Multiple sequence alignment - TraesCS7A01G467300

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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 TraesCS7A01G467300 chr7A 100.000 3065 0 0 1 3065 663605756 663602692 0.000000e+00 5661.0
1 TraesCS7A01G467300 chr4D 90.981 1907 93 26 827 2694 6462835 6460969 0.000000e+00 2495.0
2 TraesCS7A01G467300 chr4D 95.533 291 11 2 2692 2980 6460925 6460635 5.990000e-127 464.0
3 TraesCS7A01G467300 chr4D 97.500 80 2 0 720 799 6462977 6462898 1.480000e-28 137.0
4 TraesCS7A01G467300 chr4D 93.671 79 5 0 2987 3065 6460547 6460469 5.370000e-23 119.0
5 TraesCS7A01G467300 chr4B 90.731 1888 96 24 827 2674 26336881 26335033 0.000000e+00 2444.0
6 TraesCS7A01G467300 chr4B 94.928 276 10 4 2707 2980 26335034 26334761 2.180000e-116 429.0
7 TraesCS7A01G467300 chr4B 92.593 81 4 1 2987 3065 26334673 26334593 6.940000e-22 115.0
8 TraesCS7A01G467300 chr4B 90.698 86 2 2 720 799 26337039 26336954 3.230000e-20 110.0
9 TraesCS7A01G467300 chr7D 96.411 1421 21 5 812 2231 574290973 574289582 0.000000e+00 2314.0
10 TraesCS7A01G467300 chr7D 92.883 815 28 8 2 789 574291872 574291061 0.000000e+00 1157.0
11 TraesCS7A01G467300 chr7D 95.349 473 14 2 2229 2693 574289501 574289029 0.000000e+00 745.0
12 TraesCS7A01G467300 chr7D 98.270 289 3 2 2692 2980 574288984 574288698 3.530000e-139 505.0
13 TraesCS7A01G467300 chr7D 91.123 383 13 4 2 364 574295837 574295456 1.640000e-137 499.0
14 TraesCS7A01G467300 chr7D 100.000 79 0 0 2987 3065 574288608 574288530 2.460000e-31 147.0
15 TraesCS7A01G467300 chrUn 96.500 1400 27 6 812 2198 289618866 289620256 0.000000e+00 2294.0
16 TraesCS7A01G467300 chrUn 96.500 1400 27 6 812 2198 299516412 299515022 0.000000e+00 2294.0
17 TraesCS7A01G467300 chrUn 92.922 551 22 11 264 799 289618263 289618811 0.000000e+00 785.0
18 TraesCS7A01G467300 chrUn 92.922 551 22 11 264 799 299517015 299516467 0.000000e+00 785.0
19 TraesCS7A01G467300 chrUn 94.444 270 13 2 2 270 289617962 289618230 6.110000e-112 414.0
20 TraesCS7A01G467300 chrUn 94.444 270 13 2 2 270 299517316 299517048 6.110000e-112 414.0
21 TraesCS7A01G467300 chrUn 96.277 188 6 1 2799 2986 86971737 86971551 1.070000e-79 307.0
22 TraesCS7A01G467300 chrUn 98.734 79 1 0 2987 3065 86971228 86971150 1.150000e-29 141.0
23 TraesCS7A01G467300 chrUn 92.157 102 2 1 2129 2224 289620250 289620351 4.120000e-29 139.0
24 TraesCS7A01G467300 chrUn 92.929 99 1 1 2132 2224 299515025 299514927 4.120000e-29 139.0
25 TraesCS7A01G467300 chrUn 100.000 41 0 0 2759 2799 277181509 277181469 3.280000e-10 76.8
26 TraesCS7A01G467300 chrUn 100.000 41 0 0 2759 2799 337642410 337642370 3.280000e-10 76.8
