Multiple sequence alignment - TraesCS3D01G387300

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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 TraesCS3D01G387300 chr3D 100.000 3576 0 0 1 3576 502124587 502128162 0.000000e+00 6604
1 TraesCS3D01G387300 chr3D 97.186 853 23 1 1 852 600826735 600825883 0.000000e+00 1441
2 TraesCS3D01G387300 chr3D 96.600 853 27 2 1 852 496953104 496953955 0.000000e+00 1413
3 TraesCS3D01G387300 chr3D 92.000 200 13 3 3373 3571 7569628 7569825 9.780000e-71 278
4 TraesCS3D01G387300 chr3A 94.382 2759 103 31 850 3576 641557906 641560644 0.000000e+00 4189
5 TraesCS3D01G387300 chr3B 90.006 1611 105 25 1996 3576 663408409 663409993 0.000000e+00 2032
6 TraesCS3D01G387300 chr3B 89.578 1612 110 24 1996 3576 663335389 663336973 0.000000e+00 1993
7 TraesCS3D01G387300 chr3B 90.530 623 48 8 926 1544 663363947 663364562 0.000000e+00 813
8 TraesCS3D01G387300 chr3B 88.925 623 57 9 926 1544 663291125 663291739 0.000000e+00 758
9 TraesCS3D01G387300 chr6D 97.073 854 23 2 1 853 310552437 310551585 0.000000e+00 1437
10 TraesCS3D01G387300 chr5D 96.721 854 26 2 1 852 442692647 442691794 0.000000e+00 1421
11 TraesCS3D01G387300 chr5D 96.835 853 22 5 1 850 493144925 493144075 0.000000e+00 1421
12 TraesCS3D01G387300 chr5D 88.206 602 57 11 975 1564 375312395 375311796 0.000000e+00 706
13 TraesCS3D01G387300 chr5D 89.749 517 53 0 2078 2594 375310734 375310218 0.000000e+00 662
14 TraesCS3D01G387300 chr5D 87.640 356 44 0 1616 1971 375311410 375311055 7.140000e-112 414
15 TraesCS3D01G387300 chr5D 85.124 363 30 17 2993 3333 124720568 124720208 2.040000e-92 350
16 TraesCS3D01G387300 chr5D 92.040 201 12 4 3373 3571 496923824 496923626 2.720000e-71 279
17 TraesCS3D01G387300 chr5D 92.000 200 13 3 3373 3571 420457906 420458103 9.780000e-71 278
18 TraesCS3D01G387300 chr5D 91.960 199 13 3 3374 3571 420452973 420453169 3.520000e-70 276
19 TraesCS3D01G387300 chr4D 96.608 855 27 2 1 854 346062650 346061797 0.000000e+00 1417
20 TraesCS3D01G387300 chr4D 91.500 200 14 3 3373 3571 505259904 505259707 4.550000e-69 272
21 TraesCS3D01G387300 chr4D 90.541 74 7 0 2614 2687 55489307 55489234 8.170000e-17 99
22 TraesCS3D01G387300 chr2D 96.717 853 25 2 1 852 32614560 32615410 0.000000e+00 1417
23 TraesCS3D01G387300 chr1D 96.608 855 25 4 1 853 467904364 467905216 0.000000e+00 1415
24 TraesCS3D01G387300 chr1D 82.683 410 41 16 2944 3328 442456380 442455976 1.590000e-88 337
25 TraesCS3D01G387300 chr7D 96.495 856 25 5 1 854 152092361 152093213 0.000000e+00 1410
26 TraesCS3D01G387300 chr5B 92.500 520 35 4 1056 1572 448132742 448132224 0.000000e+00 741
