Multiple sequence alignment - TraesCS3D01G167900

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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 TraesCS3D01G167900 chr3D 100.000 4487 0 0 1 4487 142475504 142479990 0.000000e+00 8287
1 TraesCS3D01G167900 chr3A 94.281 4144 149 32 66 4175 161445370 161449459 0.000000e+00 6259
2 TraesCS3D01G167900 chr3A 96.552 319 8 3 4170 4487 161449536 161449852 3.980000e-145 525
3 TraesCS3D01G167900 chr3B 95.891 3675 125 14 1 3664 204280884 204284543 0.000000e+00 5927
4 TraesCS3D01G167900 chr3B 95.788 831 29 5 3661 4487 204284625 204285453 0.000000e+00 1336


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 TraesCS3D01G167900 chr3D 142475504 142479990 4486 False 8287.0 8287 100.0000 1 4487 1 chr3D.!!$F1 4486
1 TraesCS3D01G167900 chr3A 161445370 161449852 4482 False 3392.0 6259 95.4165 66 4487 2 chr3A.!!$F1 4421
2 TraesCS3D01G167900 chr3B 204280884 204285453 4569 False 3631.5 5927 95.8395 1 4487 2 chr3B.!!$F1 4486

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
334 359 0.526096 CCACAGCCATATTGCGCAAC 60.526 55.0 27.64 12.59 36.02 4.17 F
1633 1671 0.752743 TTGCCAGCTTGTTCTGCACT 60.753 50.0 0.00 0.00 32.87 4.40 F
2478 2518 0.391927 GCGGTACCAACATACCAGCA 60.392 55.0 13.54 0.00 44.36 4.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1960 1999 0.106819 AGGATGCCCACATGAAGCTC 60.107 55.0 0.0 0.0 36.35 4.09 R
3445 3485 0.179000 AGGAACTGCTCCCGCATTAG 59.821 55.0 0.0 0.0 46.81 1.73 R
4033 4158 0.038599 ATGATGCTGACCTGCCAACA 59.961 50.0 0.0 0.0 0.00 3.33 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
61 62 5.450688 GCACTACTACCTTCTGACATACCAG 60.451 48.000 0.00 0.00 35.55 4.00
86 90 9.847224 AGACTCTTCTTTCACCTGTTAATTAAA 57.153 29.630 0.00 0.00 0.00 1.52
135 139 1.527311 GCTGTTATAAGCGGCAGTAGC 59.473 52.381 1.45 0.00 38.08 3.58
141 145 1.471119 TAAGCGGCAGTAGCACTACT 58.529 50.000 1.45 4.47 46.52 2.57
182 186 3.070159 TGCTAGGAATCCTGTACTCATGC 59.930 47.826 12.96 4.15 34.61 4.06
229 233 6.403866 TTTTAGTTGCTCATGGTCATTGTT 57.596 33.333 0.00 0.00 0.00 2.83
334 359 0.526096 CCACAGCCATATTGCGCAAC 60.526 55.000 27.64 12.59 36.02 4.17
494 519 6.273071 GTGGCTGAGTAATTGTTGAAGTTTT 58.727 36.000 0.00 0.00 0.00 2.43
811 837 8.733128 GTTACATTGTGTTGATGTTATATTGCG 58.267 33.333 0.00 0.00 38.58 4.85
818 844 3.472652 TGATGTTATATTGCGGTGTCCC 58.527 45.455 0.00 0.00 0.00 4.46
