Multiple sequence alignment - TraesCS2D01G523900

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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 TraesCS2D01G523900 chr2D 100.000 5480 0 0 1 5480 612500158 612505637 0 10120
1 TraesCS2D01G523900 chr2D 90.665 1264 94 16 1 1247 218559067 218557811 0 1659
2 TraesCS2D01G523900 chr5D 95.762 5498 205 19 1 5480 291341280 291346767 0 8837
3 TraesCS2D01G523900 chr5D 90.554 5505 455 42 1 5470 421638608 421633134 0 7225
4 TraesCS2D01G523900 chr5D 93.697 4014 226 16 1 3999 499661925 499665926 0 5986
5 TraesCS2D01G523900 chr5D 94.635 1286 58 4 8 1283 427412093 427413377 0 1982
6 TraesCS2D01G523900 chr7D 95.161 5497 235 19 1 5480 75404883 75410365 0 8648
7 TraesCS2D01G523900 chr7D 95.145 5500 230 24 1 5480 75362912 75368394 0 8643
8 TraesCS2D01G523900 chr7D 96.723 4791 141 8 705 5480 243514204 243518993 0 7963
9 TraesCS2D01G523900 chr7D 96.081 4797 172 8 697 5480 75374893 75379686 0 7803
10 TraesCS2D01G523900 chr4D 95.034 5497 250 14 1 5480 218283504 218288994 0 8617
11 TraesCS2D01G523900 chr4D 95.021 5503 243 22 1 5480 385544791 385550285 0 8615
12 TraesCS2D01G523900 chr4D 93.515 3346 186 18 1 3329 486637579 486634248 0 4948
13 TraesCS2D01G523900 chr4D 93.706 2987 167 12 1 2973 105714043 105711064 0 4455
14 TraesCS2D01G523900 chr1D 94.954 5509 233 23 8 5480 285479312 285473813 0 8591
15 TraesCS2D01G523900 chr1D 95.386 4985 211 11 511 5480 119503986 119499006 0 7914
16 TraesCS2D01G523900 chr1D 89.229 3361 286 32 8 3329 255401877 255405200 0 4132
17 TraesCS2D01G523900 chr3D 94.763 5499 259 20 1 5480 288260394 288265882 0 8532
18 TraesCS2D01G523900 chr3D 92.979 3233 204 11 8 3226 426896927 426900150 0 4691


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 TraesCS2D01G523900 chr2D 612500158 612505637 5479 False 10120 10120 100.000 1 5480 1 chr2D.!!$F1 5479
1 TraesCS2D01G523900 chr2D 218557811 218559067 1256 True 1659 1659 90.665 1 1247 1 chr2D.!!$R1 1246
2 TraesCS2D01G523900 chr5D 291341280 291346767 5487 False 8837 8837 95.762 1 5480 1 chr5D.!!$F1 5479
3 TraesCS2D01G523900 chr5D 421633134 421638608 5474 True 7225 7225 90.554 1 5470 1 chr5D.!!$R1 5469
4 TraesCS2D01G523900 chr5D 499661925 499665926 4001 False 5986 5986 93.697 1 3999 1 chr5D.!!$F3 3998
5 TraesCS2D01G523900 chr5D 427412093 427413377 1284 False 1982 1982 94.635 8 1283 1 chr5D.!!$F2 1275
6 TraesCS2D01G523900 chr7D 75404883 75410365 5482 False 8648 8648 95.161 1 5480 1 chr7D.!!$F3 5479
