Multiple sequence alignment - TraesCS1A01G341600

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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 TraesCS1A01G341600 chr1A 100.000 3939 0 0 1 3939 531225405 531221467 0.000000e+00 7275
1 TraesCS1A01G341600 chr1D 94.335 3336 109 27 1 3302 432789121 432785832 0.000000e+00 5040
2 TraesCS1A01G341600 chr1D 84.982 566 53 14 3303 3857 432785740 432785196 2.680000e-151 545
3 TraesCS1A01G341600 chr1B 96.815 2606 70 11 1 2599 584142650 584140051 0.000000e+00 4340
4 TraesCS1A01G341600 chr1B 84.828 725 39 31 2623 3297 584139714 584139011 0.000000e+00 664
5 TraesCS1A01G341600 chr1B 85.980 592 44 14 3304 3889 584138916 584138358 7.290000e-167 597


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 TraesCS1A01G341600 chr1A 531221467 531225405 3938 True 7275.0 7275 100.000000 1 3939 1 chr1A.!!$R1 3938
1 TraesCS1A01G341600 chr1D 432785196 432789121 3925 True 2792.5 5040 89.658500 1 3857 2 chr1D.!!$R1 3856
2 TraesCS1A01G341600 chr1B 584138358 584142650 4292 True 1867.0 4340 89.207667 1 3889 3 chr1B.!!$R1 3888


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
873 876 0.687354 GAGGAACAGTGAAGCCTCCA 59.313 55.000 15.26 0.0 40.79 3.86 F
1915 1919 1.673920 TCAGTTTCGTGGGTGAAAAGC 59.326 47.619 0.00 0.0 39.40 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2036 2040 0.323178 AGCTTTCTGGTGGCTCATGG 60.323 55.0 0.0 0.0 0.00 3.66 R
3515 4000 0.036732 CCAGCTTCAGCCTACCACAA 59.963 55.0 0.0 0.0 43.38 3.33 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 7.611467 ACCACATTATGCTTGAACTTTGAGATA 59.389 33.333 0.00 0.00 0.00 1.98
265 266 2.161855 TGAGCCACCACATGAAACATC 58.838 47.619 0.00 0.00 0.00 3.06
344 345 2.352225 GCTCAGACCGAGGCATGTATAG 60.352 54.545 0.00 0.00 42.55 1.31
419 420 3.544684 CCCTCGATGAATGACCATTGAA 58.455 45.455 0.00 0.00 36.73 2.69
515 516 1.832998 TCACATGCAGATGCTGACCTA 59.167 47.619 6.35 0.00 42.66 3.08
529 530 9.044646 AGATGCTGACCTATATCTGATTATGTT 57.955 33.333 0.00 0.00 0.00 2.71
873 876 0.687354 GAGGAACAGTGAAGCCTCCA 59.313 55.000 15.26 0.00 40.79 3.86
1082 1085 3.181509 GCTTGTGCTCTGTTCATCTCATG 60.182 47.826 0.00 0.00 36.03 3.07
1169 1172 2.288666 TGTCACTTTGCACCTCTGTTC 58.711 47.619 0.00 0.00 0.00 3.18
1267 1271 3.196007 TCCGCTTTTTCTTTATGTGCG 57.804 42.857 0.00 0.00 41.30 5.34
1272 1276 3.121025 GCTTTTTCTTTATGTGCGGCAAC 60.121 43.478 3.23 0.00 0.00 4.17
1273 1277 3.717400 TTTTCTTTATGTGCGGCAACA 57.283 38.095 3.23 5.96 0.00 3.33
1287 1291 5.342259 GTGCGGCAACACTTTAAGAATTAAG 59.658 40.000 3.23 0.00 42.24 1.85
1289 1293 6.072175 TGCGGCAACACTTTAAGAATTAAGAT 60.072 34.615 0.00 0.00 42.24 2.40
1290 1294 6.806739 GCGGCAACACTTTAAGAATTAAGATT 59.193 34.615 0.00 0.00 42.24 2.40
1291 1295 7.328493 GCGGCAACACTTTAAGAATTAAGATTT 59.672 33.333 0.00 0.00 42.24 2.17
