Multiple sequence alignment - TraesCS6A01G309700

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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 TraesCS6A01G309700 chr6A 100.000 2336 0 0 1 2336 545831291 545828956 0.000000e+00 4314
1 TraesCS6A01G309700 chr6D 91.956 1554 66 30 412 1926 400078371 400076838 0.000000e+00 2122
2 TraesCS6A01G309700 chr6D 95.291 361 13 3 1976 2336 400076742 400076386 9.370000e-159 569
3 TraesCS6A01G309700 chr6B 84.392 1826 116 69 60 1797 599073785 599072041 0.000000e+00 1637
4 TraesCS6A01G309700 chr6B 81.889 900 82 43 483 1338 604597419 604598281 0.000000e+00 684
5 TraesCS6A01G309700 chr6B 90.638 235 12 3 1998 2222 599071717 599071483 1.050000e-78 303
6 TraesCS6A01G309700 chr6B 84.713 157 8 8 1469 1619 604598280 604598426 2.420000e-30 143
7 TraesCS6A01G309700 chr2B 89.655 348 18 13 1000 1338 224645987 224646325 5.970000e-116 427
8 TraesCS6A01G309700 chr2D 84.043 470 39 24 874 1313 163022901 163022438 9.980000e-114 420
9 TraesCS6A01G309700 chr2A 81.919 542 49 36 799 1312 176655353 176655873 1.670000e-111 412
10 TraesCS6A01G309700 chr1D 87.500 352 18 17 1000 1338 1836834 1836496 1.310000e-102 383


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 TraesCS6A01G309700 chr6A 545828956 545831291 2335 True 4314.0 4314 100.0000 1 2336 1 chr6A.!!$R1 2335
1 TraesCS6A01G309700 chr6D 400076386 400078371 1985 True 1345.5 2122 93.6235 412 2336 2 chr6D.!!$R1 1924
2 TraesCS6A01G309700 chr6B 599071483 599073785 2302 True 970.0 1637 87.5150 60 2222 2 chr6B.!!$R1 2162
3 TraesCS6A01G309700 chr6B 604597419 604598426 1007 False 413.5 684 83.3010 483 1619 2 chr6B.!!$F1 1136
4 TraesCS6A01G309700 chr2A 176655353 176655873 520 False 412.0 412 81.9190 799 1312 1 chr2A.!!$F1 513

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
19 20 0.108804 GATCAAAGACTCCACGCGGA 60.109 55.0 12.47 0.0 39.79 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1371 1523 0.315568 CAGGCTAGCTACCCATCGAC 59.684 60.0 15.72 0.0 0.0 4.2 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
18 19 2.373938 GATCAAAGACTCCACGCGG 58.626 57.895 12.47 0.00 0.00 6.46
19 20 0.108804 GATCAAAGACTCCACGCGGA 60.109 55.000 12.47 0.00 39.79 5.54
27 28 2.264480 TCCACGCGGAGTCATTGG 59.736 61.111 12.47 7.26 35.91 3.16
28 29 2.047274 CCACGCGGAGTCATTGGT 60.047 61.111 12.47 0.00 0.00 3.67
29 30 1.216977 CCACGCGGAGTCATTGGTA 59.783 57.895 12.47 0.00 0.00 3.25
30 31 0.390603 CCACGCGGAGTCATTGGTAA 60.391 55.000 12.47 0.00 0.00 2.85
