Multiple sequence alignment - TraesCS6D01G034700

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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 TraesCS6D01G034700 chr6D 100.000 2991 0 0 303 3293 14482895 14485885 0.000000e+00 5524
1 TraesCS6D01G034700 chr6D 89.859 2199 186 24 1108 3293 14437690 14439864 0.000000e+00 2791
2 TraesCS6D01G034700 chr6D 88.138 1273 140 7 1076 2347 14727352 14726090 0.000000e+00 1504
3 TraesCS6D01G034700 chr6D 84.452 1415 192 20 1091 2503 14503346 14504734 0.000000e+00 1369
4 TraesCS6D01G034700 chr6D 81.599 1413 219 31 1066 2471 14732963 14731585 0.000000e+00 1131
5 TraesCS6D01G034700 chr6D 85.918 980 78 24 2317 3293 16376579 16377501 0.000000e+00 990
6 TraesCS6D01G034700 chr6D 96.284 592 17 2 303 892 364109737 364110325 0.000000e+00 966
7 TraesCS6D01G034700 chr6D 100.000 128 0 0 1 128 14482593 14482720 1.530000e-58 237
8 TraesCS6D01G034700 chr6D 96.094 128 5 0 1 128 364109562 364109689 3.330000e-50 209
9 TraesCS6D01G034700 chr6D 91.753 97 8 0 946 1042 15344922 15344826 5.730000e-28 135
10 TraesCS6D01G034700 chr6A 92.911 2384 141 18 920 3293 15684692 15687057 0.000000e+00 3441
11 TraesCS6D01G034700 chr6A 88.825 1217 128 7 1141 2354 15914119 15912908 0.000000e+00 1487
12 TraesCS6D01G034700 chr6A 80.830 1591 256 31 948 2507 15647119 15648691 0.000000e+00 1203
13 TraesCS6D01G034700 chr6A 86.867 967 94 20 2307 3262 15924013 15923069 0.000000e+00 1051
14 TraesCS6D01G034700 chr6A 79.118 1293 235 27 1067 2349 16628963 16630230 0.000000e+00 859
15 TraesCS6D01G034700 chr6A 85.263 570 47 17 2481 3025 15688334 15688891 1.340000e-153 553
16 TraesCS6D01G034700 chr6A 83.220 590 95 3 303 889 8590483 8591071 3.740000e-149 538
17 TraesCS6D01G034700 chr6A 90.377 239 22 1 3055 3293 16652588 16652825 2.470000e-81 313
18 TraesCS6D01G034700 chr6A 95.935 123 3 2 1 122 8590308 8590429 7.210000e-47 198
19 TraesCS6D01G034700 chr6A 88.652 141 7 5 920 1051 15914301 15914161 2.630000e-36 163
20 TraesCS6D01G034700 chr6B 92.679 2090 126 12 920 3005 26488445 26490511 0.000000e+00 2987
21 TraesCS6D01G034700 chr6B 84.850 2198 279 29 1103 3293 26500525 26502675 0.000000e+00 2165
22 TraesCS6D01G034700 chr6B 83.412 2110 274 42 1208 3293 28730909 28728852 0.000000e+00 1888
23 TraesCS6D01G034700 chr6B 87.351 1257 154 5 1084 2339 26688248 26686996 0.000000e+00 1435
24 TraesCS6D01G034700 chr6B 79.710 1587 260 45 948 2507 26291158 26292709 0.000000e+00 1090
25 TraesCS6D01G034700 chr6B 84.250 400 35 12 2514 2913 28502197 28502568 6.720000e-97 364
26 TraesCS6D01G034700 chr5D 88.411 2114 210 18 1065 3169 27985522 27983435 0.000000e+00 2514
27 TraesCS6D01G034700 chr1D 96.959 592 16 1 303 892 50920085 50920676 0.000000e+00 992
28 TraesCS6D01G034700 chr1D 95.312 128 6 0 1 128 50919910 50920037 1.550000e-48 204
29 TraesCS6D01G034700 chr3D 96.791 592 17 1 303 892 590246650 590247241 0.000000e+00 987
