Multiple sequence alignment - TraesCS7A01G033900

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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 TraesCS7A01G033900 chr7A 100.000 3245 0 0 1 3245 14850272 14847028 0.000000e+00 5993
1 TraesCS7A01G033900 chr3D 96.922 3249 79 6 1 3245 584858018 584861249 0.000000e+00 5426
2 TraesCS7A01G033900 chr7D 96.831 3250 80 8 1 3245 15937480 15934249 0.000000e+00 5409
3 TraesCS7A01G033900 chr7D 94.249 539 28 3 2 538 16025314 16024777 0.000000e+00 821
4 TraesCS7A01G033900 chr7D 93.878 539 30 3 2 538 15943944 15943407 0.000000e+00 809
5 TraesCS7A01G033900 chr4A 95.288 3247 123 10 1 3245 719010667 719013885 0.000000e+00 5121
6 TraesCS7A01G033900 chr7B 85.343 1269 164 17 817 2078 711420454 711419201 0.000000e+00 1293
7 TraesCS7A01G033900 chr7B 84.115 384 48 6 1 375 711422575 711422196 3.080000e-95 359
8 TraesCS7A01G033900 chrUn 93.878 539 30 3 2 538 278082615 278082078 0.000000e+00 809
9 TraesCS7A01G033900 chrUn 93.878 539 30 3 2 538 279817731 279818268 0.000000e+00 809


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 TraesCS7A01G033900 chr7A 14847028 14850272 3244 True 5993 5993 100.000 1 3245 1 chr7A.!!$R1 3244
1 TraesCS7A01G033900 chr3D 584858018 584861249 3231 False 5426 5426 96.922 1 3245 1 chr3D.!!$F1 3244
2 TraesCS7A01G033900 chr7D 15934249 15937480 3231 True 5409 5409 96.831 1 3245 1 chr7D.!!$R1 3244
3 TraesCS7A01G033900 chr7D 16024777 16025314 537 True 821 821 94.249 2 538 1 chr7D.!!$R3 536
4 TraesCS7A01G033900 chr7D 15943407 15943944 537 True 809 809 93.878 2 538 1 chr7D.!!$R2 536
5 TraesCS7A01G033900 chr4A 719010667 719013885 3218 False 5121 5121 95.288 1 3245 1 chr4A.!!$F1 3244
6 TraesCS7A01G033900 chr7B 711419201 711422575 3374 True 826 1293 84.729 1 2078 2 chr7B.!!$R1 2077
7 TraesCS7A01G033900 chrUn 278082078 278082615 537 True 809 809 93.878 2 538 1 chrUn.!!$R1 536
8 TraesCS7A01G033900 chrUn 279817731 279818268 537 False 809 809 93.878 2 538 1 chrUn.!!$F1 536

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
281 291 3.499918 CCCTCGATGACATGATTTAAGCC 59.500 47.826 0.00 0.00 0.00 4.35 F
1880 3288 0.179004 ACGGTTGACCATTGGAGCAA 60.179 50.000 10.37 10.33 35.14 3.91 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2091 3499 0.171455 CCAGCTCGTGTACTCTCCAC 59.829 60.000 0.0 0.0 0.00 4.02 R
2782 4193 1.892474 GCCTGTAATGGTTTGCTTCCA 59.108 47.619 0.0 0.0 39.41 3.53 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
157 160 5.464168 GCTGAACTGTATGTTTTCTGCAAT 58.536 37.500 7.34 0.00 41.37 3.56
