Multiple sequence alignment - TraesCS6B01G283500

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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 TraesCS6B01G283500 chr6B 100.000 2522 0 0 1 2522 511713109 511710588 0.000000e+00 4658.0
1 TraesCS6B01G283500 chr6B 88.119 202 17 6 81 281 160661002 160660807 1.510000e-57 233.0
2 TraesCS6B01G283500 chr6B 81.017 295 27 18 1 272 158160395 158160683 9.140000e-50 207.0
3 TraesCS6B01G283500 chr6B 91.250 80 6 1 1 79 157913147 157913068 9.540000e-20 108.0
4 TraesCS6B01G283500 chr2B 92.903 2198 123 17 348 2522 441885053 441887240 0.000000e+00 3164.0
5 TraesCS6B01G283500 chr2B 90.183 927 66 7 352 1270 142989455 142988546 0.000000e+00 1184.0
6 TraesCS6B01G283500 chr2B 94.044 319 19 0 2204 2522 534409968 534410286 3.770000e-133 484.0
7 TraesCS6B01G283500 chr4D 92.179 2212 125 27 356 2522 481887026 481889234 0.000000e+00 3083.0
8 TraesCS6B01G283500 chr4D 93.202 1927 105 14 354 2263 119369760 119367843 0.000000e+00 2809.0
9 TraesCS6B01G283500 chr4D 92.950 1915 95 18 353 2239 486565784 486563882 0.000000e+00 2752.0
10 TraesCS6B01G283500 chr4D 79.252 294 28 22 1 271 223628360 223628643 9.270000e-40 174.0
11 TraesCS6B01G283500 chr4D 82.703 185 22 10 91 272 505004385 505004562 3.360000e-34 156.0
12 TraesCS6B01G283500 chr4D 80.435 184 25 10 95 272 272382526 272382348 2.040000e-26 130.0
13 TraesCS6B01G283500 chr4D 78.528 163 24 10 117 272 10756157 10755999 2.070000e-16 97.1
14 TraesCS6B01G283500 chr1D 91.640 2225 124 27 353 2522 430108487 430110704 0.000000e+00 3022.0
15 TraesCS6B01G283500 chr1D 91.712 2220 117 25 355 2522 278102468 278100264 0.000000e+00 3018.0
16 TraesCS6B01G283500 chr1D 90.942 2208 140 24 355 2512 250223367 250225564 0.000000e+00 2915.0
17 TraesCS6B01G283500 chr1D 93.580 1916 101 10 356 2255 303344960 303346869 0.000000e+00 2837.0
18 TraesCS6B01G283500 chr1D 90.299 2206 146 27 354 2522 424634905 424637079 0.000000e+00 2826.0
19 TraesCS6B01G283500 chr1D 90.901 1132 67 9 355 1473 139135263 139134155 0.000000e+00 1487.0
20 TraesCS6B01G283500 chr1D 91.434 1004 64 8 354 1345 446540375 446541368 0.000000e+00 1358.0
21 TraesCS6B01G283500 chr1D 90.661 696 48 8 354 1037 441745115 441744425 0.000000e+00 909.0
22 TraesCS6B01G283500 chr1D 88.889 459 40 5 2075 2522 236097094 236096636 2.830000e-154 555.0
23 TraesCS6B01G283500 chr1D 88.489 278 19 5 357 623 398866615 398866340 8.700000e-85 324.0
24 TraesCS6B01G283500 chr1D 82.990 194 16 13 82 271 475624161 475623981 2.600000e-35 159.0
25 TraesCS6B01G283500 chr1D 82.105 190 22 11 90 272 337212309 337212493 4.350000e-33 152.0
26 TraesCS6B01G283500 chr1D 81.026 195 17 16 92 273 478935222 478935035 1.220000e-28 137.0
27 TraesCS6B01G283500 chr1D 80.435 184 25 10 95 272 462009682 462009860 2.040000e-26 130.0
