Multiple sequence alignment - TraesCS2D01G394600

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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 TraesCS2D01G394600 chr2D 100.000 2321 0 0 1 2321 506144928 506142608 0.000000e+00 4287.0
1 TraesCS2D01G394600 chr2B 91.409 2200 109 33 1 2185 593655750 593653616 0.000000e+00 2942.0
2 TraesCS2D01G394600 chr2A 92.253 1975 85 26 1 1939 650627960 650626018 0.000000e+00 2737.0
3 TraesCS2D01G394600 chr2A 87.770 278 19 4 1937 2208 650625703 650625435 6.230000e-81 311.0
4 TraesCS2D01G394600 chr7D 94.643 56 1 1 2214 2267 1744430 1744375 4.110000e-13 86.1
5 TraesCS2D01G394600 chr6D 94.231 52 3 0 2213 2264 69269837 69269888 1.910000e-11 80.5
6 TraesCS2D01G394600 chr6B 94.340 53 1 1 2214 2264 541949832 541949884 1.910000e-11 80.5
7 TraesCS2D01G394600 chr5B 92.857 56 2 1 2214 2267 448126356 448126301 1.910000e-11 80.5
8 TraesCS2D01G394600 chr4B 94.340 53 1 1 2214 2264 526266682 526266734 1.910000e-11 80.5
9 TraesCS2D01G394600 chr7B 92.308 52 2 1 2218 2267 162140795 162140744 3.200000e-09 73.1
10 TraesCS2D01G394600 chr7A 86.765 68 6 2 2209 2274 96559211 96559145 3.200000e-09 73.1
11 TraesCS2D01G394600 chr5A 93.878 49 1 1 2218 2264 290387353 290387401 3.200000e-09 73.1
12 TraesCS2D01G394600 chr5D 88.333 60 5 1 2217 2274 346639857 346639798 1.150000e-08 71.3
13 TraesCS2D01G394600 chr3B 96.774 31 1 0 899 929 794705295 794705265 4.000000e-03 52.8


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 TraesCS2D01G394600 chr2D 506142608 506144928 2320 True 4287 4287 100.0000 1 2321 1 chr2D.!!$R1 2320
1 TraesCS2D01G394600 chr2B 593653616 593655750 2134 True 2942 2942 91.4090 1 2185 1 chr2B.!!$R1 2184
2 TraesCS2D01G394600 chr2A 650625435 650627960 2525 True 1524 2737 90.0115 1 2208 2 chr2A.!!$R1 2207

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
964 985 0.526211 TGGACTCGATCTGTTGACGG 59.474 55.0 0.0 0.0 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2102 2466 0.539051 CCTGCCCTGTCAAGTAGGAG 59.461 60.0 1.58 0.0 37.52 3.69 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
537 543 1.069159 CGATACGGATGAACGAGGAGG 60.069 57.143 0.00 0.00 37.61 4.30
591 597 1.821753 CATCGCGGAATATCTCCTCCT 59.178 52.381 6.13 0.00 42.85 3.69
592 598 1.996798 TCGCGGAATATCTCCTCCTT 58.003 50.000 6.13 0.00 42.85 3.36
593 599 1.887198 TCGCGGAATATCTCCTCCTTC 59.113 52.381 6.13 0.00 42.85 3.46
596 602 2.896039 CGGAATATCTCCTCCTTCCCT 58.104 52.381 0.00 0.00 42.85 4.20
603 609 4.521062 CCTCCTTCCCTCGCGCAG 62.521 72.222 8.75 3.84 0.00 5.18
