Multiple sequence alignment - TraesCS2B01G110900

Loading Multiple Alignment...

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 TraesCS2B01G110900 chr2B 100.000 2417 0 0 1 2417 72759663 72762079 0 4464
1 TraesCS2B01G110900 chr2B 93.152 2322 130 11 1 2304 72270524 72272834 0 3380
2 TraesCS2B01G110900 chr3D 93.291 2340 115 12 1 2305 543499204 543501536 0 3413
3 TraesCS2B01G110900 chr3D 91.206 2354 155 20 1 2306 567665596 567667945 0 3153
4 TraesCS2B01G110900 chr3D 90.663 2367 159 24 1 2306 126287998 126290363 0 3090
5 TraesCS2B01G110900 chr4D 92.928 2333 129 9 1 2304 130443087 130440762 0 3362
6 TraesCS2B01G110900 chr5D 92.157 2346 134 17 1 2304 58529691 58532028 0 3267
7 TraesCS2B01G110900 chr2D 91.951 2348 139 12 1 2305 462189843 462187503 0 3243
8 TraesCS2B01G110900 chr5B 91.117 2364 148 12 4 2306 478553178 478550816 0 3145
9 TraesCS2B01G110900 chr6A 91.022 2328 176 17 1 2304 381114848 381112530 0 3110
10 TraesCS2B01G110900 chr1D 93.260 1914 110 11 244 2140 362587846 362585935 0 2802
11 TraesCS2B01G110900 chr6D 94.482 1649 76 6 673 2308 469300985 469302631 0 2527
12 TraesCS2B01G110900 chr6D 91.073 885 70 6 1425 2305 23885625 23884746 0 1188
13 TraesCS2B01G110900 chr3B 93.192 896 61 0 1410 2305 476390911 476391806 0 1317
14 TraesCS2B01G110900 chrUn 92.212 886 55 3 1431 2305 24700679 24699797 0 1242
15 TraesCS2B01G110900 chr7A 90.470 829 66 11 1484 2304 257272824 257273647 0 1081


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 TraesCS2B01G110900 chr2B 72759663 72762079 2416 False 4464 4464 100.000 1 2417 1 chr2B.!!$F2 2416
1 TraesCS2B01G110900 chr2B 72270524 72272834 2310 False 3380 3380 93.152 1 2304 1 chr2B.!!$F1 2303
2 TraesCS2B01G110900 chr3D 543499204 543501536 2332 False 3413 3413 93.291 1 2305 1 chr3D.!!$F2 2304
3 TraesCS2B01G110900 chr3D 567665596 567667945 2349 False 3153 3153 91.206 1 2306 1 chr3D.!!$F3 2305
4 TraesCS2B01G110900 chr3D 126287998 126290363 2365 False 3090 3090 90.663 1 2306 1 chr3D.!!$F1 2305
5 TraesCS2B01G110900 chr4D 130440762 130443087 2325 True 3362 3362 92.928 1 2304 1 chr4D.!!$R1 2303
6 TraesCS2B01G110900 chr5D 58529691 58532028 2337 False 3267 3267 92.157 1 2304 1 chr5D.!!$F1 2303
7 TraesCS2B01G110900 chr2D 462187503 462189843 2340 True 3243 3243 91.951 1 2305 1 chr2D.!!$R1 2304
8 TraesCS2B01G110900 chr5B 478550816 478553178 2362 True 3145 3145 91.117 4 2306 1 chr5B.!!$R1 2302
9 TraesCS2B01G110900 chr6A 381112530 381114848 2318 True 3110 3110 91.022 1 2304 1 chr6A.!!$R1 2303
