Multiple sequence alignment - TraesCS7B01G164900

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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 TraesCS7B01G164900 chr7B 100.000 2854 0 0 1 2854 228008545 228011398 0.000000e+00 5271.0
1 TraesCS7B01G164900 chr7B 100.000 1468 0 0 3186 4653 228011730 228013197 0.000000e+00 2712.0
2 TraesCS7B01G164900 chr7B 91.593 226 15 4 616 841 194610766 194610545 4.520000e-80 309.0
3 TraesCS7B01G164900 chr7B 81.796 412 36 19 26 407 194613672 194613270 4.520000e-80 309.0
4 TraesCS7B01G164900 chr7D 97.780 2027 26 4 843 2854 251033212 251035234 0.000000e+00 3476.0
5 TraesCS7B01G164900 chr7D 95.899 634 18 6 3811 4442 251036047 251036674 0.000000e+00 1020.0
6 TraesCS7B01G164900 chr7D 94.343 654 13 5 3186 3815 251035273 251035926 0.000000e+00 981.0
7 TraesCS7B01G164900 chr7D 94.118 170 6 3 4485 4653 251036767 251036933 5.970000e-64 255.0
8 TraesCS7B01G164900 chr7D 98.000 50 0 1 4433 4482 251036696 251036744 8.300000e-13 86.1
9 TraesCS7B01G164900 chr4A 97.387 842 22 0 1 842 30138474 30139315 0.000000e+00 1434.0
10 TraesCS7B01G164900 chr4A 91.000 200 16 2 647 845 140786731 140786533 7.670000e-68 268.0
11 TraesCS7B01G164900 chr4A 91.083 157 14 0 686 842 31614255 31614411 3.650000e-51 213.0
12 TraesCS7B01G164900 chr4A 81.452 248 34 9 1 246 31613837 31614074 4.750000e-45 193.0
13 TraesCS7B01G164900 chr6A 83.051 885 117 20 1117 1974 122679566 122680444 0.000000e+00 773.0
14 TraesCS7B01G164900 chr6A 85.806 155 19 3 2700 2852 122681926 122682079 1.340000e-35 161.0
15 TraesCS7B01G164900 chr6B 82.825 885 119 21 1117 1974 186692692 186693570 0.000000e+00 761.0
16 TraesCS7B01G164900 chr6B 83.915 659 86 15 1352 1999 284660094 284659445 3.080000e-171 612.0
17 TraesCS7B01G164900 chr6B 83.240 179 23 6 2678 2852 284652075 284651900 1.730000e-34 158.0
18 TraesCS7B01G164900 chr6D 82.941 850 115 19 1152 1974 101720843 101721689 0.000000e+00 739.0
19 TraesCS7B01G164900 chr4B 87.660 235 19 7 621 847 137735985 137735753 9.930000e-67 265.0
20 TraesCS7B01G164900 chr2D 88.776 196 17 4 649 842 527726512 527726320 7.780000e-58 235.0
21 TraesCS7B01G164900 chr2D 86.316 190 13 8 1 189 527727220 527727043 1.320000e-45 195.0
22 TraesCS7B01G164900 chr5D 87.222 180 21 2 664 842 330888804 330888626 2.190000e-48 204.0
23 TraesCS7B01G164900 chr5D 86.667 180 22 2 664 842 330945597 330945775 1.020000e-46 198.0
24 TraesCS7B01G164900 chr5D 86.339 183 23 2 664 845 331055172 331054991 1.020000e-46 198.0
