Multiple sequence alignment - TraesCS6A01G146100

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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 TraesCS6A01G146100 chr6A 100.000 3643 0 0 1 3643 124421891 124425533 0.000000e+00 6728.0
1 TraesCS6A01G146100 chr6A 98.787 1237 11 1 878 2110 124917107 124915871 0.000000e+00 2198.0
2 TraesCS6A01G146100 chr6A 98.575 772 9 2 1 772 124917901 124917132 0.000000e+00 1363.0
3 TraesCS6A01G146100 chr6A 98.632 731 7 1 2913 3643 124915865 124915138 0.000000e+00 1291.0
4 TraesCS6A01G146100 chr6D 95.299 2042 83 8 920 2957 103082942 103084974 0.000000e+00 3227.0
5 TraesCS6A01G146100 chr6D 96.305 1732 57 4 920 2648 103051635 103053362 0.000000e+00 2837.0
6 TraesCS6A01G146100 chrUn 96.780 1584 45 3 920 2500 244606807 244608387 0.000000e+00 2638.0
7 TraesCS6A01G146100 chrUn 95.000 1000 40 7 1959 2957 218480242 218481232 0.000000e+00 1561.0
8 TraesCS6A01G146100 chrUn 92.253 839 51 7 2393 3227 374568661 374567833 0.000000e+00 1177.0
9 TraesCS6A01G146100 chrUn 89.396 613 34 11 25 635 472983866 472984449 0.000000e+00 743.0
10 TraesCS6A01G146100 chrUn 95.792 404 17 0 1812 2215 262506256 262506659 0.000000e+00 652.0
11 TraesCS6A01G146100 chrUn 95.792 404 17 0 1812 2215 326638841 326639244 0.000000e+00 652.0
12 TraesCS6A01G146100 chrUn 91.549 213 15 3 3413 3623 293553707 293553918 1.280000e-74 291.0
13 TraesCS6A01G146100 chrUn 91.549 213 15 3 3413 3623 314486469 314486680 1.280000e-74 291.0
14 TraesCS6A01G146100 chrUn 91.549 213 15 3 3413 3623 325383265 325383054 1.280000e-74 291.0
15 TraesCS6A01G146100 chrUn 83.333 276 18 16 3336 3583 233053275 233053550 2.830000e-56 230.0
16 TraesCS6A01G146100 chr7A 88.514 1837 122 28 1 1810 171549394 171547620 0.000000e+00 2141.0
17 TraesCS6A01G146100 chr7A 94.587 1367 61 9 2280 3643 171438297 171436941 0.000000e+00 2102.0
18 TraesCS6A01G146100 chr7A 90.347 1067 77 18 922 1982 171439644 171438598 0.000000e+00 1376.0
19 TraesCS6A01G146100 chr7A 86.571 1251 87 39 2393 3586 171547286 171546060 0.000000e+00 1304.0
20 TraesCS6A01G146100 chr7A 91.503 918 63 7 922 1837 172235272 172234368 0.000000e+00 1249.0
21 TraesCS6A01G146100 chr7A 92.133 839 52 7 2393 3227 171875846 171875018 0.000000e+00 1171.0
22 TraesCS6A01G146100 chr7A 95.577 407 18 0 1812 2218 171947193 171946787 0.000000e+00 652.0
23 TraesCS6A01G146100 chr7A 87.819 353 21 8 3291 3623 171945752 171945402 2.640000e-106 396.0
24 TraesCS6A01G146100 chr7A 94.152 171 7 3 3291 3460 172232907 172232739 1.300000e-64 257.0
25 TraesCS6A01G146100 chr7D 92.927 1329 72 12 922 2242 168990756 168992070 0.000000e+00 1914.0
26 TraesCS6A01G146100 chr7D 88.133 1660 101 39 1985 3583 169025406 169027030 0.000000e+00 1886.0
27 TraesCS6A01G146100 chr7D 86.928 1683 117 42 1985 3586 169440077 169438417 0.000000e+00 1794.0
28 TraesCS6A01G146100 chr7D 90.233 1290 84 18 2283 3536 169497935 169496652 0.000000e+00 1646.0
29 TraesCS6A01G146100 chr7D 91.519 1073 68 12 922 1981 169422797 169421735 0.000000e+00 1456.0
30 TraesCS6A01G146100 chr7D 90.769 975 61 10 1985 2957 169421686 169420739 0.000000e+00 1275.0
