Multiple sequence alignment - TraesCS1A01G155200

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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 TraesCS1A01G155200 chr1A 100.000 3806 0 0 669 4474 272610840 272614645 0.000000e+00 7029.0
1 TraesCS1A01G155200 chr1A 100.000 341 0 0 1 341 272610172 272610512 8.170000e-177 630.0
2 TraesCS1A01G155200 chr1A 88.095 168 19 1 671 838 272598759 272598925 9.820000e-47 198.0
3 TraesCS1A01G155200 chr1A 86.667 120 13 3 224 341 272598521 272598639 3.630000e-26 130.0
4 TraesCS1A01G155200 chr1B 95.913 1468 51 7 2255 3718 307427181 307428643 0.000000e+00 2370.0
5 TraesCS1A01G155200 chr1B 94.126 1430 52 7 669 2090 307425786 307427191 0.000000e+00 2146.0
6 TraesCS1A01G155200 chr1B 89.704 709 53 7 3785 4474 307435219 307435926 0.000000e+00 887.0
7 TraesCS1A01G155200 chr1B 93.696 349 11 6 1 341 307425032 307425377 3.090000e-141 512.0
8 TraesCS1A01G155200 chr1D 96.434 1430 35 7 669 2090 214398144 214399565 0.000000e+00 2344.0
9 TraesCS1A01G155200 chr1D 97.002 1301 33 5 2517 3815 214399750 214401046 0.000000e+00 2182.0
10 TraesCS1A01G155200 chr1D 95.627 343 11 3 1 341 214397675 214398015 8.460000e-152 547.0
11 TraesCS1A01G155200 chr1D 81.146 541 40 23 3823 4360 214401130 214401611 1.170000e-100 377.0
12 TraesCS1A01G155200 chr1D 96.923 195 5 1 2255 2449 214399555 214399748 4.320000e-85 326.0
13 TraesCS1A01G155200 chr3A 86.076 158 18 4 2091 2246 45604546 45604391 2.770000e-37 167.0
14 TraesCS1A01G155200 chr3A 90.769 65 4 2 4292 4355 269399351 269399288 7.970000e-13 86.1
15 TraesCS1A01G155200 chr4A 84.524 168 24 2 2087 2253 559898342 559898508 9.960000e-37 165.0
16 TraesCS1A01G155200 chr5A 84.663 163 25 0 2091 2253 619488466 619488628 3.580000e-36 163.0
17 TraesCS1A01G155200 chr5B 82.822 163 28 0 2091 2253 494202409 494202571 3.610000e-31 147.0
18 TraesCS1A01G155200 chr3B 86.364 88 5 3 4274 4355 348120506 348120420 6.160000e-14 89.8
19 TraesCS1A01G155200 chr3D 85.227 88 6 3 4274 4355 248540019 248539933 2.870000e-12 84.2


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 TraesCS1A01G155200 chr1A 272610172 272614645 4473 False 3829.5 7029 100.000000 1 4474 2 chr1A.!!$F2 4473
1 TraesCS1A01G155200 chr1B 307425032 307428643 3611 False 1676.0 2370 94.578333 1 3718 3 chr1B.!!$F2 3717
2 TraesCS1A01G155200 chr1B 307435219 307435926 707 False 887.0 887 89.704000 3785 4474 1 chr1B.!!$F1 689
3 TraesCS1A01G155200 chr1D 214397675 214401611 3936 False 1155.2 2344 93.426400 1 4360 5 chr1D.!!$F1 4359

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
864 956 1.009108 TTGTGGTGTTTGCGCGATG 60.009 52.632 12.10 0.0 0.0 3.84 F
1022 1119 0.255890 ATAAAGTCTGGCGGCATGGT 59.744 50.000 13.85 0.0 0.0 3.55 F
2217 2318 0.385390 GATTTACATTGGCTGGGCGG 59.615 55.000 0.00 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2251 2352 0.107017 CACCATGCTAAGGTCTGGGG 60.107 60.0 0.0 0.0 37.23 4.96 R
2252 2353 0.911769 TCACCATGCTAAGGTCTGGG 59.088 55.0 0.0 0.0 37.23 4.45 R
3768 3875 0.405585 CACCCCTGAATTGACACCCT 59.594 55.0 0.0 0.0 0.00 4.34 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
25 26 5.231568 CGTCGCTTTTCCTAAATCTTATCGT 59.768 40.000 0.00 0.00 0.00 3.73
