Multiple sequence alignment - TraesCS3B01G173600

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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 TraesCS3B01G173600 chr3B 100.000 3383 0 0 1 3383 173888291 173891673 0.000000e+00 6248
1 TraesCS3B01G173600 chr3B 95.980 2438 92 6 17 2450 39816313 39818748 0.000000e+00 3954
2 TraesCS3B01G173600 chr3B 94.725 891 38 4 2492 3374 669907337 669908226 0.000000e+00 1376
3 TraesCS3B01G173600 chr3B 96.364 110 4 0 2408 2517 669825288 669825179 7.460000e-42 182
4 TraesCS3B01G173600 chr7B 94.756 2517 109 14 6 2517 139542654 139540156 0.000000e+00 3895
5 TraesCS3B01G173600 chr7B 93.537 294 18 1 2492 2785 632469331 632469039 1.440000e-118 436
6 TraesCS3B01G173600 chr7B 95.455 110 5 0 2408 2517 327260168 327260277 3.470000e-40 176
7 TraesCS3B01G173600 chr7A 95.926 2381 85 5 6 2382 211291835 211294207 0.000000e+00 3849
8 TraesCS3B01G173600 chr7A 95.455 110 5 0 2408 2517 60194941 60194832 3.470000e-40 176
9 TraesCS3B01G173600 chr6B 95.975 2360 91 4 6 2361 625641652 625639293 0.000000e+00 3829
10 TraesCS3B01G173600 chr6B 94.407 894 47 3 2492 3383 264977531 264976639 0.000000e+00 1371
11 TraesCS3B01G173600 chr6B 93.870 783 32 6 2609 3383 606999046 606999820 0.000000e+00 1166
12 TraesCS3B01G173600 chr5A 95.899 2341 87 8 6 2339 534933325 534935663 0.000000e+00 3783
13 TraesCS3B01G173600 chr5A 96.404 2002 68 4 418 2415 647029609 647031610 0.000000e+00 3295
14 TraesCS3B01G173600 chr5A 95.455 110 5 0 2408 2517 16532395 16532504 3.470000e-40 176
15 TraesCS3B01G173600 chr2B 96.730 2202 67 4 139 2335 357718975 357716774 0.000000e+00 3663
16 TraesCS3B01G173600 chr2B 96.143 2204 74 9 139 2335 357344748 357342549 0.000000e+00 3589
17 TraesCS3B01G173600 chr2B 96.014 1756 63 7 6 1756 357429713 357431466 0.000000e+00 2848
18 TraesCS3B01G173600 chr2B 95.546 898 34 3 2492 3383 526491719 526490822 0.000000e+00 1432
19 TraesCS3B01G173600 chr2B 95.117 901 35 4 2492 3383 357458642 357459542 0.000000e+00 1411
20 TraesCS3B01G173600 chr2B 94.989 898 39 3 2492 3383 357336005 357336902 0.000000e+00 1404
21 TraesCS3B01G173600 chrUn 97.197 1677 38 6 747 2414 221548123 221546447 0.000000e+00 2828
22 TraesCS3B01G173600 chrUn 96.854 731 15 4 2657 3383 403405171 403405897 0.000000e+00 1216
23 TraesCS3B01G173600 chrUn 95.455 110 5 0 2408 2517 182442711 182442820 3.470000e-40 176
24 TraesCS3B01G173600 chrUn 95.455 110 5 0 2408 2517 222872361 222872470 3.470000e-40 176
