Multiple sequence alignment - TraesCS6D01G094600

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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 TraesCS6D01G094600 chr6D 100.000 4418 0 0 1 4418 58858217 58853800 0.000000e+00 8159.0
1 TraesCS6D01G094600 chr6D 95.471 1369 30 7 1 1358 429167437 429166090 0.000000e+00 2156.0
2 TraesCS6D01G094600 chr6A 96.484 2304 56 8 1357 3659 74906994 74904715 0.000000e+00 3783.0
3 TraesCS6D01G094600 chr6A 96.875 32 1 0 3434 3465 65800494 65800463 2.000000e-03 54.7
4 TraesCS6D01G094600 chr4D 92.719 2321 98 22 1357 3659 133468780 133471047 0.000000e+00 3284.0
5 TraesCS6D01G094600 chr6B 96.211 1953 53 6 1357 3303 132432563 132430626 0.000000e+00 3177.0
6 TraesCS6D01G094600 chr6B 94.030 67 4 0 3297 3363 132430443 132430377 7.820000e-18 102.0
7 TraesCS6D01G094600 chr2D 97.224 1369 26 9 1 1360 436062626 436063991 0.000000e+00 2307.0
8 TraesCS6D01G094600 chr2D 95.890 73 3 0 1285 1357 21907985 21908057 7.760000e-23 119.0
9 TraesCS6D01G094600 chr5D 96.999 1366 31 5 1 1356 50680916 50679551 0.000000e+00 2287.0
10 TraesCS6D01G094600 chr5D 96.512 1290 35 7 1 1282 525091079 525089792 0.000000e+00 2124.0
11 TraesCS6D01G094600 chr5D 94.420 1362 26 20 1 1359 543539791 543538477 0.000000e+00 2049.0
12 TraesCS6D01G094600 chr5D 97.895 760 16 0 3659 4418 514130654 514131413 0.000000e+00 1315.0
13 TraesCS6D01G094600 chr5D 97.898 761 15 1 3659 4418 558605169 558605929 0.000000e+00 1315.0
14 TraesCS6D01G094600 chr5D 97.769 762 16 1 3658 4418 384682529 384681768 0.000000e+00 1312.0
15 TraesCS6D01G094600 chr5D 97.769 762 16 1 3658 4418 421576773 421577534 0.000000e+00 1312.0
16 TraesCS6D01G094600 chr5D 97.147 771 21 1 3649 4418 495939913 495940683 0.000000e+00 1301.0
17 TraesCS6D01G094600 chr7D 97.067 1364 26 10 1 1353 179983691 179985051 0.000000e+00 2285.0
18 TraesCS6D01G094600 chr7D 96.374 1379 31 11 1 1361 40361830 40360453 0.000000e+00 2252.0
19 TraesCS6D01G094600 chr7D 95.830 1367 30 11 1 1347 544361687 544363046 0.000000e+00 2183.0
20 TraesCS6D01G094600 chr7D 95.608 1366 36 10 1 1342 578775943 578777308 0.000000e+00 2169.0
21 TraesCS6D01G094600 chr7D 95.547 1370 30 11 1 1357 587968428 587969779 0.000000e+00 2163.0
22 TraesCS6D01G094600 chr7D 97.769 762 15 1 3659 4418 549829748 549830509 0.000000e+00 1312.0
23 TraesCS6D01G094600 chr7D 97.769 762 16 1 3658 4418 593344084 593344845 0.000000e+00 1312.0
24 TraesCS6D01G094600 chr7D 76.471 782 153 27 1537 2304 591814487 591813723 3.200000e-106 396.0
25 TraesCS6D01G094600 chr1D 96.831 1357 34 6 1 1348 40200539 40201895 0.000000e+00 2259.0
26 TraesCS6D01G094600 chr1D 96.145 1375 33 7 1 1357 481103353 481101981 0.000000e+00 2228.0
27 TraesCS6D01G094600 chr1D 97.763 760 17 0 3659 4418 314157300 314156541 0.000000e+00 1310.0
28 TraesCS6D01G094600 chr1D 97.638 762 17 1 3658 4418 433932744 433933505 0.000000e+00 1306.0
