Multiple sequence alignment - TraesCS3A01G174600

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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 TraesCS3A01G174600 chr3A 100.000 7466 0 0 1 7466 193880224 193872759 0.000000e+00 13788.0
1 TraesCS3A01G174600 chr3A 96.544 6394 159 26 114 6468 33435009 33428639 0.000000e+00 10527.0
2 TraesCS3A01G174600 chr3A 98.171 3718 53 8 1 3714 194068010 194064304 0.000000e+00 6475.0
3 TraesCS3A01G174600 chr3A 98.606 3013 29 2 3776 6787 194064307 194061307 0.000000e+00 5319.0
4 TraesCS3A01G174600 chr3A 90.498 863 75 7 2800 3657 33433499 33432639 0.000000e+00 1133.0
5 TraesCS3A01G174600 chr3A 89.318 880 74 11 1608 2469 33432326 33431449 0.000000e+00 1086.0
6 TraesCS3A01G174600 chr3A 88.753 898 77 12 1589 2469 193877458 193876568 0.000000e+00 1077.0
7 TraesCS3A01G174600 chr3A 88.753 898 77 12 2767 3657 193878636 193877756 0.000000e+00 1077.0
8 TraesCS3A01G174600 chr3A 88.641 898 78 12 2767 3657 194066427 194065547 0.000000e+00 1072.0
9 TraesCS3A01G174600 chr3A 88.444 874 83 9 1612 2469 194065229 194064358 0.000000e+00 1038.0
10 TraesCS3A01G174600 chr3A 94.981 259 13 0 7058 7316 411273318 411273060 2.510000e-109 407.0
11 TraesCS3A01G174600 chr3A 92.140 229 14 3 6786 7012 411275410 411275184 3.360000e-83 320.0
12 TraesCS3A01G174600 chr3A 94.309 123 3 2 3678 3800 212122779 212122661 1.280000e-42 185.0
13 TraesCS3A01G174600 chr3A 94.309 123 3 2 3676 3798 610418847 610418965 1.280000e-42 185.0
14 TraesCS3A01G174600 chr3A 89.744 78 8 0 6119 6196 193874026 193873949 4.770000e-17 100.0
15 TraesCS3A01G174600 chr3A 89.744 78 8 0 6199 6276 193874106 193874029 4.770000e-17 100.0
16 TraesCS3A01G174600 chr3A 89.024 82 8 1 6115 6196 194061886 194061806 4.770000e-17 100.0
17 TraesCS3A01G174600 chr3A 88.750 80 9 0 6199 6278 33428988 33428909 1.710000e-16 99.0
18 TraesCS3A01G174600 chr3B 94.061 3637 120 38 3194 6787 41304910 41301327 0.000000e+00 5432.0
19 TraesCS3A01G174600 chr3B 89.293 467 41 7 2007 2469 41304910 41304449 1.810000e-160 577.0
20 TraesCS3A01G174600 chr3B 94.286 70 4 0 6127 6196 41301927 41301858 2.850000e-19 108.0
21 TraesCS3A01G174600 chr3B 90.000 80 8 0 6199 6278 41302018 41301939 3.680000e-18 104.0
22 TraesCS3A01G174600 chr3B 95.918 49 2 0 446 494 41304970 41304922 6.210000e-11 80.5
23 TraesCS3A01G174600 chr3B 90.476 42 2 2 4391 4431 594965591 594965551 4.000000e-03 54.7
24 TraesCS3A01G174600 chr5A 95.603 705 7 2 6786 7466 510196420 510197124 0.000000e+00 1109.0
25 TraesCS3A01G174600 chr5A 94.531 128 3 3 1 125 503002077 503001951 2.130000e-45 195.0
26 TraesCS3A01G174600 chr4A 95.177 705 10 2 6786 7466 557105361 557106065 0.000000e+00 1092.0
