Multiple sequence alignment - TraesCS2A01G185200

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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 TraesCS2A01G185200 chr2A 100.000 2615 0 0 1 2615 146076791 146079405 0.000000e+00 4830.0
1 TraesCS2A01G185200 chr2B 91.554 1184 81 11 776 1947 211877260 211876084 0.000000e+00 1615.0
2 TraesCS2A01G185200 chr2B 90.909 110 9 1 2500 2608 211875555 211875446 2.100000e-31 147.0
3 TraesCS2A01G185200 chr2B 81.513 119 11 4 2079 2191 211876009 211875896 1.290000e-13 87.9
4 TraesCS2A01G185200 chr2D 93.257 1053 44 9 766 1818 154633587 154632562 0.000000e+00 1526.0
5 TraesCS2A01G185200 chr2D 88.584 219 14 4 2241 2454 154631726 154631514 3.340000e-64 255.0
6 TraesCS2A01G185200 chr2D 92.424 132 9 1 1817 1947 154632403 154632272 1.240000e-43 187.0
7 TraesCS2A01G185200 chr2D 96.429 56 2 0 2560 2615 154631389 154631334 2.770000e-15 93.5
8 TraesCS2A01G185200 chr5D 88.000 775 77 4 4 762 368951165 368950391 0.000000e+00 902.0
9 TraesCS2A01G185200 chr5D 86.345 476 53 6 1 464 59887068 59887543 2.320000e-140 508.0
10 TraesCS2A01G185200 chr5D 83.544 474 55 8 4 464 357018635 357018172 3.110000e-114 422.0
11 TraesCS2A01G185200 chr5D 84.836 244 24 6 1 232 549027597 549027839 1.560000e-57 233.0
12 TraesCS2A01G185200 chr3D 85.774 478 54 5 1 464 19031819 19032296 6.500000e-136 494.0
13 TraesCS2A01G185200 chr3D 96.552 87 3 0 1945 2031 571377951 571378037 7.540000e-31 145.0
14 TraesCS2A01G185200 chr1B 85.021 474 57 10 4 464 647162889 647163361 1.100000e-128 470.0
15 TraesCS2A01G185200 chr7D 84.746 472 57 7 1 460 18833338 18832870 2.370000e-125 459.0
16 TraesCS2A01G185200 chr7D 85.761 309 33 6 458 761 18832731 18832429 1.510000e-82 316.0
17 TraesCS2A01G185200 chr7D 81.132 265 47 3 501 762 635442844 635443108 2.640000e-50 209.0
18 TraesCS2A01G185200 chr7D 85.263 190 16 7 1 178 135415516 135415327 4.440000e-43 185.0
19 TraesCS2A01G185200 chr7D 85.897 156 21 1 608 762 126704891 126705046 5.790000e-37 165.0
20 TraesCS2A01G185200 chr7D 75.472 159 33 6 1126 1281 50153439 50153594 3.610000e-09 73.1
21 TraesCS2A01G185200 chr1A 84.454 476 54 8 1 464 6200130 6200597 3.970000e-123 451.0
22 TraesCS2A01G185200 chr1A 95.745 94 4 0 1938 2031 49249646 49249739 4.510000e-33 152.0
23 TraesCS2A01G185200 chr1A 91.837 98 6 2 1942 2039 537892560 537892655 4.540000e-28 135.0
24 TraesCS2A01G185200 chr5B 85.045 448 55 6 29 464 271262220 271262667 1.850000e-121 446.0
25 TraesCS2A01G185200 chr5B 85.256 312 33 8 458 764 421719008 421718705 2.530000e-80 309.0
26 TraesCS2A01G185200 chr5B 86.063 287 39 1 181 467 421719425 421719140 9.090000e-80 307.0
27 TraesCS2A01G185200 chr5B 95.556 90 3 1 1942 2030 674496624 674496535 2.710000e-30 143.0
