Multiple sequence alignment - TraesCS7A01G211100

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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 TraesCS7A01G211100 chr7A 100.000 5464 0 0 1 5464 174194402 174199865 0.000000e+00 10091
1 TraesCS7A01G211100 chr7B 94.371 4885 181 35 637 5463 137784300 137789148 0.000000e+00 7411
2 TraesCS7A01G211100 chr7B 88.633 607 42 8 1 584 137783682 137784284 0.000000e+00 713
3 TraesCS7A01G211100 chr7D 96.050 3949 116 16 1553 5463 171303518 171307464 0.000000e+00 6392
4 TraesCS7A01G211100 chr7D 90.916 1332 51 23 222 1529 171302237 171303522 0.000000e+00 1725
5 TraesCS7A01G211100 chr7D 95.270 148 5 2 82 228 171301271 171301417 3.290000e-57 233
6 TraesCS7A01G211100 chr6B 91.667 84 7 0 2011 2094 567410247 567410164 3.460000e-22 117
7 TraesCS7A01G211100 chr6D 90.476 84 8 0 2011 2094 379564678 379564761 1.610000e-20 111


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 TraesCS7A01G211100 chr7A 174194402 174199865 5463 False 10091.000000 10091 100.000000 1 5464 1 chr7A.!!$F1 5463
1 TraesCS7A01G211100 chr7B 137783682 137789148 5466 False 4062.000000 7411 91.502000 1 5463 2 chr7B.!!$F1 5462
2 TraesCS7A01G211100 chr7D 171301271 171307464 6193 False 2783.333333 6392 94.078667 82 5463 3 chr7D.!!$F1 5381

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
30 31 0.962855 TCGCCTGAGGTGACAGAGAG 60.963 60.0 11.35 0.00 37.29 3.20 F
1242 2116 0.107508 CACCGAATCCATGGCTCTGT 60.108 55.0 6.96 5.91 0.00 3.41 F
1530 2416 0.463833 CCTGTAAGCGAATCACCCCC 60.464 60.0 0.00 0.00 0.00 5.40 F
2033 2940 0.668535 GGAGGCTCAACAACAACACC 59.331 55.0 17.69 0.00 0.00 4.16 F
3192 4106 0.322008 CCTTGCCTGAGTGGGAGTTC 60.322 60.0 0.00 0.00 37.50 3.01 F
3959 4875 0.992431 AGAAGGGAGCCATGCTGGAT 60.992 55.0 6.40 0.00 39.95 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1279 2153 0.175760 GGCCATCGTTGCAGAGACTA 59.824 55.000 0.00 0.00 0.00 2.59 R
2102 3009 0.317479 GGGTAAGAGCACGTGACAGT 59.683 55.000 22.23 3.46 0.00 3.55 R
2710 3621 0.326264 CCCTGAACTGGAACCTCCTG 59.674 60.000 0.00 0.00 40.80 3.86 R
3716 4632 2.020131 GATGGCCTCACAGCAATCG 58.980 57.895 3.32 0.00 33.61 3.34 R
4178 5095 0.179018 GCAGACCCTTGTCAACCAGT 60.179 55.000 0.00 0.00 44.33 4.00 R
5225 6156 0.391661 TTGAGTCGCTCATCAAGGGC 60.392 55.000 9.78 0.00 40.39 5.19 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 4.161295 TCCCGCTGGAATCGCCTG 62.161 66.667 0.00 0.00 37.86 4.85
30 31 0.962855 TCGCCTGAGGTGACAGAGAG 60.963 60.000 11.35 0.00 37.29 3.20
31 32 1.247419 CGCCTGAGGTGACAGAGAGT 61.247 60.000 6.07 0.00 39.94 3.24
52 53 8.378172 AGAGTTTCAGTTCGAATCAAATTACA 57.622 30.769 0.00 0.00 32.32 2.41
118 122 2.886391 GCATACTTTGGGCCTTGGGTTA 60.886 50.000 4.53 0.00 0.00 2.85
161 165 6.218019 CGATGACCAATATGAAAAATGCCAT 58.782 36.000 0.00 0.00 0.00 4.40
177 181 4.376170 ATGCCCGGACCCAAACCC 62.376 66.667 0.73 0.00 0.00 4.11
223 227 5.171337 GCGTTCATGTCTGTAACAAAACTTG 59.829 40.000 0.00 0.00 42.37 3.16