667 673 3.788766 GACTTTGACGCGCGGCAT 61.789 61.111 41.79 26.74 30.63 4.40
668 674 3.308878 GACTTTGACGCGCGGCATT 62.309 57.895 41.79 26.91 30.63 3.56
695 702 6.136541 TCTTTTCTTTTTCCTTGTCTCTGC 57.863 37.500 0.00 0.00 0.00 4.26
730 737 1.604604 CTTTGTGAAGGCCGGAAAGA 58.395 50.000 5.05 0.00 0.00 2.52
811 821 1.651240 TACGTGCGGTCTACAGAGGC 61.651 60.000 0.00 0.00 0.00 4.70
964 985 0.526211 TGGACTCGATCTGTTGACGG 59.474 55.000 0.00 0.00 0.00 4.79
1067 1088 2.857992 GTCGTCGTCGTCGTCGTG 60.858 66.667 18.44 6.23 45.27 4.35
1070 1091 2.794166 GTCGTCGTCGTCGTGGTG 60.794 66.667 11.41 0.00 38.33 4.17
1376 1405 1.483004 TGCCGAATCCATTCTTCCGTA 59.517 47.619 0.00 0.00 34.69 4.02
1403 1432 2.223479 GCAGTAGCTTCTCTTCTCTCGG 60.223 54.545 0.00 0.00 37.91 4.63
1464 1493 1.583986 CTCGCTCCGGGATCAGATC 59.416 63.158 0.00 1.18 0.00 2.75
1465 1494 2.193865 CTCGCTCCGGGATCAGATCG 62.194 65.000 0.00 0.00 0.00 3.69
1468 1497 1.960612 CTCCGGGATCAGATCGGAC 59.039 63.158 8.79 0.00 46.48 4.79
1470 1499 1.531840 CCGGGATCAGATCGGACCT 60.532 63.158 4.80 0.00 45.96 3.85
1539 1579 2.548875 CAGGATCACTACTGCTGCTTC 58.451 52.381 0.00 0.00 0.00 3.86
1570 1610 3.372060 GTTACTTTGCAGTGTTCTTGCC 58.628 45.455 0.00 0.00 34.06 4.52
1572 1612 1.035139 CTTTGCAGTGTTCTTGCCCT 58.965 50.000 0.00 0.00 0.00 5.19
1573 1613 1.410153 CTTTGCAGTGTTCTTGCCCTT 59.590 47.619 0.00 0.00 0.00 3.95
1576 1616 1.458639 GCAGTGTTCTTGCCCTTGCT 61.459 55.000 0.00 0.00 38.71 3.91
1586 1626 0.823356 TGCCCTTGCTCTTGTTCACC 60.823 55.000 0.00 0.00 38.71 4.02
1636 1676 2.160417 CCGATCAAGTGCCAACTTTCTC 59.840 50.000 0.00 0.00 44.47 2.87
1693 1733 1.708027 CGCCGAAAGTCTAAAGCGG 59.292 57.895 0.00 0.00 44.47 5.52
1696 1736 0.672401 CCGAAAGTCTAAAGCGGGCA 60.672 55.000 0.00 0.00 38.40 5.36
1697 1737 0.721718 CGAAAGTCTAAAGCGGGCAG 59.278 55.000 0.00 0.00 0.00 4.85
1827 1867 3.801997 CCCCAGGGAATGCTCGCT 61.802 66.667 7.25 0.00 45.27 4.93
1862 1902 3.153825 GGACGGGTTCCACTTCCA 58.846 61.111 0.00 0.00 45.10 3.53
1863 1903 1.302271 GGACGGGTTCCACTTCCAC 60.302 63.158 0.00 0.00 45.10 4.02
1864 1904 1.752833 GACGGGTTCCACTTCCACT 59.247 57.895 0.00 0.00 0.00 4.00
1865 1905 0.320508 GACGGGTTCCACTTCCACTC 60.321 60.000 0.00 0.00 0.00 3.51
1866 1906 1.374252 CGGGTTCCACTTCCACTCG 60.374 63.158 0.00 0.00 0.00 4.18
1867 1907 1.003718 GGGTTCCACTTCCACTCGG 60.004 63.158 0.00 0.00 0.00 4.63
1868 1908 1.003718 GGTTCCACTTCCACTCGGG 60.004 63.158 0.00 0.00 38.37 5.14
1869 1909 1.671379 GTTCCACTTCCACTCGGGC 60.671 63.158 0.00 0.00 36.21 6.13
1871 1911 2.046892 CCACTTCCACTCGGGCAG 60.047 66.667 0.00 0.00 36.21 4.85