25 TraesCS7B01G164900 chr3B 91.346 104 7 2 1 103 602295662 602295560 1.750000e-29 141.0
26 TraesCS7B01G164900 chr3D 88.000 50 6 0 1 50 610942870 610942919 5.030000e-05 60.2


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 TraesCS7B01G164900 chr7B 228008545 228013197 4652 False 3991.50 5271 100.0000 1 4653 2 chr7B.!!$F1 4652
1 TraesCS7B01G164900 chr7B 194610545 194613672 3127 True 309.00 309 86.6945 26 841 2 chr7B.!!$R1 815
2 TraesCS7B01G164900 chr7D 251033212 251036933 3721 False 1163.62 3476 96.0280 843 4653 5 chr7D.!!$F1 3810
3 TraesCS7B01G164900 chr4A 30138474 30139315 841 False 1434.00 1434 97.3870 1 842 1 chr4A.!!$F1 841
4 TraesCS7B01G164900 chr4A 31613837 31614411 574 False 203.00 213 86.2675 1 842 2 chr4A.!!$F2 841
5 TraesCS7B01G164900 chr6A 122679566 122682079 2513 False 467.00 773 84.4285 1117 2852 2 chr6A.!!$F1 1735
6 TraesCS7B01G164900 chr6B 186692692 186693570 878 False 761.00 761 82.8250 1117 1974 1 chr6B.!!$F1 857
7 TraesCS7B01G164900 chr6B 284659445 284660094 649 True 612.00 612 83.9150 1352 1999 1 chr6B.!!$R2 647
8 TraesCS7B01G164900 chr6D 101720843 101721689 846 False 739.00 739 82.9410 1152 1974 1 chr6D.!!$F1 822
9 TraesCS7B01G164900 chr2D 527726320 527727220 900 True 215.00 235 87.5460 1 842 2 chr2D.!!$R1 841

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
734 3290 0.176449 GGATTTCACATGGGCAAGGC 59.824 55.000 0.00 0.00 0.00 4.35 F
941 3512 0.179124 CTTCTTCTTCCTCCTCCGCG 60.179 60.000 0.00 0.00 0.00 6.46 F
942 3513 0.611062 TTCTTCTTCCTCCTCCGCGA 60.611 55.000 8.23 0.00 0.00 5.87 F
1597 4187 2.606826 GGGTGTTCCCGGAGACCT 60.607 66.667 0.73 0.00 44.74 3.85 F
3276 6645 3.058016 TGCTGAACTAAATTGCAGTCTGC 60.058 43.478 18.32 18.32 45.29 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1961 4570 2.461110 GCCGCACGTACCTTGATGG 61.461 63.158 0.00 0.0 42.93 3.51 R
2180 5128 3.823304 AGGACTGCAAGAAAGAAATGGAC 59.177 43.478 0.00 0.0 37.43 4.02 R
2525 5692 4.522022 CACTTACGTATTCCCCCTACCTAG 59.478 50.000 0.00 0.0 0.00 3.02 R
3376 6745 1.141881 ACGATGCCCTTGTAGCTCG 59.858 57.895 0.00 0.0 37.11 5.03 R
4358 7877 0.906282 AAGGCCTCCAAAATGCCCTG 60.906 55.000 5.23 0.0 46.55 4.45 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
50 51 5.604010 TTTGCCACTTTTCAACACAAAAG 57.396 34.783 4.49 4.49 45.33 2.27
107 108 1.351350 AGCAGAGGACAAAACTACCCC 59.649 52.381 0.00 0.00 0.00 4.95
277 374 4.416738 GGAGGAGTGCAGGTGGGC 62.417 72.222 0.00 0.00 0.00 5.36
734 3290 0.176449 GGATTTCACATGGGCAAGGC 59.824 55.000 0.00 0.00 0.00 4.35
