Multiple sequence alignment - TraesCS6A01G418100

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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 TraesCS6A01G418100 chr6A 100.000 2549 0 0 1 2549 616130724 616133272 0.000000e+00 4708.0
1 TraesCS6A01G418100 chr6A 77.222 180 37 4 342 519 616212931 616212754 4.490000e-18 102.0
2 TraesCS6A01G418100 chr2B 99.245 1988 13 2 563 2549 781094231 781096217 0.000000e+00 3587.0
3 TraesCS6A01G418100 chr2B 99.293 1980 12 2 571 2549 776222960 776224938 0.000000e+00 3578.0
4 TraesCS6A01G418100 chr4B 99.243 1981 13 2 570 2549 368430370 368428391 0.000000e+00 3574.0
5 TraesCS6A01G418100 chr3A 99.095 1988 14 3 564 2549 54951908 54953893 0.000000e+00 3568.0
6 TraesCS6A01G418100 chr5B 99.192 1979 11 2 571 2549 158571214 158569241 0.000000e+00 3561.0
7 TraesCS6A01G418100 chr5B 99.141 1979 16 1 572 2549 641128780 641126802 0.000000e+00 3559.0
8 TraesCS6A01G418100 chr7B 99.044 1987 14 3 564 2549 202776907 202778889 0.000000e+00 3559.0
9 TraesCS6A01G418100 chr7A 99.141 1979 15 2 572 2549 39015367 39017344 0.000000e+00 3559.0
10 TraesCS6A01G418100 chr3B 99.141 1980 14 2 571 2549 702857656 702855679 0.000000e+00 3559.0
11 TraesCS6A01G418100 chr6D 85.409 562 49 8 19 572 471095704 471095168 1.030000e-153 553.0
12 TraesCS6A01G418100 chr6D 76.757 185 39 3 343 524 471485461 471485278 1.610000e-17 100.0
13 TraesCS6A01G418100 chrUn 76.404 178 40 2 343 519 62959130 62959306 7.510000e-16 95.3


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 TraesCS6A01G418100 chr6A 616130724 616133272 2548 False 4708 4708 100.000 1 2549 1 chr6A.!!$F1 2548
1 TraesCS6A01G418100 chr2B 781094231 781096217 1986 False 3587 3587 99.245 563 2549 1 chr2B.!!$F2 1986
2 TraesCS6A01G418100 chr2B 776222960 776224938 1978 False 3578 3578 99.293 571 2549 1 chr2B.!!$F1 1978
3 TraesCS6A01G418100 chr4B 368428391 368430370 1979 True 3574 3574 99.243 570 2549 1 chr4B.!!$R1 1979
4 TraesCS6A01G418100 chr3A 54951908 54953893 1985 False 3568 3568 99.095 564 2549 1 chr3A.!!$F1 1985
5 TraesCS6A01G418100 chr5B 158569241 158571214 1973 True 3561 3561 99.192 571 2549 1 chr5B.!!$R1 1978
6 TraesCS6A01G418100 chr5B 641126802 641128780 1978 True 3559 3559 99.141 572 2549 1 chr5B.!!$R2 1977
7 TraesCS6A01G418100 chr7B 202776907 202778889 1982 False 3559 3559 99.044 564 2549 1 chr7B.!!$F1 1985
8 TraesCS6A01G418100 chr7A 39015367 39017344 1977 False 3559 3559 99.141 572 2549 1 chr7A.!!$F1 1977
9 TraesCS6A01G418100 chr3B 702855679 702857656 1977 True 3559 3559 99.141 571 2549 1 chr3B.!!$R1 1978
10 TraesCS6A01G418100 chr6D 471095168 471095704 536 True 553 553 85.409 19 572 1 chr6D.!!$R1 553

