Multiple sequence alignment - TraesCS3D01G463200

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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 TraesCS3D01G463200 chr3D 100.000 3158 0 0 1 3158 567225129 567221972 0.000000e+00 5832.0
1 TraesCS3D01G463200 chr3D 81.337 359 55 10 2800 3156 567226643 567226295 6.670000e-72 281.0
2 TraesCS3D01G463200 chr3D 86.239 109 13 2 1678 1785 569517278 569517385 1.990000e-22 117.0
3 TraesCS3D01G463200 chr3D 76.087 230 43 9 1506 1733 564512780 564512561 3.330000e-20 110.0
4 TraesCS3D01G463200 chr3D 100.000 51 0 0 3108 3158 567217168 567217118 9.320000e-16 95.3
5 TraesCS3D01G463200 chr3D 87.671 73 7 2 1062 1133 565982602 565982673 2.020000e-12 84.2
6 TraesCS3D01G463200 chr3A 95.156 3179 120 10 1 3158 701855551 701858716 0.000000e+00 4987.0
7 TraesCS3D01G463200 chr3A 94.208 3194 124 18 1 3158 700567123 700570291 0.000000e+00 4817.0
8 TraesCS3D01G463200 chr3A 73.611 1224 238 53 1512 2680 699251507 699250314 2.950000e-105 392.0
9 TraesCS3D01G463200 chr3A 80.780 359 57 8 2800 3156 701853930 701854278 1.440000e-68 270.0
10 TraesCS3D01G463200 chr3A 80.501 359 58 8 2800 3156 700565526 700565874 6.720000e-67 265.0
11 TraesCS3D01G463200 chr3A 81.308 214 26 11 1003 1209 697585522 697585316 9.060000e-36 161.0
12 TraesCS3D01G463200 chr3A 83.333 114 13 3 1083 1196 699455084 699454977 2.000000e-17 100.0
13 TraesCS3D01G463200 chrUn 94.873 3179 116 18 13 3158 41111960 41108796 0.000000e+00 4924.0
14 TraesCS3D01G463200 chr3B 94.544 3189 112 18 1 3158 754980653 754983810 0.000000e+00 4868.0
15 TraesCS3D01G463200 chr3B 73.333 1665 309 75 1062 2648 752122873 752121266 1.020000e-134 490.0
16 TraesCS3D01G463200 chr3B 74.023 1228 225 60 1506 2680 752178208 752177022 6.300000e-112 414.0
17 TraesCS3D01G463200 chr3B 76.733 606 109 21 1701 2286 756185900 756185307 3.060000e-80 309.0
18 TraesCS3D01G463200 chr3B 81.163 361 54 10 2800 3156 754971354 754971704 8.630000e-71 278.0
19 TraesCS3D01G463200 chr3B 86.631 187 24 1 2796 2982 756182989 756182804 4.130000e-49 206.0
20 TraesCS3D01G463200 chr3B 79.245 212 30 11 1003 1207 749685597 749685393 5.490000e-28 135.0
21 TraesCS3D01G463200 chr3B 82.581 155 21 5 1059 1207 752920186 752920032 7.110000e-27 132.0
22 TraesCS3D01G463200 chr3B 85.965 114 14 1 1678 1791 756252286 756252175 1.540000e-23 121.0
23 TraesCS3D01G463200 chr3B 87.013 77 10 0 1062 1138 754502548 754502624 1.560000e-13 87.9
24 TraesCS3D01G463200 chr3B 98.000 50 1 0 3109 3158 755041867 755041916 1.560000e-13 87.9
25 TraesCS3D01G463200 chr6A 78.723 235 31 10 2073 2288 598563993 598564227 4.250000e-29 139.0
26 TraesCS3D01G463200 chr6A 77.872 235 33 11 2073 2288 598322193 598322427 9.190000e-26 128.0
27 TraesCS3D01G463200 chr6A 77.872 235 33 11 2073 2288 598456276 598456510 9.190000e-26 128.0


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 TraesCS3D01G463200 chr3B 754980653 754983810 3157 False 4868.0 4868 94.5440 1 3158 1 chr3B.!!$F3 3157
1 TraesCS3D01G463200 chr3D 567221972 567226643 4671 True 3056.5 5832 90.6685 1 3158 2 chr3D.!!$R3 3157
2 TraesCS3D01G463200 chr3A 701853930 701858716 4786 False 2628.5 4987 87.9680 1 3158 2 chr3A.!!$F2 3157
3 TraesCS3D01G463200 chr3A 700565526 700570291 4765 False 2541.0 4817 87.3545 1 3158 2 chr3A.!!$F1 3157
4 TraesCS3D01G463200 chr3A 699250314 699251507 1193 True 392.0 392 73.6110 1512 2680 1 chr3A.!!$R2 1168
5 TraesCS3D01G463200 chrUn 41108796 41111960 3164 True 4924.0 4924 94.8730 13 3158 1 chrUn.!!$R1 3145
6 TraesCS3D01G463200 chr3B 752121266 752122873 1607 True 490.0 490 73.3330 1062 2648 1 chr3B.!!$R2 1586
7 TraesCS3D01G463200 chr3B 752177022 752178208 1186 True 414.0 414 74.0230 1506 2680 1 chr3B.!!$R3 1174
8 TraesCS3D01G463200 chr3B 756182804 756185900 3096 True 257.5 309 81.6820 1701 2982 2 chr3B.!!$R6 1281

