Multiple sequence alignment - TraesCS7A01G404500

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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 TraesCS7A01G404500 chr7A 100.000 2466 0 0 1 2466 586212912 586210447 0.000000e+00 4554.0
1 TraesCS7A01G404500 chr7A 76.033 1452 199 66 1077 2443 122867726 122869113 1.250000e-172 616.0
2 TraesCS7A01G404500 chr2A 99.354 1704 10 1 763 2466 74248121 74249823 0.000000e+00 3085.0
3 TraesCS7A01G404500 chr2A 96.078 51 2 0 753 803 509372719 509372669 1.570000e-12 84.2
4 TraesCS7A01G404500 chr5B 92.468 770 28 15 2 751 172632953 172633712 0.000000e+00 1074.0
5 TraesCS7A01G404500 chr1A 75.238 1680 241 87 867 2443 336309249 336310856 9.620000e-179 636.0
6 TraesCS7A01G404500 chr1A 89.562 297 18 7 1 290 540874889 540875179 5.010000e-97 364.0
7 TraesCS7A01G404500 chr1A 87.742 310 23 8 290 588 540884802 540885107 5.050000e-92 348.0
8 TraesCS7A01G404500 chr4B 75.895 1452 201 66 1077 2443 403388219 403386832 2.710000e-169 604.0
9 TraesCS7A01G404500 chr4B 84.615 481 48 16 290 751 233498256 233497783 2.890000e-124 455.0
10 TraesCS7A01G404500 chr4B 87.500 344 27 10 313 650 512740059 512740392 1.380000e-102 383.0
11 TraesCS7A01G404500 chr4B 77.055 584 89 25 1077 1640 382240098 382239540 6.670000e-76 294.0
12 TraesCS7A01G404500 chr4B 82.877 292 31 7 1 289 512739409 512739684 6.810000e-61 244.0
13 TraesCS7A01G404500 chr4B 86.339 183 20 1 1 183 233498884 233498707 6.960000e-46 195.0
14 TraesCS7A01G404500 chr4B 87.611 113 14 0 1643 1755 382239482 382239370 5.530000e-27 132.0
15 TraesCS7A01G404500 chr6A 74.866 1679 248 90 867 2443 501068282 501069888 9.760000e-169 603.0
16 TraesCS7A01G404500 chr3B 75.760 1448 194 71 1077 2443 56739549 56740920 3.530000e-163 584.0
17 TraesCS7A01G404500 chr3D 91.599 369 20 8 290 650 489374814 489374449 1.320000e-137 499.0
18 TraesCS7A01G404500 chr3D 89.384 292 23 4 1 289 489375351 489375065 6.480000e-96 361.0
19 TraesCS7A01G404500 chr6B 87.310 394 39 8 290 677 88373771 88373383 8.090000e-120 440.0
20 TraesCS7A01G404500 chr6B 87.056 394 40 8 290 677 88445032 88444644 3.770000e-118 435.0
21 TraesCS7A01G404500 chr6B 82.258 310 32 9 1 292 88445579 88445275 1.890000e-61 246.0
22 TraesCS7A01G404500 chr6B 81.935 310 33 9 1 292 88374318 88374014 8.810000e-60 241.0
23 TraesCS7A01G404500 chr6B 94.643 56 3 0 748 803 720445217 720445162 1.210000e-13 87.9
24 TraesCS7A01G404500 chr6B 95.745 47 2 0 748 794 691737398 691737444 2.630000e-10 76.8
25 TraesCS7A01G404500 chr2B 85.204 392 42 5 290 677 647446732 647446353 2.970000e-104 388.0
26 TraesCS7A01G404500 chr2B 85.526 304 23 9 1 289 647447281 647446984 5.160000e-77 298.0
27 TraesCS7A01G404500 chr2B 80.337 356 40 23 290 643 219909431 219909104 2.450000e-60 243.0
28 TraesCS7A01G404500 chr3A 84.211 361 40 6 290 645 735394633 735394285 3.930000e-88 335.0
29 TraesCS7A01G404500 chr3A 85.526 304 24 8 1 289 735395183 735394885 1.430000e-77 300.0
30 TraesCS7A01G404500 chrUn 84.179 335 37 6 290 620 476524769 476525091 6.620000e-81 311.0
31 TraesCS7A01G404500 chrUn 84.921 126 15 2 290 415 475728243 475728122 9.260000e-25 124.0
32 TraesCS7A01G404500 chr1B 95.918 49 2 0 748 796 30064946 30064898 2.030000e-11 80.5
33 TraesCS7A01G404500 chr4A 91.228 57 5 0 748 804 539131982 539131926 7.310000e-11 78.7
34 TraesCS7A01G404500 chr4A 96.970 33 0 1 653 685 577986299 577986330 1.000000e-03 54.7
35 TraesCS7A01G404500 chr4A 100.000 28 0 0 658 685 121018626 121018599 4.000000e-03 52.8
36 TraesCS7A01G404500 chr7B 94.000 50 3 0 748 797 453203120 453203071 2.630000e-10 76.8
37 TraesCS7A01G404500 chr7B 87.097 62 8 0 748 809 263149064 263149003 1.220000e-08 71.3
38 TraesCS7A01G404500 chr5A 94.000 50 3 0 748 797 72621054 72621005 2.630000e-10 76.8


