Multiple sequence alignment - TraesCS7B01G125200

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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 TraesCS7B01G125200 chr7B 100.000 2447 0 0 1 2447 146256283 146258729 0.000000e+00 4519
1 TraesCS7B01G125200 chr7B 86.704 1429 171 13 224 1649 653800141 653801553 0.000000e+00 1568
2 TraesCS7B01G125200 chr7D 89.472 2460 224 16 1 2433 180592745 180595196 0.000000e+00 3075
3 TraesCS7B01G125200 chr7D 87.339 1706 181 16 1 1685 585183046 585184737 0.000000e+00 1921
4 TraesCS7B01G125200 chr7D 87.163 1706 179 19 1 1685 585192066 585193752 0.000000e+00 1901
5 TraesCS7B01G125200 chr7A 91.103 1832 155 5 1 1828 185063605 185065432 0.000000e+00 2473
6 TraesCS7B01G125200 chr7A 91.043 1831 156 5 1 1828 185133062 185134887 0.000000e+00 2466
7 TraesCS7B01G125200 chr7A 90.611 1832 161 6 1 1828 184971647 184973471 0.000000e+00 2420
8 TraesCS7B01G125200 chr7A 79.631 1139 201 27 339 1467 566562665 566563782 0.000000e+00 789
9 TraesCS7B01G125200 chr7A 81.975 638 89 11 1820 2433 185135327 185135962 3.610000e-143 518
10 TraesCS7B01G125200 chr5B 86.533 1693 194 14 1 1675 684386446 684388122 0.000000e+00 1832
11 TraesCS7B01G125200 chr1A 77.355 1157 233 26 322 1467 393999147 394000285 0.000000e+00 658


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 TraesCS7B01G125200 chr7B 146256283 146258729 2446 False 4519 4519 100.000 1 2447 1 chr7B.!!$F1 2446
1 TraesCS7B01G125200 chr7B 653800141 653801553 1412 False 1568 1568 86.704 224 1649 1 chr7B.!!$F2 1425
2 TraesCS7B01G125200 chr7D 180592745 180595196 2451 False 3075 3075 89.472 1 2433 1 chr7D.!!$F1 2432
3 TraesCS7B01G125200 chr7D 585183046 585184737 1691 False 1921 1921 87.339 1 1685 1 chr7D.!!$F2 1684
4 TraesCS7B01G125200 chr7D 585192066 585193752 1686 False 1901 1901 87.163 1 1685 1 chr7D.!!$F3 1684
5 TraesCS7B01G125200 chr7A 185063605 185065432 1827 False 2473 2473 91.103 1 1828 1 chr7A.!!$F2 1827
6 TraesCS7B01G125200 chr7A 184971647 184973471 1824 False 2420 2420 90.611 1 1828 1 chr7A.!!$F1 1827
7 TraesCS7B01G125200 chr7A 185133062 185135962 2900 False 1492 2466 86.509 1 2433 2 chr7A.!!$F4 2432
8 TraesCS7B01G125200 chr7A 566562665 566563782 1117 False 789 789 79.631 339 1467 1 chr7A.!!$F3 1128
9 TraesCS7B01G125200 chr5B 684386446 684388122 1676 False 1832 1832 86.533 1 1675 1 chr5B.!!$F1 1674
10 TraesCS7B01G125200 chr1A 393999147 394000285 1138 False 658 658 77.355 322 1467 1 chr1A.!!$F1 1145

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
