Multiple sequence alignment - TraesCS1A01G130100

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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 TraesCS1A01G130100 chr1A 100.000 2720 0 0 1 2720 168443938 168446657 0 5024
1 TraesCS1A01G130100 chrUn 96.896 2738 66 10 1 2720 93417668 93420404 0 4567
2 TraesCS1A01G130100 chrUn 96.384 1051 32 5 1 1045 407706735 407707785 0 1725
3 TraesCS1A01G130100 chr5D 96.821 2737 68 11 1 2720 560879148 560876414 0 4554
4 TraesCS1A01G130100 chr5D 96.640 2738 72 12 1 2720 503212588 503209853 0 4529
5 TraesCS1A01G130100 chr5D 96.310 2141 66 6 592 2720 329196036 329193897 0 3504
6 TraesCS1A01G130100 chr3B 96.528 2736 76 12 1 2720 201521355 201518623 0 4508
7 TraesCS1A01G130100 chr6A 95.198 2707 116 9 26 2720 260126127 260128831 0 4266
8 TraesCS1A01G130100 chr6A 95.744 2279 81 12 1 2267 271184129 271181855 0 3657
9 TraesCS1A01G130100 chr7A 95.958 2400 77 13 332 2720 201367984 201370374 0 3877
10 TraesCS1A01G130100 chr7A 91.514 2734 180 24 1 2720 352187393 352190088 0 3716
11 TraesCS1A01G130100 chr1D 96.918 1979 49 9 1 1970 144237386 144235411 0 3306


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 TraesCS1A01G130100 chr1A 168443938 168446657 2719 False 5024 5024 100.000 1 2720 1 chr1A.!!$F1 2719
1 TraesCS1A01G130100 chrUn 93417668 93420404 2736 False 4567 4567 96.896 1 2720 1 chrUn.!!$F1 2719
2 TraesCS1A01G130100 chrUn 407706735 407707785 1050 False 1725 1725 96.384 1 1045 1 chrUn.!!$F2 1044
3 TraesCS1A01G130100 chr5D 560876414 560879148 2734 True 4554 4554 96.821 1 2720 1 chr5D.!!$R3 2719
4 TraesCS1A01G130100 chr5D 503209853 503212588 2735 True 4529 4529 96.640 1 2720 1 chr5D.!!$R2 2719
5 TraesCS1A01G130100 chr5D 329193897 329196036 2139 True 3504 3504 96.310 592 2720 1 chr5D.!!$R1 2128
6 TraesCS1A01G130100 chr3B 201518623 201521355 2732 True 4508 4508 96.528 1 2720 1 chr3B.!!$R1 2719
7 TraesCS1A01G130100 chr6A 260126127 260128831 2704 False 4266 4266 95.198 26 2720 1 chr6A.!!$F1 2694
8 TraesCS1A01G130100 chr6A 271181855 271184129 2274 True 3657 3657 95.744 1 2267 1 chr6A.!!$R1 2266
9 TraesCS1A01G130100 chr7A 201367984 201370374 2390 False 3877 3877 95.958 332 2720 1 chr7A.!!$F1 2388
10 TraesCS1A01G130100 chr7A 352187393 352190088 2695 False 3716 3716 91.514 1 2720 1 chr7A.!!$F2 2719
11 TraesCS1A01G130100 chr1D 144235411 144237386 1975 True 3306 3306 96.918 1 1970 1 chr1D.!!$R1 1969

