Multiple sequence alignment - TraesCS4A01G097600

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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 TraesCS4A01G097600 chr4A 100.000 2719 0 0 1 2719 108418533 108415815 0.000000e+00 5022.0
1 TraesCS4A01G097600 chr4A 90.632 918 74 9 1051 1962 742814557 742815468 0.000000e+00 1208.0
2 TraesCS4A01G097600 chr4A 85.608 674 60 22 1 641 684982188 684982857 0.000000e+00 673.0
3 TraesCS4A01G097600 chr5B 94.503 1910 92 6 61 1962 237139870 237141774 0.000000e+00 2933.0
4 TraesCS4A01G097600 chr5B 95.455 44 2 0 1 44 237139337 237139380 1.350000e-08 71.3
5 TraesCS4A01G097600 chr5D 94.559 1893 93 6 80 1966 379096516 379094628 0.000000e+00 2916.0
6 TraesCS4A01G097600 chr5D 97.766 761 13 3 1962 2719 413215459 413214700 0.000000e+00 1308.0
7 TraesCS4A01G097600 chr5D 82.932 498 51 19 174 641 58251001 58251494 4.190000e-113 418.0
8 TraesCS4A01G097600 chr5D 85.479 365 32 9 706 1050 381166241 381165878 7.160000e-96 361.0
9 TraesCS4A01G097600 chr5D 98.810 84 1 0 1 84 379110513 379110430 1.690000e-32 150.0
10 TraesCS4A01G097600 chr6A 90.120 1670 124 15 299 1962 126602439 126600805 0.000000e+00 2132.0
11 TraesCS4A01G097600 chr6A 91.694 301 24 1 1 301 126639866 126639567 1.510000e-112 416.0
12 TraesCS4A01G097600 chr4D 97.898 761 12 3 1962 2719 114296578 114297337 0.000000e+00 1314.0
13 TraesCS4A01G097600 chr4D 97.635 761 13 4 1962 2719 498643321 498642563 0.000000e+00 1301.0
14 TraesCS4A01G097600 chr1D 97.898 761 12 3 1962 2719 494180274 494179515 0.000000e+00 1314.0
15 TraesCS4A01G097600 chr1D 97.503 761 15 3 1962 2719 134668639 134667880 0.000000e+00 1297.0
16 TraesCS4A01G097600 chr1D 97.503 761 15 3 1962 2719 240525929 240525170 0.000000e+00 1297.0
17 TraesCS4A01G097600 chr7D 97.766 761 13 3 1962 2719 276261636 276262395 0.000000e+00 1308.0
18 TraesCS4A01G097600 chr7D 97.635 761 14 3 1962 2719 204843161 204843920 0.000000e+00 1303.0
19 TraesCS4A01G097600 chr7D 90.710 915 76 7 1053 1962 599795426 599796336 0.000000e+00 1210.0
20 TraesCS4A01G097600 chr6D 97.635 761 14 3 1962 2719 47247037 47246278 0.000000e+00 1303.0
21 TraesCS4A01G097600 chr6D 91.494 917 71 5 1051 1962 28152678 28153592 0.000000e+00 1254.0
22 TraesCS4A01G097600 chr3B 91.087 920 74 5 1051 1963 57322424 57321506 0.000000e+00 1238.0
23 TraesCS4A01G097600 chr3B 91.008 923 75 5 1051 1966 752239152 752238231 0.000000e+00 1238.0
24 TraesCS4A01G097600 chr3B 82.932 498 51 19 174 641 5767040 5767533 4.190000e-113 418.0
25 TraesCS4A01G097600 chr2D 91.160 905 75 3 1065 1964 48383956 48383052 0.000000e+00 1223.0
26 TraesCS4A01G097600 chr2D 90.840 917 74 7 1053 1962 557284318 557283405 0.000000e+00 1219.0
