Multiple sequence alignment - TraesCS1D01G090000

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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 TraesCS1D01G090000 chr1D 100.000 4192 0 0 1 4192 76450678 76454869 0.000000e+00 7742.0
1 TraesCS1D01G090000 chr1A 95.080 3821 126 31 1 3794 77069577 77073362 0.000000e+00 5958.0
2 TraesCS1D01G090000 chr1A 93.976 166 10 0 3789 3954 254348912 254349077 6.960000e-63 252.0
3 TraesCS1D01G090000 chr1A 96.078 51 2 0 4023 4073 77073403 77073453 2.690000e-12 84.2
4 TraesCS1D01G090000 chr1B 92.883 3822 191 34 1 3794 119765076 119768844 0.000000e+00 5476.0
5 TraesCS1D01G090000 chr1B 90.871 241 18 2 3952 4189 119768842 119769081 1.880000e-83 320.0
6 TraesCS1D01G090000 chr5D 95.122 164 7 1 3788 3950 151671543 151671706 1.500000e-64 257.0
7 TraesCS1D01G090000 chr2B 95.092 163 8 0 3792 3954 616962791 616962953 1.500000e-64 257.0
8 TraesCS1D01G090000 chr7D 94.545 165 9 0 3791 3955 94123048 94122884 5.380000e-64 255.0
9 TraesCS1D01G090000 chr6D 93.143 175 11 1 3780 3953 204160192 204160018 5.380000e-64 255.0
10 TraesCS1D01G090000 chr6D 73.333 225 43 16 3742 3957 48662249 48662033 2.700000e-07 67.6
11 TraesCS1D01G090000 chr2A 95.062 162 8 0 3792 3953 189020998 189020837 5.380000e-64 255.0
12 TraesCS1D01G090000 chr7B 94.545 165 8 1 3791 3954 411745439 411745275 1.930000e-63 254.0
13 TraesCS1D01G090000 chr4A 93.902 164 10 0 3792 3955 729701870 729702033 9.000000e-62 248.0
14 TraesCS1D01G090000 chrUn 91.573 178 14 1 3789 3965 31220492 31220669 1.160000e-60 244.0


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 TraesCS1D01G090000 chr1D 76450678 76454869 4191 False 7742.0 7742 100.000 1 4192 1 chr1D.!!$F1 4191
1 TraesCS1D01G090000 chr1A 77069577 77073453 3876 False 3021.1 5958 95.579 1 4073 2 chr1A.!!$F2 4072
2 TraesCS1D01G090000 chr1B 119765076 119769081 4005 False 2898.0 5476 91.877 1 4189 2 chr1B.!!$F1 4188

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
392 413 0.108520 TTCCATAGTCGCGTGGTTCC 60.109 55.000 12.59 0.0 36.84 3.62 F
1107 1141 0.536460 TGCCCAGAAAGAACGAACCC 60.536 55.000 0.00 0.0 0.00 4.11 F
1983 2022 2.283298 CTATGGTGTCATGGTCAGTGC 58.717 52.381 0.00 0.0 34.96 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1367 1401 0.259938 ATTCCTCCCAGCCAACATCC 59.740 55.000 0.00 0.0 0.00 3.51 R
2866 2919 1.133823 TGTGGCGCATCCCAAGATTAT 60.134 47.619 10.83 0.0 36.46 1.28 R
3952 4010 1.603802 CGGAAGCATGTGTTGTCTTGT 59.396 47.619 0.00 0.0 0.00 3.16 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 61 0.877071 AGCGGCAAAAGTCATCACAG 59.123 50.000 1.45 0.00 0.00 3.66
80 82 1.154395 GCTCAAACGGAAGCTTCGC 60.154 57.895 19.91 11.88 0.00 4.70
85 87 2.117941 AAACGGAAGCTTCGCTGCAC 62.118 55.000 19.91 4.33 39.62 4.57
88 91 3.793144 GAAGCTTCGCTGCACCCG 61.793 66.667 11.40 0.00 39.62 5.28
117 120 0.319211 TTCCGCACTCCACTTGTACG 60.319 55.000 0.00 0.00 0.00 3.67
118 121 2.380410 CCGCACTCCACTTGTACGC 61.380 63.158 0.00 0.00 0.00 4.42
119 122 1.663388 CGCACTCCACTTGTACGCA 60.663 57.895 0.00 0.00 0.00 5.24
120 123 1.860078 GCACTCCACTTGTACGCAC 59.140 57.895 0.00 0.00 0.00 5.34
121 124 1.886861 GCACTCCACTTGTACGCACG 61.887 60.000 0.00 0.00 0.00 5.34
122 125 1.663702 ACTCCACTTGTACGCACGC 60.664 57.895 0.00 0.00 0.00 5.34
123 126 1.663388 CTCCACTTGTACGCACGCA 60.663 57.895 0.00 0.00 0.00 5.24
