Multiple sequence alignment - TraesCS1D01G172500

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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 TraesCS1D01G172500 chr1D 100.000 2224 0 0 1 2224 246430854 246428631 0.000000e+00 4108.0
1 TraesCS1D01G172500 chr1D 95.439 855 38 1 1 854 131355910 131356764 0.000000e+00 1362.0
2 TraesCS1D01G172500 chr1D 97.848 604 13 0 855 1458 51860227 51860830 0.000000e+00 1044.0
3 TraesCS1D01G172500 chr1D 97.517 604 14 1 855 1458 254446844 254446242 0.000000e+00 1031.0
4 TraesCS1D01G172500 chr1D 94.676 601 28 4 1456 2053 392003081 392003680 0.000000e+00 929.0
5 TraesCS1D01G172500 chr1D 91.450 655 42 12 1456 2101 95826955 95827604 0.000000e+00 887.0
6 TraesCS1D01G172500 chr1D 94.033 553 24 3 1459 2011 95801867 95802410 0.000000e+00 830.0
7 TraesCS1D01G172500 chr1D 78.741 715 115 32 1456 2160 265287389 265288076 5.640000e-121 444.0
8 TraesCS1D01G172500 chr2D 95.673 855 36 1 1 854 432086340 432085486 0.000000e+00 1373.0
9 TraesCS1D01G172500 chr2D 93.511 601 34 4 1456 2053 626556136 626556734 0.000000e+00 889.0
10 TraesCS1D01G172500 chr2D 91.145 655 42 11 1459 2101 626548052 626548702 0.000000e+00 874.0
11 TraesCS1D01G172500 chr2D 77.826 460 74 21 1459 1909 484325741 484325301 2.190000e-65 259.0
12 TraesCS1D01G172500 chr7D 95.556 855 37 1 1 854 83060116 83059262 0.000000e+00 1367.0
13 TraesCS1D01G172500 chr7D 95.556 855 37 1 1 854 537625452 537624598 0.000000e+00 1367.0
14 TraesCS1D01G172500 chr7D 89.078 705 59 7 1461 2165 442134774 442134088 0.000000e+00 859.0
15 TraesCS1D01G172500 chr7D 97.674 86 2 0 1372 1457 141166569 141166484 4.950000e-32 148.0
16 TraesCS1D01G172500 chr7D 94.681 94 4 1 2128 2221 574744698 574744606 6.400000e-31 145.0
17 TraesCS1D01G172500 chr5D 95.460 859 36 3 1 857 512807510 512808367 0.000000e+00 1367.0
18 TraesCS1D01G172500 chr5D 98.013 604 12 0 855 1458 6264134 6264737 0.000000e+00 1050.0
19 TraesCS1D01G172500 chr5D 97.848 604 13 0 855 1458 503303678 503303075 0.000000e+00 1044.0
20 TraesCS1D01G172500 chr5D 97.020 604 18 0 855 1458 6165107 6165710 0.000000e+00 1016.0
21 TraesCS1D01G172500 chr5D 96.854 604 18 1 855 1458 329152045 329152647 0.000000e+00 1009.0
22 TraesCS1D01G172500 chr5D 93.009 658 30 11 1456 2101 447926746 447927399 0.000000e+00 946.0
23 TraesCS1D01G172500 chr5D 91.437 654 41 10 1459 2101 447918352 447919001 0.000000e+00 883.0
24 TraesCS1D01G172500 chr3D 95.460 859 36 3 1 857 429110483 429109626 0.000000e+00 1367.0
25 TraesCS1D01G172500 chr3D 95.439 855 38 1 1 854 366447391 366446537 0.000000e+00 1362.0
26 TraesCS1D01G172500 chr6D 95.444 856 35 4 1 854 449983675 449984528 0.000000e+00 1362.0
27 TraesCS1D01G172500 chr4D 95.439 855 38 1 1 854 292919819 292918965 0.000000e+00 1362.0
