Multiple sequence alignment - TraesCS3D01G397500

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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 TraesCS3D01G397500 chr3D 100.000 3711 0 0 1 3711 512259421 512263131 0.000000e+00 6854.0
1 TraesCS3D01G397500 chr3D 95.000 120 6 0 2987 3106 24157951 24158070 4.890000e-44 189.0
2 TraesCS3D01G397500 chr3D 95.000 120 6 0 2987 3106 24158465 24158584 4.890000e-44 189.0
3 TraesCS3D01G397500 chr3D 97.872 47 0 1 788 834 400336918 400336873 3.070000e-11 80.5
4 TraesCS3D01G397500 chr3D 87.879 66 5 3 770 834 180395017 180394954 1.430000e-09 75.0
5 TraesCS3D01G397500 chr3A 95.178 1825 63 8 1402 3216 648022194 648024003 0.000000e+00 2859.0
6 TraesCS3D01G397500 chr3A 93.594 562 25 7 849 1405 648021377 648021932 0.000000e+00 828.0
7 TraesCS3D01G397500 chr3A 84.509 581 60 19 1 561 648020545 648021115 7.010000e-152 547.0
8 TraesCS3D01G397500 chr3A 95.486 288 8 1 3365 3647 648024347 648024634 4.370000e-124 455.0
9 TraesCS3D01G397500 chr3A 86.344 227 16 6 568 794 648021161 648021372 2.230000e-57 233.0
10 TraesCS3D01G397500 chr3A 95.833 144 6 0 3230 3373 648023987 648024130 2.230000e-57 233.0
11 TraesCS3D01G397500 chr3A 95.833 72 3 0 3640 3711 648025898 648025969 2.340000e-22 117.0
12 TraesCS3D01G397500 chr3B 91.951 1466 46 8 1807 3239 674424289 674425715 0.000000e+00 1988.0
13 TraesCS3D01G397500 chr3B 93.368 965 52 8 849 1807 674423239 674424197 0.000000e+00 1417.0
14 TraesCS3D01G397500 chr3B 89.039 812 55 8 1 794 674422439 674423234 0.000000e+00 976.0
15 TraesCS3D01G397500 chr3B 92.593 54 2 2 793 845 10717592 10717540 3.970000e-10 76.8
16 TraesCS3D01G397500 chr3B 97.297 37 1 0 2029 2065 662809957 662809921 3.090000e-06 63.9
17 TraesCS3D01G397500 chr6A 88.277 563 50 9 3105 3660 76799249 76798696 0.000000e+00 660.0
18 TraesCS3D01G397500 chr6A 88.525 61 6 1 793 853 480648023 480647964 5.140000e-09 73.1
19 TraesCS3D01G397500 chr6B 89.448 417 29 3 3300 3711 134295482 134295076 2.560000e-141 512.0
20 TraesCS3D01G397500 chr4A 82.927 369 43 10 2516 2878 596925016 596924662 7.740000e-82 315.0
21 TraesCS3D01G397500 chrUn 95.726 117 5 0 2990 3106 298933088 298932972 4.890000e-44 189.0
22 TraesCS3D01G397500 chr5D 95.726 117 5 0 2990 3106 6242464 6242348 4.890000e-44 189.0
23 TraesCS3D01G397500 chr5D 95.000 120 6 0 2987 3106 256076463 256076582 4.890000e-44 189.0
24 TraesCS3D01G397500 chr1D 95.726 117 5 0 2990 3106 25804140 25804024 4.890000e-44 189.0
25 TraesCS3D01G397500 chr1D 97.872 47 0 1 788 834 124334330 124334375 3.070000e-11 80.5
26 TraesCS3D01G397500 chr1D 91.228 57 3 2 789 845 220878762 220878708 3.970000e-10 76.8
27 TraesCS3D01G397500 chr1B 95.000 120 6 0 2987 3106 225107676 225107795 4.890000e-44 189.0
28 TraesCS3D01G397500 chr4B 89.831 59 3 3 788 845 23660875 23660819 5.140000e-09 73.1
29 TraesCS3D01G397500 chr2A 88.333 60 5 2 788 847 593499494 593499437 1.850000e-08 71.3
30 TraesCS3D01G397500 chr2D 90.385 52 3 2 795 845 403345133 403345083 2.390000e-07 67.6


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 TraesCS3D01G397500 chr3D 512259421 512263131 3710 False 6854.000000 6854 100.000000 1 3711 1 chr3D.!!$F1 3710
1 TraesCS3D01G397500 chr3A 648020545 648025969 5424 False 753.142857 2859 92.396714 1 3711 7 chr3A.!!$F1 3710
