Multiple sequence alignment - TraesCS5B01G173000

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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 TraesCS5B01G173000 chr5B 100.000 4579 0 0 1 4579 317889437 317884859 0.000000e+00 8456.0
1 TraesCS5B01G173000 chr5B 97.010 301 9 0 4278 4578 324614480 324614780 1.470000e-139 507.0
2 TraesCS5B01G173000 chr5B 95.341 279 11 1 3997 4273 324597373 324597651 4.200000e-120 442.0
3 TraesCS5B01G173000 chr5B 83.178 107 12 5 4169 4272 614834803 614834906 4.880000e-15 93.5
4 TraesCS5B01G173000 chr5A 95.306 3451 86 20 731 4144 372931278 372934689 0.000000e+00 5406.0
5 TraesCS5B01G173000 chr5D 96.339 2595 53 16 1448 4007 280307428 280304841 0.000000e+00 4228.0
6 TraesCS5B01G173000 chr5D 97.339 451 8 2 1012 1459 280309743 280309294 0.000000e+00 763.0
7 TraesCS5B01G173000 chr5D 94.865 370 14 5 3915 4281 280304846 280304479 1.430000e-159 573.0
8 TraesCS5B01G173000 chr5D 94.702 302 7 2 4278 4579 280304312 280304020 1.160000e-125 460.0
9 TraesCS5B01G173000 chr3D 90.723 733 63 3 1 728 5057560 5058292 0.000000e+00 972.0
10 TraesCS5B01G173000 chr3D 80.544 735 134 7 1 728 468968117 468968849 1.440000e-154 556.0
11 TraesCS5B01G173000 chr3D 84.112 107 12 3 4173 4279 342717356 342717255 1.050000e-16 99.0
12 TraesCS5B01G173000 chr4A 89.139 755 75 5 1 748 86461166 86460412 0.000000e+00 933.0
13 TraesCS5B01G173000 chr4A 88.904 730 75 4 1 728 13290341 13291066 0.000000e+00 894.0
14 TraesCS5B01G173000 chr1A 88.798 732 78 3 1 730 489153669 489152940 0.000000e+00 894.0
15 TraesCS5B01G173000 chr1A 77.205 737 149 17 3 727 171042316 171043045 3.300000e-111 412.0
16 TraesCS5B01G173000 chr4B 82.466 730 118 7 8 730 72165306 72164580 8.360000e-177 630.0
17 TraesCS5B01G173000 chr4B 89.908 109 8 2 4172 4279 439317133 439317239 2.220000e-28 137.0
18 TraesCS5B01G173000 chr7A 80.628 733 133 7 1 727 513369259 513368530 4.000000e-155 558.0
19 TraesCS5B01G173000 chr7A 88.660 97 10 1 4178 4273 571312104 571312200 2.890000e-22 117.0
20 TraesCS5B01G173000 chr7B 76.461 599 123 14 139 726 248504990 248504399 4.450000e-80 309.0
21 TraesCS5B01G173000 chr2D 79.639 388 73 5 3193 3577 349732377 349731993 1.620000e-69 274.0
22 TraesCS5B01G173000 chr2D 85.714 119 12 5 4156 4273 370824167 370824281 2.240000e-23 121.0
23 TraesCS5B01G173000 chr2A 78.182 385 84 0 3193 3577 465554689 465554305 3.540000e-61 246.0
24 TraesCS5B01G173000 chr3B 83.200 125 17 2 4155 4279 776098313 776098433 1.350000e-20 111.0
25 TraesCS5B01G173000 chr3B 74.654 217 41 13 107 316 729592194 729591985 2.940000e-12 84.2
