Multiple sequence alignment - TraesCS5B01G454300

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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 TraesCS5B01G454300 chr5B 100.000 5031 0 0 1 5031 627187539 627182509 0.000000e+00 9291.0
1 TraesCS5B01G454300 chr5B 99.174 3028 15 5 1 3028 623589511 623586494 0.000000e+00 5445.0
2 TraesCS5B01G454300 chr5B 98.844 3028 26 4 1 3028 627473141 627470123 0.000000e+00 5389.0
3 TraesCS5B01G454300 chr5B 98.778 3028 32 3 1 3028 623868850 623865828 0.000000e+00 5382.0
4 TraesCS5B01G454300 chr5B 99.255 2013 6 2 3020 5031 623586421 623584417 0.000000e+00 3626.0
5 TraesCS5B01G454300 chr5B 98.075 1195 17 3 3020 4213 627470050 627468861 0.000000e+00 2074.0
6 TraesCS5B01G454300 chr5B 97.406 1195 24 3 3020 4213 623865755 623864567 0.000000e+00 2028.0
7 TraesCS5B01G454300 chr5B 91.354 960 60 16 3033 3977 627468407 627467456 0.000000e+00 1291.0
8 TraesCS5B01G454300 chr5B 91.250 960 61 16 3033 3977 623864110 623863159 0.000000e+00 1286.0
9 TraesCS5B01G454300 chr5B 78.738 1030 136 44 1659 2656 622977189 622976211 3.330000e-171 612.0
10 TraesCS5B01G454300 chr5B 78.064 816 127 26 1845 2619 633302802 633303606 7.630000e-128 468.0
11 TraesCS5B01G454300 chr5B 91.697 277 20 3 2677 2952 627468845 627468571 1.020000e-101 381.0
12 TraesCS5B01G454300 chr5B 90.378 291 25 1 1379 1666 622977715 622977425 3.680000e-101 379.0
13 TraesCS5B01G454300 chr5B 90.357 280 21 3 2677 2952 623864551 623864274 3.700000e-96 363.0
14 TraesCS5B01G454300 chr5B 91.593 226 17 2 3963 4186 627459547 627459322 1.360000e-80 311.0
15 TraesCS5B01G454300 chr5B 83.039 283 37 9 1987 2262 623148707 623148429 3.890000e-61 246.0
16 TraesCS5B01G454300 chr5B 82.253 293 42 6 1978 2262 629857561 629857271 1.400000e-60 244.0
17 TraesCS5B01G454300 chr5B 84.018 219 35 0 1379 1597 638751868 638751650 1.420000e-50 211.0
18 TraesCS5B01G454300 chr5B 86.555 119 10 4 2690 2802 633303729 633303847 5.290000e-25 126.0
19 TraesCS5B01G454300 chr5B 88.119 101 7 3 1244 1344 623118068 623117973 1.140000e-21 115.0
20 TraesCS5B01G454300 chr5B 88.119 101 7 3 1244 1344 626786000 626785905 1.140000e-21 115.0
21 TraesCS5B01G454300 chr5B 88.119 101 7 3 1244 1344 629853997 629853902 1.140000e-21 115.0
22 TraesCS5B01G454300 chr5B 87.379 103 8 3 1242 1344 623114798 623114701 4.120000e-21 113.0
23 TraesCS5B01G454300 chr5B 78.616 159 24 9 2574 2725 623148039 623147884 4.150000e-16 97.1
24 TraesCS5B01G454300 chr5B 78.616 159 24 9 2574 2725 626812746 626812591 4.150000e-16 97.1
25 TraesCS5B01G454300 chr5B 78.616 159 24 9 2574 2725 629856881 629856726 4.150000e-16 97.1
26 TraesCS5B01G454300 chr5B 91.935 62 4 1 4278 4339 110127566 110127506 8.970000e-13 86.1
27 TraesCS5B01G454300 chr5B 86.765 68 5 3 2659 2725 629281740 629281804 6.990000e-09 73.1
28 TraesCS5B01G454300 chr5B 86.765 68 5 3 2659 2725 629364034 629364098 6.990000e-09 73.1
29 TraesCS5B01G454300 chr5B 93.182 44 3 0 2681 2724 620582261 620582218 1.170000e-06 65.8
