Multiple sequence alignment - TraesCS5B01G422600

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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 TraesCS5B01G422600 chr5B 100.000 3925 0 0 1 3925 597856551 597852627 0.000000e+00 7249.0
1 TraesCS5B01G422600 chr5B 89.455 844 77 10 46 885 17578143 17578978 0.000000e+00 1055.0
2 TraesCS5B01G422600 chr5D 92.895 2463 134 24 912 3347 486444315 486441867 0.000000e+00 3541.0
3 TraesCS5B01G422600 chr5D 87.811 845 84 16 55 890 340508703 340507869 0.000000e+00 972.0
4 TraesCS5B01G422600 chr5D 88.086 512 42 9 3420 3919 486441725 486441221 1.210000e-164 590.0
5 TraesCS5B01G422600 chr5D 93.506 77 5 0 1 77 404187868 404187792 8.910000e-22 115.0
6 TraesCS5B01G422600 chr5D 86.000 100 11 3 1 99 23279378 23279475 1.930000e-18 104.0
7 TraesCS5B01G422600 chr5D 83.133 83 1 4 3358 3427 486441835 486441753 3.270000e-06 63.9
8 TraesCS5B01G422600 chr5A 92.597 2391 140 19 971 3350 606960594 606958230 0.000000e+00 3400.0
9 TraesCS5B01G422600 chr5A 87.336 837 96 9 55 888 554071921 554071092 0.000000e+00 950.0
10 TraesCS5B01G422600 chr5A 83.890 509 53 11 3420 3925 606958094 606957612 3.570000e-125 459.0
11 TraesCS5B01G422600 chr2B 89.850 867 74 9 55 913 465669182 465668322 0.000000e+00 1101.0
12 TraesCS5B01G422600 chr2B 90.334 838 74 6 56 890 24843464 24844297 0.000000e+00 1092.0
13 TraesCS5B01G422600 chr3B 88.760 863 86 7 56 913 774817841 774816985 0.000000e+00 1046.0
14 TraesCS5B01G422600 chr3B 89.513 801 76 6 56 856 239896266 239897058 0.000000e+00 1007.0
15 TraesCS5B01G422600 chr6B 87.673 868 93 13 55 913 84748809 84749671 0.000000e+00 998.0
16 TraesCS5B01G422600 chr7A 85.763 878 99 20 55 913 467784165 467785035 0.000000e+00 905.0
17 TraesCS5B01G422600 chr6D 94.805 77 4 0 1 77 451075572 451075648 1.920000e-23 121.0
18 TraesCS5B01G422600 chr3D 93.506 77 5 0 1 77 15903441 15903517 8.910000e-22 115.0
19 TraesCS5B01G422600 chr1D 93.506 77 5 0 1 77 467389091 467389167 8.910000e-22 115.0
20 TraesCS5B01G422600 chr1A 93.506 77 5 0 1 77 577153815 577153739 8.910000e-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 TraesCS5B01G422600 chr5B 597852627 597856551 3924 True 7249.0 7249 100.0000 1 3925 1 chr5B.!!$R1 3924
1 TraesCS5B01G422600 chr5B 17578143 17578978 835 False 1055.0 1055 89.4550 46 885 1 chr5B.!!$F1 839
2 TraesCS5B01G422600 chr5D 486441221 486444315 3094 True 1398.3 3541 88.0380 912 3919 3 chr5D.!!$R3 3007
3 TraesCS5B01G422600 chr5D 340507869 340508703 834 True 972.0 972 87.8110 55 890 1 chr5D.!!$R1 835
4 TraesCS5B01G422600 chr5A 606957612 606960594 2982 True 1929.5 3400 88.2435 971 3925 2 chr5A.!!$R2 2954
5 TraesCS5B01G422600 chr5A 554071092 554071921 829 True 950.0 950 87.3360 55 888 1 chr5A.!!$R1 833
6 TraesCS5B01G422600 chr2B 465668322 465669182 860 True 1101.0 1101 89.8500 55 913 1 chr2B.!!$R1 858
7 TraesCS5B01G422600 chr2B 24843464 24844297 833 False 1092.0 1092 90.3340 56 890 1 chr2B.!!$F1 834
8 TraesCS5B01G422600 chr3B 774816985 774817841 856 True 1046.0 1046 88.7600 56 913 1 chr3B.!!$R1 857
9 TraesCS5B01G422600 chr3B 239896266 239897058 792 False 1007.0 1007 89.5130 56 856 1 chr3B.!!$F1 800
10 TraesCS5B01G422600 chr6B 84748809 84749671 862 False 998.0 998 87.6730 55 913 1 chr6B.!!$F1 858
11 TraesCS5B01G422600 chr7A 467784165 467785035 870 False 905.0 905 85.7630 55 913 1 chr7A.!!$F1 858

