Multiple sequence alignment - TraesCS1B01G202300

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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 TraesCS1B01G202300 chr1B 100.000 5640 0 0 1 5640 363164274 363158635 0.000000e+00 10416.0
1 TraesCS1B01G202300 chr1A 93.687 2170 82 26 2654 4796 321396829 321398970 0.000000e+00 3197.0
2 TraesCS1B01G202300 chr1A 95.366 1791 70 6 874 2656 321394956 321396741 0.000000e+00 2835.0
3 TraesCS1B01G202300 chr1A 93.837 503 25 5 5140 5640 321402282 321402780 0.000000e+00 752.0
4 TraesCS1B01G202300 chr1A 84.000 225 28 1 4788 5012 321399012 321399228 5.730000e-50 209.0
5 TraesCS1B01G202300 chr1D 96.472 1871 59 4 787 2656 251299940 251301804 0.000000e+00 3083.0
6 TraesCS1B01G202300 chr1D 96.143 1400 31 12 2654 4048 251301885 251303266 0.000000e+00 2265.0
7 TraesCS1B01G202300 chr1D 92.374 813 34 10 4117 4913 251303280 251304080 0.000000e+00 1133.0
8 TraesCS1B01G202300 chr1D 94.432 449 22 3 5192 5640 251305405 251305850 0.000000e+00 688.0
9 TraesCS1B01G202300 chr7A 98.604 788 10 1 1 787 218257707 218258494 0.000000e+00 1393.0
10 TraesCS1B01G202300 chr2B 98.352 789 11 2 1 787 183514432 183513644 0.000000e+00 1384.0
11 TraesCS1B01G202300 chr2A 97.465 789 18 2 1 787 461024674 461023886 0.000000e+00 1345.0
12 TraesCS1B01G202300 chr6B 96.447 788 26 2 1 786 704950992 704951779 0.000000e+00 1299.0
13 TraesCS1B01G202300 chr6B 96.329 790 27 2 1 788 30131090 30130301 0.000000e+00 1297.0
14 TraesCS1B01G202300 chr5B 96.451 789 24 3 1 786 70390824 70390037 0.000000e+00 1299.0
15 TraesCS1B01G202300 chr5B 96.198 789 25 4 1 787 613634137 613633352 0.000000e+00 1286.0
16 TraesCS1B01G202300 chr6D 95.647 781 32 2 8 787 16283012 16282233 0.000000e+00 1253.0
17 TraesCS1B01G202300 chr3D 95.184 789 37 1 1 788 499861440 499862228 0.000000e+00 1245.0
18 TraesCS1B01G202300 chr3D 95.238 84 4 0 3327 3410 461562782 461562699 3.540000e-27 134.0
19 TraesCS1B01G202300 chr4B 89.247 93 8 2 1018 1109 670446805 670446714 1.280000e-21 115.0
20 TraesCS1B01G202300 chr4B 93.617 47 3 0 1178 1224 670446594 670446548 2.820000e-08 71.3
21 TraesCS1B01G202300 chr5A 89.130 92 8 2 1018 1108 708446913 708446823 4.620000e-21 113.0
22 TraesCS1B01G202300 chr5A 93.617 47 3 0 1178 1224 708446699 708446653 2.820000e-08 71.3
23 TraesCS1B01G202300 chrUn 93.617 47 3 0 1178 1224 29220731 29220777 2.820000e-08 71.3
24 TraesCS1B01G202300 chr7B 88.889 45 3 2 4276 4320 607618012 607617970 3.000000e-03 54.7


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 TraesCS1B01G202300 chr1B 363158635 363164274 5639 True 10416.00 10416 100.00000 1 5640 1 chr1B.!!$R1 5639
