Multiple sequence alignment - TraesCS1A01G129900

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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 TraesCS1A01G129900 chr1A 100.000 1820 0 0 986 2805 168260704 168262523 0.000000e+00 3362
1 TraesCS1A01G129900 chr1A 98.078 1821 32 3 986 2805 168235938 168237756 0.000000e+00 3166
2 TraesCS1A01G129900 chr1A 93.942 1073 44 12 986 2052 469356796 469355739 0.000000e+00 1602
3 TraesCS1A01G129900 chr1A 100.000 435 0 0 1 435 168259719 168260153 0.000000e+00 804
4 TraesCS1A01G129900 chr1A 96.782 435 14 0 1 435 168235477 168235911 0.000000e+00 726
5 TraesCS1A01G129900 chr1A 96.552 435 15 0 1 435 469357253 469356819 0.000000e+00 721
6 TraesCS1A01G129900 chr1A 95.632 435 19 0 1 435 469349322 469348888 0.000000e+00 699
7 TraesCS1A01G129900 chr1A 87.250 400 50 1 1 400 157582049 157582447 3.290000e-124 455
8 TraesCS1A01G129900 chr1A 82.229 332 54 3 1 331 3875830 3875503 5.920000e-72 281
9 TraesCS1A01G129900 chr1A 76.673 523 84 26 1593 2094 93889841 93890346 3.590000e-64 255
10 TraesCS1A01G129900 chr1A 76.536 537 84 35 1593 2109 367514275 367513761 3.590000e-64 255
11 TraesCS1A01G129900 chr6A 96.490 1111 30 3 986 2093 353340488 353339384 0.000000e+00 1827
12 TraesCS1A01G129900 chr6A 96.400 1111 32 2 986 2093 353348396 353347291 0.000000e+00 1823
13 TraesCS1A01G129900 chr6A 95.402 435 20 0 1 435 353340947 353340513 0.000000e+00 693
14 TraesCS1A01G129900 chr6A 95.172 435 21 0 1 435 353348855 353348421 0.000000e+00 688
15 TraesCS1A01G129900 chr6A 87.835 411 43 5 1 405 244969667 244969258 2.530000e-130 475
16 TraesCS1A01G129900 chr6A 83.127 403 59 7 1 400 302786778 302787174 2.660000e-95 359
17 TraesCS1A01G129900 chr6A 87.097 310 38 2 1 310 458081067 458081374 1.600000e-92 350
18 TraesCS1A01G129900 chr6A 93.833 227 12 1 2093 2319 141756876 141756652 9.620000e-90 340
19 TraesCS1A01G129900 chr6A 75.663 641 107 34 1491 2107 383787094 383787709 9.900000e-70 274
20 TraesCS1A01G129900 chr6A 80.936 299 39 11 1815 2104 330422132 330421843 1.310000e-53 220
21 TraesCS1A01G129900 chr4A 95.144 1112 45 3 986 2094 475579936 475578831 0.000000e+00 1746
22 TraesCS1A01G129900 chr4A 94.943 435 22 0 1 435 475588094 475587660 0.000000e+00 682
23 TraesCS1A01G129900 chr4A 94.713 435 23 0 1 435 475580395 475579961 0.000000e+00 676
24 TraesCS1A01G129900 chr4A 91.111 405 34 2 1 405 249664135 249663733 5.280000e-152 547
25 TraesCS1A01G129900 chr4A 90.148 406 37 3 1 405 249656991 249656588 2.480000e-145 525
26 TraesCS1A01G129900 chr4A 92.576 229 10 3 2093 2321 90355470 90355249 3.490000e-84 322
27 TraesCS1A01G129900 chr3A 94.947 1029 34 10 986 2011 279036915 279035902 0.000000e+00 1596
28 TraesCS1A01G129900 chr3A 93.762 1074 44 14 986 2052 271847272 271846215 0.000000e+00 1591
29 TraesCS1A01G129900 chr3A 91.324 1118 70 15 986 2089 254256444 254255340 0.000000e+00 1502
30 TraesCS1A01G129900 chr3A 95.402 435 20 0 1 435 254256901 254256467 0.000000e+00 693
31 TraesCS1A01G129900 chr3A 94.943 435 22 0 1 435 279045269 279044835 0.000000e+00 682
32 TraesCS1A01G129900 chr3A 93.392 227 9 2 2093 2319 250134378 250134158 5.790000e-87 331
33 TraesCS1A01G129900 chr3A 93.392 227 9 2 2093 2319 310546891 310546671 5.790000e-87 331
34 TraesCS1A01G129900 chr3A 83.505 291 33 12 1816 2094 279569092 279568805 9.970000e-65 257
35 TraesCS1A01G129900 chr2A 91.719 1123 61 21 986 2093 321743249 321744354 0.000000e+00 1530
36 TraesCS1A01G129900 chr2A 85.468 695 80 12 2093 2775 101987230 101987915 0.000000e+00 704
37 TraesCS1A01G129900 chr3D 95.885 486 20 0 2320 2805 505578350 505577865 0.000000e+00 787
38 TraesCS1A01G129900 chr3D 95.501 489 21 1 2317 2805 514232709 514233196 0.000000e+00 780
39 TraesCS1A01G129900 chr5D 95.679 486 21 0 2320 2805 120351622 120351137 0.000000e+00 782
40 TraesCS1A01G129900 chr5D 92.544 228 11 1 2093 2320 308365164 308365385 3.490000e-84 322
41 TraesCS1A01G129900 chr6D 95.297 489 23 0 2317 2805 318204902 318205390 0.000000e+00 776
42 TraesCS1A01G129900 chr6D 95.297 489 23 0 2317 2805 424487657 424488145 0.000000e+00 776
43 TraesCS1A01G129900 chr6D 95.297 489 23 0 2317 2805 424498719 424499207 0.000000e+00 776
44 TraesCS1A01G129900 chr6D 95.297 489 23 0 2317 2805 424509897 424510385 0.000000e+00 776
45 TraesCS1A01G129900 chr6D 92.982 228 10 2 2093 2320 334918933 334918712 7.490000e-86 327
46 TraesCS1A01G129900 chr2D 95.297 489 23 0 2317 2805 498429574 498430062 0.000000e+00 776
47 TraesCS1A01G129900 chr5A 83.824 408 60 5 1 407 158407581 158407179 1.580000e-102 383
48 TraesCS1A01G129900 chr5A 78.311 604 104 23 1514 2106 234408118 234407531 5.710000e-97 364
49 TraesCS1A01G129900 chr5A 81.735 438 71 8 1 435 158544473 158544042 9.550000e-95 357
50 TraesCS1A01G129900 chr7B 88.055 293 28 7 1815 2105 545994190 545993903 9.620000e-90 340
51 TraesCS1A01G129900 chr3B 89.919 248 16 5 2093 2339 366377674 366377913 7.540000e-81 311


