Multiple sequence alignment - TraesCS3A01G400800

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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 TraesCS3A01G400800 chr3A 100.000 2801 0 0 1 2801 647359884 647357084 0.000000e+00 5173
1 TraesCS3A01G400800 chr3A 85.790 1506 151 32 724 2195 647388881 647387405 0.000000e+00 1537
2 TraesCS3A01G400800 chr3A 86.891 923 111 6 913 1826 647444110 647443189 0.000000e+00 1026
3 TraesCS3A01G400800 chr3A 96.230 610 22 1 2192 2801 647296897 647297505 0.000000e+00 998
4 TraesCS3A01G400800 chr3A 95.717 607 26 0 2195 2801 647287282 647287888 0.000000e+00 977
5 TraesCS3A01G400800 chr3A 95.395 608 25 3 2194 2801 593053811 593053207 0.000000e+00 965
6 TraesCS3A01G400800 chr3A 94.943 613 22 9 2194 2801 24224816 24225424 0.000000e+00 952
7 TraesCS3A01G400800 chr3A 94.926 611 23 8 2194 2801 431930959 431931564 0.000000e+00 950
8 TraesCS3A01G400800 chr3A 76.409 1047 197 30 840 1860 647236851 647235829 1.150000e-143 520
9 TraesCS3A01G400800 chr3D 84.573 1640 168 51 498 2107 511262519 511260935 0.000000e+00 1548
10 TraesCS3A01G400800 chr3D 91.952 994 71 7 923 1912 511321288 511320300 0.000000e+00 1384
11 TraesCS3A01G400800 chr3D 85.803 1282 144 18 925 2195 511266254 511265000 0.000000e+00 1325
12 TraesCS3A01G400800 chr3D 91.684 950 54 8 269 1201 510858484 510857543 0.000000e+00 1293
13 TraesCS3A01G400800 chr3D 87.017 1009 120 7 913 1912 511293455 511292449 0.000000e+00 1127
14 TraesCS3A01G400800 chr3D 84.889 1125 139 22 913 2018 511129015 511127903 0.000000e+00 1107
15 TraesCS3A01G400800 chr3D 94.436 629 30 5 27 651 510912242 510911615 0.000000e+00 963
16 TraesCS3A01G400800 chr3D 91.697 277 18 3 1 273 510908091 510907816 2.040000e-101 379
17 TraesCS3A01G400800 chr3D 95.652 161 7 0 85 245 511282857 511282697 2.770000e-65 259
18 TraesCS3A01G400800 chr3D 91.566 83 6 1 428 510 511264092 511264011 2.280000e-21 113
19 TraesCS3A01G400800 chr3B 85.855 1117 135 15 970 2069 672744763 672743653 0.000000e+00 1166
20 TraesCS3A01G400800 chr3B 85.250 1139 126 27 913 2016 672770442 672769311 0.000000e+00 1134
21 TraesCS3A01G400800 chr3B 81.445 1024 171 14 913 1931 672517326 672516317 0.000000e+00 821
22 TraesCS3A01G400800 chr3B 89.910 555 51 5 1645 2195 672655231 672654678 0.000000e+00 710
23 TraesCS3A01G400800 chr3B 95.408 196 9 0 50 245 672563483 672563288 2.090000e-81 313
24 TraesCS3A01G400800 chr3B 89.069 247 23 2 3 245 672517490 672517244 1.260000e-78 303
25 TraesCS3A01G400800 chr3B 81.114 413 40 22 1716 2112 672541594 672541204 2.110000e-76 296
26 TraesCS3A01G400800 chr3B 84.082 245 36 3 446 689 672745148 672744906 1.680000e-57 233
27 TraesCS3A01G400800 chr3B 80.515 272 21 19 605 875 672535894 672535654 2.220000e-41 180
28 TraesCS3A01G400800 chr3B 80.711 197 20 8 1929 2112 672502486 672502295 1.350000e-28 137
29 TraesCS3A01G400800 chr1A 95.710 606 19 7 2198 2801 180652033 180651433 0.000000e+00 968
30 TraesCS3A01G400800 chr2A 95.545 606 21 6 2198 2801 209542859 209542258 0.000000e+00 965