31 32 0.719465 CACGCGGAGTCATTGGTAAC 59.281 55.000 12.47 0.00 0.00 2.50
53 54 6.259550 ACAGAAATTGTTCACCTGCTATTC 57.740 37.500 0.00 0.00 36.31 1.75
54 55 6.006449 ACAGAAATTGTTCACCTGCTATTCT 58.994 36.000 0.00 0.00 36.31 2.40
55 56 6.491403 ACAGAAATTGTTCACCTGCTATTCTT 59.509 34.615 0.00 0.00 36.31 2.52
56 57 7.025963 CAGAAATTGTTCACCTGCTATTCTTC 58.974 38.462 0.00 0.00 36.09 2.87
57 58 5.551760 AATTGTTCACCTGCTATTCTTCG 57.448 39.130 0.00 0.00 0.00 3.79
58 59 3.953712 TGTTCACCTGCTATTCTTCGA 57.046 42.857 0.00 0.00 0.00 3.71
86 87 1.451927 TGCCCAACCATGAGATCGC 60.452 57.895 0.00 0.00 0.00 4.58
88 89 1.224315 CCCAACCATGAGATCGCCA 59.776 57.895 0.00 0.00 0.00 5.69
96 97 0.755686 ATGAGATCGCCAGAAGACCC 59.244 55.000 0.00 0.00 0.00 4.46
131 132 2.455674 TCACAAGTTCATCCACTCGG 57.544 50.000 0.00 0.00 0.00 4.63
132 133 1.691976 TCACAAGTTCATCCACTCGGT 59.308 47.619 0.00 0.00 0.00 4.69
138 139 0.460109 TTCATCCACTCGGTGCATCG 60.460 55.000 14.66 14.66 31.34 3.84
150 151 1.902918 TGCATCGCCTTTTGCACCT 60.903 52.632 0.00 0.00 43.54 4.00
172 185 1.421485 GTGTCTGCAAATCGCTCCG 59.579 57.895 0.00 0.00 43.06 4.63
174 187 1.741770 GTCTGCAAATCGCTCCGGT 60.742 57.895 0.00 0.00 43.06 5.28
186 205 1.517832 CTCCGGTAGGTGAGCCAAG 59.482 63.158 0.00 0.00 39.05 3.61
211 230 6.460953 GCGACAAACATGGTAAATAATCCCAT 60.461 38.462 0.00 0.00 39.55 4.00
229 253 1.700042 ATGGGGATCAGCGGGAAGTC 61.700 60.000 0.00 0.00 0.00 3.01
236 260 0.603569 TCAGCGGGAAGTCTGTTCTC 59.396 55.000 0.00 0.00 0.00 2.87
242 266 3.202906 CGGGAAGTCTGTTCTCAAAACA 58.797 45.455 0.00 0.00 0.00 2.83
247 271 3.891049 AGTCTGTTCTCAAAACAAGCCT 58.109 40.909 0.00 0.00 0.00 4.58
265 289 2.416893 GCCTCATTTTCGAGTCTTCCAC 59.583 50.000 0.00 0.00 0.00 4.02
314 338 2.959030 AGACTTTGGCTGTCCCTTTTTC 59.041 45.455 0.00 0.00 35.21 2.29
316 340 1.000274 CTTTGGCTGTCCCTTTTTCCG 60.000 52.381 0.00 0.00 0.00 4.30
317 341 0.825840 TTGGCTGTCCCTTTTTCCGG 60.826 55.000 0.00 0.00 0.00 5.14
323 347 1.986631 TGTCCCTTTTTCCGGACCATA 59.013 47.619 1.83 0.00 46.78 2.74
331 355 5.335661 CCTTTTTCCGGACCATAAAAGTGAG 60.336 44.000 26.17 14.49 36.39 3.51
332 356 4.627284 TTTCCGGACCATAAAAGTGAGA 57.373 40.909 1.83 0.00 0.00 3.27
333 357 4.837093 TTCCGGACCATAAAAGTGAGAT 57.163 40.909 1.83 0.00 0.00 2.75
334 358 4.837093 TCCGGACCATAAAAGTGAGATT 57.163 40.909 0.00 0.00 0.00 2.40
335 359 4.766375 TCCGGACCATAAAAGTGAGATTC 58.234 43.478 0.00 0.00 0.00 2.52
336 360 3.555956 CCGGACCATAAAAGTGAGATTCG 59.444 47.826 0.00 0.00 0.00 3.34
337 361 4.430007 CGGACCATAAAAGTGAGATTCGA 58.570 43.478 0.00 0.00 0.00 3.71
