Multiple sequence alignment - TraesCS6B01G195200

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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 TraesCS6B01G195200 chr6B 100.000 2579 0 0 1 2579 230762831 230760253 0.000000e+00 4763
1 TraesCS6B01G195200 chr6B 96.872 1854 49 4 1 1848 661538925 661540775 0.000000e+00 3094
2 TraesCS6B01G195200 chr6B 92.537 737 26 7 1854 2579 661541471 661542189 0.000000e+00 1029
3 TraesCS6B01G195200 chr1B 97.464 1853 39 3 1 1848 460164055 460162206 0.000000e+00 3155
4 TraesCS6B01G195200 chr1B 97.086 1853 46 3 1 1848 544798278 544796429 0.000000e+00 3116
5 TraesCS6B01G195200 chr1B 96.440 1854 57 4 1 1848 569427356 569429206 0.000000e+00 3049
6 TraesCS6B01G195200 chr1B 96.386 1854 58 4 1 1848 94936245 94934395 0.000000e+00 3044
7 TraesCS6B01G195200 chr1B 96.875 1824 48 4 1 1818 668657508 668659328 0.000000e+00 3044
8 TraesCS6B01G195200 chr1B 95.872 751 21 2 1839 2579 544795760 544795010 0.000000e+00 1206
9 TraesCS6B01G195200 chr1B 94.947 752 25 3 1839 2579 460161549 460160800 0.000000e+00 1166
10 TraesCS6B01G195200 chr1B 93.085 752 23 3 1839 2579 94933742 94933009 0.000000e+00 1074
11 TraesCS6B01G195200 chr1B 92.264 698 26 2 1892 2579 364285670 364284991 0.000000e+00 965
12 TraesCS6B01G195200 chr1B 90.095 737 27 7 1854 2579 569429893 569430594 0.000000e+00 915
13 TraesCS6B01G195200 chr2B 97.086 1853 45 4 1 1848 69352021 69353869 0.000000e+00 3114
14 TraesCS6B01G195200 chr2B 96.602 1854 54 4 1 1848 23131121 23132971 0.000000e+00 3066
15 TraesCS6B01G195200 chr2B 96.405 751 16 4 1839 2579 750451921 750451172 0.000000e+00 1227
16 TraesCS6B01G195200 chr2B 94.834 755 28 2 1836 2579 69354511 69355265 0.000000e+00 1168
17 TraesCS6B01G195200 chr7B 96.926 1854 50 3 1 1848 41047019 41048871 0.000000e+00 3101
18 TraesCS6B01G195200 chr5B 97.181 745 19 2 1836 2579 69033739 69034482 0.000000e+00 1258
19 TraesCS6B01G195200 chr5B 92.693 698 23 5 1892 2579 621303727 621303048 0.000000e+00 981
20 TraesCS6B01G195200 chr5A 91.402 756 39 7 1835 2579 650153251 650153991 0.000000e+00 1013
21 TraesCS6B01G195200 chr5A 87.719 171 9 8 1836 2003 647553839 647554000 3.390000e-44 189
22 TraesCS6B01G195200 chr6A 91.270 756 40 8 1835 2579 162657123 162657863 0.000000e+00 1007
23 TraesCS6B01G195200 chr4B 92.614 704 24 5 1886 2579 654071445 654070760 0.000000e+00 987
24 TraesCS6B01G195200 chr2A 96.522 115 3 1 1835 1948 769230371 769230485 3.390000e-44 189
