Multiple sequence alignment - TraesCS6A01G083000

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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 TraesCS6A01G083000 chr6A 100.000 3371 0 0 1 3371 51879136 51882506 0.000000e+00 6226
1 TraesCS6A01G083000 chr6A 85.217 1380 189 10 667 2034 7186441 7185065 0.000000e+00 1404
2 TraesCS6A01G083000 chr6A 80.952 147 19 9 3132 3275 71700182 71700042 1.280000e-19 108
3 TraesCS6A01G083000 chr6D 96.953 2724 58 9 667 3371 41234369 41237086 0.000000e+00 4547
4 TraesCS6A01G083000 chr6D 83.754 1705 263 9 663 2355 22182988 22184690 0.000000e+00 1602
5 TraesCS6A01G083000 chr6D 84.543 1378 197 10 669 2034 7345603 7344230 0.000000e+00 1351
6 TraesCS6A01G083000 chr6D 84.443 1382 196 14 667 2034 7359145 7357769 0.000000e+00 1343
7 TraesCS6A01G083000 chr6D 84.969 1284 159 14 664 1927 7696956 7698225 0.000000e+00 1271
8 TraesCS6A01G083000 chr6D 90.411 146 12 2 2468 2611 22184867 22185012 1.230000e-44 191
9 TraesCS6A01G083000 chr6D 81.633 147 18 9 3132 3275 57109780 57109640 2.750000e-21 113
10 TraesCS6A01G083000 chr6B 95.072 1461 49 4 693 2141 96643040 96641591 0.000000e+00 2278
11 TraesCS6A01G083000 chr6B 97.643 1103 23 1 2125 3224 96638827 96637725 0.000000e+00 1890
12 TraesCS6A01G083000 chr6B 94.488 127 1 3 3223 3344 96637486 96637361 1.230000e-44 191
13 TraesCS6A01G083000 chr6B 79.377 257 33 8 2387 2624 13652007 13651752 2.690000e-36 163
14 TraesCS6A01G083000 chr6B 80.952 147 19 9 3132 3275 127746630 127746490 1.280000e-19 108
15 TraesCS6A01G083000 chrUn 85.260 1384 183 16 667 2034 80036781 80035403 0.000000e+00 1406
16 TraesCS6A01G083000 chrUn 84.851 1373 193 9 669 2030 79937468 79938836 0.000000e+00 1369
17 TraesCS6A01G083000 chrUn 84.419 1213 173 12 664 1863 79855006 79856215 0.000000e+00 1179
18 TraesCS6A01G083000 chr7D 85.033 1383 195 7 663 2034 597676778 597675397 0.000000e+00 1397
19 TraesCS6A01G083000 chr7D 93.930 659 32 6 1 657 105949359 105948707 0.000000e+00 989
20 TraesCS6A01G083000 chr7D 92.035 678 39 12 1 670 562890110 562889440 0.000000e+00 939
21 TraesCS6A01G083000 chr7D 91.876 677 41 10 1 670 16167021 16167690 0.000000e+00 933
22 TraesCS6A01G083000 chr5B 84.493 1380 200 9 667 2034 432983044 432984421 0.000000e+00 1351
23 TraesCS6A01G083000 chr5B 79.767 257 32 8 2387 2624 432984597 432984852 5.780000e-38 169
24 TraesCS6A01G083000 chr2A 93.871 669 37 3 1 669 651986417 651987081 0.000000e+00 1005
25 TraesCS6A01G083000 chr2A 91.056 682 44 12 1 669 58478562 58477885 0.000000e+00 905
26 TraesCS6A01G083000 chr5A 93.627 659 37 5 1 657 572012149 572011494 0.000000e+00 979
27 TraesCS6A01G083000 chr1D 92.024 677 43 8 1 669 38279422 38280095 0.000000e+00 941
28 TraesCS6A01G083000 chr5D 91.568 676 48 8 1 671 372493488 372492817 0.000000e+00 924
29 TraesCS6A01G083000 chr3D 90.749 681 48 12 1 673 68943100 68943773 0.000000e+00 894


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 TraesCS6A01G083000 chr6A 51879136 51882506 3370 False 6226.0 6226 100.000000 1 3371 1 chr6A.!!$F1 3370
1 TraesCS6A01G083000 chr6A 7185065 7186441 1376 True 1404.0 1404 85.217000 667 2034 1 chr6A.!!$R1 1367
2 TraesCS6A01G083000 chr6D 41234369 41237086 2717 False 4547.0 4547 96.953000 667 3371 1 chr6D.!!$F2 2704
