Multiple sequence alignment - TraesCS2D01G360300

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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 TraesCS2D01G360300 chr2D 100.000 3571 0 0 1 3571 462203363 462206933 0.000000e+00 6595
1 TraesCS2D01G360300 chr2A 96.598 2175 47 11 1404 3571 607484371 607486525 0.000000e+00 3581
2 TraesCS2D01G360300 chr2A 95.416 1418 31 6 2181 3571 610118818 610120228 0.000000e+00 2228
3 TraesCS2D01G360300 chr2A 92.721 1415 59 24 1 1396 607482905 607484294 0.000000e+00 2002
4 TraesCS2D01G360300 chr2A 91.773 1337 67 20 67 1396 610116477 610117777 0.000000e+00 1820
5 TraesCS2D01G360300 chr2A 96.081 791 24 4 1404 2190 610117854 610118641 0.000000e+00 1282
6 TraesCS2D01G360300 chr2B 95.988 2019 48 7 1411 3398 544990861 544992877 0.000000e+00 3249
7 TraesCS2D01G360300 chr2B 91.360 544 24 13 858 1400 544990254 544990775 0.000000e+00 723
8 TraesCS2D01G360300 chr2B 92.067 479 27 4 1 469 544987070 544987547 0.000000e+00 664
9 TraesCS2D01G360300 chr2B 94.183 361 14 4 490 847 544987540 544987896 8.720000e-151 544
10 TraesCS2D01G360300 chr2B 97.126 174 4 1 3398 3571 544993009 544993181 3.490000e-75 292
11 TraesCS2D01G360300 chr2B 93.902 82 3 1 3316 3395 544992994 544992913 4.840000e-24 122


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 TraesCS2D01G360300 chr2D 462203363 462206933 3570 False 6595.000000 6595 100.000000 1 3571 1 chr2D.!!$F1 3570
1 TraesCS2D01G360300 chr2A 607482905 607486525 3620 False 2791.500000 3581 94.659500 1 3571 2 chr2A.!!$F1 3570
2 TraesCS2D01G360300 chr2A 610116477 610120228 3751 False 1776.666667 2228 94.423333 67 3571 3 chr2A.!!$F2 3504
3 TraesCS2D01G360300 chr2B 544987070 544993181 6111 False 1094.400000 3249 94.144800 1 3571 5 chr2B.!!$F1 3570