27 TraesCS4A01G097600 chr2A 84.232 482 42 19 193 644 229959932 229959455 3.210000e-119 438.0
28 TraesCS4A01G097600 chr2A 83.851 483 46 17 193 645 573421543 573421063 5.380000e-117 431.0
29 TraesCS4A01G097600 chr2A 89.840 187 17 2 455 641 98884315 98884499 3.500000e-59 239.0
30 TraesCS4A01G097600 chr1B 88.593 263 27 3 202 463 77636345 77636085 1.570000e-82 316.0


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 TraesCS4A01G097600 chr4A 108415815 108418533 2718 True 5022.00 5022 100.000 1 2719 1 chr4A.!!$R1 2718
1 TraesCS4A01G097600 chr4A 742814557 742815468 911 False 1208.00 1208 90.632 1051 1962 1 chr4A.!!$F2 911
2 TraesCS4A01G097600 chr4A 684982188 684982857 669 False 673.00 673 85.608 1 641 1 chr4A.!!$F1 640
3 TraesCS4A01G097600 chr5B 237139337 237141774 2437 False 1502.15 2933 94.979 1 1962 2 chr5B.!!$F1 1961
4 TraesCS4A01G097600 chr5D 379094628 379096516 1888 True 2916.00 2916 94.559 80 1966 1 chr5D.!!$R1 1886
5 TraesCS4A01G097600 chr5D 413214700 413215459 759 True 1308.00 1308 97.766 1962 2719 1 chr5D.!!$R4 757
6 TraesCS4A01G097600 chr6A 126600805 126602439 1634 True 2132.00 2132 90.120 299 1962 1 chr6A.!!$R1 1663
7 TraesCS4A01G097600 chr4D 114296578 114297337 759 False 1314.00 1314 97.898 1962 2719 1 chr4D.!!$F1 757
8 TraesCS4A01G097600 chr4D 498642563 498643321 758 True 1301.00 1301 97.635 1962 2719 1 chr4D.!!$R1 757
9 TraesCS4A01G097600 chr1D 494179515 494180274 759 True 1314.00 1314 97.898 1962 2719 1 chr1D.!!$R3 757
10 TraesCS4A01G097600 chr1D 134667880 134668639 759 True 1297.00 1297 97.503 1962 2719 1 chr1D.!!$R1 757
11 TraesCS4A01G097600 chr1D 240525170 240525929 759 True 1297.00 1297 97.503 1962 2719 1 chr1D.!!$R2 757
12 TraesCS4A01G097600 chr7D 276261636 276262395 759 False 1308.00 1308 97.766 1962 2719 1 chr7D.!!$F2 757
13 TraesCS4A01G097600 chr7D 204843161 204843920 759 False 1303.00 1303 97.635 1962 2719 1 chr7D.!!$F1 757
14 TraesCS4A01G097600 chr7D 599795426 599796336 910 False 1210.00 1210 90.710 1053 1962 1 chr7D.!!$F3 909
15 TraesCS4A01G097600 chr6D 47246278 47247037 759 True 1303.00 1303 97.635 1962 2719 1 chr6D.!!$R1 757
16 TraesCS4A01G097600 chr6D 28152678 28153592 914 False 1254.00 1254 91.494 1051 1962 1 chr6D.!!$F1 911
17 TraesCS4A01G097600 chr3B 57321506 57322424 918 True 1238.00 1238 91.087 1051 1963 1 chr3B.!!$R1 912
18 TraesCS4A01G097600 chr3B 752238231 752239152 921 True 1238.00 1238 91.008 1051 1966 1 chr3B.!!$R2 915
19 TraesCS4A01G097600 chr2D 48383052 48383956 904 True 1223.00 1223 91.160 1065 1964 1 chr2D.!!$R1 899
20 TraesCS4A01G097600 chr2D 557283405 557284318 913 True 1219.00 1219 90.840 1053 1962 1 chr2D.!!$R2 909

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
