Multiple sequence alignment - TraesCS7A01G307800

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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 TraesCS7A01G307800 chr7A 100.000 2455 0 0 1 2455 435733609 435731155 0.000000e+00 4534
1 TraesCS7A01G307800 chr7A 95.666 2492 65 18 1 2455 563493391 563495876 0.000000e+00 3964
2 TraesCS7A01G307800 chr7A 96.112 1569 56 4 887 2455 87693049 87691486 0.000000e+00 2555
3 TraesCS7A01G307800 chr7A 96.350 904 26 3 1 898 87693974 87693072 0.000000e+00 1480
4 TraesCS7A01G307800 chr7A 88.690 840 69 12 71 898 139135876 139135051 0.000000e+00 1002
5 TraesCS7A01G307800 chr7A 89.234 548 46 8 886 1432 139135029 139134494 0.000000e+00 673
6 TraesCS7A01G307800 chr5A 96.612 2273 73 3 185 2455 690643132 690640862 0.000000e+00 3768
7 TraesCS7A01G307800 chr5A 97.064 545 16 0 185 729 698853177 698853721 0.000000e+00 918
8 TraesCS7A01G307800 chr2B 96.851 1715 47 5 92 1806 338729377 338727670 0.000000e+00 2861
9 TraesCS7A01G307800 chr1D 96.877 1569 43 5 887 2455 34022525 34020963 0.000000e+00 2621
10 TraesCS7A01G307800 chr1D 97.345 904 17 3 1 898 34023450 34022548 0.000000e+00 1530
11 TraesCS7A01G307800 chr1D 92.078 669 30 13 1801 2455 123675626 123674967 0.000000e+00 920
12 TraesCS7A01G307800 chr1D 90.244 82 6 1 1429 1508 442443034 442442953 3.340000e-19 106
13 TraesCS7A01G307800 chr3B 96.781 1367 40 4 92 1458 395707735 395706373 0.000000e+00 2278
14 TraesCS7A01G307800 chr3B 96.580 965 29 3 1493 2455 395706372 395705410 0.000000e+00 1596
15 TraesCS7A01G307800 chr5D 89.085 907 77 11 1 895 448013343 448014239 0.000000e+00 1107
16 TraesCS7A01G307800 chr5D 88.470 928 74 14 1541 2443 448014875 448015794 0.000000e+00 1090
17 TraesCS7A01G307800 chr5D 88.764 534 47 8 900 1432 448014285 448014806 2.060000e-180 641
18 TraesCS7A01G307800 chr5B 92.354 667 30 12 1801 2455 102916548 102917205 0.000000e+00 929
19 TraesCS7A01G307800 chr2D 92.042 666 31 12 1801 2455 5789776 5789122 0.000000e+00 917
20 TraesCS7A01G307800 chr4D 92.767 636 27 10 1801 2425 294681649 294682276 0.000000e+00 902
21 TraesCS7A01G307800 chr1A 88.665 547 49 8 887 1432 291624935 291624401 0.000000e+00 654


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 TraesCS7A01G307800 chr7A 435731155 435733609 2454 True 4534.0 4534 100.0000 1 2455 1 chr7A.!!$R1 2454
1 TraesCS7A01G307800 chr7A 563493391 563495876 2485 False 3964.0 3964 95.6660 1 2455 1 chr7A.!!$F1 2454
2 TraesCS7A01G307800 chr7A 87691486 87693974 2488 True 2017.5 2555 96.2310 1 2455 2 chr7A.!!$R2 2454
3 TraesCS7A01G307800 chr7A 139134494 139135876 1382 True 837.5 1002 88.9620 71 1432 2 chr7A.!!$R3 1361
4 TraesCS7A01G307800 chr5A 690640862 690643132 2270 True 3768.0 3768 96.6120 185 2455 1 chr5A.!!$R1 2270
5 TraesCS7A01G307800 chr5A 698853177 698853721 544 False 918.0 918 97.0640 185 729 1 chr5A.!!$F1 544
6 TraesCS7A01G307800 chr2B 338727670 338729377 1707 True 2861.0 2861 96.8510 92 1806 1 chr2B.!!$R1 1714
7 TraesCS7A01G307800 chr1D 34020963 34023450 2487 True 2075.5 2621 97.1110 1 2455 2 chr1D.!!$R3 2454
8 TraesCS7A01G307800 chr1D 123674967 123675626 659 True 920.0 920 92.0780 1801 2455 1 chr1D.!!$R1 654
9 TraesCS7A01G307800 chr3B 395705410 395707735 2325 True 1937.0 2278 96.6805 92 2455 2 chr3B.!!$R1 2363
10 TraesCS7A01G307800 chr5D 448013343 448015794 2451 False 946.0 1107 88.7730 1 2443 3 chr5D.!!$F1 2442
11 TraesCS7A01G307800 chr5B 102916548 102917205 657 False 929.0 929 92.3540 1801 2455 1 chr5B.!!$F1 654
12 TraesCS7A01G307800 chr2D 5789122 5789776 654 True 917.0 917 92.0420 1801 2455 1 chr2D.!!$R1 654
13 TraesCS7A01G307800 chr4D 294681649 294682276 627 False 902.0 902 92.7670 1801 2425 1 chr4D.!!$F1 624
14 TraesCS7A01G307800 chr1A 291624401 291624935 534 True 654.0 654 88.6650 887 1432 1 chr1A.!!$R1 545

