Multiple sequence alignment - TraesCS1D01G186500

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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 TraesCS1D01G186500 chr1D 100.000 6978 0 0 1 6978 257415793 257408816 0.000000e+00 12887.0
1 TraesCS1D01G186500 chr1A 93.639 6367 201 59 704 6978 331323537 331317283 0.000000e+00 9326.0
2 TraesCS1D01G186500 chr1A 100.000 30 0 0 6320 6349 576535145 576535174 1.000000e-03 56.5
3 TraesCS1D01G186500 chr1A 100.000 28 0 0 5691 5718 331318583 331318556 1.300000e-02 52.8
4 TraesCS1D01G186500 chr1B 90.833 3480 164 57 704 4079 355678966 355675538 0.000000e+00 4516.0
5 TraesCS1D01G186500 chr1B 92.790 2330 119 31 4176 6478 355675536 355673229 0.000000e+00 3326.0
6 TraesCS1D01G186500 chr1B 86.878 442 54 4 6539 6978 355673218 355672779 6.290000e-135 492.0
7 TraesCS1D01G186500 chr6D 93.352 707 42 4 1 706 62874831 62875533 0.000000e+00 1040.0
8 TraesCS1D01G186500 chr6D 93.324 704 44 2 1 703 471362605 471361904 0.000000e+00 1037.0
9 TraesCS1D01G186500 chr2D 92.676 710 49 3 1 709 50974216 50973509 0.000000e+00 1020.0
10 TraesCS1D01G186500 chr2D 92.482 705 44 5 1 703 519143717 519144414 0.000000e+00 1000.0
11 TraesCS1D01G186500 chr2D 85.638 188 23 3 6662 6847 579754541 579754356 1.990000e-45 195.0
12 TraesCS1D01G186500 chr7B 92.857 700 47 2 1 699 654079296 654079993 0.000000e+00 1013.0
13 TraesCS1D01G186500 chr5B 92.878 688 46 2 20 706 680249024 680249709 0.000000e+00 996.0
14 TraesCS1D01G186500 chr5B 85.635 181 23 2 6662 6839 646377776 646377956 3.320000e-43 187.0
15 TraesCS1D01G186500 chr7D 92.672 696 41 10 15 706 587993144 587992455 0.000000e+00 994.0
16 TraesCS1D01G186500 chr6B 92.429 700 44 5 1 699 625076570 625075879 0.000000e+00 990.0
17 TraesCS1D01G186500 chr6B 85.635 181 23 2 6662 6839 558601715 558601895 3.320000e-43 187.0
18 TraesCS1D01G186500 chr6B 100.000 29 0 0 6319 6347 675195078 675195106 4.000000e-03 54.7
19 TraesCS1D01G186500 chr6B 100.000 28 0 0 2442 2469 414606915 414606888 1.300000e-02 52.8
20 TraesCS1D01G186500 chr2B 92.174 690 49 5 20 706 82423958 82423271 0.000000e+00 970.0
21 TraesCS1D01G186500 chr2B 80.711 197 29 6 2520 2711 109297637 109297445 2.030000e-30 145.0
22 TraesCS1D01G186500 chr2B 75.704 284 38 22 2447 2716 34146569 34146303 5.720000e-21 113.0
23 TraesCS1D01G186500 chr3A 86.486 185 22 2 6662 6843 737517900 737517716 4.270000e-47 200.0
24 TraesCS1D01G186500 chr5D 86.188 181 22 2 6662 6839 552044583 552044763 7.140000e-45 193.0
25 TraesCS1D01G186500 chr5D 84.817 191 24 4 6662 6849 535902020 535902208 3.320000e-43 187.0
26 TraesCS1D01G186500 chr2A 84.080 201 25 7 6673 6867 5605348 5605547 3.320000e-43 187.0
27 TraesCS1D01G186500 chr7A 90.698 43 2 2 6320 6362 2741905 2741945 1.000000e-03 56.5
28 TraesCS1D01G186500 chr7A 94.286 35 2 0 6321 6355 2741896 2741862 4.000000e-03 54.7
