Multiple sequence alignment - TraesCS7A01G463500

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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 TraesCS7A01G463500 chr7A 100.000 3756 0 0 1 3756 660411063 660407308 0.000000e+00 6937.0
1 TraesCS7A01G463500 chr7A 90.244 123 12 0 2985 3107 636957131 636957009 1.080000e-35 161.0
2 TraesCS7A01G463500 chr7A 76.821 302 59 10 3258 3553 85029289 85029585 3.880000e-35 159.0
3 TraesCS7A01G463500 chr7B 94.534 1994 85 8 1 1979 627057759 627055775 0.000000e+00 3057.0
4 TraesCS7A01G463500 chr7B 93.573 918 37 15 2074 2987 627055496 627054597 0.000000e+00 1349.0
5 TraesCS7A01G463500 chr7B 84.652 632 64 19 3091 3716 627054598 627053994 1.930000e-167 599.0
6 TraesCS7A01G463500 chr7D 94.497 1999 77 6 1 1973 571199033 571197042 0.000000e+00 3051.0
7 TraesCS7A01G463500 chr7D 94.079 912 32 12 2085 2987 571196888 571195990 0.000000e+00 1365.0
8 TraesCS7A01G463500 chr7D 88.542 576 52 13 3152 3716 571195434 571194862 0.000000e+00 686.0
9 TraesCS7A01G463500 chr7D 77.186 263 48 9 3262 3516 99422751 99422493 3.910000e-30 143.0
10 TraesCS7A01G463500 chr7D 79.279 111 17 5 3224 3329 431077424 431077315 5.200000e-09 73.1
11 TraesCS7A01G463500 chr6B 91.080 796 55 10 1213 2000 699029750 699028963 0.000000e+00 1062.0
12 TraesCS7A01G463500 chr6B 88.889 387 40 1 2370 2756 699027951 699027568 1.220000e-129 473.0
13 TraesCS7A01G463500 chr5D 93.220 118 8 0 2978 3095 29168318 29168201 1.390000e-39 174.0
14 TraesCS7A01G463500 chr5D 79.866 149 15 9 3344 3489 547462325 547462189 1.110000e-15 95.3
15 TraesCS7A01G463500 chr1A 94.545 110 6 0 2986 3095 321291443 321291334 1.790000e-38 171.0
16 TraesCS7A01G463500 chr2A 92.982 114 8 0 2979 3092 718935047 718934934 2.320000e-37 167.0
17 TraesCS7A01G463500 chr4A 91.129 124 8 3 2974 3096 381221445 381221324 8.350000e-37 165.0
18 TraesCS7A01G463500 chr4A 91.057 123 9 2 2972 3093 625546192 625546313 8.350000e-37 165.0
19 TraesCS7A01G463500 chr4A 88.148 135 13 3 2961 3092 514346333 514346199 1.400000e-34 158.0
20 TraesCS7A01G463500 chr3A 91.597 119 10 0 2975 3093 264939820 264939938 8.350000e-37 165.0
21 TraesCS7A01G463500 chr3B 90.400 125 11 1 2986 3110 134998287 134998164 3.000000e-36 163.0
22 TraesCS7A01G463500 chr3B 75.349 215 44 7 3303 3515 411880187 411880394 1.110000e-15 95.3
23 TraesCS7A01G463500 chr3B 82.105 95 11 4 3355 3449 586158342 586158254 4.020000e-10 76.8
24 TraesCS7A01G463500 chr3B 73.543 223 47 10 3277 3496 38792625 38792412 1.450000e-09 75.0
25 TraesCS7A01G463500 chr1B 82.036 167 20 6 3273 3438 344842897 344843054 2.350000e-27 134.0
26 TraesCS7A01G463500 chr1D 79.581 191 24 9 3273 3460 267984838 267984660 5.090000e-24 122.0
27 TraesCS7A01G463500 chr4D 76.818 220 41 8 3316 3530 6526116 6525902 8.530000e-22 115.0


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 TraesCS7A01G463500 chr7A 660407308 660411063 3755 True 6937.000000 6937 100.000000 1 3756 1 chr7A.!!$R2 3755
1 TraesCS7A01G463500 chr7B 627053994 627057759 3765 True 1668.333333 3057 90.919667 1 3716 3 chr7B.!!$R1 3715
2 TraesCS7A01G463500 chr7D 571194862 571199033 4171 True 1700.666667 3051 92.372667 1 3716 3 chr7D.!!$R3 3715
3 TraesCS7A01G463500 chr6B 699027568 699029750 2182 True 767.500000 1062 89.984500 1213 2756 2 chr6B.!!$R1 1543

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
578 581 0.889186 ACATTGGCGTGGTCTCCAAC 60.889 55.0 0.0 0.0 44.23 3.77 F