26 TraesCS5B01G173000 chr6B 82.540 126 11 5 4155 4279 73356028 73356143 2.910000e-17 100.0
27 TraesCS5B01G173000 chr6B 79.545 88 18 0 105 192 712655903 712655816 3.820000e-06 63.9
28 TraesCS5B01G173000 chr4D 73.311 296 67 11 12 300 180671273 180671563 1.050000e-16 99.0


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 TraesCS5B01G173000 chr5B 317884859 317889437 4578 True 8456 8456 100.00000 1 4579 1 chr5B.!!$R1 4578
1 TraesCS5B01G173000 chr5A 372931278 372934689 3411 False 5406 5406 95.30600 731 4144 1 chr5A.!!$F1 3413
2 TraesCS5B01G173000 chr5D 280304020 280309743 5723 True 1506 4228 95.81125 1012 4579 4 chr5D.!!$R1 3567
3 TraesCS5B01G173000 chr3D 5057560 5058292 732 False 972 972 90.72300 1 728 1 chr3D.!!$F1 727
4 TraesCS5B01G173000 chr3D 468968117 468968849 732 False 556 556 80.54400 1 728 1 chr3D.!!$F2 727
5 TraesCS5B01G173000 chr4A 86460412 86461166 754 True 933 933 89.13900 1 748 1 chr4A.!!$R1 747
6 TraesCS5B01G173000 chr4A 13290341 13291066 725 False 894 894 88.90400 1 728 1 chr4A.!!$F1 727
7 TraesCS5B01G173000 chr1A 489152940 489153669 729 True 894 894 88.79800 1 730 1 chr1A.!!$R1 729
8 TraesCS5B01G173000 chr1A 171042316 171043045 729 False 412 412 77.20500 3 727 1 chr1A.!!$F1 724
9 TraesCS5B01G173000 chr4B 72164580 72165306 726 True 630 630 82.46600 8 730 1 chr4B.!!$R1 722
10 TraesCS5B01G173000 chr7A 513368530 513369259 729 True 558 558 80.62800 1 727 1 chr7A.!!$R1 726
11 TraesCS5B01G173000 chr7B 248504399 248504990 591 True 309 309 76.46100 139 726 1 chr7B.!!$R1 587

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
860 870 0.033504 TCACTCACGCCCAAGAAGTC 59.966 55.000 0.0 0.0 0.00 3.01 F
864 874 0.033504 TCACGCCCAAGAAGTCACTC 59.966 55.000 0.0 0.0 0.00 3.51 F
867 877 0.034059 CGCCCAAGAAGTCACTCACT 59.966 55.000 0.0 0.0 36.64 3.41 F
894 904 0.454196 AAGACAAAACCACGGCACAC 59.546 50.000 0.0 0.0 0.00 3.82 F
922 932 0.936600 TCGTGAGTTGTACGTGTCGA 59.063 50.000 0.0 0.0 41.91 4.20 F
1496 3392 1.830477 GTGGCTCTGTTCCTCTCTCAT 59.170 52.381 0.0 0.0 0.00 2.90 F
3380 5312 1.604308 CATCCTTGCTGTGGTGGCA 60.604 57.895 0.0 0.0 37.97 4.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2150 4081 1.488705 TTGGCTCTCGGGGTCACATT 61.489 55.000 0.00 0.0 0.00 2.71 R
2568 4500 3.338249 CGGCTTGAGAAAGGAAGATGAA 58.662 45.455 0.00 0.0 0.00 2.57 R
2825 4757 5.509498 AGCCCATTAAAAGCACTTCTATCA 58.491 37.500 0.00 0.0 0.00 2.15 R
2996 4928 1.909700 ATCCGCACACTCCAAAACAT 58.090 45.000 0.00 0.0 0.00 2.71 R
3380 5312 0.726827 CAAATGCAGGCACGTACGAT 59.273 50.000 24.41 3.1 0.00 3.73 R
3461 5393 1.005097 ACAATGCTGAGATGGAAGGCA 59.995 47.619 0.00 0.0 37.32 4.75 R
