Multiple sequence alignment - TraesCS1D01G226200

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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 TraesCS1D01G226200 chr1D 100.000 3362 0 0 1 3362 314572418 314575779 0.000000e+00 6209.0
1 TraesCS1D01G226200 chr1A 92.797 2846 131 23 562 3362 394851141 394853957 0.000000e+00 4052.0
2 TraesCS1D01G226200 chr1A 92.280 557 21 7 1 557 394850445 394850979 0.000000e+00 771.0
3 TraesCS1D01G226200 chr1B 94.761 2348 82 12 376 2690 426070941 426073280 0.000000e+00 3616.0
4 TraesCS1D01G226200 chr1B 93.548 248 7 6 1 246 426070623 426070863 8.870000e-96 361.0
5 TraesCS1D01G226200 chr1B 83.415 205 7 12 3166 3347 426073591 426073791 7.460000e-37 165.0
6 TraesCS1D01G226200 chr1B 92.188 64 0 4 271 330 426070864 426070926 5.980000e-13 86.1
7 TraesCS1D01G226200 chr7A 83.196 726 112 7 1684 2399 642254108 642253383 0.000000e+00 656.0
8 TraesCS1D01G226200 chr7D 82.735 724 115 4 1684 2397 556640247 556639524 1.320000e-178 636.0
9 TraesCS1D01G226200 chr6B 83.114 456 50 6 1477 1932 22711235 22711663 1.130000e-104 390.0
10 TraesCS1D01G226200 chr6B 87.850 321 35 2 1059 1379 22710862 22711178 1.140000e-99 374.0
11 TraesCS1D01G226200 chr6B 79.710 207 33 6 148 348 22710416 22710619 1.260000e-29 141.0
12 TraesCS1D01G226200 chr6D 88.474 321 37 0 1059 1379 12345146 12345466 4.070000e-104 388.0
13 TraesCS1D01G226200 chr6D 76.316 342 41 19 188 508 12344754 12345076 2.700000e-31 147.0


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 TraesCS1D01G226200 chr1D 314572418 314575779 3361 False 6209.000000 6209 100.0000 1 3362 1 chr1D.!!$F1 3361
1 TraesCS1D01G226200 chr1A 394850445 394853957 3512 False 2411.500000 4052 92.5385 1 3362 2 chr1A.!!$F1 3361
2 TraesCS1D01G226200 chr1B 426070623 426073791 3168 False 1057.025000 3616 90.9780 1 3347 4 chr1B.!!$F1 3346
3 TraesCS1D01G226200 chr7A 642253383 642254108 725 True 656.000000 656 83.1960 1684 2399 1 chr7A.!!$R1 715
4 TraesCS1D01G226200 chr7D 556639524 556640247 723 True 636.000000 636 82.7350 1684 2397 1 chr7D.!!$R1 713
5 TraesCS1D01G226200 chr6B 22710416 22711663 1247 False 301.666667 390 83.5580 148 1932 3 chr6B.!!$F1 1784
6 TraesCS1D01G226200 chr6D 12344754 12345466 712 False 267.500000 388 82.3950 188 1379 2 chr6D.!!$F1 1191

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
