Multiple sequence alignment - TraesCS6B01G161500

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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 TraesCS6B01G161500 chr6B 100.000 2111 0 0 1 2111 165873939 165876049 0.000000e+00 3899.0
1 TraesCS6B01G161500 chr6B 87.829 304 34 3 860 1161 166114688 166114990 9.270000e-94 353.0
2 TraesCS6B01G161500 chr6B 87.667 300 37 0 863 1162 166117147 166117446 1.200000e-92 350.0
3 TraesCS6B01G161500 chr6B 82.051 78 10 4 1861 1935 634323990 634323914 1.750000e-06 63.9
4 TraesCS6B01G161500 chr6A 90.831 698 41 7 1424 2111 105325404 105326088 0.000000e+00 913.0
5 TraesCS6B01G161500 chr6A 89.160 738 35 21 58 774 105321439 105322152 0.000000e+00 878.0
6 TraesCS6B01G161500 chr6A 91.710 193 10 5 1192 1382 105323389 105323577 1.610000e-66 263.0
7 TraesCS6B01G161500 chr6A 94.030 67 3 1 1 66 105316213 105316279 1.330000e-17 100.0
8 TraesCS6B01G161500 chr6A 91.803 61 3 2 1382 1442 105323632 105323690 1.340000e-12 84.2
9 TraesCS6B01G161500 chr6D 88.261 690 49 14 35 713 87371053 87371721 0.000000e+00 797.0
10 TraesCS6B01G161500 chr6D 86.364 704 75 11 1416 2111 87375338 87376028 0.000000e+00 749.0
11 TraesCS6B01G161500 chr6D 89.384 292 30 1 876 1166 87465774 87466065 1.190000e-97 366.0
12 TraesCS6B01G161500 chr6D 78.182 110 21 3 1860 1967 420937660 420937552 1.350000e-07 67.6
13 TraesCS6B01G161500 chr7B 88.889 306 31 3 876 1178 34614067 34614372 7.110000e-100 374.0
14 TraesCS6B01G161500 chr5B 87.847 288 29 6 874 1158 587765345 587765061 1.210000e-87 333.0
15 TraesCS6B01G161500 chr5B 87.500 288 30 6 874 1158 587790351 587790067 5.620000e-86 327.0
16 TraesCS6B01G161500 chr7A 87.285 291 34 3 876 1164 632379072 632378783 1.560000e-86 329.0
17 TraesCS6B01G161500 chr7A 86.577 298 37 2 884 1178 86073683 86073980 2.020000e-85 326.0
18 TraesCS6B01G161500 chr7D 87.108 287 36 1 876 1161 85026183 85026469 7.260000e-85 324.0
19 TraesCS6B01G161500 chr3A 82.759 261 38 7 1418 1673 46990420 46990678 2.110000e-55 226.0
20 TraesCS6B01G161500 chr1D 81.250 272 40 10 1418 1681 463859364 463859632 2.120000e-50 209.0
21 TraesCS6B01G161500 chr2D 80.220 273 40 10 1421 1681 638620308 638620038 2.140000e-45 193.0
22 TraesCS6B01G161500 chr1A 89.091 55 6 0 1593 1647 14175041 14174987 3.760000e-08 69.4


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 TraesCS6B01G161500 chr6B 165873939 165876049 2110 False 3899.00 3899 100.0000 1 2111 1 chr6B.!!$F1 2110
1 TraesCS6B01G161500 chr6B 166114688 166117446 2758 False 351.50 353 87.7480 860 1162 2 chr6B.!!$F2 302
