Multiple sequence alignment - TraesCS3D01G333600

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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 TraesCS3D01G333600 chr3D 100.000 7274 0 0 1 7274 445632883 445640156 0.000000e+00 13433.0
1 TraesCS3D01G333600 chr3A 97.078 6743 135 24 1 6687 587402290 587409026 0.000000e+00 11304.0
2 TraesCS3D01G333600 chr3B 97.886 6480 107 14 1 6473 584545468 584551924 0.000000e+00 11180.0
3 TraesCS3D01G333600 chr3B 78.230 836 106 28 6469 7273 584558687 584559477 3.970000e-127 466.0
4 TraesCS3D01G333600 chr3B 93.750 64 4 0 5787 5850 76433104 76433041 6.010000e-16 97.1
5 TraesCS3D01G333600 chr2D 88.442 199 22 1 4030 4227 410499944 410500142 9.430000e-59 239.0
6 TraesCS3D01G333600 chr6D 87.940 199 23 1 4030 4227 160853195 160853393 4.390000e-57 233.0
7 TraesCS3D01G333600 chr4B 75.284 352 77 10 5778 6124 377938639 377938293 7.550000e-35 159.0
8 TraesCS3D01G333600 chr4D 74.788 353 77 12 5778 6124 303518841 303518495 1.640000e-31 148.0
9 TraesCS3D01G333600 chr1A 98.246 57 1 0 4030 4086 533365081 533365025 4.640000e-17 100.0
10 TraesCS3D01G333600 chr4A 85.227 88 11 2 5779 5865 668094170 668094084 1.010000e-13 89.8
11 TraesCS3D01G333600 chr4A 82.192 73 10 3 5779 5850 625488056 625488126 7.880000e-05 60.2
12 TraesCS3D01G333600 chr5B 83.099 71 12 0 5780 5850 685566376 685566306 1.690000e-06 65.8
13 TraesCS3D01G333600 chr5D 82.192 73 10 3 5779 5850 543609489 543609419 7.880000e-05 60.2


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 TraesCS3D01G333600 chr3D 445632883 445640156 7273 False 13433 13433 100.000 1 7274 1 chr3D.!!$F1 7273
1 TraesCS3D01G333600 chr3A 587402290 587409026 6736 False 11304 11304 97.078 1 6687 1 chr3A.!!$F1 6686
2 TraesCS3D01G333600 chr3B 584545468 584551924 6456 False 11180 11180 97.886 1 6473 1 chr3B.!!$F1 6472
3 TraesCS3D01G333600 chr3B 584558687 584559477 790 False 466 466 78.230 6469 7273 1 chr3B.!!$F2 804

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
627 629 2.297033 TCAAGCCACCAAAGATCAAAGC 59.703 45.455 0.00 0.0 0.00 3.51 F
1586 1589 1.078001 CACCATGGGACGGGGTTAC 60.078 63.158 18.09 0.0 35.14 2.50 F
2619 2640 5.819991 ACATTTCTTCCTTCAGCCTGAATA 58.180 37.500 7.75 0.0 35.59 1.75 F
3424 3445 3.118847 ACTGTGCACTACTGATCATCTGG 60.119 47.826 19.41 0.0 33.00 3.86 F
4253 4275 2.755103 GTTTCCATCAACAGGGACATCC 59.245 50.000 0.00 0.0 30.00 3.51 F
5173 5205 4.324267 AGGTTTACAAGGGAACGATTGAG 58.676 43.478 0.00 0.0 31.45 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1881 1892 7.658575 CCATCTGGAAACAAAGAATTCATGTTT 59.341 33.333 28.13 28.13 46.67 2.83 R
3281 3302 6.471519 GTGCAGATAAAATTGATCAGAACAGC 59.528 38.462 0.00 0.00 0.00 4.40 R
3700 3722 0.537143 TGGGTGATGTTGCCAGTCAC 60.537 55.000 0.00 0.00 41.07 3.67 R
5354 5386 0.795085 CCTTGCAAGTTCTCTCGCAG 59.205 55.000 24.35 1.81 34.95 5.18 R
5802 5835 0.039165 CCGATAGCTGCTGCGTCATA 60.039 55.000 13.43 5.15 45.42 2.15 R
7075 7141 0.105039 GAACCCCATGACGAGCTAGG 59.895 60.000 0.00 0.00 0.00 3.02 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
173 174 5.698832 TGCACTTTTCTTATTGGAACATCG 58.301 37.500 0.00 0.00 39.30 3.84