281 291 3.499918 CCCTCGATGACATGATTTAAGCC 59.500 47.826 0.00 0.00 0.00 4.35
282 292 3.499918 CCTCGATGACATGATTTAAGCCC 59.500 47.826 0.00 0.00 0.00 5.19
749 1121 8.348285 TGGATAAGTCTCAAGTTTTAATTGGG 57.652 34.615 0.00 0.00 0.00 4.12
1092 2496 1.408340 CCAGATGGTTTGTTGCACACA 59.592 47.619 0.00 0.00 0.00 3.72
1327 2731 5.221501 CCATCCAACCAAAACATCACTCTTT 60.222 40.000 0.00 0.00 0.00 2.52
1335 2739 1.985473 ACATCACTCTTTGCTGCCAA 58.015 45.000 0.00 0.00 0.00 4.52
1403 2807 7.865820 TCCTATGGTCATCTCATCTTCTTTTT 58.134 34.615 0.00 0.00 0.00 1.94
1416 2820 5.492855 TCTTCTTTTTCTCCCGTGGATAA 57.507 39.130 0.00 0.00 0.00 1.75
1463 2867 0.631753 TCCAAAGTTTCACCCCCACA 59.368 50.000 0.00 0.00 0.00 4.17
1612 3019 2.025155 TGGGCACTCGATTCTCTCTAC 58.975 52.381 0.00 0.00 0.00 2.59
1663 3070 5.126779 GGTCAGAACTCAAACTTCCTTCTT 58.873 41.667 0.00 0.00 0.00 2.52
1671 3078 3.378112 TCAAACTTCCTTCTTGTGCACAG 59.622 43.478 20.59 14.08 0.00 3.66
1880 3288 0.179004 ACGGTTGACCATTGGAGCAA 60.179 50.000 10.37 10.33 35.14 3.91
2006 3414 2.928334 AGCCTTTGCAGGATGTGATAG 58.072 47.619 0.00 0.00 44.19 2.08
2091 3499 2.182030 GCCGAGAGTTCTCCACCG 59.818 66.667 3.67 0.80 39.79 4.94
2132 3540 2.484062 GCGCACATGATCCTTGGGG 61.484 63.158 0.30 0.00 0.00 4.96
2358 3766 3.129287 CACTCAAGCCTTCAAAAGTGTGT 59.871 43.478 0.00 0.00 31.69 3.72
2396 3804 2.953466 ATGTTGCACTGGATGAATGC 57.047 45.000 0.00 0.00 39.88 3.56
2484 3895 5.313520 TGGTATTCATGCATGTGTTTGAG 57.686 39.130 25.43 0.00 0.00 3.02
2496 3907 4.764679 TGTGTTTGAGCTATCGCATTTT 57.235 36.364 0.00 0.00 39.10 1.82
2524 3935 8.557864 CCTTACAAGATGTGATTTGATCATCTC 58.442 37.037 0.00 0.00 44.70 2.75
2526 3937 7.789273 ACAAGATGTGATTTGATCATCTCTC 57.211 36.000 0.00 0.00 44.70 3.20
2590 4001 1.554617 TGCTCTAGCTGGTAATGCACA 59.445 47.619 0.00 0.00 42.66 4.57
2596 4007 1.073763 AGCTGGTAATGCACACCTTCA 59.926 47.619 17.76 0.48 36.96 3.02
2609 4020 3.930229 CACACCTTCATTGCCAATTGATG 59.070 43.478 7.12 3.07 0.00 3.07
2632 4043 4.736464 GCCAGTGGTTTTTGTTCTACTTGG 60.736 45.833 11.74 0.00 0.00 3.61
2664 4075 6.701400 ACAACTTCATGCAAAAGAATGTAACC 59.299 34.615 16.58 0.00 30.96 2.85
2665 4076 6.403866 ACTTCATGCAAAAGAATGTAACCA 57.596 33.333 16.58 0.00 0.00 3.67
2672 4083 6.757237 TGCAAAAGAATGTAACCACATGATT 58.243 32.000 0.00 0.00 44.83 2.57
2690 4101 5.484173 TGATTTGGTTGCGATTATCTGTC 57.516 39.130 0.00 0.00 0.00 3.51
2696 4107 2.939103 GTTGCGATTATCTGTCAGGCTT 59.061 45.455 0.00 0.00 0.00 4.35
2705 4116 7.116948 CGATTATCTGTCAGGCTTGGTTATAAG 59.883 40.741 0.00 0.00 0.00 1.73
2741 4152 3.157087 GGTCACATTGGTTGACCTCAAT 58.843 45.455 15.70 0.00 46.22 2.57
