Multiple sequence alignment - TraesCS5B01G302500

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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 TraesCS5B01G302500 chr5B 100.000 4782 0 0 1 4782 487219473 487224254 0.000000e+00 8831
1 TraesCS5B01G302500 chr5D 93.394 3860 141 42 769 4563 406331170 406334980 0.000000e+00 5611
2 TraesCS5B01G302500 chr5D 93.447 763 29 8 1 753 406330355 406331106 0.000000e+00 1112
3 TraesCS5B01G302500 chr5A 93.261 3710 144 35 769 4408 511903498 511907171 0.000000e+00 5369
4 TraesCS5B01G302500 chr5A 91.678 757 47 9 1 753 511902690 511903434 0.000000e+00 1035
5 TraesCS5B01G302500 chr1B 85.340 382 56 0 1016 1397 655847711 655848092 3.470000e-106 396
6 TraesCS5B01G302500 chr1B 89.855 207 21 0 3323 3529 655849215 655849421 2.840000e-67 267
7 TraesCS5B01G302500 chr1D 90.338 207 20 0 3323 3529 471841334 471841540 6.100000e-69 272
8 TraesCS5B01G302500 chr1A 90.338 207 20 0 3323 3529 566111186 566111392 6.100000e-69 272


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 TraesCS5B01G302500 chr5B 487219473 487224254 4781 False 8831.0 8831 100.0000 1 4782 1 chr5B.!!$F1 4781
1 TraesCS5B01G302500 chr5D 406330355 406334980 4625 False 3361.5 5611 93.4205 1 4563 2 chr5D.!!$F1 4562
2 TraesCS5B01G302500 chr5A 511902690 511907171 4481 False 3202.0 5369 92.4695 1 4408 2 chr5A.!!$F1 4407
3 TraesCS5B01G302500 chr1B 655847711 655849421 1710 False 331.5 396 87.5975 1016 3529 2 chr1B.!!$F1 2513

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
795 856 1.164041 CGTGGCCGGTCAGTTTCTTT 61.164 55.000 10.28 0.0 0.00 2.52 F
1732 1821 1.290203 ATGTTTGCTGACGGATAGCG 58.710 50.000 0.00 0.0 44.01 4.26 F
3648 3882 1.837439 TGGGCTGAGGATCACGTATTT 59.163 47.619 0.00 0.0 42.56 1.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2581 2791 0.976073 TCTCCCTTCCACCTAAGCCG 60.976 60.0 0.00 0.0 0.00 5.52 R
3706 3940 0.770499 TGCAGACCTTGGATGTTCCA 59.230 50.0 0.00 0.0 46.61 3.53 R
4633 4904 2.286365 ACCGATGGCCAAAGAAAGAA 57.714 45.0 10.96 0.0 0.00 2.52 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
62 63 2.766828 GGAGCTTAGCCTAACTCCAAGA 59.233 50.000 19.60 0.00 46.57 3.02
212 224 4.334481 GGAGAAAACGGAAAAACAGTCTCA 59.666 41.667 0.00 0.00 0.00 3.27
226 238 2.125350 CTCAAGCAGCTCCCCGAC 60.125 66.667 0.00 0.00 0.00 4.79
345 357 3.443925 CAGCCGCTCCGTCTCTCA 61.444 66.667 0.00 0.00 0.00 3.27
418 430 1.475034 CGGGAGAGAGACAGAGAGAGG 60.475 61.905 0.00 0.00 0.00 3.69
505 517 3.138798 GGGCATGCTGCTGTGAGG 61.139 66.667 18.92 0.00 44.28 3.86
506 518 3.138798 GGCATGCTGCTGTGAGGG 61.139 66.667 18.92 0.00 44.28 4.30
676 689 5.815740 GGGTCTATTATTGCTTTCGTCAAGA 59.184 40.000 1.85 0.00 33.80 3.02
720 733 5.699097 TTATTGCTTTTGTTAAGCGGTCT 57.301 34.783 5.18 0.00 45.80 3.85
776 837 5.653507 TGGATGCTCATTTGATTTGCTAAC 58.346 37.500 0.00 0.00 0.00 2.34
