Multiple sequence alignment - TraesCS1A01G017300

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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 TraesCS1A01G017300 chr1A 100.000 2783 0 0 1 2783 9155359 9158141 0.000000e+00 5140.0
1 TraesCS1A01G017300 chr1A 97.603 1961 43 2 804 2761 9194294 9196253 0.000000e+00 3358.0
2 TraesCS1A01G017300 chr1A 86.335 161 18 4 1 157 9131232 9131392 3.690000e-39 172.0
3 TraesCS1A01G017300 chr1A 100.000 37 0 0 2747 2783 9196367 9196403 4.970000e-08 69.4
4 TraesCS1A01G017300 chr1D 94.170 2796 114 27 1 2783 7693116 7695875 0.000000e+00 4215.0
5 TraesCS1A01G017300 chr1D 91.886 1972 139 12 1 1966 7040599 7038643 0.000000e+00 2736.0
6 TraesCS1A01G017300 chr1D 85.812 1022 70 39 289 1259 7744311 7745308 0.000000e+00 1014.0
7 TraesCS1A01G017300 chr1D 82.587 982 153 10 991 1963 7707013 7707985 0.000000e+00 850.0
8 TraesCS1A01G017300 chr1D 93.464 153 6 4 10 158 7411422 7411270 1.000000e-54 224.0
9 TraesCS1A01G017300 chrUn 95.606 2367 79 14 432 2783 276780873 276778517 0.000000e+00 3771.0
10 TraesCS1A01G017300 chrUn 97.984 1885 34 2 902 2783 278893720 278891837 0.000000e+00 3267.0
11 TraesCS1A01G017300 chrUn 89.046 283 24 6 517 793 76770494 76770775 7.380000e-91 344.0
12 TraesCS1A01G017300 chr1B 91.998 1962 142 9 10 1966 9716717 9714766 0.000000e+00 2739.0
13 TraesCS1A01G017300 chr1B 90.511 822 73 3 1149 1966 9673023 9672203 0.000000e+00 1081.0
14 TraesCS1A01G017300 chr1B 85.884 758 98 5 995 1745 9845459 9846214 0.000000e+00 798.0
15 TraesCS1A01G017300 chr1B 86.600 597 73 6 167 760 9673618 9673026 0.000000e+00 652.0
16 TraesCS1A01G017300 chr1B 88.571 140 11 4 23 159 9673805 9673668 6.170000e-37 165.0
17 TraesCS1A01G017300 chr2B 91.613 155 11 2 2218 2370 523078491 523078337 2.170000e-51 213.0
18 TraesCS1A01G017300 chr3B 92.254 142 11 0 2218 2359 17036589 17036730 4.700000e-48 202.0
19 TraesCS1A01G017300 chr6B 91.156 147 11 2 2220 2366 706025228 706025372 6.080000e-47 198.0
20 TraesCS1A01G017300 chr6B 90.604 149 12 2 2218 2366 706024434 706024580 2.190000e-46 196.0
21 TraesCS1A01G017300 chr5D 90.132 152 12 2 2218 2369 545672277 545672425 7.860000e-46 195.0


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 TraesCS1A01G017300 chr1A 9155359 9158141 2782 False 5140.000000 5140 100.000000 1 2783 1 chr1A.!!$F2 2782
1 TraesCS1A01G017300 chr1A 9194294 9196403 2109 False 1713.700000 3358 98.801500 804 2783 2 chr1A.!!$F3 1979
2 TraesCS1A01G017300 chr1D 7693116 7695875 2759 False 4215.000000 4215 94.170000 1 2783 1 chr1D.!!$F1 2782
3 TraesCS1A01G017300 chr1D 7038643 7040599 1956 True 2736.000000 2736 91.886000 1 1966 1 chr1D.!!$R1 1965
4 TraesCS1A01G017300 chr1D 7744311 7745308 997 False 1014.000000 1014 85.812000 289 1259 1 chr1D.!!$F3 970
