Multiple sequence alignment - TraesCS5A01G112800

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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 TraesCS5A01G112800 chr5A 100.000 3086 0 0 1 3086 220265351 220268436 0.000000e+00 5699
1 TraesCS5A01G112800 chr5A 92.157 102 8 0 2985 3086 321615908 321616009 8.920000e-31 145
2 TraesCS5A01G112800 chr2D 95.152 2991 129 14 1 2985 340330952 340327972 0.000000e+00 4706
3 TraesCS5A01G112800 chr4B 93.409 2989 183 9 1 2984 120261641 120258662 0.000000e+00 4416
4 TraesCS5A01G112800 chr4B 92.855 2995 184 16 1 2984 40493742 40496717 0.000000e+00 4318
5 TraesCS5A01G112800 chr4B 92.573 2989 206 9 1 2984 222595969 222598946 0.000000e+00 4276
6 TraesCS5A01G112800 chr5B 93.347 2991 185 9 1 2985 10417920 10414938 0.000000e+00 4409
7 TraesCS5A01G112800 chr3A 93.108 2989 183 13 1 2984 91839316 91842286 0.000000e+00 4357
8 TraesCS5A01G112800 chr6B 92.776 2990 200 11 1 2985 706415689 706412711 0.000000e+00 4311
9 TraesCS5A01G112800 chr4A 92.852 2966 193 10 1 2961 531953452 531956403 0.000000e+00 4285
10 TraesCS5A01G112800 chr4A 94.118 102 6 0 2985 3086 319078888 319078787 4.120000e-34 156
11 TraesCS5A01G112800 chr4A 94.118 102 6 0 2985 3086 376671683 376671784 4.120000e-34 156
12 TraesCS5A01G112800 chr2B 93.112 2831 183 7 157 2984 680792838 680790017 0.000000e+00 4137
13 TraesCS5A01G112800 chr7A 94.118 102 6 0 2985 3086 588134767 588134868 4.120000e-34 156
14 TraesCS5A01G112800 chr7A 94.898 98 5 0 2989 3086 490258219 490258122 1.480000e-33 154
15 TraesCS5A01G112800 chr3D 92.157 102 8 0 2985 3086 433270652 433270753 8.920000e-31 145
16 TraesCS5A01G112800 chr6A 92.857 98 7 0 2989 3086 62091141 62091044 3.210000e-30 143
17 TraesCS5A01G112800 chr6D 91.176 102 9 0 2985 3086 365123207 365123106 4.150000e-29 139
18 TraesCS5A01G112800 chr1A 90.816 98 9 0 2989 3086 102419915 102420012 6.940000e-27 132


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 TraesCS5A01G112800 chr5A 220265351 220268436 3085 False 5699 5699 100.000 1 3086 1 chr5A.!!$F1 3085
1 TraesCS5A01G112800 chr2D 340327972 340330952 2980 True 4706 4706 95.152 1 2985 1 chr2D.!!$R1 2984
2 TraesCS5A01G112800 chr4B 120258662 120261641 2979 True 4416 4416 93.409 1 2984 1 chr4B.!!$R1 2983
3 TraesCS5A01G112800 chr4B 40493742 40496717 2975 False 4318 4318 92.855 1 2984 1 chr4B.!!$F1 2983
4 TraesCS5A01G112800 chr4B 222595969 222598946 2977 False 4276 4276 92.573 1 2984 1 chr4B.!!$F2 2983
5 TraesCS5A01G112800 chr5B 10414938 10417920 2982 True 4409 4409 93.347 1 2985 1 chr5B.!!$R1 2984
6 TraesCS5A01G112800 chr3A 91839316 91842286 2970 False 4357 4357 93.108 1 2984 1 chr3A.!!$F1 2983
7 TraesCS5A01G112800 chr6B 706412711 706415689 2978 True 4311 4311 92.776 1 2985 1 chr6B.!!$R1 2984
8 TraesCS5A01G112800 chr4A 531953452 531956403 2951 False 4285 4285 92.852 1 2961 1 chr4A.!!$F2 2960
9 TraesCS5A01G112800 chr2B 680790017 680792838 2821 True 4137 4137 93.112 157 2984 1 chr2B.!!$R1 2827

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
789 795 0.630673 TATCCCACCCTTTGCATGCT 59.369 50.0 20.33 0.0 0.00 3.79 F
