 0.00 0.00 4.02
327 2860 5.298276 GTGTATGTTTTCTTGAGTTCCACCA 59.702 40.000 0.00 0.00 0.00 4.17
328 2861 6.016276 GTGTATGTTTTCTTGAGTTCCACCAT 60.016 38.462 0.00 0.00 0.00 3.55
329 2862 5.712152 ATGTTTTCTTGAGTTCCACCATC 57.288 39.130 0.00 0.00 0.00 3.51
331 2864 3.485463 TTTCTTGAGTTCCACCATCGT 57.515 42.857 0.00 0.00 0.00 3.73
335 2868 0.602638 TGAGTTCCACCATCGTGTGC 60.603 55.000 0.00 0.00 38.41 4.57
359 2892 3.409026 TTCTTGAGAGAACCCTTGAGC 57.591 47.619 0.00 0.00 36.99 4.26
360 2893 2.614259 TCTTGAGAGAACCCTTGAGCT 58.386 47.619 0.00 0.00 0.00 4.09
364 2897 1.899142 GAGAGAACCCTTGAGCTGAGT 59.101 52.381 0.00 0.00 0.00 3.41
371 2904 1.345741 CCCTTGAGCTGAGTGAGTTGA 59.654 52.381 0.00 0.00 0.00 3.18
376 2911 1.892474 GAGCTGAGTGAGTTGAGAGGT 59.108 52.381 0.00 0.00 0.00 3.85
379 2914 2.165437 GCTGAGTGAGTTGAGAGGTAGG 59.835 54.545 0.00 0.00 0.00 3.18
383 2918 4.202577 TGAGTGAGTTGAGAGGTAGGAGAA 60.203 45.833 0.00 0.00 0.00 2.87
398 2933 4.451652 GAAGAGCGGCGCTGCAAC 62.452 66.667 41.51 31.26 39.88 4.17
422 2959 1.577328 CGGCGCCAACATCTGTTTCT 61.577 55.000 28.98 0.00 35.83 2.52
428 2965 1.884579 CCAACATCTGTTTCTGCAGCT 59.115 47.619 9.47 0.00 35.83 4.24
429 2966 2.351447 CCAACATCTGTTTCTGCAGCTG 60.351 50.000 10.11 10.11 38.25 4.24
454 2991 3.380320 GTGGTTTGGTTTGTAGTTGCTCT 59.620 43.478 0.00 0.00 0.00 4.09
483 3020 2.099263 CGATCGAGCAAGGGAAAGTAGA 59.901 50.000 10.26 0.00 0.00 2.59
518 3096 4.094887 GCTCGAGTCAAATTAATCTTGGCA 59.905 41.667 15.13 0.00 30.60 4.92
521 3099 5.705441 TCGAGTCAAATTAATCTTGGCACTT 59.295 36.000 13.64 0.00 30.60 3.16
522 3100 6.024049 CGAGTCAAATTAATCTTGGCACTTC 58.976 40.000 13.64 5.74 30.60 3.01
559 3138 4.774124 TCTGCTGAAAGATGTAATGGGAG 58.226 43.478 0.00 0.00 34.07 4.30
603 3182 5.872635 AGCATCGTGATGTTTGATAGTTTG 58.127 37.500 11.23 0.00 40.80 2.93
640 3219 1.141657 AGCAAAGAAGAGACCACTGCA 59.858 47.619 0.00 0.00 0.00 4.41
644 3223 4.216257 GCAAAGAAGAGACCACTGCATTTA 59.784 41.667 0.00 0.00 0.00 1.40
701 3429 0.667993 GCTGCAACTGTAAGGCACAA 59.332 50.000 0.00 0.00 39.30 3.33
717 3445 5.381757 AGGCACAACTGGAGTAATTAACAA 58.618 37.500 0.00 0.00 0.00 2.83
739 3475 8.532977 ACAATTTAACATTGATACTTTGTGCC 57.467 30.769 13.71 0.00 33.51 5.01
740 3476 8.147058 ACAATTTAACATTGATACTTTGTGCCA 58.853 29.630 13.71 0.00 33.51 4.92
