Multiple sequence alignment - TraesCS3A01G485300

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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 TraesCS3A01G485300 chr3A 100.000 1434 0 0 933 2366 714568159 714569592 0.000000e+00 2649.0
1 TraesCS3A01G485300 chr3A 96.559 1366 41 1 933 2292 66004004 66002639 0.000000e+00 2257.0
2 TraesCS3A01G485300 chr3A 100.000 677 0 0 1 677 714567227 714567903 0.000000e+00 1251.0
3 TraesCS3A01G485300 chr3A 96.066 610 19 4 72 677 66004641 66004033 0.000000e+00 989.0
4 TraesCS3A01G485300 chr5D 96.633 1366 40 1 933 2292 503246401 503247766 0.000000e+00 2263.0
5 TraesCS3A01G485300 chr5D 96.559 1366 41 1 933 2292 503263647 503262282 0.000000e+00 2257.0
6 TraesCS3A01G485300 chr2D 96.633 1366 40 1 933 2292 272811117 272809752 0.000000e+00 2263.0
7 TraesCS3A01G485300 chr2D 96.047 1366 48 1 933 2292 591985738 591987103 0.000000e+00 2218.0
8 TraesCS3A01G485300 chr2D 96.230 610 18 4 72 677 591985101 591985709 0.000000e+00 994.0
9 TraesCS3A01G485300 chr6D 96.486 1366 42 1 933 2292 389244693 389243328 0.000000e+00 2252.0
10 TraesCS3A01G485300 chr6D 96.066 610 19 4 72 677 389245330 389244722 0.000000e+00 989.0
11 TraesCS3A01G485300 chr2A 96.413 1366 43 1 933 2292 726905326 726903961 0.000000e+00 2246.0
12 TraesCS3A01G485300 chr3D 96.266 1366 44 2 933 2292 589262397 589261033 0.000000e+00 2233.0
13 TraesCS3A01G485300 chr3D 96.066 610 19 4 72 677 589263034 589262426 0.000000e+00 989.0
14 TraesCS3A01G485300 chr1D 96.193 1366 46 1 933 2292 254526735 254528100 0.000000e+00 2230.0
15 TraesCS3A01G485300 chr1D 96.230 610 18 4 72 677 459904225 459903617 0.000000e+00 994.0
16 TraesCS3A01G485300 chr1D 95.902 610 20 4 72 677 254526099 254526707 0.000000e+00 983.0
17 TraesCS3A01G485300 chr3B 96.393 610 17 4 72 677 201615448 201616056 0.000000e+00 1000.0
18 TraesCS3A01G485300 chr7B 96.230 610 18 4 72 677 662726896 662727504 0.000000e+00 994.0
19 TraesCS3A01G485300 chr5B 96.230 610 18 4 72 677 127808925 127809533 0.000000e+00 994.0
20 TraesCS3A01G485300 chr7D 98.701 77 1 0 2290 2366 38011139 38011215 1.140000e-28 137.0
21 TraesCS3A01G485300 chr7D 95.890 73 3 0 2290 2362 277904725 277904653 4.130000e-23 119.0
22 TraesCS3A01G485300 chr7A 90.141 71 6 1 2290 2360 316238476 316238545 9.010000e-15 91.6


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 TraesCS3A01G485300 chr3A 714567227 714569592 2365 False 1950.0 2649 100.0000 1 2366 2 chr3A.!!$F1 2365
1 TraesCS3A01G485300 chr3A 66002639 66004641 2002 True 1623.0 2257 96.3125 72 2292 2 chr3A.!!$R1 2220
2 TraesCS3A01G485300 chr5D 503246401 503247766 1365 False 2263.0 2263 96.6330 933 2292 1 chr5D.!!$F1 1359
3 TraesCS3A01G485300 chr5D 503262282 503263647 1365 True 2257.0 2257 96.5590 933 2292 1 chr5D.!!$R1 1359
