Multiple sequence alignment - TraesCS7D01G385000

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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 TraesCS7D01G385000 chr7D 100.000 2353 0 0 1 2353 498828582 498830934 0.000000e+00 4346.0
1 TraesCS7D01G385000 chr7D 95.704 582 20 3 1 580 50399060 50399638 0.000000e+00 931.0
2 TraesCS7D01G385000 chr7D 98.347 121 2 0 579 699 50399773 50399893 1.830000e-51 213.0
3 TraesCS7D01G385000 chr7D 100.000 29 0 0 1445 1473 498829940 498829968 1.000000e-03 54.7
4 TraesCS7D01G385000 chr7D 100.000 29 0 0 1359 1387 498830026 498830054 1.000000e-03 54.7
5 TraesCS7D01G385000 chr5D 98.400 1688 21 4 1 1685 419399721 419401405 0.000000e+00 2963.0
6 TraesCS7D01G385000 chr5D 98.521 676 9 1 1679 2353 419402328 419403003 0.000000e+00 1192.0
7 TraesCS7D01G385000 chr5D 97.341 677 15 3 1679 2353 324723642 324724317 0.000000e+00 1147.0
8 TraesCS7D01G385000 chr5D 86.199 413 38 18 179 580 495965203 495964799 1.670000e-116 429.0
9 TraesCS7D01G385000 chr5D 92.241 116 7 1 888 1001 419400560 419400675 1.870000e-36 163.0
10 TraesCS7D01G385000 chr5D 92.241 116 7 1 841 956 419400607 419400720 1.870000e-36 163.0
11 TraesCS7D01G385000 chr5D 93.056 72 3 1 935 1004 419400560 419400631 1.150000e-18 104.0
12 TraesCS7D01G385000 chr5D 97.059 34 1 0 463 496 419400248 419400281 9.080000e-05 58.4
13 TraesCS7D01G385000 chr5D 100.000 29 0 0 1445 1473 419401078 419401106 1.000000e-03 54.7
14 TraesCS7D01G385000 chr5D 100.000 29 0 0 1359 1387 419401164 419401192 1.000000e-03 54.7
15 TraesCS7D01G385000 chr6D 98.373 676 10 1 1679 2353 21110454 21109779 0.000000e+00 1186.0
16 TraesCS7D01G385000 chr6D 98.080 677 11 2 1679 2353 379507723 379507047 0.000000e+00 1177.0
17 TraesCS7D01G385000 chr6D 97.784 677 13 2 1679 2353 364859394 364860070 0.000000e+00 1166.0
18 TraesCS7D01G385000 chr6D 95.726 585 20 3 1 583 21112735 21112154 0.000000e+00 937.0
19 TraesCS7D01G385000 chr6D 95.556 585 21 3 1 583 379510003 379509422 0.000000e+00 931.0
20 TraesCS7D01G385000 chr6D 95.533 582 20 5 1 580 364857124 364857701 0.000000e+00 926.0
21 TraesCS7D01G385000 chr6D 99.174 121 1 0 579 699 21112022 21111902 3.940000e-53 219.0
22 TraesCS7D01G385000 chr6D 99.174 121 1 0 579 699 379509290 379509170 3.940000e-53 219.0
23 TraesCS7D01G385000 chr6D 96.694 121 4 0 579 699 364857836 364857956 3.970000e-48 202.0
24 TraesCS7D01G385000 chr6D 97.059 34 1 0 463 496 21112208 21112175 9.080000e-05 58.4
25 TraesCS7D01G385000 chr6D 97.059 34 1 0 463 496 364857650 364857683 9.080000e-05 58.4
26 TraesCS7D01G385000 chr6D 97.059 34 1 0 463 496 379509476 379509443 9.080000e-05 58.4
27 TraesCS7D01G385000 chr1D 97.637 677 14 2 1679 2353 212087542 212088218 0.000000e+00 1160.0
28 TraesCS7D01G385000 chr1D 97.341 677 16 2 1679 2353 485920448 485921124 0.000000e+00 1149.0
29 TraesCS7D01G385000 chr1D 95.017 582 23 4 1 580 212085271 212085848 0.000000e+00 909.0
30 TraesCS7D01G385000 chr1D 97.414 116 3 0 579 694 455911646 455911761 5.130000e-47 198.0
