Multiple sequence alignment - TraesCS6B01G381500

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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 TraesCS6B01G381500 chr6B 100.000 2949 0 0 1 2949 656486298 656483350 0.000000e+00 5446.0
1 TraesCS6B01G381500 chr6B 94.893 2291 90 11 1 2287 681681451 681679184 0.000000e+00 3557.0
2 TraesCS6B01G381500 chr6B 93.867 587 36 0 2363 2949 613536759 613537345 0.000000e+00 885.0
3 TraesCS6B01G381500 chr6B 92.845 587 42 0 2363 2949 106278791 106278205 0.000000e+00 852.0
4 TraesCS6B01G381500 chr6B 99.213 127 1 0 2236 2362 681679196 681679070 2.290000e-56 230.0
5 TraesCS6B01G381500 chr2A 94.639 2369 85 24 1 2362 487631010 487633343 0.000000e+00 3633.0
6 TraesCS6B01G381500 chr2A 96.078 510 20 0 1240 1749 575783447 575782938 0.000000e+00 832.0
7 TraesCS6B01G381500 chr2A 93.023 129 7 2 963 1089 468115066 468114938 1.400000e-43 187.0
8 TraesCS6B01G381500 chr2A 85.149 101 15 0 1110 1210 773400632 773400532 1.450000e-18 104.0
9 TraesCS6B01G381500 chr4A 92.808 2183 97 26 1 2151 587871466 587873620 0.000000e+00 3107.0
10 TraesCS6B01G381500 chr4A 95.359 237 11 0 997 1233 75201720 75201956 7.720000e-101 377.0
11 TraesCS6B01G381500 chr4A 93.927 247 13 1 830 1074 75201474 75201720 3.590000e-99 372.0
12 TraesCS6B01G381500 chr4A 89.922 129 11 2 963 1089 229807926 229807798 6.540000e-37 165.0
13 TraesCS6B01G381500 chr3A 91.903 1198 51 18 1153 2328 664940799 664939626 0.000000e+00 1633.0
14 TraesCS6B01G381500 chr3A 93.156 1052 42 15 1240 2287 645741146 645740121 0.000000e+00 1517.0
15 TraesCS6B01G381500 chr3A 93.857 879 29 11 1 856 664941665 664940789 0.000000e+00 1301.0
16 TraesCS6B01G381500 chr3A 83.566 286 37 8 2082 2363 740075821 740076100 2.920000e-65 259.0
17 TraesCS6B01G381500 chr3A 96.899 129 3 1 2236 2363 570196323 570196195 6.400000e-52 215.0
18 TraesCS6B01G381500 chr3A 100.000 29 0 0 274 302 597851552 597851580 1.000000e-03 54.7
19 TraesCS6B01G381500 chr7A 92.381 1155 47 14 1230 2363 627186100 627187234 0.000000e+00 1607.0
20 TraesCS6B01G381500 chr3D 91.955 1156 42 18 1230 2362 418848086 418849213 0.000000e+00 1572.0
21 TraesCS6B01G381500 chr3D 100.000 29 0 0 274 302 455596182 455596210 1.000000e-03 54.7
22 TraesCS6B01G381500 chr7B 92.593 1053 53 10 1240 2287 585597265 585596233 0.000000e+00 1489.0
23 TraesCS6B01G381500 chr7B 93.526 587 37 1 2363 2949 694945008 694945593 0.000000e+00 872.0
24 TraesCS6B01G381500 chr7B 92.845 587 41 1 2363 2949 189606379 189605794 0.000000e+00 850.0
25 TraesCS6B01G381500 chr5D 90.989 1132 46 24 1240 2362 320920074 320918990 0.000000e+00 1474.0
26 TraesCS6B01G381500 chr4B 84.807 1165 117 32 1230 2363 64456308 64457443 0.000000e+00 1116.0
27 TraesCS6B01G381500 chr4B 92.845 587 42 0 2363 2949 29531192 29531778 0.000000e+00 852.0
28 TraesCS6B01G381500 chr4B 92.675 587 43 0 2363 2949 124124212 124123626 0.000000e+00 846.0
29 TraesCS6B01G381500 chr6A 87.684 950 84 18 1427 2363 261705479 261704550 0.000000e+00 1075.0