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
30 31 0.037975 GAGCCTGGCCACACATTTTG 60.038 55.0 16.57 0.0 0.00 2.44 F
707 737 0.185901 AAATGTCCACACACCAGCCT 59.814 50.0 0.00 0.0 34.48 4.58 F
1765 1802 0.110486 TGCACCAAGAAAGGAGGACC 59.890 55.0 0.00 0.0 0.00 4.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1692 1729 0.032217 CTTCCTCCTCTGCCCTCTCT 60.032 60.0 0.00 0.0 0.00 3.10 R
1990 2027 0.035176 TTGCCATTCTTGCAAAGGCC 59.965 50.0 21.76 0.0 46.24 5.19 R
3736 3883 0.033504 ACCACAGAAACTCGATGCGT 59.966 50.0 0.00 0.0 0.00 5.24 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
18 19 2.074967 TGGGTGTTAAGGAGCCTGG 58.925 57.895 4.68 0.00 31.85 4.45
19 20 1.378646 GGGTGTTAAGGAGCCTGGC 60.379 63.158 11.65 11.65 0.00 4.85
20 21 1.378646 GGTGTTAAGGAGCCTGGCC 60.379 63.158 16.57 6.85 0.00 5.36
21 22 1.378762 GTGTTAAGGAGCCTGGCCA 59.621 57.895 16.57 4.71 0.00 5.36
22 23 0.960861 GTGTTAAGGAGCCTGGCCAC 60.961 60.000 16.57 10.55 0.00 5.01
23 24 1.378762 GTTAAGGAGCCTGGCCACA 59.621 57.895 16.57 0.00 0.00 4.17
24 25 0.960861 GTTAAGGAGCCTGGCCACAC 60.961 60.000 16.57 3.10 0.00 3.82
25 26 1.422977 TTAAGGAGCCTGGCCACACA 61.423 55.000 16.57 0.00 0.00 3.72
26 27 1.207488 TAAGGAGCCTGGCCACACAT 61.207 55.000 16.57 0.00 0.00 3.21
27 28 2.036256 GGAGCCTGGCCACACATT 59.964 61.111 16.57 0.00 0.00 2.71
28 29 1.607467 GGAGCCTGGCCACACATTT 60.607 57.895 16.57 0.00 0.00 2.32
29 30 1.187567 GGAGCCTGGCCACACATTTT 61.188 55.000 16.57 0.00 0.00 1.82
30 31 0.037975 GAGCCTGGCCACACATTTTG 60.038 55.000 16.57 0.00 0.00 2.44
31 32 0.760189 AGCCTGGCCACACATTTTGT 60.760 50.000 16.57 0.00 39.97 2.83
32 33 0.965439 GCCTGGCCACACATTTTGTA 59.035 50.000 7.66 0.00 35.67 2.41
33 34 1.550072 GCCTGGCCACACATTTTGTAT 59.450 47.619 7.66 0.00 35.67 2.29
34 35 2.674747 GCCTGGCCACACATTTTGTATG 60.675 50.000 7.66 0.00 35.67 2.39
36 37 2.562298 CTGGCCACACATTTTGTATGGT 59.438 45.455 0.00 0.00 46.28 3.55
37 38 2.298446 TGGCCACACATTTTGTATGGTG 59.702 45.455 0.00 0.00 46.28 4.17
38 39 2.298729 GGCCACACATTTTGTATGGTGT 59.701 45.455 6.80 0.00 46.28 4.16
39 40 3.574614 GCCACACATTTTGTATGGTGTC 58.425 45.455 6.80 0.00 46.28 3.67
40 41 3.255642 GCCACACATTTTGTATGGTGTCT 59.744 43.478 6.80 0.00 46.28 3.41
41 42 4.457603 GCCACACATTTTGTATGGTGTCTA 59.542 41.667 6.80 0.00 46.28 2.59
42 43 5.048364 GCCACACATTTTGTATGGTGTCTAA 60.048 40.000 6.80 0.00 46.28 2.10
43 44 6.611381 CCACACATTTTGTATGGTGTCTAAG 58.389 40.000 0.00 0.00 39.97 2.18
44 45 6.429692 CCACACATTTTGTATGGTGTCTAAGA 59.570 38.462 0.00 0.00 39.97 2.10
47 48 6.878923 CACATTTTGTATGGTGTCTAAGAGGA 59.121 38.462 0.00 0.00 0.00 3.71
51 52 4.023980 TGTATGGTGTCTAAGAGGACCAG 58.976 47.826 0.00 0.00 41.72 4.00
53 54 0.537653 GGTGTCTAAGAGGACCAGCC 59.462 60.000 0.00 0.00 35.54 4.85
87 88 3.258123 GTGTGGGCAAAATGGATAACTGT 59.742 43.478 0.00 0.00 0.00 3.55
273 285 1.411394 CATTTTGGACAACTGCAGCG 58.589 50.000 15.27 8.03 0.00 5.18
306 318 8.598202 TGTATGGTCTGGTTTACTATAGTTGA 57.402 34.615 11.40 0.00 0.00 3.18
310 322 8.598202 TGGTCTGGTTTACTATAGTTGACATA 57.402 34.615 11.40 3.30 0.00 2.29
311 323 9.209048 TGGTCTGGTTTACTATAGTTGACATAT 57.791 33.333 11.40 0.00 0.00 1.78
596 625 7.817418 AAAAGAGTTGCCATCTACTTACAAA 57.183 32.000 0.00 0.00 0.00 2.83
630 659 3.321682 AGTTGCCATGTACACTGCAAAAT 59.678 39.130 26.49 18.58 44.44 1.82
677 707 0.954449 GAGAGGAGACGGACGTGTGA 60.954 60.000 0.53 0.00 0.00 3.58
