Multiple sequence alignment - TraesCS7B01G280800

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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 TraesCS7B01G280800 chr7B 100.000 2318 0 0 1 2318 513767548 513769865 0.000000e+00 4281.0
1 TraesCS7B01G280800 chr7B 90.816 98 5 3 1633 1727 222691674 222691770 6.720000e-26 128.0
2 TraesCS7B01G280800 chr7A 90.531 1901 103 31 443 2318 554487981 554489829 0.000000e+00 2442.0
3 TraesCS7B01G280800 chr7A 95.385 260 7 4 196 451 554487470 554487728 2.140000e-110 409.0
4 TraesCS7B01G280800 chr7A 92.086 139 11 0 17 155 554487339 554487477 1.820000e-46 196.0
5 TraesCS7B01G280800 chr7D 94.186 1376 51 11 17 1377 486104087 486105448 0.000000e+00 2071.0
6 TraesCS7B01G280800 chr7D 90.067 896 53 9 1429 2318 486105442 486106307 0.000000e+00 1129.0
7 TraesCS7B01G280800 chr3A 98.718 78 1 0 1659 1736 685288882 685288959 3.110000e-29 139.0
8 TraesCS7B01G280800 chr3D 95.349 86 4 0 1649 1734 548393315 548393400 1.120000e-28 137.0
9 TraesCS7B01G280800 chr6A 95.062 81 3 1 1660 1739 591741468 591741548 2.420000e-25 126.0
10 TraesCS7B01G280800 chr1D 95.000 80 4 0 1660 1739 68453806 68453727 2.420000e-25 126.0
11 TraesCS7B01G280800 chr1B 91.209 91 8 0 1637 1727 67450872 67450782 8.700000e-25 124.0
12 TraesCS7B01G280800 chr2D 85.849 106 13 2 1636 1739 107696231 107696126 6.770000e-21 111.0
13 TraesCS7B01G280800 chr6B 100.000 31 0 0 20 50 647931602 647931572 8.950000e-05 58.4


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 TraesCS7B01G280800 chr7B 513767548 513769865 2317 False 4281.000000 4281 100.000000 1 2318 1 chr7B.!!$F2 2317
1 TraesCS7B01G280800 chr7A 554487339 554489829 2490 False 1015.666667 2442 92.667333 17 2318 3 chr7A.!!$F1 2301
2 TraesCS7B01G280800 chr7D 486104087 486106307 2220 False 1600.000000 2071 92.126500 17 2318 2 chr7D.!!$F1 2301

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
693 961 1.129058 TTTTATCTCCCTCCCCGCTC 58.871 55.0 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1900 2196 0.249405 CTGTGCGCCATGTTGGTTTT 60.249 50.0 4.18 0.0 40.46 2.43 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
100 101 3.058224 CGGTGACTTGAGAAAATCCCAAC 60.058 47.826 0.00 0.00 0.00 3.77
178 179 5.887754 AGAAATGGAAAGTTAGGGTTGCTA 58.112 37.500 0.00 0.00 0.00 3.49
196 197 3.166434 CCAGTGGTGGGGCTACAA 58.834 61.111 0.00 0.00 40.67 2.41
470 736 4.860802 TCTACATTTGGATGACCCACAT 57.139 40.909 0.00 0.00 46.62 3.21
