Multiple sequence alignment - TraesCS1B01G425400

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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 TraesCS1B01G425400 chr1B 100.000 2675 0 0 1 2675 651278169 651280843 0.000000e+00 4940.0
1 TraesCS1B01G425400 chr1D 91.272 2658 151 22 47 2675 469805510 469808115 0.000000e+00 3548.0
2 TraesCS1B01G425400 chr1D 73.476 328 49 29 42 352 469805142 469805448 3.670000e-14 89.8
3 TraesCS1B01G425400 chr1A 87.823 2710 210 59 47 2675 562911939 562914609 0.000000e+00 3066.0


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 TraesCS1B01G425400 chr1B 651278169 651280843 2674 False 4940.0 4940 100.000 1 2675 1 chr1B.!!$F1 2674
1 TraesCS1B01G425400 chr1D 469805142 469808115 2973 False 1818.9 3548 82.374 42 2675 2 chr1D.!!$F1 2633
2 TraesCS1B01G425400 chr1A 562911939 562914609 2670 False 3066.0 3066 87.823 47 2675 1 chr1A.!!$F1 2628

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
406 745 0.674895 ACGAGAGCTCACCAAATGCC 60.675 55.0 17.77 0.0 0.0 4.4 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2431 0.319728 TCAGTCCAGCAAGACAGAGC 59.68 55.0 8.62 0.0 39.34 4.09 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
29 30 9.897744 AAATATGAAACAGTGTGTGAGTAATTG 57.102 29.630 0.00 0.00 0.00 2.32
31 32 5.189928 TGAAACAGTGTGTGAGTAATTGGT 58.810 37.500 0.00 0.00 0.00 3.67
32 33 6.350103 TGAAACAGTGTGTGAGTAATTGGTA 58.650 36.000 0.00 0.00 0.00 3.25
34 35 6.801539 AACAGTGTGTGAGTAATTGGTATG 57.198 37.500 0.00 0.00 0.00 2.39
36 37 4.937620 CAGTGTGTGAGTAATTGGTATGCT 59.062 41.667 0.00 0.00 0.00 3.79
37 38 5.063944 CAGTGTGTGAGTAATTGGTATGCTC 59.936 44.000 0.00 0.00 0.00 4.26
38 39 5.046304 AGTGTGTGAGTAATTGGTATGCTCT 60.046 40.000 0.00 0.00 0.00 4.09
39 40 6.154534 AGTGTGTGAGTAATTGGTATGCTCTA 59.845 38.462 0.00 0.00 0.00 2.43
40 41 6.816640 GTGTGTGAGTAATTGGTATGCTCTAA 59.183 38.462 0.00 0.00 0.00 2.10
41 42 7.495934 GTGTGTGAGTAATTGGTATGCTCTAAT 59.504 37.037 0.00 0.00 0.00 1.73
43 44 9.542462 GTGTGAGTAATTGGTATGCTCTAATAA 57.458 33.333 0.00 0.00 0.00 1.40
45 46 9.765795 GTGAGTAATTGGTATGCTCTAATAACT 57.234 33.333 0.00 0.00 0.00 2.24
48 371 8.639761 AGTAATTGGTATGCTCTAATAACTCGT 58.360 33.333 0.00 0.00 0.00 4.18
75 398 5.897050 TGTTGGAATTTTCAACACTGTACC 58.103 37.500 17.48 0.00 46.29 3.34
88 411 8.129496 TCAACACTGTACCTAATCAATCTACA 57.871 34.615 0.00 0.00 0.00 2.74