27 TraesCS7A01G467300 chr7B 96.500 1400 27 6 812 2198 632966700 632965310 0.000000e+00 2294.0
28 TraesCS7A01G467300 chr7B 92.922 551 22 11 264 799 632967303 632966755 0.000000e+00 785.0
29 TraesCS7A01G467300 chr7B 97.924 289 5 1 2692 2980 632711894 632712181 1.640000e-137 499.0
30 TraesCS7A01G467300 chr7B 97.578 289 6 1 2692 2980 632957396 632957109 7.630000e-136 494.0
31 TraesCS7A01G467300 chr7B 94.444 270 13 2 2 270 632967604 632967336 6.110000e-112 414.0
32 TraesCS7A01G467300 chr7B 95.516 223 4 1 2478 2694 632711628 632711850 4.860000e-93 351.0
33 TraesCS7A01G467300 chr7B 95.000 220 5 1 2481 2694 632957659 632957440 1.050000e-89 340.0
34 TraesCS7A01G467300 chr7B 95.652 207 9 0 2229 2435 632711423 632711629 1.760000e-87 333.0
35 TraesCS7A01G467300 chr7B 94.686 207 9 1 2229 2435 632957865 632957661 1.370000e-83 320.0
36 TraesCS7A01G467300 chr7B 98.734 79 1 0 2987 3065 632712271 632712349 1.150000e-29 141.0
37 TraesCS7A01G467300 chr7B 98.734 79 1 0 2987 3065 632957019 632956941 1.150000e-29 141.0
38 TraesCS7A01G467300 chr7B 92.929 99 1 1 2132 2224 632965313 632965215 4.120000e-29 139.0
39 TraesCS7A01G467300 chr7B 97.727 44 1 0 2756 2799 632740399 632740442 3.280000e-10 76.8
40 TraesCS7A01G467300 chr2A 75.297 927 171 32 1152 2064 742772326 742771444 1.030000e-104 390.0
41 TraesCS7A01G467300 chr2B 75.215 815 155 22 1263 2064 744553574 744552794 2.930000e-90 342.0
42 TraesCS7A01G467300 chr2B 74.274 758 156 18 1152 1906 744482612 744481891 1.800000e-72 283.0


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 TraesCS7A01G467300 chr7A 663602692 663605756 3064 True 5661.00 5661 100.000000 1 3065 1 chr7A.!!$R1 3064
1 TraesCS7A01G467300 chr4D 6460469 6462977 2508 True 803.75 2495 94.421250 720 3065 4 chr4D.!!$R1 2345
2 TraesCS7A01G467300 chr4B 26334593 26337039 2446 True 774.50 2444 92.237500 720 3065 4 chr4B.!!$R1 2345
3 TraesCS7A01G467300 chr7D 574288530 574295837 7307 True 894.50 2314 95.672667 2 3065 6 chr7D.!!$R1 3063
4 TraesCS7A01G467300 chrUn 289617962 289620351 2389 False 908.00 2294 94.005750 2 2224 4 chrUn.!!$F1 2222
5 TraesCS7A01G467300 chrUn 299514927 299517316 2389 True 908.00 2294 94.198750 2 2224 4 chrUn.!!$R4 2222
6 TraesCS7A01G467300 chrUn 86971150 86971737 587 True 224.00 307 97.505500 2799 3065 2 chrUn.!!$R3 266
7 TraesCS7A01G467300 chr7B 632965215 632967604 2389 True 908.00 2294 94.198750 2 2224 4 chr7B.!!$R2 2222
8 TraesCS7A01G467300 chr7B 632711423 632712349 926 False 331.00 499 96.956500 2229 3065 4 chr7B.!!$F2 836
9 TraesCS7A01G467300 chr7B 632956941 632957865 924 True 323.75 494 96.499500 2229 3065 4 chr7B.!!$R1 836