10 TraesCS2B01G110900 chr1D 362585935 362587846 1911 True 2802 2802 93.260 244 2140 1 chr1D.!!$R1 1896
11 TraesCS2B01G110900 chr6D 469300985 469302631 1646 False 2527 2527 94.482 673 2308 1 chr6D.!!$F1 1635
12 TraesCS2B01G110900 chr6D 23884746 23885625 879 True 1188 1188 91.073 1425 2305 1 chr6D.!!$R1 880
13 TraesCS2B01G110900 chr3B 476390911 476391806 895 False 1317 1317 93.192 1410 2305 1 chr3B.!!$F1 895
14 TraesCS2B01G110900 chrUn 24699797 24700679 882 True 1242 1242 92.212 1431 2305 1 chrUn.!!$R1 874
15 TraesCS2B01G110900 chr7A 257272824 257273647 823 False 1081 1081 90.470 1484 2304 1 chr7A.!!$F1 820

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
305 338 0.387112 CATGACCACGCAAACGCAAT 60.387 50.0 0.0 0.0 45.53 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1817 1989 0.034756 ACGATGCCACTTGTGCACTA 59.965 50.0 19.41 9.94 42.38 2.74 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
55 56 1.134946 AGTTGAACCTTGTGCTTGTGC 59.865 47.619 0.00 0.00 40.20 4.57
138 139 5.804639 TGTTGTAGATGTATGTTCCTGCTT 58.195 37.500 0.00 0.00 0.00 3.91
154 155 2.802816 CTGCTTATAGATTGTCCGGTGC 59.197 50.000 0.00 0.00 0.00 5.01
305 338 0.387112 CATGACCACGCAAACGCAAT 60.387 50.000 0.00 0.00 45.53 3.56
352 385 2.229792 GACAACCAGTTTGCTCCATCA 58.770 47.619 0.00 0.00 39.01 3.07
555 610 1.225376 TTCATGTCCACGTTCGTGCC 61.225 55.000 18.14 11.65 35.03 5.01
654 710 3.299340 GAAGCAGGTGTTCGAGTTCTA 57.701 47.619 0.00 0.00 0.00 2.10
801 858 0.829333 CTGGAGGCAGAGCACTATGT 59.171 55.000 0.00 0.00 0.00 2.29
831 888 1.298859 GCGGTTAGCTCACAACCCTG 61.299 60.000 10.63 0.50 42.11 4.45
837 894 0.846693 AGCTCACAACCCTGTTCCTT 59.153 50.000 0.00 0.00 31.64 3.36
884 942 3.676172 TCCTAATCGCAACTAACAACACG 59.324 43.478 0.00 0.00 0.00 4.49
958 1016 2.540383 TCCAGAACTACAGCCAGATGT 58.460 47.619 0.00 0.00 37.19 3.06
1148 1206 4.480537 TGATAGGAAGAGGAAGAGAGGAGT 59.519 45.833 0.00 0.00 0.00 3.85
1159 1217 2.213310 AGAGAGGAGTCCTGATGGAGA 58.787 52.381 18.90 0.00 44.16 3.71
1237 1298 3.650950 GGGAGTGCAAGCCCCTCA 61.651 66.667 13.04 0.00 38.45 3.86
1285 1346 1.542375 ATGACCCAGGGTGGCTTCT 60.542 57.895 19.03 0.00 35.25 2.85
1288 1349 3.970410 CCCAGGGTGGCTTCTGCA 61.970 66.667 0.00 0.00 41.91 4.41
1320 1381 3.303189 GCAGCTCTCAGCCACCTA 58.697 61.111 0.00 0.00 43.77 3.08
1347 1408 3.110031 AAGGCCCAGGGTGTTGGT 61.110 61.111 7.55 0.00 36.45 3.67
1384 1445 1.152963 GCTCACAGGGTGTTGTGGT 60.153 57.895 6.33 0.00 46.55 4.16
1396 1457 0.179018 GTTGTGGTTCAGGAGCTGGT 60.179 55.000 0.00 0.00 31.51 4.00