91 414 6.668283 ACACTGTACCTAATCAATCTACAGGT 59.332 38.462 7.77 0.00 42.25 4.00
92 415 7.180408 ACACTGTACCTAATCAATCTACAGGTT 59.820 37.037 7.77 0.00 40.14 3.50
115 438 7.775561 GGTTATCTGTTCAATTCCAGTCCTAAT 59.224 37.037 0.00 0.00 0.00 1.73
163 486 9.752274 GAAATGCGAAAGATATCTTATGATGTC 57.248 33.333 18.23 9.93 39.96 3.06
166 489 6.870439 TGCGAAAGATATCTTATGATGTCTGG 59.130 38.462 18.23 10.68 46.05 3.86
178 501 8.515414 TCTTATGATGTCTGGTATACTCGATTG 58.485 37.037 2.25 0.00 0.00 2.67
182 505 8.002984 TGATGTCTGGTATACTCGATTGTAAA 57.997 34.615 2.25 0.00 0.00 2.01
184 507 9.130312 GATGTCTGGTATACTCGATTGTAAATC 57.870 37.037 2.25 0.00 0.00 2.17
204 527 1.714899 GGCGCTGCCGTTAACATGAT 61.715 55.000 7.64 0.00 39.62 2.45
212 535 3.619483 TGCCGTTAACATGATTAGGAACG 59.381 43.478 6.39 0.40 39.38 3.95
214 537 4.025979 GCCGTTAACATGATTAGGAACGAG 60.026 45.833 6.39 0.00 41.52 4.18
216 539 5.231568 CCGTTAACATGATTAGGAACGAGTC 59.768 44.000 6.39 0.00 41.52 3.36
229 552 2.949714 ACGAGTCAACAAAGCATTCG 57.050 45.000 0.00 0.00 0.00 3.34
238 561 7.871853 AGTCAACAAAGCATTCGTTACTTTAT 58.128 30.769 0.00 0.00 32.54 1.40
244 567 8.995220 ACAAAGCATTCGTTACTTTATCAAGTA 58.005 29.630 0.00 0.00 41.81 2.24
264 587 9.639601 TCAAGTATTCACAGTACAAATCTAGTG 57.360 33.333 0.00 0.00 0.00 2.74
265 588 9.639601 CAAGTATTCACAGTACAAATCTAGTGA 57.360 33.333 0.00 0.00 34.54 3.41
292 615 8.853077 ATTTAGATTAAGGATCGCAATGATGA 57.147 30.769 0.00 0.00 39.85 2.92
295 618 4.422073 TTAAGGATCGCAATGATGACCT 57.578 40.909 0.00 0.00 37.47 3.85
298 621 4.000331 AGGATCGCAATGATGACCTAAG 58.000 45.455 0.00 0.00 37.47 2.18
329 663 2.411748 CGACGAACTGAATAAGCTTGCA 59.588 45.455 9.86 3.79 0.00 4.08
330 664 3.120683 CGACGAACTGAATAAGCTTGCAA 60.121 43.478 9.86 0.00 0.00 4.08
339 673 6.643770 ACTGAATAAGCTTGCAAAATGAACAG 59.356 34.615 9.86 7.87 0.00 3.16
341 675 6.864685 TGAATAAGCTTGCAAAATGAACAGAG 59.135 34.615 9.86 0.00 0.00 3.35
344 678 3.887716 AGCTTGCAAAATGAACAGAGAGT 59.112 39.130 0.00 0.00 0.00 3.24
347 681 3.554934 TGCAAAATGAACAGAGAGTGGT 58.445 40.909 0.00 0.00 0.00 4.16
348 682 3.316029 TGCAAAATGAACAGAGAGTGGTG 59.684 43.478 0.00 0.00 0.00 4.17
360 699 2.740981 GAGAGTGGTGAAACATGCTGAG 59.259 50.000 0.00 0.00 39.98 3.35
362 701 3.141398 GAGTGGTGAAACATGCTGAGAA 58.859 45.455 0.00 0.00 39.98 2.87
