Multiple sequence alignment - TraesCS1D01G360000

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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 TraesCS1D01G360000 chr1D 100.000 2336 0 0 1 2336 443169189 443166854 0.000000e+00 4314.0
1 TraesCS1D01G360000 chr1D 85.714 126 5 4 199 324 443180995 443180883 1.130000e-23 121.0
2 TraesCS1D01G360000 chr1B 86.386 2211 141 79 201 2330 601266940 601269071 0.000000e+00 2268.0
3 TraesCS1D01G360000 chr1B 84.234 444 35 10 891 1334 601253386 601253794 1.300000e-107 399.0
4 TraesCS1D01G360000 chr1B 79.318 440 27 20 199 603 601252358 601252768 1.390000e-62 250.0
5 TraesCS1D01G360000 chr1B 94.340 106 6 0 82 187 601266772 601266877 1.860000e-36 163.0
6 TraesCS1D01G360000 chr1B 83.962 106 7 1 82 187 601255834 601255929 2.470000e-15 93.5
7 TraesCS1D01G360000 chr1B 97.778 45 1 0 1283 1327 598926111 598926155 6.920000e-11 78.7
8 TraesCS1D01G360000 chr1B 97.222 36 0 1 600 634 601252782 601252817 2.510000e-05 60.2
9 TraesCS1D01G360000 chr1B 100.000 29 0 0 606 634 601252812 601252840 1.000000e-03 54.7
10 TraesCS1D01G360000 chr1A 82.904 2445 143 110 1 2336 535856932 535859210 0.000000e+00 1945.0
11 TraesCS1D01G360000 chr1A 77.895 285 20 19 475 740 535854755 535855015 1.130000e-28 137.0
12 TraesCS1D01G360000 chr1A 88.991 109 11 1 79 187 535770540 535770647 1.460000e-27 134.0
13 TraesCS1D01G360000 chr1A 94.737 38 2 0 608 645 535857576 535857613 2.510000e-05 60.2
14 TraesCS1D01G360000 chr3B 88.435 147 17 0 1188 1334 734686483 734686337 6.630000e-41 178.0
15 TraesCS1D01G360000 chr3A 88.571 140 16 0 1195 1334 690079902 690079763 1.110000e-38 171.0


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 TraesCS1D01G360000 chr1D 443166854 443169189 2335 True 4314.000000 4314 100.000000 1 2336 1 chr1D.!!$R1 2335
1 TraesCS1D01G360000 chr1B 601266772 601269071 2299 False 1215.500000 2268 90.363000 82 2330 2 chr1B.!!$F3 2248
2 TraesCS1D01G360000 chr1A 535854755 535859210 4455 False 714.066667 1945 85.178667 1 2336 3 chr1A.!!$F2 2335

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
63 2241 0.106708 ATAGCCCGCGTGTTCATCAT 59.893 50.0 4.92 0.0 0.0 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1861 4238 0.251341 ACCCAATGCAACTGAGGGAC 60.251 55.0 16.22 0.0 42.25 4.46 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