693 723 1.089920 GTGAGCGAGATGGCAAATGT 58.910 50.000 0.00 0.00 34.64 2.71
707 737 0.185901 AAATGTCCACACACCAGCCT 59.814 50.000 0.00 0.00 34.48 4.58
760 790 1.153147 TGCTAAACGCCCACACACA 60.153 52.632 0.00 0.00 38.05 3.72
761 791 1.281656 GCTAAACGCCCACACACAC 59.718 57.895 0.00 0.00 0.00 3.82
793 826 0.806884 GTGGTGAAACGGACGTGTGA 60.807 55.000 0.00 0.00 38.12 3.58
849 882 4.009675 CCTATGTGGCACTACAAACATGT 58.990 43.478 19.83 0.00 35.07 3.21
863 896 4.022935 ACAAACATGTCAAGATTCGTGCAT 60.023 37.500 0.00 0.32 0.00 3.96
875 908 4.400251 AGATTCGTGCATTCACAAATGGAT 59.600 37.500 0.00 0.00 43.86 3.41
902 939 1.526887 CCACGCGTATAGGATGCAAAG 59.473 52.381 13.44 0.00 40.42 2.77
915 952 3.454941 GCAAAGGCACACACGTTAG 57.545 52.632 0.00 0.00 40.72 2.34
916 953 0.661020 GCAAAGGCACACACGTTAGT 59.339 50.000 0.00 0.00 40.72 2.24
917 954 1.596954 GCAAAGGCACACACGTTAGTG 60.597 52.381 11.71 11.71 46.31 2.74
934 971 5.618395 CGTTAGTGTTTCCGTTAAGAAAAGC 59.382 40.000 0.00 0.00 37.49 3.51
941 978 6.852345 TGTTTCCGTTAAGAAAAGCGTAATTC 59.148 34.615 0.00 0.00 37.49 2.17
956 993 4.882447 CGTAATTCAGTTTACGCCTTGAG 58.118 43.478 4.11 0.00 45.28 3.02
962 999 2.993899 CAGTTTACGCCTTGAGTCGATT 59.006 45.455 0.00 0.00 0.00 3.34
963 1000 4.082625 TCAGTTTACGCCTTGAGTCGATTA 60.083 41.667 0.00 0.00 0.00 1.75
977 1014 4.945246 AGTCGATTATAATGTGGTTCGCT 58.055 39.130 1.78 0.00 0.00 4.93
984 1021 0.327924 AATGTGGTTCGCTCCATCCA 59.672 50.000 2.07 0.00 39.81 3.41
1532 1569 3.338250 GGTGCACCATCAGGGGGA 61.338 66.667 31.23 0.00 46.16 4.81
1533 1570 2.693871 GGTGCACCATCAGGGGGAT 61.694 63.158 31.23 0.00 46.16 3.85
1535 1572 0.753111 GTGCACCATCAGGGGGATTC 60.753 60.000 5.22 0.00 46.16 2.52
1560 1597 2.108157 AAGTCTGTTGTCGCGGCA 59.892 55.556 10.57 10.57 0.00 5.69
1690 1727 1.201424 GTCCGAGGGGTTCAGGTTAT 58.799 55.000 0.00 0.00 33.83 1.89
1692 1729 1.200519 CCGAGGGGTTCAGGTTATCA 58.799 55.000 0.00 0.00 0.00 2.15
1695 1732 2.101582 CGAGGGGTTCAGGTTATCAGAG 59.898 54.545 0.00 0.00 0.00 3.35
1765 1802 0.110486 TGCACCAAGAAAGGAGGACC 59.890 55.000 0.00 0.00 0.00 4.46
1830 1867 2.186903 GCGAAGGAGATGGCGGAA 59.813 61.111 0.00 0.00 0.00 4.30
1896 1933 2.093394 TCTCTTGGTTTGTTCGGTGTCA 60.093 45.455 0.00 0.00 0.00 3.58
1947 1984 5.178096 TCTGCAAGTTCATGATAGGGAAA 57.822 39.130 0.00 0.00 33.76 3.13
1956 1993 8.100135 AGTTCATGATAGGGAAAGAGAGATTT 57.900 34.615 0.00 0.00 0.00 2.17
1972 2009 8.774546 AGAGAGATTTCCAAGTATACAGATGA 57.225 34.615 5.50 0.00 0.00 2.92
1986 2023 8.467598 AGTATACAGATGATCGTACAACTTTGT 58.532 33.333 5.50 0.00 44.86 2.83
1990 2027 5.062683 CAGATGATCGTACAACTTTGTGAGG 59.937 44.000 4.82 0.00 42.31 3.86
2028 2065 1.070445 GGGCGATGAGATGTGGGAG 59.930 63.158 0.00 0.00 0.00 4.30
2058 2095 3.621558 AGTGCTTTTGGATAAGGGCTAC 58.378 45.455 0.00 0.00 0.00 3.58
2076 2113 0.394565 ACTGCACAAGTGAGAGGGAC 59.605 55.000 4.04 0.00 37.88 4.46
2079 2116 1.618837 TGCACAAGTGAGAGGGACTAC 59.381 52.381 4.04 0.00 41.55 2.73
2146 2183 6.271857 AGAGGCATATGATGTGATAAAGGAGT 59.728 38.462 6.97 0.00 0.00 3.85
2363 2400 2.040813 AGCTGTTTGATCACATGGTCCT 59.959 45.455 0.00 0.00 0.00 3.85
2418 2455 7.161404 ACACATCAGTCATTACTATGTTGTGT 58.839 34.615 12.62 12.62 32.42 3.72
2448 2485 4.521146 ACAAATATGAACAGGCTGAGGAG 58.479 43.478 23.66 3.44 0.00 3.69
2454 2491 2.909006 TGAACAGGCTGAGGAGATCTTT 59.091 45.455 23.66 0.53 0.00 2.52
