Multiple sequence alignment - TraesCS7D01G253100

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 TraesCS7D01G253100 chr7D 100.000 3356 0 0 1 3356 228987849 228984494 0.000000e+00 6198.0
1 TraesCS7D01G253100 chr7D 100.000 35 0 0 1988 2022 535658825 535658791 7.770000e-07 65.8
2 TraesCS7D01G253100 chr7B 92.624 2820 108 36 18 2808 199857678 199854930 0.000000e+00 3964.0
3 TraesCS7D01G253100 chr7B 92.239 335 15 6 3029 3356 199854717 199854387 6.560000e-127 464.0
4 TraesCS7D01G253100 chr7B 100.000 35 0 0 1988 2022 577372462 577372428 7.770000e-07 65.8
5 TraesCS7D01G253100 chr7A 91.310 2923 131 39 10 2879 240958676 240955824 0.000000e+00 3877.0
6 TraesCS7D01G253100 chr7A 86.822 258 10 10 3122 3356 240955213 240954957 1.990000e-67 267.0
7 TraesCS7D01G253100 chr7A 96.739 92 2 1 3035 3126 240955635 240955545 5.800000e-33 152.0
8 TraesCS7D01G253100 chr7A 97.143 35 1 0 1988 2022 617949478 617949512 3.620000e-05 60.2
9 TraesCS7D01G253100 chr5B 78.988 257 46 4 1915 2167 462883341 462883089 5.760000e-38 169.0
10 TraesCS7D01G253100 chr5D 77.536 276 54 4 1896 2167 385604671 385604400 3.470000e-35 159.0
11 TraesCS7D01G253100 chr5A 77.536 276 54 4 1896 2167 487365619 487365348 3.470000e-35 159.0


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 TraesCS7D01G253100 chr7D 228984494 228987849 3355 True 6198 6198 100.000000 1 3356 1 chr7D.!!$R1 3355
1 TraesCS7D01G253100 chr7B 199854387 199857678 3291 True 2214 3964 92.431500 18 3356 2 chr7B.!!$R2 3338
2 TraesCS7D01G253100 chr7A 240954957 240958676 3719 True 1432 3877 91.623667 10 3356 3 chr7A.!!$R1 3346

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
411 431 0.107703 ATCATCCATCCAACGCGTGT 60.108 50.0 14.98 0.00 0.00 4.49 F
552 576 0.169672 CCCCGTATACCATACGCTCG 59.830 60.0 12.13 3.46 39.38 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1305 1362 0.179137 TAGCGAGCACTTCATCCACG 60.179 55.0 0.0 0.0 0.0 4.94 R
2507 2592 0.038435 CGTTGTCATTTGCCATGCCA 60.038 50.0 0.0 0.0 0.0 4.92 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
103 104 3.743396 GCTCAGTAACAGTTCACCTTGAG 59.257 47.826 0.00 0.00 35.20 3.02
121 122 0.238289 AGCCAAAATGCTGTCGAACG 59.762 50.000 0.00 0.00 40.90 3.95
122 123 0.237235 GCCAAAATGCTGTCGAACGA 59.763 50.000 0.00 0.00 0.00 3.85
154 160 2.657143 ACCCTTTTGCGGTTTTGACTA 58.343 42.857 0.00 0.00 0.00 2.59
155 161 2.359848 ACCCTTTTGCGGTTTTGACTAC 59.640 45.455 0.00 0.00 0.00 2.73
156 162 2.621526 CCCTTTTGCGGTTTTGACTACT 59.378 45.455 0.00 0.00 0.00 2.57
