Multiple sequence alignment - TraesCS3A01G396600

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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 TraesCS3A01G396600 chr3A 100.000 3206 0 0 1 3206 644211556 644214761 0 5921
1 TraesCS3A01G396600 chr3A 96.071 3207 125 1 1 3206 426789009 426785803 0 5223
2 TraesCS3A01G396600 chr3A 95.635 3207 137 3 1 3206 427530401 427533605 0 5144
3 TraesCS3A01G396600 chr1A 95.979 3208 126 3 1 3206 337297063 337293857 0 5206
4 TraesCS3A01G396600 chr4A 95.948 3208 127 3 1 3206 457941688 457938482 0 5201
5 TraesCS3A01G396600 chr4A 95.915 3207 127 4 1 3206 61065124 61061921 0 5193
6 TraesCS3A01G396600 chr4A 95.915 3207 126 5 1 3206 93601337 93598135 0 5192
7 TraesCS3A01G396600 chr7A 95.701 3210 132 4 1 3206 617092120 617095327 0 5158
8 TraesCS3A01G396600 chr2A 95.670 3210 135 4 1 3206 736655525 736652316 0 5155
9 TraesCS3A01G396600 chr6A 95.636 3208 138 2 1 3206 85394875 85391668 0 5147


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 TraesCS3A01G396600 chr3A 644211556 644214761 3205 False 5921 5921 100.000 1 3206 1 chr3A.!!$F2 3205
1 TraesCS3A01G396600 chr3A 426785803 426789009 3206 True 5223 5223 96.071 1 3206 1 chr3A.!!$R1 3205
2 TraesCS3A01G396600 chr3A 427530401 427533605 3204 False 5144 5144 95.635 1 3206 1 chr3A.!!$F1 3205
3 TraesCS3A01G396600 chr1A 337293857 337297063 3206 True 5206 5206 95.979 1 3206 1 chr1A.!!$R1 3205
4 TraesCS3A01G396600 chr4A 457938482 457941688 3206 True 5201 5201 95.948 1 3206 1 chr4A.!!$R3 3205
5 TraesCS3A01G396600 chr4A 61061921 61065124 3203 True 5193 5193 95.915 1 3206 1 chr4A.!!$R1 3205
6 TraesCS3A01G396600 chr4A 93598135 93601337 3202 True 5192 5192 95.915 1 3206 1 chr4A.!!$R2 3205
7 TraesCS3A01G396600 chr7A 617092120 617095327 3207 False 5158 5158 95.701 1 3206 1 chr7A.!!$F1 3205
8 TraesCS3A01G396600 chr2A 736652316 736655525 3209 True 5155 5155 95.670 1 3206 1 chr2A.!!$R1 3205
9 TraesCS3A01G396600 chr6A 85391668 85394875 3207 True 5147 5147 95.636 1 3206 1 chr6A.!!$R1 3205

