Multiple sequence alignment - TraesCS2D01G183200

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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 TraesCS2D01G183200 chr2D 100.000 2937 0 0 1 2937 127822318 127819382 0.000000e+00 5424.0
1 TraesCS2D01G183200 chr2D 87.802 2279 162 50 636 2830 83224896 83227142 0.000000e+00 2562.0
2 TraesCS2D01G183200 chr2D 92.977 1723 94 9 917 2625 83529898 83531607 0.000000e+00 2486.0
3 TraesCS2D01G183200 chr2D 86.802 1773 149 21 1056 2806 85251793 85250084 0.000000e+00 1899.0
4 TraesCS2D01G183200 chr2D 89.546 1234 83 24 538 1739 83187978 83189197 0.000000e+00 1522.0
5 TraesCS2D01G183200 chr2A 95.628 2539 81 6 428 2937 134868007 134865470 0.000000e+00 4047.0
6 TraesCS2D01G183200 chr2A 90.288 2152 145 20 731 2858 83989925 83992036 0.000000e+00 2758.0
7 TraesCS2D01G183200 chr2A 88.499 2339 176 53 538 2830 83984601 83986892 0.000000e+00 2743.0
8 TraesCS2D01G183200 chr2A 88.900 1973 145 29 917 2863 84143618 84145542 0.000000e+00 2362.0
9 TraesCS2D01G183200 chr2A 90.871 241 14 3 1 240 134868252 134868019 1.700000e-82 316.0
10 TraesCS2D01G183200 chr2A 97.006 167 5 0 684 850 733423644 733423478 6.200000e-72 281.0
11 TraesCS2D01G183200 chr2A 89.474 57 4 2 2881 2935 84146010 84146066 1.460000e-08 71.3
12 TraesCS2D01G183200 chr5A 90.451 2105 112 31 709 2769 326438158 326436099 0.000000e+00 2691.0
13 TraesCS2D01G183200 chr5A 87.049 471 54 4 248 713 326441546 326441078 2.590000e-145 525.0
14 TraesCS2D01G183200 chr2B 90.479 1964 116 26 922 2830 135357952 135359899 0.000000e+00 2525.0
15 TraesCS2D01G183200 chr2B 90.278 1296 80 15 469 1739 135126232 135127506 0.000000e+00 1653.0
16 TraesCS2D01G183200 chr2B 89.245 1153 85 26 1733 2863 135464494 135465629 0.000000e+00 1406.0
17 TraesCS2D01G183200 chr2B 89.838 1112 77 16 656 1739 135463367 135464470 0.000000e+00 1395.0
18 TraesCS2D01G183200 chr2B 90.707 990 60 18 1884 2863 182132984 182132017 0.000000e+00 1290.0
19 TraesCS2D01G183200 chr2B 90.152 924 78 10 1948 2863 136813863 136812945 0.000000e+00 1190.0
20 TraesCS2D01G183200 chr2B 92.512 828 46 2 922 1739 182153330 182152509 0.000000e+00 1171.0
21 TraesCS2D01G183200 chr2B 92.150 828 49 2 922 1739 135198035 135198856 0.000000e+00 1155.0
22 TraesCS2D01G183200 chr2B 89.964 279 26 2 162 439 135125866 135126143 2.780000e-95 359.0
23 TraesCS2D01G183200 chr2B 89.474 57 4 2 2881 2935 182131587 182131531 1.460000e-08 71.3
24 TraesCS2D01G183200 chr5D 92.478 1582 89 11 594 2162 230368712 230370276 0.000000e+00 2235.0
25 TraesCS2D01G183200 chr5D 89.062 256 28 0 183 438 230368396 230368651 4.720000e-83 318.0
26 TraesCS2D01G183200 chr7A 87.405 1850 143 38 948 2750 618195367 618193561 0.000000e+00 2043.0
27 TraesCS2D01G183200 chrUn 91.900 963 59 4 917 1869 25419699 25418746 0.000000e+00 1328.0
28 TraesCS2D01G183200 chrUn 88.677 733 56 16 636 1351 362506112 362506834 0.000000e+00 869.0
29 TraesCS2D01G183200 chrUn 90.110 91 6 3 761 851 25419861 25419774 6.650000e-22 115.0