1143 1170 0.033504 TCACTTTGTCACCTCCTCGC 59.966 55.0 0.0 0.0 0.00 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2146 2453 0.663568 GTCCTCGGATGGCGTATTCG 60.664 60.000 0.0 0.0 39.22 3.34 R
3078 3837 1.001633 TGGTTTCTACTGCCTCCGTTC 59.998 52.381 0.0 0.0 0.00 3.95 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
95 96 6.294731 GGGCTACTTCCTTTAATTATGCATGG 60.295 42.308 10.16 0.00 0.00 3.66
121 122 7.359849 GCATCATATACTACATGTCAGTTGCAG 60.360 40.741 0.00 0.00 0.00 4.41
126 127 2.795231 ACATGTCAGTTGCAGCCTAT 57.205 45.000 0.00 0.00 0.00 2.57
204 205 5.939883 TCAGTGATGTTTCTGATGGGTAAAG 59.060 40.000 0.00 0.00 36.04 1.85
508 511 9.143631 GCATTAACTATTTGCAGTCAAAATTCT 57.856 29.630 0.00 0.00 44.44 2.40
525 528 4.644103 ATTCTTGCCATCTTGTGCATAC 57.356 40.909 0.00 0.00 37.33 2.39
526 529 3.354948 TCTTGCCATCTTGTGCATACT 57.645 42.857 0.00 0.00 37.33 2.12
535 538 5.413833 CCATCTTGTGCATACTGAATATCCC 59.586 44.000 0.00 0.00 0.00 3.85
555 558 6.513806 TCCCAGTCAAAATACATGTCAATG 57.486 37.500 0.00 0.00 39.89 2.82
557 560 6.072008 TCCCAGTCAAAATACATGTCAATGTG 60.072 38.462 0.00 0.00 46.66 3.21
578 581 0.889186 ACATTGGCGTGGTCTCCAAC 60.889 55.000 0.00 0.00 44.23 3.77
708 734 5.892160 AATGTTTGACTCACATGGATCTG 57.108 39.130 0.00 0.00 34.97 2.90
796 823 7.015226 TGTTATACATTGCACATGCTACTTC 57.985 36.000 5.31 0.00 42.66 3.01
800 827 3.438087 ACATTGCACATGCTACTTCTGTC 59.562 43.478 5.31 0.00 42.66 3.51
818 845 1.269448 GTCAGGTAACACGTAACCGGA 59.731 52.381 9.46 11.06 40.88 5.14
819 846 1.959985 TCAGGTAACACGTAACCGGAA 59.040 47.619 9.46 0.00 40.88 4.30
820 847 2.061028 CAGGTAACACGTAACCGGAAC 58.939 52.381 9.46 4.83 40.88 3.62
821 848 1.000843 AGGTAACACGTAACCGGAACC 59.999 52.381 9.46 1.08 40.88 3.62
822 849 1.000843 GGTAACACGTAACCGGAACCT 59.999 52.381 9.46 0.00 38.78 3.50
823 850 2.061028 GTAACACGTAACCGGAACCTG 58.939 52.381 9.46 8.69 38.78 4.00
859 886 8.762645 TCTTCTGTTTCAGGATATAATCACTGT 58.237 33.333 0.00 0.00 32.72 3.55
902 929 6.433716 TGCTGTTATTGAACATGAAGGATGAA 59.566 34.615 0.00 0.00 44.53 2.57
903 930 7.039853 TGCTGTTATTGAACATGAAGGATGAAA 60.040 33.333 0.00 0.00 44.53 2.69
906 933 7.760794 TGTTATTGAACATGAAGGATGAAATGC 59.239 33.333 0.00 0.00 40.72 3.56
912 939 2.449464 TGAAGGATGAAATGCCTGTGG 58.551 47.619 0.00 0.00 33.77 4.17
926 953 5.290493 TGCCTGTGGTTAGATCGATATTT 57.710 39.130 0.00 0.00 0.00 1.40
976 1003 5.071250 ACAGTACAGAGGTTTGTATTGTGGA 59.929 40.000 11.77 0.00 46.29 4.02
997 1024 5.762711 TGGATCGAGAATTGAAACAACTTGA 59.237 36.000 0.00 0.00 28.09 3.02
1026 1053 6.587990 TGAGTTGTTTTTCTCGCATTTTCAAA 59.412 30.769 0.00 0.00 33.88 2.69
1035 1062 2.875933 TCGCATTTTCAAAAGGACGAGT 59.124 40.909 9.07 0.00 0.00 4.18
1084 1111 7.013220 ACTCAATGAGGGTATGAGCTCTTATA 58.987 38.462 16.19 2.25 43.41 0.98
1139 1166 8.153550 AGAATATGATATCACTTTGTCACCTCC 58.846 37.037 7.78 0.00 0.00 4.30
1141 1168 5.344743 TGATATCACTTTGTCACCTCCTC 57.655 43.478 0.00 0.00 0.00 3.71
1143 1170 0.033504 TCACTTTGTCACCTCCTCGC 59.966 55.000 0.00 0.00 0.00 5.03
1173 1200 6.664515 TGCCTTCGTTTTCACTTACATTTAG 58.335 36.000 0.00 0.00 0.00 1.85
1365 1392 6.843069 ATTGCAAGTGTTTTAAAATCGCTT 57.157 29.167 4.94 16.64 33.13 4.68
1600 1630 6.483640 GCACAAACCCTTCTAGGTAGATTATG 59.516 42.308 0.00 0.00 40.05 1.90
1626 1657 4.216257 TGCTGAACCTCTGTATTCTTTTGC 59.784 41.667 0.00 0.00 0.00 3.68
2004 2087 8.993121 TCTCATTATACTAAAATGCTAGCTTGC 58.007 33.333 17.23 13.56 34.89 4.01
2011 2094 3.294038 AAATGCTAGCTTGCCTGATCT 57.706 42.857 17.57 0.00 0.00 2.75
2012 2095 2.547299 ATGCTAGCTTGCCTGATCTC 57.453 50.000 17.57 0.00 0.00 2.75