1660 1667 0.178953 ACCTTGCTGGGCTGACATTT 60.179 50.0 1.69 0.0 41.11 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 1933 1.620822 AGTGAAAGCCTCGCCAATTT 58.379 45.000 0.0 0.0 34.9 1.82 R
2655 2672 2.038033 AGTAACACAGCCGGTAACACAT 59.962 45.455 1.9 0.0 0.0 3.21 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
25 26 8.478775 AGTTCTTGGGCTTATCTTAAAAGTTT 57.521 30.769 0.00 0.00 0.00 2.66
117 119 4.381825 GGATTCACATAATGCTGGCACAAA 60.382 41.667 0.00 0.00 38.70 2.83
118 120 3.853831 TCACATAATGCTGGCACAAAG 57.146 42.857 0.00 0.00 38.70 2.77
155 159 4.163458 GGGGTGAAGACATGGTGAGTAATA 59.837 45.833 0.00 0.00 0.00 0.98
195 199 8.397906 TGTTTTTCTGTGTCTCTTTTGTCATAG 58.602 33.333 0.00 0.00 0.00 2.23
252 256 3.127895 CCTGAAAAGAAACGACCACACAA 59.872 43.478 0.00 0.00 0.00 3.33
271 275 7.148820 CCACACAAATCAAAGGTTTATTTAGCG 60.149 37.037 0.00 0.00 0.00 4.26
284 288 6.147328 GGTTTATTTAGCGACTCACAAGAAGT 59.853 38.462 0.00 0.00 0.00 3.01
289 293 3.093057 AGCGACTCACAAGAAGTAGGAT 58.907 45.455 0.00 0.00 0.00 3.24
334 338 9.435570 AAAGATAGAAATAAGTGCCTAGTAGGA 57.564 33.333 21.02 2.33 37.67 2.94
335 339 8.644374 AGATAGAAATAAGTGCCTAGTAGGAG 57.356 38.462 21.02 0.00 37.67 3.69
420 424 9.288576 TGTATGCATGATTCTTTTCTTATAGGG 57.711 33.333 10.16 0.00 0.00 3.53
440 444 6.597832 AGGGTCGATTGGAGAATCTAATAG 57.402 41.667 0.00 0.00 46.88 1.73
503 507 1.217057 ATGGGAAGGTGATGCCCTGT 61.217 55.000 0.00 0.00 42.52 4.00
522 526 4.323562 CCTGTAGGAAGTGTTAGGGAAAGG 60.324 50.000 0.00 0.00 37.39 3.11
525 530 5.370289 TGTAGGAAGTGTTAGGGAAAGGAAA 59.630 40.000 0.00 0.00 0.00 3.13
537 542 4.968719 AGGGAAAGGAAAATTGGACAAGTT 59.031 37.500 0.00 0.00 0.00 2.66
552 557 2.299867 ACAAGTTCATGGCATGGGTTTC 59.700 45.455 26.15 12.40 0.00 2.78
718 723 7.831193 AGCAAGACCAGATTATTAAAGATGTGT 59.169 33.333 0.00 0.00 0.00 3.72
789 795 0.630673 TATCCCACCCTTTGCATGCT 59.369 50.000 20.33 0.00 0.00 3.79
909 915 8.751302 AAACAAAGGTAATGTTAATAAAGGCG 57.249 30.769 0.00 0.00 39.98 5.52
1007 1013 1.999051 CACGCTCGTCTATGCAACC 59.001 57.895 0.00 0.00 0.00 3.77
1027 1033 5.301835 ACCTGACATTCCTGAGGATAATG 57.698 43.478 0.04 6.84 0.00 1.90
1126 1132 3.052036 GCTTGCTTACCATTGTTGTGTG 58.948 45.455 0.00 0.00 0.00 3.82
1129 1135 4.764679 TGCTTACCATTGTTGTGTGATC 57.235 40.909 0.00 0.00 0.00 2.92
1199 1205 1.012086 CATCATCGCCACAAGACCTG 58.988 55.000 0.00 0.00 0.00 4.00
1255 1261 6.588373 GTGCCTTTTGAGTTTTGAAGTTGTAA 59.412 34.615 0.00 0.00 0.00 2.41
1344 1350 6.017357 GGAAACGAGGAATATAATGGGTGAAC 60.017 42.308 0.00 0.00 0.00 3.18
1357 1363 4.715534 TGGGTGAACCTATTTCAAGACA 57.284 40.909 0.00 0.00 46.09 3.41
1556 1562 7.414429 GCTCAATCTGATGTATGCAAGTAAACA 60.414 37.037 0.00 0.00 0.00 2.83
1660 1667 0.178953 ACCTTGCTGGGCTGACATTT 60.179 50.000 1.69 0.00 41.11 2.32
1661 1668 1.075374 ACCTTGCTGGGCTGACATTTA 59.925 47.619 1.69 0.00 41.11 1.40
1791 1800 2.623535 ACAAGCGGAATGTTGCGTATA 58.376 42.857 8.38 0.00 44.21 1.47
1800 1809 6.145048 GCGGAATGTTGCGTATAGTACTATTT 59.855 38.462 20.21 6.33 44.21 1.40
1863 1872 2.035066 GGTGCTGAATTTGCTCTTGTGT 59.965 45.455 6.07 0.00 0.00 3.72
1924 1933 4.473444 AGGGAAGTTTCTGATTGCAAGAA 58.527 39.130 4.94 0.00 0.00 2.52
2018 2027 8.480501 CCCTTCCACATTCTCAAATCATATTTT 58.519 33.333 0.00 0.00 0.00 1.82
2099 2108 8.443953 AAGGATAGTTGATTTACAGCTGAATC 57.556 34.615 23.35 19.55 40.16 2.52
