Multiple sequence alignment - TraesCS3A01G080400

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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 TraesCS3A01G080400 chr3A 100.000 2753 0 0 1 2753 51916341 51919093 0.000000 5084.0
1 TraesCS3A01G080400 chrUn 98.407 1758 27 1 1 1758 221548235 221546479 0.000000 3090.0
2 TraesCS3A01G080400 chrUn 98.459 1752 26 1 1 1752 186191233 186189483 0.000000 3085.0
3 TraesCS3A01G080400 chrUn 97.614 922 20 1 1834 2753 267898986 267898065 0.000000 1580.0
4 TraesCS3A01G080400 chrUn 100.000 31 0 0 1781 1811 369394633 369394663 0.000106 58.4
5 TraesCS3A01G080400 chr7B 98.289 1753 28 2 1 1752 743006245 743007996 0.000000 3070.0
6 TraesCS3A01G080400 chr7D 98.288 1752 25 2 1 1752 579029919 579031665 0.000000 3064.0
7 TraesCS3A01G080400 chr7D 97.722 922 19 1 1834 2753 382036790 382037711 0.000000 1585.0
8 TraesCS3A01G080400 chr7D 97.616 923 19 2 1834 2753 579008573 579007651 0.000000 1580.0
9 TraesCS3A01G080400 chr7D 97.186 924 22 2 1834 2753 203566844 203565921 0.000000 1559.0
10 TraesCS3A01G080400 chr7D 100.000 31 0 0 1781 1811 382096409 382096439 0.000106 58.4
11 TraesCS3A01G080400 chr4D 98.058 1751 28 2 1 1751 123654659 123652915 0.000000 3040.0
12 TraesCS3A01G080400 chr4D 97.619 924 18 2 1834 2753 123671345 123672268 0.000000 1581.0
13 TraesCS3A01G080400 chr4B 97.831 1752 37 1 1 1752 209271127 209269377 0.000000 3024.0
14 TraesCS3A01G080400 chr6D 97.660 1752 39 1 1 1752 369917824 369916075 0.000000 3007.0
15 TraesCS3A01G080400 chr6D 97.603 1752 40 2 1 1752 283153938 283152189 0.000000 3001.0
16 TraesCS3A01G080400 chr6D 96.316 923 28 4 1834 2753 102355990 102356909 0.000000 1511.0
17 TraesCS3A01G080400 chr7A 97.546 1752 39 1 1 1752 120880632 120882379 0.000000 2994.0
18 TraesCS3A01G080400 chr1A 97.746 1198 24 1 1559 2753 278508963 278510160 0.000000 2060.0
19 TraesCS3A01G080400 chr3D 96.963 922 25 2 1834 2753 154778132 154777212 0.000000 1544.0
20 TraesCS3A01G080400 chr2D 96.855 922 27 1 1834 2753 200905280 200904359 0.000000 1541.0
21 TraesCS3A01G080400 chr1B 100.000 34 0 0 1778 1811 93865857 93865824 0.000002 63.9
22 TraesCS3A01G080400 chr1B 100.000 34 0 0 1778 1811 339047771 339047804 0.000002 63.9
23 TraesCS3A01G080400 chr6B 100.000 30 0 0 1782 1811 402906291 402906320 0.000383 56.5