29 TraesCS1D01G186500 chr7A 94.286 35 2 0 6321 6355 2762666 2762632 4.000000e-03 54.7
30 TraesCS1D01G186500 chr6A 100.000 30 0 0 6320 6349 430337032 430337003 1.000000e-03 56.5
31 TraesCS1D01G186500 chr5A 100.000 29 0 0 6319 6347 437922414 437922386 4.000000e-03 54.7
32 TraesCS1D01G186500 chr5A 92.308 39 2 1 6319 6356 667326422 667326460 4.000000e-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 TraesCS1D01G186500 chr1D 257408816 257415793 6977 True 12887 12887 100.000 1 6978 1 chr1D.!!$R1 6977
1 TraesCS1D01G186500 chr1A 331317283 331323537 6254 True 9326 9326 93.639 704 6978 1 chr1A.!!$R1 6274
2 TraesCS1D01G186500 chr1B 355672779 355678966 6187 True 2778 4516 90.167 704 6978 3 chr1B.!!$R1 6274
3 TraesCS1D01G186500 chr6D 62874831 62875533 702 False 1040 1040 93.352 1 706 1 chr6D.!!$F1 705
4 TraesCS1D01G186500 chr6D 471361904 471362605 701 True 1037 1037 93.324 1 703 1 chr6D.!!$R1 702
5 TraesCS1D01G186500 chr2D 50973509 50974216 707 True 1020 1020 92.676 1 709 1 chr2D.!!$R1 708
6 TraesCS1D01G186500 chr2D 519143717 519144414 697 False 1000 1000 92.482 1 703 1 chr2D.!!$F1 702
7 TraesCS1D01G186500 chr7B 654079296 654079993 697 False 1013 1013 92.857 1 699 1 chr7B.!!$F1 698
8 TraesCS1D01G186500 chr5B 680249024 680249709 685 False 996 996 92.878 20 706 1 chr5B.!!$F2 686
9 TraesCS1D01G186500 chr7D 587992455 587993144 689 True 994 994 92.672 15 706 1 chr7D.!!$R1 691
10 TraesCS1D01G186500 chr6B 625075879 625076570 691 True 990 990 92.429 1 699 1 chr6B.!!$R2 698
11 TraesCS1D01G186500 chr2B 82423271 82423958 687 True 970 970 92.174 20 706 1 chr2B.!!$R2 686

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
331 334 0.031010 GAGGGGGATCTAGTGGGTGT 60.031 60.000 0.00 0.00 0.00 4.16 F
664 671 0.106149 GATACCGGGGCAGATTTCGT 59.894 55.000 6.32 0.00 0.00 3.85 F
1057 1080 0.599204 GAAGCGGAACCGTCTCAACA 60.599 55.000 14.63 0.00 42.09 3.33 F
2145 2249 0.036875 TTCCCACACACACACACACA 59.963 50.000 0.00 0.00 0.00 3.72 F
2458 2576 0.886563 CACTTCGTACTCCCTCCGTT 59.113 55.000 0.00 0.00 0.00 4.44 F
2459 2577 1.135460 CACTTCGTACTCCCTCCGTTC 60.135 57.143 0.00 0.00 0.00 3.95 F
3917 4048 0.823356 TGGTGCCAAAAGAGCTCCAC 60.823 55.000 10.93 9.95 46.09 4.02 F
4271 4414 0.107654 GGGACATAGCGGTCTTTGCT 60.108 55.000 0.00 0.00 46.29 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2082 2158 0.109132 GTGTACCGGGACAACCTACG 60.109 60.000 24.37 0.00 36.97 3.51 R
2083 2159 0.247460 GGTGTACCGGGACAACCTAC 59.753 60.000 25.55 9.93 36.97 3.18 R
2182 2286 0.609957 TGCATCAACCCAGGCAGAAG 60.610 55.000 0.00 0.00 0.00 2.85 R
3091 3218 2.103373 TCCTAGCAGGTGATGAGTGAC 58.897 52.381 2.68 0.00 36.53 3.67 R
3800 3931 2.368875 TCGAGAGCTAAAATCCCATCCC 59.631 50.000 0.00 0.00 0.00 3.85 R
4271 4414 2.639347 TGCCTTCTCTCCAATGAGTTCA 59.361 45.455 0.00 0.00 39.75 3.18 R
5830 5983 0.179092 ACAGTTCGCCGGCTATAACC 60.179 55.000 26.68 10.37 0.00 2.85 R
