Multiple sequence alignment - TraesCS3A01G321600

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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 TraesCS3A01G321600 chr3A 100.000 3800 0 0 1 3800 565328991 565332790 0.000000e+00 7018.0
1 TraesCS3A01G321600 chr3A 98.886 898 5 1 2903 3800 565339153 565340045 0.000000e+00 1598.0
2 TraesCS3A01G321600 chr3A 98.370 184 2 1 637 820 565343531 565343713 4.740000e-84 322.0
3 TraesCS3A01G321600 chr7B 98.726 2277 29 0 627 2903 73926582 73924306 0.000000e+00 4045.0
4 TraesCS3A01G321600 chr2B 98.680 2273 28 2 631 2903 138123824 138121554 0.000000e+00 4030.0
5 TraesCS3A01G321600 chr2B 97.669 901 6 8 2901 3800 589941367 589942253 0.000000e+00 1533.0
6 TraesCS3A01G321600 chr2B 97.553 899 6 7 2903 3800 501751254 501750371 0.000000e+00 1524.0
7 TraesCS3A01G321600 chr2B 92.600 527 31 2 2339 2864 776687410 776687929 0.000000e+00 750.0
8 TraesCS3A01G321600 chr2B 93.023 43 3 0 2865 2907 697436865 697436823 3.170000e-06 63.9
9 TraesCS3A01G321600 chr3B 97.809 1506 30 1 1401 2903 646716370 646714865 0.000000e+00 2595.0
10 TraesCS3A01G321600 chr3B 97.556 900 6 5 2902 3800 714554014 714553130 0.000000e+00 1526.0
11 TraesCS3A01G321600 chr3B 97.553 899 7 6 2903 3800 50612766 50611882 0.000000e+00 1524.0
12 TraesCS3A01G321600 chr3B 94.150 718 37 3 623 1338 646717079 646716365 0.000000e+00 1088.0
13 TraesCS3A01G321600 chr3B 90.774 607 44 7 1 606 552893295 552893890 0.000000e+00 800.0
14 TraesCS3A01G321600 chr3B 83.019 530 64 15 646 1158 129297964 129298484 1.240000e-124 457.0
15 TraesCS3A01G321600 chr3B 85.668 307 31 9 1939 2241 60257578 60257281 1.030000e-80 311.0
16 TraesCS3A01G321600 chr1A 96.547 1506 28 2 1401 2903 111989620 111988136 0.000000e+00 2471.0
17 TraesCS3A01G321600 chr1A 97.453 903 8 7 2903 3800 374260552 374261444 0.000000e+00 1526.0
18 TraesCS3A01G321600 chr1A 94.937 711 28 3 629 1338 111990318 111989615 0.000000e+00 1107.0
19 TraesCS3A01G321600 chr1A 86.986 146 13 4 636 777 357177802 357177945 3.930000e-35 159.0
20 TraesCS3A01G321600 chr1B 97.667 900 9 4 2901 3800 516943858 516942971 0.000000e+00 1535.0
21 TraesCS3A01G321600 chr1B 89.006 473 43 5 2396 2864 572288837 572288370 9.150000e-161 577.0
22 TraesCS3A01G321600 chr1B 79.042 167 29 3 604 769 616613146 616612985 4.010000e-20 110.0
23 TraesCS3A01G321600 chr1B 95.349 43 2 0 2865 2907 223853333 223853291 6.810000e-08 69.4