836 862 1.877443 CCCGAACAGGATTTTCGTTGT 59.123 47.619 4.02 0.00 43.50 3.32
837 863 3.068560 CCCGAACAGGATTTTCGTTGTA 58.931 45.455 4.02 0.00 43.50 2.41
848 875 7.480542 CAGGATTTTCGTTGTAATCGGTAAAAG 59.519 37.037 0.00 0.00 32.73 2.27
851 878 9.384682 GATTTTCGTTGTAATCGGTAAAAGAAA 57.615 29.630 0.00 0.00 0.00 2.52
860 887 8.932791 TGTAATCGGTAAAAGAAAAGTCATCTC 58.067 33.333 0.00 0.00 0.00 2.75
894 921 7.067008 AGACATGTTACGGCTATAAAAAGCAAT 59.933 33.333 0.00 0.00 44.64 3.56
1011 1038 2.568090 GCAAACATGGCTCCCGTG 59.432 61.111 0.00 2.02 45.34 4.94
1112 1145 3.515316 CTGTGGAGGTGGCGTTCGT 62.515 63.158 0.00 0.00 0.00 3.85
1254 1287 1.495951 GACGTTCAACATCGTGGCC 59.504 57.895 0.00 0.00 40.39 5.36
1458 1496 1.064017 TCCACCAGGTTTTTGCTCAGT 60.064 47.619 0.00 0.00 35.89 3.41
1534 1572 2.649034 GAGACGGTGGCGAAGTCA 59.351 61.111 7.99 0.00 43.93 3.41
1615 1653 2.657237 CTCGGCCTCGTCACCTTT 59.343 61.111 0.00 0.00 37.69 3.11
1633 1671 0.752743 TTGCCAGCTTGTTCTGCACT 60.753 50.000 0.00 0.00 32.87 4.40
1655 1693 3.423154 CGCTGCGGAAGGTGAACC 61.423 66.667 15.40 0.00 0.00 3.62
1656 1694 3.056328 GCTGCGGAAGGTGAACCC 61.056 66.667 0.00 0.00 36.42 4.11
1657 1695 2.429930 CTGCGGAAGGTGAACCCA 59.570 61.111 0.00 0.00 36.42 4.51
1663 1701 1.546773 CGGAAGGTGAACCCATTTCCA 60.547 52.381 15.51 0.00 38.09 3.53
1671 1709 3.386402 GTGAACCCATTTCCAACCAAGAA 59.614 43.478 0.00 0.00 32.58 2.52
1695 1733 3.321682 CACCACCATTTCCATGTCTTTGT 59.678 43.478 0.00 0.00 0.00 2.83
1744 1783 3.273434 TGTTTGGCAGCTCATGATACTC 58.727 45.455 0.00 0.00 0.00 2.59
1892 1931 1.881324 TGCCGTTTGTAAGCTTAACCC 59.119 47.619 7.99 0.00 0.00 4.11
1893 1932 1.881324 GCCGTTTGTAAGCTTAACCCA 59.119 47.619 7.99 0.00 0.00 4.51
1902 1941 6.767524 TGTAAGCTTAACCCACATTATTGG 57.232 37.500 7.99 0.00 36.26 3.16
1960 1999 1.047002 TGTCCAAAGCCATTGTTGGG 58.953 50.000 2.77 0.00 43.82 4.12
2080 2119 4.312443 AGTTTTACTTCGATTTCTCCGCA 58.688 39.130 0.00 0.00 0.00 5.69
2311 2351 8.304596 TCGTACTTATCAGATGTTTCAGTCTTT 58.695 33.333 0.00 0.00 0.00 2.52
2442 2482 2.878406 CAACCACTTCCACAAGAATCGT 59.122 45.455 0.00 0.00 32.82 3.73
2478 2518 0.391927 GCGGTACCAACATACCAGCA 60.392 55.000 13.54 0.00 44.36 4.41
2522 2562 2.783828 GCTCTTAGCTACGATGAGCA 57.216 50.000 21.93 0.00 46.41 4.26
2557 2597 4.282195 AGATCTTTCTGAACGAAGGACTGT 59.718 41.667 0.47 0.00 40.07 3.55
2613 2653 1.005340 CAGCCGTCTCAGCAATCTTC 58.995 55.000 0.00 0.00 0.00 2.87