30 TraesCS6D01G034700 chr3D 96.875 128 4 0 1 128 590246476 590246603 7.160000e-52 215
31 TraesCS6D01G034700 chr4B 93.243 592 38 1 303 892 659360552 659361143 0.000000e+00 870
32 TraesCS6D01G034700 chr1B 92.773 595 41 1 303 895 421435910 421435316 0.000000e+00 859
33 TraesCS6D01G034700 chr7B 92.568 592 41 2 303 892 667876983 667877573 0.000000e+00 846
34 TraesCS6D01G034700 chr7B 95.200 125 6 0 1 125 667876805 667876929 7.210000e-47 198
35 TraesCS6D01G034700 chr7D 88.055 586 68 1 303 886 577913832 577913247 0.000000e+00 693
36 TraesCS6D01G034700 chr2D 84.925 597 88 1 303 897 58992580 58993176 1.310000e-168 603
37 TraesCS6D01G034700 chr2D 94.309 123 4 3 1 122 58992406 58992526 5.610000e-43 185
38 TraesCS6D01G034700 chr4A 93.600 125 8 0 1 125 624660460 624660584 1.560000e-43 187
39 TraesCS6D01G034700 chr1A 93.600 125 8 0 1 125 569423397 569423273 1.560000e-43 187
40 TraesCS6D01G034700 chr1A 92.188 128 10 0 1 128 551869540 551869667 7.260000e-42 182


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 TraesCS6D01G034700 chr6D 14482593 14485885 3292 False 2880.5 5524 100.0000 1 3293 2 chr6D.!!$F4 3292
1 TraesCS6D01G034700 chr6D 14437690 14439864 2174 False 2791.0 2791 89.8590 1108 3293 1 chr6D.!!$F1 2185
2 TraesCS6D01G034700 chr6D 14726090 14727352 1262 True 1504.0 1504 88.1380 1076 2347 1 chr6D.!!$R1 1271
3 TraesCS6D01G034700 chr6D 14503346 14504734 1388 False 1369.0 1369 84.4520 1091 2503 1 chr6D.!!$F2 1412
4 TraesCS6D01G034700 chr6D 14731585 14732963 1378 True 1131.0 1131 81.5990 1066 2471 1 chr6D.!!$R2 1405
5 TraesCS6D01G034700 chr6D 16376579 16377501 922 False 990.0 990 85.9180 2317 3293 1 chr6D.!!$F3 976
6 TraesCS6D01G034700 chr6D 364109562 364110325 763 False 587.5 966 96.1890 1 892 2 chr6D.!!$F5 891
7 TraesCS6D01G034700 chr6A 15684692 15688891 4199 False 1997.0 3441 89.0870 920 3293 2 chr6A.!!$F5 2373
8 TraesCS6D01G034700 chr6A 15647119 15648691 1572 False 1203.0 1203 80.8300 948 2507 1 chr6A.!!$F1 1559
9 TraesCS6D01G034700 chr6A 15923069 15924013 944 True 1051.0 1051 86.8670 2307 3262 1 chr6A.!!$R1 955
10 TraesCS6D01G034700 chr6A 16628963 16630230 1267 False 859.0 859 79.1180 1067 2349 1 chr6A.!!$F2 1282
11 TraesCS6D01G034700 chr6A 15912908 15914301 1393 True 825.0 1487 88.7385 920 2354 2 chr6A.!!$R2 1434
12 TraesCS6D01G034700 chr6A 8590308 8591071 763 False 368.0 538 89.5775 1 889 2 chr6A.!!$F4 888
13 TraesCS6D01G034700 chr6B 26488445 26490511 2066 False 2987.0 2987 92.6790 920 3005 1 chr6B.!!$F2 2085
14 TraesCS6D01G034700 chr6B 26500525 26502675 2150 False 2165.0 2165 84.8500 1103 3293 1 chr6B.!!$F3 2190
15 TraesCS6D01G034700 chr6B 28728852 28730909 2057 True 1888.0 1888 83.4120 1208 3293 1 chr6B.!!$R2 2085
16 TraesCS6D01G034700 chr6B 26686996 26688248 1252 True 1435.0 1435 87.3510 1084 2339 1 chr6B.!!$R1 1255
17 TraesCS6D01G034700 chr6B 26291158 26292709 1551 False 1090.0 1090 79.7100 948 2507 1 chr6B.!!$F1 1559
