Multiple sequence alignment - TraesCS7D01G288500

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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 TraesCS7D01G288500 chr7D 100.000 2831 0 0 1 2831 321476092 321478922 0.000000e+00 5228.0
1 TraesCS7D01G288500 chr5A 90.928 2844 196 41 3 2831 41484857 41482061 0.000000e+00 3766.0
2 TraesCS7D01G288500 chr7A 90.791 2845 201 40 1 2831 46729825 46727028 0.000000e+00 3746.0
3 TraesCS7D01G288500 chr7A 90.648 2267 173 30 1 2251 7421840 7424083 0.000000e+00 2976.0
4 TraesCS7D01G288500 chr7A 93.484 1504 71 12 1331 2831 194170053 194171532 0.000000e+00 2209.0
5 TraesCS7D01G288500 chr7A 91.195 1113 56 11 1725 2831 98751761 98752837 0.000000e+00 1474.0
6 TraesCS7D01G288500 chr7A 88.042 945 82 6 1 916 194167200 194168142 0.000000e+00 1090.0
7 TraesCS7D01G288500 chr7A 85.492 386 38 8 2446 2815 7424255 7424638 1.230000e-103 387.0
8 TraesCS7D01G288500 chr7A 98.529 68 1 0 2764 2831 46764561 46764494 1.380000e-23 121.0
9 TraesCS7D01G288500 chr3B 91.086 2266 165 29 1 2251 784063665 784061422 0.000000e+00 3031.0
10 TraesCS7D01G288500 chr4A 90.957 2267 166 31 1 2251 626535091 626532848 0.000000e+00 3014.0
11 TraesCS7D01G288500 chr1B 90.909 2266 169 28 1 2251 59040166 59042409 0.000000e+00 3009.0
12 TraesCS7D01G288500 chr1B 85.013 387 39 8 2446 2815 626237727 626237343 2.660000e-100 375.0
13 TraesCS7D01G288500 chr1B 87.619 105 12 1 2314 2417 87742757 87742653 1.380000e-23 121.0
14 TraesCS7D01G288500 chr5B 90.777 2266 171 30 1 2251 457391266 457389024 0.000000e+00 2992.0
15 TraesCS7D01G288500 chr5B 90.508 2107 165 24 1 2093 493911238 493913323 0.000000e+00 2750.0
16 TraesCS7D01G288500 chr5B 86.269 386 35 8 2446 2815 457388852 457388469 1.220000e-108 403.0
17 TraesCS7D01G288500 chr5B 86.010 386 36 8 2446 2815 48320622 48321005 5.680000e-107 398.0
18 TraesCS7D01G288500 chr5B 100.000 30 0 0 2335 2364 626437529 626437500 3.940000e-04 56.5
19 TraesCS7D01G288500 chr1A 85.714 1064 110 33 427 1474 570926182 570927219 0.000000e+00 1085.0
20 TraesCS7D01G288500 chr5D 86.494 385 35 8 2446 2815 500934243 500934625 9.440000e-110 407.0
21 TraesCS7D01G288500 chr5D 100.000 30 0 0 2335 2364 296485383 296485354 3.940000e-04 56.5


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 TraesCS7D01G288500 chr7D 321476092 321478922 2830 False 5228.0 5228 100.000 1 2831 1 chr7D.!!$F1 2830