30 TraesCS6B01G381500 chr6A 91.525 295 23 2 843 1135 291221169 291220875 3.540000e-109 405.0
31 TraesCS6B01G381500 chr2D 88.000 900 72 16 1399 2287 597477931 597477057 0.000000e+00 1031.0
32 TraesCS6B01G381500 chr2D 93.220 118 8 0 1110 1227 646030918 646031035 1.090000e-39 174.0
33 TraesCS6B01G381500 chr2D 89.041 73 4 3 633 703 533131904 533131834 1.460000e-13 87.9
34 TraesCS6B01G381500 chr3B 93.356 587 39 0 2363 2949 492012763 492013349 0.000000e+00 869.0
35 TraesCS6B01G381500 chr3B 93.750 80 4 1 62 140 598910505 598910584 5.160000e-23 119.0
36 TraesCS6B01G381500 chr1B 93.015 587 41 0 2363 2949 106404060 106404646 0.000000e+00 857.0
37 TraesCS6B01G381500 chr1B 92.491 586 44 0 2364 2949 500518731 500518146 0.000000e+00 839.0
38 TraesCS6B01G381500 chr1B 96.899 129 4 0 2236 2364 506741790 506741918 1.780000e-52 217.0
39 TraesCS6B01G381500 chrUn 95.695 511 20 2 1240 1749 74793190 74793699 0.000000e+00 821.0
40 TraesCS6B01G381500 chr2B 89.222 167 14 4 2198 2362 686783959 686784123 3.850000e-49 206.0
41 TraesCS6B01G381500 chr2B 89.216 102 11 0 1110 1211 789439937 789439836 8.580000e-26 128.0
42 TraesCS6B01G381500 chr1A 93.023 129 7 2 963 1089 102469360 102469488 1.400000e-43 187.0
43 TraesCS6B01G381500 chr5A 91.473 129 9 1 963 1089 322737730 322737858 3.020000e-40 176.0


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 TraesCS6B01G381500 chr6B 656483350 656486298 2948 True 5446.0 5446 100.000 1 2949 1 chr6B.!!$R2 2948
1 TraesCS6B01G381500 chr6B 681679070 681681451 2381 True 1893.5 3557 97.053 1 2362 2 chr6B.!!$R3 2361
2 TraesCS6B01G381500 chr6B 613536759 613537345 586 False 885.0 885 93.867 2363 2949 1 chr6B.!!$F1 586
3 TraesCS6B01G381500 chr6B 106278205 106278791 586 True 852.0 852 92.845 2363 2949 1 chr6B.!!$R1 586
4 TraesCS6B01G381500 chr2A 487631010 487633343 2333 False 3633.0 3633 94.639 1 2362 1 chr2A.!!$F1 2361
5 TraesCS6B01G381500 chr2A 575782938 575783447 509 True 832.0 832 96.078 1240 1749 1 chr2A.!!$R2 509
6 TraesCS6B01G381500 chr4A 587871466 587873620 2154 False 3107.0 3107 92.808 1 2151 1 chr4A.!!$F1 2150
7 TraesCS6B01G381500 chr3A 645740121 645741146 1025 True 1517.0 1517 93.156 1240 2287 1 chr3A.!!$R2 1047
8 TraesCS6B01G381500 chr3A 664939626 664941665 2039 True 1467.0 1633 92.880 1 2328 2 chr3A.!!$R3 2327
9 TraesCS6B01G381500 chr7A 627186100 627187234 1134 False 1607.0 1607 92.381 1230 2363 1 chr7A.!!$F1 1133
10 TraesCS6B01G381500 chr3D 418848086 418849213 1127 False 1572.0 1572 91.955 1230 2362 1 chr3D.!!$F1 1132
11 TraesCS6B01G381500 chr7B 585596233 585597265 1032 True 1489.0 1489 92.593 1240 2287 1 chr7B.!!$R2 1047
12 TraesCS6B01G381500 chr7B 694945008 694945593 585 False 872.0 872 93.526 2363 2949 1 chr7B.!!$F1 586
13 TraesCS6B01G381500 chr7B 189605794 189606379 585 True 850.0 850 92.845 2363 2949 1 chr7B.!!$R1 586
14 TraesCS6B01G381500 chr5D 320918990 320920074 1084 True 1474.0 1474 90.989 1240 2362 1 chr5D.!!$R1 1122
15 TraesCS6B01G381500 chr4B 64456308 64457443 1135 False 1116.0 1116 84.807 1230 2363 1 chr4B.!!$F2 1133