18 TraesCS6D01G034700 chr5D 27983435 27985522 2087 True 2514.0 2514 88.4110 1065 3169 1 chr5D.!!$R1 2104
19 TraesCS6D01G034700 chr1D 50919910 50920676 766 False 598.0 992 96.1355 1 892 2 chr1D.!!$F1 891
20 TraesCS6D01G034700 chr3D 590246476 590247241 765 False 601.0 987 96.8330 1 892 2 chr3D.!!$F1 891
21 TraesCS6D01G034700 chr4B 659360552 659361143 591 False 870.0 870 93.2430 303 892 1 chr4B.!!$F1 589
22 TraesCS6D01G034700 chr1B 421435316 421435910 594 True 859.0 859 92.7730 303 895 1 chr1B.!!$R1 592
23 TraesCS6D01G034700 chr7B 667876805 667877573 768 False 522.0 846 93.8840 1 892 2 chr7B.!!$F1 891
24 TraesCS6D01G034700 chr7D 577913247 577913832 585 True 693.0 693 88.0550 303 886 1 chr7D.!!$R1 583
25 TraesCS6D01G034700 chr2D 58992406 58993176 770 False 394.0 603 89.6170 1 897 2 chr2D.!!$F1 896

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
912 918 0.394216 CCATGAATCACCAAGGCCGA 60.394 55.0 0.0 0.0 0.0 5.54 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2871 2957 3.258123 ACATGGCACCTCAATTGGTTTAC 59.742 43.478 5.42 0.0 38.45 2.01 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
80 81 3.246416 TCTCCCTGCCTTATACCTCTC 57.754 52.381 0.00 0.00 0.00 3.20
111 112 3.228188 ACTGATCAAGCCTTTCACCAA 57.772 42.857 0.00 0.00 0.00 3.67
113 114 4.154942 ACTGATCAAGCCTTTCACCAATT 58.845 39.130 0.00 0.00 0.00 2.32
400 401 2.742053 AGTGCACAATAACTGTTAGCCG 59.258 45.455 21.04 0.11 35.47 5.52
459 463 7.877612 TCATATGCACTGATAATGTTATCCGTT 59.122 33.333 9.59 0.00 38.98 4.44
561 565 6.719370 TGACTTTGGAGGCAATTTTGTATAGT 59.281 34.615 0.00 0.00 38.20 2.12
570 574 9.931210 GAGGCAATTTTGTATAGTACATTACAC 57.069 33.333 7.26 0.00 38.68 2.90
654 660 1.190643 TGGTGTCATATGCACTCCGA 58.809 50.000 21.55 10.02 37.07 4.55
810 816 1.578206 GCCTTGACCTCCTCGTTTGC 61.578 60.000 0.00 0.00 0.00 3.68
836 842 2.375110 GTGCACACAACAACTCATTCG 58.625 47.619 13.17 0.00 0.00 3.34
860 866 3.013921 TCCGATGTTACTTTCATTGGGC 58.986 45.455 10.95 0.00 43.42 5.36
867 873 1.244019 ACTTTCATTGGGCCGCTGTC 61.244 55.000 0.00 0.00 0.00 3.51
897 903 3.127548 GTCTCCATGTTGCTTACACCATG 59.872 47.826 0.00 0.00 44.07 3.66
898 904 3.008923 TCTCCATGTTGCTTACACCATGA 59.991 43.478 5.29 0.00 46.54 3.07
899 905 3.758023 CTCCATGTTGCTTACACCATGAA 59.242 43.478 5.29 0.00 46.54 2.57
900 906 4.343231 TCCATGTTGCTTACACCATGAAT 58.657 39.130 5.29 0.00 46.54 2.57
901 907 4.398988 TCCATGTTGCTTACACCATGAATC 59.601 41.667 5.29 0.00 46.54 2.52
902 908 4.158209 CCATGTTGCTTACACCATGAATCA 59.842 41.667 5.29 0.00 46.54 2.57
903 909 4.764679 TGTTGCTTACACCATGAATCAC 57.235 40.909 0.00 0.00 0.00 3.06
904 910 3.505680 TGTTGCTTACACCATGAATCACC 59.494 43.478 0.00 0.00 0.00 4.02
905 911 3.431673 TGCTTACACCATGAATCACCA 57.568 42.857 0.00 0.00 0.00 4.17
906 912 3.760738 TGCTTACACCATGAATCACCAA 58.239 40.909 0.00 0.00 0.00 3.67
