Multiple sequence alignment - TraesCS5B01G235600

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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 TraesCS5B01G235600 chr5B 100.000 4931 0 0 1 4931 415991777 415996707 0.000000e+00 9106.0
1 TraesCS5B01G235600 chr5B 90.099 101 9 1 2477 2576 508775502 508775602 4.010000e-26 130.0
2 TraesCS5B01G235600 chr5D 97.555 2658 46 3 441 3089 352929012 352931659 0.000000e+00 4530.0
3 TraesCS5B01G235600 chr5D 96.494 1141 21 5 3085 4212 352931963 352933097 0.000000e+00 1868.0
4 TraesCS5B01G235600 chr5D 93.730 319 17 3 4207 4522 352933127 352933445 4.470000e-130 475.0
5 TraesCS5B01G235600 chr5D 90.698 301 17 3 1 292 352928414 352928712 1.660000e-104 390.0
6 TraesCS5B01G235600 chr5D 92.982 228 14 2 4521 4747 352933600 352933826 1.020000e-86 331.0
7 TraesCS5B01G235600 chr5D 93.684 95 3 1 342 433 352928821 352928915 6.660000e-29 139.0
8 TraesCS5B01G235600 chr5D 89.109 101 10 1 2477 2576 282007018 282007118 1.860000e-24 124.0
9 TraesCS5B01G235600 chr5D 90.476 63 3 2 3537 3598 398490699 398490639 4.090000e-11 80.5
10 TraesCS5B01G235600 chr5A 93.918 1677 53 11 342 1974 452938234 452936563 0.000000e+00 2486.0
11 TraesCS5B01G235600 chr5A 93.084 1229 56 8 3005 4213 452935329 452934110 0.000000e+00 1772.0
12 TraesCS5B01G235600 chr5A 88.333 360 27 9 2641 2997 452935732 452935385 7.630000e-113 418.0
13 TraesCS5B01G235600 chr5A 88.411 302 25 5 1 292 452938645 452938344 6.070000e-94 355.0
14 TraesCS5B01G235600 chr5A 90.980 255 14 3 1978 2224 452936472 452936219 7.910000e-88 335.0
15 TraesCS5B01G235600 chr5A 80.443 271 24 11 2223 2477 452936114 452935857 3.920000e-41 180.0
16 TraesCS5B01G235600 chr5A 94.186 86 5 0 4657 4742 452933795 452933710 1.110000e-26 132.0
17 TraesCS5B01G235600 chr5A 91.667 60 4 1 3539 3598 546771306 546771364 1.140000e-11 82.4
18 TraesCS5B01G235600 chr5A 91.379 58 5 0 2993 3050 452935442 452935385 4.090000e-11 80.5
19 TraesCS5B01G235600 chr5A 100.000 35 0 0 2985 3019 452935375 452935341 1.150000e-06 65.8
20 TraesCS5B01G235600 chr3B 81.324 423 51 18 4079 4480 274669695 274669280 7.970000e-83 318.0
21 TraesCS5B01G235600 chr3B 80.465 430 54 20 4074 4480 21928462 21928884 8.020000e-78 302.0
22 TraesCS5B01G235600 chr3B 87.156 109 12 2 2477 2583 612410671 612410563 6.700000e-24 122.0
23 TraesCS5B01G235600 chr3B 91.935 62 4 1 3541 3602 94493052 94493112 8.790000e-13 86.1
24 TraesCS5B01G235600 chr3B 90.625 64 5 1 3537 3599 351291192 351291129 3.160000e-12 84.2
25 TraesCS5B01G235600 chr7B 90.099 101 9 1 2477 2576 716493531 716493431 4.010000e-26 130.0
