Multiple sequence alignment - TraesCS4A01G068200

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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 TraesCS4A01G068200 chr4A 100.000 3109 0 0 1 3109 66610979 66607871 0.000000e+00 5742.0
1 TraesCS4A01G068200 chr4A 88.420 1114 80 29 899 1986 66802673 66801583 0.000000e+00 1297.0
2 TraesCS4A01G068200 chr4A 86.560 997 61 36 779 1718 66761639 66760659 0.000000e+00 1031.0
3 TraesCS4A01G068200 chr4A 86.179 492 57 7 255 739 66772898 66772411 3.550000e-144 521.0
4 TraesCS4A01G068200 chr4A 85.396 493 58 9 255 739 66762480 66761994 1.660000e-137 499.0
5 TraesCS4A01G068200 chr4A 95.971 273 9 1 1714 1986 66755287 66755017 2.850000e-120 442.0
6 TraesCS4A01G068200 chr4A 93.590 156 8 1 1831 1986 66772026 66771873 6.710000e-57 231.0
7 TraesCS4A01G068200 chr4A 93.919 148 7 1 1839 1986 66771136 66770991 4.040000e-54 222.0
8 TraesCS4A01G068200 chr4B 88.712 2197 129 48 735 2867 471957837 471955696 0.000000e+00 2573.0
9 TraesCS4A01G068200 chr4B 86.675 773 64 18 4 741 471994589 471993821 0.000000e+00 821.0
10 TraesCS4A01G068200 chr4D 88.846 1820 101 34 779 2552 384976596 384974833 0.000000e+00 2143.0
11 TraesCS4A01G068200 chr4D 93.277 476 23 6 2415 2886 384974834 384974364 0.000000e+00 693.0
12 TraesCS4A01G068200 chr4D 82.123 179 26 3 35 209 91074879 91074703 6.950000e-32 148.0
13 TraesCS4A01G068200 chr2B 85.926 135 15 1 80 210 39373194 39373060 1.160000e-29 141.0
14 TraesCS4A01G068200 chr2B 83.871 62 7 3 2946 3005 771216634 771216574 4.330000e-04 56.5
15 TraesCS4A01G068200 chr5D 80.537 149 24 2 54 197 214855078 214854930 3.280000e-20 110.0
16 TraesCS4A01G068200 chr5D 81.119 143 18 6 78 212 5625852 5625993 4.240000e-19 106.0
17 TraesCS4A01G068200 chr3A 86.170 94 12 1 35 128 667291063 667291155 1.970000e-17 100.0
18 TraesCS4A01G068200 chr5B 83.721 86 14 0 42 127 229698498 229698413 7.150000e-12 82.4


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 TraesCS4A01G068200 chr4A 66607871 66610979 3108 True 5742.000000 5742 100.000000 1 3109 1 chr4A.!!$R1 3108
1 TraesCS4A01G068200 chr4A 66801583 66802673 1090 True 1297.000000 1297 88.420000 899 1986 1 chr4A.!!$R3 1087
2 TraesCS4A01G068200 chr4A 66760659 66762480 1821 True 765.000000 1031 85.978000 255 1718 2 chr4A.!!$R4 1463
3 TraesCS4A01G068200 chr4A 66770991 66772898 1907 True 324.666667 521 91.229333 255 1986 3 chr4A.!!$R5 1731
4 TraesCS4A01G068200 chr4B 471955696 471957837 2141 True 2573.000000 2573 88.712000 735 2867 1 chr4B.!!$R1 2132
5 TraesCS4A01G068200 chr4B 471993821 471994589 768 True 821.000000 821 86.675000 4 741 1 chr4B.!!$R2 737
6 TraesCS4A01G068200 chr4D 384974364 384976596 2232 True 1418.000000 2143 91.061500 779 2886 2 chr4D.!!$R2 2107

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
987 1361 0.736053 TATAAAAGGGCGCGGCAAAG 59.264 50.0 34.3 0.0 0.0 2.77 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2740 3611 0.037447 AAGGAGCTCAGCAAGGGTTC 59.963 55.0 17.19 0.0 0.0 3.62 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
145 146 1.145598 CATGGGAGCAGCGTGAGAT 59.854 57.895 0.00 0.00 0.00 2.75
161 162 5.746245 GCGTGAGATGTTAGATATAGATGGC 59.254 44.000 0.00 0.00 0.00 4.40
176 177 2.568062 AGATGGCTAGATGGCTCAGATG 59.432 50.000 0.00 0.00 42.34 2.90
184 185 6.408320 GGCTAGATGGCTCAGATGATATTCAT 60.408 42.308 0.00 0.00 37.79 2.57
218 219 9.649167 GTGCTTTTATAAGTAGTACTTCCTTCA 57.351 33.333 18.77 1.89 39.51 3.02
