Multiple sequence alignment - TraesCS5B01G258600

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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 TraesCS5B01G258600 chr5B 100.000 2236 0 0 1 2236 440918082 440915847 0.000000e+00 4130
1 TraesCS5B01G258600 chr5B 95.560 991 42 2 1248 2236 321871066 321872056 0.000000e+00 1585
2 TraesCS5B01G258600 chr6B 96.065 991 37 2 1248 2236 584373275 584372285 0.000000e+00 1613
3 TraesCS5B01G258600 chr6B 95.863 991 39 2 1248 2236 161171891 161172881 0.000000e+00 1602
4 TraesCS5B01G258600 chr6B 95.863 991 38 3 1248 2236 618611796 618610807 0.000000e+00 1600
5 TraesCS5B01G258600 chr2D 96.065 991 33 6 1248 2236 82608683 82609669 0.000000e+00 1609
6 TraesCS5B01G258600 chr4B 95.766 992 39 3 1248 2236 568000152 568001143 0.000000e+00 1596
7 TraesCS5B01G258600 chr4B 96.960 329 8 2 922 1248 151525871 151526199 3.250000e-153 551
8 TraesCS5B01G258600 chr2B 95.762 991 40 2 1248 2236 526021944 526020954 0.000000e+00 1596
9 TraesCS5B01G258600 chr1B 95.560 991 42 2 1248 2236 470254683 470255673 0.000000e+00 1585
10 TraesCS5B01G258600 chr1B 96.196 920 34 1 1 920 116200127 116201045 0.000000e+00 1504
11 TraesCS5B01G258600 chr3B 95.291 998 43 4 1241 2236 145064282 145065277 0.000000e+00 1580
12 TraesCS5B01G258600 chr3B 96.960 329 8 2 922 1248 201564445 201564117 3.250000e-153 551
13 TraesCS5B01G258600 chr3D 96.304 920 33 1 1 920 307026993 307027911 0.000000e+00 1509
14 TraesCS5B01G258600 chr3D 96.196 920 34 1 1 920 390378443 390379361 0.000000e+00 1504
15 TraesCS5B01G258600 chr3D 96.091 921 33 3 1 920 310737663 310738581 0.000000e+00 1498
16 TraesCS5B01G258600 chr3D 97.264 329 7 2 922 1248 589253232 589252904 6.980000e-155 556
17 TraesCS5B01G258600 chr5D 96.196 920 34 1 1 920 127583065 127583983 0.000000e+00 1504
18 TraesCS5B01G258600 chr5D 96.087 920 35 1 1 920 477419689 477420607 0.000000e+00 1498
19 TraesCS5B01G258600 chr5D 97.264 329 7 2 922 1248 449149299 449149627 6.980000e-155 556
20 TraesCS5B01G258600 chr4D 96.087 920 35 1 1 920 350225381 350224463 0.000000e+00 1498
21 TraesCS5B01G258600 chr4D 96.087 920 35 1 1 920 478878627 478879545 0.000000e+00 1498
22 TraesCS5B01G258600 chr1D 96.087 920 35 1 1 920 207608149 207609067 0.000000e+00 1498
23 TraesCS5B01G258600 chrUn 97.568 329 6 2 922 1248 430358319 430358647 1.500000e-156 562
24 TraesCS5B01G258600 chrUn 96.988 332 8 2 922 1251 351215053 351214722 6.980000e-155 556
25 TraesCS5B01G258600 chr7D 97.568 329 6 2 922 1248 231584991 231584663 1.500000e-156 562
26 TraesCS5B01G258600 chr7D 96.960 329 8 2 922 1248 231582912 231582584 3.250000e-153 551
27 TraesCS5B01G258600 chr3A 96.960 329 8 2 922 1248 695637336 695637664 3.250000e-153 551


