Multiple sequence alignment - TraesCS7A01G135500

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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 TraesCS7A01G135500 chr7A 100.000 2913 0 0 1 2913 88434910 88437822 0.000000e+00 5380.0
1 TraesCS7A01G135500 chr7A 98.411 1888 24 4 1 1887 88499282 88501164 0.000000e+00 3315.0
2 TraesCS7A01G135500 chr7A 92.818 1838 105 16 973 2795 88315480 88317305 0.000000e+00 2638.0
3 TraesCS7A01G135500 chr7A 86.718 2063 161 56 869 2913 87451165 87453132 0.000000e+00 2187.0
4 TraesCS7A01G135500 chr7A 90.285 1194 76 16 1756 2913 88122403 88123592 0.000000e+00 1526.0
5 TraesCS7A01G135500 chr7A 90.293 1195 75 17 1756 2913 88173170 88174360 0.000000e+00 1526.0
6 TraesCS7A01G135500 chr7A 89.950 1194 79 17 1756 2913 88009123 88010311 0.000000e+00 1502.0
7 TraesCS7A01G135500 chr7A 89.786 607 33 15 831 1434 88008334 88008914 0.000000e+00 750.0
8 TraesCS7A01G135500 chr7A 87.966 590 63 3 202 791 88188340 88188921 0.000000e+00 689.0
9 TraesCS7A01G135500 chr7A 86.824 592 69 4 200 791 88144408 88144990 0.000000e+00 652.0
10 TraesCS7A01G135500 chr7A 88.996 518 30 9 918 1434 88172469 88172960 1.480000e-172 616.0
11 TraesCS7A01G135500 chr7A 86.528 386 44 3 406 791 88047215 88047592 4.490000e-113 418.0
12 TraesCS7A01G135500 chr7A 83.851 322 40 6 422 740 88119764 88120076 2.190000e-76 296.0
13 TraesCS7A01G135500 chr7A 85.443 158 19 4 831 987 88121353 88121507 8.350000e-36 161.0
14 TraesCS7A01G135500 chr7A 100.000 29 0 0 804 832 88435684 88435712 1.000000e-03 54.7
15 TraesCS7A01G135500 chr7A 100.000 29 0 0 775 803 88435713 88435741 1.000000e-03 54.7
16 TraesCS7A01G135500 chr7A 100.000 29 0 0 804 832 88500053 88500081 1.000000e-03 54.7
17 TraesCS7A01G135500 chr7A 100.000 29 0 0 775 803 88500082 88500110 1.000000e-03 54.7
18 TraesCS7A01G135500 chr7D 94.972 1949 66 15 987 2913 87206445 87208383 0.000000e+00 3027.0
19 TraesCS7A01G135500 chr7D 91.046 1463 86 17 1462 2904 86919030 86920467 0.000000e+00 1934.0
20 TraesCS7A01G135500 chr7D 91.703 1362 75 14 1462 2803 86755540 86756883 0.000000e+00 1855.0
21 TraesCS7A01G135500 chr7D 95.688 1090 33 11 804 1888 87220290 87221370 0.000000e+00 1740.0
22 TraesCS7A01G135500 chr7D 93.729 606 31 3 201 803 87219717 87220318 0.000000e+00 902.0
23 TraesCS7A01G135500 chr7D 87.516 777 71 17 1416 2181 86292328 86293089 0.000000e+00 874.0
24 TraesCS7A01G135500 chr7D 82.461 764 60 27 2190 2911 86293459 86294190 4.150000e-168 601.0
25 TraesCS7A01G135500 chr7D 91.005 378 21 8 831 1201 86754993 86755364 5.610000e-137 497.0
26 TraesCS7A01G135500 chr7D 90.237 379 23 9 831 1201 86918482 86918854 1.570000e-132 483.0
27 TraesCS7A01G135500 chr7D 87.857 280 18 7 2635 2913 86796658 86796922 6.060000e-82 315.0
28 TraesCS7A01G135500 chr7D 95.745 188 7 1 1248 1434 86918849 86919036 4.720000e-78 302.0
29 TraesCS7A01G135500 chr7D 95.213 188 8 1 1248 1434 86755359 86755546 2.190000e-76 296.0
30 TraesCS7A01G135500 chr7D 92.614 176 11 2 2454 2628 86784481 86784655 4.820000e-63 252.0
31 TraesCS7A01G135500 chr7D 90.164 183 15 3 2001 2181 87221619 87221800 4.850000e-58 235.0
32 TraesCS7A01G135500 chr7D 92.982 114 4 1 2800 2913 86760522 86760631 2.320000e-36 163.0
33 TraesCS7A01G135500 chr7D 100.000 28 0 0 964 991 87206170 87206197 5.000000e-03 52.8
34 TraesCS7A01G135500 chr7B 86.667 1965 140 30 987 2913 35307638 35309518 0.000000e+00 2065.0
35 TraesCS7A01G135500 chr7B 89.180 1488 115 18 1462 2913 35507702 35509179 0.000000e+00 1814.0
36 TraesCS7A01G135500 chr7B 91.629 1111 62 11 804 1888 35637134 35638239 0.000000e+00 1507.0
37 TraesCS7A01G135500 chr7B 91.149 644 44 6 804 1440 35507076 35507713 0.000000e+00 861.0
38 TraesCS7A01G135500 chr7B 87.454 542 59 6 201 741 35636538 35637071 1.480000e-172 616.0
39 TraesCS7A01G135500 chr7B 89.140 221 23 1 201 421 28489533 28489752 1.030000e-69 274.0
40 TraesCS7A01G135500 chr7B 90.850 153 12 1 851 1003 35301965 35302115 1.370000e-48 204.0
41 TraesCS7A01G135500 chr7B 92.857 70 3 1 734 803 35637095 35637162 1.850000e-17 100.0
42 TraesCS7A01G135500 chr7B 96.774 31 1 0 2179 2209 35638567 35638597 5.000000e-03 52.8
43 TraesCS7A01G135500 chr4B 96.154 208 5 2 1 205 387795368 387795575 1.290000e-88 337.0
44 TraesCS7A01G135500 chr4B 95.673 208 6 2 1 205 387798631 387798838 6.020000e-87 331.0
45 TraesCS7A01G135500 chr5D 95.694 209 5 3 1 205 214552188 214551980 1.670000e-87 333.0
46 TraesCS7A01G135500 chr5D 94.231 208 8 3 1 205 214556978 214556772 6.060000e-82 315.0
47 TraesCS7A01G135500 chr5D 90.000 210 21 0 201 410 35562012 35562221 3.700000e-69 272.0
48 TraesCS7A01G135500 chr1A 94.737 209 7 3 1 205 296930164 296930372 3.620000e-84 322.0
49 TraesCS7A01G135500 chr1B 94.712 208 8 2 1 205 408161110 408161317 1.300000e-83 320.0
50 TraesCS7A01G135500 chr5B 94.686 207 7 3 2 205 543947325 543947120 4.680000e-83 318.0
51 TraesCS7A01G135500 chr2A 93.056 216 10 4 1 213 271898709 271898496 7.840000e-81 311.0
52 TraesCS7A01G135500 chr3D 89.091 220 23 1 201 420 417156675 417156457 3.700000e-69 272.0
53 TraesCS7A01G135500 chr3D 90.338 207 18 2 215 421 93254561 93254357 1.330000e-68 270.0
54 TraesCS7A01G135500 chr3D 88.688 221 24 1 201 421 123618826 123619045 4.780000e-68 268.0