28 TraesCS2A01G185200 chr7B 83.925 479 60 10 1 464 115231812 115232288 2.390000e-120 442.0
29 TraesCS2A01G185200 chr3B 83.193 476 57 9 1 464 646248887 646249351 5.210000e-112 414.0
30 TraesCS2A01G185200 chr3B 96.552 87 3 0 1945 2031 748777176 748777090 7.540000e-31 145.0
31 TraesCS2A01G185200 chr5A 88.024 167 19 1 597 762 287619890 287620056 2.050000e-46 196.0
32 TraesCS2A01G185200 chr7A 81.780 236 37 5 531 762 488041711 488041944 2.660000e-45 193.0
33 TraesCS2A01G185200 chr7A 77.395 261 52 5 506 763 733267523 733267779 5.830000e-32 148.0
34 TraesCS2A01G185200 chr6D 83.246 191 30 2 582 770 412445386 412445576 9.620000e-40 174.0
35 TraesCS2A01G185200 chr6D 92.208 77 6 0 1 77 430454673 430454749 2.750000e-20 110.0
36 TraesCS2A01G185200 chr3A 95.556 90 4 0 1942 2031 646921552 646921641 7.540000e-31 145.0
37 TraesCS2A01G185200 chr6B 96.512 86 3 0 1946 2031 162181262 162181177 2.710000e-30 143.0
38 TraesCS2A01G185200 chr6B 89.091 110 9 3 1946 2054 24799207 24799100 1.630000e-27 134.0
39 TraesCS2A01G185200 chr4D 94.565 92 5 0 1939 2030 509106468 509106377 2.710000e-30 143.0


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 TraesCS2A01G185200 chr2A 146076791 146079405 2614 False 4830.000000 4830 100.0000 1 2615 1 chr2A.!!$F1 2614
1 TraesCS2A01G185200 chr2B 211875446 211877260 1814 True 616.633333 1615 87.9920 776 2608 3 chr2B.!!$R1 1832
2 TraesCS2A01G185200 chr2D 154631334 154633587 2253 True 515.375000 1526 92.6735 766 2615 4 chr2D.!!$R1 1849
3 TraesCS2A01G185200 chr5D 368950391 368951165 774 True 902.000000 902 88.0000 4 762 1 chr5D.!!$R2 758
4 TraesCS2A01G185200 chr7D 18832429 18833338 909 True 387.500000 459 85.2535 1 761 2 chr7D.!!$R2 760
5 TraesCS2A01G185200 chr5B 421718705 421719425 720 True 308.000000 309 85.6595 181 764 2 chr5B.!!$R2 583

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
583 739 0.581529 GGCTCTTTTTGGCAAAACGC 59.418 50.0 24.04 23.06 41.28 4.84 F
1338 1502 0.095935 CGAAAGCTGAGCGGAACATG 59.904 55.0 0.00 0.00 0.00 3.21 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1432 1608 0.103755 TCCATGACGATCTGCAGCTC 59.896 55.0 9.47 8.39 0.0 4.09 R
2232 2648 0.383231 CGTAACCCGGTAGTGCTAGG 59.617 60.0 0.00 0.00 0.0 3.02 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
115 128 2.052690 ACGCTGGGCATCTACTCGT 61.053 57.895 0.00 0.00 0.00 4.18
194 207 4.733542 CGGTGGGGGCCAAATCGT 62.734 66.667 4.39 0.00 34.18 3.73
279 292 4.927782 GGCTCACGTGGTGGTGCA 62.928 66.667 17.00 0.00 37.83 4.57
387 400 2.123854 TAGTCTCGAGGCCGGCAT 60.124 61.111 30.85 24.69 36.24 4.40
449 462 3.853597 GACCGACGCCACCGAGTTT 62.854 63.158 0.00 0.00 38.29 2.66
452 465 1.952133 CGACGCCACCGAGTTTGAA 60.952 57.895 0.00 0.00 38.29 2.69
