Multiple sequence alignment - TraesCS3B01G237200

Loading Multiple Alignment...

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 TraesCS3B01G237200 chr3B 100.000 5624 0 0 1 5624 372234304 372239927 0.000000e+00 10386.0
1 TraesCS3B01G237200 chr3B 88.972 798 77 4 1 790 3136053 3135259 0.000000e+00 976.0
2 TraesCS3B01G237200 chr3B 100.000 341 0 0 5884 6224 372240187 372240527 1.140000e-176 630.0
3 TraesCS3B01G237200 chr3B 88.710 124 12 2 1441 1562 231187020 231187143 3.890000e-32 150.0
4 TraesCS3B01G237200 chr3B 87.719 57 7 0 3217 3273 482487885 482487829 4.030000e-07 67.6
5 TraesCS3B01G237200 chr3D 97.007 2372 60 6 2950 5317 278452938 278450574 0.000000e+00 3976.0
6 TraesCS3B01G237200 chr3D 95.462 573 19 5 849 1416 278453896 278453326 0.000000e+00 907.0
7 TraesCS3B01G237200 chr3D 98.104 211 3 1 1588 1798 278453164 278452955 3.550000e-97 366.0
8 TraesCS3B01G237200 chr3D 95.109 184 7 1 6043 6224 278450479 278450296 7.890000e-74 289.0
9 TraesCS3B01G237200 chr3D 97.391 115 3 0 5332 5446 278450592 278450478 4.920000e-46 196.0
10 TraesCS3B01G237200 chr3D 87.826 115 14 0 3068 3182 71506495 71506609 1.090000e-27 135.0
11 TraesCS3B01G237200 chr3D 86.400 125 13 4 5994 6117 583473364 583473243 3.910000e-27 134.0
12 TraesCS3B01G237200 chr3D 89.691 97 7 3 5996 6091 529483090 529483184 3.050000e-23 121.0
13 TraesCS3B01G237200 chr3D 85.217 115 17 0 3068 3182 462243469 462243583 1.100000e-22 119.0
14 TraesCS3B01G237200 chr3D 85.057 87 9 4 5994 6079 29225998 29225915 1.110000e-12 86.1
15 TraesCS3B01G237200 chr3D 84.706 85 11 2 6028 6112 182095619 182095537 4.000000e-12 84.2
16 TraesCS3B01G237200 chr3D 89.286 56 3 3 5925 5977 38185281 38185336 4.030000e-07 67.6
17 TraesCS3B01G237200 chr3D 97.222 36 1 0 3208 3243 409015478 409015443 1.870000e-05 62.1
18 TraesCS3B01G237200 chr3D 100.000 28 0 0 3209 3236 290869076 290869049 1.100000e-02 52.8
19 TraesCS3B01G237200 chr3A 97.007 2372 60 6 2950 5317 360822200 360824564 0.000000e+00 3976.0
20 TraesCS3B01G237200 chr3A 96.837 664 17 3 790 1450 360821210 360821872 0.000000e+00 1107.0
21 TraesCS3B01G237200 chr3A 93.667 300 11 3 5332 5623 360824546 360824845 5.730000e-120 442.0
22 TraesCS3B01G237200 chr3A 98.578 211 2 1 1588 1798 360821972 360822181 7.620000e-99 372.0
23 TraesCS3B01G237200 chr3A 90.558 233 15 5 5994 6224 360825001 360825228 1.010000e-77 302.0
24 TraesCS3B01G237200 chr3A 88.235 102 12 0 3068 3169 550144899 550145000 8.470000e-24 122.0
25 TraesCS3B01G237200 chr3A 93.878 49 3 0 5929 5977 647158973 647158925 2.410000e-09 75.0
26 TraesCS3B01G237200 chr3A 84.375 64 10 0 3240 3303 73610484 73610421 5.210000e-06 63.9
27 TraesCS3B01G237200 chr7D 96.181 1152 42 2 1798 2949 1205526 1204377 0.000000e+00 1882.0
28 TraesCS3B01G237200 chr7D 89.600 125 11 2 1445 1567 433883071 433882947 2.320000e-34 158.0
29 TraesCS3B01G237200 chr7D 88.889 117 8 5 6007 6120 34383203 34383089 8.410000e-29 139.0
30 TraesCS3B01G237200 chr7D 91.398 93 7 1 3071 3163 205494516 205494425 6.550000e-25 126.0
31 TraesCS3B01G237200 chr7D 87.500 104 12 1 6014 6117 111791633 111791735 1.100000e-22 119.0
