Multiple sequence alignment - TraesCS6A01G377000

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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 TraesCS6A01G377000 chr6A 100.000 2401 0 0 1 2401 598521987 598519587 0.000000e+00 4434.0
1 TraesCS6A01G377000 chr6A 99.445 1803 9 1 599 2401 598461458 598459657 0.000000e+00 3273.0
2 TraesCS6A01G377000 chr6A 99.334 1803 9 1 599 2401 598254087 598252288 0.000000e+00 3260.0
3 TraesCS6A01G377000 chr6A 99.279 1803 12 1 599 2401 598327374 598325573 0.000000e+00 3256.0
4 TraesCS6A01G377000 chr6A 99.113 1803 16 0 599 2401 598569177 598567375 0.000000e+00 3241.0
5 TraesCS6A01G377000 chr6A 98.968 969 9 1 1433 2401 598386926 598385959 0.000000e+00 1733.0
6 TraesCS6A01G377000 chr6A 86.712 888 56 20 909 1770 598576284 598575433 0.000000e+00 929.0
7 TraesCS6A01G377000 chr6A 97.047 508 3 3 1 507 598255715 598255219 0.000000e+00 845.0
8 TraesCS6A01G377000 chr6A 97.047 508 3 2 1 507 598328998 598328502 0.000000e+00 845.0
9 TraesCS6A01G377000 chr6A 97.047 508 3 2 1 507 598463100 598462604 0.000000e+00 845.0
10 TraesCS6A01G377000 chr6A 95.499 511 8 4 1 507 598388725 598388226 0.000000e+00 802.0
11 TraesCS6A01G377000 chr6A 99.419 172 1 0 599 770 598387098 598386927 1.790000e-81 313.0
12 TraesCS6A01G377000 chr6A 90.047 211 16 3 2125 2333 598574110 598573903 3.930000e-68 268.0
13 TraesCS6A01G377000 chr6A 87.963 108 12 1 593 699 598213169 598213062 2.510000e-25 126.0
14 TraesCS6A01G377000 chrUn 99.850 665 1 0 599 1263 341387204 341387868 0.000000e+00 1223.0
15 TraesCS6A01G377000 chrUn 97.047 508 3 2 1 507 341385580 341386076 0.000000e+00 845.0
16 TraesCS6A01G377000 chr6B 78.516 1415 210 54 980 2340 687413529 687412155 0.000000e+00 843.0
17 TraesCS6A01G377000 chr6B 81.745 745 69 24 805 1489 687367318 687366581 5.800000e-156 560.0
18 TraesCS6A01G377000 chr6B 89.462 446 26 5 989 1413 687372396 687371951 5.840000e-151 544.0
19 TraesCS6A01G377000 chr6B 81.250 448 36 16 1573 1998 687371913 687371492 3.850000e-83 318.0
20 TraesCS6A01G377000 chr6B 79.032 310 40 15 1194 1489 687317799 687317501 3.150000e-44 189.0
21 TraesCS6A01G377000 chr6B 83.756 197 9 4 1825 1998 687366206 687366010 5.310000e-37 165.0
22 TraesCS6A01G377000 chr6B 91.304 115 10 0 1532 1646 687366388 687366274 8.890000e-35 158.0
23 TraesCS6A01G377000 chr6B 93.976 83 4 1 593 675 687372813 687372732 9.010000e-25 124.0
24 TraesCS6A01G377000 chr6B 93.939 66 4 0 695 760 687318432 687318367 1.520000e-17 100.0
25 TraesCS6A01G377000 chr6D 77.983 1408 184 66 980 2340 452709767 452708439 0.000000e+00 767.0
26 TraesCS6A01G377000 chr6D 83.678 484 45 14 1194 1644 452641702 452641220 2.210000e-115 425.0
27 TraesCS6A01G377000 chr6D 91.093 247 22 0 1532 1778 452641234 452640988 3.820000e-88 335.0
28 TraesCS6A01G377000 chr6D 96.552 58 2 0 703 760 452642177 452642120 1.960000e-16 97.1
29 TraesCS6A01G377000 chr6D 92.424 66 5 0 695 760 452593440 452593375 7.070000e-16 95.3
30 TraesCS6A01G377000 chr6D 85.567 97 6 3 1910 1998 452640039 452639943 7.070000e-16 95.3
31 TraesCS6A01G377000 chr1D 78.010 382 63 19 36 407 410746066 410746436 1.120000e-53 220.0
32 TraesCS6A01G377000 chr7D 78.284 373 56 18 36 387 48362415 48362783 1.450000e-52 217.0
33 TraesCS6A01G377000 chr3D 77.396 407 64 21 26 413 582850208 582850605 1.450000e-52 217.0
34 TraesCS6A01G377000 chr5A 79.310 232 37 11 28 251 477005813 477005585 4.130000e-33 152.0
35 TraesCS6A01G377000 chr3B 75.229 327 50 21 89 388 546185033 546184711 2.510000e-25 126.0


