Multiple sequence alignment - TraesCS2D01G312200

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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 TraesCS2D01G312200 chr2D 100.000 2642 0 0 1 2642 401542937 401540296 0.000000e+00 4879.0
1 TraesCS2D01G312200 chr2A 87.288 1770 137 43 104 1816 538368743 538367005 0.000000e+00 1941.0
2 TraesCS2D01G312200 chr2A 86.207 551 29 18 1872 2405 538366986 538366466 1.070000e-153 553.0
3 TraesCS2D01G312200 chr2A 90.114 263 10 7 2392 2642 538366449 538366191 7.050000e-86 327.0
4 TraesCS2D01G312200 chr2A 97.674 43 1 0 1 43 538368791 538368749 1.010000e-09 75.0
5 TraesCS2D01G312200 chr2B 86.777 1452 53 47 1263 2642 475610607 475609223 0.000000e+00 1489.0
6 TraesCS2D01G312200 chr2B 89.122 1048 57 23 293 1298 475611635 475610603 0.000000e+00 1251.0
7 TraesCS2D01G312200 chr7B 91.379 58 4 1 1315 1371 612320339 612320282 7.840000e-11 78.7


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 TraesCS2D01G312200 chr2D 401540296 401542937 2641 True 4879 4879 100.00000 1 2642 1 chr2D.!!$R1 2641
1 TraesCS2D01G312200 chr2A 538366191 538368791 2600 True 724 1941 90.32075 1 2642 4 chr2A.!!$R1 2641
2 TraesCS2D01G312200 chr2B 475609223 475611635 2412 True 1370 1489 87.94950 293 2642 2 chr2B.!!$R1 2349

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
356 376 0.452585 TGCATGCACATGATCCGTTG 59.547 50.0 18.46 0.0 41.2 4.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2247 2412 1.070601 ACATGCACAGACTGTACTGCA 59.929 47.619 18.29 18.29 41.06 4.41 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
45 46 7.760131 ACAAAATTCACAAGAAGACATGTTG 57.240 32.000 0.00 0.00 37.14 3.33
46 47 6.256321 ACAAAATTCACAAGAAGACATGTTGC 59.744 34.615 0.00 0.00 35.77 4.17
47 48 5.779529 AATTCACAAGAAGACATGTTGCT 57.220 34.783 0.00 0.00 35.77 3.91
48 49 5.779529 ATTCACAAGAAGACATGTTGCTT 57.220 34.783 0.00 0.00 35.77 3.91
49 50 5.581126 TTCACAAGAAGACATGTTGCTTT 57.419 34.783 0.00 0.00 35.77 3.51
50 51 5.173774 TCACAAGAAGACATGTTGCTTTC 57.826 39.130 0.00 2.74 35.77 2.62
51 52 4.883585 TCACAAGAAGACATGTTGCTTTCT 59.116 37.500 0.00 5.04 35.77 2.52
52 53 5.357878 TCACAAGAAGACATGTTGCTTTCTT 59.642 36.000 16.33 16.33 35.77 2.52
53 54 6.038356 CACAAGAAGACATGTTGCTTTCTTT 58.962 36.000 18.11 11.44 35.77 2.52
54 55 6.532657 CACAAGAAGACATGTTGCTTTCTTTT 59.467 34.615 18.11 13.08 35.77 2.27
55 56 7.063780 CACAAGAAGACATGTTGCTTTCTTTTT 59.936 33.333 18.11 8.42 35.77 1.94
77 78 6.371809 TTTTTAGATGAAGACGTGTTGCTT 57.628 33.333 1.19 0.00 0.00 3.91
78 79 6.371809 TTTTAGATGAAGACGTGTTGCTTT 57.628 33.333 1.19 0.00 0.00 3.51
79 80 3.885484 AGATGAAGACGTGTTGCTTTG 57.115 42.857 1.19 0.00 0.00 2.77
80 81 2.549754 AGATGAAGACGTGTTGCTTTGG 59.450 45.455 1.19 0.00 0.00 3.28
81 82 2.031258 TGAAGACGTGTTGCTTTGGA 57.969 45.000 1.19 0.00 0.00 3.53
82 83 2.360844 TGAAGACGTGTTGCTTTGGAA 58.639 42.857 1.19 0.00 0.00 3.53
83 84 2.750166 TGAAGACGTGTTGCTTTGGAAA 59.250 40.909 1.19 0.00 0.00 3.13