627 629 2.297033 TCAAGCCACCAAAGATCAAAGC 59.703 45.455 0.00 0.00 0.00 3.51
1008 1011 1.227497 GGCTCTGAGAATGGAGGCG 60.227 63.158 9.28 0.00 43.25 5.52
1054 1057 2.473070 TGCTGTTGGCCAGTATACCTA 58.527 47.619 5.11 0.00 43.55 3.08
1154 1157 7.880059 ACTTTCATTGCAAAGATTTAGCTTC 57.120 32.000 1.71 0.00 36.92 3.86
1586 1589 1.078001 CACCATGGGACGGGGTTAC 60.078 63.158 18.09 0.00 35.14 2.50
1913 1932 6.648879 TTCTTTGTTTCCAGATGGTAAAGG 57.351 37.500 0.00 0.00 36.34 3.11
2341 2362 6.476378 AGACACATACAAAGCCTTAGTCATT 58.524 36.000 0.00 0.00 0.00 2.57
2392 2413 6.743575 ACTTTGGTTGTACTAATGAGATGC 57.256 37.500 0.00 0.00 0.00 3.91
2619 2640 5.819991 ACATTTCTTCCTTCAGCCTGAATA 58.180 37.500 7.75 0.00 35.59 1.75
3281 3302 6.647212 TTCTGCAAACTTCTATGATGTACG 57.353 37.500 0.00 0.00 0.00 3.67
3424 3445 3.118847 ACTGTGCACTACTGATCATCTGG 60.119 47.826 19.41 0.00 33.00 3.86
3543 3564 4.101448 CTCCGGCCCAGTTCCCAG 62.101 72.222 0.00 0.00 0.00 4.45
3601 3623 5.643379 AATTTTCTGGCGACATGTAACAT 57.357 34.783 0.00 0.00 41.51 2.71
3602 3624 5.643379 ATTTTCTGGCGACATGTAACATT 57.357 34.783 0.00 0.00 41.51 2.71
3924 3946 3.519107 TCCTGTGTGCTTGGATTCAGATA 59.481 43.478 0.00 0.00 0.00 1.98
4214 4236 4.623932 TTTCAGCAGTGATGACTACCTT 57.376 40.909 11.33 0.00 30.85 3.50
4229 4251 5.128827 TGACTACCTTCAAGTTCAAGTGAGT 59.871 40.000 0.00 0.00 0.00 3.41
4232 4254 4.446371 ACCTTCAAGTTCAAGTGAGTCTG 58.554 43.478 0.00 0.00 0.00 3.51
4253 4275 2.755103 GTTTCCATCAACAGGGACATCC 59.245 50.000 0.00 0.00 30.00 3.51
5038 5066 4.935702 TGCACCAACAATTTCTCAGAAAG 58.064 39.130 5.94 0.00 0.00 2.62
5173 5205 4.324267 AGGTTTACAAGGGAACGATTGAG 58.676 43.478 0.00 0.00 31.45 3.02
5423 5456 8.812147 AGCCTAAAAGTAAGTAAAATTTGTGC 57.188 30.769 0.00 0.00 0.00 4.57
5570 5603 9.647918 GATCCACCTATTATCCACAGAGATATA 57.352 37.037 0.00 0.00 0.00 0.86
5802 5835 3.561744 GCTATCTGGACCCCGAGTACTAT 60.562 52.174 0.00 0.00 0.00 2.12
6117 6150 0.816825 CGATGCTCCACAATGAGGGG 60.817 60.000 0.00 0.00 44.73 4.79
6300 6333 0.670546 GCACGCTCTTTGCCTACTCA 60.671 55.000 0.00 0.00 38.78 3.41
6346 6379 4.610605 TTCCTAATCAGTCGTTGGAACA 57.389 40.909 0.00 0.00 0.00 3.18
6396 6429 2.866460 GCTCGAATGCCCGATTAGCTTA 60.866 50.000 0.00 0.00 37.96 3.09
6411 6444 5.755409 TTAGCTTAAGACCAGATCAACCA 57.245 39.130 6.67 0.00 0.00 3.67
6480 6513 3.827008 AATGGAATCGAAGCTGCTCTA 57.173 42.857 1.00 0.00 0.00 2.43
6492 6525 1.929836 GCTGCTCTAAACTCGTGATGG 59.070 52.381 0.00 0.00 0.00 3.51
6517 6560 3.232213 TCGCAGCTTCGAATTAAGAGT 57.768 42.857 5.84 0.00 35.31 3.24
6524 6567 4.082447 GCTTCGAATTAAGAGTGCGTTTC 58.918 43.478 0.00 0.00 0.00 2.78
6687 6749 2.182030 GCTCCACTCCGTCTTCCG 59.818 66.667 0.00 0.00 0.00 4.30
6688 6750 2.182030 CTCCACTCCGTCTTCCGC 59.818 66.667 0.00 0.00 34.38 5.54
6689 6751 3.358076 CTCCACTCCGTCTTCCGCC 62.358 68.421 0.00 0.00 34.38 6.13
6690 6752 3.382832 CCACTCCGTCTTCCGCCT 61.383 66.667 0.00 0.00 34.38 5.52
6691 6753 2.182030 CACTCCGTCTTCCGCCTC 59.818 66.667 0.00 0.00 34.38 4.70
6692 6754 3.069318 ACTCCGTCTTCCGCCTCC 61.069 66.667 0.00 0.00 34.38 4.30
6693 6755 4.194720 CTCCGTCTTCCGCCTCCG 62.195 72.222 0.00 0.00 34.38 4.63
