Multiple sequence alignment - TraesCS3B01G363700

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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 TraesCS3B01G363700 chr3B 100.000 1708 0 0 821 2528 575683304 575681597 0 3155
1 TraesCS3B01G363700 chr3B 97.121 903 24 2 1626 2527 201634131 201633230 0 1522
2 TraesCS3B01G363700 chr3B 97.017 905 23 4 1626 2527 92181081 92181984 0 1519
3 TraesCS3B01G363700 chr3B 100.000 515 0 0 1 515 575684124 575683610 0 952
4 TraesCS3B01G363700 chr5B 97.342 903 22 2 1626 2527 713044537 713043636 0 1533
5 TraesCS3B01G363700 chr3D 97.238 905 22 3 1626 2527 202613618 202614522 0 1530
6 TraesCS3B01G363700 chr2D 97.238 905 21 3 1626 2527 635038932 635039835 0 1530
7 TraesCS3B01G363700 chr2D 97.124 904 24 2 1626 2527 17965514 17964611 0 1524
8 TraesCS3B01G363700 chr2D 98.132 803 15 0 823 1625 635038081 635038883 0 1400
9 TraesCS3B01G363700 chr7A 97.231 903 23 2 1626 2527 120827176 120826275 0 1528
10 TraesCS3B01G363700 chr7A 97.013 904 25 2 1626 2527 120924168 120923265 0 1519
11 TraesCS3B01G363700 chr7A 97.864 515 10 1 1 515 671960282 671959769 0 889
12 TraesCS3B01G363700 chr7A 97.864 515 10 1 1 515 672005439 672005952 0 889
13 TraesCS3B01G363700 chr4D 97.017 905 24 3 1626 2527 123369315 123370219 0 1519
14 TraesCS3B01G363700 chr4D 98.137 805 14 1 821 1625 123368463 123369266 0 1402
15 TraesCS3B01G363700 chr4D 98.012 805 15 1 821 1625 123579413 123580216 0 1397
16 TraesCS3B01G363700 chr4D 98.252 515 8 1 1 515 123578878 123579391 0 900
17 TraesCS3B01G363700 chr4D 97.670 515 11 1 1 515 123367927 123368440 0 883
18 TraesCS3B01G363700 chr7B 98.261 805 14 0 821 1625 743067126 743067930 0 1410
19 TraesCS3B01G363700 chr7B 97.772 808 18 0 821 1628 743112498 743111691 0 1393
20 TraesCS3B01G363700 chr7B 97.864 515 10 1 1 515 743066591 743067104 0 889
21 TraesCS3B01G363700 chr5A 98.144 808 15 0 821 1628 16622452 16621645 0 1410
22 TraesCS3B01G363700 chr5A 98.137 805 15 0 821 1625 300049387 300050191 0 1404
23 TraesCS3B01G363700 chr5A 97.864 515 10 1 1 515 300048851 300049364 0 889
24 TraesCS3B01G363700 chr7D 98.141 807 15 0 822 1628 382014050 382013244 0 1408
25 TraesCS3B01G363700 chr7D 98.058 515 9 1 1 515 382014585 382014072 0 894
26 TraesCS3B01G363700 chr1B 98.261 805 13 1 821 1625 461453044 461453847 0 1408
27 TraesCS3B01G363700 chrUn 98.058 515 9 1 1 515 273239083 273239596 0 894
28 TraesCS3B01G363700 chr2A 97.864 515 10 1 1 515 735173085 735173598 0 889


