Multiple sequence alignment - TraesCS2D01G176100

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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 TraesCS2D01G176100 chr2D 100.000 3151 0 0 1 3151 119380759 119377609 0.000000e+00 5819.0
1 TraesCS2D01G176100 chr2B 93.579 1978 71 13 8 1981 171796498 171794573 0.000000e+00 2898.0
2 TraesCS2D01G176100 chr2B 88.998 918 44 18 2257 3151 171794436 171793553 0.000000e+00 1083.0
3 TraesCS2D01G176100 chr2B 96.377 138 4 1 2020 2157 171794571 171794435 3.160000e-55 226.0
4 TraesCS2D01G176100 chr2A 88.347 1416 95 29 755 2157 121596959 121595601 0.000000e+00 1637.0
5 TraesCS2D01G176100 chr2A 95.818 837 19 11 2323 3151 121595507 121594679 0.000000e+00 1338.0
6 TraesCS2D01G176100 chr2A 92.632 95 6 1 743 836 121622632 121622538 5.480000e-28 135.0
7 TraesCS2D01G176100 chr2A 93.671 79 5 0 2180 2258 715299606 715299528 5.520000e-23 119.0
8 TraesCS2D01G176100 chr5D 93.976 83 5 0 2180 2262 118840490 118840572 3.300000e-25 126.0
9 TraesCS2D01G176100 chr1A 94.937 79 4 0 2180 2258 168567594 168567516 1.190000e-24 124.0
10 TraesCS2D01G176100 chr7A 93.750 80 5 0 2180 2259 690523753 690523832 1.540000e-23 121.0
11 TraesCS2D01G176100 chr7A 97.059 34 1 0 2148 2181 528300237 528300204 1.220000e-04 58.4
12 TraesCS2D01G176100 chr5A 91.566 83 7 0 2180 2262 128432196 128432278 7.140000e-22 115.0
13 TraesCS2D01G176100 chr4D 93.506 77 5 0 2182 2258 51798099 51798175 7.140000e-22 115.0
14 TraesCS2D01G176100 chr4D 92.405 79 6 0 2180 2258 503357954 503358032 2.570000e-21 113.0
15 TraesCS2D01G176100 chr6B 92.405 79 6 0 2180 2258 229526697 229526619 2.570000e-21 113.0
16 TraesCS2D01G176100 chr3D 92.405 79 6 0 2180 2258 1899244 1899322 2.570000e-21 113.0


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 TraesCS2D01G176100 chr2D 119377609 119380759 3150 True 5819.000000 5819 100.000000 1 3151 1 chr2D.!!$R1 3150
1 TraesCS2D01G176100 chr2B 171793553 171796498 2945 True 1402.333333 2898 92.984667 8 3151 3 chr2B.!!$R1 3143
2 TraesCS2D01G176100 chr2A 121594679 121596959 2280 True 1487.500000 1637 92.082500 755 3151 2 chr2A.!!$R3 2396

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
265 266 0.109597 GATGGTTCAGCTGCAAACGG 60.11 55.0 9.47 0.0 0.0 4.44 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2155 2174 0.251742 TTTTCCGGACGGAGGGAGTA 60.252 55.0 13.64 0.0 46.06 2.59 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
42 43 6.345298 TGATAAACATGTTCCGCAAGAGATA 58.655 36.000 12.39 0.00 43.02 1.98
45 46 6.515272 AAACATGTTCCGCAAGAGATATTT 57.485 33.333 12.39 0.00 43.02 1.40
75 76 9.844257 TTGAGTTTTTGGACAATTATTGGAAAT 57.156 25.926 9.88 0.00 34.12 2.17
103 104 1.202076 GCAAGCAAAGCGATACTCCAC 60.202 52.381 0.00 0.00 0.00 4.02
106 107 1.003118 AGCAAAGCGATACTCCACCAA 59.997 47.619 0.00 0.00 0.00 3.67
160 161 1.092345 GCTCCGATCAAGGTGAAGGC 61.092 60.000 0.00 0.00 31.22 4.35
188 189 4.873810 TTGATCCCCGCGGCATGG 62.874 66.667 22.85 16.86 0.00 3.66
215 216 2.217038 ACTGGTGGATCGTGTGGCT 61.217 57.895 0.00 0.00 0.00 4.75
221 222 1.409064 GTGGATCGTGTGGCTCTATCA 59.591 52.381 0.00 0.00 0.00 2.15
264 265 0.592637 TGATGGTTCAGCTGCAAACG 59.407 50.000 9.47 0.00 0.00 3.60
265 266 0.109597 GATGGTTCAGCTGCAAACGG 60.110 55.000 9.47 0.00 0.00 4.44