741 3477 9.153721 CAATTTAACATTGATACTTTGTGCCAT 57.846 29.630 0.00 0.00 0.00 4.40
742 3478 8.706492 ATTTAACATTGATACTTTGTGCCATG 57.294 30.769 0.00 0.00 0.00 3.66
743 3479 4.724074 ACATTGATACTTTGTGCCATGG 57.276 40.909 7.63 7.63 0.00 3.66
744 3480 3.119029 ACATTGATACTTTGTGCCATGGC 60.119 43.478 30.54 30.54 42.35 4.40
780 3517 4.971830 GTCATAATCATTGTGCCATGAACG 59.028 41.667 0.00 0.00 0.00 3.95
961 4106 4.695455 ACTGTGTATAATGTGGTGTCTTGC 59.305 41.667 0.00 0.00 0.00 4.01
967 4112 0.612732 ATGTGGTGTCTTGCCATGGG 60.613 55.000 15.13 0.00 38.40 4.00
1060 4209 0.106819 AGCTAAGCCAGATGCCTTGG 60.107 55.000 0.00 0.00 42.71 3.61
1362 5360 3.751246 GCCGCAAGCAAGCCATCA 61.751 61.111 0.00 0.00 42.97 3.07
1372 5370 3.687321 AAGCCATCAGACGCGCCAT 62.687 57.895 5.73 0.00 0.00 4.40
1423 5421 6.817765 TTCTGTTTCAGAAAGACAAAGTGT 57.182 33.333 9.34 0.00 45.84 3.55
1424 5422 6.817765 TCTGTTTCAGAAAGACAAAGTGTT 57.182 33.333 0.00 0.00 37.57 3.32
1425 5423 7.915293 TCTGTTTCAGAAAGACAAAGTGTTA 57.085 32.000 0.00 0.00 37.57 2.41
1426 5424 7.974675 TCTGTTTCAGAAAGACAAAGTGTTAG 58.025 34.615 0.00 0.00 37.57 2.34
1427 5425 7.822334 TCTGTTTCAGAAAGACAAAGTGTTAGA 59.178 33.333 0.00 0.00 37.57 2.10
1428 5426 8.506168 TGTTTCAGAAAGACAAAGTGTTAGAT 57.494 30.769 0.00 0.00 0.00 1.98
1429 5427 8.612619 TGTTTCAGAAAGACAAAGTGTTAGATC 58.387 33.333 0.00 0.00 0.00 2.75
1430 5428 8.831550 GTTTCAGAAAGACAAAGTGTTAGATCT 58.168 33.333 0.00 0.00 0.00 2.75
1431 5429 8.964476 TTCAGAAAGACAAAGTGTTAGATCTT 57.036 30.769 0.00 0.00 0.00 2.40
1436 5434 9.582223 GAAAGACAAAGTGTTAGATCTTAAACG 57.418 33.333 0.00 0.00 0.00 3.60
1437 5435 8.882415 AAGACAAAGTGTTAGATCTTAAACGA 57.118 30.769 0.00 0.00 0.00 3.85
1438 5436 8.522178 AGACAAAGTGTTAGATCTTAAACGAG 57.478 34.615 0.00 0.00 0.00 4.18
1444 5442 7.754625 AGTGTTAGATCTTAAACGAGAGAGAC 58.245 38.462 0.00 0.00 0.00 3.36
1445 5443 6.683708 GTGTTAGATCTTAAACGAGAGAGACG 59.316 42.308 0.00 0.00 0.00 4.18
1449 5447 5.522460 AGATCTTAAACGAGAGAGACGAGAG 59.478 44.000 0.00 0.00 34.70 3.20
1463 5461 5.584649 AGAGACGAGAGACAGAGATGTAAAG 59.415 44.000 0.00 0.00 0.00 1.85
1464 5462 5.492895 AGACGAGAGACAGAGATGTAAAGA 58.507 41.667 0.00 0.00 0.00 2.52