299 300 6.471233 TTGATACAGAGGAAGTGGTAGATG 57.529 41.667 0.00 0.00 0.00 2.90
306 307 5.010516 CAGAGGAAGTGGTAGATGGTAGATG 59.989 48.000 0.00 0.00 0.00 2.90
312 313 7.202011 GGAAGTGGTAGATGGTAGATGTACAAT 60.202 40.741 0.00 0.00 0.00 2.71
639 679 5.524284 TCATACAACGTGGAAAAATGTTGG 58.476 37.500 12.46 0.00 46.71 3.77
640 680 2.545731 ACAACGTGGAAAAATGTTGGC 58.454 42.857 12.46 0.00 46.71 4.52
648 688 4.213906 GTGGAAAAATGTTGGCATCCAAAG 59.786 41.667 5.37 0.00 45.73 2.77
651 691 3.967332 AAATGTTGGCATCCAAAGAGG 57.033 42.857 0.00 0.00 45.73 3.69
741 782 6.759827 TGAGTGAACTAACACACTAAAAGGTC 59.240 38.462 0.00 0.00 45.54 3.85
742 783 6.646267 AGTGAACTAACACACTAAAAGGTCA 58.354 36.000 0.00 0.00 44.06 4.02
747 788 7.875327 ACTAACACACTAAAAGGTCAACATT 57.125 32.000 0.00 0.00 0.00 2.71
768 1121 2.688666 AGATGGGCCTCGGCTTCA 60.689 61.111 4.53 7.35 41.60 3.02
804 1159 1.002069 TTCATGTTGGGCCTCCTGAT 58.998 50.000 4.53 0.00 0.00 2.90
888 1259 0.910088 GGCCTCTCCAACCAGGTACT 60.910 60.000 0.00 0.00 39.02 2.73
890 1261 1.897647 GCCTCTCCAACCAGGTACTCT 60.898 57.143 0.00 0.00 34.60 3.24
961 1335 2.600790 GATCATGGCATGAAATCCCCA 58.399 47.619 31.81 8.93 43.50 4.96
987 1361 0.736053 TATAAAAGGGCGCGGCAAAG 59.264 50.000 34.30 0.00 0.00 2.77
1026 1430 3.012518 ACAAGCGAGCAAGATAAGCATT 58.987 40.909 0.00 0.00 0.00 3.56
1078 1484 4.322274 CACTCTCTCGTTTCAATTCTCGAC 59.678 45.833 0.00 0.00 0.00 4.20
1083 1489 2.055838 CGTTTCAATTCTCGACCGACA 58.944 47.619 0.00 0.00 0.00 4.35
1098 1504 5.350365 TCGACCGACATTTAATCTTCCAAAG 59.650 40.000 0.00 0.00 0.00 2.77
1099 1505 5.310720 ACCGACATTTAATCTTCCAAAGC 57.689 39.130 0.00 0.00 0.00 3.51
1100 1506 5.010282 ACCGACATTTAATCTTCCAAAGCT 58.990 37.500 0.00 0.00 0.00 3.74
1101 1507 5.123979 ACCGACATTTAATCTTCCAAAGCTC 59.876 40.000 0.00 0.00 0.00 4.09
1102 1508 5.449177 CCGACATTTAATCTTCCAAAGCTCC 60.449 44.000 0.00 0.00 0.00 4.70
1103 1509 5.567138 ACATTTAATCTTCCAAAGCTCCG 57.433 39.130 0.00 0.00 0.00 4.63
1120 1526 1.447317 CCGTATCTGGTGCAATGGCC 61.447 60.000 0.00 0.00 40.13 5.36
1264 1679 4.742201 GCGGCGCAGGAGAACAGA 62.742 66.667 29.21 0.00 0.00 3.41
1389 1804 1.543358 GTTCGGTAAGTCCTCGTTCCT 59.457 52.381 0.00 0.00 0.00 3.36
1609 2035 2.124736 CGGATGCCGTGGGACATT 60.125 61.111 0.00 0.00 44.52 2.71
1798 2233 1.029947 TGAGCTCCTACGACATGCGA 61.030 55.000 12.15 0.72 44.57 5.10
1937 2376 2.156504 CAGTGATGAGTTTGTGCGAGAC 59.843 50.000 0.00 0.00 0.00 3.36
1938 2377 2.036475 AGTGATGAGTTTGTGCGAGACT 59.964 45.455 0.00 0.00 0.00 3.24
1962 2408 0.323178 ACCCTGCATCTGAGGCTTTG 60.323 55.000 15.78 6.00 0.00 2.77
1982 2428 0.107945 AGATTTCAGCTGTCCGAGGC 60.108 55.000 14.67 0.00 0.00 4.70
2012 2459 1.666023 CGAGTGCGTGCTCTTTGTAGA 60.666 52.381 0.00 0.00 33.55 2.59
2036 2483 1.006571 TGTGCCGTTCTTCTCCGAC 60.007 57.895 0.00 0.00 0.00 4.79
2040 2487 1.318158 GCCGTTCTTCTCCGACCCTA 61.318 60.000 0.00 0.00 0.00 3.53
2102 2549 6.253298 CGTAAATGTACTTGGCAAATCAATGG 59.747 38.462 0.00 0.00 0.00 3.16
2183 2632 4.642429 AGACATTAGTTCCCTGTTGTGTC 58.358 43.478 0.00 0.00 36.03 3.67
2184 2633 4.102524 AGACATTAGTTCCCTGTTGTGTCA 59.897 41.667 0.00 0.00 37.71 3.58
2204 2656 3.994789 CATCGTGTGATGTGATGTGTTC 58.005 45.455 0.00 0.00 45.69 3.18
2205 2657 3.385193 TCGTGTGATGTGATGTGTTCT 57.615 42.857 0.00 0.00 0.00 3.01
2228 2680 1.453155 TTCAGAATGCGGAAGAAGCC 58.547 50.000 0.00 0.00 34.76 4.35
2263 2715 4.553742 CGAGATGCTATACTATAGGCAGCG 60.554 50.000 4.43 6.01 44.32 5.18