338 362 4.267928 CGGACCATAAAAGTGAGATTCGAC 59.732 45.833 0.00 0.00 0.00 4.20
339 363 4.571176 GGACCATAAAAGTGAGATTCGACC 59.429 45.833 0.00 0.00 0.00 4.79
353 377 1.185618 TCGACCACTCTCCAACCAGG 61.186 60.000 0.00 0.00 39.47 4.45
354 378 1.679898 GACCACTCTCCAACCAGGG 59.320 63.158 0.00 0.00 38.24 4.45
373 397 0.668535 GCCAGTTGTTTCAGGTGGAC 59.331 55.000 0.00 0.00 0.00 4.02
374 398 1.750682 GCCAGTTGTTTCAGGTGGACT 60.751 52.381 0.00 0.00 0.00 3.85
375 399 2.486548 GCCAGTTGTTTCAGGTGGACTA 60.487 50.000 0.00 0.00 0.00 2.59
376 400 3.403038 CCAGTTGTTTCAGGTGGACTAG 58.597 50.000 0.00 0.00 0.00 2.57
377 401 3.403038 CAGTTGTTTCAGGTGGACTAGG 58.597 50.000 0.00 0.00 0.00 3.02
378 402 3.046374 AGTTGTTTCAGGTGGACTAGGT 58.954 45.455 0.00 0.00 0.00 3.08
379 403 4.039973 CAGTTGTTTCAGGTGGACTAGGTA 59.960 45.833 0.00 0.00 0.00 3.08
380 404 4.283722 AGTTGTTTCAGGTGGACTAGGTAG 59.716 45.833 0.00 0.00 0.00 3.18
381 405 4.122337 TGTTTCAGGTGGACTAGGTAGA 57.878 45.455 0.00 0.00 0.00 2.59
382 406 4.684724 TGTTTCAGGTGGACTAGGTAGAT 58.315 43.478 0.00 0.00 0.00 1.98
383 407 4.710375 TGTTTCAGGTGGACTAGGTAGATC 59.290 45.833 0.00 0.00 0.00 2.75
384 408 4.603094 TTCAGGTGGACTAGGTAGATCA 57.397 45.455 0.00 0.00 0.00 2.92
385 409 4.603094 TCAGGTGGACTAGGTAGATCAA 57.397 45.455 0.00 0.00 0.00 2.57
386 410 4.942944 TCAGGTGGACTAGGTAGATCAAA 58.057 43.478 0.00 0.00 0.00 2.69
387 411 4.956700 TCAGGTGGACTAGGTAGATCAAAG 59.043 45.833 0.00 0.00 0.00 2.77
388 412 3.707102 AGGTGGACTAGGTAGATCAAAGC 59.293 47.826 0.00 0.00 0.00 3.51
389 413 3.181464 GGTGGACTAGGTAGATCAAAGCC 60.181 52.174 0.00 0.00 0.00 4.35
390 414 3.039011 TGGACTAGGTAGATCAAAGCCC 58.961 50.000 0.00 0.00 0.00 5.19
391 415 3.039011 GGACTAGGTAGATCAAAGCCCA 58.961 50.000 0.00 0.00 0.00 5.36
392 416 3.454812 GGACTAGGTAGATCAAAGCCCAA 59.545 47.826 0.00 0.00 0.00 4.12
393 417 4.443598 GGACTAGGTAGATCAAAGCCCAAG 60.444 50.000 0.00 0.00 0.00 3.61
394 418 2.426842 AGGTAGATCAAAGCCCAAGC 57.573 50.000 0.00 0.00 40.32 4.01
556 580 2.357760 TAGACCAACAACCGCGCC 60.358 61.111 0.00 0.00 0.00 6.53
828 898 0.608035 CACCGCCTTTTCCCAGCTTA 60.608 55.000 0.00 0.00 0.00 3.09
829 899 0.322546 ACCGCCTTTTCCCAGCTTAG 60.323 55.000 0.00 0.00 0.00 2.18
830 900 1.657751 CCGCCTTTTCCCAGCTTAGC 61.658 60.000 0.00 0.00 0.00 3.09
832 902 1.098869 GCCTTTTCCCAGCTTAGCTC 58.901 55.000 2.68 0.00 36.40 4.09
835 911 1.004745 CTTTTCCCAGCTTAGCTCCCA 59.995 52.381 2.68 0.00 36.40 4.37
885 965 3.668980 TAGCCTTTACGCCACGCCC 62.669 63.158 0.00 0.00 0.00 6.13
