Multiple sequence alignment - TraesCS5B01G415700

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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 TraesCS5B01G415700 chr5B 100.000 3302 0 0 1 3302 589997354 590000655 0.000000e+00 6098.0
1 TraesCS5B01G415700 chr5B 87.145 1338 96 32 998 2304 589894270 589895562 0.000000e+00 1448.0
2 TraesCS5B01G415700 chr5B 85.267 991 89 26 1326 2281 589677239 589678207 0.000000e+00 968.0
3 TraesCS5B01G415700 chr5B 84.370 595 55 22 673 1247 589676521 589677097 1.730000e-152 549.0
4 TraesCS5B01G415700 chr5B 92.381 105 8 0 2474 2578 166379183 166379079 2.050000e-32 150.0
5 TraesCS5B01G415700 chr5D 90.517 1856 96 27 1343 3165 481425981 481427789 0.000000e+00 2379.0
6 TraesCS5B01G415700 chr5D 88.508 1314 71 44 1 1273 481424515 481425789 0.000000e+00 1517.0
7 TraesCS5B01G415700 chr5D 86.018 1366 106 37 962 2304 481302910 481304213 0.000000e+00 1386.0
8 TraesCS5B01G415700 chr5D 86.004 986 66 25 1345 2281 481183994 481184956 0.000000e+00 990.0
9 TraesCS5B01G415700 chr5D 82.919 603 58 23 678 1256 481183351 481183932 4.920000e-138 501.0
10 TraesCS5B01G415700 chr5D 93.939 99 6 0 2474 2572 481427203 481427105 2.050000e-32 150.0
11 TraesCS5B01G415700 chr5A 90.611 1555 85 22 1762 3291 600439046 600440564 0.000000e+00 2006.0
12 TraesCS5B01G415700 chr5A 87.346 1786 93 55 1 1726 600437328 600439040 0.000000e+00 1923.0
13 TraesCS5B01G415700 chr5A 89.441 1307 87 21 998 2281 600361472 600362750 0.000000e+00 1602.0
14 TraesCS5B01G415700 chr5A 84.453 1087 106 33 678 1726 600236562 600237623 0.000000e+00 1013.0
15 TraesCS5B01G415700 chr5A 83.877 552 44 18 1762 2281 600237629 600238167 4.950000e-133 484.0
16 TraesCS5B01G415700 chr5A 93.359 256 12 3 72 323 600433092 600433346 1.120000e-99 374.0
17 TraesCS5B01G415700 chr4B 83.006 712 82 25 1007 1703 663942170 663941483 2.820000e-170 608.0
18 TraesCS5B01G415700 chr4B 85.000 560 59 11 1734 2279 663941389 663940841 2.240000e-151 545.0
19 TraesCS5B01G415700 chr4B 92.929 99 7 0 2475 2573 511163709 511163807 9.550000e-31 145.0
20 TraesCS5B01G415700 chr4D 81.758 455 58 15 1841 2280 506482766 506483210 1.130000e-94 357.0
21 TraesCS5B01G415700 chr4D 80.000 210 8 12 1643 1843 506471048 506471232 1.240000e-24 124.0
22 TraesCS5B01G415700 chr4D 77.692 130 27 2 1109 1237 481912559 481912431 9.820000e-11 78.7
23 TraesCS5B01G415700 chr3A 93.069 101 6 1 2472 2571 470095782 470095682 2.660000e-31 147.0
24 TraesCS5B01G415700 chr2B 90.654 107 8 2 2475 2580 683025748 683025853 1.240000e-29 141.0
25 TraesCS5B01G415700 chr2A 90.654 107 8 2 2475 2580 709832403 709832508 1.240000e-29 141.0
26 TraesCS5B01G415700 chr4A 88.235 119 9 4 2475 2592 37060112 37060226 1.600000e-28 137.0


