Multiple sequence alignment - TraesCS7A01G525500

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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 TraesCS7A01G525500 chr7A 100.000 2282 0 0 1 2282 707969982 707972263 0.000000e+00 4215.0
1 TraesCS7A01G525500 chr1A 96.639 1458 42 3 1 1451 97260634 97262091 0.000000e+00 2414.0
2 TraesCS7A01G525500 chr1A 96.637 1457 42 3 1 1450 353278857 353280313 0.000000e+00 2412.0
3 TraesCS7A01G525500 chr1A 96.319 1467 47 3 1 1460 563187062 563185596 0.000000e+00 2403.0
4 TraesCS7A01G525500 chr1A 87.524 529 58 7 925 1453 571864791 571864271 2.510000e-169 604.0
5 TraesCS7A01G525500 chr2A 96.500 1457 44 3 1 1450 702408796 702410252 0.000000e+00 2401.0
6 TraesCS7A01G525500 chr2A 86.441 59 7 1 1394 1451 24910279 24910337 1.890000e-06 63.9
7 TraesCS7A01G525500 chr7D 94.118 935 48 3 1 928 41370506 41371440 0.000000e+00 1415.0
8 TraesCS7A01G525500 chr7D 91.272 928 54 13 9 928 449771211 449770303 0.000000e+00 1240.0
9 TraesCS7A01G525500 chr7D 88.438 320 32 3 1962 2280 615467491 615467806 4.600000e-102 381.0
10 TraesCS7A01G525500 chr7D 87.407 270 28 4 1570 1834 615467227 615467495 2.850000e-79 305.0
11 TraesCS7A01G525500 chr7D 85.938 128 14 3 1449 1575 615466526 615466650 1.420000e-27 134.0
12 TraesCS7A01G525500 chr1D 91.164 928 55 13 9 928 417749276 417748368 0.000000e+00 1234.0
13 TraesCS7A01G525500 chr5D 91.056 928 56 13 9 928 354746407 354745499 0.000000e+00 1229.0
14 TraesCS7A01G525500 chr5D 90.948 928 57 13 9 928 547843948 547844856 0.000000e+00 1223.0
15 TraesCS7A01G525500 chr3D 90.948 928 57 15 9 928 14358542 14357634 0.000000e+00 1223.0
16 TraesCS7A01G525500 chr3D 91.202 466 27 10 925 1389 14356009 14355557 2.490000e-174 621.0
17 TraesCS7A01G525500 chr3D 87.833 526 56 7 925 1450 49965393 49964876 5.390000e-171 610.0
18 TraesCS7A01G525500 chr3D 81.425 393 45 20 6 392 7706315 7706685 1.710000e-76 296.0
19 TraesCS7A01G525500 chr5A 90.497 926 62 6 10 928 476065898 476064992 0.000000e+00 1199.0
20 TraesCS7A01G525500 chr7B 86.930 834 73 14 1449 2279 708001224 708002024 0.000000e+00 904.0
21 TraesCS7A01G525500 chr6A 93.359 527 32 3 925 1450 610216012 610216536 0.000000e+00 776.0
22 TraesCS7A01G525500 chr6B 87.810 525 56 6 929 1450 647587299 647586780 1.940000e-170 608.0
23 TraesCS7A01G525500 chr2D 81.726 394 43 21 6 392 19528174 19527803 3.680000e-78 302.0


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 TraesCS7A01G525500 chr7A 707969982 707972263 2281 False 4215.000000 4215 100.000 1 2282 1 chr7A.!!$F1 2281
1 TraesCS7A01G525500 chr1A 97260634 97262091 1457 False 2414.000000 2414 96.639 1 1451 1 chr1A.!!$F1 1450
