Multiple sequence alignment - TraesCS7B01G442700

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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 TraesCS7B01G442700 chr7B 100.000 2264 0 0 1 2264 707616603 707618866 0.000000e+00 4181
1 TraesCS7B01G442700 chr7B 95.577 1628 53 6 637 2264 707572310 707570702 0.000000e+00 2590
2 TraesCS7B01G442700 chr7B 93.690 1569 63 10 680 2224 577212011 577213567 0.000000e+00 2316
3 TraesCS7B01G442700 chr7B 97.705 828 13 3 1 828 707572985 707572164 0.000000e+00 1419
4 TraesCS7B01G442700 chr7B 97.464 828 15 3 1 828 133432665 133431844 0.000000e+00 1408
5 TraesCS7B01G442700 chr2B 95.393 1628 65 5 637 2264 798601592 798603209 0.000000e+00 2582
6 TraesCS7B01G442700 chr2B 94.118 1564 81 5 680 2243 154584855 154583303 0.000000e+00 2368
7 TraesCS7B01G442700 chr5A 93.707 1589 71 8 637 2224 591474389 591475949 0.000000e+00 2353
8 TraesCS7B01G442700 chr5A 97.705 828 13 2 1 828 591473714 591474535 0.000000e+00 1419
9 TraesCS7B01G442700 chr6A 93.325 1588 79 6 637 2224 466679576 466681136 0.000000e+00 2320
10 TraesCS7B01G442700 chr6A 97.464 828 15 3 1 828 466678901 466679722 0.000000e+00 1408
11 TraesCS7B01G442700 chr6A 97.343 828 16 2 1 828 137872471 137873292 0.000000e+00 1402
12 TraesCS7B01G442700 chr5B 94.038 1543 65 6 637 2179 297111155 297112670 0.000000e+00 2314
13 TraesCS7B01G442700 chr5B 97.587 829 13 4 1 828 351469628 351468806 0.000000e+00 1413
14 TraesCS7B01G442700 chr5B 87.251 251 20 4 680 924 711230240 711229996 2.220000e-70 276
15 TraesCS7B01G442700 chr1B 93.266 1589 78 8 637 2224 649300657 649299097 0.000000e+00 2314
16 TraesCS7B01G442700 chr1B 97.585 828 14 3 1 828 649301332 649300511 0.000000e+00 1413
17 TraesCS7B01G442700 chr7A 93.014 1589 82 8 637 2224 497718867 497717307 0.000000e+00 2292
18 TraesCS7B01G442700 chr7A 97.585 828 14 3 1 828 497719542 497718721 0.000000e+00 1413
19 TraesCS7B01G442700 chr7D 93.770 1220 66 5 1 1211 21074602 21073384 0.000000e+00 1823


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 TraesCS7B01G442700 chr7B 707616603 707618866 2263 False 4181.0 4181 100.0000 1 2264 1 chr7B.!!$F2 2263
1 TraesCS7B01G442700 chr7B 577212011 577213567 1556 False 2316.0 2316 93.6900 680 2224 1 chr7B.!!$F1 1544
2 TraesCS7B01G442700 chr7B 707570702 707572985 2283 True 2004.5 2590 96.6410 1 2264 2 chr7B.!!$R2 2263
3 TraesCS7B01G442700 chr7B 133431844 133432665 821 True 1408.0 1408 97.4640 1 828 1 chr7B.!!$R1 827
4 TraesCS7B01G442700 chr2B 798601592 798603209 1617 False 2582.0 2582 95.3930 637 2264 1 chr2B.!!$F1 1627
5 TraesCS7B01G442700 chr2B 154583303 154584855 1552 True 2368.0 2368 94.1180 680 2243 1 chr2B.!!$R1 1563
6 TraesCS7B01G442700 chr5A 591473714 591475949 2235 False 1886.0 2353 95.7060 1 2224 2 chr5A.!!$F1 2223
7 TraesCS7B01G442700 chr6A 466678901 466681136 2235 False 1864.0 2320 95.3945 1 2224 2 chr6A.!!$F2 2223
8 TraesCS7B01G442700 chr6A 137872471 137873292 821 False 1402.0 1402 97.3430 1 828 1 chr6A.!!$F1 827
9 TraesCS7B01G442700 chr5B 297111155 297112670 1515 False 2314.0 2314 94.0380 637 2179 1 chr5B.!!$F1 1542
10 TraesCS7B01G442700 chr5B 351468806 351469628 822 True 1413.0 1413 97.5870 1 828 1 chr5B.!!$R1 827
11 TraesCS7B01G442700 chr1B 649299097 649301332 2235 True 1863.5 2314 95.4255 1 2224 2 chr1B.!!$R1 2223
12 TraesCS7B01G442700 chr7A 497717307 497719542 2235 True 1852.5 2292 95.2995 1 2224 2 chr7A.!!$R1 2223
13 TraesCS7B01G442700 chr7D 21073384 21074602 1218 True 1823.0 1823 93.7700 1 1211 1 chr7D.!!$R1 1210