26 TraesCS5B01G235600 chr7B 100.000 28 0 0 4804 4831 714252000 714252027 9.000000e-03 52.8
27 TraesCS5B01G235600 chr2D 89.109 101 10 1 2477 2576 473292205 473292305 1.860000e-24 124.0
28 TraesCS5B01G235600 chr2A 89.000 100 7 4 2485 2582 469789773 469789676 2.410000e-23 121.0
29 TraesCS5B01G235600 chr2A 88.235 102 9 3 2477 2576 727238672 727238772 8.670000e-23 119.0
30 TraesCS5B01G235600 chr2A 80.315 127 19 4 4533 4656 178180253 178180376 1.890000e-14 91.6
31 TraesCS5B01G235600 chr6D 86.364 110 12 3 2477 2584 391925885 391925993 3.120000e-22 117.0
32 TraesCS5B01G235600 chr6D 91.667 60 4 1 3541 3599 33901460 33901519 1.140000e-11 82.4
33 TraesCS5B01G235600 chr7A 90.476 63 4 1 3538 3598 281374332 281374270 1.140000e-11 82.4
34 TraesCS5B01G235600 chr4B 91.525 59 5 0 3539 3597 672320178 672320120 1.140000e-11 82.4


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 TraesCS5B01G235600 chr5B 415991777 415996707 4930 False 9106.000000 9106 100.000000 1 4931 1 chr5B.!!$F1 4930
1 TraesCS5B01G235600 chr5D 352928414 352933826 5412 False 1288.833333 4530 94.190500 1 4747 6 chr5D.!!$F2 4746
2 TraesCS5B01G235600 chr5A 452933710 452938645 4935 True 647.144444 2486 91.192667 1 4742 9 chr5A.!!$R1 4741

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
972 1156 0.097150 GCGGTTTGAGGCGAATTCTC 59.903 55.000 3.52 0.00 0.00 2.87 F
973 1157 1.726853 CGGTTTGAGGCGAATTCTCT 58.273 50.000 3.52 0.89 32.78 3.10 F
974 1158 2.076863 CGGTTTGAGGCGAATTCTCTT 58.923 47.619 3.52 0.00 32.78 2.85 F
1015 1199 2.087646 GTTTGATGCTCAAGGAGGACC 58.912 52.381 0.00 0.00 37.70 4.46 F
2452 2859 3.509442 TCAATTTTCAGGGTGATGGCTT 58.491 40.909 0.00 0.00 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2042 2327 0.320771 TGAGCTTCTGAACTTCGGCC 60.321 55.000 0.00 0.0 0.0 6.13 R
2407 2814 2.226437 AGGCAAATTACTGCGACAACAG 59.774 45.455 0.00 0.0 43.6 3.16 R
2973 3448 2.781681 AAAGGCATGCTTAGTACCGT 57.218 45.000 18.92 0.0 0.0 4.83 R
3177 4008 5.518812 TGTGAAGTCATCGAAAAACATTGG 58.481 37.500 0.00 0.0 0.0 3.16 R
4387 5282 0.802494 AGCGTGCTTGATAAAACCCG 59.198 50.000 0.00 0.0 0.0 5.28 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
19 20 2.254546 AACGTTCAAGAGGACATGCA 57.745 45.000 0.00 0.00 0.00 3.96
59 60 2.965831 AGAAATAGATAGAGCGGCCACA 59.034 45.455 2.24 0.00 0.00 4.17
100 101 2.031420 GGTTCCCTTACGCAAAGTTGTC 60.031 50.000 0.00 0.00 32.89 3.18
184 185 0.608856 TTCTGCGGCATCAACCATGT 60.609 50.000 1.75 0.00 34.56 3.21
192 202 2.297033 GGCATCAACCATGTGAACTTGT 59.703 45.455 0.00 0.00 34.56 3.16