363 702 3.755378 GAGTGGTGAAACATGCTGAGAAT 59.245 43.478 0.00 0.00 39.98 2.40
405 744 1.135859 CAACGAGAGCTCACCAAATGC 60.136 52.381 17.77 0.00 0.00 3.56
406 745 0.674895 ACGAGAGCTCACCAAATGCC 60.675 55.000 17.77 0.00 0.00 4.40
424 763 3.151022 GAGTCCTGGGAGGCGAGG 61.151 72.222 0.00 0.00 34.61 4.63
566 905 3.060615 CCTCGGGTTCGTCCTCGT 61.061 66.667 0.00 0.00 38.33 4.18
790 1134 1.841103 GGAGCAGAGGGGAGGGATC 60.841 68.421 0.00 0.00 0.00 3.36
814 1174 1.398692 TTTGCAGTTCAACCCCTGAC 58.601 50.000 0.00 0.00 33.73 3.51
824 1184 2.303022 TCAACCCCTGACACTCTTCATC 59.697 50.000 0.00 0.00 0.00 2.92
837 1197 5.152097 CACTCTTCATCAGAACAAATGTGC 58.848 41.667 0.00 0.00 0.00 4.57
888 1256 5.640732 GCAGGGCCATTTTATGATTATACG 58.359 41.667 6.18 0.00 0.00 3.06
916 1285 0.831307 AGGGCCTTAAGCTTCTACGG 59.169 55.000 0.00 0.19 43.05 4.02
1128 1509 0.317479 CCCTCGTCCTCGTCAAGTTT 59.683 55.000 0.00 0.00 38.33 2.66
1599 1980 1.519455 GGTGATCGAGAAGGTGCCG 60.519 63.158 0.00 0.00 0.00 5.69
1632 2013 2.703798 CCCGGAGTACGCCTTCGAA 61.704 63.158 14.12 0.00 45.67 3.71
1647 2028 3.684788 CCTTCGAAGAATCCGATGTGTTT 59.315 43.478 26.61 0.00 45.90 2.83
1680 2061 3.093278 CCGCGGCAGTGAGATTTC 58.907 61.111 14.67 0.00 0.00 2.17
1712 2093 2.256174 CAGGCATTTGCTCGTCATTTG 58.744 47.619 2.12 0.00 41.70 2.32
1754 2135 8.424133 AGAATTGCTTATTCCAGTTCAAAAGTT 58.576 29.630 8.05 0.00 43.08 2.66
1761 2142 9.665264 CTTATTCCAGTTCAAAAGTTTGAGTAC 57.335 33.333 6.58 4.04 46.68 2.73
1817 2198 2.034939 CAGTGCTGAATGTTTGGCTTCA 59.965 45.455 0.00 0.00 0.00 3.02
1894 2275 6.500684 ACATGTCAGGTATTTCATGTTCAC 57.499 37.500 0.00 0.00 45.30 3.18
1900 2281 4.566759 CAGGTATTTCATGTTCACGATCGT 59.433 41.667 16.60 16.60 0.00 3.73
1909 2290 3.915536 TGTTCACGATCGTATTTGTCCA 58.084 40.909 22.26 7.99 0.00 4.02
1918 2305 4.368874 TCGTATTTGTCCATTGCATTGG 57.631 40.909 19.55 19.55 38.18 3.16
1986 2381 6.360370 AAGCATCCTAACACTCAACTTCTA 57.640 37.500 0.00 0.00 0.00 2.10
1987 2382 6.552445 AGCATCCTAACACTCAACTTCTAT 57.448 37.500 0.00 0.00 0.00 1.98
1988 2383 6.344500 AGCATCCTAACACTCAACTTCTATG 58.656 40.000 0.00 0.00 0.00 2.23
1989 2384 6.070538 AGCATCCTAACACTCAACTTCTATGT 60.071 38.462 0.00 0.00 0.00 2.29
1990 2385 6.256757 GCATCCTAACACTCAACTTCTATGTC 59.743 42.308 0.00 0.00 0.00 3.06
1991 2386 6.911250 TCCTAACACTCAACTTCTATGTCA 57.089 37.500 0.00 0.00 0.00 3.58
