Multiple sequence alignment - TraesCS3B01G274100

Loading Multiple Alignment...

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 TraesCS3B01G274100 chr3B 100.000 7148 0 0 1 7148 441462088 441454941 0.000000e+00 13200.0
1 TraesCS3B01G274100 chr3B 96.907 97 3 0 5846 5942 40942762 40942858 5.740000e-36 163.0
2 TraesCS3B01G274100 chr3B 87.692 65 5 3 6940 7003 147939413 147939351 9.950000e-09 73.1
3 TraesCS3B01G274100 chr3D 98.277 5861 86 5 1 5847 342522981 342517122 0.000000e+00 10250.0
4 TraesCS3B01G274100 chr3D 95.955 890 29 4 5940 6825 342517124 342516238 0.000000e+00 1437.0
5 TraesCS3B01G274100 chr3D 94.198 293 8 7 6861 7148 342516242 342515954 8.510000e-119 438.0
6 TraesCS3B01G274100 chr3D 87.302 63 6 2 6942 7003 97118273 97118212 3.580000e-08 71.3
7 TraesCS3B01G274100 chr3D 96.774 31 1 0 7038 7068 604435835 604435805 1.300000e-02 52.8
8 TraesCS3B01G274100 chr3A 98.373 5838 80 4 24 5847 459955043 459960879 0.000000e+00 10240.0
9 TraesCS3B01G274100 chr3A 92.024 1191 67 14 5940 7117 459960877 459962052 0.000000e+00 1648.0
10 TraesCS3B01G274100 chr3A 88.333 60 4 3 6940 6996 687490892 687490833 1.290000e-07 69.4
11 TraesCS3B01G274100 chr2B 81.434 3054 468 44 251 3244 716053441 716050427 0.000000e+00 2407.0
12 TraesCS3B01G274100 chr2B 85.526 2197 305 7 3358 5552 716050337 716048152 0.000000e+00 2283.0
13 TraesCS3B01G274100 chr2B 93.458 107 7 0 5837 5943 768661134 768661028 7.420000e-35 159.0
14 TraesCS3B01G274100 chr2B 80.808 99 13 5 7044 7141 519695016 519695109 9.950000e-09 73.1
15 TraesCS3B01G274100 chr2A 80.512 3048 486 65 243 3217 725420685 725417673 0.000000e+00 2239.0
16 TraesCS3B01G274100 chr2A 83.682 2249 352 10 3317 5550 725417627 725415379 0.000000e+00 2106.0
17 TraesCS3B01G274100 chr4B 98.901 91 1 0 5846 5936 31517973 31518063 5.740000e-36 163.0
18 TraesCS3B01G274100 chr4B 92.035 113 8 1 5832 5943 21198636 21198748 2.670000e-34 158.0
19 TraesCS3B01G274100 chr7D 94.231 104 6 0 5839 5942 478795311 478795414 7.420000e-35 159.0
20 TraesCS3B01G274100 chr7D 91.304 115 8 2 5846 5958 621015981 621015867 9.600000e-34 156.0
21 TraesCS3B01G274100 chr7D 88.158 76 5 4 6432 6506 214364450 214364522 3.550000e-13 87.9
22 TraesCS3B01G274100 chr1B 94.231 104 6 0 5845 5948 359902047 359902150 7.420000e-35 159.0
23 TraesCS3B01G274100 chr1B 91.837 49 2 2 7017 7065 351537303 351537257 4.630000e-07 67.6
24 TraesCS3B01G274100 chr1B 100.000 30 0 0 6962 6991 28067493 28067464 1.000000e-03 56.5
25 TraesCS3B01G274100 chr1B 96.875 32 1 0 6963 6994 28117828 28117797 4.000000e-03 54.7
26 TraesCS3B01G274100 chr7B 93.396 106 6 1 5838 5943 589348422 589348318 9.600000e-34 156.0
