Multiple sequence alignment - TraesCS5D01G132000

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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 TraesCS5D01G132000 chr5D 100.000 3819 0 0 1 3819 209646522 209642704 0.000000e+00 7053.0
1 TraesCS5D01G132000 chr5D 100.000 541 0 0 4165 4705 209642358 209641818 0.000000e+00 1000.0
2 TraesCS5D01G132000 chr5B 97.595 3825 79 9 1 3819 223127739 223123922 0.000000e+00 6541.0
3 TraesCS5D01G132000 chr5B 92.698 315 15 7 4398 4705 223121918 223121605 9.290000e-122 448.0
4 TraesCS5D01G132000 chr5B 97.166 247 6 1 4165 4411 223123857 223123612 2.620000e-112 416.0
5 TraesCS5D01G132000 chr5B 94.737 38 2 0 295 332 96189760 96189797 5.080000e-05 60.2
6 TraesCS5D01G132000 chr5B 97.059 34 1 0 623 656 397957741 397957708 1.830000e-04 58.4
7 TraesCS5D01G132000 chr5A 97.799 3181 53 8 651 3819 271050733 271047558 0.000000e+00 5470.0
8 TraesCS5D01G132000 chr5A 94.455 541 22 3 4165 4705 271047119 271046587 0.000000e+00 826.0
9 TraesCS5D01G132000 chr5A 94.667 300 10 3 1 296 271051031 271050734 1.190000e-125 460.0
10 TraesCS5D01G132000 chr5A 74.336 226 39 13 1431 1654 51555520 51555312 1.400000e-10 78.7
11 TraesCS5D01G132000 chr5A 84.286 70 8 3 1436 1504 461484151 461484084 1.090000e-06 65.8
12 TraesCS5D01G132000 chr2B 91.060 302 24 1 301 599 583920987 583921288 5.670000e-109 405.0
13 TraesCS5D01G132000 chr6A 86.603 209 24 4 454 659 595770552 595770345 1.320000e-55 228.0
14 TraesCS5D01G132000 chr6A 93.182 44 3 0 280 323 105025822 105025779 1.090000e-06 65.8
15 TraesCS5D01G132000 chr7B 86.022 93 7 4 295 384 647817865 647817776 1.390000e-15 95.3
16 TraesCS5D01G132000 chr7B 83.871 93 9 4 295 384 647818290 647818201 3.020000e-12 84.2
17 TraesCS5D01G132000 chr7B 86.441 59 4 3 295 351 710343274 710343218 1.410000e-05 62.1
18 TraesCS5D01G132000 chr7B 92.105 38 3 0 614 651 647817828 647817865 2.000000e-03 54.7
19 TraesCS5D01G132000 chr7B 92.105 38 3 0 614 651 647818253 647818290 2.000000e-03 54.7
20 TraesCS5D01G132000 chr2A 97.297 37 1 0 295 331 450160666 450160630 3.930000e-06 63.9
21 TraesCS5D01G132000 chr3A 93.023 43 1 2 295 335 650033608 650033650 1.410000e-05 62.1
22 TraesCS5D01G132000 chr7D 82.090 67 10 2 586 651 428730230 428730165 6.580000e-04 56.5
23 TraesCS5D01G132000 chr4B 94.595 37 1 1 623 658 183813084 183813120 6.580000e-04 56.5
24 TraesCS5D01G132000 chrUn 92.105 38 3 0 614 651 254814473 254814436 2.000000e-03 54.7