69 72 2.027625 GTCACTTTGCCTCGACCCG 61.028 63.158 0.00 0.00 0.00 5.28
85 88 1.366111 CCCGACGAACGCAATGGAAT 61.366 55.000 0.00 0.00 41.07 3.01
320 331 1.424638 CCTATCCCCGTGTCCAGAAT 58.575 55.000 0.00 0.00 0.00 2.40
766 858 1.204231 GGTAGGGGTCGAACTGAAGTC 59.796 57.143 0.00 0.00 0.00 3.01
791 883 1.609208 GGCAAATAGTGGCGGATCAT 58.391 50.000 0.00 0.00 43.81 2.45
792 884 1.956477 GGCAAATAGTGGCGGATCATT 59.044 47.619 0.00 0.00 43.81 2.57
793 885 2.362077 GGCAAATAGTGGCGGATCATTT 59.638 45.455 0.00 0.00 43.81 2.32
864 956 1.009108 TTGTGGTGTTTGCGCGATG 60.009 52.632 12.10 0.00 0.00 3.84
865 957 1.440145 TTGTGGTGTTTGCGCGATGA 61.440 50.000 12.10 0.00 0.00 2.92
866 958 1.281353 GTGGTGTTTGCGCGATGAA 59.719 52.632 12.10 0.00 0.00 2.57
976 1068 1.537202 CTAAGGAGTTGGTGCACTTGC 59.463 52.381 17.98 6.87 42.50 4.01
1015 1112 7.889589 TGTTATGATATGATAAAGTCTGGCG 57.110 36.000 0.00 0.00 0.00 5.69
1022 1119 0.255890 ATAAAGTCTGGCGGCATGGT 59.744 50.000 13.85 0.00 0.00 3.55
1076 1173 5.272402 TCTGATTAGGGATCTGAACTGACA 58.728 41.667 0.00 0.00 39.07 3.58
1270 1368 0.600557 TGTATTGGCTTGTTTGGCGG 59.399 50.000 0.00 0.00 35.06 6.13
1355 1454 8.948631 TCTTGCTAAGTTAGGATGAATAACTG 57.051 34.615 14.95 0.00 41.47 3.16
1381 1480 2.002586 TCTTGCGTGCTAGAATCTTGC 58.997 47.619 9.67 9.67 33.21 4.01
1666 1766 4.744570 ACAATCATCTTTGCTGATGCTTG 58.255 39.130 19.51 19.51 46.91 4.01
1948 2049 5.255687 ACATGCATTCAGTTAGATGGTGAA 58.744 37.500 0.00 0.00 34.79 3.18
2115 2216 2.813779 CGGAGCTTCACACTAATTGC 57.186 50.000 0.00 0.00 0.00 3.56
2116 2217 2.350522 CGGAGCTTCACACTAATTGCT 58.649 47.619 0.00 0.00 0.00 3.91
2117 2218 2.094894 CGGAGCTTCACACTAATTGCTG 59.905 50.000 0.00 0.00 0.00 4.41
2118 2219 2.421424 GGAGCTTCACACTAATTGCTGG 59.579 50.000 0.00 0.00 0.00 4.85
2119 2220 2.421424 GAGCTTCACACTAATTGCTGGG 59.579 50.000 0.00 0.00 0.00 4.45
2120 2221 1.135286 GCTTCACACTAATTGCTGGGC 60.135 52.381 0.00 0.00 0.00 5.36
2121 2222 1.131126 CTTCACACTAATTGCTGGGCG 59.869 52.381 0.00 0.00 0.00 6.13
2122 2223 0.676466 TCACACTAATTGCTGGGCGG 60.676 55.000 0.00 0.00 0.00 6.13
2123 2224 1.378514 ACACTAATTGCTGGGCGGG 60.379 57.895 0.00 0.00 0.00 6.13
2124 2225 2.440247 ACTAATTGCTGGGCGGGC 60.440 61.111 0.00 0.00 0.00 6.13
2125 2226 3.219198 CTAATTGCTGGGCGGGCC 61.219 66.667 14.65 14.65 0.00 5.80
2126 2227 4.053871 TAATTGCTGGGCGGGCCA 62.054 61.111 22.99 22.99 37.98 5.36
2143 2244 4.749310 AGCGAGGCCGTGCTGAAG 62.749 66.667 21.87 0.00 40.62 3.02
2144 2245 4.742201 GCGAGGCCGTGCTGAAGA 62.742 66.667 14.18 0.00 38.24 2.87
2145 2246 2.048222 CGAGGCCGTGCTGAAGAA 60.048 61.111 0.00 0.00 0.00 2.52
2146 2247 1.667830 CGAGGCCGTGCTGAAGAAA 60.668 57.895 0.00 0.00 0.00 2.52
2147 2248 1.227999 CGAGGCCGTGCTGAAGAAAA 61.228 55.000 0.00 0.00 0.00 2.29
2148 2249 1.168714 GAGGCCGTGCTGAAGAAAAT 58.831 50.000 0.00 0.00 0.00 1.82
2149 2250 1.541588 GAGGCCGTGCTGAAGAAAATT 59.458 47.619 0.00 0.00 0.00 1.82
2150 2251 2.747446 GAGGCCGTGCTGAAGAAAATTA 59.253 45.455 0.00 0.00 0.00 1.40
2151 2252 2.488153 AGGCCGTGCTGAAGAAAATTAC 59.512 45.455 0.00 0.00 0.00 1.89
2152 2253 2.488153 GGCCGTGCTGAAGAAAATTACT 59.512 45.455 0.00 0.00 0.00 2.24
2153 2254 3.687698 GGCCGTGCTGAAGAAAATTACTA 59.312 43.478 0.00 0.00 0.00 1.82