798 991 0.450184 CGCCAACCCAGAAATTACCG 59.55 55.0 0.0 0.0 0.0 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2735 3026 0.882042 CATCCAGCGCCATAGTCCAC 60.882 60.0 2.29 0.0 0.0 4.02 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
36 37 8.908786 ATGTCTCATGTAGGTTTACCATAATG 57.091 34.615 1.13 2.21 38.89 1.90
95 96 3.612860 TCTGCTTCGAGAGTTAATTTCGC 59.387 43.478 0.00 0.00 34.52 4.70
163 165 3.552684 GGCTGCAAAGTTTGTTATCTGCA 60.553 43.478 16.70 6.71 37.46 4.41
185 187 8.830201 TGCAAATAAAACATTCAAACTATGCT 57.170 26.923 0.00 0.00 0.00 3.79
186 188 9.920133 TGCAAATAAAACATTCAAACTATGCTA 57.080 25.926 0.00 0.00 0.00 3.49
351 361 9.555727 AACTTAGACAAATTTAGCTTAGTCACA 57.444 29.630 0.00 0.00 0.00 3.58
352 362 8.989980 ACTTAGACAAATTTAGCTTAGTCACAC 58.010 33.333 0.00 0.00 0.00 3.82
353 363 8.896320 TTAGACAAATTTAGCTTAGTCACACA 57.104 30.769 0.00 0.00 0.00 3.72
354 364 7.801716 AGACAAATTTAGCTTAGTCACACAA 57.198 32.000 0.00 0.00 0.00 3.33
355 365 7.865707 AGACAAATTTAGCTTAGTCACACAAG 58.134 34.615 0.00 0.00 0.00 3.16
358 368 8.466798 ACAAATTTAGCTTAGTCACACAAGTTT 58.533 29.630 0.00 0.00 0.00 2.66
359 369 8.745837 CAAATTTAGCTTAGTCACACAAGTTTG 58.254 33.333 0.00 0.00 0.00 2.93
360 370 6.995511 TTTAGCTTAGTCACACAAGTTTGT 57.004 33.333 0.00 0.00 43.36 2.83
361 371 6.995511 TTAGCTTAGTCACACAAGTTTGTT 57.004 33.333 0.00 0.00 39.91 2.83
362 372 8.495361 TTTAGCTTAGTCACACAAGTTTGTTA 57.505 30.769 0.00 0.00 39.91 2.41
363 373 8.671384 TTAGCTTAGTCACACAAGTTTGTTAT 57.329 30.769 0.00 0.00 39.91 1.89
364 374 6.959361 AGCTTAGTCACACAAGTTTGTTATG 58.041 36.000 0.00 0.00 39.91 1.90
365 375 6.542370 AGCTTAGTCACACAAGTTTGTTATGT 59.458 34.615 0.00 0.00 39.91 2.29
366 376 6.851330 GCTTAGTCACACAAGTTTGTTATGTC 59.149 38.462 0.00 0.00 39.91 3.06
367 377 7.466725 GCTTAGTCACACAAGTTTGTTATGTCA 60.467 37.037 0.00 0.00 39.91 3.58
368 378 6.363577 AGTCACACAAGTTTGTTATGTCAG 57.636 37.500 0.00 0.00 39.91 3.51
369 379 4.970003 GTCACACAAGTTTGTTATGTCAGC 59.030 41.667 0.00 0.00 39.91 4.26
370 380 4.637977 TCACACAAGTTTGTTATGTCAGCA 59.362 37.500 0.00 0.00 39.91 4.41
371 381 5.299028 TCACACAAGTTTGTTATGTCAGCAT 59.701 36.000 0.00 0.00 39.91 3.79
372 382 5.400188 CACACAAGTTTGTTATGTCAGCATG 59.600 40.000 0.00 0.00 39.91 4.06
373 383 5.067674 ACACAAGTTTGTTATGTCAGCATGT 59.932 36.000 0.00 0.00 39.91 3.21
374 384 5.978919 CACAAGTTTGTTATGTCAGCATGTT 59.021 36.000 0.00 0.00 39.91 2.71
391 401 6.035220 CAGCATGTTACATAAGTTTGCCATTG 59.965 38.462 0.00 0.00 0.00 2.82
453 463 2.028748 ACTTCTTGCCATGCCAATCAAC 60.029 45.455 0.00 0.00 0.00 3.18
