Multiple sequence alignment - TraesCS6B01G410000

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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 TraesCS6B01G410000 chr6B 100.000 1778 0 0 512 2289 684386072 684384295 0.000000e+00 3284.0
1 TraesCS6B01G410000 chr6B 100.000 192 0 0 1 192 684386583 684386392 2.800000e-94 355.0
2 TraesCS6B01G410000 chr6B 84.967 153 20 3 1903 2054 713310386 713310536 3.940000e-33 152.0
3 TraesCS6B01G410000 chr6B 84.314 153 21 3 1903 2054 713517667 713517817 1.830000e-31 147.0
4 TraesCS6B01G410000 chr6B 84.314 153 21 3 1903 2054 713863947 713864097 1.830000e-31 147.0
5 TraesCS6B01G410000 chr6B 86.842 76 5 5 913 984 684385716 684385642 1.880000e-11 80.5
6 TraesCS6B01G410000 chr6D 85.409 1405 109 40 934 2289 450641596 450640239 0.000000e+00 1371.0
7 TraesCS6B01G410000 chr6D 83.636 440 36 21 512 937 450641968 450641551 4.610000e-102 381.0
8 TraesCS6B01G410000 chr6D 93.617 141 8 1 1 140 76080162 76080302 2.300000e-50 209.0
9 TraesCS6B01G410000 chr6D 96.226 106 4 0 41 146 450642168 450642063 8.410000e-40 174.0
10 TraesCS6B01G410000 chr6D 97.778 45 1 0 512 556 76080402 76080446 6.780000e-11 78.7
11 TraesCS6B01G410000 chr6A 87.322 1191 72 36 934 2083 596162931 596161779 0.000000e+00 1290.0
12 TraesCS6B01G410000 chr6A 83.420 386 29 15 512 892 596163279 596162924 2.190000e-85 326.0
13 TraesCS6B01G410000 chr6A 93.793 145 9 0 1 145 596163522 596163378 3.830000e-53 219.0
14 TraesCS6B01G410000 chr6A 87.879 132 11 5 1916 2044 81256999 81256870 1.420000e-32 150.0
15 TraesCS6B01G410000 chr7D 94.149 188 11 0 1102 1289 84178254 84178441 1.030000e-73 287.0
16 TraesCS6B01G410000 chr7D 93.939 99 5 1 1931 2028 549548400 549548498 5.090000e-32 148.0
17 TraesCS6B01G410000 chr7B 94.149 188 11 0 1102 1289 33805426 33805613 1.030000e-73 287.0
18 TraesCS6B01G410000 chr7A 93.085 188 13 0 1102 1289 85588719 85588906 2.240000e-70 276.0
19 TraesCS6B01G410000 chr3D 93.056 144 9 1 1 143 382820292 382820149 2.300000e-50 209.0
20 TraesCS6B01G410000 chr3D 93.056 144 9 1 1 143 554658977 554658834 2.300000e-50 209.0
21 TraesCS6B01G410000 chr3D 88.060 67 6 2 512 577 382820052 382819987 6.780000e-11 78.7
22 TraesCS6B01G410000 chr3D 88.060 67 6 2 512 577 554658737 554658672 6.780000e-11 78.7
23 TraesCS6B01G410000 chr1D 93.617 141 8 1 1 140 207148462 207148602 2.300000e-50 209.0
24 TraesCS6B01G410000 chr1D 93.578 109 5 2 1671 1778 436972427 436972320 6.540000e-36 161.0
25 TraesCS6B01G410000 chr1D 87.963 108 11 2 1921 2027 436971957 436971851 2.390000e-25 126.0
