Multiple sequence alignment - TraesCS7D01G090400

Loading Multiple Alignment...

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 TraesCS7D01G090400 chr7D 100.000 2384 0 0 1 2384 54321062 54318679 0.000000e+00 4403.0
1 TraesCS7D01G090400 chr7D 95.033 1792 71 6 598 2384 54337375 54335597 0.000000e+00 2800.0
2 TraesCS7D01G090400 chr7D 90.937 1942 120 18 89 1999 54355044 54353128 0.000000e+00 2560.0
3 TraesCS7D01G090400 chr7D 89.504 1372 99 16 99 1446 54312176 54310826 0.000000e+00 1694.0
4 TraesCS7D01G090400 chr7D 85.052 388 35 12 1656 2028 54310813 54310434 8.050000e-100 374.0
5 TraesCS7D01G090400 chr7D 100.000 108 0 0 1 108 54357047 54356940 1.450000e-47 200.0
6 TraesCS7D01G090400 chr7D 94.898 98 5 0 2197 2294 54310230 54310133 1.140000e-33 154.0
7 TraesCS7D01G090400 chr7A 87.705 2253 167 36 90 2273 57804293 57802082 0.000000e+00 2525.0
8 TraesCS7D01G090400 chr7A 94.891 1096 49 4 355 1446 57865407 57864315 0.000000e+00 1707.0
9 TraesCS7D01G090400 chr7A 93.254 756 36 7 1636 2384 57864138 57863391 0.000000e+00 1099.0
10 TraesCS7D01G090400 chr7A 100.000 32 0 0 287 318 57865510 57865479 2.560000e-05 60.2
11 TraesCS7D01G090400 chr4A 92.100 924 64 2 599 1514 669899039 669898117 0.000000e+00 1293.0
12 TraesCS7D01G090400 chr4A 85.976 763 47 24 1651 2384 669892287 669891556 0.000000e+00 761.0
13 TraesCS7D01G090400 chr4A 84.241 514 48 11 78 560 669899559 669899048 9.980000e-129 470.0
14 TraesCS7D01G090400 chr4A 85.373 335 39 8 1636 1965 669898025 669897696 2.940000e-89 339.0
15 TraesCS7D01G090400 chrUn 92.677 874 59 3 574 1446 49140767 49139898 0.000000e+00 1254.0
16 TraesCS7D01G090400 chrUn 92.449 874 61 3 574 1446 49113928 49113059 0.000000e+00 1243.0
17 TraesCS7D01G090400 chrUn 92.449 874 61 3 571 1443 384623891 384624760 0.000000e+00 1243.0
18 TraesCS7D01G090400 chrUn 85.976 763 47 28 1651 2384 49113033 49112302 0.000000e+00 761.0
19 TraesCS7D01G090400 chrUn 85.976 763 47 28 1651 2384 49139872 49139141 0.000000e+00 761.0
20 TraesCS7D01G090400 chrUn 85.386 479 29 19 1916 2384 329826064 329825617 2.160000e-125 459.0
21 TraesCS7D01G090400 chrUn 85.386 479 29 19 1916 2384 329829075 329829522 2.160000e-125 459.0
22 TraesCS7D01G090400 chrUn 84.749 459 35 19 1645 2082 384624783 384625227 6.090000e-116 427.0
23 TraesCS7D01G090400 chr7B 91.534 189 16 0 1448 1636 13895332 13895144 6.540000e-66 261.0
24 TraesCS7D01G090400 chr7B 90.476 189 18 0 1448 1636 354396447 354396259 1.410000e-62 250.0
25 TraesCS7D01G090400 chr5A 90.476 189 18 0 1448 1636 432109086 432109274 1.410000e-62 250.0
26 TraesCS7D01G090400 chr5A 90.476 189 18 0 1448 1636 535742003 535742191 1.410000e-62 250.0
27 TraesCS7D01G090400 chr3B 89.340 197 20 1 1440 1636 61788679 61788484 1.830000e-61 246.0
28 TraesCS7D01G090400 chr6B 87.204 211 25 1 1426 1636 42648544 42648752 3.060000e-59 239.0