891 971 0.829333 TTTACGCCACGCCCCTATAA 59.171 50.000 0.00 0.00 0.00 0.98
941 1029 1.383456 AACGAAAGCAACAGCCAGCA 61.383 50.000 0.00 0.00 0.00 4.41
959 1070 3.944476 AAGCTCACTTGGCTACCAG 57.056 52.632 0.00 0.00 39.30 4.00
960 1071 0.322008 AAGCTCACTTGGCTACCAGC 60.322 55.000 0.00 0.00 39.30 4.85
979 1090 1.351012 CTACCACTAGTCGCGGTCG 59.649 63.158 6.13 0.00 34.12 4.79
985 1096 3.685214 CTAGTCGCGGTCGCAGCTT 62.685 63.158 15.68 0.73 42.06 3.74
991 1102 3.188786 CGGTCGCAGCTTAGCCAC 61.189 66.667 0.00 0.00 0.00 5.01
992 1103 2.266055 GGTCGCAGCTTAGCCACT 59.734 61.111 0.00 0.00 0.00 4.00
993 1104 1.811679 GGTCGCAGCTTAGCCACTC 60.812 63.158 0.00 0.00 0.00 3.51
996 1114 1.738099 CGCAGCTTAGCCACTCGTT 60.738 57.895 0.00 0.00 0.00 3.85
1338 1471 1.685765 CACGGAGTCCCCCTGATGA 60.686 63.158 2.80 0.00 41.61 2.92
1371 1523 2.888534 CCACGTTACGCCCATCGG 60.889 66.667 4.09 0.00 43.86 4.18
1374 1526 2.952783 CGTTACGCCCATCGGTCG 60.953 66.667 0.00 0.00 43.86 4.79
1433 1588 9.020813 GCTAGCTTTTGGTTGCTATAATAAAAC 57.979 33.333 7.70 0.00 43.31 2.43
1460 1615 3.327464 TGCTATACATAGGCAAGGCATGA 59.673 43.478 0.00 0.00 0.00 3.07
1534 1697 5.105351 TGTGATTGGAGAGTGTACCTGTATG 60.105 44.000 0.00 0.00 0.00 2.39
1745 1915 1.472480 CCCATTGTTCGGTCCAATCAC 59.528 52.381 0.00 0.00 30.28 3.06
1782 1952 5.796502 TTTGATCCTTGGTTAGAAGGGAT 57.203 39.130 0.00 0.00 42.63 3.85
1845 2084 2.750888 CGCCCTGCTAACGGCTTTC 61.751 63.158 0.00 0.00 43.38 2.62
1848 2087 0.539986 CCCTGCTAACGGCTTTCCTA 59.460 55.000 0.00 0.00 42.39 2.94
1885 2128 7.340122 TCTAGATGGATTAGTTGACACTCAG 57.660 40.000 0.00 0.00 34.06 3.35
1932 2221 7.843490 TGCTCAGTACTTCATATGTTAAACC 57.157 36.000 1.90 0.00 0.00 3.27
1933 2222 6.533723 TGCTCAGTACTTCATATGTTAAACCG 59.466 38.462 1.90 0.00 0.00 4.44
2061 2378 2.161486 GCACGCAACGCCAACAAAA 61.161 52.632 0.00 0.00 0.00 2.44
2080 2397 3.455619 AACAGAGCTGAATTTAACGCG 57.544 42.857 3.53 3.53 0.00 6.01
2082 2399 2.157668 ACAGAGCTGAATTTAACGCGTG 59.842 45.455 14.98 0.00 0.00 5.34
2131 2453 6.225318 ACCAAGTTTCACGTAGCAATTAGTA 58.775 36.000 0.00 0.00 0.00 1.82
2191 2518 1.665679 CCATAACACAGCCGCTTAGTG 59.334 52.381 8.85 8.85 39.12 2.74
2244 2571 6.513393 GCATATATTTGCTTACTTGACGGCTT 60.513 38.462 10.52 0.00 39.57 4.35
2245 2572 7.307751 GCATATATTTGCTTACTTGACGGCTTA 60.308 37.037 10.52 0.00 39.57 3.09
2246 2573 4.680171 ATTTGCTTACTTGACGGCTTAC 57.320 40.909 0.00 0.00 0.00 2.34
2248 2575 3.114668 TGCTTACTTGACGGCTTACAA 57.885 42.857 0.00 0.00 0.00 2.41