31 TraesCS3A01G400800 chr7A 94.771 612 26 6 2192 2801 372525111 372525718 0.000000e+00 948
32 TraesCS3A01G400800 chr6A 94.625 614 27 6 2192 2801 81226108 81226719 0.000000e+00 946


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 TraesCS3A01G400800 chr3A 647357084 647359884 2800 True 5173.000000 5173 100.0000 1 2801 1 chr3A.!!$R3 2800
1 TraesCS3A01G400800 chr3A 647387405 647388881 1476 True 1537.000000 1537 85.7900 724 2195 1 chr3A.!!$R4 1471
2 TraesCS3A01G400800 chr3A 647443189 647444110 921 True 1026.000000 1026 86.8910 913 1826 1 chr3A.!!$R5 913
3 TraesCS3A01G400800 chr3A 647296897 647297505 608 False 998.000000 998 96.2300 2192 2801 1 chr3A.!!$F4 609
4 TraesCS3A01G400800 chr3A 647287282 647287888 606 False 977.000000 977 95.7170 2195 2801 1 chr3A.!!$F3 606
5 TraesCS3A01G400800 chr3A 593053207 593053811 604 True 965.000000 965 95.3950 2194 2801 1 chr3A.!!$R1 607
6 TraesCS3A01G400800 chr3A 24224816 24225424 608 False 952.000000 952 94.9430 2194 2801 1 chr3A.!!$F1 607
7 TraesCS3A01G400800 chr3A 431930959 431931564 605 False 950.000000 950 94.9260 2194 2801 1 chr3A.!!$F2 607
8 TraesCS3A01G400800 chr3A 647235829 647236851 1022 True 520.000000 520 76.4090 840 1860 1 chr3A.!!$R2 1020
9 TraesCS3A01G400800 chr3D 511320300 511321288 988 True 1384.000000 1384 91.9520 923 1912 1 chr3D.!!$R5 989
10 TraesCS3A01G400800 chr3D 510857543 510858484 941 True 1293.000000 1293 91.6840 269 1201 1 chr3D.!!$R1 932
11 TraesCS3A01G400800 chr3D 511292449 511293455 1006 True 1127.000000 1127 87.0170 913 1912 1 chr3D.!!$R4 999
12 TraesCS3A01G400800 chr3D 511127903 511129015 1112 True 1107.000000 1107 84.8890 913 2018 1 chr3D.!!$R2 1105
13 TraesCS3A01G400800 chr3D 511260935 511266254 5319 True 995.333333 1548 87.3140 428 2195 3 chr3D.!!$R7 1767
14 TraesCS3A01G400800 chr3D 510907816 510912242 4426 True 671.000000 963 93.0665 1 651 2 chr3D.!!$R6 650
15 TraesCS3A01G400800 chr3B 672769311 672770442 1131 True 1134.000000 1134 85.2500 913 2016 1 chr3B.!!$R6 1103
16 TraesCS3A01G400800 chr3B 672654678 672655231 553 True 710.000000 710 89.9100 1645 2195 1 chr3B.!!$R5 550
17 TraesCS3A01G400800 chr3B 672743653 672745148 1495 True 699.500000 1166 84.9685 446 2069 2 chr3B.!!$R8 1623
18 TraesCS3A01G400800 chr3B 672516317 672517490 1173 True 562.000000 821 85.2570 3 1931 2 chr3B.!!$R7 1928
19 TraesCS3A01G400800 chr1A 180651433 180652033 600 True 968.000000 968 95.7100 2198 2801 1 chr1A.!!$R1 603
20 TraesCS3A01G400800 chr2A 209542258 209542859 601 True 965.000000 965 95.5450 2198 2801 1 chr2A.!!$R1 603
21 TraesCS3A01G400800 chr7A 372525111 372525718 607 False 948.000000 948 94.7710 2192 2801 1 chr7A.!!$F1 609
22 TraesCS3A01G400800 chr6A 81226108 81226719 611 False 946.000000 946 94.6250 2192 2801 1 chr6A.!!$F1 609

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
38 39 0.603975 GTCTGTGTTCCAGTGGAGGC 60.604 60.0 12.67 10.17 42.19 4.70 F
603 3848 0.883153 CTTGGTGCAATGTGCTAGCA 59.117 50.0 14.93 14.93 45.31 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1119 4622 0.824759 AAGATCTGAGTACACCGCCC 59.175 55.0 0.0 0.0 0.0 6.13 R