6695 6757 4.796231 CCGTCTTCCGCCTCCGTG 62.796 72.222 0.00 0.00 34.38 4.94
6729 6791 4.154347 GGCTCTCCCTGCCGTGAG 62.154 72.222 0.00 0.00 41.03 3.51
6730 6792 4.828925 GCTCTCCCTGCCGTGAGC 62.829 72.222 0.00 0.00 43.75 4.26
6731 6793 4.154347 CTCTCCCTGCCGTGAGCC 62.154 72.222 0.00 0.00 42.71 4.70
6741 6803 4.308458 CGTGAGCCCGTGACCCAA 62.308 66.667 0.00 0.00 0.00 4.12
6742 6804 2.112297 GTGAGCCCGTGACCCAAA 59.888 61.111 0.00 0.00 0.00 3.28
6743 6805 1.966451 GTGAGCCCGTGACCCAAAG 60.966 63.158 0.00 0.00 0.00 2.77
6744 6806 2.144078 TGAGCCCGTGACCCAAAGA 61.144 57.895 0.00 0.00 0.00 2.52
6760 6822 3.505680 CCAAAGACCAAATGATCCGAACA 59.494 43.478 0.00 0.00 0.00 3.18
6761 6823 4.475944 CAAAGACCAAATGATCCGAACAC 58.524 43.478 0.00 0.00 0.00 3.32
6793 6855 2.358247 CGACCCGACCCAAACAGG 60.358 66.667 0.00 0.00 37.03 4.00
6802 6864 2.742372 CCAAACAGGGTCCGCTCG 60.742 66.667 0.00 0.00 0.00 5.03
6805 6867 3.530910 AAACAGGGTCCGCTCGGTG 62.531 63.158 8.28 1.87 36.47 4.94
6808 6870 3.461773 AGGGTCCGCTCGGTGATG 61.462 66.667 8.28 0.00 36.47 3.07
6816 6878 0.247814 CGCTCGGTGATGCATTTCAC 60.248 55.000 11.29 11.29 44.27 3.18
6817 6879 0.247814 GCTCGGTGATGCATTTCACG 60.248 55.000 12.98 10.10 45.63 4.35
6832 6894 0.892063 TCACGCCCAAATTTAAGCCC 59.108 50.000 6.14 0.00 0.00 5.19
6833 6895 0.457681 CACGCCCAAATTTAAGCCCG 60.458 55.000 6.14 1.60 0.00 6.13
6838 6900 2.234168 GCCCAAATTTAAGCCCGGTTTA 59.766 45.455 0.00 0.00 0.00 2.01
6841 6903 3.057386 CCAAATTTAAGCCCGGTTTACGT 60.057 43.478 0.00 0.00 42.24 3.57
6842 6904 4.160594 CAAATTTAAGCCCGGTTTACGTC 58.839 43.478 0.00 0.00 42.24 4.34
6843 6905 1.807139 TTTAAGCCCGGTTTACGTCC 58.193 50.000 0.00 0.00 42.24 4.79
6846 6908 3.113979 GCCCGGTTTACGTCCACG 61.114 66.667 0.00 0.00 46.33 4.94
6847 6909 3.113979 CCCGGTTTACGTCCACGC 61.114 66.667 0.00 0.00 44.43 5.34
6848 6910 2.356075 CCGGTTTACGTCCACGCA 60.356 61.111 0.00 0.00 44.43 5.24
6849 6911 2.377310 CCGGTTTACGTCCACGCAG 61.377 63.158 0.00 0.00 44.43 5.18
6852 6914 0.598158 GGTTTACGTCCACGCAGACA 60.598 55.000 0.00 0.00 44.43 3.41
6853 6915 0.505655 GTTTACGTCCACGCAGACAC 59.494 55.000 0.00 0.00 44.43 3.67
6854 6916 0.102663 TTTACGTCCACGCAGACACA 59.897 50.000 0.00 0.00 44.43 3.72
6855 6917 0.102663 TTACGTCCACGCAGACACAA 59.897 50.000 0.00 0.00 44.43 3.33
6856 6918 0.318360 TACGTCCACGCAGACACAAG 60.318 55.000 0.00 0.00 44.43 3.16
6857 6919 1.591594 CGTCCACGCAGACACAAGT 60.592 57.895 6.28 0.00 36.52 3.16
6868 6930 1.274596 GACACAAGTCACACGTTCGT 58.725 50.000 0.00 0.00 44.34 3.85
6876 6938 3.111098 AGTCACACGTTCGTTTAGTGTC 58.889 45.455 11.77 8.09 46.01 3.67
6877 6939 3.111098 GTCACACGTTCGTTTAGTGTCT 58.889 45.455 11.77 0.00 46.01 3.41
6879 6941 4.913924 GTCACACGTTCGTTTAGTGTCTAT 59.086 41.667 11.77 0.00 46.01 1.98
6883 6945 6.360414 CACACGTTCGTTTAGTGTCTATTACA 59.640 38.462 0.00 0.00 46.01 2.41
6888 6950 4.708421 TCGTTTAGTGTCTATTACAGGCCT 59.292 41.667 0.00 0.00 39.29 5.19
6894 6956 8.951614 TTAGTGTCTATTACAGGCCTACATAT 57.048 34.615 3.98 0.00 39.29 1.78
6902 6964 2.342279 GCCTACATATCGGCCGCA 59.658 61.111 23.51 11.56 40.43 5.69
6906 6968 0.859232 CTACATATCGGCCGCACAAC 59.141 55.000 23.51 0.00 0.00 3.32