174 180 1.524961 TCCAAGTGGAGCACGTTGT 59.475 52.632 0.00 0.00 39.78 3.32
175 181 0.813610 TCCAAGTGGAGCACGTTGTG 60.814 55.000 0.00 0.00 39.78 3.33
176 182 1.648720 CAAGTGGAGCACGTTGTGG 59.351 57.895 0.00 0.00 39.64 4.17
177 183 0.813610 CAAGTGGAGCACGTTGTGGA 60.814 55.000 0.00 0.00 39.64 4.02
178 184 0.108585 AAGTGGAGCACGTTGTGGAT 59.891 50.000 0.00 0.00 39.64 3.41
179 185 0.108585 AGTGGAGCACGTTGTGGATT 59.891 50.000 0.00 0.00 39.64 3.01
180 186 0.238289 GTGGAGCACGTTGTGGATTG 59.762 55.000 0.00 0.00 33.64 2.67
181 187 0.179032 TGGAGCACGTTGTGGATTGT 60.179 50.000 0.00 0.00 33.64 2.71
190 196 0.181587 TTGTGGATTGTGGTCGTGGT 59.818 50.000 0.00 0.00 0.00 4.16
191 197 0.181587 TGTGGATTGTGGTCGTGGTT 59.818 50.000 0.00 0.00 0.00 3.67
206 217 2.352651 CGTGGTTGGAGCATCAAGTATG 59.647 50.000 0.00 0.00 36.25 2.39
225 237 0.240945 GGCATCAAACCGGACACTTG 59.759 55.000 9.46 6.22 0.00 3.16
332 352 3.060615 CCTGCAGCCAGCTGAACC 61.061 66.667 23.40 6.33 46.30 3.62
411 431 0.107703 ATCATCCATCCAACGCGTGT 60.108 50.000 14.98 0.00 0.00 4.49
412 432 0.533032 TCATCCATCCAACGCGTGTA 59.467 50.000 14.98 0.68 0.00 2.90
552 576 0.169672 CCCCGTATACCATACGCTCG 59.830 60.000 12.13 3.46 39.38 5.03
564 588 2.365444 TACGCTCGACCGTATCACGC 62.365 60.000 8.85 0.00 40.91 5.34
854 905 5.488919 TCTCTCTTTCCTTCTCTCTCTCTCT 59.511 44.000 0.00 0.00 0.00 3.10
855 906 5.745227 TCTCTTTCCTTCTCTCTCTCTCTC 58.255 45.833 0.00 0.00 0.00 3.20
856 907 5.488919 TCTCTTTCCTTCTCTCTCTCTCTCT 59.511 44.000 0.00 0.00 0.00 3.10
857 908 5.745227 TCTTTCCTTCTCTCTCTCTCTCTC 58.255 45.833 0.00 0.00 0.00 3.20
858 909 5.488919 TCTTTCCTTCTCTCTCTCTCTCTCT 59.511 44.000 0.00 0.00 0.00 3.10
859 910 5.359194 TTCCTTCTCTCTCTCTCTCTCTC 57.641 47.826 0.00 0.00 0.00 3.20
983 1034 0.179073 TCGCTGGATCTTGCTTAGCC 60.179 55.000 0.29 0.00 0.00 3.93
1157 1208 3.015753 GGGGGAGGAGGTTGGGAC 61.016 72.222 0.00 0.00 0.00 4.46
1292 1343 2.043852 GGAGGAGGTGGAGAGCGA 60.044 66.667 0.00 0.00 0.00 4.93
1293 1344 2.124693 GGAGGAGGTGGAGAGCGAG 61.125 68.421 0.00 0.00 0.00 5.03
1294 1345 2.043450 AGGAGGTGGAGAGCGAGG 60.043 66.667 0.00 0.00 0.00 4.63
1295 1346 3.844090 GGAGGTGGAGAGCGAGGC 61.844 72.222 0.00 0.00 0.00 4.70
1296 1347 3.844090 GAGGTGGAGAGCGAGGCC 61.844 72.222 0.00 0.00 0.00 5.19
1297 1348 4.704103 AGGTGGAGAGCGAGGCCA 62.704 66.667 5.01 0.00 0.00 5.36
1631 1692 5.717178 AGTAGATCACAAAACTGGAGCTAGA 59.283 40.000 0.00 0.00 30.99 2.43
1743 1808 8.897872 AAAGATCATGGATGGATTTAATTTGC 57.102 30.769 0.00 0.00 0.00 3.68