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 TraesCS7A01G135500 chr7A 88434910 88437822 2912 False 1829.800000 5380 100.000000 1 2913 3 chr7A.!!$F9 2912
1 TraesCS7A01G135500 chr7A 88315480 88317305 1825 False 2638.000000 2638 92.818000 973 2795 1 chr7A.!!$F5 1822
2 TraesCS7A01G135500 chr7A 87451165 87453132 1967 False 2187.000000 2187 86.718000 869 2913 1 chr7A.!!$F1 2044
3 TraesCS7A01G135500 chr7A 88499282 88501164 1882 False 1141.466667 3315 99.470333 1 1887 3 chr7A.!!$F10 1886
4 TraesCS7A01G135500 chr7A 88008334 88010311 1977 False 1126.000000 1502 89.868000 831 2913 2 chr7A.!!$F6 2082
5 TraesCS7A01G135500 chr7A 88172469 88174360 1891 False 1071.000000 1526 89.644500 918 2913 2 chr7A.!!$F8 1995
6 TraesCS7A01G135500 chr7A 88188340 88188921 581 False 689.000000 689 87.966000 202 791 1 chr7A.!!$F4 589
7 TraesCS7A01G135500 chr7A 88119764 88123592 3828 False 661.000000 1526 86.526333 422 2913 3 chr7A.!!$F7 2491
8 TraesCS7A01G135500 chr7A 88144408 88144990 582 False 652.000000 652 86.824000 200 791 1 chr7A.!!$F3 591
9 TraesCS7A01G135500 chr7D 87206170 87208383 2213 False 1539.900000 3027 97.486000 964 2913 2 chr7D.!!$F6 1949
10 TraesCS7A01G135500 chr7D 87219717 87221800 2083 False 959.000000 1740 93.193667 201 2181 3 chr7D.!!$F7 1980
11 TraesCS7A01G135500 chr7D 86918482 86920467 1985 False 906.333333 1934 92.342667 831 2904 3 chr7D.!!$F5 2073
12 TraesCS7A01G135500 chr7D 86292328 86294190 1862 False 737.500000 874 84.988500 1416 2911 2 chr7D.!!$F3 1495
13 TraesCS7A01G135500 chr7D 86754993 86760631 5638 False 702.750000 1855 92.725750 831 2913 4 chr7D.!!$F4 2082
14 TraesCS7A01G135500 chr7B 35307638 35309518 1880 False 2065.000000 2065 86.667000 987 2913 1 chr7B.!!$F3 1926
15 TraesCS7A01G135500 chr7B 35507076 35509179 2103 False 1337.500000 1814 90.164500 804 2913 2 chr7B.!!$F4 2109
16 TraesCS7A01G135500 chr7B 35636538 35638597 2059 False 568.950000 1507 92.178500 201 2209 4 chr7B.!!$F5 2008
17 TraesCS7A01G135500 chr4B 387795368 387798838 3470 False 334.000000 337 95.913500 1 205 2 chr4B.!!$F1 204

