Multiple sequence alignment - TraesCS2D01G489500

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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 TraesCS2D01G489500 chr2D 100.000 3766 0 0 1 3766 588497455 588501220 0.000000e+00 6955
1 TraesCS2D01G489500 chr2D 86.154 715 99 0 1619 2333 573951932 573951218 0.000000e+00 773
2 TraesCS2D01G489500 chr2D 79.350 1138 184 40 1125 2241 588735973 588737080 0.000000e+00 752
3 TraesCS2D01G489500 chr2D 82.346 793 104 25 19 797 588734933 588735703 0.000000e+00 656
4 TraesCS2D01G489500 chr2D 89.209 417 45 0 1137 1553 573952372 573951956 4.310000e-144 521
5 TraesCS2D01G489500 chr2D 92.667 150 10 1 2769 2917 87754985 87755134 8.190000e-52 215
6 TraesCS2D01G489500 chr2D 85.930 199 28 0 3568 3766 372800503 372800305 2.950000e-51 213
7 TraesCS2D01G489500 chr2A 94.092 2793 79 28 1 2777 723100347 723103069 0.000000e+00 4165
8 TraesCS2D01G489500 chr2A 92.308 884 33 12 2900 3766 723103067 723103932 0.000000e+00 1223
9 TraesCS2D01G489500 chr2A 83.149 1086 153 17 1619 2690 712538837 712537768 0.000000e+00 965
10 TraesCS2D01G489500 chr2A 80.025 801 111 24 6 797 723511077 723511837 7.110000e-152 547
11 TraesCS2D01G489500 chr2A 87.167 413 51 2 1135 1546 712539279 712538868 5.700000e-128 468
12 TraesCS2D01G489500 chr2A 85.000 440 59 6 1112 1546 723511997 723512434 1.240000e-119 440
13 TraesCS2D01G489500 chr2A 85.122 410 59 2 1131 1539 723134379 723134787 5.820000e-113 418
14 TraesCS2D01G489500 chr2A 81.425 393 61 10 449 833 723133761 723134149 1.020000e-80 311
15 TraesCS2D01G489500 chr2A 79.618 314 60 3 39 349 723578351 723578663 4.900000e-54 222
16 TraesCS2D01G489500 chr2A 76.519 362 62 11 448 790 723578771 723579128 3.870000e-40 176
17 TraesCS2D01G489500 chr2B 93.670 2796 108 30 1 2764 712001302 712004060 0.000000e+00 4119
18 TraesCS2D01G489500 chr2B 83.932 1643 194 33 1137 2752 689777660 689776061 0.000000e+00 1507
19 TraesCS2D01G489500 chr2B 80.490 979 159 26 1118 2083 712360186 712361145 0.000000e+00 721
20 TraesCS2D01G489500 chr2B 83.354 793 103 21 19 797 712359152 712359929 0.000000e+00 706
21 TraesCS2D01G489500 chr2B 83.984 487 38 15 2902 3357 712004071 712004548 7.470000e-117 431
22 TraesCS2D01G489500 chr2B 75.391 768 161 21 41 796 712829578 712830329 2.780000e-91 346
23 TraesCS2D01G489500 chr2B 96.324 136 3 2 2775 2909 536806163 536806029 4.900000e-54 222
24 TraesCS2D01G489500 chr2B 75.956 366 64 18 449 796 712770125 712770484 2.330000e-37 167
25 TraesCS2D01G489500 chr5B 89.412 255 27 0 3509 3763 174880184 174880438 4.690000e-84 322
26 TraesCS2D01G489500 chr5B 97.794 136 2 1 2767 2902 640272875 640272741 2.260000e-57 233
27 TraesCS2D01G489500 chr5A 88.672 256 28 1 3512 3766 461592118 461592373 1.020000e-80 311
28 TraesCS2D01G489500 chr5A 87.500 256 30 2 3509 3763 205006428 205006682 1.020000e-75 294
29 TraesCS2D01G489500 chr3D 87.764 237 29 0 3530 3766 570601034 570601270 1.030000e-70 278
30 TraesCS2D01G489500 chr7D 85.156 256 36 2 3512 3766 511056077 511056331 1.040000e-65 261
31 TraesCS2D01G489500 chr6B 84.646 254 38 1 3513 3766 150473047 150472795 6.240000e-63 252
32 TraesCS2D01G489500 chr6D 100.000 129 0 0 2774 2902 323694260 323694388 4.860000e-59 239
33 TraesCS2D01G489500 chr1D 99.237 131 1 0 2772 2902 7692244 7692114 1.750000e-58 237
34 TraesCS2D01G489500 chr1D 97.692 130 3 0 2774 2903 444519295 444519424 1.360000e-54 224
35 TraesCS2D01G489500 chr4B 97.744 133 3 0 2770 2902 180671157 180671289 2.930000e-56 230
36 TraesCS2D01G489500 chr4B 81.176 255 48 0 3509 3763 184857312 184857566 4.930000e-49 206
