Multiple sequence alignment - TraesCS1B01G298400

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 TraesCS1B01G298400 chr1B 100.000 7251 0 0 1 7251 519618560 519625810 0.000000e+00 13391.0
1 TraesCS1B01G298400 chr1B 94.510 2623 79 13 1952 4517 518910057 518912671 0.000000e+00 3986.0
2 TraesCS1B01G298400 chr1B 96.460 791 16 4 4501 5290 518912838 518913617 0.000000e+00 1295.0
3 TraesCS1B01G298400 chr1B 97.841 602 13 0 1357 1958 518909305 518909906 0.000000e+00 1040.0
4 TraesCS1B01G298400 chr1B 96.364 550 15 3 5297 5844 518913723 518914269 0.000000e+00 900.0
5 TraesCS1B01G298400 chr1B 95.913 416 16 1 5844 6259 518914315 518914729 0.000000e+00 673.0
6 TraesCS1B01G298400 chr1B 89.863 365 37 0 1 365 518813097 518813461 3.060000e-128 470.0
7 TraesCS1B01G298400 chr1B 95.708 233 10 0 6031 6263 520100382 520100614 6.870000e-100 375.0
8 TraesCS1B01G298400 chr1B 95.755 212 9 0 1339 1550 519619835 519620046 6.970000e-90 342.0
9 TraesCS1B01G298400 chr1B 95.755 212 9 0 1276 1487 519619898 519620109 6.970000e-90 342.0
10 TraesCS1B01G298400 chr1B 94.845 194 10 0 1294 1487 518909305 518909498 3.290000e-78 303.0
11 TraesCS1B01G298400 chr1B 91.579 190 11 2 5844 6033 520100075 520100259 2.600000e-64 257.0
12 TraesCS1B01G298400 chr1B 96.644 149 5 0 1402 1550 519619835 519619983 1.560000e-61 248.0
13 TraesCS1B01G298400 chr1B 96.644 149 5 0 1276 1424 519619961 519620109 1.560000e-61 248.0
14 TraesCS1B01G298400 chr1B 95.973 149 6 0 1276 1424 518909350 518909498 7.270000e-60 243.0
15 TraesCS1B01G298400 chr1B 81.994 311 18 20 893 1166 518908669 518908978 5.660000e-56 230.0
16 TraesCS1B01G298400 chr1B 93.893 131 8 0 1420 1550 518909305 518909435 1.600000e-46 198.0
17 TraesCS1B01G298400 chr1B 94.958 119 5 1 5726 5844 520099847 520099964 1.240000e-42 185.0
18 TraesCS1B01G298400 chr1B 97.674 86 2 0 1465 1550 519619835 519619920 1.630000e-31 148.0
19 TraesCS1B01G298400 chr1B 97.674 86 2 0 1276 1361 519620024 519620109 1.630000e-31 148.0
20 TraesCS1B01G298400 chr1B 96.512 86 3 0 1276 1361 518909413 518909498 7.580000e-30 143.0
21 TraesCS1B01G298400 chr1B 94.118 85 5 0 363 447 440443756 440443840 5.900000e-26 130.0
22 TraesCS1B01G298400 chr1B 91.954 87 7 0 361 447 91644893 91644979 9.880000e-24 122.0
23 TraesCS1B01G298400 chr1B 91.954 87 7 0 361 447 407828956 407829042 9.880000e-24 122.0
24 TraesCS1B01G298400 chr1D 93.303 2613 92 24 2196 4750 386471440 386474027 0.000000e+00 3779.0
25 TraesCS1B01G298400 chr1D 95.982 1095 30 8 4752 5844 386474189 386475271 0.000000e+00 1766.0
26 TraesCS1B01G298400 chr1D 92.637 421 21 4 5844 6263 386475383 386475794 1.350000e-166 597.0
27 TraesCS1B01G298400 chr1D 91.594 345 17 8 1565 1901 386465880 386466220 3.960000e-127 466.0
28 TraesCS1B01G298400 chr1D 89.879 247 24 1 119 365 386464431 386464676 4.220000e-82 316.0
29 TraesCS1B01G298400 chr1D 86.667 210 18 8 438 639 21814066 21814273 2.630000e-54 224.0
30 TraesCS1B01G298400 chr1D 86.667 210 15 11 438 639 262520355 262520151 3.410000e-53 220.0
31 TraesCS1B01G298400 chr1D 85.833 120 11 4 2478 2595 386472228 386472343 9.880000e-24 122.0
32 TraesCS1B01G298400 chr1D 90.566 53 5 0 1898 1950 386471322 386471374 3.630000e-08 71.3
33 TraesCS1B01G298400 chr7B 90.892 1603 75 30 3588 5153 514515238 514513670 0.000000e+00 2085.0
34 TraesCS1B01G298400 chr7B 92.380 1168 59 14 2445 3586 514516663 514515500 0.000000e+00 1637.0
35 TraesCS1B01G298400 chr7B 90.413 1210 70 11 1953 3149 514517996 514516820 0.000000e+00 1550.0
