Multiple sequence alignment - TraesCS4D01G322100

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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 TraesCS4D01G322100 chr4D 100.000 2409 0 0 1 2409 484295254 484292846 0.000000e+00 4449
1 TraesCS4D01G322100 chr4B 91.796 2328 63 30 191 2409 615835841 615833533 0.000000e+00 3123
2 TraesCS4D01G322100 chr5A 91.357 1747 73 30 233 1909 664556013 664554275 0.000000e+00 2318
3 TraesCS4D01G322100 chr5A 95.510 490 20 2 1920 2409 664553931 664553444 0.000000e+00 782
4 TraesCS4D01G322100 chr5B 84.975 599 79 9 1 593 532562581 532563174 4.430000e-167 597
5 TraesCS4D01G322100 chr5B 83.973 599 85 9 1 593 81576115 81576708 4.500000e-157 564
6 TraesCS4D01G322100 chr5D 84.281 598 83 10 1 593 425895249 425894658 7.470000e-160 573
7 TraesCS4D01G322100 chr6A 84.764 571 81 6 1 567 524735774 524736342 3.480000e-158 568
8 TraesCS4D01G322100 chr6D 83.946 598 87 8 1 593 424710081 424710674 4.500000e-157 564
9 TraesCS4D01G322100 chr3B 83.779 598 85 9 1 593 43924518 43923928 7.520000e-155 556
10 TraesCS4D01G322100 chr3B 83.779 598 85 9 1 593 44030332 44029742 7.520000e-155 556


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 TraesCS4D01G322100 chr4D 484292846 484295254 2408 True 4449 4449 100.0000 1 2409 1 chr4D.!!$R1 2408
1 TraesCS4D01G322100 chr4B 615833533 615835841 2308 True 3123 3123 91.7960 191 2409 1 chr4B.!!$R1 2218
2 TraesCS4D01G322100 chr5A 664553444 664556013 2569 True 1550 2318 93.4335 233 2409 2 chr5A.!!$R1 2176
3 TraesCS4D01G322100 chr5B 532562581 532563174 593 False 597 597 84.9750 1 593 1 chr5B.!!$F2 592
4 TraesCS4D01G322100 chr5B 81576115 81576708 593 False 564 564 83.9730 1 593 1 chr5B.!!$F1 592
5 TraesCS4D01G322100 chr5D 425894658 425895249 591 True 573 573 84.2810 1 593 1 chr5D.!!$R1 592
6 TraesCS4D01G322100 chr6A 524735774 524736342 568 False 568 568 84.7640 1 567 1 chr6A.!!$F1 566
7 TraesCS4D01G322100 chr6D 424710081 424710674 593 False 564 564 83.9460 1 593 1 chr6D.!!$F1 592
8 TraesCS4D01G322100 chr3B 43923928 43924518 590 True 556 556 83.7790 1 593 1 chr3B.!!$R1 592
9 TraesCS4D01G322100 chr3B 44029742 44030332 590 True 556 556 83.7790 1 593 1 chr3B.!!$R2 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
123 124 2.000447 GTAGATCTTTCGGCAAAGCGT 59.0 47.619 0.0 0.0 39.23 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1710 1775 0.179145 GTCATGTGAGCAGCAATGGC 60.179 55.0 0.0 0.0 41.61 4.4 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
34 35 2.783135 ACATCTCGGCAAGTTCAACAT 58.217 42.857 0.00 0.00 0.00 2.71
38 39 2.548057 TCTCGGCAAGTTCAACATGTTC 59.452 45.455 8.48 0.00 0.00 3.18