2249 2576 3.064207 TGCTTACTTGACGGCTTACAAG 58.936 45.455 0.00 0.00 45.85 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.108804 TCCGCGTGGAGTCTTTGATC 60.109 55.000 15.21 0.00 40.17 2.92
1 2 1.972198 TCCGCGTGGAGTCTTTGAT 59.028 52.632 15.21 0.00 40.17 2.57
2 3 3.450507 TCCGCGTGGAGTCTTTGA 58.549 55.556 15.21 0.00 40.17 2.69
10 11 1.252215 TACCAATGACTCCGCGTGGA 61.252 55.000 18.43 18.43 43.88 4.02
11 12 0.390603 TTACCAATGACTCCGCGTGG 60.391 55.000 9.28 9.28 35.39 4.94
12 13 0.719465 GTTACCAATGACTCCGCGTG 59.281 55.000 4.92 0.00 0.00 5.34
13 14 0.319083 TGTTACCAATGACTCCGCGT 59.681 50.000 4.92 0.00 0.00 6.01
14 15 0.999406 CTGTTACCAATGACTCCGCG 59.001 55.000 0.00 0.00 0.00 6.46
15 16 2.380084 TCTGTTACCAATGACTCCGC 57.620 50.000 0.00 0.00 0.00 5.54
16 17 5.181245 ACAATTTCTGTTACCAATGACTCCG 59.819 40.000 0.00 0.00 32.99 4.63
17 18 6.575162 ACAATTTCTGTTACCAATGACTCC 57.425 37.500 0.00 0.00 32.99 3.85
30 31 6.006449 AGAATAGCAGGTGAACAATTTCTGT 58.994 36.000 0.00 0.00 41.27 3.41
31 32 6.506500 AGAATAGCAGGTGAACAATTTCTG 57.493 37.500 0.00 0.00 32.36 3.02
32 33 6.128172 CGAAGAATAGCAGGTGAACAATTTCT 60.128 38.462 0.00 0.00 32.36 2.52
33 34 6.024049 CGAAGAATAGCAGGTGAACAATTTC 58.976 40.000 0.00 0.00 0.00 2.17
34 35 5.705441 TCGAAGAATAGCAGGTGAACAATTT 59.295 36.000 0.00 0.00 0.00 1.82
35 36 5.122396 GTCGAAGAATAGCAGGTGAACAATT 59.878 40.000 0.00 0.00 39.69 2.32
36 37 4.631813 GTCGAAGAATAGCAGGTGAACAAT 59.368 41.667 0.00 0.00 39.69 2.71
37 38 3.994392 GTCGAAGAATAGCAGGTGAACAA 59.006 43.478 0.00 0.00 39.69 2.83
38 39 3.006430 TGTCGAAGAATAGCAGGTGAACA 59.994 43.478 0.00 0.00 39.69 3.18
39 40 3.585862 TGTCGAAGAATAGCAGGTGAAC 58.414 45.455 0.00 0.00 39.69 3.18
40 41 3.953712 TGTCGAAGAATAGCAGGTGAA 57.046 42.857 0.00 0.00 39.69 3.18
41 42 3.953712 TTGTCGAAGAATAGCAGGTGA 57.046 42.857 0.00 0.00 39.69 4.02
42 43 3.935203 ACATTGTCGAAGAATAGCAGGTG 59.065 43.478 0.00 0.00 39.69 4.00
43 44 4.207891 ACATTGTCGAAGAATAGCAGGT 57.792 40.909 0.00 0.00 39.69 4.00
44 45 4.201851 CCAACATTGTCGAAGAATAGCAGG 60.202 45.833 0.00 0.00 39.69 4.85
45 46 4.393062 ACCAACATTGTCGAAGAATAGCAG 59.607 41.667 0.00 0.00 39.69 4.24
46 47 4.154015 CACCAACATTGTCGAAGAATAGCA 59.846 41.667 0.00 0.00 39.69 3.49
47 48 4.651994 CACCAACATTGTCGAAGAATAGC 58.348 43.478 0.00 0.00 39.69 2.97
48 49 4.437390 GGCACCAACATTGTCGAAGAATAG 60.437 45.833 0.00 0.00 39.69 1.73
49 50 3.438781 GGCACCAACATTGTCGAAGAATA 59.561 43.478 0.00 0.00 39.69 1.75
50 51 2.228822 GGCACCAACATTGTCGAAGAAT 59.771 45.455 0.00 0.00 39.69 2.40