795 856 1.164041 CGTGGCCGGTCAGTTTCTTT 61.164 55.000 10.28 0.00 0.00 2.52
869 930 1.946768 ACATTTGGACCACGTGTTGAG 59.053 47.619 15.65 0.92 0.00 3.02
870 931 1.946768 CATTTGGACCACGTGTTGAGT 59.053 47.619 15.65 4.69 0.00 3.41
880 941 4.202223 ACCACGTGTTGAGTCAAGTTCTAT 60.202 41.667 15.65 0.00 0.00 1.98
883 944 3.990469 CGTGTTGAGTCAAGTTCTATGCT 59.010 43.478 5.62 0.00 0.00 3.79
887 948 7.291567 GTGTTGAGTCAAGTTCTATGCTTTAC 58.708 38.462 5.62 0.00 0.00 2.01
889 950 7.497579 TGTTGAGTCAAGTTCTATGCTTTACAA 59.502 33.333 5.62 0.00 0.00 2.41
892 953 7.715249 TGAGTCAAGTTCTATGCTTTACAAGTT 59.285 33.333 0.00 0.00 0.00 2.66
893 954 7.865707 AGTCAAGTTCTATGCTTTACAAGTTG 58.134 34.615 0.00 0.00 0.00 3.16
894 955 7.499232 AGTCAAGTTCTATGCTTTACAAGTTGT 59.501 33.333 14.05 14.05 31.86 3.32
896 957 8.128582 TCAAGTTCTATGCTTTACAAGTTGTTG 58.871 33.333 14.90 6.42 39.82 3.33
900 961 7.801716 TCTATGCTTTACAAGTTGTTGAAGT 57.198 32.000 14.90 6.92 37.10 3.01
901 962 7.861630 TCTATGCTTTACAAGTTGTTGAAGTC 58.138 34.615 14.90 13.73 37.10 3.01
904 965 4.788521 GCTTTACAAGTTGTTGAAGTCGGG 60.789 45.833 14.90 0.00 37.10 5.14
916 977 4.196626 TGAAGTCGGGTGTTTGGTATAG 57.803 45.455 0.00 0.00 0.00 1.31
923 984 4.019141 TCGGGTGTTTGGTATAGGATGTTT 60.019 41.667 0.00 0.00 0.00 2.83
952 1019 3.675502 GCCGTAAGAAGTTGGAGTCCTAC 60.676 52.174 15.13 15.13 43.02 3.18
962 1029 5.116882 AGTTGGAGTCCTACGATATTTTGC 58.883 41.667 16.62 0.00 34.62 3.68
1527 1594 4.065789 GTTTAGGTCTGTCTGTCCAAAGG 58.934 47.826 0.00 0.00 0.00 3.11
1732 1821 1.290203 ATGTTTGCTGACGGATAGCG 58.710 50.000 0.00 0.00 44.01 4.26
1883 1972 2.434702 CTGCCCCTACCTTTTATCTCGT 59.565 50.000 0.00 0.00 0.00 4.18
2082 2220 4.641541 TGTTTAGTCATGCAGATGGAATGG 59.358 41.667 0.00 0.00 0.00 3.16
2119 2257 8.859517 TTACAACAGCAAAACAATAACCTTAC 57.140 30.769 0.00 0.00 0.00 2.34
2427 2611 3.304057 GCAAGCACTACACAAAGGACTTC 60.304 47.826 0.00 0.00 0.00 3.01
2507 2691 7.571025 TGGAAGGGTAAGATTTTATCTGGTAC 58.429 38.462 0.00 0.00 40.13 3.34
2549 2759 3.372660 TTTTTGCGGGGTAATGTGTTC 57.627 42.857 0.00 0.00 0.00 3.18
2563 2773 7.189512 GGTAATGTGTTCTTTGCTAGCTATTG 58.810 38.462 17.23 4.92 0.00 1.90
2581 2791 8.579682 AGCTATTGAAGTTTGACAATTGTTTC 57.420 30.769 13.36 12.17 37.75 2.78
2608 2821 2.231380 TGGAAGGGAGAAGGCACCC 61.231 63.158 0.00 0.00 44.52 4.61
2880 3109 6.751888 GTGTGGATAATAAGACAATTTGTGCC 59.248 38.462 6.80 0.00 0.00 5.01
2881 3110 6.663093 TGTGGATAATAAGACAATTTGTGCCT 59.337 34.615 6.80 0.00 0.00 4.75
2925 3154 4.453819 CAGCTTTAGTTCTGACTTCCAAGG 59.546 45.833 0.00 0.00 37.33 3.61
2952 3182 7.693969 AGCATCAATTGTTTTAGCTTCTAGT 57.306 32.000 5.13 0.00 0.00 2.57
2953 3183 8.115490 AGCATCAATTGTTTTAGCTTCTAGTT 57.885 30.769 5.13 0.00 0.00 2.24
3277 3511 7.667219 TCTCTCCTTTGTTCAAGAGCAATTTAT 59.333 33.333 0.21 0.00 36.13 1.40
3354 3588 2.472695 TCTGCGAGCCTGTAAACATT 57.527 45.000 0.00 0.00 0.00 2.71
