Multiple sequence alignment - TraesCS4B01G212900

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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 TraesCS4B01G212900 chr4B 100.000 2513 0 0 1 2513 451481885 451479373 0 4641
1 TraesCS4B01G212900 chr4B 92.984 1297 78 10 1 1289 552005321 552006612 0 1879
2 TraesCS4B01G212900 chr1B 94.568 2522 118 12 1 2513 306219548 306222059 0 3880
3 TraesCS4B01G212900 chr1B 93.708 2527 132 17 1 2513 171628326 171630839 0 3760
4 TraesCS4B01G212900 chr1B 89.793 2420 215 25 1 2397 584636736 584634326 0 3072
5 TraesCS4B01G212900 chr5B 94.522 2519 119 12 5 2513 532513074 532510565 0 3869
6 TraesCS4B01G212900 chr5B 93.832 2529 127 18 1 2513 180053209 180055724 0 3779
7 TraesCS4B01G212900 chr5B 93.651 2347 119 11 1 2338 194199774 194197449 0 3482
8 TraesCS4B01G212900 chr5B 87.528 882 90 11 1 868 49314711 49313836 0 1002
9 TraesCS4B01G212900 chr3B 94.257 2525 109 13 1 2513 178566578 178569078 0 3827
10 TraesCS4B01G212900 chr6B 94.022 2526 121 16 1 2513 149534243 149536751 0 3801
11 TraesCS4B01G212900 chr7B 93.829 2528 135 13 1 2513 622289514 622286993 0 3784
12 TraesCS4B01G212900 chr3A 90.729 2427 184 29 1 2399 679680129 679682542 0 3197
13 TraesCS4B01G212900 chr2A 90.706 2421 185 30 5 2399 643207781 643210187 0 3188
14 TraesCS4B01G212900 chr4A 92.302 1299 85 9 1 1289 647862448 647863741 0 1831


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 TraesCS4B01G212900 chr4B 451479373 451481885 2512 True 4641 4641 100.000 1 2513 1 chr4B.!!$R1 2512
1 TraesCS4B01G212900 chr4B 552005321 552006612 1291 False 1879 1879 92.984 1 1289 1 chr4B.!!$F1 1288
2 TraesCS4B01G212900 chr1B 306219548 306222059 2511 False 3880 3880 94.568 1 2513 1 chr1B.!!$F2 2512
3 TraesCS4B01G212900 chr1B 171628326 171630839 2513 False 3760 3760 93.708 1 2513 1 chr1B.!!$F1 2512
4 TraesCS4B01G212900 chr1B 584634326 584636736 2410 True 3072 3072 89.793 1 2397 1 chr1B.!!$R1 2396
5 TraesCS4B01G212900 chr5B 532510565 532513074 2509 True 3869 3869 94.522 5 2513 1 chr5B.!!$R3 2508
6 TraesCS4B01G212900 chr5B 180053209 180055724 2515 False 3779 3779 93.832 1 2513 1 chr5B.!!$F1 2512
7 TraesCS4B01G212900 chr5B 194197449 194199774 2325 True 3482 3482 93.651 1 2338 1 chr5B.!!$R2 2337
8 TraesCS4B01G212900 chr5B 49313836 49314711 875 True 1002 1002 87.528 1 868 1 chr5B.!!$R1 867
9 TraesCS4B01G212900 chr3B 178566578 178569078 2500 False 3827 3827 94.257 1 2513 1 chr3B.!!$F1 2512
10 TraesCS4B01G212900 chr6B 149534243 149536751 2508 False 3801 3801 94.022 1 2513 1 chr6B.!!$F1 2512
11 TraesCS4B01G212900 chr7B 622286993 622289514 2521 True 3784 3784 93.829 1 2513 1 chr7B.!!$R1 2512
12 TraesCS4B01G212900 chr3A 679680129 679682542 2413 False 3197 3197 90.729 1 2399 1 chr3A.!!$F1 2398
13 TraesCS4B01G212900 chr2A 643207781 643210187 2406 False 3188 3188 90.706 5 2399 1 chr2A.!!$F1 2394