1 TraesCS7D01G288500 chr5A 41482061 41484857 2796 True 3766.0 3766 90.928 3 2831 1 chr5A.!!$R1 2828
2 TraesCS7D01G288500 chr7A 46727028 46729825 2797 True 3746.0 3746 90.791 1 2831 1 chr7A.!!$R1 2830
3 TraesCS7D01G288500 chr7A 7421840 7424638 2798 False 1681.5 2976 88.070 1 2815 2 chr7A.!!$F2 2814
4 TraesCS7D01G288500 chr7A 194167200 194171532 4332 False 1649.5 2209 90.763 1 2831 2 chr7A.!!$F3 2830
5 TraesCS7D01G288500 chr7A 98751761 98752837 1076 False 1474.0 1474 91.195 1725 2831 1 chr7A.!!$F1 1106
6 TraesCS7D01G288500 chr3B 784061422 784063665 2243 True 3031.0 3031 91.086 1 2251 1 chr3B.!!$R1 2250
7 TraesCS7D01G288500 chr4A 626532848 626535091 2243 True 3014.0 3014 90.957 1 2251 1 chr4A.!!$R1 2250
8 TraesCS7D01G288500 chr1B 59040166 59042409 2243 False 3009.0 3009 90.909 1 2251 1 chr1B.!!$F1 2250
9 TraesCS7D01G288500 chr5B 493911238 493913323 2085 False 2750.0 2750 90.508 1 2093 1 chr5B.!!$F2 2092
10 TraesCS7D01G288500 chr5B 457388469 457391266 2797 True 1697.5 2992 88.523 1 2815 2 chr5B.!!$R2 2814
11 TraesCS7D01G288500 chr1A 570926182 570927219 1037 False 1085.0 1085 85.714 427 1474 1 chr1A.!!$F1 1047

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
324 325 0.390735 ATGCCCGTCTACGAAACCAC 60.391 55.0 3.65 0.0 43.02 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2154 3719 1.063174 GCTGCAAAGGAATACTCGCTG 59.937 52.381 0.0 0.0 0.0 5.18 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
51 52 3.840078 CCCTCTCCCAAAATTTGATGGTT 59.160 43.478 7.37 0.00 34.79 3.67
63 64 0.537143 TGATGGTTGCCTGCGACTTT 60.537 50.000 9.27 0.00 0.00 2.66
72 73 1.396301 GCCTGCGACTTTGATCTCAAG 59.604 52.381 0.00 0.00 37.15 3.02
73 74 2.005451 CCTGCGACTTTGATCTCAAGG 58.995 52.381 9.29 0.95 38.67 3.61
87 88 5.408299 TGATCTCAAGGTTGTTTATGTGTCG 59.592 40.000 0.00 0.00 0.00 4.35
112 113 2.610859 GGGAGGGGTCTGCCTCAA 60.611 66.667 0.00 0.00 46.56 3.02
133 134 7.147949 CCTCAAATGCTGGAGTATTGAAATCTT 60.148 37.037 0.00 0.00 30.82 2.40
135 136 6.705863 AATGCTGGAGTATTGAAATCTTCC 57.294 37.500 0.00 0.89 0.00 3.46
160 161 2.097110 ATCGGGCTTCCATGTACCTA 57.903 50.000 0.00 0.00 0.00 3.08
165 166 1.117150 GCTTCCATGTACCTACGGGA 58.883 55.000 0.00 0.00 36.25 5.14
201 202 2.388232 CGGAGGCTACGCAAACACC 61.388 63.158 6.02 0.00 0.00 4.16
207 208 1.448922 GCTACGCAAACACCCCACAA 61.449 55.000 0.00 0.00 0.00 3.33
224 225 3.369052 CCACAATTTCTAGCTCCGTACCA 60.369 47.826 0.00 0.00 0.00 3.25
237 238 3.025978 TCCGTACCATGGAGTTCGTTAT 58.974 45.455 21.47 0.00 0.00 1.89
