Multiple sequence alignment - TraesCS7A01G201000

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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 TraesCS7A01G201000 chr7A 100.000 2369 0 0 1 2369 163155767 163158135 0.000000e+00 4375
1 TraesCS7A01G201000 chrUn 95.998 2374 89 4 1 2369 82728983 82726611 0.000000e+00 3853
2 TraesCS7A01G201000 chrUn 95.998 2374 89 4 1 2369 328865896 328863524 0.000000e+00 3853
3 TraesCS7A01G201000 chr5D 93.468 2128 118 9 14 2134 487587363 487589476 0.000000e+00 3140
4 TraesCS7A01G201000 chr5D 94.061 1667 92 2 474 2134 174804781 174803116 0.000000e+00 2523
5 TraesCS7A01G201000 chr4D 92.887 2151 127 16 2 2134 476862203 476864345 0.000000e+00 3101
6 TraesCS7A01G201000 chr4D 94.642 1661 81 4 474 2134 56944694 56946346 0.000000e+00 2567
7 TraesCS7A01G201000 chr4D 90.854 492 39 3 1 486 293372211 293372702 0.000000e+00 654
8 TraesCS7A01G201000 chr2D 92.024 2169 135 18 2 2134 127267943 127265777 0.000000e+00 3013
9 TraesCS7A01G201000 chr2D 91.614 477 36 2 9 481 6862906 6863382 0.000000e+00 656
10 TraesCS7A01G201000 chr2D 90.891 494 37 5 2 489 586776458 586775967 0.000000e+00 656
11 TraesCS7A01G201000 chr2D 90.447 492 42 3 2 489 424711398 424710908 0.000000e+00 643
12 TraesCS7A01G201000 chr2D 90.467 493 37 5 2 486 513949841 513950331 1.990000e-180 641
13 TraesCS7A01G201000 chr5A 91.925 2093 151 9 50 2134 598256787 598254705 0.000000e+00 2913
14 TraesCS7A01G201000 chr1D 94.234 1665 90 4 474 2134 495236639 495238301 0.000000e+00 2538
15 TraesCS7A01G201000 chr1D 94.583 240 12 1 2131 2369 7424178 7423939 1.030000e-98 370
16 TraesCS7A01G201000 chr1D 94.937 237 11 1 2134 2369 218259058 218258822 1.030000e-98 370
17 TraesCS7A01G201000 chr3D 93.878 1666 91 7 474 2134 594818288 594816629 0.000000e+00 2501
18 TraesCS7A01G201000 chr3D 94.937 237 11 1 2134 2369 394910347 394910583 1.030000e-98 370
19 TraesCS7A01G201000 chr3D 93.852 244 13 2 2127 2369 283239074 283239316 1.340000e-97 366
20 TraesCS7A01G201000 chr1A 87.845 798 84 5 1 791 21497399 21498190 0.000000e+00 924
21 TraesCS7A01G201000 chr7D 94.606 241 12 1 2130 2369 535899495 535899735 2.880000e-99 372
22 TraesCS7A01G201000 chr7D 94.937 237 11 1 2134 2369 156079852 156079616 1.030000e-98 370
23 TraesCS7A01G201000 chr7D 94.538 238 12 1 2133 2369 99961760 99961523 1.340000e-97 366


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 TraesCS7A01G201000 chr7A 163155767 163158135 2368 False 4375 4375 100.000 1 2369 1 chr7A.!!$F1 2368
1 TraesCS7A01G201000 chrUn 82726611 82728983 2372 True 3853 3853 95.998 1 2369 1 chrUn.!!$R1 2368
2 TraesCS7A01G201000 chrUn 328863524 328865896 2372 True 3853 3853 95.998 1 2369 1 chrUn.!!$R2 2368
3 TraesCS7A01G201000 chr5D 487587363 487589476 2113 False 3140 3140 93.468 14 2134 1 chr5D.!!$F1 2120
4 TraesCS7A01G201000 chr5D 174803116 174804781 1665 True 2523 2523 94.061 474 2134 1 chr5D.!!$R1 1660
5 TraesCS7A01G201000 chr4D 476862203 476864345 2142 False 3101 3101 92.887 2 2134 1 chr4D.!!$F3 2132
6 TraesCS7A01G201000 chr4D 56944694 56946346 1652 False 2567 2567 94.642 474 2134 1 chr4D.!!$F1 1660
7 TraesCS7A01G201000 chr2D 127265777 127267943 2166 True 3013 3013 92.024 2 2134 1 chr2D.!!$R1 2132
8 TraesCS7A01G201000 chr5A 598254705 598256787 2082 True 2913 2913 91.925 50 2134 1 chr5A.!!$R1 2084
9 TraesCS7A01G201000 chr1D 495236639 495238301 1662 False 2538 2538 94.234 474 2134 1 chr1D.!!$F1 1660
10 TraesCS7A01G201000 chr3D 594816629 594818288 1659 True 2501 2501 93.878 474 2134 1 chr3D.!!$R1 1660
11 TraesCS7A01G201000 chr1A 21497399 21498190 791 False 924 924 87.845 1 791 1 chr1A.!!$F1 790

