Multiple sequence alignment - TraesCS7B01G379300

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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 TraesCS7B01G379300 chr7B 100.000 4695 0 0 1 4695 643570615 643565921 0.000000e+00 8671.0
1 TraesCS7B01G379300 chr7B 97.434 2806 39 8 1917 4695 643626554 643623755 0.000000e+00 4752.0
2 TraesCS7B01G379300 chr7B 94.467 1934 68 17 1 1921 643628491 643626584 0.000000e+00 2942.0
3 TraesCS7B01G379300 chr7B 100.000 1212 0 0 5 1216 643611144 643609933 0.000000e+00 2239.0
4 TraesCS7B01G379300 chr7B 99.735 1134 3 0 3562 4695 643586825 643585692 0.000000e+00 2078.0
5 TraesCS7B01G379300 chr7B 85.890 1460 104 42 511 1921 643698740 643697334 0.000000e+00 1461.0
6 TraesCS7B01G379300 chr7B 83.271 1076 115 41 2693 3720 643659672 643658614 0.000000e+00 929.0
7 TraesCS7B01G379300 chr7B 85.894 397 53 3 2485 2879 643378122 643377727 2.020000e-113 420.0
8 TraesCS7B01G379300 chr7B 82.684 462 50 19 2930 3389 643377021 643376588 2.650000e-102 383.0
9 TraesCS7B01G379300 chr7B 81.549 439 67 9 4237 4665 163001832 163001398 2.690000e-92 350.0
10 TraesCS7B01G379300 chr7B 86.984 315 33 6 2384 2695 643672401 643672092 9.670000e-92 348.0
11 TraesCS7B01G379300 chr7B 74.439 446 81 20 4249 4665 39550410 39550851 1.350000e-35 161.0
12 TraesCS7B01G379300 chrUn 99.884 3449 3 1 5 3452 316972056 316975504 0.000000e+00 6346.0
13 TraesCS7B01G379300 chrUn 99.559 1134 5 0 3562 4695 369638983 369640116 0.000000e+00 2067.0
14 TraesCS7B01G379300 chr7A 89.787 3936 234 80 126 3969 671077032 671073173 0.000000e+00 4887.0
15 TraesCS7B01G379300 chr7A 85.274 1460 140 42 2280 3684 671123315 671121876 0.000000e+00 1435.0
16 TraesCS7B01G379300 chr7A 92.481 665 23 16 593 1239 671126186 671125531 0.000000e+00 926.0
17 TraesCS7B01G379300 chr7A 87.124 699 54 8 1229 1921 671124418 671123750 0.000000e+00 760.0
18 TraesCS7B01G379300 chr7A 100.000 35 0 0 3953 3987 671073142 671073108 1.090000e-06 65.8
19 TraesCS7B01G379300 chr7D 93.191 1924 103 8 1 1921 579200085 579198187 0.000000e+00 2802.0
20 TraesCS7B01G379300 chr7D 90.312 1600 84 39 2388 3959 579197784 579196228 0.000000e+00 2030.0
21 TraesCS7B01G379300 chr7D 84.406 1212 118 40 2280 3441 579251133 579249943 0.000000e+00 1125.0
22 TraesCS7B01G379300 chr7D 87.518 697 53 8 1229 1921 579252236 579251570 0.000000e+00 774.0
23 TraesCS7B01G379300 chr7D 88.866 494 23 18 764 1239 579253867 579253388 3.150000e-161 579.0
24 TraesCS7B01G379300 chr7D 95.909 220 9 0 1917 2136 579198157 579197938 1.610000e-94 357.0
25 TraesCS7B01G379300 chr7D 88.136 295 26 4 178 463 579200853 579200559 4.500000e-90 342.0
26 TraesCS7B01G379300 chr7D 77.874 461 67 16 4252 4679 628135115 628134657 2.170000e-63 254.0
27 TraesCS7B01G379300 chr7D 75.395 443 79 22 4249 4665 106980852 106980414 2.230000e-43 187.0
28 TraesCS7B01G379300 chr7D 76.190 399 66 13 4295 4665 8382739 8382342 2.890000e-42 183.0
29 TraesCS7B01G379300 chr7D 81.517 211 36 3 4019 4228 596958885 596959093 2.250000e-38 171.0
30 TraesCS7B01G379300 chr7D 89.431 123 11 2 2194 2315 579197909 579197788 2.260000e-33 154.0
31 TraesCS7B01G379300 chr7D 73.488 430 83 19 4265 4665 397386236 397385809 2.950000e-27 134.0
32 TraesCS7B01G379300 chr3B 81.707 410 61 11 4242 4641 799257838 799257433 3.500000e-86 329.0
33 TraesCS7B01G379300 chr3B 86.017 236 33 0 4254 4489 488134260 488134495 2.170000e-63 254.0
34 TraesCS7B01G379300 chr6B 78.288 479 67 18 4249 4693 556749844 556750319 1.660000e-69 274.0
35 TraesCS7B01G379300 chr6D 79.951 409 48 10 4249 4626 428261417 428261012 2.150000e-68 270.0
36 TraesCS7B01G379300 chr3D 77.871 479 69 13 4249 4693 562513991 562514466 3.600000e-66 263.0
37 TraesCS7B01G379300 chr3D 76.674 463 62 25 4257 4679 416937982 416938438 1.020000e-51 215.0
38 TraesCS7B01G379300 chr5D 85.507 207 28 2 4022 4227 495388679 495388884 1.020000e-51 215.0
39 TraesCS7B01G379300 chr5D 74.118 425 86 15 4253 4660 480370196 480370613 2.260000e-33 154.0
40 TraesCS7B01G379300 chr1B 83.886 211 33 1 4018 4228 469616095 469616304 2.870000e-47 200.0
41 TraesCS7B01G379300 chr6A 82.432 222 36 2 4008 4227 87646099 87646319 1.720000e-44 191.0
42 TraesCS7B01G379300 chr5A 85.976 164 22 1 287 449 569179317 569179154 1.740000e-39 174.0
43 TraesCS7B01G379300 chr4B 75.931 403 58 17 4294 4665 116484853 116484459 2.250000e-38 171.0
44 TraesCS7B01G379300 chr1D 86.164 159 21 1 287 445 106843497 106843654 2.250000e-38 171.0
45 TraesCS7B01G379300 chr1D 84.810 79 9 2 1 78 488678482 488678558 5.040000e-10 76.8
46 TraesCS7B01G379300 chr5B 74.889 450 70 25 4249 4665 619288423 619287984 1.050000e-36 165.0
47 TraesCS7B01G379300 chr2B 84.211 171 25 2 293 463 101064991 101064823 1.050000e-36 165.0
48 TraesCS7B01G379300 chr4A 79.325 237 41 6 3996 4228 710850281 710850513 4.860000e-35 159.0
49 TraesCS7B01G379300 chr4A 74.242 396 70 17 4330 4695 550171990 550171597 2.280000e-28 137.0
50 TraesCS7B01G379300 chr1A 78.059 237 45 6 3997 4228 9113077 9112843 4.900000e-30 143.0