1 TraesCS1B01G202300 chr1A 321394956 321402780 7824 False 1748.25 3197 91.72250 874 5640 4 chr1A.!!$F1 4766
2 TraesCS1B01G202300 chr1D 251299940 251305850 5910 False 1792.25 3083 94.85525 787 5640 4 chr1D.!!$F1 4853
3 TraesCS1B01G202300 chr7A 218257707 218258494 787 False 1393.00 1393 98.60400 1 787 1 chr7A.!!$F1 786
4 TraesCS1B01G202300 chr2B 183513644 183514432 788 True 1384.00 1384 98.35200 1 787 1 chr2B.!!$R1 786
5 TraesCS1B01G202300 chr2A 461023886 461024674 788 True 1345.00 1345 97.46500 1 787 1 chr2A.!!$R1 786
6 TraesCS1B01G202300 chr6B 704950992 704951779 787 False 1299.00 1299 96.44700 1 786 1 chr6B.!!$F1 785
7 TraesCS1B01G202300 chr6B 30130301 30131090 789 True 1297.00 1297 96.32900 1 788 1 chr6B.!!$R1 787
8 TraesCS1B01G202300 chr5B 70390037 70390824 787 True 1299.00 1299 96.45100 1 786 1 chr5B.!!$R1 785
9 TraesCS1B01G202300 chr5B 613633352 613634137 785 True 1286.00 1286 96.19800 1 787 1 chr5B.!!$R2 786
10 TraesCS1B01G202300 chr6D 16282233 16283012 779 True 1253.00 1253 95.64700 8 787 1 chr6D.!!$R1 779
11 TraesCS1B01G202300 chr3D 499861440 499862228 788 False 1245.00 1245 95.18400 1 788 1 chr3D.!!$F1 787

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
268 269 0.251354 GCTCAAGACCCTCTCATGCA 59.749 55.0 0.00 0.00 0.00 3.96 F
1266 1277 0.179089 ACATGCATGCTCCGTCTCTC 60.179 55.0 26.53 0.00 0.00 3.20 F
1431 1442 0.390603 ATCGTCCGCGTTGAATTCCA 60.391 50.0 4.92 0.00 39.49 3.53 F
2504 2517 0.678048 CTGGAGCTGGGTTAACTGGC 60.678 60.0 5.42 7.59 0.00 4.85 F
3263 3378 1.203441 AGCTGATGAGGGAAGGTGCA 61.203 55.0 0.00 0.00 0.00 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1645 1656 0.666577 CGTCAGACGGTTCCTGTTCC 60.667 60.000 15.64 0.0 38.08 3.62 R
3048 3160 1.615392 GCCAGTGAGAATTGCAAAGGT 59.385 47.619 1.71 0.0 0.00 3.50 R
3263 3378 1.806542 CCGCTTAACACAGTCTGCATT 59.193 47.619 0.00 0.0 0.00 3.56 R
4333 4461 0.744281 GACTGCAGGAGAGGCTAGTC 59.256 60.000 19.93 0.0 34.66 2.59 R
5014 5199 0.180642 CACTGCAGCCTGGATCATCT 59.819 55.000 15.27 0.0 0.00 2.90 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
268 269 0.251354 GCTCAAGACCCTCTCATGCA 59.749 55.000 0.00 0.00 0.00 3.96
357 358 2.669133 CGATGCCTCCCCACCTTGA 61.669 63.158 0.00 0.00 0.00 3.02
637 639 3.905493 TTCCCCCTATGTGGTTTTTCA 57.095 42.857 0.00 0.00 0.00 2.69
717 719 8.918202 TCTTATAAACTGGATCAAACACTTGT 57.082 30.769 0.00 0.00 33.94 3.16
817 821 2.395690 GCTGACGTACGTGCATGC 59.604 61.111 28.16 18.86 0.00 4.06
871 875 2.127869 CCTCCGATCCTCCGAAGCA 61.128 63.158 0.00 0.00 0.00 3.91
872 876 1.467678 CCTCCGATCCTCCGAAGCAT 61.468 60.000 0.00 0.00 0.00 3.79
904 909 2.932234 AATATCGCCCGGAGCCGAG 61.932 63.158 11.05 0.00 42.83 4.63