27 TraesCS3D01G387300 chr5B 89.163 526 57 0 2078 2603 448131066 448130541 0.000000e+00 656
28 TraesCS3D01G387300 chr5B 86.066 366 50 1 1616 1980 448131918 448131553 3.350000e-105 392
29 TraesCS3D01G387300 chr5A 89.492 590 51 9 985 1564 476669870 476669282 0.000000e+00 736
30 TraesCS3D01G387300 chr5A 89.163 526 57 0 2078 2603 476668242 476667717 0.000000e+00 656
31 TraesCS3D01G387300 chr5A 86.523 371 49 1 1616 1985 476668909 476668539 1.200000e-109 407
32 TraesCS3D01G387300 chr1A 84.810 395 34 14 2959 3332 518475894 518476283 1.210000e-99 374
33 TraesCS3D01G387300 chr6B 84.539 401 34 14 2959 3333 10229500 10229898 4.360000e-99 372
34 TraesCS3D01G387300 chr2B 84.308 325 19 16 2959 3254 526461484 526461805 4.520000e-74 289
35 TraesCS3D01G387300 chr2B 91.542 201 13 4 3373 3571 106743609 106743807 1.260000e-69 274
36 TraesCS3D01G387300 chr4A 92.000 200 14 2 3373 3571 740983029 740982831 2.720000e-71 279
37 TraesCS3D01G387300 chr4A 92.105 76 6 0 2612 2687 556604743 556604668 1.360000e-19 108
38 TraesCS3D01G387300 chr4B 79.195 298 40 17 3081 3363 522076216 522075926 1.700000e-43 187


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 TraesCS3D01G387300 chr3D 502124587 502128162 3575 False 6604.000000 6604 100.000000 1 3576 1 chr3D.!!$F3 3575
1 TraesCS3D01G387300 chr3D 600825883 600826735 852 True 1441.000000 1441 97.186000 1 852 1 chr3D.!!$R1 851
2 TraesCS3D01G387300 chr3D 496953104 496953955 851 False 1413.000000 1413 96.600000 1 852 1 chr3D.!!$F2 851
3 TraesCS3D01G387300 chr3A 641557906 641560644 2738 False 4189.000000 4189 94.382000 850 3576 1 chr3A.!!$F1 2726
4 TraesCS3D01G387300 chr3B 663408409 663409993 1584 False 2032.000000 2032 90.006000 1996 3576 1 chr3B.!!$F4 1580
5 TraesCS3D01G387300 chr3B 663335389 663336973 1584 False 1993.000000 1993 89.578000 1996 3576 1 chr3B.!!$F2 1580
6 TraesCS3D01G387300 chr3B 663363947 663364562 615 False 813.000000 813 90.530000 926 1544 1 chr3B.!!$F3 618
7 TraesCS3D01G387300 chr3B 663291125 663291739 614 False 758.000000 758 88.925000 926 1544 1 chr3B.!!$F1 618
8 TraesCS3D01G387300 chr6D 310551585 310552437 852 True 1437.000000 1437 97.073000 1 853 1 chr6D.!!$R1 852
9 TraesCS3D01G387300 chr5D 442691794 442692647 853 True 1421.000000 1421 96.721000 1 852 1 chr5D.!!$R2 851
10 TraesCS3D01G387300 chr5D 493144075 493144925 850 True 1421.000000 1421 96.835000 1 850 1 chr5D.!!$R3 849
11 TraesCS3D01G387300 chr5D 375310218 375312395 2177 True 594.000000 706 88.531667 975 2594 3 chr5D.!!$R5 1619
12 TraesCS3D01G387300 chr4D 346061797 346062650 853 True 1417.000000 1417 96.608000 1 854 1 chr4D.!!$R2 853
