Multiple sequence alignment - TraesCS1B01G288900

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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 TraesCS1B01G288900 chr1B 100.000 2237 0 0 1 2237 503622649 503624885 0.000000e+00 4132
1 TraesCS1B01G288900 chr1D 90.140 1785 102 46 473 2237 376859807 376861537 0.000000e+00 2254
2 TraesCS1B01G288900 chr1D 85.075 335 14 12 134 462 376859434 376859738 2.160000e-80 309
3 TraesCS1B01G288900 chr1D 89.600 125 7 4 28 152 376859303 376859421 1.070000e-33 154
4 TraesCS1B01G288900 chr1A 89.602 1029 68 26 882 1901 477022965 477023963 0.000000e+00 1271
5 TraesCS1B01G288900 chr1A 86.039 308 20 9 107 412 477022135 477022421 2.160000e-80 309
6 TraesCS1B01G288900 chr4A 95.455 88 4 0 795 882 350267429 350267516 8.330000e-30 141
7 TraesCS1B01G288900 chr2B 95.455 88 4 0 795 882 357538919 357539006 8.330000e-30 141
8 TraesCS1B01G288900 chr3B 94.318 88 5 0 795 882 797564774 797564687 3.880000e-28 135


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 TraesCS1B01G288900 chr1B 503622649 503624885 2236 False 4132.000000 4132 100.000000 1 2237 1 chr1B.!!$F1 2236
1 TraesCS1B01G288900 chr1D 376859303 376861537 2234 False 905.666667 2254 88.271667 28 2237 3 chr1D.!!$F1 2209
2 TraesCS1B01G288900 chr1A 477022135 477023963 1828 False 790.000000 1271 87.820500 107 1901 2 chr1A.!!$F1 1794

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
360 407 0.104487 GTAAGGAACCCTAGCTCGCC 59.896 60.0 0.0 0.0 31.13 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1447 1659 1.140252 ACCTGCCGTCTAGTTTGTTGT 59.86 47.619 0.0 0.0 0.0 3.32 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
21 22 2.030562 CACTGTGTGGTCCGGTCC 59.969 66.667 11.20 11.20 0.00 4.46
22 23 3.612681 ACTGTGTGGTCCGGTCCG 61.613 66.667 13.27 3.60 0.00 4.79
48 49 1.005450 GTCCATAAAAGGTCTGGGCCA 59.995 52.381 5.85 5.85 0.00 5.36
74 75 2.345760 CCATGCCAGCCCAACTCAC 61.346 63.158 0.00 0.00 0.00 3.51
76 77 1.303888 ATGCCAGCCCAACTCACAG 60.304 57.895 0.00 0.00 0.00 3.66
77 78 1.782201 ATGCCAGCCCAACTCACAGA 61.782 55.000 0.00 0.00 0.00 3.41
78 79 1.968540 GCCAGCCCAACTCACAGAC 60.969 63.158 0.00 0.00 0.00 3.51
79 80 1.451504 CCAGCCCAACTCACAGACA 59.548 57.895 0.00 0.00 0.00 3.41
80 81 0.179020 CCAGCCCAACTCACAGACAA 60.179 55.000 0.00 0.00 0.00 3.18
81 82 1.546323 CCAGCCCAACTCACAGACAAT 60.546 52.381 0.00 0.00 0.00 2.71
82 83 2.290260 CCAGCCCAACTCACAGACAATA 60.290 50.000 0.00 0.00 0.00 1.90
83 84 3.005554 CAGCCCAACTCACAGACAATAG 58.994 50.000 0.00 0.00 0.00 1.73