31 TraesCS6A01G146100 chr7D 90.247 687 50 13 2968 3643 169419716 169419036 0.000000e+00 881.0
32 TraesCS6A01G146100 chr7D 89.389 311 21 7 524 828 169499293 169499597 7.380000e-102 381.0
33 TraesCS6A01G146100 chr7B 91.364 1019 63 12 2297 3297 135018252 135017241 0.000000e+00 1371.0
34 TraesCS6A01G146100 chr7B 93.021 917 55 8 920 1832 135036656 135035745 0.000000e+00 1330.0
35 TraesCS6A01G146100 chr7B 89.845 965 74 13 1985 2938 128437600 128438551 0.000000e+00 1218.0
36 TraesCS6A01G146100 chr7B 87.324 497 33 11 3000 3469 233205976 233206469 3.200000e-150 542.0
37 TraesCS6A01G146100 chr7B 86.636 434 28 11 3063 3469 672194975 672195405 1.540000e-123 453.0
38 TraesCS6A01G146100 chr7B 85.139 323 20 15 3291 3586 135034310 135033989 4.570000e-79 305.0
39 TraesCS6A01G146100 chr7B 84.984 313 23 11 3294 3583 134494915 134495226 2.750000e-76 296.0
40 TraesCS6A01G146100 chr7B 95.902 122 5 0 1860 1981 135035747 135035626 7.980000e-47 198.0
41 TraesCS6A01G146100 chr7B 93.478 46 3 0 1885 1930 127774038 127773993 6.530000e-08 69.4
42 TraesCS6A01G146100 chr7B 93.478 46 3 0 1885 1930 128070279 128070234 6.530000e-08 69.4
43 TraesCS6A01G146100 chr1B 87.539 321 29 6 1988 2301 421097415 421097099 9.620000e-96 361.0
44 TraesCS6A01G146100 chr1A 85.329 334 27 7 1988 2301 391257423 391257092 3.510000e-85 326.0
45 TraesCS6A01G146100 chr2A 79.654 231 38 6 472 702 31910301 31910080 1.350000e-34 158.0
46 TraesCS6A01G146100 chr3B 96.875 32 1 0 453 484 39928157 39928188 2.000000e-03 54.7


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 TraesCS6A01G146100 chr6A 124421891 124425533 3642 False 6728.000000 6728 100.000000 1 3643 1 chr6A.!!$F1 3642
1 TraesCS6A01G146100 chr6A 124915138 124917901 2763 True 1617.333333 2198 98.664667 1 3643 3 chr6A.!!$R1 3642
2 TraesCS6A01G146100 chr6D 103082942 103084974 2032 False 3227.000000 3227 95.299000 920 2957 1 chr6D.!!$F2 2037
3 TraesCS6A01G146100 chr6D 103051635 103053362 1727 False 2837.000000 2837 96.305000 920 2648 1 chr6D.!!$F1 1728
4 TraesCS6A01G146100 chrUn 244606807 244608387 1580 False 2638.000000 2638 96.780000 920 2500 1 chrUn.!!$F3 1580
5 TraesCS6A01G146100 chrUn 218480242 218481232 990 False 1561.000000 1561 95.000000 1959 2957 1 chrUn.!!$F1 998
6 TraesCS6A01G146100 chrUn 374567833 374568661 828 True 1177.000000 1177 92.253000 2393 3227 1 chrUn.!!$R2 834
7 TraesCS6A01G146100 chrUn 472983866 472984449 583 False 743.000000 743 89.396000 25 635 1 chrUn.!!$F8 610
8 TraesCS6A01G146100 chr7A 171436941 171439644 2703 True 1739.000000 2102 92.467000 922 3643 2 chr7A.!!$R2 2721
9 TraesCS6A01G146100 chr7A 171546060 171549394 3334 True 1722.500000 2141 87.542500 1 3586 2 chr7A.!!$R3 3585
10 TraesCS6A01G146100 chr7A 171875018 171875846 828 True 1171.000000 1171 92.133000 2393 3227 1 chr7A.!!$R1 834
11 TraesCS6A01G146100 chr7A 172232739 172235272 2533 True 753.000000 1249 92.827500 922 3460 2 chr7A.!!$R5 2538
12 TraesCS6A01G146100 chr7A 171945402 171947193 1791 True 524.000000 652 91.698000 1812 3623 2 chr7A.!!$R4 1811