4342 6552 2.362077 ACTGCATTTGTTCTGTTGGGAC 59.638 45.455 0.00 0.0 0.00 4.46 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
26 27 1.302832 CTGTTTCTCTTGGCCGGCT 60.303 57.895 28.56 0.00 0.00 5.52
192 193 1.935327 CTGGACTTCGGACCGGAGAC 61.935 65.000 29.25 22.02 38.18 3.36
199 200 2.838693 GGACCGGAGACCTAGGCC 60.839 72.222 9.46 0.00 0.00 5.19
242 243 4.337836 TCAAACTGCTTCACATGCTTACAA 59.662 37.500 0.00 0.00 0.00 2.41
301 304 1.374947 GCTAGGGAAGTGTGGCACA 59.625 57.895 17.96 17.96 36.74 4.57
334 337 1.280998 AGCTTAACTTGGCCGTGGTAT 59.719 47.619 0.00 0.00 0.00 2.73
397 400 2.152016 CAAGGAGAGGGTTTCGGAAAC 58.848 52.381 22.26 22.26 40.65 2.78
421 424 2.484651 CTCAAGAGAGGTTTCGACTCGA 59.515 50.000 0.00 0.00 39.90 4.04
501 504 3.732849 GCCCAACAGCTAGCCCCT 61.733 66.667 12.13 0.00 0.00 4.79
543 546 6.204882 TGATCTTAAGAGATATTCGCGAGTGA 59.795 38.462 15.03 0.00 42.66 3.41
596 600 2.515854 ACGCTTTGTGAGAGAGTAGGA 58.484 47.619 0.00 0.00 0.00 2.94
615 621 2.094234 GGATTGTAATGGTGTTGGGTGC 60.094 50.000 0.00 0.00 0.00 5.01
680 689 5.703876 CCTCTCTTGTAAATTTGTTGCTCC 58.296 41.667 0.00 0.00 0.00 4.70
787 797 4.479619 GACAGAAAATCATGTGTGCTTCC 58.520 43.478 0.00 0.00 0.00 3.46
836 846 1.666553 TGCGCTTTACACGTCCCAG 60.667 57.895 9.73 0.00 0.00 4.45
849 859 0.039074 GTCCCAGTCACTCACTCACG 60.039 60.000 0.00 0.00 30.26 4.35
851 861 1.373497 CCAGTCACTCACTCACGCC 60.373 63.158 0.00 0.00 30.26 5.68
853 863 1.832608 AGTCACTCACTCACGCCCA 60.833 57.895 0.00 0.00 0.00 5.36
854 864 1.069090 GTCACTCACTCACGCCCAA 59.931 57.895 0.00 0.00 0.00 4.12
855 865 0.946221 GTCACTCACTCACGCCCAAG 60.946 60.000 0.00 0.00 0.00 3.61
856 866 1.112916 TCACTCACTCACGCCCAAGA 61.113 55.000 0.00 0.00 0.00 3.02
857 867 0.249868 CACTCACTCACGCCCAAGAA 60.250 55.000 0.00 0.00 0.00 2.52
858 868 0.034059 ACTCACTCACGCCCAAGAAG 59.966 55.000 0.00 0.00 0.00 2.85
859 869 0.034059 CTCACTCACGCCCAAGAAGT 59.966 55.000 0.00 0.00 0.00 3.01
860 870 0.033504 TCACTCACGCCCAAGAAGTC 59.966 55.000 0.00 0.00 0.00 3.01
861 871 0.249868 CACTCACGCCCAAGAAGTCA 60.250 55.000 0.00 0.00 0.00 3.41
862 872 0.249911 ACTCACGCCCAAGAAGTCAC 60.250 55.000 0.00 0.00 0.00 3.67
863 873 0.034059 CTCACGCCCAAGAAGTCACT 59.966 55.000 0.00 0.00 0.00 3.41
864 874 0.033504 TCACGCCCAAGAAGTCACTC 59.966 55.000 0.00 0.00 0.00 3.51
865 875 0.249868 CACGCCCAAGAAGTCACTCA 60.250 55.000 0.00 0.00 0.00 3.41
866 876 0.249911 ACGCCCAAGAAGTCACTCAC 60.250 55.000 0.00 0.00 0.00 3.51
867 877 0.034059 CGCCCAAGAAGTCACTCACT 59.966 55.000 0.00 0.00 36.64 3.41
868 878 1.802069 GCCCAAGAAGTCACTCACTC 58.198 55.000 0.00 0.00 32.30 3.51
869 879 1.070758 GCCCAAGAAGTCACTCACTCA 59.929 52.381 0.00 0.00 32.30 3.41
