Multiple sequence alignment - TraesCS1A01G346000

Loading Multiple Alignment...

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 TraesCS1A01G346000 chr1A 100.000 2232 0 0 1 2232 532796640 532798871 0.000000e+00 4122
1 TraesCS1A01G346000 chr1A 99.082 871 7 1 1363 2232 532805038 532805908 0.000000e+00 1563
2 TraesCS1A01G346000 chr1A 98.383 866 13 1 1366 2230 483184734 483183869 0.000000e+00 1520
3 TraesCS1A01G346000 chr1A 98.268 866 14 1 1366 2230 129451209 129450344 0.000000e+00 1515
4 TraesCS1A01G346000 chr1A 84.593 344 32 4 1 323 566636844 566636501 2.770000e-84 322
5 TraesCS1A01G346000 chr1A 88.492 252 29 0 631 882 566636478 566636227 2.780000e-79 305
6 TraesCS1A01G346000 chr1B 95.290 1380 45 5 1 1362 588515952 588517329 0.000000e+00 2170
7 TraesCS1A01G346000 chr1B 89.683 252 26 0 631 882 657406549 657406298 2.770000e-84 322
8 TraesCS1A01G346000 chr1B 84.593 344 32 5 1 323 657406915 657406572 2.770000e-84 322
9 TraesCS1A01G346000 chr1B 85.246 122 16 2 1219 1340 657406296 657406177 8.370000e-25 124
10 TraesCS1A01G346000 chr1D 94.058 1380 54 11 1 1362 435293422 435294791 0.000000e+00 2069
11 TraesCS1A01G346000 chr1D 89.489 352 20 8 881 1219 254532495 254532842 1.580000e-116 429
12 TraesCS1A01G346000 chr1D 89.683 252 26 0 631 882 472906401 472906150 2.770000e-84 322
13 TraesCS1A01G346000 chr1D 84.593 344 32 4 1 323 472906767 472906424 2.770000e-84 322
14 TraesCS1A01G346000 chr1D 85.246 122 16 1 1219 1340 472906148 472906029 8.370000e-25 124
15 TraesCS1A01G346000 chr5A 98.507 871 12 1 1361 2230 644952220 644951350 0.000000e+00 1535
16 TraesCS1A01G346000 chr6A 98.387 868 13 1 1366 2232 89919734 89918867 0.000000e+00 1524
17 TraesCS1A01G346000 chr6A 98.278 871 14 1 1363 2232 605287669 605288539 0.000000e+00 1524
18 TraesCS1A01G346000 chr6A 98.383 866 13 1 1366 2230 587461695 587460830 0.000000e+00 1520
19 TraesCS1A01G346000 chr6A 98.163 871 15 1 1363 2232 605294706 605295576 0.000000e+00 1519
20 TraesCS1A01G346000 chr6A 92.308 104 6 1 881 984 561963467 561963568 1.790000e-31 147
21 TraesCS1A01G346000 chr2A 98.278 871 14 1 1363 2232 677383629 677384499 0.000000e+00 1524
22 TraesCS1A01G346000 chr7D 85.606 924 91 9 1 882 279741323 279740400 0.000000e+00 931
23 TraesCS1A01G346000 chr7D 86.532 839 77 18 77 882 621644846 621644011 0.000000e+00 891
24 TraesCS1A01G346000 chr7B 85.606 924 91 9 1 882 253698726 253699649 0.000000e+00 931
25 TraesCS1A01G346000 chr7B 89.698 563 55 1 320 882 718361506 718362065 0.000000e+00 715
26 TraesCS1A01G346000 chr7A 85.358 922 93 9 3 882 316021009 316021930 0.000000e+00 917
