Multiple sequence alignment - TraesCS3D01G284700

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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 TraesCS3D01G284700 chr3D 100.000 4342 0 0 1 4342 394063631 394059290 0.000000e+00 8019.0
1 TraesCS3D01G284700 chr3D 77.953 127 21 2 154 279 13983165 13983285 6.020000e-09 73.1
2 TraesCS3D01G284700 chr3A 92.632 3909 175 49 1 3847 513896030 513892173 0.000000e+00 5518.0
3 TraesCS3D01G284700 chr3A 87.657 478 28 20 3886 4342 513892072 513891605 1.070000e-145 527.0
4 TraesCS3D01G284700 chr3A 82.000 100 11 2 183 282 22811025 22810933 1.290000e-10 78.7
5 TraesCS3D01G284700 chr3B 94.409 2540 97 20 406 2915 513671940 513669416 0.000000e+00 3862.0
6 TraesCS3D01G284700 chr3B 89.707 1846 98 34 342 2153 511383265 511385052 0.000000e+00 2272.0
7 TraesCS3D01G284700 chr3B 93.135 437 18 6 3887 4319 513668170 513667742 7.920000e-177 630.0
8 TraesCS3D01G284700 chr3B 93.017 358 24 1 3004 3360 513669358 513669001 4.980000e-144 521.0
9 TraesCS3D01G284700 chr3B 93.284 268 15 2 3581 3847 513668539 513668274 4.070000e-105 392.0
10 TraesCS3D01G284700 chr3B 89.437 284 24 4 1 279 513672621 513672339 1.920000e-93 353.0
11 TraesCS3D01G284700 chr3B 85.204 196 15 8 3405 3597 513668897 513668713 5.730000e-44 189.0
12 TraesCS3D01G284700 chr3B 92.105 114 6 2 2219 2330 511385062 511385174 1.620000e-34 158.0
13 TraesCS3D01G284700 chr3B 100.000 35 0 0 3359 3393 513668923 513668889 1.010000e-06 65.8
14 TraesCS3D01G284700 chr7A 83.200 125 18 2 158 279 39272395 39272271 1.280000e-20 111.0
15 TraesCS3D01G284700 chr7A 79.200 125 19 3 154 278 121639712 121639829 3.600000e-11 80.5
16 TraesCS3D01G284700 chr4D 81.301 123 19 4 154 273 12602106 12601985 3.570000e-16 97.1
17 TraesCS3D01G284700 chr5B 81.905 105 15 2 171 274 617111969 617112070 7.740000e-13 86.1
18 TraesCS3D01G284700 chr2B 94.340 53 3 0 222 274 53410934 53410986 1.000000e-11 82.4


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 TraesCS3D01G284700 chr3D 394059290 394063631 4341 True 8019.000000 8019 100.000000 1 4342 1 chr3D.!!$R1 4341
1 TraesCS3D01G284700 chr3A 513891605 513896030 4425 True 3022.500000 5518 90.144500 1 4342 2 chr3A.!!$R2 4341
2 TraesCS3D01G284700 chr3B 511383265 511385174 1909 False 1215.000000 2272 90.906000 342 2330 2 chr3B.!!$F1 1988
3 TraesCS3D01G284700 chr3B 513667742 513672621 4879 True 858.971429 3862 92.640857 1 4319 7 chr3B.!!$R1 4318

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
59 60 1.721487 CTCTGTAAAATGGCCGCCG 59.279 57.895 4.58 0.0 0.00 6.46 F