27 TraesCS3A01G174600 chr5B 90.909 682 42 3 6786 7466 397294957 397294295 0.000000e+00 898.0
28 TraesCS3A01G174600 chr5B 91.594 571 42 5 3050 3618 476450643 476451209 0.000000e+00 784.0
29 TraesCS3A01G174600 chr5B 89.860 572 48 9 1864 2430 476450643 476451209 0.000000e+00 726.0
30 TraesCS3A01G174600 chr5B 95.122 123 6 0 3676 3798 531869370 531869248 2.130000e-45 195.0
31 TraesCS3A01G174600 chr5B 95.041 121 6 0 3678 3798 531864217 531864097 2.750000e-44 191.0
32 TraesCS3A01G174600 chr5B 95.041 121 2 2 3678 3798 599612347 599612463 3.560000e-43 187.0
33 TraesCS3A01G174600 chr5D 93.695 571 34 2 3050 3618 396428969 396429539 0.000000e+00 854.0
34 TraesCS3A01G174600 chr5D 91.434 572 43 6 1864 2430 396428969 396429539 0.000000e+00 780.0
35 TraesCS3A01G174600 chr6D 89.068 558 35 3 6783 7316 79968747 79969302 0.000000e+00 669.0
36 TraesCS3A01G174600 chr6D 78.178 527 69 27 6786 7289 68695242 68695745 2.040000e-75 294.0
37 TraesCS3A01G174600 chr6D 97.143 35 1 0 4390 4424 30079407 30079373 8.090000e-05 60.2
38 TraesCS3A01G174600 chr3D 87.132 544 33 11 6786 7316 168501136 168501655 3.880000e-162 582.0
39 TraesCS3A01G174600 chr3D 94.574 129 6 1 3678 3806 511281674 511281801 1.640000e-46 198.0
40 TraesCS3A01G174600 chr3D 97.414 116 1 2 1 115 563875021 563874907 5.910000e-46 196.0
41 TraesCS3A01G174600 chr3D 97.391 115 1 2 1 114 188859260 188859147 2.130000e-45 195.0
42 TraesCS3A01G174600 chr3D 95.833 120 3 2 1 119 188820666 188820548 7.640000e-45 193.0
43 TraesCS3A01G174600 chr3D 95.082 122 6 0 3677 3798 511275934 511276055 7.640000e-45 193.0
44 TraesCS3A01G174600 chr3D 94.400 125 4 3 1 124 362017546 362017668 9.890000e-44 189.0
45 TraesCS3A01G174600 chr3D 100.000 32 0 0 4390 4421 532868835 532868866 8.090000e-05 60.2
46 TraesCS3A01G174600 chr4D 77.925 530 70 27 6786 7292 669467 668962 3.410000e-73 287.0
47 TraesCS3A01G174600 chr4D 100.000 32 0 0 4390 4421 20437815 20437784 8.090000e-05 60.2
48 TraesCS3A01G174600 chr4D 97.059 34 1 0 4390 4423 35624768 35624801 2.910000e-04 58.4
49 TraesCS3A01G174600 chr2D 78.210 514 67 29 6786 7277 550655281 550655771 3.410000e-73 287.0
50 TraesCS3A01G174600 chr2D 100.000 32 0 0 4390 4421 384255212 384255181 8.090000e-05 60.2
51 TraesCS3A01G174600 chr1A 85.787 197 24 4 117 311 112946521 112946715 9.820000e-49 206.0
52 TraesCS3A01G174600 chr7D 97.414 116 1 2 1 115 264619054 264619168 5.910000e-46 196.0
53 TraesCS3A01G174600 chr7D 97.414 116 1 2 1 115 391667033 391667147 5.910000e-46 196.0
54 TraesCS3A01G174600 chr7D 89.720 107 10 1 7360 7466 622370732 622370627 1.310000e-27 135.0