37 TraesCS2D01G489500 chr3B 96.324 136 4 1 2776 2911 236361947 236362081 4.900000e-54 222
38 TraesCS2D01G489500 chr5D 95.652 138 5 1 2766 2902 299406144 299406281 1.760000e-53 220


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 TraesCS2D01G489500 chr2D 588497455 588501220 3765 False 6955.0 6955 100.0000 1 3766 1 chr2D.!!$F2 3765
1 TraesCS2D01G489500 chr2D 588734933 588737080 2147 False 704.0 752 80.8480 19 2241 2 chr2D.!!$F3 2222
2 TraesCS2D01G489500 chr2D 573951218 573952372 1154 True 647.0 773 87.6815 1137 2333 2 chr2D.!!$R2 1196
3 TraesCS2D01G489500 chr2A 723100347 723103932 3585 False 2694.0 4165 93.2000 1 3766 2 chr2A.!!$F1 3765
4 TraesCS2D01G489500 chr2A 712537768 712539279 1511 True 716.5 965 85.1580 1135 2690 2 chr2A.!!$R1 1555
5 TraesCS2D01G489500 chr2A 723511077 723512434 1357 False 493.5 547 82.5125 6 1546 2 chr2A.!!$F3 1540
6 TraesCS2D01G489500 chr2A 723133761 723134787 1026 False 364.5 418 83.2735 449 1539 2 chr2A.!!$F2 1090
7 TraesCS2D01G489500 chr2B 712001302 712004548 3246 False 2275.0 4119 88.8270 1 3357 2 chr2B.!!$F3 3356
8 TraesCS2D01G489500 chr2B 689776061 689777660 1599 True 1507.0 1507 83.9320 1137 2752 1 chr2B.!!$R2 1615
9 TraesCS2D01G489500 chr2B 712359152 712361145 1993 False 713.5 721 81.9220 19 2083 2 chr2B.!!$F4 2064
10 TraesCS2D01G489500 chr2B 712829578 712830329 751 False 346.0 346 75.3910 41 796 1 chr2B.!!$F2 755

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
879 956 1.060308 CCCGTGCGCTTTTATGTCG 59.94 57.895 9.73 0.76 0.0 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2771 3009 0.042131 TGGGACGGAGGGAGTACAAT 59.958 55.0 0.0 0.0 0.0 2.71 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
24 25 4.918588 AGAAGTTTGGGACCGTGATAAAT 58.081 39.130 0.00 0.00 0.00 1.40
438 488 3.697747 CGTGCGGGGTTCCCAGTA 61.698 66.667 10.25 2.36 45.83 2.74
444 494 1.565067 CGGGGTTCCCAGTAACTACT 58.435 55.000 10.25 0.00 45.83 2.57
879 956 1.060308 CCCGTGCGCTTTTATGTCG 59.940 57.895 9.73 0.76 0.00 4.35
978 1160 1.542187 AAGACTAGGGTCCACGCACC 61.542 60.000 0.00 0.00 43.05 5.01
1076 1274 2.336088 CAAACAACCCTGCGGCAG 59.664 61.111 22.84 22.84 0.00 4.85
1085 1283 2.356793 CTGCGGCAGGATCGGATC 60.357 66.667 22.11 9.54 0.00 3.36
1096 1294 2.420058 GATCGGATCCAAACAACCCT 57.580 50.000 13.41 0.00 0.00 4.34
1097 1295 2.017049 GATCGGATCCAAACAACCCTG 58.983 52.381 13.41 0.00 0.00 4.45
1098 1296 0.608035 TCGGATCCAAACAACCCTGC 60.608 55.000 13.41 0.00 0.00 4.85
1102 1304 2.992817 ATCCAAACAACCCTGCGGCA 62.993 55.000 1.29 1.29 0.00 5.69
1325 1533 2.259875 GACGACTGGAGCTCCGACTG 62.260 65.000 27.43 18.90 39.43 3.51
1540 1751 2.681778 AGCTCCACCTCGACCTGG 60.682 66.667 0.00 0.00 0.00 4.45
1555 1766 4.161295 TGGGCTTCCAGATCGGCG 62.161 66.667 0.00 0.00 35.21 6.46
1557 1768 2.423446 GGCTTCCAGATCGGCGAT 59.577 61.111 24.26 24.26 33.14 4.58
1585 1799 0.742990 CCGCAAAGATAACGAGGGCA 60.743 55.000 0.00 0.00 0.00 5.36
2186 2400 1.137872 CAACCGAAGCCTAGAGAGCAT 59.862 52.381 0.00 0.00 0.00 3.79
2347 2561 2.047560 AGCGCGTTAAGGACACCC 60.048 61.111 8.43 0.00 0.00 4.61
2376 2590 4.864334 GGCACCATGGGCGAGGAG 62.864 72.222 18.09 0.00 0.00 3.69
2411 2646 2.191400 TGTGGAGAAGGAGAAGGATGG 58.809 52.381 0.00 0.00 0.00 3.51
2450 2688 0.179169 GTAGCTCCCGACGAGTTCAC 60.179 60.000 0.00 0.00 41.10 3.18
2475 2713 1.065636 CCTGATGAGGCAAGCTTCTCA 60.066 52.381 17.42 17.42 43.15 3.27
2502 2740 2.434884 CTGCGGCACCGAGTGAAT 60.435 61.111 14.43 0.00 42.83 2.57
2688 2926 5.449177 GGCCGATGTAGAAAAGATTTTCCTG 60.449 44.000 13.12 0.00 45.84 3.86
2689 2927 5.123979 GCCGATGTAGAAAAGATTTTCCTGT 59.876 40.000 13.12 0.24 45.84 4.00