1992 2387 7.297936 TCCTAACACTCAACTTCTATGTCAA 57.702 36.000 0.00 0.00 0.00 3.18
1993 2388 7.732025 TCCTAACACTCAACTTCTATGTCAAA 58.268 34.615 0.00 0.00 0.00 2.69
1994 2389 8.208224 TCCTAACACTCAACTTCTATGTCAAAA 58.792 33.333 0.00 0.00 0.00 2.44
1995 2390 9.003658 CCTAACACTCAACTTCTATGTCAAAAT 57.996 33.333 0.00 0.00 0.00 1.82
1997 2392 8.450578 AACACTCAACTTCTATGTCAAAATCA 57.549 30.769 0.00 0.00 0.00 2.57
1998 2393 8.450578 ACACTCAACTTCTATGTCAAAATCAA 57.549 30.769 0.00 0.00 0.00 2.57
1999 2394 8.902806 ACACTCAACTTCTATGTCAAAATCAAA 58.097 29.630 0.00 0.00 0.00 2.69
2000 2395 9.734620 CACTCAACTTCTATGTCAAAATCAAAA 57.265 29.630 0.00 0.00 0.00 2.44
2001 2396 9.736023 ACTCAACTTCTATGTCAAAATCAAAAC 57.264 29.630 0.00 0.00 0.00 2.43
2002 2397 9.956720 CTCAACTTCTATGTCAAAATCAAAACT 57.043 29.630 0.00 0.00 0.00 2.66
2036 2431 5.852738 ATCAAATCTTCTTGTGAGTGACG 57.147 39.130 0.00 0.00 0.00 4.35
2050 2445 3.867771 GACGCTCTGTCTTGCTGG 58.132 61.111 0.00 0.00 44.58 4.85
2086 2481 3.200165 CCCTCTTTCCAACTAGGGTAAGG 59.800 52.174 0.00 0.00 43.26 2.69
2136 2531 9.658799 TTAAGAGATAATTGACTCAACTTCTGG 57.341 33.333 13.44 0.00 35.83 3.86
2190 2585 7.173907 ACACTCTGTTTTGATTAACTGATGGAG 59.826 37.037 0.00 0.00 36.05 3.86
2245 2640 5.762218 CAGGAGATAATTGAATGTGACTCCC 59.238 44.000 0.00 0.00 42.20 4.30
2247 2642 5.163152 GGAGATAATTGAATGTGACTCCCCT 60.163 44.000 0.00 0.00 37.34 4.79
2312 2710 7.166473 GTCATGTCTTCTGTTGTTTAAAGCAAG 59.834 37.037 0.00 0.00 0.00 4.01
2315 2713 8.046294 TGTCTTCTGTTGTTTAAAGCAAGTAA 57.954 30.769 0.00 0.00 0.00 2.24
2316 2714 8.181573 TGTCTTCTGTTGTTTAAAGCAAGTAAG 58.818 33.333 0.00 2.06 0.00 2.34
2317 2715 8.182227 GTCTTCTGTTGTTTAAAGCAAGTAAGT 58.818 33.333 0.00 0.00 0.00 2.24
2318 2716 9.386010 TCTTCTGTTGTTTAAAGCAAGTAAGTA 57.614 29.630 0.00 0.00 0.00 2.24
2362 2760 5.476599 TGAAATGGTGGTGAAAACCTGATAG 59.523 40.000 0.00 0.00 38.60 2.08
2404 2802 1.045911 TTTGGCCTTTTGGGAAGCGT 61.046 50.000 3.32 0.00 40.82 5.07
2507 2918 1.169034 GCCCTTGATGAGGCGAATCC 61.169 60.000 0.00 0.00 44.85 3.01
2521 2932 2.722094 CGAATCCAGTTCCATTTCCCA 58.278 47.619 0.00 0.00 33.04 4.37
2562 2973 2.996631 AGTTGAAGCCATGACTGGATC 58.003 47.619 0.00 0.00 46.37 3.36
2579 2990 2.102578 GATCCAAGGGGGTGAATTGTG 58.897 52.381 0.00 0.00 38.11 3.33
2580 2991 0.114168 TCCAAGGGGGTGAATTGTGG 59.886 55.000 0.00 0.00 38.11 4.17
