Multiple sequence alignment - TraesCS2B01G106300

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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 TraesCS2B01G106300 chr2B 100.000 2297 0 0 1 2297 67281744 67279448 0.000000e+00 4242.0
1 TraesCS2B01G106300 chr2B 90.831 2203 108 40 1 2156 750616384 750618539 0.000000e+00 2863.0
2 TraesCS2B01G106300 chr2B 95.652 736 24 4 1 733 51008833 51009563 0.000000e+00 1175.0
3 TraesCS2B01G106300 chr2B 92.593 108 7 1 2128 2235 289215207 289215313 1.100000e-33 154.0
4 TraesCS2B01G106300 chr1B 96.471 2182 43 13 1 2156 56409072 56411245 0.000000e+00 3572.0
5 TraesCS2B01G106300 chr1B 96.335 2183 44 16 1 2156 63661736 63663909 0.000000e+00 3555.0
6 TraesCS2B01G106300 chr1B 96.286 2181 51 7 1 2156 644238885 644241060 0.000000e+00 3552.0
7 TraesCS2B01G106300 chr1B 89.941 2187 111 55 1 2156 6181530 6183638 0.000000e+00 2719.0
8 TraesCS2B01G106300 chr1B 94.971 1531 31 9 1 1517 531295688 531297186 0.000000e+00 2359.0
9 TraesCS2B01G106300 chr1B 96.154 104 2 2 2128 2231 644241114 644241215 3.920000e-38 169.0
10 TraesCS2B01G106300 chr1B 95.283 106 4 1 2128 2233 56411299 56411403 1.410000e-37 167.0
11 TraesCS2B01G106300 chr1B 95.238 105 4 1 2128 2232 63663963 63664066 5.080000e-37 165.0
12 TraesCS2B01G106300 chr1B 91.818 110 8 1 2128 2237 37665077 37665185 3.950000e-33 152.0
13 TraesCS2B01G106300 chr5B 96.288 2182 48 14 1 2156 449646037 449648211 0.000000e+00 3550.0
14 TraesCS2B01G106300 chr5B 93.590 2184 62 13 1 2156 41859148 41857015 0.000000e+00 3186.0
15 TraesCS2B01G106300 chr5B 90.778 1659 77 33 1 1616 492512873 492511248 0.000000e+00 2146.0
16 TraesCS2B01G106300 chr5B 87.461 646 33 21 1533 2156 638198171 638197552 0.000000e+00 701.0
17 TraesCS2B01G106300 chr5B 95.238 105 4 1 2128 2232 41856961 41856858 5.080000e-37 165.0
18 TraesCS2B01G106300 chr5B 93.333 105 6 1 2128 2232 669143381 669143278 1.100000e-33 154.0
19 TraesCS2B01G106300 chr5B 93.269 104 6 1 2128 2231 547254024 547253922 3.950000e-33 152.0
20 TraesCS2B01G106300 chr5B 93.269 104 6 1 2128 2231 638718852 638718750 3.950000e-33 152.0
21 TraesCS2B01G106300 chr5B 91.071 112 8 2 2128 2239 23305551 23305442 1.420000e-32 150.0
22 TraesCS2B01G106300 chr5B 93.204 103 6 1 2129 2231 449648266 449648367 1.420000e-32 150.0
23 TraesCS2B01G106300 chr5B 92.308 104 7 1 2128 2231 527734592 527734694 1.840000e-31 147.0
24 TraesCS2B01G106300 chr5B 92.424 66 5 0 2232 2297 632342262 632342197 6.760000e-16 95.3
25 TraesCS2B01G106300 chr6B 95.541 2153 48 7 3 2129 621033866 621035996 0.000000e+00 3400.0
26 TraesCS2B01G106300 chr6B 93.750 2192 63 30 1 2156 26658244 26656091 0.000000e+00 3221.0
27 TraesCS2B01G106300 chr6B 96.223 1562 35 6 1 1543 719843055 719844611 0.000000e+00 2536.0
28 TraesCS2B01G106300 chr6B 87.690 1446 102 49 749 2156 208209667 208211074 0.000000e+00 1615.0
29 TraesCS2B01G106300 chr6B 95.380 736 26 4 1 733 518305057 518305787 0.000000e+00 1164.0
30 TraesCS2B01G106300 chr6B 89.773 176 4 3 1991 2156 653396530 653396359 1.790000e-51 213.0