7 TraesCS2D01G523900 chr7D 75362912 75368394 5482 False 8643 8643 95.145 1 5480 1 chr7D.!!$F1 5479
8 TraesCS2D01G523900 chr7D 243514204 243518993 4789 False 7963 7963 96.723 705 5480 1 chr7D.!!$F4 4775
9 TraesCS2D01G523900 chr7D 75374893 75379686 4793 False 7803 7803 96.081 697 5480 1 chr7D.!!$F2 4783
10 TraesCS2D01G523900 chr4D 218283504 218288994 5490 False 8617 8617 95.034 1 5480 1 chr4D.!!$F1 5479
11 TraesCS2D01G523900 chr4D 385544791 385550285 5494 False 8615 8615 95.021 1 5480 1 chr4D.!!$F2 5479
12 TraesCS2D01G523900 chr4D 486634248 486637579 3331 True 4948 4948 93.515 1 3329 1 chr4D.!!$R2 3328
13 TraesCS2D01G523900 chr4D 105711064 105714043 2979 True 4455 4455 93.706 1 2973 1 chr4D.!!$R1 2972
14 TraesCS2D01G523900 chr1D 285473813 285479312 5499 True 8591 8591 94.954 8 5480 1 chr1D.!!$R2 5472
15 TraesCS2D01G523900 chr1D 119499006 119503986 4980 True 7914 7914 95.386 511 5480 1 chr1D.!!$R1 4969
16 TraesCS2D01G523900 chr1D 255401877 255405200 3323 False 4132 4132 89.229 8 3329 1 chr1D.!!$F1 3321
17 TraesCS2D01G523900 chr3D 288260394 288265882 5488 False 8532 8532 94.763 1 5480 1 chr3D.!!$F1 5479
18 TraesCS2D01G523900 chr3D 426896927 426900150 3223 False 4691 4691 92.979 8 3226 1 chr3D.!!$F2 3218

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
790 818 1.066858 TCACCGGCTTAGAAGAAGCAG 60.067 52.381 0.00 7.00 44.71 4.24 F
1374 1415 2.227865 GCTGTTTTATCTGAACCGCCAA 59.772 45.455 0.00 0.00 33.04 4.52 F
2903 2954 1.202533 CCGGACCGAATATGTTGAGCT 60.203 52.381 17.49 0.00 0.00 4.09 F
3329 3408 1.372128 GCAAAGCGCTTGGGACTTG 60.372 57.895 25.80 17.81 37.77 3.16 F
3974 4056 1.073706 AGGTTCCCACTCACCTGGT 60.074 57.895 0.00 0.00 42.20 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2505 2552 5.034852 TCAGAAGAATTGACTGGTTGACA 57.965 39.130 0.00 0.0 33.19 3.58 R
3272 3351 0.043940 TTGGGGGCTAATGGGCAAAT 59.956 50.000 0.00 0.0 42.84 2.32 R
3935 4017 0.108585 ATTGGACAGAGCCACAACGT 59.891 50.000 0.00 0.0 37.75 3.99 R
4290 4372 0.178987 GAGTCGGAGGGATCAGGCTA 60.179 60.000 0.00 0.0 0.00 3.93 R
5117 5240 2.105766 ACATAGTTGTCGGTACCCTCC 58.894 52.381 6.25 0.0 0.00 4.30 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
29 31 1.195115 ATCTTCCGGCTTCTGCTGTA 58.805 50.000 0.00 0.00 43.76 2.74
644 667 7.559533 AGAGCTTATGAACTTCTCTGTATCAGA 59.440 37.037 0.00 0.00 38.25 3.27
721 746 3.438360 CTGCAACCTGTGAAACTTGTTC 58.562 45.455 0.00 0.00 38.04 3.18
790 818 1.066858 TCACCGGCTTAGAAGAAGCAG 60.067 52.381 0.00 7.00 44.71 4.24