84 85 2.844122 AGACGTGTTGCTTTGGAAAC 57.156 45.000 0.00 0.00 0.00 2.78
85 86 1.404035 AGACGTGTTGCTTTGGAAACC 59.596 47.619 0.00 0.00 30.01 3.27
86 87 1.133407 GACGTGTTGCTTTGGAAACCA 59.867 47.619 0.00 0.00 30.01 3.67
87 88 1.135228 ACGTGTTGCTTTGGAAACCAC 60.135 47.619 0.00 0.00 30.78 4.16
88 89 1.134175 CGTGTTGCTTTGGAAACCACT 59.866 47.619 0.00 0.00 30.78 4.00
89 90 2.539476 GTGTTGCTTTGGAAACCACTG 58.461 47.619 0.00 0.00 30.78 3.66
90 91 2.165437 GTGTTGCTTTGGAAACCACTGA 59.835 45.455 0.00 0.00 30.78 3.41
91 92 2.828520 TGTTGCTTTGGAAACCACTGAA 59.171 40.909 0.00 0.00 30.78 3.02
92 93 3.450457 TGTTGCTTTGGAAACCACTGAAT 59.550 39.130 0.00 0.00 30.78 2.57
93 94 3.731652 TGCTTTGGAAACCACTGAATG 57.268 42.857 0.00 0.00 30.78 2.67
122 123 4.857679 CTTGGTACTGTACTACTCCCTCT 58.142 47.826 16.79 0.00 0.00 3.69
123 124 5.631009 GCTTGGTACTGTACTACTCCCTCTA 60.631 48.000 16.79 0.00 0.00 2.43
124 125 6.587560 TTGGTACTGTACTACTCCCTCTAT 57.412 41.667 16.79 0.00 0.00 1.98
127 128 6.389278 TGGTACTGTACTACTCCCTCTATCTT 59.611 42.308 16.79 0.00 0.00 2.40
134 135 9.352191 TGTACTACTCCCTCTATCTTGAATTAC 57.648 37.037 0.00 0.00 0.00 1.89
136 137 8.472007 ACTACTCCCTCTATCTTGAATTACTG 57.528 38.462 0.00 0.00 0.00 2.74
143 144 5.348986 TCTATCTTGAATTACTGGTCGCAC 58.651 41.667 0.00 0.00 0.00 5.34
147 148 5.348986 TCTTGAATTACTGGTCGCACTATC 58.651 41.667 0.00 0.00 0.00 2.08
156 157 2.236146 TGGTCGCACTATCCATTTCTGT 59.764 45.455 0.00 0.00 0.00 3.41
157 158 2.609459 GGTCGCACTATCCATTTCTGTG 59.391 50.000 0.00 0.00 0.00 3.66
159 160 4.122776 GTCGCACTATCCATTTCTGTGAT 58.877 43.478 0.00 0.00 0.00 3.06
160 161 5.289595 GTCGCACTATCCATTTCTGTGATA 58.710 41.667 0.00 0.00 0.00 2.15
162 163 6.257849 GTCGCACTATCCATTTCTGTGATAAA 59.742 38.462 0.00 0.00 0.00 1.40
163 164 6.257849 TCGCACTATCCATTTCTGTGATAAAC 59.742 38.462 0.00 0.00 0.00 2.01
171 172 6.657117 TCCATTTCTGTGATAAACAATTCGGA 59.343 34.615 0.00 0.00 38.67 4.55
173 174 7.812191 CCATTTCTGTGATAAACAATTCGGAAA 59.188 33.333 0.00 0.00 38.67 3.13
174 175 8.853345 CATTTCTGTGATAAACAATTCGGAAAG 58.147 33.333 0.00 0.00 38.67 2.62
181 184 6.311935 TGATAAACAATTCGGAAAGGAGTACG 59.688 38.462 0.00 0.00 0.00 3.67
185 188 3.947910 ATTCGGAAAGGAGTACGTTCA 57.052 42.857 3.33 0.00 39.03 3.18
186 189 3.731652 TTCGGAAAGGAGTACGTTCAA 57.268 42.857 3.33 0.00 39.03 2.69
188 191 4.057406 TCGGAAAGGAGTACGTTCAAAA 57.943 40.909 3.33 0.00 39.03 2.44
189 192 4.440880 TCGGAAAGGAGTACGTTCAAAAA 58.559 39.130 3.33 0.00 39.03 1.94
238 251 5.846203 ACAACTGCAACTTAATTTCTGCAT 58.154 33.333 0.00 0.00 43.42 3.96
241 254 6.199937 ACTGCAACTTAATTTCTGCATAGG 57.800 37.500 0.00 0.00 43.42 2.57
242 255 4.997565 TGCAACTTAATTTCTGCATAGGC 58.002 39.130 0.00 0.00 39.77 3.93
270 285 2.486191 GGGTGAAGCCTGATACATCCAG 60.486 54.545 0.00 0.00 34.14 3.86
287 302 2.647299 TCCAGGGAGCCACATTTTCTTA 59.353 45.455 0.00 0.00 0.00 2.10
289 304 3.382546 CCAGGGAGCCACATTTTCTTATG 59.617 47.826 0.00 0.00 0.00 1.90
290 305 4.272489 CAGGGAGCCACATTTTCTTATGA 58.728 43.478 0.00 0.00 0.00 2.15