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
54 55 1.062962 AGGCCCCGGATTGATTTGAAT 60.063 47.619 0.73 0.0 0.00 2.57 F
502 506 2.223758 CCTTTTCCTCCGTAGATCCGTC 60.224 54.545 0.00 0.0 0.00 4.79 F
1785 1794 1.202580 GCTAACATCCAGCTCACCGAT 60.203 52.381 0.00 0.0 36.07 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1356 1365 0.038526 ACTCAGTGCGACGGTTTAGG 60.039 55.000 0.00 0.00 0.00 2.69 R
2067 2078 0.179073 TCTTCTTATGAGCAGGCCGC 60.179 55.000 11.02 11.02 42.91 6.53 R
3057 3070 1.000233 CCACTTGCCCTTGCCCATA 60.000 57.895 0.00 0.00 36.33 2.74 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
41 42 2.006805 ATCCCCAACATTAGGCCCCG 62.007 60.000 0.00 0.0 0.00 5.73
54 55 1.062962 AGGCCCCGGATTGATTTGAAT 60.063 47.619 0.73 0.0 0.00 2.57
118 121 6.601613 ACATCTTCTTGTAGTTTGTTGAACCA 59.398 34.615 0.00 0.0 39.13 3.67
328 332 3.575630 GTCATTTCTTTTTCCCCTTCGC 58.424 45.455 0.00 0.0 0.00 4.70
502 506 2.223758 CCTTTTCCTCCGTAGATCCGTC 60.224 54.545 0.00 0.0 0.00 4.79
779 786 3.090210 TCTGTACACTTACCCATCCGA 57.910 47.619 0.00 0.0 0.00 4.55
785 792 4.569719 ACACTTACCCATCCGAAATCTT 57.430 40.909 0.00 0.0 0.00 2.40
869 878 7.178983 CGGTATATACCATTAGTCCCCTTGTTA 59.821 40.741 27.58 0.0 46.80 2.41
935 944 2.414161 GCTGTCTCCGGTTTAACATTGC 60.414 50.000 0.00 0.0 0.00 3.56
1233 1242 2.696759 CCGGGATGTTTTGGCCGAC 61.697 63.158 0.00 0.0 0.00 4.79
1350 1359 4.081420 ACAGTTGAGTTGTTCAGAGACTGT 60.081 41.667 7.10 7.1 44.61 3.55
1356 1365 4.192317 AGTTGTTCAGAGACTGTTTCCAC 58.808 43.478 0.00 0.0 32.61 4.02
1365 1374 2.436911 AGACTGTTTCCACCTAAACCGT 59.563 45.455 0.00 0.0 38.83 4.83
1497 1506 6.721208 AGTGGAATCAAACATGGTTCTATTGT 59.279 34.615 5.52 0.0 0.00 2.71
1514 1523 1.358152 TGTAAAGACACCTCCCCTGG 58.642 55.000 0.00 0.0 0.00 4.45
1531 1540 2.965147 CCTGGTGGTGAAAATCCTTTGT 59.035 45.455 0.00 0.0 0.00 2.83
1541 1550 4.648762 TGAAAATCCTTTGTCTGGCTTTCA 59.351 37.500 0.00 0.0 35.62 2.69
1655 1664 2.495669 CCTTCATGGCCAACGGTTTAAT 59.504 45.455 10.96 0.0 0.00 1.40
1710 1719 2.170607 GAGCATACTGCCCCTTAGTCAA 59.829 50.000 0.00 0.0 46.52 3.18
1785 1794 1.202580 GCTAACATCCAGCTCACCGAT 60.203 52.381 0.00 0.0 36.07 4.18
1863 1872 3.146828 AACCGGCCTGCTTCCCTTT 62.147 57.895 0.00 0.0 0.00 3.11
1885 1894 3.082579 GCCACCAACAAACCGCCAA 62.083 57.895 0.00 0.0 0.00 4.52
1939 1948 7.865706 AACTTGTTATTGATACATCTGGTCC 57.134 36.000 0.00 0.0 0.00 4.46
2007 2016 3.214328 GAGCAAGAAACTTCCACAGGAA 58.786 45.455 0.00 0.0 39.66 3.36
2136 2147 4.202493 CCTGATGATGATGTGGGTAATCCA 60.202 45.833 0.00 0.0 44.79 3.41
2157 2168 4.323028 CCAGATGTTGAGGTAGAGCTTGAA 60.323 45.833 0.00 0.0 0.00 2.69
2196 2207 3.499537 TCATGCGCCTTATTGATGATGAC 59.500 43.478 4.18 0.0 0.00 3.06
2285 2296 3.077359 CAGACCCTTTGCCTTCACTAAG 58.923 50.000 0.00 0.0 0.00 2.18
2370 2381 7.781324 ATTTCTTATGAAGACCCAACAACAT 57.219 32.000 0.00 0.0 37.23 2.71
2380 2391 0.592637 CCAACAACATGAAGCTCGCA 59.407 50.000 0.00 0.0 0.00 5.10
2427 2439 1.272212 GTTACCTCCGTCGGTTTACCA 59.728 52.381 11.88 0.0 38.49 3.25
2475 2487 6.605471 TCAGAGGTCTCTAATTTGCTTGTA 57.395 37.500 0.00 0.0 37.98 2.41
2813 2826 4.289672 AGATATACCCAATGATCCACCACC 59.710 45.833 0.00 0.0 0.00 4.61
2829 2842 1.062587 CCACCGCAAGATGACGATTTC 59.937 52.381 0.00 0.0 43.02 2.17
