Multiple sequence alignment - TraesCS3A01G078200

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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 TraesCS3A01G078200 chr3A 100.000 4107 0 0 1 4107 50642096 50637990 0.000000e+00 7585
1 TraesCS3A01G078200 chr3A 90.335 1790 101 34 1508 3253 50548184 50546423 0.000000e+00 2281
2 TraesCS3A01G078200 chr3A 86.214 515 48 11 3255 3761 50546383 50545884 1.680000e-148 536
3 TraesCS3A01G078200 chr3A 89.474 228 17 7 3881 4107 50545708 50545487 8.690000e-72 281
4 TraesCS3A01G078200 chr3A 78.896 308 45 12 1875 2170 177705292 177705591 1.510000e-44 191
5 TraesCS3A01G078200 chr3D 89.028 2552 170 42 1 2534 39303978 39301519 0.000000e+00 3061
6 TraesCS3A01G078200 chr3D 91.713 1617 57 28 2536 4107 39301472 39299888 0.000000e+00 2172
7 TraesCS3A01G078200 chr3D 89.432 757 31 15 2524 3253 39208160 39207426 0.000000e+00 909
8 TraesCS3A01G078200 chr3D 89.379 725 50 14 1824 2534 39208902 39208191 0.000000e+00 887
9 TraesCS3A01G078200 chr3D 87.216 485 35 10 3255 3732 39207396 39206932 1.010000e-145 527
10 TraesCS3A01G078200 chr3D 89.848 197 10 2 3880 4067 39206788 39206593 1.140000e-60 244
11 TraesCS3A01G078200 chr3B 89.428 1977 118 33 572 2534 62217825 62215926 0.000000e+00 2409
12 TraesCS3A01G078200 chr3B 90.653 888 42 22 3255 4107 62215127 62214246 0.000000e+00 1142
13 TraesCS3A01G078200 chr3B 88.015 801 67 20 1748 2534 62012012 62011227 0.000000e+00 920
14 TraesCS3A01G078200 chr3B 87.763 760 32 25 2524 3253 62215895 62215167 0.000000e+00 832
15 TraesCS3A01G078200 chr3B 88.421 665 49 8 2535 3174 62011183 62010522 0.000000e+00 776
16 TraesCS3A01G078200 chr3B 87.969 640 44 11 3255 3885 62010339 62009724 0.000000e+00 725
17 TraesCS3A01G078200 chr3B 86.511 556 58 13 76 628 62218346 62217805 2.730000e-166 595
18 TraesCS3A01G078200 chr3B 88.235 136 6 3 3880 4006 62009701 62009567 1.980000e-33 154
19 TraesCS3A01G078200 chr3B 93.902 82 5 0 3172 3253 62010450 62010369 1.550000e-24 124
20 TraesCS3A01G078200 chr7B 88.889 450 35 9 1557 2004 698630821 698630385 1.300000e-149 540
21 TraesCS3A01G078200 chr7B 89.294 439 32 8 1567 2003 684165019 684165444 1.680000e-148 536
22 TraesCS3A01G078200 chr7B 89.754 244 15 4 1763 2004 614249297 614249062 1.860000e-78 303
23 TraesCS3A01G078200 chr6B 88.914 451 33 7 1557 2004 68221069 68221505 1.300000e-149 540
24 TraesCS3A01G078200 chr5B 87.805 451 38 7 1557 2004 385249834 385250270 2.830000e-141 512
25 TraesCS3A01G078200 chr5A 87.556 450 41 10 1557 2004 564680197 564679761 1.320000e-139 507