484 750 3.908213 ACCCACATAAATGTCGCAAAAC 58.092 40.909 0.00 0.00 39.39 2.43
557 823 6.380560 TGTCCATTTTGAATCTGCATGGATAA 59.619 34.615 3.39 0.00 44.11 1.75
622 890 3.498082 GCGGTAAAAATAGCTTGGTGTG 58.502 45.455 0.00 0.00 0.00 3.82
623 891 3.057806 GCGGTAAAAATAGCTTGGTGTGT 60.058 43.478 0.00 0.00 0.00 3.72
693 961 1.129058 TTTTATCTCCCTCCCCGCTC 58.871 55.000 0.00 0.00 0.00 5.03
840 1108 6.049263 ACGTCTTTCTTGTGTTCAGATTTC 57.951 37.500 0.00 0.00 0.00 2.17
895 1164 6.811253 AGACGATGGCAGTAATTTGTTAAA 57.189 33.333 0.00 0.00 0.00 1.52
942 1211 2.901192 TCACCGGTTCTTGGTTCTGATA 59.099 45.455 2.97 0.00 37.72 2.15
1029 1298 2.113433 CATGGAGGAGCAGCTGCAC 61.113 63.158 38.24 32.03 45.16 4.57
1033 1302 1.078637 GAGGAGCAGCTGCACATGA 60.079 57.895 38.24 0.00 45.16 3.07
1080 1349 1.841663 CGTTGAAGAAGCACCACCCG 61.842 60.000 0.00 0.00 0.00 5.28
1101 1370 4.415150 CTCCACATGGCCCACGCT 62.415 66.667 0.00 0.00 34.44 5.07
1301 1576 1.649664 CACGAGATGGGCAAGAAGAG 58.350 55.000 0.00 0.00 0.00 2.85
1308 1583 2.354343 GGCAAGAAGAGCAGCCCT 59.646 61.111 0.00 0.00 41.25 5.19
1385 1665 2.598099 TGGTGTGCAGTGCATGGG 60.598 61.111 22.87 0.00 41.91 4.00
1395 1675 2.181975 CAGTGCATGGGAAGGGAAAAT 58.818 47.619 0.00 0.00 0.00 1.82
1396 1676 3.364549 CAGTGCATGGGAAGGGAAAATA 58.635 45.455 0.00 0.00 0.00 1.40
1400 1682 5.488561 AGTGCATGGGAAGGGAAAATATTTT 59.511 36.000 13.24 13.24 0.00 1.82
1428 1710 5.046014 TCTCTCCTTCTTTTTGGATCCTCTG 60.046 44.000 14.23 0.00 0.00 3.35
1454 1736 1.067071 GTCGACGGGGAACTTCATCTT 60.067 52.381 0.00 0.00 0.00 2.40
1457 1739 2.347731 GACGGGGAACTTCATCTTGTC 58.652 52.381 0.00 0.00 0.00 3.18
1458 1740 1.697432 ACGGGGAACTTCATCTTGTCA 59.303 47.619 0.00 0.00 0.00 3.58
1476 1758 2.784380 GTCATCTGCAGTCGACGATTAC 59.216 50.000 14.67 4.98 0.00 1.89
1496 1778 4.847365 ACGAATGTTGATCGATTCTGTG 57.153 40.909 0.00 0.00 42.76 3.66
1514 1796 2.824041 CCTGATGGAAACCGGCCG 60.824 66.667 21.04 21.04 34.57 6.13
1554 1836 2.563620 TGTACATAACTGCCGGTTCAGA 59.436 45.455 15.11 0.00 39.17 3.27
1578 1860 2.305635 TGGGCAATTGCAGAGTTCTAGA 59.694 45.455 30.32 0.00 44.36 2.43
1579 1861 3.054139 TGGGCAATTGCAGAGTTCTAGAT 60.054 43.478 30.32 0.00 44.36 1.98
1580 1862 3.563390 GGGCAATTGCAGAGTTCTAGATC 59.437 47.826 30.32 9.10 44.36 2.75
1582 1864 4.637534 GGCAATTGCAGAGTTCTAGATCAA 59.362 41.667 30.32 0.00 44.36 2.57
1583 1865 5.124457 GGCAATTGCAGAGTTCTAGATCAAA 59.876 40.000 30.32 0.00 44.36 2.69
1585 1867 6.746364 GCAATTGCAGAGTTCTAGATCAAAAG 59.254 38.462 25.36 0.00 41.59 2.27
