Multiple sequence alignment - TraesCS5B01G006300

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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 TraesCS5B01G006300 chr5B 100.000 2667 0 0 1 2667 7384265 7381599 0.000000e+00 4926.0
1 TraesCS5B01G006300 chr5B 95.351 2667 98 10 1 2667 7305677 7303037 0.000000e+00 4215.0
2 TraesCS5B01G006300 chr5B 92.579 2668 134 17 1 2667 7150198 7147594 0.000000e+00 3771.0
3 TraesCS5B01G006300 chr5B 92.544 2669 135 19 1 2667 7185937 7183331 0.000000e+00 3768.0
4 TraesCS5B01G006300 chr5B 93.000 2143 113 14 526 2667 7163305 7161199 0.000000e+00 3092.0
5 TraesCS5B01G006300 chr5D 88.394 2628 266 26 1 2603 7121000 7118387 0.000000e+00 3127.0
6 TraesCS5B01G006300 chr5D 88.798 2571 252 26 58 2603 7126237 7123678 0.000000e+00 3120.0
7 TraesCS5B01G006300 chr5D 88.029 2623 269 32 1 2597 3868827 3871430 0.000000e+00 3062.0
8 TraesCS5B01G006300 chr5D 87.652 2624 281 26 1 2592 3874399 3877011 0.000000e+00 3011.0
9 TraesCS5B01G006300 chr5D 86.667 2595 277 46 94 2655 3889440 3891998 0.000000e+00 2811.0
10 TraesCS5B01G006300 chr5D 88.170 1809 182 22 1 1794 7131576 7129785 0.000000e+00 2126.0
11 TraesCS5B01G006300 chr5D 86.629 1062 114 15 1555 2592 7135326 7134269 0.000000e+00 1149.0
12 TraesCS5B01G006300 chr5D 95.238 42 2 0 2626 2667 3882280 3882321 1.710000e-07 67.6
13 TraesCS5B01G006300 chr4A 87.961 2467 253 31 1 2448 18738366 18735925 0.000000e+00 2870.0
14 TraesCS5B01G006300 chr4A 86.058 2618 304 36 61 2655 18731963 18729384 0.000000e+00 2756.0
15 TraesCS5B01G006300 chr4A 89.046 2118 200 22 500 2603 18743503 18741404 0.000000e+00 2597.0
16 TraesCS5B01G006300 chr5A 87.231 2467 275 27 2 2448 4791863 4789417 0.000000e+00 2774.0
17 TraesCS5B01G006300 chr5A 87.917 1018 101 15 1 1002 4874776 4875787 0.000000e+00 1179.0


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 TraesCS5B01G006300 chr5B 7381599 7384265 2666 True 4926.0 4926 100.000000 1 2667 1 chr5B.!!$R5 2666
1 TraesCS5B01G006300 chr5B 7303037 7305677 2640 True 4215.0 4215 95.351000 1 2667 1 chr5B.!!$R4 2666
2 TraesCS5B01G006300 chr5B 7147594 7150198 2604 True 3771.0 3771 92.579000 1 2667 1 chr5B.!!$R1 2666
3 TraesCS5B01G006300 chr5B 7183331 7185937 2606 True 3768.0 3768 92.544000 1 2667 1 chr5B.!!$R3 2666
4 TraesCS5B01G006300 chr5B 7161199 7163305 2106 True 3092.0 3092 93.000000 526 2667 1 chr5B.!!$R2 2141
5 TraesCS5B01G006300 chr5D 3868827 3877011 8184 False 3036.5 3062 87.840500 1 2597 2 chr5D.!!$F3 2596
6 TraesCS5B01G006300 chr5D 3889440 3891998 2558 False 2811.0 2811 86.667000 94 2655 1 chr5D.!!$F2 2561
7 TraesCS5B01G006300 chr5D 7118387 7135326 16939 True 2380.5 3127 87.997750 1 2603 4 chr5D.!!$R1 2602
8 TraesCS5B01G006300 chr4A 18729384 18743503 14119 True 2741.0 2870 87.688333 1 2655 3 chr4A.!!$R1 2654
9 TraesCS5B01G006300 chr5A 4789417 4791863 2446 True 2774.0 2774 87.231000 2 2448 1 chr5A.!!$R1 2446
10 TraesCS5B01G006300 chr5A 4874776 4875787 1011 False 1179.0 1179 87.917000 1 1002 1 chr5A.!!$F1 1001