1665 1669 3.009033 AGGCAGCTGTTTTAGGTATGTCA 59.991 43.478 16.64 0.00 34.81 3.58
1915 1919 1.673920 TCAGTTTCGTGGGTGAAAAGC 59.326 47.619 0.00 0.00 39.40 3.51
2036 2040 6.198966 CCAAACAAGCTGTTGACTATTTGTTC 59.801 38.462 6.62 0.00 40.14 3.18
2060 2064 2.338785 GCCACCAGAAAGCTCCTGC 61.339 63.158 9.81 0.00 40.05 4.85
2130 2134 4.455877 GTGTCCTCAATTCTCGAAACCATT 59.544 41.667 0.00 0.00 0.00 3.16
2228 2233 7.399245 TTTGTTTTACTTTAAGTGCCTCAGT 57.601 32.000 8.00 0.00 0.00 3.41
2237 2242 1.888215 AGTGCCTCAGTGAATGTGTG 58.112 50.000 0.00 0.00 0.00 3.82
2243 2248 1.948834 CTCAGTGAATGTGTGCACCAA 59.051 47.619 15.69 2.17 35.67 3.67
2270 2275 8.409371 AGTTTTTCTTTTTCTTGACAGAGATCC 58.591 33.333 0.00 0.00 0.00 3.36
2337 2342 5.470437 TCATGTGCGTCCATTTTACAACTAA 59.530 36.000 0.00 0.00 0.00 2.24
2361 2366 0.179076 TGGATGCATGTGGAGTAGCG 60.179 55.000 2.46 0.00 0.00 4.26
2441 2449 3.691118 GCCATGACATAAAGAGCTGACAA 59.309 43.478 0.00 0.00 0.00 3.18
2586 2596 3.441922 GGAGAAGAAAATGCTGAAGGGTC 59.558 47.826 0.00 0.00 0.00 4.46
2603 2613 3.041946 GGGTCTCTCTCTCTCTCTCTCT 58.958 54.545 0.00 0.00 0.00 3.10
2604 2614 3.070302 GGGTCTCTCTCTCTCTCTCTCTC 59.930 56.522 0.00 0.00 0.00 3.20
2605 2615 3.964031 GGTCTCTCTCTCTCTCTCTCTCT 59.036 52.174 0.00 0.00 0.00 3.10
2606 2616 4.038642 GGTCTCTCTCTCTCTCTCTCTCTC 59.961 54.167 0.00 0.00 0.00 3.20
2607 2617 4.892934 GTCTCTCTCTCTCTCTCTCTCTCT 59.107 50.000 0.00 0.00 0.00 3.10
2608 2618 5.009610 GTCTCTCTCTCTCTCTCTCTCTCTC 59.990 52.000 0.00 0.00 0.00 3.20
2609 2619 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2610 2620 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2611 2621 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2612 2622 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2613 2623 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2614 2624 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2615 2625 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2616 2626 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2617 2627 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2618 2628 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2619 2629 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
2620 2630 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
2695 3018 5.680408 GCATACAGGTTAATCACTACCGACA 60.680 44.000 0.00 0.00 39.46 4.35
2718 3041 8.425577 ACACGTCTTCTTTCATCCATATTAAG 57.574 34.615 0.00 0.00 0.00 1.85
2823 3146 7.052873 ACTTCCAGGTAATCTTCATGAATCAG 58.947 38.462 8.96 0.00 0.00 2.90
2831 3176 6.939132 AATCTTCATGAATCAGTCATCACC 57.061 37.500 8.96 0.00 44.01 4.02
2832 3177 5.425196 TCTTCATGAATCAGTCATCACCA 57.575 39.130 8.96 0.00 44.01 4.17
2856 3201 0.038251 TATCCGATCTCGCCATGTGC 60.038 55.000 0.00 0.00 38.18 4.57
2998 3352 2.332063 ATACGGGATTGTTGCAGAGG 57.668 50.000 0.00 0.00 0.00 3.69