27 TraesCS3B01G274100 chr5A 90.351 114 11 0 5840 5953 687689402 687689289 4.470000e-32 150.0
28 TraesCS3B01G274100 chr5D 91.667 60 4 1 6938 6996 361896027 361896086 1.650000e-11 82.4
29 TraesCS3B01G274100 chr5D 92.593 54 2 1 7029 7082 549881100 549881049 7.690000e-10 76.8
30 TraesCS3B01G274100 chr6A 76.471 119 23 5 7022 7138 609319024 609318909 7.740000e-05 60.2
31 TraesCS3B01G274100 chr6A 100.000 29 0 0 7056 7084 270369607 270369579 4.000000e-03 54.7
32 TraesCS3B01G274100 chr1D 97.143 35 1 0 7057 7091 454490321 454490355 7.740000e-05 60.2
33 TraesCS3B01G274100 chr7A 76.613 124 15 12 7007 7127 726897466 726897578 1.000000e-03 56.5
34 TraesCS3B01G274100 chr5B 100.000 30 0 0 6962 6991 704604596 704604567 1.000000e-03 56.5
35 TraesCS3B01G274100 chr2D 86.538 52 4 3 7059 7109 179843235 179843186 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 TraesCS3B01G274100 chr3B 441454941 441462088 7147 True 13200.000000 13200 100.000000 1 7148 1 chr3B.!!$R2 7147
1 TraesCS3B01G274100 chr3D 342515954 342522981 7027 True 4041.666667 10250 96.143333 1 7148 3 chr3D.!!$R3 7147
2 TraesCS3B01G274100 chr3A 459955043 459962052 7009 False 5944.000000 10240 95.198500 24 7117 2 chr3A.!!$F1 7093
3 TraesCS3B01G274100 chr2B 716048152 716053441 5289 True 2345.000000 2407 83.480000 251 5552 2 chr2B.!!$R2 5301
4 TraesCS3B01G274100 chr2A 725415379 725420685 5306 True 2172.500000 2239 82.097000 243 5550 2 chr2A.!!$R1 5307

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
1155 1182 3.050339 CAGGCCGCAACCATTGTT 58.950 55.556 0.00 0.0 34.14 2.83 F
1321 1369 0.392998 GTTCAGGGATGGACGCATGT 60.393 55.000 0.00 0.0 0.00 3.21 F
1923 1986 0.898320 CACACTTGGGAGAGATCCGT 59.102 55.000 0.00 0.0 0.00 4.69 F
3147 3255 1.005569 AGGGGACAGACACTATCACGA 59.994 52.381 0.00 0.0 0.00 4.35 F
4062 4203 1.646912 TCAATTGTACCCTCCGTGGA 58.353 50.000 5.13 0.0 38.35 4.02 F
4792 4933 4.210724 TGGTTTTTAGTATCCTCGTGGG 57.789 45.455 3.23 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3147 3255 1.673767 ACATCATCCCCCTCACAGTT 58.326 50.000 0.00 0.0 0.00 3.16 R
3303 3411 2.237392 GGCCCTGCTATAATACCCTGAG 59.763 54.545 0.00 0.0 0.00 3.35 R
4062 4203 9.857080 ATGTACTCATGGTGTGTAACATTGCCT 62.857 40.741 0.00 0.0 40.36 4.75 R
4792 4933 1.644509 AAGATGAAGGGGGCCAAAAC 58.355 50.000 4.39 0.0 0.00 2.43 R
5742 5886 1.201181 GTGTTGTGTGGTGCTGTTTCA 59.799 47.619 0.00 0.0 0.00 2.69 R
6845 6994 0.253894 CCTGGTGGTGCATCTCATGA 59.746 55.000 0.00 0.0 0.00 3.07 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
1155 1182 3.050339 CAGGCCGCAACCATTGTT 58.950 55.556 0.00 0.00 34.14 2.83
