Multiple sequence alignment - TraesCS7A01G429900

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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 TraesCS7A01G429900 chr7A 100.000 2575 0 0 1 2575 624796857 624799431 0.000000e+00 4756.0
1 TraesCS7A01G429900 chr2A 95.162 1385 64 2 644 2025 87812062 87813446 0.000000e+00 2183.0
2 TraesCS7A01G429900 chr2A 91.517 389 30 3 646 1033 617758063 617757677 1.360000e-147 532.0
3 TraesCS7A01G429900 chr2A 97.417 271 6 1 2305 2575 87849734 87850003 6.490000e-126 460.0
4 TraesCS7A01G429900 chr2A 95.122 287 14 0 2023 2309 87840783 87841069 1.090000e-123 453.0
5 TraesCS7A01G429900 chr2D 93.136 1384 85 5 646 2026 645767898 645766522 0.000000e+00 2021.0
6 TraesCS7A01G429900 chr2D 90.081 1230 101 11 637 1863 596256003 596257214 0.000000e+00 1576.0
7 TraesCS7A01G429900 chr2D 95.841 553 23 0 2023 2575 645764162 645763610 0.000000e+00 894.0
8 TraesCS7A01G429900 chr2D 92.586 553 40 1 2023 2575 596263487 596264038 0.000000e+00 793.0
9 TraesCS7A01G429900 chr2D 81.982 222 26 7 1806 2025 596257051 596257260 2.630000e-40 176.0
10 TraesCS7A01G429900 chr2D 100.000 31 0 0 357 387 45477511 45477481 9.950000e-05 58.4
11 TraesCS7A01G429900 chr6A 94.017 1287 72 5 646 1929 581971280 581969996 0.000000e+00 1945.0
12 TraesCS7A01G429900 chr6A 92.428 383 26 2 644 1024 547338744 547339125 6.270000e-151 544.0
13 TraesCS7A01G429900 chr6A 84.536 97 13 2 1733 1828 581970088 581969993 7.590000e-16 95.3
14 TraesCS7A01G429900 chr4A 92.362 1283 91 5 646 1923 684215980 684217260 0.000000e+00 1820.0
15 TraesCS7A01G429900 chr4A 95.660 553 24 0 2023 2575 684266975 684267527 0.000000e+00 889.0
16 TraesCS7A01G429900 chr4A 95.122 246 11 1 1782 2026 684217066 684217311 1.120000e-103 387.0
17 TraesCS7A01G429900 chr4A 89.011 91 8 2 1887 1976 684217067 684217156 7.530000e-21 111.0
18 TraesCS7A01G429900 chr2B 87.294 1393 147 11 646 2023 765756818 765755441 0.000000e+00 1565.0
19 TraesCS7A01G429900 chr2B 92.196 551 43 0 2023 2573 765752804 765752254 0.000000e+00 780.0
20 TraesCS7A01G429900 chr2B 92.453 53 4 0 1258 1310 331371712 331371764 2.750000e-10 76.8
21 TraesCS7A01G429900 chr5A 90.649 524 47 1 647 1168 705355219 705355742 0.000000e+00 695.0
22 TraesCS7A01G429900 chr5A 97.318 261 7 0 2315 2575 705355734 705355994 6.540000e-121 444.0
23 TraesCS7A01G429900 chr7B 85.417 624 53 23 34 646 585465084 585465680 4.710000e-172 614.0
24 TraesCS7A01G429900 chr7D 87.747 506 40 10 1 493 541419375 541419871 2.870000e-159 571.0
