Multiple sequence alignment - TraesCS3B01G349700

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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 TraesCS3B01G349700 chr3B 100.000 3050 0 0 1 3050 559891281 559888232 0.000000e+00 5633
1 TraesCS3B01G349700 chr3B 95.359 1853 68 10 574 2412 149100696 149102544 0.000000e+00 2929
2 TraesCS3B01G349700 chr3B 94.366 639 34 1 2412 3050 559882977 559882341 0.000000e+00 979
3 TraesCS3B01G349700 chr3B 90.799 576 49 2 3 576 559883546 559882973 0.000000e+00 767
4 TraesCS3B01G349700 chr1B 97.454 1846 44 3 574 2416 665855413 665853568 0.000000e+00 3145
5 TraesCS3B01G349700 chr4B 96.576 1840 60 3 574 2412 576470061 576471898 0.000000e+00 3046
6 TraesCS3B01G349700 chr4B 96.095 1844 62 5 572 2414 611399567 611401401 0.000000e+00 2998
7 TraesCS3B01G349700 chr4B 96.037 1842 66 7 574 2412 582160949 582159112 0.000000e+00 2990
8 TraesCS3B01G349700 chr6B 96.098 1845 67 5 572 2415 659835062 659833222 0.000000e+00 3003
9 TraesCS3B01G349700 chr6B 95.341 1846 82 4 572 2415 585794164 585792321 0.000000e+00 2929
10 TraesCS3B01G349700 chr5B 96.143 1841 67 4 574 2412 416324083 416325921 0.000000e+00 3003
11 TraesCS3B01G349700 chr5B 95.215 1860 68 11 572 2414 617851153 617849298 0.000000e+00 2922
12 TraesCS3B01G349700 chr3A 97.809 639 14 0 2412 3050 557411321 557411959 0.000000e+00 1103
13 TraesCS3B01G349700 chr3A 97.561 574 14 0 3 576 557410752 557411325 0.000000e+00 983
14 TraesCS3B01G349700 chr3A 93.584 639 41 0 2412 3050 557417046 557417684 0.000000e+00 953
15 TraesCS3B01G349700 chr3A 90.451 576 55 0 1 576 557416475 557417050 0.000000e+00 760
16 TraesCS3B01G349700 chr3D 97.653 639 14 1 2412 3050 428253449 428252812 0.000000e+00 1096
17 TraesCS3B01G349700 chr3D 94.836 639 33 0 2412 3050 428247495 428246857 0.000000e+00 998
18 TraesCS3B01G349700 chr3D 97.049 576 17 0 1 576 428254020 428253445 0.000000e+00 970
19 TraesCS3B01G349700 chr3D 90.625 576 54 0 1 576 428248066 428247491 0.000000e+00 765
20 TraesCS3B01G349700 chrUn 86.278 634 87 0 2417 3050 62077782 62078415 0.000000e+00 689
21 TraesCS3B01G349700 chrUn 83.826 575 89 2 2 574 62077207 62077779 7.440000e-151 544
22 TraesCS3B01G349700 chr6D 85.759 639 91 0 2412 3050 469802204 469801566 0.000000e+00 676
23 TraesCS3B01G349700 chr6D 85.391 575 84 0 2 576 469802774 469802200 5.630000e-167 597
24 TraesCS3B01G349700 chr4A 78.194 587 122 6 2465 3048 734482155 734481572 1.340000e-98 370
25 TraesCS3B01G349700 chr4A 76.610 590 120 13 2462 3048 736758328 736757754 2.950000e-80 309
26 TraesCS3B01G349700 chr7A 76.399 572 123 12 2 567 7319709 7320274 6.390000e-77 298
27 TraesCS3B01G349700 chr7D 75.218 573 128 14 2 567 5646755 5647320 3.020000e-65 259


