Multiple sequence alignment - TraesCS5D01G301200

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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 TraesCS5D01G301200 chr5D 100.000 2540 0 0 1 2540 398244859 398247398 0.000000e+00 4691
1 TraesCS5D01G301200 chr5D 81.877 1076 124 22 644 1681 398331039 398332081 0.000000e+00 841
2 TraesCS5D01G301200 chr5D 87.115 357 37 4 270 624 398324509 398324858 1.830000e-106 396
3 TraesCS5D01G301200 chr5A 83.333 1512 180 31 215 1681 503398150 503399634 0.000000e+00 1330
4 TraesCS5D01G301200 chr5A 89.641 975 70 15 1 945 503267735 503268708 0.000000e+00 1212
5 TraesCS5D01G301200 chr5A 78.229 1502 214 55 269 1717 503485162 503486603 0.000000e+00 857
6 TraesCS5D01G301200 chr5A 93.248 548 30 6 1962 2507 503280310 503280852 0.000000e+00 800
7 TraesCS5D01G301200 chr5A 92.294 545 34 4 941 1477 503273854 503274398 0.000000e+00 767
8 TraesCS5D01G301200 chr5A 82.337 736 117 12 919 1648 503439510 503440238 5.970000e-176 627
9 TraesCS5D01G301200 chr5A 85.371 458 37 6 1473 1930 503279886 503280313 4.980000e-122 448
10 TraesCS5D01G301200 chr5A 78.756 659 78 28 270 886 503438868 503439506 3.960000e-103 385
11 TraesCS5D01G301200 chr5B 83.447 1317 145 28 218 1499 478335281 478336559 0.000000e+00 1157
12 TraesCS5D01G301200 chr5B 79.973 1478 215 53 283 1728 478425211 478426639 0.000000e+00 1014
13 TraesCS5D01G301200 chr5B 77.706 1090 188 22 678 1735 478430774 478431840 1.290000e-172 616
14 TraesCS5D01G301200 chr5B 80.137 292 36 13 461 740 478404406 478404687 5.540000e-47 198


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 TraesCS5D01G301200 chr5D 398244859 398247398 2539 False 4691 4691 100.0000 1 2540 1 chr5D.!!$F1 2539
1 TraesCS5D01G301200 chr5D 398331039 398332081 1042 False 841 841 81.8770 644 1681 1 chr5D.!!$F3 1037
2 TraesCS5D01G301200 chr5A 503398150 503399634 1484 False 1330 1330 83.3330 215 1681 1 chr5A.!!$F3 1466
3 TraesCS5D01G301200 chr5A 503267735 503268708 973 False 1212 1212 89.6410 1 945 1 chr5A.!!$F1 944
4 TraesCS5D01G301200 chr5A 503485162 503486603 1441 False 857 857 78.2290 269 1717 1 chr5A.!!$F4 1448
5 TraesCS5D01G301200 chr5A 503273854 503274398 544 False 767 767 92.2940 941 1477 1 chr5A.!!$F2 536
6 TraesCS5D01G301200 chr5A 503279886 503280852 966 False 624 800 89.3095 1473 2507 2 chr5A.!!$F5 1034
7 TraesCS5D01G301200 chr5A 503438868 503440238 1370 False 506 627 80.5465 270 1648 2 chr5A.!!$F6 1378
