Multiple sequence alignment - TraesCS4A01G337300

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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 TraesCS4A01G337300 chr4A 100.000 4479 0 0 1 4479 619376424 619371946 0.000000e+00 8272.0
1 TraesCS4A01G337300 chr4A 88.559 909 94 4 2548 3456 619384940 619384042 0.000000e+00 1094.0
2 TraesCS4A01G337300 chr4A 83.715 743 93 13 1548 2280 619418125 619417401 0.000000e+00 676.0
3 TraesCS4A01G337300 chr4A 85.021 701 56 22 3502 4202 619384045 619383394 0.000000e+00 667.0
4 TraesCS4A01G337300 chr4A 89.885 435 42 2 2636 3069 619407753 619407320 3.910000e-155 558.0
5 TraesCS4A01G337300 chr4A 84.575 577 64 2 1925 2501 619551811 619551260 2.360000e-152 549.0
6 TraesCS4A01G337300 chr4A 83.189 577 62 7 1925 2501 619491344 619490803 3.110000e-136 496.0
7 TraesCS4A01G337300 chr4A 78.884 502 75 12 1 497 11986671 11986196 1.210000e-80 311.0
8 TraesCS4A01G337300 chr4A 90.355 197 18 1 2873 3069 619490695 619490500 1.600000e-64 257.0
9 TraesCS4A01G337300 chr4A 90.355 197 18 1 2873 3069 619551152 619550957 1.600000e-64 257.0
10 TraesCS4A01G337300 chr4A 88.889 198 20 1 602 797 677114876 677114679 4.480000e-60 243.0
11 TraesCS4A01G337300 chr4A 96.000 125 5 0 673 797 677115708 677115832 2.110000e-48 204.0
12 TraesCS4A01G337300 chr4A 92.742 124 9 0 674 797 11986839 11986962 3.560000e-41 180.0
13 TraesCS4A01G337300 chr4A 92.000 125 10 0 673 797 619376593 619376717 4.600000e-40 176.0
14 TraesCS4A01G337300 chr4A 79.424 243 33 7 971 1204 619385619 619385385 6.000000e-34 156.0
15 TraesCS4A01G337300 chr4A 90.217 92 9 0 2370 2461 619416747 619416656 2.190000e-23 121.0
16 TraesCS4A01G337300 chr4A 75.940 133 23 8 1347 1472 619418302 619418172 4.840000e-05 60.2
17 TraesCS4A01G337300 chr5B 98.463 4489 45 11 1 4479 692698030 692693556 0.000000e+00 7886.0
18 TraesCS4A01G337300 chr5B 88.339 909 96 1 2548 3456 692706215 692705317 0.000000e+00 1083.0
19 TraesCS4A01G337300 chr5B 84.879 701 57 21 3502 4202 692705320 692704669 0.000000e+00 662.0
20 TraesCS4A01G337300 chr5B 82.178 505 71 11 1510 2013 692748423 692747937 2.490000e-112 416.0
21 TraesCS4A01G337300 chr5B 90.584 308 29 0 2762 3069 692747298 692746991 4.170000e-110 409.0
22 TraesCS4A01G337300 chr5B 89.251 307 21 3 2463 2757 692747920 692747614 1.520000e-99 374.0
23 TraesCS4A01G337300 chr5B 92.000 125 10 0 673 797 692698199 692698323 4.600000e-40 176.0
24 TraesCS4A01G337300 chr5B 78.776 245 33 12 971 1204 692706896 692706660 3.610000e-31 147.0
25 TraesCS4A01G337300 chr5B 100.000 28 0 0 1 28 692699079 692699052 8.000000e-03 52.8
26 TraesCS4A01G337300 chr5D 93.490 2980 152 21 848 3807 548485629 548482672 0.000000e+00 4390.0
27 TraesCS4A01G337300 chr5D 85.696 1566 165 32 1510 3069 548536140 548534628 0.000000e+00 1596.0
28 TraesCS4A01G337300 chr5D 93.627 612 24 3 3839 4450 548482249 548481653 0.000000e+00 900.0
29 TraesCS4A01G337300 chr3A 84.837 521 54 16 1 500 40283192 40282676 6.690000e-138 501.0
30 TraesCS4A01G337300 chr3A 77.778 522 75 24 1 497 77403737 77403232 2.640000e-72 283.0
31 TraesCS4A01G337300 chr3A 89.500 200 19 1 602 799 77402898 77402699 7.440000e-63 252.0
32 TraesCS4A01G337300 chr3A 89.888 178 18 0 510 687 40251694 40251517 3.480000e-56 230.0