29 TraesCS7D01G090400 chr1D 92.857 56 3 1 112 167 402837773 402837827 1.960000e-11 80.5


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 TraesCS7D01G090400 chr7D 54318679 54321062 2383 True 4403.000000 4403 100.000000 1 2384 1 chr7D.!!$R1 2383
1 TraesCS7D01G090400 chr7D 54335597 54337375 1778 True 2800.000000 2800 95.033000 598 2384 1 chr7D.!!$R2 1786
2 TraesCS7D01G090400 chr7D 54353128 54357047 3919 True 1380.000000 2560 95.468500 1 1999 2 chr7D.!!$R4 1998
3 TraesCS7D01G090400 chr7D 54310133 54312176 2043 True 740.666667 1694 89.818000 99 2294 3 chr7D.!!$R3 2195
4 TraesCS7D01G090400 chr7A 57802082 57804293 2211 True 2525.000000 2525 87.705000 90 2273 1 chr7A.!!$R1 2183
5 TraesCS7D01G090400 chr7A 57863391 57865510 2119 True 955.400000 1707 96.048333 287 2384 3 chr7A.!!$R2 2097
6 TraesCS7D01G090400 chr4A 669891556 669892287 731 True 761.000000 761 85.976000 1651 2384 1 chr4A.!!$R1 733
7 TraesCS7D01G090400 chr4A 669897696 669899559 1863 True 700.666667 1293 87.238000 78 1965 3 chr4A.!!$R2 1887
8 TraesCS7D01G090400 chrUn 49139141 49140767 1626 True 1007.500000 1254 89.326500 574 2384 2 chrUn.!!$R3 1810
9 TraesCS7D01G090400 chrUn 49112302 49113928 1626 True 1002.000000 1243 89.212500 574 2384 2 chrUn.!!$R2 1810
10 TraesCS7D01G090400 chrUn 384623891 384625227 1336 False 835.000000 1243 88.599000 571 2082 2 chrUn.!!$F2 1511

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
547 2533 0.731417 CGCTTCCAGGATGAAAGCAG 59.269 55.0 10.84 1.31 39.69 4.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2003 4108 0.102481 GGTCTTCGAATGCTCGCCTA 59.898 55.0 0.0 0.0 45.04 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
463 2416 3.725010 CGTTGGCGAGAATTGAACTAAGC 60.725 47.826 0.00 0.00 41.33 3.09
506 2463 5.883661 ACAATGATGGATGCTAAAAGAACG 58.116 37.500 0.00 0.00 0.00 3.95
507 2464 4.558538 ATGATGGATGCTAAAAGAACGC 57.441 40.909 0.00 0.00 0.00 4.84
514 2491 4.155280 GGATGCTAAAAGAACGCCAAACTA 59.845 41.667 0.00 0.00 0.00 2.24
529 2508 3.795101 CCAAACTATACAGCGGTAACTCG 59.205 47.826 0.00 0.00 32.19 4.18
547 2533 0.731417 CGCTTCCAGGATGAAAGCAG 59.269 55.000 10.84 1.31 39.69 4.24
588 2577 4.088762 CACCACGCATGCACGTCC 62.089 66.667 19.57 0.00 46.34 4.79
603 2592 2.202743 TCCTAGACGCGCATGCAC 60.203 61.111 19.57 7.15 42.97 4.57
883 2875 2.567497 ATCACCGTCGGGTCGTTGT 61.567 57.895 17.28 0.00 46.01 3.32
888 2880 4.353437 GTCGGGTCGTTGTCGCCT 62.353 66.667 0.00 0.00 36.96 5.52
1062 3054 1.172812 GGCCCTTGACGACAAAGCTT 61.173 55.000 17.20 0.00 36.35 3.74
1074 3066 1.134220 ACAAAGCTTTCCACGAGGTCA 60.134 47.619 9.23 0.00 35.89 4.02
1077 3069 1.629043 AGCTTTCCACGAGGTCACTA 58.371 50.000 0.00 0.00 35.89 2.74
1287 3279 1.066422 GATGGCGTCGATCAGCTCA 59.934 57.895 0.00 7.10 0.00 4.26
1592 3604 3.733024 CTCGATGATCCTACGAGTAGC 57.267 52.381 18.44 0.00 45.23 3.58
2002 4107 3.772025 AGGAAGCTGCTTATATAGGCGAT 59.228 43.478 15.95 3.53 0.00 4.58