2 TraesCS6B01G161500 chr6A 105321439 105326088 4649 False 534.55 913 90.8760 58 2111 4 chr6A.!!$F2 2053
3 TraesCS6B01G161500 chr6D 87371053 87376028 4975 False 773.00 797 87.3125 35 2111 2 chr6D.!!$F2 2076

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
308 323 0.534877 TTCAGTGATGGCTTGCACGT 60.535 50.0 0.0 0.0 39.88 4.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1750 9069 0.03213 GACTTGCACAGTCGACCTCA 59.968 55.0 13.01 2.16 42.82 3.86 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
29 30 3.535962 GCCAGAGGGAGAGCGGAG 61.536 72.222 0.00 0.00 35.59 4.63
30 31 2.043450 CCAGAGGGAGAGCGGAGT 60.043 66.667 0.00 0.00 35.59 3.85
31 32 2.124693 CCAGAGGGAGAGCGGAGTC 61.125 68.421 0.00 0.00 35.59 3.36
32 33 2.124487 AGAGGGAGAGCGGAGTCG 60.124 66.667 0.00 0.00 39.81 4.18
196 204 1.036481 TTGTCAGTTGCTGCAGCCAA 61.036 50.000 34.64 25.49 41.18 4.52
220 228 8.871862 CAATCTTCTGAAGTTCATCTAGACTTG 58.128 37.037 16.43 10.82 0.00 3.16
221 229 6.929625 TCTTCTGAAGTTCATCTAGACTTGG 58.070 40.000 16.43 0.00 0.00 3.61
223 231 6.274157 TCTGAAGTTCATCTAGACTTGGTC 57.726 41.667 5.91 0.00 0.00 4.02
224 232 5.060662 TGAAGTTCATCTAGACTTGGTCG 57.939 43.478 0.08 0.00 37.67 4.79
226 234 2.166664 AGTTCATCTAGACTTGGTCGCC 59.833 50.000 0.00 0.00 37.67 5.54
227 235 1.112113 TCATCTAGACTTGGTCGCCC 58.888 55.000 0.00 0.00 37.67 6.13
229 237 2.017559 ATCTAGACTTGGTCGCCCGC 62.018 60.000 0.00 0.00 37.67 6.13
230 238 3.718210 CTAGACTTGGTCGCCCGCC 62.718 68.421 0.00 0.00 37.67 6.13
300 308 5.166398 CAAGAATTCCTTTTCAGTGATGGC 58.834 41.667 0.65 0.00 31.42 4.40
305 320 1.614903 CCTTTTCAGTGATGGCTTGCA 59.385 47.619 0.00 0.00 0.00 4.08
306 321 2.608752 CCTTTTCAGTGATGGCTTGCAC 60.609 50.000 0.00 0.00 35.30 4.57
307 322 0.592637 TTTCAGTGATGGCTTGCACG 59.407 50.000 0.00 0.00 39.88 5.34
308 323 0.534877 TTCAGTGATGGCTTGCACGT 60.535 50.000 0.00 0.00 39.88 4.49
309 324 0.534877 TCAGTGATGGCTTGCACGTT 60.535 50.000 0.00 0.00 39.88 3.99
389 404 6.006449 AGTGATAACTGATGGTTCTTGCTTT 58.994 36.000 0.00 0.00 39.17 3.51
403 418 4.304110 TCTTGCTTTACACGGTACTTCTG 58.696 43.478 0.00 0.00 0.00 3.02
411 426 4.395959 ACACGGTACTTCTGTTCTTCAA 57.604 40.909 0.00 0.00 32.67 2.69
444 459 3.128242 GCTTTGTCAGGGAAGATGATGTG 59.872 47.826 0.00 0.00 0.00 3.21
483 498 5.324784 ACAGATACATGCACGAGTAGAAA 57.675 39.130 0.00 0.00 0.00 2.52
542 558 3.133901 TCAGATACGCCTGCTTCCATTTA 59.866 43.478 0.00 0.00 34.28 1.40
604 627 3.952323 CTGAACTCAATGAGGGCATTCAT 59.048 43.478 15.38 0.00 42.66 2.57
655 679 8.386606 GCTTCCGTATCAGATATGATTTTCATC 58.613 37.037 8.36 0.00 38.26 2.92