206 216 2.355837 TTGTGTCTCCGCGAGTGC 60.356 61.111 8.23 2.25 37.91 4.40
249 260 3.845178 TGTCGTCGCATGTAGAAAAGAT 58.155 40.909 0.00 0.00 0.00 2.40
260 271 9.941664 CGCATGTAGAAAAGATAATGAAGATTT 57.058 29.630 0.00 0.00 0.00 2.17
306 317 8.719560 AAATGTGCATTGATATTAATTGCACA 57.280 26.923 31.62 31.62 46.29 4.57
307 318 7.703298 ATGTGCATTGATATTAATTGCACAC 57.297 32.000 31.92 19.16 45.78 3.82
308 319 6.628185 TGTGCATTGATATTAATTGCACACA 58.372 32.000 28.45 18.99 42.71 3.72
309 320 7.095270 TGTGCATTGATATTAATTGCACACAA 58.905 30.769 28.45 14.77 42.71 3.33
311 322 8.059502 GTGCATTGATATTAATTGCACACAATG 58.940 33.333 26.23 20.40 45.90 2.82
312 323 7.224949 TGCATTGATATTAATTGCACACAATGG 59.775 33.333 20.05 10.08 45.90 3.16
314 325 9.483916 CATTGATATTAATTGCACACAATGGAT 57.516 29.630 0.00 0.00 45.90 3.41
316 327 9.887629 TTGATATTAATTGCACACAATGGATTT 57.112 25.926 0.00 0.00 45.90 2.17
317 328 9.315525 TGATATTAATTGCACACAATGGATTTG 57.684 29.630 0.00 0.00 45.90 2.32
318 329 9.531942 GATATTAATTGCACACAATGGATTTGA 57.468 29.630 0.00 0.00 45.90 2.69
319 330 7.599630 ATTAATTGCACACAATGGATTTGAC 57.400 32.000 0.00 0.00 45.90 3.18
320 331 4.603989 ATTGCACACAATGGATTTGACA 57.396 36.364 0.00 0.00 44.90 3.58
321 332 4.397481 TTGCACACAATGGATTTGACAA 57.603 36.364 0.00 0.00 38.76 3.18
322 333 4.397481 TGCACACAATGGATTTGACAAA 57.603 36.364 2.48 2.48 38.76 2.83
353 424 6.750039 TGTTTCTACAGCTGTTTTTAGTTTGC 59.250 34.615 27.06 8.82 0.00 3.68
423 497 9.573133 TGTTCTTTTCTTTGAAAGAGAAACATC 57.427 29.630 11.35 4.68 44.05 3.06
560 723 4.087892 CAGGGCCCCACGTCTGAG 62.088 72.222 21.43 0.00 0.00 3.35
701 864 1.202452 GCCCGCCACGTAGTATTAACT 60.202 52.381 0.00 0.00 41.61 2.24
899 1083 0.251832 TCACCCACCACTCTCTCTCC 60.252 60.000 0.00 0.00 0.00 3.71
970 1154 0.179189 CTGCGGTTTGAGGCGAATTC 60.179 55.000 0.00 0.00 0.00 2.17
971 1155 0.605319 TGCGGTTTGAGGCGAATTCT 60.605 50.000 3.52 0.00 0.00 2.40
972 1156 0.097150 GCGGTTTGAGGCGAATTCTC 59.903 55.000 3.52 0.00 0.00 2.87
973 1157 1.726853 CGGTTTGAGGCGAATTCTCT 58.273 50.000 3.52 0.89 32.78 3.10
974 1158 2.076863 CGGTTTGAGGCGAATTCTCTT 58.923 47.619 3.52 0.00 32.78 2.85
1015 1199 2.087646 GTTTGATGCTCAAGGAGGACC 58.912 52.381 0.00 0.00 37.70 4.46
2042 2327 4.818546 CAGGCTTATACAATGGAGTTGGAG 59.181 45.833 0.00 0.00 42.28 3.86
2452 2859 3.509442 TCAATTTTCAGGGTGATGGCTT 58.491 40.909 0.00 0.00 0.00 4.35
2973 3448 8.873186 TCTTATGGATGGTATATTAGACGTCA 57.127 34.615 19.50 0.00 0.00 4.35
3286 4117 8.608844 ACTAAATTCAGAGTTAGAACAACTGG 57.391 34.615 14.79 5.49 37.01 4.00