55 TraesCS3A01G174600 chr1D 84.236 203 30 2 116 317 98138349 98138550 5.910000e-46 196.0
56 TraesCS3A01G174600 chr1D 92.500 40 2 1 4390 4428 4762398 4762437 1.000000e-03 56.5
57 TraesCS3A01G174600 chr6A 97.391 115 1 2 1 114 259242361 259242474 2.130000e-45 195.0


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 TraesCS3A01G174600 chr3A 193872759 193880224 7465 True 13788.000000 13788 100.0000 1 7466 1 chr3A.!!$R2 7465
1 TraesCS3A01G174600 chr3A 33428639 33435009 6370 True 10527.000000 10527 96.5440 114 6468 1 chr3A.!!$R1 6354
2 TraesCS3A01G174600 chr3A 194061307 194068010 6703 True 2800.800000 6475 92.5772 1 6787 5 chr3A.!!$R6 6786
3 TraesCS3A01G174600 chr3A 33428909 33433499 4590 True 772.666667 1133 89.5220 1608 6278 3 chr3A.!!$R4 4670
4 TraesCS3A01G174600 chr3A 193873949 193878636 4687 True 588.500000 1077 89.2485 1589 6276 4 chr3A.!!$R5 4687
5 TraesCS3A01G174600 chr3A 411273060 411275410 2350 True 363.500000 407 93.5605 6786 7316 2 chr3A.!!$R7 530
6 TraesCS3A01G174600 chr3B 41301327 41304970 3643 True 1260.300000 5432 92.7116 446 6787 5 chr3B.!!$R2 6341
7 TraesCS3A01G174600 chr5A 510196420 510197124 704 False 1109.000000 1109 95.6030 6786 7466 1 chr5A.!!$F1 680
8 TraesCS3A01G174600 chr4A 557105361 557106065 704 False 1092.000000 1092 95.1770 6786 7466 1 chr4A.!!$F1 680
9 TraesCS3A01G174600 chr5B 397294295 397294957 662 True 898.000000 898 90.9090 6786 7466 1 chr5B.!!$R1 680
10 TraesCS3A01G174600 chr5B 476450643 476451209 566 False 755.000000 784 90.7270 1864 3618 2 chr5B.!!$F2 1754
11 TraesCS3A01G174600 chr5D 396428969 396429539 570 False 817.000000 854 92.5645 1864 3618 2 chr5D.!!$F1 1754
12 TraesCS3A01G174600 chr6D 79968747 79969302 555 False 669.000000 669 89.0680 6783 7316 1 chr6D.!!$F2 533
13 TraesCS3A01G174600 chr6D 68695242 68695745 503 False 294.000000 294 78.1780 6786 7289 1 chr6D.!!$F1 503
14 TraesCS3A01G174600 chr3D 168501136 168501655 519 False 582.000000 582 87.1320 6786 7316 1 chr3D.!!$F1 530
15 TraesCS3A01G174600 chr4D 668962 669467 505 True 287.000000 287 77.9250 6786 7292 1 chr4D.!!$R1 506

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
940 942 0.669318 CTGGGCTACAAACGAAGCGA 60.669 55.0 0.0 0.0 39.71 4.93 F
1467 1478 1.159285 CAGCGAATTGGTGCTTGAGA 58.841 50.0 0.0 0.0 40.03 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
6324 6383 0.110192 GACCAGTAACAAAGCAGCGC 60.110 55.0 0.0 0.0 0.00 5.92 R
6797 6888 2.004583 TCAGCGACAACTATTTCGGG 57.995 50.0 0.0 0.0 35.73 5.14 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
36 37 8.264347 TGTGCCTAGTTATGATATGTCTGAAAA 58.736 33.333 0.00 0.00 0.00 2.29