657 681 8.992835 TCCGTATCAGATATGATTTTCATCAG 57.007 34.615 8.36 0.00 42.93 2.90
677 701 3.067106 AGGTGTGCAGACTACGATTTTG 58.933 45.455 14.32 0.00 0.00 2.44
679 703 3.120649 GGTGTGCAGACTACGATTTTGTC 60.121 47.826 14.32 0.00 0.00 3.18
693 719 4.142816 CGATTTTGTCATCTGTCAAGGGAC 60.143 45.833 0.00 0.00 44.57 4.46
760 2776 8.686334 TCTTATTTCATGGCTTTTAATCCTCAC 58.314 33.333 0.00 0.00 0.00 3.51
761 2777 8.593945 TTATTTCATGGCTTTTAATCCTCACT 57.406 30.769 0.00 0.00 0.00 3.41
770 2786 6.209589 GGCTTTTAATCCTCACTTTCTTCCTT 59.790 38.462 0.00 0.00 0.00 3.36
774 2790 5.505181 AATCCTCACTTTCTTCCTTAGCA 57.495 39.130 0.00 0.00 0.00 3.49
775 2791 5.707066 ATCCTCACTTTCTTCCTTAGCAT 57.293 39.130 0.00 0.00 0.00 3.79
776 2792 5.091261 TCCTCACTTTCTTCCTTAGCATC 57.909 43.478 0.00 0.00 0.00 3.91
778 2794 5.190528 TCCTCACTTTCTTCCTTAGCATCAT 59.809 40.000 0.00 0.00 0.00 2.45
779 2795 6.384015 TCCTCACTTTCTTCCTTAGCATCATA 59.616 38.462 0.00 0.00 0.00 2.15
780 2796 7.050377 CCTCACTTTCTTCCTTAGCATCATAA 58.950 38.462 0.00 0.00 0.00 1.90
784 2800 9.565213 CACTTTCTTCCTTAGCATCATAAAAAG 57.435 33.333 0.00 0.00 0.00 2.27
785 2801 9.520515 ACTTTCTTCCTTAGCATCATAAAAAGA 57.479 29.630 0.00 0.00 0.00 2.52
788 2804 8.511604 TCTTCCTTAGCATCATAAAAAGAAGG 57.488 34.615 0.00 0.00 34.71 3.46
789 2805 8.328758 TCTTCCTTAGCATCATAAAAAGAAGGA 58.671 33.333 0.00 0.00 39.48 3.36
790 2806 8.877864 TTCCTTAGCATCATAAAAAGAAGGAA 57.122 30.769 8.35 8.35 45.17 3.36
791 2807 8.511604 TCCTTAGCATCATAAAAAGAAGGAAG 57.488 34.615 0.00 0.00 38.56 3.46
792 2808 8.328758 TCCTTAGCATCATAAAAAGAAGGAAGA 58.671 33.333 0.00 0.00 38.56 2.87
793 2809 9.129532 CCTTAGCATCATAAAAAGAAGGAAGAT 57.870 33.333 0.00 0.00 35.27 2.40
798 2814 9.298774 GCATCATAAAAAGAAGGAAGATTTCAG 57.701 33.333 0.00 0.00 0.00 3.02
799 2815 9.798994 CATCATAAAAAGAAGGAAGATTTCAGG 57.201 33.333 0.00 0.00 0.00 3.86
800 2816 7.830739 TCATAAAAAGAAGGAAGATTTCAGGC 58.169 34.615 0.00 0.00 0.00 4.85
806 2893 3.532641 AGGAAGATTTCAGGCCAAAGT 57.467 42.857 5.01 0.00 0.00 2.66
808 2895 4.998051 AGGAAGATTTCAGGCCAAAGTAA 58.002 39.130 5.01 0.00 0.00 2.24
820 2907 3.879892 GGCCAAAGTAAGCTCCTAATCAG 59.120 47.826 0.00 0.00 0.00 2.90
828 2915 6.754193 AGTAAGCTCCTAATCAGCTACAATC 58.246 40.000 0.00 0.00 46.96 2.67
836 2923 6.787458 TCCTAATCAGCTACAATCCCTGATAA 59.213 38.462 3.13 0.00 43.45 1.75
839 2926 9.593134 CTAATCAGCTACAATCCCTGATAATAC 57.407 37.037 3.13 0.00 43.45 1.89
844 2972 7.721399 CAGCTACAATCCCTGATAATACCTTTT 59.279 37.037 0.00 0.00 0.00 2.27