3305 4136 9.023962 ACAACTGGCATTATTTTTCTGAGATTA 57.976 29.630 0.00 0.00 0.00 1.75
4021 4867 0.396435 AACCGATGACCTGTGCTTGA 59.604 50.000 0.00 0.00 0.00 3.02
4097 4943 1.000019 TGTGTAGTCGAGGAGGGGG 60.000 63.158 0.00 0.00 0.00 5.40
4208 5057 3.746492 TCTTCTTCTAACTTTGCGCCTTC 59.254 43.478 4.18 0.00 0.00 3.46
4209 5058 3.120321 TCTTCTAACTTTGCGCCTTCA 57.880 42.857 4.18 0.00 0.00 3.02
4210 5059 3.067106 TCTTCTAACTTTGCGCCTTCAG 58.933 45.455 4.18 0.00 0.00 3.02
4261 5145 0.899717 AACGTCCTACACCCGGCTTA 60.900 55.000 0.00 0.00 0.00 3.09
4266 5150 1.483415 TCCTACACCCGGCTTAATGTC 59.517 52.381 0.00 0.00 0.00 3.06
4273 5157 1.583054 CCGGCTTAATGTCTGGCTAC 58.417 55.000 0.00 0.00 0.00 3.58
4314 5198 4.394729 TCCTGTTGGCTGTAGTTTTAAGG 58.605 43.478 0.00 0.00 0.00 2.69
4322 5206 2.159382 TGTAGTTTTAAGGCTGGCTGC 58.841 47.619 3.84 7.96 41.94 5.25
4355 5249 6.481954 ACGGTAGTTGTCAGATTTTGAATC 57.518 37.500 0.00 0.00 37.61 2.52
4362 5256 3.057596 TGTCAGATTTTGAATCCGTTGCC 60.058 43.478 0.00 0.00 37.61 4.52
4385 5280 6.205464 GCCTATATCTGCTCTTGTTAATTGCA 59.795 38.462 0.00 0.00 0.00 4.08
4387 5282 8.449397 CCTATATCTGCTCTTGTTAATTGCATC 58.551 37.037 0.00 0.00 33.02 3.91
4540 5592 9.734620 TGCTTATATTTTGCATGACAATAGAAC 57.265 29.630 0.00 0.00 38.31 3.01
4545 5597 9.740239 ATATTTTGCATGACAATAGAACATCAC 57.260 29.630 0.00 0.00 38.31 3.06
4546 5598 5.565592 TTGCATGACAATAGAACATCACC 57.434 39.130 0.00 0.00 31.73 4.02
4615 5668 0.248296 TGCTTTCGCGTGGTTTTCAC 60.248 50.000 5.77 0.00 42.74 3.18
4731 5784 1.466167 CAGAGTTTTCAGACATGCCCG 59.534 52.381 0.00 0.00 0.00 6.13
4747 5800 0.595053 CCCGAATCATCTGTCCGTCG 60.595 60.000 0.00 0.00 0.00 5.12
4748 5801 0.100682 CCGAATCATCTGTCCGTCGT 59.899 55.000 0.00 0.00 0.00 4.34
4749 5802 1.469251 CCGAATCATCTGTCCGTCGTT 60.469 52.381 0.00 0.00 0.00 3.85
4750 5803 2.259618 CGAATCATCTGTCCGTCGTTT 58.740 47.619 0.00 0.00 0.00 3.60
4751 5804 2.666508 CGAATCATCTGTCCGTCGTTTT 59.333 45.455 0.00 0.00 0.00 2.43
4752 5805 3.122948 CGAATCATCTGTCCGTCGTTTTT 59.877 43.478 0.00 0.00 0.00 1.94
4785 5838 9.561069 AGTGAAGTTTGTTTATAGACATGAGTT 57.439 29.630 0.00 0.00 0.00 3.01
4794 5847 9.653287 TGTTTATAGACATGAGTTTTCTAGTGG 57.347 33.333 0.00 0.00 0.00 4.00
4795 5848 9.654663 GTTTATAGACATGAGTTTTCTAGTGGT 57.345 33.333 0.00 0.00 0.00 4.16
4799 5852 7.881775 AGACATGAGTTTTCTAGTGGTTTTT 57.118 32.000 0.00 0.00 0.00 1.94
4823 5876 9.902684 TTTTTAATATACACCCTCCGTTCATAA 57.097 29.630 0.00 0.00 0.00 1.90
4824 5877 9.902684 TTTTAATATACACCCTCCGTTCATAAA 57.097 29.630 0.00 0.00 0.00 1.40