1465 5463 5.584649 AGACGAGAGACAGAGATGTAAAGAG 59.415 44.000 0.00 0.00 0.00 2.85
1466 5464 5.250200 ACGAGAGACAGAGATGTAAAGAGT 58.750 41.667 0.00 0.00 0.00 3.24
1467 5465 5.123186 ACGAGAGACAGAGATGTAAAGAGTG 59.877 44.000 0.00 0.00 0.00 3.51
1469 5467 6.128145 CGAGAGACAGAGATGTAAAGAGTGAA 60.128 42.308 0.00 0.00 0.00 3.18
1471 5469 7.546358 AGAGACAGAGATGTAAAGAGTGAATG 58.454 38.462 0.00 0.00 0.00 2.67
1472 5470 6.105333 AGACAGAGATGTAAAGAGTGAATGC 58.895 40.000 0.00 0.00 0.00 3.56
1473 5471 4.867047 ACAGAGATGTAAAGAGTGAATGCG 59.133 41.667 0.00 0.00 0.00 4.73
1478 5476 6.163476 AGATGTAAAGAGTGAATGCGTGTTA 58.837 36.000 0.00 0.00 0.00 2.41
1559 5564 3.063084 GAGAGACGCCTGTCCGGT 61.063 66.667 0.00 0.00 46.74 5.28
1579 5584 4.578898 ACCGACGCGACAGTTGCA 62.579 61.111 15.93 0.00 0.00 4.08
1602 5607 1.639298 GCAACTGCCTGCGGTTAGAG 61.639 60.000 15.47 5.77 42.97 2.43
1662 5671 4.823989 CCCCCTAATCACTGCTTTATCTTG 59.176 45.833 0.00 0.00 0.00 3.02
1705 5721 1.542547 GCTCCTCGAAAAACCCTGTGA 60.543 52.381 0.00 0.00 0.00 3.58
1859 5877 9.732130 ATAGAATCAAGAGGACAATAAATAGGC 57.268 33.333 0.00 0.00 0.00 3.93
1874 5893 9.106070 CAATAAATAGGCCGTATATACTTTCCC 57.894 37.037 11.05 5.78 0.00 3.97
1976 5998 9.256228 AGAACCTGTATAGTAAACTCATGAAGA 57.744 33.333 0.00 0.00 0.00 2.87
2050 6073 3.102204 CCCCTGATTCTTGCAAATTCCT 58.898 45.455 0.00 0.00 0.00 3.36
2258 6699 2.887152 AGCCATGAGGTCTGTTTTGAAC 59.113 45.455 0.00 0.00 37.19 3.18
2317 6805 3.878103 ACTACGCTTGTCTACGATCTGAT 59.122 43.478 0.00 0.00 0.00 2.90
2318 6806 3.071786 ACGCTTGTCTACGATCTGATG 57.928 47.619 0.00 0.00 0.00 3.07
2331 6819 3.576118 CGATCTGATGTAGTGGGGATCTT 59.424 47.826 0.00 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.530161 GGTCCACATCTGAGCCTATCTAAT 59.470 45.833 0.00 0.00 0.00 1.73
138 139 4.815308 AGAGGCACACACGTACTATACTAG 59.185 45.833 0.00 0.00 0.00 2.57
189 2720 4.410400 CCCTCACGGCCACCCTTC 62.410 72.222 2.24 0.00 0.00 3.46
211 2742 3.924144 TCACAATGGCTACATTTTTGCC 58.076 40.909 0.00 0.00 44.69 4.52
213 2744 5.750067 GGCTATCACAATGGCTACATTTTTG 59.250 40.000 0.00 0.00 44.69 2.44
225 2757 4.264253 TGTCTTCCTTGGCTATCACAATG 58.736 43.478 0.00 0.00 0.00 2.82
226 2758 4.521146 CTGTCTTCCTTGGCTATCACAAT 58.479 43.478 0.00 0.00 0.00 2.71