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 TraesCS2D01G183200 chr2D 127819382 127822318 2936 True 5424.00 5424 100.0000 1 2937 1 chr2D.!!$R2 2936
1 TraesCS2D01G183200 chr2D 83224896 83227142 2246 False 2562.00 2562 87.8020 636 2830 1 chr2D.!!$F2 2194
2 TraesCS2D01G183200 chr2D 83529898 83531607 1709 False 2486.00 2486 92.9770 917 2625 1 chr2D.!!$F3 1708
3 TraesCS2D01G183200 chr2D 85250084 85251793 1709 True 1899.00 1899 86.8020 1056 2806 1 chr2D.!!$R1 1750
4 TraesCS2D01G183200 chr2D 83187978 83189197 1219 False 1522.00 1522 89.5460 538 1739 1 chr2D.!!$F1 1201
5 TraesCS2D01G183200 chr2A 83984601 83992036 7435 False 2750.50 2758 89.3935 538 2858 2 chr2A.!!$F1 2320
6 TraesCS2D01G183200 chr2A 134865470 134868252 2782 True 2181.50 4047 93.2495 1 2937 2 chr2A.!!$R2 2936
7 TraesCS2D01G183200 chr2A 84143618 84146066 2448 False 1216.65 2362 89.1870 917 2935 2 chr2A.!!$F2 2018
8 TraesCS2D01G183200 chr5A 326436099 326441546 5447 True 1608.00 2691 88.7500 248 2769 2 chr5A.!!$R1 2521
9 TraesCS2D01G183200 chr2B 135357952 135359899 1947 False 2525.00 2525 90.4790 922 2830 1 chr2B.!!$F2 1908
10 TraesCS2D01G183200 chr2B 135463367 135465629 2262 False 1400.50 1406 89.5415 656 2863 2 chr2B.!!$F4 2207
11 TraesCS2D01G183200 chr2B 136812945 136813863 918 True 1190.00 1190 90.1520 1948 2863 1 chr2B.!!$R1 915
12 TraesCS2D01G183200 chr2B 182152509 182153330 821 True 1171.00 1171 92.5120 922 1739 1 chr2B.!!$R2 817
13 TraesCS2D01G183200 chr2B 135198035 135198856 821 False 1155.00 1155 92.1500 922 1739 1 chr2B.!!$F1 817
14 TraesCS2D01G183200 chr2B 135125866 135127506 1640 False 1006.00 1653 90.1210 162 1739 2 chr2B.!!$F3 1577
15 TraesCS2D01G183200 chr2B 182131531 182132984 1453 True 680.65 1290 90.0905 1884 2935 2 chr2B.!!$R3 1051
16 TraesCS2D01G183200 chr5D 230368396 230370276 1880 False 1276.50 2235 90.7700 183 2162 2 chr5D.!!$F1 1979
17 TraesCS2D01G183200 chr7A 618193561 618195367 1806 True 2043.00 2043 87.4050 948 2750 1 chr7A.!!$R1 1802
18 TraesCS2D01G183200 chrUn 362506112 362506834 722 False 869.00 869 88.6770 636 1351 1 chrUn.!!$F1 715
19 TraesCS2D01G183200 chrUn 25418746 25419861 1115 True 721.50 1328 91.0050 761 1869 2 chrUn.!!$R1 1108