2564 8248 0.034186 CCAAACCAGATGCAGGGCTA 60.034 55.0 0.0 0.0 0.0 3.93 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
26 27 2.919228 AGCCGAAGAAAAAGTCTGTGT 58.081 42.857 0.00 0.00 36.40 3.72
28 29 3.312697 AGCCGAAGAAAAAGTCTGTGTTC 59.687 43.478 0.00 0.00 36.40 3.18
38 39 0.603975 GTCTGTGTTCCAGTGGAGGC 60.604 60.000 12.67 10.17 42.19 4.70
96 101 0.955919 GGTAGCGGCTTCTGCTTTGT 60.956 55.000 8.26 0.00 43.71 2.83
100 105 1.086696 GCGGCTTCTGCTTTGTATCA 58.913 50.000 0.00 0.00 39.59 2.15
285 292 4.640789 ACTTTTCTGACGATAGCGAGAT 57.359 40.909 7.69 0.00 41.64 2.75
341 348 6.183360 CCGCAAGTCTAATCTTTAATTGACGT 60.183 38.462 0.00 0.00 0.00 4.34
345 352 9.530129 CAAGTCTAATCTTTAATTGACGTTGTC 57.470 33.333 0.00 0.00 0.00 3.18
356 363 3.297830 TGACGTTGTCTGTGTCTATGG 57.702 47.619 0.00 0.00 33.15 2.74
361 368 4.156190 ACGTTGTCTGTGTCTATGGTCTAG 59.844 45.833 0.00 0.00 0.00 2.43
418 425 5.359576 CGATCCCCCAATTTTCTTTCATGTA 59.640 40.000 0.00 0.00 0.00 2.29
545 3786 1.534595 CTGCTGACCTTGACTTGCTTC 59.465 52.381 0.00 0.00 0.00 3.86
603 3848 0.883153 CTTGGTGCAATGTGCTAGCA 59.117 50.000 14.93 14.93 45.31 3.49
683 3928 1.758936 GTTATAAAAGCCCCGTGCCT 58.241 50.000 0.00 0.00 42.71 4.75
714 3961 2.231478 CAGTACAGGACTACAGGTGGTG 59.769 54.545 0.00 0.00 35.64 4.17
942 4434 4.183865 CGAGTTTTGATCAGGTGATGCTA 58.816 43.478 0.00 0.00 34.37 3.49
973 4470 0.938637 CTGCTAGATTCGGCTGAGCG 60.939 60.000 0.00 0.00 35.88 5.03
1025 4528 4.058817 GCTGATAATACCAAGTTCCTCCG 58.941 47.826 0.00 0.00 0.00 4.63
1051 4554 0.894141 TCTCCTCTTGAGCAGCTCAC 59.106 55.000 25.37 0.00 40.46 3.51
1091 4594 2.050144 ACAAGATATCCGGTGCCTGAT 58.950 47.619 0.00 1.04 0.00 2.90
1119 4622 3.741860 GGCTCATTGGCTGATCCG 58.258 61.111 0.00 0.00 37.80 4.18
1159 5107 6.940739 TCTTGGAACTTTGAAAATGAAACCA 58.059 32.000 0.00 0.00 0.00 3.67
1242 5196 0.459237 CTCTGCGACTAGGCAACCTG 60.459 60.000 0.00 0.00 43.39 4.00
1352 6321 0.324943 CCTCGGGACATTTCACAGGT 59.675 55.000 0.00 0.00 0.00 4.00
1493 6462 2.986479 GTCAAATTCCACCGCAATTCAC 59.014 45.455 0.00 0.00 0.00 3.18
1571 6543 7.120726 GCCTATTCCTTCTTTGCTACAAAACTA 59.879 37.037 0.00 0.00 0.00 2.24
1661 6633 0.629596 AGGAGATGGAGACCGGTACA 59.370 55.000 7.34 7.98 0.00 2.90
1898 6974 1.915141 AGCTTGTTGCCTGCAGTAAT 58.085 45.000 13.81 0.00 44.23 1.89
2057 7166 2.101415 GGAACAAAAACAAGGCAGCTCT 59.899 45.455 0.00 0.00 0.00 4.09
2072 7181 2.162319 GCTCTGGCTAGCCTATGAAC 57.838 55.000 33.07 19.18 36.45 3.18
2075 7184 2.703007 CTCTGGCTAGCCTATGAACCTT 59.297 50.000 33.07 0.00 36.94 3.50
2148 7258 0.955178 ATGGCAGAGAGTACGGATCG 59.045 55.000 0.00 0.00 0.00 3.69
2196 7306 0.244994 CTCACGAAGAGGACACCTGG 59.755 60.000 0.00 0.00 40.84 4.45
2221 7331 3.319405 CACCCTCGATGTGACTATAGCTT 59.681 47.826 9.05 0.00 35.74 3.74
2230 7340 3.257375 TGTGACTATAGCTTCCACGTGTT 59.743 43.478 15.65 0.00 0.00 3.32
2503 8041 3.698040 TCAGGGAAAGACACGTAGTATCC 59.302 47.826 0.00 0.00 41.61 2.59
2506 8044 2.159338 GGAAAGACACGTAGTATCCGCA 60.159 50.000 0.00 0.00 41.61 5.69