225 229 6.410914 CGTTCATGTCTGTAACAAAACTTGTC 59.589 38.462 0.00 0.00 44.59 3.18
226 230 7.472543 GTTCATGTCTGTAACAAAACTTGTCT 58.527 34.615 0.00 0.00 44.59 3.41
227 231 8.609176 GTTCATGTCTGTAACAAAACTTGTCTA 58.391 33.333 0.00 0.00 44.59 2.59
288 1117 1.980784 CTGGATCCAGGCTCCCAGTG 61.981 65.000 31.14 4.89 40.84 3.66
306 1135 1.016627 TGATTGCATGCCTAGTTCGC 58.983 50.000 16.68 0.00 0.00 4.70
338 1167 3.123621 AGAGCACGCTTGTAATTTCTTCG 59.876 43.478 0.00 0.00 0.00 3.79
342 1171 3.357823 CACGCTTGTAATTTCTTCGTTGC 59.642 43.478 0.00 0.00 0.00 4.17
364 1193 3.505680 CGTGGGGTCAATCATTTTTCTGA 59.494 43.478 0.00 0.00 0.00 3.27
378 1207 3.418684 TTTCTGAGGTGGGTTTAGCTC 57.581 47.619 0.00 0.00 43.61 4.09
439 1268 2.361567 GCAATGGGCAGGAAAGGGG 61.362 63.158 0.00 0.00 43.97 4.79
520 1362 2.692273 AAACGAACCAGGGTGAGGGC 62.692 60.000 0.00 0.00 0.00 5.19
537 1379 4.918201 CCCGCCCGCCTCTCATTC 62.918 72.222 0.00 0.00 0.00 2.67
542 1384 1.745264 CCCGCCTCTCATTCTCTCC 59.255 63.158 0.00 0.00 0.00 3.71
711 1558 4.224818 TGTCATCTGTCTCTCTCTCTCTCA 59.775 45.833 0.00 0.00 0.00 3.27
720 1573 1.198867 CTCTCTCTCTCACACACCACG 59.801 57.143 0.00 0.00 0.00 4.94
841 1700 3.768922 GCCTCTCACGCCTGCTCT 61.769 66.667 0.00 0.00 0.00 4.09
842 1701 2.493973 CCTCTCACGCCTGCTCTC 59.506 66.667 0.00 0.00 0.00 3.20
843 1702 2.101965 CTCTCACGCCTGCTCTCG 59.898 66.667 0.00 0.00 0.00 4.04
844 1703 4.121669 TCTCACGCCTGCTCTCGC 62.122 66.667 0.00 0.00 0.00 5.03
846 1705 4.426112 TCACGCCTGCTCTCGCTG 62.426 66.667 0.00 0.00 36.97 5.18
851 1710 4.383861 CCTGCTCTCGCTGCCACA 62.384 66.667 0.00 0.00 36.97 4.17
852 1711 2.125229 CTGCTCTCGCTGCCACAT 60.125 61.111 0.00 0.00 36.97 3.21
853 1712 1.142531 CTGCTCTCGCTGCCACATA 59.857 57.895 0.00 0.00 36.97 2.29
854 1713 1.150567 CTGCTCTCGCTGCCACATAC 61.151 60.000 0.00 0.00 36.97 2.39
855 1714 2.233654 GCTCTCGCTGCCACATACG 61.234 63.158 0.00 0.00 0.00 3.06
856 1715 1.589993 CTCTCGCTGCCACATACGG 60.590 63.158 0.00 0.00 0.00 4.02
857 1716 2.586079 CTCGCTGCCACATACGGG 60.586 66.667 0.00 0.00 0.00 5.28
994 1868 3.093172 CTGCCTCCCTCCCTTCCC 61.093 72.222 0.00 0.00 0.00 3.97
1133 2007 0.246910 GGTTCGTGTCTCCCTCTTCC 59.753 60.000 0.00 0.00 0.00 3.46
1134 2008 0.246910 GTTCGTGTCTCCCTCTTCCC 59.753 60.000 0.00 0.00 0.00 3.97
1160 2034 1.134491 GGAATCGTTCTAGGGGGTGTG 60.134 57.143 0.00 0.00 0.00 3.82
1175 2049 2.147150 GGTGTGCTGGTTCTTCTTCTC 58.853 52.381 0.00 0.00 0.00 2.87
1242 2116 0.107508 CACCGAATCCATGGCTCTGT 60.108 55.000 6.96 5.91 0.00 3.41
1245 2119 1.134280 CCGAATCCATGGCTCTGTCTT 60.134 52.381 6.96 0.00 0.00 3.01
1255 2129 1.473080 GGCTCTGTCTTCCTCTGATGC 60.473 57.143 0.00 0.00 0.00 3.91
1256 2130 1.473080 GCTCTGTCTTCCTCTGATGCC 60.473 57.143 0.00 0.00 0.00 4.40
1271 2145 2.807967 TGATGCCGTTTCTTCAGTCAAG 59.192 45.455 0.00 0.00 0.00 3.02
1279 2153 1.621992 TCTTCAGTCAAGCCGAGAGT 58.378 50.000 0.00 0.00 31.26 3.24