845 2973 8.945193 AGCTACAATCCCTGATAATACCTTTTA 58.055 33.333 0.00 0.00 0.00 1.52
917 3072 3.431725 GGCTGTAGTGCAACGCCC 61.432 66.667 11.14 0.00 45.86 6.13
921 3087 2.187599 CTGTAGTGCAACGCCCAAGC 62.188 60.000 0.00 0.00 45.86 4.01
922 3088 2.112087 TAGTGCAACGCCCAAGCA 59.888 55.556 0.00 0.00 45.86 3.91
923 3089 1.527148 TAGTGCAACGCCCAAGCAA 60.527 52.632 0.00 0.00 45.86 3.91
924 3090 1.791103 TAGTGCAACGCCCAAGCAAC 61.791 55.000 0.00 0.00 45.86 4.17
925 3091 3.143515 TGCAACGCCCAAGCAACA 61.144 55.556 0.00 0.00 39.83 3.33
926 3092 2.355009 GCAACGCCCAAGCAACAG 60.355 61.111 0.00 0.00 39.83 3.16
927 3093 2.355009 CAACGCCCAAGCAACAGC 60.355 61.111 0.00 0.00 39.83 4.40
928 3094 2.519302 AACGCCCAAGCAACAGCT 60.519 55.556 0.00 0.00 41.23 4.24
929 3095 2.848858 AACGCCCAAGCAACAGCTG 61.849 57.895 13.48 13.48 38.93 4.24
930 3096 2.979676 CGCCCAAGCAACAGCTGA 60.980 61.111 23.35 0.00 38.93 4.26
933 3099 1.975407 CCCAAGCAACAGCTGAGGG 60.975 63.158 23.35 16.23 43.66 4.30
939 3105 2.116125 AACAGCTGAGGGCCCAAC 59.884 61.111 27.56 18.37 43.05 3.77
1096 5802 3.003394 TGAGTTGTAATGATGCCCTGG 57.997 47.619 0.00 0.00 0.00 4.45
1103 5809 0.549950 AATGATGCCCTGGGTCTCAG 59.450 55.000 15.56 0.00 43.00 3.35
1111 5817 2.772515 GCCCTGGGTCTCAGTTTATAGT 59.227 50.000 15.56 0.00 41.83 2.12
1122 5828 5.713389 TCTCAGTTTATAGTTTCCTCGACCA 59.287 40.000 0.00 0.00 0.00 4.02
1141 5847 1.066573 CACCTCTCAACTCTCCGCAAT 60.067 52.381 0.00 0.00 0.00 3.56
1158 5864 3.615056 CGCAATCGATGTGGTACTAAACA 59.385 43.478 0.00 0.00 38.10 2.83
1165 5871 5.407387 TCGATGTGGTACTAAACAAAAGAGC 59.593 40.000 0.00 0.00 0.00 4.09
1173 5879 6.073167 GGTACTAAACAAAAGAGCCAAGAGTC 60.073 42.308 0.00 0.00 0.00 3.36
1176 5882 1.777272 ACAAAAGAGCCAAGAGTCCCT 59.223 47.619 0.00 0.00 0.00 4.20
1177 5883 2.157738 CAAAAGAGCCAAGAGTCCCTG 58.842 52.381 0.00 0.00 0.00 4.45
1178 5884 0.695347 AAAGAGCCAAGAGTCCCTGG 59.305 55.000 4.74 4.74 0.00 4.45
1182 5888 3.732849 CCAAGAGTCCCTGGGCCC 61.733 72.222 17.59 17.59 0.00 5.80
1186 5892 4.423209 GAGTCCCTGGGCCCCTCT 62.423 72.222 22.27 10.18 0.00 3.69
1218 5925 1.582968 CAAGCAGCCGCAATCAACT 59.417 52.632 0.00 0.00 42.27 3.16
1219 5926 0.038892 CAAGCAGCCGCAATCAACTT 60.039 50.000 0.00 0.00 42.27 2.66
1220 5927 0.242017 AAGCAGCCGCAATCAACTTC 59.758 50.000 0.00 0.00 42.27 3.01
1221 5928 0.607489 AGCAGCCGCAATCAACTTCT 60.607 50.000 0.00 0.00 42.27 2.85
1225 5932 2.982470 CAGCCGCAATCAACTTCTTTTC 59.018 45.455 0.00 0.00 0.00 2.29
1239 5946 9.878599 TCAACTTCTTTTCTTTTTAGAATAGCG 57.121 29.630 0.00 0.00 30.47 4.26
1296 6003 0.036875 GGCCCAGTAAGAACACAGCT 59.963 55.000 0.00 0.00 0.00 4.24
