Multiple sequence alignment - TraesCS1B01G202800

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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 TraesCS1B01G202800 chr1B 100.000 4397 0 0 1 4397 364417359 364421755 0.000000e+00 8120.0
1 TraesCS1B01G202800 chr1B 94.549 587 27 2 3816 4397 402788974 402788388 0.000000e+00 902.0
2 TraesCS1B01G202800 chr1B 94.048 84 4 1 112 195 639070554 639070636 4.620000e-25 126.0
3 TraesCS1B01G202800 chr1A 90.818 2788 172 30 697 3422 320225431 320222666 0.000000e+00 3653.0
4 TraesCS1B01G202800 chr1A 97.773 898 19 1 3501 4397 388938610 388939507 0.000000e+00 1546.0
5 TraesCS1B01G202800 chr1A 94.322 317 17 1 3500 3816 388940085 388939770 6.610000e-133 484.0
6 TraesCS1B01G202800 chr1A 94.118 85 5 0 113 197 432615443 432615527 3.570000e-26 130.0
7 TraesCS1B01G202800 chr1D 91.200 2125 124 23 697 2773 250142336 250140227 0.000000e+00 2830.0
8 TraesCS1B01G202800 chr1D 88.316 659 47 14 2805 3440 250140237 250139586 0.000000e+00 763.0
9 TraesCS1B01G202800 chr1D 96.341 82 3 0 112 193 382925241 382925322 7.670000e-28 135.0
10 TraesCS1B01G202800 chr1D 95.238 84 4 0 112 195 90097161 90097078 2.760000e-27 134.0
11 TraesCS1B01G202800 chr1D 100.000 31 0 0 3473 3503 250139575 250139545 1.710000e-04 58.4
12 TraesCS1B01G202800 chr2A 97.216 898 21 2 3504 4397 144268418 144267521 0.000000e+00 1517.0
13 TraesCS1B01G202800 chr2A 97.105 898 23 3 3503 4397 161929594 161930491 0.000000e+00 1511.0
14 TraesCS1B01G202800 chr2B 97.105 898 20 3 3504 4397 749657181 749656286 0.000000e+00 1509.0
15 TraesCS1B01G202800 chr6B 96.983 895 26 1 3504 4397 483866973 483866079 0.000000e+00 1502.0
16 TraesCS1B01G202800 chr4B 96.644 894 28 2 3504 4397 49030649 49031540 0.000000e+00 1483.0
17 TraesCS1B01G202800 chr4B 94.249 313 17 1 3504 3816 49032114 49031803 1.110000e-130 477.0
18 TraesCS1B01G202800 chr5B 95.704 582 21 2 3816 4396 400099634 400099056 0.000000e+00 933.0
19 TraesCS1B01G202800 chr5B 95.238 84 4 0 112 195 711423280 711423197 2.760000e-27 134.0
20 TraesCS1B01G202800 chr5A 98.253 458 8 0 3504 3961 575215325 575215782 0.000000e+00 802.0
21 TraesCS1B01G202800 chr5A 97.303 445 10 1 3955 4397 575226251 575226695 0.000000e+00 754.0
22 TraesCS1B01G202800 chr5D 92.787 305 19 3 196 500 300315157 300314856 5.220000e-119 438.0
23 TraesCS1B01G202800 chr7A 95.294 85 4 0 112 196 67682032 67682116 7.670000e-28 135.0
24 TraesCS1B01G202800 chr3D 94.382 89 4 1 112 200 573897740 573897653 7.670000e-28 135.0
25 TraesCS1B01G202800 chr2D 95.349 86 3 1 112 196 563145308 563145393 7.670000e-28 135.0
26 TraesCS1B01G202800 chr3A 94.186 86 4 1 112 196 208116401 208116486 3.570000e-26 130.0


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 TraesCS1B01G202800 chr1B 364417359 364421755 4396 False 8120.000000 8120 100.000 1 4397 1 chr1B.!!$F1 4396
1 TraesCS1B01G202800 chr1B 402788388 402788974 586 True 902.000000 902 94.549 3816 4397 1 chr1B.!!$R1 581
2 TraesCS1B01G202800 chr1A 320222666 320225431 2765 True 3653.000000 3653 90.818 697 3422 1 chr1A.!!$R1 2725
3 TraesCS1B01G202800 chr1A 388938610 388939507 897 False 1546.000000 1546 97.773 3501 4397 1 chr1A.!!$F1 896
4 TraesCS1B01G202800 chr1D 250139545 250142336 2791 True 1217.133333 2830 93.172 697 3503 3 chr1D.!!$R2 2806
5 TraesCS1B01G202800 chr2A 144267521 144268418 897 True 1517.000000 1517 97.216 3504 4397 1 chr2A.!!$R1 893
6 TraesCS1B01G202800 chr2A 161929594 161930491 897 False 1511.000000 1511 97.105 3503 4397 1 chr2A.!!$F1 894
7 TraesCS1B01G202800 chr2B 749656286 749657181 895 True 1509.000000 1509 97.105 3504 4397 1 chr2B.!!$R1 893
8 TraesCS1B01G202800 chr6B 483866079 483866973 894 True 1502.000000 1502 96.983 3504 4397 1 chr6B.!!$R1 893
9 TraesCS1B01G202800 chr4B 49030649 49031540 891 False 1483.000000 1483 96.644 3504 4397 1 chr4B.!!$F1 893
10 TraesCS1B01G202800 chr5B 400099056 400099634 578 True 933.000000 933 95.704 3816 4396 1 chr5B.!!$R1 580


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
68 69 0.033228 CATGCCCAACCGAAAAGCAA 59.967 50.0 0.00 0.0 36.95 3.91 F
1334 1384 0.033504 CGGGCGCCATAGTATGAGTT 59.966 55.0 30.85 0.0 0.00 3.01 F
2724 2779 0.465705 ATGCAGGATACCGACTGTGG 59.534 55.0 0.00 0.0 37.07 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1903 1958 0.030908 CGAGCTCGGTTATCAGGGTC 59.969 60.0 28.40 0.0 35.37 4.46 R
3091 3154 0.036858 TGTACAAGTATGCGCTGCCA 60.037 50.0 9.73 0.0 0.00 4.92 R
3737 3829 0.807667 CTTTCGTCTAGGCGCTGCAT 60.808 55.0 12.97 0.0 0.00 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)



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

AutoCloner maintained by Alex Coulton.