3540 3774 2.490168 GCTGAAGGTACCCTCCCAAAAA 60.490 50.000 8.74 0.00 30.89 1.94
3549 3783 4.955811 ACCCTCCCAAAAATTTCAGAAC 57.044 40.909 0.00 0.00 0.00 3.01
3594 3828 6.145209 GTCACACATATACAGATGCTCATCAC 59.855 42.308 11.90 0.00 40.22 3.06
3634 3868 4.435970 TGCCTGCAGGATGGGCTG 62.436 66.667 37.21 7.51 42.93 4.85
3648 3882 1.837439 TGGGCTGAGGATCACGTATTT 59.163 47.619 0.00 0.00 42.56 1.40
3682 3916 2.431454 CAGCTGGAGAAGGAAAAGTCC 58.569 52.381 5.57 0.00 45.35 3.85
3700 3934 2.792290 CGAAGGCGCTGACATGTCG 61.792 63.158 20.54 15.64 0.00 4.35
3786 4022 1.701847 AGATGGCAAGGAGTGAACACT 59.298 47.619 7.20 7.20 45.84 3.55
4052 4288 5.066764 TGTTTTGGACCTTCTTTTAGAACGG 59.933 40.000 0.00 0.00 32.43 4.44
4146 4382 8.784043 TCTCAACTTTTAGGAGTATTTTTCTGC 58.216 33.333 0.00 0.00 0.00 4.26
4194 4431 6.377327 AGACATGGCGTTTCCTATTAATTG 57.623 37.500 0.00 0.00 35.26 2.32
4255 4493 3.304794 CCGTCTTTATTTGGTTTTCGGCA 60.305 43.478 0.00 0.00 0.00 5.69
4340 4592 5.527511 TTGAAACATGTGCACAGTTTTTG 57.472 34.783 30.41 23.93 35.77 2.44
4347 4599 5.873712 ACATGTGCACAGTTTTTGAAATTCA 59.126 32.000 25.84 0.00 0.00 2.57
4355 4607 7.412237 GCACAGTTTTTGAAATTCATGGCTATC 60.412 37.037 0.00 0.00 0.00 2.08
4491 4762 9.833182 GTGAAAAACCATTAAAAAGAAGCAAAA 57.167 25.926 0.00 0.00 0.00 2.44
4499 4770 7.384932 CCATTAAAAAGAAGCAAAAACTCGGAT 59.615 33.333 0.00 0.00 0.00 4.18
4521 4792 7.306167 CGGATAATTCCATGAAAAATCGCAAAG 60.306 37.037 0.00 0.00 42.74 2.77
4531 4802 7.333528 TGAAAAATCGCAAAGGCTATATCTT 57.666 32.000 0.00 0.00 38.10 2.40
4567 4838 4.641645 CCCGTGCTTGCCTGTGGA 62.642 66.667 0.00 0.00 0.00 4.02
4568 4839 2.594303 CCGTGCTTGCCTGTGGAA 60.594 61.111 0.00 0.00 0.00 3.53
4569 4840 2.192861 CCGTGCTTGCCTGTGGAAA 61.193 57.895 0.00 0.00 0.00 3.13
4570 4841 1.283793 CGTGCTTGCCTGTGGAAAG 59.716 57.895 0.00 0.00 0.00 2.62
4571 4842 1.165907 CGTGCTTGCCTGTGGAAAGA 61.166 55.000 8.44 0.00 0.00 2.52
4572 4843 0.595095 GTGCTTGCCTGTGGAAAGAG 59.405 55.000 8.44 0.00 0.00 2.85
4573 4844 0.473755 TGCTTGCCTGTGGAAAGAGA 59.526 50.000 8.44 0.00 0.00 3.10
4574 4845 1.163554 GCTTGCCTGTGGAAAGAGAG 58.836 55.000 8.44 0.00 0.00 3.20
4575 4846 1.818642 CTTGCCTGTGGAAAGAGAGG 58.181 55.000 0.00 0.00 0.00 3.69
4576 4847 0.401738 TTGCCTGTGGAAAGAGAGGG 59.598 55.000 0.00 0.00 0.00 4.30
4577 4848 0.768221 TGCCTGTGGAAAGAGAGGGT 60.768 55.000 0.00 0.00 0.00 4.34
4578 4849 0.402121 GCCTGTGGAAAGAGAGGGTT 59.598 55.000 0.00 0.00 0.00 4.11
4579 4850 1.884067 GCCTGTGGAAAGAGAGGGTTG 60.884 57.143 0.00 0.00 0.00 3.77
4580 4851 1.271597 CCTGTGGAAAGAGAGGGTTGG 60.272 57.143 0.00 0.00 0.00 3.77
4581 4852 1.421646 CTGTGGAAAGAGAGGGTTGGT 59.578 52.381 0.00 0.00 0.00 3.67
4582 4853 2.637872 CTGTGGAAAGAGAGGGTTGGTA 59.362 50.000 0.00 0.00 0.00 3.25
4583 4854 3.256704 TGTGGAAAGAGAGGGTTGGTAT 58.743 45.455 0.00 0.00 0.00 2.73
4584 4855 3.655777 TGTGGAAAGAGAGGGTTGGTATT 59.344 43.478 0.00 0.00 0.00 1.89