148 155 2.501222 CGGTCTTGGTCGTCGTCG 60.501 66.667 0.00 0.00 38.55 5.12
380 401 1.301716 CCGGCGGACCATTCCATAG 60.302 63.158 24.41 0.00 43.00 2.23
392 413 0.108520 TTCCATAGTCGCGTGGTTCC 60.109 55.000 12.59 0.00 36.84 3.62
436 457 0.677731 TTCCCTGCGCCAAATCTGAG 60.678 55.000 4.18 0.00 0.00 3.35
618 645 1.660264 GCCCGTTTCTTGTTTGCCG 60.660 57.895 0.00 0.00 0.00 5.69
630 657 5.571277 TCTTGTTTGCCGTAGTTGTTTAAC 58.429 37.500 0.00 0.00 37.06 2.01
649 676 8.405531 TGTTTAACTAATCTGCAGCCATTATTC 58.594 33.333 9.47 1.44 0.00 1.75
655 682 1.530293 CTGCAGCCATTATTCTCTCGC 59.470 52.381 0.00 0.00 0.00 5.03
656 683 1.134431 TGCAGCCATTATTCTCTCGCA 60.134 47.619 0.00 0.00 0.00 5.10
658 685 2.095869 GCAGCCATTATTCTCTCGCATG 60.096 50.000 0.00 0.00 0.00 4.06
659 686 3.396560 CAGCCATTATTCTCTCGCATGA 58.603 45.455 0.00 0.00 0.00 3.07
661 688 4.274214 CAGCCATTATTCTCTCGCATGAAA 59.726 41.667 0.00 0.00 0.00 2.69
662 689 4.883585 AGCCATTATTCTCTCGCATGAAAA 59.116 37.500 0.00 0.00 0.00 2.29
705 736 8.209917 GGATGACCGATGAAATAGTTTAGTTT 57.790 34.615 0.00 0.00 0.00 2.66
706 737 8.674607 GGATGACCGATGAAATAGTTTAGTTTT 58.325 33.333 0.00 0.00 0.00 2.43
777 811 3.126225 GCTCTCACCTGCTGCTGC 61.126 66.667 8.89 8.89 40.20 5.25
780 814 2.045242 CTCACCTGCTGCTGCCAT 60.045 61.111 13.47 0.00 38.71 4.40
880 914 6.809196 GCAGATGACCGAGGAATAGTATAAAG 59.191 42.308 0.00 0.00 0.00 1.85
913 947 4.622701 ACTTGTTGTTTCAGAGAAGTGC 57.377 40.909 0.00 0.00 0.00 4.40
1107 1141 0.536460 TGCCCAGAAAGAACGAACCC 60.536 55.000 0.00 0.00 0.00 4.11
1287 1321 2.897969 GTCAGTTACAAGGGTCTGAGGA 59.102 50.000 0.00 0.00 37.56 3.71
1784 1823 5.494724 TGCTTTCTTTCTGTGATCAGCTAT 58.505 37.500 0.00 0.00 41.10 2.97
1983 2022 2.283298 CTATGGTGTCATGGTCAGTGC 58.717 52.381 0.00 0.00 34.96 4.40
2236 2276 9.163894 TGTAAGAGATCTTGAATTCCCATATCT 57.836 33.333 2.27 6.24 37.40 1.98
2334 2374 3.999663 GGTTCAGAAGTCTCCATCAGTTG 59.000 47.826 0.00 0.00 0.00 3.16
2718 2765 2.601314 CGACTTTTTACATCGCCGATCA 59.399 45.455 0.00 0.00 0.00 2.92
2747 2794 3.312736 AACTGGTTGGTGAGGTTTGAT 57.687 42.857 0.00 0.00 0.00 2.57
2866 2919 2.817258 CAATTGTAACGAGCCCTTTCCA 59.183 45.455 0.00 0.00 0.00 3.53
2928 2981 4.082274 TCATTGATTTGTGTGTCGATGC 57.918 40.909 0.00 0.00 36.57 3.91
2993 3046 3.614616 GGACAACTCTTCTGCTGAATACG 59.385 47.826 6.48 1.55 0.00 3.06
3005 3058 6.640518 TCTGCTGAATACGAAGGTAAATTCT 58.359 36.000 0.00 0.00 31.15 2.40
3017 3070 1.669265 GTAAATTCTCGCTTTCCCCCG 59.331 52.381 0.00 0.00 0.00 5.73
3034 3087 1.578926 CGGAAATTCTTGCGCACCA 59.421 52.632 11.12 0.00 39.60 4.17
3038 3091 0.317799 AAATTCTTGCGCACCATGCA 59.682 45.000 11.12 0.00 45.36 3.96
3040 3093 2.552585 ATTCTTGCGCACCATGCAGC 62.553 55.000 11.12 6.20 45.36 5.25
3042 3095 2.359726 TTGCGCACCATGCAGCTA 60.360 55.556 11.12 7.90 45.36 3.32
3058 3111 7.094506 CCATGCAGCTATATAGAATCTTTTGCA 60.095 37.037 14.16 14.53 41.36 4.08
3237 3290 2.766400 CGGACCCTCTCAGAGTCGC 61.766 68.421 0.00 0.00 0.00 5.19
3238 3291 1.679305 GGACCCTCTCAGAGTCGCA 60.679 63.158 0.00 0.00 0.00 5.10
3471 3524 3.443681 TCTCGATGTACTTGATGCTCACA 59.556 43.478 0.00 0.00 0.00 3.58
3488 3541 1.065926 CACAAGCTGGTGCATCTAGGA 60.066 52.381 8.67 0.00 42.74 2.94
3561 3614 7.611855 AGATAACTCCAATGTTTCCTTAGGTTG 59.388 37.037 0.00 0.00 0.00 3.77