1193 1226 2.109126 GGCCGTGGCAGAATCTCAC 61.109 63.158 13.76 0.00 44.11 3.51
1299 1335 4.084888 GGCACACAGTTACGCCGC 62.085 66.667 0.00 0.00 34.26 6.53
1321 1369 0.392998 GTTCAGGGATGGACGCATGT 60.393 55.000 0.00 0.00 0.00 3.21
1821 1884 4.321601 GCTGTGTTTATATTGTGGTTGCCA 60.322 41.667 0.00 0.00 0.00 4.92
1847 1910 9.213777 AGTAGTTTTGATCTACCTCATGGATAA 57.786 33.333 0.00 0.00 38.66 1.75
1923 1986 0.898320 CACACTTGGGAGAGATCCGT 59.102 55.000 0.00 0.00 0.00 4.69
1945 2008 3.141398 GACATGAAACAACTGAGGCTGA 58.859 45.455 0.00 0.00 0.00 4.26
1953 2016 1.140312 AACTGAGGCTGAGGTTCCAA 58.860 50.000 5.82 0.00 0.00 3.53
2424 2514 3.517100 TCATCAAGGAAAGGACTGAGGAG 59.483 47.826 0.00 0.00 0.00 3.69
2742 2844 1.489649 CCTGATGAGGAGAATGCCACT 59.510 52.381 0.00 0.00 42.93 4.00
2757 2859 5.630415 ATGCCACTTTCTATAAGCAGGTA 57.370 39.130 0.00 0.00 33.10 3.08
2838 2946 4.838152 GCTCGGCGGAGGATTGCA 62.838 66.667 21.36 0.00 40.80 4.08
3147 3255 1.005569 AGGGGACAGACACTATCACGA 59.994 52.381 0.00 0.00 0.00 4.35
3303 3411 2.360475 GAAGGGAGTGCTGGTGGC 60.360 66.667 0.00 0.00 42.22 5.01
4062 4203 1.646912 TCAATTGTACCCTCCGTGGA 58.353 50.000 5.13 0.00 38.35 4.02
4278 4419 8.628630 TCTATTTCAACACAATGATGGTTGTA 57.371 30.769 13.38 5.34 40.17 2.41
4536 4677 4.997395 GCATCTGTTTTCTACACCTTCTCA 59.003 41.667 0.00 0.00 32.10 3.27
4792 4933 4.210724 TGGTTTTTAGTATCCTCGTGGG 57.789 45.455 3.23 0.00 0.00 4.61
5636 5780 4.455533 CCAACTCTGCACATGTTAGCTTAA 59.544 41.667 9.33 0.00 0.00 1.85
5702 5846 9.462606 TTCTTGAACTTCCTTATCCCTTATTTC 57.537 33.333 0.00 0.00 0.00 2.17
5728 5872 7.486870 CCTTGTTAGTTATTTTTATCCAACCGC 59.513 37.037 0.00 0.00 0.00 5.68
5731 5875 7.608761 TGTTAGTTATTTTTATCCAACCGCTCT 59.391 33.333 0.00 0.00 0.00 4.09
5742 5886 2.489329 CCAACCGCTCTGTTCATTGAAT 59.511 45.455 1.78 0.00 0.00 2.57
5851 5995 8.272659 ACCTTATTTCCTTATTAGGTACTCCC 57.727 38.462 0.00 0.00 42.60 4.30
5853 5997 8.595421 CCTTATTTCCTTATTAGGTACTCCCTC 58.405 40.741 0.00 0.00 44.81 4.30
5854 5998 8.502047 TTATTTCCTTATTAGGTACTCCCTCC 57.498 38.462 0.00 0.00 44.81 4.30
5855 5999 4.109877 TCCTTATTAGGTACTCCCTCCG 57.890 50.000 0.00 0.00 44.81 4.63
5856 6000 3.464833 TCCTTATTAGGTACTCCCTCCGT 59.535 47.826 0.00 0.00 44.81 4.69
5857 6001 3.825585 CCTTATTAGGTACTCCCTCCGTC 59.174 52.174 0.00 0.00 44.81 4.79
5858 6002 2.378378 ATTAGGTACTCCCTCCGTCC 57.622 55.000 0.00 0.00 44.81 4.79
5859 6003 0.259938 TTAGGTACTCCCTCCGTCCC 59.740 60.000 0.00 0.00 44.81 4.46
5860 6004 0.920763 TAGGTACTCCCTCCGTCCCA 60.921 60.000 0.00 0.00 44.81 4.37
5861 6005 1.305549 GGTACTCCCTCCGTCCCAA 60.306 63.158 0.00 0.00 0.00 4.12
5862 6006 0.906282 GGTACTCCCTCCGTCCCAAA 60.906 60.000 0.00 0.00 0.00 3.28