2 TraesCS7A01G525500 chr1A 353278857 353280313 1456 False 2412.000000 2412 96.637 1 1450 1 chr1A.!!$F2 1449
3 TraesCS7A01G525500 chr1A 563185596 563187062 1466 True 2403.000000 2403 96.319 1 1460 1 chr1A.!!$R1 1459
4 TraesCS7A01G525500 chr1A 571864271 571864791 520 True 604.000000 604 87.524 925 1453 1 chr1A.!!$R2 528
5 TraesCS7A01G525500 chr2A 702408796 702410252 1456 False 2401.000000 2401 96.500 1 1450 1 chr2A.!!$F2 1449
6 TraesCS7A01G525500 chr7D 41370506 41371440 934 False 1415.000000 1415 94.118 1 928 1 chr7D.!!$F1 927
7 TraesCS7A01G525500 chr7D 449770303 449771211 908 True 1240.000000 1240 91.272 9 928 1 chr7D.!!$R1 919
8 TraesCS7A01G525500 chr7D 615466526 615467806 1280 False 273.333333 381 87.261 1449 2280 3 chr7D.!!$F2 831
9 TraesCS7A01G525500 chr1D 417748368 417749276 908 True 1234.000000 1234 91.164 9 928 1 chr1D.!!$R1 919
10 TraesCS7A01G525500 chr5D 354745499 354746407 908 True 1229.000000 1229 91.056 9 928 1 chr5D.!!$R1 919
11 TraesCS7A01G525500 chr5D 547843948 547844856 908 False 1223.000000 1223 90.948 9 928 1 chr5D.!!$F1 919
12 TraesCS7A01G525500 chr3D 14355557 14358542 2985 True 922.000000 1223 91.075 9 1389 2 chr3D.!!$R2 1380
13 TraesCS7A01G525500 chr3D 49964876 49965393 517 True 610.000000 610 87.833 925 1450 1 chr3D.!!$R1 525
14 TraesCS7A01G525500 chr5A 476064992 476065898 906 True 1199.000000 1199 90.497 10 928 1 chr5A.!!$R1 918
15 TraesCS7A01G525500 chr7B 708001224 708002024 800 False 904.000000 904 86.930 1449 2279 1 chr7B.!!$F1 830
16 TraesCS7A01G525500 chr6A 610216012 610216536 524 False 776.000000 776 93.359 925 1450 1 chr6A.!!$F1 525
17 TraesCS7A01G525500 chr6B 647586780 647587299 519 True 608.000000 608 87.810 929 1450 1 chr6B.!!$R1 521

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
217 218 0.615331 TCAGACCATCAGAACCAGGC 59.385 55.0 0.0 0.0 0.0 4.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2069 4308 0.035152 AATCAGGTGCCGAAGATGCA 60.035 50.0 0.0 0.0 36.12 3.96 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
100 101 6.928348 TCTCCTTCCTAATACAGTTCACAA 57.072 37.500 0.00 0.00 0.00 3.33
116 117 7.572523 AGTTCACAACTGATTTCAATTCAGA 57.427 32.000 14.84 0.00 41.01 3.27
217 218 0.615331 TCAGACCATCAGAACCAGGC 59.385 55.000 0.00 0.00 0.00 4.85
224 225 3.134804 ACCATCAGAACCAGGCATACTAC 59.865 47.826 0.00 0.00 0.00 2.73
437 440 3.570975 TCAAGCGTACTTCCACTACTTCA 59.429 43.478 0.00 0.00 32.29 3.02
519 522 4.943093 TGAATTCAGAATCCGATCAGCAAA 59.057 37.500 3.38 0.00 0.00 3.68
543 546 1.614996 AAATGCCGACACCAACATCA 58.385 45.000 0.00 0.00 0.00 3.07
626 629 5.185249 GTCTCCTAGTGTTGATGAACCAGTA 59.815 44.000 0.00 0.00 0.00 2.74