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 TraesCS3B01G363700 chr3B 575681597 575684124 2527 True 2053.5 3155 100.0000 1 2528 2 chr3B.!!$R2 2527
1 TraesCS3B01G363700 chr3B 201633230 201634131 901 True 1522.0 1522 97.1210 1626 2527 1 chr3B.!!$R1 901
2 TraesCS3B01G363700 chr3B 92181081 92181984 903 False 1519.0 1519 97.0170 1626 2527 1 chr3B.!!$F1 901
3 TraesCS3B01G363700 chr5B 713043636 713044537 901 True 1533.0 1533 97.3420 1626 2527 1 chr5B.!!$R1 901
4 TraesCS3B01G363700 chr3D 202613618 202614522 904 False 1530.0 1530 97.2380 1626 2527 1 chr3D.!!$F1 901
5 TraesCS3B01G363700 chr2D 17964611 17965514 903 True 1524.0 1524 97.1240 1626 2527 1 chr2D.!!$R1 901
6 TraesCS3B01G363700 chr2D 635038081 635039835 1754 False 1465.0 1530 97.6850 823 2527 2 chr2D.!!$F1 1704
7 TraesCS3B01G363700 chr7A 120826275 120827176 901 True 1528.0 1528 97.2310 1626 2527 1 chr7A.!!$R1 901
8 TraesCS3B01G363700 chr7A 120923265 120924168 903 True 1519.0 1519 97.0130 1626 2527 1 chr7A.!!$R2 901
9 TraesCS3B01G363700 chr7A 671959769 671960282 513 True 889.0 889 97.8640 1 515 1 chr7A.!!$R3 514
10 TraesCS3B01G363700 chr7A 672005439 672005952 513 False 889.0 889 97.8640 1 515 1 chr7A.!!$F1 514
11 TraesCS3B01G363700 chr4D 123367927 123370219 2292 False 1268.0 1519 97.6080 1 2527 3 chr4D.!!$F1 2526
12 TraesCS3B01G363700 chr4D 123578878 123580216 1338 False 1148.5 1397 98.1320 1 1625 2 chr4D.!!$F2 1624
13 TraesCS3B01G363700 chr7B 743111691 743112498 807 True 1393.0 1393 97.7720 821 1628 1 chr7B.!!$R1 807
14 TraesCS3B01G363700 chr7B 743066591 743067930 1339 False 1149.5 1410 98.0625 1 1625 2 chr7B.!!$F1 1624
15 TraesCS3B01G363700 chr5A 16621645 16622452 807 True 1410.0 1410 98.1440 821 1628 1 chr5A.!!$R1 807
16 TraesCS3B01G363700 chr5A 300048851 300050191 1340 False 1146.5 1404 98.0005 1 1625 2 chr5A.!!$F1 1624
17 TraesCS3B01G363700 chr7D 382013244 382014585 1341 True 1151.0 1408 98.0995 1 1628 2 chr7D.!!$R1 1627
18 TraesCS3B01G363700 chr1B 461453044 461453847 803 False 1408.0 1408 98.2610 821 1625 1 chr1B.!!$F1 804
19 TraesCS3B01G363700 chrUn 273239083 273239596 513 False 894.0 894 98.0580 1 515 1 chrUn.!!$F1 514
20 TraesCS3B01G363700 chr2A 735173085 735173598 513 False 889.0 889 97.8640 1 515 1 chr2A.!!$F1 514