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 TraesCS6A01G377000 chr6A 598519587 598521987 2400 True 4434.000000 4434 100.000000 1 2401 1 chr6A.!!$R2 2400
1 TraesCS6A01G377000 chr6A 598567375 598569177 1802 True 3241.000000 3241 99.113000 599 2401 1 chr6A.!!$R3 1802
2 TraesCS6A01G377000 chr6A 598459657 598463100 3443 True 2059.000000 3273 98.246000 1 2401 2 chr6A.!!$R7 2400
3 TraesCS6A01G377000 chr6A 598252288 598255715 3427 True 2052.500000 3260 98.190500 1 2401 2 chr6A.!!$R4 2400
4 TraesCS6A01G377000 chr6A 598325573 598328998 3425 True 2050.500000 3256 98.163000 1 2401 2 chr6A.!!$R5 2400
5 TraesCS6A01G377000 chr6A 598385959 598388725 2766 True 949.333333 1733 97.962000 1 2401 3 chr6A.!!$R6 2400
6 TraesCS6A01G377000 chr6A 598573903 598576284 2381 True 598.500000 929 88.379500 909 2333 2 chr6A.!!$R8 1424
7 TraesCS6A01G377000 chrUn 341385580 341387868 2288 False 1034.000000 1223 98.448500 1 1263 2 chrUn.!!$F1 1262
8 TraesCS6A01G377000 chr6B 687412155 687413529 1374 True 843.000000 843 78.516000 980 2340 1 chr6B.!!$R1 1360
9 TraesCS6A01G377000 chr6B 687371492 687372813 1321 True 328.666667 544 88.229333 593 1998 3 chr6B.!!$R4 1405
10 TraesCS6A01G377000 chr6B 687366010 687367318 1308 True 294.333333 560 85.601667 805 1998 3 chr6B.!!$R3 1193
11 TraesCS6A01G377000 chr6D 452708439 452709767 1328 True 767.000000 767 77.983000 980 2340 1 chr6D.!!$R2 1360
12 TraesCS6A01G377000 chr6D 452639943 452642177 2234 True 238.100000 425 89.222500 703 1998 4 chr6D.!!$R3 1295

