Multiple sequence alignment - TraesCS4B01G333100

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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 TraesCS4B01G333100 chr4B 100.000 1963 0 0 273 2235 623347113 623345151 0.000000e+00 3626.0
1 TraesCS4B01G333100 chr4B 100.000 80 0 0 1 80 623347385 623347306 4.970000e-32 148.0
2 TraesCS4B01G333100 chr6B 98.371 1964 30 2 273 2235 596602108 596604070 0.000000e+00 3448.0
3 TraesCS4B01G333100 chrUn 98.269 1964 32 2 273 2235 171008036 171006074 0.000000e+00 3437.0
4 TraesCS4B01G333100 chrUn 100.000 30 0 0 51 80 171008060 171008031 3.100000e-04 56.5
5 TraesCS4B01G333100 chrUn 100.000 30 0 0 51 80 432742128 432742099 3.100000e-04 56.5
6 TraesCS4B01G333100 chr7A 98.216 1962 32 3 273 2232 638507914 638509874 0.000000e+00 3426.0
7 TraesCS4B01G333100 chr7A 98.066 1965 34 3 273 2235 708245375 708243413 0.000000e+00 3415.0
8 TraesCS4B01G333100 chr5B 98.015 1965 37 2 273 2235 567279746 567277782 0.000000e+00 3411.0
9 TraesCS4B01G333100 chr1B 97.963 1964 36 4 273 2235 672540972 672539012 0.000000e+00 3402.0
10 TraesCS4B01G333100 chr2B 97.558 1966 45 3 273 2235 391225491 391227456 0.000000e+00 3362.0
11 TraesCS4B01G333100 chr7D 97.505 1964 42 3 273 2235 382089549 382087592 0.000000e+00 3349.0
12 TraesCS4B01G333100 chr7D 97.457 1966 39 4 273 2235 626711445 626713402 0.000000e+00 3343.0
13 TraesCS4B01G333100 chr7D 100.000 30 0 0 51 80 307032876 307032905 3.100000e-04 56.5
14 TraesCS4B01G333100 chr4D 100.000 30 0 0 51 80 123401293 123401264 3.100000e-04 56.5
15 TraesCS4B01G333100 chr4D 100.000 30 0 0 51 80 134962787 134962758 3.100000e-04 56.5
16 TraesCS4B01G333100 chr3D 100.000 30 0 0 51 80 602860407 602860436 3.100000e-04 56.5
17 TraesCS4B01G333100 chr1D 100.000 30 0 0 51 80 212444931 212444960 3.100000e-04 56.5
18 TraesCS4B01G333100 chr1D 100.000 30 0 0 51 80 275786812 275786841 3.100000e-04 56.5
19 TraesCS4B01G333100 chr1A 100.000 30 0 0 51 80 94664167 94664196 3.100000e-04 56.5


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 TraesCS4B01G333100 chr4B 623345151 623347385 2234 True 1887.00 3626 100.0000 1 2235 2 chr4B.!!$R1 2234
1 TraesCS4B01G333100 chr6B 596602108 596604070 1962 False 3448.00 3448 98.3710 273 2235 1 chr6B.!!$F1 1962
2 TraesCS4B01G333100 chrUn 171006074 171008060 1986 True 1746.75 3437 99.1345 51 2235 2 chrUn.!!$R2 2184
3 TraesCS4B01G333100 chr7A 638507914 638509874 1960 False 3426.00 3426 98.2160 273 2232 1 chr7A.!!$F1 1959
4 TraesCS4B01G333100 chr7A 708243413 708245375 1962 True 3415.00 3415 98.0660 273 2235 1 chr7A.!!$R1 1962
