Multiple sequence alignment - TraesCS7A01G008600

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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 TraesCS7A01G008600 chr7A 100.000 7241 0 0 1 7241 3851842 3844602 0.000000e+00 13372.0
1 TraesCS7A01G008600 chr7A 94.265 3278 157 18 2457 5718 3538841 3535579 0.000000e+00 4983.0
2 TraesCS7A01G008600 chr7A 82.788 703 87 19 2862 3540 3800868 3800176 1.340000e-166 597.0
3 TraesCS7A01G008600 chr7A 87.222 360 37 2 2021 2380 3539363 3539013 1.130000e-107 401.0
4 TraesCS7A01G008600 chr7A 91.391 151 12 1 2152 2302 2658064 2657915 9.520000e-49 206.0
5 TraesCS7A01G008600 chr7A 95.876 97 4 0 2206 2302 2950618 2950714 2.700000e-34 158.0
6 TraesCS7A01G008600 chr7D 95.571 4109 133 19 2428 6520 4015980 4011905 0.000000e+00 6534.0
7 TraesCS7A01G008600 chr7D 84.633 1705 152 69 729 2380 4017782 4016135 0.000000e+00 1596.0
8 TraesCS7A01G008600 chr7D 83.264 1201 131 40 3607 4774 3565440 3564277 0.000000e+00 1040.0
9 TraesCS7A01G008600 chr7D 91.017 590 13 15 6549 7118 4011907 4011338 0.000000e+00 760.0
10 TraesCS7A01G008600 chr7D 80.336 951 116 38 5902 6800 3563561 3562630 0.000000e+00 654.0
11 TraesCS7A01G008600 chr7D 82.000 700 90 22 2862 3540 2664467 2663783 4.900000e-156 562.0
12 TraesCS7A01G008600 chr7D 87.574 338 25 7 2457 2793 3620928 3620607 6.860000e-100 375.0
13 TraesCS7A01G008600 chr7D 86.325 351 34 2 2618 2967 2507672 2507335 3.190000e-98 370.0
14 TraesCS7A01G008600 chr7D 91.453 234 19 1 3307 3540 3418560 3418328 3.260000e-83 320.0
15 TraesCS7A01G008600 chr7D 79.583 480 68 14 2862 3333 2675994 2675537 4.220000e-82 316.0
16 TraesCS7A01G008600 chr7D 85.616 292 38 4 3271 3559 3609127 3608837 3.280000e-78 303.0
17 TraesCS7A01G008600 chr7D 82.121 330 47 8 2862 3180 3420190 3419862 9.260000e-69 272.0
18 TraesCS7A01G008600 chr7D 90.960 177 16 0 2618 2794 2676169 2675993 9.390000e-59 239.0
19 TraesCS7A01G008600 chr7D 89.730 185 19 0 2618 2802 2664642 2664458 3.380000e-58 237.0
20 TraesCS7A01G008600 chr7D 84.810 158 19 2 3142 3294 4005688 4005531 3.500000e-33 154.0
21 TraesCS7A01G008600 chr7D 94.000 100 5 1 4794 4893 599718532 599718434 4.530000e-32 150.0
22 TraesCS7A01G008600 chr7D 96.610 59 1 1 7183 7241 4011334 4011277 5.980000e-16 97.1
23 TraesCS7A01G008600 chr7D 90.141 71 7 0 3859 3929 3608474 3608404 7.730000e-15 93.5
24 TraesCS7A01G008600 chr4A 95.464 2293 74 8 2517 4803 741412393 741410125 0.000000e+00 3631.0
25 TraesCS7A01G008600 chr4A 96.117 1339 35 2 2875 4212 741367998 741366676 0.000000e+00 2169.0
26 TraesCS7A01G008600 chr4A 96.386 1273 24 6 3533 4803 742012791 742014043 0.000000e+00 2076.0
27 TraesCS7A01G008600 chr4A 84.123 1795 144 69 642 2372 739595349 739597066 0.000000e+00 1605.0
28 TraesCS7A01G008600 chr4A 82.783 1545 163 57 3271 4774 739598030 739599512 0.000000e+00 1284.0