1579 1676 0.534877 ACGCTGATGGTGAACTTGCA 60.535 50.000 0.00 0.00 0.00 4.08
1586 1683 2.719531 TGGTGAACTTGCAGTGGTAA 57.280 45.000 0.00 0.00 0.00 2.85
1598 1695 2.165167 CAGTGGTAAGACGACACCCTA 58.835 52.381 0.00 0.00 35.79 3.53
1607 1704 5.687166 AAGACGACACCCTATTTTGGATA 57.313 39.130 0.00 0.00 0.00 2.59
1615 1712 4.584325 CACCCTATTTTGGATATGGTGGTG 59.416 45.833 10.73 0.00 36.94 4.17
1679 1779 6.260714 TCGTATGATCATGCATGCTTTACTTT 59.739 34.615 22.25 1.97 0.00 2.66
1799 1971 1.994794 GGTAAGGTCCCAGGGGTTTAA 59.005 52.381 5.33 0.00 36.47 1.52
1817 1989 5.243954 GGTTTAAAGTTCATGGGAAGAAGCT 59.756 40.000 0.00 0.00 32.62 3.74
1837 2009 1.207593 GTGCACAAGTGGCATCGTC 59.792 57.895 13.17 0.00 44.11 4.20
1839 2011 1.229975 TGCACAAGTGGCATCGTCTG 61.230 55.000 2.00 0.00 36.11 3.51
1840 2012 0.950555 GCACAAGTGGCATCGTCTGA 60.951 55.000 2.00 0.00 0.00 3.27
1859 2031 1.279271 GACAACAGCACCCATAGAGGT 59.721 52.381 0.00 0.00 42.40 3.85
1930 2109 2.180204 ACGGCAGCAGTGTTGACAC 61.180 57.895 13.73 6.15 46.77 3.67
1986 2195 0.603707 TGGCCTGAAGCTGAAGAACG 60.604 55.000 3.32 0.00 43.05 3.95
2042 2260 1.301401 GTGGCGTTGGTGTGCTAGA 60.301 57.895 0.00 0.00 0.00 2.43
2064 2282 2.038033 TGTGGGTAAGCTCACCAACTAC 59.962 50.000 15.07 5.23 45.29 2.73
2077 2295 4.343526 TCACCAACTACGGTACAAGGTAAA 59.656 41.667 0.00 0.00 37.07 2.01
2121 2339 0.028770 CAAACGCCGTGTTCATGTGT 59.971 50.000 0.00 0.00 40.84 3.72
2203 2421 2.224867 ACTAGATGCAGGCAACCAAACT 60.225 45.455 0.00 0.00 37.17 2.66
2308 2526 2.369532 AGTAACCAAACACGCCCTAAGA 59.630 45.455 0.00 0.00 0.00 2.10
2309 2527 1.601166 AACCAAACACGCCCTAAGAC 58.399 50.000 0.00 0.00 0.00 3.01
2310 2528 0.763035 ACCAAACACGCCCTAAGACT 59.237 50.000 0.00 0.00 0.00 3.24
2311 2529 1.270678 ACCAAACACGCCCTAAGACTC 60.271 52.381 0.00 0.00 0.00 3.36
2312 2530 1.439679 CAAACACGCCCTAAGACTCC 58.560 55.000 0.00 0.00 0.00 3.85
2313 2531 0.323957 AAACACGCCCTAAGACTCCC 59.676 55.000 0.00 0.00 0.00 4.30
2314 2532 0.544595 AACACGCCCTAAGACTCCCT 60.545 55.000 0.00 0.00 0.00 4.20
2315 2533 1.258445 ACACGCCCTAAGACTCCCTG 61.258 60.000 0.00 0.00 0.00 4.45
2316 2534 1.686110 ACGCCCTAAGACTCCCTGG 60.686 63.158 0.00 0.00 0.00 4.45
2317 2535 2.911928 GCCCTAAGACTCCCTGGC 59.088 66.667 0.00 0.00 0.00 4.85
2318 2536 3.095347 GCCCTAAGACTCCCTGGCG 62.095 68.421 0.00 0.00 0.00 5.69
2319 2537 2.435693 CCCTAAGACTCCCTGGCGG 61.436 68.421 0.00 0.00 0.00 6.13
2320 2538 1.381327 CCTAAGACTCCCTGGCGGA 60.381 63.158 0.00 0.00 38.83 5.54
2321 2539 0.760945 CCTAAGACTCCCTGGCGGAT 60.761 60.000 0.00 0.00 41.00 4.18