4 TraesCS3A01G485300 chr2D 272809752 272811117 1365 True 2263.0 2263 96.6330 933 2292 1 chr2D.!!$R1 1359
5 TraesCS3A01G485300 chr2D 591985101 591987103 2002 False 1606.0 2218 96.1385 72 2292 2 chr2D.!!$F1 2220
6 TraesCS3A01G485300 chr6D 389243328 389245330 2002 True 1620.5 2252 96.2760 72 2292 2 chr6D.!!$R1 2220
7 TraesCS3A01G485300 chr2A 726903961 726905326 1365 True 2246.0 2246 96.4130 933 2292 1 chr2A.!!$R1 1359
8 TraesCS3A01G485300 chr3D 589261033 589263034 2001 True 1611.0 2233 96.1660 72 2292 2 chr3D.!!$R1 2220
9 TraesCS3A01G485300 chr1D 254526099 254528100 2001 False 1606.5 2230 96.0475 72 2292 2 chr1D.!!$F1 2220
10 TraesCS3A01G485300 chr1D 459903617 459904225 608 True 994.0 994 96.2300 72 677 1 chr1D.!!$R1 605
11 TraesCS3A01G485300 chr3B 201615448 201616056 608 False 1000.0 1000 96.3930 72 677 1 chr3B.!!$F1 605
12 TraesCS3A01G485300 chr7B 662726896 662727504 608 False 994.0 994 96.2300 72 677 1 chr7B.!!$F1 605
13 TraesCS3A01G485300 chr5B 127808925 127809533 608 False 994.0 994 96.2300 72 677 1 chr5B.!!$F1 605

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
76 77 0.179124 CTTCCTGCGGCTCTACTGAC 60.179 60.0 0.0 0.0 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1751 1762 0.449388 GGCTCATTCTTCAACAGGCG 59.551 55.0 0.0 0.0 0.0 5.52 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
17 18 4.095400 GGGGGAGGAGGAGGCTCA 62.095 72.222 17.69 0.00 0.00 4.26
18 19 2.445654 GGGGAGGAGGAGGCTCAG 60.446 72.222 17.69 0.00 0.00 3.35
19 20 2.445654 GGGAGGAGGAGGCTCAGG 60.446 72.222 17.69 0.00 0.00 3.86
20 21 2.693017 GGAGGAGGAGGCTCAGGA 59.307 66.667 17.69 0.00 0.00 3.86
21 22 1.457455 GGAGGAGGAGGCTCAGGAG 60.457 68.421 17.69 0.00 0.00 3.69
22 23 1.309688 GAGGAGGAGGCTCAGGAGT 59.690 63.158 17.69 0.00 0.00 3.85
23 24 0.755327 GAGGAGGAGGCTCAGGAGTC 60.755 65.000 17.69 4.35 0.00 3.36
24 25 2.124693 GGAGGAGGCTCAGGAGTCG 61.125 68.421 17.69 0.00 38.27 4.18
25 26 1.379309 GAGGAGGCTCAGGAGTCGT 60.379 63.158 17.69 0.00 38.27 4.34
26 27 0.968393 GAGGAGGCTCAGGAGTCGTT 60.968 60.000 17.69 0.00 38.27 3.85
27 28 0.968393 AGGAGGCTCAGGAGTCGTTC 60.968 60.000 17.69 0.00 38.27 3.95
28 29 1.137825 GAGGCTCAGGAGTCGTTCG 59.862 63.158 10.25 0.00 38.27 3.95
29 30 1.303398 AGGCTCAGGAGTCGTTCGA 60.303 57.895 0.00 0.00 38.27 3.71
30 31 1.137825 GGCTCAGGAGTCGTTCGAG 59.862 63.158 0.00 0.00 0.00 4.04
31 32 1.515304 GCTCAGGAGTCGTTCGAGC 60.515 63.158 8.79 8.79 41.98 5.03
32 33 1.137825 CTCAGGAGTCGTTCGAGCC 59.862 63.158 0.00 0.86 0.00 4.70
33 34 2.202492 CAGGAGTCGTTCGAGCCG 60.202 66.667 0.00 0.00 0.00 5.52
34 35 3.441290 AGGAGTCGTTCGAGCCGG 61.441 66.667 0.00 0.00 0.00 6.13
35 36 3.745803 GGAGTCGTTCGAGCCGGT 61.746 66.667 1.90 0.00 0.00 5.28
36 37 2.504244 GAGTCGTTCGAGCCGGTG 60.504 66.667 1.90 0.00 0.00 4.94
37 38 3.966026 GAGTCGTTCGAGCCGGTGG 62.966 68.421 1.90 0.00 0.00 4.61
