Multiple sequence alignment - TraesCS7A01G290700

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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 TraesCS7A01G290700 chr7A 100.000 2210 0 0 1 2210 352678560 352676351 0.000000e+00 4082
1 TraesCS7A01G290700 chr1B 93.971 2239 100 14 1 2210 633729984 633727752 0.000000e+00 3354
2 TraesCS7A01G290700 chr2D 94.039 2231 100 20 1 2210 272802777 272800559 0.000000e+00 3352
3 TraesCS7A01G290700 chr2D 94.493 1816 85 10 1 1805 630268109 630269920 0.000000e+00 2785
4 TraesCS7A01G290700 chr2D 94.714 1627 67 15 600 2210 33933300 33934923 0.000000e+00 2510
5 TraesCS7A01G290700 chr3A 93.904 2231 108 14 1 2208 672879547 672877322 0.000000e+00 3341
6 TraesCS7A01G290700 chr3B 93.753 2241 104 15 1 2210 201561895 201559660 0.000000e+00 3330
7 TraesCS7A01G290700 chr5B 93.683 2232 110 19 1 2210 432875612 432877834 0.000000e+00 3312
8 TraesCS7A01G290700 chr5B 92.600 527 22 8 1701 2210 413608023 413608549 0.000000e+00 741
9 TraesCS7A01G290700 chr5D 93.190 2232 125 13 1 2210 432293831 432291605 0.000000e+00 3254
10 TraesCS7A01G290700 chr4A 92.867 2215 138 15 1 2208 219340976 219338775 0.000000e+00 3197
11 TraesCS7A01G290700 chr4A 92.518 2232 140 14 1 2210 310761294 310763520 0.000000e+00 3171
12 TraesCS7A01G290700 chr4D 92.390 933 56 3 1293 2210 245648863 245649795 0.000000e+00 1315
13 TraesCS7A01G290700 chr5A 92.441 807 44 8 1421 2210 442270687 442271493 0.000000e+00 1136
14 TraesCS7A01G290700 chr5A 94.118 204 8 3 1970 2170 468919449 468919651 7.660000e-80 307
15 TraesCS7A01G290700 chr2B 89.167 360 32 6 98 453 626305097 626305453 2.010000e-120 442


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 TraesCS7A01G290700 chr7A 352676351 352678560 2209 True 4082 4082 100.000 1 2210 1 chr7A.!!$R1 2209
1 TraesCS7A01G290700 chr1B 633727752 633729984 2232 True 3354 3354 93.971 1 2210 1 chr1B.!!$R1 2209
2 TraesCS7A01G290700 chr2D 272800559 272802777 2218 True 3352 3352 94.039 1 2210 1 chr2D.!!$R1 2209
3 TraesCS7A01G290700 chr2D 630268109 630269920 1811 False 2785 2785 94.493 1 1805 1 chr2D.!!$F2 1804
4 TraesCS7A01G290700 chr2D 33933300 33934923 1623 False 2510 2510 94.714 600 2210 1 chr2D.!!$F1 1610
5 TraesCS7A01G290700 chr3A 672877322 672879547 2225 True 3341 3341 93.904 1 2208 1 chr3A.!!$R1 2207
6 TraesCS7A01G290700 chr3B 201559660 201561895 2235 True 3330 3330 93.753 1 2210 1 chr3B.!!$R1 2209
7 TraesCS7A01G290700 chr5B 432875612 432877834 2222 False 3312 3312 93.683 1 2210 1 chr5B.!!$F2 2209
8 TraesCS7A01G290700 chr5B 413608023 413608549 526 False 741 741 92.600 1701 2210 1 chr5B.!!$F1 509
9 TraesCS7A01G290700 chr5D 432291605 432293831 2226 True 3254 3254 93.190 1 2210 1 chr5D.!!$R1 2209
10 TraesCS7A01G290700 chr4A 219338775 219340976 2201 True 3197 3197 92.867 1 2208 1 chr4A.!!$R1 2207
11 TraesCS7A01G290700 chr4A 310761294 310763520 2226 False 3171 3171 92.518 1 2210 1 chr4A.!!$F1 2209
12 TraesCS7A01G290700 chr4D 245648863 245649795 932 False 1315 1315 92.390 1293 2210 1 chr4D.!!$F1 917
13 TraesCS7A01G290700 chr5A 442270687 442271493 806 False 1136 1136 92.441 1421 2210 1 chr5A.!!$F1 789

