Multiple sequence alignment - TraesCS1B01G043700

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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 TraesCS1B01G043700 chr1B 100.000 2708 0 0 1 2708 23816295 23819002 0.000000e+00 5001.0
1 TraesCS1B01G043700 chr1B 94.959 1845 69 2 1 1844 48530101 48531922 0.000000e+00 2870.0
2 TraesCS1B01G043700 chr1B 94.286 735 29 6 1986 2708 666991387 666990654 0.000000e+00 1112.0
3 TraesCS1B01G043700 chr1B 95.098 102 3 1 1845 1944 388032449 388032550 2.790000e-35 159.0
4 TraesCS1B01G043700 chr1B 95.000 100 5 0 1845 1944 48532430 48532529 1.000000e-34 158.0
5 TraesCS1B01G043700 chr5B 98.080 2708 48 3 1 2708 701465276 701467979 0.000000e+00 4710.0
6 TraesCS1B01G043700 chr7A 97.769 1793 40 0 1 1793 206573907 206575699 0.000000e+00 3090.0
7 TraesCS1B01G043700 chr7A 96.399 722 21 3 1986 2703 206576216 206576936 0.000000e+00 1184.0
8 TraesCS1B01G043700 chr2B 95.612 1823 67 3 1 1823 142887636 142889445 0.000000e+00 2911.0
9 TraesCS1B01G043700 chr2B 92.643 734 39 5 1986 2708 573751799 573752528 0.000000e+00 1042.0
10 TraesCS1B01G043700 chr3B 96.296 1161 42 1 1 1161 607522624 607521465 0.000000e+00 1905.0
11 TraesCS1B01G043700 chr3B 97.529 688 17 0 1157 1844 607501966 607501279 0.000000e+00 1177.0
12 TraesCS1B01G043700 chr3B 94.223 727 35 5 1986 2708 487852967 487852244 0.000000e+00 1103.0
13 TraesCS1B01G043700 chr3B 96.970 99 3 0 1846 1944 607500771 607500673 1.670000e-37 167.0
14 TraesCS1B01G043700 chr3B 100.000 39 0 0 1942 1980 487853550 487853512 3.740000e-09 73.1
15 TraesCS1B01G043700 chr5A 95.198 1187 51 5 1 1183 670476317 670475133 0.000000e+00 1871.0
16 TraesCS1B01G043700 chr5A 94.682 1147 60 1 1 1147 696328415 696327270 0.000000e+00 1779.0
17 TraesCS1B01G043700 chr5A 95.735 680 26 2 1144 1823 670475032 670474356 0.000000e+00 1092.0
18 TraesCS1B01G043700 chr1A 95.031 1147 55 2 1 1147 374208219 374209363 0.000000e+00 1801.0
19 TraesCS1B01G043700 chr1A 94.338 1148 63 2 1 1147 449450500 449451646 0.000000e+00 1759.0
20 TraesCS1B01G043700 chr1A 95.000 680 31 2 1144 1823 449451784 449452460 0.000000e+00 1064.0
21 TraesCS1B01G043700 chr1A 92.643 734 39 8 1986 2708 387225355 387224626 0.000000e+00 1042.0
22 TraesCS1B01G043700 chr1A 100.000 39 0 0 1942 1980 387225935 387225897 3.740000e-09 73.1
23 TraesCS1B01G043700 chr2D 94.769 1147 60 0 1 1147 197522953 197521807 0.000000e+00 1786.0
24 TraesCS1B01G043700 chr2D 95.448 681 26 3 1144 1823 197521669 197520993 0.000000e+00 1081.0
25 TraesCS1B01G043700 chr5D 94.643 728 33 4 1986 2708 498378946 498379672 0.000000e+00 1123.0
26 TraesCS1B01G043700 chr3A 95.441 680 23 4 1144 1823 1715090 1714419 0.000000e+00 1077.0
27 TraesCS1B01G043700 chr4A 92.906 733 40 6 1986 2708 706560986 706560256 0.000000e+00 1055.0
28 TraesCS1B01G043700 chr4A 91.873 726 31 14 1986 2706 324709708 324709006 0.000000e+00 989.0
29 TraesCS1B01G043700 chr4A 90.358 726 41 16 1986 2706 551275275 551275976 0.000000e+00 926.0
30 TraesCS1B01G043700 chr4A 94.872 39 2 0 1942 1980 324710292 324710254 8.100000e-06 62.1