32 2210 0.173481 CGAATCTGAACGGAGGCAGA 59.827 55.000 0.00 0.00 44.48 4.26
35 2213 0.820871 ATCTGAACGGAGGCAGAGTC 59.179 55.000 0.00 0.00 43.85 3.36
36 2214 0.539669 TCTGAACGGAGGCAGAGTCA 60.540 55.000 0.00 0.00 37.94 3.41
37 2215 0.318441 CTGAACGGAGGCAGAGTCAA 59.682 55.000 0.00 0.00 36.40 3.18
38 2216 0.976641 TGAACGGAGGCAGAGTCAAT 59.023 50.000 0.00 0.00 0.00 2.57
39 2217 2.166459 CTGAACGGAGGCAGAGTCAATA 59.834 50.000 0.00 0.00 36.40 1.90
40 2218 2.166459 TGAACGGAGGCAGAGTCAATAG 59.834 50.000 0.00 0.00 0.00 1.73
41 2219 1.115467 ACGGAGGCAGAGTCAATAGG 58.885 55.000 0.00 0.00 0.00 2.57
63 2241 0.106708 ATAGCCCGCGTGTTCATCAT 59.893 50.000 4.92 0.00 0.00 2.45
73 2251 1.952296 GTGTTCATCATCATCTGGCCC 59.048 52.381 0.00 0.00 0.00 5.80
74 2252 1.848388 TGTTCATCATCATCTGGCCCT 59.152 47.619 0.00 0.00 0.00 5.19
75 2253 2.228059 GTTCATCATCATCTGGCCCTG 58.772 52.381 0.00 0.00 0.00 4.45
77 2255 0.894184 CATCATCATCTGGCCCTGGC 60.894 60.000 0.00 0.00 41.06 4.85
114 2292 1.217882 CCACTCGTTTGACAGTGTCC 58.782 55.000 20.43 4.45 38.74 4.02
122 2300 1.890876 TTGACAGTGTCCCCAAATCG 58.109 50.000 20.43 0.00 0.00 3.34
132 2310 3.564027 CCAAATCGGACGCGAGCC 61.564 66.667 15.93 13.31 36.56 4.70
402 2653 0.107945 GCAGCAACCAAACCAACCAA 60.108 50.000 0.00 0.00 0.00 3.67
405 2656 1.425267 GCAACCAAACCAACCAACGC 61.425 55.000 0.00 0.00 0.00 4.84
414 2665 4.675029 AACCAACGCCGTCCTCCG 62.675 66.667 0.00 0.00 0.00 4.63
488 2741 1.725557 CGATGATCGACGGAGGTGGT 61.726 60.000 9.62 0.00 43.74 4.16
489 2742 0.460311 GATGATCGACGGAGGTGGTT 59.540 55.000 0.00 0.00 0.00 3.67
490 2743 0.175760 ATGATCGACGGAGGTGGTTG 59.824 55.000 0.00 0.00 0.00 3.77
492 2745 3.310860 ATCGACGGAGGTGGTTGCC 62.311 63.158 0.00 0.00 0.00 4.52
536 2813 1.180456 TCAGGGTACGACTCGGCAAA 61.180 55.000 2.98 0.00 0.00 3.68
561 2838 2.177950 CAGTTGATGGCAGCTGGAC 58.822 57.895 17.12 0.00 46.03 4.02
649 2943 5.709164 AGCAGGCAGATATATTTTCCATCAC 59.291 40.000 0.00 0.00 0.00 3.06
651 2945 6.005823 CAGGCAGATATATTTTCCATCACCA 58.994 40.000 0.00 0.00 0.00 4.17
652 2946 6.150641 CAGGCAGATATATTTTCCATCACCAG 59.849 42.308 0.00 0.00 0.00 4.00
656 2950 7.663081 GCAGATATATTTTCCATCACCAGAAGA 59.337 37.037 0.00 0.00 0.00 2.87
657 2951 9.565090 CAGATATATTTTCCATCACCAGAAGAA 57.435 33.333 0.00 0.00 0.00 2.52