28 TraesCS6B01G283500 chr1D 81.657 169 18 11 110 274 50989390 50989549 7.320000e-26 128.0
29 TraesCS6B01G283500 chr1D 80.000 195 16 21 82 273 111980057 111980231 3.410000e-24 122.0
30 TraesCS6B01G283500 chr1D 88.298 94 10 1 179 272 66379350 66379442 7.370000e-21 111.0
31 TraesCS6B01G283500 chr1D 86.735 98 7 6 179 273 250703682 250703776 1.230000e-18 104.0
32 TraesCS6B01G283500 chr1D 84.466 103 10 6 176 275 208854896 208854995 2.070000e-16 97.1
33 TraesCS6B01G283500 chr6D 91.434 2218 125 27 354 2522 325418870 325416669 0.000000e+00 2983.0
34 TraesCS6B01G283500 chr6D 90.836 2117 112 33 355 2420 447882347 447880262 0.000000e+00 2760.0
35 TraesCS6B01G283500 chr6D 92.451 1934 113 17 352 2263 347439908 347437986 0.000000e+00 2732.0
36 TraesCS6B01G283500 chr6D 92.901 1296 66 8 353 1627 421840966 421842256 0.000000e+00 1860.0
37 TraesCS6B01G283500 chr6D 92.668 1132 60 13 354 1473 41924608 41923488 0.000000e+00 1609.0
38 TraesCS6B01G283500 chr6D 78.596 285 34 20 4 273 83174870 83174598 2.010000e-36 163.0
39 TraesCS6B01G283500 chr6D 81.579 190 23 9 89 273 412196980 412197162 2.020000e-31 147.0
40 TraesCS6B01G283500 chr6D 79.042 167 20 13 117 274 139575054 139574894 1.600000e-17 100.0
41 TraesCS6B01G283500 chr6D 78.528 163 25 10 117 272 63718777 63718936 5.740000e-17 99.0
42 TraesCS6B01G283500 chr6D 78.916 166 20 11 112 275 147894399 147894247 5.740000e-17 99.0
43 TraesCS6B01G283500 chr2D 90.769 2210 157 19 354 2522 644015512 644013309 0.000000e+00 2907.0
44 TraesCS6B01G283500 chr2D 92.499 1933 94 18 354 2263 500667213 500665309 0.000000e+00 2719.0
45 TraesCS6B01G283500 chr2D 91.505 671 38 6 355 1011 50139065 50138400 0.000000e+00 905.0
46 TraesCS6B01G283500 chr2D 83.889 180 19 9 97 272 26455785 26455958 2.010000e-36 163.0
47 TraesCS6B01G283500 chr2D 85.542 83 4 5 272 354 21532136 21532210 2.080000e-11 80.5
48 TraesCS6B01G283500 chr7D 93.691 1918 94 16 354 2255 85019321 85021227 0.000000e+00 2846.0
49 TraesCS6B01G283500 chr7D 91.297 1195 67 12 353 1533 56936786 56937957 0.000000e+00 1596.0
50 TraesCS6B01G283500 chr7B 93.584 1917 101 9 355 2255 442357638 442359548 0.000000e+00 2839.0
51 TraesCS6B01G283500 chr7B 91.635 526 25 9 2016 2522 8457989 8457464 0.000000e+00 710.0
52 TraesCS6B01G283500 chr7B 87.000 200 15 9 80 277 1880477 1880287 5.460000e-52 215.0
53 TraesCS6B01G283500 chrUn 93.184 1922 100 13 355 2258 105335964 105334056 0.000000e+00 2795.0
54 TraesCS6B01G283500 chrUn 90.511 822 55 10 351 1160 108802910 108803720 0.000000e+00 1064.0
55 TraesCS6B01G283500 chrUn 80.928 194 19 16 82 272 32325533 32325355 1.220000e-28 137.0
56 TraesCS6B01G283500 chrUn 86.139 101 9 5 179 275 410432203 410432302 1.230000e-18 104.0