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
82 83 0.040351 TCACTCTCCAGCCAGCTACT 59.96 55.0 0.0 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2183 2194 2.018515 CTAAACACCACAAACCCACGT 58.981 47.619 0.0 0.0 0.0 4.49 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
32 33 2.184579 GACCAGGCAGCTACCGAC 59.815 66.667 0.00 0.00 33.69 4.79
37 38 1.913762 AGGCAGCTACCGACCTGTT 60.914 57.895 0.00 0.00 33.69 3.16
39 40 0.248289 GGCAGCTACCGACCTGTTAA 59.752 55.000 0.00 0.00 0.00 2.01
66 67 5.869753 AAAGATGCATGTCACTAGTTCAC 57.130 39.130 2.46 0.00 0.00 3.18
80 81 0.898320 GTTCACTCTCCAGCCAGCTA 59.102 55.000 0.00 0.00 0.00 3.32
81 82 0.898320 TTCACTCTCCAGCCAGCTAC 59.102 55.000 0.00 0.00 0.00 3.58
82 83 0.040351 TCACTCTCCAGCCAGCTACT 59.960 55.000 0.00 0.00 0.00 2.57
83 84 0.459489 CACTCTCCAGCCAGCTACTC 59.541 60.000 0.00 0.00 0.00 2.59
95 96 3.012518 CCAGCTACTCCTTGATTGTTGG 58.987 50.000 0.00 0.00 0.00 3.77
102 103 4.170292 CTCCTTGATTGTTGGAGCAAAG 57.830 45.455 0.00 0.00 40.52 2.77
104 105 4.410099 TCCTTGATTGTTGGAGCAAAGAT 58.590 39.130 0.00 0.00 31.63 2.40
169 177 1.165907 TGGCTCTGTGTTTTCGCCAG 61.166 55.000 0.00 0.00 45.08 4.85
184 192 0.676782 GCCAGGTACTCGGCAAACAT 60.677 55.000 17.80 0.00 46.65 2.71
191 199 2.248280 ACTCGGCAAACATGTACACA 57.752 45.000 0.00 0.00 0.00 3.72
200 208 6.212955 GGCAAACATGTACACATTAACAAGT 58.787 36.000 0.00 0.00 33.61 3.16
207 215 4.986034 TGTACACATTAACAAGTGTCTCGG 59.014 41.667 11.95 0.00 45.16 4.63
209 217 2.066262 ACATTAACAAGTGTCTCGGCG 58.934 47.619 0.00 0.00 0.00 6.46
213 221 0.670546 AACAAGTGTCTCGGCGGATG 60.671 55.000 7.21 1.33 0.00 3.51
239 247 3.835978 TGAACAGATCCCGGAGAAAGTTA 59.164 43.478 0.73 0.00 0.00 2.24
250 258 4.023707 CCGGAGAAAGTTATCATTGCATCC 60.024 45.833 0.00 0.00 0.00 3.51
266 274 3.599046 CATCCGTGCTCTTTTATCTGC 57.401 47.619 0.00 0.00 0.00 4.26
274 282 2.095263 GCTCTTTTATCTGCGCCACAAA 60.095 45.455 4.18 0.00 0.00 2.83
286 294 2.384382 CGCCACAAACAAATCAGTGTC 58.616 47.619 0.00 0.00 0.00 3.67
287 295 2.742774 GCCACAAACAAATCAGTGTCC 58.257 47.619 0.00 0.00 0.00 4.02
288 296 2.545742 GCCACAAACAAATCAGTGTCCC 60.546 50.000 0.00 0.00 0.00 4.46
289 297 2.035832 CCACAAACAAATCAGTGTCCCC 59.964 50.000 0.00 0.00 0.00 4.81
290 298 2.035832 CACAAACAAATCAGTGTCCCCC 59.964 50.000 0.00 0.00 0.00 5.40
303 311 4.497291 GTGTCCCCCACAATAAGTATGA 57.503 45.455 0.00 0.00 43.92 2.15
342 350 3.864583 TGCTGTGCTTTTTGCTTAACAAG 59.135 39.130 0.00 0.00 40.06 3.16
372 380 5.426504 CTCTGCTTTGATCTCATACCTTGT 58.573 41.667 0.00 0.00 0.00 3.16