31 TraesCS2B01G106300 chr6B 94.231 104 5 1 2128 2231 26656037 26655935 8.500000e-35 158.0
32 TraesCS2B01G106300 chr7B 94.566 2153 48 11 1 2129 39763451 39765558 0.000000e+00 3264.0
33 TraesCS2B01G106300 chr7B 93.773 2184 76 27 1 2130 724303941 724301764 0.000000e+00 3225.0
34 TraesCS2B01G106300 chr7B 90.054 2202 113 55 1 2156 715338356 715336215 0.000000e+00 2756.0
35 TraesCS2B01G106300 chr7B 89.837 2204 127 46 1 2156 655321098 655318944 0.000000e+00 2739.0
36 TraesCS2B01G106300 chr7B 89.831 2183 110 52 3 2156 46780008 46782107 0.000000e+00 2699.0
37 TraesCS2B01G106300 chr7B 94.293 736 32 5 1 733 3659145 3659873 0.000000e+00 1118.0
38 TraesCS2B01G106300 chr7B 97.170 106 2 1 2128 2233 39765635 39765739 6.520000e-41 178.0
39 TraesCS2B01G106300 chrUn 92.443 2157 83 31 5 2129 315137690 315135582 0.000000e+00 3007.0
40 TraesCS2B01G106300 chrUn 90.181 2210 124 50 1 2138 236931566 236933754 0.000000e+00 2793.0
41 TraesCS2B01G106300 chrUn 92.557 1787 66 27 5 1770 34511107 34512847 0.000000e+00 2501.0
42 TraesCS2B01G106300 chrUn 92.557 1787 66 27 5 1770 301822865 301821125 0.000000e+00 2501.0
43 TraesCS2B01G106300 chrUn 85.470 936 59 37 1265 2156 281295642 281294740 0.000000e+00 904.0
44 TraesCS2B01G106300 chrUn 85.470 936 59 37 1265 2156 281302562 281301660 0.000000e+00 904.0
45 TraesCS2B01G106300 chrUn 85.470 936 59 40 1265 2156 291784333 291785235 0.000000e+00 904.0
46 TraesCS2B01G106300 chrUn 85.470 936 59 40 1265 2156 291786814 291785912 0.000000e+00 904.0
47 TraesCS2B01G106300 chrUn 85.470 936 59 40 1265 2156 389950436 389949534 0.000000e+00 904.0
48 TraesCS2B01G106300 chrUn 91.984 499 23 6 1670 2156 294405654 294405161 0.000000e+00 684.0
49 TraesCS2B01G106300 chrUn 94.340 318 6 3 1822 2129 449003962 449003647 5.740000e-131 477.0
50 TraesCS2B01G106300 chrUn 91.339 127 6 3 2030 2156 314860805 314860926 3.920000e-38 169.0
51 TraesCS2B01G106300 chrUn 91.346 104 8 1 2128 2231 40675226 40675124 8.560000e-30 141.0
52 TraesCS2B01G106300 chrUn 91.346 104 8 1 2128 2231 357524124 357524226 8.560000e-30 141.0
53 TraesCS2B01G106300 chrUn 90.385 104 9 1 2128 2231 48530722 48530620 3.980000e-28 135.0
54 TraesCS2B01G106300 chrUn 90.476 105 7 2 2128 2231 147957306 147957204 3.980000e-28 135.0
55 TraesCS2B01G106300 chrUn 88.991 109 11 1 2128 2236 280614260 280614153 1.430000e-27 134.0
56 TraesCS2B01G106300 chrUn 89.423 104 10 1 2128 2231 1843070 1843172 1.850000e-26 130.0
57 TraesCS2B01G106300 chrUn 89.423 104 10 1 2128 2231 201690848 201690950 1.850000e-26 130.0
58 TraesCS2B01G106300 chrUn 88.679 106 11 1 2128 2233 50159806 50159910 6.660000e-26 128.0
59 TraesCS2B01G106300 chrUn 88.679 106 11 1 2128 2233 346136537 346136433 6.660000e-26 128.0
60 TraesCS2B01G106300 chr3B 92.930 2051 58 27 135 2156 177462969 177460977 0.000000e+00 2904.0
61 TraesCS2B01G106300 chr3B 90.444 2208 120 40 1 2156 29816236 29818404 0.000000e+00 2824.0
62 TraesCS2B01G106300 chr3B 95.558 1531 35 9 1 1517 60549066 60547555 0.000000e+00 2420.0
