Multiple sequence alignment - TraesCS3B01G609300

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 TraesCS3B01G609300 chr3B 100.000 3127 0 0 424 3550 828416437 828419563 0.000000e+00 5775
1 TraesCS3B01G609300 chr3B 97.333 2287 38 2 1278 3550 828768063 828765786 0.000000e+00 3864
2 TraesCS3B01G609300 chr3B 88.768 276 21 5 667 941 828768391 828768125 2.640000e-86 329
3 TraesCS3B01G609300 chr3B 95.098 204 7 1 424 624 828768922 828768719 5.720000e-83 318
4 TraesCS3B01G609300 chr3B 100.000 58 0 0 1 58 828416014 828416071 1.350000e-19 108
5 TraesCS3B01G609300 chr3D 92.033 2749 137 39 500 3225 610799808 610802497 0.000000e+00 3788
6 TraesCS3B01G609300 chr3D 86.383 235 25 5 3192 3420 610802518 610802751 2.120000e-62 250
7 TraesCS3B01G609300 chr3D 93.878 49 3 0 425 473 610799761 610799809 1.370000e-09 75
8 TraesCS3B01G609300 chr3A 88.499 1739 120 29 667 2365 745508480 745510178 0.000000e+00 2030
9 TraesCS3B01G609300 chr3A 90.404 198 19 0 424 621 745507899 745508096 9.780000e-66 261
10 TraesCS3B01G609300 chr5A 81.037 1350 203 39 1037 2366 382291596 382292912 0.000000e+00 1026
11 TraesCS3B01G609300 chr5D 80.826 1356 217 31 1028 2366 289008155 289009484 0.000000e+00 1024
12 TraesCS3B01G609300 chr5D 81.009 1348 201 37 1037 2366 288818034 288819344 0.000000e+00 1020
13 TraesCS3B01G609300 chr5B 80.537 1341 228 25 1037 2365 328233601 328234920 0.000000e+00 1000


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 TraesCS3B01G609300 chr3B 828416014 828419563 3549 False 2941.500000 5775 100.000000 1 3550 2 chr3B.!!$F1 3549
1 TraesCS3B01G609300 chr3B 828765786 828768922 3136 True 1503.666667 3864 93.733000 424 3550 3 chr3B.!!$R1 3126
2 TraesCS3B01G609300 chr3D 610799761 610802751 2990 False 1371.000000 3788 90.764667 425 3420 3 chr3D.!!$F1 2995
3 TraesCS3B01G609300 chr3A 745507899 745510178 2279 False 1145.500000 2030 89.451500 424 2365 2 chr3A.!!$F1 1941
4 TraesCS3B01G609300 chr5A 382291596 382292912 1316 False 1026.000000 1026 81.037000 1037 2366 1 chr5A.!!$F1 1329
5 TraesCS3B01G609300 chr5D 289008155 289009484 1329 False 1024.000000 1024 80.826000 1028 2366 1 chr5D.!!$F2 1338
6 TraesCS3B01G609300 chr5D 288818034 288819344 1310 False 1020.000000 1020 81.009000 1037 2366 1 chr5D.!!$F1 1329
7 TraesCS3B01G609300 chr5B 328233601 328234920 1319 False 1000.000000 1000 80.537000 1037 2365 1 chr5B.!!$F1 1328

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
646 665 1.361543 ACCTTGCCTGACCTCCTAGTA 59.638 52.381 0.00 0.0 0.0 1.82 F
1009 1376 1.084370 GCTCTTGATCGACCAACCCG 61.084 60.000 0.00 0.0 0.0 5.28 F
1384 1760 1.213926 GGCAGAAGGTCATGGGAGATT 59.786 52.381 0.00 0.0 0.0 2.40 F
2020 2434 0.033504 CGGCAAGGCGGTATGATAGT 59.966 55.000 8.26 0.0 0.0 2.12 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1946 2360 0.388649 AGATGCACCTTGTCGTCGTC 60.389 55.000 0.00 0.00 0.00 4.2 R