252 253 9.099454 GGAGTTCGTTATCATCTACAAGATTTT 57.901 33.333 0.00 0.00 31.32 1.82
265 266 3.074538 ACAAGATTTTGGTAGAGGTGGCT 59.925 43.478 0.57 0.00 38.66 4.75
270 271 1.605058 TTGGTAGAGGTGGCTCTCGC 61.605 60.000 0.00 0.00 38.71 5.03
291 292 3.552890 GCCCAAAGAATGCGAAAGAACTT 60.553 43.478 0.00 0.00 0.00 2.66
318 319 1.038681 TAAGGCATGCCCGTCTACGA 61.039 55.000 33.14 6.74 43.02 3.43
324 325 0.390735 ATGCCCGTCTACGAAACCAC 60.391 55.000 3.65 0.00 43.02 4.16
334 335 1.710013 ACGAAACCACATAGAGCGTG 58.290 50.000 0.00 0.00 0.00 5.34
345 346 1.438651 TAGAGCGTGCAATTGGTGTC 58.561 50.000 7.72 0.00 0.00 3.67
349 350 1.580942 CGTGCAATTGGTGTCTGGG 59.419 57.895 7.72 0.00 0.00 4.45
380 381 6.813152 CGATTTCCTATTTTGAAAGTTGGCAT 59.187 34.615 0.00 0.00 35.36 4.40
381 382 7.201461 CGATTTCCTATTTTGAAAGTTGGCATG 60.201 37.037 0.00 0.00 35.36 4.06
396 397 3.039743 TGGCATGCATTACCCAATTGAT 58.960 40.909 21.36 0.00 0.00 2.57
412 413 8.090214 ACCCAATTGATACTCAAGTCAAAATTG 58.910 33.333 7.12 12.70 40.05 2.32
415 416 8.644619 CAATTGATACTCAAGTCAAAATTGCTG 58.355 33.333 0.00 0.00 40.05 4.41
447 448 6.037062 CAGCTGTATTTCACAACATAATCCGA 59.963 38.462 5.25 0.00 36.48 4.55
448 449 6.258727 AGCTGTATTTCACAACATAATCCGAG 59.741 38.462 0.00 0.00 36.48 4.63
462 467 1.186200 TCCGAGGTGAGGTGATGAAG 58.814 55.000 0.00 0.00 0.00 3.02
468 473 2.915604 AGGTGAGGTGATGAAGAATGGT 59.084 45.455 0.00 0.00 0.00 3.55
584 589 4.042271 TCAAAGGGACCTTGGTAATTCC 57.958 45.455 4.03 0.00 36.26 3.01
633 638 6.381498 TGTGGGTGGACTATCAAAGAATTA 57.619 37.500 0.00 0.00 0.00 1.40
639 644 7.496263 GGGTGGACTATCAAAGAATTAGAAGAC 59.504 40.741 0.00 0.00 0.00 3.01
673 679 5.760253 ACGGAGATCTGTTGGCTAATAATTG 59.240 40.000 0.00 0.00 29.59 2.32
777 806 8.906867 AGGATGACATTTGAGTTATGTTATTGG 58.093 33.333 0.00 0.00 36.41 3.16
783 812 7.838696 ACATTTGAGTTATGTTATTGGGGATCA 59.161 33.333 0.00 0.00 32.48 2.92
873 902 9.524106 TTGCATTTTCAGATTCTTATATTGCTG 57.476 29.630 0.00 0.00 0.00 4.41
889 919 9.571816 TTATATTGCTGAATGTGATGTTGGATA 57.428 29.630 0.00 0.00 0.00 2.59
890 920 6.971726 ATTGCTGAATGTGATGTTGGATAT 57.028 33.333 0.00 0.00 0.00 1.63
891 921 6.778834 TTGCTGAATGTGATGTTGGATATT 57.221 33.333 0.00 0.00 0.00 1.28
892 922 6.381481 TGCTGAATGTGATGTTGGATATTC 57.619 37.500 0.00 0.00 0.00 1.75
893 923 5.887035 TGCTGAATGTGATGTTGGATATTCA 59.113 36.000 0.00 0.00 34.50 2.57
897 927 8.756486 TGAATGTGATGTTGGATATTCAGATT 57.244 30.769 0.00 0.00 35.52 2.40