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 TraesCS5B01G415700 chr5B 589997354 590000655 3301 False 6098.000000 6098 100.000000 1 3302 1 chr5B.!!$F2 3301
1 TraesCS5B01G415700 chr5B 589894270 589895562 1292 False 1448.000000 1448 87.145000 998 2304 1 chr5B.!!$F1 1306
2 TraesCS5B01G415700 chr5B 589676521 589678207 1686 False 758.500000 968 84.818500 673 2281 2 chr5B.!!$F3 1608
3 TraesCS5B01G415700 chr5D 481424515 481427789 3274 False 1948.000000 2379 89.512500 1 3165 2 chr5D.!!$F3 3164
4 TraesCS5B01G415700 chr5D 481302910 481304213 1303 False 1386.000000 1386 86.018000 962 2304 1 chr5D.!!$F1 1342
5 TraesCS5B01G415700 chr5D 481183351 481184956 1605 False 745.500000 990 84.461500 678 2281 2 chr5D.!!$F2 1603
6 TraesCS5B01G415700 chr5A 600361472 600362750 1278 False 1602.000000 1602 89.441000 998 2281 1 chr5A.!!$F1 1283
7 TraesCS5B01G415700 chr5A 600433092 600440564 7472 False 1434.333333 2006 90.438667 1 3291 3 chr5A.!!$F3 3290
8 TraesCS5B01G415700 chr5A 600236562 600238167 1605 False 748.500000 1013 84.165000 678 2281 2 chr5A.!!$F2 1603
9 TraesCS5B01G415700 chr4B 663940841 663942170 1329 True 576.500000 608 84.003000 1007 2279 2 chr4B.!!$R1 1272

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
530 4789 0.399233 ATAGGACCCAGTCAGAGGCC 60.399 60.0 0.0 0.0 33.68 5.19 F
1607 6100 0.460109 CCGACTGGATGATGCACGAA 60.460 55.0 0.0 0.0 37.49 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2008 6648 0.243907 CCCACCTGACTGACGTACTG 59.756 60.0 0.0 0.0 0.00 2.74 R
3177 7880 0.322098 TTTGTATGACCTGTGGGCGG 60.322 55.0 0.0 0.0 35.63 6.13 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
103 4343 1.904144 CATTGCTCACATTTGCTCCG 58.096 50.000 0.00 0.00 0.00 4.63
152 4392 1.611148 GCTCCTCTCCATCATCCATGC 60.611 57.143 0.00 0.00 0.00 4.06
170 4424 5.637810 TCCATGCTTCTTTTACGACTTACTG 59.362 40.000 0.00 0.00 0.00 2.74
176 4433 3.737266 TCTTTTACGACTTACTGCAACCG 59.263 43.478 0.00 0.00 0.00 4.44
178 4435 2.624316 TACGACTTACTGCAACCGAG 57.376 50.000 0.00 0.00 0.00 4.63
194 4452 6.653320 TGCAACCGAGTTTACTTTTGATCTAT 59.347 34.615 0.00 0.00 0.00 1.98
213 4471 9.793259 TGATCTATCAAAAACAACCTACTTTCT 57.207 29.630 0.00 0.00 33.08 2.52
220 4478 9.849166 TCAAAAACAACCTACTTTCTTACTTTG 57.151 29.630 0.00 0.00 0.00 2.77
221 4479 8.592155 CAAAAACAACCTACTTTCTTACTTTGC 58.408 33.333 0.00 0.00 0.00 3.68
222 4480 7.640597 AAACAACCTACTTTCTTACTTTGCT 57.359 32.000 0.00 0.00 0.00 3.91
223 4481 6.862711 ACAACCTACTTTCTTACTTTGCTC 57.137 37.500 0.00 0.00 0.00 4.26
224 4482 5.763698 ACAACCTACTTTCTTACTTTGCTCC 59.236 40.000 0.00 0.00 0.00 4.70
225 4483 4.566987 ACCTACTTTCTTACTTTGCTCCG 58.433 43.478 0.00 0.00 0.00 4.63
226 4484 3.371285 CCTACTTTCTTACTTTGCTCCGC 59.629 47.826 0.00 0.00 0.00 5.54