1266 1277 0.179089 ACATGCATGCTCCGTCTCTC 60.179 55.000 26.53 0.00 0.00 3.20
1431 1442 0.390603 ATCGTCCGCGTTGAATTCCA 60.391 50.000 4.92 0.00 39.49 3.53
1434 1445 0.953960 GTCCGCGTTGAATTCCACCT 60.954 55.000 4.92 0.00 0.00 4.00
1635 1646 3.266376 ACAACACGTGTTCGGCGG 61.266 61.111 30.24 20.53 37.01 6.13
1645 1656 2.813474 TTCGGCGGCGACAATGAG 60.813 61.111 34.85 0.97 0.00 2.90
1649 1660 2.750888 GGCGGCGACAATGAGGAAC 61.751 63.158 12.98 0.00 0.00 3.62
1650 1661 2.032634 GCGGCGACAATGAGGAACA 61.033 57.895 12.98 0.00 0.00 3.18
1651 1662 1.970917 GCGGCGACAATGAGGAACAG 61.971 60.000 12.98 0.00 0.00 3.16
1658 1669 1.420138 ACAATGAGGAACAGGAACCGT 59.580 47.619 0.00 0.00 0.00 4.83
1747 1758 1.755959 CTGTACATGCTCCTCTCAGCT 59.244 52.381 0.00 0.00 40.39 4.24
1855 1866 0.737715 GACTGATCGCGACTTGGCTT 60.738 55.000 12.93 0.00 0.00 4.35
1881 1892 5.118990 CGTCAAGTGGATCAAGATGGTAAT 58.881 41.667 0.00 0.00 0.00 1.89
1908 1919 2.785868 ATTCCTCCAGAATGCGCAC 58.214 52.632 14.90 0.00 43.81 5.34
1916 1927 1.200716 CCAGAATGCGCACAATGAAGT 59.799 47.619 14.90 0.00 31.97 3.01
1917 1928 2.247637 CAGAATGCGCACAATGAAGTG 58.752 47.619 14.90 0.00 42.37 3.16
1920 1931 1.525718 ATGCGCACAATGAAGTGGCA 61.526 50.000 14.90 10.86 44.07 4.92
2035 2047 2.394563 GGCTGCAGCGAAAGAGGAC 61.395 63.158 31.19 11.21 43.26 3.85
2089 2101 1.675641 GTGGCAGAAATGGAGGCGT 60.676 57.895 0.00 0.00 0.00 5.68
2095 2107 2.938798 AAATGGAGGCGTGGGGGA 60.939 61.111 0.00 0.00 0.00 4.81
2153 2165 1.841556 GCCATCTCCGGGGGTGATA 60.842 63.158 18.84 0.00 34.65 2.15
2166 2179 5.828859 CCGGGGGTGATAATATGTTAAACAA 59.171 40.000 0.00 0.00 0.00 2.83
2201 2214 1.233919 TGATGAGATCTCTCCGCGAG 58.766 55.000 22.95 3.02 42.20 5.03
2210 2223 2.884685 CTCCGCGAGCTGCTGAAG 60.885 66.667 8.23 0.00 43.27 3.02
2230 2243 5.635280 TGAAGTAGCTGTCTCGATCTTTTTG 59.365 40.000 0.00 0.00 0.00 2.44
2451 2464 4.084013 CCACAAGTCTTTAATCGTCCACAC 60.084 45.833 0.00 0.00 0.00 3.82
2453 2466 4.750098 ACAAGTCTTTAATCGTCCACACTG 59.250 41.667 0.00 0.00 0.00 3.66
2504 2517 0.678048 CTGGAGCTGGGTTAACTGGC 60.678 60.000 5.42 7.59 0.00 4.85
2644 2657 4.136796 TGCACTGTCTTGCTGTATTTTCT 58.863 39.130 0.00 0.00 43.41 2.52
2884 2989 6.150140 CCCATTCCTTAGCAGCATATTCTTAC 59.850 42.308 0.00 0.00 0.00 2.34
2969 3081 7.345653 TCAGATAACATGGATAGAGGTGAGTTT 59.654 37.037 0.00 0.00 0.00 2.66
2982 3094 3.370978 AGGTGAGTTTCGCGTAATTCATG 59.629 43.478 22.45 0.00 0.00 3.07
3048 3160 8.486210 AGAATCTTACCATGCATAACTAGACAA 58.514 33.333 0.00 0.00 0.00 3.18
3167 3279 8.570488 GGCATCAAGTAATGTTCATGATTCATA 58.430 33.333 12.26 0.32 0.00 2.15
3200 3315 4.408694 GTTCCGCACACGCTTTAAATAAT 58.591 39.130 0.00 0.00 38.22 1.28