2742 4153 3.191371 GGTCACATTGGTTGACCTCAATC 59.809 47.826 15.70 0.00 46.22 2.67
2777 4188 5.957842 ATTTCTGAAGTCAAACGCCAATA 57.042 34.783 0.00 0.00 0.00 1.90
2778 4189 5.957842 TTTCTGAAGTCAAACGCCAATAT 57.042 34.783 0.00 0.00 0.00 1.28
2779 4190 5.957842 TTCTGAAGTCAAACGCCAATATT 57.042 34.783 0.00 0.00 0.00 1.28
2780 4191 7.441890 TTTCTGAAGTCAAACGCCAATATTA 57.558 32.000 0.00 0.00 0.00 0.98
2781 4192 7.441890 TTCTGAAGTCAAACGCCAATATTAA 57.558 32.000 0.00 0.00 0.00 1.40
2782 4193 7.624360 TCTGAAGTCAAACGCCAATATTAAT 57.376 32.000 0.00 0.00 0.00 1.40
2824 4235 5.127682 GGCATGATACCTTGTTCCTTCATTT 59.872 40.000 0.00 0.00 0.00 2.32
2836 4247 7.536895 TGTTCCTTCATTTTGTTGAACAATG 57.463 32.000 11.97 8.35 39.12 2.82
3023 4434 3.041211 AGCCTATAGACCATGTTCAGCA 58.959 45.455 0.00 0.00 0.00 4.41
3024 4435 3.455910 AGCCTATAGACCATGTTCAGCAA 59.544 43.478 0.00 0.00 0.00 3.91
3025 4436 4.103785 AGCCTATAGACCATGTTCAGCAAT 59.896 41.667 0.00 0.00 0.00 3.56
3026 4437 4.453819 GCCTATAGACCATGTTCAGCAATC 59.546 45.833 0.00 0.00 0.00 2.67
3027 4438 5.614308 CCTATAGACCATGTTCAGCAATCA 58.386 41.667 0.00 0.00 0.00 2.57
3028 4439 5.699915 CCTATAGACCATGTTCAGCAATCAG 59.300 44.000 0.00 0.00 0.00 2.90
3029 4440 2.089980 AGACCATGTTCAGCAATCAGC 58.910 47.619 0.00 0.00 46.19 4.26
3062 4473 7.308770 CCAGAAAACTGAAGCTAATGACAATGA 60.309 37.037 0.00 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
157 160 3.963374 TGTCTCCCGCTAGTCTAGTAGTA 59.037 47.826 8.68 0.00 0.00 1.82
265 275 4.613437 AGTTGGGGCTTAAATCATGTCAT 58.387 39.130 0.00 0.00 0.00 3.06
281 291 6.538742 CCGTTAATATATGGCAGATAGTTGGG 59.461 42.308 7.43 3.66 0.00 4.12
282 292 7.103641 ACCGTTAATATATGGCAGATAGTTGG 58.896 38.462 7.43 9.75 0.00 3.77
749 1121 2.514824 GCGAATGTCTCAGGCCCC 60.515 66.667 0.00 0.00 0.00 5.80
1241 2645 0.247736 AGATGGAACGTGAGGAGCAC 59.752 55.000 0.00 0.00 44.21 4.40
1327 2731 4.603989 TTTCTTCATCAATTTGGCAGCA 57.396 36.364 0.00 0.00 0.00 4.41
1403 2807 3.104512 ACAAGACATTATCCACGGGAGA 58.895 45.455 0.00 0.00 34.05 3.71
1416 2820 4.277476 TGAAAGGGTCAACAACAAGACAT 58.723 39.130 0.00 0.00 36.50 3.06
1481 2888 1.034292 GGTAGGACTAACCCGCTCGT 61.034 60.000 0.00 0.00 40.05 4.18
1612 3019 1.067354 GCTTCCAACTGGCCAATCAAG 60.067 52.381 7.01 6.07 34.44 3.02
1663 3070 4.152223 CACGATTTGAGTTATCTGTGCACA 59.848 41.667 20.37 20.37 0.00 4.57
1671 3078 7.189512 CCTTGAATTCCACGATTTGAGTTATC 58.810 38.462 2.27 0.00 0.00 1.75
1880 3288 7.830201 TCAAAATACCACCATCCTTAATACGTT 59.170 33.333 0.00 0.00 0.00 3.99
2006 3414 9.453572 TCATATTAGATAATGGCATGTTCTTCC 57.546 33.333 15.19 0.00 0.00 3.46
