Multiple sequence alignment - TraesCS1D01G334700

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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 TraesCS1D01G334700 chr1D 100.000 3050 0 0 1 3050 424866757 424869806 0.000000e+00 5633.0
1 TraesCS1D01G334700 chr1D 95.367 777 32 3 2275 3050 174653319 174652546 0.000000e+00 1232.0
2 TraesCS1D01G334700 chr1A 89.733 1646 94 28 78 1687 520762159 520763765 0.000000e+00 2034.0
3 TraesCS1D01G334700 chr1A 82.198 455 36 19 1759 2189 520763803 520764236 1.740000e-92 350.0
4 TraesCS1D01G334700 chr1B 89.197 1657 84 36 583 2189 573936782 573938393 0.000000e+00 1980.0
5 TraesCS1D01G334700 chr1B 89.655 580 37 14 31 594 573936189 573936761 0.000000e+00 717.0
6 TraesCS1D01G334700 chr5D 96.401 778 25 3 2275 3050 241141707 241142483 0.000000e+00 1279.0
7 TraesCS1D01G334700 chr5D 95.501 778 30 3 2275 3050 426139912 426140686 0.000000e+00 1238.0
8 TraesCS1D01G334700 chr5D 95.367 777 32 3 2275 3050 321161582 321160809 0.000000e+00 1232.0
9 TraesCS1D01G334700 chr5D 95.478 774 31 3 2275 3047 505192558 505193328 0.000000e+00 1232.0
10 TraesCS1D01G334700 chr5D 88.592 412 32 7 541 946 115700106 115700508 1.270000e-133 486.0
11 TraesCS1D01G334700 chr2D 96.144 778 27 3 2275 3050 429845861 429845085 0.000000e+00 1267.0
12 TraesCS1D01G334700 chr2D 100.000 40 0 0 2204 2243 595646476 595646515 1.170000e-09 75.0
13 TraesCS1D01G334700 chr2D 88.525 61 4 3 2204 2262 111513315 111513374 1.520000e-08 71.3
14 TraesCS1D01G334700 chr6D 95.769 780 25 7 2275 3050 351428146 351428921 0.000000e+00 1251.0
15 TraesCS1D01G334700 chr7D 95.753 777 29 2 2275 3050 436449519 436450292 0.000000e+00 1249.0
16 TraesCS1D01G334700 chr7D 95.635 779 28 5 2275 3050 593318388 593319163 0.000000e+00 1245.0
17 TraesCS1D01G334700 chrUn 95.349 43 2 0 2204 2246 245878028 245877986 5.460000e-08 69.4
18 TraesCS1D01G334700 chrUn 97.500 40 1 0 2204 2243 260280891 260280930 5.460000e-08 69.4
19 TraesCS1D01G334700 chrUn 95.349 43 2 0 2204 2246 321616967 321616925 5.460000e-08 69.4
20 TraesCS1D01G334700 chrUn 95.349 43 2 0 2204 2246 321705727 321705685 5.460000e-08 69.4
21 TraesCS1D01G334700 chrUn 95.349 43 2 0 2204 2246 456201538 456201496 5.460000e-08 69.4
22 TraesCS1D01G334700 chr4D 95.349 43 2 0 2204 2246 3440655 3440613 5.460000e-08 69.4
23 TraesCS1D01G334700 chr4D 95.349 43 2 0 2204 2246 233052979 233052937 5.460000e-08 69.4


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 TraesCS1D01G334700 chr1D 424866757 424869806 3049 False 5633.0 5633 100.0000 1 3050 1 chr1D.!!$F1 3049
1 TraesCS1D01G334700 chr1D 174652546 174653319 773 True 1232.0 1232 95.3670 2275 3050 1 chr1D.!!$R1 775
2 TraesCS1D01G334700 chr1A 520762159 520764236 2077 False 1192.0 2034 85.9655 78 2189 2 chr1A.!!$F1 2111
3 TraesCS1D01G334700 chr1B 573936189 573938393 2204 False 1348.5 1980 89.4260 31 2189 2 chr1B.!!$F1 2158
4 TraesCS1D01G334700 chr5D 241141707 241142483 776 False 1279.0 1279 96.4010 2275 3050 1 chr5D.!!$F2 775
5 TraesCS1D01G334700 chr5D 426139912 426140686 774 False 1238.0 1238 95.5010 2275 3050 1 chr5D.!!$F3 775
6 TraesCS1D01G334700 chr5D 321160809 321161582 773 True 1232.0 1232 95.3670 2275 3050 1 chr5D.!!$R1 775
7 TraesCS1D01G334700 chr5D 505192558 505193328 770 False 1232.0 1232 95.4780 2275 3047 1 chr5D.!!$F4 772
