Multiple sequence alignment - TraesCS7A01G119600

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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 TraesCS7A01G119600 chr7A 100.000 2270 0 0 1 2270 77093174 77090905 0.000000e+00 4193
1 TraesCS7A01G119600 chr1A 93.255 1883 126 1 388 2270 521913201 521911320 0.000000e+00 2772
2 TraesCS7A01G119600 chr2B 93.202 1883 128 0 388 2270 197702545 197700663 0.000000e+00 2769
3 TraesCS7A01G119600 chr3B 90.967 1882 166 2 388 2269 718858880 718857003 0.000000e+00 2531
4 TraesCS7A01G119600 chrUn 98.048 922 17 1 1 921 349331191 349330270 0.000000e+00 1602
5 TraesCS7A01G119600 chr4A 90.513 780 73 1 1491 2270 742296769 742295991 0.000000e+00 1029
6 TraesCS7A01G119600 chr5D 97.954 391 8 0 1 391 210619024 210618634 0.000000e+00 678
7 TraesCS7A01G119600 chr5D 97.698 391 9 0 1 391 457836115 457836505 0.000000e+00 673
8 TraesCS7A01G119600 chr7D 97.698 391 9 0 1 391 289493547 289493937 0.000000e+00 673
9 TraesCS7A01G119600 chr7D 97.698 391 9 0 1 391 460405971 460405581 0.000000e+00 673
10 TraesCS7A01G119600 chr3D 97.698 391 9 0 1 391 438493080 438493470 0.000000e+00 673
11 TraesCS7A01G119600 chr2D 97.698 391 9 0 1 391 560889666 560890056 0.000000e+00 673
12 TraesCS7A01G119600 chr1D 97.698 391 9 0 1 391 56916422 56916032 0.000000e+00 673
13 TraesCS7A01G119600 chr1D 97.698 391 9 0 1 391 58682961 58683351 0.000000e+00 673
14 TraesCS7A01G119600 chr1B 96.927 358 11 0 1913 2270 670967752 670968109 3.230000e-168 601


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 TraesCS7A01G119600 chr7A 77090905 77093174 2269 True 4193 4193 100.000 1 2270 1 chr7A.!!$R1 2269
1 TraesCS7A01G119600 chr1A 521911320 521913201 1881 True 2772 2772 93.255 388 2270 1 chr1A.!!$R1 1882
2 TraesCS7A01G119600 chr2B 197700663 197702545 1882 True 2769 2769 93.202 388 2270 1 chr2B.!!$R1 1882
3 TraesCS7A01G119600 chr3B 718857003 718858880 1877 True 2531 2531 90.967 388 2269 1 chr3B.!!$R1 1881
4 TraesCS7A01G119600 chrUn 349330270 349331191 921 True 1602 1602 98.048 1 921 1 chrUn.!!$R1 920
5 TraesCS7A01G119600 chr4A 742295991 742296769 778 True 1029 1029 90.513 1491 2270 1 chr4A.!!$R1 779