26 TraesCS6B01G410000 chr1D 97.778 45 1 0 512 556 207148702 207148746 6.780000e-11 78.7
27 TraesCS6B01G410000 chr5B 89.844 128 7 4 1652 1778 13842016 13842138 2.350000e-35 159.0
28 TraesCS6B01G410000 chr5B 88.976 127 8 5 1653 1778 36190840 36190719 3.940000e-33 152.0
29 TraesCS6B01G410000 chr5B 88.189 127 8 6 1653 1778 13830494 13830614 6.590000e-31 145.0
30 TraesCS6B01G410000 chr5A 89.844 128 7 4 1652 1778 12541416 12541538 2.350000e-35 159.0
31 TraesCS6B01G410000 chr1B 93.396 106 5 2 1674 1778 503627531 503627635 3.040000e-34 156.0
32 TraesCS6B01G410000 chr5D 89.516 124 7 5 1656 1778 17855176 17855058 3.940000e-33 152.0
33 TraesCS6B01G410000 chr1A 91.753 97 7 1 1932 2027 533779290 533779194 1.430000e-27 134.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6B01G410000 chr6B 684384295 684386583 2288 True 1239.833333 3284 95.614000 1 2289 3 chr6B.!!$R1 2288
1 TraesCS6B01G410000 chr6D 450640239 450642168 1929 True 642.000000 1371 88.423667 41 2289 3 chr6D.!!$R1 2248
2 TraesCS6B01G410000 chr6A 596161779 596163522 1743 True 611.666667 1290 88.178333 1 2083 3 chr6A.!!$R2 2082

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
769 779 0.744414 CCTAACAGGCCACATCCACG 60.744 60.0 5.01 0.0 0.0 4.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2200 2275 0.108329 GGATTTCCAGCGAAGACGGA 60.108 55.0 0.0 0.0 36.6 4.69 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
34 35 3.349006 GTGCTGTGGGTGAGCGTG 61.349 66.667 0.00 0.00 39.47 5.34
35 36 4.624364 TGCTGTGGGTGAGCGTGG 62.624 66.667 0.00 0.00 39.47 4.94
129 130 4.637489 CGGAGATCCTCGCCTGCG 62.637 72.222 4.92 4.92 37.84 5.18
130 131 4.292178 GGAGATCCTCGCCTGCGG 62.292 72.222 12.06 2.50 40.25 5.69
131 132 3.219928 GAGATCCTCGCCTGCGGA 61.220 66.667 12.06 2.24 40.25 5.54
132 133 3.206211 GAGATCCTCGCCTGCGGAG 62.206 68.421 12.06 0.00 40.25 4.63
133 134 3.219928 GATCCTCGCCTGCGGAGA 61.220 66.667 5.10 9.08 40.25 3.71
134 135 2.759973 ATCCTCGCCTGCGGAGAA 60.760 61.111 5.10 0.00 40.25 2.87
135 136 2.691674 GATCCTCGCCTGCGGAGAAG 62.692 65.000 5.10 0.00 40.25 2.85
136 137 3.452786 CCTCGCCTGCGGAGAAGA 61.453 66.667 5.10 3.17 40.25 2.87
137 138 2.573869 CTCGCCTGCGGAGAAGAA 59.426 61.111 5.10 0.00 40.25 2.52
138 139 1.518133 CTCGCCTGCGGAGAAGAAG 60.518 63.158 5.10 0.00 40.25 2.85
139 140 1.938657 CTCGCCTGCGGAGAAGAAGA 61.939 60.000 5.10 0.00 40.25 2.87
140 141 1.079819 CGCCTGCGGAGAAGAAGAA 60.080 57.895 5.10 0.00 35.56 2.52
146 147 3.306364 CCTGCGGAGAAGAAGAAGAAGAA 60.306 47.826 5.10 0.00 0.00 2.52
147 148 3.654414 TGCGGAGAAGAAGAAGAAGAAC 58.346 45.455 0.00 0.00 0.00 3.01