8 TraesCS1D01G334700 chr2D 429845085 429845861 776 True 1267.0 1267 96.1440 2275 3050 1 chr2D.!!$R1 775
9 TraesCS1D01G334700 chr6D 351428146 351428921 775 False 1251.0 1251 95.7690 2275 3050 1 chr6D.!!$F1 775
10 TraesCS1D01G334700 chr7D 436449519 436450292 773 False 1249.0 1249 95.7530 2275 3050 1 chr7D.!!$F1 775
11 TraesCS1D01G334700 chr7D 593318388 593319163 775 False 1245.0 1245 95.6350 2275 3050 1 chr7D.!!$F2 775

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
237 242 0.793861 TATCCGCACAACAAAGACGC 59.206 50.0 0.0 0.0 0.00 5.19 F
1843 1960 0.253610 TTTCCCGTGTGGTTGTGTCT 59.746 50.0 0.0 0.0 34.77 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2005 2122 0.181114 TTGGATTGGCCTCTGGATCG 59.819 55.0 3.32 0.0 37.63 3.69 R
2868 3016 0.249573 TCCGTTCGCCTCTTTTTCGT 60.250 50.0 0.00 0.0 0.00 3.85 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
39 40 4.024387 TGAAGGACGTTGAGTTAATGTTGC 60.024 41.667 0.00 0.00 38.60 4.17
63 64 7.829211 TGCACCTCATAGTTTAGCTAGATTTTT 59.171 33.333 0.00 0.00 32.45 1.94
65 66 9.606631 CACCTCATAGTTTAGCTAGATTTTTCT 57.393 33.333 0.00 0.00 32.45 2.52
66 67 9.825109 ACCTCATAGTTTAGCTAGATTTTTCTC 57.175 33.333 0.00 0.00 32.45 2.87
111 112 3.443681 CCATGTGTGGTTTACTCAATCCC 59.556 47.826 0.00 0.00 40.83 3.85
120 121 3.819564 TTACTCAATCCCACGATCCAG 57.180 47.619 0.00 0.00 0.00 3.86
127 128 2.754946 TCCCACGATCCAGTTTGTAC 57.245 50.000 0.00 0.00 0.00 2.90
132 133 1.278127 ACGATCCAGTTTGTACCCCAG 59.722 52.381 0.00 0.00 0.00 4.45
137 138 2.158579 TCCAGTTTGTACCCCAGAAACC 60.159 50.000 2.98 0.00 40.43 3.27
146 147 1.003928 ACCCCAGAAACCGTGGTATTC 59.996 52.381 0.00 0.00 32.62 1.75
204 209 1.210931 CAAACTGCCCATGTCTGCG 59.789 57.895 0.00 0.00 0.00 5.18
213 218 0.805322 CCATGTCTGCGTCTGCTCTC 60.805 60.000 0.00 0.00 43.34 3.20
230 235 3.126858 GCTCTCATTTTATCCGCACAACA 59.873 43.478 0.00 0.00 0.00 3.33
237 242 0.793861 TATCCGCACAACAAAGACGC 59.206 50.000 0.00 0.00 0.00 5.19
255 260 3.331150 ACGCCATCACGTTTCTTAATCA 58.669 40.909 0.00 0.00 45.75 2.57
281 286 4.215185 CAGCTCTTCCTTCTTTCCTCAAAC 59.785 45.833 0.00 0.00 0.00 2.93
446 483 3.008594 TCGAAAAAGGGATAAGGCTCACA 59.991 43.478 0.00 0.00 0.00 3.58
447 484 3.127030 CGAAAAAGGGATAAGGCTCACAC 59.873 47.826 0.00 0.00 0.00 3.82
469 506 3.653344 GCTTTCCTGTTTTTCCATGTCC 58.347 45.455 0.00 0.00 0.00 4.02
559 596 1.342074 TCAGGTTCTCCACACCAGAG 58.658 55.000 0.00 0.00 36.67 3.35
570 608 2.041081 CCACACCAGAGGAAACCCAATA 59.959 50.000 0.00 0.00 0.00 1.90
589 627 5.512921 CCAATACCAAAAAGGCCACAGATTT 60.513 40.000 5.01 0.00 43.14 2.17
591 629 6.926630 ATACCAAAAAGGCCACAGATTTAA 57.073 33.333 5.01 0.00 43.14 1.52
593 631 4.202315 ACCAAAAAGGCCACAGATTTAACC 60.202 41.667 5.01 0.00 43.14 2.85
702 774 3.056821 CCAACACTACTACTGCTGCTACA 60.057 47.826 0.00 0.00 0.00 2.74
703 775 4.556233 CAACACTACTACTGCTGCTACAA 58.444 43.478 0.00 0.00 0.00 2.41
822 897 5.691754 TGACGAATTCCATTCATACTCATCG 59.308 40.000 0.00 0.00 39.22 3.84
936 1014 1.298667 AACCATCGGTGGGTGCTAC 59.701 57.895 21.19 0.00 46.12 3.58
937 1015 1.198759 AACCATCGGTGGGTGCTACT 61.199 55.000 21.19 0.00 46.12 2.57
938 1016 1.898094 AACCATCGGTGGGTGCTACTA 60.898 52.381 21.19 0.00 46.12 1.82
942 1020 0.973496 TCGGTGGGTGCTACTATGCA 60.973 55.000 0.00 0.00 41.05 3.96
945 1023 2.224185 CGGTGGGTGCTACTATGCAATA 60.224 50.000 0.00 0.00 45.12 1.90
1092 1195 1.926426 CTCCCACCCATTGACTCCCC 61.926 65.000 0.00 0.00 0.00 4.81