1401 1706 1.045350 CAGCAGCTGCCTACTCCCTA 61.045 60.000 34.39 0.0 43.38 3.53 F
2903 3250 0.037326 TCACCGAATCACTCCAGTGC 60.037 55.000 1.49 0.0 45.25 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1410 1715 1.331756 GCCTTGTATGCAATCGACAGG 59.668 52.381 0.00 0.0 33.65 4.00 R
2987 3364 0.099436 GCGCAACTGCCCAGATTTAG 59.901 55.000 0.30 0.0 37.91 1.85 R
3858 4526 0.034896 TCGCTTTTTCTCCGGAGCTT 59.965 50.000 27.39 0.0 33.09 3.74 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
59 60 1.721487 CTCTGTAAAATGGCCGCCG 59.279 57.895 4.58 0.00 0.00 6.46
181 182 3.002102 ACGGTCGTTGTTGTAGTTTGTT 58.998 40.909 0.00 0.00 0.00 2.83
189 190 6.757478 TCGTTGTTGTAGTTTGTTGATCACTA 59.243 34.615 0.00 0.00 0.00 2.74
245 251 6.704310 TCGCTTAGGTATAAGTTTGGTCTTT 58.296 36.000 0.00 0.00 40.55 2.52
987 1291 3.884037 AGGAACACAAATCCAGAACCT 57.116 42.857 0.00 0.00 39.55 3.50
1401 1706 1.045350 CAGCAGCTGCCTACTCCCTA 61.045 60.000 34.39 0.00 43.38 3.53
1410 1715 1.137282 GCCTACTCCCTAGCACAACTC 59.863 57.143 0.00 0.00 0.00 3.01
1443 1748 4.021981 GCATACAAGGCCTTGAAGAAAGTT 60.022 41.667 44.50 25.49 42.93 2.66
1453 1758 4.402474 CCTTGAAGAAAGTTCCTGTGGTTT 59.598 41.667 0.00 0.00 33.66 3.27
1520 1825 8.902806 GGTATGTTATGGTGATTTTGATCTGAA 58.097 33.333 0.00 0.00 0.00 3.02
1698 2005 2.308690 GGGTCAGTAGCCAGTACTAGG 58.691 57.143 0.00 0.70 40.27 3.02
1891 2200 5.069318 TGTGCATCATTTTGTGTTAGGAGA 58.931 37.500 0.00 0.00 0.00 3.71
1897 2206 7.977853 GCATCATTTTGTGTTAGGAGAAATCAT 59.022 33.333 0.00 0.00 0.00 2.45
1920 2230 4.832266 TCAAAATGGTGCCAGTCTTTACAT 59.168 37.500 0.00 0.00 0.00 2.29
2354 2691 0.389948 GCGGCGGTATAGGGATTCAG 60.390 60.000 9.78 0.00 0.00 3.02
2395 2732 2.215942 AGTCCATAAGGGGTGTTTGC 57.784 50.000 0.00 0.00 37.22 3.68
2402 2739 2.595124 AAGGGGTGTTTGCTTTTTCG 57.405 45.000 0.00 0.00 0.00 3.46
2414 2751 8.113675 GTGTTTGCTTTTTCGTCAAAATATTGT 58.886 29.630 0.00 0.00 37.79 2.71
2417 2754 7.621832 TGCTTTTTCGTCAAAATATTGTGAG 57.378 32.000 8.66 4.08 37.79 3.51
2428 2765 9.612620 GTCAAAATATTGTGAGTTAAACTCCAG 57.387 33.333 8.66 0.00 38.60 3.86
2437 2774 1.807142 GTTAAACTCCAGAGTGGCAGC 59.193 52.381 0.05 0.00 41.58 5.25
2541 2878 4.394920 ACATAGTTGGTATGGCGTTTCTTG 59.605 41.667 0.00 0.00 42.74 3.02
2585 2922 6.602803 TGATACATGGTAAATGCACATCTTGT 59.397 34.615 0.00 0.00 0.00 3.16
2696 3042 5.629079 ATCTTAGCAAGCAAACTACCAAC 57.371 39.130 0.00 0.00 0.00 3.77
2724 3070 5.839621 TCATTACCGAATCCTTAGTAGCAC 58.160 41.667 0.00 0.00 0.00 4.40
2726 3072 2.463752 ACCGAATCCTTAGTAGCACCA 58.536 47.619 0.00 0.00 0.00 4.17