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
489 491 0.03213 GCTTATCTCCGACATCGCCA 59.968 55.0 0.0 0.0 38.18 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1689 1691 0.250234 TCTTCAATCTGTGCCCTCCG 59.75 55.0 0.0 0.0 0.0 4.63 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
64 65 9.853555 TTGATTCGAATGCTTATTTGTTGTTAT 57.146 25.926 16.96 0.00 0.00 1.89
93 94 2.357009 CTGAGTTGGCCAATATGTCAGC 59.643 50.000 23.66 5.85 0.00 4.26
130 131 6.202762 CACTATCGTAAAGAAATGCATGCCTA 59.797 38.462 16.68 0.00 0.00 3.93
300 301 3.334583 TCAACTAGGGATGTCAACTGC 57.665 47.619 0.00 0.00 0.00 4.40
454 456 2.297597 GACTCTGTTGCTACTGTCACCT 59.702 50.000 0.00 0.00 0.00 4.00
455 457 2.297597 ACTCTGTTGCTACTGTCACCTC 59.702 50.000 0.00 0.00 0.00 3.85
489 491 0.032130 GCTTATCTCCGACATCGCCA 59.968 55.000 0.00 0.00 38.18 5.69
923 925 4.283403 GCGCCAGCCTGCAAACAA 62.283 61.111 0.00 0.00 37.42 2.83
932 934 1.956477 GCCTGCAAACAAGAGGAAGAA 59.044 47.619 0.00 0.00 0.00 2.52
950 952 0.968393 AAACTTGCGGGTGTGGTTGT 60.968 50.000 0.00 0.00 0.00 3.32
955 957 2.604174 GCGGGTGTGGTTGTCTTCG 61.604 63.158 0.00 0.00 0.00 3.79
963 965 0.742505 TGGTTGTCTTCGACACGACT 59.257 50.000 12.00 0.00 42.60 4.18
1004 1006 3.058708 CGAGCAAAGAACAGAAAGATGCA 60.059 43.478 0.00 0.00 34.89 3.96
1069 1071 6.774656 GGGAATCATAGATGAAGGACAACAAT 59.225 38.462 0.00 0.00 40.69 2.71
1138 1140 2.851263 ACCGGACATAGCTGTTTCAA 57.149 45.000 9.46 0.00 35.14 2.69
1339 1341 4.561326 GCTACAACCCTGAAATGCATGTTT 60.561 41.667 0.00 0.00 0.00 2.83
1342 1344 6.112927 ACAACCCTGAAATGCATGTTTTAT 57.887 33.333 0.00 0.00 0.00 1.40
1493 1495 3.432749 GCCTAGAGCTGATCATGTTTGGA 60.433 47.826 0.00 0.00 38.99 3.53
1602 1604 2.147315 ATCGTCGCGCTGCCATCTAT 62.147 55.000 5.56 0.00 0.00 1.98
1623 1625 1.751924 GAGACCGTCAATGCTACTCCT 59.248 52.381 0.40 0.00 0.00 3.69
1666 1668 1.758440 AACCAAGCTCGAGCAGGTCA 61.758 55.000 38.08 0.00 46.26 4.02
1682 1684 1.338020 GGTCAACCCTTTCACTGCTTG 59.662 52.381 0.00 0.00 0.00 4.01
1689 1691 0.595095 CTTTCACTGCTTGCCACCTC 59.405 55.000 0.00 0.00 0.00 3.85
1720 1722 6.444633 CACAGATTGAAGAACTTTGCTCAAT 58.555 36.000 0.00 0.00 0.00 2.57
1726 1728 5.125356 TGAAGAACTTTGCTCAATGTCTGA 58.875 37.500 2.31 0.00 0.00 3.27
1744 1746 3.824469 CATTGGGCATTCGCGGCA 61.824 61.111 6.13 0.00 39.92 5.69
1783 1785 3.056465 GGATGAGAACTTTGTCTCCGTCT 60.056 47.826 0.01 0.00 42.97 4.18
1814 1816 2.558359 CCTTCGGTGCATTTTTCCTCTT 59.442 45.455 0.00 0.00 0.00 2.85
1841 1843 3.708403 AGTCACCATTGCTTCATCAGA 57.292 42.857 0.00 0.00 0.00 3.27
1896 1898 3.330267 GACTCGAAGCAACCTCAAAGAT 58.670 45.455 0.00 0.00 0.00 2.40
1911 1913 3.074390 TCAAAGATGCCTTCTTCCAGGAA 59.926 43.478 0.71 0.71 44.09 3.36
2069 2071 5.161358 TGTGTGTGAGCTTAAAGAGATACG 58.839 41.667 0.00 0.00 0.00 3.06
2118 2120 1.369625 ACGAGCGAAATGATCCAACC 58.630 50.000 0.00 0.00 0.00 3.77
2142 2144 3.255888 TGAGCAAGCTCGACTCTTTCTTA 59.744 43.478 16.45 0.00 45.48 2.10
2157 2159 7.114754 ACTCTTTCTTATGCAATGAGGAATGA 58.885 34.615 0.00 0.00 25.71 2.57