898 928 9.192642 TGAATGTGATGTTGGATATTCAGATTT 57.807 29.630 0.00 0.00 33.70 2.17
899 929 9.459640 GAATGTGATGTTGGATATTCAGATTTG 57.540 33.333 0.00 0.00 33.70 2.32
900 930 7.943079 TGTGATGTTGGATATTCAGATTTGT 57.057 32.000 0.00 0.00 0.00 2.83
901 931 9.631257 ATGTGATGTTGGATATTCAGATTTGTA 57.369 29.630 0.00 0.00 0.00 2.41
902 932 9.631257 TGTGATGTTGGATATTCAGATTTGTAT 57.369 29.630 0.00 0.00 0.00 2.29
962 992 8.975410 TTGCTTAATTTGATCAGATTCTTGTG 57.025 30.769 14.30 4.21 0.00 3.33
1033 1064 1.308783 GGCTAAGTGGACAGCAAGGC 61.309 60.000 0.00 0.00 39.63 4.35
1042 1073 1.888512 GGACAGCAAGGCATGAGAAAA 59.111 47.619 0.00 0.00 0.00 2.29
1107 1138 1.549037 GGCCAAAATGGGTGGACTACA 60.549 52.381 0.00 0.00 41.44 2.74
1116 1147 1.134371 GGGTGGACTACAGAAGGATGC 60.134 57.143 0.00 0.00 0.00 3.91
1161 1192 7.118723 TGAACAATTTATATCCAGAGGCAAGT 58.881 34.615 0.00 0.00 0.00 3.16
1196 1227 2.432510 AGGTCCAAGATAAGGAAGCTCG 59.567 50.000 0.00 0.00 36.80 5.03
1229 1260 7.145932 AGCACTACAAAAATATCAAGTCCAC 57.854 36.000 0.00 0.00 0.00 4.02
1231 1262 7.230510 AGCACTACAAAAATATCAAGTCCACAA 59.769 33.333 0.00 0.00 0.00 3.33
1239 1270 2.631160 TCAAGTCCACAATCAACCGT 57.369 45.000 0.00 0.00 0.00 4.83
1258 1289 5.308825 ACCGTTCTGGAATATCATGGAATC 58.691 41.667 0.00 0.00 42.00 2.52
1268 1299 8.909923 TGGAATATCATGGAATCATATTGCATC 58.090 33.333 11.70 0.00 28.83 3.91
1294 1325 3.451141 TCAACACCATGCCTGAAAAAC 57.549 42.857 0.00 0.00 0.00 2.43
1365 2927 9.807649 ATTTCCTTATATGTGCATGAACTTTTC 57.192 29.630 5.18 0.00 0.00 2.29
1432 2994 2.232208 GAGGACCCAAAGCTCAAAATGG 59.768 50.000 0.00 0.00 0.00 3.16
1466 3029 3.129287 AGCTTTCCATTTTACGAGGCATG 59.871 43.478 0.00 0.00 0.00 4.06
1492 3055 4.910195 TGTGCTCTATGAAGGACACATTT 58.090 39.130 0.33 0.00 41.90 2.32
1494 3057 5.181748 GTGCTCTATGAAGGACACATTTCT 58.818 41.667 0.00 0.00 37.53 2.52
1529 3092 1.558756 CCTCACATCAAGGAAGCCTCT 59.441 52.381 0.00 0.00 35.83 3.69
1535 3098 3.009916 ACATCAAGGAAGCCTCTGATTGT 59.990 43.478 0.00 0.00 32.94 2.71
1543 3106 4.219288 GGAAGCCTCTGATTGTCACAAAAT 59.781 41.667 0.00 0.00 0.00 1.82
1696 3259 6.211384 TGATGTGGATGAAAGAGAGAACACTA 59.789 38.462 0.00 0.00 0.00 2.74
1765 3328 7.648142 TCAACCACAAATAAGTGAATCAAGTC 58.352 34.615 0.00 0.00 42.05 3.01
1767 3330 6.306987 ACCACAAATAAGTGAATCAAGTCCT 58.693 36.000 0.00 0.00 42.05 3.85
1770 3333 8.454106 CCACAAATAAGTGAATCAAGTCCTAAG 58.546 37.037 0.00 0.00 42.05 2.18