63 TraesCS2B01G106300 chr3B 94.766 726 30 4 2 724 142227092 142227812 0.000000e+00 1123.0
64 TraesCS2B01G106300 chr3B 92.098 734 23 12 1444 2156 60547486 60546767 0.000000e+00 1002.0
65 TraesCS2B01G106300 chr3B 96.154 104 3 1 2128 2231 177460923 177460821 3.920000e-38 169.0
66 TraesCS2B01G106300 chr4B 90.819 2211 108 47 1 2156 668343781 668341611 0.000000e+00 2870.0
67 TraesCS2B01G106300 chr4B 89.342 2205 115 42 1 2156 39579709 39577576 0.000000e+00 2660.0
68 TraesCS2B01G106300 chr4B 88.442 770 30 16 1396 2138 366558973 366558236 0.000000e+00 874.0
69 TraesCS2B01G106300 chr4B 92.308 104 7 1 2128 2231 213029533 213029431 1.840000e-31 147.0
70 TraesCS2B01G106300 chr4B 92.308 104 7 1 2128 2231 236162368 236162266 1.840000e-31 147.0
71 TraesCS2B01G106300 chr4B 92.308 104 7 1 2128 2231 275551867 275551969 1.840000e-31 147.0
72 TraesCS2B01G106300 chr4B 92.308 104 7 1 2128 2231 654351255 654351153 1.840000e-31 147.0
73 TraesCS2B01G106300 chr4B 92.308 104 7 1 2128 2231 668533167 668533065 1.840000e-31 147.0
74 TraesCS2B01G106300 chr4B 91.429 105 7 2 2128 2232 117429640 117429742 2.380000e-30 143.0
75 TraesCS2B01G106300 chr4B 90.000 110 9 2 2128 2236 106634997 106634889 8.560000e-30 141.0
76 TraesCS2B01G106300 chr4B 90.000 110 10 1 2128 2237 365510828 365510936 8.560000e-30 141.0
77 TraesCS2B01G106300 chr4A 86.330 1229 96 33 958 2155 29673212 29672025 0.000000e+00 1273.0
78 TraesCS2B01G106300 chr4A 86.533 995 70 30 1187 2156 691376516 691375561 0.000000e+00 1037.0
79 TraesCS2B01G106300 chr4A 83.099 1207 129 48 958 2129 24489635 24490801 0.000000e+00 1029.0
80 TraesCS2B01G106300 chr4A 92.570 498 20 6 1670 2156 660551006 660551497 0.000000e+00 699.0
81 TraesCS2B01G106300 chr4A 92.523 107 7 1 2128 2234 727044105 727044210 3.950000e-33 152.0
82 TraesCS2B01G106300 chr4A 92.308 104 7 1 2128 2231 644728888 644728990 1.840000e-31 147.0
83 TraesCS2B01G106300 chr4A 89.565 115 8 3 2128 2242 647851252 647851142 2.380000e-30 143.0
84 TraesCS2B01G106300 chr1A 84.202 1247 108 43 958 2156 471034492 471035697 0.000000e+00 1129.0
85 TraesCS2B01G106300 chr1A 93.342 736 39 6 1 733 54871295 54870567 0.000000e+00 1079.0
86 TraesCS2B01G106300 chr1A 90.179 112 10 1 2128 2239 287038841 287038731 6.610000e-31 145.0
87 TraesCS2B01G106300 chr3A 93.886 736 37 4 1 733 153244997 153244267 0.000000e+00 1103.0
88 TraesCS2B01G106300 chr6A 88.945 597 30 12 1571 2156 11910597 11910026 0.000000e+00 704.0
89 TraesCS2B01G106300 chr6A 93.333 105 6 1 2128 2232 571219301 571219198 1.100000e-33 154.0
90 TraesCS2B01G106300 chr6A 90.385 104 9 1 2128 2231 1329509 1329611 3.980000e-28 135.0
91 TraesCS2B01G106300 chr6A 90.385 104 9 1 2128 2231 245227186 245227084 3.980000e-28 135.0
92 TraesCS2B01G106300 chr6A 90.385 104 9 1 2128 2231 485253224 485253122 3.980000e-28 135.0
93 TraesCS2B01G106300 chr5A 89.421 501 32 8 1667 2156 501878634 501879124 1.510000e-171 612.0
94 TraesCS2B01G106300 chr1D 86.307 482 44 10 1685 2156 336728468 336727999 2.630000e-139 505.0