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
181 183 2.920724 TGAAAGGACATTCGTGGACA 57.079 45.0 0.0 0.0 31.8 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2163 5320 1.742308 TGAAGGCTAGTGGGACCTTT 58.258 50.0 0.78 0.0 43.82 3.11 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
181 183 2.920724 TGAAAGGACATTCGTGGACA 57.079 45.000 0.00 0.00 31.80 4.02
326 329 7.607250 ACACTTGAGAATGTTTACCACAAAAA 58.393 30.769 0.00 0.00 39.50 1.94
534 539 3.908737 GGGGTACATATGACCGCTC 57.091 57.895 22.66 11.39 44.42 5.03
537 542 3.097614 GGGGTACATATGACCGCTCTAT 58.902 50.000 22.66 0.00 44.42 1.98
539 544 4.708421 GGGGTACATATGACCGCTCTATTA 59.292 45.833 22.66 0.00 44.42 0.98
541 546 5.393896 GGGTACATATGACCGCTCTATTACC 60.394 48.000 10.38 6.51 37.90 2.85
543 548 6.600822 GGTACATATGACCGCTCTATTACCTA 59.399 42.308 10.38 0.00 0.00 3.08
545 550 6.921914 ACATATGACCGCTCTATTACCTAAC 58.078 40.000 10.38 0.00 0.00 2.34
548 553 8.737175 CATATGACCGCTCTATTACCTAACTTA 58.263 37.037 0.00 0.00 0.00 2.24
549 554 7.778185 ATGACCGCTCTATTACCTAACTTAT 57.222 36.000 0.00 0.00 0.00 1.73
554 559 8.262933 ACCGCTCTATTACCTAACTTATTTGTT 58.737 33.333 0.00 0.00 0.00 2.83
555 560 9.106070 CCGCTCTATTACCTAACTTATTTGTTT 57.894 33.333 0.00 0.00 0.00 2.83
556 561 9.916397 CGCTCTATTACCTAACTTATTTGTTTG 57.084 33.333 0.00 0.00 0.00 2.93
564 569 8.943594 ACCTAACTTATTTGTTTGGGTATGAA 57.056 30.769 11.21 0.00 43.60 2.57
565 570 9.369672 ACCTAACTTATTTGTTTGGGTATGAAA 57.630 29.630 11.21 0.00 43.60 2.69
575 1194 9.898152 TTTGTTTGGGTATGAAAAGAAAAGATT 57.102 25.926 0.00 0.00 28.94 2.40
1523 2843 3.650942 TCTGTCATCAGGGGTGTAAAAGT 59.349 43.478 0.00 0.00 41.59 2.66
2163 5320 1.265635 CATGTCGCAAGGTTTTTCCGA 59.734 47.619 0.00 0.00 41.99 4.55
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
446 451 5.982356 TCCATTGGTGAAACACATGAAAAA 58.018 33.333 0.00 0.00 39.98 1.94
507 512 6.292923 CGGTCATATGTACCCCTGAATAAAA 58.707 40.000 14.80 0.00 33.10 1.52
508 513 5.743714 GCGGTCATATGTACCCCTGAATAAA 60.744 44.000 14.80 0.00 33.10 1.40
511 516 2.038557 GCGGTCATATGTACCCCTGAAT 59.961 50.000 14.80 0.00 33.10 2.57
512 517 1.414919 GCGGTCATATGTACCCCTGAA 59.585 52.381 14.80 0.00 33.10 3.02
513 518 1.045407 GCGGTCATATGTACCCCTGA 58.955 55.000 14.80 0.00 33.10 3.86
514 519 1.000955 GAGCGGTCATATGTACCCCTG 59.999 57.143 10.30 5.40 33.10 4.45
515 520 1.133136 AGAGCGGTCATATGTACCCCT 60.133 52.381 18.15 12.32 33.10 4.79
516 521 1.339097 AGAGCGGTCATATGTACCCC 58.661 55.000 18.15 8.84 33.10 4.95
517 522 4.803098 AATAGAGCGGTCATATGTACCC 57.197 45.455 18.15 8.16 33.10 3.69
518 523 5.418209 AGGTAATAGAGCGGTCATATGTACC 59.582 44.000 18.15 17.94 0.00 3.34
519 524 6.512342 AGGTAATAGAGCGGTCATATGTAC 57.488 41.667 18.15 10.60 0.00 2.90
520 525 7.886970 AGTTAGGTAATAGAGCGGTCATATGTA 59.113 37.037 18.15 0.00 0.00 2.29
521 526 6.720288 AGTTAGGTAATAGAGCGGTCATATGT 59.280 38.462 18.15 0.00 0.00 2.29
525 530 7.778185 ATAAGTTAGGTAATAGAGCGGTCAT 57.222 36.000 18.15 5.59 0.00 3.06
526 531 7.592885 AATAAGTTAGGTAATAGAGCGGTCA 57.407 36.000 18.15 3.22 0.00 4.02
527 532 7.924947 ACAAATAAGTTAGGTAATAGAGCGGTC 59.075 37.037 6.48 6.48 0.00 4.79
539 544 8.943594 TTCATACCCAAACAAATAAGTTAGGT 57.056 30.769 0.00 0.00 39.87 3.08
549 554 9.898152 AATCTTTTCTTTTCATACCCAAACAAA 57.102 25.926 0.00 0.00 0.00 2.83
581 1200 9.915629 GTCCGATGTAATATGAGAAAGATACTT 57.084 33.333 0.00 0.00 0.00 2.24
582 1201 9.078990 TGTCCGATGTAATATGAGAAAGATACT 57.921 33.333 0.00 0.00 0.00 2.12
583 1202 9.347934 CTGTCCGATGTAATATGAGAAAGATAC 57.652 37.037 0.00 0.00 0.00 2.24
585 1204 6.870965 GCTGTCCGATGTAATATGAGAAAGAT 59.129 38.462 0.00 0.00 0.00 2.40
589 1208 5.163457 TGTGCTGTCCGATGTAATATGAGAA 60.163 40.000 0.00 0.00 0.00 2.87
590 1209 4.340950 TGTGCTGTCCGATGTAATATGAGA 59.659 41.667 0.00 0.00 0.00 3.27
2163 5320 1.742308 TGAAGGCTAGTGGGACCTTT 58.258 50.000 0.78 0.00 43.82 3.11


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

AutoCloner maintained by Alex Coulton.