661 2955 5.627499 TTTTCCATCACCAGAAGAAATCG 57.373 39.130 0.00 0.00 33.08 3.34
662 2956 3.266510 TCCATCACCAGAAGAAATCGG 57.733 47.619 0.00 0.00 0.00 4.18
663 2957 2.571653 TCCATCACCAGAAGAAATCGGT 59.428 45.455 0.00 0.00 36.01 4.69
664 2958 2.679837 CCATCACCAGAAGAAATCGGTG 59.320 50.000 0.00 0.00 45.76 4.94
666 2960 3.981071 TCACCAGAAGAAATCGGTGAT 57.019 42.857 6.03 0.00 46.80 3.06
699 2993 8.783833 AATAGCACTATCATACAATCATCACC 57.216 34.615 0.00 0.00 0.00 4.02
700 2994 6.430962 AGCACTATCATACAATCATCACCT 57.569 37.500 0.00 0.00 0.00 4.00
704 2998 7.664758 CACTATCATACAATCATCACCTGAGA 58.335 38.462 0.00 0.00 37.28 3.27
705 2999 7.813627 CACTATCATACAATCATCACCTGAGAG 59.186 40.741 0.00 0.00 37.28 3.20
706 3000 6.990908 ATCATACAATCATCACCTGAGAGA 57.009 37.500 0.00 0.00 37.28 3.10
711 3008 6.566197 ACAATCATCACCTGAGAGAAAAAC 57.434 37.500 0.00 0.00 37.28 2.43
742 3039 1.093159 CTCTGTTAGGGCTCGTACGT 58.907 55.000 16.05 0.00 0.00 3.57
744 3041 2.009774 TCTGTTAGGGCTCGTACGTAC 58.990 52.381 15.90 15.90 0.00 3.67
756 3053 2.095567 TCGTACGTACCTGAAGCTGAAC 60.096 50.000 19.67 0.00 0.00 3.18
764 3061 3.119096 GAAGCTGAACGGACCGGC 61.119 66.667 20.00 11.85 36.21 6.13
858 3160 2.588877 CGCGTCATCCCATCCACC 60.589 66.667 0.00 0.00 0.00 4.61
868 3170 3.264052 CATCCACCCCACCCCACA 61.264 66.667 0.00 0.00 0.00 4.17
941 3247 2.124693 ACAAGCACCAAACCCCACG 61.125 57.895 0.00 0.00 0.00 4.94
977 3287 1.309013 AGAGCATTCCCCATCCCCA 60.309 57.895 0.00 0.00 0.00 4.96
979 3289 1.623686 AGCATTCCCCATCCCCACT 60.624 57.895 0.00 0.00 0.00 4.00
980 3290 1.152673 GCATTCCCCATCCCCACTC 60.153 63.158 0.00 0.00 0.00 3.51
981 3291 1.538666 CATTCCCCATCCCCACTCC 59.461 63.158 0.00 0.00 0.00 3.85
982 3292 2.078665 ATTCCCCATCCCCACTCCG 61.079 63.158 0.00 0.00 0.00 4.63
1381 3721 2.824880 CCCCGTCCAGGTTGGTTGA 61.825 63.158 0.00 0.00 39.03 3.18
1391 3731 2.165030 CAGGTTGGTTGATTGAGATGCC 59.835 50.000 0.00 0.00 0.00 4.40
1583 3941 1.202394 TGCGCTGCTTGTTGATTTTGT 60.202 42.857 9.73 0.00 0.00 2.83
1584 3942 1.860326 GCGCTGCTTGTTGATTTTGTT 59.140 42.857 0.00 0.00 0.00 2.83
1585 3943 2.347846 GCGCTGCTTGTTGATTTTGTTG 60.348 45.455 0.00 0.00 0.00 3.33
1586 3944 3.114809 CGCTGCTTGTTGATTTTGTTGA 58.885 40.909 0.00 0.00 0.00 3.18
1587 3945 3.737266 CGCTGCTTGTTGATTTTGTTGAT 59.263 39.130 0.00 0.00 0.00 2.57