48 49 8.615211 TGATATGTCTGAAAATACTCAATGCAC 58.385 33.333 0.00 0.00 0.00 4.57
637 638 7.017055 GCACATTTTTCATAAATTGCAGGAAC 58.983 34.615 0.00 0.00 31.13 3.62
939 941 1.635663 CCTGGGCTACAAACGAAGCG 61.636 60.000 0.00 0.00 39.71 4.68
940 942 0.669318 CTGGGCTACAAACGAAGCGA 60.669 55.000 0.00 0.00 39.71 4.93
941 943 0.669318 TGGGCTACAAACGAAGCGAG 60.669 55.000 0.00 0.00 39.71 5.03
942 944 1.359459 GGGCTACAAACGAAGCGAGG 61.359 60.000 0.00 0.00 39.71 4.63
943 945 1.420312 GCTACAAACGAAGCGAGGC 59.580 57.895 0.00 0.00 0.00 4.70
1127 1133 1.612146 TGACGGCTCCCTGAATCCA 60.612 57.895 0.00 0.00 0.00 3.41
1356 1367 1.493311 GTCTTCCTTTGCTGTCGCG 59.507 57.895 0.00 0.00 39.65 5.87
1467 1478 1.159285 CAGCGAATTGGTGCTTGAGA 58.841 50.000 0.00 0.00 40.03 3.27
1469 1480 2.163010 CAGCGAATTGGTGCTTGAGATT 59.837 45.455 0.00 0.00 40.03 2.40
1473 1484 3.686241 CGAATTGGTGCTTGAGATTCTCA 59.314 43.478 12.38 12.38 38.87 3.27
6324 6383 1.271597 ACTGCCCCTCTTTTAGCACTG 60.272 52.381 0.00 0.00 0.00 3.66
6362 6421 6.379988 ACTGGTCAATGGAAGTACTTGTTTTT 59.620 34.615 14.14 0.00 0.00 1.94
6572 6631 5.086104 TGGCAGCTAACTCTACCTTTTAG 57.914 43.478 0.00 0.00 0.00 1.85
6584 6651 6.436847 ACTCTACCTTTTAGTCTCCCACTTAC 59.563 42.308 0.00 0.00 36.43 2.34
6686 6753 5.350365 ACATTACTTAAAGCGCGAGATTGAA 59.650 36.000 12.10 0.00 39.83 2.69
6702 6792 4.940046 AGATTGAACTGGTGCTATTGTCTG 59.060 41.667 0.00 0.00 0.00 3.51
6703 6793 3.769739 TGAACTGGTGCTATTGTCTGT 57.230 42.857 0.00 0.00 0.00 3.41
6704 6794 3.402110 TGAACTGGTGCTATTGTCTGTG 58.598 45.455 0.00 0.00 0.00 3.66
6705 6795 3.181455 TGAACTGGTGCTATTGTCTGTGT 60.181 43.478 0.00 0.00 0.00 3.72
6706 6796 2.771089 ACTGGTGCTATTGTCTGTGTG 58.229 47.619 0.00 0.00 0.00 3.82
6707 6797 2.104792 ACTGGTGCTATTGTCTGTGTGT 59.895 45.455 0.00 0.00 0.00 3.72
6708 6798 3.323691 ACTGGTGCTATTGTCTGTGTGTA 59.676 43.478 0.00 0.00 0.00 2.90
6709 6799 4.202315 ACTGGTGCTATTGTCTGTGTGTAA 60.202 41.667 0.00 0.00 0.00 2.41
6710 6800 4.905429 TGGTGCTATTGTCTGTGTGTAAT 58.095 39.130 0.00 0.00 0.00 1.89
6711 6801 6.043854 TGGTGCTATTGTCTGTGTGTAATA 57.956 37.500 0.00 0.00 0.00 0.98
6712 6802 6.468543 TGGTGCTATTGTCTGTGTGTAATAA 58.531 36.000 0.00 0.00 0.00 1.40
6713 6803 6.593770 TGGTGCTATTGTCTGTGTGTAATAAG 59.406 38.462 0.00 0.00 0.00 1.73
6772 6862 8.082242 GCTTCCACTGTTTCTATACAACAAAAT 58.918 33.333 0.00 0.00 33.74 1.82
6797 6888 3.386402 AGCTGCTAATTACTCCCTCTGTC 59.614 47.826 0.00 0.00 0.00 3.51
6816 6909 1.546923 TCCCGAAATAGTTGTCGCTGA 59.453 47.619 0.00 0.00 35.93 4.26
6942 7082 4.167359 TCGCTCGTGCTCTCTCGC 62.167 66.667 7.97 0.00 36.97 5.03
7321 9327 0.094901 CGTCGTCGTCTTCGTCAGAT 59.905 55.000 0.00 0.00 38.33 2.90