8 TraesCS5D01G301200 chr5B 478335281 478336559 1278 False 1157 1157 83.4470 218 1499 1 chr5B.!!$F1 1281
9 TraesCS5D01G301200 chr5B 478425211 478426639 1428 False 1014 1014 79.9730 283 1728 1 chr5B.!!$F3 1445
10 TraesCS5D01G301200 chr5B 478430774 478431840 1066 False 616 616 77.7060 678 1735 1 chr5B.!!$F4 1057

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
171 172 0.179163 GGCAAAGCTGATACCGTTGC 60.179 55.0 8.24 8.24 43.67 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1949 2112 0.308684 TGACGACGACACGTTTAGCT 59.691 50.0 0.0 0.0 46.52 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
72 73 4.135306 TGTCCGTAGATGTACCATCTCTC 58.865 47.826 9.86 5.06 0.00 3.20
75 76 4.039609 TCCGTAGATGTACCATCTCTCGTA 59.960 45.833 19.80 9.84 0.00 3.43
77 78 5.107026 CCGTAGATGTACCATCTCTCGTAAG 60.107 48.000 19.80 9.37 0.00 2.34
117 118 3.282021 TGGGACTACATACTCCACGTAC 58.718 50.000 0.00 0.00 0.00 3.67
118 119 2.620585 GGGACTACATACTCCACGTACC 59.379 54.545 0.00 0.00 0.00 3.34
134 135 2.444351 GTACCGTGTGCGACTACATAC 58.556 52.381 0.00 0.00 41.33 2.39
137 138 1.401800 CCGTGTGCGACTACATACACA 60.402 52.381 0.00 0.00 42.55 3.72
141 142 1.647213 GTGCGACTACATACACACACG 59.353 52.381 0.00 0.00 33.23 4.49
151 152 0.955905 TACACACACGCAGTAGAGCA 59.044 50.000 0.00 0.00 41.61 4.26
160 161 0.676151 GCAGTAGAGCAGGCAAAGCT 60.676 55.000 0.00 0.00 46.82 3.74
165 166 2.035530 AGAGCAGGCAAAGCTGATAC 57.964 50.000 3.84 0.00 43.58 2.24
171 172 0.179163 GGCAAAGCTGATACCGTTGC 60.179 55.000 8.24 8.24 43.67 4.17
172 173 0.521291 GCAAAGCTGATACCGTTGCA 59.479 50.000 11.23 0.00 43.78 4.08
194 195 0.515127 TGCACGACAAGCAAATACCG 59.485 50.000 0.00 0.00 39.39 4.02
207 208 2.579207 AATACCGTGTGAGACCATCG 57.421 50.000 0.00 0.00 0.00 3.84
210 211 0.524862 ACCGTGTGAGACCATCGTAC 59.475 55.000 0.00 0.00 0.00 3.67
216 217 1.822990 GTGAGACCATCGTACTCCCAA 59.177 52.381 0.00 0.00 0.00 4.12
224 225 3.429547 CCATCGTACTCCCAAGTCTTCAG 60.430 52.174 0.00 0.00 36.92 3.02
247 248 3.395639 TCCGTAATGGTGTTGTGACTTC 58.604 45.455 0.00 0.00 39.52 3.01
256 257 4.155826 TGGTGTTGTGACTTCTGAGTTTTG 59.844 41.667 0.00 0.00 35.88 2.44
257 258 4.394920 GGTGTTGTGACTTCTGAGTTTTGA 59.605 41.667 0.00 0.00 35.88 2.69
261 262 5.084818 TGTGACTTCTGAGTTTTGACAGA 57.915 39.130 0.00 0.00 40.66 3.41
265 293 6.313905 GTGACTTCTGAGTTTTGACAGAGAAA 59.686 38.462 0.00 0.00 42.72 2.52
335 369 0.527565 TTTGTACGGGTAGACGAGCC 59.472 55.000 0.00 0.00 42.83 4.70
431 473 0.586802 GGAAAAACAGAGACGCGCTT 59.413 50.000 5.73 0.00 0.00 4.68
