Multiple sequence alignment - TraesCS5D01G552300

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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 TraesCS5D01G552300 chr5D 100.000 2480 0 0 1 2480 557793951 557796430 0 4580
1 TraesCS5D01G552300 chr5D 96.691 967 28 4 749 1713 565809433 565810397 0 1605
2 TraesCS5D01G552300 chr5D 97.250 909 24 1 1573 2480 565810202 565811110 0 1539
3 TraesCS5D01G552300 chr2D 99.114 2482 19 3 1 2480 621997766 622000246 0 4458
4 TraesCS5D01G552300 chr3D 98.353 1700 24 3 1 1700 359527468 359525773 0 2981
5 TraesCS5D01G552300 chr3D 98.460 909 13 1 1573 2480 359525955 359525047 0 1600
6 TraesCS5D01G552300 chr4D 98.076 1715 28 5 1 1713 393458506 393460217 0 2979
7 TraesCS5D01G552300 chr4D 98.350 909 14 1 1573 2480 393460022 393460930 0 1594
8 TraesCS5D01G552300 chr1D 97.608 1714 37 4 1 1713 251020562 251022272 0 2935
9 TraesCS5D01G552300 chr1D 97.690 909 20 1 1573 2480 251022077 251022985 0 1561
10 TraesCS5D01G552300 chr3B 97.116 1699 46 3 1 1699 389719858 389721553 0 2863
11 TraesCS5D01G552300 chr3B 96.791 1714 52 3 1 1713 361795829 361797540 0 2857
12 TraesCS5D01G552300 chr3B 97.250 909 24 1 1573 2480 361797345 361798253 0 1539
13 TraesCS5D01G552300 chr2B 96.674 1714 54 3 1 1713 728070272 728068561 0 2846
14 TraesCS5D01G552300 chr2B 96.429 924 29 4 1560 2480 728068770 728067848 0 1520
15 TraesCS5D01G552300 chr6B 96.558 1714 53 4 1 1713 587366781 587365073 0 2833
16 TraesCS5D01G552300 chr6B 96.320 924 30 4 1560 2480 587365282 587364360 0 1515
17 TraesCS5D01G552300 chr6A 94.248 1721 80 9 1 1713 583326533 583328242 0 2612
18 TraesCS5D01G552300 chr6A 95.055 910 43 2 1573 2480 583328046 583328955 0 1430


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 TraesCS5D01G552300 chr5D 557793951 557796430 2479 False 4580.0 4580 100.0000 1 2480 1 chr5D.!!$F1 2479
1 TraesCS5D01G552300 chr5D 565809433 565811110 1677 False 1572.0 1605 96.9705 749 2480 2 chr5D.!!$F2 1731
2 TraesCS5D01G552300 chr2D 621997766 622000246 2480 False 4458.0 4458 99.1140 1 2480 1 chr2D.!!$F1 2479
3 TraesCS5D01G552300 chr3D 359525047 359527468 2421 True 2290.5 2981 98.4065 1 2480 2 chr3D.!!$R1 2479
4 TraesCS5D01G552300 chr4D 393458506 393460930 2424 False 2286.5 2979 98.2130 1 2480 2 chr4D.!!$F1 2479
5 TraesCS5D01G552300 chr1D 251020562 251022985 2423 False 2248.0 2935 97.6490 1 2480 2 chr1D.!!$F1 2479
6 TraesCS5D01G552300 chr3B 389719858 389721553 1695 False 2863.0 2863 97.1160 1 1699 1 chr3B.!!$F1 1698
7 TraesCS5D01G552300 chr3B 361795829 361798253 2424 False 2198.0 2857 97.0205 1 2480 2 chr3B.!!$F2 2479
8 TraesCS5D01G552300 chr2B 728067848 728070272 2424 True 2183.0 2846 96.5515 1 2480 2 chr2B.!!$R1 2479
