Multiple sequence alignment - TraesCS1A01G290600

Loading Multiple Alignment...

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 TraesCS1A01G290600 chr1A 100.000 2740 0 0 1 2740 487080353 487077614 0.000000e+00 5060
1 TraesCS1A01G290600 chr1A 91.637 837 57 10 1914 2740 423952812 423953645 0.000000e+00 1146
2 TraesCS1A01G290600 chr1B 85.258 1221 97 39 234 1426 520682828 520681663 0.000000e+00 1181
3 TraesCS1A01G290600 chr1B 92.308 247 15 4 1471 1717 520681648 520681406 5.620000e-92 348
4 TraesCS1A01G290600 chr7A 92.019 827 54 5 1914 2730 475261887 475261063 0.000000e+00 1151
5 TraesCS1A01G290600 chr7A 91.707 832 58 11 1915 2740 226688517 226689343 0.000000e+00 1144
6 TraesCS1A01G290600 chr7A 91.429 840 57 8 1914 2740 526163224 526164061 0.000000e+00 1138
7 TraesCS1A01G290600 chr7A 90.826 109 3 3 392 494 618184450 618184343 3.680000e-29 139
8 TraesCS1A01G290600 chr1D 91.727 834 62 7 1910 2740 31227453 31228282 0.000000e+00 1151
9 TraesCS1A01G290600 chr1D 91.388 836 60 8 1914 2740 31220492 31221324 0.000000e+00 1134
10 TraesCS1A01G290600 chr1D 86.630 920 66 29 995 1889 387329645 387328758 0.000000e+00 965
11 TraesCS1A01G290600 chr1D 84.170 777 83 19 229 996 387330423 387329678 0.000000e+00 717
12 TraesCS1A01G290600 chr1D 86.345 249 17 3 1 233 387330890 387330643 3.500000e-64 255
13 TraesCS1A01G290600 chr6D 91.657 839 54 8 1913 2740 273157010 273156177 0.000000e+00 1147
14 TraesCS1A01G290600 chr6D 91.274 848 53 16 1910 2740 86204163 86205006 0.000000e+00 1136
15 TraesCS1A01G290600 chr2A 91.340 843 56 11 1910 2740 84256597 84257434 0.000000e+00 1136
16 TraesCS1A01G290600 chr3B 95.745 94 2 2 388 480 479988673 479988581 1.700000e-32 150
17 TraesCS1A01G290600 chr5D 92.857 98 5 2 392 488 446400805 446400709 1.020000e-29 141
18 TraesCS1A01G290600 chr5A 92.857 98 6 1 388 484 650290022 650290119 1.020000e-29 141
19 TraesCS1A01G290600 chr5A 88.793 116 10 3 378 490 644821011 644821126 3.680000e-29 139
20 TraesCS1A01G290600 chr5B 91.346 104 6 3 381 482 658381132 658381030 3.680000e-29 139
21 TraesCS1A01G290600 chr5B 90.000 110 6 3 386 490 650023823 650023932 1.320000e-28 137


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 TraesCS1A01G290600 chr1A 487077614 487080353 2739 True 5060.000000 5060 100.000 1 2740 1 chr1A.!!$R1 2739
1 TraesCS1A01G290600 chr1A 423952812 423953645 833 False 1146.000000 1146 91.637 1914 2740 1 chr1A.!!$F1 826
2 TraesCS1A01G290600 chr1B 520681406 520682828 1422 True 764.500000 1181 88.783 234 1717 2 chr1B.!!$R1 1483
3 TraesCS1A01G290600 chr7A 475261063 475261887 824 True 1151.000000 1151 92.019 1914 2730 1 chr7A.!!$R1 816
4 TraesCS1A01G290600 chr7A 226688517 226689343 826 False 1144.000000 1144 91.707 1915 2740 1 chr7A.!!$F1 825
5 TraesCS1A01G290600 chr7A 526163224 526164061 837 False 1138.000000 1138 91.429 1914 2740 1 chr7A.!!$F2 826
6 TraesCS1A01G290600 chr1D 31227453 31228282 829 False 1151.000000 1151 91.727 1910 2740 1 chr1D.!!$F2 830
7 TraesCS1A01G290600 chr1D 31220492 31221324 832 False 1134.000000 1134 91.388 1914 2740 1 chr1D.!!$F1 826
8 TraesCS1A01G290600 chr1D 387328758 387330890 2132 True 645.666667 965 85.715 1 1889 3 chr1D.!!$R1 1888