1821 3385 2.283298 CATCTGTACAGCGGCTTGAAT 58.717 47.619 18.45 0.75 0.00 2.57
1855 3419 6.690530 TGGCTTATGTGAATTTCAAGAAAGG 58.309 36.000 0.00 0.00 33.32 3.11
1896 3461 7.015584 AGGAAAAAGTGTCATAGCAAGGAAAAT 59.984 33.333 0.00 0.00 0.00 1.82
1919 3484 5.116084 AGCCCTCAATTACAGAATGCTTA 57.884 39.130 0.00 0.00 42.53 3.09
1920 3485 5.128919 AGCCCTCAATTACAGAATGCTTAG 58.871 41.667 0.00 0.00 42.53 2.18
1948 3513 6.094464 GTCTTGAATGACATGGATGATGTTCA 59.906 38.462 0.00 0.00 45.90 3.18
1952 3517 4.141233 TGACATGGATGATGTTCACGAT 57.859 40.909 0.00 0.00 45.90 3.73
1991 3556 4.082354 GCCTCTGATGTTTTCAAAGATGCT 60.082 41.667 0.00 0.00 36.41 3.79
1997 3562 5.234757 TGATGTTTTCAAAGATGCTGCAAAC 59.765 36.000 6.36 4.49 0.00 2.93
2009 3574 2.100584 TGCTGCAAACCGTGAGATTTTT 59.899 40.909 0.00 0.00 0.00 1.94
2194 3759 2.611518 CTCGACTTTCATCTGGTGGTC 58.388 52.381 0.00 0.00 0.00 4.02
2257 3823 4.092383 TCGTGCTCCTTTTATTTTCGCTAC 59.908 41.667 0.00 0.00 0.00 3.58
2260 3826 5.062558 GTGCTCCTTTTATTTTCGCTACGTA 59.937 40.000 0.00 0.00 0.00 3.57
2303 3869 3.700538 TCTTCATTATTGCTTGCCCTGT 58.299 40.909 0.00 0.00 0.00 4.00
2304 3870 4.088634 TCTTCATTATTGCTTGCCCTGTT 58.911 39.130 0.00 0.00 0.00 3.16
2305 3871 4.527816 TCTTCATTATTGCTTGCCCTGTTT 59.472 37.500 0.00 0.00 0.00 2.83
2306 3872 5.714333 TCTTCATTATTGCTTGCCCTGTTTA 59.286 36.000 0.00 0.00 0.00 2.01
2307 3873 6.380846 TCTTCATTATTGCTTGCCCTGTTTAT 59.619 34.615 0.00 0.00 0.00 1.40
2308 3874 6.543430 TCATTATTGCTTGCCCTGTTTATT 57.457 33.333 0.00 0.00 0.00 1.40
2309 3875 6.339730 TCATTATTGCTTGCCCTGTTTATTG 58.660 36.000 0.00 0.00 0.00 1.90
2310 3876 2.453983 TTGCTTGCCCTGTTTATTGC 57.546 45.000 0.00 0.00 0.00 3.56
2311 3877 1.336131 TGCTTGCCCTGTTTATTGCA 58.664 45.000 0.00 0.00 0.00 4.08
2312 3878 1.273048 TGCTTGCCCTGTTTATTGCAG 59.727 47.619 0.00 0.00 34.81 4.41
2322 3888 3.924144 TGTTTATTGCAGGATTGGTTGC 58.076 40.909 0.00 0.00 40.67 4.17
2323 3889 3.261580 GTTTATTGCAGGATTGGTTGCC 58.738 45.455 0.00 0.00 39.54 4.52
2324 3890 1.484038 TATTGCAGGATTGGTTGCCC 58.516 50.000 0.00 0.00 39.54 5.36
2325 3891 0.252375 ATTGCAGGATTGGTTGCCCT 60.252 50.000 0.00 0.00 39.54 5.19
2326 3892 0.899717 TTGCAGGATTGGTTGCCCTC 60.900 55.000 0.00 0.00 39.54 4.30
2367 3934 3.442625 GCCCTGTTTATTGGGTTCTACAC 59.557 47.826 0.00 0.00 45.06 2.90
2377 3944 2.976185 TGGGTTCTACACATGGTCTCAA 59.024 45.455 0.00 0.00 0.00 3.02
2391 3958 7.276658 CACATGGTCTCAACTTCAGAGTTATAC 59.723 40.741 0.00 0.00 44.14 1.47