9 TraesCS5D01G552300 chr6B 587364360 587366781 2421 True 2174.0 2833 96.4390 1 2480 2 chr6B.!!$R1 2479
10 TraesCS5D01G552300 chr6A 583326533 583328955 2422 False 2021.0 2612 94.6515 1 2480 2 chr6A.!!$F1 2479

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
957 968 4.410099 TCTGGAGCATCTTTCCAAAATGT 58.59 39.13 0.0 0.0 43.79 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1962 2031 0.84203 AGGCATTCACCTGGAGTCCA 60.842 55.0 12.4 12.4 39.13 4.02 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
957 968 4.410099 TCTGGAGCATCTTTCCAAAATGT 58.590 39.130 0.0 0.0 43.79 2.71
1575 1588 7.698130 GGAGTGAACTATTTTGTCATTGTATGC 59.302 37.037 0.0 0.0 0.00 3.14
1576 1589 7.538575 AGTGAACTATTTTGTCATTGTATGCC 58.461 34.615 0.0 0.0 0.00 4.40
1577 1590 7.176515 AGTGAACTATTTTGTCATTGTATGCCA 59.823 33.333 0.0 0.0 0.00 4.92
1578 1591 7.273381 GTGAACTATTTTGTCATTGTATGCCAC 59.727 37.037 0.0 0.0 0.00 5.01
1579 1592 7.176515 TGAACTATTTTGTCATTGTATGCCACT 59.823 33.333 0.0 0.0 0.00 4.00
1580 1593 7.466746 ACTATTTTGTCATTGTATGCCACTT 57.533 32.000 0.0 0.0 0.00 3.16
1581 1594 7.315142 ACTATTTTGTCATTGTATGCCACTTG 58.685 34.615 0.0 0.0 0.00 3.16
1582 1595 5.781210 TTTTGTCATTGTATGCCACTTGA 57.219 34.783 0.0 0.0 0.00 3.02
1583 1596 5.781210 TTTGTCATTGTATGCCACTTGAA 57.219 34.783 0.0 0.0 0.00 2.69
1584 1597 4.764679 TGTCATTGTATGCCACTTGAAC 57.235 40.909 0.0 0.0 0.00 3.18
1585 1598 4.397420 TGTCATTGTATGCCACTTGAACT 58.603 39.130 0.0 0.0 0.00 3.01
1586 1599 5.555966 TGTCATTGTATGCCACTTGAACTA 58.444 37.500 0.0 0.0 0.00 2.24
1587 1600 6.179756 TGTCATTGTATGCCACTTGAACTAT 58.820 36.000 0.0 0.0 0.00 2.12
1588 1601 6.658816 TGTCATTGTATGCCACTTGAACTATT 59.341 34.615 0.0 0.0 0.00 1.73
1589 1602 7.176515 TGTCATTGTATGCCACTTGAACTATTT 59.823 33.333 0.0 0.0 0.00 1.40
1590 1603 7.485913 GTCATTGTATGCCACTTGAACTATTTG 59.514 37.037 0.0 0.0 0.00 2.32
1591 1604 5.309323 TGTATGCCACTTGAACTATTTGC 57.691 39.130 0.0 0.0 0.00 3.68
1592 1605 5.009631 TGTATGCCACTTGAACTATTTGCT 58.990 37.500 0.0 0.0 0.00 3.91
1593 1606 5.476599 TGTATGCCACTTGAACTATTTGCTT 59.523 36.000 0.0 0.0 0.00 3.91
1594 1607 4.935352 TGCCACTTGAACTATTTGCTTT 57.065 36.364 0.0 0.0 0.00 3.51
1595 1608 6.588719 ATGCCACTTGAACTATTTGCTTTA 57.411 33.333 0.0 0.0 0.00 1.85
1596 1609 6.588719 TGCCACTTGAACTATTTGCTTTAT 57.411 33.333 0.0 0.0 0.00 1.40
1597 1610 6.389091 TGCCACTTGAACTATTTGCTTTATG 58.611 36.000 0.0 0.0 0.00 1.90
1598 1611 6.015519 TGCCACTTGAACTATTTGCTTTATGT 60.016 34.615 0.0 0.0 0.00 2.29
1599 1612 7.175816 TGCCACTTGAACTATTTGCTTTATGTA 59.824 33.333 0.0 0.0 0.00 2.29
1600 1613 8.190784 GCCACTTGAACTATTTGCTTTATGTAT 58.809 33.333 0.0 0.0 0.00 2.29
1601 1614 9.507280 CCACTTGAACTATTTGCTTTATGTATG 57.493 33.333 0.0 0.0 0.00 2.39
1605 1618 9.853555 TTGAACTATTTGCTTTATGTATGTTGG 57.146 29.630 0.0 0.0 0.00 3.77