25 TraesCS3B01G173600 chr3A 96.702 1698 53 3 747 2441 51916454 51918151 0.000000e+00 2822
26 TraesCS3B01G173600 chr6A 95.861 894 35 2 2492 3383 597224281 597225174 0.000000e+00 1445
27 TraesCS3B01G173600 chr4A 92.729 894 55 5 2492 3383 199398744 199399629 0.000000e+00 1282
28 TraesCS3B01G173600 chr4D 92.764 539 28 5 2493 3029 285137400 285137929 0.000000e+00 769
29 TraesCS3B01G173600 chr5B 95.455 110 5 0 2408 2517 130583512 130583403 3.470000e-40 176
30 TraesCS3B01G173600 chr4B 95.455 110 5 0 2408 2517 209218385 209218494 3.470000e-40 176
31 TraesCS3B01G173600 chr1B 95.455 110 5 0 2408 2517 583573732 583573623 3.470000e-40 176


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 TraesCS3B01G173600 chr3B 173888291 173891673 3382 False 6248 6248 100.000 1 3383 1 chr3B.!!$F2 3382
1 TraesCS3B01G173600 chr3B 39816313 39818748 2435 False 3954 3954 95.980 17 2450 1 chr3B.!!$F1 2433
2 TraesCS3B01G173600 chr3B 669907337 669908226 889 False 1376 1376 94.725 2492 3374 1 chr3B.!!$F3 882
3 TraesCS3B01G173600 chr7B 139540156 139542654 2498 True 3895 3895 94.756 6 2517 1 chr7B.!!$R1 2511
4 TraesCS3B01G173600 chr7A 211291835 211294207 2372 False 3849 3849 95.926 6 2382 1 chr7A.!!$F1 2376
5 TraesCS3B01G173600 chr6B 625639293 625641652 2359 True 3829 3829 95.975 6 2361 1 chr6B.!!$R2 2355
6 TraesCS3B01G173600 chr6B 264976639 264977531 892 True 1371 1371 94.407 2492 3383 1 chr6B.!!$R1 891
7 TraesCS3B01G173600 chr6B 606999046 606999820 774 False 1166 1166 93.870 2609 3383 1 chr6B.!!$F1 774
8 TraesCS3B01G173600 chr5A 534933325 534935663 2338 False 3783 3783 95.899 6 2339 1 chr5A.!!$F2 2333
9 TraesCS3B01G173600 chr5A 647029609 647031610 2001 False 3295 3295 96.404 418 2415 1 chr5A.!!$F3 1997
10 TraesCS3B01G173600 chr2B 357716774 357718975 2201 True 3663 3663 96.730 139 2335 1 chr2B.!!$R2 2196
11 TraesCS3B01G173600 chr2B 357342549 357344748 2199 True 3589 3589 96.143 139 2335 1 chr2B.!!$R1 2196
12 TraesCS3B01G173600 chr2B 357429713 357431466 1753 False 2848 2848 96.014 6 1756 1 chr2B.!!$F2 1750
13 TraesCS3B01G173600 chr2B 526490822 526491719 897 True 1432 1432 95.546 2492 3383 1 chr2B.!!$R3 891
14 TraesCS3B01G173600 chr2B 357458642 357459542 900 False 1411 1411 95.117 2492 3383 1 chr2B.!!$F3 891
15 TraesCS3B01G173600 chr2B 357336005 357336902 897 False 1404 1404 94.989 2492 3383 1 chr2B.!!$F1 891
16 TraesCS3B01G173600 chrUn 221546447 221548123 1676 True 2828 2828 97.197 747 2414 1 chrUn.!!$R1 1667
17 TraesCS3B01G173600 chrUn 403405171 403405897 726 False 1216 1216 96.854 2657 3383 1 chrUn.!!$F3 726
