Multiple sequence alignment - TraesCS6D01G273600

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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 TraesCS6D01G273600 chr6D 100.000 2485 0 0 1 2485 382549852 382552336 0.000000e+00 4590.0
1 TraesCS6D01G273600 chr6B 88.763 2198 143 49 291 2430 572090129 572092280 0.000000e+00 2595.0
2 TraesCS6D01G273600 chr6B 88.779 303 26 4 1 295 572085213 572085515 5.050000e-97 364.0
3 TraesCS6D01G273600 chr6A 87.904 1331 105 33 435 1741 524331406 524332704 0.000000e+00 1515.0
4 TraesCS6D01G273600 chr6A 89.234 548 37 13 1783 2318 524332697 524333234 0.000000e+00 665.0
5 TraesCS6D01G273600 chr6A 87.469 407 42 5 2 405 524329824 524330224 6.260000e-126 460.0
6 TraesCS6D01G273600 chr6A 93.519 108 6 1 2367 2473 524333220 524333327 2.560000e-35 159.0
7 TraesCS6D01G273600 chr5A 81.392 618 65 27 1897 2473 8059473 8058865 2.250000e-125 459.0
8 TraesCS6D01G273600 chr5D 80.757 634 59 24 1897 2480 10038592 10037972 1.060000e-118 436.0
9 TraesCS6D01G273600 chr5B 79.030 639 64 37 1894 2471 42157838 42158467 8.390000e-100 374.0
10 TraesCS6D01G273600 chr4B 96.970 33 1 0 1154 1186 134047193 134047225 3.450000e-04 56.5
11 TraesCS6D01G273600 chr4A 96.970 33 1 0 1154 1186 485708820 485708788 3.450000e-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 TraesCS6D01G273600 chr6D 382549852 382552336 2484 False 4590.00 4590 100.0000 1 2485 1 chr6D.!!$F1 2484
1 TraesCS6D01G273600 chr6B 572090129 572092280 2151 False 2595.00 2595 88.7630 291 2430 1 chr6B.!!$F2 2139
2 TraesCS6D01G273600 chr6A 524329824 524333327 3503 False 699.75 1515 89.5315 2 2473 4 chr6A.!!$F1 2471
3 TraesCS6D01G273600 chr5A 8058865 8059473 608 True 459.00 459 81.3920 1897 2473 1 chr5A.!!$R1 576
4 TraesCS6D01G273600 chr5D 10037972 10038592 620 True 436.00 436 80.7570 1897 2480 1 chr5D.!!$R1 583
5 TraesCS6D01G273600 chr5B 42157838 42158467 629 False 374.00 374 79.0300 1894 2471 1 chr5B.!!$F1 577

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
106 108 0.034896 TTCGCTCCTGGTCTTGTTCC 59.965 55.0 0.0 0.0 0.0 3.62 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1599 2822 0.463654 AGAACAAGAGTGCACGGCAA 60.464 50.0 12.01 0.0 41.47 4.52 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
24 25 1.402968 TGTCGTACACTTCGGCCTATC 59.597 52.381 0.00 0.00 31.61 2.08
25 26 1.674962 GTCGTACACTTCGGCCTATCT 59.325 52.381 0.00 0.00 0.00 1.98