2114 2123 4.018597 AGCTGAATCCTTGGATCAAGAAGT 60.019 41.667 9.01 0.00 43.42 3.01
2119 2128 8.884124 TGAATCCTTGGATCAAGAAGTAAATT 57.116 30.769 9.01 0.74 43.42 1.82
2229 2238 5.276270 GTCGAATTGATGCAAATGCTATGT 58.724 37.500 6.97 0.00 42.66 2.29
2243 2252 6.817765 AATGCTATGTTGTAATATTCCCCG 57.182 37.500 0.00 0.00 0.00 5.73
2318 2328 8.768957 ATGCATATGTATCATACACTCTTGTC 57.231 34.615 0.00 0.00 42.23 3.18
2682 2699 5.163622 TGTTACCGGCTGTGTTACTATAGTC 60.164 44.000 9.12 0.00 0.00 2.59
2685 2702 3.490419 CCGGCTGTGTTACTATAGTCACC 60.490 52.174 17.54 9.33 0.00 4.02
2693 2710 8.054152 TGTGTTACTATAGTCACCGAAACATA 57.946 34.615 17.54 13.01 0.00 2.29
2704 2721 4.696402 TCACCGAAACATATTACCACCAAC 59.304 41.667 0.00 0.00 0.00 3.77
2874 2892 4.365723 ACAGTTGACACCACTTAGTAACG 58.634 43.478 0.00 0.00 0.00 3.18
2917 2936 9.860650 ATTTCAAACTATGTTACTATATGGCCA 57.139 29.630 8.56 8.56 0.00 5.36
2934 2953 2.223947 GGCCAAGTAACACACTTTTGGG 60.224 50.000 0.00 0.00 45.54 4.12
2956 2975 4.081309 GGCCTGTAGTAACACAAGATGGTA 60.081 45.833 0.00 0.00 0.00 3.25
2985 3004 3.845860 AGGTCTGTCCTCTTGTAGTGAA 58.154 45.455 0.00 0.00 44.42 3.18
2986 3005 3.574826 AGGTCTGTCCTCTTGTAGTGAAC 59.425 47.826 0.00 0.00 44.42 3.18
2987 3006 3.321111 GGTCTGTCCTCTTGTAGTGAACA 59.679 47.826 0.00 0.00 35.88 3.18
2988 3007 4.299978 GTCTGTCCTCTTGTAGTGAACAC 58.700 47.826 0.00 0.00 38.00 3.32
2989 3008 4.038162 GTCTGTCCTCTTGTAGTGAACACT 59.962 45.833 12.10 12.10 45.02 3.55
2990 3009 4.649674 TCTGTCCTCTTGTAGTGAACACTT 59.350 41.667 12.66 0.00 42.54 3.16
2991 3010 4.945246 TGTCCTCTTGTAGTGAACACTTC 58.055 43.478 12.66 8.49 42.54 3.01
2992 3011 4.202223 TGTCCTCTTGTAGTGAACACTTCC 60.202 45.833 12.66 5.32 42.54 3.46
2993 3012 4.039366 GTCCTCTTGTAGTGAACACTTCCT 59.961 45.833 12.66 0.00 42.54 3.36
2994 3013 4.654262 TCCTCTTGTAGTGAACACTTCCTT 59.346 41.667 12.66 0.00 42.54 3.36
2995 3014 4.991687 CCTCTTGTAGTGAACACTTCCTTC 59.008 45.833 12.66 1.27 42.54 3.46
2996 3015 5.221541 CCTCTTGTAGTGAACACTTCCTTCT 60.222 44.000 12.66 0.00 42.54 2.85
2997 3016 6.015350 CCTCTTGTAGTGAACACTTCCTTCTA 60.015 42.308 12.66 0.00 42.54 2.10
2998 3017 7.356089 TCTTGTAGTGAACACTTCCTTCTAA 57.644 36.000 12.66 0.00 42.54 2.10
2999 3018 7.434492 TCTTGTAGTGAACACTTCCTTCTAAG 58.566 38.462 12.66 7.31 42.54 2.18
3000 3019 6.971726 TGTAGTGAACACTTCCTTCTAAGA 57.028 37.500 12.66 0.00 42.54 2.10
3001 3020 7.540474 TGTAGTGAACACTTCCTTCTAAGAT 57.460 36.000 12.66 0.00 42.54 2.40
3002 3021 7.378966 TGTAGTGAACACTTCCTTCTAAGATG 58.621 38.462 12.66 0.00 42.54 2.90
3003 3022 6.672266 AGTGAACACTTCCTTCTAAGATGA 57.328 37.500 1.32 0.00 38.83 2.92
3004 3023 6.696411 AGTGAACACTTCCTTCTAAGATGAG 58.304 40.000 1.32 0.00 38.83 2.90
3005 3024 5.350091 GTGAACACTTCCTTCTAAGATGAGC 59.650 44.000 0.00 0.00 0.00 4.26
3006 3025 5.012046 TGAACACTTCCTTCTAAGATGAGCA 59.988 40.000 0.00 0.00 0.00 4.26
3007 3026 5.083533 ACACTTCCTTCTAAGATGAGCAG 57.916 43.478 0.00 0.00 0.00 4.24
3008 3027 4.530161 ACACTTCCTTCTAAGATGAGCAGT 59.470 41.667 0.00 0.00 0.00 4.40
3009 3028 4.869297 CACTTCCTTCTAAGATGAGCAGTG 59.131 45.833 0.00 0.00 0.00 3.66
3010 3029 4.530161 ACTTCCTTCTAAGATGAGCAGTGT 59.470 41.667 0.00 0.00 0.00 3.55