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 TraesCS5B01G258600 chr5B 440915847 440918082 2235 True 4130.0 4130 100.000 1 2236 1 chr5B.!!$R1 2235
1 TraesCS5B01G258600 chr5B 321871066 321872056 990 False 1585.0 1585 95.560 1248 2236 1 chr5B.!!$F1 988
2 TraesCS5B01G258600 chr6B 584372285 584373275 990 True 1613.0 1613 96.065 1248 2236 1 chr6B.!!$R1 988
3 TraesCS5B01G258600 chr6B 161171891 161172881 990 False 1602.0 1602 95.863 1248 2236 1 chr6B.!!$F1 988
4 TraesCS5B01G258600 chr6B 618610807 618611796 989 True 1600.0 1600 95.863 1248 2236 1 chr6B.!!$R2 988
5 TraesCS5B01G258600 chr2D 82608683 82609669 986 False 1609.0 1609 96.065 1248 2236 1 chr2D.!!$F1 988
6 TraesCS5B01G258600 chr4B 568000152 568001143 991 False 1596.0 1596 95.766 1248 2236 1 chr4B.!!$F2 988
7 TraesCS5B01G258600 chr2B 526020954 526021944 990 True 1596.0 1596 95.762 1248 2236 1 chr2B.!!$R1 988
8 TraesCS5B01G258600 chr1B 470254683 470255673 990 False 1585.0 1585 95.560 1248 2236 1 chr1B.!!$F2 988
9 TraesCS5B01G258600 chr1B 116200127 116201045 918 False 1504.0 1504 96.196 1 920 1 chr1B.!!$F1 919
10 TraesCS5B01G258600 chr3B 145064282 145065277 995 False 1580.0 1580 95.291 1241 2236 1 chr3B.!!$F1 995
11 TraesCS5B01G258600 chr3D 307026993 307027911 918 False 1509.0 1509 96.304 1 920 1 chr3D.!!$F1 919
12 TraesCS5B01G258600 chr3D 390378443 390379361 918 False 1504.0 1504 96.196 1 920 1 chr3D.!!$F3 919
13 TraesCS5B01G258600 chr3D 310737663 310738581 918 False 1498.0 1498 96.091 1 920 1 chr3D.!!$F2 919
14 TraesCS5B01G258600 chr5D 127583065 127583983 918 False 1504.0 1504 96.196 1 920 1 chr5D.!!$F1 919
15 TraesCS5B01G258600 chr5D 477419689 477420607 918 False 1498.0 1498 96.087 1 920 1 chr5D.!!$F3 919
16 TraesCS5B01G258600 chr4D 350224463 350225381 918 True 1498.0 1498 96.087 1 920 1 chr4D.!!$R1 919
17 TraesCS5B01G258600 chr4D 478878627 478879545 918 False 1498.0 1498 96.087 1 920 1 chr4D.!!$F1 919
18 TraesCS5B01G258600 chr1D 207608149 207609067 918 False 1498.0 1498 96.087 1 920 1 chr1D.!!$F1 919
19 TraesCS5B01G258600 chr7D 231582584 231584991 2407 True 556.5 562 97.264 922 1248 2 chr7D.!!$R1 326