1588 3946 4.209703 CGCTGCTTGTTGATTTTGTTGATT 59.790 37.500 0.00 0.00 0.00 2.57
1589 3947 5.276963 CGCTGCTTGTTGATTTTGTTGATTT 60.277 36.000 0.00 0.00 0.00 2.17
1592 3950 7.742963 GCTGCTTGTTGATTTTGTTGATTTATG 59.257 33.333 0.00 0.00 0.00 1.90
1593 3951 8.085720 TGCTTGTTGATTTTGTTGATTTATGG 57.914 30.769 0.00 0.00 0.00 2.74
1611 3986 7.650834 TTTATGGTTGTCTGCTTATTTTTGC 57.349 32.000 0.00 0.00 0.00 3.68
1619 3994 4.620184 GTCTGCTTATTTTTGCTGCTTCTG 59.380 41.667 0.00 0.00 0.00 3.02
1621 3996 4.947645 TGCTTATTTTTGCTGCTTCTGTT 58.052 34.783 0.00 0.00 0.00 3.16
1647 4024 7.215789 AGTCTGAATGTCTGATAATTAGGCTG 58.784 38.462 0.00 0.00 0.00 4.85
1661 4038 2.046507 GCTGGCACTAGCTGCTGT 60.047 61.111 13.43 5.67 46.25 4.40
1699 4076 0.658829 TTGCAAATTTCGGTCGTGCG 60.659 50.000 0.00 0.00 38.05 5.34
1822 4199 5.350914 GCCTAGCTGCTGTAATGATTCATAG 59.649 44.000 13.43 0.00 0.00 2.23
1824 4201 7.606349 CCTAGCTGCTGTAATGATTCATAGTA 58.394 38.462 13.43 0.00 0.00 1.82
1825 4202 7.543868 CCTAGCTGCTGTAATGATTCATAGTAC 59.456 40.741 13.43 0.98 0.00 2.73
1826 4203 7.060383 AGCTGCTGTAATGATTCATAGTACT 57.940 36.000 0.00 0.00 0.00 2.73
1828 4205 7.440556 AGCTGCTGTAATGATTCATAGTACTTG 59.559 37.037 0.00 0.00 0.00 3.16
1830 4207 7.275183 TGCTGTAATGATTCATAGTACTTGCT 58.725 34.615 0.00 0.00 0.00 3.91
1861 4238 2.057316 TGCAAATTTCGATTTGTGCCG 58.943 42.857 11.91 0.00 42.02 5.69
1879 4256 1.308069 CGTCCCTCAGTTGCATTGGG 61.308 60.000 0.00 0.00 39.22 4.12
1880 4257 0.251341 GTCCCTCAGTTGCATTGGGT 60.251 55.000 8.97 0.00 38.95 4.51
1881 4258 1.004277 GTCCCTCAGTTGCATTGGGTA 59.996 52.381 8.97 0.00 38.95 3.69
1959 4336 4.901927 AGAATGGTTCTAGGAGGGAGATT 58.098 43.478 0.00 0.00 38.49 2.40
1960 4337 4.657969 AGAATGGTTCTAGGAGGGAGATTG 59.342 45.833 0.00 0.00 38.49 2.67
1961 4338 2.119495 TGGTTCTAGGAGGGAGATTGC 58.881 52.381 0.00 0.00 0.00 3.56
1962 4339 2.293184 TGGTTCTAGGAGGGAGATTGCT 60.293 50.000 0.00 0.00 0.00 3.91
1963 4340 2.367241 GGTTCTAGGAGGGAGATTGCTC 59.633 54.545 0.00 0.00 40.54 4.26
2096 4474 3.063485 TGAAATTCGATCTCGTTGTGCA 58.937 40.909 0.00 0.00 40.80 4.57
2105 4483 4.034258 CGTTGTGCAGCAGCTGGG 62.034 66.667 24.13 0.00 42.74 4.45
2106 4484 2.595463 GTTGTGCAGCAGCTGGGA 60.595 61.111 24.13 3.24 42.74 4.37
2107 4485 1.975407 GTTGTGCAGCAGCTGGGAT 60.975 57.895 24.13 0.00 42.74 3.85