257 4516 1.145119 GAGTGTCCCCCAAGGTTTCTT 59.855 52.381 0.00 0.00 36.75 2.52
258 4517 1.145119 AGTGTCCCCCAAGGTTTCTTC 59.855 52.381 0.00 0.00 36.75 2.87
259 4518 1.145119 GTGTCCCCCAAGGTTTCTTCT 59.855 52.381 0.00 0.00 36.75 2.85
263 4522 1.004862 CCCCCAAGGTTTCTTCTCCTC 59.995 57.143 0.00 0.00 33.09 3.71
278 4537 0.887387 TCCTCTTTTTCGTTGCCCGG 60.887 55.000 0.00 0.00 37.11 5.73
288 4547 1.749258 GTTGCCCGGTTCATCTCCC 60.749 63.158 0.00 0.00 0.00 4.30
434 4693 2.166664 AGTCGTGCAACTAAGATCTCCC 59.833 50.000 0.00 0.00 31.75 4.30
435 4694 2.166664 GTCGTGCAACTAAGATCTCCCT 59.833 50.000 0.00 0.00 31.75 4.20
436 4695 3.380637 GTCGTGCAACTAAGATCTCCCTA 59.619 47.826 0.00 0.00 31.75 3.53
437 4696 3.632604 TCGTGCAACTAAGATCTCCCTAG 59.367 47.826 0.00 0.00 31.75 3.02
496 4755 5.310720 ACGTTGGCAAATATTCCTTTCTC 57.689 39.130 0.00 0.00 0.00 2.87
500 4759 6.457528 CGTTGGCAAATATTCCTTTCTCTCTC 60.458 42.308 0.00 0.00 0.00 3.20
501 4760 6.319048 TGGCAAATATTCCTTTCTCTCTCT 57.681 37.500 0.00 0.00 0.00 3.10
502 4761 6.118170 TGGCAAATATTCCTTTCTCTCTCTG 58.882 40.000 0.00 0.00 0.00 3.35
503 4762 6.118852 GGCAAATATTCCTTTCTCTCTCTGT 58.881 40.000 0.00 0.00 0.00 3.41
504 4763 6.601217 GGCAAATATTCCTTTCTCTCTCTGTT 59.399 38.462 0.00 0.00 0.00 3.16
505 4764 7.770897 GGCAAATATTCCTTTCTCTCTCTGTTA 59.229 37.037 0.00 0.00 0.00 2.41
506 4765 9.336171 GCAAATATTCCTTTCTCTCTCTGTTAT 57.664 33.333 0.00 0.00 0.00 1.89
530 4789 0.399233 ATAGGACCCAGTCAGAGGCC 60.399 60.000 0.00 0.00 33.68 5.19
542 4802 5.337894 CCAGTCAGAGGCCATATATGTAAGG 60.338 48.000 5.01 0.00 0.00 2.69
619 4885 1.522668 TCCCATTCGCACAGACAAAG 58.477 50.000 0.00 0.00 0.00 2.77
632 4898 5.753921 GCACAGACAAAGTAACACTCTTACT 59.246 40.000 0.00 0.00 36.85 2.24
633 4899 6.258068 GCACAGACAAAGTAACACTCTTACTT 59.742 38.462 0.54 0.54 44.45 2.24
634 4900 7.437267 GCACAGACAAAGTAACACTCTTACTTA 59.563 37.037 6.03 0.00 42.48 2.24
635 4901 8.753175 CACAGACAAAGTAACACTCTTACTTAC 58.247 37.037 6.03 2.87 42.48 2.34
663 4932 3.548770 ACACATGCAAGCACAGCTATAT 58.451 40.909 0.00 0.00 38.25 0.86
664 4933 4.707105 ACACATGCAAGCACAGCTATATA 58.293 39.130 0.00 0.00 38.25 0.86
783 5052 4.207165 TCCTTTAACTTGTTGCAGAGCTT 58.793 39.130 0.00 0.00 0.00 3.74
794 5072 8.526147 ACTTGTTGCAGAGCTTTCATTTATAAT 58.474 29.630 0.00 0.00 0.00 1.28
799 5077 5.047731 GCAGAGCTTTCATTTATAATCCCCC 60.048 44.000 0.00 0.00 0.00 5.40
800 5078 5.182001 CAGAGCTTTCATTTATAATCCCCCG 59.818 44.000 0.00 0.00 0.00 5.73
802 5080 5.701224 AGCTTTCATTTATAATCCCCCGAA 58.299 37.500 0.00 0.00 0.00 4.30
803 5081 6.314917 AGCTTTCATTTATAATCCCCCGAAT 58.685 36.000 0.00 0.00 0.00 3.34
861 5147 3.462021 CACCAAGAGCTTGCTATCCTAC 58.538 50.000 4.72 0.00 39.16 3.18
862 5148 2.101582 ACCAAGAGCTTGCTATCCTACG 59.898 50.000 4.72 0.00 39.16 3.51
