Multiple sequence alignment - TraesCS6D01G356500

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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 TraesCS6D01G356500 chr6D 100.000 4496 0 0 1 4496 450647503 450651998 0.000000e+00 8303
1 TraesCS6D01G356500 chr6D 93.789 322 17 2 3727 4046 467774027 467774347 8.750000e-132 481
2 TraesCS6D01G356500 chr6A 97.558 3645 69 3 851 4495 596169084 596172708 0.000000e+00 6220
3 TraesCS6D01G356500 chr6A 92.416 356 17 6 3749 4103 613834827 613835173 2.410000e-137 499
4 TraesCS6D01G356500 chr6A 89.277 401 28 8 443 834 596168458 596168852 5.230000e-134 488
5 TraesCS6D01G356500 chr6A 82.949 434 32 14 1 433 596168020 596168412 1.990000e-93 353
6 TraesCS6D01G356500 chr6B 97.043 3652 94 6 846 4496 684410684 684414322 0.000000e+00 6133
7 TraesCS6D01G356500 chr6B 88.034 468 35 7 3727 4184 712994727 712995183 6.620000e-148 534
8 TraesCS6D01G356500 chr6B 85.057 435 62 3 1 432 684391806 684392240 1.480000e-119 440
9 TraesCS6D01G356500 chr7A 90.385 3172 268 24 452 3615 101218719 101221861 0.000000e+00 4133
10 TraesCS6D01G356500 chr7A 93.902 82 4 1 3614 3694 101221901 101221982 6.110000e-24 122
11 TraesCS6D01G356500 chr7D 92.662 2862 189 15 769 3615 98660473 98663328 0.000000e+00 4102
12 TraesCS6D01G356500 chr7D 93.902 82 4 1 3614 3694 98663368 98663449 6.110000e-24 122
13 TraesCS6D01G356500 chr7B 93.602 2407 152 1 1209 3615 54311087 54313491 0.000000e+00 3591
14 TraesCS6D01G356500 chr7B 78.120 1234 187 51 1 1218 54309963 54311129 0.000000e+00 706
15 TraesCS6D01G356500 chr7B 93.902 82 4 1 3614 3694 54313531 54313612 6.110000e-24 122
16 TraesCS6D01G356500 chrUn 94.236 399 23 0 2130 2528 478902044 478901646 1.070000e-170 610


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 TraesCS6D01G356500 chr6D 450647503 450651998 4495 False 8303.000000 8303 100.000000 1 4496 1 chr6D.!!$F1 4495
1 TraesCS6D01G356500 chr6A 596168020 596172708 4688 False 2353.666667 6220 89.928000 1 4495 3 chr6A.!!$F2 4494
2 TraesCS6D01G356500 chr6B 684410684 684414322 3638 False 6133.000000 6133 97.043000 846 4496 1 chr6B.!!$F2 3650
3 TraesCS6D01G356500 chr7A 101218719 101221982 3263 False 2127.500000 4133 92.143500 452 3694 2 chr7A.!!$F1 3242
4 TraesCS6D01G356500 chr7D 98660473 98663449 2976 False 2112.000000 4102 93.282000 769 3694 2 chr7D.!!$F1 2925
5 TraesCS6D01G356500 chr7B 54309963 54313612 3649 False 1473.000000 3591 88.541333 1 3694 3 chr7B.!!$F1 3693

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
218 219 0.249120 CCAGGTCGCCACTCATGTAA 59.751 55.000 0.00 0.0 0.00 2.41 F