18 TraesCS3B01G173600 chr3A 51916454 51918151 1697 False 2822 2822 96.702 747 2441 1 chr3A.!!$F1 1694
19 TraesCS3B01G173600 chr6A 597224281 597225174 893 False 1445 1445 95.861 2492 3383 1 chr6A.!!$F1 891
20 TraesCS3B01G173600 chr4A 199398744 199399629 885 False 1282 1282 92.729 2492 3383 1 chr4A.!!$F1 891
21 TraesCS3B01G173600 chr4D 285137400 285137929 529 False 769 769 92.764 2493 3029 1 chr4D.!!$F1 536

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
180 181 0.252742 ACCGGAGATTCAAGACCCCT 60.253 55.0 9.46 0.0 0.0 4.79 F
648 650 1.246737 CCCAAGAGCAAGGCAAGTCC 61.247 60.0 0.00 0.0 0.0 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1320 1331 0.238289 CAGGTCCACGCATGTTGAAC 59.762 55.0 0.0 0.0 0.00 3.18 R
2470 2492 0.827925 CTCCCTACATCTGCGGGCTA 60.828 60.0 0.0 0.0 37.89 3.93 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
136 137 5.538118 TCTTTCTAGTTTGTGCTTCATCGA 58.462 37.500 0.00 0.00 0.00 3.59
180 181 0.252742 ACCGGAGATTCAAGACCCCT 60.253 55.000 9.46 0.00 0.00 4.79
199 200 4.156477 CCCTAGGCTCTAGCTCATTTAGT 58.844 47.826 2.05 0.00 41.70 2.24
200 201 4.021544 CCCTAGGCTCTAGCTCATTTAGTG 60.022 50.000 2.05 0.00 41.70 2.74
222 223 5.363005 GTGGGGCTAAACTTCTATCTGAGTA 59.637 44.000 0.00 0.00 0.00 2.59
250 251 1.707427 GCAGGATCTGGGATGGGTTAT 59.293 52.381 0.00 0.00 31.21 1.89
373 374 5.573219 AGATGTCATTCAGGAATTTGTGGA 58.427 37.500 0.00 0.00 0.00 4.02
397 398 4.950475 GCTTTATCAAAGAGTAGGGCCTTT 59.050 41.667 13.45 0.00 41.02 3.11
398 399 5.066634 GCTTTATCAAAGAGTAGGGCCTTTC 59.933 44.000 13.45 10.71 41.02 2.62
445 447 2.686405 TGAAGCGCTTCGTTCCTATCTA 59.314 45.455 37.03 18.36 42.28 1.98
648 650 1.246737 CCCAAGAGCAAGGCAAGTCC 61.247 60.000 0.00 0.00 0.00 3.85
742 750 4.929146 AAGTGGGGTAGCTCAGTAATTT 57.071 40.909 1.76 0.00 0.00 1.82
838 847 5.808366 AATATGGTTCGATGGCTCTTCTA 57.192 39.130 0.00 0.00 0.00 2.10
925 934 3.195610 ACATGCTTCTCCGTACTGATTCA 59.804 43.478 0.00 0.00 0.00 2.57
987 996 9.736023 GTGGGAATCATCAACTTTATAATGTTC 57.264 33.333 12.48 2.36 0.00 3.18
1388 1399 2.244695 TGTGTGGTCCGTTCTAGTGAT 58.755 47.619 0.00 0.00 0.00 3.06
1418 1429 8.652810 TTCCTACTTTTATTATCACTTACGGC 57.347 34.615 0.00 0.00 0.00 5.68
1612 1625 3.533547 TCGACCTTTTCAAGAAAACCGA 58.466 40.909 3.98 9.98 35.57 4.69
1786 1800 8.742777 CAGGAATCAAAATCTTTAGTTGGATCA 58.257 33.333 0.00 0.00 0.00 2.92
1958 1972 7.063308 GGTTGCACATTTCCATTATGTACTTTG 59.937 37.037 0.00 0.00 34.59 2.77