1387 6768 2.921069 GCTCGTTCTGCTCGTTGTCTTA 60.921 50.000 0.00 0.00 0.00 2.10
1456 8775 2.804647 TGACGAGGTGTTATATGCGTG 58.195 47.619 0.00 0.00 31.58 5.34
1484 8803 7.595311 AAAATTTGGCGAAGAAATGATTACC 57.405 32.000 0.00 0.00 0.00 2.85
1485 8804 4.349663 TTTGGCGAAGAAATGATTACCG 57.650 40.909 0.00 0.00 0.00 4.02
1702 9021 9.461312 AAATTGAATACAAGTGCTCCTATGTTA 57.539 29.630 0.00 0.00 39.46 2.41
1704 9023 9.632638 ATTGAATACAAGTGCTCCTATGTTATT 57.367 29.630 0.00 0.00 39.46 1.40
1737 9056 6.842437 ATTAGCCTACTATCATCATCGTGT 57.158 37.500 0.00 0.00 0.00 4.49
1743 9062 4.244425 ACTATCATCATCGTGTGTAGCC 57.756 45.455 0.00 0.00 0.00 3.93
1750 9069 2.100749 TCATCGTGTGTAGCCATCGATT 59.899 45.455 0.00 0.00 37.93 3.34
1861 9187 7.176515 TCACTTCCAATGCAAAAGCTAATAAGA 59.823 33.333 0.00 0.00 0.00 2.10
1882 9208 1.139853 GCATCTTTGGTCGATCCCTCT 59.860 52.381 0.00 0.00 34.77 3.69
1935 9261 4.748701 TGAGGAGTTAAACTGGACCTAGT 58.251 43.478 0.00 0.00 0.00 2.57
1986 9313 5.733620 AAATTTACTCCTCGAGTGGTACA 57.266 39.130 12.31 7.40 43.30 2.90
2021 9348 5.450550 CGCTTCTTTGGATATTTTTCCTCCC 60.451 44.000 0.00 0.00 36.68 4.30
2040 9367 1.811266 CATCCACGCCCGTCTTCTG 60.811 63.158 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.535962 CTCCGCTCTCCCTCTGGC 61.536 72.222 0.00 0.00 0.00 4.85
13 14 2.043450 ACTCCGCTCTCCCTCTGG 60.043 66.667 0.00 0.00 0.00 3.86
14 15 2.477176 CGACTCCGCTCTCCCTCTG 61.477 68.421 0.00 0.00 0.00 3.35
15 16 2.124487 CGACTCCGCTCTCCCTCT 60.124 66.667 0.00 0.00 0.00 3.69
26 27 4.070552 ACCGGCAGAAGCGACTCC 62.071 66.667 0.00 0.00 43.41 3.85
27 28 2.564553 ATCACCGGCAGAAGCGACTC 62.565 60.000 0.00 0.00 43.41 3.36
28 29 2.650116 ATCACCGGCAGAAGCGACT 61.650 57.895 0.00 0.00 43.41 4.18
29 30 2.125512 ATCACCGGCAGAAGCGAC 60.126 61.111 0.00 0.00 43.41 5.19
30 31 2.125552 CATCACCGGCAGAAGCGA 60.126 61.111 0.00 0.00 43.41 4.93
31 32 3.197790 CCATCACCGGCAGAAGCG 61.198 66.667 0.00 0.00 43.41 4.68
55 56 3.110178 GCAAGTCGTCCCCGTTCG 61.110 66.667 0.00 0.00 35.01 3.95
80 81 1.202510 CGATCTTGAGGGAAGAGCCAG 60.203 57.143 0.00 0.00 43.10 4.85
86 87 1.339055 TGTTGCCGATCTTGAGGGAAG 60.339 52.381 0.00 0.00 38.51 3.46
133 134 9.405587 GTCGTTTTCAATTCTTTGGAATCATAA 57.594 29.630 0.00 0.00 40.86 1.90
139 140 7.429920 CGTTAAGTCGTTTTCAATTCTTTGGAA 59.570 33.333 0.00 0.00 33.44 3.53
196 204 7.180051 ACCAAGTCTAGATGAACTTCAGAAGAT 59.820 37.037 17.56 4.70 0.00 2.40
229 237 0.455464 TACACATTGCGACGACGAGG 60.455 55.000 12.29 0.00 42.66 4.63
230 238 1.333115 TTACACATTGCGACGACGAG 58.667 50.000 12.29 0.00 42.66 4.18