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
654 675 0.035439 AATAGCGGTGGGAACTGTGG 60.035 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 2143 4.469657 TGGTCCAGGTAAATCCATTATGC 58.53 43.478 0.0 0.0 39.02 3.14 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
140 141 6.209986 TCAAGTAGTACTTTCTTCGGATTCCA 59.790 38.462 13.00 0.00 36.03 3.53
234 236 7.932683 TTTTCTTTTTAAATACCCCCTTCCA 57.067 32.000 0.00 0.00 0.00 3.53
235 237 6.921486 TTCTTTTTAAATACCCCCTTCCAC 57.079 37.500 0.00 0.00 0.00 4.02
316 333 5.105187 TCCTTCCTCTATCCATATTCATGCG 60.105 44.000 0.00 0.00 0.00 4.73
337 354 5.588246 TGCGGAATTGCTCATGAACTAATAA 59.412 36.000 0.00 0.00 35.36 1.40
464 481 3.135348 AGGATGAGATCAATTCGGAAGCA 59.865 43.478 0.00 0.00 0.00 3.91
602 623 6.950842 TCCTTTTTCTGATCATAGAGAAGCA 58.049 36.000 0.00 0.00 30.03 3.91
610 631 8.419922 TCTGATCATAGAGAAGCAGTATGAAT 57.580 34.615 0.00 0.00 39.69 2.57
654 675 0.035439 AATAGCGGTGGGAACTGTGG 60.035 55.000 0.00 0.00 0.00 4.17
695 716 8.703604 TGATTGTCTAATAGTTCAAGTACAGC 57.296 34.615 0.00 0.00 0.00 4.40
722 743 7.595875 TGATATTGTTGAAGCACAGTCAAAATG 59.404 33.333 0.00 0.00 36.77 2.32
768 790 2.866762 CGTCAGCCTATAGGTTTTCTGC 59.133 50.000 20.10 12.40 37.57 4.26
846 869 3.451178 AGCGGAGGAAGAATTAGTAGCAA 59.549 43.478 0.00 0.00 0.00 3.91
950 974 9.337396 CTATTTGTAACATTCTATACTTGGGCA 57.663 33.333 0.00 0.00 0.00 5.36
968 992 5.776358 TGGGCAGGTGGAATTTATCTATTT 58.224 37.500 0.00 0.00 0.00 1.40
971 995 5.243954 GGCAGGTGGAATTTATCTATTTCCC 59.756 44.000 0.00 0.00 38.51 3.97
972 996 6.071320 GCAGGTGGAATTTATCTATTTCCCT 58.929 40.000 0.00 0.00 38.51 4.20
973 997 7.231467 GCAGGTGGAATTTATCTATTTCCCTA 58.769 38.462 0.00 0.00 38.51 3.53
974 998 7.890655 GCAGGTGGAATTTATCTATTTCCCTAT 59.109 37.037 0.00 0.00 38.51 2.57
1259 1286 9.468532 GAATATTTTCAACACAAAAGCTCTCTT 57.531 29.630 0.00 0.00 0.00 2.85
1489 1516 4.142600 CGAGGGTGAATCCACTTTGAATTC 60.143 45.833 0.00 0.00 42.77 2.17
1503 1530 9.787532 CCACTTTGAATTCGATAAATGTATTGT 57.212 29.630 0.04 0.00 0.00 2.71
1513 1540 9.605955 TTCGATAAATGTATTGTTTGTGAAGTG 57.394 29.630 0.00 0.00 0.00 3.16
1522 1549 5.384063 TTGTTTGTGAAGTGTGTGTTCAT 57.616 34.783 0.00 0.00 36.35 2.57
1533 1560 4.991056 AGTGTGTGTTCATGTATGTCTGAC 59.009 41.667 0.00 0.00 0.00 3.51
1545 1572 5.730550 TGTATGTCTGACAGATTTACCCAC 58.269 41.667 16.46 1.66 0.00 4.61
1547 1574 6.666113 TGTATGTCTGACAGATTTACCCACTA 59.334 38.462 16.46 0.00 0.00 2.74
1635 1662 8.153550 TGGAGTTTGTATATTTTGTGGCAATTT 58.846 29.630 0.00 0.00 0.00 1.82
1664 1691 8.282455 TGAGTATTGTCCAACAAGTTGTTTAA 57.718 30.769 18.59 11.56 41.94 1.52
1755 1782 5.019785 AGTCGGTTACCAATCTCCATAAC 57.980 43.478 1.13 0.00 0.00 1.89
1758 1785 3.181473 CGGTTACCAATCTCCATAACGGA 60.181 47.826 1.13 0.00 43.61 4.69
1781 1808 8.427012 CGGAAGATTACACAATTCAAACAATTG 58.573 33.333 3.24 3.24 41.91 2.32
2044 2096 7.955750 TCCTTTTTCCTTCCTTGAATCCTTTAT 59.044 33.333 0.00 0.00 0.00 1.40
2045 2097 8.253810 CCTTTTTCCTTCCTTGAATCCTTTATC 58.746 37.037 0.00 0.00 0.00 1.75
2188 2240 9.413734 GGTCTAGGAGTAGTATTACTTACCAAA 57.586 37.037 0.85 0.00 40.21 3.28