2690 2928 6.315393 GCCGATGTAGAAAAGATTTTCCTGTA 59.685 38.462 13.12 0.00 45.84 2.74
2756 2994 6.318648 ACATGATTAGTTTCGTGCCATGTTAT 59.681 34.615 0.00 0.00 39.76 1.89
2788 3026 3.345508 AAAATTGTACTCCCTCCGTCC 57.654 47.619 0.00 0.00 0.00 4.79
2789 3027 1.201424 AATTGTACTCCCTCCGTCCC 58.799 55.000 0.00 0.00 0.00 4.46
2790 3028 0.042131 ATTGTACTCCCTCCGTCCCA 59.958 55.000 0.00 0.00 0.00 4.37
2791 3029 0.178926 TTGTACTCCCTCCGTCCCAA 60.179 55.000 0.00 0.00 0.00 4.12
2792 3030 0.178926 TGTACTCCCTCCGTCCCAAA 60.179 55.000 0.00 0.00 0.00 3.28
2793 3031 0.978907 GTACTCCCTCCGTCCCAAAA 59.021 55.000 0.00 0.00 0.00 2.44
2794 3032 1.558294 GTACTCCCTCCGTCCCAAAAT 59.442 52.381 0.00 0.00 0.00 1.82
2795 3033 1.073098 ACTCCCTCCGTCCCAAAATT 58.927 50.000 0.00 0.00 0.00 1.82
2796 3034 1.004394 ACTCCCTCCGTCCCAAAATTC 59.996 52.381 0.00 0.00 0.00 2.17
2797 3035 1.282157 CTCCCTCCGTCCCAAAATTCT 59.718 52.381 0.00 0.00 0.00 2.40
2798 3036 1.708551 TCCCTCCGTCCCAAAATTCTT 59.291 47.619 0.00 0.00 0.00 2.52
2799 3037 1.818674 CCCTCCGTCCCAAAATTCTTG 59.181 52.381 0.00 0.00 0.00 3.02
2800 3038 2.514803 CCTCCGTCCCAAAATTCTTGT 58.485 47.619 0.00 0.00 0.00 3.16
2801 3039 2.488153 CCTCCGTCCCAAAATTCTTGTC 59.512 50.000 0.00 0.00 0.00 3.18
2802 3040 3.412386 CTCCGTCCCAAAATTCTTGTCT 58.588 45.455 0.00 0.00 0.00 3.41
2803 3041 3.821033 CTCCGTCCCAAAATTCTTGTCTT 59.179 43.478 0.00 0.00 0.00 3.01
2804 3042 4.975631 TCCGTCCCAAAATTCTTGTCTTA 58.024 39.130 0.00 0.00 0.00 2.10
2805 3043 5.001232 TCCGTCCCAAAATTCTTGTCTTAG 58.999 41.667 0.00 0.00 0.00 2.18
2806 3044 5.001232 CCGTCCCAAAATTCTTGTCTTAGA 58.999 41.667 0.00 0.00 0.00 2.10
2807 3045 5.648092 CCGTCCCAAAATTCTTGTCTTAGAT 59.352 40.000 0.00 0.00 0.00 1.98
2808 3046 6.151144 CCGTCCCAAAATTCTTGTCTTAGATT 59.849 38.462 0.00 0.00 0.00 2.40
2809 3047 7.309194 CCGTCCCAAAATTCTTGTCTTAGATTT 60.309 37.037 0.00 0.00 0.00 2.17
2810 3048 7.538678 CGTCCCAAAATTCTTGTCTTAGATTTG 59.461 37.037 0.00 0.00 29.84 2.32
2811 3049 8.360390 GTCCCAAAATTCTTGTCTTAGATTTGT 58.640 33.333 0.00 0.00 28.79 2.83
2812 3050 8.576442 TCCCAAAATTCTTGTCTTAGATTTGTC 58.424 33.333 0.00 0.00 28.79 3.18
2813 3051 8.579863 CCCAAAATTCTTGTCTTAGATTTGTCT 58.420 33.333 0.00 0.00 28.79 3.41
2821 3059 8.622157 TCTTGTCTTAGATTTGTCTAGATACGG 58.378 37.037 0.00 0.00 0.00 4.02
2822 3060 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
2823 3061 8.693120 TGTCTTAGATTTGTCTAGATACGGAT 57.307 34.615 0.00 0.00 0.00 4.18
2824 3062 8.568794 TGTCTTAGATTTGTCTAGATACGGATG 58.431 37.037 0.00 0.00 0.00 3.51
2825 3063 8.569641 GTCTTAGATTTGTCTAGATACGGATGT 58.430 37.037 0.00 0.00 0.00 3.06
2826 3064 9.788889 TCTTAGATTTGTCTAGATACGGATGTA 57.211 33.333 0.00 0.00 34.45 2.29
2827 3065 9.828852 CTTAGATTTGTCTAGATACGGATGTAC 57.171 37.037 0.00 0.00 32.26 2.90
2828 3066 7.216973 AGATTTGTCTAGATACGGATGTACC 57.783 40.000 0.00 0.00 32.26 3.34
2829 3067 7.005296 AGATTTGTCTAGATACGGATGTACCT 58.995 38.462 0.00 0.00 36.31 3.08
2830 3068 8.162085 AGATTTGTCTAGATACGGATGTACCTA 58.838 37.037 0.00 0.00 36.31 3.08
2831 3069 8.701908 ATTTGTCTAGATACGGATGTACCTAA 57.298 34.615 0.00 0.00 36.31 2.69
2832 3070 8.701908 TTTGTCTAGATACGGATGTACCTAAT 57.298 34.615 0.00 0.00 36.31 1.73
2833 3071 9.797642 TTTGTCTAGATACGGATGTACCTAATA 57.202 33.333 0.00 0.00 36.31 0.98
2834 3072 8.783833 TGTCTAGATACGGATGTACCTAATAC 57.216 38.462 0.00 0.00 36.31 1.89
2835 3073 7.547019 TGTCTAGATACGGATGTACCTAATACG 59.453 40.741 0.00 0.00 36.47 3.06
2836 3074 7.761704 GTCTAGATACGGATGTACCTAATACGA 59.238 40.741 3.49 0.00 36.47 3.43
2837 3075 8.314021 TCTAGATACGGATGTACCTAATACGAA 58.686 37.037 3.49 0.00 36.47 3.85
