Multiple sequence alignment - TraesCS3B01G572100

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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 TraesCS3B01G572100 chr3B 100.000 2846 0 0 1 2846 803175710 803178555 0 5256
1 TraesCS3B01G572100 chr3B 95.937 2215 88 2 1 2214 807745334 807747547 0 3591
2 TraesCS3B01G572100 chr3B 96.651 627 20 1 2219 2844 804273201 804273827 0 1040
3 TraesCS3B01G572100 chr3B 96.172 627 23 1 2219 2844 804264593 804265219 0 1024
4 TraesCS3B01G572100 chr6A 96.343 2215 79 2 1 2214 300400 302613 0 3640
5 TraesCS3B01G572100 chr6A 96.332 627 21 2 2219 2844 302662 303287 0 1029
6 TraesCS3B01G572100 chr6B 95.939 2216 87 3 1 2214 3397150 3399364 0 3591
7 TraesCS3B01G572100 chr6B 95.937 2215 88 2 1 2214 6265431 6263218 0 3591
8 TraesCS3B01G572100 chr6B 97.129 627 17 1 2219 2844 3399413 3400039 0 1057
9 TraesCS3B01G572100 chr6B 96.332 627 20 2 2219 2844 6263170 6262546 0 1027
10 TraesCS3B01G572100 chr5B 95.801 2215 92 1 1 2214 521485518 521487732 0 3574
11 TraesCS3B01G572100 chr5B 96.178 628 22 2 2221 2846 521487783 521488410 0 1026
12 TraesCS3B01G572100 chr2B 95.307 2216 102 2 1 2214 489888 487673 0 3515
13 TraesCS3B01G572100 chr7B 95.309 2217 99 4 1 2214 745378043 745375829 0 3513
14 TraesCS3B01G572100 chr7B 95.305 2215 98 4 1 2214 750189047 750186838 0 3509
15 TraesCS3B01G572100 chr7B 95.880 631 18 7 2219 2846 745375780 745375155 0 1014
16 TraesCS3B01G572100 chr7B 95.411 632 25 3 2219 2846 708229079 708228448 0 1003
17 TraesCS3B01G572100 chr4A 95.217 2216 103 3 1 2214 717091173 717088959 0 3502
18 TraesCS3B01G572100 chr4B 95.527 626 26 2 2223 2846 8774397 8773772 0 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 TraesCS3B01G572100 chr3B 803175710 803178555 2845 False 5256.0 5256 100.0000 1 2846 1 chr3B.!!$F1 2845
1 TraesCS3B01G572100 chr3B 807745334 807747547 2213 False 3591.0 3591 95.9370 1 2214 1 chr3B.!!$F4 2213
2 TraesCS3B01G572100 chr3B 804273201 804273827 626 False 1040.0 1040 96.6510 2219 2844 1 chr3B.!!$F3 625
3 TraesCS3B01G572100 chr3B 804264593 804265219 626 False 1024.0 1024 96.1720 2219 2844 1 chr3B.!!$F2 625
4 TraesCS3B01G572100 chr6A 300400 303287 2887 False 2334.5 3640 96.3375 1 2844 2 chr6A.!!$F1 2843
5 TraesCS3B01G572100 chr6B 3397150 3400039 2889 False 2324.0 3591 96.5340 1 2844 2 chr6B.!!$F1 2843
6 TraesCS3B01G572100 chr6B 6262546 6265431 2885 True 2309.0 3591 96.1345 1 2844 2 chr6B.!!$R1 2843
7 TraesCS3B01G572100 chr5B 521485518 521488410 2892 False 2300.0 3574 95.9895 1 2846 2 chr5B.!!$F1 2845
8 TraesCS3B01G572100 chr2B 487673 489888 2215 True 3515.0 3515 95.3070 1 2214 1 chr2B.!!$R1 2213
9 TraesCS3B01G572100 chr7B 750186838 750189047 2209 True 3509.0 3509 95.3050 1 2214 1 chr7B.!!$R2 2213
10 TraesCS3B01G572100 chr7B 745375155 745378043 2888 True 2263.5 3513 95.5945 1 2846 2 chr7B.!!$R3 2845
11 TraesCS3B01G572100 chr7B 708228448 708229079 631 True 1003.0 1003 95.4110 2219 2846 1 chr7B.!!$R1 627
