Multiple sequence alignment - TraesCS7D01G516300

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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 TraesCS7D01G516300 chr7D 100.000 2875 0 0 1 2875 615955111 615952237 0.000000e+00 5310
1 TraesCS7D01G516300 chr7D 92.484 1610 79 20 1 1581 437417509 437419105 0.000000e+00 2265
2 TraesCS7D01G516300 chr3D 94.301 2316 80 15 1 2266 543498703 543501016 0.000000e+00 3498
3 TraesCS7D01G516300 chr3D 91.268 836 45 10 1 810 97111694 97110861 0.000000e+00 1114
4 TraesCS7D01G516300 chr3D 93.814 485 29 1 2268 2751 542836390 542836874 0.000000e+00 728
5 TraesCS7D01G516300 chr3D 93.621 486 29 2 2268 2751 478122097 478122582 0.000000e+00 725
6 TraesCS7D01G516300 chr2D 93.187 2319 106 14 1 2269 634063713 634061397 0.000000e+00 3360
7 TraesCS7D01G516300 chr2D 94.141 495 28 1 2265 2758 417208776 417209270 0.000000e+00 752
8 TraesCS7D01G516300 chr2D 93.827 486 28 2 2268 2751 634061359 634060874 0.000000e+00 730
9 TraesCS7D01G516300 chr2D 93.456 489 30 2 2268 2754 388059348 388058860 0.000000e+00 725
10 TraesCS7D01G516300 chr2D 92.126 508 36 4 2268 2773 648340131 648340636 0.000000e+00 713
11 TraesCS7D01G516300 chr1B 93.043 2300 117 10 1 2270 641639994 641637708 0.000000e+00 3321
12 TraesCS7D01G516300 chr5B 92.845 2320 114 15 1 2270 478553683 478551366 0.000000e+00 3317
13 TraesCS7D01G516300 chr5B 92.541 2306 122 12 1 2270 345850387 345852678 0.000000e+00 3260
14 TraesCS7D01G516300 chr5B 89.522 544 40 5 1 529 315918084 315917543 0.000000e+00 673
15 TraesCS7D01G516300 chr1A 92.724 2309 125 11 1 2269 506521226 506523531 0.000000e+00 3293
16 TraesCS7D01G516300 chr1A 92.928 1923 109 16 1 1900 587376002 587374084 0.000000e+00 2772
17 TraesCS7D01G516300 chr4D 92.783 2314 105 19 1 2270 65098991 65096696 0.000000e+00 3291
18 TraesCS7D01G516300 chr4D 94.433 485 26 1 2268 2751 130441246 130440762 0.000000e+00 745
19 TraesCS7D01G516300 chr4B 92.251 2323 122 16 1 2270 41787144 41784827 0.000000e+00 3240
20 TraesCS7D01G516300 chr4B 93.306 1987 96 13 1 1954 519348225 519350207 0.000000e+00 2898
21 TraesCS7D01G516300 chr4A 91.990 2297 148 13 1 2263 104136026 104138320 0.000000e+00 3190
22 TraesCS7D01G516300 chr3B 91.894 2307 139 22 1 2269 643838932 643836636 0.000000e+00 3181
23 TraesCS7D01G516300 chr7B 91.166 2298 160 26 1 2270 721423809 721426091 0.000000e+00 3079
24 TraesCS7D01G516300 chr7B 92.800 125 5 1 2752 2872 709089000 709088876 8.190000e-41 178
25 TraesCS7D01G516300 chr2B 89.983 2316 178 25 1 2269 503341817 503344125 0.000000e+00 2942
26 TraesCS7D01G516300 chr2B 92.938 1770 104 10 49 1802 629077295 629075531 0.000000e+00 2556
27 TraesCS7D01G516300 chr5D 94.529 1901 80 9 393 2269 58529595 58531495 0.000000e+00 2913
28 TraesCS7D01G516300 chr5D 93.608 485 30 1 2268 2751 238123871 238124355 0.000000e+00 723
29 TraesCS7D01G516300 chr6D 94.373 1173 45 7 1 1156 469298108 469299276 0.000000e+00 1781
30 TraesCS7D01G516300 chr6D 95.277 487 22 1 2268 2753 36286379 36286865 0.000000e+00 771
31 TraesCS7D01G516300 chr6D 91.209 546 33 2 1 532 470941533 470942077 0.000000e+00 728
32 TraesCS7D01G516300 chr1D 93.220 708 31 6 1 694 362593077 362592373 0.000000e+00 1026
33 TraesCS7D01G516300 chr1D 92.833 600 31 6 1679 2267 247384982 247384384 0.000000e+00 859
34 TraesCS7D01G516300 chr7A 93.846 65 4 0 2811 2875 708778391 708778327 6.560000e-17 99