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 TraesCS1A01G129900 chr1A 168259719 168262523 2804 False 2083.0 3362 100.0000 1 2805 2 chr1A.!!$F4 2804
1 TraesCS1A01G129900 chr1A 168235477 168237756 2279 False 1946.0 3166 97.4300 1 2805 2 chr1A.!!$F3 2804
2 TraesCS1A01G129900 chr1A 469355739 469357253 1514 True 1161.5 1602 95.2470 1 2052 2 chr1A.!!$R4 2051
3 TraesCS1A01G129900 chr1A 93889841 93890346 505 False 255.0 255 76.6730 1593 2094 1 chr1A.!!$F1 501
4 TraesCS1A01G129900 chr1A 367513761 367514275 514 True 255.0 255 76.5360 1593 2109 1 chr1A.!!$R2 516
5 TraesCS1A01G129900 chr6A 353339384 353340947 1563 True 1260.0 1827 95.9460 1 2093 2 chr6A.!!$R4 2092
6 TraesCS1A01G129900 chr6A 353347291 353348855 1564 True 1255.5 1823 95.7860 1 2093 2 chr6A.!!$R5 2092
7 TraesCS1A01G129900 chr6A 383787094 383787709 615 False 274.0 274 75.6630 1491 2107 1 chr6A.!!$F2 616
8 TraesCS1A01G129900 chr4A 475578831 475580395 1564 True 1211.0 1746 94.9285 1 2094 2 chr4A.!!$R5 2093
9 TraesCS1A01G129900 chr3A 279035902 279036915 1013 True 1596.0 1596 94.9470 986 2011 1 chr3A.!!$R3 1025
10 TraesCS1A01G129900 chr3A 271846215 271847272 1057 True 1591.0 1591 93.7620 986 2052 1 chr3A.!!$R2 1066
11 TraesCS1A01G129900 chr3A 254255340 254256901 1561 True 1097.5 1502 93.3630 1 2089 2 chr3A.!!$R7 2088
12 TraesCS1A01G129900 chr2A 321743249 321744354 1105 False 1530.0 1530 91.7190 986 2093 1 chr2A.!!$F2 1107
13 TraesCS1A01G129900 chr2A 101987230 101987915 685 False 704.0 704 85.4680 2093 2775 1 chr2A.!!$F1 682
14 TraesCS1A01G129900 chr5A 234407531 234408118 587 True 364.0 364 78.3110 1514 2106 1 chr5A.!!$R3 592