5991 6144 1.244019 ACAAGCAGGATTTGACCCGC 61.244 55.000 0.00 0.00 0.00 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
77 78 8.838741 TCATTATACCTAACCCTAACAAAACCT 58.161 33.333 0.00 0.00 0.00 3.50
291 294 4.098960 GTGATGCAAATGACCTCAATCCAT 59.901 41.667 0.00 0.00 0.00 3.41
293 296 3.972133 TGCAAATGACCTCAATCCATCT 58.028 40.909 0.00 0.00 0.00 2.90
296 299 2.251409 ATGACCTCAATCCATCTGCG 57.749 50.000 0.00 0.00 0.00 5.18
331 334 0.031010 GAGGGGGATCTAGTGGGTGT 60.031 60.000 0.00 0.00 0.00 4.16
338 341 3.264964 GGGATCTAGTGGGTGTTTTGGTA 59.735 47.826 0.00 0.00 0.00 3.25
339 342 4.514401 GGATCTAGTGGGTGTTTTGGTAG 58.486 47.826 0.00 0.00 0.00 3.18
420 425 2.124403 GAGCAGCACATCCCCCTG 60.124 66.667 0.00 0.00 0.00 4.45
659 664 3.312736 AAAATTGATACCGGGGCAGAT 57.687 42.857 6.32 0.00 0.00 2.90
660 665 3.312736 AAATTGATACCGGGGCAGATT 57.687 42.857 6.32 0.00 0.00 2.40
664 671 0.106149 GATACCGGGGCAGATTTCGT 59.894 55.000 6.32 0.00 0.00 3.85
681 688 7.908082 CAGATTTCGTTTTTATATGCCGAAAGA 59.092 33.333 10.62 0.00 46.54 2.52
709 716 5.486735 AACATGAAATTTTGCCTCCATGA 57.513 34.783 17.43 0.00 36.29 3.07
714 721 1.125633 ATTTTGCCTCCATGATGGGC 58.874 50.000 12.26 8.69 45.45 5.36
823 836 5.450550 CGAAAAAGAAAAGAGAAGCCCAACT 60.451 40.000 0.00 0.00 0.00 3.16
927 946 2.103581 TAAAAACCCACGCGTCGCAC 62.104 55.000 18.75 0.00 0.00 5.34
957 976 2.559998 AACCGCCAGCAAAATTATCG 57.440 45.000 0.00 0.00 0.00 2.92
983 1002 1.937546 CTTTCCATCAGCCAACCGCC 61.938 60.000 0.00 0.00 38.78 6.13
1057 1080 0.599204 GAAGCGGAACCGTCTCAACA 60.599 55.000 14.63 0.00 42.09 3.33
1111 1171 4.199310 CAACAGAACAGAAAACCCTCTCA 58.801 43.478 0.00 0.00 0.00 3.27
1201 1270 3.071206 AGCGCAGATGGAGACCGT 61.071 61.111 11.47 0.00 0.00 4.83
1658 1730 4.660938 GTGCCGGGCTCCAGGTTT 62.661 66.667 21.46 0.00 0.00 3.27
1802 1878 2.724977 TCTTCCACTTGTCAGCTACG 57.275 50.000 0.00 0.00 0.00 3.51
1803 1879 1.272490 TCTTCCACTTGTCAGCTACGG 59.728 52.381 0.00 0.00 0.00 4.02
1804 1880 1.272490 CTTCCACTTGTCAGCTACGGA 59.728 52.381 0.00 0.00 0.00 4.69
1805 1881 0.888619 TCCACTTGTCAGCTACGGAG 59.111 55.000 0.00 0.00 0.00 4.63
1807 1883 1.816835 CCACTTGTCAGCTACGGAGTA 59.183 52.381 0.00 0.00 45.11 2.59
1808 1884 2.415625 CCACTTGTCAGCTACGGAGTAC 60.416 54.545 0.00 0.00 45.11 2.73
1809 1885 2.488545 CACTTGTCAGCTACGGAGTACT 59.511 50.000 0.00 0.00 45.11 2.73
1810 1886 3.057456 CACTTGTCAGCTACGGAGTACTT 60.057 47.826 0.00 0.00 45.11 2.24
1811 1887 4.155462 CACTTGTCAGCTACGGAGTACTTA 59.845 45.833 0.00 0.00 45.11 2.24
1812 1888 4.155644 ACTTGTCAGCTACGGAGTACTTAC 59.844 45.833 0.00 0.00 45.11 2.34
1850 1926 1.993301 AGCTAGGTAGGTTGCCCTTTT 59.007 47.619 0.00 0.00 42.66 2.27
1930 2006 5.350365 TGTCACGTAATCAAAGGAAGCATAC 59.650 40.000 0.00 0.00 0.00 2.39
1931 2007 5.581085 GTCACGTAATCAAAGGAAGCATACT 59.419 40.000 0.00 0.00 0.00 2.12
1932 2008 5.580691 TCACGTAATCAAAGGAAGCATACTG 59.419 40.000 0.00 0.00 0.00 2.74