38 39 4.047059 GTCGTTCGAGCCGGTGGA 62.047 66.667 1.90 0.00 0.00 4.02
39 40 3.744719 TCGTTCGAGCCGGTGGAG 61.745 66.667 1.90 0.00 0.00 3.86
40 41 4.796231 CGTTCGAGCCGGTGGAGG 62.796 72.222 1.90 0.00 0.00 4.30
41 42 3.379445 GTTCGAGCCGGTGGAGGA 61.379 66.667 1.90 0.00 0.00 3.71
42 43 3.379445 TTCGAGCCGGTGGAGGAC 61.379 66.667 1.90 0.00 0.00 3.85
45 46 3.827898 GAGCCGGTGGAGGACGAG 61.828 72.222 1.90 0.00 0.00 4.18
46 47 4.680537 AGCCGGTGGAGGACGAGT 62.681 66.667 1.90 0.00 0.00 4.18
47 48 3.692406 GCCGGTGGAGGACGAGTT 61.692 66.667 1.90 0.00 0.00 3.01
48 49 2.261671 CCGGTGGAGGACGAGTTG 59.738 66.667 0.00 0.00 0.00 3.16
49 50 2.261671 CGGTGGAGGACGAGTTGG 59.738 66.667 0.00 0.00 0.00 3.77
50 51 2.571216 CGGTGGAGGACGAGTTGGT 61.571 63.158 0.00 0.00 0.00 3.67
51 52 1.004918 GGTGGAGGACGAGTTGGTG 60.005 63.158 0.00 0.00 0.00 4.17
52 53 1.668151 GTGGAGGACGAGTTGGTGC 60.668 63.158 0.00 0.00 0.00 5.01
53 54 1.837051 TGGAGGACGAGTTGGTGCT 60.837 57.895 0.00 0.00 41.62 4.40
54 55 1.374758 GGAGGACGAGTTGGTGCTG 60.375 63.158 0.00 0.00 38.82 4.41
55 56 2.029844 GAGGACGAGTTGGTGCTGC 61.030 63.158 0.00 0.00 38.82 5.25
56 57 2.280797 GGACGAGTTGGTGCTGCA 60.281 61.111 0.00 0.00 0.00 4.41
57 58 2.607892 GGACGAGTTGGTGCTGCAC 61.608 63.158 24.02 24.02 0.00 4.57
58 59 1.595382 GACGAGTTGGTGCTGCACT 60.595 57.895 29.54 12.21 34.40 4.40
59 60 1.153168 ACGAGTTGGTGCTGCACTT 60.153 52.632 29.54 14.51 34.40 3.16
60 61 1.160329 ACGAGTTGGTGCTGCACTTC 61.160 55.000 29.54 20.03 34.40 3.01
61 62 1.845809 CGAGTTGGTGCTGCACTTCC 61.846 60.000 29.54 15.91 34.40 3.46
62 63 0.536006 GAGTTGGTGCTGCACTTCCT 60.536 55.000 29.54 21.46 34.40 3.36
63 64 0.820891 AGTTGGTGCTGCACTTCCTG 60.821 55.000 29.54 0.00 34.40 3.86
76 77 0.179124 CTTCCTGCGGCTCTACTGAC 60.179 60.000 0.00 0.00 0.00 3.51
97 100 2.744202 CACATGCCACTGAAAGACTACC 59.256 50.000 0.00 0.00 37.43 3.18
114 117 3.581332 ACTACCGAGACAAAAAGATGGGA 59.419 43.478 0.00 0.00 0.00 4.37
142 146 4.901785 AAAGGTAGAGAGGTAGGATGGA 57.098 45.455 0.00 0.00 0.00 3.41
167 171 6.613271 ACAGTTGGTCAGATCTAGTATGGATT 59.387 38.462 0.00 0.00 35.97 3.01
206 210 4.444081 ACGGCGGCTCTCCTAGGT 62.444 66.667 13.24 0.00 0.00 3.08
251 255 1.376649 AGAGGATCAAGTTGGCCCTT 58.623 50.000 15.10 0.00 37.82 3.95
276 280 5.817296 TGCGAATAACTTGATGCACTATCTT 59.183 36.000 0.00 0.00 36.71 2.40
414 418 1.035932 CACGGACCGACCATAGACCT 61.036 60.000 23.38 0.00 38.90 3.85
416 420 1.064463 ACGGACCGACCATAGACCTTA 60.064 52.381 23.38 0.00 38.90 2.69
500 504 4.148891 GCAATCACTCGTTCTTAAAACCG 58.851 43.478 0.00 0.00 0.00 4.44
510 514 5.121142 TCGTTCTTAAAACCGGCATTCTTAG 59.879 40.000 0.00 0.00 0.00 2.18
528 532 0.984230 AGGATCAAAGAGTCGGGCAA 59.016 50.000 0.00 0.00 0.00 4.52
561 565 0.905337 CTCCCCGTTCCTGGTTCTCT 60.905 60.000 0.00 0.00 0.00 3.10
613 617 6.745857 AATCCTTAGAATGGGATTCCAACTT 58.254 36.000 0.00 0.00 45.84 2.66