31 TraesCS1B01G043700 chr2A 94.000 100 6 0 1845 1944 729535047 729534948 4.670000e-33 152.0


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 TraesCS1B01G043700 chr1B 23816295 23819002 2707 False 5001.00 5001 100.0000 1 2708 1 chr1B.!!$F1 2707
1 TraesCS1B01G043700 chr1B 48530101 48532529 2428 False 1514.00 2870 94.9795 1 1944 2 chr1B.!!$F3 1943
2 TraesCS1B01G043700 chr1B 666990654 666991387 733 True 1112.00 1112 94.2860 1986 2708 1 chr1B.!!$R1 722
3 TraesCS1B01G043700 chr5B 701465276 701467979 2703 False 4710.00 4710 98.0800 1 2708 1 chr5B.!!$F1 2707
4 TraesCS1B01G043700 chr7A 206573907 206576936 3029 False 2137.00 3090 97.0840 1 2703 2 chr7A.!!$F1 2702
5 TraesCS1B01G043700 chr2B 142887636 142889445 1809 False 2911.00 2911 95.6120 1 1823 1 chr2B.!!$F1 1822
6 TraesCS1B01G043700 chr2B 573751799 573752528 729 False 1042.00 1042 92.6430 1986 2708 1 chr2B.!!$F2 722
7 TraesCS1B01G043700 chr3B 607521465 607522624 1159 True 1905.00 1905 96.2960 1 1161 1 chr3B.!!$R1 1160
8 TraesCS1B01G043700 chr3B 607500673 607501966 1293 True 672.00 1177 97.2495 1157 1944 2 chr3B.!!$R3 787
9 TraesCS1B01G043700 chr3B 487852244 487853550 1306 True 588.05 1103 97.1115 1942 2708 2 chr3B.!!$R2 766
10 TraesCS1B01G043700 chr5A 696327270 696328415 1145 True 1779.00 1779 94.6820 1 1147 1 chr5A.!!$R1 1146
11 TraesCS1B01G043700 chr5A 670474356 670476317 1961 True 1481.50 1871 95.4665 1 1823 2 chr5A.!!$R2 1822
12 TraesCS1B01G043700 chr1A 374208219 374209363 1144 False 1801.00 1801 95.0310 1 1147 1 chr1A.!!$F1 1146
13 TraesCS1B01G043700 chr1A 449450500 449452460 1960 False 1411.50 1759 94.6690 1 1823 2 chr1A.!!$F2 1822
14 TraesCS1B01G043700 chr1A 387224626 387225935 1309 True 557.55 1042 96.3215 1942 2708 2 chr1A.!!$R1 766
15 TraesCS1B01G043700 chr2D 197520993 197522953 1960 True 1433.50 1786 95.1085 1 1823 2 chr2D.!!$R1 1822
16 TraesCS1B01G043700 chr5D 498378946 498379672 726 False 1123.00 1123 94.6430 1986 2708 1 chr5D.!!$F1 722
17 TraesCS1B01G043700 chr3A 1714419 1715090 671 True 1077.00 1077 95.4410 1144 1823 1 chr3A.!!$R1 679
18 TraesCS1B01G043700 chr4A 706560256 706560986 730 True 1055.00 1055 92.9060 1986 2708 1 chr4A.!!$R1 722
19 TraesCS1B01G043700 chr4A 551275275 551275976 701 False 926.00 926 90.3580 1986 2706 1 chr4A.!!$F1 720
20 TraesCS1B01G043700 chr4A 324709006 324710292 1286 True 525.55 989 93.3725 1942 2706 2 chr4A.!!$R2 764

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
627 629 0.603065 GCTTGACCACAACAATCCCC 59.397 55.000 0.0 0.0 32.27 4.81 F
1238 1385 2.364632 TGTATCAATTCCGCAAGTGGG 58.635 47.619 0.0 0.0 0.00 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1616 1764 2.689471 TCTCGATTCATTGGGCATTTGG 59.311 45.455 0.0 0.0 0.0 3.28 R
2457 3667 2.799126 ACACTTCAACCCACTGACAA 57.201 45.000 0.0 0.0 0.0 3.18 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
85 86 0.898320 AGGCGGCGCTCATCTAATAT 59.102 50.000 32.30 0.32 0.00 1.28
110 111 2.097110 ATGCCGACCATAGGGAGTTA 57.903 50.000 0.00 0.00 38.05 2.24
257 259 3.314913 CGGCATGTGCTGTATTCCATAAA 59.685 43.478 5.66 0.00 42.29 1.40
297 299 2.158623 GGTGATGAGGCATGGTTGGATA 60.159 50.000 0.00 0.00 0.00 2.59