1813 1878 4.487948 CATCAACAACAGGCCAAATACTG 58.512 43.478 5.01 0.00 40.48 2.74
1814 1879 2.295909 TCAACAACAGGCCAAATACTGC 59.704 45.455 5.01 0.00 38.25 4.40
1815 1880 2.292828 ACAACAGGCCAAATACTGCT 57.707 45.000 5.01 0.00 38.25 4.24
1861 1926 1.252904 CCATGGAGTGTTTGCCCTGG 61.253 60.000 5.56 0.00 34.37 4.45
1914 1979 2.364448 AGGAGGGGCCTCTCGAAC 60.364 66.667 26.53 12.92 46.97 3.95
2253 2330 2.664851 CACAGCGCGTCCCAGAAA 60.665 61.111 8.43 0.00 0.00 2.52
2277 2354 1.893137 AGCGTCATGAGTAGGAACACA 59.107 47.619 0.00 0.00 0.00 3.72
2401 2478 2.045634 GAGATGGTGCTGCTGCCA 60.046 61.111 13.47 16.23 39.33 4.92
2435 2512 8.228035 ACTGTATAATCAAGAGGTCTCTACAC 57.772 38.462 0.43 0.00 39.39 2.90
2469 2554 8.770438 ACATTAATTTGTTGTGTTTGTCTGTT 57.230 26.923 0.00 0.00 0.00 3.16
2470 2555 9.213799 ACATTAATTTGTTGTGTTTGTCTGTTT 57.786 25.926 0.00 0.00 0.00 2.83
2471 2556 9.475505 CATTAATTTGTTGTGTTTGTCTGTTTG 57.524 29.630 0.00 0.00 0.00 2.93
2472 2557 8.594881 TTAATTTGTTGTGTTTGTCTGTTTGT 57.405 26.923 0.00 0.00 0.00 2.83
2501 2586 3.812167 GCCTCTTCTTGAATCACCTGGTT 60.812 47.826 0.00 0.00 0.00 3.67
2502 2587 3.755378 CCTCTTCTTGAATCACCTGGTTG 59.245 47.826 0.00 0.00 0.00 3.77
2503 2588 3.754965 TCTTCTTGAATCACCTGGTTGG 58.245 45.455 0.00 0.00 42.93 3.77
2504 2589 1.909700 TCTTGAATCACCTGGTTGGC 58.090 50.000 0.00 0.00 40.22 4.52
2505 2590 1.144708 TCTTGAATCACCTGGTTGGCA 59.855 47.619 0.00 0.00 40.22 4.92
2507 2592 2.307496 TGAATCACCTGGTTGGCAAT 57.693 45.000 1.92 0.00 40.22 3.56
2508 2593 1.894466 TGAATCACCTGGTTGGCAATG 59.106 47.619 1.92 0.00 40.22 2.82
2509 2594 1.205417 GAATCACCTGGTTGGCAATGG 59.795 52.381 1.92 9.15 40.22 3.16
2510 2595 1.259840 ATCACCTGGTTGGCAATGGC 61.260 55.000 1.92 0.00 40.22 4.40
2511 2596 2.200930 ACCTGGTTGGCAATGGCA 59.799 55.556 5.05 5.05 43.71 4.92
2512 2597 1.229272 ACCTGGTTGGCAATGGCAT 60.229 52.632 11.08 0.00 43.71 4.40
2513 2598 1.219664 CCTGGTTGGCAATGGCATG 59.780 57.895 11.08 1.75 43.71 4.06
2514 2599 1.219664 CTGGTTGGCAATGGCATGG 59.780 57.895 11.08 0.00 43.71 3.66
2515 2600 2.125024 GGTTGGCAATGGCATGGC 60.125 61.111 18.82 18.82 45.44 4.40
2521 2606 0.107606 GGCAATGGCATGGCAAATGA 60.108 50.000 30.30 10.12 44.66 2.57
2525 2610 2.389962 ATGGCATGGCAAATGACAAC 57.610 45.000 27.04 0.00 40.90 3.32
2533 2618 1.605202 GGCAAATGACAACGGCAACAT 60.605 47.619 0.00 0.00 0.00 2.71
2558 2643 0.040067 GGCCGTTTCTGTCAGCAAAG 60.040 55.000 0.00 0.00 0.00 2.77
2561 2646 2.143122 CCGTTTCTGTCAGCAAAGCTA 58.857 47.619 0.00 0.00 36.40 3.32
