Multiple sequence alignment - TraesCS3B01G511000

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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 TraesCS3B01G511000 chr3B 100.000 3164 0 0 1 3164 754980655 754983818 0.000000e+00 5843.0
1 TraesCS3B01G511000 chr3B 73.665 1667 316 78 1062 2667 752122873 752121269 1.670000e-147 532.0
2 TraesCS3B01G511000 chr3B 73.953 1194 222 63 1518 2667 752178202 752177054 1.770000e-107 399.0
3 TraesCS3B01G511000 chr3B 76.423 615 114 24 1707 2311 756185900 756185307 1.430000e-78 303.0
4 TraesCS3B01G511000 chr3B 81.337 359 52 11 2803 3158 754971361 754971707 8.640000e-71 278.0
5 TraesCS3B01G511000 chr3B 85.027 187 27 1 2794 2980 756182989 756182804 4.170000e-44 189.0
6 TraesCS3B01G511000 chr3B 81.646 158 29 0 1059 1216 752920186 752920029 7.120000e-27 132.0
7 TraesCS3B01G511000 chr3B 78.140 215 39 6 1003 1216 749685597 749685390 2.560000e-26 130.0
8 TraesCS3B01G511000 chr3B 86.792 106 12 1 1692 1797 756252278 756252175 1.990000e-22 117.0
9 TraesCS3B01G511000 chr3B 100.000 55 0 0 3107 3161 755041867 755041921 5.580000e-18 102.0
10 TraesCS3B01G511000 chr3B 78.571 154 25 7 1062 1211 754502548 754502697 9.340000e-16 95.3
11 TraesCS3B01G511000 chrUn 95.359 3189 97 16 11 3164 41111960 41108788 0.000000e+00 5022.0
12 TraesCS3B01G511000 chr3D 94.554 3195 112 18 1 3164 567225127 567221964 0.000000e+00 4879.0
13 TraesCS3B01G511000 chr3D 81.267 363 53 12 2799 3158 567226642 567226292 2.400000e-71 279.0
14 TraesCS3B01G511000 chr3D 74.909 275 57 10 1523 1791 569517117 569517385 7.170000e-22 115.0
15 TraesCS3B01G511000 chr3D 74.194 310 57 16 1442 1739 564512859 564512561 1.200000e-19 108.0
16 TraesCS3B01G511000 chr3D 96.610 59 2 0 3106 3164 567217168 567217110 7.220000e-17 99.0
17 TraesCS3B01G511000 chr3D 86.667 75 8 2 1062 1135 565982602 565982675 7.270000e-12 82.4
18 TraesCS3B01G511000 chr3A 93.713 3197 143 18 1 3164 701855553 701858724 0.000000e+00 4737.0
19 TraesCS3B01G511000 chr3A 92.801 3209 152 22 1 3164 700567125 700570299 0.000000e+00 4573.0
20 TraesCS3B01G511000 chr3A 83.442 308 38 9 2853 3158 701853985 701854281 1.120000e-69 274.0
21 TraesCS3B01G511000 chr3A 80.465 215 34 6 1003 1216 697585522 697585315 1.170000e-34 158.0
22 TraesCS3B01G511000 chr5D 72.251 764 165 38 1779 2517 547932579 547931838 3.220000e-45 193.0
23 TraesCS3B01G511000 chr6A 81.590 239 36 6 2079 2313 598322193 598322427 1.160000e-44 191.0
24 TraesCS3B01G511000 chr6A 81.590 239 36 6 2079 2313 598456276 598456510 1.160000e-44 191.0
