Multiple sequence alignment - TraesCS1D01G357700

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 TraesCS1D01G357700 chr1D 100.000 2318 0 0 1 2318 441576004 441578321 0.000000e+00 4281
1 TraesCS1D01G357700 chr1D 91.828 1860 140 11 5 1858 441737724 441739577 0.000000e+00 2582
2 TraesCS1D01G357700 chr1D 92.121 1320 95 8 749 2062 441630801 441632117 0.000000e+00 1853
3 TraesCS1D01G357700 chr1D 91.896 691 50 5 1 690 441630116 441630801 0.000000e+00 961
4 TraesCS1D01G357700 chr1D 90.871 241 21 1 1889 2128 441739569 441739809 2.870000e-84 322
5 TraesCS1D01G357700 chr1D 87.407 135 16 1 2128 2262 307455641 307455508 1.110000e-33 154
6 TraesCS1D01G357700 chr1D 86.667 135 17 1 2128 2262 356144957 356144824 5.160000e-32 148
7 TraesCS1D01G357700 chr1B 91.717 2137 162 12 1 2128 599704966 599707096 0.000000e+00 2952
8 TraesCS1D01G357700 chr1B 91.717 2137 154 14 1 2128 599834472 599836594 0.000000e+00 2944
9 TraesCS1D01G357700 chr1B 91.577 2137 166 11 1 2128 599633757 599635888 0.000000e+00 2937
10 TraesCS1D01G357700 chr1B 91.577 2137 166 11 1 2128 599980326 599982457 0.000000e+00 2937
11 TraesCS1D01G357700 chr1B 91.343 2137 170 12 1 2128 599923011 599925141 0.000000e+00 2907
12 TraesCS1D01G357700 chr1B 90.973 2138 173 16 1 2128 599575430 599577557 0.000000e+00 2861
13 TraesCS1D01G357700 chr1B 91.591 2081 159 13 58 2128 599762984 599765058 0.000000e+00 2859
14 TraesCS1D01G357700 chr7D 87.943 141 15 2 2128 2268 85933749 85933611 5.120000e-37 165
15 TraesCS1D01G357700 chr1A 88.148 135 15 1 2128 2262 386705099 386704966 2.380000e-35 159
16 TraesCS1D01G357700 chr6B 87.313 134 16 1 2128 2261 521525164 521525032 3.990000e-33 152
17 TraesCS1D01G357700 chr5D 86.861 137 16 2 2126 2261 220729373 220729508 3.990000e-33 152
18 TraesCS1D01G357700 chr5B 87.407 135 14 3 2128 2261 136825632 136825500 3.990000e-33 152
19 TraesCS1D01G357700 chr4D 87.313 134 16 1 2128 2261 123938763 123938631 3.990000e-33 152
20 TraesCS1D01G357700 chr3D 86.765 136 14 4 2128 2261 355998209 355998076 5.160000e-32 148


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 TraesCS1D01G357700 chr1D 441576004 441578321 2317 False 4281 4281 100.0000 1 2318 1 chr1D.!!$F1 2317
1 TraesCS1D01G357700 chr1D 441737724 441739809 2085 False 1452 2582 91.3495 5 2128 2 chr1D.!!$F3 2123
2 TraesCS1D01G357700 chr1D 441630116 441632117 2001 False 1407 1853 92.0085 1 2062 2 chr1D.!!$F2 2061
3 TraesCS1D01G357700 chr1B 599704966 599707096 2130 False 2952 2952 91.7170 1 2128 1 chr1B.!!$F3 2127
4 TraesCS1D01G357700 chr1B 599834472 599836594 2122 False 2944 2944 91.7170 1 2128 1 chr1B.!!$F5 2127
5 TraesCS1D01G357700 chr1B 599633757 599635888 2131 False 2937 2937 91.5770 1 2128 1 chr1B.!!$F2 2127
6 TraesCS1D01G357700 chr1B 599980326 599982457 2131 False 2937 2937 91.5770 1 2128 1 chr1B.!!$F7 2127
7 TraesCS1D01G357700 chr1B 599923011 599925141 2130 False 2907 2907 91.3430 1 2128 1 chr1B.!!$F6 2127
8 TraesCS1D01G357700 chr1B 599575430 599577557 2127 False 2861 2861 90.9730 1 2128 1 chr1B.!!$F1 2127
9 TraesCS1D01G357700 chr1B 599762984 599765058 2074 False 2859 2859 91.5910 58 2128 1 chr1B.!!$F4 2070

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