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
216 217 0.527113 CCAACGCCATTCATCTTGCA 59.473 50.0 0.00 0.00 0.00 4.08 F
274 275 1.166950 CGCTACTACGTTCGTCGAAC 58.833 55.0 24.91 24.91 42.86 3.95 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1394 1395 0.324614 ATCCAACATGCAGGACACGA 59.675 50.0 4.84 0.00 36.60 4.35 R
1772 1823 0.817013 TAGCCGTTACCCGAATTCGT 59.183 50.0 25.10 11.33 39.56 3.85 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
22 23 1.127343 GGCCTTCAGATAGGTGCTCT 58.873 55.000 0.00 0.00 37.63 4.09
79 80 9.823647 GAGACACTATCTTGGATGAGATAAAAA 57.176 33.333 0.00 0.00 38.00 1.94
216 217 0.527113 CCAACGCCATTCATCTTGCA 59.473 50.000 0.00 0.00 0.00 4.08
274 275 1.166950 CGCTACTACGTTCGTCGAAC 58.833 55.000 24.91 24.91 42.86 3.95
284 285 2.098021 CGTTCGTCGAACACTTCTTGAC 60.098 50.000 31.26 7.49 42.05 3.18
1129 1130 2.183478 ACGATTGATTGGTCTGTGCA 57.817 45.000 0.00 0.00 0.00 4.57
1138 1139 4.216902 TGATTGGTCTGTGCATTTCTCTTG 59.783 41.667 0.00 0.00 0.00 3.02
1394 1395 9.529325 TCTAATTCGTGAATTTCTAATGATCGT 57.471 29.630 12.62 0.00 40.99 3.73
1408 1409 0.458543 GATCGTCGTGTCCTGCATGT 60.459 55.000 0.00 0.00 35.64 3.21
1650 1699 3.890527 GGTACCTCGTAGGACCTCA 57.109 57.895 4.06 0.00 37.67 3.86
1702 1751 0.914902 GGAAGGGGTGCTCCTAGGTT 60.915 60.000 9.08 0.00 35.80 3.50
1724 1773 2.291670 TGTGTAGGGGGTGTGTTTGTTT 60.292 45.455 0.00 0.00 0.00 2.83
1964 2018 1.183549 TGGCGAAGAGACCTTAGGAC 58.816 55.000 4.77 0.00 31.62 3.85
2075 2130 2.383855 CCCCCTTCCAAATAAATGCGA 58.616 47.619 0.00 0.00 0.00 5.10
2184 2240 3.197664 GCAGGAAGCAGGCCTAAAT 57.802 52.632 3.98 0.00 44.79 1.40
2298 2354 1.004277 GTGGTCTAATGACAAGGGCCA 59.996 52.381 6.18 0.00 44.61 5.36
2446 2503 6.019748 CCTGACTCTACCATCATTATAGGGT 58.980 44.000 0.00 0.00 32.17 4.34
2456 2513 6.800606 ACCATCATTATAGGGTTATGGGGTTA 59.199 38.462 0.00 0.00 38.54 2.85
2527 2584 9.774742 CTTTACTTGGATCTGTTTTTATGCTAC 57.225 33.333 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
22 23 8.822805 CCCCATAAAATAGATAAGCCTGTAGTA 58.177 37.037 0.00 0.00 0.00 1.82
79 80 6.328672 AGTGGAAGGATCAACTATCTATTGCT 59.671 38.462 0.00 0.00 38.11 3.91
94 95 1.078143 GCTTCGGCAGTGGAAGGAT 60.078 57.895 10.12 0.00 40.92 3.24
216 217 3.355378 TGCATGAAAGACCGGATTTGAT 58.645 40.909 9.46 5.71 0.00 2.57
274 275 0.798776 GATGGTGCCGTCAAGAAGTG 59.201 55.000 5.61 0.00 32.55 3.16
284 285 2.146342 GGTAATGAGATGATGGTGCCG 58.854 52.381 0.00 0.00 0.00 5.69
314 315 1.404391 GTCATAGCCGAAGTCGAAGGA 59.596 52.381 1.43 0.00 43.02 3.36
1394 1395 0.324614 ATCCAACATGCAGGACACGA 59.675 50.000 4.84 0.00 36.60 4.35
1408 1409 9.661954 AAGAACATAGAATAGTAGAGGATCCAA 57.338 33.333 15.82 0.00 33.66 3.53
1473 1474 3.007290 TGATCCCAGCGAATAGAAGATGG 59.993 47.826 0.00 0.00 43.02 3.51
1540 1541 2.171027 ACTTTACGACAACAAGGGACCA 59.829 45.455 0.00 0.00 0.00 4.02
1547 1548 6.701400 GGACCTTTACTACTTTACGACAACAA 59.299 38.462 0.00 0.00 0.00 2.83
1548 1549 6.215845 GGACCTTTACTACTTTACGACAACA 58.784 40.000 0.00 0.00 0.00 3.33
1551 1552 5.391312 GGGACCTTTACTACTTTACGACA 57.609 43.478 0.00 0.00 0.00 4.35
1702 1751 1.285373 ACAAACACACCCCCTACACAA 59.715 47.619 0.00 0.00 0.00 3.33
1724 1773 2.094234 TGACGAGGAATTCATTCTCGCA 60.094 45.455 23.84 20.13 39.12 5.10
1772 1823 0.817013 TAGCCGTTACCCGAATTCGT 59.183 50.000 25.10 11.33 39.56 3.85
1822 1873 1.982958 AGTTTACGTCCATCCCTGGTT 59.017 47.619 0.00 0.00 43.61 3.67
1910 1964 2.595238 ACGACAGAGGAACTAACCTGT 58.405 47.619 0.00 0.00 41.55 4.00
1964 2018 4.041723 CCTCCGTTTGTTTTAGCAACTTG 58.958 43.478 0.00 0.00 0.00 3.16
2075 2130 1.908340 CTGCCAAGCTCTACCCTGCT 61.908 60.000 0.00 0.00 41.82 4.24
2158 2214 1.302832 CTGCTTCCTGCCCGAAAGT 60.303 57.895 0.00 0.00 42.00 2.66
2298 2354 2.257676 GTCCGAGCTTCCGTCGTT 59.742 61.111 0.00 0.00 35.59 3.85
2446 2503 7.324388 TCTTTCTTTGTCTCTAACCCCATAA 57.676 36.000 0.00 0.00 0.00 1.90
2456 2513 4.978099 TGCCTTGATCTTTCTTTGTCTCT 58.022 39.130 0.00 0.00 0.00 3.10


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

AutoCloner maintained by Alex Coulton.