5863 6007 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
5864 6008 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
5865 6009 1.961133 ACTCCCTCCGTCCCAAAATA 58.039 50.000 0.00 0.00 0.00 1.40
5866 6010 2.271777 ACTCCCTCCGTCCCAAAATAA 58.728 47.619 0.00 0.00 0.00 1.40
5867 6011 2.238898 ACTCCCTCCGTCCCAAAATAAG 59.761 50.000 0.00 0.00 0.00 1.73
5868 6012 2.238898 CTCCCTCCGTCCCAAAATAAGT 59.761 50.000 0.00 0.00 0.00 2.24
5869 6013 2.026636 TCCCTCCGTCCCAAAATAAGTG 60.027 50.000 0.00 0.00 0.00 3.16
5870 6014 2.290705 CCCTCCGTCCCAAAATAAGTGT 60.291 50.000 0.00 0.00 0.00 3.55
5871 6015 3.007635 CCTCCGTCCCAAAATAAGTGTC 58.992 50.000 0.00 0.00 0.00 3.67
5872 6016 3.307480 CCTCCGTCCCAAAATAAGTGTCT 60.307 47.826 0.00 0.00 0.00 3.41
5873 6017 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
5874 6018 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
5875 6019 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
5876 6020 4.154195 CCGTCCCAAAATAAGTGTCTCAAG 59.846 45.833 0.00 0.00 0.00 3.02
5877 6021 4.378459 CGTCCCAAAATAAGTGTCTCAAGC 60.378 45.833 0.00 0.00 0.00 4.01
5878 6022 4.762251 GTCCCAAAATAAGTGTCTCAAGCT 59.238 41.667 0.00 0.00 0.00 3.74
5879 6023 5.241728 GTCCCAAAATAAGTGTCTCAAGCTT 59.758 40.000 0.00 0.00 0.00 3.74
5880 6024 6.430000 GTCCCAAAATAAGTGTCTCAAGCTTA 59.570 38.462 0.00 0.00 0.00 3.09
5881 6025 6.655003 TCCCAAAATAAGTGTCTCAAGCTTAG 59.345 38.462 0.00 0.00 0.00 2.18
5882 6026 6.431234 CCCAAAATAAGTGTCTCAAGCTTAGT 59.569 38.462 0.00 0.00 0.00 2.24
5883 6027 7.040409 CCCAAAATAAGTGTCTCAAGCTTAGTT 60.040 37.037 0.00 0.00 35.44 2.24
5884 6028 8.017946 CCAAAATAAGTGTCTCAAGCTTAGTTC 58.982 37.037 0.00 0.00 33.67 3.01
5885 6029 8.559536 CAAAATAAGTGTCTCAAGCTTAGTTCA 58.440 33.333 0.00 0.00 33.67 3.18
5886 6030 8.677148 AAATAAGTGTCTCAAGCTTAGTTCAA 57.323 30.769 0.00 0.00 30.44 2.69
5887 6031 5.993106 AAGTGTCTCAAGCTTAGTTCAAC 57.007 39.130 0.00 0.00 0.00 3.18
5888 6032 5.283457 AGTGTCTCAAGCTTAGTTCAACT 57.717 39.130 0.00 0.00 0.00 3.16
5889 6033 5.675538 AGTGTCTCAAGCTTAGTTCAACTT 58.324 37.500 0.00 0.00 0.00 2.66
5890 6034 6.116126 AGTGTCTCAAGCTTAGTTCAACTTT 58.884 36.000 0.00 0.00 0.00 2.66
5891 6035 6.037610 AGTGTCTCAAGCTTAGTTCAACTTTG 59.962 38.462 0.00 0.00 0.00 2.77
5892 6036 5.880332 TGTCTCAAGCTTAGTTCAACTTTGT 59.120 36.000 0.00 0.00 0.00 2.83
5893 6037 7.011109 GTGTCTCAAGCTTAGTTCAACTTTGTA 59.989 37.037 0.00 0.00 0.00 2.41
5894 6038 7.011109 TGTCTCAAGCTTAGTTCAACTTTGTAC 59.989 37.037 0.00 0.00 0.00 2.90
5895 6039 7.224949 GTCTCAAGCTTAGTTCAACTTTGTACT 59.775 37.037 0.00 6.50 40.98 2.73
5896 6040 8.418662 TCTCAAGCTTAGTTCAACTTTGTACTA 58.581 33.333 0.00 4.78 39.18 1.82