879 888 6.398918 TGTTGTAAGATCTTCAAGTCTAGCC 58.601 40.000 12.24 3.92 0.00 3.93
891 900 1.104630 GTCTAGCCGTAGCAGGAGTT 58.895 55.000 0.00 0.00 43.56 3.01
1442 3092 0.332972 GCCCCCAAAATCTCAGGACT 59.667 55.000 0.00 0.00 0.00 3.85
1444 3094 1.635487 CCCCCAAAATCTCAGGACTGA 59.365 52.381 1.61 1.61 38.06 3.41
1524 3175 7.259161 AGTTAAACGACAATAACAAAAAGGCA 58.741 30.769 0.00 0.00 35.06 4.75
1527 3178 5.000012 ACGACAATAACAAAAAGGCACAA 58.000 34.783 0.00 0.00 0.00 3.33
1609 3842 3.977427 TCACCGAGATAATTCACCGATG 58.023 45.455 0.00 0.00 0.00 3.84
1631 3864 8.438513 CGATGTAATTCTAATCATGGACACATC 58.561 37.037 0.00 0.00 36.70 3.06
1632 3865 7.713764 TGTAATTCTAATCATGGACACATCG 57.286 36.000 0.00 0.00 34.35 3.84
1639 3874 7.219322 TCTAATCATGGACACATCGAATCATT 58.781 34.615 0.00 0.00 34.35 2.57
1658 3893 8.524870 AATCATTCTCACAAACACAATTAAGC 57.475 30.769 0.00 0.00 0.00 3.09
1661 3896 8.196771 TCATTCTCACAAACACAATTAAGCTTT 58.803 29.630 3.20 0.00 0.00 3.51
1682 3917 8.103935 AGCTTTAAATGGCTAGGATTAGGATAC 58.896 37.037 0.34 0.00 37.00 2.24
1702 3938 4.411256 ACCTCTAACCGAACTCACAAAA 57.589 40.909 0.00 0.00 0.00 2.44
1703 3939 4.124970 ACCTCTAACCGAACTCACAAAAC 58.875 43.478 0.00 0.00 0.00 2.43
1704 3940 3.183775 CCTCTAACCGAACTCACAAAACG 59.816 47.826 0.00 0.00 0.00 3.60
1744 3980 4.578928 TCTGCAAACCTTAACTCCTCAAAC 59.421 41.667 0.00 0.00 0.00 2.93
1746 3982 4.097286 TGCAAACCTTAACTCCTCAAACAC 59.903 41.667 0.00 0.00 0.00 3.32
1759 3998 5.516090 TCCTCAAACACGAGTTAAAAATGC 58.484 37.500 0.00 0.00 36.84 3.56
1794 4033 8.085296 AGCATAACTCTCAAATATAACTCCTCG 58.915 37.037 0.00 0.00 0.00 4.63
1795 4034 7.329717 GCATAACTCTCAAATATAACTCCTCGG 59.670 40.741 0.00 0.00 0.00 4.63
1802 4041 5.839063 TCAAATATAACTCCTCGGATCCAGT 59.161 40.000 13.41 4.45 0.00 4.00
1814 4053 2.223688 CGGATCCAGTTTGTGCACAAAA 60.224 45.455 38.81 26.82 46.08 2.44
1834 4073 8.667463 CACAAAAACCTCATTCAAAACTCAAAT 58.333 29.630 0.00 0.00 0.00 2.32
1858 4097 9.787435 AATTTGAAAGTATACTAAGACCACACA 57.213 29.630 5.65 0.00 0.00 3.72
1865 4104 5.932619 ATACTAAGACCACACAGTGCATA 57.067 39.130 0.00 0.00 31.34 3.14
1906 4145 7.441890 AACACAACATCACGGTTCATAATTA 57.558 32.000 0.00 0.00 0.00 1.40
1907 4146 7.441890 ACACAACATCACGGTTCATAATTAA 57.558 32.000 0.00 0.00 0.00 1.40
1908 4147 7.877003 ACACAACATCACGGTTCATAATTAAA 58.123 30.769 0.00 0.00 0.00 1.52
1909 4148 8.353684 ACACAACATCACGGTTCATAATTAAAA 58.646 29.630 0.00 0.00 0.00 1.52
1910 4149 8.849490 CACAACATCACGGTTCATAATTAAAAG 58.151 33.333 0.00 0.00 0.00 2.27
1911 4150 8.573035 ACAACATCACGGTTCATAATTAAAAGT 58.427 29.630 0.00 0.00 0.00 2.66
1914 4153 9.444600 ACATCACGGTTCATAATTAAAAGTAGT 57.555 29.630 0.00 0.00 0.00 2.73