9 TraesCS1A01G290600 chr6D 273156177 273157010 833 True 1147.000000 1147 91.657 1913 2740 1 chr6D.!!$R1 827
10 TraesCS1A01G290600 chr6D 86204163 86205006 843 False 1136.000000 1136 91.274 1910 2740 1 chr6D.!!$F1 830
11 TraesCS1A01G290600 chr2A 84256597 84257434 837 False 1136.000000 1136 91.340 1910 2740 1 chr2A.!!$F1 830

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
378 633 0.669619 CACATCAAGCTGTGTGCCAA 59.33 50.0 12.42 0.0 44.23 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1865 2204 0.034863 ATACCCCAAATGCGAACCGT 60.035 50.0 0.0 0.0 0.0 4.83 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
33 34 6.228258 GTGGTGTATTCAGTTGTTTAGAGGA 58.772 40.000 0.00 0.00 0.00 3.71
55 56 2.282040 GGTGCTGCTGTGAGGCTT 60.282 61.111 0.00 0.00 0.00 4.35
91 107 4.205385 CGAAGAATAACTAGCGAGCAACTC 59.795 45.833 0.00 0.00 0.00 3.01
121 137 7.010923 TGTGTTATTTGCTTTGAACCAATTGTC 59.989 33.333 4.43 0.00 0.00 3.18
133 149 2.365293 ACCAATTGTCTTCTTTGGGCAC 59.635 45.455 4.43 0.00 43.39 5.01
159 175 5.643777 AGTAGTGTTGACATGGACTATTTGC 59.356 40.000 0.00 0.00 0.00 3.68
175 191 5.932303 ACTATTTGCTGTCAACTCGTGTTAT 59.068 36.000 2.02 0.00 34.60 1.89
182 198 5.590104 TGTCAACTCGTGTTATTGTCATG 57.410 39.130 2.02 0.00 34.60 3.07
186 202 5.755861 TCAACTCGTGTTATTGTCATGAACA 59.244 36.000 0.00 0.00 34.60 3.18
203 219 5.749596 TGAACAATTTGATGTCAACTCGT 57.250 34.783 2.79 0.00 35.28 4.18
222 238 7.757097 ACTCGTATTGTTGTCATGAACTATC 57.243 36.000 0.00 0.00 0.00 2.08
223 239 7.320399 ACTCGTATTGTTGTCATGAACTATCA 58.680 34.615 0.00 0.00 40.57 2.15
225 241 7.320399 TCGTATTGTTGTCATGAACTATCAGT 58.680 34.615 0.00 0.00 39.39 3.41
269 512 2.352034 AGACCAGACGATATATAGCGCG 59.648 50.000 19.65 0.00 38.91 6.86
281 524 2.365095 ATAGCGCGTAAGTCCTGGGC 62.365 60.000 8.43 0.00 41.35 5.36
283 526 4.430765 CGCGTAAGTCCTGGGCGT 62.431 66.667 0.00 0.00 41.75 5.68
286 529 2.388232 CGTAAGTCCTGGGCGTTGC 61.388 63.158 0.00 0.00 0.00 4.17
293 536 1.602323 CCTGGGCGTTGCTTGGTTA 60.602 57.895 0.00 0.00 0.00 2.85
318 561 7.905604 TGTTTACTCATCAACTGTATTCTGG 57.094 36.000 0.00 0.00 0.00 3.86
327 570 3.560636 ACTGTATTCTGGCCACCATAC 57.439 47.619 17.64 17.64 30.82 2.39
357 600 1.895020 TAAGCCTGCGTTCGGGACAT 61.895 55.000 0.00 0.00 41.45 3.06
361 616 1.082117 CCTGCGTTCGGGACATACAC 61.082 60.000 0.00 0.00 41.45 2.90
364 619 0.928229 GCGTTCGGGACATACACATC 59.072 55.000 0.00 0.00 0.00 3.06
370 625 1.935873 CGGGACATACACATCAAGCTG 59.064 52.381 0.00 0.00 0.00 4.24
377 632 2.333291 CACATCAAGCTGTGTGCCA 58.667 52.632 12.42 0.00 44.23 4.92
378 633 0.669619 CACATCAAGCTGTGTGCCAA 59.330 50.000 12.42 0.00 44.23 4.52
496 761 3.405689 TTTTTCCTACGCTGGTGCA 57.594 47.368 0.00 0.00 39.64 4.57
511 777 2.550606 TGGTGCATTTCTTACAACGTCC 59.449 45.455 0.00 0.00 0.00 4.79
519 785 4.545823 TTCTTACAACGTCCAAAAGCAG 57.454 40.909 0.00 0.00 0.00 4.24
540 806 3.501445 AGCAGCACTGAAGACATCTTTTC 59.499 43.478 0.81 0.00 36.11 2.29
551 817 4.093998 AAGACATCTTTTCTGCATGTAGCG 59.906 41.667 5.85 0.00 38.55 4.26
567 833 6.508880 GCATGTAGCGTATCGTCAACAATTTA 60.509 38.462 0.00 0.00 0.00 1.40
572 838 4.523813 CGTATCGTCAACAATTTATGCCC 58.476 43.478 0.00 0.00 0.00 5.36
