Multiple sequence alignment - TraesCS3A01G376000

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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 TraesCS3A01G376000 chr3A 100.000 2955 0 0 1 2955 624943982 624941028 0.000000e+00 5457.0
1 TraesCS3A01G376000 chr3A 82.511 223 28 8 416 635 623816798 623817012 5.030000e-43 185.0
2 TraesCS3A01G376000 chr3B 87.398 2206 106 58 831 2951 643858037 643855919 0.000000e+00 2375.0
3 TraesCS3A01G376000 chr3B 81.614 223 30 8 416 635 434310536 434310750 1.090000e-39 174.0
4 TraesCS3A01G376000 chr3D 87.560 2074 90 67 831 2824 481740652 481738667 0.000000e+00 2246.0
5 TraesCS3A01G376000 chr3D 89.815 108 9 2 735 841 491175336 491175442 1.430000e-28 137.0
6 TraesCS3A01G376000 chr4A 97.971 838 15 2 1 838 201756506 201755671 0.000000e+00 1452.0
7 TraesCS3A01G376000 chr4A 96.310 840 25 6 1 837 726802159 726802995 0.000000e+00 1375.0
8 TraesCS3A01G376000 chr4A 87.379 103 11 2 735 837 174726742 174726842 1.860000e-22 117.0
9 TraesCS3A01G376000 chr6A 94.682 771 31 8 1 771 613742458 613743218 0.000000e+00 1188.0
10 TraesCS3A01G376000 chr1D 87.273 220 25 2 1582 1798 370885335 370885554 6.320000e-62 248.0
11 TraesCS3A01G376000 chr1D 82.759 174 27 2 665 837 159875455 159875626 5.100000e-33 152.0
12 TraesCS3A01G376000 chr1B 87.273 220 25 2 1582 1798 494222761 494222980 6.320000e-62 248.0
13 TraesCS3A01G376000 chr1A 86.878 221 24 4 1582 1798 469645069 469645288 2.940000e-60 243.0
14 TraesCS3A01G376000 chr4B 78.803 401 38 23 1 369 54324438 54324053 2.960000e-55 226.0
15 TraesCS3A01G376000 chr4B 82.511 223 28 8 416 635 33816320 33816106 5.030000e-43 185.0
16 TraesCS3A01G376000 chr5B 81.356 295 34 11 1 284 350400506 350400790 1.380000e-53 220.0
17 TraesCS3A01G376000 chr5B 82.511 223 28 8 416 635 448802675 448802889 5.030000e-43 185.0
18 TraesCS3A01G376000 chr7A 82.511 223 28 8 416 635 493458282 493458496 5.030000e-43 185.0
19 TraesCS3A01G376000 chr7A 87.097 93 12 0 744 836 195522620 195522528 4.030000e-19 106.0
20 TraesCS3A01G376000 chr2B 82.511 223 28 8 416 635 180560720 180560506 5.030000e-43 185.0
21 TraesCS3A01G376000 chr2B 90.476 105 8 2 735 838 690932114 690932011 1.430000e-28 137.0
22 TraesCS3A01G376000 chr7B 88.043 92 9 2 748 838 582694420 582694330 1.120000e-19 108.0
23 TraesCS3A01G376000 chr6B 77.326 172 31 6 670 837 658812298 658812465 8.720000e-16 95.3