990 995 1.553704 CCTAAGAGGCGGTGGTTTACT 59.446 52.381 0.00 0.00 0.00 2.24
1007 1012 1.188219 ACTCTGTGGCGGATGTCAGT 61.188 55.000 0.00 0.00 0.00 3.41
1138 1149 7.378966 TGATAAGATCCTTCCATTTAGTAGCG 58.621 38.462 0.00 0.00 0.00 4.26
1230 1241 1.305381 CCCAGAGACGAGGAAGGGT 60.305 63.158 0.00 0.00 0.00 4.34
1248 1259 1.060698 GGTGTAGCAAGCGACGAAATC 59.939 52.381 0.00 0.00 0.00 2.17
1278 1289 6.073003 GGGGAGTTGAAAATAAGCATAGATCG 60.073 42.308 0.00 0.00 0.00 3.69
1325 1336 1.251251 AAACTGCCTGCTGAATCCAC 58.749 50.000 2.88 0.00 0.00 4.02
1372 1383 5.812642 CGAACTGAAACATCTTAGTAGCCAT 59.187 40.000 0.00 0.00 0.00 4.40
1521 1532 2.040178 ACCCTAGATGGCTAAAGTCCG 58.960 52.381 0.00 0.00 0.00 4.79
1569 1580 1.001120 TGACCCGAGTAGCATGGGA 59.999 57.895 3.03 0.00 46.41 4.37
1630 1641 2.127708 AGGCTAAATACTCCTGGGTGG 58.872 52.381 0.00 0.00 37.10 4.61
1657 1668 1.068741 GCGAAGTAGTACCATGAGGGG 59.931 57.143 0.00 0.00 42.91 4.79
1704 1715 6.149807 GGGTAATGAAATAGAACGTGAAACCA 59.850 38.462 0.00 0.00 0.00 3.67
1751 1762 0.737715 AAAGTGATCTCTGACCGCGC 60.738 55.000 0.00 0.00 0.00 6.86
1951 1962 3.254060 ACCGACTGATGTTGAAGAATCG 58.746 45.455 0.00 0.00 0.00 3.34
1955 1966 2.270923 CTGATGTTGAAGAATCGGCGA 58.729 47.619 13.87 13.87 0.00 5.54
1984 1995 1.148027 TGGTTAGGGGTGAAATGCCAA 59.852 47.619 0.00 0.00 0.00 4.52
1987 1998 3.096092 GTTAGGGGTGAAATGCCAATCA 58.904 45.455 0.00 0.00 0.00 2.57
2001 2012 2.619074 GCCAATCAAACCCAGAGCTAGT 60.619 50.000 0.00 0.00 0.00 2.57
2018 2029 3.118519 GCTAGTTGGTTCTCCCCGAAATA 60.119 47.826 0.00 0.00 32.41 1.40
2076 2088 3.416490 CACTGTTTCGGTGCGGTT 58.584 55.556 0.00 0.00 33.85 4.44
2188 2200 3.243434 GGGATAAGCTTCATCGTCGAGAA 60.243 47.826 0.00 4.27 0.00 2.87
2196 2208 3.653539 TCATCGTCGAGAAGGAAACAA 57.346 42.857 0.00 0.00 0.00 2.83
2233 2245 1.887707 GCCCCTAAATGACCGCTCG 60.888 63.158 0.00 0.00 0.00 5.03
2292 2304 1.651737 TTGCCTAGAAGTAGCCACCA 58.348 50.000 0.00 0.00 0.00 4.17
2293 2305 1.879575 TGCCTAGAAGTAGCCACCAT 58.120 50.000 0.00 0.00 0.00 3.55
2294 2306 3.040655 TGCCTAGAAGTAGCCACCATA 57.959 47.619 0.00 0.00 0.00 2.74
2295 2307 3.587498 TGCCTAGAAGTAGCCACCATAT 58.413 45.455 0.00 0.00 0.00 1.78
2296 2308 3.973973 TGCCTAGAAGTAGCCACCATATT 59.026 43.478 0.00 0.00 0.00 1.28
2297 2309 4.412199 TGCCTAGAAGTAGCCACCATATTT 59.588 41.667 0.00 0.00 0.00 1.40
2298 2310 5.104109 TGCCTAGAAGTAGCCACCATATTTT 60.104 40.000 0.00 0.00 0.00 1.82
2299 2311 5.470437 GCCTAGAAGTAGCCACCATATTTTC 59.530 44.000 0.00 0.00 0.00 2.29
2300 2312 6.591935 CCTAGAAGTAGCCACCATATTTTCA 58.408 40.000 0.00 0.00 0.00 2.69
2301 2313 7.227156 CCTAGAAGTAGCCACCATATTTTCAT 58.773 38.462 0.00 0.00 0.00 2.57
2302 2314 7.721399 CCTAGAAGTAGCCACCATATTTTCATT 59.279 37.037 0.00 0.00 0.00 2.57
2303 2315 7.573968 AGAAGTAGCCACCATATTTTCATTC 57.426 36.000 0.00 0.00 0.00 2.67