291 306 4.706476 CAGGGAGCCACATTTTCTTATGAA 59.294 41.667 0.00 0.00 0.00 2.57
325 340 3.117794 CGAGTTGTGGTCGTACAAAAGA 58.882 45.455 0.00 0.00 41.75 2.52
329 344 6.445357 AGTTGTGGTCGTACAAAAGAAAAT 57.555 33.333 0.00 0.00 41.75 1.82
334 349 8.844441 TGTGGTCGTACAAAAGAAAATTAAAG 57.156 30.769 0.00 0.00 0.00 1.85
335 350 8.675504 TGTGGTCGTACAAAAGAAAATTAAAGA 58.324 29.630 0.00 0.00 0.00 2.52
336 351 9.673454 GTGGTCGTACAAAAGAAAATTAAAGAT 57.327 29.630 0.00 0.00 0.00 2.40
349 369 7.820386 AGAAAATTAAAGATTGCATGCACATGA 59.180 29.630 22.58 5.97 41.20 3.07
356 376 0.452585 TGCATGCACATGATCCGTTG 59.547 50.000 18.46 0.00 41.20 4.10
360 380 0.606130 TGCACATGATCCGTTGCACT 60.606 50.000 0.00 0.00 0.00 4.40
391 411 5.516696 AGCAGCTTTTTCGTTTCTTTCTTTC 59.483 36.000 0.00 0.00 0.00 2.62
428 448 1.227380 CCTACCGTGAGCATGAGCC 60.227 63.158 0.00 0.00 43.56 4.70
429 449 1.517361 CTACCGTGAGCATGAGCCA 59.483 57.895 0.00 0.00 43.56 4.75
466 486 1.574134 ACGTGTTTGAACCACTACCG 58.426 50.000 0.00 0.00 0.00 4.02
545 565 6.273071 ACTGAAAACAAATGTACTGCTTTCC 58.727 36.000 6.89 0.00 31.02 3.13
546 566 6.096846 ACTGAAAACAAATGTACTGCTTTCCT 59.903 34.615 6.89 0.00 31.02 3.36
599 622 3.552699 TGAACTGTACGCTACACAAACAC 59.447 43.478 0.00 0.00 34.46 3.32
601 624 3.120792 ACTGTACGCTACACAAACACTG 58.879 45.455 0.00 0.00 34.46 3.66
685 716 3.244875 TGCCATCCTCAAGCACTCTTAAA 60.245 43.478 0.00 0.00 0.00 1.52
686 717 3.758554 GCCATCCTCAAGCACTCTTAAAA 59.241 43.478 0.00 0.00 0.00 1.52
687 718 4.400567 GCCATCCTCAAGCACTCTTAAAAT 59.599 41.667 0.00 0.00 0.00 1.82
688 719 5.449725 GCCATCCTCAAGCACTCTTAAAATC 60.450 44.000 0.00 0.00 0.00 2.17
689 720 5.884792 CCATCCTCAAGCACTCTTAAAATCT 59.115 40.000 0.00 0.00 0.00 2.40
690 721 6.183360 CCATCCTCAAGCACTCTTAAAATCTG 60.183 42.308 0.00 0.00 0.00 2.90
692 723 6.299141 TCCTCAAGCACTCTTAAAATCTGTT 58.701 36.000 0.00 0.00 0.00 3.16
693 724 6.428159 TCCTCAAGCACTCTTAAAATCTGTTC 59.572 38.462 0.00 0.00 0.00 3.18
694 725 6.228273 TCAAGCACTCTTAAAATCTGTTCG 57.772 37.500 0.00 0.00 0.00 3.95
695 726 4.670227 AGCACTCTTAAAATCTGTTCGC 57.330 40.909 0.00 0.00 0.00 4.70
696 727 4.319177 AGCACTCTTAAAATCTGTTCGCT 58.681 39.130 0.00 0.00 0.00 4.93
697 728 4.757149 AGCACTCTTAAAATCTGTTCGCTT 59.243 37.500 0.00 0.00 0.00 4.68
698 729 5.932303 AGCACTCTTAAAATCTGTTCGCTTA 59.068 36.000 0.00 0.00 0.00 3.09
705 737 2.246719 ATCTGTTCGCTTATGAGGCC 57.753 50.000 0.00 0.00 0.00 5.19
743 781 6.721318 AGCCAACTTTTGTAGGAGAATATGA 58.279 36.000 0.00 0.00 0.00 2.15
832 870 9.944376 ATAATCAGACAGGTGCGTAATAATAAT 57.056 29.630 0.00 0.00 0.00 1.28
868 907 3.812053 GCAAAGAGAGGCAGGTATGTATG 59.188 47.826 0.00 0.00 0.00 2.39
904 943 9.513906 TCTGGTGAAATTCAGTACAATTATCAA 57.486 29.630 0.00 0.00 33.13 2.57
905 944 9.778993 CTGGTGAAATTCAGTACAATTATCAAG 57.221 33.333 0.00 0.00 0.00 3.02
906 945 9.295825 TGGTGAAATTCAGTACAATTATCAAGT 57.704 29.630 0.00 0.00 0.00 3.16
1022 1062 4.346734 AGATTCGTTCATGCATGTTCAC 57.653 40.909 25.43 18.38 0.00 3.18