967 998 4.104696 CGGCTTAAATTTGAACCGGAAT 57.895 40.909 9.46 0.00 37.04 3.01
1177 1217 5.497474 ACGGAGAGGTTGTTATATTTGCTT 58.503 37.500 0.00 0.00 0.00 3.91
1374 1415 2.227865 GCTGTTTTATCTGAACCGCCAA 59.772 45.455 0.00 0.00 33.04 4.52
2026 2070 3.153369 TGACCATGAGGCTGCTAAAAA 57.847 42.857 0.00 0.00 39.06 1.94
2483 2530 9.713713 GAGGTTATCTCCAACTTATATCCTTTC 57.286 37.037 0.00 0.00 36.52 2.62
2505 2552 2.978010 CTTTGGCGGGCGTCACTT 60.978 61.111 0.00 0.00 0.00 3.16
2514 2561 1.507141 GGGCGTCACTTGTCAACCAG 61.507 60.000 0.00 0.00 0.00 4.00
2605 2652 1.292223 CTTTCAAGACCGCTCCCGA 59.708 57.895 0.00 0.00 36.29 5.14
2713 2761 6.039829 CAGCAAGAGGGAAAAGAAAAGTAACT 59.960 38.462 0.00 0.00 0.00 2.24
2903 2954 1.202533 CCGGACCGAATATGTTGAGCT 60.203 52.381 17.49 0.00 0.00 4.09
3104 3155 7.134815 CAGCAAAAATCTGAGGTATAATTCCG 58.865 38.462 0.00 0.00 33.54 4.30
3329 3408 1.372128 GCAAAGCGCTTGGGACTTG 60.372 57.895 25.80 17.81 37.77 3.16
3692 3773 2.870435 GCTCTTACTGAAAGAACCGCCA 60.870 50.000 0.00 0.00 43.66 5.69
3710 3791 2.492088 GCCAAACTCTCCGGCTTAAAAT 59.508 45.455 0.00 0.00 42.78 1.82
3762 3843 7.058023 TCTTTGGTAAGTTACTCTGTAAGCA 57.942 36.000 12.65 0.00 32.98 3.91
3764 3846 7.602644 TCTTTGGTAAGTTACTCTGTAAGCATG 59.397 37.037 12.65 0.00 32.98 4.06
3829 3911 2.533266 TCAGCTCACCTGACTTTGTC 57.467 50.000 0.00 0.00 45.44 3.18
3840 3922 1.985159 TGACTTTGTCATACAGGCCCT 59.015 47.619 0.00 0.00 37.67 5.19
3869 3951 3.624410 TCCAATCTCAATCAGAACATGCG 59.376 43.478 0.00 0.00 33.62 4.73
3870 3952 3.624410 CCAATCTCAATCAGAACATGCGA 59.376 43.478 0.00 0.00 33.62 5.10
3935 4017 1.870580 CGGGTCACAACGTGCTTTAGA 60.871 52.381 0.00 0.00 32.98 2.10
3974 4056 1.073706 AGGTTCCCACTCACCTGGT 60.074 57.895 0.00 0.00 42.20 4.00
4137 4219 1.760405 ACCCCAACCTGAAGGAAGAT 58.240 50.000 2.62 0.00 38.94 2.40
4290 4372 3.067106 CACTCCACGTTATGAAGCAGTT 58.933 45.455 0.00 0.00 0.00 3.16
4318 4400 0.249073 CCCTCCGACTCGTAAGCATG 60.249 60.000 0.00 0.00 37.18 4.06
4537 4619 1.542547 GCCTCACCTTTTTGACTCGGA 60.543 52.381 0.00 0.00 0.00 4.55
4582 4665 4.911514 AACACTTAATTTTGTCGTGCCT 57.088 36.364 0.00 0.00 0.00 4.75
4590 4673 0.743688 TTTGTCGTGCCTTTGTGCAT 59.256 45.000 0.00 0.00 44.30 3.96
4713 4827 2.226962 AGTCTCTAGGCGGTTTACCA 57.773 50.000 0.00 0.00 35.14 3.25
4966 5084 0.605319 TAAGAACCGCCCTTGCACAG 60.605 55.000 0.00 0.00 37.32 3.66
4979 5097 4.400251 CCCTTGCACAGTGTTGATATGATT 59.600 41.667 1.61 0.00 0.00 2.57