1872 1912 2.743928 CACTTCCACTCGGGCAGC 60.744 66.667 0.00 0.00 36.21 5.25
1882 1922 3.264897 CGGGCAGCGATCTTTCGG 61.265 66.667 0.00 0.00 45.59 4.30
1914 1955 3.069158 CGGGTGTTATCTTAGGTAGGTGG 59.931 52.174 0.00 0.00 0.00 4.61
1999 2360 7.511959 AAGAGGATCCAAGTAAACTTTTGTC 57.488 36.000 15.82 0.00 33.66 3.18
2014 2375 7.678947 AACTTTTGTCATCTTGTCATCCTAG 57.321 36.000 0.00 0.00 0.00 3.02
2034 2398 5.745294 CCTAGTTTAACAAGATAGCGCGTTA 59.255 40.000 8.43 6.54 0.00 3.18
2098 2462 4.162320 GTGTGATGAGAGATTCCCAGGTTA 59.838 45.833 0.00 0.00 0.00 2.85
2099 2463 4.162320 TGTGATGAGAGATTCCCAGGTTAC 59.838 45.833 0.00 0.00 0.00 2.50
2100 2464 4.407296 GTGATGAGAGATTCCCAGGTTACT 59.593 45.833 0.00 0.00 0.00 2.24
2101 2465 5.598830 GTGATGAGAGATTCCCAGGTTACTA 59.401 44.000 0.00 0.00 0.00 1.82
2102 2466 5.598830 TGATGAGAGATTCCCAGGTTACTAC 59.401 44.000 0.00 0.00 0.00 2.73
2103 2467 5.208294 TGAGAGATTCCCAGGTTACTACT 57.792 43.478 0.00 0.00 0.00 2.57
2104 2468 5.202004 TGAGAGATTCCCAGGTTACTACTC 58.798 45.833 0.00 0.00 0.00 2.59
2105 2469 4.548669 AGAGATTCCCAGGTTACTACTCC 58.451 47.826 0.00 0.00 0.00 3.85
2106 2470 4.233287 AGAGATTCCCAGGTTACTACTCCT 59.767 45.833 0.00 0.00 33.96 3.69
2144 2508 3.224884 GATGCGATAGGAGCCTAGTTC 57.775 52.381 2.33 0.00 42.54 3.01
2210 2574 8.777865 TCTGAATTACAAGATGTTCTACTTGG 57.222 34.615 0.00 0.00 45.03 3.61
2211 2575 8.593679 TCTGAATTACAAGATGTTCTACTTGGA 58.406 33.333 0.00 0.00 45.03 3.53
2212 2576 8.777865 TGAATTACAAGATGTTCTACTTGGAG 57.222 34.615 0.00 0.00 45.03 3.86
2213 2577 7.334421 TGAATTACAAGATGTTCTACTTGGAGC 59.666 37.037 0.00 0.00 45.03 4.70
2214 2578 4.623932 ACAAGATGTTCTACTTGGAGCA 57.376 40.909 0.00 0.00 45.03 4.26
2215 2579 5.171339 ACAAGATGTTCTACTTGGAGCAT 57.829 39.130 0.00 0.00 45.03 3.79
2216 2580 4.940046 ACAAGATGTTCTACTTGGAGCATG 59.060 41.667 0.00 0.00 45.03 4.06
2217 2581 4.833478 AGATGTTCTACTTGGAGCATGT 57.167 40.909 0.00 0.00 37.30 3.21
2218 2582 5.171339 AGATGTTCTACTTGGAGCATGTT 57.829 39.130 0.00 0.00 37.30 2.71
2219 2583 5.564550 AGATGTTCTACTTGGAGCATGTTT 58.435 37.500 0.00 0.00 37.30 2.83
2220 2584 6.006449 AGATGTTCTACTTGGAGCATGTTTT 58.994 36.000 0.00 0.00 37.30 2.43
2221 2585 7.168219 AGATGTTCTACTTGGAGCATGTTTTA 58.832 34.615 0.00 0.00 37.30 1.52
2222 2586 6.801539 TGTTCTACTTGGAGCATGTTTTAG 57.198 37.500 0.00 0.00 0.00 1.85
2223 2587 6.296026 TGTTCTACTTGGAGCATGTTTTAGT 58.704 36.000 0.00 0.00 0.00 2.24
2224 2588 6.204688 TGTTCTACTTGGAGCATGTTTTAGTG 59.795 38.462 0.00 0.00 0.00 2.74
2225 2589 5.865085 TCTACTTGGAGCATGTTTTAGTGT 58.135 37.500 0.00 0.00 0.00 3.55