3201 3316 4.688511 TCCGCACACGCTTTAAATAATT 57.311 36.364 0.00 0.00 38.22 1.40
3263 3378 1.203441 AGCTGATGAGGGAAGGTGCA 61.203 55.000 0.00 0.00 0.00 4.57
3344 3459 4.380233 GCTGCTGCAGATTTTATTGACAGT 60.380 41.667 32.30 0.00 39.41 3.55
3636 3752 2.024176 TTTCCAGGCCTGTCACTCTA 57.976 50.000 30.63 6.44 0.00 2.43
3696 3812 4.826733 TGTTTGCAGGAATTAGCTCTTTCA 59.173 37.500 9.91 0.00 0.00 2.69
3761 3878 7.876896 GCAGGAGCATAATTAAGTAGAGTAC 57.123 40.000 0.00 0.00 41.58 2.73
3762 3879 7.434492 GCAGGAGCATAATTAAGTAGAGTACA 58.566 38.462 0.00 0.00 41.58 2.90
3763 3880 8.091449 GCAGGAGCATAATTAAGTAGAGTACAT 58.909 37.037 0.00 0.00 41.58 2.29
3807 3925 1.222936 CCGCTTGGAGCTGAGGAAT 59.777 57.895 0.00 0.00 39.60 3.01
3890 4008 7.307396 CGCTAAATGTCTACCAATATGGAGTTG 60.307 40.741 2.85 0.00 40.96 3.16
4033 4151 5.423886 GCAGTAGCTATTCTGACCTTCTTT 58.576 41.667 13.98 0.00 37.91 2.52
4035 4153 6.036626 GCAGTAGCTATTCTGACCTTCTTTTC 59.963 42.308 13.98 0.00 37.91 2.29
4048 4166 2.740506 TCTTTTCCCCAAGAAACCGT 57.259 45.000 0.00 0.00 44.20 4.83
4049 4167 2.303175 TCTTTTCCCCAAGAAACCGTG 58.697 47.619 0.00 0.00 44.20 4.94
4060 4178 4.211389 CAAGAAACCGTGAGAATTGTTCG 58.789 43.478 0.00 0.00 34.02 3.95
4067 4185 3.485216 CCGTGAGAATTGTTCGTATTGGC 60.485 47.826 0.00 0.00 34.02 4.52
4082 4200 5.879777 TCGTATTGGCATGAATTGAAGAGAA 59.120 36.000 0.00 0.00 0.00 2.87
4153 4271 4.778213 ACACAGCTGAACCCATATGTAT 57.222 40.909 23.35 0.00 0.00 2.29
4272 4390 3.963383 ATGCTCTTTGTTTTTCGTCGT 57.037 38.095 0.00 0.00 0.00 4.34
4273 4391 3.313274 TGCTCTTTGTTTTTCGTCGTC 57.687 42.857 0.00 0.00 0.00 4.20
4345 4473 2.297701 CTCTGACAGACTAGCCTCTCC 58.702 57.143 0.00 0.00 0.00 3.71
4452 4580 0.387367 CACCCGACTGAGTGAACTCG 60.387 60.000 6.01 3.90 45.72 4.18
4453 4581 0.822532 ACCCGACTGAGTGAACTCGT 60.823 55.000 6.01 6.78 45.72 4.18
4454 4582 0.314302 CCCGACTGAGTGAACTCGTT 59.686 55.000 6.01 0.00 45.72 3.85
4570 4701 0.398239 AGCAGATCCTGGAGCAGCTA 60.398 55.000 27.24 0.00 38.89 3.32
4737 4868 6.216801 AGGAAACTTTTGTTGTAAGGGAAC 57.783 37.500 0.00 0.00 42.67 3.62
4775 4907 5.809051 GGGTACTTGTAGTCTGTTTTATCCG 59.191 44.000 0.00 0.00 0.00 4.18
4796 4980 4.508124 CCGTAAGTCAGCATTTCCATAGAC 59.492 45.833 0.00 0.00 0.00 2.59
4798 4982 4.574674 AAGTCAGCATTTCCATAGACCA 57.425 40.909 0.00 0.00 0.00 4.02
4817 5001 4.251268 ACCAGTTTGACTAGCGAAATACC 58.749 43.478 0.00 0.00 0.00 2.73
4819 5003 3.306166 CAGTTTGACTAGCGAAATACCCG 59.694 47.826 0.00 0.00 0.00 5.28
4847 5031 1.583054 AAAAGCTGACACCGTGAGTC 58.417 50.000 5.28 0.00 36.55 3.36
4856 5040 3.440522 TGACACCGTGAGTCTAGAAGATG 59.559 47.826 5.28 0.00 36.94 2.90
4857 5041 2.164624 ACACCGTGAGTCTAGAAGATGC 59.835 50.000 5.28 0.00 0.00 3.91