29 TraesCS6D01G094600 chr4A 89.985 1338 85 19 2327 3659 428164105 428162812 0.000000e+00 1683.0
30 TraesCS6D01G094600 chr4A 94.460 704 30 5 1357 2055 428259759 428259060 0.000000e+00 1075.0
31 TraesCS6D01G094600 chr4A 91.901 284 11 1 2051 2334 428253791 428253520 1.930000e-103 387.0
32 TraesCS6D01G094600 chr4A 86.364 154 20 1 1204 1357 718881360 718881512 2.730000e-37 167.0
33 TraesCS6D01G094600 chr4A 83.871 155 23 2 1200 1353 743498671 743498824 3.560000e-31 147.0
34 TraesCS6D01G094600 chr4B 96.009 426 17 0 2782 3207 161620195 161619770 0.000000e+00 693.0
35 TraesCS6D01G094600 chr4B 93.939 165 7 2 1395 1558 161621173 161621011 3.410000e-61 246.0
36 TraesCS6D01G094600 chr5B 82.768 737 113 10 2504 3227 622605437 622606172 0.000000e+00 645.0
37 TraesCS6D01G094600 chr3B 82.353 765 106 20 2478 3217 620454966 620454206 4.820000e-179 638.0
38 TraesCS6D01G094600 chr3B 78.980 804 146 18 1536 2332 620455890 620455103 1.090000e-145 527.0
39 TraesCS6D01G094600 chr3B 88.095 168 19 1 1186 1353 77643661 77643827 9.690000e-47 198.0
40 TraesCS6D01G094600 chr3B 96.970 33 1 0 3482 3514 636131202 636131170 6.170000e-04 56.5
41 TraesCS6D01G094600 chr3A 82.609 736 106 13 2507 3222 609687759 609687026 8.060000e-177 630.0
42 TraesCS6D01G094600 chr3A 79.827 808 132 26 1536 2332 609688715 609687928 1.070000e-155 560.0
43 TraesCS6D01G094600 chr3D 81.830 765 110 21 2478 3217 466679143 466678383 2.260000e-172 616.0
44 TraesCS6D01G094600 chr3D 79.579 808 134 26 1536 2332 466680067 466679280 2.320000e-152 549.0
45 TraesCS6D01G094600 chr7B 77.968 758 134 29 1562 2304 671702117 671702856 1.130000e-120 444.0
46 TraesCS6D01G094600 chr7B 76.913 758 142 28 1562 2304 685666792 685667531 2.480000e-107 399.0
47 TraesCS6D01G094600 chr7A 77.704 758 136 29 1562 2304 727276696 727277435 2.440000e-117 433.0
48 TraesCS6D01G094600 chr7A 78.134 718 121 31 1601 2302 726605943 726605246 1.470000e-114 424.0
49 TraesCS6D01G094600 chr7A 78.025 719 125 27 1601 2304 682899100 682898400 5.280000e-114 422.0


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 TraesCS6D01G094600 chr6D 58853800 58858217 4417 True 8159.0 8159 100.0000 1 4418 1 chr6D.!!$R1 4417
1 TraesCS6D01G094600 chr6D 429166090 429167437 1347 True 2156.0 2156 95.4710 1 1358 1 chr6D.!!$R2 1357
2 TraesCS6D01G094600 chr6A 74904715 74906994 2279 True 3783.0 3783 96.4840 1357 3659 1 chr6A.!!$R2 2302
3 TraesCS6D01G094600 chr4D 133468780 133471047 2267 False 3284.0 3284 92.7190 1357 3659 1 chr4D.!!$F1 2302
4 TraesCS6D01G094600 chr6B 132430377 132432563 2186 True 1639.5 3177 95.1205 1357 3363 2 chr6B.!!$R1 2006
5 TraesCS6D01G094600 chr2D 436062626 436063991 1365 False 2307.0 2307 97.2240 1 1360 1 chr2D.!!$F2 1359
6 TraesCS6D01G094600 chr5D 50679551 50680916 1365 True 2287.0 2287 96.9990 1 1356 1 chr5D.!!$R1 1355