2226 2590 4.836125 ACTTGGAGCATGTTTTAGTGTG 57.164 40.909 0.00 0.00 0.00 3.82
2227 2591 4.207165 ACTTGGAGCATGTTTTAGTGTGT 58.793 39.130 0.00 0.00 0.00 3.72
2228 2592 4.644685 ACTTGGAGCATGTTTTAGTGTGTT 59.355 37.500 0.00 0.00 0.00 3.32
2229 2593 5.127031 ACTTGGAGCATGTTTTAGTGTGTTT 59.873 36.000 0.00 0.00 0.00 2.83
2230 2594 4.930963 TGGAGCATGTTTTAGTGTGTTTG 58.069 39.130 0.00 0.00 0.00 2.93
2231 2595 4.400884 TGGAGCATGTTTTAGTGTGTTTGT 59.599 37.500 0.00 0.00 0.00 2.83
2232 2596 5.105554 TGGAGCATGTTTTAGTGTGTTTGTT 60.106 36.000 0.00 0.00 0.00 2.83
2233 2597 5.810074 GGAGCATGTTTTAGTGTGTTTGTTT 59.190 36.000 0.00 0.00 0.00 2.83
2234 2598 6.975772 GGAGCATGTTTTAGTGTGTTTGTTTA 59.024 34.615 0.00 0.00 0.00 2.01
2235 2599 7.043656 GGAGCATGTTTTAGTGTGTTTGTTTAC 60.044 37.037 0.00 0.00 0.00 2.01
2236 2600 7.543756 AGCATGTTTTAGTGTGTTTGTTTACT 58.456 30.769 0.00 0.00 0.00 2.24
2237 2601 7.700656 AGCATGTTTTAGTGTGTTTGTTTACTC 59.299 33.333 0.00 0.00 0.00 2.59
2238 2602 7.486551 GCATGTTTTAGTGTGTTTGTTTACTCA 59.513 33.333 0.00 0.00 0.00 3.41
2239 2603 9.515020 CATGTTTTAGTGTGTTTGTTTACTCAT 57.485 29.630 0.00 0.00 0.00 2.90
2241 2605 9.915629 TGTTTTAGTGTGTTTGTTTACTCATTT 57.084 25.926 0.00 0.00 0.00 2.32
2244 2608 9.781834 TTTAGTGTGTTTGTTTACTCATTTCAG 57.218 29.630 0.00 0.00 0.00 3.02
2245 2609 7.391148 AGTGTGTTTGTTTACTCATTTCAGT 57.609 32.000 0.00 0.00 0.00 3.41
2246 2610 7.472543 AGTGTGTTTGTTTACTCATTTCAGTC 58.527 34.615 0.00 0.00 0.00 3.51
2247 2611 7.336931 AGTGTGTTTGTTTACTCATTTCAGTCT 59.663 33.333 0.00 0.00 0.00 3.24
2248 2612 8.609176 GTGTGTTTGTTTACTCATTTCAGTCTA 58.391 33.333 0.00 0.00 0.00 2.59
2249 2613 9.337396 TGTGTTTGTTTACTCATTTCAGTCTAT 57.663 29.630 0.00 0.00 0.00 1.98
2250 2614 9.599322 GTGTTTGTTTACTCATTTCAGTCTATG 57.401 33.333 0.00 0.00 0.00 2.23
2251 2615 9.337396 TGTTTGTTTACTCATTTCAGTCTATGT 57.663 29.630 0.00 0.00 0.00 2.29
2285 2649 9.775854 ATTGACATCTTCTAATAGTGAATGGAG 57.224 33.333 0.00 0.00 0.00 3.86
2286 2650 7.730084 TGACATCTTCTAATAGTGAATGGAGG 58.270 38.462 0.00 0.00 0.00 4.30
2287 2651 7.072263 ACATCTTCTAATAGTGAATGGAGGG 57.928 40.000 0.00 0.00 0.00 4.30
2288 2652 6.846505 ACATCTTCTAATAGTGAATGGAGGGA 59.153 38.462 0.00 0.00 0.00 4.20
2289 2653 6.985653 TCTTCTAATAGTGAATGGAGGGAG 57.014 41.667 0.00 0.00 0.00 4.30
2290 2654 6.444704 TCTTCTAATAGTGAATGGAGGGAGT 58.555 40.000 0.00 0.00 0.00 3.85
2291 2655 7.592736 TCTTCTAATAGTGAATGGAGGGAGTA 58.407 38.462 0.00 0.00 0.00 2.59
2292 2656 7.726291 TCTTCTAATAGTGAATGGAGGGAGTAG 59.274 40.741 0.00 0.00 0.00 2.57
2293 2657 7.162973 TCTAATAGTGAATGGAGGGAGTAGA 57.837 40.000 0.00 0.00 0.00 2.59