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 TraesCS3B01G349700 chr3B 559888232 559891281 3049 True 5633.0 5633 100.0000 1 3050 1 chr3B.!!$R1 3049
1 TraesCS3B01G349700 chr3B 149100696 149102544 1848 False 2929.0 2929 95.3590 574 2412 1 chr3B.!!$F1 1838
2 TraesCS3B01G349700 chr3B 559882341 559883546 1205 True 873.0 979 92.5825 3 3050 2 chr3B.!!$R2 3047
3 TraesCS3B01G349700 chr1B 665853568 665855413 1845 True 3145.0 3145 97.4540 574 2416 1 chr1B.!!$R1 1842
4 TraesCS3B01G349700 chr4B 576470061 576471898 1837 False 3046.0 3046 96.5760 574 2412 1 chr4B.!!$F1 1838
5 TraesCS3B01G349700 chr4B 611399567 611401401 1834 False 2998.0 2998 96.0950 572 2414 1 chr4B.!!$F2 1842
6 TraesCS3B01G349700 chr4B 582159112 582160949 1837 True 2990.0 2990 96.0370 574 2412 1 chr4B.!!$R1 1838
7 TraesCS3B01G349700 chr6B 659833222 659835062 1840 True 3003.0 3003 96.0980 572 2415 1 chr6B.!!$R2 1843
8 TraesCS3B01G349700 chr6B 585792321 585794164 1843 True 2929.0 2929 95.3410 572 2415 1 chr6B.!!$R1 1843
9 TraesCS3B01G349700 chr5B 416324083 416325921 1838 False 3003.0 3003 96.1430 574 2412 1 chr5B.!!$F1 1838
10 TraesCS3B01G349700 chr5B 617849298 617851153 1855 True 2922.0 2922 95.2150 572 2414 1 chr5B.!!$R1 1842
11 TraesCS3B01G349700 chr3A 557410752 557411959 1207 False 1043.0 1103 97.6850 3 3050 2 chr3A.!!$F1 3047
12 TraesCS3B01G349700 chr3A 557416475 557417684 1209 False 856.5 953 92.0175 1 3050 2 chr3A.!!$F2 3049
13 TraesCS3B01G349700 chr3D 428252812 428254020 1208 True 1033.0 1096 97.3510 1 3050 2 chr3D.!!$R2 3049
14 TraesCS3B01G349700 chr3D 428246857 428248066 1209 True 881.5 998 92.7305 1 3050 2 chr3D.!!$R1 3049
15 TraesCS3B01G349700 chrUn 62077207 62078415 1208 False 616.5 689 85.0520 2 3050 2 chrUn.!!$F1 3048
16 TraesCS3B01G349700 chr6D 469801566 469802774 1208 True 636.5 676 85.5750 2 3050 2 chr6D.!!$R1 3048
17 TraesCS3B01G349700 chr4A 734481572 734482155 583 True 370.0 370 78.1940 2465 3048 1 chr4A.!!$R1 583
18 TraesCS3B01G349700 chr4A 736757754 736758328 574 True 309.0 309 76.6100 2462 3048 1 chr4A.!!$R2 586
19 TraesCS3B01G349700 chr7A 7319709 7320274 565 False 298.0 298 76.3990 2 567 1 chr7A.!!$F1 565
20 TraesCS3B01G349700 chr7D 5646755 5647320 565 False 259.0 259 75.2180 2 567 1 chr7D.!!$F1 565

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
557 558 0.035317 TCAACATGCTGGAGCGAAGT 59.965 50.0 0.00 0.0 45.83 3.01 F
563 564 0.321671 TGCTGGAGCGAAGTTAGCTT 59.678 50.0 12.01 0.0 46.13 3.74 F
567 568 0.391793 GGAGCGAAGTTAGCTTGCCT 60.392 55.0 12.01 0.0 46.13 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1619 0.037046 ATGACATGCTGCACGAGACA 60.037 50.0 3.57 5.36 0.0 3.41 R
1743 1753 0.257616 CGTCCTTCCTCCTCTCCTCT 59.742 60.0 0.00 0.00 0.0 3.69 R
2304 2506 1.593196 CTGTGTTCATTGGGTCGTGT 58.407 50.0 0.00 0.00 0.0 4.49 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