513 548 8.453681 TCCTCTACATCAGTATATTTGGGTAGA 58.546 37.037 0.00 0.00 34.64 2.59
557 592 8.692110 TCTGATTGAATATTTGTGATTGTTGC 57.308 30.769 0.00 0.00 0.00 4.17
639 832 5.357596 AGCATAATGTTGCACACATGACATA 59.642 36.000 13.05 5.10 46.23 2.29
777 970 3.610677 GGAAAATATTTGTTTCCCACGCG 59.389 43.478 3.53 3.53 45.62 6.01
798 991 0.450184 CGCCAACCCAGAAATTACCG 59.550 55.000 0.00 0.00 0.00 4.02
815 1008 8.514136 AAATTACCGTTTGACATGTTGTTATG 57.486 30.769 0.00 0.00 0.00 1.90
839 1032 4.982295 GGCAACATAGTTTTCCTTCACAAC 59.018 41.667 0.00 0.00 0.00 3.32
871 1064 4.705507 AGTCTTTAGTTACAGAGATGCCGA 59.294 41.667 0.00 0.00 0.00 5.54
880 1073 1.203287 CAGAGATGCCGAGTGAAGTCA 59.797 52.381 0.00 0.00 0.00 3.41
881 1074 1.895798 AGAGATGCCGAGTGAAGTCAA 59.104 47.619 0.00 0.00 0.00 3.18
897 1090 9.778741 AGTGAAGTCAAGAAAGTATTCATGTTA 57.221 29.630 0.00 0.00 38.06 2.41
911 1109 7.836183 AGTATTCATGTTAGCTTCCCTTTCAAT 59.164 33.333 0.00 0.00 0.00 2.57
956 1154 1.354031 TCTGTATGTGGGTTGGTGCAT 59.646 47.619 0.00 0.00 0.00 3.96
1056 1273 8.687824 TTCTCTTCAGTTTGTTGATGTTTTTC 57.312 30.769 0.00 0.00 0.00 2.29
1057 1274 7.825681 TCTCTTCAGTTTGTTGATGTTTTTCA 58.174 30.769 0.00 0.00 0.00 2.69
1313 1536 3.011144 TCTGCAATTAGATTCACCCCCAA 59.989 43.478 0.00 0.00 0.00 4.12
1332 1555 3.431922 AATGATTCCATTGCTCAAGCG 57.568 42.857 0.00 0.00 41.18 4.68
1659 1910 2.433604 TGGATCATCTGAGCAGAAGGAC 59.566 50.000 4.06 0.00 41.36 3.85
2430 2688 2.048222 CGAGGCGTTCCTTGCTCA 60.048 61.111 0.00 0.00 44.46 4.26
2495 2753 0.818040 GGTTTCTGGCGTGTCCTGTT 60.818 55.000 0.00 0.00 35.49 3.16
2530 2788 1.947456 GTGGGTGGTCTGTTGAACTTC 59.053 52.381 0.00 0.00 0.00 3.01
2582 2840 0.693049 AATGGGACTCGTTTCAGGCT 59.307 50.000 0.00 0.00 0.00 4.58
2583 2841 1.568504 ATGGGACTCGTTTCAGGCTA 58.431 50.000 0.00 0.00 0.00 3.93
2668 2930 8.404765 CACCACATCACTATTTTATGCATGTTA 58.595 33.333 10.16 0.00 0.00 2.41
2673 2935 8.551205 CATCACTATTTTATGCATGTTAGTCGT 58.449 33.333 10.16 0.00 0.00 4.34
2674 2936 8.126871 TCACTATTTTATGCATGTTAGTCGTC 57.873 34.615 10.16 0.00 0.00 4.20
2675 2937 7.043656 TCACTATTTTATGCATGTTAGTCGTCG 60.044 37.037 10.16 0.00 0.00 5.12
2676 2938 3.918258 TTTATGCATGTTAGTCGTCGC 57.082 42.857 10.16 0.00 0.00 5.19
2677 2939 1.472990 TATGCATGTTAGTCGTCGCG 58.527 50.000 10.16 0.00 0.00 5.87
2735 3026 5.006165 CGCAGCTTTTCTACTTCAGAATAGG 59.994 44.000 6.60 0.00 42.88 2.57
2745 3036 5.878406 ACTTCAGAATAGGTGGACTATGG 57.122 43.478 0.00 0.00 41.54 2.74