2562 2647 2.096218 CCGTTTCTGTCAGCAAAGCTAC 60.096 50.000 0.00 0.00 36.40 3.58
2563 2648 2.410262 CGTTTCTGTCAGCAAAGCTACG 60.410 50.000 0.00 0.00 36.40 3.51
2621 2706 1.511850 TGTTGAGCTGATGTCGTTGG 58.488 50.000 0.00 0.00 0.00 3.77
2707 2792 1.673767 AATGGTGGGTGATGAGTCCT 58.326 50.000 0.00 0.00 0.00 3.85
2718 2803 2.224450 TGATGAGTCCTATGCATGCCTG 60.224 50.000 16.68 4.95 0.00 4.85
2753 2838 2.874701 GCATCATCCAGTTGTTAGCGAT 59.125 45.455 0.00 0.00 0.00 4.58
2822 2941 6.636705 TCTAAAAGCTAAGCATACGGAAAGA 58.363 36.000 0.00 0.00 0.00 2.52
2879 2998 3.963476 TCCCTCCCAAAAAGTTGAAGA 57.037 42.857 0.00 0.00 36.83 2.87
2881 3000 4.814967 TCCCTCCCAAAAAGTTGAAGATT 58.185 39.130 0.00 0.00 36.83 2.40
2882 3001 5.959512 TCCCTCCCAAAAAGTTGAAGATTA 58.040 37.500 0.00 0.00 36.83 1.75
2883 3002 5.773176 TCCCTCCCAAAAAGTTGAAGATTAC 59.227 40.000 0.00 0.00 36.83 1.89
2884 3003 5.538433 CCCTCCCAAAAAGTTGAAGATTACA 59.462 40.000 0.00 0.00 36.83 2.41
2886 3005 7.092716 CCTCCCAAAAAGTTGAAGATTACATG 58.907 38.462 0.00 0.00 36.83 3.21
2887 3006 7.039784 CCTCCCAAAAAGTTGAAGATTACATGA 60.040 37.037 0.00 0.00 36.83 3.07
2888 3007 7.885297 TCCCAAAAAGTTGAAGATTACATGAG 58.115 34.615 0.00 0.00 36.83 2.90
2895 3046 5.123502 AGTTGAAGATTACATGAGCAGCAAG 59.876 40.000 0.00 0.00 0.00 4.01
2920 3071 4.507710 GTCTGTAGATCATCTGGCACAAA 58.492 43.478 0.00 0.00 38.70 2.83
2949 3127 1.074752 CCTCACGAGAGCAAAAGCTC 58.925 55.000 9.34 9.34 40.68 4.09
2958 3136 3.683802 AGAGCAAAAGCTCATAACTGCT 58.316 40.909 18.46 0.00 42.57 4.24
3005 3187 2.752322 TTTGACGGGTCGCCACGTAG 62.752 60.000 0.00 0.00 44.24 3.51
3007 3189 2.359850 ACGGGTCGCCACGTAGTA 60.360 61.111 0.00 0.00 41.61 1.82
3009 3191 2.689785 CGGGTCGCCACGTAGTACA 61.690 63.158 0.38 0.00 41.61 2.90
3010 3192 1.153958 GGGTCGCCACGTAGTACAC 60.154 63.158 0.38 0.00 41.61 2.90
3068 3250 2.010582 GCAGGAGAGAACCGCGATCT 62.011 60.000 8.23 11.37 34.73 2.75
3119 3306 2.334946 GCAGCAGGCGGATCACAAA 61.335 57.895 0.00 0.00 0.00 2.83
3133 3655 5.751028 CGGATCACAAACCTTAATCTCTCTC 59.249 44.000 0.00 0.00 0.00 3.20
3149 3674 4.865925 TCTCTCTCGATTAGTATAGCTCGC 59.134 45.833 0.00 0.00 30.63 5.03
3151 3676 4.389382 TCTCTCGATTAGTATAGCTCGCAC 59.611 45.833 0.00 0.00 30.63 5.34
3260 3803 2.748058 TTTCGAAGGGGCAGGCAGAC 62.748 60.000 0.00 0.00 0.00 3.51
3279 3822 0.926846 CGAGATGAGCTTTCTTCGGC 59.073 55.000 2.07 0.00 0.00 5.54
3352 3896 6.154192 TCCTATGCTATGCTAATCCTCTCTTG 59.846 42.308 0.00 0.00 0.00 3.02