95 TraesCS2B01G106300 chr6D 86.200 471 38 15 1698 2156 446362675 446362220 3.430000e-133 484.0
96 TraesCS2B01G106300 chr4D 85.745 470 40 11 1698 2156 236670926 236670473 2.670000e-129 472.0
97 TraesCS2B01G106300 chr3D 91.667 108 7 2 2128 2234 9495259 9495153 5.110000e-32 148.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS2B01G106300 chr2B 67279448 67281744 2296 True 4242.0 4242 100.0000 1 2297 1 chr2B.!!$R1 2296
1 TraesCS2B01G106300 chr2B 750616384 750618539 2155 False 2863.0 2863 90.8310 1 2156 1 chr2B.!!$F3 2155
2 TraesCS2B01G106300 chr2B 51008833 51009563 730 False 1175.0 1175 95.6520 1 733 1 chr2B.!!$F1 732
3 TraesCS2B01G106300 chr1B 6181530 6183638 2108 False 2719.0 2719 89.9410 1 2156 1 chr1B.!!$F1 2155
4 TraesCS2B01G106300 chr1B 531295688 531297186 1498 False 2359.0 2359 94.9710 1 1517 1 chr1B.!!$F3 1516
5 TraesCS2B01G106300 chr1B 56409072 56411403 2331 False 1869.5 3572 95.8770 1 2233 2 chr1B.!!$F4 2232
6 TraesCS2B01G106300 chr1B 644238885 644241215 2330 False 1860.5 3552 96.2200 1 2231 2 chr1B.!!$F6 2230
7 TraesCS2B01G106300 chr1B 63661736 63664066 2330 False 1860.0 3555 95.7865 1 2232 2 chr1B.!!$F5 2231
8 TraesCS2B01G106300 chr5B 492511248 492512873 1625 True 2146.0 2146 90.7780 1 1616 1 chr5B.!!$R2 1615
9 TraesCS2B01G106300 chr5B 449646037 449648367 2330 False 1850.0 3550 94.7460 1 2231 2 chr5B.!!$F2 2230
10 TraesCS2B01G106300 chr5B 41856858 41859148 2290 True 1675.5 3186 94.4140 1 2232 2 chr5B.!!$R8 2231
11 TraesCS2B01G106300 chr5B 638197552 638198171 619 True 701.0 701 87.4610 1533 2156 1 chr5B.!!$R5 623
12 TraesCS2B01G106300 chr6B 621033866 621035996 2130 False 3400.0 3400 95.5410 3 2129 1 chr6B.!!$F3 2126
13 TraesCS2B01G106300 chr6B 719843055 719844611 1556 False 2536.0 2536 96.2230 1 1543 1 chr6B.!!$F4 1542
14 TraesCS2B01G106300 chr6B 26655935 26658244 2309 True 1689.5 3221 93.9905 1 2231 2 chr6B.!!$R2 2230
15 TraesCS2B01G106300 chr6B 208209667 208211074 1407 False 1615.0 1615 87.6900 749 2156 1 chr6B.!!$F1 1407
16 TraesCS2B01G106300 chr6B 518305057 518305787 730 False 1164.0 1164 95.3800 1 733 1 chr6B.!!$F2 732
17 TraesCS2B01G106300 chr7B 724301764 724303941 2177 True 3225.0 3225 93.7730 1 2130 1 chr7B.!!$R3 2129
18 TraesCS2B01G106300 chr7B 715336215 715338356 2141 True 2756.0 2756 90.0540 1 2156 1 chr7B.!!$R2 2155
19 TraesCS2B01G106300 chr7B 655318944 655321098 2154 True 2739.0 2739 89.8370 1 2156 1 chr7B.!!$R1 2155
20 TraesCS2B01G106300 chr7B 46780008 46782107 2099 False 2699.0 2699 89.8310 3 2156 1 chr7B.!!$F2 2153
21 TraesCS2B01G106300 chr7B 39763451 39765739 2288 False 1721.0 3264 95.8680 1 2233 2 chr7B.!!$F3 2232
22 TraesCS2B01G106300 chr7B 3659145 3659873 728 False 1118.0 1118 94.2930 1 733 1 chr7B.!!$F1 732
23 TraesCS2B01G106300 chrUn 315135582 315137690 2108 True 3007.0 3007 92.4430 5 2129 1 chrUn.!!$R10 2124
24 TraesCS2B01G106300 chrUn 236931566 236933754 2188 False 2793.0 2793 90.1810 1 2138 1 chrUn.!!$F5 2137
25 TraesCS2B01G106300 chrUn 34511107 34512847 1740 False 2501.0 2501 92.5570 5 1770 1 chrUn.!!$F2 1765
