Multiple sequence alignment - TraesCS2B01G210400

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 TraesCS2B01G210400 chr2B 100.000 2824 0 0 1 2824 193389788 193392611 0.000000e+00 5216
1 TraesCS2B01G210400 chr2D 93.049 2834 102 38 17 2824 135600330 135603094 0.000000e+00 4054
2 TraesCS2B01G210400 chr2D 91.111 90 7 1 2395 2483 572683042 572682953 1.370000e-23 121
3 TraesCS2B01G210400 chr2D 90.805 87 8 0 2394 2480 23305959 23306045 1.780000e-22 117
4 TraesCS2B01G210400 chr2A 90.924 2446 121 42 1 2396 143722689 143725083 0.000000e+00 3193
5 TraesCS2B01G210400 chr2A 85.160 748 74 16 927 1663 143835523 143836244 0.000000e+00 732
6 TraesCS2B01G210400 chr2A 89.916 357 26 1 2478 2824 143725082 143725438 4.290000e-123 451
7 TraesCS2B01G210400 chr2A 90.805 87 8 0 2394 2480 25484393 25484307 1.780000e-22 117
8 TraesCS2B01G210400 chr7A 90.816 98 8 1 2383 2479 252187698 252187601 2.280000e-26 130
9 TraesCS2B01G210400 chr7A 91.860 86 7 0 2395 2480 68236049 68235964 1.370000e-23 121
10 TraesCS2B01G210400 chr6A 90.000 90 8 1 2391 2479 55552640 55552551 6.390000e-22 115
11 TraesCS2B01G210400 chr1A 90.000 90 8 1 2395 2483 587861394 587861305 6.390000e-22 115
12 TraesCS2B01G210400 chr7B 86.735 98 13 0 2391 2488 529956387 529956290 2.970000e-20 110


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 TraesCS2B01G210400 chr2B 193389788 193392611 2823 False 5216 5216 100.000 1 2824 1 chr2B.!!$F1 2823
1 TraesCS2B01G210400 chr2D 135600330 135603094 2764 False 4054 4054 93.049 17 2824 1 chr2D.!!$F2 2807
2 TraesCS2B01G210400 chr2A 143722689 143725438 2749 False 1822 3193 90.420 1 2824 2 chr2A.!!$F2 2823
3 TraesCS2B01G210400 chr2A 143835523 143836244 721 False 732 732 85.160 927 1663 1 chr2A.!!$F1 736

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
868 910 0.389948 GACCCACTTGTCAGCCTACG 60.39 60.0 0.0 0.0 35.29 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1871 1926 1.133482 AGGTGAGACAACCCCCAAAAG 60.133 52.381 0.0 0.0 41.54 2.27 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
321 339 1.461127 CTTTTCTTCCTCGTCGCCTTG 59.539 52.381 0.00 0.00 0.00 3.61
332 350 3.710722 CGCCTTGCTCCTCCTGGT 61.711 66.667 0.00 0.00 34.23 4.00
752 789 6.966534 ACACATTTGACATTCCTTCTTCTT 57.033 33.333 0.00 0.00 0.00 2.52
753 790 9.739276 ATACACATTTGACATTCCTTCTTCTTA 57.261 29.630 0.00 0.00 0.00 2.10
761 798 9.823647 TTGACATTCCTTCTTCTTATAGATGAC 57.176 33.333 0.00 0.00 29.48 3.06
762 799 9.206690 TGACATTCCTTCTTCTTATAGATGACT 57.793 33.333 0.00 0.00 29.48 3.41
774 816 9.587772 TTCTTATAGATGACTAAAGTGCAGTTC 57.412 33.333 7.36 0.00 32.04 3.01
792 834 5.056480 CAGTTCATAGTGGGCAATTCGATA 58.944 41.667 0.00 0.00 0.00 2.92