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
294 306 0.250901 TTCTGAACCCTGAAGCCAGC 60.251 55.0 0.0 0.0 39.07 4.85 F
1005 3375 1.528292 GCGAGGGTCTAGCGATGGAT 61.528 60.0 0.0 0.0 0.00 3.41 F
1583 4035 0.324943 TTGGGTTGCTCTGCTAGTCC 59.675 55.0 0.0 0.0 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1408 3789 0.031994 AACAAAACCTGGTCATGCGC 59.968 50.0 0.0 0.0 0.00 6.09 R
2352 4995 1.020437 GCTAAGGACTCATGCTTGCC 58.980 55.0 0.0 0.0 37.06 4.52 R
3071 5716 0.322975 CTGAGGCTGTGGCAACTACT 59.677 55.0 0.0 0.0 40.87 2.57 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
25 27 3.009723 TGTCTTAGCCAAGCACATAAGC 58.990 45.455 0.00 0.00 0.00 3.09
26 28 3.009723 GTCTTAGCCAAGCACATAAGCA 58.990 45.455 0.00 0.00 36.85 3.91
165 168 2.281484 TTCCAGCGTTGGTCCTGC 60.281 61.111 18.51 0.00 45.26 4.85
212 215 1.676014 CCCTGAGAAATCGACACCCAC 60.676 57.143 0.00 0.00 0.00 4.61
252 255 2.590821 GCTGGACCATAAGATTGCCAT 58.409 47.619 0.00 0.00 0.00 4.40
257 261 1.858910 ACCATAAGATTGCCATCCCCA 59.141 47.619 0.00 0.00 0.00 4.96
262 266 3.986996 AAGATTGCCATCCCCAAAAAG 57.013 42.857 0.00 0.00 0.00 2.27
293 305 2.503895 ATTCTGAACCCTGAAGCCAG 57.496 50.000 0.00 0.00 40.09 4.85
294 306 0.250901 TTCTGAACCCTGAAGCCAGC 60.251 55.000 0.00 0.00 39.07 4.85
468 480 7.301054 CAGTTGTCTTCTGAATTCACATTACC 58.699 38.462 3.38 0.00 35.20 2.85
564 579 2.671177 CGTCGTTGAGCTGCAAGGG 61.671 63.158 1.02 5.31 41.47 3.95
567 582 1.597854 CGTTGAGCTGCAAGGGACA 60.598 57.895 1.02 0.00 38.40 4.02
905 3274 2.282462 ACTCTTTTGCCCCTGCCG 60.282 61.111 0.00 0.00 36.33 5.69
908 3277 3.752339 CTTTTGCCCCTGCCGCTC 61.752 66.667 0.00 0.00 36.33 5.03
996 3366 2.601868 GGGGAGAGCGAGGGTCTA 59.398 66.667 0.00 0.00 40.67 2.59
998 3368 2.197605 GGGAGAGCGAGGGTCTAGC 61.198 68.421 0.00 0.00 40.67 3.42
1005 3375 1.528292 GCGAGGGTCTAGCGATGGAT 61.528 60.000 0.00 0.00 0.00 3.41
1014 3384 1.744320 TAGCGATGGATGTGGGGTCG 61.744 60.000 0.00 0.00 35.56 4.79
1370 3743 4.876107 TGCTTGCTACTGCTTTTACTATCC 59.124 41.667 0.00 0.00 40.48 2.59
1371 3744 4.025647 GCTTGCTACTGCTTTTACTATCCG 60.026 45.833 0.00 0.00 40.48 4.18
1396 3777 9.212687 CGAGTAAATTTCGAAACAAAACTGTTA 57.787 29.630 13.81 0.00 40.36 2.41
1406 3787 9.843334 TCGAAACAAAACTGTTATGTAAAAACT 57.157 25.926 0.00 0.00 0.00 2.66
1426 3877 0.823356 AGCGCATGACCAGGTTTTGT 60.823 50.000 11.47 0.00 0.00 2.83
1429 3880 2.287909 GCGCATGACCAGGTTTTGTTTA 60.288 45.455 0.30 0.00 0.00 2.01
1583 4035 0.324943 TTGGGTTGCTCTGCTAGTCC 59.675 55.000 0.00 0.00 0.00 3.85
1607 4059 6.420903 CCTCTTGAAATGCATTGCTCATATTG 59.579 38.462 18.39 7.85 0.00 1.90
1787 4244 5.703592 TGTATGACCAAATTACACAGGTGTC 59.296 40.000 8.56 0.00 43.74 3.67
2066 4523 1.735973 GGAAAGCCCATCGAATGCC 59.264 57.895 0.00 0.00 34.14 4.40
2285 4928 1.945387 CAGATGTCGTATTGGCTGCT 58.055 50.000 0.00 0.00 0.00 4.24
2680 5323 7.736447 AATTTATAGCTAGGCATTCACAGTC 57.264 36.000 0.00 0.00 0.00 3.51
2708 5351 7.230510 TCAGTATTTGTTGTAAGCTTCCACAAT 59.769 33.333 15.88 6.75 37.04 2.71
2724 5367 7.495934 GCTTCCACAATACTTTGAAGCTATCTA 59.504 37.037 13.60 0.00 37.29 1.98
2788 5431 3.201290 GACTGGTGCATAGAAGTGATGG 58.799 50.000 7.80 0.00 0.00 3.51
3060 5705 9.874205 GGATCATTGTTTTTCTTGGATGAAATA 57.126 29.630 0.00 0.00 36.07 1.40
3071 5716 6.720309 TCTTGGATGAAATATGAGGTGTTGA 58.280 36.000 0.00 0.00 0.00 3.18
3106 5751 2.197324 AGCGGGCCAAAACAAGGA 59.803 55.556 4.39 0.00 0.00 3.36
3107 5752 2.200337 AGCGGGCCAAAACAAGGAC 61.200 57.895 4.39 0.00 0.00 3.85
3376 6050 7.307493 TCGGTGAAAATAATGAAGACATGAG 57.693 36.000 0.00 0.00 36.79 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 28 4.457257 GCTTGTCTTTTGATCAGGCTAACT 59.543 41.667 0.00 0.00 33.43 2.24