2272 2724 0.318441 TATAGGCAGCGCATCCTGAC 59.682 55.000 24.93 11.13 41.31 3.51
2277 2729 1.930100 CAGCGCATCCTGACGAATC 59.070 57.895 11.47 0.00 34.77 2.52
2282 2734 2.809446 CGCATCCTGACGAATCTGTAA 58.191 47.619 0.00 0.00 0.00 2.41
2517 3109 5.890985 TCAGGAGTTCTTGAAAATCAACCAA 59.109 36.000 0.00 0.00 32.21 3.67
2518 3110 5.979517 CAGGAGTTCTTGAAAATCAACCAAC 59.020 40.000 0.00 0.00 32.21 3.77
2529 3121 4.836125 AATCAACCAACACACACAGATC 57.164 40.909 0.00 0.00 0.00 2.75
2540 3132 2.358898 ACACACAGATCTGTTGTTTGCC 59.641 45.455 25.84 0.00 42.83 4.52
2547 3139 4.921515 CAGATCTGTTGTTTGCCTCAATTG 59.078 41.667 14.95 0.00 0.00 2.32
2554 3240 2.627699 TGTTTGCCTCAATTGGAAGGAC 59.372 45.455 15.62 6.88 0.00 3.85
2563 3249 3.571828 TCAATTGGAAGGACAAATCGCAA 59.428 39.130 5.42 0.00 33.48 4.85
2662 3353 0.528466 CCGCGTACTGCATCATCTGT 60.528 55.000 4.92 0.00 46.97 3.41
2708 3579 0.536006 ACTCTGACCTTGGTTGCTGC 60.536 55.000 0.00 0.00 0.00 5.25
2734 3605 4.563168 GCTTGCATCTGCTGGAGATAGTAT 60.563 45.833 11.50 0.00 39.64 2.12
2740 3611 4.148079 TCTGCTGGAGATAGTATGGTGAG 58.852 47.826 0.00 0.00 0.00 3.51
2856 3727 1.372251 CGCCATAGTAGCTCTGCGG 60.372 63.158 0.00 0.00 38.46 5.69
2943 3816 4.049393 GCTTATAGCCGTGGCAGG 57.951 61.111 14.29 0.00 44.88 4.85
2944 3817 1.598130 GCTTATAGCCGTGGCAGGG 60.598 63.158 21.55 21.55 44.88 4.45
2951 3824 2.676121 CCGTGGCAGGGCAAATCA 60.676 61.111 14.01 0.00 0.00 2.57
2952 3825 2.274645 CCGTGGCAGGGCAAATCAA 61.275 57.895 14.01 0.00 0.00 2.57
2953 3826 1.664873 CGTGGCAGGGCAAATCAAA 59.335 52.632 0.00 0.00 0.00 2.69
2954 3827 0.667184 CGTGGCAGGGCAAATCAAAC 60.667 55.000 0.00 0.00 0.00 2.93
2955 3828 0.392336 GTGGCAGGGCAAATCAAACA 59.608 50.000 0.00 0.00 0.00 2.83
2956 3829 1.002315 GTGGCAGGGCAAATCAAACAT 59.998 47.619 0.00 0.00 0.00 2.71
2957 3830 1.698532 TGGCAGGGCAAATCAAACATT 59.301 42.857 0.00 0.00 0.00 2.71
2958 3831 2.106166 TGGCAGGGCAAATCAAACATTT 59.894 40.909 0.00 0.00 0.00 2.32
2959 3832 3.148412 GGCAGGGCAAATCAAACATTTT 58.852 40.909 0.00 0.00 0.00 1.82
2960 3833 3.569277 GGCAGGGCAAATCAAACATTTTT 59.431 39.130 0.00 0.00 0.00 1.94
2961 3834 4.759183 GGCAGGGCAAATCAAACATTTTTA 59.241 37.500 0.00 0.00 0.00 1.52
2962 3835 5.240403 GGCAGGGCAAATCAAACATTTTTAA 59.760 36.000 0.00 0.00 0.00 1.52
2963 3836 6.072008 GGCAGGGCAAATCAAACATTTTTAAT 60.072 34.615 0.00 0.00 0.00 1.40
2964 3837 6.802834 GCAGGGCAAATCAAACATTTTTAATG 59.197 34.615 0.00 0.00 0.00 1.90
2965 3838 7.306953 CAGGGCAAATCAAACATTTTTAATGG 58.693 34.615 4.61 0.00 0.00 3.16
2966 3839 6.072008 AGGGCAAATCAAACATTTTTAATGGC 60.072 34.615 4.61 0.00 0.00 4.40
2967 3840 6.294397 GGGCAAATCAAACATTTTTAATGGCA 60.294 34.615 0.00 0.00 0.00 4.92
2968 3841 7.144000 GGCAAATCAAACATTTTTAATGGCAA 58.856 30.769 0.00 0.00 0.00 4.52
2969 3842 7.813627 GGCAAATCAAACATTTTTAATGGCAAT 59.186 29.630 0.00 0.00 0.00 3.56
2970 3843 9.194271 GCAAATCAAACATTTTTAATGGCAATT 57.806 25.926 0.00 0.00 0.00 2.32
2982 3855 8.572828 TTTTAATGGCAATTTATATCAGCACG 57.427 30.769 0.00 0.00 0.00 5.34
2983 3856 3.624326 TGGCAATTTATATCAGCACGC 57.376 42.857 0.00 0.00 0.00 5.34
2984 3857 2.948315 TGGCAATTTATATCAGCACGCA 59.052 40.909 0.00 0.00 0.00 5.24
2985 3858 3.379688 TGGCAATTTATATCAGCACGCAA 59.620 39.130 0.00 0.00 0.00 4.85
2986 3859 4.037803 TGGCAATTTATATCAGCACGCAAT 59.962 37.500 0.00 0.00 0.00 3.56
2987 3860 4.383649 GGCAATTTATATCAGCACGCAATG 59.616 41.667 0.00 0.00 0.00 2.82