26 TraesCS3A01G078200 chr5A 85.156 384 44 9 1782 2160 632224342 632223967 8.330000e-102 381
27 TraesCS3A01G078200 chr4A 86.577 447 45 8 1560 2004 661807955 661807522 2.870000e-131 479
28 TraesCS3A01G078200 chr4A 82.759 203 35 0 2843 3045 173932155 173931953 9.070000e-42 182
29 TraesCS3A01G078200 chr2B 80.392 204 38 2 2842 3044 84817752 84817954 1.980000e-33 154
30 TraesCS3A01G078200 chr2A 80.392 204 38 2 2842 3044 54817556 54817354 1.980000e-33 154


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 TraesCS3A01G078200 chr3A 50637990 50642096 4106 True 7585.000000 7585 100.000000 1 4107 1 chr3A.!!$R1 4106
1 TraesCS3A01G078200 chr3A 50545487 50548184 2697 True 1032.666667 2281 88.674333 1508 4107 3 chr3A.!!$R2 2599
2 TraesCS3A01G078200 chr3D 39299888 39303978 4090 True 2616.500000 3061 90.370500 1 4107 2 chr3D.!!$R2 4106
3 TraesCS3A01G078200 chr3D 39206593 39208902 2309 True 641.750000 909 88.968750 1824 4067 4 chr3D.!!$R1 2243
4 TraesCS3A01G078200 chr3B 62214246 62218346 4100 True 1244.500000 2409 88.588750 76 4107 4 chr3B.!!$R2 4031
5 TraesCS3A01G078200 chr3B 62009567 62012012 2445 True 539.800000 920 89.308400 1748 4006 5 chr3B.!!$R1 2258

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
324 327 0.041833 AGAGGCAGAGGTAGAGGCAA 59.958 55.0 0.0 0.0 0.00 4.52 F
1843 1910 0.030638 TTTGGCTTTTGCTCAGCGAC 59.969 50.0 0.0 0.0 46.54 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2147 2237 0.039798 CATGTGGTGTGCTTGCAGAC 60.040 55.0 13.47 13.47 0.00 3.51 R
3632 3994 1.601166 GCTTGGGTTTTCACCGTAGT 58.399 50.0 0.00 0.00 45.39 2.73 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
20 21 2.706890 ACATGGCTCGAACCGTTAAAT 58.293 42.857 0.00 0.00 0.00 1.40
24 25 3.340034 TGGCTCGAACCGTTAAATTGAT 58.660 40.909 0.00 0.00 0.00 2.57
29 30 5.539582 TCGAACCGTTAAATTGATCCTTG 57.460 39.130 0.00 0.00 0.00 3.61
38 39 6.093495 CGTTAAATTGATCCTTGCCAACTCTA 59.907 38.462 0.00 0.00 0.00 2.43
41 42 9.866655 TTAAATTGATCCTTGCCAACTCTATAT 57.133 29.630 0.00 0.00 0.00 0.86
61 62 3.288290 CGCTCCGCCCGATCTAGT 61.288 66.667 0.00 0.00 0.00 2.57
83 84 0.105778 CTCCAGAAGCTCCCGAATCC 59.894 60.000 0.00 0.00 0.00 3.01
89 90 1.627297 AAGCTCCCGAATCCCCTGAC 61.627 60.000 0.00 0.00 0.00 3.51
91 92 2.366435 TCCCGAATCCCCTGACCC 60.366 66.667 0.00 0.00 0.00 4.46
122 125 3.055719 GTGCACCACATCCACCCG 61.056 66.667 5.22 0.00 34.08 5.28
135 138 1.517832 CACCCGCAGAGGTAGAAGG 59.482 63.158 0.00 0.00 38.39 3.46
147 150 4.020543 GAGGTAGAAGGAGATGACACTGT 58.979 47.826 0.00 0.00 0.00 3.55
163 166 1.332195 CTGTCCTCCCATATCTCGCA 58.668 55.000 0.00 0.00 0.00 5.10