4831 5884 7.369551 ACACCCTCCGTTCATAAATATAAGA 57.630 36.000 0.00 0.00 0.00 2.10
4832 5885 7.974504 ACACCCTCCGTTCATAAATATAAGAT 58.025 34.615 0.00 0.00 0.00 2.40
4833 5886 7.878127 ACACCCTCCGTTCATAAATATAAGATG 59.122 37.037 0.00 0.00 0.00 2.90
4834 5887 7.878127 CACCCTCCGTTCATAAATATAAGATGT 59.122 37.037 0.00 0.00 0.00 3.06
4835 5888 7.878127 ACCCTCCGTTCATAAATATAAGATGTG 59.122 37.037 0.00 0.00 0.00 3.21
4836 5889 7.148407 CCCTCCGTTCATAAATATAAGATGTGC 60.148 40.741 0.00 0.00 0.00 4.57
4837 5890 7.604164 CCTCCGTTCATAAATATAAGATGTGCT 59.396 37.037 0.00 0.00 0.00 4.40
4838 5891 9.639601 CTCCGTTCATAAATATAAGATGTGCTA 57.360 33.333 0.00 0.00 0.00 3.49
4839 5892 9.990360 TCCGTTCATAAATATAAGATGTGCTAA 57.010 29.630 0.00 0.00 0.00 3.09
4891 5944 6.511416 CACATTTTAGTGTTCACCCATTTCA 58.489 36.000 0.00 0.00 34.83 2.69
4892 5945 6.642131 CACATTTTAGTGTTCACCCATTTCAG 59.358 38.462 0.00 0.00 34.83 3.02
4893 5946 6.323739 ACATTTTAGTGTTCACCCATTTCAGT 59.676 34.615 0.00 0.00 0.00 3.41
4894 5947 6.385649 TTTTAGTGTTCACCCATTTCAGTC 57.614 37.500 0.00 0.00 0.00 3.51
4895 5948 2.863809 AGTGTTCACCCATTTCAGTCC 58.136 47.619 0.00 0.00 0.00 3.85
4896 5949 1.535462 GTGTTCACCCATTTCAGTCCG 59.465 52.381 0.00 0.00 0.00 4.79
4897 5950 0.521735 GTTCACCCATTTCAGTCCGC 59.478 55.000 0.00 0.00 0.00 5.54
4898 5951 0.109532 TTCACCCATTTCAGTCCGCA 59.890 50.000 0.00 0.00 0.00 5.69
4899 5952 0.327924 TCACCCATTTCAGTCCGCAT 59.672 50.000 0.00 0.00 0.00 4.73
4900 5953 1.557371 TCACCCATTTCAGTCCGCATA 59.443 47.619 0.00 0.00 0.00 3.14
4901 5954 2.172505 TCACCCATTTCAGTCCGCATAT 59.827 45.455 0.00 0.00 0.00 1.78
4902 5955 3.389656 TCACCCATTTCAGTCCGCATATA 59.610 43.478 0.00 0.00 0.00 0.86
4903 5956 3.748048 CACCCATTTCAGTCCGCATATAG 59.252 47.826 0.00 0.00 0.00 1.31
4904 5957 3.391296 ACCCATTTCAGTCCGCATATAGT 59.609 43.478 0.00 0.00 0.00 2.12
4905 5958 3.748048 CCCATTTCAGTCCGCATATAGTG 59.252 47.826 0.00 0.00 0.00 2.74
4928 5981 9.139734 AGTGCATATTCAAATATCCAAACATCT 57.860 29.630 0.00 0.00 29.35 2.90
4929 5982 9.754382 GTGCATATTCAAATATCCAAACATCTT 57.246 29.630 0.00 0.00 29.35 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 5.723672 TTCTTCTTCGGTAGTTGAGTGAT 57.276 39.130 0.00 0.00 0.00 3.06
100 101 1.548081 TGGTGATGCAACCCTTCATG 58.452 50.000 5.11 0.00 39.70 3.07
154 155 0.872021 GCCGCAGAATAGAGTCACCG 60.872 60.000 0.00 0.00 0.00 4.94
184 185 0.318699 CTCGCGGAGACACAAGTTCA 60.319 55.000 6.13 0.00 0.00 3.18
192 202 1.372997 GAAAGCACTCGCGGAGACA 60.373 57.895 6.13 0.00 45.49 3.41
231 242 6.510746 TCATTATCTTTTCTACATGCGACG 57.489 37.500 0.00 0.00 0.00 5.12
