Multiple sequence alignment - TraesCS5D01G430300

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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 TraesCS5D01G430300 chr5D 100.000 3562 0 0 1 3562 487600882 487597321 0.000000e+00 6578.0
1 TraesCS5D01G430300 chr5D 92.364 1100 75 4 907 1997 487836890 487835791 0.000000e+00 1557.0
2 TraesCS5D01G430300 chr5D 87.173 382 38 3 3 373 394597596 394597977 1.180000e-114 424.0
3 TraesCS5D01G430300 chr5D 81.734 542 57 12 3046 3562 564448130 564447606 7.110000e-112 414.0
4 TraesCS5D01G430300 chr5D 86.494 385 40 4 1 374 368324002 368324385 2.560000e-111 412.0
5 TraesCS5D01G430300 chr5D 79.952 419 48 18 3178 3562 376942966 376943382 3.500000e-70 276.0
6 TraesCS5D01G430300 chr5D 94.118 136 8 0 2314 2449 487834352 487834217 1.300000e-49 207.0
7 TraesCS5D01G430300 chr5D 79.668 241 21 17 2024 2260 487835794 487835578 7.970000e-32 148.0
8 TraesCS5D01G430300 chr5A 93.821 2282 107 15 590 2848 608362163 608359893 0.000000e+00 3402.0
9 TraesCS5D01G430300 chr5A 92.463 1088 70 7 920 1997 608447785 608446700 0.000000e+00 1544.0
10 TraesCS5D01G430300 chr5A 87.583 604 56 10 1 591 608362800 608362203 0.000000e+00 682.0
11 TraesCS5D01G430300 chr5A 88.127 379 41 3 1 375 515496733 515496355 7.010000e-122 448.0
12 TraesCS5D01G430300 chr5A 82.322 379 41 14 3108 3461 480178566 480178189 4.470000e-79 305.0
13 TraesCS5D01G430300 chr5A 78.151 357 50 21 1639 1984 42259926 42260265 6.030000e-48 202.0
14 TraesCS5D01G430300 chr5A 78.486 251 23 17 2013 2260 608446717 608446495 6.200000e-28 135.0
15 TraesCS5D01G430300 chr5B 92.102 2393 107 45 590 2912 600135590 600133210 0.000000e+00 3297.0
16 TraesCS5D01G430300 chr5B 92.029 1104 73 9 907 1997 600338639 600337538 0.000000e+00 1537.0
17 TraesCS5D01G430300 chr5B 88.980 608 50 4 1 591 600136240 600135633 0.000000e+00 736.0
18 TraesCS5D01G430300 chr5B 84.543 427 49 12 3044 3461 692745520 692745938 1.190000e-109 407.0
19 TraesCS5D01G430300 chr5B 86.100 259 15 1 2191 2449 600337357 600337120 3.530000e-65 259.0
20 TraesCS5D01G430300 chr5B 77.060 449 66 19 3149 3562 354503154 354502708 1.290000e-54 224.0
21 TraesCS5D01G430300 chr5B 90.541 74 4 1 2013 2083 600337555 600337482 1.050000e-15 95.3
22 TraesCS5D01G430300 chr7A 86.279 430 50 7 3042 3464 136538007 136537580 3.240000e-125 459.0
23 TraesCS5D01G430300 chr4B 87.500 384 37 3 1 373 639085949 639086332 1.960000e-117 433.0
24 TraesCS5D01G430300 chr4B 83.295 431 60 5 3046 3464 44080102 44079672 1.550000e-103 387.0
25 TraesCS5D01G430300 chr4B 78.557 485 66 21 3105 3562 640021818 640022291 5.820000e-73 285.0
26 TraesCS5D01G430300 chr4B 80.328 122 22 2 2319 2439 464953857 464953737 1.360000e-14 91.6
27 TraesCS5D01G430300 chr4D 85.142 424 49 9 3044 3461 374784883 374784468 4.250000e-114 422.0
28 TraesCS5D01G430300 chr4D 80.800 125 22 2 2316 2439 378449413 378449290 2.930000e-16 97.1
29 TraesCS5D01G430300 chr6D 84.706 425 57 5 3044 3464 311807070 311806650 5.500000e-113 418.0
30 TraesCS5D01G430300 chr6D 90.385 52 2 3 636 687 58046110 58046158 8.250000e-07 65.8
31 TraesCS5D01G430300 chr1D 86.269 386 42 3 1 375 46490764 46491149 3.310000e-110 409.0
32 TraesCS5D01G430300 chr1D 84.400 250 27 4 141 378 491756946 491756697 5.950000e-58 235.0
33 TraesCS5D01G430300 chr1D 92.157 51 3 1 712 761 394271113 394271163 1.770000e-08 71.3
34 TraesCS5D01G430300 chr1A 86.234 385 42 8 1 374 46312339 46312723 1.190000e-109 407.0
35 TraesCS5D01G430300 chr1A 79.144 561 73 10 3043 3562 574508125 574507568 7.320000e-92 348.0
36 TraesCS5D01G430300 chr2B 85.901 383 42 4 1 372 639247398 639247779 7.170000e-107 398.0
37 TraesCS5D01G430300 chr2B 88.024 334 35 3 3135 3464 198274947 198274615 1.200000e-104 390.0
38 TraesCS5D01G430300 chr2B 82.160 426 60 9 3041 3461 423823592 423824006 5.660000e-93 351.0
39 TraesCS5D01G430300 chr2B 78.858 473 65 9 3112 3552 759544408 759544877 1.620000e-73 287.0
40 TraesCS5D01G430300 chrUn 85.523 373 41 4 12 373 82327434 82327804 9.330000e-101 377.0
41 TraesCS5D01G430300 chrUn 85.523 373 41 4 12 373 82333658 82334028 9.330000e-101 377.0
42 TraesCS5D01G430300 chrUn 85.637 369 42 3 19 376 234380386 234380018 9.330000e-101 377.0
43 TraesCS5D01G430300 chrUn 85.637 369 42 3 19 376 327347213 327346845 9.330000e-101 377.0
44 TraesCS5D01G430300 chr4A 84.051 395 56 6 3076 3464 515882072 515881679 1.210000e-99 374.0
45 TraesCS5D01G430300 chr4A 80.672 119 21 2 2313 2430 86991425 86991542 1.360000e-14 91.6
46 TraesCS5D01G430300 chr3A 82.974 417 59 7 3048 3460 69061778 69062186 2.020000e-97 366.0
47 TraesCS5D01G430300 chr3A 81.681 464 60 15 3113 3553 505527816 505528277 2.610000e-96 363.0
48 TraesCS5D01G430300 chr2D 88.489 278 31 1 1 277 20375439 20375716 5.700000e-88 335.0
49 TraesCS5D01G430300 chr2D 78.664 539 65 14 3046 3552 63917216 63917736 2.670000e-81 313.0