33 TraesCS4A01G337300 chr3A 95.200 125 6 0 673 797 40249809 40249685 9.830000e-47 198.0
34 TraesCS4A01G337300 chr3A 93.600 125 8 0 673 797 77403872 77403996 2.130000e-43 187.0
35 TraesCS4A01G337300 chr3A 100.000 37 0 0 815 851 40249697 40249661 8.040000e-08 69.4
36 TraesCS4A01G337300 chr3A 90.698 43 4 0 815 857 77402713 77402671 1.740000e-04 58.4


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 TraesCS4A01G337300 chr4A 619371946 619376424 4478 True 8272.000000 8272 100.000000 1 4479 1 chr4A.!!$R2 4478
1 TraesCS4A01G337300 chr4A 619383394 619385619 2225 True 639.000000 1094 84.334667 971 4202 3 chr4A.!!$R5 3231
2 TraesCS4A01G337300 chr4A 619550957 619551811 854 True 403.000000 549 87.465000 1925 3069 2 chr4A.!!$R8 1144
3 TraesCS4A01G337300 chr4A 619490500 619491344 844 True 376.500000 496 86.772000 1925 3069 2 chr4A.!!$R7 1144
4 TraesCS4A01G337300 chr4A 619416656 619418302 1646 True 285.733333 676 83.290667 1347 2461 3 chr4A.!!$R6 1114
5 TraesCS4A01G337300 chr5B 692693556 692699079 5523 True 3969.400000 7886 99.231500 1 4479 2 chr5B.!!$R1 4478
6 TraesCS4A01G337300 chr5B 692704669 692706896 2227 True 630.666667 1083 83.998000 971 4202 3 chr5B.!!$R2 3231
7 TraesCS4A01G337300 chr5B 692746991 692748423 1432 True 399.666667 416 87.337667 1510 3069 3 chr5B.!!$R3 1559
8 TraesCS4A01G337300 chr5D 548481653 548485629 3976 True 2645.000000 4390 93.558500 848 4450 2 chr5D.!!$R2 3602
9 TraesCS4A01G337300 chr5D 548534628 548536140 1512 True 1596.000000 1596 85.696000 1510 3069 1 chr5D.!!$R1 1559
10 TraesCS4A01G337300 chr3A 40282676 40283192 516 True 501.000000 501 84.837000 1 500 1 chr3A.!!$R1 499

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
28 1078 4.262635 CCACCATAGATCGTGATAAAGGCT 60.263 45.833 3.11 0.0 31.36 4.58 F
3134 5201 5.450818 TGTAGCCCATTGGATAAGTTCTT 57.549 39.130 3.62 0.0 33.44 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3134 5201 0.473755 TCTTGGAGGCAGCTTGACAA 59.526 50.0 0.0 0.0 0.0 3.18 R
4359 6820 0.538287 GGAAGGGAACAAGCAGCACT 60.538 55.0 0.0 0.0 0.0 4.40 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
28 1078 4.262635 CCACCATAGATCGTGATAAAGGCT 60.263 45.833 3.11 0.00 31.36 4.58
3134 5201 5.450818 TGTAGCCCATTGGATAAGTTCTT 57.549 39.130 3.62 0.00 33.44 2.52
3145 5212 4.216257 TGGATAAGTTCTTTGTCAAGCTGC 59.784 41.667 0.00 0.00 0.00 5.25
3530 5598 6.480524 TTTCTGACAGATATGGACAAAACG 57.519 37.500 5.87 0.00 0.00 3.60
3879 6338 1.302383 CTGTGACTCCGAGCTCGACT 61.302 60.000 36.59 18.02 43.02 4.18
4023 6482 3.739300 ACTGAACGTGTACCGAAAGATTG 59.261 43.478 10.17 0.00 40.70 2.67
4032 6491 6.074835 CGTGTACCGAAAGATTGTATCATCTG 60.075 42.308 0.00 0.00 39.56 2.90
4074 6533 5.543507 ACCACCATTTCTTTATTTGTGCA 57.456 34.783 0.00 0.00 0.00 4.57
4075 6534 5.923204 ACCACCATTTCTTTATTTGTGCAA 58.077 33.333 0.00 0.00 0.00 4.08
4149 6608 1.371558 GGGGCTCGAAACAGTGACT 59.628 57.895 0.00 0.00 0.00 3.41
4187 6646 9.509956 TTTCGGTTGAAAGAATTAGATTAAGGA 57.490 29.630 0.00 0.00 39.13 3.36
4236 6695 4.766891 ACCAACCAGGAAAGTAATGTGATG 59.233 41.667 0.00 0.00 41.22 3.07
4237 6696 4.766891 CCAACCAGGAAAGTAATGTGATGT 59.233 41.667 0.00 0.00 41.22 3.06
4238 6697 5.243730 CCAACCAGGAAAGTAATGTGATGTT 59.756 40.000 0.00 0.00 41.22 2.71