29 TraesCS7A01G008600 chr4A 91.315 829 56 6 4885 5699 742014042 742014868 0.000000e+00 1118.0
30 TraesCS7A01G008600 chr4A 96.128 594 12 4 4214 4803 741366609 741366023 0.000000e+00 959.0
31 TraesCS7A01G008600 chr4A 91.987 599 37 4 2378 2976 739597118 739597705 0.000000e+00 830.0
32 TraesCS7A01G008600 chr4A 86.776 673 73 9 5091 5752 739599516 739600183 0.000000e+00 736.0
33 TraesCS7A01G008600 chr4A 85.503 676 75 15 5091 5752 740154256 740153590 0.000000e+00 684.0
34 TraesCS7A01G008600 chr4A 80.988 931 113 42 5610 6491 741181268 741182183 0.000000e+00 680.0
35 TraesCS7A01G008600 chr4A 84.167 720 82 24 5747 6443 741365387 741364677 0.000000e+00 669.0
36 TraesCS7A01G008600 chr4A 84.167 720 82 24 5747 6443 741409489 741408779 0.000000e+00 669.0
37 TraesCS7A01G008600 chr4A 93.519 432 25 2 4885 5315 741366024 741365595 2.200000e-179 640.0
38 TraesCS7A01G008600 chr4A 93.519 432 25 2 4885 5315 741410126 741409697 2.200000e-179 640.0
39 TraesCS7A01G008600 chr4A 83.449 719 86 26 5747 6443 742014998 742015705 7.920000e-179 638.0
40 TraesCS7A01G008600 chr4A 83.478 690 90 17 2862 3540 740133369 740132693 7.980000e-174 621.0
41 TraesCS7A01G008600 chr4A 82.994 688 85 16 2862 3540 733809447 733810111 1.740000e-165 593.0
42 TraesCS7A01G008600 chr4A 81.297 802 79 31 5747 6520 739600236 739600994 1.050000e-162 584.0
43 TraesCS7A01G008600 chr4A 82.066 697 92 25 2862 3540 739610437 739611118 1.360000e-156 564.0
44 TraesCS7A01G008600 chr4A 80.228 703 103 21 2862 3540 739758037 739757347 5.050000e-136 496.0
45 TraesCS7A01G008600 chr4A 84.881 463 64 5 3083 3540 742024681 742025142 5.120000e-126 462.0
46 TraesCS7A01G008600 chr4A 91.525 236 19 1 2686 2920 741178254 741178489 2.520000e-84 324.0
47 TraesCS7A01G008600 chr4A 82.436 353 41 14 5784 6118 740153494 740153145 9.190000e-74 289.0
48 TraesCS7A01G008600 chr4A 97.484 159 4 0 5594 5752 741365598 741365440 9.260000e-69 272.0
49 TraesCS7A01G008600 chr4A 97.484 159 4 0 5594 5752 741409700 741409542 9.260000e-69 272.0
50 TraesCS7A01G008600 chr4A 79.582 431 46 16 6538 6946 739990227 739989817 3.330000e-68 270.0
51 TraesCS7A01G008600 chr4A 93.785 177 11 0 2618 2794 739610262 739610438 4.310000e-67 267.0
52 TraesCS7A01G008600 chr4A 92.655 177 13 0 2618 2794 733809272 733809448 9.320000e-64 255.0
53 TraesCS7A01G008600 chr4A 97.241 145 4 0 5608 5752 739997050 739996906 5.610000e-61 246.0
54 TraesCS7A01G008600 chr4A 85.654 237 17 8 6523 6745 739603267 739603500 4.370000e-57 233.0
55 TraesCS7A01G008600 chr4A 87.778 180 18 3 2866 3042 740498621 740498799 2.650000e-49 207.0
56 TraesCS7A01G008600 chr4A 82.329 249 33 6 1881 2118 741048118 741048366 9.520000e-49 206.0
57 TraesCS7A01G008600 chr4A 83.410 217 22 8 566 781 688787295 688787092 9.590000e-44 189.0