184 185 4.021925 GGGTCAGCCTCACCGCTT 62.022 66.667 0.00 0.00 36.82 4.68
185 186 2.743928 GGTCAGCCTCACCGCTTG 60.744 66.667 0.00 0.00 36.82 4.01
604 605 2.841988 GCATCTCGCCTCCCCTCT 60.842 66.667 0.00 0.00 32.94 3.69
606 607 1.152567 CATCTCGCCTCCCCTCTCT 60.153 63.158 0.00 0.00 0.00 3.10
608 609 1.360393 ATCTCGCCTCCCCTCTCTCT 61.360 60.000 0.00 0.00 0.00 3.10
756 766 1.279846 CTCTTTTACGGGCCCCTAACA 59.720 52.381 18.66 7.73 0.00 2.41
767 777 1.570857 CCCCTAACAGGCCACATCCA 61.571 60.000 5.01 0.00 32.73 3.41
769 779 0.744414 CCTAACAGGCCACATCCACG 60.744 60.000 5.01 0.00 0.00 4.94
770 780 0.744414 CTAACAGGCCACATCCACGG 60.744 60.000 5.01 0.00 0.00 4.94
812 832 2.828549 GCCCACGGCCCACATAAG 60.829 66.667 0.00 0.00 44.06 1.73
813 833 2.994699 CCCACGGCCCACATAAGA 59.005 61.111 0.00 0.00 0.00 2.10
814 834 1.301623 CCCACGGCCCACATAAGAA 59.698 57.895 0.00 0.00 0.00 2.52
815 835 1.029947 CCCACGGCCCACATAAGAAC 61.030 60.000 0.00 0.00 0.00 3.01
816 836 1.366111 CCACGGCCCACATAAGAACG 61.366 60.000 0.00 0.00 0.00 3.95
870 890 3.722147 CCGTCTAGGGTTGATTCATCTG 58.278 50.000 0.00 0.00 35.97 2.90
916 939 4.856607 GAGCGCTCCCCGTTCTCG 62.857 72.222 27.22 0.00 42.89 4.04
955 978 4.070552 GCTCGAGTGCTCCCCGTT 62.071 66.667 15.13 0.00 0.00 4.44
956 979 2.182030 CTCGAGTGCTCCCCGTTC 59.818 66.667 3.62 0.00 0.00 3.95
957 980 2.282958 TCGAGTGCTCCCCGTTCT 60.283 61.111 0.00 0.00 0.00 3.01
958 981 2.182030 CGAGTGCTCCCCGTTCTC 59.818 66.667 0.00 0.00 0.00 2.87
959 982 2.182030 GAGTGCTCCCCGTTCTCG 59.818 66.667 0.00 0.00 0.00 4.04
960 983 2.600769 AGTGCTCCCCGTTCTCGT 60.601 61.111 0.00 0.00 35.01 4.18
961 984 2.126031 GTGCTCCCCGTTCTCGTC 60.126 66.667 0.00 0.00 35.01 4.20
962 985 3.744719 TGCTCCCCGTTCTCGTCG 61.745 66.667 0.00 0.00 35.01 5.12
964 987 4.493747 CTCCCCGTTCTCGTCGCC 62.494 72.222 0.00 0.00 35.01 5.54
967 990 4.409218 CCCGTTCTCGTCGCCGAA 62.409 66.667 0.00 0.00 43.69 4.30
968 991 2.874780 CCGTTCTCGTCGCCGAAG 60.875 66.667 0.00 0.00 43.69 3.79
969 992 3.533691 CGTTCTCGTCGCCGAAGC 61.534 66.667 0.00 0.00 43.69 3.86
1019 1042 1.414181 CATGGGTAACGATCTGCTCCT 59.586 52.381 0.00 0.00 29.61 3.69
1022 1045 0.389757 GGTAACGATCTGCTCCTCCC 59.610 60.000 0.00 0.00 0.00 4.30
1024 1047 0.759436 TAACGATCTGCTCCTCCCCC 60.759 60.000 0.00 0.00 0.00 5.40
1027 1050 1.235696 GATCTGCTCCTCCCCCTCT 59.764 63.158 0.00 0.00 0.00 3.69
1028 1051 0.399806 GATCTGCTCCTCCCCCTCTT 60.400 60.000 0.00 0.00 0.00 2.85
1029 1052 0.045469 ATCTGCTCCTCCCCCTCTTT 59.955 55.000 0.00 0.00 0.00 2.52
1032 1055 1.307430 GCTCCTCCCCCTCTTTCCT 60.307 63.158 0.00 0.00 0.00 3.36