2547 2584 3.705051 ACAAGGTATTCCTGTCCTCGTA 58.295 45.455 0.00 0.00 44.35 3.43
2548 2585 4.287552 ACAAGGTATTCCTGTCCTCGTAT 58.712 43.478 0.00 0.00 44.35 3.06
2550 2587 5.895534 ACAAGGTATTCCTGTCCTCGTATTA 59.104 40.000 0.00 0.00 44.35 0.98
2551 2588 6.040616 ACAAGGTATTCCTGTCCTCGTATTAG 59.959 42.308 0.00 0.00 44.35 1.73
2581 2619 7.268447 CGCTTGCTGTTTTAGTTATTCTGTTAC 59.732 37.037 0.00 0.00 0.00 2.50
2675 2713 6.545298 GTCTTCCATCCAATATTGAGAGCTTT 59.455 38.462 17.23 0.00 0.00 3.51
2840 2878 1.276421 GCTAGCCTTCAACCTGTCAGA 59.724 52.381 2.29 0.00 0.00 3.27
2855 2893 4.511826 CCTGTCAGAAAGTTGGTCTGTTAC 59.488 45.833 0.00 0.00 42.63 2.50
2986 3026 2.570415 TTACCAAGAATGCCCGAACA 57.430 45.000 0.00 0.00 0.00 3.18
2991 3032 2.568623 AAGAATGCCCGAACAGTCTT 57.431 45.000 12.55 12.55 46.81 3.01
2992 3033 1.813513 AGAATGCCCGAACAGTCTTG 58.186 50.000 2.37 0.00 41.93 3.02
2993 3034 1.347707 AGAATGCCCGAACAGTCTTGA 59.652 47.619 2.37 0.00 41.93 3.02
2994 3035 1.734465 GAATGCCCGAACAGTCTTGAG 59.266 52.381 0.00 0.00 32.10 3.02
2995 3036 0.976641 ATGCCCGAACAGTCTTGAGA 59.023 50.000 0.00 0.00 0.00 3.27
3001 3045 2.493675 CCGAACAGTCTTGAGATGGAGA 59.506 50.000 0.00 0.00 0.00 3.71
3013 3057 1.417145 AGATGGAGATCAGGCTTCAGC 59.583 52.381 0.00 0.00 41.14 4.26
3025 3069 1.063174 GGCTTCAGCGCATTACTTCAG 59.937 52.381 11.47 0.00 43.26 3.02
3059 3104 3.159213 ACTTCCCTGTGATGCATTGAA 57.841 42.857 0.00 0.00 0.00 2.69
3062 3107 5.263599 ACTTCCCTGTGATGCATTGAATTA 58.736 37.500 0.00 0.00 0.00 1.40
3077 3123 9.970395 TGCATTGAATTATCAGAATTACCAATC 57.030 29.630 0.00 0.00 36.78 2.67
3078 3124 9.121517 GCATTGAATTATCAGAATTACCAATCG 57.878 33.333 0.00 0.00 36.78 3.34
3092 3138 2.747446 ACCAATCGAAAAATGACCGAGG 59.253 45.455 0.00 0.00 35.70 4.63
3093 3139 3.006940 CCAATCGAAAAATGACCGAGGA 58.993 45.455 0.00 0.00 35.70 3.71
3096 3142 5.393027 CCAATCGAAAAATGACCGAGGATTT 60.393 40.000 0.00 0.00 35.70 2.17
3099 3145 6.804770 TCGAAAAATGACCGAGGATTTTTA 57.195 33.333 11.72 0.16 40.29 1.52
3100 3146 7.204496 TCGAAAAATGACCGAGGATTTTTAA 57.796 32.000 11.72 4.47 40.29 1.52
3162 3210 4.747108 CGAGGTATCATTTCTTTCGCATCT 59.253 41.667 0.00 0.00 0.00 2.90
3193 3241 9.961265 TTACTGTAGATCATTAGTATCCGTTTG 57.039 33.333 0.00 0.00 0.00 2.93
3194 3242 6.924060 ACTGTAGATCATTAGTATCCGTTTGC 59.076 38.462 0.00 0.00 0.00 3.68
3195 3243 7.050970 TGTAGATCATTAGTATCCGTTTGCT 57.949 36.000 0.00 0.00 0.00 3.91
3196 3244 7.497595 TGTAGATCATTAGTATCCGTTTGCTT 58.502 34.615 0.00 0.00 0.00 3.91
3212 3269 5.569059 CGTTTGCTTTGATTATGTGACTTCC 59.431 40.000 0.00 0.00 0.00 3.46
3232 3289 4.992688 TCCGTAATTTTGTGCCATCATTC 58.007 39.130 0.00 0.00 0.00 2.67
3234 3291 5.036737 CCGTAATTTTGTGCCATCATTCTC 58.963 41.667 0.00 0.00 0.00 2.87
3392 3489 7.029563 GGTGTTTATTGGTCTTATGCTTTGAG 58.970 38.462 0.00 0.00 0.00 3.02
3401 3498 4.336713 GTCTTATGCTTTGAGGATGGTTCC 59.663 45.833 0.00 0.00 42.96 3.62
3468 3600 2.755469 GCCAATGGCGGTGATGGT 60.755 61.111 9.14 0.00 39.62 3.55
3469 3601 3.067480 GCCAATGGCGGTGATGGTG 62.067 63.158 9.14 0.00 39.62 4.17
3470 3602 1.378382 CCAATGGCGGTGATGGTGA 60.378 57.895 0.00 0.00 0.00 4.02
3471 3603 0.752743 CCAATGGCGGTGATGGTGAT 60.753 55.000 0.00 0.00 0.00 3.06
3472 3604 0.382873 CAATGGCGGTGATGGTGATG 59.617 55.000 0.00 0.00 0.00 3.07
3486 3618 2.577563 TGGTGATGGTGGATCAGAATGT 59.422 45.455 0.00 0.00 42.00 2.71
3487 3619 3.010472 TGGTGATGGTGGATCAGAATGTT 59.990 43.478 0.00 0.00 42.00 2.71
