Multiple sequence alignment - TraesCS3D01G472800

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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 TraesCS3D01G472800 chr3D 100.000 2624 0 0 1 2624 574781291 574778668 0.000000e+00 4846.0
1 TraesCS3D01G472800 chr3D 89.184 1470 146 5 1 1459 575480272 575481739 0.000000e+00 1821.0
2 TraesCS3D01G472800 chr3D 82.033 1653 267 21 1 1629 575546948 575548594 0.000000e+00 1380.0
3 TraesCS3D01G472800 chr3D 81.740 1632 272 18 1 1611 574769778 574768152 0.000000e+00 1339.0
4 TraesCS3D01G472800 chr3D 81.740 1632 272 18 1 1611 575488399 575490025 0.000000e+00 1339.0
5 TraesCS3D01G472800 chr3D 82.385 1476 235 14 1 1455 575527737 575529208 0.000000e+00 1262.0
6 TraesCS3D01G472800 chr3D 89.810 422 26 5 2209 2624 575481909 575482319 2.310000e-145 525.0
7 TraesCS3D01G472800 chr3D 91.349 289 18 4 1838 2121 575481732 575482018 3.170000e-104 388.0
8 TraesCS3D01G472800 chr3D 93.636 110 7 0 2012 2121 574779083 574778974 5.810000e-37 165.0
9 TraesCS3D01G472800 chr3D 93.636 110 7 0 2209 2318 574779280 574779171 5.810000e-37 165.0
10 TraesCS3D01G472800 chr3D 81.034 174 10 8 2117 2267 575529865 575530038 1.650000e-22 117.0
11 TraesCS3D01G472800 chr3A 94.918 2125 88 4 1 2121 710838584 710840692 0.000000e+00 3308.0
12 TraesCS3D01G472800 chr3A 81.862 1676 271 24 1 1651 710937871 710939538 0.000000e+00 1380.0
13 TraesCS3D01G472800 chr3A 81.495 1632 274 18 1 1611 711058289 711059913 0.000000e+00 1315.0
14 TraesCS3D01G472800 chr3A 82.632 1140 159 28 1 1109 710948692 710949823 0.000000e+00 972.0
15 TraesCS3D01G472800 chr3A 92.874 421 24 4 2209 2624 710840584 710841003 8.030000e-170 606.0
16 TraesCS3D01G472800 chr3A 82.235 349 62 0 5 353 747609805 747609457 4.240000e-78 302.0
17 TraesCS3D01G472800 chr3B 92.552 1987 101 15 1 1970 765549535 765551491 0.000000e+00 2806.0
18 TraesCS3D01G472800 chr3B 81.470 1673 278 24 1 1650 765928837 765930500 0.000000e+00 1343.0
19 TraesCS3D01G472800 chr3B 81.534 1630 277 17 1 1611 765670644 765672268 0.000000e+00 1321.0
20 TraesCS3D01G472800 chr3B 79.146 1640 289 35 1 1601 765855255 765856880 0.000000e+00 1085.0
21 TraesCS3D01G472800 chr3B 76.762 1674 314 48 1 1619 765589491 765591144 0.000000e+00 867.0
22 TraesCS3D01G472800 chr3B 90.802 424 30 3 2209 2624 765551567 765551989 2.280000e-155 558.0
23 TraesCS3D01G472800 chr3B 81.404 285 40 5 2227 2503 765599796 765600075 1.220000e-53 220.0
24 TraesCS3D01G472800 chr3B 95.327 107 5 0 2009 2115 765551564 765551670 1.250000e-38 171.0
25 TraesCS3D01G472800 chr3B 89.706 68 7 0 2051 2118 765599820 765599887 1.290000e-13 87.9
26 TraesCS3D01G472800 chr3B 88.406 69 8 0 2050 2118 765678123 765678191 1.670000e-12 84.2
27 TraesCS3D01G472800 chr3B 93.333 45 3 0 2126 2170 765936180 765936224 1.690000e-07 67.6
28 TraesCS3D01G472800 chr5B 87.879 99 11 1 2527 2624 358627898 358627996 5.930000e-22 115.0


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 TraesCS3D01G472800 chr3D 574778668 574781291 2623 True 1725.333333 4846 95.757333 1 2624 3 chr3D.!!$R2 2623