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
382 385 0.457337 GCTACGATCAACGACCGGTT 60.457 55.000 9.42 0.0 45.77 4.44 F
540 619 1.002544 CTGGGCTTCTCTTTCGGAAGT 59.997 52.381 2.72 0.0 41.36 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1919 10171 2.583024 TGACAGGCAATGGTGATTGA 57.417 45.000 0.0 0.0 41.49 2.57 R
2289 10549 6.403866 AATTGCAGTACATGAGTTTCCAAA 57.596 33.333 0.0 0.0 0.00 3.28 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
29 30 3.946558 GCTTTGAGGCATTCATCTTCTCT 59.053 43.478 0.00 0.00 35.27 3.10
44 45 3.565063 TCTTCTCTCGCATCTCTCTCATG 59.435 47.826 0.00 0.00 0.00 3.07
68 69 1.474879 GTCTCACACCTCTCACCTAGC 59.525 57.143 0.00 0.00 0.00 3.42
75 76 1.896465 ACCTCTCACCTAGCAGTTCAC 59.104 52.381 0.00 0.00 0.00 3.18
77 78 1.895798 CTCTCACCTAGCAGTTCACCA 59.104 52.381 0.00 0.00 0.00 4.17
110 111 2.433145 ACTCCATGCGCACTGTCG 60.433 61.111 14.90 2.73 0.00 4.35
151 153 2.288642 CTGTCATGATGGGGTGGGGG 62.289 65.000 0.00 0.00 0.00 5.40
152 154 3.428664 TCATGATGGGGTGGGGGC 61.429 66.667 0.00 0.00 0.00 5.80
285 288 2.357034 GACACCATGACCGTGCGT 60.357 61.111 0.00 0.00 34.45 5.24
312 315 1.154016 CGCGTCGTCCTCATCTGTT 60.154 57.895 0.00 0.00 0.00 3.16
382 385 0.457337 GCTACGATCAACGACCGGTT 60.457 55.000 9.42 0.00 45.77 4.44
414 417 3.474570 GACAGGGGGAGATGCGCT 61.475 66.667 9.73 0.00 0.00 5.92
540 619 1.002544 CTGGGCTTCTCTTTCGGAAGT 59.997 52.381 2.72 0.00 41.36 3.01
550 629 7.412020 GCTTCTCTTTCGGAAGTACATTTAGTG 60.412 40.741 2.72 0.00 41.36 2.74
914 3972 7.700656 ACGTTCCATTTGTTCTTCAGTTAAAAG 59.299 33.333 0.00 0.00 0.00 2.27
1101 4179 1.850998 TCCCGATCTCCAGACCTAGAA 59.149 52.381 0.00 0.00 0.00 2.10
1539 4637 2.050350 CACGGAGAACCTAGCCCGA 61.050 63.158 6.66 0.00 44.29 5.14
1817 10066 2.269241 GGCTCTACACCACTGCCC 59.731 66.667 0.00 0.00 37.81 5.36
1919 10171 3.867216 GCTGCAAGATTCCCAAGCAAAAT 60.867 43.478 0.00 0.00 34.07 1.82
2054 10309 9.897744 TTCACACATGAGTTTCATTTAATCTTC 57.102 29.630 0.00 0.00 34.28 2.87
2782 11343 0.598562 AGTGTGTACTGAGGCACGAG 59.401 55.000 0.00 0.00 38.36 4.18
2880 11466 3.140623 GGTTGCAATCAAATTGGCAAGT 58.859 40.909 4.39 0.00 40.57 3.16
2925 11699 5.049828 GCAGCTATTTGACAAACAGGTTTT 58.950 37.500 8.15 0.00 0.00 2.43
2926 11700 5.523552 GCAGCTATTTGACAAACAGGTTTTT 59.476 36.000 8.15 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.790091 CGAGAGAAGATGAATGCCTCAA 58.210 45.455 0.00 0.00 37.67 3.02
12 13 2.134346 GCGAGAGAAGATGAATGCCTC 58.866 52.381 0.00 0.00 0.00 4.70
15 16 3.391965 AGATGCGAGAGAAGATGAATGC 58.608 45.455 0.00 0.00 0.00 3.56
44 45 0.109504 GTGAGAGGTGTGAGACGAGC 60.110 60.000 0.00 0.00 0.00 5.03
75 76 0.179000 GTGATGGCTACCACCTCTGG 59.821 60.000 0.00 0.00 44.26 3.86
77 78 1.490574 GAGTGATGGCTACCACCTCT 58.509 55.000 0.00 0.00 35.80 3.69
156 158 4.593864 GATGACCTCGCCCTCGCC 62.594 72.222 0.00 0.00 35.26 5.54
157 159 4.933064 CGATGACCTCGCCCTCGC 62.933 72.222 0.00 0.00 41.14 5.03
361 364 0.248907 CCGGTCGTTGATCGTAGCAT 60.249 55.000 0.00 0.00 40.80 3.79
382 385 1.650314 CTGTCATGGCTTGCATCGCA 61.650 55.000 10.21 0.00 36.47 5.10
426 429 3.923864 ACCGACGGTTGCAGCTCA 61.924 61.111 15.37 0.00 27.29 4.26
513 592 3.384668 GAAAGAGAAGCCCAGCAAAAAC 58.615 45.455 0.00 0.00 0.00 2.43
540 619 8.364142 CACAAATTTTCCCTTCCACTAAATGTA 58.636 33.333 0.00 0.00 0.00 2.29
550 629 5.047306 CCTTCCTACACAAATTTTCCCTTCC 60.047 44.000 0.00 0.00 0.00 3.46
682 781 2.029110 TCTTAAGCACAGCCCAAAATGC 60.029 45.455 0.00 0.00 38.39 3.56
914 3972 1.002366 AATCTCACGCGCTCATTCAC 58.998 50.000 5.73 0.00 0.00 3.18
1817 10066 4.374702 GGCGCAACAGCAGTGACG 62.375 66.667 10.83 0.55 39.27 4.35
1919 10171 2.583024 TGACAGGCAATGGTGATTGA 57.417 45.000 0.00 0.00 41.49 2.57
2289 10549 6.403866 AATTGCAGTACATGAGTTTCCAAA 57.596 33.333 0.00 0.00 0.00 3.28
2660 10964 1.702182 TTGCACAGATTCAGGCCAAA 58.298 45.000 5.01 0.00 0.00 3.28
2782 11343 6.544931 TGAAATCAGAGATGAATCCATTGGAC 59.455 38.462 7.76 0.00 32.98 4.02
2834 11395 7.257722 CAATAACTGTCCCAAACATGGTTATC 58.742 38.462 0.00 0.00 37.84 1.75
2880 11466 4.616604 GCACTATGATGCAAGCTTTTCACA 60.617 41.667 0.00 0.00 45.39 3.58


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

AutoCloner maintained by Alex Coulton.