25 TraesCS6B01G195200 chr4A 87.135 171 11 7 1836 2003 521947975 521948137 1.580000e-42 183


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 TraesCS6B01G195200 chr6B 230760253 230762831 2578 True 4763.0 4763 100.0000 1 2579 1 chr6B.!!$R1 2578
1 TraesCS6B01G195200 chr6B 661538925 661542189 3264 False 2061.5 3094 94.7045 1 2579 2 chr6B.!!$F1 2578
2 TraesCS6B01G195200 chr1B 668657508 668659328 1820 False 3044.0 3044 96.8750 1 1818 1 chr1B.!!$F1 1817
3 TraesCS6B01G195200 chr1B 544795010 544798278 3268 True 2161.0 3116 96.4790 1 2579 2 chr1B.!!$R4 2578
4 TraesCS6B01G195200 chr1B 460160800 460164055 3255 True 2160.5 3155 96.2055 1 2579 2 chr1B.!!$R3 2578
5 TraesCS6B01G195200 chr1B 94933009 94936245 3236 True 2059.0 3044 94.7355 1 2579 2 chr1B.!!$R2 2578
6 TraesCS6B01G195200 chr1B 569427356 569430594 3238 False 1982.0 3049 93.2675 1 2579 2 chr1B.!!$F2 2578
7 TraesCS6B01G195200 chr1B 364284991 364285670 679 True 965.0 965 92.2640 1892 2579 1 chr1B.!!$R1 687
8 TraesCS6B01G195200 chr2B 23131121 23132971 1850 False 3066.0 3066 96.6020 1 1848 1 chr2B.!!$F1 1847
9 TraesCS6B01G195200 chr2B 69352021 69355265 3244 False 2141.0 3114 95.9600 1 2579 2 chr2B.!!$F2 2578
10 TraesCS6B01G195200 chr2B 750451172 750451921 749 True 1227.0 1227 96.4050 1839 2579 1 chr2B.!!$R1 740
11 TraesCS6B01G195200 chr7B 41047019 41048871 1852 False 3101.0 3101 96.9260 1 1848 1 chr7B.!!$F1 1847
12 TraesCS6B01G195200 chr5B 69033739 69034482 743 False 1258.0 1258 97.1810 1836 2579 1 chr5B.!!$F1 743
13 TraesCS6B01G195200 chr5B 621303048 621303727 679 True 981.0 981 92.6930 1892 2579 1 chr5B.!!$R1 687
14 TraesCS6B01G195200 chr5A 650153251 650153991 740 False 1013.0 1013 91.4020 1835 2579 1 chr5A.!!$F2 744
15 TraesCS6B01G195200 chr6A 162657123 162657863 740 False 1007.0 1007 91.2700 1835 2579 1 chr6A.!!$F1 744
16 TraesCS6B01G195200 chr4B 654070760 654071445 685 True 987.0 987 92.6140 1886 2579 1 chr4B.!!$R1 693

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
741 746 0.469892 CCACTGTGGAGCCCCTTTTT 60.47 55.0 22.33 0.0 40.96 1.94 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2174 3634 0.674895 CCAGGTCAGCTACTGCCAAC 60.675 60.0 6.7 0.0 40.8 3.77 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
61 62 3.834373 CTACCAAACGCGCGGTCG 61.834 66.667 35.22 23.42 36.69 4.79
120 121 4.015872 TCTAACCATTTTTCTGACGGCT 57.984 40.909 0.00 0.00 0.00 5.52
242 245 2.348888 GGTCGGTCGGGATCACACT 61.349 63.158 0.00 0.00 0.00 3.55