6907 6969 0.531090 TACATATCGGCCGCACAACC 60.531 55.000 23.51 0.00 0.00 3.77
6910 6972 0.884704 ATATCGGCCGCACAACCATC 60.885 55.000 23.51 0.00 0.00 3.51
6912 6974 4.101790 CGGCCGCACAACCATCAC 62.102 66.667 14.67 0.00 0.00 3.06
6915 6977 1.153978 GCCGCACAACCATCACATG 60.154 57.895 0.00 0.00 0.00 3.21
6916 6978 1.865788 GCCGCACAACCATCACATGT 61.866 55.000 0.00 0.00 0.00 3.21
6917 6979 0.597568 CCGCACAACCATCACATGTT 59.402 50.000 0.00 0.00 0.00 2.71
6920 6982 2.543445 CGCACAACCATCACATGTTGTT 60.543 45.455 0.00 0.00 37.87 2.83
6923 6985 4.498850 GCACAACCATCACATGTTGTTGTA 60.499 41.667 22.36 0.00 40.91 2.41
6924 6986 5.586339 CACAACCATCACATGTTGTTGTAA 58.414 37.500 22.36 0.00 40.91 2.41
6932 6994 7.253717 CCATCACATGTTGTTGTAATAAATGCG 60.254 37.037 0.00 0.00 0.00 4.73
6933 6995 6.673106 TCACATGTTGTTGTAATAAATGCGT 58.327 32.000 0.00 0.00 0.00 5.24
6936 6998 4.713806 TGTTGTTGTAATAAATGCGTCCG 58.286 39.130 0.00 0.00 0.00 4.79
6937 6999 3.392769 TGTTGTAATAAATGCGTCCGC 57.607 42.857 4.42 4.42 42.35 5.54
6946 7008 2.221906 AATGCGTCCGCCTAACTCGT 62.222 55.000 9.43 0.00 41.09 4.18
6947 7009 2.879462 GCGTCCGCCTAACTCGTG 60.879 66.667 0.00 0.00 34.56 4.35
6949 7011 2.572284 GTCCGCCTAACTCGTGCT 59.428 61.111 0.00 0.00 0.00 4.40
6956 7018 1.065102 GCCTAACTCGTGCTCGTATGA 59.935 52.381 8.17 0.00 38.33 2.15
6957 7019 2.287668 GCCTAACTCGTGCTCGTATGAT 60.288 50.000 8.17 0.00 38.33 2.45
6974 7036 1.482182 TGATAGCGTGTGGAAGCATCT 59.518 47.619 0.00 0.00 35.48 2.90
6976 7038 0.108186 TAGCGTGTGGAAGCATCTGG 60.108 55.000 0.00 0.00 35.48 3.86
6978 7040 1.915614 GCGTGTGGAAGCATCTGGTG 61.916 60.000 0.00 0.00 0.00 4.17
6979 7041 0.603707 CGTGTGGAAGCATCTGGTGT 60.604 55.000 0.00 0.00 0.00 4.16
6983 7045 0.764271 TGGAAGCATCTGGTGTGTCA 59.236 50.000 0.00 0.00 0.00 3.58
6985 7047 2.012673 GGAAGCATCTGGTGTGTCATC 58.987 52.381 0.00 0.00 0.00 2.92
6992 7054 4.083537 GCATCTGGTGTGTCATCGTTTTTA 60.084 41.667 0.00 0.00 0.00 1.52
6995 7057 6.627395 TCTGGTGTGTCATCGTTTTTAAAT 57.373 33.333 0.00 0.00 0.00 1.40
6996 7058 6.434596 TCTGGTGTGTCATCGTTTTTAAATG 58.565 36.000 0.00 0.00 0.00 2.32
6998 7060 4.979197 GGTGTGTCATCGTTTTTAAATGCA 59.021 37.500 0.00 0.00 0.00 3.96
7000 7062 6.345723 GGTGTGTCATCGTTTTTAAATGCAAG 60.346 38.462 0.00 0.00 0.00 4.01
7001 7063 5.174761 TGTGTCATCGTTTTTAAATGCAAGC 59.825 36.000 0.00 0.00 0.00 4.01
7002 7064 4.381270 TGTCATCGTTTTTAAATGCAAGCG 59.619 37.500 0.00 0.00 0.00 4.68
7003 7065 3.363426 TCATCGTTTTTAAATGCAAGCGC 59.637 39.130 0.00 0.00 39.24 5.92
7004 7066 1.711298 TCGTTTTTAAATGCAAGCGCG 59.289 42.857 0.00 0.00 42.97 6.86
7006 7068 1.125930 GTTTTTAAATGCAAGCGCGGG 59.874 47.619 8.83 0.00 42.97 6.13
7007 7069 0.389166 TTTTAAATGCAAGCGCGGGG 60.389 50.000 8.83 0.00 42.97 5.73
7008 7070 1.528292 TTTAAATGCAAGCGCGGGGT 61.528 50.000 8.83 0.00 42.97 4.95
7043 7109 4.489771 CCCCGTCCACATCTGGCC 62.490 72.222 0.00 0.00 37.49 5.36
7045 7111 2.591753 CCGTCCACATCTGGCCAT 59.408 61.111 5.51 0.00 37.49 4.40
7050 7116 0.177836 TCCACATCTGGCCATACGTG 59.822 55.000 5.51 8.38 37.49 4.49
7054 7120 1.340017 ACATCTGGCCATACGTGCTTT 60.340 47.619 5.51 0.00 0.00 3.51