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
819 828 1.48424 GCTGGTAGTGGAAGAGATGCT 59.516 52.381 0.0 0.0 0.0 3.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2299 2325 1.682451 TTTCGCCGCCCAGTAGCTAT 61.682 55.0 0.0 0.0 0.0 2.97 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
21 22 4.537135 AAGGCTTCAAGTGTATCGAAGA 57.463 40.909 0.00 0.00 45.75 2.87
22 23 3.851098 AGGCTTCAAGTGTATCGAAGAC 58.149 45.455 0.00 0.00 43.81 3.01
23 24 3.851098 GGCTTCAAGTGTATCGAAGACT 58.149 45.455 0.00 0.00 42.51 3.24
24 25 3.860536 GGCTTCAAGTGTATCGAAGACTC 59.139 47.826 0.00 0.00 42.51 3.36
25 26 3.544285 GCTTCAAGTGTATCGAAGACTCG 59.456 47.826 0.00 0.00 46.87 4.18
147 152 6.712241 TCTAAAATTCAAGCGAAGAGACTG 57.288 37.500 0.00 0.00 33.74 3.51
242 247 7.587028 TCGTAAAATTTGTACAAAATGTCGACC 59.413 33.333 23.97 7.56 33.56 4.79
255 260 3.993103 CGACCGATTCGTAGGTGC 58.007 61.111 5.20 0.00 43.24 5.01
315 320 8.585018 CATAAACAAAGACAGGGGTAATCTTTT 58.415 33.333 0.00 0.00 39.98 2.27
571 580 7.493743 TGTAGGAATGCACGTTTTAGTTTAA 57.506 32.000 0.00 0.00 0.00 1.52
599 608 5.989777 AGAGTGCACGTAGAATAACAAAAGT 59.010 36.000 12.01 0.00 0.00 2.66
601 610 5.526111 AGTGCACGTAGAATAACAAAAGTGT 59.474 36.000 12.01 0.00 40.75 3.55
722 731 5.068198 TCAAAAGCTCAAGAAAAGCATCACT 59.932 36.000 0.00 0.00 42.35 3.41
775 784 6.317642 TGCTATTCGTACAATAGGTTTGCAAT 59.682 34.615 18.52 0.00 32.32 3.56
819 828 1.484240 GCTGGTAGTGGAAGAGATGCT 59.516 52.381 0.00 0.00 0.00 3.79
903 912 1.540146 CCGCATAATGGATGTCGACCA 60.540 52.381 14.12 4.10 41.83 4.02
1089 1100 5.875359 AGATAGTAAGCGCCTTTATTATGGC 59.125 40.000 2.29 0.00 45.25 4.40
1209 1220 2.223711 ACGTGCAAAATTTGGGAGTGTC 60.224 45.455 7.89 0.00 0.00 3.67
1351 1362 7.490000 CGTCAAAGGTCCTAGATACATAACTT 58.510 38.462 0.00 0.00 0.00 2.66
1355 1366 8.919145 CAAAGGTCCTAGATACATAACTTCTCT 58.081 37.037 0.00 0.00 0.00 3.10
1548 1559 3.495193 CATGCCTGTTCGAAATGTGAAG 58.505 45.455 0.00 0.00 0.00 3.02
1596 1611 7.936584 TGGAAATGAAAAACACGAGATACTTT 58.063 30.769 0.00 0.00 0.00 2.66
1676 1691 9.173939 GGCTTCTCGTAATTTGATTGATTTATG 57.826 33.333 0.00 0.00 0.00 1.90
1717 1732 0.537653 GGAAGAGGGCGCTAGTTTCT 59.462 55.000 7.64 0.42 0.00 2.52
1731 1746 9.569167 GGCGCTAGTTTCTAAGAAAATAAAAAT 57.431 29.630 7.64 0.00 0.00 1.82
1754 1769 5.610429 AGGTTTACTCCACCCCTTTTTAT 57.390 39.130 0.00 0.00 34.44 1.40
2157 2181 4.700692 GGGAAGATTCACTTGGAAGTAACC 59.299 45.833 0.00 0.00 39.30 2.85
2271 2295 4.585879 TGCTCCAATACCTAACCAAAGAC 58.414 43.478 0.00 0.00 0.00 3.01
2369 2395 7.903145 TCTAGAAAAGGTACTGTCAATAAGCA 58.097 34.615 0.00 0.00 40.86 3.91
2374 2400 8.630054 AAAAGGTACTGTCAATAAGCATGTTA 57.370 30.769 0.00 0.00 40.86 2.41
2516 2542 3.196254 GGTTCACCAATCATTGATGGCTT 59.804 43.478 0.00 0.00 35.64 4.35
2669 2695 9.547753 TCTTAATACAGGATCATTTAAGTCTGC 57.452 33.333 8.92 0.00 33.61 4.26
2705 2731 4.715297 TGGGATAGGTGAACTCTTTAGGAC 59.285 45.833 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 3.312973 TCTTCGCTATCCTTCGAGTCTTC 59.687 47.826 0.00 0.0 36.02 2.87
18 19 3.280295 TCTTCGCTATCCTTCGAGTCTT 58.720 45.455 0.00 0.0 36.02 3.01
20 21 3.907894 ATCTTCGCTATCCTTCGAGTC 57.092 47.619 0.00 0.0 36.02 3.36