583 739 0.581529 GGCTCTTTTTGGCAAAACGC 59.418 50.000 24.04 23.06 41.28 4.84
597 753 2.401583 AAACGCTATGCCACATCAGA 57.598 45.000 0.00 0.00 0.00 3.27
712 872 5.880054 TTGCAAAGAAACTGTATCCTAGC 57.120 39.130 0.00 0.00 0.00 3.42
744 905 5.009610 GCAAATCTAAACCTCAAAGTGGTGA 59.990 40.000 0.00 0.00 37.93 4.02
753 914 4.220602 ACCTCAAAGTGGTGATTTTATGCC 59.779 41.667 0.00 0.00 36.30 4.40
764 925 5.067283 GGTGATTTTATGCCATTTACTCGGT 59.933 40.000 0.00 0.00 0.00 4.69
768 929 6.671614 TTTTATGCCATTTACTCGGTAGTG 57.328 37.500 0.00 0.00 36.36 2.74
983 1144 1.730547 GCCAACACAAGCACATCGC 60.731 57.895 0.00 0.00 42.91 4.58
992 1153 3.313750 GCACATCGCTCGATCCAC 58.686 61.111 1.30 0.00 37.77 4.02
1013 1177 1.381191 TAGGCATGTCGAGGCAGGA 60.381 57.895 6.07 0.00 0.00 3.86
1022 1186 4.436998 GAGGCAGGACGTGGACGG 62.437 72.222 0.00 0.00 44.95 4.79
1337 1501 2.460330 CGAAAGCTGAGCGGAACAT 58.540 52.632 0.00 0.00 0.00 2.71
1338 1502 0.095935 CGAAAGCTGAGCGGAACATG 59.904 55.000 0.00 0.00 0.00 3.21
1339 1503 0.449388 GAAAGCTGAGCGGAACATGG 59.551 55.000 0.00 0.00 0.00 3.66
1340 1504 1.589716 AAAGCTGAGCGGAACATGGC 61.590 55.000 0.00 0.00 0.00 4.40
1341 1505 3.869272 GCTGAGCGGAACATGGCG 61.869 66.667 0.00 0.00 0.00 5.69
1342 1506 2.434884 CTGAGCGGAACATGGCGT 60.435 61.111 0.00 0.00 0.00 5.68
1343 1507 2.434185 TGAGCGGAACATGGCGTC 60.434 61.111 0.00 0.00 0.00 5.19
1344 1508 3.554692 GAGCGGAACATGGCGTCG 61.555 66.667 0.00 0.00 0.00 5.12
1386 1562 2.310233 CGTCACGCTCAAGGTGGTG 61.310 63.158 0.00 0.00 36.09 4.17
1437 1613 2.169789 CAGGATGAACGCCGAGCTG 61.170 63.158 0.00 0.00 39.69 4.24
1775 1956 1.403679 CCGTTTCTGGCTTCACAAACA 59.596 47.619 0.00 0.00 31.57 2.83
1787 1968 4.508861 GCTTCACAAACAACAATGCTCATT 59.491 37.500 0.00 0.00 0.00 2.57
1805 1986 6.885918 TGCTCATTTGATTTTCAGATAGTGGA 59.114 34.615 0.00 0.00 0.00 4.02
1807 1988 7.861372 GCTCATTTGATTTTCAGATAGTGGATG 59.139 37.037 0.00 0.00 0.00 3.51
1815 1996 9.956720 GATTTTCAGATAGTGGATGGTAAAATG 57.043 33.333 0.00 0.00 0.00 2.32
1843 2187 3.678056 TCCAACTAGTCATTTCGCTGT 57.322 42.857 0.00 0.00 0.00 4.40
1846 2190 3.123621 CCAACTAGTCATTTCGCTGTGTC 59.876 47.826 0.00 0.00 0.00 3.67
1848 2192 5.161358 CAACTAGTCATTTCGCTGTGTCTA 58.839 41.667 0.00 0.00 0.00 2.59
1858 2202 1.673033 CGCTGTGTCTAAGGGTCCTTG 60.673 57.143 12.20 3.30 37.47 3.61
1866 2210 6.183361 TGTGTCTAAGGGTCCTTGTTTATTCA 60.183 38.462 12.20 1.53 37.47 2.57
1944 2289 4.272489 TCCTATCTGGATTGCTTGGTTTG 58.728 43.478 0.00 0.00 40.56 2.93
1945 2290 4.019174 CCTATCTGGATTGCTTGGTTTGT 58.981 43.478 0.00 0.00 38.35 2.83
1946 2291 5.045213 TCCTATCTGGATTGCTTGGTTTGTA 60.045 40.000 0.00 0.00 40.56 2.41
1947 2292 5.066505 CCTATCTGGATTGCTTGGTTTGTAC 59.933 44.000 0.00 0.00 38.35 2.90