832 3388 4.039124 CCAAGTAAGTGGTGGCAAGAAATT 59.961 41.667 0.00 0.00 33.63 1.82
861 3417 1.270907 CTTGTAGAGTGGCCAGGAGT 58.729 55.000 5.11 0.00 0.00 3.85
885 3442 2.807045 GCTCTCTCACACACGCCG 60.807 66.667 0.00 0.00 0.00 6.46
939 3510 1.754226 CCTCTTCTTCTTCCTCCTCCG 59.246 57.143 0.00 0.00 0.00 4.63
940 3511 1.136110 CTCTTCTTCTTCCTCCTCCGC 59.864 57.143 0.00 0.00 0.00 5.54
941 3512 0.179124 CTTCTTCTTCCTCCTCCGCG 60.179 60.000 0.00 0.00 0.00 6.46
942 3513 0.611062 TTCTTCTTCCTCCTCCGCGA 60.611 55.000 8.23 0.00 0.00 5.87
1094 3665 4.742201 CCCGGTGTCGCCTGTCTG 62.742 72.222 0.00 0.00 34.25 3.51
1404 3987 3.121030 CCCTTCGCCAGCTTCACG 61.121 66.667 0.00 0.00 0.00 4.35
1597 4187 2.606826 GGGTGTTCCCGGAGACCT 60.607 66.667 0.73 0.00 44.74 3.85
2180 5128 3.617263 GCAACTACTCTGGTAATCGGTTG 59.383 47.826 0.00 0.00 35.41 3.77
2288 5236 7.163441 AGTTTTGGGAATTTTCATCAATGAGG 58.837 34.615 0.00 0.00 38.19 3.86
2328 5276 5.739161 GCACTTAAGATTAATGAACTTGCCG 59.261 40.000 10.09 0.00 0.00 5.69
2386 5334 7.645340 CAGAACTGTCCAACTTTTACATTTCAG 59.355 37.037 0.00 0.00 36.07 3.02
2525 5692 4.314961 GAATTCACATTTTGGGGGAACAC 58.685 43.478 0.00 0.00 0.00 3.32
3275 6644 4.754372 TGCTGAACTAAATTGCAGTCTG 57.246 40.909 0.00 0.00 0.00 3.51
3276 6645 3.058016 TGCTGAACTAAATTGCAGTCTGC 60.058 43.478 18.32 18.32 45.29 4.26
3376 6745 2.789339 GCTCAAGACTTTGTTTTTCCGC 59.211 45.455 0.00 0.00 35.73 5.54
3442 6811 1.720301 GGAGAATGCGCAGAAGCTG 59.280 57.895 18.32 0.00 39.10 4.24
3487 6856 1.885163 AAGACCTGAGTTACCCCGCG 61.885 60.000 0.00 0.00 0.00 6.46
3572 6941 3.834489 AGATGCTATTCAGGACCAGTG 57.166 47.619 0.00 0.00 0.00 3.66
3604 6973 1.271762 GGTGGTACCCCTTTCAACCTC 60.272 57.143 10.07 0.00 32.99 3.85
3628 6997 6.998074 TCGCAATGGGAGTAGATTTATCATTT 59.002 34.615 0.00 0.00 0.00 2.32
3733 7116 8.842280 ACTAGTATCAGTAGCTTTACTTGCTAG 58.158 37.037 0.00 9.92 42.74 3.42
3734 7117 7.648039 AGTATCAGTAGCTTTACTTGCTAGT 57.352 36.000 6.00 6.00 44.63 2.57
3735 7118 7.708998 AGTATCAGTAGCTTTACTTGCTAGTC 58.291 38.462 3.45 0.00 42.68 2.59
3736 7119 5.977489 TCAGTAGCTTTACTTGCTAGTCA 57.023 39.130 3.45 0.00 42.68 3.41
3781 7174 2.742053 TGATAGCTTCAACGAACTTGGC 59.258 45.455 0.00 0.00 0.00 4.52
3783 7176 1.725973 GCTTCAACGAACTTGGCGC 60.726 57.895 0.00 0.00 0.00 6.53
3809 7202 1.648504 GGTGGCGGTACTTGTACATC 58.351 55.000 12.23 3.89 0.00 3.06
3863 7381 4.020485 AGTTCATGTGGTAGTAACAGGGAC 60.020 45.833 0.00 0.00 37.95 4.46
3927 7445 2.234908 AGTTTCTCCTCGATGGTCCTTG 59.765 50.000 0.00 0.00 37.07 3.61