608 612 0.037975 CCACTCCATTTGCCTTGTGC 60.038 55.0 0.0 0.0 41.77 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2259 2274 0.18135 GGGATAGCAAGGGTCTGGTG 59.819 60.0 0.0 0.0 0.0 4.17 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
43 44 9.474920 CACATTTGTTTGGTATAGTTTGTCAAT 57.525 29.630 0.00 0.00 0.00 2.57
44 45 9.474920 ACATTTGTTTGGTATAGTTTGTCAATG 57.525 29.630 0.00 0.00 0.00 2.82
90 91 7.333174 TGTGTCTTGCAATCATATTAGTTTCGA 59.667 33.333 0.00 0.00 0.00 3.71
176 177 7.652727 TGTAATTCATCGTGAAAAATGGAACA 58.347 30.769 4.87 0.00 41.28 3.18
177 178 8.138074 TGTAATTCATCGTGAAAAATGGAACAA 58.862 29.630 4.87 0.00 40.63 2.83
212 213 3.931285 TTTGCATGAGATTCGTCATCG 57.069 42.857 0.00 0.00 34.81 3.84
234 235 0.328258 AACTTGGTTCCCCGGATCAG 59.672 55.000 0.73 0.00 0.00 2.90
250 251 3.371380 GGATCAGTCCTGAAAGAAGCCAT 60.371 47.826 0.37 0.00 43.58 4.40
256 257 1.661341 CTGAAAGAAGCCATCGAGGG 58.339 55.000 12.83 12.83 34.30 4.30
306 308 4.947645 AGAGATTTGTCTATGCTCTGCTC 58.052 43.478 0.00 0.00 34.85 4.26
308 310 5.832595 AGAGATTTGTCTATGCTCTGCTCTA 59.167 40.000 0.00 0.00 34.85 2.43
318 320 2.167281 TGCTCTGCTCTAGTTAAGCCAG 59.833 50.000 0.00 0.00 39.05 4.85
328 330 6.986817 GCTCTAGTTAAGCCAGTATTGATTGA 59.013 38.462 0.00 0.00 33.53 2.57
341 343 3.634397 TTGATTGACCTGTCTCCCATC 57.366 47.619 0.00 0.00 0.00 3.51
345 347 2.919772 TGACCTGTCTCCCATCTACA 57.080 50.000 0.00 0.00 0.00 2.74
370 372 3.388024 TGCATTAGTGGTGGGTCTAGATC 59.612 47.826 0.00 0.00 0.00 2.75
398 400 4.059511 ACATGTTGTGCATTTTGTGGATG 58.940 39.130 0.00 0.00 35.19 3.51
421 424 9.472361 GATGTGATGAAATATTTCCTCCATTTG 57.528 33.333 22.42 0.00 36.36 2.32
424 427 7.223387 GTGATGAAATATTTCCTCCATTTGTGC 59.777 37.037 22.42 2.07 36.36 4.57
431 435 4.751767 TTCCTCCATTTGTGCTTTTTGT 57.248 36.364 0.00 0.00 0.00 2.83
476 480 1.692519 AGGGAATCGGCATACACCTAC 59.307 52.381 0.00 0.00 0.00 3.18
565 569 1.967319 GGTGGTACCAATGATCGCAT 58.033 50.000 18.31 0.00 38.42 4.73
570 574 1.265095 GTACCAATGATCGCATGCCTG 59.735 52.381 13.15 0.00 34.26 4.85
572 576 1.658114 CAATGATCGCATGCCTGGG 59.342 57.895 13.15 0.00 34.26 4.45
579 583 4.175337 GCATGCCTGGGCGTAGGA 62.175 66.667 6.36 0.00 45.51 2.94
598 602 3.270433 AGGAAATCCATGTCCACTCCATT 59.730 43.478 1.67 0.00 38.89 3.16
608 612 0.037975 CCACTCCATTTGCCTTGTGC 60.038 55.000 0.00 0.00 41.77 4.57
635 639 1.171308 CCAAGGCTGTGAGACCAATG 58.829 55.000 0.00 0.00 0.00 2.82
649 653 2.368878 AATGAGAGGGGAGGGGGC 60.369 66.667 0.00 0.00 0.00 5.80
685 689 6.487299 AACCAAAAATTTAGCTAACCACCA 57.513 33.333 5.45 0.00 0.00 4.17
690 694 1.515081 TTTAGCTAACCACCACACGC 58.485 50.000 5.45 0.00 0.00 5.34
698 702 1.594293 CCACCACACGCGTTTCTCT 60.594 57.895 10.22 0.00 0.00 3.10
764 768 1.599071 AGCGGTGCATGATTAATGTCG 59.401 47.619 0.00 0.00 38.65 4.35
774 778 3.977427 TGATTAATGTCGTGATCCTCCG 58.023 45.455 0.00 0.00 0.00 4.63
779 783 3.822192 TCGTGATCCTCCGCACCG 61.822 66.667 0.00 0.00 0.00 4.94
801 807 0.935196 GTGTCGTCACAGGGTTGTTC 59.065 55.000 7.95 0.00 43.37 3.18
804 810 0.249155 TCGTCACAGGGTTGTTCGTC 60.249 55.000 0.00 0.00 34.62 4.20
865 871 2.554344 TGAAGAAATCAAAGGGGGACCG 60.554 50.000 0.00 0.00 46.42 4.79
891 897 5.186021 ACCACCTAAGACTCAAGATGTACAG 59.814 44.000 0.33 0.00 0.00 2.74