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
90 1769 1.078918 CAGGTCTTCATCGGCAGCA 60.079 57.895 0.0 0.0 0.00 4.41 F
1058 2746 2.125512 GTGCCTCTTCGCCACGAT 60.126 61.111 0.0 0.0 35.23 3.73 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1427 3136 0.108851 CCAATAACCGCAAGCCCAAC 60.109 55.000 0.0 0.0 0.00 3.77 R
2539 4727 3.251484 TGACTCAAGGAAGAGGGACATT 58.749 45.455 0.0 0.0 39.97 2.71 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
83 1762 1.225704 CCAGGGCCAGGTCTTCATC 59.774 63.158 6.18 0.00 0.00 2.92
85 1764 2.190578 GGGCCAGGTCTTCATCGG 59.809 66.667 4.39 0.00 0.00 4.18
90 1769 1.078918 CAGGTCTTCATCGGCAGCA 60.079 57.895 0.00 0.00 0.00 4.41
172 1852 4.111016 TTCGAGCGACGCACCGAT 62.111 61.111 28.43 8.10 42.26 4.18
202 1886 2.263077 GACGTCGTCAAGCTCATCATT 58.737 47.619 20.28 0.00 32.09 2.57
248 1932 5.450818 AGAGAGATAAGAGACAGTGTCCT 57.549 43.478 19.71 13.22 32.18 3.85
272 1956 3.181433 GCTAAGGGGCCACTAATTACCAT 60.181 47.826 8.71 0.00 0.00 3.55
473 2157 8.191110 AGAACCCCCAGTATCCTATATTAATCA 58.809 37.037 0.00 0.00 0.00 2.57
475 2159 8.766492 ACCCCCAGTATCCTATATTAATCAAA 57.234 34.615 0.00 0.00 0.00 2.69
619 2304 4.129380 GGGTAAACCGTGTCTTTGTTACT 58.871 43.478 0.00 0.00 36.71 2.24
700 2385 8.349983 GCTCTGTCAATAAGTGTTTCCTTTTAA 58.650 33.333 0.00 0.00 0.00 1.52
731 2416 7.534085 TTGTATATTTTCAAGTAGCAGTCGG 57.466 36.000 0.00 0.00 0.00 4.79
930 2617 2.243994 TCCCCTTTCTATCGTCTCCTCA 59.756 50.000 0.00 0.00 0.00 3.86
1058 2746 2.125512 GTGCCTCTTCGCCACGAT 60.126 61.111 0.00 0.00 35.23 3.73
1180 2868 4.410400 CTCCACCCGTGCCTTCCC 62.410 72.222 0.00 0.00 0.00 3.97
1278 2987 3.390521 CCGCCCAGCTCCACACTA 61.391 66.667 0.00 0.00 0.00 2.74
1346 3055 2.423660 CCTTCTCGTCCTCTCCAGGTAT 60.424 54.545 0.00 0.00 41.28 2.73
1386 3095 7.285401 ACACCATTGATTTCTCAGTTTGTAACT 59.715 33.333 0.00 0.00 44.06 2.24
1427 3136 4.256920 CTCCCCTTCAACAACTACATGAG 58.743 47.826 0.00 0.00 0.00 2.90
1496 3205 6.866179 GAGTATCGATTGTTACTTGAACGT 57.134 37.500 1.71 0.00 41.35 3.99
1865 3593 5.381757 TGGGTATTGCAGAACTACAAAAGT 58.618 37.500 0.00 0.00 41.49 2.66
2356 4516 1.928868 CTTTTCTTGGCACCCTGGAT 58.071 50.000 0.00 0.00 0.00 3.41
2719 4917 0.036952 TGTAGAGCAGCTTGAGCACC 60.037 55.000 5.70 0.00 45.16 5.01
2799 6339 4.486125 AGCAAACCAAACCTTTGTTCAT 57.514 36.364 0.00 0.00 36.45 2.57
2819 6430 7.438757 TGTTCATTGAATTTTGTGGAAGTCATG 59.561 33.333 1.78 0.00 34.14 3.07
2864 6479 5.335191 GCAAAGATTCCGCAATATCTTAGGG 60.335 44.000 0.00 0.00 39.53 3.53
2868 6483 5.998363 AGATTCCGCAATATCTTAGGGTTTC 59.002 40.000 0.00 0.00 0.00 2.78
2965 6580 4.396166 CCCTTGCAGATTTTATTCAGTCGT 59.604 41.667 0.00 0.00 0.00 4.34