2154 2255 4.436986 GGCCGTGCTGAAGAAAATTACTAC 60.437 45.833 0.00 0.00 0.00 2.73
2155 2256 4.153475 GCCGTGCTGAAGAAAATTACTACA 59.847 41.667 0.00 0.00 0.00 2.74
2156 2257 5.334569 GCCGTGCTGAAGAAAATTACTACAA 60.335 40.000 0.00 0.00 0.00 2.41
2157 2258 6.077838 CCGTGCTGAAGAAAATTACTACAAC 58.922 40.000 0.00 0.00 0.00 3.32
2158 2259 5.783654 CGTGCTGAAGAAAATTACTACAACG 59.216 40.000 0.00 0.00 0.00 4.10
2159 2260 6.563381 CGTGCTGAAGAAAATTACTACAACGT 60.563 38.462 0.00 0.00 0.00 3.99
2160 2261 7.130269 GTGCTGAAGAAAATTACTACAACGTT 58.870 34.615 0.00 0.00 0.00 3.99
2161 2262 7.642586 GTGCTGAAGAAAATTACTACAACGTTT 59.357 33.333 0.00 0.00 0.00 3.60
2162 2263 8.185505 TGCTGAAGAAAATTACTACAACGTTTT 58.814 29.630 0.00 0.00 0.00 2.43
2163 2264 9.016623 GCTGAAGAAAATTACTACAACGTTTTT 57.983 29.630 0.00 0.00 0.00 1.94
2165 2266 9.843334 TGAAGAAAATTACTACAACGTTTTTGT 57.157 25.926 0.00 1.89 36.49 2.83
2172 2273 7.972623 TTACTACAACGTTTTTGTTTCATGG 57.027 32.000 6.84 0.00 34.11 3.66
2173 2274 4.801516 ACTACAACGTTTTTGTTTCATGGC 59.198 37.500 0.00 0.00 34.11 4.40
2174 2275 2.933260 ACAACGTTTTTGTTTCATGGCC 59.067 40.909 0.00 0.00 0.00 5.36
2175 2276 3.194062 CAACGTTTTTGTTTCATGGCCT 58.806 40.909 3.32 0.00 0.00 5.19
2176 2277 4.142138 ACAACGTTTTTGTTTCATGGCCTA 60.142 37.500 3.32 0.00 0.00 3.93
2177 2278 4.657436 ACGTTTTTGTTTCATGGCCTAA 57.343 36.364 3.32 0.00 0.00 2.69
2178 2279 5.208463 ACGTTTTTGTTTCATGGCCTAAT 57.792 34.783 3.32 0.00 0.00 1.73
2179 2280 6.334102 ACGTTTTTGTTTCATGGCCTAATA 57.666 33.333 3.32 0.00 0.00 0.98
2180 2281 6.386654 ACGTTTTTGTTTCATGGCCTAATAG 58.613 36.000 3.32 0.00 0.00 1.73
2181 2282 5.288472 CGTTTTTGTTTCATGGCCTAATAGC 59.712 40.000 3.32 0.00 0.00 2.97
2182 2283 5.991933 TTTTGTTTCATGGCCTAATAGCA 57.008 34.783 3.32 0.00 0.00 3.49
2183 2284 5.581126 TTTGTTTCATGGCCTAATAGCAG 57.419 39.130 3.32 0.00 0.00 4.24
2184 2285 3.554934 TGTTTCATGGCCTAATAGCAGG 58.445 45.455 3.32 0.00 38.86 4.85
2185 2286 3.053693 TGTTTCATGGCCTAATAGCAGGT 60.054 43.478 3.32 0.00 38.05 4.00
2186 2287 2.936919 TCATGGCCTAATAGCAGGTG 57.063 50.000 3.32 0.00 38.05 4.00
2187 2288 2.126882 TCATGGCCTAATAGCAGGTGT 58.873 47.619 3.32 0.00 38.05 4.16
2188 2289 3.313791 TCATGGCCTAATAGCAGGTGTA 58.686 45.455 3.32 0.00 38.05 2.90
2189 2290 3.909995 TCATGGCCTAATAGCAGGTGTAT 59.090 43.478 3.32 0.00 38.05 2.29
2190 2291 5.090845 TCATGGCCTAATAGCAGGTGTATA 58.909 41.667 3.32 0.00 38.05 1.47
2191 2292 5.726308 TCATGGCCTAATAGCAGGTGTATAT 59.274 40.000 3.32 0.00 38.05 0.86
2192 2293 6.215431 TCATGGCCTAATAGCAGGTGTATATT 59.785 38.462 3.32 0.00 38.05 1.28
2193 2294 7.401782 TCATGGCCTAATAGCAGGTGTATATTA 59.598 37.037 3.32 0.00 38.05 0.98
2194 2295 6.942976 TGGCCTAATAGCAGGTGTATATTAC 58.057 40.000 3.32 0.00 38.05 1.89
2195 2296 6.499000 TGGCCTAATAGCAGGTGTATATTACA 59.501 38.462 3.32 0.00 38.05 2.41
2196 2297 7.042335 GGCCTAATAGCAGGTGTATATTACAG 58.958 42.308 0.00 0.00 39.77 2.74
2197 2298 7.093465 GGCCTAATAGCAGGTGTATATTACAGA 60.093 40.741 0.00 0.00 39.77 3.41
2198 2299 7.976734 GCCTAATAGCAGGTGTATATTACAGAG 59.023 40.741 0.00 0.00 39.77 3.35
2199 2300 9.244292 CCTAATAGCAGGTGTATATTACAGAGA 57.756 37.037 0.00 0.00 39.77 3.10
2205 2306 8.924303 AGCAGGTGTATATTACAGAGATTTACA 58.076 33.333 0.00 0.00 39.77 2.41