7058 7124 0.739462 TGGCCATACGTGCTTTCTCG 60.739 55.000 0.00 0.00 35.54 4.04
7072 7138 2.352704 TTCTCGTCGGCGACCACAAA 62.353 55.000 31.86 18.57 42.81 2.83
7075 7141 2.635338 GTCGGCGACCACAAAACC 59.365 61.111 28.72 0.05 0.00 3.27
7080 7146 1.583495 GGCGACCACAAAACCCTAGC 61.583 60.000 0.00 0.00 0.00 3.42
7082 7148 1.439679 CGACCACAAAACCCTAGCTC 58.560 55.000 0.00 0.00 0.00 4.09
7089 7155 2.009774 CAAAACCCTAGCTCGTCATGG 58.990 52.381 0.00 0.00 0.00 3.66
7091 7157 1.338136 AACCCTAGCTCGTCATGGGG 61.338 60.000 0.00 0.00 42.00 4.96
7103 7169 0.322456 TCATGGGGTTCTTCGGCAAG 60.322 55.000 0.00 0.00 0.00 4.01
7115 7181 1.007387 CGGCAAGAACAAGGGCAAC 60.007 57.895 0.00 0.00 0.00 4.17
7157 7223 3.487202 CGCGCGCCTTCTTTGCTA 61.487 61.111 27.72 0.00 0.00 3.49
7158 7224 2.098489 GCGCGCCTTCTTTGCTAC 59.902 61.111 23.24 0.00 0.00 3.58
7160 7226 2.785258 GCGCCTTCTTTGCTACCG 59.215 61.111 0.00 0.00 0.00 4.02
7161 7227 2.033194 GCGCCTTCTTTGCTACCGT 61.033 57.895 0.00 0.00 0.00 4.83
7165 7231 1.359459 CCTTCTTTGCTACCGTCGCC 61.359 60.000 0.00 0.00 0.00 5.54
7201 7267 2.358737 GCCACGGGAGAGGTTGTG 60.359 66.667 0.00 0.00 43.07 3.33
7208 7274 1.077429 GGAGAGGTTGTGCATCCCC 60.077 63.158 0.00 0.00 0.00 4.81
7231 7297 1.968017 ACCAAGCGTGATGGCACTG 60.968 57.895 0.00 0.00 42.93 3.66
7232 7298 1.672030 CCAAGCGTGATGGCACTGA 60.672 57.895 0.00 0.00 42.93 3.41
7246 7312 2.207229 ACTGACAGTACCGCCAGCA 61.207 57.895 6.24 0.00 0.00 4.41
7247 7313 1.738099 CTGACAGTACCGCCAGCAC 60.738 63.158 0.00 0.00 0.00 4.40
7248 7314 2.159819 CTGACAGTACCGCCAGCACT 62.160 60.000 0.00 0.00 0.00 4.40
7249 7315 1.738099 GACAGTACCGCCAGCACTG 60.738 63.158 6.97 6.97 44.20 3.66
7250 7316 2.343758 CAGTACCGCCAGCACTGT 59.656 61.111 0.00 0.00 35.91 3.55
7251 7317 1.738099 CAGTACCGCCAGCACTGTC 60.738 63.158 0.00 0.00 35.91 3.51
7252 7318 2.809601 GTACCGCCAGCACTGTCG 60.810 66.667 0.00 0.00 0.00 4.35
7253 7319 3.299977 TACCGCCAGCACTGTCGT 61.300 61.111 0.15 0.00 29.00 4.34
7254 7320 1.972752 TACCGCCAGCACTGTCGTA 60.973 57.895 0.15 0.00 29.00 3.43
7255 7321 2.203972 TACCGCCAGCACTGTCGTAC 62.204 60.000 0.15 0.00 29.00 3.67
7256 7322 2.809601 CGCCAGCACTGTCGTACC 60.810 66.667 0.00 0.00 0.00 3.34
7260 7326 2.282674 AGCACTGTCGTACCCCGA 60.283 61.111 0.00 0.00 45.00 5.14
7273 7339 2.046285 CCCCGAATGTCAACCTGCC 61.046 63.158 0.00 0.00 0.00 4.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
41 42 9.588774 CACAATGCATCTTCTAATTTTGTTTTG 57.411 29.630 0.00 0.00 0.00 2.44
173 174 4.886489 ACGTAGGGACTAGAGTTATTGACC 59.114 45.833 0.00 0.00 44.14 4.02
627 629 1.676014 CCTTCACGGGTCTAGGCTTTG 60.676 57.143 0.00 0.00 0.00 2.77
684 686 3.162666 AGGATTACTGACTGTTCCGTCA 58.837 45.455 0.00 0.00 41.33 4.35
1008 1011 3.065925 ACAGCAGCAGAAACTTTCTCAAC 59.934 43.478 0.67 0.00 38.11 3.18
1154 1157 4.641541 TGGCTTGTCACCTTCAATATGATG 59.358 41.667 0.00 0.00 0.00 3.07
1881 1892 7.658575 CCATCTGGAAACAAAGAATTCATGTTT 59.341 33.333 28.13 28.13 46.67 2.83
1913 1932 8.450964 TCTGTTAAAATGTTATAAGCTCTGCAC 58.549 33.333 0.00 0.00 0.00 4.57
2341 2362 8.424133 TCAGCAGAGCTTAATAATAATGTGAGA 58.576 33.333 0.00 0.00 36.40 3.27