27 TraesCS1A01G346000 chr7A 89.343 563 57 1 320 882 717086490 717085931 0.000000e+00 704
28 TraesCS1A01G346000 chr7A 89.714 350 22 6 881 1219 352681140 352680794 3.400000e-118 435
29 TraesCS1A01G346000 chrUn 91.813 342 23 4 881 1219 363863629 363863290 2.590000e-129 472
30 TraesCS1A01G346000 chrUn 89.744 351 22 5 881 1219 430358280 430358628 9.460000e-119 436
31 TraesCS1A01G346000 chrUn 88.604 351 26 7 881 1219 354743915 354743567 4.430000e-112 414
32 TraesCS1A01G346000 chr2D 91.813 342 23 4 881 1219 272805352 272805013 2.590000e-129 472
33 TraesCS1A01G346000 chr2D 91.545 343 22 5 881 1219 196967432 196967093 1.210000e-127 466
34 TraesCS1A01G346000 chr5D 83.846 520 53 13 51 543 557181712 557182227 1.210000e-127 466
35 TraesCS1A01G346000 chr5D 88.701 354 20 9 881 1219 128182190 128181842 4.430000e-112 414
36 TraesCS1A01G346000 chr3B 89.971 349 19 7 881 1216 201550199 201550544 9.460000e-119 436
37 TraesCS1A01G346000 chr5B 88.596 342 33 5 881 1219 432873047 432873385 5.740000e-111 411
38 TraesCS1A01G346000 chr5B 85.663 279 30 8 51 323 709423386 709423112 3.630000e-73 285
39 TraesCS1A01G346000 chr5B 93.269 104 5 1 881 984 555191679 555191578 3.840000e-33 152
40 TraesCS1A01G346000 chr4D 94.419 215 10 2 1007 1219 354587271 354587485 1.650000e-86 329
41 TraesCS1A01G346000 chr4A 86.992 246 29 2 1 246 605665439 605665681 7.850000e-70 274


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 TraesCS1A01G346000 chr1A 532796640 532798871 2231 False 4122.0 4122 100.000000 1 2232 1 chr1A.!!$F1 2231
1 TraesCS1A01G346000 chr1A 532805038 532805908 870 False 1563.0 1563 99.082000 1363 2232 1 chr1A.!!$F2 869
2 TraesCS1A01G346000 chr1A 483183869 483184734 865 True 1520.0 1520 98.383000 1366 2230 1 chr1A.!!$R2 864
3 TraesCS1A01G346000 chr1A 129450344 129451209 865 True 1515.0 1515 98.268000 1366 2230 1 chr1A.!!$R1 864
4 TraesCS1A01G346000 chr1A 566636227 566636844 617 True 313.5 322 86.542500 1 882 2 chr1A.!!$R3 881
5 TraesCS1A01G346000 chr1B 588515952 588517329 1377 False 2170.0 2170 95.290000 1 1362 1 chr1B.!!$F1 1361
6 TraesCS1A01G346000 chr1B 657406177 657406915 738 True 256.0 322 86.507333 1 1340 3 chr1B.!!$R1 1339
7 TraesCS1A01G346000 chr1D 435293422 435294791 1369 False 2069.0 2069 94.058000 1 1362 1 chr1D.!!$F2 1361
8 TraesCS1A01G346000 chr1D 472906029 472906767 738 True 256.0 322 86.507333 1 1340 3 chr1D.!!$R1 1339
9 TraesCS1A01G346000 chr5A 644951350 644952220 870 True 1535.0 1535 98.507000 1361 2230 1 chr5A.!!$R1 869