2206 2307 9.712305 GCAGGTGTATATTACAGAGATTTACAT 57.288 33.333 0.00 0.00 39.77 2.29
2213 2314 6.949352 ATTACAGAGATTTACATTGGCTGG 57.051 37.500 0.00 0.00 0.00 4.85
2214 2315 3.624777 ACAGAGATTTACATTGGCTGGG 58.375 45.455 0.00 0.00 0.00 4.45
2215 2316 2.360165 CAGAGATTTACATTGGCTGGGC 59.640 50.000 0.00 0.00 0.00 5.36
2216 2317 1.334869 GAGATTTACATTGGCTGGGCG 59.665 52.381 0.00 0.00 0.00 6.13
2217 2318 0.385390 GATTTACATTGGCTGGGCGG 59.615 55.000 0.00 0.00 0.00 6.13
2218 2319 1.042559 ATTTACATTGGCTGGGCGGG 61.043 55.000 0.00 0.00 0.00 6.13
2219 2320 4.813235 TACATTGGCTGGGCGGGC 62.813 66.667 0.00 0.00 0.00 6.13
2258 2359 4.208686 CGTAGCTCCGCCCCAGAC 62.209 72.222 0.00 0.00 0.00 3.51
2259 2360 3.851128 GTAGCTCCGCCCCAGACC 61.851 72.222 0.00 0.00 0.00 3.85
2340 2443 7.237055 ACTCACCCCTAACTTGTAAGATTAGTT 59.763 37.037 0.00 0.00 36.23 2.24
2346 2449 8.047310 CCCTAACTTGTAAGATTAGTTGGACAT 58.953 37.037 0.00 0.00 33.70 3.06
2453 2556 8.867097 AGTCTCAGTTATGGTGTTTCTTAGTTA 58.133 33.333 0.00 0.00 0.00 2.24
2458 2561 8.230486 CAGTTATGGTGTTTCTTAGTTAGCTTG 58.770 37.037 0.00 0.00 0.00 4.01
2481 2584 5.695816 TGAAAAGCCATGCAAAGTTCAATAC 59.304 36.000 0.00 0.00 0.00 1.89
2695 2798 2.285977 GGTGTCCAAGTTTCTGACGTT 58.714 47.619 0.00 0.00 0.00 3.99
2737 2840 4.338682 GGTAATCACTCGTCCAGTCAGTAT 59.661 45.833 0.00 0.00 30.26 2.12
2871 2974 6.494491 TGTTGTCAGATCCATTTTCCTTCATT 59.506 34.615 0.00 0.00 0.00 2.57
3110 3216 2.949644 AGCCTTTTAACACGCTGAGTTT 59.050 40.909 0.00 0.00 0.00 2.66
3309 3415 3.582647 TCTTCCCATGCTTCTACTTGTCA 59.417 43.478 0.00 0.00 0.00 3.58
3344 3450 5.532779 TGTGTGACCACATTAATTTGTAGCA 59.467 36.000 6.10 0.00 46.45 3.49
3345 3451 6.208402 TGTGTGACCACATTAATTTGTAGCAT 59.792 34.615 6.10 0.00 46.45 3.79
3450 3556 1.882989 GCTGTCAGAGGAGAAGGCGT 61.883 60.000 3.32 0.00 0.00 5.68
3534 3640 5.253330 TGAATAAATGAAACCTTCCGCTCT 58.747 37.500 0.00 0.00 0.00 4.09
3670 3776 2.154462 ACAGGACAGTACATTTGCTGC 58.846 47.619 9.02 0.00 38.97 5.25
3753 3859 5.654650 ACAACAAGTCACATAAAAACTCCCA 59.345 36.000 0.00 0.00 0.00 4.37
3768 3875 7.663043 AAAACTCCCAAAAACTGGTTATACA 57.337 32.000 0.00 0.00 44.76 2.29
3896 4079 9.350357 GGCATATGCAAGATTATTTTATCACTG 57.650 33.333 28.07 0.00 44.36 3.66
3957 4140 7.489113 AGTTGAACATCACTTCAAAACACAATC 59.511 33.333 0.00 0.00 40.89 2.67
4058 4241 5.061179 TGCACCATATGAGAGAACATCATG 58.939 41.667 3.65 0.00 37.91 3.07
4136 4321 2.168947 CACACTGCCATGTGCTCTC 58.831 57.895 4.66 0.00 43.29 3.20
4137 4322 1.002868 ACACTGCCATGTGCTCTCC 60.003 57.895 7.54 0.00 41.30 3.71
4143 4328 0.105778 GCCATGTGCTCTCCTACCTC 59.894 60.000 0.00 0.00 36.87 3.85
4170 4355 5.220529 GCCATCTTTGATGCTAAATTTGTGC 60.221 40.000 0.00 6.03 0.00 4.57
4222 4407 5.859205 AGTCTTGCTCCATTTTGTTTCTT 57.141 34.783 0.00 0.00 0.00 2.52
4255 4441 7.124599 TGCCTTCAATTAGGATGTTGATTTGAT 59.875 33.333 0.00 0.00 37.50 2.57
4268 4454 1.680207 GATTTGATGGAAGCCAGGCTC 59.320 52.381 16.53 8.41 38.25 4.70
4314 4500 1.210931 CCTCACATGCCACTTTGCG 59.789 57.895 0.00 0.00 0.00 4.85
4351 4537 2.526888 ACCTCGGACCATCTCAAGTA 57.473 50.000 0.00 0.00 0.00 2.24
4385 4590 4.618920 TTCTTCCAACTTACCAGGAGAC 57.381 45.455 0.00 0.00 32.11 3.36
4391 4596 1.987855 CTTACCAGGAGACCCGCCA 60.988 63.158 0.00 0.00 37.58 5.69