25 TraesCS3B01G511000 chr6A 81.172 239 37 6 2079 2313 598563993 598564227 5.390000e-43 185.0
26 TraesCS3B01G511000 chr6A 94.286 35 1 1 830 863 603926958 603926992 6.000000e-03 52.8
27 TraesCS3B01G511000 chr7B 94.643 56 3 0 3106 3161 611462382 611462437 1.560000e-13 87.9
28 TraesCS3B01G511000 chr5B 94.643 56 3 0 3106 3161 619014504 619014559 1.560000e-13 87.9
29 TraesCS3B01G511000 chr2B 94.643 56 3 0 3109 3164 726562746 726562691 1.560000e-13 87.9
30 TraesCS3B01G511000 chr2B 76.866 134 18 9 736 863 230886584 230886710 2.630000e-06 63.9
31 TraesCS3B01G511000 chr1A 81.707 82 12 3 783 863 581917505 581917426 7.330000e-07 65.8
32 TraesCS3B01G511000 chr2D 85.965 57 6 2 808 863 306770429 306770484 3.410000e-05 60.2
33 TraesCS3B01G511000 chr2A 81.081 74 11 3 791 863 418914387 418914316 4.410000e-04 56.5


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 TraesCS3B01G511000 chr3B 754980655 754983818 3163 False 5843.0 5843 100.0000 1 3164 1 chr3B.!!$F3 3163
1 TraesCS3B01G511000 chr3B 752121269 752122873 1604 True 532.0 532 73.6650 1062 2667 1 chr3B.!!$R2 1605
2 TraesCS3B01G511000 chr3B 752177054 752178202 1148 True 399.0 399 73.9530 1518 2667 1 chr3B.!!$R3 1149
3 TraesCS3B01G511000 chr3B 756182804 756185900 3096 True 246.0 303 80.7250 1707 2980 2 chr3B.!!$R6 1273
4 TraesCS3B01G511000 chrUn 41108788 41111960 3172 True 5022.0 5022 95.3590 11 3164 1 chrUn.!!$R1 3153
5 TraesCS3B01G511000 chr3D 567221964 567226642 4678 True 2579.0 4879 87.9105 1 3164 2 chr3D.!!$R3 3163
6 TraesCS3B01G511000 chr3A 700567125 700570299 3174 False 4573.0 4573 92.8010 1 3164 1 chr3A.!!$F1 3163
7 TraesCS3B01G511000 chr3A 701853985 701858724 4739 False 2505.5 4737 88.5775 1 3164 2 chr3A.!!$F2 3163

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
88 1741 1.078918 CAGGTCTTCATCGGCAGCA 60.079 57.895 0.0 0.0 0.00 4.41 F
1056 2719 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
1425 3109 0.108851 CCAATAACCGCAAGCCCAAC 60.109 55.0 0.0 0.0 0.0 3.77 R
2176 4287 1.131638 AGAAGCACCACCTCACTCAA 58.868 50.0 0.0 0.0 0.0 3.02 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
81 1734 1.225704 CCAGGGCCAGGTCTTCATC 59.774 63.158 6.18 0.00 0.00 2.92
83 1736 2.190578 GGGCCAGGTCTTCATCGG 59.809 66.667 4.39 0.00 0.00 4.18
88 1741 1.078918 CAGGTCTTCATCGGCAGCA 60.079 57.895 0.00 0.00 0.00 4.41
170 1824 4.111016 TTCGAGCGACGCACCGAT 62.111 61.111 28.43 8.10 42.26 4.18
200 1858 2.263077 GACGTCGTCAAGCTCATCATT 58.737 47.619 20.28 0.00 32.09 2.57
246 1904 5.450818 AGAGAGATAAGAGACAGTGTCCT 57.549 43.478 19.71 13.22 32.18 3.85