12 TraesCS3B01G572100 chr4A 717088959 717091173 2214 True 3502.0 3502 95.2170 1 2214 1 chr4A.!!$R1 2213
13 TraesCS3B01G572100 chr4B 8773772 8774397 625 True 1000.0 1000 95.5270 2223 2846 1 chr4B.!!$R1 623

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
265 267 1.148759 GCTCGTCGGAAATGGAGAGC 61.149 60.0 0.0 0.0 43.11 4.09 F
1388 1393 0.676782 GCAGATTTGCCCCGTAGTGT 60.677 55.0 0.0 0.0 44.74 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1622 1627 0.249911 GATAACCTCAAGCCGCGGAT 60.250 55.0 33.48 23.9 0.0 4.18 R
2482 2534 0.394352 CCAATACACCAGGGGCTCAC 60.394 60.0 0.00 0.0 0.0 3.51 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
156 158 1.227853 GTGTCCGGATACCCATGGC 60.228 63.158 19.92 0.00 0.00 4.40
265 267 1.148759 GCTCGTCGGAAATGGAGAGC 61.149 60.000 0.00 0.00 43.11 4.09
332 334 4.959460 TGGGGCCCCAAGGAGGTT 62.959 66.667 42.66 0.00 44.12 3.50
390 392 2.685380 CCTTCCGGACTCCAGGCT 60.685 66.667 1.83 0.00 0.00 4.58
442 444 2.045143 GACCCTCGTCCGGACTCT 60.045 66.667 30.92 9.33 32.40 3.24
741 745 3.734463 TGATGCTTAGTTCGGTGTTTGA 58.266 40.909 0.00 0.00 0.00 2.69
753 757 3.193691 TCGGTGTTTGAAAAGAAAAGCCA 59.806 39.130 0.00 0.00 0.00 4.75
871 875 3.265791 GAGGTCAATACACTGAAGCAGG 58.734 50.000 0.00 0.00 35.51 4.85
876 880 3.327757 TCAATACACTGAAGCAGGACCTT 59.672 43.478 0.00 0.00 35.51 3.50
1109 1114 3.393149 GAGAGAAAGGGGAGGCGCC 62.393 68.421 21.89 21.89 36.67 6.53
1147 1152 1.110442 AGAGCTCCAGATTCTCGTGG 58.890 55.000 10.93 0.00 34.87 4.94
1330 1335 8.728088 AAGCAAGAATGTAAAAGTCAATTACG 57.272 30.769 0.00 0.00 36.31 3.18
1344 1349 7.100458 AGTCAATTACGTATTACTTACCCGT 57.900 36.000 0.00 0.00 35.68 5.28
1388 1393 0.676782 GCAGATTTGCCCCGTAGTGT 60.677 55.000 0.00 0.00 44.74 3.55
1593 1598 1.224592 CATGCCCGGGAGCTACTTT 59.775 57.895 29.31 0.00 0.00 2.66
1622 1627 4.175337 GCGGCTGGTGGATGCCTA 62.175 66.667 0.00 0.00 46.42 3.93
1635 1640 2.663188 GCCTATCCGCGGCTTGAG 60.663 66.667 23.51 14.03 44.17 3.02
1666 1671 0.250234 CTCCGTCTGCATTGAAGGGA 59.750 55.000 7.84 4.53 36.48 4.20
1789 1794 4.263068 CCGAAATGTATTATGAGGGCCTCT 60.263 45.833 32.28 20.32 0.00 3.69
1853 1859 6.102006 TGTAATTTTTGAATAGACTCGCGG 57.898 37.500 6.13 0.00 0.00 6.46
1869 1876 2.095314 TCGCGGTTGTTATTCTGTACGA 60.095 45.455 6.13 0.00 0.00 3.43
1882 1889 9.659830 GTTATTCTGTACGATGAAAACTTGTTT 57.340 29.630 0.00 0.00 0.00 2.83
1935 1943 0.397187 TACTACCTTTTGTGCGGCCA 59.603 50.000 2.24 0.00 0.00 5.36
2017 2025 3.335579 GTGTTCGGGATAAACTTGAGCT 58.664 45.455 0.00 0.00 0.00 4.09
2085 2093 1.534163 GAACAAGGCAACCGGACTTAC 59.466 52.381 9.46 0.00 45.50 2.34
2100 2108 4.024048 CGGACTTACAATGCTTGAACACTT 60.024 41.667 3.37 0.00 0.00 3.16
2214 2222 1.187974 TAATTCCGGTTCCTCGCTCA 58.812 50.000 0.00 0.00 0.00 4.26
2215 2223 0.541863 AATTCCGGTTCCTCGCTCAT 59.458 50.000 0.00 0.00 0.00 2.90
2216 2224 0.179073 ATTCCGGTTCCTCGCTCATG 60.179 55.000 0.00 0.00 0.00 3.07
2217 2225 2.852495 TTCCGGTTCCTCGCTCATGC 62.852 60.000 0.00 0.00 0.00 4.06
2227 2279 4.166888 GCTCATGCCCGGCTCTCA 62.167 66.667 11.61 0.00 0.00 3.27