2988 3861 5.214417 GCAATTTATATCAGCACGCAATGA 58.786 37.500 0.00 0.00 0.00 2.57
2989 3862 5.116074 GCAATTTATATCAGCACGCAATGAC 59.884 40.000 0.00 0.00 0.00 3.06
2990 3863 6.200808 CAATTTATATCAGCACGCAATGACA 58.799 36.000 0.00 0.00 0.00 3.58
2991 3864 5.809719 TTTATATCAGCACGCAATGACAA 57.190 34.783 0.00 0.00 0.00 3.18
2992 3865 5.809719 TTATATCAGCACGCAATGACAAA 57.190 34.783 0.00 0.00 0.00 2.83
2993 3866 4.906065 ATATCAGCACGCAATGACAAAT 57.094 36.364 0.00 0.00 0.00 2.32
2994 3867 3.581024 ATCAGCACGCAATGACAAATT 57.419 38.095 0.00 0.00 0.00 1.82
2995 3868 3.367992 TCAGCACGCAATGACAAATTT 57.632 38.095 0.00 0.00 0.00 1.82
2996 3869 4.495911 TCAGCACGCAATGACAAATTTA 57.504 36.364 0.00 0.00 0.00 1.40
2997 3870 4.475028 TCAGCACGCAATGACAAATTTAG 58.525 39.130 0.00 0.00 0.00 1.85
2998 3871 4.023279 TCAGCACGCAATGACAAATTTAGT 60.023 37.500 0.00 0.00 0.00 2.24
2999 3872 4.681025 CAGCACGCAATGACAAATTTAGTT 59.319 37.500 0.00 0.00 0.00 2.24
3000 3873 5.175491 CAGCACGCAATGACAAATTTAGTTT 59.825 36.000 0.00 0.00 0.00 2.66
3013 3886 6.372981 CAAATTTAGTTTGCAATTTCCTGGC 58.627 36.000 0.00 0.00 40.62 4.85
3014 3887 4.679373 TTTAGTTTGCAATTTCCTGGCA 57.321 36.364 0.00 0.00 35.41 4.92
3015 3888 4.679373 TTAGTTTGCAATTTCCTGGCAA 57.321 36.364 0.00 0.00 44.97 4.52
3042 3915 9.683069 AAAAGTTGAATCACAGATTTGTCATAC 57.317 29.630 0.00 0.00 34.62 2.39
3043 3916 8.627208 AAGTTGAATCACAGATTTGTCATACT 57.373 30.769 0.00 0.00 34.62 2.12
3044 3917 8.261492 AGTTGAATCACAGATTTGTCATACTC 57.739 34.615 0.00 0.00 34.62 2.59
3045 3918 6.892310 TGAATCACAGATTTGTCATACTCG 57.108 37.500 0.00 0.00 34.62 4.18
3046 3919 5.291858 TGAATCACAGATTTGTCATACTCGC 59.708 40.000 0.00 0.00 34.62 5.03
3047 3920 3.521560 TCACAGATTTGTCATACTCGCC 58.478 45.455 0.00 0.00 34.62 5.54
3048 3921 3.056179 TCACAGATTTGTCATACTCGCCA 60.056 43.478 0.00 0.00 34.62 5.69
3049 3922 3.684305 CACAGATTTGTCATACTCGCCAA 59.316 43.478 0.00 0.00 34.62 4.52
3050 3923 4.333649 CACAGATTTGTCATACTCGCCAAT 59.666 41.667 0.00 0.00 34.62 3.16
3051 3924 4.943705 ACAGATTTGTCATACTCGCCAATT 59.056 37.500 0.00 0.00 29.46 2.32
3052 3925 6.037062 CACAGATTTGTCATACTCGCCAATTA 59.963 38.462 0.00 0.00 34.62 1.40
3053 3926 6.597672 ACAGATTTGTCATACTCGCCAATTAA 59.402 34.615 0.00 0.00 29.46 1.40
3054 3927 7.120579 ACAGATTTGTCATACTCGCCAATTAAA 59.879 33.333 0.00 0.00 29.46 1.52
3055 3928 7.429340 CAGATTTGTCATACTCGCCAATTAAAC 59.571 37.037 0.00 0.00 0.00 2.01
3056 3929 6.811253 TTTGTCATACTCGCCAATTAAACT 57.189 33.333 0.00 0.00 0.00 2.66
3057 3930 6.811253 TTGTCATACTCGCCAATTAAACTT 57.189 33.333 0.00 0.00 0.00 2.66
3058 3931 6.176975 TGTCATACTCGCCAATTAAACTTG 57.823 37.500 0.00 0.00 0.00 3.16
3059 3932 5.703592 TGTCATACTCGCCAATTAAACTTGT 59.296 36.000 0.00 0.00 0.00 3.16
3060 3933 6.874664 TGTCATACTCGCCAATTAAACTTGTA 59.125 34.615 0.00 0.00 0.00 2.41
3061 3934 7.148540 TGTCATACTCGCCAATTAAACTTGTAC 60.149 37.037 0.00 0.00 0.00 2.90
3062 3935 4.657075 ACTCGCCAATTAAACTTGTACG 57.343 40.909 0.00 0.00 0.00 3.67
3063 3936 4.309099 ACTCGCCAATTAAACTTGTACGA 58.691 39.130 0.00 4.90 34.07 3.43
3064 3937 4.751098 ACTCGCCAATTAAACTTGTACGAA 59.249 37.500 0.00 0.00 34.50 3.85
3065 3938 5.021120 TCGCCAATTAAACTTGTACGAAC 57.979 39.130 0.00 0.00 32.98 3.95
3066 3939 4.510711 TCGCCAATTAAACTTGTACGAACA 59.489 37.500 0.00 0.00 32.98 3.18
3067 3940 5.179742 TCGCCAATTAAACTTGTACGAACAT 59.820 36.000 0.00 0.00 34.97 2.71
3068 3941 6.368243 TCGCCAATTAAACTTGTACGAACATA 59.632 34.615 0.00 0.00 34.97 2.29