2782 3128 8.226543 TCAAAATTAATGCTGCTTAAAAGACG 57.773 30.769 0.00 0.00 0.00 4.18
2859 3205 7.149569 TCACATTGAAGTGATTGAGGAAATC 57.850 36.000 0.00 0.00 43.18 2.17
2867 3213 7.503566 TGAAGTGATTGAGGAAATCTGAAAGTT 59.496 33.333 0.30 0.00 44.42 2.66
2895 3242 7.148306 ACCACATAAAAATAGTCACCGAATCAC 60.148 37.037 0.00 0.00 0.00 3.06
2902 3249 1.273606 AGTCACCGAATCACTCCAGTG 59.726 52.381 0.00 0.00 46.91 3.66
2903 3250 0.037326 TCACCGAATCACTCCAGTGC 60.037 55.000 1.49 0.00 45.25 4.40
2907 3254 1.903877 CGAATCACTCCAGTGCCCCT 61.904 60.000 1.49 0.00 45.25 4.79
2908 3255 1.204146 GAATCACTCCAGTGCCCCTA 58.796 55.000 1.49 0.00 45.25 3.53
2909 3256 0.912486 AATCACTCCAGTGCCCCTAC 59.088 55.000 1.49 0.00 45.25 3.18
2910 3257 0.983378 ATCACTCCAGTGCCCCTACC 60.983 60.000 1.49 0.00 45.25 3.18
2911 3258 1.918293 CACTCCAGTGCCCCTACCA 60.918 63.158 0.00 0.00 39.39 3.25
2912 3259 1.151899 ACTCCAGTGCCCCTACCAA 60.152 57.895 0.00 0.00 0.00 3.67
2925 3302 2.827921 CCCTACCAATGCAAGCTTTCTT 59.172 45.455 0.00 0.00 0.00 2.52
2937 3314 4.143535 GCAAGCTTTCTTTACGATGTTTGC 60.144 41.667 0.00 0.00 36.45 3.68
2943 3320 6.636562 TTTCTTTACGATGTTTGCCCTTAA 57.363 33.333 0.00 0.00 0.00 1.85
2946 3323 2.200373 ACGATGTTTGCCCTTAAGCT 57.800 45.000 0.00 0.00 0.00 3.74
2977 3354 1.760029 TCCAAACTTTGTTTCCCAGGC 59.240 47.619 0.88 0.00 0.00 4.85
2979 3356 2.483538 CCAAACTTTGTTTCCCAGGCAG 60.484 50.000 0.88 0.00 0.00 4.85
2980 3357 0.752658 AACTTTGTTTCCCAGGCAGC 59.247 50.000 0.00 0.00 0.00 5.25
2981 3358 1.286880 CTTTGTTTCCCAGGCAGCG 59.713 57.895 0.00 0.00 0.00 5.18
2982 3359 1.454847 TTTGTTTCCCAGGCAGCGT 60.455 52.632 0.00 0.00 0.00 5.07
2983 3360 1.733402 TTTGTTTCCCAGGCAGCGTG 61.733 55.000 8.20 8.20 0.00 5.34
2984 3361 2.281484 GTTTCCCAGGCAGCGTGA 60.281 61.111 16.85 0.00 0.00 4.35
2985 3362 2.032528 TTTCCCAGGCAGCGTGAG 59.967 61.111 16.85 3.13 0.00 3.51
2986 3363 2.515979 TTTCCCAGGCAGCGTGAGA 61.516 57.895 16.85 5.88 0.00 3.27
2987 3364 2.731691 TTTCCCAGGCAGCGTGAGAC 62.732 60.000 16.85 0.00 0.00 3.36
2988 3365 3.699894 CCCAGGCAGCGTGAGACT 61.700 66.667 16.85 0.00 0.00 3.24
2989 3366 2.351244 CCCAGGCAGCGTGAGACTA 61.351 63.158 16.85 0.00 0.00 2.59
2990 3367 1.591703 CCAGGCAGCGTGAGACTAA 59.408 57.895 16.85 0.00 0.00 2.24
2991 3368 0.037326 CCAGGCAGCGTGAGACTAAA 60.037 55.000 16.85 0.00 0.00 1.85
2992 3369 1.406069 CCAGGCAGCGTGAGACTAAAT 60.406 52.381 16.85 0.00 0.00 1.40
2993 3370 1.929836 CAGGCAGCGTGAGACTAAATC 59.070 52.381 9.63 0.00 0.00 2.17
2994 3371 1.827969 AGGCAGCGTGAGACTAAATCT 59.172 47.619 0.00 0.00 41.91 2.40
2995 3372 1.929836 GGCAGCGTGAGACTAAATCTG 59.070 52.381 0.00 0.00 38.00 2.90