910 916 3.118738 ACAGACCCTTTATAAGCACCTCG 60.119 47.826 0.00 0.00 0.00 4.63
913 919 1.217882 CCTTTATAAGCACCTCGCCG 58.782 55.000 0.00 0.00 44.04 6.46
932 938 2.094659 CGTCGCTTTCCACGCATCT 61.095 57.895 0.00 0.00 0.00 2.90
937 943 0.874390 GCTTTCCACGCATCTGAACA 59.126 50.000 0.00 0.00 0.00 3.18
938 944 1.400242 GCTTTCCACGCATCTGAACAC 60.400 52.381 0.00 0.00 0.00 3.32
991 997 4.218635 ACATACAGTGAGACAGGTACACAG 59.781 45.833 0.00 0.00 37.05 3.66
993 999 1.341209 CAGTGAGACAGGTACACAGCA 59.659 52.381 0.00 0.00 37.05 4.41
1068 1074 0.321564 TGAAGCCCCTGATGTTGACG 60.322 55.000 0.00 0.00 0.00 4.35
1098 1106 3.787001 GGCCAGGAGAAGGGTCCG 61.787 72.222 0.00 0.00 42.05 4.79
1118 1126 0.620030 CCACACCATGAGGATGACCA 59.380 55.000 0.00 0.00 38.69 4.02
1127 1135 1.003580 TGAGGATGACCAACAAGCTCC 59.996 52.381 0.00 0.00 38.94 4.70
1132 1140 1.429930 TGACCAACAAGCTCCAGGTA 58.570 50.000 0.00 0.00 31.57 3.08
1183 1192 4.217035 GTGACATATGGCACGGCA 57.783 55.556 25.43 0.00 45.07 5.69
1197 1206 1.338337 CACGGCATCTTCCTCTACGAT 59.662 52.381 0.00 0.00 0.00 3.73
1201 1210 1.069204 GCATCTTCCTCTACGATGGCA 59.931 52.381 0.00 0.00 36.07 4.92
1232 1241 0.841289 GGAAATATGACCCCGGTGGA 59.159 55.000 15.08 0.00 38.00 4.02
1284 1293 5.916883 CGATTTCTTTGAACATATGGATGGC 59.083 40.000 7.80 0.00 37.39 4.40
1303 1312 0.105964 CGGAGCCGGACCATTCATTA 59.894 55.000 5.05 0.00 35.56 1.90
1334 1343 7.740246 TCTATGTAGTATGTCGATCGATGTTC 58.260 38.462 22.50 8.85 0.00 3.18
1346 1355 1.809619 GATGTTCGCGCACTAGGCA 60.810 57.895 10.81 0.00 45.17 4.75
1364 1374 7.225931 CACTAGGCAGAGTTGTTGTAACTTAAA 59.774 37.037 0.00 0.00 0.00 1.52
1453 1463 9.956720 CGGCTCAAAATATTAGATTCTTTGAAT 57.043 29.630 0.00 0.00 36.03 2.57
1486 1496 8.750416 CGCTCATGTATTATCATTACTATCTGC 58.250 37.037 0.00 0.00 0.00 4.26
1513 1523 4.944619 TGGGAGTGCTCATTAGTATCTG 57.055 45.455 1.41 0.00 0.00 2.90
1594 1604 8.510505 ACAAATGTTGTGTGTAATTTTGCTTTT 58.489 25.926 0.00 0.00 43.48 2.27
1634 1644 7.887996 TTCTTATTGCTATTTTGTTTGCCTG 57.112 32.000 0.00 0.00 0.00 4.85
1738 1751 8.090831 TGCATAGAGAAGTACCATATTGATGTC 58.909 37.037 0.00 0.00 0.00 3.06
1763 1776 8.784043 TCTTTCTAAGATTTTCAGTGTTTAGCC 58.216 33.333 0.00 0.00 31.20 3.93
1766 1779 8.635765 TCTAAGATTTTCAGTGTTTAGCCAAT 57.364 30.769 0.00 0.00 0.00 3.16
1809 1822 7.378181 CACCTGCACCTTTTTATTTGTTCTAT 58.622 34.615 0.00 0.00 0.00 1.98
1814 1827 8.637986 TGCACCTTTTTATTTGTTCTATGACTT 58.362 29.630 0.00 0.00 0.00 3.01
1848 1861 0.106967 GGAGGGGCTCTTGGATTCAC 60.107 60.000 0.00 0.00 0.00 3.18
1966 1979 4.635765 AGTAAATGAGTACGTGCAATGCAT 59.364 37.500 12.38 0.00 41.91 3.96
2084 2099 9.484326 TTGCATATTAATTATGTAATTAGCGCG 57.516 29.630 0.00 0.00 37.79 6.86
2100 2115 8.627487 AATTAGCGCGAAATTTTGATATTTGA 57.373 26.923 12.10 0.00 0.00 2.69
2128 2143 6.912051 TGCTATTAATTGCACGCTAAAGATTG 59.088 34.615 18.70 0.00 33.81 2.67
2129 2144 6.912591 GCTATTAATTGCACGCTAAAGATTGT 59.087 34.615 15.67 0.00 0.00 2.71
2130 2145 7.432252 GCTATTAATTGCACGCTAAAGATTGTT 59.568 33.333 15.67 0.00 0.00 2.83
2131 2146 6.926280 TTAATTGCACGCTAAAGATTGTTG 57.074 33.333 0.00 0.00 0.00 3.33
2132 2147 3.980646 TTGCACGCTAAAGATTGTTGT 57.019 38.095 0.00 0.00 0.00 3.32
