Multiple sequence alignment - TraesCS1B01G461500

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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 TraesCS1B01G461500 chr1B 100.000 2201 0 0 1 2201 674494007 674496207 0.000000e+00 4065.0
1 TraesCS1B01G461500 chr1B 80.986 710 116 16 844 1547 674053720 674054416 1.490000e-151 545.0
2 TraesCS1B01G461500 chr1D 93.348 1353 79 7 856 2201 484251353 484252701 0.000000e+00 1989.0
3 TraesCS1B01G461500 chr1D 95.470 861 37 2 2 860 484250454 484251314 0.000000e+00 1373.0
4 TraesCS1B01G461500 chr1D 82.609 138 21 3 217 352 484112641 484112777 3.840000e-23 119.0
5 TraesCS1B01G461500 chr1A 91.906 1186 77 9 859 2042 581433579 581434747 0.000000e+00 1640.0
6 TraesCS1B01G461500 chr1A 92.157 867 53 6 2 860 581432678 581433537 0.000000e+00 1210.0
7 TraesCS1B01G461500 chr1A 80.282 710 128 12 844 1547 581206029 581206732 1.940000e-145 525.0
8 TraesCS1B01G461500 chr1A 80.704 653 114 9 859 1508 581245158 581245801 4.220000e-137 497.0
9 TraesCS1B01G461500 chr1A 80.545 550 96 11 844 1388 581110299 581110842 1.570000e-111 412.0
10 TraesCS1B01G461500 chr1A 83.942 137 21 1 217 352 581254344 581254480 1.770000e-26 130.0
11 TraesCS1B01G461500 chr5A 74.218 671 150 20 861 1520 643922179 643922837 2.170000e-65 259.0
12 TraesCS1B01G461500 chr5A 86.047 86 9 3 73 156 827888 827972 3.010000e-14 89.8
13 TraesCS1B01G461500 chr5A 79.661 118 17 3 35 150 825600 825712 6.520000e-11 78.7
14 TraesCS1B01G461500 chr5B 75.494 506 103 19 1019 1520 648287364 648287852 6.110000e-56 228.0
15 TraesCS1B01G461500 chr7D 82.000 150 23 3 2 150 596094448 596094302 8.250000e-25 124.0
16 TraesCS1B01G461500 chr3B 89.535 86 8 1 72 156 819011272 819011187 8.310000e-20 108.0
17 TraesCS1B01G461500 chr7B 79.470 151 25 5 2 150 674197585 674197439 3.870000e-18 102.0
18 TraesCS1B01G461500 chr7B 93.617 47 2 1 164 209 265707021 265707067 3.920000e-08 69.4
19 TraesCS1B01G461500 chr7B 93.333 45 3 0 166 210 436412603 436412647 1.410000e-07 67.6
20 TraesCS1B01G461500 chr3D 84.884 86 12 1 72 156 608566561 608566476 3.890000e-13 86.1
21 TraesCS1B01G461500 chr3D 89.796 49 5 0 161 209 276961208 276961160 1.820000e-06 63.9
22 TraesCS1B01G461500 chr7A 92.453 53 3 1 157 209 48613782 48613731 8.430000e-10 75.0
23 TraesCS1B01G461500 chr2B 93.478 46 3 0 164 209 187232711 187232666 3.920000e-08 69.4
24 TraesCS1B01G461500 chr2B 90.000 50 2 2 161 209 571046430 571046383 6.560000e-06 62.1
25 TraesCS1B01G461500 chr6A 88.000 50 4 2 162 210 489291394 489291442 8.490000e-05 58.4


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 TraesCS1B01G461500 chr1B 674494007 674496207 2200 False 4065 4065 100.0000 1 2201 1 chr1B.!!$F2 2200
1 TraesCS1B01G461500 chr1B 674053720 674054416 696 False 545 545 80.9860 844 1547 1 chr1B.!!$F1 703
2 TraesCS1B01G461500 chr1D 484250454 484252701 2247 False 1681 1989 94.4090 2 2201 2 chr1D.!!$F2 2199
3 TraesCS1B01G461500 chr1A 581432678 581434747 2069 False 1425 1640 92.0315 2 2042 2 chr1A.!!$F5 2040
4 TraesCS1B01G461500 chr1A 581206029 581206732 703 False 525 525 80.2820 844 1547 1 chr1A.!!$F2 703
5 TraesCS1B01G461500 chr1A 581245158 581245801 643 False 497 497 80.7040 859 1508 1 chr1A.!!$F3 649
6 TraesCS1B01G461500 chr1A 581110299 581110842 543 False 412 412 80.5450 844 1388 1 chr1A.!!$F1 544
7 TraesCS1B01G461500 chr5A 643922179 643922837 658 False 259 259 74.2180 861 1520 1 chr5A.!!$F1 659