863 5149 2.131183 CAAGAGCTTGCTATCCTACGC 58.869 52.381 0.00 0.00 33.45 4.42
922 5208 3.619419 GAGAGGGTCCGTAGAACTAAGT 58.381 50.000 0.00 0.00 0.00 2.24
924 5210 3.009916 AGAGGGTCCGTAGAACTAAGTGA 59.990 47.826 0.00 0.00 0.00 3.41
925 5211 3.354467 AGGGTCCGTAGAACTAAGTGAG 58.646 50.000 0.00 0.00 0.00 3.51
926 5212 2.159268 GGGTCCGTAGAACTAAGTGAGC 60.159 54.545 0.00 0.00 0.00 4.26
933 5219 3.760580 AGAACTAAGTGAGCAAGCAGT 57.239 42.857 0.00 0.00 0.00 4.40
934 5220 4.873746 AGAACTAAGTGAGCAAGCAGTA 57.126 40.909 0.00 0.00 0.00 2.74
935 5221 4.561105 AGAACTAAGTGAGCAAGCAGTAC 58.439 43.478 0.00 0.00 0.00 2.73
936 5222 4.039245 AGAACTAAGTGAGCAAGCAGTACA 59.961 41.667 0.00 0.00 0.00 2.90
939 5225 5.308825 ACTAAGTGAGCAAGCAGTACAAAT 58.691 37.500 0.00 0.00 0.00 2.32
940 5226 4.494350 AAGTGAGCAAGCAGTACAAATG 57.506 40.909 0.00 0.00 0.00 2.32
943 5229 3.748048 GTGAGCAAGCAGTACAAATGAGA 59.252 43.478 0.00 0.00 0.00 3.27
945 5231 2.746362 AGCAAGCAGTACAAATGAGAGC 59.254 45.455 0.00 0.00 0.00 4.09
946 5232 2.485426 GCAAGCAGTACAAATGAGAGCA 59.515 45.455 0.00 0.00 0.00 4.26
947 5233 3.058016 GCAAGCAGTACAAATGAGAGCAA 60.058 43.478 0.00 0.00 0.00 3.91
949 5235 5.152097 CAAGCAGTACAAATGAGAGCAAAG 58.848 41.667 0.00 0.00 0.00 2.77
953 5239 5.278463 GCAGTACAAATGAGAGCAAAGGAAA 60.278 40.000 0.00 0.00 0.00 3.13
954 5240 6.376978 CAGTACAAATGAGAGCAAAGGAAAG 58.623 40.000 0.00 0.00 0.00 2.62
957 5243 6.264841 ACAAATGAGAGCAAAGGAAAGATC 57.735 37.500 0.00 0.00 0.00 2.75
958 5244 5.106396 ACAAATGAGAGCAAAGGAAAGATCG 60.106 40.000 0.00 0.00 0.00 3.69
959 5245 2.350522 TGAGAGCAAAGGAAAGATCGC 58.649 47.619 0.00 0.00 0.00 4.58
960 5246 2.289631 TGAGAGCAAAGGAAAGATCGCA 60.290 45.455 0.00 0.00 0.00 5.10
962 5248 2.746362 AGAGCAAAGGAAAGATCGCAAG 59.254 45.455 0.00 0.00 0.00 4.01
1303 5760 6.701400 GCCATGACTTGAACAAATACAGTTTT 59.299 34.615 0.00 0.00 0.00 2.43
1351 5835 3.554934 TCTGACAGAGTGTGGCAAATTT 58.445 40.909 0.00 0.00 46.64 1.82
1421 5908 1.988406 GAGGGGCAGGAAGTACCGT 60.988 63.158 0.00 0.00 44.74 4.83
1559 6052 4.190001 TGAAGAAGTCGCTCGTCTACTAT 58.810 43.478 0.00 0.00 34.04 2.12
1607 6100 0.460109 CCGACTGGATGATGCACGAA 60.460 55.000 0.00 0.00 37.49 3.85
1905 6524 4.117661 GCCGCCGACTCGAACTCT 62.118 66.667 0.00 0.00 0.00 3.24
2007 6647 3.738246 CAGCAGCAGCACCAGCAG 61.738 66.667 3.17 0.00 45.49 4.24
2065 6705 1.811359 ACTTCTTCTACGAGGACACCG 59.189 52.381 0.00 0.00 0.00 4.94
2098 6747 2.940467 TCCAGGGGCAATGGAGCA 60.940 61.111 5.86 0.00 41.96 4.26
2106 6773 3.443045 CAATGGAGCACCGCACCC 61.443 66.667 0.00 0.00 38.50 4.61
2142 6809 0.247736 AGCAGAAACTACAGAGCCCG 59.752 55.000 0.00 0.00 0.00 6.13
2281 6957 1.353076 GGCAGGGTTTTACGACTACG 58.647 55.000 0.00 0.00 45.75 3.51
2282 6958 1.067635 GGCAGGGTTTTACGACTACGA 60.068 52.381 0.00 0.00 42.66 3.43