594 860 1.226746 AGCAAAAGACTGCACGGTAC 58.773 50.000 0.00 0.00 45.18 3.34
647 913 3.764237 TCCTCGCCTATTTATTGGTCC 57.236 47.619 0.00 0.00 0.00 4.46
696 963 4.954118 TGGACGCCTCCCACAGGT 62.954 66.667 0.00 0.00 45.61 4.00
697 964 2.682494 GGACGCCTCCCACAGGTA 60.682 66.667 0.00 0.00 45.61 3.08
698 965 2.577593 GACGCCTCCCACAGGTAC 59.422 66.667 0.00 0.00 45.61 3.34
724 991 6.908870 TCTCGATTTCACGATTGATTGATT 57.091 33.333 0.00 0.00 41.39 2.57
725 992 6.708676 TCTCGATTTCACGATTGATTGATTG 58.291 36.000 0.00 0.00 41.39 2.67
726 993 5.809464 TCGATTTCACGATTGATTGATTGG 58.191 37.500 0.00 0.00 37.37 3.16
727 994 5.353956 TCGATTTCACGATTGATTGATTGGT 59.646 36.000 0.00 0.00 37.37 3.67
728 995 6.536941 TCGATTTCACGATTGATTGATTGGTA 59.463 34.615 0.00 0.00 37.37 3.25
729 996 7.226523 TCGATTTCACGATTGATTGATTGGTAT 59.773 33.333 0.00 0.00 37.37 2.73
730 997 7.531871 CGATTTCACGATTGATTGATTGGTATC 59.468 37.037 0.00 0.00 35.09 2.24
767 1040 5.723492 TCATTCATCTTTACACGAGCATG 57.277 39.130 0.00 0.00 0.00 4.06
801 1074 1.376037 GGAAACTCCCCTCTGCACG 60.376 63.158 0.00 0.00 0.00 5.34
803 1076 2.731691 GAAACTCCCCTCTGCACGCA 62.732 60.000 0.00 0.00 0.00 5.24
805 1078 4.007644 CTCCCCTCTGCACGCACA 62.008 66.667 0.00 0.00 0.00 4.57
850 1123 3.501828 TGTTGATTGTTCGATCCTGGTTG 59.498 43.478 0.00 0.00 0.00 3.77
888 1161 1.872952 CAATGGCGTCAGAGAAACACA 59.127 47.619 0.00 0.00 0.00 3.72
912 1185 1.850640 GCGTCGCCGGTAATGTATG 59.149 57.895 5.75 0.00 33.68 2.39
913 1186 1.850640 CGTCGCCGGTAATGTATGC 59.149 57.895 1.90 0.00 0.00 3.14
944 1220 2.597455 CTGGTTTGGTTTGGTCCTCAT 58.403 47.619 0.00 0.00 0.00 2.90
950 1226 3.025322 TGGTTTGGTCCTCATGTGTTT 57.975 42.857 0.00 0.00 0.00 2.83
951 1227 3.370104 TGGTTTGGTCCTCATGTGTTTT 58.630 40.909 0.00 0.00 0.00 2.43
961 1237 4.280677 TCCTCATGTGTTTTGATTGGGAAC 59.719 41.667 0.00 0.00 0.00 3.62
965 1241 0.676736 TGTTTTGATTGGGAACGGGC 59.323 50.000 0.00 0.00 0.00 6.13
1130 1452 4.456253 CGTCGCTACCACGTCGCT 62.456 66.667 0.00 0.00 37.72 4.93
1159 1482 2.416680 TGCAAATGATCGATGTCCCA 57.583 45.000 0.54 0.00 0.00 4.37
1355 1692 0.896226 AAGGCCCTCTTCGACTACAC 59.104 55.000 0.00 0.00 0.00 2.90
1356 1693 1.139095 GGCCCTCTTCGACTACACG 59.861 63.158 0.00 0.00 0.00 4.49
1431 1768 1.296867 CGCGTCGTACCGTCGTAAT 60.297 57.895 0.00 0.00 40.04 1.89
1432 1769 0.043396 CGCGTCGTACCGTCGTAATA 60.043 55.000 0.00 0.00 40.04 0.98
1501 1838 3.557290 GGTGGCCGGGATAGGGAC 61.557 72.222 2.18 0.00 0.00 4.46
1644 1982 3.011635 GCCTCGCTCTTCTGGCTCA 62.012 63.158 0.00 0.00 41.92 4.26
1650 1988 1.146637 GCTCTTCTGGCTCATATGCG 58.853 55.000 0.00 0.00 0.00 4.73
1661 1999 2.130395 CTCATATGCGTCATGCTCGTT 58.870 47.619 0.00 3.68 46.63 3.85
1676 2014 3.412061 GTTGGCAACGTCACGGAA 58.588 55.556 15.49 0.00 42.51 4.30
1727 2065 3.224324 GACGGAGGCGCAGGGATA 61.224 66.667 10.83 0.00 0.00 2.59
1729 2067 3.996124 CGGAGGCGCAGGGATAGG 61.996 72.222 10.83 0.00 0.00 2.57
1730 2068 2.524394 GGAGGCGCAGGGATAGGA 60.524 66.667 10.83 0.00 0.00 2.94
1736 2074 0.316841 GCGCAGGGATAGGAGAGAAG 59.683 60.000 0.30 0.00 0.00 2.85
1738 2076 1.339610 CGCAGGGATAGGAGAGAAGTG 59.660 57.143 0.00 0.00 0.00 3.16
1741 2079 3.645687 GCAGGGATAGGAGAGAAGTGAAT 59.354 47.826 0.00 0.00 0.00 2.57