3032 3386 3.005539 AGGAGACATGCCTGGCGT 61.006 61.111 14.98 11.57 34.62 5.68
3059 3429 6.260936 AGTTCATTAATGCCTGAAAGATACCG 59.739 38.462 10.76 0.00 34.07 4.02
3175 3548 0.596600 ATGTCCGCGCTTATGTACGG 60.597 55.000 5.56 0.00 46.97 4.02
3211 3584 2.096713 CGAGCTTGCAAGTGTCTGTTAC 60.097 50.000 26.55 7.50 0.00 2.50
3212 3585 1.867233 AGCTTGCAAGTGTCTGTTACG 59.133 47.619 26.55 0.00 0.00 3.18
3213 3586 1.069906 GCTTGCAAGTGTCTGTTACGG 60.070 52.381 26.55 0.00 0.00 4.02
3215 3588 2.148916 TGCAAGTGTCTGTTACGGAG 57.851 50.000 0.00 0.00 0.00 4.63
3218 3591 3.257375 TGCAAGTGTCTGTTACGGAGTAT 59.743 43.478 0.00 0.00 45.21 2.12
3219 3592 4.243270 GCAAGTGTCTGTTACGGAGTATT 58.757 43.478 0.00 0.00 45.21 1.89
3220 3593 5.047872 TGCAAGTGTCTGTTACGGAGTATTA 60.048 40.000 0.00 0.00 45.21 0.98
3221 3594 5.865552 GCAAGTGTCTGTTACGGAGTATTAA 59.134 40.000 0.00 0.00 45.21 1.40
3222 3595 6.534079 GCAAGTGTCTGTTACGGAGTATTAAT 59.466 38.462 0.00 0.00 45.21 1.40
3223 3596 7.064253 GCAAGTGTCTGTTACGGAGTATTAATT 59.936 37.037 0.00 0.00 45.21 1.40
3224 3597 9.577110 CAAGTGTCTGTTACGGAGTATTAATTA 57.423 33.333 0.00 0.00 45.21 1.40
3272 3648 2.222007 TGAATGTTTGCACAACAGCC 57.778 45.000 16.01 11.72 36.16 4.85
3297 3673 7.917505 CCAACTGGAAAGCAATAGTCATATTTC 59.082 37.037 0.00 0.00 37.39 2.17
3300 3676 9.905713 ACTGGAAAGCAATAGTCATATTTCTTA 57.094 29.630 0.00 0.00 34.89 2.10
3352 3823 8.205131 TCTATTACTGGCCGTTCTTTTTATTC 57.795 34.615 0.00 0.00 0.00 1.75
3427 3899 1.448119 GCTTCGCCTTTATCTGCCCC 61.448 60.000 0.00 0.00 0.00 5.80
3441 3926 1.281867 CTGCCCCTATTTGTCCAGACA 59.718 52.381 0.00 0.00 39.98 3.41
3452 3937 2.997315 CCAGACAGCGAGGGGTCA 60.997 66.667 0.00 0.00 36.50 4.02
3453 3938 2.362369 CCAGACAGCGAGGGGTCAT 61.362 63.158 0.00 0.00 36.50 3.06
3454 3939 1.599047 CAGACAGCGAGGGGTCATT 59.401 57.895 0.00 0.00 36.50 2.57
3455 3940 0.460987 CAGACAGCGAGGGGTCATTC 60.461 60.000 0.00 0.00 36.50 2.67
3456 3941 1.153349 GACAGCGAGGGGTCATTCC 60.153 63.158 0.00 0.00 34.22 3.01
3467 3952 0.039527 GGTCATTCCGTTGTTGTGCC 60.040 55.000 0.00 0.00 0.00 5.01
3477 3962 2.540769 CGTTGTTGTGCCGAGTTGAAAT 60.541 45.455 0.00 0.00 0.00 2.17
3478 3963 3.443976 GTTGTTGTGCCGAGTTGAAATT 58.556 40.909 0.00 0.00 0.00 1.82
3531 4016 1.340017 TGGATTGTGGTAGGCTGAAGC 60.340 52.381 0.00 0.00 41.14 3.86
3589 4074 4.998788 TCTAATCAACGTCTGATGGACAG 58.001 43.478 12.06 0.00 44.43 3.51
3656 4142 5.477510 CATGACTGAGCTACCAAGGATATC 58.522 45.833 0.00 0.00 0.00 1.63
3657 4143 4.809193 TGACTGAGCTACCAAGGATATCT 58.191 43.478 2.05 0.00 0.00 1.98
3658 4144 4.830046 TGACTGAGCTACCAAGGATATCTC 59.170 45.833 2.05 0.00 0.00 2.75
3686 4172 0.975040 TGCCAAACTTGTTGCAGGGT 60.975 50.000 0.00 0.00 0.00 4.34
3690 4176 2.223711 CCAAACTTGTTGCAGGGTGTAC 60.224 50.000 0.00 0.00 0.00 2.90
3697 4183 1.812571 GTTGCAGGGTGTACTGATTGG 59.187 52.381 0.00 0.00 40.97 3.16