25 TraesCS7A01G429900 chr7D 85.149 101 3 1 539 639 541419893 541419981 2.730000e-15 93.5
26 TraesCS7A01G429900 chr6B 96.774 31 1 0 357 387 682117571 682117541 5.000000e-03 52.8


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 TraesCS7A01G429900 chr7A 624796857 624799431 2574 False 4756.000000 4756 100.0000 1 2575 1 chr7A.!!$F1 2574
1 TraesCS7A01G429900 chr2A 87812062 87813446 1384 False 2183.000000 2183 95.1620 644 2025 1 chr2A.!!$F1 1381
2 TraesCS7A01G429900 chr2D 645763610 645767898 4288 True 1457.500000 2021 94.4885 646 2575 2 chr2D.!!$R2 1929
3 TraesCS7A01G429900 chr2D 596256003 596257260 1257 False 876.000000 1576 86.0315 637 2025 2 chr2D.!!$F2 1388
4 TraesCS7A01G429900 chr2D 596263487 596264038 551 False 793.000000 793 92.5860 2023 2575 1 chr2D.!!$F1 552
5 TraesCS7A01G429900 chr6A 581969993 581971280 1287 True 1020.150000 1945 89.2765 646 1929 2 chr6A.!!$R1 1283
6 TraesCS7A01G429900 chr4A 684266975 684267527 552 False 889.000000 889 95.6600 2023 2575 1 chr4A.!!$F1 552
7 TraesCS7A01G429900 chr4A 684215980 684217311 1331 False 772.666667 1820 92.1650 646 2026 3 chr4A.!!$F2 1380
8 TraesCS7A01G429900 chr2B 765752254 765756818 4564 True 1172.500000 1565 89.7450 646 2573 2 chr2B.!!$R1 1927
9 TraesCS7A01G429900 chr5A 705355219 705355994 775 False 569.500000 695 93.9835 647 2575 2 chr5A.!!$F1 1928
10 TraesCS7A01G429900 chr7B 585465084 585465680 596 False 614.000000 614 85.4170 34 646 1 chr7B.!!$F1 612
11 TraesCS7A01G429900 chr7D 541419375 541419981 606 False 332.250000 571 86.4480 1 639 2 chr7D.!!$F1 638

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
43 44 4.075682 TGCATAGCTCGATAGTTAGCTCT 58.924 43.478 0.0 0.0 45.92 4.09 F
1076 1108 0.389426 GGTATGTTGTCGCTCGTGGT 60.389 55.000 0.0 0.0 0.00 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1088 1120 0.400213 AATGGTGTCACGGACATGGT 59.600 50.000 9.47 0.0 44.63 3.55 R
2209 5223 3.266772 ACTGCTCCCTGGTATGAATTTGA 59.733 43.478 0.00 0.0 0.00 2.69 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
43 44 4.075682 TGCATAGCTCGATAGTTAGCTCT 58.924 43.478 0.00 0.00 45.92 4.09
97 98 5.411669 CAGCCCGTTAGTTCTTACAGATTTT 59.588 40.000 0.00 0.00 0.00 1.82
121 122 6.817184 TGGGGTTTTCGTATTTTTCATTTCA 58.183 32.000 0.00 0.00 0.00 2.69
158 159 9.071221 CATACATATTGCACATGTTTTTACGTT 57.929 29.630 16.13 0.00 37.74 3.99
166 167 6.146898 GCACATGTTTTTACGTTGGAAGTAT 58.853 36.000 0.00 0.00 0.00 2.12