1933 2009 5.351465 CACGTAATCAAAGGAAGCATACTGT 59.649 40.000 0.00 0.00 0.00 3.55
1934 2010 5.351465 ACGTAATCAAAGGAAGCATACTGTG 59.649 40.000 0.00 0.00 0.00 3.66
1935 2011 5.351465 CGTAATCAAAGGAAGCATACTGTGT 59.649 40.000 0.00 0.00 0.00 3.72
1936 2012 5.633830 AATCAAAGGAAGCATACTGTGTG 57.366 39.130 0.00 0.00 0.00 3.82
1937 2013 3.411446 TCAAAGGAAGCATACTGTGTGG 58.589 45.455 6.67 0.00 0.00 4.17
1938 2014 2.489329 CAAAGGAAGCATACTGTGTGGG 59.511 50.000 6.67 0.00 0.00 4.61
1939 2015 1.656587 AGGAAGCATACTGTGTGGGA 58.343 50.000 6.67 0.00 0.00 4.37
1940 2016 1.556911 AGGAAGCATACTGTGTGGGAG 59.443 52.381 6.67 0.00 0.00 4.30
2080 2156 0.819582 GATCCGTCCGTCCTTGGTTA 59.180 55.000 0.00 0.00 0.00 2.85
2081 2157 0.822164 ATCCGTCCGTCCTTGGTTAG 59.178 55.000 0.00 0.00 0.00 2.34
2082 2158 1.447314 CCGTCCGTCCTTGGTTAGC 60.447 63.158 0.00 0.00 0.00 3.09
2083 2159 1.804326 CGTCCGTCCTTGGTTAGCG 60.804 63.158 0.00 0.00 0.00 4.26
2084 2160 1.291272 GTCCGTCCTTGGTTAGCGT 59.709 57.895 0.00 0.00 0.00 5.07
2085 2161 0.527565 GTCCGTCCTTGGTTAGCGTA 59.472 55.000 0.00 0.00 0.00 4.42
2086 2162 0.813184 TCCGTCCTTGGTTAGCGTAG 59.187 55.000 0.00 0.00 0.00 3.51
2145 2249 0.036875 TTCCCACACACACACACACA 59.963 50.000 0.00 0.00 0.00 3.72
2182 2286 5.405571 CAGTGTGGTGTAGTAGATGTTTGAC 59.594 44.000 0.00 0.00 0.00 3.18
2189 2293 5.348997 GTGTAGTAGATGTTTGACTTCTGCC 59.651 44.000 6.71 0.00 36.25 4.85
2458 2576 0.886563 CACTTCGTACTCCCTCCGTT 59.113 55.000 0.00 0.00 0.00 4.44
2459 2577 1.135460 CACTTCGTACTCCCTCCGTTC 60.135 57.143 0.00 0.00 0.00 3.95
2605 2726 4.084171 CGTATCCATTGATGTGCATCTGAC 60.084 45.833 12.64 0.00 38.60 3.51
3017 3143 3.825328 ACTCAACTGAGCAAGTGGAAAT 58.175 40.909 6.63 0.00 45.79 2.17
3089 3216 3.181516 GCAGTTCACTCTTATTTCTGCCG 60.182 47.826 0.00 0.00 40.23 5.69
3091 3218 3.997021 AGTTCACTCTTATTTCTGCCGTG 59.003 43.478 0.00 0.00 0.00 4.94
3917 4048 0.823356 TGGTGCCAAAAGAGCTCCAC 60.823 55.000 10.93 9.95 46.09 4.02
3994 4137 3.319972 ACTTGTGCAGCAATTCAACTGAT 59.680 39.130 0.00 0.00 36.36 2.90
4125 4268 4.616802 TCGGTTCAACGTCGTATTTTACTC 59.383 41.667 0.00 0.00 34.94 2.59
4128 4271 6.470235 CGGTTCAACGTCGTATTTTACTCTAT 59.530 38.462 0.00 0.00 0.00 1.98
4130 4273 9.289303 GGTTCAACGTCGTATTTTACTCTATTA 57.711 33.333 0.00 0.00 0.00 0.98
4271 4414 0.107654 GGGACATAGCGGTCTTTGCT 60.108 55.000 0.00 0.00 46.29 3.91
4346 4489 2.900528 CCATACGGCAATCGAGTCC 58.099 57.895 0.00 0.00 42.43 3.85
4417 4560 3.028850 CTGATGGAAATTGCCAGGTGAT 58.971 45.455 11.82 0.00 42.15 3.06
4549 4693 2.882137 GGGAATCGAAGTCACAAAACCA 59.118 45.455 0.00 0.00 0.00 3.67
4625 4769 2.300723 TGCGTACTGTATGTTCCCTGTT 59.699 45.455 8.69 0.00 0.00 3.16
4637 4781 2.764010 GTTCCCTGTTTCCCTGTGTTTT 59.236 45.455 0.00 0.00 0.00 2.43
4638 4782 3.955524 TCCCTGTTTCCCTGTGTTTTA 57.044 42.857 0.00 0.00 0.00 1.52
