Multiple sequence alignment - TraesCS7A01G315900

Loading Multiple Alignment...

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 TraesCS7A01G315900 chr7A 100.000 2946 0 0 1 2946 450364423 450361478 0.000000e+00 5441
1 TraesCS7A01G315900 chr7A 96.260 2139 67 6 1 2134 577480913 577483043 0.000000e+00 3494
2 TraesCS7A01G315900 chr7A 94.107 2138 103 9 1 2134 496901235 496899117 0.000000e+00 3229
3 TraesCS7A01G315900 chr7A 95.215 815 36 3 2134 2946 456355354 456354541 0.000000e+00 1286
4 TraesCS7A01G315900 chr7A 95.167 807 37 2 2141 2946 495905663 495904858 0.000000e+00 1273
5 TraesCS7A01G315900 chr7A 94.397 821 41 3 2129 2946 496328324 496327506 0.000000e+00 1256
6 TraesCS7A01G315900 chr1A 96.077 2141 66 9 1 2134 238650163 238648034 0.000000e+00 3472
7 TraesCS7A01G315900 chr5A 93.124 2138 106 16 1 2134 228645327 228643227 0.000000e+00 3096
8 TraesCS7A01G315900 chr5A 95.110 818 33 3 2134 2946 228261796 228262611 0.000000e+00 1282
9 TraesCS7A01G315900 chr5A 94.853 816 38 3 2134 2946 289189408 289188594 0.000000e+00 1271
10 TraesCS7A01G315900 chr5A 94.847 815 37 3 2133 2946 272297364 272298174 0.000000e+00 1267
11 TraesCS7A01G315900 chr5A 94.608 816 39 3 2134 2946 273286637 273285824 0.000000e+00 1258
12 TraesCS7A01G315900 chr2A 96.673 992 33 0 1 992 427173430 427174421 0.000000e+00 1650
13 TraesCS7A01G315900 chr2A 94.215 968 42 2 1170 2134 427174422 427175378 0.000000e+00 1465
14 TraesCS7A01G315900 chr2A 94.383 819 43 2 2129 2946 176496198 176497014 0.000000e+00 1254
15 TraesCS7A01G315900 chr3A 94.621 818 37 3 2134 2946 463559285 463558470 0.000000e+00 1260
16 TraesCS7A01G315900 chrUn 95.694 720 31 0 908 1627 96518701 96517982 0.000000e+00 1158
17 TraesCS7A01G315900 chr3B 97.347 603 12 4 1 601 1265681 1266281 0.000000e+00 1022
18 TraesCS7A01G315900 chr3B 93.297 552 16 7 1586 2134 1266270 1266803 0.000000e+00 795
19 TraesCS7A01G315900 chr6A 95.688 603 20 5 1 601 447423725 447423127 0.000000e+00 965
20 TraesCS7A01G315900 chr6A 95.109 552 15 5 1586 2134 447423138 447422596 0.000000e+00 859
21 TraesCS7A01G315900 chr6A 87.898 157 16 2 1436 1591 181911392 181911546 6.490000e-42 182
22 TraesCS7A01G315900 chr4B 79.619 525 74 24 1607 2128 446513564 446514058 2.170000e-91 346
23 TraesCS7A01G315900 chr7B 80.878 319 42 13 1822 2128 558893134 558893445 1.770000e-57 233
24 TraesCS7A01G315900 chr7B 87.898 157 16 2 1436 1591 558892738 558892892 6.490000e-42 182
25 TraesCS7A01G315900 chr6B 77.724 413 45 26 1743 2128 505706318 505705926 2.980000e-50 209
26 TraesCS7A01G315900 chr6B 87.261 157 17 2 1436 1591 505706614 505706460 3.020000e-40 176