2196 2198 2.676839 ACATCTTCTGCATGCTCTTTCG 59.323 45.455 20.33 4.68 0.00 3.46
2201 2203 2.771089 TCTGCATGCTCTTTCGTCTTT 58.229 42.857 20.33 0.00 0.00 2.52
2229 2231 0.329596 ACCATTGCCCACTTCTCCTC 59.670 55.000 0.00 0.00 0.00 3.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
64 65 1.578897 TGGCCAACTCAGGTATAGCA 58.421 50.000 0.61 0.00 0.00 3.49
130 131 9.147732 AGGAAAAGTTAAGGACTCAAATGAAAT 57.852 29.630 0.00 0.00 37.72 2.17
300 301 7.201705 GGACTTTAATCAGGATTAAAAGGGACG 60.202 40.741 21.20 13.94 46.45 4.79
454 456 0.899720 AAGCGTTAGTGGGAATCCGA 59.100 50.000 0.00 0.00 35.24 4.55
455 457 2.589798 TAAGCGTTAGTGGGAATCCG 57.410 50.000 0.00 0.00 35.24 4.18
489 491 0.110678 TGTCTCGAGAGGTGGTGAGT 59.889 55.000 17.22 0.00 0.00 3.41
923 925 0.765510 ACCCGCAAGTTTCTTCCTCT 59.234 50.000 0.00 0.00 0.00 3.69
932 934 1.379309 ACAACCACACCCGCAAGTT 60.379 52.632 0.00 0.00 0.00 2.66
950 952 0.520404 GCACCTAGTCGTGTCGAAGA 59.480 55.000 0.00 0.00 37.72 2.87
955 957 1.446272 GGCTGCACCTAGTCGTGTC 60.446 63.158 0.50 0.00 36.08 3.67
1040 1042 5.370584 TGTCCTTCATCTATGATTCCCATGT 59.629 40.000 0.00 0.00 36.56 3.21
1069 1071 1.462616 CCAATGGCGTCTTCCATGAA 58.537 50.000 0.00 0.00 45.64 2.57
1095 1097 2.549992 CCTTCCCTGAAACATGTCGACA 60.550 50.000 22.48 22.48 0.00 4.35
1150 1152 3.013921 GGTCACAGTCAAGGTTGAACAA 58.986 45.455 0.00 0.00 39.21 2.83
1396 1398 5.068987 ACAATTGCAACACACATCTAAAGGT 59.931 36.000 0.00 0.00 0.00 3.50
1399 1401 6.825284 CAACAATTGCAACACACATCTAAA 57.175 33.333 0.00 0.00 0.00 1.85
1493 1495 2.564947 GGATTACATCGGAGGAGCAGAT 59.435 50.000 0.00 0.00 31.20 2.90
1602 1604 1.476891 GGAGTAGCATTGACGGTCTCA 59.523 52.381 9.88 0.00 0.00 3.27
1666 1668 0.396974 TGGCAAGCAGTGAAAGGGTT 60.397 50.000 0.00 0.00 0.00 4.11
1689 1691 0.250234 TCTTCAATCTGTGCCCTCCG 59.750 55.000 0.00 0.00 0.00 4.63
1720 1722 1.452110 CGAATGCCCAATGTCAGACA 58.548 50.000 5.50 5.50 0.00 3.41
1726 1728 3.825611 GCCGCGAATGCCCAATGT 61.826 61.111 8.23 0.00 38.08 2.71
1814 1816 1.412079 AGCAATGGTGACTTTGGCAA 58.588 45.000 0.00 0.00 43.61 4.52
1841 1843 6.000219 ACAGATGTTAGCTTGAATGAAGTGT 59.000 36.000 0.00 0.00 33.73 3.55
1911 1913 3.334054 GGCTTCTCCTGGGCCAGT 61.334 66.667 30.68 0.00 44.69 4.00
1997 1999 2.352651 CGACTCCGATCAACATTTGCAT 59.647 45.455 0.00 0.00 38.22 3.96
2048 2050 4.174009 GCGTATCTCTTTAAGCTCACACA 58.826 43.478 0.00 0.00 0.00 3.72
2069 2071 1.877637 AAATTTCCGGTTTTGCAGGC 58.122 45.000 0.00 0.00 32.16 4.85
2118 2120 2.007360 AAGAGTCGAGCTTGCTCATG 57.993 50.000 20.59 7.20 0.00 3.07
2142 2144 3.201290 GACGTCTCATTCCTCATTGCAT 58.799 45.455 8.70 0.00 0.00 3.96
2157 2159 0.865769 GTGTGCCAAATTCGACGTCT 59.134 50.000 14.70 0.00 0.00 4.18
2196 2198 2.161211 GCAATGGTCAGAGAGCAAAGAC 59.839 50.000 2.83 0.00 43.29 3.01
2201 2203 1.300963 GGGCAATGGTCAGAGAGCA 59.699 57.895 1.08 1.08 44.17 4.26
2229 2231 1.654220 CGGCCCTTTATCATTGGCG 59.346 57.895 0.00 0.00 44.96 5.69


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

AutoCloner maintained by Alex Coulton.