2003 4108 4.223923 AGGAAGCTGCTTATATAGGCGATT 59.776 41.667 15.95 10.92 0.00 3.34
2004 4109 5.422331 AGGAAGCTGCTTATATAGGCGATTA 59.578 40.000 15.95 0.00 0.00 1.75
2005 4110 5.751028 GGAAGCTGCTTATATAGGCGATTAG 59.249 44.000 15.95 5.21 0.00 1.73
2006 4111 5.269505 AGCTGCTTATATAGGCGATTAGG 57.730 43.478 11.75 0.55 0.00 2.69
2152 4301 2.597510 GACAACCCAGTGGCACCC 60.598 66.667 15.27 0.00 33.59 4.61
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
506 2463 3.528532 AGTTACCGCTGTATAGTTTGGC 58.471 45.455 0.00 0.00 0.00 4.52
507 2464 3.795101 CGAGTTACCGCTGTATAGTTTGG 59.205 47.826 0.00 0.00 0.00 3.28
529 2508 1.742268 GTCTGCTTTCATCCTGGAAGC 59.258 52.381 12.29 12.29 0.00 3.86
530 2509 3.063510 TGTCTGCTTTCATCCTGGAAG 57.936 47.619 0.00 0.00 0.00 3.46
531 2510 3.507162 TTGTCTGCTTTCATCCTGGAA 57.493 42.857 0.00 0.00 0.00 3.53
532 2511 3.349927 CATTGTCTGCTTTCATCCTGGA 58.650 45.455 0.00 0.00 0.00 3.86
533 2512 2.426024 CCATTGTCTGCTTTCATCCTGG 59.574 50.000 0.00 0.00 0.00 4.45
534 2513 3.349927 TCCATTGTCTGCTTTCATCCTG 58.650 45.455 0.00 0.00 0.00 3.86
535 2514 3.265221 TCTCCATTGTCTGCTTTCATCCT 59.735 43.478 0.00 0.00 0.00 3.24
547 2533 3.390639 AGGATCACTCCATCTCCATTGTC 59.609 47.826 0.00 0.00 44.79 3.18
576 2562 3.693245 GTCTAGGACGTGCATGCG 58.307 61.111 14.09 1.59 37.94 4.73
588 2577 3.001067 CAGTGCATGCGCGTCTAG 58.999 61.111 24.54 10.34 42.97 2.43
603 2592 5.004821 CGCAATCAACTACTACTAAGTGCAG 59.995 44.000 0.00 0.00 36.36 4.41
1062 3054 2.005370 ACCTTAGTGACCTCGTGGAA 57.995 50.000 11.17 0.00 37.04 3.53
1074 3066 1.373812 GCCCACGTCCAACCTTAGT 59.626 57.895 0.00 0.00 0.00 2.24
1077 3069 4.636435 CCGCCCACGTCCAACCTT 62.636 66.667 0.00 0.00 37.70 3.50
1287 3279 3.782443 CCCTCCCTACGCGGCTTT 61.782 66.667 12.47 0.00 0.00 3.51
1396 3391 9.868277 TTTATAGTTGATTGATTTTGCCGAATT 57.132 25.926 0.00 0.00 0.00 2.17
1592 3604 8.810427 TTAACTAGTTAACTTGCCGATTAATCG 58.190 33.333 27.19 27.19 38.66 3.34
1703 3764 1.003476 CCCAAAACCCTGGCAATGC 60.003 57.895 0.00 0.00 34.88 3.56
1965 4059 2.808567 GCTTCCTGCTGGAACTATAGCC 60.809 54.545 20.15 4.46 46.57 3.93
2002 4107 1.470979 GGTCTTCGAATGCTCGCCTAA 60.471 52.381 0.00 0.00 45.04 2.69
2003 4108 0.102481 GGTCTTCGAATGCTCGCCTA 59.898 55.000 0.00 0.00 45.04 3.93
2004 4109 1.153549 GGTCTTCGAATGCTCGCCT 60.154 57.895 0.00 0.00 45.04 5.52
2005 4110 0.102481 TAGGTCTTCGAATGCTCGCC 59.898 55.000 0.00 0.00 45.04 5.54
2006 4111 1.482278 CTAGGTCTTCGAATGCTCGC 58.518 55.000 0.00 0.00 45.04 5.03
2007 4112 1.482278 GCTAGGTCTTCGAATGCTCG 58.518 55.000 0.00 0.00 46.87 5.03
2008 4113 1.137086 TGGCTAGGTCTTCGAATGCTC 59.863 52.381 0.00 0.00 0.00 4.26
2009 4114 1.137872 CTGGCTAGGTCTTCGAATGCT 59.862 52.381 0.00 0.00 0.00 3.79
2050 4194 1.726853 ACGAAGCAAGAAAGATCGGG 58.273 50.000 0.00 0.00 37.81 5.14
2152 4301 1.608590 ACGCCCTGTGAGATTGTTTTG 59.391 47.619 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.