292 303 9.531942 TCAAATCCATTGTGTGCAATTAATATC 57.468 29.630 0.00 0.00 42.91 1.63
294 305 8.309656 TGTCAAATCCATTGTGTGCAATTAATA 58.690 29.630 0.00 0.00 42.91 0.98
295 306 7.160049 TGTCAAATCCATTGTGTGCAATTAAT 58.840 30.769 0.00 0.00 42.91 1.40
296 307 6.519382 TGTCAAATCCATTGTGTGCAATTAA 58.481 32.000 0.00 0.00 42.91 1.40
297 308 6.094193 TGTCAAATCCATTGTGTGCAATTA 57.906 33.333 0.00 0.00 42.91 1.40
299 310 4.603989 TGTCAAATCCATTGTGTGCAAT 57.396 36.364 0.00 0.00 45.42 3.56
301 312 4.397481 TTTGTCAAATCCATTGTGTGCA 57.603 36.364 0.00 0.00 40.11 4.57
321 332 8.546597 AAAAACAGCTGTAGAAACACATTTTT 57.453 26.923 22.01 15.21 0.00 1.94
322 333 9.301153 CTAAAAACAGCTGTAGAAACACATTTT 57.699 29.630 22.01 19.86 0.00 1.82
325 336 7.568199 ACTAAAAACAGCTGTAGAAACACAT 57.432 32.000 22.01 0.00 0.00 3.21
329 340 6.972901 AGCAAACTAAAAACAGCTGTAGAAAC 59.027 34.615 22.01 6.56 0.00 2.78
330 341 7.095695 AGCAAACTAAAAACAGCTGTAGAAA 57.904 32.000 22.01 5.75 0.00 2.52
331 342 6.693315 AGCAAACTAAAAACAGCTGTAGAA 57.307 33.333 22.01 5.37 0.00 2.10
332 343 6.693315 AAGCAAACTAAAAACAGCTGTAGA 57.307 33.333 22.01 4.77 31.88 2.59
334 345 7.865385 CCAATAAGCAAACTAAAAACAGCTGTA 59.135 33.333 22.01 2.85 31.88 2.74
338 349 7.477144 AACCAATAAGCAAACTAAAAACAGC 57.523 32.000 0.00 0.00 0.00 4.40
353 424 8.631480 AACCTTGGAGTAGTTTAACCAATAAG 57.369 34.615 0.00 0.00 40.78 1.73
433 507 7.654520 GGGGGTTTTGTTCTTTACAATTTCTAC 59.345 37.037 0.00 0.00 45.72 2.59
435 509 6.385759 AGGGGGTTTTGTTCTTTACAATTTCT 59.614 34.615 0.00 0.00 45.72 2.52
436 510 6.481976 CAGGGGGTTTTGTTCTTTACAATTTC 59.518 38.462 0.00 0.00 45.72 2.17
437 511 6.353323 CAGGGGGTTTTGTTCTTTACAATTT 58.647 36.000 0.00 0.00 45.72 1.82
438 512 5.686387 GCAGGGGGTTTTGTTCTTTACAATT 60.686 40.000 0.00 0.00 45.72 2.32
439 513 4.202315 GCAGGGGGTTTTGTTCTTTACAAT 60.202 41.667 0.00 0.00 45.72 2.71
899 1083 3.879295 GAGACAGATGAGACAGAGAGAGG 59.121 52.174 0.00 0.00 0.00 3.69
970 1154 0.814457 CGGACACCAGGAGAGAAGAG 59.186 60.000 0.00 0.00 0.00 2.85
971 1155 0.112606 ACGGACACCAGGAGAGAAGA 59.887 55.000 0.00 0.00 0.00 2.87
972 1156 0.244994 CACGGACACCAGGAGAGAAG 59.755 60.000 0.00 0.00 0.00 2.85
973 1157 0.469331 ACACGGACACCAGGAGAGAA 60.469 55.000 0.00 0.00 0.00 2.87
974 1158 0.894184 GACACGGACACCAGGAGAGA 60.894 60.000 0.00 0.00 0.00 3.10
1750 1940 3.468326 GATCCTCGCTCCCCTTGCC 62.468 68.421 0.00 0.00 0.00 4.52
2042 2327 0.320771 TGAGCTTCTGAACTTCGGCC 60.321 55.000 0.00 0.00 0.00 6.13
2407 2814 2.226437 AGGCAAATTACTGCGACAACAG 59.774 45.455 0.00 0.00 43.60 3.16
2452 2859 8.579850 AGCAACACTTCCAAATATGAGAATAA 57.420 30.769 0.00 0.00 0.00 1.40