2841 2881 4.400251 GGTGTCATGTTGATGATCATTGGT 59.600 41.667 10.14 0.00 40.78 3.67
2874 2914 3.008330 GCTCATGCATGACTTCAAGACT 58.992 45.455 25.42 0.00 39.41 3.24
2883 2923 4.808414 TGACTTCAAGACTGGATACCTG 57.192 45.455 0.00 0.00 0.00 4.00
2895 2935 2.225267 TGGATACCTGACACTCACCTCA 60.225 50.000 0.00 0.00 0.00 3.86
2973 3013 1.543429 CCGCTTGTCTTCCTGTCCTTT 60.543 52.381 0.00 0.00 0.00 3.11
3017 3057 2.110006 GGGAGAAGCTGGATCGGC 59.890 66.667 0.00 1.67 35.73 5.54
3150 3190 1.550072 GCCTTTTGCTTGGATTGCCTA 59.450 47.619 0.00 0.00 36.87 3.93
3174 3214 2.958355 AGCAGTAGCCAAAGCAAAGAAA 59.042 40.909 0.00 0.00 43.56 2.52
3440 3480 6.682746 TGAAGTTCTTGTCTAGTCATCAGAC 58.317 40.000 4.17 0.00 45.31 3.51
3445 3485 3.876274 TGTCTAGTCATCAGACCAAGC 57.124 47.619 0.38 0.00 46.15 4.01
3484 3524 3.775316 CCTACCCAAAGTGACTACCTCAT 59.225 47.826 0.00 0.00 0.00 2.90
3513 3553 7.814587 TGATACAGACAAGTACTGACAGAAATG 59.185 37.037 10.08 5.25 38.55 2.32
3588 3628 4.717877 ACACATGTGAATTCCTTGAGTCA 58.282 39.130 31.94 0.00 0.00 3.41
3721 3846 6.211184 AGGATCAAAATATGCTTGACACCAAA 59.789 34.615 17.95 0.00 35.70 3.28
3767 3892 3.193479 GGAACAGGCTTTTAATCACCAGG 59.807 47.826 0.00 0.00 0.00 4.45
3777 3902 2.414994 AATCACCAGGTCATGCTGAG 57.585 50.000 2.22 0.00 27.09 3.35
3791 3916 3.518634 TGCTGAGAAACCAAACAAACC 57.481 42.857 0.00 0.00 0.00 3.27
3797 3922 4.024725 TGAGAAACCAAACAAACCGATACG 60.025 41.667 0.00 0.00 0.00 3.06
3909 4034 6.381133 GGTTAATGAAGATGAAGGTGGGAAAT 59.619 38.462 0.00 0.00 0.00 2.17
4033 4158 4.806952 AGACTAGTAATCTCCTGGCTCT 57.193 45.455 0.00 0.00 0.00 4.09
4086 4211 8.863049 CAATTTCAGCTGTTATCCAACAATAAC 58.137 33.333 14.67 0.00 43.92 1.89
4166 4291 3.637769 TGCTACTTTTCCAGGGTGTTTT 58.362 40.909 0.00 0.00 0.00 2.43
4332 4543 2.238898 GGGGGCTCAAACAGTACACTAT 59.761 50.000 0.00 0.00 0.00 2.12
4396 4607 6.963049 TGTCCGCTTAGAACTTTTAGATTC 57.037 37.500 0.00 0.00 0.00 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 5.008415 GGATGCTTTTCTCTGTGATGTATGG 59.992 44.000 0.00 0.00 0.00 2.74
13 14 7.658982 TGCTATATTAGGATGCTTTTCTCTGTG 59.341 37.037 0.00 0.00 0.00 3.66
86 90 5.003804 GGTTGTGAGTTCTGACCATACAAT 58.996 41.667 0.00 0.00 31.00 2.71
88 92 3.244422 GGGTTGTGAGTTCTGACCATACA 60.244 47.826 0.00 0.00 32.00 2.29
89 93 3.244422 TGGGTTGTGAGTTCTGACCATAC 60.244 47.826 0.00 0.00 32.00 2.39
90 94 2.976185 TGGGTTGTGAGTTCTGACCATA 59.024 45.455 0.00 0.00 32.00 2.74
