Multiple sequence alignment - TraesCS1A01G063100

Loading Multiple Alignment...

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 TraesCS1A01G063100 chr1A 100.000 2766 0 0 1 2766 43272537 43269772 0.000000e+00 5108
1 TraesCS1A01G063100 chr1A 93.955 2779 124 19 1 2766 43393158 43390411 0.000000e+00 4161
2 TraesCS1A01G063100 chr1A 81.624 468 42 14 2309 2766 43952523 43952956 5.670000e-92 348
3 TraesCS1A01G063100 chr1A 85.577 104 12 3 353 454 386500133 386500235 3.770000e-19 106
4 TraesCS1A01G063100 chr1B 90.703 2732 206 28 55 2761 63807952 63810660 0.000000e+00 3594
5 TraesCS1A01G063100 chr1B 91.702 2603 183 21 183 2766 63479076 63481664 0.000000e+00 3579
6 TraesCS1A01G063100 chr1B 91.049 2603 191 27 183 2766 63467844 63470423 0.000000e+00 3478
7 TraesCS1A01G063100 chr1B 90.709 2594 189 31 61 2628 63758353 63760920 0.000000e+00 3408
8 TraesCS1A01G063100 chr1B 91.883 2082 151 11 61 2128 63613357 63615434 0.000000e+00 2892
9 TraesCS1A01G063100 chr1B 92.204 1847 127 12 61 1894 63888247 63890089 0.000000e+00 2597
10 TraesCS1A01G063100 chr1B 87.500 624 54 14 2132 2741 63624149 63624762 0.000000e+00 699
11 TraesCS1A01G063100 chr1B 89.623 106 8 3 49 151 63467737 63467842 6.220000e-27 132
12 TraesCS1A01G063100 chr1B 89.286 84 6 3 49 129 63478116 63478199 4.870000e-18 102
13 TraesCS1A01G063100 chr1D 90.699 2032 138 21 753 2766 44275023 44277021 0.000000e+00 2658
14 TraesCS1A01G063100 chr1D 90.255 2042 147 26 753 2766 43823105 43825122 0.000000e+00 2621
15 TraesCS1A01G063100 chr1D 90.673 1576 117 22 621 2188 44628791 44630344 0.000000e+00 2069
16 TraesCS1A01G063100 chr1D 89.831 1239 98 14 1548 2766 44370324 44371554 0.000000e+00 1565
17 TraesCS1A01G063100 chr1D 90.361 747 52 13 2033 2766 44160031 44160770 0.000000e+00 963
18 TraesCS1A01G063100 chr1D 89.680 281 27 2 455 733 43822414 43822694 9.420000e-95 357
19 TraesCS1A01G063100 chr1D 89.630 270 27 1 465 733 44309541 44309810 2.640000e-90 342


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 TraesCS1A01G063100 chr1A 43269772 43272537 2765 True 5108.0 5108 100.0000 1 2766 1 chr1A.!!$R1 2765
1 TraesCS1A01G063100 chr1A 43390411 43393158 2747 True 4161.0 4161 93.9550 1 2766 1 chr1A.!!$R2 2765
2 TraesCS1A01G063100 chr1B 63807952 63810660 2708 False 3594.0 3594 90.7030 55 2761 1 chr1B.!!$F4 2706
3 TraesCS1A01G063100 chr1B 63758353 63760920 2567 False 3408.0 3408 90.7090 61 2628 1 chr1B.!!$F3 2567
4 TraesCS1A01G063100 chr1B 63613357 63615434 2077 False 2892.0 2892 91.8830 61 2128 1 chr1B.!!$F1 2067
5 TraesCS1A01G063100 chr1B 63888247 63890089 1842 False 2597.0 2597 92.2040 61 1894 1 chr1B.!!$F5 1833
6 TraesCS1A01G063100 chr1B 63478116 63481664 3548 False 1840.5 3579 90.4940 49 2766 2 chr1B.!!$F7 2717
7 TraesCS1A01G063100 chr1B 63467737 63470423 2686 False 1805.0 3478 90.3360 49 2766 2 chr1B.!!$F6 2717
8 TraesCS1A01G063100 chr1B 63624149 63624762 613 False 699.0 699 87.5000 2132 2741 1 chr1B.!!$F2 609
9 TraesCS1A01G063100 chr1D 44275023 44277021 1998 False 2658.0 2658 90.6990 753 2766 1 chr1D.!!$F2 2013
10 TraesCS1A01G063100 chr1D 44628791 44630344 1553 False 2069.0 2069 90.6730 621 2188 1 chr1D.!!$F5 1567
11 TraesCS1A01G063100 chr1D 44370324 44371554 1230 False 1565.0 1565 89.8310 1548 2766 1 chr1D.!!$F4 1218
12 TraesCS1A01G063100 chr1D 43822414 43825122 2708 False 1489.0 2621 89.9675 455 2766 2 chr1D.!!$F6 2311
13 TraesCS1A01G063100 chr1D 44160031 44160770 739 False 963.0 963 90.3610 2033 2766 1 chr1D.!!$F1 733