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 TraesCS7D01G516300 chr7D 615952237 615955111 2874 True 5310 5310 100.000 1 2875 1 chr7D.!!$R1 2874
1 TraesCS7D01G516300 chr7D 437417509 437419105 1596 False 2265 2265 92.484 1 1581 1 chr7D.!!$F1 1580
2 TraesCS7D01G516300 chr3D 543498703 543501016 2313 False 3498 3498 94.301 1 2266 1 chr3D.!!$F3 2265
3 TraesCS7D01G516300 chr3D 97110861 97111694 833 True 1114 1114 91.268 1 810 1 chr3D.!!$R1 809
4 TraesCS7D01G516300 chr2D 634060874 634063713 2839 True 2045 3360 93.507 1 2751 2 chr2D.!!$R2 2750
5 TraesCS7D01G516300 chr2D 648340131 648340636 505 False 713 713 92.126 2268 2773 1 chr2D.!!$F2 505
6 TraesCS7D01G516300 chr1B 641637708 641639994 2286 True 3321 3321 93.043 1 2270 1 chr1B.!!$R1 2269
7 TraesCS7D01G516300 chr5B 478551366 478553683 2317 True 3317 3317 92.845 1 2270 1 chr5B.!!$R2 2269
8 TraesCS7D01G516300 chr5B 345850387 345852678 2291 False 3260 3260 92.541 1 2270 1 chr5B.!!$F1 2269
9 TraesCS7D01G516300 chr5B 315917543 315918084 541 True 673 673 89.522 1 529 1 chr5B.!!$R1 528
10 TraesCS7D01G516300 chr1A 506521226 506523531 2305 False 3293 3293 92.724 1 2269 1 chr1A.!!$F1 2268
11 TraesCS7D01G516300 chr1A 587374084 587376002 1918 True 2772 2772 92.928 1 1900 1 chr1A.!!$R1 1899
12 TraesCS7D01G516300 chr4D 65096696 65098991 2295 True 3291 3291 92.783 1 2270 1 chr4D.!!$R1 2269
13 TraesCS7D01G516300 chr4B 41784827 41787144 2317 True 3240 3240 92.251 1 2270 1 chr4B.!!$R1 2269
14 TraesCS7D01G516300 chr4B 519348225 519350207 1982 False 2898 2898 93.306 1 1954 1 chr4B.!!$F1 1953
15 TraesCS7D01G516300 chr4A 104136026 104138320 2294 False 3190 3190 91.990 1 2263 1 chr4A.!!$F1 2262
16 TraesCS7D01G516300 chr3B 643836636 643838932 2296 True 3181 3181 91.894 1 2269 1 chr3B.!!$R1 2268
17 TraesCS7D01G516300 chr7B 721423809 721426091 2282 False 3079 3079 91.166 1 2270 1 chr7B.!!$F1 2269
18 TraesCS7D01G516300 chr2B 503341817 503344125 2308 False 2942 2942 89.983 1 2269 1 chr2B.!!$F1 2268
19 TraesCS7D01G516300 chr2B 629075531 629077295 1764 True 2556 2556 92.938 49 1802 1 chr2B.!!$R1 1753
20 TraesCS7D01G516300 chr5D 58529595 58531495 1900 False 2913 2913 94.529 393 2269 1 chr5D.!!$F1 1876
21 TraesCS7D01G516300 chr6D 469298108 469299276 1168 False 1781 1781 94.373 1 1156 1 chr6D.!!$F2 1155
22 TraesCS7D01G516300 chr6D 470941533 470942077 544 False 728 728 91.209 1 532 1 chr6D.!!$F3 531
23 TraesCS7D01G516300 chr1D 362592373 362593077 704 True 1026 1026 93.220 1 694 1 chr1D.!!$R2 693
24 TraesCS7D01G516300 chr1D 247384384 247384982 598 True 859 859 92.833 1679 2267 1 chr1D.!!$R1 588

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
295 313 0.669318 GCGTTGATCTTCCACGACCA 60.669 55.0 5.44 0.0 0.0 4.02 F
1116 1228 1.088306 ACTTGAACACCGTTGCGAAA 58.912 45.0 0.00 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1126 1238 0.846693 ACCTCTTGCCCACAGAACTT 59.153 50.0 0.0 0.0 0.0 2.66 R
2827 3060 0.031449 TTCGATGTCACGCTCACACA 59.969 50.0 0.0 0.0 0.0 3.72 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
187 202 0.898789 TCCCTCCGTTCGAGCTTTCT 60.899 55.000 0.00 0.00 37.27 2.52
238 256 3.788766 GCGGCGCAACTTCATCGT 61.789 61.111 29.21 0.00 0.00 3.73
295 313 0.669318 GCGTTGATCTTCCACGACCA 60.669 55.000 5.44 0.00 0.00 4.02
318 336 2.507992 CCTCGTCCTCAAGCTGCG 60.508 66.667 0.00 0.00 0.00 5.18
494 515 1.336125 GGGCTAGATGTTCAAGCATGC 59.664 52.381 10.51 10.51 38.01 4.06