1281 2155 2.750166 TCTTCAGTCAAGCCGAGAGTAG 59.250 50.000 0.00 0.00 31.26 2.57
1354 2228 7.851822 ATTATTATTATCGGTTTTGCGCAAG 57.148 32.000 23.68 11.90 43.44 4.01
1530 2416 0.463833 CCTGTAAGCGAATCACCCCC 60.464 60.000 0.00 0.00 0.00 5.40
1549 2435 2.623416 CCCTTTCCTGTTTCACTTCACC 59.377 50.000 0.00 0.00 0.00 4.02
1552 2438 1.967319 TCCTGTTTCACTTCACCTGC 58.033 50.000 0.00 0.00 0.00 4.85
1568 2454 5.858381 TCACCTGCACCTAATCATATTCTC 58.142 41.667 0.00 0.00 0.00 2.87
1587 2473 7.750229 ATTCTCTGCATGTTTTTACTTCTCA 57.250 32.000 0.00 0.00 0.00 3.27
1594 2483 5.617751 GCATGTTTTTACTTCTCATCACGCT 60.618 40.000 0.00 0.00 0.00 5.07
1595 2484 5.342806 TGTTTTTACTTCTCATCACGCTG 57.657 39.130 0.00 0.00 0.00 5.18
1598 2487 4.990543 TTTACTTCTCATCACGCTGTTG 57.009 40.909 0.00 0.00 0.00 3.33
1604 2493 3.059884 TCTCATCACGCTGTTGTTCTTC 58.940 45.455 0.00 0.00 0.00 2.87
1605 2494 1.792367 TCATCACGCTGTTGTTCTTCG 59.208 47.619 0.00 0.00 0.00 3.79
1642 2531 1.209019 GCTCCAAGCCAGAATCTCTCA 59.791 52.381 0.00 0.00 34.48 3.27
1745 2634 5.138125 TCAGAGTTCCATTTTCCATTTGC 57.862 39.130 0.00 0.00 0.00 3.68
1935 2824 3.093057 CCAGTACCTGTGAGCTCTACTT 58.907 50.000 16.19 0.00 0.00 2.24
1936 2825 3.129638 CCAGTACCTGTGAGCTCTACTTC 59.870 52.174 16.19 1.32 0.00 3.01
1937 2826 4.013728 CAGTACCTGTGAGCTCTACTTCT 58.986 47.826 16.19 2.32 0.00 2.85
1939 2828 2.088423 ACCTGTGAGCTCTACTTCTCG 58.912 52.381 16.19 0.00 32.20 4.04
1940 2829 2.088423 CCTGTGAGCTCTACTTCTCGT 58.912 52.381 16.19 0.00 32.20 4.18
1941 2830 2.096819 CCTGTGAGCTCTACTTCTCGTC 59.903 54.545 16.19 0.00 32.20 4.20
1942 2831 2.744741 CTGTGAGCTCTACTTCTCGTCA 59.255 50.000 16.19 0.00 32.20 4.35
1943 2832 3.348119 TGTGAGCTCTACTTCTCGTCAT 58.652 45.455 16.19 0.00 32.20 3.06
1944 2833 3.127721 TGTGAGCTCTACTTCTCGTCATG 59.872 47.826 16.19 0.00 32.20 3.07
1945 2834 3.375610 GTGAGCTCTACTTCTCGTCATGA 59.624 47.826 16.19 0.00 32.20 3.07
1946 2835 4.010349 TGAGCTCTACTTCTCGTCATGAA 58.990 43.478 16.19 0.00 32.20 2.57
1947 2836 4.459337 TGAGCTCTACTTCTCGTCATGAAA 59.541 41.667 16.19 0.00 32.20 2.69
1948 2837 5.126222 TGAGCTCTACTTCTCGTCATGAAAT 59.874 40.000 16.19 0.00 32.20 2.17
1950 2839 6.500041 AGCTCTACTTCTCGTCATGAAATAC 58.500 40.000 0.00 0.00 0.00 1.89
1951 2840 5.688176 GCTCTACTTCTCGTCATGAAATACC 59.312 44.000 0.00 0.00 0.00 2.73
1953 2842 5.892119 TCTACTTCTCGTCATGAAATACCCT 59.108 40.000 0.00 0.00 0.00 4.34
1954 2843 7.058525 TCTACTTCTCGTCATGAAATACCCTA 58.941 38.462 0.00 0.00 0.00 3.53
1955 2844 5.903810 ACTTCTCGTCATGAAATACCCTAC 58.096 41.667 0.00 0.00 0.00 3.18
1956 2845 4.931661 TCTCGTCATGAAATACCCTACC 57.068 45.455 0.00 0.00 0.00 3.18
1957 2846 4.543689 TCTCGTCATGAAATACCCTACCT 58.456 43.478 0.00 0.00 0.00 3.08
1958 2847 4.583489 TCTCGTCATGAAATACCCTACCTC 59.417 45.833 0.00 0.00 0.00 3.85
1965 2872 5.450818 TGAAATACCCTACCTCTTGCATT 57.549 39.130 0.00 0.00 0.00 3.56
1969 2876 8.719596 TGAAATACCCTACCTCTTGCATTATTA 58.280 33.333 0.00 0.00 0.00 0.98