196 199 3.423154 GCAACTTCGAGCCCCACG 61.423 66.667 0.00 0.00 0.00 4.94
197 200 2.342279 CAACTTCGAGCCCCACGA 59.658 61.111 0.00 0.00 37.99 4.35
240 243 3.781307 CGTCGGGGCTCCCATCAA 61.781 66.667 7.34 0.00 45.83 2.57
248 251 1.410083 GGGCTCCCATCAAGTATGCAA 60.410 52.381 0.00 0.00 33.92 4.08
276 279 1.142314 CGGGGTCGCCGAGAATTAA 59.858 57.895 23.09 0.00 0.00 1.40
286 289 1.138266 CCGAGAATTAAGGAAGGGCGA 59.862 52.381 0.00 0.00 0.00 5.54
304 307 1.152383 GACGGGTTGCGAGAATAGGC 61.152 60.000 0.00 0.00 0.00 3.93
305 308 1.153449 CGGGTTGCGAGAATAGGCA 60.153 57.895 0.00 0.00 37.39 4.75
311 314 1.329913 TGCGAGAATAGGCAGAGGCA 61.330 55.000 0.00 0.00 43.71 4.75
316 319 1.127343 GAATAGGCAGAGGCAGAGGT 58.873 55.000 0.00 0.00 43.71 3.85
323 326 0.685785 CAGAGGCAGAGGTAGAGGCA 60.686 60.000 0.00 0.00 0.00 4.75
324 327 0.041833 AGAGGCAGAGGTAGAGGCAA 59.958 55.000 0.00 0.00 0.00 4.52
326 329 0.908198 AGGCAGAGGTAGAGGCAAAG 59.092 55.000 0.00 0.00 0.00 2.77
327 330 0.905357 GGCAGAGGTAGAGGCAAAGA 59.095 55.000 0.00 0.00 0.00 2.52
328 331 1.134551 GGCAGAGGTAGAGGCAAAGAG 60.135 57.143 0.00 0.00 0.00 2.85
329 332 1.827969 GCAGAGGTAGAGGCAAAGAGA 59.172 52.381 0.00 0.00 0.00 3.10
330 333 2.433970 GCAGAGGTAGAGGCAAAGAGAT 59.566 50.000 0.00 0.00 0.00 2.75
333 336 4.280677 CAGAGGTAGAGGCAAAGAGATAGG 59.719 50.000 0.00 0.00 0.00 2.57
339 342 0.107654 GGCAAAGAGATAGGTGGCGT 60.108 55.000 0.00 0.00 0.00 5.68
347 350 2.131294 GATAGGTGGCGTCGCGAGAT 62.131 60.000 10.24 1.02 45.19 2.75
480 484 3.221964 ACAAGAAATCAAATCGCAGCC 57.778 42.857 0.00 0.00 0.00 4.85
548 552 6.300354 TCACATCGAAACCTTTTTCTTCTC 57.700 37.500 0.00 0.00 39.29 2.87
551 555 5.470437 ACATCGAAACCTTTTTCTTCTCCTC 59.530 40.000 0.00 0.00 39.29 3.71
624 663 4.278419 GCTGGTACTTGACTGATTTGGTTT 59.722 41.667 0.00 0.00 0.00 3.27
654 693 0.548031 GATCTGTGGGGGCATCTGAA 59.452 55.000 0.00 0.00 0.00 3.02
655 694 0.257039 ATCTGTGGGGGCATCTGAAC 59.743 55.000 0.00 0.00 0.00 3.18
657 696 2.438434 GTGGGGGCATCTGAACGG 60.438 66.667 0.00 0.00 0.00 4.44
661 701 0.610785 GGGGGCATCTGAACGGAAAA 60.611 55.000 0.00 0.00 0.00 2.29
688 728 4.861462 CGGAGGAGATACGATCATGATTTG 59.139 45.833 10.14 8.40 37.47 2.32
689 729 4.629200 GGAGGAGATACGATCATGATTTGC 59.371 45.833 10.14 0.00 0.00 3.68
690 730 5.477510 GAGGAGATACGATCATGATTTGCT 58.522 41.667 10.14 3.67 0.00 3.91
691 731 5.477510 AGGAGATACGATCATGATTTGCTC 58.522 41.667 10.14 11.77 0.00 4.26
724 764 3.467119 CCGCGACGTGTGTAGTGC 61.467 66.667 8.23 0.00 30.85 4.40
747 787 3.243737 ACAAGTGAAGTCTGTATGCGTCA 60.244 43.478 0.00 0.00 0.00 4.35
776 816 2.858476 TGGTGGACACATGGGGCT 60.858 61.111 0.00 0.00 0.00 5.19