2111 4489 4.189188 GCAGCAGCTGGGATTGCG 62.189 66.667 24.13 0.00 44.80 4.85
2291 4687 1.876416 CGATTCACGTGTGTTTCCCCT 60.876 52.381 16.51 0.00 37.22 4.79
2298 4694 1.439679 GTGTGTTTCCCCTTCTAGCG 58.560 55.000 0.00 0.00 0.00 4.26
2331 4727 6.197168 TCTTCCAATTTTTATCCATGGAGCT 58.803 36.000 21.33 6.86 40.96 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.541379 TCAGATTCGGTCGTCCTTCA 58.459 50.000 0.00 0.00 0.00 3.02
16 2194 0.820871 GACTCTGCCTCCGTTCAGAT 59.179 55.000 0.00 0.00 38.50 2.90
41 2219 1.714899 ATGAACACGCGGGCTATTGC 61.715 55.000 9.12 0.00 38.76 3.56
73 2251 1.424493 GCGACTTTCTGATCGGCCAG 61.424 60.000 2.24 0.00 38.78 4.85
74 2252 1.447838 GCGACTTTCTGATCGGCCA 60.448 57.895 2.24 0.00 38.78 5.36
75 2253 1.447838 TGCGACTTTCTGATCGGCC 60.448 57.895 0.00 0.00 38.78 6.13
77 2255 1.084370 GGGTGCGACTTTCTGATCGG 61.084 60.000 0.00 0.00 38.78 4.18
78 2256 0.389817 TGGGTGCGACTTTCTGATCG 60.390 55.000 0.00 0.00 41.32 3.69
79 2257 1.079503 GTGGGTGCGACTTTCTGATC 58.920 55.000 0.00 0.00 0.00 2.92
80 2258 0.687354 AGTGGGTGCGACTTTCTGAT 59.313 50.000 0.00 0.00 0.00 2.90
114 2292 3.564027 GCTCGCGTCCGATTTGGG 61.564 66.667 5.77 0.00 43.47 4.12
132 2310 0.729116 CAAGGTTAGAGGCATGTGCG 59.271 55.000 0.00 0.00 43.26 5.34
285 2512 3.041940 GTCCAGTGGAACCGTGCG 61.042 66.667 15.09 0.00 37.80 5.34
287 2514 1.301716 CCAGTCCAGTGGAACCGTG 60.302 63.158 15.09 9.11 40.44 4.94
288 2515 1.458777 TCCAGTCCAGTGGAACCGT 60.459 57.895 15.09 0.00 44.01 4.83
291 2518 1.003233 GGCTCCAGTCCAGTGGAAC 60.003 63.158 15.09 8.52 46.29 3.62
292 2519 1.152030 AGGCTCCAGTCCAGTGGAA 60.152 57.895 15.09 0.00 46.29 3.53
294 2521 2.177594 GACAGGCTCCAGTCCAGTGG 62.178 65.000 1.40 1.40 39.19 4.00
295 2522 1.294780 GACAGGCTCCAGTCCAGTG 59.705 63.158 0.48 0.00 0.00 3.66
296 2523 2.279069 CGACAGGCTCCAGTCCAGT 61.279 63.158 5.97 0.00 0.00 4.00
297 2524 1.979155 TCGACAGGCTCCAGTCCAG 60.979 63.158 5.97 0.00 0.00 3.86
298 2525 2.117423 TCGACAGGCTCCAGTCCA 59.883 61.111 5.97 0.00 0.00 4.02
299 2526 2.574399 GTCGACAGGCTCCAGTCC 59.426 66.667 11.55 0.00 0.00 3.85
300 2527 2.574399 GGTCGACAGGCTCCAGTC 59.426 66.667 18.91 1.79 0.00 3.51
385 2612 0.174617 CGTTGGTTGGTTTGGTTGCT 59.825 50.000 0.00 0.00 0.00 3.91
414 2665 1.207570 TGCAATGAAATGATGGTGGGC 59.792 47.619 0.00 0.00 0.00 5.36