2581 2992 0.904394 CCAAGGGGGTGAATTGTGGG 60.904 60.000 0.00 0.00 0.00 4.61
2591 3002 2.428171 GTGAATTGTGGGTCATGGATGG 59.572 50.000 0.00 0.00 0.00 3.51
2594 3005 1.508667 TTGTGGGTCATGGATGGGCT 61.509 55.000 0.00 0.00 0.00 5.19
2650 3071 1.808945 GCTTGTGTCCATCCTGAAGTG 59.191 52.381 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.897744 CAATTACTCACACACTGTTTCATATTT 57.102 29.630 0.00 0.00 0.00 1.40
4 5 8.514594 CCAATTACTCACACACTGTTTCATATT 58.485 33.333 0.00 0.00 0.00 1.28
5 6 7.665559 ACCAATTACTCACACACTGTTTCATAT 59.334 33.333 0.00 0.00 0.00 1.78
6 7 6.995686 ACCAATTACTCACACACTGTTTCATA 59.004 34.615 0.00 0.00 0.00 2.15
7 8 5.827797 ACCAATTACTCACACACTGTTTCAT 59.172 36.000 0.00 0.00 0.00 2.57
10 11 6.293955 GCATACCAATTACTCACACACTGTTT 60.294 38.462 0.00 0.00 0.00 2.83
11 12 5.181245 GCATACCAATTACTCACACACTGTT 59.819 40.000 0.00 0.00 0.00 3.16
12 13 4.695455 GCATACCAATTACTCACACACTGT 59.305 41.667 0.00 0.00 0.00 3.55
13 14 4.937620 AGCATACCAATTACTCACACACTG 59.062 41.667 0.00 0.00 0.00 3.66
16 17 5.420725 AGAGCATACCAATTACTCACACA 57.579 39.130 0.00 0.00 0.00 3.72
18 19 9.542462 GTTATTAGAGCATACCAATTACTCACA 57.458 33.333 0.00 0.00 0.00 3.58
19 20 9.765795 AGTTATTAGAGCATACCAATTACTCAC 57.234 33.333 0.00 0.00 0.00 3.51
21 22 9.130312 CGAGTTATTAGAGCATACCAATTACTC 57.870 37.037 0.00 0.00 35.36 2.59
22 23 8.639761 ACGAGTTATTAGAGCATACCAATTACT 58.360 33.333 0.00 0.00 0.00 2.24
23 24 8.813643 ACGAGTTATTAGAGCATACCAATTAC 57.186 34.615 0.00 0.00 0.00 1.89
28 29 8.418662 ACAATAACGAGTTATTAGAGCATACCA 58.581 33.333 17.61 0.00 42.11 3.25
29 30 8.813643 ACAATAACGAGTTATTAGAGCATACC 57.186 34.615 17.61 0.00 42.11 2.73
31 32 9.256477 CCAACAATAACGAGTTATTAGAGCATA 57.744 33.333 17.61 0.00 42.11 3.14
32 33 7.985184 TCCAACAATAACGAGTTATTAGAGCAT 59.015 33.333 17.61 0.00 42.11 3.79
34 35 7.766219 TCCAACAATAACGAGTTATTAGAGC 57.234 36.000 17.61 0.00 42.11 4.09
41 42 9.453325 GTTGAAAATTCCAACAATAACGAGTTA 57.547 29.630 14.93 0.00 42.40 2.24
43 44 7.924103 GTTGAAAATTCCAACAATAACGAGT 57.076 32.000 14.93 0.00 42.40 4.18
88 411 5.251700 AGGACTGGAATTGAACAGATAACCT 59.748 40.000 8.03 0.00 38.09 3.50
97 420 6.823689 TGCTCTTATTAGGACTGGAATTGAAC 59.176 38.462 0.00 0.00 0.00 3.18
98 421 6.823689 GTGCTCTTATTAGGACTGGAATTGAA 59.176 38.462 0.00 0.00 35.17 2.69
100 423 6.115446 TGTGCTCTTATTAGGACTGGAATTG 58.885 40.000 0.00 0.00 38.53 2.32
