Multiple sequence alignment - TraesCS4A01G283800

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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 TraesCS4A01G283800 chr4A 100.000 2723 0 0 1 2723 590624494 590627216 0.000000e+00 5029
1 TraesCS4A01G283800 chr4A 93.718 1385 57 13 1 1374 604682991 604684356 0.000000e+00 2049
2 TraesCS4A01G283800 chr4A 96.595 1116 27 4 1619 2723 586665615 586664500 0.000000e+00 1840
3 TraesCS4A01G283800 chr3A 94.887 2738 107 16 1 2723 71903692 71906411 0.000000e+00 4250
4 TraesCS4A01G283800 chr3A 95.612 1823 62 8 913 2723 37765724 37767540 0.000000e+00 2907
5 TraesCS4A01G283800 chr2A 93.277 2112 91 17 1 2098 35224251 35226325 0.000000e+00 3066
6 TraesCS4A01G283800 chr2A 93.179 1378 65 17 1 1374 35026208 35027560 0.000000e+00 1997
7 TraesCS4A01G283800 chr2A 97.133 1116 21 5 1619 2723 196308731 196307616 0.000000e+00 1873
8 TraesCS4A01G283800 chr5B 92.999 1557 86 12 1 1549 546010351 546011892 0.000000e+00 2250
9 TraesCS4A01G283800 chr5B 95.569 1151 34 9 1587 2723 546011892 546013039 0.000000e+00 1827
10 TraesCS4A01G283800 chr5B 96.279 833 16 7 1904 2723 622318207 622319037 0.000000e+00 1352
11 TraesCS4A01G283800 chr5B 96.158 833 17 7 1904 2723 622279547 622280377 0.000000e+00 1347
12 TraesCS4A01G283800 chr5B 92.244 361 10 1 1654 1996 453116550 453116190 1.880000e-136 496
13 TraesCS4A01G283800 chr6B 92.494 1572 78 23 1 1554 616363069 616364618 0.000000e+00 2213
14 TraesCS4A01G283800 chr6B 95.098 612 29 1 944 1554 696463187 696463798 0.000000e+00 963
15 TraesCS4A01G283800 chr3B 94.352 1381 61 12 1 1374 172155717 172154347 0.000000e+00 2102
16 TraesCS4A01G283800 chr3B 93.974 614 36 1 942 1554 665495906 665496519 0.000000e+00 928
17 TraesCS4A01G283800 chr5A 93.981 1379 54 9 1 1374 43769930 43768576 0.000000e+00 2060
18 TraesCS4A01G283800 chr7A 93.471 1256 61 15 1 1250 418347150 418348390 0.000000e+00 1845
19 TraesCS4A01G283800 chr7A 89.709 447 17 5 1644 2061 418348430 418348876 6.630000e-151 544
20 TraesCS4A01G283800 chr7A 86.456 443 22 16 1650 2060 108809028 108808592 4.130000e-123 451
21 TraesCS4A01G283800 chr1A 96.685 1116 25 6 1619 2723 512280990 512282104 0.000000e+00 1845
22 TraesCS4A01G283800 chr1A 91.905 1050 44 15 1 1044 591447174 591448188 0.000000e+00 1430
23 TraesCS4A01G283800 chr1B 93.049 1194 62 10 1 1185 3841357 3842538 0.000000e+00 1725
24 TraesCS4A01G283800 chr7B 95.798 833 20 7 1904 2723 134438912 134438082 0.000000e+00 1330
25 TraesCS4A01G283800 chr4B 95.678 833 21 7 1904 2723 106582260 106583090 0.000000e+00 1325