876 886 1.069090 GTCACTCACTCACGCCCAA 59.931 57.895 0.00 0.00 0.00 4.12
894 904 0.454196 AAGACAAAACCACGGCACAC 59.546 50.000 0.00 0.00 0.00 3.82
898 908 2.025155 ACAAAACCACGGCACACATAA 58.975 42.857 0.00 0.00 0.00 1.90
899 909 2.625790 ACAAAACCACGGCACACATAAT 59.374 40.909 0.00 0.00 0.00 1.28
911 921 4.181578 GCACACATAATACCTCGTGAGTT 58.818 43.478 0.00 0.00 33.56 3.01
922 932 0.936600 TCGTGAGTTGTACGTGTCGA 59.063 50.000 0.00 0.00 41.91 4.20
997 1007 2.158330 CGTACGCGATTGCTGCTGA 61.158 57.895 15.93 0.00 41.33 4.26
1261 1274 6.555315 GTCAGTATCTACCCAAATTTGCTTG 58.445 40.000 12.92 5.93 0.00 4.01
1269 1282 3.582208 ACCCAAATTTGCTTGGCATCTTA 59.418 39.130 12.92 0.00 43.97 2.10
1333 1352 3.293337 AGAATATTGGAGCTGCAATGCA 58.707 40.909 35.42 21.71 36.92 3.96
1496 3392 1.830477 GTGGCTCTGTTCCTCTCTCAT 59.170 52.381 0.00 0.00 0.00 2.90
1500 3396 3.197549 GGCTCTGTTCCTCTCTCATCTTT 59.802 47.826 0.00 0.00 0.00 2.52
1889 3814 8.675705 TCGCATGATCTCTTTATTCCAAAATA 57.324 30.769 0.00 0.00 0.00 1.40
1952 3878 9.783256 AGTCATGTAACAAGTTTTTGTAAAGAC 57.217 29.630 0.00 0.00 46.54 3.01
2240 4172 6.426937 TGTGTATTCTACTTTTCCTGTTGCTC 59.573 38.462 0.00 0.00 0.00 4.26
2329 4261 8.766994 ATAATTGGCACTACTTTTATGGTGAT 57.233 30.769 0.00 0.00 33.10 3.06
2825 4757 2.094545 GCTTTTCGACCATCCATTTGCT 60.095 45.455 0.00 0.00 0.00 3.91
2996 4928 7.856145 TGTATGTATCATGTTTGTGTATGCA 57.144 32.000 0.00 0.00 0.00 3.96
3380 5312 1.604308 CATCCTTGCTGTGGTGGCA 60.604 57.895 0.00 0.00 37.97 4.92
3461 5393 1.738099 CGCTTTCGTGCTGCCTACT 60.738 57.895 0.00 0.00 0.00 2.57
3578 5510 3.239449 TGGAACCTTCACTGCTCTCTAA 58.761 45.455 0.00 0.00 0.00 2.10
3640 5572 0.602905 GGTGTGTACAGGTCAGGTGC 60.603 60.000 0.00 0.00 0.00 5.01
3662 5594 7.548780 GGTGCAATTATAAACCACATGACAAAT 59.451 33.333 0.00 0.00 32.69 2.32
3664 5596 9.149225 TGCAATTATAAACCACATGACAAATTC 57.851 29.630 0.00 0.00 0.00 2.17
3707 5639 8.814038 AGCAATAGAAAAGAAACACCATCTAT 57.186 30.769 0.00 0.00 32.90 1.98
3729 5661 9.467258 TCTATAAGAAGACGACGAAAAGAAAAA 57.533 29.630 0.00 0.00 0.00 1.94
3794 5726 0.820871 CTCGAAGGAAGCCTAGCTGT 59.179 55.000 0.00 0.00 39.62 4.40
3877 5809 2.548067 GGTAGCGCATGGTAGCTTATGT 60.548 50.000 11.47 0.00 44.15 2.29
4016 6036 5.594926 TCGTATAAAAACGAGGAAGGATCC 58.405 41.667 2.48 2.48 46.29 3.36
4024 6044 3.426917 GGAAGGATCCTTGGGGCA 58.573 61.111 31.79 0.00 42.93 5.36
4025 6045 1.933629 GGAAGGATCCTTGGGGCAT 59.066 57.895 31.79 5.52 42.93 4.40
4026 6046 0.262876 GGAAGGATCCTTGGGGCATT 59.737 55.000 31.79 4.65 42.93 3.56
4027 6047 1.697284 GAAGGATCCTTGGGGCATTC 58.303 55.000 31.79 10.89 36.26 2.67