4585 4856 4.105697 TGTGGAAAGAGAGGGTTGGTATTT 59.894 41.667 0.00 0.00 0.00 1.40
4586 4857 5.077564 GTGGAAAGAGAGGGTTGGTATTTT 58.922 41.667 0.00 0.00 0.00 1.82
4587 4858 5.538813 GTGGAAAGAGAGGGTTGGTATTTTT 59.461 40.000 0.00 0.00 0.00 1.94
4610 4881 6.879188 TTTTTCTGGTTTTGTTTCTTAGCG 57.121 33.333 0.00 0.00 0.00 4.26
4611 4882 5.821516 TTTCTGGTTTTGTTTCTTAGCGA 57.178 34.783 0.00 0.00 0.00 4.93
4612 4883 5.418310 TTCTGGTTTTGTTTCTTAGCGAG 57.582 39.130 0.00 0.00 0.00 5.03
4613 4884 3.813166 TCTGGTTTTGTTTCTTAGCGAGG 59.187 43.478 0.00 0.00 0.00 4.63
4614 4885 3.547746 TGGTTTTGTTTCTTAGCGAGGT 58.452 40.909 0.00 0.00 0.00 3.85
4615 4886 3.949113 TGGTTTTGTTTCTTAGCGAGGTT 59.051 39.130 0.00 0.00 0.00 3.50
4616 4887 4.201970 TGGTTTTGTTTCTTAGCGAGGTTG 60.202 41.667 0.00 0.00 0.00 3.77
4617 4888 4.201980 GGTTTTGTTTCTTAGCGAGGTTGT 60.202 41.667 0.00 0.00 0.00 3.32
4618 4889 5.337554 GTTTTGTTTCTTAGCGAGGTTGTT 58.662 37.500 0.00 0.00 0.00 2.83
4619 4890 5.570234 TTTGTTTCTTAGCGAGGTTGTTT 57.430 34.783 0.00 0.00 0.00 2.83
4620 4891 5.570234 TTGTTTCTTAGCGAGGTTGTTTT 57.430 34.783 0.00 0.00 0.00 2.43
4621 4892 5.164606 TGTTTCTTAGCGAGGTTGTTTTC 57.835 39.130 0.00 0.00 0.00 2.29
4622 4893 4.879545 TGTTTCTTAGCGAGGTTGTTTTCT 59.120 37.500 0.00 0.00 0.00 2.52
4623 4894 6.050432 TGTTTCTTAGCGAGGTTGTTTTCTA 58.950 36.000 0.00 0.00 0.00 2.10
4624 4895 6.708949 TGTTTCTTAGCGAGGTTGTTTTCTAT 59.291 34.615 0.00 0.00 0.00 1.98
4625 4896 6.721571 TTCTTAGCGAGGTTGTTTTCTATG 57.278 37.500 0.00 0.00 0.00 2.23
4626 4897 5.175859 TCTTAGCGAGGTTGTTTTCTATGG 58.824 41.667 0.00 0.00 0.00 2.74
4627 4898 3.418684 AGCGAGGTTGTTTTCTATGGT 57.581 42.857 0.00 0.00 0.00 3.55
4628 4899 3.751518 AGCGAGGTTGTTTTCTATGGTT 58.248 40.909 0.00 0.00 0.00 3.67
4629 4900 4.901868 AGCGAGGTTGTTTTCTATGGTTA 58.098 39.130 0.00 0.00 0.00 2.85
4630 4901 5.497474 AGCGAGGTTGTTTTCTATGGTTAT 58.503 37.500 0.00 0.00 0.00 1.89
4631 4902 5.585047 AGCGAGGTTGTTTTCTATGGTTATC 59.415 40.000 0.00 0.00 0.00 1.75
4632 4903 5.585047 GCGAGGTTGTTTTCTATGGTTATCT 59.415 40.000 0.00 0.00 0.00 1.98
4633 4904 6.093633 GCGAGGTTGTTTTCTATGGTTATCTT 59.906 38.462 0.00 0.00 0.00 2.40
4634 4905 7.361799 GCGAGGTTGTTTTCTATGGTTATCTTT 60.362 37.037 0.00 0.00 0.00 2.52
4635 4906 8.175716 CGAGGTTGTTTTCTATGGTTATCTTTC 58.824 37.037 0.00 0.00 0.00 2.62
4636 4907 9.232473 GAGGTTGTTTTCTATGGTTATCTTTCT 57.768 33.333 0.00 0.00 0.00 2.52
4637 4908 9.588096 AGGTTGTTTTCTATGGTTATCTTTCTT 57.412 29.630 0.00 0.00 0.00 2.52
4645 4916 8.281212 TCTATGGTTATCTTTCTTTCTTTGGC 57.719 34.615 0.00 0.00 0.00 4.52
4646 4917 5.722021 TGGTTATCTTTCTTTCTTTGGCC 57.278 39.130 0.00 0.00 0.00 5.36
4647 4918 5.144100 TGGTTATCTTTCTTTCTTTGGCCA 58.856 37.500 0.00 0.00 0.00 5.36
4648 4919 5.779771 TGGTTATCTTTCTTTCTTTGGCCAT 59.220 36.000 6.09 0.00 0.00 4.40
4649 4920 6.071391 TGGTTATCTTTCTTTCTTTGGCCATC 60.071 38.462 6.09 0.00 0.00 3.51