1956 2370 1.269936 GCAAGCAAACAAGATGCACCT 60.270 47.619 0.00 0.00 46.22 4.0 R
2432 2853 2.283145 AGCTGCAACCTTCAACTGAT 57.717 45.000 1.02 0.00 0.00 2.9 R
3421 3923 4.443394 CGTATACGGAAATTCCAGTAGTGC 59.557 45.833 17.61 8.31 35.91 4.4 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
25 26 8.650143 TTATATTCCTCTGCTTTTCACCTTTT 57.350 30.769 0.00 0.00 0.00 2.27
26 27 4.654091 TTCCTCTGCTTTTCACCTTTTG 57.346 40.909 0.00 0.00 0.00 2.44
44 45 7.803279 CCTTTTGGTAAGTATCTGGATTACC 57.197 40.000 6.44 6.44 45.71 2.85
51 52 8.834749 GGTAAGTATCTGGATTACCAAGATTC 57.165 38.462 8.17 0.00 46.32 2.52
52 53 7.878644 GGTAAGTATCTGGATTACCAAGATTCC 59.121 40.741 8.17 0.00 46.32 3.01
53 54 6.441088 AGTATCTGGATTACCAAGATTCCC 57.559 41.667 0.00 0.00 46.32 3.97
54 55 4.731313 ATCTGGATTACCAAGATTCCCC 57.269 45.455 0.00 0.00 46.32 4.81
55 56 2.783510 TCTGGATTACCAAGATTCCCCC 59.216 50.000 0.00 0.00 46.32 5.40
565 566 5.047377 TCCATTTTGCCGCTTTCTATTTCTT 60.047 36.000 0.00 0.00 0.00 2.52
646 665 1.361543 ACCTTGCCTGACCTCCTAGTA 59.638 52.381 0.00 0.00 0.00 1.82
657 676 1.689273 CCTCCTAGTATGTGAGCCCAC 59.311 57.143 0.00 0.00 43.46 4.61
806 1159 2.791158 CCGTTGACGAGCAAAATATGCC 60.791 50.000 4.91 0.00 45.84 4.40
942 1296 5.006455 CAGCATTATGACAGAGCTAGTGTTG 59.994 44.000 0.00 0.00 33.59 3.33
955 1309 7.596995 CAGAGCTAGTGTTGCTTAATATACTCC 59.403 40.741 0.00 0.00 41.30 3.85
956 1310 7.507616 AGAGCTAGTGTTGCTTAATATACTCCT 59.492 37.037 0.00 0.00 41.30 3.69
957 1311 8.707796 AGCTAGTGTTGCTTAATATACTCCTA 57.292 34.615 0.00 0.00 37.52 2.94
958 1312 8.798402 AGCTAGTGTTGCTTAATATACTCCTAG 58.202 37.037 0.00 0.00 37.52 3.02
964 1318 7.926555 TGTTGCTTAATATACTCCTAGTCAAGC 59.073 37.037 0.00 0.00 37.09 4.01
1005 1372 1.404181 CCGAAGCTCTTGATCGACCAA 60.404 52.381 6.33 0.00 38.82 3.67
1006 1373 1.656095 CGAAGCTCTTGATCGACCAAC 59.344 52.381 0.00 0.00 38.82 3.77
1009 1376 1.084370 GCTCTTGATCGACCAACCCG 61.084 60.000 0.00 0.00 0.00 5.28
1132 1502 2.992847 TCCTCTTGTACCTCACCTCA 57.007 50.000 0.00 0.00 0.00 3.86
1192 1562 2.321060 CGCCGCATCATCGTTGAC 59.679 61.111 0.00 0.00 33.85 3.18
1207 1577 1.531578 GTTGACGCAAACTTCCTCTCC 59.468 52.381 0.00 0.00 0.00 3.71
1215 1585 4.579869 GCAAACTTCCTCTCCTACATTGA 58.420 43.478 0.00 0.00 0.00 2.57
1384 1760 1.213926 GGCAGAAGGTCATGGGAGATT 59.786 52.381 0.00 0.00 0.00 2.40
1428 1804 2.915604 TCCTCCTTGCCAAGAAGAAGAT 59.084 45.455 5.89 0.00 0.00 2.40
1675 2080 1.333619 GATAACATTGGCACGGCGAAT 59.666 47.619 16.62 0.00 37.45 3.34
1696 2101 1.226603 CTACGCGTTCGAAGAGGGG 60.227 63.158 20.78 12.29 38.43 4.79
1905 2319 4.101790 CGCATTGCCGGACCACAC 62.102 66.667 5.05 0.00 0.00 3.82
1942 2356 5.097742 TGTGGGTTCTCAATATCAACGAT 57.902 39.130 0.00 0.00 0.00 3.73
1946 2360 4.209288 GGGTTCTCAATATCAACGATGACG 59.791 45.833 0.00 0.00 45.75 4.35