2525 2932 6.635641 CGCTTAAACGAATGTATCTAGCACTA 59.364 38.462 0.00 0.00 34.06 2.74
2973 3448 2.781681 AAAGGCATGCTTAGTACCGT 57.218 45.000 18.92 0.00 0.00 4.83
3177 4008 5.518812 TGTGAAGTCATCGAAAAACATTGG 58.481 37.500 0.00 0.00 0.00 3.16
3350 4181 2.645510 CGACTTCGACACCACGCAC 61.646 63.158 0.00 0.00 43.02 5.34
4021 4867 5.248380 AGAAAGGAAACTAGCAGGTCAAT 57.752 39.130 0.00 0.00 42.68 2.57
4208 5057 6.422100 CCCATGACTTACTTACATCGATTCTG 59.578 42.308 0.00 0.00 0.00 3.02
4209 5058 6.323996 TCCCATGACTTACTTACATCGATTCT 59.676 38.462 0.00 0.00 0.00 2.40
4210 5059 6.513180 TCCCATGACTTACTTACATCGATTC 58.487 40.000 0.00 0.00 0.00 2.52
4261 5145 1.899814 TCGGTTGAGTAGCCAGACATT 59.100 47.619 0.00 0.00 0.00 2.71
4266 5150 2.457366 AACTTCGGTTGAGTAGCCAG 57.543 50.000 0.00 0.00 36.72 4.85
4273 5157 8.765219 CAACAGGATATATAAACTTCGGTTGAG 58.235 37.037 0.00 0.00 38.30 3.02
4314 5198 3.271706 TTGAACGCATGCAGCCAGC 62.272 57.895 19.57 0.82 45.96 4.85
4355 5249 3.062763 CAAGAGCAGATATAGGCAACGG 58.937 50.000 1.43 0.00 46.39 4.44
4362 5256 8.167345 CGATGCAATTAACAAGAGCAGATATAG 58.833 37.037 0.00 0.00 38.75 1.31
4385 5280 1.400494 GCGTGCTTGATAAAACCCGAT 59.600 47.619 0.00 0.00 0.00 4.18
4387 5282 0.802494 AGCGTGCTTGATAAAACCCG 59.198 50.000 0.00 0.00 0.00 5.28
4504 5400 6.790282 TGCAAAATATAAGCAACGCATTCTA 58.210 32.000 0.00 0.00 34.97 2.10
4506 5402 5.947503 TGCAAAATATAAGCAACGCATTC 57.052 34.783 0.00 0.00 34.97 2.67
4546 5598 3.518992 AAATATGGGATGTTACGGGGG 57.481 47.619 0.00 0.00 0.00 5.40
4577 5630 7.410087 CGAAAGCAATGTTATGAAGCTTCAAAG 60.410 37.037 31.55 16.61 44.03 2.77
4634 5687 7.988028 GCATAGGGAGAGTATAATATGGAAACC 59.012 40.741 0.00 0.00 0.00 3.27
4639 5692 8.643324 GGTTAGCATAGGGAGAGTATAATATGG 58.357 40.741 0.00 0.00 0.00 2.74
4649 5702 2.964209 TCCTGGTTAGCATAGGGAGAG 58.036 52.381 0.00 0.00 32.39 3.20
4731 5784 4.663636 AAAAACGACGGACAGATGATTC 57.336 40.909 0.00 0.00 0.00 2.52
4759 5812 9.561069 AACTCATGTCTATAAACAAACTTCACT 57.439 29.630 0.00 0.00 31.81 3.41
4768 5821 9.653287 CCACTAGAAAACTCATGTCTATAAACA 57.347 33.333 0.00 0.00 0.00 2.83
4769 5822 9.654663 ACCACTAGAAAACTCATGTCTATAAAC 57.345 33.333 0.00 0.00 0.00 2.01
4773 5826 9.574516 AAAAACCACTAGAAAACTCATGTCTAT 57.425 29.630 0.00 0.00 0.00 1.98
4774 5827 8.974060 AAAAACCACTAGAAAACTCATGTCTA 57.026 30.769 0.00 0.00 0.00 2.59
4775 5828 7.881775 AAAAACCACTAGAAAACTCATGTCT 57.118 32.000 0.00 0.00 0.00 3.41
4797 5850 9.902684 TTATGAACGGAGGGTGTATATTAAAAA 57.097 29.630 0.00 0.00 0.00 1.94