2322 2540 0.676736 CTAAGACTCCCTGGCGGATC 59.323 60.000 0.00 0.00 41.00 3.36
2323 2541 0.261991 TAAGACTCCCTGGCGGATCT 59.738 55.000 0.00 0.00 41.00 2.75
2324 2542 0.618968 AAGACTCCCTGGCGGATCTT 60.619 55.000 0.00 0.00 41.00 2.40
2325 2543 1.144936 GACTCCCTGGCGGATCTTG 59.855 63.158 0.00 0.00 41.00 3.02
2326 2544 2.203126 CTCCCTGGCGGATCTTGC 60.203 66.667 0.00 0.00 41.00 4.01
2327 2545 3.008517 TCCCTGGCGGATCTTGCA 61.009 61.111 11.61 0.00 34.86 4.08
2328 2546 2.045045 CCCTGGCGGATCTTGCAA 60.045 61.111 0.00 0.00 0.00 4.08
2329 2547 2.409870 CCCTGGCGGATCTTGCAAC 61.410 63.158 11.61 0.00 0.00 4.17
2330 2548 1.377725 CCTGGCGGATCTTGCAACT 60.378 57.895 11.61 0.00 0.00 3.16
2331 2549 0.962356 CCTGGCGGATCTTGCAACTT 60.962 55.000 11.61 0.00 0.00 2.66
2332 2550 0.169672 CTGGCGGATCTTGCAACTTG 59.830 55.000 11.61 0.00 0.00 3.16
2333 2551 0.537143 TGGCGGATCTTGCAACTTGT 60.537 50.000 11.61 0.00 0.00 3.16
2334 2552 1.271108 TGGCGGATCTTGCAACTTGTA 60.271 47.619 11.61 0.00 0.00 2.41
2335 2553 2.017049 GGCGGATCTTGCAACTTGTAT 58.983 47.619 11.61 0.00 0.00 2.29
2336 2554 3.202906 GGCGGATCTTGCAACTTGTATA 58.797 45.455 11.61 0.00 0.00 1.47
2337 2555 3.625764 GGCGGATCTTGCAACTTGTATAA 59.374 43.478 11.61 0.00 0.00 0.98
2338 2556 4.095782 GGCGGATCTTGCAACTTGTATAAA 59.904 41.667 11.61 0.00 0.00 1.40
2339 2557 5.028375 GCGGATCTTGCAACTTGTATAAAC 58.972 41.667 0.00 0.00 0.00 2.01
2340 2558 5.569413 CGGATCTTGCAACTTGTATAAACC 58.431 41.667 0.00 0.00 0.00 3.27
2341 2559 5.123186 CGGATCTTGCAACTTGTATAAACCA 59.877 40.000 0.00 0.00 0.00 3.67
2342 2560 6.348950 CGGATCTTGCAACTTGTATAAACCAA 60.349 38.462 0.00 0.00 0.00 3.67
2343 2561 7.547227 GGATCTTGCAACTTGTATAAACCAAT 58.453 34.615 0.00 0.00 0.00 3.16
2344 2562 7.702348 GGATCTTGCAACTTGTATAAACCAATC 59.298 37.037 0.00 0.00 0.00 2.67
2345 2563 6.607689 TCTTGCAACTTGTATAAACCAATCG 58.392 36.000 0.00 0.00 0.00 3.34
2346 2564 6.428465 TCTTGCAACTTGTATAAACCAATCGA 59.572 34.615 0.00 0.00 0.00 3.59
2347 2565 6.176975 TGCAACTTGTATAAACCAATCGAG 57.823 37.500 0.00 0.00 0.00 4.04
2348 2566 5.703592 TGCAACTTGTATAAACCAATCGAGT 59.296 36.000 0.00 0.00 0.00 4.18
2349 2567 6.021596 GCAACTTGTATAAACCAATCGAGTG 58.978 40.000 5.75 5.75 0.00 3.51
2350 2568 6.542852 CAACTTGTATAAACCAATCGAGTGG 58.457 40.000 29.20 29.20 44.92 4.00
2357 2575 3.540211 CCAATCGAGTGGTTCTGCT 57.460 52.632 23.45 0.00 33.63 4.24
2358 2576 1.363744 CCAATCGAGTGGTTCTGCTC 58.636 55.000 23.45 0.00 33.63 4.26
2362 2580 4.154613 GAGTGGTTCTGCTCGACG 57.845 61.111 0.00 0.00 0.00 5.12