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 TraesCS3A01G376000 chr3A 624941028 624943982 2954 True 5457 5457 100.000 1 2955 1 chr3A.!!$R1 2954
1 TraesCS3A01G376000 chr3B 643855919 643858037 2118 True 2375 2375 87.398 831 2951 1 chr3B.!!$R1 2120
2 TraesCS3A01G376000 chr3D 481738667 481740652 1985 True 2246 2246 87.560 831 2824 1 chr3D.!!$R1 1993
3 TraesCS3A01G376000 chr4A 201755671 201756506 835 True 1452 1452 97.971 1 838 1 chr4A.!!$R1 837
4 TraesCS3A01G376000 chr4A 726802159 726802995 836 False 1375 1375 96.310 1 837 1 chr4A.!!$F2 836
5 TraesCS3A01G376000 chr6A 613742458 613743218 760 False 1188 1188 94.682 1 771 1 chr6A.!!$F1 770

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
772 776 2.048603 GGGACAGTTGGCATCCTGC 61.049 63.158 12.94 7.31 44.08 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2000 2047 0.033796 TGGAGGAGTACTACGGGTGG 60.034 60.0 0.0 0.0 30.06 4.61 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
110 111 2.289547 GTGAGGTTAAACATGTGTGCGT 59.710 45.455 0.00 0.00 0.00 5.24
268 269 4.695455 GTCTTTATGCCTGTAACTCTGCAA 59.305 41.667 0.00 0.00 37.27 4.08
310 311 9.354673 GATTTTTGATTCTATATCAAGGGTCCA 57.645 33.333 0.00 0.00 38.98 4.02
619 621 4.779993 GACCTCATCCTGGTCCTTTAAT 57.220 45.455 1.76 0.00 46.01 1.40
772 776 2.048603 GGGACAGTTGGCATCCTGC 61.049 63.158 12.94 7.31 44.08 4.85
838 843 4.261656 CGGATGTAGAATAGACAGTCCCAC 60.262 50.000 0.00 0.00 0.00 4.61
880 888 4.862823 GTCCTCCTCCTCCCCGGG 62.863 77.778 15.80 15.80 0.00 5.73
925 933 2.582498 CTTTACTCGCCCTCGCCG 60.582 66.667 0.00 0.00 35.26 6.46
980 988 4.776349 CCCCATTAATATATAGCGCCACA 58.224 43.478 2.29 0.00 0.00 4.17
981 989 4.816385 CCCCATTAATATATAGCGCCACAG 59.184 45.833 2.29 0.00 0.00 3.66
1013 1021 2.885861 CTCCGAGAACTCCACCCG 59.114 66.667 0.00 0.00 0.00 5.28
1064 1080 4.277593 CCTCGCTCTAGCCAGCCG 62.278 72.222 0.00 0.00 35.84 5.52
1065 1081 4.940593 CTCGCTCTAGCCAGCCGC 62.941 72.222 0.00 0.00 35.84 6.53
1095 1111 4.148825 AAGCGAGCTAGCCCGGTG 62.149 66.667 24.04 4.58 36.58 4.94
1433 1449 3.066190 CTGTACGAGGACCCGGCA 61.066 66.667 0.00 5.08 0.00 5.69
1816 1851 2.035632 CCAGTTCTAGCTACCCTCCTG 58.964 57.143 0.00 0.00 0.00 3.86
1818 1853 1.289530 AGTTCTAGCTACCCTCCTGCT 59.710 52.381 0.00 0.00 40.43 4.24
1819 1854 1.684450 GTTCTAGCTACCCTCCTGCTC 59.316 57.143 0.00 0.00 38.15 4.26
1826 1861 0.186386 TACCCTCCTGCTCCTAGCTC 59.814 60.000 0.00 0.00 42.97 4.09
1913 1957 2.895404 TCACACTCTTACCACCAGTACC 59.105 50.000 0.00 0.00 0.00 3.34