377 385 5.448360 GCTTTGATCTCATACCTTGTTGAGC 60.448 44.000 0.00 0.00 39.36 4.26
389 397 3.425359 CCTTGTTGAGCAATAACAGAGCG 60.425 47.826 0.00 0.00 39.03 5.03
391 399 1.086696 TTGAGCAATAACAGAGCGGC 58.913 50.000 0.00 0.00 0.00 6.53
395 403 1.766143 GCAATAACAGAGCGGCCTCG 61.766 60.000 0.00 0.00 43.05 4.63
397 405 0.179108 AATAACAGAGCGGCCTCGAC 60.179 55.000 0.00 0.00 43.05 4.20
410 418 1.798813 GCCTCGACACAGGTAAACAAG 59.201 52.381 0.00 0.00 35.72 3.16
428 436 0.250513 AGTCAAGGATGGCTTCGACC 59.749 55.000 0.00 0.00 38.74 4.79
444 452 0.878416 GACCGCAGTATTGTGCCAAA 59.122 50.000 0.00 0.00 40.62 3.28
451 459 4.734854 CGCAGTATTGTGCCAAACATAATC 59.265 41.667 0.00 0.00 39.14 1.75
452 460 5.649557 GCAGTATTGTGCCAAACATAATCA 58.350 37.500 0.00 0.00 39.14 2.57
453 461 6.275335 GCAGTATTGTGCCAAACATAATCAT 58.725 36.000 0.00 0.00 39.14 2.45
454 462 6.418819 GCAGTATTGTGCCAAACATAATCATC 59.581 38.462 0.00 0.00 39.14 2.92
455 463 7.482474 CAGTATTGTGCCAAACATAATCATCA 58.518 34.615 0.00 0.00 39.14 3.07
456 464 8.139350 CAGTATTGTGCCAAACATAATCATCAT 58.861 33.333 0.00 0.00 39.14 2.45
457 465 8.139350 AGTATTGTGCCAAACATAATCATCATG 58.861 33.333 0.00 0.00 39.14 3.07
458 466 5.918426 TGTGCCAAACATAATCATCATGT 57.082 34.783 0.00 0.00 38.25 3.21
459 467 7.401955 TTGTGCCAAACATAATCATCATGTA 57.598 32.000 0.00 0.00 38.99 2.29
460 468 7.585579 TGTGCCAAACATAATCATCATGTAT 57.414 32.000 0.00 0.00 35.58 2.29
461 469 8.009622 TGTGCCAAACATAATCATCATGTATT 57.990 30.769 0.00 0.00 35.58 1.89
462 470 8.476447 TGTGCCAAACATAATCATCATGTATTT 58.524 29.630 0.00 0.00 35.58 1.40
463 471 8.971321 GTGCCAAACATAATCATCATGTATTTC 58.029 33.333 0.00 0.00 35.58 2.17
497 505 0.394352 AGCCTCCAACCGCCAATAAG 60.394 55.000 0.00 0.00 0.00 1.73
537 545 6.509317 TCTGTGAAAATTGACGCAAAAATC 57.491 33.333 0.00 0.00 0.00 2.17
557 565 2.169561 TCTTAGCGAACATGGGCACATA 59.830 45.455 0.00 0.00 34.99 2.29
562 570 2.680841 GCGAACATGGGCACATAACTAA 59.319 45.455 0.00 0.00 34.99 2.24
564 572 4.202010 GCGAACATGGGCACATAACTAATT 60.202 41.667 0.00 0.00 34.99 1.40
565 573 5.510671 CGAACATGGGCACATAACTAATTC 58.489 41.667 0.00 0.00 34.99 2.17
2183 2194 1.911766 GGACTCGAACCCAGGACCA 60.912 63.158 0.00 0.00 0.00 4.02
2228 2239 1.664321 CGCTGGTAACCGCTAGGACT 61.664 60.000 0.00 0.00 41.02 3.85
2243 2254 4.383118 GCTAGGACTGATGGCAAGACTTTA 60.383 45.833 0.00 0.00 0.00 1.85
2536 2549 2.610859 GGCTTCTCACCCCCTCCA 60.611 66.667 0.00 0.00 0.00 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 1.376609 CCTGGTCGTGCTAATTGGCC 61.377 60.000 11.64 0.00 0.00 5.36
3 4 1.993369 GCCTGGTCGTGCTAATTGGC 61.993 60.000 6.88 6.88 0.00 4.52
4 5 0.676466 TGCCTGGTCGTGCTAATTGG 60.676 55.000 0.00 0.00 0.00 3.16
