Multiple sequence alignment - TraesCS1D01G059200

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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 TraesCS1D01G059200 chr1D 100.000 5814 0 0 1 5814 39292865 39287052 0.000000e+00 10737.0
1 TraesCS1D01G059200 chr1B 93.259 5889 229 77 3 5814 59192377 59198174 0.000000e+00 8521.0
2 TraesCS1D01G059200 chr1A 95.651 4001 123 26 3 3976 38734040 38730064 0.000000e+00 6377.0
3 TraesCS1D01G059200 chr1A 92.865 1892 71 24 3977 5814 38730000 38728119 0.000000e+00 2687.0
4 TraesCS1D01G059200 chr5B 86.667 75 5 4 3172 3246 532610873 532610804 1.740000e-10 78.7
5 TraesCS1D01G059200 chr5B 86.667 75 5 3 3172 3246 532616156 532616087 1.740000e-10 78.7
6 TraesCS1D01G059200 chr3A 86.667 75 5 3 3172 3246 462635862 462635931 1.740000e-10 78.7
7 TraesCS1D01G059200 chr6A 93.182 44 3 0 461 504 617977586 617977543 1.350000e-06 65.8


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 TraesCS1D01G059200 chr1D 39287052 39292865 5813 True 10737 10737 100.000 1 5814 1 chr1D.!!$R1 5813
1 TraesCS1D01G059200 chr1B 59192377 59198174 5797 False 8521 8521 93.259 3 5814 1 chr1B.!!$F1 5811
2 TraesCS1D01G059200 chr1A 38728119 38734040 5921 True 4532 6377 94.258 3 5814 2 chr1A.!!$R1 5811

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
122 127 0.099259 CCAATGTCGCAATGCACGAT 59.901 50.000 5.91 0.0 42.26 3.73 F
239 244 0.260230 AAATGTGGTGGTGGTGGTGA 59.740 50.000 0.00 0.0 0.00 4.02 F
240 245 0.482446 AATGTGGTGGTGGTGGTGAT 59.518 50.000 0.00 0.0 0.00 3.06 F
665 677 0.698818 AAAGCTCCCACCTTTCCGAT 59.301 50.000 0.00 0.0 0.00 4.18 F
2241 2277 0.815734 GCTCCAAGTACAGAGGCGTA 59.184 55.000 8.96 0.0 0.00 4.42 F
3728 3774 1.138883 GCATGTCGACGCCACTCTA 59.861 57.895 11.62 0.0 0.00 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2004 2040 1.762708 ACACTGGTTGGTGTCTTTGG 58.237 50.000 0.0 0.0 45.94 3.28 R
2107 2143 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.0 0.0 0.00 3.33 R
2113 2149 5.178252 CCATCAAACAACAACAACAACAACA 59.822 36.000 0.0 0.0 0.00 3.33 R
2555 2596 1.689273 CCCTGTCCACTGCCTACTATC 59.311 57.143 0.0 0.0 0.00 2.08 R
3868 3914 0.171455 ATGACTCCGAACTCGACAGC 59.829 55.000 0.0 0.0 43.02 4.40 R
5186 5343 1.639722 TCAGCAGTGGTAGTTGGCTA 58.360 50.000 0.0 0.0 32.71 3.93 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