10 TraesCS1A01G346000 chr6A 89918867 89919734 867 True 1524.0 1524 98.387000 1366 2232 1 chr6A.!!$R1 866
11 TraesCS1A01G346000 chr6A 605287669 605288539 870 False 1524.0 1524 98.278000 1363 2232 1 chr6A.!!$F2 869
12 TraesCS1A01G346000 chr6A 587460830 587461695 865 True 1520.0 1520 98.383000 1366 2230 1 chr6A.!!$R2 864
13 TraesCS1A01G346000 chr6A 605294706 605295576 870 False 1519.0 1519 98.163000 1363 2232 1 chr6A.!!$F3 869
14 TraesCS1A01G346000 chr2A 677383629 677384499 870 False 1524.0 1524 98.278000 1363 2232 1 chr2A.!!$F1 869
15 TraesCS1A01G346000 chr7D 279740400 279741323 923 True 931.0 931 85.606000 1 882 1 chr7D.!!$R1 881
16 TraesCS1A01G346000 chr7D 621644011 621644846 835 True 891.0 891 86.532000 77 882 1 chr7D.!!$R2 805
17 TraesCS1A01G346000 chr7B 253698726 253699649 923 False 931.0 931 85.606000 1 882 1 chr7B.!!$F1 881
18 TraesCS1A01G346000 chr7B 718361506 718362065 559 False 715.0 715 89.698000 320 882 1 chr7B.!!$F2 562
19 TraesCS1A01G346000 chr7A 316021009 316021930 921 False 917.0 917 85.358000 3 882 1 chr7A.!!$F1 879
20 TraesCS1A01G346000 chr7A 717085931 717086490 559 True 704.0 704 89.343000 320 882 1 chr7A.!!$R2 562
21 TraesCS1A01G346000 chr5D 557181712 557182227 515 False 466.0 466 83.846000 51 543 1 chr5D.!!$F1 492

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
362 414 1.419762 TGCTTGTTTCTACTGCCTCCA 59.58 47.619 0.0 0.0 0.0 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1753 1806 1.202604 AGTCACCCAGTTACGTTGTGG 60.203 52.381 0.0 0.0 0.0 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
46 47 3.594568 GCACCTGCTGCATGCTTA 58.405 55.556 20.33 4.10 46.29 3.09
55 56 4.380761 CCTGCTGCATGCTTAACACATTAA 60.381 41.667 20.33 0.00 43.37 1.40
144 163 3.623703 TGGCTCATGCAAAGACACATAT 58.376 40.909 3.96 0.00 41.91 1.78
159 181 6.179756 AGACACATATTGCTGGTTCAACATA 58.820 36.000 0.00 0.00 0.00 2.29
323 372 7.324935 TGTTTCTGTTGTAGAATATTCGGCTA 58.675 34.615 9.78 1.82 44.54 3.93
362 414 1.419762 TGCTTGTTTCTACTGCCTCCA 59.580 47.619 0.00 0.00 0.00 3.86
466 518 2.125310 CCGACTGCATGGCCGTTA 60.125 61.111 0.00 0.00 0.00 3.18
481 533 1.670087 CCGTTAGCTGTGTCTGTGGAG 60.670 57.143 0.00 0.00 0.00 3.86
710 762 3.244146 TGCCTTTGTGCAGCATAAACATT 60.244 39.130 12.93 0.00 36.04 2.71
826 878 2.730382 TCTGCCCGATGTTAGTGAGTA 58.270 47.619 0.00 0.00 0.00 2.59
843 895 6.217294 AGTGAGTAAAGAAGCTTGTACAGAC 58.783 40.000 2.10 4.63 0.00 3.51
847 899 6.921914 AGTAAAGAAGCTTGTACAGACGTAT 58.078 36.000 2.10 0.00 0.00 3.06
890 942 4.695396 TGTTGCTGAGACATTGCAAATTT 58.305 34.783 1.71 0.00 46.22 1.82