3069 3942 7.016466 CGCCAATTAAACTTGTACGAACATAA 58.984 34.615 0.00 0.00 34.97 1.90
3070 3943 7.694784 CGCCAATTAAACTTGTACGAACATAAT 59.305 33.333 0.00 0.00 34.97 1.28
3071 3944 8.794406 GCCAATTAAACTTGTACGAACATAATG 58.206 33.333 0.00 0.00 34.97 1.90
3072 3945 9.284594 CCAATTAAACTTGTACGAACATAATGG 57.715 33.333 0.00 0.00 34.97 3.16
3073 3946 9.834628 CAATTAAACTTGTACGAACATAATGGT 57.165 29.630 0.00 0.00 34.97 3.55
3076 3949 7.499321 AAACTTGTACGAACATAATGGTTCA 57.501 32.000 6.82 0.00 45.82 3.18
3077 3950 7.499321 AACTTGTACGAACATAATGGTTCAA 57.501 32.000 6.82 0.00 45.82 2.69
3078 3951 7.499321 ACTTGTACGAACATAATGGTTCAAA 57.501 32.000 6.82 0.00 45.82 2.69
3079 3952 7.932335 ACTTGTACGAACATAATGGTTCAAAA 58.068 30.769 6.82 0.00 45.82 2.44
3080 3953 8.407064 ACTTGTACGAACATAATGGTTCAAAAA 58.593 29.630 6.82 0.00 45.82 1.94
3099 3972 5.731599 AAAAACATGCGATTTTGCTGAAA 57.268 30.435 0.00 0.00 35.36 2.69
3100 3973 4.713854 AAACATGCGATTTTGCTGAAAC 57.286 36.364 0.00 0.00 35.36 2.78
3101 3974 2.676076 ACATGCGATTTTGCTGAAACC 58.324 42.857 0.00 0.00 35.36 3.27
3102 3975 2.297033 ACATGCGATTTTGCTGAAACCT 59.703 40.909 0.00 0.00 35.36 3.50
3103 3976 3.505680 ACATGCGATTTTGCTGAAACCTA 59.494 39.130 0.00 0.00 35.36 3.08
3104 3977 4.022416 ACATGCGATTTTGCTGAAACCTAA 60.022 37.500 0.00 0.00 35.36 2.69
3105 3978 4.576216 TGCGATTTTGCTGAAACCTAAA 57.424 36.364 0.00 0.00 35.36 1.85
3106 3979 4.938080 TGCGATTTTGCTGAAACCTAAAA 58.062 34.783 0.00 0.00 35.36 1.52
3107 3980 5.352284 TGCGATTTTGCTGAAACCTAAAAA 58.648 33.333 0.00 0.00 35.36 1.94
3108 3981 5.988561 TGCGATTTTGCTGAAACCTAAAAAT 59.011 32.000 0.00 0.00 34.14 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
113 114 4.223700 TGCTCCCATGATGTATCTATCACC 59.776 45.833 0.00 0.00 39.68 4.02
117 118 3.118847 CGCTGCTCCCATGATGTATCTAT 60.119 47.826 0.00 0.00 0.00 1.98
145 146 7.128751 AGCCATCTAGCCATCTATATCTAACA 58.871 38.462 0.00 0.00 0.00 2.41
268 269 7.824779 ACCACTTCCTCTGTATCAAAATCTAAC 59.175 37.037 0.00 0.00 0.00 2.34
272 273 7.556844 TCTACCACTTCCTCTGTATCAAAATC 58.443 38.462 0.00 0.00 0.00 2.17
713 754 9.268268 CCTTTTAGTGTGTTAGTTCACTCATTA 57.732 33.333 1.08 0.00 42.77 1.90
725 766 7.710044 TCGTAATGTTGACCTTTTAGTGTGTTA 59.290 33.333 0.00 0.00 0.00 2.41
741 782 2.213499 GAGGCCCATCTCGTAATGTTG 58.787 52.381 0.00 0.00 0.00 3.33
742 783 2.622064 GAGGCCCATCTCGTAATGTT 57.378 50.000 0.00 0.00 0.00 2.71
768 1121 7.598493 CCAACATGAAAATTTATTTCAGACCGT 59.402 33.333 0.00 2.43 41.13 4.83
771 1124 7.148423 GGCCCAACATGAAAATTTATTTCAGAC 60.148 37.037 0.00 0.00 41.13 3.51
804 1159 1.733041 CTTTCTCGGCACTTCGCGA 60.733 57.895 3.71 3.71 43.84 5.87
888 1259 2.661537 CAACGCACACCGCTCAGA 60.662 61.111 0.00 0.00 41.76 3.27
890 1261 2.964925 GACAACGCACACCGCTCA 60.965 61.111 0.00 0.00 41.76 4.26
961 1335 0.532196 GCGCCCTTTTATAGAGCGGT 60.532 55.000 0.00 0.00 46.50 5.68
987 1361 3.014085 TTCGGTGGGAGATGGCGAC 62.014 63.158 0.00 0.00 0.00 5.19
1026 1430 1.301401 CGTTGGAACTCGGAAGCCA 60.301 57.895 0.00 0.00 0.00 4.75
1078 1484 5.449177 GGAGCTTTGGAAGATTAAATGTCGG 60.449 44.000 0.00 0.00 0.00 4.79
1083 1489 7.227512 CAGATACGGAGCTTTGGAAGATTAAAT 59.772 37.037 0.00 0.00 0.00 1.40
1098 1504 0.940126 CATTGCACCAGATACGGAGC 59.060 55.000 0.00 0.00 42.40 4.70
1099 1505 1.586422 CCATTGCACCAGATACGGAG 58.414 55.000 0.00 0.00 0.00 4.63
1100 1506 0.463654 GCCATTGCACCAGATACGGA 60.464 55.000 0.00 0.00 37.47 4.69