1586 1868 7.574592 GCAATTGCAGAGTTCTAGATCAAAAGT 60.575 37.037 25.36 0.00 41.59 2.66
1587 1869 7.992754 ATTGCAGAGTTCTAGATCAAAAGTT 57.007 32.000 3.70 0.00 0.00 2.66
1588 1870 7.807977 TTGCAGAGTTCTAGATCAAAAGTTT 57.192 32.000 3.70 0.00 0.00 2.66
1589 1871 7.807977 TGCAGAGTTCTAGATCAAAAGTTTT 57.192 32.000 3.70 0.00 0.00 2.43
1590 1872 7.865707 TGCAGAGTTCTAGATCAAAAGTTTTC 58.134 34.615 0.00 0.00 0.00 2.29
1591 1873 7.041098 TGCAGAGTTCTAGATCAAAAGTTTTCC 60.041 37.037 0.00 0.00 0.00 3.13
1592 1874 7.574030 GCAGAGTTCTAGATCAAAAGTTTTCCC 60.574 40.741 0.00 0.00 0.00 3.97
1593 1875 7.663493 CAGAGTTCTAGATCAAAAGTTTTCCCT 59.337 37.037 0.00 0.00 0.00 4.20
1594 1876 7.880713 AGAGTTCTAGATCAAAAGTTTTCCCTC 59.119 37.037 0.00 0.00 0.00 4.30
1595 1877 7.518188 AGTTCTAGATCAAAAGTTTTCCCTCA 58.482 34.615 0.00 0.00 0.00 3.86
1598 1880 8.760980 TCTAGATCAAAAGTTTTCCCTCAAAA 57.239 30.769 0.00 0.00 0.00 2.44
1736 2028 2.332063 ACTCGGCCATATCAACTTGG 57.668 50.000 2.24 0.00 36.03 3.61
1743 2036 3.508744 CCATATCAACTTGGTGGCAAC 57.491 47.619 0.00 0.00 0.00 4.17
1763 2056 2.170187 ACAATCCTCCTGCAGAGATCAC 59.830 50.000 17.39 0.00 46.50 3.06
1791 2084 6.049149 CGCTTTCTACCATCATCCTTCTTAA 58.951 40.000 0.00 0.00 0.00 1.85
1792 2085 6.018669 CGCTTTCTACCATCATCCTTCTTAAC 60.019 42.308 0.00 0.00 0.00 2.01
1800 2093 7.442656 ACCATCATCCTTCTTAACTAATACCG 58.557 38.462 0.00 0.00 0.00 4.02
1900 2196 7.573710 AGTATTGGGACTAAGCATCATGTAAA 58.426 34.615 0.00 0.00 0.00 2.01
1901 2197 8.052748 AGTATTGGGACTAAGCATCATGTAAAA 58.947 33.333 0.00 0.00 0.00 1.52
1942 2238 2.238898 ACCTGATAACTTGGCCACCTAC 59.761 50.000 3.88 0.00 0.00 3.18
1984 2280 3.186909 TGATGATAACGAGCGAAACAGG 58.813 45.455 0.00 0.00 0.00 4.00
2005 2301 3.307059 GGCAGAGGTGACACTCTACAAAT 60.307 47.826 5.39 0.00 45.71 2.32
2047 2343 1.665735 GGCAACCAACAACATGCTACG 60.666 52.381 0.00 0.00 38.79 3.51
2186 2491 5.687166 AATGTACTCGGGGTAGATGAAAA 57.313 39.130 0.00 0.00 35.07 2.29
2287 2592 0.881796 GTTTCCCAAAAGGCTCGGAG 59.118 55.000 0.00 0.00 34.51 4.63
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.934645 TGTATTTAGTGGAGTTCAAGTGAAGG 59.065 38.462 0.00 0.00 34.27 3.46
1 2 7.962964 TGTATTTAGTGGAGTTCAAGTGAAG 57.037 36.000 0.00 0.00 34.27 3.02
2 3 8.740123 TTTGTATTTAGTGGAGTTCAAGTGAA 57.260 30.769 0.00 0.00 0.00 3.18
3 4 8.918202 ATTTGTATTTAGTGGAGTTCAAGTGA 57.082 30.769 0.00 0.00 0.00 3.41
4 5 9.612620 GAATTTGTATTTAGTGGAGTTCAAGTG 57.387 33.333 0.00 0.00 0.00 3.16