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
285 290 4.433615 GAGCAGAGATTGATACCGTGAAA 58.566 43.478 0.0 0.0 0.0 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2223 6511 4.993705 AATAATAAAGGCCCTGATCCGA 57.006 40.909 0.0 0.0 0.0 4.55 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
51 55 5.586243 CAGACTCCTATTACAATTGGGTGTG 59.414 44.000 10.83 5.28 33.00 3.82
240 245 8.712285 TCTAGTCCAATTGAAACCTATTTACG 57.288 34.615 7.12 0.00 0.00 3.18
285 290 4.433615 GAGCAGAGATTGATACCGTGAAA 58.566 43.478 0.00 0.00 0.00 2.69
2125 6033 0.976641 TCCACGAGATCTGGCACTTT 59.023 50.000 0.00 0.00 0.00 2.66
2223 6511 2.875296 TCAAAGTGTGCCCTTTATGCT 58.125 42.857 0.00 0.00 33.00 3.79
2271 6567 6.909550 ACAGAGGCTCTATTATGTCTAAGG 57.090 41.667 18.26 2.31 0.00 2.69
2352 6650 1.152333 GGTGCCCCCTTTTGGTTCT 60.152 57.895 0.00 0.00 38.10 3.01
2408 6706 0.035439 GGACGCATTCCTTTCCTGGA 60.035 55.000 0.00 0.00 41.95 3.86
2458 6756 4.349048 CCCAATCTTGATCTCTGGATGGTA 59.651 45.833 0.00 0.00 31.46 3.25
2466 6764 3.367646 TCTCTGGATGGTAGACGTCTT 57.632 47.619 25.44 5.05 35.38 3.01
2519 6839 2.024176 TCGCTTGAGGCCTTGATTAC 57.976 50.000 6.77 0.00 37.74 1.89
2592 6912 1.434188 TTGGGCAACTCTGAAGAGGA 58.566 50.000 11.87 0.00 46.13 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
25 26 6.180472 CACCCAATTGTAATAGGAGTCTGTT 58.820 40.000 4.43 0.00 0.00 3.16
51 55 0.177373 CGTAGAAGGTTACCCTGCCC 59.823 60.000 0.00 0.00 41.56 5.36
240 245 7.622464 GCTCGAAGAAATACTCCAAAGACTTTC 60.622 40.741 0.00 0.00 34.09 2.62
436 445 1.469423 GCCGGGACTTAGAGAAACTCG 60.469 57.143 2.18 0.00 35.36 4.18
2125 6033 5.473504 GCTTGGGAAAACTCATTCTAGACAA 59.526 40.000 0.00 0.00 0.00 3.18
2223 6511 4.993705 AATAATAAAGGCCCTGATCCGA 57.006 40.909 0.00 0.00 0.00 4.55
2309 6605 0.921347 CTTCGACGGCCAAGATAACG 59.079 55.000 2.24 0.00 0.00 3.18
2345 6643 1.697082 TACCCGTGTGCCAGAACCAA 61.697 55.000 0.00 0.00 0.00 3.67
2352 6650 3.196939 GGTATAAATACCCGTGTGCCA 57.803 47.619 7.80 0.00 45.62 4.92
2408 6706 2.665185 GCGTTCGCAACCAGGAGT 60.665 61.111 12.33 0.00 0.00 3.85
2458 6756 0.321996 GGAAAGAGGCCAAGACGTCT 59.678 55.000 13.58 13.58 36.38 4.18
2466 6764 2.144078 TCACACGGGAAAGAGGCCA 61.144 57.895 5.01 0.00 0.00 5.36
2519 6839 7.840342 ACTTGTATGCTAAAGAGAACATCTG 57.160 36.000 0.00 0.00 38.67 2.90
2592 6912 0.887836 CATACCGCATCATGCCAGCT 60.888 55.000 3.38 0.00 41.12 4.24


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

AutoCloner maintained by Alex Coulton.