236 237 0.630134 AACCTCTACGAGCCTACCCT 59.370 55.000 0.00 0.0 0.00 4.34 F
443 446 0.672401 TCGAAATTCGAGGCACACCC 60.672 55.000 14.59 0.0 44.82 4.61 F
591 632 0.673644 ATGAGCCCGTGAACGAAAGG 60.674 55.000 4.03 0.0 43.02 3.11 F
973 1256 1.225704 CCTCCTGCTCAATCCCACC 59.774 63.158 0.00 0.0 0.00 4.61 F
2374 2657 1.203237 AGGGTCTGACACCTGACAGAT 60.203 52.381 6.40 0.0 45.38 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1361 1644 2.685387 GATCTCGGCGTAGGTGGCAG 62.685 65.000 6.85 0.00 0.00 4.85 R
1777 2060 3.567585 GCTTTGTCTGCCTTCTTTTCTCT 59.432 43.478 0.00 0.00 0.00 3.10 R
2271 2554 5.413833 AGCATCCATAGCAATGTTATACAGC 59.586 40.000 0.00 0.00 0.00 4.40 R
2374 2657 5.523552 CCTTGATCACGCATGTATAGTGAAA 59.476 40.000 15.38 8.53 46.22 2.69 R
3493 3776 3.139397 TGCCTTTCCCTCAAGGTTTTCTA 59.861 43.478 1.56 0.00 44.84 2.10 R
3908 4235 4.992951 CCTGCAAAGAATTTCCTCTTTTGG 59.007 41.667 9.53 0.00 41.81 3.28 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
22 23 4.579869 AGACGTATCACCTTGAAAATGCT 58.420 39.130 0.00 0.00 0.00 3.79
48 49 5.357032 ACAAGAAGGAAACGACACTCAAAAT 59.643 36.000 0.00 0.00 0.00 1.82
51 52 4.813296 AGGAAACGACACTCAAAATCAC 57.187 40.909 0.00 0.00 0.00 3.06
93 94 2.036387 TGACCGGAGACAAGACTTTCA 58.964 47.619 9.46 0.00 0.00 2.69
149 150 0.389426 TCGAAAGCCTACCAACGAGC 60.389 55.000 0.00 0.00 0.00 5.03
197 198 0.688087 CCCTCCCACACCTACTCCTC 60.688 65.000 0.00 0.00 0.00 3.71
214 215 4.457496 CGCCAGGTCGCCACTCAT 62.457 66.667 0.00 0.00 0.00 2.90
215 216 2.821366 GCCAGGTCGCCACTCATG 60.821 66.667 0.00 0.00 0.00 3.07
218 219 0.249120 CCAGGTCGCCACTCATGTAA 59.751 55.000 0.00 0.00 0.00 2.41
222 223 1.641577 GTCGCCACTCATGTAACCTC 58.358 55.000 0.00 0.00 0.00 3.85
223 224 1.204941 GTCGCCACTCATGTAACCTCT 59.795 52.381 0.00 0.00 0.00 3.69
232 233 4.135306 CTCATGTAACCTCTACGAGCCTA 58.865 47.826 0.00 0.00 0.00 3.93
236 237 0.630134 AACCTCTACGAGCCTACCCT 59.370 55.000 0.00 0.00 0.00 4.34
294 296 1.740718 GCTCTCCCCAAACGACATCTC 60.741 57.143 0.00 0.00 0.00 2.75
312 314 0.690192 TCGGGGCTTGTCAAAGATGA 59.310 50.000 0.00 0.00 35.19 2.92
331 333 2.158652 TGACTAGGAGCTATGCGGTAGT 60.159 50.000 0.00 0.00 32.72 2.73
348 350 3.071206 TGAGAGGAGTCGGCCTGC 61.071 66.667 0.00 0.00 38.73 4.85
364 367 1.124839 CCTGCGCGAAAATTTGAAAGC 59.875 47.619 12.10 0.00 0.00 3.51
414 417 5.491070 CAATGAAGTCCATGGTCTGAGTTA 58.509 41.667 12.50 0.00 35.24 2.24
418 421 4.559862 AGTCCATGGTCTGAGTTAAAGG 57.440 45.455 12.58 0.00 0.00 3.11
424 427 3.256704 TGGTCTGAGTTAAAGGGGACAT 58.743 45.455 0.00 0.00 0.00 3.06
