Multiple sequence alignment - TraesCS4A01G392900

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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 TraesCS4A01G392900 chr4A 100.000 2333 0 0 1 2333 668642195 668639863 0.000000e+00 4309
1 TraesCS4A01G392900 chr4A 86.695 1646 212 7 3 1645 438690795 438689154 0.000000e+00 1820
2 TraesCS4A01G392900 chr6B 98.055 1645 32 0 1 1645 59939089 59940733 0.000000e+00 2861
3 TraesCS4A01G392900 chr1B 98.055 1645 32 0 1 1645 410047225 410045581 0.000000e+00 2861
4 TraesCS4A01G392900 chr1B 95.313 1643 76 1 3 1645 24201189 24202830 0.000000e+00 2606
5 TraesCS4A01G392900 chr1B 82.878 695 112 6 1639 2331 567372027 567371338 3.290000e-173 617
6 TraesCS4A01G392900 chr5B 97.730 1586 36 0 60 1645 80274032 80272447 0.000000e+00 2730
7 TraesCS4A01G392900 chr5B 97.541 1586 39 0 60 1645 80678821 80677236 0.000000e+00 2713
8 TraesCS4A01G392900 chr7A 88.741 1652 174 11 3 1647 12891348 12892994 0.000000e+00 2010
9 TraesCS4A01G392900 chr7A 89.001 691 57 6 1639 2329 117640604 117639933 0.000000e+00 837
10 TraesCS4A01G392900 chr7A 83.954 698 99 10 1639 2331 136352626 136351937 0.000000e+00 656
11 TraesCS4A01G392900 chr6A 88.554 1660 178 11 3 1654 133819583 133821238 0.000000e+00 2002
12 TraesCS4A01G392900 chr5A 86.165 1648 214 13 3 1645 602240361 602241999 0.000000e+00 1768
13 TraesCS4A01G392900 chr5A 90.831 698 55 8 1639 2332 219241769 219242461 0.000000e+00 926
14 TraesCS4A01G392900 chr2A 91.799 695 54 1 1639 2333 62239610 62238919 0.000000e+00 965
15 TraesCS4A01G392900 chr4B 89.984 629 45 9 1639 2252 347582368 347582993 0.000000e+00 797
16 TraesCS4A01G392900 chr2B 83.931 697 102 8 1639 2331 157281951 157281261 0.000000e+00 658
17 TraesCS4A01G392900 chr7D 83.965 686 97 7 1651 2331 162132677 162133354 0.000000e+00 645
18 TraesCS4A01G392900 chr3B 83.165 695 109 7 1639 2331 145893910 145893222 1.520000e-176 628


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 TraesCS4A01G392900 chr4A 668639863 668642195 2332 True 4309 4309 100.000 1 2333 1 chr4A.!!$R2 2332
1 TraesCS4A01G392900 chr4A 438689154 438690795 1641 True 1820 1820 86.695 3 1645 1 chr4A.!!$R1 1642
2 TraesCS4A01G392900 chr6B 59939089 59940733 1644 False 2861 2861 98.055 1 1645 1 chr6B.!!$F1 1644
3 TraesCS4A01G392900 chr1B 410045581 410047225 1644 True 2861 2861 98.055 1 1645 1 chr1B.!!$R1 1644
4 TraesCS4A01G392900 chr1B 24201189 24202830 1641 False 2606 2606 95.313 3 1645 1 chr1B.!!$F1 1642
5 TraesCS4A01G392900 chr1B 567371338 567372027 689 True 617 617 82.878 1639 2331 1 chr1B.!!$R2 692
6 TraesCS4A01G392900 chr5B 80272447 80274032 1585 True 2730 2730 97.730 60 1645 1 chr5B.!!$R1 1585
7 TraesCS4A01G392900 chr5B 80677236 80678821 1585 True 2713 2713 97.541 60 1645 1 chr5B.!!$R2 1585
8 TraesCS4A01G392900 chr7A 12891348 12892994 1646 False 2010 2010 88.741 3 1647 1 chr7A.!!$F1 1644
9 TraesCS4A01G392900 chr7A 117639933 117640604 671 True 837 837 89.001 1639 2329 1 chr7A.!!$R1 690
10 TraesCS4A01G392900 chr7A 136351937 136352626 689 True 656 656 83.954 1639 2331 1 chr7A.!!$R2 692
11 TraesCS4A01G392900 chr6A 133819583 133821238 1655 False 2002 2002 88.554 3 1654 1 chr6A.!!$F1 1651
12 TraesCS4A01G392900 chr5A 602240361 602241999 1638 False 1768 1768 86.165 3 1645 1 chr5A.!!$F2 1642
13 TraesCS4A01G392900 chr5A 219241769 219242461 692 False 926 926 90.831 1639 2332 1 chr5A.!!$F1 693
14 TraesCS4A01G392900 chr2A 62238919 62239610 691 True 965 965 91.799 1639 2333 1 chr2A.!!$R1 694
15 TraesCS4A01G392900 chr4B 347582368 347582993 625 False 797 797 89.984 1639 2252 1 chr4B.!!$F1 613
16 TraesCS4A01G392900 chr2B 157281261 157281951 690 True 658 658 83.931 1639 2331 1 chr2B.!!$R1 692
17 TraesCS4A01G392900 chr7D 162132677 162133354 677 False 645 645 83.965 1651 2331 1 chr7D.!!$F1 680
18 TraesCS4A01G392900 chr3B 145893222 145893910 688 True 628 628 83.165 1639 2331 1 chr3B.!!$R1 692