10 TraesCS7A01G467300 chr2A 742771444 742772326 882 True 390.00 390 75.297000 1152 2064 1 chr2A.!!$R1 912
11 TraesCS7A01G467300 chr2B 744552794 744553574 780 True 342.00 342 75.215000 1263 2064 1 chr2B.!!$R2 801
12 TraesCS7A01G467300 chr2B 744481891 744482612 721 True 283.00 283 74.274000 1152 1906 1 chr2B.!!$R1 754

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
799 4854 0.405973 AAGAAAGGGGGCAAGACCTC 59.594 55.0 0.0 0.0 38.78 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 6735 0.901124 AACACAAGTGGGCTGCAAAA 59.099 45.0 0.5 0.0 34.19 2.44 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
113 114 4.701956 AAATAAGAGGCATTTGACACCG 57.298 40.909 0.00 0.00 0.00 4.94
117 118 2.988684 GGCATTTGACACCGCCCA 60.989 61.111 0.00 0.00 38.67 5.36
124 125 2.208132 TTGACACCGCCCATTAACAT 57.792 45.000 0.00 0.00 0.00 2.71
207 209 8.183536 GTGATGAAAACAATATAGACACATGCA 58.816 33.333 0.00 0.00 0.00 3.96
229 231 7.885297 TGCATGTAAAGTTTTTAGCTCAAGAT 58.115 30.769 0.00 0.00 0.00 2.40
343 4354 1.075212 TGGCAACTCATTGGATCCACA 59.925 47.619 15.91 6.51 36.23 4.17
476 4493 6.920569 ACTATTGGTTCCTGTAAATTAGCG 57.079 37.500 0.00 0.00 0.00 4.26
480 4497 2.941064 GGTTCCTGTAAATTAGCGGGAC 59.059 50.000 8.71 5.62 39.64 4.46
570 4587 3.118038 GCCTATAACAACCTCACCCATGA 60.118 47.826 0.00 0.00 0.00 3.07
799 4854 0.405973 AAGAAAGGGGGCAAGACCTC 59.594 55.000 0.00 0.00 38.78 3.85
824 4930 4.728102 CCGTCGCCGCAGTAACCA 62.728 66.667 0.00 0.00 0.00 3.67
840 4952 1.922570 ACCAATTCGATTCGTCGAGG 58.077 50.000 5.89 0.00 43.33 4.63
894 5006 5.476945 GCTCCCAAAACTTAATCTTTCCTGA 59.523 40.000 0.00 0.00 0.00 3.86
1674 5808 4.785453 CGCCAGTGGAGGAAGGCC 62.785 72.222 15.20 0.00 44.18 5.19
1676 5810 4.785453 CCAGTGGAGGAAGGCCGC 62.785 72.222 1.68 0.00 39.96 6.53
1729 5863 4.473520 ATGTCCCCGAGCTTGGCG 62.474 66.667 15.36 6.37 0.00 5.69
1884 6018 2.503546 GGCTGCCTGCTCTACCTC 59.496 66.667 12.43 0.00 42.39 3.85
2318 6626 3.382227 CAGCAATGTTGGCAGGATATTCA 59.618 43.478 0.00 0.00 0.00 2.57
2337 6667 1.071987 CAGCTTCTCCAGGTGTGCA 59.928 57.895 10.32 0.00 44.77 4.57
2379 6709 5.468746 CCACTCTTTCCTTCACGATTTTGTA 59.531 40.000 0.00 0.00 0.00 2.41
2405 6735 2.091885 AGGTTCATCAACAACAGTGGGT 60.092 45.455 0.00 0.00 33.70 4.51
2438 6769 5.297547 CACTTGTGTTATCACCTGTACACT 58.702 41.667 0.00 0.00 43.26 3.55
2496 6829 9.157104 GGGATACTACGTAGTATAGGAGTAAAC 57.843 40.741 36.29 24.01 46.46 2.01
2678 7019 3.678056 TCTGATATTCGGGCATACCAC 57.322 47.619 0.00 0.00 40.22 4.16
2847 7237 6.071952 GGATTAGCTCAACATAGAGGAGAGAG 60.072 46.154 0.00 0.00 36.15 3.20
2848 7238 4.518278 AGCTCAACATAGAGGAGAGAGA 57.482 45.455 0.00 0.00 36.15 3.10
