Multiple sequence alignment - TraesCS3A01G320000

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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 TraesCS3A01G320000 chr3A 100.000 2657 0 0 1 2657 562572305 562569649 0.000000e+00 4907.0
1 TraesCS3A01G320000 chr3A 100.000 329 0 0 2788 3116 562569518 562569190 2.660000e-170 608.0
2 TraesCS3A01G320000 chr3A 78.678 469 62 25 41 498 535572979 535573420 8.510000e-71 278.0
3 TraesCS3A01G320000 chr3A 75.789 380 69 19 164 530 535573068 535573437 1.490000e-38 171.0
4 TraesCS3A01G320000 chr3B 97.847 1347 17 5 833 2173 555925735 555927075 0.000000e+00 2316.0
5 TraesCS3A01G320000 chr3B 97.179 1347 26 5 833 2173 555736960 555738300 0.000000e+00 2266.0
6 TraesCS3A01G320000 chr3B 96.499 457 16 0 2197 2653 555927638 555928094 0.000000e+00 756.0
7 TraesCS3A01G320000 chr3B 95.415 458 20 1 2197 2653 555738863 555739320 0.000000e+00 728.0
8 TraesCS3A01G320000 chr3B 92.593 216 13 2 2789 3004 555739342 555739554 1.090000e-79 307.0
9 TraesCS3A01G320000 chr3B 92.308 143 8 2 2862 3004 556006404 556006543 1.900000e-47 200.0
10 TraesCS3A01G320000 chr3B 97.368 114 3 0 3003 3116 556008867 556008980 8.820000e-46 195.0
11 TraesCS3A01G320000 chr3B 88.696 115 9 3 3002 3116 556007166 556007276 1.510000e-28 137.0
12 TraesCS3A01G320000 chr3B 87.931 116 10 3 3001 3116 555740162 555740273 1.950000e-27 134.0
13 TraesCS3A01G320000 chr3B 95.181 83 4 0 2789 2871 555928119 555928201 7.010000e-27 132.0
14 TraesCS3A01G320000 chr3B 100.000 28 0 0 2173 2200 555927093 555927120 6.000000e-03 52.8
15 TraesCS3A01G320000 chr2A 93.649 803 26 10 1 780 281880145 281879345 0.000000e+00 1177.0
16 TraesCS3A01G320000 chr2A 81.835 1101 148 23 1066 2115 52568402 52567303 0.000000e+00 878.0
17 TraesCS3A01G320000 chr2A 88.208 212 22 3 839 1048 52568660 52568450 1.860000e-62 250.0
18 TraesCS3A01G320000 chr2B 83.703 1172 139 27 839 1967 79704728 79703566 0.000000e+00 1059.0
19 TraesCS3A01G320000 chr2B 84.069 929 114 20 1061 1967 79702775 79701859 0.000000e+00 865.0
20 TraesCS3A01G320000 chr2B 76.642 411 59 24 207 595 678009767 678010162 3.170000e-45 193.0
21 TraesCS3A01G320000 chr2B 79.447 253 42 9 174 422 214128281 214128527 1.490000e-38 171.0
22 TraesCS3A01G320000 chr6A 87.167 826 35 21 1 780 33169697 33168897 0.000000e+00 872.0
23 TraesCS3A01G320000 chr6A 77.914 489 78 26 122 593 18471113 18471588 8.510000e-71 278.0
24 TraesCS3A01G320000 chr6A 76.978 278 43 18 41 306 18469993 18470261 4.190000e-29 139.0
25 TraesCS3A01G320000 chr6D 85.821 804 46 33 1 739 422942869 422942069 0.000000e+00 791.0
26 TraesCS3A01G320000 chr7D 83.397 789 79 24 1 780 209830829 209830084 0.000000e+00 684.0