34 35 2.812499 GGCCTATCTTGACGGCGA 59.188 61.111 16.62 0.00 44.68 5.54
38 39 0.389391 CCTATCTTGACGGCGATGGT 59.611 55.000 16.62 0.00 0.00 3.55
42 43 4.321966 TTGACGGCGATGGTGGCA 62.322 61.111 16.62 0.00 0.00 4.92
53 54 4.062293 GCGATGGTGGCAATAGTATTGTA 58.938 43.478 21.15 10.32 0.00 2.41
55 56 5.334105 GCGATGGTGGCAATAGTATTGTAAG 60.334 44.000 21.15 8.15 0.00 2.34
56 57 5.334105 CGATGGTGGCAATAGTATTGTAAGC 60.334 44.000 21.15 18.27 0.00 3.09
57 58 4.849518 TGGTGGCAATAGTATTGTAAGCA 58.150 39.130 21.15 20.09 0.00 3.91
58 59 5.445069 TGGTGGCAATAGTATTGTAAGCAT 58.555 37.500 21.15 0.00 0.00 3.79
59 60 5.299028 TGGTGGCAATAGTATTGTAAGCATG 59.701 40.000 21.15 0.00 0.00 4.06
60 61 5.215160 GTGGCAATAGTATTGTAAGCATGC 58.785 41.667 21.15 10.51 0.00 4.06
61 62 5.009010 GTGGCAATAGTATTGTAAGCATGCT 59.991 40.000 16.30 16.30 0.00 3.79
62 63 5.239306 TGGCAATAGTATTGTAAGCATGCTC 59.761 40.000 22.93 10.31 0.00 4.26
65 67 6.854892 GCAATAGTATTGTAAGCATGCTCTTG 59.145 38.462 22.93 8.88 0.00 3.02
89 91 4.092968 GTCACTGGGTATGTTGATTCGTTC 59.907 45.833 0.00 0.00 0.00 3.95
96 98 1.428448 TGTTGATTCGTTCGCTCCTG 58.572 50.000 0.00 0.00 0.00 3.86
102 104 0.319555 TTCGTTCGCTCCTGGTCTTG 60.320 55.000 0.00 0.00 0.00 3.02
103 105 1.006102 CGTTCGCTCCTGGTCTTGT 60.006 57.895 0.00 0.00 0.00 3.16
104 106 0.600255 CGTTCGCTCCTGGTCTTGTT 60.600 55.000 0.00 0.00 0.00 2.83
106 108 0.034896 TTCGCTCCTGGTCTTGTTCC 59.965 55.000 0.00 0.00 0.00 3.62
107 109 1.376037 CGCTCCTGGTCTTGTTCCC 60.376 63.158 0.00 0.00 0.00 3.97
110 112 0.036875 CTCCTGGTCTTGTTCCCCAC 59.963 60.000 0.00 0.00 0.00 4.61
111 113 1.302511 CCTGGTCTTGTTCCCCACG 60.303 63.158 0.00 0.00 0.00 4.94
112 114 1.302511 CTGGTCTTGTTCCCCACGG 60.303 63.158 0.00 0.00 0.00 4.94
113 115 2.052047 CTGGTCTTGTTCCCCACGGT 62.052 60.000 0.00 0.00 0.00 4.83
115 117 0.321034 GGTCTTGTTCCCCACGGTAC 60.321 60.000 0.00 0.00 0.00 3.34
143 145 8.349983 ACACAAAGTAATAGTGTTCAACAATCC 58.650 33.333 0.00 0.00 43.40 3.01
165 167 0.035439 CTTGCAACCCCGTCCATACT 60.035 55.000 0.00 0.00 0.00 2.12
179 181 4.712476 GTCCATACTGCCTTCAATGATCT 58.288 43.478 0.00 0.00 0.00 2.75
193 195 8.260818 CCTTCAATGATCTTAAGTTCTCACCTA 58.739 37.037 13.38 0.00 0.00 3.08
224 226 3.314635 GGCAGCTCATCGAAGATTTTGAT 59.685 43.478 0.00 0.00 45.12 2.57
235 237 9.778993 CATCGAAGATTTTGATGTTATTTCAGT 57.221 29.630 9.79 0.00 43.54 3.41
270 272 5.775686 TGGTCTTCTGCATTTTCTTCATTG 58.224 37.500 0.00 0.00 0.00 2.82