533 535 8.943594 AAATTTAACTAGTACCCCATTGTTGA 57.056 30.769 0.00 0.00 0.00 3.18
627 629 0.603065 GCTTGACCACAACAATCCCC 59.397 55.000 0.00 0.00 32.27 4.81
632 634 3.761897 TGACCACAACAATCCCCTTTAG 58.238 45.455 0.00 0.00 0.00 1.85
748 751 8.781951 ACAAATCCAAGAGAAGGATAAGGATTA 58.218 33.333 0.00 0.00 44.94 1.75
845 848 5.529581 TCATCGCTGAACCTGTAATATGA 57.470 39.130 0.00 0.00 0.00 2.15
846 849 5.912892 TCATCGCTGAACCTGTAATATGAA 58.087 37.500 0.00 0.00 0.00 2.57
992 995 4.386711 AGGGTAAAGAAGTTCCGTTCAAG 58.613 43.478 0.00 0.00 0.00 3.02
1043 1046 5.036117 ACACTACATGAAGGTGTGTTTCT 57.964 39.130 17.09 0.00 41.75 2.52
1238 1385 2.364632 TGTATCAATTCCGCAAGTGGG 58.635 47.619 0.00 0.00 0.00 4.61
1282 1429 6.393897 TCTCCTATGGATTCCTCTACCAATT 58.606 40.000 3.95 0.00 37.24 2.32
1333 1480 6.554605 TGTTGATGATGGTATGTCCTCATCTA 59.445 38.462 19.00 14.17 43.31 1.98
2001 3204 6.211515 AGCACTACAGCTTGATTTGAAAAAG 58.788 36.000 0.00 0.00 43.70 2.27
2108 3311 8.965819 AGGACAACATTTTATTATGTGTGCATA 58.034 29.630 0.00 0.00 38.69 3.14
2207 3410 6.512297 ACAACACTGTTCTTTCTTGTTTTGT 58.488 32.000 0.00 0.00 28.57 2.83
2267 3470 3.885297 AGTTGATGGTGGAAGTTTCAGTG 59.115 43.478 0.00 0.00 0.00 3.66
2407 3614 4.789012 AAAACCATGATTAGCACACCTG 57.211 40.909 0.00 0.00 0.00 4.00
2457 3667 6.973843 TCGATATGTATAACTGGTTAGCGTT 58.026 36.000 0.00 0.00 0.00 4.84
2492 3702 7.865385 GGTTGAAGTGTTATTTTGCTGATTACA 59.135 33.333 0.00 0.00 0.00 2.41
2559 3780 8.589701 TCTAGTACTTTGTGTCATTCCTGATA 57.410 34.615 0.00 0.00 32.98 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 3.642848 GGATTGCATGGGTATGGTTGAAT 59.357 43.478 0.00 0.00 34.79 2.57
257 259 5.809001 TCACCACTTTGAGCTCTAATGATT 58.191 37.500 16.19 2.97 0.00 2.57
297 299 2.624364 GTGGAATTAACGGTGGTTGGTT 59.376 45.455 0.00 0.00 36.90 3.67
405 407 1.866601 CCACATTTGCATCGCGATCTA 59.133 47.619 20.85 8.27 0.00 1.98
627 629 3.081804 ACCCATTTTGACCTCGCTAAAG 58.918 45.455 0.00 0.00 0.00 1.85
632 634 0.608035 TCCACCCATTTTGACCTCGC 60.608 55.000 0.00 0.00 0.00 5.03
692 695 6.721208 TGGAGAAATGAGCTAGTGGAAATTTT 59.279 34.615 0.00 0.00 0.00 1.82
748 751 8.650143 TCTCACTGCCTTATAATTTCCTTTTT 57.350 30.769 0.00 0.00 0.00 1.94
992 995 6.896431 CAATGACTTGAAGAGCATGAATGGTC 60.896 42.308 13.35 13.35 43.23 4.02
1043 1046 5.045215 GGTCGACGGAAATACATGATACAA 58.955 41.667 9.92 0.00 0.00 2.41
1238 1385 1.089920 AATGGCATCGCTTGTGAGAC 58.910 50.000 0.00 0.00 0.00 3.36
1282 1429 8.561536 TTGGTAGAGGAGATATGGTTCAAATA 57.438 34.615 0.00 0.00 0.00 1.40
1333 1480 0.033109 GCCCCTTGCCCTTGTAGATT 60.033 55.000 0.00 0.00 0.00 2.40
1616 1764 2.689471 TCTCGATTCATTGGGCATTTGG 59.311 45.455 0.00 0.00 0.00 3.28
1980 2640 6.096846 ACACCTTTTTCAAATCAAGCTGTAGT 59.903 34.615 0.00 0.00 0.00 2.73
2001 3204 6.494893 TCATTGCTTTGTCACTAATACACC 57.505 37.500 0.00 0.00 0.00 4.16
2267 3470 7.181143 TGTTTGTTGTCGAAATAGTTACTCC 57.819 36.000 0.00 0.00 0.00 3.85
2407 3614 5.929992 TCGCATAAATAACATAGCACTACCC 59.070 40.000 0.00 0.00 0.00 3.69
2457 3667 2.799126 ACACTTCAACCCACTGACAA 57.201 45.000 0.00 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.