24 TraesCS3A01G321600 chr1B 97.436 39 1 0 2865 2903 130938746 130938708 2.450000e-07 67.6
25 TraesCS3A01G321600 chr1B 97.436 39 1 0 2865 2903 575124533 575124571 2.450000e-07 67.6
26 TraesCS3A01G321600 chr7A 97.550 898 7 6 2903 3800 595196023 595195141 0.000000e+00 1522.0
27 TraesCS3A01G321600 chr5A 96.937 914 10 6 2890 3800 391600398 391599500 0.000000e+00 1517.0
28 TraesCS3A01G321600 chr5A 90.409 563 45 3 2303 2864 565941080 565940526 0.000000e+00 732.0
29 TraesCS3A01G321600 chr5A 93.313 329 20 2 1456 1783 566039731 566039404 5.710000e-133 484.0
30 TraesCS3A01G321600 chr2D 92.185 563 37 3 2303 2864 633593201 633593757 0.000000e+00 789.0
31 TraesCS3A01G321600 chr2D 92.517 147 8 1 1376 1519 73913171 73913025 1.380000e-49 207.0
32 TraesCS3A01G321600 chr3D 89.106 615 35 7 1 608 423861947 423861358 0.000000e+00 736.0
33 TraesCS3A01G321600 chr3D 90.809 544 33 6 1703 2241 112301237 112300706 0.000000e+00 712.0
34 TraesCS3A01G321600 chr3D 87.906 339 31 5 1325 1658 112301567 112301234 1.280000e-104 390.0
35 TraesCS3A01G321600 chr6B 90.055 543 39 4 1703 2241 668008202 668007671 0.000000e+00 689.0
36 TraesCS3A01G321600 chr6B 87.879 363 40 2 803 1165 95585461 95585819 1.260000e-114 424.0
37 TraesCS3A01G321600 chr6B 88.201 339 29 6 1325 1658 668008531 668008199 9.890000e-106 394.0
38 TraesCS3A01G321600 chr2A 91.952 497 31 3 2369 2864 780743858 780743370 0.000000e+00 688.0
39 TraesCS3A01G321600 chr2A 88.807 545 43 7 1703 2241 5960129 5959597 0.000000e+00 652.0
40 TraesCS3A01G321600 chr2A 87.332 371 38 6 801 1168 662740790 662740426 2.110000e-112 416.0
41 TraesCS3A01G321600 chr2A 87.021 339 33 6 1325 1658 5960458 5960126 4.640000e-99 372.0
42 TraesCS3A01G321600 chr2A 78.075 187 27 7 602 781 391915503 391915324 5.190000e-19 106.0
43 TraesCS3A01G321600 chr6A 88.398 543 46 8 1703 2241 587376512 587375983 4.140000e-179 638.0
44 TraesCS3A01G321600 chr6A 87.705 366 42 3 801 1165 569260192 569260555 1.260000e-114 424.0
45 TraesCS3A01G321600 chr6A 89.298 299 23 4 1365 1658 587376803 587376509 2.160000e-97 366.0
46 TraesCS3A01G321600 chr1D 89.006 473 41 4 2396 2864 423036034 423035569 3.290000e-160 575.0
47 TraesCS3A01G321600 chr4D 84.030 526 71 12 645 1168 115198394 115197880 9.480000e-136 494.0
48 TraesCS3A01G321600 chr4A 78.947 171 23 10 607 769 695915872 695916037 1.870000e-18 104.0


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 TraesCS3A01G321600 chr3A 565328991 565332790 3799 False 7018.0 7018 100.0000 1 3800 1 chr3A.!!$F1 3799