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
247 248 3.000819 CAGGGCCACACCGAGGTA 61.001 66.667 6.18 0.0 40.62 3.08 F
405 406 3.049674 CGGGCGAGCAAAAGAGCA 61.050 61.111 0.00 0.0 36.85 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1248 1249 1.201429 ATTCTCGTGGCCCTGACCTT 61.201 55.000 0.00 0.0 0.00 3.50 R
1989 2018 2.223386 TGTGCATTGCATCATGTCATCG 60.223 45.455 15.49 0.0 41.91 3.84 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)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
247 248 3.000819 CAGGGCCACACCGAGGTA 61.001 66.667 6.18 0.0 40.62 3.08
405 406 3.049674 CGGGCGAGCAAAAGAGCA 61.050 61.111 0.00 0.0 36.85 4.26
1263 1264 3.636231 CCAAGGTCAGGGCCACGA 61.636 66.667 6.18 0.0 0.00 4.35
1400 1405 0.397535 TCGCTAGGTTTACGGGGGAT 60.398 55.000 0.00 0.0 0.00 3.85
1474 1479 3.815407 CTGGGCTGCACTGGGGTTT 62.815 63.158 2.50 0.0 0.00 3.27
1731 1752 4.714308 AGTCCAAAAATGTTGGGAAGACAA 59.286 37.500 1.78 0.0 38.67 3.18
1755 1776 6.399743 AGAAGAGTCTCGATAAAAGGGAAAC 58.600 40.000 0.00 0.0 0.00 2.78
1849 1875 6.576662 TTGCGGTTAATTCCAAACTAATGA 57.423 33.333 0.00 0.0 0.00 2.57
1989 2018 8.623903 TGTAAAAGATTTATGAGATGATGGCAC 58.376 33.333 0.00 0.0 0.00 5.01
2315 2361 0.912486 ACCCAGGGATAGTTGCACTC 59.088 55.000 14.54 0.0 0.00 3.51
2579 2626 4.320861 CCATGTGTTAATGCTTTGTTCCGA 60.321 41.667 0.00 0.0 0.00 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
239 240 1.988406 GGCCACCTTCTACCTCGGT 60.988 63.158 0.00 0.0 0.00 4.69
271 272 1.746220 GTACGACAGCTGATGACCTCT 59.254 52.381 23.35 0.0 0.00 3.69
405 406 0.390866 CTCAGTCATGGCACTTCGCT 60.391 55.000 0.00 0.0 41.91 4.93
1248 1249 1.201429 ATTCTCGTGGCCCTGACCTT 61.201 55.000 0.00 0.0 0.00 3.50
1474 1479 3.686978 CGAGAGAATGAGGGAGAGAGGAA 60.687 52.174 0.00 0.0 0.00 3.36
1731 1752 6.399743 GTTTCCCTTTTATCGAGACTCTTCT 58.600 40.000 0.03 0.0 33.37 2.85
1755 1776 3.452474 TCCAAACTTTGCCAACAATTCG 58.548 40.909 0.00 0.0 35.21 3.34
1989 2018 2.223386 TGTGCATTGCATCATGTCATCG 60.223 45.455 15.49 0.0 41.91 3.84
2177 2222 2.497273 GGAATGTGGACCCCTCAAAATG 59.503 50.000 0.00 0.0 30.64 2.32


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

AutoCloner maintained by Alex Coulton.