550 571 2.362077 ACCTTGTGCTTGTGTTGAATCC 59.638 45.455 0.00 0.00 0.00 3.01
715 781 4.398358 CAGATGTGCTTTCATGGATTGTCT 59.602 41.667 0.00 0.00 0.00 3.41
831 897 2.290367 CGACAACCAGTTTGCTTCATCA 59.710 45.455 0.00 0.00 39.01 3.07
1116 1228 1.088306 ACTTGAACACCGTTGCGAAA 58.912 45.000 0.00 0.00 0.00 3.46
1126 1238 0.375454 CGTTGCGAAACAGGTGTTCA 59.625 50.000 7.15 0.00 37.25 3.18
1188 1300 2.251818 CACCTGAGGAAGTGGAGAAGA 58.748 52.381 4.99 0.00 0.00 2.87
1223 1335 2.563179 TGTCCAAGCTGAGAGACCTTAC 59.437 50.000 0.00 0.00 0.00 2.34
1460 1572 1.757118 CACATCTTCTCCTTCGGGCTA 59.243 52.381 0.00 0.00 34.44 3.93
1520 1632 1.272147 GGTTCTCCCATGCCAGACTTT 60.272 52.381 0.00 0.00 0.00 2.66
1792 1904 0.107800 GCTCTCATGGCAGCTCTCAA 60.108 55.000 8.99 0.00 32.48 3.02
2075 2247 0.108019 GGACGACACCCTCTTTTGGT 59.892 55.000 0.00 0.00 36.21 3.67
2093 2265 2.778850 TGGTTGTGGTGGTAGGTTAACT 59.221 45.455 5.42 0.00 0.00 2.24
2156 2334 5.583854 TCATGCATGCTTTACTTCTCTTCTC 59.416 40.000 22.25 0.00 0.00 2.87
2294 2525 2.826428 AGTGGCATCGTATAGCAACAG 58.174 47.619 0.00 0.00 37.15 3.16
2349 2580 2.891580 AGAACAAGCTTACTCCGAGTGA 59.108 45.455 11.52 1.80 0.00 3.41
2357 2588 4.467232 CTCCGAGTGAGTGCGAAG 57.533 61.111 0.00 0.00 36.27 3.79
2378 2609 1.006086 CACGACAGCAGTGTTGACAA 58.994 50.000 14.47 0.00 40.21 3.18
2380 2611 1.599071 ACGACAGCAGTGTTGACAATG 59.401 47.619 14.47 7.17 43.96 2.82
2457 2688 2.787473 TCATCTTCGCCCAGTTCATT 57.213 45.000 0.00 0.00 0.00 2.57
2465 2696 0.609662 GCCCAGTTCATTGCCATTGT 59.390 50.000 0.00 0.00 0.00 2.71
2468 2699 2.613474 CCCAGTTCATTGCCATTGTTGG 60.613 50.000 0.00 0.00 46.66 3.77
2476 2708 3.457484 CCATTGTTGGCTGTGGCA 58.543 55.556 0.00 0.00 40.87 4.92
2599 2831 2.681848 CAATGCAGGCAACCAAACAAAA 59.318 40.909 0.00 0.00 37.17 2.44
2608 2840 3.682921 CAACCAAACAAAATGCACTTGC 58.317 40.909 9.70 0.00 42.50 4.01
2641 2873 3.384168 TGCAGGGACATTAGATACAGGT 58.616 45.455 0.00 0.00 0.00 4.00
2661 2894 5.122396 CAGGTAACCAAACAACTAGCAGATC 59.878 44.000 0.00 0.00 37.17 2.75
2663 2896 3.402628 ACCAAACAACTAGCAGATCGT 57.597 42.857 0.00 0.00 0.00 3.73
2697 2930 1.114722 TTTTGCTCAACCAGGCTGGG 61.115 55.000 35.34 19.93 43.37 4.45
2719 2952 2.971307 TGAGAAGTGTATGCGATGCAA 58.029 42.857 0.00 0.00 43.62 4.08
2720 2953 3.333804 TGAGAAGTGTATGCGATGCAAA 58.666 40.909 0.00 0.00 43.62 3.68
2722 2955 3.073678 AGAAGTGTATGCGATGCAAACA 58.926 40.909 0.00 0.00 43.62 2.83
2754 2987 1.813192 CAACCAAACACGCCCTTGT 59.187 52.632 0.00 0.00 0.00 3.16
2756 2989 0.174617 AACCAAACACGCCCTTGTTG 59.825 50.000 0.00 0.00 39.70 3.33
2757 2990 0.681564 ACCAAACACGCCCTTGTTGA 60.682 50.000 0.00 0.00 39.70 3.18
2759 2992 0.248866 CAAACACGCCCTTGTTGACC 60.249 55.000 0.00 0.00 39.70 4.02
2760 2993 1.388837 AAACACGCCCTTGTTGACCC 61.389 55.000 0.00 0.00 39.70 4.46
2762 2995 1.528309 CACGCCCTTGTTGACCCTT 60.528 57.895 0.00 0.00 0.00 3.95
2763 2996 1.528309 ACGCCCTTGTTGACCCTTG 60.528 57.895 0.00 0.00 0.00 3.61
2765 2998 1.908299 GCCCTTGTTGACCCTTGGG 60.908 63.158 3.77 3.77 37.76 4.12
2766 2999 1.908299 CCCTTGTTGACCCTTGGGC 60.908 63.158 5.46 0.00 0.00 5.36
2767 3000 1.152567 CCTTGTTGACCCTTGGGCA 60.153 57.895 5.46 2.27 40.08 5.36
2768 3001 0.542702 CCTTGTTGACCCTTGGGCAT 60.543 55.000 5.46 0.00 42.18 4.40
2773 3006 0.409092 TTGACCCTTGGGCATCATGT 59.591 50.000 5.46 0.00 42.18 3.21
2774 3007 1.294041 TGACCCTTGGGCATCATGTA 58.706 50.000 5.46 0.00 34.69 2.29