434 476 1.436195 AAAACAGAGACGCGCTTGCA 61.436 50.000 5.73 0.00 39.07 4.08
475 517 4.778143 GAATCACACGGCGGGGCT 62.778 66.667 16.11 0.00 0.00 5.19
842 940 4.331717 CCGACTACAAATACACCATTGGAC 59.668 45.833 10.37 0.00 0.00 4.02
865 963 0.971386 CAGAACAAAGCCCATGCCTT 59.029 50.000 0.00 0.00 38.69 4.35
894 992 1.173043 CAGCTTCTCTCGTCTCTGGT 58.827 55.000 0.00 0.00 0.00 4.00
899 997 0.699399 TCTCTCGTCTCTGGTTCCCT 59.301 55.000 0.00 0.00 0.00 4.20
1158 1282 2.741985 CGCATTGTGGCTGACCGA 60.742 61.111 0.00 0.00 39.70 4.69
1241 1371 1.852157 ATGGGGGTGACTTGGCAGA 60.852 57.895 0.00 0.00 0.00 4.26
1246 1376 1.004277 GGGGTGACTTGGCAGACAATA 59.996 52.381 0.00 0.00 38.65 1.90
1383 1531 2.149578 GATGATGTGCTACTGGATGCC 58.850 52.381 0.00 0.00 0.00 4.40
1399 1547 0.321346 TGCCTGCGATCAAGAAGACA 59.679 50.000 0.00 0.00 0.00 3.41
1407 1555 3.367932 GCGATCAAGAAGACAACGATGAA 59.632 43.478 0.00 0.00 0.00 2.57
1413 1561 4.181309 AGAAGACAACGATGAACTCTCC 57.819 45.455 0.00 0.00 0.00 3.71
1460 1608 1.700186 AGAGGTTGAGGGTTTGGAGTC 59.300 52.381 0.00 0.00 0.00 3.36
1571 1727 2.621338 CACATGCATGTACCTCGAGTT 58.379 47.619 30.92 2.47 39.39 3.01
1577 1733 3.187700 GCATGTACCTCGAGTTTAGGTG 58.812 50.000 12.31 4.34 46.90 4.00
1661 1823 3.708631 AGGAGCTGATACTTAGCACACAT 59.291 43.478 0.00 0.00 43.53 3.21
1717 1880 6.605471 TTGTTAGCAACTAAGATCCTCAGA 57.395 37.500 0.00 0.00 0.00 3.27
1750 1913 1.632018 CCCCTCTATTGTTGCCCCGA 61.632 60.000 0.00 0.00 0.00 5.14
1771 1934 2.111043 CACCCGTGCCTCACAAGT 59.889 61.111 0.00 0.00 33.40 3.16
1808 1971 2.438254 TGCTGCTATGGTTGGGCG 60.438 61.111 0.00 0.00 0.00 6.13
1817 1980 3.367910 GCTATGGTTGGGCGAAATTTCAA 60.368 43.478 17.99 2.68 0.00 2.69
1819 1982 3.543680 TGGTTGGGCGAAATTTCAAAA 57.456 38.095 17.99 3.81 0.00 2.44
1820 1983 3.873910 TGGTTGGGCGAAATTTCAAAAA 58.126 36.364 17.99 4.13 0.00 1.94
1846 2009 9.457110 AAAATAAAATTTGCGGGAACAATTTTC 57.543 25.926 7.59 0.00 34.01 2.29
1858 2021 7.307751 GCGGGAACAATTTTCGATCTATTCATA 60.308 37.037 0.00 0.00 0.00 2.15
1870 2033 7.951591 TCGATCTATTCATAAACTGTCATGGA 58.048 34.615 0.00 0.00 0.00 3.41
1871 2034 8.588472 TCGATCTATTCATAAACTGTCATGGAT 58.412 33.333 0.00 2.72 0.00 3.41
1884 2047 2.042464 TCATGGATCTAGTGGGAGCAC 58.958 52.381 0.00 0.00 0.00 4.40
1885 2048 2.045524 CATGGATCTAGTGGGAGCACT 58.954 52.381 0.00 0.00 39.08 4.40
1926 2089 4.767578 TCATGTCCGTAGACTACCTAGT 57.232 45.455 7.05 0.00 43.91 2.57