79 80 5.047802 GCAAATGAGTTCCTTGGATCAAGAA 60.048 40.000 9.01 0.33 43.42 2.52
123 124 2.000447 GTAGATCTTTCGGCAAAGCGT 59.000 47.619 0.00 0.00 39.23 5.07
129 130 5.353123 AGATCTTTCGGCAAAGCGTTTATTA 59.647 36.000 0.00 0.00 39.23 0.98
141 142 7.253190 GCAAAGCGTTTATTAAACTCGGTAATG 60.253 37.037 15.38 12.11 39.23 1.90
160 161 3.367992 TGATTTGGTCATGCACAACAC 57.632 42.857 0.00 1.48 0.00 3.32
174 175 8.183536 TCATGCACAACACTGAATATTTCATAC 58.816 33.333 0.00 0.00 39.30 2.39
175 176 7.446001 TGCACAACACTGAATATTTCATACA 57.554 32.000 0.00 0.00 39.30 2.29
178 179 7.970061 GCACAACACTGAATATTTCATACATGT 59.030 33.333 2.69 2.69 39.30 3.21
187 188 9.325198 TGAATATTTCATACATGTAGTGGTGAC 57.675 33.333 11.91 0.00 34.08 3.67
189 190 9.679661 AATATTTCATACATGTAGTGGTGACAA 57.320 29.630 11.91 7.64 46.06 3.18
275 277 6.372659 TGTTTGGCAATGTAATGTTGTGTTTT 59.627 30.769 0.00 0.00 0.00 2.43
278 280 7.470289 TGGCAATGTAATGTTGTGTTTTAAC 57.530 32.000 0.00 0.00 0.00 2.01
409 412 5.927689 TGATCTTTCCATTGCAAACATTGTC 59.072 36.000 1.71 0.00 0.00 3.18
438 441 8.950208 ACTCATTAGTCTTGCCTAATAGTTTC 57.050 34.615 0.00 0.00 35.87 2.78
473 480 5.350091 GCAAGTGCAAAAAGACCAAAACTTA 59.650 36.000 0.00 0.00 41.59 2.24
621 629 2.987213 ATGCAACAACGCGTGCAGTG 62.987 55.000 23.53 16.19 40.78 3.66
858 866 5.105997 GGGATCAATCTGAAACAACCAGAAG 60.106 44.000 0.00 0.00 43.07 2.85
963 971 7.386025 TGATTATGAATCGAATCCATGTCTGAC 59.614 37.037 0.00 0.00 40.84 3.51
1417 1434 2.048127 AGCGGCTGAGGTTTCGAC 60.048 61.111 0.00 0.00 0.00 4.20
1418 1435 2.357034 GCGGCTGAGGTTTCGACA 60.357 61.111 0.00 0.00 0.00 4.35
1428 1446 0.030235 GGTTTCGACAGGTTGTTGCC 59.970 55.000 0.00 0.00 31.81 4.52
1474 1492 2.470196 CAATGCATGCAGCTAGTGAC 57.530 50.000 26.69 0.00 45.94 3.67
1475 1493 1.741145 CAATGCATGCAGCTAGTGACA 59.259 47.619 26.69 0.00 45.94 3.58
1476 1494 2.343484 ATGCATGCAGCTAGTGACAT 57.657 45.000 26.69 1.43 45.94 3.06
1477 1495 1.660167 TGCATGCAGCTAGTGACATC 58.340 50.000 18.46 0.00 45.94 3.06
1478 1496 1.208776 TGCATGCAGCTAGTGACATCT 59.791 47.619 18.46 0.00 45.94 2.90
1479 1497 2.286872 GCATGCAGCTAGTGACATCTT 58.713 47.619 14.21 0.00 41.15 2.40
1480 1498 3.118665 TGCATGCAGCTAGTGACATCTTA 60.119 43.478 18.46 0.00 45.94 2.10
1481 1499 4.063689 GCATGCAGCTAGTGACATCTTAT 58.936 43.478 14.21 0.00 41.15 1.73
1596 1637 2.736721 CACAAGTGTCCACCTTGTATCG 59.263 50.000 5.56 0.00 39.01 2.92
1638 1679 6.767902 TGGCATGAATGTACCTCTTAAAGATC 59.232 38.462 0.00 0.00 0.00 2.75
1649 1690 9.886132 GTACCTCTTAAAGATCTTTGGTATTGA 57.114 33.333 25.97 16.14 33.15 2.57