2619 2640 8.692710 ACACTTCATATTGATCATGCATTCTTT 58.307 29.630 0.00 0.00 0.00 2.52
3281 3302 6.471519 GTGCAGATAAAATTGATCAGAACAGC 59.528 38.462 0.00 0.00 0.00 4.40
3700 3722 0.537143 TGGGTGATGTTGCCAGTCAC 60.537 55.000 0.00 0.00 41.07 3.67
3924 3946 0.951040 CAAAAGAAGCGGCTCGAGGT 60.951 55.000 15.58 0.00 0.00 3.85
4214 4236 4.876107 GGAAACAGACTCACTTGAACTTGA 59.124 41.667 0.00 0.00 0.00 3.02
4232 4254 2.755103 GGATGTCCCTGTTGATGGAAAC 59.245 50.000 0.00 0.00 31.03 2.78
4253 4275 2.613730 TCAGTTCTGACGTAGCGAAG 57.386 50.000 0.00 0.00 0.00 3.79
5038 5066 4.041444 AGCCTCCTGATCCTATTTCATGAC 59.959 45.833 0.00 0.00 0.00 3.06
5173 5205 1.327303 TTGCAACACCTGTTCCATCC 58.673 50.000 0.00 0.00 35.83 3.51
5354 5386 0.795085 CCTTGCAAGTTCTCTCGCAG 59.205 55.000 24.35 1.81 34.95 5.18
5414 5447 5.360714 TGTGAAGGAGAAGAAGCACAAATTT 59.639 36.000 0.00 0.00 33.81 1.82
5416 5449 4.464008 TGTGAAGGAGAAGAAGCACAAAT 58.536 39.130 0.00 0.00 33.81 2.32
5423 5456 3.879295 TGCAAGTTGTGAAGGAGAAGAAG 59.121 43.478 4.48 0.00 0.00 2.85
5570 5603 7.454380 TCATCCAAAAGGATATTTGTGGACTTT 59.546 33.333 1.74 0.00 38.37 2.66
5802 5835 0.039165 CCGATAGCTGCTGCGTCATA 60.039 55.000 13.43 5.15 45.42 2.15
6396 6429 1.420138 ACCGTTGGTTGATCTGGTCTT 59.580 47.619 0.00 0.00 27.29 3.01
6411 6444 1.005294 CGAATTCACCGTCGACCGTT 61.005 55.000 10.58 0.00 39.64 4.44
6480 6513 2.165641 TGCGATCTACCATCACGAGTTT 59.834 45.455 0.00 0.00 0.00 2.66
6492 6525 4.976731 TCTTAATTCGAAGCTGCGATCTAC 59.023 41.667 19.65 0.00 40.35 2.59
6517 6560 2.127042 GCCGCAAATCGAAACGCA 60.127 55.556 0.00 0.00 41.67 5.24
6524 6567 3.732892 ACCAACGGCCGCAAATCG 61.733 61.111 28.58 9.46 38.08 3.34
6728 6790 2.430367 GTCTTTGGGTCACGGGCT 59.570 61.111 0.00 0.00 0.00 5.19
6729 6791 2.671963 GGTCTTTGGGTCACGGGC 60.672 66.667 0.00 0.00 0.00 6.13
6730 6792 0.466555 TTTGGTCTTTGGGTCACGGG 60.467 55.000 0.00 0.00 0.00 5.28
6731 6793 1.269448 CATTTGGTCTTTGGGTCACGG 59.731 52.381 0.00 0.00 0.00 4.94
6732 6794 2.226330 TCATTTGGTCTTTGGGTCACG 58.774 47.619 0.00 0.00 0.00 4.35
6733 6795 3.193479 GGATCATTTGGTCTTTGGGTCAC 59.807 47.826 0.00 0.00 0.00 3.67
6734 6796 3.430453 GGATCATTTGGTCTTTGGGTCA 58.570 45.455 0.00 0.00 0.00 4.02
6735 6797 2.423538 CGGATCATTTGGTCTTTGGGTC 59.576 50.000 0.00 0.00 0.00 4.46
6736 6798 2.041081 TCGGATCATTTGGTCTTTGGGT 59.959 45.455 0.00 0.00 0.00 4.51
6737 6799 2.722094 TCGGATCATTTGGTCTTTGGG 58.278 47.619 0.00 0.00 0.00 4.12
6738 6800 3.505680 TGTTCGGATCATTTGGTCTTTGG 59.494 43.478 0.00 0.00 0.00 3.28
6739 6801 4.475944 GTGTTCGGATCATTTGGTCTTTG 58.524 43.478 0.00 0.00 0.00 2.77
6740 6802 3.506067 GGTGTTCGGATCATTTGGTCTTT 59.494 43.478 0.00 0.00 0.00 2.52
6741 6803 3.081804 GGTGTTCGGATCATTTGGTCTT 58.918 45.455 0.00 0.00 0.00 3.01
6742 6804 2.711542 GGTGTTCGGATCATTTGGTCT 58.288 47.619 0.00 0.00 0.00 3.85
6743 6805 1.396996 CGGTGTTCGGATCATTTGGTC 59.603 52.381 0.00 0.00 34.75 4.02
6744 6806 1.448985 CGGTGTTCGGATCATTTGGT 58.551 50.000 0.00 0.00 34.75 3.67
6774 6836 4.629523 TGTTTGGGTCGGGTCGGC 62.630 66.667 0.00 0.00 0.00 5.54
6775 6837 2.358247 CTGTTTGGGTCGGGTCGG 60.358 66.667 0.00 0.00 0.00 4.79
6776 6838 2.358247 CCTGTTTGGGTCGGGTCG 60.358 66.667 0.00 0.00 0.00 4.79