2 TraesCS3D01G397500 chr3B 674422439 674425715 3276 False 1460.333333 1988 91.452667 1 3239 3 chr3B.!!$F1 3238
3 TraesCS3D01G397500 chr6A 76798696 76799249 553 True 660.000000 660 88.277000 3105 3660 1 chr6A.!!$R1 555

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
120 121 0.038526 GTCGTCTTTCCTGGAGCGAA 60.039 55.0 13.35 0.0 0.0 4.70 F
531 567 0.392327 GGGGTGCAGAGAAGAAGAGC 60.392 60.0 0.00 0.0 0.0 4.09 F
596 671 0.460722 TGCTTTGCTTGCTTGCTTGA 59.539 45.0 3.47 0.0 0.0 3.02 F
1505 1860 0.550914 TGGGGCTGACTGTCTGTTTT 59.449 50.0 14.85 0.0 0.0 2.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2501 0.028242 CATCTTCGTCCTCGTCCTCG 59.972 60.000 0.0 0.0 38.33 4.63 R
2340 2801 1.315257 CCTTGACAATGGCCCTTCCG 61.315 60.000 0.0 0.0 37.80 4.30 R
2554 3015 2.357836 CCTGGGCTCACCTGCAAT 59.642 61.111 0.0 0.0 41.11 3.56 R
3238 3731 0.108329 GCTAGCTTCGCCAACTACCA 60.108 55.000 7.7 0.0 0.00 3.25 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
19 20 2.629050 GATCCTCTGCGCCGCTTACA 62.629 60.000 11.67 0.00 0.00 2.41
30 31 1.141881 CGCTTACATCACCGGCTCT 59.858 57.895 0.00 0.00 0.00 4.09
98 99 4.803426 GTCTCTGCAGCCCGTCGG 62.803 72.222 9.47 3.60 0.00 4.79
120 121 0.038526 GTCGTCTTTCCTGGAGCGAA 60.039 55.000 13.35 0.00 0.00 4.70
191 192 2.203523 TCTTCGGTCCACGGGTCA 60.204 61.111 0.00 0.00 44.45 4.02
235 236 5.151389 GCCTACTGTAAAAATGTTTCACCG 58.849 41.667 0.00 0.00 0.00 4.94
247 248 2.420466 TTTCACCGGCTTTCCCTCCC 62.420 60.000 0.00 0.00 0.00 4.30
271 272 1.162698 GTCTCAAAGCAGCATCAGCA 58.837 50.000 0.00 0.00 45.49 4.41
272 273 1.130749 GTCTCAAAGCAGCATCAGCAG 59.869 52.381 0.00 0.00 45.49 4.24
273 274 1.166129 CTCAAAGCAGCATCAGCAGT 58.834 50.000 0.00 0.00 45.49 4.40
274 275 1.540267 CTCAAAGCAGCATCAGCAGTT 59.460 47.619 0.00 0.00 45.49 3.16
275 276 1.538512 TCAAAGCAGCATCAGCAGTTC 59.461 47.619 0.00 0.00 45.49 3.01
294 295 3.819188 GCACCAGCTGCAGTATCC 58.181 61.111 16.64 0.00 46.29 2.59
298 299 0.829333 ACCAGCTGCAGTATCCAGAG 59.171 55.000 16.64 0.00 32.03 3.35
306 307 3.173151 TGCAGTATCCAGAGGAAGAACA 58.827 45.455 0.00 0.00 34.34 3.18
309 310 3.196469 CAGTATCCAGAGGAAGAACAGCA 59.804 47.826 0.00 0.00 34.34 4.41
394 417 4.197498 CCCGGCGGTAGGTACGTG 62.197 72.222 26.32 1.35 0.00 4.49
395 418 4.860261 CCGGCGGTAGGTACGTGC 62.860 72.222 19.97 0.00 0.00 5.34
399 422 2.180017 CGGTAGGTACGTGCGCTT 59.820 61.111 9.73 0.00 0.00 4.68
401 424 1.509923 GGTAGGTACGTGCGCTTCT 59.490 57.895 9.73 0.00 0.00 2.85
402 425 0.801067 GGTAGGTACGTGCGCTTCTG 60.801 60.000 9.73 0.00 0.00 3.02
404 427 1.940883 TAGGTACGTGCGCTTCTGGG 61.941 60.000 9.73 0.00 0.00 4.45
528 564 1.681166 CCATGGGGTGCAGAGAAGAAG 60.681 57.143 2.85 0.00 0.00 2.85
529 565 1.280133 CATGGGGTGCAGAGAAGAAGA 59.720 52.381 0.00 0.00 0.00 2.87
530 566 0.979665 TGGGGTGCAGAGAAGAAGAG 59.020 55.000 0.00 0.00 0.00 2.85
531 567 0.392327 GGGGTGCAGAGAAGAAGAGC 60.392 60.000 0.00 0.00 0.00 4.09
550 586 2.339418 GCGAGCTAGCTAGACGAGATA 58.661 52.381 30.42 0.00 0.00 1.98
593 668 0.748450 TCTTGCTTTGCTTGCTTGCT 59.252 45.000 3.47 0.00 0.00 3.91
594 669 1.137479 TCTTGCTTTGCTTGCTTGCTT 59.863 42.857 3.47 0.00 0.00 3.91
595 670 1.260561 CTTGCTTTGCTTGCTTGCTTG 59.739 47.619 3.47 0.00 0.00 4.01
596 671 0.460722 TGCTTTGCTTGCTTGCTTGA 59.539 45.000 3.47 0.00 0.00 3.02