4798 5851 9.902684 TTTATGAACGGAGGGTGTATATTAAAA 57.097 29.630 0.00 0.00 0.00 1.52
4805 5858 9.096823 TCTTATATTTATGAACGGAGGGTGTAT 57.903 33.333 0.00 0.00 0.00 2.29
4806 5859 8.481492 TCTTATATTTATGAACGGAGGGTGTA 57.519 34.615 0.00 0.00 0.00 2.90
4807 5860 7.369551 TCTTATATTTATGAACGGAGGGTGT 57.630 36.000 0.00 0.00 0.00 4.16
4808 5861 7.878127 ACATCTTATATTTATGAACGGAGGGTG 59.122 37.037 0.00 0.00 0.00 4.61
4809 5862 7.878127 CACATCTTATATTTATGAACGGAGGGT 59.122 37.037 0.00 0.00 0.00 4.34
4810 5863 7.148407 GCACATCTTATATTTATGAACGGAGGG 60.148 40.741 0.00 0.00 0.00 4.30
4811 5864 7.604164 AGCACATCTTATATTTATGAACGGAGG 59.396 37.037 0.00 0.00 0.00 4.30
4812 5865 8.539770 AGCACATCTTATATTTATGAACGGAG 57.460 34.615 0.00 0.00 0.00 4.63
4813 5866 9.990360 TTAGCACATCTTATATTTATGAACGGA 57.010 29.630 0.00 0.00 0.00 4.69
4867 5920 6.511416 TGAAATGGGTGAACACTAAAATGTG 58.489 36.000 4.96 0.00 43.07 3.21
4868 5921 6.323739 ACTGAAATGGGTGAACACTAAAATGT 59.676 34.615 4.96 0.00 0.00 2.71
4869 5922 6.748132 ACTGAAATGGGTGAACACTAAAATG 58.252 36.000 4.96 0.00 0.00 2.32
4870 5923 6.015434 GGACTGAAATGGGTGAACACTAAAAT 60.015 38.462 4.96 0.00 0.00 1.82
4871 5924 5.300792 GGACTGAAATGGGTGAACACTAAAA 59.699 40.000 4.96 0.00 0.00 1.52
4872 5925 4.825085 GGACTGAAATGGGTGAACACTAAA 59.175 41.667 4.96 0.00 0.00 1.85
4873 5926 4.394729 GGACTGAAATGGGTGAACACTAA 58.605 43.478 4.96 0.00 0.00 2.24
4874 5927 3.556213 CGGACTGAAATGGGTGAACACTA 60.556 47.826 4.96 0.00 0.00 2.74
4875 5928 2.810400 CGGACTGAAATGGGTGAACACT 60.810 50.000 4.96 0.00 0.00 3.55
4876 5929 1.535462 CGGACTGAAATGGGTGAACAC 59.465 52.381 0.00 0.00 0.00 3.32
4877 5930 1.890876 CGGACTGAAATGGGTGAACA 58.109 50.000 0.00 0.00 0.00 3.18
4878 5931 0.521735 GCGGACTGAAATGGGTGAAC 59.478 55.000 0.00 0.00 0.00 3.18
4879 5932 0.109532 TGCGGACTGAAATGGGTGAA 59.890 50.000 0.00 0.00 0.00 3.18
4880 5933 0.327924 ATGCGGACTGAAATGGGTGA 59.672 50.000 0.00 0.00 0.00 4.02
4881 5934 2.036958 TATGCGGACTGAAATGGGTG 57.963 50.000 0.00 0.00 0.00 4.61
4882 5935 3.391296 ACTATATGCGGACTGAAATGGGT 59.609 43.478 0.00 0.00 0.00 4.51
4883 5936 3.748048 CACTATATGCGGACTGAAATGGG 59.252 47.826 0.00 0.00 0.00 4.00
4884 5937 3.187227 GCACTATATGCGGACTGAAATGG 59.813 47.826 0.00 0.00 46.55 3.16
4885 5938 4.395581 GCACTATATGCGGACTGAAATG 57.604 45.455 0.00 0.00 46.55 2.32
4902 5955 9.139734 AGATGTTTGGATATTTGAATATGCACT 57.860 29.630 14.86 7.91 45.43 4.40
4903 5956 9.754382 AAGATGTTTGGATATTTGAATATGCAC 57.246 29.630 14.86 7.72 45.43 4.57


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

AutoCloner maintained by Alex Coulton.