35 36 6.455360 AAGGTTGTCCGTTACGATTATAGA 57.545 37.500 6.24 0.00 39.05 1.98
43 44 7.080724 GTCCGTTACGATTATAGACCTAAAGG 58.919 42.308 6.24 0.00 42.17 3.11
66 67 4.022676 GCCCGGTGAAAAGTAATCAAAAGA 60.023 41.667 0.00 0.00 0.00 2.52
76 77 8.816640 AAAAGTAATCAAAAGATGAATTGCGT 57.183 26.923 0.00 0.00 42.54 5.24
86 88 5.283060 AGATGAATTGCGTAGACAACAAC 57.717 39.130 0.00 0.00 31.03 3.32
106 108 1.529438 CAAAAACTCGTCGCTAGCCAA 59.471 47.619 9.66 0.00 0.00 4.52
122 127 0.099259 CCAATGTCGCAATGCACGAT 59.901 50.000 5.91 0.00 42.26 3.73
208 213 7.930217 TCAAACAAAATTCTAGGAGTGTTCAG 58.070 34.615 0.00 0.00 0.00 3.02
235 240 1.804151 CGTAGAAATGTGGTGGTGGTG 59.196 52.381 0.00 0.00 0.00 4.17
236 241 2.159382 GTAGAAATGTGGTGGTGGTGG 58.841 52.381 0.00 0.00 0.00 4.61
237 242 0.555769 AGAAATGTGGTGGTGGTGGT 59.444 50.000 0.00 0.00 0.00 4.16
238 243 0.673437 GAAATGTGGTGGTGGTGGTG 59.327 55.000 0.00 0.00 0.00 4.17
239 244 0.260230 AAATGTGGTGGTGGTGGTGA 59.740 50.000 0.00 0.00 0.00 4.02
240 245 0.482446 AATGTGGTGGTGGTGGTGAT 59.518 50.000 0.00 0.00 0.00 3.06
241 246 1.367346 ATGTGGTGGTGGTGGTGATA 58.633 50.000 0.00 0.00 0.00 2.15
246 251 2.708861 TGGTGGTGGTGGTGATATATCC 59.291 50.000 10.25 1.94 0.00 2.59
258 263 6.590292 GTGGTGATATATCCGTAAGACCAATG 59.410 42.308 17.44 0.00 43.02 2.82
260 265 6.295688 GGTGATATATCCGTAAGACCAATGGT 60.296 42.308 3.74 3.74 39.44 3.55
274 280 2.229784 CCAATGGTCTGTCCTCAAAAGC 59.770 50.000 0.00 0.00 37.07 3.51
275 281 2.886523 CAATGGTCTGTCCTCAAAAGCA 59.113 45.455 0.00 0.00 37.07 3.91
591 603 4.011517 TCTCCGGCCGTTTCCCAC 62.012 66.667 26.12 0.00 0.00 4.61
632 644 5.627172 TCGCAAAGCTTTTGTCACATATAC 58.373 37.500 9.53 0.00 0.00 1.47
633 645 5.180304 TCGCAAAGCTTTTGTCACATATACA 59.820 36.000 9.53 0.00 0.00 2.29
662 674 0.969149 CCAAAAGCTCCCACCTTTCC 59.031 55.000 0.00 0.00 31.69 3.13
665 677 0.698818 AAAGCTCCCACCTTTCCGAT 59.301 50.000 0.00 0.00 0.00 4.18
946 962 8.642935 TTGAGATTGTTTGGGTTTGATACATA 57.357 30.769 0.00 0.00 0.00 2.29
980 996 5.862924 TCTCGTTGATTGATTGGAAGTTC 57.137 39.130 0.00 0.00 0.00 3.01
1323 1339 2.544359 CCGCAACAACTCGTCACG 59.456 61.111 0.00 0.00 0.00 4.35
1707 1733 5.351458 ACAAATTTTCTTGCTCCTGTTCAC 58.649 37.500 0.00 0.00 0.00 3.18