1948 2293 4.098914 TCTGGATTGCTTGGTTTGTACT 57.901 40.909 0.00 0.00 0.00 2.73
1949 2294 4.072131 TCTGGATTGCTTGGTTTGTACTC 58.928 43.478 0.00 0.00 0.00 2.59
1950 2295 3.153919 TGGATTGCTTGGTTTGTACTCC 58.846 45.455 0.00 0.00 0.00 3.85
1951 2296 2.492088 GGATTGCTTGGTTTGTACTCCC 59.508 50.000 0.00 0.00 0.00 4.30
1952 2297 3.421844 GATTGCTTGGTTTGTACTCCCT 58.578 45.455 0.00 0.00 0.00 4.20
1953 2298 2.561478 TGCTTGGTTTGTACTCCCTC 57.439 50.000 0.00 0.00 0.00 4.30
1954 2299 2.054799 TGCTTGGTTTGTACTCCCTCT 58.945 47.619 0.00 0.00 0.00 3.69
1955 2300 2.224523 TGCTTGGTTTGTACTCCCTCTG 60.225 50.000 0.00 0.00 0.00 3.35
1956 2301 2.224548 GCTTGGTTTGTACTCCCTCTGT 60.225 50.000 0.00 0.00 0.00 3.41
1957 2302 3.007614 GCTTGGTTTGTACTCCCTCTGTA 59.992 47.826 0.00 0.00 0.00 2.74
1958 2303 4.504340 GCTTGGTTTGTACTCCCTCTGTAA 60.504 45.833 0.00 0.00 0.00 2.41
1959 2304 5.617252 CTTGGTTTGTACTCCCTCTGTAAA 58.383 41.667 0.00 0.00 0.00 2.01
1960 2305 4.964593 TGGTTTGTACTCCCTCTGTAAAC 58.035 43.478 0.00 0.00 0.00 2.01
1961 2306 4.657039 TGGTTTGTACTCCCTCTGTAAACT 59.343 41.667 0.00 0.00 0.00 2.66
1962 2307 5.840149 TGGTTTGTACTCCCTCTGTAAACTA 59.160 40.000 0.00 0.00 0.00 2.24
1963 2308 6.327104 TGGTTTGTACTCCCTCTGTAAACTAA 59.673 38.462 0.00 0.00 0.00 2.24
1964 2309 7.016858 TGGTTTGTACTCCCTCTGTAAACTAAT 59.983 37.037 0.00 0.00 0.00 1.73
1965 2310 8.534496 GGTTTGTACTCCCTCTGTAAACTAATA 58.466 37.037 0.00 0.00 0.00 0.98
2026 2371 9.710818 ACACTCTTATATTAGTTTACAGAGGGA 57.289 33.333 2.59 0.00 34.50 4.20
2036 2381 4.712337 AGTTTACAGAGGGAGTATGACTGG 59.288 45.833 0.00 0.00 33.57 4.00
2060 2405 8.410912 TGGATCATCATGCAAAAGAATTTCTAG 58.589 33.333 0.00 0.00 37.28 2.43
2065 2410 9.031360 CATCATGCAAAAGAATTTCTAGGATTG 57.969 33.333 0.00 4.94 37.28 2.67
2067 2412 8.805175 TCATGCAAAAGAATTTCTAGGATTGAA 58.195 29.630 0.00 0.00 37.28 2.69
2068 2413 9.426837 CATGCAAAAGAATTTCTAGGATTGAAA 57.573 29.630 0.00 0.00 37.28 2.69
2069 2414 8.816640 TGCAAAAGAATTTCTAGGATTGAAAC 57.183 30.769 0.00 0.00 37.28 2.78
2070 2415 8.641541 TGCAAAAGAATTTCTAGGATTGAAACT 58.358 29.630 0.00 0.00 37.28 2.66
2072 2454 8.919661 CAAAAGAATTTCTAGGATTGAAACTGC 58.080 33.333 0.00 0.00 37.28 4.40
2129 2545 8.458573 AATCCTTGTACTTTTTGTATGACACA 57.541 30.769 0.00 0.00 33.23 3.72
2139 2555 6.513806 TTTTGTATGACACAGCAATGCTAT 57.486 33.333 7.70 0.00 36.40 2.97
2141 2557 3.878699 TGTATGACACAGCAATGCTATGG 59.121 43.478 18.33 8.30 37.40 2.74
2142 2558 2.495155 TGACACAGCAATGCTATGGT 57.505 45.000 18.33 11.46 37.40 3.55
2143 2559 2.794103 TGACACAGCAATGCTATGGTT 58.206 42.857 18.33 0.00 37.40 3.67
2177 2593 6.650427 ACTATTTCCAGTTTTTCCACTTCC 57.350 37.500 0.00 0.00 0.00 3.46