2408 3975 6.003950 AGTTATACTGTTGGTGCTGATGTTT 58.996 36.000 0.00 0.00 0.00 2.83
2462 4103 1.532868 GTGTAGACTTGTTGCTGCCTG 59.467 52.381 0.00 0.00 0.00 4.85
2522 4166 3.670627 GCCATGTTGTTTCTTCATCGGTC 60.671 47.826 0.00 0.00 0.00 4.79
2580 4224 2.771372 TGACATGCTATGGCTACCTTGA 59.229 45.455 1.68 0.00 39.69 3.02
2595 4239 0.329261 CTTGAACCATCTGGCTCCCA 59.671 55.000 0.00 0.00 39.32 4.37
2616 4260 6.500049 TCCCATTGGTAATTCAGGATTTTGTT 59.500 34.615 1.20 0.00 0.00 2.83
2647 4291 7.502226 TCTTTTTGACATACATGGTTGTTCTCT 59.498 33.333 0.00 0.00 37.28 3.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
51 52 0.321346 TGAGATCAAAGTCGCAGGCA 59.679 50.000 0.00 0.00 0.00 4.75
63 64 5.408299 CGACACATAAACAACCTTGAGATCA 59.592 40.000 0.00 0.00 0.00 2.92
72 73 1.199097 CCAGCCGACACATAAACAACC 59.801 52.381 0.00 0.00 0.00 3.77
73 74 1.877443 ACCAGCCGACACATAAACAAC 59.123 47.619 0.00 0.00 0.00 3.32
87 88 4.048470 GACCCCTCCCAACCAGCC 62.048 72.222 0.00 0.00 0.00 4.85
112 113 6.189859 TGGAAGATTTCAATACTCCAGCATT 58.810 36.000 0.00 0.00 30.12 3.56
133 134 0.623194 TGGAAGCCCGATTGAATGGA 59.377 50.000 0.00 0.00 34.29 3.41
135 136 2.026641 ACATGGAAGCCCGATTGAATG 58.973 47.619 0.00 0.00 34.29 2.67
160 161 4.999311 GTCAACCAAATAGTACTTTCCCGT 59.001 41.667 0.00 0.00 0.00 5.28
165 166 5.243207 CCTCCGTCAACCAAATAGTACTTT 58.757 41.667 0.00 0.00 0.00 2.66
201 202 2.403252 ACGGAGCTAGAAATTGTGGG 57.597 50.000 0.00 0.00 0.00 4.61
207 208 3.305720 TCCATGGTACGGAGCTAGAAAT 58.694 45.455 12.58 0.00 0.00 2.17
224 225 7.348080 TCTTGTAGATGATAACGAACTCCAT 57.652 36.000 0.00 0.00 0.00 3.41
237 238 7.331026 CACCTCTACCAAAATCTTGTAGATGA 58.669 38.462 0.00 0.00 34.65 2.92
270 271 3.923017 AGTTCTTTCGCATTCTTTGGG 57.077 42.857 0.00 0.00 39.56 4.12
279 280 6.668323 CCTTAGATTGAAAAGTTCTTTCGCA 58.332 36.000 0.00 0.00 0.00 5.10
280 281 5.569441 GCCTTAGATTGAAAAGTTCTTTCGC 59.431 40.000 0.00 0.00 0.00 4.70
282 283 7.062722 GCATGCCTTAGATTGAAAAGTTCTTTC 59.937 37.037 6.36 0.00 0.00 2.62
291 292 2.023673 CGGGCATGCCTTAGATTGAAA 58.976 47.619 34.70 0.00 36.10 2.69
318 319 1.890876 TTGCACGCTCTATGTGGTTT 58.109 45.000 0.00 0.00 37.80 3.27
324 325 1.739466 ACACCAATTGCACGCTCTATG 59.261 47.619 0.00 0.00 0.00 2.23
334 335 2.932187 GCATTTCCCAGACACCAATTGC 60.932 50.000 0.00 0.00 0.00 3.56
349 350 8.466086 ACTTTCAAAATAGGAAATCGCATTTC 57.534 30.769 11.08 11.08 46.05 2.17
369 370 2.233431 TGGGTAATGCATGCCAACTTTC 59.767 45.455 16.68 1.76 35.05 2.62