1038 1078 3.236816 GTTCACATTGTCATTTCAGCGG 58.763 45.455 0.00 0.00 0.00 5.52
1164 1223 4.181010 CACAGCCCATCCCCTCCG 62.181 72.222 0.00 0.00 0.00 4.63
1213 1284 2.218603 GAGAGCGGTTGAGGAAAACAA 58.781 47.619 0.00 0.00 0.00 2.83
1222 1293 4.390603 GGTTGAGGAAAACAAAAACCACAC 59.609 41.667 0.00 0.00 37.57 3.82
1240 1312 1.140589 CCGAGCTGAGCCTACTGTG 59.859 63.158 0.00 0.00 0.00 3.66
1290 1403 3.256631 GCAAAGCCCAATCAAGAAGAAGA 59.743 43.478 0.00 0.00 0.00 2.87
1293 1406 3.694926 AGCCCAATCAAGAAGAAGAAGG 58.305 45.455 0.00 0.00 0.00 3.46
1644 1766 2.838225 GCGGGGCAGGAGTAGCTA 60.838 66.667 0.00 0.00 0.00 3.32
1689 1817 3.213506 CCTGTGACCATGAAGACAACAA 58.786 45.455 0.00 0.00 0.00 2.83
1792 1930 3.369147 AGCGATTCGTTGATGTCTGAAAG 59.631 43.478 8.03 0.00 0.00 2.62
1846 1985 5.065859 GCTCTTTCTCTGGATTTCCTTTAGC 59.934 44.000 0.00 0.00 36.82 3.09
1850 1989 5.350504 TCTCTGGATTTCCTTTAGCTCTG 57.649 43.478 0.00 0.00 36.82 3.35
1854 1993 4.589908 TGGATTTCCTTTAGCTCTGTTCC 58.410 43.478 0.00 0.00 36.82 3.62
1865 2004 7.826744 CCTTTAGCTCTGTTCCTTTTAAGATCT 59.173 37.037 0.00 0.00 0.00 2.75
1868 2007 7.680442 AGCTCTGTTCCTTTTAAGATCTTTC 57.320 36.000 14.36 0.00 0.00 2.62
1869 2008 7.457561 AGCTCTGTTCCTTTTAAGATCTTTCT 58.542 34.615 14.36 0.00 0.00 2.52
1870 2009 7.941790 AGCTCTGTTCCTTTTAAGATCTTTCTT 59.058 33.333 14.36 0.00 44.44 2.52
1871 2010 8.572185 GCTCTGTTCCTTTTAAGATCTTTCTTT 58.428 33.333 14.36 0.00 42.29 2.52
1901 2040 1.609208 TCCAAAGCAGAGGCAAGTTC 58.391 50.000 0.00 0.00 44.61 3.01
1944 2093 5.632347 GCTATAGCAATTCCAATCATGTTGC 59.368 40.000 20.01 6.80 43.97 4.17
1984 2133 3.128764 TGCTTGTGATCTACTAGTGGACG 59.871 47.826 11.56 0.00 35.04 4.79
2022 2180 6.040247 TGTACTGCGAAACGATAATTGATCT 58.960 36.000 0.00 0.00 31.70 2.75
2059 2224 0.778815 CGATATTCTCGGCGTTGAGC 59.221 55.000 6.85 0.00 43.82 4.26
2083 2248 3.018856 CTGCTCCATGCTCACCAATAAA 58.981 45.455 0.00 0.00 43.37 1.40
2084 2249 3.634504 TGCTCCATGCTCACCAATAAAT 58.365 40.909 0.00 0.00 43.37 1.40
2085 2250 4.790937 TGCTCCATGCTCACCAATAAATA 58.209 39.130 0.00 0.00 43.37 1.40
2086 2251 5.199723 TGCTCCATGCTCACCAATAAATAA 58.800 37.500 0.00 0.00 43.37 1.40
2087 2252 5.834742 TGCTCCATGCTCACCAATAAATAAT 59.165 36.000 0.00 0.00 43.37 1.28
2088 2253 6.154445 GCTCCATGCTCACCAATAAATAATG 58.846 40.000 0.00 0.00 38.95 1.90
2089 2254 6.088016 TCCATGCTCACCAATAAATAATGC 57.912 37.500 0.00 0.00 0.00 3.56
2090 2255 5.834742 TCCATGCTCACCAATAAATAATGCT 59.165 36.000 0.00 0.00 0.00 3.79
2091 2256 5.924254 CCATGCTCACCAATAAATAATGCTG 59.076 40.000 0.00 0.00 0.00 4.41
2092 2257 5.518848 TGCTCACCAATAAATAATGCTGG 57.481 39.130 0.00 0.00 0.00 4.85
2093 2258 5.199723 TGCTCACCAATAAATAATGCTGGA 58.800 37.500 0.00 0.00 0.00 3.86
2094 2259 5.300034 TGCTCACCAATAAATAATGCTGGAG 59.700 40.000 0.00 0.00 0.00 3.86
2095 2260 5.532406 GCTCACCAATAAATAATGCTGGAGA 59.468 40.000 0.00 0.00 0.00 3.71
2124 2289 3.181473 ACAAGCAATGAAGCAAAGCAAGA 60.181 39.130 0.00 0.00 36.85 3.02
