Multiple sequence alignment - TraesCS6B01G045900

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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 TraesCS6B01G045900 chr6B 100.000 2438 0 0 1 2438 27352995 27350558 0 4503
1 TraesCS6B01G045900 chr6B 96.148 623 24 0 1816 2438 27342144 27341522 0 1018
2 TraesCS6B01G045900 chr6B 94.099 627 35 2 1814 2438 557131637 557132263 0 952
3 TraesCS6B01G045900 chr7B 96.861 1816 55 2 1 1815 22623725 22625539 0 3037
4 TraesCS6B01G045900 chr7B 96.755 1818 53 4 1 1815 22731191 22733005 0 3025
5 TraesCS6B01G045900 chr7B 96.643 1817 58 3 1 1815 22802816 22804631 0 3014
6 TraesCS6B01G045900 chr7B 96.423 1817 63 2 1 1815 22849775 22851591 0 2994
7 TraesCS6B01G045900 chr7B 96.258 1817 66 2 1 1815 22910565 22912381 0 2977
8 TraesCS6B01G045900 chr7B 96.203 1817 64 3 1 1815 22980043 22981856 0 2968
9 TraesCS6B01G045900 chr7B 94.418 627 32 3 1815 2438 705738482 705739108 0 961
10 TraesCS6B01G045900 chr2B 96.753 1817 56 3 1 1815 357927641 357929456 0 3025
11 TraesCS6B01G045900 chr4B 95.118 1823 81 8 1 1819 44959919 44961737 0 2867
12 TraesCS6B01G045900 chr4B 94.382 623 32 2 1816 2435 294407099 294406477 0 953
13 TraesCS6B01G045900 chr4A 91.690 1817 141 8 1 1811 26443704 26441892 0 2510
14 TraesCS6B01G045900 chr4A 93.800 629 35 3 1811 2436 571497035 571497662 0 942
15 TraesCS6B01G045900 chr3B 95.666 623 25 2 1816 2438 652406972 652407592 0 1000
16 TraesCS6B01G045900 chr3B 95.506 623 28 0 1816 2438 652397941 652398563 0 996
17 TraesCS6B01G045900 chr2D 94.071 624 33 3 1815 2436 413215011 413215632 0 944
18 TraesCS6B01G045900 chr2A 93.930 626 35 2 1816 2438 47860334 47859709 0 942


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 TraesCS6B01G045900 chr6B 27350558 27352995 2437 True 4503 4503 100.000 1 2438 1 chr6B.!!$R2 2437
1 TraesCS6B01G045900 chr6B 27341522 27342144 622 True 1018 1018 96.148 1816 2438 1 chr6B.!!$R1 622
2 TraesCS6B01G045900 chr6B 557131637 557132263 626 False 952 952 94.099 1814 2438 1 chr6B.!!$F1 624
3 TraesCS6B01G045900 chr7B 22623725 22625539 1814 False 3037 3037 96.861 1 1815 1 chr7B.!!$F1 1814
4 TraesCS6B01G045900 chr7B 22731191 22733005 1814 False 3025 3025 96.755 1 1815 1 chr7B.!!$F2 1814
5 TraesCS6B01G045900 chr7B 22802816 22804631 1815 False 3014 3014 96.643 1 1815 1 chr7B.!!$F3 1814
6 TraesCS6B01G045900 chr7B 22849775 22851591 1816 False 2994 2994 96.423 1 1815 1 chr7B.!!$F4 1814
7 TraesCS6B01G045900 chr7B 22910565 22912381 1816 False 2977 2977 96.258 1 1815 1 chr7B.!!$F5 1814
8 TraesCS6B01G045900 chr7B 22980043 22981856 1813 False 2968 2968 96.203 1 1815 1 chr7B.!!$F6 1814
9 TraesCS6B01G045900 chr7B 705738482 705739108 626 False 961 961 94.418 1815 2438 1 chr7B.!!$F7 623
10 TraesCS6B01G045900 chr2B 357927641 357929456 1815 False 3025 3025 96.753 1 1815 1 chr2B.!!$F1 1814
11 TraesCS6B01G045900 chr4B 44959919 44961737 1818 False 2867 2867 95.118 1 1819 1 chr4B.!!$F1 1818
12 TraesCS6B01G045900 chr4B 294406477 294407099 622 True 953 953 94.382 1816 2435 1 chr4B.!!$R1 619
13 TraesCS6B01G045900 chr4A 26441892 26443704 1812 True 2510 2510 91.690 1 1811 1 chr4A.!!$R1 1810
14 TraesCS6B01G045900 chr4A 571497035 571497662 627 False 942 942 93.800 1811 2436 1 chr4A.!!$F1 625
15 TraesCS6B01G045900 chr3B 652406972 652407592 620 False 1000 1000 95.666 1816 2438 1 chr3B.!!$F2 622
16 TraesCS6B01G045900 chr3B 652397941 652398563 622 False 996 996 95.506 1816 2438 1 chr3B.!!$F1 622
17 TraesCS6B01G045900 chr2D 413215011 413215632 621 False 944 944 94.071 1815 2436 1 chr2D.!!$F1 621
18 TraesCS6B01G045900 chr2A 47859709 47860334 625 True 942 942 93.930 1816 2438 1 chr2A.!!$R1 622

