Multiple sequence alignment - TraesCS7D01G229600

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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 TraesCS7D01G229600 chr7D 100.000 2798 0 0 684 3481 190079435 190082232 0.000000e+00 5168
1 TraesCS7D01G229600 chr7D 100.000 254 0 0 1 254 190078752 190079005 1.460000e-128 470
2 TraesCS7D01G229600 chr7B 96.676 2196 66 4 684 2875 334770676 334772868 0.000000e+00 3644
3 TraesCS7D01G229600 chr7B 90.132 456 43 2 2876 3331 334772950 334773403 2.990000e-165 592
4 TraesCS7D01G229600 chr7B 91.760 267 3 2 7 254 334769844 334770110 1.540000e-93 353
5 TraesCS7D01G229600 chr7B 93.421 152 9 1 3331 3481 334773440 334773591 1.260000e-54 224
6 TraesCS7D01G229600 chr7A 95.178 2136 87 7 756 2875 198940717 198942852 0.000000e+00 3360
7 TraesCS7D01G229600 chr7A 97.424 427 10 1 2905 3331 198942946 198943371 0.000000e+00 726
8 TraesCS7D01G229600 chr7A 92.308 234 4 3 1 220 198940148 198940381 1.560000e-83 320
9 TraesCS7D01G229600 chr7A 98.013 151 3 0 3331 3481 198943408 198943558 2.660000e-66 263


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 TraesCS7D01G229600 chr7D 190078752 190082232 3480 False 2819.00 5168 100.00000 1 3481 2 chr7D.!!$F1 3480
1 TraesCS7D01G229600 chr7B 334769844 334773591 3747 False 1203.25 3644 92.99725 7 3481 4 chr7B.!!$F1 3474
2 TraesCS7D01G229600 chr7A 198940148 198943558 3410 False 1167.25 3360 95.73075 1 3481 4 chr7A.!!$F1 3480