30 TraesCS5B01G454300 chr5B 85.714 56 7 1 4227 4282 559118902 559118956 1.960000e-04 58.4
31 TraesCS5B01G454300 chr5A 81.928 1566 203 44 1311 2818 599556974 599555431 0.000000e+00 1251.0
32 TraesCS5B01G454300 chr5A 79.207 1034 152 34 1634 2619 626018385 626019403 0.000000e+00 660.0
33 TraesCS5B01G454300 chr5A 76.765 1218 190 48 1398 2552 629372514 629373701 3.350000e-166 595.0
34 TraesCS5B01G454300 chr5A 76.702 1219 189 48 1398 2552 629250500 629249313 1.560000e-164 590.0
35 TraesCS5B01G454300 chr5A 83.755 554 67 14 3489 4035 599554783 599554246 2.090000e-138 503.0
36 TraesCS5B01G454300 chr5A 85.036 274 36 4 1993 2263 629371116 629371387 1.780000e-69 274.0
37 TraesCS5B01G454300 chr5A 77.189 434 62 24 4278 4700 666938801 666939208 8.480000e-53 219.0
38 TraesCS5B01G454300 chr5A 85.047 214 27 5 754 965 492997452 492997662 3.950000e-51 213.0
39 TraesCS5B01G454300 chr5A 90.323 62 5 1 4278 4339 609803668 609803728 4.180000e-11 80.5
40 TraesCS5B01G454300 chr3B 76.000 1650 257 70 1277 2818 462100140 462098522 0.000000e+00 725.0
41 TraesCS5B01G454300 chr3B 84.255 470 51 16 4487 4939 7279183 7278720 2.150000e-118 436.0
42 TraesCS5B01G454300 chr3B 81.970 538 70 11 427 963 755227932 755227421 1.000000e-116 431.0
43 TraesCS5B01G454300 chr3B 91.803 122 10 0 1 122 374533409 374533530 2.410000e-38 171.0
44 TraesCS5B01G454300 chr2B 85.388 657 71 19 4278 4919 737773222 737773868 0.000000e+00 658.0
45 TraesCS5B01G454300 chr2B 87.290 417 34 14 4627 5031 737773714 737774123 4.590000e-125 459.0
46 TraesCS5B01G454300 chr2B 81.116 466 65 16 4577 5031 662514985 662515438 8.010000e-93 351.0
47 TraesCS5B01G454300 chr2B 78.424 533 81 20 4391 4918 246569642 246569139 2.920000e-82 316.0
48 TraesCS5B01G454300 chr2B 86.957 184 22 2 783 965 732883981 732884163 6.600000e-49 206.0
49 TraesCS5B01G454300 chr2B 92.623 122 9 0 1 122 223191098 223190977 5.180000e-40 176.0
50 TraesCS5B01G454300 chr2B 96.000 50 2 0 4222 4271 737773190 737773239 1.160000e-11 82.4
51 TraesCS5B01G454300 chr2B 91.071 56 5 0 4226 4281 103439077 103439132 5.400000e-10 76.8
52 TraesCS5B01G454300 chr1B 85.321 654 70 22 4390 5031 515487040 515486401 0.000000e+00 652.0
53 TraesCS5B01G454300 chr1B 83.913 460 45 22 4583 5031 15751912 15752353 3.620000e-111 412.0
54 TraesCS5B01G454300 chr1B 90.984 122 11 0 1 122 151006893 151006772 1.120000e-36 165.0
55 TraesCS5B01G454300 chr7B 85.355 437 47 15 4499 4925 503440559 503440130 2.150000e-118 436.0
56 TraesCS5B01G454300 chr7B 92.500 40 0 3 4232 4270 562174981 562175018 3.000000e-03 54.7
57 TraesCS5B01G454300 chr3D 79.452 657 92 22 4278 4901 484938037 484937391 4.660000e-115 425.0
58 TraesCS5B01G454300 chr3D 78.788 561 82 29 4278 4816 103818638 103819183 4.820000e-90 342.0
59 TraesCS5B01G454300 chr3D 78.759 532 85 18 4278 4798 78105689 78105175 1.040000e-86 331.0
60 TraesCS5B01G454300 chr3D 78.033 610 67 34 4321 4918 164543548 164544102 6.280000e-84 322.0