1 TraesCS3D01G472800 chr3D 575546948 575548594 1646 False 1380.000000 1380 82.033000 1 1629 1 chr3D.!!$F2 1628
2 TraesCS3D01G472800 chr3D 574768152 574769778 1626 True 1339.000000 1339 81.740000 1 1611 1 chr3D.!!$R1 1610
3 TraesCS3D01G472800 chr3D 575488399 575490025 1626 False 1339.000000 1339 81.740000 1 1611 1 chr3D.!!$F1 1610
4 TraesCS3D01G472800 chr3D 575480272 575482319 2047 False 911.333333 1821 90.114333 1 2624 3 chr3D.!!$F3 2623
5 TraesCS3D01G472800 chr3D 575527737 575530038 2301 False 689.500000 1262 81.709500 1 2267 2 chr3D.!!$F4 2266
6 TraesCS3D01G472800 chr3A 710838584 710841003 2419 False 1957.000000 3308 93.896000 1 2624 2 chr3A.!!$F4 2623
7 TraesCS3D01G472800 chr3A 710937871 710939538 1667 False 1380.000000 1380 81.862000 1 1651 1 chr3A.!!$F1 1650
8 TraesCS3D01G472800 chr3A 711058289 711059913 1624 False 1315.000000 1315 81.495000 1 1611 1 chr3A.!!$F3 1610
9 TraesCS3D01G472800 chr3A 710948692 710949823 1131 False 972.000000 972 82.632000 1 1109 1 chr3A.!!$F2 1108
10 TraesCS3D01G472800 chr3B 765928837 765930500 1663 False 1343.000000 1343 81.470000 1 1650 1 chr3B.!!$F5 1649
11 TraesCS3D01G472800 chr3B 765670644 765672268 1624 False 1321.000000 1321 81.534000 1 1611 1 chr3B.!!$F2 1610
12 TraesCS3D01G472800 chr3B 765549535 765551989 2454 False 1178.333333 2806 92.893667 1 2624 3 chr3B.!!$F7 2623
13 TraesCS3D01G472800 chr3B 765855255 765856880 1625 False 1085.000000 1085 79.146000 1 1601 1 chr3B.!!$F4 1600
14 TraesCS3D01G472800 chr3B 765589491 765591144 1653 False 867.000000 867 76.762000 1 1619 1 chr3B.!!$F1 1618

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
923 952 0.247736 AAGGACCTCGATGCTGTGAC 59.752 55.0 0.0 0.0 0.0 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2578 2889 0.250727 TGTGAGTGGCCCAGCTAAAC 60.251 55.0 0.0 0.0 0.0 2.01 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
193 194 9.905713 TTGTTTGTTATATCTTAGCATCTTCCT 57.094 29.630 0.00 0.00 0.00 3.36
466 479 1.039856 GGCACAGGAAGAAAAAGGCA 58.960 50.000 0.00 0.00 0.00 4.75
735 760 4.463891 CCACTGAAATTGGGAAGCTACAAT 59.536 41.667 5.63 5.63 38.85 2.71
923 952 0.247736 AAGGACCTCGATGCTGTGAC 59.752 55.000 0.00 0.00 0.00 3.67
1039 1101 2.833794 TGTGCAAACTGGACAGTCTAC 58.166 47.619 5.30 3.96 43.78 2.59
1197 1271 5.163457 CCTTTCTCTCCTCACCTATCTTCAC 60.163 48.000 0.00 0.00 0.00 3.18
1237 1311 0.179073 ATCCGAGGCGATCCAACTTG 60.179 55.000 0.00 0.00 33.74 3.16
1255 1329 0.112995 TGTTGGGATGCTTCCTGCTT 59.887 50.000 17.48 0.00 42.20 3.91
1350 1436 1.579084 TTGCGTTATTCCCGTGTGCC 61.579 55.000 0.00 0.00 0.00 5.01
1352 1438 1.373590 GCGTTATTCCCGTGTGCCAT 61.374 55.000 0.00 0.00 0.00 4.40
1489 1650 1.080637 GATTTGTGCATGCGCCACA 60.081 52.632 27.42 16.47 37.32 4.17
1638 1812 2.615447 ACATTGACGCATGCATAGGAAG 59.385 45.455 19.57 1.32 0.00 3.46
1677 1877 6.942005 AGGTGTTCATTCTTATGTGTCATTGA 59.058 34.615 0.00 0.00 33.34 2.57
1680 1880 8.453320 GTGTTCATTCTTATGTGTCATTGATCA 58.547 33.333 0.00 0.00 33.34 2.92
1730 1970 4.278669 CGGAGGCTAGCTAGAGAAATACAA 59.721 45.833 25.15 0.00 0.00 2.41
1779 2019 5.619607 CGTGTATTCTTTTGTTTTCTCACCG 59.380 40.000 0.00 0.00 0.00 4.94