2757 3048 2.111669 CTATGGCGCTGGATGGCA 59.888 61.111 7.64 0.00 46.52 4.92
2766 3057 1.303309 GCTGGATGGCATGTCTGTAC 58.697 55.000 3.81 0.00 0.00 2.90
2777 3068 4.093998 GGCATGTCTGTACTGTGAATTCAG 59.906 45.833 8.80 0.24 40.80 3.02
2839 3144 4.881273 TGCACTAGTTTTGACACACTTCAT 59.119 37.500 0.00 0.00 0.00 2.57
2843 3148 7.466725 GCACTAGTTTTGACACACTTCATGTTA 60.467 37.037 0.00 0.00 40.64 2.41
2865 3170 7.434897 TGTTATTTTGAAGTTGCAACATGAGTC 59.565 33.333 30.11 18.09 0.00 3.36
2875 3180 8.165239 AGTTGCAACATGAGTCTTTGTTTATA 57.835 30.769 30.11 0.00 33.93 0.98
2878 3183 8.969121 TGCAACATGAGTCTTTGTTTATATTG 57.031 30.769 0.00 1.36 33.93 1.90
2881 3186 9.069078 CAACATGAGTCTTTGTTTATATTGCAG 57.931 33.333 0.00 0.00 33.93 4.41
2922 3228 0.757512 ATGAGGTCGAGCATCTGCAT 59.242 50.000 18.15 8.90 45.16 3.96
2952 3260 2.908073 CGCGGGCTGAGCTTGTTTT 61.908 57.895 3.72 0.00 0.00 2.43
2964 3272 5.194432 TGAGCTTGTTTTAACTTGGGTGTA 58.806 37.500 0.00 0.00 0.00 2.90
2968 3276 6.016276 AGCTTGTTTTAACTTGGGTGTATCTG 60.016 38.462 0.00 0.00 0.00 2.90
2996 3304 7.933577 AGAACCCTTTTGATCCAATTCTTTTTC 59.066 33.333 0.00 0.00 0.00 2.29
3010 3318 8.143835 CCAATTCTTTTTCTGTGGTATTGAACT 58.856 33.333 0.00 0.00 0.00 3.01
3021 3329 6.702329 TGTGGTATTGAACTTGTTTGGTTTT 58.298 32.000 0.00 0.00 0.00 2.43
3022 3330 7.837863 TGTGGTATTGAACTTGTTTGGTTTTA 58.162 30.769 0.00 0.00 0.00 1.52
3027 3335 9.758651 GTATTGAACTTGTTTGGTTTTAAGGAT 57.241 29.630 0.00 0.00 0.00 3.24
3071 3379 0.675083 TGGGTCGCTTTCGTACTCAA 59.325 50.000 0.00 0.00 36.96 3.02
3101 3409 0.848053 TTTTCCTTTCCCGTGGACCT 59.152 50.000 0.00 0.00 31.24 3.85
3103 3411 1.823169 TTCCTTTCCCGTGGACCTCG 61.823 60.000 9.00 9.00 31.24 4.63
3109 3417 2.657237 CCGTGGACCTCGAGCTTT 59.343 61.111 17.27 0.00 0.00 3.51
3110 3418 1.004918 CCGTGGACCTCGAGCTTTT 60.005 57.895 17.27 0.00 0.00 2.27
3136 3444 5.763444 AATGTTCTTTCATGTCTACGACG 57.237 39.130 0.00 0.00 34.95 5.12
3137 3445 4.492791 TGTTCTTTCATGTCTACGACGA 57.507 40.909 0.00 0.00 34.95 4.20
3160 3469 4.281688 ACCATGCATGTTTTAGACAGCTTT 59.718 37.500 24.58 0.00 42.62 3.51
3161 3470 4.624024 CCATGCATGTTTTAGACAGCTTTG 59.376 41.667 24.58 0.22 42.62 2.77
3191 3500 2.055838 TGCTAGTACGTTTGCAGTTCG 58.944 47.619 0.00 5.89 0.00 3.95
3239 3556 2.743636 TGGACGCTTTTCCTACTCTG 57.256 50.000 0.00 0.00 36.51 3.35
3240 3557 1.275291 TGGACGCTTTTCCTACTCTGG 59.725 52.381 0.00 0.00 36.51 3.86
3241 3558 1.405661 GGACGCTTTTCCTACTCTGGG 60.406 57.143 0.00 0.00 32.24 4.45