318 319 1.247567 GTTTGCAGCCTACCATGTGT 58.752 50.000 0.00 0.00 0.00 3.72
401 402 3.010027 TGGCCATCCAACACTCAGAATTA 59.990 43.478 0.00 0.00 39.99 1.40
439 441 4.036971 GTCGATTCTTCTAAGGCTCTAGCA 59.963 45.833 4.07 0.00 44.36 3.49
444 446 4.551671 TCTTCTAAGGCTCTAGCAATCCT 58.448 43.478 4.07 0.00 44.36 3.24
447 449 5.991933 TCTAAGGCTCTAGCAATCCTATG 57.008 43.478 4.07 0.00 44.36 2.23
448 450 5.645201 TCTAAGGCTCTAGCAATCCTATGA 58.355 41.667 4.07 0.00 44.36 2.15
506 508 2.096174 GCAGCAGAGATCAAAGCTCTTG 59.904 50.000 0.00 0.00 40.60 3.02
555 557 8.153550 ACAGAAGCTCAATAGGGAACATAATAG 58.846 37.037 0.00 0.00 0.00 1.73
556 558 7.605691 CAGAAGCTCAATAGGGAACATAATAGG 59.394 40.741 0.00 0.00 0.00 2.57
557 559 7.514127 AGAAGCTCAATAGGGAACATAATAGGA 59.486 37.037 0.00 0.00 0.00 2.94
558 560 7.821134 AGCTCAATAGGGAACATAATAGGAT 57.179 36.000 0.00 0.00 0.00 3.24
559 561 8.917414 AGCTCAATAGGGAACATAATAGGATA 57.083 34.615 0.00 0.00 0.00 2.59
560 562 8.986991 AGCTCAATAGGGAACATAATAGGATAG 58.013 37.037 0.00 0.00 0.00 2.08
603 605 7.464710 GCTTGTACATATGAAGTCTTGTACTGC 60.465 40.741 10.38 11.17 42.98 4.40
628 630 2.058595 GCTCCTTAGAGGTCCGCCA 61.059 63.158 0.00 0.00 40.79 5.69
637 639 2.050144 AGAGGTCCGCCATGTATCAAT 58.950 47.619 0.00 0.00 37.19 2.57
699 701 6.806217 TGGAATAAAACTCCTATTTTCCCCA 58.194 36.000 0.00 0.00 33.80 4.96
727 732 5.555966 AGAAAAAGTGGCTCTTCTCCTTAG 58.444 41.667 1.81 0.00 35.02 2.18
876 889 4.402056 AAATCGATACCATGGTTCGAGT 57.598 40.909 34.14 31.90 39.20 4.18
884 899 1.134965 CCATGGTTCGAGTGAGACTCC 60.135 57.143 2.57 0.00 42.12 3.85
899 914 7.171653 AGTGAGACTCCGATCAGATGATATAA 58.828 38.462 0.00 0.00 34.37 0.98
901 916 6.375736 TGAGACTCCGATCAGATGATATAACC 59.624 42.308 0.00 0.00 34.37 2.85
932 947 1.810755 ACACACGATCGAACTAGCAGA 59.189 47.619 24.34 0.00 0.00 4.26
953 968 6.293955 GCAGAACAAGCCAAGAACTTATGTTA 60.294 38.462 0.00 0.00 36.39 2.41
955 972 7.805071 CAGAACAAGCCAAGAACTTATGTTAAG 59.195 37.037 0.00 0.00 36.39 1.85
1331 1348 1.509923 GACCTGTACTTCCGGTCGG 59.490 63.158 0.00 2.52 39.80 4.79
1373 1390 2.593978 CCTGCTGGATCACCTGGG 59.406 66.667 2.92 0.00 35.96 4.45
1485 1502 2.414559 CGCTTCTCGTAACCGTCCTTTA 60.415 50.000 0.00 0.00 35.01 1.85
1526 1543 3.443925 CTCTGACTCTCGGGCGCA 61.444 66.667 10.83 0.00 0.00 6.09
1578 1595 1.474332 AAGAAGGTTCACCGGCGGTA 61.474 55.000 33.65 15.50 42.08 4.02
1729 1746 2.044352 TCGATCAGGGCACGGAGA 60.044 61.111 0.00 0.00 0.00 3.71
1733 1750 1.112113 GATCAGGGCACGGAGAGTAA 58.888 55.000 0.00 0.00 0.00 2.24
1887 1904 0.247736 GTGACCTGGAGACGCATCTT 59.752 55.000 0.00 0.00 34.34 2.40
1888 1905 1.476891 GTGACCTGGAGACGCATCTTA 59.523 52.381 0.00 0.00 34.34 2.10
1889 1906 1.751351 TGACCTGGAGACGCATCTTAG 59.249 52.381 0.00 0.00 34.34 2.18
1965 1983 1.521423 GCCGTACACGCATGAATCTAC 59.479 52.381 0.00 0.00 38.18 2.59
1969 1987 4.261072 CCGTACACGCATGAATCTACTAGT 60.261 45.833 0.00 0.00 38.18 2.57
1970 1988 5.049886 CCGTACACGCATGAATCTACTAGTA 60.050 44.000 1.89 1.89 38.18 1.82
1971 1989 6.072098 CGTACACGCATGAATCTACTAGTAG 58.928 44.000 21.87 21.87 34.56 2.57
1972 1990 6.073927 CGTACACGCATGAATCTACTAGTAGA 60.074 42.308 29.96 29.96 45.24 2.59
1973 1991 6.307031 ACACGCATGAATCTACTAGTAGAG 57.693 41.667 30.78 20.42 44.47 2.43