664 678 4.404394 TGATAGAGTTAAATGCACCGGAGA 59.596 41.667 9.46 0.00 0.00 3.71
791 805 4.400961 GCTCGCTGACCTGCCCTT 62.401 66.667 0.00 0.00 0.00 3.95
886 905 4.713792 AACACTCTTCTTCACATTCCCT 57.286 40.909 0.00 0.00 0.00 4.20
1024 1053 4.714555 CGTCGTCGTCAGCGTCGT 62.715 66.667 6.55 0.00 46.29 4.34
1025 1054 2.426425 GTCGTCGTCAGCGTCGTT 60.426 61.111 6.55 0.00 46.29 3.85
1026 1055 2.426261 TCGTCGTCAGCGTCGTTG 60.426 61.111 2.22 2.22 46.29 4.10
1027 1056 2.724721 CGTCGTCAGCGTCGTTGT 60.725 61.111 9.00 0.00 42.66 3.32
1038 1070 1.081242 GTCGTTGTCGCTTCCGGTA 60.081 57.895 0.00 0.00 36.96 4.02
1076 1108 0.389426 GGTATGTTGTCGCTCGTGGT 60.389 55.000 0.00 0.00 0.00 4.16
1088 1120 1.876416 GCTCGTGGTTTGTCCTTGCTA 60.876 52.381 0.00 0.00 37.07 3.49
1493 1525 6.647229 TGATGTTGTGAAGAAGCTAGATGAT 58.353 36.000 0.00 0.00 0.00 2.45
1592 1628 7.463544 TGAAATGAATGAAGTACATGTAAGCG 58.536 34.615 7.25 0.00 39.39 4.68
1598 1634 7.923878 TGAATGAAGTACATGTAAGCGCTATTA 59.076 33.333 12.05 0.00 39.39 0.98
1638 1674 9.604626 GAATGAAGTGTTTAATCTGAACTGAAG 57.395 33.333 0.00 0.00 0.00 3.02
1652 1688 5.614308 TGAACTGAAGAGCAAGATTGAGAA 58.386 37.500 0.00 0.00 0.00 2.87
1780 1911 6.647334 TGAATAGCTTCATTTTGGTCAACA 57.353 33.333 0.00 0.00 36.46 3.33
1792 1923 1.666553 GTCAACATGGACGGTCGCA 60.667 57.895 1.43 2.06 0.00 5.10
1832 1964 8.133024 TGATGGTTAGCTTATTTTGGTTTCAT 57.867 30.769 0.00 0.00 0.00 2.57
2072 5086 3.196685 GTGGAAGCTCTGTAGATCCAGTT 59.803 47.826 1.20 0.00 39.53 3.16
2101 5115 6.317140 CACACATCATCAAAGCCTATGTTACT 59.683 38.462 0.00 0.00 0.00 2.24
2158 5172 4.523083 TGCTGAAACTTAGGAACAACAGT 58.477 39.130 0.00 0.00 0.00 3.55
2195 5209 4.631813 GTGTCTGTATCCCTGTCAACAATC 59.368 45.833 0.00 0.00 0.00 2.67
2209 5223 3.009723 CAACAATCCGCAGTCCTGTATT 58.990 45.455 0.00 0.00 0.00 1.89
2231 5245 3.266772 TCAAATTCATACCAGGGAGCAGT 59.733 43.478 0.00 0.00 0.00 4.40
2334 5348 8.464404 CAACTTCACATCCATCAAAATACTCAT 58.536 33.333 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 6.817184 TGAAATGAAAAATACGAAAACCCCA 58.183 32.000 0.00 0.00 0.00 4.96
144 145 9.589111 AAAAATACTTCCAACGTAAAAACATGT 57.411 25.926 0.00 0.00 0.00 3.21
404 405 7.421599 ACAATGTCAACGAAAAACATACATGA 58.578 30.769 0.00 0.00 33.42 3.07
412 413 8.695284 TGCAAATATACAATGTCAACGAAAAAC 58.305 29.630 0.00 0.00 0.00 2.43
535 549 9.123902 TGCTATAATGTGTATGAAGAAAATGCT 57.876 29.630 0.00 0.00 0.00 3.79
536 550 9.903682 ATGCTATAATGTGTATGAAGAAAATGC 57.096 29.630 0.00 0.00 0.00 3.56
639 653 5.680619 TCCGGTGCATTTAACTCTATCAAT 58.319 37.500 0.00 0.00 0.00 2.57