4395 4600 1.987855 CCAGGAGACCCGCCAACTA 60.988 63.158 0.00 0.00 37.58 2.24
4397 4602 2.183555 GGAGACCCGCCAACTACG 59.816 66.667 0.00 0.00 0.00 3.51
4403 4608 0.743097 ACCCGCCAACTACGACTATC 59.257 55.000 0.00 0.00 0.00 2.08
4422 4627 3.934457 TCGTCCATGTACGATGCATAT 57.066 42.857 9.68 0.00 46.29 1.78
4432 4637 7.062722 CCATGTACGATGCATATAGTCTTGAAG 59.937 40.741 0.00 0.00 0.00 3.02
4438 4643 9.935241 ACGATGCATATAGTCTTGAAGATTATT 57.065 29.630 14.19 0.00 30.98 1.40
4470 4675 7.560368 TCATTCCTTTATCTTTCTCACCTCTC 58.440 38.462 0.00 0.00 0.00 3.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 5.522460 TGGACGATAAGATTTAGGAAAAGCG 59.478 40.000 0.00 0.00 36.11 4.68
42 43 3.353836 CAAAGTGACGCCGTGGGG 61.354 66.667 0.00 0.80 0.00 4.96
69 72 1.062587 CTGGATTCCATTGCGTTCGTC 59.937 52.381 5.70 0.00 30.82 4.20
85 88 1.199615 TGTCAGTGTGGTTGTCTGGA 58.800 50.000 0.00 0.00 0.00 3.86
168 171 0.243907 CTACCGGGCTCATACCATCG 59.756 60.000 6.32 0.00 0.00 3.84
171 174 1.382009 TGCTACCGGGCTCATACCA 60.382 57.895 6.32 0.00 0.00 3.25
766 858 0.096976 CGCCACTATTTGCCACTTCG 59.903 55.000 0.00 0.00 0.00 3.79
791 883 2.289694 GCAGTGAGCTCTCCCACTTAAA 60.290 50.000 16.19 0.00 41.26 1.52
792 884 1.276421 GCAGTGAGCTCTCCCACTTAA 59.724 52.381 16.19 0.00 41.26 1.85
793 885 0.898320 GCAGTGAGCTCTCCCACTTA 59.102 55.000 16.19 0.00 41.26 2.24
864 956 3.080319 GCCCATCAGATCAGCCTATTTC 58.920 50.000 0.00 0.00 0.00 2.17
865 957 2.715336 AGCCCATCAGATCAGCCTATTT 59.285 45.455 0.00 0.00 0.00 1.40
866 958 2.346529 AGCCCATCAGATCAGCCTATT 58.653 47.619 0.00 0.00 0.00 1.73
976 1068 9.447040 CATATCATAACAAGCAAATCAGTTCAG 57.553 33.333 0.00 0.00 0.00 3.02
1015 1112 0.609662 ATCTGCACCAAAACCATGCC 59.390 50.000 0.00 0.00 38.63 4.40
1022 1119 0.690192 TCCCGAGATCTGCACCAAAA 59.310 50.000 0.00 0.00 0.00 2.44
1076 1173 4.566004 TCACTTACGAATTAACAGCAGCT 58.434 39.130 0.00 0.00 0.00 4.24
1270 1368 2.984471 CACTTCATGTGTTGCATTGAGC 59.016 45.455 0.00 0.00 41.53 4.26
1355 1454 6.777526 AGATTCTAGCACGCAAGAATTATC 57.222 37.500 0.00 0.00 41.40 1.75
1638 1738 5.787953 TCAGCAAAGATGATTGTCCAAAA 57.212 34.783 0.00 0.00 32.80 2.44
1639 1739 5.716094 CATCAGCAAAGATGATTGTCCAAA 58.284 37.500 7.75 0.00 46.51 3.28
1666 1766 6.154021 TCCTATAGTGTACCAACAGAAGGTTC 59.846 42.308 0.00 0.00 40.54 3.62
1721 1821 1.202394 GCAACATTCACACCAGTGCAA 60.202 47.619 0.00 0.00 45.49 4.08
2088 2189 4.704833 TGAAGCTCCGCCACTGGC 62.705 66.667 10.35 10.35 46.75 4.85
2089 2190 2.743928 GTGAAGCTCCGCCACTGG 60.744 66.667 0.00 0.00 0.00 4.00
2090 2191 2.031012 TGTGAAGCTCCGCCACTG 59.969 61.111 0.00 0.00 0.00 3.66
2091 2192 1.185618 TAGTGTGAAGCTCCGCCACT 61.186 55.000 11.47 11.47 0.00 4.00
2092 2193 0.320421 TTAGTGTGAAGCTCCGCCAC 60.320 55.000 0.00 0.00 0.00 5.01
2093 2194 0.613260 ATTAGTGTGAAGCTCCGCCA 59.387 50.000 0.00 0.00 0.00 5.69
2094 2195 1.398390 CAATTAGTGTGAAGCTCCGCC 59.602 52.381 0.00 0.00 0.00 6.13
2095 2196 1.202076 GCAATTAGTGTGAAGCTCCGC 60.202 52.381 0.00 0.00 0.00 5.54
2096 2197 2.094894 CAGCAATTAGTGTGAAGCTCCG 59.905 50.000 0.00 0.00 0.00 4.63
2097 2198 2.421424 CCAGCAATTAGTGTGAAGCTCC 59.579 50.000 0.00 0.00 0.00 4.70
2098 2199 2.421424 CCCAGCAATTAGTGTGAAGCTC 59.579 50.000 0.00 0.00 0.00 4.09
