Multiple sequence alignment - TraesCS3A01G249600

Loading Multiple Alignment...

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 TraesCS3A01G249600 chr3A 100.000 2394 0 0 1 2394 467894076 467896469 0 4421
1 TraesCS3A01G249600 chr1D 95.428 1553 61 6 1 1551 77843245 77841701 0 2466
2 TraesCS3A01G249600 chr2D 94.394 1552 78 5 1 1551 468952954 468951411 0 2375
3 TraesCS3A01G249600 chr2D 87.967 1471 167 5 3 1470 427568005 427569468 0 1727
4 TraesCS3A01G249600 chr7D 94.262 1551 80 4 1 1551 13888660 13887119 0 2362
5 TraesCS3A01G249600 chr7D 94.068 1551 84 4 1 1551 48270002 48268460 0 2348
6 TraesCS3A01G249600 chr7D 97.291 849 21 2 1547 2394 616650663 616649816 0 1439
7 TraesCS3A01G249600 chr7D 97.288 848 21 2 1548 2394 64537615 64538461 0 1437
8 TraesCS3A01G249600 chr6D 94.455 1533 75 5 1 1533 19503046 19501524 0 2351
9 TraesCS3A01G249600 chr6D 97.288 848 21 2 1548 2394 124648060 124648906 0 1437
10 TraesCS3A01G249600 chr6D 97.285 847 22 1 1548 2394 157608046 157607201 0 1435
11 TraesCS3A01G249600 chr7A 90.874 1545 130 4 1 1544 34345432 34343898 0 2061
12 TraesCS3A01G249600 chr2B 90.206 1552 132 13 1 1546 396930977 396929440 0 2006
13 TraesCS3A01G249600 chr5A 89.923 1558 136 14 1 1551 527780378 527778835 0 1988
14 TraesCS3A01G249600 chr6A 89.586 1546 142 12 1 1538 606067639 606069173 0 1945
15 TraesCS3A01G249600 chrUn 97.291 849 21 2 1547 2394 68446135 68445288 0 1439
16 TraesCS3A01G249600 chrUn 97.066 852 23 2 1544 2394 109035594 109036444 0 1434
17 TraesCS3A01G249600 chr4D 97.285 847 23 0 1548 2394 382339063 382338217 0 1437
18 TraesCS3A01G249600 chr4D 97.288 848 21 2 1548 2394 508708470 508707624 0 1437
19 TraesCS3A01G249600 chr5D 97.285 847 22 1 1548 2394 472600034 472599189 0 1435
20 TraesCS3A01G249600 chr4B 92.221 797 56 1 1 797 481518842 481519632 0 1123


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 TraesCS3A01G249600 chr3A 467894076 467896469 2393 False 4421 4421 100.000 1 2394 1 chr3A.!!$F1 2393
1 TraesCS3A01G249600 chr1D 77841701 77843245 1544 True 2466 2466 95.428 1 1551 1 chr1D.!!$R1 1550
2 TraesCS3A01G249600 chr2D 468951411 468952954 1543 True 2375 2375 94.394 1 1551 1 chr2D.!!$R1 1550
3 TraesCS3A01G249600 chr2D 427568005 427569468 1463 False 1727 1727 87.967 3 1470 1 chr2D.!!$F1 1467
4 TraesCS3A01G249600 chr7D 13887119 13888660 1541 True 2362 2362 94.262 1 1551 1 chr7D.!!$R1 1550
5 TraesCS3A01G249600 chr7D 48268460 48270002 1542 True 2348 2348 94.068 1 1551 1 chr7D.!!$R2 1550
6 TraesCS3A01G249600 chr7D 616649816 616650663 847 True 1439 1439 97.291 1547 2394 1 chr7D.!!$R3 847
7 TraesCS3A01G249600 chr7D 64537615 64538461 846 False 1437 1437 97.288 1548 2394 1 chr7D.!!$F1 846
8 TraesCS3A01G249600 chr6D 19501524 19503046 1522 True 2351 2351 94.455 1 1533 1 chr6D.!!$R1 1532
9 TraesCS3A01G249600 chr6D 124648060 124648906 846 False 1437 1437 97.288 1548 2394 1 chr6D.!!$F1 846
10 TraesCS3A01G249600 chr6D 157607201 157608046 845 True 1435 1435 97.285 1548 2394 1 chr6D.!!$R2 846
11 TraesCS3A01G249600 chr7A 34343898 34345432 1534 True 2061 2061 90.874 1 1544 1 chr7A.!!$R1 1543
12 TraesCS3A01G249600 chr2B 396929440 396930977 1537 True 2006 2006 90.206 1 1546 1 chr2B.!!$R1 1545
13 TraesCS3A01G249600 chr5A 527778835 527780378 1543 True 1988 1988 89.923 1 1551 1 chr5A.!!$R1 1550
14 TraesCS3A01G249600 chr6A 606067639 606069173 1534 False 1945 1945 89.586 1 1538 1 chr6A.!!$F1 1537
15 TraesCS3A01G249600 chrUn 68445288 68446135 847 True 1439 1439 97.291 1547 2394 1 chrUn.!!$R1 847
16 TraesCS3A01G249600 chrUn 109035594 109036444 850 False 1434 1434 97.066 1544 2394 1 chrUn.!!$F1 850
17 TraesCS3A01G249600 chr4D 382338217 382339063 846 True 1437 1437 97.285 1548 2394 1 chr4D.!!$R1 846
18 TraesCS3A01G249600 chr4D 508707624 508708470 846 True 1437 1437 97.288 1548 2394 1 chr4D.!!$R2 846
19 TraesCS3A01G249600 chr5D 472599189 472600034 845 True 1435 1435 97.285 1548 2394 1 chr5D.!!$R1 846
20 TraesCS3A01G249600 chr4B 481518842 481519632 790 False 1123 1123 92.221 1 797 1 chr4B.!!$F1 796