231 239 1.452773 GTTTACACATTGCGACGACGA 59.547 47.619 12.29 0.00 42.66 4.20
232 240 1.461237 GGTTTACACATTGCGACGACG 60.461 52.381 2.12 2.12 42.93 5.12
233 241 1.527736 TGGTTTACACATTGCGACGAC 59.472 47.619 0.00 0.00 0.00 4.34
234 242 1.867166 TGGTTTACACATTGCGACGA 58.133 45.000 0.00 0.00 0.00 4.20
235 243 2.672188 TTGGTTTACACATTGCGACG 57.328 45.000 0.00 0.00 0.00 5.12
236 244 7.044314 GCTATATTTTGGTTTACACATTGCGAC 60.044 37.037 0.00 0.00 0.00 5.19
237 245 6.970043 GCTATATTTTGGTTTACACATTGCGA 59.030 34.615 0.00 0.00 0.00 5.10
238 246 6.749578 TGCTATATTTTGGTTTACACATTGCG 59.250 34.615 0.00 0.00 0.00 4.85
300 308 5.121611 TCTGAACCATAATGTAACGTGCAAG 59.878 40.000 0.00 0.00 0.00 4.01
305 320 5.488341 AGCTTCTGAACCATAATGTAACGT 58.512 37.500 0.00 0.00 0.00 3.99
306 321 6.092122 TCAAGCTTCTGAACCATAATGTAACG 59.908 38.462 0.00 0.00 0.00 3.18
307 322 7.377766 TCAAGCTTCTGAACCATAATGTAAC 57.622 36.000 0.00 0.00 0.00 2.50
308 323 7.816640 GTTCAAGCTTCTGAACCATAATGTAA 58.183 34.615 17.09 0.00 46.29 2.41
309 324 7.377766 GTTCAAGCTTCTGAACCATAATGTA 57.622 36.000 17.09 0.00 46.29 2.29
333 348 4.481112 GCAGCGATTTGTGGCCCG 62.481 66.667 0.00 0.00 0.00 6.13
366 381 5.886960 AAGCAAGAACCATCAGTTATCAC 57.113 39.130 0.00 0.00 39.40 3.06
367 382 6.939730 TGTAAAGCAAGAACCATCAGTTATCA 59.060 34.615 0.00 0.00 39.40 2.15
368 383 7.244192 GTGTAAAGCAAGAACCATCAGTTATC 58.756 38.462 0.00 0.00 39.40 1.75
369 384 6.128282 CGTGTAAAGCAAGAACCATCAGTTAT 60.128 38.462 0.00 0.00 39.40 1.89
370 385 5.178623 CGTGTAAAGCAAGAACCATCAGTTA 59.821 40.000 0.00 0.00 39.40 2.24
371 386 4.024048 CGTGTAAAGCAAGAACCATCAGTT 60.024 41.667 0.00 0.00 43.07 3.16
372 387 3.498397 CGTGTAAAGCAAGAACCATCAGT 59.502 43.478 0.00 0.00 0.00 3.41
389 404 5.068198 AGTTGAAGAACAGAAGTACCGTGTA 59.932 40.000 0.00 0.00 34.17 2.90
403 418 5.506686 AAGCTTTTCCAGAGTTGAAGAAC 57.493 39.130 0.00 0.00 0.00 3.01
411 426 3.217626 CCTGACAAAGCTTTTCCAGAGT 58.782 45.455 26.86 15.36 0.00 3.24
483 498 6.709846 GTGCATAAAAGGAAGCTATCATCTCT 59.290 38.462 0.00 0.00 0.00 3.10
542 558 8.996651 ATTAACGAGAAATCTCCCCATTTTAT 57.003 30.769 4.90 0.00 39.79 1.40
579 599 3.507162 TGCCCTCATTGAGTTCAGAAA 57.493 42.857 12.54 0.00 0.00 2.52
633 656 7.821359 ACCTGATGAAAATCATATCTGATACGG 59.179 37.037 0.00 0.00 41.34 4.02
635 658 9.499479 ACACCTGATGAAAATCATATCTGATAC 57.501 33.333 0.00 0.00 41.34 2.24
655 679 2.370281 AATCGTAGTCTGCACACCTG 57.630 50.000 0.00 0.00 0.00 4.00
657 681 2.806244 ACAAAATCGTAGTCTGCACACC 59.194 45.455 0.00 0.00 0.00 4.16