4880 5064 4.359706 GTCATTTTATGCCGGATCAAACC 58.640 43.478 5.05 0.00 0.00 3.27
4898 5082 5.067674 TCAAACCATTGAACTCAAGAACTGG 59.932 40.000 7.84 7.84 42.47 4.00
4908 5092 1.071542 TCAAGAACTGGTCGCATTCCA 59.928 47.619 0.00 0.00 0.00 3.53
4915 5099 0.880441 TGGTCGCATTCCATGTGTTG 59.120 50.000 0.00 0.00 41.38 3.33
4959 5143 5.461526 GTTAGGAGCAACATTTTCAGGTTC 58.538 41.667 0.00 0.00 0.00 3.62
4975 5160 4.888239 TCAGGTTCGAAAATTGGTTGGTTA 59.112 37.500 0.00 0.00 0.00 2.85
4996 5181 6.446318 GTTAAGCATGAGAATTGTTTGTCCA 58.554 36.000 0.00 0.00 0.00 4.02
5002 5187 7.557358 AGCATGAGAATTGTTTGTCCATGTATA 59.443 33.333 0.00 0.00 0.00 1.47
5012 5197 3.916035 TGTCCATGTATAGCTCCAGTCT 58.084 45.455 0.00 0.00 0.00 3.24
5014 5199 5.454966 TGTCCATGTATAGCTCCAGTCTAA 58.545 41.667 0.00 0.00 0.00 2.10
5015 5200 5.536538 TGTCCATGTATAGCTCCAGTCTAAG 59.463 44.000 0.00 0.00 0.00 2.18
5016 5201 5.770663 GTCCATGTATAGCTCCAGTCTAAGA 59.229 44.000 0.00 0.00 0.00 2.10
5017 5202 6.435904 GTCCATGTATAGCTCCAGTCTAAGAT 59.564 42.308 0.00 0.00 0.00 2.40
5021 8172 7.695480 TGTATAGCTCCAGTCTAAGATGATC 57.305 40.000 0.00 0.00 0.00 2.92
5037 8188 1.976132 GATCCAGGCTGCAGTGGCTA 61.976 60.000 16.64 1.37 41.04 3.93
5038 8189 1.565390 ATCCAGGCTGCAGTGGCTAA 61.565 55.000 16.64 0.63 41.04 3.09
5059 8210 0.461961 GGCAGGCGATACTCACTCTT 59.538 55.000 0.00 0.00 0.00 2.85
5064 8215 4.678309 GCAGGCGATACTCACTCTTAGTTT 60.678 45.833 0.00 0.00 0.00 2.66
5108 8259 4.495184 CCGGCGTAGGAATTGTTGAATAAC 60.495 45.833 6.01 0.00 37.32 1.89
5115 8266 8.447833 CGTAGGAATTGTTGAATAACTAAGCAA 58.552 33.333 0.00 0.00 37.68 3.91
5217 8958 5.391312 AACTATTCACAAGGGTGCATTTC 57.609 39.130 0.00 0.00 44.87 2.17
5234 8975 4.202090 GCATTTCAGCCCAGGATTAGAAAG 60.202 45.833 0.00 0.00 0.00 2.62
5235 8976 2.717639 TCAGCCCAGGATTAGAAAGC 57.282 50.000 0.00 0.00 0.00 3.51
5240 8981 2.590821 CCCAGGATTAGAAAGCCCATG 58.409 52.381 0.00 0.00 37.80 3.66
5252 8993 2.690778 GCCCATGTCCGCACAGAAC 61.691 63.158 0.00 0.00 35.41 3.01
5253 8994 1.003355 CCCATGTCCGCACAGAACT 60.003 57.895 0.00 0.00 35.41 3.01
5254 8995 0.606401 CCCATGTCCGCACAGAACTT 60.606 55.000 0.00 0.00 35.41 2.66
5255 8996 1.338674 CCCATGTCCGCACAGAACTTA 60.339 52.381 0.00 0.00 35.41 2.24
5257 8998 3.009723 CCATGTCCGCACAGAACTTATT 58.990 45.455 0.00 0.00 35.41 1.40
5258 8999 3.063997 CCATGTCCGCACAGAACTTATTC 59.936 47.826 0.00 0.00 35.41 1.75
5288 9029 3.435327 TCGTCATGGGAAAATTGAAGTCG 59.565 43.478 0.00 0.00 0.00 4.18
5302 9043 5.462530 TTGAAGTCGACTCCATTGAACTA 57.537 39.130 20.33 0.00 0.00 2.24
5309 9050 5.694910 GTCGACTCCATTGAACTAAACAGAA 59.305 40.000 8.70 0.00 0.00 3.02