26 TraesCS2B01G106300 chrUn 301821125 301822865 1740 True 2501.0 2501 92.5570 5 1770 1 chrUn.!!$R9 1765
27 TraesCS2B01G106300 chrUn 281294740 281295642 902 True 904.0 904 85.4700 1265 2156 1 chrUn.!!$R5 891
28 TraesCS2B01G106300 chrUn 281301660 281302562 902 True 904.0 904 85.4700 1265 2156 1 chrUn.!!$R6 891
29 TraesCS2B01G106300 chrUn 291784333 291785235 902 False 904.0 904 85.4700 1265 2156 1 chrUn.!!$F6 891
30 TraesCS2B01G106300 chrUn 291785912 291786814 902 True 904.0 904 85.4700 1265 2156 1 chrUn.!!$R7 891
31 TraesCS2B01G106300 chrUn 389949534 389950436 902 True 904.0 904 85.4700 1265 2156 1 chrUn.!!$R12 891
32 TraesCS2B01G106300 chr3B 29816236 29818404 2168 False 2824.0 2824 90.4440 1 2156 1 chr3B.!!$F1 2155
33 TraesCS2B01G106300 chr3B 60546767 60549066 2299 True 1711.0 2420 93.8280 1 2156 2 chr3B.!!$R1 2155
34 TraesCS2B01G106300 chr3B 177460821 177462969 2148 True 1536.5 2904 94.5420 135 2231 2 chr3B.!!$R2 2096
35 TraesCS2B01G106300 chr3B 142227092 142227812 720 False 1123.0 1123 94.7660 2 724 1 chr3B.!!$F2 722
36 TraesCS2B01G106300 chr4B 668341611 668343781 2170 True 2870.0 2870 90.8190 1 2156 1 chr4B.!!$R7 2155
37 TraesCS2B01G106300 chr4B 39577576 39579709 2133 True 2660.0 2660 89.3420 1 2156 1 chr4B.!!$R1 2155
38 TraesCS2B01G106300 chr4B 366558236 366558973 737 True 874.0 874 88.4420 1396 2138 1 chr4B.!!$R5 742
39 TraesCS2B01G106300 chr4A 29672025 29673212 1187 True 1273.0 1273 86.3300 958 2155 1 chr4A.!!$R1 1197
40 TraesCS2B01G106300 chr4A 691375561 691376516 955 True 1037.0 1037 86.5330 1187 2156 1 chr4A.!!$R3 969
41 TraesCS2B01G106300 chr4A 24489635 24490801 1166 False 1029.0 1029 83.0990 958 2129 1 chr4A.!!$F1 1171
42 TraesCS2B01G106300 chr1A 471034492 471035697 1205 False 1129.0 1129 84.2020 958 2156 1 chr1A.!!$F1 1198
43 TraesCS2B01G106300 chr1A 54870567 54871295 728 True 1079.0 1079 93.3420 1 733 1 chr1A.!!$R1 732
44 TraesCS2B01G106300 chr3A 153244267 153244997 730 True 1103.0 1103 93.8860 1 733 1 chr3A.!!$R1 732
45 TraesCS2B01G106300 chr6A 11910026 11910597 571 True 704.0 704 88.9450 1571 2156 1 chr6A.!!$R1 585

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
873 938 1.811965 TGTTCCAATTGCATGTCTCCG 59.188 47.619 0.0 0.0 0.0 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2263 2863 0.037975 TGTTTCTAGGCGGTTCGTCC 60.038 55.0 0.0 0.0 28.67 4.79 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
83 84 6.385033 GCAAATAAAGTCAGCATCAAGTCTT 58.615 36.000 0.00 0.00 0.00 3.01
392 396 8.806429 TTGGATAACATTTCTGATTCTTGCTA 57.194 30.769 0.00 0.00 0.00 3.49
844 909 5.044846 ACCACCATTCTAGGCTTAATGAAGT 60.045 40.000 18.59 11.85 35.53 3.01
873 938 1.811965 TGTTCCAATTGCATGTCTCCG 59.188 47.619 0.00 0.00 0.00 4.63
1609 2056 4.005650 AGTTATGTGGATCACTTGTGCAG 58.994 43.478 0.00 0.00 35.11 4.41
1810 2309 6.539826 GCATAGCAGAAAATAAAAAGGCCAAT 59.460 34.615 5.01 0.00 0.00 3.16
2139 2739 5.239963 TGGTCGTAAAATCTTTTGACCTTCC 59.760 40.000 18.31 7.36 40.81 3.46
2141 2741 5.049886 GTCGTAAAATCTTTTGACCTTCCGT 60.050 40.000 0.00 0.00 0.00 4.69
