Multiple sequence alignment - TraesCS1B01G181000

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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 TraesCS1B01G181000 chr1B 100.000 5847 0 0 1 5847 327580098 327574252 0.000000e+00 10798.0
1 TraesCS1B01G181000 chr1D 96.894 5280 104 17 2 5266 228073555 228068321 0.000000e+00 8787.0
2 TraesCS1B01G181000 chr1D 97.245 3484 54 9 2388 5847 208086699 208090164 0.000000e+00 5864.0
3 TraesCS1B01G181000 chr1D 98.604 2364 16 8 2 2362 208084357 208086706 0.000000e+00 4167.0
4 TraesCS1B01G181000 chr1D 93.399 606 22 4 5259 5847 228068160 228067556 0.000000e+00 881.0
5 TraesCS1B01G181000 chr1A 94.873 3784 124 33 2126 5847 295587929 295584154 0.000000e+00 5849.0
6 TraesCS1B01G181000 chr1A 94.351 1540 53 15 365 1899 295589643 295588133 0.000000e+00 2331.0
7 TraesCS1B01G181000 chr1A 96.739 368 11 1 1 368 295590127 295589761 3.870000e-171 612.0
8 TraesCS1B01G181000 chr1A 83.439 314 37 8 3344 3651 295586756 295586452 1.600000e-70 278.0
9 TraesCS1B01G181000 chr1A 93.333 90 5 1 2036 2125 90725839 90725927 1.320000e-26 132.0
10 TraesCS1B01G181000 chr1A 96.226 53 2 0 1893 1945 295587979 295587927 2.900000e-13 87.9
11 TraesCS1B01G181000 chr5D 93.407 91 5 1 2036 2126 449674921 449675010 3.680000e-27 134.0
12 TraesCS1B01G181000 chr4A 91.667 96 7 1 2034 2129 647205474 647205568 1.320000e-26 132.0
13 TraesCS1B01G181000 chr3D 93.333 90 5 1 2036 2125 611923109 611923197 1.320000e-26 132.0
14 TraesCS1B01G181000 chr2D 94.253 87 4 1 2039 2125 645152810 645152725 1.320000e-26 132.0
15 TraesCS1B01G181000 chr2A 92.553 94 4 3 2039 2130 310535727 310535635 1.320000e-26 132.0
16 TraesCS1B01G181000 chr5B 90.722 97 8 1 2039 2135 115054068 115053973 1.710000e-25 128.0


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 TraesCS1B01G181000 chr1B 327574252 327580098 5846 True 10798.00 10798 100.0000 1 5847 1 chr1B.!!$R1 5846
1 TraesCS1B01G181000 chr1D 208084357 208090164 5807 False 5015.50 5864 97.9245 2 5847 2 chr1D.!!$F1 5845
2 TraesCS1B01G181000 chr1D 228067556 228073555 5999 True 4834.00 8787 95.1465 2 5847 2 chr1D.!!$R1 5845
3 TraesCS1B01G181000 chr1A 295584154 295590127 5973 True 1831.58 5849 93.1256 1 5847 5 chr1A.!!$R1 5846