3715 4205 0.601057 GGTTTGTTTACATGCGCCCT 59.399 50.000 4.18 0.00 0.00 5.19
3716 4206 1.402325 GGTTTGTTTACATGCGCCCTC 60.402 52.381 4.18 0.00 0.00 4.30
3717 4207 1.268352 GTTTGTTTACATGCGCCCTCA 59.732 47.619 4.18 0.00 0.00 3.86
3718 4208 0.878416 TTGTTTACATGCGCCCTCAC 59.122 50.000 4.18 0.00 0.00 3.51
3734 4224 2.594592 ACGCTTTGTGGCCTGACC 60.595 61.111 3.32 0.00 39.84 4.02
3803 4293 2.084546 GGAAACCAAGATGAACTCCCG 58.915 52.381 0.00 0.00 0.00 5.14
3804 4294 1.468914 GAAACCAAGATGAACTCCCGC 59.531 52.381 0.00 0.00 0.00 6.13
3805 4295 0.322546 AACCAAGATGAACTCCCGCC 60.323 55.000 0.00 0.00 0.00 6.13
3806 4296 1.201429 ACCAAGATGAACTCCCGCCT 61.201 55.000 0.00 0.00 0.00 5.52
3807 4297 0.462759 CCAAGATGAACTCCCGCCTC 60.463 60.000 0.00 0.00 0.00 4.70
3808 4298 0.462759 CAAGATGAACTCCCGCCTCC 60.463 60.000 0.00 0.00 0.00 4.30
3809 4299 1.627297 AAGATGAACTCCCGCCTCCC 61.627 60.000 0.00 0.00 0.00 4.30
3810 4300 3.447025 GATGAACTCCCGCCTCCCG 62.447 68.421 0.00 0.00 0.00 5.14
3826 4317 2.345991 CGGTGCCGAAGAAGGGAA 59.654 61.111 4.35 0.00 42.83 3.97
3828 4319 1.375326 GGTGCCGAAGAAGGGAAGT 59.625 57.895 0.00 0.00 31.97 3.01
3833 4324 1.946283 GCCGAAGAAGGGAAGTGGAAG 60.946 57.143 0.00 0.00 0.00 3.46
3836 4327 3.496160 CCGAAGAAGGGAAGTGGAAGAAA 60.496 47.826 0.00 0.00 0.00 2.52
3847 4338 0.882927 TGGAAGAAACTTCGCACCGG 60.883 55.000 0.00 0.00 0.00 5.28
3848 4339 0.601841 GGAAGAAACTTCGCACCGGA 60.602 55.000 9.46 0.00 0.00 5.14
3849 4340 0.790814 GAAGAAACTTCGCACCGGAG 59.209 55.000 9.46 0.00 38.61 4.63
3877 4368 2.042831 GCCTCTGCACGCAGGAAAT 61.043 57.895 18.47 0.00 43.75 2.17
3881 4372 0.250684 TCTGCACGCAGGAAATCCAA 60.251 50.000 18.47 0.00 43.75 3.53
3889 4380 2.230992 CGCAGGAAATCCAATTGACCAA 59.769 45.455 7.12 0.00 38.89 3.67
3890 4381 3.305950 CGCAGGAAATCCAATTGACCAAA 60.306 43.478 7.12 0.00 38.89 3.28
3891 4382 4.640364 GCAGGAAATCCAATTGACCAAAA 58.360 39.130 7.12 0.00 38.89 2.44
3892 4383 5.062528 GCAGGAAATCCAATTGACCAAAAA 58.937 37.500 7.12 0.00 38.89 1.94
3893 4384 5.706833 GCAGGAAATCCAATTGACCAAAAAT 59.293 36.000 7.12 0.00 38.89 1.82
3894 4385 6.878389 GCAGGAAATCCAATTGACCAAAAATA 59.122 34.615 7.12 0.00 38.89 1.40
3895 4386 7.148423 GCAGGAAATCCAATTGACCAAAAATAC 60.148 37.037 7.12 0.00 38.89 1.89
3896 4387 7.877097 CAGGAAATCCAATTGACCAAAAATACA 59.123 33.333 7.12 0.00 38.89 2.29
3897 4388 7.877612 AGGAAATCCAATTGACCAAAAATACAC 59.122 33.333 7.12 0.00 38.89 2.90
3898 4389 7.148656 GGAAATCCAATTGACCAAAAATACACG 60.149 37.037 7.12 0.00 35.64 4.49
3899 4390 5.776173 TCCAATTGACCAAAAATACACGT 57.224 34.783 7.12 0.00 0.00 4.49
3900 4391 6.150396 TCCAATTGACCAAAAATACACGTT 57.850 33.333 7.12 0.00 0.00 3.99
3901 4392 6.574350 TCCAATTGACCAAAAATACACGTTT 58.426 32.000 7.12 0.00 0.00 3.60
3902 4393 6.477033 TCCAATTGACCAAAAATACACGTTTG 59.523 34.615 7.12 0.00 35.03 2.93