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
58 59 1.694169 AATGCCTCGTCTGGGGGAT 60.694 57.895 0.0 0.0 35.17 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1707 1729 0.45826 GGTTGCACCGGTTTGAAACT 59.542 50.0 2.97 0.0 35.57 2.66 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
58 59 1.694169 AATGCCTCGTCTGGGGGAT 60.694 57.895 0.00 0.00 35.17 3.85
368 369 5.187186 TGAAAGCTAAGTACTTCAGTAGGGG 59.813 44.000 12.39 0.00 0.00 4.79
488 489 2.340337 GCAATCTGGAAACATTGCCAC 58.660 47.619 5.49 0.00 45.97 5.01
538 539 2.477245 TCCCTATGGCTGAGCAGTTTA 58.523 47.619 6.82 0.00 0.00 2.01
651 652 5.939764 ATAGTGAGCTTAATGACCAGTGA 57.060 39.130 0.00 0.00 0.00 3.41
881 882 2.692557 CTGTCCTGACTAGGGATGTGAG 59.307 54.545 0.00 0.00 44.70 3.51
1031 1032 4.036027 CACTGCTTTGTGCCCTGATAATAG 59.964 45.833 0.00 0.00 42.00 1.73
1148 1150 5.062558 CGTATCGTAACAGGGTTACTTTTGG 59.937 44.000 15.01 2.48 0.00 3.28
1306 1308 4.643463 GATGATGATGAGGATCTGTGCTT 58.357 43.478 0.00 0.00 34.92 3.91
1434 1438 3.357079 GTTGTGAGCCTGGGTGCG 61.357 66.667 1.59 0.00 36.02 5.34
1482 1489 6.042093 CCTGGTTCCTAGCTTTAGATGTATGA 59.958 42.308 0.00 0.00 0.00 2.15
1501 1508 3.770424 GTCGTCGGGTTTTCGCCG 61.770 66.667 0.00 0.00 35.84 6.46
1577 1585 1.807142 GAACTCGCTTCCCCTTTTCTG 59.193 52.381 0.00 0.00 0.00 3.02
1841 1863 5.067674 CAGATCGAGGAACTTCTTCATCTCT 59.932 44.000 10.34 3.60 41.55 3.10
1843 1865 7.004086 AGATCGAGGAACTTCTTCATCTCTAT 58.996 38.462 2.18 0.00 41.55 1.98
1871 1894 1.154197 GCCCACTACGGAACAAAGTC 58.846 55.000 0.00 0.00 36.56 3.01
1872 1895 1.425412 CCCACTACGGAACAAAGTCG 58.575 55.000 0.00 0.00 36.56 4.18
2033 2061 1.903860 TGGTTAGGGCTCGTACAATGT 59.096 47.619 0.00 0.00 0.00 2.71
2084 2112 2.905075 TGCATCATCCGGACTACTTTG 58.095 47.619 6.12 0.00 0.00 2.77
2123 2152 4.530161 AGCCTAGAGTCTGACACTGAAAAT 59.470 41.667 16.50 0.00 34.41 1.82
2184 2213 8.087136 TGTGCATGTTAATTTGCTCAAGATTTA 58.913 29.630 12.22 0.00 38.84 1.40
2217 2248 1.448013 GTGCCGGCCTTAGAGTGAC 60.448 63.158 26.77 8.15 0.00 3.67
2218 2249 2.187163 GCCGGCCTTAGAGTGACC 59.813 66.667 18.11 0.00 0.00 4.02
2294 2328 6.922957 TGAAAACTAATTCCACATGAGTTTGC 59.077 34.615 0.00 2.32 39.60 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
117 118 8.871629 TGGCAAGTATAGTTTTGGATAAAAGA 57.128 30.769 0.00 0.00 36.51 2.52
368 369 6.854496 TCATTTTAATATCAGCCACGGTAC 57.146 37.500 0.00 0.00 0.00 3.34