147 148 3.057969 TGTTCTAACCGTCCGTCTCTA 57.942 47.619 0.00 0.00 0.00 2.43
152 153 0.754587 AACCGTCCGTCTCTATCCCC 60.755 60.000 0.00 0.00 0.00 4.81
155 156 0.890090 CGTCCGTCTCTATCCCCTCC 60.890 65.000 0.00 0.00 0.00 4.30
156 157 0.479378 GTCCGTCTCTATCCCCTCCT 59.521 60.000 0.00 0.00 0.00 3.69
157 158 0.772384 TCCGTCTCTATCCCCTCCTC 59.228 60.000 0.00 0.00 0.00 3.71
158 159 0.251430 CCGTCTCTATCCCCTCCTCC 60.251 65.000 0.00 0.00 0.00 4.30
196 228 2.408022 CCGTTCTCCGCTCCGTAG 59.592 66.667 0.00 0.00 34.38 3.51
199 231 0.169672 CGTTCTCCGCTCCGTAGAAA 59.830 55.000 0.00 0.00 31.41 2.52
200 232 1.401931 CGTTCTCCGCTCCGTAGAAAA 60.402 52.381 0.00 0.00 31.41 2.29
201 233 2.260481 GTTCTCCGCTCCGTAGAAAAG 58.740 52.381 0.00 0.00 31.41 2.27
202 234 1.830279 TCTCCGCTCCGTAGAAAAGA 58.170 50.000 0.00 0.00 0.00 2.52
203 235 2.165167 TCTCCGCTCCGTAGAAAAGAA 58.835 47.619 0.00 0.00 0.00 2.52
204 236 2.559668 TCTCCGCTCCGTAGAAAAGAAA 59.440 45.455 0.00 0.00 0.00 2.52
216 248 4.797912 AGAAAAGAAAAGGACAGGGACT 57.202 40.909 0.00 0.00 43.88 3.85
231 263 1.726533 GGACTAGAGCCGTTCTCCCG 61.727 65.000 0.00 0.00 42.90 5.14
256 288 2.365408 GGAATCCGAACTCGTCAACT 57.635 50.000 0.00 0.00 37.74 3.16
257 289 2.260481 GGAATCCGAACTCGTCAACTC 58.740 52.381 0.00 0.00 37.74 3.01
258 290 1.912110 GAATCCGAACTCGTCAACTCG 59.088 52.381 0.00 0.00 37.74 4.18
259 291 1.162698 ATCCGAACTCGTCAACTCGA 58.837 50.000 0.00 0.00 37.74 4.04
260 292 0.236711 TCCGAACTCGTCAACTCGAC 59.763 55.000 0.00 0.00 41.62 4.20
267 299 4.647654 GTCAACTCGACGAGCCAA 57.352 55.556 24.38 7.15 34.19 4.52
268 300 2.895039 GTCAACTCGACGAGCCAAA 58.105 52.632 24.38 5.32 34.19 3.28
269 301 0.507358 GTCAACTCGACGAGCCAAAC 59.493 55.000 24.38 13.44 34.19 2.93
270 302 0.599204 TCAACTCGACGAGCCAAACC 60.599 55.000 24.38 0.00 32.04 3.27
271 303 0.600255 CAACTCGACGAGCCAAACCT 60.600 55.000 24.38 0.06 32.04 3.50
272 304 0.319641 AACTCGACGAGCCAAACCTC 60.320 55.000 24.38 0.00 32.04 3.85
360 407 0.104487 GTAAGGAACCCTAGCTCGCC 59.896 60.000 0.00 0.00 31.13 5.54
445 505 2.936829 TTCAGAGCGCGCGATCGATT 62.937 55.000 37.90 21.77 38.10 3.34
517 677 9.559958 GGGATAAAACAGCATAATTCATAATCG 57.440 33.333 0.00 0.00 0.00 3.34
534 719 2.519377 TCGGCAGGATTTATACCGTG 57.481 50.000 0.00 0.00 44.17 4.94
535 720 1.069513 TCGGCAGGATTTATACCGTGG 59.930 52.381 0.00 0.00 44.17 4.94
545 730 5.361571 GGATTTATACCGTGGTTGGGAAAAT 59.638 40.000 0.00 0.00 0.00 1.82
554 741 5.992217 CCGTGGTTGGGAAAATTTTAATTGA 59.008 36.000 2.75 0.00 0.00 2.57
596 783 5.815233 TTGAACTTATTTTGAATGGGGCA 57.185 34.783 0.00 0.00 0.00 5.36