1049 1072 5.251005 TCTTTCCTCGCTAGATCCCTATCTA 59.749 44.000 0.00 0.00 42.61 1.98
1055 1078 4.409574 TCGCTAGATCCCTATCTACCCTAG 59.590 50.000 0.00 0.00 42.61 3.02
1223 1250 1.155889 CAAGCGCATCCAGTACAACA 58.844 50.000 11.47 0.00 0.00 3.33
1225 1252 0.391661 AGCGCATCCAGTACAACAGG 60.392 55.000 11.47 0.00 0.00 4.00
1289 1316 2.448453 CCAACTCCTCCGAGAAGTAGT 58.552 52.381 0.00 0.00 38.52 2.73
1290 1317 3.618351 CCAACTCCTCCGAGAAGTAGTA 58.382 50.000 0.00 0.00 38.52 1.82
1291 1318 3.628487 CCAACTCCTCCGAGAAGTAGTAG 59.372 52.174 0.00 0.00 38.52 2.57
1296 1323 5.131475 ACTCCTCCGAGAAGTAGTAGATCTT 59.869 44.000 0.00 0.00 38.52 2.40
1426 1483 5.316167 TCTCACTGCATTGTCCAGTTAATT 58.684 37.500 3.77 0.00 41.34 1.40
1427 1484 5.769662 TCTCACTGCATTGTCCAGTTAATTT 59.230 36.000 3.77 0.00 41.34 1.82
1493 1553 6.920210 GGCAATCTGCTTCTGTTATTTTATCC 59.080 38.462 0.00 0.00 44.28 2.59
1568 1636 3.261580 TGAACGATCCAGCATTAGTGTG 58.738 45.455 0.00 0.00 0.00 3.82
1573 1641 0.692476 TCCAGCATTAGTGTGCCAGT 59.308 50.000 0.00 0.00 46.19 4.00
1575 1643 1.339438 CCAGCATTAGTGTGCCAGTCT 60.339 52.381 0.00 0.00 46.19 3.24
1582 1650 4.893424 TTAGTGTGCCAGTCTGTTTTTC 57.107 40.909 0.00 0.00 0.00 2.29
1584 1652 4.150897 AGTGTGCCAGTCTGTTTTTCTA 57.849 40.909 0.00 0.00 0.00 2.10
1596 1664 4.578928 TCTGTTTTTCTAGGTCTTGTTGCC 59.421 41.667 0.00 0.00 0.00 4.52
1624 1692 6.472163 TGCTTTGTCTCGATTTGAAAACTTTC 59.528 34.615 0.00 0.00 37.69 2.62
1631 1699 8.126700 GTCTCGATTTGAAAACTTTCCAACTTA 58.873 33.333 0.00 0.00 36.36 2.24
1632 1700 8.679100 TCTCGATTTGAAAACTTTCCAACTTAA 58.321 29.630 0.00 0.00 36.36 1.85
1672 1741 4.799564 TTGCTTCTTTTCCAGTTTGTGT 57.200 36.364 0.00 0.00 0.00 3.72
1793 1867 4.701651 CAGCCATCACTTTGAAGTTCCATA 59.298 41.667 0.00 0.00 37.08 2.74
1857 1931 3.278574 GGCAACTATGTATCCTTGTGCA 58.721 45.455 0.00 0.00 0.00 4.57
1859 1933 4.339247 GGCAACTATGTATCCTTGTGCATT 59.661 41.667 0.00 0.00 0.00 3.56
1860 1934 5.506317 GGCAACTATGTATCCTTGTGCATTC 60.506 44.000 0.00 0.00 0.00 2.67
1886 1960 0.246635 GAGCCTTCTCTGCCGTGTTA 59.753 55.000 0.00 0.00 36.42 2.41
1889 1963 1.676014 GCCTTCTCTGCCGTGTTATGT 60.676 52.381 0.00 0.00 0.00 2.29
1892 1966 3.865745 CCTTCTCTGCCGTGTTATGTTAG 59.134 47.826 0.00 0.00 0.00 2.34
1899 1973 3.194861 GCCGTGTTATGTTAGCATCTCA 58.805 45.455 0.00 0.00 36.58 3.27
1900 1975 3.246226 GCCGTGTTATGTTAGCATCTCAG 59.754 47.826 0.00 0.00 36.58 3.35
2099 2174 6.214191 TCTAGTTTTGTGCTATCTCTGGAG 57.786 41.667 0.00 0.00 0.00 3.86
2127 2202 5.933463 AGGTTGTCAATTGGCATTTTATGTG 59.067 36.000 14.57 0.00 0.00 3.21