2195 2795 3.644966 AGTGACCTTTCAGTGACCAAA 57.355 42.857 0.00 0.00 33.82 3.28
2233 2833 9.317936 CAAGATAGCATATTTCTTGTAGTGTGA 57.682 33.333 4.20 0.00 40.80 3.58
2234 2834 8.879342 AGATAGCATATTTCTTGTAGTGTGAC 57.121 34.615 0.00 0.00 0.00 3.67
2235 2835 7.928706 AGATAGCATATTTCTTGTAGTGTGACC 59.071 37.037 0.00 0.00 0.00 4.02
2236 2836 6.054860 AGCATATTTCTTGTAGTGTGACCT 57.945 37.500 0.00 0.00 0.00 3.85
2237 2837 5.877012 AGCATATTTCTTGTAGTGTGACCTG 59.123 40.000 0.00 0.00 0.00 4.00
2238 2838 5.643777 GCATATTTCTTGTAGTGTGACCTGT 59.356 40.000 0.00 0.00 0.00 4.00
2239 2839 6.816640 GCATATTTCTTGTAGTGTGACCTGTA 59.183 38.462 0.00 0.00 0.00 2.74
2240 2840 7.010552 GCATATTTCTTGTAGTGTGACCTGTAG 59.989 40.741 0.00 0.00 0.00 2.74
2241 2841 6.665992 ATTTCTTGTAGTGTGACCTGTAGA 57.334 37.500 0.00 0.00 0.00 2.59
2242 2842 5.707242 TTCTTGTAGTGTGACCTGTAGAG 57.293 43.478 0.00 0.00 0.00 2.43
2243 2843 3.506455 TCTTGTAGTGTGACCTGTAGAGC 59.494 47.826 0.00 0.00 0.00 4.09
2244 2844 1.810755 TGTAGTGTGACCTGTAGAGCG 59.189 52.381 0.00 0.00 0.00 5.03
2245 2845 2.082231 GTAGTGTGACCTGTAGAGCGA 58.918 52.381 0.00 0.00 0.00 4.93
2246 2846 1.840737 AGTGTGACCTGTAGAGCGAT 58.159 50.000 0.00 0.00 0.00 4.58
2247 2847 1.474478 AGTGTGACCTGTAGAGCGATG 59.526 52.381 0.00 0.00 0.00 3.84
2248 2848 1.472878 GTGTGACCTGTAGAGCGATGA 59.527 52.381 0.00 0.00 0.00 2.92
2249 2849 1.472878 TGTGACCTGTAGAGCGATGAC 59.527 52.381 0.00 0.00 0.00 3.06
2250 2850 1.103803 TGACCTGTAGAGCGATGACC 58.896 55.000 0.00 0.00 0.00 4.02
2251 2851 0.029567 GACCTGTAGAGCGATGACCG 59.970 60.000 0.00 0.00 42.21 4.79
2252 2852 0.393944 ACCTGTAGAGCGATGACCGA 60.394 55.000 0.00 0.00 41.76 4.69
2253 2853 0.738975 CCTGTAGAGCGATGACCGAA 59.261 55.000 0.00 0.00 41.76 4.30
2254 2854 1.268794 CCTGTAGAGCGATGACCGAAG 60.269 57.143 0.00 0.00 41.76 3.79
2255 2855 1.671328 CTGTAGAGCGATGACCGAAGA 59.329 52.381 0.00 0.00 41.76 2.87
2256 2856 1.671328 TGTAGAGCGATGACCGAAGAG 59.329 52.381 0.00 0.00 41.76 2.85
2258 2858 1.590259 GAGCGATGACCGAAGAGGC 60.590 63.158 0.00 0.00 46.52 4.70
2259 2859 2.184322 GCGATGACCGAAGAGGCA 59.816 61.111 0.00 0.00 46.52 4.75
2260 2860 1.880340 GCGATGACCGAAGAGGCAG 60.880 63.158 0.00 0.00 46.52 4.85
2261 2861 1.880340 CGATGACCGAAGAGGCAGC 60.880 63.158 0.00 0.00 46.52 5.25
2262 2862 1.219124 GATGACCGAAGAGGCAGCA 59.781 57.895 0.00 0.00 46.52 4.41
2263 2863 0.809241 GATGACCGAAGAGGCAGCAG 60.809 60.000 0.00 0.00 46.52 4.24
2264 2864 2.125350 GACCGAAGAGGCAGCAGG 60.125 66.667 0.00 0.00 46.52 4.85
2265 2865 2.604686 ACCGAAGAGGCAGCAGGA 60.605 61.111 0.00 0.00 46.52 3.86
2266 2866 2.125350 CCGAAGAGGCAGCAGGAC 60.125 66.667 0.00 0.00 0.00 3.85
2267 2867 2.507992 CGAAGAGGCAGCAGGACG 60.508 66.667 0.00 0.00 0.00 4.79
2268 2868 2.973899 GAAGAGGCAGCAGGACGA 59.026 61.111 0.00 0.00 0.00 4.20
2269 2869 1.293498 GAAGAGGCAGCAGGACGAA 59.707 57.895 0.00 0.00 0.00 3.85
2270 2870 1.004440 AAGAGGCAGCAGGACGAAC 60.004 57.895 0.00 0.00 0.00 3.95
2271 2871 2.435059 GAGGCAGCAGGACGAACC 60.435 66.667 0.00 0.00 39.35 3.62