2996 3373 1.929836 GCAGCGTGAGACTAAATCTGG 59.070 52.381 0.00 0.00 38.00 3.86
2997 3374 2.544685 CAGCGTGAGACTAAATCTGGG 58.455 52.381 0.00 0.00 38.00 4.45
2998 3375 1.134670 AGCGTGAGACTAAATCTGGGC 60.135 52.381 0.00 0.00 38.00 5.36
2999 3376 1.405526 GCGTGAGACTAAATCTGGGCA 60.406 52.381 0.00 0.00 38.00 5.36
3000 3377 2.544685 CGTGAGACTAAATCTGGGCAG 58.455 52.381 0.00 0.00 38.00 4.85
3001 3378 2.093973 CGTGAGACTAAATCTGGGCAGT 60.094 50.000 0.00 0.00 38.00 4.40
3002 3379 3.617531 CGTGAGACTAAATCTGGGCAGTT 60.618 47.826 0.00 0.00 38.00 3.16
3016 3393 0.670546 GCAGTTGCGCCTTCAGTAGA 60.671 55.000 4.18 0.00 0.00 2.59
3088 3465 4.991056 TCTGCTAGTGTCTGACATTTCAAC 59.009 41.667 14.37 0.00 0.00 3.18
3093 3470 4.389374 AGTGTCTGACATTTCAACGGAAT 58.611 39.130 14.37 0.00 31.93 3.01
3119 3496 0.469494 ATGATACGGCTGGTGCATCA 59.531 50.000 0.00 0.00 41.91 3.07
3137 3515 0.447801 CATGGCAGGTCTTTGCGTAC 59.552 55.000 0.00 0.00 45.00 3.67
3320 3698 0.784178 CATCCGCCGTAATCGATGTG 59.216 55.000 0.00 0.00 39.71 3.21
3355 3733 9.979578 GTCAAATCTGTGAGAATATGAGATAGT 57.020 33.333 0.00 0.00 0.00 2.12
3400 3858 0.762418 TCCTTCGCAGGGAGTTCAAA 59.238 50.000 0.00 0.00 41.25 2.69
3401 3859 1.142060 TCCTTCGCAGGGAGTTCAAAA 59.858 47.619 0.00 0.00 41.25 2.44
3402 3860 1.266989 CCTTCGCAGGGAGTTCAAAAC 59.733 52.381 0.00 0.00 36.36 2.43
3403 3861 2.222027 CTTCGCAGGGAGTTCAAAACT 58.778 47.619 0.00 0.00 46.38 2.66
3406 3864 2.616842 TCGCAGGGAGTTCAAAACTTTC 59.383 45.455 0.00 0.00 43.03 2.62
3417 3875 0.752658 AAAACTTTCCAGGGTGCTGC 59.247 50.000 0.00 0.00 0.00 5.25
3428 3886 2.399356 GGTGCTGCGCCTTTAGGAC 61.399 63.158 24.33 6.77 37.39 3.85
3723 4383 8.092249 GTCTACATTGACAGTAGTGAGTACACG 61.092 44.444 4.09 0.00 42.34 4.49
3758 4418 0.035152 ATCGCACTCCCAATCAGCAA 60.035 50.000 0.00 0.00 0.00 3.91
3759 4419 0.250684 TCGCACTCCCAATCAGCAAA 60.251 50.000 0.00 0.00 0.00 3.68
3760 4420 0.813184 CGCACTCCCAATCAGCAAAT 59.187 50.000 0.00 0.00 0.00 2.32
3761 4421 2.016318 CGCACTCCCAATCAGCAAATA 58.984 47.619 0.00 0.00 0.00 1.40
3762 4422 2.223340 CGCACTCCCAATCAGCAAATAC 60.223 50.000 0.00 0.00 0.00 1.89
3763 4423 2.099756 GCACTCCCAATCAGCAAATACC 59.900 50.000 0.00 0.00 0.00 2.73
3764 4424 2.689983 CACTCCCAATCAGCAAATACCC 59.310 50.000 0.00 0.00 0.00 3.69
3765 4425 2.310538 CTCCCAATCAGCAAATACCCC 58.689 52.381 0.00 0.00 0.00 4.95
3766 4426 1.929494 TCCCAATCAGCAAATACCCCT 59.071 47.619 0.00 0.00 0.00 4.79
3771 4431 3.864789 ATCAGCAAATACCCCTACCTG 57.135 47.619 0.00 0.00 0.00 4.00
3833 4501 3.055209 AGCAGCAGCCATATCTGTATG 57.945 47.619 0.00 0.00 43.56 2.39