2099 2200 2.440409 CCCAGCAATTAGTGTGAAGCT 58.560 47.619 0.00 0.00 0.00 3.74
2100 2201 1.135286 GCCCAGCAATTAGTGTGAAGC 60.135 52.381 0.00 0.00 0.00 3.86
2101 2202 1.131126 CGCCCAGCAATTAGTGTGAAG 59.869 52.381 0.00 0.00 0.00 3.02
2102 2203 1.164411 CGCCCAGCAATTAGTGTGAA 58.836 50.000 0.00 0.00 0.00 3.18
2103 2204 0.676466 CCGCCCAGCAATTAGTGTGA 60.676 55.000 0.00 0.00 0.00 3.58
2104 2205 1.656818 CCCGCCCAGCAATTAGTGTG 61.657 60.000 0.00 0.00 0.00 3.82
2105 2206 1.378514 CCCGCCCAGCAATTAGTGT 60.379 57.895 0.00 0.00 0.00 3.55
2106 2207 2.774799 GCCCGCCCAGCAATTAGTG 61.775 63.158 0.00 0.00 0.00 2.74
2107 2208 2.440247 GCCCGCCCAGCAATTAGT 60.440 61.111 0.00 0.00 0.00 2.24
2108 2209 3.219198 GGCCCGCCCAGCAATTAG 61.219 66.667 0.00 0.00 0.00 1.73
2109 2210 4.053871 TGGCCCGCCCAGCAATTA 62.054 61.111 0.00 0.00 39.18 1.40
2126 2227 4.749310 CTTCAGCACGGCCTCGCT 62.749 66.667 9.82 9.82 40.63 4.93
2127 2228 4.742201 TCTTCAGCACGGCCTCGC 62.742 66.667 0.00 2.52 40.63 5.03
2128 2229 1.227999 TTTTCTTCAGCACGGCCTCG 61.228 55.000 0.00 0.00 43.02 4.63
2129 2230 1.168714 ATTTTCTTCAGCACGGCCTC 58.831 50.000 0.00 0.00 0.00 4.70
2130 2231 1.620822 AATTTTCTTCAGCACGGCCT 58.379 45.000 0.00 0.00 0.00 5.19
2131 2232 2.488153 AGTAATTTTCTTCAGCACGGCC 59.512 45.455 0.00 0.00 0.00 6.13
2132 2233 3.831715 AGTAATTTTCTTCAGCACGGC 57.168 42.857 0.00 0.00 0.00 5.68
2133 2234 5.856126 TGTAGTAATTTTCTTCAGCACGG 57.144 39.130 0.00 0.00 0.00 4.94
2134 2235 5.783654 CGTTGTAGTAATTTTCTTCAGCACG 59.216 40.000 0.00 0.00 0.00 5.34
2135 2236 6.656003 ACGTTGTAGTAATTTTCTTCAGCAC 58.344 36.000 0.00 0.00 0.00 4.40
2136 2237 6.854496 ACGTTGTAGTAATTTTCTTCAGCA 57.146 33.333 0.00 0.00 0.00 4.41
2137 2238 8.556517 AAAACGTTGTAGTAATTTTCTTCAGC 57.443 30.769 0.00 0.00 0.00 4.26
2139 2240 9.843334 ACAAAAACGTTGTAGTAATTTTCTTCA 57.157 25.926 0.00 0.00 0.00 3.02
2146 2247 9.026074 CCATGAAACAAAAACGTTGTAGTAATT 57.974 29.630 0.00 0.00 31.50 1.40
2147 2248 7.168469 GCCATGAAACAAAAACGTTGTAGTAAT 59.832 33.333 0.00 0.00 31.50 1.89
2148 2249 6.472808 GCCATGAAACAAAAACGTTGTAGTAA 59.527 34.615 0.00 0.00 31.50 2.24
2149 2250 5.972382 GCCATGAAACAAAAACGTTGTAGTA 59.028 36.000 0.00 0.00 31.50 1.82
2150 2251 4.801516 GCCATGAAACAAAAACGTTGTAGT 59.198 37.500 0.00 0.00 31.50 2.73
2151 2252 4.208253 GGCCATGAAACAAAAACGTTGTAG 59.792 41.667 0.00 0.00 31.50 2.74
2152 2253 4.113354 GGCCATGAAACAAAAACGTTGTA 58.887 39.130 0.00 0.00 31.50 2.41
2153 2254 2.933260 GGCCATGAAACAAAAACGTTGT 59.067 40.909 0.00 0.00 0.00 3.32
2154 2255 3.194062 AGGCCATGAAACAAAAACGTTG 58.806 40.909 5.01 0.00 0.00 4.10
2155 2256 3.535280 AGGCCATGAAACAAAAACGTT 57.465 38.095 5.01 0.00 0.00 3.99
2156 2257 4.657436 TTAGGCCATGAAACAAAAACGT 57.343 36.364 5.01 0.00 0.00 3.99
2157 2258 5.288472 GCTATTAGGCCATGAAACAAAAACG 59.712 40.000 5.01 0.00 0.00 3.60
2158 2259 6.162777 TGCTATTAGGCCATGAAACAAAAAC 58.837 36.000 5.01 0.00 0.00 2.43
2159 2260 6.352016 TGCTATTAGGCCATGAAACAAAAA 57.648 33.333 5.01 0.00 0.00 1.94
2160 2261 5.105392 CCTGCTATTAGGCCATGAAACAAAA 60.105 40.000 5.01 0.00 0.00 2.44
2161 2262 4.402155 CCTGCTATTAGGCCATGAAACAAA 59.598 41.667 5.01 0.00 0.00 2.83
2162 2263 3.953612 CCTGCTATTAGGCCATGAAACAA 59.046 43.478 5.01 0.00 0.00 2.83
2163 2264 3.053693 ACCTGCTATTAGGCCATGAAACA 60.054 43.478 5.01 0.00 41.75 2.83