3944 7462 5.127682 GGTCCTTGATGCAACCAAATTAGAT 59.872 40.000 0.00 0.00 0.00 1.98
3945 7463 6.321181 GGTCCTTGATGCAACCAAATTAGATA 59.679 38.462 0.00 0.00 0.00 1.98
3946 7464 7.420800 GTCCTTGATGCAACCAAATTAGATAG 58.579 38.462 0.00 0.00 0.00 2.08
3979 7497 2.767960 TGCAGCAGGATATCTCACTTGA 59.232 45.455 2.05 0.00 0.00 3.02
4039 7557 3.304458 GGGGCTTTTGAAGAACTGTTACG 60.304 47.826 0.00 0.00 0.00 3.18
4086 7604 1.053835 TGTGTGAAGTGGGAGCTCCA 61.054 55.000 33.29 17.15 44.79 3.86
4110 7628 4.623932 TGATGGAGCAGTAGAACACTTT 57.376 40.909 0.00 0.00 34.26 2.66
4132 7650 9.197306 ACTTTAGTGAACCTTAATTTGGAGTTT 57.803 29.630 4.47 0.00 0.00 2.66
4337 7856 8.900983 AATTTGTGTAGCAACCATAACAAATT 57.099 26.923 15.04 15.04 45.90 1.82
4346 7865 7.096551 AGCAACCATAACAAATTTGTATGGTC 58.903 34.615 34.99 29.04 44.81 4.02
4356 7875 1.672854 TTGTATGGTCTCGCTCGGGG 61.673 60.000 0.00 0.00 0.00 5.73
4379 7898 0.692476 GGGCATTTTGGAGGCCTTTT 59.308 50.000 6.77 0.00 46.87 2.27
4380 7899 1.905894 GGGCATTTTGGAGGCCTTTTA 59.094 47.619 6.77 0.00 46.87 1.52
4482 8032 5.876651 TGAGGATGAATAGTACATGTGCT 57.123 39.130 20.58 20.58 0.00 4.40
4493 8063 9.265901 GAATAGTACATGTGCTCATAGATTTGT 57.734 33.333 20.38 0.00 32.47 2.83
4566 8137 2.684374 TGTGCATCATGCCATCAAGTAC 59.316 45.455 7.30 0.00 44.23 2.73
4569 8140 3.316868 TGCATCATGCCATCAAGTACATG 59.683 43.478 7.30 0.00 44.23 3.21
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
734 3290 6.490040 TCTTAGTTGGAACTTTGAGGATTTGG 59.510 38.462 0.00 0.00 40.37 3.28
832 3388 4.855298 CCACTCTACAAGGGGGATTTTA 57.145 45.455 0.00 0.00 45.89 1.52
861 3417 0.469892 TGTGTGAGAGAGCCTCCACA 60.470 55.000 15.58 15.58 43.87 4.17
885 3442 2.273179 GGAGGGTTTTGGGCGAACC 61.273 63.158 7.33 7.33 44.62 3.62
1063 3634 2.183555 CGGGAAGGAGGCGTACAC 59.816 66.667 0.00 0.00 0.00 2.90
1094 3665 1.607801 GCAAAGGGAGGGGAATGTGC 61.608 60.000 0.00 0.00 0.00 4.57
1404 3987 1.282875 GCCGTCCAAGAAACTGCAC 59.717 57.895 0.00 0.00 0.00 4.57
1961 4570 2.461110 GCCGCACGTACCTTGATGG 61.461 63.158 0.00 0.00 42.93 3.51
1985 4594 4.645535 TGGAAAGTCAGAAATGAGGTGAG 58.354 43.478 0.00 0.00 0.00 3.51
2180 5128 3.823304 AGGACTGCAAGAAAGAAATGGAC 59.177 43.478 0.00 0.00 37.43 4.02
2306 5254 7.448748 AACGGCAAGTTCATTAATCTTAAGT 57.551 32.000 1.63 0.00 39.16 2.24
2328 5276 8.741101 TGCAATTATGTGTTGTATCTTCAAAC 57.259 30.769 0.00 0.00 0.00 2.93
2525 5692 4.522022 CACTTACGTATTCCCCCTACCTAG 59.478 50.000 0.00 0.00 0.00 3.02
3275 6644 2.577593 GGGTCCACTAGTGTCCGC 59.422 66.667 21.18 14.56 0.00 5.54