3646 3704 4.343231 TCAATGCCAGAAATTCTGCCTTA 58.657 39.130 17.03 3.76 42.98 2.69
3655 3713 6.369615 CCAGAAATTCTGCCTTAATTGGTTTG 59.630 38.462 17.03 0.00 42.98 2.93
3694 3752 6.017109 GCTTGTTCAACCTCTCAATGACTTTA 60.017 38.462 0.00 0.00 0.00 1.85
3797 3855 7.396540 AGATGACACAAAATGAAATACTCCC 57.603 36.000 0.00 0.00 0.00 4.30
3798 3856 7.177878 AGATGACACAAAATGAAATACTCCCT 58.822 34.615 0.00 0.00 0.00 4.20
3799 3857 6.817765 TGACACAAAATGAAATACTCCCTC 57.182 37.500 0.00 0.00 0.00 4.30
3800 3858 5.710099 TGACACAAAATGAAATACTCCCTCC 59.290 40.000 0.00 0.00 0.00 4.30
3801 3859 4.700213 ACACAAAATGAAATACTCCCTCCG 59.300 41.667 0.00 0.00 0.00 4.63
3802 3860 4.700213 CACAAAATGAAATACTCCCTCCGT 59.300 41.667 0.00 0.00 0.00 4.69
3803 3861 5.183140 CACAAAATGAAATACTCCCTCCGTT 59.817 40.000 0.00 0.00 0.00 4.44
3804 3862 5.414765 ACAAAATGAAATACTCCCTCCGTTC 59.585 40.000 0.00 0.00 0.00 3.95
3805 3863 3.840124 ATGAAATACTCCCTCCGTTCC 57.160 47.619 0.00 0.00 0.00 3.62
3806 3864 2.829023 TGAAATACTCCCTCCGTTCCT 58.171 47.619 0.00 0.00 0.00 3.36
3807 3865 3.985127 TGAAATACTCCCTCCGTTCCTA 58.015 45.455 0.00 0.00 0.00 2.94
3808 3866 4.355549 TGAAATACTCCCTCCGTTCCTAA 58.644 43.478 0.00 0.00 0.00 2.69
3809 3867 4.778958 TGAAATACTCCCTCCGTTCCTAAA 59.221 41.667 0.00 0.00 0.00 1.85
3810 3868 5.427481 TGAAATACTCCCTCCGTTCCTAAAT 59.573 40.000 0.00 0.00 0.00 1.40
3811 3869 6.612456 TGAAATACTCCCTCCGTTCCTAAATA 59.388 38.462 0.00 0.00 0.00 1.40
3812 3870 7.291651 TGAAATACTCCCTCCGTTCCTAAATAT 59.708 37.037 0.00 0.00 0.00 1.28
3813 3871 8.731591 AAATACTCCCTCCGTTCCTAAATATA 57.268 34.615 0.00 0.00 0.00 0.86
3814 3872 8.731591 AATACTCCCTCCGTTCCTAAATATAA 57.268 34.615 0.00 0.00 0.00 0.98
3815 3873 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
3816 3874 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
3817 3875 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
3818 3876 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3819 3877 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3820 3878 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3821 3879 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
3822 3880 7.441458 CCTCCGTTCCTAAATATAAGTCTTTGG 59.559 40.741 0.00 0.00 0.00 3.28
3823 3881 8.081517 TCCGTTCCTAAATATAAGTCTTTGGA 57.918 34.615 0.00 0.00 0.00 3.53
3824 3882 8.542080 TCCGTTCCTAAATATAAGTCTTTGGAA 58.458 33.333 0.00 0.00 0.00 3.53
3825 3883 9.169592 CCGTTCCTAAATATAAGTCTTTGGAAA 57.830 33.333 0.00 0.00 33.62 3.13
3850 3908 4.442401 TCCACTATGGACTACATACGGA 57.558 45.455 0.00 0.00 42.67 4.69
3851 3909 4.395625 TCCACTATGGACTACATACGGAG 58.604 47.826 0.00 0.00 42.67 4.63
3852 3910 3.057456 CCACTATGGACTACATACGGAGC 60.057 52.174 0.00 0.00 40.96 4.70
3853 3911 3.568430 CACTATGGACTACATACGGAGCA 59.432 47.826 0.00 0.00 41.03 4.26
3854 3912 4.037565 CACTATGGACTACATACGGAGCAA 59.962 45.833 0.00 0.00 41.03 3.91
3855 3913 4.647853 ACTATGGACTACATACGGAGCAAA 59.352 41.667 0.00 0.00 41.03 3.68
3856 3914 3.965379 TGGACTACATACGGAGCAAAA 57.035 42.857 0.00 0.00 0.00 2.44
3857 3915 4.481368 TGGACTACATACGGAGCAAAAT 57.519 40.909 0.00 0.00 0.00 1.82
3858 3916 4.188462 TGGACTACATACGGAGCAAAATG 58.812 43.478 0.00 0.00 0.00 2.32
3859 3917 4.081365 TGGACTACATACGGAGCAAAATGA 60.081 41.667 0.00 0.00 0.00 2.57
3860 3918 4.508124 GGACTACATACGGAGCAAAATGAG 59.492 45.833 0.00 0.00 0.00 2.90