1151 1254 0.915364 GGATGAAGCAGGAGAAGGGT 59.085 55.000 0.00 0.00 0.00 4.34
1631 1734 1.448540 CGCCACGATCAAGAAGGCT 60.449 57.895 0.00 0.00 43.07 4.58
1632 1735 1.699656 CGCCACGATCAAGAAGGCTG 61.700 60.000 0.00 0.00 43.07 4.85
1633 1736 1.986575 GCCACGATCAAGAAGGCTGC 61.987 60.000 0.00 0.00 42.01 5.25
1841 1958 1.546961 TTTTTCCCGTGTGGTTGTGT 58.453 45.000 0.00 0.00 34.77 3.72
1842 1959 1.096416 TTTTCCCGTGTGGTTGTGTC 58.904 50.000 0.00 0.00 34.77 3.67
1843 1960 0.253610 TTTCCCGTGTGGTTGTGTCT 59.746 50.000 0.00 0.00 34.77 3.41
1855 1972 3.115554 GGTTGTGTCTTGTGTGAATTGC 58.884 45.455 0.00 0.00 0.00 3.56
1884 2001 9.793259 ATTTTCTAGTGGTTAGATTTTGTCAGA 57.207 29.630 0.00 0.00 38.19 3.27
1968 2085 9.865321 GTTGTTAATTGGTAGAGTACACATCTA 57.135 33.333 0.00 0.00 0.00 1.98
2037 2158 2.393764 CAATCCAAACAAGTTCGGTGC 58.606 47.619 0.00 0.00 0.00 5.01
2042 2163 0.578211 AAACAAGTTCGGTGCGTACG 59.422 50.000 11.84 11.84 32.71 3.67
2100 2244 3.733443 ATGCTATGCTCGTGTCATACA 57.267 42.857 0.00 0.00 0.00 2.29
2106 2250 4.655762 ATGCTCGTGTCATACATACACT 57.344 40.909 4.99 0.00 44.05 3.55
2109 2253 3.547868 GCTCGTGTCATACATACACTGTG 59.452 47.826 6.19 6.19 44.05 3.66
2110 2254 4.104696 TCGTGTCATACATACACTGTGG 57.895 45.455 13.09 0.00 44.05 4.17
2112 2256 4.401202 TCGTGTCATACATACACTGTGGAT 59.599 41.667 13.09 6.16 44.05 3.41
2145 2289 1.830477 CCTCTGACTTTCCTAGCAGCT 59.170 52.381 0.00 0.00 31.88 4.24
2189 2333 2.997897 GGACTGGGAGGTGTCGCT 60.998 66.667 0.00 0.00 36.58 4.93
2190 2334 2.262915 GACTGGGAGGTGTCGCTG 59.737 66.667 0.00 0.00 39.59 5.18
2191 2335 2.524394 ACTGGGAGGTGTCGCTGT 60.524 61.111 0.00 0.00 41.25 4.40
2192 2336 2.100879 GACTGGGAGGTGTCGCTGTT 62.101 60.000 4.01 0.00 44.53 3.16
2193 2337 1.374758 CTGGGAGGTGTCGCTGTTC 60.375 63.158 0.00 0.00 36.58 3.18
2194 2338 1.821061 CTGGGAGGTGTCGCTGTTCT 61.821 60.000 0.00 0.00 36.58 3.01
2195 2339 1.374758 GGGAGGTGTCGCTGTTCTG 60.375 63.158 0.00 0.00 32.83 3.02
2196 2340 1.666011 GGAGGTGTCGCTGTTCTGA 59.334 57.895 0.00 0.00 0.00 3.27
2197 2341 0.667792 GGAGGTGTCGCTGTTCTGAC 60.668 60.000 0.00 0.00 35.67 3.51
2198 2342 0.032130 GAGGTGTCGCTGTTCTGACA 59.968 55.000 0.00 0.00 42.49 3.58
2200 2344 4.319249 TGTCGCTGTTCTGACACG 57.681 55.556 0.00 0.00 40.02 4.49
2201 2345 1.949133 TGTCGCTGTTCTGACACGC 60.949 57.895 0.00 0.00 40.02 5.34
2202 2346 2.355837 TCGCTGTTCTGACACGCC 60.356 61.111 0.00 0.00 33.41 5.68
2203 2347 2.661537 CGCTGTTCTGACACGCCA 60.662 61.111 0.00 0.00 30.86 5.69
2204 2348 2.661566 CGCTGTTCTGACACGCCAG 61.662 63.158 0.00 0.00 35.55 4.85
2205 2349 2.320587 GCTGTTCTGACACGCCAGG 61.321 63.158 0.00 0.00 34.99 4.45
2206 2350 1.669115 CTGTTCTGACACGCCAGGG 60.669 63.158 0.00 0.00 34.99 4.45
2207 2351 3.050275 GTTCTGACACGCCAGGGC 61.050 66.667 0.00 0.00 34.99 5.19
2208 2352 4.329545 TTCTGACACGCCAGGGCC 62.330 66.667 4.42 0.00 37.98 5.80
2216 2360 2.844362 CGCCAGGGCCCAGAGATA 60.844 66.667 27.56 0.00 37.98 1.98
2217 2361 2.832498 GCCAGGGCCCAGAGATAC 59.168 66.667 27.56 1.39 34.56 2.24
2218 2362 2.823758 GCCAGGGCCCAGAGATACC 61.824 68.421 27.56 0.00 34.56 2.73
2219 2363 1.074167 CCAGGGCCCAGAGATACCT 60.074 63.158 27.56 0.00 0.00 3.08
2220 2364 1.124477 CCAGGGCCCAGAGATACCTC 61.124 65.000 27.56 0.00 39.72 3.85
2235 2379 7.209471 GAGATACCTCTTCGATACATGAAGT 57.791 40.000 0.00 0.00 42.68 3.01