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
398 400 0.75831 GTAGAGTTACCCCCTCCCCG 60.758 65.0 0.0 0.0 0.0 5.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1936 2006 0.392998 CATGAGCGGGCTGTTAAGGT 60.393 55.0 0.0 0.0 0.0 3.5 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
25 26 2.920912 GGACGGAGGGGTGTGACA 60.921 66.667 0.00 0.00 0.00 3.58
51 52 3.188786 GATCGGCTGTGCACGTCC 61.189 66.667 13.13 14.25 0.00 4.79
75 76 3.675225 CGTATAGCTCATACATGCCACAC 59.325 47.826 0.00 0.00 39.71 3.82
159 161 2.159099 TGTACCGAAGCAAGGCTCTATG 60.159 50.000 0.00 0.00 38.25 2.23
177 179 8.786898 GGCTCTATGAATATAGCATGAAACAAA 58.213 33.333 0.00 0.00 36.92 2.83
398 400 0.758310 GTAGAGTTACCCCCTCCCCG 60.758 65.000 0.00 0.00 0.00 5.73
404 407 3.815407 TACCCCCTCCCCGCGTATC 62.815 68.421 4.92 0.00 0.00 2.24
411 414 2.026590 CCCCGCGTATCGTGTACC 59.973 66.667 4.92 0.00 35.46 3.34
423 426 6.365247 GCGTATCGTGTACCAAATCTGAATAT 59.635 38.462 0.00 0.00 0.00 1.28
502 505 1.000521 TGGCCTGCCAAGATCCAAG 60.001 57.895 8.75 0.00 44.12 3.61
515 518 6.738731 GCCAAGATCCAAGAGTTATATCGTGA 60.739 42.308 0.00 0.00 31.24 4.35
710 718 9.783081 AAAAGAGATTTTGCTTGGTTAATTCAT 57.217 25.926 0.00 0.00 0.00 2.57
838 847 3.127425 AGGAGGCATTTACTATTCGCC 57.873 47.619 0.00 0.00 43.31 5.54
933 993 4.373156 AAGTGAGTATTTGCTTGGACCT 57.627 40.909 0.00 0.00 0.00 3.85
956 1016 5.554822 AACACAAACATACAACTGAACGT 57.445 34.783 0.00 0.00 0.00 3.99
998 1058 7.661536 TCTACTGCTCTATGTGAATTTAGGT 57.338 36.000 0.00 0.00 0.00 3.08
1016 1076 6.633500 TTAGGTGATGGCAAATAATAGCAC 57.367 37.500 0.00 0.00 0.00 4.40
1046 1106 7.331687 CCAAGTCTTTGTTGTTTTTCTCATTGT 59.668 33.333 0.00 0.00 32.21 2.71
1056 1116 7.094508 TGTTTTTCTCATTGTGCAAGTCTTA 57.905 32.000 0.00 0.00 0.00 2.10
1210 1270 4.037208 CCATGAAGCCTTGATATGTGGTTC 59.963 45.833 0.00 0.00 0.00 3.62
1394 1461 4.922692 TGTGCCGCAAAGAGATTAAAATTG 59.077 37.500 0.00 0.00 0.00 2.32
1399 1466 6.148948 CCGCAAAGAGATTAAAATTGTGTCA 58.851 36.000 0.00 0.00 31.41 3.58
1697 1767 0.843309 TGCCAAAGACTCCTCCACAA 59.157 50.000 0.00 0.00 0.00 3.33
1715 1785 6.361433 TCCACAAGAGTCCTTCAATTTTACA 58.639 36.000 0.00 0.00 0.00 2.41
1716 1786 6.831353 TCCACAAGAGTCCTTCAATTTTACAA 59.169 34.615 0.00 0.00 0.00 2.41
1818 1888 9.847224 AGAGAAATCAAGAGGTAAAACTAACAA 57.153 29.630 0.00 0.00 0.00 2.83
1936 2006 7.174946 GTCTCATTTTTGGTGTTCCTCTCAATA 59.825 37.037 0.00 0.00 34.23 1.90
1970 2040 0.249120 TCATGCTTGTCCGACCGATT 59.751 50.000 0.00 0.00 0.00 3.34
1972 2042 0.249120 ATGCTTGTCCGACCGATTCA 59.751 50.000 0.00 0.00 0.00 2.57
1988 2058 5.066505 ACCGATTCAATTTAGACAAGGCATC 59.933 40.000 0.00 0.00 0.00 3.91
1989 2059 5.066375 CCGATTCAATTTAGACAAGGCATCA 59.934 40.000 0.00 0.00 0.00 3.07
2021 2091 9.912634 ACTTTTTGTGTGGACATTATGATAAAG 57.087 29.630 0.00 0.00 30.13 1.85
2062 2132 4.899502 AGACAAGTGTGGTTTGGATAGAG 58.100 43.478 0.00 0.00 0.00 2.43