2363 2581 1.444553 GAGTGGTTCTGCTCGACGG 60.445 63.158 0.00 0.00 0.00 4.79
2364 2582 1.863662 GAGTGGTTCTGCTCGACGGA 61.864 60.000 0.00 0.00 0.00 4.69
2365 2583 1.733399 GTGGTTCTGCTCGACGGAC 60.733 63.158 0.00 0.00 31.67 4.79
2366 2584 2.126031 GGTTCTGCTCGACGGACC 60.126 66.667 0.00 0.00 31.67 4.46
2367 2585 2.504244 GTTCTGCTCGACGGACCG 60.504 66.667 13.61 13.61 31.67 4.79
2368 2586 2.670592 TTCTGCTCGACGGACCGA 60.671 61.111 23.38 0.00 37.03 4.69
2374 2592 2.818714 TCGACGGACCGAGCTCTC 60.819 66.667 23.38 6.10 34.19 3.20
2375 2593 3.125573 CGACGGACCGAGCTCTCA 61.126 66.667 23.38 0.00 0.00 3.27
2376 2594 2.687805 CGACGGACCGAGCTCTCAA 61.688 63.158 23.38 0.00 0.00 3.02
2377 2595 1.153997 GACGGACCGAGCTCTCAAC 60.154 63.158 23.38 0.53 0.00 3.18
2378 2596 2.182030 CGGACCGAGCTCTCAACC 59.818 66.667 8.64 8.82 0.00 3.77
2379 2597 2.636412 CGGACCGAGCTCTCAACCA 61.636 63.158 8.64 0.00 0.00 3.67
2380 2598 1.901085 GGACCGAGCTCTCAACCAT 59.099 57.895 12.85 0.00 0.00 3.55
2381 2599 1.112113 GGACCGAGCTCTCAACCATA 58.888 55.000 12.85 0.00 0.00 2.74
2382 2600 1.067821 GGACCGAGCTCTCAACCATAG 59.932 57.143 12.85 0.00 0.00 2.23
2383 2601 1.067821 GACCGAGCTCTCAACCATAGG 59.932 57.143 12.85 4.54 0.00 2.57
2384 2602 1.115467 CCGAGCTCTCAACCATAGGT 58.885 55.000 12.85 0.00 37.65 3.08
2386 2604 2.693591 CCGAGCTCTCAACCATAGGTTA 59.306 50.000 12.85 0.00 45.01 2.85
2387 2605 3.132289 CCGAGCTCTCAACCATAGGTTAA 59.868 47.826 12.85 0.00 45.01 2.01
2388 2606 4.202264 CCGAGCTCTCAACCATAGGTTAAT 60.202 45.833 12.85 0.00 45.01 1.40
2389 2607 5.360591 CGAGCTCTCAACCATAGGTTAATT 58.639 41.667 12.85 0.00 45.01 1.40
2390 2608 5.235186 CGAGCTCTCAACCATAGGTTAATTG 59.765 44.000 12.85 0.00 45.01 2.32
2391 2609 6.313519 AGCTCTCAACCATAGGTTAATTGA 57.686 37.500 0.40 0.00 45.01 2.57
2392 2610 6.904626 AGCTCTCAACCATAGGTTAATTGAT 58.095 36.000 0.40 0.00 45.01 2.57
2393 2611 6.995091 AGCTCTCAACCATAGGTTAATTGATC 59.005 38.462 0.40 0.00 45.01 2.92
2394 2612 6.995091 GCTCTCAACCATAGGTTAATTGATCT 59.005 38.462 0.40 0.00 45.01 2.75
2395 2613 7.172361 GCTCTCAACCATAGGTTAATTGATCTC 59.828 40.741 0.40 0.00 45.01 2.75
2396 2614 7.509546 TCTCAACCATAGGTTAATTGATCTCC 58.490 38.462 0.40 0.00 45.01 3.71
2397 2615 7.127186 TCTCAACCATAGGTTAATTGATCTCCA 59.873 37.037 0.40 0.00 45.01 3.86
2398 2616 7.638444 TCAACCATAGGTTAATTGATCTCCAA 58.362 34.615 0.40 0.00 45.01 3.53
2399 2617 8.281531 TCAACCATAGGTTAATTGATCTCCAAT 58.718 33.333 0.40 0.00 45.01 3.16
2400 2618 8.917088 CAACCATAGGTTAATTGATCTCCAATT 58.083 33.333 0.40 7.93 45.01 2.32