135 139 5.106197 TGCATAACATCAAAAGGCAGTAGTG 60.106 40.000 0.00 0.00 0.00 2.74
141 145 3.196039 AGCATGCATAACATCAAAAGGCA 59.804 39.130 21.98 0.00 36.64 4.75
142 146 3.788937 AGCATGCATAACATCAAAAGGC 58.211 40.909 21.98 0.00 36.64 4.35
316 341 0.862701 CGTTGCGCAATATGGCTGTG 60.863 55.000 27.79 4.22 0.00 3.66
334 359 5.630680 AGCTTTGAACATGTCAATTTTAGCG 59.369 36.000 17.23 0.00 45.22 4.26
494 519 4.360405 GGCGGGAAAAGGGCAGGA 62.360 66.667 0.00 0.00 0.00 3.86
727 752 4.880120 CCATTTGATCTCTAAAGCTCAGCA 59.120 41.667 0.00 0.00 29.84 4.41
811 837 1.810755 GAAAATCCTGTTCGGGACACC 59.189 52.381 2.18 0.00 38.30 4.16
825 851 8.938047 TTCTTTTACCGATTACAACGAAAATC 57.062 30.769 0.00 0.00 0.00 2.17
836 862 8.319146 AGGAGATGACTTTTCTTTTACCGATTA 58.681 33.333 0.00 0.00 0.00 1.75
837 863 7.119846 CAGGAGATGACTTTTCTTTTACCGATT 59.880 37.037 0.00 0.00 0.00 3.34
894 921 6.701145 TTTTAACTGTCACCAACATAAGCA 57.299 33.333 0.00 0.00 37.23 3.91
1254 1287 1.219393 GAAGAACCCGAGGAGGCTG 59.781 63.158 0.00 0.00 39.21 4.85
1266 1299 2.408704 CCACGACTTGATCACGAAGAAC 59.591 50.000 10.77 0.00 0.00 3.01
1427 1460 1.094785 CCTGGTGGAAAATAGCGTGG 58.905 55.000 0.00 0.00 34.57 4.94
1429 1462 2.579410 AACCTGGTGGAAAATAGCGT 57.421 45.000 0.00 0.00 37.04 5.07
1431 1464 3.745975 GCAAAAACCTGGTGGAAAATAGC 59.254 43.478 0.00 0.00 37.04 2.97
1433 1466 4.651503 TGAGCAAAAACCTGGTGGAAAATA 59.348 37.500 0.00 0.00 37.04 1.40
1434 1467 3.454082 TGAGCAAAAACCTGGTGGAAAAT 59.546 39.130 0.00 0.00 37.04 1.82
1435 1468 2.834549 TGAGCAAAAACCTGGTGGAAAA 59.165 40.909 0.00 0.00 37.04 2.29
1615 1653 1.152902 AGTGCAGAACAAGCTGGCA 60.153 52.632 0.00 0.00 36.41 4.92
1654 1692 3.055891 GGTGATTCTTGGTTGGAAATGGG 60.056 47.826 0.00 0.00 0.00 4.00
1655 1693 3.577848 TGGTGATTCTTGGTTGGAAATGG 59.422 43.478 0.00 0.00 0.00 3.16
1656 1694 4.559153 GTGGTGATTCTTGGTTGGAAATG 58.441 43.478 0.00 0.00 0.00 2.32
1657 1695 3.578282 GGTGGTGATTCTTGGTTGGAAAT 59.422 43.478 0.00 0.00 0.00 2.17
1663 1701 3.578282 GGAAATGGTGGTGATTCTTGGTT 59.422 43.478 0.00 0.00 0.00 3.67
1671 1709 3.744940 AGACATGGAAATGGTGGTGAT 57.255 42.857 0.00 0.00 0.00 3.06
1892 1931 4.884164 GGGAGGAGAGAAACCAATAATGTG 59.116 45.833 0.00 0.00 0.00 3.21
1893 1932 4.079730 GGGGAGGAGAGAAACCAATAATGT 60.080 45.833 0.00 0.00 0.00 2.71
1902 1941 1.959710 AAGGAGGGGAGGAGAGAAAC 58.040 55.000 0.00 0.00 0.00 2.78
1960 1999 0.106819 AGGATGCCCACATGAAGCTC 60.107 55.000 0.00 0.00 36.35 4.09