232 2764 1.589414 AGGCTGTCTTCCTTGGCTAT 58.411 50.000 0.00 0.00 33.53 2.97
233 2765 2.247699 TAGGCTGTCTTCCTTGGCTA 57.752 50.000 0.00 0.00 36.69 3.93
235 2767 1.673168 CATAGGCTGTCTTCCTTGGC 58.327 55.000 0.00 0.00 35.21 4.52
256 2788 4.082125 AGGAAGGACACAAATAGGCTTTG 58.918 43.478 0.00 0.00 35.64 2.77
257 2789 4.388577 AGGAAGGACACAAATAGGCTTT 57.611 40.909 0.00 0.00 0.00 3.51
260 2792 2.755103 CCAAGGAAGGACACAAATAGGC 59.245 50.000 0.00 0.00 0.00 3.93
261 2793 4.034285 ACCAAGGAAGGACACAAATAGG 57.966 45.455 0.00 0.00 0.00 2.57
265 2797 3.935818 TGTACCAAGGAAGGACACAAA 57.064 42.857 0.00 0.00 0.00 2.83
269 2801 1.338674 CGCATGTACCAAGGAAGGACA 60.339 52.381 0.00 0.00 0.00 4.02
270 2802 1.338769 ACGCATGTACCAAGGAAGGAC 60.339 52.381 0.00 0.00 0.00 3.85
278 2811 2.739379 CACATACACACGCATGTACCAA 59.261 45.455 1.73 0.00 37.88 3.67
289 2822 5.666969 AACATACACACACACATACACAC 57.333 39.130 0.00 0.00 0.00 3.82
290 2823 6.540551 AGAAAACATACACACACACATACACA 59.459 34.615 0.00 0.00 0.00 3.72
291 2824 6.954944 AGAAAACATACACACACACATACAC 58.045 36.000 0.00 0.00 0.00 2.90
292 2825 7.281100 TCAAGAAAACATACACACACACATACA 59.719 33.333 0.00 0.00 0.00 2.29
295 2828 6.318648 ACTCAAGAAAACATACACACACACAT 59.681 34.615 0.00 0.00 0.00 3.21
307 2840 4.216257 CGATGGTGGAACTCAAGAAAACAT 59.784 41.667 0.00 0.00 36.74 2.71
324 2857 0.531974 AAGAACACGCACACGATGGT 60.532 50.000 0.00 0.00 43.93 3.55
325 2858 0.110688 CAAGAACACGCACACGATGG 60.111 55.000 0.00 0.00 43.93 3.51
327 2860 1.139989 CTCAAGAACACGCACACGAT 58.860 50.000 0.00 0.00 43.93 3.73
328 2861 0.101579 TCTCAAGAACACGCACACGA 59.898 50.000 0.00 0.00 43.93 4.35
329 2862 3.362758 TTCTCTCAAGAACACGCACACG 61.363 50.000 0.00 0.00 39.96 4.49
331 2864 2.595124 TTCTCTCAAGAACACGCACA 57.405 45.000 0.00 0.00 36.59 4.57
353 2886 3.577667 CTCTCAACTCACTCAGCTCAAG 58.422 50.000 0.00 0.00 0.00 3.02
354 2887 2.298446 CCTCTCAACTCACTCAGCTCAA 59.702 50.000 0.00 0.00 0.00 3.02
355 2888 1.891811 CCTCTCAACTCACTCAGCTCA 59.108 52.381 0.00 0.00 0.00 4.26
356 2889 1.892474 ACCTCTCAACTCACTCAGCTC 59.108 52.381 0.00 0.00 0.00 4.09
357 2890 2.008242 ACCTCTCAACTCACTCAGCT 57.992 50.000 0.00 0.00 0.00 4.24
359 2892 3.691575 TCCTACCTCTCAACTCACTCAG 58.308 50.000 0.00 0.00 0.00 3.35
360 2893 3.330998 TCTCCTACCTCTCAACTCACTCA 59.669 47.826 0.00 0.00 0.00 3.41