51 52 1.606668 GGCACCAACATTGTCGAAGAA 59.393 47.619 0.00 0.00 39.69 2.52
52 53 1.234821 GGCACCAACATTGTCGAAGA 58.765 50.000 0.00 0.00 0.00 2.87
53 54 3.773117 GGCACCAACATTGTCGAAG 57.227 52.632 0.00 0.00 0.00 3.79
80 81 2.066999 GGGGGTCTTCTGGCGATCT 61.067 63.158 0.00 0.00 0.00 2.75
99 100 3.235292 TTGTGAAGAAAGGCGCGCG 62.235 57.895 28.44 28.44 0.00 6.86
105 106 4.823989 AGTGGATGAACTTGTGAAGAAAGG 59.176 41.667 0.00 0.00 0.00 3.11
109 110 3.554960 CCGAGTGGATGAACTTGTGAAGA 60.555 47.826 0.00 0.00 37.49 2.87
150 151 3.863681 GCGATTTGCAGACACCAAA 57.136 47.368 0.00 0.00 45.45 3.28
160 161 1.153429 ACCTACCGGAGCGATTTGC 60.153 57.895 9.46 0.00 46.98 3.68
161 162 0.174845 TCACCTACCGGAGCGATTTG 59.825 55.000 9.46 0.00 0.00 2.32
172 185 1.448013 GTCGCTTGGCTCACCTACC 60.448 63.158 0.00 0.00 36.63 3.18
174 187 0.394938 TTTGTCGCTTGGCTCACCTA 59.605 50.000 0.00 0.00 36.63 3.08
186 205 5.163602 TGGGATTATTTACCATGTTTGTCGC 60.164 40.000 0.00 0.00 0.00 5.19
211 230 2.285368 ACTTCCCGCTGATCCCCA 60.285 61.111 0.00 0.00 0.00 4.96
212 231 2.066999 AGACTTCCCGCTGATCCCC 61.067 63.158 0.00 0.00 0.00 4.81
222 246 4.498177 GCTTGTTTTGAGAACAGACTTCCC 60.498 45.833 0.00 0.00 0.00 3.97
229 253 4.843220 ATGAGGCTTGTTTTGAGAACAG 57.157 40.909 0.00 0.00 0.00 3.16
236 260 4.610945 ACTCGAAAATGAGGCTTGTTTTG 58.389 39.130 13.31 7.24 40.39 2.44
247 271 3.762407 TGGTGGAAGACTCGAAAATGA 57.238 42.857 0.00 0.00 0.00 2.57
265 289 1.733402 TTGCTTTGTGCCGGACTTGG 61.733 55.000 5.05 0.00 42.00 3.61
289 313 3.032265 AGGGACAGCCAAAGTCTTTTT 57.968 42.857 0.00 0.00 36.29 1.94
296 320 1.000274 CGGAAAAAGGGACAGCCAAAG 60.000 52.381 0.00 0.00 35.15 2.77
314 338 3.555956 CGAATCTCACTTTTATGGTCCGG 59.444 47.826 0.00 0.00 0.00 5.14
316 340 4.571176 GGTCGAATCTCACTTTTATGGTCC 59.429 45.833 0.00 0.00 0.00 4.46
317 341 5.063564 GTGGTCGAATCTCACTTTTATGGTC 59.936 44.000 0.00 0.00 0.00 4.02
323 347 4.561105 GAGAGTGGTCGAATCTCACTTTT 58.439 43.478 7.35 5.72 41.24 2.27
331 355 1.275291 TGGTTGGAGAGTGGTCGAATC 59.725 52.381 0.00 0.00 0.00 2.52
332 356 1.276421 CTGGTTGGAGAGTGGTCGAAT 59.724 52.381 0.00 0.00 0.00 3.34
333 357 0.679505 CTGGTTGGAGAGTGGTCGAA 59.320 55.000 0.00 0.00 0.00 3.71
334 358 1.185618 CCTGGTTGGAGAGTGGTCGA 61.186 60.000 0.00 0.00 38.35 4.20
335 359 1.293498 CCTGGTTGGAGAGTGGTCG 59.707 63.158 0.00 0.00 38.35 4.79
336 360 1.679898 CCCTGGTTGGAGAGTGGTC 59.320 63.158 0.00 0.00 38.35 4.02
337 361 2.529744 GCCCTGGTTGGAGAGTGGT 61.530 63.158 0.00 0.00 38.35 4.16
338 362 2.352805 GCCCTGGTTGGAGAGTGG 59.647 66.667 0.00 0.00 38.35 4.00
