Multiple sequence alignment - TraesCS7D01G453600

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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 TraesCS7D01G453600 chr7D 100.000 2807 0 0 1 2807 573191838 573194644 0.000000e+00 5184
1 TraesCS7D01G453600 chr7B 93.979 2840 103 29 3 2794 631404216 631407035 0.000000e+00 4235
2 TraesCS7D01G453600 chr7A 95.197 2644 91 19 2 2623 662966052 662968681 0.000000e+00 4146
3 TraesCS7D01G453600 chr7A 96.216 185 7 0 2623 2807 662968942 662969126 1.260000e-78 303
4 TraesCS7D01G453600 chr6B 88.395 405 47 0 1043 1447 178273236 178272832 3.250000e-134 488
5 TraesCS7D01G453600 chr6B 85.974 385 54 0 1054 1438 687525398 687525014 2.010000e-111 412
6 TraesCS7D01G453600 chr6D 87.059 425 52 3 1043 1464 94602359 94602783 7.030000e-131 477
7 TraesCS7D01G453600 chr6A 86.437 435 56 3 1043 1474 114459020 114458586 9.100000e-130 473
8 TraesCS7D01G453600 chr6A 85.714 385 55 0 1054 1438 598619721 598619337 9.360000e-110 407
9 TraesCS7D01G453600 chrUn 87.648 421 25 12 2401 2794 294908612 294908192 5.480000e-127 464
10 TraesCS7D01G453600 chr2A 86.889 389 49 2 1051 1438 626589669 626589282 4.290000e-118 435
11 TraesCS7D01G453600 chr1B 85.049 408 59 2 1044 1450 422563215 422562809 5.590000e-112 414


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 TraesCS7D01G453600 chr7D 573191838 573194644 2806 False 5184.0 5184 100.0000 1 2807 1 chr7D.!!$F1 2806
1 TraesCS7D01G453600 chr7B 631404216 631407035 2819 False 4235.0 4235 93.9790 3 2794 1 chr7B.!!$F1 2791
2 TraesCS7D01G453600 chr7A 662966052 662969126 3074 False 2224.5 4146 95.7065 2 2807 2 chr7A.!!$F1 2805