3011 3030 4.727507 TCCTTCTAAGATGAGCAGTGTC 57.272 45.455 0.00 0.00 0.00 3.67
3012 3031 4.089361 TCCTTCTAAGATGAGCAGTGTCA 58.911 43.478 0.00 0.00 0.00 3.58
3013 3032 4.713814 TCCTTCTAAGATGAGCAGTGTCAT 59.286 41.667 7.62 7.62 40.00 3.06
3014 3033 5.893824 TCCTTCTAAGATGAGCAGTGTCATA 59.106 40.000 7.81 0.00 37.29 2.15
3015 3034 5.982516 CCTTCTAAGATGAGCAGTGTCATAC 59.017 44.000 7.81 3.98 37.29 2.39
3016 3035 5.175090 TCTAAGATGAGCAGTGTCATACG 57.825 43.478 7.81 0.00 37.29 3.06
3017 3036 4.881850 TCTAAGATGAGCAGTGTCATACGA 59.118 41.667 7.81 2.22 37.29 3.43
3018 3037 3.706802 AGATGAGCAGTGTCATACGAG 57.293 47.619 7.81 0.00 37.29 4.18
3019 3038 3.020274 AGATGAGCAGTGTCATACGAGT 58.980 45.455 7.81 0.00 37.29 4.18
3020 3039 3.445450 AGATGAGCAGTGTCATACGAGTT 59.555 43.478 7.81 0.00 37.29 3.01
3021 3040 2.946564 TGAGCAGTGTCATACGAGTTG 58.053 47.619 0.00 0.00 0.00 3.16
3022 3041 2.296190 TGAGCAGTGTCATACGAGTTGT 59.704 45.455 0.00 0.00 0.00 3.32
3023 3042 3.504520 TGAGCAGTGTCATACGAGTTGTA 59.495 43.478 0.00 0.00 37.49 2.41
3024 3043 4.022676 TGAGCAGTGTCATACGAGTTGTAA 60.023 41.667 0.00 0.00 36.44 2.41
3025 3044 5.073311 AGCAGTGTCATACGAGTTGTAAT 57.927 39.130 0.00 0.00 36.44 1.89
3026 3045 5.103000 AGCAGTGTCATACGAGTTGTAATC 58.897 41.667 0.00 0.00 36.44 1.75
3027 3046 5.103000 GCAGTGTCATACGAGTTGTAATCT 58.897 41.667 0.00 0.00 36.44 2.40
3028 3047 6.095021 AGCAGTGTCATACGAGTTGTAATCTA 59.905 38.462 0.00 0.00 36.44 1.98
3029 3048 6.918569 GCAGTGTCATACGAGTTGTAATCTAT 59.081 38.462 0.00 0.00 36.44 1.98
3030 3049 7.096436 GCAGTGTCATACGAGTTGTAATCTATG 60.096 40.741 0.00 0.00 36.44 2.23
3031 3050 8.129211 CAGTGTCATACGAGTTGTAATCTATGA 58.871 37.037 0.00 0.00 36.44 2.15
3032 3051 8.683615 AGTGTCATACGAGTTGTAATCTATGAA 58.316 33.333 0.00 0.00 36.44 2.57
3033 3052 8.959058 GTGTCATACGAGTTGTAATCTATGAAG 58.041 37.037 0.00 0.00 36.44 3.02
3034 3053 8.899771 TGTCATACGAGTTGTAATCTATGAAGA 58.100 33.333 0.00 0.00 36.44 2.87
3035 3054 9.731819 GTCATACGAGTTGTAATCTATGAAGAA 57.268 33.333 0.00 0.00 36.44 2.52
3039 3058 8.827177 ACGAGTTGTAATCTATGAAGAAAACA 57.173 30.769 0.00 0.00 34.73 2.83
3040 3059 9.436957 ACGAGTTGTAATCTATGAAGAAAACAT 57.563 29.630 0.00 0.00 34.73 2.71
3041 3060 9.694520 CGAGTTGTAATCTATGAAGAAAACATG 57.305 33.333 0.00 0.00 34.73 3.21
3042 3061 9.495754 GAGTTGTAATCTATGAAGAAAACATGC 57.504 33.333 0.00 0.00 34.73 4.06
3043 3062 9.236006 AGTTGTAATCTATGAAGAAAACATGCT 57.764 29.630 0.00 0.00 34.73 3.79
3044 3063 9.495754 GTTGTAATCTATGAAGAAAACATGCTC 57.504 33.333 0.00 0.00 34.73 4.26
3045 3064 8.791327 TGTAATCTATGAAGAAAACATGCTCA 57.209 30.769 0.00 0.00 34.73 4.26
3046 3065 9.399797 TGTAATCTATGAAGAAAACATGCTCAT 57.600 29.630 0.00 0.00 34.73 2.90
3047 3066 9.661187 GTAATCTATGAAGAAAACATGCTCATG 57.339 33.333 8.21 8.21 38.85 3.07
3048 3067 6.688637 TCTATGAAGAAAACATGCTCATGG 57.311 37.500 13.69 0.00 42.91 3.66
3049 3068 6.417258 TCTATGAAGAAAACATGCTCATGGA 58.583 36.000 13.69 0.00 42.91 3.41
3050 3069 5.988310 ATGAAGAAAACATGCTCATGGAA 57.012 34.783 13.69 0.00 42.91 3.53
3051 3070 5.381174 TGAAGAAAACATGCTCATGGAAG 57.619 39.130 13.69 0.00 42.91 3.46
3052 3071 5.072055 TGAAGAAAACATGCTCATGGAAGA 58.928 37.500 13.69 0.00 42.91 2.87
3053 3072 5.535783 TGAAGAAAACATGCTCATGGAAGAA 59.464 36.000 13.69 0.00 42.91 2.52