5 TraesCS4B01G333100 chr5B 567277782 567279746 1964 True 3411.00 3411 98.0150 273 2235 1 chr5B.!!$R1 1962
6 TraesCS4B01G333100 chr1B 672539012 672540972 1960 True 3402.00 3402 97.9630 273 2235 1 chr1B.!!$R1 1962
7 TraesCS4B01G333100 chr2B 391225491 391227456 1965 False 3362.00 3362 97.5580 273 2235 1 chr2B.!!$F1 1962
8 TraesCS4B01G333100 chr7D 382087592 382089549 1957 True 3349.00 3349 97.5050 273 2235 1 chr7D.!!$R1 1962
9 TraesCS4B01G333100 chr7D 626711445 626713402 1957 False 3343.00 3343 97.4570 273 2235 1 chr7D.!!$F2 1962

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
531 534 0.114954 AATTGGCTGGCTTCCCTCAA 59.885 50.0 2.0 0.0 0.0 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1372 1379 0.461961 CGGGAGGCTCTCGAAAAGAT 59.538 55.0 32.33 0.0 44.6 2.4 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
29 30 4.752879 GTGCCGCGTTAGAGCCCA 62.753 66.667 4.92 0.00 0.00 5.36
30 31 4.451150 TGCCGCGTTAGAGCCCAG 62.451 66.667 4.92 0.00 0.00 4.45
32 33 4.530857 CCGCGTTAGAGCCCAGGG 62.531 72.222 4.92 0.00 0.00 4.45
33 34 3.458163 CGCGTTAGAGCCCAGGGA 61.458 66.667 10.89 0.00 0.00 4.20
34 35 2.987125 GCGTTAGAGCCCAGGGAA 59.013 61.111 10.89 0.00 0.00 3.97
35 36 1.153349 GCGTTAGAGCCCAGGGAAG 60.153 63.158 10.89 0.00 0.00 3.46
36 37 1.153349 CGTTAGAGCCCAGGGAAGC 60.153 63.158 10.89 0.00 0.00 3.86
37 38 1.899437 CGTTAGAGCCCAGGGAAGCA 61.899 60.000 10.89 0.00 0.00 3.91
38 39 0.393132 GTTAGAGCCCAGGGAAGCAC 60.393 60.000 10.89 0.00 0.00 4.40
39 40 0.547712 TTAGAGCCCAGGGAAGCACT 60.548 55.000 10.89 0.00 34.24 4.40
40 41 0.338467 TAGAGCCCAGGGAAGCACTA 59.662 55.000 10.89 0.00 32.07 2.74
41 42 0.980231 AGAGCCCAGGGAAGCACTAG 60.980 60.000 10.89 0.00 0.00 2.57
42 43 1.229658 AGCCCAGGGAAGCACTAGT 60.230 57.895 10.89 0.00 0.00 2.57
43 44 1.078143 GCCCAGGGAAGCACTAGTG 60.078 63.158 18.93 18.93 0.00 2.74
44 45 1.553690 GCCCAGGGAAGCACTAGTGA 61.554 60.000 27.08 0.00 0.00 3.41
45 46 0.250513 CCCAGGGAAGCACTAGTGAC 59.749 60.000 27.08 16.83 0.00 3.67
46 47 0.976641 CCAGGGAAGCACTAGTGACA 59.023 55.000 27.08 0.00 0.00 3.58
47 48 1.556911 CCAGGGAAGCACTAGTGACAT 59.443 52.381 27.08 10.94 0.00 3.06
48 49 2.625737 CAGGGAAGCACTAGTGACATG 58.374 52.381 27.08 15.46 0.00 3.21
49 50 1.556911 AGGGAAGCACTAGTGACATGG 59.443 52.381 27.08 0.00 0.00 3.66
74 75 3.129988 CAGCAGGATTTTAAGGGCTTCTG 59.870 47.826 0.00 0.00 0.00 3.02
75 76 3.092301 GCAGGATTTTAAGGGCTTCTGT 58.908 45.455 0.00 0.00 0.00 3.41
76 77 3.511540 GCAGGATTTTAAGGGCTTCTGTT 59.488 43.478 0.00 0.00 0.00 3.16