360 381 0.03467 GGTTCTGCTCCTTGCCATCT 60.035 55.0 0.0 0.0 42.0 2.9 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2405 0.10576 TCCATGTGCCTTTTGTGGGT 60.106 50.0 0.0 0.0 0.0 4.51 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
165 186 2.433970 GCAGGAGCCTCTTTCTACTCAT 59.566 50.000 0.00 0.00 33.58 2.90
183 204 1.468127 CATTACATCGTGCAAGCACCA 59.532 47.619 18.54 7.30 43.49 4.17
220 241 9.635404 TCCCCAATACTTAATTATGTAAAGGTG 57.365 33.333 19.82 14.16 0.00 4.00
268 289 4.499183 TGTTAAACCAAAGCAAACCACAG 58.501 39.130 0.00 0.00 0.00 3.66
275 296 3.305335 CCAAAGCAAACCACAGACATACC 60.305 47.826 0.00 0.00 0.00 2.73
276 297 2.949177 AGCAAACCACAGACATACCA 57.051 45.000 0.00 0.00 0.00 3.25
301 322 7.009631 CACATACTACAGTTAGTTGCTAGCAAG 59.990 40.741 29.99 18.88 39.43 4.01
309 330 2.213499 AGTTGCTAGCAAGACACACAC 58.787 47.619 29.99 16.34 36.52 3.82
310 331 1.939934 GTTGCTAGCAAGACACACACA 59.060 47.619 29.99 1.96 36.52 3.72
317 338 4.541973 AGCAAGACACACACATCATCTA 57.458 40.909 0.00 0.00 0.00 1.98
331 352 3.998913 TCATCTAGTCAACATGGCCAA 57.001 42.857 10.96 0.00 0.00 4.52
345 366 1.745890 GCCAACCCACCAAAGGTTC 59.254 57.895 0.00 0.00 44.42 3.62
360 381 0.034670 GGTTCTGCTCCTTGCCATCT 60.035 55.000 0.00 0.00 42.00 2.90
402 423 0.603065 TTCAGTTCTAGCAGCTCGCA 59.397 50.000 0.00 0.00 46.13 5.10
422 443 2.740981 CAAGCTCAGTGATGACTTGTCC 59.259 50.000 16.73 0.00 34.43 4.02
432 453 3.132824 TGATGACTTGTCCATCGTAGCAT 59.867 43.478 0.00 0.00 42.37 3.79
482 503 0.796312 GTGTGTACAAGGATGCCACG 59.204 55.000 0.00 0.00 35.54 4.94
500 521 2.932614 CACGGAGAAGGCTCATAAGTTG 59.067 50.000 0.00 0.00 43.14 3.16
696 717 0.877071 CGTGAGCTTGGATGCACTTT 59.123 50.000 0.00 0.00 34.99 2.66
737 758 2.847234 AAGGGTGCGGTCACTCCA 60.847 61.111 0.00 0.00 44.83 3.86
773 796 5.065988 GGGCCAATGTTGTAAGTACATAGTG 59.934 44.000 4.39 0.00 35.26 2.74
876 904 2.363680 TGTAGGTTGTTGTTGGGCATTG 59.636 45.455 0.00 0.00 0.00 2.82
904 932 3.094062 GCTGCTACCGAGGGCATCA 62.094 63.158 0.00 0.00 37.83 3.07
940 968 5.023533 TGGCAAGCTTATCTCTTTATCGT 57.976 39.130 0.00 0.00 0.00 3.73
1191 1219 4.062293 TCGTGAACCAACCTATTTCAGTG 58.938 43.478 0.00 0.00 29.97 3.66
1228 1256 5.151389 GTGACATGACGTTCCAATTTTACC 58.849 41.667 0.00 0.00 0.00 2.85
1298 1326 5.510179 GCATTGCAGCTATTGGTTATGGAAT 60.510 40.000 3.15 0.00 32.97 3.01
1344 1372 8.622572 ATTGGTTATTGAAGAATTTATGGGGT 57.377 30.769 0.00 0.00 0.00 4.95
1356 1384 0.553819 TATGGGGTACAACATGGGGC 59.446 55.000 10.70 0.00 0.00 5.80
1362 1390 1.084289 GTACAACATGGGGCGAGAAC 58.916 55.000 0.00 0.00 0.00 3.01
1368 1396 2.728435 ATGGGGCGAGAACGGGTAC 61.728 63.158 0.00 0.00 40.15 3.34
1417 1445 2.540383 AGAGAGGCATGTGTGGTCTTA 58.460 47.619 0.00 0.00 0.00 2.10