3353 3897 4.000331 TGCTATGCTAATCCTCTCTTGC 58.000 45.455 0.00 0.00 0.00 4.01
3354 3898 3.645212 TGCTATGCTAATCCTCTCTTGCT 59.355 43.478 0.00 0.00 0.00 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.776969 TGACCAGAGAAGTAATCCTGCAT 59.223 43.478 0.00 0.00 0.00 3.96
1 2 3.173151 TGACCAGAGAAGTAATCCTGCA 58.827 45.455 0.00 0.00 0.00 4.41
2 3 3.895232 TGACCAGAGAAGTAATCCTGC 57.105 47.619 0.00 0.00 0.00 4.85
3 4 4.223923 ACCTTGACCAGAGAAGTAATCCTG 59.776 45.833 0.00 0.00 0.00 3.86
4 5 4.430441 ACCTTGACCAGAGAAGTAATCCT 58.570 43.478 0.00 0.00 0.00 3.24
5 6 4.828072 ACCTTGACCAGAGAAGTAATCC 57.172 45.455 0.00 0.00 0.00 3.01
6 7 9.886132 TTAATTACCTTGACCAGAGAAGTAATC 57.114 33.333 0.00 0.00 0.00 1.75
7 8 9.668497 GTTAATTACCTTGACCAGAGAAGTAAT 57.332 33.333 0.00 0.00 0.00 1.89
8 9 8.098912 GGTTAATTACCTTGACCAGAGAAGTAA 58.901 37.037 0.00 0.00 41.90 2.24
103 104 0.237235 TCGTTCGACAGCATTTTGGC 59.763 50.000 0.00 0.00 0.00 4.52
121 122 2.109425 AAAGGGTAATCGTGGCTGTC 57.891 50.000 0.00 0.00 0.00 3.51
122 123 2.159382 CAAAAGGGTAATCGTGGCTGT 58.841 47.619 0.00 0.00 0.00 4.40
126 132 0.450184 CCGCAAAAGGGTAATCGTGG 59.550 55.000 0.00 0.00 0.00 4.94
129 135 2.983803 CAAAACCGCAAAAGGGTAATCG 59.016 45.455 0.00 0.00 36.57 3.34
156 162 0.813610 CACAACGTGCTCCACTTGGA 60.814 55.000 0.00 0.00 43.08 3.53
167 173 0.234625 CGACCACAATCCACAACGTG 59.765 55.000 0.00 0.00 0.00 4.49
174 180 0.536233 CCAACCACGACCACAATCCA 60.536 55.000 0.00 0.00 0.00 3.41
175 181 0.250553 TCCAACCACGACCACAATCC 60.251 55.000 0.00 0.00 0.00 3.01
176 182 1.156736 CTCCAACCACGACCACAATC 58.843 55.000 0.00 0.00 0.00 2.67
177 183 0.889186 GCTCCAACCACGACCACAAT 60.889 55.000 0.00 0.00 0.00 2.71
178 184 1.525077 GCTCCAACCACGACCACAA 60.525 57.895 0.00 0.00 0.00 3.33
179 185 2.050836 ATGCTCCAACCACGACCACA 62.051 55.000 0.00 0.00 0.00 4.17
180 186 1.298859 GATGCTCCAACCACGACCAC 61.299 60.000 0.00 0.00 0.00 4.16
181 187 1.003839 GATGCTCCAACCACGACCA 60.004 57.895 0.00 0.00 0.00 4.02
190 196 2.804986 TGCCATACTTGATGCTCCAA 57.195 45.000 0.00 0.00 33.79 3.53
191 197 2.173143 TGATGCCATACTTGATGCTCCA 59.827 45.455 0.00 0.00 33.79 3.86
206 217 0.240945 CAAGTGTCCGGTTTGATGCC 59.759 55.000 0.00 0.00 0.00 4.40
225 237 2.159517 GGTCCGATTCACAATCAAGCAC 60.160 50.000 0.00 0.00 37.78 4.40
332 352 0.250901 CTCTGTCCACCCAAACCCAG 60.251 60.000 0.00 0.00 0.00 4.45
369 389 1.153549 GGACGGATCGCTTTCTGCT 60.154 57.895 0.00 0.00 40.11 4.24
552 576 3.384927 GCTGTGCGTGATACGGTC 58.615 61.111 3.41 0.00 42.82 4.79