57 TraesCS6B01G283500 chr5B 89.428 2204 184 32 356 2522 615401475 615399284 0.000000e+00 2734.0
58 TraesCS6B01G283500 chr5B 89.955 2011 155 18 356 2325 635767314 635765310 0.000000e+00 2551.0
59 TraesCS6B01G283500 chr5B 89.060 521 42 7 353 871 128209013 128208506 1.270000e-177 632.0
60 TraesCS6B01G283500 chr5B 87.766 188 15 6 85 272 158732819 158732998 1.970000e-51 213.0
61 TraesCS6B01G283500 chr5B 89.634 164 10 5 108 271 105756185 105756341 4.250000e-48 202.0
62 TraesCS6B01G283500 chr5B 87.500 168 15 6 106 273 106354658 106354497 3.310000e-44 189.0
63 TraesCS6B01G283500 chr3D 93.763 1443 70 10 353 1781 576579536 576578100 0.000000e+00 2148.0
64 TraesCS6B01G283500 chr3D 92.581 1240 67 8 341 1567 580656345 580657572 0.000000e+00 1757.0
65 TraesCS6B01G283500 chr3D 89.950 398 25 9 354 740 515671975 515672368 1.350000e-137 499.0
66 TraesCS6B01G283500 chr3D 93.691 317 20 0 2206 2522 576576212 576575896 2.270000e-130 475.0
67 TraesCS6B01G283500 chr3D 81.481 189 25 9 89 274 2253483 2253302 2.020000e-31 147.0
68 TraesCS6B01G283500 chr3D 80.874 183 24 5 92 273 231161742 231161570 1.570000e-27 134.0
69 TraesCS6B01G283500 chr5A 89.736 341 20 8 353 682 655728954 655729290 3.000000e-114 422.0
70 TraesCS6B01G283500 chr5A 88.563 341 24 8 353 682 655800047 655800383 1.410000e-107 399.0
71 TraesCS6B01G283500 chr5A 87.683 341 26 9 353 682 655646392 655646727 1.420000e-102 383.0
72 TraesCS6B01G283500 chr5A 82.734 278 34 11 1 272 404664799 404665068 4.190000e-58 235.0
73 TraesCS6B01G283500 chr5A 84.043 188 20 9 93 273 338409852 338410036 3.340000e-39 172.0
74 TraesCS6B01G283500 chr5A 83.516 182 20 9 95 271 624753090 624753266 7.220000e-36 161.0
75 TraesCS6B01G283500 chr4B 90.391 281 25 2 353 633 554219909 554220187 3.960000e-98 368.0
76 TraesCS6B01G283500 chr4B 87.329 292 12 10 1 273 436261598 436261313 6.770000e-81 311.0
77 TraesCS6B01G283500 chr4B 83.158 190 23 7 90 272 242718651 242718838 5.580000e-37 165.0
78 TraesCS6B01G283500 chr3B 85.811 296 14 11 1 272 741431653 741431944 3.170000e-74 289.0
79 TraesCS6B01G283500 chr3B 90.674 193 11 3 80 271 16836340 16836154 1.500000e-62 250.0
80 TraesCS6B01G283500 chr3B 89.175 194 15 5 80 273 539563880 539563693 1.170000e-58 237.0
81 TraesCS6B01G283500 chr3B 82.432 296 23 15 1 273 466660491 466660780 5.430000e-57 231.0
82 TraesCS6B01G283500 chr3B 89.071 183 13 5 92 272 254847583 254847760 1.170000e-53 220.0
83 TraesCS6B01G283500 chr3B 95.312 64 3 0 1 64 16836687 16836624 4.440000e-18 102.0
84 TraesCS6B01G283500 chr1B 93.000 200 7 3 80 277 573413411 573413217 4.110000e-73 285.0
85 TraesCS6B01G283500 chr1B 84.512 297 18 10 1 273 7335756 7336048 4.140000e-68 268.0
86 TraesCS6B01G283500 chr1B 83.217 286 30 16 1 272 161379874 161379593 1.940000e-61 246.0