415 2666 2.419021 GGTGCAATGAAATGATGGTGGG 60.419 50.000 0.00 0.00 0.00 4.61
418 2669 3.579586 AGTTGGTGCAATGAAATGATGGT 59.420 39.130 0.00 0.00 0.00 3.55
536 2813 2.045926 GCCATCAACTGCTCCGGT 60.046 61.111 0.00 0.00 0.00 5.28
561 2838 3.920231 TCCATCTTGATCTTGGTGAGG 57.080 47.619 0.00 0.00 0.00 3.86
593 2870 4.530857 CTGACCGGTCGCCATCCC 62.531 72.222 28.70 4.29 0.00 3.85
649 2943 2.159099 TCCGATCACCGATTTCTTCTGG 60.159 50.000 0.00 0.00 41.76 3.86
651 2945 5.531122 TTATCCGATCACCGATTTCTTCT 57.469 39.130 0.00 0.00 41.76 2.85
652 2946 6.598753 TTTTATCCGATCACCGATTTCTTC 57.401 37.500 0.00 0.00 41.76 2.87
656 2950 5.995282 TGCTATTTTATCCGATCACCGATTT 59.005 36.000 0.00 0.00 41.76 2.17
657 2951 5.408604 GTGCTATTTTATCCGATCACCGATT 59.591 40.000 0.00 0.00 41.76 3.34
658 2952 4.929808 GTGCTATTTTATCCGATCACCGAT 59.070 41.667 0.00 0.00 41.76 4.18
659 2953 4.038763 AGTGCTATTTTATCCGATCACCGA 59.961 41.667 0.00 0.00 41.76 4.69
660 2954 4.307432 AGTGCTATTTTATCCGATCACCG 58.693 43.478 0.00 0.00 38.18 4.94
661 2955 7.097192 TGATAGTGCTATTTTATCCGATCACC 58.903 38.462 0.00 0.00 0.00 4.02
662 2956 8.709386 ATGATAGTGCTATTTTATCCGATCAC 57.291 34.615 0.00 0.00 0.00 3.06
663 2957 9.803315 GTATGATAGTGCTATTTTATCCGATCA 57.197 33.333 0.00 0.00 0.00 2.92
664 2958 9.803315 TGTATGATAGTGCTATTTTATCCGATC 57.197 33.333 0.00 0.00 0.00 3.69
695 2989 5.874810 CGGAATATGTTTTTCTCTCAGGTGA 59.125 40.000 0.00 0.00 0.00 4.02
696 2990 5.874810 TCGGAATATGTTTTTCTCTCAGGTG 59.125 40.000 0.00 0.00 0.00 4.00
697 2991 6.049955 TCGGAATATGTTTTTCTCTCAGGT 57.950 37.500 0.00 0.00 0.00 4.00
698 2992 7.497249 AGAATCGGAATATGTTTTTCTCTCAGG 59.503 37.037 0.00 0.00 0.00 3.86
699 2993 8.430801 AGAATCGGAATATGTTTTTCTCTCAG 57.569 34.615 0.00 0.00 0.00 3.35
700 2994 8.260818 AGAGAATCGGAATATGTTTTTCTCTCA 58.739 33.333 9.35 0.00 42.42 3.27
704 2998 8.567285 AACAGAGAATCGGAATATGTTTTTCT 57.433 30.769 0.00 0.00 42.67 2.52
705 2999 9.922305 CTAACAGAGAATCGGAATATGTTTTTC 57.078 33.333 6.57 0.00 42.67 2.29
706 3000 8.893727 CCTAACAGAGAATCGGAATATGTTTTT 58.106 33.333 6.57 0.00 42.67 1.94
711 3008 4.932200 GCCCTAACAGAGAATCGGAATATG 59.068 45.833 0.00 0.00 42.67 1.78
742 3039 0.606604 GGTCCGTTCAGCTTCAGGTA 59.393 55.000 0.00 0.00 0.00 3.08
744 3041 1.738099 CGGTCCGTTCAGCTTCAGG 60.738 63.158 2.08 0.00 0.00 3.86