670 749 1.530771 CCCCATTCTCTCTGCCTGG 59.469 63.158 0.00 0.00 0.00 4.45
685 764 1.325476 CCTGGCCTGCCTCCAATTTC 61.325 60.000 9.97 0.00 36.94 2.17
689 768 1.379642 GCCTGCCTCCAATTTCCTCG 61.380 60.000 0.00 0.00 0.00 4.63
696 775 2.633488 CTCCAATTTCCTCGGTTCTCC 58.367 52.381 0.00 0.00 0.00 3.71
780 859 3.922850 GCTTTGCTCCTTTACATTTCTGC 59.077 43.478 0.00 0.00 0.00 4.26
797 876 4.392921 TCTGCAGCCAGAATTCTACTAC 57.607 45.455 9.47 4.46 44.79 2.73
798 877 4.026744 TCTGCAGCCAGAATTCTACTACT 58.973 43.478 9.47 0.41 44.79 2.57
799 878 4.098654 TCTGCAGCCAGAATTCTACTACTC 59.901 45.833 9.47 3.05 44.79 2.59
800 879 3.133003 TGCAGCCAGAATTCTACTACTCC 59.867 47.826 7.86 0.00 0.00 3.85
801 880 3.493524 GCAGCCAGAATTCTACTACTCCC 60.494 52.174 7.86 0.00 0.00 4.30
802 881 3.964031 CAGCCAGAATTCTACTACTCCCT 59.036 47.826 7.86 0.00 0.00 4.20
803 882 4.038642 CAGCCAGAATTCTACTACTCCCTC 59.961 50.000 7.86 0.00 0.00 4.30
804 883 4.078863 AGCCAGAATTCTACTACTCCCTCT 60.079 45.833 7.86 0.00 0.00 3.69
805 884 4.038642 GCCAGAATTCTACTACTCCCTCTG 59.961 50.000 7.86 0.00 0.00 3.35
806 885 5.205056 CCAGAATTCTACTACTCCCTCTGT 58.795 45.833 7.86 0.00 0.00 3.41
807 886 5.300792 CCAGAATTCTACTACTCCCTCTGTC 59.699 48.000 7.86 0.00 0.00 3.51
808 887 5.300792 CAGAATTCTACTACTCCCTCTGTCC 59.699 48.000 7.86 0.00 0.00 4.02
809 888 3.666345 TTCTACTACTCCCTCTGTCCC 57.334 52.381 0.00 0.00 0.00 4.46
810 889 2.570098 TCTACTACTCCCTCTGTCCCA 58.430 52.381 0.00 0.00 0.00 4.37
811 890 3.132056 TCTACTACTCCCTCTGTCCCAT 58.868 50.000 0.00 0.00 0.00 4.00
812 891 4.313362 TCTACTACTCCCTCTGTCCCATA 58.687 47.826 0.00 0.00 0.00 2.74
813 892 4.730392 TCTACTACTCCCTCTGTCCCATAA 59.270 45.833 0.00 0.00 0.00 1.90
814 893 4.561254 ACTACTCCCTCTGTCCCATAAT 57.439 45.455 0.00 0.00 0.00 1.28
815 894 5.681494 ACTACTCCCTCTGTCCCATAATA 57.319 43.478 0.00 0.00 0.00 0.98
816 895 6.234404 ACTACTCCCTCTGTCCCATAATAT 57.766 41.667 0.00 0.00 0.00 1.28
817 896 7.358255 ACTACTCCCTCTGTCCCATAATATA 57.642 40.000 0.00 0.00 0.00 0.86
818 897 7.776745 ACTACTCCCTCTGTCCCATAATATAA 58.223 38.462 0.00 0.00 0.00 0.98
819 898 7.896496 ACTACTCCCTCTGTCCCATAATATAAG 59.104 40.741 0.00 0.00 0.00 1.73
820 899 6.875469 ACTCCCTCTGTCCCATAATATAAGA 58.125 40.000 0.00 0.00 0.00 2.10
821 900 6.957020 ACTCCCTCTGTCCCATAATATAAGAG 59.043 42.308 0.00 0.00 0.00 2.85
822 901 5.721960 TCCCTCTGTCCCATAATATAAGAGC 59.278 44.000 0.00 0.00 0.00 4.09
823 902 5.394663 CCCTCTGTCCCATAATATAAGAGCG 60.395 48.000 0.00 0.00 0.00 5.03
824 903 5.186021 CCTCTGTCCCATAATATAAGAGCGT 59.814 44.000 0.00 0.00 0.00 5.07
825 904 6.295349 CCTCTGTCCCATAATATAAGAGCGTT 60.295 42.308 0.00 0.00 0.00 4.84
826 905 7.062749 TCTGTCCCATAATATAAGAGCGTTT 57.937 36.000 0.00 0.00 0.00 3.60
827 906 7.506114 TCTGTCCCATAATATAAGAGCGTTTT 58.494 34.615 0.00 0.00 0.00 2.43
828 907 7.990886 TCTGTCCCATAATATAAGAGCGTTTTT 59.009 33.333 0.00 0.00 0.00 1.94
829 908 7.925993 TGTCCCATAATATAAGAGCGTTTTTG 58.074 34.615 0.00 0.00 0.00 2.44
830 909 7.771361 TGTCCCATAATATAAGAGCGTTTTTGA 59.229 33.333 0.00 0.00 0.00 2.69
831 910 8.068380 GTCCCATAATATAAGAGCGTTTTTGAC 58.932 37.037 0.00 0.00 0.00 3.18
832 911 7.771361 TCCCATAATATAAGAGCGTTTTTGACA 59.229 33.333 0.00 0.00 0.00 3.58
833 912 7.855904 CCCATAATATAAGAGCGTTTTTGACAC 59.144 37.037 0.00 0.00 0.00 3.67
834 913 7.582679 CCATAATATAAGAGCGTTTTTGACACG 59.417 37.037 0.00 0.00 40.75 4.49