16 TraesCS6B01G381500 chr4B 29531192 29531778 586 False 852.0 852 92.845 2363 2949 1 chr4B.!!$F1 586
17 TraesCS6B01G381500 chr4B 124123626 124124212 586 True 846.0 846 92.675 2363 2949 1 chr4B.!!$R1 586
18 TraesCS6B01G381500 chr6A 261704550 261705479 929 True 1075.0 1075 87.684 1427 2363 1 chr6A.!!$R1 936
19 TraesCS6B01G381500 chr2D 597477057 597477931 874 True 1031.0 1031 88.000 1399 2287 1 chr2D.!!$R2 888
20 TraesCS6B01G381500 chr3B 492012763 492013349 586 False 869.0 869 93.356 2363 2949 1 chr3B.!!$F1 586
21 TraesCS6B01G381500 chr1B 106404060 106404646 586 False 857.0 857 93.015 2363 2949 1 chr1B.!!$F1 586
22 TraesCS6B01G381500 chr1B 500518146 500518731 585 True 839.0 839 92.491 2364 2949 1 chr1B.!!$R1 585
23 TraesCS6B01G381500 chrUn 74793190 74793699 509 False 821.0 821 95.695 1240 1749 1 chrUn.!!$F1 509

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
712 745 2.69084 GTACTATCCTGTGGTGGGGAT 58.309 52.381 0.0 0.0 43.77 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1983 2067 1.004745 CCACCACCAGCCTAAACAGAT 59.995 52.381 0.0 0.0 0.0 2.9 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
71 72 2.985896 AGTGAACAATGGATGTACGGG 58.014 47.619 0.00 0.00 42.99 5.28
308 310 9.830975 TGAAACTGTATGTTGCATACTGTATAT 57.169 29.630 22.64 15.70 39.19 0.86
515 518 5.825679 AGTGTGGTTGTAGAACTAAATTGCA 59.174 36.000 2.43 0.00 32.15 4.08
712 745 2.690840 GTACTATCCTGTGGTGGGGAT 58.309 52.381 0.00 0.00 43.77 3.85
861 897 9.775854 ATATTGAATTGTGTTTTTGTCCAATCA 57.224 25.926 0.00 0.00 0.00 2.57
867 903 7.678947 TTGTGTTTTTGTCCAATCATTTGTT 57.321 28.000 0.00 0.00 0.00 2.83
882 918 9.386010 CAATCATTTGTTGGATTATGTGGAAAT 57.614 29.630 0.00 0.00 32.71 2.17
1089 1125 1.979469 CATATGCCGACGACGAAGATC 59.021 52.381 9.28 0.00 42.66 2.75
1165 1201 6.127758 TGTTGCTTGTTTGTTCTATTGTCACT 60.128 34.615 0.00 0.00 0.00 3.41
1195 1231 1.288127 GCTCTTTTGGCAGCCAGTG 59.712 57.895 15.50 9.04 33.81 3.66
1196 1232 1.458639 GCTCTTTTGGCAGCCAGTGT 61.459 55.000 15.50 0.00 33.81 3.55
1211 1247 6.456988 GCAGCCAGTGTCATAATTGTACTTAC 60.457 42.308 0.00 0.00 0.00 2.34
1713 1796 5.118050 TCTGATGCGTACTAACAAGTTTTCG 59.882 40.000 0.00 0.00 0.00 3.46
1727 1810 3.476552 AGTTTTCGCTTTCCTGACATGA 58.523 40.909 0.00 0.00 0.00 3.07
1728 1811 3.251004 AGTTTTCGCTTTCCTGACATGAC 59.749 43.478 0.00 0.00 0.00 3.06
1729 1812 1.808411 TTCGCTTTCCTGACATGACC 58.192 50.000 0.00 0.00 0.00 4.02
1730 1813 0.389817 TCGCTTTCCTGACATGACCG 60.390 55.000 0.00 0.00 0.00 4.79
1731 1814 0.670546 CGCTTTCCTGACATGACCGT 60.671 55.000 0.00 0.00 0.00 4.83
1732 1815 1.403647 CGCTTTCCTGACATGACCGTA 60.404 52.381 0.00 0.00 0.00 4.02
1733 1816 2.271800 GCTTTCCTGACATGACCGTAG 58.728 52.381 0.00 0.00 0.00 3.51
1913 1997 0.391263 GGACCTCGACGCCATCTTTT 60.391 55.000 0.00 0.00 0.00 2.27
2040 2126 0.462937 CCACCTTCGGTTGTGTGTGA 60.463 55.000 0.00 0.00 31.02 3.58
2397 2543 3.411446 CATAGTGTGTTTTGCTCCCTGA 58.589 45.455 0.00 0.00 0.00 3.86
2450 2596 6.641474 ACTAGACATAGGCTTTTACCTTCAC 58.359 40.000 0.00 0.00 41.50 3.18