2026 2041 3.189910 GGGTAAAATCTTTGGTCGGACAC 59.810 47.826 10.76 0.17 0.00 3.67
2112 2128 1.684983 CCCATGCATTTCTTAGGGCTG 59.315 52.381 0.00 0.00 0.00 4.85
2244 2260 3.466836 AGTTGTCGCAATCACTTCAAGA 58.533 40.909 0.00 0.00 0.00 3.02
2378 2394 4.035909 TCCTGCGGTAAAAGAGACAAAAAC 59.964 41.667 0.00 0.00 0.00 2.43
2426 2448 2.681097 GCCTCTTTCTGGCTCCGTATTT 60.681 50.000 0.00 0.00 46.38 1.40
2427 2449 3.198872 CCTCTTTCTGGCTCCGTATTTC 58.801 50.000 0.00 0.00 0.00 2.17
2428 2450 3.118592 CCTCTTTCTGGCTCCGTATTTCT 60.119 47.826 0.00 0.00 0.00 2.52
2434 2456 4.021229 TCTGGCTCCGTATTTCTAACTCA 58.979 43.478 0.00 0.00 0.00 3.41
2521 2543 8.173292 CTCTTGAACTGAGAAATCAAAGGGACT 61.173 40.741 0.00 0.00 34.79 3.85
2565 2587 4.684485 CGGCTCTTATCTGGTTTGAATCCT 60.684 45.833 0.00 0.00 0.00 3.24
2748 2788 8.074370 TCGTTTCATATATGCGCTAGGATATAC 58.926 37.037 9.73 0.00 43.30 1.47
2857 2899 6.423905 TGAAGGTCGAAATGTCTAGTTTGAAG 59.576 38.462 0.00 0.00 0.00 3.02
2959 3001 5.105756 CCCGTTCAATTGAAATAGCTTCCTT 60.106 40.000 22.07 0.00 35.58 3.36
2989 3031 5.103000 CAGTTCGATACCCACTGAAACTAG 58.897 45.833 8.23 0.00 40.43 2.57
3086 3131 9.114952 GAAATAAAGAGGACCTTCTTAATCCTG 57.885 37.037 0.00 0.00 43.12 3.86
3158 3203 3.414700 CCAACTCGACACGGCTGC 61.415 66.667 0.00 0.00 0.00 5.25
3309 3354 2.040939 AGGAGAGATGCAGACCAGATG 58.959 52.381 0.00 0.00 0.00 2.90
3376 3421 5.066634 GTCTGTGGAAGAGAAGTATCGATCA 59.933 44.000 0.00 0.00 38.31 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
118 119 3.123621 GGTGTCGATGAAGCACAAACTAG 59.876 47.826 5.60 0.00 35.05 2.57
124 125 0.037326 GGAGGTGTCGATGAAGCACA 60.037 55.000 5.60 0.00 35.05 4.57
136 137 3.513515 GAGAGTGATCAGAAAGGAGGTGT 59.486 47.826 0.00 0.00 0.00 4.16
180 181 3.898123 CCCACTAAATGAGCTAGAGCCTA 59.102 47.826 0.00 0.00 43.38 3.93
199 200 4.362677 ACTCAGATAGAAGTTTAGCCCCA 58.637 43.478 0.00 0.00 0.00 4.96
200 201 6.673839 ATACTCAGATAGAAGTTTAGCCCC 57.326 41.667 0.00 0.00 0.00 5.80
222 223 2.398588 TCCCAGATCCTGCTCGTAAAT 58.601 47.619 0.00 0.00 0.00 1.40
373 374 3.783082 AGGCCCTACTCTTTGATAAAGCT 59.217 43.478 0.00 0.00 38.39 3.74
397 398 1.826921 GTAGGGCTCGATCGGTGGA 60.827 63.158 16.41 0.00 0.00 4.02
398 399 1.392710 AAGTAGGGCTCGATCGGTGG 61.393 60.000 16.41 7.25 0.00 4.61
445 447 6.715280 AGAATCAGTTGTGTGAATATGGTCT 58.285 36.000 0.00 0.00 0.00 3.85
580 582 0.984230 CTTCCAGGCACCTCCTTGTA 59.016 55.000 0.00 0.00 44.75 2.41
581 583 1.062488 ACTTCCAGGCACCTCCTTGT 61.062 55.000 0.00 0.00 44.75 3.16
648 650 1.075425 CTCGTGCTCAGCTCTTTCGG 61.075 60.000 0.00 0.00 0.00 4.30
