Multiple sequence alignment - TraesCS3A01G337400

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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 TraesCS3A01G337400 chr3A 100.000 2891 0 0 1 2891 584282307 584285197 0.000000e+00 5339
1 TraesCS3A01G337400 chr3A 92.955 2470 102 28 449 2891 15355097 15357521 0.000000e+00 3531
2 TraesCS3A01G337400 chr3A 96.172 209 8 0 2675 2883 15357857 15358065 3.140000e-90 342
3 TraesCS3A01G337400 chr3A 94.470 217 12 0 2675 2891 15357353 15357569 5.260000e-88 335
4 TraesCS3A01G337400 chr3A 100.000 71 0 0 3221 3291 15357897 15357967 7.410000e-27 132
5 TraesCS3A01G337400 chr3A 100.000 71 0 0 3221 3291 584285527 584285597 7.410000e-27 132
6 TraesCS3A01G337400 chr3A 98.592 71 1 0 3221 3291 15357489 15357559 3.450000e-25 126
7 TraesCS3A01G337400 chr3A 98.592 71 1 0 3221 3291 584285021 584285091 3.450000e-25 126
8 TraesCS3A01G337400 chr6A 95.993 2446 59 20 449 2891 36425334 36422925 0.000000e+00 3938
9 TraesCS3A01G337400 chr6A 94.019 2274 91 23 624 2891 21289920 21287686 0.000000e+00 3404
10 TraesCS3A01G337400 chr6A 95.853 217 9 0 2675 2891 36423045 36422829 5.220000e-93 351
11 TraesCS3A01G337400 chr6A 92.627 217 16 0 2675 2891 21287854 21287638 2.470000e-81 313
12 TraesCS3A01G337400 chr6A 100.000 71 0 0 3221 3291 36422450 36422380 7.410000e-27 132
13 TraesCS3A01G337400 chr6A 100.000 71 0 0 3221 3291 36423005 36422935 7.410000e-27 132
14 TraesCS3A01G337400 chr6A 98.592 71 1 0 3221 3291 36413631 36413561 3.450000e-25 126
15 TraesCS3A01G337400 chr6A 98.592 71 1 0 3221 3291 36422546 36422476 3.450000e-25 126
16 TraesCS3A01G337400 chr7A 94.656 2470 100 14 448 2891 10616608 10614145 0.000000e+00 3801
17 TraesCS3A01G337400 chr7A 94.144 2459 108 16 456 2891 27539866 27542311 0.000000e+00 3711
18 TraesCS3A01G337400 chr7A 94.470 217 12 0 2675 2891 10614313 10614097 5.260000e-88 335
19 TraesCS3A01G337400 chr7A 93.088 217 13 1 2675 2891 27542145 27542359 1.910000e-82 316
20 TraesCS3A01G337400 chr7A 98.592 71 1 0 3221 3291 10614177 10614107 3.450000e-25 126
21 TraesCS3A01G337400 chr4B 94.451 2469 93 23 449 2891 567645746 567648196 0.000000e+00 3760
22 TraesCS3A01G337400 chr4B 100.000 69 0 0 3223 3291 567648118 567648186 9.590000e-26 128
23 TraesCS3A01G337400 chr5B 92.364 2475 116 28 449 2891 643322857 643320424 0.000000e+00 3456
24 TraesCS3A01G337400 chr5B 89.268 820 63 14 440 1245 607064447 607065255 0.000000e+00 1003