5423 9164 9.479549 TGGATATATGTACTAGCATCTGAATGA 57.520 33.333 0.00 0.00 34.61 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
268 269 1.508632 CTCACCAAAACGGACGACAT 58.491 50.000 0.00 0.00 38.63 3.06
357 358 0.530650 CAGCAGGCCGACACGATTAT 60.531 55.000 0.00 0.00 0.00 1.28
685 687 9.974980 GTTTGATCCAGTTTATAAGAAAAACCA 57.025 29.630 0.00 0.00 37.51 3.67
717 719 2.037901 TGCTCAAAGTGGCCAAAATGA 58.962 42.857 7.24 11.31 0.00 2.57
797 801 3.659089 ATGCACGTACGTCAGCCCC 62.659 63.158 19.94 3.56 0.00 5.80
871 875 1.330521 GATATTGCGTGCAACCGACAT 59.669 47.619 9.79 0.00 38.88 3.06
872 876 0.724549 GATATTGCGTGCAACCGACA 59.275 50.000 9.79 0.00 38.88 4.35
1236 1247 1.813092 GCATGCATGTGAGAGGTAGGG 60.813 57.143 26.79 0.00 0.00 3.53
1237 1248 1.140452 AGCATGCATGTGAGAGGTAGG 59.860 52.381 26.79 0.00 0.00 3.18
1266 1277 2.961721 CCATGACACGCCGGATCG 60.962 66.667 5.05 1.69 0.00 3.69
1635 1646 1.464997 GTTCCTGTTCCTCATTGTCGC 59.535 52.381 0.00 0.00 0.00 5.19
1645 1656 0.666577 CGTCAGACGGTTCCTGTTCC 60.667 60.000 15.64 0.00 38.08 3.62
1649 1660 4.554163 GTCGTCAGACGGTTCCTG 57.446 61.111 22.66 0.00 42.81 3.86
1693 1704 2.038975 TAGTCCTTGGAGCGCCCT 59.961 61.111 2.29 0.00 35.38 5.19
1798 1809 2.577593 GCGTCGTAGCCCTTCCTT 59.422 61.111 0.00 0.00 0.00 3.36
1837 1848 1.016130 CAAGCCAAGTCGCGATCAGT 61.016 55.000 14.06 0.00 0.00 3.41
1855 1866 3.588955 CATCTTGATCCACTTGACGTCA 58.411 45.455 15.76 15.76 0.00 4.35
1881 1892 2.342406 TCTGGAGGAATGGAGGTTGA 57.658 50.000 0.00 0.00 0.00 3.18
1908 1919 2.022195 AGCTAGCATGCCACTTCATTG 58.978 47.619 18.83 0.00 0.00 2.82
1916 1927 1.500474 AGGAACTAGCTAGCATGCCA 58.500 50.000 20.91 0.00 36.02 4.92
1917 1928 3.033368 GTAGGAACTAGCTAGCATGCC 57.967 52.381 20.91 15.50 44.14 4.40
2035 2047 4.739453 ACGTACTTTCACGCGATTTCTCG 61.739 47.826 15.93 10.20 45.77 4.04
2089 2101 4.562425 GCGCCGATGATTCCCCCA 62.562 66.667 0.00 0.00 0.00 4.96
2166 2179 6.829229 TCTCATCAAGATTGCTTTTGACAT 57.171 33.333 0.00 0.00 36.26 3.06
2210 2223 3.679980 TGCAAAAAGATCGAGACAGCTAC 59.320 43.478 0.00 0.00 0.00 3.58
2214 2227 3.070018 ACCTGCAAAAAGATCGAGACAG 58.930 45.455 0.00 0.00 0.00 3.51
2217 2230 3.685139 AGACCTGCAAAAAGATCGAGA 57.315 42.857 0.00 0.00 0.00 4.04
2220 2233 3.063180 CAGCTAGACCTGCAAAAAGATCG 59.937 47.826 0.00 0.00 0.00 3.69
2221 2234 4.612932 CAGCTAGACCTGCAAAAAGATC 57.387 45.455 0.00 0.00 0.00 2.75
2504 2517 4.456566 CCAATTCTTTTGGCCATTTTGGAG 59.543 41.667 6.09 0.00 40.96 3.86
2703 2808 3.670637 CTGCTAGGCGCTGCAAGGA 62.671 63.158 19.54 8.29 38.81 3.36
2704 2809 3.200593 CTGCTAGGCGCTGCAAGG 61.201 66.667 19.54 9.12 38.81 3.61
2723 2828 3.129113 CGAATCCAGAAACCATGATGCAA 59.871 43.478 0.00 0.00 0.00 4.08