793 835 5.527214 CAGTTCATAGTGGGCAATTCGATAA 59.473 40.000 0.00 0.00 0.00 1.75
794 836 6.205464 CAGTTCATAGTGGGCAATTCGATAAT 59.795 38.462 0.00 0.00 0.00 1.28
795 837 7.387673 CAGTTCATAGTGGGCAATTCGATAATA 59.612 37.037 0.00 0.00 0.00 0.98
796 838 7.387948 AGTTCATAGTGGGCAATTCGATAATAC 59.612 37.037 0.00 0.00 0.00 1.89
798 840 6.873605 TCATAGTGGGCAATTCGATAATACTG 59.126 38.462 0.00 0.00 0.00 2.74
800 842 5.057149 AGTGGGCAATTCGATAATACTGTC 58.943 41.667 0.00 0.00 0.00 3.51
814 856 7.411480 CGATAATACTGTCTTGTTTTCGCTTCA 60.411 37.037 0.00 0.00 0.00 3.02
815 857 6.371809 AATACTGTCTTGTTTTCGCTTCAA 57.628 33.333 0.00 0.00 0.00 2.69
830 872 4.977963 TCGCTTCAATTTCTGCAAAAAGAG 59.022 37.500 0.00 0.00 0.00 2.85
868 910 0.389948 GACCCACTTGTCAGCCTACG 60.390 60.000 0.00 0.00 35.29 3.51
870 912 1.741770 CCACTTGTCAGCCTACGCC 60.742 63.158 0.00 0.00 34.57 5.68
871 913 1.005037 CACTTGTCAGCCTACGCCA 60.005 57.895 0.00 0.00 34.57 5.69
872 914 1.016130 CACTTGTCAGCCTACGCCAG 61.016 60.000 0.00 0.00 34.57 4.85
873 915 1.293498 CTTGTCAGCCTACGCCAGT 59.707 57.895 0.00 0.00 34.57 4.00
874 916 0.737715 CTTGTCAGCCTACGCCAGTC 60.738 60.000 0.00 0.00 34.57 3.51
875 917 2.202623 GTCAGCCTACGCCAGTCG 60.203 66.667 0.00 0.00 45.38 4.18
876 918 2.360726 TCAGCCTACGCCAGTCGA 60.361 61.111 0.00 0.00 41.67 4.20
877 919 1.974875 TCAGCCTACGCCAGTCGAA 60.975 57.895 0.00 0.00 41.67 3.71
878 920 1.517257 CAGCCTACGCCAGTCGAAG 60.517 63.158 0.00 0.00 41.67 3.79
879 921 2.886124 GCCTACGCCAGTCGAAGC 60.886 66.667 0.00 0.00 41.67 3.86
880 922 2.202756 CCTACGCCAGTCGAAGCC 60.203 66.667 0.00 0.00 41.67 4.35
881 923 2.711922 CCTACGCCAGTCGAAGCCT 61.712 63.158 0.00 0.00 41.67 4.58
896 938 2.032071 CCTTCGCCTCAACGGGTT 59.968 61.111 0.00 0.00 0.00 4.11
906 948 1.890041 CAACGGGTTGCGTTCTCCA 60.890 57.895 0.00 0.00 33.45 3.86
972 1014 1.374125 CGCACCGGTTCAGTGATCA 60.374 57.895 2.97 0.00 37.42 2.92
980 1022 1.197721 GGTTCAGTGATCAACCGCAAG 59.802 52.381 0.00 0.00 33.01 4.01
1064 1115 2.203126 GGCTCAGATCAAGGCCGG 60.203 66.667 0.00 0.00 35.08 6.13
1154 1206 0.387622 CCGTCTCGCTCGGTTGTTAA 60.388 55.000 4.97 0.00 42.62 2.01
1189 1241 2.363147 GTCTCGAGCCCCTGACCT 60.363 66.667 7.81 0.00 0.00 3.85
1327 1379 4.431131 CCTGGTTGGCTCCCGCAT 62.431 66.667 0.00 0.00 38.10 4.73
1338 1390 1.954927 CTCCCGCATCTTACCTTTCC 58.045 55.000 0.00 0.00 0.00 3.13
1513 1568 1.099295 TCTATGACATCGTCGGCCGT 61.099 55.000 27.15 3.60 34.95 5.68
1578 1633 3.181469 GGCCACATTATTCACCGAGTCTA 60.181 47.826 0.00 0.00 0.00 2.59
1871 1926 7.645340 GCACAATACATTTATGAATGACTGTCC 59.355 37.037 16.43 3.92 44.37 4.02
1895 1950 1.705997 GGGGGTTGTCTCACCTGTGT 61.706 60.000 0.00 0.00 36.97 3.72
1897 1952 0.468226 GGGTTGTCTCACCTGTGTCA 59.532 55.000 0.00 0.00 36.97 3.58