1848 1882 4.283722 CCTGAACTACCTGTACTGAAACCT 59.716 45.833 0.60 0.00 0.00 3.50
2004 2040 1.662629 CGACATGAAGCAGGTGATCAC 59.337 52.381 17.91 17.91 0.00 3.06
2088 2124 7.985184 AGTACTGTTGTTGAAACTGATGAACTA 59.015 33.333 0.00 0.00 0.00 2.24
2103 2139 9.213799 ACTGATGAACTAAAGAAATTCTGACTC 57.786 33.333 0.00 0.00 0.00 3.36
2106 2142 9.213799 GATGAACTAAAGAAATTCTGACTCTGT 57.786 33.333 0.00 0.00 0.00 3.41
2107 2143 8.964476 TGAACTAAAGAAATTCTGACTCTGTT 57.036 30.769 0.00 0.00 0.00 3.16
2108 2144 8.830580 TGAACTAAAGAAATTCTGACTCTGTTG 58.169 33.333 0.00 0.00 0.00 3.33
2110 2146 8.738645 ACTAAAGAAATTCTGACTCTGTTGTT 57.261 30.769 0.00 0.00 0.00 2.83
2111 2147 8.616076 ACTAAAGAAATTCTGACTCTGTTGTTG 58.384 33.333 0.00 0.00 0.00 3.33
2112 2148 7.396540 AAAGAAATTCTGACTCTGTTGTTGT 57.603 32.000 0.00 0.00 0.00 3.32
2113 2149 7.396540 AAGAAATTCTGACTCTGTTGTTGTT 57.603 32.000 0.00 0.00 0.00 2.83
2114 2150 6.789262 AGAAATTCTGACTCTGTTGTTGTTG 58.211 36.000 0.00 0.00 0.00 3.33
2115 2151 6.375455 AGAAATTCTGACTCTGTTGTTGTTGT 59.625 34.615 0.00 0.00 0.00 3.32
2134 2170 5.580691 TGTTGTTGTTGTTGTTGTTGTTTGA 59.419 32.000 0.00 0.00 0.00 2.69
2241 2277 0.815734 GCTCCAAGTACAGAGGCGTA 59.184 55.000 8.96 0.00 0.00 4.42
2305 2341 4.062991 GTTCCTCGGCAAGAAGTAAGAAA 58.937 43.478 0.00 0.00 0.00 2.52
2308 2344 5.313712 TCCTCGGCAAGAAGTAAGAAAAAT 58.686 37.500 0.00 0.00 0.00 1.82
2412 2450 2.303890 TCTCTGGATGTGATTGTGCTGT 59.696 45.455 0.00 0.00 0.00 4.40
2523 2562 7.875327 AAGCAGTAGTTCTTAGGTTGAAAAA 57.125 32.000 0.00 0.00 0.00 1.94
2571 2615 4.946478 AATGAGATAGTAGGCAGTGGAC 57.054 45.455 0.00 0.00 0.00 4.02
2821 2865 3.616821 CGATCAAATGCAACGGTAGAGAA 59.383 43.478 0.00 0.00 0.00 2.87
2979 3024 4.672587 ATTCTGCGTTGGAGATTAGCTA 57.327 40.909 0.00 0.00 0.00 3.32
2988 3033 6.510317 GCGTTGGAGATTAGCTAATGAACTTC 60.510 42.308 23.51 13.25 0.00 3.01
3400 3446 4.817464 TCACCACACAGTAACATGTTTACC 59.183 41.667 17.78 5.49 0.00 2.85
3551 3597 2.093973 GGTCGCAATCCCTCATCGATAT 60.094 50.000 0.00 0.00 0.00 1.63
3643 3689 8.736244 GGTGAGGTGATACTAAATTTTAAAGCA 58.264 33.333 0.00 0.00 0.00 3.91
3688 3734 1.604185 GGCTCTGATGACGCCAGATAC 60.604 57.143 1.16 0.00 43.25 2.24
3695 3741 1.729838 GACGCCAGATACGGATCGC 60.730 63.158 0.92 0.00 37.15 4.58
3728 3774 1.138883 GCATGTCGACGCCACTCTA 59.861 57.895 11.62 0.00 0.00 2.43