1927 2090 4.449131 TCATGTCCGTAGACTACCTAGTG 58.551 47.826 7.05 1.22 43.91 2.74
1928 2091 4.162888 TCATGTCCGTAGACTACCTAGTGA 59.837 45.833 7.05 3.35 43.91 3.41
1929 2092 3.866651 TGTCCGTAGACTACCTAGTGAC 58.133 50.000 7.05 6.91 43.91 3.67
1930 2093 3.261643 TGTCCGTAGACTACCTAGTGACA 59.738 47.826 7.05 9.02 43.91 3.58
1931 2094 4.256920 GTCCGTAGACTACCTAGTGACAA 58.743 47.826 7.05 0.00 40.10 3.18
1932 2095 4.094146 GTCCGTAGACTACCTAGTGACAAC 59.906 50.000 7.05 0.00 40.10 3.32
1933 2096 4.019860 TCCGTAGACTACCTAGTGACAACT 60.020 45.833 7.05 0.00 40.67 3.16
1934 2097 5.187772 TCCGTAGACTACCTAGTGACAACTA 59.812 44.000 7.05 0.00 37.88 2.24
1935 2098 5.293079 CCGTAGACTACCTAGTGACAACTAC 59.707 48.000 7.05 0.00 37.88 2.73
1936 2099 5.871524 CGTAGACTACCTAGTGACAACTACA 59.128 44.000 7.05 0.00 37.88 2.74
1937 2100 6.369890 CGTAGACTACCTAGTGACAACTACAA 59.630 42.308 7.05 0.00 37.88 2.41
1938 2101 7.065563 CGTAGACTACCTAGTGACAACTACAAT 59.934 40.741 7.05 0.00 37.88 2.71
1939 2102 7.393841 AGACTACCTAGTGACAACTACAATC 57.606 40.000 0.00 0.00 37.88 2.67
1940 2103 6.093771 AGACTACCTAGTGACAACTACAATCG 59.906 42.308 0.00 0.00 37.88 3.34
1941 2104 3.846360 ACCTAGTGACAACTACAATCGC 58.154 45.455 0.00 0.00 37.88 4.58
1942 2105 3.510360 ACCTAGTGACAACTACAATCGCT 59.490 43.478 0.00 0.00 37.88 4.93
1943 2106 3.859961 CCTAGTGACAACTACAATCGCTG 59.140 47.826 0.00 0.00 37.88 5.18
1944 2107 2.688507 AGTGACAACTACAATCGCTGG 58.311 47.619 0.00 0.00 33.79 4.85
1945 2108 1.732259 GTGACAACTACAATCGCTGGG 59.268 52.381 0.00 0.00 0.00 4.45
1946 2109 1.338674 TGACAACTACAATCGCTGGGG 60.339 52.381 0.00 0.00 0.00 4.96
1947 2110 0.676782 ACAACTACAATCGCTGGGGC 60.677 55.000 0.00 0.00 0.00 5.80
1957 2120 3.195698 GCTGGGGCGAGCTAAACG 61.196 66.667 0.00 0.00 35.95 3.60
1958 2121 2.264794 CTGGGGCGAGCTAAACGT 59.735 61.111 0.00 0.00 0.00 3.99
1959 2122 2.047655 TGGGGCGAGCTAAACGTG 60.048 61.111 0.00 0.00 0.00 4.49
1960 2123 2.047560 GGGGCGAGCTAAACGTGT 60.048 61.111 0.00 0.00 0.00 4.49
1963 2126 1.731969 GGCGAGCTAAACGTGTCGT 60.732 57.895 0.00 0.00 43.97 4.34
1974 2137 2.879462 GTGTCGTCGTCATCGCCC 60.879 66.667 0.00 0.00 36.96 6.13
1977 2140 3.066190 TCGTCGTCATCGCCCCTT 61.066 61.111 0.00 0.00 36.96 3.95
1980 2143 1.218316 GTCGTCATCGCCCCTTTCT 59.782 57.895 0.00 0.00 36.96 2.52
1981 2144 0.391263 GTCGTCATCGCCCCTTTCTT 60.391 55.000 0.00 0.00 36.96 2.52
1982 2145 1.134907 GTCGTCATCGCCCCTTTCTTA 60.135 52.381 0.00 0.00 36.96 2.10
1983 2146 1.551430 TCGTCATCGCCCCTTTCTTAA 59.449 47.619 0.00 0.00 36.96 1.85