3054 3073 5.640189 AGAAAACATGCTCATGGAAGAAG 57.360 39.130 13.69 0.00 42.91 2.85
3055 3074 5.075493 AGAAAACATGCTCATGGAAGAAGT 58.925 37.500 13.69 0.00 42.91 3.01
3056 3075 5.182760 AGAAAACATGCTCATGGAAGAAGTC 59.817 40.000 13.69 2.64 42.91 3.01
3057 3076 3.708403 ACATGCTCATGGAAGAAGTCA 57.292 42.857 13.69 0.00 42.91 3.41
3058 3077 4.025040 ACATGCTCATGGAAGAAGTCAA 57.975 40.909 13.69 0.00 42.91 3.18
3059 3078 3.755378 ACATGCTCATGGAAGAAGTCAAC 59.245 43.478 13.69 0.00 42.91 3.18
3060 3079 3.490439 TGCTCATGGAAGAAGTCAACA 57.510 42.857 0.00 0.00 0.00 3.33
3061 3080 3.405831 TGCTCATGGAAGAAGTCAACAG 58.594 45.455 0.00 0.00 0.00 3.16
3062 3081 2.161211 GCTCATGGAAGAAGTCAACAGC 59.839 50.000 0.00 0.00 0.00 4.40
3063 3082 2.746362 CTCATGGAAGAAGTCAACAGCC 59.254 50.000 0.00 0.00 0.00 4.85
3064 3083 2.373169 TCATGGAAGAAGTCAACAGCCT 59.627 45.455 0.00 0.00 0.00 4.58
3065 3084 3.152341 CATGGAAGAAGTCAACAGCCTT 58.848 45.455 0.00 0.00 0.00 4.35
3066 3085 2.575532 TGGAAGAAGTCAACAGCCTTG 58.424 47.619 0.00 0.00 0.00 3.61
3067 3086 2.172505 TGGAAGAAGTCAACAGCCTTGA 59.827 45.455 0.00 0.00 0.00 3.02
3068 3087 3.214328 GGAAGAAGTCAACAGCCTTGAA 58.786 45.455 0.00 0.00 0.00 2.69
3069 3088 3.823304 GGAAGAAGTCAACAGCCTTGAAT 59.177 43.478 0.00 0.00 0.00 2.57
3070 3089 4.279420 GGAAGAAGTCAACAGCCTTGAATT 59.721 41.667 7.03 7.03 39.10 2.17
3071 3090 5.221322 GGAAGAAGTCAACAGCCTTGAATTT 60.221 40.000 8.36 2.16 36.94 1.82
3072 3091 5.859205 AGAAGTCAACAGCCTTGAATTTT 57.141 34.783 8.36 1.79 36.94 1.82
3073 3092 6.225981 AGAAGTCAACAGCCTTGAATTTTT 57.774 33.333 8.36 0.32 36.94 1.94
3074 3093 6.044682 AGAAGTCAACAGCCTTGAATTTTTG 58.955 36.000 8.36 0.00 36.94 2.44
3075 3094 4.122046 AGTCAACAGCCTTGAATTTTTGC 58.878 39.130 0.00 0.00 0.00 3.68
3076 3095 4.122046 GTCAACAGCCTTGAATTTTTGCT 58.878 39.130 0.00 0.00 0.00 3.91
3077 3096 4.571984 GTCAACAGCCTTGAATTTTTGCTT 59.428 37.500 0.00 0.00 0.00 3.91
3078 3097 4.810491 TCAACAGCCTTGAATTTTTGCTTC 59.190 37.500 0.00 0.00 0.00 3.86
3079 3098 4.677673 ACAGCCTTGAATTTTTGCTTCT 57.322 36.364 0.00 0.00 0.00 2.85
3080 3099 5.027293 ACAGCCTTGAATTTTTGCTTCTT 57.973 34.783 0.00 0.00 0.00 2.52
3081 3100 4.812626 ACAGCCTTGAATTTTTGCTTCTTG 59.187 37.500 0.00 0.00 0.00 3.02
3082 3101 4.212636 CAGCCTTGAATTTTTGCTTCTTGG 59.787 41.667 0.00 0.00 0.00 3.61
3083 3102 4.101430 AGCCTTGAATTTTTGCTTCTTGGA 59.899 37.500 0.00 0.00 0.00 3.53
3084 3103 4.450080 GCCTTGAATTTTTGCTTCTTGGAG 59.550 41.667 0.00 0.00 0.00 3.86
3085 3104 5.739935 GCCTTGAATTTTTGCTTCTTGGAGA 60.740 40.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
48 49 0.539438 TTCTCGGCAAGGGCATGTTT 60.539 50.000 0.00 0.00 43.71 2.83
117 119 2.375174 TCACCCCAACAAGCATAACTCT 59.625 45.455 0.00 0.00 0.00 3.24
118 120 2.790433 TCACCCCAACAAGCATAACTC 58.210 47.619 0.00 0.00 0.00 3.01
155 159 7.147846 ACACAGAAAAACACTTCAGGAATCAAT 60.148 33.333 0.00 0.00 0.00 2.57
195 199 3.603158 ACAAAACAGAAACAACACCCC 57.397 42.857 0.00 0.00 0.00 4.95
252 256 7.174253 TGTGAGTCGCTAAATAAACCTTTGATT 59.826 33.333 5.11 0.00 0.00 2.57
271 275 4.808364 GCATCATCCTACTTCTTGTGAGTC 59.192 45.833 0.00 0.00 0.00 3.36
420 424 6.682746 TCAGCTATTAGATTCTCCAATCGAC 58.317 40.000 0.00 0.00 43.05 4.20