835 914 3.806316 ATAAGAGCGTTTTTGACACGG 57.194 42.857 0.00 0.00 38.13 4.94
836 915 1.658994 AAGAGCGTTTTTGACACGGA 58.341 45.000 0.00 0.00 38.13 4.69
837 916 1.217882 AGAGCGTTTTTGACACGGAG 58.782 50.000 0.00 0.00 38.13 4.63
839 918 2.129607 GAGCGTTTTTGACACGGAGTA 58.870 47.619 0.00 0.00 41.61 2.59
840 919 2.132762 AGCGTTTTTGACACGGAGTAG 58.867 47.619 0.00 0.00 41.61 2.57
841 920 1.398071 GCGTTTTTGACACGGAGTAGC 60.398 52.381 0.00 0.00 41.61 3.58
842 921 2.132762 CGTTTTTGACACGGAGTAGCT 58.867 47.619 0.00 0.00 41.61 3.32
843 922 2.096909 CGTTTTTGACACGGAGTAGCTG 60.097 50.000 0.00 0.00 41.61 4.24
844 923 2.870411 GTTTTTGACACGGAGTAGCTGT 59.130 45.455 0.00 0.00 41.61 4.40
856 935 4.815308 CGGAGTAGCTGTGTATGTAGTACT 59.185 45.833 0.00 0.00 34.27 2.73
863 942 5.035443 GCTGTGTATGTAGTACTGTGTAGC 58.965 45.833 5.39 1.35 34.27 3.58
988 1070 3.831911 CCACATGTTTTTATCACAGGGGT 59.168 43.478 0.00 0.00 26.84 4.95
996 1078 4.919774 TTTATCACAGGGGTAAAGCAGA 57.080 40.909 0.00 0.00 0.00 4.26
1043 1125 3.165606 GAGGTCGTCGTCCTCCTAA 57.834 57.895 23.14 0.00 43.90 2.69
1065 1147 3.264450 ACAAGGTGGGTTCTAGGATTCTG 59.736 47.826 0.00 0.00 0.00 3.02
1066 1148 1.840635 AGGTGGGTTCTAGGATTCTGC 59.159 52.381 0.00 0.00 0.00 4.26
1067 1149 1.840635 GGTGGGTTCTAGGATTCTGCT 59.159 52.381 0.00 0.00 0.00 4.24
1068 1150 2.239907 GGTGGGTTCTAGGATTCTGCTT 59.760 50.000 0.00 0.00 0.00 3.91
1069 1151 3.536570 GTGGGTTCTAGGATTCTGCTTC 58.463 50.000 0.00 0.00 0.00 3.86
1070 1152 3.198853 GTGGGTTCTAGGATTCTGCTTCT 59.801 47.826 0.00 0.00 0.00 2.85
1071 1153 3.198635 TGGGTTCTAGGATTCTGCTTCTG 59.801 47.826 0.00 0.00 0.00 3.02
1079 1161 4.734266 AGGATTCTGCTTCTGGTTCTTTT 58.266 39.130 0.00 0.00 0.00 2.27
1114 1196 5.892568 ACTGAGTTGGACACGATTAGTATC 58.107 41.667 0.00 0.00 0.00 2.24
1190 1272 1.098712 TTCAAGCCGAAAGTGCCGTT 61.099 50.000 0.00 0.00 0.00 4.44
1263 1346 3.784701 TTGAGCTGCTACTGCTAGTAC 57.215 47.619 0.15 0.00 38.70 2.73
1324 1411 8.941977 CAGTTTACTACATTACCAAGCACATTA 58.058 33.333 0.00 0.00 0.00 1.90
1341 1428 2.315925 TTATCTGCTCTTTCAGGCCG 57.684 50.000 0.00 0.00 34.91 6.13
1386 1473 7.907045 CCAATTGATGAAGAGTTAATGAAGACG 59.093 37.037 7.12 0.00 0.00 4.18
1433 1785 5.948481 ATTATGTATTGGGATTGGGGTCT 57.052 39.130 0.00 0.00 0.00 3.85
1505 1860 0.550914 TGGGGCTGACTGTCTGTTTT 59.449 50.000 14.85 0.00 0.00 2.43
1573 1933 5.049267 TGCGAGTTATAAAAGGTTGGTCAAC 60.049 40.000 5.35 5.35 40.45 3.18
1747 2107 2.664851 TTCCAAGCGGCACAGTCG 60.665 61.111 1.45 0.00 0.00 4.18
1927 2381 1.396653 CCTGCCAATCCAGGTGAATC 58.603 55.000 0.10 0.00 45.87 2.52
2041 2501 2.796383 CGGTGATGAAGATGACGAGGAC 60.796 54.545 0.00 0.00 0.00 3.85
2042 2502 2.455032 GTGATGAAGATGACGAGGACG 58.545 52.381 0.00 0.00 45.75 4.79
2043 2503 2.097629 GTGATGAAGATGACGAGGACGA 59.902 50.000 0.00 0.00 42.66 4.20
2044 2504 2.356069 TGATGAAGATGACGAGGACGAG 59.644 50.000 0.00 0.00 42.66 4.18
2045 2505 1.095600 TGAAGATGACGAGGACGAGG 58.904 55.000 0.00 0.00 42.66 4.63
2046 2506 1.339727 TGAAGATGACGAGGACGAGGA 60.340 52.381 0.00 0.00 42.66 3.71
2047 2507 1.064357 GAAGATGACGAGGACGAGGAC 59.936 57.143 0.00 0.00 42.66 3.85
2048 2508 1.090625 AGATGACGAGGACGAGGACG 61.091 60.000 0.00 0.00 42.66 4.79
2049 2509 1.078637 ATGACGAGGACGAGGACGA 60.079 57.895 0.00 0.00 42.66 4.20