2013 2096 0.467384 TGCTAGCTTGCCTGATCTCC 59.533 55.000 17.57 0.00 0.00 3.71
2014 2097 0.467384 GCTAGCTTGCCTGATCTCCA 59.533 55.000 9.15 0.00 0.00 3.86
2015 2098 1.072015 GCTAGCTTGCCTGATCTCCAT 59.928 52.381 9.15 0.00 0.00 3.41
2016 2099 2.768698 CTAGCTTGCCTGATCTCCATG 58.231 52.381 0.00 0.00 0.00 3.66
2017 2100 0.183014 AGCTTGCCTGATCTCCATGG 59.817 55.000 4.97 4.97 0.00 3.66
2018 2101 0.106819 GCTTGCCTGATCTCCATGGT 60.107 55.000 12.58 0.00 0.00 3.55
2020 2103 2.421952 GCTTGCCTGATCTCCATGGTTA 60.422 50.000 12.58 0.94 0.00 2.85
2021 2104 3.474600 CTTGCCTGATCTCCATGGTTAG 58.525 50.000 12.58 2.42 0.00 2.34
2023 2106 1.072965 GCCTGATCTCCATGGTTAGGG 59.927 57.143 12.58 8.94 0.00 3.53
2024 2107 1.072965 CCTGATCTCCATGGTTAGGGC 59.927 57.143 12.58 0.00 0.00 5.19
2025 2108 2.053244 CTGATCTCCATGGTTAGGGCT 58.947 52.381 12.58 0.00 0.00 5.19
2027 2110 0.475906 ATCTCCATGGTTAGGGCTGC 59.524 55.000 12.58 0.00 0.00 5.25
2053 2239 6.670695 AAGCACATTAAGATTGGGAAAAGT 57.329 33.333 0.00 0.00 0.00 2.66
2146 2453 0.393132 GCAGAGGTTACTTGGCTCCC 60.393 60.000 0.00 0.00 0.00 4.30
2167 2474 0.389391 AATACGCCATCCGAGGACAG 59.611 55.000 0.00 0.00 41.02 3.51
2328 3078 4.481368 TGTTCATCGTAGGCCTGTTTAT 57.519 40.909 17.99 0.14 0.00 1.40
2461 3218 2.697761 CGACGACCTGGACGTGGAT 61.698 63.158 27.34 3.98 43.97 3.41
2691 3448 4.099170 CTCCTCGCCGTCGTCGTT 62.099 66.667 0.71 0.00 36.96 3.85
2877 3635 3.000727 GCTTGTATGGTCTGTGTGGTAC 58.999 50.000 0.00 0.00 0.00 3.34
2906 3664 8.999431 TGGTCTTCATACTTTCATTCACTTTAC 58.001 33.333 0.00 0.00 0.00 2.01
2907 3665 9.220767 GGTCTTCATACTTTCATTCACTTTACT 57.779 33.333 0.00 0.00 0.00 2.24
2999 3758 7.562454 TTTTAATCAATACTCCATCCGTTCC 57.438 36.000 0.00 0.00 0.00 3.62
3000 3759 4.771114 AATCAATACTCCATCCGTTCCA 57.229 40.909 0.00 0.00 0.00 3.53
3001 3760 4.771114 ATCAATACTCCATCCGTTCCAA 57.229 40.909 0.00 0.00 0.00 3.53
3002 3761 4.561500 TCAATACTCCATCCGTTCCAAA 57.438 40.909 0.00 0.00 0.00 3.28
3003 3762 5.110814 TCAATACTCCATCCGTTCCAAAT 57.889 39.130 0.00 0.00 0.00 2.32
3004 3763 5.505780 TCAATACTCCATCCGTTCCAAATT 58.494 37.500 0.00 0.00 0.00 1.82
3005 3764 6.654959 TCAATACTCCATCCGTTCCAAATTA 58.345 36.000 0.00 0.00 0.00 1.40
3006 3765 6.540914 TCAATACTCCATCCGTTCCAAATTAC 59.459 38.462 0.00 0.00 0.00 1.89
3007 3766 4.569719 ACTCCATCCGTTCCAAATTACT 57.430 40.909 0.00 0.00 0.00 2.24
3008 3767 4.514401 ACTCCATCCGTTCCAAATTACTC 58.486 43.478 0.00 0.00 0.00 2.59
3009 3768 3.527533 TCCATCCGTTCCAAATTACTCG 58.472 45.455 0.00 0.00 0.00 4.18
3010 3769 3.055675 TCCATCCGTTCCAAATTACTCGT 60.056 43.478 0.00 0.00 0.00 4.18
3011 3770 3.308866 CCATCCGTTCCAAATTACTCGTC 59.691 47.826 0.00 0.00 0.00 4.20
3012 3771 3.663995 TCCGTTCCAAATTACTCGTCA 57.336 42.857 0.00 0.00 0.00 4.35
3013 3772 3.319755 TCCGTTCCAAATTACTCGTCAC 58.680 45.455 0.00 0.00 0.00 3.67
3014 3773 3.061322 CCGTTCCAAATTACTCGTCACA 58.939 45.455 0.00 0.00 0.00 3.58
3015 3774 3.495377 CCGTTCCAAATTACTCGTCACAA 59.505 43.478 0.00 0.00 0.00 3.33
3016 3775 4.024725 CCGTTCCAAATTACTCGTCACAAA 60.025 41.667 0.00 0.00 0.00 2.83
3017 3776 5.503498 CGTTCCAAATTACTCGTCACAAAA 58.497 37.500 0.00 0.00 0.00 2.44
3018 3777 5.966503 CGTTCCAAATTACTCGTCACAAAAA 59.033 36.000 0.00 0.00 0.00 1.94
3019 3778 6.635239 CGTTCCAAATTACTCGTCACAAAAAT 59.365 34.615 0.00 0.00 0.00 1.82
3020 3779 7.357206 CGTTCCAAATTACTCGTCACAAAAATG 60.357 37.037 0.00 0.00 0.00 2.32
3021 3780 6.442952 TCCAAATTACTCGTCACAAAAATGG 58.557 36.000 0.00 0.00 0.00 3.16
3022 3781 6.263392 TCCAAATTACTCGTCACAAAAATGGA 59.737 34.615 0.00 0.00 0.00 3.41