27 TraesCS3A01G320000 chr7D 78.723 470 61 27 41 498 87368045 87368487 8.510000e-71 278.0
28 TraesCS3A01G320000 chr7D 97.500 40 1 0 1 40 87367976 87368015 5.580000e-08 69.4
29 TraesCS3A01G320000 chr1D 77.924 607 76 40 32 598 31670004 31669416 3.000000e-85 326.0
30 TraesCS3A01G320000 chr5A 79.904 418 61 20 191 595 436818604 436818197 5.090000e-73 285.0
31 TraesCS3A01G320000 chr7A 77.586 406 62 21 205 595 630620499 630620108 5.230000e-53 219.0
32 TraesCS3A01G320000 chr7A 75.000 408 77 22 163 559 148496945 148497338 6.910000e-37 165.0
33 TraesCS3A01G320000 chr3D 98.198 111 2 0 3001 3111 425461154 425461044 8.820000e-46 195.0
34 TraesCS3A01G320000 chr3D 91.667 84 3 3 3029 3112 425463301 425463222 2.540000e-21 113.0
35 TraesCS3A01G320000 chr4B 75.399 439 76 24 169 595 547312393 547311975 1.910000e-42 183.0
36 TraesCS3A01G320000 chr5B 80.385 260 32 15 345 594 398151076 398151326 2.470000e-41 180.0
37 TraesCS3A01G320000 chr1B 79.915 234 29 14 366 589 386199622 386199847 4.160000e-34 156.0


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 TraesCS3A01G320000 chr3A 562569190 562572305 3115 True 2757.50 4907 100.00000 1 3116 2 chr3A.!!$R1 3115
1 TraesCS3A01G320000 chr3B 555736960 555740273 3313 False 858.75 2266 93.27950 833 3116 4 chr3B.!!$F1 2283
2 TraesCS3A01G320000 chr3B 555925735 555928201 2466 False 814.20 2316 97.38175 833 2871 4 chr3B.!!$F2 2038
3 TraesCS3A01G320000 chr2A 281879345 281880145 800 True 1177.00 1177 93.64900 1 780 1 chr2A.!!$R1 779
4 TraesCS3A01G320000 chr2A 52567303 52568660 1357 True 564.00 878 85.02150 839 2115 2 chr2A.!!$R2 1276
5 TraesCS3A01G320000 chr2B 79701859 79704728 2869 True 962.00 1059 83.88600 839 1967 2 chr2B.!!$R1 1128
6 TraesCS3A01G320000 chr6A 33168897 33169697 800 True 872.00 872 87.16700 1 780 1 chr6A.!!$R1 779
7 TraesCS3A01G320000 chr6A 18469993 18471588 1595 False 208.50 278 77.44600 41 593 2 chr6A.!!$F1 552
8 TraesCS3A01G320000 chr6D 422942069 422942869 800 True 791.00 791 85.82100 1 739 1 chr6D.!!$R1 738
9 TraesCS3A01G320000 chr7D 209830084 209830829 745 True 684.00 684 83.39700 1 780 1 chr7D.!!$R1 779
10 TraesCS3A01G320000 chr1D 31669416 31670004 588 True 326.00 326 77.92400 32 598 1 chr1D.!!$R1 566

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
831 2076 1.48424 AGATCCTCTTTCCTTCCTGCG 59.516 52.381 0.0 0.0 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2807 5439 0.112606 AACCTGACCGTCTGAGAGGA 59.887 55.0 3.35 0.0 0.0 3.71 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
161 1210 8.783093 ACTAATTTGAGAACATTCATCGTTTCA 58.217 29.630 0.00 0.00 0.00 2.69
694 1939 3.250744 CAGTGAGATCGCGACCTAAAAA 58.749 45.455 12.93 0.00 0.00 1.94