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
221 222 0.040204 AACCTGCCTGGCTAGCATTT 59.96 50.0 21.03 6.23 40.04 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1745 1755 0.253207 TTCTCTCCCCTCCCTTTCCC 60.253 60.0 0.0 0.0 0.0 3.97 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
144 145 6.437162 CCCCTGATAGACAAAATCCTCAAAAA 59.563 38.462 0.00 0.00 0.00 1.94
221 222 0.040204 AACCTGCCTGGCTAGCATTT 59.960 50.000 21.03 6.23 40.04 2.32
237 241 7.394816 GCTAGCATTTCCATATACCTCCTTTA 58.605 38.462 10.63 0.00 0.00 1.85
355 359 0.598065 CCAACTGGCACCTACTTTGC 59.402 55.000 0.00 0.00 39.41 3.68
386 390 0.778479 ACATGGGGGTTTAGGGGTGT 60.778 55.000 0.00 0.00 0.00 4.16
524 528 6.649557 CCCTAATATCTTTGCTAGTAAACCCG 59.350 42.308 1.42 0.00 0.00 5.28
668 673 3.272285 TCTCCCCTCTCAGTCCAATTCTA 59.728 47.826 0.00 0.00 0.00 2.10
694 699 4.761739 CACTTTACACCATCTGTCACCAAT 59.238 41.667 0.00 0.00 33.91 3.16
710 715 6.099701 TGTCACCAATAATGCTCTACCATAGT 59.900 38.462 0.00 0.00 0.00 2.12
778 783 8.370940 GGATTTTCACATCTACTATGATGGAGA 58.629 37.037 8.96 4.31 45.78 3.71
840 845 0.041982 GGGAGGAGGGTGACTCTCTT 59.958 60.000 12.89 4.20 45.83 2.85
1239 1248 3.999001 CAGTCTGTGCATGTGTTCTATGT 59.001 43.478 0.00 0.00 0.00 2.29
1250 1259 5.357742 TGTGTTCTATGTGCTATGTGGAT 57.642 39.130 0.00 0.00 0.00 3.41
1458 1468 4.884668 ATTGTCGAAAGGGAAGACACTA 57.115 40.909 0.00 0.00 43.54 2.74
1534 1544 2.005370 ATCATAAAGGGGCCAGCATG 57.995 50.000 4.39 2.99 0.00 4.06
1657 1667 0.183492 AAGAAGCTCAAGGTGGTGCA 59.817 50.000 0.00 0.00 0.00 4.57
1745 1755 2.234908 AGTGGAAGAAATCTGGTCTCCG 59.765 50.000 0.00 0.00 0.00 4.63
1790 1804 7.039784 AGTGTTGGTTATTACAGATTTGTGCAT 60.040 33.333 0.00 0.00 38.23 3.96
1837 1851 1.797025 TGACACACAAACACGTCACA 58.203 45.000 0.00 0.00 33.61 3.58
2153 2172 1.812571 GTTGTTCAATCGGCCATCACT 59.187 47.619 2.24 0.00 0.00 3.41
2160 2181 0.179009 ATCGGCCATCACTCCCAATG 60.179 55.000 2.24 0.00 0.00 2.82