5 6 0.729116 CTGCCTGGTCGTGCTAATTG 59.271 55.000 0.00 0.00 0.00 2.32
7 8 1.450312 GCTGCCTGGTCGTGCTAAT 60.450 57.895 0.00 0.00 0.00 1.73
8 9 1.254975 TAGCTGCCTGGTCGTGCTAA 61.255 55.000 0.00 0.00 33.94 3.09
9 10 1.680989 TAGCTGCCTGGTCGTGCTA 60.681 57.895 0.00 2.12 35.47 3.49
10 11 2.997315 TAGCTGCCTGGTCGTGCT 60.997 61.111 0.00 3.07 37.72 4.40
11 12 2.815647 GTAGCTGCCTGGTCGTGC 60.816 66.667 0.00 0.00 0.00 5.34
12 13 2.125512 GGTAGCTGCCTGGTCGTG 60.126 66.667 14.43 0.00 0.00 4.35
13 14 3.760035 CGGTAGCTGCCTGGTCGT 61.760 66.667 19.36 0.00 0.00 4.34
14 15 3.449227 TCGGTAGCTGCCTGGTCG 61.449 66.667 19.36 5.18 0.00 4.79
15 16 2.184579 GTCGGTAGCTGCCTGGTC 59.815 66.667 19.36 2.80 0.00 4.02
16 17 3.391382 GGTCGGTAGCTGCCTGGT 61.391 66.667 19.36 0.00 0.00 4.00
17 18 3.077556 AGGTCGGTAGCTGCCTGG 61.078 66.667 19.36 4.27 30.51 4.45
32 33 7.062605 GTGACATGCATCTTTTTCATTAACAGG 59.937 37.037 0.00 0.00 0.00 4.00
37 38 8.565896 ACTAGTGACATGCATCTTTTTCATTA 57.434 30.769 0.00 0.00 0.00 1.90
39 40 7.175467 TGAACTAGTGACATGCATCTTTTTCAT 59.825 33.333 0.00 0.00 0.00 2.57
66 67 0.396974 AGGAGTAGCTGGCTGGAGAG 60.397 60.000 5.25 0.00 0.00 3.20
82 83 3.831323 TCTTTGCTCCAACAATCAAGGA 58.169 40.909 0.00 0.00 0.00 3.36
83 84 4.796038 ATCTTTGCTCCAACAATCAAGG 57.204 40.909 0.00 0.00 0.00 3.61
97 98 7.080724 GGTAAGCAGAGCATTTATATCTTTGC 58.919 38.462 0.00 0.00 37.97 3.68
98 99 8.158169 TGGTAAGCAGAGCATTTATATCTTTG 57.842 34.615 0.00 0.00 0.00 2.77
101 102 8.790718 CATTTGGTAAGCAGAGCATTTATATCT 58.209 33.333 0.00 0.00 0.00 1.98
102 103 8.025445 CCATTTGGTAAGCAGAGCATTTATATC 58.975 37.037 0.00 0.00 0.00 1.63
104 105 7.059788 TCCATTTGGTAAGCAGAGCATTTATA 58.940 34.615 0.00 0.00 36.34 0.98
149 157 1.282875 GGCGAAAACACAGAGCCAC 59.717 57.895 0.00 0.00 46.48 5.01
169 177 2.414138 GTGTACATGTTTGCCGAGTACC 59.586 50.000 2.30 0.00 35.41 3.34
184 192 4.986034 CCGAGACACTTGTTAATGTGTACA 59.014 41.667 10.41 0.00 45.94 2.90
191 199 1.274167 TCCGCCGAGACACTTGTTAAT 59.726 47.619 0.00 0.00 0.00 1.40
207 215 0.590195 GATCTGTTCATGGCATCCGC 59.410 55.000 0.00 0.00 37.44 5.54
209 217 1.613836 GGGATCTGTTCATGGCATCC 58.386 55.000 0.00 0.00 33.46 3.51
213 221 0.533755 CTCCGGGATCTGTTCATGGC 60.534 60.000 0.00 0.00 0.00 4.40
217 225 2.257207 ACTTTCTCCGGGATCTGTTCA 58.743 47.619 0.00 0.00 0.00 3.18
250 258 0.026803 GGCGCAGATAAAAGAGCACG 59.973 55.000 10.83 0.00 31.88 5.34
254 262 3.058293 TGTTTGTGGCGCAGATAAAAGAG 60.058 43.478 10.83 0.00 0.00 2.85
266 274 2.384382 GACACTGATTTGTTTGTGGCG 58.616 47.619 0.00 0.00 35.02 5.69
274 282 3.745723 GTGGGGGACACTGATTTGT 57.254 52.632 0.00 0.00 46.72 2.83