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
815 816 0.95104 CCGTGGAAGAACTGGCAGAC 60.951 60.0 23.66 14.4 0.0 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2095 2916 0.040058 AGAAAGCATGGTGGATGGCA 59.96 50.0 0.0 0.0 31.99 4.92 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
62 63 4.336153 TCACGGTTTATCATACGAGCAGTA 59.664 41.667 0.00 0.00 40.03 2.74
117 118 1.469126 CTGTGCGCCGACGTATACAC 61.469 60.000 4.18 0.00 42.83 2.90
266 267 9.710900 TGACATATAAGCAACTATGTATCTTGG 57.289 33.333 5.41 0.00 38.38 3.61
272 273 5.360591 AGCAACTATGTATCTTGGTACAGC 58.639 41.667 0.00 0.00 42.39 4.40
306 307 6.753279 CAGTTAATTGAGGCCACAATGTAATG 59.247 38.462 26.35 20.89 39.88 1.90
316 317 6.070078 AGGCCACAATGTAATGAATTCCAAAT 60.070 34.615 5.01 0.00 0.00 2.32
365 366 3.496884 TGGAACACTCACATTAAACTCGC 59.503 43.478 0.00 0.00 0.00 5.03
706 707 5.244851 TGCATTCCACTAAATTTAAGCACCA 59.755 36.000 0.00 0.00 0.00 4.17
731 732 5.726980 ATTTGCAGAAATAAGCAGACCAA 57.273 34.783 0.00 0.00 42.39 3.67
743 744 1.670967 GCAGACCAAAATGCCTCTTGC 60.671 52.381 0.00 0.00 36.41 4.01
815 816 0.951040 CCGTGGAAGAACTGGCAGAC 60.951 60.000 23.66 14.40 0.00 3.51
920 921 9.739276 TCTTTTAGATTGTGTTGGTCATTCTAT 57.261 29.630 0.00 0.00 32.04 1.98
1063 1065 8.463930 TGAATTTCAAGTATTCAGTTTCACCT 57.536 30.769 0.00 0.00 37.15 4.00
1064 1066 8.912988 TGAATTTCAAGTATTCAGTTTCACCTT 58.087 29.630 0.00 0.00 37.15 3.50
1085 1087 5.875359 CCTTTAAGATACGGAGACTTGCTTT 59.125 40.000 0.00 0.00 0.00 3.51
1351 1354 2.572290 ACTAAAACTGAGGTGTGTGCC 58.428 47.619 0.00 0.00 0.00 5.01
1396 1400 5.358442 CGATAGGAGATAGACATCCCGAAAT 59.642 44.000 0.00 0.00 36.14 2.17
1435 1439 7.138736 ACATACCTATTTGCGCAAATATGAAC 58.861 34.615 40.41 4.12 41.02 3.18
1696 1702 4.737855 ATGTTAGCGGTGTGAGAGTTAT 57.262 40.909 0.00 0.00 0.00 1.89
1721 1727 6.033341 GTGTAACTGCAAGAACACAATTCAA 58.967 36.000 16.18 0.00 46.25 2.69
1779 1785 2.481185 GTGGTGGCATTGCTTCAATTTG 59.519 45.455 8.82 0.00 31.05 2.32
1985 2047 1.136305 TCCTCGGCGACATTTTCCTAG 59.864 52.381 4.99 0.00 0.00 3.02
2131 3318 5.163561 TGCTTTCTTCGTCTTTTCAACCAAT 60.164 36.000 0.00 0.00 0.00 3.16
2169 3425 4.553678 CCAGTATCTACTACTTTCCCCCA 58.446 47.826 0.00 0.00 38.68 4.96
2178 3434 4.706616 ACTACTTTCCCCCATTTCCTCTA 58.293 43.478 0.00 0.00 0.00 2.43
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 8.116753 CGAACGAGTGCTCTATTTCATTAAAAT 58.883 33.333 0.00 0.00 40.67 1.82
117 118 4.574828 ACCTGCAGTGTTTACAAGTACTTG 59.425 41.667 29.76 29.76 45.58 3.16
136 137 0.981183 TACAAGTGGGGTAGCACCTG 59.019 55.000 0.00 0.00 38.64 4.00
137 138 1.628846 CTTACAAGTGGGGTAGCACCT 59.371 52.381 0.00 0.00 38.64 4.00
174 175 2.036571 CGAGCTGAGCCAATGTGCA 61.037 57.895 0.00 0.00 0.00 4.57
266 267 1.156736 AACTGCATGAACCGCTGTAC 58.843 50.000 0.00 0.00 40.19 2.90
272 273 3.731867 GCCTCAATTAACTGCATGAACCG 60.732 47.826 0.00 0.00 0.00 4.44
306 307 3.900941 AGCGTGTGAACATTTGGAATTC 58.099 40.909 0.00 0.00 0.00 2.17
316 317 1.860676 GTTGGACTAGCGTGTGAACA 58.139 50.000 0.00 0.00 0.00 3.18
706 707 7.408756 TGGTCTGCTTATTTCTGCAAATAAT 57.591 32.000 4.45 0.00 41.55 1.28
743 744 1.733402 TTTTTGGACAGGTGCGCAGG 61.733 55.000 12.22 6.16 0.00 4.85
815 816 2.672961 TCCTAGTTCGGAATGCACTG 57.327 50.000 0.00 0.00 0.00 3.66
827 828 4.342092 AGCAAAAACAACTGCATCCTAGTT 59.658 37.500 0.00 0.00 41.17 2.24
1063 1065 7.380536 TGTAAAGCAAGTCTCCGTATCTTAAA 58.619 34.615 0.00 0.00 0.00 1.52
1064 1066 6.927416 TGTAAAGCAAGTCTCCGTATCTTAA 58.073 36.000 0.00 0.00 0.00 1.85
1158 1161 2.231964 TCTTTGCCAAATAAGCCAGCAG 59.768 45.455 0.00 0.00 34.45 4.24
1214 1217 7.639113 AAATTACTGCTCCCGAATATTCAAA 57.361 32.000 15.57 0.00 0.00 2.69
1306 1309 0.171679 TGCGCAAAATGAGATGGCTG 59.828 50.000 8.16 0.00 0.00 4.85
1351 1354 3.354397 GTTTCTATCCGCGCAATCAAAG 58.646 45.455 8.75 0.00 0.00 2.77
1396 1400 8.588472 CAAATAGGTATGTCTGTCTCCATATCA 58.412 37.037 0.00 0.00 28.94 2.15
1414 1418 5.835113 AGTTCATATTTGCGCAAATAGGT 57.165 34.783 42.26 31.79 43.85 3.08
1696 1702 5.124617 TGAATTGTGTTCTTGCAGTTACACA 59.875 36.000 19.59 19.59 46.41 3.72
1709 1715 6.928492 TGCTTTATTTCCCTTGAATTGTGTTC 59.072 34.615 0.00 0.00 0.00 3.18
1721 1727 3.713826 TCCGTCTTGCTTTATTTCCCT 57.286 42.857 0.00 0.00 0.00 4.20
1779 1785 0.172803 AATGGTCTAGTGCCGTCGAC 59.827 55.000 5.18 5.18 0.00 4.20
1985 2047 3.873952 GGTCTAGATTTCATGTGCTCACC 59.126 47.826 0.00 0.00 0.00 4.02
2095 2916 0.040058 AGAAAGCATGGTGGATGGCA 59.960 50.000 0.00 0.00 31.99 4.92
2131 3318 0.974010 CTGGCTACCCAACCGGTCTA 60.974 60.000 8.04 0.00 43.58 2.59
2169 3425 6.960542 TCTAGGACTTGGTTCTTAGAGGAAAT 59.039 38.462 0.00 0.00 31.19 2.17
2178 3434 5.045286 AGCATGAATCTAGGACTTGGTTCTT 60.045 40.000 0.00 0.37 0.00 2.52


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

AutoCloner maintained by Alex Coulton.