396 397 4.261572 GCCACAGCAATTTTGACTTGAGTA 60.262 41.667 0.00 0.00 39.53 2.59
415 416 1.305219 TGAAATACAGCTGCCGCCAC 61.305 55.000 15.27 2.03 36.60 5.01
447 448 2.915604 ACCATTCTTCATCACCTCACCT 59.084 45.455 0.00 0.00 0.00 4.00
448 449 3.356529 ACCATTCTTCATCACCTCACC 57.643 47.619 0.00 0.00 0.00 4.02
462 467 5.455525 GCATTTGTTGCGTATCTAACCATTC 59.544 40.000 0.00 0.00 42.54 2.67
584 589 5.319140 TGTTGGCAATTTCATCTCTCATG 57.681 39.130 1.92 0.00 0.00 3.07
633 638 4.703897 TCTCCGTGACATTTTTGTCTTCT 58.296 39.130 7.55 0.00 39.41 2.85
639 644 5.149273 CAACAGATCTCCGTGACATTTTTG 58.851 41.667 0.00 0.00 0.00 2.44
643 648 2.936993 GCCAACAGATCTCCGTGACATT 60.937 50.000 0.00 0.00 0.00 2.71
731 738 9.685276 TCATCCTTACATAACTCAAATGTCATT 57.315 29.630 0.00 0.00 38.49 2.57
834 863 8.246908 TCTGAAAATGCAAAATCACATCAATC 57.753 30.769 0.00 0.00 0.00 2.67
835 864 8.786826 ATCTGAAAATGCAAAATCACATCAAT 57.213 26.923 0.00 0.00 0.00 2.57
873 902 9.459640 CAAATCTGAATATCCAACATCACATTC 57.540 33.333 0.00 0.00 0.00 2.67
936 966 9.582431 CACAAGAATCTGATCAAATTAAGCAAT 57.418 29.630 0.00 0.00 0.00 3.56
1042 1073 3.008813 TCTGTAAGTACCTCCACGAGACT 59.991 47.826 0.00 0.00 33.76 3.24
1107 1138 4.401022 TGACAACTTGATTGCATCCTTCT 58.599 39.130 0.00 0.00 42.62 2.85
1116 1147 6.979817 TGTTCAATTCCTTGACAACTTGATTG 59.020 34.615 0.00 0.00 41.05 2.67
1196 1227 9.255304 TGATATTTTTGTAGTGCTTTTTCAACC 57.745 29.630 0.00 0.00 0.00 3.77
1229 1260 6.432936 CATGATATTCCAGAACGGTTGATTG 58.567 40.000 0.00 0.00 35.57 2.67
1231 1262 5.065914 CCATGATATTCCAGAACGGTTGAT 58.934 41.667 0.00 0.00 35.57 2.57
1239 1270 8.963725 GCAATATGATTCCATGATATTCCAGAA 58.036 33.333 0.00 0.00 28.54 3.02
1283 1314 1.142060 TCTCTTCCCGTTTTTCAGGCA 59.858 47.619 0.00 0.00 0.00 4.75
1294 1325 2.322355 ACTGCAATGATCTCTTCCCG 57.678 50.000 0.00 0.00 0.00 5.14
1336 2897 8.162878 AGTTCATGCACATATAAGGAAATCAG 57.837 34.615 0.00 0.00 0.00 2.90
1455 3018 1.298340 CACACCCCATGCCTCGTAA 59.702 57.895 0.00 0.00 0.00 3.18
1466 3029 1.134371 GTCCTTCATAGAGCACACCCC 60.134 57.143 0.00 0.00 0.00 4.95
1492 3055 2.639347 TGAGGCAATGTCTTCCTTGAGA 59.361 45.455 0.00 0.00 0.00 3.27
1494 3057 2.106338 TGTGAGGCAATGTCTTCCTTGA 59.894 45.455 0.00 0.00 0.00 3.02
1529 3092 7.230510 AGTTGCTACCTAATTTTGTGACAATCA 59.769 33.333 0.00 0.00 0.00 2.57
1535 3098 6.547880 TCCAAAGTTGCTACCTAATTTTGTGA 59.452 34.615 8.37 4.39 34.73 3.58