7 TraesCS6D01G094600 chr5D 525089792 525091079 1287 True 2124.0 2124 96.5120 1 1282 1 chr5D.!!$R3 1281
8 TraesCS6D01G094600 chr5D 543538477 543539791 1314 True 2049.0 2049 94.4200 1 1359 1 chr5D.!!$R4 1358
9 TraesCS6D01G094600 chr5D 514130654 514131413 759 False 1315.0 1315 97.8950 3659 4418 1 chr5D.!!$F3 759
10 TraesCS6D01G094600 chr5D 558605169 558605929 760 False 1315.0 1315 97.8980 3659 4418 1 chr5D.!!$F4 759
11 TraesCS6D01G094600 chr5D 384681768 384682529 761 True 1312.0 1312 97.7690 3658 4418 1 chr5D.!!$R2 760
12 TraesCS6D01G094600 chr5D 421576773 421577534 761 False 1312.0 1312 97.7690 3658 4418 1 chr5D.!!$F1 760
13 TraesCS6D01G094600 chr5D 495939913 495940683 770 False 1301.0 1301 97.1470 3649 4418 1 chr5D.!!$F2 769
14 TraesCS6D01G094600 chr7D 179983691 179985051 1360 False 2285.0 2285 97.0670 1 1353 1 chr7D.!!$F1 1352
15 TraesCS6D01G094600 chr7D 40360453 40361830 1377 True 2252.0 2252 96.3740 1 1361 1 chr7D.!!$R1 1360
16 TraesCS6D01G094600 chr7D 544361687 544363046 1359 False 2183.0 2183 95.8300 1 1347 1 chr7D.!!$F2 1346
17 TraesCS6D01G094600 chr7D 578775943 578777308 1365 False 2169.0 2169 95.6080 1 1342 1 chr7D.!!$F4 1341
18 TraesCS6D01G094600 chr7D 587968428 587969779 1351 False 2163.0 2163 95.5470 1 1357 1 chr7D.!!$F5 1356
19 TraesCS6D01G094600 chr7D 549829748 549830509 761 False 1312.0 1312 97.7690 3659 4418 1 chr7D.!!$F3 759
20 TraesCS6D01G094600 chr7D 593344084 593344845 761 False 1312.0 1312 97.7690 3658 4418 1 chr7D.!!$F6 760
21 TraesCS6D01G094600 chr7D 591813723 591814487 764 True 396.0 396 76.4710 1537 2304 1 chr7D.!!$R2 767
22 TraesCS6D01G094600 chr1D 40200539 40201895 1356 False 2259.0 2259 96.8310 1 1348 1 chr1D.!!$F1 1347
23 TraesCS6D01G094600 chr1D 481101981 481103353 1372 True 2228.0 2228 96.1450 1 1357 1 chr1D.!!$R2 1356
24 TraesCS6D01G094600 chr1D 314156541 314157300 759 True 1310.0 1310 97.7630 3659 4418 1 chr1D.!!$R1 759
25 TraesCS6D01G094600 chr1D 433932744 433933505 761 False 1306.0 1306 97.6380 3658 4418 1 chr1D.!!$F2 760
26 TraesCS6D01G094600 chr4A 428162812 428164105 1293 True 1683.0 1683 89.9850 2327 3659 1 chr4A.!!$R1 1332
27 TraesCS6D01G094600 chr4A 428259060 428259759 699 True 1075.0 1075 94.4600 1357 2055 1 chr4A.!!$R3 698
28 TraesCS6D01G094600 chr4B 161619770 161621173 1403 True 469.5 693 94.9740 1395 3207 2 chr4B.!!$R1 1812
29 TraesCS6D01G094600 chr5B 622605437 622606172 735 False 645.0 645 82.7680 2504 3227 1 chr5B.!!$F1 723
30 TraesCS6D01G094600 chr3B 620454206 620455890 1684 True 582.5 638 80.6665 1536 3217 2 chr3B.!!$R2 1681
31 TraesCS6D01G094600 chr3A 609687026 609688715 1689 True 595.0 630 81.2180 1536 3222 2 chr3A.!!$R1 1686
32 TraesCS6D01G094600 chr3D 466678383 466680067 1684 True 582.5 616 80.7045 1536 3217 2 chr3D.!!$R1 1681
33 TraesCS6D01G094600 chr7B 671702117 671702856 739 False 444.0 444 77.9680 1562 2304 1 chr7B.!!$F1 742