25 TraesCS5D01G132000 chr2D 81.429 70 9 2 584 651 611482267 611482334 2.000000e-03 54.7


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 TraesCS5D01G132000 chr5D 209641818 209646522 4704 True 4026.500000 7053 100.000000 1 4705 2 chr5D.!!$R1 4704
1 TraesCS5D01G132000 chr5B 223121605 223127739 6134 True 2468.333333 6541 95.819667 1 4705 3 chr5B.!!$R2 4704
2 TraesCS5D01G132000 chr5A 271046587 271051031 4444 True 2252.000000 5470 95.640333 1 4705 3 chr5A.!!$R3 4704

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
573 578 0.323302 TTGAACGCATAGCCAGTGGA 59.677 50.0 15.2 0.0 0.0 4.02 F
574 579 0.323302 TGAACGCATAGCCAGTGGAA 59.677 50.0 15.2 0.0 0.0 3.53 F
1107 1116 2.036475 TCGCAGAGGGAAATCTCATAGC 59.964 50.0 0.0 0.0 36.3 2.97 F
2601 2619 2.409948 ACTAGTGCTGCCATTCTTCC 57.590 50.0 0.0 0.0 0.0 3.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2504 2522 1.605968 GCATTTGCTGTGGTGCATTCA 60.606 47.619 0.0 0.0 42.96 2.57 R
2579 2597 4.164988 AGGAAGAATGGCAGCACTAGTTAT 59.835 41.667 0.0 0.0 0.00 1.89 R
3026 3044 3.074538 ACCTACAGCTTGTTTTCCCTGAT 59.925 43.478 0.0 0.0 0.00 2.90 R
4314 4425 0.250467 TGCTGAGACAAGGCAAGACC 60.250 55.000 0.0 0.0 39.61 3.85 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
230 235 1.771565 CTGGTGCATCATGGTGGAAT 58.228 50.000 8.33 0.0 0.00 3.01
239 244 3.497103 TCATGGTGGAATGGCATAGAG 57.503 47.619 0.00 0.0 0.00 2.43
303 308 5.902431 GGATGGATTGCTATATACTCCCTCT 59.098 44.000 0.00 0.0 0.00 3.69
383 388 0.451783 ATGGCGTTTGATTTCCGAGC 59.548 50.000 0.00 0.0 0.00 5.03
403 408 0.749454 GGGGCAGCAACGAATCAGAT 60.749 55.000 0.00 0.0 0.00 2.90
467 472 1.656429 CGTATTTAGCCAATCACGCGC 60.656 52.381 5.73 0.0 0.00 6.86
534 539 1.672881 GCCTCTTCGCATGCAACTAAT 59.327 47.619 19.57 0.0 0.00 1.73
573 578 0.323302 TTGAACGCATAGCCAGTGGA 59.677 50.000 15.20 0.0 0.00 4.02
574 579 0.323302 TGAACGCATAGCCAGTGGAA 59.677 50.000 15.20 0.0 0.00 3.53
608 613 4.279922 GGGGCCTTATAAAAACATATGCGT 59.720 41.667 0.84 0.0 0.00 5.24
616 621 9.864034 CTTATAAAAACATATGCGTCTAGTTGG 57.136 33.333 1.58 0.0 0.00 3.77
999 1008 6.761099 TTACTGTGCTTGTTTTTGGAGTAA 57.239 33.333 0.00 0.0 0.00 2.24
1107 1116 2.036475 TCGCAGAGGGAAATCTCATAGC 59.964 50.000 0.00 0.0 36.30 2.97
1648 1660 6.564328 AGCTTGACTTAGGAACAAAACAAAG 58.436 36.000 0.00 0.0 0.00 2.77
1811 1823 5.780984 AGTCTACACAAACTTACTACCTGC 58.219 41.667 0.00 0.0 0.00 4.85
1930 1948 5.970317 TGTGAAGAATGCAAGATCACAAT 57.030 34.783 19.30 0.0 45.17 2.71
2486 2504 7.041030 TGTCTAGTCTTGAAGTCAACTCTGTAG 60.041 40.741 0.00 0.0 0.00 2.74