21 22 4.098044 TCAAATCTTCGCTATCCTTCGAGT 59.902 41.667 0.00 0.0 36.02 4.18
22 23 4.611943 TCAAATCTTCGCTATCCTTCGAG 58.388 43.478 0.00 0.0 36.02 4.04
23 24 4.649088 TCAAATCTTCGCTATCCTTCGA 57.351 40.909 0.00 0.0 0.00 3.71
24 25 4.210120 CCTTCAAATCTTCGCTATCCTTCG 59.790 45.833 0.00 0.0 0.00 3.79
25 26 5.360591 TCCTTCAAATCTTCGCTATCCTTC 58.639 41.667 0.00 0.0 0.00 3.46
26 27 5.359194 TCCTTCAAATCTTCGCTATCCTT 57.641 39.130 0.00 0.0 0.00 3.36
28 29 5.350091 GCTATCCTTCAAATCTTCGCTATCC 59.650 44.000 0.00 0.0 0.00 2.59
242 247 1.937846 CGTCCGCACCTACGAATCG 60.938 63.158 0.00 0.0 41.55 3.34
253 258 3.520290 AATGACTCTAATTCGTCCGCA 57.480 42.857 0.00 0.0 0.00 5.69
255 260 3.865745 AGCAAATGACTCTAATTCGTCCG 59.134 43.478 0.00 0.0 0.00 4.79
283 288 3.502211 CCCTGTCTTTGTTTATGCTTCGT 59.498 43.478 0.00 0.0 0.00 3.85
571 580 4.219944 TGTTATTCTACGTGCACTCTTCCT 59.780 41.667 16.19 0.0 0.00 3.36
599 608 8.845227 TGAAACTAGCTTGAACATGAATAAACA 58.155 29.630 0.00 0.0 0.00 2.83
601 610 9.677567 GTTGAAACTAGCTTGAACATGAATAAA 57.322 29.630 0.00 0.0 0.00 1.40
683 692 3.500680 GCTTTTGAATCCACAAGTACCGA 59.499 43.478 0.00 0.0 33.72 4.69
722 731 4.713553 TGCTGTTCTTTGACCAACATAGA 58.286 39.130 0.00 0.0 35.44 1.98
775 784 4.843728 CCCTTTACCATAACTTCTGCTCA 58.156 43.478 0.00 0.0 0.00 4.26
913 923 5.163794 CGGGTTAATTCTTTTACATGCGTCT 60.164 40.000 0.00 0.0 0.00 4.18
914 924 5.025826 CGGGTTAATTCTTTTACATGCGTC 58.974 41.667 0.00 0.0 0.00 5.19
915 925 4.673320 GCGGGTTAATTCTTTTACATGCGT 60.673 41.667 0.00 0.0 0.00 5.24
916 926 3.789224 GCGGGTTAATTCTTTTACATGCG 59.211 43.478 0.00 0.0 0.00 4.73
917 927 4.993905 AGCGGGTTAATTCTTTTACATGC 58.006 39.130 0.00 0.0 0.00 4.06
918 928 7.087639 TGAAAGCGGGTTAATTCTTTTACATG 58.912 34.615 0.00 0.0 0.00 3.21
1089 1100 1.644786 GCGGGGACAGAATGAAACGG 61.645 60.000 0.00 0.0 39.69 4.44
1209 1220 2.572191 TTGTAGAATACTCGTGCGGG 57.428 50.000 0.00 0.0 43.54 6.13
1351 1362 6.068461 AGGCGGTAAGATGATATCTAGAGA 57.932 41.667 3.98 0.0 39.08 3.10
1355 1366 4.398358 CGGAAGGCGGTAAGATGATATCTA 59.602 45.833 3.98 0.0 39.08 1.98
1548 1559 9.403583 TCCATTCCCACAAGAAAAATACTATAC 57.596 33.333 0.00 0.0 0.00 1.47
1676 1691 1.725164 CCGCGTGTAGAAAAGGAAGAC 59.275 52.381 4.92 0.0 0.00 3.01
1731 1746 6.723471 ATAAAAAGGGGTGGAGTAAACCTA 57.277 37.500 0.00 0.0 37.85 3.08
2059 2083 8.810652 TTGTACCAAAGATGCTAAATTGTTTC 57.189 30.769 0.00 0.0 0.00 2.78
2157 2181 9.090103 TGAAGTACCATAGGTATCTAGGAAATG 57.910 37.037 0.00 0.0 40.54 2.32
2271 2295 6.473455 CCGTTTTTAATCGGTACTGTAGTAGG 59.527 42.308 0.64 0.0 41.58 3.18
2299 2325 1.682451 TTTCGCCGCCCAGTAGCTAT 61.682 55.000 0.00 0.0 0.00 2.97
2369 2395 8.177119 TCTTTTAATGGTTTCTGTGCTAACAT 57.823 30.769 0.00 0.0 35.22 2.71
2374 2400 5.519722 CGTTCTTTTAATGGTTTCTGTGCT 58.480 37.500 0.00 0.0 0.00 4.40
2468 2494 3.452627 AGATCCGTTTGCAACTCCTCTAT 59.547 43.478 0.00 0.0 0.00 1.98
2469 2495 2.832129 AGATCCGTTTGCAACTCCTCTA 59.168 45.455 0.00 0.0 0.00 2.43
2516 2542 4.546829 AATGTAGGTTTAGCGGTTCTCA 57.453 40.909 0.00 0.0 0.00 3.27
2669 2695 7.938140 TCACCTATCCCAATAACAAAGAAAG 57.062 36.000 0.00 0.0 0.00 2.62


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

AutoCloner maintained by Alex Coulton.