2236 2380 6.976088 AGATACCTCTTCGATACATGAAGTG 58.024 40.000 0.00 1.10 42.68 3.16
2237 2381 6.773200 AGATACCTCTTCGATACATGAAGTGA 59.227 38.462 0.00 0.00 42.68 3.41
2238 2382 5.000012 ACCTCTTCGATACATGAAGTGAC 58.000 43.478 0.00 0.00 42.68 3.67
2239 2383 4.462834 ACCTCTTCGATACATGAAGTGACA 59.537 41.667 0.00 0.00 42.68 3.58
2240 2384 5.047306 ACCTCTTCGATACATGAAGTGACAA 60.047 40.000 0.00 0.00 42.68 3.18
2241 2385 5.869344 CCTCTTCGATACATGAAGTGACAAA 59.131 40.000 0.00 0.00 42.68 2.83
2242 2386 6.536582 CCTCTTCGATACATGAAGTGACAAAT 59.463 38.462 0.00 0.00 42.68 2.32
2243 2387 7.065085 CCTCTTCGATACATGAAGTGACAAATT 59.935 37.037 0.00 0.00 42.68 1.82
2244 2388 7.963981 TCTTCGATACATGAAGTGACAAATTC 58.036 34.615 0.00 0.00 42.68 2.17
2245 2389 7.819415 TCTTCGATACATGAAGTGACAAATTCT 59.181 33.333 0.00 0.00 42.68 2.40
2246 2390 7.525688 TCGATACATGAAGTGACAAATTCTC 57.474 36.000 0.00 0.00 0.00 2.87
2247 2391 7.323420 TCGATACATGAAGTGACAAATTCTCT 58.677 34.615 0.00 0.00 0.00 3.10
2248 2392 7.489435 TCGATACATGAAGTGACAAATTCTCTC 59.511 37.037 0.00 0.00 0.00 3.20
2249 2393 7.490725 CGATACATGAAGTGACAAATTCTCTCT 59.509 37.037 0.00 0.00 0.00 3.10
2250 2394 6.798315 ACATGAAGTGACAAATTCTCTCTG 57.202 37.500 0.00 0.00 0.00 3.35
2251 2395 6.528321 ACATGAAGTGACAAATTCTCTCTGA 58.472 36.000 0.00 0.00 0.00 3.27
2252 2396 7.166851 ACATGAAGTGACAAATTCTCTCTGAT 58.833 34.615 0.00 0.00 0.00 2.90
2253 2397 7.119407 ACATGAAGTGACAAATTCTCTCTGATG 59.881 37.037 0.00 0.00 0.00 3.07
2254 2398 5.410746 TGAAGTGACAAATTCTCTCTGATGC 59.589 40.000 3.96 0.00 0.00 3.91
2255 2399 5.163281 AGTGACAAATTCTCTCTGATGCT 57.837 39.130 0.00 0.00 0.00 3.79
2256 2400 5.558818 AGTGACAAATTCTCTCTGATGCTT 58.441 37.500 0.00 0.00 0.00 3.91
2257 2401 6.002704 AGTGACAAATTCTCTCTGATGCTTT 58.997 36.000 0.00 0.00 0.00 3.51
2258 2402 6.072618 AGTGACAAATTCTCTCTGATGCTTTG 60.073 38.462 0.00 0.00 0.00 2.77
2259 2403 5.999600 TGACAAATTCTCTCTGATGCTTTGA 59.000 36.000 0.00 0.00 0.00 2.69
2260 2404 6.072838 TGACAAATTCTCTCTGATGCTTTGAC 60.073 38.462 0.00 0.00 0.00 3.18
2261 2405 5.766670 ACAAATTCTCTCTGATGCTTTGACA 59.233 36.000 0.00 0.00 0.00 3.58
2262 2406 6.433404 ACAAATTCTCTCTGATGCTTTGACAT 59.567 34.615 0.00 0.00 0.00 3.06
2263 2407 6.438259 AATTCTCTCTGATGCTTTGACATG 57.562 37.500 0.00 0.00 0.00 3.21
2264 2408 4.548451 TCTCTCTGATGCTTTGACATGT 57.452 40.909 0.00 0.00 0.00 3.21
2265 2409 4.502016 TCTCTCTGATGCTTTGACATGTC 58.498 43.478 19.27 19.27 0.00 3.06
2266 2410 4.020839 TCTCTCTGATGCTTTGACATGTCA 60.021 41.667 24.56 24.56 37.91 3.58
2267 2411 4.251268 TCTCTGATGCTTTGACATGTCAG 58.749 43.478 26.48 17.95 41.13 3.51
2268 2412 3.340928 TCTGATGCTTTGACATGTCAGG 58.659 45.455 26.48 22.67 41.13 3.86
2269 2413 2.422479 CTGATGCTTTGACATGTCAGGG 59.578 50.000 26.48 22.36 41.13 4.45
2270 2414 1.133790 GATGCTTTGACATGTCAGGGC 59.866 52.381 30.81 30.81 41.13 5.19
2271 2415 0.178995 TGCTTTGACATGTCAGGGCA 60.179 50.000 33.68 33.68 42.14 5.36
2272 2416 1.180029 GCTTTGACATGTCAGGGCAT 58.820 50.000 31.68 0.00 41.13 4.40
2273 2417 2.290832 TGCTTTGACATGTCAGGGCATA 60.291 45.455 33.68 22.19 40.79 3.14
2286 2430 8.469200 CATGTCAGGGCATAAAAAGATTTCTAA 58.531 33.333 0.00 0.00 0.00 2.10
2612 2760 8.587608 ACAATATCATTGTCCACATGTTTCTTT 58.412 29.630 0.00 0.00 0.00 2.52
2652 2800 9.023962 ACAAATCAACAAAGCTATTTAGATGGA 57.976 29.630 0.00 0.00 0.00 3.41