3242 3559 1.549170 GACGCTTTTCCTACTCTGGGA 59.451 52.381 0.00 0.00 0.00 4.37
3243 3560 1.550976 ACGCTTTTCCTACTCTGGGAG 59.449 52.381 0.00 0.00 34.06 4.30
3265 3590 0.613012 AATCCTGCCAAGAGCCAACC 60.613 55.000 0.00 0.00 42.71 3.77
3285 3610 5.568620 ACCAAACATTCTCTAGTGGAGTT 57.431 39.130 3.16 0.00 42.40 3.01
3323 3661 5.426509 AGTCATGACTGGACATCCTATCAAA 59.573 40.000 27.37 0.11 40.75 2.69
3349 3687 7.333174 ACAATGTTTTTCGTTTTGGAATCACTT 59.667 29.630 0.00 0.00 0.00 3.16
3350 3688 6.639671 TGTTTTTCGTTTTGGAATCACTTG 57.360 33.333 0.00 0.00 0.00 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 6.765989 TGCATTATGGTAAACCTACATGAGAC 59.234 38.462 0.00 0.00 36.82 3.36
58 59 7.387673 TCTCGAAGCAGAAACTCAATGATTTAA 59.612 33.333 0.00 0.00 0.00 1.52
59 60 6.873605 TCTCGAAGCAGAAACTCAATGATTTA 59.126 34.615 0.00 0.00 0.00 1.40
60 61 5.702670 TCTCGAAGCAGAAACTCAATGATTT 59.297 36.000 0.00 0.00 0.00 2.17
95 96 5.065218 GCCAGTCTTCATTACACCATGTTAG 59.935 44.000 0.00 0.00 0.00 2.34
348 358 4.919206 TGCTGACATAACAAACTTGTGTG 58.081 39.130 0.00 1.89 41.31 3.82
349 359 5.067674 ACATGCTGACATAACAAACTTGTGT 59.932 36.000 0.00 0.00 36.44 3.72
350 360 5.522456 ACATGCTGACATAACAAACTTGTG 58.478 37.500 0.00 0.00 36.44 3.33
351 361 5.772825 ACATGCTGACATAACAAACTTGT 57.227 34.783 0.00 0.00 37.43 3.16
352 362 7.138081 TGTAACATGCTGACATAACAAACTTG 58.862 34.615 0.00 0.00 33.67 3.16
353 363 7.270757 TGTAACATGCTGACATAACAAACTT 57.729 32.000 0.00 0.00 33.67 2.66
354 364 6.875948 TGTAACATGCTGACATAACAAACT 57.124 33.333 0.00 0.00 33.67 2.66
355 365 9.277565 CTTATGTAACATGCTGACATAACAAAC 57.722 33.333 17.34 0.00 39.78 2.93
358 368 8.560355 AACTTATGTAACATGCTGACATAACA 57.440 30.769 17.34 5.56 39.78 2.41
359 369 9.277565 CAAACTTATGTAACATGCTGACATAAC 57.722 33.333 17.34 0.00 39.78 1.89
360 370 7.967854 GCAAACTTATGTAACATGCTGACATAA 59.032 33.333 18.96 18.96 41.46 1.90
361 371 7.415095 GGCAAACTTATGTAACATGCTGACATA 60.415 37.037 9.66 9.66 35.48 2.29
362 372 6.324819 GCAAACTTATGTAACATGCTGACAT 58.675 36.000 11.24 11.24 37.55 3.06
363 373 5.335583 GGCAAACTTATGTAACATGCTGACA 60.336 40.000 0.00 0.00 33.09 3.58
364 374 5.095490 GGCAAACTTATGTAACATGCTGAC 58.905 41.667 0.00 0.00 33.09 3.51
365 375 4.764308 TGGCAAACTTATGTAACATGCTGA 59.236 37.500 0.00 0.00 33.09 4.26
366 376 5.058149 TGGCAAACTTATGTAACATGCTG 57.942 39.130 0.00 0.00 33.09 4.41
367 377 5.920193 ATGGCAAACTTATGTAACATGCT 57.080 34.783 0.00 0.00 33.09 3.79