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 TraesCS7A01G404500 chr7A 586210447 586212912 2465 True 4554.0 4554 100.0000 1 2466 1 chr7A.!!$R1 2465
1 TraesCS7A01G404500 chr7A 122867726 122869113 1387 False 616.0 616 76.0330 1077 2443 1 chr7A.!!$F1 1366
2 TraesCS7A01G404500 chr2A 74248121 74249823 1702 False 3085.0 3085 99.3540 763 2466 1 chr2A.!!$F1 1703
3 TraesCS7A01G404500 chr5B 172632953 172633712 759 False 1074.0 1074 92.4680 2 751 1 chr5B.!!$F1 749
4 TraesCS7A01G404500 chr1A 336309249 336310856 1607 False 636.0 636 75.2380 867 2443 1 chr1A.!!$F1 1576
5 TraesCS7A01G404500 chr4B 403386832 403388219 1387 True 604.0 604 75.8950 1077 2443 1 chr4B.!!$R1 1366
6 TraesCS7A01G404500 chr4B 233497783 233498884 1101 True 325.0 455 85.4770 1 751 2 chr4B.!!$R2 750
7 TraesCS7A01G404500 chr4B 512739409 512740392 983 False 313.5 383 85.1885 1 650 2 chr4B.!!$F1 649
8 TraesCS7A01G404500 chr4B 382239370 382240098 728 True 213.0 294 82.3330 1077 1755 2 chr4B.!!$R3 678
9 TraesCS7A01G404500 chr6A 501068282 501069888 1606 False 603.0 603 74.8660 867 2443 1 chr6A.!!$F1 1576
10 TraesCS7A01G404500 chr3B 56739549 56740920 1371 False 584.0 584 75.7600 1077 2443 1 chr3B.!!$F1 1366
11 TraesCS7A01G404500 chr3D 489374449 489375351 902 True 430.0 499 90.4915 1 650 2 chr3D.!!$R1 649
12 TraesCS7A01G404500 chr6B 88373383 88374318 935 True 340.5 440 84.6225 1 677 2 chr6B.!!$R2 676
13 TraesCS7A01G404500 chr6B 88444644 88445579 935 True 340.5 435 84.6570 1 677 2 chr6B.!!$R3 676
14 TraesCS7A01G404500 chr2B 647446353 647447281 928 True 343.0 388 85.3650 1 677 2 chr2B.!!$R2 676
15 TraesCS7A01G404500 chr3A 735394285 735395183 898 True 317.5 335 84.8685 1 645 2 chr3A.!!$R1 644

