Multiple sequence alignment - TraesCS3D01G154900

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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 TraesCS3D01G154900 chr3D 100.000 2725 0 0 1 2725 121882240 121884964 0.000000e+00 5033.0
1 TraesCS3D01G154900 chr3D 95.810 1074 33 3 3 1073 121803476 121804540 0.000000e+00 1724.0
2 TraesCS3D01G154900 chr3D 95.531 1074 35 4 3 1073 121736927 121737990 0.000000e+00 1705.0
3 TraesCS3D01G154900 chr3D 96.257 748 23 2 1633 2376 121753390 121754136 0.000000e+00 1221.0
4 TraesCS3D01G154900 chr3D 95.789 570 23 1 1068 1637 121749645 121750213 0.000000e+00 918.0
5 TraesCS3D01G154900 chr3D 95.789 570 23 1 1068 1637 121812506 121813074 0.000000e+00 918.0
6 TraesCS3D01G154900 chr3D 95.870 339 9 2 2387 2725 121754388 121754721 6.640000e-151 544.0
7 TraesCS3D01G154900 chr3D 95.280 339 11 2 2387 2725 121816305 121816638 1.440000e-147 532.0
8 TraesCS3D01G154900 chr3B 87.662 2237 176 57 378 2576 173372865 173375039 0.000000e+00 2510.0
9 TraesCS3D01G154900 chr3B 88.048 753 53 10 946 1690 173335597 173336320 0.000000e+00 857.0
10 TraesCS3D01G154900 chr3B 89.341 516 39 5 1675 2175 173364593 173365107 3.830000e-178 634.0
11 TraesCS3D01G154900 chr3B 92.037 427 27 4 2151 2576 173370417 173370837 6.500000e-166 593.0
12 TraesCS3D01G154900 chr3B 87.731 432 41 5 529 948 173327678 173328109 6.780000e-136 494.0
13 TraesCS3D01G154900 chr3B 95.652 92 4 0 2634 2725 173371168 173371259 6.080000e-32 148.0
14 TraesCS3D01G154900 chr3B 96.629 89 3 0 2634 2722 173375376 173375464 6.080000e-32 148.0
15 TraesCS3D01G154900 chr3A 89.453 1280 71 13 1464 2725 128127538 128128771 0.000000e+00 1557.0
16 TraesCS3D01G154900 chr3A 90.944 519 38 6 953 1467 128126929 128127442 0.000000e+00 689.0
17 TraesCS3D01G154900 chr3A 86.965 537 41 17 378 891 128102555 128103085 6.540000e-161 577.0
18 TraesCS3D01G154900 chrUn 95.941 271 8 1 806 1073 324187269 324187539 1.160000e-118 436.0
19 TraesCS3D01G154900 chrUn 96.875 32 1 0 1816 1847 91331544 91331575 1.000000e-03 54.7
20 TraesCS3D01G154900 chr7D 92.887 239 13 1 1 239 240638207 240638441 7.220000e-91 344.0
21 TraesCS3D01G154900 chr2D 92.149 242 15 1 1 242 384147203 384147440 3.360000e-89 339.0
22 TraesCS3D01G154900 chr1B 92.469 239 14 1 1 239 523787304 523787538 3.360000e-89 339.0
23 TraesCS3D01G154900 chr1B 92.083 240 14 2 4 243 612400447 612400213 1.560000e-87 333.0
24 TraesCS3D01G154900 chr4B 92.083 240 14 2 4 243 70104449 70104683 1.560000e-87 333.0
25 TraesCS3D01G154900 chr4B 90.688 247 19 1 1 247 284629720 284629962 2.620000e-85 326.0
26 TraesCS3D01G154900 chr5B 91.322 242 17 1 1 242 155814083 155813846 7.280000e-86 327.0
27 TraesCS3D01G154900 chr7A 90.244 41 4 0 1816 1856 91300068 91300028 1.000000e-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 TraesCS3D01G154900 chr3D 121882240 121884964 2724 False 5033.000000 5033 100.0000 1 2725 1 chr3D.!!$F3 2724