3903 4394 6.477033 CCAATTGACCAAAAATACACGTTTGA 59.523 34.615 7.12 0.00 36.96 2.69
3904 4395 7.334009 CAATTGACCAAAAATACACGTTTGAC 58.666 34.615 0.00 0.00 36.96 3.18
3905 4396 4.922719 TGACCAAAAATACACGTTTGACC 58.077 39.130 0.00 0.00 36.96 4.02
3906 4397 4.398358 TGACCAAAAATACACGTTTGACCA 59.602 37.500 0.00 0.00 36.96 4.02
3907 4398 5.105877 TGACCAAAAATACACGTTTGACCAA 60.106 36.000 0.00 0.00 36.96 3.67
3908 4399 5.344884 ACCAAAAATACACGTTTGACCAAG 58.655 37.500 0.00 0.00 36.96 3.61
3909 4400 5.125739 ACCAAAAATACACGTTTGACCAAGA 59.874 36.000 0.00 0.00 36.96 3.02
3910 4401 6.037098 CCAAAAATACACGTTTGACCAAGAA 58.963 36.000 0.00 0.00 36.96 2.52
3911 4402 6.699642 CCAAAAATACACGTTTGACCAAGAAT 59.300 34.615 0.00 0.00 36.96 2.40
3912 4403 7.863375 CCAAAAATACACGTTTGACCAAGAATA 59.137 33.333 0.00 0.00 36.96 1.75
3913 4404 9.405587 CAAAAATACACGTTTGACCAAGAATAT 57.594 29.630 0.00 0.00 36.96 1.28
3914 4405 9.974980 AAAAATACACGTTTGACCAAGAATATT 57.025 25.926 0.00 0.00 0.00 1.28
3915 4406 8.964420 AAATACACGTTTGACCAAGAATATTG 57.036 30.769 0.00 0.00 0.00 1.90
3916 4407 7.915293 ATACACGTTTGACCAAGAATATTGA 57.085 32.000 0.00 0.00 0.00 2.57
3917 4408 6.627395 ACACGTTTGACCAAGAATATTGAA 57.373 33.333 0.00 0.00 0.00 2.69
3918 4409 7.033530 ACACGTTTGACCAAGAATATTGAAA 57.966 32.000 0.00 0.00 0.00 2.69
3919 4410 7.484975 ACACGTTTGACCAAGAATATTGAAAA 58.515 30.769 0.00 0.00 0.00 2.29
3920 4411 7.976734 ACACGTTTGACCAAGAATATTGAAAAA 59.023 29.630 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 8.508883 TGGTATAACAAAACTAGTGTTTGTGT 57.491 30.769 24.20 19.98 44.70 3.72
290 291 6.718454 AGTCCAAGAATCAAGACAATGAACAT 59.282 34.615 0.00 0.00 32.06 2.71
310 311 2.103373 GTCTGAGCATACTGGAGTCCA 58.897 52.381 12.40 12.40 0.00 4.02
344 345 5.652014 TGAGGAACATTTACATGGGTTCATC 59.348 40.000 16.71 16.71 45.83 2.92
816 819 8.787852 GTGGAAGTGAAGATATTTTGAAGTTCT 58.212 33.333 4.17 0.00 0.00 3.01
873 876 8.486210 TGAACATCAGGTTGTTTATATAGCTCT 58.514 33.333 0.00 0.00 40.63 4.09
1082 1085 4.865925 TGCATGAACTTTGATGCTTAATGC 59.134 37.500 13.48 0.00 46.03 3.56
1095 1098 5.356751 TGACAAGTGTTTACTGCATGAACTT 59.643 36.000 0.00 0.00 37.19 2.66
1169 1172 5.828299 TTCTAAGGTGTGTCAAAGTTTGG 57.172 39.130 15.47 0.00 0.00 3.28
1234 1238 6.977213 AGAAAAAGCGGAATTTAAGCACTAA 58.023 32.000 4.10 0.00 0.00 2.24
1291 1295 5.838521 AGGAGAGTTCCAAAATGGCTAAAAA 59.161 36.000 0.00 0.00 46.64 1.94
1295 1299 4.657814 AAGGAGAGTTCCAAAATGGCTA 57.342 40.909 0.00 0.00 46.64 3.93
1297 1301 4.281941 AGAAAAGGAGAGTTCCAAAATGGC 59.718 41.667 0.00 0.00 46.64 4.40
1548 1552 7.986085 AGATACTGCTTAACAACAATTGACT 57.014 32.000 13.59 0.00 0.00 3.41
1944 1948 6.634436 CAGATTAAGTTCTGCAAACTTGTGAC 59.366 38.462 24.73 16.95 40.38 3.67
1948 1952 6.638468 GGTTCAGATTAAGTTCTGCAAACTTG 59.362 38.462 24.73 15.08 42.37 3.16
