Multiple sequence alignment - TraesCS3A01G110600

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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 TraesCS3A01G110600 chr3A 100.000 2971 0 0 1 2971 77593780 77596750 0.000000e+00 5487.0
1 TraesCS3A01G110600 chr3A 99.623 2121 8 0 1 2121 77707334 77709454 0.000000e+00 3873.0
2 TraesCS3A01G110600 chr3A 94.821 2240 67 15 761 2971 77548000 77550219 0.000000e+00 3448.0
3 TraesCS3A01G110600 chr3A 88.372 387 25 5 2169 2547 77709456 77709830 5.840000e-122 448.0
4 TraesCS3A01G110600 chr3A 97.973 148 3 0 1 148 340370207 340370354 1.060000e-64 257.0
5 TraesCS3A01G110600 chr3A 94.771 153 6 2 2536 2686 77710759 77710911 1.380000e-58 237.0
6 TraesCS3A01G110600 chr3A 80.534 262 36 6 2725 2971 77712375 77712636 1.410000e-43 187.0
7 TraesCS3A01G110600 chr3A 75.221 226 40 12 2531 2745 674991054 674991274 3.150000e-15 93.5
8 TraesCS3A01G110600 chr3D 90.044 2280 138 28 761 2971 66552979 66555238 0.000000e+00 2870.0
9 TraesCS3A01G110600 chr3D 88.327 1542 117 32 894 2412 66561416 66562917 0.000000e+00 1792.0
10 TraesCS3A01G110600 chr3D 87.167 639 37 7 147 741 29783481 29784118 0.000000e+00 684.0
11 TraesCS3A01G110600 chr3D 84.927 617 34 19 147 721 593291171 593290572 1.190000e-158 569.0
12 TraesCS3A01G110600 chr3D 96.250 160 5 1 740 899 66557693 66557851 8.170000e-66 261.0
13 TraesCS3A01G110600 chr3D 75.943 212 42 5 259 463 23576531 23576740 1.880000e-17 100.0
14 TraesCS3A01G110600 chr3D 77.483 151 25 9 2599 2745 540111377 540111522 6.830000e-12 82.4
15 TraesCS3A01G110600 chr3B 89.886 1315 86 16 761 2043 110735573 110736872 0.000000e+00 1648.0
16 TraesCS3A01G110600 chr3B 89.558 1063 59 10 740 1789 110741389 110742412 0.000000e+00 1301.0
17 TraesCS3A01G110600 chr3B 88.523 941 67 19 2064 2971 110738010 110738942 0.000000e+00 1101.0
18 TraesCS3A01G110600 chr3B 85.909 220 12 10 1848 2053 110742413 110742627 1.790000e-52 217.0
19 TraesCS3A01G110600 chr4A 87.179 741 62 21 1168 1876 697432888 697433627 0.000000e+00 811.0
20 TraesCS3A01G110600 chr4A 86.803 735 64 20 1174 1876 697439333 697440066 0.000000e+00 789.0
21 TraesCS3A01G110600 chr4A 86.342 637 42 15 148 739 484685891 484685255 0.000000e+00 652.0
22 TraesCS3A01G110600 chr4A 85.808 613 48 20 147 740 320492234 320491642 5.440000e-172 614.0
23 TraesCS3A01G110600 chr4A 89.268 205 21 1 1215 1419 697511916 697512119 3.800000e-64 255.0
24 TraesCS3A01G110600 chr4A 79.618 157 24 3 313 462 700937931 700937776 4.050000e-19 106.0
25 TraesCS3A01G110600 chr7D 90.232 604 43 9 147 740 104606032 104605435 0.000000e+00 774.0
26 TraesCS3A01G110600 chr7D 86.066 732 72 21 1175 1876 31101997 31101266 0.000000e+00 760.0
27 TraesCS3A01G110600 chr7D 81.499 854 97 38 1000 1810 31070934 31070099 0.000000e+00 645.0
28 TraesCS3A01G110600 chr7D 84.762 630 36 21 147 733 587445768 587446380 7.140000e-161 577.0
29 TraesCS3A01G110600 chr7D 84.469 631 34 21 147 733 460082150 460081540 5.560000e-157 564.0
30 TraesCS3A01G110600 chr7D 90.977 399 36 0 1478 1876 31055803 31055405 3.370000e-149 538.0
31 TraesCS3A01G110600 chr7A 85.849 742 72 19 1168 1876 31511965 31511224 0.000000e+00 758.0
32 TraesCS3A01G110600 chr7A 87.455 558 47 8 147 681 717475968 717475411 3.250000e-174 621.0
33 TraesCS3A01G110600 chr7A 97.945 146 3 0 1 146 253114485 253114630 1.370000e-63 254.0
34 TraesCS3A01G110600 chr2D 87.678 633 37 8 147 739 30361352 30360721 0.000000e+00 699.0
35 TraesCS3A01G110600 chr2D 87.618 638 33 13 147 740 498283940 498283305 0.000000e+00 699.0
36 TraesCS3A01G110600 chr2D 85.321 654 33 22 147 739 638285405 638286056 4.210000e-173 617.0
37 TraesCS3A01G110600 chr2D 82.500 80 10 4 2599 2676 638825807 638825884 1.910000e-07 67.6
38 TraesCS3A01G110600 chr6D 87.500 640 35 10 147 741 435883928 435883289 0.000000e+00 697.0
39 TraesCS3A01G110600 chr6A 87.682 617 50 8 148 739 613706071 613705456 0.000000e+00 695.0
40 TraesCS3A01G110600 chr6A 86.212 631 43 10 148 734 9496534 9495904 0.000000e+00 643.0
41 TraesCS3A01G110600 chr6A 97.279 147 4 0 1 147 439742700 439742846 1.770000e-62 250.0
42 TraesCS3A01G110600 chr6A 97.260 146 4 0 1 146 111959312 111959167 6.360000e-62 248.0
43 TraesCS3A01G110600 chr5A 86.342 637 43 10 148 740 698083744 698083108 0.000000e+00 654.0
44 TraesCS3A01G110600 chr5A 91.489 47 4 0 2599 2645 460475025 460475071 6.870000e-07 65.8
45 TraesCS3A01G110600 chr1D 85.714 637 44 10 147 739 40358398 40359031 1.940000e-176 628.0
46 TraesCS3A01G110600 chr1D 84.786 631 34 23 147 733 303062222 303062834 7.140000e-161 577.0
47 TraesCS3A01G110600 chr1D 73.010 515 93 29 259 739 13125014 13125516 3.990000e-29 139.0
48 TraesCS3A01G110600 chr1D 78.014 141 20 9 2613 2745 57319518 57319381 8.830000e-11 78.7
49 TraesCS3A01G110600 chrUn 84.885 655 33 18 147 739 137755614 137756264 4.240000e-168 601.0
50 TraesCS3A01G110600 chrUn 76.410 195 29 10 2205 2397 378542037 378542216 4.080000e-14 89.8
51 TraesCS3A01G110600 chr4D 84.469 631 35 22 147 733 338449398 338448787 5.560000e-157 564.0
52 TraesCS3A01G110600 chr4D 79.487 156 18 9 2531 2676 104634954 104635105 6.780000e-17 99.0
53 TraesCS3A01G110600 chr4D 77.707 157 23 7 2531 2676 104633894 104634049 5.280000e-13 86.1
54 TraesCS3A01G110600 chr4D 95.238 42 2 0 2599 2640 104633804 104633845 1.910000e-07 67.6
55 TraesCS3A01G110600 chr4D 90.000 50 5 0 2599 2648 104634864 104634913 6.870000e-07 65.8
56 TraesCS3A01G110600 chr4B 90.432 324 24 1 147 463 478839136 478838813 1.270000e-113 420.0
57 TraesCS3A01G110600 chr1A 97.297 148 4 0 1 148 246096859 246097006 4.920000e-63 252.0
58 TraesCS3A01G110600 chr1A 97.260 146 4 0 1 146 221225814 221225669 6.360000e-62 248.0
59 TraesCS3A01G110600 chr1A 96.026 151 5 1 1 151 349502955 349503104 8.230000e-61 244.0
60 TraesCS3A01G110600 chr1A 95.425 153 6 1 1 153 128277006 128276855 2.960000e-60 243.0
61 TraesCS3A01G110600 chr5D 83.766 154 18 5 1168 1315 37207160 37207008 3.990000e-29 139.0
62 TraesCS3A01G110600 chr5D 95.122 41 2 0 2611 2651 110326736 110326696 6.870000e-07 65.8
63 TraesCS3A01G110600 chr2B 76.410 195 29 10 2205 2397 49888106 49888285 4.080000e-14 89.8
64 TraesCS3A01G110600 chr2B 76.410 195 29 10 2205 2397 49891487 49891666 4.080000e-14 89.8