2042 2205 3.650139 TCTCTACAAGTCGCCAAAACTC 58.350 45.455 0.00 0.00 0.00 3.01
2077 2240 4.756084 AGTTGTATCTTCTGCTTGTTGC 57.244 40.909 0.00 0.00 43.25 4.17
2087 2250 3.822594 CTGCTTGTTGCGGTTATGTTA 57.177 42.857 0.00 0.00 46.63 2.41
2119 2283 3.173599 CAAGCACTGTGACACTTTGTTG 58.826 45.455 12.86 7.29 0.00 3.33
2127 2291 2.639065 TGACACTTTGTTGGGTCACTC 58.361 47.619 0.00 0.00 35.51 3.51
2145 2309 2.264794 GTGACCCCGCATCGAACT 59.735 61.111 0.00 0.00 0.00 3.01
2152 2316 1.030457 CCCGCATCGAACTACCTAGT 58.970 55.000 0.00 0.00 38.39 2.57
2319 2484 4.422840 TGCGCATGTCATTTTAGATTTGG 58.577 39.130 5.66 0.00 0.00 3.28
2327 2492 6.923012 TGTCATTTTAGATTTGGACATGGTG 58.077 36.000 0.00 0.00 30.99 4.17
2340 2505 1.275291 ACATGGTGTCCAAGGACTACG 59.725 52.381 19.20 6.91 44.80 3.51
2386 2551 9.676195 TTGTTTCATGTGAATGTGTTTGTATAG 57.324 29.630 0.00 0.00 33.54 1.31
2477 2642 3.916035 TGTCCTGTATATGGAGTGAGCT 58.084 45.455 0.00 0.00 33.78 4.09
2500 2665 0.179134 CCTAGTTCCAACTCGGCTCG 60.179 60.000 0.00 0.00 40.37 5.03
2507 2672 1.546923 TCCAACTCGGCTCGTATTTCA 59.453 47.619 0.00 0.00 33.14 2.69
2508 2673 2.028839 TCCAACTCGGCTCGTATTTCAA 60.029 45.455 0.00 0.00 33.14 2.69
2509 2674 2.093783 CCAACTCGGCTCGTATTTCAAC 59.906 50.000 0.00 0.00 0.00 3.18
2510 2675 2.993899 CAACTCGGCTCGTATTTCAACT 59.006 45.455 0.00 0.00 0.00 3.16
2511 2676 4.171005 CAACTCGGCTCGTATTTCAACTA 58.829 43.478 0.00 0.00 0.00 2.24
2512 2677 4.445452 ACTCGGCTCGTATTTCAACTAA 57.555 40.909 0.00 0.00 0.00 2.24
2513 2678 4.421948 ACTCGGCTCGTATTTCAACTAAG 58.578 43.478 0.00 0.00 0.00 2.18
2514 2679 3.184541 TCGGCTCGTATTTCAACTAAGC 58.815 45.455 0.00 0.00 0.00 3.09
2515 2680 3.119245 TCGGCTCGTATTTCAACTAAGCT 60.119 43.478 0.00 0.00 0.00 3.74
2516 2681 4.096833 TCGGCTCGTATTTCAACTAAGCTA 59.903 41.667 0.00 0.00 0.00 3.32
2517 2682 4.982916 CGGCTCGTATTTCAACTAAGCTAT 59.017 41.667 0.00 0.00 0.00 2.97
2518 2683 5.462398 CGGCTCGTATTTCAACTAAGCTATT 59.538 40.000 0.00 0.00 0.00 1.73
2519 2684 6.018994 CGGCTCGTATTTCAACTAAGCTATTT 60.019 38.462 0.00 0.00 0.00 1.40
2520 2685 7.465513 CGGCTCGTATTTCAACTAAGCTATTTT 60.466 37.037 0.00 0.00 0.00 1.82
2521 2686 8.182227 GGCTCGTATTTCAACTAAGCTATTTTT 58.818 33.333 0.00 0.00 0.00 1.94
2539 2704 2.992124 TTTTCACCCTCACGAGAACA 57.008 45.000 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
72 73 8.830580 CCATGCATATATAGGGATTTTCTTACG 58.169 37.037 0.00 0.00 0.00 3.18