751 955 2.965831 AGCTTATGCCGGATGAACTCTA 59.034 45.455 5.05 0.00 40.80 2.43
765 971 0.381089 ACTCTAGTGCGCGATACACC 59.619 55.000 12.10 0.00 38.87 4.16
825 1031 6.151817 AGGAAATGTTTCAGACAGAATAAGGC 59.848 38.462 7.69 0.00 42.62 4.35
849 1055 4.275936 GCTGGAGTGAAGAAGCTACAAAAA 59.724 41.667 0.00 0.00 32.82 1.94
890 1096 5.880332 ACCGAGAACTACATTACAATTGCAT 59.120 36.000 5.05 0.00 0.00 3.96
942 1149 4.998033 CAGAGGGTTAAAAAGGACTGTCTC 59.002 45.833 7.85 0.00 0.00 3.36
1006 1213 1.832998 CTTATTTTGCAGGCATGGGGT 59.167 47.619 0.00 0.00 0.00 4.95
1038 1245 3.719871 TCTTGAGGGTGTCCTGCTTATA 58.280 45.455 0.00 0.00 45.05 0.98
1164 1371 3.517100 AGATGATTGGCCTCATATACGCT 59.483 43.478 7.44 0.00 36.01 5.07
1259 1466 4.907875 ACAGTGGGAAGTGGTATGCTATAT 59.092 41.667 0.00 0.00 0.00 0.86
1280 1490 2.495084 AGTTCTTCGGTTTGCTTCCTC 58.505 47.619 0.00 0.00 0.00 3.71
1313 1524 5.819901 AGATATTTGCACTCAACTAGGCTTC 59.180 40.000 0.00 0.00 30.75 3.86
1347 1558 0.955919 GTGCTTCACCCCTTCTTCCG 60.956 60.000 0.00 0.00 0.00 4.30
1384 1596 2.420022 GGTTGTATAGCTGTGCCTTGTG 59.580 50.000 0.00 0.00 0.00 3.33
1441 1653 7.876068 TCAGCTACTAATTTATTGGTTATCCGG 59.124 37.037 0.00 0.00 33.39 5.14
1442 1654 7.119262 CAGCTACTAATTTATTGGTTATCCGGG 59.881 40.741 0.00 0.00 33.39 5.73
1443 1655 7.016858 AGCTACTAATTTATTGGTTATCCGGGA 59.983 37.037 0.00 0.00 33.39 5.14
1444 1656 7.118825 GCTACTAATTTATTGGTTATCCGGGAC 59.881 40.741 0.00 0.00 33.39 4.46
1445 1657 6.902408 ACTAATTTATTGGTTATCCGGGACA 58.098 36.000 0.00 0.00 36.30 4.02
1446 1658 7.348033 ACTAATTTATTGGTTATCCGGGACAA 58.652 34.615 0.00 0.00 36.30 3.18
1447 1659 7.835181 ACTAATTTATTGGTTATCCGGGACAAA 59.165 33.333 0.00 0.00 36.30 2.83
1453 1665 2.885894 GGTTATCCGGGACAAACAACAA 59.114 45.455 19.95 0.00 0.00 2.83
1463 1675 3.547413 GGACAAACAACAAACTAGACGGC 60.547 47.826 0.00 0.00 0.00 5.68
1503 1715 9.681692 TGATCTTTCATTGTTCTTTTGTATGTG 57.318 29.630 0.00 0.00 0.00 3.21
1526 1738 4.207635 GCATGATGTATTTGCATTTGTCCG 59.792 41.667 0.00 0.00 36.40 4.79
1587 1799 8.415553 TGCATGATGGACTTTTTATTATGAAGG 58.584 33.333 0.00 0.00 0.00 3.46
1642 1855 6.291648 AGCATCAGAGAAGTTCTTATGTGA 57.708 37.500 6.88 8.90 38.98 3.58
1672 1885 2.420687 GGAGTGCCTCTCATAAACCAGG 60.421 54.545 8.01 0.00 44.40 4.45
1695 1910 7.802117 AGGCACTGTAGTATTATATGTTTGGT 58.198 34.615 0.00 0.00 37.18 3.67
1697 1912 8.899771 GGCACTGTAGTATTATATGTTTGGTTT 58.100 33.333 0.00 0.00 0.00 3.27
1715 1930 4.652822 GGTTTTCACCACTTCTATGGAGT 58.347 43.478 0.00 0.00 43.02 3.85
1718 1933 6.295688 GGTTTTCACCACTTCTATGGAGTAGA 60.296 42.308 0.00 0.00 43.02 2.59