3847 4515 4.229432 TCTGTATGTGCAGTGACGCAGT 62.229 50.000 0.00 0.00 44.05 4.40
3848 4516 4.918879 TCTGTATGTGCAGTGACGCAGTA 61.919 47.826 0.00 0.00 44.05 2.74
3849 4517 6.172438 TCTGTATGTGCAGTGACGCAGTAT 62.172 45.833 0.00 4.15 44.05 2.12
3886 4589 2.096860 GGAGAAAAAGCGAAGACGACAC 60.097 50.000 0.00 0.00 42.66 3.67
3887 4590 1.521423 AGAAAAAGCGAAGACGACACG 59.479 47.619 0.00 0.00 42.66 4.49
3909 4643 2.546321 CACGCACGCAACTCACTC 59.454 61.111 0.00 0.00 0.00 3.51
3997 4734 1.339610 TCCTTTTCAACCGCCACATTG 59.660 47.619 0.00 0.00 0.00 2.82
4011 4748 1.522355 CATTGCTCTCGCGGGTGAT 60.522 57.895 13.09 0.00 39.65 3.06
4012 4749 1.091771 CATTGCTCTCGCGGGTGATT 61.092 55.000 13.09 0.00 39.65 2.57
4013 4750 0.811616 ATTGCTCTCGCGGGTGATTC 60.812 55.000 13.09 0.00 39.65 2.52
4070 4821 2.741092 GTCTCCACTCCACCGCAA 59.259 61.111 0.00 0.00 0.00 4.85
4134 4885 0.038159 GCTCGCACTCACCAGTAAGT 60.038 55.000 0.00 0.00 0.00 2.24
4136 4887 2.352421 GCTCGCACTCACCAGTAAGTAA 60.352 50.000 0.00 0.00 0.00 2.24
4137 4888 3.859627 GCTCGCACTCACCAGTAAGTAAA 60.860 47.826 0.00 0.00 0.00 2.01
4138 4889 4.495422 CTCGCACTCACCAGTAAGTAAAT 58.505 43.478 0.00 0.00 0.00 1.40
4139 4890 4.890088 TCGCACTCACCAGTAAGTAAATT 58.110 39.130 0.00 0.00 0.00 1.82
4219 4981 2.989571 AGGGATCTGAGAGGTGGTTTTT 59.010 45.455 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.099436 GCGGCCATTTTACAGAGCTG 59.901 55.000 2.24 0.00 0.00 4.24
59 60 8.336080 CAAAGAACAGACCTTTAGTAGTTCAAC 58.664 37.037 0.00 0.00 42.11 3.18
893 1191 6.432581 GGGGTTGGAGGATTCTAGTAAAAAT 58.567 40.000 0.00 0.00 0.00 1.82
987 1291 1.304381 GCCCATTCCTGTTGCTCCA 60.304 57.895 0.00 0.00 0.00 3.86
1029 1333 1.523258 CTGGATGCCAAGCTCCGAG 60.523 63.158 0.00 0.00 34.05 4.63
1310 1614 3.449018 ACTCAGTATTCTGCACGGAGATT 59.551 43.478 9.15 0.00 39.63 2.40
1401 1706 1.800805 CAATCGACAGGAGTTGTGCT 58.199 50.000 0.00 0.00 41.05 4.40
1410 1715 1.331756 GCCTTGTATGCAATCGACAGG 59.668 52.381 0.00 0.00 33.65 4.00
1597 1904 7.605449 CAGACATCACAAACAGGGAAATAAAT 58.395 34.615 0.00 0.00 29.94 1.40
1698 2005 2.109425 AACTCAACCAACCGCCTATC 57.891 50.000 0.00 0.00 0.00 2.08
1891 2200 4.529377 AGACTGGCACCATTTTGATGATTT 59.471 37.500 0.00 0.00 0.00 2.17
1897 2206 4.211125 TGTAAAGACTGGCACCATTTTGA 58.789 39.130 0.00 0.00 0.00 2.69
1935 2245 6.745450 TCTTTGCGTTTGTTTTTCTGACTTAG 59.255 34.615 0.00 0.00 0.00 2.18
1941 2252 5.344665 TGTTCTCTTTGCGTTTGTTTTTCTG 59.655 36.000 0.00 0.00 0.00 3.02
1942 2253 5.465935 TGTTCTCTTTGCGTTTGTTTTTCT 58.534 33.333 0.00 0.00 0.00 2.52
1949 2260 4.621034 AGTTTGTTGTTCTCTTTGCGTTTG 59.379 37.500 0.00 0.00 0.00 2.93