4640 4784 4.403734 TCCCTGTTTCCCTGTGTTTTATC 58.596 43.478 0.00 0.00 0.00 1.75
4668 4812 1.339055 GCCTAATGGTGCAGTGACAGA 60.339 52.381 0.00 0.00 35.27 3.41
4778 4926 2.279741 GTTGCTCGCCACTGATTATGA 58.720 47.619 0.00 0.00 0.00 2.15
4787 4935 4.454678 GCCACTGATTATGATTGTCTGGA 58.545 43.478 0.00 0.00 0.00 3.86
4823 4972 0.383231 GGCCATTTCTGGATGAAGCG 59.617 55.000 0.00 0.00 46.37 4.68
5196 5345 3.807538 TACGACGTCGAGGCCTGC 61.808 66.667 41.52 0.00 43.02 4.85
5293 5442 7.490079 CCCTTCATTTGTGTTCACAATATGATG 59.510 37.037 24.91 24.71 37.11 3.07
5396 5545 4.919754 GCTCTAATTTTGCCAGTCTTGTTG 59.080 41.667 0.00 0.00 0.00 3.33
5427 5576 5.948842 ACCACAAATACTACCAAGGTTCTT 58.051 37.500 0.00 0.00 0.00 2.52
5435 5584 8.879427 AATACTACCAAGGTTCTTATTTTGCT 57.121 30.769 0.00 0.00 0.00 3.91
5511 5662 5.649831 ACCATCTGAAATTCTAACTTGAGGC 59.350 40.000 0.00 0.00 0.00 4.70
5638 5789 2.640184 CTGATGAGATCAAGCAAGCCA 58.360 47.619 0.00 0.00 39.11 4.75
5754 5905 5.643777 TCTTAAGCAACTAATTGACTGAGCC 59.356 40.000 0.00 0.00 38.15 4.70
5830 5983 5.909610 GCAGTTGCTCTTTGTTGTAACTAAG 59.090 40.000 11.12 11.12 41.17 2.18
5991 6144 3.730761 GTCCACGCTGCAGCCAAG 61.731 66.667 32.07 20.74 37.91 3.61
6025 6180 7.938140 TCCTGCTTGTTAAATGCTTTATACT 57.062 32.000 0.00 0.00 0.00 2.12
6045 6200 3.894427 ACTAGTGCTGGATCCATGTCTAG 59.106 47.826 27.29 27.29 0.00 2.43
6047 6202 2.964464 AGTGCTGGATCCATGTCTAGAG 59.036 50.000 16.63 1.52 0.00 2.43
6050 6205 2.368221 GCTGGATCCATGTCTAGAGCTT 59.632 50.000 16.63 0.00 0.00 3.74
6051 6206 3.576118 GCTGGATCCATGTCTAGAGCTTA 59.424 47.826 16.63 0.00 0.00 3.09
6052 6207 4.560513 GCTGGATCCATGTCTAGAGCTTAC 60.561 50.000 16.63 0.00 0.00 2.34
6091 6248 4.036734 GTGGACTCTGAAATTTGCTGAACA 59.963 41.667 0.00 0.00 0.00 3.18
6140 6300 2.550208 CCTCTGGTTGCTTACGAACCTT 60.550 50.000 0.00 0.00 43.00 3.50
6224 6387 8.194769 TGCAATTTGTAATCAGAGTACGAGATA 58.805 33.333 3.66 0.00 0.00 1.98
6228 6391 6.862711 TGTAATCAGAGTACGAGATACAGG 57.137 41.667 3.66 0.00 36.09 4.00
6346 6518 9.751542 AAAACGTCTTATATTATGAGACAGAGG 57.248 33.333 21.66 11.85 43.73 3.69
6412 6584 4.438148 ACAAAAATAACAAGCAAACGCCT 58.562 34.783 0.00 0.00 0.00 5.52
6422 6601 0.602905 GCAAACGCCTGACCTACAGT 60.603 55.000 0.00 0.00 44.40 3.55
6452 6631 6.375174 ACCAACGCACATGCATATATAATCAT 59.625 34.615 0.00 0.00 42.21 2.45
6511 6690 3.348119 CCTAGGCAGAGGGAAAAACTTC 58.652 50.000 0.00 0.00 32.39 3.01
6532 6711 4.735985 TCAAAGCGATCAAAACATCATGG 58.264 39.130 0.00 0.00 0.00 3.66
6695 6874 0.529992 CCAACGAGGGAGGCGATAAC 60.530 60.000 0.00 0.00 0.00 1.89
6792 6972 5.883503 TTATTTCGGGTGTTCATTGTACC 57.116 39.130 0.00 0.00 0.00 3.34
6797 6977 0.519961 GGTGTTCATTGTACCGCCAC 59.480 55.000 0.00 0.00 0.00 5.01
6922 7102 8.158169 AGAAATCAAAAGATTTTCAAAAGGCC 57.842 30.769 0.00 0.00 35.18 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 7.231925 GGGTTAAGGTTATGGTTATGGTTATGG 59.768 40.741 0.00 0.00 0.00 2.74