2050 2510 1.090625 ATGACGAGGACGAGGACGAG 61.091 60.000 0.00 0.00 42.66 4.18
2051 2511 2.436292 ACGAGGACGAGGACGAGG 60.436 66.667 0.00 0.00 42.66 4.63
2052 2512 2.125229 CGAGGACGAGGACGAGGA 60.125 66.667 0.00 0.00 42.66 3.71
2104 2564 6.475504 AGATGACAATGATGTTGAGTTACCA 58.524 36.000 0.00 0.00 40.74 3.25
2124 2584 2.500910 CAGAGTCTCTCCCAAGCTCAAT 59.499 50.000 0.00 0.00 0.00 2.57
2536 2997 5.117135 CACGATATCGATATGTGTGGTGTTC 59.883 44.000 30.75 10.63 43.02 3.18
2554 3015 4.879545 GTGTTCACTGTTTAGGTTCTTCCA 59.120 41.667 0.00 0.00 39.02 3.53
2650 3111 1.907739 CCAGCTTGGGGAGATCGAA 59.092 57.895 0.00 0.00 32.67 3.71
2653 3114 4.063815 CCAGCTTGGGGAGATCGAAAGA 62.064 54.545 0.00 0.00 38.16 2.52
2800 3264 5.027737 CGTATGCGTTTTAACTGCATGATT 58.972 37.500 22.76 9.78 43.49 2.57
2944 3437 2.202932 CAGAAGGCGCGGCAGTAT 60.203 61.111 34.94 16.56 0.00 2.12
2958 3451 2.102749 GTATGCCGCGTCCGTGTA 59.897 61.111 4.92 0.00 0.00 2.90
2962 3455 0.032952 ATGCCGCGTCCGTGTATAAT 59.967 50.000 4.92 0.00 0.00 1.28
2988 3481 6.730619 CACGTTGTTGTTTGAGTTATATCGAC 59.269 38.462 0.00 0.00 0.00 4.20
3089 3582 6.115448 TCCTATTTAGAGGAATTAGCTGCC 57.885 41.667 0.00 0.00 42.90 4.85
3274 3767 2.485266 AGCGTTGGTAAAAACAGCAC 57.515 45.000 0.00 0.00 34.34 4.40
3287 3780 2.108514 CAGCACTGGTATGGCCGTG 61.109 63.158 8.05 4.63 41.41 4.94
3407 4125 3.256879 TGTTTTTCCATGGCAGCGAAATA 59.743 39.130 6.96 5.66 0.00 1.40
3444 4163 4.458989 GCAACATACCAGAACAATTGAGGA 59.541 41.667 13.59 0.00 0.00 3.71
3451 4170 3.349927 CAGAACAATTGAGGAGCCATGA 58.650 45.455 13.59 0.00 0.00 3.07
3468 4187 6.739112 AGCCATGACAAAACTTTTTCTAGTC 58.261 36.000 0.00 0.00 0.00 2.59
3700 5695 1.208614 GCAAGCACGGAAGCAGAAG 59.791 57.895 0.00 0.00 36.85 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 0.030369 GAGGACACGTGTTCACTCGT 59.970 55.000 28.21 13.90 45.34 4.18
53 54 1.007271 CGCAGAGAGGACACGTGTT 60.007 57.895 24.26 7.79 0.00 3.32
77 78 2.267006 CGGGCTGCAGAGACACAT 59.733 61.111 20.43 0.00 0.00 3.21
98 99 1.446272 CTCCAGGAAAGACGACGGC 60.446 63.158 0.00 0.00 0.00 5.68
120 121 1.753463 GGAGGATCGGGTGAGACGT 60.753 63.158 0.00 0.00 34.37 4.34
142 143 2.125512 CGAGGCGGGAGAAGGTTG 60.126 66.667 0.00 0.00 0.00 3.77
176 177 2.522436 AGTGACCCGTGGACCGAA 60.522 61.111 0.00 0.00 39.56 4.30
208 209 5.300539 TGAAACATTTTTACAGTAGGCAGCA 59.699 36.000 0.00 0.00 0.00 4.41
235 236 1.228459 ACGTTTGGGAGGGAAAGCC 60.228 57.895 0.00 0.00 0.00 4.35
247 248 2.031769 TGATGCTGCTTTGAGACGTTTG 60.032 45.455 0.00 0.00 0.00 2.93
294 295 1.440708 CAGCTGCTGTTCTTCCTCTG 58.559 55.000 21.21 0.00 0.00 3.35
298 299 2.684843 CCGCAGCTGCTGTTCTTCC 61.685 63.158 34.22 11.47 39.32 3.46
362 383 2.352032 CGGGAGTGAGGGACAGGAC 61.352 68.421 0.00 0.00 0.00 3.85
374 397 2.440980 GTACCTACCGCCGGGAGT 60.441 66.667 15.62 7.42 36.97 3.85
383 406 0.801067 CAGAAGCGCACGTACCTACC 60.801 60.000 11.47 0.00 0.00 3.18
394 417 0.464554 AAATCCTAGCCCAGAAGCGC 60.465 55.000 0.00 0.00 38.01 5.92
395 418 1.672881 CAAAATCCTAGCCCAGAAGCG 59.327 52.381 0.00 0.00 38.01 4.68
399 422 0.926293 CCCCAAAATCCTAGCCCAGA 59.074 55.000 0.00 0.00 0.00 3.86
401 424 0.926293 CTCCCCAAAATCCTAGCCCA 59.074 55.000 0.00 0.00 0.00 5.36
402 425 0.186143 CCTCCCCAAAATCCTAGCCC 59.814 60.000 0.00 0.00 0.00 5.19
404 427 3.602205 AATCCTCCCCAAAATCCTAGC 57.398 47.619 0.00 0.00 0.00 3.42