1917 4156 9.491675 TCACGGTTCATAATTAAAAGTAGTTCA 57.508 29.630 0.00 0.00 0.00 3.18
2006 4245 8.171840 GCTAAAACAAGCACTAATCAGAGTTAG 58.828 37.037 0.00 0.00 42.30 2.34
2011 4250 4.026744 AGCACTAATCAGAGTTAGAGCCA 58.973 43.478 10.86 0.00 44.28 4.75
2033 4272 3.016736 AGTTTTATCATTGCCGACCTGG 58.983 45.455 0.00 0.00 42.50 4.45
2069 4308 2.034066 CATTGTGGGCGTCCCTGT 59.966 61.111 2.12 0.00 45.70 4.00
2086 4325 3.067985 TGCATCTTCGGCACCTGA 58.932 55.556 0.00 0.00 36.11 3.86
2189 4428 2.755469 CCTCCACCATTTGCCCGG 60.755 66.667 0.00 0.00 0.00 5.73
2195 4434 4.060667 CCATTTGCCCGGGGGTCT 62.061 66.667 25.28 0.00 37.65 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 3.359950 GGCCCTCTGAATTGAAATCAGT 58.640 45.455 9.83 0.00 43.77 3.41
116 117 1.920835 GACCAAGACTGAGGGCCCT 60.921 63.158 29.18 29.18 0.00 5.19
217 218 4.083003 ACGGCCAAACACAAATGTAGTATG 60.083 41.667 2.24 0.00 38.45 2.39
224 225 0.319469 GGGACGGCCAAACACAAATG 60.319 55.000 11.00 0.00 35.15 2.32
292 294 3.514645 GCATGCTAAAACACAATCCTGG 58.485 45.455 11.37 0.00 0.00 4.45
355 358 7.410485 CAATTTATCTACGGCCTTCTTCTTTC 58.590 38.462 0.00 0.00 0.00 2.62
437 440 4.261801 CCAACTCATCACCTCGGTTTATT 58.738 43.478 0.00 0.00 0.00 1.40
519 522 2.428890 TGTTGGTGTCGGCATTTTCTTT 59.571 40.909 0.00 0.00 0.00 2.52
543 546 3.211045 AGCCACTTACATTGTTGTCGTT 58.789 40.909 0.00 0.00 37.28 3.85
794 797 6.705863 AGCCATTTTCTATCATGTTTCTCC 57.294 37.500 0.00 0.00 0.00 3.71
879 888 3.018149 AGGAACTCTAACTCCTGCTACG 58.982 50.000 0.00 0.00 40.70 3.51
891 900 4.962362 TCCATCATGTGCTAAGGAACTCTA 59.038 41.667 0.00 0.00 38.49 2.43
966 2603 7.707624 TGGCAAAGTGAATCTCATAATCTTT 57.292 32.000 0.00 0.00 0.00 2.52
1378 3028 5.457633 GGGGCCCTTAGTAAACACATCATAT 60.458 44.000 24.38 0.00 0.00 1.78
1420 3070 1.387737 CTGAGATTTTGGGGGCCCA 59.612 57.895 26.86 7.88 45.63 5.36
1442 3092 3.398318 TTCTAGACATAGGCAGGGTCA 57.602 47.619 0.00 0.00 34.04 4.02
1444 3094 4.104831 AGTTTTCTAGACATAGGCAGGGT 58.895 43.478 0.00 0.00 0.00 4.34
1500 3150 7.009357 TGTGCCTTTTTGTTATTGTCGTTTAAC 59.991 33.333 0.00 0.00 0.00 2.01
1501 3151 7.033791 TGTGCCTTTTTGTTATTGTCGTTTAA 58.966 30.769 0.00 0.00 0.00 1.52
1502 3152 6.561614 TGTGCCTTTTTGTTATTGTCGTTTA 58.438 32.000 0.00 0.00 0.00 2.01
1503 3153 5.411781 TGTGCCTTTTTGTTATTGTCGTTT 58.588 33.333 0.00 0.00 0.00 3.60
1524 3175 6.655078 ATCTAAAGTGATGCTTTTGGTTGT 57.345 33.333 0.00 0.00 44.41 3.32
1553 3204 1.340502 TGTGCCGCCATGAGGAATTAA 60.341 47.619 10.78 0.00 36.89 1.40
1609 3842 7.946655 TCGATGTGTCCATGATTAGAATTAC 57.053 36.000 0.00 0.00 0.00 1.89
1631 3864 8.726650 TTAATTGTGTTTGTGAGAATGATTCG 57.273 30.769 0.00 0.00 34.02 3.34
