Multiple sequence alignment - TraesCS7A01G237700

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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 TraesCS7A01G237700 chr7A 100.000 2528 0 0 1 2528 211279017 211276490 0 4669
1 TraesCS7A01G237700 chr7A 97.977 1681 32 1 848 2528 120828002 120826324 0 2915
2 TraesCS7A01G237700 chr7A 97.749 844 19 0 1 844 4905807 4904964 0 1454
3 TraesCS7A01G237700 chr5A 98.038 1682 32 1 848 2528 16622425 16620744 0 2922
4 TraesCS7A01G237700 chr2D 98.038 1682 32 1 848 2528 635038106 635039787 0 2922
5 TraesCS7A01G237700 chr2D 97.918 1681 35 0 848 2528 17966340 17964660 0 2911
6 TraesCS7A01G237700 chr5B 97.977 1681 32 1 848 2528 713045363 713043685 0 2915
7 TraesCS7A01G237700 chr7B 97.919 1682 34 1 848 2528 743067153 743068834 0 2911
8 TraesCS7A01G237700 chr3B 97.918 1681 33 2 848 2528 201634957 201633279 0 2909
9 TraesCS7A01G237700 chr2A 97.856 1679 34 2 848 2525 735173648 735175325 0 2900
10 TraesCS7A01G237700 chr3D 97.741 1682 37 1 848 2528 202612792 202614473 0 2894
11 TraesCS7A01G237700 chr3D 97.512 844 21 0 1 844 202623268 202622425 0 1443
12 TraesCS7A01G237700 chr3D 97.393 844 22 0 1 844 478088148 478087305 0 1437
13 TraesCS7A01G237700 chrUn 97.867 844 18 0 1 844 45132176 45131333 0 1459
14 TraesCS7A01G237700 chrUn 97.867 844 18 0 1 844 304292474 304293317 0 1459
15 TraesCS7A01G237700 chrUn 97.867 844 18 0 1 844 369087759 369086916 0 1459
16 TraesCS7A01G237700 chr6D 97.630 844 20 0 1 844 430464571 430463728 0 1448
17 TraesCS7A01G237700 chr4A 97.038 844 25 0 1 844 67510904 67511747 0 1421
18 TraesCS7A01G237700 chr3A 97.038 844 25 0 1 844 653793116 653793959 0 1421


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 TraesCS7A01G237700 chr7A 211276490 211279017 2527 True 4669 4669 100.000 1 2528 1 chr7A.!!$R3 2527
1 TraesCS7A01G237700 chr7A 120826324 120828002 1678 True 2915 2915 97.977 848 2528 1 chr7A.!!$R2 1680
2 TraesCS7A01G237700 chr7A 4904964 4905807 843 True 1454 1454 97.749 1 844 1 chr7A.!!$R1 843
3 TraesCS7A01G237700 chr5A 16620744 16622425 1681 True 2922 2922 98.038 848 2528 1 chr5A.!!$R1 1680
4 TraesCS7A01G237700 chr2D 635038106 635039787 1681 False 2922 2922 98.038 848 2528 1 chr2D.!!$F1 1680
5 TraesCS7A01G237700 chr2D 17964660 17966340 1680 True 2911 2911 97.918 848 2528 1 chr2D.!!$R1 1680
6 TraesCS7A01G237700 chr5B 713043685 713045363 1678 True 2915 2915 97.977 848 2528 1 chr5B.!!$R1 1680
7 TraesCS7A01G237700 chr7B 743067153 743068834 1681 False 2911 2911 97.919 848 2528 1 chr7B.!!$F1 1680
8 TraesCS7A01G237700 chr3B 201633279 201634957 1678 True 2909 2909 97.918 848 2528 1 chr3B.!!$R1 1680
9 TraesCS7A01G237700 chr2A 735173648 735175325 1677 False 2900 2900 97.856 848 2525 1 chr2A.!!$F1 1677
10 TraesCS7A01G237700 chr3D 202612792 202614473 1681 False 2894 2894 97.741 848 2528 1 chr3D.!!$F1 1680
11 TraesCS7A01G237700 chr3D 202622425 202623268 843 True 1443 1443 97.512 1 844 1 chr3D.!!$R1 843
12 TraesCS7A01G237700 chr3D 478087305 478088148 843 True 1437 1437 97.393 1 844 1 chr3D.!!$R2 843
13 TraesCS7A01G237700 chrUn 45131333 45132176 843 True 1459 1459 97.867 1 844 1 chrUn.!!$R1 843
14 TraesCS7A01G237700 chrUn 304292474 304293317 843 False 1459 1459 97.867 1 844 1 chrUn.!!$F1 843
15 TraesCS7A01G237700 chrUn 369086916 369087759 843 True 1459 1459 97.867 1 844 1 chrUn.!!$R2 843
16 TraesCS7A01G237700 chr6D 430463728 430464571 843 True 1448 1448 97.630 1 844 1 chr6D.!!$R1 843
17 TraesCS7A01G237700 chr4A 67510904 67511747 843 False 1421 1421 97.038 1 844 1 chr4A.!!$F1 843
18 TraesCS7A01G237700 chr3A 653793116 653793959 843 False 1421 1421 97.038 1 844 1 chr3A.!!$F1 843