32 TraesCS3B01G237200 chr7D 97.222 36 1 0 3208 3243 261820140 261820175 1.870000e-05 62.1
33 TraesCS3B01G237200 chr7D 100.000 30 0 0 3210 3239 378490923 378490952 8.720000e-04 56.5
34 TraesCS3B01G237200 chr7D 100.000 28 0 0 3319 3346 56543506 56543479 1.100000e-02 52.8
35 TraesCS3B01G237200 chr7B 95.462 1146 50 2 1800 2945 695112107 695110964 0.000000e+00 1827.0
36 TraesCS3B01G237200 chr7B 94.709 1153 59 2 1798 2949 99221131 99219980 0.000000e+00 1790.0
37 TraesCS3B01G237200 chr7B 95.556 45 2 0 5930 5974 75778114 75778158 8.650000e-09 73.1
38 TraesCS3B01G237200 chr7B 95.556 45 2 0 5930 5974 100880558 100880602 8.650000e-09 73.1
39 TraesCS3B01G237200 chr7B 86.441 59 6 2 3209 3266 749563793 749563736 5.210000e-06 63.9
40 TraesCS3B01G237200 chr6B 94.719 1155 59 2 1796 2949 717855873 717854720 0.000000e+00 1794.0
41 TraesCS3B01G237200 chr6B 85.393 89 11 2 3130 3218 522091644 522091558 2.390000e-14 91.6
42 TraesCS3B01G237200 chr2B 94.719 1155 59 2 1796 2949 199167239 199166086 0.000000e+00 1794.0
43 TraesCS3B01G237200 chr2B 94.705 1152 59 2 1799 2949 528830266 528831416 0.000000e+00 1788.0
44 TraesCS3B01G237200 chr2B 88.847 798 77 5 1 790 477531383 477530590 0.000000e+00 970.0
45 TraesCS3B01G237200 chr2B 89.218 742 77 2 1 742 486845329 486844591 0.000000e+00 924.0
46 TraesCS3B01G237200 chr2B 89.516 124 11 2 1447 1568 26591559 26591436 8.350000e-34 156.0
47 TraesCS3B01G237200 chr2B 90.083 121 10 2 1444 1562 723434230 723434350 8.350000e-34 156.0
48 TraesCS3B01G237200 chr5B 94.709 1153 59 2 1798 2949 362955799 362954648 0.000000e+00 1790.0
49 TraesCS3B01G237200 chr5B 94.700 1151 59 2 1800 2949 63282309 63281160 0.000000e+00 1786.0
50 TraesCS3B01G237200 chr5B 86.614 127 11 6 5991 6114 96754703 96754826 1.090000e-27 135.0
51 TraesCS3B01G237200 chr5B 82.946 129 17 5 5994 6119 702796913 702796787 1.830000e-20 111.0
52 TraesCS3B01G237200 chr5B 88.608 79 7 2 3301 3379 688804608 688804532 1.850000e-15 95.3
53 TraesCS3B01G237200 chr5B 88.608 79 7 2 3301 3379 688840307 688840231 1.850000e-15 95.3
54 TraesCS3B01G237200 chr5B 94.444 36 2 0 3208 3243 70445127 70445092 8.720000e-04 56.5
55 TraesCS3B01G237200 chr5B 84.211 57 9 0 3212 3268 440026012 440026068 8.720000e-04 56.5
56 TraesCS3B01G237200 chr5B 100.000 30 0 0 3214 3243 696291939 696291968 8.720000e-04 56.5
57 TraesCS3B01G237200 chr2A 94.705 1152 59 2 1799 2949 55884066 55882916 0.000000e+00 1788.0
58 TraesCS3B01G237200 chr2A 89.000 800 76 6 1 791 549954216 549955012 0.000000e+00 979.0
59 TraesCS3B01G237200 chr2A 90.909 121 9 2 1443 1561 62286365 62286245 1.800000e-35 161.0
60 TraesCS3B01G237200 chr2A 83.846 130 15 5 5994 6120 516306371 516306245 1.100000e-22 119.0
61 TraesCS3B01G237200 chr2A 82.692 104 14 3 3301 3403 7411396 7411496 8.590000e-14 89.8
62 TraesCS3B01G237200 chr2A 100.000 36 0 0 3301 3336 66794231 66794196 4.030000e-07 67.6
63 TraesCS3B01G237200 chr2A 79.817 109 5 10 3210 3304 27741361 27741256 5.210000e-06 63.9
64 TraesCS3B01G237200 chr5D 89.599 798 73 4 1 790 69325428 69326223 0.000000e+00 1005.0