2884 2989 6.020281 TGTTTACTTGTTGCAACATTAAAGCG 60.020 34.615 31.48 15.82 38.95 4.68
2969 3081 4.930463 TGCTAAAACATGAATTACGCGA 57.070 36.364 15.93 0.00 0.00 5.87
3048 3160 1.615392 GCCAGTGAGAATTGCAAAGGT 59.385 47.619 1.71 0.00 0.00 3.50
3263 3378 1.806542 CCGCTTAACACAGTCTGCATT 59.193 47.619 0.00 0.00 0.00 3.56
3344 3459 3.055747 TGTCAATAGCAACGGACCATGTA 60.056 43.478 0.00 0.00 0.00 2.29
3547 3662 9.700831 AGGGTTTACTGAATTATTTAGATTGCT 57.299 29.630 3.71 0.00 0.00 3.91
3575 3690 3.354948 AATTAGCTCCATGCAGACACA 57.645 42.857 0.00 0.00 45.94 3.72
3636 3752 2.482721 CGCACCGAGTGAAAAACCTATT 59.517 45.455 8.04 0.00 35.23 1.73
3696 3812 2.961062 AGGATACGTACCGTTATTGCCT 59.039 45.455 0.00 0.00 41.54 4.75
3756 3873 8.712285 TGGCTAACATTTACAGTTATGTACTC 57.288 34.615 0.00 0.00 41.62 2.59
3761 3878 9.897744 CCATATTGGCTAACATTTACAGTTATG 57.102 33.333 0.00 0.00 31.64 1.90
3762 3879 9.860650 TCCATATTGGCTAACATTTACAGTTAT 57.139 29.630 0.00 0.00 37.47 1.89
3763 3880 9.116067 GTCCATATTGGCTAACATTTACAGTTA 57.884 33.333 0.00 0.00 37.47 2.24
3764 3881 7.068226 GGTCCATATTGGCTAACATTTACAGTT 59.932 37.037 0.00 0.00 37.47 3.16
3890 4008 4.829064 TTGTCAGCTGAATAACACAACC 57.171 40.909 20.19 2.06 0.00 3.77
3896 4014 7.809331 TCATGTTCAATTTGTCAGCTGAATAAC 59.191 33.333 20.19 14.23 30.96 1.89
4033 4151 1.133363 TCTCACGGTTTCTTGGGGAA 58.867 50.000 0.00 0.00 0.00 3.97
4035 4153 2.200373 ATTCTCACGGTTTCTTGGGG 57.800 50.000 0.00 0.00 0.00 4.96
4048 4166 4.940654 TCATGCCAATACGAACAATTCTCA 59.059 37.500 0.00 0.00 0.00 3.27
4049 4167 5.484173 TCATGCCAATACGAACAATTCTC 57.516 39.130 0.00 0.00 0.00 2.87
4060 4178 7.709947 TGATTCTCTTCAATTCATGCCAATAC 58.290 34.615 0.00 0.00 0.00 1.89
4082 4200 4.776308 TGATGCAGAGCCTGATAGTATGAT 59.224 41.667 6.40 0.00 32.44 2.45
4232 4350 4.828829 CATTCAGGGTTACGAGTTACCTT 58.171 43.478 10.66 1.18 33.14 3.50
4289 4407 1.078143 ATGCAGAGGCCGAGGTTTC 60.078 57.895 0.00 0.00 40.13 2.78
4333 4461 0.744281 GACTGCAGGAGAGGCTAGTC 59.256 60.000 19.93 0.00 34.66 2.59
4436 4564 2.135664 AAACGAGTTCACTCAGTCGG 57.864 50.000 7.71 0.00 42.85 4.79
4452 4580 7.498239 AGTCAAGAAAAGTACTCCCTTGTAAAC 59.502 37.037 21.16 15.76 36.53 2.01
4453 4581 7.571025 AGTCAAGAAAAGTACTCCCTTGTAAA 58.429 34.615 21.16 8.52 36.53 2.01
4454 4582 7.133133 AGTCAAGAAAAGTACTCCCTTGTAA 57.867 36.000 21.16 9.00 36.53 2.41
4570 4701 3.890147 CCGGGTAGTAAGTATTGAGCTCT 59.110 47.826 16.19 0.00 0.00 4.09
4576 4707 5.334724 AGAACACCGGGTAGTAAGTATTG 57.665 43.478 6.32 0.00 0.00 1.90
4737 4868 1.001624 GTACCCCGATCGTTTTTCCG 58.998 55.000 15.09 0.00 0.00 4.30
4775 4907 5.428253 TGGTCTATGGAAATGCTGACTTAC 58.572 41.667 0.00 0.00 0.00 2.34