538 539 7.440523 AATTGCAAATAGAGAAAAGACGAGT 57.559 32.000 1.71 0.00 0.00 4.18
587 588 4.040047 TGAGGAGGGATCAGCATTTAAGA 58.960 43.478 0.00 0.00 0.00 2.10
651 652 6.296026 TCTAGCCAATTTACTCACAACAACT 58.704 36.000 0.00 0.00 0.00 3.16
839 840 2.036346 GCATCCTGAAAAAGTTGCCACT 59.964 45.455 0.00 0.00 33.11 4.00
1031 1032 3.056607 ACACCATGAATAAGCTTGCCAAC 60.057 43.478 9.86 0.00 0.00 3.77
1127 1129 4.202493 ACCCAAAAGTAACCCTGTTACGAT 60.202 41.667 10.50 3.07 0.00 3.73
1148 1150 2.544277 GGGTTTGTAAGCGGTTTGAACC 60.544 50.000 21.22 21.22 45.76 3.62
1306 1308 0.599204 GACGCCTCTTCGTGGTTTGA 60.599 55.000 0.00 0.00 43.42 2.69
1434 1438 0.759060 AACAGCCCCCAAAAGTCACC 60.759 55.000 0.00 0.00 0.00 4.02
1482 1489 2.030958 GGCGAAAACCCGACGACAT 61.031 57.895 0.00 0.00 35.00 3.06
1577 1585 5.461526 GGAAATACAACAGTCCAAGAAAGC 58.538 41.667 0.00 0.00 0.00 3.51
1707 1729 0.458260 GGTTGCACCGGTTTGAAACT 59.542 50.000 2.97 0.00 35.57 2.66
1709 1731 0.895530 TTGGTTGCACCGGTTTGAAA 59.104 45.000 2.97 0.00 42.58 2.69
1792 1814 7.147949 TGCATGGGTTTGTTTCATTGAAAATTT 60.148 29.630 13.21 0.00 33.14 1.82
1841 1863 6.268158 TGTTCCGTAGTGGGCATCTTATTATA 59.732 38.462 0.00 0.00 38.76 0.98
1843 1865 4.406326 TGTTCCGTAGTGGGCATCTTATTA 59.594 41.667 0.00 0.00 38.76 0.98
1853 1876 1.269936 ACGACTTTGTTCCGTAGTGGG 60.270 52.381 0.00 0.00 38.76 4.61
1931 1954 9.645059 CTGAACCGTTATTGATCATGTATATCT 57.355 33.333 0.00 0.00 0.00 1.98
1947 1970 4.000988 GAGATGGCTTTTCTGAACCGTTA 58.999 43.478 0.00 0.00 0.00 3.18
1950 1973 2.417933 CTGAGATGGCTTTTCTGAACCG 59.582 50.000 0.00 0.00 0.00 4.44
1951 1974 3.416156 ACTGAGATGGCTTTTCTGAACC 58.584 45.455 5.15 0.00 0.00 3.62
2033 2061 2.441750 AGGATTTTATTCCTAGCGCCCA 59.558 45.455 2.29 0.00 44.50 5.36
2070 2098 0.107654 GCCAGCAAAGTAGTCCGGAT 60.108 55.000 7.81 0.00 0.00 4.18
2074 2102 1.009829 CGATGCCAGCAAAGTAGTCC 58.990 55.000 0.00 0.00 0.00 3.85
2076 2104 1.001974 TGTCGATGCCAGCAAAGTAGT 59.998 47.619 0.00 0.00 0.00 2.73
2084 2112 1.502163 GGCTATGTGTCGATGCCAGC 61.502 60.000 0.00 0.00 42.79 4.85
2123 2152 7.392673 GCCCTAGTAGCTACATTGTGTATACTA 59.607 40.741 25.28 5.61 33.32 1.82
2184 2213 0.102300 GGCACCAACAAGAGCGTTTT 59.898 50.000 0.00 0.00 0.00 2.43
2217 2248 7.272244 ACCAACAGATGAAAAGGTTAAAAAGG 58.728 34.615 0.00 0.00 0.00 3.11
2218 2249 7.167468 CGACCAACAGATGAAAAGGTTAAAAAG 59.833 37.037 0.00 0.00 0.00 2.27


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

AutoCloner maintained by Alex Coulton.