2401 2619 9.136323 AACCATAGGTTAATTGATCTCCAATTC 57.864 33.333 6.32 0.00 44.94 2.17
2410 2628 6.956202 ATTGATCTCCAATTCTCCATTGAC 57.044 37.500 0.00 0.00 44.78 3.18
2411 2629 5.705397 TGATCTCCAATTCTCCATTGACT 57.295 39.130 0.00 0.00 44.78 3.41
2412 2630 6.070951 TGATCTCCAATTCTCCATTGACTT 57.929 37.500 0.00 0.00 44.78 3.01
2413 2631 5.884232 TGATCTCCAATTCTCCATTGACTTG 59.116 40.000 0.00 0.00 44.78 3.16
2414 2632 4.592942 TCTCCAATTCTCCATTGACTTGG 58.407 43.478 7.13 7.13 44.78 3.61
2415 2633 3.091545 TCCAATTCTCCATTGACTTGGC 58.908 45.455 8.23 0.00 44.78 4.52
2416 2634 2.167075 CCAATTCTCCATTGACTTGGCC 59.833 50.000 0.00 0.00 44.78 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
55 56 9.827411 CAAATCACATATCTAAGCATGATTCAG 57.173 33.333 0.00 0.00 0.00 3.02
138 139 1.037493 AGCGCACCGGACAATCTATA 58.963 50.000 9.46 0.00 0.00 1.31
305 338 2.693591 CGACAAGGGCCTGACTAAGATA 59.306 50.000 6.92 0.00 0.00 1.98
555 610 2.407090 TGAGCTCACACATCTTGTTCG 58.593 47.619 13.74 0.00 35.67 3.95
654 710 1.001641 GCAGACACCTCTTGCCCAT 60.002 57.895 0.00 0.00 0.00 4.00
801 858 3.709880 CTAACCGCGACATGGCCGA 62.710 63.158 8.23 0.00 0.00 5.54
831 888 4.394729 TGGTGGACAGTATGAAAAGGAAC 58.605 43.478 0.00 0.00 39.69 3.62
837 894 3.088532 GGCAATGGTGGACAGTATGAAA 58.911 45.455 0.00 0.00 39.69 2.69
884 942 4.215613 GGTGGTCCTAAGAATGAAACACAC 59.784 45.833 0.00 0.00 0.00 3.82
1049 1107 2.806237 GGACCTCGATGTCCGGTC 59.194 66.667 21.85 16.54 44.98 4.79
1057 1115 1.832912 GGCCATCAAGGACCTCGAT 59.167 57.895 0.00 0.00 40.85 3.59
1148 1206 3.695357 TGATCTCCTTCTCCATCAGGA 57.305 47.619 0.00 0.00 43.21 3.86
1159 1217 4.082354 GCTGCAAAAGACATTGATCTCCTT 60.082 41.667 0.00 0.00 31.84 3.36
1237 1298 0.470456 TACAGGTCAGGGTGGACGTT 60.470 55.000 0.00 0.00 38.70 3.99
1285 1346 1.078918 CCATGAGAGCCTCGTTGCA 60.079 57.895 0.00 0.00 32.35 4.08
1288 1349 1.220206 CTGCCATGAGAGCCTCGTT 59.780 57.895 0.00 0.00 32.35 3.85
1320 1381 0.468029 CCTGGGCCTTGTTGTCAAGT 60.468 55.000 4.53 0.00 46.70 3.16
1347 1408 0.527113 CATCAGCCATGGCAACGAAA 59.473 50.000 37.18 16.14 44.88 3.46
1384 1445 2.005606 TTGCCCAACCAGCTCCTGAA 62.006 55.000 0.00 0.00 32.44 3.02
1396 1457 3.437213 TCTAGTAGTAGTGCTTGCCCAA 58.563 45.455 4.51 0.00 0.00 4.12
1579 1676 2.592102 TAGGGTGTCGTCTTACCACT 57.408 50.000 0.00 0.00 38.74 4.00
1586 1683 5.454755 CCATATCCAAAATAGGGTGTCGTCT 60.455 44.000 0.00 0.00 0.00 4.18
1598 1695 3.774842 ACCCACCACCATATCCAAAAT 57.225 42.857 0.00 0.00 0.00 1.82