34 TraesCS6D01G094600 chr7B 685666792 685667531 739 False 399.0 399 76.9130 1562 2304 1 chr7B.!!$F2 742
35 TraesCS6D01G094600 chr7A 727276696 727277435 739 False 433.0 433 77.7040 1562 2304 1 chr7A.!!$F1 742
36 TraesCS6D01G094600 chr7A 726605246 726605943 697 True 424.0 424 78.1340 1601 2302 1 chr7A.!!$R2 701
37 TraesCS6D01G094600 chr7A 682898400 682899100 700 True 422.0 422 78.0250 1601 2304 1 chr7A.!!$R1 703

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
512 516 1.837450 CGACTTGTGTGTGACGTCG 59.163 57.895 11.62 0.0 40.92 5.12 F
1944 1993 1.349357 GTCAAGAGCTTTCCAGGGAGT 59.651 52.381 0.00 0.0 0.00 3.85 F
2456 2545 1.160329 GCTCAAGTCGTGCAAGTGGT 61.160 55.000 0.00 0.0 34.19 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2148 2211 0.108992 AGAAAGCGCCATCGTCGTTA 60.109 50.0 2.29 0.00 38.14 3.18 R
3340 4381 0.250234 TCTCGGCCAATTGAGACCTG 59.750 55.0 7.12 2.98 36.36 4.00 R
3787 4832 0.533491 CAGACGAACCGGGACCAATA 59.467 55.0 6.32 0.00 0.00 1.90 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
83 84 6.547510 GCATCCTAACCTTTCATTTATGTCCT 59.452 38.462 0.00 0.00 0.00 3.85
112 113 2.685850 ATAGCACCGTTCCAACCTAC 57.314 50.000 0.00 0.00 0.00 3.18
145 146 7.658525 AATGCCATGTTACAGGATTTAATGA 57.341 32.000 0.00 0.00 0.00 2.57
150 151 6.404184 CCATGTTACAGGATTTAATGACGCAA 60.404 38.462 0.00 0.00 0.00 4.85
400 404 3.616219 CTCCGGAATGTTAACCCAATGA 58.384 45.455 5.23 0.00 0.00 2.57
512 516 1.837450 CGACTTGTGTGTGACGTCG 59.163 57.895 11.62 0.00 40.92 5.12
535 539 8.074972 GTCGACTAGGATAATACATTCGACTTT 58.925 37.037 8.70 0.00 46.57 2.66
536 540 8.288208 TCGACTAGGATAATACATTCGACTTTC 58.712 37.037 0.00 0.00 29.78 2.62
539 543 8.074972 ACTAGGATAATACATTCGACTTTCGTC 58.925 37.037 0.00 0.00 41.35 4.20
557 568 3.635373 TCGTCATGTGGACTATCCCTAAC 59.365 47.826 0.00 0.00 44.68 2.34
1042 1069 4.957296 ACCACACGTCAGTTAGAAAGAAT 58.043 39.130 0.00 0.00 0.00 2.40
1050 1084 6.420008 ACGTCAGTTAGAAAGAATACACACAC 59.580 38.462 0.00 0.00 0.00 3.82
1259 1293 2.517402 GTGACGGTGGGTTTGCCA 60.517 61.111 0.00 0.00 36.17 4.92
1353 1387 5.391097 CCGGCGTACATGAAAATTTCAGTAA 60.391 40.000 14.10 0.00 43.98 2.24
1388 1422 8.592529 TCAATCATGGAAGAATCATAACCAAA 57.407 30.769 0.00 0.00 34.28 3.28
1389 1423 8.469200 TCAATCATGGAAGAATCATAACCAAAC 58.531 33.333 0.00 0.00 34.28 2.93
1390 1424 6.435430 TCATGGAAGAATCATAACCAAACG 57.565 37.500 0.00 0.00 34.28 3.60
1487 1536 6.551736 CGCCAATATTAACTATGGTTATGGC 58.448 40.000 23.98 23.98 46.33 4.40
1944 1993 1.349357 GTCAAGAGCTTTCCAGGGAGT 59.651 52.381 0.00 0.00 0.00 3.85
2350 2419 6.407979 GGTGTACTACTACTACTACTGGCTCT 60.408 46.154 0.00 0.00 0.00 4.09
2456 2545 1.160329 GCTCAAGTCGTGCAAGTGGT 61.160 55.000 0.00 0.00 34.19 4.16
3389 4430 7.118723 AGCAAATCTAAGTCAAATGGTATGGA 58.881 34.615 0.00 0.00 0.00 3.41
3523 4565 8.109634 AGATTTAACAAATTCTCTTCCCTGCTA 58.890 33.333 0.00 0.00 0.00 3.49