2133 2148 3.980646 TGCACGCTAAAGATTGTTGTT 57.019 38.095 0.00 0.00 0.00 2.83
2134 2149 4.300189 TGCACGCTAAAGATTGTTGTTT 57.700 36.364 0.00 0.00 0.00 2.83
2135 2150 5.425577 TGCACGCTAAAGATTGTTGTTTA 57.574 34.783 0.00 0.00 0.00 2.01
2136 2151 6.007936 TGCACGCTAAAGATTGTTGTTTAT 57.992 33.333 0.00 0.00 0.00 1.40
2137 2152 5.855925 TGCACGCTAAAGATTGTTGTTTATG 59.144 36.000 0.00 0.00 0.00 1.90
2138 2153 5.856455 GCACGCTAAAGATTGTTGTTTATGT 59.144 36.000 0.00 0.00 0.00 2.29
2139 2154 7.018826 GCACGCTAAAGATTGTTGTTTATGTA 58.981 34.615 0.00 0.00 0.00 2.29
2140 2155 7.696453 GCACGCTAAAGATTGTTGTTTATGTAT 59.304 33.333 0.00 0.00 0.00 2.29
2141 2156 9.210426 CACGCTAAAGATTGTTGTTTATGTATC 57.790 33.333 0.00 0.00 0.00 2.24
2142 2157 8.395633 ACGCTAAAGATTGTTGTTTATGTATCC 58.604 33.333 0.00 0.00 0.00 2.59
2143 2158 8.394877 CGCTAAAGATTGTTGTTTATGTATCCA 58.605 33.333 0.00 0.00 0.00 3.41
2165 2180 8.795842 TCCATACATGTATTTAAGTTTTCGGT 57.204 30.769 15.85 0.00 0.00 4.69
2166 2181 8.885722 TCCATACATGTATTTAAGTTTTCGGTC 58.114 33.333 15.85 0.00 0.00 4.79
2167 2182 8.670135 CCATACATGTATTTAAGTTTTCGGTCA 58.330 33.333 15.85 0.00 0.00 4.02
2174 2189 9.275398 TGTATTTAAGTTTTCGGTCAATACACT 57.725 29.630 0.00 0.00 33.03 3.55
2177 2192 8.441312 TTTAAGTTTTCGGTCAATACACTTCT 57.559 30.769 0.00 0.00 0.00 2.85
2178 2193 9.545105 TTTAAGTTTTCGGTCAATACACTTCTA 57.455 29.630 0.00 0.00 0.00 2.10
2179 2194 9.545105 TTAAGTTTTCGGTCAATACACTTCTAA 57.455 29.630 0.00 0.00 0.00 2.10
2180 2195 7.417496 AGTTTTCGGTCAATACACTTCTAAC 57.583 36.000 0.00 0.00 0.00 2.34
2181 2196 6.987992 AGTTTTCGGTCAATACACTTCTAACA 59.012 34.615 0.00 0.00 0.00 2.41
2182 2197 7.660208 AGTTTTCGGTCAATACACTTCTAACAT 59.340 33.333 0.00 0.00 0.00 2.71
2183 2198 6.961359 TTCGGTCAATACACTTCTAACATG 57.039 37.500 0.00 0.00 0.00 3.21
2184 2199 6.275494 TCGGTCAATACACTTCTAACATGA 57.725 37.500 0.00 0.00 0.00 3.07
2185 2200 6.693466 TCGGTCAATACACTTCTAACATGAA 58.307 36.000 0.00 0.00 0.00 2.57
2186 2201 7.327975 TCGGTCAATACACTTCTAACATGAAT 58.672 34.615 0.00 0.00 0.00 2.57
2187 2202 8.471609 TCGGTCAATACACTTCTAACATGAATA 58.528 33.333 0.00 0.00 0.00 1.75
2188 2203 8.755941 CGGTCAATACACTTCTAACATGAATAG 58.244 37.037 0.00 1.66 0.00 1.73
2189 2204 9.601217 GGTCAATACACTTCTAACATGAATAGT 57.399 33.333 0.00 0.00 0.00 2.12
2267 2282 3.288092 GGAATATTCCCAACACCAGACC 58.712 50.000 22.09 0.00 41.62 3.85
2268 2283 3.288092 GAATATTCCCAACACCAGACCC 58.712 50.000 3.92 0.00 0.00 4.46
2269 2284 2.053747 TATTCCCAACACCAGACCCT 57.946 50.000 0.00 0.00 0.00 4.34
2270 2285 1.158007 ATTCCCAACACCAGACCCTT 58.842 50.000 0.00 0.00 0.00 3.95
2271 2286 0.184933 TTCCCAACACCAGACCCTTG 59.815 55.000 0.00 0.00 0.00 3.61
2272 2287 1.903404 CCCAACACCAGACCCTTGC 60.903 63.158 0.00 0.00 0.00 4.01
2273 2288 1.151450 CCAACACCAGACCCTTGCT 59.849 57.895 0.00 0.00 0.00 3.91
2274 2289 0.400213 CCAACACCAGACCCTTGCTA 59.600 55.000 0.00 0.00 0.00 3.49
2275 2290 1.004745 CCAACACCAGACCCTTGCTAT 59.995 52.381 0.00 0.00 0.00 2.97
2276 2291 2.359900 CAACACCAGACCCTTGCTATC 58.640 52.381 0.00 0.00 0.00 2.08
2277 2292 0.912486 ACACCAGACCCTTGCTATCC 59.088 55.000 0.00 0.00 0.00 2.59
2278 2293 0.181350 CACCAGACCCTTGCTATCCC 59.819 60.000 0.00 0.00 0.00 3.85