277 279 6.094719 TCTGCATTTTCTTCATTGCATGTAC 58.905 36.000 0.00 0.00 43.51 2.90
303 305 5.987098 AGAAAAGCAGAGATGCAAGAGATA 58.013 37.500 2.73 0.00 37.25 1.98
319 325 9.503399 TGCAAGAGATAGATCTATAGTAAACGA 57.497 33.333 15.31 0.00 37.25 3.85
379 386 5.369833 TGACCTTCTATTGGTTCGTTTTCA 58.630 37.500 0.00 0.00 38.03 2.69
395 402 9.180678 GTTCGTTTTCATTCAATTTGATGTACT 57.819 29.630 0.00 0.00 0.00 2.73
401 408 9.474920 TTTCATTCAATTTGATGTACTTTGTCC 57.525 29.630 0.00 0.00 0.00 4.02
406 413 9.829507 TTCAATTTGATGTACTTTGTCCAATTT 57.170 25.926 0.00 0.00 0.00 1.82
435 1570 5.470777 CAGTAAAGTCGGATTGTTTACCCAA 59.529 40.000 12.95 0.00 37.36 4.12
500 1658 0.317160 CCACGACAAGTCTACTGGCA 59.683 55.000 0.00 0.00 0.00 4.92
587 1756 2.982470 CAATGAAACTTCTTTCCAGCGC 59.018 45.455 0.00 0.00 35.75 5.92
625 1794 4.219288 GCCACCTTTGATTCTCAGTTTCAT 59.781 41.667 0.00 0.00 0.00 2.57
632 1801 7.490402 CCTTTGATTCTCAGTTTCATATTTGGC 59.510 37.037 0.00 0.00 0.00 4.52
830 2011 4.988598 CGCGCACCAACTCCACCT 62.989 66.667 8.75 0.00 0.00 4.00
950 2135 1.346538 GCAGCTCGTTCGATCTTGC 59.653 57.895 0.00 3.23 0.00 4.01
952 2137 0.459237 CAGCTCGTTCGATCTTGCCT 60.459 55.000 0.00 0.00 0.00 4.75
955 2140 1.746727 CTCGTTCGATCTTGCCTGCG 61.747 60.000 0.00 0.00 0.00 5.18
957 2142 1.710339 GTTCGATCTTGCCTGCGAC 59.290 57.895 0.00 0.00 31.91 5.19
964 2149 0.667487 TCTTGCCTGCGACTTCGAAG 60.667 55.000 23.43 23.43 44.50 3.79
965 2150 2.233007 CTTGCCTGCGACTTCGAAGC 62.233 60.000 24.86 15.90 43.57 3.86
969 2154 1.347817 CCTGCGACTTCGAAGCTGAC 61.348 60.000 24.86 12.37 43.57 3.51
976 2161 1.269831 ACTTCGAAGCTGACTGTCACC 60.270 52.381 24.86 0.03 0.00 4.02
992 2177 4.582869 TGTCACCGTCACTAGTAGTGTAT 58.417 43.478 25.83 10.35 46.03 2.29
1030 2215 1.758440 AAGAGGCAGTGCGAGGAACA 61.758 55.000 9.45 0.00 0.00 3.18
1032 2217 3.426568 GGCAGTGCGAGGAACAGC 61.427 66.667 9.45 0.00 0.00 4.40
1228 2413 3.554692 CCGCCGCTCGCTAGTTTG 61.555 66.667 0.00 0.00 36.73 2.93
1231 2416 1.472276 CGCCGCTCGCTAGTTTGTAG 61.472 60.000 0.00 0.00 34.21 2.74
1232 2417 1.146358 GCCGCTCGCTAGTTTGTAGG 61.146 60.000 0.00 0.00 0.00 3.18
1235 2420 1.132643 CGCTCGCTAGTTTGTAGGAGT 59.867 52.381 0.00 0.00 0.00 3.85
1236 2421 2.353889 CGCTCGCTAGTTTGTAGGAGTA 59.646 50.000 0.00 0.00 0.00 2.59
1237 2422 3.181503 CGCTCGCTAGTTTGTAGGAGTAA 60.182 47.826 0.00 0.00 0.00 2.24