243 246 1.139095 GTCGGTCGGGATCACACTC 59.861 63.158 0.00 0.00 0.00 3.51
244 247 2.102357 CGGTCGGGATCACACTCG 59.898 66.667 0.00 0.00 0.00 4.18
475 478 3.393609 GGGTTAGGGTTAGGATTAGGTGG 59.606 52.174 0.00 0.00 0.00 4.61
476 479 3.181447 GGTTAGGGTTAGGATTAGGTGGC 60.181 52.174 0.00 0.00 0.00 5.01
512 515 2.357009 CAGCCATGGATGTTGCTTAGTC 59.643 50.000 22.12 0.00 30.08 2.59
542 545 4.094146 TGTTGTTGTGTGTGTGATACTGTG 59.906 41.667 0.00 0.00 0.00 3.66
550 553 4.821260 TGTGTGTGATACTGTGCTTGATTT 59.179 37.500 0.00 0.00 0.00 2.17
606 611 4.684724 ACCTAGGGTTCATCTCTGTACAA 58.315 43.478 14.81 0.00 27.29 2.41
655 660 6.922957 GGATTTAATGAACAGTGCAAGTTGAA 59.077 34.615 7.16 0.00 0.00 2.69
657 662 9.624697 GATTTAATGAACAGTGCAAGTTGAATA 57.375 29.630 7.16 0.00 0.00 1.75
670 675 6.095300 TGCAAGTTGAATATGGTATTGAGTGG 59.905 38.462 7.16 0.00 0.00 4.00
741 746 0.469892 CCACTGTGGAGCCCCTTTTT 60.470 55.000 22.33 0.00 40.96 1.94
840 845 2.754946 CTGTAACAGGGAGGCGTTTA 57.245 50.000 0.00 0.00 0.00 2.01
911 921 6.377712 TGGATGTTCAGTTTGATATGATGCAA 59.622 34.615 0.00 0.00 0.00 4.08
931 941 6.207928 TGCAACAGTTTGTTTGATATGACAG 58.792 36.000 0.00 0.00 38.77 3.51
958 968 7.665690 ACACATATGTATTTTTGCCACTTTGA 58.334 30.769 8.32 0.00 37.26 2.69
1490 1500 5.880901 TGTTCTTAAGAAGGAGAAGGCAAT 58.119 37.500 18.22 0.00 34.27 3.56
1501 1511 1.817447 AGAAGGCAATGCTTGAGCTTC 59.183 47.619 4.82 8.98 42.66 3.86
1513 1523 2.916702 TGAGCTTCTTGTTGCTGAGA 57.083 45.000 0.00 0.00 39.91 3.27
1743 1753 9.396022 CCTATGTTGTTAAGTTGTAATGGATCT 57.604 33.333 0.00 0.00 0.00 2.75
2003 3410 8.359060 TGTTATTACAAACCAAATCAAACAGC 57.641 30.769 0.00 0.00 0.00 4.40
2174 3634 0.252479 AAGATCCAGTGCCAGCTCTG 59.748 55.000 13.42 13.42 37.32 3.35
2194 3654 2.124942 GGCAGTAGCTGACCTGGC 60.125 66.667 16.68 16.68 41.70 4.85
2198 3658 0.320771 CAGTAGCTGACCTGGCGTTT 60.321 55.000 0.00 0.00 32.44 3.60
2263 3731 3.393426 AGACCTTGATCCATTGCCATT 57.607 42.857 0.00 0.00 0.00 3.16
2264 3732 3.028850 AGACCTTGATCCATTGCCATTG 58.971 45.455 0.00 0.00 0.00 2.82
2266 3734 2.762327 ACCTTGATCCATTGCCATTGAC 59.238 45.455 0.00 0.00 0.00 3.18
2419 3887 4.515191 TGTTGACTCATTTGTTACTGGAGC 59.485 41.667 0.00 0.00 0.00 4.70
2424 3892 4.202461 ACTCATTTGTTACTGGAGCAGGAA 60.202 41.667 0.00 0.00 35.51 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
100 101 4.475944 CAAGCCGTCAGAAAAATGGTTAG 58.524 43.478 0.00 0.00 0.00 2.34
120 121 2.356278 GCTGACAGATGGGCCCAA 59.644 61.111 32.58 13.16 0.00 4.12