2080 2119 3.048602 CCCACACCGACGAGACTT 58.951 61.111 0.00 0.00 0.00 3.01
2478 2518 8.031277 GCTGTTTGTTTATCTGAATTTCCATCT 58.969 33.333 0.00 0.00 0.00 2.90
2522 2562 3.937706 CAGAAAGATCTTGTTCCTGCGAT 59.062 43.478 9.17 0.00 32.03 4.58
2557 2597 1.813859 CAACCGAGACATAGCCCGA 59.186 57.895 0.00 0.00 0.00 5.14
2805 2845 2.203394 ACACCACAGGCAGCAAGG 60.203 61.111 0.00 0.00 0.00 3.61
2841 2881 1.162181 GCATGAGCTCAGCGGCATTA 61.162 55.000 22.96 0.00 37.91 1.90
2874 2914 2.225267 TGAGGTGAGTGTCAGGTATCCA 60.225 50.000 0.00 0.00 0.00 3.41
2883 2923 0.753262 ACAGTGGTGAGGTGAGTGTC 59.247 55.000 0.00 0.00 0.00 3.67
2895 2935 3.347216 GCTTATGAACATGGACAGTGGT 58.653 45.455 0.00 0.00 0.00 4.16
2973 3013 3.733684 GCTCTTTGCCGACAAGTTTTTCA 60.734 43.478 0.00 0.00 37.04 2.69
2998 3038 1.907739 CCGATCCAGCTTCTCCCAA 59.092 57.895 0.00 0.00 0.00 4.12
3017 3057 3.204827 CCAAGGGCGCCGAGAATG 61.205 66.667 22.54 13.91 0.00 2.67
3108 3148 4.700213 GCCATAAGGAAGAAAGCTACACAA 59.300 41.667 0.00 0.00 36.89 3.33
3150 3190 2.205022 TTGCTTTGGCTACTGCTGAT 57.795 45.000 0.00 0.00 39.59 2.90
3174 3214 5.193679 GGAATGTAGTTACTTGCCTTCCAT 58.806 41.667 13.86 0.00 0.00 3.41
3388 3428 1.616374 GGGTGGCTCGATTTGGAAAAA 59.384 47.619 0.00 0.00 0.00 1.94
3440 3480 1.442526 CTGCTCCCGCATTAGCTTGG 61.443 60.000 0.00 0.00 46.74 3.61
3445 3485 0.179000 AGGAACTGCTCCCGCATTAG 59.821 55.000 0.00 0.00 46.81 1.73
3459 3499 3.581770 AGGTAGTCACTTTGGGTAGGAAC 59.418 47.826 0.00 0.00 0.00 3.62
3484 3524 6.659242 TCTGTCAGTACTTGTCTGTATCATCA 59.341 38.462 0.00 0.00 34.86 3.07
3604 3644 6.266558 ACACTGGAAAAATATTTACACAGGCA 59.733 34.615 20.61 6.21 34.37 4.75
3721 3846 2.875296 TCTTTTACTGGCAATGTGGCT 58.125 42.857 3.34 0.00 44.10 4.75
3767 3892 3.988379 TGTTTGGTTTCTCAGCATGAC 57.012 42.857 0.00 0.00 42.56 3.06
3777 3902 4.471157 TCGTATCGGTTTGTTTGGTTTC 57.529 40.909 0.00 0.00 0.00 2.78
3791 3916 4.360563 ACTATGCTTGACCTTTCGTATCG 58.639 43.478 0.00 0.00 0.00 2.92
3797 3922 9.294030 CAAAATGAATACTATGCTTGACCTTTC 57.706 33.333 0.00 0.00 0.00 2.62
4033 4158 0.038599 ATGATGCTGACCTGCCAACA 59.961 50.000 0.00 0.00 0.00 3.33
4086 4211 8.729529 ATTCGTATAACTATCGTGATGAGTTG 57.270 34.615 11.56 0.00 35.17 3.16
4197 4404 7.080353 TCGTTCATATCGTAGAGAAACTGAA 57.920 36.000 0.00 0.00 43.63 3.02


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

AutoCloner maintained by Alex Coulton.