Multiple sequence alignment - TraesCS7A01G029100

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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 TraesCS7A01G029100 chr7A 100.000 3351 0 0 1 3351 11881879 11885229 0.000000e+00 6189.0
1 TraesCS7A01G029100 chr7A 99.314 3351 18 2 1 3351 11928863 11932208 0.000000e+00 6056.0
2 TraesCS7A01G029100 chr7A 97.163 2467 46 9 13 2455 11801867 11804333 0.000000e+00 4146.0
3 TraesCS7A01G029100 chr7A 96.419 1480 22 11 13 1461 11828369 11829848 0.000000e+00 2410.0
4 TraesCS7A01G029100 chr7A 98.124 906 17 0 2446 3351 11804926 11805831 0.000000e+00 1580.0
5 TraesCS7A01G029100 chr7A 98.077 208 4 0 22 229 80221517 80221310 2.460000e-96 363.0
6 TraesCS7A01G029100 chrUn 96.419 1480 22 11 13 1461 341054422 341052943 0.000000e+00 2410.0
7 TraesCS7A01G029100 chrUn 96.997 999 23 3 1463 2455 349443138 349442141 0.000000e+00 1672.0
8 TraesCS7A01G029100 chr5D 96.899 903 28 0 2449 3351 482484822 482483920 0.000000e+00 1513.0
9 TraesCS7A01G029100 chr5D 96.899 903 27 1 2449 3351 420688670 420687769 0.000000e+00 1511.0
10 TraesCS7A01G029100 chr5D 96.788 903 29 0 2449 3351 76124362 76123460 0.000000e+00 1507.0
11 TraesCS7A01G029100 chr5D 96.689 906 30 0 2446 3351 261363700 261364605 0.000000e+00 1507.0
12 TraesCS7A01G029100 chr5D 96.689 906 30 0 2446 3351 447802087 447802992 0.000000e+00 1507.0
13 TraesCS7A01G029100 chr5D 96.689 906 30 0 2446 3351 464502576 464503481 0.000000e+00 1507.0
14 TraesCS7A01G029100 chr5D 92.416 356 23 4 1732 2085 297633584 297633937 3.860000e-139 505.0
15 TraesCS7A01G029100 chr5D 91.618 346 24 5 1741 2084 240868866 240869208 1.090000e-129 473.0
16 TraesCS7A01G029100 chr5D 90.816 98 9 0 560 657 526139274 526139177 7.540000e-27 132.0
17 TraesCS7A01G029100 chr2D 96.799 906 27 1 2446 3351 460638278 460639181 0.000000e+00 1511.0
18 TraesCS7A01G029100 chr2D 92.416 356 22 3 1736 2088 198455382 198455029 1.390000e-138 503.0
19 TraesCS7A01G029100 chr2D 90.000 360 31 4 2113 2470 201839765 201839409 8.470000e-126 460.0
20 TraesCS7A01G029100 chr2D 90.323 341 26 4 2091 2428 204932703 204933039 1.100000e-119 440.0
21 TraesCS7A01G029100 chr2D 89.933 149 15 0 2091 2239 42493782 42493930 3.410000e-45 193.0
22 TraesCS7A01G029100 chr4A 92.782 762 48 3 975 1736 725838036 725837282 0.000000e+00 1096.0
23 TraesCS7A01G029100 chr4A 92.982 285 18 2 656 939 725838319 725838036 6.690000e-112 414.0
24 TraesCS7A01G029100 chr4A 87.395 357 23 13 225 562 725838719 725838366 1.130000e-104 390.0
25 TraesCS7A01G029100 chr4A 96.330 218 6 2 29 245 45489376 45489160 1.140000e-94 357.0
26 TraesCS7A01G029100 chr1D 93.220 354 23 1 1732 2085 289723772 289724124 1.380000e-143 520.0
27 TraesCS7A01G029100 chr1D 92.437 357 22 5 1732 2085 246668310 246668664 3.860000e-139 505.0
28 TraesCS7A01G029100 chr1D 92.635 353 23 3 1735 2085 298085394 298085745 3.860000e-139 505.0
29 TraesCS7A01G029100 chr1D 90.251 359 28 6 1732 2085 406951731 406952087 2.360000e-126 462.0
30 TraesCS7A01G029100 chr7D 92.593 351 24 2 1736 2085 165171344 165171693 1.390000e-138 503.0
31 TraesCS7A01G029100 chr5A 90.423 355 28 5 1741 2094 575431967 575431618 2.360000e-126 462.0
32 TraesCS7A01G029100 chr5A 89.751 361 33 3 1735 2094 337295580 337295223 3.050000e-125 459.0
33 TraesCS7A01G029100 chr5A 90.085 353 31 2 2107 2455 510073803 510074155 3.940000e-124 455.0
34 TraesCS7A01G029100 chr5A 89.286 364 33 5 1738 2097 75067018 75066657 5.100000e-123 451.0
35 TraesCS7A01G029100 chr5A 98.077 208 4 0 22 229 160956525 160956732 2.460000e-96 363.0
36 TraesCS7A01G029100 chr3A 89.972 359 29 5 1732 2085 649015986 649016342 1.100000e-124 457.0
37 TraesCS7A01G029100 chr3A 95.349 43 2 0 656 698 47157079 47157121 6.000000e-08 69.4
38 TraesCS7A01G029100 chr1B 90.435 345 30 2 2113 2455 259048928 259048585 5.100000e-123 451.0
39 TraesCS7A01G029100 chr7B 88.859 368 36 4 2113 2478 446932684 446933048 6.600000e-122 448.0
40 TraesCS7A01G029100 chr7B 89.418 189 20 0 2091 2279 75186765 75186577 4.320000e-59 239.0
41 TraesCS7A01G029100 chr4B 90.145 345 32 1 2113 2455 360014929 360015273 6.600000e-122 448.0
42 TraesCS7A01G029100 chr4B 92.784 97 7 0 561 657 664775714 664775618 1.250000e-29 141.0
43 TraesCS7A01G029100 chr3D 88.981 363 34 5 2113 2470 276170725 276170364 8.530000e-121 444.0
44 TraesCS7A01G029100 chr6D 89.676 339 30 2 2091 2427 100944384 100944049 8.590000e-116 427.0
45 TraesCS7A01G029100 chr2B 87.193 367 45 1 2091 2455 207357988 207358354 1.860000e-112 416.0
46 TraesCS7A01G029100 chr6A 99.015 203 2 0 27 229 593106544 593106342 6.830000e-97 364.0
47 TraesCS7A01G029100 chr1A 99.010 202 2 0 28 229 495751533 495751734 2.460000e-96 363.0
48 TraesCS7A01G029100 chr4D 89.947 189 19 0 2091 2279 189995200 189995012 9.290000e-61 244.0
49 TraesCS7A01G029100 chr4D 94.505 91 5 0 561 651 31822000 31822090 1.250000e-29 141.0
50 TraesCS7A01G029100 chr4D 92.000 100 8 0 561 660 360449785 360449686 1.250000e-29 141.0
51 TraesCS7A01G029100 chr3B 93.000 100 7 0 558 657 327059389 327059290 2.690000e-31 147.0
52 TraesCS7A01G029100 chr6B 100.000 37 0 0 656 692 681466863 681466899 6.000000e-08 69.4