6793 6855 3.740128 ATGCATCACCGAGCGGACC 62.740 63.158 16.83 0.00 38.96 4.46
6794 6856 1.369091 AAATGCATCACCGAGCGGAC 61.369 55.000 16.83 0.35 38.96 4.79
6816 6878 1.140804 CCGGGCTTAAATTTGGGCG 59.859 57.895 0.00 3.49 0.00 6.13
6817 6879 0.611200 AACCGGGCTTAAATTTGGGC 59.389 50.000 6.32 6.02 0.00 5.36
6832 6894 1.372004 TCTGCGTGGACGTAAACCG 60.372 57.895 0.52 0.00 42.22 4.44
6833 6895 0.598158 TGTCTGCGTGGACGTAAACC 60.598 55.000 0.52 0.00 42.22 3.27
6838 6900 1.591594 CTTGTGTCTGCGTGGACGT 60.592 57.895 0.52 0.00 42.22 4.34
6841 6903 0.529773 GTGACTTGTGTCTGCGTGGA 60.530 55.000 0.00 0.00 43.29 4.02
6842 6904 0.809636 TGTGACTTGTGTCTGCGTGG 60.810 55.000 0.00 0.00 43.29 4.94
6843 6905 0.301687 GTGTGACTTGTGTCTGCGTG 59.698 55.000 0.00 0.00 43.29 5.34
6846 6908 1.004927 GAACGTGTGACTTGTGTCTGC 60.005 52.381 0.00 0.00 43.29 4.26
6847 6909 1.255342 CGAACGTGTGACTTGTGTCTG 59.745 52.381 0.00 0.00 43.29 3.51
6848 6910 1.135199 ACGAACGTGTGACTTGTGTCT 60.135 47.619 0.00 0.00 43.29 3.41
6849 6911 1.274596 ACGAACGTGTGACTTGTGTC 58.725 50.000 0.00 0.00 43.20 3.67
6852 6914 3.305094 CACTAAACGAACGTGTGACTTGT 59.695 43.478 9.55 0.00 0.00 3.16
6853 6915 3.305094 ACACTAAACGAACGTGTGACTTG 59.695 43.478 18.09 7.47 40.11 3.16
6854 6916 3.514645 ACACTAAACGAACGTGTGACTT 58.485 40.909 18.09 5.27 40.11 3.01
6855 6917 3.111098 GACACTAAACGAACGTGTGACT 58.889 45.455 18.09 2.63 41.53 3.41
6856 6918 3.111098 AGACACTAAACGAACGTGTGAC 58.889 45.455 18.09 13.55 41.53 3.67
6857 6919 3.425577 AGACACTAAACGAACGTGTGA 57.574 42.857 18.09 1.17 41.53 3.58
6861 6923 6.088824 CCTGTAATAGACACTAAACGAACGT 58.911 40.000 0.00 0.00 33.31 3.99
6865 6927 4.708421 AGGCCTGTAATAGACACTAAACGA 59.292 41.667 3.11 0.00 33.31 3.85
6866 6928 5.007385 AGGCCTGTAATAGACACTAAACG 57.993 43.478 3.11 0.00 33.31 3.60
6868 6930 7.670605 ATGTAGGCCTGTAATAGACACTAAA 57.329 36.000 17.99 0.00 33.31 1.85
6888 6950 0.531090 GGTTGTGCGGCCGATATGTA 60.531 55.000 33.48 5.02 0.00 2.29
6894 6956 4.321966 TGATGGTTGTGCGGCCGA 62.322 61.111 33.48 11.82 0.00 5.54
6906 6968 7.253717 CGCATTTATTACAACAACATGTGATGG 60.254 37.037 0.00 0.00 34.40 3.51
6907 6969 7.273164 ACGCATTTATTACAACAACATGTGATG 59.727 33.333 0.00 1.39 36.15 3.07
6910 6972 6.033407 GGACGCATTTATTACAACAACATGTG 59.967 38.462 0.00 0.00 34.75 3.21
6912 6974 5.226978 CGGACGCATTTATTACAACAACATG 59.773 40.000 0.00 0.00 0.00 3.21
6915 6977 3.540738 GCGGACGCATTTATTACAACAAC 59.459 43.478 12.31 0.00 41.49 3.32
6916 6978 3.426426 GGCGGACGCATTTATTACAACAA 60.426 43.478 18.95 0.00 44.11 2.83
6917 6979 2.096174 GGCGGACGCATTTATTACAACA 59.904 45.455 18.95 0.00 44.11 3.33
6920 6982 2.319136 AGGCGGACGCATTTATTACA 57.681 45.000 18.95 0.00 44.11 2.41
6923 6985 2.870411 GAGTTAGGCGGACGCATTTATT 59.130 45.455 18.95 0.28 44.11 1.40
6924 6986 2.480845 GAGTTAGGCGGACGCATTTAT 58.519 47.619 18.95 0.87 44.11 1.40
6932 6994 1.516603 GAGCACGAGTTAGGCGGAC 60.517 63.158 0.00 0.00 0.00 4.79
6933 6995 2.882876 GAGCACGAGTTAGGCGGA 59.117 61.111 0.00 0.00 0.00 5.54
6936 6998 1.065102 TCATACGAGCACGAGTTAGGC 59.935 52.381 11.40 0.00 42.66 3.93