58 TraesCS7A01G008600 chr4A 77.344 256 32 16 6523 6756 739601091 739601342 2.120000e-25 128.0
59 TraesCS7A01G008600 chr4A 81.818 99 8 6 6832 6926 733826675 733826583 2.800000e-09 75.0
60 TraesCS7A01G008600 chrUn 100.000 395 0 0 4830 5224 479299730 479300124 0.000000e+00 730.0
61 TraesCS7A01G008600 chrUn 89.091 110 9 3 7000 7109 287061832 287061726 4.560000e-27 134.0
62 TraesCS7A01G008600 chr4B 85.000 220 20 6 342 557 584073752 584073962 2.050000e-50 211.0
63 TraesCS7A01G008600 chr6A 95.000 100 3 2 4799 4898 172113269 172113172 9.730000e-34 156.0
64 TraesCS7A01G008600 chr1A 94.792 96 5 0 4799 4894 551438020 551437925 4.530000e-32 150.0
65 TraesCS7A01G008600 chr3B 90.179 112 9 2 4783 4893 15111127 15111017 2.110000e-30 145.0
66 TraesCS7A01G008600 chr3B 91.579 95 7 1 6998 7092 621537376 621537469 5.900000e-26 130.0
67 TraesCS7A01G008600 chr3A 93.000 100 5 2 4795 4892 492755870 492755969 2.110000e-30 145.0
68 TraesCS7A01G008600 chr3A 97.531 81 2 0 7004 7084 99426270 99426190 9.800000e-29 139.0
69 TraesCS7A01G008600 chr1D 97.619 84 2 0 4890 4973 225405130 225405047 2.110000e-30 145.0
70 TraesCS7A01G008600 chr2A 93.684 95 4 2 4878 4971 515955457 515955364 2.720000e-29 141.0
71 TraesCS7A01G008600 chr2A 90.090 111 7 4 4783 4890 724029778 724029887 2.720000e-29 141.0
72 TraesCS7A01G008600 chr2A 89.109 101 9 2 4791 4890 695156866 695156767 2.740000e-24 124.0
73 TraesCS7A01G008600 chr5D 94.505 91 3 2 4881 4971 535711526 535711614 9.800000e-29 139.0
74 TraesCS7A01G008600 chr3D 93.478 92 3 3 6998 7086 149291980 149292071 4.560000e-27 134.0
75 TraesCS7A01G008600 chr3D 89.091 110 9 3 7000 7109 570116478 570116372 4.560000e-27 134.0
76 TraesCS7A01G008600 chr1B 93.407 91 3 2 7005 7095 593927161 593927074 1.640000e-26 132.0
77 TraesCS7A01G008600 chr5B 94.186 86 4 1 7000 7085 13722193 13722277 5.900000e-26 130.0
78 TraesCS7A01G008600 chr2D 87.736 106 11 2 7005 7109 379699523 379699419 9.860000e-24 122.0
79 TraesCS7A01G008600 chr6B 80.909 110 11 5 1186 1295 641468663 641468762 2.170000e-10 78.7


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 TraesCS7A01G008600 chr7A 3844602 3851842 7240 True 13372.000000 13372 100.000000 1 7241 1 chr7A.!!$R3 7240
1 TraesCS7A01G008600 chr7A 3535579 3539363 3784 True 2692.000000 4983 90.743500 2021 5718 2 chr7A.!!$R4 3697
2 TraesCS7A01G008600 chr7A 3800176 3800868 692 True 597.000000 597 82.788000 2862 3540 1 chr7A.!!$R2 678
3 TraesCS7A01G008600 chr7D 4011277 4017782 6505 True 2246.775000 6534 91.957750 729 7241 4 chr7D.!!$R10 6512
4 TraesCS7A01G008600 chr7D 3562630 3565440 2810 True 847.000000 1040 81.800000 3607 6800 2 chr7D.!!$R8 3193
5 TraesCS7A01G008600 chr7D 2663783 2664642 859 True 399.500000 562 85.865000 2618 3540 2 chr7D.!!$R5 922
6 TraesCS7A01G008600 chr7D 3418328 3420190 1862 True 296.000000 320 86.787000 2862 3540 2 chr7D.!!$R7 678