907 913 3.758023 TGCTTACACCATGAATCACCAAG 59.242 43.478 0.00 0.00 0.00 3.61
908 914 3.129287 GCTTACACCATGAATCACCAAGG 59.871 47.826 0.00 0.00 0.00 3.61
909 915 1.549203 ACACCATGAATCACCAAGGC 58.451 50.000 0.00 0.00 0.00 4.35
910 916 0.819582 CACCATGAATCACCAAGGCC 59.180 55.000 0.00 0.00 0.00 5.19
911 917 0.680921 ACCATGAATCACCAAGGCCG 60.681 55.000 0.00 0.00 0.00 6.13
912 918 0.394216 CCATGAATCACCAAGGCCGA 60.394 55.000 0.00 0.00 0.00 5.54
913 919 1.019673 CATGAATCACCAAGGCCGAG 58.980 55.000 0.00 0.00 0.00 4.63
914 920 0.749454 ATGAATCACCAAGGCCGAGC 60.749 55.000 0.00 0.00 0.00 5.03
915 921 1.078143 GAATCACCAAGGCCGAGCT 60.078 57.895 0.00 0.00 0.00 4.09
916 922 1.078143 AATCACCAAGGCCGAGCTC 60.078 57.895 2.73 2.73 0.00 4.09
917 923 2.543067 AATCACCAAGGCCGAGCTCC 62.543 60.000 8.47 0.00 0.00 4.70
918 924 4.785453 CACCAAGGCCGAGCTCCC 62.785 72.222 8.47 4.33 0.00 4.30
935 941 3.374367 GCTCCCAATTCGAAGAGGTAAAC 59.626 47.826 15.18 1.83 38.43 2.01
1025 1036 3.411517 CCATTCTCACCGGCCCCT 61.412 66.667 0.00 0.00 0.00 4.79
1045 1071 4.017126 CCTATTTCTTTCCTTCCCCACAC 58.983 47.826 0.00 0.00 0.00 3.82
1053 1079 1.225983 CTTCCCCACACACCACACA 59.774 57.895 0.00 0.00 0.00 3.72
1327 1379 1.270907 GAAGCTCTCCCACCTCAAGA 58.729 55.000 0.00 0.00 0.00 3.02
1514 1566 4.514577 CATCGCCCGCCTCGTCTT 62.515 66.667 0.00 0.00 0.00 3.01
1599 1651 3.057104 TCTTCGGCTCATTCGACAACTTA 60.057 43.478 0.00 0.00 36.30 2.24
1635 1693 0.603569 GCGACTCCAACCTTCTCTCA 59.396 55.000 0.00 0.00 0.00 3.27
2056 2118 3.018149 CCGGTAGTTCTCAGTCTTAGCT 58.982 50.000 0.00 0.00 0.00 3.32
2119 2181 4.579869 TCTCAAGGAAAATGGACTGCTAC 58.420 43.478 0.00 0.00 0.00 3.58
2154 2216 3.062774 GCTTCTTTACTGCGGTCAAGATC 59.937 47.826 20.23 12.74 36.13 2.75
2408 2477 7.421530 TCACTATCTTTTCTAGTGTGTTTGC 57.578 36.000 9.56 0.00 44.16 3.68
2864 2950 8.632679 TCTTAACATTTGCATCCCTCATTAATC 58.367 33.333 0.00 0.00 0.00 1.75
2865 2951 6.795144 AACATTTGCATCCCTCATTAATCA 57.205 33.333 0.00 0.00 0.00 2.57
2871 2957 5.557866 TGCATCCCTCATTAATCATCAGAG 58.442 41.667 0.00 0.00 0.00 3.35
3104 3198 1.305201 TTCTGCCTTGAAACGACACC 58.695 50.000 0.00 0.00 0.00 4.16
3129 3225 4.288105 AGACCTTCAATCTGTTGTCCATCT 59.712 41.667 0.00 0.00 36.69 2.90
3223 3327 2.226330 TGCAACCAAATTAGTGTCGCT 58.774 42.857 0.00 0.00 0.00 4.93
3264 3368 2.369394 CCTGGGCACTTGTAATCCTTC 58.631 52.381 0.00 0.00 0.00 3.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 2.289002 GCTTGATCAGTTTATGCCGAGG 59.711 50.000 0.00 0.00 0.00 4.63
400 401 9.476059 TCATTTTATGAAGCGGAGCAAAGCTAC 62.476 40.741 0.39 0.00 46.76 3.58
459 463 0.107066 TCGTACCGGGCAGACTCATA 60.107 55.000 6.32 0.00 0.00 2.15
810 816 1.601903 AGTTGTTGTGTGCACCATACG 59.398 47.619 15.69 0.00 0.00 3.06
836 842 4.332819 CCCAATGAAAGTAACATCGGAGAC 59.667 45.833 0.00 0.00 42.51 3.36
867 873 8.246481 TGTAAGCAACATGGAGACTGTCCTAG 62.246 46.154 3.76 0.00 38.66 3.02