3488 3620 3.379372 GGTGATGGTGGATCAGAATGTTG 59.621 47.826 0.00 0.00 42.00 3.33
3489 3621 3.379372 GTGATGGTGGATCAGAATGTTGG 59.621 47.826 0.00 0.00 42.00 3.77
3490 3622 3.010472 TGATGGTGGATCAGAATGTTGGT 59.990 43.478 0.00 0.00 36.06 3.67
3491 3623 2.794103 TGGTGGATCAGAATGTTGGTG 58.206 47.619 0.00 0.00 37.40 4.17
3492 3624 2.094675 GGTGGATCAGAATGTTGGTGG 58.905 52.381 0.00 0.00 37.40 4.61
3502 3640 2.717639 ATGTTGGTGGCTAGTGGATC 57.282 50.000 0.00 0.00 0.00 3.36
3509 3647 2.026262 GGTGGCTAGTGGATCCTGAAAA 60.026 50.000 14.23 0.00 0.00 2.29
3566 3705 4.750021 TTCTTGTCCATCTCATCTCCTG 57.250 45.455 0.00 0.00 0.00 3.86
3574 3719 2.771562 TCTCATCTCCTGCTCCTCAT 57.228 50.000 0.00 0.00 0.00 2.90
3609 3754 1.761198 TCTCTGAGGGATGCATCAGTG 59.239 52.381 27.25 22.69 42.86 3.66
3669 3816 3.431626 CGTACATTGCATCTAAGGTCCCA 60.432 47.826 0.00 0.00 0.00 4.37
3674 3821 1.340017 TGCATCTAAGGTCCCAGTTGC 60.340 52.381 13.63 13.63 37.78 4.17
3679 3826 0.251916 TAAGGTCCCAGTTGCGGATG 59.748 55.000 0.00 0.00 0.00 3.51
3696 3843 3.397482 GGATGCAGCTCGATTTATGTCT 58.603 45.455 0.22 0.00 0.00 3.41
3714 3861 4.643463 TGTCTTGAAAACAAGGGCGTATA 58.357 39.130 9.54 0.00 33.26 1.47
3734 3881 3.733443 ACTGCACTCCATTTTTGGAAC 57.267 42.857 0.00 0.00 37.55 3.62
3735 3882 2.365293 ACTGCACTCCATTTTTGGAACC 59.635 45.455 0.00 0.00 37.55 3.62
3736 3883 2.364970 CTGCACTCCATTTTTGGAACCA 59.635 45.455 0.00 0.00 37.55 3.67
3757 3904 1.531149 CGCATCGAGTTTCTGTGGTTT 59.469 47.619 0.00 0.00 0.00 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.074967 CCAGGCTCCTTAACACCCA 58.925 57.895 0.00 0.00 0.00 4.51
1 2 1.378646 GCCAGGCTCCTTAACACCC 60.379 63.158 3.29 0.00 0.00 4.61
2 3 1.378646 GGCCAGGCTCCTTAACACC 60.379 63.158 12.43 0.00 0.00 4.16
3 4 0.960861 GTGGCCAGGCTCCTTAACAC 60.961 60.000 5.11 5.13 0.00 3.32
4 5 1.378762 GTGGCCAGGCTCCTTAACA 59.621 57.895 5.11 0.00 0.00 2.41
7 8 1.207488 ATGTGTGGCCAGGCTCCTTA 61.207 55.000 5.11 0.00 0.00 2.69
8 9 2.085343 AATGTGTGGCCAGGCTCCTT 62.085 55.000 5.11 0.00 0.00 3.36
9 10 2.085343 AAATGTGTGGCCAGGCTCCT 62.085 55.000 5.11 0.00 0.00 3.69
10 11 1.187567 AAAATGTGTGGCCAGGCTCC 61.188 55.000 5.11 2.39 0.00 4.70
12 13 0.760189 ACAAAATGTGTGGCCAGGCT 60.760 50.000 5.11 0.00 39.72 4.58
14 15 3.235157 CATACAAAATGTGTGGCCAGG 57.765 47.619 5.11 0.00 41.89 4.45
20 21 7.361201 CCTCTTAGACACCATACAAAATGTGTG 60.361 40.741 0.00 0.81 41.89 3.82
21 22 6.655003 CCTCTTAGACACCATACAAAATGTGT 59.345 38.462 0.00 0.00 44.82 3.72
22 23 6.878923 TCCTCTTAGACACCATACAAAATGTG 59.121 38.462 0.00 0.00 0.00 3.21
23 24 6.879458 GTCCTCTTAGACACCATACAAAATGT 59.121 38.462 0.00 0.00 36.73 2.71
24 25 6.316390 GGTCCTCTTAGACACCATACAAAATG 59.684 42.308 1.70 0.00 38.59 2.32
25 26 6.012858 TGGTCCTCTTAGACACCATACAAAAT 60.013 38.462 4.60 0.00 38.59 1.82
26 27 5.308497 TGGTCCTCTTAGACACCATACAAAA 59.692 40.000 4.60 0.00 38.59 2.44
27 28 4.841813 TGGTCCTCTTAGACACCATACAAA 59.158 41.667 4.60 0.00 38.59 2.83
28 29 4.422057 TGGTCCTCTTAGACACCATACAA 58.578 43.478 4.60 0.00 38.59 2.41
29 30 4.023980 CTGGTCCTCTTAGACACCATACA 58.976 47.826 8.33 0.00 38.26 2.29
30 31 3.181474 GCTGGTCCTCTTAGACACCATAC 60.181 52.174 8.33 2.40 38.26 2.39
31 32 3.031736 GCTGGTCCTCTTAGACACCATA 58.968 50.000 8.33 0.00 38.26 2.74
32 33 1.834263 GCTGGTCCTCTTAGACACCAT 59.166 52.381 8.33 0.00 38.26 3.55
33 34 1.267121 GCTGGTCCTCTTAGACACCA 58.733 55.000 7.77 7.77 38.59 4.17