2775 3008 1.852309 TGACCCTTGGGCATCATGTAT 59.148 47.619 5.46 0.00 34.69 2.29
2776 3009 2.233271 GACCCTTGGGCATCATGTATG 58.767 52.381 5.46 0.00 38.74 2.39
2777 3010 1.133388 ACCCTTGGGCATCATGTATGG 60.133 52.381 5.46 0.00 35.99 2.74
2778 3011 1.145531 CCCTTGGGCATCATGTATGGA 59.854 52.381 0.00 0.00 35.99 3.41
2779 3012 2.225192 CCCTTGGGCATCATGTATGGAT 60.225 50.000 0.00 0.00 35.99 3.41
2780 3013 3.087031 CCTTGGGCATCATGTATGGATC 58.913 50.000 0.00 0.00 35.99 3.36
2781 3014 3.245158 CCTTGGGCATCATGTATGGATCT 60.245 47.826 0.00 0.00 35.99 2.75
2782 3015 3.708403 TGGGCATCATGTATGGATCTC 57.292 47.619 0.00 0.00 35.99 2.75
2783 3016 2.981081 TGGGCATCATGTATGGATCTCA 59.019 45.455 0.00 0.00 35.99 3.27
2784 3017 3.590182 TGGGCATCATGTATGGATCTCAT 59.410 43.478 0.00 0.00 39.78 2.90
2785 3018 4.043686 TGGGCATCATGTATGGATCTCATT 59.956 41.667 2.58 0.00 37.30 2.57
2786 3019 4.639310 GGGCATCATGTATGGATCTCATTC 59.361 45.833 2.58 0.00 37.30 2.67
2787 3020 5.250982 GGCATCATGTATGGATCTCATTCA 58.749 41.667 2.58 4.55 37.51 2.57
2788 3021 5.354513 GGCATCATGTATGGATCTCATTCAG 59.645 44.000 2.58 0.72 36.76 3.02
2789 3022 5.163744 GCATCATGTATGGATCTCATTCAGC 60.164 44.000 2.58 1.53 36.76 4.26
2790 3023 5.820404 TCATGTATGGATCTCATTCAGCT 57.180 39.130 2.58 0.00 36.76 4.24
2791 3024 6.183810 TCATGTATGGATCTCATTCAGCTT 57.816 37.500 2.58 0.00 36.76 3.74
2792 3025 6.598503 TCATGTATGGATCTCATTCAGCTTT 58.401 36.000 2.58 0.00 36.76 3.51
2793 3026 6.709397 TCATGTATGGATCTCATTCAGCTTTC 59.291 38.462 2.58 0.00 36.76 2.62
2794 3027 5.371526 TGTATGGATCTCATTCAGCTTTCC 58.628 41.667 2.58 0.00 37.30 3.13
2795 3028 4.792513 ATGGATCTCATTCAGCTTTCCT 57.207 40.909 0.00 0.00 30.55 3.36
2796 3029 4.581309 TGGATCTCATTCAGCTTTCCTT 57.419 40.909 0.00 0.00 0.00 3.36
2797 3030 4.267536 TGGATCTCATTCAGCTTTCCTTG 58.732 43.478 0.00 0.00 0.00 3.61
2798 3031 3.631227 GGATCTCATTCAGCTTTCCTTGG 59.369 47.826 0.00 0.00 0.00 3.61
2799 3032 3.795688 TCTCATTCAGCTTTCCTTGGT 57.204 42.857 0.00 0.00 0.00 3.67
2800 3033 3.679389 TCTCATTCAGCTTTCCTTGGTC 58.321 45.455 0.00 0.00 0.00 4.02
2801 3034 2.417933 CTCATTCAGCTTTCCTTGGTCG 59.582 50.000 0.00 0.00 0.00 4.79
2802 3035 2.154462 CATTCAGCTTTCCTTGGTCGT 58.846 47.619 0.00 0.00 0.00 4.34
2803 3036 2.341846 TTCAGCTTTCCTTGGTCGTT 57.658 45.000 0.00 0.00 0.00 3.85
2804 3037 1.878953 TCAGCTTTCCTTGGTCGTTC 58.121 50.000 0.00 0.00 0.00 3.95
2805 3038 1.416401 TCAGCTTTCCTTGGTCGTTCT 59.584 47.619 0.00 0.00 0.00 3.01
2806 3039 2.631062 TCAGCTTTCCTTGGTCGTTCTA 59.369 45.455 0.00 0.00 0.00 2.10
2807 3040 2.996621 CAGCTTTCCTTGGTCGTTCTAG 59.003 50.000 0.00 0.00 0.00 2.43
2808 3041 2.633481 AGCTTTCCTTGGTCGTTCTAGT 59.367 45.455 0.00 0.00 0.00 2.57
2809 3042 3.830755 AGCTTTCCTTGGTCGTTCTAGTA 59.169 43.478 0.00 0.00 0.00 1.82
2810 3043 3.925299 GCTTTCCTTGGTCGTTCTAGTAC 59.075 47.826 0.00 0.00 0.00 2.73
2811 3044 4.321824 GCTTTCCTTGGTCGTTCTAGTACT 60.322 45.833 0.00 0.00 0.00 2.73
2812 3045 5.780984 CTTTCCTTGGTCGTTCTAGTACTT 58.219 41.667 0.00 0.00 0.00 2.24
2813 3046 4.778534 TCCTTGGTCGTTCTAGTACTTG 57.221 45.455 0.00 0.00 0.00 3.16
2814 3047 3.508793 TCCTTGGTCGTTCTAGTACTTGG 59.491 47.826 0.00 0.00 0.00 3.61
2815 3048 3.257624 CCTTGGTCGTTCTAGTACTTGGT 59.742 47.826 0.00 0.00 0.00 3.67
2816 3049 3.928727 TGGTCGTTCTAGTACTTGGTG 57.071 47.619 0.00 0.00 0.00 4.17
2817 3050 2.029649 TGGTCGTTCTAGTACTTGGTGC 60.030 50.000 0.00 0.00 0.00 5.01