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
155 10637 1.755008 GCGCCTACTCTCCCACTCT 60.755 63.158 0.00 0.00 0.00 3.24 F
274 10756 2.043953 AATTGGGAAGCTCCGCCC 60.044 61.111 11.34 11.34 44.93 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1152 11650 0.307760 GAGAAGGCAAACACACCACG 59.692 55.0 0.0 0.0 0.0 4.94 R
1984 12510 1.663695 ACCAAACACCACACTCTTCG 58.336 50.0 0.0 0.0 0.0 3.79 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
24 5224 7.899178 CCAAACATAATTGGGGTTTTAAGAC 57.101 36.000 0.00 0.00 45.03 3.01
155 10637 1.755008 GCGCCTACTCTCCCACTCT 60.755 63.158 0.00 0.00 0.00 3.24
274 10756 2.043953 AATTGGGAAGCTCCGCCC 60.044 61.111 11.34 11.34 44.93 6.13
295 10777 5.565834 GCCCAACGAAATTTTCCATAGTCAA 60.566 40.000 3.61 0.00 0.00 3.18
864 11362 7.220300 GCTATGACAAAGCATCAATTTGAGAAG 59.780 37.037 5.21 0.00 39.50 2.85
1058 11556 9.330063 CATACACTTATCAACTCCACATACAAT 57.670 33.333 0.00 0.00 0.00 2.71
1080 11578 8.594550 ACAATAGTACCACCTATTAATAGCCTG 58.405 37.037 15.86 12.37 35.87 4.85
1152 11650 7.252965 ACTTGTGCTACTTTCTTTTCTTCTC 57.747 36.000 0.00 0.00 0.00 2.87
1165 11663 1.295792 TCTTCTCGTGGTGTGTTTGC 58.704 50.000 0.00 0.00 0.00 3.68
1169 11667 0.307760 CTCGTGGTGTGTTTGCCTTC 59.692 55.000 0.00 0.00 0.00 3.46
1442 11942 6.263392 CAGATCTTGGAGAATGCTTCATCAAT 59.737 38.462 0.00 0.00 27.28 2.57
1727 12231 5.193124 TGATTGTCTCCTCCTAGGTGTACTA 59.807 44.000 9.08 2.31 36.53 1.82
1752 12256 3.804325 CGTGGAACTATGATGGACATCAC 59.196 47.826 16.47 4.53 42.30 3.06
1770 12275 6.688578 ACATCACGACAAAATGTACTCTAGT 58.311 36.000 0.00 0.00 32.05 2.57
1771 12276 6.807230 ACATCACGACAAAATGTACTCTAGTC 59.193 38.462 0.00 0.00 32.05 2.59
1772 12277 6.570672 TCACGACAAAATGTACTCTAGTCT 57.429 37.500 0.00 0.00 0.00 3.24
1773 12278 6.978338 TCACGACAAAATGTACTCTAGTCTT 58.022 36.000 0.00 0.00 0.00 3.01
1816 12341 2.723314 CGCGTGCGTTAACATCATTCAA 60.723 45.455 6.00 0.00 34.35 2.69
1889 12414 8.531622 TGTGAAGCACCAAATATTGTAATTTG 57.468 30.769 2.97 2.97 43.45 2.32
2090 12616 3.014604 AGTGCGTGTAGAAGAAGTGAC 57.985 47.619 0.00 0.00 0.00 3.67
2091 12617 2.361119 AGTGCGTGTAGAAGAAGTGACA 59.639 45.455 0.00 0.00 0.00 3.58
2120 12646 2.163815 GCGTCCTCTAGCTACAAGTCAA 59.836 50.000 0.00 0.00 0.00 3.18
2180 12706 3.117657 TCCATCTAGGACCGCTGAG 57.882 57.895 0.00 0.00 43.07 3.35
2218 12747 3.371102 TCGAACCAGAGTTGAACTGAG 57.629 47.619 0.90 0.00 35.94 3.35
2296 12827 9.396022 TGCAAAATAAGTCTAGATTTCCTAAGG 57.604 33.333 3.43 0.00 0.00 2.69
