Multiple sequence alignment - TraesCS4B01G237800

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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 TraesCS4B01G237800 chr4B 100.000 2465 0 0 1 2465 495480789 495478325 0 4553
1 TraesCS4B01G237800 chr1A 98.160 1685 28 3 782 2465 278520899 278522581 0 2937
2 TraesCS4B01G237800 chr3A 98.042 1685 31 2 782 2465 495105055 495103372 0 2928
3 TraesCS4B01G237800 chr3A 97.970 788 16 0 1 788 495105909 495105122 0 1367
4 TraesCS4B01G237800 chrUn 98.040 1684 32 1 782 2465 217907373 217909055 0 2926
5 TraesCS4B01G237800 chrUn 97.716 788 18 0 1 788 217906519 217907306 0 1356
6 TraesCS4B01G237800 chr3B 98.040 1684 32 1 782 2465 6011061 6009379 0 2926
7 TraesCS4B01G237800 chr3B 98.044 1687 26 5 782 2465 92297027 92295345 0 2926
8 TraesCS4B01G237800 chr3B 97.970 788 16 0 1 788 92297881 92297094 0 1367
9 TraesCS4B01G237800 chr3B 97.716 788 18 0 1 788 6011915 6011128 0 1356
10 TraesCS4B01G237800 chr6A 97.982 1685 29 3 782 2465 597253288 597251608 0 2918
11 TraesCS4B01G237800 chr2B 97.923 1685 33 2 782 2465 234541455 234539772 0 2916
12 TraesCS4B01G237800 chr2B 97.970 788 16 0 1 788 234542309 234541522 0 1367
13 TraesCS4B01G237800 chr4A 97.864 1685 34 2 782 2465 67519203 67520886 0 2911
14 TraesCS4B01G237800 chr1B 97.799 1681 36 1 786 2465 619195623 619193943 0 2898
15 TraesCS4B01G237800 chr1B 97.970 788 16 0 1 788 461438972 461439759 0 1367
16 TraesCS4B01G237800 chr4D 97.843 788 17 0 1 788 123450135 123449348 0 1362
17 TraesCS4B01G237800 chr7A 97.716 788 18 0 1 788 563523247 563522460 0 1356
18 TraesCS4B01G237800 chr6D 97.592 789 17 2 1 788 108484059 108484846 0 1351


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 TraesCS4B01G237800 chr4B 495478325 495480789 2464 True 4553.0 4553 100.0000 1 2465 1 chr4B.!!$R1 2464
1 TraesCS4B01G237800 chr1A 278520899 278522581 1682 False 2937.0 2937 98.1600 782 2465 1 chr1A.!!$F1 1683
2 TraesCS4B01G237800 chr3A 495103372 495105909 2537 True 2147.5 2928 98.0060 1 2465 2 chr3A.!!$R1 2464
3 TraesCS4B01G237800 chrUn 217906519 217909055 2536 False 2141.0 2926 97.8780 1 2465 2 chrUn.!!$F1 2464
4 TraesCS4B01G237800 chr3B 92295345 92297881 2536 True 2146.5 2926 98.0070 1 2465 2 chr3B.!!$R2 2464
5 TraesCS4B01G237800 chr3B 6009379 6011915 2536 True 2141.0 2926 97.8780 1 2465 2 chr3B.!!$R1 2464
6 TraesCS4B01G237800 chr6A 597251608 597253288 1680 True 2918.0 2918 97.9820 782 2465 1 chr6A.!!$R1 1683
7 TraesCS4B01G237800 chr2B 234539772 234542309 2537 True 2141.5 2916 97.9465 1 2465 2 chr2B.!!$R1 2464
8 TraesCS4B01G237800 chr4A 67519203 67520886 1683 False 2911.0 2911 97.8640 782 2465 1 chr4A.!!$F1 1683
9 TraesCS4B01G237800 chr1B 619193943 619195623 1680 True 2898.0 2898 97.7990 786 2465 1 chr1B.!!$R1 1679
10 TraesCS4B01G237800 chr1B 461438972 461439759 787 False 1367.0 1367 97.9700 1 788 1 chr1B.!!$F1 787
11 TraesCS4B01G237800 chr4D 123449348 123450135 787 True 1362.0 1362 97.8430 1 788 1 chr4D.!!$R1 787
12 TraesCS4B01G237800 chr7A 563522460 563523247 787 True 1356.0 1356 97.7160 1 788 1 chr7A.!!$R1 787
13 TraesCS4B01G237800 chr6D 108484059 108484846 787 False 1351.0 1351 97.5920 1 788 1 chr6D.!!$F1 787