2091 3499 0.171455 CCAGCTCGTGTACTCTCCAC 59.829 60.000 0.00 0.00 0.00 4.02
2132 3540 2.437359 ACTGCCTGATGGAAGCGC 60.437 61.111 0.00 0.00 43.11 5.92
2334 3742 1.334869 ACTTTTGAAGGCTTGAGTGCG 59.665 47.619 3.46 0.00 0.00 5.34
2426 3837 0.528249 AGCAGTTGCCGCAAAACAAG 60.528 50.000 7.54 0.00 43.38 3.16
2427 3838 0.741326 TAGCAGTTGCCGCAAAACAA 59.259 45.000 7.54 0.00 43.38 2.83
2428 3839 0.741326 TTAGCAGTTGCCGCAAAACA 59.259 45.000 7.54 0.00 43.38 2.83
2496 3907 5.945191 TGATCAAATCACATCTTGTAAGGCA 59.055 36.000 0.00 0.00 33.59 4.75
2512 3923 7.400439 TCAAAGGTTCTGAGAGATGATCAAAT 58.600 34.615 0.00 0.00 0.00 2.32
2524 3935 9.775854 ATAATATCACATCTCAAAGGTTCTGAG 57.224 33.333 0.00 0.00 41.47 3.35
2590 4001 3.255969 GCATCAATTGGCAATGAAGGT 57.744 42.857 14.47 0.34 0.00 3.50
2609 4020 4.359706 CAAGTAGAACAAAAACCACTGGC 58.640 43.478 0.00 0.00 0.00 4.85
2664 4075 5.684184 CAGATAATCGCAACCAAATCATGTG 59.316 40.000 0.00 0.00 0.00 3.21
2665 4076 5.357878 ACAGATAATCGCAACCAAATCATGT 59.642 36.000 0.00 0.00 0.00 3.21
2672 4083 3.270027 CCTGACAGATAATCGCAACCAA 58.730 45.455 3.32 0.00 0.00 3.67
2690 4101 8.556213 TTAACAGTTACTTATAACCAAGCCTG 57.444 34.615 0.00 0.00 41.54 4.85
2705 4116 7.443272 ACCAATGTGACCTAACTTAACAGTTAC 59.557 37.037 0.00 0.00 41.81 2.50
2741 4152 8.208224 TGACTTCAGAAATTACTGTTACCTTGA 58.792 33.333 0.00 0.00 38.79 3.02
2742 4153 8.378172 TGACTTCAGAAATTACTGTTACCTTG 57.622 34.615 0.00 0.00 38.79 3.61
2751 4162 4.819630 TGGCGTTTGACTTCAGAAATTACT 59.180 37.500 0.00 0.00 0.00 2.24
2781 4192 2.497273 GCCTGTAATGGTTTGCTTCCAT 59.503 45.455 2.89 2.89 46.20 3.41
2782 4193 1.892474 GCCTGTAATGGTTTGCTTCCA 59.108 47.619 0.00 0.00 39.41 3.53
2824 4235 4.828939 AGAGGCATCTTCATTGTTCAACAA 59.171 37.500 5.18 5.18 35.80 2.83
2836 4247 7.467131 GCTCAATTTCTTAAGAGAGGCATCTTC 60.467 40.741 16.83 0.00 40.08 2.87
3023 4434 4.037208 CAGTTTTCTGGTTCAGTGCTGATT 59.963 41.667 2.47 0.00 43.61 2.57
3024 4435 3.567164 CAGTTTTCTGGTTCAGTGCTGAT 59.433 43.478 2.47 0.00 43.61 2.90
3025 4436 2.945008 CAGTTTTCTGGTTCAGTGCTGA 59.055 45.455 0.00 0.00 43.61 4.26
3026 4437 2.945008 TCAGTTTTCTGGTTCAGTGCTG 59.055 45.455 0.00 0.00 46.94 4.41
3027 4438 3.281727 TCAGTTTTCTGGTTCAGTGCT 57.718 42.857 0.00 0.00 46.94 4.40
3028 4439 3.793465 GCTTCAGTTTTCTGGTTCAGTGC 60.793 47.826 0.00 0.00 46.94 4.40
3029 4440 3.629398 AGCTTCAGTTTTCTGGTTCAGTG 59.371 43.478 0.00 0.00 46.94 3.66
3062 4473 5.157940 ACACTTGTGCTGAGACTTGATAT 57.842 39.130 0.10 0.00 0.00 1.63


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

AutoCloner maintained by Alex Coulton.