2074 2144 6.264518 TGGTTTGGATAGAGTCAAAGGAAAAC 59.735 38.462 0.00 0.00 34.11 2.43
2076 2146 7.201875 GGTTTGGATAGAGTCAAAGGAAAACAA 60.202 37.037 0.00 0.00 34.11 2.83
2196 2268 4.965200 AATAGACAGGCTATCCAGTTCC 57.035 45.455 0.00 0.00 38.88 3.62
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
194 196 9.000018 GCATCAAAATTCTGATACGTCTTAAAC 58.000 33.333 0.00 0.00 34.20 2.01
198 200 6.992063 AGCATCAAAATTCTGATACGTCTT 57.008 33.333 0.00 0.00 34.20 3.01
398 400 3.441163 TCAGATTTGGTACACGATACGC 58.559 45.455 0.00 0.00 39.29 4.42
469 472 1.779092 AGGCCATGGAGATATGCACTT 59.221 47.619 18.40 0.00 0.00 3.16
471 474 1.531423 CAGGCCATGGAGATATGCAC 58.469 55.000 18.40 0.00 0.00 4.57
588 595 8.535335 ACTAGTAATACATGCTTCCTGGATATG 58.465 37.037 0.00 5.94 0.00 1.78
778 787 3.695830 TGGGACAATGAACCTAGACAC 57.304 47.619 0.00 0.00 31.92 3.67
882 934 6.835174 AGATACCATGACATGAAGCTTGTAT 58.165 36.000 17.24 13.30 0.00 2.29
883 935 6.239217 AGATACCATGACATGAAGCTTGTA 57.761 37.500 17.24 9.31 0.00 2.41
915 968 5.001232 GTGTTAGGTCCAAGCAAATACTCA 58.999 41.667 0.00 0.00 0.00 3.41
933 993 6.665474 ACGTTCAGTTGTATGTTTGTGTTA 57.335 33.333 0.00 0.00 0.00 2.41
998 1058 5.065914 GGAGAGTGCTATTATTTGCCATCA 58.934 41.667 0.00 0.00 0.00 3.07
1016 1076 6.856895 AGAAAAACAACAAAGACTTGGAGAG 58.143 36.000 0.00 0.00 36.82 3.20
1056 1116 2.693074 TGCTGCAATCATCATGAGCAAT 59.307 40.909 0.00 0.00 34.45 3.56
1176 1236 1.162800 GCTTCATGGAGGATGCGGTC 61.163 60.000 2.40 0.00 31.32 4.79
1210 1270 7.600752 CCTAGCTTATTTATCGGAGGAGAAAAG 59.399 40.741 0.00 0.00 36.98 2.27
1394 1461 9.696917 ATCCTCTAAAAACATTGAATTTGACAC 57.303 29.630 0.00 0.00 0.00 3.67
1575 1645 7.933396 TCAATTATGCTACAATGGAATGACAG 58.067 34.615 0.00 0.00 0.00 3.51
1612 1682 6.364701 CCCTTGGGTGAATAACATTATCTCA 58.635 40.000 0.00 0.00 0.00 3.27
1630 1700 0.762461 TGCCAAAAGAACCCCCTTGG 60.762 55.000 0.00 0.00 41.11 3.61
1697 1767 7.823745 ACATGTTGTAAAATTGAAGGACTCT 57.176 32.000 0.00 0.00 0.00 3.24
1715 1785 5.711506 TCATTAGCAAGGATCACAACATGTT 59.288 36.000 4.92 4.92 0.00 2.71
1716 1786 5.255687 TCATTAGCAAGGATCACAACATGT 58.744 37.500 0.00 0.00 0.00 3.21
1727 1797 8.730680 GTTGAGTAAGAATTTCATTAGCAAGGA 58.269 33.333 0.00 0.00 0.00 3.36
1882 1952 5.824542 AATAATGGGTAGGAAAAAGGGGA 57.175 39.130 0.00 0.00 0.00 4.81
1883 1953 6.679542 AGTAATAATGGGTAGGAAAAAGGGG 58.320 40.000 0.00 0.00 0.00 4.79
1884 1954 8.474831 CAAAGTAATAATGGGTAGGAAAAAGGG 58.525 37.037 0.00 0.00 0.00 3.95
1885 1955 9.031537 ACAAAGTAATAATGGGTAGGAAAAAGG 57.968 33.333 0.00 0.00 0.00 3.11
1936 2006 0.392998 CATGAGCGGGCTGTTAAGGT 60.393 55.000 0.00 0.00 0.00 3.50
1970 2040 5.357878 GTCCATGATGCCTTGTCTAAATTGA 59.642 40.000 0.00 0.00 0.00 2.57
1972 2042 5.126061 GTGTCCATGATGCCTTGTCTAAATT 59.874 40.000 0.00 0.00 0.00 1.82
2081 2151 7.556733 TGACCACGTCTTTAAACAAACTTAT 57.443 32.000 0.00 0.00 33.15 1.73


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

AutoCloner maintained by Alex Coulton.