1996 2903 2.280628 CTTGAGATGTTAACCCGAGGC 58.719 52.381 2.48 0.00 0.00 4.70
2030 2937 0.954452 CCAGGAGGCTCAACAACAAC 59.046 55.000 17.69 0.00 0.00 3.32
2033 2940 0.668535 GGAGGCTCAACAACAACACC 59.331 55.000 17.69 0.00 0.00 4.16
2039 2946 1.676006 CTCAACAACAACACCCTGTCC 59.324 52.381 0.00 0.00 0.00 4.02
2057 2964 1.227263 CGGTCCATTCCCTACAGCG 60.227 63.158 0.00 0.00 0.00 5.18
2089 2996 1.002792 GTCGCACCTTGTTTTCCTGTC 60.003 52.381 0.00 0.00 0.00 3.51
2102 3009 6.843752 TGTTTTCCTGTCAGTAATTTCCCTA 58.156 36.000 0.00 0.00 0.00 3.53
2113 3020 2.094762 ATTTCCCTACTGTCACGTGC 57.905 50.000 11.67 6.86 0.00 5.34
2126 3037 1.831106 TCACGTGCTCTTACCCATGAT 59.169 47.619 11.67 0.00 0.00 2.45
2129 3040 3.063997 CACGTGCTCTTACCCATGATTTC 59.936 47.826 0.82 0.00 0.00 2.17
2132 3043 4.201851 CGTGCTCTTACCCATGATTTCTTG 60.202 45.833 0.00 0.00 0.00 3.02
2156 3067 1.160137 GGGATGTTCTCACTGTGCAC 58.840 55.000 10.75 10.75 0.00 4.57
2192 3103 7.066163 TGCAGAGATTTGTCATACAATAACCTG 59.934 37.037 0.00 0.00 38.00 4.00
2473 3384 1.461888 CGACGAAAGCTAAAAGCCACG 60.462 52.381 0.00 2.43 43.77 4.94
2566 3477 2.197605 TGGAGACAGCGTCGGAACA 61.198 57.895 0.00 0.50 37.67 3.18
2710 3621 5.220796 GGATAACGTTAGCCTTGGAAATGTC 60.221 44.000 30.45 10.95 36.32 3.06
2851 3762 2.417719 GCTGTCAAACGACTCAAGGAT 58.582 47.619 0.00 0.00 34.31 3.24
3068 3979 0.322456 TGCCTTTCCTTGACATCCCG 60.322 55.000 0.00 0.00 0.00 5.14
3110 4021 3.611766 ACTAGCTCATTTTGGCGTAGT 57.388 42.857 0.00 0.00 0.00 2.73
3143 4054 1.261480 TTGCTTTGTTGGGTGTGTGT 58.739 45.000 0.00 0.00 0.00 3.72
3192 4106 0.322008 CCTTGCCTGAGTGGGAGTTC 60.322 60.000 0.00 0.00 37.50 3.01
3282 4196 4.431416 TTGTCATGTTACCAAGTGACCT 57.569 40.909 0.00 0.00 40.07 3.85
3716 4632 2.186826 AGCCAACGTGTTGCTGGAC 61.187 57.895 7.41 0.00 39.16 4.02
3749 4665 1.151777 CCATCGTCGGTGATTTCGGG 61.152 60.000 7.17 0.00 0.00 5.14
3779 4695 2.831333 CTCCTTGATCACCAGGATTCG 58.169 52.381 15.13 2.48 36.00 3.34
3959 4875 0.992431 AGAAGGGAGCCATGCTGGAT 60.992 55.000 6.40 0.00 39.95 3.41
3968 4884 2.041701 GCCATGCTGGATTGGGTAATT 58.958 47.619 6.40 0.00 40.96 1.40
3990 4906 7.651027 ATTAAGCCTCTGCAATTTACTTGAT 57.349 32.000 0.00 0.00 41.13 2.57
3991 4907 8.752005 ATTAAGCCTCTGCAATTTACTTGATA 57.248 30.769 0.00 0.00 41.13 2.15
4004 4921 8.430063 CAATTTACTTGATAAAACTGCTGCAAG 58.570 33.333 3.02 0.00 36.35 4.01
4087 5004 6.142817 GTCGAAACTGTTCATAACTGCAAAT 58.857 36.000 0.00 0.00 32.89 2.32
4124 5041 4.805719 TGATGCTTAAGTTAGCTCATGACG 59.194 41.667 4.02 0.00 41.76 4.35
4125 5042 4.188247 TGCTTAAGTTAGCTCATGACGT 57.812 40.909 4.02 0.00 41.76 4.34
4126 5043 5.319140 TGCTTAAGTTAGCTCATGACGTA 57.681 39.130 4.02 0.00 41.76 3.57
4178 5095 5.470098 GCACCAAGAGAAGAAACTTGATGTA 59.530 40.000 0.00 0.00 43.98 2.29
4193 5110 2.708861 TGATGTACTGGTTGACAAGGGT 59.291 45.455 0.00 0.00 0.00 4.34
4277 5194 4.000620 TACCTCCCAGGCCACCGA 62.001 66.667 5.01 0.00 39.63 4.69