2133 2208 6.002704 TCAATTGGCATTTTATGTGGCTTTT 58.997 32.000 5.42 0.00 42.13 2.27
2147 2222 4.953579 TGTGGCTTTTAGAGGTTTTTGTCT 59.046 37.500 0.00 0.00 0.00 3.41
2181 2256 1.034838 TTGTCCGTTGGCTGCAACTT 61.035 50.000 0.50 0.00 33.21 2.66
2182 2257 1.282875 GTCCGTTGGCTGCAACTTC 59.717 57.895 0.50 0.00 33.21 3.01
2183 2258 1.148273 TCCGTTGGCTGCAACTTCT 59.852 52.632 0.50 0.00 33.21 2.85
2195 2270 5.278463 GGCTGCAACTTCTCATTTGACTTTA 60.278 40.000 0.50 0.00 0.00 1.85
2200 2275 6.238759 GCAACTTCTCATTTGACTTTAGTGGT 60.239 38.462 0.00 0.00 0.00 4.16
2201 2276 7.355778 CAACTTCTCATTTGACTTTAGTGGTC 58.644 38.462 0.00 0.00 0.00 4.02
2210 2286 1.336609 ACTTTAGTGGTCCGTCTTCGC 60.337 52.381 0.00 0.00 35.54 4.70
2215 2291 2.204461 TGGTCCGTCTTCGCTGGAA 61.204 57.895 0.00 0.00 32.60 3.53
2217 2293 0.391263 GGTCCGTCTTCGCTGGAAAT 60.391 55.000 0.00 0.00 32.60 2.17
2253 2345 4.659529 TTATGTTGTGTCCATGGGGTTA 57.340 40.909 13.02 0.00 34.93 2.85
2267 2359 4.348020 TGGGGTTATCTCTGACTTAGGT 57.652 45.455 0.00 0.00 0.00 3.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 1.915489 TCACCCACAGCACCATAGAAT 59.085 47.619 0.00 0.00 0.00 2.40
19 20 4.314440 TCCACGCTCACCCACAGC 62.314 66.667 0.00 0.00 0.00 4.40
34 35 1.456705 ATCGGTCAGCCTCCTCTCC 60.457 63.158 0.00 0.00 0.00 3.71
35 36 1.040339 ACATCGGTCAGCCTCCTCTC 61.040 60.000 0.00 0.00 0.00 3.20
129 130 7.213678 TCTTCTTGTTCTTCTTCTTCTTCTCC 58.786 38.462 0.00 0.00 0.00 3.71
130 131 8.655651 TTCTTCTTGTTCTTCTTCTTCTTCTC 57.344 34.615 0.00 0.00 0.00 2.87
131 132 7.714813 CCTTCTTCTTGTTCTTCTTCTTCTTCT 59.285 37.037 0.00 0.00 0.00 2.85
132 133 7.713073 TCCTTCTTCTTGTTCTTCTTCTTCTTC 59.287 37.037 0.00 0.00 0.00 2.87
133 134 7.569240 TCCTTCTTCTTGTTCTTCTTCTTCTT 58.431 34.615 0.00 0.00 0.00 2.52
134 135 7.070571 TCTCCTTCTTCTTGTTCTTCTTCTTCT 59.929 37.037 0.00 0.00 0.00 2.85
135 136 7.213678 TCTCCTTCTTCTTGTTCTTCTTCTTC 58.786 38.462 0.00 0.00 0.00 2.87
136 137 7.130681 TCTCCTTCTTCTTGTTCTTCTTCTT 57.869 36.000 0.00 0.00 0.00 2.52
137 138 6.739331 TCTCCTTCTTCTTGTTCTTCTTCT 57.261 37.500 0.00 0.00 0.00 2.85
138 139 8.931775 GTTATCTCCTTCTTCTTGTTCTTCTTC 58.068 37.037 0.00 0.00 0.00 2.87
139 140 7.880713 GGTTATCTCCTTCTTCTTGTTCTTCTT 59.119 37.037 0.00 0.00 0.00 2.52
140 141 7.390823 GGTTATCTCCTTCTTCTTGTTCTTCT 58.609 38.462 0.00 0.00 0.00 2.85
146 147 3.197983 CCGGGTTATCTCCTTCTTCTTGT 59.802 47.826 0.00 0.00 0.00 3.16
147 148 3.432326 CCCGGGTTATCTCCTTCTTCTTG 60.432 52.174 14.18 0.00 0.00 3.02
542 543 3.612004 GCCGGAGATATTCTACAACGAGG 60.612 52.174 5.05 0.00 0.00 4.63