1719 1934 6.531503 TTTCACCACTTCTATGGAGTAGAG 57.468 41.667 0.00 0.00 43.02 2.43
1727 1942 8.138712 CCACTTCTATGGAGTAGAGTATTTCAC 58.861 40.741 0.00 0.00 43.02 3.18
1814 2031 2.422127 CGTGGGTGTCATTTATTGGACC 59.578 50.000 0.00 0.00 33.09 4.46
1818 2035 3.119137 GGGTGTCATTTATTGGACCTTGC 60.119 47.826 0.00 0.00 33.09 4.01
1856 2074 7.238723 TGAATACAGGTTATGGCCATTCCTATA 59.761 37.037 29.49 25.59 35.26 1.31
1863 2081 7.184570 AGGTTATGGCCATTCCTATATGTGTAT 59.815 37.037 29.17 10.81 35.26 2.29
1982 2200 9.359653 TCCTTGAGATTTGAATTTTCTTCTTCT 57.640 29.630 0.00 0.00 0.00 2.85
1983 2201 9.978044 CCTTGAGATTTGAATTTTCTTCTTCTT 57.022 29.630 0.00 0.00 0.00 2.52
2021 2239 2.029728 GTCATCATCAAAGACGGAAGCG 59.970 50.000 0.00 0.00 0.00 4.68
2051 2269 5.039333 GGATAAATTCTTGCATGTGCTCAC 58.961 41.667 6.55 0.00 42.66 3.51
2075 2293 5.670792 ACGGAGTGTAGAACCATGATTTA 57.329 39.130 0.00 0.00 42.51 1.40
2133 2359 2.349297 ACACAGTTGCTACTAGTCGC 57.651 50.000 12.27 12.27 31.96 5.19
2136 2362 1.616865 ACAGTTGCTACTAGTCGCCAA 59.383 47.619 16.05 7.63 31.96 4.52
2142 2368 6.037172 CAGTTGCTACTAGTCGCCAAATTTAT 59.963 38.462 16.05 0.00 31.96 1.40
2149 2375 4.609691 AGTCGCCAAATTTATTGTACCG 57.390 40.909 0.00 0.00 0.00 4.02
2180 2406 8.846943 ATACAAAACATTTTCCAAAATCCTCC 57.153 30.769 0.00 0.00 36.52 4.30
2181 2407 6.657875 ACAAAACATTTTCCAAAATCCTCCA 58.342 32.000 0.00 0.00 36.52 3.86
2182 2408 7.289310 ACAAAACATTTTCCAAAATCCTCCAT 58.711 30.769 0.00 0.00 36.52 3.41
2183 2409 7.229106 ACAAAACATTTTCCAAAATCCTCCATG 59.771 33.333 0.00 0.00 36.52 3.66
2184 2410 6.684897 AACATTTTCCAAAATCCTCCATGA 57.315 33.333 0.00 0.00 36.52 3.07
2185 2411 6.684897 ACATTTTCCAAAATCCTCCATGAA 57.315 33.333 0.00 0.00 36.52 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 2.030562 GGACCGGACCACACAGTG 59.969 66.667 18.62 0.00 0.00 3.66
5 6 3.612681 CGGACCGGACCACACAGT 61.613 66.667 22.85 0.00 0.00 3.55
18 19 2.490509 CCTTTTATGGACCAAACCGGAC 59.509 50.000 9.46 0.00 38.63 4.79
19 20 2.108601 ACCTTTTATGGACCAAACCGGA 59.891 45.455 9.46 0.00 38.63 5.14
20 21 2.490509 GACCTTTTATGGACCAAACCGG 59.509 50.000 0.00 0.00 42.50 5.28
21 22 3.190535 CAGACCTTTTATGGACCAAACCG 59.809 47.826 0.00 0.00 0.00 4.44
22 23 3.509967 CCAGACCTTTTATGGACCAAACC 59.490 47.826 0.00 0.00 36.09 3.27
23 24 3.509967 CCCAGACCTTTTATGGACCAAAC 59.490 47.826 0.00 0.00 36.09 2.93
24 25 3.773560 CCCAGACCTTTTATGGACCAAA 58.226 45.455 0.00 0.00 36.09 3.28
25 26 2.556559 GCCCAGACCTTTTATGGACCAA 60.557 50.000 0.00 0.00 36.09 3.67
26 27 1.005450 GCCCAGACCTTTTATGGACCA 59.995 52.381 0.00 0.00 36.09 4.02