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
60 61 6.040391 CGATCCCTTTTATGGGCAAAAATCTA 59.960 38.462 0.00 0.00 46.67 1.98
81 82 7.472543 ACAAATTGCAAGTCCTTATTACGATC 58.527 34.615 4.94 0.00 0.00 3.69
156 157 5.774690 AGCCATTTCCTTAACAAGTGAATGA 59.225 36.000 10.56 0.00 33.93 2.57
231 233 3.178865 ACTATTCTTCTTTCCCCGTGGA 58.821 45.455 0.00 0.00 39.54 4.02
316 333 7.333528 TGGTTATTAGTTCATGAGCAATTCC 57.666 36.000 12.41 13.38 0.00 3.01
435 452 9.845740 TTCCGAATTGATCTCATCCTTTATAAA 57.154 29.630 0.00 0.00 0.00 1.40
464 481 9.692325 ATTCCATCTGCTAGAATAAGAAAAAGT 57.308 29.630 0.00 0.00 0.00 2.66
543 564 1.913762 CTATCCCCTGGGGCGTAGG 60.914 68.421 27.93 10.82 43.94 3.18
562 583 9.599866 CAGAAAAAGGAAAGGACTATTTTGTTT 57.400 29.630 0.00 0.00 0.00 2.83
570 591 9.046846 TCTATGATCAGAAAAAGGAAAGGACTA 57.953 33.333 0.09 0.00 0.00 2.59
602 623 7.926555 CCGTACATGAAACCTTAGATTCATACT 59.073 37.037 0.00 5.00 42.72 2.12
610 631 6.289834 TCAAAACCGTACATGAAACCTTAGA 58.710 36.000 0.00 0.00 0.00 2.10
681 702 8.311109 TCAACAATATCAGCTGTACTTGAACTA 58.689 33.333 22.48 0.41 0.00 2.24
695 716 5.868043 TGACTGTGCTTCAACAATATCAG 57.132 39.130 0.00 0.00 0.00 2.90
702 723 3.119209 TGCATTTTGACTGTGCTTCAACA 60.119 39.130 0.00 0.00 39.52 3.33
782 805 5.640189 ATCTTTCACATTCTGCCAAAGAG 57.360 39.130 0.00 0.00 34.10 2.85
846 869 5.812286 ACCGGAATATTCAGTTTGGTAACT 58.188 37.500 17.07 0.00 45.40 2.24
924 947 9.337396 TGCCCAAGTATAGAATGTTACAAATAG 57.663 33.333 0.00 0.00 0.00 1.73
940 964 3.473113 AAATTCCACCTGCCCAAGTAT 57.527 42.857 0.00 0.00 0.00 2.12
996 1020 7.966246 AATTGCAAGTGCTTTATTCATTTGA 57.034 28.000 4.94 0.00 42.66 2.69
1012 1036 6.375377 CCATTGTCATTTCCAAAATTGCAAG 58.625 36.000 4.94 0.00 0.00 4.01
1016 1040 9.835389 ATATACCCATTGTCATTTCCAAAATTG 57.165 29.630 0.00 0.00 0.00 2.32
1147 1174 4.405756 TGCCCAGGGAAATAGGTAAAAA 57.594 40.909 10.89 0.00 0.00 1.94
1489 1516 8.839914 CACACTTCACAAACAATACATTTATCG 58.160 33.333 0.00 0.00 0.00 2.92
1503 1530 6.094742 ACATACATGAACACACACTTCACAAA 59.905 34.615 0.00 0.00 30.46 2.83
1513 1540 5.230182 TCTGTCAGACATACATGAACACAC 58.770 41.667 2.97 0.00 0.00 3.82
1522 1549 5.483937 AGTGGGTAAATCTGTCAGACATACA 59.516 40.000 20.36 8.57 0.00 2.29
1533 1560 5.940617 TCCAATCCATAGTGGGTAAATCTG 58.059 41.667 0.00 0.00 41.33 2.90
1545 1572 7.886629 TCCTTTTCAAATCTCCAATCCATAG 57.113 36.000 0.00 0.00 0.00 2.23
1547 1574 9.443365 AATATCCTTTTCAAATCTCCAATCCAT 57.557 29.630 0.00 0.00 0.00 3.41
1699 1726 8.686397 TTTGATTGTAATTCAATTCATGACGG 57.314 30.769 0.00 0.00 45.49 4.79
1727 1754 4.874396 GGAGATTGGTAACCGACTTAAAGG 59.126 45.833 0.00 0.00 0.00 3.11
1755 1782 8.427012 CAATTGTTTGAATTGTGTAATCTTCCG 58.573 33.333 0.00 0.00 34.60 4.30
1758 1785 8.428063 TCCCAATTGTTTGAATTGTGTAATCTT 58.572 29.630 4.43 0.00 36.24 2.40
1781 1808 9.338291 GTTTATTTTACTTTCAGACGAATTCCC 57.662 33.333 0.00 0.00 0.00 3.97
2091 2143 4.469657 TGGTCCAGGTAAATCCATTATGC 58.530 43.478 0.00 0.00 39.02 3.14


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

AutoCloner maintained by Alex Coulton.