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
263 264 0.60813 CGTGTGAATGGAGAGTGGGA 59.392 55.0 0.0 0.0 0.0 4.37 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1498 1572 0.887387 GGCAGAACCGTTGTTGCCTA 60.887 55.0 21.23 0.0 39.35 3.93 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
252 253 2.418628 CCGCTTTGATAACCGTGTGAAT 59.581 45.455 0.00 0.00 0.00 2.57
263 264 0.608130 CGTGTGAATGGAGAGTGGGA 59.392 55.000 0.00 0.00 0.00 4.37
268 269 2.834549 GTGAATGGAGAGTGGGAAGAGA 59.165 50.000 0.00 0.00 0.00 3.10
309 310 1.285950 CGGAGTCGCACACTTGAGA 59.714 57.895 0.00 0.00 34.41 3.27
372 373 2.933906 GGCCGATTAAATCACAGACGAA 59.066 45.455 0.00 0.00 0.00 3.85
379 380 7.167481 CGATTAAATCACAGACGAAGAACTTC 58.833 38.462 4.67 4.67 36.29 3.01
731 733 3.694058 CTGCAAGCAGGCGGGATCT 62.694 63.158 14.10 0.00 40.17 2.75
762 764 2.782222 CCCTCCGATTCGAAGCCGA 61.782 63.158 19.95 12.97 43.96 5.54
964 1038 5.971895 AAAGCTGTCGTAAAGTTTCGTTA 57.028 34.783 0.00 0.00 0.00 3.18
998 1072 7.140048 GTCGTTGACCCTATCTATGTTTCTAG 58.860 42.308 0.00 0.00 0.00 2.43
1012 1086 3.075283 TGTTTCTAGGATGGCCCAAGAAA 59.925 43.478 0.00 4.56 41.09 2.52
1317 1391 6.118170 AGATATTGATTCCTCCACACAACAG 58.882 40.000 0.00 0.00 0.00 3.16
1356 1430 6.030849 CGACGAATTAGAAGAGATGTCAACT 58.969 40.000 0.00 0.00 0.00 3.16
1410 1484 2.928801 TTGGTACTGTCACTGCACAT 57.071 45.000 0.00 0.00 0.00 3.21
1687 1761 0.098728 CGGGCCATCAACATTCGAAC 59.901 55.000 4.39 0.00 0.00 3.95
1688 1762 1.173043 GGGCCATCAACATTCGAACA 58.827 50.000 4.39 0.00 0.00 3.18
1986 2060 1.277326 CTCGCCAAATTCGTCGATCA 58.723 50.000 0.00 0.00 0.00 2.92
2072 2146 1.778803 CCCCTTTCCCCCTATCCCC 60.779 68.421 0.00 0.00 0.00 4.81
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
124 125 3.244044 GCTCCTATCTCTCGGCAAAGATT 60.244 47.826 0.00 0.0 34.21 2.40
252 253 3.073062 CCTTTTTCTCTTCCCACTCTCCA 59.927 47.826 0.00 0.0 0.00 3.86
263 264 3.074687 GGACCTCCTTCCCTTTTTCTCTT 59.925 47.826 0.00 0.0 0.00 2.85
309 310 0.832135 TTCTCCAGTCTCCCGCACTT 60.832 55.000 0.00 0.0 0.00 3.16
750 752 2.373938 CCACACTCGGCTTCGAATC 58.626 57.895 0.00 0.0 42.80 2.52
816 890 5.067413 GCCATGCTATTCCATGATATTGGAG 59.933 44.000 0.00 0.0 46.22 3.86
998 1072 1.215382 GCGTTTTCTTGGGCCATCC 59.785 57.895 7.26 0.0 0.00 3.51
1012 1086 0.320771 ACGGCTGAAGAATGAGCGTT 60.321 50.000 0.00 0.0 35.95 4.84
1279 1353 5.219343 TCAATATCTCGACATGAGCCAAT 57.781 39.130 0.00 0.0 44.86 3.16
1286 1360 5.636965 GTGGAGGAATCAATATCTCGACATG 59.363 44.000 0.00 0.0 35.83 3.21
1356 1430 1.072489 TGTTTCCAGATACGGTTGCCA 59.928 47.619 0.00 0.0 0.00 4.92
1410 1484 2.925966 ATCCCCAATCCTTTGCTTGA 57.074 45.000 0.00 0.0 0.00 3.02
1498 1572 0.887387 GGCAGAACCGTTGTTGCCTA 60.887 55.000 21.23 0.0 39.35 3.93
1680 1754 2.930826 AGGACCAACACTGTTCGAAT 57.069 45.000 0.00 0.0 0.00 3.34
2072 2146 1.202770 CCCGCTCCTAAACATAAGGGG 60.203 57.143 0.00 0.0 40.51 4.79


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

AutoCloner maintained by Alex Coulton.