640 654 5.092554 TCCGGTGCATTTAACTCTATCAA 57.907 39.130 0.00 0.00 0.00 2.57
641 655 4.404394 TCTCCGGTGCATTTAACTCTATCA 59.596 41.667 0.00 0.00 0.00 2.15
642 656 4.945246 TCTCCGGTGCATTTAACTCTATC 58.055 43.478 0.00 0.00 0.00 2.08
659 673 3.546670 CGACGAAACTTTTAGGATCTCCG 59.453 47.826 0.00 0.00 42.08 4.63
664 678 4.319261 GCACAACGACGAAACTTTTAGGAT 60.319 41.667 0.00 0.00 0.00 3.24
791 805 2.904866 GTGGGTCAAAGCGCCACA 60.905 61.111 2.29 0.00 33.13 4.17
850 869 5.917545 AGAGTGTTTCTAGGGGGTTTTTA 57.082 39.130 0.00 0.00 33.23 1.52
886 905 3.054361 GGAAGAAATAGAGCAAGGGACCA 60.054 47.826 0.00 0.00 0.00 4.02
1024 1053 0.947180 GCTTGTACCGGAAGCGACAA 60.947 55.000 9.46 9.27 36.74 3.18
1025 1054 1.373748 GCTTGTACCGGAAGCGACA 60.374 57.895 9.46 0.66 36.74 4.35
1026 1055 3.471399 GCTTGTACCGGAAGCGAC 58.529 61.111 9.46 0.00 36.74 5.19
1032 1064 2.706890 GAAATTGGAGCTTGTACCGGA 58.293 47.619 9.46 0.00 0.00 5.14
1038 1070 2.154462 CCAGACGAAATTGGAGCTTGT 58.846 47.619 0.00 0.00 36.55 3.16
1076 1108 2.790433 GGACATGGTAGCAAGGACAAA 58.210 47.619 0.00 0.00 0.00 2.83
1088 1120 0.400213 AATGGTGTCACGGACATGGT 59.600 50.000 9.47 0.00 44.63 3.55
1150 1182 1.865788 CGATGGTTGGGGCACTTGTG 61.866 60.000 0.00 0.00 0.00 3.33
1265 1297 2.814805 AGTAGTGCTGGCATGGATTT 57.185 45.000 0.00 0.00 0.00 2.17
1331 1363 4.712051 TCTTGCAATAGATATGTGGCCT 57.288 40.909 3.32 0.00 0.00 5.19
1493 1525 6.609212 AGAACATCCTAACTAAGCAGATCAGA 59.391 38.462 0.00 0.00 0.00 3.27
1598 1634 8.641498 AACACTTCATTCAAATAGTTCATCCT 57.359 30.769 0.00 0.00 0.00 3.24
1633 1669 6.150641 TCCAAATTCTCAATCTTGCTCTTCAG 59.849 38.462 0.00 0.00 0.00 3.02
1638 1674 5.100943 GCTTCCAAATTCTCAATCTTGCTC 58.899 41.667 0.00 0.00 0.00 4.26
1652 1688 9.947433 TTCATTTAGATCAAAATGCTTCCAAAT 57.053 25.926 0.00 0.00 43.49 2.32
1741 1871 4.993584 GCTATTCATCAATGTGGACGATCT 59.006 41.667 0.00 0.00 0.00 2.75
1780 1911 3.774959 GATCGCTGCGACCGTCCAT 62.775 63.158 28.41 9.58 39.18 3.41
1792 1923 1.586422 CATCATTGGGAACGATCGCT 58.414 50.000 16.60 1.61 39.17 4.93
2072 5086 3.623703 AGGCTTTGATGATGTGTGCATA 58.376 40.909 0.00 0.00 35.07 3.14
2195 5209 3.689161 TGAATTTGAATACAGGACTGCGG 59.311 43.478 0.00 0.00 0.00 5.69
2209 5223 3.266772 ACTGCTCCCTGGTATGAATTTGA 59.733 43.478 0.00 0.00 0.00 2.69
2231 5245 4.667573 TGGCCCAGTGTAATGTTTATTGA 58.332 39.130 0.00 0.00 0.00 2.57
2499 5513 8.262601 AGGGTTTCAGTTCTAAATTCCAAAAT 57.737 30.769 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.