3023 3782 7.040062 TCCAAATTACTCGTCACAAAAATGGAT 60.040 33.333 0.00 0.00 0.00 3.41
3024 3783 7.062138 CCAAATTACTCGTCACAAAAATGGATG 59.938 37.037 0.00 0.00 0.00 3.51
3025 3784 6.817765 ATTACTCGTCACAAAAATGGATGT 57.182 33.333 0.00 0.00 0.00 3.06
3026 3785 7.915293 ATTACTCGTCACAAAAATGGATGTA 57.085 32.000 0.00 0.00 0.00 2.29
3027 3786 7.915293 TTACTCGTCACAAAAATGGATGTAT 57.085 32.000 0.00 0.00 0.00 2.29
3028 3787 6.422776 ACTCGTCACAAAAATGGATGTATC 57.577 37.500 0.00 0.00 0.00 2.24
3029 3788 6.173339 ACTCGTCACAAAAATGGATGTATCT 58.827 36.000 0.00 0.00 0.00 1.98
3030 3789 7.327975 ACTCGTCACAAAAATGGATGTATCTA 58.672 34.615 0.00 0.00 0.00 1.98
3031 3790 7.492669 ACTCGTCACAAAAATGGATGTATCTAG 59.507 37.037 0.00 0.00 0.00 2.43
3032 3791 7.552459 TCGTCACAAAAATGGATGTATCTAGA 58.448 34.615 0.00 0.00 0.00 2.43
3033 3792 8.038351 TCGTCACAAAAATGGATGTATCTAGAA 58.962 33.333 0.00 0.00 0.00 2.10
3034 3793 8.116753 CGTCACAAAAATGGATGTATCTAGAAC 58.883 37.037 0.00 0.00 0.00 3.01
3035 3794 9.167311 GTCACAAAAATGGATGTATCTAGAACT 57.833 33.333 0.00 0.00 0.00 3.01
3064 3823 6.537453 ACATCTAGATACATCCATACCTGC 57.463 41.667 4.54 0.00 0.00 4.85
3065 3824 5.126222 ACATCTAGATACATCCATACCTGCG 59.874 44.000 4.54 0.00 0.00 5.18
3066 3825 4.918588 TCTAGATACATCCATACCTGCGA 58.081 43.478 0.00 0.00 0.00 5.10
3067 3826 5.510430 TCTAGATACATCCATACCTGCGAT 58.490 41.667 0.00 0.00 0.00 4.58
3068 3827 6.659824 TCTAGATACATCCATACCTGCGATA 58.340 40.000 0.00 0.00 0.00 2.92
3069 3828 7.116736 TCTAGATACATCCATACCTGCGATAA 58.883 38.462 0.00 0.00 0.00 1.75
3070 3829 6.605471 AGATACATCCATACCTGCGATAAA 57.395 37.500 0.00 0.00 0.00 1.40
3071 3830 7.187824 AGATACATCCATACCTGCGATAAAT 57.812 36.000 0.00 0.00 0.00 1.40
3072 3831 8.306313 AGATACATCCATACCTGCGATAAATA 57.694 34.615 0.00 0.00 0.00 1.40
3073 3832 8.758829 AGATACATCCATACCTGCGATAAATAA 58.241 33.333 0.00 0.00 0.00 1.40
3074 3833 9.547753 GATACATCCATACCTGCGATAAATAAT 57.452 33.333 0.00 0.00 0.00 1.28
3075 3834 9.905713 ATACATCCATACCTGCGATAAATAATT 57.094 29.630 0.00 0.00 0.00 1.40
3076 3835 8.268850 ACATCCATACCTGCGATAAATAATTC 57.731 34.615 0.00 0.00 0.00 2.17
3077 3836 7.882791 ACATCCATACCTGCGATAAATAATTCA 59.117 33.333 0.00 0.00 0.00 2.57
3078 3837 7.905604 TCCATACCTGCGATAAATAATTCAG 57.094 36.000 0.00 0.00 0.00 3.02
3079 3838 7.676004 TCCATACCTGCGATAAATAATTCAGA 58.324 34.615 0.00 0.00 0.00 3.27
3080 3839 8.154203 TCCATACCTGCGATAAATAATTCAGAA 58.846 33.333 0.00 0.00 0.00 3.02
3081 3840 8.230486 CCATACCTGCGATAAATAATTCAGAAC 58.770 37.037 0.00 0.00 0.00 3.01
3082 3841 6.287107 ACCTGCGATAAATAATTCAGAACG 57.713 37.500 0.00 0.00 0.00 3.95
3083 3842 5.236478 ACCTGCGATAAATAATTCAGAACGG 59.764 40.000 0.00 0.00 0.00 4.44
3084 3843 5.465390 CCTGCGATAAATAATTCAGAACGGA 59.535 40.000 0.00 0.00 0.00 4.69
3085 3844 6.346919 CCTGCGATAAATAATTCAGAACGGAG 60.347 42.308 0.00 0.00 36.71 4.63
3086 3845 5.465390 TGCGATAAATAATTCAGAACGGAGG 59.535 40.000 0.00 0.00 0.00 4.30
3089 3848 6.346919 CGATAAATAATTCAGAACGGAGGCAG 60.347 42.308 0.00 0.00 0.00 4.85
3252 4508 8.891671 ATGCAATTTTCTACAGTGTGAAAAAT 57.108 26.923 24.36 21.22 42.80 1.82
3329 4588 2.093869 ACAGTACACTTTCACACGTGGT 60.094 45.455 21.57 8.52 35.51 4.16
3407 4668 4.974399 TGGGCCGGAATTTTGTTTATTTT 58.026 34.783 5.05 0.00 0.00 1.82
3481 4747 7.825681 TGTTCAACATGTATAAGTTTCCATGG 58.174 34.615 4.97 4.97 39.14 3.66
3482 4748 7.667635 TGTTCAACATGTATAAGTTTCCATGGA 59.332 33.333 11.44 11.44 39.14 3.41
3564 4832 2.557452 CCCAGGAGCTTGGTTACCATTT 60.557 50.000 4.38 0.00 36.45 2.32