1956 2370 0.041047 AACGATGACGACGACGACAA 60.041 50.000 15.32 0.00 45.19 3.18
2020 2434 0.033504 CGGCAAGGCGGTATGATAGT 59.966 55.000 8.26 0.00 0.00 2.12
2074 2488 1.076485 GGAGGCTACCCGTGGACTA 60.076 63.158 0.00 0.00 35.76 2.59
2321 2739 1.631071 TACCAGATGGGGCAATCGCA 61.631 55.000 3.48 0.00 42.91 5.10
2432 2853 5.084818 TCTGAATGCAAGGACTTAATCGA 57.915 39.130 0.00 0.00 0.00 3.59
2439 2860 4.631377 TGCAAGGACTTAATCGATCAGTTG 59.369 41.667 10.67 7.32 0.00 3.16
2778 3214 4.586421 TGTTTTTGGTATCAGCATTCACCA 59.414 37.500 0.00 0.00 39.27 4.17
3421 3923 5.457799 CGGTAGGTTGATGTTTATCTACACG 59.542 44.000 0.00 0.00 39.72 4.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 8.522830 CAAAAGGTGAAAAGCAGAGGAATATAA 58.477 33.333 0.00 0.00 0.00 0.98
1 2 7.122650 CCAAAAGGTGAAAAGCAGAGGAATATA 59.877 37.037 0.00 0.00 0.00 0.86
2 3 6.071165 CCAAAAGGTGAAAAGCAGAGGAATAT 60.071 38.462 0.00 0.00 0.00 1.28
3 4 5.243730 CCAAAAGGTGAAAAGCAGAGGAATA 59.756 40.000 0.00 0.00 0.00 1.75
4 5 4.039609 CCAAAAGGTGAAAAGCAGAGGAAT 59.960 41.667 0.00 0.00 0.00 3.01
5 6 3.384467 CCAAAAGGTGAAAAGCAGAGGAA 59.616 43.478 0.00 0.00 0.00 3.36
6 7 2.958355 CCAAAAGGTGAAAAGCAGAGGA 59.042 45.455 0.00 0.00 0.00 3.71
7 8 2.695147 ACCAAAAGGTGAAAAGCAGAGG 59.305 45.455 0.00 0.00 0.00 3.69
8 9 5.067805 ACTTACCAAAAGGTGAAAAGCAGAG 59.932 40.000 0.00 0.00 0.00 3.35
9 10 4.953579 ACTTACCAAAAGGTGAAAAGCAGA 59.046 37.500 0.00 0.00 0.00 4.26
10 11 5.262588 ACTTACCAAAAGGTGAAAAGCAG 57.737 39.130 0.00 0.00 0.00 4.24
11 12 6.775629 AGATACTTACCAAAAGGTGAAAAGCA 59.224 34.615 0.00 0.00 0.00 3.91
12 13 7.084486 CAGATACTTACCAAAAGGTGAAAAGC 58.916 38.462 0.00 0.00 0.00 3.51
13 14 7.447238 TCCAGATACTTACCAAAAGGTGAAAAG 59.553 37.037 0.00 0.00 0.00 2.27
14 15 7.291566 TCCAGATACTTACCAAAAGGTGAAAA 58.708 34.615 0.00 0.00 0.00 2.29
15 16 6.843752 TCCAGATACTTACCAAAAGGTGAAA 58.156 36.000 0.00 0.00 0.00 2.69
16 17 6.442541 TCCAGATACTTACCAAAAGGTGAA 57.557 37.500 0.00 0.00 0.00 3.18
17 18 6.636454 ATCCAGATACTTACCAAAAGGTGA 57.364 37.500 0.00 0.00 0.00 4.02
18 19 7.282450 GGTAATCCAGATACTTACCAAAAGGTG 59.718 40.741 5.97 0.00 42.52 4.00
19 20 7.037153 TGGTAATCCAGATACTTACCAAAAGGT 60.037 37.037 10.18 0.00 46.97 3.50
20 21 7.343357 TGGTAATCCAGATACTTACCAAAAGG 58.657 38.462 10.18 0.00 46.97 3.11
26 27 7.878644 GGAATCTTGGTAATCCAGATACTTACC 59.121 40.741 4.20 4.20 45.22 2.85
27 28 7.878644 GGGAATCTTGGTAATCCAGATACTTAC 59.121 40.741 0.00 0.00 45.22 2.34
28 29 7.017254 GGGGAATCTTGGTAATCCAGATACTTA 59.983 40.741 0.00 0.00 45.22 2.24
29 30 6.183361 GGGGAATCTTGGTAATCCAGATACTT 60.183 42.308 0.00 0.00 45.22 2.24
30 31 5.310857 GGGGAATCTTGGTAATCCAGATACT 59.689 44.000 0.00 0.00 45.22 2.12
31 32 5.515008 GGGGGAATCTTGGTAATCCAGATAC 60.515 48.000 0.00 0.00 45.22 2.24
32 33 4.601857 GGGGGAATCTTGGTAATCCAGATA 59.398 45.833 0.00 0.00 45.22 1.98