61 TraesCS5B01G454300 chr3D 94.444 54 2 1 4228 4281 103818612 103818664 1.160000e-11 82.4
62 TraesCS5B01G454300 chr6A 78.930 617 85 24 1984 2574 30719998 30720595 1.320000e-100 377.0
63 TraesCS5B01G454300 chr6A 78.396 611 63 37 4327 4919 74153832 74153273 2.900000e-87 333.0
64 TraesCS5B01G454300 chr6A 100.000 28 0 0 365 392 592036212 592036239 9.000000e-03 52.8
65 TraesCS5B01G454300 chr6D 78.734 616 82 28 1984 2574 27502619 27502028 2.860000e-97 366.0
66 TraesCS5B01G454300 chr6D 80.752 452 53 21 517 965 129168681 129169101 6.280000e-84 322.0
67 TraesCS5B01G454300 chr6D 93.388 121 8 0 3 123 348675141 348675021 4.000000e-41 180.0
68 TraesCS5B01G454300 chr6D 92.063 63 5 0 1094 1156 66631630 66631568 6.940000e-14 89.8
69 TraesCS5B01G454300 chr7D 81.132 477 64 21 4569 5031 37828189 37828653 4.790000e-95 359.0
70 TraesCS5B01G454300 chr7D 77.603 634 94 27 4321 4918 37827735 37828356 1.730000e-89 340.0
71 TraesCS5B01G454300 chr3A 80.562 463 61 20 4581 5031 523379481 523379926 3.750000e-86 329.0
72 TraesCS5B01G454300 chr3A 90.476 126 11 1 1 125 346367374 346367249 1.120000e-36 165.0
73 TraesCS5B01G454300 chr3A 86.325 117 13 3 3277 3391 33434919 33435034 1.900000e-24 124.0
74 TraesCS5B01G454300 chrUn 80.044 451 57 19 517 965 46035492 46035073 2.280000e-78 303.0
75 TraesCS5B01G454300 chr2D 79.039 458 65 20 517 971 136177832 136177403 8.240000e-73 285.0
76 TraesCS5B01G454300 chr2D 84.874 119 12 6 3277 3391 56196859 56196743 1.140000e-21 115.0
77 TraesCS5B01G454300 chr2D 84.746 118 14 4 3277 3391 645896650 645896534 1.140000e-21 115.0
78 TraesCS5B01G454300 chr6B 91.935 124 9 1 1 123 345147675 345147798 6.700000e-39 172.0
79 TraesCS5B01G454300 chr5D 78.341 217 25 14 2581 2781 498927967 498927757 2.460000e-23 121.0
80 TraesCS5B01G454300 chr5D 78.341 217 25 14 2581 2781 501709503 501709293 2.460000e-23 121.0
81 TraesCS5B01G454300 chr5D 88.350 103 7 3 1242 1344 501824661 501824564 8.850000e-23 119.0
82 TraesCS5B01G454300 chr5D 88.000 100 7 3 1245 1344 471632837 471632931 4.120000e-21 113.0
83 TraesCS5B01G454300 chr2A 84.746 118 14 4 3277 3391 771620289 771620173 1.140000e-21 115.0
84 TraesCS5B01G454300 chr4A 91.667 60 4 1 4281 4340 726343436 726343378 1.160000e-11 82.4
85 TraesCS5B01G454300 chr4D 97.436 39 0 1 366 403 252362634 252362672 1.170000e-06 65.8
86 TraesCS5B01G454300 chr4D 97.436 39 0 1 366 403 252627804 252627842 1.170000e-06 65.8


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 TraesCS5B01G454300 chr5B 627182509 627187539 5030 True 9291.00 9291 100.000000 1 5031 1 chr5B.!!$R5 5030
1 TraesCS5B01G454300 chr5B 623584417 623589511 5094 True 4535.50 5445 99.214500 1 5031 2 chr5B.!!$R11 5030
2 TraesCS5B01G454300 chr5B 627467456 627473141 5685 True 2283.75 5389 94.992500 1 4213 4 chr5B.!!$R13 4212
3 TraesCS5B01G454300 chr5B 623863159 623868850 5691 True 2264.75 5382 94.447750 1 4213 4 chr5B.!!$R12 4212
4 TraesCS5B01G454300 chr5B 622976211 622977715 1504 True 495.50 612 84.558000 1379 2656 2 chr5B.!!$R8 1277