1 TraesCS3D01G154900 chr3D 121803476 121804540 1064 False 1724.000000 1724 95.8100 3 1073 1 chr3D.!!$F2 1070
2 TraesCS3D01G154900 chr3D 121736927 121737990 1063 False 1705.000000 1705 95.5310 3 1073 1 chr3D.!!$F1 1070
3 TraesCS3D01G154900 chr3D 121749645 121754721 5076 False 894.333333 1221 95.9720 1068 2725 3 chr3D.!!$F4 1657
4 TraesCS3D01G154900 chr3D 121812506 121816638 4132 False 725.000000 918 95.5345 1068 2725 2 chr3D.!!$F5 1657
5 TraesCS3D01G154900 chr3B 173335597 173336320 723 False 857.000000 857 88.0480 946 1690 1 chr3B.!!$F2 744
6 TraesCS3D01G154900 chr3B 173370417 173375464 5047 False 849.750000 2510 92.9950 378 2725 4 chr3B.!!$F4 2347
7 TraesCS3D01G154900 chr3B 173364593 173365107 514 False 634.000000 634 89.3410 1675 2175 1 chr3B.!!$F3 500
8 TraesCS3D01G154900 chr3A 128126929 128128771 1842 False 1123.000000 1557 90.1985 953 2725 2 chr3A.!!$F2 1772
9 TraesCS3D01G154900 chr3A 128102555 128103085 530 False 577.000000 577 86.9650 378 891 1 chr3A.!!$F1 513

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
564 2666 0.459759 CCTACCCGACGCTTCCTTTC 60.460 60.0 0.0 0.0 0.0 2.62 F
1176 3295 0.526662 ACGTCGTGGATGTCTTCTCC 59.473 55.0 0.0 0.0 0.0 3.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 3848 3.569277 TGATGTCATTGTTCAACACCCAG 59.431 43.478 0.00 0.0 0.00 4.45 R
2199 10318 6.912591 AGCAAAGCTTTTATACATATGCGAAC 59.087 34.615 9.53 0.0 33.89 3.95 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
180 181 9.256228 CTACCCACTATGATGGTAGTAACATAT 57.744 37.037 0.00 0.00 44.28 1.78
271 272 6.183360 CGATATGAGTACATAGCTTCGGATGA 60.183 42.308 0.00 0.00 41.47 2.92
562 2664 1.304713 TCCTACCCGACGCTTCCTT 60.305 57.895 0.00 0.00 0.00 3.36
563 2665 0.901580 TCCTACCCGACGCTTCCTTT 60.902 55.000 0.00 0.00 0.00 3.11
564 2666 0.459759 CCTACCCGACGCTTCCTTTC 60.460 60.000 0.00 0.00 0.00 2.62
565 2667 0.459759 CTACCCGACGCTTCCTTTCC 60.460 60.000 0.00 0.00 0.00 3.13
566 2668 0.901580 TACCCGACGCTTCCTTTCCT 60.902 55.000 0.00 0.00 0.00 3.36
573 2675 3.490933 CGACGCTTCCTTTCCTCATATCA 60.491 47.826 0.00 0.00 0.00 2.15
762 2873 2.569134 GTCTTCCTCGAGCTGCGT 59.431 61.111 6.99 0.00 41.80 5.24
767 2878 3.753434 CCTCGAGCTGCGTGACCT 61.753 66.667 6.99 0.00 41.80 3.85
891 3007 3.764049 GTGTTCGACTGCGGCGTC 61.764 66.667 9.37 12.71 38.28 5.19
892 3008 3.973516 TGTTCGACTGCGGCGTCT 61.974 61.111 9.37 0.00 38.28 4.18
966 3085 1.374947 GCTGCAGTGGGTGGAGTTA 59.625 57.895 16.64 0.00 46.21 2.24
1176 3295 0.526662 ACGTCGTGGATGTCTTCTCC 59.473 55.000 0.00 0.00 0.00 3.71
1180 3299 2.428890 GTCGTGGATGTCTTCTCCTCAT 59.571 50.000 0.00 0.00 33.69 2.90
1223 3342 0.688487 TCGTTTGTTCGGGAAGGGAT 59.312 50.000 0.00 0.00 0.00 3.85
1257 3376 1.804326 CGCCGGTTGTAGGTCGAAG 60.804 63.158 1.90 0.00 32.73 3.79
1422 3549 3.187227 CACACAGCAACTACATTCCAGAC 59.813 47.826 0.00 0.00 0.00 3.51
1622 3848 3.181489 ACGAGACGTATGGAAAGATGGAC 60.181 47.826 0.00 0.00 38.73 4.02
1796 9509 0.469705 AGATTGGGTTGCCAAGCACA 60.470 50.000 9.09 1.56 38.71 4.57