2790 2937 6.961359 ATTCACGTCTTCATCGACAAAATA 57.039 33.333 0.00 0.00 33.54 1.40
2890 3037 1.596752 ACCGTGAAGCGTGCATTCA 60.597 52.632 0.00 0.00 39.32 2.57
2911 3058 0.761187 CGGATGTGTCCATGGGATCT 59.239 55.000 13.02 0.00 45.37 2.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
71 72 3.277142 ACTATTCGGTCCCAATGGAAC 57.723 47.619 0.00 0.00 45.66 3.62
225 226 3.927481 GAACTGGCAGTCCTGGGGC 62.927 68.421 22.31 1.14 35.80 5.80
308 310 2.375014 TGATGGTCGGCTAGGTGATA 57.625 50.000 0.00 0.00 0.00 2.15
486 489 9.623000 AATTTAGTTCTACAACCACACTAACTT 57.377 29.630 0.00 0.00 31.25 2.66
515 518 5.241728 GCTCTTCCTATTGGTGTTCAACTTT 59.758 40.000 0.00 0.00 38.31 2.66
628 661 4.019174 ACCAGACAAGGATTAAGCAATGG 58.981 43.478 0.00 0.00 0.00 3.16
712 745 6.884295 CGCCCCATAATCTATCCAGAAAAATA 59.116 38.462 0.00 0.00 33.50 1.40
763 799 5.076182 TGTATCCAGCAAAAGATTGGACAA 58.924 37.500 0.00 0.00 43.32 3.18
861 897 7.166851 TGCAATTTCCACATAATCCAACAAAT 58.833 30.769 0.00 0.00 0.00 2.32
867 903 4.381398 CGGTTGCAATTTCCACATAATCCA 60.381 41.667 0.59 0.00 0.00 3.41
882 918 5.276461 ACATATAGAGATCACGGTTGCAA 57.724 39.130 0.00 0.00 0.00 4.08
978 1014 2.095059 GCTAAACCACTGTTGCATCAGG 60.095 50.000 24.80 13.92 39.48 3.86
1089 1125 3.760684 GCTCCCTCAGCCAATAAATATGG 59.239 47.826 0.00 0.00 43.17 2.74
1165 1201 3.870419 GCCAAAAGAGCATCAAACAAACA 59.130 39.130 0.00 0.00 37.82 2.83
1211 1247 6.712241 TCTGAAAAGAGAGCAATTTAGACG 57.288 37.500 0.00 0.00 0.00 4.18
1661 1744 9.747898 TTCAAATCTGCTAGGGTATTTTCTTTA 57.252 29.630 0.00 0.00 0.00 1.85
1677 1760 2.417933 ACGCATCAGAGTTCAAATCTGC 59.582 45.455 10.09 0.00 43.20 4.26
1713 1796 2.271800 CTACGGTCATGTCAGGAAAGC 58.728 52.381 0.00 0.00 0.00 3.51
1728 1811 3.453559 GTGTCAATCACCCCTACGG 57.546 57.895 0.00 0.00 40.84 4.02
1736 1819 2.301870 TCACCCCTACAGTGTCAATCAC 59.698 50.000 0.00 0.00 46.46 3.06
1737 1820 2.615391 TCACCCCTACAGTGTCAATCA 58.385 47.619 0.00 0.00 36.58 2.57
1738 1821 3.914426 ATCACCCCTACAGTGTCAATC 57.086 47.619 0.00 0.00 36.58 2.67
1739 1822 3.587061 TCAATCACCCCTACAGTGTCAAT 59.413 43.478 0.00 0.00 36.58 2.57
1740 1823 2.976185 TCAATCACCCCTACAGTGTCAA 59.024 45.455 0.00 0.00 36.58 3.18
1741 1824 2.301870 GTCAATCACCCCTACAGTGTCA 59.698 50.000 0.00 0.00 36.58 3.58
1742 1825 2.301870 TGTCAATCACCCCTACAGTGTC 59.698 50.000 0.00 0.00 36.58 3.67
1743 1826 2.038557 GTGTCAATCACCCCTACAGTGT 59.961 50.000 0.00 0.00 40.84 3.55
1744 1827 2.699954 GTGTCAATCACCCCTACAGTG 58.300 52.381 0.00 0.00 40.84 3.66
1913 1997 2.721167 CGAATCCTCCCTCACGCCA 61.721 63.158 0.00 0.00 0.00 5.69
1983 2067 1.004745 CCACCACCAGCCTAAACAGAT 59.995 52.381 0.00 0.00 0.00 2.90
2040 2126 7.810766 CACGTCCAGTGCAAAATAAATTAAT 57.189 32.000 0.00 0.00 44.72 1.40
2397 2543 6.448369 TGGAATTATTGGGGTCTCGATAAT 57.552 37.500 0.00 0.00 36.03 1.28
2450 2596 1.039233 TACTAGTTCGGCCCCTTCGG 61.039 60.000 0.00 0.00 0.00 4.30
2911 3058 1.627864 TCAGACACCGGTTCAGATCA 58.372 50.000 2.97 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.