13 TraesCS3D01G387300 chr2D 32614560 32615410 850 False 1417.000000 1417 96.717000 1 852 1 chr2D.!!$F1 851
14 TraesCS3D01G387300 chr1D 467904364 467905216 852 False 1415.000000 1415 96.608000 1 853 1 chr1D.!!$F1 852
15 TraesCS3D01G387300 chr7D 152092361 152093213 852 False 1410.000000 1410 96.495000 1 854 1 chr7D.!!$F1 853
16 TraesCS3D01G387300 chr5B 448130541 448132742 2201 True 596.333333 741 89.243000 1056 2603 3 chr5B.!!$R1 1547
17 TraesCS3D01G387300 chr5A 476667717 476669870 2153 True 599.666667 736 88.392667 985 2603 3 chr5A.!!$R1 1618

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
418 421 1.332375 CGTTTTGGTGATCCACGTTGT 59.668 47.619 0.00 0.00 44.22 3.32 F
1666 2117 0.888619 TGAGGTGTGATCACTCGGTC 59.111 55.000 25.55 20.13 43.41 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 2205 0.391661 CCGGTGTCTATGCTGCAGTT 60.392 55.000 16.64 6.05 0.00 3.16 R
3342 4239 1.837747 CATTTCCGAAATACGCGTTGC 59.162 47.619 20.78 0.00 41.07 4.17 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
227 229 6.690957 TGCTTCAAATTTTGTAAGAGTTGTCG 59.309 34.615 17.80 0.00 0.00 4.35
228 230 6.910433 GCTTCAAATTTTGTAAGAGTTGTCGA 59.090 34.615 17.80 0.00 0.00 4.20
418 421 1.332375 CGTTTTGGTGATCCACGTTGT 59.668 47.619 0.00 0.00 44.22 3.32
511 514 2.569059 TCCTCCGTTGATAGGTAGTCG 58.431 52.381 0.00 0.00 34.30 4.18
760 767 4.142469 CGCGGGAGGTTTTTCATTTTCTAT 60.142 41.667 0.00 0.00 0.00 1.98
854 861 3.249687 CCAGGTAGGCAAGTCCAAC 57.750 57.895 0.00 0.00 37.29 3.77
865 872 8.188799 GGTAGGCAAGTCCAACTTTATTTTATC 58.811 37.037 0.00 0.00 36.03 1.75
967 974 5.624738 GCACAACAGCTATAGTACCACTCTT 60.625 44.000 0.84 0.00 0.00 2.85
970 977 3.884091 ACAGCTATAGTACCACTCTTCGG 59.116 47.826 0.84 0.00 0.00 4.30
1586 1837 2.355513 CCTCACTTGCTATCACTGGCTT 60.356 50.000 0.00 0.00 0.00 4.35
1599 1850 1.414919 ACTGGCTTGTTACCGAGACAA 59.585 47.619 0.00 0.00 39.74 3.18
1600 1851 2.038557 ACTGGCTTGTTACCGAGACAAT 59.961 45.455 0.00 0.00 39.74 2.71
1605 1856 3.368236 GCTTGTTACCGAGACAATGAGAC 59.632 47.826 0.00 0.00 36.51 3.36
1666 2117 0.888619 TGAGGTGTGATCACTCGGTC 59.111 55.000 25.55 20.13 43.41 4.79
1754 2205 3.471680 TCAAACAACACGATCATCACCA 58.528 40.909 0.00 0.00 0.00 4.17
1801 2252 0.539051 CGATCTGCCCCAAGTCTCTT 59.461 55.000 0.00 0.00 0.00 2.85
1852 2303 1.592669 CTGCCGGATCCGCACTAAG 60.593 63.158 29.12 14.77 38.24 2.18
1883 2334 3.815856 TCAAATTTGGAAGTGCAAGCA 57.184 38.095 17.90 0.00 0.00 3.91
1884 2335 4.134379 TCAAATTTGGAAGTGCAAGCAA 57.866 36.364 17.90 0.00 0.00 3.91
2051 2727 0.100325 TTGACTGCAACTTTGTGGCG 59.900 50.000 0.00 0.00 34.77 5.69