1974 1992 6.056236 ACACGCATGAATCTACTAGTAGAGA 58.944 40.000 30.78 20.13 44.47 3.10
1975 1993 6.712998 ACACGCATGAATCTACTAGTAGAGAT 59.287 38.462 30.78 23.64 44.47 2.75
1976 1994 7.094975 ACACGCATGAATCTACTAGTAGAGATC 60.095 40.741 30.78 28.46 44.47 2.75
1977 1995 6.091577 ACGCATGAATCTACTAGTAGAGATCG 59.908 42.308 30.78 26.22 44.47 3.69
1978 1996 6.311690 CGCATGAATCTACTAGTAGAGATCGA 59.688 42.308 30.78 21.50 44.47 3.59
1979 1997 7.148557 CGCATGAATCTACTAGTAGAGATCGAA 60.149 40.741 30.78 18.84 44.47 3.71
1980 1998 8.673711 GCATGAATCTACTAGTAGAGATCGAAT 58.326 37.037 30.78 19.85 44.47 3.34
2139 2158 1.900351 TGGTTCGATGAGGAGCCAG 59.100 57.895 0.00 0.00 41.63 4.85
2165 2184 5.609533 TTCCTTAGAAAATACTCCCTCCG 57.390 43.478 0.00 0.00 0.00 4.63
2166 2185 4.617593 TCCTTAGAAAATACTCCCTCCGT 58.382 43.478 0.00 0.00 0.00 4.69
2167 2186 4.648307 TCCTTAGAAAATACTCCCTCCGTC 59.352 45.833 0.00 0.00 0.00 4.79
2168 2187 4.202233 CCTTAGAAAATACTCCCTCCGTCC 60.202 50.000 0.00 0.00 0.00 4.79
2169 2188 1.755380 AGAAAATACTCCCTCCGTCCG 59.245 52.381 0.00 0.00 0.00 4.79
2170 2189 0.828677 AAAATACTCCCTCCGTCCGG 59.171 55.000 0.00 0.00 0.00 5.14
2171 2190 0.032813 AAATACTCCCTCCGTCCGGA 60.033 55.000 0.00 0.00 42.90 5.14
2172 2191 0.032813 AATACTCCCTCCGTCCGGAA 60.033 55.000 5.23 0.00 44.66 4.30
2173 2192 0.032813 ATACTCCCTCCGTCCGGAAA 60.033 55.000 5.23 0.00 44.66 3.13
2174 2193 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
2175 2194 1.123246 ACTCCCTCCGTCCGGAAAAA 61.123 55.000 5.23 0.00 44.66 1.94
2176 2195 0.672711 CTCCCTCCGTCCGGAAAAAC 60.673 60.000 5.23 0.00 44.66 2.43
2177 2196 1.123246 TCCCTCCGTCCGGAAAAACT 61.123 55.000 5.23 0.00 44.66 2.66
2178 2197 0.672711 CCCTCCGTCCGGAAAAACTC 60.673 60.000 5.23 0.00 44.66 3.01
2179 2198 1.012486 CCTCCGTCCGGAAAAACTCG 61.012 60.000 5.23 3.90 44.66 4.18
2180 2199 0.319297 CTCCGTCCGGAAAAACTCGT 60.319 55.000 5.23 0.00 44.66 4.18
2181 2200 0.958091 TCCGTCCGGAAAAACTCGTA 59.042 50.000 5.23 0.00 42.05 3.43
2182 2201 1.545582 TCCGTCCGGAAAAACTCGTAT 59.454 47.619 5.23 0.00 42.05 3.06
2183 2202 2.029110 TCCGTCCGGAAAAACTCGTATT 60.029 45.455 5.23 0.00 42.05 1.89
2184 2203 2.738314 CCGTCCGGAAAAACTCGTATTT 59.262 45.455 5.23 0.00 37.50 1.40
2185 2204 3.925913 CCGTCCGGAAAAACTCGTATTTA 59.074 43.478 5.23 0.00 37.50 1.40
2186 2205 4.032104 CCGTCCGGAAAAACTCGTATTTAG 59.968 45.833 5.23 0.00 37.50 1.85
2187 2206 4.491441 CGTCCGGAAAAACTCGTATTTAGC 60.491 45.833 5.23 0.00 0.00 3.09
2188 2207 4.389687 GTCCGGAAAAACTCGTATTTAGCA 59.610 41.667 5.23 0.00 0.00 3.49
2189 2208 4.389687 TCCGGAAAAACTCGTATTTAGCAC 59.610 41.667 0.00 0.00 0.00 4.40
2190 2209 4.436451 CCGGAAAAACTCGTATTTAGCACC 60.436 45.833 0.00 0.00 0.00 5.01
2191 2210 4.152759 CGGAAAAACTCGTATTTAGCACCA 59.847 41.667 0.00 0.00 0.00 4.17
2192 2211 5.334260 CGGAAAAACTCGTATTTAGCACCAA 60.334 40.000 0.00 0.00 0.00 3.67
2193 2212 6.084277 GGAAAAACTCGTATTTAGCACCAAG 58.916 40.000 0.00 0.00 0.00 3.61
2194 2213 6.293790 GGAAAAACTCGTATTTAGCACCAAGT 60.294 38.462 0.00 0.00 0.00 3.16
2195 2214 6.628919 AAAACTCGTATTTAGCACCAAGTT 57.371 33.333 0.00 0.00 0.00 2.66
2196 2215 7.733402 AAAACTCGTATTTAGCACCAAGTTA 57.267 32.000 0.00 0.00 0.00 2.24
2197 2216 7.733402 AAACTCGTATTTAGCACCAAGTTAA 57.267 32.000 0.00 0.00 0.00 2.01