77 78 4.619160 GCAGGATTTTAAGGGCTTCTGTTG 60.619 45.833 0.00 0.00 0.00 3.33
78 79 4.766891 CAGGATTTTAAGGGCTTCTGTTGA 59.233 41.667 0.00 0.00 0.00 3.18
79 80 5.243730 CAGGATTTTAAGGGCTTCTGTTGAA 59.756 40.000 0.00 0.00 0.00 2.69
379 382 2.329379 GCGAACATCTAATCTAGGCCG 58.671 52.381 0.00 0.00 0.00 6.13
531 534 0.114954 AATTGGCTGGCTTCCCTCAA 59.885 50.000 2.00 0.00 0.00 3.02
750 753 2.658807 GGTTCCAGACCCAAGAGTTT 57.341 50.000 0.00 0.00 43.06 2.66
1296 1303 0.034337 CGAGTTTTTCGGGGTCCTCA 59.966 55.000 0.00 0.00 45.54 3.86
1327 1334 2.687700 TAGGTCGAGTAGAGACGCTT 57.312 50.000 0.00 0.00 39.38 4.68
1372 1379 4.139786 GCATTTCAAGATGGCCTCTATCA 58.860 43.478 3.32 0.00 32.41 2.15
1449 1456 0.531974 GCAGTCCCACACGAAACTGA 60.532 55.000 5.59 0.00 41.26 3.41
1619 1626 5.200368 TCCAATTCTTCCAAAGACAAAGC 57.800 39.130 0.00 0.00 37.23 3.51
1727 1735 0.831711 GGGGCTTGCTCCCTTTTTCA 60.832 55.000 0.00 0.00 45.80 2.69
1894 1902 2.117423 CCCGGCCCTTTGTTCCTT 59.883 61.111 0.00 0.00 0.00 3.36
2001 2010 0.400213 ACTTGTCGGGCTTGGATTCA 59.600 50.000 0.00 0.00 0.00 2.57
2148 2159 5.525199 GGCCAATTCACTTCGAAAAACTAA 58.475 37.500 0.00 0.00 37.12 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 4.752879 TGGGCTCTAACGCGGCAC 62.753 66.667 12.47 5.10 0.00 5.01
13 14 4.451150 CTGGGCTCTAACGCGGCA 62.451 66.667 12.47 0.00 0.00 5.69
15 16 4.530857 CCCTGGGCTCTAACGCGG 62.531 72.222 12.47 0.00 0.00 6.46
16 17 2.907897 CTTCCCTGGGCTCTAACGCG 62.908 65.000 8.22 3.53 0.00 6.01
17 18 1.153349 CTTCCCTGGGCTCTAACGC 60.153 63.158 8.22 0.00 0.00 4.84
18 19 1.153349 GCTTCCCTGGGCTCTAACG 60.153 63.158 8.22 0.00 0.00 3.18
19 20 0.393132 GTGCTTCCCTGGGCTCTAAC 60.393 60.000 8.22 0.00 0.00 2.34
20 21 0.547712 AGTGCTTCCCTGGGCTCTAA 60.548 55.000 8.22 0.00 31.77 2.10
21 22 0.338467 TAGTGCTTCCCTGGGCTCTA 59.662 55.000 8.22 4.58 34.72 2.43
22 23 0.980231 CTAGTGCTTCCCTGGGCTCT 60.980 60.000 8.22 5.58 36.48 4.09
23 24 1.268283 ACTAGTGCTTCCCTGGGCTC 61.268 60.000 8.22 0.00 0.00 4.70
24 25 1.229658 ACTAGTGCTTCCCTGGGCT 60.230 57.895 8.22 0.97 0.00 5.19
25 26 1.078143 CACTAGTGCTTCCCTGGGC 60.078 63.158 10.54 0.00 0.00 5.36
26 27 0.250513 GTCACTAGTGCTTCCCTGGG 59.749 60.000 18.45 6.33 0.00 4.45
27 28 0.976641 TGTCACTAGTGCTTCCCTGG 59.023 55.000 18.45 0.00 0.00 4.45
28 29 2.625737 CATGTCACTAGTGCTTCCCTG 58.374 52.381 18.45 5.79 0.00 4.45
29 30 1.556911 CCATGTCACTAGTGCTTCCCT 59.443 52.381 18.45 0.00 0.00 4.20
30 31 1.555075 TCCATGTCACTAGTGCTTCCC 59.445 52.381 18.45 4.03 0.00 3.97
31 32 2.898705 CTCCATGTCACTAGTGCTTCC 58.101 52.381 18.45 6.39 0.00 3.46