4028 6048 1.216427 GAAGGATCCTTGGGGCATTCT 59.784 52.381 31.79 2.94 36.26 2.40
4029 6049 0.849417 AGGATCCTTGGGGCATTCTC 59.151 55.000 9.02 0.00 0.00 2.87
4030 6050 0.178978 GGATCCTTGGGGCATTCTCC 60.179 60.000 3.84 0.00 0.00 3.71
4031 6051 0.178978 GATCCTTGGGGCATTCTCCC 60.179 60.000 0.00 0.00 45.80 4.30
4105 6143 1.089920 GTGGCTGCATAGGTGTTCTG 58.910 55.000 0.50 0.00 0.00 3.02
4273 6313 2.224549 CGTGAAGTCCGTGCCAAATTTA 59.775 45.455 0.00 0.00 0.00 1.40
4340 6550 1.012486 CGGAAGAAAACCGTCTCCCG 61.012 60.000 0.00 0.00 44.57 5.14
4341 6551 0.319405 GGAAGAAAACCGTCTCCCGA 59.681 55.000 0.00 0.00 39.56 5.14
4342 6552 1.672145 GGAAGAAAACCGTCTCCCGAG 60.672 57.143 0.00 0.00 39.56 4.63
4343 6553 1.000618 GAAGAAAACCGTCTCCCGAGT 59.999 52.381 0.00 0.00 39.56 4.18
4344 6554 0.602060 AGAAAACCGTCTCCCGAGTC 59.398 55.000 0.00 0.00 39.56 3.36
4345 6555 0.389556 GAAAACCGTCTCCCGAGTCC 60.390 60.000 0.00 0.00 39.56 3.85
4346 6556 1.824224 AAAACCGTCTCCCGAGTCCC 61.824 60.000 0.00 0.00 39.56 4.46
4357 6567 1.476110 CCCGAGTCCCAACAGAACAAA 60.476 52.381 0.00 0.00 0.00 2.83
4459 6669 5.278315 GCGAACTTTGGGATTCAAGTAAGTT 60.278 40.000 0.00 0.00 36.93 2.66
4460 6670 6.072893 GCGAACTTTGGGATTCAAGTAAGTTA 60.073 38.462 0.00 0.00 35.36 2.24
4537 6747 5.904362 AGAGTTTGTTCACTTCTTTGCTT 57.096 34.783 0.00 0.00 0.00 3.91
4541 6751 8.470002 AGAGTTTGTTCACTTCTTTGCTTAAAT 58.530 29.630 0.00 0.00 0.00 1.40
4546 6756 9.730420 TTGTTCACTTCTTTGCTTAAATAACTC 57.270 29.630 0.00 0.00 0.00 3.01
4556 6766 8.862325 TTTGCTTAAATAACTCCATCTTCTCA 57.138 30.769 0.00 0.00 0.00 3.27
4557 6767 8.862325 TTGCTTAAATAACTCCATCTTCTCAA 57.138 30.769 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 4.244066 AGTACGTCGATCTCGCAGTATAT 58.756 43.478 0.00 0.00 39.60 0.86
192 193 3.711059 CTTGCAGCCCAGGCCTAGG 62.711 68.421 13.73 13.73 43.17 3.02
242 243 1.202371 TGTTCAGCGTTGTCTTCGTCT 60.202 47.619 0.00 0.00 0.00 4.18
301 304 5.587844 CCAAGTTAAGCTCATGTAAGCATCT 59.412 40.000 8.91 0.00 45.00 2.90
309 312 1.271379 ACGGCCAAGTTAAGCTCATGT 60.271 47.619 2.24 0.00 0.00 3.21
334 337 0.331616 TCATCCTCTCTGGTCGGTCA 59.668 55.000 0.00 0.00 37.07 4.02
397 400 4.420168 GAGTCGAAACCTCTCTTGAGATG 58.580 47.826 0.41 1.40 42.73 2.90
421 424 3.640407 AGCCACCGCTGTCACCAT 61.640 61.111 0.00 0.00 46.19 3.55
471 474 3.255642 GCTGTTGGGCTGTTCTATTGAAA 59.744 43.478 0.00 0.00 33.52 2.69
501 504 1.919240 TCACTTCCACTAGCTCCGAA 58.081 50.000 0.00 0.00 0.00 4.30
543 546 0.695803 CCCCTAGACCTGCATCCCTT 60.696 60.000 0.00 0.00 0.00 3.95
596 600 1.543802 CGCACCCAACACCATTACAAT 59.456 47.619 0.00 0.00 0.00 2.71
680 689 6.925165 TCGCGTACCTTAATTTTATAGAAGGG 59.075 38.462 5.77 0.00 42.39 3.95