2198 2217 7.916914 AACTCGTATTTAGCACCAAGTTAAT 57.083 32.000 0.00 0.00 0.00 1.40
2199 2218 7.303634 ACTCGTATTTAGCACCAAGTTAATG 57.696 36.000 0.00 0.00 0.00 1.90
2200 2219 6.114221 TCGTATTTAGCACCAAGTTAATGC 57.886 37.500 2.91 2.91 39.74 3.56
2209 2228 6.867662 GCACCAAGTTAATGCTAGATACAT 57.132 37.500 0.00 0.00 36.40 2.29
2210 2229 6.892691 GCACCAAGTTAATGCTAGATACATC 58.107 40.000 0.00 0.00 36.40 3.06
2211 2230 6.073003 GCACCAAGTTAATGCTAGATACATCC 60.073 42.308 0.00 0.00 36.40 3.51
2212 2231 6.992123 CACCAAGTTAATGCTAGATACATCCA 59.008 38.462 0.00 0.00 0.00 3.41
2213 2232 7.172190 CACCAAGTTAATGCTAGATACATCCAG 59.828 40.741 0.00 0.00 0.00 3.86
2214 2233 7.147479 ACCAAGTTAATGCTAGATACATCCAGT 60.147 37.037 0.00 0.00 0.00 4.00
2215 2234 7.716998 CCAAGTTAATGCTAGATACATCCAGTT 59.283 37.037 0.00 0.00 0.00 3.16
2216 2235 8.554528 CAAGTTAATGCTAGATACATCCAGTTG 58.445 37.037 0.00 0.00 0.00 3.16
2217 2236 8.023021 AGTTAATGCTAGATACATCCAGTTGA 57.977 34.615 0.00 0.00 0.00 3.18
2218 2237 8.147058 AGTTAATGCTAGATACATCCAGTTGAG 58.853 37.037 0.00 0.00 0.00 3.02
2219 2238 6.737720 AATGCTAGATACATCCAGTTGAGA 57.262 37.500 0.00 0.00 0.00 3.27
2220 2239 5.781210 TGCTAGATACATCCAGTTGAGAG 57.219 43.478 0.00 0.00 0.00 3.20
2221 2240 5.449553 TGCTAGATACATCCAGTTGAGAGA 58.550 41.667 0.00 0.00 0.00 3.10
2222 2241 5.300539 TGCTAGATACATCCAGTTGAGAGAC 59.699 44.000 0.00 0.00 0.00 3.36
2223 2242 5.300539 GCTAGATACATCCAGTTGAGAGACA 59.699 44.000 0.00 0.00 0.00 3.41
2224 2243 6.183360 GCTAGATACATCCAGTTGAGAGACAA 60.183 42.308 0.00 0.00 36.02 3.18
2225 2244 6.219417 AGATACATCCAGTTGAGAGACAAG 57.781 41.667 0.00 0.00 39.30 3.16
2226 2245 3.051081 ACATCCAGTTGAGAGACAAGC 57.949 47.619 0.00 0.00 39.30 4.01
2227 2246 2.636893 ACATCCAGTTGAGAGACAAGCT 59.363 45.455 0.00 0.00 39.30 3.74
2228 2247 3.072184 ACATCCAGTTGAGAGACAAGCTT 59.928 43.478 0.00 0.00 39.30 3.74
2229 2248 3.117491 TCCAGTTGAGAGACAAGCTTG 57.883 47.619 24.84 24.84 39.30 4.01
2230 2249 2.700371 TCCAGTTGAGAGACAAGCTTGA 59.300 45.455 32.50 6.30 39.30 3.02
2231 2250 3.065655 CCAGTTGAGAGACAAGCTTGAG 58.934 50.000 32.50 7.94 39.30 3.02
2232 2251 3.244009 CCAGTTGAGAGACAAGCTTGAGA 60.244 47.826 32.50 6.59 39.30 3.27
2233 2252 3.740321 CAGTTGAGAGACAAGCTTGAGAC 59.260 47.826 32.50 20.78 39.30 3.36
2234 2253 3.386078 AGTTGAGAGACAAGCTTGAGACA 59.614 43.478 32.50 19.34 39.30 3.41
2235 2254 4.122776 GTTGAGAGACAAGCTTGAGACAA 58.877 43.478 32.50 23.06 39.30 3.18
2236 2255 3.987547 TGAGAGACAAGCTTGAGACAAG 58.012 45.455 32.50 4.70 0.00 3.16
2237 2256 3.386078 TGAGAGACAAGCTTGAGACAAGT 59.614 43.478 32.50 8.41 0.00 3.16
2238 2257 4.141846 TGAGAGACAAGCTTGAGACAAGTT 60.142 41.667 32.50 7.60 0.00 2.66
2239 2258 4.775236 AGAGACAAGCTTGAGACAAGTTT 58.225 39.130 32.50 6.80 0.00 2.66
2240 2259 5.189180 AGAGACAAGCTTGAGACAAGTTTT 58.811 37.500 32.50 5.99 0.00 2.43
2241 2260 5.649831 AGAGACAAGCTTGAGACAAGTTTTT 59.350 36.000 32.50 5.43 0.00 1.94
2280 2299 8.001875 AGTAAGAAGCTGAGGATTCATAGTAGA 58.998 37.037 0.00 0.00 39.98 2.59
2305 2324 0.038983 TCCGATTCGTCTGCGTCAAA 60.039 50.000 5.20 0.00 39.49 2.69
2308 2327 1.057847 CGATTCGTCTGCGTCAAAGAC 59.942 52.381 0.00 0.00 40.59 3.01
2385 2435 2.294233 TGTTTCAATGTGCCTGAGCTTC 59.706 45.455 0.00 0.00 40.80 3.86
2651 2704 2.711547 ACCAAACCTAGGAAAGAGCACT 59.288 45.455 17.98 0.00 0.00 4.40