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 TraesCS3A01G110600 chr3A 77593780 77596750 2970 False 5487.00 5487 100.000000 1 2971 1 chr3A.!!$F2 2970
1 TraesCS3A01G110600 chr3A 77548000 77550219 2219 False 3448.00 3448 94.821000 761 2971 1 chr3A.!!$F1 2210
2 TraesCS3A01G110600 chr3A 77707334 77712636 5302 False 1186.25 3873 90.825000 1 2971 4 chr3A.!!$F5 2970
3 TraesCS3A01G110600 chr3D 66552979 66562917 9938 False 1641.00 2870 91.540333 740 2971 3 chr3D.!!$F4 2231
4 TraesCS3A01G110600 chr3D 29783481 29784118 637 False 684.00 684 87.167000 147 741 1 chr3D.!!$F2 594
5 TraesCS3A01G110600 chr3D 593290572 593291171 599 True 569.00 569 84.927000 147 721 1 chr3D.!!$R1 574
6 TraesCS3A01G110600 chr3B 110735573 110742627 7054 False 1066.75 1648 88.469000 740 2971 4 chr3B.!!$F1 2231
7 TraesCS3A01G110600 chr4A 697432888 697433627 739 False 811.00 811 87.179000 1168 1876 1 chr4A.!!$F1 708
8 TraesCS3A01G110600 chr4A 697439333 697440066 733 False 789.00 789 86.803000 1174 1876 1 chr4A.!!$F2 702
9 TraesCS3A01G110600 chr4A 484685255 484685891 636 True 652.00 652 86.342000 148 739 1 chr4A.!!$R2 591
10 TraesCS3A01G110600 chr4A 320491642 320492234 592 True 614.00 614 85.808000 147 740 1 chr4A.!!$R1 593
11 TraesCS3A01G110600 chr7D 104605435 104606032 597 True 774.00 774 90.232000 147 740 1 chr7D.!!$R4 593
12 TraesCS3A01G110600 chr7D 31101266 31101997 731 True 760.00 760 86.066000 1175 1876 1 chr7D.!!$R3 701
13 TraesCS3A01G110600 chr7D 31070099 31070934 835 True 645.00 645 81.499000 1000 1810 1 chr7D.!!$R2 810
14 TraesCS3A01G110600 chr7D 587445768 587446380 612 False 577.00 577 84.762000 147 733 1 chr7D.!!$F1 586
15 TraesCS3A01G110600 chr7D 460081540 460082150 610 True 564.00 564 84.469000 147 733 1 chr7D.!!$R5 586
16 TraesCS3A01G110600 chr7A 31511224 31511965 741 True 758.00 758 85.849000 1168 1876 1 chr7A.!!$R1 708
17 TraesCS3A01G110600 chr7A 717475411 717475968 557 True 621.00 621 87.455000 147 681 1 chr7A.!!$R2 534
18 TraesCS3A01G110600 chr2D 30360721 30361352 631 True 699.00 699 87.678000 147 739 1 chr2D.!!$R1 592
19 TraesCS3A01G110600 chr2D 498283305 498283940 635 True 699.00 699 87.618000 147 740 1 chr2D.!!$R2 593
20 TraesCS3A01G110600 chr2D 638285405 638286056 651 False 617.00 617 85.321000 147 739 1 chr2D.!!$F1 592
21 TraesCS3A01G110600 chr6D 435883289 435883928 639 True 697.00 697 87.500000 147 741 1 chr6D.!!$R1 594
22 TraesCS3A01G110600 chr6A 613705456 613706071 615 True 695.00 695 87.682000 148 739 1 chr6A.!!$R3 591
23 TraesCS3A01G110600 chr6A 9495904 9496534 630 True 643.00 643 86.212000 148 734 1 chr6A.!!$R1 586
24 TraesCS3A01G110600 chr5A 698083108 698083744 636 True 654.00 654 86.342000 148 740 1 chr5A.!!$R1 592
25 TraesCS3A01G110600 chr1D 40358398 40359031 633 False 628.00 628 85.714000 147 739 1 chr1D.!!$F2 592
26 TraesCS3A01G110600 chr1D 303062222 303062834 612 False 577.00 577 84.786000 147 733 1 chr1D.!!$F3 586
27 TraesCS3A01G110600 chrUn 137755614 137756264 650 False 601.00 601 84.885000 147 739 1 chrUn.!!$F1 592
28 TraesCS3A01G110600 chr4D 338448787 338449398 611 True 564.00 564 84.469000 147 733 1 chr4D.!!$R1 586