87 TraesCS6B01G283500 chr1B 81.145 297 26 16 1 273 130105834 130106124 7.070000e-51 211.0
88 TraesCS6B01G283500 chr1B 87.135 171 16 5 106 273 6578746 6578913 3.310000e-44 189.0
89 TraesCS6B01G283500 chr1B 87.059 170 16 5 105 271 562470704 562470538 1.190000e-43 187.0
90 TraesCS6B01G283500 chr4A 86.705 173 13 7 105 271 651086437 651086605 1.540000e-42 183.0
91 TraesCS6B01G283500 chr4A 83.770 191 22 9 86 273 512026073 512026257 3.340000e-39 172.0
92 TraesCS6B01G283500 chr4A 100.000 27 0 0 1 27 436436890 436436916 1.600000e-02 51.0
93 TraesCS6B01G283500 chr1A 79.667 300 25 21 4 272 513590144 513589850 1.540000e-42 183.0
94 TraesCS6B01G283500 chr1A 83.436 163 13 12 112 271 492136526 492136677 3.380000e-29 139.0
95 TraesCS6B01G283500 chr1A 83.226 155 17 8 118 271 269576126 269575980 1.570000e-27 134.0
96 TraesCS6B01G283500 chr6A 79.522 293 29 19 1 268 457611361 457611075 1.990000e-41 180.0
97 TraesCS6B01G283500 chr6A 82.812 192 23 9 95 281 609673185 609673371 2.010000e-36 163.0
98 TraesCS6B01G283500 chr6A 77.517 298 36 20 4 275 161148984 161148692 1.560000e-32 150.0
99 TraesCS6B01G283500 chr6A 97.674 43 1 0 1 43 102139846 102139804 9.680000e-10 75.0
100 TraesCS6B01G283500 chr5D 86.585 164 14 8 112 271 459140553 459140712 9.270000e-40 174.0
101 TraesCS6B01G283500 chr5D 85.629 167 13 10 117 281 110346009 110346166 5.580000e-37 165.0
102 TraesCS6B01G283500 chr5D 82.162 185 20 12 95 272 484783402 484783580 2.020000e-31 147.0


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 TraesCS6B01G283500 chr6B 511710588 511713109 2521 True 4658.0 4658 100.000 1 2522 1 chr6B.!!$R3 2521
1 TraesCS6B01G283500 chr2B 441885053 441887240 2187 False 3164.0 3164 92.903 348 2522 1 chr2B.!!$F1 2174
2 TraesCS6B01G283500 chr2B 142988546 142989455 909 True 1184.0 1184 90.183 352 1270 1 chr2B.!!$R1 918
3 TraesCS6B01G283500 chr4D 481887026 481889234 2208 False 3083.0 3083 92.179 356 2522 1 chr4D.!!$F2 2166
4 TraesCS6B01G283500 chr4D 119367843 119369760 1917 True 2809.0 2809 93.202 354 2263 1 chr4D.!!$R2 1909
5 TraesCS6B01G283500 chr4D 486563882 486565784 1902 True 2752.0 2752 92.950 353 2239 1 chr4D.!!$R4 1886
6 TraesCS6B01G283500 chr1D 430108487 430110704 2217 False 3022.0 3022 91.640 353 2522 1 chr1D.!!$F10 2169
7 TraesCS6B01G283500 chr1D 278100264 278102468 2204 True 3018.0 3018 91.712 355 2522 1 chr1D.!!$R3 2167
8 TraesCS6B01G283500 chr1D 250223367 250225564 2197 False 2915.0 2915 90.942 355 2512 1 chr1D.!!$F5 2157
9 TraesCS6B01G283500 chr1D 303344960 303346869 1909 False 2837.0 2837 93.580 356 2255 1 chr1D.!!$F7 1899
10 TraesCS6B01G283500 chr1D 424634905 424637079 2174 False 2826.0 2826 90.299 354 2522 1 chr1D.!!$F9 2168
11 TraesCS6B01G283500 chr1D 139134155 139135263 1108 True 1487.0 1487 90.901 355 1473 1 chr1D.!!$R1 1118