433 436 4.634443 AGTTAAAGGGGACATCGAAATTCG 59.366 41.667 9.38 9.38 42.10 3.34
443 446 0.672401 TCGAAATTCGAGGCACACCC 60.672 55.000 14.59 0.00 44.82 4.61
456 495 4.856801 CACCCCCTTCGCCGGATG 62.857 72.222 5.05 0.00 0.00 3.51
531 570 3.712187 TCCAAACGATTTCAACCAAAGC 58.288 40.909 0.00 0.00 0.00 3.51
541 580 4.481930 TTCAACCAAAGCGAACATGTAG 57.518 40.909 0.00 0.00 0.00 2.74
549 589 4.483476 AAGCGAACATGTAGGACAAAAC 57.517 40.909 0.00 0.00 0.00 2.43
586 627 2.223249 CCATTTTATGAGCCCGTGAACG 60.223 50.000 0.00 0.00 39.44 3.95
591 632 0.673644 ATGAGCCCGTGAACGAAAGG 60.674 55.000 4.03 0.00 43.02 3.11
600 642 2.668550 AACGAAAGGAGCACGCCC 60.669 61.111 0.00 0.00 0.00 6.13
688 734 2.988636 TGGATGAATTGGTGGTGGAA 57.011 45.000 0.00 0.00 0.00 3.53
689 735 3.251016 TGGATGAATTGGTGGTGGAAA 57.749 42.857 0.00 0.00 0.00 3.13
767 813 3.408851 GTGCCGTTCCGTTCCGTC 61.409 66.667 0.00 0.00 0.00 4.79
973 1256 1.225704 CCTCCTGCTCAATCCCACC 59.774 63.158 0.00 0.00 0.00 4.61
1638 1921 2.202892 GGAATCGTCCCGGCAGTC 60.203 66.667 0.00 0.00 38.08 3.51
1668 1951 6.088016 TGCAACATACTTCTCAAATTTGCT 57.912 33.333 13.54 0.00 39.07 3.91
1777 2060 7.874252 AGTCCTTATCACTAGGTCTCTCTTTA 58.126 38.462 0.00 0.00 34.29 1.85
2057 2340 3.008049 AGACAAGGGTTCACACCAGATAC 59.992 47.826 0.00 0.00 46.43 2.24
2374 2657 1.203237 AGGGTCTGACACCTGACAGAT 60.203 52.381 6.40 0.00 45.38 2.90
3219 3502 6.112734 TGTTCTTAGAACAAAGCAGAACAGA 58.887 36.000 23.50 0.00 45.28 3.41
3493 3776 8.520351 GTGTACTGGCCTTTTCTGTATTAAATT 58.480 33.333 3.32 0.00 0.00 1.82
3544 3827 2.284952 TGACATGTATGATTTCGCTGCG 59.715 45.455 17.25 17.25 0.00 5.18
3908 4235 2.034221 GTCCCAAGGCACTGGTCC 59.966 66.667 5.09 0.00 40.86 4.46
3926 4253 5.215845 TGGTCCCAAAAGAGGAAATTCTTT 58.784 37.500 0.00 0.00 46.50 2.52
3937 4264 5.833131 AGAGGAAATTCTTTGCAGGTTTGTA 59.167 36.000 0.00 0.00 32.92 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 17 5.298276 TGTCGTTTCCTTCTTGTTAGCATTT 59.702 36.000 0.00 0.00 0.00 2.32
22 23 5.013568 TGAGTGTCGTTTCCTTCTTGTTA 57.986 39.130 0.00 0.00 0.00 2.41
48 49 1.401905 CAGAGTCGACGATGATGGTGA 59.598 52.381 15.43 0.00 0.00 4.02
51 52 0.741326 ACCAGAGTCGACGATGATGG 59.259 55.000 20.38 19.75 0.00 3.51
93 94 0.916358 CTTGGGAGGTGGATCCAGGT 60.916 60.000 16.81 4.84 41.52 4.00
149 150 1.613437 GTCTGGATTTGGTTGTGGTGG 59.387 52.381 0.00 0.00 0.00 4.61
222 223 1.420891 AGGTAGAGGGTAGGCTCGTAG 59.579 57.143 0.00 0.00 0.00 3.51
223 224 1.419387 GAGGTAGAGGGTAGGCTCGTA 59.581 57.143 0.00 0.00 0.00 3.43
232 233 0.544595 AACAAGCGGAGGTAGAGGGT 60.545 55.000 0.00 0.00 37.06 4.34
236 237 1.134367 CGATCAACAAGCGGAGGTAGA 59.866 52.381 0.00 0.00 37.06 2.59