2232 3103 4.219288 AGAAGGCACCATTTCAGATGTTTC 59.781 41.667 0.00 0.00 0.00 2.78
2582 3453 3.310774 CCTGAATGTTCAATAGCAGACCG 59.689 47.826 0.00 0.00 36.64 4.79
2688 3559 6.098679 TGTTGGCACATACTGAAATATTTGC 58.901 36.000 5.17 0.57 39.30 3.68
2729 3602 5.767665 TCAGCAATTTTACAGTGGTGTACAT 59.232 36.000 0.00 0.00 38.95 2.29
2816 3690 2.060050 TTCAGTCCTTTGGCCGAAAA 57.940 45.000 6.92 0.00 0.00 2.29
2826 3700 1.370778 GGCCGAAAACGAAAACGGG 60.371 57.895 0.00 0.00 44.61 5.28
2900 3774 9.551339 TTACTATAATAAGGAATGATACCGGGT 57.449 33.333 6.32 4.46 0.00 5.28
2964 3838 3.244735 TGGATTCGAAACCATGACCTCAA 60.245 43.478 21.96 0.00 0.00 3.02
3070 3945 5.639082 GCGATTTTCCATTTCATTTTCACCT 59.361 36.000 0.00 0.00 0.00 4.00
3073 3948 4.952071 TTCCATTTCATTTTCACCTGCA 57.048 36.364 0.00 0.00 0.00 4.41
3131 4015 2.678336 CCTATGGGTCTGCGAAAGTTTC 59.322 50.000 5.47 5.47 0.00 2.78
3403 4300 2.054021 TCCTTCTCATGTGGGTTGTGA 58.946 47.619 0.00 0.00 0.00 3.58
3412 4319 0.693049 GTGGGTTGTGAGGAGATGGT 59.307 55.000 0.00 0.00 0.00 3.55
3454 4361 0.323178 CCAATGAGGTGCAGAAGCCT 60.323 55.000 0.00 0.00 41.13 4.58
3505 4413 6.981210 GTCATTTGGACTTTGCACGTGAGTA 61.981 44.000 22.23 0.98 42.94 2.59
3567 4475 3.146847 AGTGGGACGAAAAATCAGTTCC 58.853 45.455 0.00 0.00 34.14 3.62
3571 4479 3.408634 GGACGAAAAATCAGTTCCTCCA 58.591 45.455 0.00 0.00 33.10 3.86
3572 4480 3.818773 GGACGAAAAATCAGTTCCTCCAA 59.181 43.478 0.00 0.00 33.10 3.53
3573 4481 4.083271 GGACGAAAAATCAGTTCCTCCAAG 60.083 45.833 0.00 0.00 33.10 3.61
3574 4482 3.821033 ACGAAAAATCAGTTCCTCCAAGG 59.179 43.478 0.00 0.00 36.46 3.61
3575 4483 3.191371 CGAAAAATCAGTTCCTCCAAGGG 59.809 47.826 0.00 0.00 35.59 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
227 229 6.768029 TGCAACAACTTTGCTATGATTTTC 57.232 33.333 10.15 0.00 45.13 2.29
228 230 6.707161 ACATGCAACAACTTTGCTATGATTTT 59.293 30.769 19.23 4.03 45.13 1.82
340 342 1.747355 GCCATCCAATGAGTCCAACTG 59.253 52.381 0.00 0.00 0.00 3.16
418 421 9.309516 CTAAATCGCCTAACATAAAGACAACTA 57.690 33.333 0.00 0.00 0.00 2.24
511 514 6.879276 AAAGCAACTCCTTTTTCCTAGTAC 57.121 37.500 0.00 0.00 31.25 2.73
594 598 8.568617 AACTAGATCCCATATGAGTAGGTTTT 57.431 34.615 3.65 0.00 0.00 2.43
707 713 4.482990 CCACCTGCATTTATTAGGGGATT 58.517 43.478 0.00 0.00 37.16 3.01
760 767 4.111016 CGCCGCGTCAGGACAGTA 62.111 66.667 4.92 0.00 0.00 2.74
844 851 9.476202 ACAAAGATAAAATAAAGTTGGACTTGC 57.524 29.630 0.00 0.00 38.66 4.01
898 905 8.592998 GTTCGGTGAGTGTGTAATAAATCTAAG 58.407 37.037 0.00 0.00 0.00 2.18
899 906 8.308931 AGTTCGGTGAGTGTGTAATAAATCTAA 58.691 33.333 0.00 0.00 0.00 2.10