368 378 5.868801 ACAATGGCAAACTTATGTAACATGC 59.131 36.000 0.00 0.00 0.00 4.06
369 379 8.243426 AGTACAATGGCAAACTTATGTAACATG 58.757 33.333 0.00 0.00 0.00 3.21
370 380 8.348285 AGTACAATGGCAAACTTATGTAACAT 57.652 30.769 0.00 0.00 0.00 2.71
371 381 7.753309 AGTACAATGGCAAACTTATGTAACA 57.247 32.000 0.00 0.00 0.00 2.41
453 463 1.663702 GCCAAGCTGCAGTGCAAAG 60.664 57.895 20.22 9.72 38.41 2.77
639 832 2.650116 AACTCCCGCTGTCTCGCAT 61.650 57.895 0.00 0.00 0.00 4.73
674 867 1.344953 TAGAAGCCATGCGTCCCCAT 61.345 55.000 0.00 0.00 37.75 4.00
748 941 6.927933 GGAAACAAATATTTTCCTGTGACG 57.072 37.500 9.32 0.00 45.94 4.35
761 954 1.877367 GCCGCGTGGGAAACAAATA 59.123 52.632 18.41 0.00 38.47 1.40
777 970 0.172578 GTAATTTCTGGGTTGGCGCC 59.827 55.000 22.73 22.73 0.00 6.53
798 991 4.250116 TGCCCATAACAACATGTCAAAC 57.750 40.909 0.00 0.00 0.00 2.93
815 1008 3.572255 TGTGAAGGAAAACTATGTTGCCC 59.428 43.478 0.00 0.00 0.00 5.36
871 1064 8.682936 AACATGAATACTTTCTTGACTTCACT 57.317 30.769 0.00 0.00 38.60 3.41
880 1073 7.406104 AGGGAAGCTAACATGAATACTTTCTT 58.594 34.615 0.00 0.00 32.78 2.52
881 1074 6.963322 AGGGAAGCTAACATGAATACTTTCT 58.037 36.000 0.00 0.00 32.78 2.52
942 1140 2.073252 TTGTAATGCACCAACCCACA 57.927 45.000 0.00 0.00 0.00 4.17
956 1154 9.364989 CACAGTTTTGATTCCTTCTTTTTGTAA 57.635 29.630 0.00 0.00 0.00 2.41
1030 1247 9.139174 GAAAAACATCAACAAACTGAAGAGAAA 57.861 29.630 0.00 0.00 0.00 2.52
1313 1536 2.617308 CTCGCTTGAGCAATGGAATCAT 59.383 45.455 3.65 0.00 42.21 2.45
1332 1555 3.287222 AGGCTCTGAGACTGTGATACTC 58.713 50.000 13.36 0.00 27.71 2.59
1484 1735 5.227569 TGTCTTGCTGTTATCTTCCTTGA 57.772 39.130 0.00 0.00 0.00 3.02
1659 1910 1.398390 GACTGCCCTTTGTTATCAGCG 59.602 52.381 0.00 0.00 0.00 5.18
2495 2753 2.425592 CACCGTTCCAGACCAGCA 59.574 61.111 0.00 0.00 0.00 4.41
2582 2840 5.391312 TCGCATAGCAGAAGAAGCATATA 57.609 39.130 0.00 0.00 0.00 0.86
2583 2841 4.263018 TCGCATAGCAGAAGAAGCATAT 57.737 40.909 0.00 0.00 0.00 1.78
2654 2916 4.550063 CGCGACGACTAACATGCATAAAAT 60.550 41.667 0.00 0.00 0.00 1.82
2668 2930 1.954146 ATGTGCAAACGCGACGACT 60.954 52.632 15.93 0.00 0.00 4.18
2673 2935 1.914634 AAAAACATGTGCAAACGCGA 58.085 40.000 15.93 0.00 0.00 5.87
2735 3026 0.882042 CATCCAGCGCCATAGTCCAC 60.882 60.000 2.29 0.00 0.00 4.02
2745 3036 2.515523 AGACATGCCATCCAGCGC 60.516 61.111 0.00 0.00 34.65 5.92
2766 3057 5.530915 TGGTAAAACCAGACTGAATTCACAG 59.469 40.000 3.38 0.00 44.79 3.66
2839 3144 7.264221 ACTCATGTTGCAACTTCAAAATAACA 58.736 30.769 28.61 6.52 0.00 2.41