2746 2894 4.574892 TCACAAGATTCAGCATCGGTAAA 58.425 39.130 0.00 0.00 36.93 2.01
2758 2906 3.194861 CATCGGTAAAAGGAGCAATCGA 58.805 45.455 0.00 0.00 0.00 3.59
2866 3014 0.304705 ACACGAGCAAACAAGAAGCG 59.695 50.000 0.00 0.00 0.00 4.68
2868 3016 1.003972 CACGAGCAAACAAGAAGCGAA 60.004 47.619 0.00 0.00 0.00 4.70
2928 3079 1.492993 AAGGGTGAAGTGGGGAGAGC 61.493 60.000 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 7.974675 ACGTCCTTCAGACATAAAATTACATG 58.025 34.615 0.00 0.00 46.69 3.21
1 2 8.450964 CAACGTCCTTCAGACATAAAATTACAT 58.549 33.333 0.00 0.00 46.69 2.29
2 3 7.658167 TCAACGTCCTTCAGACATAAAATTACA 59.342 33.333 0.00 0.00 46.69 2.41
3 4 8.025243 TCAACGTCCTTCAGACATAAAATTAC 57.975 34.615 0.00 0.00 46.69 1.89
4 5 7.876068 ACTCAACGTCCTTCAGACATAAAATTA 59.124 33.333 0.00 0.00 46.69 1.40
5 6 6.710744 ACTCAACGTCCTTCAGACATAAAATT 59.289 34.615 0.00 0.00 46.69 1.82
6 7 6.231211 ACTCAACGTCCTTCAGACATAAAAT 58.769 36.000 0.00 0.00 46.69 1.82
7 8 5.607477 ACTCAACGTCCTTCAGACATAAAA 58.393 37.500 0.00 0.00 46.69 1.52
8 9 5.209818 ACTCAACGTCCTTCAGACATAAA 57.790 39.130 0.00 0.00 46.69 1.40
9 10 4.866508 ACTCAACGTCCTTCAGACATAA 57.133 40.909 0.00 0.00 46.69 1.90
10 11 4.866508 AACTCAACGTCCTTCAGACATA 57.133 40.909 0.00 0.00 46.69 2.29
11 12 3.753294 AACTCAACGTCCTTCAGACAT 57.247 42.857 0.00 0.00 46.69 3.06
12 13 4.659111 TTAACTCAACGTCCTTCAGACA 57.341 40.909 0.00 0.00 46.69 3.41
13 14 4.989168 ACATTAACTCAACGTCCTTCAGAC 59.011 41.667 0.00 0.00 42.54 3.51
14 15 5.209818 ACATTAACTCAACGTCCTTCAGA 57.790 39.130 0.00 0.00 0.00 3.27
15 16 5.679906 CAACATTAACTCAACGTCCTTCAG 58.320 41.667 0.00 0.00 0.00 3.02
16 17 4.024387 GCAACATTAACTCAACGTCCTTCA 60.024 41.667 0.00 0.00 0.00 3.02
17 18 4.024387 TGCAACATTAACTCAACGTCCTTC 60.024 41.667 0.00 0.00 0.00 3.46
18 19 3.880490 TGCAACATTAACTCAACGTCCTT 59.120 39.130 0.00 0.00 0.00 3.36
19 20 3.250040 GTGCAACATTAACTCAACGTCCT 59.750 43.478 0.00 0.00 36.32 3.85
20 21 3.551551 GTGCAACATTAACTCAACGTCC 58.448 45.455 0.00 0.00 36.32 4.79
21 22 3.250040 AGGTGCAACATTAACTCAACGTC 59.750 43.478 3.64 0.00 39.98 4.34
22 23 3.211045 AGGTGCAACATTAACTCAACGT 58.789 40.909 3.64 0.00 39.98 3.99
23 24 3.249799 TGAGGTGCAACATTAACTCAACG 59.750 43.478 3.64 0.00 39.98 4.10
24 25 4.829064 TGAGGTGCAACATTAACTCAAC 57.171 40.909 3.64 0.00 39.98 3.18
25 26 6.237901 ACTATGAGGTGCAACATTAACTCAA 58.762 36.000 3.64 0.00 39.98 3.02
26 27 5.804639 ACTATGAGGTGCAACATTAACTCA 58.195 37.500 3.64 0.00 39.98 3.41
27 28 6.743575 AACTATGAGGTGCAACATTAACTC 57.256 37.500 3.64 0.00 39.98 3.01
28 29 7.148239 GCTAAACTATGAGGTGCAACATTAACT 60.148 37.037 3.64 0.00 39.98 2.24
29 30 6.967199 GCTAAACTATGAGGTGCAACATTAAC 59.033 38.462 3.64 0.00 39.98 2.01
39 40 9.606631 AGAAAAATCTAGCTAAACTATGAGGTG 57.393 33.333 0.00 0.00 0.00 4.00
76 77 1.339438 ACACATGGCGCTCTTGATCTT 60.339 47.619 7.64 0.00 0.00 2.40
101 102 2.747177 ACTGGATCGTGGGATTGAGTA 58.253 47.619 0.00 0.00 31.51 2.59
111 112 1.002659 TGGGGTACAAACTGGATCGTG 59.997 52.381 0.00 0.00 0.00 4.35
120 121 1.605232 CACGGTTTCTGGGGTACAAAC 59.395 52.381 0.00 0.00 0.00 2.93
127 128 1.746470 GAATACCACGGTTTCTGGGG 58.254 55.000 0.00 0.00 32.45 4.96
132 133 6.592798 TTATTCATCGAATACCACGGTTTC 57.407 37.500 0.00 0.00 34.73 2.78
137 138 5.651172 TGCTTTATTCATCGAATACCACG 57.349 39.130 0.00 0.00 34.73 4.94
175 177 3.037549 TGGGCAGTTTGTGGAGATTTTT 58.962 40.909 0.00 0.00 0.00 1.94