339 363 2.352805 GGCCCTGGTTGGAGAGTG 59.647 66.667 0.00 0.00 38.35 3.51
353 377 0.467290 TCCACCTGAAACAACTGGCC 60.467 55.000 0.00 0.00 33.18 5.36
354 378 0.668535 GTCCACCTGAAACAACTGGC 59.331 55.000 0.00 0.00 33.18 4.85
373 397 3.471680 GCTTGGGCTTTGATCTACCTAG 58.528 50.000 0.00 0.00 35.22 3.02
374 398 3.560636 GCTTGGGCTTTGATCTACCTA 57.439 47.619 0.00 0.00 35.22 3.08
375 399 2.426842 GCTTGGGCTTTGATCTACCT 57.573 50.000 0.00 0.00 35.22 3.08
387 411 2.298729 TGTTTTCCAATGTAGCTTGGGC 59.701 45.455 2.34 0.00 44.85 5.36
388 412 3.306019 GGTGTTTTCCAATGTAGCTTGGG 60.306 47.826 2.34 0.00 44.85 4.12
389 413 3.306019 GGGTGTTTTCCAATGTAGCTTGG 60.306 47.826 0.00 0.00 45.91 3.61
390 414 3.306019 GGGGTGTTTTCCAATGTAGCTTG 60.306 47.826 0.00 0.00 0.00 4.01
391 415 2.897326 GGGGTGTTTTCCAATGTAGCTT 59.103 45.455 0.00 0.00 0.00 3.74
392 416 2.158385 TGGGGTGTTTTCCAATGTAGCT 60.158 45.455 0.00 0.00 0.00 3.32
393 417 2.029380 GTGGGGTGTTTTCCAATGTAGC 60.029 50.000 0.00 0.00 34.47 3.58
394 418 3.005367 GTGTGGGGTGTTTTCCAATGTAG 59.995 47.826 0.00 0.00 34.47 2.74
608 637 1.065600 TTGAGTTGGTTGCTTGCGC 59.934 52.632 0.00 0.00 0.00 6.09
696 746 0.701303 GTGTGAATGACGTCGACGAC 59.299 55.000 41.52 34.87 43.02 4.34
859 935 0.870735 GCGTAAAGGCTACGAGGAGC 60.871 60.000 13.66 0.00 42.94 4.70
885 965 2.604174 CGCGCCGGGCTTTTATAGG 61.604 63.158 18.34 0.00 40.44 2.57
941 1029 0.322008 GCTGGTAGCCAAGTGAGCTT 60.322 55.000 0.00 0.00 41.83 3.74
957 1068 1.064296 CGCGACTAGTGGTAGGCTG 59.936 63.158 0.00 0.00 31.04 4.85
958 1069 2.119655 CCGCGACTAGTGGTAGGCT 61.120 63.158 8.23 0.00 45.30 4.58
959 1070 2.412112 CCGCGACTAGTGGTAGGC 59.588 66.667 8.23 0.00 45.30 3.93
979 1090 0.670546 TCAACGAGTGGCTAAGCTGC 60.671 55.000 0.00 0.00 0.00 5.25
985 1096 3.832704 CCATGTCAACGAGTGGCTA 57.167 52.632 0.00 0.00 30.97 3.93
988 1099 1.300971 CTGGCCATGTCAACGAGTGG 61.301 60.000 5.51 0.00 34.84 4.00
990 1101 1.672356 GCTGGCCATGTCAACGAGT 60.672 57.895 5.51 0.00 0.00 4.18
991 1102 1.236616 TTGCTGGCCATGTCAACGAG 61.237 55.000 5.51 0.00 0.00 4.18
992 1103 1.228094 TTGCTGGCCATGTCAACGA 60.228 52.632 5.51 0.00 0.00 3.85
993 1104 1.210931 CTTGCTGGCCATGTCAACG 59.789 57.895 5.51 0.00 0.00 4.10
996 1114 1.672030 CGACTTGCTGGCCATGTCA 60.672 57.895 5.51 1.46 44.55 3.58
1017 1135 2.420890 GCGAGGATCAGCAGGGAG 59.579 66.667 0.00 0.00 35.34 4.30
1097 1224 3.277211 TTCACCGCGTCCTCCTTCG 62.277 63.158 4.92 0.00 0.00 3.79
1338 1471 1.469251 CGTGGACGAGTTCGATCCATT 60.469 52.381 20.46 0.00 44.61 3.16