4650 4921 4.708726 ATCTTTCTTTCTTTGGCCATCG 57.291 40.909 6.09 0.00 0.00 3.84
4651 4922 2.819608 TCTTTCTTTCTTTGGCCATCGG 59.180 45.455 6.09 0.00 0.00 4.18
4652 4923 2.286365 TTCTTTCTTTGGCCATCGGT 57.714 45.000 6.09 0.00 0.00 4.69
4653 4924 2.286365 TCTTTCTTTGGCCATCGGTT 57.714 45.000 6.09 0.00 0.00 4.44
4654 4925 2.593026 TCTTTCTTTGGCCATCGGTTT 58.407 42.857 6.09 0.00 0.00 3.27
4655 4926 2.962421 TCTTTCTTTGGCCATCGGTTTT 59.038 40.909 6.09 0.00 0.00 2.43
4656 4927 4.145807 TCTTTCTTTGGCCATCGGTTTTA 58.854 39.130 6.09 0.00 0.00 1.52
4657 4928 4.770010 TCTTTCTTTGGCCATCGGTTTTAT 59.230 37.500 6.09 0.00 0.00 1.40
4658 4929 5.245075 TCTTTCTTTGGCCATCGGTTTTATT 59.755 36.000 6.09 0.00 0.00 1.40
4659 4930 6.434652 TCTTTCTTTGGCCATCGGTTTTATTA 59.565 34.615 6.09 0.00 0.00 0.98
4660 4931 5.828299 TCTTTGGCCATCGGTTTTATTAG 57.172 39.130 6.09 0.00 0.00 1.73
4661 4932 5.258051 TCTTTGGCCATCGGTTTTATTAGT 58.742 37.500 6.09 0.00 0.00 2.24
4662 4933 5.712917 TCTTTGGCCATCGGTTTTATTAGTT 59.287 36.000 6.09 0.00 0.00 2.24
4663 4934 5.986501 TTGGCCATCGGTTTTATTAGTTT 57.013 34.783 6.09 0.00 0.00 2.66
4664 4935 5.986501 TGGCCATCGGTTTTATTAGTTTT 57.013 34.783 0.00 0.00 0.00 2.43
4665 4936 7.463961 TTGGCCATCGGTTTTATTAGTTTTA 57.536 32.000 6.09 0.00 0.00 1.52
4666 4937 7.648039 TGGCCATCGGTTTTATTAGTTTTAT 57.352 32.000 0.00 0.00 0.00 1.40
4667 4938 7.484975 TGGCCATCGGTTTTATTAGTTTTATG 58.515 34.615 0.00 0.00 0.00 1.90
4668 4939 7.122948 TGGCCATCGGTTTTATTAGTTTTATGT 59.877 33.333 0.00 0.00 0.00 2.29
4669 4940 7.434013 GGCCATCGGTTTTATTAGTTTTATGTG 59.566 37.037 0.00 0.00 0.00 3.21
4670 4941 7.971722 GCCATCGGTTTTATTAGTTTTATGTGT 59.028 33.333 0.00 0.00 0.00 3.72
4671 4942 9.849166 CCATCGGTTTTATTAGTTTTATGTGTT 57.151 29.630 0.00 0.00 0.00 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 60 0.671251 GCTGGATCGGATCGTCTCTT 59.329 55.000 11.62 0.00 0.00 2.85
62 63 1.982660 TTAGCTGGATCGGATCGTCT 58.017 50.000 11.62 10.22 0.00 4.18
212 224 3.394836 GGAGTCGGGGAGCTGCTT 61.395 66.667 2.53 0.00 0.00 3.91
226 238 1.279271 ACCGAAAACTGATGGAGGGAG 59.721 52.381 0.00 0.00 0.00 4.30
533 545 4.598894 CCGCCTCCGCCAGATCTG 62.599 72.222 16.24 16.24 0.00 2.90
676 689 4.471904 TGAATGAATGACTAGCCGACTT 57.528 40.909 0.00 0.00 0.00 3.01
724 737 4.856801 ACACGATGGCGGATGGGC 62.857 66.667 0.00 0.00 43.17 5.36
725 738 2.896854 CACACGATGGCGGATGGG 60.897 66.667 0.00 0.00 43.17 4.00
738 751 0.323725 ATCCATCACCAAGGCCACAC 60.324 55.000 5.01 0.00 0.00 3.82
776 837 1.164041 AAAGAAACTGACCGGCCACG 61.164 55.000 0.00 0.00 40.55 4.94
847 908 3.542648 TCAACACGTGGTCCAAATGTAA 58.457 40.909 21.57 0.34 0.00 2.41
848 909 3.135225 CTCAACACGTGGTCCAAATGTA 58.865 45.455 21.57 0.00 0.00 2.29
849 910 1.946768 CTCAACACGTGGTCCAAATGT 59.053 47.619 21.57 0.00 0.00 2.71
850 911 1.946768 ACTCAACACGTGGTCCAAATG 59.053 47.619 21.57 0.00 0.00 2.32