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 TraesCS7A01G315900 chr7A 450361478 450364423 2945 True 5441.0 5441 100.0000 1 2946 1 chr7A.!!$R1 2945
1 TraesCS7A01G315900 chr7A 577480913 577483043 2130 False 3494.0 3494 96.2600 1 2134 1 chr7A.!!$F1 2133
2 TraesCS7A01G315900 chr7A 496899117 496901235 2118 True 3229.0 3229 94.1070 1 2134 1 chr7A.!!$R5 2133
3 TraesCS7A01G315900 chr7A 456354541 456355354 813 True 1286.0 1286 95.2150 2134 2946 1 chr7A.!!$R2 812
4 TraesCS7A01G315900 chr7A 495904858 495905663 805 True 1273.0 1273 95.1670 2141 2946 1 chr7A.!!$R3 805
5 TraesCS7A01G315900 chr7A 496327506 496328324 818 True 1256.0 1256 94.3970 2129 2946 1 chr7A.!!$R4 817
6 TraesCS7A01G315900 chr1A 238648034 238650163 2129 True 3472.0 3472 96.0770 1 2134 1 chr1A.!!$R1 2133
7 TraesCS7A01G315900 chr5A 228643227 228645327 2100 True 3096.0 3096 93.1240 1 2134 1 chr5A.!!$R1 2133
8 TraesCS7A01G315900 chr5A 228261796 228262611 815 False 1282.0 1282 95.1100 2134 2946 1 chr5A.!!$F1 812
9 TraesCS7A01G315900 chr5A 289188594 289189408 814 True 1271.0 1271 94.8530 2134 2946 1 chr5A.!!$R3 812
10 TraesCS7A01G315900 chr5A 272297364 272298174 810 False 1267.0 1267 94.8470 2133 2946 1 chr5A.!!$F2 813
11 TraesCS7A01G315900 chr5A 273285824 273286637 813 True 1258.0 1258 94.6080 2134 2946 1 chr5A.!!$R2 812
12 TraesCS7A01G315900 chr2A 427173430 427175378 1948 False 1557.5 1650 95.4440 1 2134 2 chr2A.!!$F2 2133
13 TraesCS7A01G315900 chr2A 176496198 176497014 816 False 1254.0 1254 94.3830 2129 2946 1 chr2A.!!$F1 817
14 TraesCS7A01G315900 chr3A 463558470 463559285 815 True 1260.0 1260 94.6210 2134 2946 1 chr3A.!!$R1 812
15 TraesCS7A01G315900 chrUn 96517982 96518701 719 True 1158.0 1158 95.6940 908 1627 1 chrUn.!!$R1 719
16 TraesCS7A01G315900 chr3B 1265681 1266803 1122 False 908.5 1022 95.3220 1 2134 2 chr3B.!!$F1 2133
17 TraesCS7A01G315900 chr6A 447422596 447423725 1129 True 912.0 965 95.3985 1 2134 2 chr6A.!!$R1 2133
18 TraesCS7A01G315900 chr7B 558892738 558893445 707 False 207.5 233 84.3880 1436 2128 2 chr7B.!!$F1 692