2369 2706 7.676004 CAAACACCCCTTATGGACTTTTATTT 58.324 34.615 0.00 0.00 35.39 1.40
2388 2725 8.113675 ACAATATTTTGACGAAAAAGCAAACAC 58.886 29.630 2.69 0.00 41.00 3.32
2402 2739 9.612620 CTGGAGTTTAACTCACAATATTTTGAC 57.387 33.333 24.09 5.12 46.79 3.18
2414 2751 2.703536 TGCCACTCTGGAGTTTAACTCA 59.296 45.455 24.09 11.11 46.79 3.41
2417 2754 1.807142 GCTGCCACTCTGGAGTTTAAC 59.193 52.381 0.00 0.00 40.96 2.01
2428 2765 0.674895 CACCTAGTTGGCTGCCACTC 60.675 60.000 23.30 17.20 40.22 3.51
2437 2774 3.077359 CCTTTGCTCTTCACCTAGTTGG 58.923 50.000 0.00 0.00 42.93 3.77
2541 2878 4.154347 CTCCTGCGAGGGCCAGTC 62.154 72.222 6.18 0.00 38.85 3.51
2605 2942 6.090483 TGAGAAAACAATGCCGGATAAAAA 57.910 33.333 5.05 0.00 0.00 1.94
2606 2943 5.713792 TGAGAAAACAATGCCGGATAAAA 57.286 34.783 5.05 0.00 0.00 1.52
2607 2944 5.649557 CATGAGAAAACAATGCCGGATAAA 58.350 37.500 5.05 0.00 0.00 1.40
2608 2945 4.439974 GCATGAGAAAACAATGCCGGATAA 60.440 41.667 5.05 0.00 32.56 1.75
2611 2948 1.202114 GCATGAGAAAACAATGCCGGA 59.798 47.619 5.05 0.00 32.56 5.14
2612 2949 1.203052 AGCATGAGAAAACAATGCCGG 59.797 47.619 0.00 0.00 38.90 6.13
2678 3024 6.712998 TGAATTAGTTGGTAGTTTGCTTGCTA 59.287 34.615 0.00 0.00 0.00 3.49
2684 3030 6.964934 CGGTAATGAATTAGTTGGTAGTTTGC 59.035 38.462 0.00 0.00 0.00 3.68
2696 3042 9.141400 GCTACTAAGGATTCGGTAATGAATTAG 57.859 37.037 0.00 0.00 38.65 1.73
2724 3070 6.384224 AGTGCGAAAATAATCATATGCATGG 58.616 36.000 10.16 1.18 33.25 3.66
2726 3072 6.432162 AGGAGTGCGAAAATAATCATATGCAT 59.568 34.615 3.79 3.79 33.25 3.96
2782 3128 6.865205 AGTGCTCAAAAGAAACAGATAAATGC 59.135 34.615 0.00 0.00 0.00 3.56
2817 3163 4.397420 TGTGACTTGTCAAATGGCATAGT 58.603 39.130 0.00 0.00 0.00 2.12
2825 3171 6.698008 TCACTTCAATGTGACTTGTCAAAT 57.302 33.333 4.93 2.78 41.43 2.32
2853 3199 9.974980 TTTTATGTGGTAAACTTTCAGATTTCC 57.025 29.630 0.00 0.00 32.17 3.13
2867 3213 8.795842 ATTCGGTGACTATTTTTATGTGGTAA 57.204 30.769 0.00 0.00 0.00 2.85
2895 3242 0.107017 CATTGGTAGGGGCACTGGAG 60.107 60.000 0.00 0.00 0.00 3.86
2902 3249 0.972471 AAGCTTGCATTGGTAGGGGC 60.972 55.000 0.00 0.00 0.00 5.80
2903 3250 1.478105 GAAAGCTTGCATTGGTAGGGG 59.522 52.381 0.00 0.00 0.00 4.79
2907 3254 4.757657 TCGTAAAGAAAGCTTGCATTGGTA 59.242 37.500 7.33 0.00 33.79 3.25
2908 3255 3.568007 TCGTAAAGAAAGCTTGCATTGGT 59.432 39.130 7.33 0.00 33.79 3.67
2909 3256 4.159377 TCGTAAAGAAAGCTTGCATTGG 57.841 40.909 7.33 0.00 33.79 3.16
2910 3257 5.156355 ACATCGTAAAGAAAGCTTGCATTG 58.844 37.500 7.33 0.00 33.79 2.82
2911 3258 5.376854 ACATCGTAAAGAAAGCTTGCATT 57.623 34.783 7.33 3.32 33.79 3.56