2294 2658 7.235079 TCTAATAGTGAATGGAGGGAGTAGAG 58.765 42.308 0.00 0.00 0.00 2.43
2295 2659 3.767309 AGTGAATGGAGGGAGTAGAGT 57.233 47.619 0.00 0.00 0.00 3.24
2296 2660 4.883021 AGTGAATGGAGGGAGTAGAGTA 57.117 45.455 0.00 0.00 0.00 2.59
2297 2661 5.208294 AGTGAATGGAGGGAGTAGAGTAA 57.792 43.478 0.00 0.00 0.00 2.24
2298 2662 5.782925 AGTGAATGGAGGGAGTAGAGTAAT 58.217 41.667 0.00 0.00 0.00 1.89
2299 2663 6.923670 AGTGAATGGAGGGAGTAGAGTAATA 58.076 40.000 0.00 0.00 0.00 0.98
2300 2664 7.540183 AGTGAATGGAGGGAGTAGAGTAATAT 58.460 38.462 0.00 0.00 0.00 1.28
2301 2665 8.013667 AGTGAATGGAGGGAGTAGAGTAATATT 58.986 37.037 0.00 0.00 0.00 1.28
2302 2666 8.091449 GTGAATGGAGGGAGTAGAGTAATATTG 58.909 40.741 0.00 0.00 0.00 1.90
2303 2667 6.613153 ATGGAGGGAGTAGAGTAATATTGC 57.387 41.667 0.00 0.00 0.00 3.56
2304 2668 4.523173 TGGAGGGAGTAGAGTAATATTGCG 59.477 45.833 0.00 0.00 0.00 4.85
2305 2669 4.765856 GGAGGGAGTAGAGTAATATTGCGA 59.234 45.833 0.00 0.00 0.00 5.10
2306 2670 5.106078 GGAGGGAGTAGAGTAATATTGCGAG 60.106 48.000 0.00 0.00 0.00 5.03
2307 2671 4.767928 AGGGAGTAGAGTAATATTGCGAGG 59.232 45.833 0.00 0.00 0.00 4.63
2308 2672 4.082136 GGGAGTAGAGTAATATTGCGAGGG 60.082 50.000 0.00 0.00 0.00 4.30
2309 2673 4.082136 GGAGTAGAGTAATATTGCGAGGGG 60.082 50.000 0.00 0.00 0.00 4.79
2310 2674 4.737578 AGTAGAGTAATATTGCGAGGGGA 58.262 43.478 0.00 0.00 0.00 4.81
2311 2675 5.145564 AGTAGAGTAATATTGCGAGGGGAA 58.854 41.667 0.00 0.00 0.00 3.97
2312 2676 5.780793 AGTAGAGTAATATTGCGAGGGGAAT 59.219 40.000 0.00 0.00 37.92 3.01
2313 2677 5.568620 AGAGTAATATTGCGAGGGGAATT 57.431 39.130 0.00 0.00 35.64 2.17
2314 2678 5.941788 AGAGTAATATTGCGAGGGGAATTT 58.058 37.500 0.00 0.00 35.64 1.82
2315 2679 5.765182 AGAGTAATATTGCGAGGGGAATTTG 59.235 40.000 0.00 0.00 35.64 2.32
2316 2680 4.827284 AGTAATATTGCGAGGGGAATTTGG 59.173 41.667 0.00 0.00 35.64 3.28
2317 2681 3.593442 ATATTGCGAGGGGAATTTGGA 57.407 42.857 0.00 0.00 35.64 3.53
2318 2682 2.230130 ATTGCGAGGGGAATTTGGAA 57.770 45.000 0.00 0.00 28.79 3.53
2319 2683 2.002505 TTGCGAGGGGAATTTGGAAA 57.997 45.000 0.00 0.00 0.00 3.13
2320 2684 1.253100 TGCGAGGGGAATTTGGAAAC 58.747 50.000 0.00 0.00 0.00 2.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 1.299620 GCGGACGTACGGTATGCAT 60.300 57.895 23.80 3.79 0.00 3.96
64 65 2.664851 TTGTTCACAGCCGCCGAG 60.665 61.111 0.00 0.00 0.00 4.63
250 251 2.002586 CTCAGTCCACGAAATGCGAAT 58.997 47.619 0.00 0.00 44.57 3.34
591 597 4.314440 AAGTGCTGCGCGAGGGAA 62.314 61.111 12.10 0.00 0.00 3.97
668 674 9.423061 CAGAGACAAGGAAAAAGAAAAGAAAAA 57.577 29.630 0.00 0.00 0.00 1.94