2818 3051 2.230750 GGTCGTTCTAGTACTTGGTGCT 59.769 50.000 0.00 0.00 32.46 4.40
2819 3052 3.500014 GTCGTTCTAGTACTTGGTGCTC 58.500 50.000 0.00 0.00 30.04 4.26
2820 3053 2.490903 TCGTTCTAGTACTTGGTGCTCC 59.509 50.000 0.00 0.00 30.04 4.70
2821 3054 2.492484 CGTTCTAGTACTTGGTGCTCCT 59.508 50.000 0.00 0.00 30.04 3.69
2822 3055 3.056749 CGTTCTAGTACTTGGTGCTCCTT 60.057 47.826 0.00 0.00 30.04 3.36
2823 3056 4.246458 GTTCTAGTACTTGGTGCTCCTTG 58.754 47.826 0.00 1.52 30.04 3.61
2824 3057 3.507411 TCTAGTACTTGGTGCTCCTTGT 58.493 45.455 0.00 7.33 30.04 3.16
2825 3058 2.550830 AGTACTTGGTGCTCCTTGTG 57.449 50.000 6.34 0.00 34.23 3.33
2826 3059 2.047061 AGTACTTGGTGCTCCTTGTGA 58.953 47.619 6.34 0.00 34.23 3.58
2827 3060 2.639839 AGTACTTGGTGCTCCTTGTGAT 59.360 45.455 6.34 0.00 34.23 3.06
2828 3061 1.901591 ACTTGGTGCTCCTTGTGATG 58.098 50.000 6.34 0.00 34.23 3.07
2829 3062 1.143684 ACTTGGTGCTCCTTGTGATGT 59.856 47.619 6.34 0.00 34.23 3.06
2830 3063 1.538512 CTTGGTGCTCCTTGTGATGTG 59.461 52.381 6.34 0.00 34.23 3.21
2831 3064 0.473755 TGGTGCTCCTTGTGATGTGT 59.526 50.000 6.34 0.00 34.23 3.72
2832 3065 0.877071 GGTGCTCCTTGTGATGTGTG 59.123 55.000 0.00 0.00 0.00 3.82
2833 3066 1.543208 GGTGCTCCTTGTGATGTGTGA 60.543 52.381 0.00 0.00 0.00 3.58
2834 3067 1.802960 GTGCTCCTTGTGATGTGTGAG 59.197 52.381 0.00 0.00 0.00 3.51
2835 3068 0.801251 GCTCCTTGTGATGTGTGAGC 59.199 55.000 0.00 0.00 38.51 4.26
2836 3069 1.073964 CTCCTTGTGATGTGTGAGCG 58.926 55.000 0.00 0.00 0.00 5.03
2837 3070 0.392706 TCCTTGTGATGTGTGAGCGT 59.607 50.000 0.00 0.00 0.00 5.07
2838 3071 0.514255 CCTTGTGATGTGTGAGCGTG 59.486 55.000 0.00 0.00 0.00 5.34
2839 3072 1.501169 CTTGTGATGTGTGAGCGTGA 58.499 50.000 0.00 0.00 0.00 4.35
2840 3073 1.193203 CTTGTGATGTGTGAGCGTGAC 59.807 52.381 0.00 0.00 0.00 3.67
2841 3074 0.103937 TGTGATGTGTGAGCGTGACA 59.896 50.000 0.00 0.00 0.00 3.58
2842 3075 1.270252 TGTGATGTGTGAGCGTGACAT 60.270 47.619 0.00 0.00 32.95 3.06
2843 3076 1.391485 GTGATGTGTGAGCGTGACATC 59.609 52.381 11.84 11.84 44.17 3.06
2844 3077 0.642291 GATGTGTGAGCGTGACATCG 59.358 55.000 0.00 0.00 37.37 3.84
2845 3078 0.243636 ATGTGTGAGCGTGACATCGA 59.756 50.000 0.00 0.00 0.00 3.59
2846 3079 0.031449 TGTGTGAGCGTGACATCGAA 59.969 50.000 0.00 0.00 0.00 3.71
2847 3080 1.336795 TGTGTGAGCGTGACATCGAAT 60.337 47.619 0.00 0.00 0.00 3.34
2848 3081 1.726791 GTGTGAGCGTGACATCGAATT 59.273 47.619 0.00 0.00 0.00 2.17
2849 3082 1.992667 TGTGAGCGTGACATCGAATTC 59.007 47.619 0.00 0.00 0.00 2.17
2850 3083 2.263077 GTGAGCGTGACATCGAATTCT 58.737 47.619 3.52 0.00 0.00 2.40
2851 3084 2.668457 GTGAGCGTGACATCGAATTCTT 59.332 45.455 3.52 0.00 0.00 2.52
2852 3085 2.923655 TGAGCGTGACATCGAATTCTTC 59.076 45.455 3.52 0.00 0.00 2.87
2853 3086 2.271800 AGCGTGACATCGAATTCTTCC 58.728 47.619 3.52 0.00 0.00 3.46
2854 3087 2.093973 AGCGTGACATCGAATTCTTCCT 60.094 45.455 3.52 0.00 0.00 3.36
2855 3088 2.673368 GCGTGACATCGAATTCTTCCTT 59.327 45.455 3.52 0.00 0.00 3.36
2856 3089 3.125316 GCGTGACATCGAATTCTTCCTTT 59.875 43.478 3.52 0.00 0.00 3.11
2857 3090 4.725169 GCGTGACATCGAATTCTTCCTTTC 60.725 45.833 3.52 0.00 0.00 2.62
2858 3091 4.490959 CGTGACATCGAATTCTTCCTTTCG 60.491 45.833 3.52 0.00 44.53 3.46
2859 3092 4.389077 GTGACATCGAATTCTTCCTTTCGT 59.611 41.667 3.52 0.00 43.81 3.85
2860 3093 4.994852 TGACATCGAATTCTTCCTTTCGTT 59.005 37.500 3.52 0.00 43.81 3.85
2861 3094 5.107104 TGACATCGAATTCTTCCTTTCGTTG 60.107 40.000 3.52 12.12 44.51 4.10