3089 6704 1.206371 GCGGCTAGGTTAGAAAGACCA 59.794 52.381 0.00 0.00 39.71 4.02
3090 6705 2.158943 GCGGCTAGGTTAGAAAGACCAT 60.159 50.000 0.00 0.00 39.71 3.55
3104 6719 2.036098 CCATTGCCTGTCCCAGCA 59.964 61.111 0.00 0.00 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.607187 GTACTTCATGGACACCGTCAG 58.393 52.381 0.00 0.00 33.68 3.51
4 5 1.274167 GGTACTTCATGGACACCGTCA 59.726 52.381 0.00 0.00 33.68 4.35
83 1762 2.124193 TCCAATGGGATGCTGCCG 60.124 61.111 0.00 0.00 38.64 5.69
172 1852 3.964221 GACGACGTCGAGGCATGCA 62.964 63.158 41.52 0.00 43.02 3.96
202 1886 3.716872 AGAACTTCCCTCACTCTTTGGAA 59.283 43.478 0.00 0.00 35.64 3.53
272 1956 0.692476 CCCATCACCAGGAGTTGACA 59.308 55.000 0.00 0.00 0.00 3.58
338 2022 3.949754 TCTTCCTTGTATACGTCATCGGT 59.050 43.478 0.00 0.00 41.85 4.69
341 2025 7.426410 TCTGAATCTTCCTTGTATACGTCATC 58.574 38.462 0.00 0.00 0.00 2.92
345 2029 7.093902 TGTCTTCTGAATCTTCCTTGTATACGT 60.094 37.037 0.00 0.00 0.00 3.57
547 2231 2.406130 CTAAGTCCCGCGTGTGTTTTA 58.594 47.619 4.92 0.00 0.00 1.52
548 2232 1.223187 CTAAGTCCCGCGTGTGTTTT 58.777 50.000 4.92 0.00 0.00 2.43
556 2241 2.094338 GGATAATACCCTAAGTCCCGCG 60.094 54.545 0.00 0.00 0.00 6.46
619 2304 3.014304 ACTAGGCGTCTAGGAATGACA 57.986 47.619 26.79 0.00 45.50 3.58
727 2412 0.098728 CCATCCATTTCGTTGCCGAC 59.901 55.000 0.00 0.00 44.13 4.79
731 2416 2.250188 CGTTTCCATCCATTTCGTTGC 58.750 47.619 0.00 0.00 0.00 4.17
1153 2841 3.661648 GGGTGGAGGTGGCATGGT 61.662 66.667 0.00 0.00 0.00 3.55
1220 2908 5.394224 GGTGAGGATGTATTCTTCGTCTGAA 60.394 44.000 8.61 0.00 33.24 3.02
1278 2987 0.749454 GCCTTGTCAAGATGGGCGAT 60.749 55.000 14.42 0.00 33.30 4.58
1346 3055 5.372373 TCAATGGTGTCAGTCATGTTGTTA 58.628 37.500 0.00 0.00 0.00 2.41
1386 3095 0.313672 GCAAATTGACGAGTGGCCAA 59.686 50.000 7.24 0.00 0.00 4.52
1427 3136 0.108851 CCAATAACCGCAAGCCCAAC 60.109 55.000 0.00 0.00 0.00 3.77
1496 3205 5.961272 TCAGTCGTTTCATTGTAGCTATCA 58.039 37.500 0.00 0.00 0.00 2.15
1865 3593 4.994852 CGATACTTGAAGTTCCAAACCTCA 59.005 41.667 1.97 0.00 30.33 3.86
2356 4516 8.407832 CAACATACAGAATATTCATTTCAGCCA 58.592 33.333 17.56 0.00 0.00 4.75
2539 4727 3.251484 TGACTCAAGGAAGAGGGACATT 58.749 45.455 0.00 0.00 39.97 2.71
2799 6339 5.867903 ACCATGACTTCCACAAAATTCAA 57.132 34.783 0.00 0.00 0.00 2.69
2819 6430 5.828747 TGCACTGTCGAGTAGATATTAACC 58.171 41.667 3.79 0.00 0.00 2.85
2868 6483 6.764877 ACTATGTTCTATATTTTCGGTGCG 57.235 37.500 0.00 0.00 0.00 5.34
2908 6523 4.095782 GCATTCACCGTATACATTGTTGGT 59.904 41.667 3.32 0.00 0.00 3.67
3104 6719 7.218228 TCATCACAAGTTAATGTTGCAAGAT 57.782 32.000 2.67 2.67 0.00 2.40


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

AutoCloner maintained by Alex Coulton.