3861 3919 5.086104 ACTACATACGGAGCAAAATGAGT 57.914 39.130 0.00 0.00 0.00 3.41
3862 3920 4.870426 ACTACATACGGAGCAAAATGAGTG 59.130 41.667 0.00 0.00 0.00 3.51
3863 3921 3.937814 ACATACGGAGCAAAATGAGTGA 58.062 40.909 0.00 0.00 0.00 3.41
3864 3922 4.323417 ACATACGGAGCAAAATGAGTGAA 58.677 39.130 0.00 0.00 0.00 3.18
3865 3923 4.943705 ACATACGGAGCAAAATGAGTGAAT 59.056 37.500 0.00 0.00 0.00 2.57
3866 3924 6.112734 ACATACGGAGCAAAATGAGTGAATA 58.887 36.000 0.00 0.00 0.00 1.75
3867 3925 6.767902 ACATACGGAGCAAAATGAGTGAATAT 59.232 34.615 0.00 0.00 0.00 1.28
3868 3926 7.931407 ACATACGGAGCAAAATGAGTGAATATA 59.069 33.333 0.00 0.00 0.00 0.86
3869 3927 8.939929 CATACGGAGCAAAATGAGTGAATATAT 58.060 33.333 0.00 0.00 0.00 0.86
3871 3929 8.311650 ACGGAGCAAAATGAGTGAATATATAC 57.688 34.615 0.00 0.00 0.00 1.47
3872 3930 8.150945 ACGGAGCAAAATGAGTGAATATATACT 58.849 33.333 0.00 0.00 0.00 2.12
3873 3931 8.651588 CGGAGCAAAATGAGTGAATATATACTC 58.348 37.037 8.23 8.23 42.77 2.59
3874 3932 9.717942 GGAGCAAAATGAGTGAATATATACTCT 57.282 33.333 14.09 1.56 42.86 3.24
3896 3954 8.031864 ACTCTAAATTGCATCTAGATACATCCG 58.968 37.037 4.54 0.00 0.00 4.18
3897 3955 7.896811 TCTAAATTGCATCTAGATACATCCGT 58.103 34.615 4.54 0.00 0.00 4.69
3898 3956 9.020731 TCTAAATTGCATCTAGATACATCCGTA 57.979 33.333 4.54 0.00 0.00 4.02
3899 3957 9.809096 CTAAATTGCATCTAGATACATCCGTAT 57.191 33.333 4.54 0.00 41.16 3.06
3900 3958 8.484641 AAATTGCATCTAGATACATCCGTATG 57.515 34.615 4.54 0.00 38.48 2.39
3902 3960 5.954335 TGCATCTAGATACATCCGTATGTG 58.046 41.667 4.54 0.00 45.99 3.21
3903 3961 5.105756 TGCATCTAGATACATCCGTATGTGG 60.106 44.000 4.54 0.00 45.99 4.17
3904 3962 5.105716 GCATCTAGATACATCCGTATGTGGT 60.106 44.000 4.54 0.00 45.99 4.16
3905 3963 6.556212 CATCTAGATACATCCGTATGTGGTC 58.444 44.000 4.54 2.46 45.99 4.02
3906 3964 5.008331 TCTAGATACATCCGTATGTGGTCC 58.992 45.833 3.56 0.00 45.99 4.46
3907 3965 3.572642 AGATACATCCGTATGTGGTCCA 58.427 45.455 3.56 0.00 45.99 4.02
3908 3966 3.964688 AGATACATCCGTATGTGGTCCAA 59.035 43.478 3.56 0.00 45.99 3.53
3909 3967 4.407621 AGATACATCCGTATGTGGTCCAAA 59.592 41.667 3.56 0.00 45.99 3.28
3910 3968 2.985896 ACATCCGTATGTGGTCCAAAG 58.014 47.619 0.00 0.00 44.79 2.77
3911 3969 2.304761 ACATCCGTATGTGGTCCAAAGT 59.695 45.455 0.00 0.00 44.79 2.66
3912 3970 3.516300 ACATCCGTATGTGGTCCAAAGTA 59.484 43.478 0.00 0.00 44.79 2.24
3913 3971 4.020039 ACATCCGTATGTGGTCCAAAGTAA 60.020 41.667 0.00 0.00 44.79 2.24
3914 3972 4.620589 TCCGTATGTGGTCCAAAGTAAA 57.379 40.909 0.00 0.00 0.00 2.01
3915 3973 4.970711 TCCGTATGTGGTCCAAAGTAAAA 58.029 39.130 0.00 0.00 0.00 1.52
3916 3974 5.562635 TCCGTATGTGGTCCAAAGTAAAAT 58.437 37.500 0.00 0.00 0.00 1.82
3917 3975 5.644636 TCCGTATGTGGTCCAAAGTAAAATC 59.355 40.000 0.00 0.00 0.00 2.17
3918 3976 5.646360 CCGTATGTGGTCCAAAGTAAAATCT 59.354 40.000 0.00 0.00 0.00 2.40
3919 3977 6.183360 CCGTATGTGGTCCAAAGTAAAATCTC 60.183 42.308 0.00 0.00 0.00 2.75
3920 3978 6.594159 CGTATGTGGTCCAAAGTAAAATCTCT 59.406 38.462 0.00 0.00 0.00 3.10
3921 3979 7.762615 CGTATGTGGTCCAAAGTAAAATCTCTA 59.237 37.037 0.00 0.00 0.00 2.43
3922 3980 7.923414 ATGTGGTCCAAAGTAAAATCTCTAC 57.077 36.000 0.00 0.00 0.00 2.59
3923 3981 6.833041 TGTGGTCCAAAGTAAAATCTCTACA 58.167 36.000 0.00 0.00 0.00 2.74
3924 3982 7.284074 TGTGGTCCAAAGTAAAATCTCTACAA 58.716 34.615 0.00 0.00 0.00 2.41