2164 2265 3.316308 CACCTGCTATTAGGCCATGAAAC 59.684 47.826 5.01 0.00 41.75 2.78
2165 2266 3.053693 ACACCTGCTATTAGGCCATGAAA 60.054 43.478 5.01 0.00 41.75 2.69
2166 2267 2.509548 ACACCTGCTATTAGGCCATGAA 59.490 45.455 5.01 0.00 41.75 2.57
2167 2268 2.126882 ACACCTGCTATTAGGCCATGA 58.873 47.619 5.01 0.00 41.75 3.07
2168 2269 2.645838 ACACCTGCTATTAGGCCATG 57.354 50.000 5.01 0.00 41.75 3.66
2169 2270 6.642733 AATATACACCTGCTATTAGGCCAT 57.357 37.500 5.01 0.00 41.75 4.40
2170 2271 6.499000 TGTAATATACACCTGCTATTAGGCCA 59.501 38.462 5.01 0.00 41.75 5.36
2171 2272 6.942976 TGTAATATACACCTGCTATTAGGCC 58.057 40.000 0.00 0.00 41.75 5.19
2172 2273 7.837863 TCTGTAATATACACCTGCTATTAGGC 58.162 38.462 0.00 0.00 41.75 3.93
2173 2274 9.244292 TCTCTGTAATATACACCTGCTATTAGG 57.756 37.037 0.00 0.00 43.71 2.69
2179 2280 8.924303 TGTAAATCTCTGTAATATACACCTGCT 58.076 33.333 0.00 0.00 34.46 4.24
2180 2281 9.712305 ATGTAAATCTCTGTAATATACACCTGC 57.288 33.333 0.00 0.00 34.46 4.85
2187 2288 9.725019 CCAGCCAATGTAAATCTCTGTAATATA 57.275 33.333 0.00 0.00 0.00 0.86
2188 2289 7.667219 CCCAGCCAATGTAAATCTCTGTAATAT 59.333 37.037 0.00 0.00 0.00 1.28
2189 2290 6.998074 CCCAGCCAATGTAAATCTCTGTAATA 59.002 38.462 0.00 0.00 0.00 0.98
2190 2291 5.829924 CCCAGCCAATGTAAATCTCTGTAAT 59.170 40.000 0.00 0.00 0.00 1.89
2191 2292 5.192927 CCCAGCCAATGTAAATCTCTGTAA 58.807 41.667 0.00 0.00 0.00 2.41
2192 2293 4.780815 CCCAGCCAATGTAAATCTCTGTA 58.219 43.478 0.00 0.00 0.00 2.74
2193 2294 3.624777 CCCAGCCAATGTAAATCTCTGT 58.375 45.455 0.00 0.00 0.00 3.41
2194 2295 2.360165 GCCCAGCCAATGTAAATCTCTG 59.640 50.000 0.00 0.00 0.00 3.35
2195 2296 2.659428 GCCCAGCCAATGTAAATCTCT 58.341 47.619 0.00 0.00 0.00 3.10
2196 2297 1.334869 CGCCCAGCCAATGTAAATCTC 59.665 52.381 0.00 0.00 0.00 2.75
2197 2298 1.392589 CGCCCAGCCAATGTAAATCT 58.607 50.000 0.00 0.00 0.00 2.40
2198 2299 0.385390 CCGCCCAGCCAATGTAAATC 59.615 55.000 0.00 0.00 0.00 2.17
2199 2300 1.042559 CCCGCCCAGCCAATGTAAAT 61.043 55.000 0.00 0.00 0.00 1.40
2200 2301 1.680651 CCCGCCCAGCCAATGTAAA 60.681 57.895 0.00 0.00 0.00 2.01
2201 2302 2.044451 CCCGCCCAGCCAATGTAA 60.044 61.111 0.00 0.00 0.00 2.41
2202 2303 4.813235 GCCCGCCCAGCCAATGTA 62.813 66.667 0.00 0.00 0.00 2.29
2246 2347 3.095347 GCTAAGGTCTGGGGCGGAG 62.095 68.421 0.00 0.00 0.00 4.63
2247 2348 3.081409 GCTAAGGTCTGGGGCGGA 61.081 66.667 0.00 0.00 0.00 5.54
2248 2349 2.746375 ATGCTAAGGTCTGGGGCGG 61.746 63.158 0.00 0.00 0.00 6.13
2249 2350 1.524621 CATGCTAAGGTCTGGGGCG 60.525 63.158 0.00 0.00 0.00 6.13
2250 2351 1.152881 CCATGCTAAGGTCTGGGGC 60.153 63.158 0.00 0.00 0.00 5.80
2251 2352 0.107017 CACCATGCTAAGGTCTGGGG 60.107 60.000 0.00 0.00 37.23 4.96
2252 2353 0.911769 TCACCATGCTAAGGTCTGGG 59.088 55.000 0.00 0.00 37.23 4.45
2253 2354 2.569059 CATCACCATGCTAAGGTCTGG 58.431 52.381 0.00 0.00 37.23 3.86
2340 2443 6.775142 TGTGAACAAATAAAGAGGAATGTCCA 59.225 34.615 0.00 0.00 39.61 4.02
2346 2449 9.739276 ATACAGATGTGAACAAATAAAGAGGAA 57.261 29.630 0.00 0.00 0.00 3.36
2356 2459 5.561919 GCGTCCAAATACAGATGTGAACAAA 60.562 40.000 0.00 0.00 0.00 2.83
2458 2561 5.164061 CGTATTGAACTTTGCATGGCTTTTC 60.164 40.000 0.00 0.00 0.00 2.29
2507 2610 9.552114 CAAAAACAGCACAAAAATGTGAATTTA 57.448 25.926 12.80 0.00 42.02 1.40