2248 2325 5.301551 TGCTGTCCTTCAACACATTACAATT 59.698 36.000 0.00 0.00 0.00 2.32
2305 2382 4.882842 TGTGTAGTGATGCTTTGGTAGA 57.117 40.909 0.00 0.00 0.00 2.59
2368 2445 7.389053 ACAGAGTTCCTGATATTTGAACTTGAC 59.611 37.037 13.42 5.24 46.37 3.18
2399 2476 9.197694 CTTGCATACTACAGTAATTGATACTCC 57.802 37.037 0.00 0.00 43.12 3.85
2404 2481 7.589958 ACTACAGTAATTGATACTCCCTCTG 57.410 40.000 0.00 0.00 43.12 3.35
2405 2482 7.126733 ACTACAGTAATTGATACTCCCTCTGT 58.873 38.462 0.00 0.00 43.12 3.41
2406 2483 8.280084 ACTACAGTAATTGATACTCCCTCTGTA 58.720 37.037 0.00 0.00 43.12 2.74
2408 2485 8.375493 ACAGTAATTGATACTCCCTCTGTAAA 57.625 34.615 0.00 0.00 43.12 2.01
2409 2486 8.478877 ACAGTAATTGATACTCCCTCTGTAAAG 58.521 37.037 0.00 0.00 43.12 1.85
2410 2487 8.696374 CAGTAATTGATACTCCCTCTGTAAAGA 58.304 37.037 0.00 0.00 43.12 2.52
2411 2488 9.268282 AGTAATTGATACTCCCTCTGTAAAGAA 57.732 33.333 0.00 0.00 41.04 2.52
2412 2489 9.886132 GTAATTGATACTCCCTCTGTAAAGAAA 57.114 33.333 0.00 0.00 0.00 2.52
2414 2491 8.970859 ATTGATACTCCCTCTGTAAAGAAATG 57.029 34.615 0.00 0.00 0.00 2.32
2415 2492 7.496346 TGATACTCCCTCTGTAAAGAAATGT 57.504 36.000 0.00 0.00 0.00 2.71
2416 2493 8.603898 TGATACTCCCTCTGTAAAGAAATGTA 57.396 34.615 0.00 0.00 0.00 2.29
2417 2494 9.042450 TGATACTCCCTCTGTAAAGAAATGTAA 57.958 33.333 0.00 0.00 0.00 2.41
2418 2495 9.535878 GATACTCCCTCTGTAAAGAAATGTAAG 57.464 37.037 0.00 0.00 0.00 2.34
2419 2496 7.554959 ACTCCCTCTGTAAAGAAATGTAAGA 57.445 36.000 0.00 0.00 0.00 2.10
2420 2497 7.616313 ACTCCCTCTGTAAAGAAATGTAAGAG 58.384 38.462 0.00 0.00 0.00 2.85
2421 2498 7.235812 ACTCCCTCTGTAAAGAAATGTAAGAGT 59.764 37.037 0.00 0.00 0.00 3.24
2422 2499 7.974504 TCCCTCTGTAAAGAAATGTAAGAGTT 58.025 34.615 0.00 0.00 0.00 3.01
2423 2500 8.437575 TCCCTCTGTAAAGAAATGTAAGAGTTT 58.562 33.333 0.00 0.00 0.00 2.66
2498 2575 8.958506 GGGAGTATATTCCAGTATACTACAGTG 58.041 40.741 15.53 0.00 44.81 3.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
63 64 0.584876 CACGTTTTGACGGGGAGAAC 59.415 55.000 3.90 0.00 37.45 3.01
161 166 2.309162 TCTCCTGAGGCAGTGTACTACT 59.691 50.000 0.00 0.00 41.36 2.57
321 339 4.459089 GTCGCCACCAGGAGGAGC 62.459 72.222 7.20 0.00 38.69 4.70
592 613 0.035152 AGCCACGATCCAAGCATGAA 60.035 50.000 0.00 0.00 0.00 2.57
593 614 0.745486 CAGCCACGATCCAAGCATGA 60.745 55.000 0.00 0.00 0.00 3.07
668 703 3.525268 AAACACTGGAGCCAACAAAAG 57.475 42.857 0.00 0.00 0.00 2.27
753 790 8.700051 ACTATGAACTGCACTTTAGTCATCTAT 58.300 33.333 0.00 0.00 0.00 1.98
761 798 3.375299 GCCCACTATGAACTGCACTTTAG 59.625 47.826 0.00 0.00 0.00 1.85
762 799 3.244735 TGCCCACTATGAACTGCACTTTA 60.245 43.478 0.00 0.00 0.00 1.85