13 TraesCS6A01G146100 chr7D 168990756 168992070 1314 False 1914.000000 1914 92.927000 922 2242 1 chr7D.!!$F1 1320
14 TraesCS6A01G146100 chr7D 169025406 169027030 1624 False 1886.000000 1886 88.133000 1985 3583 1 chr7D.!!$F2 1598
15 TraesCS6A01G146100 chr7D 169438417 169440077 1660 True 1794.000000 1794 86.928000 1985 3586 1 chr7D.!!$R1 1601
16 TraesCS6A01G146100 chr7D 169496652 169497935 1283 True 1646.000000 1646 90.233000 2283 3536 1 chr7D.!!$R2 1253
17 TraesCS6A01G146100 chr7D 169419036 169422797 3761 True 1204.000000 1456 90.845000 922 3643 3 chr7D.!!$R3 2721
18 TraesCS6A01G146100 chr7B 135017241 135018252 1011 True 1371.000000 1371 91.364000 2297 3297 1 chr7B.!!$R3 1000
19 TraesCS6A01G146100 chr7B 128437600 128438551 951 False 1218.000000 1218 89.845000 1985 2938 1 chr7B.!!$F1 953
20 TraesCS6A01G146100 chr7B 135033989 135036656 2667 True 611.000000 1330 91.354000 920 3586 3 chr7B.!!$R4 2666

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
813 831 0.476338 TGGCCTCAACTGCTTTGGTA 59.524 50.0 3.32 0.0 35.69 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2660 3071 2.186076 CGTCGATAACAGAGCAGGAAC 58.814 52.381 0.0 0.0 0.0 3.62 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
200 202 2.203195 GCATCCATGGCGGCTACA 60.203 61.111 17.25 0.0 33.14 2.74
498 500 2.026636 CCCTCCCATCAACGGTTTTCTA 60.027 50.000 0.00 0.0 0.00 2.10
668 671 7.626144 AAACGGTGGTTATTTTACAATTTCG 57.374 32.000 0.00 0.0 34.62 3.46
781 799 2.305927 ACCCTGATGAGTGACGGATTTT 59.694 45.455 0.00 0.0 0.00 1.82
813 831 0.476338 TGGCCTCAACTGCTTTGGTA 59.524 50.000 3.32 0.0 35.69 3.25
819 837 4.642429 CCTCAACTGCTTTGGTAAGTACT 58.358 43.478 0.00 0.0 35.69 2.73
820 838 5.790593 CCTCAACTGCTTTGGTAAGTACTA 58.209 41.667 0.00 0.0 35.69 1.82
821 839 6.407202 CCTCAACTGCTTTGGTAAGTACTAT 58.593 40.000 0.00 0.0 35.69 2.12
822 840 6.313905 CCTCAACTGCTTTGGTAAGTACTATG 59.686 42.308 0.00 0.0 35.69 2.23
823 841 6.170506 TCAACTGCTTTGGTAAGTACTATGG 58.829 40.000 0.00 0.0 35.69 2.74
826 844 3.521937 TGCTTTGGTAAGTACTATGGGCT 59.478 43.478 0.00 0.0 33.74 5.19
827 845 3.877508 GCTTTGGTAAGTACTATGGGCTG 59.122 47.826 0.00 0.0 33.74 4.85
828 846 4.451900 CTTTGGTAAGTACTATGGGCTGG 58.548 47.826 0.00 0.0 0.00 4.85
829 847 3.124856 TGGTAAGTACTATGGGCTGGT 57.875 47.619 0.00 0.0 0.00 4.00
830 848 3.036091 TGGTAAGTACTATGGGCTGGTC 58.964 50.000 0.00 0.0 0.00 4.02
831 849 3.306613 GGTAAGTACTATGGGCTGGTCT 58.693 50.000 0.00 0.0 0.00 3.85
832 850 3.710165 GGTAAGTACTATGGGCTGGTCTT 59.290 47.826 0.00 0.0 0.00 3.01
833 851 3.914426 AAGTACTATGGGCTGGTCTTG 57.086 47.619 0.00 0.0 0.00 3.02
834 852 2.119495 AGTACTATGGGCTGGTCTTGG 58.881 52.381 0.00 0.0 0.00 3.61
845 863 1.142870 CTGGTCTTGGTGAAAGGTCCA 59.857 52.381 0.00 0.0 37.69 4.02
846 864 1.142870 TGGTCTTGGTGAAAGGTCCAG 59.857 52.381 0.00 0.0 36.28 3.86
857 875 3.655777 TGAAAGGTCCAGGAGTATGGTTT 59.344 43.478 0.00 0.0 41.43 3.27
869 887 8.971073 CCAGGAGTATGGTTTAAAGAAATGAAT 58.029 33.333 0.00 0.0 35.47 2.57
1049 1098 0.472471 TCCCACAACACCTTCCTGAC 59.528 55.000 0.00 0.0 0.00 3.51
1487 1590 2.125912 CAAGGTCGGCGAGGTCAG 60.126 66.667 11.20 0.0 0.00 3.51