1829 2070 4.388499 TTTCAGGCGGCCGGAGTC 62.388 66.667 29.38 9.97 0.00 3.36
1991 2260 4.766375 TCTACTTATGCTGCAAAGGTACC 58.234 43.478 20.54 2.73 0.00 3.34
2009 2282 7.253905 AGGTACCAACATATGTGAAGTACTT 57.746 36.000 26.31 21.47 33.41 2.24
2011 2284 7.038587 AGGTACCAACATATGTGAAGTACTTCA 60.039 37.037 30.07 30.07 46.27 3.02
2024 2297 6.993079 TGAAGTACTTCAGATTAGTGAGCAA 58.007 36.000 30.07 6.34 43.90 3.91
2025 2298 7.615403 TGAAGTACTTCAGATTAGTGAGCAAT 58.385 34.615 30.07 0.00 43.90 3.56
2026 2299 7.761704 TGAAGTACTTCAGATTAGTGAGCAATC 59.238 37.037 30.07 3.17 43.90 2.67
2027 2300 6.578023 AGTACTTCAGATTAGTGAGCAATCC 58.422 40.000 0.00 0.00 33.67 3.01
2029 2302 5.181748 ACTTCAGATTAGTGAGCAATCCAC 58.818 41.667 0.00 0.00 33.67 4.02
2030 2303 5.046014 ACTTCAGATTAGTGAGCAATCCACT 60.046 40.000 0.00 0.00 45.75 4.00
2031 2304 6.155221 ACTTCAGATTAGTGAGCAATCCACTA 59.845 38.462 0.00 0.00 43.79 2.74
2043 2316 6.483307 TGAGCAATCCACTAAGTAATATGCAC 59.517 38.462 0.00 0.00 33.89 4.57
2047 2320 7.227512 GCAATCCACTAAGTAATATGCACTTCT 59.772 37.037 6.31 0.00 37.42 2.85
2048 2321 9.764363 CAATCCACTAAGTAATATGCACTTCTA 57.236 33.333 6.31 0.00 37.42 2.10
2051 2324 9.764363 TCCACTAAGTAATATGCACTTCTATTG 57.236 33.333 6.31 2.05 37.42 1.90
2052 2325 8.993121 CCACTAAGTAATATGCACTTCTATTGG 58.007 37.037 6.31 6.01 37.42 3.16
2053 2326 9.764363 CACTAAGTAATATGCACTTCTATTGGA 57.236 33.333 6.31 0.00 37.42 3.53
2057 2330 9.851686 AAGTAATATGCACTTCTATTGGATGAA 57.148 29.630 0.00 0.00 30.36 2.57
2058 2331 9.851686 AGTAATATGCACTTCTATTGGATGAAA 57.148 29.630 0.00 0.00 0.00 2.69
2059 2332 9.884465 GTAATATGCACTTCTATTGGATGAAAC 57.116 33.333 0.00 0.00 0.00 2.78
2060 2333 8.523915 AATATGCACTTCTATTGGATGAAACA 57.476 30.769 0.00 0.00 0.00 2.83
2061 2334 8.701908 ATATGCACTTCTATTGGATGAAACAT 57.298 30.769 0.00 0.00 0.00 2.71
2062 2335 6.198650 TGCACTTCTATTGGATGAAACATG 57.801 37.500 0.00 0.00 0.00 3.21
2063 2336 5.711506 TGCACTTCTATTGGATGAAACATGT 59.288 36.000 0.00 0.00 0.00 3.21
2064 2337 6.032094 GCACTTCTATTGGATGAAACATGTG 58.968 40.000 0.00 0.00 0.00 3.21
2065 2338 6.558009 CACTTCTATTGGATGAAACATGTGG 58.442 40.000 0.00 0.00 0.00 4.17
2066 2339 6.151648 CACTTCTATTGGATGAAACATGTGGT 59.848 38.462 0.00 0.00 0.00 4.16
2067 2340 6.375455 ACTTCTATTGGATGAAACATGTGGTC 59.625 38.462 0.00 0.39 0.00 4.02
2068 2341 6.065976 TCTATTGGATGAAACATGTGGTCT 57.934 37.500 0.00 0.00 0.00 3.85
2069 2342 6.484288 TCTATTGGATGAAACATGTGGTCTT 58.516 36.000 0.00 0.00 0.00 3.01
2070 2343 6.947733 TCTATTGGATGAAACATGTGGTCTTT 59.052 34.615 0.00 0.00 0.00 2.52
2071 2344 8.106462 TCTATTGGATGAAACATGTGGTCTTTA 58.894 33.333 0.00 0.00 0.00 1.85
2072 2345 7.722949 ATTGGATGAAACATGTGGTCTTTAT 57.277 32.000 0.00 0.00 0.00 1.40
2073 2346 7.537596 TTGGATGAAACATGTGGTCTTTATT 57.462 32.000 0.00 0.00 0.00 1.40
2074 2347 7.537596 TGGATGAAACATGTGGTCTTTATTT 57.462 32.000 0.00 0.00 0.00 1.40
2075 2348 7.961351 TGGATGAAACATGTGGTCTTTATTTT 58.039 30.769 0.00 0.00 0.00 1.82
2076 2349 8.087750 TGGATGAAACATGTGGTCTTTATTTTC 58.912 33.333 0.00 0.00 0.00 2.29
2077 2350 8.306761 GGATGAAACATGTGGTCTTTATTTTCT 58.693 33.333 0.00 0.00 0.00 2.52