65 TraesCS3B01G237200 chr5D 88.889 99 11 0 3071 3169 459068815 459068717 8.470000e-24 122.0
66 TraesCS3B01G237200 chr5D 83.607 61 10 0 3245 3305 345624760 345624820 2.420000e-04 58.4
67 TraesCS3B01G237200 chr5D 79.545 88 13 3 3216 3302 444729968 444729885 2.420000e-04 58.4
68 TraesCS3B01G237200 chr5D 78.302 106 10 7 3210 3303 266749459 266749355 8.720000e-04 56.5
69 TraesCS3B01G237200 chr1D 88.861 799 79 6 1 790 16204780 16205577 0.000000e+00 974.0
70 TraesCS3B01G237200 chr1D 93.617 47 3 0 6071 6117 160989762 160989716 3.110000e-08 71.3
71 TraesCS3B01G237200 chr1B 88.736 799 72 10 1 790 530956309 530955520 0.000000e+00 961.0
72 TraesCS3B01G237200 chr6D 88.346 798 80 9 1 790 143084639 143085431 0.000000e+00 946.0
73 TraesCS3B01G237200 chr6D 89.113 744 75 5 1 742 306352477 306351738 0.000000e+00 920.0
74 TraesCS3B01G237200 chr6D 87.500 104 12 1 6014 6117 438839804 438839702 1.100000e-22 119.0
75 TraesCS3B01G237200 chr6D 82.301 113 7 3 6014 6114 430832480 430832591 1.110000e-12 86.1
76 TraesCS3B01G237200 chr6D 95.349 43 2 0 5932 5974 97352513 97352555 1.120000e-07 69.4
77 TraesCS3B01G237200 chr6D 91.489 47 3 1 6068 6114 156316588 156316633 5.210000e-06 63.9
78 TraesCS3B01G237200 chr4A 91.057 123 8 3 1447 1566 702148793 702148915 4.990000e-36 163.0
79 TraesCS3B01G237200 chr4A 86.607 112 13 2 6007 6117 59383447 59383337 8.470000e-24 122.0
80 TraesCS3B01G237200 chr4A 95.556 45 2 0 5933 5977 248663 248619 8.650000e-09 73.1
81 TraesCS3B01G237200 chr4B 90.323 124 9 3 1444 1565 97922024 97922146 6.460000e-35 159.0
82 TraesCS3B01G237200 chr4B 90.756 119 9 2 1445 1561 165306627 165306509 2.320000e-34 158.0
83 TraesCS3B01G237200 chr4B 89.423 104 10 1 6014 6117 562580417 562580519 5.060000e-26 130.0
84 TraesCS3B01G237200 chr4B 85.246 122 14 4 5994 6114 50830881 50830999 8.470000e-24 122.0
85 TraesCS3B01G237200 chr4B 82.812 64 11 0 3239 3302 1049110 1049173 2.420000e-04 58.4
86 TraesCS3B01G237200 chr4D 89.600 125 11 2 1447 1569 389210116 389210240 2.320000e-34 158.0
87 TraesCS3B01G237200 chr4D 87.705 122 13 2 3098 3218 423392217 423392097 2.340000e-29 141.0
88 TraesCS3B01G237200 chr4D 87.619 105 12 1 6013 6117 437033690 437033587 3.050000e-23 121.0
89 TraesCS3B01G237200 chr4D 86.517 89 10 2 6028 6116 1360272 1360186 5.140000e-16 97.1
90 TraesCS3B01G237200 chr4D 86.585 82 11 0 3137 3218 70576979 70577060 2.390000e-14 91.6
91 TraesCS3B01G237200 chr4D 79.259 135 20 7 5991 6120 5696765 5696634 3.090000e-13 87.9
92 TraesCS3B01G237200 chr4D 92.982 57 2 2 6061 6116 396626910 396626965 1.440000e-11 82.4
93 TraesCS3B01G237200 chr4D 93.617 47 2 1 6068 6114 304643193 304643238 1.120000e-07 69.4
94 TraesCS3B01G237200 chr4D 80.000 105 8 7 3210 3302 170210360 170210463 1.450000e-06 65.8
95 TraesCS3B01G237200 chr4D 79.808 104 8 6 3212 3303 205963543 205963441 5.210000e-06 63.9
96 TraesCS3B01G237200 chr4D 80.000 85 15 2 6028 6112 14438166 14438084 1.870000e-05 62.1
97 TraesCS3B01G237200 chr4D 78.723 94 19 1 6023 6116 338024419 338024511 1.870000e-05 62.1
98 TraesCS3B01G237200 chr5A 88.000 125 11 4 5994 6117 26532044 26532165 1.810000e-30 145.0