28 TraesCS1D01G172500 chr4D 96.523 604 20 1 855 1458 19880297 19879695 0.000000e+00 998.0
29 TraesCS1D01G172500 chr4D 93.750 96 6 0 2129 2224 100693111 100693206 6.400000e-31 145.0
30 TraesCS1D01G172500 chr4D 82.222 90 12 3 2133 2221 488151805 488151719 8.520000e-10 75.0
31 TraesCS1D01G172500 chr4D 81.111 90 13 3 2133 2221 488143494 488143408 3.960000e-08 69.4
32 TraesCS1D01G172500 chr3B 98.013 604 12 0 855 1458 101908339 101908942 0.000000e+00 1050.0
33 TraesCS1D01G172500 chr4A 96.854 604 18 1 855 1458 309478514 309479116 0.000000e+00 1009.0
34 TraesCS1D01G172500 chr4A 90.268 596 49 5 1456 2050 706254013 706253426 0.000000e+00 771.0
35 TraesCS1D01G172500 chr4A 91.382 557 40 4 1491 2046 706261927 706261378 0.000000e+00 756.0
36 TraesCS1D01G172500 chr6B 80.111 719 99 33 1456 2161 439140765 439141452 1.530000e-136 496.0
37 TraesCS1D01G172500 chr6B 96.250 80 3 0 2129 2208 386315631 386315552 4.980000e-27 132.0
38 TraesCS1D01G172500 chr6B 95.000 80 4 0 2129 2208 386323005 386322926 2.320000e-25 126.0
39 TraesCS1D01G172500 chr1B 78.303 719 113 37 1459 2165 252835877 252836564 7.340000e-115 424.0
40 TraesCS1D01G172500 chr1B 100.000 58 0 0 1401 1458 260783974 260783917 8.400000e-20 108.0
41 TraesCS1D01G172500 chr5A 95.349 129 6 0 1330 1458 267861326 267861198 2.890000e-49 206.0
42 TraesCS1D01G172500 chr2A 73.684 399 79 25 1456 1841 533686680 533687065 4.980000e-27 132.0
43 TraesCS1D01G172500 chr7B 96.203 79 3 0 2129 2207 322586369 322586447 1.790000e-26 130.0


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 TraesCS1D01G172500 chr1D 246428631 246430854 2223 True 4108 4108 100.000 1 2224 1 chr1D.!!$R1 2223
1 TraesCS1D01G172500 chr1D 131355910 131356764 854 False 1362 1362 95.439 1 854 1 chr1D.!!$F4 853
2 TraesCS1D01G172500 chr1D 51860227 51860830 603 False 1044 1044 97.848 855 1458 1 chr1D.!!$F1 603
3 TraesCS1D01G172500 chr1D 254446242 254446844 602 True 1031 1031 97.517 855 1458 1 chr1D.!!$R2 603
4 TraesCS1D01G172500 chr1D 392003081 392003680 599 False 929 929 94.676 1456 2053 1 chr1D.!!$F6 597
5 TraesCS1D01G172500 chr1D 95826955 95827604 649 False 887 887 91.450 1456 2101 1 chr1D.!!$F3 645
6 TraesCS1D01G172500 chr1D 95801867 95802410 543 False 830 830 94.033 1459 2011 1 chr1D.!!$F2 552
7 TraesCS1D01G172500 chr1D 265287389 265288076 687 False 444 444 78.741 1456 2160 1 chr1D.!!$F5 704
8 TraesCS1D01G172500 chr2D 432085486 432086340 854 True 1373 1373 95.673 1 854 1 chr2D.!!$R1 853
9 TraesCS1D01G172500 chr2D 626556136 626556734 598 False 889 889 93.511 1456 2053 1 chr2D.!!$F2 597
10 TraesCS1D01G172500 chr2D 626548052 626548702 650 False 874 874 91.145 1459 2101 1 chr2D.!!$F1 642
11 TraesCS1D01G172500 chr7D 83059262 83060116 854 True 1367 1367 95.556 1 854 1 chr7D.!!$R1 853