3745 3791 6.115446 CCACTCTATTTTGCAATCAGGACTA 58.885 40.000 0.00 0.00 0.00 2.59
3851 3897 2.967887 AGCTCAAGTTGGCCTGATTTTT 59.032 40.909 3.32 0.00 0.00 1.94
3866 3912 5.300286 CCTGATTTTTCATAGTCCACCCATC 59.700 44.000 0.00 0.00 0.00 3.51
3868 3914 3.275617 TTTTCATAGTCCACCCATCCG 57.724 47.619 0.00 0.00 0.00 4.18
3880 3926 1.874019 CCATCCGCTGTCGAGTTCG 60.874 63.158 0.00 0.00 38.10 3.95
4008 4119 9.003658 AGTATAAATATGCTTGATTTTCCTCCG 57.996 33.333 0.00 0.00 0.00 4.63
4191 4319 7.607991 AGAAAACAGATCTGAATCGTACCAATT 59.392 33.333 29.27 5.39 36.97 2.32
4247 4375 4.313277 ACTTGGAAGCAAAAGAAAGCTC 57.687 40.909 0.00 0.00 40.90 4.09
4265 4393 0.036765 TCGCAAGTCGGCACCTTATT 60.037 50.000 0.00 0.00 39.05 1.40
4278 4417 5.358725 CGGCACCTTATTGTAATAGGGTTTT 59.641 40.000 13.79 0.00 45.76 2.43
4297 4436 7.613411 AGGGTTTTCCATTTGTTTTGAAAATCA 59.387 29.630 8.54 0.00 38.79 2.57
4341 4488 8.313292 CCTAAATTATCCTCTCAGATTCCTCAG 58.687 40.741 0.00 0.00 0.00 3.35
4344 4491 2.386779 TCCTCTCAGATTCCTCAGCTG 58.613 52.381 7.63 7.63 0.00 4.24
4345 4492 1.413445 CCTCTCAGATTCCTCAGCTGG 59.587 57.143 15.13 4.45 0.00 4.85
4350 4497 4.161189 TCTCAGATTCCTCAGCTGGTAAAG 59.839 45.833 15.13 3.26 0.00 1.85
4362 4509 6.769512 TCAGCTGGTAAAGTTCAAGAGTATT 58.230 36.000 15.13 0.00 0.00 1.89
4375 4522 6.466308 TCAAGAGTATTTTCACATGTGTCG 57.534 37.500 24.63 0.02 0.00 4.35
4420 4572 7.756722 CCAAAAGAAAGTTTAGCTGGACATATG 59.243 37.037 0.00 0.00 0.00 1.78
4427 4579 5.900123 AGTTTAGCTGGACATATGTACCTCT 59.100 40.000 15.66 13.64 0.00 3.69
4440 4592 4.978083 TGTACCTCTCCTTTATGTCGAC 57.022 45.455 9.11 9.11 0.00 4.20
4542 4694 8.158169 TCCTACATGAGCAAGCTAAATTATTG 57.842 34.615 0.00 0.00 0.00 1.90
4545 4697 9.793252 CTACATGAGCAAGCTAAATTATTGTTT 57.207 29.630 0.00 0.00 0.00 2.83
4969 5126 4.829492 CCAAGTGAAATGTCCCTTCTTCTT 59.171 41.667 0.00 0.00 0.00 2.52
4985 5142 0.037046 TCTTTGCGCTCTCTGCATCA 60.037 50.000 9.73 0.00 42.84 3.07
5186 5343 4.829492 AGTTGGCTCTTGTTTTTGCTCTAT 59.171 37.500 0.00 0.00 0.00 1.98
5224 5381 5.804473 TGCTGAATTGTACTGTTGTTTGTTG 59.196 36.000 0.00 0.00 0.00 3.33
5264 5421 1.679032 GGCTCTAACGGATGCCAAAGT 60.679 52.381 0.00 0.00 44.34 2.66
5381 5564 9.941664 CAAAGTATGCCTAGAAATGTCAATTAG 57.058 33.333 0.00 0.00 0.00 1.73