4370 5287 1.217882 CCGACTCACACAAGTTCACC 58.782 55.000 0.00 0.00 0.00 4.02
4415 5332 1.991099 GCTACTCCGACCTGACCGAC 61.991 65.000 0.00 0.00 0.00 4.79
4421 5338 2.479650 GACCTGACCGACGACTCG 59.520 66.667 0.00 0.00 39.83 4.18
4451 5368 4.200283 CAGGCCGTCGAGCTCTCC 62.200 72.222 12.85 5.07 0.00 3.71
4468 5385 1.825191 CCGGGCCAAGATGACATGG 60.825 63.158 4.39 0.00 37.85 3.66
4477 5394 3.415212 CAAGATGACATGGTCACCAAGT 58.585 45.455 3.81 3.81 45.65 3.16
4479 5396 2.639347 AGATGACATGGTCACCAAGTGA 59.361 45.455 10.07 0.37 45.65 3.41
4501 5424 1.285023 CAGAACACCAAGCAGCAGC 59.715 57.895 0.00 0.00 42.56 5.25
4754 5677 6.959639 TTGTATTTTCTCTTTGGCAGTCTT 57.040 33.333 0.00 0.00 0.00 3.01
4755 5678 6.959639 TGTATTTTCTCTTTGGCAGTCTTT 57.040 33.333 0.00 0.00 0.00 2.52
4756 5679 8.458573 TTGTATTTTCTCTTTGGCAGTCTTTA 57.541 30.769 0.00 0.00 0.00 1.85
4807 5735 7.994425 TCAGATTGAAACAGGTGCTAAAATA 57.006 32.000 0.00 0.00 0.00 1.40
4818 5746 8.162878 ACAGGTGCTAAAATATGATCAGAATG 57.837 34.615 0.09 0.00 37.54 2.67
5007 5938 4.592942 TCATCAACCATCAAAGGAGAAGG 58.407 43.478 0.00 0.00 0.00 3.46
5015 5946 0.385974 CAAAGGAGAAGGCGCAAACG 60.386 55.000 10.83 0.00 44.07 3.60
5024 5955 2.548295 GGCGCAAACGAAGGTTCCA 61.548 57.895 10.83 0.00 43.93 3.53
5025 5956 1.370051 GCGCAAACGAAGGTTCCAC 60.370 57.895 0.30 0.00 43.93 4.02
5099 6030 3.068590 GGTTGGTGATATTGCCCATCTTG 59.931 47.826 0.00 0.00 0.00 3.02
5243 6174 1.219124 GCCCTTGATGAGCGACTCA 59.781 57.895 11.12 11.12 44.99 3.41
5314 6245 2.178876 TTGTCGTCGCCACCATCCAT 62.179 55.000 0.00 0.00 0.00 3.41
5463 6394 7.088905 GGATCCTTCAATGCAAATGTCATATC 58.911 38.462 3.84 0.00 0.00 1.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 4.303282 GAACTGAAACTCTCTGTCACCTC 58.697 47.826 0.00 0.00 35.33 3.85
118 122 1.994463 CAAAGTCTAGCCTGGGCCT 59.006 57.895 4.53 0.00 43.17 5.19
177 181 1.654023 GGAATGTTTTCCGGGCCTCG 61.654 60.000 0.84 4.41 42.04 4.63
251 1080 6.830838 GGATCCAGATTAGTTCCAGACATTTT 59.169 38.462 6.95 0.00 0.00 1.82
288 1117 1.262683 GAGCGAACTAGGCATGCAATC 59.737 52.381 21.36 8.51 0.00 2.67
338 1167 0.887933 AATGATTGACCCCACGCAAC 59.112 50.000 0.00 0.00 0.00 4.17
342 1171 3.505680 TCAGAAAAATGATTGACCCCACG 59.494 43.478 0.00 0.00 0.00 4.94
364 1193 2.327325 TCTGAGAGCTAAACCCACCT 57.673 50.000 0.00 0.00 0.00 4.00
378 1207 8.781196 TCTTTTCTTGATTGATTGTCTTCTGAG 58.219 33.333 0.00 0.00 0.00 3.35
439 1268 2.043980 TCCGGGATTTTTGCGAGCC 61.044 57.895 0.00 0.00 0.00 4.70
520 1362 4.918201 GAATGAGAGGCGGGCGGG 62.918 72.222 0.00 0.00 0.00 6.13
523 1365 1.068921 GAGAGAATGAGAGGCGGGC 59.931 63.158 0.00 0.00 0.00 6.13
527 1369 2.141312 GGGGGAGAGAATGAGAGGC 58.859 63.158 0.00 0.00 0.00 4.70
542 1384 2.627699 CCGGAATGATAAACAATGGGGG 59.372 50.000 0.00 0.00 0.00 5.40
847 1706 4.910585 GGCCTCGCCCGTATGTGG 62.911 72.222 0.00 0.00 44.06 4.17
857 1716 4.043200 GTGCAACCTTGGCCTCGC 62.043 66.667 3.32 0.00 0.00 5.03
858 1717 2.281761 AGTGCAACCTTGGCCTCG 60.282 61.111 3.32 0.00 37.80 4.63