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
791 793 0.674895 CAAGTGCTAGAGGTGGTGGC 60.675 60.0 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2225 2306 0.038251 CTCACGTCTGCTAACCTGCA 60.038 55.0 0.0 0.0 41.05 4.41 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
189 190 2.363711 GACTCGGTGGTGTCAGTGCA 62.364 60.000 0.00 0.00 36.81 4.57
459 460 3.350992 TCAGGGGTGATATGGATGACT 57.649 47.619 0.00 0.00 0.00 3.41
550 551 4.265056 GGTGTGCGGTGAAGGGGT 62.265 66.667 0.00 0.00 0.00 4.95
551 552 2.203294 GTGTGCGGTGAAGGGGTT 60.203 61.111 0.00 0.00 0.00 4.11
766 768 1.668101 GCTAGAGGTGGTGGTCGAGG 61.668 65.000 0.00 0.00 0.00 4.63
767 769 1.000019 TAGAGGTGGTGGTCGAGGG 60.000 63.158 0.00 0.00 0.00 4.30
791 793 0.674895 CAAGTGCTAGAGGTGGTGGC 60.675 60.000 0.00 0.00 0.00 5.01
988 1043 6.639632 ATGTCTTGTGCTAACAATTGTTCT 57.360 33.333 26.46 7.57 45.12 3.01
1444 1499 2.798689 CGCCGATTCGAGGAGTCA 59.201 61.111 7.83 0.00 0.00 3.41
1574 1629 3.183793 CAAGAAAACTTGCAAGGGCTT 57.816 42.857 29.18 21.07 41.91 4.35
1629 1684 2.271173 GGGAAAGTGGCCCCGTAG 59.729 66.667 0.00 0.00 39.81 3.51
1780 1835 6.775088 AGATTATGTGCAAACTATGTTCGTG 58.225 36.000 0.00 0.00 0.00 4.35
1890 1948 5.522097 TGCTAAGCAAAAACTTTAACAAGCC 59.478 36.000 0.00 0.00 34.76 4.35
1926 1984 4.033776 CCCACACCCAGACGCCAT 62.034 66.667 0.00 0.00 0.00 4.40
1943 2001 4.954118 TGGTCCCTGGCGTCTGGT 62.954 66.667 12.29 0.00 0.00 4.00
1945 2003 2.358737 GTCCCTGGCGTCTGGTTG 60.359 66.667 12.29 0.00 0.00 3.77
1952 2010 1.896660 GGCGTCTGGTTGGCTTTCA 60.897 57.895 0.00 0.00 0.00 2.69
2011 2069 3.240134 GACAGCCAGACGCCAAGGA 62.240 63.158 0.00 0.00 38.78 3.36
2094 2152 2.122413 AGGTGACCAGACAGGCCA 60.122 61.111 5.01 0.00 43.14 5.36
2127 2208 3.695606 GGACAGCCAGACGCCAGA 61.696 66.667 0.00 0.00 38.78 3.86
2179 2260 3.399181 GGGTCCATGGCGTCTGGA 61.399 66.667 6.96 4.37 40.49 3.86
2225 2306 4.295119 GGCCGTCTGGTGTGTCGT 62.295 66.667 0.00 0.00 37.67 4.34
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
189 190 5.221742 GCCAATGATACTTACTAGGCCTCTT 60.222 44.000 9.68 0.00 34.94 2.85
459 460 0.625316 ATGCCAGTGTATCCAGCCAA 59.375 50.000 0.00 0.00 0.00 4.52
550 551 0.804364 GCATGTCCGCTCATTGTGAA 59.196 50.000 0.00 0.00 0.00 3.18
551 552 0.321475 TGCATGTCCGCTCATTGTGA 60.321 50.000 0.00 0.00 0.00 3.58
766 768 0.610687 ACCTCTAGCACTTGTGCTCC 59.389 55.000 28.34 0.41 45.00 4.70
767 769 1.674221 CCACCTCTAGCACTTGTGCTC 60.674 57.143 28.34 1.13 45.00 4.26
791 793 0.319555 TTGTGCTTCCTCTTCGACGG 60.320 55.000 0.00 0.00 0.00 4.79
1444 1499 1.322538 GCTCCAATCCCCGTGCAAAT 61.323 55.000 0.00 0.00 0.00 2.32
1508 1563 0.320771 TCTTTGCGTGCCCTCTCTTC 60.321 55.000 0.00 0.00 0.00 2.87
1574 1629 2.491621 CTCCTCTCGTGCATCGCA 59.508 61.111 0.00 0.00 39.67 5.10
1629 1684 5.351740 GCCTTTCCATTTGTCTACTGAGTAC 59.648 44.000 0.00 0.00 0.00 2.73
1780 1835 7.916450 ACAAAGCATACTAACTAGTCTCGAATC 59.084 37.037 0.00 0.00 37.73 2.52
1890 1948 1.665169 GGCCTGTTGTTTTTGCACAAG 59.335 47.619 0.00 0.00 37.33 3.16
1926 1984 4.954118 ACCAGACGCCAGGGACCA 62.954 66.667 0.00 0.00 0.00 4.02
1943 2001 0.537143 ACCTGCGTGATGAAAGCCAA 60.537 50.000 0.00 0.00 31.40 4.52
1945 2003 0.955428 TCACCTGCGTGATGAAAGCC 60.955 55.000 0.00 0.00 44.20 4.35
2053 2111 0.884704 GAGCAAACCAAGCCAGACGA 60.885 55.000 0.00 0.00 0.00 4.20
2168 2249 0.606401 CAAACCTGTCCAGACGCCAT 60.606 55.000 0.00 0.00 0.00 4.40
2197 2278 2.982130 GACGGCCTGTCTGGTCAT 59.018 61.111 17.12 0.00 44.58 3.06
2225 2306 0.038251 CTCACGTCTGCTAACCTGCA 60.038 55.000 0.00 0.00 41.05 4.41


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

AutoCloner maintained by Alex Coulton.