5 TraesCS1A01G017300 chr1D 7707013 7707985 972 False 850.000000 850 82.587000 991 1963 1 chr1D.!!$F2 972
6 TraesCS1A01G017300 chrUn 276778517 276780873 2356 True 3771.000000 3771 95.606000 432 2783 1 chrUn.!!$R1 2351
7 TraesCS1A01G017300 chrUn 278891837 278893720 1883 True 3267.000000 3267 97.984000 902 2783 1 chrUn.!!$R2 1881
8 TraesCS1A01G017300 chr1B 9714766 9716717 1951 True 2739.000000 2739 91.998000 10 1966 1 chr1B.!!$R1 1956
9 TraesCS1A01G017300 chr1B 9845459 9846214 755 False 798.000000 798 85.884000 995 1745 1 chr1B.!!$F1 750
10 TraesCS1A01G017300 chr1B 9672203 9673805 1602 True 632.666667 1081 88.560667 23 1966 3 chr1B.!!$R2 1943

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
736 824 0.778815 CACTGAAGTCTTCGTCGTGC 59.221 55.0 8.06 0.0 0.0 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2033 2154 2.026822 AGTTGGGGCACTAAGAGTCATG 60.027 50.0 0.0 0.0 0.0 3.07 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
38 39 3.324556 TGTGAGTTGTGATGGAGTGATGA 59.675 43.478 0.00 0.00 0.00 2.92
90 95 6.156083 TGAATGTATGGACTGTGGTTGATAGA 59.844 38.462 0.00 0.00 0.00 1.98
128 134 1.376553 GCTTGACTCCCCTGCTGTC 60.377 63.158 0.00 0.00 0.00 3.51
356 406 5.110940 ACATGGCATGAAAAATTGTTTGC 57.889 34.783 32.74 0.00 0.00 3.68
415 471 5.912149 ATTGCAAGTATCTGGGAAGGATA 57.088 39.130 4.94 0.00 0.00 2.59
420 476 5.605534 CAAGTATCTGGGAAGGATACACTG 58.394 45.833 13.81 8.28 44.51 3.66
500 558 1.746787 TGTCATGGATGCATGCTTGAC 59.253 47.619 38.10 38.10 46.30 3.18
584 665 1.753930 TAACGATGACTGACCGGCTA 58.246 50.000 0.00 0.00 0.00 3.93
630 718 4.595781 TCTGTTTACTTCCCAGCCTTCTTA 59.404 41.667 0.00 0.00 0.00 2.10
635 723 2.507471 ACTTCCCAGCCTTCTTATCCAG 59.493 50.000 0.00 0.00 0.00 3.86
664 752 5.470368 TGACTAATGTCTCGAGAAACTTGG 58.530 41.667 18.55 14.34 43.29 3.61
693 781 5.699097 AGTTAACTAATCCGCAAGCAAAA 57.301 34.783 6.26 0.00 0.00 2.44
694 782 6.267496 AGTTAACTAATCCGCAAGCAAAAT 57.733 33.333 6.26 0.00 0.00 1.82
710 798 7.384932 GCAAGCAAAATACCTTGACTAATGTTT 59.615 33.333 4.70 0.00 40.59 2.83
711 799 9.260002 CAAGCAAAATACCTTGACTAATGTTTT 57.740 29.630 0.00 0.00 40.59 2.43
727 815 7.934120 ACTAATGTTTTCTAAGCACTGAAGTCT 59.066 33.333 0.00 0.00 0.00 3.24
729 817 6.604735 TGTTTTCTAAGCACTGAAGTCTTC 57.395 37.500 5.58 5.58 0.00 2.87
731 819 4.585955 TTCTAAGCACTGAAGTCTTCGT 57.414 40.909 8.06 6.24 0.00 3.85
736 824 0.778815 CACTGAAGTCTTCGTCGTGC 59.221 55.000 8.06 0.00 0.00 5.34
1041 1152 2.676608 CTGCTGGGTACATGGGCA 59.323 61.111 0.00 0.00 0.00 5.36
1104 1215 2.622436 GGCTTGAGCTATGAGAACGTT 58.378 47.619 0.00 0.00 41.70 3.99
1151 1262 3.394836 GCTCCTCGCCTCCAACCT 61.395 66.667 0.00 0.00 0.00 3.50
2027 2148 4.391216 CGAGAGCACATCAATCTTTGTTCT 59.609 41.667 0.00 0.00 32.84 3.01
2033 2154 6.094603 AGCACATCAATCTTTGTTCTATGGAC 59.905 38.462 0.00 0.00 0.00 4.02