74 75 5.784750 TTCGAAAGCACATCTATTGTCTG 57.215 39.130 0.00 0.00 36.00 3.51
76 77 6.408858 TCTTTCGAAAGCACATCTATTGTC 57.591 37.500 29.10 0.00 33.74 3.18
77 78 6.801539 TTCTTTCGAAAGCACATCTATTGT 57.198 33.333 29.10 0.00 35.27 2.71
78 79 8.506140 TTTTTCTTTCGAAAGCACATCTATTG 57.494 30.769 29.10 6.08 40.04 1.90
79 80 7.809806 CCTTTTTCTTTCGAAAGCACATCTATT 59.190 33.333 29.10 0.00 40.04 1.73
80 81 7.174946 TCCTTTTTCTTTCGAAAGCACATCTAT 59.825 33.333 29.10 0.00 40.04 1.98
81 82 6.485313 TCCTTTTTCTTTCGAAAGCACATCTA 59.515 34.615 29.10 10.62 40.04 1.98
82 83 5.299279 TCCTTTTTCTTTCGAAAGCACATCT 59.701 36.000 29.10 0.00 40.04 2.90
83 84 5.519722 TCCTTTTTCTTTCGAAAGCACATC 58.480 37.500 29.10 0.00 40.04 3.06
87 88 5.212194 CGATTCCTTTTTCTTTCGAAAGCA 58.788 37.500 29.10 18.79 40.04 3.91
120 121 1.538512 GGACGGTTAGAACAAAAGGCC 59.461 52.381 0.00 0.00 0.00 5.19
196 228 5.866207 TCTAGTCCCTGTCCTTTTCTTTTC 58.134 41.667 0.00 0.00 0.00 2.29
199 231 3.262151 GCTCTAGTCCCTGTCCTTTTCTT 59.738 47.826 0.00 0.00 0.00 2.52
200 232 2.835156 GCTCTAGTCCCTGTCCTTTTCT 59.165 50.000 0.00 0.00 0.00 2.52
201 233 2.093394 GGCTCTAGTCCCTGTCCTTTTC 60.093 54.545 0.00 0.00 0.00 2.29
202 234 1.909986 GGCTCTAGTCCCTGTCCTTTT 59.090 52.381 0.00 0.00 0.00 2.27
203 235 1.574263 GGCTCTAGTCCCTGTCCTTT 58.426 55.000 0.00 0.00 0.00 3.11
204 236 0.684805 CGGCTCTAGTCCCTGTCCTT 60.685 60.000 0.00 0.00 0.00 3.36
256 288 2.257371 CGAGGTTTGGCTCGTCGA 59.743 61.111 11.87 0.00 42.95 4.20
257 289 3.479269 GCGAGGTTTGGCTCGTCG 61.479 66.667 0.00 12.55 44.03 5.12
258 290 3.119096 GGCGAGGTTTGGCTCGTC 61.119 66.667 0.00 0.00 44.03 4.20
261 293 3.119096 GACGGCGAGGTTTGGCTC 61.119 66.667 16.62 0.00 0.00 4.70
360 407 3.250762 TCTCACGAATCAAAAACAGGCAG 59.749 43.478 0.00 0.00 0.00 4.85
445 505 0.043637 AATCCTACGGGTGGGAGGAA 59.956 55.000 9.81 0.00 43.65 3.36
465 525 8.022550 CGACATATGTATACAAACCACGGTATA 58.977 37.037 10.14 0.00 32.72 1.47
466 526 6.864685 CGACATATGTATACAAACCACGGTAT 59.135 38.462 10.14 0.00 34.72 2.73
468 528 5.045215 CGACATATGTATACAAACCACGGT 58.955 41.667 10.14 1.93 0.00 4.83
469 529 4.446385 CCGACATATGTATACAAACCACGG 59.554 45.833 20.62 20.62 0.00 4.94
471 531 5.603596 TCCCGACATATGTATACAAACCAC 58.396 41.667 10.14 1.66 0.00 4.16
472 532 5.873146 TCCCGACATATGTATACAAACCA 57.127 39.130 10.14 0.00 0.00 3.67
476 536 9.483916 CTGTTTTATCCCGACATATGTATACAA 57.516 33.333 10.14 0.05 0.00 2.41
517 677 2.616842 CAACCACGGTATAAATCCTGCC 59.383 50.000 0.00 0.00 0.00 4.85
534 719 9.243637 GCTTTTTCAATTAAAATTTTCCCAACC 57.756 29.630 6.72 0.00 36.94 3.77