2838 3076 7.750229 AGATACGGATGTACCTAATACGAAA 57.250 36.000 3.49 0.00 36.47 3.46
2839 3077 8.169977 AGATACGGATGTACCTAATACGAAAA 57.830 34.615 3.49 0.00 36.47 2.29
2840 3078 8.078596 AGATACGGATGTACCTAATACGAAAAC 58.921 37.037 3.49 0.00 36.47 2.43
2841 3079 5.036737 ACGGATGTACCTAATACGAAAACG 58.963 41.667 3.49 0.00 36.47 3.60
2842 3080 5.036737 CGGATGTACCTAATACGAAAACGT 58.963 41.667 0.00 0.00 36.47 3.99
2843 3081 5.052172 CGGATGTACCTAATACGAAAACGTG 60.052 44.000 5.54 0.00 36.47 4.49
2844 3082 6.035843 GGATGTACCTAATACGAAAACGTGA 58.964 40.000 5.54 0.00 36.47 4.35
2845 3083 6.020360 GGATGTACCTAATACGAAAACGTGAC 60.020 42.308 5.54 0.00 36.47 3.67
2846 3084 6.012658 TGTACCTAATACGAAAACGTGACT 57.987 37.500 5.54 0.00 36.47 3.41
2847 3085 6.446318 TGTACCTAATACGAAAACGTGACTT 58.554 36.000 5.54 0.31 36.47 3.01
2848 3086 5.834239 ACCTAATACGAAAACGTGACTTG 57.166 39.130 5.54 0.00 0.00 3.16
2849 3087 5.531634 ACCTAATACGAAAACGTGACTTGA 58.468 37.500 5.54 0.00 0.00 3.02
2850 3088 6.161381 ACCTAATACGAAAACGTGACTTGAT 58.839 36.000 5.54 0.00 0.00 2.57
2851 3089 7.315142 ACCTAATACGAAAACGTGACTTGATA 58.685 34.615 5.54 0.00 0.00 2.15
2852 3090 7.274250 ACCTAATACGAAAACGTGACTTGATAC 59.726 37.037 5.54 0.00 0.00 2.24
2853 3091 7.274033 CCTAATACGAAAACGTGACTTGATACA 59.726 37.037 5.54 0.00 0.00 2.29
2854 3092 7.591006 AATACGAAAACGTGACTTGATACAT 57.409 32.000 5.54 0.00 0.00 2.29
2855 3093 5.511088 ACGAAAACGTGACTTGATACATC 57.489 39.130 0.00 0.00 0.00 3.06
2856 3094 4.387862 ACGAAAACGTGACTTGATACATCC 59.612 41.667 0.00 0.00 0.00 3.51
2857 3095 4.490319 CGAAAACGTGACTTGATACATCCG 60.490 45.833 0.00 0.00 0.00 4.18
2858 3096 3.587797 AACGTGACTTGATACATCCGT 57.412 42.857 0.00 0.00 0.00 4.69
2859 3097 4.707030 AACGTGACTTGATACATCCGTA 57.293 40.909 0.00 0.00 0.00 4.02
2860 3098 4.913335 ACGTGACTTGATACATCCGTAT 57.087 40.909 0.00 0.00 41.16 3.06
2861 3099 5.258456 ACGTGACTTGATACATCCGTATT 57.742 39.130 0.00 0.00 38.48 1.89
2862 3100 5.657474 ACGTGACTTGATACATCCGTATTT 58.343 37.500 0.00 0.00 38.48 1.40
2863 3101 6.798482 ACGTGACTTGATACATCCGTATTTA 58.202 36.000 0.00 0.00 38.48 1.40
2864 3102 6.916387 ACGTGACTTGATACATCCGTATTTAG 59.084 38.462 0.00 0.00 38.48 1.85
2865 3103 7.136772 CGTGACTTGATACATCCGTATTTAGA 58.863 38.462 0.00 0.00 38.48 2.10
2866 3104 7.113124 CGTGACTTGATACATCCGTATTTAGAC 59.887 40.741 0.00 0.00 38.48 2.59
2867 3105 7.919091 GTGACTTGATACATCCGTATTTAGACA 59.081 37.037 0.00 0.00 38.48 3.41
2868 3106 8.471609 TGACTTGATACATCCGTATTTAGACAA 58.528 33.333 0.00 0.00 38.48 3.18
2869 3107 9.309516 GACTTGATACATCCGTATTTAGACAAA 57.690 33.333 0.00 0.00 38.48 2.83
2870 3108 9.832445 ACTTGATACATCCGTATTTAGACAAAT 57.168 29.630 0.00 0.00 38.48 2.32
2877 3115 9.530633 ACATCCGTATTTAGACAAATCTAAGAC 57.469 33.333 0.00 0.83 45.93 3.01
2878 3116 9.529325 CATCCGTATTTAGACAAATCTAAGACA 57.471 33.333 9.81 0.00 45.93 3.41
2880 3118 9.582431 TCCGTATTTAGACAAATCTAAGACAAG 57.418 33.333 9.81 3.88 45.93 3.16
2881 3119 9.582431 CCGTATTTAGACAAATCTAAGACAAGA 57.418 33.333 9.81 0.00 45.93 3.02
2889 3127 9.971922 AGACAAATCTAAGACAAGAATTTTTGG 57.028 29.630 12.83 0.00 31.65 3.28
2890 3128 9.965824 GACAAATCTAAGACAAGAATTTTTGGA 57.034 29.630 12.83 1.24 31.65 3.53
2891 3129 9.750125 ACAAATCTAAGACAAGAATTTTTGGAC 57.250 29.630 12.83 6.81 31.65 4.02
2892 3130 8.905702 CAAATCTAAGACAAGAATTTTTGGACG 58.094 33.333 12.83 0.00 32.32 4.79
2893 3131 6.554334 TCTAAGACAAGAATTTTTGGACGG 57.446 37.500 12.83 0.70 32.32 4.79
2894 3132 6.292923 TCTAAGACAAGAATTTTTGGACGGA 58.707 36.000 12.83 2.72 32.32 4.69
2895 3133 5.438761 AAGACAAGAATTTTTGGACGGAG 57.561 39.130 12.83 0.00 32.32 4.63