688 694 0.595095 CCAAAGGCAACAGCAGAGAC 59.405 55.000 0.00 0.00 41.41 3.36
730 737 2.069273 CCTTTCGACAACAGCGATCTT 58.931 47.619 0.00 0.00 37.64 2.40
823 833 4.127171 CCAGTCTCTAGTCTCTACTGCTC 58.873 52.174 0.00 0.00 36.96 4.26
835 845 0.028242 CGTGCGCTACCAGTCTCTAG 59.972 60.000 9.73 0.00 0.00 2.43
936 957 1.344438 AGATCGAGTCCAAGTGTTGCA 59.656 47.619 0.00 0.00 0.00 4.08
984 1005 0.458669 CCATGGAAGGCTACGTACGT 59.541 55.000 25.98 25.98 0.00 3.57
1376 1405 0.534412 AGAGAAGCTACTGCATGCGT 59.466 50.000 14.09 15.84 42.74 5.24
1415 1444 5.343325 GCAGCAGAGCAAACTAATTAAACAC 59.657 40.000 0.00 0.00 0.00 3.32
1464 1493 1.135083 GTGTACATCTGGTCAGGTCCG 60.135 57.143 0.00 0.00 0.00 4.79
1465 1494 1.899814 TGTGTACATCTGGTCAGGTCC 59.100 52.381 0.00 0.00 0.00 4.46
1468 1497 1.406069 GGCTGTGTACATCTGGTCAGG 60.406 57.143 0.00 0.00 0.00 3.86
1470 1499 1.347062 TGGCTGTGTACATCTGGTCA 58.653 50.000 0.00 0.00 0.00 4.02
1539 1579 3.001939 ACTGCAAAGTAACGAAGAAACCG 59.998 43.478 0.00 0.00 0.00 4.44
1570 1610 1.237285 CGGGGTGAACAAGAGCAAGG 61.237 60.000 0.00 0.00 0.00 3.61
1572 1612 1.896660 GCGGGGTGAACAAGAGCAA 60.897 57.895 0.00 0.00 0.00 3.91
1573 1613 2.281484 GCGGGGTGAACAAGAGCA 60.281 61.111 0.00 0.00 0.00 4.26
1576 1616 1.070786 GTCTGCGGGGTGAACAAGA 59.929 57.895 0.00 0.00 0.00 3.02
1586 1626 2.434359 GGGAAGAACGTCTGCGGG 60.434 66.667 0.00 0.00 43.45 6.13
1636 1676 1.792057 GTTTGCGCGTGAACGGATG 60.792 57.895 8.43 0.00 40.23 3.51
1696 1736 4.427661 GCACACTCTCGCTCGCCT 62.428 66.667 0.00 0.00 0.00 5.52
1705 1745 2.715532 ATTCGGCACACGCACACTCT 62.716 55.000 0.00 0.00 43.86 3.24
1807 1847 4.529731 GAGCATTCCCTGGGGCCC 62.530 72.222 18.17 18.17 34.68 5.80
1827 1867 1.459539 CCTATCCGGCAAGAGGGGA 60.460 63.158 0.00 0.00 0.00 4.81
1914 1955 4.992381 AAATCCTTATCGCTAATCGCAC 57.008 40.909 0.00 0.00 39.08 5.34
1999 2360 8.777865 TCTTGTTAAACTAGGATGACAAGATG 57.222 34.615 22.38 8.54 44.51 2.90
2014 2375 4.328169 ACCTAACGCGCTATCTTGTTAAAC 59.672 41.667 5.73 0.00 0.00 2.01
2034 2398 1.524863 CGGTGACTGGACTCGAACCT 61.525 60.000 9.25 0.00 0.00 3.50
2098 2462 2.225293 TGCCCTGTCAAGTAGGAGTAGT 60.225 50.000 0.00 0.00 37.52 2.73
2099 2463 2.428890 CTGCCCTGTCAAGTAGGAGTAG 59.571 54.545 0.00 0.00 37.52 2.57
2100 2464 2.457598 CTGCCCTGTCAAGTAGGAGTA 58.542 52.381 0.00 0.00 37.52 2.59
2101 2465 1.270907 CTGCCCTGTCAAGTAGGAGT 58.729 55.000 0.00 0.00 37.52 3.85
2102 2466 0.539051 CCTGCCCTGTCAAGTAGGAG 59.461 60.000 1.58 0.00 37.52 3.69
2103 2467 1.553690 GCCTGCCCTGTCAAGTAGGA 61.554 60.000 9.95 0.00 37.52 2.94