3057 3070 2.608752 CGCCAAAGAAGAATTTGCTGCT 60.609 45.455 0.00 0.0 38.57 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
54 55 6.061022 TGCTAAAGGATTGACATGAACCTA 57.939 37.500 0.00 0.00 0.00 3.08
118 121 2.167281 CCAGAGAAGATGACATCACGGT 59.833 50.000 17.57 0.00 0.00 4.83
328 332 1.355066 GAAGACGAAGCAGAAGGGCG 61.355 60.000 0.00 0.00 39.27 6.13
444 448 0.250513 CCGAGGAAGAAACAGAGGGG 59.749 60.000 0.00 0.00 0.00 4.79
447 451 1.404851 GGAGCCGAGGAAGAAACAGAG 60.405 57.143 0.00 0.00 0.00 3.35
502 506 4.202472 ACTGAAGAACTTGGAAACCCTAGG 60.202 45.833 0.06 0.06 31.99 3.02
562 566 2.622942 GCAAAGGTTCACAGGTTCATCA 59.377 45.455 0.00 0.00 0.00 3.07
785 792 5.584649 CCGGATCTAAGCATTGAAACAGTTA 59.415 40.000 0.00 0.00 0.00 2.24
869 878 0.031994 GCAACAACATCTGGCGGTTT 59.968 50.000 0.00 0.00 0.00 3.27
935 944 7.910162 GCATTGATTAAAGTACACTGGTATGTG 59.090 37.037 0.00 0.00 43.07 3.21
1195 1204 2.749076 GGTAAAATTTAGAACCGGGCGT 59.251 45.455 6.32 0.00 0.00 5.68
1233 1242 0.593128 CTTGTGGGCGGAGTTGAAAG 59.407 55.000 0.00 0.00 0.00 2.62
1301 1310 4.314121 CTCCTCTTGAAAGAACACCTCAG 58.686 47.826 0.00 0.00 34.03 3.35
1350 1359 0.106335 TGCGACGGTTTAGGTGGAAA 59.894 50.000 0.00 0.00 0.00 3.13
1356 1365 0.038526 ACTCAGTGCGACGGTTTAGG 60.039 55.000 0.00 0.00 0.00 2.69
1365 1374 1.335597 CCGTCAGTAAACTCAGTGCGA 60.336 52.381 0.00 0.00 0.00 5.10
1432 1441 3.053395 AGTTTGGCATGAGGGTATGTGAT 60.053 43.478 0.00 0.00 0.00 3.06
1497 1506 3.906115 ACCAGGGGAGGTGTCTTTA 57.094 52.632 0.00 0.00 41.30 1.85
1514 1523 3.552890 GCCAGACAAAGGATTTTCACCAC 60.553 47.826 0.00 0.00 35.03 4.16
1655 1664 1.735376 GCGAGCGAGATCAACCCCTA 61.735 60.000 0.00 0.00 0.00 3.53
1710 1719 2.325082 GCACATCAAACCGGAGCGT 61.325 57.895 9.46 0.00 0.00 5.07
1785 1794 3.777106 ACAGCCTCTGTGATTTCTTCA 57.223 42.857 0.00 0.00 43.63 3.02
1863 1872 1.513158 CGGTTTGTTGGTGGCACAA 59.487 52.632 20.82 4.91 44.16 3.33
1914 1923 8.109634 AGGACCAGATGTATCAATAACAAGTTT 58.890 33.333 0.00 0.00 0.00 2.66
1918 1927 7.402054 ACAAGGACCAGATGTATCAATAACAA 58.598 34.615 0.00 0.00 0.00 2.83
1930 1939 8.906867 ACATTGATATTAAACAAGGACCAGATG 58.093 33.333 10.36 0.00 33.13 2.90
2067 2078 0.179073 TCTTCTTATGAGCAGGCCGC 60.179 55.000 11.02 11.02 42.91 6.53
2136 2147 5.188555 TGATTCAAGCTCTACCTCAACATCT 59.811 40.000 0.00 0.00 0.00 2.90
2139 2150 4.284490 AGTGATTCAAGCTCTACCTCAACA 59.716 41.667 0.00 0.00 0.00 3.33
2140 2151 4.826556 AGTGATTCAAGCTCTACCTCAAC 58.173 43.478 0.00 0.00 0.00 3.18
2157 2168 5.104374 CGCATGAAAAATAAGCCAAGTGAT 58.896 37.500 0.00 0.00 0.00 3.06
2196 2207 4.790766 GCTTCGGCATCATCCTAACAAATG 60.791 45.833 0.00 0.00 41.33 2.32
2285 2296 1.794222 CGGTTTGCCTGACGGATTC 59.206 57.895 0.00 0.00 0.00 2.52
2370 2381 2.253758 GGTTGTGCTGCGAGCTTCA 61.254 57.895 9.12 6.24 42.97 3.02
2813 2826 2.780014 GCAATGAAATCGTCATCTTGCG 59.220 45.455 0.44 0.00 46.80 4.85
2829 2842 4.400251 TCAATAGGCCTTTCTTCAGCAATG 59.600 41.667 12.58 0.00 0.00 2.82
3057 3070 1.000233 CCACTTGCCCTTGCCCATA 60.000 57.895 0.00 0.00 36.33 2.74
3066 3079 1.620822 AGTCAACATTCCACTTGCCC 58.379 50.000 0.00 0.00 0.00 5.36


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

AutoCloner maintained by Alex Coulton.