Multiple sequence alignment - TraesCS2B01G081100

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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 TraesCS2B01G081100 chr2B 100.000 3370 0 0 1 3370 45535295 45538664 0.000000e+00 6224.0
1 TraesCS2B01G081100 chr2B 97.059 1938 37 3 3 1920 45040348 45038411 0.000000e+00 3245.0
2 TraesCS2B01G081100 chr2B 99.875 802 1 0 2569 3370 45534886 45534085 0.000000e+00 1476.0
3 TraesCS2B01G081100 chr2B 94.396 803 28 7 2569 3370 318118118 318117332 0.000000e+00 1218.0
4 TraesCS2B01G081100 chr2B 84.235 1091 150 19 1334 2422 44752458 44751388 0.000000e+00 1042.0
5 TraesCS2B01G081100 chr2B 83.106 1172 163 23 1260 2422 45134616 45133471 0.000000e+00 1035.0
6 TraesCS2B01G081100 chr2B 82.675 1114 163 21 1313 2421 44926721 44927809 0.000000e+00 961.0
7 TraesCS2B01G081100 chr2B 94.847 524 25 1 1911 2432 45038391 45037868 0.000000e+00 817.0
8 TraesCS2B01G081100 chr2B 87.844 691 64 2 1 671 45032139 45031449 0.000000e+00 793.0
9 TraesCS2B01G081100 chr2B 87.699 691 65 2 1 671 45135827 45135137 0.000000e+00 787.0
10 TraesCS2B01G081100 chr2B 87.583 604 73 2 1313 1915 45625375 45625977 0.000000e+00 699.0
11 TraesCS2B01G081100 chr2B 84.540 718 91 2 1 698 44925446 44926163 0.000000e+00 693.0
12 TraesCS2B01G081100 chr2B 84.419 706 90 2 13 698 45701622 45702327 0.000000e+00 676.0
13 TraesCS2B01G081100 chr2B 83.983 718 95 2 1 698 45624100 45624817 0.000000e+00 671.0
14 TraesCS2B01G081100 chr2D 97.371 1940 31 3 1 1920 28008239 28006300 0.000000e+00 3282.0
15 TraesCS2B01G081100 chr2D 83.518 1171 162 24 1260 2422 27959002 27960149 0.000000e+00 1064.0
16 TraesCS2B01G081100 chr2D 83.993 1112 156 19 1313 2422 27999507 27998416 0.000000e+00 1048.0
17 TraesCS2B01G081100 chr2D 94.260 662 33 4 1911 2568 28006280 28005620 0.000000e+00 1007.0
18 TraesCS2B01G081100 chr2D 83.094 1112 162 18 1313 2421 28416345 28415257 0.000000e+00 989.0
19 TraesCS2B01G081100 chr2D 89.146 691 55 2 1 671 27957792 27958482 0.000000e+00 843.0
20 TraesCS2B01G081100 chr2D 85.515 718 84 5 1 698 28093754 28093037 0.000000e+00 732.0
21 TraesCS2B01G081100 chr2A 97.372 1941 30 4 1 1920 30187081 30185141 0.000000e+00 3282.0
22 TraesCS2B01G081100 chr2A 84.007 1113 147 20 1314 2422 30162658 30161573 0.000000e+00 1040.0
23 TraesCS2B01G081100 chr2A 83.542 1118 153 24 1313 2422 30303208 30304302 0.000000e+00 1016.0
24 TraesCS2B01G081100 chr2A 93.646 661 30 3 1911 2568 30185122 30184471 0.000000e+00 977.0
25 TraesCS2B01G081100 chr2A 82.862 1097 160 19 1334 2427 30269850 30268779 0.000000e+00 959.0
26 TraesCS2B01G081100 chr2A 82.379 1118 169 19 1313 2427 30254223 30253131 0.000000e+00 948.0
27 TraesCS2B01G081100 chr2A 84.701 719 88 11 1 698 30301957 30302674 0.000000e+00 699.0
28 TraesCS2B01G081100 chr5A 99.502 803 3 1 2569 3370 612787671 612788473 0.000000e+00 1459.0
29 TraesCS2B01G081100 chr5A 92.191 461 30 6 2591 3049 536448710 536449166 0.000000e+00 647.0
30 TraesCS2B01G081100 chr5A 91.282 195 12 3 3177 3370 536449293 536449483 9.270000e-66 261.0
31 TraesCS2B01G081100 chr6B 96.758 802 11 4 2569 3370 705430667 705429881 0.000000e+00 1323.0
32 TraesCS2B01G081100 chr7D 89.219 807 40 16 2569 3370 137011307 137012071 0.000000e+00 965.0
33 TraesCS2B01G081100 chr5B 91.189 488 36 5 2569 3052 100830385 100830869 0.000000e+00 656.0