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
212 313 0.865769 GCAGTGTGTACGTCTTTGGG 59.134 55.0 0.0 0.0 0.0 4.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1739 2417 6.974932 ATTAGCACTTGTGTACATCTTGAG 57.025 37.5 0.0 0.0 0.0 3.02 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
155 166 4.142182 CCATCCGATTGTTTTTAGGTGCAT 60.142 41.667 0.00 0.00 0.00 3.96
197 298 7.255242 CCATCCGATCTAATTTGTAAATGCAGT 60.255 37.037 0.00 0.00 0.00 4.40
203 304 9.490663 GATCTAATTTGTAAATGCAGTGTGTAC 57.509 33.333 0.00 0.00 0.00 2.90
212 313 0.865769 GCAGTGTGTACGTCTTTGGG 59.134 55.000 0.00 0.00 0.00 4.12
227 349 2.589724 GGGTACATTACGCCGCCC 60.590 66.667 0.00 0.00 35.79 6.13
327 825 4.537015 TGATGACGTATATGTTCTCTGCG 58.463 43.478 0.00 0.00 0.00 5.18
377 875 7.058525 TCCTTCTGATGCATATGAACTGATTT 58.941 34.615 6.97 0.00 0.00 2.17
457 962 8.043113 TGGATGAATGCATATATGTACTCCTTC 58.957 37.037 14.14 10.34 34.11 3.46
520 1027 2.648059 AGAAACTGCAGCACACTCTTT 58.352 42.857 15.27 4.64 0.00 2.52
651 1165 4.769688 TGGCAGTACATACTCCTTGAATG 58.230 43.478 0.00 0.00 33.46 2.67
702 1228 7.783042 ACTACTTAAAAGGCTGTATAGACCTG 58.217 38.462 3.83 0.00 32.89 4.00
760 1287 6.755206 GCGTTGGGCACATATATATATAGGA 58.245 40.000 18.72 0.00 42.87 2.94
761 1288 7.214381 GCGTTGGGCACATATATATATAGGAA 58.786 38.462 18.72 2.34 42.87 3.36
780 1307 8.865244 ATAGGAAAATGGGTTAGTACTCCTAA 57.135 34.615 0.00 0.00 37.73 2.69
834 1361 2.430546 TTTTGTTTGCCCGTGCTATG 57.569 45.000 0.00 0.00 38.71 2.23
1739 2417 6.366061 CAGCTGCCTAAATAAACTTTTGTTCC 59.634 38.462 0.00 0.00 42.67 3.62
1981 2668 5.932883 TGCAATGCATGTAAATTTGTGTGAT 59.067 32.000 2.72 0.00 31.71 3.06
2067 2765 9.905713 AGACATAATCCTTTTCTTTGTAGCATA 57.094 29.630 0.00 0.00 0.00 3.14
2122 2823 5.817816 AGTCCTTTTTGCTTGATCGGTATAG 59.182 40.000 0.00 0.00 0.00 1.31
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 114 9.589461 TCCCTAATTGTTTACCAGAATTTGTAA 57.411 29.630 0.00 0.00 0.00 2.41
104 115 9.762381 ATCCCTAATTGTTTACCAGAATTTGTA 57.238 29.630 0.00 0.00 0.00 2.41
105 116 8.531146 CATCCCTAATTGTTTACCAGAATTTGT 58.469 33.333 0.00 0.00 0.00 2.83
155 166 6.462552 TCGGATGGCATTAATTCATTGAAA 57.537 33.333 0.00 0.00 0.00 2.69
197 298 4.339872 AATGTACCCAAAGACGTACACA 57.660 40.909 2.40 0.00 45.52 3.72
203 304 1.662122 GGCGTAATGTACCCAAAGACG 59.338 52.381 0.00 0.00 0.00 4.18
212 313 2.589724 GGGGGCGGCGTAATGTAC 60.590 66.667 9.37 0.00 0.00 2.90
427 930 9.387257 GAGTACATATATGCATTCATCCATTCA 57.613 33.333 12.79 0.00 34.22 2.57
677 1191 7.399478 ACAGGTCTATACAGCCTTTTAAGTAGT 59.601 37.037 0.00 0.00 0.00 2.73
678 1192 7.783042 ACAGGTCTATACAGCCTTTTAAGTAG 58.217 38.462 0.00 0.00 0.00 2.57
680 1194 6.622427 ACAGGTCTATACAGCCTTTTAAGT 57.378 37.500 0.00 0.00 0.00 2.24
681 1195 7.923414 AAACAGGTCTATACAGCCTTTTAAG 57.077 36.000 0.00 0.00 0.00 1.85
754 1281 9.956558 TTAGGAGTACTAACCCATTTTCCTATA 57.043 33.333 0.00 0.00 36.76 1.31
755 1282 8.865244 TTAGGAGTACTAACCCATTTTCCTAT 57.135 34.615 0.00 0.00 36.76 2.57
756 1283 8.683776 TTTAGGAGTACTAACCCATTTTCCTA 57.316 34.615 0.00 0.00 41.24 2.94
757 1284 7.578458 TTTAGGAGTACTAACCCATTTTCCT 57.422 36.000 0.00 0.00 41.24 3.36
758 1285 7.886970 ACTTTTAGGAGTACTAACCCATTTTCC 59.113 37.037 0.00 0.00 41.24 3.13
759 1286 8.859236 ACTTTTAGGAGTACTAACCCATTTTC 57.141 34.615 0.00 0.00 41.24 2.29
761 1288 9.901172 CATACTTTTAGGAGTACTAACCCATTT 57.099 33.333 0.00 0.00 41.24 2.32
780 1307 5.709164 AGACGTGTGTAGGAGTACATACTTT 59.291 40.000 0.00 0.00 44.83 2.66
818 1345 1.677300 CCCATAGCACGGGCAAACA 60.677 57.895 14.57 0.00 44.61 2.83
892 1420 5.360714 ACCACATTAAAATCGGAGCAATGAT 59.639 36.000 9.31 0.00 32.29 2.45
1739 2417 6.974932 ATTAGCACTTGTGTACATCTTGAG 57.025 37.500 0.00 0.00 0.00 3.02
1784 2462 8.641498 ACTTCTCAATTTGTTTACATCAGGAT 57.359 30.769 0.00 0.00 0.00 3.24
2067 2765 8.926092 ACTACTTTTAGATCTTCAAAAAGGCT 57.074 30.769 23.59 12.49 42.05 4.58
2068 2766 9.399403 CAACTACTTTTAGATCTTCAAAAAGGC 57.601 33.333 23.59 0.00 42.05 4.35


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

AutoCloner maintained by Alex Coulton.