2178 2594 6.373759 ACTATTTCCAGTTTTTCCACTTCCT 58.626 36.000 0.00 0.00 0.00 3.36
2179 2595 7.523415 ACTATTTCCAGTTTTTCCACTTCCTA 58.477 34.615 0.00 0.00 0.00 2.94
2180 2596 6.650427 ATTTCCAGTTTTTCCACTTCCTAC 57.350 37.500 0.00 0.00 0.00 3.18
2181 2597 5.382664 TTCCAGTTTTTCCACTTCCTACT 57.617 39.130 0.00 0.00 0.00 2.57
2182 2598 4.714632 TCCAGTTTTTCCACTTCCTACTG 58.285 43.478 0.00 0.00 33.21 2.74
2183 2599 4.410883 TCCAGTTTTTCCACTTCCTACTGA 59.589 41.667 0.00 0.00 34.87 3.41
2184 2600 5.104277 TCCAGTTTTTCCACTTCCTACTGAA 60.104 40.000 0.00 0.00 34.87 3.02
2195 2611 4.628074 CTTCCTACTGAAGGTCGTTTTCA 58.372 43.478 0.00 0.00 45.66 2.69
2196 2612 4.675976 TCCTACTGAAGGTCGTTTTCAA 57.324 40.909 0.00 0.00 46.62 2.69
2197 2613 5.026038 TCCTACTGAAGGTCGTTTTCAAA 57.974 39.130 0.00 0.00 46.62 2.69
2198 2614 5.430007 TCCTACTGAAGGTCGTTTTCAAAA 58.570 37.500 0.00 0.00 46.62 2.44
2230 2646 5.584551 ACTGAAGGTAGAAGTCCCATTTT 57.415 39.130 0.00 0.00 0.00 1.82
2231 2647 6.697641 ACTGAAGGTAGAAGTCCCATTTTA 57.302 37.500 0.00 0.00 0.00 1.52
2232 2648 6.473758 ACTGAAGGTAGAAGTCCCATTTTAC 58.526 40.000 0.00 0.00 0.00 2.01
2233 2649 5.812286 TGAAGGTAGAAGTCCCATTTTACC 58.188 41.667 0.00 0.00 0.00 2.85
2234 2650 5.550403 TGAAGGTAGAAGTCCCATTTTACCT 59.450 40.000 3.55 3.55 41.87 3.08
2235 2651 6.731919 TGAAGGTAGAAGTCCCATTTTACCTA 59.268 38.462 8.59 0.00 39.83 3.08
2236 2652 6.809976 AGGTAGAAGTCCCATTTTACCTAG 57.190 41.667 6.86 0.00 39.17 3.02
2237 2653 5.130643 AGGTAGAAGTCCCATTTTACCTAGC 59.869 44.000 6.86 0.00 39.17 3.42
2238 2654 5.104652 GGTAGAAGTCCCATTTTACCTAGCA 60.105 44.000 0.00 0.00 0.00 3.49
2243 2958 4.163649 AGTCCCATTTTACCTAGCACTACC 59.836 45.833 0.00 0.00 0.00 3.18
2331 3050 1.425448 AGCCCTGCTTAGAAAACCAGT 59.575 47.619 0.00 0.00 33.89 4.00
2354 3074 5.948742 TCTTTTGGGTTTGACCTGAAATT 57.051 34.783 0.00 0.00 38.64 1.82
2357 3077 6.836527 TCTTTTGGGTTTGACCTGAAATTCTA 59.163 34.615 0.00 0.00 38.64 2.10
2365 3086 8.847196 GGTTTGACCTGAAATTCTAAACTAAGT 58.153 33.333 0.00 0.00 34.73 2.24
2372 3093 6.403878 TGAAATTCTAAACTAAGTCCCTCCG 58.596 40.000 0.00 0.00 0.00 4.63
2423 3144 6.382869 AAAGTGATGAAAGGAGTGAACAAG 57.617 37.500 0.00 0.00 0.00 3.16
2425 3146 5.874093 AGTGATGAAAGGAGTGAACAAGAT 58.126 37.500 0.00 0.00 0.00 2.40
2426 3147 6.302269 AGTGATGAAAGGAGTGAACAAGATT 58.698 36.000 0.00 0.00 0.00 2.40
2427 3148 6.774656 AGTGATGAAAGGAGTGAACAAGATTT 59.225 34.615 0.00 0.00 0.00 2.17
2428 3149 7.286316 AGTGATGAAAGGAGTGAACAAGATTTT 59.714 33.333 0.00 0.00 0.00 1.82
2429 3150 7.922811 GTGATGAAAGGAGTGAACAAGATTTTT 59.077 33.333 0.00 0.00 0.00 1.94
2487 3283 4.265073 CAGAAGTAATTTGGGACAGAGGG 58.735 47.826 0.00 0.00 42.39 4.30
2489 3285 4.601857 AGAAGTAATTTGGGACAGAGGGAA 59.398 41.667 0.00 0.00 42.39 3.97