591 592 1.528309 GAGAGAGAGGGGAGGCGAG 60.528 68.421 0.00 0.00 0.00 5.03
592 593 1.990160 GAGAGAGAGAGGGGAGGCGA 61.990 65.000 0.00 0.00 0.00 5.54
593 594 1.528309 GAGAGAGAGAGGGGAGGCG 60.528 68.421 0.00 0.00 0.00 5.52
594 595 0.178990 GAGAGAGAGAGAGGGGAGGC 60.179 65.000 0.00 0.00 0.00 4.70
595 596 1.421646 GAGAGAGAGAGAGAGGGGAGG 59.578 61.905 0.00 0.00 0.00 4.30
596 597 1.421646 GGAGAGAGAGAGAGAGGGGAG 59.578 61.905 0.00 0.00 0.00 4.30
597 598 1.010793 AGGAGAGAGAGAGAGAGGGGA 59.989 57.143 0.00 0.00 0.00 4.81
598 599 1.421646 GAGGAGAGAGAGAGAGAGGGG 59.578 61.905 0.00 0.00 0.00 4.79
599 600 1.421646 GGAGGAGAGAGAGAGAGAGGG 59.578 61.905 0.00 0.00 0.00 4.30
600 601 1.070758 CGGAGGAGAGAGAGAGAGAGG 59.929 61.905 0.00 0.00 0.00 3.69
604 605 1.529796 GGCGGAGGAGAGAGAGAGA 59.470 63.158 0.00 0.00 0.00 3.10
606 607 2.190843 CGGCGGAGGAGAGAGAGA 59.809 66.667 0.00 0.00 0.00 3.10
691 698 2.041405 CTCCTCCTCCTCCCCCAC 60.041 72.222 0.00 0.00 0.00 4.61
692 699 3.368501 CCTCCTCCTCCTCCCCCA 61.369 72.222 0.00 0.00 0.00 4.96
693 700 3.036959 TCCTCCTCCTCCTCCCCC 61.037 72.222 0.00 0.00 0.00 5.40
694 701 2.612251 CTCCTCCTCCTCCTCCCC 59.388 72.222 0.00 0.00 0.00 4.81
695 702 2.612251 CCTCCTCCTCCTCCTCCC 59.388 72.222 0.00 0.00 0.00 4.30
696 703 2.015726 TCCCTCCTCCTCCTCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
697 704 1.541672 CTCCCTCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
698 705 2.018086 CCTCCCTCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
699 706 2.015726 TCCTCCCTCCTCCTCCTCC 61.016 68.421 0.00 0.00 0.00 4.30
700 707 1.541672 CTCCTCCCTCCTCCTCCTC 59.458 68.421 0.00 0.00 0.00 3.71
701 708 2.018086 CCTCCTCCCTCCTCCTCCT 61.018 68.421 0.00 0.00 0.00 3.69
732 742 0.465642 GGGGCCCGTAAAAGAGATGG 60.466 60.000 17.79 0.00 0.00 3.51
734 744 2.172082 GTTAGGGGCCCGTAAAAGAGAT 59.828 50.000 33.05 0.00 0.00 2.75
735 745 1.556451 GTTAGGGGCCCGTAAAAGAGA 59.444 52.381 33.05 12.38 0.00 3.10
806 826 1.405121 GGGCTCCGTTCGTTCTTATGT 60.405 52.381 0.00 0.00 0.00 2.29
812 832 2.506438 CGAGGGCTCCGTTCGTTC 60.506 66.667 4.08 0.00 0.00 3.95
813 833 4.736896 GCGAGGGCTCCGTTCGTT 62.737 66.667 11.29 0.00 35.83 3.85
938 961 3.991536 GAACGGGGAGCACTCGAGC 62.992 68.421 13.61 0.00 0.00 5.03
939 962 2.182030 GAACGGGGAGCACTCGAG 59.818 66.667 11.84 11.84 0.00 4.04
940 963 2.282958 AGAACGGGGAGCACTCGA 60.283 61.111 7.73 0.00 0.00 4.04
941 964 2.182030 GAGAACGGGGAGCACTCG 59.818 66.667 0.00 0.00 0.00 4.18
942 965 2.182030 CGAGAACGGGGAGCACTC 59.818 66.667 0.00 0.00 35.72 3.51
943 966 2.600769 ACGAGAACGGGGAGCACT 60.601 61.111 0.00 0.00 44.46 4.40
