Multiple sequence alignment - TraesCS1A01G406100

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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 TraesCS1A01G406100 chr1A 100.000 3504 0 0 1 3504 568718755 568715252 0 6471
1 TraesCS1A01G406100 chr1A 98.232 3507 58 4 1 3504 521305225 521308730 0 6130
2 TraesCS1A01G406100 chr1A 98.176 3509 59 5 1 3504 531033310 531036818 0 6120
3 TraesCS1A01G406100 chr1B 98.374 3505 55 2 1 3504 65600597 65597094 0 6156
4 TraesCS1A01G406100 chr1B 98.290 3509 54 6 1 3504 167986970 167983463 0 6143
5 TraesCS1A01G406100 chr1B 98.289 3506 57 3 1 3504 419953946 419957450 0 6139
6 TraesCS1A01G406100 chr1B 97.865 3513 66 9 1 3504 303595686 303592174 0 6063
7 TraesCS1A01G406100 chr5B 98.317 3506 57 2 1 3504 158883262 158886767 0 6146
8 TraesCS1A01G406100 chr5B 98.034 3510 63 6 1 3504 474303101 474306610 0 6095
9 TraesCS1A01G406100 chr5B 91.810 3541 231 35 1 3504 218929182 218932700 0 4878
10 TraesCS1A01G406100 chr5B 90.755 1774 117 31 1755 3504 157578173 157579923 0 2324


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 TraesCS1A01G406100 chr1A 568715252 568718755 3503 True 6471 6471 100.000 1 3504 1 chr1A.!!$R1 3503
1 TraesCS1A01G406100 chr1A 521305225 521308730 3505 False 6130 6130 98.232 1 3504 1 chr1A.!!$F1 3503
2 TraesCS1A01G406100 chr1A 531033310 531036818 3508 False 6120 6120 98.176 1 3504 1 chr1A.!!$F2 3503
3 TraesCS1A01G406100 chr1B 65597094 65600597 3503 True 6156 6156 98.374 1 3504 1 chr1B.!!$R1 3503
4 TraesCS1A01G406100 chr1B 167983463 167986970 3507 True 6143 6143 98.290 1 3504 1 chr1B.!!$R2 3503
5 TraesCS1A01G406100 chr1B 419953946 419957450 3504 False 6139 6139 98.289 1 3504 1 chr1B.!!$F1 3503
6 TraesCS1A01G406100 chr1B 303592174 303595686 3512 True 6063 6063 97.865 1 3504 1 chr1B.!!$R3 3503
7 TraesCS1A01G406100 chr5B 158883262 158886767 3505 False 6146 6146 98.317 1 3504 1 chr5B.!!$F2 3503
8 TraesCS1A01G406100 chr5B 474303101 474306610 3509 False 6095 6095 98.034 1 3504 1 chr5B.!!$F4 3503
9 TraesCS1A01G406100 chr5B 218929182 218932700 3518 False 4878 4878 91.810 1 3504 1 chr5B.!!$F3 3503
10 TraesCS1A01G406100 chr5B 157578173 157579923 1750 False 2324 2324 90.755 1755 3504 1 chr5B.!!$F1 1749