2279 2294 1.338136 ACCAGACCCTTGCTATCCCG 61.338 60.000 0.00 0.00 0.00 5.14
2280 2295 1.227674 CAGACCCTTGCTATCCCGC 60.228 63.158 0.00 0.00 0.00 6.13
2281 2296 1.689233 AGACCCTTGCTATCCCGCA 60.689 57.895 0.00 0.00 38.31 5.69
2282 2297 1.227674 GACCCTTGCTATCCCGCAG 60.228 63.158 0.00 0.00 41.55 5.18
2283 2298 2.592861 CCCTTGCTATCCCGCAGC 60.593 66.667 0.00 0.00 41.55 5.25
2284 2299 2.507944 CCTTGCTATCCCGCAGCT 59.492 61.111 0.00 0.00 41.55 4.24
2285 2300 1.748403 CCTTGCTATCCCGCAGCTA 59.252 57.895 0.00 0.00 41.55 3.32
2286 2301 0.320247 CCTTGCTATCCCGCAGCTAG 60.320 60.000 0.00 0.00 41.55 3.42
2287 2302 0.676184 CTTGCTATCCCGCAGCTAGA 59.324 55.000 0.00 0.00 42.25 2.43
2288 2303 0.676184 TTGCTATCCCGCAGCTAGAG 59.324 55.000 0.00 0.00 41.55 2.43
2289 2304 1.080161 GCTATCCCGCAGCTAGAGC 60.080 63.158 0.00 0.00 42.49 4.09
2290 2305 1.589113 CTATCCCGCAGCTAGAGCC 59.411 63.158 0.00 0.00 43.38 4.70
2291 2306 1.882989 CTATCCCGCAGCTAGAGCCC 61.883 65.000 0.00 0.00 43.38 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 0.037303 AATGTGGGGAGTGCAGACAG 59.963 55.000 0.00 0.00 0.00 3.51
8 9 1.411977 CAAACAAATGTGGGGAGTGCA 59.588 47.619 0.00 0.00 0.00 4.57
9 10 1.270252 CCAAACAAATGTGGGGAGTGC 60.270 52.381 0.00 0.00 0.00 4.40
70 71 7.972832 TGCAATTCGAAACTAATATGATTGCAA 59.027 29.630 20.06 0.00 44.73 4.08
83 84 1.131126 CGCATCCTGCAATTCGAAACT 59.869 47.619 0.00 0.00 45.36 2.66
90 91 2.821969 AGACTTTTCGCATCCTGCAATT 59.178 40.909 0.00 0.00 45.36 2.32
102 103 2.574322 CGATTGTGGCAAGACTTTTCG 58.426 47.619 0.00 0.00 0.00 3.46
106 107 1.880027 GAACCGATTGTGGCAAGACTT 59.120 47.619 0.00 0.00 0.00 3.01
107 108 1.202758 TGAACCGATTGTGGCAAGACT 60.203 47.619 0.00 0.00 0.00 3.24
108 109 1.234821 TGAACCGATTGTGGCAAGAC 58.765 50.000 0.00 0.00 0.00 3.01
110 111 2.791383 TTTGAACCGATTGTGGCAAG 57.209 45.000 0.00 0.00 0.00 4.01
111 112 3.068732 TCATTTTGAACCGATTGTGGCAA 59.931 39.130 0.00 0.00 0.00 4.52
112 113 2.625314 TCATTTTGAACCGATTGTGGCA 59.375 40.909 0.00 0.00 0.00 4.92
113 114 3.296322 TCATTTTGAACCGATTGTGGC 57.704 42.857 0.00 0.00 0.00 5.01
161 162 6.843069 AGGAAATTTGTTCCATTTTTCACG 57.157 33.333 7.80 0.00 41.00 4.35
192 193 2.609002 CCGATGACGAATCTCATGCAAA 59.391 45.455 0.00 0.00 42.66 3.68
193 194 2.204237 CCGATGACGAATCTCATGCAA 58.796 47.619 0.00 0.00 42.66 4.08
206 207 0.521735 GGAACCAAGTTGCCGATGAC 59.478 55.000 0.00 0.00 0.00 3.06
234 235 2.275318 CTCGATGGCTTCTTTCAGGAC 58.725 52.381 0.00 0.00 0.00 3.85
250 251 0.563173 AGGAATCTCCCATCCCTCGA 59.437 55.000 0.00 0.00 37.19 4.04
256 257 5.815233 TCATAGTGAAGGAATCTCCCATC 57.185 43.478 0.00 0.00 37.19 3.51
306 308 7.225538 CAGGTCAATCAATACTGGCTTAACTAG 59.774 40.741 0.00 0.00 0.00 2.57
308 310 5.882557 CAGGTCAATCAATACTGGCTTAACT 59.117 40.000 0.00 0.00 0.00 2.24
318 320 4.487714 TGGGAGACAGGTCAATCAATAC 57.512 45.455 1.84 0.00 0.00 1.89
328 330 3.370953 GCAAATGTAGATGGGAGACAGGT 60.371 47.826 0.00 0.00 0.00 4.00
341 343 4.016444 ACCCACCACTAATGCAAATGTAG 58.984 43.478 0.00 0.00 0.00 2.74
345 347 3.456380 AGACCCACCACTAATGCAAAT 57.544 42.857 0.00 0.00 0.00 2.32
392 394 6.547141 TGGAGGAAATATTTCATCACATCCAC 59.453 38.462 32.31 19.32 46.50 4.02
398 400 7.223387 GCACAAATGGAGGAAATATTTCATCAC 59.777 37.037 32.31 24.39 46.50 3.06