3276 6645 2.882876 CGGGTCCACTAGTGTCCG 59.117 66.667 24.69 24.69 33.28 4.79
3376 6745 1.141881 ACGATGCCCTTGTAGCTCG 59.858 57.895 0.00 0.00 37.11 5.03
3442 6811 2.366916 CACCCAGATGTACATCCTCTCC 59.633 54.545 28.26 7.02 38.58 3.71
3487 6856 3.857157 TTGGCACCCATAGATACCTTC 57.143 47.619 0.00 0.00 31.53 3.46
3572 6941 3.000684 GGTACCACCTCCAGGAAATTC 57.999 52.381 7.15 0.00 38.94 2.17
3604 6973 6.808008 AATGATAAATCTACTCCCATTGCG 57.192 37.500 0.00 0.00 0.00 4.85
3628 6997 3.068881 CAGAAGAAGGGGTCGGCA 58.931 61.111 0.00 0.00 0.00 5.69
3733 7116 8.893219 TCATCATCCAGATACTAACAAATGAC 57.107 34.615 0.00 0.00 34.43 3.06
3783 7176 3.113979 GTACCGCCACCGAAACCG 61.114 66.667 0.00 0.00 36.29 4.44
3809 7202 7.095940 CCACATGCTTTTCAGAATTTTGTACTG 60.096 37.037 0.00 0.00 0.00 2.74
3863 7381 3.034635 ACCAGCTCAGGTAATGTCTAGG 58.965 50.000 0.00 0.00 40.98 3.02
3927 7445 8.276325 CGTTCTACTATCTAATTTGGTTGCATC 58.724 37.037 0.00 0.00 0.00 3.91
3944 7462 3.119602 CCTGCTGCAACTACGTTCTACTA 60.120 47.826 3.02 0.00 0.00 1.82
3945 7463 2.352814 CCTGCTGCAACTACGTTCTACT 60.353 50.000 3.02 0.00 0.00 2.57
3946 7464 1.993370 CCTGCTGCAACTACGTTCTAC 59.007 52.381 3.02 0.00 0.00 2.59
3979 7497 5.046014 AGCCAAGTTCACTGATAAGATGAGT 60.046 40.000 0.00 0.00 0.00 3.41
4039 7557 3.214328 CTGACCCCAACAAGTATATGCC 58.786 50.000 0.00 0.00 0.00 4.40
4086 7604 5.171339 AGTGTTCTACTGCTCCATCAATT 57.829 39.130 0.00 0.00 38.49 2.32
4090 7608 5.578727 CACTAAAGTGTTCTACTGCTCCATC 59.421 44.000 1.81 0.00 40.26 3.51
4097 7615 8.882415 TTAAGGTTCACTAAAGTGTTCTACTG 57.118 34.615 9.81 0.00 45.76 2.74
4110 7628 9.191479 TGAAAAACTCCAAATTAAGGTTCACTA 57.809 29.630 0.00 0.00 0.00 2.74
4119 7637 5.751028 CCGCTTGTGAAAAACTCCAAATTAA 59.249 36.000 0.00 0.00 0.00 1.40
4120 7638 5.067936 TCCGCTTGTGAAAAACTCCAAATTA 59.932 36.000 0.00 0.00 0.00 1.40
4132 7650 1.878953 GGAAGAGTCCGCTTGTGAAA 58.121 50.000 0.00 0.00 33.05 2.69
4207 7725 0.996462 CGCGCAATAGACCGAAGAAA 59.004 50.000 8.75 0.00 0.00 2.52
4337 7856 1.672854 CCCCGAGCGAGACCATACAA 61.673 60.000 0.00 0.00 0.00 2.41
4356 7875 3.022710 GCCTCCAAAATGCCCTGCC 62.023 63.158 0.00 0.00 0.00 4.85
4358 7877 0.906282 AAGGCCTCCAAAATGCCCTG 60.906 55.000 5.23 0.00 46.55 4.45
4429 7949 9.970395 TCATGATTATTTTTCATCCTTGCATAC 57.030 29.630 0.00 0.00 31.50 2.39
4519 8090 6.853872 TGTGTAAATTTTCAGGACGAAATTCG 59.146 34.615 14.35 14.35 43.12 3.34


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

AutoCloner maintained by Alex Coulton.