1742 2080 4.262420 GCAGGGATAGGAGAGAAGTGAATC 60.262 50.000 0.00 0.00 0.00 2.52
1743 2081 5.147032 CAGGGATAGGAGAGAAGTGAATCT 58.853 45.833 0.00 0.00 0.00 2.40
1744 2082 5.243730 CAGGGATAGGAGAGAAGTGAATCTC 59.756 48.000 0.00 0.00 45.06 2.75
1745 2083 5.103301 AGGGATAGGAGAGAAGTGAATCTCA 60.103 44.000 7.04 0.00 46.73 3.27
1746 2084 5.243730 GGGATAGGAGAGAAGTGAATCTCAG 59.756 48.000 7.04 0.00 46.73 3.35
1747 2085 5.833131 GGATAGGAGAGAAGTGAATCTCAGT 59.167 44.000 7.04 0.00 46.73 3.41
1748 2086 6.323739 GGATAGGAGAGAAGTGAATCTCAGTT 59.676 42.308 7.04 0.00 46.73 3.16
1749 2087 7.147742 GGATAGGAGAGAAGTGAATCTCAGTTT 60.148 40.741 7.04 0.00 46.73 2.66
1750 2088 6.432403 AGGAGAGAAGTGAATCTCAGTTTT 57.568 37.500 7.04 0.00 46.73 2.43
1751 2089 6.463360 AGGAGAGAAGTGAATCTCAGTTTTC 58.537 40.000 7.04 6.64 46.73 2.29
1752 2090 6.042552 AGGAGAGAAGTGAATCTCAGTTTTCA 59.957 38.462 13.95 0.00 46.73 2.69
1753 2091 6.147000 GGAGAGAAGTGAATCTCAGTTTTCAC 59.853 42.308 13.95 12.59 46.73 3.18
1770 2108 1.023502 CACAATATGCGGCATCCACA 58.976 50.000 20.34 1.59 0.00 4.17
1789 2127 8.862074 CATCCACATACACATTGTAAATTTGTG 58.138 33.333 0.00 3.26 41.37 3.33
1795 2133 9.242477 CATACACATTGTAAATTTGTGACAACA 57.758 29.630 12.90 0.24 38.71 3.33
1807 2145 3.905339 GTGACAACACAAACATGCAAC 57.095 42.857 0.00 0.00 45.32 4.17
1808 2146 2.278615 GTGACAACACAAACATGCAACG 59.721 45.455 0.00 0.00 45.32 4.10
1809 2147 1.255084 GACAACACAAACATGCAACGC 59.745 47.619 0.00 0.00 0.00 4.84
1810 2148 1.275505 CAACACAAACATGCAACGCA 58.724 45.000 0.00 0.00 44.86 5.24
1811 2149 1.657594 CAACACAAACATGCAACGCAA 59.342 42.857 0.00 0.00 43.62 4.85
1812 2150 2.222007 ACACAAACATGCAACGCAAT 57.778 40.000 0.00 0.00 43.62 3.56
1813 2151 3.361794 ACACAAACATGCAACGCAATA 57.638 38.095 0.00 0.00 43.62 1.90
1814 2152 3.049206 ACACAAACATGCAACGCAATAC 58.951 40.909 0.00 0.00 43.62 1.89
1839 2177 4.499183 GTCATCTTCATGTCGAGGACTTT 58.501 43.478 17.87 0.00 37.80 2.66
1843 2181 5.462530 TCTTCATGTCGAGGACTTTTGTA 57.537 39.130 0.00 0.00 33.15 2.41
1848 2186 3.784338 TGTCGAGGACTTTTGTACGTTT 58.216 40.909 0.00 0.00 38.61 3.60
1849 2187 4.930963 TGTCGAGGACTTTTGTACGTTTA 58.069 39.130 0.00 0.00 38.61 2.01
1878 2217 1.124658 CAATTGCACGGTTCGCATTTG 59.875 47.619 11.25 11.25 41.51 2.32
1885 2224 0.661020 CGGTTCGCATTTGGGGTATC 59.339 55.000 0.00 0.00 0.00 2.24
1889 2228 2.614057 GTTCGCATTTGGGGTATCAGAG 59.386 50.000 0.00 0.00 0.00 3.35
1890 2229 0.947244 CGCATTTGGGGTATCAGAGC 59.053 55.000 0.00 0.00 0.00 4.09
1891 2230 1.746861 CGCATTTGGGGTATCAGAGCA 60.747 52.381 0.00 0.00 0.00 4.26
1892 2231 2.590821 GCATTTGGGGTATCAGAGCAT 58.409 47.619 0.00 0.00 0.00 3.79
1893 2232 2.555757 GCATTTGGGGTATCAGAGCATC 59.444 50.000 0.00 0.00 0.00 3.91
1904 2243 2.107953 GAGCATCTCCACTCGCCC 59.892 66.667 0.00 0.00 0.00 6.13
1905 2244 3.453070 GAGCATCTCCACTCGCCCC 62.453 68.421 0.00 0.00 0.00 5.80
1906 2245 4.554036 GCATCTCCACTCGCCCCC 62.554 72.222 0.00 0.00 0.00 5.40
1907 2246 2.765807 CATCTCCACTCGCCCCCT 60.766 66.667 0.00 0.00 0.00 4.79
1908 2247 2.041265 ATCTCCACTCGCCCCCTT 59.959 61.111 0.00 0.00 0.00 3.95
1934 2273 5.490159 CCTGTTGGGGAACGTAGTAATTTA 58.510 41.667 0.00 0.00 45.00 1.40