1975 9859 2.023673 CCGTACATGCCATGTTGGATT 58.976 47.619 16.67 0.00 41.63 3.01
2015 9899 5.652452 AGCCATTATAGAACCCAGTTTTGTC 59.348 40.000 0.00 0.00 0.00 3.18
2100 10219 7.994425 TTTAGGCTCTTGTATCACATTTTGA 57.006 32.000 0.00 0.00 39.11 2.69
2104 10223 8.757982 AGGCTCTTGTATCACATTTTGATAAT 57.242 30.769 0.00 0.00 46.72 1.28
2140 10259 0.787908 GTACGTTTTGCGACATGGCG 60.788 55.000 18.99 18.99 44.77 5.69
2191 10310 2.014010 TTGCCTTTTCATCTGGCCTT 57.986 45.000 3.32 0.00 45.56 4.35
2199 10318 4.589216 TTTCATCTGGCCTTGTTGAAAG 57.411 40.909 20.94 4.37 32.88 2.62
2551 10912 2.985847 GGAAAGCTGCTGCCCGTT 60.986 61.111 12.44 4.26 40.80 4.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 33 4.100373 AGCACCTCTCTCCTCATTAACTT 58.900 43.478 0.00 0.00 0.00 2.66
71 72 3.197265 GGGTGCGTTATGTTACGGTAAT 58.803 45.455 3.59 0.00 41.65 1.89
222 223 7.339721 TCGATTCCTAAGGCTAGTCATAATAGG 59.660 40.741 0.00 3.33 0.00 2.57
226 227 8.687242 CATATCGATTCCTAAGGCTAGTCATAA 58.313 37.037 1.71 0.00 0.00 1.90
271 272 3.040147 TGCGAACGATCTTTTCCTTCT 57.960 42.857 0.00 0.00 0.00 2.85
405 2477 4.748679 ACGTAGACGCGCCGTGTC 62.749 66.667 22.31 22.31 41.37 3.67
562 2664 5.070313 TGTCCATGTCGATTGATATGAGGAA 59.930 40.000 18.65 1.99 44.05 3.36
563 2665 4.588528 TGTCCATGTCGATTGATATGAGGA 59.411 41.667 18.65 7.72 44.05 3.71
564 2666 4.886579 TGTCCATGTCGATTGATATGAGG 58.113 43.478 18.65 5.67 44.05 3.86
565 2667 6.090493 GTCATGTCCATGTCGATTGATATGAG 59.910 42.308 18.65 10.31 44.05 2.90
566 2668 5.928264 GTCATGTCCATGTCGATTGATATGA 59.072 40.000 18.65 9.89 44.05 2.15
573 2675 2.420547 CCTGGTCATGTCCATGTCGATT 60.421 50.000 12.25 0.00 39.72 3.34
762 2873 4.270153 AGGGGCAGGTCCAGGTCA 62.270 66.667 0.00 0.00 36.21 4.02
891 3007 2.103042 GCCGTTGCAGCAGTCCTAG 61.103 63.158 0.24 0.00 37.47 3.02
892 3008 2.047274 GCCGTTGCAGCAGTCCTA 60.047 61.111 0.24 0.00 37.47 2.94
1176 3295 1.219124 CCACTCACCGGTCCATGAG 59.781 63.158 16.12 16.12 46.49 2.90
1180 3299 2.214216 CCTTCCACTCACCGGTCCA 61.214 63.158 2.59 0.00 0.00 4.02
1244 3363 2.985139 CGTCTTTCCTTCGACCTACAAC 59.015 50.000 0.00 0.00 0.00 3.32
1292 3411 1.455248 AGAGACGTAGAGTGCTCCAC 58.545 55.000 0.00 0.00 31.66 4.02
1422 3549 7.752239 GCAAAATATGGGATCATCATTAGAACG 59.248 37.037 6.18 0.00 34.96 3.95
1622 3848 3.569277 TGATGTCATTGTTCAACACCCAG 59.431 43.478 0.00 0.00 0.00 4.45
1796 9509 8.608844 AGAAAATCAATTGTCGAGTTAGAACT 57.391 30.769 5.13 0.00 43.16 3.01
2015 9899 7.630242 AACATCATGACTTTAACCACTATGG 57.370 36.000 0.00 0.00 45.02 2.74
2104 10223 8.723311 CAAAACGTACCCATAGATAAGAACAAA 58.277 33.333 0.00 0.00 0.00 2.83
2140 10259 6.934561 AATCAAATTCAAGCTTTCTTACGC 57.065 33.333 0.00 0.00 0.00 4.42
2191 10310 9.767684 CTTTTATACATATGCGAACTTTCAACA 57.232 29.630 1.58 0.00 0.00 3.33
2199 10318 6.912591 AGCAAAGCTTTTATACATATGCGAAC 59.087 34.615 9.53 0.00 33.89 3.95


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

AutoCloner maintained by Alex Coulton.