75 76 7.943076 TCCCATGCATATATAGGGATTTTCTT 58.057 34.615 15.95 0.00 43.39 2.52
82 83 5.849140 TGTAGTCCCATGCATATATAGGGA 58.151 41.667 15.95 15.95 45.94 4.20
83 84 6.753913 ATGTAGTCCCATGCATATATAGGG 57.246 41.667 11.96 11.96 40.98 3.53
117 118 1.265568 GTGTATGTAGTCGCACACGG 58.734 55.000 0.00 0.00 40.63 4.94
118 119 1.971792 TGTGTATGTAGTCGCACACG 58.028 50.000 0.00 0.00 43.30 4.49
124 125 1.911464 CTGCGTGTGTGTATGTAGTCG 59.089 52.381 0.00 0.00 0.00 4.18
134 135 1.010935 CCTGCTCTACTGCGTGTGTG 61.011 60.000 0.00 0.00 35.36 3.82
137 138 2.099652 TTGCCTGCTCTACTGCGTGT 62.100 55.000 0.00 0.00 35.36 4.49
141 142 0.676151 AGCTTTGCCTGCTCTACTGC 60.676 55.000 0.00 0.00 35.67 4.40
151 152 1.453155 CAACGGTATCAGCTTTGCCT 58.547 50.000 0.00 0.00 0.00 4.75
171 172 2.124011 ATTTGCTTGTCGTGCACTTG 57.876 45.000 16.19 0.00 40.40 3.16
172 173 2.031157 GGTATTTGCTTGTCGTGCACTT 60.031 45.455 16.19 0.00 40.40 3.16
194 195 1.134560 GGGAGTACGATGGTCTCACAC 59.865 57.143 0.00 0.00 32.56 3.82
207 208 2.093921 GGAGCTGAAGACTTGGGAGTAC 60.094 54.545 0.00 0.00 35.88 2.73
210 211 0.108424 CGGAGCTGAAGACTTGGGAG 60.108 60.000 0.00 0.00 0.00 4.30
216 217 2.093973 CACCATTACGGAGCTGAAGACT 60.094 50.000 0.00 0.00 38.63 3.24
224 225 1.463444 GTCACAACACCATTACGGAGC 59.537 52.381 0.00 0.00 38.63 4.70
247 248 6.484643 TCTTCCATTTCTCTGTCAAAACTCAG 59.515 38.462 0.00 0.00 0.00 3.35
256 257 7.219484 TCCATTTTTCTTCCATTTCTCTGTC 57.781 36.000 0.00 0.00 0.00 3.51
257 258 7.601705 TTCCATTTTTCTTCCATTTCTCTGT 57.398 32.000 0.00 0.00 0.00 3.41
261 262 6.295518 GGAGCTTCCATTTTTCTTCCATTTCT 60.296 38.462 0.00 0.00 36.28 2.52
265 293 3.771479 GGGAGCTTCCATTTTTCTTCCAT 59.229 43.478 6.02 0.00 38.64 3.41
335 369 1.303074 TCCCTGCTCTTTGCTGCTG 60.303 57.895 0.00 0.00 43.37 4.41
350 384 0.179234 GTAGCTTTGCCTCTCCTCCC 59.821 60.000 0.00 0.00 0.00 4.30
431 473 3.204526 CAAAATTCCAAAGGTTGCTGCA 58.795 40.909 0.00 0.00 0.00 4.41
434 476 2.487086 GCCCAAAATTCCAAAGGTTGCT 60.487 45.455 0.00 0.00 0.00 3.91
475 517 2.069776 CTTTCCTCAGTGGCCTCCA 58.930 57.895 3.32 0.00 35.26 3.86
483 526 2.348998 CGGGCAGCTTTCCTCAGT 59.651 61.111 0.00 0.00 0.00 3.41
842 940 1.134907 GCATGGGCTTTGTTCTGATGG 60.135 52.381 0.00 0.00 36.96 3.51
865 963 2.498167 GAGAGAAGCTGGCTTGAAACA 58.502 47.619 12.79 0.00 36.26 2.83
894 992 4.600111 AGAAATGGTGTAGGTTACAGGGAA 59.400 41.667 0.00 0.00 39.77 3.97
899 997 8.528044 AAAAGAAAGAAATGGTGTAGGTTACA 57.472 30.769 0.00 0.00 36.08 2.41
1241 1371 4.100035 TCGCCAACTGATGAGAGATATTGT 59.900 41.667 0.00 0.00 0.00 2.71