2078 2351 9.132521 GATGAAACATGTGGTCTTTATTTTCTG 57.867 33.333 0.00 0.00 0.00 3.02
2079 2352 8.006298 TGAAACATGTGGTCTTTATTTTCTGT 57.994 30.769 0.00 0.00 0.00 3.41
2080 2353 8.474025 TGAAACATGTGGTCTTTATTTTCTGTT 58.526 29.630 0.00 0.00 0.00 3.16
2081 2354 8.871686 AAACATGTGGTCTTTATTTTCTGTTC 57.128 30.769 0.00 0.00 0.00 3.18
2082 2355 6.668323 ACATGTGGTCTTTATTTTCTGTTCG 58.332 36.000 0.00 0.00 0.00 3.95
2083 2356 5.682943 TGTGGTCTTTATTTTCTGTTCGG 57.317 39.130 0.00 0.00 0.00 4.30
2084 2357 5.369833 TGTGGTCTTTATTTTCTGTTCGGA 58.630 37.500 0.00 0.00 0.00 4.55
2085 2358 5.823570 TGTGGTCTTTATTTTCTGTTCGGAA 59.176 36.000 0.00 0.00 0.00 4.30
2086 2359 6.140786 GTGGTCTTTATTTTCTGTTCGGAAC 58.859 40.000 13.86 13.86 0.00 3.62
2087 2360 5.823570 TGGTCTTTATTTTCTGTTCGGAACA 59.176 36.000 21.30 21.30 39.52 3.18
2088 2361 6.488683 TGGTCTTTATTTTCTGTTCGGAACAT 59.511 34.615 22.65 11.01 41.26 2.71
2089 2362 7.013846 TGGTCTTTATTTTCTGTTCGGAACATT 59.986 33.333 22.65 9.14 41.26 2.71
2090 2363 7.865889 GGTCTTTATTTTCTGTTCGGAACATTT 59.134 33.333 22.65 9.43 41.26 2.32
2091 2364 8.690840 GTCTTTATTTTCTGTTCGGAACATTTG 58.309 33.333 22.65 12.29 41.26 2.32
2092 2365 8.625651 TCTTTATTTTCTGTTCGGAACATTTGA 58.374 29.630 22.65 14.30 41.26 2.69
2093 2366 8.568732 TTTATTTTCTGTTCGGAACATTTGAC 57.431 30.769 22.65 0.00 41.26 3.18
2094 2367 5.828299 TTTTCTGTTCGGAACATTTGACT 57.172 34.783 22.65 0.00 41.26 3.41
2095 2368 4.811555 TTCTGTTCGGAACATTTGACTG 57.188 40.909 22.65 10.28 41.26 3.51
2096 2369 4.066646 TCTGTTCGGAACATTTGACTGA 57.933 40.909 22.65 12.30 41.26 3.41
2097 2370 4.447290 TCTGTTCGGAACATTTGACTGAA 58.553 39.130 22.65 0.00 41.26 3.02
2098 2371 4.272504 TCTGTTCGGAACATTTGACTGAAC 59.727 41.667 22.65 17.85 44.88 3.18
2099 2372 3.314080 TGTTCGGAACATTTGACTGAACC 59.686 43.478 19.07 0.00 44.38 3.62
2100 2373 3.201353 TCGGAACATTTGACTGAACCA 57.799 42.857 0.00 0.00 0.00 3.67
2101 2374 3.750371 TCGGAACATTTGACTGAACCAT 58.250 40.909 0.00 0.00 0.00 3.55
2102 2375 4.141287 TCGGAACATTTGACTGAACCATT 58.859 39.130 0.00 0.00 0.00 3.16
2103 2376 4.582656 TCGGAACATTTGACTGAACCATTT 59.417 37.500 0.00 0.00 0.00 2.32
2104 2377 4.681025 CGGAACATTTGACTGAACCATTTG 59.319 41.667 0.00 0.00 0.00 2.32
2105 2378 5.600696 GGAACATTTGACTGAACCATTTGT 58.399 37.500 0.00 0.00 0.00 2.83
2106 2379 6.514212 CGGAACATTTGACTGAACCATTTGTA 60.514 38.462 0.00 0.00 0.00 2.41
2107 2380 7.378181 GGAACATTTGACTGAACCATTTGTAT 58.622 34.615 0.00 0.00 0.00 2.29
2108 2381 7.329226 GGAACATTTGACTGAACCATTTGTATG 59.671 37.037 0.00 0.00 0.00 2.39
2109 2382 6.158598 ACATTTGACTGAACCATTTGTATGC 58.841 36.000 0.00 0.00 0.00 3.14
2110 2383 4.782019 TTGACTGAACCATTTGTATGCC 57.218 40.909 0.00 0.00 0.00 4.40
2111 2384 4.032960 TGACTGAACCATTTGTATGCCT 57.967 40.909 0.00 0.00 0.00 4.75
2112 2385 3.758023 TGACTGAACCATTTGTATGCCTG 59.242 43.478 0.00 0.00 0.00 4.85
2113 2386 3.758554 GACTGAACCATTTGTATGCCTGT 59.241 43.478 0.00 0.00 0.00 4.00
2114 2387 3.507233 ACTGAACCATTTGTATGCCTGTG 59.493 43.478 0.00 0.00 0.00 3.66
2115 2388 2.230992 TGAACCATTTGTATGCCTGTGC 59.769 45.455 0.00 0.00 38.26 4.57