1507 1535 9.715123 CACGAAGATTAAATAAACATATGCACA 57.285 29.630 1.58 0.00 0.00 4.57
1527 1557 1.688772 TCCTCTAGGGATTCCGTTCG 58.311 55.000 2.75 0.00 39.58 3.95
1535 1565 2.236395 AGGGATTCCGTTCGATGTCTTT 59.764 45.455 0.00 0.00 38.33 2.52
1537 1567 3.554731 GGGATTCCGTTCGATGTCTTTAC 59.445 47.826 0.00 0.00 0.00 2.01
1685 1717 7.289310 TGCTATATTTGATTTCATGGTCCTCA 58.711 34.615 0.00 0.00 0.00 3.86
1702 1734 4.996122 GTCCTCATGAGAATGAGCCTATTG 59.004 45.833 24.62 2.45 44.98 1.90
1705 1737 6.044054 TCCTCATGAGAATGAGCCTATTGAAT 59.956 38.462 24.62 0.00 44.98 2.57
1709 1741 8.654094 TCATGAGAATGAGCCTATTGAATTCTA 58.346 33.333 7.05 0.00 37.63 2.10
1710 1742 8.719648 CATGAGAATGAGCCTATTGAATTCTAC 58.280 37.037 7.05 0.00 37.63 2.59
1712 1744 7.055667 AGAATGAGCCTATTGAATTCTACGA 57.944 36.000 7.05 0.00 36.17 3.43
1714 1746 8.807118 AGAATGAGCCTATTGAATTCTACGATA 58.193 33.333 7.05 0.19 36.17 2.92
1715 1747 8.764524 AATGAGCCTATTGAATTCTACGATAC 57.235 34.615 7.05 0.00 0.00 2.24
1718 1750 5.243283 AGCCTATTGAATTCTACGATACGGT 59.757 40.000 7.05 0.00 0.00 4.83
1720 1752 6.746364 GCCTATTGAATTCTACGATACGGTAG 59.254 42.308 7.05 0.00 40.98 3.18
1739 1771 4.141711 GGTAGGTGATCCATGTGTGTATGT 60.142 45.833 0.00 0.00 35.89 2.29
1747 1779 6.885918 TGATCCATGTGTGTATGTTTCTCATT 59.114 34.615 0.00 0.00 37.91 2.57
1770 1802 5.526115 TGTTTACTGTCCTACAAGTTCTCG 58.474 41.667 0.00 0.00 0.00 4.04
1800 1833 3.443976 ACAACGAATTCAACTTGTTGGC 58.556 40.909 20.24 1.54 43.08 4.52
1806 1839 5.298276 ACGAATTCAACTTGTTGGCTTTCTA 59.702 36.000 12.75 0.00 0.00 2.10
1819 1852 7.342581 TGTTGGCTTTCTACATGGTATTATGA 58.657 34.615 0.00 0.00 0.00 2.15
1822 1855 8.995027 TGGCTTTCTACATGGTATTATGAATT 57.005 30.769 0.00 0.00 0.00 2.17
1861 2342 8.273557 GTGCGTGATTTTAATACGTAAGATGAT 58.726 33.333 0.00 0.00 39.79 2.45
1863 2344 7.266335 GCGTGATTTTAATACGTAAGATGATGC 59.734 37.037 0.00 0.00 39.79 3.91
1875 2356 6.071952 ACGTAAGATGATGCCTGAATTTGTTT 60.072 34.615 0.00 0.00 43.62 2.83
1876 2357 6.252015 CGTAAGATGATGCCTGAATTTGTTTG 59.748 38.462 0.00 0.00 43.02 2.93
1877 2358 5.988310 AGATGATGCCTGAATTTGTTTGA 57.012 34.783 0.00 0.00 0.00 2.69
1878 2359 6.349243 AGATGATGCCTGAATTTGTTTGAA 57.651 33.333 0.00 0.00 0.00 2.69
1884 2365 9.504708 TGATGCCTGAATTTGTTTGAATATTTT 57.495 25.926 0.00 0.00 0.00 1.82
1928 2409 8.943594 AAGAGGTGTGTTTTAATATTTACCCA 57.056 30.769 0.00 0.00 0.00 4.51
1929 2410 8.344446 AGAGGTGTGTTTTAATATTTACCCAC 57.656 34.615 0.00 0.00 0.00 4.61
1941 2422 3.742433 TTTACCCACAAAAGGCACATG 57.258 42.857 0.00 0.00 0.00 3.21
1944 2425 0.604578 CCCACAAAAGGCACATGGAG 59.395 55.000 0.00 0.00 31.69 3.86