778 818 2.436646 GTGGACACATGGGGCTCG 60.437 66.667 0.00 0.00 0.00 5.03
895 936 2.086426 CACCGTCCGTCGACATGTG 61.086 63.158 17.16 10.42 42.86 3.21
937 978 3.106986 GCTGAGCTTGGCCCGGATA 62.107 63.158 0.73 0.00 0.00 2.59
938 979 1.070445 CTGAGCTTGGCCCGGATAG 59.930 63.158 0.73 0.00 0.00 2.08
974 1015 4.752142 CGCGCGCGTTCCCATTTT 62.752 61.111 42.49 0.00 34.35 1.82
991 1032 4.988716 TCCGACCACCGACAGGCT 62.989 66.667 0.00 0.00 42.76 4.58
1015 1056 0.744414 AATCATGGAGTTCCCGCACG 60.744 55.000 0.00 0.00 37.93 5.34
1257 1298 0.818445 GCGAGGATGAGTACGGAGGA 60.818 60.000 0.00 0.00 0.00 3.71
1714 1774 2.752354 AGATCGATCCAAGATCGGCTAG 59.248 50.000 21.66 0.00 46.60 3.42
1812 1879 7.419634 CCTTGTCCTTTTCTAATTGGGGAAAAA 60.420 37.037 13.01 3.40 39.76 1.94
1839 1906 1.682854 TCCTGTTTGGCTTTTGCTCAG 59.317 47.619 0.00 0.00 46.54 3.35
1840 1907 1.494824 CTGTTTGGCTTTTGCTCAGC 58.505 50.000 0.00 0.00 46.54 4.26
1841 1908 0.248990 TGTTTGGCTTTTGCTCAGCG 60.249 50.000 0.00 0.00 46.54 5.18
1843 1910 0.030638 TTTGGCTTTTGCTCAGCGAC 59.969 50.000 0.00 0.00 46.54 5.19
1848 1917 2.047040 GCTTTTGCTCAGCGACTTTTC 58.953 47.619 0.00 0.00 43.35 2.29
1880 1949 4.005650 TGTTTCTTCTCTGATCATGTGGC 58.994 43.478 0.00 0.00 0.00 5.01
1899 1968 5.469760 TGTGGCTGATGGATTTGAATATACG 59.530 40.000 0.00 0.00 0.00 3.06
2066 2135 4.410228 CCTCCTTCCTTCAGTTCATCCATA 59.590 45.833 0.00 0.00 0.00 2.74
2112 2201 4.735132 TGCGTGCACGGTAGAGCC 62.735 66.667 37.47 20.74 40.23 4.70
2126 2215 2.496899 AGAGCCGACATGATTTTGGT 57.503 45.000 0.00 0.00 0.00 3.67
2128 2217 3.270877 AGAGCCGACATGATTTTGGTAC 58.729 45.455 0.00 0.00 0.00 3.34
2147 2237 8.771920 TTGGTACATTTAGACATAACAGAGTG 57.228 34.615 0.00 0.00 39.30 3.51
2164 2258 1.077858 TGTCTGCAAGCACACCACA 60.078 52.632 0.00 0.00 0.00 4.17
2165 2259 0.466007 TGTCTGCAAGCACACCACAT 60.466 50.000 0.00 0.00 0.00 3.21
2166 2260 0.039798 GTCTGCAAGCACACCACATG 60.040 55.000 0.00 0.00 0.00 3.21
2167 2261 1.372499 CTGCAAGCACACCACATGC 60.372 57.895 0.00 0.00 43.74 4.06
2168 2262 2.048877 GCAAGCACACCACATGCC 60.049 61.111 0.00 0.00 44.53 4.40
2169 2263 2.858862 GCAAGCACACCACATGCCA 61.859 57.895 0.00 0.00 44.53 4.92
2170 2264 1.287815 CAAGCACACCACATGCCAG 59.712 57.895 0.00 0.00 44.53 4.85
2171 2265 1.152694 AAGCACACCACATGCCAGT 60.153 52.632 0.00 0.00 44.53 4.00
2172 2266 1.457823 AAGCACACCACATGCCAGTG 61.458 55.000 8.39 8.39 44.53 3.66
2267 2364 9.428097 GAATGGATAAGCTTGAACAAAAAGAAT 57.572 29.630 9.86 0.00 0.00 2.40
2283 2380 9.822185 ACAAAAAGAATCACTTTGAGCTTATTT 57.178 25.926 12.13 0.00 46.55 1.40
2314 2411 2.287788 GCCTGTGGTGTTTCAGTGAATG 60.288 50.000 6.36 0.00 0.00 2.67