2679 2733 0.306533 GCAGACGGCGAGTTGAAAAA 59.693 50.000 16.62 0.00 0.00 1.94
2692 2746 2.825532 GTTGAAAAATAGCAGGCCCAGA 59.174 45.455 0.00 0.00 0.00 3.86
2774 2837 3.264193 AGGCTACACCACATGATTCTTCA 59.736 43.478 0.00 0.00 43.14 3.02
2980 3052 1.239347 GCAGTTCCAGTTCCAGTTCC 58.761 55.000 0.00 0.00 0.00 3.62
2981 3053 1.476833 GCAGTTCCAGTTCCAGTTCCA 60.477 52.381 0.00 0.00 0.00 3.53
2982 3054 2.498167 CAGTTCCAGTTCCAGTTCCAG 58.502 52.381 0.00 0.00 0.00 3.86
2983 3055 2.127708 AGTTCCAGTTCCAGTTCCAGT 58.872 47.619 0.00 0.00 0.00 4.00
2984 3056 2.509964 AGTTCCAGTTCCAGTTCCAGTT 59.490 45.455 0.00 0.00 0.00 3.16
2985 3057 2.879026 GTTCCAGTTCCAGTTCCAGTTC 59.121 50.000 0.00 0.00 0.00 3.01
3005 3077 3.462982 TCCATTCCATAATCGGACAACG 58.537 45.455 0.00 0.00 46.11 4.10
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 8.490355 CAAAAACTCAACCAAAATATCTCTTGC 58.510 33.333 0.00 0.00 0.00 4.01
42 43 7.936496 AATTGTCCAAAAACTCAACCAAAAT 57.064 28.000 0.00 0.00 0.00 1.82
45 46 7.497249 CCAATAATTGTCCAAAAACTCAACCAA 59.503 33.333 0.00 0.00 0.00 3.67
75 76 2.150390 TCGCTTTGCTTGCACAATAGA 58.850 42.857 0.00 0.00 0.00 1.98
103 104 4.034048 CGTTCCCTTTAATCATCTCGTTGG 59.966 45.833 0.00 0.00 0.00 3.77
106 107 4.081862 TCACGTTCCCTTTAATCATCTCGT 60.082 41.667 0.00 0.00 0.00 4.18
171 172 4.873810 CCATGCCGCGGGGATCAA 62.874 66.667 29.38 4.30 29.13 2.57
212 213 2.435805 TGACCCATCAACTGATAGAGCC 59.564 50.000 0.00 0.00 32.63 4.70
215 216 6.962182 AGAAAATGACCCATCAACTGATAGA 58.038 36.000 0.00 0.00 38.69 1.98
221 222 7.890127 TCATTAGAAGAAAATGACCCATCAACT 59.110 33.333 0.00 0.00 38.19 3.16
264 265 0.654683 GCACGTCTCAGAATCATGCC 59.345 55.000 0.00 0.00 0.00 4.40
265 266 1.649664 AGCACGTCTCAGAATCATGC 58.350 50.000 0.00 0.00 0.00 4.06
273 274 4.485554 GCCACTAGCACGTCTCAG 57.514 61.111 0.00 0.00 42.97 3.35
292 293 0.821711 GTAGGCTGCAAACACCACCA 60.822 55.000 0.50 0.00 0.00 4.17
337 338 3.120095 TGCATGAATCTCTGCTTTCAACG 60.120 43.478 0.00 0.00 39.16 4.10
342 343 3.682696 TGAGTGCATGAATCTCTGCTTT 58.317 40.909 0.00 0.00 39.16 3.51
401 402 1.671979 TCGACTGGACGATAATCGGT 58.328 50.000 0.00 0.00 45.59 4.69
439 441 9.401058 CTGAAAAGGTTATCACTTCATAGGATT 57.599 33.333 0.00 0.00 0.00 3.01
444 446 7.110155 GGACCTGAAAAGGTTATCACTTCATA 58.890 38.462 0.00 0.00 43.24 2.15
447 449 4.392138 CGGACCTGAAAAGGTTATCACTTC 59.608 45.833 0.00 0.00 43.24 3.01
448 450 4.324267 CGGACCTGAAAAGGTTATCACTT 58.676 43.478 0.00 0.00 43.24 3.16
520 522 6.774656 CCCTATTGAGCTTCTGTGGAATAAAT 59.225 38.462 0.00 0.00 0.00 1.40
541 543 7.130775 GCTACCCTATCCTATTATGTTCCCTA 58.869 42.308 0.00 0.00 0.00 3.53
555 557 2.031495 ACTGATGGGCTACCCTATCC 57.969 55.000 3.93 0.00 45.73 2.59
556 558 2.039084 CCAACTGATGGGCTACCCTATC 59.961 54.545 3.93 6.24 46.30 2.08
557 559 2.057922 CCAACTGATGGGCTACCCTAT 58.942 52.381 3.93 0.00 46.27 2.57
558 560 1.507140 CCAACTGATGGGCTACCCTA 58.493 55.000 3.93 0.00 46.27 3.53
559 561 2.311287 CCAACTGATGGGCTACCCT 58.689 57.895 3.93 0.00 46.27 4.34
560 562 4.986467 CCAACTGATGGGCTACCC 57.014 61.111 0.00 0.00 46.27 3.69
571 573 5.877012 AGACTTCATATGTACAAGCCAACTG 59.123 40.000 0.00 0.00 0.00 3.16
603 605 3.282885 GGACCTCTAAGGAGCCAAATTG 58.717 50.000 0.00 0.00 37.67 2.32