242 245 2.456948 CGAGAGAGTGAGCGAGCGA 61.457 63.158 0.00 0.00 0.00 4.93
243 246 2.022623 CGAGAGAGTGAGCGAGCG 59.977 66.667 0.00 0.00 0.00 5.03
244 247 0.796491 CAACGAGAGAGTGAGCGAGC 60.796 60.000 0.00 0.00 0.00 5.03
335 338 2.920912 AAGGAGGTCGACGGCCAA 60.921 61.111 22.54 0.00 0.00 4.52
413 416 2.233271 CATAAGTCCCATGTCCATGCC 58.767 52.381 1.64 0.00 37.49 4.40
467 470 2.104963 GCCTAAGCTACTGCCACCTAAT 59.895 50.000 0.00 0.00 40.80 1.73
512 515 4.153296 TCACACACACAACAACAACACTAG 59.847 41.667 0.00 0.00 0.00 2.57
542 545 0.109597 CGCACCCTCACAAATCAAGC 60.110 55.000 0.00 0.00 0.00 4.01
550 553 0.179004 AATCAAACCGCACCCTCACA 60.179 50.000 0.00 0.00 0.00 3.58
655 660 7.721399 GGTTTCAATCTCCACTCAATACCATAT 59.279 37.037 0.00 0.00 0.00 1.78
657 662 5.888161 GGTTTCAATCTCCACTCAATACCAT 59.112 40.000 0.00 0.00 0.00 3.55
670 675 6.106003 ACCAACAAAAACTGGTTTCAATCTC 58.894 36.000 0.00 0.00 43.62 2.75
741 746 0.746063 CAAGCTCAAGTTGGCCACAA 59.254 50.000 3.88 0.00 0.00 3.33
840 845 1.713005 CCTGGACTGGGCAGCCATAT 61.713 60.000 15.19 0.00 35.29 1.78
911 921 6.017109 GTGTCCTGTCATATCAAACAAACTGT 60.017 38.462 0.00 0.00 0.00 3.55
931 941 6.207691 AGTGGCAAAAATACATATGTGTCC 57.792 37.500 18.81 9.16 39.77 4.02
1057 1067 4.320057 GCACAAACATCTCTGAAGAACAGG 60.320 45.833 0.00 0.00 45.76 4.00
1490 1500 1.335810 CAGCAACAAGAAGCTCAAGCA 59.664 47.619 4.59 0.00 45.16 3.91
1501 1511 3.439129 TCATTCAGCATCTCAGCAACAAG 59.561 43.478 0.00 0.00 36.85 3.16
1513 1523 2.091720 TGCCATACCCTTCATTCAGCAT 60.092 45.455 0.00 0.00 0.00 3.79
1573 1583 5.048504 CCAACATATCACAGCAAGTTCAAGT 60.049 40.000 0.00 0.00 0.00 3.16
1743 1753 8.994500 TCCATTACAACACTTAATACCATAGGA 58.006 33.333 0.00 0.00 0.00 2.94
1952 3359 5.949952 TGCCTCACTAAGTACTTGATACTGA 59.050 40.000 18.56 9.59 43.79 3.41
2003 3410 3.316029 TGTTGAACTCCAAGTGCTTCATG 59.684 43.478 0.00 0.00 35.03 3.07
2174 3634 0.674895 CCAGGTCAGCTACTGCCAAC 60.675 60.000 6.70 0.00 40.80 3.77
2198 3658 3.576078 TCAAGGTCTTCTCCAGCAAAA 57.424 42.857 0.00 0.00 0.00 2.44
2263 3731 4.635765 CCAAGAAGAAGAACACAACTGTCA 59.364 41.667 0.00 0.00 0.00 3.58
2264 3732 4.496507 GCCAAGAAGAAGAACACAACTGTC 60.497 45.833 0.00 0.00 0.00 3.51
2266 3734 3.378112 TGCCAAGAAGAAGAACACAACTG 59.622 43.478 0.00 0.00 0.00 3.16
2419 3887 1.588082 GCACCTGCACCAATTCCTG 59.412 57.895 0.00 0.00 41.59 3.86


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

AutoCloner maintained by Alex Coulton.