5897 6041 8.951787 TCAAGCTTAGTTCAACTTTGTACTAA 57.048 30.769 16.00 16.00 43.82 2.24
5898 6042 9.386010 TCAAGCTTAGTTCAACTTTGTACTAAA 57.614 29.630 16.99 4.97 44.65 1.85
5899 6043 9.651718 CAAGCTTAGTTCAACTTTGTACTAAAG 57.348 33.333 16.99 13.08 44.65 1.85
5900 6044 8.959705 AGCTTAGTTCAACTTTGTACTAAAGT 57.040 30.769 16.99 14.04 44.65 2.66
5929 6073 9.673454 GTACAAAGTTAAGACACTAATTTTGGG 57.327 33.333 12.82 0.00 40.26 4.12
5930 6074 8.528044 ACAAAGTTAAGACACTAATTTTGGGA 57.472 30.769 12.82 0.00 40.26 4.37
5931 6075 8.410912 ACAAAGTTAAGACACTAATTTTGGGAC 58.589 33.333 12.82 0.00 40.26 4.46
5932 6076 6.796705 AGTTAAGACACTAATTTTGGGACG 57.203 37.500 0.00 0.00 0.00 4.79
5933 6077 5.704053 AGTTAAGACACTAATTTTGGGACGG 59.296 40.000 0.00 0.00 0.00 4.79
5934 6078 4.360951 AAGACACTAATTTTGGGACGGA 57.639 40.909 0.00 0.00 0.00 4.69
5935 6079 3.939066 AGACACTAATTTTGGGACGGAG 58.061 45.455 0.00 0.00 0.00 4.63
5936 6080 3.581332 AGACACTAATTTTGGGACGGAGA 59.419 43.478 0.00 0.00 0.00 3.71
5937 6081 3.933332 GACACTAATTTTGGGACGGAGAG 59.067 47.826 0.00 0.00 0.00 3.20
5938 6082 3.581332 ACACTAATTTTGGGACGGAGAGA 59.419 43.478 0.00 0.00 0.00 3.10
5939 6083 4.184629 CACTAATTTTGGGACGGAGAGAG 58.815 47.826 0.00 0.00 0.00 3.20
5940 6084 3.838903 ACTAATTTTGGGACGGAGAGAGT 59.161 43.478 0.00 0.00 0.00 3.24
5941 6085 5.021458 ACTAATTTTGGGACGGAGAGAGTA 58.979 41.667 0.00 0.00 0.00 2.59
6008 6152 5.064452 CACCTGCAATCAGATACTTGTTCTC 59.936 44.000 0.00 0.00 42.95 2.87
6013 6157 3.895232 TCAGATACTTGTTCTCCAGCC 57.105 47.619 0.00 0.00 0.00 4.85
6164 6308 5.078256 AGTGTAGGTACAGCTGTTCTAACT 58.922 41.667 27.06 23.14 36.78 2.24
6263 6407 5.220681 GGCGACATCTTTACCTTGATTCTTC 60.221 44.000 0.00 0.00 0.00 2.87
6289 6433 7.064609 CGTAACTTGATGTACACATGGATTTCT 59.935 37.037 0.00 0.00 36.57 2.52
6464 6608 9.868277 CATATTTTTGTTGTAAAGCTGGGAATA 57.132 29.630 0.00 0.00 0.00 1.75
6533 6677 9.128107 GATTGTAATCTTGTACACCAATTGTTG 57.872 33.333 4.43 2.60 33.73 3.33
6585 6729 2.252346 CGCTGCTGGCTGATCCATC 61.252 63.158 0.00 0.00 45.50 3.51
6644 6791 3.823330 GCATGCTGCAGTCTGGGC 61.823 66.667 16.64 8.75 44.26 5.36
6671 6818 1.129998 CATGTTCTTCAGCTCTTGCCG 59.870 52.381 0.00 0.00 40.80 5.69
6757 6904 0.390472 TTATGTGTGCGGTGATGCGA 60.390 50.000 0.00 0.00 37.81 5.10
6830 6979 4.487412 GCTTGCGCCATGCTGTCC 62.487 66.667 4.18 0.00 46.63 4.02
6845 6994 3.936203 TCCGCTCCGCCTTGTGTT 61.936 61.111 0.00 0.00 0.00 3.32
6858 7007 2.163010 CCTTGTGTTCATGAGATGCACC 59.837 50.000 14.66 0.00 32.48 5.01
6859 7008 2.565046 TGTGTTCATGAGATGCACCA 57.435 45.000 14.66 0.00 32.48 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