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
171 1031 0.395862 CTCGTTCTCCAGAGCCCCTA 60.396 60.000 0.00 0.0 0.0 3.53 F
332 1198 1.713246 CAACACACAACAGTCGCGT 59.287 52.632 5.77 0.0 0.0 6.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1177 2445 0.108662 TCGCATTCGTCAGCTGACAT 60.109 50.0 38.31 25.97 44.99 3.06 R
2130 3419 1.541310 CGTGACCCTAGGTGAAGGCA 61.541 60.0 8.29 0.00 35.25 4.75 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
26 27 6.382869 GGACAAACCCTAGATTGATGAATG 57.617 41.667 9.08 0.00 0.00 2.67
33 34 5.126061 ACCCTAGATTGATGAATGCACAAAC 59.874 40.000 0.00 0.00 0.00 2.93
85 86 5.592282 TGAGCAAGAAACAATAACTGGACAA 59.408 36.000 0.00 0.00 0.00 3.18
171 1031 0.395862 CTCGTTCTCCAGAGCCCCTA 60.396 60.000 0.00 0.00 0.00 3.53
224 1089 5.413499 CAAAATGAATGCGAGGGAGAAAAT 58.587 37.500 0.00 0.00 0.00 1.82
249 1115 1.819288 CTGAGAGAGACAAACGGCCTA 59.181 52.381 0.00 0.00 0.00 3.93
277 1143 2.074547 ACTATCGTGACAAACACCCG 57.925 50.000 0.00 0.00 45.73 5.28
305 1171 4.572389 CGCTACTAGCATCAACCTGAAAAT 59.428 41.667 8.78 0.00 42.58 1.82
315 1181 3.746889 CTGAAAATGGGCCGCGCA 61.747 61.111 13.06 13.06 0.00 6.09
332 1198 1.713246 CAACACACAACAGTCGCGT 59.287 52.632 5.77 0.00 0.00 6.01
394 1260 6.137794 TCTTGAAGATAGACGAGATCCAAC 57.862 41.667 0.00 0.00 0.00 3.77
415 1281 3.628487 ACGGCTCTAGACTTAGATGTGAC 59.372 47.826 0.00 0.00 35.43 3.67
439 1305 9.517609 GACGTAGTTATTTCACATCTAGATGTT 57.482 33.333 31.39 20.91 46.55 2.71
599 1467 9.678941 TGTAATTAATGCACACGTTCATTTTTA 57.321 25.926 11.24 8.33 34.95 1.52
770 2033 9.687210 GTATAATGTGTCGATGTGGAGTTAATA 57.313 33.333 0.00 0.00 0.00 0.98
823 2090 9.800433 CATATCTTCAAGGTATAGCATGTAGAG 57.200 37.037 17.43 10.24 0.00 2.43
948 2216 2.212812 TGCTTGACATGGTGCCATAA 57.787 45.000 3.07 0.00 34.91 1.90
961 2229 7.663081 ACATGGTGCCATAACTTCAAGATATAG 59.337 37.037 3.07 0.00 34.91 1.31
1177 2445 1.009060 TCCTCACTATTGGGGTAGCCA 59.991 52.381 14.06 0.00 45.01 4.75
1182 2450 2.172505 CACTATTGGGGTAGCCATGTCA 59.827 50.000 14.06 0.00 0.00 3.58
1512 2780 9.004717 TGTTATTCTTTGGATTCACACGATTTA 57.995 29.630 0.00 0.00 0.00 1.40
1616 2884 0.683504 TTCCCTCCTCTGGCGTAGTC 60.684 60.000 0.00 0.00 0.00 2.59
1675 2945 2.487775 ACATTCCATGTACCTGGCCTA 58.512 47.619 12.04 1.40 42.78 3.93
1682 2952 4.475381 TCCATGTACCTGGCCTAACAATAA 59.525 41.667 12.04 0.00 36.16 1.40
1737 3008 7.575414 TGTGCCAGAAAACTTTATGTTAAGA 57.425 32.000 0.00 0.00 38.03 2.10
2130 3419 7.287466 AGCTAGACTAATGAATGATGTGTCTCT 59.713 37.037 0.00 0.00 35.36 3.10
2296 3602 4.685169 ACGTTGTGCAGAATATGGAAAG 57.315 40.909 0.00 0.00 0.00 2.62
2383 3692 9.833917 AAAACCTCTATATAAGCAGGTTAGTTC 57.166 33.333 15.85 0.00 41.22 3.01