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
674 675 0.784778 CAGCGGTTTCGAAGACTGAC 59.215 55.0 17.82 6.06 39.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1625 1672 0.537653 TGTGGTTCAGTGGTTCGACA 59.462 50.0 0.0 0.0 0.0 4.35 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
195 196 1.686355 ACGTGTTGATCAAGGCCAAA 58.314 45.000 8.80 0.00 0.00 3.28
198 199 2.489329 CGTGTTGATCAAGGCCAAAGAT 59.511 45.455 8.80 4.69 0.00 2.40
247 248 8.258007 TGAAGAACGAGGTATGATGATTACTTT 58.742 33.333 0.00 0.00 0.00 2.66
288 289 6.541934 TCATGCAAATGACCATATTTTCCA 57.458 33.333 0.00 0.00 0.00 3.53
313 314 6.161855 CTGCAATACAGGTAGAAGATACCA 57.838 41.667 6.82 0.00 43.19 3.25
321 322 6.838382 ACAGGTAGAAGATACCAAGTTGTTT 58.162 36.000 6.82 0.00 39.99 2.83
355 356 5.716703 CAGGAAATCCATGGGAAAAACTACT 59.283 40.000 13.02 0.00 38.89 2.57
434 435 1.908619 TGGCATTGCTCCTGAGTTAGA 59.091 47.619 8.82 0.00 0.00 2.10
674 675 0.784778 CAGCGGTTTCGAAGACTGAC 59.215 55.000 17.82 6.06 39.00 3.51
746 747 5.067273 TGTGGTCGAAATCAAATGGTAACT 58.933 37.500 0.00 0.00 37.61 2.24
800 801 6.150976 ACAAGCTTTAGCAGTATGTTTGCATA 59.849 34.615 0.00 0.00 43.92 3.14
844 845 0.895100 TGTGAATGGGCAGAGGCAAC 60.895 55.000 0.00 0.00 43.71 4.17
845 846 1.675310 TGAATGGGCAGAGGCAACG 60.675 57.895 0.00 0.00 43.71 4.10
846 847 2.361610 AATGGGCAGAGGCAACGG 60.362 61.111 0.00 0.00 43.71 4.44
883 884 2.233922 CACCTAACCCACCTACTCACTG 59.766 54.545 0.00 0.00 0.00 3.66
950 951 3.579534 TTAGTAATTTGGCGCCCCATA 57.420 42.857 26.77 9.18 41.78 2.74
1443 1481 9.804758 CTACTATTCTATGTTCTTTCCGAAAGT 57.195 33.333 18.32 4.28 39.52 2.66
1465 1503 1.272369 TGCCAATCCCTATGTTGTGCA 60.272 47.619 0.00 0.00 32.80 4.57
1480 1518 0.727970 GTGCAGAGCTGAGCATCTTG 59.272 55.000 7.39 0.00 43.44 3.02
1509 1547 2.376518 TGGGATCAAGCTTTTCCTCTGT 59.623 45.455 19.72 0.00 0.00 3.41
1568 1615 5.393461 CCCCTGTCGTCGTAAAGTAGTAAAT 60.393 44.000 0.00 0.00 0.00 1.40
1998 2061 2.347490 GCCGGAGAGTTCTTGGCA 59.653 61.111 5.05 0.00 43.23 4.92
2153 2217 3.082579 GCTCGGCAGAGGGTTCGAT 62.083 63.158 15.89 0.00 44.51 3.59
2171 2235 6.261603 GGTTCGATAATAGGGTAGGGTTTTTG 59.738 42.308 0.00 0.00 0.00 2.44
2294 2358 1.247567 CACCACCCGAGAAGCAAAAT 58.752 50.000 0.00 0.00 0.00 1.82
2335 2399 5.582665 GGAAAAGACAAGCATAGTGGTCTAG 59.417 44.000 0.00 0.00 39.55 2.43
2352 2416 0.968901 TAGTGACAAGGGCCGACGAT 60.969 55.000 0.00 0.00 0.00 3.73