132 133 6.210385 TGATGCATTTAGGGTAATGTTTGTGT 59.790 34.615 0.00 0.00 37.72 3.72
162 163 9.205719 CATGATTTTGTTGTGGTGAAATCAATA 57.794 29.630 12.56 0.00 45.85 1.90
184 185 7.815840 TTTTGTTGGAATCACTAGTTCATGA 57.184 32.000 0.00 0.00 0.00 3.07
259 262 3.701040 GTCATTTGCATCACCCAAGGTAT 59.299 43.478 0.00 0.00 32.11 2.73
291 294 2.421073 CCATTGCTTGAGATTTCGCAGA 59.579 45.455 0.00 0.00 33.48 4.26
293 296 2.421073 CTCCATTGCTTGAGATTTCGCA 59.579 45.455 0.00 0.00 0.00 5.10
296 299 2.692041 CCCCTCCATTGCTTGAGATTTC 59.308 50.000 0.00 0.00 0.00 2.17
345 348 0.326143 AAGCTCTCTCCCCCTCTTCC 60.326 60.000 0.00 0.00 0.00 3.46
420 425 1.408822 CCTGGATAAGGTTGTGAGGGC 60.409 57.143 0.00 0.00 41.74 5.19
549 554 2.053865 CGTGGCGGTAGGTTCCCTA 61.054 63.158 0.00 0.00 34.61 3.53
645 650 0.106149 ACGAAATCTGCCCCGGTATC 59.894 55.000 0.00 0.00 0.00 2.24
655 660 7.962934 TTTCGGCATATAAAAACGAAATCTG 57.037 32.000 6.47 0.00 45.12 2.90
659 664 7.095144 TGACTCTTTCGGCATATAAAAACGAAA 60.095 33.333 9.67 9.67 46.96 3.46
660 665 6.369340 TGACTCTTTCGGCATATAAAAACGAA 59.631 34.615 0.00 0.00 41.16 3.85
664 671 8.353684 TGTTTTGACTCTTTCGGCATATAAAAA 58.646 29.630 0.00 0.00 0.00 1.94
823 836 1.798223 GAACTTGTCGCATGTGTAGCA 59.202 47.619 6.09 1.80 0.00 3.49
928 947 3.864160 CTGGCGGTTTGGGCTTTGC 62.864 63.158 0.00 0.00 0.00 3.68
929 948 2.339712 CTGGCGGTTTGGGCTTTG 59.660 61.111 0.00 0.00 0.00 2.77
930 949 3.615709 GCTGGCGGTTTGGGCTTT 61.616 61.111 0.00 0.00 0.00 3.51
957 976 0.171231 GGCTGATGGAAAGCGGAAAC 59.829 55.000 0.00 0.00 41.78 2.78
983 1002 0.753848 GACTCTTCCTCTCCCCTCCG 60.754 65.000 0.00 0.00 0.00 4.63
1057 1080 4.338539 GCGTGACGTCCGTGTCCT 62.339 66.667 21.74 0.00 38.11 3.85
1111 1171 2.281761 GCGGGGCCATTCGATGAT 60.282 61.111 15.03 0.00 0.00 2.45
1658 1730 0.549950 CCCAGTAGTAGACCTCCCGA 59.450 60.000 0.00 0.00 0.00 5.14
1802 1878 9.101655 CTTCTGTCTTCTAGTAGTAAGTACTCC 57.898 40.741 0.00 0.00 41.42 3.85
1803 1879 9.657419 ACTTCTGTCTTCTAGTAGTAAGTACTC 57.343 37.037 0.00 0.00 41.42 2.59
1806 1882 9.598517 GCTACTTCTGTCTTCTAGTAGTAAGTA 57.401 37.037 0.00 6.35 41.22 2.24
1807 1883 8.323567 AGCTACTTCTGTCTTCTAGTAGTAAGT 58.676 37.037 0.00 5.67 41.22 2.24
1808 1884 8.726870 AGCTACTTCTGTCTTCTAGTAGTAAG 57.273 38.462 0.00 0.74 41.22 2.34
1809 1885 9.820725 CTAGCTACTTCTGTCTTCTAGTAGTAA 57.179 37.037 0.00 0.00 41.22 2.24
1810 1886 8.423349 CCTAGCTACTTCTGTCTTCTAGTAGTA 58.577 40.741 0.00 0.00 41.22 1.82
1811 1887 7.092757 ACCTAGCTACTTCTGTCTTCTAGTAGT 60.093 40.741 0.00 0.00 41.22 2.73
1812 1888 7.277396 ACCTAGCTACTTCTGTCTTCTAGTAG 58.723 42.308 0.00 0.00 41.77 2.57
1850 1926 0.390124 ACGTAAGCCCGAAACAGTCA 59.610 50.000 0.00 0.00 45.62 3.41
1930 2006 2.281761 GCCCACACTCCCACACAG 60.282 66.667 0.00 0.00 0.00 3.66
1931 2007 4.248842 CGCCCACACTCCCACACA 62.249 66.667 0.00 0.00 0.00 3.72
1938 2014 4.643387 AACCAGCCGCCCACACTC 62.643 66.667 0.00 0.00 0.00 3.51