2315 2412 2.951642 CCTGTGGTGTTTCAGTGAATGT 59.048 45.455 6.36 0.00 0.00 2.71
2335 2435 3.901222 TGTTCACCACTAGGATTCAGTGA 59.099 43.478 4.11 0.00 45.10 3.41
2443 2551 6.143118 TGTTCAGCAAACGTTGTAAATTATGC 59.857 34.615 0.00 5.29 41.02 3.14
2468 2577 7.648142 CCAGTGTCAAAAGTTAAATCTGCTAA 58.352 34.615 0.00 0.00 0.00 3.09
2506 2615 7.221450 TGCCATACAAGACCATAACTATAACC 58.779 38.462 0.00 0.00 0.00 2.85
2605 2804 8.914011 TGCACATATATCACAGTAGTTCTAACT 58.086 33.333 0.39 0.39 42.91 2.24
2612 2811 3.673809 CACAGTAGTTCTAACTCGGTTGC 59.326 47.826 0.00 0.00 40.37 4.17
2632 2831 1.067212 CCCATGACCGCTCTAGTGTAC 59.933 57.143 0.00 0.00 0.00 2.90
2681 2880 4.812626 GGTGAACTCGTTAGACAAAAGGAA 59.187 41.667 0.00 0.00 0.00 3.36
2688 2887 4.333372 TCGTTAGACAAAAGGAACAACACC 59.667 41.667 0.00 0.00 0.00 4.16
2693 2892 2.563620 ACAAAAGGAACAACACCGGTTT 59.436 40.909 2.97 0.00 34.21 3.27
2710 2911 5.708230 ACCGGTTTCAGAATAATTTGCTACA 59.292 36.000 0.00 0.00 0.00 2.74
2778 2983 4.523943 TGCAGCTCCAGTATTGTGAATTTT 59.476 37.500 0.00 0.00 0.00 1.82
3091 3326 2.838736 TGCTCCAGTTCAGTTTCACTC 58.161 47.619 0.00 0.00 0.00 3.51
3196 3510 4.794278 TGACACGAGCAAGGTATTTCTA 57.206 40.909 0.00 0.00 0.00 2.10
3253 3606 1.605710 GCAGGAACGATGCATATGCTT 59.394 47.619 27.13 21.42 43.31 3.91
3287 3640 8.360390 ACTGAATGTTTCTGGAATAAAAAGGAC 58.640 33.333 0.00 0.00 33.45 3.85
3493 3849 7.949565 TGGTTTATCCCATCATATTGCTGTAAT 59.050 33.333 0.00 0.00 34.77 1.89
3528 3890 7.772166 TCTATATAGTTGTGGCGGATATTCAG 58.228 38.462 9.58 0.00 0.00 3.02
3652 4014 0.515564 CTACGGTGAAAACCCAAGCG 59.484 55.000 0.00 0.00 40.43 4.68
3677 4039 6.981762 TTCGACCAGTACAAAAACAAGTTA 57.018 33.333 0.00 0.00 0.00 2.24
3769 4145 6.660521 TGAAAATTGACAGGAGCTGTATGAAT 59.339 34.615 0.00 0.00 45.44 2.57
3920 4343 2.769663 AGGTCCCCTCCAAAACAAAAAC 59.230 45.455 0.00 0.00 0.00 2.43
4049 4481 4.835615 GGTATCATGTCCTGTCCACTAGAT 59.164 45.833 0.00 0.00 0.00 1.98
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 4.142773 GCAAGGATCAATTTAACGGTTCGA 60.143 41.667 0.00 0.00 0.00 3.71
8 9 4.095610 GCAAGGATCAATTTAACGGTTCG 58.904 43.478 0.00 0.00 0.00 3.95
15 16 9.866655 ATATAGAGTTGGCAAGGATCAATTTAA 57.133 29.630 0.00 0.00 0.00 1.52
20 21 5.221925 GGGATATAGAGTTGGCAAGGATCAA 60.222 44.000 0.00 0.00 0.00 2.57
24 25 2.632996 CGGGATATAGAGTTGGCAAGGA 59.367 50.000 0.00 0.00 0.00 3.36
29 30 1.066787 GGAGCGGGATATAGAGTTGGC 60.067 57.143 0.00 0.00 0.00 4.52
61 62 0.040646 TTCGGGAGCTTCTGGAGGTA 59.959 55.000 0.00 0.00 35.91 3.08
83 84 4.016706 GGTGGTGTCGGGTCAGGG 62.017 72.222 0.00 0.00 0.00 4.45