564 588 1.337071 AGACATACCGGTATCGCTGTG 59.663 52.381 24.45 15.87 34.56 3.66
570 594 3.635373 TGACCTGAAGACATACCGGTATC 59.365 47.826 24.45 15.28 0.00 2.24
854 905 5.013547 AGGACAAGAAATCTTCGAGAGAGA 58.986 41.667 0.00 0.00 43.69 3.10
855 906 5.323371 AGGACAAGAAATCTTCGAGAGAG 57.677 43.478 0.00 0.00 43.69 3.20
856 907 4.142578 CGAGGACAAGAAATCTTCGAGAGA 60.143 45.833 0.73 0.79 45.56 3.10
857 908 4.101942 CGAGGACAAGAAATCTTCGAGAG 58.898 47.826 0.73 0.00 45.56 3.20
858 909 3.506455 ACGAGGACAAGAAATCTTCGAGA 59.494 43.478 12.60 0.00 45.56 4.04
859 910 3.839293 ACGAGGACAAGAAATCTTCGAG 58.161 45.455 12.60 0.00 45.56 4.04
1157 1208 4.567385 GCTCTCGCAGCTCCTCCG 62.567 72.222 0.00 0.00 45.83 4.63
1170 1221 2.655077 ATAGCGCCTCCTCCAGCTCT 62.655 60.000 2.29 0.00 40.73 4.09
1224 1275 2.081425 CTTCCCCGATCGAGGAGCTG 62.081 65.000 18.33 9.32 32.57 4.24
1296 1347 4.776322 TCATCCACGGGCGCCTTG 62.776 66.667 28.56 22.70 0.00 3.61
1297 1348 3.976701 CTTCATCCACGGGCGCCTT 62.977 63.158 28.56 11.31 0.00 4.35
1305 1362 0.179137 TAGCGAGCACTTCATCCACG 60.179 55.000 0.00 0.00 0.00 4.94
1560 1621 0.400213 ACAACTGGCCGAGGAATCAA 59.600 50.000 0.00 0.00 0.00 2.57
1631 1692 2.159382 CAGAACGGGCATACTGGTTTT 58.841 47.619 0.00 0.00 0.00 2.43
1640 1703 1.981256 AAGTTCAACAGAACGGGCAT 58.019 45.000 3.04 0.00 44.89 4.40
1743 1808 5.220662 CGGGATTTCAGCTAATTACACACAG 60.221 44.000 0.00 0.00 0.00 3.66
1830 1895 4.279145 ACACTCCATGGGTACTACTGTAG 58.721 47.826 13.02 13.13 0.00 2.74
1834 1899 3.307480 GCAAACACTCCATGGGTACTACT 60.307 47.826 13.02 0.00 0.00 2.57
1835 1900 3.007635 GCAAACACTCCATGGGTACTAC 58.992 50.000 13.02 0.00 0.00 2.73
1861 1926 8.044060 TCATTCATCTTGGTCAGTTAATGTTC 57.956 34.615 0.00 0.00 0.00 3.18
1914 1979 1.810030 GGACTTGCCGGCGTAGAAG 60.810 63.158 28.80 24.30 0.00 2.85
1974 2039 1.821332 CTTGGCGATCTCCTTGGCC 60.821 63.158 2.88 0.00 45.76 5.36
2168 2245 2.480610 CCATTGCCGCTGCCGTTAT 61.481 57.895 0.00 0.00 36.33 1.89
2253 2330 0.748367 TCCTACTCATGACGCTCGCT 60.748 55.000 0.00 0.00 0.00 4.93
2277 2354 2.271800 GAGCTCGTGTTCGGATTGATT 58.728 47.619 0.00 0.00 37.69 2.57
2401 2478 6.462207 CCTCTTGATTATACAGTAGCAGCAGT 60.462 42.308 0.00 0.00 0.00 4.40
2469 2554 2.172505 TCAAGAAGAGGCCAACAGACAA 59.827 45.455 5.01 0.00 0.00 3.18
2470 2555 1.768275 TCAAGAAGAGGCCAACAGACA 59.232 47.619 5.01 0.00 0.00 3.41
2471 2556 2.550830 TCAAGAAGAGGCCAACAGAC 57.449 50.000 5.01 0.00 0.00 3.51
2472 2557 3.072915 TGATTCAAGAAGAGGCCAACAGA 59.927 43.478 5.01 0.00 0.00 3.41