3 TraesCS6A01G083000 chr6D 7344230 7345603 1373 True 1351.0 1351 84.543000 669 2034 1 chr6D.!!$R1 1365
4 TraesCS6A01G083000 chr6D 7357769 7359145 1376 True 1343.0 1343 84.443000 667 2034 1 chr6D.!!$R2 1367
5 TraesCS6A01G083000 chr6D 7696956 7698225 1269 False 1271.0 1271 84.969000 664 1927 1 chr6D.!!$F1 1263
6 TraesCS6A01G083000 chr6D 22182988 22185012 2024 False 896.5 1602 87.082500 663 2611 2 chr6D.!!$F3 1948
7 TraesCS6A01G083000 chr6B 96637361 96643040 5679 True 1453.0 2278 95.734333 693 3344 3 chr6B.!!$R3 2651
8 TraesCS6A01G083000 chrUn 80035403 80036781 1378 True 1406.0 1406 85.260000 667 2034 1 chrUn.!!$R1 1367
9 TraesCS6A01G083000 chrUn 79937468 79938836 1368 False 1369.0 1369 84.851000 669 2030 1 chrUn.!!$F2 1361
10 TraesCS6A01G083000 chrUn 79855006 79856215 1209 False 1179.0 1179 84.419000 664 1863 1 chrUn.!!$F1 1199
11 TraesCS6A01G083000 chr7D 597675397 597676778 1381 True 1397.0 1397 85.033000 663 2034 1 chr7D.!!$R3 1371
12 TraesCS6A01G083000 chr7D 105948707 105949359 652 True 989.0 989 93.930000 1 657 1 chr7D.!!$R1 656
13 TraesCS6A01G083000 chr7D 562889440 562890110 670 True 939.0 939 92.035000 1 670 1 chr7D.!!$R2 669
14 TraesCS6A01G083000 chr7D 16167021 16167690 669 False 933.0 933 91.876000 1 670 1 chr7D.!!$F1 669
15 TraesCS6A01G083000 chr5B 432983044 432984852 1808 False 760.0 1351 82.130000 667 2624 2 chr5B.!!$F1 1957
16 TraesCS6A01G083000 chr2A 651986417 651987081 664 False 1005.0 1005 93.871000 1 669 1 chr2A.!!$F1 668
17 TraesCS6A01G083000 chr2A 58477885 58478562 677 True 905.0 905 91.056000 1 669 1 chr2A.!!$R1 668
18 TraesCS6A01G083000 chr5A 572011494 572012149 655 True 979.0 979 93.627000 1 657 1 chr5A.!!$R1 656
19 TraesCS6A01G083000 chr1D 38279422 38280095 673 False 941.0 941 92.024000 1 669 1 chr1D.!!$F1 668
20 TraesCS6A01G083000 chr5D 372492817 372493488 671 True 924.0 924 91.568000 1 671 1 chr5D.!!$R1 670
21 TraesCS6A01G083000 chr3D 68943100 68943773 673 False 894.0 894 90.749000 1 673 1 chr3D.!!$F1 672

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
594 617 0.251474 AACATCACCATGGCTGCTGT 60.251 50.0 13.04 13.83 33.82 4.40 F
859 895 0.829333 ATGCTGGAGGTAGCTGTCAG 59.171 55.0 14.22 14.22 44.01 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2101 5.514169 TCCAGTATGAAATAACCCATGCAA 58.486 37.500 0.0 0.0 39.69 4.08 R
2637 5545 5.799681 CAAACCTGCAAACAAATGTTCTT 57.200 34.783 0.0 0.0 37.25 2.52 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
200 201 6.828502 ACGTATGTTGTAGCTGTATGATTG 57.171 37.500 0.00 0.00 0.00 2.67
427 434 2.495409 CCCTGTGACCCGCGCTATA 61.495 63.158 5.56 0.00 0.00 1.31
428 435 1.666011 CCTGTGACCCGCGCTATAT 59.334 57.895 5.56 0.00 0.00 0.86
594 617 0.251474 AACATCACCATGGCTGCTGT 60.251 50.000 13.04 13.83 33.82 4.40
744 770 1.656652 CACTTCGAAGAATGCCCGAT 58.343 50.000 31.08 2.56 45.90 4.18
805 841 4.327982 CTCAAAGGTCTCTGTGTTGAGA 57.672 45.455 5.94 0.00 45.16 3.27
856 892 1.065854 GTTGATGCTGGAGGTAGCTGT 60.066 52.381 0.00 0.00 44.01 4.40
859 895 0.829333 ATGCTGGAGGTAGCTGTCAG 59.171 55.000 14.22 14.22 44.01 3.51
947 986 6.668323 GCTTACAGCTTACTTTGTGAAATGA 58.332 36.000 0.00 0.00 38.45 2.57
1024 1064 2.028839 TGCAAGGTTCAAGCAATGGATG 60.029 45.455 0.00 0.00 34.97 3.51