266 267 0.887387 TTTGGGGAGAGCGGTTTTCG 60.887 55.000 0.00 0.00 42.76 3.46
278 280 1.594833 CCGAGATGTCGTTTGGGGA 59.405 57.895 11.66 0.00 45.30 4.81
294 296 3.248043 TCATCTTTGACAAGCCCCG 57.752 52.632 0.00 0.00 0.00 5.73
312 314 2.158652 TCACTACCGCATAGCTCCTAGT 60.159 50.000 0.00 0.00 33.73 2.57
331 333 3.071206 GCAGGCCGACTCCTCTCA 61.071 66.667 0.00 0.00 33.25 3.27
348 350 1.404477 ACCGCTTTCAAATTTTCGCG 58.596 45.000 0.00 0.00 40.22 5.87
414 417 3.343941 TCGAATTTCGATGTCCCCTTT 57.656 42.857 17.08 0.00 44.82 3.11
440 443 3.988050 TACATCCGGCGAAGGGGGT 62.988 63.158 9.30 0.00 0.00 4.95
443 446 0.810031 CTTGTACATCCGGCGAAGGG 60.810 60.000 9.30 0.00 0.00 3.95
456 495 2.607187 CCTCGATGACACCACTTGTAC 58.393 52.381 0.00 0.00 39.17 2.90
486 525 3.425404 CAAGGCCGTGACGATTAAAATG 58.575 45.455 14.14 0.00 0.00 2.32
531 570 4.688879 TGCTAGTTTTGTCCTACATGTTCG 59.311 41.667 2.30 0.00 0.00 3.95
541 580 8.250332 TGGAATTTTATCATGCTAGTTTTGTCC 58.750 33.333 0.00 0.00 0.00 4.02
577 618 1.301401 TGCTCCTTTCGTTCACGGG 60.301 57.895 0.00 0.00 40.29 5.28
586 627 3.119096 GTCGGGCGTGCTCCTTTC 61.119 66.667 0.00 0.00 0.00 2.62
591 632 1.782028 AAAACTTGTCGGGCGTGCTC 61.782 55.000 0.00 0.00 0.00 4.26
600 642 5.509771 TCAATGATGACACAAAACTTGTCG 58.490 37.500 0.00 0.00 45.44 4.35
849 916 2.190578 CGATGGCCCAAGGAGGAC 59.809 66.667 0.00 0.00 41.22 3.85
1228 1511 4.851214 AGAGCTCCTCCTCCGGGC 62.851 72.222 10.93 0.00 32.17 6.13
1361 1644 2.685387 GATCTCGGCGTAGGTGGCAG 62.685 65.000 6.85 0.00 0.00 4.85
1638 1921 4.318332 TGAGAAGTATGTTGCAAGTCCAG 58.682 43.478 0.00 0.00 0.00 3.86
1668 1951 3.695606 GAGTCACCGCCCTCAGCA 61.696 66.667 0.00 0.00 44.04 4.41
1777 2060 3.567585 GCTTTGTCTGCCTTCTTTTCTCT 59.432 43.478 0.00 0.00 0.00 3.10
2057 2340 8.633561 TCCGAATGAGATAGCTATAACCATATG 58.366 37.037 6.13 0.00 0.00 1.78
2271 2554 5.413833 AGCATCCATAGCAATGTTATACAGC 59.586 40.000 0.00 0.00 0.00 4.40
2374 2657 5.523552 CCTTGATCACGCATGTATAGTGAAA 59.476 40.000 15.38 8.53 46.22 2.69
3493 3776 3.139397 TGCCTTTCCCTCAAGGTTTTCTA 59.861 43.478 1.56 0.00 44.84 2.10
3544 3827 6.513180 TGACGAGATTTCAGTGGATATAACC 58.487 40.000 0.00 0.00 0.00 2.85
3697 4024 6.654582 TGTATAAAGAAGATGTCTGCAAAGCA 59.345 34.615 0.00 0.00 36.40 3.91
3908 4235 4.992951 CCTGCAAAGAATTTCCTCTTTTGG 59.007 41.667 9.53 0.00 41.81 3.28
3926 4253 5.561679 TGGTACATGTATTACAAACCTGCA 58.438 37.500 9.18 0.00 33.35 4.41
4160 4487 7.547370 TGGGAAAAACAAACTTCTGTAACAATG 59.453 33.333 0.00 0.00 0.00 2.82


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

AutoCloner maintained by Alex Coulton.