764 3061 1.378882 CGGGTGGATGAATGCACTGG 61.379 60.000 13.64 3.81 46.65 4.00
795 3092 2.326550 GCGTGACACCAACCAACG 59.673 61.111 0.00 0.00 0.00 4.10
858 3160 3.330720 GAGAGGGTGTGGGGTGGG 61.331 72.222 0.00 0.00 0.00 4.61
868 3170 1.606889 GGTGACAGACGGAGAGGGT 60.607 63.158 0.00 0.00 0.00 4.34
920 3226 2.421314 GGGTTTGGTGCTTGTGCC 59.579 61.111 0.00 0.00 38.71 5.01
941 3247 4.056125 GCTTTCTTGGGTGCGGGC 62.056 66.667 0.00 0.00 0.00 6.13
977 3287 1.539124 AGGAAGGGGAAAGCGGAGT 60.539 57.895 0.00 0.00 0.00 3.85
979 3289 2.656069 CGAGGAAGGGGAAAGCGGA 61.656 63.158 0.00 0.00 0.00 5.54
980 3290 2.125106 CGAGGAAGGGGAAAGCGG 60.125 66.667 0.00 0.00 0.00 5.52
981 3291 2.820037 GCGAGGAAGGGGAAAGCG 60.820 66.667 0.00 0.00 0.00 4.68
982 3292 2.438614 GGCGAGGAAGGGGAAAGC 60.439 66.667 0.00 0.00 0.00 3.51
1362 3698 2.448931 AACCAACCTGGACGGGGA 60.449 61.111 0.00 0.00 40.96 4.81
1368 3704 3.689347 CATCTCAATCAACCAACCTGGA 58.311 45.455 0.00 0.00 40.96 3.86
1371 3707 2.450476 GGCATCTCAATCAACCAACCT 58.550 47.619 0.00 0.00 0.00 3.50
1381 3721 1.522355 CACGGAGCGGCATCTCAAT 60.522 57.895 1.45 0.00 34.84 2.57
1419 3759 7.627939 GCATGAAAGAAATGTACTCTGCATCTT 60.628 37.037 0.00 0.00 0.00 2.40
1583 3941 9.995003 AAAAATAAGCAGACAACCATAAATCAA 57.005 25.926 0.00 0.00 0.00 2.57
1584 3942 9.421806 CAAAAATAAGCAGACAACCATAAATCA 57.578 29.630 0.00 0.00 0.00 2.57
1585 3943 8.382875 GCAAAAATAAGCAGACAACCATAAATC 58.617 33.333 0.00 0.00 0.00 2.17
1586 3944 8.096414 AGCAAAAATAAGCAGACAACCATAAAT 58.904 29.630 0.00 0.00 0.00 1.40
1587 3945 7.384660 CAGCAAAAATAAGCAGACAACCATAAA 59.615 33.333 0.00 0.00 0.00 1.40
1588 3946 6.867816 CAGCAAAAATAAGCAGACAACCATAA 59.132 34.615 0.00 0.00 0.00 1.90
1589 3947 6.389091 CAGCAAAAATAAGCAGACAACCATA 58.611 36.000 0.00 0.00 0.00 2.74
1592 3950 3.429881 GCAGCAAAAATAAGCAGACAACC 59.570 43.478 0.00 0.00 0.00 3.77
1593 3951 4.301628 AGCAGCAAAAATAAGCAGACAAC 58.698 39.130 0.00 0.00 0.00 3.32
1611 3986 5.348179 CAGACATTCAGACTAACAGAAGCAG 59.652 44.000 0.00 0.00 0.00 4.24
1619 3994 8.983724 GCCTAATTATCAGACATTCAGACTAAC 58.016 37.037 0.00 0.00 0.00 2.34
1621 3996 8.363390 CAGCCTAATTATCAGACATTCAGACTA 58.637 37.037 0.00 0.00 0.00 2.59
1661 4038 3.498397 GCAAGTGGAAGAAAGAATCGTCA 59.502 43.478 0.00 0.00 38.18 4.35