2896 3134 3.821033 AGACAAGAATTTTTGGACGGAGG 59.179 43.478 12.83 0.00 32.32 4.30
2897 3135 2.890945 ACAAGAATTTTTGGACGGAGGG 59.109 45.455 12.83 0.00 32.32 4.30
2898 3136 3.153919 CAAGAATTTTTGGACGGAGGGA 58.846 45.455 0.76 0.00 0.00 4.20
2926 3164 6.204075 CTTCTACACGCATAGAAGCAATAC 57.796 41.667 18.29 0.00 46.84 1.89
3185 3430 4.222145 ACACATTGGTATTACTGACTCCGT 59.778 41.667 0.00 0.00 0.00 4.69
3187 3432 5.747197 CACATTGGTATTACTGACTCCGTAC 59.253 44.000 0.00 0.00 0.00 3.67
3189 3434 6.097839 ACATTGGTATTACTGACTCCGTACAT 59.902 38.462 0.00 0.00 0.00 2.29
3241 3493 9.672086 AAATTGAATCATTGAAGTTTGCAATTG 57.328 25.926 0.00 0.00 34.72 2.32
3245 3497 9.058174 TGAATCATTGAAGTTTGCAATTGATTT 57.942 25.926 10.34 0.00 35.78 2.17
3330 3604 4.741321 AATGGTAAAATGATGGGTGCAG 57.259 40.909 0.00 0.00 0.00 4.41
3361 3635 6.551385 ACATGAAGAAGTTGATCAACACTC 57.449 37.500 33.92 28.11 43.47 3.51
3363 3637 4.693283 TGAAGAAGTTGATCAACACTCGT 58.307 39.130 33.92 26.74 43.47 4.18
3369 3643 8.154649 AGAAGTTGATCAACACTCGTAAAAAT 57.845 30.769 33.92 11.28 43.47 1.82
3470 3745 4.265904 ACGTACAATGGAAGACATGACA 57.734 40.909 0.00 0.00 40.44 3.58
3494 3769 7.712639 ACACACATACATCCTTGATAGATGAAC 59.287 37.037 7.70 0.00 43.15 3.18
3510 3785 8.734218 ATAGATGAACATGATATTGGCTCATC 57.266 34.615 0.00 10.76 38.77 2.92
3553 3828 7.201565 GCATGAGAACCTAAAGTTGTACATCTC 60.202 40.741 6.90 8.33 39.40 2.75
3600 3875 2.758423 GCCCCCGAAGATAATTTTGTGT 59.242 45.455 0.00 0.00 0.00 3.72
3647 3922 3.257393 CATACCTCAGCTCAACACAGAC 58.743 50.000 0.00 0.00 0.00 3.51
3669 3944 3.848019 CGAAAATGAGATTTTGTCTGCCG 59.152 43.478 0.00 0.00 42.15 5.69
3670 3945 2.927553 AATGAGATTTTGTCTGCCGC 57.072 45.000 0.00 0.00 37.29 6.53
3715 3990 2.355132 ACGCGGTAACACAAATGAAACA 59.645 40.909 12.47 0.00 0.00 2.83
3745 4020 6.444704 AGTCTCCTAGACCTAATGGATTTCA 58.555 40.000 3.49 0.00 46.18 2.69
3752 4027 5.435291 AGACCTAATGGATTTCAAGCAGAG 58.565 41.667 0.00 0.00 37.04 3.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
259 267 2.101380 GTCGCTGGAGACGCTCTC 59.899 66.667 6.78 6.63 42.66 3.20
438 488 4.833380 TCAAGCTCAGGTACAAGAGTAGTT 59.167 41.667 13.32 4.81 35.63 2.24
444 494 1.961394 ACGTCAAGCTCAGGTACAAGA 59.039 47.619 0.00 0.00 0.00 3.02
879 956 2.202756 ATCGGAAGTCGGAAGCGC 60.203 61.111 0.00 0.00 39.77 5.92
978 1160 2.696506 GACGGTTTCTCCAGGGTTTAG 58.303 52.381 0.00 0.00 35.57 1.85
1077 1275 2.017049 CAGGGTTGTTTGGATCCGATC 58.983 52.381 7.39 5.12 0.00 3.69
1078 1276 1.955208 GCAGGGTTGTTTGGATCCGAT 60.955 52.381 7.39 0.00 0.00 4.18
1079 1277 0.608035 GCAGGGTTGTTTGGATCCGA 60.608 55.000 7.39 1.27 0.00 4.55
1080 1278 1.883021 GCAGGGTTGTTTGGATCCG 59.117 57.895 7.39 0.00 0.00 4.18
1081 1279 1.883021 CGCAGGGTTGTTTGGATCC 59.117 57.895 4.20 4.20 0.00 3.36
1095 1293 1.073964 CCATATCGATCTTGCCGCAG 58.926 55.000 0.00 0.00 0.00 5.18
1096 1294 0.950555 GCCATATCGATCTTGCCGCA 60.951 55.000 0.00 0.00 0.00 5.69
1097 1295 0.671781 AGCCATATCGATCTTGCCGC 60.672 55.000 0.00 1.57 0.00 6.53
1098 1296 1.728971 GAAGCCATATCGATCTTGCCG 59.271 52.381 0.00 0.00 0.00 5.69
1102 1304 4.051922 GTTGACGAAGCCATATCGATCTT 58.948 43.478 0.00 0.00 42.76 2.40
1325 1533 2.065906 CTTCTCCTCGGCCTCGTAGC 62.066 65.000 0.00 0.00 37.69 3.58
1540 1751 0.247736 ATATCGCCGATCTGGAAGCC 59.752 55.000 1.25 0.00 42.00 4.35
1555 1766 1.852942 TCTTTGCGGCGACAGATATC 58.147 50.000 12.98 0.00 0.00 1.63
1557 1768 3.120792 GTTATCTTTGCGGCGACAGATA 58.879 45.455 12.98 14.42 0.00 1.98
1585 1799 2.358247 GCCGTCATGGTCGTGGTT 60.358 61.111 9.50 0.00 41.21 3.67
1594 1808 1.811266 CTTCCTCACGGCCGTCATG 60.811 63.158 31.80 18.72 0.00 3.07