1939 2015 4.204028 AAACCAGCCGCCCACACT 62.204 61.111 0.00 0.00 0.00 3.55
1940 2016 3.977244 CAAACCAGCCGCCCACAC 61.977 66.667 0.00 0.00 0.00 3.82
1953 2029 6.127563 ACGTCCCATCCCATATAAAAACAAAC 60.128 38.462 0.00 0.00 0.00 2.93
2080 2156 1.304381 TACCGGGACAACCTACGCT 60.304 57.895 6.32 0.00 36.97 5.07
2081 2157 1.153765 GTACCGGGACAACCTACGC 60.154 63.158 13.46 0.00 36.97 4.42
2082 2158 0.109132 GTGTACCGGGACAACCTACG 60.109 60.000 24.37 0.00 36.97 3.51
2083 2159 0.247460 GGTGTACCGGGACAACCTAC 59.753 60.000 25.55 9.93 36.97 3.18
2084 2160 2.669878 GGTGTACCGGGACAACCTA 58.330 57.895 25.55 0.00 36.97 3.08
2085 2161 3.475192 GGTGTACCGGGACAACCT 58.525 61.111 25.55 0.00 36.97 3.50
2153 2257 3.840991 TCTACTACACCACACTGTCCTT 58.159 45.455 0.00 0.00 0.00 3.36
2154 2258 3.520691 TCTACTACACCACACTGTCCT 57.479 47.619 0.00 0.00 0.00 3.85
2161 2265 5.801531 AGTCAAACATCTACTACACCACA 57.198 39.130 0.00 0.00 0.00 4.17
2182 2286 0.609957 TGCATCAACCCAGGCAGAAG 60.610 55.000 0.00 0.00 0.00 2.85
2189 2293 3.659850 CATGCATGCATCAACCCAG 57.340 52.632 30.07 13.50 33.90 4.45
2499 2619 6.484308 CCTATATAAACCCGGTCGAAATTTGT 59.516 38.462 0.00 0.00 0.00 2.83
2504 2625 4.222336 TCCCTATATAAACCCGGTCGAAA 58.778 43.478 0.00 0.00 0.00 3.46
2507 2628 4.605640 TTTCCCTATATAAACCCGGTCG 57.394 45.455 0.00 0.00 0.00 4.79
2511 2632 8.996271 GTAGATTGTTTTCCCTATATAAACCCG 58.004 37.037 0.00 0.00 32.25 5.28
2637 2758 4.398044 TCAAACTTTCCAAACTCTGACCAC 59.602 41.667 0.00 0.00 0.00 4.16
2760 2882 9.845740 AGGCATATAGTTCAACACATAATACAA 57.154 29.630 0.00 0.00 0.00 2.41
3043 3169 2.579410 AATTTGCACCGGGTAGACTT 57.421 45.000 6.32 0.00 0.00 3.01
3089 3216 2.417924 CCTAGCAGGTGATGAGTGACAC 60.418 54.545 0.00 0.00 36.44 3.67
3091 3218 2.103373 TCCTAGCAGGTGATGAGTGAC 58.897 52.381 2.68 0.00 36.53 3.67
3633 3764 7.590279 ACCAGCATAGTTAACAACACAATAAC 58.410 34.615 8.61 0.00 0.00 1.89
3800 3931 2.368875 TCGAGAGCTAAAATCCCATCCC 59.631 50.000 0.00 0.00 0.00 3.85
3917 4048 7.285172 TGGTACACATTATGATTTTGATCCCAG 59.715 37.037 0.00 0.00 0.00 4.45
3994 4137 6.072948 CGAATGTTGTTACCAAGGTTGTCATA 60.073 38.462 0.00 0.00 0.00 2.15
4125 4268 6.759272 TCCAAGCTAAGGTGTAGCATAATAG 58.241 40.000 8.00 0.00 42.68 1.73
4128 4271 5.188948 TCTTCCAAGCTAAGGTGTAGCATAA 59.811 40.000 8.00 0.00 42.68 1.90
4130 4273 3.519510 TCTTCCAAGCTAAGGTGTAGCAT 59.480 43.478 8.00 0.00 42.68 3.79
4271 4414 2.639347 TGCCTTCTCTCCAATGAGTTCA 59.361 45.455 0.00 0.00 39.75 3.18
4346 4489 5.012239 TCCATCTCAGAATTCCACAAAAGG 58.988 41.667 0.65 0.00 0.00 3.11
4417 4560 6.544197 AGATCAAGCTGATTTACTCTACGAGA 59.456 38.462 0.00 0.00 37.20 4.04
4534 4678 3.479505 TGTTGTGGTTTTGTGACTTCG 57.520 42.857 0.00 0.00 0.00 3.79
4549 4693 5.527582 ACGAAGTTAGAAGCAAAGATGTTGT 59.472 36.000 0.00 0.00 37.78 3.32
4625 4769 5.415701 GCATGAGAAGATAAAACACAGGGAA 59.584 40.000 0.00 0.00 0.00 3.97