1699 4076 5.522460 CCAAATCAACAAGCAATCATGGATC 59.478 40.000 0.00 0.00 0.00 3.36
1792 4169 5.059161 TCATTACAGCAGCTAGGCTAATTG 58.941 41.667 0.00 0.00 43.68 2.32
1822 4199 3.181480 TGCAAGGGAAACAAAGCAAGTAC 60.181 43.478 0.00 0.00 0.00 2.73
1824 4201 1.830477 TGCAAGGGAAACAAAGCAAGT 59.170 42.857 0.00 0.00 0.00 3.16
1825 4202 2.600470 TGCAAGGGAAACAAAGCAAG 57.400 45.000 0.00 0.00 0.00 4.01
1826 4203 3.340814 TTTGCAAGGGAAACAAAGCAA 57.659 38.095 0.00 0.00 39.00 3.91
1828 4205 4.552572 CGAAATTTGCAAGGGAAACAAAGC 60.553 41.667 0.00 0.00 36.78 3.51
1830 4207 4.759782 TCGAAATTTGCAAGGGAAACAAA 58.240 34.783 0.00 0.00 37.66 2.83
1861 4238 0.251341 ACCCAATGCAACTGAGGGAC 60.251 55.000 16.22 0.00 42.25 4.46
1879 4256 2.872245 TCGAGGCAATAGCAAAGCATAC 59.128 45.455 0.00 0.00 44.61 2.39
1880 4257 3.192541 TCGAGGCAATAGCAAAGCATA 57.807 42.857 0.00 0.00 44.61 3.14
1881 4258 2.042686 TCGAGGCAATAGCAAAGCAT 57.957 45.000 0.00 0.00 44.61 3.79
1885 4262 3.002791 CTCTGTTCGAGGCAATAGCAAA 58.997 45.455 0.00 0.00 44.61 3.68
1960 4337 3.623934 AAAATGGGGGCAGGGGAGC 62.624 63.158 0.00 0.00 0.00 4.70
1961 4338 1.381735 GAAAATGGGGGCAGGGGAG 60.382 63.158 0.00 0.00 0.00 4.30
1962 4339 2.777146 GAAAATGGGGGCAGGGGA 59.223 61.111 0.00 0.00 0.00 4.81
1963 4340 2.365502 GGAAAATGGGGGCAGGGG 60.366 66.667 0.00 0.00 0.00 4.79
1964 4341 1.080907 AAGGAAAATGGGGGCAGGG 59.919 57.895 0.00 0.00 0.00 4.45
1965 4342 1.266867 CCAAGGAAAATGGGGGCAGG 61.267 60.000 0.00 0.00 34.15 4.85
1966 4343 0.252193 TCCAAGGAAAATGGGGGCAG 60.252 55.000 0.00 0.00 38.54 4.85
2096 4474 3.272364 TTCCGCAATCCCAGCTGCT 62.272 57.895 8.66 0.00 36.38 4.24
2105 4483 0.109132 CTTTGGCCAGTTCCGCAATC 60.109 55.000 5.11 0.00 0.00 2.67
2106 4484 1.535204 CCTTTGGCCAGTTCCGCAAT 61.535 55.000 5.11 0.00 0.00 3.56
2107 4485 2.199652 CCTTTGGCCAGTTCCGCAA 61.200 57.895 5.11 0.00 0.00 4.85
2111 4489 0.247460 GCAATCCTTTGGCCAGTTCC 59.753 55.000 5.11 0.00 33.22 3.62
2154 4546 1.475403 GTTCTGGACGGAGGAGATCA 58.525 55.000 0.00 0.00 0.00 2.92
2236 4632 0.249398 TCCCTTCTTAACCGAGCTGC 59.751 55.000 0.00 0.00 0.00 5.25
2291 4687 0.392461 AAGAAATGGCGCCGCTAGAA 60.392 50.000 23.90 2.33 0.00 2.10
2298 4694 2.385013 AAATTGGAAGAAATGGCGCC 57.615 45.000 22.73 22.73 0.00 6.53


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

AutoCloner maintained by Alex Coulton.