1101 1507 1.447317 GGCCATTGCACCAGATACGG 61.447 60.000 0.00 0.00 40.13 4.02
1102 1508 1.775039 CGGCCATTGCACCAGATACG 61.775 60.000 2.24 0.00 40.13 3.06
1103 1509 2.024918 CGGCCATTGCACCAGATAC 58.975 57.895 2.24 0.00 40.13 2.24
1175 1587 3.706373 GGCTCTCCAGGCACGGAA 61.706 66.667 0.00 0.00 44.88 4.30
1306 1721 1.155859 ATTGCCCTGCTGGTTTCCA 59.844 52.632 9.00 0.00 36.04 3.53
1389 1804 7.484975 ACAAAATTCCGTGTAAAAGAACATCA 58.515 30.769 0.00 0.00 0.00 3.07
1609 2035 1.569548 ACCTCCTTCTCGTCCTCCATA 59.430 52.381 0.00 0.00 0.00 2.74
1937 2376 1.411977 CCTCAGATGCAGGGTACAGAG 59.588 57.143 0.00 0.00 0.00 3.35
1938 2377 1.489481 CCTCAGATGCAGGGTACAGA 58.511 55.000 0.00 0.00 0.00 3.41
1962 2408 1.933247 CCTCGGACAGCTGAAATCTC 58.067 55.000 23.35 6.73 0.00 2.75
2012 2459 0.672342 AGAAGAACGGCACACTACGT 59.328 50.000 0.00 0.00 46.48 3.57
2036 2483 3.774959 AACGAGCGCGCAGATAGGG 62.775 63.158 35.10 15.35 42.48 3.53
2077 2524 6.253298 CCATTGATTTGCCAAGTACATTTACG 59.747 38.462 0.00 0.00 32.93 3.18
2102 2549 2.742053 TCAAGCAGCCGAACACTTATTC 59.258 45.455 0.00 0.00 0.00 1.75
2152 2599 5.067936 CAGGGAACTAATGTCTCGATACAGT 59.932 44.000 9.63 9.27 40.21 3.55
2153 2600 5.067936 ACAGGGAACTAATGTCTCGATACAG 59.932 44.000 9.63 0.00 40.21 2.74
2154 2601 4.954202 ACAGGGAACTAATGTCTCGATACA 59.046 41.667 6.06 6.06 40.21 2.29
2184 2633 3.930336 AGAACACATCACATCACACGAT 58.070 40.909 0.00 0.00 0.00 3.73
2228 2680 7.468441 AGTATAGCATCTCGATTCAGTTATCG 58.532 38.462 0.00 0.00 46.63 2.92
2246 2698 2.941453 TGCGCTGCCTATAGTATAGC 57.059 50.000 9.73 7.83 0.00 2.97
2247 2699 3.634448 AGGATGCGCTGCCTATAGTATAG 59.366 47.826 18.06 9.87 31.31 1.31
2248 2700 3.381590 CAGGATGCGCTGCCTATAGTATA 59.618 47.826 18.87 0.00 32.03 1.47
2252 2704 0.605083 TCAGGATGCGCTGCCTATAG 59.395 55.000 18.87 9.25 34.76 1.31
2263 2715 4.046938 TCTTACAGATTCGTCAGGATGC 57.953 45.455 0.00 0.00 34.76 3.91
2272 2724 4.103365 AGACTGCACTCTTACAGATTCG 57.897 45.455 0.00 0.00 37.35 3.34
2277 2729 3.119316 CCCAGTAGACTGCACTCTTACAG 60.119 52.174 4.03 0.00 42.47 2.74
2282 2734 0.542938 TGCCCAGTAGACTGCACTCT 60.543 55.000 4.03 1.37 42.47 3.24
2517 3109 3.181497 GCAAACAACAGATCTGTGTGTGT 60.181 43.478 29.34 25.87 44.13 3.72
2518 3110 3.365832 GCAAACAACAGATCTGTGTGTG 58.634 45.455 28.52 27.74 44.13 3.82
2529 3121 3.731652 TCCAATTGAGGCAAACAACAG 57.268 42.857 7.12 0.00 0.00 3.16
2540 3132 3.191162 TGCGATTTGTCCTTCCAATTGAG 59.809 43.478 7.12 0.00 0.00 3.02
2547 3139 2.369394 AGGATTGCGATTTGTCCTTCC 58.631 47.619 0.00 0.00 37.84 3.46
2554 3240 3.941483 ACTCAGGTTAGGATTGCGATTTG 59.059 43.478 0.00 0.00 0.00 2.32
2563 3249 1.115467 CCAGCGACTCAGGTTAGGAT 58.885 55.000 0.00 0.00 0.00 3.24
2708 3579 1.377366 CTCCAGCAGATGCAAGCAGG 61.377 60.000 7.68 12.42 45.16 4.85
2734 3605 0.397941 CTCAGCAAGGGTTCTCACCA 59.602 55.000 0.00 0.00 46.43 4.17
2740 3611 0.037447 AAGGAGCTCAGCAAGGGTTC 59.963 55.000 17.19 0.00 0.00 3.62
2926 3799 1.598130 CCCTGCCACGGCTATAAGC 60.598 63.158 9.92 0.00 42.51 3.09
2927 3800 1.598130 GCCCTGCCACGGCTATAAG 60.598 63.158 9.92 0.00 43.48 1.73
2928 3801 2.508928 GCCCTGCCACGGCTATAA 59.491 61.111 9.92 0.00 43.48 0.98
2934 3807 1.814772 TTTGATTTGCCCTGCCACGG 61.815 55.000 0.00 0.00 0.00 4.94
2935 3808 0.667184 GTTTGATTTGCCCTGCCACG 60.667 55.000 0.00 0.00 0.00 4.94
2936 3809 0.392336 TGTTTGATTTGCCCTGCCAC 59.608 50.000 0.00 0.00 0.00 5.01
2937 3810 1.350071 ATGTTTGATTTGCCCTGCCA 58.650 45.000 0.00 0.00 0.00 4.92