5504 5687 7.233389 ACAGATACTTCAGAAGCACTAGAAA 57.767 36.000 10.33 0.00 0.00 2.52
5505 5688 7.671302 ACAGATACTTCAGAAGCACTAGAAAA 58.329 34.615 10.33 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.893489 GGACAACCTTTCCAGCTCATTT 59.107 45.455 0.00 0.00 32.82 2.32
1 2 2.519013 GGACAACCTTTCCAGCTCATT 58.481 47.619 0.00 0.00 32.82 2.57
35 36 0.479378 TTTTCACCGGGCCTTTAGGT 59.521 50.000 6.32 4.69 39.12 3.08
43 44 3.926821 TTTGATTACTTTTCACCGGGC 57.073 42.857 6.32 0.00 0.00 6.13
66 67 5.431420 TTGTTGTTGTCTACGCAATTCAT 57.569 34.783 0.00 0.00 0.00 2.57
76 77 4.492895 GCGACGAGTTTTTGTTGTTGTCTA 60.493 41.667 0.00 0.00 0.00 2.59
86 88 1.144969 TGGCTAGCGACGAGTTTTTG 58.855 50.000 9.00 0.00 0.00 2.44
106 108 2.224079 GGATAATCGTGCATTGCGACAT 59.776 45.455 3.84 0.00 41.33 3.06
122 127 1.421268 AGAGCCATTCCATGCGGATAA 59.579 47.619 0.00 0.00 42.41 1.75
208 213 3.930848 CCACCACATTTCTACGGTTCTAC 59.069 47.826 0.00 0.00 0.00 2.59
235 240 6.106673 CCATTGGTCTTACGGATATATCACC 58.893 44.000 14.60 11.81 0.00 4.02
236 241 6.698380 ACCATTGGTCTTACGGATATATCAC 58.302 40.000 14.60 2.95 0.00 3.06
237 242 6.928348 ACCATTGGTCTTACGGATATATCA 57.072 37.500 14.60 0.00 0.00 2.15
258 263 3.149196 TCAATGCTTTTGAGGACAGACC 58.851 45.455 0.00 0.00 39.35 3.85
260 265 5.126869 TGTTTTCAATGCTTTTGAGGACAGA 59.873 36.000 12.15 0.00 0.00 3.41
361 369 4.202253 GGGGGCAAATTATAAGGAGCAAAG 60.202 45.833 7.74 0.00 0.00 2.77
610 622 5.389778 TGTATATGTGACAAAAGCTTTGCG 58.610 37.500 13.54 9.82 0.00 4.85
613 625 7.944729 AGGATGTATATGTGACAAAAGCTTT 57.055 32.000 5.69 5.69 0.00 3.51
624 636 7.467811 GCTTTTGGAGTGAAGGATGTATATGTG 60.468 40.741 0.00 0.00 0.00 3.21
625 637 6.543831 GCTTTTGGAGTGAAGGATGTATATGT 59.456 38.462 0.00 0.00 0.00 2.29
632 644 2.751806 GGAGCTTTTGGAGTGAAGGATG 59.248 50.000 0.00 0.00 0.00 3.51
633 645 2.291217 GGGAGCTTTTGGAGTGAAGGAT 60.291 50.000 0.00 0.00 0.00 3.24
946 962 6.873997 TCAATCAACGAGAACACACCTATAT 58.126 36.000 0.00 0.00 0.00 0.86
952 968 4.213270 TCCAATCAATCAACGAGAACACAC 59.787 41.667 0.00 0.00 0.00 3.82
953 969 4.384940 TCCAATCAATCAACGAGAACACA 58.615 39.130 0.00 0.00 0.00 3.72
980 996 1.519455 GCCGAGATCACCACTTCCG 60.519 63.158 0.00 0.00 0.00 4.30
1848 1882 4.141733 TGAACAGAGTGGACATGACTTCAA 60.142 41.667 0.00 0.00 0.00 2.69
2004 2040 1.762708 ACACTGGTTGGTGTCTTTGG 58.237 50.000 0.00 0.00 45.94 3.28