25 TraesCS3A01G337400 chr7D 92.522 2113 90 27 450 2530 35846000 35843924 0.000000e+00 2964
26 TraesCS3A01G337400 chr7D 81.315 289 35 11 2604 2891 35843923 35843653 1.990000e-52 217
27 TraesCS3A01G337400 chr4A 95.192 1872 68 13 1022 2891 707776348 707778199 0.000000e+00 2939
28 TraesCS3A01G337400 chr5A 97.359 1628 41 2 773 2398 44145581 44147208 0.000000e+00 2767
29 TraesCS3A01G337400 chr5A 94.931 217 11 0 2675 2891 44156404 44156620 1.130000e-89 340
30 TraesCS3A01G337400 chr3D 89.130 460 30 7 1 448 443264458 443264909 3.710000e-154 555
31 TraesCS3A01G337400 chr3B 91.810 232 14 2 1 232 581075497 581075723 5.300000e-83 318
32 TraesCS3A01G337400 chr3B 92.157 204 11 4 250 448 581075901 581076104 1.930000e-72 283
33 TraesCS3A01G337400 chr6D 92.627 217 16 0 2675 2891 155819665 155819449 2.470000e-81 313


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 TraesCS3A01G337400 chr3A 584282307 584285597 3290 False 1865.666667 5339 99.530667 1 3291 3 chr3A.!!$F2 3290
1 TraesCS3A01G337400 chr3A 15355097 15358065 2968 False 893.200000 3531 96.437800 449 3291 5 chr3A.!!$F1 2842
2 TraesCS3A01G337400 chr6A 21287638 21289920 2282 True 1858.500000 3404 93.323000 624 2891 2 chr6A.!!$R2 2267
3 TraesCS3A01G337400 chr6A 36422380 36425334 2954 True 935.800000 3938 98.087600 449 3291 5 chr6A.!!$R3 2842
4 TraesCS3A01G337400 chr7A 27539866 27542359 2493 False 2013.500000 3711 93.616000 456 2891 2 chr7A.!!$F1 2435
5 TraesCS3A01G337400 chr7A 10614097 10616608 2511 True 1420.666667 3801 95.906000 448 3291 3 chr7A.!!$R1 2843
6 TraesCS3A01G337400 chr4B 567645746 567648196 2450 False 1944.000000 3760 97.225500 449 3291 2 chr4B.!!$F1 2842
7 TraesCS3A01G337400 chr5B 643320424 643322857 2433 True 3456.000000 3456 92.364000 449 2891 1 chr5B.!!$R1 2442
8 TraesCS3A01G337400 chr5B 607064447 607065255 808 False 1003.000000 1003 89.268000 440 1245 1 chr5B.!!$F1 805
9 TraesCS3A01G337400 chr7D 35843653 35846000 2347 True 1590.500000 2964 86.918500 450 2891 2 chr7D.!!$R1 2441
10 TraesCS3A01G337400 chr4A 707776348 707778199 1851 False 2939.000000 2939 95.192000 1022 2891 1 chr4A.!!$F1 1869
11 TraesCS3A01G337400 chr5A 44145581 44147208 1627 False 2767.000000 2767 97.359000 773 2398 1 chr5A.!!$F1 1625
12 TraesCS3A01G337400 chr3B 581075497 581076104 607 False 300.500000 318 91.983500 1 448 2 chr3B.!!$F1 447

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
753 938 0.033601 TGCTCTCCTCTCCTCACTCC 60.034 60.000 0.0 0.0 0.00 3.85 F