2283 6959 1.988467 GCAGGGTTTTACGACTACGAC 59.012 52.381 0.00 0.00 42.66 4.34
2284 6960 2.352127 GCAGGGTTTTACGACTACGACT 60.352 50.000 0.00 0.00 42.66 4.18
2285 6961 3.119849 GCAGGGTTTTACGACTACGACTA 60.120 47.826 0.00 0.00 42.66 2.59
2286 6962 4.406943 CAGGGTTTTACGACTACGACTAC 58.593 47.826 0.00 0.00 42.66 2.73
2348 7024 3.813724 GAGTTGTTCAGGGTAGACAAACC 59.186 47.826 0.00 0.00 38.94 3.27
2507 7198 5.107837 CGATCCATAATAAGTGTCGCAGTTC 60.108 44.000 3.66 0.00 0.00 3.01
2517 7208 3.318275 AGTGTCGCAGTTCTGAACTAAGA 59.682 43.478 21.65 19.26 40.46 2.10
2776 7468 6.826893 AAATCGAAACAAATGAACAACAGG 57.173 33.333 0.00 0.00 0.00 4.00
2835 7528 5.432645 TCCTGTTAGTGTTTGATGTGTTCA 58.567 37.500 0.00 0.00 0.00 3.18
2976 7674 4.989279 AATGGGCAAGAACATGTATGTC 57.011 40.909 0.00 0.09 40.80 3.06
3014 7715 0.822811 TGGCGCCCGTACAAGTATTA 59.177 50.000 26.77 0.00 0.00 0.98
3020 7721 3.473625 GCCCGTACAAGTATTATTGGCT 58.526 45.455 0.00 0.00 34.36 4.75
3045 7746 5.310594 AGCAGGAGCATATATACCAAGGAAA 59.689 40.000 0.00 0.00 45.49 3.13
3050 7751 7.502561 AGGAGCATATATACCAAGGAAACAAAC 59.497 37.037 0.00 0.00 0.00 2.93
3052 7753 8.225603 AGCATATATACCAAGGAAACAAACAG 57.774 34.615 0.00 0.00 0.00 3.16
3053 7754 6.918022 GCATATATACCAAGGAAACAAACAGC 59.082 38.462 0.00 0.00 0.00 4.40
3075 7778 5.457473 AGCGAAATGTAAAAGTGTTTTTCCG 59.543 36.000 0.00 0.00 37.64 4.30
3081 7784 3.320673 AAAAGTGTTTTTCCGCACCAA 57.679 38.095 0.00 0.00 36.35 3.67
3093 7796 5.713792 TTCCGCACCAAATTTCTTATCAA 57.286 34.783 0.00 0.00 0.00 2.57
3130 7833 6.961554 GGTGAGCAAAAATAATCAGTTCTACG 59.038 38.462 0.00 0.00 0.00 3.51
3139 7842 0.459899 TCAGTTCTACGCGCATCCAT 59.540 50.000 5.73 0.00 0.00 3.41
3157 7860 4.843728 TCCATTTTGTCGCTCCTAGATTT 58.156 39.130 0.00 0.00 0.00 2.17
3161 7864 6.483307 CCATTTTGTCGCTCCTAGATTTATCA 59.517 38.462 0.00 0.00 0.00 2.15
3166 7869 2.028020 CGCTCCTAGATTTATCACCCCC 60.028 54.545 0.00 0.00 0.00 5.40
3167 7870 2.028020 GCTCCTAGATTTATCACCCCCG 60.028 54.545 0.00 0.00 0.00 5.73
3168 7871 1.975680 TCCTAGATTTATCACCCCCGC 59.024 52.381 0.00 0.00 0.00 6.13
3169 7872 1.003233 CCTAGATTTATCACCCCCGCC 59.997 57.143 0.00 0.00 0.00 6.13
3170 7873 1.003233 CTAGATTTATCACCCCCGCCC 59.997 57.143 0.00 0.00 0.00 6.13
3171 7874 1.228459 GATTTATCACCCCCGCCCC 60.228 63.158 0.00 0.00 0.00 5.80
3172 7875 2.708593 GATTTATCACCCCCGCCCCC 62.709 65.000 0.00 0.00 0.00 5.40
3198 7901 1.199097 CGCCCACAGGTCATACAAAAC 59.801 52.381 0.00 0.00 34.57 2.43
3212 7915 3.648339 ACAAAACTGCGCATGATCTTT 57.352 38.095 12.24 3.49 0.00 2.52
3214 7917 2.642139 AAACTGCGCATGATCTTTGG 57.358 45.000 12.24 0.00 0.00 3.28
3216 7919 1.538047 ACTGCGCATGATCTTTGGTT 58.462 45.000 12.24 0.00 0.00 3.67
3223 7926 0.168788 ATGATCTTTGGTTGCGTGCG 59.831 50.000 0.00 0.00 0.00 5.34