364 2897 4.594970 CTCTTCTCCTACCTCTCAACTCA 58.405 47.826 0.00 0.00 0.00 3.41
371 2904 0.753848 GCCGCTCTTCTCCTACCTCT 60.754 60.000 0.00 0.00 0.00 3.69
376 2911 2.440430 AGCGCCGCTCTTCTCCTA 60.440 61.111 5.39 0.00 30.62 2.94
422 2959 2.521465 CAAACCACCCCAGCTGCA 60.521 61.111 8.66 0.00 0.00 4.41
428 2965 1.288335 ACTACAAACCAAACCACCCCA 59.712 47.619 0.00 0.00 0.00 4.96
429 2966 2.076207 ACTACAAACCAAACCACCCC 57.924 50.000 0.00 0.00 0.00 4.95
454 2991 0.104855 CTTGCTCGATCGATTCCCCA 59.895 55.000 19.78 8.19 0.00 4.96
498 3035 5.551760 AGTGCCAAGATTAATTTGACTCG 57.448 39.130 10.22 0.00 0.00 4.18
559 3138 9.364989 GATGCTACAGATCTCACCTTATAATTC 57.635 37.037 0.00 0.00 0.00 2.17
603 3182 1.566018 GCTCGCCCACTTGTGTACAC 61.566 60.000 19.36 19.36 0.00 2.90
614 3193 0.320771 GTCTCTTCTTTGCTCGCCCA 60.321 55.000 0.00 0.00 0.00 5.36
616 3195 0.320771 TGGTCTCTTCTTTGCTCGCC 60.321 55.000 0.00 0.00 0.00 5.54
640 3219 5.555017 ACACTGCTCAGTTCAGTCATAAAT 58.445 37.500 0.00 0.00 42.38 1.40
644 3223 3.136763 CAACACTGCTCAGTTCAGTCAT 58.863 45.455 0.00 0.00 42.38 3.06
794 3531 1.538849 GCAACAAAGGAAACTGCAGGG 60.539 52.381 19.93 0.00 42.68 4.45
961 4106 5.072741 CCACTAGATATGAAAACCCCATGG 58.927 45.833 4.14 4.14 37.80 3.66
967 4112 8.798859 ATGATATGCCACTAGATATGAAAACC 57.201 34.615 0.00 0.00 0.00 3.27
1421 5419 6.592994 TCGTCTCTCTCGTTTAAGATCTAACA 59.407 38.462 8.68 0.00 0.00 2.41
1422 5420 7.002816 TCGTCTCTCTCGTTTAAGATCTAAC 57.997 40.000 0.00 0.00 0.00 2.34
1423 5421 7.040494 TCTCGTCTCTCTCGTTTAAGATCTAA 58.960 38.462 0.00 0.00 0.00 2.10
1424 5422 6.571605 TCTCGTCTCTCTCGTTTAAGATCTA 58.428 40.000 0.00 0.00 0.00 1.98
1425 5423 5.421277 TCTCGTCTCTCTCGTTTAAGATCT 58.579 41.667 0.00 0.00 0.00 2.75
1426 5424 5.521010 TCTCTCGTCTCTCTCGTTTAAGATC 59.479 44.000 0.00 0.00 0.00 2.75
1427 5425 5.292589 GTCTCTCGTCTCTCTCGTTTAAGAT 59.707 44.000 0.00 0.00 0.00 2.40
1428 5426 4.626604 GTCTCTCGTCTCTCTCGTTTAAGA 59.373 45.833 0.00 0.00 0.00 2.10
1429 5427 4.389382 TGTCTCTCGTCTCTCTCGTTTAAG 59.611 45.833 0.00 0.00 0.00 1.85
1430 5428 4.313282 TGTCTCTCGTCTCTCTCGTTTAA 58.687 43.478 0.00 0.00 0.00 1.52
1431 5429 3.922910 TGTCTCTCGTCTCTCTCGTTTA 58.077 45.455 0.00 0.00 0.00 2.01