851 912 2.218603 GACTCAACACGTGGTCCAAAT 58.781 47.619 21.57 0.00 0.00 2.32
856 917 1.935933 ACTTGACTCAACACGTGGTC 58.064 50.000 21.57 16.99 0.00 4.02
883 944 4.095185 CACCCGACTTCAACAACTTGTAAA 59.905 41.667 0.00 0.00 0.00 2.01
887 948 2.014128 ACACCCGACTTCAACAACTTG 58.986 47.619 0.00 0.00 0.00 3.16
889 950 2.413310 AACACCCGACTTCAACAACT 57.587 45.000 0.00 0.00 0.00 3.16
892 953 1.340211 ACCAAACACCCGACTTCAACA 60.340 47.619 0.00 0.00 0.00 3.33
893 954 1.385528 ACCAAACACCCGACTTCAAC 58.614 50.000 0.00 0.00 0.00 3.18
894 955 3.495434 ATACCAAACACCCGACTTCAA 57.505 42.857 0.00 0.00 0.00 2.69
896 957 3.196254 TCCTATACCAAACACCCGACTTC 59.804 47.826 0.00 0.00 0.00 3.01
900 961 3.109151 ACATCCTATACCAAACACCCGA 58.891 45.455 0.00 0.00 0.00 5.14
901 962 3.553828 ACATCCTATACCAAACACCCG 57.446 47.619 0.00 0.00 0.00 5.28
904 965 8.760569 CAAACAAAAACATCCTATACCAAACAC 58.239 33.333 0.00 0.00 0.00 3.32
916 977 4.612943 TCTTACGGCAAACAAAAACATCC 58.387 39.130 0.00 0.00 0.00 3.51
923 984 3.695060 TCCAACTTCTTACGGCAAACAAA 59.305 39.130 0.00 0.00 0.00 2.83
952 1019 5.400485 GCTTTAAGATGGCAGCAAAATATCG 59.600 40.000 5.19 0.00 32.17 2.92
962 1029 7.359514 GCAAGTTAAAAAGCTTTAAGATGGCAG 60.360 37.037 13.10 0.00 37.61 4.85
1498 1565 4.451900 ACAGACAGACCTAAACCTTTGTG 58.548 43.478 0.00 0.00 0.00 3.33
1911 2000 7.085746 ACCAAACCATTACGTATTTGCTAAAC 58.914 34.615 11.99 0.00 31.95 2.01
1962 2051 4.219288 GGACAATGTTTTCAAGGATCAGCT 59.781 41.667 0.00 0.00 0.00 4.24
1963 2052 4.488879 GGACAATGTTTTCAAGGATCAGC 58.511 43.478 0.00 0.00 0.00 4.26
2041 2179 2.462889 ACAAAACTGCAACATTCTGCG 58.537 42.857 0.00 0.00 45.74 5.18
2048 2186 4.803088 GCATGACTAAACAAAACTGCAACA 59.197 37.500 0.00 0.00 0.00 3.33
2082 2220 8.699749 GTTTTGCTGTTGTAATATGTTTTCCTC 58.300 33.333 0.00 0.00 0.00 3.71
2119 2257 5.695851 AACATTTAGTTTCAGTCAGCTGG 57.304 39.130 15.13 0.00 37.03 4.85
2549 2759 6.902341 TGTCAAACTTCAATAGCTAGCAAAG 58.098 36.000 18.83 13.54 0.00 2.77
2563 2773 4.359706 AGCCGAAACAATTGTCAAACTTC 58.640 39.130 12.39 10.38 0.00 3.01
2581 2791 0.976073 TCTCCCTTCCACCTAAGCCG 60.976 60.000 0.00 0.00 0.00 5.52
2768 2981 4.881850 AGTACCGGATTTGATAGCAAAAGG 59.118 41.667 9.46 15.43 46.19 3.11
2769 2982 5.220854 CCAGTACCGGATTTGATAGCAAAAG 60.221 44.000 9.46 5.25 46.19 2.27
2880 3109 6.293298 GCTGCAGTCCATTAATTGTCATCTAG 60.293 42.308 16.64 0.00 0.00 2.43
2881 3110 5.528690 GCTGCAGTCCATTAATTGTCATCTA 59.471 40.000 16.64 0.00 0.00 1.98
2925 3154 6.638168 GAAGCTAAAACAATTGATGCTTCC 57.362 37.500 25.55 16.64 45.02 3.46
2971 3201 4.641396 TCTGTCGACTGGAAATCAACATT 58.359 39.130 20.57 0.00 0.00 2.71
3168 3402 4.592942 ACTCATTAGGAACACATGTGCAT 58.407 39.130 25.68 14.92 0.00 3.96
3354 3588 2.766313 CTCACCATTTCGTCACTTCCA 58.234 47.619 0.00 0.00 0.00 3.53
3540 3774 9.657419 AACAGAACAAAAAGAATGTTCTGAAAT 57.343 25.926 36.60 25.24 37.65 2.17
3549 3783 7.008628 GTGTGACTGAACAGAACAAAAAGAATG 59.991 37.037 8.87 0.00 33.11 2.67