828 1014 2.048222 CATGGTGTCGTGGAGCGT 60.048 61.111 0.0 0.0 42.13 5.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1954 2234 0.764369 ACTCCACACCCTTCTGCTGA 60.764 55.000 0.00 0.0 0.00 4.26 R
2785 3291 2.321720 CCCCTAGGGCCATTCTGTT 58.678 57.895 23.84 0.0 35.35 3.16 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
43 44 6.413269 GCCATTAATTGCTTCTTATTTTGCG 58.587 36.000 4.31 0.00 0.00 4.85
99 100 1.295792 TGCCGTATCATTCGCCTTTC 58.704 50.000 0.00 0.00 0.00 2.62
140 141 1.081556 TTGTAGCGCGCACATACCTG 61.082 55.000 35.10 0.00 0.00 4.00
179 180 2.612212 TCGTTTTGGAAAGTCTGCACTC 59.388 45.455 0.00 0.00 29.93 3.51
181 182 2.687935 GTTTTGGAAAGTCTGCACTCCA 59.312 45.455 0.00 0.00 29.93 3.86
192 193 5.535333 AGTCTGCACTCCAAATTTGATTTG 58.465 37.500 19.86 12.83 46.98 2.32
232 233 3.381045 CAGTCACGCGTGTGGAATATAT 58.619 45.455 35.74 11.59 46.42 0.86
234 235 4.979815 CAGTCACGCGTGTGGAATATATTA 59.020 41.667 35.74 11.84 46.42 0.98
235 236 5.117135 CAGTCACGCGTGTGGAATATATTAG 59.883 44.000 35.74 8.13 46.42 1.73
238 239 3.987868 ACGCGTGTGGAATATATTAGCTG 59.012 43.478 12.93 0.00 0.00 4.24
239 240 3.987868 CGCGTGTGGAATATATTAGCTGT 59.012 43.478 0.00 0.00 0.00 4.40
240 241 4.090066 CGCGTGTGGAATATATTAGCTGTC 59.910 45.833 0.00 0.00 0.00 3.51
241 242 4.389077 GCGTGTGGAATATATTAGCTGTCC 59.611 45.833 0.00 0.00 0.00 4.02
243 244 5.864474 CGTGTGGAATATATTAGCTGTCCTC 59.136 44.000 0.00 0.00 0.00 3.71
244 245 5.864474 GTGTGGAATATATTAGCTGTCCTCG 59.136 44.000 0.00 0.00 0.00 4.63
245 246 5.773176 TGTGGAATATATTAGCTGTCCTCGA 59.227 40.000 0.00 0.00 0.00 4.04
246 247 6.437477 TGTGGAATATATTAGCTGTCCTCGAT 59.563 38.462 0.00 0.00 0.00 3.59
248 249 8.634444 GTGGAATATATTAGCTGTCCTCGATAT 58.366 37.037 0.00 0.00 0.00 1.63
249 250 9.862149 TGGAATATATTAGCTGTCCTCGATATA 57.138 33.333 0.00 0.00 0.00 0.86
266 428 9.322776 CCTCGATATATAAACTTACACACGTAC 57.677 37.037 0.00 0.00 0.00 3.67
268 430 7.530525 TCGATATATAAACTTACACACGTACGC 59.469 37.037 16.72 0.00 0.00 4.42
285 447 3.036429 GCAGCCAAGGACTCCCGAT 62.036 63.158 0.00 0.00 37.58 4.18
317 479 3.021788 GAGCGAGCACGATCGAGC 61.022 66.667 27.02 27.02 44.45 5.03
391 557 4.021925 GGTGGTCCGGCTGCTCTT 62.022 66.667 0.00 0.00 0.00 2.85
401 567 1.365368 GGCTGCTCTTTCTTCTCGCC 61.365 60.000 0.00 0.00 0.00 5.54
437 603 1.065358 CGCTACAAACCCACAGTACG 58.935 55.000 0.00 0.00 0.00 3.67
468 634 5.105997 GCTAGAGTGAATTGCAGAAAACCAT 60.106 40.000 0.00 0.00 0.00 3.55