7440 9446 5.309323 TGGTTACTTGCTCAATACAATGC 57.691 39.130 0.00 0.00 0.00 3.56
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 5.050490 GGACTAATCGTGTGCATTGAGTAT 58.950 41.667 0.00 0.00 0.00 2.12
48 49 1.075542 TGCTTTGCGGACTAATCGTG 58.924 50.000 0.00 0.00 0.00 4.35
915 917 1.228737 GTTTGTAGCCCAGGCCCAA 60.229 57.895 4.70 6.17 43.17 4.12
1084 1090 1.372997 GAGAAGACACCGCGCTTCA 60.373 57.895 21.07 0.00 42.21 3.02
1311 1322 0.323633 TACGGTGAGAATCGACCCCA 60.324 55.000 0.00 0.00 38.61 4.96
1356 1367 2.668550 GGCACACCCGAAGTCCAC 60.669 66.667 0.00 0.00 0.00 4.02
1467 1478 0.106519 CCGGGCCCAAATCTGAGAAT 60.107 55.000 24.92 0.00 0.00 2.40
1469 1480 2.679342 CCCGGGCCCAAATCTGAGA 61.679 63.158 24.92 0.00 0.00 3.27
1473 1484 1.609210 CAAACCCGGGCCCAAATCT 60.609 57.895 24.08 0.00 0.00 2.40
6324 6383 0.110192 GACCAGTAACAAAGCAGCGC 60.110 55.000 0.00 0.00 0.00 5.92
6572 6631 5.916661 TGAGATAACAGTAAGTGGGAGAC 57.083 43.478 0.00 0.00 0.00 3.36
6584 6651 5.928976 TGGGTAATGTCCATGAGATAACAG 58.071 41.667 0.00 0.00 0.00 3.16
6686 6753 2.104792 ACACACAGACAATAGCACCAGT 59.895 45.455 0.00 0.00 0.00 4.00
6702 6792 6.816640 TCTTCAGTATGCACCTTATTACACAC 59.183 38.462 0.00 0.00 34.76 3.82
6703 6793 6.941857 TCTTCAGTATGCACCTTATTACACA 58.058 36.000 0.00 0.00 34.76 3.72
6704 6794 7.549488 ACTTCTTCAGTATGCACCTTATTACAC 59.451 37.037 0.00 0.00 31.97 2.90
6705 6795 7.620880 ACTTCTTCAGTATGCACCTTATTACA 58.379 34.615 0.00 0.00 31.97 2.41
6706 6796 9.032420 GTACTTCTTCAGTATGCACCTTATTAC 57.968 37.037 0.00 0.00 40.29 1.89
6707 6797 7.919091 CGTACTTCTTCAGTATGCACCTTATTA 59.081 37.037 0.00 0.00 40.29 0.98
6708 6798 6.757010 CGTACTTCTTCAGTATGCACCTTATT 59.243 38.462 0.00 0.00 40.29 1.40
6709 6799 6.273825 CGTACTTCTTCAGTATGCACCTTAT 58.726 40.000 0.00 0.00 40.29 1.73
6710 6800 5.393787 CCGTACTTCTTCAGTATGCACCTTA 60.394 44.000 0.00 0.00 41.96 2.69
6711 6801 4.495422 CGTACTTCTTCAGTATGCACCTT 58.505 43.478 0.00 0.00 40.29 3.50
6712 6802 3.119101 CCGTACTTCTTCAGTATGCACCT 60.119 47.826 0.00 0.00 41.96 4.00
6713 6803 3.187700 CCGTACTTCTTCAGTATGCACC 58.812 50.000 0.00 0.00 41.96 5.01
6772 6862 4.830046 CAGAGGGAGTAATTAGCAGCTCTA 59.170 45.833 0.00 0.00 0.00 2.43
6797 6888 2.004583 TCAGCGACAACTATTTCGGG 57.995 50.000 0.00 0.00 35.73 5.14
6816 6909 4.025145 CGCGAAAGTTGAACTAGAAACCTT 60.025 41.667 0.00 0.00 0.00 3.50
6896 6989 3.474486 TTGGGCAAGCGAGTGAGCA 62.474 57.895 0.00 0.00 40.15 4.26
7321 9327 3.311110 GTCAGCGAGGTGGGGACA 61.311 66.667 2.30 0.00 38.70 4.02
7440 9446 2.413765 CCAAACAGCAAAGAGATGAGCG 60.414 50.000 0.00 0.00 37.02 5.03


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

AutoCloner maintained by Alex Coulton.