1965 2306 2.168326 ACGCACACACAAGATCATGA 57.832 45.000 4.68 0.00 0.00 3.07
2019 2361 1.468520 CGTACCCTCGTAGACCGAAAA 59.531 52.381 0.00 0.00 46.75 2.29
2020 2362 2.095263 CGTACCCTCGTAGACCGAAAAA 60.095 50.000 0.00 0.00 46.75 1.94
2021 2363 3.428045 CGTACCCTCGTAGACCGAAAAAT 60.428 47.826 0.00 0.00 46.75 1.82
2131 2473 0.099259 ACACGTTCAACTCGACGACA 59.901 50.000 0.00 0.00 41.53 4.35
2141 2483 0.663688 CTCGACGACATCCCTCGAAT 59.336 55.000 0.00 0.00 36.08 3.34
2270 2613 2.174854 TCGAGGTGGACTATGATGGAGA 59.825 50.000 0.00 0.00 0.00 3.71
2300 2644 3.119531 CGCACATGGCTAAAAGATCCAAA 60.120 43.478 0.00 0.00 41.67 3.28
2304 2648 6.690530 CACATGGCTAAAAGATCCAAAAGAA 58.309 36.000 0.00 0.00 33.04 2.52
2358 2702 4.106825 TCCCCGTATATAAAGGAGTGGAGA 59.893 45.833 7.00 0.00 0.00 3.71
2372 2716 2.041265 GAGAAGGAGGAGGGGGCA 59.959 66.667 0.00 0.00 0.00 5.36
2464 2814 1.216930 AGTAGGAGAGGAGAGGGAAGC 59.783 57.143 0.00 0.00 0.00 3.86
2467 2817 1.048160 GGAGAGGAGAGGGAAGCAGG 61.048 65.000 0.00 0.00 0.00 4.85
2472 2822 0.618968 GGAGAGGGAAGCAGGGAGAA 60.619 60.000 0.00 0.00 0.00 2.87
2627 2993 1.133356 ACCCCCAGTACTCCGGTATAC 60.133 57.143 0.00 5.51 0.00 1.47
2677 3043 2.858344 GTCCGAACATAGTCGTCCAATG 59.142 50.000 0.00 0.00 39.43 2.82
2696 3062 6.038936 TCCAATGTATCGATCTTTACGTCTCA 59.961 38.462 0.00 0.00 0.00 3.27
2698 3064 7.222031 CCAATGTATCGATCTTTACGTCTCAAA 59.778 37.037 0.00 0.00 0.00 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 5.120208 CCTCTAAACAACTGAATACACCACG 59.880 44.000 0.00 0.00 0.00 4.94
12 13 6.698380 TCCTCCTCTAAACAACTGAATACAC 58.302 40.000 0.00 0.00 0.00 2.90
20 21 3.307762 GCACCATCCTCCTCTAAACAACT 60.308 47.826 0.00 0.00 0.00 3.16
33 34 1.298993 CTCACAGCAGCACCATCCT 59.701 57.895 0.00 0.00 0.00 3.24
55 56 0.750249 TTCTTCGTCACAGCCACTCA 59.250 50.000 0.00 0.00 0.00 3.41
91 107 6.215121 TGGTTCAAAGCAAATAACACATCTG 58.785 36.000 0.00 0.00 32.80 2.90
121 137 2.154462 CACTACTGGTGCCCAAAGAAG 58.846 52.381 9.05 2.35 39.22 2.85
133 149 3.685139 AGTCCATGTCAACACTACTGG 57.315 47.619 0.00 0.00 0.00 4.00
135 151 5.643777 GCAAATAGTCCATGTCAACACTACT 59.356 40.000 0.00 0.00 0.00 2.57
145 161 4.655963 AGTTGACAGCAAATAGTCCATGT 58.344 39.130 0.00 0.00 35.42 3.21
146 162 4.201753 CGAGTTGACAGCAAATAGTCCATG 60.202 45.833 0.00 0.00 35.42 3.66
159 175 5.405269 TCATGACAATAACACGAGTTGACAG 59.595 40.000 8.59 0.00 38.69 3.51
182 198 7.803189 ACAATACGAGTTGACATCAAATTGTTC 59.197 33.333 17.45 2.23 43.54 3.18
203 219 9.500785 TCAAACTGATAGTTCATGACAACAATA 57.499 29.630 0.00 0.00 37.47 1.90
222 238 7.202016 TGTGATTTAAGGCTAGTTCAAACTG 57.798 36.000 5.66 0.00 40.07 3.16
223 239 9.167311 CTATGTGATTTAAGGCTAGTTCAAACT 57.833 33.333 0.46 0.46 42.91 2.66
225 241 9.162764 GTCTATGTGATTTAAGGCTAGTTCAAA 57.837 33.333 0.00 0.00 0.00 2.69
269 512 0.605589 AAGCAACGCCCAGGACTTAC 60.606 55.000 0.00 0.00 0.00 2.34
281 524 5.351233 TGAGTAAACATAACCAAGCAACG 57.649 39.130 0.00 0.00 0.00 4.10
283 526 7.230510 AGTTGATGAGTAAACATAACCAAGCAA 59.769 33.333 0.00 0.00 0.00 3.91
286 529 8.099364 ACAGTTGATGAGTAAACATAACCAAG 57.901 34.615 0.00 0.00 0.00 3.61
293 536 7.066284 GCCAGAATACAGTTGATGAGTAAACAT 59.934 37.037 0.00 0.00 0.00 2.71