2843 3148 6.152932 AGACTCATGTTGCAACTTCAAAAT 57.847 33.333 28.61 11.23 0.00 1.82
2851 3156 8.970691 ATATAAACAAAGACTCATGTTGCAAC 57.029 30.769 22.83 22.83 39.57 4.17
2905 3211 1.339610 AGTATGCAGATGCTCGACCTC 59.660 52.381 6.35 0.00 42.66 3.85
2922 3228 1.107538 AGCCCGCGCTTGATAGAGTA 61.108 55.000 5.56 0.00 45.55 2.59
2952 3260 5.188359 GGGTTCTACAGATACACCCAAGTTA 59.812 44.000 11.28 0.00 40.63 2.24
2964 3272 5.779241 TGGATCAAAAGGGTTCTACAGAT 57.221 39.130 0.00 0.00 0.00 2.90
2968 3276 7.468141 AAGAATTGGATCAAAAGGGTTCTAC 57.532 36.000 0.00 0.00 0.00 2.59
2996 3304 5.514274 ACCAAACAAGTTCAATACCACAG 57.486 39.130 0.00 0.00 0.00 3.66
3027 3335 5.407387 CGTGAAAACTTTCCGAGGATTCTAA 59.593 40.000 0.00 0.00 36.36 2.10
3037 3345 1.003223 GACCCACGTGAAAACTTTCCG 60.003 52.381 19.30 9.87 36.36 4.30
3043 3351 0.379316 AAAGCGACCCACGTGAAAAC 59.621 50.000 19.30 4.59 44.60 2.43
3046 3354 1.952133 CGAAAGCGACCCACGTGAA 60.952 57.895 19.30 0.00 44.60 3.18
3071 3379 5.362717 ACGGGAAAGGAAAATTCTTTTGAGT 59.637 36.000 7.83 3.35 36.73 3.41
3094 3402 0.034896 TCCAAAAGCTCGAGGTCCAC 59.965 55.000 18.90 0.00 0.00 4.02
3101 3409 5.067153 TGAAAGAACATTTCCAAAAGCTCGA 59.933 36.000 0.00 0.00 0.00 4.04
3103 3411 6.703165 ACATGAAAGAACATTTCCAAAAGCTC 59.297 34.615 0.00 0.00 0.00 4.09
3109 3417 6.708502 TCGTAGACATGAAAGAACATTTCCAA 59.291 34.615 0.00 0.00 30.21 3.53
3110 3418 6.227522 TCGTAGACATGAAAGAACATTTCCA 58.772 36.000 0.00 0.00 30.21 3.53
3136 3444 3.441572 AGCTGTCTAAAACATGCATGGTC 59.558 43.478 29.41 12.23 37.23 4.02
3137 3445 3.424703 AGCTGTCTAAAACATGCATGGT 58.575 40.909 29.41 22.35 37.23 3.55
3160 3469 8.884726 TGCAAACGTACTAGCAATAAATAATCA 58.115 29.630 0.00 0.00 33.48 2.57
3161 3470 9.370126 CTGCAAACGTACTAGCAATAAATAATC 57.630 33.333 0.00 0.00 36.44 1.75
3239 3556 1.228510 CTTGGCAGGATTCCCTCCC 59.771 63.158 0.00 0.00 46.27 4.30
3240 3557 0.182299 CTCTTGGCAGGATTCCCTCC 59.818 60.000 0.00 1.45 42.02 4.30
3241 3558 0.465278 GCTCTTGGCAGGATTCCCTC 60.465 60.000 0.00 0.00 42.02 4.30
3242 3559 1.611965 GCTCTTGGCAGGATTCCCT 59.388 57.895 0.00 0.00 45.74 4.20
3243 3560 1.454663 GGCTCTTGGCAGGATTCCC 60.455 63.158 0.00 0.00 44.01 3.97
3265 3590 7.155328 AGTACAACTCCACTAGAGAATGTTTG 58.845 38.462 0.00 1.58 46.50 2.93
3285 3610 6.149308 CCAGTCATGACTTGCAAATTAGTACA 59.851 38.462 25.84 0.00 40.20 2.90
3323 3661 6.816140 AGTGATTCCAAAACGAAAAACATTGT 59.184 30.769 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.