1246 1376 2.433604 ACATCGCCAACTGATGAGAGAT 59.566 45.455 9.72 0.00 44.76 2.75
1383 1531 2.328473 TCGTTGTCTTCTTGATCGCAG 58.672 47.619 0.00 0.00 0.00 5.18
1399 1547 2.417379 CCATGACGGAGAGTTCATCGTT 60.417 50.000 0.00 0.00 36.56 3.85
1413 1561 2.752121 CTCCTGATCACATCCATGACG 58.248 52.381 0.00 0.00 0.00 4.35
1460 1608 2.507058 TCAATCTCCTCCTCCATGTTGG 59.493 50.000 0.00 0.00 39.43 3.77
1591 1748 2.471815 ATCCAGTGGATACCCGAAGA 57.528 50.000 23.67 0.00 41.16 2.87
1593 1750 3.605726 TCTATCCAGTGGATACCCGAA 57.394 47.619 25.30 8.65 41.16 4.30
1594 1751 3.605726 TTCTATCCAGTGGATACCCGA 57.394 47.619 25.30 18.68 41.16 5.14
1750 1913 4.008933 GTGAGGCACGGGTGAGCT 62.009 66.667 2.38 0.00 31.76 4.09
1819 1982 9.809096 AAAATTGTTCCCGCAAATTTTATTTTT 57.191 22.222 4.08 0.00 30.07 1.94
1820 1983 9.457110 GAAAATTGTTCCCGCAAATTTTATTTT 57.543 25.926 5.57 0.00 33.27 1.82
1821 1984 7.800847 CGAAAATTGTTCCCGCAAATTTTATTT 59.199 29.630 5.57 0.00 33.27 1.40
1822 1985 7.171678 TCGAAAATTGTTCCCGCAAATTTTATT 59.828 29.630 5.57 0.00 33.27 1.40
1823 1986 6.647067 TCGAAAATTGTTCCCGCAAATTTTAT 59.353 30.769 5.57 0.00 33.27 1.40
1825 1988 4.811557 TCGAAAATTGTTCCCGCAAATTTT 59.188 33.333 5.32 5.32 33.27 1.82
1826 1989 4.372656 TCGAAAATTGTTCCCGCAAATTT 58.627 34.783 0.00 0.00 35.08 1.82
1827 1990 3.983741 TCGAAAATTGTTCCCGCAAATT 58.016 36.364 0.00 0.00 31.63 1.82
1828 1991 3.651803 TCGAAAATTGTTCCCGCAAAT 57.348 38.095 0.00 0.00 31.63 2.32
1846 2009 8.768957 ATCCATGACAGTTTATGAATAGATCG 57.231 34.615 0.00 0.00 0.00 3.69
1858 2021 4.104086 TCCCACTAGATCCATGACAGTTT 58.896 43.478 0.00 0.00 0.00 2.66
1875 2038 5.761165 TTTGTTACTTTTAGTGCTCCCAC 57.239 39.130 0.00 0.00 42.39 4.61
1908 2071 3.261643 TGTCACTAGGTAGTCTACGGACA 59.738 47.826 3.92 9.12 44.36 4.02
1926 2089 1.338674 CCCCAGCGATTGTAGTTGTCA 60.339 52.381 0.00 0.00 0.00 3.58
1927 2090 1.369625 CCCCAGCGATTGTAGTTGTC 58.630 55.000 0.00 0.00 0.00 3.18
1928 2091 0.676782 GCCCCAGCGATTGTAGTTGT 60.677 55.000 0.00 0.00 0.00 3.32
1929 2092 2.098293 GCCCCAGCGATTGTAGTTG 58.902 57.895 0.00 0.00 0.00 3.16
1930 2093 4.637771 GCCCCAGCGATTGTAGTT 57.362 55.556 0.00 0.00 0.00 2.24
1940 2103 3.195698 CGTTTAGCTCGCCCCAGC 61.196 66.667 0.00 0.00 39.99 4.85
1941 2104 2.100631 CACGTTTAGCTCGCCCCAG 61.101 63.158 0.00 0.00 0.00 4.45
1942 2105 2.047655 CACGTTTAGCTCGCCCCA 60.048 61.111 0.00 0.00 0.00 4.96
1943 2106 2.047560 ACACGTTTAGCTCGCCCC 60.048 61.111 0.00 0.00 0.00 5.80