4796 4980 3.621715 GGGTATTTCGCTAGTCAAACTGG 59.378 47.826 0.00 0.00 0.00 4.00
4798 4982 3.056322 ACGGGTATTTCGCTAGTCAAACT 60.056 43.478 0.00 0.00 0.00 2.66
4817 5001 1.136336 GTCAGCTTTTTACTCGCACGG 60.136 52.381 0.00 0.00 0.00 4.94
4819 5003 2.349532 GGTGTCAGCTTTTTACTCGCAC 60.350 50.000 0.00 0.00 0.00 5.34
4847 5031 5.683859 GGCATAAAATGACGCATCTTCTAG 58.316 41.667 0.00 0.00 0.00 2.43
4880 5064 3.364366 GCGACCAGTTCTTGAGTTCAATG 60.364 47.826 0.00 0.00 35.02 2.82
4908 5092 4.998671 TGTTTGGACATGAACAACACAT 57.001 36.364 0.00 0.00 33.19 3.21
4915 5099 3.130340 ACCACTGTTGTTTGGACATGAAC 59.870 43.478 0.00 0.00 36.28 3.18
4959 5143 5.226396 TCATGCTTAACCAACCAATTTTCG 58.774 37.500 0.00 0.00 0.00 3.46
4969 5153 6.815089 ACAAACAATTCTCATGCTTAACCAA 58.185 32.000 0.00 0.00 0.00 3.67
4975 5160 5.011329 ACATGGACAAACAATTCTCATGCTT 59.989 36.000 0.00 0.00 35.34 3.91
4996 5181 7.341769 GGATCATCTTAGACTGGAGCTATACAT 59.658 40.741 0.00 0.00 0.00 2.29
5002 5187 3.896888 CTGGATCATCTTAGACTGGAGCT 59.103 47.826 0.00 0.00 0.00 4.09
5012 5197 2.121948 ACTGCAGCCTGGATCATCTTA 58.878 47.619 15.27 0.00 0.00 2.10
5014 5199 0.180642 CACTGCAGCCTGGATCATCT 59.819 55.000 15.27 0.00 0.00 2.90
5015 5200 0.818445 CCACTGCAGCCTGGATCATC 60.818 60.000 16.55 0.00 0.00 2.92
5016 5201 1.226542 CCACTGCAGCCTGGATCAT 59.773 57.895 16.55 0.00 0.00 2.45
5017 5202 2.672908 CCACTGCAGCCTGGATCA 59.327 61.111 16.55 0.00 0.00 2.92
5021 8172 1.748122 CTTAGCCACTGCAGCCTGG 60.748 63.158 15.27 16.34 41.13 4.45
5037 8188 1.522569 GTGAGTATCGCCTGCCCTT 59.477 57.895 0.00 0.00 40.45 3.95
5038 8189 3.221222 GTGAGTATCGCCTGCCCT 58.779 61.111 0.00 0.00 40.45 5.19
5059 8210 7.526608 CGGTCATTAGCTTTGATGAAAAACTA 58.473 34.615 0.00 0.00 34.34 2.24
5064 8215 3.128589 GGCGGTCATTAGCTTTGATGAAA 59.871 43.478 0.00 0.00 34.34 2.69
5073 8224 4.891727 CGCCGGCGGTCATTAGCT 62.892 66.667 40.50 0.00 35.56 3.32
5217 8958 1.685148 GGCTTTCTAATCCTGGGCTG 58.315 55.000 0.00 0.00 0.00 4.85
5234 8975 2.359850 TTCTGTGCGGACATGGGC 60.360 61.111 11.16 0.00 0.00 5.36
5235 8976 0.606401 AAGTTCTGTGCGGACATGGG 60.606 55.000 11.16 0.00 0.00 4.00
5240 8981 5.358298 AAAAGAATAAGTTCTGTGCGGAC 57.642 39.130 0.00 0.00 43.80 4.79
5264 9005 4.651778 ACTTCAATTTTCCCATGACGAGA 58.348 39.130 0.00 0.00 0.00 4.04
5267 9008 3.435327 TCGACTTCAATTTTCCCATGACG 59.565 43.478 0.00 0.00 0.00 4.35
5288 9029 6.655003 TCCATTCTGTTTAGTTCAATGGAGTC 59.345 38.462 7.46 0.00 44.91 3.36
5302 9043 6.097412 GGAGCCAGATTTATTCCATTCTGTTT 59.903 38.462 0.00 0.00 35.01 2.83
5309 9050 5.163374 GCTTTTGGAGCCAGATTTATTCCAT 60.163 40.000 0.00 0.00 46.01 3.41


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

AutoCloner maintained by Alex Coulton.