2247 2412 4.473520 CGCCGGCCTCCATTCTGT 62.474 66.667 23.46 0.00 0.00 3.41
2248 2413 2.825836 GCCGGCCTCCATTCTGTG 60.826 66.667 18.11 0.00 0.00 3.66
2313 2478 0.323816 ATGTCAGGCCAGTCTCTCGA 60.324 55.000 5.01 0.00 0.00 4.04
2378 2543 2.356793 CCGAGGCGATGATGGAGC 60.357 66.667 0.00 0.00 0.00 4.70
2382 2547 4.996434 GGCGATGATGGAGCCGGG 62.996 72.222 2.18 0.00 41.53 5.73
2384 2549 3.550431 CGATGATGGAGCCGGGGT 61.550 66.667 2.18 0.00 0.00 4.95
2557 2782 1.817881 TGCCAATGCATTGCTAGCC 59.182 52.632 30.15 16.36 44.23 3.93
2561 2786 1.829533 AATGCATTGCTAGCCCGGG 60.830 57.895 19.09 19.09 0.00 5.73
2626 2858 2.421529 CCAAACCTACTACCCTCATGGC 60.422 54.545 0.00 0.00 37.83 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
28 29 4.883585 AGAAAGCAACATGTCTTCTTGTGA 59.116 37.500 0.00 0.00 33.29 3.58
54 55 6.371809 AAGCAACACGTCTTCATCTAAAAA 57.628 33.333 0.00 0.00 0.00 1.94
55 56 6.198687 CAAAGCAACACGTCTTCATCTAAAA 58.801 36.000 0.00 0.00 0.00 1.52
56 57 5.277779 CCAAAGCAACACGTCTTCATCTAAA 60.278 40.000 0.00 0.00 0.00 1.85
57 58 4.213270 CCAAAGCAACACGTCTTCATCTAA 59.787 41.667 0.00 0.00 0.00 2.10
58 59 3.745975 CCAAAGCAACACGTCTTCATCTA 59.254 43.478 0.00 0.00 0.00 1.98
59 60 2.549754 CCAAAGCAACACGTCTTCATCT 59.450 45.455 0.00 0.00 0.00 2.90
60 61 2.548057 TCCAAAGCAACACGTCTTCATC 59.452 45.455 0.00 0.00 0.00 2.92
61 62 2.571212 TCCAAAGCAACACGTCTTCAT 58.429 42.857 0.00 0.00 0.00 2.57
62 63 2.031258 TCCAAAGCAACACGTCTTCA 57.969 45.000 0.00 0.00 0.00 3.02
63 64 3.105937 GTTTCCAAAGCAACACGTCTTC 58.894 45.455 0.00 0.00 0.00 2.87
64 65 2.159296 GGTTTCCAAAGCAACACGTCTT 60.159 45.455 0.00 0.00 36.47 3.01
65 66 1.404035 GGTTTCCAAAGCAACACGTCT 59.596 47.619 0.00 0.00 36.47 4.18
66 67 1.133407 TGGTTTCCAAAGCAACACGTC 59.867 47.619 1.45 0.00 42.72 4.34
67 68 1.135228 GTGGTTTCCAAAGCAACACGT 60.135 47.619 5.53 0.00 46.50 4.49
68 69 1.134175 AGTGGTTTCCAAAGCAACACG 59.866 47.619 5.53 0.00 46.50 4.49
69 70 2.165437 TCAGTGGTTTCCAAAGCAACAC 59.835 45.455 5.53 0.00 46.50 3.32
70 71 2.451490 TCAGTGGTTTCCAAAGCAACA 58.549 42.857 5.53 0.00 46.50 3.33
71 72 3.518634 TTCAGTGGTTTCCAAAGCAAC 57.481 42.857 5.53 1.73 46.50 4.17
72 73 3.181467 CCATTCAGTGGTTTCCAAAGCAA 60.181 43.478 5.53 0.00 46.50 3.91
73 74 2.364970 CCATTCAGTGGTTTCCAAAGCA 59.635 45.455 0.00 0.00 43.44 3.91
74 75 3.030668 CCATTCAGTGGTTTCCAAAGC 57.969 47.619 0.00 0.00 43.44 3.51
85 86 1.274167 ACCAAGCAATGCCATTCAGTG 59.726 47.619 0.00 0.00 43.15 3.66
86 87 1.636148 ACCAAGCAATGCCATTCAGT 58.364 45.000 0.00 0.00 0.00 3.41
87 88 2.756760 AGTACCAAGCAATGCCATTCAG 59.243 45.455 0.00 0.00 0.00 3.02
88 89 2.492881 CAGTACCAAGCAATGCCATTCA 59.507 45.455 0.00 0.00 0.00 2.57
89 90 2.493278 ACAGTACCAAGCAATGCCATTC 59.507 45.455 0.00 0.00 0.00 2.67
90 91 2.528564 ACAGTACCAAGCAATGCCATT 58.471 42.857 0.00 0.00 0.00 3.16
91 92 2.220653 ACAGTACCAAGCAATGCCAT 57.779 45.000 0.00 0.00 0.00 4.40
92 93 2.039746 AGTACAGTACCAAGCAATGCCA 59.960 45.455 7.13 0.00 0.00 4.92