34 TraesCS2B01G081100 chr5B 88.608 237 15 7 3139 3370 100830962 100831191 9.210000e-71 278.0
35 TraesCS2B01G081100 chr7A 86.977 215 24 3 2569 2783 37264390 37264180 4.350000e-59 239.0
36 TraesCS2B01G081100 chr7A 93.571 140 9 0 3001 3140 720423023 720423162 3.410000e-50 209.0
37 TraesCS2B01G081100 chr1A 87.264 212 24 2 2569 2780 153408193 153408401 4.350000e-59 239.0
38 TraesCS2B01G081100 chr1A 95.000 140 7 0 3001 3140 153408513 153408652 1.570000e-53 220.0
39 TraesCS2B01G081100 chr1A 94.872 39 1 1 3178 3216 153408734 153408771 3.630000e-05 60.2
40 TraesCS2B01G081100 chr6A 94.872 39 1 1 3178 3216 179812717 179812754 3.630000e-05 60.2


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 TraesCS2B01G081100 chr2B 45535295 45538664 3369 False 6224.0 6224 100.0000 1 3370 1 chr2B.!!$F1 3369
1 TraesCS2B01G081100 chr2B 45037868 45040348 2480 True 2031.0 3245 95.9530 3 2432 2 chr2B.!!$R5 2429
2 TraesCS2B01G081100 chr2B 45534085 45534886 801 True 1476.0 1476 99.8750 2569 3370 1 chr2B.!!$R3 801
3 TraesCS2B01G081100 chr2B 318117332 318118118 786 True 1218.0 1218 94.3960 2569 3370 1 chr2B.!!$R4 801
4 TraesCS2B01G081100 chr2B 44751388 44752458 1070 True 1042.0 1042 84.2350 1334 2422 1 chr2B.!!$R1 1088
5 TraesCS2B01G081100 chr2B 45133471 45135827 2356 True 911.0 1035 85.4025 1 2422 2 chr2B.!!$R6 2421
6 TraesCS2B01G081100 chr2B 44925446 44927809 2363 False 827.0 961 83.6075 1 2421 2 chr2B.!!$F3 2420
7 TraesCS2B01G081100 chr2B 45031449 45032139 690 True 793.0 793 87.8440 1 671 1 chr2B.!!$R2 670
8 TraesCS2B01G081100 chr2B 45624100 45625977 1877 False 685.0 699 85.7830 1 1915 2 chr2B.!!$F4 1914
9 TraesCS2B01G081100 chr2B 45701622 45702327 705 False 676.0 676 84.4190 13 698 1 chr2B.!!$F2 685
10 TraesCS2B01G081100 chr2D 28005620 28008239 2619 True 2144.5 3282 95.8155 1 2568 2 chr2D.!!$R4 2567
11 TraesCS2B01G081100 chr2D 27998416 27999507 1091 True 1048.0 1048 83.9930 1313 2422 1 chr2D.!!$R1 1109
12 TraesCS2B01G081100 chr2D 28415257 28416345 1088 True 989.0 989 83.0940 1313 2421 1 chr2D.!!$R3 1108
13 TraesCS2B01G081100 chr2D 27957792 27960149 2357 False 953.5 1064 86.3320 1 2422 2 chr2D.!!$F1 2421
14 TraesCS2B01G081100 chr2D 28093037 28093754 717 True 732.0 732 85.5150 1 698 1 chr2D.!!$R2 697
15 TraesCS2B01G081100 chr2A 30184471 30187081 2610 True 2129.5 3282 95.5090 1 2568 2 chr2A.!!$R4 2567
16 TraesCS2B01G081100 chr2A 30161573 30162658 1085 True 1040.0 1040 84.0070 1314 2422 1 chr2A.!!$R1 1108
17 TraesCS2B01G081100 chr2A 30268779 30269850 1071 True 959.0 959 82.8620 1334 2427 1 chr2A.!!$R3 1093
18 TraesCS2B01G081100 chr2A 30253131 30254223 1092 True 948.0 948 82.3790 1313 2427 1 chr2A.!!$R2 1114
19 TraesCS2B01G081100 chr2A 30301957 30304302 2345 False 857.5 1016 84.1215 1 2422 2 chr2A.!!$F1 2421
20 TraesCS2B01G081100 chr5A 612787671 612788473 802 False 1459.0 1459 99.5020 2569 3370 1 chr5A.!!$F1 801
21 TraesCS2B01G081100 chr5A 536448710 536449483 773 False 454.0 647 91.7365 2591 3370 2 chr5A.!!$F2 779
22 TraesCS2B01G081100 chr6B 705429881 705430667 786 True 1323.0 1323 96.7580 2569 3370 1 chr6B.!!$R1 801
23 TraesCS2B01G081100 chr7D 137011307 137012071 764 False 965.0 965 89.2190 2569 3370 1 chr7D.!!$F1 801
24 TraesCS2B01G081100 chr5B 100830385 100831191 806 False 467.0 656 89.8985 2569 3370 2 chr5B.!!$F1 801

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