3594 3828 6.082338 CAGAATTTGGATTCAGTTTGACGAG 58.918 40.000 0.00 0.00 43.35 4.18
3634 3868 6.238484 CCTTGATCCAAAAATACGTGATCCTC 60.238 42.308 0.00 0.00 32.70 3.71
3648 3882 1.615116 CCAGCTGCTCCTTGATCCAAA 60.615 52.381 8.66 0.00 0.00 3.28
3682 3916 2.792290 CGACATGTCAGCGCCTTCG 61.792 63.158 24.93 5.07 39.07 3.79
3689 3923 0.870393 CCATATGCCGACATGTCAGC 59.130 55.000 24.24 24.24 37.04 4.26
3691 3925 2.093235 TGTTCCATATGCCGACATGTCA 60.093 45.455 24.93 7.42 37.04 3.58
3706 3940 0.770499 TGCAGACCTTGGATGTTCCA 59.230 50.000 0.00 0.00 46.61 3.53
4008 4244 9.806203 CAAAACAATGGCTCATAAATATCTCAA 57.194 29.630 0.00 0.00 0.00 3.02
4020 4256 2.380064 AGGTCCAAAACAATGGCTCA 57.620 45.000 0.00 0.00 40.46 4.26
4194 4431 2.333014 GCATCTAACTATGCCTCGAGC 58.667 52.381 6.99 3.23 45.31 5.03
4207 4444 1.404986 CCGTTCGACTTGGGCATCTAA 60.405 52.381 0.00 0.00 0.00 2.10
4255 4493 9.424319 GAAGAAAGGAAGAAACAAAGAAAAAGT 57.576 29.630 0.00 0.00 0.00 2.66
4307 4559 5.189625 GCACATGTTTCAAAAATGTTCACG 58.810 37.500 2.88 0.00 32.27 4.35
4308 4560 5.958949 GTGCACATGTTTCAAAAATGTTCAC 59.041 36.000 17.17 17.17 39.82 3.18
4499 4770 5.580297 GCCTTTGCGATTTTTCATGGAATTA 59.420 36.000 0.00 0.00 0.00 1.40
4531 4802 3.146066 GGGCTATATTTCACAATCGGCA 58.854 45.455 0.00 0.00 0.00 5.69
4535 4806 4.147219 GCACGGGCTATATTTCACAATC 57.853 45.455 0.00 0.00 36.96 2.67
4563 4834 4.302559 AATACCAACCCTCTCTTTCCAC 57.697 45.455 0.00 0.00 0.00 4.02
4564 4835 5.333566 AAAATACCAACCCTCTCTTTCCA 57.666 39.130 0.00 0.00 0.00 3.53
4587 4858 6.622549 TCGCTAAGAAACAAAACCAGAAAAA 58.377 32.000 0.00 0.00 0.00 1.94
4588 4859 6.197364 TCGCTAAGAAACAAAACCAGAAAA 57.803 33.333 0.00 0.00 0.00 2.29
4589 4860 5.220970 CCTCGCTAAGAAACAAAACCAGAAA 60.221 40.000 0.00 0.00 0.00 2.52
4590 4861 4.274950 CCTCGCTAAGAAACAAAACCAGAA 59.725 41.667 0.00 0.00 0.00 3.02
4591 4862 3.813166 CCTCGCTAAGAAACAAAACCAGA 59.187 43.478 0.00 0.00 0.00 3.86
4592 4863 3.564225 ACCTCGCTAAGAAACAAAACCAG 59.436 43.478 0.00 0.00 0.00 4.00
4593 4864 3.547746 ACCTCGCTAAGAAACAAAACCA 58.452 40.909 0.00 0.00 0.00 3.67
4594 4865 4.201980 ACAACCTCGCTAAGAAACAAAACC 60.202 41.667 0.00 0.00 0.00 3.27
4595 4866 4.916870 ACAACCTCGCTAAGAAACAAAAC 58.083 39.130 0.00 0.00 0.00 2.43
4596 4867 5.570234 AACAACCTCGCTAAGAAACAAAA 57.430 34.783 0.00 0.00 0.00 2.44
4597 4868 5.570234 AAACAACCTCGCTAAGAAACAAA 57.430 34.783 0.00 0.00 0.00 2.83
4598 4869 5.355910 AGAAAACAACCTCGCTAAGAAACAA 59.644 36.000 0.00 0.00 0.00 2.83
4599 4870 4.879545 AGAAAACAACCTCGCTAAGAAACA 59.120 37.500 0.00 0.00 0.00 2.83
4600 4871 5.419760 AGAAAACAACCTCGCTAAGAAAC 57.580 39.130 0.00 0.00 0.00 2.78
4601 4872 6.148811 CCATAGAAAACAACCTCGCTAAGAAA 59.851 38.462 0.00 0.00 0.00 2.52
4602 4873 5.642063 CCATAGAAAACAACCTCGCTAAGAA 59.358 40.000 0.00 0.00 0.00 2.52
4603 4874 5.175859 CCATAGAAAACAACCTCGCTAAGA 58.824 41.667 0.00 0.00 0.00 2.10