5429 5555 1.902508 ACGATCATAAGCCGGATCCAT 59.097 47.619 13.41 0.00 37.26 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.229784 CAGCAGAAGCCGGAAGATTTTT 59.770 45.455 5.05 0.00 43.56 1.94
131 134 7.290248 TCGGGATGGTCTTTAAAGATAAGATCT 59.710 37.037 20.41 0.00 42.61 2.75
337 353 2.650116 GCCGAGGCTGAGGAAGACA 61.650 63.158 6.90 0.00 35.71 3.41
721 746 5.051508 GCAGTTTTTGTCTAAGTGTTGCATG 60.052 40.000 0.00 0.00 0.00 4.06
790 818 1.792367 GCCGGAAATTTCACAAAGCAC 59.208 47.619 19.49 0.00 0.00 4.40
893 924 2.304761 CGGCTTATGAAGGGGCCTAATA 59.695 50.000 0.84 0.00 42.13 0.98
967 998 5.300792 ACGGAAGCCTATGACAAAAGAAAAA 59.699 36.000 0.00 0.00 0.00 1.94
1177 1217 0.916086 AAACCCCGGCTCATGTGATA 59.084 50.000 0.00 0.00 0.00 2.15
1374 1415 2.184167 CCCGTTGGCACACTCGTTT 61.184 57.895 0.00 0.00 39.29 3.60
2505 2552 5.034852 TCAGAAGAATTGACTGGTTGACA 57.965 39.130 0.00 0.00 33.19 3.58
2605 2652 8.616076 GCACAAAGTAAGCTAATCATCATTACT 58.384 33.333 0.00 0.00 38.09 2.24
2961 3012 2.180086 AGTGATATCCAGTCTGGCCCTA 59.820 50.000 14.64 6.11 37.47 3.53
3104 3155 7.494952 GGTAAGGATGACTATGGAGTAAACAAC 59.505 40.741 0.00 0.00 35.45 3.32
3272 3351 0.043940 TTGGGGGCTAATGGGCAAAT 59.956 50.000 0.00 0.00 42.84 2.32
3329 3408 3.963383 ACAGTGTCGGTTCATGAAAAC 57.037 42.857 10.35 9.51 0.00 2.43
3413 3492 8.190122 GTGATTATCATGCAACATTAAAGTCCA 58.810 33.333 0.00 0.00 0.00 4.02
3692 3773 2.492088 GGCATTTTAAGCCGGAGAGTTT 59.508 45.455 5.05 0.00 43.15 2.66
3710 3791 0.469494 ACCATCTGCGATACATGGCA 59.531 50.000 0.00 0.00 40.85 4.92
3829 3911 1.346068 GGAGCTTCTAGGGCCTGTATG 59.654 57.143 18.53 7.36 0.00 2.39
3840 3922 6.070596 TGTTCTGATTGAGATTGGAGCTTCTA 60.071 38.462 0.00 0.00 0.00 2.10
3935 4017 0.108585 ATTGGACAGAGCCACAACGT 59.891 50.000 0.00 0.00 37.75 3.99
3974 4056 0.679002 AAGCCGCCTGAGTACGTCTA 60.679 55.000 0.00 0.00 0.00 2.59
4290 4372 0.178987 GAGTCGGAGGGATCAGGCTA 60.179 60.000 0.00 0.00 0.00 3.93
4590 4673 0.249868 AGAGTTAAGCGCTGCACACA 60.250 50.000 12.58 0.00 0.00 3.72
4713 4827 6.839134 TGTGTAAGGTATATGACTCTCCATGT 59.161 38.462 0.00 0.00 0.00 3.21
4778 4892 6.961359 TGGTTATCGCGAAGATATAATTGG 57.039 37.500 15.24 0.00 41.13 3.16
4979 5097 8.465999 TCTTTTGATTTGCAACAAGTTCTTCTA 58.534 29.630 0.00 0.00 35.91 2.10
5117 5240 2.105766 ACATAGTTGTCGGTACCCTCC 58.894 52.381 6.25 0.00 0.00 4.30
5131 5254 7.281774 TCGTATTCGAACCTAAGAGAACATAGT 59.718 37.037 0.00 0.00 43.34 2.12
5429 5555 2.631062 ACATTACGTGGTCACTTGGAGA 59.369 45.455 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.