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
809 856 0.248498 CGCACGTGATAGACATCGGT 60.248 55.0 22.23 0.0 33.51 4.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1823 1881 0.908198 CCTCCTCCCTTGAGTCCTTG 59.092 60.0 0.0 0.0 36.86 3.61 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
130 131 3.036577 GTGGACACGAGACGGACA 58.963 61.111 0.00 0.00 0.00 4.02
131 132 1.585006 GTGGACACGAGACGGACAT 59.415 57.895 0.00 0.00 0.00 3.06
207 214 8.003629 TCATTTTCTTCCATTTTCCCCAAAAAT 58.996 29.630 0.00 0.00 46.23 1.82
345 353 1.654220 GAAAGGCAAGCTTCGTGCA 59.346 52.632 10.85 0.00 44.07 4.57
506 544 3.764466 AACGAGGGAGGCGCTCTG 61.764 66.667 7.64 0.00 40.57 3.35
613 652 1.380302 GTGATGCCCAACTCACCCT 59.620 57.895 0.00 0.00 36.59 4.34
693 733 2.919043 GGGGAATGCTCACCCGAT 59.081 61.111 0.00 0.00 46.42 4.18
796 843 3.335534 GCACGAGGAAACGCACGT 61.336 61.111 0.00 0.00 39.17 4.49
804 851 1.271379 AGGAAACGCACGTGATAGACA 59.729 47.619 22.23 0.00 0.00 3.41
809 856 0.248498 CGCACGTGATAGACATCGGT 60.248 55.000 22.23 0.00 33.51 4.69
1014 1061 1.742761 CCTTCATGCGTGATCAGGTT 58.257 50.000 15.84 2.64 33.56 3.50
1090 1138 0.251386 AGAGGAAGAGGACGAGTGCA 60.251 55.000 0.00 0.00 0.00 4.57
1337 1385 3.511146 CCACCTTACCAATTTGTGAGCAT 59.489 43.478 0.00 0.00 0.00 3.79
1367 1415 2.617021 GGGTCTCAATTTCCAAGCGGTA 60.617 50.000 0.00 0.00 0.00 4.02
1421 1469 1.079543 CCACCCTTGAGAGCGTCAG 60.080 63.158 0.00 0.00 36.21 3.51
1478 1526 2.092484 TGGTATGATAGCAAGCAAGCCA 60.092 45.455 1.25 0.00 32.53 4.75
1628 1677 1.425066 TGCTTCAACCTCTCCCATTGT 59.575 47.619 0.00 0.00 0.00 2.71
1780 1835 1.205893 GAAGGAGGACAAGCGAGATGT 59.794 52.381 0.00 0.00 0.00 3.06
1823 1881 0.027586 GCGTGGACGGCATGATTAAC 59.972 55.000 0.00 0.00 40.23 2.01
2234 2292 4.431131 CATGGGCCGGGCTTGAGT 62.431 66.667 28.80 6.65 0.00 3.41
2252 2310 3.391296 TGAGTCTAAGTTTTGAGCCCACT 59.609 43.478 0.00 0.00 0.00 4.00
2258 2316 1.168714 GTTTTGAGCCCACTAGCAGG 58.831 55.000 0.00 0.00 34.23 4.85
2308 2366 1.405463 GCATTTTAAGGAAGAGGCCCG 59.595 52.381 0.00 0.00 0.00 6.13
2363 2421 0.968393 TTTTTACCAGATGGGCCGGC 60.968 55.000 21.18 21.18 42.05 6.13
2364 2422 1.858739 TTTTACCAGATGGGCCGGCT 61.859 55.000 28.56 6.33 42.05 5.52
2366 2424 2.550699 TTACCAGATGGGCCGGCTTG 62.551 60.000 28.56 16.10 42.05 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 1.530419 TGCCGCCACTTTTGTCCAT 60.530 52.632 0.00 0.0 0.00 3.41
240 247 0.668535 CGATGTCGTCCTCATGGCTA 59.331 55.000 0.00 0.0 34.11 3.93
613 652 2.103934 GTTGCAAGCCAACGCACA 59.896 55.556 0.00 0.0 43.85 4.57
726 772 3.700970 TTGAGGTCGATGGGCGCA 61.701 61.111 10.83 5.7 40.61 6.09
796 843 0.816421 TCGCCGACCGATGTCTATCA 60.816 55.000 0.00 0.0 41.89 2.15
990 1037 3.687321 ATCACGCATGAAGGCCGCT 62.687 57.895 0.00 0.0 38.69 5.52
1014 1061 3.770040 CCGTCCAGGTCGATGCCA 61.770 66.667 7.77 0.0 34.51 4.92
1090 1138 3.214328 ACAAAAGCTCCACTTCGATGTT 58.786 40.909 0.39 0.0 37.75 2.71
1123 1171 2.840066 CGGCGGCTTGGTTGACAAA 61.840 57.895 7.61 0.0 38.91 2.83
1367 1415 2.304180 CACTCTTGTTGGATCACCCTCT 59.696 50.000 0.00 0.0 35.38 3.69
1628 1677 2.380941 TCGTCCTTGATGACCCGATAA 58.619 47.619 0.00 0.0 31.35 1.75
1823 1881 0.908198 CCTCCTCCCTTGAGTCCTTG 59.092 60.000 0.00 0.0 36.86 3.61
1852 1910 1.205417 CCATTTGCTCCGCCTTGAAAT 59.795 47.619 0.00 0.0 0.00 2.17
2067 2125 1.078143 GCCTCTTCCTTGGCGACAT 60.078 57.895 0.00 0.0 42.32 3.06
2234 2292 3.326588 TGCTAGTGGGCTCAAAACTTAGA 59.673 43.478 0.00 0.0 0.00 2.10


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

AutoCloner maintained by Alex Coulton.