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 0.105039 GTGAAGCTCTATCCACGGGG 59.895 60.0 0.00 0.0 0.00 5.73 F
98 99 1.048724 TGAAGCTCTATCCACGGGGG 61.049 60.0 2.42 0.0 38.37 5.40 F
1164 1172 0.178992 TGGCTGCTATATGTTGGGCC 60.179 55.0 0.00 0.0 38.67 5.80 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1164 1172 1.106285 GGTTCCTGGCTAGCCAAATG 58.894 55.0 35.07 25.34 46.63 2.32 R
1250 1259 1.195115 GAGACCTGCCCAGTACATCA 58.805 55.0 0.00 0.00 0.00 3.07 R
2177 2198 0.886563 ATTCGATCGTCGGTATCCCC 59.113 55.0 15.94 0.00 40.88 4.81 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
93 94 5.069781 ACTGGATTAGTGAAGCTCTATCCAC 59.930 44.000 0.00 0.00 40.57 4.02
94 95 4.038042 TGGATTAGTGAAGCTCTATCCACG 59.962 45.833 0.00 0.00 40.57 4.94
95 96 4.551388 GATTAGTGAAGCTCTATCCACGG 58.449 47.826 0.00 0.00 34.93 4.94
96 97 1.115467 AGTGAAGCTCTATCCACGGG 58.885 55.000 0.00 0.00 34.93 5.28
97 98 0.105039 GTGAAGCTCTATCCACGGGG 59.895 60.000 0.00 0.00 0.00 5.73
98 99 1.048724 TGAAGCTCTATCCACGGGGG 61.049 60.000 2.42 0.00 38.37 5.40
150 152 6.351327 GTGCTGTCACATATTCCTACTTTC 57.649 41.667 0.00 0.00 42.66 2.62
151 153 5.005779 GTGCTGTCACATATTCCTACTTTCG 59.994 44.000 0.00 0.00 42.66 3.46
203 205 2.422803 CCTTGGAGAAGTGGGACAAACA 60.423 50.000 0.00 0.00 44.16 2.83
324 329 5.535030 GGGTGTTAAAGACTTGAGGAAACAT 59.465 40.000 0.00 0.00 0.00 2.71
355 360 4.022329 GTCTTTTAGTGAAATGGTGGTGGG 60.022 45.833 0.00 0.00 0.00 4.61
501 507 5.191722 AGTGAAAGACCTTTATATGCTGGGA 59.808 40.000 0.00 0.00 32.11 4.37
521 527 7.093945 GCTGGGAAGAGGTATTAATTTGAACAA 60.094 37.037 0.00 0.00 0.00 2.83
552 558 3.226777 GGCTAGACTCTGGCTTGATAGA 58.773 50.000 13.56 0.00 38.07 1.98
569 575 5.970289 TGATAGACTGGATGGTAGAATCCT 58.030 41.667 4.93 0.00 45.57 3.24
680 686 3.954904 TCTTTTAGGAGGAGGATGTCTCG 59.045 47.826 0.00 0.00 43.34 4.04
864 871 4.524802 ATGGATCTGGGATGCAAAACTA 57.475 40.909 5.88 0.00 0.00 2.24
1081 1089 6.662755 ACTGATTGTTGCCCTAATTCTATCA 58.337 36.000 0.00 0.00 0.00 2.15
1164 1172 0.178992 TGGCTGCTATATGTTGGGCC 60.179 55.000 0.00 0.00 38.67 5.80
1212 1220 7.023575 CCACTTTCGAACTCAAATGGATTAAG 58.976 38.462 0.00 0.00 0.00 1.85
1250 1259 6.155475 TGTATTTACAGCTTGTGCCTTTTT 57.845 33.333 0.00 0.00 40.80 1.94
1297 1306 2.158249 CCAGAGATAGGGGAGATGGTGA 60.158 54.545 0.00 0.00 0.00 4.02
1345 1354 4.898320 AGAACACAACACAGATGATGCTA 58.102 39.130 0.00 0.00 31.96 3.49
1418 1428 2.036862 AGAAGACGTTGTGGACCCTAAC 59.963 50.000 0.00 0.00 0.00 2.34
1472 1487 3.432588 CGACGCGTCCTGGAGTCT 61.433 66.667 31.84 0.00 35.00 3.24
1521 1541 2.510382 TCTTTGGTCCTTGTTGTGGGTA 59.490 45.455 0.00 0.00 0.00 3.69