2010 2014 5.127031 ACAAATAGTCAACAGCTTGTTTGGT 59.873 36.000 7.63 0.00 38.77 3.67
2036 2040 0.323178 AGCTTTCTGGTGGCTCATGG 60.323 55.000 0.00 0.00 0.00 3.66
2228 2233 3.883830 AAACTTTGGTGCACACATTCA 57.116 38.095 20.43 3.64 0.00 2.57
2237 2242 7.015289 GTCAAGAAAAAGAAAAACTTTGGTGC 58.985 34.615 0.00 0.00 46.55 5.01
2243 2248 9.794685 GATCTCTGTCAAGAAAAAGAAAAACTT 57.205 29.630 0.00 0.00 34.28 2.66
2270 2275 5.934625 AGCAATATAAATCTCTGCGTTAGGG 59.065 40.000 0.00 0.00 38.07 3.53
2337 2342 2.811410 ACTCCACATGCATCCAACATT 58.189 42.857 0.00 0.00 0.00 2.71
2361 2366 5.643379 TCATCTGTAAAAGGCCAATGTTC 57.357 39.130 5.01 0.00 0.00 3.18
2586 2596 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
2603 2613 3.963374 CAGGAGAGAGAGAGAGAGAGAGA 59.037 52.174 0.00 0.00 0.00 3.10
2604 2614 3.494048 GCAGGAGAGAGAGAGAGAGAGAG 60.494 56.522 0.00 0.00 0.00 3.20
2605 2615 2.435805 GCAGGAGAGAGAGAGAGAGAGA 59.564 54.545 0.00 0.00 0.00 3.10
2606 2616 2.437281 AGCAGGAGAGAGAGAGAGAGAG 59.563 54.545 0.00 0.00 0.00 3.20
2607 2617 2.481441 AGCAGGAGAGAGAGAGAGAGA 58.519 52.381 0.00 0.00 0.00 3.10
2608 2618 3.287867 AAGCAGGAGAGAGAGAGAGAG 57.712 52.381 0.00 0.00 0.00 3.20
2609 2619 4.853468 TTAAGCAGGAGAGAGAGAGAGA 57.147 45.455 0.00 0.00 0.00 3.10
2610 2620 6.772716 ACTAATTAAGCAGGAGAGAGAGAGAG 59.227 42.308 0.00 0.00 0.00 3.20
2611 2621 6.668645 ACTAATTAAGCAGGAGAGAGAGAGA 58.331 40.000 0.00 0.00 0.00 3.10
2612 2622 6.959639 ACTAATTAAGCAGGAGAGAGAGAG 57.040 41.667 0.00 0.00 0.00 3.20
2613 2623 6.097554 CCAACTAATTAAGCAGGAGAGAGAGA 59.902 42.308 0.00 0.00 0.00 3.10
2614 2624 6.127196 ACCAACTAATTAAGCAGGAGAGAGAG 60.127 42.308 0.00 0.00 0.00 3.20
2615 2625 5.721960 ACCAACTAATTAAGCAGGAGAGAGA 59.278 40.000 0.00 0.00 0.00 3.10
2616 2626 5.983540 ACCAACTAATTAAGCAGGAGAGAG 58.016 41.667 0.00 0.00 0.00 3.20
2617 2627 6.374417 AACCAACTAATTAAGCAGGAGAGA 57.626 37.500 0.00 0.00 0.00 3.10
2618 2628 6.258947 GCTAACCAACTAATTAAGCAGGAGAG 59.741 42.308 0.00 0.00 0.00 3.20
2619 2629 6.113411 GCTAACCAACTAATTAAGCAGGAGA 58.887 40.000 0.00 0.00 0.00 3.71
2620 2630 5.880332 TGCTAACCAACTAATTAAGCAGGAG 59.120 40.000 2.38 0.00 0.00 3.69
2733 3056 2.847327 TCTGGAAAGTTCTCCTGCAG 57.153 50.000 6.78 6.78 36.35 4.41
2823 3146 3.452755 TCGGATACACATGGTGATGAC 57.547 47.619 2.98 0.00 36.96 3.06
2831 3176 1.000274 TGGCGAGATCGGATACACATG 60.000 52.381 4.18 0.00 40.23 3.21
2832 3177 1.328279 TGGCGAGATCGGATACACAT 58.672 50.000 4.18 0.00 40.23 3.21
2856 3201 5.008019 GTGTGGCCATGTCATGTTATTAGAG 59.992 44.000 9.72 0.00 0.00 2.43
2988 3342 1.072331 GGGTCTTCTTCCTCTGCAACA 59.928 52.381 0.00 0.00 0.00 3.33
2998 3352 1.978580 TCCTGTTCCTGGGTCTTCTTC 59.021 52.381 0.00 0.00 0.00 2.87
3030 3384 7.072177 TCTTTCAGGCATTAATGAACTAACG 57.928 36.000 19.73 5.63 35.25 3.18
3031 3385 9.937175 GTATCTTTCAGGCATTAATGAACTAAC 57.063 33.333 19.73 0.00 35.25 2.34