1949 2430 4.012374 CACAAAAGGCACATGGAGATAGT 58.988 43.478 0.00 0.00 0.00 2.12
1950 2431 4.012374 ACAAAAGGCACATGGAGATAGTG 58.988 43.478 0.00 0.00 36.39 2.74
1956 2437 3.434167 GGCACATGGAGATAGTGAACCAT 60.434 47.826 0.00 0.00 42.83 3.55
2023 2504 4.082190 GTGTAACATCAGGTGAGAGTAGCA 60.082 45.833 0.00 0.00 36.32 3.49
2033 2514 5.413833 CAGGTGAGAGTAGCAATTTTCACAT 59.586 40.000 11.16 3.42 37.31 3.21
2035 2516 7.281774 CAGGTGAGAGTAGCAATTTTCACATAT 59.718 37.037 11.16 0.00 37.31 1.78
2038 2520 6.598850 TGAGAGTAGCAATTTTCACATATGCA 59.401 34.615 1.58 0.00 39.42 3.96
2045 2527 6.655848 AGCAATTTTCACATATGCATTTTGGT 59.344 30.769 3.54 3.07 39.42 3.67
2055 2537 0.179034 GCATTTTGGTTTGGCCCACA 60.179 50.000 0.00 0.00 33.14 4.17
2067 2549 3.093057 TGGCCCACATATTACTTGCAA 57.907 42.857 0.00 0.00 0.00 4.08
2100 2582 6.420903 GTCTAAGTTTTTGAGTTGGCAATTCC 59.579 38.462 18.52 4.38 0.00 3.01
2127 2609 4.745620 AGTTCACTCGAAAGCTCAAAGTAC 59.254 41.667 0.00 0.00 31.43 2.73
2131 2613 4.025979 CACTCGAAAGCTCAAAGTACGTTT 60.026 41.667 0.00 0.00 0.00 3.60
2149 2631 8.794553 AGTACGTTTGAACCATCTATCCTATAG 58.205 37.037 0.00 0.00 0.00 1.31
2166 2648 2.113860 TAGGGAACATGAGCAACTGC 57.886 50.000 0.00 0.00 42.49 4.40
2183 2665 7.905031 GCAACTGCTCAAGATCATAAAATAC 57.095 36.000 0.00 0.00 38.21 1.89
2241 2732 6.072112 ACAACACAAGAACATTACATGACC 57.928 37.500 0.00 0.00 0.00 4.02
2244 2735 3.126858 CACAAGAACATTACATGACCCGG 59.873 47.826 0.00 0.00 0.00 5.73
2248 2739 3.199946 AGAACATTACATGACCCGGTGAT 59.800 43.478 0.00 0.00 0.00 3.06
2320 2818 9.790344 ATGATATAAGGAAAGGAGATTCAGTTG 57.210 33.333 0.00 0.00 0.00 3.16
2329 2827 7.660208 GGAAAGGAGATTCAGTTGTAACAAGTA 59.340 37.037 0.00 0.00 0.00 2.24
2333 2831 7.657761 AGGAGATTCAGTTGTAACAAGTAAGTG 59.342 37.037 0.00 0.00 0.00 3.16
2334 2832 7.656137 GGAGATTCAGTTGTAACAAGTAAGTGA 59.344 37.037 0.00 0.00 33.33 3.41
2338 2839 8.556213 TTCAGTTGTAACAAGTAAGTGAACTT 57.444 30.769 0.71 0.71 38.27 2.66
2355 2856 9.975218 AAGTGAACTTGGGTATTTAATCACTAT 57.025 29.630 5.62 0.00 43.82 2.12
2356 2857 9.975218 AGTGAACTTGGGTATTTAATCACTATT 57.025 29.630 3.47 0.00 43.07 1.73
2360 2861 8.588290 ACTTGGGTATTTAATCACTATTGCAA 57.412 30.769 0.00 0.00 0.00 4.08
2380 2882 6.170506 TGCAAAAACTCTATTAGTGACGGAT 58.829 36.000 0.00 0.00 38.88 4.18
2400 2902 2.178580 TCCAAAAGGCCCATCAATGAC 58.821 47.619 0.00 0.00 0.00 3.06
2401 2903 1.135024 CCAAAAGGCCCATCAATGACG 60.135 52.381 0.00 0.00 0.00 4.35
2403 2905 2.214376 AAAGGCCCATCAATGACGAA 57.786 45.000 0.00 0.00 0.00 3.85
2409 2911 0.652592 CCATCAATGACGAACGAGCC 59.347 55.000 0.14 0.00 0.00 4.70