3585 4853 2.811431 TGCATTTTCCATTTCGACTCGT 59.189 40.909 0.00 0.00 0.00 4.18
3599 4867 7.515957 TTTCGACTCGTAGTATTCCATTTTC 57.484 36.000 0.00 0.00 0.00 2.29
3600 4868 6.198650 TCGACTCGTAGTATTCCATTTTCA 57.801 37.500 0.00 0.00 0.00 2.69
3606 4874 6.046593 TCGTAGTATTCCATTTTCAATCGCT 58.953 36.000 0.00 0.00 0.00 4.93
3609 4877 2.652941 TTCCATTTTCAATCGCTGCC 57.347 45.000 0.00 0.00 0.00 4.85
3636 4904 4.323477 CCCCCAAACTGCCGACGA 62.323 66.667 0.00 0.00 0.00 4.20
3644 4912 3.554692 CTGCCGACGATTCGCACC 61.555 66.667 5.86 0.00 44.43 5.01
3645 4913 4.365505 TGCCGACGATTCGCACCA 62.366 61.111 5.86 0.00 44.43 4.17
3692 4962 1.864711 CGGCCCATTGTGTAGATAACG 59.135 52.381 0.00 0.00 0.00 3.18
3715 4985 2.237893 AGGTACTACCCCATCCGTTTTG 59.762 50.000 1.19 0.00 39.75 2.44
3716 4986 2.236893 GGTACTACCCCATCCGTTTTGA 59.763 50.000 0.00 0.00 30.04 2.69
3717 4987 3.118149 GGTACTACCCCATCCGTTTTGAT 60.118 47.826 0.00 0.00 30.04 2.57
3718 4988 3.732048 ACTACCCCATCCGTTTTGATT 57.268 42.857 0.00 0.00 0.00 2.57
3719 4989 4.042271 ACTACCCCATCCGTTTTGATTT 57.958 40.909 0.00 0.00 0.00 2.17
3720 4990 4.412843 ACTACCCCATCCGTTTTGATTTT 58.587 39.130 0.00 0.00 0.00 1.82
3721 4991 4.836175 ACTACCCCATCCGTTTTGATTTTT 59.164 37.500 0.00 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
95 96 6.424812 TGCAACTGACATGTAGTATATGATGC 59.575 38.462 13.28 13.43 0.00 3.91
101 102 4.405680 AGGCTGCAACTGACATGTAGTATA 59.594 41.667 0.00 0.00 33.63 1.47
126 127 7.936847 ACTAACAACCAACTATCACTGATTTGA 59.063 33.333 0.00 0.00 0.00 2.69
204 205 5.186996 TCAAACTTGAATGTTTCTGGAGC 57.813 39.130 0.00 0.00 37.98 4.70
236 237 3.826157 ACAGCAAAGCCACTTAAGCATTA 59.174 39.130 1.29 0.00 30.53 1.90
411 414 3.448686 CTCGGGTAGTTTGCTGACATAG 58.551 50.000 0.00 0.00 0.00 2.23
508 511 3.070476 TCAGTATGCACAAGATGGCAA 57.930 42.857 0.00 0.00 44.20 4.52
525 528 8.455903 ACATGTATTTTGACTGGGATATTCAG 57.544 34.615 0.00 5.73 38.16 3.02
526 529 8.052141 TGACATGTATTTTGACTGGGATATTCA 58.948 33.333 0.00 0.00 0.00 2.57
535 538 7.861872 TGTTCACATTGACATGTATTTTGACTG 59.138 33.333 0.00 0.00 42.14 3.51
555 558 0.517316 GAGACCACGCCAATGTTCAC 59.483 55.000 0.00 0.00 0.00 3.18
557 560 0.605319 TGGAGACCACGCCAATGTTC 60.605 55.000 0.00 0.00 42.60 3.18
569 572 2.069273 CAGAATGTCACGTTGGAGACC 58.931 52.381 1.75 0.00 33.42 3.85
578 581 7.912949 TTTCAAAGAAATTCAGAATGTCACG 57.087 32.000 14.77 3.84 37.40 4.35
683 709 7.014518 TCAGATCCATGTGAGTCAAACATTTTT 59.985 33.333 0.00 0.00 36.10 1.94
796 823 2.322161 CGGTTACGTGTTACCTGACAG 58.678 52.381 0.00 0.00 34.81 3.51
800 827 2.061028 GTTCCGGTTACGTGTTACCTG 58.939 52.381 0.00 0.00 38.78 4.00
818 845 4.526970 ACAGAAGAACATGAACACAGGTT 58.473 39.130 0.00 0.00 40.40 3.50
819 846 4.156455 ACAGAAGAACATGAACACAGGT 57.844 40.909 0.00 0.00 0.00 4.00
820 847 5.066375 TGAAACAGAAGAACATGAACACAGG 59.934 40.000 0.00 0.00 0.00 4.00
821 848 6.122850 TGAAACAGAAGAACATGAACACAG 57.877 37.500 0.00 0.00 0.00 3.66
822 849 5.066375 CCTGAAACAGAAGAACATGAACACA 59.934 40.000 0.00 0.00 32.44 3.72
823 850 5.296780 TCCTGAAACAGAAGAACATGAACAC 59.703 40.000 0.00 0.00 32.44 3.32
836 863 8.321353 ACAACAGTGATTATATCCTGAAACAGA 58.679 33.333 0.00 0.00 34.09 3.41
838 865 8.729756 CAACAACAGTGATTATATCCTGAAACA 58.270 33.333 0.00 0.00 34.09 2.83
859 886 3.057104 CAGCAATCATCAGCCTTCAACAA 60.057 43.478 0.00 0.00 0.00 2.83
902 929 3.845781 ATCGATCTAACCACAGGCATT 57.154 42.857 0.00 0.00 0.00 3.56
903 930 5.489792 AATATCGATCTAACCACAGGCAT 57.510 39.130 0.00 0.00 0.00 4.40