93 94 2.711542 AGTACAGTACCAAGCAATGCC 58.288 47.619 7.13 0.00 0.00 4.40
94 95 4.504858 AGTAGTACAGTACCAAGCAATGC 58.495 43.478 7.13 0.00 0.00 3.56
95 96 5.109903 GGAGTAGTACAGTACCAAGCAATG 58.890 45.833 7.13 0.00 0.00 2.82
96 97 4.161754 GGGAGTAGTACAGTACCAAGCAAT 59.838 45.833 7.13 0.00 0.00 3.56
97 98 3.512724 GGGAGTAGTACAGTACCAAGCAA 59.487 47.826 7.13 0.00 0.00 3.91
98 99 3.094572 GGGAGTAGTACAGTACCAAGCA 58.905 50.000 7.13 0.00 0.00 3.91
99 100 3.363627 AGGGAGTAGTACAGTACCAAGC 58.636 50.000 7.13 0.00 0.00 4.01
100 101 4.857679 AGAGGGAGTAGTACAGTACCAAG 58.142 47.826 7.13 0.00 0.00 3.61
101 102 4.942363 AGAGGGAGTAGTACAGTACCAA 57.058 45.455 7.13 0.00 0.00 3.67
102 103 5.910003 AGATAGAGGGAGTAGTACAGTACCA 59.090 44.000 7.13 0.00 0.00 3.25
122 123 5.339008 AGTGCGACCAGTAATTCAAGATA 57.661 39.130 0.00 0.00 0.00 1.98
123 124 4.207891 AGTGCGACCAGTAATTCAAGAT 57.792 40.909 0.00 0.00 0.00 2.40
124 125 3.678056 AGTGCGACCAGTAATTCAAGA 57.322 42.857 0.00 0.00 0.00 3.02
127 128 3.449377 TGGATAGTGCGACCAGTAATTCA 59.551 43.478 0.00 0.00 31.03 2.57
134 135 2.868583 CAGAAATGGATAGTGCGACCAG 59.131 50.000 0.00 0.00 37.12 4.00
136 137 2.609459 CACAGAAATGGATAGTGCGACC 59.391 50.000 0.00 0.00 0.00 4.79
143 144 9.655769 CGAATTGTTTATCACAGAAATGGATAG 57.344 33.333 0.00 0.00 36.48 2.08
147 148 6.851609 TCCGAATTGTTTATCACAGAAATGG 58.148 36.000 0.00 0.00 36.48 3.16
156 157 6.311935 CGTACTCCTTTCCGAATTGTTTATCA 59.688 38.462 0.00 0.00 0.00 2.15
157 158 6.312180 ACGTACTCCTTTCCGAATTGTTTATC 59.688 38.462 0.00 0.00 0.00 1.75
159 160 5.540911 ACGTACTCCTTTCCGAATTGTTTA 58.459 37.500 0.00 0.00 0.00 2.01
160 161 4.383173 ACGTACTCCTTTCCGAATTGTTT 58.617 39.130 0.00 0.00 0.00 2.83
162 163 3.672767 ACGTACTCCTTTCCGAATTGT 57.327 42.857 0.00 0.00 0.00 2.71
163 164 3.991773 TGAACGTACTCCTTTCCGAATTG 59.008 43.478 0.00 0.00 0.00 2.32
167 168 3.731652 TTTGAACGTACTCCTTTCCGA 57.268 42.857 0.00 0.00 0.00 4.55
186 189 8.308207 AGGTAAATGTATGCATTAACGGTTTTT 58.692 29.630 9.58 0.53 43.89 1.94
188 191 7.338449 AGAGGTAAATGTATGCATTAACGGTTT 59.662 33.333 9.58 6.31 43.89 3.27
189 192 6.826741 AGAGGTAAATGTATGCATTAACGGTT 59.173 34.615 9.58 0.00 43.89 4.44
193 196 9.931210 GTTGTAGAGGTAAATGTATGCATTAAC 57.069 33.333 9.58 0.00 43.89 2.01
197 200 6.260936 GCAGTTGTAGAGGTAAATGTATGCAT 59.739 38.462 3.79 3.79 36.80 3.96
199 202 5.584649 TGCAGTTGTAGAGGTAAATGTATGC 59.415 40.000 0.00 0.00 0.00 3.14
238 251 1.340991 GGCTTCACCCTTTCATGCCTA 60.341 52.381 0.00 0.00 36.32 3.93
241 254 0.529378 CAGGCTTCACCCTTTCATGC 59.471 55.000 0.00 0.00 40.58 4.06
242 255 2.205022 TCAGGCTTCACCCTTTCATG 57.795 50.000 0.00 0.00 40.58 3.07
243 256 3.266772 TGTATCAGGCTTCACCCTTTCAT 59.733 43.478 0.00 0.00 40.58 2.57
244 257 2.642311 TGTATCAGGCTTCACCCTTTCA 59.358 45.455 0.00 0.00 40.58 2.69
270 285 5.659440 TTTCATAAGAAAATGTGGCTCCC 57.341 39.130 0.00 0.00 40.61 4.30
287 302 6.751888 CACAACTCGGTTTCTTTTCTTTTCAT 59.248 34.615 0.00 0.00 0.00 2.57
289 304 5.515270 CCACAACTCGGTTTCTTTTCTTTTC 59.485 40.000 0.00 0.00 0.00 2.29