1927 1974 4.935808 CACCAGTACCACTCCTGTTTATTC 59.064 45.833 0.00 0.00 0.00 1.75
1928 1975 4.844655 ACCAGTACCACTCCTGTTTATTCT 59.155 41.667 0.00 0.00 0.00 2.40
1977 2024 3.499157 CCTAGTAGTAGCACCTGATCGAC 59.501 52.174 0.00 0.00 0.00 4.20
1998 2045 4.330250 ACCGTCAGTCTGTTAACTAGCTA 58.670 43.478 7.22 0.00 0.00 3.32
1999 2046 4.395542 ACCGTCAGTCTGTTAACTAGCTAG 59.604 45.833 19.44 19.44 0.00 3.42
2000 2047 4.344448 CGTCAGTCTGTTAACTAGCTAGC 58.656 47.826 20.91 6.62 0.00 3.42
2001 2048 4.674475 GTCAGTCTGTTAACTAGCTAGCC 58.326 47.826 20.91 6.98 0.00 3.93
2094 2155 1.000827 CGAGATGCGCCTAGTCTTCAT 60.001 52.381 4.18 0.00 0.00 2.57
2104 2165 4.556501 CGCCTAGTCTTCATCTCAAGCTAG 60.557 50.000 0.00 0.00 33.91 3.42
2127 2202 5.824624 AGTAAGCATGATGGTGTAATCCAAG 59.175 40.000 0.00 0.00 41.09 3.61
2128 2203 2.954318 AGCATGATGGTGTAATCCAAGC 59.046 45.455 0.00 0.00 41.09 4.01
2145 2220 5.498393 TCCAAGCCAATGTAACCGTTATTA 58.502 37.500 0.00 0.00 0.00 0.98
2146 2221 6.123651 TCCAAGCCAATGTAACCGTTATTAT 58.876 36.000 0.00 0.00 0.00 1.28
2147 2222 6.603997 TCCAAGCCAATGTAACCGTTATTATT 59.396 34.615 0.00 0.00 0.00 1.40
2148 2223 6.915843 CCAAGCCAATGTAACCGTTATTATTC 59.084 38.462 0.00 0.00 0.00 1.75
2149 2224 7.415765 CCAAGCCAATGTAACCGTTATTATTCA 60.416 37.037 0.00 0.00 0.00 2.57
2150 2225 7.817418 AGCCAATGTAACCGTTATTATTCAT 57.183 32.000 0.00 0.00 0.00 2.57
2151 2226 7.648142 AGCCAATGTAACCGTTATTATTCATG 58.352 34.615 0.00 0.00 0.00 3.07
2204 2279 5.390613 GGCATGGCGTTGTAATGATATAAC 58.609 41.667 2.41 0.00 31.78 1.89
2207 2282 7.234384 GCATGGCGTTGTAATGATATAACTAC 58.766 38.462 0.00 0.00 32.64 2.73
2209 2284 6.818233 TGGCGTTGTAATGATATAACTACCA 58.182 36.000 0.00 0.00 36.04 3.25
2210 2285 6.702723 TGGCGTTGTAATGATATAACTACCAC 59.297 38.462 0.00 0.00 34.79 4.16
2212 2287 8.084073 GGCGTTGTAATGATATAACTACCACTA 58.916 37.037 0.00 0.00 32.64 2.74
2213 2288 8.909671 GCGTTGTAATGATATAACTACCACTAC 58.090 37.037 0.00 0.00 32.64 2.73
2220 2295 9.830186 AATGATATAACTACCACTACTCCTCAT 57.170 33.333 0.00 0.00 0.00 2.90
2221 2296 8.637196 TGATATAACTACCACTACTCCTCATG 57.363 38.462 0.00 0.00 0.00 3.07
2222 2297 8.225416 TGATATAACTACCACTACTCCTCATGT 58.775 37.037 0.00 0.00 0.00 3.21
2240 2315 5.761003 TCATGTTGTTTGTGCATCAAGTAG 58.239 37.500 0.00 0.00 37.35 2.57
2241 2316 5.299028 TCATGTTGTTTGTGCATCAAGTAGT 59.701 36.000 0.00 0.00 37.35 2.73
2242 2317 6.484977 TCATGTTGTTTGTGCATCAAGTAGTA 59.515 34.615 0.00 0.00 37.35 1.82
2243 2318 6.055231 TGTTGTTTGTGCATCAAGTAGTAC 57.945 37.500 0.00 0.00 37.35 2.73