628 630 7.994911 TCAAGAGGCAATAACTCATTGATACAT 59.005 33.333 1.26 0.00 45.99 2.29
637 639 9.679661 TTATTACAATCAAGAGGCAATAACTCA 57.320 29.630 0.00 0.00 37.43 3.41
680 682 5.954757 TGTGTGGGGAAAATAGGAGTTTTA 58.045 37.500 0.00 0.00 31.80 1.52
699 701 4.273318 AGAAGAGCCACTTTTTCTTGTGT 58.727 39.130 0.00 0.00 39.13 3.72
727 732 3.746492 TCGCTCTTTGCTCCTAGTTTTTC 59.254 43.478 0.00 0.00 40.11 2.29
876 889 6.375736 GGTTATATCATCTGATCGGAGTCTCA 59.624 42.308 10.61 0.00 36.05 3.27
884 899 6.071672 ACTGTGGAGGTTATATCATCTGATCG 60.072 42.308 0.00 0.00 36.05 3.69
899 914 1.830145 GTGTGTGGACTGTGGAGGT 59.170 57.895 0.00 0.00 0.00 3.85
901 916 0.318441 ATCGTGTGTGGACTGTGGAG 59.682 55.000 0.00 0.00 0.00 3.86
932 947 7.817418 TCTTAACATAAGTTCTTGGCTTGTT 57.183 32.000 0.00 0.00 39.15 2.83
1506 1523 2.046864 CGCCCGAGAGTCAGAGGAA 61.047 63.158 0.00 0.00 0.00 3.36
1526 1543 2.670148 GCCAATGGGGGAGACGAGT 61.670 63.158 0.00 0.00 37.04 4.18
1578 1595 4.070552 GCGTTCTCCAGGGCGTCT 62.071 66.667 0.00 0.00 0.00 4.18
1869 1886 1.751351 CTAAGATGCGTCTCCAGGTCA 59.249 52.381 9.35 0.00 32.15 4.02
1871 1888 0.461961 GCTAAGATGCGTCTCCAGGT 59.538 55.000 9.35 0.00 32.15 4.00
1989 2007 6.958752 CAGCAATGATTCGTATACGTCAAAAA 59.041 34.615 23.67 11.48 40.80 1.94
1990 2008 6.474364 CAGCAATGATTCGTATACGTCAAAA 58.526 36.000 23.67 11.84 40.80 2.44
1991 2009 5.501736 GCAGCAATGATTCGTATACGTCAAA 60.502 40.000 23.67 12.19 40.80 2.69
1992 2010 4.026062 GCAGCAATGATTCGTATACGTCAA 60.026 41.667 23.67 12.89 40.80 3.18
1993 2011 3.489416 GCAGCAATGATTCGTATACGTCA 59.511 43.478 23.67 20.38 40.80 4.35
1994 2012 3.120991 GGCAGCAATGATTCGTATACGTC 60.121 47.826 23.67 15.65 40.80 4.34
1995 2013 2.800544 GGCAGCAATGATTCGTATACGT 59.199 45.455 23.67 6.63 40.80 3.57
1996 2014 2.799978 TGGCAGCAATGATTCGTATACG 59.200 45.455 19.23 19.23 41.45 3.06
1997 2015 4.273480 ACTTGGCAGCAATGATTCGTATAC 59.727 41.667 0.00 0.00 0.00 1.47
1998 2016 4.450976 ACTTGGCAGCAATGATTCGTATA 58.549 39.130 0.00 0.00 0.00 1.47
1999 2017 3.282021 ACTTGGCAGCAATGATTCGTAT 58.718 40.909 0.00 0.00 0.00 3.06
2000 2018 2.710377 ACTTGGCAGCAATGATTCGTA 58.290 42.857 0.00 0.00 0.00 3.43
2001 2019 1.538047 ACTTGGCAGCAATGATTCGT 58.462 45.000 0.00 0.00 0.00 3.85
2155 2174 0.251742 TTTTCCGGACGGAGGGAGTA 60.252 55.000 13.64 0.00 46.06 2.59
2156 2175 1.123246 TTTTTCCGGACGGAGGGAGT 61.123 55.000 13.64 0.00 46.06 3.85
2157 2176 0.672711 GTTTTTCCGGACGGAGGGAG 60.673 60.000 13.64 0.00 46.06 4.30
2158 2177 1.123246 AGTTTTTCCGGACGGAGGGA 61.123 55.000 13.64 1.83 46.06 4.20
2159 2178 0.672711 GAGTTTTTCCGGACGGAGGG 60.673 60.000 13.64 0.00 46.06 4.30
2160 2179 1.012486 CGAGTTTTTCCGGACGGAGG 61.012 60.000 13.64 0.00 46.06 4.30
2161 2180 0.319297 ACGAGTTTTTCCGGACGGAG 60.319 55.000 13.64 3.15 46.06 4.63
2162 2181 0.958091 TACGAGTTTTTCCGGACGGA 59.042 50.000 1.83 9.76 43.52 4.69
2163 2182 2.000429 ATACGAGTTTTTCCGGACGG 58.000 50.000 1.83 3.96 0.00 4.79
2164 2183 4.491441 GCTAAATACGAGTTTTTCCGGACG 60.491 45.833 1.83 5.89 0.00 4.79
2165 2184 4.389687 TGCTAAATACGAGTTTTTCCGGAC 59.610 41.667 1.83 0.00 0.00 4.79
2166 2185 4.389687 GTGCTAAATACGAGTTTTTCCGGA 59.610 41.667 0.00 0.00 0.00 5.14
2167 2186 4.436451 GGTGCTAAATACGAGTTTTTCCGG 60.436 45.833 0.00 0.00 0.00 5.14
2168 2187 4.152759 TGGTGCTAAATACGAGTTTTTCCG 59.847 41.667 0.00 0.00 0.00 4.30