904 911 6.158598 GGTAGTTCGGTGAGTGTGTAATAAA 58.841 40.000 0.00 0.00 0.00 1.40
913 920 1.067776 GGAGTGGTAGTTCGGTGAGTG 60.068 57.143 0.00 0.00 0.00 3.51
914 921 1.254954 GGAGTGGTAGTTCGGTGAGT 58.745 55.000 0.00 0.00 0.00 3.41
967 974 3.093057 CTCTTTCCTCTTCTCTTCCCGA 58.907 50.000 0.00 0.00 0.00 5.14
970 977 5.234752 GTTGACTCTTTCCTCTTCTCTTCC 58.765 45.833 0.00 0.00 0.00 3.46
977 984 1.605712 CGGCGTTGACTCTTTCCTCTT 60.606 52.381 0.00 0.00 0.00 2.85
1109 1142 3.740397 CCGCCGTGTCGTACCTGA 61.740 66.667 0.00 0.00 0.00 3.86
1569 1606 2.867109 ACAAGCCAGTGATAGCAAGT 57.133 45.000 0.00 0.00 0.00 3.16
1572 1823 2.676750 CGGTAACAAGCCAGTGATAGCA 60.677 50.000 0.00 0.00 0.00 3.49
1575 1826 3.093814 TCTCGGTAACAAGCCAGTGATA 58.906 45.455 0.00 0.00 0.00 2.15
1586 1837 2.815503 TCGTCTCATTGTCTCGGTAACA 59.184 45.455 0.00 0.00 0.00 2.41
1605 1856 2.554142 TGCAAGCATATTGGAGACTCG 58.446 47.619 0.00 0.00 0.00 4.18
1666 2117 3.602489 CGTATATGGAGACGTTGCGTATG 59.398 47.826 11.42 0.00 41.37 2.39
1754 2205 0.391661 CCGGTGTCTATGCTGCAGTT 60.392 55.000 16.64 6.05 0.00 3.16
1801 2252 1.071814 GTTGTGAACAGGGCCCGTA 59.928 57.895 18.44 0.28 0.00 4.02
1852 2303 7.467623 CACTTCCAAATTTGATAGCACTAGAC 58.532 38.462 19.86 0.00 0.00 2.59
1883 2334 2.620585 GCAGCCTCTCAAAGTTGAAGTT 59.379 45.455 0.00 0.00 36.64 2.66
1884 2335 2.158696 AGCAGCCTCTCAAAGTTGAAGT 60.159 45.455 0.00 0.00 36.64 3.01
1994 2447 5.614308 TGAATAAGATGCCACCTGATAGTG 58.386 41.667 0.00 0.00 37.51 2.74
2232 3103 3.801698 ACCGATGAGATGTTGATGAAGG 58.198 45.455 0.00 0.00 0.00 3.46
2582 3453 6.309980 CAGATACATACGATTGAGATTCAGGC 59.690 42.308 0.00 0.00 0.00 4.85
2688 3559 2.100749 GCTGAAATATTTTGACCGGGGG 59.899 50.000 6.32 0.00 0.00 5.40
2772 3646 2.165030 CCCACCTGCATTTGATTGAGAC 59.835 50.000 0.00 0.00 0.00 3.36
2816 3690 5.952526 ATTTAAGTGATTCCCGTTTTCGT 57.047 34.783 0.00 0.00 42.35 3.85
2877 3751 8.074613 TCACCCGGTATCATTCCTTATTATAG 57.925 38.462 0.00 0.00 0.00 1.31
2964 3838 2.017049 GTGTTGCAAGGACTTCACACT 58.983 47.619 0.00 0.00 0.00 3.55
3185 4079 8.850452 GGCAGTTGTAATTTTTCTTAGATTTCG 58.150 33.333 0.00 0.00 0.00 3.46
3342 4239 1.837747 CATTTCCGAAATACGCGTTGC 59.162 47.619 20.78 0.00 41.07 4.17
3403 4300 2.579860 AGGCTTCAAATGACCATCTCCT 59.420 45.455 0.00 0.00 0.00 3.69
3505 4413 3.137360 GGAGGGTAAAAGCATCCTCATCT 59.863 47.826 9.96 0.00 42.66 2.90
3510 4418 2.175715 GGATGGAGGGTAAAAGCATCCT 59.824 50.000 10.67 0.00 45.79 3.24
3553 4461 3.191371 CCCTTGGAGGAACTGATTTTTCG 59.809 47.826 0.00 0.00 41.55 3.46


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

AutoCloner maintained by Alex Coulton.