290 305 5.047590 ACCACAACTCGGTTTCTTTTCTTTT 60.048 36.000 0.00 0.00 30.53 2.27
291 306 4.461431 ACCACAACTCGGTTTCTTTTCTTT 59.539 37.500 0.00 0.00 30.53 2.52
304 319 3.117794 TCTTTTGTACGACCACAACTCG 58.882 45.455 0.00 0.00 38.12 4.18
325 340 7.908827 TCATGTGCATGCAATCTTTAATTTT 57.091 28.000 24.58 0.00 38.65 1.82
329 344 5.593968 GGATCATGTGCATGCAATCTTTAA 58.406 37.500 24.58 4.88 38.65 1.52
334 349 1.335810 ACGGATCATGTGCATGCAATC 59.664 47.619 24.58 20.57 38.65 2.67
335 350 1.395635 ACGGATCATGTGCATGCAAT 58.604 45.000 24.58 12.61 38.65 3.56
336 351 1.135344 CAACGGATCATGTGCATGCAA 60.135 47.619 24.58 13.36 38.65 4.08
428 448 2.224079 CGTTTGTCAGGACAGACCATTG 59.776 50.000 15.00 0.92 41.68 2.82
429 449 2.158813 ACGTTTGTCAGGACAGACCATT 60.159 45.455 15.00 0.74 41.68 3.16
466 486 1.507141 CTTGACACGTCCAGGCAACC 61.507 60.000 0.00 0.00 37.17 3.77
545 565 8.925788 GCTCGAAGCTAAAACATTAATATCAG 57.074 34.615 0.00 0.00 38.45 2.90
599 622 6.260936 CCACACTTATCCCAATTAAGTAGCAG 59.739 42.308 0.00 0.00 33.26 4.24
601 624 5.008712 GCCACACTTATCCCAATTAAGTAGC 59.991 44.000 0.00 0.00 33.26 3.58
685 716 2.092968 TGGCCTCATAAGCGAACAGATT 60.093 45.455 3.32 0.00 0.00 2.40
686 717 1.486310 TGGCCTCATAAGCGAACAGAT 59.514 47.619 3.32 0.00 0.00 2.90
687 718 0.901827 TGGCCTCATAAGCGAACAGA 59.098 50.000 3.32 0.00 0.00 3.41
688 719 1.134699 TCTGGCCTCATAAGCGAACAG 60.135 52.381 3.32 0.00 0.00 3.16
689 720 0.901827 TCTGGCCTCATAAGCGAACA 59.098 50.000 3.32 0.00 0.00 3.18
690 721 1.666189 GTTCTGGCCTCATAAGCGAAC 59.334 52.381 3.32 0.66 0.00 3.95
692 723 0.901827 TGTTCTGGCCTCATAAGCGA 59.098 50.000 3.32 0.00 0.00 4.93
693 724 1.737838 TTGTTCTGGCCTCATAAGCG 58.262 50.000 3.32 0.00 0.00 4.68
694 725 4.276926 CCTAATTGTTCTGGCCTCATAAGC 59.723 45.833 3.32 0.00 0.00 3.09
695 726 5.684704 TCCTAATTGTTCTGGCCTCATAAG 58.315 41.667 3.32 0.00 0.00 1.73
696 727 5.708736 TCCTAATTGTTCTGGCCTCATAA 57.291 39.130 3.32 0.00 0.00 1.90
697 728 5.684704 CTTCCTAATTGTTCTGGCCTCATA 58.315 41.667 3.32 0.00 0.00 2.15
698 729 4.530875 CTTCCTAATTGTTCTGGCCTCAT 58.469 43.478 3.32 0.00 0.00 2.90
705 737 5.712152 AAGTTGGCTTCCTAATTGTTCTG 57.288 39.130 0.00 0.00 0.00 3.02
743 781 1.957877 GGTAGAGCCGTAGAGCTGAAT 59.042 52.381 0.00 0.00 45.15 2.57
797 835 7.931407 ACGCACCTGTCTGATTATATTGATAAA 59.069 33.333 0.00 0.00 31.28 1.40
832 870 6.295067 GCCTCTCTTTGCCTTTTTGGTAATTA 60.295 38.462 0.00 0.00 40.09 1.40
845 884 1.065126 ACATACCTGCCTCTCTTTGCC 60.065 52.381 0.00 0.00 0.00 4.52
904 943 6.817184 TGTGTCTTTGAAAAGAGCTACTACT 58.183 36.000 5.74 0.00 45.01 2.57
905 944 7.600752 AGATGTGTCTTTGAAAAGAGCTACTAC 59.399 37.037 5.74 5.33 45.01 2.73
906 945 7.600375 CAGATGTGTCTTTGAAAAGAGCTACTA 59.400 37.037 5.74 0.10 45.01 1.82
970 1009 3.217681 ACATACGTGTGGGGTCTTTTT 57.782 42.857 17.05 0.00 37.14 1.94
977 1017 2.486592 GGAAAAGAACATACGTGTGGGG 59.513 50.000 17.05 0.00 38.92 4.96
1022 1062 1.469703 TGCTCCGCTGAAATGACAATG 59.530 47.619 0.00 0.00 0.00 2.82