2938 3811 2.477845 AATGTTTGATTTGCCCTGCC 57.522 45.000 0.00 0.00 0.00 4.85
2939 3812 4.834357 AAAAATGTTTGATTTGCCCTGC 57.166 36.364 0.00 0.00 0.00 4.85
2940 3813 7.306953 CCATTAAAAATGTTTGATTTGCCCTG 58.693 34.615 0.00 0.00 0.00 4.45
2941 3814 6.072008 GCCATTAAAAATGTTTGATTTGCCCT 60.072 34.615 0.00 0.00 0.00 5.19
2942 3815 6.092092 GCCATTAAAAATGTTTGATTTGCCC 58.908 36.000 0.00 0.00 0.00 5.36
2943 3816 6.675987 TGCCATTAAAAATGTTTGATTTGCC 58.324 32.000 0.00 0.00 0.00 4.52
2944 3817 8.745464 ATTGCCATTAAAAATGTTTGATTTGC 57.255 26.923 0.00 0.00 0.00 3.68
2956 3829 9.029243 CGTGCTGATATAAATTGCCATTAAAAA 57.971 29.630 0.00 0.00 0.00 1.94
2957 3830 7.168972 GCGTGCTGATATAAATTGCCATTAAAA 59.831 33.333 0.00 0.00 0.00 1.52
2958 3831 6.640499 GCGTGCTGATATAAATTGCCATTAAA 59.360 34.615 0.00 0.00 0.00 1.52
2959 3832 6.148948 GCGTGCTGATATAAATTGCCATTAA 58.851 36.000 0.00 0.00 0.00 1.40
2960 3833 5.240403 TGCGTGCTGATATAAATTGCCATTA 59.760 36.000 0.00 0.00 0.00 1.90
2961 3834 4.037803 TGCGTGCTGATATAAATTGCCATT 59.962 37.500 0.00 0.00 0.00 3.16
2962 3835 3.569277 TGCGTGCTGATATAAATTGCCAT 59.431 39.130 0.00 0.00 0.00 4.40
2963 3836 2.948315 TGCGTGCTGATATAAATTGCCA 59.052 40.909 0.00 0.00 0.00 4.92
2964 3837 3.624326 TGCGTGCTGATATAAATTGCC 57.376 42.857 0.00 0.00 0.00 4.52
2965 3838 5.116074 GTCATTGCGTGCTGATATAAATTGC 59.884 40.000 0.00 0.00 0.00 3.56
2966 3839 6.200808 TGTCATTGCGTGCTGATATAAATTG 58.799 36.000 0.00 0.00 0.00 2.32
2967 3840 6.375945 TGTCATTGCGTGCTGATATAAATT 57.624 33.333 0.00 0.00 0.00 1.82
2968 3841 6.375945 TTGTCATTGCGTGCTGATATAAAT 57.624 33.333 0.00 0.00 0.00 1.40
2969 3842 5.809719 TTGTCATTGCGTGCTGATATAAA 57.190 34.783 0.00 0.00 0.00 1.40
2970 3843 5.809719 TTTGTCATTGCGTGCTGATATAA 57.190 34.783 0.00 0.00 0.00 0.98
2971 3844 6.375945 AATTTGTCATTGCGTGCTGATATA 57.624 33.333 0.00 0.00 0.00 0.86
2972 3845 4.906065 ATTTGTCATTGCGTGCTGATAT 57.094 36.364 0.00 0.00 0.00 1.63
2973 3846 4.700268 AATTTGTCATTGCGTGCTGATA 57.300 36.364 0.00 0.00 0.00 2.15
2974 3847 3.581024 AATTTGTCATTGCGTGCTGAT 57.419 38.095 0.00 0.00 0.00 2.90
2975 3848 3.367992 AAATTTGTCATTGCGTGCTGA 57.632 38.095 0.00 0.00 0.00 4.26
2976 3849 4.229096 ACTAAATTTGTCATTGCGTGCTG 58.771 39.130 0.00 0.00 0.00 4.41
2977 3850 4.503741 ACTAAATTTGTCATTGCGTGCT 57.496 36.364 0.00 0.00 0.00 4.40
2978 3851 5.365133 CAAACTAAATTTGTCATTGCGTGC 58.635 37.500 0.00 0.00 42.46 5.34
2990 3863 6.060788 TGCCAGGAAATTGCAAACTAAATTT 58.939 32.000 1.71 0.00 38.39 1.82
2991 3864 5.619220 TGCCAGGAAATTGCAAACTAAATT 58.381 33.333 1.71 0.00 30.85 1.82
2992 3865 5.226194 TGCCAGGAAATTGCAAACTAAAT 57.774 34.783 1.71 0.00 30.85 1.40
2993 3866 4.679373 TGCCAGGAAATTGCAAACTAAA 57.321 36.364 1.71 0.00 30.85 1.85
2994 3867 4.679373 TTGCCAGGAAATTGCAAACTAA 57.321 36.364 1.71 0.00 41.63 2.24
2995 3868 4.679373 TTTGCCAGGAAATTGCAAACTA 57.321 36.364 1.71 0.00 46.63 2.24
2996 3869 3.557228 TTTGCCAGGAAATTGCAAACT 57.443 38.095 1.71 0.00 46.63 2.66
3016 3889 9.683069 GTATGACAAATCTGTGATTCAACTTTT 57.317 29.630 0.00 0.00 35.30 2.27
3017 3890 9.071276 AGTATGACAAATCTGTGATTCAACTTT 57.929 29.630 0.00 0.00 35.30 2.66
3018 3891 8.627208 AGTATGACAAATCTGTGATTCAACTT 57.373 30.769 0.00 0.00 35.30 2.66
3019 3892 7.063898 CGAGTATGACAAATCTGTGATTCAACT 59.936 37.037 0.00 0.00 35.30 3.16
3020 3893 7.176075 CGAGTATGACAAATCTGTGATTCAAC 58.824 38.462 0.00 0.00 35.30 3.18
3021 3894 6.183360 GCGAGTATGACAAATCTGTGATTCAA 60.183 38.462 0.00 0.00 35.30 2.69