2862 3095 4.154195 ACATCGAATTCTTCCTTTCGTTGG 59.846 41.667 15.99 6.50 43.83 3.77
2863 3096 3.735591 TCGAATTCTTCCTTTCGTTGGT 58.264 40.909 3.52 0.00 43.81 3.67
2864 3097 3.744426 TCGAATTCTTCCTTTCGTTGGTC 59.256 43.478 3.52 0.00 43.81 4.02
2865 3098 3.423123 CGAATTCTTCCTTTCGTTGGTCG 60.423 47.826 3.52 0.00 39.77 4.79
2866 3099 2.607631 TTCTTCCTTTCGTTGGTCGT 57.392 45.000 0.00 0.00 40.80 4.34
2867 3100 2.144482 TCTTCCTTTCGTTGGTCGTC 57.856 50.000 0.00 0.00 40.80 4.20
2868 3101 1.409790 TCTTCCTTTCGTTGGTCGTCA 59.590 47.619 0.00 0.00 40.80 4.35
2869 3102 1.792949 CTTCCTTTCGTTGGTCGTCAG 59.207 52.381 0.00 0.00 40.80 3.51
2870 3103 0.032952 TCCTTTCGTTGGTCGTCAGG 59.967 55.000 0.00 0.00 39.44 3.86
2871 3104 0.032952 CCTTTCGTTGGTCGTCAGGA 59.967 55.000 0.00 0.00 40.01 3.86
2872 3105 1.419374 CTTTCGTTGGTCGTCAGGAG 58.581 55.000 0.00 0.00 40.80 3.69
2873 3106 0.599204 TTTCGTTGGTCGTCAGGAGC 60.599 55.000 0.00 0.00 43.52 4.70
2874 3107 1.461091 TTCGTTGGTCGTCAGGAGCT 61.461 55.000 0.00 0.00 43.60 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
216 234 0.953471 ATGAAGTTGCGCCGCTTACA 60.953 50.000 11.67 9.70 0.00 2.41
494 515 9.563748 AAACTCTACTACTAATCTAGCCTACAG 57.436 37.037 0.00 0.00 0.00 2.74
550 571 6.047870 AGCTACAAATCACAGATCTAAGCAG 58.952 40.000 0.00 0.00 0.00 4.24
715 781 3.348647 AGCATAGCACACAACATACCA 57.651 42.857 0.00 0.00 0.00 3.25
831 897 1.338200 GGCTGTGAGTCCTCGACAAAT 60.338 52.381 0.00 0.00 34.60 2.32
1116 1228 2.643551 CCACAGAACTTGAACACCTGT 58.356 47.619 0.00 0.00 38.48 4.00
1126 1238 0.846693 ACCTCTTGCCCACAGAACTT 59.153 50.000 0.00 0.00 0.00 2.66
1188 1300 3.894759 CTTGGACACTTGGATCCATCAT 58.105 45.455 17.06 1.23 44.49 2.45
1268 1380 2.280457 GGCCGGCATAGTGCTCTC 60.280 66.667 30.85 1.84 44.28 3.20
1460 1572 1.980772 GGCATGCTTCCCAGTTGCT 60.981 57.895 18.92 0.00 33.87 3.91
1792 1904 1.392589 CTTGTTGTCAAGCAGGTGGT 58.607 50.000 0.00 0.00 43.34 4.16
1874 1987 1.645710 AGTAGTAGTGCTTGCCCAGT 58.354 50.000 0.00 0.00 0.00 4.00
1942 2055 1.392168 ACAAAATGTACATCGTCGCCG 59.608 47.619 9.23 0.00 0.00 6.46
2049 2221 1.930908 GAGGGTGTCGTCCTACCACG 61.931 65.000 0.00 0.00 38.74 4.94
2075 2247 3.047115 TGGAGTTAACCTACCACCACAA 58.953 45.455 0.88 0.00 0.00 3.33
2093 2265 3.468071 TCTTCCTAGCACTACCTTGGA 57.532 47.619 0.00 0.00 35.43 3.53
2156 2334 2.101249 AGCACACAAACAACAATGGAGG 59.899 45.455 0.00 0.00 0.00 4.30
2357 2588 1.887242 TCAACACTGCTGTCGTGCC 60.887 57.895 0.00 0.00 35.84 5.01
2378 2609 0.251341 GACACCTCCAACCTTGCCAT 60.251 55.000 0.00 0.00 0.00 4.40
2380 2611 0.467290 TTGACACCTCCAACCTTGCC 60.467 55.000 0.00 0.00 0.00 4.52
2465 2696 1.457267 ACACCAATGCCACAGCCAA 60.457 52.632 0.00 0.00 38.69 4.52
2468 2699 2.048877 GCACACCAATGCCACAGC 60.049 61.111 0.00 0.00 39.86 4.40
2476 2708 0.038166 CCCACACCTAGCACACCAAT 59.962 55.000 0.00 0.00 0.00 3.16
2608 2840 4.330944 TGTCCCTGCATTAGGTAATACG 57.669 45.455 0.00 0.00 45.80 3.06
2630 2862 7.820872 GCTAGTTGTTTGGTTACCTGTATCTAA 59.179 37.037 2.07 0.00 0.00 2.10
2636 2868 4.134563 CTGCTAGTTGTTTGGTTACCTGT 58.865 43.478 2.07 0.00 0.00 4.00
2641 2873 4.688879 CACGATCTGCTAGTTGTTTGGTTA 59.311 41.667 0.00 0.00 0.00 2.85
2661 2894 3.672241 GCAAAAACAGGCCCTAATACACG 60.672 47.826 0.00 0.00 0.00 4.49
2663 2896 3.761752 GAGCAAAAACAGGCCCTAATACA 59.238 43.478 0.00 0.00 0.00 2.29
2697 2930 2.672874 TGCATCGCATACACTTCTCAAC 59.327 45.455 0.00 0.00 31.71 3.18
2719 2952 1.064952 GTTGCCGTTTGCTACAGTGTT 59.935 47.619 0.00 0.00 43.93 3.32