3925 3983 7.776030 TGTGGTCCAAAGTAAAATCTCTACAAA 59.224 33.333 0.00 0.00 0.00 2.83
3926 3984 8.290325 GTGGTCCAAAGTAAAATCTCTACAAAG 58.710 37.037 0.00 0.00 0.00 2.77
3927 3985 8.215050 TGGTCCAAAGTAAAATCTCTACAAAGA 58.785 33.333 0.00 0.00 0.00 2.52
3928 3986 8.504815 GGTCCAAAGTAAAATCTCTACAAAGAC 58.495 37.037 0.00 0.00 0.00 3.01
3929 3987 9.274206 GTCCAAAGTAAAATCTCTACAAAGACT 57.726 33.333 0.00 0.00 0.00 3.24
3930 3988 9.847224 TCCAAAGTAAAATCTCTACAAAGACTT 57.153 29.630 0.00 0.00 0.00 3.01
3946 4004 8.943909 ACAAAGACTTATATTTAGGAACGGAG 57.056 34.615 0.00 0.00 0.00 4.63
3947 4005 7.985752 ACAAAGACTTATATTTAGGAACGGAGG 59.014 37.037 0.00 0.00 0.00 4.30
3948 4006 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3949 4007 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3950 4008 7.017531 AGACTTATATTTAGGAACGGAGGGAT 58.982 38.462 0.00 0.00 0.00 3.85
3951 4009 7.513091 AGACTTATATTTAGGAACGGAGGGATT 59.487 37.037 0.00 0.00 0.00 3.01
3952 4010 8.731591 ACTTATATTTAGGAACGGAGGGATTA 57.268 34.615 0.00 0.00 0.00 1.75
3953 4011 8.591940 ACTTATATTTAGGAACGGAGGGATTAC 58.408 37.037 0.00 0.00 0.00 1.89
3954 4012 8.495160 TTATATTTAGGAACGGAGGGATTACA 57.505 34.615 0.00 0.00 0.00 2.41
3955 4013 5.703730 ATTTAGGAACGGAGGGATTACAA 57.296 39.130 0.00 0.00 0.00 2.41
3964 4022 3.556213 CGGAGGGATTACAAGACAACACA 60.556 47.826 0.00 0.00 0.00 3.72
4128 4189 1.336877 GTTTTCGGAATTTCGCTGGC 58.663 50.000 0.00 0.00 0.00 4.85
4160 4221 1.137086 TCTTGCATCGGCTAACTCCTC 59.863 52.381 0.00 0.00 41.91 3.71
4175 4236 2.023461 CTCCGCGAGTGCTCTACG 59.977 66.667 8.23 4.24 39.65 3.51
4191 4252 3.005898 CGGCATCATGGTCGTTCG 58.994 61.111 0.00 0.00 0.00 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
59 61 2.514505 GAAGCTTCCGTTTGAGCGCC 62.515 60.000 15.97 0.00 0.00 6.53
85 87 3.110139 CGGAATGTGGAATGCGGG 58.890 61.111 0.00 0.00 0.00 6.13
88 91 0.099436 GAGTGCGGAATGTGGAATGC 59.901 55.000 0.00 0.00 0.00 3.56
148 155 2.501610 GGGTGGAGAGATGCGGAC 59.498 66.667 0.00 0.00 0.00 4.79
293 306 4.379243 AAGGTGGCGACTGGCGAG 62.379 66.667 7.31 0.00 44.92 5.03
294 307 4.680237 CAAGGTGGCGACTGGCGA 62.680 66.667 7.31 0.00 44.92 5.54
295 308 3.583276 TACAAGGTGGCGACTGGCG 62.583 63.158 0.00 0.00 44.92 5.69
296 309 2.033194 GTACAAGGTGGCGACTGGC 61.033 63.158 0.00 0.00 42.51 4.85
297 310 1.736645 CGTACAAGGTGGCGACTGG 60.737 63.158 0.00 0.00 0.00 4.00
298 311 0.599204 AACGTACAAGGTGGCGACTG 60.599 55.000 0.00 0.00 0.00 3.51
299 312 0.319297 GAACGTACAAGGTGGCGACT 60.319 55.000 0.00 0.00 0.00 4.18
300 313 1.287041 GGAACGTACAAGGTGGCGAC 61.287 60.000 0.00 0.00 0.00 5.19
380 401 4.688419 TCGACGGAACCACGCGAC 62.688 66.667 15.93 0.00 37.43 5.19
392 413 0.429736 CAAGTACAACGCACTCGACG 59.570 55.000 0.00 0.00 39.41 5.12
436 457 7.201504 CCAATCATCTAGCACGATTGATATCAC 60.202 40.741 20.93 0.00 45.73 3.06
618 645 6.148811 TGGCTGCAGATTAGTTAAACAACTAC 59.851 38.462 20.43 0.00 35.20 2.73
630 657 5.348179 CGAGAGAATAATGGCTGCAGATTAG 59.652 44.000 20.43 0.00 0.00 1.73
638 665 3.396560 TCATGCGAGAGAATAATGGCTG 58.603 45.455 0.00 0.00 0.00 4.85
661 688 3.157087 TCCGTCGGTAAGGTCTACTTTT 58.843 45.455 11.88 0.00 40.64 2.27
662 689 2.795329 TCCGTCGGTAAGGTCTACTTT 58.205 47.619 11.88 0.00 40.64 2.66
665 692 2.032675 GTCATCCGTCGGTAAGGTCTAC 59.967 54.545 11.88 0.00 0.00 2.59