6937 6999 3.627732 ATCATACGAGCACGAGTTAGG 57.372 47.619 11.40 0.00 42.66 2.69
6946 7008 1.269051 CCACACGCTATCATACGAGCA 60.269 52.381 0.00 0.00 38.69 4.26
6947 7009 1.001706 TCCACACGCTATCATACGAGC 60.002 52.381 0.00 0.00 35.24 5.03
6949 7011 2.543031 GCTTCCACACGCTATCATACGA 60.543 50.000 0.00 0.00 0.00 3.43
6956 7018 1.473965 CCAGATGCTTCCACACGCTAT 60.474 52.381 0.00 0.00 0.00 2.97
6957 7019 0.108186 CCAGATGCTTCCACACGCTA 60.108 55.000 0.00 0.00 0.00 4.26
6974 7036 4.979197 GCATTTAAAAACGATGACACACCA 59.021 37.500 0.00 0.00 0.00 4.17
6976 7038 6.503616 TTGCATTTAAAAACGATGACACAC 57.496 33.333 0.00 0.00 0.00 3.82
6978 7040 5.598783 GCTTGCATTTAAAAACGATGACAC 58.401 37.500 0.00 0.00 0.00 3.67
6979 7041 4.381270 CGCTTGCATTTAAAAACGATGACA 59.619 37.500 0.00 0.00 0.00 3.58
6983 7045 2.341168 CGCGCTTGCATTTAAAAACGAT 59.659 40.909 5.56 0.00 39.07 3.73
6985 7047 1.201651 CCGCGCTTGCATTTAAAAACG 60.202 47.619 5.56 0.00 39.07 3.60
6992 7054 4.054825 CACCCCGCGCTTGCATTT 62.055 61.111 5.56 0.00 39.07 2.32
7001 7063 4.530857 GGATGAGGTCACCCCGCG 62.531 72.222 0.00 0.00 38.74 6.46
7002 7064 3.399181 TGGATGAGGTCACCCCGC 61.399 66.667 0.00 0.00 38.74 6.13
7003 7065 1.553690 AAGTGGATGAGGTCACCCCG 61.554 60.000 0.00 0.00 38.74 5.73
7004 7066 0.253327 GAAGTGGATGAGGTCACCCC 59.747 60.000 0.00 0.00 34.67 4.95
7006 7068 1.208293 GGAGAAGTGGATGAGGTCACC 59.792 57.143 0.00 0.00 34.67 4.02
7007 7069 1.208293 GGGAGAAGTGGATGAGGTCAC 59.792 57.143 0.00 0.00 0.00 3.67
7008 7070 1.573108 GGGAGAAGTGGATGAGGTCA 58.427 55.000 0.00 0.00 0.00 4.02
7010 7072 0.621862 GGGGGAGAAGTGGATGAGGT 60.622 60.000 0.00 0.00 0.00 3.85
7018 7084 1.553690 ATGTGGACGGGGGAGAAGTG 61.554 60.000 0.00 0.00 0.00 3.16
7020 7086 0.978146 AGATGTGGACGGGGGAGAAG 60.978 60.000 0.00 0.00 0.00 2.85
7043 7109 0.914551 CCGACGAGAAAGCACGTATG 59.085 55.000 0.00 0.00 41.33 2.39
7045 7111 1.443194 GCCGACGAGAAAGCACGTA 60.443 57.895 0.00 0.00 41.33 3.57
7058 7124 2.635338 GGTTTTGTGGTCGCCGAC 59.365 61.111 9.15 9.15 0.00 4.79
7072 7138 1.338136 CCCCATGACGAGCTAGGGTT 61.338 60.000 0.00 0.00 37.84 4.11
7075 7141 0.105039 GAACCCCATGACGAGCTAGG 59.895 60.000 0.00 0.00 0.00 3.02
7080 7146 0.460284 CCGAAGAACCCCATGACGAG 60.460 60.000 0.00 0.00 0.00 4.18
7082 7148 2.106683 GCCGAAGAACCCCATGACG 61.107 63.158 0.00 0.00 0.00 4.35
7103 7169 1.179174 GGGTGAGGTTGCCCTTGTTC 61.179 60.000 0.00 0.00 42.86 3.18
7144 7210 1.683790 CGACGGTAGCAAAGAAGGCG 61.684 60.000 0.00 0.00 36.08 5.52
7208 7274 1.138036 CCATCACGCTTGGTGCATG 59.862 57.895 0.00 0.00 46.56 4.06
7225 7291 2.434359 GGCGGTACTGTCAGTGCC 60.434 66.667 25.69 25.69 45.96 5.01
7231 7297 2.657237 AGTGCTGGCGGTACTGTC 59.343 61.111 16.65 0.00 39.36 3.51
7251 7317 0.248289 AGGTTGACATTCGGGGTACG 59.752 55.000 0.00 0.00 46.11 3.67
7252 7318 1.734163 CAGGTTGACATTCGGGGTAC 58.266 55.000 0.00 0.00 0.00 3.34
7253 7319 0.035820 GCAGGTTGACATTCGGGGTA 60.036 55.000 0.00 0.00 0.00 3.69
7254 7320 1.303317 GCAGGTTGACATTCGGGGT 60.303 57.895 0.00 0.00 0.00 4.95
7255 7321 2.046285 GGCAGGTTGACATTCGGGG 61.046 63.158 0.00 0.00 0.00 5.73
7256 7322 3.590824 GGCAGGTTGACATTCGGG 58.409 61.111 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.