180 182 0.478072 ACATGGGCAGTTTGTGGAGA 59.522 50.000 0.00 0.00 0.00 3.71
181 183 0.883833 GACATGGGCAGTTTGTGGAG 59.116 55.000 0.00 0.00 0.00 3.86
182 184 0.478072 AGACATGGGCAGTTTGTGGA 59.522 50.000 0.00 0.00 0.00 4.02
183 185 0.599558 CAGACATGGGCAGTTTGTGG 59.400 55.000 0.00 0.00 0.00 4.17
185 187 1.518056 CGCAGACATGGGCAGTTTGT 61.518 55.000 0.00 0.00 32.05 2.83
187 189 1.228245 ACGCAGACATGGGCAGTTT 60.228 52.632 0.00 0.00 42.93 2.66
204 209 3.001736 GTGCGGATAAAATGAGAGCAGAC 59.998 47.826 0.00 0.00 33.60 3.51
213 218 4.320690 CGTCTTTGTTGTGCGGATAAAATG 59.679 41.667 0.00 0.00 0.00 2.32
230 235 1.878953 AGAAACGTGATGGCGTCTTT 58.121 45.000 8.40 0.15 45.00 2.52
237 242 5.569059 GCTGTTTGATTAAGAAACGTGATGG 59.431 40.000 0.00 0.00 36.30 3.51
255 260 4.141390 TGAGGAAAGAAGGAAGAGCTGTTT 60.141 41.667 0.00 0.00 0.00 2.83
446 483 2.693074 ACATGGAAAAACAGGAAAGCGT 59.307 40.909 0.00 0.00 0.00 5.07
447 484 3.308530 GACATGGAAAAACAGGAAAGCG 58.691 45.455 0.00 0.00 0.00 4.68
469 506 1.254026 TACCTGTCCTGTCTTGTCCG 58.746 55.000 0.00 0.00 0.00 4.79
559 596 3.558321 GGCCTTTTTGGTATTGGGTTTCC 60.558 47.826 0.00 0.00 38.35 3.13
570 608 4.202315 GGTTAAATCTGTGGCCTTTTTGGT 60.202 41.667 3.32 0.00 38.35 3.67
589 627 4.234019 GCATCCATGCGTGGGTTA 57.766 55.556 24.78 6.18 46.06 2.85
608 676 3.625764 ACACTCAAACGTTTAGCATGTGT 59.374 39.130 14.20 18.35 0.00 3.72
609 677 4.209452 ACACTCAAACGTTTAGCATGTG 57.791 40.909 14.20 17.80 0.00 3.21
615 683 6.145696 AGCTAGCTTAACACTCAAACGTTTAG 59.854 38.462 12.68 13.34 0.00 1.85
671 739 4.645136 CAGTAGTAGTGTTGGATCTGGCTA 59.355 45.833 0.00 0.00 0.00 3.93
702 774 3.222603 CTTGGGCAGTTTGTACTCCTTT 58.777 45.455 0.00 0.00 30.26 3.11
703 775 2.863809 CTTGGGCAGTTTGTACTCCTT 58.136 47.619 0.00 0.00 30.26 3.36
846 921 1.708341 AATGTTCAGCAACTGGGCTT 58.292 45.000 0.00 0.00 42.71 4.35
922 1000 0.393077 GCATAGTAGCACCCACCGAT 59.607 55.000 0.00 0.00 0.00 4.18
923 1001 0.973496 TGCATAGTAGCACCCACCGA 60.973 55.000 0.00 0.00 40.11 4.69
936 1014 7.592938 TGAAACTTTGAACCAGTATTGCATAG 58.407 34.615 0.00 0.00 0.00 2.23
937 1015 7.517614 TGAAACTTTGAACCAGTATTGCATA 57.482 32.000 0.00 0.00 0.00 3.14
938 1016 6.403866 TGAAACTTTGAACCAGTATTGCAT 57.596 33.333 0.00 0.00 0.00 3.96
942 1020 7.176589 TGGTTTGAAACTTTGAACCAGTATT 57.823 32.000 8.09 0.00 44.72 1.89
1105 1208 1.619983 GTCGACGCCTTTCTCTTCTC 58.380 55.000 0.00 0.00 0.00 2.87
1470 1573 4.939915 CGCGTCCTCGTCGATCCG 62.940 72.222 0.00 0.00 38.23 4.18
1616 1719 1.372087 GGGCAGCCTTCTTGATCGTG 61.372 60.000 12.43 0.00 0.00 4.35
1713 1819 4.710695 CGCGGGCACACGTACAGA 62.711 66.667 0.00 0.00 35.98 3.41
1740 1846 3.406361 CGCGTGCAGTGACTGTCC 61.406 66.667 14.82 4.12 33.43 4.02
1741 1847 3.406361 CCGCGTGCAGTGACTGTC 61.406 66.667 14.82 7.23 33.43 3.51
1837 1954 3.419264 GTGCAATTCACACAAGACACA 57.581 42.857 0.00 0.00 44.98 3.72
1855 1972 9.612620 GACAAAATCTAACCACTAGAAAATGTG 57.387 33.333 0.00 0.00 40.12 3.21
1884 2001 1.884067 GCTGCTAACTGCTTCCAGGTT 60.884 52.381 0.00 0.00 43.53 3.50
1968 2085 0.534877 TGGCACGTCACATGCTTCTT 60.535 50.000 0.00 0.00 42.93 2.52
2003 2120 0.689623 GGATTGGCCTCTGGATCGAT 59.310 55.000 3.32 0.00 0.00 3.59
2004 2121 0.690744 TGGATTGGCCTCTGGATCGA 60.691 55.000 3.32 0.00 37.63 3.59
2005 2122 0.181114 TTGGATTGGCCTCTGGATCG 59.819 55.000 3.32 0.00 37.63 3.69
2006 2123 2.027385 GTTTGGATTGGCCTCTGGATC 58.973 52.381 3.32 0.00 37.63 3.36
