Multiple sequence alignment - TraesCS3A01G066300

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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 TraesCS3A01G066300 chr3A 100.000 2527 0 0 1 2527 39657697 39660223 0.000000e+00 4667.0
1 TraesCS3A01G066300 chr3A 94.876 2537 106 13 1 2527 39677357 39679879 0.000000e+00 3943.0
2 TraesCS3A01G066300 chr3A 94.181 2406 99 19 1 2386 39697588 39699972 0.000000e+00 3629.0
3 TraesCS3A01G066300 chr3A 94.281 1976 92 15 555 2527 39307172 39309129 0.000000e+00 3003.0
4 TraesCS3A01G066300 chr3A 94.281 1976 92 15 555 2527 39323904 39325861 0.000000e+00 3003.0
5 TraesCS3A01G066300 chr3A 92.821 1978 113 18 555 2527 39185054 39187007 0.000000e+00 2839.0
6 TraesCS3A01G066300 chr3A 93.885 1897 78 20 633 2527 39573909 39575769 0.000000e+00 2826.0
7 TraesCS3A01G066300 chr3A 92.759 1975 107 13 555 2527 39858271 39860211 0.000000e+00 2822.0
8 TraesCS3A01G066300 chr3A 93.161 1667 87 15 873 2527 38692360 38694011 0.000000e+00 2422.0
9 TraesCS3A01G066300 chr3A 94.638 746 38 2 94 838 39442576 39443320 0.000000e+00 1155.0
10 TraesCS3A01G066300 chr3A 94.474 561 26 4 1 559 39857568 39858125 0.000000e+00 859.0
11 TraesCS3A01G066300 chr3A 94.255 557 28 4 3 559 39573167 39573719 0.000000e+00 848.0
12 TraesCS3A01G066300 chr3A 93.393 560 29 6 1 559 38690900 38691452 0.000000e+00 822.0
13 TraesCS3A01G066300 chr3A 94.041 537 32 0 1 537 39248240 39248776 0.000000e+00 815.0
14 TraesCS3A01G066300 chr3A 92.665 559 37 3 1 559 39183879 39184433 0.000000e+00 802.0
15 TraesCS3A01G066300 chr3A 93.884 327 17 3 555 881 38692084 38692407 8.120000e-135 490.0
16 TraesCS3A01G066300 chr3D 87.333 971 92 13 1587 2527 29371740 29372709 0.000000e+00 1083.0
17 TraesCS3A01G066300 chr3D 86.842 532 58 8 932 1453 29361723 29362252 3.620000e-163 584.0
18 TraesCS3A01G066300 chr3D 84.669 287 21 8 1 264 29360993 29361279 5.360000e-67 265.0
19 TraesCS3A01G066300 chr3D 83.929 280 29 6 1 264 29284728 29285007 1.160000e-63 254.0
20 TraesCS3A01G066300 chr3D 91.398 93 8 0 1448 1540 29371642 29371734 7.340000e-26 128.0
21 TraesCS3A01G066300 chr2A 86.572 283 33 3 261 543 729070867 729071144 8.780000e-80 307.0
22 TraesCS3A01G066300 chr1A 86.111 72 8 2 1743 1814 182151437 182151506 2.700000e-10 76.8


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 TraesCS3A01G066300 chr3A 39657697 39660223 2526 False 4667.000000 4667 100.000000 1 2527 1 chr3A.!!$F5 2526
1 TraesCS3A01G066300 chr3A 39677357 39679879 2522 False 3943.000000 3943 94.876000 1 2527 1 chr3A.!!$F6 2526
2 TraesCS3A01G066300 chr3A 39697588 39699972 2384 False 3629.000000 3629 94.181000 1 2386 1 chr3A.!!$F7 2385
3 TraesCS3A01G066300 chr3A 39307172 39309129 1957 False 3003.000000 3003 94.281000 555 2527 1 chr3A.!!$F2 1972
4 TraesCS3A01G066300 chr3A 39323904 39325861 1957 False 3003.000000 3003 94.281000 555 2527 1 chr3A.!!$F3 1972
5 TraesCS3A01G066300 chr3A 39857568 39860211 2643 False 1840.500000 2822 93.616500 1 2527 2 chr3A.!!$F11 2526
6 TraesCS3A01G066300 chr3A 39573167 39575769 2602 False 1837.000000 2826 94.070000 3 2527 2 chr3A.!!$F10 2524
7 TraesCS3A01G066300 chr3A 39183879 39187007 3128 False 1820.500000 2839 92.743000 1 2527 2 chr3A.!!$F9 2526
8 TraesCS3A01G066300 chr3A 38690900 38694011 3111 False 1244.666667 2422 93.479333 1 2527 3 chr3A.!!$F8 2526
9 TraesCS3A01G066300 chr3A 39442576 39443320 744 False 1155.000000 1155 94.638000 94 838 1 chr3A.!!$F4 744
10 TraesCS3A01G066300 chr3A 39248240 39248776 536 False 815.000000 815 94.041000 1 537 1 chr3A.!!$F1 536
11 TraesCS3A01G066300 chr3D 29371642 29372709 1067 False 605.500000 1083 89.365500 1448 2527 2 chr3D.!!$F3 1079
12 TraesCS3A01G066300 chr3D 29360993 29362252 1259 False 424.500000 584 85.755500 1 1453 2 chr3D.!!$F2 1452

