Multiple sequence alignment - TraesCS7A01G080700

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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 TraesCS7A01G080700 chr7A 100.000 2487 0 0 1 2487 46402290 46404776 0.000000e+00 4593.0
1 TraesCS7A01G080700 chr7A 96.285 1669 52 4 822 2487 563584005 563585666 0.000000e+00 2730.0
2 TraesCS7A01G080700 chr7A 98.857 1050 9 2 1 1047 4970649 4971698 0.000000e+00 1869.0
3 TraesCS7A01G080700 chr7A 91.517 389 24 4 1486 1873 162829682 162830062 6.090000e-146 527.0
4 TraesCS7A01G080700 chr7A 98.134 268 5 0 1 268 708267938 708268205 3.750000e-128 468.0
5 TraesCS7A01G080700 chr7A 100.000 42 0 0 2188 2229 367137586 367137627 7.370000e-11 78.7
6 TraesCS7A01G080700 chr7A 91.071 56 4 1 2150 2204 83934764 83934709 9.540000e-10 75.0
7 TraesCS7A01G080700 chr7A 92.500 40 3 0 1239 1278 683423962 683423923 9.610000e-05 58.4
8 TraesCS7A01G080700 chr6B 97.713 2492 52 3 1 2487 596620321 596622812 0.000000e+00 4281.0
9 TraesCS7A01G080700 chrUn 97.673 2493 51 5 1 2487 282364699 282362208 0.000000e+00 4276.0
10 TraesCS7A01G080700 chrUn 97.513 2493 55 5 1 2487 86510015 86507524 0.000000e+00 4253.0
11 TraesCS7A01G080700 chr3B 97.391 2491 59 5 1 2487 92317835 92320323 0.000000e+00 4235.0
12 TraesCS7A01G080700 chr2B 97.231 2492 59 8 1 2487 30670614 30668128 0.000000e+00 4211.0
13 TraesCS7A01G080700 chr6A 97.075 2496 63 5 1 2487 84434141 84436635 0.000000e+00 4196.0
14 TraesCS7A01G080700 chr3D 97.110 2491 66 4 1 2487 154704963 154702475 0.000000e+00 4196.0
15 TraesCS7A01G080700 chr5A 98.400 125 2 0 255 379 322365510 322365634 1.160000e-53 220.0
16 TraesCS7A01G080700 chr5A 94.167 120 6 1 1376 1495 358783651 358783533 5.460000e-42 182.0
17 TraesCS7A01G080700 chr5A 84.184 196 13 6 618 806 130541528 130541712 9.140000e-40 174.0
18 TraesCS7A01G080700 chr5A 85.161 155 14 3 1980 2134 17131011 17131156 1.540000e-32 150.0
19 TraesCS7A01G080700 chr5A 97.674 43 1 0 693 735 306572748 306572706 9.540000e-10 75.0


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 TraesCS7A01G080700 chr7A 46402290 46404776 2486 False 4593 4593 100.000 1 2487 1 chr7A.!!$F2 2486
1 TraesCS7A01G080700 chr7A 563584005 563585666 1661 False 2730 2730 96.285 822 2487 1 chr7A.!!$F5 1665
2 TraesCS7A01G080700 chr7A 4970649 4971698 1049 False 1869 1869 98.857 1 1047 1 chr7A.!!$F1 1046
3 TraesCS7A01G080700 chr6B 596620321 596622812 2491 False 4281 4281 97.713 1 2487 1 chr6B.!!$F1 2486
4 TraesCS7A01G080700 chrUn 282362208 282364699 2491 True 4276 4276 97.673 1 2487 1 chrUn.!!$R2 2486
5 TraesCS7A01G080700 chrUn 86507524 86510015 2491 True 4253 4253 97.513 1 2487 1 chrUn.!!$R1 2486
6 TraesCS7A01G080700 chr3B 92317835 92320323 2488 False 4235 4235 97.391 1 2487 1 chr3B.!!$F1 2486
7 TraesCS7A01G080700 chr2B 30668128 30670614 2486 True 4211 4211 97.231 1 2487 1 chr2B.!!$R1 2486
8 TraesCS7A01G080700 chr6A 84434141 84436635 2494 False 4196 4196 97.075 1 2487 1 chr6A.!!$F1 2486
9 TraesCS7A01G080700 chr3D 154702475 154704963 2488 True 4196 4196 97.110 1 2487 1 chr3D.!!$R1 2486