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
174 175 2.283145 AGTCCCATATGCTTGGATGC 57.717 50.0 0.00 0.0 39.25 3.91 F
1385 1508 0.250234 TCAGAGAACATGAAGCCCCG 59.750 55.0 0.00 0.0 0.00 5.73 F
3306 3642 0.603569 CACTGTACGGAAGACCTGCT 59.396 55.0 9.17 0.0 0.00 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 2230 0.392706 CCCAAACAAACAGGGCCTTC 59.607 55.000 1.32 0.00 35.44 3.46 R
3634 3997 1.134946 GTTTGGTCTGCCATATGGTGC 59.865 52.381 22.79 10.11 45.56 5.01 R
5080 5483 2.736721 CAGGTTCCGTGTGTACAATGAG 59.263 50.000 0.00 0.00 0.00 2.90 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
174 175 2.283145 AGTCCCATATGCTTGGATGC 57.717 50.000 0.00 0.00 39.25 3.91
658 780 7.601886 CCATGTTTCTTTGTGCCAATTACATAA 59.398 33.333 0.00 0.00 0.00 1.90
764 886 7.027874 TGGTAGATTTGAATCTGGTAACCTT 57.972 36.000 17.72 0.00 45.01 3.50
1385 1508 0.250234 TCAGAGAACATGAAGCCCCG 59.750 55.000 0.00 0.00 0.00 5.73
1942 2230 4.508861 CCAAGAAATTTGCCAGTTCAGTTG 59.491 41.667 0.00 0.00 0.00 3.16
2380 2704 3.378112 CACCGCTACCACATGAAAATCAT 59.622 43.478 0.00 0.00 37.65 2.45
3306 3642 0.603569 CACTGTACGGAAGACCTGCT 59.396 55.000 9.17 0.00 0.00 4.24
3358 3694 1.526917 CCTTATGGAAGGCCTGCCG 60.527 63.158 25.82 10.47 45.91 5.69
3423 3759 0.890996 GGCCTGCTAATGATTCCCCG 60.891 60.000 0.00 0.00 0.00 5.73
3634 3997 4.208632 GGAGACCTGCCAACGATG 57.791 61.111 0.00 0.00 0.00 3.84
3904 4267 3.264193 TCAGCAATTAGGCCTCTCAAGAA 59.736 43.478 9.68 0.00 0.00 2.52
4226 4626 4.085357 TGTCTGGTTCTGTTTATGCTGT 57.915 40.909 0.00 0.00 0.00 4.40
4403 4803 5.745476 GCTCATCTCCCTTCTGAAATGCTAT 60.745 44.000 0.00 0.00 0.00 2.97
4421 4821 6.778834 TGCTATGTGGAAATTGTCATTGAT 57.221 33.333 0.00 0.00 0.00 2.57
4461 4861 5.809562 CAGGTATTCAAGTAGCTCTGTTGAG 59.190 44.000 0.00 0.00 42.96 3.02
4870 5272 2.093764 CCTAGAGGCTTGTGGTGAAGAG 60.094 54.545 0.00 0.00 0.00 2.85
4928 5330 3.343617 TGCTGCCACATTAACTAGGTTC 58.656 45.455 0.00 0.00 0.00 3.62
5000 5402 4.338400 GGTTATTTCCAAGGATGTACTGCC 59.662 45.833 0.00 0.00 0.00 4.85
5016 5418 2.164624 ACTGCCAAACGTGCTTGTTTTA 59.835 40.909 4.45 0.00 39.94 1.52
5068 5471 2.998670 ACATCTGATGACAAGAGTTGCG 59.001 45.455 23.59 0.00 0.00 4.85
5236 5639 1.285078 AGGAGGCCATAGTTTCCAACC 59.715 52.381 5.01 0.00 32.02 3.77
5367 5946 4.508861 AGACAATGCTTTGTGATTTGCAAC 59.491 37.500 21.41 5.06 46.01 4.17
5405 5987 6.909357 GTGCTCAGTAACAATTATCTTGATGC 59.091 38.462 0.00 0.00 0.00 3.91
5514 6096 5.388111 GTTTCTAGGGCGAACATAAAACAC 58.612 41.667 0.00 0.00 0.00 3.32
5522 6104 7.088272 AGGGCGAACATAAAACACTTTAATTC 58.912 34.615 0.00 0.00 30.87 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
742 864 7.281100 CAGGAAGGTTACCAGATTCAAATCTAC 59.719 40.741 3.51 0.84 43.65 2.59
794 916 7.230510 TGTTCACAAGTGCAAGAAAAGGTATAT 59.769 33.333 0.00 0.00 0.00 0.86
1385 1508 2.731217 ACGCATCTTGAGCAAAACAAC 58.269 42.857 0.00 0.00 0.00 3.32
1681 1804 0.732571 AGCTGGAACACAACACAACG 59.267 50.000 0.00 0.00 0.00 4.10
1925 2213 3.493176 GCCTTCAACTGAACTGGCAAATT 60.493 43.478 14.62 0.00 41.97 1.82
1942 2230 0.392706 CCCAAACAAACAGGGCCTTC 59.607 55.000 1.32 0.00 35.44 3.46
3634 3997 1.134946 GTTTGGTCTGCCATATGGTGC 59.865 52.381 22.79 10.11 45.56 5.01
3904 4267 8.766994 AATTGTTGCATATTACTATTCCCAGT 57.233 30.769 0.00 0.00 0.00 4.00
4421 4821 7.811282 TGAATACCTGCCAAAAGGATTATCTA 58.189 34.615 0.00 0.00 40.02 1.98
4461 4861 5.526846 CAGAGAACTATTTGGAATCCTCAGC 59.473 44.000 0.00 0.00 0.00 4.26
4928 5330 4.433615 ACATGATCTAAGTTACACCGCTG 58.566 43.478 0.00 0.00 0.00 5.18
5000 5402 7.908193 AAGACTAATAAAACAAGCACGTTTG 57.092 32.000 4.49 0.00 39.04 2.93
5016 5418 7.232737 CACTCAAAAGGGGGTAAAAAGACTAAT 59.767 37.037 0.00 0.00 0.00 1.73
5080 5483 2.736721 CAGGTTCCGTGTGTACAATGAG 59.263 50.000 0.00 0.00 0.00 2.90
5236 5639 7.856145 ATTCCTGCTACAAACAGAATTCTAG 57.144 36.000 7.86 5.56 37.32 2.43
5681 6277 1.589716 CTTTTGCCTTCTCGCCAGGG 61.590 60.000 0.00 0.00 31.20 4.45
5687 6283 1.537202 CTGGGTTCTTTTGCCTTCTCG 59.463 52.381 0.00 0.00 0.00 4.04
5690 6286 2.820197 CCTACTGGGTTCTTTTGCCTTC 59.180 50.000 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.