12 TraesCS1D01G172500 chr7D 537624598 537625452 854 True 1367 1367 95.556 1 854 1 chr7D.!!$R4 853
13 TraesCS1D01G172500 chr7D 442134088 442134774 686 True 859 859 89.078 1461 2165 1 chr7D.!!$R3 704
14 TraesCS1D01G172500 chr5D 512807510 512808367 857 False 1367 1367 95.460 1 857 1 chr5D.!!$F6 856
15 TraesCS1D01G172500 chr5D 6264134 6264737 603 False 1050 1050 98.013 855 1458 1 chr5D.!!$F2 603
16 TraesCS1D01G172500 chr5D 503303075 503303678 603 True 1044 1044 97.848 855 1458 1 chr5D.!!$R1 603
17 TraesCS1D01G172500 chr5D 6165107 6165710 603 False 1016 1016 97.020 855 1458 1 chr5D.!!$F1 603
18 TraesCS1D01G172500 chr5D 329152045 329152647 602 False 1009 1009 96.854 855 1458 1 chr5D.!!$F3 603
19 TraesCS1D01G172500 chr5D 447926746 447927399 653 False 946 946 93.009 1456 2101 1 chr5D.!!$F5 645
20 TraesCS1D01G172500 chr5D 447918352 447919001 649 False 883 883 91.437 1459 2101 1 chr5D.!!$F4 642
21 TraesCS1D01G172500 chr3D 429109626 429110483 857 True 1367 1367 95.460 1 857 1 chr3D.!!$R2 856
22 TraesCS1D01G172500 chr3D 366446537 366447391 854 True 1362 1362 95.439 1 854 1 chr3D.!!$R1 853
23 TraesCS1D01G172500 chr6D 449983675 449984528 853 False 1362 1362 95.444 1 854 1 chr6D.!!$F1 853
24 TraesCS1D01G172500 chr4D 292918965 292919819 854 True 1362 1362 95.439 1 854 1 chr4D.!!$R2 853
25 TraesCS1D01G172500 chr4D 19879695 19880297 602 True 998 998 96.523 855 1458 1 chr4D.!!$R1 603
26 TraesCS1D01G172500 chr3B 101908339 101908942 603 False 1050 1050 98.013 855 1458 1 chr3B.!!$F1 603
27 TraesCS1D01G172500 chr4A 309478514 309479116 602 False 1009 1009 96.854 855 1458 1 chr4A.!!$F1 603
28 TraesCS1D01G172500 chr4A 706253426 706254013 587 True 771 771 90.268 1456 2050 1 chr4A.!!$R1 594
29 TraesCS1D01G172500 chr4A 706261378 706261927 549 True 756 756 91.382 1491 2046 1 chr4A.!!$R2 555
30 TraesCS1D01G172500 chr6B 439140765 439141452 687 False 496 496 80.111 1456 2161 1 chr6B.!!$F1 705
31 TraesCS1D01G172500 chr1B 252835877 252836564 687 False 424 424 78.303 1459 2165 1 chr1B.!!$F1 706

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
593 597 0.179056 TGCTAAGCTAACGGATGGGC 60.179 55.0 0.0 0.0 0.0 5.36 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2052 2094 0.533032 GAGGAAGAGAGGGGAACGTG 59.467 60.0 0.0 0.0 0.0 4.49 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
71 72 2.894126 AGACATGACCGAGACACTTCTT 59.106 45.455 0.00 0.00 29.47 2.52
389 393 6.294010 CGGAGTGACAAATCCTAATCTCGATA 60.294 42.308 6.43 0.00 33.12 2.92
469 473 6.706716 TCCAGTTATGTTGTGACGTTTGATAA 59.293 34.615 0.00 0.00 0.00 1.75
593 597 0.179056 TGCTAAGCTAACGGATGGGC 60.179 55.000 0.00 0.00 0.00 5.36
759 763 3.124636 CACACATGTACTAAGTTTCCGGC 59.875 47.826 0.00 0.00 0.00 6.13
853 857 4.387026 CCCCTATGGCATATTTCCTTCA 57.613 45.455 7.81 0.00 0.00 3.02