2304 2316 6.547510 AGAAGTAGCCACCATATTTTCATTCC 59.452 38.462 0.00 0.00 0.00 3.01
2305 2317 6.018433 AGTAGCCACCATATTTTCATTCCT 57.982 37.500 0.00 0.00 0.00 3.36
2306 2318 6.064717 AGTAGCCACCATATTTTCATTCCTC 58.935 40.000 0.00 0.00 0.00 3.71
2307 2319 5.134725 AGCCACCATATTTTCATTCCTCT 57.865 39.130 0.00 0.00 0.00 3.69
2308 2320 5.136105 AGCCACCATATTTTCATTCCTCTC 58.864 41.667 0.00 0.00 0.00 3.20
2309 2321 4.279420 GCCACCATATTTTCATTCCTCTCC 59.721 45.833 0.00 0.00 0.00 3.71
2310 2322 5.699143 CCACCATATTTTCATTCCTCTCCT 58.301 41.667 0.00 0.00 0.00 3.69
2311 2323 6.691491 GCCACCATATTTTCATTCCTCTCCTA 60.691 42.308 0.00 0.00 0.00 2.94
2312 2324 7.290061 CCACCATATTTTCATTCCTCTCCTAA 58.710 38.462 0.00 0.00 0.00 2.69
2313 2325 7.229506 CCACCATATTTTCATTCCTCTCCTAAC 59.770 40.741 0.00 0.00 0.00 2.34
2314 2326 7.775093 CACCATATTTTCATTCCTCTCCTAACA 59.225 37.037 0.00 0.00 0.00 2.41
2315 2327 8.506083 ACCATATTTTCATTCCTCTCCTAACAT 58.494 33.333 0.00 0.00 0.00 2.71
2329 2341 5.086104 TCCTAACATAGAGGAGCAAACAC 57.914 43.478 0.00 0.00 38.22 3.32
2330 2342 3.865745 CCTAACATAGAGGAGCAAACACG 59.134 47.826 0.00 0.00 35.99 4.49
2331 2343 3.678056 AACATAGAGGAGCAAACACGA 57.322 42.857 0.00 0.00 0.00 4.35
2332 2344 3.678056 ACATAGAGGAGCAAACACGAA 57.322 42.857 0.00 0.00 0.00 3.85
2333 2345 4.002906 ACATAGAGGAGCAAACACGAAA 57.997 40.909 0.00 0.00 0.00 3.46
2334 2346 4.579869 ACATAGAGGAGCAAACACGAAAT 58.420 39.130 0.00 0.00 0.00 2.17
2335 2347 4.393062 ACATAGAGGAGCAAACACGAAATG 59.607 41.667 0.00 0.00 0.00 2.32
2336 2348 2.851195 AGAGGAGCAAACACGAAATGT 58.149 42.857 0.00 0.00 46.42 2.71
2337 2349 4.002906 AGAGGAGCAAACACGAAATGTA 57.997 40.909 0.00 0.00 42.31 2.29
2338 2350 4.579869 AGAGGAGCAAACACGAAATGTAT 58.420 39.130 0.00 0.00 42.31 2.29
2339 2351 4.393062 AGAGGAGCAAACACGAAATGTATG 59.607 41.667 0.00 0.00 42.31 2.39
2340 2352 4.323417 AGGAGCAAACACGAAATGTATGA 58.677 39.130 0.00 0.00 42.31 2.15
2341 2353 4.943705 AGGAGCAAACACGAAATGTATGAT 59.056 37.500 0.00 0.00 42.31 2.45
2342 2354 5.415701 AGGAGCAAACACGAAATGTATGATT 59.584 36.000 0.00 0.00 42.31 2.57
2343 2355 6.597672 AGGAGCAAACACGAAATGTATGATTA 59.402 34.615 0.00 0.00 42.31 1.75
2344 2356 7.283127 AGGAGCAAACACGAAATGTATGATTAT 59.717 33.333 0.00 0.00 42.31 1.28
2345 2357 7.587757 GGAGCAAACACGAAATGTATGATTATC 59.412 37.037 0.00 0.00 42.31 1.75
2346 2358 7.984391 AGCAAACACGAAATGTATGATTATCA 58.016 30.769 0.00 0.00 42.31 2.15
2347 2359 7.910162 AGCAAACACGAAATGTATGATTATCAC 59.090 33.333 0.00 0.00 42.31 3.06
2348 2360 7.910162 GCAAACACGAAATGTATGATTATCACT 59.090 33.333 0.00 0.00 42.31 3.41
2349 2361 9.773328 CAAACACGAAATGTATGATTATCACTT 57.227 29.630 0.00 0.00 42.31 3.16
2352 2364 9.594478 ACACGAAATGTATGATTATCACTTACA 57.406 29.630 10.04 10.04 40.88 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.095400 TGAGCCTCCTCCTCCCCC 62.095 72.222 0.00 0.00 37.29 5.40