104 427 4.353777 ACTGTGCTCTTATTAGGACTGGA 58.646 43.478 7.18 0.00 39.84 3.86
151 474 8.815565 ATCGAGTATACCAGACATCATAAGAT 57.184 34.615 0.00 0.00 33.87 2.40
152 475 8.515414 CAATCGAGTATACCAGACATCATAAGA 58.485 37.037 0.00 0.00 0.00 2.10
156 479 6.656632 ACAATCGAGTATACCAGACATCAT 57.343 37.500 0.00 0.00 0.00 2.45
163 486 5.345202 GCCGATTTACAATCGAGTATACCAG 59.655 44.000 18.22 2.12 43.59 4.00
166 489 4.201466 GCGCCGATTTACAATCGAGTATAC 60.201 45.833 18.22 0.00 43.59 1.47
204 527 3.799366 TGCTTTGTTGACTCGTTCCTAA 58.201 40.909 0.00 0.00 0.00 2.69
212 535 5.344207 AGTAACGAATGCTTTGTTGACTC 57.656 39.130 10.17 2.24 37.79 3.36
214 537 7.801315 TGATAAAGTAACGAATGCTTTGTTGAC 59.199 33.333 15.13 6.33 42.88 3.18
216 539 8.500837 TTGATAAAGTAACGAATGCTTTGTTG 57.499 30.769 15.13 0.00 42.88 3.33
238 561 9.639601 CACTAGATTTGTACTGTGAATACTTGA 57.360 33.333 0.00 0.00 0.00 3.02
263 586 9.942850 TCATTGCGATCCTTAATCTAAATATCA 57.057 29.630 0.00 0.00 31.68 2.15
274 597 4.422073 AGGTCATCATTGCGATCCTTAA 57.578 40.909 0.00 0.00 26.22 1.85
275 598 5.070446 ACTTAGGTCATCATTGCGATCCTTA 59.930 40.000 0.00 0.00 32.10 2.69
295 618 2.129607 GTTCGTCGCTTCAACCACTTA 58.870 47.619 0.00 0.00 0.00 2.24
298 621 0.232303 CAGTTCGTCGCTTCAACCAC 59.768 55.000 0.00 0.00 0.00 4.16
329 663 5.652014 TGTTTCACCACTCTCTGTTCATTTT 59.348 36.000 0.00 0.00 0.00 1.82
330 664 5.192927 TGTTTCACCACTCTCTGTTCATTT 58.807 37.500 0.00 0.00 0.00 2.32
339 673 2.740981 CTCAGCATGTTTCACCACTCTC 59.259 50.000 0.00 0.00 37.40 3.20
341 675 2.771089 TCTCAGCATGTTTCACCACTC 58.229 47.619 0.00 0.00 37.40 3.51
344 678 5.164620 TCTATTCTCAGCATGTTTCACCA 57.835 39.130 0.00 0.00 37.40 4.17
347 681 4.330894 CGCTTCTATTCTCAGCATGTTTCA 59.669 41.667 0.00 0.00 37.40 2.69
348 682 4.260538 CCGCTTCTATTCTCAGCATGTTTC 60.261 45.833 0.00 0.00 37.40 2.78
360 699 3.324035 CGGCTGCCGCTTCTATTC 58.676 61.111 29.58 0.00 41.17 1.75
386 725 1.160137 GCATTTGGTGAGCTCTCGTT 58.840 50.000 16.19 0.00 0.00 3.85
387 726 0.674895 GGCATTTGGTGAGCTCTCGT 60.675 55.000 16.19 0.00 0.00 4.18
406 745 3.522731 CTCGCCTCCCAGGACTCG 61.523 72.222 0.00 0.00 37.67 4.18
559 898 2.753043 TGGGACCGCTACGAGGAC 60.753 66.667 0.00 0.00 0.00 3.85
566 905 1.987855 CCTCCAACTGGGACCGCTA 60.988 63.158 0.00 0.00 42.15 4.26
790 1134 3.016736 AGGGGTTGAACTGCAAATATCG 58.983 45.455 0.00 0.00 38.44 2.92