535 720 9.794685 TGCTTTTTCAATTAAAATTTTCCCAAC 57.205 25.926 6.72 0.00 36.94 3.77
545 730 7.548780 ACTGCAGTTCTGCTTTTTCAATTAAAA 59.451 29.630 15.25 0.15 35.24 1.52
554 741 4.098349 TCAATCACTGCAGTTCTGCTTTTT 59.902 37.500 18.94 8.93 35.49 1.94
559 746 2.551459 AGTTCAATCACTGCAGTTCTGC 59.449 45.455 18.94 16.65 0.00 4.26
596 783 5.922544 GCAGCAAATTAATCTGACACAAACT 59.077 36.000 6.79 0.00 0.00 2.66
653 840 0.811915 CCTACAGTCACAGTCCCTCG 59.188 60.000 0.00 0.00 0.00 4.63
751 955 0.100682 CTAGTGGTGTATCGCGCACT 59.899 55.000 16.87 16.87 37.07 4.40
765 971 6.094603 CCTTTTCCACAGAATGAATCCTAGTG 59.905 42.308 0.00 0.00 39.69 2.74
825 1031 1.067565 TGTAGCTTCTTCACTCCAGCG 60.068 52.381 0.00 0.00 37.35 5.18
901 1107 5.934043 CCCTCTGAATTTTGTTTCCAAATCC 59.066 40.000 0.00 0.00 40.14 3.01
942 1149 1.180029 CACAAGGAAAGGAGCCCATG 58.820 55.000 0.00 0.00 0.00 3.66
1006 1213 3.221771 CACCCTCAAGAAATGACCACAA 58.778 45.455 0.00 0.00 33.47 3.33
1259 1466 3.660865 GAGGAAGCAAACCGAAGAACTA 58.339 45.455 0.00 0.00 0.00 2.24
1280 1490 6.594284 TGAGTGCAAATATCTCAATCTTCG 57.406 37.500 1.72 0.00 35.65 3.79
1305 1515 6.199908 CACGAGAAGATTTACATGAAGCCTAG 59.800 42.308 0.00 0.00 0.00 3.02
1306 1516 6.042777 CACGAGAAGATTTACATGAAGCCTA 58.957 40.000 0.00 0.00 0.00 3.93
1313 1524 5.446473 GGTGAAGCACGAGAAGATTTACATG 60.446 44.000 0.00 0.00 34.83 3.21
1347 1558 8.552034 GCTATACAACCATCAACAAAGACTATC 58.448 37.037 0.00 0.00 0.00 2.08
1384 1596 2.679837 CACATCTCAACAGGGTGCATAC 59.320 50.000 0.00 0.00 0.00 2.39
1392 1604 2.031420 CACAACTGCACATCTCAACAGG 60.031 50.000 0.00 0.00 34.40 4.00
1422 1634 7.811117 TTGTCCCGGATAACCAATAAATTAG 57.189 36.000 0.73 0.00 35.59 1.73
1441 1653 3.547413 GCCGTCTAGTTTGTTGTTTGTCC 60.547 47.826 0.00 0.00 0.00 4.02
1442 1654 3.064271 TGCCGTCTAGTTTGTTGTTTGTC 59.936 43.478 0.00 0.00 0.00 3.18
1443 1655 3.011119 TGCCGTCTAGTTTGTTGTTTGT 58.989 40.909 0.00 0.00 0.00 2.83
1444 1656 3.548014 CCTGCCGTCTAGTTTGTTGTTTG 60.548 47.826 0.00 0.00 0.00 2.93
1445 1657 2.616842 CCTGCCGTCTAGTTTGTTGTTT 59.383 45.455 0.00 0.00 0.00 2.83
1446 1658 2.218603 CCTGCCGTCTAGTTTGTTGTT 58.781 47.619 0.00 0.00 0.00 2.83
1447 1659 1.140252 ACCTGCCGTCTAGTTTGTTGT 59.860 47.619 0.00 0.00 0.00 3.32
1463 1675 3.902881 AAGATCAGAGTTAGGCACCTG 57.097 47.619 0.00 0.00 0.00 4.00
1476 1688 9.903682 ACATACAAAAGAACAATGAAAGATCAG 57.096 29.630 0.00 0.00 39.39 2.90
1503 1715 4.207635 CGGACAAATGCAAATACATCATGC 59.792 41.667 0.00 0.00 40.45 4.06
1605 1818 6.060136 TCTCTGATGCTTCTATGAAAATGGG 58.940 40.000 0.88 0.00 0.00 4.00