666 693 2.292267 GTCATCCGTCGGTAAGGTCTA 58.708 52.381 11.88 0.00 0.00 2.59
731 765 1.876156 GAACCAAGACAAGCAGGACAG 59.124 52.381 0.00 0.00 0.00 3.51
777 811 6.422776 AAACTATAGCACACGAGAAAATGG 57.577 37.500 0.00 0.00 0.00 3.16
880 914 5.009610 TGAAACAACAAGTATTTCTCCTGCC 59.990 40.000 9.76 0.00 34.18 4.85
913 947 1.675310 TTTGATGCGTCTGCCTGGG 60.675 57.895 7.58 0.00 41.78 4.45
1023 1057 0.232303 CCGAAACGATCATAAGGCGC 59.768 55.000 0.00 0.00 0.00 6.53
1107 1141 1.934589 TGTTCAGACACAACAGTCCG 58.065 50.000 0.00 0.00 39.34 4.79
1367 1401 0.259938 ATTCCTCCCAGCCAACATCC 59.740 55.000 0.00 0.00 0.00 3.51
1784 1823 9.901172 TCCGCTACTATAGATTATCTTCACATA 57.099 33.333 6.78 0.00 0.00 2.29
2718 2765 4.202326 CCTCACCAACCAGTTACTTGTACT 60.202 45.833 0.00 0.00 0.00 2.73
2747 2794 6.183360 CGAGTATACCTTCCATTTCCCAGTTA 60.183 42.308 0.00 0.00 0.00 2.24
2866 2919 1.133823 TGTGGCGCATCCCAAGATTAT 60.134 47.619 10.83 0.00 36.46 1.28
2928 2981 3.931468 CCTGAGTGTGACAGAAGCATTAG 59.069 47.826 0.00 0.00 37.54 1.73
2993 3046 3.377485 GGGGAAAGCGAGAATTTACCTTC 59.623 47.826 0.02 0.00 40.08 3.46
3017 3070 1.632422 CATGGTGCGCAAGAATTTCC 58.368 50.000 14.00 8.03 43.02 3.13
3034 3087 7.446319 TGTGCAAAAGATTCTATATAGCTGCAT 59.554 33.333 4.75 0.00 38.25 3.96
3038 3091 7.989741 ACTGTGTGCAAAAGATTCTATATAGCT 59.010 33.333 4.75 0.00 0.00 3.32
3058 3111 4.202419 TGGGTAGTTCAGCATAAACTGTGT 60.202 41.667 8.21 0.00 37.52 3.72
3207 3260 1.623811 GAGGGTCCGTGCATATATGGT 59.376 52.381 14.51 0.00 0.00 3.55
3415 3468 6.007936 TGTAATTACAACATTCTGGTGCAC 57.992 37.500 15.92 8.80 39.04 4.57
3445 3498 6.108687 TGAGCATCAAGTACATCGAGAAATT 58.891 36.000 0.00 0.00 45.97 1.82
3471 3524 1.630369 TGTTCCTAGATGCACCAGCTT 59.370 47.619 0.00 0.00 42.74 3.74
3488 3541 3.087031 CTGTCATGGGCAAGATTCTGTT 58.913 45.455 0.00 0.00 0.00 3.16
3646 3704 5.757808 GCAAGGTGTCATTTACAAACCAATT 59.242 36.000 0.00 0.00 40.63 2.32
3655 3713 5.181690 TGAACAAGCAAGGTGTCATTTAC 57.818 39.130 0.00 0.00 0.00 2.01
3794 3852 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
3795 3853 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
3796 3854 7.441458 CCAAAGACTTATATTTAGGAACGGAGG 59.559 40.741 0.00 0.00 0.00 4.30
3797 3855 8.202137 TCCAAAGACTTATATTTAGGAACGGAG 58.798 37.037 0.00 0.00 0.00 4.63
3798 3856 8.081517 TCCAAAGACTTATATTTAGGAACGGA 57.918 34.615 0.00 0.00 0.00 4.69
3799 3857 8.726870 TTCCAAAGACTTATATTTAGGAACGG 57.273 34.615 0.00 0.00 29.25 4.44
3829 3887 4.395625 CTCCGTATGTAGTCCATAGTGGA 58.604 47.826 0.00 0.00 45.98 4.02
3830 3888 3.057456 GCTCCGTATGTAGTCCATAGTGG 60.057 52.174 0.00 0.00 36.71 4.00
3831 3889 3.568430 TGCTCCGTATGTAGTCCATAGTG 59.432 47.826 0.00 0.00 36.71 2.74
3832 3890 3.828921 TGCTCCGTATGTAGTCCATAGT 58.171 45.455 0.00 0.00 36.71 2.12
3833 3891 4.848562 TTGCTCCGTATGTAGTCCATAG 57.151 45.455 0.00 0.00 36.71 2.23
3834 3892 5.601583 TTTTGCTCCGTATGTAGTCCATA 57.398 39.130 0.00 0.00 34.86 2.74
3835 3893 4.481368 TTTTGCTCCGTATGTAGTCCAT 57.519 40.909 0.00 0.00 37.58 3.41
3836 3894 3.965379 TTTTGCTCCGTATGTAGTCCA 57.035 42.857 0.00 0.00 0.00 4.02
3837 3895 4.439057 TCATTTTGCTCCGTATGTAGTCC 58.561 43.478 0.00 0.00 0.00 3.85
3838 3896 5.005779 CACTCATTTTGCTCCGTATGTAGTC 59.994 44.000 0.00 0.00 0.00 2.59
3839 3897 4.870426 CACTCATTTTGCTCCGTATGTAGT 59.130 41.667 0.00 0.00 0.00 2.73