1615 1712 1.066645 CCACTACCTCGGTGTTAACCC 60.067 57.143 2.48 3.20 44.42 4.11
1626 1723 4.621038 GCAAGTTCTTCCTACCACTACCTC 60.621 50.000 0.00 0.00 0.00 3.85
1679 1779 5.350914 CACAAACAACAATGGAGCAAAAGAA 59.649 36.000 0.00 0.00 0.00 2.52
1799 1971 4.583871 CACTAGCTTCTTCCCATGAACTT 58.416 43.478 0.00 0.00 0.00 2.66
1817 1989 0.034756 ACGATGCCACTTGTGCACTA 59.965 50.000 19.41 9.94 42.38 2.74
1837 2009 2.625737 CTCTATGGGTGCTGTTGTCAG 58.374 52.381 0.00 0.00 43.87 3.51
1839 2011 1.279271 ACCTCTATGGGTGCTGTTGTC 59.721 52.381 0.00 0.00 41.11 3.18
1840 2012 1.362224 ACCTCTATGGGTGCTGTTGT 58.638 50.000 0.00 0.00 41.11 3.32
1859 2031 1.611673 GCTGCCTGCCTAGTCTTGAAA 60.612 52.381 0.00 0.00 35.15 2.69
1930 2109 0.951040 GACACCTCCAACCTTGCGAG 60.951 60.000 0.00 0.00 0.00 5.03
2042 2260 1.705186 AGTTGGTGAGCTTACCCACAT 59.295 47.619 27.24 13.74 38.48 3.21
2064 2282 4.273969 ACATGTTGTGTTTACCTTGTACCG 59.726 41.667 0.00 0.00 38.01 4.02
2077 2295 2.354510 GCATACGGCATACATGTTGTGT 59.645 45.455 2.30 8.12 43.03 3.72
2203 2421 3.762288 CCCTAATACGCCATCTGCTAGTA 59.238 47.826 0.00 0.00 38.05 1.82
2229 2447 1.345415 CCAGCCTGGTTGAGCAAAAAT 59.655 47.619 12.54 0.00 31.35 1.82
2289 2507 2.369532 AGTCTTAGGGCGTGTTTGGTTA 59.630 45.455 0.00 0.00 0.00 2.85
2311 2529 2.045045 TTGCAAGATCCGCCAGGG 60.045 61.111 0.00 0.00 38.33 4.45
2312 2530 0.962356 AAGTTGCAAGATCCGCCAGG 60.962 55.000 0.00 0.00 39.46 4.45
2313 2531 0.169672 CAAGTTGCAAGATCCGCCAG 59.830 55.000 0.00 0.00 0.00 4.85
2314 2532 0.537143 ACAAGTTGCAAGATCCGCCA 60.537 50.000 0.00 0.00 0.00 5.69
2315 2533 1.448985 TACAAGTTGCAAGATCCGCC 58.551 50.000 0.00 0.00 0.00 6.13
2316 2534 4.875544 TTATACAAGTTGCAAGATCCGC 57.124 40.909 0.00 0.00 0.00 5.54
2317 2535 5.123186 TGGTTTATACAAGTTGCAAGATCCG 59.877 40.000 0.00 0.00 0.00 4.18
2318 2536 6.509418 TGGTTTATACAAGTTGCAAGATCC 57.491 37.500 0.00 0.65 0.00 3.36
2319 2537 7.429340 CGATTGGTTTATACAAGTTGCAAGATC 59.571 37.037 0.00 0.00 0.00 2.75
2320 2538 7.120579 TCGATTGGTTTATACAAGTTGCAAGAT 59.879 33.333 0.00 0.00 0.00 2.40
2321 2539 6.428465 TCGATTGGTTTATACAAGTTGCAAGA 59.572 34.615 0.00 0.00 0.00 3.02
2322 2540 6.607689 TCGATTGGTTTATACAAGTTGCAAG 58.392 36.000 0.00 0.00 0.00 4.01
2323 2541 6.205853 ACTCGATTGGTTTATACAAGTTGCAA 59.794 34.615 1.81 0.00 0.00 4.08
2324 2542 5.703592 ACTCGATTGGTTTATACAAGTTGCA 59.296 36.000 1.81 0.00 0.00 4.08
2325 2543 6.021596 CACTCGATTGGTTTATACAAGTTGC 58.978 40.000 1.81 0.00 0.00 4.17
2326 2544 6.542852 CCACTCGATTGGTTTATACAAGTTG 58.457 40.000 13.44 0.00 0.00 3.16