31 TraesCS7D01G385000 chr1D 97.059 34 1 0 463 496 212085797 212085830 9.080000e-05 58.4
32 TraesCS7D01G385000 chr4D 97.489 677 15 2 1679 2353 129493425 129494101 0.000000e+00 1155.0
33 TraesCS7D01G385000 chr4D 97.194 677 17 2 1679 2353 502959254 502958578 0.000000e+00 1144.0
34 TraesCS7D01G385000 chr4D 97.880 566 10 1 888 1451 9435122 9435687 0.000000e+00 977.0
35 TraesCS7D01G385000 chr4D 97.719 263 6 0 694 956 9434975 9435237 9.910000e-124 453.0
36 TraesCS7D01G385000 chr4D 80.992 363 56 11 1001 1356 9442175 9442531 2.300000e-70 276.0
37 TraesCS7D01G385000 chr4D 97.872 141 1 2 1506 1644 9435690 9435830 2.340000e-60 243.0
38 TraesCS7D01G385000 chr4D 93.056 72 3 1 935 1004 9435122 9435193 1.150000e-18 104.0
39 TraesCS7D01G385000 chr4D 100.000 29 0 0 1445 1473 9435595 9435623 1.000000e-03 54.7
40 TraesCS7D01G385000 chr2D 95.704 582 20 3 1 580 476467788 476468366 0.000000e+00 931.0
41 TraesCS7D01G385000 chr2D 95.361 582 22 3 1 580 174944192 174944770 0.000000e+00 920.0
42 TraesCS7D01G385000 chr2D 94.701 585 21 4 1 583 175749671 175749095 0.000000e+00 900.0
43 TraesCS7D01G385000 chr2D 98.347 121 2 0 579 699 174944905 174945025 1.830000e-51 213.0
44 TraesCS7D01G385000 chr2D 98.347 121 2 0 579 699 175748963 175748843 1.830000e-51 213.0
45 TraesCS7D01G385000 chr2D 98.347 121 2 0 579 699 476468501 476468621 1.830000e-51 213.0
46 TraesCS7D01G385000 chr2D 97.059 34 1 0 463 496 174944719 174944752 9.080000e-05 58.4
47 TraesCS7D01G385000 chr2D 97.059 34 1 0 463 496 476468315 476468348 9.080000e-05 58.4
48 TraesCS7D01G385000 chr4A 93.560 559 27 5 896 1452 594037034 594036483 0.000000e+00 824.0
49 TraesCS7D01G385000 chr4A 94.024 251 14 1 706 956 594037176 594036927 1.710000e-101 379.0
50 TraesCS7D01G385000 chr4A 81.020 353 60 7 1007 1356 594005872 594005524 8.280000e-70 274.0
51 TraesCS7D01G385000 chr4A 91.379 174 15 0 1010 1183 594028905 594028732 3.020000e-59 239.0
52 TraesCS7D01G385000 chr4A 92.806 139 5 5 1510 1644 594036477 594036340 1.840000e-46 196.0
53 TraesCS7D01G385000 chr4A 92.857 70 3 1 935 1002 594037042 594036973 1.490000e-17 100.0
54 TraesCS7D01G385000 chr4A 100.000 29 0 0 1445 1473 594036576 594036548 1.000000e-03 54.7
55 TraesCS7D01G385000 chr4B 92.014 576 34 6 888 1451 17492587 17493162 0.000000e+00 798.0
56 TraesCS7D01G385000 chr4B 92.040 201 15 1 757 956 17492503 17492703 4.950000e-72 281.0
57 TraesCS7D01G385000 chr4B 81.163 361 57 11 1001 1356 17998467 17998821 1.780000e-71 279.0
58 TraesCS7D01G385000 chr4B 91.241 137 5 5 1510 1644 17493169 17493300 1.860000e-41 180.0
59 TraesCS7D01G385000 chr4B 86.765 68 7 1 935 1000 17492587 17492654 9.020000e-10 75.0
60 TraesCS7D01G385000 chr3D 97.059 34 1 0 463 496 48643914 48643947 9.080000e-05 58.4
61 TraesCS7D01G385000 chr6A 89.130 46 4 1 452 496 61395238 61395193 3.270000e-04 56.5


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 TraesCS7D01G385000 chr7D 498828582 498830934 2352 False 1485.133333 4346 100.000000 1 2353 3 chr7D.!!$F2 2352