763 800 2.162681 GCCCACTATGAACTGCACTTT 58.837 47.619 0.00 0.00 0.00 2.66
774 816 6.650807 ACAGTATTATCGAATTGCCCACTATG 59.349 38.462 0.00 0.00 0.00 2.23
792 834 6.371809 TTGAAGCGAAAACAAGACAGTATT 57.628 33.333 0.00 0.00 0.00 1.89
793 835 6.560253 ATTGAAGCGAAAACAAGACAGTAT 57.440 33.333 0.00 0.00 0.00 2.12
794 836 6.371809 AATTGAAGCGAAAACAAGACAGTA 57.628 33.333 0.00 0.00 0.00 2.74
795 837 4.900635 ATTGAAGCGAAAACAAGACAGT 57.099 36.364 0.00 0.00 0.00 3.55
796 838 5.973565 AGAAATTGAAGCGAAAACAAGACAG 59.026 36.000 0.00 0.00 0.00 3.51
798 840 5.331830 GCAGAAATTGAAGCGAAAACAAGAC 60.332 40.000 0.00 0.00 0.00 3.01
800 842 4.503734 TGCAGAAATTGAAGCGAAAACAAG 59.496 37.500 0.00 0.00 0.00 3.16
814 856 5.217978 TGCCATCTCTTTTTGCAGAAATT 57.782 34.783 2.48 0.00 0.00 1.82
815 857 4.877378 TGCCATCTCTTTTTGCAGAAAT 57.123 36.364 2.48 0.00 0.00 2.17
846 888 3.050275 GCTGACAAGTGGGTCCGC 61.050 66.667 0.00 0.00 40.05 5.54
850 892 1.671742 CGTAGGCTGACAAGTGGGT 59.328 57.895 0.00 0.00 0.00 4.51
879 921 2.032071 AACCCGTTGAGGCGAAGG 59.968 61.111 0.00 0.00 39.21 3.46
880 922 2.966309 GCAACCCGTTGAGGCGAAG 61.966 63.158 11.70 0.00 42.93 3.79
881 923 2.975799 GCAACCCGTTGAGGCGAA 60.976 61.111 11.70 0.00 42.93 4.70
896 938 2.962569 CGGAGACTGGAGAACGCA 59.037 61.111 0.00 0.00 0.00 5.24
955 997 0.517316 GTTGATCACTGAACCGGTGC 59.483 55.000 8.52 6.80 40.25 5.01
960 1002 1.197721 CTTGCGGTTGATCACTGAACC 59.802 52.381 0.00 0.00 38.65 3.62
963 1005 1.291184 CGCTTGCGGTTGATCACTGA 61.291 55.000 7.16 0.00 32.74 3.41
1050 1101 3.089874 CCCCCGGCCTTGATCTGA 61.090 66.667 0.00 0.00 0.00 3.27
1154 1206 3.204827 GGCGAGGCGTGCATGAAT 61.205 61.111 10.93 0.00 0.00 2.57
1327 1379 0.978907 GTGGGGACGGAAAGGTAAGA 59.021 55.000 0.00 0.00 0.00 2.10
1578 1633 6.989169 CCATTCCTCTAATCGAGAATTTCACT 59.011 38.462 0.00 0.00 42.62 3.41
1871 1926 1.133482 AGGTGAGACAACCCCCAAAAG 60.133 52.381 0.00 0.00 41.54 2.27
1932 1987 6.496565 CAGGAAGACCTTACCTAGATGATCAT 59.503 42.308 8.25 8.25 45.36 2.45
1942 1997 1.903183 GCACTCAGGAAGACCTTACCT 59.097 52.381 0.00 0.00 45.36 3.08
2095 2150 2.373169 AGAAGGTGATGCTGGTTTCTCA 59.627 45.455 0.00 0.00 0.00 3.27
2142 2219 3.254060 ACTCAATGATTTCACGGTCTCG 58.746 45.455 0.00 0.00 43.02 4.04
2264 2341 7.288810 ACACAAAAGCATCATAGGAAAAGAA 57.711 32.000 0.00 0.00 0.00 2.52
2368 2445 6.533723 TCAATTACTGTAGTATGCAAGAACCG 59.466 38.462 0.00 0.00 0.00 4.44
2459 2536 8.483758 TGGAATATACTCCCTCTGTAAAGAAAC 58.516 37.037 0.00 0.00 34.22 2.78
2498 2575 8.112449 GCTCATTTGCAAAATTAACTATGCTTC 58.888 33.333 17.19 0.00 39.49 3.86
2777 2864 3.596214 AGATCGCGGTGTTATTGTCTTT 58.404 40.909 6.13 0.00 0.00 2.52


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

AutoCloner maintained by Alex Coulton.