2169 2188 5.616488 TGGTGCTAAATACGAGTTTTTCC 57.384 39.130 0.00 0.00 0.00 3.13
2170 2189 6.665465 ACTTGGTGCTAAATACGAGTTTTTC 58.335 36.000 0.00 0.00 0.00 2.29
2171 2190 6.628919 ACTTGGTGCTAAATACGAGTTTTT 57.371 33.333 0.00 0.00 0.00 1.94
2172 2191 6.628919 AACTTGGTGCTAAATACGAGTTTT 57.371 33.333 0.00 0.00 0.00 2.43
2173 2192 7.733402 TTAACTTGGTGCTAAATACGAGTTT 57.267 32.000 0.00 0.00 31.79 2.66
2174 2193 7.625606 GCATTAACTTGGTGCTAAATACGAGTT 60.626 37.037 0.00 0.00 36.02 3.01
2175 2194 6.183360 GCATTAACTTGGTGCTAAATACGAGT 60.183 38.462 0.00 0.00 36.02 4.18
2176 2195 6.037172 AGCATTAACTTGGTGCTAAATACGAG 59.963 38.462 0.00 0.00 46.54 4.18
2177 2196 5.878116 AGCATTAACTTGGTGCTAAATACGA 59.122 36.000 0.00 0.00 46.54 3.43
2178 2197 6.119144 AGCATTAACTTGGTGCTAAATACG 57.881 37.500 0.00 0.00 46.54 3.06
2184 2203 7.119709 TGTATCTAGCATTAACTTGGTGCTA 57.880 36.000 7.35 7.35 46.54 3.49
2186 2205 6.073003 GGATGTATCTAGCATTAACTTGGTGC 60.073 42.308 0.00 0.00 39.10 5.01
2187 2206 6.992123 TGGATGTATCTAGCATTAACTTGGTG 59.008 38.462 0.00 0.00 0.00 4.17
2188 2207 7.136822 TGGATGTATCTAGCATTAACTTGGT 57.863 36.000 0.00 0.00 0.00 3.67
2189 2208 7.220030 ACTGGATGTATCTAGCATTAACTTGG 58.780 38.462 5.29 0.00 38.79 3.61
2190 2209 8.554528 CAACTGGATGTATCTAGCATTAACTTG 58.445 37.037 5.29 0.00 38.79 3.16
2191 2210 8.486210 TCAACTGGATGTATCTAGCATTAACTT 58.514 33.333 5.29 0.00 38.79 2.66
2192 2211 8.023021 TCAACTGGATGTATCTAGCATTAACT 57.977 34.615 5.29 0.00 38.79 2.24
2193 2212 8.144478 TCTCAACTGGATGTATCTAGCATTAAC 58.856 37.037 5.29 0.00 38.79 2.01
2194 2213 8.250143 TCTCAACTGGATGTATCTAGCATTAA 57.750 34.615 5.29 0.00 38.79 1.40
2195 2214 7.725844 TCTCTCAACTGGATGTATCTAGCATTA 59.274 37.037 5.29 0.00 38.79 1.90
2196 2215 6.552725 TCTCTCAACTGGATGTATCTAGCATT 59.447 38.462 5.29 0.00 38.79 3.56
2197 2216 6.015519 GTCTCTCAACTGGATGTATCTAGCAT 60.016 42.308 5.29 0.00 38.79 3.79
2198 2217 5.300539 GTCTCTCAACTGGATGTATCTAGCA 59.699 44.000 5.29 0.00 38.79 3.49
2199 2218 5.300539 TGTCTCTCAACTGGATGTATCTAGC 59.699 44.000 5.29 0.00 38.79 3.42
2200 2219 6.951062 TGTCTCTCAACTGGATGTATCTAG 57.049 41.667 3.98 3.98 40.74 2.43
2201 2220 6.183360 GCTTGTCTCTCAACTGGATGTATCTA 60.183 42.308 0.00 0.00 32.18 1.98
2202 2221 5.395103 GCTTGTCTCTCAACTGGATGTATCT 60.395 44.000 0.00 0.00 32.18 1.98
2203 2222 4.808364 GCTTGTCTCTCAACTGGATGTATC 59.192 45.833 0.00 0.00 32.18 2.24
2204 2223 4.469227 AGCTTGTCTCTCAACTGGATGTAT 59.531 41.667 0.00 0.00 32.18 2.29
2205 2224 3.834813 AGCTTGTCTCTCAACTGGATGTA 59.165 43.478 0.00 0.00 32.18 2.29
2206 2225 2.636893 AGCTTGTCTCTCAACTGGATGT 59.363 45.455 0.00 0.00 32.18 3.06
2207 2226 3.331478 AGCTTGTCTCTCAACTGGATG 57.669 47.619 0.00 0.00 32.18 3.51
2208 2227 3.326006 TCAAGCTTGTCTCTCAACTGGAT 59.674 43.478 25.19 0.00 32.18 3.41
2209 2228 2.700371 TCAAGCTTGTCTCTCAACTGGA 59.300 45.455 25.19 0.00 32.18 3.86
2210 2229 3.065655 CTCAAGCTTGTCTCTCAACTGG 58.934 50.000 25.19 0.00 32.18 4.00
2211 2230 3.740321 GTCTCAAGCTTGTCTCTCAACTG 59.260 47.826 25.19 0.00 32.18 3.16
2212 2231 3.386078 TGTCTCAAGCTTGTCTCTCAACT 59.614 43.478 25.19 0.00 32.18 3.16
2213 2232 3.722147 TGTCTCAAGCTTGTCTCTCAAC 58.278 45.455 25.19 13.68 32.18 3.18
2214 2233 4.141846 ACTTGTCTCAAGCTTGTCTCTCAA 60.142 41.667 25.19 19.91 34.61 3.02