1596 1810 3.691342 CCTTCCTCACGGCCGTCA 61.691 66.667 31.80 17.39 0.00 4.35
1605 1819 1.846124 GTCCACCACCCCTTCCTCA 60.846 63.158 0.00 0.00 0.00 3.86
2347 2561 3.257375 CCCATGGTGCCATATTGATCTTG 59.743 47.826 11.73 0.00 34.91 3.02
2376 2590 5.282055 TCTCCACAACATCATCCTCATAC 57.718 43.478 0.00 0.00 0.00 2.39
2411 2646 4.935885 ACAAACAAATCATCGCTCTCTC 57.064 40.909 0.00 0.00 0.00 3.20
2450 2688 1.372087 GCTTGCCTCATCAGGAACCG 61.372 60.000 0.00 0.00 43.65 4.44
2502 2740 2.865119 AGTGCACCATGTTGATCTCA 57.135 45.000 14.63 0.00 0.00 3.27
2535 2773 2.173519 CTGGCCATCATCCTTTGTGTT 58.826 47.619 5.51 0.00 0.00 3.32
2699 2937 8.380644 CAAGATTATTTTGAGATTACGTGACGT 58.619 33.333 17.03 17.03 44.35 4.34
2771 3009 0.042131 TGGGACGGAGGGAGTACAAT 59.958 55.000 0.00 0.00 0.00 2.71
2773 3011 0.178926 TTTGGGACGGAGGGAGTACA 60.179 55.000 0.00 0.00 0.00 2.90
2774 3012 0.978907 TTTTGGGACGGAGGGAGTAC 59.021 55.000 0.00 0.00 0.00 2.73
2775 3013 1.961133 ATTTTGGGACGGAGGGAGTA 58.039 50.000 0.00 0.00 0.00 2.59
2776 3014 1.004394 GAATTTTGGGACGGAGGGAGT 59.996 52.381 0.00 0.00 0.00 3.85
2777 3015 1.282157 AGAATTTTGGGACGGAGGGAG 59.718 52.381 0.00 0.00 0.00 4.30
2778 3016 1.368374 AGAATTTTGGGACGGAGGGA 58.632 50.000 0.00 0.00 0.00 4.20
2779 3017 1.818674 CAAGAATTTTGGGACGGAGGG 59.181 52.381 0.00 0.00 0.00 4.30
2780 3018 2.488153 GACAAGAATTTTGGGACGGAGG 59.512 50.000 0.00 0.00 0.00 4.30
2781 3019 3.412386 AGACAAGAATTTTGGGACGGAG 58.588 45.455 0.00 0.00 0.00 4.63
2782 3020 3.502123 AGACAAGAATTTTGGGACGGA 57.498 42.857 0.00 0.00 0.00 4.69
2783 3021 5.001232 TCTAAGACAAGAATTTTGGGACGG 58.999 41.667 0.00 0.00 0.00 4.79
2784 3022 6.743575 ATCTAAGACAAGAATTTTGGGACG 57.256 37.500 5.68 0.00 0.00 4.79
2785 3023 8.360390 ACAAATCTAAGACAAGAATTTTGGGAC 58.640 33.333 0.00 0.00 33.04 4.46
2786 3024 8.477419 ACAAATCTAAGACAAGAATTTTGGGA 57.523 30.769 0.00 0.00 33.04 4.37
2787 3025 8.579863 AGACAAATCTAAGACAAGAATTTTGGG 58.420 33.333 0.00 0.00 33.04 4.12
2795 3033 8.622157 CCGTATCTAGACAAATCTAAGACAAGA 58.378 37.037 0.00 0.00 36.98 3.02
2796 3034 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
2797 3035 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
2798 3036 8.568794 CATCCGTATCTAGACAAATCTAAGACA 58.431 37.037 0.00 0.00 36.98 3.41
2799 3037 8.569641 ACATCCGTATCTAGACAAATCTAAGAC 58.430 37.037 0.00 0.00 36.98 3.01
2800 3038 8.693120 ACATCCGTATCTAGACAAATCTAAGA 57.307 34.615 0.00 0.00 36.98 2.10
2801 3039 9.828852 GTACATCCGTATCTAGACAAATCTAAG 57.171 37.037 0.00 0.00 36.98 2.18
2802 3040 8.790718 GGTACATCCGTATCTAGACAAATCTAA 58.209 37.037 0.00 0.00 36.98 2.10
2803 3041 8.162085 AGGTACATCCGTATCTAGACAAATCTA 58.838 37.037 0.00 0.00 37.29 1.98
2804 3042 7.005296 AGGTACATCCGTATCTAGACAAATCT 58.995 38.462 0.00 0.00 37.29 2.40
2805 3043 7.216973 AGGTACATCCGTATCTAGACAAATC 57.783 40.000 0.00 0.00 37.29 2.17
2806 3044 8.701908 TTAGGTACATCCGTATCTAGACAAAT 57.298 34.615 0.00 0.00 41.33 2.32
2807 3045 8.701908 ATTAGGTACATCCGTATCTAGACAAA 57.298 34.615 0.00 0.00 41.33 2.83
2808 3046 9.224267 GTATTAGGTACATCCGTATCTAGACAA 57.776 37.037 0.00 0.00 41.33 3.18
2809 3047 7.547019 CGTATTAGGTACATCCGTATCTAGACA 59.453 40.741 0.00 0.00 41.33 3.41
2810 3048 7.761704 TCGTATTAGGTACATCCGTATCTAGAC 59.238 40.741 0.00 0.00 41.33 2.59
2811 3049 7.840931 TCGTATTAGGTACATCCGTATCTAGA 58.159 38.462 0.00 0.00 41.33 2.43
2812 3050 8.484641 TTCGTATTAGGTACATCCGTATCTAG 57.515 38.462 0.00 0.00 41.33 2.43
2813 3051 8.846943 TTTCGTATTAGGTACATCCGTATCTA 57.153 34.615 0.00 0.00 39.80 1.98
2814 3052 7.750229 TTTCGTATTAGGTACATCCGTATCT 57.250 36.000 0.00 0.00 41.99 1.98