1541 1562 4.285260 GGTACTCTGGTAGTTCTTTTGGGA 59.715 45.833 0.00 0.00 39.80 4.37
1682 1703 7.112122 ACATGTGTGAATACATAGACCACAAT 58.888 34.615 0.00 0.00 39.17 2.71
1844 1865 4.330074 GCATAGCACAAGATCGTGTAGTTT 59.670 41.667 14.10 3.41 39.19 2.66
2177 2198 4.738740 GGTAACGAGATTGAACGAGGTATG 59.261 45.833 0.00 0.00 0.00 2.39
2239 2260 8.215050 ACCGATTGACAAAGGGAATTGTATATA 58.785 33.333 13.19 0.00 43.31 0.86
2347 2368 2.375174 TGTTGGTTATTGGCCAGAGAGT 59.625 45.455 5.11 0.00 37.31 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 5.758296 TCACTAATCCAGTTTTCACAGTGAC 59.242 40.000 1.52 0.00 36.99 3.67
150 152 6.366061 TGTTCAGAAGAAACATAGACATGTCG 59.634 38.462 19.85 8.81 44.83 4.35
151 153 7.658179 TGTTCAGAAGAAACATAGACATGTC 57.342 36.000 18.47 18.47 44.83 3.06
203 205 8.181904 TCTATGCCAGAAAAATTTTCTTCTGT 57.818 30.769 22.31 12.37 44.66 3.41
355 360 3.571828 AGCCCTTTCTTTTTCTCAAGCTC 59.428 43.478 0.00 0.00 0.00 4.09
420 426 4.743493 CTTTGTGTTTAACCACAGCAACT 58.257 39.130 5.94 0.00 45.42 3.16
501 507 8.390921 TCTCCCTTGTTCAAATTAATACCTCTT 58.609 33.333 0.00 0.00 0.00 2.85
521 527 1.573376 AGAGTCTAGCCACATCTCCCT 59.427 52.381 0.00 0.00 0.00 4.20
552 558 8.390921 TCTTTAAAAAGGATTCTACCATCCAGT 58.609 33.333 2.62 0.00 44.93 4.00
569 575 5.833131 AGCAGTGGGAATCTGTCTTTAAAAA 59.167 36.000 0.00 0.00 35.60 1.94
680 686 4.337555 CCTCCCATTGTTTCATCATCTCAC 59.662 45.833 0.00 0.00 0.00 3.51
884 891 3.862877 TCTATGCCATATGCCACAAGT 57.137 42.857 0.00 0.00 40.16 3.16
1081 1089 8.605947 ACTATACATCCACACATAATATTGCCT 58.394 33.333 0.00 0.00 0.00 4.75
1164 1172 1.106285 GGTTCCTGGCTAGCCAAATG 58.894 55.000 35.07 25.34 46.63 2.32
1212 1220 9.076596 GCTGTAAATACAATTTCAAATGGAGAC 57.923 33.333 0.00 0.00 35.50 3.36
1250 1259 1.195115 GAGACCTGCCCAGTACATCA 58.805 55.000 0.00 0.00 0.00 3.07
1472 1487 1.511850 CTGTTCATCCAGCACACGAA 58.488 50.000 0.00 0.00 0.00 3.85
1521 1541 4.351111 ACATCCCAAAAGAACTACCAGAGT 59.649 41.667 0.00 0.00 41.56 3.24
1541 1562 4.095946 AGGGCATATTTCCAACACAACAT 58.904 39.130 0.00 0.00 0.00 2.71
1682 1703 5.926580 ACTAGAGGCTTACTAGGGACATA 57.073 43.478 13.13 0.00 40.86 2.29
1800 1821 3.610911 CTTAGGATTGGGTCTTGTCCAC 58.389 50.000 0.00 0.00 33.43 4.02
1844 1865 7.228507 TGACATTAGAAAAGCTCTAGCAAAACA 59.771 33.333 4.54 0.00 45.16 2.83
2139 2160 3.005684 TCGTTACCGGCAAGTCTCTTTAA 59.994 43.478 0.00 0.00 33.95 1.52
2177 2198 0.886563 ATTCGATCGTCGGTATCCCC 59.113 55.000 15.94 0.00 40.88 4.81
2325 2346 3.181434 ACTCTCTGGCCAATAACCAACAA 60.181 43.478 7.01 0.00 36.56 2.83
2347 2368 3.531934 ATGCAGACATGATCGAGACAA 57.468 42.857 0.00 0.00 34.35 3.18


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

AutoCloner maintained by Alex Coulton.