906 933 9.489084 TCAATTAAATATCGATCTAACCACAGG 57.511 33.333 0.00 0.00 0.00 4.00
936 963 4.591498 TGTACTGTGGTTCACTTGGTAGAT 59.409 41.667 0.00 0.00 35.11 1.98
950 977 5.305585 ACAATACAAACCTCTGTACTGTGG 58.694 41.667 16.62 16.62 39.91 4.17
974 1001 6.241207 TCAAGTTGTTTCAATTCTCGATCC 57.759 37.500 2.11 0.00 0.00 3.36
976 1003 9.778993 CATTATCAAGTTGTTTCAATTCTCGAT 57.221 29.630 2.11 0.00 0.00 3.59
997 1024 8.816640 AAAATGCGAGAAAAACAACTCATTAT 57.183 26.923 0.00 0.00 33.86 1.28
1026 1053 1.913762 CTGACCCCCACTCGTCCTT 60.914 63.158 0.00 0.00 0.00 3.36
1035 1062 0.754957 CAGTTTGTTGCTGACCCCCA 60.755 55.000 0.00 0.00 36.12 4.96
1084 1111 5.067283 AGCGATTTTCAACAAAACTGTAGGT 59.933 36.000 0.00 0.00 34.24 3.08
1143 1170 2.554032 AGTGAAAACGAAGGCAGAATGG 59.446 45.455 0.00 0.00 35.86 3.16
1317 1344 3.627395 AAGGTCCAGCATCGAATACAA 57.373 42.857 0.00 0.00 0.00 2.41
1324 1351 4.275689 TGCAATAATTAAGGTCCAGCATCG 59.724 41.667 0.00 0.00 0.00 3.84
1365 1392 3.153919 GTGTTCCCTGAAATGGCAAGTA 58.846 45.455 0.00 0.00 0.00 2.24
1600 1630 6.749923 AAAGAATACAGAGGTTCAGCAATC 57.250 37.500 0.00 0.00 0.00 2.67
1626 1657 5.355350 ACGGCATCTGAAATTTTTCTAGGAG 59.645 40.000 4.80 0.00 38.02 3.69
1935 1966 4.712763 CAAAGCAGACAGGTTCGATTAAC 58.287 43.478 0.00 0.00 36.83 2.01
2000 2083 2.431954 AACCATGGAGATCAGGCAAG 57.568 50.000 21.47 0.00 0.00 4.01
2004 2087 1.072965 GCCCTAACCATGGAGATCAGG 59.927 57.143 21.47 15.42 0.00 3.86
2011 2094 1.517238 TATGCAGCCCTAACCATGGA 58.483 50.000 21.47 0.00 0.00 3.41
2012 2095 2.233271 CTTATGCAGCCCTAACCATGG 58.767 52.381 11.19 11.19 0.00 3.66
2013 2096 1.610522 GCTTATGCAGCCCTAACCATG 59.389 52.381 0.00 0.00 43.65 3.66
2014 2097 1.986882 GCTTATGCAGCCCTAACCAT 58.013 50.000 0.00 0.00 43.65 3.55
2015 2098 3.494850 GCTTATGCAGCCCTAACCA 57.505 52.632 0.00 0.00 43.65 3.67
2027 2110 8.253113 ACTTTTCCCAATCTTAATGTGCTTATG 58.747 33.333 0.00 0.00 0.00 1.90
2146 2453 0.663568 GTCCTCGGATGGCGTATTCG 60.664 60.000 0.00 0.00 39.22 3.34
2167 2474 1.065418 ACATCTGATTTCCGGGTCACC 60.065 52.381 0.00 0.00 0.00 4.02
2305 2612 2.851263 ACAGGCCTACGATGAACAAA 57.149 45.000 3.98 0.00 0.00 2.83
2438 3195 3.998672 GTCCAGGTCGTCGCCCAA 61.999 66.667 0.00 0.00 0.00 4.12
2461 3218 3.241530 AGGAACCTGCACGCCTCA 61.242 61.111 0.00 0.00 0.00 3.86
2853 3610 1.460743 CACACAGACCATACAAGCACG 59.539 52.381 0.00 0.00 0.00 5.34
2877 3635 6.652481 AGTGAATGAAAGTATGAAGACCACTG 59.348 38.462 0.00 0.00 0.00 3.66
2921 3679 4.660938 AAGTGAAGTGCCCCGCCC 62.661 66.667 0.00 0.00 0.00 6.13
2979 3738 4.771114 TGGAACGGATGGAGTATTGATT 57.229 40.909 0.00 0.00 0.00 2.57
2980 3739 4.771114 TTGGAACGGATGGAGTATTGAT 57.229 40.909 0.00 0.00 0.00 2.57
2981 3740 4.561500 TTTGGAACGGATGGAGTATTGA 57.438 40.909 0.00 0.00 0.00 2.57
2982 3741 5.835113 AATTTGGAACGGATGGAGTATTG 57.165 39.130 0.00 0.00 0.00 1.90
2983 3742 6.659824 AGTAATTTGGAACGGATGGAGTATT 58.340 36.000 0.00 0.00 0.00 1.89
2984 3743 6.248569 AGTAATTTGGAACGGATGGAGTAT 57.751 37.500 0.00 0.00 0.00 2.12
2985 3744 5.667466 GAGTAATTTGGAACGGATGGAGTA 58.333 41.667 0.00 0.00 0.00 2.59
2986 3745 4.514401 GAGTAATTTGGAACGGATGGAGT 58.486 43.478 0.00 0.00 0.00 3.85
2987 3746 3.555956 CGAGTAATTTGGAACGGATGGAG 59.444 47.826 0.00 0.00 0.00 3.86
2988 3747 3.055675 ACGAGTAATTTGGAACGGATGGA 60.056 43.478 0.00 0.00 0.00 3.41
2989 3748 3.267483 ACGAGTAATTTGGAACGGATGG 58.733 45.455 0.00 0.00 0.00 3.51
2990 3749 3.930229 TGACGAGTAATTTGGAACGGATG 59.070 43.478 0.00 0.00 0.00 3.51
2991 3750 3.930848 GTGACGAGTAATTTGGAACGGAT 59.069 43.478 0.00 0.00 0.00 4.18