3840 3898 5.109210 TCACTCATTTTGCTCCGTATGTAG 58.891 41.667 0.00 0.00 0.00 2.74
3841 3899 5.079689 TCACTCATTTTGCTCCGTATGTA 57.920 39.130 0.00 0.00 0.00 2.29
3842 3900 3.937814 TCACTCATTTTGCTCCGTATGT 58.062 40.909 0.00 0.00 0.00 2.29
3843 3901 4.944962 TTCACTCATTTTGCTCCGTATG 57.055 40.909 0.00 0.00 0.00 2.39
3845 3903 9.419297 GTATATATTCACTCATTTTGCTCCGTA 57.581 33.333 0.00 0.00 0.00 4.02
3846 3904 8.150945 AGTATATATTCACTCATTTTGCTCCGT 58.849 33.333 0.00 0.00 0.00 4.69
3847 3905 8.539770 AGTATATATTCACTCATTTTGCTCCG 57.460 34.615 0.00 0.00 0.00 4.63
3848 3906 9.717942 AGAGTATATATTCACTCATTTTGCTCC 57.282 33.333 15.06 0.00 42.99 4.70
3870 3928 8.031864 CGGATGTATCTAGATGCAATTTAGAGT 58.968 37.037 24.65 8.10 42.45 3.24
3871 3929 8.031864 ACGGATGTATCTAGATGCAATTTAGAG 58.968 37.037 24.65 14.61 42.45 2.43
3872 3930 7.896811 ACGGATGTATCTAGATGCAATTTAGA 58.103 34.615 24.65 2.73 43.21 2.10
3873 3931 9.809096 ATACGGATGTATCTAGATGCAATTTAG 57.191 33.333 24.65 16.57 36.56 1.85
3874 3932 9.586435 CATACGGATGTATCTAGATGCAATTTA 57.414 33.333 24.65 14.55 39.28 1.40
3875 3933 8.097038 ACATACGGATGTATCTAGATGCAATTT 58.903 33.333 24.65 10.85 44.77 1.82
3876 3934 7.547019 CACATACGGATGTATCTAGATGCAATT 59.453 37.037 24.65 11.54 44.82 2.32
3877 3935 7.038048 CACATACGGATGTATCTAGATGCAAT 58.962 38.462 24.65 14.37 44.82 3.56
3878 3936 6.389906 CACATACGGATGTATCTAGATGCAA 58.610 40.000 24.65 10.52 44.82 4.08
3879 3937 5.105756 CCACATACGGATGTATCTAGATGCA 60.106 44.000 23.38 23.38 44.82 3.96
3880 3938 5.105716 ACCACATACGGATGTATCTAGATGC 60.106 44.000 14.23 14.54 44.82 3.91
3881 3939 6.404844 GGACCACATACGGATGTATCTAGATG 60.405 46.154 14.23 0.00 44.82 2.90
3882 3940 5.652891 GGACCACATACGGATGTATCTAGAT 59.347 44.000 14.23 10.73 44.82 1.98
3883 3941 5.008331 GGACCACATACGGATGTATCTAGA 58.992 45.833 14.23 0.00 44.82 2.43
3884 3942 4.765339 TGGACCACATACGGATGTATCTAG 59.235 45.833 14.23 0.00 44.82 2.43
3885 3943 4.732065 TGGACCACATACGGATGTATCTA 58.268 43.478 14.23 9.44 44.82 1.98
3886 3944 3.572642 TGGACCACATACGGATGTATCT 58.427 45.455 14.23 0.00 44.82 1.98
3887 3945 4.330944 TTGGACCACATACGGATGTATC 57.669 45.455 14.23 13.80 44.82 2.24
3888 3946 4.163458 ACTTTGGACCACATACGGATGTAT 59.837 41.667 14.23 4.48 44.82 2.29
3889 3947 3.516300 ACTTTGGACCACATACGGATGTA 59.484 43.478 14.23 0.00 44.82 2.29
3891 3949 2.985896 ACTTTGGACCACATACGGATG 58.014 47.619 5.94 5.94 39.16 3.51
3892 3950 4.829872 TTACTTTGGACCACATACGGAT 57.170 40.909 0.00 0.00 0.00 4.18
3893 3951 4.620589 TTTACTTTGGACCACATACGGA 57.379 40.909 0.00 0.00 0.00 4.69
3894 3952 5.646360 AGATTTTACTTTGGACCACATACGG 59.354 40.000 0.00 0.00 0.00 4.02
3895 3953 6.594159 AGAGATTTTACTTTGGACCACATACG 59.406 38.462 0.00 0.00 0.00 3.06
3896 3954 7.923414 AGAGATTTTACTTTGGACCACATAC 57.077 36.000 0.00 0.00 0.00 2.39
3897 3955 8.598916 TGTAGAGATTTTACTTTGGACCACATA 58.401 33.333 0.00 0.00 0.00 2.29
3898 3956 7.458397 TGTAGAGATTTTACTTTGGACCACAT 58.542 34.615 0.00 0.00 0.00 3.21
3899 3957 6.833041 TGTAGAGATTTTACTTTGGACCACA 58.167 36.000 0.00 0.00 0.00 4.17
3900 3958 7.739498 TTGTAGAGATTTTACTTTGGACCAC 57.261 36.000 0.00 0.00 0.00 4.16
3901 3959 8.215050 TCTTTGTAGAGATTTTACTTTGGACCA 58.785 33.333 0.00 0.00 0.00 4.02
3902 3960 8.504815 GTCTTTGTAGAGATTTTACTTTGGACC 58.495 37.037 0.00 0.00 0.00 4.46
3903 3961 9.274206 AGTCTTTGTAGAGATTTTACTTTGGAC 57.726 33.333 0.00 0.00 0.00 4.02