1606 1619 9.237187 TGAACTATTTGCTTTATGTATGTTGGA 57.763 29.630 0.0 0.0 0.00 3.53
1607 1620 9.722056 GAACTATTTGCTTTATGTATGTTGGAG 57.278 33.333 0.0 0.0 0.00 3.86
1608 1621 8.807948 ACTATTTGCTTTATGTATGTTGGAGT 57.192 30.769 0.0 0.0 0.00 3.85
1609 1622 8.677300 ACTATTTGCTTTATGTATGTTGGAGTG 58.323 33.333 0.0 0.0 0.00 3.51
1610 1623 7.701539 ATTTGCTTTATGTATGTTGGAGTGA 57.298 32.000 0.0 0.0 0.00 3.41
1611 1624 7.517614 TTTGCTTTATGTATGTTGGAGTGAA 57.482 32.000 0.0 0.0 0.00 3.18
1612 1625 6.494893 TGCTTTATGTATGTTGGAGTGAAC 57.505 37.500 0.0 0.0 0.00 3.18
1613 1626 6.237901 TGCTTTATGTATGTTGGAGTGAACT 58.762 36.000 0.0 0.0 0.00 3.01
1614 1627 7.390823 TGCTTTATGTATGTTGGAGTGAACTA 58.609 34.615 0.0 0.0 0.00 2.24
1615 1628 8.046708 TGCTTTATGTATGTTGGAGTGAACTAT 58.953 33.333 0.0 0.0 0.00 2.12
1616 1629 8.893727 GCTTTATGTATGTTGGAGTGAACTATT 58.106 33.333 0.0 0.0 0.00 1.73
1620 1633 8.635765 ATGTATGTTGGAGTGAACTATTTTGT 57.364 30.769 0.0 0.0 0.00 2.83
1621 1634 8.094798 TGTATGTTGGAGTGAACTATTTTGTC 57.905 34.615 0.0 0.0 0.00 3.18
1622 1635 7.717436 TGTATGTTGGAGTGAACTATTTTGTCA 59.283 33.333 0.0 0.0 0.00 3.58
1623 1636 7.765695 ATGTTGGAGTGAACTATTTTGTCAT 57.234 32.000 0.0 0.0 0.00 3.06
1624 1637 7.581213 TGTTGGAGTGAACTATTTTGTCATT 57.419 32.000 0.0 0.0 0.00 2.57
1625 1638 7.424803 TGTTGGAGTGAACTATTTTGTCATTG 58.575 34.615 0.0 0.0 0.00 2.82
1626 1639 7.068103 TGTTGGAGTGAACTATTTTGTCATTGT 59.932 33.333 0.0 0.0 0.00 2.71
1627 1640 8.564574 GTTGGAGTGAACTATTTTGTCATTGTA 58.435 33.333 0.0 0.0 0.00 2.41
1628 1641 8.862325 TGGAGTGAACTATTTTGTCATTGTAT 57.138 30.769 0.0 0.0 0.00 2.29
1629 1642 8.729756 TGGAGTGAACTATTTTGTCATTGTATG 58.270 33.333 0.0 0.0 0.00 2.39
1929 1998 2.401583 TCCACCGAGGACATCAATTG 57.598 50.000 0.0 0.0 43.07 2.32
1962 2031 2.887152 GGATGGTTGCAAGAGACTTTGT 59.113 45.455 0.0 0.0 0.00 2.83
2106 2176 5.595952 AGTCTTGCAATGTTCCTCTTCTTTT 59.404 36.000 0.0 0.0 0.00 2.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
496 505 3.785325 TCCATTGAATCACCCTGACCATA 59.215 43.478 0.0 0.0 0.00 2.74
957 968 9.993454 TGTTCATCATTCAAAATATCACCAAAA 57.007 25.926 0.0 0.0 0.00 2.44
1575 1588 9.507280 CATACATAAAGCAAATAGTTCAAGTGG 57.493 33.333 0.0 0.0 0.00 4.00
1579 1592 9.853555 CCAACATACATAAAGCAAATAGTTCAA 57.146 29.630 0.0 0.0 0.00 2.69
1580 1593 9.237187 TCCAACATACATAAAGCAAATAGTTCA 57.763 29.630 0.0 0.0 0.00 3.18
1581 1594 9.722056 CTCCAACATACATAAAGCAAATAGTTC 57.278 33.333 0.0 0.0 0.00 3.01
1582 1595 9.243105 ACTCCAACATACATAAAGCAAATAGTT 57.757 29.630 0.0 0.0 0.00 2.24
1583 1596 8.677300 CACTCCAACATACATAAAGCAAATAGT 58.323 33.333 0.0 0.0 0.00 2.12
1584 1597 8.892723 TCACTCCAACATACATAAAGCAAATAG 58.107 33.333 0.0 0.0 0.00 1.73
1585 1598 8.800370 TCACTCCAACATACATAAAGCAAATA 57.200 30.769 0.0 0.0 0.00 1.40