421 424 8.455598 TCTAACAACACTAAAACAAAAAGCAC 57.544 30.769 0.00 0.00 0.00 4.40
452 456 0.105964 TGTATGCCGATTCCCTTCCG 59.894 55.000 0.00 0.00 0.00 4.30
496 500 2.037367 CCTCCACCCCTCTCGTGA 59.963 66.667 0.00 0.00 32.77 4.35
551 555 1.596603 CAGGCATGCGATCATTGGTA 58.403 50.000 12.44 0.00 0.00 3.25
565 569 1.223487 GATTTCCTACGCCCAGGCA 59.777 57.895 9.78 0.00 42.06 4.75
570 574 1.594331 GACATGGATTTCCTACGCCC 58.406 55.000 0.00 0.00 36.82 6.13
572 576 1.940613 GTGGACATGGATTTCCTACGC 59.059 52.381 0.00 0.00 36.82 4.42
579 583 3.196254 GCAAATGGAGTGGACATGGATTT 59.804 43.478 0.00 0.00 0.00 2.17
608 612 2.234661 TCTCACAGCCTTGGTACTCATG 59.765 50.000 0.00 0.00 0.00 3.07
609 613 2.234908 GTCTCACAGCCTTGGTACTCAT 59.765 50.000 0.00 0.00 0.00 2.90
635 639 4.153330 TACGCCCCCTCCCCTCTC 62.153 72.222 0.00 0.00 0.00 3.20
649 653 6.757026 AATTTTTGGTTCGGATTTTGTACG 57.243 33.333 0.00 0.00 34.65 3.67
690 694 6.812481 TTATGATCAATGACGAGAGAAACG 57.188 37.500 0.00 0.00 0.00 3.60
698 702 5.696270 CGGAGGATTTTATGATCAATGACGA 59.304 40.000 0.00 0.00 0.00 4.20
764 768 2.202756 GTCGGTGCGGAGGATCAC 60.203 66.667 0.00 0.00 36.25 3.06
785 789 0.249155 GACGAACAACCCTGTGACGA 60.249 55.000 10.46 0.00 38.58 4.20
801 807 1.869132 TCTGGTGATACGATACGGACG 59.131 52.381 0.00 0.00 0.00 4.79
804 810 5.813080 TCATATCTGGTGATACGATACGG 57.187 43.478 0.00 0.00 37.92 4.02
827 833 9.525409 GATTTCTTCAATCCAATTCGAATCAAT 57.475 29.630 11.83 2.74 36.02 2.57
865 871 5.153950 ACATCTTGAGTCTTAGGTGGTTC 57.846 43.478 9.82 0.00 0.00 3.62
891 897 2.210961 GCGAGGTGCTTATAAAGGGTC 58.789 52.381 0.00 0.00 41.73 4.46
919 925 1.872952 TGTGTTCAGATGCGTGGAAAG 59.127 47.619 0.00 0.00 0.00 2.62
932 938 3.055747 TGGTGTCTGTGTAGTTGTGTTCA 60.056 43.478 0.00 0.00 0.00 3.18
937 943 1.805120 GCGTGGTGTCTGTGTAGTTGT 60.805 52.381 0.00 0.00 0.00 3.32
938 944 0.859232 GCGTGGTGTCTGTGTAGTTG 59.141 55.000 0.00 0.00 0.00 3.16
980 986 0.035458 GGCTTCTGCTGTGTACCTGT 59.965 55.000 0.00 0.00 39.59 4.00
991 997 3.869272 CGGCGACATGGCTTCTGC 61.869 66.667 0.00 0.00 42.02 4.26
1058 1064 2.038426 ACCACCTTGATCGTCAACATCA 59.962 45.455 0.00 0.00 32.21 3.07
1059 1065 2.416547 CACCACCTTGATCGTCAACATC 59.583 50.000 0.00 0.00 32.21 3.06
1068 1074 1.379044 CTGGCCCACCACCTTGATC 60.379 63.158 0.00 0.00 42.67 2.92
1098 1106 0.749454 GGTCATCCTCATGGTGTGGC 60.749 60.000 0.00 0.00 31.43 5.01
1118 1126 2.026822 CCATGAGTACCTGGAGCTTGTT 60.027 50.000 0.00 0.00 34.45 2.83
1127 1135 1.404181 CCACACGTCCATGAGTACCTG 60.404 57.143 0.00 0.00 0.00 4.00
1132 1140 0.606604 GGTACCACACGTCCATGAGT 59.393 55.000 7.15 0.00 0.00 3.41
1159 1167 1.324005 TGCCATATGTCACGTCGGGA 61.324 55.000 0.00 0.00 0.00 5.14
1183 1192 2.289320 GCATGCCATCGTAGAGGAAGAT 60.289 50.000 6.36 0.00 43.16 2.40
1201 1210 0.465460 ATATTTCCACGCACCCGCAT 60.465 50.000 0.00 0.00 38.40 4.73
1213 1222 0.841289 TCCACCGGGGTCATATTTCC 59.159 55.000 6.32 0.00 38.11 3.13
1232 1241 1.516110 CCCATCCTCCATCTCAAGGT 58.484 55.000 0.00 0.00 34.12 3.50
1260 1269 5.916883 GCCATCCATATGTTCAAAGAAATCG 59.083 40.000 1.24 0.00 0.00 3.34
1284 1293 0.105964 TAATGAATGGTCCGGCTCCG 59.894 55.000 0.00 0.48 39.44 4.63
1290 1299 6.881065 ACATAGATCCAATAATGAATGGTCCG 59.119 38.462 0.00 0.00 37.94 4.79