4604 4875 4.935808 ACCATAGAAAACAACCTCGCTAAG 59.064 41.667 0.00 0.00 0.00 2.18
4605 4876 4.901868 ACCATAGAAAACAACCTCGCTAA 58.098 39.130 0.00 0.00 0.00 3.09
4606 4877 4.546829 ACCATAGAAAACAACCTCGCTA 57.453 40.909 0.00 0.00 0.00 4.26
4607 4878 3.418684 ACCATAGAAAACAACCTCGCT 57.581 42.857 0.00 0.00 0.00 4.93
4608 4879 5.585047 AGATAACCATAGAAAACAACCTCGC 59.415 40.000 0.00 0.00 0.00 5.03
4609 4880 7.611213 AAGATAACCATAGAAAACAACCTCG 57.389 36.000 0.00 0.00 0.00 4.63
4610 4881 9.232473 AGAAAGATAACCATAGAAAACAACCTC 57.768 33.333 0.00 0.00 0.00 3.85
4611 4882 9.588096 AAGAAAGATAACCATAGAAAACAACCT 57.412 29.630 0.00 0.00 0.00 3.50
4619 4890 8.739972 GCCAAAGAAAGAAAGATAACCATAGAA 58.260 33.333 0.00 0.00 0.00 2.10
4620 4891 7.339466 GGCCAAAGAAAGAAAGATAACCATAGA 59.661 37.037 0.00 0.00 0.00 1.98
4621 4892 7.122650 TGGCCAAAGAAAGAAAGATAACCATAG 59.877 37.037 0.61 0.00 0.00 2.23
4622 4893 6.951198 TGGCCAAAGAAAGAAAGATAACCATA 59.049 34.615 0.61 0.00 0.00 2.74
4623 4894 5.779771 TGGCCAAAGAAAGAAAGATAACCAT 59.220 36.000 0.61 0.00 0.00 3.55
4624 4895 5.144100 TGGCCAAAGAAAGAAAGATAACCA 58.856 37.500 0.61 0.00 0.00 3.67
4625 4896 5.722021 TGGCCAAAGAAAGAAAGATAACC 57.278 39.130 0.61 0.00 0.00 2.85
4626 4897 6.030228 CGATGGCCAAAGAAAGAAAGATAAC 58.970 40.000 10.96 0.00 0.00 1.89
4627 4898 5.125417 CCGATGGCCAAAGAAAGAAAGATAA 59.875 40.000 10.96 0.00 0.00 1.75
4628 4899 4.640201 CCGATGGCCAAAGAAAGAAAGATA 59.360 41.667 10.96 0.00 0.00 1.98
4629 4900 3.445096 CCGATGGCCAAAGAAAGAAAGAT 59.555 43.478 10.96 0.00 0.00 2.40
4630 4901 2.819608 CCGATGGCCAAAGAAAGAAAGA 59.180 45.455 10.96 0.00 0.00 2.52
4631 4902 2.558359 ACCGATGGCCAAAGAAAGAAAG 59.442 45.455 10.96 0.00 0.00 2.62
4632 4903 2.593026 ACCGATGGCCAAAGAAAGAAA 58.407 42.857 10.96 0.00 0.00 2.52
4633 4904 2.286365 ACCGATGGCCAAAGAAAGAA 57.714 45.000 10.96 0.00 0.00 2.52
4634 4905 2.286365 AACCGATGGCCAAAGAAAGA 57.714 45.000 10.96 0.00 0.00 2.52
4635 4906 3.385193 AAAACCGATGGCCAAAGAAAG 57.615 42.857 10.96 0.00 0.00 2.62
4636 4907 5.476091 AATAAAACCGATGGCCAAAGAAA 57.524 34.783 10.96 0.00 0.00 2.52
4637 4908 5.712917 ACTAATAAAACCGATGGCCAAAGAA 59.287 36.000 10.96 0.00 0.00 2.52
4638 4909 5.258051 ACTAATAAAACCGATGGCCAAAGA 58.742 37.500 10.96 0.00 0.00 2.52
4639 4910 5.576447 ACTAATAAAACCGATGGCCAAAG 57.424 39.130 10.96 6.70 0.00 2.77
4640 4911 5.986501 AACTAATAAAACCGATGGCCAAA 57.013 34.783 10.96 0.00 0.00 3.28
4641 4912 5.986501 AAACTAATAAAACCGATGGCCAA 57.013 34.783 10.96 0.00 0.00 4.52
4642 4913 5.986501 AAAACTAATAAAACCGATGGCCA 57.013 34.783 8.56 8.56 0.00 5.36
4643 4914 7.434013 CACATAAAACTAATAAAACCGATGGCC 59.566 37.037 0.00 0.00 0.00 5.36
4644 4915 7.971722 ACACATAAAACTAATAAAACCGATGGC 59.028 33.333 0.00 0.00 0.00 4.40
4645 4916 9.849166 AACACATAAAACTAATAAAACCGATGG 57.151 29.630 0.00 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.