440 444 1.569479 GCCAACTCTGGTCGTTCAGC 61.569 60.000 3.54 0.00 45.53 4.26
474 478 0.693049 ACCTTCCCATGCGACTCTTT 59.307 50.000 0.00 0.00 0.00 2.52
503 507 6.518516 TTTTCCTTTCCCTAACACTTCCTA 57.481 37.500 0.00 0.00 0.00 2.94
522 526 4.630111 TGCCATGAACTTGTCCAATTTTC 58.370 39.130 0.00 0.00 0.00 2.29
525 530 3.055675 CCATGCCATGAACTTGTCCAATT 60.056 43.478 6.18 0.00 0.00 2.32
537 542 1.619432 GGAAGGAAACCCATGCCATGA 60.619 52.381 6.18 0.00 0.00 3.07
552 557 3.008485 AGACTTGCTTAGGAGTTGGAAGG 59.992 47.826 0.00 0.00 34.24 3.46
727 732 7.917003 TCTATGCCATTATTGACATAGCCTTA 58.083 34.615 13.20 0.00 41.04 2.69
825 831 9.713684 TTATCATTTGATTGGAGGTTTTCCTAT 57.286 29.630 0.00 0.00 43.01 2.57
909 915 5.611796 TCAAGTGACAAGCAATGATGTAC 57.388 39.130 0.00 0.00 0.00 2.90
967 973 6.461927 CGTGCCTTAATAGGTCCATTACACTA 60.462 42.308 0.00 0.00 44.00 2.74
972 978 3.389983 AGCGTGCCTTAATAGGTCCATTA 59.610 43.478 0.00 0.00 44.00 1.90
985 991 1.519455 GCATAGACGAGCGTGCCTT 60.519 57.895 0.00 0.00 0.00 4.35
1007 1013 9.736414 ATAAATCATTATCCTCAGGAATGTCAG 57.264 33.333 0.00 0.00 34.34 3.51
1062 1068 7.152645 TCTTTGTGACATGAGTAAGAGTAACC 58.847 38.462 0.00 0.00 0.00 2.85
1126 1132 1.557651 GTCGCCAACCTAGTTCGATC 58.442 55.000 0.00 0.00 28.02 3.69
1129 1135 4.180496 GGTCGCCAACCTAGTTCG 57.820 61.111 0.00 0.00 45.45 3.95
1187 1193 2.790433 TCAATAACCAGGTCTTGTGGC 58.210 47.619 12.44 0.00 38.83 5.01
1199 1205 5.675538 ACCTCTAGCACAGAATCAATAACC 58.324 41.667 0.00 0.00 31.12 2.85
1255 1261 6.360370 TCATACCTTGAAGCTACAGAAAGT 57.640 37.500 0.00 0.00 0.00 2.66
1306 1312 1.345415 TCGTTTCCCTCACCTACCAAC 59.655 52.381 0.00 0.00 0.00 3.77
1344 1350 6.294176 CCTTGTTGGTTCTGTCTTGAAATAGG 60.294 42.308 0.00 0.00 0.00 2.57
1357 1363 3.974642 AGTTCTAGTCCCTTGTTGGTTCT 59.025 43.478 0.00 0.00 0.00 3.01
1646 1653 4.400567 AGATCTTTTAAATGTCAGCCCAGC 59.599 41.667 0.00 0.00 0.00 4.85
1791 1800 5.895534 TTGGATCGGTACTCCAAATAGTACT 59.104 40.000 11.57 0.00 47.00 2.73
1800 1809 5.163343 CCTTAATTCTTGGATCGGTACTCCA 60.163 44.000 0.00 0.00 41.03 3.86
1808 1817 3.313526 CACCAGCCTTAATTCTTGGATCG 59.686 47.826 0.00 0.00 0.00 3.69
1819 1828 4.650972 AACTCAATACCACCAGCCTTAA 57.349 40.909 0.00 0.00 0.00 1.85
1863 1872 5.592104 TCAAGAATAGGTTCGTCTATGCA 57.408 39.130 0.00 0.00 39.38 3.96
1898 1907 4.985538 TGCAATCAGAAACTTCCCTTACT 58.014 39.130 0.00 0.00 0.00 2.24
1924 1933 1.620822 AGTGAAAGCCTCGCCAATTT 58.379 45.000 0.00 0.00 34.90 1.82
2089 2098 3.265221 TCTTGATCCAAGGATTCAGCTGT 59.735 43.478 14.67 0.00 41.33 4.40
2187 2196 8.758633 ATTCGACGAAAGAAAAAGATCTTCTA 57.241 30.769 15.22 0.00 38.69 2.10
2229 2238 6.052405 ACACAACTACGGGGAATATTACAA 57.948 37.500 0.00 0.00 0.00 2.41
2243 2252 9.612620 CATTTTGAGGATAGAAAACACAACTAC 57.387 33.333 0.00 0.00 0.00 2.73
2655 2672 2.038033 AGTAACACAGCCGGTAACACAT 59.962 45.455 1.90 0.00 0.00 3.21
2665 2682 3.379372 TCGGTGACTATAGTAACACAGCC 59.621 47.826 20.07 10.25 35.33 4.85
2667 2684 6.384224 TGTTTCGGTGACTATAGTAACACAG 58.616 40.000 20.07 17.07 35.33 3.66
2682 2699 4.436317 CGTTGGTGGTAATATGTTTCGGTG 60.436 45.833 0.00 0.00 0.00 4.94
2685 2702 4.932268 ACGTTGGTGGTAATATGTTTCG 57.068 40.909 0.00 0.00 0.00 3.46