944 967 2.126031 GACGAGAACGGGGAGCAC 60.126 66.667 0.00 0.00 44.46 4.40
945 968 3.744719 CGACGAGAACGGGGAGCA 61.745 66.667 0.00 0.00 44.46 4.26
947 970 4.493747 GGCGACGAGAACGGGGAG 62.494 72.222 0.00 0.00 44.46 4.30
1019 1042 0.397254 CTAGCGAGGAAAGAGGGGGA 60.397 60.000 0.00 0.00 0.00 4.81
1022 1045 1.616374 GGATCTAGCGAGGAAAGAGGG 59.384 57.143 0.00 0.00 0.00 4.30
1024 1047 2.593026 AGGGATCTAGCGAGGAAAGAG 58.407 52.381 0.00 0.00 0.00 2.85
1027 1050 4.390129 AGATAGGGATCTAGCGAGGAAA 57.610 45.455 0.00 0.00 40.85 3.13
1028 1051 4.846040 GTAGATAGGGATCTAGCGAGGAA 58.154 47.826 0.00 0.00 43.84 3.36
1029 1052 4.490899 GTAGATAGGGATCTAGCGAGGA 57.509 50.000 0.00 0.00 43.84 3.71
1049 1072 1.125633 AACCACGACAACACTAGGGT 58.874 50.000 0.00 0.00 0.00 4.34
1055 1078 1.085501 ACCGACAACCACGACAACAC 61.086 55.000 0.00 0.00 0.00 3.32
1289 1316 0.738975 CGCGAGACCACCAAGATCTA 59.261 55.000 0.00 0.00 0.00 1.98
1290 1317 1.513158 CGCGAGACCACCAAGATCT 59.487 57.895 0.00 0.00 0.00 2.75
1291 1318 2.167861 GCGCGAGACCACCAAGATC 61.168 63.158 12.10 0.00 0.00 2.75
1331 1358 2.710377 AGCATGCATACTGGAACGAAA 58.290 42.857 21.98 0.00 0.00 3.46
1561 1629 4.523083 AGAAAAACAGACTGGCACACTAA 58.477 39.130 7.51 0.00 0.00 2.24
1568 1636 4.009370 AGACCTAGAAAAACAGACTGGC 57.991 45.455 7.51 0.00 0.00 4.85
1573 1641 4.578928 GGCAACAAGACCTAGAAAAACAGA 59.421 41.667 0.00 0.00 0.00 3.41
1575 1643 3.314080 CGGCAACAAGACCTAGAAAAACA 59.686 43.478 0.00 0.00 0.00 2.83
1582 1650 1.009829 GCATCGGCAACAAGACCTAG 58.990 55.000 0.00 0.00 40.72 3.02
1584 1652 0.250901 AAGCATCGGCAACAAGACCT 60.251 50.000 0.00 0.00 44.61 3.85
1596 1664 3.997319 TCAAATCGAGACAAAGCATCG 57.003 42.857 0.00 0.00 37.79 3.84
1672 1741 1.199789 GCAAATCGTCACTGCCATCAA 59.800 47.619 0.00 0.00 0.00 2.57
1727 1796 8.411683 GGCATACAAATCAATCTCAAAAGAGAT 58.588 33.333 2.29 2.29 43.18 2.75
1799 1873 8.154203 AGAAAACCAAACCTTTTCAAAAGAGAA 58.846 29.630 11.73 0.00 39.24 2.87
1800 1874 7.676004 AGAAAACCAAACCTTTTCAAAAGAGA 58.324 30.769 11.73 0.00 39.24 3.10
1801 1875 7.905604 AGAAAACCAAACCTTTTCAAAAGAG 57.094 32.000 11.73 4.34 39.24 2.85
1802 1876 8.684386 AAAGAAAACCAAACCTTTTCAAAAGA 57.316 26.923 11.73 0.00 39.24 2.52
1813 1887 6.529829 GCCAATTTTCAAAAGAAAACCAAACC 59.470 34.615 5.62 0.00 36.95 3.27
1815 1889 7.219484 TGCCAATTTTCAAAAGAAAACCAAA 57.781 28.000 5.62 0.00 36.95 3.28
1834 1908 3.694072 GCACAAGGATACATAGTTGCCAA 59.306 43.478 0.00 0.00 41.41 4.52
1838 1912 6.932356 AGAATGCACAAGGATACATAGTTG 57.068 37.500 0.00 0.00 41.41 3.16