270 1928 3.181433 GCTAAGGGGCCACTAATTACCAT 60.181 47.826 8.71 0.00 0.00 3.55
471 2129 8.191110 AGAACCCCCAGTATCCTATATTAATCA 58.809 37.037 0.00 0.00 0.00 2.57
473 2131 8.766492 ACCCCCAGTATCCTATATTAATCAAA 57.234 34.615 0.00 0.00 0.00 2.69
617 2276 4.129380 GGGTAAACCGTGTCTTTGTTACT 58.871 43.478 0.00 0.00 36.71 2.24
698 2357 8.349983 GCTCTGTCAATAAGTGTTTCCTTTTAA 58.650 33.333 0.00 0.00 0.00 1.52
729 2388 7.534085 TTGTATATTTTCAAGTAGCAGTCGG 57.466 36.000 0.00 0.00 0.00 4.79
928 2590 2.243994 TCCCCTTTCTATCGTCTCCTCA 59.756 50.000 0.00 0.00 0.00 3.86
1056 2719 2.125512 GTGCCTCTTCGCCACGAT 60.126 61.111 0.00 0.00 35.23 3.73
1178 2841 4.410400 CTCCACCCGTGCCTTCCC 62.410 72.222 0.00 0.00 0.00 3.97
1276 2960 3.390521 CCGCCCAGCTCCACACTA 61.391 66.667 0.00 0.00 0.00 2.74
1344 3028 2.423660 CCTTCTCGTCCTCTCCAGGTAT 60.424 54.545 0.00 0.00 41.28 2.73
1384 3068 7.285401 ACACCATTGATTTCTCAGTTTGTAACT 59.715 33.333 0.00 0.00 44.06 2.24
1425 3109 4.256920 CTCCCCTTCAACAACTACATGAG 58.743 47.826 0.00 0.00 0.00 2.90
1494 3178 6.866179 GAGTATCGATTGTTACTTGAACGT 57.134 37.500 1.71 0.00 41.35 3.99
1513 3197 4.740268 ACGTGATAGCTACAATGAAACGA 58.260 39.130 0.00 0.00 33.10 3.85
1863 3566 5.381757 TGGGTATTGCAGAACTACAAAAGT 58.618 37.500 0.00 0.00 41.49 2.66
2014 3717 1.611977 CTGGTCGGTGTCTGTCTTACA 59.388 52.381 0.00 0.00 0.00 2.41
2174 4285 7.742767 TCACCATTCATCTGATGTCTATTGAT 58.257 34.615 16.66 0.34 0.00 2.57
2175 4286 8.873144 TCACCATTCATCTGATGTCTATTGATA 58.127 33.333 16.66 0.00 0.00 2.15
2176 4287 9.668497 CACCATTCATCTGATGTCTATTGATAT 57.332 33.333 16.66 0.00 0.00 1.63
2354 4492 1.928868 CTTTTCTTGGCACCCTGGAT 58.071 50.000 0.00 0.00 0.00 3.41
2717 4891 0.036952 TGTAGAGCAGCTTGAGCACC 60.037 55.000 5.70 0.00 45.16 5.01
2797 6313 4.486125 AGCAAACCAAACCTTTGTTCAT 57.514 36.364 0.00 0.00 36.45 2.57
2817 6404 7.438757 TGTTCATTGAATTTTGTGGAAGTCATG 59.561 33.333 1.78 0.00 34.14 3.07
2862 6453 5.335191 GCAAAGATTCCGCAATATCTTAGGG 60.335 44.000 0.00 0.00 39.53 3.53
2866 6457 5.998363 AGATTCCGCAATATCTTAGGGTTTC 59.002 40.000 0.00 0.00 0.00 2.78
2963 6554 4.396166 CCCTTGCAGATTTTATTCAGTCGT 59.604 41.667 0.00 0.00 0.00 4.34
3087 6678 1.206371 GCGGCTAGGTTAGAAAGACCA 59.794 52.381 0.00 0.00 39.71 4.02
3088 6679 2.158943 GCGGCTAGGTTAGAAAGACCAT 60.159 50.000 0.00 0.00 39.71 3.55
3102 6693 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
81 1734 2.124193 TCCAATGGGATGCTGCCG 60.124 61.111 0.00 0.00 38.64 5.69
170 1824 3.964221 GACGACGTCGAGGCATGCA 62.964 63.158 41.52 0.00 43.02 3.96