318 561 2.128771 AGATGTGGTTGTATGGTGGC 57.871 50.000 0.00 0.00 0.00 5.01
327 570 1.131126 CGCAGGCTTAAGATGTGGTTG 59.869 52.381 6.67 0.00 0.00 3.77
361 616 0.669619 TGTTGGCACACAGCTTGATG 59.330 50.000 0.00 0.00 44.79 3.07
364 619 0.029834 GACTGTTGGCACACAGCTTG 59.970 55.000 21.64 7.21 44.79 4.01
370 625 0.027586 GTGTTCGACTGTTGGCACAC 59.972 55.000 12.67 12.67 39.29 3.82
377 632 2.132762 GACGGATTGTGTTCGACTGTT 58.867 47.619 0.00 0.00 0.00 3.16
378 633 1.779569 GACGGATTGTGTTCGACTGT 58.220 50.000 0.00 0.00 0.00 3.55
381 636 1.909532 CTACGACGGATTGTGTTCGAC 59.090 52.381 0.00 0.00 0.00 4.20
384 639 3.213249 AGACTACGACGGATTGTGTTC 57.787 47.619 0.00 0.00 0.00 3.18
436 691 2.350134 GGACTTGAACCCGGGTCC 59.650 66.667 30.40 17.39 40.86 4.46
484 749 3.000041 TGTAAGAAATGCACCAGCGTAG 59.000 45.455 0.00 0.00 46.23 3.51
496 761 5.508200 TGCTTTTGGACGTTGTAAGAAAT 57.492 34.783 0.00 0.00 0.00 2.17
511 777 1.335810 TCTTCAGTGCTGCTGCTTTTG 59.664 47.619 17.00 11.63 44.66 2.44
519 785 3.501445 AGAAAAGATGTCTTCAGTGCTGC 59.499 43.478 0.00 0.00 34.61 5.25
535 801 3.551890 ACGATACGCTACATGCAGAAAAG 59.448 43.478 0.00 0.00 43.06 2.27
540 806 2.119671 TGACGATACGCTACATGCAG 57.880 50.000 0.00 0.00 43.06 4.41
551 817 4.271533 TCGGGCATAAATTGTTGACGATAC 59.728 41.667 0.00 0.00 0.00 2.24
572 838 0.384725 CCGTGCAGTCTTTTGCTTCG 60.385 55.000 0.00 4.80 44.38 3.79
578 844 1.554042 CGCGTACCGTGCAGTCTTTT 61.554 55.000 0.00 0.00 0.00 2.27
579 845 2.019951 CGCGTACCGTGCAGTCTTT 61.020 57.895 0.00 0.00 0.00 2.52
663 930 1.464997 GTCCAACTGAGCGGTTGAATC 59.535 52.381 20.63 8.81 46.55 2.52
696 963 8.349983 TCAATCAATCGTGAAATCGAGATAGTA 58.650 33.333 0.00 0.00 43.00 1.82
697 964 7.203218 TCAATCAATCGTGAAATCGAGATAGT 58.797 34.615 0.00 0.00 43.00 2.12
698 965 7.629027 TCAATCAATCGTGAAATCGAGATAG 57.371 36.000 0.00 0.00 43.00 2.08
724 991 2.481441 AGGGAAGAGCATGTGATACCA 58.519 47.619 0.00 0.00 0.00 3.25
725 992 3.118261 TGAAGGGAAGAGCATGTGATACC 60.118 47.826 0.00 0.00 0.00 2.73
726 993 4.142609 TGAAGGGAAGAGCATGTGATAC 57.857 45.455 0.00 0.00 0.00 2.24
727 994 5.104402 TGAATGAAGGGAAGAGCATGTGATA 60.104 40.000 0.00 0.00 0.00 2.15
728 995 3.947612 ATGAAGGGAAGAGCATGTGAT 57.052 42.857 0.00 0.00 0.00 3.06
729 996 3.009363 TGAATGAAGGGAAGAGCATGTGA 59.991 43.478 0.00 0.00 0.00 3.58
730 997 3.349927 TGAATGAAGGGAAGAGCATGTG 58.650 45.455 0.00 0.00 0.00 3.21
784 1057 2.035442 GCGTGCAGAGGGGAGTTTC 61.035 63.158 0.00 0.00 0.00 2.78
794 1067 0.536724 AGGTATCATGTGCGTGCAGA 59.463 50.000 0.00 0.00 0.00 4.26
801 1074 3.365832 CATTTTCGCAGGTATCATGTGC 58.634 45.455 0.00 0.00 0.00 4.57
803 1076 2.032054 CGCATTTTCGCAGGTATCATGT 59.968 45.455 0.00 0.00 0.00 3.21
826 1099 3.502211 ACCAGGATCGAACAATCAACAAC 59.498 43.478 0.00 0.00 0.00 3.32
850 1123 1.218854 GCCATGCATTTGGGTCACC 59.781 57.895 8.41 0.00 37.24 4.02
913 1186 0.745845 CCAAACCAGGCTGAGATCGG 60.746 60.000 17.94 5.82 0.00 4.18
944 1220 1.683917 CCCGTTCCCAATCAAAACACA 59.316 47.619 0.00 0.00 0.00 3.72
950 1226 2.360600 CCGCCCGTTCCCAATCAA 60.361 61.111 0.00 0.00 0.00 2.57
961 1237 1.863662 ATACACTATCTCGCCGCCCG 61.864 60.000 0.00 0.00 38.61 6.13
965 1241 5.700846 ACTAATCAATACACTATCTCGCCG 58.299 41.667 0.00 0.00 0.00 6.46