1303 1312 7.553044 TCGATCGACATACTACATAGATCCAAT 59.447 37.037 15.15 0.00 31.96 3.16
1334 1343 2.125912 AACTCTGCCTAGTGCGCG 60.126 61.111 0.00 0.00 45.60 6.86
1346 1355 9.284968 ACATATGCTTTAAGTTACAACAACTCT 57.715 29.630 1.58 0.00 0.00 3.24
1407 1417 3.064545 CCGCTCACATCAGAAATTTCCTC 59.935 47.826 14.61 0.00 0.00 3.71
1479 1489 2.421424 GCACTCCCAAACAAGCAGATAG 59.579 50.000 0.00 0.00 0.00 2.08
1486 1496 4.074970 ACTAATGAGCACTCCCAAACAAG 58.925 43.478 0.00 0.00 0.00 3.16
1489 1499 5.525378 CAGATACTAATGAGCACTCCCAAAC 59.475 44.000 0.00 0.00 0.00 2.93
1513 1523 6.978080 ACCACTGTTCAAACATATGACAAAAC 59.022 34.615 10.38 8.87 38.41 2.43
1564 1574 8.573801 GCAAAATTACACACAACATTTGTTTTG 58.426 29.630 7.79 7.79 43.23 2.44
1616 1626 3.067461 ACGACAGGCAAACAAAATAGCAA 59.933 39.130 0.00 0.00 0.00 3.91
1623 1633 2.490115 ACAAGAACGACAGGCAAACAAA 59.510 40.909 0.00 0.00 0.00 2.83
1634 1644 1.719780 CACTAGCGGAACAAGAACGAC 59.280 52.381 0.00 0.00 0.00 4.34
1738 1751 8.567948 TGGCTAAACACTGAAAATCTTAGAAAG 58.432 33.333 0.00 0.00 0.00 2.62
1761 1774 5.109210 GGACCAAATACAAAAGCTATTGGC 58.891 41.667 2.44 0.00 42.19 4.52
1763 1776 6.071391 AGGTGGACCAAATACAAAAGCTATTG 60.071 38.462 0.00 0.00 38.89 1.90
1766 1779 4.764823 CAGGTGGACCAAATACAAAAGCTA 59.235 41.667 0.00 0.00 38.89 3.32
1781 1794 4.202212 ACAAATAAAAAGGTGCAGGTGGAC 60.202 41.667 0.00 0.00 35.50 4.02
1809 1822 6.490040 CCCTCCTTAGTTGAATCAAAAAGTCA 59.510 38.462 14.40 4.48 0.00 3.41
1814 1827 4.086457 GCCCCTCCTTAGTTGAATCAAAA 58.914 43.478 0.00 0.00 0.00 2.44
1818 1831 2.774809 AGAGCCCCTCCTTAGTTGAATC 59.225 50.000 0.00 0.00 0.00 2.52
1830 1843 0.620556 TGTGAATCCAAGAGCCCCTC 59.379 55.000 0.00 0.00 0.00 4.30
1897 1910 5.985530 CCTACGATCAAAATAGCTCACATCA 59.014 40.000 0.00 0.00 0.00 3.07
1898 1911 6.216569 TCCTACGATCAAAATAGCTCACATC 58.783 40.000 0.00 0.00 0.00 3.06
2075 2090 8.627487 TCAAATATCAAAATTTCGCGCTAATT 57.373 26.923 5.56 8.67 0.00 1.40
2100 2115 8.322906 TCTTTAGCGTGCAATTAATAGCATAT 57.677 30.769 0.00 0.00 43.44 1.78
2139 2154 9.403583 ACCGAAAACTTAAATACATGTATGGAT 57.596 29.630 18.94 10.89 31.06 3.41
2140 2155 8.795842 ACCGAAAACTTAAATACATGTATGGA 57.204 30.769 18.94 7.42 0.00 3.41
2141 2156 8.670135 TGACCGAAAACTTAAATACATGTATGG 58.330 33.333 18.94 13.17 0.00 2.74
2148 2163 9.275398 AGTGTATTGACCGAAAACTTAAATACA 57.725 29.630 0.00 0.00 36.93 2.29
2151 2166 9.063615 AGAAGTGTATTGACCGAAAACTTAAAT 57.936 29.630 0.00 0.00 0.00 1.40
2152 2167 8.441312 AGAAGTGTATTGACCGAAAACTTAAA 57.559 30.769 0.00 0.00 0.00 1.52
2153 2168 9.545105 TTAGAAGTGTATTGACCGAAAACTTAA 57.455 29.630 0.00 0.00 0.00 1.85
2154 2169 8.981647 GTTAGAAGTGTATTGACCGAAAACTTA 58.018 33.333 0.00 0.00 0.00 2.24
2155 2170 7.496591 TGTTAGAAGTGTATTGACCGAAAACTT 59.503 33.333 0.00 0.00 0.00 2.66
2156 2171 6.987992 TGTTAGAAGTGTATTGACCGAAAACT 59.012 34.615 0.00 0.00 0.00 2.66
2157 2172 7.181143 TGTTAGAAGTGTATTGACCGAAAAC 57.819 36.000 0.00 0.00 0.00 2.43
2158 2173 7.658167 TCATGTTAGAAGTGTATTGACCGAAAA 59.342 33.333 0.00 0.00 0.00 2.29
2159 2174 7.156000 TCATGTTAGAAGTGTATTGACCGAAA 58.844 34.615 0.00 0.00 0.00 3.46
2160 2175 6.693466 TCATGTTAGAAGTGTATTGACCGAA 58.307 36.000 0.00 0.00 0.00 4.30
2161 2176 6.275494 TCATGTTAGAAGTGTATTGACCGA 57.725 37.500 0.00 0.00 0.00 4.69