3904 3962 9.847224 AAGTCTTTGTAGAGATTTTACTTTGGA 57.153 29.630 0.00 0.00 0.00 3.53
3921 3979 7.985752 CCTCCGTTCCTAAATATAAGTCTTTGT 59.014 37.037 0.00 0.00 0.00 2.83
3922 3980 7.441458 CCCTCCGTTCCTAAATATAAGTCTTTG 59.559 40.741 0.00 0.00 0.00 2.77
3923 3981 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
3924 3982 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
3925 3983 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
3926 3984 6.661304 TCCCTCCGTTCCTAAATATAAGTC 57.339 41.667 0.00 0.00 0.00 3.01
3927 3985 7.628501 AATCCCTCCGTTCCTAAATATAAGT 57.371 36.000 0.00 0.00 0.00 2.24
3928 3986 8.591072 TGTAATCCCTCCGTTCCTAAATATAAG 58.409 37.037 0.00 0.00 0.00 1.73
3929 3987 8.495160 TGTAATCCCTCCGTTCCTAAATATAA 57.505 34.615 0.00 0.00 0.00 0.98
3930 3988 8.495160 TTGTAATCCCTCCGTTCCTAAATATA 57.505 34.615 0.00 0.00 0.00 0.86
3931 3989 7.291651 TCTTGTAATCCCTCCGTTCCTAAATAT 59.708 37.037 0.00 0.00 0.00 1.28
3932 3990 6.612456 TCTTGTAATCCCTCCGTTCCTAAATA 59.388 38.462 0.00 0.00 0.00 1.40
3933 3991 5.427481 TCTTGTAATCCCTCCGTTCCTAAAT 59.573 40.000 0.00 0.00 0.00 1.40
3934 3992 4.778958 TCTTGTAATCCCTCCGTTCCTAAA 59.221 41.667 0.00 0.00 0.00 1.85
3935 3993 4.161001 GTCTTGTAATCCCTCCGTTCCTAA 59.839 45.833 0.00 0.00 0.00 2.69
3936 3994 3.703052 GTCTTGTAATCCCTCCGTTCCTA 59.297 47.826 0.00 0.00 0.00 2.94
3937 3995 2.500504 GTCTTGTAATCCCTCCGTTCCT 59.499 50.000 0.00 0.00 0.00 3.36
3938 3996 2.235402 TGTCTTGTAATCCCTCCGTTCC 59.765 50.000 0.00 0.00 0.00 3.62
3939 3997 3.604875 TGTCTTGTAATCCCTCCGTTC 57.395 47.619 0.00 0.00 0.00 3.95
3940 3998 3.071892 TGTTGTCTTGTAATCCCTCCGTT 59.928 43.478 0.00 0.00 0.00 4.44
3941 3999 2.635915 TGTTGTCTTGTAATCCCTCCGT 59.364 45.455 0.00 0.00 0.00 4.69
3942 4000 3.000727 GTGTTGTCTTGTAATCCCTCCG 58.999 50.000 0.00 0.00 0.00 4.63
3943 4001 4.015872 TGTGTTGTCTTGTAATCCCTCC 57.984 45.455 0.00 0.00 0.00 4.30
3944 4002 4.142600 GCATGTGTTGTCTTGTAATCCCTC 60.143 45.833 0.00 0.00 0.00 4.30
3945 4003 3.758554 GCATGTGTTGTCTTGTAATCCCT 59.241 43.478 0.00 0.00 0.00 4.20
3946 4004 3.758554 AGCATGTGTTGTCTTGTAATCCC 59.241 43.478 0.00 0.00 0.00 3.85
3947 4005 5.376854 AAGCATGTGTTGTCTTGTAATCC 57.623 39.130 0.00 0.00 0.00 3.01
3948 4006 5.393962 GGAAGCATGTGTTGTCTTGTAATC 58.606 41.667 0.00 0.00 0.00 1.75
3949 4007 4.083324 CGGAAGCATGTGTTGTCTTGTAAT 60.083 41.667 0.00 0.00 0.00 1.89
3950 4008 3.249799 CGGAAGCATGTGTTGTCTTGTAA 59.750 43.478 0.00 0.00 0.00 2.41
3951 4009 2.805671 CGGAAGCATGTGTTGTCTTGTA 59.194 45.455 0.00 0.00 0.00 2.41
3952 4010 1.603802 CGGAAGCATGTGTTGTCTTGT 59.396 47.619 0.00 0.00 0.00 3.16
3953 4011 2.320805 CGGAAGCATGTGTTGTCTTG 57.679 50.000 0.00 0.00 0.00 3.02
4003 4061 3.075005 CCGATCCACCGTCCACCT 61.075 66.667 0.00 0.00 0.00 4.00
4034 4092 1.063266 AGAATCTTCCTCCTCGGAGCT 60.063 52.381 7.46 0.00 44.28 4.09
4107 4168 1.402325 CCAGCGAAATTCCGAAAACCC 60.402 52.381 0.00 0.00 0.00 4.11
4114 4175 2.098298 CACGCCAGCGAAATTCCG 59.902 61.111 20.32 0.00 42.83 4.30
4137 4198 2.945668 GGAGTTAGCCGATGCAAGAATT 59.054 45.455 0.00 0.00 41.13 2.17
4142 4203 0.178068 GGAGGAGTTAGCCGATGCAA 59.822 55.000 0.00 0.00 41.13 4.08
4151 4212 1.226717 GCACTCGCGGAGGAGTTAG 60.227 63.158 6.13 0.00 44.65 2.34


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

AutoCloner maintained by Alex Coulton.