2849 7239 4.464008 AGCTCAACATAGAGGAGAGAGAG 58.536 47.826 0.00 0.00 36.15 3.20
2980 7371 4.669318 CTGGCAGCTTTATCAATGTTCAG 58.331 43.478 0.00 0.00 0.00 3.02
2983 7374 3.119388 GCAGCTTTATCAATGTTCAGCCA 60.119 43.478 0.00 0.00 0.00 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
289 4300 6.267471 TGCAAAATATTGAAAGACCTGGTCTT 59.733 34.615 31.40 31.40 43.98 3.01
343 4354 1.002134 CGCCTGGAAAGGACCACAT 60.002 57.895 0.00 0.00 35.91 3.21
476 4493 6.458210 ACTGAATTGATGAACAAATTGTCCC 58.542 36.000 0.00 0.00 42.03 4.46
480 4497 8.843733 CGACTAACTGAATTGATGAACAAATTG 58.156 33.333 0.00 0.00 42.03 2.32
589 4606 7.784633 ATGTTTATGTTTTTGGGTTTCTGTG 57.215 32.000 0.00 0.00 0.00 3.66
661 4680 5.928976 TGGAGTATATTGCATGCAAGTACT 58.071 37.500 36.49 36.49 40.59 2.73
662 4681 6.348786 CCATGGAGTATATTGCATGCAAGTAC 60.349 42.308 34.15 32.60 43.19 2.73
810 4916 1.355796 CGAATTGGTTACTGCGGCGA 61.356 55.000 12.98 0.00 0.00 5.54
854 4966 0.761802 GAGCAGCAATACCTAGCCCT 59.238 55.000 0.00 0.00 0.00 5.19
855 4967 0.250510 GGAGCAGCAATACCTAGCCC 60.251 60.000 0.00 0.00 0.00 5.19
856 4968 0.250510 GGGAGCAGCAATACCTAGCC 60.251 60.000 0.00 0.00 0.00 3.93
857 4969 0.469917 TGGGAGCAGCAATACCTAGC 59.530 55.000 0.00 0.00 0.00 3.42
858 4970 3.281727 TTTGGGAGCAGCAATACCTAG 57.718 47.619 0.00 0.00 0.00 3.02
859 4971 3.010138 AGTTTTGGGAGCAGCAATACCTA 59.990 43.478 0.00 0.00 0.00 3.08
894 5006 5.770162 ACCAAACAGAAGGAGAAAAATCGAT 59.230 36.000 0.00 0.00 0.00 3.59
983 5096 1.004277 TCATTTACCTGCCCTGTCACC 59.996 52.381 0.00 0.00 0.00 4.02
1729 5863 1.450312 CCATGCCGAACCAGAGGTC 60.450 63.158 0.00 0.00 33.12 3.85
1780 5914 2.888863 GTCGAGGCTGGAGAGGTG 59.111 66.667 0.00 0.00 0.00 4.00
1884 6018 3.737172 CAAAACCTGCCGGCTCCG 61.737 66.667 29.70 16.89 39.44 4.63
1968 6105 2.202053 ACCACCTCCACACCGGTA 59.798 61.111 6.87 0.00 35.57 4.02
2318 6626 1.072159 GCACACCTGGAGAAGCTGT 59.928 57.895 0.00 0.00 0.00 4.40
2337 6667 1.922447 TGGTCAAGGATGGTATGCCTT 59.078 47.619 0.16 0.00 45.07 4.35
2379 6709 3.701040 ACTGTTGTTGATGAACCTTTGCT 59.299 39.130 0.00 0.00 0.00 3.91
2405 6735 0.901124 AACACAAGTGGGCTGCAAAA 59.099 45.000 0.50 0.00 34.19 2.44
2496 6829 3.326733 TTCGACACACATGTTTTTCCG 57.673 42.857 0.00 0.00 39.95 4.30
2678 7019 0.916809 ATGGGACCGGTAAAGAAGGG 59.083 55.000 7.34 0.00 0.00 3.95
2847 7237 6.060028 TGACACTTGTGCTGTATTTTTCTC 57.940 37.500 0.10 0.00 0.00 2.87
2848 7238 6.449635 TTGACACTTGTGCTGTATTTTTCT 57.550 33.333 0.10 0.00 0.00 2.52
2849 7239 7.698836 AATTGACACTTGTGCTGTATTTTTC 57.301 32.000 0.10 0.00 0.00 2.29
2980 7371 8.677148 TTGAGATTGAATAAACCTAGTATGGC 57.323 34.615 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.