693 719 3.811722 TGTTGCTTATGTCGCTTCTTG 57.188 42.857 0.00 0.00 0.00 3.02
774 2790 8.473219 GCCTGAAATCTTCCTTCTTTTTATGAT 58.527 33.333 0.00 0.00 0.00 2.45
775 2791 7.093771 GGCCTGAAATCTTCCTTCTTTTTATGA 60.094 37.037 0.00 0.00 0.00 2.15
776 2792 7.038048 GGCCTGAAATCTTCCTTCTTTTTATG 58.962 38.462 0.00 0.00 0.00 1.90
778 2794 6.074648 TGGCCTGAAATCTTCCTTCTTTTTA 58.925 36.000 3.32 0.00 0.00 1.52
779 2795 4.901250 TGGCCTGAAATCTTCCTTCTTTTT 59.099 37.500 3.32 0.00 0.00 1.94
780 2796 4.482990 TGGCCTGAAATCTTCCTTCTTTT 58.517 39.130 3.32 0.00 0.00 2.27
784 2800 3.829026 ACTTTGGCCTGAAATCTTCCTTC 59.171 43.478 3.32 0.00 0.00 3.46
785 2801 3.849527 ACTTTGGCCTGAAATCTTCCTT 58.150 40.909 3.32 0.00 0.00 3.36
786 2802 3.532641 ACTTTGGCCTGAAATCTTCCT 57.467 42.857 3.32 0.00 0.00 3.36
787 2803 4.380973 GCTTACTTTGGCCTGAAATCTTCC 60.381 45.833 3.32 0.00 0.00 3.46
788 2804 4.460731 AGCTTACTTTGGCCTGAAATCTTC 59.539 41.667 3.32 0.00 0.00 2.87
789 2805 4.411013 AGCTTACTTTGGCCTGAAATCTT 58.589 39.130 3.32 0.00 0.00 2.40
790 2806 4.013050 GAGCTTACTTTGGCCTGAAATCT 58.987 43.478 3.32 0.00 0.00 2.40
791 2807 3.129462 GGAGCTTACTTTGGCCTGAAATC 59.871 47.826 3.32 0.00 0.00 2.17
792 2808 3.092301 GGAGCTTACTTTGGCCTGAAAT 58.908 45.455 3.32 0.00 0.00 2.17
793 2809 2.108250 AGGAGCTTACTTTGGCCTGAAA 59.892 45.455 3.32 0.00 0.00 2.69
796 2812 3.350219 TTAGGAGCTTACTTTGGCCTG 57.650 47.619 3.32 0.00 0.00 4.85
798 2814 3.879892 CTGATTAGGAGCTTACTTTGGCC 59.120 47.826 0.00 0.00 0.00 5.36
799 2815 3.313803 GCTGATTAGGAGCTTACTTTGGC 59.686 47.826 0.00 0.00 33.37 4.52
800 2816 4.775236 AGCTGATTAGGAGCTTACTTTGG 58.225 43.478 0.00 0.00 44.65 3.28
806 2893 5.012148 GGGATTGTAGCTGATTAGGAGCTTA 59.988 44.000 0.00 0.00 44.65 3.09
820 2907 9.569122 TTAAAAGGTATTATCAGGGATTGTAGC 57.431 33.333 0.00 0.00 0.00 3.58
828 2915 9.586435 CAAAGCTTTTAAAAGGTATTATCAGGG 57.414 33.333 27.78 10.97 45.17 4.45
836 2923 9.336171 TGAATTTGCAAAGCTTTTAAAAGGTAT 57.664 25.926 27.78 16.14 45.17 2.73
839 2926 8.908172 TTTGAATTTGCAAAGCTTTTAAAAGG 57.092 26.923 25.40 12.39 33.61 3.11
845 2973 9.022915 GCTAAAATTTGAATTTGCAAAGCTTTT 57.977 25.926 18.19 15.89 40.68 2.27
870 2998 0.179059 CACCCCAACCAAAACAAGGC 60.179 55.000 0.00 0.00 0.00 4.35
921 3087 2.115910 TTGGGCCCTCAGCTGTTG 59.884 61.111 25.70 8.01 43.05 3.33
922 3088 2.116125 GTTGGGCCCTCAGCTGTT 59.884 61.111 25.70 0.00 43.05 3.16
923 3089 4.335647 CGTTGGGCCCTCAGCTGT 62.336 66.667 25.70 0.00 43.05 4.40
939 3105 1.140161 CCATCACAATGGCTTGCCG 59.860 57.895 7.18 0.00 45.88 5.69
996 3163 1.845791 TCTGATATGTGGGCCATGTGT 59.154 47.619 10.70 0.00 34.86 3.72