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
686 1359 0.700564 TTCTTTGCAGATGGGAGCCT 59.299 50.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1831 2585 0.111061 ACACATGGTGTCCACATGCT 59.889 50.0 5.41 0.0 43.92 3.79 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
68 70 3.031736 TCCCCCGTTCAAACATTTTCAA 58.968 40.909 0.00 0.00 0.00 2.69
278 306 5.465532 TTGACAAAGCTGAAATGGCAATA 57.534 34.783 6.32 0.00 37.17 1.90
296 324 6.601613 TGGCAATAGTCCAAGGTAATTAAGTG 59.398 38.462 0.00 0.00 0.00 3.16
321 351 1.029681 AGCTACGTCCGTGCATATCA 58.970 50.000 1.98 0.00 0.00 2.15
460 490 9.552114 GTGAGAACATTCACTTTATGATCAAAG 57.448 33.333 0.00 2.15 43.23 2.77
472 502 7.071698 ACTTTATGATCAAAGGGAGCAGAGATA 59.928 37.037 11.02 0.00 46.56 1.98
509 539 7.609960 TGGGTACGTAAACACTATTCACAATA 58.390 34.615 0.00 0.00 0.00 1.90
681 1354 2.892852 TGAGGTTTTCTTTGCAGATGGG 59.107 45.455 0.00 0.00 0.00 4.00
686 1359 0.700564 TTCTTTGCAGATGGGAGCCT 59.299 50.000 0.00 0.00 0.00 4.58
827 1501 8.865590 TCTTCGATTGACATGAATTCGTTATA 57.134 30.769 0.00 0.00 0.00 0.98
962 1687 9.289303 GTACGTGAATTAAAGCATTGATCAATT 57.711 29.630 18.41 7.67 0.00 2.32
1064 1799 8.375493 AGACAGGAAGAAATTGTATGTAGGTA 57.625 34.615 0.00 0.00 0.00 3.08
1265 2004 7.409358 AGAGAAGAAGATTAAGGGCATTTTCT 58.591 34.615 0.00 0.00 28.67 2.52
1271 2010 9.706529 AGAAGATTAAGGGCATTTTCTAGATTT 57.293 29.630 0.00 0.00 0.00 2.17
1402 2143 0.033504 ACCGACGACAAGTGCAAGAT 59.966 50.000 0.00 0.00 0.00 2.40
1492 2233 7.851228 TGATGTCCTGTCATTCAAGTATAAGT 58.149 34.615 0.00 0.00 0.00 2.24
1603 2344 2.679837 CCCGGACTCATCAAGATGTTTG 59.320 50.000 0.73 4.92 39.72 2.93
1759 2512 3.537337 TGAGAAGGAGGATTAACCCCAA 58.463 45.455 0.00 0.00 40.05 4.12
1831 2585 5.127845 TCTCAAACAAAAATGGTGGTTGCTA 59.872 36.000 0.00 0.00 42.32 3.49
1838 2592 1.466856 ATGGTGGTTGCTAGCATGTG 58.533 50.000 20.13 0.00 35.18 3.21
1893 2665 6.042437 TGAGTAGATGAGCATGGTATGTGATT 59.958 38.462 0.00 0.00 0.00 2.57
1905 2677 7.857885 GCATGGTATGTGATTAAGCTCTTTTAC 59.142 37.037 0.00 0.00 0.00 2.01
1921 2693 6.459670 TCTTTTACCCTTTCAAACTTGACC 57.540 37.500 0.00 0.00 36.83 4.02
1959 2731 0.767375 ACAGGTCCAGTGCATGTTCT 59.233 50.000 0.00 0.00 0.00 3.01
2412 3198 6.627395 TTGAGTCCAACGTCATAAATTGTT 57.373 33.333 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