283 757 0.905357 TCTAGAAGGTGCTTGGGCTC 59.095 55.000 0.00 0.00 39.59 4.7 F
921 1430 2.238395 GGATATTGATGAGAGGCCTCCC 59.762 54.545 29.54 19.35 38.66 4.3 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1586 2101 0.032952 GTGTAGCCCTGTTGTCGACA 59.967 55.000 15.76 15.76 36.65 4.35 R
2288 2816 3.521126 ACAAGTTCTCCCTGAGTATGCAT 59.479 43.478 3.79 3.79 0.00 3.96 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
44 45 1.271543 TGGCAACATAGCTGCAGTTCT 60.272 47.619 16.64 7.36 46.17 3.01
50 51 5.706916 CAACATAGCTGCAGTTCTCATTTT 58.293 37.500 16.64 0.00 0.00 1.82
283 757 0.905357 TCTAGAAGGTGCTTGGGCTC 59.095 55.000 0.00 0.00 39.59 4.70
331 805 2.836372 TCTCACATGGATCTTCACTGCT 59.164 45.455 0.00 0.00 0.00 4.24
377 852 5.151297 TGTCAATTCTACATGTCTGCTCA 57.849 39.130 0.00 0.00 0.00 4.26
405 880 2.329267 CATGGTGCTAGATGGTCCCTA 58.671 52.381 0.00 0.00 0.00 3.53
419 894 7.978925 AGATGGTCCCTATTTAGTTAATCCAG 58.021 38.462 0.00 0.00 0.00 3.86
513 1018 5.348164 AGACACACAACAATAAACTTTGCC 58.652 37.500 0.00 0.00 0.00 4.52
615 1120 6.753180 TGTTTGAACTGCATTTTATAGCCAA 58.247 32.000 0.00 0.00 0.00 4.52
642 1147 9.715123 GTTTTTATGTGTTGCTTTTATTTTGCT 57.285 25.926 0.00 0.00 0.00 3.91
671 1176 7.351166 ACCTTTATGGCCAGTAAGCTTAATTA 58.649 34.615 13.05 0.00 40.22 1.40
807 1312 9.023962 ACATGGATGCTTTTAATGAGTTTTAGA 57.976 29.630 0.00 0.00 0.00 2.10
898 1405 4.623932 TCATCTGCCTGACACTTTAGTT 57.376 40.909 0.00 0.00 0.00 2.24
921 1430 2.238395 GGATATTGATGAGAGGCCTCCC 59.762 54.545 29.54 19.35 38.66 4.30
1057 1566 3.119849 GCTGTACAAATTCATCGCAAGGT 60.120 43.478 0.00 0.00 38.47 3.50
1081 1591 3.551846 GGTCAGTCCCAAAGTTCAAAGA 58.448 45.455 0.00 0.00 0.00 2.52
1231 1742 4.343526 CCTGGTGAGCACTACTTAGATGAT 59.656 45.833 0.16 0.00 0.00 2.45
1323 1837 5.514274 TCATCAAAGACAAGAAAACACCC 57.486 39.130 0.00 0.00 0.00 4.61
1332 1846 3.818773 ACAAGAAAACACCCGACCATTAG 59.181 43.478 0.00 0.00 0.00 1.73
1380 1894 3.932822 TGCTACTGACGGCAAAAGAATA 58.067 40.909 3.72 0.00 35.40 1.75
1490 2005 7.815068 CAGTACTTTAGCACACACTTCTCTAAT 59.185 37.037 0.00 0.00 0.00 1.73
1643 2162 3.736126 GCAGCTTCCATAAGGCAAACATC 60.736 47.826 0.00 0.00 32.98 3.06
1710 2233 2.497273 GGCCTCTGCATGGTTGTTTATT 59.503 45.455 0.00 0.00 40.13 1.40
1738 2261 5.955959 TCTAAGCAGGTCACAATAGTCCTTA 59.044 40.000 0.00 0.00 0.00 2.69
2175 2703 6.268617 TCTGTTATATGCTAGGCTCATCAAGT 59.731 38.462 0.00 0.00 0.00 3.16
2288 2816 2.349438 GCACGAAGAACTTTCGCAATGA 60.349 45.455 9.00 0.00 44.98 2.57
2453 2983 3.272574 TGTGCCTTTGATCTCCATCTC 57.727 47.619 0.00 0.00 0.00 2.75
2484 3014 3.625649 TCATGATTTCCATCGTCACCA 57.374 42.857 0.00 0.00 31.94 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
87 561 8.805175 TGGAGATGAATTTTGTGTTCAATACAT 58.195 29.630 0.00 0.00 38.89 2.29