2116 2389 2.220653 ACCATTTGTATGCCTGTGCT 57.779 45.000 0.00 0.00 38.71 4.40
2117 2390 2.528564 ACCATTTGTATGCCTGTGCTT 58.471 42.857 0.00 0.00 38.71 3.91
2118 2391 2.231964 ACCATTTGTATGCCTGTGCTTG 59.768 45.455 0.00 0.00 38.71 4.01
2124 2397 2.423185 TGTATGCCTGTGCTTGCAATAC 59.577 45.455 0.00 3.14 41.50 1.89
2138 2411 5.277490 GCTTGCAATACGAATCTATTCAGCA 60.277 40.000 0.00 0.00 36.61 4.41
2154 2427 3.429492 TCAGCATTGGCCTGTTCATTTA 58.571 40.909 3.32 0.00 42.56 1.40
2160 2433 3.084536 TGGCCTGTTCATTTATGCTGA 57.915 42.857 3.32 0.00 0.00 4.26
2182 2457 5.433712 TGAAAAGATACATAGGGCCCCTTAA 59.566 40.000 21.43 1.27 34.61 1.85
2202 2477 6.860023 CCTTAATTGCTATTTCTGCATGCTAC 59.140 38.462 20.33 0.00 40.34 3.58
2204 2479 5.840243 ATTGCTATTTCTGCATGCTACAA 57.160 34.783 20.33 8.77 40.34 2.41
2318 2621 0.883153 TTGTATGCCTGTGCTTGCAG 59.117 50.000 0.00 0.00 41.46 4.41
2346 2650 4.275196 CACATCTGCATGTATTTGCTAGCT 59.725 41.667 17.23 0.00 41.69 3.32
2355 2664 6.128200 GCATGTATTTGCTAGCTGTATATGCA 60.128 38.462 28.83 19.67 38.74 3.96
2373 2682 4.574674 TGCACCTATCTGAAGTTCCAAT 57.425 40.909 0.00 0.00 0.00 3.16
2387 2696 8.347004 TGAAGTTCCAATAAATCTGCAATGTA 57.653 30.769 0.00 0.00 0.00 2.29
2405 2714 3.255725 TGTAGATTTCGCCTTGGTTACG 58.744 45.455 0.00 0.00 0.00 3.18
2425 2734 8.437742 GGTTACGTATGGTGCATAAATACATAC 58.562 37.037 13.51 12.36 40.07 2.39
2492 2801 5.297527 TGCTCCACATTACATTATCAAGCAG 59.702 40.000 0.00 0.00 32.70 4.24
2503 2813 6.574350 ACATTATCAAGCAGTCCACTAGTAC 58.426 40.000 0.00 0.00 0.00 2.73
2541 2851 1.463674 CCCTGTATGTGTGCCCTTTC 58.536 55.000 0.00 0.00 0.00 2.62
2557 2868 2.280628 CTTTCCGTAGTTGGATGGAGC 58.719 52.381 0.00 0.00 38.00 4.70
2578 2889 5.990408 AGCATGTTTTCTTCTTCTGTAACG 58.010 37.500 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
193 194 7.632861 TCCTTTCATAATCTTGTGATCTTCCA 58.367 34.615 0.00 0.00 31.51 3.53
370 383 2.299013 ACCATGTCATGTACACGACACT 59.701 45.455 25.49 12.79 44.45 3.55
452 465 6.686484 ACCAAATTATGCCTTTTTCTTCCT 57.314 33.333 0.00 0.00 0.00 3.36
463 476 3.715628 ATCTGCGAACCAAATTATGCC 57.284 42.857 0.00 0.00 0.00 4.40
466 479 4.704540 TGGACAATCTGCGAACCAAATTAT 59.295 37.500 0.00 0.00 0.00 1.28
923 952 1.341285 TGGTCAGATGGCCCAATTCTG 60.341 52.381 7.87 7.87 39.61 3.02
981 1013 4.464008 CCATCAAAGCTTTATCCAGGCTA 58.536 43.478 12.25 0.00 35.06 3.93
1039 1101 4.956085 TCTCCACCACGGACATAAATATG 58.044 43.478 0.00 0.00 39.64 1.78
1197 1271 2.890311 TGGCACTTCAACCACCTTTATG 59.110 45.455 0.00 0.00 0.00 1.90
1255 1329 9.613428 AATATCCATTATCTCGAGAACACAAAA 57.387 29.630 20.91 7.57 0.00 2.44
1350 1436 3.480470 ACAAAGGAAGTGACACTCCATG 58.520 45.455 19.74 18.74 0.00 3.66
1352 1438 4.974645 ATACAAAGGAAGTGACACTCCA 57.025 40.909 19.74 5.63 0.00 3.86
1428 1514 0.532573 TAGCTGAGAAGGTGAAGCCG 59.467 55.000 0.00 0.00 43.70 5.52
1489 1650 0.618968 ACTCGCTCCAAGGAAGGGAT 60.619 55.000 0.00 0.00 33.04 3.85
1638 1812 5.909621 TGAACACCTAGTGTATGTACCTC 57.090 43.478 0.00 0.00 46.79 3.85
1677 1877 9.741647 GAAACTGAGAAAGAAACAAAGAATGAT 57.258 29.630 0.00 0.00 0.00 2.45
1680 1880 9.525409 CATGAAACTGAGAAAGAAACAAAGAAT 57.475 29.630 0.00 0.00 0.00 2.40