856 883 1.298413 CGTAGATGGGCGTGACGAG 60.298 63.158 10.10 0.00 35.59 4.18
888 915 2.752238 CGGCTGGACTCGACCTCT 60.752 66.667 0.00 0.00 0.00 3.69
1043 1070 3.716006 CAGTCTTGCGCACACGGG 61.716 66.667 11.12 4.30 40.57 5.28
1059 1086 3.744719 CGGACCTCGACGAAGCCA 61.745 66.667 0.00 0.00 42.43 4.75
1147 1174 1.250154 CCATCCCACGCAACAATGGT 61.250 55.000 0.00 0.00 33.66 3.55
1155 1182 1.480212 AAGTCTCACCATCCCACGCA 61.480 55.000 0.00 0.00 0.00 5.24
1221 1257 1.067565 GTGATGAAGACGGTGAGCAGA 60.068 52.381 0.00 0.00 0.00 4.26
1222 1258 1.354040 GTGATGAAGACGGTGAGCAG 58.646 55.000 0.00 0.00 0.00 4.24
1299 1335 2.885644 CGTCCATCCCTGAACGCG 60.886 66.667 3.53 3.53 0.00 6.01
1821 1884 7.682787 ATCCATGAGGTAGATCAAAACTACT 57.317 36.000 0.00 0.00 39.77 2.57
1923 1986 2.880268 CAGCCTCAGTTGTTTCATGTCA 59.120 45.455 0.00 0.00 0.00 3.58
2424 2514 3.534970 TTGCGTCACAATGCCGTGC 62.535 57.895 0.00 0.00 36.52 5.34
2742 2844 2.800629 GCGCCGTACCTGCTTATAGAAA 60.801 50.000 0.00 0.00 0.00 2.52
2838 2946 8.610248 TCATGAACAATGAATTGCTGAAAAAT 57.390 26.923 2.92 0.00 42.49 1.82
3147 3255 1.673767 ACATCATCCCCCTCACAGTT 58.326 50.000 0.00 0.00 0.00 3.16
3303 3411 2.237392 GGCCCTGCTATAATACCCTGAG 59.763 54.545 0.00 0.00 0.00 3.35
4062 4203 9.857080 ATGTACTCATGGTGTGTAACATTGCCT 62.857 40.741 0.00 0.00 40.36 4.75
4278 4419 5.877012 CCAGACAAATGCATAGACAGTTAGT 59.123 40.000 0.00 0.00 0.00 2.24
4536 4677 7.069826 CCATAATAATGTGTCTTGGTTCCCATT 59.930 37.037 0.00 0.00 31.53 3.16
4792 4933 1.644509 AAGATGAAGGGGGCCAAAAC 58.355 50.000 4.39 0.00 0.00 2.43
5564 5705 4.518970 GGCATCCTTACAAAGAGACACAAA 59.481 41.667 0.00 0.00 0.00 2.83
5702 5846 7.486870 GCGGTTGGATAAAAATAACTAACAAGG 59.513 37.037 0.00 0.00 0.00 3.61
5742 5886 1.201181 GTGTTGTGTGGTGCTGTTTCA 59.799 47.619 0.00 0.00 0.00 2.69
5847 5991 2.238898 ACTTATTTTGGGACGGAGGGAG 59.761 50.000 0.00 0.00 0.00 4.30
5848 5992 2.026636 CACTTATTTTGGGACGGAGGGA 60.027 50.000 0.00 0.00 0.00 4.20
5849 5993 2.290705 ACACTTATTTTGGGACGGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
5850 5994 3.007635 GACACTTATTTTGGGACGGAGG 58.992 50.000 0.00 0.00 0.00 4.30
5851 5995 3.933332 GAGACACTTATTTTGGGACGGAG 59.067 47.826 0.00 0.00 0.00 4.63
5852 5996 3.325425 TGAGACACTTATTTTGGGACGGA 59.675 43.478 0.00 0.00 0.00 4.69
5853 5997 3.670625 TGAGACACTTATTTTGGGACGG 58.329 45.455 0.00 0.00 0.00 4.79
5854 5998 4.378459 GCTTGAGACACTTATTTTGGGACG 60.378 45.833 0.00 0.00 0.00 4.79
5855 5999 4.762251 AGCTTGAGACACTTATTTTGGGAC 59.238 41.667 0.00 0.00 0.00 4.46
5856 6000 4.985538 AGCTTGAGACACTTATTTTGGGA 58.014 39.130 0.00 0.00 0.00 4.37
5857 6001 5.712152 AAGCTTGAGACACTTATTTTGGG 57.288 39.130 0.00 0.00 0.00 4.12