1 TraesCS3A01G321600 chr3A 565339153 565343713 4560 False 960.0 1598 98.6280 637 3800 2 chr3A.!!$F2 3163
2 TraesCS3A01G321600 chr7B 73924306 73926582 2276 True 4045.0 4045 98.7260 627 2903 1 chr7B.!!$R1 2276
3 TraesCS3A01G321600 chr2B 138121554 138123824 2270 True 4030.0 4030 98.6800 631 2903 1 chr2B.!!$R1 2272
4 TraesCS3A01G321600 chr2B 589941367 589942253 886 False 1533.0 1533 97.6690 2901 3800 1 chr2B.!!$F1 899
5 TraesCS3A01G321600 chr2B 501750371 501751254 883 True 1524.0 1524 97.5530 2903 3800 1 chr2B.!!$R2 897
6 TraesCS3A01G321600 chr2B 776687410 776687929 519 False 750.0 750 92.6000 2339 2864 1 chr2B.!!$F2 525
7 TraesCS3A01G321600 chr3B 646714865 646717079 2214 True 1841.5 2595 95.9795 623 2903 2 chr3B.!!$R4 2280
8 TraesCS3A01G321600 chr3B 714553130 714554014 884 True 1526.0 1526 97.5560 2902 3800 1 chr3B.!!$R3 898
9 TraesCS3A01G321600 chr3B 50611882 50612766 884 True 1524.0 1524 97.5530 2903 3800 1 chr3B.!!$R1 897
10 TraesCS3A01G321600 chr3B 552893295 552893890 595 False 800.0 800 90.7740 1 606 1 chr3B.!!$F2 605
11 TraesCS3A01G321600 chr3B 129297964 129298484 520 False 457.0 457 83.0190 646 1158 1 chr3B.!!$F1 512
12 TraesCS3A01G321600 chr1A 111988136 111990318 2182 True 1789.0 2471 95.7420 629 2903 2 chr1A.!!$R1 2274
13 TraesCS3A01G321600 chr1A 374260552 374261444 892 False 1526.0 1526 97.4530 2903 3800 1 chr1A.!!$F2 897
14 TraesCS3A01G321600 chr1B 516942971 516943858 887 True 1535.0 1535 97.6670 2901 3800 1 chr1B.!!$R3 899
15 TraesCS3A01G321600 chr7A 595195141 595196023 882 True 1522.0 1522 97.5500 2903 3800 1 chr7A.!!$R1 897
16 TraesCS3A01G321600 chr5A 391599500 391600398 898 True 1517.0 1517 96.9370 2890 3800 1 chr5A.!!$R1 910
17 TraesCS3A01G321600 chr5A 565940526 565941080 554 True 732.0 732 90.4090 2303 2864 1 chr5A.!!$R2 561
18 TraesCS3A01G321600 chr2D 633593201 633593757 556 False 789.0 789 92.1850 2303 2864 1 chr2D.!!$F1 561
19 TraesCS3A01G321600 chr3D 423861358 423861947 589 True 736.0 736 89.1060 1 608 1 chr3D.!!$R1 607
20 TraesCS3A01G321600 chr3D 112300706 112301567 861 True 551.0 712 89.3575 1325 2241 2 chr3D.!!$R2 916
21 TraesCS3A01G321600 chr6B 668007671 668008531 860 True 541.5 689 89.1280 1325 2241 2 chr6B.!!$R1 916
22 TraesCS3A01G321600 chr2A 5959597 5960458 861 True 512.0 652 87.9140 1325 2241 2 chr2A.!!$R4 916
23 TraesCS3A01G321600 chr6A 587375983 587376803 820 True 502.0 638 88.8480 1365 2241 2 chr6A.!!$R1 876