2162 2177 6.961359 TTCATGTTAGAAGTGTATTGACCG 57.039 37.500 0.00 0.00 0.00 4.79
2163 2178 9.601217 ACTATTCATGTTAGAAGTGTATTGACC 57.399 33.333 10.94 0.00 0.00 4.02
2233 2248 9.847224 GTTGGGAATATTCCTTTAGAGACAATA 57.153 33.333 29.24 4.43 46.72 1.90
2234 2249 8.336235 TGTTGGGAATATTCCTTTAGAGACAAT 58.664 33.333 29.24 0.00 46.72 2.71
2235 2250 7.610305 GTGTTGGGAATATTCCTTTAGAGACAA 59.390 37.037 29.24 19.89 46.72 3.18
2236 2251 7.110155 GTGTTGGGAATATTCCTTTAGAGACA 58.890 38.462 29.24 19.69 46.72 3.41
2237 2252 6.542735 GGTGTTGGGAATATTCCTTTAGAGAC 59.457 42.308 29.24 18.71 46.72 3.36
2238 2253 6.216662 TGGTGTTGGGAATATTCCTTTAGAGA 59.783 38.462 29.24 10.32 46.72 3.10
2239 2254 6.423182 TGGTGTTGGGAATATTCCTTTAGAG 58.577 40.000 29.24 0.00 46.72 2.43
2240 2255 6.216662 TCTGGTGTTGGGAATATTCCTTTAGA 59.783 38.462 29.24 19.79 46.72 2.10
2241 2256 6.318900 GTCTGGTGTTGGGAATATTCCTTTAG 59.681 42.308 29.24 18.30 46.72 1.85
2242 2257 6.184789 GTCTGGTGTTGGGAATATTCCTTTA 58.815 40.000 29.24 15.93 46.72 1.85
2243 2258 5.016831 GTCTGGTGTTGGGAATATTCCTTT 58.983 41.667 29.24 0.00 46.72 3.11
2244 2259 4.569865 GGTCTGGTGTTGGGAATATTCCTT 60.570 45.833 29.24 0.00 46.72 3.36
2245 2260 3.053619 GGTCTGGTGTTGGGAATATTCCT 60.054 47.826 29.24 0.00 46.72 3.36
2246 2261 3.288092 GGTCTGGTGTTGGGAATATTCC 58.712 50.000 24.14 24.14 46.82 3.01
2247 2262 3.053619 AGGGTCTGGTGTTGGGAATATTC 60.054 47.826 6.93 6.93 0.00 1.75
2248 2263 2.926329 AGGGTCTGGTGTTGGGAATATT 59.074 45.455 0.00 0.00 0.00 1.28
2249 2264 2.573463 AGGGTCTGGTGTTGGGAATAT 58.427 47.619 0.00 0.00 0.00 1.28
2250 2265 2.041081 CAAGGGTCTGGTGTTGGGAATA 59.959 50.000 0.00 0.00 0.00 1.75
2251 2266 1.158007 AAGGGTCTGGTGTTGGGAAT 58.842 50.000 0.00 0.00 0.00 3.01
2252 2267 0.184933 CAAGGGTCTGGTGTTGGGAA 59.815 55.000 0.00 0.00 0.00 3.97
2253 2268 1.843421 CAAGGGTCTGGTGTTGGGA 59.157 57.895 0.00 0.00 0.00 4.37
2254 2269 1.903404 GCAAGGGTCTGGTGTTGGG 60.903 63.158 0.00 0.00 0.00 4.12
2255 2270 0.400213 TAGCAAGGGTCTGGTGTTGG 59.600 55.000 0.00 0.00 0.00 3.77
2256 2271 2.359900 GATAGCAAGGGTCTGGTGTTG 58.640 52.381 0.00 0.00 0.00 3.33
2257 2272 1.282157 GGATAGCAAGGGTCTGGTGTT 59.718 52.381 0.00 0.00 0.00 3.32
2258 2273 0.912486 GGATAGCAAGGGTCTGGTGT 59.088 55.000 0.00 0.00 0.00 4.16
2259 2274 0.181350 GGGATAGCAAGGGTCTGGTG 59.819 60.000 0.00 0.00 0.00 4.17
2260 2275 1.338136 CGGGATAGCAAGGGTCTGGT 61.338 60.000 0.00 0.00 0.00 4.00
2261 2276 1.447643 CGGGATAGCAAGGGTCTGG 59.552 63.158 0.00 0.00 0.00 3.86
2262 2277 1.227674 GCGGGATAGCAAGGGTCTG 60.228 63.158 0.00 0.00 37.05 3.51
2263 2278 1.689233 TGCGGGATAGCAAGGGTCT 60.689 57.895 0.00 0.00 45.06 3.85
2264 2279 2.908015 TGCGGGATAGCAAGGGTC 59.092 61.111 0.00 0.00 45.06 4.46
2270 2285 1.810606 GCTCTAGCTGCGGGATAGCA 61.811 60.000 0.00 0.00 45.96 3.49
2271 2286 1.080161 GCTCTAGCTGCGGGATAGC 60.080 63.158 0.00 0.00 41.43 2.97
2272 2287 1.589113 GGCTCTAGCTGCGGGATAG 59.411 63.158 0.00 0.00 41.70 2.08
2273 2288 1.908793 GGGCTCTAGCTGCGGGATA 60.909 63.158 0.00 0.00 41.70 2.59
2274 2289 3.237741 GGGCTCTAGCTGCGGGAT 61.238 66.667 0.00 0.00 41.70 3.85


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

AutoCloner maintained by Alex Coulton.