34 35 0.537653 GGCTGGTCCTCTTAGACACC 59.462 60.000 0.00 0.00 38.59 4.16
35 36 0.537653 GGGCTGGTCCTCTTAGACAC 59.462 60.000 0.00 0.00 38.59 3.67
36 37 0.116342 TGGGCTGGTCCTCTTAGACA 59.884 55.000 0.00 0.00 38.59 3.41
37 38 0.537653 GTGGGCTGGTCCTCTTAGAC 59.462 60.000 0.00 0.00 35.95 2.59
38 39 0.116342 TGTGGGCTGGTCCTCTTAGA 59.884 55.000 0.00 0.00 34.39 2.10
39 40 0.250513 GTGTGGGCTGGTCCTCTTAG 59.749 60.000 0.00 0.00 34.39 2.18
40 41 1.541310 CGTGTGGGCTGGTCCTCTTA 61.541 60.000 0.00 0.00 34.39 2.10
41 42 2.883828 CGTGTGGGCTGGTCCTCTT 61.884 63.158 0.00 0.00 34.39 2.85
42 43 3.314331 CGTGTGGGCTGGTCCTCT 61.314 66.667 0.00 0.00 34.39 3.69
87 88 1.244697 GGCTGAGAGAGGTCGTGTGA 61.245 60.000 0.00 0.00 0.00 3.58
151 157 1.279025 ACCATGGCAACTACGGGGAT 61.279 55.000 13.04 0.00 37.61 3.85
523 543 1.813786 TGTTTTGCAAGGTATACGGCC 59.186 47.619 0.00 0.00 0.00 6.13
529 549 2.632028 TGCCATGTGTTTTGCAAGGTAT 59.368 40.909 0.00 0.00 0.00 2.73
574 600 6.204882 GTGTTTGTAAGTAGATGGCAACTCTT 59.795 38.462 0.00 7.49 37.61 2.85
596 625 1.128200 TGGCAACTGTCCTAGTGTGT 58.872 50.000 0.00 0.00 40.26 3.72
630 659 4.002982 CTCAAGTTGCTAGTTGCCATGTA 58.997 43.478 10.43 0.00 42.00 2.29
651 681 1.304547 CCGTCTCCTCTCCCACACT 60.305 63.158 0.00 0.00 0.00 3.55
677 707 0.035152 TGGACATTTGCCATCTCGCT 60.035 50.000 0.00 0.00 0.00 4.93
693 723 0.751277 CACAAAGGCTGGTGTGTGGA 60.751 55.000 18.72 0.00 40.22 4.02
707 737 2.744741 TCAGTTTTCACTCACGCACAAA 59.255 40.909 0.00 0.00 0.00 2.83
793 826 2.746277 GGCATTCACCCGTTCGCT 60.746 61.111 0.00 0.00 0.00 4.93
813 846 2.236146 CACATAGGACAAGGCTGGTGTA 59.764 50.000 0.00 0.00 0.00 2.90
913 950 4.810491 ACGCTTTTCTTAACGGAAACACTA 59.190 37.500 0.00 0.00 35.31 2.74
914 951 3.624410 ACGCTTTTCTTAACGGAAACACT 59.376 39.130 0.00 0.00 35.31 3.55
915 952 3.943958 ACGCTTTTCTTAACGGAAACAC 58.056 40.909 0.00 0.00 35.31 3.32
916 953 5.731599 TTACGCTTTTCTTAACGGAAACA 57.268 34.783 0.00 0.00 35.31 2.83
917 954 6.852345 TGAATTACGCTTTTCTTAACGGAAAC 59.148 34.615 0.00 0.00 35.31 2.78
918 955 6.957150 TGAATTACGCTTTTCTTAACGGAAA 58.043 32.000 0.00 0.00 31.14 3.13
919 956 6.203338 ACTGAATTACGCTTTTCTTAACGGAA 59.797 34.615 0.00 0.00 32.06 4.30
920 957 5.697633 ACTGAATTACGCTTTTCTTAACGGA 59.302 36.000 0.00 0.00 0.00 4.69
921 958 5.923665 ACTGAATTACGCTTTTCTTAACGG 58.076 37.500 0.00 0.00 0.00 4.44
922 959 7.831750 AAACTGAATTACGCTTTTCTTAACG 57.168 32.000 0.00 0.00 0.00 3.18
941 978 2.060326 TCGACTCAAGGCGTAAACTG 57.940 50.000 4.99 0.00 0.00 3.16
954 991 4.982916 AGCGAACCACATTATAATCGACTC 59.017 41.667 7.83 0.00 32.38 3.36
956 993 4.150098 GGAGCGAACCACATTATAATCGAC 59.850 45.833 7.83 2.19 32.38 4.20
962 999 3.389656 TGGATGGAGCGAACCACATTATA 59.610 43.478 3.25 0.00 43.03 0.98
963 1000 2.172505 TGGATGGAGCGAACCACATTAT 59.827 45.455 3.25 0.00 43.03 1.28
1335 1372 4.400961 AGGGAGTTGCAGAGCGGC 62.401 66.667 0.00 0.00 0.00 6.53
1342 1379 4.704833 GGCGAGCAGGGAGTTGCA 62.705 66.667 0.52 0.00 46.47 4.08
1455 1492 0.749818 TGCCCACACTCTTCGCAAAA 60.750 50.000 0.00 0.00 0.00 2.44
1526 1563 1.916181 ACTTGTTGATCGAATCCCCCT 59.084 47.619 0.00 0.00 0.00 4.79
1529 1566 3.600388 ACAGACTTGTTGATCGAATCCC 58.400 45.455 0.00 0.00 32.28 3.85
1560 1597 2.224523 ACACAGACCATCGACAACCATT 60.225 45.455 0.00 0.00 0.00 3.16
1572 1609 3.680786 CGCTCCCGACACAGACCA 61.681 66.667 0.00 0.00 36.29 4.02