1 2 2.445654 CTGAGCCTCCTCCTCCCC 60.446 72.222 0.00 0.00 37.29 4.81
2 3 2.445654 CCTGAGCCTCCTCCTCCC 60.446 72.222 0.00 0.00 37.29 4.30
3 4 1.457455 CTCCTGAGCCTCCTCCTCC 60.457 68.421 0.00 0.00 37.29 4.30
4 5 0.755327 GACTCCTGAGCCTCCTCCTC 60.755 65.000 0.00 0.00 37.29 3.71
5 6 1.309688 GACTCCTGAGCCTCCTCCT 59.690 63.158 0.00 0.00 37.29 3.69
6 7 2.124693 CGACTCCTGAGCCTCCTCC 61.125 68.421 0.00 0.00 37.29 4.30
7 8 0.968393 AACGACTCCTGAGCCTCCTC 60.968 60.000 0.00 0.00 38.62 3.71
8 9 0.968393 GAACGACTCCTGAGCCTCCT 60.968 60.000 0.00 0.00 0.00 3.69
9 10 1.513622 GAACGACTCCTGAGCCTCC 59.486 63.158 0.00 0.00 0.00 4.30
10 11 1.137825 CGAACGACTCCTGAGCCTC 59.862 63.158 0.00 0.00 0.00 4.70
11 12 1.303398 TCGAACGACTCCTGAGCCT 60.303 57.895 0.00 0.00 0.00 4.58
12 13 1.137825 CTCGAACGACTCCTGAGCC 59.862 63.158 0.00 0.00 0.00 4.70
13 14 1.515304 GCTCGAACGACTCCTGAGC 60.515 63.158 0.00 0.00 44.37 4.26
14 15 1.137825 GGCTCGAACGACTCCTGAG 59.862 63.158 0.00 0.00 0.00 3.35
15 16 2.687805 CGGCTCGAACGACTCCTGA 61.688 63.158 3.30 0.00 0.00 3.86
16 17 2.202492 CGGCTCGAACGACTCCTG 60.202 66.667 3.30 0.00 0.00 3.86
17 18 3.441290 CCGGCTCGAACGACTCCT 61.441 66.667 10.38 0.00 0.00 3.69
18 19 3.745803 ACCGGCTCGAACGACTCC 61.746 66.667 0.00 0.00 0.00 3.85
19 20 2.504244 CACCGGCTCGAACGACTC 60.504 66.667 0.00 0.00 0.00 3.36
20 21 4.052229 CCACCGGCTCGAACGACT 62.052 66.667 0.00 0.00 0.00 4.18
21 22 3.966026 CTCCACCGGCTCGAACGAC 62.966 68.421 0.00 0.00 0.00 4.34
22 23 3.744719 CTCCACCGGCTCGAACGA 61.745 66.667 0.00 0.00 0.00 3.85
23 24 4.796231 CCTCCACCGGCTCGAACG 62.796 72.222 0.00 2.46 0.00 3.95
24 25 3.379445 TCCTCCACCGGCTCGAAC 61.379 66.667 0.00 0.00 0.00 3.95
25 26 3.379445 GTCCTCCACCGGCTCGAA 61.379 66.667 0.00 0.00 0.00 3.71
28 29 3.827898 CTCGTCCTCCACCGGCTC 61.828 72.222 0.00 0.00 0.00 4.70
29 30 4.680537 ACTCGTCCTCCACCGGCT 62.681 66.667 0.00 0.00 0.00 5.52
30 31 3.692406 AACTCGTCCTCCACCGGC 61.692 66.667 0.00 0.00 0.00 6.13
31 32 2.261671 CAACTCGTCCTCCACCGG 59.738 66.667 0.00 0.00 0.00 5.28
32 33 2.261671 CCAACTCGTCCTCCACCG 59.738 66.667 0.00 0.00 0.00 4.94
33 34 1.004918 CACCAACTCGTCCTCCACC 60.005 63.158 0.00 0.00 0.00 4.61
34 35 1.668151 GCACCAACTCGTCCTCCAC 60.668 63.158 0.00 0.00 0.00 4.02
35 36 1.837051 AGCACCAACTCGTCCTCCA 60.837 57.895 0.00 0.00 0.00 3.86
36 37 1.374758 CAGCACCAACTCGTCCTCC 60.375 63.158 0.00 0.00 0.00 4.30
37 38 2.029844 GCAGCACCAACTCGTCCTC 61.030 63.158 0.00 0.00 0.00 3.71
38 39 2.031163 GCAGCACCAACTCGTCCT 59.969 61.111 0.00 0.00 0.00 3.85
39 40 2.280797 TGCAGCACCAACTCGTCC 60.281 61.111 0.00 0.00 0.00 4.79
40 41 1.160329 AAGTGCAGCACCAACTCGTC 61.160 55.000 22.41 0.00 34.49 4.20
41 42 1.153168 AAGTGCAGCACCAACTCGT 60.153 52.632 22.41 0.00 34.49 4.18
42 43 1.571460 GAAGTGCAGCACCAACTCG 59.429 57.895 22.41 0.00 34.49 4.18