1238 2423 4.497674 CGCTCGCTAGTTTGTAGGAGTAAT 60.498 45.833 0.00 0.00 0.00 1.89
1239 2424 5.277683 CGCTCGCTAGTTTGTAGGAGTAATA 60.278 44.000 0.00 0.00 0.00 0.98
1248 2433 8.813643 AGTTTGTAGGAGTAATATATGCGTTC 57.186 34.615 0.00 0.00 0.00 3.95
1349 2562 4.436998 GCGGCGTACCAGAGCTGT 62.437 66.667 9.37 0.00 41.51 4.40
1469 2682 0.254178 AGGCCAACATGAAGATCGCT 59.746 50.000 5.01 0.00 0.00 4.93
1485 2698 0.387202 CGCTGTCAGGGTCATCTAGG 59.613 60.000 8.71 0.00 0.00 3.02
1487 2700 1.689575 GCTGTCAGGGTCATCTAGGGA 60.690 57.143 1.14 0.00 0.00 4.20
1488 2701 2.035632 CTGTCAGGGTCATCTAGGGAC 58.964 57.143 6.86 6.86 34.52 4.46
1511 2728 4.262463 CCAGAAGTGGCTAGTGACTTGTTA 60.262 45.833 11.82 0.00 36.89 2.41
1512 2729 4.686554 CAGAAGTGGCTAGTGACTTGTTAC 59.313 45.833 11.82 0.00 32.47 2.50
1599 2822 3.573967 CCAACTGTTAGTTTGCTTCCCAT 59.426 43.478 0.00 0.00 36.03 4.00
1601 2824 4.853924 ACTGTTAGTTTGCTTCCCATTG 57.146 40.909 0.00 0.00 0.00 2.82
1625 2853 3.329386 GTGCACTCTTGTTCTAGATGCA 58.671 45.455 10.32 10.16 36.86 3.96
1630 2858 3.999663 ACTCTTGTTCTAGATGCAGCAAC 59.000 43.478 4.07 0.04 0.00 4.17
1640 2868 1.635663 ATGCAGCAACCGCGAGTTAC 61.636 55.000 8.23 5.06 45.49 2.50
1672 2900 9.736023 CTGTTAATTTGAATATGGGTCTAAAGC 57.264 33.333 0.00 0.00 0.00 3.51
1677 2905 8.829373 ATTTGAATATGGGTCTAAAGCTTTCT 57.171 30.769 16.57 0.00 0.00 2.52
1678 2906 7.630242 TTGAATATGGGTCTAAAGCTTTCTG 57.370 36.000 16.57 10.22 0.00 3.02
1683 2911 5.767816 TGGGTCTAAAGCTTTCTGAAAAC 57.232 39.130 16.57 9.25 0.00 2.43
1713 2945 2.365293 AGCGCTTTTCCATCCTTTGTTT 59.635 40.909 2.64 0.00 0.00 2.83
1743 2975 7.754851 GGAAAAACCTAACCAGTAAATCTCA 57.245 36.000 0.00 0.00 35.41 3.27
1799 3031 1.869767 GATAGCAAATCGGGCACTCAG 59.130 52.381 0.00 0.00 0.00 3.35
1808 3040 1.225704 GGGCACTCAGGGGAAGATG 59.774 63.158 0.00 0.00 0.00 2.90
1832 3064 6.045072 ACGACACAAGAGGTTCCATTTATA 57.955 37.500 0.00 0.00 0.00 0.98
1833 3065 6.106673 ACGACACAAGAGGTTCCATTTATAG 58.893 40.000 0.00 0.00 0.00 1.31
1871 3103 7.761038 AGTGCCATAATATATCGATCGGATA 57.239 36.000 16.41 13.42 41.71 2.59
1895 3127 5.599999 TTGCATACCTTCTCTCCTACTTC 57.400 43.478 0.00 0.00 0.00 3.01
1913 3150 9.211485 TCCTACTTCAAAAATACTAAGGTTTCG 57.789 33.333 0.00 0.00 0.00 3.46
1939 3177 1.541588 GAGATCCACAAACCTTGCCAC 59.458 52.381 0.00 0.00 0.00 5.01
1968 3212 2.118679 TCACAGCTACCCACTATGCAT 58.881 47.619 3.79 3.79 0.00 3.96
1973 3217 1.068588 GCTACCCACTATGCATCGTCA 59.931 52.381 0.19 0.00 0.00 4.35