2358 2422 3.031417 AAGGGCCGACGATGGAAGG 62.031 63.158 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 3.960102 ACAAAGGCAGAATGGAAGAACAA 59.040 39.130 0.00 0.00 35.86 2.83
135 136 8.556589 TCAGGATTTGTCCTTAAAATAGGATCA 58.443 33.333 0.00 0.00 45.69 2.92
141 142 8.748412 CCAACATCAGGATTTGTCCTTAAAATA 58.252 33.333 0.00 0.00 38.22 1.40
195 196 5.889853 TCTTTTCATGGCTGCTTCATTATCT 59.110 36.000 0.00 0.00 0.00 1.98
198 199 6.153170 TCAATCTTTTCATGGCTGCTTCATTA 59.847 34.615 0.00 0.00 0.00 1.90
247 248 4.997395 GCATGAAGAACAGAAAGTAGTCCA 59.003 41.667 0.00 0.00 0.00 4.02
312 313 9.965824 ATTTCCTGTAAACATCTAAACAACTTG 57.034 29.630 0.00 0.00 0.00 3.16
321 322 6.159575 TCCCATGGATTTCCTGTAAACATCTA 59.840 38.462 15.22 0.00 36.82 1.98
434 435 2.028930 ACTTCTTCCGCGATCTCTTTGT 60.029 45.455 8.23 0.00 0.00 2.83
674 675 3.433274 TGTTGATACTTGCAAGAAGAGCG 59.567 43.478 32.50 5.71 33.85 5.03
800 801 3.140623 GCTGTTTGGCCAAAAACATGAT 58.859 40.909 31.92 0.00 46.12 2.45
883 884 3.932710 TCAGCTGAACACCGTAATTGATC 59.067 43.478 15.67 0.00 0.00 2.92
1016 1017 9.717942 GACCACTTAGATAGAAATAGCATTCAT 57.282 33.333 0.00 0.00 0.00 2.57
1030 1031 7.005296 GGACAGAGAATAGGACCACTTAGATA 58.995 42.308 0.00 0.00 0.00 1.98
1393 1431 2.359107 CAGCATGCAGGACACGGT 60.359 61.111 21.98 0.00 0.00 4.83
1443 1481 2.445427 CACAACATAGGGATTGGCACA 58.555 47.619 0.00 0.00 0.00 4.57
1465 1503 3.715495 CGAATACAAGATGCTCAGCTCT 58.285 45.455 0.00 0.00 0.00 4.09
1480 1518 2.246719 AGCTTGATCCCAGCGAATAC 57.753 50.000 8.05 0.00 0.00 1.89
1509 1547 1.068948 TTTACTGCACAAGGCCCCTA 58.931 50.000 0.00 0.00 43.89 3.53
1548 1586 6.086222 GGACATTTACTACTTTACGACGACA 58.914 40.000 0.00 0.00 0.00 4.35
1568 1615 2.358247 GAAAGCTTCGCGGGGACA 60.358 61.111 6.13 0.00 0.00 4.02
1623 1670 2.011222 GTGGTTCAGTGGTTCGACAAA 58.989 47.619 0.00 0.00 0.00 2.83
1625 1672 0.537653 TGTGGTTCAGTGGTTCGACA 59.462 50.000 0.00 0.00 0.00 4.35
1998 2061 6.628644 AGCAACTTATCCTAAGGTCTCTTT 57.371 37.500 0.00 0.00 34.59 2.52
2153 2217 4.535692 ACCGTCAAAAACCCTACCCTATTA 59.464 41.667 0.00 0.00 0.00 0.98
2294 2358 4.724074 TTTCCGCCTTTACTCTCGAATA 57.276 40.909 0.00 0.00 0.00 1.75
2335 2399 2.100631 CATCGTCGGCCCTTGTCAC 61.101 63.158 0.00 0.00 0.00 3.67
2352 2416 2.678934 CTCCGTCCCGACCTTCCA 60.679 66.667 0.00 0.00 0.00 3.53


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

AutoCloner maintained by Alex Coulton.