859 1718 1.973812 GGAGTGCAACCTTGGCCTC 60.974 63.158 3.32 0.00 37.80 4.70
860 1719 2.116125 GGAGTGCAACCTTGGCCT 59.884 61.111 3.32 0.00 37.80 5.19
861 1720 2.203480 TGGAGTGCAACCTTGGCC 60.203 61.111 11.60 0.00 37.80 5.36
862 1721 2.908073 CGTGGAGTGCAACCTTGGC 61.908 63.158 11.60 0.00 37.80 4.52
863 1722 2.908073 GCGTGGAGTGCAACCTTGG 61.908 63.158 11.60 3.57 37.80 3.61
864 1723 2.121564 CTGCGTGGAGTGCAACCTTG 62.122 60.000 11.60 6.01 42.70 3.61
865 1724 1.893808 CTGCGTGGAGTGCAACCTT 60.894 57.895 11.60 0.00 42.70 3.50
866 1725 2.281070 CTGCGTGGAGTGCAACCT 60.281 61.111 11.60 0.00 42.70 3.50
867 1726 4.030452 GCTGCGTGGAGTGCAACC 62.030 66.667 4.46 4.46 42.70 3.77
941 1805 3.322466 AGGGGCGTGACAAGGGAG 61.322 66.667 0.00 0.00 0.00 4.30
976 1850 3.093172 GGAAGGGAGGGAGGCAGG 61.093 72.222 0.00 0.00 0.00 4.85
977 1851 3.093172 GGGAAGGGAGGGAGGCAG 61.093 72.222 0.00 0.00 0.00 4.85
978 1852 4.760220 GGGGAAGGGAGGGAGGCA 62.760 72.222 0.00 0.00 0.00 4.75
984 1858 3.420482 ATTGCCGGGGAAGGGAGG 61.420 66.667 7.18 0.00 31.78 4.30
985 1859 2.124151 CATTGCCGGGGAAGGGAG 60.124 66.667 7.18 0.00 31.78 4.30
1133 2007 1.067212 CCTAGAACGATTCCAGGACGG 59.933 57.143 4.59 0.00 40.50 4.79
1134 2008 1.067212 CCCTAGAACGATTCCAGGACG 59.933 57.143 11.64 0.00 40.50 4.79
1160 2034 1.905894 AGAGGGAGAAGAAGAACCAGC 59.094 52.381 0.00 0.00 0.00 4.85
1175 2049 1.404851 GCGGAGAAGAAAGACAGAGGG 60.405 57.143 0.00 0.00 0.00 4.30
1203 2077 5.450688 CGGTGGGAATAACAGAGTAGAGAAG 60.451 48.000 0.00 0.00 0.00 2.85
1242 2116 1.902508 AGAAACGGCATCAGAGGAAGA 59.097 47.619 0.00 0.00 0.00 2.87
1245 2119 1.623311 TGAAGAAACGGCATCAGAGGA 59.377 47.619 0.00 0.00 0.00 3.71
1255 2129 0.512952 CGGCTTGACTGAAGAAACGG 59.487 55.000 0.00 0.00 32.82 4.44
1256 2130 1.457303 CTCGGCTTGACTGAAGAAACG 59.543 52.381 0.00 0.00 32.82 3.60
1279 2153 0.175760 GGCCATCGTTGCAGAGACTA 59.824 55.000 0.00 0.00 0.00 2.59
1281 2155 2.456119 CGGCCATCGTTGCAGAGAC 61.456 63.158 2.24 0.00 0.00 3.36
1354 2228 2.352127 GGCAGGCAGATGTTTCAGAAAC 60.352 50.000 17.85 17.85 41.73 2.78
1530 2416 3.243201 GCAGGTGAAGTGAAACAGGAAAG 60.243 47.826 0.00 0.00 41.43 2.62
1549 2435 5.303165 TGCAGAGAATATGATTAGGTGCAG 58.697 41.667 0.00 0.00 33.65 4.41
1552 2438 7.741027 AACATGCAGAGAATATGATTAGGTG 57.259 36.000 0.00 0.00 0.00 4.00
1568 2454 5.791974 CGTGATGAGAAGTAAAAACATGCAG 59.208 40.000 0.00 0.00 0.00 4.41
1584 2470 2.159920 CGAAGAACAACAGCGTGATGAG 60.160 50.000 0.00 0.00 0.00 2.90
1587 2473 2.148916 TCGAAGAACAACAGCGTGAT 57.851 45.000 0.00 0.00 0.00 3.06
1594 2483 4.384940 TGTGGATGATTCGAAGAACAACA 58.615 39.130 3.35 2.59 45.90 3.33
1595 2484 4.142816 CCTGTGGATGATTCGAAGAACAAC 60.143 45.833 3.35 3.11 45.90 3.32
1598 2487 2.939103 CCCTGTGGATGATTCGAAGAAC 59.061 50.000 3.35 0.00 45.90 3.01
1604 2493 0.533755 GCCTCCCTGTGGATGATTCG 60.534 60.000 0.00 0.00 40.80 3.34
1605 2494 0.842635 AGCCTCCCTGTGGATGATTC 59.157 55.000 0.00 0.00 40.80 2.52