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
122 123 3.576982 ACGAATAACTGGAAGACACCTGA 59.423 43.478 0.0 0.0 37.43 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1984 2255 3.243941 ACATGTGCGTGTACTACTCCAAA 60.244 43.478 0.0 0.0 0.0 3.28 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
122 123 3.576982 ACGAATAACTGGAAGACACCTGA 59.423 43.478 0.00 0.00 37.43 3.86
1984 2255 6.379988 ACCAGAAGTTGAATAAAGGTTGTTGT 59.620 34.615 0.00 0.00 0.00 3.32
2160 3549 1.071228 GGTAAACCACCGAACACTCCT 59.929 52.381 0.00 0.00 37.63 3.69
2171 3560 3.073735 CACTCCTGCTCGAGCCCT 61.074 66.667 33.23 9.12 41.18 5.19
2195 3584 1.068541 GCAAAGAAAAAGGGCGATCGT 60.069 47.619 17.81 0.00 0.00 3.73
2259 3648 2.761767 TCTCCATCCGATAACCGAAACA 59.238 45.455 0.00 0.00 41.76 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1984 2255 3.243941 ACATGTGCGTGTACTACTCCAAA 60.244 43.478 0.00 0.00 0.00 3.28
2171 3560 0.673437 CGCCCTTTTTCTTTGCTCCA 59.327 50.000 0.00 0.00 0.00 3.86
2195 3584 7.279313 GGCAAGTAAAGGACGAATTACTCATAA 59.721 37.037 0.00 0.00 40.51 1.90
2259 3648 3.438297 AGAAGCATGATTAGTACGCGT 57.562 42.857 19.17 19.17 0.00 6.01
2376 3765 1.208165 ATCCCGGCACCTTCTCCTTT 61.208 55.000 0.00 0.00 0.00 3.11


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

AutoCloner maintained by Alex Coulton.