2912 3259 5.376854 AACATCGTAAAGAAAGCTTGCAT 57.623 34.783 7.33 0.00 33.79 3.96
2925 3302 3.681593 AGCTTAAGGGCAAACATCGTAA 58.318 40.909 4.29 0.00 34.17 3.18
2943 3320 4.206477 AGTTTGGAAGCAAACAAAAGCT 57.794 36.364 1.99 0.00 44.86 3.74
2946 3323 6.625873 AACAAAGTTTGGAAGCAAACAAAA 57.374 29.167 19.45 0.00 44.86 2.44
2977 3354 2.544685 CCCAGATTTAGTCTCACGCTG 58.455 52.381 0.00 0.00 34.00 5.18
2979 3356 1.291132 GCCCAGATTTAGTCTCACGC 58.709 55.000 0.00 0.00 34.00 5.34
2980 3357 2.093973 ACTGCCCAGATTTAGTCTCACG 60.094 50.000 1.69 0.00 34.00 4.35
2981 3358 3.618690 ACTGCCCAGATTTAGTCTCAC 57.381 47.619 1.69 0.00 34.00 3.51
2982 3359 3.869912 GCAACTGCCCAGATTTAGTCTCA 60.870 47.826 1.69 0.00 32.38 3.27
2983 3360 2.680339 GCAACTGCCCAGATTTAGTCTC 59.320 50.000 1.69 0.00 32.38 3.36
2984 3361 2.716217 GCAACTGCCCAGATTTAGTCT 58.284 47.619 1.69 0.00 34.16 3.24
2985 3362 1.398390 CGCAACTGCCCAGATTTAGTC 59.602 52.381 1.69 0.00 37.91 2.59
2986 3363 1.453155 CGCAACTGCCCAGATTTAGT 58.547 50.000 1.69 0.00 37.91 2.24
2987 3364 0.099436 GCGCAACTGCCCAGATTTAG 59.901 55.000 0.30 0.00 37.91 1.85
2988 3365 2.179764 GCGCAACTGCCCAGATTTA 58.820 52.632 0.30 0.00 37.91 1.40
2989 3366 2.964978 GCGCAACTGCCCAGATTT 59.035 55.556 0.30 0.00 37.91 2.17
2997 3374 0.670546 TCTACTGAAGGCGCAACTGC 60.671 55.000 10.83 0.00 37.78 4.40
2998 3375 1.929836 GATCTACTGAAGGCGCAACTG 59.070 52.381 10.83 6.40 0.00 3.16
2999 3376 1.550524 TGATCTACTGAAGGCGCAACT 59.449 47.619 10.83 0.00 0.00 3.16
3000 3377 2.010145 TGATCTACTGAAGGCGCAAC 57.990 50.000 10.83 0.00 0.00 4.17
3001 3378 2.168313 TCATGATCTACTGAAGGCGCAA 59.832 45.455 10.83 0.00 0.00 4.85
3002 3379 1.756538 TCATGATCTACTGAAGGCGCA 59.243 47.619 10.83 0.00 0.00 6.09
3016 3393 4.225942 TCAAAGCTAACAGAGGGTCATGAT 59.774 41.667 0.00 0.00 0.00 2.45
3060 3437 2.226674 TGTCAGACACTAGCAGAGTTCG 59.773 50.000 0.00 0.00 35.64 3.95
3088 3465 3.809832 AGCCGTATCATTCTTCAATTCCG 59.190 43.478 0.00 0.00 0.00 4.30
3093 3470 3.270027 CACCAGCCGTATCATTCTTCAA 58.730 45.455 0.00 0.00 0.00 2.69
3102 3479 0.870393 CATGATGCACCAGCCGTATC 59.130 55.000 0.00 0.00 41.13 2.24
3119 3496 1.019278 CGTACGCAAAGACCTGCCAT 61.019 55.000 0.52 0.00 39.26 4.40
3320 3698 3.603532 TCACAGATTTGACAGCCAGATC 58.396 45.455 0.00 0.00 36.83 2.75
3355 3733 5.953548 TGTACTAGTTTGCCACCATCTAGTA 59.046 40.000 0.00 0.00 38.63 1.82
3356 3734 4.775780 TGTACTAGTTTGCCACCATCTAGT 59.224 41.667 0.00 0.00 39.74 2.57
3357 3735 5.105310 AGTGTACTAGTTTGCCACCATCTAG 60.105 44.000 0.00 0.00 34.74 2.43
3400 3858 1.898574 CGCAGCACCCTGGAAAGTT 60.899 57.895 0.00 0.00 39.54 2.66