5858 6002 7.440523 ACTAAGCTTGAGACACTTATTTTGG 57.559 36.000 9.86 0.00 0.00 3.28
5859 6003 8.559536 TGAACTAAGCTTGAGACACTTATTTTG 58.440 33.333 9.86 0.00 0.00 2.44
5860 6004 8.677148 TGAACTAAGCTTGAGACACTTATTTT 57.323 30.769 9.86 0.00 0.00 1.82
5861 6005 8.560374 GTTGAACTAAGCTTGAGACACTTATTT 58.440 33.333 9.86 0.00 0.00 1.40
5862 6006 7.934120 AGTTGAACTAAGCTTGAGACACTTATT 59.066 33.333 9.86 0.00 0.00 1.40
5863 6007 7.445945 AGTTGAACTAAGCTTGAGACACTTAT 58.554 34.615 9.86 0.00 0.00 1.73
5864 6008 6.817184 AGTTGAACTAAGCTTGAGACACTTA 58.183 36.000 9.86 0.00 0.00 2.24
5865 6009 5.675538 AGTTGAACTAAGCTTGAGACACTT 58.324 37.500 9.86 0.00 0.00 3.16
5866 6010 5.283457 AGTTGAACTAAGCTTGAGACACT 57.717 39.130 9.86 1.30 0.00 3.55
5867 6011 5.993106 AAGTTGAACTAAGCTTGAGACAC 57.007 39.130 9.86 0.00 0.00 3.67
5868 6012 5.880332 ACAAAGTTGAACTAAGCTTGAGACA 59.120 36.000 9.86 1.72 0.00 3.41
5869 6013 6.364945 ACAAAGTTGAACTAAGCTTGAGAC 57.635 37.500 9.86 0.00 0.00 3.36
5870 6014 7.272978 AGTACAAAGTTGAACTAAGCTTGAGA 58.727 34.615 9.86 0.53 0.00 3.27
5871 6015 7.484035 AGTACAAAGTTGAACTAAGCTTGAG 57.516 36.000 9.86 5.36 0.00 3.02
5872 6016 8.951787 TTAGTACAAAGTTGAACTAAGCTTGA 57.048 30.769 9.86 0.00 0.00 3.02
5873 6017 9.651718 CTTTAGTACAAAGTTGAACTAAGCTTG 57.348 33.333 9.86 1.99 0.00 4.01
5874 6018 9.392259 ACTTTAGTACAAAGTTGAACTAAGCTT 57.608 29.630 3.48 3.48 37.18 3.74
5875 6019 8.959705 ACTTTAGTACAAAGTTGAACTAAGCT 57.040 30.769 14.04 0.00 37.18 3.74
5903 6047 9.673454 CCCAAAATTAGTGTCTTAACTTTGTAC 57.327 33.333 0.00 0.00 31.38 2.90
5904 6048 9.629878 TCCCAAAATTAGTGTCTTAACTTTGTA 57.370 29.630 0.00 0.00 31.38 2.41
5905 6049 8.410912 GTCCCAAAATTAGTGTCTTAACTTTGT 58.589 33.333 0.00 0.00 31.38 2.83
5906 6050 7.589954 CGTCCCAAAATTAGTGTCTTAACTTTG 59.410 37.037 0.00 0.00 32.47 2.77
5907 6051 7.255346 CCGTCCCAAAATTAGTGTCTTAACTTT 60.255 37.037 0.00 0.00 0.00 2.66
5908 6052 6.206048 CCGTCCCAAAATTAGTGTCTTAACTT 59.794 38.462 0.00 0.00 0.00 2.66
5909 6053 5.704053 CCGTCCCAAAATTAGTGTCTTAACT 59.296 40.000 0.00 0.00 0.00 2.24
5910 6054 5.702209 TCCGTCCCAAAATTAGTGTCTTAAC 59.298 40.000 0.00 0.00 0.00 2.01
5911 6055 5.867330 TCCGTCCCAAAATTAGTGTCTTAA 58.133 37.500 0.00 0.00 0.00 1.85
5912 6056 5.246656 TCTCCGTCCCAAAATTAGTGTCTTA 59.753 40.000 0.00 0.00 0.00 2.10
5913 6057 4.041198 TCTCCGTCCCAAAATTAGTGTCTT 59.959 41.667 0.00 0.00 0.00 3.01
5914 6058 3.581332 TCTCCGTCCCAAAATTAGTGTCT 59.419 43.478 0.00 0.00 0.00 3.41
5915 6059 3.933332 CTCTCCGTCCCAAAATTAGTGTC 59.067 47.826 0.00 0.00 0.00 3.67
5916 6060 3.581332 TCTCTCCGTCCCAAAATTAGTGT 59.419 43.478 0.00 0.00 0.00 3.55