3022 3895 5.291858 GCGAGTATGACAAATCTGTGATTCA 59.708 40.000 0.00 0.00 35.30 2.57
3023 3896 5.277058 GGCGAGTATGACAAATCTGTGATTC 60.277 44.000 0.00 0.00 35.30 2.52
3024 3897 4.572389 GGCGAGTATGACAAATCTGTGATT 59.428 41.667 0.00 0.00 35.30 2.57
3025 3898 4.122776 GGCGAGTATGACAAATCTGTGAT 58.877 43.478 0.00 0.00 35.30 3.06
3026 3899 3.056179 TGGCGAGTATGACAAATCTGTGA 60.056 43.478 0.00 0.00 35.30 3.58
3027 3900 3.261580 TGGCGAGTATGACAAATCTGTG 58.738 45.455 0.00 0.00 35.30 3.66
3028 3901 3.610040 TGGCGAGTATGACAAATCTGT 57.390 42.857 0.00 0.00 38.98 3.41
3029 3902 5.490139 AATTGGCGAGTATGACAAATCTG 57.510 39.130 0.00 0.00 40.98 2.90
3030 3903 7.336931 AGTTTAATTGGCGAGTATGACAAATCT 59.663 33.333 0.00 0.00 40.98 2.40
3031 3904 7.472543 AGTTTAATTGGCGAGTATGACAAATC 58.527 34.615 0.00 0.00 40.98 2.17
3032 3905 7.391148 AGTTTAATTGGCGAGTATGACAAAT 57.609 32.000 0.00 0.00 40.98 2.32
3033 3906 6.811253 AGTTTAATTGGCGAGTATGACAAA 57.189 33.333 0.00 0.00 40.98 2.83
3034 3907 6.205853 ACAAGTTTAATTGGCGAGTATGACAA 59.794 34.615 0.00 0.00 42.06 3.18
3035 3908 5.703592 ACAAGTTTAATTGGCGAGTATGACA 59.296 36.000 0.00 0.00 34.36 3.58
3036 3909 6.178239 ACAAGTTTAATTGGCGAGTATGAC 57.822 37.500 0.00 0.00 34.36 3.06
3037 3910 6.035220 CGTACAAGTTTAATTGGCGAGTATGA 59.965 38.462 0.00 0.00 35.89 2.15
3038 3911 6.035220 TCGTACAAGTTTAATTGGCGAGTATG 59.965 38.462 7.40 0.00 37.04 2.39
3039 3912 6.101332 TCGTACAAGTTTAATTGGCGAGTAT 58.899 36.000 7.40 0.00 37.04 2.12
3040 3913 5.468592 TCGTACAAGTTTAATTGGCGAGTA 58.531 37.500 7.40 0.00 37.04 2.59
3041 3914 4.309099 TCGTACAAGTTTAATTGGCGAGT 58.691 39.130 7.40 0.00 37.04 4.18
3042 3915 4.914312 TCGTACAAGTTTAATTGGCGAG 57.086 40.909 7.40 0.00 37.04 5.03
3043 3916 4.510711 TGTTCGTACAAGTTTAATTGGCGA 59.489 37.500 0.00 7.40 38.74 5.54
3044 3917 4.774586 TGTTCGTACAAGTTTAATTGGCG 58.225 39.130 0.00 0.10 35.48 5.69
3045 3918 8.794406 CATTATGTTCGTACAAGTTTAATTGGC 58.206 33.333 0.00 0.00 37.91 4.52
3046 3919 9.284594 CCATTATGTTCGTACAAGTTTAATTGG 57.715 33.333 0.00 1.23 37.91 3.16
3047 3920 9.834628 ACCATTATGTTCGTACAAGTTTAATTG 57.165 29.630 0.00 0.00 37.91 2.32
3050 3923 9.053840 TGAACCATTATGTTCGTACAAGTTTAA 57.946 29.630 0.00 0.00 46.04 1.52
3051 3924 8.604640 TGAACCATTATGTTCGTACAAGTTTA 57.395 30.769 0.00 0.00 46.04 2.01
3052 3925 7.499321 TGAACCATTATGTTCGTACAAGTTT 57.501 32.000 0.00 0.00 46.04 2.66
3053 3926 7.499321 TTGAACCATTATGTTCGTACAAGTT 57.501 32.000 0.00 0.00 46.04 2.66
3054 3927 7.499321 TTTGAACCATTATGTTCGTACAAGT 57.501 32.000 0.00 0.00 46.04 3.16
3055 3928 8.789881 TTTTTGAACCATTATGTTCGTACAAG 57.210 30.769 0.00 0.00 46.04 3.16
3077 3950 5.500825 GTTTCAGCAAAATCGCATGTTTTT 58.499 33.333 0.00 0.00 0.00 1.94
3078 3951 4.024977 GGTTTCAGCAAAATCGCATGTTTT 60.025 37.500 0.00 0.00 0.00 2.43
3079 3952 3.494251 GGTTTCAGCAAAATCGCATGTTT 59.506 39.130 0.00 0.00 0.00 2.83
3080 3953 3.059166 GGTTTCAGCAAAATCGCATGTT 58.941 40.909 0.00 0.00 0.00 2.71
3081 3954 2.297033 AGGTTTCAGCAAAATCGCATGT 59.703 40.909 0.00 0.00 32.91 3.21
3082 3955 2.950433 AGGTTTCAGCAAAATCGCATG 58.050 42.857 0.00 0.00 32.91 4.06
3083 3956 4.782019 TTAGGTTTCAGCAAAATCGCAT 57.218 36.364 0.00 0.00 32.91 4.73
3084 3957 4.576216 TTTAGGTTTCAGCAAAATCGCA 57.424 36.364 0.00 0.00 32.91 5.10
3085 3958 5.898630 TTTTTAGGTTTCAGCAAAATCGC 57.101 34.783 0.00 0.00 32.91 4.58


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

AutoCloner maintained by Alex Coulton.