2720 2953 0.661020 GTTGCCGTTTGCTACAGTGT 59.339 50.000 0.00 0.00 43.93 3.55
2722 2955 0.464735 TGGTTGCCGTTTGCTACAGT 60.465 50.000 1.62 0.00 45.92 3.55
2754 2987 0.409092 ACATGATGCCCAAGGGTCAA 59.591 50.000 7.05 0.00 37.65 3.18
2756 2989 2.233271 CATACATGATGCCCAAGGGTC 58.767 52.381 7.05 0.00 37.65 4.46
2757 2990 1.133388 CCATACATGATGCCCAAGGGT 60.133 52.381 7.05 0.00 37.65 4.34
2759 2992 2.662535 TCCATACATGATGCCCAAGG 57.337 50.000 0.00 0.00 33.79 3.61
2760 2993 4.008330 GAGATCCATACATGATGCCCAAG 58.992 47.826 0.00 0.00 33.79 3.61
2762 2995 2.981081 TGAGATCCATACATGATGCCCA 59.019 45.455 0.00 0.00 33.79 5.36
2763 2996 3.708403 TGAGATCCATACATGATGCCC 57.292 47.619 0.00 0.00 33.79 5.36
2765 2998 5.163744 GCTGAATGAGATCCATACATGATGC 60.164 44.000 0.00 0.00 34.45 3.91
2766 2999 6.174049 AGCTGAATGAGATCCATACATGATG 58.826 40.000 0.00 0.00 34.45 3.07
2767 3000 6.375830 AGCTGAATGAGATCCATACATGAT 57.624 37.500 0.00 0.00 34.45 2.45
2768 3001 5.820404 AGCTGAATGAGATCCATACATGA 57.180 39.130 0.00 0.00 34.45 3.07
2773 3006 5.901413 AGGAAAGCTGAATGAGATCCATA 57.099 39.130 0.00 0.00 34.45 2.74
2774 3007 4.792513 AGGAAAGCTGAATGAGATCCAT 57.207 40.909 0.00 0.00 36.99 3.41
2775 3008 4.267536 CAAGGAAAGCTGAATGAGATCCA 58.732 43.478 0.00 0.00 0.00 3.41
2776 3009 3.631227 CCAAGGAAAGCTGAATGAGATCC 59.369 47.826 0.00 0.00 0.00 3.36
2777 3010 4.268359 ACCAAGGAAAGCTGAATGAGATC 58.732 43.478 0.00 0.00 0.00 2.75
2778 3011 4.268359 GACCAAGGAAAGCTGAATGAGAT 58.732 43.478 0.00 0.00 0.00 2.75
2779 3012 3.679389 GACCAAGGAAAGCTGAATGAGA 58.321 45.455 0.00 0.00 0.00 3.27
2780 3013 2.417933 CGACCAAGGAAAGCTGAATGAG 59.582 50.000 0.00 0.00 0.00 2.90
2781 3014 2.224523 ACGACCAAGGAAAGCTGAATGA 60.225 45.455 0.00 0.00 0.00 2.57
2782 3015 2.154462 ACGACCAAGGAAAGCTGAATG 58.846 47.619 0.00 0.00 0.00 2.67
2783 3016 2.568623 ACGACCAAGGAAAGCTGAAT 57.431 45.000 0.00 0.00 0.00 2.57
2784 3017 2.158813 AGAACGACCAAGGAAAGCTGAA 60.159 45.455 0.00 0.00 0.00 3.02
2785 3018 1.416401 AGAACGACCAAGGAAAGCTGA 59.584 47.619 0.00 0.00 0.00 4.26
2786 3019 1.884235 AGAACGACCAAGGAAAGCTG 58.116 50.000 0.00 0.00 0.00 4.24
2787 3020 2.633481 ACTAGAACGACCAAGGAAAGCT 59.367 45.455 0.00 0.00 0.00 3.74
2788 3021 3.041508 ACTAGAACGACCAAGGAAAGC 57.958 47.619 0.00 0.00 0.00 3.51
2789 3022 5.388408 AGTACTAGAACGACCAAGGAAAG 57.612 43.478 0.00 0.00 0.00 2.62
2790 3023 5.510179 CCAAGTACTAGAACGACCAAGGAAA 60.510 44.000 0.00 0.00 0.00 3.13
2791 3024 4.021719 CCAAGTACTAGAACGACCAAGGAA 60.022 45.833 0.00 0.00 0.00 3.36
2792 3025 3.508793 CCAAGTACTAGAACGACCAAGGA 59.491 47.826 0.00 0.00 0.00 3.36
2793 3026 3.257624 ACCAAGTACTAGAACGACCAAGG 59.742 47.826 0.00 0.00 0.00 3.61
2794 3027 4.235360 CACCAAGTACTAGAACGACCAAG 58.765 47.826 0.00 0.00 0.00 3.61
2795 3028 3.553508 GCACCAAGTACTAGAACGACCAA 60.554 47.826 0.00 0.00 0.00 3.67
2796 3029 2.029649 GCACCAAGTACTAGAACGACCA 60.030 50.000 0.00 0.00 0.00 4.02
2797 3030 2.230750 AGCACCAAGTACTAGAACGACC 59.769 50.000 0.00 0.00 0.00 4.79
2798 3031 3.500014 GAGCACCAAGTACTAGAACGAC 58.500 50.000 0.00 0.00 0.00 4.34
2799 3032 2.490903 GGAGCACCAAGTACTAGAACGA 59.509 50.000 0.00 0.00 35.97 3.85
2800 3033 2.492484 AGGAGCACCAAGTACTAGAACG 59.508 50.000 2.07 0.00 38.94 3.95
2801 3034 4.246458 CAAGGAGCACCAAGTACTAGAAC 58.754 47.826 2.07 0.00 38.94 3.01
2802 3035 3.901844 ACAAGGAGCACCAAGTACTAGAA 59.098 43.478 2.07 0.00 38.94 2.10