1093 1405 3.126831 CGGAGCCAGCTAACAGAATTAG 58.873 50.000 0.00 0.00 0.00 1.73
1099 1411 1.517257 CGACGGAGCCAGCTAACAG 60.517 63.158 0.00 0.00 0.00 3.16
1101 1413 2.001361 TAGCGACGGAGCCAGCTAAC 62.001 60.000 0.00 0.00 38.99 2.34
1130 1452 2.602694 CGATCATTTGCATGCACGCATA 60.603 45.455 22.58 3.75 42.62 3.14
1355 1692 2.434884 AAGACGTGGAGCATGGCG 60.435 61.111 0.00 0.00 32.87 5.69
1356 1693 0.674895 AAGAAGACGTGGAGCATGGC 60.675 55.000 0.00 0.00 0.00 4.40
1394 1731 1.017387 GGTGCTTGGTGGATTCGATC 58.983 55.000 0.00 0.00 0.00 3.69
1398 1735 2.877691 GCGGTGCTTGGTGGATTC 59.122 61.111 0.00 0.00 0.00 2.52
1480 1817 4.235762 CTATCCCGGCCACCGTGG 62.236 72.222 13.71 13.71 46.80 4.94
1481 1818 4.235762 CCTATCCCGGCCACCGTG 62.236 72.222 2.24 0.00 46.80 4.94
1557 1894 4.078516 GCAGGCGTACCCGAGGTT 62.079 66.667 0.72 0.00 37.09 3.50
1644 1982 1.220529 CCAACGAGCATGACGCATAT 58.779 50.000 11.51 0.00 46.13 1.78
1650 1988 4.847255 GTTGCCAACGAGCATGAC 57.153 55.556 0.00 0.00 43.64 3.06
1661 1999 1.593209 GTCTTCCGTGACGTTGCCA 60.593 57.895 3.64 0.00 0.00 4.92
1672 2010 0.522915 GCCGTCGAAGTAGTCTTCCG 60.523 60.000 0.00 2.28 45.02 4.30
1676 2014 2.404995 CCGGCCGTCGAAGTAGTCT 61.405 63.158 26.12 0.00 42.43 3.24
1721 2059 5.103301 TGAGATTCACTTCTCTCCTATCCCT 60.103 44.000 3.41 0.00 42.22 4.20
1727 2065 6.042552 TGAAAACTGAGATTCACTTCTCTCCT 59.957 38.462 3.41 0.00 42.22 3.69
1738 2076 5.967674 CCGCATATTGTGAAAACTGAGATTC 59.032 40.000 0.00 0.00 0.00 2.52
1741 2079 3.126858 GCCGCATATTGTGAAAACTGAGA 59.873 43.478 0.00 0.00 0.00 3.27
1742 2080 3.119884 TGCCGCATATTGTGAAAACTGAG 60.120 43.478 0.00 0.00 0.00 3.35
1743 2081 2.816672 TGCCGCATATTGTGAAAACTGA 59.183 40.909 0.00 0.00 0.00 3.41
1744 2082 3.214697 TGCCGCATATTGTGAAAACTG 57.785 42.857 0.00 0.00 0.00 3.16
1745 2083 3.181487 GGATGCCGCATATTGTGAAAACT 60.181 43.478 5.67 0.00 0.00 2.66
1746 2084 3.115554 GGATGCCGCATATTGTGAAAAC 58.884 45.455 5.67 0.00 0.00 2.43
1747 2085 2.757314 TGGATGCCGCATATTGTGAAAA 59.243 40.909 5.67 0.00 0.00 2.29
1748 2086 2.098934 GTGGATGCCGCATATTGTGAAA 59.901 45.455 5.67 0.00 33.65 2.69
1749 2087 1.675483 GTGGATGCCGCATATTGTGAA 59.325 47.619 5.67 0.00 33.65 3.18
1750 2088 1.308047 GTGGATGCCGCATATTGTGA 58.692 50.000 5.67 0.00 33.65 3.58
1751 2089 1.023502 TGTGGATGCCGCATATTGTG 58.976 50.000 5.67 0.00 39.28 3.33
1752 2090 3.493028 TGTGGATGCCGCATATTGT 57.507 47.368 5.67 0.00 39.28 2.71
1770 2108 9.243637 GTGTTGTCACAAATTTACAATGTGTAT 57.756 29.630 7.96 0.00 43.72 2.29
1789 2127 1.255084 GCGTTGCATGTTTGTGTTGTC 59.745 47.619 0.00 0.00 0.00 3.18
1795 2133 2.315011 CGTATTGCGTTGCATGTTTGT 58.685 42.857 0.00 0.00 38.76 2.83
1799 2137 4.763593 GCGTATTGCGTTGCATGT 57.236 50.000 0.00 0.00 43.66 3.21
1808 2146 2.285220 ACATGAAGATGACGCGTATTGC 59.715 45.455 13.97 0.00 35.18 3.56
1809 2147 3.361051 CGACATGAAGATGACGCGTATTG 60.361 47.826 13.97 3.76 40.05 1.90
1810 2148 2.789339 CGACATGAAGATGACGCGTATT 59.211 45.455 13.97 4.77 40.05 1.89
1811 2149 2.032924 TCGACATGAAGATGACGCGTAT 59.967 45.455 13.97 6.30 44.24 3.06
1812 2150 1.399089 TCGACATGAAGATGACGCGTA 59.601 47.619 13.97 0.41 44.24 4.42
