Multiple sequence alignment - TraesCS5A01G387900

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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 TraesCS5A01G387900 chr5A 100.000 5773 0 0 1 5773 584715273 584721045 0.000000e+00 10661.0
1 TraesCS5A01G387900 chr5A 82.989 629 100 6 1890 2513 698646637 698646011 3.910000e-156 562.0
2 TraesCS5A01G387900 chr5A 89.944 179 13 2 2662 2835 469102672 469102494 5.820000e-55 226.0
3 TraesCS5A01G387900 chr5A 90.476 168 14 1 2662 2829 382961945 382961780 2.710000e-53 220.0
4 TraesCS5A01G387900 chr5A 93.694 111 7 0 5269 5379 260334158 260334268 3.580000e-37 167.0
5 TraesCS5A01G387900 chr5A 93.636 110 7 0 5268 5377 688927655 688927546 1.290000e-36 165.0
6 TraesCS5A01G387900 chr5A 91.379 116 10 0 5268 5383 606350783 606350668 5.990000e-35 159.0
7 TraesCS5A01G387900 chr5A 86.047 129 16 2 4971 5098 584859279 584859406 2.810000e-28 137.0
8 TraesCS5A01G387900 chr5A 91.358 81 6 1 392 472 227926528 227926449 6.120000e-20 110.0
9 TraesCS5A01G387900 chr5B 91.758 1650 81 23 3512 5142 571483938 571485551 0.000000e+00 2242.0
10 TraesCS5A01G387900 chr5B 84.778 1465 148 30 3709 5142 571490668 571492088 0.000000e+00 1400.0
11 TraesCS5A01G387900 chr5B 93.673 727 41 2 1887 2609 571480879 571481604 0.000000e+00 1083.0
12 TraesCS5A01G387900 chr5B 91.195 795 47 12 1117 1889 571480060 571480853 0.000000e+00 1059.0
13 TraesCS5A01G387900 chr5B 81.172 1041 117 29 3708 4722 571508829 571509816 0.000000e+00 763.0
14 TraesCS5A01G387900 chr5B 91.536 319 20 5 3142 3455 387152098 387152414 3.200000e-117 433.0
15 TraesCS5A01G387900 chr5B 85.610 410 48 8 4738 5144 571510083 571510484 2.490000e-113 420.0
16 TraesCS5A01G387900 chr5B 86.335 161 14 3 1 161 571476417 571476569 9.950000e-38 169.0
17 TraesCS5A01G387900 chr5B 84.000 125 14 5 2969 3093 571490285 571490403 1.310000e-21 115.0
18 TraesCS5A01G387900 chr5B 93.333 75 5 0 392 466 460658924 460658998 1.700000e-20 111.0
19 TraesCS5A01G387900 chr5D 83.122 1499 180 35 3671 5135 464395246 464396705 0.000000e+00 1299.0
20 TraesCS5A01G387900 chr5D 93.676 759 41 2 1887 2645 464325574 464326325 0.000000e+00 1129.0
21 TraesCS5A01G387900 chr5D 92.201 795 39 12 1117 1889 464324755 464325548 0.000000e+00 1103.0
22 TraesCS5A01G387900 chr5D 90.520 538 39 7 4611 5142 464347634 464348165 0.000000e+00 701.0
23 TraesCS5A01G387900 chr5D 90.614 277 15 5 5508 5773 464403110 464403386 1.980000e-94 357.0
24 TraesCS5A01G387900 chr5D 84.639 319 24 14 2829 3144 464326333 464326629 1.570000e-75 294.0
25 TraesCS5A01G387900 chr5D 87.912 182 18 3 2655 2835 104489784 104489962 1.630000e-50 211.0
26 TraesCS5A01G387900 chr5D 89.032 155 6 1 5128 5271 464401561 464401715 1.280000e-41 182.0
27 TraesCS5A01G387900 chr5D 92.913 127 5 2 5374 5498 464401712 464401836 1.280000e-41 182.0
28 TraesCS5A01G387900 chr5D 87.770 139 11 4 2969 3107 464394941 464395073 2.150000e-34 158.0
29 TraesCS5A01G387900 chr5D 87.805 82 10 0 391 472 268343147 268343066 4.760000e-16 97.1
30 TraesCS5A01G387900 chr2A 78.412 1436 245 45 1119 2509 30222935 30224350 0.000000e+00 874.0
31 TraesCS5A01G387900 chr2A 90.698 172 15 1 2662 2833 59330929 59331099 1.620000e-55 228.0
32 TraesCS5A01G387900 chr2A 93.519 108 7 0 5270 5377 650256593 650256700 1.660000e-35 161.0
33 TraesCS5A01G387900 chr2A 91.304 115 10 0 5270 5384 527504725 527504611 2.150000e-34 158.0