2028 2064 6.808829 TGCATCTGAATAATTTGGTTGGATC 58.191 36.000 0.00 0.00 0.00 3.36
2088 2124 7.396540 ACAACAACAGAGTCAGAATTTCTTT 57.603 32.000 0.00 0.00 0.00 2.52
2103 2139 5.006165 ACAACAACAACAACAACAACAACAG 59.994 36.000 0.00 0.00 0.00 3.16
2106 2142 5.351465 ACAACAACAACAACAACAACAACAA 59.649 32.000 0.00 0.00 0.00 2.83
2107 2143 4.870426 ACAACAACAACAACAACAACAACA 59.130 33.333 0.00 0.00 0.00 3.33
2108 2144 5.396750 ACAACAACAACAACAACAACAAC 57.603 34.783 0.00 0.00 0.00 3.32
2110 2146 5.580691 TCAAACAACAACAACAACAACAACA 59.419 32.000 0.00 0.00 0.00 3.33
2111 2147 6.037423 TCAAACAACAACAACAACAACAAC 57.963 33.333 0.00 0.00 0.00 3.32
2112 2148 6.293081 CCATCAAACAACAACAACAACAACAA 60.293 34.615 0.00 0.00 0.00 2.83
2113 2149 5.178252 CCATCAAACAACAACAACAACAACA 59.822 36.000 0.00 0.00 0.00 3.33
2114 2150 5.406780 TCCATCAAACAACAACAACAACAAC 59.593 36.000 0.00 0.00 0.00 3.32
2115 2151 5.541845 TCCATCAAACAACAACAACAACAA 58.458 33.333 0.00 0.00 0.00 2.83
2134 2170 5.456330 CCTTCATCTGATCCAGAACATCCAT 60.456 44.000 0.43 0.00 44.04 3.41
2241 2277 2.906897 CCGCACTTGTGCAGGGTT 60.907 61.111 22.97 0.00 34.41 4.11
2305 2341 5.133491 TGGTTCAAAATGGAAGGGGAAATTT 59.867 36.000 0.00 0.00 0.00 1.82
2308 2344 3.658725 TGGTTCAAAATGGAAGGGGAAA 58.341 40.909 0.00 0.00 0.00 3.13
2412 2450 4.486839 TCAGATTCAGATCAGATAGGCCA 58.513 43.478 5.01 0.00 34.60 5.36
2555 2596 1.689273 CCCTGTCCACTGCCTACTATC 59.311 57.143 0.00 0.00 0.00 2.08
2821 2865 1.081376 CTCGAAGTTCGTCACGGCT 60.081 57.895 23.67 0.00 41.35 5.52
2988 3033 5.217393 CCTGCCAATCGTCATAATCAAATG 58.783 41.667 0.00 0.00 0.00 2.32
3168 3214 1.963515 GTGAAATTGGACTGGTTGCCT 59.036 47.619 0.00 0.00 0.00 4.75
3400 3446 3.356529 AACCATAGTCAGGCAGGAAAG 57.643 47.619 0.00 0.00 0.00 2.62
3499 3545 2.487934 GAGCATCGACCTGCATAACAT 58.512 47.619 13.17 0.00 44.77 2.71
3551 3597 1.306141 ATGCTCGGTCAGAAGGGGA 60.306 57.895 0.00 0.00 0.00 4.81
3643 3689 7.373617 ACCATGAAAATTTTAGGTGAAAGGT 57.626 32.000 16.86 8.87 0.00 3.50
3695 3741 3.182372 CGACATGCTCAATATGTACGGTG 59.818 47.826 0.00 0.00 38.78 4.94
3728 3774 4.592942 TCAGCTAGTCCTGATTGCAAAAT 58.407 39.130 1.71 0.00 36.96 1.82
3745 3791 2.483363 GCACTATCAGTCTGCATCAGCT 60.483 50.000 0.00 0.00 42.74 4.24