2494 3290 5.536497 AATTTGGGACAGAGGGAATAGTT 57.464 39.130 0.00 0.00 42.39 2.24
2509 3310 6.070767 AGGGAATAGTTTCGAAAGACATGAGA 60.071 38.462 11.66 0.00 41.84 3.27
2551 3353 4.442192 GGAGGACTACAATAGAAGCACCTG 60.442 50.000 0.00 0.00 0.00 4.00
2602 3404 1.990563 CGTCGAACCACACAATACTCC 59.009 52.381 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
34 35 4.699522 GAGGAGCCGCCCAACGTT 62.700 66.667 0.00 0.00 41.42 3.99
97 110 2.052690 ACGAGTAGATGCCCAGCGT 61.053 57.895 0.00 0.00 0.00 5.07
100 113 1.589993 CGCACGAGTAGATGCCCAG 60.590 63.158 0.00 0.00 38.69 4.45
106 119 1.076923 ACCTCCCGCACGAGTAGAT 60.077 57.895 0.00 0.00 0.00 1.98
110 123 1.827399 ATTTGACCTCCCGCACGAGT 61.827 55.000 0.00 0.00 0.00 4.18
115 128 2.267642 CCGATTTGACCTCCCGCA 59.732 61.111 0.00 0.00 0.00 5.69
176 189 4.733542 CGATTTGGCCCCCACCGT 62.734 66.667 0.00 0.00 30.78 4.83
420 433 4.595538 GTCGGTCACCACCACGCA 62.596 66.667 0.00 0.00 44.02 5.24
449 462 2.048222 CTCCCGCAGCGTTCTTCA 60.048 61.111 15.05 0.00 0.00 3.02
468 622 0.463116 ACAAACCGTTCGTCAGCCTT 60.463 50.000 0.00 0.00 0.00 4.35
528 682 1.416030 AGCAAAAACACCCCCAACATC 59.584 47.619 0.00 0.00 0.00 3.06
614 773 3.308866 GCTCGGTTAAGTGCGTTTATGAT 59.691 43.478 0.00 0.00 0.00 2.45
690 850 4.391830 CGCTAGGATACAGTTTCTTTGCAA 59.608 41.667 0.00 0.00 41.41 4.08
695 855 6.128634 CGAAAAACGCTAGGATACAGTTTCTT 60.129 38.462 0.00 0.00 34.42 2.52
712 872 5.209240 TGAGGTTTAGATTTGCGAAAAACG 58.791 37.500 0.00 0.00 45.66 3.60
730 891 4.220602 GGCATAAAATCACCACTTTGAGGT 59.779 41.667 0.00 0.00 40.85 3.85
744 905 6.826741 ACACTACCGAGTAAATGGCATAAAAT 59.173 34.615 0.00 0.00 33.32 1.82
753 914 8.430801 ACTACTACTACACTACCGAGTAAATG 57.569 38.462 0.00 0.00 33.32 2.32
764 925 9.135189 TGTTCTTTTCCAACTACTACTACACTA 57.865 33.333 0.00 0.00 0.00 2.74
912 1073 2.794282 CGCGCTGCTTATAAAATGGCAA 60.794 45.455 5.56 0.00 34.21 4.52
913 1074 1.268488 CGCGCTGCTTATAAAATGGCA 60.268 47.619 5.56 0.00 0.00 4.92
983 1144 0.319040 CATGCCTACGGTGGATCGAG 60.319 60.000 0.00 0.00 0.00 4.04
987 1148 1.040893 TCGACATGCCTACGGTGGAT 61.041 55.000 0.00 0.00 0.00 3.41
990 1151 1.226974 CCTCGACATGCCTACGGTG 60.227 63.158 0.00 0.00 0.00 4.94
991 1152 3.077519 GCCTCGACATGCCTACGGT 62.078 63.158 0.00 0.00 0.00 4.83
992 1153 2.279517 GCCTCGACATGCCTACGG 60.280 66.667 0.00 0.00 0.00 4.02
1239 1403 2.364186 TCCATCTGGAGCTCCGCA 60.364 61.111 27.43 16.73 39.78 5.69
1432 1608 0.103755 TCCATGACGATCTGCAGCTC 59.896 55.000 9.47 8.39 0.00 4.09
1437 1613 0.877649 ACGCATCCATGACGATCTGC 60.878 55.000 0.00 0.00 33.66 4.26
1626 1802 8.623903 GGTGAAGTGCAATGAGAATATGAAATA 58.376 33.333 0.00 0.00 0.00 1.40
1629 1805 5.945191 TGGTGAAGTGCAATGAGAATATGAA 59.055 36.000 0.00 0.00 0.00 2.57