2244 2319 4.983215 TGTTTGTGCATCAAGTAGTACG 57.017 40.909 0.00 0.00 37.35 3.67
2245 2320 4.373527 TGTTTGTGCATCAAGTAGTACGT 58.626 39.130 0.00 0.00 37.35 3.57
2246 2321 4.210328 TGTTTGTGCATCAAGTAGTACGTG 59.790 41.667 9.67 9.67 37.35 4.49
2247 2322 3.653539 TGTGCATCAAGTAGTACGTGT 57.346 42.857 14.66 1.78 0.00 4.49
2248 2323 3.313690 TGTGCATCAAGTAGTACGTGTG 58.686 45.455 14.66 12.85 0.00 3.82
2249 2324 2.092211 GTGCATCAAGTAGTACGTGTGC 59.908 50.000 23.32 23.32 36.28 4.57
2250 2325 2.029380 TGCATCAAGTAGTACGTGTGCT 60.029 45.455 26.61 11.29 36.48 4.40
2251 2326 3.191791 TGCATCAAGTAGTACGTGTGCTA 59.808 43.478 26.61 17.94 36.48 3.49
2252 2327 3.546670 GCATCAAGTAGTACGTGTGCTAC 59.453 47.826 23.06 17.23 45.29 3.58
2259 2334 5.076911 GTAGTACGTGTGCTACTACTAGC 57.923 47.826 17.54 0.00 45.19 3.42
2264 2339 4.197750 ACGTGTGCTACTACTAGCTATGT 58.802 43.478 0.00 0.00 45.20 2.29
2284 2359 2.254546 AATCGTTCACTGCTCAACCA 57.745 45.000 0.00 0.00 0.00 3.67
2288 2363 2.948979 TCGTTCACTGCTCAACCATTTT 59.051 40.909 0.00 0.00 0.00 1.82
2290 2365 3.730715 CGTTCACTGCTCAACCATTTTTC 59.269 43.478 0.00 0.00 0.00 2.29
2293 2368 4.935702 TCACTGCTCAACCATTTTTCTTG 58.064 39.130 0.00 0.00 0.00 3.02
2295 2370 4.741676 CACTGCTCAACCATTTTTCTTGTC 59.258 41.667 0.00 0.00 0.00 3.18
2296 2371 3.963665 TGCTCAACCATTTTTCTTGTCG 58.036 40.909 0.00 0.00 0.00 4.35
2297 2372 3.243367 TGCTCAACCATTTTTCTTGTCGG 60.243 43.478 0.00 0.00 0.00 4.79
2315 2408 4.638421 TGTCGGTCATCTTTCACTGTTTTT 59.362 37.500 0.00 0.00 0.00 1.94
2316 2409 5.818336 TGTCGGTCATCTTTCACTGTTTTTA 59.182 36.000 0.00 0.00 0.00 1.52
2318 2411 5.237779 TCGGTCATCTTTCACTGTTTTTACC 59.762 40.000 0.00 0.00 0.00 2.85
2319 2412 5.449304 GGTCATCTTTCACTGTTTTTACCG 58.551 41.667 0.00 0.00 0.00 4.02
2320 2413 5.237779 GGTCATCTTTCACTGTTTTTACCGA 59.762 40.000 0.00 0.00 0.00 4.69
2321 2414 6.134061 GTCATCTTTCACTGTTTTTACCGAC 58.866 40.000 0.00 0.00 0.00 4.79
2322 2415 5.818336 TCATCTTTCACTGTTTTTACCGACA 59.182 36.000 0.00 0.00 0.00 4.35
2323 2416 5.728351 TCTTTCACTGTTTTTACCGACAG 57.272 39.130 2.22 2.22 46.65 3.51
2343 2436 3.634202 CCACTGGGCTGCTAGCTA 58.366 61.111 17.23 1.31 41.99 3.32
2358 2451 1.389555 AGCTAGCCATTTTTACCGCC 58.610 50.000 12.13 0.00 0.00 6.13
2409 2502 5.229469 CGTCCTGTCAACTCGTGAAATATAC 59.771 44.000 0.00 0.00 38.23 1.47
2430 2523 2.357034 CCACTACGTGCCGCACTT 60.357 61.111 20.87 14.49 31.34 3.16
2431 2524 2.667318 CCACTACGTGCCGCACTTG 61.667 63.158 20.87 12.57 31.34 3.16