2410 2912 1.358877 CATCAATGACGAACGAGCCA 58.641 50.000 0.14 0.00 0.00 4.75
2412 2914 0.032815 TCAATGACGAACGAGCCACA 59.967 50.000 0.14 0.00 0.00 4.17
2414 2916 1.078709 AATGACGAACGAGCCACATG 58.921 50.000 0.14 0.00 0.00 3.21
2418 2920 1.654105 GACGAACGAGCCACATGTTAG 59.346 52.381 0.00 0.00 0.00 2.34
2426 2928 1.604147 GCCACATGTTAGGGTTGGCC 61.604 60.000 9.51 0.00 35.15 5.36
2427 2929 0.039618 CCACATGTTAGGGTTGGCCT 59.960 55.000 3.32 0.00 34.45 5.19
2429 2931 1.545582 CACATGTTAGGGTTGGCCTTG 59.454 52.381 3.32 0.00 34.45 3.61
2430 2932 1.146982 ACATGTTAGGGTTGGCCTTGT 59.853 47.619 3.32 0.00 34.45 3.16
2431 2933 1.818674 CATGTTAGGGTTGGCCTTGTC 59.181 52.381 3.32 0.00 34.45 3.18
2432 2934 0.847373 TGTTAGGGTTGGCCTTGTCA 59.153 50.000 3.32 0.00 34.45 3.58
2433 2935 1.427368 TGTTAGGGTTGGCCTTGTCAT 59.573 47.619 3.32 0.00 34.45 3.06
2434 2936 2.158385 TGTTAGGGTTGGCCTTGTCATT 60.158 45.455 3.32 0.00 34.45 2.57
2435 2937 2.214376 TAGGGTTGGCCTTGTCATTG 57.786 50.000 3.32 0.00 34.45 2.82
2436 2938 0.542702 AGGGTTGGCCTTGTCATTGG 60.543 55.000 3.32 0.00 34.45 3.16
2437 2939 0.831711 GGGTTGGCCTTGTCATTGGT 60.832 55.000 3.32 0.00 34.45 3.67
2438 2940 1.549037 GGGTTGGCCTTGTCATTGGTA 60.549 52.381 3.32 0.00 34.45 3.25
2439 2941 2.243810 GGTTGGCCTTGTCATTGGTAA 58.756 47.619 3.32 0.00 0.00 2.85
2440 2942 2.029380 GGTTGGCCTTGTCATTGGTAAC 60.029 50.000 3.32 0.00 0.00 2.50
2441 2943 2.890945 GTTGGCCTTGTCATTGGTAACT 59.109 45.455 3.32 0.00 37.61 2.24
2442 2944 2.513753 TGGCCTTGTCATTGGTAACTG 58.486 47.619 3.32 0.00 37.61 3.16
2443 2945 1.818674 GGCCTTGTCATTGGTAACTGG 59.181 52.381 0.00 0.00 37.61 4.00
2444 2946 1.818674 GCCTTGTCATTGGTAACTGGG 59.181 52.381 0.00 0.00 37.61 4.45
2445 2947 2.817839 GCCTTGTCATTGGTAACTGGGT 60.818 50.000 0.00 0.00 37.61 4.51
2446 2948 3.496331 CCTTGTCATTGGTAACTGGGTT 58.504 45.455 0.00 0.00 37.61 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 55 1.470890 ACCGGCCAACGTTTGATTATG 59.529 47.619 0.00 0.00 42.24 1.90
165 186 1.819928 ATGGTGCTTGCACGATGTAA 58.180 45.000 19.45 3.26 0.00 2.41
232 253 8.763984 TTTGGTTTAACAAATGGAACTAGGTA 57.236 30.769 0.00 0.00 35.57 3.08
268 289 7.222224 GCAACTAACTGTAGTATGTGGTATGTC 59.778 40.741 0.00 0.00 39.79 3.06
275 296 6.330278 TGCTAGCAACTAACTGTAGTATGTG 58.670 40.000 16.84 0.00 39.79 3.21
276 297 6.525578 TGCTAGCAACTAACTGTAGTATGT 57.474 37.500 16.84 0.00 39.79 2.29
301 322 5.230182 TGTTGACTAGATGATGTGTGTGTC 58.770 41.667 0.00 0.00 0.00 3.67
309 330 3.812262 TGGCCATGTTGACTAGATGATG 58.188 45.455 0.00 0.00 29.12 3.07
310 331 4.202441 GTTGGCCATGTTGACTAGATGAT 58.798 43.478 6.09 0.00 29.12 2.45