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
864 1021 0.737715 CCGCCTTCTTCTTCCACTCG 60.738 60.0 0.0 0.0 0.0 4.18 F
930 1087 0.884704 TCCTCCTCAAGTGCGTTTGC 60.885 55.0 0.0 0.0 43.2 3.68 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1934 2091 0.827507 ACCCCTTGCCAACATGTCAC 60.828 55.0 0.00 0.0 0.0 3.67 R
2665 2827 1.818959 TTGCAAGCAACCCCATCAGC 61.819 55.0 2.89 0.0 0.0 4.26 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
705 862 2.438434 CCGCACATCTTCCCCCAC 60.438 66.667 0.00 0.00 0.00 4.61
709 866 1.221840 CACATCTTCCCCCACCTCG 59.778 63.158 0.00 0.00 0.00 4.63
810 967 2.636830 CATCATTCCTTCAACTCCGCT 58.363 47.619 0.00 0.00 0.00 5.52
864 1021 0.737715 CCGCCTTCTTCTTCCACTCG 60.738 60.000 0.00 0.00 0.00 4.18
930 1087 0.884704 TCCTCCTCAAGTGCGTTTGC 60.885 55.000 0.00 0.00 43.20 3.68
1044 1201 5.465724 GGATAAGTTCACATATTCCACGGTC 59.534 44.000 0.00 0.00 0.00 4.79
1182 1339 1.090052 GTGCCGGAGATGTTACAGGC 61.090 60.000 5.05 5.73 44.93 4.85
1440 1597 2.861147 AGAAGGGTCTTGCACCTAAC 57.139 50.000 0.00 0.00 45.95 2.34
1644 1801 5.359009 AGAGATGGTTGAGGCAAAATGTATG 59.641 40.000 0.00 0.00 0.00 2.39
2037 2194 2.777692 CCTTCCTAGGGCAATGGACTTA 59.222 50.000 9.46 0.00 37.94 2.24
2256 2413 1.478105 GCCATTTTGGAGATGGTGGTC 59.522 52.381 0.00 0.00 44.75 4.02
2472 2631 9.681692 TCAAGATTTTGACACAATAAAGTGATG 57.318 29.630 0.57 0.00 38.78 3.07
2624 2784 4.818546 ACTTGTCCTTCATCTTCTGTTGTG 59.181 41.667 0.00 0.00 0.00 3.33
2665 2827 5.496556 TGACTCTGTCTCTTCTTCCTAGAG 58.503 45.833 0.00 0.00 40.39 2.43
2886 3150 6.491383 TCCTCTACCACATGTACTTCTTAGT 58.509 40.000 0.00 0.00 38.44 2.24
2887 3151 7.636579 TCCTCTACCACATGTACTTCTTAGTA 58.363 38.462 0.00 0.00 35.78 1.82
2967 3231 4.155826 GTGTGAACAGTGGCAGCAAATATA 59.844 41.667 0.00 0.00 0.00 0.86
3090 3354 7.611855 CAGTTCTCCATGAAAAGGTAGGTTATT 59.388 37.037 0.00 0.00 36.30 1.40
3229 3493 7.362920 GCTTCATTTGGGCAGTTTCTATCTAAA 60.363 37.037 0.00 0.00 0.00 1.85
3321 3585 6.051074 AGGTTTCTTTCCTTGCAATTTTCTG 58.949 36.000 0.00 0.00 30.18 3.02
3327 3591 7.596494 TCTTTCCTTGCAATTTTCTGTATCAG 58.404 34.615 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 1.470979 CGCTCGCACTAGGGTTTACAT 60.471 52.381 0.00 0.00 0.00 2.29
810 967 1.233369 GAGGGGGAATCGGAGGAGA 59.767 63.158 0.00 0.00 0.00 3.71
846 1003 1.355066 GCGAGTGGAAGAAGAAGGCG 61.355 60.000 0.00 0.00 0.00 5.52
930 1087 1.944177 TCCTTGGGACCAGAGAGAAG 58.056 55.000 0.00 0.00 0.00 2.85
987 1144 1.817099 CCCTGGAATGCTCTCGTGC 60.817 63.158 0.00 0.00 0.00 5.34
1128 1285 3.018856 CAGCACAGGATTAAATGCCTCA 58.981 45.455 0.00 0.00 38.92 3.86
1182 1339 2.406452 AAGAAAACAGCTTGGCCGCG 62.406 55.000 0.00 0.00 34.40 6.46
1236 1393 2.642139 GCAGCAGCACATTGTATGTT 57.358 45.000 0.00 0.00 42.70 2.71
1644 1801 6.813649 TCGAGCTATAAGTCATGATATTTGGC 59.186 38.462 0.00 0.30 0.00 4.52
1934 2091 0.827507 ACCCCTTGCCAACATGTCAC 60.828 55.000 0.00 0.00 0.00 3.67
2256 2413 3.726517 CGCCGGCAAACACCTCTG 61.727 66.667 28.98 0.98 0.00 3.35
2284 2441 4.378770 CCAACATTTGTCAATCACTCTCCG 60.379 45.833 0.00 0.00 0.00 4.63
2472 2631 8.905702 CGAAAACAAGCATAATGATTAATAGCC 58.094 33.333 0.00 0.00 0.00 3.93
2563 2723 3.429492 TGGCAAAAGCATCACCATAGAA 58.571 40.909 0.00 0.00 0.00 2.10
2624 2784 5.703130 AGAGTCAGAAACAAATAGGTCAAGC 59.297 40.000 0.00 0.00 0.00 4.01
2665 2827 1.818959 TTGCAAGCAACCCCATCAGC 61.819 55.000 2.89 0.00 0.00 4.26
2754 2920 5.576384 GCGAATGTCAAGGCAATCATTTAAA 59.424 36.000 0.00 0.00 31.87 1.52
2887 3151 9.448438 AAGGAAAGAAATGTTTTTACTTGCTTT 57.552 25.926 0.00 0.00 36.39 3.51
2901 3165 5.726397 TGATGCATCCAAAGGAAAGAAATG 58.274 37.500 23.67 0.00 34.34 2.32
2967 3231 6.906848 TCTCCGGTAAAAATATCCAGGAAAT 58.093 36.000 0.00 0.00 0.00 2.17
3229 3493 7.173218 AGTTTCTCATGTACGTTTTCACATCAT 59.827 33.333 0.00 0.00 33.12 2.45
3294 3558 7.928167 AGAAAATTGCAAGGAAAGAAACCTAAG 59.072 33.333 4.94 0.00 36.67 2.18
3321 3585 6.113411 ACCAGTTTAATGCACCTACTGATAC 58.887 40.000 17.02 0.00 38.74 2.24
3327 3591 3.254657 TGCAACCAGTTTAATGCACCTAC 59.745 43.478 0.00 0.00 43.32 3.18


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

AutoCloner maintained by Alex Coulton.