1730 1970 1.178276 CAGAGGTTAGCTCGTGGAGT 58.822 55.000 5.75 0.00 31.39 3.85
1779 2019 6.468543 AGAAGTGGAGAGGAATTAAACACTC 58.531 40.000 0.00 0.00 36.77 3.51
1829 2070 2.222027 GATTTGGTGAATCGGCCTAGG 58.778 52.381 3.67 3.67 35.21 3.02
1957 2221 8.474831 TGCAGCATAAGTAGAAGTAGTTCATAA 58.525 33.333 12.77 0.00 34.82 1.90
2009 2282 6.544928 TTAGTGGATTGCTCACTAATCTGA 57.455 37.500 11.25 0.00 46.48 3.27
2015 2288 7.872993 GCATATTACTTAGTGGATTGCTCACTA 59.127 37.037 0.00 0.00 42.91 2.74
2016 2289 6.708054 GCATATTACTTAGTGGATTGCTCACT 59.292 38.462 0.00 0.00 46.02 3.41
2017 2290 6.483307 TGCATATTACTTAGTGGATTGCTCAC 59.517 38.462 0.00 0.00 35.51 3.51
2018 2291 6.483307 GTGCATATTACTTAGTGGATTGCTCA 59.517 38.462 0.00 0.00 0.00 4.26
2019 2292 6.708054 AGTGCATATTACTTAGTGGATTGCTC 59.292 38.462 0.00 1.35 0.00 4.26
2020 2293 6.595682 AGTGCATATTACTTAGTGGATTGCT 58.404 36.000 0.00 0.00 0.00 3.91
2021 2294 6.867662 AGTGCATATTACTTAGTGGATTGC 57.132 37.500 0.00 0.47 0.00 3.56
2022 2295 8.668510 AGAAGTGCATATTACTTAGTGGATTG 57.331 34.615 0.00 0.00 38.42 2.67
2025 2298 9.764363 CAATAGAAGTGCATATTACTTAGTGGA 57.236 33.333 0.00 0.00 38.42 4.02
2026 2299 8.993121 CCAATAGAAGTGCATATTACTTAGTGG 58.007 37.037 0.00 4.25 38.42 4.00
2027 2300 9.764363 TCCAATAGAAGTGCATATTACTTAGTG 57.236 33.333 0.00 0.00 38.42 2.74
2031 2304 9.851686 TTCATCCAATAGAAGTGCATATTACTT 57.148 29.630 0.00 2.55 40.84 2.24
2032 2305 9.851686 TTTCATCCAATAGAAGTGCATATTACT 57.148 29.630 0.00 0.00 0.00 2.24
2034 2307 9.625747 TGTTTCATCCAATAGAAGTGCATATTA 57.374 29.630 0.00 0.00 0.00 0.98
2036 2309 8.573885 CATGTTTCATCCAATAGAAGTGCATAT 58.426 33.333 0.00 0.00 0.00 1.78
2037 2310 7.557358 ACATGTTTCATCCAATAGAAGTGCATA 59.443 33.333 0.00 0.00 0.00 3.14
2038 2311 6.379133 ACATGTTTCATCCAATAGAAGTGCAT 59.621 34.615 0.00 0.00 0.00 3.96
2039 2312 5.711506 ACATGTTTCATCCAATAGAAGTGCA 59.288 36.000 0.00 0.00 0.00 4.57
2043 2316 6.600822 AGACCACATGTTTCATCCAATAGAAG 59.399 38.462 0.00 0.00 0.00 2.85
2047 2320 8.821686 ATAAAGACCACATGTTTCATCCAATA 57.178 30.769 0.00 0.00 0.00 1.90
2048 2321 7.722949 ATAAAGACCACATGTTTCATCCAAT 57.277 32.000 0.00 0.00 0.00 3.16
2049 2322 7.537596 AATAAAGACCACATGTTTCATCCAA 57.462 32.000 0.00 0.00 0.00 3.53
2050 2323 7.537596 AAATAAAGACCACATGTTTCATCCA 57.462 32.000 0.00 0.00 0.00 3.41
2051 2324 8.306761 AGAAAATAAAGACCACATGTTTCATCC 58.693 33.333 0.00 0.00 0.00 3.51
2052 2325 9.132521 CAGAAAATAAAGACCACATGTTTCATC 57.867 33.333 0.00 0.00 0.00 2.92
2053 2326 8.641541 ACAGAAAATAAAGACCACATGTTTCAT 58.358 29.630 0.00 0.00 0.00 2.57
2054 2327 8.006298 ACAGAAAATAAAGACCACATGTTTCA 57.994 30.769 0.00 0.00 0.00 2.69
2055 2328 8.871686 AACAGAAAATAAAGACCACATGTTTC 57.128 30.769 0.00 0.00 0.00 2.78
2056 2329 7.647715 CGAACAGAAAATAAAGACCACATGTTT 59.352 33.333 0.00 0.00 0.00 2.83
2057 2330 7.138736 CGAACAGAAAATAAAGACCACATGTT 58.861 34.615 0.00 0.00 0.00 2.71
2058 2331 6.293955 CCGAACAGAAAATAAAGACCACATGT 60.294 38.462 0.00 0.00 0.00 3.21
2059 2332 6.072728 TCCGAACAGAAAATAAAGACCACATG 60.073 38.462 0.00 0.00 0.00 3.21
2060 2333 6.001460 TCCGAACAGAAAATAAAGACCACAT 58.999 36.000 0.00 0.00 0.00 3.21