1839 1913 7.944729 AAAGAATGCACAAGGATACATAGTT 57.055 32.000 0.00 0.00 41.41 2.24
1840 1914 7.831193 AGAAAAGAATGCACAAGGATACATAGT 59.169 33.333 0.00 0.00 41.41 2.12
1841 1915 8.127327 CAGAAAAGAATGCACAAGGATACATAG 58.873 37.037 0.00 0.00 41.41 2.23
1842 1916 7.828717 TCAGAAAAGAATGCACAAGGATACATA 59.171 33.333 0.00 0.00 41.41 2.29
1843 1917 6.660521 TCAGAAAAGAATGCACAAGGATACAT 59.339 34.615 0.00 0.00 41.41 2.29
1857 1931 4.009002 GCAGAGAAGGCTCAGAAAAGAAT 58.991 43.478 0.00 0.00 43.81 2.40
1859 1933 2.289945 GGCAGAGAAGGCTCAGAAAAGA 60.290 50.000 0.00 0.00 43.81 2.52
1860 1934 2.083002 GGCAGAGAAGGCTCAGAAAAG 58.917 52.381 0.00 0.00 43.81 2.27
1918 1993 9.773328 CATCACGTGATACTGTAAAAATCAATT 57.227 29.630 29.52 0.00 31.77 2.32
1919 1994 9.161629 TCATCACGTGATACTGTAAAAATCAAT 57.838 29.630 29.52 0.31 31.77 2.57
1920 1995 8.541133 TCATCACGTGATACTGTAAAAATCAA 57.459 30.769 29.52 0.00 31.77 2.57
1921 1996 8.541133 TTCATCACGTGATACTGTAAAAATCA 57.459 30.769 29.52 0.00 36.54 2.57
1922 1997 9.262472 GTTTCATCACGTGATACTGTAAAAATC 57.738 33.333 29.52 10.31 36.31 2.17
1923 1998 8.234546 GGTTTCATCACGTGATACTGTAAAAAT 58.765 33.333 29.52 2.14 38.41 1.82
1929 2004 4.537135 AGGTTTCATCACGTGATACTGT 57.463 40.909 29.52 13.42 38.41 3.55
1938 2013 5.762045 AGATTGTTTCAAGGTTTCATCACG 58.238 37.500 0.00 0.00 0.00 4.35
2099 2174 4.519540 AATGCCAATTGACAACCTGTAC 57.480 40.909 7.12 0.00 0.00 2.90
2105 2180 5.390779 GCCACATAAAATGCCAATTGACAAC 60.391 40.000 7.12 0.00 0.00 3.32
2108 2183 4.506758 AGCCACATAAAATGCCAATTGAC 58.493 39.130 7.12 0.00 0.00 3.18
2110 2185 5.883503 AAAGCCACATAAAATGCCAATTG 57.116 34.783 0.00 0.00 0.00 2.32
2112 2187 6.945218 TCTAAAAGCCACATAAAATGCCAAT 58.055 32.000 0.00 0.00 0.00 3.16
2127 2202 5.515797 ACAGACAAAAACCTCTAAAAGCC 57.484 39.130 0.00 0.00 0.00 4.35
2181 2256 4.039973 ACGGACCACTAAAGTCAAATGAGA 59.960 41.667 0.00 0.00 35.89 3.27
2182 2257 4.315803 ACGGACCACTAAAGTCAAATGAG 58.684 43.478 0.00 0.00 35.89 2.90
2183 2258 4.039973 AGACGGACCACTAAAGTCAAATGA 59.960 41.667 0.00 0.00 35.89 2.57
2195 2270 2.651361 CAGCGAAGACGGACCACT 59.349 61.111 0.00 0.00 40.15 4.00
2200 2275 0.108329 GGATTTCCAGCGAAGACGGA 60.108 55.000 0.00 0.00 36.60 4.69
2201 2276 1.090052 GGGATTTCCAGCGAAGACGG 61.090 60.000 0.00 0.00 37.63 4.79
2215 2291 7.334921 CACAACATAAAGCAATGAAATGGGATT 59.665 33.333 1.26 0.00 0.00 3.01
2217 2293 6.164876 CACAACATAAAGCAATGAAATGGGA 58.835 36.000 1.26 0.00 0.00 4.37
2253 2345 5.753721 AAAGAGCAACCTAAGTCAGAGAT 57.246 39.130 0.00 0.00 0.00 2.75


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

AutoCloner maintained by Alex Coulton.