317 338 0.827507 GTGGGTTGGCCATGTTGACT 60.828 55.000 6.09 0.00 36.17 3.41
331 352 0.178990 GAGCAGAACCTTTGGTGGGT 60.179 55.000 0.00 0.00 35.34 4.51
360 381 2.217038 AGAGGCAGAGGCAACCGAA 61.217 57.895 0.00 0.00 43.71 4.30
402 423 2.369860 TGGACAAGTCATCACTGAGCTT 59.630 45.455 2.29 0.00 31.06 3.74
422 443 0.249031 TCTCGTGCCATGCTACGATG 60.249 55.000 18.69 13.97 46.66 3.84
432 453 1.296392 CCATCCAACTCTCGTGCCA 59.704 57.895 0.00 0.00 0.00 4.92
482 503 4.195416 CCTTCAACTTATGAGCCTTCTCC 58.805 47.826 0.00 0.00 39.77 3.71
500 521 1.963515 ACATTGGCCTTGAACACCTTC 59.036 47.619 3.32 0.00 0.00 3.46
606 627 4.761739 TCCTTTGTTAGCCTTTGTCATCTG 59.238 41.667 0.00 0.00 0.00 2.90
696 717 1.207089 CCTCCAATCTACTGTTGCCGA 59.793 52.381 0.00 0.00 0.00 5.54
737 758 2.023695 ACATTGGCCCTGATCCTTGATT 60.024 45.455 0.00 0.00 0.00 2.57
876 904 2.391389 GGTAGCAGCAACAGCGGAC 61.391 63.158 0.00 0.00 37.01 4.79
904 932 3.575687 AGCTTGCCAGTTTTTAGCTTGAT 59.424 39.130 0.00 0.00 38.99 2.57
940 968 7.450074 ACATCACAATCTACCAACTCTTGTTA 58.550 34.615 0.00 0.00 34.60 2.41
1191 1219 1.675641 GTCACCACCATCCACAGCC 60.676 63.158 0.00 0.00 0.00 4.85
1228 1256 1.349026 ACCAGTCATCACTCCACCTTG 59.651 52.381 0.00 0.00 0.00 3.61
1298 1326 1.960417 TTTTGTGCCATCACTCGTCA 58.040 45.000 0.00 0.00 43.49 4.35
1337 1365 0.553819 GCCCCATGTTGTACCCCATA 59.446 55.000 0.00 0.00 0.00 2.74
1344 1372 0.390603 CGTTCTCGCCCCATGTTGTA 60.391 55.000 0.00 0.00 0.00 2.41
1356 1384 4.110482 CCATTCTTAAGTACCCGTTCTCG 58.890 47.826 1.63 0.00 0.00 4.04
1362 1390 4.404715 TCCTTCTCCATTCTTAAGTACCCG 59.595 45.833 1.63 0.00 0.00 5.28
1368 1396 7.826252 TCAGAAATGTCCTTCTCCATTCTTAAG 59.174 37.037 0.00 0.00 33.25 1.85
1417 1445 0.988678 GGGTAGGAAGGCTCCATGGT 60.989 60.000 12.58 0.00 45.24 3.55
1469 1497 7.780008 TTTAATCTTCGTGTATGTATGTGGG 57.220 36.000 0.00 0.00 0.00 4.61
1509 1537 1.688772 TCGAACGGAATCCCTAGAGG 58.311 55.000 0.00 0.00 0.00 3.69
1526 1556 9.825972 ATATTTTGACACAAAGTAAAGACATCG 57.174 29.630 0.00 0.00 0.00 3.84
1685 1717 7.601886 CGTAGAATTCAATAGGCTCATTCTCAT 59.398 37.037 8.44 0.00 36.03 2.90
1690 1722 7.542477 CGTATCGTAGAATTCAATAGGCTCATT 59.458 37.037 8.44 0.00 43.58 2.57
1702 1734 5.679734 TCACCTACCGTATCGTAGAATTC 57.320 43.478 0.00 0.00 43.58 2.17
1705 1737 4.067896 GGATCACCTACCGTATCGTAGAA 58.932 47.826 0.00 0.00 43.58 2.10
1709 1741 2.353357 TGGATCACCTACCGTATCGT 57.647 50.000 0.00 0.00 37.04 3.73
1710 1742 2.557056 ACATGGATCACCTACCGTATCG 59.443 50.000 0.00 0.00 37.04 2.92
1712 1744 3.069586 CACACATGGATCACCTACCGTAT 59.930 47.826 0.00 0.00 37.04 3.06
1714 1746 1.207089 CACACATGGATCACCTACCGT 59.793 52.381 0.00 0.00 37.04 4.83