2466 19336 6.650120 AGATAGCGAGACAATTTTTAAGGGA 58.350 36.000 0.00 0.00 0.00 4.20
2604 19474 2.158623 TCAAACACTTGTGATCTGCCCT 60.159 45.455 7.83 0.00 33.94 5.19
2655 19525 4.142093 GCAATTGATCATGTAGCAACCCTT 60.142 41.667 10.34 0.00 36.05 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
155 10637 0.598942 CGACACGAATGGACACCACA 60.599 55.000 0.00 0.00 35.80 4.17
274 10756 5.572896 GCCTTGACTATGGAAAATTTCGTTG 59.427 40.000 0.00 0.00 0.00 4.10
295 10777 1.001378 GTGAAAATGTCGCACTTGCCT 60.001 47.619 0.00 0.00 36.70 4.75
601 11095 5.828299 AAAATTCAACAAGACTCGTCCAA 57.172 34.783 0.00 0.00 0.00 3.53
1058 11556 9.833179 AATACAGGCTATTAATAGGTGGTACTA 57.167 33.333 21.30 0.00 0.00 1.82
1080 11578 6.812160 ACTTTGTCATCGTCACTAAGGAATAC 59.188 38.462 8.95 0.00 32.75 1.89
1117 11615 1.242076 AGCACAAGTCCTTGCACATC 58.758 50.000 6.94 0.00 44.03 3.06
1152 11650 0.307760 GAGAAGGCAAACACACCACG 59.692 55.000 0.00 0.00 0.00 4.94
1165 11663 3.474600 CATATGTGCCTCCAAGAGAAGG 58.525 50.000 0.00 0.00 0.00 3.46
1169 11667 4.422073 TTACCATATGTGCCTCCAAGAG 57.578 45.455 1.24 0.00 0.00 2.85
1290 11790 5.534654 TGTTTCTCCCCTTGTTGTTTATGAG 59.465 40.000 0.00 0.00 0.00 2.90
1727 12231 4.753516 TGTCCATCATAGTTCCACGATT 57.246 40.909 0.00 0.00 0.00 3.34
1752 12256 8.024285 AGAGAAAGACTAGAGTACATTTTGTCG 58.976 37.037 0.00 0.00 0.00 4.35
1770 12275 5.721480 TGAGAGAGAGAGAGAGAGAGAAAGA 59.279 44.000 0.00 0.00 0.00 2.52
1771 12276 5.814705 GTGAGAGAGAGAGAGAGAGAGAAAG 59.185 48.000 0.00 0.00 0.00 2.62
1772 12277 5.624509 CGTGAGAGAGAGAGAGAGAGAGAAA 60.625 48.000 0.00 0.00 0.00 2.52
1773 12278 4.142160 CGTGAGAGAGAGAGAGAGAGAGAA 60.142 50.000 0.00 0.00 0.00 2.87
1830 12355 8.601047 TGAAATTATTGTTCACCCATCCAATA 57.399 30.769 0.00 0.00 30.08 1.90
1984 12510 1.663695 ACCAAACACCACACTCTTCG 58.336 50.000 0.00 0.00 0.00 3.79
2090 12616 1.994507 CTAGAGGACGCCGACACCTG 61.995 65.000 6.93 0.00 33.89 4.00
2091 12617 1.749638 CTAGAGGACGCCGACACCT 60.750 63.158 0.00 0.00 36.68 4.00
2120 12646 8.496707 AAATGCAGTTTTTGAAAGAGTCAATT 57.503 26.923 0.00 0.00 45.71 2.32
2218 12747 4.484236 TGTGAATTCCATCAAAATCACGC 58.516 39.130 2.27 0.00 37.56 5.34
2296 12827 1.875963 CATGTGGGTTGGAACGCTC 59.124 57.895 7.93 5.19 41.84 5.03
2604 19474 4.646945 TGGGCAGTGTGTTTTCTTCATTTA 59.353 37.500 0.00 0.00 0.00 1.40


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

AutoCloner maintained by Alex Coulton.