533 701 8.655970 GTTTTTGCTGTAGAAAACACTGATTTT 58.344 29.630 6.78 0.00 42.43 1.82
534 702 8.770438 TTTTGCTGTAGAAAACACTGATTTTT 57.230 26.923 0.00 0.00 31.90 1.94
753 938 0.033601 TGCTCTCCTCTCCTCACTCC 60.034 60.000 0.00 0.00 0.00 3.85
806 992 2.747855 CCGTTCTGCTGCTTCCCC 60.748 66.667 0.00 0.00 0.00 4.81
828 1014 2.048222 CATGGTGTCGTGGAGCGT 60.048 61.111 0.00 0.00 42.13 5.07
869 1061 2.103941 GTCATGAACATCTCCTCCTCCC 59.896 54.545 0.00 0.00 0.00 4.30
1738 2018 5.698545 GGAGAATTATGACAGTCTGTATGCC 59.301 44.000 5.21 0.00 0.00 4.40
1954 2234 0.851469 ATGCTCTCTTGGATGCCCAT 59.149 50.000 0.00 0.00 43.12 4.00
2083 2363 6.043706 TGTCAAAGAAAGAGGAGGAGAAGAAT 59.956 38.462 0.00 0.00 0.00 2.40
2089 2372 6.443527 AGAAAGAGGAGGAGAAGAATAAGCTT 59.556 38.462 3.48 3.48 0.00 3.74
2298 2581 3.912248 TCTTAGATGAGTAGGGGTGTCC 58.088 50.000 0.00 0.00 0.00 4.02
2785 3291 4.525996 ACCACCATTTCATCGATTCATCA 58.474 39.130 0.00 0.00 0.00 3.07
2877 3599 4.098349 CCATGACCACCATTTCATCGATTT 59.902 41.667 0.00 0.00 31.94 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 3.207265 TGGCGTATGTTTGGCTATCAT 57.793 42.857 0.00 0.00 0.00 2.45
16 17 7.221838 GCAAAATAAGAAGCAATTAATGGCGTA 59.778 33.333 9.20 1.84 34.54 4.42
17 18 6.035975 GCAAAATAAGAAGCAATTAATGGCGT 59.964 34.615 9.20 6.04 34.54 5.68
18 19 6.413269 GCAAAATAAGAAGCAATTAATGGCG 58.587 36.000 9.20 0.00 34.54 5.69
99 100 5.705609 AAGGCATATTAATTTGTAGCCGG 57.294 39.130 0.00 0.00 44.97 6.13
108 109 4.783242 CGCGCTACAAAGGCATATTAATT 58.217 39.130 5.56 0.00 0.00 1.40
109 110 3.364964 GCGCGCTACAAAGGCATATTAAT 60.365 43.478 26.67 0.00 0.00 1.40
110 111 2.032377 GCGCGCTACAAAGGCATATTAA 60.032 45.455 26.67 0.00 0.00 1.40
111 112 1.529438 GCGCGCTACAAAGGCATATTA 59.471 47.619 26.67 0.00 0.00 0.98
192 193 3.658757 TGCTTTAATGGCAGTTGGAAC 57.341 42.857 0.00 0.00 34.56 3.62
213 214 4.143389 GCTAATATATTCCACACGCGTGAC 60.143 45.833 42.94 11.50 46.80 3.67
215 216 3.987868 AGCTAATATATTCCACACGCGTG 59.012 43.478 35.99 35.99 43.21 5.34
218 219 4.389077 GGACAGCTAATATATTCCACACGC 59.611 45.833 0.00 0.00 0.00 5.34
234 235 8.298140 GTGTAAGTTTATATATCGAGGACAGCT 58.702 37.037 0.00 0.00 0.00 4.24
235 236 8.080417 TGTGTAAGTTTATATATCGAGGACAGC 58.920 37.037 0.00 0.00 0.00 4.40
238 239 8.072567 ACGTGTGTAAGTTTATATATCGAGGAC 58.927 37.037 0.00 0.00 0.00 3.85
239 240 8.158169 ACGTGTGTAAGTTTATATATCGAGGA 57.842 34.615 0.00 0.00 0.00 3.71
240 241 9.322776 GTACGTGTGTAAGTTTATATATCGAGG 57.677 37.037 0.00 0.00 30.94 4.63