2815 3053 7.059945 CGTTTTCGTATTAGGTACATCCGTATC 59.940 40.741 0.00 0.00 38.78 2.24
2816 3054 6.857964 CGTTTTCGTATTAGGTACATCCGTAT 59.142 38.462 0.00 0.00 38.78 3.06
2817 3055 6.198687 CGTTTTCGTATTAGGTACATCCGTA 58.801 40.000 0.00 0.00 38.78 4.02
2818 3056 5.036737 CGTTTTCGTATTAGGTACATCCGT 58.963 41.667 0.00 0.00 38.78 4.69
2819 3057 5.550701 CGTTTTCGTATTAGGTACATCCG 57.449 43.478 0.00 0.00 38.78 4.18
2834 3072 8.825668 ATACGGATGTATCAAGTCACGTTTTCG 61.826 40.741 0.00 0.00 42.29 3.46
2835 3073 4.387862 ACGGATGTATCAAGTCACGTTTTC 59.612 41.667 0.00 0.00 0.00 2.29
2836 3074 4.312443 ACGGATGTATCAAGTCACGTTTT 58.688 39.130 0.00 0.00 0.00 2.43
2837 3075 3.921677 ACGGATGTATCAAGTCACGTTT 58.078 40.909 0.00 0.00 0.00 3.60
2838 3076 3.587797 ACGGATGTATCAAGTCACGTT 57.412 42.857 0.00 0.00 0.00 3.99
2839 3077 4.913335 ATACGGATGTATCAAGTCACGT 57.087 40.909 0.00 0.00 36.56 4.49
2840 3078 7.113124 GTCTAAATACGGATGTATCAAGTCACG 59.887 40.741 0.00 0.00 40.42 4.35
2841 3079 7.919091 TGTCTAAATACGGATGTATCAAGTCAC 59.081 37.037 0.00 0.00 40.42 3.67
2842 3080 8.002984 TGTCTAAATACGGATGTATCAAGTCA 57.997 34.615 0.00 0.00 40.42 3.41
2843 3081 8.867112 TTGTCTAAATACGGATGTATCAAGTC 57.133 34.615 0.00 0.00 40.42 3.01
2844 3082 9.832445 ATTTGTCTAAATACGGATGTATCAAGT 57.168 29.630 0.00 0.00 40.42 3.16
2851 3089 9.530633 GTCTTAGATTTGTCTAAATACGGATGT 57.469 33.333 0.26 0.00 36.66 3.06
2852 3090 9.529325 TGTCTTAGATTTGTCTAAATACGGATG 57.471 33.333 0.26 0.00 36.66 3.51
2854 3092 9.582431 CTTGTCTTAGATTTGTCTAAATACGGA 57.418 33.333 0.26 0.00 36.66 4.69
2855 3093 9.582431 TCTTGTCTTAGATTTGTCTAAATACGG 57.418 33.333 0.26 0.99 36.66 4.02
2863 3101 9.971922 CCAAAAATTCTTGTCTTAGATTTGTCT 57.028 29.630 0.00 0.00 0.00 3.41
2864 3102 9.965824 TCCAAAAATTCTTGTCTTAGATTTGTC 57.034 29.630 0.00 0.00 0.00 3.18
2865 3103 9.750125 GTCCAAAAATTCTTGTCTTAGATTTGT 57.250 29.630 0.00 0.00 0.00 2.83
2866 3104 8.905702 CGTCCAAAAATTCTTGTCTTAGATTTG 58.094 33.333 0.00 0.00 0.00 2.32
2867 3105 8.082242 CCGTCCAAAAATTCTTGTCTTAGATTT 58.918 33.333 0.00 0.00 0.00 2.17
2868 3106 7.447238 TCCGTCCAAAAATTCTTGTCTTAGATT 59.553 33.333 0.00 0.00 0.00 2.40
2869 3107 6.940298 TCCGTCCAAAAATTCTTGTCTTAGAT 59.060 34.615 0.00 0.00 0.00 1.98
2870 3108 6.292923 TCCGTCCAAAAATTCTTGTCTTAGA 58.707 36.000 0.00 0.00 0.00 2.10
2871 3109 6.348540 CCTCCGTCCAAAAATTCTTGTCTTAG 60.349 42.308 0.00 0.00 0.00 2.18
2872 3110 5.472137 CCTCCGTCCAAAAATTCTTGTCTTA 59.528 40.000 0.00 0.00 0.00 2.10
2873 3111 4.278419 CCTCCGTCCAAAAATTCTTGTCTT 59.722 41.667 0.00 0.00 0.00 3.01
2874 3112 3.821033 CCTCCGTCCAAAAATTCTTGTCT 59.179 43.478 0.00 0.00 0.00 3.41
2875 3113 3.057526 CCCTCCGTCCAAAAATTCTTGTC 60.058 47.826 0.00 0.00 0.00 3.18
2876 3114 2.890945 CCCTCCGTCCAAAAATTCTTGT 59.109 45.455 0.00 0.00 0.00 3.16
2877 3115 3.153919 TCCCTCCGTCCAAAAATTCTTG 58.846 45.455 0.00 0.00 0.00 3.02
2878 3116 3.181433 ACTCCCTCCGTCCAAAAATTCTT 60.181 43.478 0.00 0.00 0.00 2.52
2879 3117 2.375509 ACTCCCTCCGTCCAAAAATTCT 59.624 45.455 0.00 0.00 0.00 2.40
2880 3118 2.791655 ACTCCCTCCGTCCAAAAATTC 58.208 47.619 0.00 0.00 0.00 2.17
2881 3119 2.971901 ACTCCCTCCGTCCAAAAATT 57.028 45.000 0.00 0.00 0.00 1.82
2882 3120 2.355818 GCTACTCCCTCCGTCCAAAAAT 60.356 50.000 0.00 0.00 0.00 1.82
2883 3121 1.002773 GCTACTCCCTCCGTCCAAAAA 59.997 52.381 0.00 0.00 0.00 1.94
2884 3122 0.611714 GCTACTCCCTCCGTCCAAAA 59.388 55.000 0.00 0.00 0.00 2.44
2885 3123 0.252103 AGCTACTCCCTCCGTCCAAA 60.252 55.000 0.00 0.00 0.00 3.28
2886 3124 0.252103 AAGCTACTCCCTCCGTCCAA 60.252 55.000 0.00 0.00 0.00 3.53
2887 3125 0.683504 GAAGCTACTCCCTCCGTCCA 60.684 60.000 0.00 0.00 0.00 4.02