3246 7949 5.289193 CGCAATCTAAACATTTGATTGGGTG 59.711 40.000 23.06 8.67 46.51 4.61
3247 7950 5.581874 GCAATCTAAACATTTGATTGGGTGG 59.418 40.000 20.59 0.00 44.05 4.61
3263 7966 4.483950 TGGGTGGATTTTGTCATTTACCA 58.516 39.130 0.00 0.00 0.00 3.25
3265 7968 5.221541 TGGGTGGATTTTGTCATTTACCAAC 60.222 40.000 0.00 0.00 33.53 3.77
3277 7980 8.958175 TGTCATTTACCAACGAAAAATGTATC 57.042 30.769 0.00 1.99 40.10 2.24
3278 7981 8.568794 TGTCATTTACCAACGAAAAATGTATCA 58.431 29.630 0.00 3.89 40.10 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 4251 0.669318 TCCAGAAGGTGCGCTTAACG 60.669 55.000 9.73 0.00 39.78 3.18
54 4291 5.851047 AACACGTAAACAACTAGGCATAC 57.149 39.130 0.00 0.00 0.00 2.39
59 4299 4.622313 TGCGATAACACGTAAACAACTAGG 59.378 41.667 0.00 0.00 35.59 3.02
68 4308 2.222931 GCAATGCTGCGATAACACGTAA 60.223 45.455 0.00 0.00 39.20 3.18
103 4343 0.605589 AGGTAGCCTTTGTTGACGGC 60.606 55.000 0.00 0.00 44.09 5.68
152 4392 5.611844 CGGTTGCAGTAAGTCGTAAAAGAAG 60.612 44.000 0.00 0.00 0.00 2.85
170 4424 5.358298 AGATCAAAAGTAAACTCGGTTGC 57.642 39.130 0.00 0.00 0.00 4.17
194 4452 9.849166 CAAAGTAAGAAAGTAGGTTGTTTTTGA 57.151 29.630 0.00 0.00 0.00 2.69
236 4494 0.251209 GAAACCTTGGGGGACACTCC 60.251 60.000 0.00 0.00 38.76 3.85
257 4516 1.892209 GGGCAACGAAAAAGAGGAGA 58.108 50.000 0.00 0.00 37.60 3.71
278 4537 2.019984 ACGTACGGTAGGGAGATGAAC 58.980 52.381 21.06 0.00 0.00 3.18
288 4547 4.380974 GTCAACTGAAGAAACGTACGGTAG 59.619 45.833 21.06 9.43 0.00 3.18
434 4693 6.975197 CGAGATCTAGAGACAGAGATAGCTAG 59.025 46.154 0.00 0.00 32.47 3.42
435 4694 6.127451 CCGAGATCTAGAGACAGAGATAGCTA 60.127 46.154 4.15 0.00 32.47 3.32
436 4695 5.337571 CCGAGATCTAGAGACAGAGATAGCT 60.338 48.000 4.15 0.00 32.47 3.32
437 4696 4.870426 CCGAGATCTAGAGACAGAGATAGC 59.130 50.000 4.15 0.00 32.47 2.97
479 4738 6.118852 ACAGAGAGAGAAAGGAATATTTGCC 58.881 40.000 0.00 0.00 0.00 4.52
496 4755 7.453126 ACTGGGTCCTATGATAATAACAGAGAG 59.547 40.741 0.00 0.00 0.00 3.20
500 4759 7.233553 TCTGACTGGGTCCTATGATAATAACAG 59.766 40.741 0.00 0.00 0.00 3.16
501 4760 7.073208 TCTGACTGGGTCCTATGATAATAACA 58.927 38.462 0.00 0.00 0.00 2.41
502 4761 7.310113 CCTCTGACTGGGTCCTATGATAATAAC 60.310 44.444 0.00 0.00 0.00 1.89
503 4762 6.726299 CCTCTGACTGGGTCCTATGATAATAA 59.274 42.308 0.00 0.00 0.00 1.40
504 4763 6.256819 CCTCTGACTGGGTCCTATGATAATA 58.743 44.000 0.00 0.00 0.00 0.98
505 4764 5.090139 CCTCTGACTGGGTCCTATGATAAT 58.910 45.833 0.00 0.00 0.00 1.28
506 4765 4.483950 CCTCTGACTGGGTCCTATGATAA 58.516 47.826 0.00 0.00 0.00 1.75
512 4771 1.001760 GGCCTCTGACTGGGTCCTA 59.998 63.158 0.00 0.00 0.00 2.94
542 4802 4.577693 TCAAAAGGCATGAGCTCATACATC 59.422 41.667 28.27 16.83 41.70 3.06
619 4885 7.596621 GTGTTACCCTGTAAGTAAGAGTGTTAC 59.403 40.741 1.96 1.96 30.59 2.50