1632 3865 8.642020 GCTTAATTGTGTTTGTGAGAATGATTC 58.358 33.333 0.00 0.00 0.00 2.52
1658 3893 8.606830 AGGTATCCTAATCCTAGCCATTTAAAG 58.393 37.037 0.00 0.00 28.47 1.85
1661 3896 7.488205 AGAGGTATCCTAATCCTAGCCATTTA 58.512 38.462 0.00 0.00 31.76 1.40
1682 3917 3.183775 CGTTTTGTGAGTTCGGTTAGAGG 59.816 47.826 0.00 0.00 0.00 3.69
1702 3938 5.163561 TGCAGAGAAAATTGAAAGGAAACGT 60.164 36.000 0.00 0.00 0.00 3.99
1703 3939 5.280945 TGCAGAGAAAATTGAAAGGAAACG 58.719 37.500 0.00 0.00 0.00 3.60
1704 3940 7.401860 GTTTGCAGAGAAAATTGAAAGGAAAC 58.598 34.615 0.00 0.00 0.00 2.78
1746 3982 1.643810 GCTGCACGCATTTTTAACTCG 59.356 47.619 0.00 0.00 38.92 4.18
1763 4002 9.703892 AGTTATATTTGAGAGTTATGCTAGCTG 57.296 33.333 17.23 0.00 0.00 4.24
1772 4011 8.707796 ATCCGAGGAGTTATATTTGAGAGTTA 57.292 34.615 0.00 0.00 0.00 2.24
1784 4023 3.775316 ACAAACTGGATCCGAGGAGTTAT 59.225 43.478 13.90 5.06 0.00 1.89
1794 4033 3.451141 TTTTGTGCACAAACTGGATCC 57.549 42.857 37.72 4.20 44.56 3.36
1795 4034 3.555547 GGTTTTTGTGCACAAACTGGATC 59.444 43.478 37.72 23.37 44.56 3.36
1802 4041 4.825422 TGAATGAGGTTTTTGTGCACAAA 58.175 34.783 35.10 35.10 43.36 2.83
1814 4053 9.447157 TTTCAAATTTGAGTTTTGAATGAGGTT 57.553 25.926 19.64 0.00 46.63 3.50
1834 4073 8.426489 ACTGTGTGGTCTTAGTATACTTTCAAA 58.574 33.333 11.40 0.00 0.00 2.69
1923 4162 8.923683 GCTCGAAAGTAAGTGTTATCTACTTTT 58.076 33.333 7.62 0.00 39.97 2.27
1945 4184 7.955864 AGCTCGTTTTAACTTTAATTTAGCTCG 59.044 33.333 0.00 0.00 0.00 5.03
1956 4195 8.512138 AGCATAAATGTAGCTCGTTTTAACTTT 58.488 29.630 0.00 0.00 36.72 2.66
2006 4245 3.128589 TCGGCAATGATAAAACTTGGCTC 59.871 43.478 6.52 0.00 41.69 4.70
2011 4250 3.443681 CCAGGTCGGCAATGATAAAACTT 59.556 43.478 0.00 0.00 0.00 2.66
2033 4272 3.248029 CGATGCATTAGGCTCCGC 58.752 61.111 0.00 0.00 45.15 5.54
2042 4281 1.817881 CCCACAATGGCGATGCATT 59.182 52.632 0.00 0.00 35.79 3.56
2069 4308 0.035152 AATCAGGTGCCGAAGATGCA 60.035 50.000 0.00 0.00 36.12 3.96
2084 4323 5.760743 TGAATCTTAACACGGACAACAATCA 59.239 36.000 0.00 0.00 0.00 2.57
2086 4325 5.997385 GTGAATCTTAACACGGACAACAAT 58.003 37.500 0.00 0.00 0.00 2.71
2181 4420 4.278513 CACAGACCCCCGGGCAAA 62.279 66.667 17.73 0.00 39.32 3.68
2189 4428 2.529389 ACCCTCCACACAGACCCC 60.529 66.667 0.00 0.00 0.00 4.95
2195 4434 1.145156 CGTCAACACCCTCCACACA 59.855 57.895 0.00 0.00 0.00 3.72
2199 4438 2.050836 ATGCACGTCAACACCCTCCA 62.051 55.000 0.00 0.00 0.00 3.86
2228 4468 2.358737 CCGAGCCACCAAGGTGTC 60.359 66.667 17.36 5.28 44.02 3.67
2229 4469 3.168528 ACCGAGCCACCAAGGTGT 61.169 61.111 17.36 0.20 44.02 4.16


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

AutoCloner maintained by Alex Coulton.