14 TraesCS4B01G212900 chr4A 647862448 647863741 1293 False 1831 1831 92.302 1 1289 1 chr4A.!!$F1 1288

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
97 98 1.072266 ACCATTAGAAGTGCCACCCA 58.928 50.0 0.0 0.0 0.0 4.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1994 2062 1.578897 TCAACCTACCATGCTAGCCA 58.421 50.0 13.29 0.24 0.0 4.75 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
72 73 2.557056 GTGCCTGCAGATACGGTATCTA 59.443 50.000 25.77 13.63 43.41 1.98
97 98 1.072266 ACCATTAGAAGTGCCACCCA 58.928 50.000 0.00 0.00 0.00 4.51
174 175 1.247567 CGAATTCAGGGCCACAAAGT 58.752 50.000 6.18 0.00 0.00 2.66
286 287 6.721208 ACCACACCACATAATCTCTCATTTTT 59.279 34.615 0.00 0.00 0.00 1.94
506 520 4.019174 CTGTGAGGCCAAATGGTAGAATT 58.981 43.478 5.01 0.00 37.57 2.17
588 602 7.703621 GTGCTGACAAAATAATCATGCATTACT 59.296 33.333 0.00 0.00 34.12 2.24
650 664 5.411831 AAATCCTGAGGAAGAATTTTGCC 57.588 39.130 4.76 0.00 34.34 4.52
673 694 1.618837 ACACGGTAGCTCACACTGAAT 59.381 47.619 0.87 0.00 0.00 2.57
679 700 6.019801 CACGGTAGCTCACACTGAATAAATAC 60.020 42.308 0.87 0.00 0.00 1.89
701 723 3.244112 CGTGAGTACTCCTTCCCTGTTTT 60.244 47.826 20.11 0.00 0.00 2.43
702 724 4.021719 CGTGAGTACTCCTTCCCTGTTTTA 60.022 45.833 20.11 0.00 0.00 1.52
703 725 5.236282 GTGAGTACTCCTTCCCTGTTTTAC 58.764 45.833 20.11 3.13 0.00 2.01
705 727 5.221581 TGAGTACTCCTTCCCTGTTTTACAC 60.222 44.000 20.11 0.00 0.00 2.90
771 814 2.953466 ATGTGGCAGATGTTTCATGC 57.047 45.000 0.00 0.00 39.25 4.06
798 841 1.227999 GCTGCCGTGCAAACTGACTA 61.228 55.000 0.00 0.00 38.41 2.59
802 845 2.225491 TGCCGTGCAAACTGACTATTTC 59.775 45.455 0.00 0.00 34.76 2.17
853 898 7.445707 TGTGGCAACTTCATAGTAAAATACACA 59.554 33.333 0.00 0.00 33.17 3.72
1121 1170 1.135689 GCTTGATTCAATGCGTTCGGT 60.136 47.619 0.00 0.00 0.00 4.69
1149 1198 0.647410 CAGACCTTACTTCGCATGCG 59.353 55.000 33.61 33.61 41.35 4.73
1163 1212 2.724349 GCATGCGGAATTCTTCATCAC 58.276 47.619 0.00 1.09 0.00 3.06
1215 1264 7.175641 CACTATGAAAACTCAAAGGTCCAGATT 59.824 37.037 0.00 0.00 0.00 2.40
1355 1408 9.013229 TGAATTGAAGTTTATCACTGCTATGTT 57.987 29.630 0.00 0.00 35.12 2.71
1362 1416 6.942576 AGTTTATCACTGCTATGTTTGTCCTT 59.057 34.615 0.00 0.00 32.83 3.36
1390 1445 4.083961 GCGAGTTTACCTGACTCTTTTTCC 60.084 45.833 3.17 0.00 41.02 3.13
1511 1566 5.188163 TCCGGAAAATCTACACATGGAACTA 59.812 40.000 0.00 0.00 0.00 2.24
1669 1724 7.308710 CCGAGGAATGTAAGGTACTATCTCTTC 60.309 44.444 0.00 0.00 38.49 2.87
1693 1749 7.703328 TCTGTTCTTGTCAAAAACTATGTTCC 58.297 34.615 3.55 0.00 0.00 3.62
1865 1926 3.394674 TTCATCGTTTGTAGCACCAGA 57.605 42.857 0.00 0.00 0.00 3.86
1882 1944 3.947196 ACCAGATTGCTATTTCGAATGCA 59.053 39.130 14.22 14.22 0.00 3.96
1884 1946 5.764686 ACCAGATTGCTATTTCGAATGCATA 59.235 36.000 17.42 5.19 35.27 3.14
1994 2062 4.065088 TCTTTTTCATCGCTAACTGCACT 58.935 39.130 0.00 0.00 43.06 4.40