1813 2151 0.170339 TCGACATGAAGATGACGCGT 59.830 50.000 13.85 13.85 44.24 6.01
1814 2152 0.842613 CTCGACATGAAGATGACGCG 59.157 55.000 3.53 3.53 44.24 6.01
1815 2153 1.202302 TCCTCGACATGAAGATGACGC 60.202 52.381 0.00 0.00 44.24 5.19
1816 2154 2.098280 AGTCCTCGACATGAAGATGACG 59.902 50.000 17.14 0.00 45.41 4.35
1817 2155 3.791973 AGTCCTCGACATGAAGATGAC 57.208 47.619 16.21 16.21 34.60 3.06
1818 2156 4.808414 AAAGTCCTCGACATGAAGATGA 57.192 40.909 0.00 0.00 34.60 2.92
1819 2157 4.692625 ACAAAAGTCCTCGACATGAAGATG 59.307 41.667 0.00 0.00 34.60 2.90
1820 2158 4.899502 ACAAAAGTCCTCGACATGAAGAT 58.100 39.130 0.00 0.00 34.60 2.40
1824 2162 3.005050 ACGTACAAAAGTCCTCGACATGA 59.995 43.478 0.00 0.00 34.60 3.07
1839 2177 7.559835 CAATTGATGCACAATAAACGTACAA 57.440 32.000 12.78 0.00 46.90 2.41
1865 2204 0.034863 ATACCCCAAATGCGAACCGT 60.035 50.000 0.00 0.00 0.00 4.83
1866 2205 0.661020 GATACCCCAAATGCGAACCG 59.339 55.000 0.00 0.00 0.00 4.44
1871 2210 0.947244 GCTCTGATACCCCAAATGCG 59.053 55.000 0.00 0.00 0.00 4.73
1878 2217 1.346068 GTGGAGATGCTCTGATACCCC 59.654 57.143 0.00 0.00 0.00 4.95
1885 2224 1.227205 GGCGAGTGGAGATGCTCTG 60.227 63.158 0.00 0.00 0.00 3.35
1889 2228 4.554036 GGGGGCGAGTGGAGATGC 62.554 72.222 0.00 0.00 0.00 3.91
1890 2229 2.317149 GAAGGGGGCGAGTGGAGATG 62.317 65.000 0.00 0.00 0.00 2.90
1891 2230 2.041265 AAGGGGGCGAGTGGAGAT 59.959 61.111 0.00 0.00 0.00 2.75
1892 2231 2.683933 GAAGGGGGCGAGTGGAGA 60.684 66.667 0.00 0.00 0.00 3.71
1893 2232 3.787001 GGAAGGGGGCGAGTGGAG 61.787 72.222 0.00 0.00 0.00 3.86
1899 2238 4.995058 AACAGGGGAAGGGGGCGA 62.995 66.667 0.00 0.00 0.00 5.54
1900 2239 4.740822 CAACAGGGGAAGGGGGCG 62.741 72.222 0.00 0.00 0.00 6.13
1901 2240 4.382541 CCAACAGGGGAAGGGGGC 62.383 72.222 0.00 0.00 0.00 5.80
1911 2250 3.622166 ATTACTACGTTCCCCAACAGG 57.378 47.619 0.00 0.00 32.14 4.00
1965 2306 2.549563 CCCTCTCGTTGCTATGCATCAT 60.550 50.000 0.19 0.00 38.76 2.45
2019 2361 1.196808 CGTTGTGCTAACGCTTCCATT 59.803 47.619 12.46 0.00 36.82 3.16
2020 2362 0.796312 CGTTGTGCTAACGCTTCCAT 59.204 50.000 12.46 0.00 36.82 3.41
2021 2363 2.230892 CGTTGTGCTAACGCTTCCA 58.769 52.632 12.46 0.00 36.82 3.53
2141 2483 1.899437 AAAGCTCGGCTGGATCGGAA 61.899 55.000 0.00 0.00 39.62 4.30
2193 2535 3.921677 ACGGTAGAACATCAACATCGTT 58.078 40.909 0.00 0.00 0.00 3.85
2300 2644 6.209391 CCCTTGGAGACATAACAATTGTTCTT 59.791 38.462 26.46 13.22 42.32 2.52
2304 2648 4.202673 ACCCCTTGGAGACATAACAATTGT 60.203 41.667 4.92 4.92 42.32 2.71
2431 2775 3.519510 CTCTCCTACTCCCACATGGAAAA 59.480 47.826 0.00 0.00 44.57 2.29
2464 2814 2.291217 CCTTTCCTTTCCCTTCTCCCTG 60.291 54.545 0.00 0.00 0.00 4.45
2467 2817 1.617263 GCCCTTTCCTTTCCCTTCTCC 60.617 57.143 0.00 0.00 0.00 3.71
2472 2822 2.558147 GGGGCCCTTTCCTTTCCCT 61.558 63.158 24.38 0.00 37.16 4.20
2613 2978 3.027419 GGGCGTATACCGGAGTACT 57.973 57.895 9.46 0.00 36.94 2.73
2627 2993 1.302192 TTTCAGGGAGTTTCGGGCG 60.302 57.895 0.00 0.00 0.00 6.13
2677 3043 7.681125 ATGTTTGAGACGTAAAGATCGATAC 57.319 36.000 0.00 0.00 0.00 2.24
2696 3062 2.814336 GACGAGGAGCCTTGAAATGTTT 59.186 45.455 10.74 0.00 0.00 2.83
2698 3064 1.347707 TGACGAGGAGCCTTGAAATGT 59.652 47.619 10.74 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.