33 34 3.399305 GGGGGAATCTTGGTAATCCAGAT 59.601 47.826 0.00 0.00 45.22 2.90
34 35 2.783510 GGGGGAATCTTGGTAATCCAGA 59.216 50.000 0.00 0.00 45.22 3.86
35 36 3.229697 GGGGGAATCTTGGTAATCCAG 57.770 52.381 0.00 0.00 45.22 3.86
468 469 3.552273 CCCTATGCTTTGCTGAATCATGC 60.552 47.826 0.00 0.00 0.00 4.06
565 566 8.556213 ACTAGAACCGCAATAAAACATTTCTA 57.444 30.769 0.00 0.00 0.00 2.10
571 572 6.348704 GGCTAAACTAGAACCGCAATAAAACA 60.349 38.462 0.00 0.00 0.00 2.83
657 676 1.518325 TACCTGTGAACGCCATGTTG 58.482 50.000 0.00 0.00 42.09 3.33
658 677 2.151202 CTTACCTGTGAACGCCATGTT 58.849 47.619 0.00 0.00 45.61 2.71
662 681 2.851263 ATTCTTACCTGTGAACGCCA 57.149 45.000 0.00 0.00 0.00 5.69
806 1159 3.486383 AGTAGTGGTTGTGGTTGGATTG 58.514 45.455 0.00 0.00 0.00 2.67
882 1236 1.066071 GCCCTCCAAGTAGGTCTGAAC 60.066 57.143 0.00 0.00 39.02 3.18
942 1296 6.014499 TGGGCTTGACTAGGAGTATATTAAGC 60.014 42.308 0.00 0.00 37.77 3.09
957 1311 8.890472 TCCTTGTTTATATATATGGGCTTGACT 58.110 33.333 5.44 0.00 0.00 3.41
958 1312 9.167311 CTCCTTGTTTATATATATGGGCTTGAC 57.833 37.037 5.44 0.00 0.00 3.18
964 1318 6.884832 TCGGCTCCTTGTTTATATATATGGG 58.115 40.000 5.44 0.00 0.00 4.00
1006 1373 4.837797 TTGGCCATGGGATGCGGG 62.838 66.667 15.13 0.00 0.00 6.13
1009 1376 1.380246 TCTGTTGGCCATGGGATGC 60.380 57.895 15.13 0.00 0.00 3.91
1192 1562 2.743636 TGTAGGAGAGGAAGTTTGCG 57.256 50.000 0.00 0.00 0.00 4.85
1207 1577 1.215173 TGGGGGCTGGAATCAATGTAG 59.785 52.381 0.00 0.00 0.00 2.74
1215 1585 2.046855 AGGGATGGGGGCTGGAAT 59.953 61.111 0.00 0.00 0.00 3.01
1327 1703 3.394836 AGGGAGAAGTGGCGGCTC 61.395 66.667 11.43 6.75 0.00 4.70
1384 1760 1.376683 GGTGTGGCGGCTATCAACA 60.377 57.895 11.43 2.22 0.00 3.33
1428 1804 0.899720 GGTATGACGTCTCCACCCAA 59.100 55.000 17.92 0.00 0.00 4.12
1675 2080 1.154093 CTCTTCGAACGCGTAGGCA 60.154 57.895 14.46 0.00 39.92 4.75
1917 2331 5.765677 TCGTTGATATTGAGAACCCACAAAA 59.234 36.000 0.00 0.00 0.00 2.44
1942 2356 1.009335 CACCTTGTCGTCGTCGTCA 60.009 57.895 1.33 0.00 38.33 4.35
1946 2360 0.388649 AGATGCACCTTGTCGTCGTC 60.389 55.000 0.00 0.00 0.00 4.20
1956 2370 1.269936 GCAAGCAAACAAGATGCACCT 60.270 47.619 0.00 0.00 46.22 4.00
2074 2488 1.366319 ACTCATCCTTGTGCCCTTCT 58.634 50.000 0.00 0.00 0.00 2.85
2321 2739 8.638873 TCGACATATACAAATACCAGAACATCT 58.361 33.333 0.00 0.00 0.00 2.90
2432 2853 2.283145 AGCTGCAACCTTCAACTGAT 57.717 45.000 1.02 0.00 0.00 2.90
2650 3086 5.070981 TGATGGTAGATAAAGCCAAGAGGAG 59.929 44.000 0.00 0.00 36.89 3.69
2919 3355 5.337554 CATTCGCATCAGTCACATCAAAAT 58.662 37.500 0.00 0.00 0.00 1.82
3350 3852 9.606631 ATCCTGACTGTCATTAAAGAAATAGAC 57.393 33.333 11.45 0.00 0.00 2.59
3421 3923 4.443394 CGTATACGGAAATTCCAGTAGTGC 59.557 45.833 17.61 8.31 35.91 4.40


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

AutoCloner maintained by Alex Coulton.