34 TraesCS5A01G387900 chr2A 89.431 123 10 3 5262 5384 102329260 102329379 1.000000e-32 152.0
35 TraesCS5A01G387900 chr2D 77.817 1429 255 42 1117 2509 28407749 28409151 0.000000e+00 826.0
36 TraesCS5A01G387900 chr2D 92.727 110 8 0 5268 5377 637342564 637342673 5.990000e-35 159.0
37 TraesCS5A01G387900 chr2B 77.645 1427 261 37 1117 2509 44942775 44941373 0.000000e+00 815.0
38 TraesCS5A01G387900 chr2B 77.622 1430 256 44 1117 2509 45608344 45609746 0.000000e+00 809.0
39 TraesCS5A01G387900 chr2B 77.289 1431 263 38 1117 2509 45642133 45640727 0.000000e+00 785.0
40 TraesCS5A01G387900 chr2B 74.460 787 166 20 1755 2511 18320291 18319510 2.020000e-79 307.0
41 TraesCS5A01G387900 chr2B 73.418 790 169 27 1755 2511 18386670 18385889 2.060000e-64 257.0
42 TraesCS5A01G387900 chr2B 92.241 116 7 2 5270 5383 621062527 621062642 4.630000e-36 163.0
43 TraesCS5A01G387900 chr4D 83.201 631 98 8 1890 2515 509838252 509837625 6.490000e-159 571.0
44 TraesCS5A01G387900 chr4D 82.553 470 70 8 1125 1591 509839016 509838556 2.510000e-108 403.0
45 TraesCS5A01G387900 chr4B 82.965 634 94 13 1890 2515 656892479 656893106 1.400000e-155 560.0
46 TraesCS5A01G387900 chr4B 78.249 754 113 31 1122 1865 656891695 656892407 2.470000e-118 436.0
47 TraesCS5A01G387900 chr7D 93.082 318 16 4 3142 3454 115140773 115141089 1.470000e-125 460.0
48 TraesCS5A01G387900 chr7D 91.515 165 13 1 2662 2826 576654104 576654267 5.820000e-55 226.0
49 TraesCS5A01G387900 chr3D 92.767 318 17 4 3142 3454 601009702 601010018 6.820000e-124 455.0
50 TraesCS5A01G387900 chr3D 92.453 318 18 4 3142 3454 601035507 601035823 3.170000e-122 449.0
51 TraesCS5A01G387900 chr3D 91.824 318 20 4 3142 3454 601018647 601018963 6.870000e-119 438.0
52 TraesCS5A01G387900 chr3D 88.235 85 10 0 388 472 107672338 107672254 1.020000e-17 102.0
53 TraesCS5A01G387900 chr3A 92.523 321 17 5 3142 3457 181668816 181669134 2.450000e-123 453.0
54 TraesCS5A01G387900 chr3A 91.824 318 20 4 3142 3454 731579344 731579028 6.870000e-119 438.0
55 TraesCS5A01G387900 chr3A 91.277 321 22 4 3142 3457 553946027 553946346 3.200000e-117 433.0
56 TraesCS5A01G387900 chr3B 91.824 318 20 4 3142 3454 808278282 808278598 6.870000e-119 438.0
57 TraesCS5A01G387900 chr3B 91.667 72 6 0 388 459 127932633 127932704 3.680000e-17 100.0
58 TraesCS5A01G387900 chr1B 72.831 1406 299 58 1121 2482 557412403 557411037 2.510000e-108 403.0
59 TraesCS5A01G387900 chr6A 91.954 174 13 1 2662 2835 64662417 64662245 5.780000e-60 243.0
60 TraesCS5A01G387900 chr6A 87.582 153 18 1 9 161 251565851 251565700 5.950000e-40 176.0
61 TraesCS5A01G387900 chr6A 87.179 78 9 1 881 957 108851916 108851839 2.870000e-13 87.9
62 TraesCS5A01G387900 chr6A 84.416 77 11 1 882 957 251565274 251565198 2.230000e-09 75.0
63 TraesCS5A01G387900 chr1D 75.941 478 98 13 1121 1588 413234463 413233993 4.500000e-56 230.0
64 TraesCS5A01G387900 chr1D 90.419 167 15 1 2662 2828 42271754 42271589 9.740000e-53 219.0
65 TraesCS5A01G387900 chr1D 80.791 177 26 6 4690 4865 243461882 243461713 1.310000e-26 132.0
66 TraesCS5A01G387900 chr1D 90.361 83 7 1 390 472 205490289 205490370 2.200000e-19 108.0
67 TraesCS5A01G387900 chrUn 75.770 487 98 16 1117 1587 12467689 12468171 1.620000e-55 228.0
68 TraesCS5A01G387900 chrUn 86.747 83 11 0 390 472 79505465 79505383 6.160000e-15 93.5
69 TraesCS5A01G387900 chr7A 89.560 182 14 3 2662 2838 543447842 543447661 5.820000e-55 226.0
70 TraesCS5A01G387900 chr7A 90.058 171 15 2 2668 2836 84295677 84295847 2.710000e-53 220.0