26 TraesCS4A01G283800 chr7D 85.393 445 27 20 1650 2061 104566858 104566419 6.970000e-116 427
27 TraesCS4A01G283800 chr6D 83.598 189 18 8 1476 1654 463448280 463448095 6.030000e-37 165


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 TraesCS4A01G283800 chr4A 590624494 590627216 2722 False 5029.0 5029 100.000 1 2723 1 chr4A.!!$F1 2722
1 TraesCS4A01G283800 chr4A 604682991 604684356 1365 False 2049.0 2049 93.718 1 1374 1 chr4A.!!$F2 1373
2 TraesCS4A01G283800 chr4A 586664500 586665615 1115 True 1840.0 1840 96.595 1619 2723 1 chr4A.!!$R1 1104
3 TraesCS4A01G283800 chr3A 71903692 71906411 2719 False 4250.0 4250 94.887 1 2723 1 chr3A.!!$F2 2722
4 TraesCS4A01G283800 chr3A 37765724 37767540 1816 False 2907.0 2907 95.612 913 2723 1 chr3A.!!$F1 1810
5 TraesCS4A01G283800 chr2A 35224251 35226325 2074 False 3066.0 3066 93.277 1 2098 1 chr2A.!!$F2 2097
6 TraesCS4A01G283800 chr2A 35026208 35027560 1352 False 1997.0 1997 93.179 1 1374 1 chr2A.!!$F1 1373
7 TraesCS4A01G283800 chr2A 196307616 196308731 1115 True 1873.0 1873 97.133 1619 2723 1 chr2A.!!$R1 1104
8 TraesCS4A01G283800 chr5B 546010351 546013039 2688 False 2038.5 2250 94.284 1 2723 2 chr5B.!!$F3 2722
9 TraesCS4A01G283800 chr5B 622318207 622319037 830 False 1352.0 1352 96.279 1904 2723 1 chr5B.!!$F2 819
10 TraesCS4A01G283800 chr5B 622279547 622280377 830 False 1347.0 1347 96.158 1904 2723 1 chr5B.!!$F1 819
11 TraesCS4A01G283800 chr6B 616363069 616364618 1549 False 2213.0 2213 92.494 1 1554 1 chr6B.!!$F1 1553
12 TraesCS4A01G283800 chr6B 696463187 696463798 611 False 963.0 963 95.098 944 1554 1 chr6B.!!$F2 610
13 TraesCS4A01G283800 chr3B 172154347 172155717 1370 True 2102.0 2102 94.352 1 1374 1 chr3B.!!$R1 1373
14 TraesCS4A01G283800 chr3B 665495906 665496519 613 False 928.0 928 93.974 942 1554 1 chr3B.!!$F1 612
15 TraesCS4A01G283800 chr5A 43768576 43769930 1354 True 2060.0 2060 93.981 1 1374 1 chr5A.!!$R1 1373
16 TraesCS4A01G283800 chr7A 418347150 418348876 1726 False 1194.5 1845 91.590 1 2061 2 chr7A.!!$F1 2060
17 TraesCS4A01G283800 chr1A 512280990 512282104 1114 False 1845.0 1845 96.685 1619 2723 1 chr1A.!!$F1 1104
18 TraesCS4A01G283800 chr1A 591447174 591448188 1014 False 1430.0 1430 91.905 1 1044 1 chr1A.!!$F2 1043
19 TraesCS4A01G283800 chr1B 3841357 3842538 1181 False 1725.0 1725 93.049 1 1185 1 chr1B.!!$F1 1184
20 TraesCS4A01G283800 chr7B 134438082 134438912 830 True 1330.0 1330 95.798 1904 2723 1 chr7B.!!$R1 819
21 TraesCS4A01G283800 chr4B 106582260 106583090 830 False 1325.0 1325 95.678 1904 2723 1 chr4B.!!$F1 819