4637 4781 4.102996 TGCACCATTAGGCATGAGAAGATA 59.897 41.667 0.00 0.00 39.06 1.98
4638 4782 3.117776 TGCACCATTAGGCATGAGAAGAT 60.118 43.478 0.00 0.00 39.06 2.40
4640 4784 2.617308 CTGCACCATTAGGCATGAGAAG 59.383 50.000 0.00 0.00 39.65 2.85
4668 4812 7.924947 GCTATTATACTTTTCGGTACTTCCTGT 59.075 37.037 0.00 0.00 0.00 4.00
4733 4881 5.825593 AAGGGTGAATGTTCAGAGAGTTA 57.174 39.130 0.00 0.00 37.98 2.24
4787 4935 1.712056 GCCCCAAACCTGGTTAAGTT 58.288 50.000 13.37 0.00 41.72 2.66
4823 4972 5.291614 GCTTCTCATGACTCTCACTGATTTC 59.708 44.000 0.00 0.00 0.00 2.17
5217 5366 4.638865 GTCCATACCTGTGGTTTGTATTCC 59.361 45.833 6.47 0.00 40.27 3.01
5293 5442 8.028938 ACCATTTATCAAGTACAAACATGCTTC 58.971 33.333 0.00 0.00 0.00 3.86
5396 5545 4.521256 TGGTAGTATTTGTGGTTTTGAGGC 59.479 41.667 0.00 0.00 0.00 4.70
5427 5576 5.321102 TGAGGAAACAAGGCTAGCAAAATA 58.679 37.500 18.24 0.00 0.00 1.40
5435 5584 4.042311 TGTGGTTATGAGGAAACAAGGCTA 59.958 41.667 0.00 0.00 0.00 3.93
5476 5627 4.826274 TTTCAGATGGTAGTTGGAGGAG 57.174 45.455 0.00 0.00 0.00 3.69
5477 5628 5.488919 AGAATTTCAGATGGTAGTTGGAGGA 59.511 40.000 0.00 0.00 0.00 3.71
5511 5662 3.496130 GTCTGCAGAATGATATCCAACGG 59.504 47.826 20.19 0.00 39.69 4.44
5638 5789 6.265196 TGTGCACATTTTTCTTCTGATAAGGT 59.735 34.615 17.42 0.00 0.00 3.50
5754 5905 6.169094 AGACTAGACACACAATCAATCAAGG 58.831 40.000 0.00 0.00 0.00 3.61
5830 5983 0.179092 ACAGTTCGCCGGCTATAACC 60.179 55.000 26.68 10.37 0.00 2.85
5934 6087 9.383519 CACTCTGTACCACAAGAATGTAAATAT 57.616 33.333 0.00 0.00 37.82 1.28
5991 6144 1.244019 ACAAGCAGGATTTGACCCGC 61.244 55.000 0.00 0.00 0.00 6.13
6025 6180 4.148079 CTCTAGACATGGATCCAGCACTA 58.852 47.826 21.33 18.97 0.00 2.74
6050 6205 4.942483 GTCCACAGACTGAGCTTACTAGTA 59.058 45.833 10.08 0.00 40.10 1.82
6051 6206 3.759618 GTCCACAGACTGAGCTTACTAGT 59.240 47.826 10.08 0.00 40.10 2.57
6052 6207 4.364415 GTCCACAGACTGAGCTTACTAG 57.636 50.000 10.08 0.00 40.10 2.57
6091 6248 7.574021 TCCCTGTCTTAATGCTATAATCCAT 57.426 36.000 0.00 0.00 0.00 3.41
6224 6387 6.271624 ACCAAAAGTACACTTATAGGACCTGT 59.728 38.462 3.53 0.00 34.61 4.00
6228 6391 6.070366 AGGGACCAAAAGTACACTTATAGGAC 60.070 42.308 11.91 7.44 34.61 3.85
6422 6601 1.358402 GCATGTGCGTTGGTGTTGA 59.642 52.632 0.00 0.00 0.00 3.18
6452 6631 2.727544 GTTTTGCTCTTGCCGGCA 59.272 55.556 29.03 29.03 38.71 5.69
6503 6682 6.959671 TGTTTTGATCGCTTTGAAGTTTTT 57.040 29.167 0.00 0.00 0.00 1.94
6511 6690 4.735985 TCCATGATGTTTTGATCGCTTTG 58.264 39.130 0.00 0.00 0.00 2.77
6532 6711 4.878397 AGGAGTCGATGAACCAAATCATTC 59.122 41.667 0.00 0.00 40.08 2.67
6792 6972 5.155509 TCTATTCATTTTCAATCGTGGCG 57.844 39.130 0.00 0.00 0.00 5.69
6862 7042 7.489574 TTGGTTGCCATCTTTAAACATTTTC 57.510 32.000 0.00 0.00 31.53 2.29
6877 7057 9.267084 GATTTCTACTTTTATTTTTGGTTGCCA 57.733 29.630 0.00 0.00 0.00 4.92


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

AutoCloner maintained by Alex Coulton.