165 168 3.499737 CAAACCGCTGCTAGCCGG 61.500 66.667 25.18 25.18 38.18 6.13
212 215 2.430465 CCTCTCAAATGTCACAGGTGG 58.570 52.381 0.00 0.00 0.00 4.61
252 255 2.969628 TCCAAGCAATCTTTTTGGGGA 58.030 42.857 2.96 0.00 41.31 4.81
257 261 8.037166 GGTTCAGAATATCCAAGCAATCTTTTT 58.963 33.333 0.00 0.00 0.00 1.94
262 266 5.009410 CAGGGTTCAGAATATCCAAGCAATC 59.991 44.000 0.00 0.00 0.00 2.67
293 305 0.674895 ACTCTGCTGAAATGTCGGGC 60.675 55.000 0.00 0.00 0.00 6.13
294 306 2.271800 GTACTCTGCTGAAATGTCGGG 58.728 52.381 0.00 0.00 0.00 5.14
343 355 1.468914 GATTTGGCGTTCCTTCTGTCC 59.531 52.381 0.00 0.00 0.00 4.02
431 443 2.863809 AGACAACTGGTTGATGGGAAC 58.136 47.619 18.63 0.00 42.93 3.62
468 480 2.786495 ATCCCTGGTGCTAGTCGCG 61.786 63.158 0.00 0.00 43.27 5.87
480 495 4.080919 TCTCTTGGTCAATGTACATCCCTG 60.081 45.833 9.23 4.19 0.00 4.45
541 556 2.598632 GCAGCTCAACGACGTGCTT 61.599 57.895 8.44 0.00 33.63 3.91
591 606 3.425404 GCATTGGCAAATACGTACTGTG 58.575 45.455 3.01 0.00 40.72 3.66
905 3274 1.135575 CCCAAATCGTTGAGCTTGAGC 60.136 52.381 0.00 0.00 36.83 4.26
908 3277 1.135575 GCTCCCAAATCGTTGAGCTTG 60.136 52.381 0.00 0.00 36.83 4.01
964 3333 3.083349 CCCCGGATGCAGACCTCA 61.083 66.667 0.73 0.00 0.00 3.86
969 3338 2.444706 CTCTCCCCCGGATGCAGA 60.445 66.667 0.73 0.00 0.00 4.26
996 3366 2.911143 GACCCCACATCCATCGCT 59.089 61.111 0.00 0.00 0.00 4.93
998 3368 1.521457 CACGACCCCACATCCATCG 60.521 63.158 0.00 0.00 38.71 3.84
1126 3496 3.432588 GTCCTGCTGCTGCTGCTG 61.433 66.667 27.67 25.97 40.48 4.41
1152 3525 1.289380 GGAGAAGAGCGACACGGTT 59.711 57.895 0.00 0.00 37.83 4.44
1370 3743 7.659290 ACAGTTTTGTTTCGAAATTTACTCG 57.341 32.000 14.69 11.42 32.28 4.18
1396 3777 4.006989 TGGTCATGCGCTAGTTTTTACAT 58.993 39.130 9.73 0.00 0.00 2.29
1398 3779 3.181510 CCTGGTCATGCGCTAGTTTTTAC 60.182 47.826 9.73 0.00 0.00 2.01
1399 3780 3.006940 CCTGGTCATGCGCTAGTTTTTA 58.993 45.455 9.73 0.00 0.00 1.52
1400 3781 1.812571 CCTGGTCATGCGCTAGTTTTT 59.187 47.619 9.73 0.00 0.00 1.94
1401 3782 1.271379 ACCTGGTCATGCGCTAGTTTT 60.271 47.619 9.73 0.00 0.00 2.43
1402 3783 0.324943 ACCTGGTCATGCGCTAGTTT 59.675 50.000 9.73 0.00 0.00 2.66
1403 3784 0.324943 AACCTGGTCATGCGCTAGTT 59.675 50.000 9.73 0.00 0.00 2.24
1405 3786 1.131126 CAAAACCTGGTCATGCGCTAG 59.869 52.381 9.73 0.14 0.00 3.42
1406 3787 1.164411 CAAAACCTGGTCATGCGCTA 58.836 50.000 9.73 0.00 0.00 4.26
1408 3789 0.031994 AACAAAACCTGGTCATGCGC 59.968 50.000 0.00 0.00 0.00 6.09
1409 3790 2.507339 AAACAAAACCTGGTCATGCG 57.493 45.000 0.00 0.00 0.00 4.73
1426 3877 6.655848 ACGCCTTTAGTATGAACATTGGTAAA 59.344 34.615 0.00 0.00 0.00 2.01
1429 3880 4.585879 ACGCCTTTAGTATGAACATTGGT 58.414 39.130 0.00 0.00 0.00 3.67
1583 4035 6.978659 ACAATATGAGCAATGCATTTCAAGAG 59.021 34.615 15.80 9.85 0.00 2.85
1639 4091 2.253610 TCAGTACGGAATTCACCAGGT 58.746 47.619 7.93 0.00 0.00 4.00
2066 4523 4.921515 TGAGTCTTCTTATTCCGAAACACG 59.078 41.667 0.00 0.00 42.18 4.49
2285 4928 1.284657 CAAAACCGTTGTGCATGCAA 58.715 45.000 24.58 10.26 0.00 4.08
2352 4995 1.020437 GCTAAGGACTCATGCTTGCC 58.980 55.000 0.00 0.00 37.06 4.52
2650 5293 8.713271 GTGAATGCCTAGCTATAAATTAGACAC 58.287 37.037 0.00 0.00 0.00 3.67
2680 5323 7.023575 GTGGAAGCTTACAACAAATACTGATG 58.976 38.462 14.43 0.00 34.11 3.07
2724 5367 7.436118 ACAGTTTGTGCTCAAATAACATGAAT 58.564 30.769 16.24 0.00 43.92 2.57
2788 5431 6.256757 GGTAGATGTCTAGATTGTTGCTGAAC 59.743 42.308 0.00 0.00 0.00 3.18
3060 5705 2.371841 TGGCAACTACTCAACACCTCAT 59.628 45.455 0.00 0.00 37.61 2.90
3071 5716 0.322975 CTGAGGCTGTGGCAACTACT 59.677 55.000 0.00 0.00 40.87 2.57
3237 5909 6.178607 AGAACTTTCTGGGAAAATGCAAAT 57.821 33.333 0.00 0.00 35.89 2.32


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

AutoCloner maintained by Alex Coulton.