1 TraesCS7D01G385000 chr7D 50399060 50399893 833 False 572.000000 931 97.025500 1 699 2 chr7D.!!$F1 698
2 TraesCS7D01G385000 chr5D 324723642 324724317 675 False 1147.000000 1147 97.341000 1679 2353 1 chr5D.!!$F1 674
3 TraesCS7D01G385000 chr5D 419399721 419403003 3282 False 594.100000 2963 96.439750 1 2353 8 chr5D.!!$F2 2352
4 TraesCS7D01G385000 chr6D 21109779 21112735 2956 True 600.100000 1186 97.583000 1 2353 4 chr6D.!!$R1 2352
5 TraesCS7D01G385000 chr6D 379507047 379510003 2956 True 596.350000 1177 97.467250 1 2353 4 chr6D.!!$R2 2352
6 TraesCS7D01G385000 chr6D 364857124 364860070 2946 False 588.100000 1166 96.767500 1 2353 4 chr6D.!!$F1 2352
7 TraesCS7D01G385000 chr1D 485920448 485921124 676 False 1149.000000 1149 97.341000 1679 2353 1 chr1D.!!$F2 674
8 TraesCS7D01G385000 chr1D 212085271 212088218 2947 False 709.133333 1160 96.571000 1 2353 3 chr1D.!!$F3 2352
9 TraesCS7D01G385000 chr4D 129493425 129494101 676 False 1155.000000 1155 97.489000 1679 2353 1 chr4D.!!$F2 674
10 TraesCS7D01G385000 chr4D 502958578 502959254 676 True 1144.000000 1144 97.194000 1679 2353 1 chr4D.!!$R1 674
11 TraesCS7D01G385000 chr4D 9434975 9435830 855 False 366.340000 977 97.305400 694 1644 5 chr4D.!!$F3 950
12 TraesCS7D01G385000 chr2D 175748843 175749671 828 True 556.500000 900 96.524000 1 699 2 chr2D.!!$R1 698
13 TraesCS7D01G385000 chr2D 476467788 476468621 833 False 400.800000 931 97.036667 1 699 3 chr2D.!!$F2 698
14 TraesCS7D01G385000 chr2D 174944192 174945025 833 False 397.133333 920 96.922333 1 699 3 chr2D.!!$F1 698
15 TraesCS7D01G385000 chr4A 594036340 594037176 836 True 310.740000 824 94.649400 706 1644 5 chr4A.!!$R3 938
16 TraesCS7D01G385000 chr4B 17492503 17493300 797 False 333.500000 798 90.515000 757 1644 4 chr4B.!!$F2 887

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
137 138 0.040646 TCGAGGAACTTGGCTCCCTA 59.959 55.000 0.0 0.0 41.55 3.53 F
493 495 3.569194 TTTGAGTCTTGTTGGTAGGCA 57.431 42.857 0.0 0.0 0.00 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1005 1480 0.107703 TAGGGTCCAGCTCAATTGCG 60.108 55.0 0.0 0.0 38.13 4.85 R
2002 3428 1.544825 CCCTCCTTGCTCGTCCTTCA 61.545 60.0 0.0 0.0 0.00 3.02 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
137 138 0.040646 TCGAGGAACTTGGCTCCCTA 59.959 55.000 0.00 0.00 41.55 3.53
162 163 8.995027 ATACAGATCATTTTGCTAATGGGTAA 57.005 30.769 10.78 0.00 0.00 2.85
335 337 6.183309 AGTGAACTTCCTAAATCAATTCGC 57.817 37.500 0.00 0.00 0.00 4.70
454 456 7.817418 AAAGTAACAGGCATTTCTTACTGAA 57.183 32.000 0.00 0.00 35.08 3.02
484 486 8.689972 AGTTTTTGAGAATGATTTGAGTCTTGT 58.310 29.630 0.00 0.00 0.00 3.16
486 488 8.861033 TTTTGAGAATGATTTGAGTCTTGTTG 57.139 30.769 0.00 0.00 0.00 3.33
487 489 6.564709 TGAGAATGATTTGAGTCTTGTTGG 57.435 37.500 0.00 0.00 0.00 3.77
489 491 7.223584 TGAGAATGATTTGAGTCTTGTTGGTA 58.776 34.615 0.00 0.00 0.00 3.25