24 TraesCS3A01G321600 chr4D 115197880 115198394 514 True 494.0 494 84.0300 645 1168 1 chr4D.!!$R1 523

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
322 324 0.031585 GCCGGTTTTGACTTCCCAAC 59.968 55.000 1.90 0.0 0.00 3.77 F
347 349 0.691078 TCCAGGTGGGAGCCTCATAC 60.691 60.000 0.00 0.0 42.15 2.39 F
671 673 0.811616 AATCACCGATCGCTTCTGGC 60.812 55.000 10.32 0.0 37.64 4.85 F
1347 1368 3.244665 TGTTCTCCTACTGTCAGGTCGTA 60.245 47.826 4.53 0.0 36.99 3.43 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1142 1163 3.560251 AGTGGAAGGTGGCGCTGT 61.560 61.111 7.64 0.00 0.00 4.40 R
1193 1214 3.765511 CCCATCCTGCAAAAATTGAGAGA 59.234 43.478 0.00 0.00 0.00 3.10 R
2629 2662 0.319297 GTTGACGGGTCGTACAGCTT 60.319 55.000 0.00 0.00 41.37 3.74 R
3467 3521 2.286121 TCCTAGGTGCCTTGGGGG 60.286 66.667 16.52 6.05 39.01 5.40 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
159 161 3.138304 GCCAAGAGTGTGTTATGTGTGA 58.862 45.455 0.00 0.00 0.00 3.58
203 205 1.142748 CGCGCTCTTCCTCTGGATT 59.857 57.895 5.56 0.00 0.00 3.01
207 209 0.545646 GCTCTTCCTCTGGATTGCCT 59.454 55.000 0.00 0.00 34.31 4.75
208 210 1.765314 GCTCTTCCTCTGGATTGCCTA 59.235 52.381 0.00 0.00 34.31 3.93
213 215 4.102210 TCTTCCTCTGGATTGCCTAATCAG 59.898 45.833 0.00 0.00 43.62 2.90
221 223 3.181483 GGATTGCCTAATCAGCTTGGTTG 60.181 47.826 0.00 0.00 43.62 3.77
253 255 3.148279 GGATCTGTCCGGGCGAGT 61.148 66.667 0.00 0.00 34.13 4.18
254 256 2.105128 GATCTGTCCGGGCGAGTG 59.895 66.667 0.00 0.00 0.00 3.51
259 261 4.477975 GTCCGGGCGAGTGTCGAG 62.478 72.222 0.00 0.00 43.74 4.04
265 267 2.354656 GCGAGTGTCGAGTGCACA 60.355 61.111 21.04 0.00 43.74 4.57
274 276 1.792949 GTCGAGTGCACACCTAACAAG 59.207 52.381 21.04 0.00 0.00 3.16
279 281 2.143925 GTGCACACCTAACAAGGACTC 58.856 52.381 13.17 0.00 0.00 3.36
281 283 2.438021 TGCACACCTAACAAGGACTCTT 59.562 45.455 0.00 0.00 0.00 2.85
296 298 3.196685 GGACTCTTGTAGATGCTCTGGTT 59.803 47.826 0.00 0.00 0.00 3.67
306 308 2.125912 CTCTGGTTGAGTCGGCCG 60.126 66.667 22.12 22.12 37.99 6.13
314 316 1.161563 TTGAGTCGGCCGGTTTTGAC 61.162 55.000 27.83 15.24 0.00 3.18
322 324 0.031585 GCCGGTTTTGACTTCCCAAC 59.968 55.000 1.90 0.00 0.00 3.77
331 333 1.418264 TGACTTCCCAACGTCATTCCA 59.582 47.619 0.00 0.00 35.40 3.53
345 347 2.456364 TCCAGGTGGGAGCCTCAT 59.544 61.111 0.00 0.00 42.15 2.90
346 348 1.709711 TCCAGGTGGGAGCCTCATA 59.290 57.895 0.00 0.00 42.15 2.15
347 349 0.691078 TCCAGGTGGGAGCCTCATAC 60.691 60.000 0.00 0.00 42.15 2.39