1775 1956 9.582431 CTATCTGAAAATCAAATGAGCATTGTT 57.418 29.630 0.00 0.00 0.00 2.83
1787 1968 9.527157 TTTTACCATCCACTATCTGAAAATCAA 57.473 29.630 0.00 0.00 0.00 2.57
1843 2187 6.442541 TGAATAAACAAGGACCCTTAGACA 57.557 37.500 0.29 0.00 34.50 3.41
1846 2190 8.404107 TCTTTTGAATAAACAAGGACCCTTAG 57.596 34.615 0.29 0.00 34.50 2.18
1848 2192 7.730332 AGATCTTTTGAATAAACAAGGACCCTT 59.270 33.333 0.00 0.00 36.60 3.95
1866 2210 8.985315 TGGCACATCTTATATGAAGATCTTTT 57.015 30.769 9.87 3.34 34.96 2.27
2000 2345 9.710818 TCCCTCTGTAAACTAATATAAGAGTGT 57.289 33.333 0.00 0.00 0.00 3.55
2002 2347 9.939424 ACTCCCTCTGTAAACTAATATAAGAGT 57.061 33.333 0.00 0.00 0.00 3.24
2008 2353 9.884814 AGTCATACTCCCTCTGTAAACTAATAT 57.115 33.333 0.00 0.00 0.00 1.28
2009 2354 9.132923 CAGTCATACTCCCTCTGTAAACTAATA 57.867 37.037 0.00 0.00 0.00 0.98
2010 2355 7.070074 CCAGTCATACTCCCTCTGTAAACTAAT 59.930 40.741 0.00 0.00 0.00 1.73
2011 2356 6.380274 CCAGTCATACTCCCTCTGTAAACTAA 59.620 42.308 0.00 0.00 0.00 2.24
2012 2357 5.892119 CCAGTCATACTCCCTCTGTAAACTA 59.108 44.000 0.00 0.00 0.00 2.24
2013 2358 4.712337 CCAGTCATACTCCCTCTGTAAACT 59.288 45.833 0.00 0.00 0.00 2.66
2014 2359 4.710375 TCCAGTCATACTCCCTCTGTAAAC 59.290 45.833 0.00 0.00 0.00 2.01
2015 2360 4.942944 TCCAGTCATACTCCCTCTGTAAA 58.057 43.478 0.00 0.00 0.00 2.01
2016 2361 4.603094 TCCAGTCATACTCCCTCTGTAA 57.397 45.455 0.00 0.00 0.00 2.41
2017 2362 4.168088 TGATCCAGTCATACTCCCTCTGTA 59.832 45.833 0.00 0.00 0.00 2.74
2018 2363 3.052566 TGATCCAGTCATACTCCCTCTGT 60.053 47.826 0.00 0.00 0.00 3.41
2019 2364 3.570540 TGATCCAGTCATACTCCCTCTG 58.429 50.000 0.00 0.00 0.00 3.35
2020 2365 3.981516 TGATCCAGTCATACTCCCTCT 57.018 47.619 0.00 0.00 0.00 3.69
2036 2381 8.627403 TCCTAGAAATTCTTTTGCATGATGATC 58.373 33.333 0.00 0.00 0.00 2.92
2093 2505 6.697641 AAGTACAAGGATTCAAAGGTAGGA 57.302 37.500 0.00 0.00 0.00 2.94
2096 2508 8.528044 ACAAAAAGTACAAGGATTCAAAGGTA 57.472 30.769 0.00 0.00 0.00 3.08
2154 2570 6.373759 AGGAAGTGGAAAAACTGGAAATAGT 58.626 36.000 0.00 0.00 0.00 2.12
2219 2635 4.929146 AGTGCTAGGTAAAATGGGACTT 57.071 40.909 0.00 0.00 0.00 3.01
2220 2636 4.163649 GGTAGTGCTAGGTAAAATGGGACT 59.836 45.833 0.00 0.00 34.35 3.85
2221 2637 4.449131 GGTAGTGCTAGGTAAAATGGGAC 58.551 47.826 0.00 0.00 0.00 4.46
2222 2638 3.133362 CGGTAGTGCTAGGTAAAATGGGA 59.867 47.826 0.00 0.00 0.00 4.37
2223 2639 3.463944 CGGTAGTGCTAGGTAAAATGGG 58.536 50.000 0.00 0.00 0.00 4.00
2225 2641 3.118519 ACCCGGTAGTGCTAGGTAAAATG 60.119 47.826 0.00 0.00 0.00 2.32
2226 2642 3.109928 ACCCGGTAGTGCTAGGTAAAAT 58.890 45.455 0.00 0.00 0.00 1.82
2227 2643 2.539302 ACCCGGTAGTGCTAGGTAAAA 58.461 47.619 0.00 0.00 0.00 1.52
2228 2644 2.236489 ACCCGGTAGTGCTAGGTAAA 57.764 50.000 0.00 0.00 0.00 2.01