2504 2522 8.317679 ACTCTGTAGAAGTGAATTTGCTAGATT 58.682 33.333 0.00 0.0 0.00 2.40
2601 2619 2.409948 ACTAGTGCTGCCATTCTTCC 57.590 50.000 0.00 0.0 0.00 3.46
3042 3060 3.565307 TCACAATCAGGGAAAACAAGCT 58.435 40.909 0.00 0.0 0.00 3.74
3161 3179 1.471676 CCTAGGCGGATGAACTGTGTC 60.472 57.143 0.00 0.0 33.16 3.67
3218 3236 0.677731 GCACTGTTCTATGCCAGCCA 60.678 55.000 0.00 0.0 35.73 4.75
3271 3289 2.592102 TTTGGCAGCATCTCCTTCTT 57.408 45.000 0.00 0.0 0.00 2.52
3539 3557 4.329545 GCTGAAGCACCGACCCCA 62.330 66.667 0.00 0.0 41.59 4.96
3638 3656 2.432874 CACAATGGACTACCGATACCCA 59.567 50.000 0.00 0.0 39.42 4.51
3777 3795 3.625897 CTGGGACCGCCACAGTGA 61.626 66.667 0.62 0.0 35.15 3.41
4207 4318 5.613358 TTTAACAGCTTGCTTTCTAGAGC 57.387 39.130 0.00 0.0 43.00 4.09
4213 4324 2.415224 GCTTGCTTTCTAGAGCCTTTGC 60.415 50.000 1.83 0.0 42.01 3.68
4270 4381 2.954989 TGATACTTTGCTTGTGTTGCCA 59.045 40.909 0.00 0.0 0.00 4.92
4314 4425 8.901748 CATCTGTGGTTAAGTTACAAATTTTCG 58.098 33.333 0.00 0.0 0.00 3.46
4315 4426 7.419204 TCTGTGGTTAAGTTACAAATTTTCGG 58.581 34.615 0.00 0.0 0.00 4.30
4359 4470 4.775236 AGCCTATCAGTTTGAAGGATCAC 58.225 43.478 0.00 0.0 34.61 3.06
4476 6296 1.660560 GACGGCCGCCAGAACTACTA 61.661 60.000 28.58 0.0 0.00 1.82
4664 6490 1.628846 AGATTGTGCTACCCGAGGTTT 59.371 47.619 0.72 0.0 37.09 3.27
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
103 107 5.066505 CCATCTTAACACAGGGCATAAGAAC 59.933 44.000 3.32 0.00 37.76 3.01
230 235 1.271856 TTCGTCCAACCTCTATGCCA 58.728 50.000 0.00 0.00 0.00 4.92
303 308 1.000646 GGCCCAATAAACCCGGACA 60.001 57.895 0.73 0.00 0.00 4.02
383 388 2.745884 TGATTCGTTGCTGCCCCG 60.746 61.111 0.00 0.00 0.00 5.73
395 400 8.677300 TGCCATGACTACTTTAAAATCTGATTC 58.323 33.333 2.92 0.00 0.00 2.52
403 408 5.622007 GCTGCATGCCATGACTACTTTAAAA 60.622 40.000 16.68 0.00 35.15 1.52
428 433 1.937546 GAAGGGGAAATGTGCAGCCG 61.938 60.000 0.00 0.00 0.00 5.52
467 472 1.999051 CTGCTAGCGCTAAACGTGG 59.001 57.895 19.37 6.67 46.11 4.94
534 539 4.580995 TCAATTGGTTAGGTTTTCTCGCAA 59.419 37.500 5.42 0.00 0.00 4.85
544 549 3.377172 GCTATGCGTTCAATTGGTTAGGT 59.623 43.478 5.42 0.00 0.00 3.08
545 550 3.243068 GGCTATGCGTTCAATTGGTTAGG 60.243 47.826 5.42 0.00 0.00 2.69
573 578 3.178611 GGCCCCCTCGATCCCATT 61.179 66.667 0.00 0.00 0.00 3.16
574 579 2.340909 TAAGGCCCCCTCGATCCCAT 62.341 60.000 0.00 0.00 30.89 4.00
608 613 2.978824 GCCCACGAGCCAACTAGA 59.021 61.111 0.00 0.00 0.00 2.43