814 1174 5.152097 GCACATTTGTTCTGATGAAGAGTG 58.848 41.667 0.00 0.00 35.91 3.51
824 1184 1.061799 GCGAGCGCACATTTGTTCTG 61.062 55.000 11.47 0.00 41.49 3.02
837 1197 2.351336 ATAGAAACCCTCGGCGAGCG 62.351 60.000 30.55 24.81 0.00 5.03
888 1256 1.087501 CTTAAGGCCCTCGTGAAAGC 58.912 55.000 0.00 0.00 0.00 3.51
916 1285 2.435059 GCGGAACTGTCCTGAGGC 60.435 66.667 0.00 0.00 42.44 4.70
946 1315 1.530655 ACGGAAGGGTTTTGCCTGG 60.531 57.895 0.00 0.00 37.43 4.45
1506 1887 3.064987 CTGGTACCCGAGGAGCACG 62.065 68.421 10.07 0.00 0.00 5.34
1581 1962 1.519455 CGGCACCTTCTCGATCACC 60.519 63.158 0.00 0.00 0.00 4.02
1632 2013 2.744202 GAGCACAAACACATCGGATTCT 59.256 45.455 0.00 0.00 0.00 2.40
1754 2135 5.237815 CAGCCATCACAACTAAGTACTCAA 58.762 41.667 0.00 0.00 0.00 3.02
1761 2142 3.057969 TCACCAGCCATCACAACTAAG 57.942 47.619 0.00 0.00 0.00 2.18
1843 2224 1.451651 GCAAAACATCGGCGAAACTTG 59.548 47.619 15.93 15.70 0.00 3.16
1894 2275 3.942539 TGCAATGGACAAATACGATCG 57.057 42.857 14.88 14.88 0.00 3.69
1900 2281 4.092279 TCACCCAATGCAATGGACAAATA 58.908 39.130 22.85 0.00 43.54 1.40
1909 2290 2.127271 TGTCGATCACCCAATGCAAT 57.873 45.000 0.00 0.00 0.00 3.56
1918 2305 6.863126 ACATTGAATTTCTTTTGTCGATCACC 59.137 34.615 0.00 0.00 0.00 4.02
1986 2381 7.546358 TGACACAGAAGTTTTGATTTTGACAT 58.454 30.769 0.00 0.00 0.00 3.06
1987 2382 6.918626 TGACACAGAAGTTTTGATTTTGACA 58.081 32.000 0.00 0.00 0.00 3.58
1988 2383 7.810766 TTGACACAGAAGTTTTGATTTTGAC 57.189 32.000 0.00 0.00 0.00 3.18
1989 2384 8.824159 TTTTGACACAGAAGTTTTGATTTTGA 57.176 26.923 0.00 0.00 0.00 2.69
1990 2385 9.693157 GATTTTGACACAGAAGTTTTGATTTTG 57.307 29.630 0.00 0.00 0.00 2.44
1991 2386 9.434420 TGATTTTGACACAGAAGTTTTGATTTT 57.566 25.926 0.00 0.00 0.00 1.82
1992 2387 9.434420 TTGATTTTGACACAGAAGTTTTGATTT 57.566 25.926 0.00 0.00 0.00 2.17
1993 2388 9.434420 TTTGATTTTGACACAGAAGTTTTGATT 57.566 25.926 0.00 0.00 0.00 2.57
1994 2389 9.603921 ATTTGATTTTGACACAGAAGTTTTGAT 57.396 25.926 0.00 0.00 0.00 2.57
1995 2390 9.086336 GATTTGATTTTGACACAGAAGTTTTGA 57.914 29.630 0.00 0.00 0.00 2.69
1996 2391 9.090692 AGATTTGATTTTGACACAGAAGTTTTG 57.909 29.630 0.00 0.00 0.00 2.44
1997 2392 9.657419 AAGATTTGATTTTGACACAGAAGTTTT 57.343 25.926 0.00 0.00 0.00 2.43
1998 2393 9.305925 GAAGATTTGATTTTGACACAGAAGTTT 57.694 29.630 0.00 0.00 0.00 2.66
1999 2394 8.689972 AGAAGATTTGATTTTGACACAGAAGTT 58.310 29.630 0.00 0.00 0.00 2.66