1371 1523 0.315568 CAGGCTAGCTACCCATCGAC 59.684 60.000 15.72 0.00 0.00 4.20
1374 1526 1.633774 TAGCAGGCTAGCTACCCATC 58.366 55.000 15.72 0.00 44.50 3.51
1433 1588 4.753233 CCTTGCCTATGTATAGCAGCTAG 58.247 47.826 8.43 0.00 0.00 3.42
1444 1599 3.748083 CATACTCATGCCTTGCCTATGT 58.252 45.455 0.00 0.00 0.00 2.29
1460 1615 1.676529 AGTCGCTGATACACGCATACT 59.323 47.619 0.00 0.00 0.00 2.12
1467 1622 4.478195 ACGCAGTCGCTGATACAC 57.522 55.556 10.46 0.00 29.74 2.90
1568 1732 3.411415 AAGCAAAGCGAGATATGCAAC 57.589 42.857 0.00 0.00 41.18 4.17
1570 1734 2.749076 ACAAAGCAAAGCGAGATATGCA 59.251 40.909 0.00 0.00 41.18 3.96
1659 1824 5.181433 ACATAGCAAGCTTCATCATGCATAG 59.819 40.000 0.00 0.00 41.18 2.23
1745 1915 7.544566 CCAAGGATCAAATTCAGATTTTCACTG 59.455 37.037 0.00 0.00 33.25 3.66
1782 1952 4.713553 TGCCTAGATCACTGAAAACAACA 58.286 39.130 0.00 0.00 0.00 3.33
1845 2084 5.336055 CCATCTAGAACATTAGACGCCTAGG 60.336 48.000 3.67 3.67 32.78 3.02
1848 2087 4.215908 TCCATCTAGAACATTAGACGCCT 58.784 43.478 0.00 0.00 32.78 5.52
1926 2169 5.534207 TTGTGTCTTAGGACTCGGTTTAA 57.466 39.130 6.54 0.00 42.54 1.52
1927 2170 5.534207 TTTGTGTCTTAGGACTCGGTTTA 57.466 39.130 6.54 0.00 42.54 2.01
1932 2221 4.252971 TCCTTTTGTGTCTTAGGACTCG 57.747 45.455 6.54 0.00 42.54 4.18
1933 2222 6.511282 CGTTTTCCTTTTGTGTCTTAGGACTC 60.511 42.308 6.54 3.36 42.54 3.36
2061 2378 2.157668 CACGCGTTAAATTCAGCTCTGT 59.842 45.455 10.22 0.00 0.00 3.41
2080 2397 3.637998 TCGTGTCTAAGTTCACCTCAC 57.362 47.619 0.00 0.00 0.00 3.51
2082 2399 4.806330 TCAATCGTGTCTAAGTTCACCTC 58.194 43.478 0.00 0.00 0.00 3.85
2170 2497 1.278127 ACTAAGCGGCTGTGTTATGGT 59.722 47.619 1.81 0.00 0.00 3.55
2191 2518 4.493545 CGACTCGTTTACAAATGGTATGCC 60.494 45.833 0.00 0.00 0.00 4.40
2236 2563 0.942410 GCGTGACTTGTAAGCCGTCA 60.942 55.000 0.00 0.00 35.49 4.35
2244 2571 4.062293 AGTAAAGCATTGCGTGACTTGTA 58.938 39.130 8.61 0.00 0.00 2.41
2245 2572 2.878406 AGTAAAGCATTGCGTGACTTGT 59.122 40.909 8.61 0.00 0.00 3.16
2246 2573 3.482786 GAGTAAAGCATTGCGTGACTTG 58.517 45.455 14.74 0.00 0.00 3.16
2248 2575 2.076863 GGAGTAAAGCATTGCGTGACT 58.923 47.619 13.66 13.66 0.00 3.41
2249 2576 1.201921 CGGAGTAAAGCATTGCGTGAC 60.202 52.381 4.05 4.05 0.00 3.67
2250 2577 1.075542 CGGAGTAAAGCATTGCGTGA 58.924 50.000 2.38 0.00 0.00 4.35
2251 2578 0.096976 CCGGAGTAAAGCATTGCGTG 59.903 55.000 0.00 0.00 0.00 5.34
2252 2579 1.644786 GCCGGAGTAAAGCATTGCGT 61.645 55.000 5.05 0.00 0.00 5.24
2253 2580 1.062525 GCCGGAGTAAAGCATTGCG 59.937 57.895 5.05 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.