1586 1599 7.701539 TCACTCCAACATACATAAAGCAAAT 57.298 32.000 0.0 0.0 0.00 2.32
1587 1600 7.230510 AGTTCACTCCAACATACATAAAGCAAA 59.769 33.333 0.0 0.0 0.00 3.68
1588 1601 6.714810 AGTTCACTCCAACATACATAAAGCAA 59.285 34.615 0.0 0.0 0.00 3.91
1589 1602 6.237901 AGTTCACTCCAACATACATAAAGCA 58.762 36.000 0.0 0.0 0.00 3.91
1590 1603 6.743575 AGTTCACTCCAACATACATAAAGC 57.256 37.500 0.0 0.0 0.00 3.51
1594 1607 9.733556 ACAAAATAGTTCACTCCAACATACATA 57.266 29.630 0.0 0.0 0.00 2.29
1595 1608 8.635765 ACAAAATAGTTCACTCCAACATACAT 57.364 30.769 0.0 0.0 0.00 2.29
1596 1609 7.717436 TGACAAAATAGTTCACTCCAACATACA 59.283 33.333 0.0 0.0 0.00 2.29
1597 1610 8.094798 TGACAAAATAGTTCACTCCAACATAC 57.905 34.615 0.0 0.0 0.00 2.39
1598 1611 8.862325 ATGACAAAATAGTTCACTCCAACATA 57.138 30.769 0.0 0.0 0.00 2.29
1599 1612 7.765695 ATGACAAAATAGTTCACTCCAACAT 57.234 32.000 0.0 0.0 0.00 2.71
1600 1613 7.068103 ACAATGACAAAATAGTTCACTCCAACA 59.932 33.333 0.0 0.0 0.00 3.33
1601 1614 7.425606 ACAATGACAAAATAGTTCACTCCAAC 58.574 34.615 0.0 0.0 0.00 3.77
1602 1615 7.581213 ACAATGACAAAATAGTTCACTCCAA 57.419 32.000 0.0 0.0 0.00 3.53
1603 1616 8.729756 CATACAATGACAAAATAGTTCACTCCA 58.270 33.333 0.0 0.0 0.00 3.86
1604 1617 7.698130 GCATACAATGACAAAATAGTTCACTCC 59.302 37.037 0.0 0.0 0.00 3.85
1605 1618 7.698130 GGCATACAATGACAAAATAGTTCACTC 59.302 37.037 0.0 0.0 38.49 3.51
1606 1619 7.538575 GGCATACAATGACAAAATAGTTCACT 58.461 34.615 0.0 0.0 38.49 3.41
1607 1620 7.740519 GGCATACAATGACAAAATAGTTCAC 57.259 36.000 0.0 0.0 38.49 3.18
1619 1632 6.683974 ATAGTTCAAGTGGCATACAATGAC 57.316 37.500 0.0 0.0 39.32 3.06
1620 1633 7.701539 AAATAGTTCAAGTGGCATACAATGA 57.298 32.000 0.0 0.0 0.00 2.57
1621 1634 8.246180 AGAAAATAGTTCAAGTGGCATACAATG 58.754 33.333 0.0 0.0 0.00 2.82
1622 1635 8.353423 AGAAAATAGTTCAAGTGGCATACAAT 57.647 30.769 0.0 0.0 0.00 2.71
1623 1636 7.759489 AGAAAATAGTTCAAGTGGCATACAA 57.241 32.000 0.0 0.0 0.00 2.41
1624 1637 7.759489 AAGAAAATAGTTCAAGTGGCATACA 57.241 32.000 0.0 0.0 0.00 2.29
1627 1640 9.247861 AGATAAAGAAAATAGTTCAAGTGGCAT 57.752 29.630 0.0 0.0 0.00 4.40
1628 1641 8.635765 AGATAAAGAAAATAGTTCAAGTGGCA 57.364 30.769 0.0 0.0 0.00 4.92
1787 1856 6.878389 TGTCACTATCAAACATCTGCATACAA 59.122 34.615 0.0 0.0 0.00 2.41
1929 1998 2.949644 GCAACCATCCCATACCACTTAC 59.050 50.000 0.0 0.0 0.00 2.34
1962 2031 0.842030 AGGCATTCACCTGGAGTCCA 60.842 55.000 12.4 12.4 39.13 4.02
2106 2176 4.531854 TCTGTTGGACTCATTTCCACAAA 58.468 39.130 0.0 0.0 45.80 2.83
2108 2178 3.855255 TCTGTTGGACTCATTTCCACA 57.145 42.857 0.0 0.0 45.80 4.17
2381 2451 5.422214 AGAACATTTTGAGTCGGTATCCT 57.578 39.130 0.0 0.0 0.00 3.24


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

AutoCloner maintained by Alex Coulton.