2048 2118 0.813184 CTTTCCTGCGGTTGATGCAT 59.187 50.000 0.00 0.00 42.32 3.96
2050 2120 1.936436 TTCCTGCGGTTGATGCATGC 61.936 55.000 11.82 11.82 42.32 4.06
2192 2270 1.667724 CAGTACAGCTAACATGGCAGC 59.332 52.381 11.70 11.70 38.09 5.25
2195 2273 1.171308 ACAGCTAACATGGCAGCTTG 58.829 50.000 17.82 15.32 45.80 4.01
2218 2296 1.967319 ACAAACAACACGGCAGATCT 58.033 45.000 0.00 0.00 0.00 2.75
2372 2475 8.623903 CATGGCAGATTAACTACACATAACATT 58.376 33.333 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.406442 AGGACCTCCTCTGCAATGA 57.594 52.632 0.00 0.00 44.77 2.57
72 73 4.385310 GGTGGCACTTCTAATGGTATCCTT 60.385 45.833 18.45 0.00 0.00 3.36
174 175 1.913778 TCGTACAGCTGGGTCTGTTA 58.086 50.000 19.93 0.00 44.26 2.41
320 322 7.968956 CGTAAGCGGATCATGTATAGAAAGTAT 59.031 37.037 0.00 0.00 0.00 2.12
455 469 1.030457 GATCACCCAGGTCGACGTAT 58.970 55.000 10.91 0.00 0.00 3.06
506 520 2.093625 GCATGCAACTACATTCGTCGAA 59.906 45.455 14.21 10.61 0.00 3.71
588 602 2.824936 CCCATATTTTGCAGGTCACACA 59.175 45.455 0.00 0.00 0.00 3.72
650 664 0.033504 AGTGTGAGCTACCGTGTTGG 59.966 55.000 0.00 0.00 46.41 3.77
673 694 5.359009 CAGGGAAGGAGTACTCACGTATTTA 59.641 44.000 23.91 0.00 0.00 1.40
679 700 1.546961 ACAGGGAAGGAGTACTCACG 58.453 55.000 23.91 6.54 0.00 4.35
798 841 3.510719 CACGGGATGCAAAAATCGAAAT 58.489 40.909 0.00 0.00 0.00 2.17
1121 1170 3.181486 CGAAGTAAGGTCTGCATCAGCTA 60.181 47.826 0.00 0.00 42.74 3.32
1149 1198 3.751175 TGACGTTGGTGATGAAGAATTCC 59.249 43.478 0.65 0.00 46.93 3.01
1180 1229 5.235616 TTGAGTTTTCATAGTGACGGTTCAC 59.764 40.000 0.00 0.00 41.86 3.18
1181 1230 4.951254 TGAGTTTTCATAGTGACGGTTCA 58.049 39.130 0.00 0.00 0.00 3.18
1194 1243 6.710744 GTCTAATCTGGACCTTTGAGTTTTCA 59.289 38.462 0.00 0.00 0.00 2.69
1215 1264 4.468510 ACATACTCAACCGGGAAATGTCTA 59.531 41.667 6.32 0.00 0.00 2.59
1362 1416 4.448210 AGAGTCAGGTAAACTCGCAAAAA 58.552 39.130 0.00 0.00 46.23 1.94
1374 1428 3.135712 TGCACAGGAAAAAGAGTCAGGTA 59.864 43.478 0.00 0.00 0.00 3.08
1390 1445 1.665916 CACAGTCCGTCCTGCACAG 60.666 63.158 0.00 0.00 35.83 3.66
1511 1566 6.618287 TGTTGAAATCTTCATTCGTCAACT 57.382 33.333 13.61 0.00 38.98 3.16
1669 1724 7.645340 CAGGAACATAGTTTTTGACAAGAACAG 59.355 37.037 20.15 13.05 0.00 3.16
1693 1749 4.201851 GGTTGCAGTCATAACATAGCACAG 60.202 45.833 0.00 0.00 32.23 3.66
1865 1926 7.595311 TCGTATATGCATTCGAAATAGCAAT 57.405 32.000 21.60 17.86 40.76 3.56
1994 2062 1.578897 TCAACCTACCATGCTAGCCA 58.421 50.000 13.29 0.24 0.00 4.75
2192 2270 2.353269 TGCCGTGTTGTTTGTACTCAAG 59.647 45.455 0.00 0.00 34.88 3.02
2195 2273 2.206750 TCTGCCGTGTTGTTTGTACTC 58.793 47.619 0.00 0.00 0.00 2.59
2218 2296 6.541907 TGGATCTGCCATGTTAATTATGCTA 58.458 36.000 0.00 0.00 43.33 3.49
2372 2475 6.061441 CCATGTTATGGGTACTTAATCTGCA 58.939 40.000 0.00 0.00 46.86 4.41
2476 2602 6.539173 TGTTTTGTACCCTAGATGTTGTGAT 58.461 36.000 0.00 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.