1745 2634 5.413213 AGAGAACGGTAAGATATCTCCATCG 59.587 44.000 15.00 15.00 37.77 3.84
1935 2824 4.543689 AGGTAGGGTATTTCATGACGAGA 58.456 43.478 0.00 0.00 0.00 4.04
1936 2825 4.585162 AGAGGTAGGGTATTTCATGACGAG 59.415 45.833 0.00 0.00 0.00 4.18
1937 2826 4.543689 AGAGGTAGGGTATTTCATGACGA 58.456 43.478 0.00 0.00 0.00 4.20
1939 2828 4.816925 GCAAGAGGTAGGGTATTTCATGAC 59.183 45.833 0.00 0.00 0.00 3.06
1940 2829 4.473196 TGCAAGAGGTAGGGTATTTCATGA 59.527 41.667 0.00 0.00 0.00 3.07
1941 2830 4.780815 TGCAAGAGGTAGGGTATTTCATG 58.219 43.478 0.00 0.00 0.00 3.07
1942 2831 5.653255 ATGCAAGAGGTAGGGTATTTCAT 57.347 39.130 0.00 0.00 0.00 2.57
1943 2832 5.450818 AATGCAAGAGGTAGGGTATTTCA 57.549 39.130 0.00 0.00 0.00 2.69
1944 2833 9.740710 ATAATAATGCAAGAGGTAGGGTATTTC 57.259 33.333 0.00 0.00 0.00 2.17
1946 2835 9.520515 CAATAATAATGCAAGAGGTAGGGTATT 57.479 33.333 0.00 0.00 0.00 1.89
1947 2836 8.669571 ACAATAATAATGCAAGAGGTAGGGTAT 58.330 33.333 0.00 0.00 0.00 2.73
1948 2837 8.041143 ACAATAATAATGCAAGAGGTAGGGTA 57.959 34.615 0.00 0.00 0.00 3.69
1950 2839 7.040409 GGAACAATAATAATGCAAGAGGTAGGG 60.040 40.741 0.00 0.00 0.00 3.53
1951 2840 7.721399 AGGAACAATAATAATGCAAGAGGTAGG 59.279 37.037 0.00 0.00 0.00 3.18
1953 2842 8.902806 CAAGGAACAATAATAATGCAAGAGGTA 58.097 33.333 0.00 0.00 0.00 3.08
1954 2843 7.615365 TCAAGGAACAATAATAATGCAAGAGGT 59.385 33.333 0.00 0.00 0.00 3.85
1955 2844 7.999679 TCAAGGAACAATAATAATGCAAGAGG 58.000 34.615 0.00 0.00 0.00 3.69
1956 2845 8.896744 TCTCAAGGAACAATAATAATGCAAGAG 58.103 33.333 0.00 0.00 0.00 2.85
1957 2846 8.806429 TCTCAAGGAACAATAATAATGCAAGA 57.194 30.769 0.00 0.00 0.00 3.02
1958 2847 9.459640 CATCTCAAGGAACAATAATAATGCAAG 57.540 33.333 0.00 0.00 0.00 4.01
1965 2872 9.403583 GGGTTAACATCTCAAGGAACAATAATA 57.596 33.333 8.10 0.00 0.00 0.98
1969 2876 4.700213 CGGGTTAACATCTCAAGGAACAAT 59.300 41.667 8.10 0.00 0.00 2.71
1996 2903 3.369892 CCTCCTGGTCAGATTACAACAGG 60.370 52.174 0.00 0.00 45.18 4.00
2030 2937 1.078426 GAATGGACCGGACAGGGTG 60.078 63.158 9.46 0.00 46.96 4.61
2039 2946 1.227263 CGCTGTAGGGAATGGACCG 60.227 63.158 0.00 0.00 0.00 4.79
2102 3009 0.317479 GGGTAAGAGCACGTGACAGT 59.683 55.000 22.23 3.46 0.00 3.55
2113 3020 6.350445 CCAAACCAAGAAATCATGGGTAAGAG 60.350 42.308 9.29 0.00 38.92 2.85
2126 3037 4.340950 GTGAGAACATCCCAAACCAAGAAA 59.659 41.667 0.00 0.00 0.00 2.52
2129 3040 3.254166 CAGTGAGAACATCCCAAACCAAG 59.746 47.826 0.00 0.00 0.00 3.61
2132 3043 2.554032 CACAGTGAGAACATCCCAAACC 59.446 50.000 0.00 0.00 0.00 3.27
2156 3067 2.486472 AATCTCTGCAGGACACAAGG 57.514 50.000 15.13 0.00 0.00 3.61
2192 3103 1.122019 ATCCTGGTATCGGGCCACTC 61.122 60.000 4.39 0.00 39.31 3.51
2284 3195 7.194112 TGATACAGGTTCATACTTCCATGAA 57.806 36.000 0.00 0.00 41.49 2.57
2566 3477 3.130516 TCGTCATCGAAAAGTATCTGCCT 59.869 43.478 0.00 0.00 43.34 4.75
2710 3621 0.326264 CCCTGAACTGGAACCTCCTG 59.674 60.000 0.00 0.00 40.80 3.86
2851 3762 2.045438 CCACCCGCAGCATTACCA 60.045 61.111 0.00 0.00 0.00 3.25