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 TraesCS5D01G430300 chr5D 487597321 487600882 3561 True 6578.000000 6578 100.000000 1 3562 1 chr5D.!!$R1 3561
1 TraesCS5D01G430300 chr5D 487834217 487836890 2673 True 637.333333 1557 88.716667 907 2449 3 chr5D.!!$R3 1542
2 TraesCS5D01G430300 chr5D 564447606 564448130 524 True 414.000000 414 81.734000 3046 3562 1 chr5D.!!$R2 516
3 TraesCS5D01G430300 chr5A 608359893 608362800 2907 True 2042.000000 3402 90.702000 1 2848 2 chr5A.!!$R3 2847
4 TraesCS5D01G430300 chr5A 608446495 608447785 1290 True 839.500000 1544 85.474500 920 2260 2 chr5A.!!$R4 1340
5 TraesCS5D01G430300 chr5B 600133210 600136240 3030 True 2016.500000 3297 90.541000 1 2912 2 chr5B.!!$R2 2911
6 TraesCS5D01G430300 chr5B 600337120 600338639 1519 True 630.433333 1537 89.556667 907 2449 3 chr5B.!!$R3 1542
7 TraesCS5D01G430300 chr1A 574507568 574508125 557 True 348.000000 348 79.144000 3043 3562 1 chr1A.!!$R1 519
8 TraesCS5D01G430300 chr2D 63917216 63917736 520 False 313.000000 313 78.664000 3046 3552 1 chr2D.!!$F2 506


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
264 266 0.331616 ACCCTTGCTTGTATGGGACC 59.668 55.000 14.64 0.0 42.11 4.46 F
295 307 1.192428 GAGGCTTCGAAACTCCCCTA 58.808 55.000 15.21 0.0 0.00 3.53 F
513 531 1.343465 GCCGGTATATAGTGTGGCAGT 59.657 52.381 1.90 0.0 42.03 4.40 F
2378 3715 0.104304 TATTCCGCGGGAAGAAGCTC 59.896 55.000 27.83 0.0 45.48 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2103 2203 2.893637 TGCAAGCGAAGGTAGAGAATC 58.106 47.619 0.00 0.00 37.06 2.52 R
2360 3697 1.153349 GAGCTTCTTCCCGCGGAAT 60.153 57.895 30.73 3.33 41.23 3.01 R
2426 3763 2.651361 CGGTCGTGCTCCTTGACT 59.349 61.111 0.00 0.00 33.21 3.41 R
3500 4921 1.001641 GGTGGAGCAGCAGGAACAT 60.002 57.895 0.00 0.00 0.00 2.71 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.