2670 8544 6.238759 GCTTAAAGGTGAGGCAAGGTAATATG 60.239 42.308 0.00 0.00 0.00 1.78
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 2.919228 ACACAGACTTTTTCTTCGGCT 58.081 42.857 0.00 0.00 28.96 5.52
9 10 4.875544 TGGAACACAGACTTTTTCTTCG 57.124 40.909 0.00 0.00 28.96 3.79
26 27 1.070786 GACAACGCCTCCACTGGAA 59.929 57.895 0.00 0.00 0.00 3.53
28 29 2.358737 GGACAACGCCTCCACTGG 60.359 66.667 0.00 0.00 0.00 4.00
38 39 3.303791 GCACAACTCTTAAAGGGACAACG 60.304 47.826 0.00 0.00 0.00 4.10
83 88 4.970662 TGATTGATACAAAGCAGAAGCC 57.029 40.909 0.00 0.00 43.56 4.35
96 101 7.223584 TCAGAAAACTCACCAGTTGATTGATA 58.776 34.615 0.00 0.00 42.45 2.15
100 105 5.440610 ACTCAGAAAACTCACCAGTTGATT 58.559 37.500 0.00 0.00 42.45 2.57
142 147 9.856488 GTAAGAATACTTGATCACTGTACTTGA 57.144 33.333 9.20 0.00 37.53 3.02
149 154 6.311445 ACTTGCGTAAGAATACTTGATCACTG 59.689 38.462 20.61 0.00 43.02 3.66
285 292 8.096414 TGAAGATTGAAGAAGTCATCACATGTA 58.904 33.333 0.00 0.00 35.70 2.29
341 348 3.128764 CGCTAGACCATAGACACAGACAA 59.871 47.826 0.00 0.00 0.00 3.18
345 352 3.316588 ACATCGCTAGACCATAGACACAG 59.683 47.826 0.00 0.00 0.00 3.66
444 2180 9.654663 AGTTAACTATGTTAGGAGTTCAATCAC 57.345 33.333 6.26 0.00 37.16 3.06
471 2207 5.842328 TGTCTTAGAAAGTCTAGGTTTGGGA 59.158 40.000 0.00 0.00 29.56 4.37
603 3848 7.549488 CCTGTTAATTTCCGAAGTCTTGTAGAT 59.451 37.037 0.00 0.00 0.00 1.98
714 3961 3.971702 AGAAGCCACCAGCCCACC 61.972 66.667 0.00 0.00 45.47 4.61
942 4434 4.450053 GAATCTAGCAGCTTGTCAATCCT 58.550 43.478 0.00 0.00 0.00 3.24
973 4470 1.264288 CGAGGAGTGAAACAAACAGCC 59.736 52.381 0.00 0.00 41.43 4.85
1051 4554 3.692101 TGTTCAGTACCAAAACACAGTGG 59.308 43.478 5.31 0.00 41.00 4.00
1091 4594 2.875672 GCCAATGAGCCTTGTACAGACA 60.876 50.000 0.00 0.00 0.00 3.41
1119 4622 0.824759 AAGATCTGAGTACACCGCCC 59.175 55.000 0.00 0.00 0.00 6.13
1242 5196 1.550524 GGAAATTGGCCTTGAAGTCCC 59.449 52.381 3.32 0.00 0.00 4.46
1352 6321 3.005155 CAGAGATGTCAGATACGGCATCA 59.995 47.826 8.11 0.00 39.90 3.07
1661 6633 0.886563 GAGCCTGTGCAGCTTGATTT 59.113 50.000 0.00 0.00 41.75 2.17
1914 6991 5.335191 GCTAATTGCCAGGCATACTATCAAC 60.335 44.000 17.09 0.00 38.76 3.18
2057 7166 2.683742 GCAAAGGTTCATAGGCTAGCCA 60.684 50.000 34.70 20.88 38.92 4.75
2091 7200 2.358898 CGCATCGAAATGGGGAGAAAAT 59.641 45.455 0.00 0.00 41.01 1.82
2196 7306 3.802948 ATAGTCACATCGAGGGTGTTC 57.197 47.619 16.69 12.16 37.52 3.18
2230 7340 0.898326 TGCCTCTAAGTCGTGCCTCA 60.898 55.000 0.00 0.00 0.00 3.86
2503 8041 1.134530 GTTCGACGAGGACTCATGCG 61.135 60.000 0.00 0.39 0.00 4.73
2506 8044 1.096416 GGAGTTCGACGAGGACTCAT 58.904 55.000 23.95 0.00 41.15 2.90
2564 8248 0.034186 CCAAACCAGATGCAGGGCTA 60.034 55.000 0.00 0.00 0.00 3.93
2565 8249 1.304713 CCAAACCAGATGCAGGGCT 60.305 57.895 0.00 0.00 0.00 5.19
2655 8529 4.035675 GCTTCACACATATTACCTTGCCTC 59.964 45.833 0.00 0.00 0.00 4.70
2670 8544 1.371389 GCTTGCTGCAGCTTCACAC 60.371 57.895 36.61 17.60 42.66 3.82


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

AutoCloner maintained by Alex Coulton.