3851 3897 0.398522 AGCGGATGGGTGGACTATGA 60.399 55.000 0.00 0.00 0.00 2.15
3866 3912 2.202492 CTCCGAACTCGACAGCGG 60.202 66.667 0.00 8.37 44.83 5.52
3868 3914 0.171455 ATGACTCCGAACTCGACAGC 59.829 55.000 0.00 0.00 43.02 4.40
3880 3926 7.573968 AATTGTGCTAGGAATTAATGACTCC 57.426 36.000 0.00 0.00 0.00 3.85
3913 3959 6.042093 ACAGTTTGTGAGAACTCAAGATCCTA 59.958 38.462 6.08 0.00 41.85 2.94
3926 3972 5.304686 ACCCAATTAGACAGTTTGTGAGA 57.695 39.130 0.00 0.00 0.00 3.27
4008 4119 6.103330 GTCAACTCTCTAGGATGTTCCTTTC 58.897 44.000 0.59 0.00 46.91 2.62
4117 4245 9.706691 CTGAATGGTGGTCGTACTATTATAAAT 57.293 33.333 0.00 0.00 32.76 1.40
4118 4246 8.916062 TCTGAATGGTGGTCGTACTATTATAAA 58.084 33.333 0.00 0.00 32.76 1.40
4119 4247 8.467963 TCTGAATGGTGGTCGTACTATTATAA 57.532 34.615 0.00 0.00 32.76 0.98
4120 4248 7.176165 CCTCTGAATGGTGGTCGTACTATTATA 59.824 40.741 0.00 0.00 32.76 0.98
4121 4249 6.015350 CCTCTGAATGGTGGTCGTACTATTAT 60.015 42.308 0.00 0.00 32.76 1.28
4122 4250 5.301045 CCTCTGAATGGTGGTCGTACTATTA 59.699 44.000 0.00 0.00 32.76 0.98
4123 4251 4.099573 CCTCTGAATGGTGGTCGTACTATT 59.900 45.833 0.00 0.00 34.91 1.73
4124 4252 3.637229 CCTCTGAATGGTGGTCGTACTAT 59.363 47.826 0.00 0.00 0.00 2.12
4125 4253 3.021695 CCTCTGAATGGTGGTCGTACTA 58.978 50.000 0.00 0.00 0.00 1.82
4126 4254 1.825474 CCTCTGAATGGTGGTCGTACT 59.175 52.381 0.00 0.00 0.00 2.73
4127 4255 1.549170 ACCTCTGAATGGTGGTCGTAC 59.451 52.381 0.00 0.00 36.30 3.67
4128 4256 1.933021 ACCTCTGAATGGTGGTCGTA 58.067 50.000 0.00 0.00 36.30 3.43
4129 4257 1.056660 AACCTCTGAATGGTGGTCGT 58.943 50.000 0.00 0.00 37.93 4.34
4130 4258 2.185004 AAACCTCTGAATGGTGGTCG 57.815 50.000 0.00 0.00 37.93 4.79
4171 4299 8.824159 AATAGAATTGGTACGATTCAGATCTG 57.176 34.615 17.07 17.07 36.26 2.90
4191 4319 8.915057 AGCCGTACTCATACTACTAAAATAGA 57.085 34.615 0.00 0.00 0.00 1.98
4247 4375 0.096976 CAATAAGGTGCCGACTTGCG 59.903 55.000 0.00 0.00 40.47 4.85
4265 4393 8.705594 TCAAAACAAATGGAAAACCCTATTACA 58.294 29.630 0.00 0.00 35.38 2.41
4297 4436 8.978874 AATTTAGGAAAAGTGAAATGGCTTTT 57.021 26.923 0.00 0.00 44.55 2.27
4301 4440 8.478066 AGGATAATTTAGGAAAAGTGAAATGGC 58.522 33.333 0.00 0.00 0.00 4.40
4307 4454 9.046846 TCTGAGAGGATAATTTAGGAAAAGTGA 57.953 33.333 0.00 0.00 0.00 3.41
4308 4455 9.844257 ATCTGAGAGGATAATTTAGGAAAAGTG 57.156 33.333 0.00 0.00 0.00 3.16