286 294 4.503714 ACTGTCATACTTATTGTGGGGG 57.496 45.455 0.00 0.00 0.00 5.40
344 352 3.345508 TGAGATCAAAGCAGAGCATGT 57.654 42.857 0.00 0.00 0.00 3.21
359 367 7.112122 TGTTATTGCTCAACAAGGTATGAGAT 58.888 34.615 6.95 0.00 44.64 2.75
372 380 1.086696 GCCGCTCTGTTATTGCTCAA 58.913 50.000 0.00 0.00 0.00 3.02
377 385 0.179111 TCGAGGCCGCTCTGTTATTG 60.179 55.000 4.53 0.00 35.37 1.90
389 397 0.034337 TGTTTACCTGTGTCGAGGCC 59.966 55.000 0.00 0.00 36.46 5.19
391 399 3.057734 GACTTGTTTACCTGTGTCGAGG 58.942 50.000 0.00 0.00 39.28 4.63
395 403 4.448210 TCCTTGACTTGTTTACCTGTGTC 58.552 43.478 0.00 0.00 0.00 3.67
397 405 4.216257 CCATCCTTGACTTGTTTACCTGTG 59.784 45.833 0.00 0.00 0.00 3.66
410 418 1.084370 CGGTCGAAGCCATCCTTGAC 61.084 60.000 0.00 0.00 32.78 3.18
444 452 8.172070 TGGGATGGAAATACATGATGATTATGT 58.828 33.333 7.97 7.97 41.36 2.29
451 459 4.585581 TGCTTGGGATGGAAATACATGATG 59.414 41.667 0.00 0.00 0.00 3.07
452 460 4.806892 TGCTTGGGATGGAAATACATGAT 58.193 39.130 0.00 0.00 0.00 2.45
453 461 4.248174 TGCTTGGGATGGAAATACATGA 57.752 40.909 0.00 0.00 0.00 3.07
454 462 4.646040 TCTTGCTTGGGATGGAAATACATG 59.354 41.667 0.00 0.00 0.00 3.21
455 463 4.870636 TCTTGCTTGGGATGGAAATACAT 58.129 39.130 0.00 0.00 0.00 2.29
456 464 4.314522 TCTTGCTTGGGATGGAAATACA 57.685 40.909 0.00 0.00 0.00 2.29
457 465 4.440663 GCTTCTTGCTTGGGATGGAAATAC 60.441 45.833 0.00 0.00 38.95 1.89
458 466 3.701040 GCTTCTTGCTTGGGATGGAAATA 59.299 43.478 0.00 0.00 38.95 1.40
459 467 2.498885 GCTTCTTGCTTGGGATGGAAAT 59.501 45.455 0.00 0.00 38.95 2.17
460 468 1.895131 GCTTCTTGCTTGGGATGGAAA 59.105 47.619 0.00 0.00 38.95 3.13
461 469 1.549203 GCTTCTTGCTTGGGATGGAA 58.451 50.000 0.00 0.00 38.95 3.53
462 470 0.323725 GGCTTCTTGCTTGGGATGGA 60.324 55.000 0.00 0.00 42.39 3.41
463 471 0.324091 AGGCTTCTTGCTTGGGATGG 60.324 55.000 0.00 0.00 42.39 3.51
486 494 1.682854 CATGGCAATCTTATTGGCGGT 59.317 47.619 17.85 9.06 46.47 5.68
497 505 1.299620 GATGTGCGGCATGGCAATC 60.300 57.895 20.37 11.91 45.93 2.67
529 537 3.859386 CCCATGTTCGCTAAGATTTTTGC 59.141 43.478 0.00 0.00 0.00 3.68
537 545 1.382522 ATGTGCCCATGTTCGCTAAG 58.617 50.000 0.00 0.00 0.00 2.18
545 553 7.480760 AAAAGAATTAGTTATGTGCCCATGT 57.519 32.000 0.00 0.00 32.29 3.21
565 573 9.378551 GGCAAAAGGATAATTAACCCTAAAAAG 57.621 33.333 8.09 1.40 0.00 2.27
2183 2194 2.018515 CTAAACACCACAAACCCACGT 58.981 47.619 0.00 0.00 0.00 4.49
2228 2239 3.763360 CCCATGTTAAAGTCTTGCCATCA 59.237 43.478 0.00 0.00 0.00 3.07
2243 2254 2.993863 ACCTTCTTTCCCTACCCATGTT 59.006 45.455 0.00 0.00 0.00 2.71


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

AutoCloner maintained by Alex Coulton.