74 75 6.145535 GGCAACTGCTAATTGATAAGTATGC 58.854 40.000 1.06 0.00 41.70 3.14
80 81 6.364701 TGCTAATTGATAAGTATGCAAGGGT 58.635 36.000 0.00 0.00 0.00 4.34
118 119 2.728922 ACGTTTTCAGAGTCGAGACAC 58.271 47.619 5.99 0.00 0.00 3.67
156 157 0.327259 AGCAATGCCTGAAGAGCTCA 59.673 50.000 17.77 0.00 0.00 4.26
264 265 4.481368 ACTTGGATACGTGGCAGATTTA 57.519 40.909 0.00 0.00 42.51 1.40
349 350 5.555017 ACTGTAAACTGTCATCTGCATTCT 58.445 37.500 0.00 0.00 0.00 2.40
500 501 0.978907 TTCATGTCTCTGAGCTGCCA 59.021 50.000 0.00 0.00 0.00 4.92
544 545 6.981762 TTTGCACACAAAAATCTTCAACAT 57.018 29.167 0.00 0.00 42.73 2.71
545 546 5.970140 TGCACACAAAAATCTTCAACATG 57.030 34.783 0.00 0.00 0.00 3.21
546 547 4.270566 TGCACACAAAAATCTTCAACATGC 59.729 37.500 0.00 0.00 0.00 4.06
547 548 4.508861 GCACACAAAAATCTTCAACATGCT 59.491 37.500 0.00 0.00 0.00 3.79
548 549 5.557514 GCACACAAAAATCTTCAACATGCTG 60.558 40.000 0.00 0.00 0.00 4.41
549 550 5.050634 CACACAAAAATCTTCAACATGCTGG 60.051 40.000 0.00 0.00 0.00 4.85
550 551 5.163426 ACACAAAAATCTTCAACATGCTGGA 60.163 36.000 0.00 0.00 0.00 3.86
551 552 5.404366 CACAAAAATCTTCAACATGCTGGAG 59.596 40.000 0.00 0.00 0.00 3.86
552 553 3.863142 AAATCTTCAACATGCTGGAGC 57.137 42.857 0.00 0.00 42.50 4.70
553 554 1.376543 ATCTTCAACATGCTGGAGCG 58.623 50.000 0.00 0.00 45.83 5.03
554 555 0.321346 TCTTCAACATGCTGGAGCGA 59.679 50.000 0.00 0.00 45.83 4.93
555 556 1.159285 CTTCAACATGCTGGAGCGAA 58.841 50.000 0.00 0.00 45.83 4.70
556 557 1.129998 CTTCAACATGCTGGAGCGAAG 59.870 52.381 0.00 0.00 45.83 3.79
557 558 0.035317 TCAACATGCTGGAGCGAAGT 59.965 50.000 0.00 0.00 45.83 3.01
558 559 0.877071 CAACATGCTGGAGCGAAGTT 59.123 50.000 0.00 0.00 45.83 2.66
559 560 2.076100 CAACATGCTGGAGCGAAGTTA 58.924 47.619 0.00 0.00 45.83 2.24
560 561 2.015736 ACATGCTGGAGCGAAGTTAG 57.984 50.000 0.00 0.00 45.83 2.34
561 562 0.654683 CATGCTGGAGCGAAGTTAGC 59.345 55.000 0.00 0.00 45.83 3.09
563 564 0.321671 TGCTGGAGCGAAGTTAGCTT 59.678 50.000 12.01 0.00 46.13 3.74
564 565 0.723981 GCTGGAGCGAAGTTAGCTTG 59.276 55.000 12.01 6.99 46.13 4.01
565 566 0.723981 CTGGAGCGAAGTTAGCTTGC 59.276 55.000 12.01 0.25 46.13 4.01
566 567 0.673644 TGGAGCGAAGTTAGCTTGCC 60.674 55.000 12.01 9.91 46.13 4.52
567 568 0.391793 GGAGCGAAGTTAGCTTGCCT 60.392 55.000 12.01 0.00 46.13 4.75
568 569 1.134788 GGAGCGAAGTTAGCTTGCCTA 60.135 52.381 12.01 0.00 46.13 3.93
569 570 2.483889 GGAGCGAAGTTAGCTTGCCTAT 60.484 50.000 12.01 0.00 46.13 2.57
570 571 3.243771 GGAGCGAAGTTAGCTTGCCTATA 60.244 47.826 12.01 0.00 46.13 1.31
1226 1227 0.681887 TATTGGGAGACGAGGACGCA 60.682 55.000 0.00 0.00 43.96 5.24
1743 1753 2.046023 CAGATGGCGGCCTTGACA 60.046 61.111 21.46 0.00 0.00 3.58
2459 2671 5.718607 TCATACATCCTGTATCCCAGATCAG 59.281 44.000 0.00 0.00 41.28 2.90