3605 4648 2.739784 CCTGCCTAGGCGATCAGG 59.260 66.667 28.28 23.95 45.51 3.86
3686 4730 3.642141 AGAAAAGAGGGCTTTGGTTCAA 58.358 40.909 0.00 0.00 43.32 2.69
3745 4790 4.702274 ACCAATGGGGGCACTGGC 62.702 66.667 3.55 0.00 42.91 4.85
3977 5022 0.324923 ATATATACCCCTCGCCCGCA 60.325 55.000 0.00 0.00 0.00 5.69
4087 5132 1.168407 CGATGAAATGCCCGAGCCAT 61.168 55.000 0.00 0.00 38.69 4.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
83 84 0.036765 ACGGTGCTATTTCGAGGCAA 60.037 50.000 6.14 0.00 37.73 4.52
150 151 0.318762 GCTCCTCTTCAACAGTCCGT 59.681 55.000 0.00 0.00 0.00 4.69
400 404 3.207321 AGATCATCTTGAGGAGGAGAGGT 59.793 47.826 0.00 0.00 38.18 3.85
512 516 8.074972 ACGAAAGTCGAATGTATTATCCTAGTC 58.925 37.037 4.40 0.00 44.19 2.59
539 543 5.482908 GCATAGTTAGGGATAGTCCACATG 58.517 45.833 0.00 0.00 38.64 3.21
557 568 8.753497 TCTAGTCCACACATATATAGGCATAG 57.247 38.462 0.00 0.00 0.00 2.23
686 699 6.375455 GTCAAGCTATTTCTTTTCTGATCCCA 59.625 38.462 0.00 0.00 0.00 4.37
1026 1053 6.419710 TGTGTGTGTATTCTTTCTAACTGACG 59.580 38.462 0.00 0.00 0.00 4.35
1259 1293 1.583054 GTTTGCCGAGTGTCACTCTT 58.417 50.000 26.46 0.00 42.92 2.85
1353 1387 9.941325 GATTCTTCCATGATTGATACTACTCAT 57.059 33.333 0.00 0.00 0.00 2.90
1371 1405 4.698304 TGGTCGTTTGGTTATGATTCTTCC 59.302 41.667 0.00 0.00 0.00 3.46
1375 1409 5.151389 GTGTTGGTCGTTTGGTTATGATTC 58.849 41.667 0.00 0.00 0.00 2.52
1376 1410 4.580995 TGTGTTGGTCGTTTGGTTATGATT 59.419 37.500 0.00 0.00 0.00 2.57
1884 1933 4.514577 CCGGCGAAGGACTGCGAT 62.515 66.667 9.30 0.00 0.00 4.58
1996 2045 1.134965 GTAGAGCTGCGTGAAGATGGT 60.135 52.381 0.00 0.00 0.00 3.55
2141 2204 3.320078 CATCGTCGTTAGCGCCGG 61.320 66.667 2.29 0.00 40.06 6.13
2142 2205 3.320078 CCATCGTCGTTAGCGCCG 61.320 66.667 2.29 0.00 41.05 6.46
2143 2206 3.627218 GCCATCGTCGTTAGCGCC 61.627 66.667 2.29 0.00 38.14 6.53
2148 2211 0.108992 AGAAAGCGCCATCGTCGTTA 60.109 50.000 2.29 0.00 38.14 3.18
2327 2393 6.805016 AGAGCCAGTAGTAGTAGTAGTACA 57.195 41.667 20.04 1.70 37.48 2.90
2350 2419 3.324846 TCTTGCTGGAGCTCTCTTTTGTA 59.675 43.478 14.64 0.00 42.66 2.41
3340 4381 0.250234 TCTCGGCCAATTGAGACCTG 59.750 55.000 7.12 2.98 36.36 4.00
3450 4492 5.466819 CCTTAGCCGATGTTATATTCGTGA 58.533 41.667 0.00 0.00 33.60 4.35
3605 4648 1.507174 CGGACGAGTCACTTCCCTC 59.493 63.158 5.55 0.00 33.98 4.30
3787 4832 0.533491 CAGACGAACCGGGACCAATA 59.467 55.000 6.32 0.00 0.00 1.90
3822 4867 2.349755 CCGGTTCGTCCCACCAAT 59.650 61.111 0.00 0.00 33.36 3.16
3977 5022 2.433446 CACTGGAGTGCCCTGCTT 59.567 61.111 0.00 0.00 39.39 3.91
4025 5070 1.694150 TGAGCTAGAGCACCACAAAGT 59.306 47.619 4.01 0.00 45.16 2.66
4087 5132 6.413052 TCGAGAGGAGAAAGCTTAACTAGTA 58.587 40.000 0.00 0.00 0.00 1.82
4230 5275 4.472833 AGATAAGAACAAGAGGCTCACCAT 59.527 41.667 18.26 0.00 39.06 3.55


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

AutoCloner maintained by Alex Coulton.