2888 3126 0.396001 AGAAGCTACTCCCTCCGTCC 60.396 60.000 0.00 0.00 0.00 4.79
2889 3127 1.948834 GTAGAAGCTACTCCCTCCGTC 59.051 57.143 0.00 0.00 0.00 4.79
2890 3128 1.284198 TGTAGAAGCTACTCCCTCCGT 59.716 52.381 6.21 0.00 0.00 4.69
2891 3129 1.677052 GTGTAGAAGCTACTCCCTCCG 59.323 57.143 6.21 0.00 0.00 4.63
2892 3130 1.677052 CGTGTAGAAGCTACTCCCTCC 59.323 57.143 6.21 0.00 0.00 4.30
2893 3131 1.065851 GCGTGTAGAAGCTACTCCCTC 59.934 57.143 6.21 0.00 0.00 4.30
2894 3132 1.104630 GCGTGTAGAAGCTACTCCCT 58.895 55.000 6.21 0.00 0.00 4.20
2895 3133 0.815734 TGCGTGTAGAAGCTACTCCC 59.184 55.000 0.00 0.00 0.00 4.30
2896 3134 2.873133 ATGCGTGTAGAAGCTACTCC 57.127 50.000 0.00 0.00 0.00 3.85
2897 3135 4.815040 TCTATGCGTGTAGAAGCTACTC 57.185 45.455 0.00 2.16 0.00 2.59
2898 3136 5.176407 CTTCTATGCGTGTAGAAGCTACT 57.824 43.478 19.08 0.00 46.15 2.57
2926 3164 4.690748 TCTGTTCTTTACATCTCCTTTGCG 59.309 41.667 0.00 0.00 35.85 4.85
3273 3525 5.999044 ACAATATCAGTTGAGCCATCTCTT 58.001 37.500 0.00 0.00 40.03 2.85
3274 3526 5.627182 ACAATATCAGTTGAGCCATCTCT 57.373 39.130 0.00 0.00 40.03 3.10
3275 3527 7.976135 AATACAATATCAGTTGAGCCATCTC 57.024 36.000 0.00 0.00 39.78 2.75
3330 3604 7.307694 TGATCAACTTCTTCATGTATTGCAAC 58.692 34.615 0.00 0.00 0.00 4.17
3361 3635 9.626332 GAACACAATTTTGGTTACATTTTTACG 57.374 29.630 0.00 0.00 0.00 3.18
3369 3643 9.823647 ACAAATATGAACACAATTTTGGTTACA 57.176 25.926 0.00 0.00 30.73 2.41
3396 3670 6.405538 AGGAAGCTGTTTCATTTGACAAAAA 58.594 32.000 4.41 0.00 37.54 1.94
3397 3671 5.976458 AGGAAGCTGTTTCATTTGACAAAA 58.024 33.333 4.41 0.00 37.54 2.44
3398 3672 5.591099 GAGGAAGCTGTTTCATTTGACAAA 58.409 37.500 2.48 2.48 37.54 2.83
3399 3673 4.261155 CGAGGAAGCTGTTTCATTTGACAA 60.261 41.667 6.58 0.00 37.54 3.18
3400 3674 3.250762 CGAGGAAGCTGTTTCATTTGACA 59.749 43.478 6.58 0.00 37.54 3.58
3401 3675 3.365364 CCGAGGAAGCTGTTTCATTTGAC 60.365 47.826 6.58 0.00 37.54 3.18
3402 3676 2.813754 CCGAGGAAGCTGTTTCATTTGA 59.186 45.455 6.58 0.00 37.54 2.69
3403 3677 2.554032 ACCGAGGAAGCTGTTTCATTTG 59.446 45.455 6.58 0.00 37.54 2.32
3404 3678 2.814336 GACCGAGGAAGCTGTTTCATTT 59.186 45.455 6.58 0.00 37.54 2.32
3405 3679 2.224523 TGACCGAGGAAGCTGTTTCATT 60.225 45.455 6.58 0.00 37.54 2.57
3406 3680 1.347707 TGACCGAGGAAGCTGTTTCAT 59.652 47.619 6.58 0.00 37.54 2.57
3407 3681 0.756294 TGACCGAGGAAGCTGTTTCA 59.244 50.000 6.58 0.00 37.54 2.69
3408 3682 2.003301 GATGACCGAGGAAGCTGTTTC 58.997 52.381 0.00 0.00 34.93 2.78
3409 3683 1.347707 TGATGACCGAGGAAGCTGTTT 59.652 47.619 0.00 0.00 0.00 2.83
3410 3684 0.976641 TGATGACCGAGGAAGCTGTT 59.023 50.000 0.00 0.00 0.00 3.16
3411 3685 1.137872 GATGATGACCGAGGAAGCTGT 59.862 52.381 0.00 0.00 0.00 4.40
3470 3745 7.795047 TGTTCATCTATCAAGGATGTATGTGT 58.205 34.615 0.00 0.00 40.76 3.72
3494 3769 4.030314 ACCCTGATGAGCCAATATCATG 57.970 45.455 0.00 0.00 37.52 3.07
3510 3785 0.828022 TGCCCTACAATCGTACCCTG 59.172 55.000 0.00 0.00 0.00 4.45
3576 3851 1.231963 AAATTATCTTCGGGGGCCCT 58.768 50.000 24.38 3.25 0.00 5.19
3580 3855 3.064820 CGACACAAAATTATCTTCGGGGG 59.935 47.826 0.00 0.00 0.00 5.40
3616 3891 2.116238 GCTGAGGTATGTCCCCAACTA 58.884 52.381 0.00 0.00 36.75 2.24
3647 3922 3.848019 CGGCAGACAAAATCTCATTTTCG 59.152 43.478 0.00 0.00 40.27 3.46
3669 3944 3.391049 ACACCTCTTTCTCAGTAAACGC 58.609 45.455 0.00 0.00 0.00 4.84
3670 3945 5.522460 TCAAACACCTCTTTCTCAGTAAACG 59.478 40.000 0.00 0.00 0.00 3.60
3715 3990 7.827787 TCCATTAGGTCTAGGAGACTTATTCT 58.172 38.462 6.58 0.00 44.46 2.40


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

AutoCloner maintained by Alex Coulton.