2506 2718 8.742554 ACTTGCTTAATTTACATAGTTTGTGC 57.257 30.769 0.00 0.00 39.48 4.57
2722 2934 4.988540 TGAAGTACCTGACTGAAAACATCG 59.011 41.667 0.00 0.00 38.87 3.84
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
74 75 0.954452 GTGTCTTCCAGCAACCCTTG 59.046 55.000 0.00 0.00 0.00 3.61
80 81 2.333926 CGTTATCGTGTCTTCCAGCAA 58.666 47.619 0.00 0.00 0.00 3.91
156 157 3.177228 AGAAGACCTGCCACTCAATACT 58.823 45.455 0.00 0.00 0.00 2.12
172 173 2.233676 TCGATTGCAGTGCCTTAGAAGA 59.766 45.455 13.72 0.20 0.00 2.87
500 501 2.269940 AGCAGAAGGGGTATGAGTTGT 58.730 47.619 0.00 0.00 0.00 3.32
541 542 2.009042 GCTAACTTCGCTCCAGCATGT 61.009 52.381 0.00 0.00 42.21 3.21
542 543 0.654683 GCTAACTTCGCTCCAGCATG 59.345 55.000 0.00 0.00 42.21 4.06
543 544 0.539051 AGCTAACTTCGCTCCAGCAT 59.461 50.000 0.00 0.00 42.21 3.79
544 545 0.321671 AAGCTAACTTCGCTCCAGCA 59.678 50.000 0.00 0.00 42.21 4.41
545 546 0.723981 CAAGCTAACTTCGCTCCAGC 59.276 55.000 0.00 0.00 36.56 4.85
546 547 0.723981 GCAAGCTAACTTCGCTCCAG 59.276 55.000 0.00 0.00 36.56 3.86
547 548 0.673644 GGCAAGCTAACTTCGCTCCA 60.674 55.000 0.00 0.00 36.56 3.86
548 549 0.391793 AGGCAAGCTAACTTCGCTCC 60.392 55.000 0.00 0.00 36.56 4.70
549 550 2.295253 TAGGCAAGCTAACTTCGCTC 57.705 50.000 0.00 0.00 36.56 5.03
550 551 2.990066 ATAGGCAAGCTAACTTCGCT 57.010 45.000 0.00 0.00 39.94 4.93
551 552 5.348997 CCTTATATAGGCAAGCTAACTTCGC 59.651 44.000 0.00 0.00 37.17 4.70
552 553 6.952935 CCTTATATAGGCAAGCTAACTTCG 57.047 41.667 0.00 0.00 37.17 3.79
566 567 3.864921 GCGGTGGAGTTGGCCTTATATAG 60.865 52.174 3.32 0.00 0.00 1.31
567 568 2.038033 GCGGTGGAGTTGGCCTTATATA 59.962 50.000 3.32 0.00 0.00 0.86
568 569 1.202770 GCGGTGGAGTTGGCCTTATAT 60.203 52.381 3.32 0.00 0.00 0.86
569 570 0.179468 GCGGTGGAGTTGGCCTTATA 59.821 55.000 3.32 0.00 0.00 0.98
570 571 1.077716 GCGGTGGAGTTGGCCTTAT 60.078 57.895 3.32 0.00 0.00 1.73
623 624 2.620627 CCGCCTCCTTTGTCCCTTTTAT 60.621 50.000 0.00 0.00 0.00 1.40
1137 1138 4.256180 GCGGGGGCGATGGAGAAT 62.256 66.667 0.00 0.00 0.00 2.40
1226 1227 2.835431 CGTCGCTCCAGGGGATCT 60.835 66.667 0.00 0.00 39.09 2.75
1443 1444 1.594293 CGTGCCGGCGAAATAGGAT 60.594 57.895 23.90 0.00 0.00 3.24
1554 1564 4.286320 GGCGATGGAGACGGCGAT 62.286 66.667 16.62 0.11 45.03 4.58
1609 1619 0.037046 ATGACATGCTGCACGAGACA 60.037 50.000 3.57 5.36 0.00 3.41
1743 1753 0.257616 CGTCCTTCCTCCTCTCCTCT 59.742 60.000 0.00 0.00 0.00 3.69
2304 2506 1.593196 CTGTGTTCATTGGGTCGTGT 58.407 50.000 0.00 0.00 0.00 4.49
2459 2671 3.821421 ACGACATCTTGAAGGGTATCC 57.179 47.619 0.00 0.00 0.00 2.59
2506 2718 3.434299 ACCATAAAGTTACGAGTTTGCCG 59.566 43.478 0.00 0.00 31.14 5.69
2722 2934 3.201290 CCCACTTACAGATGATGTGAGC 58.799 50.000 0.00 0.00 46.76 4.26


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

AutoCloner maintained by Alex Coulton.