2054 2198 3.093814 TCAGCATGCCATGTTCTCAAAT 58.906 40.909 15.66 0.00 34.76 2.32
2059 2203 2.139323 ATGTCAGCATGCCATGTTCT 57.861 45.000 15.66 0.00 34.76 3.01
2100 2244 2.362397 CGCCTGTCTATCCACAGTGTAT 59.638 50.000 0.00 0.00 42.10 2.29
2106 2250 1.897423 CCACGCCTGTCTATCCACA 59.103 57.895 0.00 0.00 0.00 4.17
2109 2253 2.109181 GGCCACGCCTGTCTATCC 59.891 66.667 0.00 0.00 46.69 2.59
2145 2289 1.155889 CAAATGCACCGCACTGACTA 58.844 50.000 0.00 0.00 43.04 2.59
2189 2333 2.425592 CCCTGGCGTGTCAGAACA 59.574 61.111 2.41 0.00 36.93 3.18
2190 2334 3.050275 GCCCTGGCGTGTCAGAAC 61.050 66.667 2.41 0.00 36.93 3.01
2191 2335 4.329545 GGCCCTGGCGTGTCAGAA 62.330 66.667 2.41 0.00 43.06 3.02
2198 2342 3.696518 TATCTCTGGGCCCTGGCGT 62.697 63.158 26.94 15.36 43.06 5.68
2199 2343 2.844362 TATCTCTGGGCCCTGGCG 60.844 66.667 26.94 18.26 43.06 5.69
2200 2344 2.823758 GGTATCTCTGGGCCCTGGC 61.824 68.421 26.94 12.63 41.06 4.85
2201 2345 1.074167 AGGTATCTCTGGGCCCTGG 60.074 63.158 26.94 17.69 0.00 4.45
2202 2346 2.446512 GAGGTATCTCTGGGCCCTG 58.553 63.158 25.70 23.93 37.07 4.45
2211 2355 7.041030 TCACTTCATGTATCGAAGAGGTATCTC 60.041 40.741 6.89 0.00 43.63 2.75
2212 2356 6.773200 TCACTTCATGTATCGAAGAGGTATCT 59.227 38.462 6.89 0.00 43.63 1.98
2213 2357 6.858993 GTCACTTCATGTATCGAAGAGGTATC 59.141 42.308 6.89 0.00 43.63 2.24
2214 2358 6.321435 TGTCACTTCATGTATCGAAGAGGTAT 59.679 38.462 6.89 0.00 43.63 2.73
2215 2359 5.650703 TGTCACTTCATGTATCGAAGAGGTA 59.349 40.000 6.89 0.00 43.63 3.08
2216 2360 4.462834 TGTCACTTCATGTATCGAAGAGGT 59.537 41.667 6.89 0.00 43.63 3.85
2217 2361 4.998788 TGTCACTTCATGTATCGAAGAGG 58.001 43.478 6.89 0.00 43.63 3.69
2218 2362 6.951256 TTTGTCACTTCATGTATCGAAGAG 57.049 37.500 6.89 0.00 43.63 2.85
2219 2363 7.819415 AGAATTTGTCACTTCATGTATCGAAGA 59.181 33.333 6.89 0.00 42.05 2.87
2220 2364 7.968246 AGAATTTGTCACTTCATGTATCGAAG 58.032 34.615 0.00 0.00 44.46 3.79
2221 2365 7.819415 AGAGAATTTGTCACTTCATGTATCGAA 59.181 33.333 0.00 0.00 0.00 3.71
2222 2366 7.323420 AGAGAATTTGTCACTTCATGTATCGA 58.677 34.615 0.00 0.00 0.00 3.59
2223 2367 7.490725 AGAGAGAATTTGTCACTTCATGTATCG 59.509 37.037 0.00 0.00 0.00 2.92
2224 2368 8.602328 CAGAGAGAATTTGTCACTTCATGTATC 58.398 37.037 0.00 0.00 0.00 2.24
2225 2369 8.316946 TCAGAGAGAATTTGTCACTTCATGTAT 58.683 33.333 0.00 0.00 0.00 2.29
2226 2370 7.670364 TCAGAGAGAATTTGTCACTTCATGTA 58.330 34.615 0.00 0.00 0.00 2.29
2227 2371 6.528321 TCAGAGAGAATTTGTCACTTCATGT 58.472 36.000 0.00 0.00 0.00 3.21
2228 2372 7.465173 CATCAGAGAGAATTTGTCACTTCATG 58.535 38.462 0.00 0.00 0.00 3.07
2229 2373 6.093771 GCATCAGAGAGAATTTGTCACTTCAT 59.906 38.462 0.00 0.00 0.00 2.57
2230 2374 5.410746 GCATCAGAGAGAATTTGTCACTTCA 59.589 40.000 0.00 0.00 0.00 3.02
2231 2375 5.642919 AGCATCAGAGAGAATTTGTCACTTC 59.357 40.000 0.00 0.00 0.00 3.01
2232 2376 5.558818 AGCATCAGAGAGAATTTGTCACTT 58.441 37.500 0.00 0.00 0.00 3.16
2233 2377 5.163281 AGCATCAGAGAGAATTTGTCACT 57.837 39.130 0.00 0.00 0.00 3.41
2234 2378 5.876612 AAGCATCAGAGAGAATTTGTCAC 57.123 39.130 0.00 0.00 0.00 3.67
2235 2379 5.999600 TCAAAGCATCAGAGAGAATTTGTCA 59.000 36.000 0.00 0.00 33.49 3.58
2236 2380 6.072838 TGTCAAAGCATCAGAGAGAATTTGTC 60.073 38.462 0.00 0.00 33.49 3.18
2237 2381 5.766670 TGTCAAAGCATCAGAGAGAATTTGT 59.233 36.000 0.00 0.00 33.49 2.83
2238 2382 6.250344 TGTCAAAGCATCAGAGAGAATTTG 57.750 37.500 0.00 0.00 33.25 2.32