2433 2526 1.663702 ACTACGTGCCGCACTTGTC 60.664 57.895 20.87 0.00 31.34 3.18
2434 2527 1.663388 CTACGTGCCGCACTTGTCA 60.663 57.895 20.87 0.00 31.34 3.58
2436 2529 4.354212 CGTGCCGCACTTGTCACG 62.354 66.667 20.87 2.44 44.62 4.35
2438 2531 2.964925 TGCCGCACTTGTCACGTC 60.965 61.111 0.00 0.00 0.00 4.34
2441 2540 4.059459 CGCACTTGTCACGTCCGC 62.059 66.667 0.00 0.00 0.00 5.54
2446 2545 2.280524 TTGTCACGTCCGCCCAAG 60.281 61.111 0.00 0.00 0.00 3.61
2453 2552 3.062466 GTCCGCCCAAGCCCTTTC 61.062 66.667 0.00 0.00 34.57 2.62
2550 2668 2.106683 CCCGAGGCCGATTTGTGTC 61.107 63.158 0.00 0.00 38.22 3.67
2552 2670 2.106683 CGAGGCCGATTTGTGTCCC 61.107 63.158 0.00 0.00 38.22 4.46
2555 2673 3.131478 GCCGATTTGTGTCCCCGG 61.131 66.667 0.00 0.00 42.74 5.73
2556 2674 3.131478 CCGATTTGTGTCCCCGGC 61.131 66.667 0.00 0.00 33.47 6.13
2557 2675 2.046314 CGATTTGTGTCCCCGGCT 60.046 61.111 0.00 0.00 0.00 5.52
2558 2676 2.106683 CGATTTGTGTCCCCGGCTC 61.107 63.158 0.00 0.00 0.00 4.70
2559 2677 1.749258 GATTTGTGTCCCCGGCTCC 60.749 63.158 0.00 0.00 0.00 4.70
2628 2758 2.428071 GCAACGACAAGCAGCTGC 60.428 61.111 31.53 31.53 42.49 5.25
2652 2782 2.276740 GTTGGGGCCTGGATGAGG 59.723 66.667 0.84 0.00 46.13 3.86
2707 2837 2.914777 GATCTCGCCACAGTGCCCTC 62.915 65.000 0.00 0.00 0.00 4.30
2720 2850 3.941188 CCCTCGCACTGTGTGGGT 61.941 66.667 18.99 0.00 44.89 4.51
2796 2926 3.303135 AGTGCCGGCTCGTCTCAA 61.303 61.111 29.70 0.07 0.00 3.02
2821 2952 6.609616 ACGTATTCATGGGGGTAAATTTTCAT 59.390 34.615 0.00 0.00 0.00 2.57
2825 2956 3.990959 TGGGGGTAAATTTTCATTGGC 57.009 42.857 0.00 0.00 0.00 4.52
2828 2959 2.092646 GGGGTAAATTTTCATTGGCCCC 60.093 50.000 0.00 0.00 44.11 5.80
2880 3011 0.734889 GCGGTCCTTGCTACGTAGTA 59.265 55.000 22.98 16.78 45.11 1.82
2912 3043 4.594920 AGTAGGATAATACTGTGCCTGCAT 59.405 41.667 0.00 0.00 34.68 3.96
2918 3049 2.128290 TACTGTGCCTGCATGCTGGT 62.128 55.000 35.31 22.28 37.37 4.00
2919 3050 2.986979 TGTGCCTGCATGCTGGTG 60.987 61.111 35.31 18.06 37.37 4.17
2920 3051 4.430765 GTGCCTGCATGCTGGTGC 62.431 66.667 35.31 26.24 45.25 5.01
2941 3072 2.825836 CCAACCGCTCCTGGCATC 60.826 66.667 0.00 0.00 41.91 3.91
2942 3073 3.197790 CAACCGCTCCTGGCATCG 61.198 66.667 0.00 0.00 41.91 3.84
2943 3074 4.473520 AACCGCTCCTGGCATCGG 62.474 66.667 15.89 15.89 46.61 4.18
2945 3076 4.899239 CCGCTCCTGGCATCGGTC 62.899 72.222 11.26 0.00 41.91 4.79
2947 3078 4.899239 GCTCCTGGCATCGGTCGG 62.899 72.222 0.00 0.00 41.35 4.79