2365 2417 1.304052 CCAAAACATGGGAGCCGGA 60.304 57.895 5.05 0.00 46.27 5.14
2482 2534 6.633500 ATCACACCATAATTTTGGGATACG 57.367 37.500 17.83 4.93 41.35 3.06
2533 2585 2.387445 TACGGTTGCAGCATGTCGC 61.387 57.895 2.05 0.00 39.31 5.19
2544 2596 1.250476 GCATGTCGCGAAATGAACAC 58.750 50.000 37.21 18.99 0.00 3.32
2618 2675 9.606631 ATTGTTTATTCAAAAAGGTACTGCAAA 57.393 25.926 0.00 0.00 40.86 3.68
2697 2754 2.284331 TCCAGGGGTAAGCTGCGA 60.284 61.111 0.00 0.00 0.00 5.10
2713 2771 4.640201 AGCTGCGAATGGTATGTAAAACAT 59.360 37.500 0.00 0.00 42.35 2.71
2836 2894 1.153745 CGAAGGCGGAGTCCTGAAG 60.154 63.158 7.77 0.00 34.48 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
331 333 2.289444 CGCTACCTCCTCTTGACCAAAA 60.289 50.000 0.00 0.00 0.00 2.44
332 334 1.275291 CGCTACCTCCTCTTGACCAAA 59.725 52.381 0.00 0.00 0.00 3.28
442 444 1.227527 CGCTGATGGTTCCGGCATA 60.228 57.895 0.00 0.00 0.00 3.14
495 497 2.918802 ACACCGGCGTCTTACCCA 60.919 61.111 6.01 0.00 0.00 4.51
612 614 0.246635 GCTCTTGGCGGACTGAACTA 59.753 55.000 0.00 0.00 0.00 2.24
741 745 4.170468 TCCTCAGTCTGGCTTTTCTTTT 57.830 40.909 0.00 0.00 0.00 2.27
753 757 8.301002 GCGTATATCTTTTTAGATCCTCAGTCT 58.699 37.037 0.00 0.00 0.00 3.24
1032 1037 0.546747 CCACCACTTCCCTCAGGGTA 60.547 60.000 10.50 0.00 44.74 3.69
1147 1152 2.143925 CTCCAAACCCTCGTGTTTCTC 58.856 52.381 0.00 0.00 36.33 2.87
1388 1393 3.881952 AACGCGGCAGCATCAGACA 62.882 57.895 12.47 0.00 45.49 3.41
1622 1627 0.249911 GATAACCTCAAGCCGCGGAT 60.250 55.000 33.48 23.90 0.00 4.18
1635 1640 2.271800 CAGACGGAGCACTTGATAACC 58.728 52.381 0.00 0.00 0.00 2.85
1747 1752 2.816958 CGTGCGATGCTCCTTGCT 60.817 61.111 0.00 0.00 43.37 3.91
1789 1794 2.463589 ATTCGGCGAGCACCCTTCAA 62.464 55.000 10.46 0.00 0.00 2.69
1853 1859 9.103048 CAAGTTTTCATCGTACAGAATAACAAC 57.897 33.333 0.00 0.00 0.00 3.32
1869 1876 7.432252 GCTTAGCGCATATAAACAAGTTTTCAT 59.568 33.333 11.47 0.00 38.92 2.57
1918 1926 0.887933 AATGGCCGCACAAAAGGTAG 59.112 50.000 0.00 0.00 0.00 3.18
1925 1933 3.883830 AATTGATAAATGGCCGCACAA 57.116 38.095 0.00 0.00 0.00 3.33
1935 1943 8.755977 ACTTGCCATCTCTCAAAATTGATAAAT 58.244 29.630 0.00 0.00 36.46 1.40
2214 2222 1.056700 ATAAGGTGAGAGCCGGGCAT 61.057 55.000 23.09 9.38 0.00 4.40
2215 2223 1.686325 GATAAGGTGAGAGCCGGGCA 61.686 60.000 23.09 0.00 0.00 5.36
2216 2224 1.069935 GATAAGGTGAGAGCCGGGC 59.930 63.158 12.11 12.11 0.00 6.13
2217 2225 1.051812 ATGATAAGGTGAGAGCCGGG 58.948 55.000 2.18 0.00 0.00 5.73
2227 2279 4.553330 AAACTGACCGTCATGATAAGGT 57.447 40.909 16.94 16.94 40.11 3.50
2355 2407 3.961414 GGGTTTGTCCGGCTCCCA 61.961 66.667 0.00 0.00 38.15 4.37
2365 2417 3.603965 TGGGTCAATAGTTGGGTTTGT 57.396 42.857 0.00 0.00 0.00 2.83
2482 2534 0.394352 CCAATACACCAGGGGCTCAC 60.394 60.000 0.00 0.00 0.00 3.51
2618 2675 5.812642 CACTATTTGTATCGTTCTGCTTCCT 59.187 40.000 0.00 0.00 0.00 3.36
2713 2771 7.210174 GTGGTCTCTGTTATGAGCATTATACA 58.790 38.462 0.00 0.00 41.67 2.29


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

AutoCloner maintained by Alex Coulton.