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
38 39 0.169451 GAAATACAAACACGGGCGGG 59.831 55.0 0.0 0.0 0.0 6.13 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1948 1975 6.073167 ACAATAGTACGTTCATCGATCGATCT 60.073 38.462 27.2 20.12 42.86 2.75 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
38 39 0.169451 GAAATACAAACACGGGCGGG 59.831 55.000 0.00 0.00 0.00 6.13
55 56 4.770874 GCGGGTGGGTGCATACGT 62.771 66.667 0.00 0.00 0.00 3.57
94 95 1.379710 AACACTGTTGCACCTGCCA 60.380 52.632 0.00 0.00 41.18 4.92
158 159 1.304217 TCTCCGTCTCCCCACTCAC 60.304 63.158 0.00 0.00 0.00 3.51
159 160 1.304547 CTCCGTCTCCCCACTCACT 60.305 63.158 0.00 0.00 0.00 3.41
604 605 1.855978 CGCGTGTGTGTCAGTTTCTTA 59.144 47.619 0.00 0.00 0.00 2.10
753 758 2.116713 TCCCCCTTTAGGAAACCCTAGT 59.883 50.000 0.00 0.00 37.58 2.57
769 774 3.325870 CCTAGTGTCAGATTTTCGTGCA 58.674 45.455 0.00 0.00 0.00 4.57
779 784 0.319555 TTTTCGTGCACCCTCGAGAG 60.320 55.000 15.71 2.13 38.10 3.20
830 835 2.097685 CGATGCTTAGCTTGATTCGTCG 60.098 50.000 5.60 0.00 0.00 5.12
840 847 0.179111 TGATTCGTCGGCTCACCATC 60.179 55.000 0.00 0.00 34.57 3.51
862 881 1.093159 CTGAGCTGAAGAACCATGCC 58.907 55.000 0.00 0.00 0.00 4.40
874 893 2.711311 CATGCCGCGAACTGATGG 59.289 61.111 8.23 0.00 0.00 3.51
985 1012 3.731264 GCATGCAGATCTGAAGTCAAAGC 60.731 47.826 27.04 16.93 0.00 3.51
2225 2253 0.935196 GTTGCGTTCTTCCTGTCGTT 59.065 50.000 0.00 0.00 0.00 3.85
2261 2289 7.923414 ACTGATGTGTTCCTAGGATTTTAAC 57.077 36.000 13.57 8.00 0.00 2.01
2283 2311 7.986085 AACTTGTTCTTATGACTAGCATTGT 57.014 32.000 5.22 0.00 38.44 2.71
2383 2434 9.755804 TGCTTTCACTGTATATTTCTCTATCTG 57.244 33.333 0.00 0.00 0.00 2.90
2633 2946 6.406370 TGTTAGATGTTTGGTATCTGACAGG 58.594 40.000 1.81 0.00 42.56 4.00
2646 2959 4.028993 TCTGACAGGGGTTTGGTATTTC 57.971 45.455 1.81 0.00 0.00 2.17
2739 3056 1.144691 TCATTTGGGTGTGGAGACCA 58.855 50.000 0.00 0.00 37.80 4.02
2776 3094 4.517453 AGACAGTTCTATATCTCTCGCCAC 59.483 45.833 0.00 0.00 0.00 5.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.136800 TGTATTTCTGCATGCGATTTATGAATT 58.863 29.630 14.09 7.43 0.00 2.17
38 39 3.374012 TACGTATGCACCCACCCGC 62.374 63.158 0.00 0.00 0.00 6.13
55 56 6.018751 GTGTTCCTGATGTATCTACGTACGTA 60.019 42.308 25.41 25.41 0.00 3.57
94 95 3.308401 GACCCCAATCATTTAAGCCCAT 58.692 45.455 0.00 0.00 0.00 4.00
151 152 2.262915 GCGGGTGAGAGTGAGTGG 59.737 66.667 0.00 0.00 0.00 4.00
158 159 4.899239 GATGCGGGCGGGTGAGAG 62.899 72.222 0.00 0.00 0.00 3.20
639 640 0.250234 TCCAAGACGGCCTGAATCTG 59.750 55.000 0.00 0.00 33.14 2.90
640 641 1.134280 CATCCAAGACGGCCTGAATCT 60.134 52.381 0.00 0.00 33.14 2.40
641 642 1.303309 CATCCAAGACGGCCTGAATC 58.697 55.000 0.00 0.00 33.14 2.52
753 758 1.202758 AGGGTGCACGAAAATCTGACA 60.203 47.619 11.45 0.00 0.00 3.58
769 774 2.158534 ACATGCTATCTCTCTCGAGGGT 60.159 50.000 13.10 0.00 37.86 4.34
779 784 5.240623 AGTCTGTAGCTGTACATGCTATCTC 59.759 44.000 21.80 13.87 43.66 2.75
781 786 5.240623 AGAGTCTGTAGCTGTACATGCTATC 59.759 44.000 21.80 16.70 43.66 2.08
862 881 2.906182 TAGCTGCCCATCAGTTCGCG 62.906 60.000 0.00 0.00 44.66 5.87
874 893 2.513435 GCCAGTGAGCTAGCTGCC 60.513 66.667 24.99 12.15 44.23 4.85
985 1012 1.142748 GCATGTCCGTCCTCTCCTG 59.857 63.158 0.00 0.00 0.00 3.86
1948 1975 6.073167 ACAATAGTACGTTCATCGATCGATCT 60.073 38.462 27.20 20.12 42.86 2.75
1949 1976 6.078479 ACAATAGTACGTTCATCGATCGATC 58.922 40.000 27.20 15.68 42.86 3.69
2261 2289 7.601073 TGACAATGCTAGTCATAAGAACAAG 57.399 36.000 2.97 0.00 40.80 3.16
2283 2311 6.146510 GCAAAATTCTGCAGAAAATGTCATGA 59.853 34.615 31.55 6.55 42.17 3.07
2336 2387 5.126061 AGCATACGAGAAATCAAGGCAAAAT 59.874 36.000 0.00 0.00 0.00 1.82
2337 2388 4.458989 AGCATACGAGAAATCAAGGCAAAA 59.541 37.500 0.00 0.00 0.00 2.44
2338 2389 4.009675 AGCATACGAGAAATCAAGGCAAA 58.990 39.130 0.00 0.00 0.00 3.68
2339 2390 3.609853 AGCATACGAGAAATCAAGGCAA 58.390 40.909 0.00 0.00 0.00 4.52
2340 2391 3.266510 AGCATACGAGAAATCAAGGCA 57.733 42.857 0.00 0.00 0.00 4.75
2381 2432 4.589216 TCAAGATTTTTCTTGCCCACAG 57.411 40.909 10.19 0.00 44.82 3.66
2383 2434 5.540911 TGAATCAAGATTTTTCTTGCCCAC 58.459 37.500 10.19 4.02 44.82 4.61
2494 2546 5.517770 GCTGTGTGGATTTTCTATGCAAATC 59.482 40.000 0.00 0.00 39.14 2.17
2632 2945 5.126545 GGTCTACAATGAAATACCAAACCCC 59.873 44.000 0.00 0.00 0.00 4.95
2633 2946 5.126545 GGGTCTACAATGAAATACCAAACCC 59.873 44.000 0.00 0.00 35.12 4.11
2776 3094 4.830826 TGTCTGTGTGGCGTATATCTAG 57.169 45.455 0.00 0.00 0.00 2.43


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

AutoCloner maintained by Alex Coulton.