2028 3311 5.182190 TCTGTCATGTCAGAGTACACTTCTC 59.818 44.000 17.19 0.00 39.20 2.87
2222 3512 0.034863 TACCACCGAAAAGCCCCATC 60.035 55.000 0.00 0.00 0.00 3.51
2331 3641 8.278729 TGATACAAAATGATTGCTGTCATGTA 57.721 30.769 5.38 5.97 38.76 2.29
2347 3657 4.389077 GTCATGTAGCAGAAACACACTACC 59.611 45.833 0.00 0.00 35.25 3.18
2350 3660 3.389983 TGTAGCAGAAACACACTACCCTT 59.610 43.478 0.00 0.00 35.25 3.95
2360 3679 3.888930 ACACACTACCCTTTCCAAACATG 59.111 43.478 0.00 0.00 0.00 3.21
2365 3684 1.970640 ACCCTTTCCAAACATGAAGCC 59.029 47.619 0.00 0.00 0.00 4.35
2458 3799 7.554118 TCATTTCTTCAGATTCCAACCTCATAC 59.446 37.037 0.00 0.00 0.00 2.39
2473 3814 7.444183 CCAACCTCATACGTTTGGTCATTATAT 59.556 37.037 6.15 0.00 31.64 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 0.997196 GGCCGAAGTGTACGACAATC 59.003 55.000 0.00 0.00 0.00 2.67
2 3 0.606604 AGGCCGAAGTGTACGACAAT 59.393 50.000 0.00 0.00 0.00 2.71
4 5 1.402968 GATAGGCCGAAGTGTACGACA 59.597 52.381 0.00 0.00 0.00 4.35
5 6 1.674962 AGATAGGCCGAAGTGTACGAC 59.325 52.381 0.00 0.00 0.00 4.34
6 7 2.048444 AGATAGGCCGAAGTGTACGA 57.952 50.000 0.00 0.00 0.00 3.43
7 8 2.098607 TCAAGATAGGCCGAAGTGTACG 59.901 50.000 0.00 0.00 0.00 3.67
18 19 0.946221 CCATCGCCGTCAAGATAGGC 60.946 60.000 8.78 8.78 46.88 3.93
24 25 3.499737 GCCACCATCGCCGTCAAG 61.500 66.667 0.00 0.00 0.00 3.02
25 26 3.716145 TATTGCCACCATCGCCGTCAA 62.716 52.381 0.00 0.00 0.00 3.18
34 35 5.445069 TGCTTACAATACTATTGCCACCAT 58.555 37.500 8.47 0.00 0.00 3.55
38 39 5.132502 AGCATGCTTACAATACTATTGCCA 58.867 37.500 16.30 2.73 0.00 4.92
42 43 7.056635 ACCAAGAGCATGCTTACAATACTATT 58.943 34.615 23.61 0.00 0.00 1.73
53 54 1.531423 CAGTGACCAAGAGCATGCTT 58.469 50.000 23.61 4.81 0.00 3.91
55 56 1.310933 CCCAGTGACCAAGAGCATGC 61.311 60.000 10.51 10.51 0.00 4.06
56 57 0.037303 ACCCAGTGACCAAGAGCATG 59.963 55.000 0.00 0.00 0.00 4.06
57 58 1.656587 TACCCAGTGACCAAGAGCAT 58.343 50.000 0.00 0.00 0.00 3.79
58 59 1.278985 CATACCCAGTGACCAAGAGCA 59.721 52.381 0.00 0.00 0.00 4.26
59 60 1.279271 ACATACCCAGTGACCAAGAGC 59.721 52.381 0.00 0.00 0.00 4.09
60 61 3.007940 TCAACATACCCAGTGACCAAGAG 59.992 47.826 0.00 0.00 0.00 2.85
61 62 2.976185 TCAACATACCCAGTGACCAAGA 59.024 45.455 0.00 0.00 0.00 3.02
62 63 3.417069 TCAACATACCCAGTGACCAAG 57.583 47.619 0.00 0.00 0.00 3.61
65 67 2.936498 CGAATCAACATACCCAGTGACC 59.064 50.000 0.00 0.00 0.00 4.02