3068 3979 7.279750 AGTTCTATCTAGCCTAGTTAAGCAC 57.720 40.000 0.00 0.00 0.00 4.40
3143 4054 2.033141 GCTGCAGCCTCCAACTGA 59.967 61.111 28.76 0.00 37.32 3.41
3192 4106 2.158885 GGAGGAGGCTAGCCAAAGTAAG 60.159 54.545 34.70 0.00 38.92 2.34
3716 4632 2.020131 GATGGCCTCACAGCAATCG 58.980 57.895 3.32 0.00 33.61 3.34
3779 4695 2.588877 ACTGCAGTGGTGACGTGC 60.589 61.111 20.97 0.00 37.73 5.34
3959 4875 3.730215 TGCAGAGGCTTAATTACCCAA 57.270 42.857 0.00 0.00 41.91 4.12
3968 4884 8.574251 TTTATCAAGTAAATTGCAGAGGCTTA 57.426 30.769 0.00 0.00 41.91 3.09
4040 4957 5.581874 ACAAAAGTGCTTTTCATTTCAGGTG 59.418 36.000 6.92 0.00 40.45 4.00
4087 5004 1.228033 CATCATCGATGGCAGGGCA 60.228 57.895 24.61 4.33 36.51 5.36
4124 5041 6.317140 TCTTCACCTGATCATCAAGCAATTAC 59.683 38.462 0.00 0.00 0.00 1.89
4125 5042 6.417258 TCTTCACCTGATCATCAAGCAATTA 58.583 36.000 0.00 0.00 0.00 1.40
4126 5043 5.258841 TCTTCACCTGATCATCAAGCAATT 58.741 37.500 0.00 0.00 0.00 2.32
4160 5077 6.426646 ACCAGTACATCAAGTTTCTTCTCT 57.573 37.500 0.00 0.00 0.00 3.10
4178 5095 0.179018 GCAGACCCTTGTCAACCAGT 60.179 55.000 0.00 0.00 44.33 4.00
4325 5242 3.723348 GACGCTTGCCACCGTTCC 61.723 66.667 0.00 0.00 37.87 3.62
4370 5287 0.249868 TGAAGGTGAACTCAGGCACG 60.250 55.000 0.00 0.00 35.91 5.34
4403 5320 2.479650 GAGTCGTCGGTCAGGTCG 59.520 66.667 0.00 0.00 0.00 4.79
4415 5332 1.959899 GCACCAGCAATGACGAGTCG 61.960 60.000 11.85 11.85 41.58 4.18
4451 5368 1.077501 ACCATGTCATCTTGGCCCG 60.078 57.895 0.00 0.00 40.99 6.13
4477 5394 0.254462 TGCTTGGTGTTCTGTGGTCA 59.746 50.000 0.00 0.00 0.00 4.02
4479 5396 1.103398 GCTGCTTGGTGTTCTGTGGT 61.103 55.000 0.00 0.00 0.00 4.16
4501 5424 4.978099 AGGATTATCATGCTGTACAAGGG 58.022 43.478 0.00 0.00 27.88 3.95
4807 5735 4.584743 ACATCAGCAATGCATTCTGATCAT 59.415 37.500 30.65 24.10 43.44 2.45
4818 5746 7.809665 TGATATTATGTACACATCAGCAATGC 58.190 34.615 0.00 0.00 39.12 3.56
4878 5809 8.721133 TTGGCTGTATGGAGTAATAGAGAATA 57.279 34.615 0.00 0.00 0.00 1.75
5007 5938 1.370051 GTGGAACCTTCGTTTGCGC 60.370 57.895 0.00 0.00 38.14 6.09
5024 5955 2.831685 TCGTGAACACATAAGCTGGT 57.168 45.000 5.80 0.00 0.00 4.00
5025 5956 3.935203 AGATTCGTGAACACATAAGCTGG 59.065 43.478 5.80 0.00 0.00 4.85
5099 6030 1.134965 CAGTTCTCGGACTCCATGGTC 60.135 57.143 12.58 2.28 35.66 4.02
5225 6156 0.391661 TTGAGTCGCTCATCAAGGGC 60.392 55.000 9.78 0.00 40.39 5.19
5239 6170 3.034721 TCGACAACGCCTATTTTGAGT 57.965 42.857 0.00 0.00 39.58 3.41
5243 6174 2.740447 GACCTTCGACAACGCCTATTTT 59.260 45.455 0.00 0.00 39.58 1.82
5266 6197 3.986054 TGGACAGCCACACTTCCT 58.014 55.556 0.00 0.00 39.92 3.36
5314 6245 1.920325 CTCAAGGAGGTCTGCCCCA 60.920 63.158 0.00 0.00 34.57 4.96
5323 6254 0.392729 CCTCAGCAAGCTCAAGGAGG 60.393 60.000 12.53 11.54 36.33 4.30
5420 6351 1.024046 CCCACACGATTGGATTCGCA 61.024 55.000 8.42 0.00 42.82 5.10


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

AutoCloner maintained by Alex Coulton.