1661 1725 8.964476 ATCTTTGGTATTGATGTATCGAAGTT 57.036 30.769 0.00 0.00 31.08 2.66
1701 1765 2.042464 AGTGAGGAGCAGAGTGTGAAA 58.958 47.619 0.00 0.00 0.00 2.69
1712 1777 0.536006 AGTGTGAAACTCTGCTGGCC 60.536 55.000 0.00 0.00 39.54 5.36
1713 1778 0.819259 GTGTGAAACTCTGCTGGCCA 60.819 55.000 4.71 4.71 38.04 5.36
1718 1803 0.541296 AAACTCTGCTGGCCATTGCT 60.541 50.000 17.08 0.00 37.74 3.91
1744 1829 5.941733 TCACATGACAATACAATGAACTGC 58.058 37.500 0.00 0.00 0.00 4.40
1746 1831 3.469899 TGACAATACAATGAACTGCGC 57.530 42.857 0.00 0.00 0.00 6.09
1753 1838 1.881973 ACAATGAACTGCGCTTCACAT 59.118 42.857 13.58 9.08 32.95 3.21
1754 1839 2.247637 CAATGAACTGCGCTTCACATG 58.752 47.619 13.58 11.83 32.95 3.21
1755 1840 1.812235 ATGAACTGCGCTTCACATGA 58.188 45.000 13.58 0.00 32.95 3.07
1756 1841 0.867746 TGAACTGCGCTTCACATGAC 59.132 50.000 9.73 0.00 0.00 3.06
1757 1842 0.867746 GAACTGCGCTTCACATGACA 59.132 50.000 9.73 0.00 0.00 3.58
1792 1877 6.861055 ACGCACACAAAATCTAAATACCAAAG 59.139 34.615 0.00 0.00 0.00 2.77
1876 1976 5.745312 ATCTCCAAAATTCCAAGGTTTCC 57.255 39.130 0.00 0.00 0.00 3.13
1881 1981 5.606329 TCCAAAATTCCAAGGTTTCCAAGAT 59.394 36.000 0.00 0.00 0.00 2.40
1893 1993 9.059260 CAAGGTTTCCAAGATTTGAATGAAAAT 57.941 29.630 0.00 0.00 32.43 1.82
1980 2412 2.480419 GAACGCAGTGATAGCACAACTT 59.520 45.455 14.51 0.00 45.00 2.66
2009 2441 1.967319 ACAGAAACGAGTGGCACAAT 58.033 45.000 21.41 0.00 44.16 2.71
2099 2536 7.464830 AGCTGTATGTACTTAAAAGTATGCG 57.535 36.000 5.90 0.00 42.88 4.73
2398 2835 0.688487 TACCCACACCAGCCAAGTAC 59.312 55.000 0.00 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
7 8 2.632377 ACTTGCCGAGATGTATGTTGG 58.368 47.619 0.00 0.00 0.00 3.77
34 35 6.552859 TGCTAATTTTGATGAAGACGAACA 57.447 33.333 0.00 0.00 0.00 3.18
38 39 7.752239 ACTCATTTGCTAATTTTGATGAAGACG 59.248 33.333 0.00 0.00 0.00 4.18
79 80 5.543714 TCAATTGTTGAGATGCATTGCTTT 58.456 33.333 10.49 0.00 34.08 3.51
129 130 5.393027 GCATGACCAAATCATTACCGAGTTT 60.393 40.000 0.00 0.00 46.54 2.66
141 142 3.004629 TCAGTGTTGTGCATGACCAAATC 59.995 43.478 0.00 0.00 0.00 2.17
160 161 9.546428 TCACCACTACATGTATGAAATATTCAG 57.454 33.333 5.91 0.00 43.98 3.02
174 175 6.876789 TGGTAACTTATTGTCACCACTACATG 59.123 38.462 0.00 0.00 34.40 3.21
175 176 7.011499 TGGTAACTTATTGTCACCACTACAT 57.989 36.000 0.00 0.00 34.40 2.29
178 179 8.158132 TCAAATGGTAACTTATTGTCACCACTA 58.842 33.333 0.00 0.00 41.82 2.74
187 188 6.386654 GTGGTGGTCAAATGGTAACTTATTG 58.613 40.000 0.00 0.00 37.61 1.90
189 190 4.698304 CGTGGTGGTCAAATGGTAACTTAT 59.302 41.667 0.00 0.00 37.61 1.73
409 412 6.992063 ATTAGGCAAGACTAATGAGTTGTG 57.008 37.500 7.37 0.00 40.98 3.33