1096 5802 6.035217 GTCGAGGAAACTATAAACTGAGACC 58.965 44.000 0.00 0.00 44.43 3.85
1103 5809 5.082251 AGGTGGTCGAGGAAACTATAAAC 57.918 43.478 0.00 0.00 44.43 2.01
1111 5817 1.343465 GTTGAGAGGTGGTCGAGGAAA 59.657 52.381 0.00 0.00 0.00 3.13
1122 5828 1.205893 GATTGCGGAGAGTTGAGAGGT 59.794 52.381 0.00 0.00 0.00 3.85
1141 5847 5.407387 GCTCTTTTGTTTAGTACCACATCGA 59.593 40.000 0.00 0.00 0.00 3.59
1158 5864 1.074566 CCAGGGACTCTTGGCTCTTTT 59.925 52.381 0.00 0.00 34.60 2.27
1165 5871 3.732849 GGGCCCAGGGACTCTTGG 61.733 72.222 19.95 0.00 34.60 3.61
1173 5879 4.101077 AGAGAGAGGGGCCCAGGG 62.101 72.222 27.72 0.00 0.00 4.45
1178 5884 4.154347 CACGCAGAGAGAGGGGCC 62.154 72.222 0.00 0.00 0.00 5.80
1180 5886 1.388065 CCTACACGCAGAGAGAGGGG 61.388 65.000 0.00 0.00 0.00 4.79
1181 5887 2.010582 GCCTACACGCAGAGAGAGGG 62.011 65.000 0.00 0.00 0.00 4.30
1182 5888 1.315981 TGCCTACACGCAGAGAGAGG 61.316 60.000 0.00 0.00 33.92 3.69
1186 5892 1.079819 GCTTGCCTACACGCAGAGA 60.080 57.895 0.00 0.00 40.61 3.10
1213 5920 9.878599 CGCTATTCTAAAAAGAAAAGAAGTTGA 57.121 29.630 0.00 0.00 33.05 3.18
1218 5925 7.209471 TGCCGCTATTCTAAAAAGAAAAGAA 57.791 32.000 0.00 0.00 34.00 2.52
1219 5926 6.811253 TGCCGCTATTCTAAAAAGAAAAGA 57.189 33.333 0.00 0.00 0.00 2.52
1220 5927 6.033937 GCTTGCCGCTATTCTAAAAAGAAAAG 59.966 38.462 0.00 0.00 35.14 2.27
1221 5928 5.861787 GCTTGCCGCTATTCTAAAAAGAAAA 59.138 36.000 0.00 0.00 35.14 2.29
1225 5932 4.355543 TGCTTGCCGCTATTCTAAAAAG 57.644 40.909 0.00 0.00 40.11 2.27
1248 5955 2.357517 AAACGAGAGGCGCACAGG 60.358 61.111 10.83 1.27 46.04 4.00
1373 6754 1.585668 CTCGCATAAGACAACGAGCAG 59.414 52.381 0.00 0.00 44.56 4.24
1387 6768 0.460284 CTGTAGTTTCGGCCTCGCAT 60.460 55.000 0.00 0.00 36.13 4.73
1463 8782 4.398044 ACGGTAATCATTTCTTCGCCAAAT 59.602 37.500 0.00 0.00 0.00 2.32
1470 8789 7.222999 CCTGAACTCTACGGTAATCATTTCTTC 59.777 40.741 0.00 0.00 0.00 2.87
1674 8993 9.632638 ACATAGGAGCACTTGTATTCAATTTAT 57.367 29.630 0.00 0.00 32.82 1.40
1737 9056 1.067060 CGACCTCAATCGATGGCTACA 59.933 52.381 0.00 0.00 45.13 2.74
1750 9069 0.032130 GACTTGCACAGTCGACCTCA 59.968 55.000 13.01 2.16 42.82 3.86
1761 9080 3.329300 ACCTCATGGTGACTTGCAC 57.671 52.632 0.00 0.00 46.51 4.57
1861 9187 1.139853 GAGGGATCGACCAAAGATGCT 59.860 52.381 6.41 0.00 41.20 3.79
1935 9261 7.291566 AGGAGTTAAAGAGGATAAGAGATCGA 58.708 38.462 0.00 0.00 0.00 3.59
1986 9313 1.600957 CAAAGAAGCGGCATCGATCAT 59.399 47.619 1.45 0.00 39.00 2.45
2021 9348 2.511600 GAAGACGGGCGTGGATGG 60.512 66.667 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.