2829 2847 7.760437 TGTCACACATAATAATTGTCACCATG 58.240 34.615 0.00 0.00 0.00 3.66
2835 2853 8.503196 TGTCAACTGTCACACATAATAATTGTC 58.497 33.333 0.00 0.00 0.00 3.18
2874 2892 5.957842 TGAAATGTGTTCCATTAGACCAC 57.042 39.130 0.00 0.00 43.04 4.16
2934 2953 3.939066 ACCATCTTGTGTTACTACAGGC 58.061 45.455 0.00 0.00 34.24 4.85
2985 3004 4.530161 ACTGCTCATCTTAGAAGGAAGTGT 59.470 41.667 0.00 0.00 0.00 3.55
2986 3005 4.869297 CACTGCTCATCTTAGAAGGAAGTG 59.131 45.833 6.32 6.32 0.00 3.16
2987 3006 4.530161 ACACTGCTCATCTTAGAAGGAAGT 59.470 41.667 0.00 0.00 0.00 3.01
2988 3007 5.083533 ACACTGCTCATCTTAGAAGGAAG 57.916 43.478 0.00 0.00 0.00 3.46
2989 3008 4.528206 TGACACTGCTCATCTTAGAAGGAA 59.472 41.667 0.00 0.00 0.00 3.36
2990 3009 4.089361 TGACACTGCTCATCTTAGAAGGA 58.911 43.478 0.00 0.00 0.00 3.36
2991 3010 4.462508 TGACACTGCTCATCTTAGAAGG 57.537 45.455 0.00 0.00 0.00 3.46
2992 3011 5.685068 CGTATGACACTGCTCATCTTAGAAG 59.315 44.000 0.00 0.00 32.86 2.85
2993 3012 5.357032 TCGTATGACACTGCTCATCTTAGAA 59.643 40.000 0.00 0.00 32.86 2.10
2994 3013 4.881850 TCGTATGACACTGCTCATCTTAGA 59.118 41.667 0.00 0.00 32.86 2.10
2995 3014 5.175090 TCGTATGACACTGCTCATCTTAG 57.825 43.478 0.00 0.00 32.86 2.18
2996 3015 4.640647 ACTCGTATGACACTGCTCATCTTA 59.359 41.667 0.00 0.00 32.86 2.10
2997 3016 3.445450 ACTCGTATGACACTGCTCATCTT 59.555 43.478 0.00 0.00 32.86 2.40
2998 3017 3.020274 ACTCGTATGACACTGCTCATCT 58.980 45.455 0.00 0.00 32.86 2.90
2999 3018 3.428746 ACTCGTATGACACTGCTCATC 57.571 47.619 0.00 0.00 32.86 2.92
3000 3019 3.056536 ACAACTCGTATGACACTGCTCAT 60.057 43.478 0.00 0.00 35.05 2.90
3001 3020 2.296190 ACAACTCGTATGACACTGCTCA 59.704 45.455 0.00 0.00 0.00 4.26
3002 3021 2.947852 ACAACTCGTATGACACTGCTC 58.052 47.619 0.00 0.00 0.00 4.26
3003 3022 4.514781 TTACAACTCGTATGACACTGCT 57.485 40.909 0.00 0.00 0.00 4.24
3004 3023 5.103000 AGATTACAACTCGTATGACACTGC 58.897 41.667 0.00 0.00 0.00 4.40
3005 3024 8.129211 TCATAGATTACAACTCGTATGACACTG 58.871 37.037 0.00 0.00 0.00 3.66
3006 3025 8.221965 TCATAGATTACAACTCGTATGACACT 57.778 34.615 0.00 0.00 0.00 3.55
3007 3026 8.851960 TTCATAGATTACAACTCGTATGACAC 57.148 34.615 0.00 0.00 0.00 3.67
3008 3027 8.899771 TCTTCATAGATTACAACTCGTATGACA 58.100 33.333 0.00 0.00 0.00 3.58
3009 3028 9.731819 TTCTTCATAGATTACAACTCGTATGAC 57.268 33.333 0.00 0.00 0.00 3.06
3013 3032 9.917129 TGTTTTCTTCATAGATTACAACTCGTA 57.083 29.630 0.00 0.00 0.00 3.43
3014 3033 8.827177 TGTTTTCTTCATAGATTACAACTCGT 57.173 30.769 0.00 0.00 0.00 4.18
3015 3034 9.694520 CATGTTTTCTTCATAGATTACAACTCG 57.305 33.333 0.00 0.00 31.77 4.18
3016 3035 9.495754 GCATGTTTTCTTCATAGATTACAACTC 57.504 33.333 0.00 0.00 31.77 3.01
3017 3036 9.236006 AGCATGTTTTCTTCATAGATTACAACT 57.764 29.630 0.00 0.00 31.77 3.16
3018 3037 9.495754 GAGCATGTTTTCTTCATAGATTACAAC 57.504 33.333 0.00 0.00 31.77 3.32
3019 3038 9.230122 TGAGCATGTTTTCTTCATAGATTACAA 57.770 29.630 0.00 0.00 31.77 2.41
3020 3039 8.791327 TGAGCATGTTTTCTTCATAGATTACA 57.209 30.769 0.00 0.00 32.23 2.41
3021 3040 9.661187 CATGAGCATGTTTTCTTCATAGATTAC 57.339 33.333 2.34 0.00 34.23 1.89
3022 3041 8.843262 CCATGAGCATGTTTTCTTCATAGATTA 58.157 33.333 9.39 0.00 37.11 1.75
3023 3042 7.558807 TCCATGAGCATGTTTTCTTCATAGATT 59.441 33.333 9.39 0.00 37.11 2.40