948 952 1.485294 TTGCTCAAAGGGGTCGCCTA 61.485 55.000 9.21 0.00 0.00 3.93
1225 1230 4.016444 GGTGTTCCATCTTGCAAATAGGA 58.984 43.478 0.00 4.93 0.00 2.94
1226 1231 4.646492 GGTGTTCCATCTTGCAAATAGGAT 59.354 41.667 12.52 4.06 0.00 3.24
1275 1280 6.327365 GGAAATGATCCCTTTATTCCCATGTT 59.673 38.462 0.00 0.00 43.00 2.71
1308 1313 7.797121 ACTTTATCCCCAACTTTGATTTCAT 57.203 32.000 0.00 0.00 0.00 2.57
1388 1393 1.007271 ATCGATAACGCGCCCTCTG 60.007 57.895 5.73 0.00 39.58 3.35
1516 1521 2.183478 AATGATGCCACGTCACTTCA 57.817 45.000 5.66 5.66 0.00 3.02
1568 1573 6.304445 TCGAAACCGATTCAAATTCAAATTCG 59.696 34.615 0.00 0.00 37.96 3.34
1965 2001 3.970410 CCCAGCTGGCCACTCCAA 61.970 66.667 28.39 0.00 46.01 3.53
1966 2002 2.115910 CCAGCTGGCCACTCCAAA 59.884 61.111 22.33 0.00 46.01 3.28
1975 2011 2.672996 CACTCCAAACGGCCTGGG 60.673 66.667 9.53 1.32 34.46 4.45
2067 2109 1.918800 CCCCACGTTCCCCTCTCTT 60.919 63.158 0.00 0.00 0.00 2.85
2075 2117 0.324460 TTCCCCTCTCTTCCTCGTCC 60.324 60.000 0.00 0.00 0.00 4.79
2079 2121 1.040339 CCTCTCTTCCTCGTCCCCTG 61.040 65.000 0.00 0.00 0.00 4.45
2080 2122 0.323908 CTCTCTTCCTCGTCCCCTGT 60.324 60.000 0.00 0.00 0.00 4.00
2183 2247 4.760047 CCTGCCTCCCCAACGTCG 62.760 72.222 0.00 0.00 0.00 5.12
2201 2265 3.507009 CCCGTCGTCTCCGTCCTC 61.507 72.222 0.00 0.00 35.01 3.71
2202 2266 3.507009 CCGTCGTCTCCGTCCTCC 61.507 72.222 0.00 0.00 35.01 4.30
2203 2267 2.436292 CGTCGTCTCCGTCCTCCT 60.436 66.667 0.00 0.00 35.01 3.69
2204 2268 2.462782 CGTCGTCTCCGTCCTCCTC 61.463 68.421 0.00 0.00 35.01 3.71
2205 2269 2.114051 GTCGTCTCCGTCCTCCTCC 61.114 68.421 0.00 0.00 35.01 4.30
2206 2270 2.829458 CGTCTCCGTCCTCCTCCC 60.829 72.222 0.00 0.00 0.00 4.30
2207 2271 2.442458 GTCTCCGTCCTCCTCCCC 60.442 72.222 0.00 0.00 0.00 4.81
2208 2272 2.944954 TCTCCGTCCTCCTCCCCA 60.945 66.667 0.00 0.00 0.00 4.96
2209 2273 2.760385 CTCCGTCCTCCTCCCCAC 60.760 72.222 0.00 0.00 0.00 4.61
2210 2274 4.753662 TCCGTCCTCCTCCCCACG 62.754 72.222 0.00 0.00 0.00 4.94
2218 2282 4.820744 CCTCCCCACGCCCCATTG 62.821 72.222 0.00 0.00 0.00 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
88 89 0.758734 TATGAGCATCCAGGTTCCGG 59.241 55.000 0.00 0.0 0.00 5.14
299 301 6.247229 TCACTATAAGCCTTGGAAGCAATA 57.753 37.500 0.00 0.0 0.00 1.90
307 309 3.544684 TGCACATCACTATAAGCCTTGG 58.455 45.455 0.00 0.0 0.00 3.61
389 393 3.894427 TGGTGTTTGTTGAGTTGGCATAT 59.106 39.130 0.00 0.0 0.00 1.78
444 448 4.443621 TCAAACGTCACAACATAACTGGA 58.556 39.130 0.00 0.0 0.00 3.86
487 491 7.212976 TGAGATTATGCAACTCCTGAATACTC 58.787 38.462 0.00 0.0 29.04 2.59
593 597 4.778579 AGAGAATGATGTGATGGACAAGG 58.221 43.478 0.00 0.0 38.36 3.61
832 836 4.387026 TGAAGGAAATATGCCATAGGGG 57.613 45.455 0.00 0.0 40.85 4.79
833 837 5.388654 ACTTGAAGGAAATATGCCATAGGG 58.611 41.667 0.00 0.0 37.18 3.53