2104 2468 1.078143 GCCTGCCCTGTCAAGTAGG 60.078 63.158 3.12 3.12 35.01 3.18
2105 2469 1.448540 CGCCTGCCCTGTCAAGTAG 60.449 63.158 0.00 0.00 0.00 2.57
2106 2470 2.662596 CGCCTGCCCTGTCAAGTA 59.337 61.111 0.00 0.00 0.00 2.24
2132 2496 2.792370 TCCTATCAGGAACTAGGCTCCT 59.208 50.000 9.34 9.34 42.51 3.69
2144 2508 6.961360 TGAACTATGTACTGTCCTATCAGG 57.039 41.667 0.00 0.00 39.48 3.86
2208 2572 4.400884 ACAAACACACTAAAACATGCTCCA 59.599 37.500 0.00 0.00 0.00 3.86
2209 2573 4.932146 ACAAACACACTAAAACATGCTCC 58.068 39.130 0.00 0.00 0.00 4.70
2210 2574 6.885735 AAACAAACACACTAAAACATGCTC 57.114 33.333 0.00 0.00 0.00 4.26
2211 2575 7.543756 AGTAAACAAACACACTAAAACATGCT 58.456 30.769 0.00 0.00 0.00 3.79
2212 2576 7.486551 TGAGTAAACAAACACACTAAAACATGC 59.513 33.333 0.00 0.00 0.00 4.06
2213 2577 8.903570 TGAGTAAACAAACACACTAAAACATG 57.096 30.769 0.00 0.00 0.00 3.21
2215 2579 9.915629 AAATGAGTAAACAAACACACTAAAACA 57.084 25.926 0.00 0.00 0.00 2.83
2218 2582 9.781834 CTGAAATGAGTAAACAAACACACTAAA 57.218 29.630 0.00 0.00 0.00 1.85
2219 2583 8.952278 ACTGAAATGAGTAAACAAACACACTAA 58.048 29.630 0.00 0.00 0.00 2.24
2220 2584 8.500753 ACTGAAATGAGTAAACAAACACACTA 57.499 30.769 0.00 0.00 0.00 2.74
2221 2585 7.336931 AGACTGAAATGAGTAAACAAACACACT 59.663 33.333 0.00 0.00 0.00 3.55
2222 2586 7.472543 AGACTGAAATGAGTAAACAAACACAC 58.527 34.615 0.00 0.00 0.00 3.82
2223 2587 7.624360 AGACTGAAATGAGTAAACAAACACA 57.376 32.000 0.00 0.00 0.00 3.72
2224 2588 9.599322 CATAGACTGAAATGAGTAAACAAACAC 57.401 33.333 0.00 0.00 0.00 3.32
2225 2589 9.337396 ACATAGACTGAAATGAGTAAACAAACA 57.663 29.630 0.00 0.00 0.00 2.83
2259 2623 9.775854 CTCCATTCACTATTAGAAGATGTCAAT 57.224 33.333 0.00 0.00 0.00 2.57
2260 2624 8.206867 CCTCCATTCACTATTAGAAGATGTCAA 58.793 37.037 0.00 0.00 0.00 3.18
2261 2625 7.202038 CCCTCCATTCACTATTAGAAGATGTCA 60.202 40.741 0.00 0.00 0.00 3.58
2262 2626 7.015682 TCCCTCCATTCACTATTAGAAGATGTC 59.984 40.741 0.00 0.00 0.00 3.06
2263 2627 6.846505 TCCCTCCATTCACTATTAGAAGATGT 59.153 38.462 0.00 0.00 0.00 3.06
2264 2628 7.016072 ACTCCCTCCATTCACTATTAGAAGATG 59.984 40.741 0.00 0.00 0.00 2.90
2265 2629 7.079048 ACTCCCTCCATTCACTATTAGAAGAT 58.921 38.462 0.00 0.00 0.00 2.40
2266 2630 6.444704 ACTCCCTCCATTCACTATTAGAAGA 58.555 40.000 0.00 0.00 0.00 2.87
2267 2631 6.739331 ACTCCCTCCATTCACTATTAGAAG 57.261 41.667 0.00 0.00 0.00 2.85
2268 2632 7.592736 TCTACTCCCTCCATTCACTATTAGAA 58.407 38.462 0.00 0.00 0.00 2.10
2269 2633 7.147105 ACTCTACTCCCTCCATTCACTATTAGA 60.147 40.741 0.00 0.00 0.00 2.10
2270 2634 7.007723 ACTCTACTCCCTCCATTCACTATTAG 58.992 42.308 0.00 0.00 0.00 1.73