5 6 9.574516 AGAATTTGTATTTAGTGGAGTTCAAGT 57.425 29.630 0.00 0.00 0.00 3.16
6 7 9.831737 CAGAATTTGTATTTAGTGGAGTTCAAG 57.168 33.333 0.00 0.00 0.00 3.02
7 8 8.296713 GCAGAATTTGTATTTAGTGGAGTTCAA 58.703 33.333 0.00 0.00 0.00 2.69
8 9 7.665559 AGCAGAATTTGTATTTAGTGGAGTTCA 59.334 33.333 0.00 0.00 0.00 3.18
9 10 8.045176 AGCAGAATTTGTATTTAGTGGAGTTC 57.955 34.615 0.00 0.00 0.00 3.01
10 11 7.665559 TGAGCAGAATTTGTATTTAGTGGAGTT 59.334 33.333 0.00 0.00 0.00 3.01
11 12 7.168219 TGAGCAGAATTTGTATTTAGTGGAGT 58.832 34.615 0.00 0.00 0.00 3.85
12 13 7.615582 TGAGCAGAATTTGTATTTAGTGGAG 57.384 36.000 0.00 0.00 0.00 3.86
13 14 7.994425 TTGAGCAGAATTTGTATTTAGTGGA 57.006 32.000 0.00 0.00 0.00 4.02
14 15 8.081633 TGTTTGAGCAGAATTTGTATTTAGTGG 58.918 33.333 0.00 0.00 0.00 4.00
15 16 9.121517 CTGTTTGAGCAGAATTTGTATTTAGTG 57.878 33.333 0.00 0.00 38.70 2.74
58 59 1.476488 GCCGGTTTCCAACAATATGCT 59.524 47.619 1.90 0.00 0.00 3.79
59 60 1.797348 CGCCGGTTTCCAACAATATGC 60.797 52.381 1.90 0.00 0.00 3.14
70 71 1.566018 CTCAAGTCACCGCCGGTTTC 61.566 60.000 5.76 2.14 31.02 2.78
100 101 2.642139 AATTGCTCAAATGCGTCCTG 57.358 45.000 0.00 0.00 35.36 3.86
178 179 1.772567 TTGTAGCCCCACCACTGGT 60.773 57.895 0.00 0.00 35.46 4.00
191 192 4.601084 TCTCCCTCTGAAGGTAGTTGTAG 58.399 47.826 0.00 0.00 41.59 2.74
192 193 4.669866 TCTCCCTCTGAAGGTAGTTGTA 57.330 45.455 0.00 0.00 41.59 2.41
193 194 3.544698 TCTCCCTCTGAAGGTAGTTGT 57.455 47.619 0.00 0.00 41.59 3.32
194 195 4.528596 TCTTTCTCCCTCTGAAGGTAGTTG 59.471 45.833 0.00 0.00 41.59 3.16
195 196 4.753186 TCTTTCTCCCTCTGAAGGTAGTT 58.247 43.478 0.00 0.00 41.59 2.24
196 197 4.405756 TCTTTCTCCCTCTGAAGGTAGT 57.594 45.455 0.00 0.00 41.59 2.73
217 218 3.896888 TGAAACTGATTGCCTTTCCACAT 59.103 39.130 0.00 0.00 0.00 3.21
386 391 7.913789 TGGTACATTCTACCTAATTGTTCTGT 58.086 34.615 0.00 0.00 38.39 3.41
470 736 6.621316 TTTAGAGTGGTTTTGCGACATTTA 57.379 33.333 0.00 0.00 0.00 1.40
484 750 5.437191 AGGGGACACTATTTTTAGAGTGG 57.563 43.478 6.94 0.00 46.05 4.00
575 843 1.355796 CGAATTCGTTGGCGCCACTA 61.356 55.000 32.95 14.07 38.14 2.74
693 961 3.660501 TGTAGTGGTGAGCAGTAACAG 57.339 47.619 0.11 0.00 0.00 3.16
745 1013 4.009675 TGTGCAGTAAATTGTGGATCCTC 58.990 43.478 14.23 10.39 0.00 3.71
840 1108 1.635487 TCTCATCCAAACCCTCCCAAG 59.365 52.381 0.00 0.00 0.00 3.61
918 1187 2.290641 CAGAACCAAGAACCGGTGAAAG 59.709 50.000 8.52 0.00 36.67 2.62
942 1211 4.128643 TCTACCATTCCAACGAACGTTTT 58.871 39.130 9.87 0.00 36.00 2.43