742 750 4.082125 GGGCTGGAAGAGAAAAGAATCAA 58.918 43.478 0.00 0.00 34.07 2.57
838 847 6.619852 AGTCCCAATATCCTTGTGGTTAGTAT 59.380 38.462 0.00 0.00 34.23 2.12
925 934 1.278127 CGGGTCGGGCTAATTCCATAT 59.722 52.381 0.00 0.00 0.00 1.78
948 957 6.441284 TGATGATTCCCACCAAGAATTTGATT 59.559 34.615 0.00 0.00 36.36 2.57
1009 1018 7.212274 GCCAGCATAACCATAAAAAGATCATT 58.788 34.615 0.00 0.00 0.00 2.57
1011 1020 5.221028 CGCCAGCATAACCATAAAAAGATCA 60.221 40.000 0.00 0.00 0.00 2.92
1012 1021 5.008613 TCGCCAGCATAACCATAAAAAGATC 59.991 40.000 0.00 0.00 0.00 2.75
1013 1022 4.887071 TCGCCAGCATAACCATAAAAAGAT 59.113 37.500 0.00 0.00 0.00 2.40
1014 1023 4.265893 TCGCCAGCATAACCATAAAAAGA 58.734 39.130 0.00 0.00 0.00 2.52
1015 1024 4.630894 TCGCCAGCATAACCATAAAAAG 57.369 40.909 0.00 0.00 0.00 2.27
1320 1331 0.238289 CAGGTCCACGCATGTTGAAC 59.762 55.000 0.00 0.00 0.00 3.18
1418 1429 2.044451 TAATTGCCCCCGCCAGTG 60.044 61.111 0.00 0.00 0.00 3.66
1612 1625 3.983410 ACCATGCCTAGATACCCAAAGAT 59.017 43.478 0.00 0.00 0.00 2.40
1786 1800 1.286248 GAACCTCCCCACATGGTAGT 58.714 55.000 0.00 0.00 33.17 2.73
2026 2041 5.394553 GGATTTGGCCTAAAGTTTCAGGATG 60.395 44.000 3.32 0.00 33.42 3.51
2067 2082 3.585732 AGAAGGTCAGATTAACCCCGAAA 59.414 43.478 0.00 0.00 37.52 3.46
2112 2128 2.244651 GCGACATGGCATACCCGAC 61.245 63.158 16.04 6.71 35.87 4.79
2378 2394 4.402793 AGTTAGGACATATATGCGCCTAGG 59.597 45.833 23.48 3.67 38.52 3.02
2426 2448 7.333423 CCGACACTAAATCCAATTTGAGTTAGA 59.667 37.037 24.97 0.00 42.55 2.10
2427 2449 7.464358 CCGACACTAAATCCAATTTGAGTTAG 58.536 38.462 19.48 19.48 44.39 2.34
2428 2450 6.128117 GCCGACACTAAATCCAATTTGAGTTA 60.128 38.462 0.00 0.32 33.82 2.24
2434 2456 3.443681 CCAGCCGACACTAAATCCAATTT 59.556 43.478 0.00 0.00 36.29 1.82
2470 2492 0.827925 CTCCCTACATCTGCGGGCTA 60.828 60.000 0.00 0.00 37.89 3.93
2521 2543 3.551846 GTGTGTTCCCTTCTTTCCAAGA 58.448 45.455 0.00 0.00 35.26 3.02
2823 2863 0.838554 TTCGACCTTCATCCCACCCA 60.839 55.000 0.00 0.00 0.00 4.51
3031 3073 6.420913 TCAACAAGAAAGACTTAGTAGCCT 57.579 37.500 0.00 0.00 37.03 4.58
3036 3078 5.701290 CCGGAATCAACAAGAAAGACTTAGT 59.299 40.000 0.00 0.00 37.03 2.24
3158 3203 0.667487 AGTGAACAGGCGTCATCGTG 60.667 55.000 0.00 0.00 39.49 4.35
3309 3354 7.573968 ATTTACAGAGTATTCTTGCATTCCC 57.426 36.000 0.00 0.00 0.00 3.97
3347 3392 6.970043 CGATACTTCTCTTCCACAGACTAAAG 59.030 42.308 0.00 0.00 0.00 1.85


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

AutoCloner maintained by Alex Coulton.