2501 2586 0.393132 CATTTGCCATGCCATTGCCA 60.393 50.000 0.00 0.00 36.33 4.92
2502 2587 0.107606 TCATTTGCCATGCCATTGCC 60.108 50.000 0.00 0.00 36.33 4.52
2503 2588 1.011333 GTCATTTGCCATGCCATTGC 58.989 50.000 0.00 0.00 38.26 3.56
2504 2589 2.388310 TGTCATTTGCCATGCCATTG 57.612 45.000 0.00 0.00 0.00 2.82
2505 2590 2.702261 GTTGTCATTTGCCATGCCATT 58.298 42.857 0.00 0.00 0.00 3.16
2507 2592 0.038435 CGTTGTCATTTGCCATGCCA 60.038 50.000 0.00 0.00 0.00 4.92
2508 2593 0.737019 CCGTTGTCATTTGCCATGCC 60.737 55.000 0.00 0.00 0.00 4.40
2509 2594 1.353609 GCCGTTGTCATTTGCCATGC 61.354 55.000 0.00 0.00 0.00 4.06
2510 2595 0.038435 TGCCGTTGTCATTTGCCATG 60.038 50.000 0.00 0.00 0.00 3.66
2511 2596 0.678395 TTGCCGTTGTCATTTGCCAT 59.322 45.000 0.00 0.00 0.00 4.40
2512 2597 0.249238 GTTGCCGTTGTCATTTGCCA 60.249 50.000 0.00 0.00 0.00 4.92
2513 2598 0.249238 TGTTGCCGTTGTCATTTGCC 60.249 50.000 0.00 0.00 0.00 4.52
2514 2599 1.456544 CATGTTGCCGTTGTCATTTGC 59.543 47.619 0.00 0.00 0.00 3.68
2515 2600 3.010624 TCATGTTGCCGTTGTCATTTG 57.989 42.857 0.00 0.00 0.00 2.32
2516 2601 3.068024 ACTTCATGTTGCCGTTGTCATTT 59.932 39.130 0.00 0.00 0.00 2.32
2517 2602 2.622942 ACTTCATGTTGCCGTTGTCATT 59.377 40.909 0.00 0.00 0.00 2.57
2521 2606 0.667993 CCACTTCATGTTGCCGTTGT 59.332 50.000 0.00 0.00 0.00 3.32
2525 2610 2.568090 GGCCACTTCATGTTGCCG 59.432 61.111 0.00 0.00 45.61 5.69
2533 2618 0.179234 TGACAGAAACGGCCACTTCA 59.821 50.000 14.53 6.74 0.00 3.02
2558 2643 5.169295 AGAACATGGTTAAGAACTCGTAGC 58.831 41.667 0.00 0.00 0.00 3.58
2561 2646 5.209818 TGAGAACATGGTTAAGAACTCGT 57.790 39.130 0.00 0.00 0.00 4.18
2562 2647 5.004821 CGATGAGAACATGGTTAAGAACTCG 59.995 44.000 0.00 0.00 36.82 4.18
2563 2648 6.100004 TCGATGAGAACATGGTTAAGAACTC 58.900 40.000 0.00 0.00 36.82 3.01
2621 2706 7.326063 GCAACAATTAAACCAGTAATCTGTCAC 59.674 37.037 0.00 0.00 39.82 3.67
2632 2717 6.266168 TGGTCATAGCAACAATTAAACCAG 57.734 37.500 0.00 0.00 31.08 4.00
2649 2734 1.228245 AGCAAACACCGCTGGTCAT 60.228 52.632 0.00 0.00 38.60 3.06
2718 2803 2.462456 TGATGCTTATCGGATGAGGC 57.538 50.000 11.24 7.95 0.00 4.70
2719 2804 3.055602 TGGATGATGCTTATCGGATGAGG 60.056 47.826 11.24 0.00 0.00 3.86
2720 2805 4.182339 CTGGATGATGCTTATCGGATGAG 58.818 47.826 5.47 5.47 0.00 2.90
2721 2806 3.580022 ACTGGATGATGCTTATCGGATGA 59.420 43.478 0.00 0.00 0.00 2.92
2753 2838 2.236395 AGCTAAAGAGGCCTAAAGCGAA 59.764 45.455 4.42 0.00 45.17 4.70
2784 2870 9.712305 CTTAGCTTTTAGATTAGCTGGCTAATA 57.288 33.333 22.64 9.84 45.88 0.98