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
61 64 2.283604 TAGGACCGAGTGCAGGCA 60.284 61.111 0.0 0.0 0.0 4.75 F
1043 1103 2.126463 CGATCACCACGTCGCTGT 60.126 61.111 0.0 0.0 0.0 4.40 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1155 1216 1.952193 GCACTTTGCAAACCAACCAT 58.048 45.000 8.05 0.0 44.26 3.55 R
2409 2570 2.990967 CGCCACCCCACATTGCTT 60.991 61.111 0.00 0.0 0.00 3.91 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
61 64 2.283604 TAGGACCGAGTGCAGGCA 60.284 61.111 0.00 0.00 0.00 4.75
90 93 2.575279 AGGATCAACAGCAGGAGACAAT 59.425 45.455 0.00 0.00 0.00 2.71
195 198 2.668280 GCGCGGAGACTTGTTCCAC 61.668 63.158 8.83 0.00 34.24 4.02
596 610 6.804677 TGAAAGAACTAAAAGAAATGCAGCA 58.195 32.000 0.00 0.00 0.00 4.41
645 659 8.504815 CAATTTTGGAGATCACAGAGCTATATG 58.495 37.037 0.00 0.00 0.00 1.78
672 686 6.349973 ACGAGTTATTATGTTGATGCACAG 57.650 37.500 0.00 0.00 0.00 3.66
1037 1097 2.261671 GCTCCACGATCACCACGT 59.738 61.111 0.00 0.00 44.83 4.49
1043 1103 2.126463 CGATCACCACGTCGCTGT 60.126 61.111 0.00 0.00 0.00 4.40
1155 1216 7.749377 TCCCTCTACTGGATCTGAATTTTTA 57.251 36.000 0.00 0.00 0.00 1.52
1478 1539 5.032220 GGTGTTCAACCTTAGTTCAAAACG 58.968 41.667 0.00 0.00 46.55 3.60
1485 1546 2.482721 CCTTAGTTCAAAACGGCGACAT 59.517 45.455 16.62 0.00 36.23 3.06
1537 1598 7.924358 TGCCAATTAGTATAGTCCCTTAAGA 57.076 36.000 3.36 0.00 0.00 2.10
1631 1712 1.737838 TGTAGGCTTGTAGTGCATGC 58.262 50.000 11.82 11.82 44.59 4.06
1803 1886 7.252612 TCACTAGAATTTGGTTGGACTATGA 57.747 36.000 0.00 0.00 0.00 2.15
1999 2084 5.557576 ATGATGTTCATCCTGCTAAGCTA 57.442 39.130 9.83 0.00 29.59 3.32
2018 2106 3.388350 GCTACAGGGGTAATAGTGCTTCT 59.612 47.826 0.00 0.00 0.00 2.85
2081 2227 4.901250 TGGATCAGATGGCTTAGTATGTGA 59.099 41.667 0.00 2.34 32.17 3.58
2378 2539 3.969976 TCCTCAGGTGGATCTAATCAAGG 59.030 47.826 0.00 0.00 0.00 3.61
2409 2570 3.181459 TGACCGTCTTCCATTTCAACTGA 60.181 43.478 0.00 0.00 0.00 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
61 64 0.745845 GCTGTTGATCCTGGTCGCAT 60.746 55.000 0.00 0.00 0.00 4.73
90 93 9.232473 TGTATTAATAACAGCCACAATGTAACA 57.768 29.630 0.00 0.00 0.00 2.41
147 150 1.609208 GTGAACAAGTGCCCATCTGT 58.391 50.000 0.00 0.00 0.00 3.41
621 635 7.743749 ACATATAGCTCTGTGATCTCCAAAAT 58.256 34.615 2.80 0.00 0.00 1.82
645 659 8.172484 TGTGCATCAACATAATAACTCGTTAAC 58.828 33.333 0.00 0.00 0.00 2.01
672 686 5.464168 ACAAGCTCACTAAATTGAATGCAC 58.536 37.500 0.00 0.00 0.00 4.57
840 856 7.439157 TTTACAAAGACACAGATGATTCAGG 57.561 36.000 0.00 0.00 0.00 3.86
1037 1097 2.604686 AAGGCCAGGAGACAGCGA 60.605 61.111 5.01 0.00 33.06 4.93
1155 1216 1.952193 GCACTTTGCAAACCAACCAT 58.048 45.000 8.05 0.00 44.26 3.55
1478 1539 4.250464 TCCGATCCATAATAAATGTCGCC 58.750 43.478 0.00 0.00 0.00 5.54
1485 1546 7.850935 ACTACTTCCTCCGATCCATAATAAA 57.149 36.000 0.00 0.00 0.00 1.40
1537 1598 7.516209 TCCCATATCCTATGCTACTTTTTAGGT 59.484 37.037 0.00 0.00 34.18 3.08
1631 1712 3.011119 AGTTCTAGCTCGTACAGGTGAG 58.989 50.000 0.00 0.37 33.71 3.51
1764 1847 6.605471 TTCTAGTGATGTGGCCGATATAAT 57.395 37.500 0.00 0.00 0.00 1.28
1773 1856 4.380867 CCAACCAAATTCTAGTGATGTGGC 60.381 45.833 14.31 0.00 0.00 5.01
1803 1886 5.106157 CCCTCTTTCGACTTAAACATGCAAT 60.106 40.000 0.00 0.00 0.00 3.56
1999 2084 4.621769 ACTAGAAGCACTATTACCCCTGT 58.378 43.478 0.00 0.00 0.00 4.00
2034 2122 8.418662 CCATAACTGATCAATTGACCATGATTT 58.581 33.333 11.07 1.22 36.45 2.17
2056 2172 6.725834 TCACATACTAAGCCATCTGATCCATA 59.274 38.462 0.00 0.00 0.00 2.74
2378 2539 3.071479 TGGAAGACGGTCAATAAGTTGC 58.929 45.455 11.27 0.76 35.26 4.17
2409 2570 2.990967 CGCCACCCCACATTGCTT 60.991 61.111 0.00 0.00 0.00 3.91


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

AutoCloner maintained by Alex Coulton.