2271 2635 6.923670 ACTCTACTCCCTCCATTCACTATTA 58.076 40.000 0.00 0.00 0.00 0.98
2272 2636 5.782925 ACTCTACTCCCTCCATTCACTATT 58.217 41.667 0.00 0.00 0.00 1.73
2273 2637 5.411103 ACTCTACTCCCTCCATTCACTAT 57.589 43.478 0.00 0.00 0.00 2.12
2274 2638 4.883021 ACTCTACTCCCTCCATTCACTA 57.117 45.455 0.00 0.00 0.00 2.74
2275 2639 3.767309 ACTCTACTCCCTCCATTCACT 57.233 47.619 0.00 0.00 0.00 3.41
2276 2640 7.784470 ATATTACTCTACTCCCTCCATTCAC 57.216 40.000 0.00 0.00 0.00 3.18
2277 2641 7.256332 GCAATATTACTCTACTCCCTCCATTCA 60.256 40.741 0.00 0.00 0.00 2.57
2278 2642 7.100409 GCAATATTACTCTACTCCCTCCATTC 58.900 42.308 0.00 0.00 0.00 2.67
2279 2643 6.295349 CGCAATATTACTCTACTCCCTCCATT 60.295 42.308 0.00 0.00 0.00 3.16
2280 2644 5.186021 CGCAATATTACTCTACTCCCTCCAT 59.814 44.000 0.00 0.00 0.00 3.41
2281 2645 4.523173 CGCAATATTACTCTACTCCCTCCA 59.477 45.833 0.00 0.00 0.00 3.86
2282 2646 4.765856 TCGCAATATTACTCTACTCCCTCC 59.234 45.833 0.00 0.00 0.00 4.30
2283 2647 5.106078 CCTCGCAATATTACTCTACTCCCTC 60.106 48.000 0.00 0.00 0.00 4.30
2284 2648 4.767928 CCTCGCAATATTACTCTACTCCCT 59.232 45.833 0.00 0.00 0.00 4.20
2285 2649 4.082136 CCCTCGCAATATTACTCTACTCCC 60.082 50.000 0.00 0.00 0.00 4.30
2286 2650 4.082136 CCCCTCGCAATATTACTCTACTCC 60.082 50.000 0.00 0.00 0.00 3.85
2287 2651 4.765856 TCCCCTCGCAATATTACTCTACTC 59.234 45.833 0.00 0.00 0.00 2.59
2288 2652 4.737578 TCCCCTCGCAATATTACTCTACT 58.262 43.478 0.00 0.00 0.00 2.57
2289 2653 5.464030 TTCCCCTCGCAATATTACTCTAC 57.536 43.478 0.00 0.00 0.00 2.59
2290 2654 6.681729 AATTCCCCTCGCAATATTACTCTA 57.318 37.500 0.00 0.00 0.00 2.43
2291 2655 5.568620 AATTCCCCTCGCAATATTACTCT 57.431 39.130 0.00 0.00 0.00 3.24
2292 2656 5.048713 CCAAATTCCCCTCGCAATATTACTC 60.049 44.000 0.00 0.00 0.00 2.59
2293 2657 4.827284 CCAAATTCCCCTCGCAATATTACT 59.173 41.667 0.00 0.00 0.00 2.24
2294 2658 4.825085 TCCAAATTCCCCTCGCAATATTAC 59.175 41.667 0.00 0.00 0.00 1.89
2295 2659 5.055265 TCCAAATTCCCCTCGCAATATTA 57.945 39.130 0.00 0.00 0.00 0.98
2296 2660 3.909732 TCCAAATTCCCCTCGCAATATT 58.090 40.909 0.00 0.00 0.00 1.28
2297 2661 3.593442 TCCAAATTCCCCTCGCAATAT 57.407 42.857 0.00 0.00 0.00 1.28
2298 2662 3.374042 TTCCAAATTCCCCTCGCAATA 57.626 42.857 0.00 0.00 0.00 1.90
2299 2663 2.230130 TTCCAAATTCCCCTCGCAAT 57.770 45.000 0.00 0.00 0.00 3.56
2300 2664 1.616374 GTTTCCAAATTCCCCTCGCAA 59.384 47.619 0.00 0.00 0.00 4.85
2301 2665 1.253100 GTTTCCAAATTCCCCTCGCA 58.747 50.000 0.00 0.00 0.00 5.10


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

AutoCloner maintained by Alex Coulton.