891 943 4.508492 TGTTGCTGAGACATTGCAAATTTG 59.492 37.500 14.03 14.03 46.22 2.32
1017 1069 8.768397 GGGGGATTTATGGTTAAAGAAGAAAAT 58.232 33.333 0.00 0.00 31.07 1.82
1027 1079 9.862149 TGGTTAAAGAAGAAAATAGGAGTTCTT 57.138 29.630 0.00 0.00 44.72 2.52
1133 1185 1.964223 AGAGGTCTGCGAGACTTTTGA 59.036 47.619 13.59 0.00 44.46 2.69
1145 1197 4.148348 CGAGACTTTTGAGAAAACGTCGAT 59.852 41.667 0.00 0.00 35.55 3.59
1180 1232 8.650714 GCTTATTTGGCAAAGAAAAATAGAGTG 58.349 33.333 19.29 7.15 29.93 3.51
1284 1336 5.238868 GGAAGTCCAGGAGTTGTTTTAGAAC 59.761 44.000 14.84 0.00 34.58 3.01
1352 1404 0.473755 TGTGGAAAGCTGAGAGGCAA 59.526 50.000 0.00 0.00 34.17 4.52
1353 1405 1.163554 GTGGAAAGCTGAGAGGCAAG 58.836 55.000 0.00 0.00 34.17 4.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
46 47 4.887071 TCTTGGAACTGTGCTTAATGTGTT 59.113 37.500 0.00 0.00 0.00 3.32
55 56 1.602311 CAGCTTCTTGGAACTGTGCT 58.398 50.000 0.00 0.00 0.00 4.40
94 113 0.524862 GGCTCTCAGGCAAACATGTG 59.475 55.000 0.00 0.00 40.97 3.21
159 181 5.336150 TGAATGTCCAACAAACACAACAT 57.664 34.783 0.00 0.00 0.00 2.71
323 372 2.662866 CACAGGGCTCCATTCATCAAT 58.337 47.619 0.00 0.00 0.00 2.57
353 405 3.960102 TCAAAAATCTGTTTGGAGGCAGT 59.040 39.130 0.00 0.00 38.72 4.40
362 414 4.338118 TCGAGCAACCTCAAAAATCTGTTT 59.662 37.500 0.00 0.00 38.00 2.83
463 515 1.433534 GCTCCACAGACACAGCTAAC 58.566 55.000 0.00 0.00 0.00 2.34
466 518 2.341543 CGCTCCACAGACACAGCT 59.658 61.111 0.00 0.00 0.00 4.24
626 678 4.730949 ATTTATCAGCAGCAGCAAATGT 57.269 36.364 3.17 0.00 45.49 2.71
810 862 4.567159 GCTTCTTTACTCACTAACATCGGG 59.433 45.833 0.00 0.00 0.00 5.14
826 878 5.798934 CGTATACGTCTGTACAAGCTTCTTT 59.201 40.000 17.16 0.00 32.26 2.52
843 895 2.475111 CTGGCAGCCAAATACGTATACG 59.525 50.000 23.24 23.24 38.10 3.06
847 899 0.746563 GCCTGGCAGCCAAATACGTA 60.747 55.000 17.03 0.00 30.80 3.57
1027 1079 9.528018 GGTGAAACTGAATACTTGAAATTCAAA 57.472 29.630 9.85 0.00 41.50 2.69
1133 1185 3.181510 GCCAGCAAATATCGACGTTTTCT 60.182 43.478 0.00 0.00 0.00 2.52
1145 1197 4.815533 TTGCCAAATAAGCCAGCAAATA 57.184 36.364 0.00 0.00 40.26 1.40
1273 1325 8.630054 AACATATGCTACCTGTTCTAAAACAA 57.370 30.769 1.58 0.00 44.53 2.83
1284 1336 8.299570 ACTTTCTTGAAAAACATATGCTACCTG 58.700 33.333 1.58 0.00 0.00 4.00
1352 1404 6.407299 GGGCATATTTCCATCAAAATGTGACT 60.407 38.462 10.47 0.00 42.33 3.41
1353 1405 5.754890 GGGCATATTTCCATCAAAATGTGAC 59.245 40.000 9.40 6.79 42.11 3.67
1753 1806 1.202604 AGTCACCCAGTTACGTTGTGG 60.203 52.381 0.00 0.00 0.00 4.17


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

AutoCloner maintained by Alex Coulton.