89 91 1.376037 GGGAACAAGACCAGGAGCG 60.376 63.158 0.00 0.00 0.00 5.03
96 98 0.321034 GTACCGTGGGGAACAAGACC 60.321 60.000 0.00 0.00 36.97 3.85
102 104 1.373371 GTGTCGTACCGTGGGGAAC 60.373 63.158 0.00 0.00 36.97 3.62
103 105 1.398174 TTGTGTCGTACCGTGGGGAA 61.398 55.000 0.00 0.00 36.97 3.97
104 106 1.398174 TTTGTGTCGTACCGTGGGGA 61.398 55.000 0.00 0.00 36.97 4.81
106 108 0.249573 ACTTTGTGTCGTACCGTGGG 60.250 55.000 0.00 0.00 0.00 4.61
107 109 2.420628 TACTTTGTGTCGTACCGTGG 57.579 50.000 0.00 0.00 0.00 4.94
110 112 5.156355 ACACTATTACTTTGTGTCGTACCG 58.844 41.667 0.00 0.00 40.39 4.02
111 113 6.642131 TGAACACTATTACTTTGTGTCGTACC 59.358 38.462 0.00 0.00 43.11 3.34
112 114 7.627585 TGAACACTATTACTTTGTGTCGTAC 57.372 36.000 0.00 0.00 43.11 3.67
113 115 7.705752 TGTTGAACACTATTACTTTGTGTCGTA 59.294 33.333 0.00 0.00 43.11 3.43
115 117 6.939627 TGTTGAACACTATTACTTTGTGTCG 58.060 36.000 0.00 0.00 43.11 4.35
116 118 9.382244 GATTGTTGAACACTATTACTTTGTGTC 57.618 33.333 0.00 0.00 43.11 3.67
118 120 7.533900 CGGATTGTTGAACACTATTACTTTGTG 59.466 37.037 0.00 0.00 37.67 3.33
119 121 7.227910 ACGGATTGTTGAACACTATTACTTTGT 59.772 33.333 0.00 0.00 0.00 2.83
120 122 7.581476 ACGGATTGTTGAACACTATTACTTTG 58.419 34.615 0.00 0.00 0.00 2.77
123 125 6.698380 AGACGGATTGTTGAACACTATTACT 58.302 36.000 0.00 0.00 0.00 2.24
124 126 6.963049 AGACGGATTGTTGAACACTATTAC 57.037 37.500 0.00 0.00 0.00 1.89
125 127 6.128391 GCAAGACGGATTGTTGAACACTATTA 60.128 38.462 0.00 0.00 32.56 0.98
128 130 3.496884 GCAAGACGGATTGTTGAACACTA 59.503 43.478 0.00 0.00 32.56 2.74
143 145 3.047877 GGACGGGGTTGCAAGACG 61.048 66.667 0.00 7.63 0.00 4.18
165 167 6.372659 GTGAGAACTTAAGATCATTGAAGGCA 59.627 38.462 10.09 0.00 0.00 4.75
193 195 0.682209 GATGAGCTGCCCACCACAAT 60.682 55.000 0.00 0.00 0.00 2.71
205 207 7.798596 ATAACATCAAAATCTTCGATGAGCT 57.201 32.000 7.14 0.00 39.09 4.09
224 226 7.122948 ACCAAACCTACACAAACTGAAATAACA 59.877 33.333 0.00 0.00 0.00 2.41
235 237 3.630312 GCAGAAGACCAAACCTACACAAA 59.370 43.478 0.00 0.00 0.00 2.83
238 240 2.846193 TGCAGAAGACCAAACCTACAC 58.154 47.619 0.00 0.00 0.00 2.90
270 272 2.346803 TCTGCTTTTCTCCGTACATGC 58.653 47.619 0.00 0.00 0.00 4.06
316 322 5.407407 ACATCAAAGTTCTCCATAGTCGT 57.593 39.130 0.00 0.00 0.00 4.34
317 323 7.036220 AGTTACATCAAAGTTCTCCATAGTCG 58.964 38.462 0.00 0.00 0.00 4.18
318 324 8.779354 AAGTTACATCAAAGTTCTCCATAGTC 57.221 34.615 0.00 0.00 0.00 2.59