99 TraesCS3B01G237200 chr5A 84.874 119 12 6 5991 6106 436260453 436260568 1.420000e-21 115.0
100 TraesCS3B01G237200 chr5A 88.710 62 4 3 3158 3218 237940966 237940907 8.650000e-09 73.1
101 TraesCS3B01G237200 chr5A 80.198 101 15 4 3205 3302 659866865 659866963 3.110000e-08 71.3
102 TraesCS3B01G237200 chr6A 89.796 98 10 0 3071 3168 233395624 233395527 6.550000e-25 126.0
103 TraesCS3B01G237200 chr6A 83.168 101 12 3 3121 3218 85574159 85574257 3.090000e-13 87.9
104 TraesCS3B01G237200 chr6A 93.333 45 3 0 5933 5977 523352314 523352270 4.030000e-07 67.6
105 TraesCS3B01G237200 chr6A 93.182 44 3 0 5933 5976 59814804 59814761 1.450000e-06 65.8
106 TraesCS3B01G237200 chr2D 87.129 101 12 1 6014 6114 578600786 578600885 5.100000e-21 113.0
107 TraesCS3B01G237200 chr2D 81.481 135 17 8 5991 6120 538842900 538843031 3.070000e-18 104.0
108 TraesCS3B01G237200 chr2D 76.543 162 30 7 3301 3457 8374520 8374678 1.440000e-11 82.4
109 TraesCS3B01G237200 chr2D 81.905 105 6 6 3212 3304 427953776 427953673 6.690000e-10 76.8
110 TraesCS3B01G237200 chr2D 79.208 101 17 4 3217 3315 98555035 98554937 4.030000e-07 67.6
111 TraesCS3B01G237200 chr2D 96.774 31 1 0 3239 3269 302304691 302304721 1.100000e-02 52.8
112 TraesCS3B01G237200 chr1A 84.821 112 13 4 6008 6118 496629222 496629330 6.600000e-20 110.0
113 TraesCS3B01G237200 chr1A 84.466 103 14 2 6013 6114 308573584 308573685 3.970000e-17 100.0
114 TraesCS3B01G237200 chr1A 81.553 103 15 4 6014 6114 392054408 392054508 1.440000e-11 82.4
115 TraesCS3B01G237200 chr1A 91.489 47 4 0 5933 5979 513129328 513129374 1.450000e-06 65.8
116 TraesCS3B01G237200 chr1A 100.000 31 0 0 5949 5979 531617482 531617512 2.420000e-04 58.4
117 TraesCS3B01G237200 chr1A 78.641 103 9 6 3212 3302 49276355 49276254 8.720000e-04 56.5
118 TraesCS3B01G237200 chr7A 89.855 69 6 1 3303 3371 14375201 14375134 3.090000e-13 87.9
119 TraesCS3B01G237200 chr7A 95.556 45 2 0 5933 5977 69967077 69967033 8.650000e-09 73.1
120 TraesCS3B01G237200 chr7A 95.556 45 2 0 5930 5974 676892780 676892824 8.650000e-09 73.1
121 TraesCS3B01G237200 chrUn 87.671 73 5 3 6017 6087 31222614 31222544 1.440000e-11 82.4
122 TraesCS3B01G237200 chrUn 90.566 53 2 3 6070 6120 12876733 12876682 4.030000e-07 67.6
123 TraesCS3B01G237200 chrUn 90.566 53 2 3 6070 6120 274067754 274067703 4.030000e-07 67.6
124 TraesCS3B01G237200 chrUn 91.489 47 3 1 6068 6114 197787968 197788013 5.210000e-06 63.9
125 TraesCS3B01G237200 chrUn 91.489 47 3 1 6068 6114 230513036 230513081 5.210000e-06 63.9
126 TraesCS3B01G237200 chrUn 88.679 53 5 1 6068 6120 468628800 468628749 5.210000e-06 63.9
127 TraesCS3B01G237200 chrUn 96.875 32 1 0 3206 3237 67353048 67353079 3.000000e-03 54.7


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 TraesCS3B01G237200 chr3B 372234304 372240527 6223 False 5508.0 10386 100.0000 1 6224 2 chr3B.!!$F2 6223
1 TraesCS3B01G237200 chr3B 3135259 3136053 794 True 976.0 976 88.9720 1 790 1 chr3B.!!$R1 789
2 TraesCS3B01G237200 chr3D 278450296 278453896 3600 True 1146.8 3976 96.6146 849 6224 5 chr3D.!!$R6 5375