1715 1747 1.207089 ACACACATGGATCACCTACCG 59.793 52.381 0.00 0.00 37.04 4.02
1718 1750 5.692115 AACATACACACATGGATCACCTA 57.308 39.130 0.00 0.00 37.04 3.08
1720 1752 4.943705 AGAAACATACACACATGGATCACC 59.056 41.667 0.00 0.00 0.00 4.02
1739 1771 7.990886 ACTTGTAGGACAGTAAACAATGAGAAA 59.009 33.333 0.00 0.00 31.88 2.52
1747 1779 5.508489 CCGAGAACTTGTAGGACAGTAAACA 60.508 44.000 0.00 0.00 0.00 2.83
1770 1802 1.066303 TGAATTCGTTGTTGCCACACC 59.934 47.619 0.04 0.00 30.32 4.16
1791 1824 3.832527 ACCATGTAGAAAGCCAACAAGT 58.167 40.909 0.00 0.00 0.00 3.16
1793 1826 7.831690 TCATAATACCATGTAGAAAGCCAACAA 59.168 33.333 0.00 0.00 0.00 2.83
1798 1831 9.899226 GAAATTCATAATACCATGTAGAAAGCC 57.101 33.333 0.00 0.00 0.00 4.35
1819 1852 9.638239 AAATCACGCACTAAAATATGTGAAATT 57.362 25.926 0.00 0.00 39.49 1.82
1837 2318 7.266335 GCATCATCTTACGTATTAAAATCACGC 59.734 37.037 0.00 0.00 39.23 5.34
1849 2330 6.112734 ACAAATTCAGGCATCATCTTACGTA 58.887 36.000 0.00 0.00 0.00 3.57
1852 2333 7.315142 TCAAACAAATTCAGGCATCATCTTAC 58.685 34.615 0.00 0.00 0.00 2.34
1853 2334 7.465353 TCAAACAAATTCAGGCATCATCTTA 57.535 32.000 0.00 0.00 0.00 2.10
1861 2342 8.899427 TGAAAATATTCAAACAAATTCAGGCA 57.101 26.923 0.00 0.00 42.47 4.75
1906 2387 8.480133 TTGTGGGTAAATATTAAAACACACCT 57.520 30.769 19.95 0.00 43.95 4.00
1919 2400 4.221703 CCATGTGCCTTTTGTGGGTAAATA 59.778 41.667 0.00 0.00 0.00 1.40
1923 2404 1.145945 TCCATGTGCCTTTTGTGGGTA 59.854 47.619 0.00 0.00 0.00 3.69
1924 2405 0.105760 TCCATGTGCCTTTTGTGGGT 60.106 50.000 0.00 0.00 0.00 4.51
1926 2407 1.619654 TCTCCATGTGCCTTTTGTGG 58.380 50.000 0.00 0.00 0.00 4.17
1928 2409 4.012374 CACTATCTCCATGTGCCTTTTGT 58.988 43.478 0.00 0.00 0.00 2.83
1929 2410 4.264253 TCACTATCTCCATGTGCCTTTTG 58.736 43.478 0.00 0.00 0.00 2.44
1934 2415 2.092968 TGGTTCACTATCTCCATGTGCC 60.093 50.000 0.00 0.00 0.00 5.01
2000 2481 4.082190 TGCTACTCTCACCTGATGTTACAC 60.082 45.833 0.00 0.00 0.00 2.90
2002 2483 4.720649 TGCTACTCTCACCTGATGTTAC 57.279 45.455 0.00 0.00 0.00 2.50
2010 2491 4.973168 TGTGAAAATTGCTACTCTCACCT 58.027 39.130 0.00 0.00 33.78 4.00
2012 2493 6.909357 GCATATGTGAAAATTGCTACTCTCAC 59.091 38.462 4.29 0.00 34.99 3.51
2016 2497 8.638685 AAATGCATATGTGAAAATTGCTACTC 57.361 30.769 0.00 0.00 34.47 2.59
2023 2504 8.298140 CCAAACCAAAATGCATATGTGAAAATT 58.702 29.630 0.00 0.00 0.00 1.82
2033 2514 1.980765 TGGGCCAAACCAAAATGCATA 59.019 42.857 2.13 0.00 42.05 3.14
2035 2516 0.179034 GTGGGCCAAACCAAAATGCA 60.179 50.000 8.40 0.00 43.34 3.96
2038 2520 4.925390 AATATGTGGGCCAAACCAAAAT 57.075 36.364 8.40 0.00 43.34 1.82
2045 2527 3.435275 TGCAAGTAATATGTGGGCCAAA 58.565 40.909 8.40 1.64 0.00 3.28