5917 6061 4.184629 CTCTCTCCGTCCCAAAATTAGTG 58.815 47.826 0.00 0.00 0.00 2.74
5918 6062 3.838903 ACTCTCTCCGTCCCAAAATTAGT 59.161 43.478 0.00 0.00 0.00 2.24
5919 6063 4.473477 ACTCTCTCCGTCCCAAAATTAG 57.527 45.455 0.00 0.00 0.00 1.73
5920 6064 5.897824 AGATACTCTCTCCGTCCCAAAATTA 59.102 40.000 0.00 0.00 0.00 1.40
5921 6065 4.717280 AGATACTCTCTCCGTCCCAAAATT 59.283 41.667 0.00 0.00 0.00 1.82
5922 6066 4.290942 AGATACTCTCTCCGTCCCAAAAT 58.709 43.478 0.00 0.00 0.00 1.82
5923 6067 3.709587 AGATACTCTCTCCGTCCCAAAA 58.290 45.455 0.00 0.00 0.00 2.44
5924 6068 3.383698 AGATACTCTCTCCGTCCCAAA 57.616 47.619 0.00 0.00 0.00 3.28
5925 6069 4.515028 TTAGATACTCTCTCCGTCCCAA 57.485 45.455 0.00 0.00 35.28 4.12
5926 6070 4.205587 GTTTAGATACTCTCTCCGTCCCA 58.794 47.826 0.00 0.00 35.28 4.37
5927 6071 4.205587 TGTTTAGATACTCTCTCCGTCCC 58.794 47.826 0.00 0.00 35.28 4.46
5928 6072 5.124645 TCTGTTTAGATACTCTCTCCGTCC 58.875 45.833 0.00 0.00 35.28 4.79
5929 6073 6.680874 TTCTGTTTAGATACTCTCTCCGTC 57.319 41.667 0.00 0.00 35.28 4.79
5930 6074 7.463961 TTTTCTGTTTAGATACTCTCTCCGT 57.536 36.000 0.00 0.00 35.28 4.69
5931 6075 8.410141 AGATTTTCTGTTTAGATACTCTCTCCG 58.590 37.037 0.00 0.00 35.28 4.63
5932 6076 9.528018 CAGATTTTCTGTTTAGATACTCTCTCC 57.472 37.037 0.00 0.00 39.58 3.71
5950 6094 6.509317 TGCGATTCAAACAAACAGATTTTC 57.491 33.333 0.00 0.00 0.00 2.29
6008 6152 3.473923 ACAAAAGGTGAATTTGGCTGG 57.526 42.857 4.29 0.00 41.08 4.85
6013 6157 6.536224 AGCTGAAAGAACAAAAGGTGAATTTG 59.464 34.615 0.00 0.00 38.89 2.32
6164 6308 5.476945 TGCAGAGTAGTCTCAATGTTAGTGA 59.523 40.000 0.00 0.00 42.66 3.41
6263 6407 6.662414 AATCCATGTGTACATCAAGTTACG 57.338 37.500 0.00 0.00 33.61 3.18
6289 6433 8.565896 AGTTTGATTGCATCATTTCTACTACA 57.434 30.769 0.00 0.00 39.39 2.74
6533 6677 0.652592 CAGCCGATGACATTTCCGAC 59.347 55.000 0.00 0.00 0.00 4.79
6585 6729 5.598416 TGACATGAGTAGTACATCCCAAG 57.402 43.478 0.00 0.00 0.00 3.61
6643 6790 1.674962 GCTGAAGAACATGATCAGGGC 59.325 52.381 12.66 3.39 40.68 5.19
6644 6791 3.118334 AGAGCTGAAGAACATGATCAGGG 60.118 47.826 12.66 3.94 40.68 4.45
6671 6818 8.945758 CAGCATGCATAAACTAGACAATAATC 57.054 34.615 21.98 0.00 0.00 1.75
6757 6904 2.098614 AGACGACATGAGCTGATGAGT 58.901 47.619 20.64 17.65 0.00 3.41
6836 6985 1.814394 TGCATCTCATGAACACAAGGC 59.186 47.619 0.00 0.00 0.00 4.35
6845 6994 0.253894 CCTGGTGGTGCATCTCATGA 59.746 55.000 0.00 0.00 0.00 3.07
6858 7007 2.745152 CGGGTAAAAGATAGCCCTGGTG 60.745 54.545 0.00 0.00 38.97 4.17
6859 7008 1.489230 CGGGTAAAAGATAGCCCTGGT 59.511 52.381 0.00 0.00 38.97 4.00


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

AutoCloner maintained by Alex Coulton.