419 440 1.794116 CATTGGAAAGCTGCAAAACCG 59.206 47.619 1.02 0.0 36.37 4.44 F
945 969 3.126831 GTTGGACAAGCTGGATCTATCG 58.873 50.000 0.00 0.0 0.00 2.92 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1609 1701 1.022735 CATCTGTCAAGGCTGCCATC 58.977 55.0 22.65 8.33 0.00 3.51 R
2475 2608 0.895530 TAGCCAACTGTCGCTAGCTT 59.104 50.0 13.93 0.00 36.53 3.74 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
98 99 4.707105 TGCTTGATCTTTCAGACAACTCA 58.293 39.130 0.00 0.00 32.27 3.41
231 232 2.360801 TGCACCCAGCTTACAAAGTTTC 59.639 45.455 0.00 0.00 45.94 2.78
419 440 1.794116 CATTGGAAAGCTGCAAAACCG 59.206 47.619 1.02 0.00 36.37 4.44
683 704 6.711277 ACAACAAGCTCATAGGAGAAATACA 58.289 36.000 8.95 0.00 44.26 2.29
945 969 3.126831 GTTGGACAAGCTGGATCTATCG 58.873 50.000 0.00 0.00 0.00 2.92
948 972 3.570125 TGGACAAGCTGGATCTATCGTAG 59.430 47.826 0.00 0.00 0.00 3.51
1228 1303 9.826574 GTAATAAGATTCCTGGTGTGTTATGTA 57.173 33.333 0.00 0.00 0.00 2.29
1609 1701 3.885297 ACTGGTCTTCAAGTTCATGGTTG 59.115 43.478 0.00 0.00 0.00 3.77
1980 2105 3.192001 CCCTTCATGTATGTATGCATGGC 59.808 47.826 18.53 2.61 46.54 4.40
2035 2160 1.077930 TGGGCTGCAAGATCTCTGC 60.078 57.895 17.68 17.68 34.07 4.26
2276 2403 0.036765 TTGGGCTGTCATGTACCGTC 60.037 55.000 0.00 0.00 0.00 4.79
2284 2411 3.014623 TGTCATGTACCGTCGAATCTCT 58.985 45.455 0.00 0.00 0.00 3.10
2381 2508 6.933130 TCATGACGATTGACGAATATTTGAC 58.067 36.000 9.79 4.02 45.77 3.18
2475 2608 2.288948 GCAAGTGCCCAATGTGATTTGA 60.289 45.455 0.00 0.00 34.31 2.69
2478 2611 2.028748 AGTGCCCAATGTGATTTGAAGC 60.029 45.455 0.00 0.00 0.00 3.86
2479 2612 2.028748 GTGCCCAATGTGATTTGAAGCT 60.029 45.455 0.00 0.00 31.16 3.74
2483 2616 3.488047 CCCAATGTGATTTGAAGCTAGCG 60.488 47.826 9.55 0.00 0.00 4.26
2532 2666 0.875474 CTTTGTTGCGGGTTTGCTGG 60.875 55.000 0.00 0.00 35.36 4.85
2535 2669 1.591327 GTTGCGGGTTTGCTGGTTG 60.591 57.895 0.00 0.00 35.36 3.77
2554 2688 8.825745 GCTGGTTGTTTTCATTTTGATCTTAAA 58.174 29.630 0.00 0.00 0.00 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
231 232 0.454600 CTGCAGGTAAGCTGCCATTG 59.545 55.000 5.57 2.32 46.35 2.82
683 704 6.418057 TTGCCAAATTACCAACTTCTGATT 57.582 33.333 0.00 0.00 0.00 2.57
773 794 6.494893 TGCGCAAGAACAATAAAGTAAGAT 57.505 33.333 8.16 0.00 43.02 2.40
945 969 3.219281 TGGCCCTTCAAAGTTGTTCTAC 58.781 45.455 0.00 0.00 0.00 2.59
948 972 3.751479 ATTGGCCCTTCAAAGTTGTTC 57.249 42.857 0.00 0.00 0.00 3.18
1228 1303 1.770294 TTCTTCCGGTTGGCAACTTT 58.230 45.000 27.77 0.00 34.14 2.66
1229 1304 1.770294 TTTCTTCCGGTTGGCAACTT 58.230 45.000 27.77 0.00 34.14 2.66
1609 1701 1.022735 CATCTGTCAAGGCTGCCATC 58.977 55.000 22.65 8.33 0.00 3.51
1980 2105 8.112099 GCAAATGCACTCAAATACTCAATAAG 57.888 34.615 0.00 0.00 41.59 1.73
2035 2160 3.784701 AACTATACACGTCAGCTCCTG 57.215 47.619 0.00 0.00 0.00 3.86
2284 2411 2.619931 TCATTCCAGGTCTGTCCTTCA 58.380 47.619 0.00 0.00 45.67 3.02
2381 2508 2.975732 TCAGCATGCTCTAACAGAGG 57.024 50.000 19.68 3.08 42.54 3.69
2475 2608 0.895530 TAGCCAACTGTCGCTAGCTT 59.104 50.000 13.93 0.00 36.53 3.74
2498 2631 5.452777 GCAACAAAGGATAGTTGACACTTC 58.547 41.667 9.25 0.00 46.01 3.01
2554 2688 1.134098 GCCACTGGCCATACATACACT 60.134 52.381 5.51 0.00 44.06 3.55
2684 2819 7.965655 TGAACGTTTGAAATGCGATTAATGTAT 59.034 29.630 0.46 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.