2239 2383 6.433404 ACATGTCAAAGCATCAGAGAGAATTT 59.567 34.615 0.00 0.00 0.00 1.82
2240 2384 5.944599 ACATGTCAAAGCATCAGAGAGAATT 59.055 36.000 0.00 0.00 0.00 2.17
2241 2385 5.498393 ACATGTCAAAGCATCAGAGAGAAT 58.502 37.500 0.00 0.00 0.00 2.40
2242 2386 4.903054 ACATGTCAAAGCATCAGAGAGAA 58.097 39.130 0.00 0.00 0.00 2.87
2243 2387 4.020839 TGACATGTCAAAGCATCAGAGAGA 60.021 41.667 26.02 0.00 36.53 3.10
2244 2388 4.251268 TGACATGTCAAAGCATCAGAGAG 58.749 43.478 26.02 0.00 36.53 3.20
2245 2389 4.251268 CTGACATGTCAAAGCATCAGAGA 58.749 43.478 27.63 1.95 39.39 3.10
2246 2390 3.374367 CCTGACATGTCAAAGCATCAGAG 59.626 47.826 27.63 12.69 39.39 3.35
2247 2391 3.340928 CCTGACATGTCAAAGCATCAGA 58.659 45.455 27.63 2.67 39.39 3.27
2248 2392 2.422479 CCCTGACATGTCAAAGCATCAG 59.578 50.000 27.63 14.03 39.39 2.90
2249 2393 2.439409 CCCTGACATGTCAAAGCATCA 58.561 47.619 27.63 4.78 39.39 3.07
2250 2394 1.133790 GCCCTGACATGTCAAAGCATC 59.866 52.381 30.64 15.44 39.39 3.91
2251 2395 1.180029 GCCCTGACATGTCAAAGCAT 58.820 50.000 30.64 0.00 39.39 3.79
2252 2396 0.178995 TGCCCTGACATGTCAAAGCA 60.179 50.000 32.83 32.83 42.04 3.91
2253 2397 1.180029 ATGCCCTGACATGTCAAAGC 58.820 50.000 29.67 29.67 39.39 3.51
2254 2398 5.389859 TTTTATGCCCTGACATGTCAAAG 57.610 39.130 27.63 21.65 39.39 2.77
2255 2399 5.538053 TCTTTTTATGCCCTGACATGTCAAA 59.462 36.000 27.63 15.83 39.39 2.69
2256 2400 5.076182 TCTTTTTATGCCCTGACATGTCAA 58.924 37.500 27.63 14.62 39.39 3.18
2257 2401 4.661222 TCTTTTTATGCCCTGACATGTCA 58.339 39.130 26.33 26.33 38.06 3.58
2258 2402 5.841957 ATCTTTTTATGCCCTGACATGTC 57.158 39.130 19.27 19.27 0.00 3.06
2259 2403 6.438425 AGAAATCTTTTTATGCCCTGACATGT 59.562 34.615 0.00 0.00 0.00 3.21
2260 2404 6.870769 AGAAATCTTTTTATGCCCTGACATG 58.129 36.000 0.00 0.00 0.00 3.21
2261 2405 8.593945 TTAGAAATCTTTTTATGCCCTGACAT 57.406 30.769 0.00 0.00 0.00 3.06
2262 2406 8.415950 TTTAGAAATCTTTTTATGCCCTGACA 57.584 30.769 0.00 0.00 0.00 3.58
2263 2407 9.358872 CTTTTAGAAATCTTTTTATGCCCTGAC 57.641 33.333 0.00 0.00 0.00 3.51
2264 2408 8.034804 GCTTTTAGAAATCTTTTTATGCCCTGA 58.965 33.333 0.00 0.00 0.00 3.86
2265 2409 7.818930 TGCTTTTAGAAATCTTTTTATGCCCTG 59.181 33.333 0.00 0.00 0.00 4.45
2266 2410 7.906327 TGCTTTTAGAAATCTTTTTATGCCCT 58.094 30.769 0.00 0.00 0.00 5.19
2267 2411 8.546597 TTGCTTTTAGAAATCTTTTTATGCCC 57.453 30.769 0.00 0.00 0.00 5.36
2286 2430 3.399440 TGCCGGATTGAATTTTGCTTT 57.601 38.095 5.05 0.00 0.00 3.51
2440 2584 2.896685 CCCTCCGCTAAGATCATCTCTT 59.103 50.000 0.00 0.00 46.16 2.85
2484 2631 6.899393 TTCTTGGAATAAGTGCAAAGATGT 57.101 33.333 0.00 0.00 37.08 3.06
2523 2670 4.450082 AAACTTGGTTTTCGTCTTTGCT 57.550 36.364 0.00 0.00 31.10 3.91
2612 2760 5.640783 TGTTGATTTGTGTGACATGCAAAAA 59.359 32.000 5.62 0.00 36.00 1.94
2652 2800 2.598565 TCCTAGTGAAGATGCCGCTAT 58.401 47.619 0.00 0.00 0.00 2.97
2677 2825 3.378112 TGTCATGAAAGATCAATTCGCCC 59.622 43.478 0.00 0.00 39.49 6.13
2758 2906 7.439056 CCAACAACAATGATTTTCTTAGCACTT 59.561 33.333 0.00 0.00 0.00 3.16
2866 3014 1.398071 CCGTTCGCCTCTTTTTCGTTC 60.398 52.381 0.00 0.00 0.00 3.95
2868 3016 0.249573 TCCGTTCGCCTCTTTTTCGT 60.250 50.000 0.00 0.00 0.00 3.85
2928 3079 1.000385 TGCCATTTGCCTCTCGTTTTG 60.000 47.619 0.00 0.00 40.16 2.44


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

AutoCloner maintained by Alex Coulton.