2948 3079 3.461773 CTCCTGGCATCGGTCGGT 61.462 66.667 0.00 0.00 0.00 4.69
2949 3080 3.432051 CTCCTGGCATCGGTCGGTC 62.432 68.421 0.00 0.00 0.00 4.79
2950 3081 4.873129 CCTGGCATCGGTCGGTCG 62.873 72.222 0.00 0.00 0.00 4.79
2951 3082 4.873129 CTGGCATCGGTCGGTCGG 62.873 72.222 0.00 0.00 0.00 4.79
2953 3084 4.867599 GGCATCGGTCGGTCGGTC 62.868 72.222 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 1.075374 AGCCACCATTTGTGCTAGGAA 59.925 47.619 0.00 0.00 44.01 3.36
268 269 7.534085 TCAAAAATCTGCTCGAAATACGTAT 57.466 32.000 1.14 1.14 43.13 3.06
453 454 8.289618 GTGTAAGATGCAATGAAAAAGACACTA 58.710 33.333 0.00 0.00 31.79 2.74
619 621 3.312736 AAGCAAAACAAAGGGAGGAGA 57.687 42.857 0.00 0.00 0.00 3.71
695 698 7.110155 TCTGCCCCAACTTTTAAATAGACTAG 58.890 38.462 0.00 0.00 0.00 2.57
772 776 4.826733 TCATCCATATTTTCCATCCAACCG 59.173 41.667 0.00 0.00 0.00 4.44
838 843 8.031864 ACGAGCATGTGAAGAGGATAATTATAG 58.968 37.037 0.00 0.00 0.00 1.31
925 933 1.352156 CGTGAGCGAGGCCAGTAAAC 61.352 60.000 5.01 0.00 41.33 2.01
946 954 2.623094 TAATGGGGCGCCATGTGAGG 62.623 60.000 33.53 0.00 0.00 3.86
1000 1008 1.079750 GAGTGCGGGTGGAGTTCTC 60.080 63.158 0.00 0.00 0.00 2.87
1013 1021 1.375268 GTGAGTGAGCTGGGAGTGC 60.375 63.158 0.00 0.00 0.00 4.40
1121 1137 3.842126 CTCGACATGGCGTGCGTG 61.842 66.667 22.59 13.98 0.00 5.34
1889 1933 1.611977 CTGGTGGTAAGAGTGTGACGA 59.388 52.381 0.00 0.00 0.00 4.20
1895 1939 2.897969 AGTGGTACTGGTGGTAAGAGTG 59.102 50.000 0.00 0.00 31.56 3.51
1913 1957 8.718734 GGTTACAGTAAAGAATAAACAGGAGTG 58.281 37.037 0.00 0.00 0.00 3.51
1977 2024 3.851976 AGCTAGTTAACAGACTGACGG 57.148 47.619 10.08 0.00 0.00 4.79
1998 2045 0.395448 GAGGAGTACTACGGGTGGCT 60.395 60.000 0.00 0.00 0.00 4.75
1999 2046 1.390383 GGAGGAGTACTACGGGTGGC 61.390 65.000 0.00 0.00 0.00 5.01
2000 2047 0.033796 TGGAGGAGTACTACGGGTGG 60.034 60.000 0.00 0.00 30.06 4.61
2001 2048 1.681793 CATGGAGGAGTACTACGGGTG 59.318 57.143 0.00 0.00 30.06 4.61
2104 2165 5.506317 GCTTGGATTACACCATCATGCTTAC 60.506 44.000 0.00 0.00 39.82 2.34
2127 2202 6.362283 GCATGAATAATAACGGTTACATTGGC 59.638 38.462 2.10 6.14 0.00 4.52
2128 2203 7.421599 TGCATGAATAATAACGGTTACATTGG 58.578 34.615 2.10 0.98 0.00 3.16
2161 2236 2.940510 CACGCGCACGCATCATTG 60.941 61.111 16.04 0.00 45.53 2.82
2182 2257 6.241207 AGTTATATCATTACAACGCCATGC 57.759 37.500 0.00 0.00 0.00 4.06
2204 2279 5.407407 AACAACATGAGGAGTAGTGGTAG 57.593 43.478 0.00 0.00 0.00 3.18