2215 2234 3.386078 ACTTGTCTCAAGCTTGTCTCTCA 59.614 43.478 25.19 15.00 0.00 3.27
2216 2235 3.988819 ACTTGTCTCAAGCTTGTCTCTC 58.011 45.455 25.19 12.90 0.00 3.20
2217 2236 4.414337 AACTTGTCTCAAGCTTGTCTCT 57.586 40.909 25.19 1.20 0.00 3.10
2218 2237 5.491635 AAAACTTGTCTCAAGCTTGTCTC 57.508 39.130 25.19 16.00 0.00 3.36
2219 2238 5.904362 AAAAACTTGTCTCAAGCTTGTCT 57.096 34.783 25.19 0.72 0.00 3.41
2238 2257 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
2239 2258 1.547372 CTTACTCCCTCCGTCCGAAAA 59.453 52.381 0.00 0.00 0.00 2.29
2240 2259 1.180029 CTTACTCCCTCCGTCCGAAA 58.820 55.000 0.00 0.00 0.00 3.46
2241 2260 0.329261 TCTTACTCCCTCCGTCCGAA 59.671 55.000 0.00 0.00 0.00 4.30
2242 2261 0.329261 TTCTTACTCCCTCCGTCCGA 59.671 55.000 0.00 0.00 0.00 4.55
2243 2262 0.739561 CTTCTTACTCCCTCCGTCCG 59.260 60.000 0.00 0.00 0.00 4.79
2244 2263 0.460722 GCTTCTTACTCCCTCCGTCC 59.539 60.000 0.00 0.00 0.00 4.79
2245 2264 1.135333 CAGCTTCTTACTCCCTCCGTC 59.865 57.143 0.00 0.00 0.00 4.79
2246 2265 1.187087 CAGCTTCTTACTCCCTCCGT 58.813 55.000 0.00 0.00 0.00 4.69
2247 2266 1.407258 CTCAGCTTCTTACTCCCTCCG 59.593 57.143 0.00 0.00 0.00 4.63
2248 2267 1.760029 CCTCAGCTTCTTACTCCCTCC 59.240 57.143 0.00 0.00 0.00 4.30
2249 2268 2.741145 TCCTCAGCTTCTTACTCCCTC 58.259 52.381 0.00 0.00 0.00 4.30
2250 2269 2.930109 TCCTCAGCTTCTTACTCCCT 57.070 50.000 0.00 0.00 0.00 4.20
2251 2270 3.452627 TGAATCCTCAGCTTCTTACTCCC 59.547 47.826 0.00 0.00 0.00 4.30
2252 2271 4.744795 TGAATCCTCAGCTTCTTACTCC 57.255 45.455 0.00 0.00 0.00 3.85
2253 2272 7.049799 ACTATGAATCCTCAGCTTCTTACTC 57.950 40.000 0.00 0.00 34.23 2.59
2254 2273 8.001875 TCTACTATGAATCCTCAGCTTCTTACT 58.998 37.037 0.00 0.00 34.23 2.24
2255 2274 8.172352 TCTACTATGAATCCTCAGCTTCTTAC 57.828 38.462 0.00 0.00 34.23 2.34
2280 2299 1.799181 CGCAGACGAATCGGATTGTCT 60.799 52.381 20.39 20.39 43.93 3.41
2305 2324 1.447489 GCGAGCACATCAGCAGTCT 60.447 57.895 0.00 0.00 36.85 3.24
2308 2327 1.146957 GAGAGCGAGCACATCAGCAG 61.147 60.000 0.00 0.00 36.85 4.24
2385 2435 2.225727 GCCCGAAACTGTCCTGTAAAAG 59.774 50.000 0.00 0.00 0.00 2.27
2424 2475 6.042552 TGGTATTGCTTGATTTTCTTCCCAAA 59.957 34.615 0.00 0.00 0.00 3.28
2427 2478 5.659440 TGGTATTGCTTGATTTTCTTCCC 57.341 39.130 0.00 0.00 0.00 3.97
2430 2481 9.807649 GTAATCATGGTATTGCTTGATTTTCTT 57.192 29.630 0.00 0.00 39.07 2.52
2469 2521 5.939883 CCATGTGAGATTTCCTGTTAACTGA 59.060 40.000 13.56 4.39 0.00 3.41
2651 2704 3.785859 GCCGTCTGCCCCTCATGA 61.786 66.667 0.00 0.00 0.00 3.07
2692 2746 3.636764 GGATAAACCATGATTCGCCCTTT 59.363 43.478 0.00 0.00 38.79 3.11
2774 2837 1.416401 TCCAGTCTTCCTTTCGCAAGT 59.584 47.619 0.00 0.00 39.48 3.16
2980 3052 4.450976 TGTCCGATTATGGAATGGAACTG 58.549 43.478 0.00 0.00 40.44 3.16
2981 3053 4.771114 TGTCCGATTATGGAATGGAACT 57.229 40.909 0.00 0.00 40.44 3.01
2982 3054 4.260620 CGTTGTCCGATTATGGAATGGAAC 60.261 45.833 0.00 0.00 40.44 3.62
2983 3055 3.874543 CGTTGTCCGATTATGGAATGGAA 59.125 43.478 0.00 0.00 40.44 3.53
2984 3056 3.133183 TCGTTGTCCGATTATGGAATGGA 59.867 43.478 0.00 0.00 41.60 3.41
2985 3057 3.462982 TCGTTGTCCGATTATGGAATGG 58.537 45.455 0.00 0.00 41.60 3.16
3005 3077 3.471680 GGATGGTGATGCTTACTTCCTC 58.528 50.000 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.