4341 4488 7.803659 GTGAAAATACTCTTGAACTTTACCAGC 59.196 37.037 0.00 0.00 0.00 4.85
4344 4491 9.612620 CATGTGAAAATACTCTTGAACTTTACC 57.387 33.333 0.00 0.00 0.00 2.85
4350 4497 6.792250 CGACACATGTGAAAATACTCTTGAAC 59.208 38.462 31.94 0.00 0.00 3.18
4362 4509 8.918961 AAAATAAGAAAACGACACATGTGAAA 57.081 26.923 31.94 5.08 0.00 2.69
4396 4543 8.409358 ACATATGTCCAGCTAAACTTTCTTTT 57.591 30.769 1.41 0.00 0.00 2.27
4401 4550 6.958767 AGGTACATATGTCCAGCTAAACTTT 58.041 36.000 12.68 0.00 0.00 2.66
4407 4556 4.106502 AGGAGAGGTACATATGTCCAGCTA 59.893 45.833 12.68 0.00 0.00 3.32
4420 4572 3.698040 TGGTCGACATAAAGGAGAGGTAC 59.302 47.826 18.91 0.00 0.00 3.34
4427 4579 2.028839 TCGCTTTGGTCGACATAAAGGA 60.029 45.455 29.62 24.26 33.25 3.36
4440 4592 2.678336 GGTCTAATTCCTGTCGCTTTGG 59.322 50.000 0.00 0.00 0.00 3.28
4489 4641 7.804843 ATTCAACAAAATTGGCAGAAATTGA 57.195 28.000 10.12 4.75 30.21 2.57
4542 4694 6.542370 TCTGGCTGCTTCCTACATAAATAAAC 59.458 38.462 0.00 0.00 0.00 2.01
4545 4697 5.602561 TCTCTGGCTGCTTCCTACATAAATA 59.397 40.000 0.00 0.00 0.00 1.40
4553 4709 2.165357 TGATCTCTGGCTGCTTCCTA 57.835 50.000 0.00 0.00 0.00 2.94
4985 5142 1.956477 GAATTATGGGACCAATGCGCT 59.044 47.619 9.73 0.00 0.00 5.92
5186 5343 1.639722 TCAGCAGTGGTAGTTGGCTA 58.360 50.000 0.00 0.00 32.71 3.93
5224 5381 3.735746 GCCAAATCTTGTAACAGTGCAAC 59.264 43.478 0.00 0.00 0.00 4.17
5307 5483 6.771267 AGTCATGCATGTCAGATGTTATCATT 59.229 34.615 25.43 0.00 34.06 2.57
5314 5490 2.504585 AGGAGTCATGCATGTCAGATGT 59.495 45.455 25.43 4.52 0.00 3.06
5315 5491 3.195471 AGGAGTCATGCATGTCAGATG 57.805 47.619 25.43 0.16 0.00 2.90
5316 5492 5.363562 TTTAGGAGTCATGCATGTCAGAT 57.636 39.130 25.43 12.89 0.00 2.90
5317 5493 4.824479 TTTAGGAGTCATGCATGTCAGA 57.176 40.909 25.43 4.01 0.00 3.27
5318 5494 5.821470 AGAATTTAGGAGTCATGCATGTCAG 59.179 40.000 25.43 0.54 0.00 3.51
5319 5495 5.587443 CAGAATTTAGGAGTCATGCATGTCA 59.413 40.000 25.43 5.20 0.00 3.58
5320 5496 5.587844 ACAGAATTTAGGAGTCATGCATGTC 59.412 40.000 25.43 20.17 0.00 3.06
5321 5497 5.503927 ACAGAATTTAGGAGTCATGCATGT 58.496 37.500 25.43 8.12 0.00 3.21
5381 5564 8.614469 TTTCCATTGGAAATCACCATTTTTAC 57.386 30.769 23.89 0.00 45.42 2.01


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

AutoCloner maintained by Alex Coulton.