1647 1684 5.351465 CACAATCCTGTACGCTACAAAATCT 59.649 40.000 0.00 0.00 38.38 2.40
1690 1727 1.217747 TCCTCCTCTGCCCTCTCTGA 61.218 60.000 0.00 0.00 0.00 3.27
1692 1729 0.032217 CTTCCTCCTCTGCCCTCTCT 60.032 60.000 0.00 0.00 0.00 3.10
1695 1732 2.069430 CCCTTCCTCCTCTGCCCTC 61.069 68.421 0.00 0.00 0.00 4.30
1755 1792 1.132689 ACCTCTCTGTGGTCCTCCTTT 60.133 52.381 0.00 0.00 31.03 3.11
1765 1802 1.334419 CGCAAGCAAAACCTCTCTGTG 60.334 52.381 0.00 0.00 0.00 3.66
1827 1864 2.750948 TCGCCTAATACAATCGCTTCC 58.249 47.619 0.00 0.00 0.00 3.46
1830 1867 3.746492 GGAAATCGCCTAATACAATCGCT 59.254 43.478 0.00 0.00 0.00 4.93
1896 1933 2.017623 GCAGCATCAGCATCAACCTCT 61.018 52.381 0.00 0.00 45.49 3.69
1947 1984 8.774546 TCATCTGTATACTTGGAAATCTCTCT 57.225 34.615 4.17 0.00 0.00 3.10
1956 1993 7.284716 AGTTGTACGATCATCTGTATACTTGGA 59.715 37.037 4.17 0.80 0.00 3.53
1972 2009 2.423577 GCCCTCACAAAGTTGTACGAT 58.576 47.619 0.00 0.00 39.91 3.73
1986 2023 1.259609 CATTCTTGCAAAGGCCCTCA 58.740 50.000 0.00 0.00 46.24 3.86
1990 2027 0.035176 TTGCCATTCTTGCAAAGGCC 59.965 50.000 21.76 0.00 46.24 5.19
2028 2065 7.415653 CCCTTATCCAAAAGCACTCTAAACATC 60.416 40.741 0.00 0.00 0.00 3.06
2058 2095 0.683973 AGTCCCTCTCACTTGTGCAG 59.316 55.000 0.00 0.00 0.00 4.41
2064 2101 3.264450 CCAAATGGTAGTCCCTCTCACTT 59.736 47.826 0.00 0.00 0.00 3.16
2146 2183 7.112779 CCAGGATCTAGCTTCTTCCTTTTTAA 58.887 38.462 7.98 0.00 36.45 1.52
2363 2400 1.067295 ATCTGGTGCCACTCCTTTCA 58.933 50.000 0.00 0.00 0.00 2.69
2418 2455 7.014134 TCAGCCTGTTCATATTTGTTTTCTTGA 59.986 33.333 0.00 0.00 0.00 3.02
2448 2485 6.106877 TGCGCTACAGATTTGTTAAAGATC 57.893 37.500 9.73 0.00 38.76 2.75
2509 2546 4.275936 ACCTTGTTTACAGAGTGCAATGAC 59.724 41.667 0.00 0.00 0.00 3.06
2547 2584 5.243207 ACTAAAACAGCAAGCGTACCTAAT 58.757 37.500 0.00 0.00 0.00 1.73
2548 2585 4.634199 ACTAAAACAGCAAGCGTACCTAA 58.366 39.130 0.00 0.00 0.00 2.69
2550 2587 3.121738 ACTAAAACAGCAAGCGTACCT 57.878 42.857 0.00 0.00 0.00 3.08
2551 2588 3.891056 AACTAAAACAGCAAGCGTACC 57.109 42.857 0.00 0.00 0.00 3.34
2556 2593 7.537649 GGTAACAGAATAACTAAAACAGCAAGC 59.462 37.037 0.00 0.00 0.00 4.01
2581 2619 4.189231 CAAGGACGGTATTTACAAGGAGG 58.811 47.826 0.00 0.00 0.00 4.30
2634 2672 3.751698 GGAAGACTTGACATAACACCCAC 59.248 47.826 0.00 0.00 0.00 4.61
2675 2713 8.291740 CACTTCAACAGAATGACATGTGAATTA 58.708 33.333 1.15 0.00 39.69 1.40
2840 2878 7.990886 TGAGAATGTAAGTAACAGACCAACTTT 59.009 33.333 0.00 0.00 42.70 2.66
2855 2893 3.356529 ACAAGCCCCTGAGAATGTAAG 57.643 47.619 0.00 0.00 0.00 2.34
2969 3009 0.110486 ACTGTTCGGGCATTCTTGGT 59.890 50.000 0.00 0.00 0.00 3.67
2986 3026 2.699846 GCCTGATCTCCATCTCAAGACT 59.300 50.000 0.00 0.00 0.00 3.24
2991 3032 2.699321 CTGAAGCCTGATCTCCATCTCA 59.301 50.000 0.00 0.00 0.00 3.27
2992 3033 2.548493 GCTGAAGCCTGATCTCCATCTC 60.548 54.545 0.00 0.00 34.31 2.75
2993 3034 1.417145 GCTGAAGCCTGATCTCCATCT 59.583 52.381 0.00 0.00 34.31 2.90
2994 3035 1.873069 CGCTGAAGCCTGATCTCCATC 60.873 57.143 0.00 0.00 37.91 3.51
2995 3036 0.106335 CGCTGAAGCCTGATCTCCAT 59.894 55.000 0.00 0.00 37.91 3.41
3001 3045 1.134280 AGTAATGCGCTGAAGCCTGAT 60.134 47.619 9.73 0.00 37.91 2.90
3013 3057 5.062183 TCAATCTCGTTTCTGAAGTAATGCG 59.938 40.000 0.00 0.00 0.00 4.73
3025 3069 5.292101 CACAGGGAAGTATCAATCTCGTTTC 59.708 44.000 0.00 0.00 0.00 2.78
3062 3107 8.190784 GGTCATTTTTCGATTGGTAATTCTGAT 58.809 33.333 0.00 0.00 0.00 2.90