1944 2107 2.442188 CGACACGTTTAGCTCGCCC 61.442 63.158 0.00 0.00 0.00 6.13
1945 2108 1.671880 GACGACACGTTTAGCTCGCC 61.672 60.000 0.00 0.00 41.37 5.54
1946 2109 1.694962 GACGACACGTTTAGCTCGC 59.305 57.895 0.00 0.00 41.37 5.03
1947 2110 0.723790 ACGACGACACGTTTAGCTCG 60.724 55.000 0.00 0.00 44.14 5.03
1948 2111 0.973423 GACGACGACACGTTTAGCTC 59.027 55.000 0.00 0.00 46.52 4.09
1949 2112 0.308684 TGACGACGACACGTTTAGCT 59.691 50.000 0.00 0.00 46.52 3.32
1950 2113 1.316735 GATGACGACGACACGTTTAGC 59.683 52.381 0.00 2.15 46.52 3.09
1951 2114 1.571840 CGATGACGACGACACGTTTAG 59.428 52.381 0.00 0.00 46.52 1.85
1952 2115 1.594517 CGATGACGACGACACGTTTA 58.405 50.000 0.00 3.06 46.52 2.01
1953 2116 1.602877 GCGATGACGACGACACGTTT 61.603 55.000 17.32 0.00 46.52 3.60
1954 2117 2.078914 GCGATGACGACGACACGTT 61.079 57.895 17.32 0.00 46.52 3.99
1956 2119 3.238241 GGCGATGACGACGACACG 61.238 66.667 0.00 9.59 42.66 4.49
1963 2126 1.187974 TAAGAAAGGGGCGATGACGA 58.812 50.000 0.00 0.00 42.66 4.20
1974 2137 6.937465 GGATAGGCTCCAGTAATTAAGAAAGG 59.063 42.308 0.00 0.00 44.26 3.11
1999 2162 6.268566 AGAAAGAAAAACACTAGCAAGCAAG 58.731 36.000 0.00 0.00 0.00 4.01
2042 2205 5.749462 AGATACAACTTCCAGAGAAATGGG 58.251 41.667 0.00 0.00 41.01 4.00
2077 2240 4.541779 TGCAAAGCAAGTTAACATAACCG 58.458 39.130 8.61 0.00 34.76 4.44
2107 2271 2.639065 GAGTGACCCAACAAAGTGTCA 58.361 47.619 0.00 0.00 35.50 3.58
2127 2291 2.274232 TAGTTCGATGCGGGGTCACG 62.274 60.000 0.00 0.00 0.00 4.35
2167 2331 9.676861 GAGGCCTTTAAGGTTATAAAACTAGAA 57.323 33.333 6.77 0.00 37.80 2.10
2178 2342 6.243148 CCTTAAACTGAGGCCTTTAAGGTTA 58.757 40.000 30.07 22.89 46.34 2.85
2250 2415 8.464404 GCCATGCAAATACACATATCATTCTAT 58.536 33.333 0.00 0.00 0.00 1.98
2255 2420 7.170277 TCTAGCCATGCAAATACACATATCAT 58.830 34.615 0.00 0.00 0.00 2.45
2300 2465 6.477688 CCATGTCCAAATCTAAAATGACATGC 59.522 38.462 19.65 0.00 44.01 4.06
2304 2469 6.924111 ACACCATGTCCAAATCTAAAATGAC 58.076 36.000 0.00 0.00 0.00 3.06
2319 2484 2.674177 CGTAGTCCTTGGACACCATGTC 60.674 54.545 20.36 0.10 46.23 3.06
2327 2492 1.134560 CCTAGTGCGTAGTCCTTGGAC 59.865 57.143 11.59 11.59 0.00 4.02
2340 2505 9.937175 GAAACAATAATCAAAGATACCTAGTGC 57.063 33.333 0.00 0.00 0.00 4.40
2477 2642 1.481871 CCGAGTTGGAACTAGGGCTA 58.518 55.000 10.07 0.00 44.91 3.93
2519 2684 3.269538 TGTTCTCGTGAGGGTGAAAAA 57.730 42.857 0.00 0.00 0.00 1.94
2520 2685 2.992124 TGTTCTCGTGAGGGTGAAAA 57.008 45.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.