278 306 6.947376 ACTACCACTTAATTACCTTGGACT 57.053 37.500 11.49 0.00 0.00 3.85
296 324 0.028637 GCACGGACGTAGCTACTACC 59.971 60.000 21.20 20.24 33.79 3.18
435 465 8.733458 CCTTTGATCATAAAGTGAATGTTCTCA 58.267 33.333 0.00 0.00 40.97 3.27
460 490 3.640967 AGATGTCTTGTATCTCTGCTCCC 59.359 47.826 0.00 0.00 29.05 4.30
472 502 3.764237 ACGTACCCAAAGATGTCTTGT 57.236 42.857 0.00 0.00 36.12 3.16
560 1233 9.063615 GGTTTGACTAGATTAAGAAAGTTCCAA 57.936 33.333 0.00 0.00 0.00 3.53
681 1354 9.252962 CATTAAAAATGTCCATTTCATAGGCTC 57.747 33.333 5.77 0.00 39.88 4.70
926 1624 9.915629 TGCTTTAATTCACGTACCAAATTAATT 57.084 25.926 13.48 0.00 35.75 1.40
928 1626 9.915629 AATGCTTTAATTCACGTACCAAATTAA 57.084 25.926 10.68 10.68 34.63 1.40
929 1627 9.347934 CAATGCTTTAATTCACGTACCAAATTA 57.652 29.630 0.00 0.00 0.00 1.40
930 1628 8.085296 TCAATGCTTTAATTCACGTACCAAATT 58.915 29.630 0.00 0.00 0.00 1.82
936 1661 8.841444 ATTGATCAATGCTTTAATTCACGTAC 57.159 30.769 20.11 0.00 0.00 3.67
1064 1799 3.822607 CAGGAGTCTGCTTACGCTT 57.177 52.632 0.00 0.00 36.97 4.68
1087 1822 3.493767 TGCCATGGTGTACAGTACAAA 57.506 42.857 15.24 7.34 40.93 2.83
1244 1983 9.706529 AATCTAGAAAATGCCCTTAATCTTCTT 57.293 29.630 0.00 0.00 0.00 2.52
1402 2143 1.837538 GCCTACGCTGTCGCAAAACA 61.838 55.000 0.00 0.00 39.84 2.83
1469 2210 7.624549 ACACTTATACTTGAATGACAGGACAT 58.375 34.615 0.00 0.00 0.00 3.06
1548 2289 3.077484 TGGAAGCTCCCAGATCAAAAG 57.923 47.619 0.00 0.00 35.03 2.27
1603 2344 7.248381 CGAAAAGTCGGTTTACAATGATTTC 57.752 36.000 0.00 0.00 43.81 2.17
1741 2493 3.732048 TGTTGGGGTTAATCCTCCTTC 57.268 47.619 4.37 0.00 35.35 3.46
1831 2585 0.111061 ACACATGGTGTCCACATGCT 59.889 50.000 5.41 0.00 43.92 3.79
1838 2592 3.632145 AGAAACAAGAACACATGGTGTCC 59.368 43.478 2.07 0.00 46.79 4.02
1893 2665 7.558444 TCAAGTTTGAAAGGGTAAAAGAGCTTA 59.442 33.333 0.00 0.00 33.55 3.09
1905 2677 3.230134 TCATGGGTCAAGTTTGAAAGGG 58.770 45.455 0.00 0.00 39.21 3.95
1921 2693 4.334759 CCTGTAGAAAGACTTGCATCATGG 59.665 45.833 0.00 0.00 0.00 3.66
2108 2886 4.895297 ACTTCCGATAATGCCCATCAATTT 59.105 37.500 0.00 0.00 0.00 1.82
2376 3162 5.238650 CGTTGGACTCAATAGAACCTTGTTT 59.761 40.000 0.00 0.00 35.10 2.83


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

AutoCloner maintained by Alex Coulton.