3024 3043 7.058525 TCCATGAGCATGTTTTCTTCATAGAT 58.941 34.615 9.39 0.00 37.11 1.98
3025 3044 6.417258 TCCATGAGCATGTTTTCTTCATAGA 58.583 36.000 9.39 0.00 37.11 1.98
3026 3045 6.688637 TCCATGAGCATGTTTTCTTCATAG 57.311 37.500 9.39 0.00 37.11 2.23
3027 3046 6.885918 TCTTCCATGAGCATGTTTTCTTCATA 59.114 34.615 9.39 0.00 37.11 2.15
3028 3047 5.713389 TCTTCCATGAGCATGTTTTCTTCAT 59.287 36.000 9.39 0.00 37.11 2.57
3029 3048 5.072055 TCTTCCATGAGCATGTTTTCTTCA 58.928 37.500 9.39 0.00 37.11 3.02
3030 3049 5.633830 TCTTCCATGAGCATGTTTTCTTC 57.366 39.130 9.39 0.00 37.11 2.87
3031 3050 5.537674 ACTTCTTCCATGAGCATGTTTTCTT 59.462 36.000 9.39 0.00 37.11 2.52
3032 3051 5.075493 ACTTCTTCCATGAGCATGTTTTCT 58.925 37.500 9.39 0.00 37.11 2.52
3033 3052 5.048504 TGACTTCTTCCATGAGCATGTTTTC 60.049 40.000 9.39 0.00 37.11 2.29
3034 3053 4.828939 TGACTTCTTCCATGAGCATGTTTT 59.171 37.500 9.39 0.00 37.11 2.43
3035 3054 4.401022 TGACTTCTTCCATGAGCATGTTT 58.599 39.130 9.39 0.00 37.11 2.83
3036 3055 4.025040 TGACTTCTTCCATGAGCATGTT 57.975 40.909 9.39 0.00 37.11 2.71
3037 3056 3.708403 TGACTTCTTCCATGAGCATGT 57.292 42.857 9.39 0.00 37.11 3.21
3038 3057 3.754850 TGTTGACTTCTTCCATGAGCATG 59.245 43.478 3.50 3.50 38.51 4.06
3039 3058 4.008330 CTGTTGACTTCTTCCATGAGCAT 58.992 43.478 0.00 0.00 0.00 3.79
3040 3059 3.405831 CTGTTGACTTCTTCCATGAGCA 58.594 45.455 0.00 0.00 0.00 4.26
3041 3060 2.161211 GCTGTTGACTTCTTCCATGAGC 59.839 50.000 0.00 0.00 0.00 4.26
3042 3061 2.746362 GGCTGTTGACTTCTTCCATGAG 59.254 50.000 0.00 0.00 0.00 2.90
3043 3062 2.373169 AGGCTGTTGACTTCTTCCATGA 59.627 45.455 0.00 0.00 0.00 3.07
3044 3063 2.787994 AGGCTGTTGACTTCTTCCATG 58.212 47.619 0.00 0.00 0.00 3.66
3045 3064 3.152341 CAAGGCTGTTGACTTCTTCCAT 58.848 45.455 0.00 0.00 40.08 3.41
3046 3065 2.172505 TCAAGGCTGTTGACTTCTTCCA 59.827 45.455 0.00 0.00 40.08 3.53
3047 3066 2.851195 TCAAGGCTGTTGACTTCTTCC 58.149 47.619 0.00 0.00 40.08 3.46
3048 3067 5.444663 AATTCAAGGCTGTTGACTTCTTC 57.555 39.130 2.01 0.00 40.08 2.87
3049 3068 5.859205 AAATTCAAGGCTGTTGACTTCTT 57.141 34.783 2.01 0.00 40.08 2.52
3050 3069 5.859205 AAAATTCAAGGCTGTTGACTTCT 57.141 34.783 2.01 0.00 40.08 2.85
3051 3070 5.277011 GCAAAAATTCAAGGCTGTTGACTTC 60.277 40.000 2.01 0.00 40.08 3.01
3052 3071 4.571984 GCAAAAATTCAAGGCTGTTGACTT 59.428 37.500 2.01 1.47 43.54 3.01
3053 3072 4.122046 GCAAAAATTCAAGGCTGTTGACT 58.878 39.130 2.01 0.00 0.00 3.41
3054 3073 4.122046 AGCAAAAATTCAAGGCTGTTGAC 58.878 39.130 2.01 0.00 32.76 3.18
3055 3074 4.405116 AGCAAAAATTCAAGGCTGTTGA 57.595 36.364 0.00 0.00 32.76 3.18
3056 3075 4.812626 AGAAGCAAAAATTCAAGGCTGTTG 59.187 37.500 0.00 0.00 34.56 3.33
3057 3076 5.027293 AGAAGCAAAAATTCAAGGCTGTT 57.973 34.783 0.00 0.00 34.56 3.16
3058 3077 4.677673 AGAAGCAAAAATTCAAGGCTGT 57.322 36.364 0.00 0.00 34.56 4.40
3059 3078 4.212636 CCAAGAAGCAAAAATTCAAGGCTG 59.787 41.667 0.00 0.00 34.56 4.85
3060 3079 4.101430 TCCAAGAAGCAAAAATTCAAGGCT 59.899 37.500 0.00 0.00 36.13 4.58
3061 3080 4.379652 TCCAAGAAGCAAAAATTCAAGGC 58.620 39.130 0.00 0.00 0.00 4.35
3062 3081 5.846203 TCTCCAAGAAGCAAAAATTCAAGG 58.154 37.500 0.00 0.00 0.00 3.61


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

AutoCloner maintained by Alex Coulton.