1690 1905 5.450453 TCCATAGAAGTGGTGAAAACCAAA 58.550 37.500 0.00 0.00 42.10 3.28
1695 1910 6.497259 ACTCTACTCCATAGAAGTGGTGAAAA 59.503 38.462 2.38 0.00 39.52 2.29
1697 1912 5.580998 ACTCTACTCCATAGAAGTGGTGAA 58.419 41.667 2.38 0.00 39.52 3.18
1762 1977 9.241919 ACATTGAACACATATGATAAGAAACCA 57.758 29.630 10.38 0.00 0.00 3.67
1768 1983 9.213819 CGTTTGACATTGAACACATATGATAAG 57.786 33.333 10.38 0.00 0.00 1.73
1814 2031 5.447413 CTGTATTCAGAGCAATCACTGCAAG 60.447 44.000 0.00 0.00 46.06 4.01
1818 2035 4.511527 ACCTGTATTCAGAGCAATCACTG 58.488 43.478 0.12 0.00 43.76 3.66
1836 2053 5.649395 CACATATAGGAATGGCCATAACCTG 59.351 44.000 35.23 26.77 40.02 4.00
1863 2081 8.683615 TCTAAGCTCGTGTATCTTCAGAAATTA 58.316 33.333 0.00 0.00 0.00 1.40
1956 2174 9.359653 AGAAGAAGAAAATTCAAATCTCAAGGA 57.640 29.630 0.00 0.00 0.00 3.36
1975 2193 9.482627 ACAGTCAAGTAATAGTTCAAGAAGAAG 57.517 33.333 0.00 0.00 36.78 2.85
1978 2196 8.818141 TGACAGTCAAGTAATAGTTCAAGAAG 57.182 34.615 0.00 0.00 0.00 2.85
1980 2198 8.585018 TGATGACAGTCAAGTAATAGTTCAAGA 58.415 33.333 7.50 0.00 0.00 3.02
1981 2199 8.763049 TGATGACAGTCAAGTAATAGTTCAAG 57.237 34.615 7.50 0.00 0.00 3.02
1982 2200 9.371136 GATGATGACAGTCAAGTAATAGTTCAA 57.629 33.333 7.50 0.00 0.00 2.69
1983 2201 8.531146 TGATGATGACAGTCAAGTAATAGTTCA 58.469 33.333 7.50 3.78 0.00 3.18
1984 2202 8.932945 TGATGATGACAGTCAAGTAATAGTTC 57.067 34.615 7.50 0.00 0.00 3.01
1986 2204 9.376075 CTTTGATGATGACAGTCAAGTAATAGT 57.624 33.333 7.50 0.00 33.82 2.12
1987 2205 9.591792 TCTTTGATGATGACAGTCAAGTAATAG 57.408 33.333 7.50 0.98 33.82 1.73
1988 2206 9.371136 GTCTTTGATGATGACAGTCAAGTAATA 57.629 33.333 7.50 0.00 33.82 0.98
1989 2207 7.063898 CGTCTTTGATGATGACAGTCAAGTAAT 59.936 37.037 7.50 0.00 33.82 1.89
1990 2208 6.366061 CGTCTTTGATGATGACAGTCAAGTAA 59.634 38.462 7.50 0.00 33.82 2.24
1991 2209 5.863935 CGTCTTTGATGATGACAGTCAAGTA 59.136 40.000 7.50 0.00 33.82 2.24
1998 2216 3.063180 GCTTCCGTCTTTGATGATGACAG 59.937 47.826 0.00 0.00 33.27 3.51
2021 2239 7.464977 GCACATGCAAGAATTTATCCAAATGTC 60.465 37.037 0.00 0.00 41.59 3.06
2051 2269 1.471287 TCATGGTTCTACACTCCGTCG 59.529 52.381 0.00 0.00 0.00 5.12
2107 2333 7.585867 CGACTAGTAGCAACTGTGTATCATAT 58.414 38.462 0.00 0.00 36.36 1.78
2119 2345 4.680171 AAATTTGGCGACTAGTAGCAAC 57.320 40.909 26.27 12.65 32.66 4.17
2160 2386 7.077050 TCATGGAGGATTTTGGAAAATGTTT 57.923 32.000 2.06 0.00 38.64 2.83
2163 2389 7.982761 TTTTCATGGAGGATTTTGGAAAATG 57.017 32.000 2.06 0.00 38.64 2.32


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

AutoCloner maintained by Alex Coulton.