4239 6698 5.964958 ACCAGGAAAGTAATGTGATGTTG 57.035 39.130 0.00 0.00 0.00 3.33
4240 6699 5.630121 ACCAGGAAAGTAATGTGATGTTGA 58.370 37.500 0.00 0.00 0.00 3.18
4241 6700 6.248433 ACCAGGAAAGTAATGTGATGTTGAT 58.752 36.000 0.00 0.00 0.00 2.57
4242 6701 6.151648 ACCAGGAAAGTAATGTGATGTTGATG 59.848 38.462 0.00 0.00 0.00 3.07
4243 6702 6.375174 CCAGGAAAGTAATGTGATGTTGATGA 59.625 38.462 0.00 0.00 0.00 2.92
4244 6703 7.067859 CCAGGAAAGTAATGTGATGTTGATGAT 59.932 37.037 0.00 0.00 0.00 2.45
4245 6704 7.913821 CAGGAAAGTAATGTGATGTTGATGATG 59.086 37.037 0.00 0.00 0.00 3.07
4246 6705 7.830697 AGGAAAGTAATGTGATGTTGATGATGA 59.169 33.333 0.00 0.00 0.00 2.92
4247 6706 8.627403 GGAAAGTAATGTGATGTTGATGATGAT 58.373 33.333 0.00 0.00 0.00 2.45
4293 6754 3.754850 AGTTAGGTTTTATCACGGGTTGC 59.245 43.478 0.00 0.00 0.00 4.17
4319 6780 1.032014 GCCAGAAACAAAGCTCACCA 58.968 50.000 0.00 0.00 0.00 4.17
4359 6820 2.066340 CTAACACTCTGCCCCCACA 58.934 57.895 0.00 0.00 0.00 4.17
4372 6833 1.656441 CCCACAGTGCTGCTTGTTC 59.344 57.895 0.00 0.00 0.00 3.18
4450 6911 7.944554 CCCACTAATCAAACCCTGTTATGATAT 59.055 37.037 0.00 0.00 32.47 1.63
4451 6912 9.003658 CCACTAATCAAACCCTGTTATGATATC 57.996 37.037 0.00 0.00 32.47 1.63
4454 6915 7.823745 AATCAAACCCTGTTATGATATCCAC 57.176 36.000 0.00 0.00 32.47 4.02
4455 6916 5.690865 TCAAACCCTGTTATGATATCCACC 58.309 41.667 0.00 0.00 0.00 4.61
4473 6944 1.000739 CATCATGGCAGGTGGGGTT 59.999 57.895 0.00 0.00 0.00 4.11
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
322 1389 1.872313 GATACTCTCCTACGTGACGGG 59.128 57.143 10.66 1.28 0.00 5.28
595 1666 2.202837 GTGTCCACGGGCGATACC 60.203 66.667 0.00 0.00 37.93 2.73
3134 5201 0.473755 TCTTGGAGGCAGCTTGACAA 59.526 50.000 0.00 0.00 0.00 3.18
3530 5598 1.454653 GTCAGTTGTTCCGTTAGACGC 59.545 52.381 0.00 0.00 40.91 5.19
3879 6338 2.343101 GTGTACAAACTGCAGCGGATA 58.657 47.619 15.27 0.00 0.00 2.59
4074 6533 7.246171 TGTCAGTATAGCCTCTTCTTCTTTT 57.754 36.000 0.00 0.00 0.00 2.27
4075 6534 6.859112 TGTCAGTATAGCCTCTTCTTCTTT 57.141 37.500 0.00 0.00 0.00 2.52
4149 6608 6.932400 TCTTTCAACCGAAATCTACTGCTTTA 59.068 34.615 0.00 0.00 40.32 1.85
4187 6646 7.611467 TGATTGCAAGGTATGAGTTGATTAGTT 59.389 33.333 4.94 0.00 0.00 2.24
4244 6703 8.840321 GCATCATCATTATCATCATCATCATCA 58.160 33.333 0.00 0.00 0.00 3.07
4245 6704 8.840321 TGCATCATCATTATCATCATCATCATC 58.160 33.333 0.00 0.00 0.00 2.92
4246 6705 8.752005 TGCATCATCATTATCATCATCATCAT 57.248 30.769 0.00 0.00 0.00 2.45
4247 6706 7.829211 ACTGCATCATCATTATCATCATCATCA 59.171 33.333 0.00 0.00 0.00 3.07
4293 6754 2.363359 AGCTTTGTTTCTGGCAGAAAGG 59.637 45.455 35.98 26.12 44.07 3.11
4319 6780 6.576778 AGCTACCAGGTCCTTATTGTTTAT 57.423 37.500 0.00 0.00 0.00 1.40
4359 6820 0.538287 GGAAGGGAACAAGCAGCACT 60.538 55.000 0.00 0.00 0.00 4.40
4372 6833 4.340617 TGTGCTTAATTAACTGGGAAGGG 58.659 43.478 0.00 0.00 0.00 3.95
4450 6911 1.303948 CACCTGCCATGATGGTGGA 59.696 57.895 24.78 6.30 45.29 4.02
4451 6912 3.929002 CACCTGCCATGATGGTGG 58.071 61.111 13.84 17.00 45.29 4.61
4454 6915 2.123597 CCCCACCTGCCATGATGG 60.124 66.667 7.21 7.21 41.55 3.51
4455 6916 1.000739 AACCCCACCTGCCATGATG 59.999 57.895 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.