3032 3386 9.120538 GGTATCTTTCAGGCATTAATGAACTAA 57.879 33.333 19.73 7.42 35.25 2.24
3086 3456 8.614814 ACATGGTGCCCTTATGATTATATTACT 58.385 33.333 0.00 0.00 0.00 2.24
3087 3457 8.807948 ACATGGTGCCCTTATGATTATATTAC 57.192 34.615 0.00 0.00 0.00 1.89
3090 3463 6.664816 CCAACATGGTGCCCTTATGATTATAT 59.335 38.462 4.81 0.00 31.35 0.86
3106 3479 5.356719 ATCCAACAGGACACCAACATGGT 62.357 47.826 0.00 0.00 41.88 3.55
3175 3548 4.619760 GCAAGCTCGGTTGGTTTTATTTAC 59.380 41.667 10.43 0.00 0.00 2.01
3223 3596 9.474313 ACAGGCTCCTTGTCAATAAATTAATTA 57.526 29.630 0.01 0.00 0.00 1.40
3224 3597 8.253113 CACAGGCTCCTTGTCAATAAATTAATT 58.747 33.333 0.00 0.00 0.00 1.40
3225 3598 7.615365 TCACAGGCTCCTTGTCAATAAATTAAT 59.385 33.333 0.00 0.00 0.00 1.40
3226 3599 6.945435 TCACAGGCTCCTTGTCAATAAATTAA 59.055 34.615 0.00 0.00 0.00 1.40
3227 3600 6.480763 TCACAGGCTCCTTGTCAATAAATTA 58.519 36.000 0.00 0.00 0.00 1.40
3228 3601 5.324409 TCACAGGCTCCTTGTCAATAAATT 58.676 37.500 0.00 0.00 0.00 1.82
3229 3602 4.922206 TCACAGGCTCCTTGTCAATAAAT 58.078 39.130 0.00 0.00 0.00 1.40
3230 3603 4.365514 TCACAGGCTCCTTGTCAATAAA 57.634 40.909 0.00 0.00 0.00 1.40
3236 3609 2.479566 TCATTCACAGGCTCCTTGTC 57.520 50.000 0.00 0.00 0.00 3.18
3241 3617 3.841643 CAAACATTCATTCACAGGCTCC 58.158 45.455 0.00 0.00 0.00 4.70
3242 3618 3.248266 GCAAACATTCATTCACAGGCTC 58.752 45.455 0.00 0.00 0.00 4.70
3246 3622 4.804665 TGTTGTGCAAACATTCATTCACAG 59.195 37.500 9.46 0.00 36.09 3.66
3272 3648 8.680903 AGAAATATGACTATTGCTTTCCAGTTG 58.319 33.333 0.00 0.00 30.11 3.16
3316 3786 7.927048 ACGGCCAGTAATAGATTTCAATTAAC 58.073 34.615 2.24 0.00 0.00 2.01
3336 3807 6.549061 ACTAAATCGAATAAAAAGAACGGCC 58.451 36.000 0.00 0.00 0.00 6.13
3427 3899 2.544685 CCTCGCTGTCTGGACAAATAG 58.455 52.381 4.94 2.86 41.33 1.73
3441 3926 2.291043 AACGGAATGACCCCTCGCT 61.291 57.895 0.00 0.00 34.64 4.93
3452 3937 0.534203 ACTCGGCACAACAACGGAAT 60.534 50.000 0.00 0.00 0.00 3.01
3453 3938 0.745128 AACTCGGCACAACAACGGAA 60.745 50.000 0.00 0.00 0.00 4.30
3454 3939 1.153329 AACTCGGCACAACAACGGA 60.153 52.632 0.00 0.00 0.00 4.69
3455 3940 1.010125 CAACTCGGCACAACAACGG 60.010 57.895 0.00 0.00 0.00 4.44
3456 3941 0.375454 TTCAACTCGGCACAACAACG 59.625 50.000 0.00 0.00 0.00 4.10
3467 3952 8.368126 GCACATGAGATTAAAAATTTCAACTCG 58.632 33.333 0.00 0.00 0.00 4.18
3477 3962 3.749088 ACCGACGCACATGAGATTAAAAA 59.251 39.130 0.00 0.00 0.00 1.94
3478 3963 3.124466 CACCGACGCACATGAGATTAAAA 59.876 43.478 0.00 0.00 0.00 1.52
3514 3999 1.340405 CCAGCTTCAGCCTACCACAAT 60.340 52.381 0.00 0.00 43.38 2.71
3515 4000 0.036732 CCAGCTTCAGCCTACCACAA 59.963 55.000 0.00 0.00 43.38 3.33
3516 4001 0.835971 TCCAGCTTCAGCCTACCACA 60.836 55.000 0.00 0.00 43.38 4.17
3517 4002 0.107945 CTCCAGCTTCAGCCTACCAC 60.108 60.000 0.00 0.00 43.38 4.16