407 430 3.468625 AGCATAATCCTCCCCAAAATCCT 59.531 43.478 0.00 0.00 0.00 3.24
528 564 0.511221 CTCGTCTAGCTAGCTCGCTC 59.489 60.000 23.26 10.42 41.30 5.03
529 565 0.105224 TCTCGTCTAGCTAGCTCGCT 59.895 55.000 23.26 17.70 43.83 4.93
530 566 1.153353 ATCTCGTCTAGCTAGCTCGC 58.847 55.000 23.26 11.53 0.00 5.03
531 567 2.669434 GGTATCTCGTCTAGCTAGCTCG 59.331 54.545 23.26 18.97 0.00 5.03
550 586 2.093447 CAGAAATCTTAGGAGCACGGGT 60.093 50.000 0.00 0.00 0.00 5.28
593 668 6.599244 CCTAGCAAACTGGTAATCAGAATCAA 59.401 38.462 0.00 0.00 46.18 2.57
594 669 6.115446 CCTAGCAAACTGGTAATCAGAATCA 58.885 40.000 0.00 0.00 46.18 2.57
595 670 6.116126 ACCTAGCAAACTGGTAATCAGAATC 58.884 40.000 0.00 0.00 46.18 2.52
596 671 6.067217 ACCTAGCAAACTGGTAATCAGAAT 57.933 37.500 0.00 0.00 46.18 2.40
670 749 1.379642 CGAGGAAATTGGAGGCAGGC 61.380 60.000 0.00 0.00 0.00 4.85
711 790 6.961086 GGGCTACCAGAATCACAGGAAGTG 62.961 54.167 0.00 0.00 42.56 3.16
712 791 2.237392 GGCTACCAGAATCACAGGAAGT 59.763 50.000 0.00 0.00 0.00 3.01
713 792 2.420687 GGGCTACCAGAATCACAGGAAG 60.421 54.545 0.00 0.00 36.50 3.46
754 833 0.608035 TGTAAAGGAGCAAAGCCCCG 60.608 55.000 0.00 0.00 0.00 5.73
767 846 4.771590 TTCTGGCTGCAGAAATGTAAAG 57.228 40.909 20.43 2.18 38.15 1.85
769 848 5.012239 AGAATTCTGGCTGCAGAAATGTAA 58.988 37.500 20.43 3.48 43.44 2.41
771 850 3.428532 AGAATTCTGGCTGCAGAAATGT 58.571 40.909 20.43 6.30 43.44 2.71
780 859 3.964031 AGGGAGTAGTAGAATTCTGGCTG 59.036 47.826 18.47 0.00 0.00 4.85
805 884 8.068380 GTCAAAAACGCTCTTATATTATGGGAC 58.932 37.037 0.00 0.00 0.00 4.46
806 885 7.771361 TGTCAAAAACGCTCTTATATTATGGGA 59.229 33.333 0.00 0.00 0.00 4.37
807 886 7.855904 GTGTCAAAAACGCTCTTATATTATGGG 59.144 37.037 0.00 0.00 35.42 4.00
808 887 7.582679 CGTGTCAAAAACGCTCTTATATTATGG 59.417 37.037 0.00 0.00 36.18 2.74
809 888 7.582679 CCGTGTCAAAAACGCTCTTATATTATG 59.417 37.037 0.00 0.00 39.69 1.90
810 889 7.493320 TCCGTGTCAAAAACGCTCTTATATTAT 59.507 33.333 0.00 0.00 39.69 1.28
811 890 6.812656 TCCGTGTCAAAAACGCTCTTATATTA 59.187 34.615 0.00 0.00 39.69 0.98
812 891 5.640357 TCCGTGTCAAAAACGCTCTTATATT 59.360 36.000 0.00 0.00 39.69 1.28
813 892 5.172934 TCCGTGTCAAAAACGCTCTTATAT 58.827 37.500 0.00 0.00 39.69 0.86
814 893 4.558178 TCCGTGTCAAAAACGCTCTTATA 58.442 39.130 0.00 0.00 39.69 0.98
815 894 3.395639 TCCGTGTCAAAAACGCTCTTAT 58.604 40.909 0.00 0.00 39.69 1.73
816 895 2.798283 CTCCGTGTCAAAAACGCTCTTA 59.202 45.455 0.00 0.00 39.69 2.10
817 896 1.597663 CTCCGTGTCAAAAACGCTCTT 59.402 47.619 0.00 0.00 39.69 2.85
818 897 1.217882 CTCCGTGTCAAAAACGCTCT 58.782 50.000 0.00 0.00 39.69 4.09
819 898 0.935196 ACTCCGTGTCAAAAACGCTC 59.065 50.000 0.00 0.00 39.69 5.03
820 899 2.132762 CTACTCCGTGTCAAAAACGCT 58.867 47.619 0.00 0.00 39.69 5.07
821 900 1.398071 GCTACTCCGTGTCAAAAACGC 60.398 52.381 0.00 0.00 39.69 4.84
822 901 2.096909 CAGCTACTCCGTGTCAAAAACG 60.097 50.000 0.00 0.00 40.70 3.60
823 902 2.870411 ACAGCTACTCCGTGTCAAAAAC 59.130 45.455 0.00 0.00 0.00 2.43
824 903 2.869801 CACAGCTACTCCGTGTCAAAAA 59.130 45.455 0.00 0.00 0.00 1.94
825 904 2.159014 ACACAGCTACTCCGTGTCAAAA 60.159 45.455 1.14 0.00 39.64 2.44
826 905 1.411246 ACACAGCTACTCCGTGTCAAA 59.589 47.619 1.14 0.00 39.64 2.69
827 906 1.037493 ACACAGCTACTCCGTGTCAA 58.963 50.000 1.14 0.00 39.64 3.18
828 907 1.900245 TACACAGCTACTCCGTGTCA 58.100 50.000 9.80 0.00 42.65 3.58