2272 2872 4.379243 AGGCAGCAGGACGAACCG 62.379 66.667 0.00 0.00 44.74 4.44
2275 2875 4.379243 CAGCAGGACGAACCGCCT 62.379 66.667 0.00 0.00 44.74 5.52
2276 2876 2.678934 AGCAGGACGAACCGCCTA 60.679 61.111 0.00 0.00 44.74 3.93
2277 2877 2.202756 GCAGGACGAACCGCCTAG 60.203 66.667 0.00 0.00 44.74 3.02
2278 2878 2.707849 GCAGGACGAACCGCCTAGA 61.708 63.158 0.00 0.00 44.74 2.43
2279 2879 1.888018 CAGGACGAACCGCCTAGAA 59.112 57.895 0.00 0.00 44.74 2.10
2280 2880 0.245539 CAGGACGAACCGCCTAGAAA 59.754 55.000 0.00 0.00 44.74 2.52
2281 2881 0.245813 AGGACGAACCGCCTAGAAAC 59.754 55.000 0.00 0.00 44.74 2.78
2282 2882 0.037975 GGACGAACCGCCTAGAAACA 60.038 55.000 0.00 0.00 0.00 2.83
2283 2883 1.066136 GACGAACCGCCTAGAAACAC 58.934 55.000 0.00 0.00 0.00 3.32
2284 2884 0.390124 ACGAACCGCCTAGAAACACA 59.610 50.000 0.00 0.00 0.00 3.72
2285 2885 1.202557 ACGAACCGCCTAGAAACACAA 60.203 47.619 0.00 0.00 0.00 3.33
2286 2886 1.459592 CGAACCGCCTAGAAACACAAG 59.540 52.381 0.00 0.00 0.00 3.16
2287 2887 1.197036 GAACCGCCTAGAAACACAAGC 59.803 52.381 0.00 0.00 0.00 4.01
2288 2888 0.107831 ACCGCCTAGAAACACAAGCA 59.892 50.000 0.00 0.00 0.00 3.91
2289 2889 0.517316 CCGCCTAGAAACACAAGCAC 59.483 55.000 0.00 0.00 0.00 4.40
2290 2890 0.517316 CGCCTAGAAACACAAGCACC 59.483 55.000 0.00 0.00 0.00 5.01
2291 2891 1.878102 CGCCTAGAAACACAAGCACCT 60.878 52.381 0.00 0.00 0.00 4.00
2292 2892 1.537202 GCCTAGAAACACAAGCACCTG 59.463 52.381 0.00 0.00 0.00 4.00
2293 2893 1.537202 CCTAGAAACACAAGCACCTGC 59.463 52.381 0.00 0.00 42.49 4.85
2294 2894 2.221169 CTAGAAACACAAGCACCTGCA 58.779 47.619 0.00 0.00 45.16 4.41
2295 2895 1.027357 AGAAACACAAGCACCTGCAG 58.973 50.000 6.78 6.78 45.16 4.41
2296 2896 1.024271 GAAACACAAGCACCTGCAGA 58.976 50.000 17.39 0.00 45.16 4.26
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.253894 TCCGTCAGATCAGGTACCGA 59.746 55.000 6.18 7.58 0.00 4.69
235 236 5.209818 TCTTGTTCGACACATAGGTTTCT 57.790 39.130 0.00 0.00 34.43 2.52
873 938 5.105146 ACAAGAAGATGATGACTAGTGACCC 60.105 44.000 0.00 0.00 0.00 4.46
1609 2056 0.610232 AAGTGATCCACAAGCCCAGC 60.610 55.000 0.00 0.00 36.74 4.85
1782 2281 5.650543 CCTTTTTATTTTCTGCTATGCGGT 58.349 37.500 0.00 0.00 36.18 5.68
1784 2283 4.504097 GGCCTTTTTATTTTCTGCTATGCG 59.496 41.667 0.00 0.00 0.00 4.73
1810 2309 2.039216 TGGTCTAGTTCGAATTTGGGCA 59.961 45.455 0.00 0.00 0.00 5.36
1870 2371 6.029346 TGGAGCCTTTTTCTGATGAAATTC 57.971 37.500 0.00 0.00 41.24 2.17
1873 2375 5.047092 GGAATGGAGCCTTTTTCTGATGAAA 60.047 40.000 0.00 0.00 40.08 2.69
2195 2795 2.906389 TGCTATCTTGTGACCTCCACTT 59.094 45.455 0.00 0.00 45.86 3.16
2233 2833 0.393944 TCGGTCATCGCTCTACAGGT 60.394 55.000 0.00 0.00 39.05 4.00
2234 2834 0.738975 TTCGGTCATCGCTCTACAGG 59.261 55.000 0.00 0.00 39.05 4.00
2235 2835 1.671328 TCTTCGGTCATCGCTCTACAG 59.329 52.381 0.00 0.00 39.05 2.74
2236 2836 1.671328 CTCTTCGGTCATCGCTCTACA 59.329 52.381 0.00 0.00 39.05 2.74
2237 2837 1.002251 CCTCTTCGGTCATCGCTCTAC 60.002 57.143 0.00 0.00 39.05 2.59
2238 2838 1.309950 CCTCTTCGGTCATCGCTCTA 58.690 55.000 0.00 0.00 39.05 2.43