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 TraesCS7A01G029100 chr7A 11881879 11885229 3350 False 6189.000000 6189 100.0000 1 3351 1 chr7A.!!$F2 3350
1 TraesCS7A01G029100 chr7A 11928863 11932208 3345 False 6056.000000 6056 99.3140 1 3351 1 chr7A.!!$F3 3350
2 TraesCS7A01G029100 chr7A 11801867 11805831 3964 False 2863.000000 4146 97.6435 13 3351 2 chr7A.!!$F4 3338
3 TraesCS7A01G029100 chr7A 11828369 11829848 1479 False 2410.000000 2410 96.4190 13 1461 1 chr7A.!!$F1 1448
4 TraesCS7A01G029100 chrUn 341052943 341054422 1479 True 2410.000000 2410 96.4190 13 1461 1 chrUn.!!$R1 1448
5 TraesCS7A01G029100 chrUn 349442141 349443138 997 True 1672.000000 1672 96.9970 1463 2455 1 chrUn.!!$R2 992
6 TraesCS7A01G029100 chr5D 482483920 482484822 902 True 1513.000000 1513 96.8990 2449 3351 1 chr5D.!!$R3 902
7 TraesCS7A01G029100 chr5D 420687769 420688670 901 True 1511.000000 1511 96.8990 2449 3351 1 chr5D.!!$R2 902
8 TraesCS7A01G029100 chr5D 76123460 76124362 902 True 1507.000000 1507 96.7880 2449 3351 1 chr5D.!!$R1 902
9 TraesCS7A01G029100 chr5D 261363700 261364605 905 False 1507.000000 1507 96.6890 2446 3351 1 chr5D.!!$F2 905
10 TraesCS7A01G029100 chr5D 447802087 447802992 905 False 1507.000000 1507 96.6890 2446 3351 1 chr5D.!!$F4 905
11 TraesCS7A01G029100 chr5D 464502576 464503481 905 False 1507.000000 1507 96.6890 2446 3351 1 chr5D.!!$F5 905
12 TraesCS7A01G029100 chr2D 460638278 460639181 903 False 1511.000000 1511 96.7990 2446 3351 1 chr2D.!!$F3 905
13 TraesCS7A01G029100 chr4A 725837282 725838719 1437 True 633.333333 1096 91.0530 225 1736 3 chr4A.!!$R2 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
1198 1268 1.559368 CTTTCCATGGCCATCACCAA 58.441 50.0 17.61 5.64 44.65 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2605 3283 4.390603 TCCCGTTAATCAAATGACAACTCG 59.609 41.667 7.65 0.0 0.0 4.18 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
1198 1268 1.559368 CTTTCCATGGCCATCACCAA 58.441 50.0 17.61 5.64 44.65 3.67
2605 3283 5.758784 GGTTATGTTTCCTAGCCATAGACAC 59.241 44.0 0.00 0.00 0.00 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1198 1268 1.813513 CTTGGTGTCGGAAGCTTGAT 58.186 50.000 2.10 0.0 0.0 2.57
1768 1838 0.899720 TCGCAGACCCTAAAACCGAT 59.100 50.000 0.00 0.0 0.0 4.18
2605 3283 4.390603 TCCCGTTAATCAAATGACAACTCG 59.609 41.667 7.65 0.0 0.0 4.18


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

AutoCloner maintained by Alex Coulton.