122 125 3.027412 TGTCATCTCCTTCTACCTCTGC 58.973 50.000 0.00 0.00 0.00 4.26
123 126 4.097741 CAGTGTCATCTCCTTCTACCTCTG 59.902 50.000 0.00 0.00 0.00 3.35
135 138 1.561643 TGGGAGGACAGTGTCATCTC 58.438 55.000 30.56 28.87 43.15 2.75
147 150 1.964223 GTTCTGCGAGATATGGGAGGA 59.036 52.381 0.00 0.00 0.00 3.71
163 166 1.360393 TTGCCTTGGGACCCAGTTCT 61.360 55.000 14.35 0.00 33.81 3.01
196 199 1.950909 CATCCCACTCTCTACTCGGTC 59.049 57.143 0.00 0.00 0.00 4.79
197 200 1.564818 TCATCCCACTCTCTACTCGGT 59.435 52.381 0.00 0.00 0.00 4.69
203 206 1.393603 CTGCGTCATCCCACTCTCTA 58.606 55.000 0.00 0.00 0.00 2.43
236 239 3.445096 GGCCTCAACTTTGCATACTTGAT 59.555 43.478 0.00 0.00 0.00 2.57
240 243 1.453155 CGGCCTCAACTTTGCATACT 58.547 50.000 0.00 0.00 0.00 2.12
248 251 4.016706 CGACCCCGGCCTCAACTT 62.017 66.667 0.00 0.00 0.00 2.66
271 274 0.107361 CCCGTCGCCCTTCCTTAATT 60.107 55.000 0.00 0.00 0.00 1.40
276 279 4.016706 CAACCCGTCGCCCTTCCT 62.017 66.667 0.00 0.00 0.00 3.36
286 289 1.153429 GCCTATTCTCGCAACCCGT 60.153 57.895 0.00 0.00 38.35 5.28
298 301 2.091055 TCTACCTCTGCCTCTGCCTATT 60.091 50.000 0.00 0.00 36.33 1.73
299 302 1.501170 TCTACCTCTGCCTCTGCCTAT 59.499 52.381 0.00 0.00 36.33 2.57
304 307 0.685785 TGCCTCTACCTCTGCCTCTG 60.686 60.000 0.00 0.00 0.00 3.35
305 308 0.041833 TTGCCTCTACCTCTGCCTCT 59.958 55.000 0.00 0.00 0.00 3.69
311 314 4.078863 ACCTATCTCTTTGCCTCTACCTCT 60.079 45.833 0.00 0.00 0.00 3.69
316 319 2.700897 GCCACCTATCTCTTTGCCTCTA 59.299 50.000 0.00 0.00 0.00 2.43
323 326 0.179108 GCGACGCCACCTATCTCTTT 60.179 55.000 9.14 0.00 0.00 2.52
324 327 1.437986 GCGACGCCACCTATCTCTT 59.562 57.895 9.14 0.00 0.00 2.85
326 329 2.353607 CGCGACGCCACCTATCTC 60.354 66.667 15.34 0.00 0.00 2.75
327 330 2.827190 TCGCGACGCCACCTATCT 60.827 61.111 15.34 0.00 0.00 1.98
328 331 2.131294 ATCTCGCGACGCCACCTATC 62.131 60.000 15.34 0.00 0.00 2.08
329 332 2.131294 GATCTCGCGACGCCACCTAT 62.131 60.000 15.34 0.80 0.00 2.57
330 333 2.827190 ATCTCGCGACGCCACCTA 60.827 61.111 15.34 0.00 0.00 3.08
333 336 2.092291 TTTGATCTCGCGACGCCAC 61.092 57.895 15.34 2.06 0.00 5.01
339 342 4.740741 TTCAAAATGTTTGATCTCGCGA 57.259 36.364 9.26 9.26 0.00 5.87
480 484 2.461110 GGATAGTGCGGTTGGTGCG 61.461 63.158 0.00 0.00 34.24 5.34
624 663 2.893489 CCCCACAGATCAGATCGTATCA 59.107 50.000 4.67 0.00 0.00 2.15
654 693 0.754472 TCTCCTCCGTTGTTTTCCGT 59.246 50.000 0.00 0.00 0.00 4.69
655 694 2.094762 ATCTCCTCCGTTGTTTTCCG 57.905 50.000 0.00 0.00 0.00 4.30
657 696 3.841643 TCGTATCTCCTCCGTTGTTTTC 58.158 45.455 0.00 0.00 0.00 2.29
661 701 2.651455 TGATCGTATCTCCTCCGTTGT 58.349 47.619 0.00 0.00 0.00 3.32