2992 3751 3.243805 TGTGACGAGTAATTTGGAACGGA 60.244 43.478 0.00 0.00 0.00 4.69
2993 3752 3.061322 TGTGACGAGTAATTTGGAACGG 58.939 45.455 0.00 0.00 0.00 4.44
2994 3753 4.718858 TTGTGACGAGTAATTTGGAACG 57.281 40.909 0.00 0.00 0.00 3.95
2995 3754 7.096230 CCATTTTTGTGACGAGTAATTTGGAAC 60.096 37.037 0.00 0.00 0.00 3.62
2996 3755 6.920758 CCATTTTTGTGACGAGTAATTTGGAA 59.079 34.615 0.00 0.00 0.00 3.53
2997 3756 6.263392 TCCATTTTTGTGACGAGTAATTTGGA 59.737 34.615 0.00 0.00 0.00 3.53
2998 3757 6.442952 TCCATTTTTGTGACGAGTAATTTGG 58.557 36.000 0.00 0.00 0.00 3.28
2999 3758 7.594758 ACATCCATTTTTGTGACGAGTAATTTG 59.405 33.333 0.00 0.00 0.00 2.32
3000 3759 7.657336 ACATCCATTTTTGTGACGAGTAATTT 58.343 30.769 0.00 0.00 0.00 1.82
3001 3760 7.214467 ACATCCATTTTTGTGACGAGTAATT 57.786 32.000 0.00 0.00 0.00 1.40
3002 3761 6.817765 ACATCCATTTTTGTGACGAGTAAT 57.182 33.333 0.00 0.00 0.00 1.89
3003 3762 7.822334 AGATACATCCATTTTTGTGACGAGTAA 59.178 33.333 0.00 0.00 0.00 2.24
3004 3763 7.327975 AGATACATCCATTTTTGTGACGAGTA 58.672 34.615 0.00 0.00 0.00 2.59
3005 3764 6.173339 AGATACATCCATTTTTGTGACGAGT 58.827 36.000 0.00 0.00 0.00 4.18
3006 3765 6.668541 AGATACATCCATTTTTGTGACGAG 57.331 37.500 0.00 0.00 0.00 4.18
3007 3766 7.552459 TCTAGATACATCCATTTTTGTGACGA 58.448 34.615 0.00 0.00 0.00 4.20
3008 3767 7.770801 TCTAGATACATCCATTTTTGTGACG 57.229 36.000 0.00 0.00 0.00 4.35
3009 3768 9.167311 AGTTCTAGATACATCCATTTTTGTGAC 57.833 33.333 0.00 0.00 0.00 3.67
3038 3797 8.700051 GCAGGTATGGATGTATCTAGATGTATT 58.300 37.037 15.79 0.00 0.00 1.89
3039 3798 7.013750 CGCAGGTATGGATGTATCTAGATGTAT 59.986 40.741 15.79 9.11 0.00 2.29
3040 3799 6.318900 CGCAGGTATGGATGTATCTAGATGTA 59.681 42.308 15.79 4.44 0.00 2.29
3041 3800 5.126222 CGCAGGTATGGATGTATCTAGATGT 59.874 44.000 15.79 1.25 0.00 3.06
3042 3801 5.358160 TCGCAGGTATGGATGTATCTAGATG 59.642 44.000 15.79 0.00 0.00 2.90
3043 3802 5.510430 TCGCAGGTATGGATGTATCTAGAT 58.490 41.667 10.73 10.73 0.00 1.98
3044 3803 4.918588 TCGCAGGTATGGATGTATCTAGA 58.081 43.478 0.00 0.00 0.00 2.43
3045 3804 5.843673 ATCGCAGGTATGGATGTATCTAG 57.156 43.478 0.00 0.00 0.00 2.43
3046 3805 7.712204 TTTATCGCAGGTATGGATGTATCTA 57.288 36.000 0.00 0.00 0.00 1.98
3047 3806 6.605471 TTTATCGCAGGTATGGATGTATCT 57.395 37.500 0.00 0.00 0.00 1.98
3048 3807 8.942338 TTATTTATCGCAGGTATGGATGTATC 57.058 34.615 0.00 0.00 0.00 2.24
3049 3808 9.905713 AATTATTTATCGCAGGTATGGATGTAT 57.094 29.630 0.00 0.00 0.00 2.29
3050 3809 9.378551 GAATTATTTATCGCAGGTATGGATGTA 57.621 33.333 0.00 0.00 0.00 2.29
3051 3810 7.882791 TGAATTATTTATCGCAGGTATGGATGT 59.117 33.333 0.00 0.00 0.00 3.06
3052 3811 8.267620 TGAATTATTTATCGCAGGTATGGATG 57.732 34.615 0.00 0.00 0.00 3.51
3053 3812 8.321353 TCTGAATTATTTATCGCAGGTATGGAT 58.679 33.333 0.00 0.00 0.00 3.41
3054 3813 7.676004 TCTGAATTATTTATCGCAGGTATGGA 58.324 34.615 0.00 0.00 0.00 3.41
3055 3814 7.905604 TCTGAATTATTTATCGCAGGTATGG 57.094 36.000 0.00 0.00 0.00 2.74
3056 3815 7.952101 CGTTCTGAATTATTTATCGCAGGTATG 59.048 37.037 0.00 0.00 0.00 2.39
3057 3816 7.117812 CCGTTCTGAATTATTTATCGCAGGTAT 59.882 37.037 0.00 0.00 0.00 2.73
3058 3817 6.422701 CCGTTCTGAATTATTTATCGCAGGTA 59.577 38.462 0.00 0.00 0.00 3.08
3059 3818 5.236478 CCGTTCTGAATTATTTATCGCAGGT 59.764 40.000 0.00 0.00 0.00 4.00
3060 3819 5.465390 TCCGTTCTGAATTATTTATCGCAGG 59.535 40.000 0.00 0.00 0.00 4.85
3061 3820 6.346919 CCTCCGTTCTGAATTATTTATCGCAG 60.347 42.308 0.00 0.00 0.00 5.18
3062 3821 5.465390 CCTCCGTTCTGAATTATTTATCGCA 59.535 40.000 0.00 0.00 0.00 5.10