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
789 826 0.030908 CGAACCCTAGCGTCATCTCC 59.969 60.0 0.0 0.0 0.0 3.71 F
791 828 0.325296 AACCCTAGCGTCATCTCCCA 60.325 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
1720 1785 1.982958 GGGGAGGTTGGACTTGAACTA 59.017 52.381 0.0 0.0 0.00 2.24 R
2035 2129 2.877786 CAATGGACACACTGCACAAGTA 59.122 45.455 0.0 0.0 36.83 2.24 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
40 41 8.602472 TGCAATAATTATTTGGTAGGTCCTTT 57.398 30.769 8.01 0.00 37.07 3.11
111 115 6.039616 CGTCCAAAGAAAATGAAAACTTCCA 58.960 36.000 0.00 0.00 0.00 3.53
408 417 9.912634 TGTCACTCCAAAAATAGAAAATGATTC 57.087 29.630 0.00 0.00 0.00 2.52
409 418 9.358872 GTCACTCCAAAAATAGAAAATGATTCC 57.641 33.333 0.00 0.00 0.00 3.01
411 420 7.765819 CACTCCAAAAATAGAAAATGATTCCCC 59.234 37.037 0.00 0.00 0.00 4.81
627 638 8.540492 CAATTTAGATGGTCATAACGTGTACTC 58.460 37.037 0.00 0.00 0.00 2.59
788 825 0.595310 GCGAACCCTAGCGTCATCTC 60.595 60.000 0.00 0.00 0.00 2.75
789 826 0.030908 CGAACCCTAGCGTCATCTCC 59.969 60.000 0.00 0.00 0.00 3.71
790 827 0.389757 GAACCCTAGCGTCATCTCCC 59.610 60.000 0.00 0.00 0.00 4.30
791 828 0.325296 AACCCTAGCGTCATCTCCCA 60.325 55.000 0.00 0.00 0.00 4.37
792 829 0.325296 ACCCTAGCGTCATCTCCCAA 60.325 55.000 0.00 0.00 0.00 4.12
935 997 2.285743 GCCTGACCTTCTCCCCCT 60.286 66.667 0.00 0.00 0.00 4.79
936 998 2.371259 GCCTGACCTTCTCCCCCTC 61.371 68.421 0.00 0.00 0.00 4.30
937 999 1.081092 CCTGACCTTCTCCCCCTCA 59.919 63.158 0.00 0.00 0.00 3.86
938 1000 0.980231 CCTGACCTTCTCCCCCTCAG 60.980 65.000 0.00 0.00 0.00 3.35
948 1010 4.421554 CCCCTCAGCTCCCCTCCA 62.422 72.222 0.00 0.00 0.00 3.86
951 1013 1.614824 CCTCAGCTCCCCTCCACTT 60.615 63.158 0.00 0.00 0.00 3.16
1099 1161 0.674895 GTTCTTGGCCATGCTCTCGT 60.675 55.000 6.09 0.00 0.00 4.18
1199 1263 0.672342 AACCAGTACGAGAGCACGTT 59.328 50.000 8.64 0.00 44.14 3.99
1436 1501 0.669077 CTAGCTAGCCGATTGACCGT 59.331 55.000 12.13 0.00 0.00 4.83
1438 1503 1.108776 AGCTAGCCGATTGACCGTTA 58.891 50.000 12.13 0.00 0.00 3.18
1459 1524 2.360350 CCCTGTTGGCTCACGCAT 60.360 61.111 0.00 0.00 38.10 4.73
1489 1554 2.725312 GCCAGCTGATCCTGTCCGA 61.725 63.158 17.39 0.00 0.00 4.55
1569 1634 7.730084 TCTGCATAGTCTTCTTGTAGCATAAT 58.270 34.615 0.00 0.00 0.00 1.28
1573 1638 9.261180 GCATAGTCTTCTTGTAGCATAATACAA 57.739 33.333 0.00 0.00 42.01 2.41
1601 1666 2.160822 ATATCGCATCTGGACAGTGC 57.839 50.000 13.31 13.31 34.45 4.40
1971 2054 1.479730 TGTGTTGCATTTTGTCCTGCA 59.520 42.857 0.00 0.00 46.08 4.41