2067 2549 8.076178 CCAACTCAAAAACTTAGACGATCATTT 58.924 33.333 0.00 0.00 0.00 2.32
2100 2582 0.946221 AGCTTTCGAGTGAACTGGCG 60.946 55.000 0.00 0.00 32.71 5.69
2127 2609 6.210784 TCCCTATAGGATAGATGGTTCAAACG 59.789 42.308 21.07 0.00 40.93 3.60
2131 2613 6.630131 TGTTCCCTATAGGATAGATGGTTCA 58.370 40.000 21.07 3.31 46.94 3.18
2138 2620 5.903923 TGCTCATGTTCCCTATAGGATAGA 58.096 41.667 21.07 6.24 46.94 1.98
2139 2621 6.212388 AGTTGCTCATGTTCCCTATAGGATAG 59.788 42.308 21.07 3.69 46.94 2.08
2159 2641 6.630443 CGTATTTTATGATCTTGAGCAGTTGC 59.370 38.462 0.00 0.00 42.49 4.17
2166 2648 9.655769 CACATTTCCGTATTTTATGATCTTGAG 57.344 33.333 0.00 0.00 0.00 3.02
2181 2663 1.057471 TGGTGGACCACATTTCCGTA 58.943 50.000 25.75 0.00 42.01 4.02
2183 2665 4.811206 TGGTGGACCACATTTCCG 57.189 55.556 25.75 0.00 42.01 4.30
2300 2798 7.741785 TGTTACAACTGAATCTCCTTTCCTTA 58.258 34.615 0.00 0.00 0.00 2.69
2303 2801 6.486993 ACTTGTTACAACTGAATCTCCTTTCC 59.513 38.462 0.00 0.00 0.00 3.13
2304 2802 7.497925 ACTTGTTACAACTGAATCTCCTTTC 57.502 36.000 0.00 0.00 0.00 2.62
2312 2810 8.732746 AGTTCACTTACTTGTTACAACTGAAT 57.267 30.769 0.00 0.00 0.00 2.57
2329 2827 9.975218 ATAGTGATTAAATACCCAAGTTCACTT 57.025 29.630 7.46 0.00 41.80 3.16
2333 2831 8.682710 TGCAATAGTGATTAAATACCCAAGTTC 58.317 33.333 0.00 0.00 0.00 3.01
2334 2832 8.588290 TGCAATAGTGATTAAATACCCAAGTT 57.412 30.769 0.00 0.00 0.00 2.66
2338 2839 9.646427 GTTTTTGCAATAGTGATTAAATACCCA 57.354 29.630 0.00 0.00 0.00 4.51
2349 2850 9.719355 TCACTAATAGAGTTTTTGCAATAGTGA 57.281 29.630 21.25 21.25 42.40 3.41
2355 2856 5.992829 TCCGTCACTAATAGAGTTTTTGCAA 59.007 36.000 0.00 0.00 35.64 4.08
2356 2857 5.543714 TCCGTCACTAATAGAGTTTTTGCA 58.456 37.500 0.00 0.00 35.64 4.08
2360 2861 6.540438 TGGATCCGTCACTAATAGAGTTTT 57.460 37.500 7.39 0.00 35.64 2.43
2380 2882 2.178580 GTCATTGATGGGCCTTTTGGA 58.821 47.619 4.53 0.00 44.07 3.53
2400 2902 0.999406 CCTAACATGTGGCTCGTTCG 59.001 55.000 0.00 0.00 0.00 3.95
2401 2903 1.338769 ACCCTAACATGTGGCTCGTTC 60.339 52.381 0.00 0.00 0.00 3.95
2403 2905 0.690762 AACCCTAACATGTGGCTCGT 59.309 50.000 0.00 0.00 0.00 4.18
2409 2911 1.545582 CAAGGCCAACCCTAACATGTG 59.454 52.381 5.01 0.00 45.62 3.21
2410 2912 1.146982 ACAAGGCCAACCCTAACATGT 59.853 47.619 5.01 0.00 45.62 3.21
2412 2914 1.427368 TGACAAGGCCAACCCTAACAT 59.573 47.619 5.01 0.00 45.62 2.71
2414 2916 2.215942 ATGACAAGGCCAACCCTAAC 57.784 50.000 5.01 0.00 45.62 2.34
2418 2920 0.831711 ACCAATGACAAGGCCAACCC 60.832 55.000 5.01 0.00 36.11 4.11


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

AutoCloner maintained by Alex Coulton.