1096 1136 7.596494 CATAGCTCTTGATGAAAGGAAACAAA 58.404 34.615 0.00 0.00 36.46 2.83
1098 1138 5.124457 GCATAGCTCTTGATGAAAGGAAACA 59.876 40.000 0.00 0.00 36.46 2.83
1099 1139 5.124457 TGCATAGCTCTTGATGAAAGGAAAC 59.876 40.000 0.00 0.00 36.46 2.78
1104 1144 5.511571 CATGTGCATAGCTCTTGATGAAAG 58.488 41.667 0.00 0.00 37.22 2.62
1164 1223 3.660865 CGTGTGGTATATAAAGAGGGGC 58.339 50.000 0.00 0.00 0.00 5.80
1213 1284 1.166531 GCTCAGCTCGGTGTGGTTTT 61.167 55.000 0.00 0.00 0.00 2.43
1222 1293 1.140589 CACAGTAGGCTCAGCTCGG 59.859 63.158 0.00 0.00 0.00 4.63
1290 1403 2.378634 CGCCTCCCCCATTCTCCTT 61.379 63.158 0.00 0.00 0.00 3.36
1293 1406 4.570874 GGCGCCTCCCCCATTCTC 62.571 72.222 22.15 0.00 0.00 2.87
1644 1766 1.913762 ACCGTCACCAGCTAGGCTT 60.914 57.895 0.00 0.00 43.14 4.35
1706 1835 4.399618 TCTCCATTGAGCAGTAGTGAGTAC 59.600 45.833 0.42 0.00 38.58 2.73
1792 1930 4.952262 TGTAGCAATGCAATCTTCAGAC 57.048 40.909 8.35 0.00 0.00 3.51
1901 2040 1.640428 CACAGTACCATACAGCACCG 58.360 55.000 0.00 0.00 0.00 4.94
2009 2167 5.463392 CACGGAATCACAGATCAATTATCGT 59.537 40.000 0.00 1.50 39.79 3.73
2083 2248 5.221422 GCTTGTAGTCTCTCTCCAGCATTAT 60.221 44.000 0.00 0.00 0.00 1.28
2084 2249 4.098654 GCTTGTAGTCTCTCTCCAGCATTA 59.901 45.833 0.00 0.00 0.00 1.90
2085 2250 3.118811 GCTTGTAGTCTCTCTCCAGCATT 60.119 47.826 0.00 0.00 0.00 3.56
2086 2251 2.430332 GCTTGTAGTCTCTCTCCAGCAT 59.570 50.000 0.00 0.00 0.00 3.79
2087 2252 1.821753 GCTTGTAGTCTCTCTCCAGCA 59.178 52.381 0.00 0.00 0.00 4.41
2088 2253 1.821753 TGCTTGTAGTCTCTCTCCAGC 59.178 52.381 0.00 0.00 0.00 4.85
2089 2254 4.159321 TCATTGCTTGTAGTCTCTCTCCAG 59.841 45.833 0.00 0.00 0.00 3.86
2090 2255 4.089361 TCATTGCTTGTAGTCTCTCTCCA 58.911 43.478 0.00 0.00 0.00 3.86
2091 2256 4.727507 TCATTGCTTGTAGTCTCTCTCC 57.272 45.455 0.00 0.00 0.00 3.71
2092 2257 4.566360 GCTTCATTGCTTGTAGTCTCTCTC 59.434 45.833 0.00 0.00 0.00 3.20
2093 2258 4.020751 TGCTTCATTGCTTGTAGTCTCTCT 60.021 41.667 0.00 0.00 0.00 3.10
2094 2259 4.248859 TGCTTCATTGCTTGTAGTCTCTC 58.751 43.478 0.00 0.00 0.00 3.20
2095 2260 4.277515 TGCTTCATTGCTTGTAGTCTCT 57.722 40.909 0.00 0.00 0.00 3.10
2124 2289 1.737793 GATCACGGAATTTCGGCAACT 59.262 47.619 11.59 0.00 0.00 3.16
2247 2412 1.070601 ACATGCACAGACTGTACTGCA 59.929 47.619 18.29 18.29 41.06 4.41
2248 2413 1.462283 CACATGCACAGACTGTACTGC 59.538 52.381 8.02 8.65 41.06 4.40
2333 2498 4.327680 CCGACTTCAATCCTCTCCTTTTT 58.672 43.478 0.00 0.00 0.00 1.94
2367 2532 3.106986 AACCCCGGCTCCATCATCG 62.107 63.158 0.00 0.00 0.00 3.84
2378 2543 3.053896 GGCTTCGTTCAACCCCGG 61.054 66.667 0.00 0.00 0.00 5.73
2381 2546 2.677979 GCTCGGCTTCGTTCAACCC 61.678 63.158 0.00 0.00 35.06 4.11
2382 2547 2.677979 GGCTCGGCTTCGTTCAACC 61.678 63.158 0.00 0.00 35.06 3.77
2384 2549 1.227704 TTGGCTCGGCTTCGTTCAA 60.228 52.632 0.00 0.00 35.06 2.69
2597 2825 0.688487 TAGTAGGTTTGGCTGGCGTT 59.312 50.000 0.00 0.00 0.00 4.84


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

AutoCloner maintained by Alex Coulton.