829 908 2.163815 ACATACACAGCTACTCCGTGTC 59.836 50.000 9.80 0.00 42.65 3.67
830 909 2.168496 ACATACACAGCTACTCCGTGT 58.832 47.619 11.09 11.09 45.42 4.49
831 910 2.941453 ACATACACAGCTACTCCGTG 57.059 50.000 0.00 0.00 36.70 4.94
832 911 3.618351 ACTACATACACAGCTACTCCGT 58.382 45.455 0.00 0.00 0.00 4.69
833 912 4.815308 AGTACTACATACACAGCTACTCCG 59.185 45.833 0.00 0.00 36.09 4.63
834 913 5.589452 ACAGTACTACATACACAGCTACTCC 59.411 44.000 0.00 0.00 36.09 3.85
835 914 6.093771 ACACAGTACTACATACACAGCTACTC 59.906 42.308 0.00 0.00 36.09 2.59
836 915 5.944599 ACACAGTACTACATACACAGCTACT 59.055 40.000 0.00 0.00 36.09 2.57
837 916 6.192234 ACACAGTACTACATACACAGCTAC 57.808 41.667 0.00 0.00 36.09 3.58
838 917 6.037940 GCTACACAGTACTACATACACAGCTA 59.962 42.308 0.00 0.00 36.09 3.32
839 918 5.163642 GCTACACAGTACTACATACACAGCT 60.164 44.000 0.00 0.00 36.09 4.24
840 919 5.035443 GCTACACAGTACTACATACACAGC 58.965 45.833 0.00 0.00 36.09 4.40
841 920 5.064325 TCGCTACACAGTACTACATACACAG 59.936 44.000 0.00 0.00 36.09 3.66
842 921 4.937015 TCGCTACACAGTACTACATACACA 59.063 41.667 0.00 0.00 36.09 3.72
843 922 5.292834 TCTCGCTACACAGTACTACATACAC 59.707 44.000 0.00 0.00 36.09 2.90
844 923 5.422145 TCTCGCTACACAGTACTACATACA 58.578 41.667 0.00 0.00 36.09 2.29
845 924 5.980698 TCTCGCTACACAGTACTACATAC 57.019 43.478 0.00 0.00 0.00 2.39
847 926 4.698780 TGTTCTCGCTACACAGTACTACAT 59.301 41.667 0.00 0.00 0.00 2.29
851 930 3.409570 TCTGTTCTCGCTACACAGTACT 58.590 45.455 0.00 0.00 39.24 2.73
856 935 0.243907 GGCTCTGTTCTCGCTACACA 59.756 55.000 0.00 0.00 0.00 3.72
863 942 1.447489 CTGCCAGGCTCTGTTCTCG 60.447 63.158 14.15 0.00 0.00 4.04
890 972 1.337260 CCTGACTGTCCCTCAACTTCG 60.337 57.143 5.17 0.00 0.00 3.79
938 1020 4.517285 CTCAGTGTGGCCATAAGTAACAT 58.483 43.478 9.72 0.00 0.00 2.71
988 1070 3.611530 GCTGCGTCCATTTTTCTGCTTTA 60.612 43.478 0.00 0.00 0.00 1.85
996 1078 1.539827 GTACCTGCTGCGTCCATTTTT 59.460 47.619 0.00 0.00 0.00 1.94
1043 1125 3.264450 CAGAATCCTAGAACCCACCTTGT 59.736 47.826 0.00 0.00 0.00 3.16
1065 1147 5.139435 AGCCATTAAAAAGAACCAGAAGC 57.861 39.130 0.00 0.00 0.00 3.86
1066 1148 9.788960 GTATTAGCCATTAAAAAGAACCAGAAG 57.211 33.333 0.00 0.00 0.00 2.85
1067 1149 9.528489 AGTATTAGCCATTAAAAAGAACCAGAA 57.472 29.630 0.00 0.00 0.00 3.02
1068 1150 8.956426 CAGTATTAGCCATTAAAAAGAACCAGA 58.044 33.333 0.00 0.00 0.00 3.86
1069 1151 8.956426 TCAGTATTAGCCATTAAAAAGAACCAG 58.044 33.333 0.00 0.00 0.00 4.00
1070 1152 8.871629 TCAGTATTAGCCATTAAAAAGAACCA 57.128 30.769 0.00 0.00 0.00 3.67
1071 1153 8.957466 ACTCAGTATTAGCCATTAAAAAGAACC 58.043 33.333 0.00 0.00 0.00 3.62
1079 1161 6.821665 GTGTCCAACTCAGTATTAGCCATTAA 59.178 38.462 0.00 0.00 0.00 1.40
1114 1196 8.154649 ACAACAAGAAAACACCTATCAGTAAG 57.845 34.615 0.00 0.00 0.00 2.34
1190 1272 1.067250 GGTTTCTTTGGCTTGCGCA 59.933 52.632 5.66 5.66 38.10 6.09
1263 1346 9.350357 CAGGTGAACAAAATTTGAGAGATATTG 57.650 33.333 13.19 0.00 0.00 1.90
1324 1411 1.451028 GCGGCCTGAAAGAGCAGAT 60.451 57.895 0.00 0.00 38.14 2.90
1341 1428 2.687935 TGGTTTTGTCTCTTCCAGTTGC 59.312 45.455 0.00 0.00 0.00 4.17
1386 1473 2.497675 TGACTAATCACTCACCCTCAGC 59.502 50.000 0.00 0.00 0.00 4.26
1573 1933 2.654749 TGTGTACTTCGCTGATCTGG 57.345 50.000 1.46 0.00 0.00 3.86