369 376 9.180678 AGTACATCAAATTGAATGAAAACGAAC 57.819 29.630 0.00 0.00 0.00 3.95
406 413 9.754382 GGTAAACAATCCGACTTTACTGATATA 57.246 33.333 0.00 0.00 32.97 0.86
407 414 7.713942 GGGTAAACAATCCGACTTTACTGATAT 59.286 37.037 0.00 0.00 32.97 1.63
500 1658 1.751351 TCGATCTCGGAAGTGCATCTT 59.249 47.619 0.00 0.00 40.29 2.40
541 1699 2.543037 TTTTTAGGGGAGGGAATGGC 57.457 50.000 0.00 0.00 0.00 4.40
587 1756 3.827634 GGCGGTGCCTATCTTTGG 58.172 61.111 0.00 0.00 46.69 3.28
632 1801 4.355720 TGCAGCAGGCCTTCCCAG 62.356 66.667 0.00 0.00 43.89 4.45
837 2018 0.321671 TGGCAGTAGTGTTGAGGAGC 59.678 55.000 0.00 0.00 0.00 4.70
939 2124 0.737715 AGTCGCAGGCAAGATCGAAC 60.738 55.000 0.00 0.00 32.49 3.95
950 2135 1.080501 TCAGCTTCGAAGTCGCAGG 60.081 57.895 25.24 9.55 39.60 4.85
952 2137 0.664466 CAGTCAGCTTCGAAGTCGCA 60.664 55.000 25.24 5.68 39.60 5.10
955 2140 2.055100 GTGACAGTCAGCTTCGAAGTC 58.945 52.381 25.24 17.29 0.00 3.01
957 2142 1.423395 GGTGACAGTCAGCTTCGAAG 58.577 55.000 23.03 21.02 41.34 3.79
992 2177 2.125552 CCAGAGCCATCGACGCAA 60.126 61.111 8.86 0.00 0.00 4.85
1228 2413 6.248001 CGAACGAACGCATATATTACTCCTAC 59.752 42.308 0.00 0.00 0.00 3.18
1231 2416 4.913924 ACGAACGAACGCATATATTACTCC 59.086 41.667 0.14 0.00 36.70 3.85
1232 2417 5.622448 TCACGAACGAACGCATATATTACTC 59.378 40.000 0.14 0.00 36.70 2.59
1235 2420 5.171874 GTGTCACGAACGAACGCATATATTA 59.828 40.000 0.14 0.00 36.70 0.98
1236 2421 4.027132 GTGTCACGAACGAACGCATATATT 60.027 41.667 0.14 0.00 36.70 1.28
1237 2422 3.484649 GTGTCACGAACGAACGCATATAT 59.515 43.478 0.14 0.00 36.70 0.86
1238 2423 2.847717 GTGTCACGAACGAACGCATATA 59.152 45.455 0.14 0.00 36.70 0.86
1239 2424 1.652124 GTGTCACGAACGAACGCATAT 59.348 47.619 0.14 0.00 36.70 1.78
1469 2682 1.343075 GGTCCCTAGATGACCCTGACA 60.343 57.143 16.52 0.00 45.38 3.58
1485 2698 1.066787 GTCACTAGCCACTTCTGGTCC 60.067 57.143 0.00 0.00 40.17 4.46
1487 2700 2.016905 AGTCACTAGCCACTTCTGGT 57.983 50.000 0.00 0.00 40.17 4.00
1488 2701 2.037772 ACAAGTCACTAGCCACTTCTGG 59.962 50.000 4.30 0.00 41.13 3.86
1489 2702 3.393089 ACAAGTCACTAGCCACTTCTG 57.607 47.619 4.30 0.00 30.06 3.02
1511 2728 4.952071 ATCGATCTGATCTGAATGTGGT 57.048 40.909 15.16 0.00 28.49 4.16
1599 2822 0.463654 AGAACAAGAGTGCACGGCAA 60.464 50.000 12.01 0.00 41.47 4.52
1601 2824 1.071605 CTAGAACAAGAGTGCACGGC 58.928 55.000 12.01 7.96 0.00 5.68
1625 2853 1.463444 GAATTGTAACTCGCGGTTGCT 59.537 47.619 21.67 8.49 40.41 3.91