632 4898 2.817258 GCTTGCATGTGTTACCCTGTAA 59.183 45.455 1.14 0.00 0.00 2.41
633 4899 2.224646 TGCTTGCATGTGTTACCCTGTA 60.225 45.455 1.14 0.00 0.00 2.74
634 4900 1.247567 GCTTGCATGTGTTACCCTGT 58.752 50.000 1.14 0.00 0.00 4.00
635 4901 1.068333 GTGCTTGCATGTGTTACCCTG 60.068 52.381 0.00 0.00 0.00 4.45
663 4932 1.144913 ACCTTCTGGTTTTGCTGGCTA 59.855 47.619 0.00 0.00 46.05 3.93
664 4933 0.106015 ACCTTCTGGTTTTGCTGGCT 60.106 50.000 0.00 0.00 46.05 4.75
670 4939 1.007387 GCCGCACCTTCTGGTTTTG 60.007 57.895 0.00 0.00 46.05 2.44
783 5052 6.606069 TCACATTCGGGGGATTATAAATGAA 58.394 36.000 0.00 0.00 0.00 2.57
794 5072 0.404040 AAAGCTTCACATTCGGGGGA 59.596 50.000 0.00 0.00 0.00 4.81
922 5208 3.999001 CTCTCATTTGTACTGCTTGCTCA 59.001 43.478 0.00 0.00 0.00 4.26
924 5210 2.746362 GCTCTCATTTGTACTGCTTGCT 59.254 45.455 0.00 0.00 0.00 3.91
925 5211 2.485426 TGCTCTCATTTGTACTGCTTGC 59.515 45.455 0.00 0.00 0.00 4.01
926 5212 4.754372 TTGCTCTCATTTGTACTGCTTG 57.246 40.909 0.00 0.00 0.00 4.01
933 5219 6.092670 CGATCTTTCCTTTGCTCTCATTTGTA 59.907 38.462 0.00 0.00 0.00 2.41
934 5220 5.106396 CGATCTTTCCTTTGCTCTCATTTGT 60.106 40.000 0.00 0.00 0.00 2.83
935 5221 5.330295 CGATCTTTCCTTTGCTCTCATTTG 58.670 41.667 0.00 0.00 0.00 2.32
936 5222 4.142513 GCGATCTTTCCTTTGCTCTCATTT 60.143 41.667 0.00 0.00 0.00 2.32
939 5225 2.289631 TGCGATCTTTCCTTTGCTCTCA 60.290 45.455 0.00 0.00 0.00 3.27
940 5226 2.350522 TGCGATCTTTCCTTTGCTCTC 58.649 47.619 0.00 0.00 0.00 3.20
943 5229 2.746362 CTCTTGCGATCTTTCCTTTGCT 59.254 45.455 0.00 0.00 0.00 3.91
945 5231 3.338249 TCCTCTTGCGATCTTTCCTTTG 58.662 45.455 0.00 0.00 0.00 2.77
946 5232 3.604582 CTCCTCTTGCGATCTTTCCTTT 58.395 45.455 0.00 0.00 0.00 3.11
947 5233 2.679349 GCTCCTCTTGCGATCTTTCCTT 60.679 50.000 0.00 0.00 0.00 3.36
949 5235 1.134551 AGCTCCTCTTGCGATCTTTCC 60.135 52.381 0.00 0.00 35.28 3.13
953 5239 3.756739 CAAGCTCCTCTTGCGATCT 57.243 52.632 0.00 0.00 44.85 2.75
973 5259 8.894731 CGTGGATCTATAAATCTTAGCTAGCTA 58.105 37.037 20.67 20.67 0.00 3.32
1038 5347 2.509336 CCGTCGCTCATCGCCTTT 60.509 61.111 0.00 0.00 38.27 3.11
1421 5908 0.963355 GGTTTGGCCGGATGCTGTTA 60.963 55.000 5.05 0.00 40.92 2.41
1574 6067 1.228154 GTCGGTCTTGGTGCCCTTT 60.228 57.895 0.00 0.00 0.00 3.11
1905 6524 0.896940 ACTCGAAGCTCCCCGTGTTA 60.897 55.000 0.00 0.00 0.00 2.41
2005 6645 0.598562 ACCTGACTGACGTACTGCTG 59.401 55.000 0.00 0.00 0.00 4.41
2006 6646 0.598562 CACCTGACTGACGTACTGCT 59.401 55.000 0.00 0.00 0.00 4.24
2007 6647 0.388649 CCACCTGACTGACGTACTGC 60.389 60.000 0.00 0.00 0.00 4.40
2008 6648 0.243907 CCCACCTGACTGACGTACTG 59.756 60.000 0.00 0.00 0.00 2.74
2009 6649 1.533469 GCCCACCTGACTGACGTACT 61.533 60.000 0.00 0.00 0.00 2.73
2010 6650 1.080025 GCCCACCTGACTGACGTAC 60.080 63.158 0.00 0.00 0.00 3.67