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
151 152 1.991121 ACTCAACCCTGACGAGTACA 58.009 50.000 0.0 0.0 38.22 2.9 F
1047 1052 3.104512 TCCTGATGTAGTGGGATCGTTT 58.895 45.455 0.0 0.0 0.00 3.6 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1344 1350 0.529833 TGCGGCACAAACCCATATTG 59.470 50.000 0.0 0.0 0.00 1.90 R
1975 1983 1.266989 GGCTTGCGAAACAAAGTAGCT 59.733 47.619 0.0 0.0 37.96 3.32 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
151 152 1.991121 ACTCAACCCTGACGAGTACA 58.009 50.000 0.00 0.00 38.22 2.90
728 732 4.082190 TCGCTTATGCTTAGTCAAGTGAGT 60.082 41.667 0.00 0.00 33.76 3.41
783 787 3.326588 TCTTCAAAACTTCTCGGGATCCA 59.673 43.478 15.23 0.00 0.00 3.41
1047 1052 3.104512 TCCTGATGTAGTGGGATCGTTT 58.895 45.455 0.00 0.00 0.00 3.60
1167 1172 7.985184 CCAGTGGCTACATTTATGTTAAGTCTA 59.015 37.037 2.02 0.00 41.97 2.59
1198 1203 4.883006 GGGCCGTTGTACCTTTTGATTATA 59.117 41.667 0.00 0.00 0.00 0.98
1199 1204 5.533528 GGGCCGTTGTACCTTTTGATTATAT 59.466 40.000 0.00 0.00 0.00 0.86
1247 1252 4.591072 AGGGCTACTTTATTTGTTTGCCAA 59.409 37.500 0.00 0.00 37.47 4.52
1248 1253 5.248248 AGGGCTACTTTATTTGTTTGCCAAT 59.752 36.000 0.00 0.00 37.47 3.16
1387 1393 5.652891 AGGTGTTGAACGATCTACTCTACAT 59.347 40.000 8.53 0.00 33.23 2.29
1447 1453 3.263170 TCTTTCATTCATCAAGGGGTCGA 59.737 43.478 0.00 0.00 0.00 4.20
1540 1546 4.009370 AGAGGAAAGGTAGCTTGTCAAC 57.991 45.455 8.16 6.29 0.00 3.18
1624 1632 0.102663 GCTACTAAGGACCTGACGGC 59.897 60.000 0.00 0.00 0.00 5.68
1733 1741 0.806492 GAGTTTTCCTAGCCTCGCCG 60.806 60.000 0.00 0.00 0.00 6.46
1998 2006 2.208326 ACTTTGTTTCGCAAGCCTTG 57.792 45.000 0.00 0.00 38.47 3.61
2001 2009 1.681538 TTGTTTCGCAAGCCTTGGTA 58.318 45.000 6.57 0.00 32.52 3.25
2186 2194 1.316266 AGGTAGATGCCTCCCAGCT 59.684 57.895 0.00 0.00 43.77 4.24
2455 2471 2.177531 GGCGTCGTCGTCTAAGCA 59.822 61.111 3.66 0.00 38.74 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
151 152 0.550914 TGCTCCCTGACCAAGTTTGT 59.449 50.000 0.00 0.0 0.00 2.83
564 566 7.657354 CCATTTTATGTATCCATCTTGACTCGA 59.343 37.037 0.00 0.0 32.29 4.04
621 623 6.128282 GCGAAAGAAAGTGAAATGTCCTATCA 60.128 38.462 0.00 0.0 0.00 2.15
686 690 2.798283 CGAAAACGTGGCTGAGAGTAAA 59.202 45.455 0.00 0.0 0.00 2.01
728 732 6.753279 CCTGTTACGTTACTTCGAATGGAATA 59.247 38.462 6.24 0.0 33.26 1.75
1016 1021 3.133003 CACTACATCAGGACCCTTTCGAT 59.867 47.826 0.00 0.0 0.00 3.59
1047 1052 4.530553 TCTGCTAGAGGTTGTAACAATCCA 59.469 41.667 0.00 0.0 0.00 3.41
1167 1172 2.874664 TACAACGGCCCAAGCGACT 61.875 57.895 0.00 0.0 41.24 4.18
1198 1203 6.826668 TGTTCGGATCTGACAATACCATAAT 58.173 36.000 2.94 0.0 0.00 1.28
1199 1204 6.228616 TGTTCGGATCTGACAATACCATAA 57.771 37.500 2.94 0.0 0.00 1.90
1247 1252 5.353394 TCCATAAACACCTAGCGAAGAAT 57.647 39.130 0.00 0.0 0.00 2.40
1248 1253 4.811969 TCCATAAACACCTAGCGAAGAA 57.188 40.909 0.00 0.0 0.00 2.52
1310 1315 3.066342 CCGTATATCATAGGCGACCGAAT 59.934 47.826 0.00 0.0 0.00 3.34
1343 1348 0.814457 GCGGCACAAACCCATATTGA 59.186 50.000 0.00 0.0 0.00 2.57
1344 1350 0.529833 TGCGGCACAAACCCATATTG 59.470 50.000 0.00 0.0 0.00 1.90
1347 1353 1.677300 CCTGCGGCACAAACCCATA 60.677 57.895 0.00 0.0 0.00 2.74
1387 1393 1.559065 GCCCTGTAAGCCCACACCTA 61.559 60.000 0.00 0.0 0.00 3.08
1540 1546 5.749462 AGAATTTCCAATAGTGAGACCAGG 58.251 41.667 0.00 0.0 0.00 4.45
1580 1588 1.416401 ACAAAGAAGAAGAGCCGGTGA 59.584 47.619 1.90 0.0 0.00 4.02
1624 1632 3.459232 TTCATCCATCAAGTAGGCGAG 57.541 47.619 0.00 0.0 0.00 5.03
1720 1728 2.516460 GAGTCGGCGAGGCTAGGA 60.516 66.667 11.20 0.0 33.03 2.94
1733 1741 2.222819 CGCTCGCCTACAAAAATGAGTC 60.223 50.000 0.00 0.0 0.00 3.36
1975 1983 1.266989 GGCTTGCGAAACAAAGTAGCT 59.733 47.619 0.00 0.0 37.96 3.32
2186 2194 3.923864 CGATTCGATCCGCCCCCA 61.924 66.667 0.00 0.0 0.00 4.96
2231 2246 6.420913 AGCACAGAAGTTTAAGGAGAACTA 57.579 37.500 0.00 0.0 36.38 2.24
2363 2378 7.256190 CCCGAAGATGGGTAATATGTTCTCTAA 60.256 40.741 0.00 0.0 44.76 2.10
2452 2468 5.182760 GGAGATCAAAACAAGAAGTCATGCT 59.817 40.000 0.00 0.0 0.00 3.79
2455 2471 5.012893 GGGGAGATCAAAACAAGAAGTCAT 58.987 41.667 0.00 0.0 0.00 3.06


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

AutoCloner maintained by Alex Coulton.