7 TraesCS7A01G008600 chr7D 2675537 2676169 632 True 277.500000 316 85.271500 2618 3333 2 chr7D.!!$R6 715
8 TraesCS7A01G008600 chr4A 741408779 741412393 3614 True 1303.000000 3631 92.658500 2517 6443 4 chr4A.!!$R9 3926
9 TraesCS7A01G008600 chr4A 742012791 742015705 2914 False 1277.333333 2076 90.383333 3533 6443 3 chr4A.!!$F8 2910
10 TraesCS7A01G008600 chr4A 741364677 741367998 3321 True 941.800000 2169 93.483000 2875 6443 5 chr4A.!!$R8 3568
11 TraesCS7A01G008600 chr4A 739595349 739603500 8151 False 771.428571 1605 84.280571 642 6756 7 chr4A.!!$F5 6114
12 TraesCS7A01G008600 chr4A 740132693 740133369 676 True 621.000000 621 83.478000 2862 3540 1 chr4A.!!$R6 678
13 TraesCS7A01G008600 chr4A 741178254 741182183 3929 False 502.000000 680 86.256500 2686 6491 2 chr4A.!!$F7 3805
14 TraesCS7A01G008600 chr4A 739757347 739758037 690 True 496.000000 496 80.228000 2862 3540 1 chr4A.!!$R3 678
15 TraesCS7A01G008600 chr4A 740153145 740154256 1111 True 486.500000 684 83.969500 5091 6118 2 chr4A.!!$R7 1027
16 TraesCS7A01G008600 chr4A 733809272 733810111 839 False 424.000000 593 87.824500 2618 3540 2 chr4A.!!$F4 922
17 TraesCS7A01G008600 chr4A 739610262 739611118 856 False 415.500000 564 87.925500 2618 3540 2 chr4A.!!$F6 922


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
844 861 0.036858 GTGACCTCTCTGTGGCCTTC 60.037 60.000 3.32 0.0 0.00 3.46 F
1457 1520 0.266152 CCCCTCCTCTACCACCAGAT 59.734 60.000 0.00 0.0 0.00 2.90 F
1865 1952 0.319405 AAATTGGGACTGCTGCTTGC 59.681 50.000 0.00 0.0 43.25 4.01 F
1866 1953 0.541296 AATTGGGACTGCTGCTTGCT 60.541 50.000 0.00 0.0 43.37 3.91 F
2454 2706 0.613260 TTCCTGCACGGCTAGAACAT 59.387 50.000 0.00 0.0 0.00 2.71 F
2807 3063 2.711009 TGAAGGATTCCTGTCACCTGTT 59.289 45.455 5.84 0.0 46.93 3.16 F
4778 8492 1.253100 GGTTCGATTTGCAAAGGGGA 58.747 50.000 18.19 11.2 0.00 4.81 F
5442 9249 0.461516 CATGCAGGTGTCATCTCGCT 60.462 55.000 0.00 0.0 0.00 4.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2795 3051 0.035458 GAGGACCAACAGGTGACAGG 59.965 60.000 0.00 0.0 35.25 4.00 R
3111 3449 1.222567 ACTTCTGGGGTTCTTGTGGT 58.777 50.000 0.00 0.0 0.00 4.16 R
3702 7303 0.033366 GGGGCAAATGTTGTGTCCAC 59.967 55.000 0.00 0.0 0.00 4.02 R
4201 7821 8.858003 TCGAAATAGAAAGTACTGATGCTAAG 57.142 34.615 0.00 0.0 0.00 2.18 R
4388 8095 4.997395 TCAACAATCTAAAGTGCAGGAGTC 59.003 41.667 0.00 0.0 0.00 3.36 R
4803 8591 8.081025 CACTCTTATATTAGTTTACGGAGGGAC 58.919 40.741 0.00 0.0 0.00 4.46 R
5782 9737 0.181350 ATCTTAGGCAAGCCCTTCCG 59.819 55.000 7.62 0.0 43.06 4.30 R
6281 10283 0.975556 TAGCATCGCCAGACCAGGAA 60.976 55.000 0.00 0.0 0.00 3.36 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)



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

AutoCloner maintained by Alex Coulton.