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 TraesCS3A01G080400 chr3A 51916341 51919093 2752 False 5084 5084 100.000 1 2753 1 chr3A.!!$F1 2752
1 TraesCS3A01G080400 chrUn 221546479 221548235 1756 True 3090 3090 98.407 1 1758 1 chrUn.!!$R2 1757
2 TraesCS3A01G080400 chrUn 186189483 186191233 1750 True 3085 3085 98.459 1 1752 1 chrUn.!!$R1 1751
3 TraesCS3A01G080400 chrUn 267898065 267898986 921 True 1580 1580 97.614 1834 2753 1 chrUn.!!$R3 919
4 TraesCS3A01G080400 chr7B 743006245 743007996 1751 False 3070 3070 98.289 1 1752 1 chr7B.!!$F1 1751
5 TraesCS3A01G080400 chr7D 579029919 579031665 1746 False 3064 3064 98.288 1 1752 1 chr7D.!!$F3 1751
6 TraesCS3A01G080400 chr7D 382036790 382037711 921 False 1585 1585 97.722 1834 2753 1 chr7D.!!$F1 919
7 TraesCS3A01G080400 chr7D 579007651 579008573 922 True 1580 1580 97.616 1834 2753 1 chr7D.!!$R2 919
8 TraesCS3A01G080400 chr7D 203565921 203566844 923 True 1559 1559 97.186 1834 2753 1 chr7D.!!$R1 919
9 TraesCS3A01G080400 chr4D 123652915 123654659 1744 True 3040 3040 98.058 1 1751 1 chr4D.!!$R1 1750
10 TraesCS3A01G080400 chr4D 123671345 123672268 923 False 1581 1581 97.619 1834 2753 1 chr4D.!!$F1 919
11 TraesCS3A01G080400 chr4B 209269377 209271127 1750 True 3024 3024 97.831 1 1752 1 chr4B.!!$R1 1751
12 TraesCS3A01G080400 chr6D 369916075 369917824 1749 True 3007 3007 97.660 1 1752 1 chr6D.!!$R2 1751
13 TraesCS3A01G080400 chr6D 283152189 283153938 1749 True 3001 3001 97.603 1 1752 1 chr6D.!!$R1 1751
14 TraesCS3A01G080400 chr6D 102355990 102356909 919 False 1511 1511 96.316 1834 2753 1 chr6D.!!$F1 919
15 TraesCS3A01G080400 chr7A 120880632 120882379 1747 False 2994 2994 97.546 1 1752 1 chr7A.!!$F1 1751
16 TraesCS3A01G080400 chr1A 278508963 278510160 1197 False 2060 2060 97.746 1559 2753 1 chr1A.!!$F1 1194
17 TraesCS3A01G080400 chr3D 154777212 154778132 920 True 1544 1544 96.963 1834 2753 1 chr3D.!!$R1 919
18 TraesCS3A01G080400 chr2D 200904359 200905280 921 True 1541 1541 96.855 1834 2753 1 chr2D.!!$R1 919