2207 2282 4.214119 CACAAACAACATGAGGAGTAGTGG 59.786 45.833 0.00 0.00 0.00 4.00
2209 2284 3.815401 GCACAAACAACATGAGGAGTAGT 59.185 43.478 0.00 0.00 0.00 2.73
2210 2285 3.814842 TGCACAAACAACATGAGGAGTAG 59.185 43.478 0.00 0.00 0.00 2.57
2212 2287 2.653726 TGCACAAACAACATGAGGAGT 58.346 42.857 0.00 0.00 0.00 3.85
2213 2288 3.253921 TGATGCACAAACAACATGAGGAG 59.746 43.478 0.00 0.00 0.00 3.69
2214 2289 3.220940 TGATGCACAAACAACATGAGGA 58.779 40.909 0.00 0.00 0.00 3.71
2215 2290 3.646611 TGATGCACAAACAACATGAGG 57.353 42.857 0.00 0.00 0.00 3.86
2216 2291 4.613944 ACTTGATGCACAAACAACATGAG 58.386 39.130 0.00 0.00 38.08 2.90
2217 2292 4.652421 ACTTGATGCACAAACAACATGA 57.348 36.364 0.00 0.00 38.08 3.07
2218 2293 5.522456 ACTACTTGATGCACAAACAACATG 58.478 37.500 0.00 0.00 38.08 3.21
2219 2294 5.772825 ACTACTTGATGCACAAACAACAT 57.227 34.783 0.00 0.00 38.08 2.71
2220 2295 5.277106 CGTACTACTTGATGCACAAACAACA 60.277 40.000 0.00 0.00 38.08 3.33
2221 2296 5.137403 CGTACTACTTGATGCACAAACAAC 58.863 41.667 0.00 0.00 38.08 3.32
2222 2297 4.812091 ACGTACTACTTGATGCACAAACAA 59.188 37.500 0.00 0.00 38.08 2.83
2249 2324 8.991026 AGTGAACGATTACATAGCTAGTAGTAG 58.009 37.037 0.00 0.00 0.00 2.57
2250 2325 8.771766 CAGTGAACGATTACATAGCTAGTAGTA 58.228 37.037 0.00 0.00 0.00 1.82
2251 2326 7.640852 CAGTGAACGATTACATAGCTAGTAGT 58.359 38.462 0.00 0.52 0.00 2.73
2252 2327 6.579292 GCAGTGAACGATTACATAGCTAGTAG 59.421 42.308 0.00 0.00 0.00 2.57
2253 2328 6.262496 AGCAGTGAACGATTACATAGCTAGTA 59.738 38.462 0.00 0.00 31.24 1.82
2259 2334 5.005779 GGTTGAGCAGTGAACGATTACATAG 59.994 44.000 0.00 0.00 0.00 2.23
2264 2339 3.394674 TGGTTGAGCAGTGAACGATTA 57.605 42.857 0.00 0.00 0.00 1.75
2284 2359 6.263168 AGTGAAAGATGACCGACAAGAAAAAT 59.737 34.615 0.00 0.00 0.00 1.82
2288 2363 4.058124 CAGTGAAAGATGACCGACAAGAA 58.942 43.478 0.00 0.00 0.00 2.52
2290 2365 3.393800 ACAGTGAAAGATGACCGACAAG 58.606 45.455 0.00 0.00 0.00 3.16
2293 2368 4.813296 AAAACAGTGAAAGATGACCGAC 57.187 40.909 0.00 0.00 0.00 4.79
2295 2370 5.449304 GGTAAAAACAGTGAAAGATGACCG 58.551 41.667 0.00 0.00 0.00 4.79
2296 2371 5.237779 TCGGTAAAAACAGTGAAAGATGACC 59.762 40.000 0.00 0.00 0.00 4.02
2297 2372 6.134061 GTCGGTAAAAACAGTGAAAGATGAC 58.866 40.000 0.00 0.00 0.00 3.06
2315 2408 2.579657 CCCAGTGGCACTGTCGGTA 61.580 63.158 37.43 0.00 44.50 4.02
2316 2409 3.941188 CCCAGTGGCACTGTCGGT 61.941 66.667 37.43 7.94 44.50 4.69
2337 2430 2.548480 GGCGGTAAAAATGGCTAGCTAG 59.452 50.000 16.84 16.84 0.00 3.42