36 TraesCS1B01G298400 chr7B 94.648 654 31 3 5194 5844 514512994 514512342 0.000000e+00 1011.0
37 TraesCS1B01G298400 chr7B 87.621 622 45 14 5844 6460 514512230 514511636 0.000000e+00 693.0
38 TraesCS1B01G298400 chr7B 92.053 302 17 6 1655 1949 514518459 514518158 1.130000e-112 418.0
39 TraesCS1B01G298400 chr7B 88.333 120 11 3 2478 2595 514516111 514515993 2.730000e-29 141.0
40 TraesCS1B01G298400 chr7B 85.833 120 12 5 2478 2595 514516974 514516858 9.880000e-24 122.0
41 TraesCS1B01G298400 chr7B 88.660 97 6 4 1565 1656 514518691 514518595 5.950000e-21 113.0
42 TraesCS1B01G298400 chr1A 91.898 1444 49 12 2708 4103 486399850 486401273 0.000000e+00 1956.0
43 TraesCS1B01G298400 chr1A 96.390 831 20 3 4913 5743 486403284 486404104 0.000000e+00 1360.0
44 TraesCS1B01G298400 chr1A 94.471 832 36 4 4102 4926 486402223 486403051 0.000000e+00 1273.0
45 TraesCS1B01G298400 chr1A 95.122 533 23 3 2187 2716 486389185 486389717 0.000000e+00 837.0
46 TraesCS1B01G298400 chr1A 91.905 420 32 2 5844 6263 486411106 486411523 2.910000e-163 586.0
47 TraesCS1B01G298400 chr1A 89.344 366 37 2 1 365 486386788 486387152 6.630000e-125 459.0
48 TraesCS1B01G298400 chr1A 90.400 250 8 5 7003 7251 531372254 531372020 1.520000e-81 315.0
49 TraesCS1B01G298400 chr1A 93.137 204 14 0 1949 2152 486388974 486389177 4.250000e-77 300.0
50 TraesCS1B01G298400 chr1A 98.261 115 2 0 5730 5844 486410880 486410994 1.230000e-47 202.0
51 TraesCS1B01G298400 chr1A 92.361 144 7 1 6317 6460 486411603 486411742 1.230000e-47 202.0
52 TraesCS1B01G298400 chr1A 89.116 147 10 5 827 969 486388661 486388805 2.080000e-40 178.0
53 TraesCS1B01G298400 chr1A 87.500 120 9 4 2478 2595 486400136 486400251 4.560000e-27 134.0
54 TraesCS1B01G298400 chr1A 87.500 64 5 2 6272 6335 372550073 372550013 3.630000e-08 71.3
55 TraesCS1B01G298400 chr7A 92.857 574 24 6 6679 7251 296574316 296573759 0.000000e+00 817.0
56 TraesCS1B01G298400 chr7A 92.135 356 12 3 6897 7251 299252411 299252751 8.450000e-134 488.0
57 TraesCS1B01G298400 chr7A 88.596 228 12 1 6465 6678 296574604 296574377 1.550000e-66 265.0
58 TraesCS1B01G298400 chr2A 90.777 206 12 6 440 639 244909758 244909554 1.200000e-67 268.0
59 TraesCS1B01G298400 chr2A 89.202 213 14 6 435 639 593720880 593720669 2.600000e-64 257.0
60 TraesCS1B01G298400 chr2A 89.372 207 16 5 438 639 244828387 244828592 9.340000e-64 255.0
61 TraesCS1B01G298400 chr2A 88.942 208 16 5 438 639 244908341 244908547 4.340000e-62 250.0
62 TraesCS1B01G298400 chr4D 85.577 208 23 6 438 639 416131218 416131012 2.050000e-50 211.0
63 TraesCS1B01G298400 chr4D 85.577 208 23 6 438 639 421204813 421204607 2.050000e-50 211.0
64 TraesCS1B01G298400 chr4D 91.954 87 6 1 361 447 319063883 319063968 3.550000e-23 121.0
65 TraesCS1B01G298400 chr6B 85.096 208 24 6 438 639 201209573 201209779 9.540000e-49 206.0
66 TraesCS1B01G298400 chr2D 87.037 162 12 3 2593 2749 554694339 554694496 2.690000e-39 174.0
67 TraesCS1B01G298400 chr7D 92.941 85 6 0 363 447 178507094 178507178 2.750000e-24 124.0
68 TraesCS1B01G298400 chr4B 90.426 94 9 0 354 447 46010119 46010212 2.750000e-24 124.0
69 TraesCS1B01G298400 chr4B 95.833 48 1 1 6269 6315 49514846 49514893 7.800000e-10 76.8
70 TraesCS1B01G298400 chr3D 92.857 84 6 0 364 447 476397729 476397646 9.880000e-24 122.0
71 TraesCS1B01G298400 chr3D 92.857 84 6 0 364 447 476404747 476404664 9.880000e-24 122.0