2254 2377 6.218108 ACGTGTTAGTTAGGAATTAGGAGG 57.782 41.667 0.00 0.00 0.00 4.30
2395 2518 8.830915 TTCCAGCCATCCTACAATTTTTATAA 57.169 30.769 0.00 0.00 0.00 0.98
2492 2615 9.241317 CAAAATTAAGCATTAGATTAGCACCTG 57.759 33.333 0.00 0.00 0.00 4.00
2574 2697 2.406130 GTCACAATTTACCCGTGACGA 58.594 47.619 6.54 0.00 46.99 4.20
2599 2722 5.798125 TGGCAAACCATATTTCACTTTCA 57.202 34.783 0.00 0.00 42.67 2.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 0.472352 AACTCACAAGGGTACGGGGA 60.472 55.000 0.00 0.00 0.00 4.81
8 9 2.519377 TCACAACTCACAAGGGTACG 57.481 50.000 0.00 0.00 0.00 3.67
38 39 7.327975 TCTGTACAATGTTTCGACAAGGATAT 58.672 34.615 0.00 0.00 0.00 1.63
90 95 9.110502 GTCAAGCACCTAATTAATTAGTTAGCT 57.889 33.333 26.18 25.62 39.38 3.32
128 134 8.092521 AGTGCAGAGGATAAATAAATCAATCG 57.907 34.615 0.00 0.00 0.00 3.34
189 237 6.317789 TCTCAAAATATTTGATGCGATCCC 57.682 37.500 0.39 0.00 0.00 3.85
304 353 9.601217 GATATATACTGTTAATGTGGATGGGAC 57.399 37.037 0.00 0.00 0.00 4.46
345 394 7.076983 CACAAAGACAAACAGCAAACAATTTT 58.923 30.769 0.00 0.00 0.00 1.82
356 406 3.067180 AGGACATGCACAAAGACAAACAG 59.933 43.478 0.00 0.00 0.00 3.16
415 471 5.683876 AATACTTATGCTCCAGTCAGTGT 57.316 39.130 0.00 0.00 0.00 3.55
420 476 9.209175 CAAATACCTAATACTTATGCTCCAGTC 57.791 37.037 0.00 0.00 0.00 3.51
584 665 0.980231 GCAGAGTCCTGGACATCCCT 60.980 60.000 27.48 15.43 40.72 4.20
664 752 5.229921 TGCGGATTAGTTAACTTTCATGC 57.770 39.130 14.49 16.89 0.00 4.06
693 781 8.947115 GTGCTTAGAAAACATTAGTCAAGGTAT 58.053 33.333 0.00 0.00 0.00 2.73
694 782 8.154856 AGTGCTTAGAAAACATTAGTCAAGGTA 58.845 33.333 0.00 0.00 0.00 3.08
710 798 4.547532 GACGAAGACTTCAGTGCTTAGAA 58.452 43.478 15.36 0.00 0.00 2.10
711 799 3.365064 CGACGAAGACTTCAGTGCTTAGA 60.365 47.826 15.36 0.00 0.00 2.10
727 815 2.159824 TGTTTTGAAACAGCACGACGAA 59.840 40.909 0.00 0.00 43.45 3.85
729 817 2.166741 TGTTTTGAAACAGCACGACG 57.833 45.000 5.25 0.00 43.45 5.12
793 884 6.204359 GGACATTGAATATACTTGCTGCTTG 58.796 40.000 0.00 0.00 0.00 4.01
829 938 6.701400 GTCAAGGACACTTATTTTGCACAATT 59.299 34.615 2.94 0.00 34.49 2.32
1041 1152 2.854076 CTGGAAACCCAGGGGCTT 59.146 61.111 11.37 2.05 45.86 4.35
1104 1215 1.112916 TGTTGTCGAGGTCCTGCTCA 61.113 55.000 0.00 0.00 0.00 4.26
1254 1365 1.072505 GTCAACGGGCAGGAAGGAA 59.927 57.895 0.00 0.00 0.00 3.36
1334 1445 7.540400 TGTGAAATCAACAACACAAAACACTAG 59.460 33.333 0.00 0.00 39.70 2.57
2027 2148 3.388024 GGGCACTAAGAGTCATGTCCATA 59.612 47.826 0.00 0.00 36.80 2.74
2033 2154 2.026822 AGTTGGGGCACTAAGAGTCATG 60.027 50.000 0.00 0.00 0.00 3.07
2395 2518 3.173965 TCTAAAACAGCCCACTAGAGCT 58.826 45.455 0.00 0.00 40.89 4.09
2492 2615 5.371115 TTGGGAAAAAGTCGTGATCATTC 57.629 39.130 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.