Multiple sequence alignment - TraesCS4A01G280200

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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 TraesCS4A01G280200 chr4A 100.000 2288 0 0 1 2288 588660109 588657822 0.000000e+00 4226
1 TraesCS4A01G280200 chr7A 98.077 2288 44 0 1 2288 141312580 141310293 0.000000e+00 3982
2 TraesCS4A01G280200 chr7A 97.948 2290 39 3 1 2288 140768966 140766683 0.000000e+00 3962
3 TraesCS4A01G280200 chr7A 97.770 2287 48 1 2 2288 141058408 141056125 0.000000e+00 3938
4 TraesCS4A01G280200 chr7A 96.991 2293 42 2 1 2288 141652942 141650672 0.000000e+00 3827
5 TraesCS4A01G280200 chr7A 98.019 1868 36 1 1 1867 141903682 141901815 0.000000e+00 3243
6 TraesCS4A01G280200 chr7A 96.760 463 15 0 1826 2288 141901814 141901352 0.000000e+00 773
7 TraesCS4A01G280200 chr2D 92.724 1718 111 8 3 1713 591013982 591015692 0.000000e+00 2468
8 TraesCS4A01G280200 chr1A 92.753 1711 114 8 4 1709 46320932 46319227 0.000000e+00 2464
9 TraesCS4A01G280200 chr1A 92.519 1711 117 8 4 1709 46224668 46222964 0.000000e+00 2440
10 TraesCS4A01G280200 chr1A 92.344 1711 120 8 4 1709 46268618 46266914 0.000000e+00 2423
11 TraesCS4A01G280200 chr4D 92.808 292 12 3 2000 2288 13344928 13345213 4.550000e-112 414
12 TraesCS4A01G280200 chr4D 93.421 76 5 0 2119 2194 13357306 13357381 1.860000e-21 113
13 TraesCS4A01G280200 chr6A 84.536 291 12 5 2001 2288 201645705 201645445 8.110000e-65 257
14 TraesCS4A01G280200 chr7D 91.667 144 12 0 1709 1852 426987879 426987736 1.390000e-47 200


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 TraesCS4A01G280200 chr4A 588657822 588660109 2287 True 4226 4226 100.0000 1 2288 1 chr4A.!!$R1 2287
1 TraesCS4A01G280200 chr7A 141310293 141312580 2287 True 3982 3982 98.0770 1 2288 1 chr7A.!!$R3 2287
2 TraesCS4A01G280200 chr7A 140766683 140768966 2283 True 3962 3962 97.9480 1 2288 1 chr7A.!!$R1 2287
3 TraesCS4A01G280200 chr7A 141056125 141058408 2283 True 3938 3938 97.7700 2 2288 1 chr7A.!!$R2 2286
4 TraesCS4A01G280200 chr7A 141650672 141652942 2270 True 3827 3827 96.9910 1 2288 1 chr7A.!!$R4 2287
5 TraesCS4A01G280200 chr7A 141901352 141903682 2330 True 2008 3243 97.3895 1 2288 2 chr7A.!!$R5 2287
6 TraesCS4A01G280200 chr2D 591013982 591015692 1710 False 2468 2468 92.7240 3 1713 1 chr2D.!!$F1 1710
7 TraesCS4A01G280200 chr1A 46319227 46320932 1705 True 2464 2464 92.7530 4 1709 1 chr1A.!!$R3 1705
8 TraesCS4A01G280200 chr1A 46222964 46224668 1704 True 2440 2440 92.5190 4 1709 1 chr1A.!!$R1 1705
9 TraesCS4A01G280200 chr1A 46266914 46268618 1704 True 2423 2423 92.3440 4 1709 1 chr1A.!!$R2 1705

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
138 139 1.32769 CCCTTGCTGGCATCTGCATT 61.328 55.0 4.33 0.0 45.06 3.56 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1440 1454 0.035534 TCGGCACAACCATGTAGCAT 60.036 50.0 0.0 0.0 37.82 3.79 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
37 38 4.019051 TGGCCTTCATCTTCTTCTTCATCA 60.019 41.667 3.32 0.0 0.00 3.07
138 139 1.327690 CCCTTGCTGGCATCTGCATT 61.328 55.000 4.33 0.0 45.06 3.56
636 640 3.009143 CAGGGTGAGTAAATATAGGGGCC 59.991 52.174 0.00 0.0 0.00 5.80
669 673 1.973515 AGAAGAGTGACAGTCATGCCA 59.026 47.619 6.51 0.0 0.00 4.92
1065 1074 2.945668 GTTCAAGCTCAGGAACAACACT 59.054 45.455 16.52 0.0 42.23 3.55
1102 1111 1.069978 TGACGGTGAAGCTGATGAACA 59.930 47.619 0.00 0.0 0.00 3.18
1221 1230 2.169352 CCTCAAGGTCACCATCTTCGAT 59.831 50.000 0.00 0.0 0.00 3.59
1295 1304 1.001248 CCAAGGAGTAGGGTCGGGA 59.999 63.158 0.00 0.0 0.00 5.14
1439 1453 2.836262 ACTCTGCTCTGCTTATGATGC 58.164 47.619 0.00 0.0 0.00 3.91
1440 1454 2.169978 ACTCTGCTCTGCTTATGATGCA 59.830 45.455 0.00 0.0 38.81 3.96
2022 2081 2.484651 GCATCGATCGGAGTAGCTAGAA 59.515 50.000 16.41 0.0 0.00 2.10
2056 2115 1.339631 CCGGAAATGGTCAGTTGCCTA 60.340 52.381 0.00 0.0 0.00 3.93
2232 2291 4.489679 AAGACAAAGCCAAAATCTCGAC 57.510 40.909 0.00 0.0 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
636 640 2.694628 CACTCTTCTCCTCCTCTCCATG 59.305 54.545 0.00 0.00 0.00 3.66
779 783 0.459489 GCTTGCCCTTGTTGTCAACA 59.541 50.000 14.48 14.48 40.21 3.33
1065 1074 2.530151 ACCTTCCAGGAGCAGCCA 60.530 61.111 0.00 0.00 37.67 4.75
1221 1230 1.337728 ACGACCTCAATGCAATCGTCA 60.338 47.619 0.00 0.00 41.96 4.35
1295 1304 4.659835 AGACTCGATAGTACTTAGGGAGGT 59.340 45.833 0.00 0.00 35.56 3.85
1439 1453 0.099259 CGGCACAACCATGTAGCATG 59.901 55.000 2.38 2.38 37.82 4.06
1440 1454 0.035534 TCGGCACAACCATGTAGCAT 60.036 50.000 0.00 0.00 37.82 3.79
1575 1592 1.589716 GCATGGGCAGAACCACACTC 61.590 60.000 0.00 0.00 44.72 3.51
1648 1665 3.769300 TGCATAGCCTTCTCAACTCAGTA 59.231 43.478 0.00 0.00 0.00 2.74
1985 2044 1.559965 ATGCTGGAGAGCTTGCTGGA 61.560 55.000 0.00 0.00 46.39 3.86
2022 2081 3.878160 TTTCCGGTTTCTTGCAAGTTT 57.122 38.095 25.19 0.00 0.00 2.66
2056 2115 4.507512 GGAAGATTCTGGGAGGACTTTGTT 60.508 45.833 0.00 0.00 0.00 2.83
2232 2291 2.223688 TGTTTGTTTCGGTGAATGCTGG 60.224 45.455 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.