689 729 4.514577 ATCGGCTCGGCGTTGGAG 62.515 66.667 6.85 0.00 34.62 3.86
690 730 4.508128 GATCGGCTCGGCGTTGGA 62.508 66.667 6.85 0.69 0.00 3.53
724 764 3.059884 ACGCATACAGACTTCACTTGTG 58.940 45.455 0.00 0.00 0.00 3.33
747 787 2.901840 CCACCACGTGCACAGCTT 60.902 61.111 18.64 0.00 31.34 3.74
794 834 3.730761 GATGGCGATGGCGATGGC 61.731 66.667 7.17 7.17 37.76 4.40
795 835 3.417224 CGATGGCGATGGCGATGG 61.417 66.667 1.13 0.00 37.76 3.51
796 836 4.081030 GCGATGGCGATGGCGATG 62.081 66.667 1.13 0.00 37.76 3.84
799 839 4.662961 TAGGCGATGGCGATGGCG 62.663 66.667 9.43 0.00 41.24 5.69
800 840 2.740055 CTAGGCGATGGCGATGGC 60.740 66.667 7.17 7.17 41.24 4.40
801 841 1.069765 AACTAGGCGATGGCGATGG 59.930 57.895 0.00 0.00 41.24 3.51
802 842 1.835483 GCAACTAGGCGATGGCGATG 61.835 60.000 0.00 0.00 41.24 3.84
815 855 2.147958 ACCGCTTCAATTTCGCAACTA 58.852 42.857 0.00 0.00 0.00 2.24
874 914 1.970114 ATGTCGACGGACGGTGAGT 60.970 57.895 11.62 0.00 46.49 3.41
881 921 1.805945 GGAGCACATGTCGACGGAC 60.806 63.158 11.62 4.22 43.71 4.79
882 922 2.571757 GGAGCACATGTCGACGGA 59.428 61.111 11.62 0.00 0.00 4.69
938 979 2.073101 GGGGAGTGGAGGTGGATCC 61.073 68.421 4.20 4.20 40.03 3.36
974 1015 3.572447 TAGCCTGTCGGTGGTCGGA 62.572 63.158 0.00 0.00 39.77 4.55
991 1032 2.158957 GCGGGAACTCCATGATTGACTA 60.159 50.000 0.00 0.00 37.91 2.59
1554 1613 2.992689 TACGTCGGCTGCCTGGAA 60.993 61.111 17.92 0.00 0.00 3.53
1555 1614 3.755628 GTACGTCGGCTGCCTGGA 61.756 66.667 17.92 4.49 0.00 3.86
1714 1774 2.354259 GATCGGGATCATGGAAGCATC 58.646 52.381 3.84 0.00 37.74 3.91
1760 1825 1.202879 ACGCCAAGTTTTCAGATCCCA 60.203 47.619 0.00 0.00 0.00 4.37
1839 1906 8.895932 AGAAACAATAATACATGAAAAGTCGC 57.104 30.769 0.00 0.00 0.00 5.19
1880 1949 9.101655 TCATATGCGTATATTCAAATCCATCAG 57.898 33.333 2.96 0.00 0.00 2.90
2110 2199 4.370364 AATGTACCAAAATCATGTCGGC 57.630 40.909 0.00 0.00 0.00 5.54
2112 2201 7.747888 TGTCTAAATGTACCAAAATCATGTCG 58.252 34.615 0.00 0.00 0.00 4.35
2147 2237 0.039798 CATGTGGTGTGCTTGCAGAC 60.040 55.000 13.47 13.47 0.00 3.51
2167 2261 0.813184 GGAATGTGTGGCATCACTGG 59.187 55.000 17.03 0.00 43.94 4.00
2168 2262 1.536940 TGGAATGTGTGGCATCACTG 58.463 50.000 17.03 0.00 43.94 3.66
2169 2263 2.291209 TTGGAATGTGTGGCATCACT 57.709 45.000 17.03 0.09 43.94 3.41
2170 2264 3.255725 CATTTGGAATGTGTGGCATCAC 58.744 45.455 11.62 11.62 43.87 3.06
2171 2265 2.353903 GCATTTGGAATGTGTGGCATCA 60.354 45.455 0.00 0.00 36.67 3.07
2172 2266 2.273557 GCATTTGGAATGTGTGGCATC 58.726 47.619 0.00 0.00 36.67 3.91
2283 2380 2.146724 ACCACAGGCCACACTGCTA 61.147 57.895 5.01 0.00 42.21 3.49