392 394 2.553602 TCAATCATGCACTGAAAAGCGT 59.446 40.909 0.00 0.00 37.44 5.07
393 395 2.907910 ATCATGCACTGAAAAGCGTC 57.092 45.000 0.00 0.00 37.44 5.19
400 402 1.665679 CACTGAAAAGCGTCTGTGTGT 59.334 47.619 13.31 0.00 40.60 3.72
404 406 1.724582 AAAAGCGTCTGTGTGTGGGC 61.725 55.000 0.00 0.00 0.00 5.36
417 419 1.202348 GTGTGGGCCATTAGTTTCAGC 59.798 52.381 10.70 0.00 0.00 4.26
450 452 3.023832 ACTATTGTGCCTACCCAATTGC 58.976 45.455 0.00 0.00 33.54 3.56
456 458 1.098050 GCCTACCCAATTGCACTCTG 58.902 55.000 0.00 0.00 0.00 3.35
481 483 0.958822 ACGTTTCAGGTTTGGGATGC 59.041 50.000 0.00 0.00 0.00 3.91
542 544 4.016706 CTTCGCCCACCCGGACTT 62.017 66.667 0.73 0.00 0.00 3.01
543 545 4.323477 TTCGCCCACCCGGACTTG 62.323 66.667 0.73 0.00 0.00 3.16
549 551 2.430244 CACCCGGACTTGTCGTCG 60.430 66.667 0.73 0.00 43.79 5.12
671 673 0.811616 AATCACCGATCGCTTCTGGC 60.812 55.000 10.32 0.00 37.64 4.85
824 845 4.722535 TCCCTCCTGCCCTCGCTT 62.723 66.667 0.00 0.00 35.36 4.68
1142 1163 3.712907 GCCACCCCGCTCAACCTA 61.713 66.667 0.00 0.00 0.00 3.08
1193 1214 5.486775 TGGAGAACCTCATCTCTCTGATTTT 59.513 40.000 4.50 0.00 44.30 1.82
1347 1368 3.244665 TGTTCTCCTACTGTCAGGTCGTA 60.245 47.826 4.53 0.00 36.99 3.43
2164 2192 5.510179 CCTCCTGTGAATGAACAAGCAAATT 60.510 40.000 0.00 0.00 0.00 1.82
2542 2575 5.607939 TCATGTTTATACGGATGAGGTGT 57.392 39.130 0.00 0.00 0.00 4.16
2629 2662 3.389656 TCCTGACTTCAACACCATGTACA 59.610 43.478 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
70 72 2.507992 CACAGCGAGGAGAAGCCG 60.508 66.667 0.00 0.00 43.43 5.52
113 115 2.240493 AAGAGTGGTCAAGTGTTCCG 57.760 50.000 0.00 0.00 0.00 4.30
141 143 4.811024 CACACTCACACATAACACACTCTT 59.189 41.667 0.00 0.00 0.00 2.85
203 205 1.075374 ACCAACCAAGCTGATTAGGCA 59.925 47.619 0.00 0.00 0.00 4.75
253 255 0.747852 TGTTAGGTGTGCACTCGACA 59.252 50.000 19.41 15.87 0.00 4.35
254 256 1.792949 CTTGTTAGGTGTGCACTCGAC 59.207 52.381 19.41 13.65 0.00 4.20
259 261 2.143925 GAGTCCTTGTTAGGTGTGCAC 58.856 52.381 10.75 10.75 42.60 4.57
260 262 2.047061 AGAGTCCTTGTTAGGTGTGCA 58.953 47.619 0.00 0.00 42.60 4.57
296 298 1.595929 GTCAAAACCGGCCGACTCA 60.596 57.895 30.73 1.40 0.00 3.41
306 308 2.018515 TGACGTTGGGAAGTCAAAACC 58.981 47.619 0.00 0.00 43.47 3.27
314 316 1.271379 ACCTGGAATGACGTTGGGAAG 60.271 52.381 0.00 0.00 0.00 3.46
322 324 1.450312 GCTCCCACCTGGAATGACG 60.450 63.158 0.00 0.00 44.57 4.35
331 333 0.692419 CCTGTATGAGGCTCCCACCT 60.692 60.000 12.86 0.00 45.04 4.00