5 TraesCS5B01G454300 chr5B 633302802 633303847 1045 False 297.00 468 82.309500 1845 2802 2 chr5B.!!$F4 957
6 TraesCS5B01G454300 chr5A 599554246 599556974 2728 True 877.00 1251 82.841500 1311 4035 2 chr5A.!!$R2 2724
7 TraesCS5B01G454300 chr5A 626018385 626019403 1018 False 660.00 660 79.207000 1634 2619 1 chr5A.!!$F3 985
8 TraesCS5B01G454300 chr5A 629249313 629250500 1187 True 590.00 590 76.702000 1398 2552 1 chr5A.!!$R1 1154
9 TraesCS5B01G454300 chr5A 629371116 629373701 2585 False 434.50 595 80.900500 1398 2552 2 chr5A.!!$F5 1154
10 TraesCS5B01G454300 chr3B 462098522 462100140 1618 True 725.00 725 76.000000 1277 2818 1 chr3B.!!$R2 1541
11 TraesCS5B01G454300 chr3B 755227421 755227932 511 True 431.00 431 81.970000 427 963 1 chr3B.!!$R3 536
12 TraesCS5B01G454300 chr2B 737773190 737774123 933 False 399.80 658 89.559333 4222 5031 3 chr2B.!!$F4 809
13 TraesCS5B01G454300 chr2B 246569139 246569642 503 True 316.00 316 78.424000 4391 4918 1 chr2B.!!$R2 527
14 TraesCS5B01G454300 chr1B 515486401 515487040 639 True 652.00 652 85.321000 4390 5031 1 chr1B.!!$R2 641
15 TraesCS5B01G454300 chr3D 484937391 484938037 646 True 425.00 425 79.452000 4278 4901 1 chr3D.!!$R2 623
16 TraesCS5B01G454300 chr3D 78105175 78105689 514 True 331.00 331 78.759000 4278 4798 1 chr3D.!!$R1 520
17 TraesCS5B01G454300 chr3D 164543548 164544102 554 False 322.00 322 78.033000 4321 4918 1 chr3D.!!$F1 597
18 TraesCS5B01G454300 chr3D 103818612 103819183 571 False 212.20 342 86.616000 4228 4816 2 chr3D.!!$F2 588
19 TraesCS5B01G454300 chr6A 30719998 30720595 597 False 377.00 377 78.930000 1984 2574 1 chr6A.!!$F1 590
20 TraesCS5B01G454300 chr6A 74153273 74153832 559 True 333.00 333 78.396000 4327 4919 1 chr6A.!!$R1 592
21 TraesCS5B01G454300 chr6D 27502028 27502619 591 True 366.00 366 78.734000 1984 2574 1 chr6D.!!$R1 590
22 TraesCS5B01G454300 chr7D 37827735 37828653 918 False 349.50 359 79.367500 4321 5031 2 chr7D.!!$F1 710

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
635 637 0.551131 ACTGAGGGGAGGGAGCAATT 60.551 55.0 0.0 0.0 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
4180 4985 4.070552 AGAACCAGCGCGAGGGAC 62.071 66.667 22.89 16.21 0.0 4.46 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
475 476 2.184579 CGGGGCGAGGAAGAAGAC 59.815 66.667 0.00 0.0 0.00 3.01
635 637 0.551131 ACTGAGGGGAGGGAGCAATT 60.551 55.000 0.00 0.0 0.00 2.32
636 638 0.627986 CTGAGGGGAGGGAGCAATTT 59.372 55.000 0.00 0.0 0.00 1.82
755 757 1.067821 GGAGGACCACGCAGATTAGAG 59.932 57.143 0.00 0.0 35.97 2.43
4180 4985 2.022240 GAGGCCAGCTACTCCCGAAG 62.022 65.000 5.01 0.0 0.00 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
475 476 0.035439 AAGGACGGCCACCAACTATG 60.035 55.000 11.69 0.00 36.29 2.23
755 757 2.650813 ATCGTCCAAGCTCGCATCCC 62.651 60.000 0.00 0.00 0.00 3.85
4180 4985 4.070552 AGAACCAGCGCGAGGGAC 62.071 66.667 22.89 16.21 0.00 4.46


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

AutoCloner maintained by Alex Coulton.