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
612 625 2.009774 GCCACATACACGCTCTTGAAT 58.990 47.619 0.00 0.0 0.00 2.57 F
1386 1410 2.105134 TGTATGAACCTTGTCAACCCGT 59.895 45.455 0.00 0.0 0.00 5.28 F
1768 1792 2.223805 GCTTGCTACTGCCAGTGTTTTT 60.224 45.455 7.83 0.0 38.71 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1542 1566 0.035458 CGGGTGAACAGCTCTTCCTT 59.965 55.0 0.00 0.00 0.0 3.36 R
2383 2410 0.541392 TAACAGCGCTGATGGTCCAT 59.459 50.0 42.03 15.97 0.0 3.41 R
3447 3500 0.878523 CGAGCAGAAACACGGGTTGA 60.879 55.0 2.46 0.00 37.3 3.18 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
63 65 5.619086 CGCGAGAATTGTAAGGGTGATTTTT 60.619 40.000 0.00 0.00 0.00 1.94
202 205 3.118519 ACCTGAAGAAACGTGGTAGTTGT 60.119 43.478 0.00 0.00 34.14 3.32
490 503 3.316308 GCCACAAATGTGTTCTCTTCTGT 59.684 43.478 12.21 0.00 44.21 3.41
529 542 3.988976 ACTGACTGTCATAGTTGCCAT 57.011 42.857 11.45 0.00 40.53 4.40
612 625 2.009774 GCCACATACACGCTCTTGAAT 58.990 47.619 0.00 0.00 0.00 2.57
1055 1074 3.805066 TTTCATGGATCCACCTCAACA 57.195 42.857 18.99 0.00 39.86 3.33
1153 1176 5.500234 TGTTATTTGTTGGCAGCTAGATCT 58.500 37.500 0.00 0.00 0.00 2.75
1225 1249 3.020274 TGGCAACAGCTCAACACTTTTA 58.980 40.909 0.00 0.00 46.17 1.52
1369 1393 2.677914 TCTGATGGATGTCCGGTGTAT 58.322 47.619 0.00 0.00 39.43 2.29
1386 1410 2.105134 TGTATGAACCTTGTCAACCCGT 59.895 45.455 0.00 0.00 0.00 5.28
1542 1566 6.294342 CCCGTACGAGGTTAATAATGAGATCA 60.294 42.308 18.76 0.00 0.00 2.92
1557 1581 3.580022 TGAGATCAAGGAAGAGCTGTTCA 59.420 43.478 23.53 4.96 33.80 3.18
1768 1792 2.223805 GCTTGCTACTGCCAGTGTTTTT 60.224 45.455 7.83 0.00 38.71 1.94
2383 2410 2.491298 TCACAAGTTTGCTGTTTCTGCA 59.509 40.909 0.00 0.00 36.58 4.41
2401 2428 1.028330 CATGGACCATCAGCGCTGTT 61.028 55.000 34.70 25.37 0.00 3.16
2408 2435 1.473257 CCATCAGCGCTGTTAAGGCTA 60.473 52.381 34.70 15.28 34.75 3.93
2632 2662 6.482973 GCCTCAAAAATTTGAAAAGTGGATGA 59.517 34.615 9.63 0.00 45.61 2.92
3028 3058 2.586792 GGCCTCAGCAAGGACGAT 59.413 61.111 9.23 0.00 45.69 3.73
3040 3070 1.464734 AGGACGATGACGATGACACT 58.535 50.000 0.00 0.00 42.66 3.55
3281 3332 9.683069 CTCAATTTTAGTTTTCTGCTGTGTATT 57.317 29.630 0.00 0.00 0.00 1.89
3439 3492 1.344763 AGCAGCTACGAAGAAACAGGT 59.655 47.619 0.00 0.00 0.00 4.00
3447 3500 1.021968 GAAGAAACAGGTGCCAACGT 58.978 50.000 0.00 0.00 0.00 3.99
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 65 2.557924 CAATGGCAACTGCTTCAACCTA 59.442 45.455 1.06 0.00 41.70 3.08
490 503 6.265196 AGTCAGTTTCAGAAAATATGTTGCCA 59.735 34.615 0.00 0.00 0.00 4.92
1369 1393 3.142951 CATAACGGGTTGACAAGGTTCA 58.857 45.455 3.29 0.00 0.00 3.18
1386 1410 0.323302 TCACCAAGCCAGTCGCATAA 59.677 50.000 0.00 0.00 41.38 1.90
1542 1566 0.035458 CGGGTGAACAGCTCTTCCTT 59.965 55.000 0.00 0.00 0.00 3.36
1557 1581 1.616367 ACCCAGGAAACAAACGGGT 59.384 52.632 0.00 0.00 45.53 5.28
1768 1792 2.161808 TCAAAACGGAAGAAACGCAACA 59.838 40.909 0.00 0.00 34.00 3.33
1932 1956 6.861065 ATAAATACCATTAAGTGCAGACGG 57.139 37.500 0.00 0.00 0.00 4.79
1969 1993 7.086230 ACGTTATAAACAAAGGTTCACACAA 57.914 32.000 0.00 0.00 35.82 3.33
2100 2126 5.940617 TGCTAATATGAAGGTAGTTGCCAT 58.059 37.500 0.00 0.00 0.00 4.40
2383 2410 0.541392 TAACAGCGCTGATGGTCCAT 59.459 50.000 42.03 15.97 0.00 3.41
2632 2662 2.356313 CGGAGCTGAGTGCACGTT 60.356 61.111 12.01 0.00 45.94 3.99
3028 3058 1.810151 TCGTCATCAGTGTCATCGTCA 59.190 47.619 0.00 0.00 0.00 4.35
3040 3070 1.067915 TCAGCGTGTTCATCGTCATCA 60.068 47.619 0.00 0.00 0.00 3.07
3146 3197 1.351076 CTTGATGGCAAAACCCCCTT 58.649 50.000 0.00 0.00 37.83 3.95
3281 3332 7.358770 TGGATGAGATTGTTCCAAAGAAAAA 57.641 32.000 0.00 0.00 36.62 1.94
3439 3492 2.897846 CACGGGTTGACGTTGGCA 60.898 61.111 0.00 0.00 46.25 4.92
3447 3500 0.878523 CGAGCAGAAACACGGGTTGA 60.879 55.000 2.46 0.00 37.30 3.18


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

AutoCloner maintained by Alex Coulton.