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 TraesCS7B01G379300 chr7B 643565921 643570615 4694 True 8671.000000 8671 100.0000 1 4695 1 chr7B.!!$R2 4694
1 TraesCS7B01G379300 chr7B 643623755 643628491 4736 True 3847.000000 4752 95.9505 1 4695 2 chr7B.!!$R9 4694
2 TraesCS7B01G379300 chr7B 643609933 643611144 1211 True 2239.000000 2239 100.0000 5 1216 1 chr7B.!!$R4 1211
3 TraesCS7B01G379300 chr7B 643585692 643586825 1133 True 2078.000000 2078 99.7350 3562 4695 1 chr7B.!!$R3 1133
4 TraesCS7B01G379300 chr7B 643697334 643698740 1406 True 1461.000000 1461 85.8900 511 1921 1 chr7B.!!$R7 1410
5 TraesCS7B01G379300 chr7B 643658614 643659672 1058 True 929.000000 929 83.2710 2693 3720 1 chr7B.!!$R5 1027
6 TraesCS7B01G379300 chr7B 643376588 643378122 1534 True 401.500000 420 84.2890 2485 3389 2 chr7B.!!$R8 904
7 TraesCS7B01G379300 chrUn 316972056 316975504 3448 False 6346.000000 6346 99.8840 5 3452 1 chrUn.!!$F1 3447
8 TraesCS7B01G379300 chrUn 369638983 369640116 1133 False 2067.000000 2067 99.5590 3562 4695 1 chrUn.!!$F2 1133
9 TraesCS7B01G379300 chr7A 671073108 671077032 3924 True 2476.400000 4887 94.8935 126 3987 2 chr7A.!!$R1 3861
10 TraesCS7B01G379300 chr7A 671121876 671126186 4310 True 1040.333333 1435 88.2930 593 3684 3 chr7A.!!$R2 3091
11 TraesCS7B01G379300 chr7D 579196228 579200853 4625 True 1137.000000 2802 91.3958 1 3959 5 chr7D.!!$R5 3958
12 TraesCS7B01G379300 chr7D 579249943 579253867 3924 True 826.000000 1125 86.9300 764 3441 3 chr7D.!!$R6 2677