12 TraesCS6B01G283500 chr1D 446540375 446541368 993 False 1358.0 1358 91.434 354 1345 1 chr1D.!!$F11 991
13 TraesCS6B01G283500 chr1D 441744425 441745115 690 True 909.0 909 90.661 354 1037 1 chr1D.!!$R5 683
14 TraesCS6B01G283500 chr6D 325416669 325418870 2201 True 2983.0 2983 91.434 354 2522 1 chr6D.!!$R5 2168
15 TraesCS6B01G283500 chr6D 447880262 447882347 2085 True 2760.0 2760 90.836 355 2420 1 chr6D.!!$R7 2065
16 TraesCS6B01G283500 chr6D 347437986 347439908 1922 True 2732.0 2732 92.451 352 2263 1 chr6D.!!$R6 1911
17 TraesCS6B01G283500 chr6D 421840966 421842256 1290 False 1860.0 1860 92.901 353 1627 1 chr6D.!!$F3 1274
18 TraesCS6B01G283500 chr6D 41923488 41924608 1120 True 1609.0 1609 92.668 354 1473 1 chr6D.!!$R1 1119
19 TraesCS6B01G283500 chr2D 644013309 644015512 2203 True 2907.0 2907 90.769 354 2522 1 chr2D.!!$R3 2168
20 TraesCS6B01G283500 chr2D 500665309 500667213 1904 True 2719.0 2719 92.499 354 2263 1 chr2D.!!$R2 1909
21 TraesCS6B01G283500 chr2D 50138400 50139065 665 True 905.0 905 91.505 355 1011 1 chr2D.!!$R1 656
22 TraesCS6B01G283500 chr7D 85019321 85021227 1906 False 2846.0 2846 93.691 354 2255 1 chr7D.!!$F2 1901
23 TraesCS6B01G283500 chr7D 56936786 56937957 1171 False 1596.0 1596 91.297 353 1533 1 chr7D.!!$F1 1180
24 TraesCS6B01G283500 chr7B 442357638 442359548 1910 False 2839.0 2839 93.584 355 2255 1 chr7B.!!$F1 1900
25 TraesCS6B01G283500 chr7B 8457464 8457989 525 True 710.0 710 91.635 2016 2522 1 chr7B.!!$R2 506
26 TraesCS6B01G283500 chrUn 105334056 105335964 1908 True 2795.0 2795 93.184 355 2258 1 chrUn.!!$R2 1903
27 TraesCS6B01G283500 chrUn 108802910 108803720 810 False 1064.0 1064 90.511 351 1160 1 chrUn.!!$F1 809
28 TraesCS6B01G283500 chr5B 615399284 615401475 2191 True 2734.0 2734 89.428 356 2522 1 chr5B.!!$R3 2166
29 TraesCS6B01G283500 chr5B 635765310 635767314 2004 True 2551.0 2551 89.955 356 2325 1 chr5B.!!$R4 1969
30 TraesCS6B01G283500 chr5B 128208506 128209013 507 True 632.0 632 89.060 353 871 1 chr5B.!!$R2 518
31 TraesCS6B01G283500 chr3D 580656345 580657572 1227 False 1757.0 1757 92.581 341 1567 1 chr3D.!!$F2 1226
32 TraesCS6B01G283500 chr3D 576575896 576579536 3640 True 1311.5 2148 93.727 353 2522 2 chr3D.!!$R3 2169


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
198 199 0.109964 GTGTTTGTGCGTGTGTGTGT 60.11 50.0 0.0 0.0 0.0 3.72 F
200 201 0.109964 GTTTGTGCGTGTGTGTGTGT 60.11 50.0 0.0 0.0 0.0 3.72 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1259 1350 1.004745 ACCTCTGGTTATGGCCAACAG 59.995 52.381 10.96 16.16 38.18 3.16 R
2090 3615 1.350684 TGGCCAGAGCTAACAACATCA 59.649 47.619 0.00 0.00 39.73 3.07 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)



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AutoCloner maintained by Alex Coulton.