3077 3123 6.858993 TGTTAAAAATCCTCGGTCATTTTTCG 59.141 34.615 12.26 0.00 40.02 3.46
3078 3124 8.582433 TTGTTAAAAATCCTCGGTCATTTTTC 57.418 30.769 12.26 4.40 40.02 2.29
3092 3138 8.275632 GCACAAACCAGATCTTTGTTAAAAATC 58.724 33.333 8.28 0.00 39.34 2.17
3093 3139 7.986889 AGCACAAACCAGATCTTTGTTAAAAAT 59.013 29.630 8.28 0.00 39.34 1.82
3096 3142 6.096141 TCAGCACAAACCAGATCTTTGTTAAA 59.904 34.615 8.28 0.00 39.34 1.52
3099 3145 3.953612 TCAGCACAAACCAGATCTTTGTT 59.046 39.130 8.28 5.26 39.34 2.83
3100 3146 3.554934 TCAGCACAAACCAGATCTTTGT 58.445 40.909 5.60 5.60 41.52 2.83
3190 3238 5.240623 ACGGAAGTCACATAATCAAAGCAAA 59.759 36.000 0.00 0.00 44.19 3.68
3191 3239 4.759693 ACGGAAGTCACATAATCAAAGCAA 59.240 37.500 0.00 0.00 44.19 3.91
3193 3241 4.946784 ACGGAAGTCACATAATCAAAGC 57.053 40.909 0.00 0.00 44.19 3.51
3242 3299 3.455543 TGTCTTGATGATATCTGTGGGCA 59.544 43.478 3.98 0.00 0.00 5.36
3392 3489 3.815401 CTCAATGTAATCCGGAACCATCC 59.185 47.826 9.01 0.00 42.80 3.51
3401 3498 1.570813 TGCTCGCTCAATGTAATCCG 58.429 50.000 0.00 0.00 0.00 4.18
3467 3599 3.379372 CCAACATTCTGATCCACCATCAC 59.621 47.826 0.00 0.00 36.51 3.06
3468 3600 3.010472 ACCAACATTCTGATCCACCATCA 59.990 43.478 0.00 0.00 39.39 3.07
3469 3601 3.379372 CACCAACATTCTGATCCACCATC 59.621 47.826 0.00 0.00 0.00 3.51
3470 3602 3.359033 CACCAACATTCTGATCCACCAT 58.641 45.455 0.00 0.00 0.00 3.55
3471 3603 2.555006 CCACCAACATTCTGATCCACCA 60.555 50.000 0.00 0.00 0.00 4.17
3472 3604 2.094675 CCACCAACATTCTGATCCACC 58.905 52.381 0.00 0.00 0.00 4.61
3486 3618 0.911769 CAGGATCCACTAGCCACCAA 59.088 55.000 15.82 0.00 35.45 3.67
3487 3619 0.042581 TCAGGATCCACTAGCCACCA 59.957 55.000 15.82 0.00 35.45 4.17
3488 3620 1.204146 TTCAGGATCCACTAGCCACC 58.796 55.000 15.82 0.00 35.45 4.61
3489 3621 3.350219 TTTTCAGGATCCACTAGCCAC 57.650 47.619 15.82 0.00 35.45 5.01
3490 3622 3.523157 TCATTTTCAGGATCCACTAGCCA 59.477 43.478 15.82 0.00 35.45 4.75
3491 3623 3.879892 GTCATTTTCAGGATCCACTAGCC 59.120 47.826 15.82 0.00 0.00 3.93
3492 3624 3.879892 GGTCATTTTCAGGATCCACTAGC 59.120 47.826 15.82 0.00 0.00 3.42
3509 3647 6.957631 TCTATAACACAATGAACCTGGTCAT 58.042 36.000 0.00 2.86 40.01 3.06
3566 3705 5.017294 ACTTTTAGCAGTCTATGAGGAGC 57.983 43.478 0.00 0.00 0.00 4.70
3574 3719 5.186021 CCCTCAGAGAACTTTTAGCAGTCTA 59.814 44.000 0.00 0.00 0.00 2.59
3609 3754 1.131126 CCACCAAGACACGATCATTGC 59.869 52.381 0.00 0.00 0.00 3.56
3613 3758 0.324614 ATGCCACCAAGACACGATCA 59.675 50.000 0.00 0.00 0.00 2.92
3617 3762 1.336440 TGAAAATGCCACCAAGACACG 59.664 47.619 0.00 0.00 0.00 4.49
3648 3793 4.130118 CTGGGACCTTAGATGCAATGTAC 58.870 47.826 0.00 0.00 0.00 2.90
3674 3821 2.138320 ACATAAATCGAGCTGCATCCG 58.862 47.619 1.02 2.46 0.00 4.18
3679 3826 4.864916 TTCAAGACATAAATCGAGCTGC 57.135 40.909 0.00 0.00 0.00 5.25
3696 3843 3.189702 GCAGTATACGCCCTTGTTTTCAA 59.810 43.478 8.05 0.00 38.21 2.69
3714 3861 2.365293 GGTTCCAAAAATGGAGTGCAGT 59.635 45.455 0.00 0.00 39.43 4.40
3734 3881 0.439985 CACAGAAACTCGATGCGTGG 59.560 55.000 0.00 0.00 0.00 4.94
3735 3882 0.439985 CCACAGAAACTCGATGCGTG 59.560 55.000 0.00 0.00 0.00 5.34
3736 3883 0.033504 ACCACAGAAACTCGATGCGT 59.966 50.000 0.00 0.00 0.00 5.24
3791 3938 9.193806 ACAATCTATTGAGGCATCTAAAATGTT 57.806 29.630 9.60 0.00 40.14 2.71


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

AutoCloner maintained by Alex Coulton.