3518 4003 0.545309 ACTCCAGCTTCAGCCTACCA 60.545 55.000 0.00 0.00 43.38 3.25
3519 4004 0.107945 CACTCCAGCTTCAGCCTACC 60.108 60.000 0.00 0.00 43.38 3.18
3520 4005 0.610687 ACACTCCAGCTTCAGCCTAC 59.389 55.000 0.00 0.00 43.38 3.18
3531 4016 1.218316 GGCGGTCCTAACACTCCAG 59.782 63.158 0.00 0.00 0.00 3.86
3589 4074 1.188863 TTCCCCCGTTAGCTCAGTAC 58.811 55.000 0.00 0.00 0.00 2.73
3656 4142 4.573900 ACAAGTTTGGCATAGTGAGAGAG 58.426 43.478 0.00 0.00 0.00 3.20
3657 4143 4.623932 ACAAGTTTGGCATAGTGAGAGA 57.376 40.909 0.00 0.00 0.00 3.10
3658 4144 4.614535 GCAACAAGTTTGGCATAGTGAGAG 60.615 45.833 0.00 0.00 0.00 3.20
3686 4172 6.442952 GCATGTAAACAAACCAATCAGTACA 58.557 36.000 0.00 0.00 0.00 2.90
3690 4176 3.364621 GCGCATGTAAACAAACCAATCAG 59.635 43.478 0.30 0.00 0.00 2.90
3697 4183 1.268352 TGAGGGCGCATGTAAACAAAC 59.732 47.619 10.83 0.00 0.00 2.93
3717 4207 2.594592 GGTCAGGCCACAAAGCGT 60.595 61.111 5.01 0.00 37.17 5.07
3718 4208 3.726517 CGGTCAGGCCACAAAGCG 61.727 66.667 5.01 4.59 36.97 4.68
3734 4224 0.597637 AGAGTGGTTGCGACTTCACG 60.598 55.000 3.59 0.00 35.50 4.35
3805 4295 2.125512 CTTCTTCGGCACCGGGAG 60.126 66.667 6.32 8.02 40.25 4.30
3806 4296 3.702048 CCTTCTTCGGCACCGGGA 61.702 66.667 6.32 5.47 40.25 5.14
3807 4297 4.778143 CCCTTCTTCGGCACCGGG 62.778 72.222 6.32 1.70 40.25 5.73
3808 4298 3.248446 TTCCCTTCTTCGGCACCGG 62.248 63.158 9.58 0.00 40.25 5.28
3809 4299 1.741770 CTTCCCTTCTTCGGCACCG 60.742 63.158 1.73 1.73 41.35 4.94
3810 4300 0.955919 CACTTCCCTTCTTCGGCACC 60.956 60.000 0.00 0.00 0.00 5.01
3826 4317 1.594331 GGTGCGAAGTTTCTTCCACT 58.406 50.000 19.57 0.00 0.00 4.00
3828 4319 0.882927 CCGGTGCGAAGTTTCTTCCA 60.883 55.000 0.00 1.66 0.00 3.53
3833 4324 1.503818 TTGCTCCGGTGCGAAGTTTC 61.504 55.000 22.46 0.00 35.36 2.78
3836 4327 2.110213 TTTGCTCCGGTGCGAAGT 59.890 55.556 23.99 0.00 32.99 3.01
3867 4358 1.818674 GGTCAATTGGATTTCCTGCGT 59.181 47.619 5.42 0.00 36.82 5.24
3872 4363 7.148656 CGTGTATTTTTGGTCAATTGGATTTCC 60.149 37.037 5.42 2.19 0.00 3.13
3877 4368 5.776173 ACGTGTATTTTTGGTCAATTGGA 57.224 34.783 5.42 0.00 0.00 3.53
3881 4372 5.980715 GGTCAAACGTGTATTTTTGGTCAAT 59.019 36.000 0.00 0.00 34.14 2.57
3889 4380 9.405587 CAATATTCTTGGTCAAACGTGTATTTT 57.594 29.630 0.00 0.00 0.00 1.82
3890 4381 8.788806 TCAATATTCTTGGTCAAACGTGTATTT 58.211 29.630 0.00 0.00 0.00 1.40
3891 4382 8.330466 TCAATATTCTTGGTCAAACGTGTATT 57.670 30.769 0.00 0.00 0.00 1.89
3892 4383 7.915293 TCAATATTCTTGGTCAAACGTGTAT 57.085 32.000 0.00 0.00 0.00 2.29
3893 4384 7.731882 TTCAATATTCTTGGTCAAACGTGTA 57.268 32.000 0.00 0.00 0.00 2.90
3894 4385 6.627395 TTCAATATTCTTGGTCAAACGTGT 57.373 33.333 0.00 0.00 0.00 4.49
3895 4386 7.922505 TTTTCAATATTCTTGGTCAAACGTG 57.077 32.000 0.00 0.00 0.00 4.49



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

AutoCloner maintained by Alex Coulton.