283 757 2.854777 CAGCTAATCGGTCAGAGAAACG 59.145 50.000 0.00 0.00 0.00 3.60
355 830 5.151297 TGAGCAGACATGTAGAATTGACA 57.849 39.130 0.00 0.00 0.00 3.58
495 999 6.601741 ACATTGGCAAAGTTTATTGTTGTG 57.398 33.333 3.01 0.00 32.80 3.33
513 1018 6.419791 TGTTGGAATAGGTAGGGTTACATTG 58.580 40.000 0.00 0.00 0.00 2.82
615 1120 9.715123 GCAAAATAAAAGCAACACATAAAAACT 57.285 25.926 0.00 0.00 0.00 2.66
642 1147 4.018779 AGCTTACTGGCCATAAAGGTACAA 60.019 41.667 23.27 4.23 40.61 2.41
702 1207 2.094390 TCTCAAGAAAATGCATGCAGCC 60.094 45.455 26.69 13.95 44.83 4.85
736 1241 5.946972 TGGTGTTTTGTTACCTCTTTTCTCA 59.053 36.000 0.00 0.00 37.84 3.27
779 1284 5.490139 ACTCATTAAAAGCATCCATGTCG 57.510 39.130 0.00 0.00 0.00 4.35
827 1332 4.584638 TTTGTGGAGGCTACCATATTGT 57.415 40.909 8.58 0.00 42.17 2.71
898 1405 4.357325 GGAGGCCTCTCATCAATATCCTA 58.643 47.826 31.36 0.00 41.69 2.94
921 1430 5.613358 ACTTTTGAAGCTTAGACCATTCG 57.387 39.130 0.00 0.00 0.00 3.34
1032 1541 2.677836 TGCGATGAATTTGTACAGCCTC 59.322 45.455 0.00 0.00 0.00 4.70
1091 1602 6.855763 ATGTATTTTCCAGCTTCCAAATGA 57.144 33.333 4.64 0.00 0.00 2.57
1098 1609 5.502606 GCGAGTAATGTATTTTCCAGCTTC 58.497 41.667 0.00 0.00 0.00 3.86
1231 1742 0.034574 ACACACAGTGGGCAGTGAAA 60.035 50.000 1.44 0.00 37.94 2.69
1323 1837 3.047796 GTGGCATACGTACTAATGGTCG 58.952 50.000 0.00 0.00 0.00 4.79
1332 1846 3.159353 TCTGTCATGTGGCATACGTAC 57.841 47.619 0.00 0.00 0.00 3.67
1405 1919 4.406456 TGGCATGTTCTTGTAGGAAACAT 58.594 39.130 0.00 0.00 38.10 2.71
1490 2005 0.902984 TGTGCGGGAAGAGGCTTCTA 60.903 55.000 0.00 0.00 31.96 2.10
1586 2101 0.032952 GTGTAGCCCTGTTGTCGACA 59.967 55.000 15.76 15.76 36.65 4.35
1643 2162 2.756760 AGCATATGCACACCCTTTCTTG 59.243 45.455 28.62 0.00 45.16 3.02
1710 2233 6.299805 ACTATTGTGACCTGCTTAGATTGA 57.700 37.500 0.00 0.00 0.00 2.57
1772 2295 8.985315 AAATGATGCCAGATATAAAAGTCTCA 57.015 30.769 0.00 0.00 0.00 3.27
1831 2357 4.082190 ACGGATTGATGATAGTCATACGGG 60.082 45.833 0.00 0.00 37.20 5.28
1881 2408 8.743085 AAGAGTGTGCATCAAAATATGTAGAT 57.257 30.769 0.00 0.00 0.00 1.98
2030 2557 4.693283 GTGATGATCGGACATGGTTTAGA 58.307 43.478 0.00 0.00 0.00 2.10
2175 2703 3.680937 CACGCGGAATACTCAGGTTAAAA 59.319 43.478 12.47 0.00 0.00 1.52
2288 2816 3.521126 ACAAGTTCTCCCTGAGTATGCAT 59.479 43.478 3.79 3.79 0.00 3.96
2339 2869 3.790288 GCTTAGTTCGACGGTAGCTTTAG 59.210 47.826 0.00 0.00 0.00 1.85
2421 2951 4.338012 TCAAAGGCACAAGATGATGATGT 58.662 39.130 0.00 0.00 0.00 3.06
2453 2983 5.270893 TGGAAATCATGATGATGCTTTGG 57.729 39.130 9.46 0.00 37.15 3.28
2484 3014 7.221381 ATGATGGAGATCATGGTGTCATGCT 62.221 44.000 5.37 0.00 45.90 3.79


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

AutoCloner maintained by Alex Coulton.