616 621 1.663379 GGTTTATTGGGCCCACGAGC 61.663 60.000 28.70 16.28 0.00 5.03
999 1008 3.666902 GCACAATGCTACGAAACGACATT 60.667 43.478 0.00 0.00 40.96 2.71
1048 1057 5.046529 CACATCAAACCCTCTTCGAGATAG 58.953 45.833 0.00 0.00 0.00 2.08
1068 1077 1.881925 CGATGGCCAAGAAACCTCACA 60.882 52.381 10.96 0.00 0.00 3.58
1525 1534 8.251026 ACATATTTTCAGAGTGTATTGACTCGA 58.749 33.333 0.00 0.00 46.04 4.04
1648 1660 2.167075 CCATCCCAAAATGCAAGTCCTC 59.833 50.000 0.00 0.00 0.00 3.71
1873 1885 2.559668 CTGCAGATGAAGGCAAAGGAAA 59.440 45.455 8.42 0.00 39.93 3.13
1930 1948 6.701145 TGGTTGTTACAGTAAAAAGCATGA 57.299 33.333 19.93 2.78 38.17 3.07
2486 2504 7.008992 GTGCATTCAATCTAGCAAATTCACTTC 59.991 37.037 0.00 0.00 38.91 3.01
2504 2522 1.605968 GCATTTGCTGTGGTGCATTCA 60.606 47.619 0.00 0.00 42.96 2.57
2579 2597 4.164988 AGGAAGAATGGCAGCACTAGTTAT 59.835 41.667 0.00 0.00 0.00 1.89
2601 2619 4.191544 TGAGAACAAGTTGACAACTGGAG 58.808 43.478 26.29 18.34 41.91 3.86
2883 2901 4.160642 AGGAAACTGATGCAGCATATCA 57.839 40.909 8.22 2.87 41.13 2.15
2886 2904 4.142622 CGAAAAGGAAACTGATGCAGCATA 60.143 41.667 8.22 0.00 42.68 3.14
2898 2916 3.975035 GCACAATCAGACGAAAAGGAAAC 59.025 43.478 0.00 0.00 0.00 2.78
3026 3044 3.074538 ACCTACAGCTTGTTTTCCCTGAT 59.925 43.478 0.00 0.00 0.00 2.90
3042 3060 4.748701 ACCTTCCTTGAGTAGAACCTACA 58.251 43.478 6.86 0.00 0.00 2.74
3161 3179 2.171237 TGAGGCAGGTATGGAGTTCATG 59.829 50.000 0.00 0.00 37.30 3.07
3218 3236 0.250467 AATGAGCAACGGCACTGTCT 60.250 50.000 0.00 0.00 44.61 3.41
3777 3795 9.520515 AGTTAAAAGACCATGAACAATAGACAT 57.479 29.630 0.00 0.00 0.00 3.06
4207 4318 6.374333 TGCTAGTTATTACAGAAAGGCAAAGG 59.626 38.462 0.00 0.00 0.00 3.11
4213 4324 9.871238 TTAAGTCTGCTAGTTATTACAGAAAGG 57.129 33.333 0.00 0.00 40.61 3.11
4270 4381 7.046652 CACAGATGAATATGTGGAACTCTTCT 58.953 38.462 9.66 0.00 44.02 2.85
4314 4425 0.250467 TGCTGAGACAAGGCAAGACC 60.250 55.000 0.00 0.00 39.61 3.85
4315 4426 1.597742 TTGCTGAGACAAGGCAAGAC 58.402 50.000 0.00 0.00 40.38 3.01
4359 4470 2.556189 TGTTCCAACGATTCACCATTGG 59.444 45.455 0.00 0.00 42.55 3.16
4476 6296 3.360867 TCACCAGAACCAATGTTGTTGT 58.639 40.909 0.00 0.00 33.97 3.32
4518 6338 3.521765 TTGGCCGCAACCTCCCATT 62.522 57.895 0.00 0.00 0.00 3.16
4596 6421 4.193334 CCAGAGTCGATCGCGCCA 62.193 66.667 11.09 0.00 37.46 5.69
4648 6473 0.250124 CACAAACCTCGGGTAGCACA 60.250 55.000 0.00 0.00 33.12 4.57
4664 6490 4.143543 TCATTCTCATTGCAGGAAACACA 58.856 39.130 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.