2061 2334 5.369833 TCCGAACAGAAAATAAAGACCACA 58.630 37.500 0.00 0.00 0.00 4.17
2062 2335 5.934935 TCCGAACAGAAAATAAAGACCAC 57.065 39.130 0.00 0.00 0.00 4.16
2063 2336 5.823570 TGTTCCGAACAGAAAATAAAGACCA 59.176 36.000 9.99 0.00 36.25 4.02
2064 2337 6.308371 TGTTCCGAACAGAAAATAAAGACC 57.692 37.500 9.99 0.00 36.25 3.85
2065 2338 8.690840 CAAATGTTCCGAACAGAAAATAAAGAC 58.309 33.333 18.46 0.00 45.95 3.01
2066 2339 8.625651 TCAAATGTTCCGAACAGAAAATAAAGA 58.374 29.630 18.46 4.80 45.95 2.52
2067 2340 8.690840 GTCAAATGTTCCGAACAGAAAATAAAG 58.309 33.333 18.46 2.86 45.95 1.85
2068 2341 8.410141 AGTCAAATGTTCCGAACAGAAAATAAA 58.590 29.630 18.46 0.00 45.95 1.40
2069 2342 7.860373 CAGTCAAATGTTCCGAACAGAAAATAA 59.140 33.333 18.46 0.00 45.95 1.40
2070 2343 7.227711 TCAGTCAAATGTTCCGAACAGAAAATA 59.772 33.333 18.46 0.94 45.95 1.40
2071 2344 6.039270 TCAGTCAAATGTTCCGAACAGAAAAT 59.961 34.615 18.46 0.00 45.95 1.82
2072 2345 5.355630 TCAGTCAAATGTTCCGAACAGAAAA 59.644 36.000 18.46 3.20 45.95 2.29
2073 2346 4.878971 TCAGTCAAATGTTCCGAACAGAAA 59.121 37.500 18.46 2.87 45.95 2.52
2074 2347 4.447290 TCAGTCAAATGTTCCGAACAGAA 58.553 39.130 18.46 2.55 45.95 3.02
2075 2348 4.066646 TCAGTCAAATGTTCCGAACAGA 57.933 40.909 18.46 8.54 45.95 3.41
2076 2349 4.527564 GTTCAGTCAAATGTTCCGAACAG 58.472 43.478 18.46 6.41 45.95 3.16
2077 2350 3.314080 GGTTCAGTCAAATGTTCCGAACA 59.686 43.478 16.15 16.15 46.94 3.18
2078 2351 3.314080 TGGTTCAGTCAAATGTTCCGAAC 59.686 43.478 4.18 4.18 0.00 3.95
2079 2352 3.546724 TGGTTCAGTCAAATGTTCCGAA 58.453 40.909 0.00 0.00 0.00 4.30
2080 2353 3.201353 TGGTTCAGTCAAATGTTCCGA 57.799 42.857 0.00 0.00 0.00 4.55
2081 2354 4.503741 AATGGTTCAGTCAAATGTTCCG 57.496 40.909 0.00 0.00 0.00 4.30
2082 2355 5.600696 ACAAATGGTTCAGTCAAATGTTCC 58.399 37.500 0.00 0.00 0.00 3.62
2083 2356 7.148755 GCATACAAATGGTTCAGTCAAATGTTC 60.149 37.037 0.00 0.00 33.38 3.18
2084 2357 6.646240 GCATACAAATGGTTCAGTCAAATGTT 59.354 34.615 0.00 0.00 33.38 2.71
2085 2358 6.158598 GCATACAAATGGTTCAGTCAAATGT 58.841 36.000 0.00 0.00 33.38 2.71
2086 2359 5.577945 GGCATACAAATGGTTCAGTCAAATG 59.422 40.000 0.00 0.00 33.38 2.32
2087 2360 5.481473 AGGCATACAAATGGTTCAGTCAAAT 59.519 36.000 0.00 0.00 33.38 2.32
2088 2361 4.832266 AGGCATACAAATGGTTCAGTCAAA 59.168 37.500 0.00 0.00 33.38 2.69
2089 2362 4.218200 CAGGCATACAAATGGTTCAGTCAA 59.782 41.667 0.00 0.00 33.38 3.18
2090 2363 3.758023 CAGGCATACAAATGGTTCAGTCA 59.242 43.478 0.00 0.00 33.38 3.41
2091 2364 3.758554 ACAGGCATACAAATGGTTCAGTC 59.241 43.478 0.00 0.00 33.38 3.51
2092 2365 3.507233 CACAGGCATACAAATGGTTCAGT 59.493 43.478 0.00 0.00 33.38 3.41
2093 2366 3.674138 GCACAGGCATACAAATGGTTCAG 60.674 47.826 0.00 0.00 40.72 3.02
2094 2367 2.230992 GCACAGGCATACAAATGGTTCA 59.769 45.455 0.00 0.00 40.72 3.18
2095 2368 2.493278 AGCACAGGCATACAAATGGTTC 59.507 45.455 0.00 0.00 44.61 3.62
2096 2369 2.528564 AGCACAGGCATACAAATGGTT 58.471 42.857 0.00 0.00 44.61 3.67
2097 2370 2.220653 AGCACAGGCATACAAATGGT 57.779 45.000 0.00 0.00 44.61 3.55
2098 2371 2.883574 CAAGCACAGGCATACAAATGG 58.116 47.619 0.00 0.00 44.61 3.16