834 838 7.453393 TCTACTTGAAGGAAATATGCCATAGG 58.547 38.462 0.00 0.0 0.00 2.57
835 839 8.778358 GTTCTACTTGAAGGAAATATGCCATAG 58.222 37.037 0.00 0.0 35.01 2.23
836 840 7.441157 CGTTCTACTTGAAGGAAATATGCCATA 59.559 37.037 0.00 0.0 41.55 2.74
837 841 6.260936 CGTTCTACTTGAAGGAAATATGCCAT 59.739 38.462 0.00 0.0 41.55 4.40
838 842 5.584649 CGTTCTACTTGAAGGAAATATGCCA 59.415 40.000 0.00 0.0 41.55 4.92
839 843 5.504173 GCGTTCTACTTGAAGGAAATATGCC 60.504 44.000 0.00 0.0 41.55 4.40
840 844 5.502606 GCGTTCTACTTGAAGGAAATATGC 58.497 41.667 0.00 0.0 41.55 3.14
841 845 5.007724 GGGCGTTCTACTTGAAGGAAATATG 59.992 44.000 0.00 0.0 41.55 1.78
842 846 5.123936 GGGCGTTCTACTTGAAGGAAATAT 58.876 41.667 0.00 0.0 41.55 1.28
843 847 4.020039 TGGGCGTTCTACTTGAAGGAAATA 60.020 41.667 0.00 0.0 41.55 1.40
844 848 3.244770 TGGGCGTTCTACTTGAAGGAAAT 60.245 43.478 0.00 0.0 41.55 2.17
845 849 2.105134 TGGGCGTTCTACTTGAAGGAAA 59.895 45.455 0.00 0.0 41.55 3.13
846 850 1.695242 TGGGCGTTCTACTTGAAGGAA 59.305 47.619 0.00 0.0 41.55 3.36
847 851 1.344065 TGGGCGTTCTACTTGAAGGA 58.656 50.000 0.00 0.0 41.55 3.36
848 852 2.009774 CATGGGCGTTCTACTTGAAGG 58.990 52.381 0.00 0.0 41.83 3.46
849 853 2.972625 TCATGGGCGTTCTACTTGAAG 58.027 47.619 0.00 0.0 35.01 3.02
850 854 3.410631 TTCATGGGCGTTCTACTTGAA 57.589 42.857 0.00 0.0 0.00 2.69
851 855 3.627395 ATTCATGGGCGTTCTACTTGA 57.373 42.857 0.00 0.0 0.00 3.02
852 856 4.701956 AAATTCATGGGCGTTCTACTTG 57.298 40.909 0.00 0.0 0.00 3.16
853 857 5.010282 AGAAAATTCATGGGCGTTCTACTT 58.990 37.500 0.00 0.0 0.00 2.24
920 924 2.310538 CCCTTTGAGCAACCTGTTCTT 58.689 47.619 0.00 0.0 0.00 2.52
1275 1280 2.198336 TGGGGATAAAGTAGCCGGAAA 58.802 47.619 5.05 0.0 34.30 3.13
1308 1313 8.497554 GGTTCGTGTGTATATTTTACAGAAACA 58.502 33.333 0.00 0.0 0.00 2.83
1325 1330 2.029244 GCTCGACATAATGGTTCGTGTG 59.971 50.000 0.00 0.0 0.00 3.82
1516 1521 2.604914 CGCGAGATTAGCAACAGTGATT 59.395 45.455 0.00 0.0 34.19 2.57
1778 1787 4.471904 TCAACTTAGCCCATAGTCACAG 57.528 45.455 0.00 0.0 0.00 3.66
1988 2027 1.273438 GGGTTAGTAGGTGAGGTGGGA 60.273 57.143 0.00 0.0 0.00 4.37
2052 2094 0.533032 GAGGAAGAGAGGGGAACGTG 59.467 60.000 0.00 0.0 0.00 4.49
2067 2109 1.453379 GATCGACAGGGGACGAGGA 60.453 63.158 0.00 0.0 43.76 3.71
2143 2207 3.827898 GAGGGAGGCGTGGTCGAG 61.828 72.222 0.00 0.0 39.71 4.04
2166 2230 4.760047 CGACGTTGGGGAGGCAGG 62.760 72.222 0.00 0.0 0.00 4.85
2190 2254 2.442458 GGGGAGGAGGACGGAGAC 60.442 72.222 0.00 0.0 0.00 3.36
2191 2255 2.944954 TGGGGAGGAGGACGGAGA 60.945 66.667 0.00 0.0 0.00 3.71
2192 2256 2.760385 GTGGGGAGGAGGACGGAG 60.760 72.222 0.00 0.0 0.00 4.63
2193 2257 4.753662 CGTGGGGAGGAGGACGGA 62.754 72.222 0.00 0.0 0.00 4.69
2201 2265 4.820744 CAATGGGGCGTGGGGAGG 62.821 72.222 0.00 0.0 0.00 4.30


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

AutoCloner maintained by Alex Coulton.