897 903 1.078143 AGCTCGGCCTTGGTGATTC 60.078 57.895 0.00 0.00 0.00 2.52
898 904 1.078143 GAGCTCGGCCTTGGTGATT 60.078 57.895 0.00 0.00 0.00 2.57
899 905 2.586792 GAGCTCGGCCTTGGTGAT 59.413 61.111 0.00 0.00 0.00 3.06
900 906 3.706373 GGAGCTCGGCCTTGGTGA 61.706 66.667 7.83 0.00 0.00 4.02
901 907 4.785453 GGGAGCTCGGCCTTGGTG 62.785 72.222 7.83 0.00 0.00 4.17
903 909 2.843912 AATTGGGAGCTCGGCCTTGG 62.844 60.000 7.83 0.00 0.00 3.61
904 910 1.379044 AATTGGGAGCTCGGCCTTG 60.379 57.895 7.83 0.00 0.00 3.61
905 911 1.077429 GAATTGGGAGCTCGGCCTT 60.077 57.895 7.83 0.00 0.00 4.35
906 912 2.592308 GAATTGGGAGCTCGGCCT 59.408 61.111 7.83 0.00 0.00 5.19
907 913 2.869503 TTCGAATTGGGAGCTCGGCC 62.870 60.000 7.83 4.74 33.44 6.13
908 914 1.432270 CTTCGAATTGGGAGCTCGGC 61.432 60.000 7.83 0.00 33.44 5.54
909 915 0.175760 TCTTCGAATTGGGAGCTCGG 59.824 55.000 7.83 0.00 33.44 4.63
910 916 1.565305 CTCTTCGAATTGGGAGCTCG 58.435 55.000 7.83 0.00 0.00 5.03
911 917 1.208293 ACCTCTTCGAATTGGGAGCTC 59.792 52.381 17.28 4.71 0.00 4.09
912 918 1.280457 ACCTCTTCGAATTGGGAGCT 58.720 50.000 17.28 0.00 0.00 4.09
913 919 2.981859 TACCTCTTCGAATTGGGAGC 57.018 50.000 17.28 0.00 0.00 4.70
914 920 3.939592 GGTTTACCTCTTCGAATTGGGAG 59.060 47.826 17.28 11.79 0.00 4.30
915 921 3.307904 GGGTTTACCTCTTCGAATTGGGA 60.308 47.826 17.28 8.92 35.85 4.37
916 922 3.014623 GGGTTTACCTCTTCGAATTGGG 58.985 50.000 17.28 13.17 35.85 4.12
1025 1036 4.403734 GTGTGTGGGGAAGGAAAGAAATA 58.596 43.478 0.00 0.00 0.00 1.40
1045 1071 2.351350 GCGGAGGTATTTTTGTGTGGTG 60.351 50.000 0.00 0.00 0.00 4.17
1053 1079 2.110352 CGGCGGCGGAGGTATTTTT 61.110 57.895 25.36 0.00 0.00 1.94
1307 1359 0.979665 CTTGAGGTGGGAGAGCTTCA 59.020 55.000 0.00 0.00 30.42 3.02
1327 1379 4.926162 GTTGGGTTTGGCGGGGGT 62.926 66.667 0.00 0.00 0.00 4.95
1599 1651 2.345244 CACTTGAGCAGCCGGAGT 59.655 61.111 5.05 0.00 0.00 3.85
2154 2216 5.152623 TCTCCACAAATACCTTCTCAGTG 57.847 43.478 0.00 0.00 0.00 3.66
2249 2311 8.783093 TCCATCTAAATATGAAATTAGTTGGCG 58.217 33.333 13.85 0.00 42.95 5.69
2408 2477 3.829948 CAATGAGCAAACTGGCAAGTAG 58.170 45.455 0.00 0.00 34.77 2.57
2477 2558 4.072131 TCTAAGGAATGACAACAACAGCC 58.928 43.478 0.00 0.00 0.00 4.85
2598 2681 6.980593 TGAACCGCAAACTTAGTACTAACTA 58.019 36.000 11.38 0.00 37.15 2.24
2843 2929 6.551975 TGATGATTAATGAGGGATGCAAATGT 59.448 34.615 0.00 0.00 0.00 2.71
2864 2950 5.392380 GCACCTCAATTGGTTTACTCTGATG 60.392 44.000 5.42 0.00 38.45 3.07
2865 2951 4.702131 GCACCTCAATTGGTTTACTCTGAT 59.298 41.667 5.42 0.00 38.45 2.90
2871 2957 3.258123 ACATGGCACCTCAATTGGTTTAC 59.742 43.478 5.42 0.00 38.45 2.01
3104 3198 2.996621 GGACAACAGATTGAAGGTCTCG 59.003 50.000 0.00 0.00 39.30 4.04
3223 3327 1.067846 GCACTGACTCGTGGACATGTA 60.068 52.381 0.00 0.00 35.47 2.29
3264 3368 7.987268 ACAGATACATACATCACTAAACACG 57.013 36.000 0.00 0.00 0.00 4.49


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

AutoCloner maintained by Alex Coulton.