2174 2195 4.838986 ACTCCCAATGTATATAAGAGGCGT 59.161 41.667 0.00 0.00 0.00 5.68
2183 2204 5.597182 TGTATATAAGAGGCGTCTGGACTTT 59.403 40.000 10.16 0.00 29.96 2.66
2202 2223 6.429078 GGACTTTCCGTACAAGTAAAGGATTT 59.571 38.462 6.55 0.00 43.42 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
144 145 1.336632 GCCTCTCCAGCCAGACATCT 61.337 60.000 0.00 0.0 0.00 2.90
350 354 3.592059 CATGTTTCTTCCCCATGCAAAG 58.408 45.455 0.00 0.0 30.63 2.77
355 359 1.488390 CCCCATGTTTCTTCCCCATG 58.512 55.000 0.00 0.0 36.56 3.66
477 481 5.402398 GGAAGTTGTGGATGTATTTCTTGC 58.598 41.667 0.00 0.0 0.00 4.01
668 673 2.371841 TGACAGATGGTGTAAAGTGGCT 59.628 45.455 0.00 0.0 40.56 4.75
694 699 7.039434 CCAGATCTCAACTATGGTAGAGCATTA 60.039 40.741 0.00 0.0 0.00 1.90
710 715 5.272402 TCTCATAGTTGTCCCAGATCTCAA 58.728 41.667 0.00 0.0 0.00 3.02
763 768 7.310671 GGCATACCAATTCTCCATCATAGTAGA 60.311 40.741 0.00 0.0 35.26 2.59
778 783 3.951563 TTGCTCTAGGGCATACCAATT 57.048 42.857 20.21 0.0 43.89 2.32
862 867 5.818678 AGTGAACTAGTGGTGTATTTCCA 57.181 39.130 0.00 0.0 0.00 3.53
1239 1248 9.625747 TGTGAATTTCTATTTATCCACATAGCA 57.374 29.630 0.00 0.0 0.00 3.49
1280 1289 6.419484 TCCGTTTCACATCAGTCCATATAT 57.581 37.500 0.00 0.0 0.00 0.86
1438 1448 4.675976 TTAGTGTCTTCCCTTTCGACAA 57.324 40.909 0.00 0.0 39.16 3.18
1534 1544 2.496899 TCTTGGTGGAGAGATTTGGC 57.503 50.000 0.00 0.0 0.00 4.52
1745 1755 0.253207 TTCTCTCCCCTCCCTTTCCC 60.253 60.000 0.00 0.0 0.00 3.97
1837 1851 3.524606 CCGGCGTCGAGGGTACAT 61.525 66.667 12.93 0.0 39.00 2.29
1966 1982 4.007644 CCGCTGCACTCCCTGACA 62.008 66.667 0.00 0.0 0.00 3.58
2153 2172 5.047306 CAGACGCCTCTTATATACATTGGGA 60.047 44.000 0.00 0.0 0.00 4.37
2160 2181 5.708877 AAGTCCAGACGCCTCTTATATAC 57.291 43.478 0.00 0.0 36.20 1.47
2174 2195 5.510179 CCTTTACTTGTACGGAAAGTCCAGA 60.510 44.000 0.67 0.0 38.73 3.86
2183 2204 8.636213 CCTAGATAAATCCTTTACTTGTACGGA 58.364 37.037 0.00 0.0 0.00 4.69


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

AutoCloner maintained by Alex Coulton.