3401 3859 2.281761 CGCAGCACCCTGGAAAGT 60.282 61.111 0.00 0.00 39.54 2.66
3417 3875 2.871427 GCGCATCGTCCTAAAGGCG 61.871 63.158 0.30 0.00 46.47 5.52
3428 3886 2.813474 TTCAGGTTCGGCGCATCG 60.813 61.111 10.83 4.34 0.00 3.84
3619 4275 0.314935 AACTGAAGCGGCAACCAATG 59.685 50.000 1.45 0.00 0.00 2.82
3684 4341 6.183360 TGTCAATGTAGACAAGTGTCAGTGTA 60.183 38.462 13.66 0.00 44.92 2.90
3723 4383 1.993370 GCGATGTAGACAAGTGTCCAC 59.007 52.381 7.82 5.51 45.85 4.02
3758 4418 6.126273 GGAATTTAGGAACAGGTAGGGGTATT 60.126 42.308 0.00 0.00 0.00 1.89
3759 4419 5.371769 GGAATTTAGGAACAGGTAGGGGTAT 59.628 44.000 0.00 0.00 0.00 2.73
3760 4420 4.723285 GGAATTTAGGAACAGGTAGGGGTA 59.277 45.833 0.00 0.00 0.00 3.69
3761 4421 3.526430 GGAATTTAGGAACAGGTAGGGGT 59.474 47.826 0.00 0.00 0.00 4.95
3762 4422 3.526019 TGGAATTTAGGAACAGGTAGGGG 59.474 47.826 0.00 0.00 0.00 4.79
3763 4423 4.855298 TGGAATTTAGGAACAGGTAGGG 57.145 45.455 0.00 0.00 0.00 3.53
3764 4424 4.948004 GGTTGGAATTTAGGAACAGGTAGG 59.052 45.833 0.00 0.00 0.00 3.18
3765 4425 5.414765 GTGGTTGGAATTTAGGAACAGGTAG 59.585 44.000 0.00 0.00 0.00 3.18
3766 4426 5.073965 AGTGGTTGGAATTTAGGAACAGGTA 59.926 40.000 0.00 0.00 0.00 3.08
3771 4431 8.027189 GTCATTAAGTGGTTGGAATTTAGGAAC 58.973 37.037 0.00 0.00 0.00 3.62
3833 4501 0.994995 CTGATACTGCGTCACTGCAC 59.005 55.000 0.00 0.00 40.62 4.57
3854 4522 2.614520 GCTTTTTCTCCGGAGCTTATCC 59.385 50.000 27.39 9.65 45.64 2.59
3855 4523 2.285488 CGCTTTTTCTCCGGAGCTTATC 59.715 50.000 27.39 12.18 33.09 1.75
3856 4524 2.093658 TCGCTTTTTCTCCGGAGCTTAT 60.094 45.455 27.39 0.00 33.09 1.73
3857 4525 1.274167 TCGCTTTTTCTCCGGAGCTTA 59.726 47.619 27.39 11.48 33.09 3.09
3858 4526 0.034896 TCGCTTTTTCTCCGGAGCTT 59.965 50.000 27.39 0.00 33.09 3.74
3888 4591 4.415501 GAGTTGCGTGCGTGCGAG 62.416 66.667 5.04 0.00 37.81 5.03
3909 4643 2.416547 AGTGAATGAATCGAAACGGCAG 59.583 45.455 0.00 0.00 0.00 4.85
4011 4748 6.075984 AGGTAGAGTACAAGTGGAAGAAGAA 58.924 40.000 0.00 0.00 0.00 2.52
4012 4749 5.642165 AGGTAGAGTACAAGTGGAAGAAGA 58.358 41.667 0.00 0.00 0.00 2.87
4013 4750 5.105675 GGAGGTAGAGTACAAGTGGAAGAAG 60.106 48.000 0.00 0.00 0.00 2.85
4070 4821 2.676471 GACACCTTGGGCGGCATT 60.676 61.111 12.47 0.00 0.00 3.56
4149 4910 2.417719 GTGACTGACTAAAGTGGCCAG 58.582 52.381 5.11 0.00 0.00 4.85
4188 4950 1.002544 CTCAGATCCCTAATTCCGGCC 59.997 57.143 0.00 0.00 0.00 6.13
4198 4960 2.350863 AAACCACCTCTCAGATCCCT 57.649 50.000 0.00 0.00 0.00 4.20
4219 4981 0.179043 TTACCTGCAAGCCACGAACA 60.179 50.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.