72 TraesCS1B01G298400 chr3D 97.778 45 1 0 6272 6316 530356817 530356861 2.170000e-10 78.7
73 TraesCS1B01G298400 chr3D 90.741 54 3 2 6272 6324 208707531 208707479 3.630000e-08 71.3
74 TraesCS1B01G298400 chr6D 92.771 83 6 0 365 447 47326771 47326689 3.550000e-23 121.0
75 TraesCS1B01G298400 chr6D 100.000 42 0 0 6272 6313 249445838 249445797 2.170000e-10 78.7
76 TraesCS1B01G298400 chr2B 89.062 64 7 0 6274 6337 21651938 21651875 6.030000e-11 80.5
77 TraesCS1B01G298400 chr5D 92.453 53 2 2 6272 6323 339105104 339105053 2.810000e-09 75.0
78 TraesCS1B01G298400 chr3B 94.000 50 1 2 6265 6312 611171535 611171486 2.810000e-09 75.0
79 TraesCS1B01G298400 chr5A 87.097 62 3 5 6272 6330 32129195 32129254 1.690000e-06 65.8


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 TraesCS1B01G298400 chr1B 519618560 519625810 7250 False 13391.000000 13391 100.000000 1 7251 1 chr1B.!!$F5 7250
1 TraesCS1B01G298400 chr1B 518908669 518914729 6060 False 901.100000 3986 94.430500 893 6259 10 chr1B.!!$F6 5366
2 TraesCS1B01G298400 chr1B 520099847 520100614 767 False 272.333333 375 94.081667 5726 6263 3 chr1B.!!$F8 537
3 TraesCS1B01G298400 chr1D 386471322 386475794 4472 False 1267.060000 3779 91.664200 1898 6263 5 chr1D.!!$F3 4365
4 TraesCS1B01G298400 chr1D 386464431 386466220 1789 False 391.000000 466 90.736500 119 1901 2 chr1D.!!$F2 1782
5 TraesCS1B01G298400 chr7B 514511636 514518691 7055 True 863.333333 2085 90.092556 1565 6460 9 chr7B.!!$R1 4895
6 TraesCS1B01G298400 chr1A 486399850 486404104 4254 False 1180.750000 1956 92.564750 2478 5743 4 chr1A.!!$F2 3265
7 TraesCS1B01G298400 chr1A 486386788 486389717 2929 False 443.500000 837 91.679750 1 2716 4 chr1A.!!$F1 2715
8 TraesCS1B01G298400 chr1A 486410880 486411742 862 False 330.000000 586 94.175667 5730 6460 3 chr1A.!!$F3 730
9 TraesCS1B01G298400 chr7A 296573759 296574604 845 True 541.000000 817 90.726500 6465 7251 2 chr7A.!!$R1 786


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
398 400 0.035739 TGTGCCCTTAACTCGAACCC 59.964 55.000 0.00 0.0 0.00 4.11 F
1099 2634 0.032403 ATGACCGTCGTTGTTTCCGA 59.968 50.000 0.00 0.0 0.00 4.55 F
1303 2863 0.104777 TGATGCCTGCCTCCTCCTAT 60.105 55.000 0.00 0.0 0.00 2.57 F
1304 2864 0.324285 GATGCCTGCCTCCTCCTATG 59.676 60.000 0.00 0.0 0.00 2.23 F
2060 4107 0.807667 GACATGGTAGAGCTGCGGTG 60.808 60.000 0.00 0.0 0.00 4.94 F
2109 4156 2.365068 CGTGTGTTGACTCGCTCCG 61.365 63.158 0.00 0.0 32.82 4.63 F
2529 4581 2.765699 GAGAGGGAAAGAGAGACAGCAT 59.234 50.000 0.00 0.0 0.00 3.79 F
3788 6997 0.111253 AGCTTTTAGCCTGCCACACT 59.889 50.000 0.00 0.0 43.77 3.55 F
4590 8968 0.176910 TGGACGGCGATTATGAAGCA 59.823 50.000 16.62 0.0 0.00 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1284 2844 0.104777 ATAGGAGGAGGCAGGCATCA 60.105 55.000 8.27 0.00 0.00 3.07 R
1987 4034 0.956902 ATCGCTTGCTGCACATGACA 60.957 50.000 0.00 0.00 43.06 3.58 R
2783 4844 2.002586 TGAGAAATCTACAGCTTGCGC 58.997 47.619 0.00 0.00 0.00 6.09 R
2871 4933 3.379372 GCGCCGTATTCTCAGGGTATATA 59.621 47.826 0.00 0.00 0.00 0.86 R
3413 6362 1.444933 ATCACAAGACCAGTGGGGAA 58.555 50.000 15.21 0.00 41.15 3.97 R
3415 6364 3.433306 TTTATCACAAGACCAGTGGGG 57.567 47.619 15.21 2.42 44.81 4.96 R
4247 8436 0.959372 CTGGAGACCCGTCGTACAGT 60.959 60.000 0.00 0.00 34.29 3.55 R
5290 10715 0.320334 TGGCGCTCGAAACTGAATGA 60.320 50.000 7.64 0.00 0.00 2.57 R
6259 12096 0.108329 AGAAATGGTGCCCTACGTCG 60.108 55.000 0.00 0.00 0.00 5.12 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.