1129 1169 1.795768 TTCATCAGGACAGTGCGAAC 58.204 50.000 0.00 0.00 0.00 3.95
1136 1176 2.591715 ACAGTGCGAACAGGTGGC 60.592 61.111 0.00 0.00 0.00 5.01
1235 1276 2.352960 GCAAGAGTAGAAGATTTGCGGG 59.647 50.000 0.00 0.00 35.39 6.13
1333 1374 4.383173 TGCATATGCTATGGAACAGTCAG 58.617 43.478 27.13 0.00 42.31 3.51
1981 2041 6.071391 TGGAATGATAGATGATGCGTTAGCTA 60.071 38.462 0.00 0.00 45.42 3.32
1996 2056 5.228012 GCGTTAGCTATTTTCAGTGAAATGC 59.772 40.000 18.69 20.19 41.01 3.56
2004 2064 4.998671 TTTCAGTGAAATGCTGGACAAA 57.001 36.364 14.35 0.00 34.89 2.83
2155 4995 6.779860 ACCTACAACATAATTCTCAGTGGTT 58.220 36.000 0.00 0.00 0.00 3.67
2637 5545 5.871396 AGTGATTTTAGCTAATCGAGGGA 57.129 39.130 7.08 0.00 37.34 4.20
2647 5555 4.878397 AGCTAATCGAGGGAAGAACATTTG 59.122 41.667 0.00 0.00 0.00 2.32
2728 5636 6.658391 GGTCACTTCTCTTAGTAGTAAGTCCA 59.342 42.308 15.43 0.00 37.50 4.02
2764 5672 2.522185 AGTAGTAAACGCCTGACTGGA 58.478 47.619 1.91 0.00 38.35 3.86
2840 5751 2.334946 GGAGCTGCACATTTCGCCA 61.335 57.895 0.00 0.00 0.00 5.69
2932 5843 4.750098 TCACTGAAGTTGTTAGCAGTAAGC 59.250 41.667 0.00 0.00 39.40 3.09
2998 5909 2.457366 ACATGTGGTCCTCGAAGAAC 57.543 50.000 0.00 0.00 34.09 3.01
3020 5931 3.007940 CCAGTGTTCCATCACCACTTAGA 59.992 47.826 0.00 0.00 37.34 2.10
3157 6068 7.624360 TTTCAAGTGGGTAGTTATGCTTATG 57.376 36.000 0.00 0.00 0.00 1.90
3164 6075 6.821665 GTGGGTAGTTATGCTTATGTTCTTCA 59.178 38.462 0.00 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
200 201 4.084433 TCGTCACAACTTAATTGCCGTTAC 60.084 41.667 0.00 0.00 42.62 2.50
492 501 1.912417 CCTAGATCGGTAGGGAGTGG 58.088 60.000 0.00 0.00 36.63 4.00
594 617 1.238439 CTTCCCTTGCGAGCTTGAAA 58.762 50.000 4.70 0.00 0.00 2.69
744 770 4.640789 AACATTCGGTGTGCAGTTAAAA 57.359 36.364 0.00 0.00 41.14 1.52
856 892 1.656587 AGGACACCACATTAGGCTGA 58.343 50.000 0.00 0.00 0.00 4.26
859 895 3.071023 TGCTATAGGACACCACATTAGGC 59.929 47.826 1.04 0.00 0.00 3.93
947 986 3.045634 TCGGTGAAATCCCCTGATGTAT 58.954 45.455 0.00 0.00 0.00 2.29
1129 1169 5.902613 TTCTTGAAAATATGAGCCACCTG 57.097 39.130 0.00 0.00 0.00 4.00
1314 1355 4.655649 TGGACTGACTGTTCCATAGCATAT 59.344 41.667 0.00 0.00 0.00 1.78
1333 1374 6.206048 TCAATGAGACAATGCATATCATGGAC 59.794 38.462 13.97 3.58 35.13 4.02
1981 2041 5.534207 TTGTCCAGCATTTCACTGAAAAT 57.466 34.783 8.28 0.00 37.32 1.82
2041 2101 5.514169 TCCAGTATGAAATAACCCATGCAA 58.486 37.500 0.00 0.00 39.69 4.08
2155 4995 7.220740 TCATCCACACAGTTATTTCTACACAA 58.779 34.615 0.00 0.00 0.00 3.33
2330 5170 8.508875 TCATTAATCTATACGTAACAGCATCGA 58.491 33.333 0.00 0.00 0.00 3.59
2575 5483 7.036863 ACCAGTTCCCTATTCCAGAAAAGAATA 60.037 37.037 0.00 0.00 35.59 1.75
2637 5545 5.799681 CAAACCTGCAAACAAATGTTCTT 57.200 34.783 0.00 0.00 37.25 2.52
2728 5636 8.081025 CGTTTACTACTAGTCAAAGTTTCTCCT 58.919 37.037 0.00 0.00 0.00 3.69
2764 5672 7.011763 CACAGATAGTCGATCATCAAAATGGTT 59.988 37.037 10.68 0.00 36.98 3.67
2890 5801 3.023119 TGAGTGAACAGGCACAACAATT 58.977 40.909 0.00 0.00 41.19 2.32
3157 6068 8.200792 ACTACAGGACAGAATCATATGAAGAAC 58.799 37.037 9.99 2.01 0.00 3.01
3164 6075 7.563188 AGTTCAGACTACAGGACAGAATCATAT 59.437 37.037 0.00 0.00 33.32 1.78
3313 6464 8.715998 CACTGGATTTAGACATGCTTATACATC 58.284 37.037 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.