1576 1936 7.234187 TCATTTTATGTGTACTTCGCTGATC 57.766 36.000 0.00 0.00 0.00 2.92
1741 2101 0.603975 GCTTCTGCTTTCCCGACTGT 60.604 55.000 0.00 0.00 36.03 3.55
1747 2107 1.039856 TTGGTTGCTTCTGCTTTCCC 58.960 50.000 0.00 0.00 40.48 3.97
1927 2381 2.947852 ACGAATGAACCGAAGTCTCAG 58.052 47.619 0.00 0.00 0.00 3.35
2041 2501 0.028242 CATCTTCGTCCTCGTCCTCG 59.972 60.000 0.00 0.00 38.33 4.63
2042 2502 1.380524 TCATCTTCGTCCTCGTCCTC 58.619 55.000 0.00 0.00 38.33 3.71
2043 2503 1.678627 CATCATCTTCGTCCTCGTCCT 59.321 52.381 0.00 0.00 38.33 3.85
2044 2504 1.676529 TCATCATCTTCGTCCTCGTCC 59.323 52.381 0.00 0.00 38.33 4.79
2045 2505 3.634568 ATCATCATCTTCGTCCTCGTC 57.365 47.619 0.00 0.00 38.33 4.20
2046 2506 5.010112 ACATTATCATCATCTTCGTCCTCGT 59.990 40.000 0.00 0.00 38.33 4.18
2047 2507 5.465051 ACATTATCATCATCTTCGTCCTCG 58.535 41.667 0.00 0.00 38.55 4.63
2048 2508 6.703607 ACAACATTATCATCATCTTCGTCCTC 59.296 38.462 0.00 0.00 0.00 3.71
2049 2509 6.586344 ACAACATTATCATCATCTTCGTCCT 58.414 36.000 0.00 0.00 0.00 3.85
2050 2510 6.851222 ACAACATTATCATCATCTTCGTCC 57.149 37.500 0.00 0.00 0.00 4.79
2051 2511 7.043391 TCGAACAACATTATCATCATCTTCGTC 60.043 37.037 0.00 0.00 0.00 4.20
2052 2512 6.756542 TCGAACAACATTATCATCATCTTCGT 59.243 34.615 0.00 0.00 0.00 3.85
2104 2564 2.317371 TTGAGCTTGGGAGAGACTCT 57.683 50.000 4.14 4.14 0.00 3.24
2124 2584 4.486125 TGGATGGAAGATTCACATTCGA 57.514 40.909 0.00 0.00 0.00 3.71
2340 2801 1.315257 CCTTGACAATGGCCCTTCCG 61.315 60.000 0.00 0.00 37.80 4.30
2536 2997 4.278170 TGCAATGGAAGAACCTAAACAGTG 59.722 41.667 0.00 0.00 39.86 3.66
2554 3015 2.357836 CCTGGGCTCACCTGCAAT 59.642 61.111 0.00 0.00 41.11 3.56
2650 3111 0.392706 TCACCACGACATGCTGTCTT 59.607 50.000 12.45 3.08 44.85 3.01
2653 3114 4.361253 GTCACCACGACATGCTGT 57.639 55.556 0.00 0.00 44.69 4.40
2940 3433 1.731433 ATACACGGACGCGGCATACT 61.731 55.000 17.00 0.00 0.00 2.12
2942 3435 0.667453 TTATACACGGACGCGGCATA 59.333 50.000 17.00 0.00 0.00 3.14
2944 3437 0.595567 GATTATACACGGACGCGGCA 60.596 55.000 17.00 0.00 0.00 5.69
2962 3455 6.641723 TCGATATAACTCAAACAACAACGTGA 59.358 34.615 0.00 0.00 0.00 4.35
2988 3481 8.574196 AGAATTCATTGGTGTTAAGAAAAACG 57.426 30.769 8.44 0.00 31.76 3.60
3015 3508 7.382759 GGAGCTATCGTTTTCCTCTAACATTAG 59.617 40.741 0.00 0.00 0.00 1.73
3021 3514 5.670792 TTGGAGCTATCGTTTTCCTCTAA 57.329 39.130 0.00 0.00 0.00 2.10
3087 3580 1.523758 ACATCAAAGGTCGTTGAGGC 58.476 50.000 10.21 0.00 41.78 4.70
3089 3582 3.362986 CGACAACATCAAAGGTCGTTGAG 60.363 47.826 8.02 0.00 45.73 3.02
3153 3646 9.769093 ATTTCGTTTTTGCTATGTAACTGTATC 57.231 29.630 0.00 0.00 0.00 2.24
3238 3731 0.108329 GCTAGCTTCGCCAACTACCA 60.108 55.000 7.70 0.00 0.00 3.25
3274 3767 2.514592 CCAGCACGGCCATACCAG 60.515 66.667 2.24 0.00 39.03 4.00
3287 3780 1.143401 GCCTACCGTCCTAACCAGC 59.857 63.158 0.00 0.00 0.00 4.85
3378 4096 5.389725 CGCTGCCATGGAAAAACAATTTTAG 60.390 40.000 18.40 0.00 38.83 1.85
3407 4125 8.584157 TCTGGTATGTTGCTATGAACAATTTTT 58.416 29.630 0.00 0.00 39.25 1.94
3444 4163 6.513393 CGACTAGAAAAAGTTTTGTCATGGCT 60.513 38.462 13.74 3.13 0.00 4.75
3451 4170 9.028185 CAGTACTACGACTAGAAAAAGTTTTGT 57.972 33.333 0.61 0.00 0.00 2.83
3468 4187 3.206964 TCTGGAGATGCTCAGTACTACG 58.793 50.000 0.00 0.00 31.08 3.51


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

AutoCloner maintained by Alex Coulton.