2338 2431 2.567985 GGCGGTAAAAATGGCTAGCTA 58.432 47.619 15.72 9.47 0.00 3.32
2339 2432 1.389555 GGCGGTAAAAATGGCTAGCT 58.610 50.000 15.72 0.00 0.00 3.32
2343 2436 1.248101 AAGCGGCGGTAAAAATGGCT 61.248 50.000 13.69 0.00 0.00 4.75
2375 2468 0.531974 TGACAGGACGGTGAGCAAAC 60.532 55.000 0.00 0.00 0.00 2.93
2429 2522 2.280524 CTTGGGCGGACGTGACAA 60.281 61.111 0.00 0.00 0.00 3.18
2430 2523 4.980805 GCTTGGGCGGACGTGACA 62.981 66.667 0.00 0.00 0.00 3.58
2436 2529 3.062466 GAAAGGGCTTGGGCGGAC 61.062 66.667 0.00 0.00 39.81 4.79
2441 2540 2.751837 GAGCGGAAAGGGCTTGGG 60.752 66.667 0.00 0.00 41.72 4.12
2446 2545 2.815647 CACGAGAGCGGAAAGGGC 60.816 66.667 0.00 0.00 43.17 5.19
2540 2658 2.046314 AGCCGGGGACACAAATCG 60.046 61.111 2.18 0.00 0.00 3.34
2555 2673 3.672295 CTGGAGCCAACGGAGGAGC 62.672 68.421 0.00 0.00 0.00 4.70
2556 2674 2.581354 CTGGAGCCAACGGAGGAG 59.419 66.667 0.00 0.00 0.00 3.69
2557 2675 3.706373 GCTGGAGCCAACGGAGGA 61.706 66.667 0.00 0.00 34.31 3.71
2652 2782 0.811616 CGCCTGCTATCCACTCCAAC 60.812 60.000 0.00 0.00 0.00 3.77
2707 2837 0.667993 AATGAAACCCACACAGTGCG 59.332 50.000 0.00 0.00 31.34 5.34
2720 2850 3.059386 GGCCCCGACGCAATGAAA 61.059 61.111 0.00 0.00 0.00 2.69
2765 2895 2.126307 CACTGTGGCTCCGTCGAG 60.126 66.667 0.00 0.00 39.33 4.04
2796 2926 5.952947 TGAAAATTTACCCCCATGAATACGT 59.047 36.000 0.00 0.00 0.00 3.57
2806 2936 2.092646 GGGCCAATGAAAATTTACCCCC 60.093 50.000 4.39 0.00 0.00 5.40
2821 2952 1.747367 CGCTTTATGACGGGGCCAA 60.747 57.895 4.39 0.00 0.00 4.52
2825 2956 1.849097 GTAGACGCTTTATGACGGGG 58.151 55.000 0.00 0.00 0.00 5.73
2828 2959 2.512885 ACACGTAGACGCTTTATGACG 58.487 47.619 1.14 0.00 44.43 4.35
2854 2985 1.377366 TAGCAAGGACCGCGAGAGAG 61.377 60.000 8.23 0.00 0.00 3.20
2858 2989 1.985447 TACGTAGCAAGGACCGCGAG 61.985 60.000 8.23 0.00 0.00 5.03
2860 2991 1.585521 CTACGTAGCAAGGACCGCG 60.586 63.158 10.14 0.00 0.00 6.46
2880 3011 9.723601 GCACAGTATTATCCTACTACTACTACT 57.276 37.037 0.00 0.00 30.78 2.57
2881 3012 8.945057 GGCACAGTATTATCCTACTACTACTAC 58.055 40.741 0.00 0.00 30.78 2.73
2882 3013 8.888419 AGGCACAGTATTATCCTACTACTACTA 58.112 37.037 0.00 0.00 30.78 1.82
2883 3014 7.666388 CAGGCACAGTATTATCCTACTACTACT 59.334 40.741 0.00 0.00 30.78 2.57
2884 3015 7.575343 GCAGGCACAGTATTATCCTACTACTAC 60.575 44.444 0.00 0.00 30.78 2.73
2885 3016 6.433404 GCAGGCACAGTATTATCCTACTACTA 59.567 42.308 0.00 0.00 30.78 1.82


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

AutoCloner maintained by Alex Coulton.