200 1858 3.716872 AGAACTTCCCTCACTCTTTGGAA 59.283 43.478 0.00 0.00 35.64 3.53
270 1928 0.692476 CCCATCACCAGGAGTTGACA 59.308 55.000 0.00 0.00 0.00 3.58
336 1994 3.949754 TCTTCCTTGTATACGTCATCGGT 59.050 43.478 0.00 0.00 41.85 4.69
339 1997 7.426410 TCTGAATCTTCCTTGTATACGTCATC 58.574 38.462 0.00 0.00 0.00 2.92
343 2001 7.093902 TGTCTTCTGAATCTTCCTTGTATACGT 60.094 37.037 0.00 0.00 0.00 3.57
545 2203 2.406130 CTAAGTCCCGCGTGTGTTTTA 58.594 47.619 4.92 0.00 0.00 1.52
546 2204 1.223187 CTAAGTCCCGCGTGTGTTTT 58.777 50.000 4.92 0.00 0.00 2.43
554 2213 2.094338 GGATAATACCCTAAGTCCCGCG 60.094 54.545 0.00 0.00 0.00 6.46
617 2276 3.014304 ACTAGGCGTCTAGGAATGACA 57.986 47.619 26.79 0.00 45.50 3.58
725 2384 0.098728 CCATCCATTTCGTTGCCGAC 59.901 55.000 0.00 0.00 44.13 4.79
729 2388 2.250188 CGTTTCCATCCATTTCGTTGC 58.750 47.619 0.00 0.00 0.00 4.17
1151 2814 3.661648 GGGTGGAGGTGGCATGGT 61.662 66.667 0.00 0.00 0.00 3.55
1218 2881 5.394224 GGTGAGGATGTATTCTTCGTCTGAA 60.394 44.000 8.61 0.00 33.24 3.02
1276 2960 0.749454 GCCTTGTCAAGATGGGCGAT 60.749 55.000 14.42 0.00 33.30 4.58
1344 3028 5.372373 TCAATGGTGTCAGTCATGTTGTTA 58.628 37.500 0.00 0.00 0.00 2.41
1384 3068 0.313672 GCAAATTGACGAGTGGCCAA 59.686 50.000 7.24 0.00 0.00 4.52
1425 3109 0.108851 CCAATAACCGCAAGCCCAAC 60.109 55.000 0.00 0.00 0.00 3.77
1494 3178 5.961272 TCAGTCGTTTCATTGTAGCTATCA 58.039 37.500 0.00 0.00 0.00 2.15
1513 3197 2.706190 AGTAGCCAAGTTGGTCTTCAGT 59.294 45.455 22.85 7.09 40.46 3.41
1863 3566 4.994852 CGATACTTGAAGTTCCAAACCTCA 59.005 41.667 1.97 0.00 30.33 3.86
2014 3717 6.604396 TCAATCAGCTTACCATCATTGTCAAT 59.396 34.615 0.00 0.00 0.00 2.57
2174 4285 2.906389 AGAAGCACCACCTCACTCAATA 59.094 45.455 0.00 0.00 0.00 1.90
2175 4286 1.701847 AGAAGCACCACCTCACTCAAT 59.298 47.619 0.00 0.00 0.00 2.57
2176 4287 1.131638 AGAAGCACCACCTCACTCAA 58.868 50.000 0.00 0.00 0.00 3.02
2177 4288 1.131638 AAGAAGCACCACCTCACTCA 58.868 50.000 0.00 0.00 0.00 3.41
2178 4289 2.966050 CTAAGAAGCACCACCTCACTC 58.034 52.381 0.00 0.00 0.00 3.51
2354 4492 8.407832 CAACATACAGAATATTCATTTCAGCCA 58.592 33.333 17.56 0.00 0.00 4.75
2537 4703 3.251484 TGACTCAAGGAAGAGGGACATT 58.749 45.455 0.00 0.00 39.97 2.71
2797 6313 5.867903 ACCATGACTTCCACAAAATTCAA 57.132 34.783 0.00 0.00 0.00 2.69
2817 6404 5.828747 TGCACTGTCGAGTAGATATTAACC 58.171 41.667 3.79 0.00 0.00 2.85
2866 6457 6.764877 ACTATGTTCTATATTTTCGGTGCG 57.235 37.500 0.00 0.00 0.00 5.34
2906 6497 4.095782 GCATTCACCGTATACATTGTTGGT 59.904 41.667 3.32 0.00 0.00 3.67
3102 6693 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.