2284 2381 3.492353 ACCACAGGCCACACTGCT 61.492 61.111 5.01 0.00 42.21 4.24
2293 2390 1.388547 TTCACTGAAACACCACAGGC 58.611 50.000 0.00 0.00 38.30 4.85
2314 2411 4.537135 TCACTGAATCCTAGTGGTGAAC 57.463 45.455 5.42 0.00 44.33 3.18
2315 2412 5.762179 AATCACTGAATCCTAGTGGTGAA 57.238 39.130 5.42 0.00 44.33 3.18
2443 2551 6.076981 AGCAGATTTAACTTTTGACACTGG 57.923 37.500 0.00 0.00 0.00 4.00
2506 2615 3.745975 ACATGAACACACGTGGAAGTATG 59.254 43.478 21.57 18.83 34.19 2.39
2612 2811 1.067212 GTACACTAGAGCGGTCATGGG 59.933 57.143 18.15 12.14 0.00 4.00
2632 2831 8.642885 CATATTATTTTAGAGCTAGTGTCGCTG 58.357 37.037 0.00 0.00 37.96 5.18
2681 2880 6.212955 CAAATTATTCTGAAACCGGTGTTGT 58.787 36.000 8.52 0.00 34.13 3.32
2688 2887 6.842163 AGTGTAGCAAATTATTCTGAAACCG 58.158 36.000 0.00 0.00 0.00 4.44
2693 2892 9.890629 AACTCATAGTGTAGCAAATTATTCTGA 57.109 29.630 0.00 0.00 0.00 3.27
2710 2911 4.890158 TGACCATGTGACAACTCATAGT 57.110 40.909 0.00 0.00 0.00 2.12
2969 3176 2.379907 ACAGAATGAGGGTGGTTCCATT 59.620 45.455 0.00 0.00 39.69 3.16
3196 3510 7.180766 AGACACAAATCAATCCCCAATTGTAAT 59.819 33.333 4.43 0.00 44.36 1.89
3253 3606 6.109156 TCCAGAAACATTCAGTACTTGCTA 57.891 37.500 0.00 0.00 0.00 3.49
3287 3640 3.803082 CCACTCACATTGGCGCCG 61.803 66.667 23.90 10.49 0.00 6.46
3362 3715 3.742882 CCATCACACATAATCTACGCCAG 59.257 47.826 0.00 0.00 0.00 4.85
3493 3849 7.283354 CGCCACAACTATATAGATAGATCTCCA 59.717 40.741 16.79 0.00 37.81 3.86
3528 3890 2.596904 TATGCTACCTTGAGCCGAAC 57.403 50.000 0.00 0.00 42.11 3.95
3590 3952 9.814899 TGTACATGTCTGAATTTTTCATGTTTT 57.185 25.926 0.00 4.22 43.97 2.43
3591 3953 9.985730 ATGTACATGTCTGAATTTTTCATGTTT 57.014 25.926 7.78 7.34 43.97 2.83
3592 3954 9.414295 CATGTACATGTCTGAATTTTTCATGTT 57.586 29.630 24.91 5.18 43.97 2.71
3593 3955 8.975410 CATGTACATGTCTGAATTTTTCATGT 57.025 30.769 24.91 17.00 46.62 3.21
3632 3994 1.601166 GCTTGGGTTTTCACCGTAGT 58.399 50.000 0.00 0.00 45.39 2.73
3652 4014 5.633927 ACTTGTTTTTGTACTGGTCGAAAC 58.366 37.500 0.00 0.00 0.00 2.78
3677 4039 2.094675 AGCGCCAGAAAATAAGCACAT 58.905 42.857 2.29 0.00 0.00 3.21
3751 4115 5.876651 ACATATTCATACAGCTCCTGTCA 57.123 39.130 0.48 0.00 41.21 3.58
3854 4246 3.331478 AGTCTCTGCACCTCAAAGATG 57.669 47.619 0.00 0.00 0.00 2.90
3906 4328 8.472683 TGAGTACATTTGTTTTTGTTTTGGAG 57.527 30.769 0.00 0.00 0.00 3.86
3920 4343 6.017400 AGCAATTGACCTTGAGTACATTTG 57.983 37.500 10.34 0.00 0.00 2.32
4049 4481 2.037367 AGGGCGAGCCAGACACTA 59.963 61.111 16.65 0.00 37.98 2.74


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

AutoCloner maintained by Alex Coulton.