2401 3710 8.430828 GGTTAGTTCTGTTCGTTATTTACAGAC 58.569 37.037 0.00 0.00 45.64 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 2.306847 TCCCCTCTTCTTTGTTTGTGC 58.693 47.619 0.00 0.00 0.00 4.57
33 34 1.005215 AGCACCATCCCCTCTTCTTTG 59.995 52.381 0.00 0.00 0.00 2.77
171 1031 0.031616 ATTCCTCTTCGGCCTCCTCT 60.032 55.000 0.00 0.00 0.00 3.69
224 1089 3.057456 GCCGTTTGTCTCTCTCAGAGTAA 60.057 47.826 0.36 0.00 42.83 2.24
277 1143 2.040009 TTGATGCTAGTAGCGGGCCC 62.040 60.000 13.57 13.57 46.26 5.80
315 1181 1.713246 CACGCGACTGTTGTGTGTT 59.287 52.632 26.25 0.00 41.64 3.32
343 1209 4.320348 CGCAAACCTATTTTTGTCCCGTTA 60.320 41.667 0.00 0.00 38.51 3.18
394 1260 3.303461 CGTCACATCTAAGTCTAGAGCCG 60.303 52.174 0.00 0.00 37.58 5.52
653 1522 6.429078 CCATTAGTTGCACATCTACATGCTAT 59.571 38.462 0.00 0.00 42.55 2.97
770 2033 7.734924 ATAGCATCGAACAATGAATGTGTAT 57.265 32.000 0.00 0.00 42.99 2.29
777 2040 9.276590 AGATATGAAATAGCATCGAACAATGAA 57.723 29.630 0.00 0.00 37.75 2.57
891 2158 7.597288 TTAATTGCACTCTAGAGGCTACATA 57.403 36.000 23.50 13.35 0.00 2.29
948 2216 8.209584 ACATGCATCAGTTCTATATCTTGAAGT 58.790 33.333 0.00 0.00 0.00 3.01
961 2229 1.108776 ATGGGCACATGCATCAGTTC 58.891 50.000 0.00 0.00 44.36 3.01
1177 2445 0.108662 TCGCATTCGTCAGCTGACAT 60.109 50.000 38.31 25.97 44.99 3.06
1182 2450 2.185350 CCCTCGCATTCGTCAGCT 59.815 61.111 0.00 0.00 36.96 4.24
1557 2825 7.838696 AGACCATTCAATTTGACCCAACATATA 59.161 33.333 0.00 0.00 0.00 0.86
1616 2884 3.118956 CCTCCCACAGCTAAACTAGAGTG 60.119 52.174 0.00 0.00 34.90 3.51
1675 2945 8.697507 ACAGATCTGAAAGGAAAGTTATTGTT 57.302 30.769 29.27 0.00 0.00 2.83
1682 2952 7.118390 CACGAATTACAGATCTGAAAGGAAAGT 59.882 37.037 29.27 14.71 0.00 2.66
1737 3008 6.671614 TCACAAACGTTCTCATACAAAGTT 57.328 33.333 0.00 0.00 0.00 2.66
1828 3101 3.484649 GCAACGCATGAGCATATTTTCTG 59.515 43.478 0.00 0.00 42.27 3.02
1912 3194 9.942526 AATTTAAAGGTCCCAATCTCATCTTAT 57.057 29.630 0.00 0.00 0.00 1.73
1913 3195 9.189156 CAATTTAAAGGTCCCAATCTCATCTTA 57.811 33.333 0.00 0.00 0.00 2.10
2130 3419 1.541310 CGTGACCCTAGGTGAAGGCA 61.541 60.000 8.29 0.00 35.25 4.75
2271 3575 4.068599 TCCATATTCTGCACAACGTTGAA 58.931 39.130 33.66 17.57 0.00 2.69
2383 3692 4.929808 AGCAGGTCTGTAAATAACGAACAG 59.070 41.667 0.00 0.00 41.58 3.16
2484 3796 8.735315 TCGCCAAAAATACTCATGATTTAAGAA 58.265 29.630 0.00 0.00 0.00 2.52
2485 3797 8.275015 TCGCCAAAAATACTCATGATTTAAGA 57.725 30.769 0.00 0.00 0.00 2.10
2488 3800 7.821652 TGTTCGCCAAAAATACTCATGATTTA 58.178 30.769 0.00 0.00 0.00 1.40
2646 3964 8.768397 AGGAAGTCATAACATGTCCAGTATTTA 58.232 33.333 0.00 0.00 0.00 1.40
2722 4040 6.460399 CGGGATTTCCAAAAGTTGTCAGTTTA 60.460 38.462 0.00 0.00 37.91 2.01


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

AutoCloner maintained by Alex Coulton.