2695 2798 9.111519 TGATTACCCCAGATAATAGCATTCTTA 57.888 33.333 0.00 0.00 0.00 2.10
2737 2840 2.308570 AGTGGCATGGTTAACATCAGGA 59.691 45.455 8.10 0.00 37.84 3.86
2752 2855 1.053835 TGGGAGTCTTCACAGTGGCA 61.054 55.000 0.00 0.00 29.84 4.92
2845 2948 5.474532 TGAAGGAAAATGGATCTGACAACAG 59.525 40.000 0.00 0.00 44.66 3.16
2871 2974 8.742125 AGAGGATAACACCATTATTAGATCCA 57.258 34.615 0.00 0.00 35.14 3.41
3049 3152 1.423584 CCAAAAAGGTCCAAGGGCTT 58.576 50.000 0.00 0.00 0.00 4.35
3110 3216 3.156293 CAAATGTTCCCTGTGATCCACA 58.844 45.455 0.00 0.00 42.45 4.17
3437 3543 2.665603 GCCAACGCCTTCTCCTCT 59.334 61.111 0.00 0.00 0.00 3.69
3467 3573 2.031683 CCTTCGAATGTGGATTTACGCC 59.968 50.000 0.00 0.00 0.00 5.68
3603 3709 4.655963 ACAAGCCTCATTCATACACACTT 58.344 39.130 0.00 0.00 0.00 3.16
3670 3776 5.745294 CAGGTGTCAAATTGTTTCACTCTTG 59.255 40.000 13.92 2.41 0.00 3.02
3720 3826 5.869753 ATGTGACTTGTTGTAGATGCTTC 57.130 39.130 0.00 0.00 0.00 3.86
3721 3827 7.744087 TTTATGTGACTTGTTGTAGATGCTT 57.256 32.000 0.00 0.00 0.00 3.91
3753 3859 5.697067 TGACACCCTGTATAACCAGTTTTT 58.303 37.500 0.00 0.00 0.00 1.94
3768 3875 0.405585 CACCCCTGAATTGACACCCT 59.594 55.000 0.00 0.00 0.00 4.34
3932 4115 6.942886 TTGTGTTTTGAAGTGATGTTCAAC 57.057 33.333 0.00 0.00 44.29 3.18
4136 4321 3.634397 TCAAAGATGGCAAGAGGTAGG 57.366 47.619 0.00 0.00 0.00 3.18
4137 4322 3.314635 GCATCAAAGATGGCAAGAGGTAG 59.685 47.826 8.87 0.00 0.00 3.18
4143 4328 6.592607 ACAAATTTAGCATCAAAGATGGCAAG 59.407 34.615 8.87 0.00 0.00 4.01
4176 4361 3.014304 AGCTTCCGTACCATGAGTAGA 57.986 47.619 0.00 0.00 0.00 2.59
4177 4362 3.119101 ACAAGCTTCCGTACCATGAGTAG 60.119 47.826 0.00 0.00 0.00 2.57
4178 4363 2.829720 ACAAGCTTCCGTACCATGAGTA 59.170 45.455 0.00 0.00 0.00 2.59
4179 4364 1.623811 ACAAGCTTCCGTACCATGAGT 59.376 47.619 0.00 0.00 0.00 3.41
4180 4365 2.386661 ACAAGCTTCCGTACCATGAG 57.613 50.000 0.00 0.00 0.00 2.90
4181 4366 2.829720 ACTACAAGCTTCCGTACCATGA 59.170 45.455 0.00 0.00 0.00 3.07
4182 4367 3.119101 AGACTACAAGCTTCCGTACCATG 60.119 47.826 0.00 0.00 0.00 3.66
4183 4368 3.097614 AGACTACAAGCTTCCGTACCAT 58.902 45.455 0.00 0.00 0.00 3.55
4184 4369 2.522185 AGACTACAAGCTTCCGTACCA 58.478 47.619 0.00 0.00 0.00 3.25
4185 4370 3.251571 CAAGACTACAAGCTTCCGTACC 58.748 50.000 0.00 0.00 0.00 3.34
4186 4371 2.666994 GCAAGACTACAAGCTTCCGTAC 59.333 50.000 0.00 0.00 0.00 3.67
4190 4375 2.289694 TGGAGCAAGACTACAAGCTTCC 60.290 50.000 0.00 0.00 35.76 3.46
4222 4407 3.966979 TCCTAATTGAAGGCATTGCAGA 58.033 40.909 11.39 0.00 36.51 4.26
4255 4441 3.952508 TTGCGAGCCTGGCTTCCA 61.953 61.111 24.26 19.08 39.88 3.53
4268 4454 3.358993 GCAATCGAAGAAAAGAAGTTGCG 59.641 43.478 0.00 0.00 43.58 4.85
4314 4500 3.092301 AGGTTTAAGGCAATGAAGGAGC 58.908 45.455 0.00 0.00 0.00 4.70
4365 4551 2.904434 GGTCTCCTGGTAAGTTGGAAGA 59.096 50.000 0.00 0.00 0.00 2.87
4385 4590 0.317603 CGATAGTCGTAGTTGGCGGG 60.318 60.000 0.00 0.00 34.72 6.13
4403 4608 4.733850 ACTATATGCATCGTACATGGACG 58.266 43.478 24.84 24.84 44.29 4.79
4438 4643 9.573166 TGAGAAAGATAAAGGAATGAAGAAACA 57.427 29.630 0.00 0.00 0.00 2.83
4445 4650 7.365117 GGAGAGGTGAGAAAGATAAAGGAATGA 60.365 40.741 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.