43 44 0.536006 AGGAAGTGCAGCACCAACTC 60.536 55.000 22.41 12.99 34.49 3.01
44 45 0.820891 CAGGAAGTGCAGCACCAACT 60.821 55.000 22.41 14.08 34.49 3.16
45 46 1.656441 CAGGAAGTGCAGCACCAAC 59.344 57.895 22.41 11.98 34.49 3.77
46 47 4.162592 CAGGAAGTGCAGCACCAA 57.837 55.556 22.41 0.00 34.49 3.67
61 62 0.174389 ATGTGTCAGTAGAGCCGCAG 59.826 55.000 0.00 0.00 0.00 5.18
62 63 0.108662 CATGTGTCAGTAGAGCCGCA 60.109 55.000 0.00 0.00 0.00 5.69
63 64 1.424493 GCATGTGTCAGTAGAGCCGC 61.424 60.000 0.00 0.00 0.00 6.53
64 65 0.807667 GGCATGTGTCAGTAGAGCCG 60.808 60.000 0.00 0.00 0.00 5.52
65 66 0.250234 TGGCATGTGTCAGTAGAGCC 59.750 55.000 0.00 0.00 40.93 4.70
66 67 1.066573 AGTGGCATGTGTCAGTAGAGC 60.067 52.381 0.00 0.00 30.39 4.09
67 68 2.232208 TCAGTGGCATGTGTCAGTAGAG 59.768 50.000 0.00 0.00 31.11 2.43
68 69 2.247358 TCAGTGGCATGTGTCAGTAGA 58.753 47.619 0.00 0.00 31.11 2.59
69 70 2.749280 TCAGTGGCATGTGTCAGTAG 57.251 50.000 0.00 0.00 31.11 2.57
70 71 3.070878 TCTTTCAGTGGCATGTGTCAGTA 59.929 43.478 0.00 0.00 31.11 2.74
76 77 2.744202 GGTAGTCTTTCAGTGGCATGTG 59.256 50.000 0.00 0.00 0.00 3.21
97 100 4.002982 TGACATCCCATCTTTTTGTCTCG 58.997 43.478 0.00 0.00 38.00 4.04
114 117 6.023603 TCCTACCTCTCTACCTTTTTGACAT 58.976 40.000 0.00 0.00 0.00 3.06
142 146 5.519808 TCCATACTAGATCTGACCAACTGT 58.480 41.667 5.18 0.00 0.00 3.55
167 171 4.097437 GTCTCCAACTATCGTCCATGTACA 59.903 45.833 0.00 0.00 0.00 2.90
189 193 3.959329 AACCTAGGAGAGCCGCCGT 62.959 63.158 17.98 0.00 39.96 5.68
251 255 5.817296 AGATAGTGCATCAAGTTATTCGCAA 59.183 36.000 0.00 0.00 35.96 4.85
276 280 0.762418 TCGCTCAAAGGGTTGAAGGA 59.238 50.000 0.00 0.00 43.18 3.36
354 358 0.105039 CCTTGGGGTGATCTCGTAGC 59.895 60.000 0.00 0.00 0.00 3.58
414 418 8.682710 GGCTAATGTGTTCCACTTATTGAATAA 58.317 33.333 0.00 0.00 35.11 1.40
416 420 6.183360 CGGCTAATGTGTTCCACTTATTGAAT 60.183 38.462 0.00 0.00 35.11 2.57
500 504 4.509600 CGACTCTTTGATCCTAAGAATGCC 59.490 45.833 8.27 0.23 31.67 4.40
510 514 1.821216 TTTGCCCGACTCTTTGATCC 58.179 50.000 0.00 0.00 0.00 3.36
561 565 1.659022 TCCGGGGAATCCAGTTACAA 58.341 50.000 0.00 0.00 34.36 2.41
613 617 7.068103 TCTCAAAATCTCAAAACAAAGGTGCTA 59.932 33.333 0.00 0.00 0.00 3.49
941 946 1.063114 ACGGGTTCTACCATAGAGGCT 60.063 52.381 0.00 0.00 41.02 4.58
973 978 1.002087 CAGAGTAAACCACCGCCTCTT 59.998 52.381 0.00 0.00 30.31 2.85
990 995 1.293179 CACTGACATCCGCCACAGA 59.707 57.895 0.00 0.00 34.88 3.41
1007 1012 1.404391 GAGATAAGCGGACTCGAACCA 59.596 52.381 8.65 0.00 39.00 3.67
1230 1241 1.067142 AGGATTTCGTCGCTTGCTACA 60.067 47.619 0.00 0.00 0.00 2.74
1325 1336 1.294659 GGTTGTCTCTTGCCTGCTCG 61.295 60.000 0.00 0.00 0.00 5.03
1372 1383 5.705609 ATCGCTTTTGCTTTCTTTTCCTA 57.294 34.783 0.00 0.00 44.80 2.94
1480 1491 3.345808 GCACTCAACCGCTTCGCA 61.346 61.111 0.00 0.00 0.00 5.10