2099 2372 2.264813 GCAAGCACAGGCATACAAATG 58.735 47.619 0.00 0.00 44.61 2.32
2100 2373 1.894466 TGCAAGCACAGGCATACAAAT 59.106 42.857 0.00 0.00 44.61 2.32
2101 2374 1.326328 TGCAAGCACAGGCATACAAA 58.674 45.000 0.00 0.00 44.61 2.83
2102 2375 1.326328 TTGCAAGCACAGGCATACAA 58.674 45.000 0.00 0.00 44.61 2.41
2103 2376 1.548081 ATTGCAAGCACAGGCATACA 58.452 45.000 4.94 0.00 44.61 2.29
2104 2377 2.539547 CGTATTGCAAGCACAGGCATAC 60.540 50.000 4.94 0.00 44.61 2.39
2105 2378 1.670295 CGTATTGCAAGCACAGGCATA 59.330 47.619 4.94 0.00 44.61 3.14
2106 2379 0.452987 CGTATTGCAAGCACAGGCAT 59.547 50.000 4.94 0.00 44.61 4.40
2107 2380 0.605050 TCGTATTGCAAGCACAGGCA 60.605 50.000 4.94 0.00 44.61 4.75
2108 2381 0.521291 TTCGTATTGCAAGCACAGGC 59.479 50.000 4.94 0.00 41.61 4.85
2109 2382 2.679837 AGATTCGTATTGCAAGCACAGG 59.320 45.455 4.94 0.00 0.00 4.00
2110 2383 5.663795 ATAGATTCGTATTGCAAGCACAG 57.336 39.130 4.94 2.94 0.00 3.66
2111 2384 5.584251 TGAATAGATTCGTATTGCAAGCACA 59.416 36.000 4.94 0.00 39.62 4.57
2112 2385 6.048073 TGAATAGATTCGTATTGCAAGCAC 57.952 37.500 4.94 4.56 39.62 4.40
2113 2386 5.277490 GCTGAATAGATTCGTATTGCAAGCA 60.277 40.000 4.94 0.00 39.62 3.91
2114 2387 5.142962 GCTGAATAGATTCGTATTGCAAGC 58.857 41.667 4.94 0.00 39.62 4.01
2115 2388 6.291067 TGCTGAATAGATTCGTATTGCAAG 57.709 37.500 4.94 0.00 39.62 4.01
2116 2389 6.866010 ATGCTGAATAGATTCGTATTGCAA 57.134 33.333 0.00 0.00 39.62 4.08
2117 2390 6.293571 CCAATGCTGAATAGATTCGTATTGCA 60.294 38.462 19.61 14.45 39.21 4.08
2118 2391 6.082338 CCAATGCTGAATAGATTCGTATTGC 58.918 40.000 19.61 11.21 39.21 3.56
2124 2397 3.058432 CAGGCCAATGCTGAATAGATTCG 60.058 47.826 5.01 0.00 39.62 3.34
2138 2411 4.025360 TCAGCATAAATGAACAGGCCAAT 58.975 39.130 5.01 0.00 0.00 3.16
2154 2427 4.401925 GGCCCTATGTATCTTTTCAGCAT 58.598 43.478 0.00 0.00 0.00 3.79
2160 2433 6.545860 ATTAAGGGGCCCTATGTATCTTTT 57.454 37.500 29.08 8.61 31.13 2.27
2182 2457 5.591472 TCTTGTAGCATGCAGAAATAGCAAT 59.409 36.000 21.98 0.00 46.27 3.56
2202 2477 7.215789 AGTGGATTGCTCACTAATCTATCTTG 58.784 38.462 0.00 0.00 42.91 3.02
2204 2479 6.992664 AGTGGATTGCTCACTAATCTATCT 57.007 37.500 0.00 0.00 42.91 1.98
2286 2582 4.012374 AGGCATACAAATGGTTCAGTCAG 58.988 43.478 0.00 0.00 33.38 3.51
2318 2621 4.558095 GCAAATACATGCAGATGTGGATCC 60.558 45.833 4.20 4.20 45.70 3.36
2346 2650 6.326323 TGGAACTTCAGATAGGTGCATATACA 59.674 38.462 0.00 0.00 27.32 2.29
2355 2664 7.500559 GCAGATTTATTGGAACTTCAGATAGGT 59.499 37.037 0.00 0.00 0.00 3.08
2387 2696 2.467566 ACGTAACCAAGGCGAAATCT 57.532 45.000 0.00 0.00 0.00 2.40
2405 2714 8.560355 TGATGGTATGTATTTATGCACCATAC 57.440 34.615 4.14 0.00 37.96 2.39
2425 2734 4.614535 GCAAGCAGAAGTAACAACTGATGG 60.615 45.833 0.00 0.00 34.07 3.51
2485 2794 4.919793 AGTAGTACTAGTGGACTGCTTGA 58.080 43.478 9.52 0.00 35.39 3.02
2541 2851 1.134401 ACATGCTCCATCCAACTACGG 60.134 52.381 0.00 0.00 0.00 4.02
2557 2868 9.370126 CTAAACGTTACAGAAGAAGAAAACATG 57.630 33.333 0.00 0.00 0.00 3.21
2578 2889 0.250727 TGTGAGTGGCCCAGCTAAAC 60.251 55.000 0.00 0.00 0.00 2.01


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

AutoCloner maintained by Alex Coulton.