2327 2545 6.737254 CCACTCGATTGGTTTATACAAGTT 57.263 37.500 13.44 0.00 0.00 2.66
2339 2557 1.363744 GAGCAGAACCACTCGATTGG 58.636 55.000 19.45 19.45 43.04 3.16
2345 2563 1.444553 CCGTCGAGCAGAACCACTC 60.445 63.158 0.00 0.00 0.00 3.51
2346 2564 1.901948 TCCGTCGAGCAGAACCACT 60.902 57.895 0.00 0.00 0.00 4.00
2347 2565 1.733399 GTCCGTCGAGCAGAACCAC 60.733 63.158 0.00 0.00 0.00 4.16
2348 2566 2.649034 GTCCGTCGAGCAGAACCA 59.351 61.111 0.00 0.00 0.00 3.67
2349 2567 2.126031 GGTCCGTCGAGCAGAACC 60.126 66.667 0.00 0.00 36.48 3.62
2350 2568 2.504244 CGGTCCGTCGAGCAGAAC 60.504 66.667 2.08 0.00 36.22 3.01
2351 2569 2.670592 TCGGTCCGTCGAGCAGAA 60.671 61.111 11.88 0.00 36.22 3.02
2357 2575 2.818714 GAGAGCTCGGTCCGTCGA 60.819 66.667 11.88 0.00 37.60 4.20
2358 2576 2.687805 TTGAGAGCTCGGTCCGTCG 61.688 63.158 11.88 5.08 0.00 5.12
2359 2577 1.153997 GTTGAGAGCTCGGTCCGTC 60.154 63.158 11.88 1.28 0.00 4.79
2360 2578 2.637383 GGTTGAGAGCTCGGTCCGT 61.637 63.158 11.88 0.00 0.00 4.69
2361 2579 1.949847 ATGGTTGAGAGCTCGGTCCG 61.950 60.000 8.37 4.39 0.00 4.79
2362 2580 1.067821 CTATGGTTGAGAGCTCGGTCC 59.932 57.143 8.37 10.27 0.00 4.46
2363 2581 1.067821 CCTATGGTTGAGAGCTCGGTC 59.932 57.143 8.37 1.63 0.00 4.79
2364 2582 1.115467 CCTATGGTTGAGAGCTCGGT 58.885 55.000 8.37 0.00 0.00 4.69
2365 2583 1.115467 ACCTATGGTTGAGAGCTCGG 58.885 55.000 8.37 2.37 27.29 4.63
2366 2584 2.969628 AACCTATGGTTGAGAGCTCG 57.030 50.000 8.37 0.00 45.07 5.03
2367 2585 6.349300 TCAATTAACCTATGGTTGAGAGCTC 58.651 40.000 5.27 5.27 46.35 4.09
2368 2586 6.313519 TCAATTAACCTATGGTTGAGAGCT 57.686 37.500 11.78 0.00 46.35 4.09
2369 2587 6.995091 AGATCAATTAACCTATGGTTGAGAGC 59.005 38.462 11.78 7.16 46.35 4.09
2370 2588 7.659390 GGAGATCAATTAACCTATGGTTGAGAG 59.341 40.741 11.78 1.85 46.35 3.20
2371 2589 7.127186 TGGAGATCAATTAACCTATGGTTGAGA 59.873 37.037 11.78 5.23 46.35 3.27
2372 2590 7.282585 TGGAGATCAATTAACCTATGGTTGAG 58.717 38.462 11.78 0.47 46.35 3.02
2373 2591 7.206789 TGGAGATCAATTAACCTATGGTTGA 57.793 36.000 11.78 4.44 46.35 3.18
2374 2592 7.880160 TTGGAGATCAATTAACCTATGGTTG 57.120 36.000 11.78 0.00 46.35 3.77
2388 2606 6.070951 AGTCAATGGAGAATTGGAGATCAA 57.929 37.500 0.00 0.00 45.00 2.57
2389 2607 5.705397 AGTCAATGGAGAATTGGAGATCA 57.295 39.130 0.00 0.00 45.00 2.92
2390 2608 6.374565 CAAGTCAATGGAGAATTGGAGATC 57.625 41.667 0.00 0.00 45.00 2.75
2396 2614 3.515330 GGCCAAGTCAATGGAGAATTG 57.485 47.619 0.00 0.00 46.10 2.32


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

AutoCloner maintained by Alex Coulton.