1996 2079 8.206867 CACCTTGAGAATGACTAGGATTTATGA 58.793 37.037 0.00 0.00 0.00 2.15
1998 2081 9.217278 CCTTGAGAATGACTAGGATTTATGATG 57.783 37.037 0.00 0.00 0.00 3.07
1999 2082 9.993454 CTTGAGAATGACTAGGATTTATGATGA 57.007 33.333 0.00 0.00 0.00 2.92
2008 2102 9.915629 GACTAGGATTTATGATGAAATAGTCGT 57.084 33.333 0.00 0.00 29.19 4.34
2055 2149 2.057137 ACTTGTGCAGTGTGTCCATT 57.943 45.000 0.00 0.00 32.83 3.16
2065 2159 4.561530 GCAGTGTGTCCATTGAGAGTAGAA 60.562 45.833 0.00 0.00 30.28 2.10
2125 2219 7.986889 TGCTCTTATATGCAAGTTTGTATCTGA 59.013 33.333 0.00 0.00 36.15 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 15 8.782137 AAGGACCTACCAAATAATTATTGCAT 57.218 30.769 11.42 3.12 42.04 3.96
627 638 1.811266 CGTGGACCAATCAGAGCCG 60.811 63.158 0.00 0.00 0.00 5.52
784 821 0.719015 TCTGGAGAGGGTTGGGAGAT 59.281 55.000 0.00 0.00 0.00 2.75
788 825 0.621571 TGGATCTGGAGAGGGTTGGG 60.622 60.000 0.00 0.00 0.00 4.12
789 826 0.835941 CTGGATCTGGAGAGGGTTGG 59.164 60.000 0.00 0.00 0.00 3.77
790 827 1.871418 TCTGGATCTGGAGAGGGTTG 58.129 55.000 0.00 0.00 0.00 3.77
791 828 2.688477 GATCTGGATCTGGAGAGGGTT 58.312 52.381 3.58 0.00 35.04 4.11
792 829 1.132881 GGATCTGGATCTGGAGAGGGT 60.133 57.143 9.96 0.00 37.92 4.34
921 975 1.613630 GCTGAGGGGGAGAAGGTCA 60.614 63.158 0.00 0.00 0.00 4.02
935 997 1.613630 GGAAGTGGAGGGGAGCTGA 60.614 63.158 0.00 0.00 0.00 4.26
936 998 2.674220 GGGAAGTGGAGGGGAGCTG 61.674 68.421 0.00 0.00 0.00 4.24
937 999 2.285743 GGGAAGTGGAGGGGAGCT 60.286 66.667 0.00 0.00 0.00 4.09
938 1000 2.285743 AGGGAAGTGGAGGGGAGC 60.286 66.667 0.00 0.00 0.00 4.70
948 1010 2.606826 GGGACACGGGAGGGAAGT 60.607 66.667 0.00 0.00 36.77 3.01
1057 1119 0.321475 GCTGCTCACCTCTTGAAGCT 60.321 55.000 0.00 0.00 35.81 3.74
1099 1161 2.158971 TGAAATGAATCGCCAGATCCGA 60.159 45.455 0.00 0.00 35.74 4.55
1402 1467 1.003118 AGCTAGACGGGATGCAAACAA 59.997 47.619 0.00 0.00 0.00 2.83
1489 1554 5.457148 CGTCGTCTATTACTACTAGACACGT 59.543 44.000 18.11 0.00 43.41 4.49
1569 1634 6.071896 CCAGATGCGATATTAGAGGAGTTGTA 60.072 42.308 0.00 0.00 0.00 2.41
1573 1638 4.461081 GTCCAGATGCGATATTAGAGGAGT 59.539 45.833 0.00 0.00 0.00 3.85
1720 1785 1.982958 GGGGAGGTTGGACTTGAACTA 59.017 52.381 0.00 0.00 0.00 2.24
1971 2054 8.324191 TCATAAATCCTAGTCATTCTCAAGGT 57.676 34.615 0.00 0.00 0.00 3.50
2035 2129 2.877786 CAATGGACACACTGCACAAGTA 59.122 45.455 0.00 0.00 36.83 2.24
2125 2219 7.040201 ACAAACTTCTGTCATGCATAAGACATT 60.040 33.333 17.42 8.50 43.18 2.71


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

AutoCloner maintained by Alex Coulton.