2000 2395 8.230472 AGAAGATTTGATTTTGACACAGAAGT 57.770 30.769 0.00 0.00 0.00 3.01
2001 2396 8.965172 CAAGAAGATTTGATTTTGACACAGAAG 58.035 33.333 0.00 0.00 0.00 2.85
2002 2397 8.469200 ACAAGAAGATTTGATTTTGACACAGAA 58.531 29.630 0.00 0.00 0.00 3.02
2003 2398 7.916977 CACAAGAAGATTTGATTTTGACACAGA 59.083 33.333 0.00 0.00 0.00 3.41
2036 2431 0.319728 TCAGTCCAGCAAGACAGAGC 59.680 55.000 8.62 0.00 39.34 4.09
2047 2442 1.064166 AGGGGCATTTCATCAGTCCAG 60.064 52.381 0.00 0.00 0.00 3.86
2050 2445 2.725221 AGAGGGGCATTTCATCAGTC 57.275 50.000 0.00 0.00 0.00 3.51
2136 2531 6.668323 TCACAAAGAAGATTTGATTTCGACC 58.332 36.000 7.30 0.00 33.83 4.79
2190 2585 2.356227 GGAGGAGGGACATTTCCAGTTC 60.356 54.545 0.00 0.00 44.98 3.01
2245 2640 4.454678 TCAGCTAGATTTTGCATACCAGG 58.545 43.478 0.00 0.00 0.00 4.45
2247 2642 5.102953 ACTCAGCTAGATTTTGCATACCA 57.897 39.130 0.00 0.00 0.00 3.25
2312 2710 3.074412 ACCACAGCAGCAACATACTTAC 58.926 45.455 0.00 0.00 0.00 2.34
2315 2713 2.276732 AACCACAGCAGCAACATACT 57.723 45.000 0.00 0.00 0.00 2.12
2316 2714 3.369546 AAAACCACAGCAGCAACATAC 57.630 42.857 0.00 0.00 0.00 2.39
2317 2715 4.764308 TCATAAAACCACAGCAGCAACATA 59.236 37.500 0.00 0.00 0.00 2.29
2318 2716 3.573538 TCATAAAACCACAGCAGCAACAT 59.426 39.130 0.00 0.00 0.00 2.71
2362 2760 4.327680 ACTAGTGGCTCTTTCACAAATCC 58.672 43.478 0.00 0.00 37.58 3.01
2404 2802 2.027561 AGTTCAAGCCGTATAAGCACCA 60.028 45.455 0.00 0.00 0.00 4.17
2449 2848 4.216042 CACAGTTTCAATGTGCCATAGACA 59.784 41.667 0.00 0.00 41.39 3.41
2507 2918 6.358974 AGGTAAAAATGGGAAATGGAACTG 57.641 37.500 0.00 0.00 0.00 3.16
2521 2932 8.097662 TCAACTTCAACACCAAAAGGTAAAAAT 58.902 29.630 0.00 0.00 0.00 1.82
2562 2973 0.904394 CCCACAATTCACCCCCTTGG 60.904 60.000 0.00 0.00 41.37 3.61
2579 2990 1.039233 CAACAGCCCATCCATGACCC 61.039 60.000 0.00 0.00 0.00 4.46
2580 2991 0.034186 TCAACAGCCCATCCATGACC 60.034 55.000 0.00 0.00 0.00 4.02
2581 2992 1.747355 CTTCAACAGCCCATCCATGAC 59.253 52.381 0.00 0.00 0.00 3.06
2594 3005 0.516877 CGGAATCGCAAGCTTCAACA 59.483 50.000 0.00 0.00 43.92 3.33
2606 3017 0.315382 GCGCAAATCACTCGGAATCG 60.315 55.000 0.30 0.00 37.82 3.34
2641 3062 2.042464 AGCAAGAGACACACTTCAGGA 58.958 47.619 0.00 0.00 0.00 3.86
2650 3071 2.162408 GCATAACCCAAGCAAGAGACAC 59.838 50.000 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.