462 469 7.554118 TGATTCCTCTGATCATAAGTTTTGGTC 59.446 37.037 0.00 0.03 0.00 4.02
473 480 3.498121 GGTGGCATGATTCCTCTGATCAT 60.498 47.826 0.00 0.00 35.61 2.45
621 629 9.076596 GTGTTTCATCATCCAACTAAAAATAGC 57.923 33.333 0.00 0.00 0.00 2.97
858 866 7.672983 TGATTCTGGTGAAAACAGAGATAAC 57.327 36.000 0.00 0.00 44.91 1.89
963 971 0.583438 CGATGCCACAAGATTAGCCG 59.417 55.000 0.00 0.00 0.00 5.52
1318 1335 0.320771 GCTTCTTCGCCTTCAGGTCA 60.321 55.000 0.00 0.00 37.57 4.02
1417 1434 2.575532 TCTTCTCAAGGCAACAACCTG 58.424 47.619 0.00 0.00 39.93 4.00
1418 1435 3.297134 TTCTTCTCAAGGCAACAACCT 57.703 42.857 0.00 0.00 43.91 3.50
1428 1446 6.732154 TGAAAGCTGTTTCATTCTTCTCAAG 58.268 36.000 0.00 0.00 45.82 3.02
1496 1532 9.748708 GAAGATTAAAGCACAATAATATGCCAA 57.251 29.630 0.00 0.00 43.12 4.52
1596 1637 1.467342 GCCACAGTTTACCACGGATTC 59.533 52.381 0.00 0.00 0.00 2.52
1638 1679 7.429340 GCAAACTTCGATACATCAATACCAAAG 59.571 37.037 0.00 0.00 0.00 2.77
1649 1690 7.945033 AAAACAAATGCAAACTTCGATACAT 57.055 28.000 0.00 0.00 0.00 2.29
1650 1691 7.763172 AAAAACAAATGCAAACTTCGATACA 57.237 28.000 0.00 0.00 0.00 2.29
1675 1739 3.834813 ACACTCTGCTCCTCACTTAATGA 59.165 43.478 0.00 0.00 35.45 2.57
1693 1757 0.536006 GGCCAGCAGAGTTTCACACT 60.536 55.000 0.00 0.00 39.07 3.55
1701 1765 1.677966 CAGCAATGGCCAGCAGAGT 60.678 57.895 18.35 0.00 42.56 3.24
1710 1775 0.179145 GTCATGTGAGCAGCAATGGC 60.179 55.000 0.00 0.00 41.61 4.40
1712 1777 3.503827 ATTGTCATGTGAGCAGCAATG 57.496 42.857 0.00 0.00 30.28 2.82
1713 1778 4.011698 TGTATTGTCATGTGAGCAGCAAT 58.988 39.130 0.00 0.00 33.43 3.56
1718 1803 5.706833 AGTTCATTGTATTGTCATGTGAGCA 59.293 36.000 0.00 0.00 0.00 4.26
1744 1829 3.551485 TCATCGTATTGTCATGTGAAGCG 59.449 43.478 0.00 0.00 0.00 4.68
1746 1831 5.484085 CGTTCATCGTATTGTCATGTGAAG 58.516 41.667 0.00 0.00 34.52 3.02
1753 1838 2.410392 GTGTGCGTTCATCGTATTGTCA 59.590 45.455 0.00 0.00 42.13 3.58
1754 1839 2.410392 TGTGTGCGTTCATCGTATTGTC 59.590 45.455 0.00 0.00 42.13 3.18
1755 1840 2.409012 TGTGTGCGTTCATCGTATTGT 58.591 42.857 0.00 0.00 42.13 2.71
1756 1841 3.447752 TTGTGTGCGTTCATCGTATTG 57.552 42.857 0.00 0.00 42.13 1.90
1757 1842 4.475763 TTTTGTGTGCGTTCATCGTATT 57.524 36.364 0.00 0.00 42.13 1.89
1956 2388 0.721718 GTGCTATCACTGCGTTCACC 59.278 55.000 0.00 0.00 40.03 4.02
1958 2390 1.798223 GTTGTGCTATCACTGCGTTCA 59.202 47.619 0.00 0.00 43.49 3.18
2009 2441 7.715249 GGATGTTAATATCAGTACTTGCTTGGA 59.285 37.037 13.45 0.00 0.00 3.53
2099 2536 6.872920 TGGAAAATGGATGCCACTTTTATAC 58.127 36.000 0.00 0.00 32.91 1.47


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

AutoCloner maintained by Alex Coulton.