1521 1532 2.869192 GCTAGTGATGCTTTCAGCTACC 59.131 50.000 0.00 0.00 42.97 3.18
1630 1641 1.605710 TGGTACTACTTCGCTATCGGC 59.394 52.381 0.00 0.00 36.13 5.54
1657 1668 2.239400 CTGGGGGTTCTTTTCACCTTC 58.761 52.381 0.00 0.00 34.36 3.46
1684 1695 5.415701 AGCATGGTTTCACGTTCTATTTCAT 59.584 36.000 0.00 0.00 0.00 2.57
1751 1762 0.449388 GGCTCATTCTTCAACAGGCG 59.551 55.000 0.00 0.00 0.00 5.52
1951 1962 1.737793 CCTAACCACAACTCATTCGCC 59.262 52.381 0.00 0.00 0.00 5.54
1955 1966 2.714250 TCACCCCTAACCACAACTCATT 59.286 45.455 0.00 0.00 0.00 2.57
1984 1995 2.644798 ACCAACTAGCTCTGGGTTTGAT 59.355 45.455 12.64 0.00 37.00 2.57
1987 1998 2.711547 AGAACCAACTAGCTCTGGGTTT 59.288 45.455 12.64 0.49 41.65 3.27
2001 2012 1.624813 ACGTATTTCGGGGAGAACCAA 59.375 47.619 0.00 0.00 44.69 3.67
2018 2029 4.609018 ACTGCTGCGCCTCAACGT 62.609 61.111 4.18 0.00 34.88 3.99
2075 2087 0.949588 TTTGGTACCGATCGCGCAAA 60.950 50.000 10.32 0.02 35.83 3.68
2076 2088 0.741574 ATTTGGTACCGATCGCGCAA 60.742 50.000 10.32 0.00 35.83 4.85
2084 2096 0.609151 TTGCCTCGATTTGGTACCGA 59.391 50.000 7.57 1.50 0.00 4.69
2188 2200 0.037734 GGTGATCCGGGTTGTTTCCT 59.962 55.000 0.00 0.00 0.00 3.36
2233 2245 1.639108 ACCCCCACCTTCTTTATCACC 59.361 52.381 0.00 0.00 0.00 4.02
2243 2255 1.152546 GTCTTTGCACCCCCACCTT 60.153 57.895 0.00 0.00 0.00 3.50
2307 2319 4.381612 CGTGTTTGCTCCTCTATGTTAGGA 60.382 45.833 0.00 0.00 40.92 2.94
2308 2320 3.865745 CGTGTTTGCTCCTCTATGTTAGG 59.134 47.826 0.00 0.00 35.26 2.69
2309 2321 4.744570 TCGTGTTTGCTCCTCTATGTTAG 58.255 43.478 0.00 0.00 0.00 2.34
2310 2322 4.794278 TCGTGTTTGCTCCTCTATGTTA 57.206 40.909 0.00 0.00 0.00 2.41
2311 2323 3.678056 TCGTGTTTGCTCCTCTATGTT 57.322 42.857 0.00 0.00 0.00 2.71
2312 2324 3.678056 TTCGTGTTTGCTCCTCTATGT 57.322 42.857 0.00 0.00 0.00 2.29
2313 2325 4.393062 ACATTTCGTGTTTGCTCCTCTATG 59.607 41.667 0.00 0.00 38.01 2.23
2314 2326 4.579869 ACATTTCGTGTTTGCTCCTCTAT 58.420 39.130 0.00 0.00 38.01 1.98
2315 2327 4.002906 ACATTTCGTGTTTGCTCCTCTA 57.997 40.909 0.00 0.00 38.01 2.43
2316 2328 2.851195 ACATTTCGTGTTTGCTCCTCT 58.149 42.857 0.00 0.00 38.01 3.69
2317 2329 4.391830 TCATACATTTCGTGTTTGCTCCTC 59.608 41.667 0.00 0.00 42.29 3.71
2318 2330 4.323417 TCATACATTTCGTGTTTGCTCCT 58.677 39.130 0.00 0.00 42.29 3.69
2319 2331 4.678509 TCATACATTTCGTGTTTGCTCC 57.321 40.909 0.00 0.00 42.29 4.70
2320 2332 8.122330 TGATAATCATACATTTCGTGTTTGCTC 58.878 33.333 0.00 0.00 42.29 4.26
2321 2333 7.910162 GTGATAATCATACATTTCGTGTTTGCT 59.090 33.333 0.00 0.00 42.29 3.91
2322 2334 7.910162 AGTGATAATCATACATTTCGTGTTTGC 59.090 33.333 0.00 0.00 42.29 3.68
2323 2335 9.773328 AAGTGATAATCATACATTTCGTGTTTG 57.227 29.630 0.00 0.00 42.29 2.93
2326 2338 9.594478 TGTAAGTGATAATCATACATTTCGTGT 57.406 29.630 0.00 0.00 44.95 4.49


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

AutoCloner maintained by Alex Coulton.