2097 2458 7.830099 AGATGGTTTTGATCTTGAAGAACTT 57.170 32.000 0.00 0.0 0.00 2.66
2144 2505 0.033504 GAAGTTGAGCCGGTCACTGA 59.966 55.000 1.90 0.0 33.71 3.41
2345 2709 0.103026 TCGGATCTTGACGCTCCATG 59.897 55.000 0.00 0.0 0.00 3.66
2660 3071 9.169468 CAAGCTACTATAAAACTGTTGTTGTTG 57.831 33.333 0.00 0.0 36.39 3.33
2724 3145 4.322349 CCTGCACTAGTACTTCTTCTGCTT 60.322 45.833 0.00 0.0 32.18 3.91
2769 3192 8.574196 TGTTAAAACTGCTCTTATCTTTTTGC 57.426 30.769 0.00 0.0 0.00 3.68
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
498 500 7.201857 GGCAAAATTTTCAGCTCCATCTATACT 60.202 37.037 11.65 0.0 0.00 2.12
668 671 2.823747 ACAAATTCCGTAGAAAAGGCCC 59.176 45.455 0.00 0.0 35.09 5.80
801 819 5.497474 CCCATAGTACTTACCAAAGCAGTT 58.503 41.667 0.00 0.0 36.05 3.16
813 831 2.505819 CCAAGACCAGCCCATAGTACTT 59.494 50.000 0.00 0.0 0.00 2.24
819 837 1.367346 TTCACCAAGACCAGCCCATA 58.633 50.000 0.00 0.0 0.00 2.74
820 838 0.482446 TTTCACCAAGACCAGCCCAT 59.518 50.000 0.00 0.0 0.00 4.00
821 839 0.178992 CTTTCACCAAGACCAGCCCA 60.179 55.000 0.00 0.0 33.80 5.36
822 840 0.895559 CCTTTCACCAAGACCAGCCC 60.896 60.000 0.00 0.0 33.80 5.19
823 841 0.178990 ACCTTTCACCAAGACCAGCC 60.179 55.000 0.00 0.0 33.80 4.85
826 844 1.142870 CTGGACCTTTCACCAAGACCA 59.857 52.381 0.00 0.0 36.82 4.02
827 845 1.545651 CCTGGACCTTTCACCAAGACC 60.546 57.143 0.00 0.0 35.67 3.85
828 846 1.420138 TCCTGGACCTTTCACCAAGAC 59.580 52.381 0.00 0.0 35.67 3.01
829 847 1.699634 CTCCTGGACCTTTCACCAAGA 59.300 52.381 0.00 0.0 35.67 3.02
830 848 1.421646 ACTCCTGGACCTTTCACCAAG 59.578 52.381 0.00 0.0 35.67 3.61
831 849 1.518367 ACTCCTGGACCTTTCACCAA 58.482 50.000 0.00 0.0 35.67 3.67
832 850 2.409064 TACTCCTGGACCTTTCACCA 57.591 50.000 0.00 0.0 34.81 4.17
833 851 2.092914 CCATACTCCTGGACCTTTCACC 60.093 54.545 0.00 0.0 38.69 4.02
834 852 2.572104 ACCATACTCCTGGACCTTTCAC 59.428 50.000 0.00 0.0 39.73 3.18
845 863 9.190317 GGATTCATTTCTTTAAACCATACTCCT 57.810 33.333 0.00 0.0 0.00 3.69
846 864 8.966868 TGGATTCATTTCTTTAAACCATACTCC 58.033 33.333 0.00 0.0 0.00 3.85
1049 1098 1.966451 GAGTGGTTTGTCTGCGGGG 60.966 63.158 0.00 0.0 0.00 5.73
1487 1590 3.771577 TCTTCTTGAAGGACAGGTTCC 57.228 47.619 10.08 0.0 46.33 3.62
2097 2458 4.039245 GGGTCGTCTTCCATCATTCTCATA 59.961 45.833 0.00 0.0 0.00 2.15
2345 2709 2.224159 TGGTCCTGTCCCTGAAGCC 61.224 63.158 0.00 0.0 0.00 4.35
2386 2753 2.357009 CTGCTTCAAATGGATCGAAGGG 59.643 50.000 8.71 0.0 37.27 3.95
2644 3055 5.047660 AGCAGGAACAACAACAACAGTTTTA 60.048 36.000 0.00 0.0 0.00 1.52
2645 3056 3.993736 GCAGGAACAACAACAACAGTTTT 59.006 39.130 0.00 0.0 0.00 2.43
2660 3071 2.186076 CGTCGATAACAGAGCAGGAAC 58.814 52.381 0.00 0.0 0.00 3.62
2724 3145 3.156293 CATGGTCCATCACAGGAAACAA 58.844 45.455 0.00 0.0 39.92 2.83
2769 3192 4.132336 TGCTTGCTTATCTGAGCCTAATG 58.868 43.478 0.00 0.0 42.01 1.90
2850 3282 6.035843 TCAAGAGCAGTGAAACAATTTTGAC 58.964 36.000 0.00 0.0 41.43 3.18
3339 4853 8.484214 TGCTCACTAGATCTTTATAATCTGGT 57.516 34.615 0.00 0.0 43.31 4.00


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

AutoCloner maintained by Alex Coulton.