2229 2645 2.236489 AACCCGGTAGTGCTAGGTAA 57.764 50.000 0.00 0.00 0.00 2.85
2230 2646 2.654863 GTAACCCGGTAGTGCTAGGTA 58.345 52.381 0.00 0.00 0.00 3.08
2231 2647 1.478631 GTAACCCGGTAGTGCTAGGT 58.521 55.000 0.00 0.00 0.00 3.08
2232 2648 0.383231 CGTAACCCGGTAGTGCTAGG 59.617 60.000 0.00 0.00 0.00 3.02
2233 2649 1.064654 GACGTAACCCGGTAGTGCTAG 59.935 57.143 0.00 0.00 42.24 3.42
2234 2650 1.094785 GACGTAACCCGGTAGTGCTA 58.905 55.000 0.00 0.00 42.24 3.49
2235 2651 1.885871 GACGTAACCCGGTAGTGCT 59.114 57.895 0.00 0.00 42.24 4.40
2236 2652 1.514873 CGACGTAACCCGGTAGTGC 60.515 63.158 0.00 0.00 42.24 4.40
2237 2653 0.521291 TTCGACGTAACCCGGTAGTG 59.479 55.000 0.00 0.00 42.24 2.74
2238 2654 1.200020 CTTTCGACGTAACCCGGTAGT 59.800 52.381 0.00 0.00 42.24 2.73
2243 2958 1.453148 GTCAACTTTCGACGTAACCCG 59.547 52.381 0.00 0.00 44.03 5.28
2331 3050 5.948742 ATTTCAGGTCAAACCCAAAAGAA 57.051 34.783 0.00 0.00 39.75 2.52
2354 3074 4.400567 GCTTACGGAGGGACTTAGTTTAGA 59.599 45.833 0.00 0.00 41.55 2.10
2357 3077 3.056035 CAGCTTACGGAGGGACTTAGTTT 60.056 47.826 0.00 0.00 41.55 2.66
2365 3086 2.253610 TCTTTTCAGCTTACGGAGGGA 58.746 47.619 0.00 0.00 0.00 4.20
2372 3093 4.390264 AGGTCCAGTTCTTTTCAGCTTAC 58.610 43.478 0.00 0.00 0.00 2.34
2454 3175 6.994496 CCCAAATTACTTCTGCAGATAGATGA 59.006 38.462 19.04 0.00 0.00 2.92
2455 3176 6.994496 TCCCAAATTACTTCTGCAGATAGATG 59.006 38.462 19.04 10.24 0.00 2.90
2456 3177 6.995091 GTCCCAAATTACTTCTGCAGATAGAT 59.005 38.462 19.04 6.89 0.00 1.98
2458 3179 6.115446 TGTCCCAAATTACTTCTGCAGATAG 58.885 40.000 19.04 18.71 0.00 2.08
2461 3182 4.041567 TCTGTCCCAAATTACTTCTGCAGA 59.958 41.667 13.74 13.74 0.00 4.26
2462 3183 4.326826 TCTGTCCCAAATTACTTCTGCAG 58.673 43.478 7.63 7.63 0.00 4.41
2463 3184 4.326826 CTCTGTCCCAAATTACTTCTGCA 58.673 43.478 0.00 0.00 0.00 4.41
2464 3185 3.691609 CCTCTGTCCCAAATTACTTCTGC 59.308 47.826 0.00 0.00 0.00 4.26
2466 3187 4.175962 TCCCTCTGTCCCAAATTACTTCT 58.824 43.478 0.00 0.00 0.00 2.85
2467 3188 4.569719 TCCCTCTGTCCCAAATTACTTC 57.430 45.455 0.00 0.00 0.00 3.01
2468 3189 5.536497 ATTCCCTCTGTCCCAAATTACTT 57.464 39.130 0.00 0.00 0.00 2.24
2487 3283 8.467402 TTCTCTCATGTCTTTCGAAACTATTC 57.533 34.615 6.47 0.00 0.00 1.75
2489 3285 8.833231 TTTTCTCTCATGTCTTTCGAAACTAT 57.167 30.769 6.47 0.00 0.00 2.12
2518 3319 3.474798 TGTAGTCCTCCCTGTTCAGAT 57.525 47.619 1.00 0.00 0.00 2.90
2519 3320 2.992847 TGTAGTCCTCCCTGTTCAGA 57.007 50.000 1.00 0.00 0.00 3.27
2522 3323 5.682730 GCTTCTATTGTAGTCCTCCCTGTTC 60.683 48.000 0.00 0.00 0.00 3.18
2551 3353 5.629020 TGATTTGTTCTATTTTTGCACGAGC 59.371 36.000 0.00 0.00 42.57 5.03


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

AutoCloner maintained by Alex Coulton.