2803 3036 3.258372 CACAAGGAGCACCAAGTACTAGA 59.742 47.826 2.07 0.00 38.94 2.43
2804 3037 3.258372 TCACAAGGAGCACCAAGTACTAG 59.742 47.826 2.07 0.00 38.94 2.57
2805 3038 3.236047 TCACAAGGAGCACCAAGTACTA 58.764 45.455 2.07 0.00 38.94 1.82
2806 3039 2.047061 TCACAAGGAGCACCAAGTACT 58.953 47.619 2.07 0.00 38.94 2.73
2807 3040 2.543777 TCACAAGGAGCACCAAGTAC 57.456 50.000 2.07 0.00 38.94 2.73
2808 3041 2.371841 ACATCACAAGGAGCACCAAGTA 59.628 45.455 2.07 0.00 38.94 2.24
2809 3042 1.143684 ACATCACAAGGAGCACCAAGT 59.856 47.619 2.07 0.00 38.94 3.16
2810 3043 1.538512 CACATCACAAGGAGCACCAAG 59.461 52.381 2.07 0.00 38.94 3.61
2811 3044 1.133823 ACACATCACAAGGAGCACCAA 60.134 47.619 2.07 0.00 38.94 3.67
2812 3045 0.473755 ACACATCACAAGGAGCACCA 59.526 50.000 2.07 0.00 38.94 4.17
2813 3046 0.877071 CACACATCACAAGGAGCACC 59.123 55.000 0.00 0.00 0.00 5.01
2814 3047 1.802960 CTCACACATCACAAGGAGCAC 59.197 52.381 0.00 0.00 0.00 4.40
2815 3048 1.879372 GCTCACACATCACAAGGAGCA 60.879 52.381 0.00 0.00 45.23 4.26
2816 3049 0.801251 GCTCACACATCACAAGGAGC 59.199 55.000 0.00 0.00 40.63 4.70
2817 3050 1.073964 CGCTCACACATCACAAGGAG 58.926 55.000 0.00 0.00 0.00 3.69
2818 3051 0.392706 ACGCTCACACATCACAAGGA 59.607 50.000 0.00 0.00 0.00 3.36
2819 3052 0.514255 CACGCTCACACATCACAAGG 59.486 55.000 0.00 0.00 0.00 3.61
2820 3053 1.193203 GTCACGCTCACACATCACAAG 59.807 52.381 0.00 0.00 0.00 3.16
2821 3054 1.217001 GTCACGCTCACACATCACAA 58.783 50.000 0.00 0.00 0.00 3.33
2822 3055 0.103937 TGTCACGCTCACACATCACA 59.896 50.000 0.00 0.00 0.00 3.58
2823 3056 1.391485 GATGTCACGCTCACACATCAC 59.609 52.381 6.44 0.00 43.98 3.06
2824 3057 1.713597 GATGTCACGCTCACACATCA 58.286 50.000 6.44 0.00 43.98 3.07
2825 3058 0.642291 CGATGTCACGCTCACACATC 59.358 55.000 0.00 0.00 42.02 3.06
2826 3059 0.243636 TCGATGTCACGCTCACACAT 59.756 50.000 0.00 0.00 33.32 3.21
2827 3060 0.031449 TTCGATGTCACGCTCACACA 59.969 50.000 0.00 0.00 0.00 3.72
2828 3061 1.350193 ATTCGATGTCACGCTCACAC 58.650 50.000 0.00 0.00 0.00 3.82
2829 3062 1.992667 GAATTCGATGTCACGCTCACA 59.007 47.619 0.00 0.00 0.00 3.58
2830 3063 2.263077 AGAATTCGATGTCACGCTCAC 58.737 47.619 0.00 0.00 0.00 3.51
2831 3064 2.654749 AGAATTCGATGTCACGCTCA 57.345 45.000 0.00 0.00 0.00 4.26
2832 3065 3.561155 GAAGAATTCGATGTCACGCTC 57.439 47.619 0.00 0.00 34.17 5.03
2844 3077 3.497262 ACGACCAACGAAAGGAAGAATTC 59.503 43.478 0.00 0.00 44.52 2.17
2845 3078 3.473625 ACGACCAACGAAAGGAAGAATT 58.526 40.909 0.00 0.00 45.77 2.17
2846 3079 3.064931 GACGACCAACGAAAGGAAGAAT 58.935 45.455 0.00 0.00 45.77 2.40
2847 3080 2.159071 TGACGACCAACGAAAGGAAGAA 60.159 45.455 0.00 0.00 45.77 2.52
2848 3081 1.409790 TGACGACCAACGAAAGGAAGA 59.590 47.619 0.00 0.00 45.77 2.87
2849 3082 1.792949 CTGACGACCAACGAAAGGAAG 59.207 52.381 0.00 0.00 45.77 3.46
2850 3083 1.539496 CCTGACGACCAACGAAAGGAA 60.539 52.381 0.00 0.00 44.38 3.36
2851 3084 0.032952 CCTGACGACCAACGAAAGGA 59.967 55.000 0.00 0.00 44.38 3.36
2852 3085 0.032952 TCCTGACGACCAACGAAAGG 59.967 55.000 0.00 0.00 45.77 3.11
2853 3086 1.419374 CTCCTGACGACCAACGAAAG 58.581 55.000 0.00 0.00 45.77 2.62
2854 3087 0.599204 GCTCCTGACGACCAACGAAA 60.599 55.000 0.00 0.00 45.77 3.46
2855 3088 1.006571 GCTCCTGACGACCAACGAA 60.007 57.895 0.00 0.00 45.77 3.85
2856 3089 1.901948 AGCTCCTGACGACCAACGA 60.902 57.895 0.00 0.00 45.77 3.85


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

AutoCloner maintained by Alex Coulton.