340 342 2.787473 TTGTCCTTGCCTGTATGAGG 57.213 50.000 0.00 0.00 46.13 3.86
341 343 2.947652 CCATTGTCCTTGCCTGTATGAG 59.052 50.000 0.00 0.00 0.00 2.90
342 344 2.945440 GCCATTGTCCTTGCCTGTATGA 60.945 50.000 0.00 0.00 0.00 2.15
343 345 1.406539 GCCATTGTCCTTGCCTGTATG 59.593 52.381 0.00 0.00 0.00 2.39
344 346 1.005805 TGCCATTGTCCTTGCCTGTAT 59.994 47.619 0.00 0.00 0.00 2.29
345 347 0.403655 TGCCATTGTCCTTGCCTGTA 59.596 50.000 0.00 0.00 0.00 2.74
346 348 0.251922 ATGCCATTGTCCTTGCCTGT 60.252 50.000 0.00 0.00 0.00 4.00
347 349 1.406539 GTATGCCATTGTCCTTGCCTG 59.593 52.381 0.00 0.00 0.00 4.85
373 375 2.816087 AGACGCTTTTCAGTGCATGATT 59.184 40.909 0.00 0.00 37.89 2.57
392 394 1.064003 ACTAATGGCCCACACACAGA 58.936 50.000 0.00 0.00 0.00 3.41
393 395 1.909700 AACTAATGGCCCACACACAG 58.090 50.000 0.00 0.00 0.00 3.66
400 402 1.312371 GCGCTGAAACTAATGGCCCA 61.312 55.000 0.00 0.00 0.00 5.36
404 406 2.898705 AGAGAGCGCTGAAACTAATGG 58.101 47.619 18.48 0.00 0.00 3.16
417 419 2.784380 GCACAATAGTACGAAGAGAGCG 59.216 50.000 0.00 0.00 0.00 5.03
450 452 2.027625 GAAACGTCGGGCCAGAGTG 61.028 63.158 5.57 4.55 0.00 3.51
481 483 0.798776 GTGACGACCTCAGGCAATTG 59.201 55.000 0.00 0.00 0.00 2.32
537 539 2.048503 CCCCACGACGACAAGTCC 60.049 66.667 0.00 0.00 46.92 3.85
542 544 3.066190 CTAGGCCCCACGACGACA 61.066 66.667 0.00 0.00 0.00 4.35
543 545 4.509737 GCTAGGCCCCACGACGAC 62.510 72.222 0.00 0.00 0.00 4.34
565 567 4.010667 ACTAGTATTCCAAAACACGCCA 57.989 40.909 0.00 0.00 0.00 5.69
640 642 5.345202 GCGATCGGTGATTTATTAGTAGGTG 59.655 44.000 18.30 0.00 0.00 4.00
671 673 3.927163 AAAGGGCAGCGACGTACGG 62.927 63.158 21.06 3.45 42.83 4.02
1142 1163 3.560251 AGTGGAAGGTGGCGCTGT 61.560 61.111 7.64 0.00 0.00 4.40
1193 1214 3.765511 CCCATCCTGCAAAAATTGAGAGA 59.234 43.478 0.00 0.00 0.00 3.10
1347 1368 9.452287 CCCACAAAATTGATAAAAAGAATCCAT 57.548 29.630 0.00 0.00 0.00 3.41
1948 1975 5.190677 AGGGGAAAATACACGATTTACTGG 58.809 41.667 0.00 0.00 36.71 4.00
2542 2575 1.461268 TCTCAGCCACCCCTGACAA 60.461 57.895 0.00 0.00 36.96 3.18
2629 2662 0.319297 GTTGACGGGTCGTACAGCTT 60.319 55.000 0.00 0.00 41.37 3.74
3467 3521 2.286121 TCCTAGGTGCCTTGGGGG 60.286 66.667 16.52 6.05 39.01 5.40
3468 3522 2.378634 CCTCCTAGGTGCCTTGGGG 61.379 68.421 16.52 13.87 38.80 4.96
3469 3523 3.324713 CCTCCTAGGTGCCTTGGG 58.675 66.667 16.52 10.22 39.01 4.12


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

AutoCloner maintained by Alex Coulton.