2042 6682 3.255149 GGTGTCCTCGTAGAAGAAGTTGA 59.745 47.826 0.00 0.00 34.09 3.18
2065 6705 1.360192 GGAACTGCTGGTTGTGCAC 59.640 57.895 10.75 10.75 38.41 4.57
2114 6781 2.501223 TAGTTTCTGCTCCGGCACCG 62.501 60.000 1.02 1.02 44.28 4.94
2198 6865 2.194271 CCTCGACCTTGTAGAAATCGC 58.806 52.381 2.11 0.00 32.89 4.58
2348 7024 1.798368 CTAGCGTGTCGGCGAATTCG 61.798 60.000 23.34 23.34 43.27 3.34
2517 7208 8.135529 GCAGTTTTGAACTAAGGTTGAACTAAT 58.864 33.333 0.00 0.00 40.46 1.73
2650 7342 6.127253 ACTGATTGAATTAAAAGATGCCTGGG 60.127 38.462 0.00 0.00 0.00 4.45
2659 7351 9.850628 ATCACACATGACTGATTGAATTAAAAG 57.149 29.630 0.00 0.00 37.79 2.27
2794 7486 5.754782 ACAGGAGGAACATGCACATAATAA 58.245 37.500 0.00 0.00 33.22 1.40
2957 7653 3.719268 AGACATACATGTTCTTGCCCA 57.281 42.857 2.30 0.00 41.95 5.36
2999 7700 3.473625 AGCCAATAATACTTGTACGGGC 58.526 45.455 0.00 0.00 39.14 6.13
3006 7707 4.453819 GCTCCTGCTAGCCAATAATACTTG 59.546 45.833 13.29 0.00 36.45 3.16
3014 7715 5.163258 GGTATATATGCTCCTGCTAGCCAAT 60.163 44.000 13.29 0.00 42.05 3.16
3020 7721 5.589831 TCCTTGGTATATATGCTCCTGCTA 58.410 41.667 0.62 0.00 40.48 3.49
3045 7746 5.646606 ACACTTTTACATTTCGCTGTTTGT 58.353 33.333 0.00 0.00 0.00 2.83
3050 7751 6.559521 CGGAAAAACACTTTTACATTTCGCTG 60.560 38.462 0.00 0.00 35.37 5.18
3052 7753 5.652699 CGGAAAAACACTTTTACATTTCGC 58.347 37.500 0.00 0.00 35.37 4.70
3053 7754 5.230306 TGCGGAAAAACACTTTTACATTTCG 59.770 36.000 0.00 0.00 35.37 3.46
3075 7778 8.761575 TCTGAAATTGATAAGAAATTTGGTGC 57.238 30.769 0.00 0.00 37.35 5.01
3093 7796 6.959639 TTTTTGCTCACCTAACTCTGAAAT 57.040 33.333 0.00 0.00 0.00 2.17
3105 7808 6.961554 CGTAGAACTGATTATTTTTGCTCACC 59.038 38.462 0.00 0.00 0.00 4.02
3130 7833 0.863119 GAGCGACAAAATGGATGCGC 60.863 55.000 0.00 0.00 40.80 6.09
3139 7842 5.815740 GGTGATAAATCTAGGAGCGACAAAA 59.184 40.000 0.00 0.00 0.00 2.44
3175 7878 3.087253 TATGACCTGTGGGCGGGG 61.087 66.667 0.00 0.00 45.50 5.73
3176 7879 2.189521 GTATGACCTGTGGGCGGG 59.810 66.667 0.00 0.00 46.63 6.13
3177 7880 0.322098 TTTGTATGACCTGTGGGCGG 60.322 55.000 0.00 0.00 35.63 6.13
3185 7888 1.890876 TGCGCAGTTTTGTATGACCT 58.109 45.000 5.66 0.00 0.00 3.85
3186 7889 2.161410 TCATGCGCAGTTTTGTATGACC 59.839 45.455 18.32 0.00 0.00 4.02
3198 7901 1.904144 CAACCAAAGATCATGCGCAG 58.096 50.000 18.32 8.46 0.00 5.18
3219 7922 5.220265 CCAATCAAATGTTTAGATTGCGCAC 60.220 40.000 11.12 0.00 44.40 5.34
3223 7926 5.581874 CCACCCAATCAAATGTTTAGATTGC 59.418 40.000 16.48 0.00 44.40 3.56
3246 7949 7.701809 TTTTCGTTGGTAAATGACAAAATCC 57.298 32.000 0.00 0.00 30.90 3.01
3247 7950 9.579610 CATTTTTCGTTGGTAAATGACAAAATC 57.420 29.630 0.00 0.00 40.14 2.17


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

AutoCloner maintained by Alex Coulton.