32 33 2.275318 GCTCCATGTCACTAGTGCTTC 58.725 52.381 18.45 11.04 0.00 3.86
33 34 1.625315 TGCTCCATGTCACTAGTGCTT 59.375 47.619 18.45 8.63 0.00 3.91
34 35 1.206610 CTGCTCCATGTCACTAGTGCT 59.793 52.381 18.45 2.39 0.00 4.40
35 36 1.649664 CTGCTCCATGTCACTAGTGC 58.350 55.000 18.45 13.34 0.00 4.40
36 37 1.066645 TGCTGCTCCATGTCACTAGTG 60.067 52.381 17.17 17.17 0.00 2.74
37 38 1.206610 CTGCTGCTCCATGTCACTAGT 59.793 52.381 0.00 0.00 0.00 2.57
38 39 1.472904 CCTGCTGCTCCATGTCACTAG 60.473 57.143 0.00 0.00 0.00 2.57
39 40 0.538584 CCTGCTGCTCCATGTCACTA 59.461 55.000 0.00 0.00 0.00 2.74
40 41 1.196766 TCCTGCTGCTCCATGTCACT 61.197 55.000 0.00 0.00 0.00 3.41
41 42 0.107312 ATCCTGCTGCTCCATGTCAC 60.107 55.000 0.00 0.00 0.00 3.67
42 43 0.622136 AATCCTGCTGCTCCATGTCA 59.378 50.000 0.00 0.00 0.00 3.58
43 44 1.760192 AAATCCTGCTGCTCCATGTC 58.240 50.000 0.00 0.00 0.00 3.06
44 45 2.226962 AAAATCCTGCTGCTCCATGT 57.773 45.000 0.00 0.00 0.00 3.21
45 46 3.067742 CCTTAAAATCCTGCTGCTCCATG 59.932 47.826 0.00 0.00 0.00 3.66
46 47 3.294214 CCTTAAAATCCTGCTGCTCCAT 58.706 45.455 0.00 0.00 0.00 3.41
47 48 2.621407 CCCTTAAAATCCTGCTGCTCCA 60.621 50.000 0.00 0.00 0.00 3.86
48 49 2.027385 CCCTTAAAATCCTGCTGCTCC 58.973 52.381 0.00 0.00 0.00 4.70
49 50 1.406898 GCCCTTAAAATCCTGCTGCTC 59.593 52.381 0.00 0.00 0.00 4.26
379 382 1.954927 CCTTCATAGAAAGGCGACCC 58.045 55.000 0.00 0.00 39.47 4.46
531 534 1.832608 TGGCGACACCAGTCTGAGT 60.833 57.895 0.00 0.00 46.36 3.41
676 679 1.305046 CGTCCACTCTAGGGGGTGT 60.305 63.158 0.00 0.00 0.00 4.16
744 747 4.222145 TGCTCATACGGGAAAGTAAACTCT 59.778 41.667 0.00 0.00 0.00 3.24
750 753 3.491964 CCGAATGCTCATACGGGAAAGTA 60.492 47.826 0.00 0.00 41.41 2.24
834 837 2.292323 ACCCTCAGACGACCCTTCTAAT 60.292 50.000 0.00 0.00 0.00 1.73
1296 1303 4.124851 ACTCGACCTAAAATGCGATCTT 57.875 40.909 0.00 0.00 31.87 2.40
1327 1334 2.224159 GGAAGCCCACAGACTCCCA 61.224 63.158 0.00 0.00 0.00 4.37
1372 1379 0.461961 CGGGAGGCTCTCGAAAAGAT 59.538 55.000 32.33 0.00 44.60 2.40
1619 1626 5.689068 GCAAACTCCTCAAAATGAAGTTCTG 59.311 40.000 4.17 0.00 0.00 3.02
1727 1735 1.872773 CAGGTCCTTCCTTAGCTCCT 58.127 55.000 0.00 0.00 45.67 3.69
1854 1862 6.155393 GGGGAGATCATCGAAATTACCTCTAT 59.845 42.308 0.00 0.00 0.00 1.98
2067 2077 4.622701 GCGATTGGCTTCACTTTAGATT 57.377 40.909 0.00 0.00 39.11 2.40
2124 2135 2.697431 TTTTCGAAGTGAATTGGCCG 57.303 45.000 0.00 0.00 36.22 6.13
2148 2159 7.068716 ACCAATTTTTCTGCTCAAGTTAGAACT 59.931 33.333 0.00 0.00 42.04 3.01


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

AutoCloner maintained by Alex Coulton.