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
502 506 5.420725 TTGTAGAAGGAATGCAGCTCTTA 57.579 39.13 0.0 0.0 0.0 2.1 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2226 2300 0.035739 GCGAGGGTCTTGGGTTTGTA 59.964 55.0 0.0 0.0 0.0 2.41 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
498 502 5.990120 AATTTTGTAGAAGGAATGCAGCT 57.010 34.783 0.00 0.00 0.00 4.24
502 506 5.420725 TTGTAGAAGGAATGCAGCTCTTA 57.579 39.130 0.00 0.00 0.00 2.10
679 684 6.977213 ACACATAATGTTGGTTGTTAACTCC 58.023 36.000 7.22 9.86 38.98 3.85
1007 1012 8.164058 TGATGATTTCAGTAACACATGTTCAA 57.836 30.769 0.00 0.00 39.31 2.69
1167 1172 2.756283 AGAAGACCTAGCGCCGCT 60.756 61.111 18.67 18.67 43.41 5.52
1205 1210 1.186200 CTAGCTATAGATGGCGGCCA 58.814 55.000 26.11 26.11 39.47 5.36
1277 1282 1.536072 GCGCATGACATTCGAGGACTA 60.536 52.381 11.76 0.00 0.00 2.59
1304 1309 1.453562 TGTGCTGGCTGCTCAACAA 60.454 52.632 17.00 0.00 41.46 2.83
1347 1352 2.502093 GACGTGTCCACCCACACA 59.498 61.111 0.00 0.00 46.09 3.72
1403 1408 0.798776 CAAACGGCTCCATGTCACTC 59.201 55.000 0.00 0.00 0.00 3.51
1604 1633 6.913873 TTTACAGTGTACAACTTCTTCACC 57.086 37.500 1.43 0.00 36.83 4.02
2137 2210 7.835822 TCCATCTTTCTTTTCTGTTTTTGTCA 58.164 30.769 0.00 0.00 0.00 3.58
2157 2230 2.841317 GTTCTGGGAACGGGGGTT 59.159 61.111 0.00 0.00 37.31 4.11
2170 2243 1.078347 GGGGTTCCCAGAATTGCCA 59.922 57.895 10.25 0.00 44.65 4.92
2226 2300 2.224159 ACGGCCCATCTTCACCAGT 61.224 57.895 0.00 0.00 0.00 4.00
2297 2371 4.400961 GCTTCCTCAGGCACGGCT 62.401 66.667 0.00 0.00 0.00 5.52
2496 2570 0.109319 GGTTGCCGTTTCGATGCAAT 60.109 50.000 13.03 0.00 45.66 3.56
2502 2576 2.002586 CCGTTTCGATGCAATGAGACT 58.997 47.619 9.53 0.00 0.00 3.24
2525 2599 2.583101 AGACCAGGAGGACTATGAGACA 59.417 50.000 0.00 0.00 38.17 3.41
2590 2664 2.157863 GCGCAGGTGAAGACTACTTTTC 59.842 50.000 0.30 0.00 36.39 2.29
2629 2703 2.378547 TGCTGTCCCCCTTCAAATTAGT 59.621 45.455 0.00 0.00 0.00 2.24
2820 2903 2.270205 CCAGCAGTTCATCGCCCT 59.730 61.111 0.00 0.00 0.00 5.19
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 5.978814 TCTAGCTTTCTCAATACAGGGTTC 58.021 41.667 0.00 0.00 0.00 3.62
332 335 4.074970 CTGCTGAATGAAGTAAACCCACT 58.925 43.478 0.00 0.00 0.00 4.00
465 469 7.168219 TCCTTCTACAAAATTACTGCATCTGT 58.832 34.615 0.00 0.00 0.00 3.41
679 684 8.722394 TGTAGAGCTCTAGTGATATTATGTTCG 58.278 37.037 23.87 0.00 0.00 3.95
1007 1012 6.127591 ACACACTCTCGAGCTCACTATTATTT 60.128 38.462 15.40 0.00 0.00 1.40
1167 1172 4.202357 GCTAGGGGATGTGTCATCATTGTA 60.202 45.833 11.08 0.00 0.00 2.41
1205 1210 3.090219 GCCAAGGGATCTACGCCGT 62.090 63.158 0.00 0.00 0.00 5.68
1304 1309 1.821061 CTGGAAGGTGACGTGGAGCT 61.821 60.000 0.00 0.00 0.00 4.09
1403 1408 2.661566 CGTGAACAGCCGCTGTGAG 61.662 63.158 26.37 13.75 44.62 3.51
1604 1633 8.079203 AGAAGATACAGCTACTGAATAATGTCG 58.921 37.037 0.78 0.00 35.18 4.35
1915 1981 2.559668 CACCTGATCAACATGCTTTGGT 59.440 45.455 0.00 0.00 0.00 3.67
2081 2148 6.069963 AGGAGGAGAGCAAAGCTAGAAAATAA 60.070 38.462 0.00 0.00 39.88 1.40
2137 2210 4.016706 CCCCGTTCCCAGAACGCT 62.017 66.667 21.18 0.00 41.85 5.07
2157 2230 1.000521 CAGGCTGGCAATTCTGGGA 60.001 57.895 6.61 0.00 0.00 4.37
2226 2300 0.035739 GCGAGGGTCTTGGGTTTGTA 59.964 55.000 0.00 0.00 0.00 2.41
2297 2371 2.669569 GCGAGCCAGCCTGACAAA 60.670 61.111 0.00 0.00 0.00 2.83
2368 2442 2.885113 CGCCCTGAGTCGTCATGA 59.115 61.111 0.00 0.00 30.18 3.07
2490 2564 3.776969 TCCTGGTCTTAGTCTCATTGCAT 59.223 43.478 0.00 0.00 0.00 3.96
2496 2570 2.650322 AGTCCTCCTGGTCTTAGTCTCA 59.350 50.000 0.00 0.00 34.23 3.27
2502 2576 4.229812 TGTCTCATAGTCCTCCTGGTCTTA 59.770 45.833 0.00 0.00 33.85 2.10
2525 2599 2.997897 GGCTCCACGGTGACCTCT 60.998 66.667 10.28 0.00 0.00 3.69
2590 2664 5.911752 ACAGCAAGTATCAACTATCCTGAG 58.088 41.667 0.00 0.00 33.75 3.35
2820 2903 0.895530 CGAGGGTCTGTTCTTGGCTA 59.104 55.000 0.00 0.00 0.00 3.93
2847 2930 6.440647 TGATAGTGGACAGTACAAGGAAGAAT 59.559 38.462 0.00 0.00 0.00 2.40


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

AutoCloner maintained by Alex Coulton.