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
1360 3380 8.401709 AGTTTCTTGTTTTCAGATGACTTCTTC 58.598 33.333 0.0 0.00 29.93 2.87 F
1421 3448 6.491062 TCATCTTATTGGCCATGGATTTACAG 59.509 38.462 18.4 3.93 0.00 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3452 6336 6.567050 AGCAAACCAAAACATATATGAGCAG 58.433 36.00 19.63 6.4 0.00 4.24 R
4644 7602 5.779529 ACTTGTAGTAGACAGTCGGAAAA 57.220 39.13 0.00 0.0 39.88 2.29 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
1360 3380 8.401709 AGTTTCTTGTTTTCAGATGACTTCTTC 58.598 33.333 0.00 0.00 29.93 2.87
1421 3448 6.491062 TCATCTTATTGGCCATGGATTTACAG 59.509 38.462 18.40 3.93 0.00 2.74
3452 6336 7.336931 ACAATTTGGTGATCCAGTATACTTGAC 59.663 37.037 8.73 4.70 45.22 3.18
4644 7602 1.069765 CCGGCCTTAGCACGATGAT 59.930 57.895 0.00 0.00 42.56 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1322 3342 8.536175 TGAAAACAAGAAACTTCCTTTATGGTT 58.464 29.630 0.00 0.00 29.82 3.67
1323 3343 8.073467 TGAAAACAAGAAACTTCCTTTATGGT 57.927 30.769 0.00 0.00 37.07 3.55
1324 3344 8.413229 TCTGAAAACAAGAAACTTCCTTTATGG 58.587 33.333 0.00 0.00 37.10 2.74
1325 3345 9.971922 ATCTGAAAACAAGAAACTTCCTTTATG 57.028 29.630 0.00 0.00 0.00 1.90
1326 3346 9.971922 CATCTGAAAACAAGAAACTTCCTTTAT 57.028 29.630 0.00 0.00 0.00 1.40
1327 3347 9.184523 TCATCTGAAAACAAGAAACTTCCTTTA 57.815 29.630 0.00 0.00 0.00 1.85
1328 3348 7.976175 GTCATCTGAAAACAAGAAACTTCCTTT 59.024 33.333 0.00 0.00 0.00 3.11
1329 3349 7.340487 AGTCATCTGAAAACAAGAAACTTCCTT 59.660 33.333 0.00 0.00 0.00 3.36
1330 3350 6.830838 AGTCATCTGAAAACAAGAAACTTCCT 59.169 34.615 0.00 0.00 0.00 3.36
1331 3351 7.032377 AGTCATCTGAAAACAAGAAACTTCC 57.968 36.000 0.00 0.00 0.00 3.46
1332 3352 8.401709 AGAAGTCATCTGAAAACAAGAAACTTC 58.598 33.333 16.48 16.48 43.01 3.01
1333 3353 8.286191 AGAAGTCATCTGAAAACAAGAAACTT 57.714 30.769 0.00 0.00 36.88 2.66
1334 3354 7.872113 AGAAGTCATCTGAAAACAAGAAACT 57.128 32.000 0.00 0.00 36.88 2.66
1335 3355 8.184192 TGAAGAAGTCATCTGAAAACAAGAAAC 58.816 33.333 0.00 0.00 38.79 2.78
1336 3356 8.279970 TGAAGAAGTCATCTGAAAACAAGAAA 57.720 30.769 0.00 0.00 38.79 2.52
1337 3357 7.864108 TGAAGAAGTCATCTGAAAACAAGAA 57.136 32.000 0.00 0.00 38.79 2.52
1421 3448 4.642429 ACTTAACCAGGAAGACATCACAC 58.358 43.478 0.00 0.00 0.00 3.82
3452 6336 6.567050 AGCAAACCAAAACATATATGAGCAG 58.433 36.000 19.63 6.40 0.00 4.24
4644 7602 5.779529 ACTTGTAGTAGACAGTCGGAAAA 57.220 39.130 0.00 0.00 39.88 2.29


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

AutoCloner maintained by Alex Coulton.