490 492 7.388776 TGAGAATGATTTGAGTCTTGTTGGTAG 59.611 37.037 0.00 0.00 0.00 3.18
491 493 6.656693 AGAATGATTTGAGTCTTGTTGGTAGG 59.343 38.462 0.00 0.00 0.00 3.18
492 494 4.072131 TGATTTGAGTCTTGTTGGTAGGC 58.928 43.478 0.00 0.00 0.00 3.93
493 495 3.569194 TTTGAGTCTTGTTGGTAGGCA 57.431 42.857 0.00 0.00 0.00 4.75
582 720 8.810427 GGCATTGTTCAATAGTCAACATAATTG 58.190 33.333 0.00 0.00 32.60 2.32
892 1366 9.967451 TGGAATCATTATTGTCTTGTTAACCTA 57.033 29.630 2.48 0.00 0.00 3.08
1005 1480 6.205464 ACCTGTATGTTATTGCTGATATGCAC 59.795 38.462 0.00 0.00 43.20 4.57
1659 2146 5.918608 ACAGACACTGAGAATGTACTGTTT 58.081 37.500 5.76 0.00 36.18 2.83
2002 3428 0.607489 GGTCTGCTGTTGTGATGGCT 60.607 55.000 0.00 0.00 0.00 4.75
2009 3435 1.808945 CTGTTGTGATGGCTGAAGGAC 59.191 52.381 0.00 0.00 0.00 3.85
2099 3525 1.350351 GGGTAGCAGATCATGGCTGAT 59.650 52.381 17.21 14.14 44.93 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
137 138 8.850156 GTTACCCATTAGCAAAATGATCTGTAT 58.150 33.333 12.07 0.0 0.00 2.29
470 472 4.072131 GCCTACCAACAAGACTCAAATCA 58.928 43.478 0.00 0.0 0.00 2.57
471 473 4.072131 TGCCTACCAACAAGACTCAAATC 58.928 43.478 0.00 0.0 0.00 2.17
473 475 3.569194 TGCCTACCAACAAGACTCAAA 57.431 42.857 0.00 0.0 0.00 2.69
474 476 3.788227 ATGCCTACCAACAAGACTCAA 57.212 42.857 0.00 0.0 0.00 3.02
475 477 3.788227 AATGCCTACCAACAAGACTCA 57.212 42.857 0.00 0.0 0.00 3.41
476 478 5.122396 CACTTAATGCCTACCAACAAGACTC 59.878 44.000 0.00 0.0 0.00 3.36
478 480 4.760204 ACACTTAATGCCTACCAACAAGAC 59.240 41.667 0.00 0.0 0.00 3.01
479 481 4.980573 ACACTTAATGCCTACCAACAAGA 58.019 39.130 0.00 0.0 0.00 3.02
480 482 5.705609 AACACTTAATGCCTACCAACAAG 57.294 39.130 0.00 0.0 0.00 3.16
483 485 4.022329 AGCAAACACTTAATGCCTACCAAC 60.022 41.667 0.00 0.0 40.93 3.77
484 486 4.022416 CAGCAAACACTTAATGCCTACCAA 60.022 41.667 0.00 0.0 40.93 3.67
486 488 3.506067 ACAGCAAACACTTAATGCCTACC 59.494 43.478 0.00 0.0 40.93 3.18
487 489 4.766404 ACAGCAAACACTTAATGCCTAC 57.234 40.909 0.00 0.0 40.93 3.18
489 491 4.670896 AAACAGCAAACACTTAATGCCT 57.329 36.364 0.00 0.0 40.93 4.75
490 492 6.868339 AGATAAAACAGCAAACACTTAATGCC 59.132 34.615 0.00 0.0 40.93 4.40
491 493 7.873739 AGATAAAACAGCAAACACTTAATGC 57.126 32.000 0.00 0.0 40.34 3.56
492 494 9.462174 TCAAGATAAAACAGCAAACACTTAATG 57.538 29.630 0.00 0.0 0.00 1.90
582 720 3.876274 TCTCAGGATCTGTGTAAGCAC 57.124 47.619 0.00 0.0 45.44 4.40
892 1366 8.640063 TTCCAAGCATATCAGCAATAACATAT 57.360 30.769 0.00 0.0 36.85 1.78
1005 1480 0.107703 TAGGGTCCAGCTCAATTGCG 60.108 55.000 0.00 0.0 38.13 4.85
1659 2146 2.443632 TCAGTGGTTTATTGTGGTGGGA 59.556 45.455 0.00 0.0 0.00 4.37
1731 3157 2.093921 TGCATGCAATTCTGAACATGGG 60.094 45.455 20.30 0.0 40.17 4.00
1860 3286 6.015350 AGGATCATGTTAGGTTGAGGTATACG 60.015 42.308 0.00 0.0 0.00 3.06
2002 3428 1.544825 CCCTCCTTGCTCGTCCTTCA 61.545 60.000 0.00 0.0 0.00 3.02
2009 3435 3.474570 CCTCCCCCTCCTTGCTCG 61.475 72.222 0.00 0.0 0.00 5.03


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

AutoCloner maintained by Alex Coulton.