3063 3822 5.614887 GCCTCCGTTCTGAATTATTTATCGC 60.615 44.000 0.00 0.00 0.00 4.58
3064 3823 5.465390 TGCCTCCGTTCTGAATTATTTATCG 59.535 40.000 0.00 0.00 0.00 2.92
3065 3824 6.483640 ACTGCCTCCGTTCTGAATTATTTATC 59.516 38.462 0.00 0.00 0.00 1.75
3066 3825 6.357367 ACTGCCTCCGTTCTGAATTATTTAT 58.643 36.000 0.00 0.00 0.00 1.40
3067 3826 5.741011 ACTGCCTCCGTTCTGAATTATTTA 58.259 37.500 0.00 0.00 0.00 1.40
3068 3827 4.589908 ACTGCCTCCGTTCTGAATTATTT 58.410 39.130 0.00 0.00 0.00 1.40
3069 3828 4.222124 ACTGCCTCCGTTCTGAATTATT 57.778 40.909 0.00 0.00 0.00 1.40
3070 3829 3.914426 ACTGCCTCCGTTCTGAATTAT 57.086 42.857 0.00 0.00 0.00 1.28
3071 3830 4.021229 TCTACTGCCTCCGTTCTGAATTA 58.979 43.478 0.00 0.00 0.00 1.40
3072 3831 2.832129 TCTACTGCCTCCGTTCTGAATT 59.168 45.455 0.00 0.00 0.00 2.17
3073 3832 2.457598 TCTACTGCCTCCGTTCTGAAT 58.542 47.619 0.00 0.00 0.00 2.57
3074 3833 1.919240 TCTACTGCCTCCGTTCTGAA 58.081 50.000 0.00 0.00 0.00 3.02
3075 3834 1.919240 TTCTACTGCCTCCGTTCTGA 58.081 50.000 0.00 0.00 0.00 3.27
3076 3835 2.338500 GTTTCTACTGCCTCCGTTCTG 58.662 52.381 0.00 0.00 0.00 3.02
3077 3836 1.275573 GGTTTCTACTGCCTCCGTTCT 59.724 52.381 0.00 0.00 0.00 3.01
3078 3837 1.001633 TGGTTTCTACTGCCTCCGTTC 59.998 52.381 0.00 0.00 0.00 3.95
3079 3838 1.053424 TGGTTTCTACTGCCTCCGTT 58.947 50.000 0.00 0.00 0.00 4.44
3080 3839 1.002087 CTTGGTTTCTACTGCCTCCGT 59.998 52.381 0.00 0.00 0.00 4.69
3081 3840 1.726853 CTTGGTTTCTACTGCCTCCG 58.273 55.000 0.00 0.00 0.00 4.63
3082 3841 1.003696 AGCTTGGTTTCTACTGCCTCC 59.996 52.381 0.00 0.00 0.00 4.30
3083 3842 2.289694 TGAGCTTGGTTTCTACTGCCTC 60.290 50.000 0.00 0.00 0.00 4.70
3084 3843 1.699634 TGAGCTTGGTTTCTACTGCCT 59.300 47.619 0.00 0.00 0.00 4.75
3085 3844 2.185004 TGAGCTTGGTTTCTACTGCC 57.815 50.000 0.00 0.00 0.00 4.85
3086 3845 3.077359 ACATGAGCTTGGTTTCTACTGC 58.923 45.455 0.00 0.00 0.00 4.40
3110 3869 3.181485 GGGGAGAATCGTTCTACTGTGAG 60.181 52.174 9.04 0.00 40.62 3.51
3117 3876 2.504175 CCTTTGGGGGAGAATCGTTCTA 59.496 50.000 1.08 0.00 40.87 2.10
3353 4614 7.481275 AAACAACCAGCACATTTTAGAAATG 57.519 32.000 10.86 10.86 0.00 2.32
3371 4632 1.395262 CGGCCCAACAACAAAAACAAC 59.605 47.619 0.00 0.00 0.00 3.32
3460 4721 9.874205 AAAATCCATGGAAACTTATACATGTTG 57.126 29.630 20.67 0.00 39.14 3.33
3528 4795 1.341080 CTGGGGCTTGGTGTTTGAAT 58.659 50.000 0.00 0.00 0.00 2.57
3535 4802 3.215587 AAGCTCCTGGGGCTTGGTG 62.216 63.158 32.11 0.00 46.53 4.17
3564 4832 2.811431 ACGAGTCGAAATGGAAAATGCA 59.189 40.909 21.50 0.00 0.00 3.96
3585 4853 5.008613 GGCAGCGATTGAAAATGGAATACTA 59.991 40.000 0.00 0.00 0.00 1.82
3606 4874 4.440829 GGGGGAAGAATGGCGGCA 62.441 66.667 16.34 16.34 0.00 5.69
3609 4877 0.611896 AGTTTGGGGGAAGAATGGCG 60.612 55.000 0.00 0.00 0.00 5.69
3651 4919 4.704833 ATTGCACCGCTCGGCTGT 62.705 61.111 8.41 0.00 39.32 4.40
3666 4934 2.506884 TACACAATGGGCCGGCCATT 62.507 55.000 44.46 34.64 38.26 3.16
3670 4938 0.107831 TATCTACACAATGGGCCGGC 59.892 55.000 21.18 21.18 0.00 6.13
3671 4939 2.218603 GTTATCTACACAATGGGCCGG 58.781 52.381 0.00 0.00 0.00 6.13
3673 4941 2.914059 ACGTTATCTACACAATGGGCC 58.086 47.619 0.00 0.00 0.00 5.80
3674 4942 4.056050 CCTACGTTATCTACACAATGGGC 58.944 47.826 0.00 0.00 0.00 5.36
3675 4943 5.272283 ACCTACGTTATCTACACAATGGG 57.728 43.478 0.00 0.00 0.00 4.00
3678 4946 7.229506 GGGTAGTACCTACGTTATCTACACAAT 59.770 40.741 18.85 0.00 37.79 2.71
3692 4962 2.371658 ACGGATGGGGTAGTACCTAC 57.628 55.000 18.85 12.50 38.64 3.18


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

AutoCloner maintained by Alex Coulton.