1543 3106 3.780804 TGCTCCAAAGTTGCTACCTAA 57.219 42.857 0.00 0.00 0.00 2.69
1569 3132 2.159462 GCTAGTGCTTGCAACCATCTTC 60.159 50.000 0.00 0.00 36.03 2.87
1696 3259 5.059833 GCCTAATTCTTCCTCGTCATTGAT 58.940 41.667 0.00 0.00 0.00 2.57
1781 3345 3.594134 TGTGGCACCTTTTTGTTTCTTG 58.406 40.909 16.26 0.00 0.00 3.02
1821 3385 8.481492 AAATTCACATAAGCCATCATGGAATA 57.519 30.769 8.30 0.00 40.96 1.75
1855 3419 3.346426 TCCTTCTTGGAAGCTTGCC 57.654 52.632 15.98 11.27 42.94 4.52
1884 3449 4.584638 TTGAGGGCTATTTTCCTTGCTA 57.415 40.909 0.00 0.00 32.74 3.49
1896 3461 4.778213 AGCATTCTGTAATTGAGGGCTA 57.222 40.909 0.00 0.00 0.00 3.93
1919 3484 4.472470 TCATCCATGTCATTCAAGACCTCT 59.528 41.667 0.00 0.00 37.73 3.69
1920 3485 4.774124 TCATCCATGTCATTCAAGACCTC 58.226 43.478 0.00 0.00 37.73 3.85
1948 3513 3.191371 GGCAAAGATTTTGACCTCATCGT 59.809 43.478 5.77 0.00 0.00 3.73
1952 3517 3.822735 CAGAGGCAAAGATTTTGACCTCA 59.177 43.478 27.23 0.00 41.18 3.86
1991 3556 3.243367 CCAGAAAAATCTCACGGTTTGCA 60.243 43.478 0.00 0.00 0.00 4.08
1997 3562 4.069304 TGTAACCCAGAAAAATCTCACGG 58.931 43.478 0.00 0.00 0.00 4.94
2009 3574 4.072131 GCAATCTTGAGTTGTAACCCAGA 58.928 43.478 0.00 0.00 0.00 3.86
2151 3716 3.407698 TGCAAAGGAATACTCGCTGAAA 58.592 40.909 0.00 0.00 0.00 2.69
2154 3719 1.063174 GCTGCAAAGGAATACTCGCTG 59.937 52.381 0.00 0.00 0.00 5.18
2194 3759 4.015084 AGCACCAGATTGATTGAAGGAAG 58.985 43.478 0.00 0.00 0.00 3.46
2290 3856 2.302445 TGCAATAAACAGGGCAAGCAAT 59.698 40.909 0.00 0.00 32.54 3.56
2303 3869 3.608316 GGCAACCAATCCTGCAATAAA 57.392 42.857 0.00 0.00 40.46 1.40
2318 3884 4.660789 ATCATGCAATAAAGAGGGCAAC 57.339 40.909 0.00 0.00 40.02 4.17
2319 3885 5.013568 CAATCATGCAATAAAGAGGGCAA 57.986 39.130 0.00 0.00 40.02 4.52
2320 3886 4.659111 CAATCATGCAATAAAGAGGGCA 57.341 40.909 0.00 0.00 41.00 5.36
2367 3934 7.490725 CAGTATAACTCTGAAGTTGAGACCATG 59.509 40.741 1.17 0.00 45.37 3.66
2377 3944 5.012148 AGCACCAACAGTATAACTCTGAAGT 59.988 40.000 0.00 0.00 37.32 3.01
2391 3958 3.713858 TTGAAACATCAGCACCAACAG 57.286 42.857 0.00 0.00 0.00 3.16
2408 3975 2.323999 ATGTTGCAAAGGGGGATTGA 57.676 45.000 0.00 0.00 0.00 2.57
2580 4224 0.032813 CCAATGGGAGCCAGATGGTT 60.033 55.000 0.00 0.00 38.70 3.67
2616 4260 9.295825 ACAACCATGTATGTCAAAAAGATTAGA 57.704 29.630 0.00 0.00 38.24 2.10
2654 4298 6.000219 GTGCTCTATGAATGATACCAACCAT 59.000 40.000 0.00 0.00 0.00 3.55


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

AutoCloner maintained by Alex Coulton.