3 TraesCS3B01G237200 chr3A 360821210 360825228 4018 False 1239.8 3976 95.3294 790 6224 5 chr3A.!!$F2 5434
4 TraesCS3B01G237200 chr7D 1204377 1205526 1149 True 1882.0 1882 96.1810 1798 2949 1 chr7D.!!$R1 1151
5 TraesCS3B01G237200 chr7B 695110964 695112107 1143 True 1827.0 1827 95.4620 1800 2945 1 chr7B.!!$R2 1145
6 TraesCS3B01G237200 chr7B 99219980 99221131 1151 True 1790.0 1790 94.7090 1798 2949 1 chr7B.!!$R1 1151
7 TraesCS3B01G237200 chr6B 717854720 717855873 1153 True 1794.0 1794 94.7190 1796 2949 1 chr6B.!!$R2 1153
8 TraesCS3B01G237200 chr2B 199166086 199167239 1153 True 1794.0 1794 94.7190 1796 2949 1 chr2B.!!$R2 1153
9 TraesCS3B01G237200 chr2B 528830266 528831416 1150 False 1788.0 1788 94.7050 1799 2949 1 chr2B.!!$F1 1150
10 TraesCS3B01G237200 chr2B 477530590 477531383 793 True 970.0 970 88.8470 1 790 1 chr2B.!!$R3 789
11 TraesCS3B01G237200 chr2B 486844591 486845329 738 True 924.0 924 89.2180 1 742 1 chr2B.!!$R4 741
12 TraesCS3B01G237200 chr5B 362954648 362955799 1151 True 1790.0 1790 94.7090 1798 2949 1 chr5B.!!$R3 1151
13 TraesCS3B01G237200 chr5B 63281160 63282309 1149 True 1786.0 1786 94.7000 1800 2949 1 chr5B.!!$R1 1149
14 TraesCS3B01G237200 chr2A 55882916 55884066 1150 True 1788.0 1788 94.7050 1799 2949 1 chr2A.!!$R2 1150
15 TraesCS3B01G237200 chr2A 549954216 549955012 796 False 979.0 979 89.0000 1 791 1 chr2A.!!$F2 790
16 TraesCS3B01G237200 chr5D 69325428 69326223 795 False 1005.0 1005 89.5990 1 790 1 chr5D.!!$F1 789
17 TraesCS3B01G237200 chr1D 16204780 16205577 797 False 974.0 974 88.8610 1 790 1 chr1D.!!$F1 789
18 TraesCS3B01G237200 chr1B 530955520 530956309 789 True 961.0 961 88.7360 1 790 1 chr1B.!!$R1 789
19 TraesCS3B01G237200 chr6D 143084639 143085431 792 False 946.0 946 88.3460 1 790 1 chr6D.!!$F2 789
20 TraesCS3B01G237200 chr6D 306351738 306352477 739 True 920.0 920 89.1130 1 742 1 chr6D.!!$R1 741

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
737 738 0.040425 GCCGCACAAAAACAGACGAT 60.040 50.000 0.00 0.0 0.00 3.73 F
1461 1490 0.035152 TAAGTACTGCCTCCGTCCGA 60.035 55.000 0.00 0.0 0.00 4.55 F
1464 1493 0.037975 GTACTGCCTCCGTCCGAAAA 60.038 55.000 0.00 0.0 0.00 2.29 F
2752 2972 0.251354 GGGATGAGCTGAGCACTTGA 59.749 55.000 7.39 0.0 0.00 3.02 F
3429 3650 2.168106 ACAAAACATTCCAGCAACAGCA 59.832 40.909 0.00 0.0 0.00 4.41 F
5142 5372 1.254026 ACGAGCTGTACAAGGTAGCA 58.746 50.000 6.79 0.0 39.84 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1742 1848 0.113776 ACAGACGGTCCCTCAGGTAA 59.886 55.000 4.14 0.00 0.00 2.85 R
3107 3328 0.454600 GAGGTGACATGCTTGCATGG 59.545 55.000 30.86 17.56 36.91 3.66 R
3283 3504 1.497161 ATACTCCCTCGGTCCCAAAG 58.503 55.000 0.00 0.00 0.00 2.77 R
4428 4654 1.846439 CCCATGACATCAAGTAGGGGT 59.154 52.381 0.00 0.00 34.76 4.95 R
5166 5396 0.994995 CAATGACTGCGGAGAAGTCG 59.005 55.000 12.26 0.00 45.81 4.18 R
6153 6400 2.091278 TCCTCCCTCCGATCACTGTTAT 60.091 50.000 0.00 0.00 0.00 1.89 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)


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

AutoCloner maintained by Alex Coulton.