765 775 4.217118 AGGAAGCACACATGATTTTCTGTC 59.783 41.667 0.00 0.00 33.63 3.51
836 846 0.946221 CTTGGGCGTGAGTGAGTGAC 60.946 60.000 0.00 0.00 0.00 3.67
849 859 1.070758 TGAGTGAGTGACTTCTTGGGC 59.929 52.381 0.00 0.00 33.83 5.36
851 861 2.398498 CGTGAGTGAGTGACTTCTTGG 58.602 52.381 0.00 0.00 33.83 3.61
853 863 1.269831 GGCGTGAGTGAGTGACTTCTT 60.270 52.381 0.00 0.00 33.83 2.52
854 864 0.315568 GGCGTGAGTGAGTGACTTCT 59.684 55.000 0.00 0.00 33.83 2.85
855 865 0.667792 GGGCGTGAGTGAGTGACTTC 60.668 60.000 0.00 0.00 33.83 3.01
856 866 1.367840 GGGCGTGAGTGAGTGACTT 59.632 57.895 0.00 0.00 33.83 3.01
857 867 1.399744 TTGGGCGTGAGTGAGTGACT 61.400 55.000 0.00 0.00 37.76 3.41
858 868 0.946221 CTTGGGCGTGAGTGAGTGAC 60.946 60.000 0.00 0.00 0.00 3.67
859 869 1.112916 TCTTGGGCGTGAGTGAGTGA 61.113 55.000 0.00 0.00 0.00 3.41
860 870 0.946221 GTCTTGGGCGTGAGTGAGTG 60.946 60.000 0.00 0.00 0.00 3.51
861 871 1.367840 GTCTTGGGCGTGAGTGAGT 59.632 57.895 0.00 0.00 0.00 3.41
862 872 0.249868 TTGTCTTGGGCGTGAGTGAG 60.250 55.000 0.00 0.00 0.00 3.51
863 873 0.179234 TTTGTCTTGGGCGTGAGTGA 59.821 50.000 0.00 0.00 0.00 3.41
864 874 1.021202 TTTTGTCTTGGGCGTGAGTG 58.979 50.000 0.00 0.00 0.00 3.51
865 875 1.021968 GTTTTGTCTTGGGCGTGAGT 58.978 50.000 0.00 0.00 0.00 3.41
866 876 0.310854 GGTTTTGTCTTGGGCGTGAG 59.689 55.000 0.00 0.00 0.00 3.51
867 877 0.394488 TGGTTTTGTCTTGGGCGTGA 60.394 50.000 0.00 0.00 0.00 4.35
868 878 0.248866 GTGGTTTTGTCTTGGGCGTG 60.249 55.000 0.00 0.00 0.00 5.34
869 879 1.720694 CGTGGTTTTGTCTTGGGCGT 61.721 55.000 0.00 0.00 0.00 5.68
876 886 0.678366 TGTGTGCCGTGGTTTTGTCT 60.678 50.000 0.00 0.00 0.00 3.41
894 904 5.454554 CACGTACAACTCACGAGGTATTATG 59.545 44.000 1.43 0.00 41.91 1.90
898 908 2.816087 ACACGTACAACTCACGAGGTAT 59.184 45.455 1.43 0.00 41.91 2.73
899 909 2.221169 ACACGTACAACTCACGAGGTA 58.779 47.619 1.43 0.00 41.91 3.08
911 921 3.271014 GAGGCCTCGACACGTACA 58.729 61.111 19.06 0.00 0.00 2.90
997 1007 2.273449 CTTTGCCTCCGCCATCCT 59.727 61.111 0.00 0.00 0.00 3.24
1217 1230 1.118838 GAGGAGGAGCATGCAGTAGT 58.881 55.000 21.98 0.00 0.00 2.73
1261 1274 6.128145 GGAGAGAAACAAAAGAGTAAGATGCC 60.128 42.308 0.00 0.00 0.00 4.40
1269 1282 2.104963 AGCGGGAGAGAAACAAAAGAGT 59.895 45.455 0.00 0.00 0.00 3.24
1333 1352 6.043590 TCACCCAATCTGCATATAGACAGAAT 59.956 38.462 10.56 1.60 45.49 2.40
1562 3467 3.930229 CCACCGATTTCATAACGAGACAA 59.070 43.478 0.00 0.00 0.00 3.18
1622 3529 6.463995 AATAGCGCAATCCTTAAAATCCAA 57.536 33.333 11.47 0.00 0.00 3.53
1952 3878 4.752661 TCTTAAACCCGGTTTGAATTCG 57.247 40.909 23.45 5.76 36.37 3.34