1080 1349 1.678970 GTGGGCCATGTGGAGGTTC 60.679 63.158 10.70 0.00 37.39 3.62
1400 1682 7.069344 AGGATCCAAAAAGAAGGAGAGAAAAA 58.931 34.615 15.82 0.00 37.34 1.94
1428 1710 2.662527 TTCCCCGTCGACGCAAAC 60.663 61.111 31.73 0.00 38.18 2.93
1454 1736 0.811281 ATCGTCGACTGCAGATGACA 59.189 50.000 29.00 20.82 36.59 3.58
1457 1739 1.775770 CGTAATCGTCGACTGCAGATG 59.224 52.381 23.35 12.25 0.00 2.90
1458 1740 1.669265 TCGTAATCGTCGACTGCAGAT 59.331 47.619 23.35 4.35 38.33 2.90
1476 1758 3.544834 GGCACAGAATCGATCAACATTCG 60.545 47.826 0.00 0.00 34.68 3.34
1496 1778 3.140814 GGCCGGTTTCCATCAGGC 61.141 66.667 1.90 0.00 43.41 4.85
1554 1836 2.901839 AGAACTCTGCAATTGCCCATTT 59.098 40.909 26.94 14.87 41.18 2.32
1651 1943 3.243401 GGTTCAAATCCCACTGTCAACAC 60.243 47.826 0.00 0.00 0.00 3.32
1736 2028 0.895100 TGCAGGAGGATTGTTGCCAC 60.895 55.000 0.00 0.00 35.75 5.01
1743 2036 2.802415 CGTGATCTCTGCAGGAGGATTG 60.802 54.545 15.13 6.36 42.10 2.67
1763 2056 2.540101 GGATGATGGTAGAAAGCGTTCG 59.460 50.000 6.74 0.00 38.90 3.95
1791 2084 9.836076 GAAAATGTTTTAGAAAGCGGTATTAGT 57.164 29.630 0.00 0.00 0.00 2.24
1800 2093 8.634475 ACAGTTCAGAAAATGTTTTAGAAAGC 57.366 30.769 6.98 0.00 40.58 3.51
1865 2159 8.319146 TGCTTAGTCCCAATACTATAATTAGCC 58.681 37.037 0.00 0.00 33.10 3.93
1866 2160 9.892130 ATGCTTAGTCCCAATACTATAATTAGC 57.108 33.333 0.00 0.00 33.99 3.09
1870 2164 9.896645 CATGATGCTTAGTCCCAATACTATAAT 57.103 33.333 0.00 0.00 32.16 1.28
1871 2165 8.880244 ACATGATGCTTAGTCCCAATACTATAA 58.120 33.333 0.00 0.00 32.16 0.98
1900 2196 0.249405 CTGTGCGCCATGTTGGTTTT 60.249 50.000 4.18 0.00 40.46 2.43
1901 2197 1.363443 CTGTGCGCCATGTTGGTTT 59.637 52.632 4.18 0.00 40.46 3.27
1942 2238 2.431419 AGATGATCAGACTGCACAGAGG 59.569 50.000 4.31 0.00 0.00 3.69
1984 2280 3.386768 TTTGTAGAGTGTCACCTCTGC 57.613 47.619 12.51 11.78 41.81 4.26
2005 2301 4.005650 CACTTTCTTTGCTATGCTCTGGA 58.994 43.478 0.00 0.00 0.00 3.86
2047 2343 3.070159 TCTGAATATAGTGTGCCTGCTCC 59.930 47.826 0.00 0.00 0.00 4.70
2114 2410 5.450818 TTATCCTGTTGCCTAAAGACCAT 57.549 39.130 0.00 0.00 0.00 3.55
2173 2472 8.062065 TGTATGTTTCAATTTTCATCTACCCC 57.938 34.615 0.00 0.00 0.00 4.95
2174 2473 9.520204 CATGTATGTTTCAATTTTCATCTACCC 57.480 33.333 0.00 0.00 0.00 3.69
2186 2491 9.135189 ACCATTAGCATACATGTATGTTTCAAT 57.865 29.630 34.92 26.02 43.57 2.57
2287 2592 5.596268 TCGCTATATGTTCACATGATTGC 57.404 39.130 0.00 4.84 37.15 3.56


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

AutoCloner maintained by Alex Coulton.