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
329 330 0.248621 CCCGGCGATCAAATTCTTGC 60.249 55.0 9.3 0.0 32.14 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1863 1866 0.557729 CCCGGTAGGTAAGTAGGGGA 59.442 60.0 0.0 0.0 35.16 4.81 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
47 48 7.934665 GGAGGATCTTAGAAGGGAATTAGAAAC 59.065 40.741 0.00 0.0 33.73 2.78
98 99 1.747444 TCTTTTCTCTTCCAGCCCCT 58.253 50.000 0.00 0.0 0.00 4.79
329 330 0.248621 CCCGGCGATCAAATTCTTGC 60.249 55.000 9.30 0.0 32.14 4.01
516 517 2.427095 GTTGTTGCCACCAAGTCTCTTT 59.573 45.455 0.00 0.0 0.00 2.52
648 649 7.355778 CAATTTTTAGTCTTCATCTATCGGGC 58.644 38.462 0.00 0.0 0.00 6.13
709 710 1.621317 TCTTCAACATGCGTGGACCTA 59.379 47.619 11.36 0.0 0.00 3.08
798 799 3.387947 CTTCCGGTACTGGCGGGT 61.388 66.667 16.58 0.0 0.00 5.28
823 824 9.296400 GTGCAATTACAATGTTATTAACCGATT 57.704 29.630 4.17 0.0 0.00 3.34
1155 1156 9.093458 ACAGGAATCAAAATCTTTAGTTGGATT 57.907 29.630 0.00 0.0 34.14 3.01
1354 1355 4.062293 GGGAGCCGTTTTTGCTTTATTTT 58.938 39.130 0.00 0.0 39.69 1.82
1495 1496 1.152756 GGGCTTTCGGGTATGCCAT 60.153 57.895 1.04 0.0 46.53 4.40
1732 1733 2.158813 ACTTTTGGAGAACTTCCTGCGA 60.159 45.455 0.00 0.0 46.92 5.10
1863 1866 3.300388 TCAGGAAATAGAGATGCCGAGT 58.700 45.455 0.00 0.0 0.00 4.18
2005 2016 6.457122 CGATAGCGAATTCATACGAGGACTAT 60.457 42.308 6.22 0.0 40.82 2.12
2046 2057 4.056125 CAGGAGGTCGAGCGCACA 62.056 66.667 19.80 0.0 0.00 4.57
2061 2072 1.939934 CGCACACTTTCCTCAGTTTCA 59.060 47.619 0.00 0.0 0.00 2.69
2113 2124 1.728490 GCAAAGGGGATAGCCTTGCG 61.728 60.000 6.70 0.0 34.48 4.85
2256 2267 8.102676 TGAATTCATGAATCCTGTTTCTAGTGA 58.897 33.333 20.95 0.0 0.00 3.41
2302 2313 1.047801 AAACGGGAAAGGCAAAGCAT 58.952 45.000 0.00 0.0 0.00 3.79
2568 2579 1.822371 TGCTGTAGTGAACCGCATCTA 59.178 47.619 0.00 0.0 42.57 1.98
2591 2602 2.522436 ACCGGGAGTCGTGAACCA 60.522 61.111 6.32 0.0 37.11 3.67
2592 2603 1.911766 ACCGGGAGTCGTGAACCAT 60.912 57.895 6.32 0.0 37.11 3.55
2749 2760 6.010219 TCCCTCCTTATTTTCACTCCAAAAG 58.990 40.000 0.00 0.0 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
516 517 5.459505 ACTAAGGCTGAGCTTAATAGGAGA 58.540 41.667 3.72 0.00 0.00 3.71
645 646 6.643388 AGAACCTAAAATTGATGAAATGCCC 58.357 36.000 0.00 0.00 0.00 5.36
709 710 8.200024 AGTGGTAATCTATGCATAGTCATTCT 57.800 34.615 28.51 17.32 0.00 2.40
798 799 9.295214 CAATCGGTTAATAACATTGTAATTGCA 57.705 29.630 5.45 0.00 0.00 4.08
1123 1124 3.716431 AGATTTTGATTCCTGTGGGCAT 58.284 40.909 0.00 0.00 0.00 4.40
1155 1156 1.229820 ACCTCCCCACATGGTAGCA 60.230 57.895 0.00 0.00 31.50 3.49
1174 1175 5.124776 ACATGGGTGTTTTGTATTGTATCGG 59.875 40.000 0.00 0.00 34.01 4.18
1354 1355 4.542525 ACCCACCCAATAGTAAAATCCAGA 59.457 41.667 0.00 0.00 0.00 3.86
1495 1496 3.387699 TCTGGATAATCTGGAATGCGACA 59.612 43.478 0.00 0.00 0.00 4.35
1732 1733 5.392057 GCGCCTAGCTTTTTGTCTCTTTTAT 60.392 40.000 0.00 0.00 44.04 1.40
1841 1842 3.900601 ACTCGGCATCTCTATTTCCTGAT 59.099 43.478 0.00 0.00 0.00 2.90
1863 1866 0.557729 CCCGGTAGGTAAGTAGGGGA 59.442 60.000 0.00 0.00 35.16 4.81
2005 2016 5.450412 GGAAGGAATGCAATTATTCGCTTCA 60.450 40.000 20.02 0.00 40.85 3.02
2046 2057 5.302823 CCCTTGATTTGAAACTGAGGAAAGT 59.697 40.000 4.46 0.00 0.00 2.66
2061 2072 7.218314 AGGATCTATCTTTGTCCCTTGATTT 57.782 36.000 0.00 0.00 0.00 2.17
2256 2267 5.062308 CGTACCTTTCGTAGTAGTTACTCGT 59.938 44.000 0.00 0.00 37.73 4.18
2568 2579 0.968901 TCACGACTCCCGGTGCTTAT 60.969 55.000 0.00 0.00 43.93 1.73
2591 2602 4.729868 AGTTTAAGAAGGACCTTGTGCAT 58.270 39.130 12.68 0.00 0.00 3.96
2592 2603 4.164843 AGTTTAAGAAGGACCTTGTGCA 57.835 40.909 12.68 0.00 0.00 4.57


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

AutoCloner maintained by Alex Coulton.