2879 2998 1.019673 CCGCTTGCTGCTCATGTAAT 58.980 50.000 0.00 0.00 40.11 1.89
2881 3000 0.740868 GACCGCTTGCTGCTCATGTA 60.741 55.000 0.00 0.00 40.11 2.29
2882 3001 2.033141 ACCGCTTGCTGCTCATGT 59.967 55.556 0.00 0.00 40.11 3.21
2883 3002 1.744368 AGACCGCTTGCTGCTCATG 60.744 57.895 0.00 0.00 40.11 3.07
2884 3003 1.744368 CAGACCGCTTGCTGCTCAT 60.744 57.895 0.00 0.00 40.11 2.90
2886 3005 1.079819 TACAGACCGCTTGCTGCTC 60.080 57.895 0.00 0.00 40.11 4.26
2887 3006 1.079543 CTACAGACCGCTTGCTGCT 60.080 57.895 0.00 0.00 40.11 4.24
2888 3007 0.460987 ATCTACAGACCGCTTGCTGC 60.461 55.000 0.00 0.00 35.57 5.25
2895 3046 1.604185 GCCAGATGATCTACAGACCGC 60.604 57.143 0.00 0.00 0.00 5.68
2898 3049 3.808466 TGTGCCAGATGATCTACAGAC 57.192 47.619 0.00 0.00 0.00 3.51
2903 3054 4.641541 CCATTGTTTGTGCCAGATGATCTA 59.358 41.667 0.00 0.00 0.00 1.98
2920 3071 0.976641 TCTCGTGAGGAAGCCATTGT 59.023 50.000 0.00 0.00 0.00 2.71
2949 3127 8.948631 TTTCCACTCTTTCTATAGCAGTTATG 57.051 34.615 0.00 0.00 0.00 1.90
2958 3136 7.068839 AGCTTCTCGATTTCCACTCTTTCTATA 59.931 37.037 0.00 0.00 0.00 1.31
3017 3199 4.260702 CCGGTGTACTACGCTTTTCAAAAA 60.261 41.667 0.00 0.00 0.00 1.94
3018 3200 3.248125 CCGGTGTACTACGCTTTTCAAAA 59.752 43.478 0.00 0.00 0.00 2.44
3019 3201 2.801679 CCGGTGTACTACGCTTTTCAAA 59.198 45.455 0.00 0.00 0.00 2.69
3020 3202 2.224018 ACCGGTGTACTACGCTTTTCAA 60.224 45.455 6.12 0.00 0.00 2.69
3021 3203 1.340889 ACCGGTGTACTACGCTTTTCA 59.659 47.619 6.12 0.00 0.00 2.69
3022 3204 2.070262 ACCGGTGTACTACGCTTTTC 57.930 50.000 6.12 0.00 0.00 2.29
3023 3205 2.531522 AACCGGTGTACTACGCTTTT 57.468 45.000 8.52 0.00 0.00 2.27
3024 3206 3.317150 GTTAACCGGTGTACTACGCTTT 58.683 45.455 8.52 0.00 0.00 3.51
3025 3207 2.668279 CGTTAACCGGTGTACTACGCTT 60.668 50.000 8.52 0.00 0.00 4.68
3026 3208 1.135689 CGTTAACCGGTGTACTACGCT 60.136 52.381 8.52 0.00 0.00 5.07
3027 3209 1.135803 TCGTTAACCGGTGTACTACGC 60.136 52.381 8.52 0.00 37.11 4.42
3028 3210 2.892373 TCGTTAACCGGTGTACTACG 57.108 50.000 8.52 13.91 37.11 3.51
3068 3250 2.561297 CCTCCCCAGGTTAACTAGTCCA 60.561 54.545 5.42 0.00 34.60 4.02
3133 3655 3.184649 ACGTGCGAGCTATACTAATCG 57.815 47.619 0.00 0.00 38.19 3.34
3167 3692 1.549203 AATTTGAATGCCCAGTCGCT 58.451 45.000 0.00 0.00 0.00 4.93
3260 3803 0.926846 GCCGAAGAAAGCTCATCTCG 59.073 55.000 2.73 7.89 0.00 4.04
3314 3857 3.768833 ATAGGATGCCCCGTCCCGT 62.769 63.158 0.00 0.00 40.21 5.28


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

AutoCloner maintained by Alex Coulton.