2239 2839 2.010582 GCCTCTTCGGTCATCGCTCT 62.011 60.000 0.00 0.00 39.05 4.09
2240 2840 1.590259 GCCTCTTCGGTCATCGCTC 60.590 63.158 0.00 0.00 39.05 5.03
2241 2841 2.290122 CTGCCTCTTCGGTCATCGCT 62.290 60.000 0.00 0.00 39.05 4.93
2242 2842 1.880340 CTGCCTCTTCGGTCATCGC 60.880 63.158 0.00 0.00 39.05 4.58
2243 2843 1.880340 GCTGCCTCTTCGGTCATCG 60.880 63.158 0.00 0.00 40.90 3.84
2244 2844 0.809241 CTGCTGCCTCTTCGGTCATC 60.809 60.000 0.00 0.00 34.25 2.92
2245 2845 1.220206 CTGCTGCCTCTTCGGTCAT 59.780 57.895 0.00 0.00 34.25 3.06
2246 2846 2.659016 CTGCTGCCTCTTCGGTCA 59.341 61.111 0.00 0.00 34.25 4.02
2247 2847 2.125350 CCTGCTGCCTCTTCGGTC 60.125 66.667 0.00 0.00 34.25 4.79
2248 2848 2.604686 TCCTGCTGCCTCTTCGGT 60.605 61.111 0.00 0.00 34.25 4.69
2249 2849 2.125350 GTCCTGCTGCCTCTTCGG 60.125 66.667 0.00 0.00 0.00 4.30
2250 2850 2.492449 TTCGTCCTGCTGCCTCTTCG 62.492 60.000 0.00 0.00 0.00 3.79
2251 2851 1.016653 GTTCGTCCTGCTGCCTCTTC 61.017 60.000 0.00 0.00 0.00 2.87
2252 2852 1.004440 GTTCGTCCTGCTGCCTCTT 60.004 57.895 0.00 0.00 0.00 2.85
2253 2853 2.659610 GTTCGTCCTGCTGCCTCT 59.340 61.111 0.00 0.00 0.00 3.69
2254 2854 2.435059 GGTTCGTCCTGCTGCCTC 60.435 66.667 0.00 0.00 0.00 4.70
2255 2855 4.379243 CGGTTCGTCCTGCTGCCT 62.379 66.667 0.00 0.00 0.00 4.75
2258 2858 2.890847 CTAGGCGGTTCGTCCTGCTG 62.891 65.000 11.45 0.00 35.69 4.41
2259 2859 2.678934 TAGGCGGTTCGTCCTGCT 60.679 61.111 11.45 0.00 35.69 4.24
2260 2860 2.202756 CTAGGCGGTTCGTCCTGC 60.203 66.667 11.45 0.14 35.69 4.85
2261 2861 0.245539 TTTCTAGGCGGTTCGTCCTG 59.754 55.000 11.45 4.76 35.69 3.86
2262 2862 0.245813 GTTTCTAGGCGGTTCGTCCT 59.754 55.000 7.98 7.98 37.25 3.85
2263 2863 0.037975 TGTTTCTAGGCGGTTCGTCC 60.038 55.000 0.00 0.00 28.67 4.79
2264 2864 1.066136 GTGTTTCTAGGCGGTTCGTC 58.934 55.000 0.00 0.00 0.00 4.20
2265 2865 0.390124 TGTGTTTCTAGGCGGTTCGT 59.610 50.000 0.00 0.00 0.00 3.85
2266 2866 1.459592 CTTGTGTTTCTAGGCGGTTCG 59.540 52.381 0.00 0.00 0.00 3.95
2267 2867 1.197036 GCTTGTGTTTCTAGGCGGTTC 59.803 52.381 0.00 0.00 0.00 3.62
2268 2868 1.235724 GCTTGTGTTTCTAGGCGGTT 58.764 50.000 0.00 0.00 0.00 4.44
2269 2869 0.107831 TGCTTGTGTTTCTAGGCGGT 59.892 50.000 0.00 0.00 0.00 5.68
2270 2870 0.517316 GTGCTTGTGTTTCTAGGCGG 59.483 55.000 0.00 0.00 0.00 6.13
2271 2871 0.517316 GGTGCTTGTGTTTCTAGGCG 59.483 55.000 0.00 0.00 0.00 5.52
2272 2872 1.537202 CAGGTGCTTGTGTTTCTAGGC 59.463 52.381 0.00 0.00 0.00 3.93
2273 2873 1.537202 GCAGGTGCTTGTGTTTCTAGG 59.463 52.381 0.00 0.00 38.21 3.02
2274 2874 2.221169 TGCAGGTGCTTGTGTTTCTAG 58.779 47.619 3.18 0.00 42.66 2.43
2275 2875 2.158827 TCTGCAGGTGCTTGTGTTTCTA 60.159 45.455 15.13 0.00 42.66 2.10
2276 2876 1.027357 CTGCAGGTGCTTGTGTTTCT 58.973 50.000 5.57 0.00 42.66 2.52
2277 2877 1.024271 TCTGCAGGTGCTTGTGTTTC 58.976 50.000 15.13 0.00 42.66 2.78
2278 2878 3.189568 TCTGCAGGTGCTTGTGTTT 57.810 47.368 15.13 0.00 42.66 2.83
2279 2879 4.984194 TCTGCAGGTGCTTGTGTT 57.016 50.000 15.13 0.00 42.66 3.32


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

AutoCloner maintained by Alex Coulton.