241 242 9.034299 CGTACGTGTGTAAGTTTATATATCGAG 57.966 37.037 7.22 0.00 30.94 4.04
243 244 7.321034 TGCGTACGTGTGTAAGTTTATATATCG 59.679 37.037 17.90 0.00 33.27 2.92
244 245 8.492920 TGCGTACGTGTGTAAGTTTATATATC 57.507 34.615 17.90 0.00 33.27 1.63
245 246 7.113965 GCTGCGTACGTGTGTAAGTTTATATAT 59.886 37.037 17.90 0.00 33.27 0.86
246 247 6.414694 GCTGCGTACGTGTGTAAGTTTATATA 59.585 38.462 17.90 0.00 33.27 0.86
248 249 4.558470 GCTGCGTACGTGTGTAAGTTTATA 59.442 41.667 17.90 0.00 33.27 0.98
249 250 3.365820 GCTGCGTACGTGTGTAAGTTTAT 59.634 43.478 17.90 0.00 33.27 1.40
250 251 2.725723 GCTGCGTACGTGTGTAAGTTTA 59.274 45.455 17.90 0.00 33.27 2.01
251 252 1.523934 GCTGCGTACGTGTGTAAGTTT 59.476 47.619 17.90 0.00 33.27 2.66
253 254 0.665369 GGCTGCGTACGTGTGTAAGT 60.665 55.000 17.90 0.00 33.27 2.24
254 255 0.665068 TGGCTGCGTACGTGTGTAAG 60.665 55.000 17.90 6.51 33.78 2.34
256 257 0.665068 CTTGGCTGCGTACGTGTGTA 60.665 55.000 17.90 0.00 0.00 2.90
268 430 0.105039 GTATCGGGAGTCCTTGGCTG 59.895 60.000 9.58 0.00 0.00 4.85
285 447 3.139850 CTCGCTCGATCCTTCCTTAGTA 58.860 50.000 0.00 0.00 0.00 1.82
346 508 2.654079 CGGTGAGAGCCTCCTTGCT 61.654 63.158 0.00 0.00 46.37 3.91
391 557 2.742372 GCAAGCCGGCGAGAAGAA 60.742 61.111 23.20 0.00 0.00 2.52
417 583 0.794473 GTACTGTGGGTTTGTAGCGC 59.206 55.000 0.00 0.00 0.00 5.92
419 585 1.435577 CCGTACTGTGGGTTTGTAGC 58.564 55.000 0.00 0.00 0.00 3.58
437 603 2.223665 GCAATTCACTCTAGCCATTGCC 60.224 50.000 4.19 0.00 42.54 4.52
468 634 3.888323 TGCAAACCTAAGCTGAAATGTGA 59.112 39.130 0.00 0.00 0.00 3.58
753 938 2.181021 CGTCGGGGGAGAAGAACG 59.819 66.667 0.00 0.00 0.00 3.95
802 987 3.338250 GACACCATGGCCAGGGGA 61.338 66.667 37.81 0.63 36.39 4.81
806 992 2.747460 CCACGACACCATGGCCAG 60.747 66.667 13.05 4.61 0.00 4.85
828 1014 2.095461 CTGAATCCTCACTGGTCTCGA 58.905 52.381 0.00 0.00 37.07 4.04
1738 2018 2.897436 TCCAAGAGAGCATTGACATCG 58.103 47.619 0.00 0.00 0.00 3.84
1954 2234 0.764369 ACTCCACACCCTTCTGCTGA 60.764 55.000 0.00 0.00 0.00 4.26
2083 2363 6.467677 AGTCTCATACTTTTGCAGAAGCTTA 58.532 36.000 16.43 3.59 36.99 3.09
2089 2372 6.434340 TCACTAGAGTCTCATACTTTTGCAGA 59.566 38.462 0.00 0.00 39.07 4.26
2785 3291 2.321720 CCCCTAGGGCCATTCTGTT 58.678 57.895 23.84 0.00 35.35 3.16
2856 3578 7.206981 GATAAATCGATGAAATGGTGGTCAT 57.793 36.000 0.00 0.00 37.19 3.06


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

AutoCloner maintained by Alex Coulton.