1630 2858 1.722011 ACAGGAATTGTAACTCGCGG 58.278 50.000 6.13 0.00 38.56 6.46
1640 2868 9.533253 GACCCATATTCAAATTAACAGGAATTG 57.467 33.333 0.00 0.00 32.62 2.32
1668 2896 4.580580 AGTCCATCGTTTTCAGAAAGCTTT 59.419 37.500 12.53 12.53 0.00 3.51
1672 2900 4.201628 CGCTAGTCCATCGTTTTCAGAAAG 60.202 45.833 0.00 0.00 0.00 2.62
1676 2904 1.324736 GCGCTAGTCCATCGTTTTCAG 59.675 52.381 0.00 0.00 0.00 3.02
1677 2905 1.067142 AGCGCTAGTCCATCGTTTTCA 60.067 47.619 8.99 0.00 0.00 2.69
1678 2906 1.641577 AGCGCTAGTCCATCGTTTTC 58.358 50.000 8.99 0.00 0.00 2.29
1683 2911 0.931005 GGAAAAGCGCTAGTCCATCG 59.069 55.000 26.56 0.00 0.00 3.84
1756 2988 7.145474 TCTCTTCCTTACTGGTTAGGTTTTT 57.855 36.000 5.82 0.00 37.07 1.94
1799 3031 1.275291 TCTTGTGTCGTCATCTTCCCC 59.725 52.381 0.00 0.00 0.00 4.81
1808 3040 2.457366 ATGGAACCTCTTGTGTCGTC 57.543 50.000 0.00 0.00 0.00 4.20
1832 3064 2.889045 TGGCACTAGTACGAGTTTCACT 59.111 45.455 5.83 0.00 0.00 3.41
1833 3065 3.293311 TGGCACTAGTACGAGTTTCAC 57.707 47.619 5.83 0.00 0.00 3.18
1841 3073 7.740781 CGATCGATATATTATGGCACTAGTACG 59.259 40.741 10.26 0.00 0.00 3.67
1871 3103 6.156949 TGAAGTAGGAGAGAAGGTATGCAAAT 59.843 38.462 0.00 0.00 0.00 2.32
1913 3150 4.333926 GCAAGGTTTGTGGATCTCTATGAC 59.666 45.833 0.00 0.00 0.00 3.06
1919 3157 1.541588 GTGGCAAGGTTTGTGGATCTC 59.458 52.381 0.00 0.00 0.00 2.75
1939 3177 4.876107 AGTGGGTAGCTGTGAAATTTATCG 59.124 41.667 0.00 0.00 0.00 2.92
1983 3227 6.984474 ACAGAAACGTGATCTTCAAGAACTTA 59.016 34.615 0.00 0.00 30.40 2.24
1984 3228 5.817816 ACAGAAACGTGATCTTCAAGAACTT 59.182 36.000 0.00 0.00 30.40 2.66
1985 3229 5.360591 ACAGAAACGTGATCTTCAAGAACT 58.639 37.500 0.00 0.00 30.40 3.01
1986 3230 5.234329 TGACAGAAACGTGATCTTCAAGAAC 59.766 40.000 0.00 0.00 30.40 3.01
1987 3231 5.356426 TGACAGAAACGTGATCTTCAAGAA 58.644 37.500 0.00 0.00 30.40 2.52
2222 3512 1.344942 CGTCTCCAGGTTTTCTCGCG 61.345 60.000 0.00 0.00 0.00 5.87
2331 3641 3.477530 GAAAGGGTAGTGTGTTTCTGCT 58.522 45.455 0.00 0.00 0.00 4.24
2347 3657 3.749665 TTGGCTTCATGTTTGGAAAGG 57.250 42.857 0.00 0.00 0.00 3.11
2350 3660 4.100653 TGTCATTTGGCTTCATGTTTGGAA 59.899 37.500 0.00 0.00 0.00 3.53
2360 3679 4.500477 GCGAAATATGTGTCATTTGGCTTC 59.500 41.667 7.32 0.00 41.27 3.86
2365 3684 6.545508 TCTTCTGCGAAATATGTGTCATTTG 58.454 36.000 0.00 0.00 0.00 2.32


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

AutoCloner maintained by Alex Coulton.