71 TraesCS5A01G387900 chr7A 93.519 108 7 0 5270 5377 188030228 188030335 1.660000e-35 161.0
72 TraesCS5A01G387900 chr7B 91.765 85 7 0 388 472 511462090 511462174 1.020000e-22 119.0
73 TraesCS5A01G387900 chr1A 90.361 83 7 1 391 472 463825451 463825369 2.200000e-19 108.0


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 TraesCS5A01G387900 chr5A 584715273 584721045 5772 False 10661.000000 10661 100.00000 1 5773 1 chr5A.!!$F2 5772
1 TraesCS5A01G387900 chr5A 698646011 698646637 626 True 562.000000 562 82.98900 1890 2513 1 chr5A.!!$R6 623
2 TraesCS5A01G387900 chr5B 571476417 571485551 9134 False 1138.250000 2242 90.74025 1 5142 4 chr5B.!!$F3 5141
3 TraesCS5A01G387900 chr5B 571490285 571492088 1803 False 757.500000 1400 84.38900 2969 5142 2 chr5B.!!$F4 2173
4 TraesCS5A01G387900 chr5B 571508829 571510484 1655 False 591.500000 763 83.39100 3708 5144 2 chr5B.!!$F5 1436
5 TraesCS5A01G387900 chr5D 464324755 464326629 1874 False 842.000000 1129 90.17200 1117 3144 3 chr5D.!!$F3 2027
6 TraesCS5A01G387900 chr5D 464394941 464396705 1764 False 728.500000 1299 85.44600 2969 5135 2 chr5D.!!$F4 2166
7 TraesCS5A01G387900 chr5D 464347634 464348165 531 False 701.000000 701 90.52000 4611 5142 1 chr5D.!!$F2 531
8 TraesCS5A01G387900 chr5D 464401561 464403386 1825 False 240.333333 357 90.85300 5128 5773 3 chr5D.!!$F5 645
9 TraesCS5A01G387900 chr2A 30222935 30224350 1415 False 874.000000 874 78.41200 1119 2509 1 chr2A.!!$F1 1390
10 TraesCS5A01G387900 chr2D 28407749 28409151 1402 False 826.000000 826 77.81700 1117 2509 1 chr2D.!!$F1 1392
11 TraesCS5A01G387900 chr2B 44941373 44942775 1402 True 815.000000 815 77.64500 1117 2509 1 chr2B.!!$R3 1392
12 TraesCS5A01G387900 chr2B 45608344 45609746 1402 False 809.000000 809 77.62200 1117 2509 1 chr2B.!!$F1 1392
13 TraesCS5A01G387900 chr2B 45640727 45642133 1406 True 785.000000 785 77.28900 1117 2509 1 chr2B.!!$R4 1392
14 TraesCS5A01G387900 chr2B 18319510 18320291 781 True 307.000000 307 74.46000 1755 2511 1 chr2B.!!$R1 756
15 TraesCS5A01G387900 chr2B 18385889 18386670 781 True 257.000000 257 73.41800 1755 2511 1 chr2B.!!$R2 756
16 TraesCS5A01G387900 chr4D 509837625 509839016 1391 True 487.000000 571 82.87700 1125 2515 2 chr4D.!!$R1 1390
17 TraesCS5A01G387900 chr4B 656891695 656893106 1411 False 498.000000 560 80.60700 1122 2515 2 chr4B.!!$F1 1393
18 TraesCS5A01G387900 chr1B 557411037 557412403 1366 True 403.000000 403 72.83100 1121 2482 1 chr1B.!!$R1 1361


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
523 524 0.036388 GACAAGCAACTCCGGATGGA 60.036 55.0 3.57 0.0 43.88 3.41 F
1058 1098 0.108138 AAGCCACATCGAGCCTGTAC 60.108 55.0 0.00 0.0 0.00 2.90 F
2553 5644 0.251297 TCAGTTCTGGCACCCATTGG 60.251 55.0 0.00 0.0 30.82 3.16 F
3317 6443 0.256752 ATCTAGTGGCCAAGCATGCA 59.743 50.0 21.98 0.0 0.00 3.96 F
3446 6572 0.183971 TTGAGCCAACCGGAAAAGGA 59.816 50.0 9.46 0.0 34.73 3.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 4854 2.511600 ACGTAGCCTTGGCGCATC 60.512 61.111 10.83 0.0 0.00 3.91 R
2609 5700 0.675633 AAACAGATGGTGCCACAAGC 59.324 50.000 0.00 0.0 44.14 4.01 R
3427 6553 0.183971 TCCTTTTCCGGTTGGCTCAA 59.816 50.000 0.00 0.0 34.14 3.02 R
4660 9900 0.247460 CTGCACACCGAGATCAAGGA 59.753 55.000 12.65 0.0 0.00 3.36 R
4887 10378 1.067846 TCGTCTGTCAGTGGCATGTAC 60.068 52.381 0.00 0.0 0.00 2.90 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.