1432 5430 2.739913 CTGTCTCTCGTCTCTCTCGTTT 59.260 50.000 0.00 0.00 0.00 3.60
1433 5431 2.028839 TCTGTCTCTCGTCTCTCTCGTT 60.029 50.000 0.00 0.00 0.00 3.85
1434 5432 1.546923 TCTGTCTCTCGTCTCTCTCGT 59.453 52.381 0.00 0.00 0.00 4.18
1435 5433 2.159296 TCTCTGTCTCTCGTCTCTCTCG 60.159 54.545 0.00 0.00 0.00 4.04
1436 5434 3.520290 TCTCTGTCTCTCGTCTCTCTC 57.480 52.381 0.00 0.00 0.00 3.20
1437 5435 3.197766 ACATCTCTGTCTCTCGTCTCTCT 59.802 47.826 0.00 0.00 0.00 3.10
1438 5436 3.531538 ACATCTCTGTCTCTCGTCTCTC 58.468 50.000 0.00 0.00 0.00 3.20
1444 5442 5.352846 TCACTCTTTACATCTCTGTCTCTCG 59.647 44.000 0.00 0.00 36.79 4.04
1445 5443 6.751514 TCACTCTTTACATCTCTGTCTCTC 57.248 41.667 0.00 0.00 36.79 3.20
1449 5447 5.005203 CGCATTCACTCTTTACATCTCTGTC 59.995 44.000 0.00 0.00 36.79 3.51
1463 5461 7.684670 TCAATAAAGATAACACGCATTCACTC 58.315 34.615 0.00 0.00 0.00 3.51
1464 5462 7.609760 TCAATAAAGATAACACGCATTCACT 57.390 32.000 0.00 0.00 0.00 3.41
1465 5463 8.122330 TCATCAATAAAGATAACACGCATTCAC 58.878 33.333 0.00 0.00 0.00 3.18
1466 5464 8.207521 TCATCAATAAAGATAACACGCATTCA 57.792 30.769 0.00 0.00 0.00 2.57
1467 5465 9.110617 CATCATCAATAAAGATAACACGCATTC 57.889 33.333 0.00 0.00 0.00 2.67
1469 5467 8.071967 CACATCATCAATAAAGATAACACGCAT 58.928 33.333 0.00 0.00 0.00 4.73
1471 5469 7.630026 TCACATCATCAATAAAGATAACACGC 58.370 34.615 0.00 0.00 0.00 5.34
1472 5470 9.803130 GATCACATCATCAATAAAGATAACACG 57.197 33.333 0.00 0.00 0.00 4.49
1559 5564 1.947146 CAACTGTCGCGTCGGTTCA 60.947 57.895 24.36 7.04 35.10 3.18
1579 5584 2.730094 CCGCAGGCAGTTGCTTTT 59.270 55.556 3.88 0.00 46.14 2.27
1662 5671 8.485976 AGCTTTTCAAGATGATGTCTACTAAC 57.514 34.615 0.00 0.00 35.67 2.34
1705 5721 9.003658 CAAACACTATACTCCTCACATTTTTCT 57.996 33.333 0.00 0.00 0.00 2.52
1857 5875 5.221106 GGTTTTTGGGAAAGTATATACGGCC 60.221 44.000 7.23 9.54 0.00 6.13
1859 5877 5.300034 GGGGTTTTTGGGAAAGTATATACGG 59.700 44.000 7.23 0.00 0.00 4.02
2050 6073 7.958088 TCATGGAATTGGTATATGACGACTTA 58.042 34.615 0.00 0.00 0.00 2.24
2317 6805 4.480115 ACATCGATAAGATCCCCACTACA 58.520 43.478 0.00 0.00 37.52 2.74
2318 6806 6.183360 GGATACATCGATAAGATCCCCACTAC 60.183 46.154 16.36 0.00 37.52 2.73


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

AutoCloner maintained by Alex Coulton.