1987 3913 6.932400 TCACAATGTGAAAACGGTATTCTAGT 59.068 34.615 14.37 0.00 39.78 2.57
2136 4064 4.862574 GGGTCACATTCCGCTTTAAAAATC 59.137 41.667 0.00 0.00 0.00 2.17
2137 4065 4.322424 GGGGTCACATTCCGCTTTAAAAAT 60.322 41.667 0.00 0.00 35.46 1.82
2143 4074 1.674322 CGGGGTCACATTCCGCTTT 60.674 57.895 0.00 0.00 37.25 3.51
2150 4081 1.488705 TTGGCTCTCGGGGTCACATT 61.489 55.000 0.00 0.00 0.00 2.71
2198 4130 8.966868 AGAATACACATGTTTAACCATTTAGGG 58.033 33.333 0.00 0.00 43.89 3.53
2335 4267 5.878332 AAGATTCGTCATAATGCACACAA 57.122 34.783 0.00 0.00 0.00 3.33
2568 4500 3.338249 CGGCTTGAGAAAGGAAGATGAA 58.662 45.455 0.00 0.00 0.00 2.57
2825 4757 5.509498 AGCCCATTAAAAGCACTTCTATCA 58.491 37.500 0.00 0.00 0.00 2.15
2996 4928 1.909700 ATCCGCACACTCCAAAACAT 58.090 45.000 0.00 0.00 0.00 2.71
3380 5312 0.726827 CAAATGCAGGCACGTACGAT 59.273 50.000 24.41 3.10 0.00 3.73
3461 5393 1.005097 ACAATGCTGAGATGGAAGGCA 59.995 47.619 0.00 0.00 37.32 4.75
3662 5594 5.247862 TGCTTTCTCTCATGTGCATTAGAA 58.752 37.500 0.00 0.00 0.00 2.10
3664 5596 5.556355 TTGCTTTCTCTCATGTGCATTAG 57.444 39.130 0.00 0.00 0.00 1.73
3794 5726 7.202011 GGGATTCTAGTAGATCTTTGTGCCTTA 60.202 40.741 0.00 0.00 0.00 2.69
3877 5809 4.637534 CACCCTACTGCTTAGTACTCGTAA 59.362 45.833 0.00 0.00 0.00 3.18
4030 6050 6.439058 TCCTCATTTTAACTAAACATTGGGGG 59.561 38.462 0.00 0.00 0.00 5.40
4031 6051 7.475137 TCCTCATTTTAACTAAACATTGGGG 57.525 36.000 0.00 0.00 0.00 4.96
4032 6052 8.531146 ACATCCTCATTTTAACTAAACATTGGG 58.469 33.333 0.00 0.00 0.00 4.12
4037 6075 7.721842 TCACCACATCCTCATTTTAACTAAACA 59.278 33.333 0.00 0.00 0.00 2.83
4105 6143 4.273318 AGCTATCATGTTGGTCCCTTTTC 58.727 43.478 0.00 0.00 0.00 2.29
4167 6206 2.901192 TGAATTTACTGTCCACCTCGGA 59.099 45.455 0.00 0.00 43.61 4.55
4273 6313 5.652324 AGACCCTTATACGGATATTCCACT 58.348 41.667 0.00 0.00 35.91 4.00
4340 6550 2.622942 TGCATTTGTTCTGTTGGGACTC 59.377 45.455 0.00 0.00 0.00 3.36
4341 6551 2.624838 CTGCATTTGTTCTGTTGGGACT 59.375 45.455 0.00 0.00 0.00 3.85
4342 6552 2.362077 ACTGCATTTGTTCTGTTGGGAC 59.638 45.455 0.00 0.00 0.00 4.46
4343 6553 2.665165 ACTGCATTTGTTCTGTTGGGA 58.335 42.857 0.00 0.00 0.00 4.37
4344 6554 3.317711 TGTACTGCATTTGTTCTGTTGGG 59.682 43.478 0.00 0.00 0.00 4.12
4345 6555 4.566545 TGTACTGCATTTGTTCTGTTGG 57.433 40.909 0.00 0.00 0.00 3.77
4346 6556 8.746922 AAATATGTACTGCATTTGTTCTGTTG 57.253 30.769 0.00 0.00 38.94 3.33
4357 6567 6.989169 GGTTCTCTCTGAAATATGTACTGCAT 59.011 38.462 0.00 0.00 37.73 3.96
4485 6695 4.973663 GGTACACATCAAAACTTCCGTTTG 59.026 41.667 0.00 0.00 42.28 2.93


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

AutoCloner maintained by Alex Coulton.