770 2015 2.553602 CAGTGTGCTGCATCCTTAAACA 59.446 45.455 5.27 0.00 35.77 2.83
780 2025 4.476846 TGCATCCTTAAACAAGGGATCCTA 59.523 41.667 12.58 0.00 40.38 2.94
781 2026 5.134339 TGCATCCTTAAACAAGGGATCCTAT 59.866 40.000 12.58 0.00 40.38 2.57
782 2027 6.331572 TGCATCCTTAAACAAGGGATCCTATA 59.668 38.462 12.58 0.00 40.38 1.31
783 2028 6.881602 GCATCCTTAAACAAGGGATCCTATAG 59.118 42.308 12.58 2.14 40.38 1.31
784 2029 7.398024 CATCCTTAAACAAGGGATCCTATAGG 58.602 42.308 13.07 13.07 40.38 2.57
785 2030 6.699688 TCCTTAAACAAGGGATCCTATAGGA 58.300 40.000 23.76 23.76 43.45 2.94
786 2031 7.143741 TCCTTAAACAAGGGATCCTATAGGAA 58.856 38.462 25.20 9.29 42.98 3.36
787 2032 7.292591 TCCTTAAACAAGGGATCCTATAGGAAG 59.707 40.741 25.20 12.66 42.98 3.46
788 2033 7.474936 CCTTAAACAAGGGATCCTATAGGAAGG 60.475 44.444 25.20 17.35 40.91 3.46
799 2044 6.553554 TCCTATAGGAAGGAAAGAGGATCT 57.446 41.667 19.59 0.00 44.53 2.75
829 2074 8.409358 TTTTAAAAGATCCTCTTTCCTTCCTG 57.591 34.615 0.00 0.00 45.19 3.86
830 2075 3.643199 AAGATCCTCTTTCCTTCCTGC 57.357 47.619 0.00 0.00 31.57 4.85
831 2076 1.484240 AGATCCTCTTTCCTTCCTGCG 59.516 52.381 0.00 0.00 0.00 5.18
1058 2325 3.532155 GGCGGGGCACAACAACAA 61.532 61.111 0.00 0.00 0.00 2.83
1059 2326 2.279186 GCGGGGCACAACAACAAC 60.279 61.111 0.00 0.00 0.00 3.32
1060 2327 3.069980 GCGGGGCACAACAACAACA 62.070 57.895 0.00 0.00 0.00 3.33
1061 2328 1.513158 CGGGGCACAACAACAACAA 59.487 52.632 0.00 0.00 0.00 2.83
1135 2420 2.138320 CATCGATATGCGCCAAGACTT 58.862 47.619 4.18 0.00 40.61 3.01
1159 2444 1.866853 CGATCGATGGGGCGAGATGA 61.867 60.000 10.26 0.00 44.26 2.92
1819 3127 3.570212 ACAGTCAGTGCCCCACCC 61.570 66.667 0.00 0.00 34.49 4.61
2120 3473 2.233186 TCAAGTCTGTGCTCTGATGAGG 59.767 50.000 0.00 0.00 40.53 3.86
2390 5022 7.639039 CAGCTCACACTTCTGTAACAATAAAA 58.361 34.615 0.00 0.00 0.00 1.52
2474 5106 6.155827 TGAAACAAGGAAAACAACACTTCTG 58.844 36.000 0.00 0.00 0.00 3.02
2508 5140 7.957002 TGTTCTTCAGATCTCTTAGTTTGAGT 58.043 34.615 0.00 0.00 33.59 3.41
2511 5143 8.415950 TCTTCAGATCTCTTAGTTTGAGTTCT 57.584 34.615 0.00 0.00 39.68 3.01
2601 5233 5.045215 CACGACGCCTCCACTATTATTTTA 58.955 41.667 0.00 0.00 0.00 1.52
2807 5439 1.824230 TGGTTGCTTGCTGTTTCTTGT 59.176 42.857 0.00 0.00 0.00 3.16
2819 5451 2.035961 TGTTTCTTGTCCTCTCAGACGG 59.964 50.000 0.00 0.00 39.77 4.79
2820 5452 1.996798 TTCTTGTCCTCTCAGACGGT 58.003 50.000 0.00 0.00 39.77 4.83
2872 5504 5.765182 AGAGTTGTTGGGTGTGAATTTAGAG 59.235 40.000 0.00 0.00 0.00 2.43
2891 5523 1.750778 AGTTGTGGTGTTTTGCCAGAG 59.249 47.619 0.00 0.00 36.57 3.35
2930 5562 4.551388 CTTCGGAGGTAGCAATAGATGTC 58.449 47.826 0.00 0.00 0.00 3.06
2933 5565 3.305676 CGGAGGTAGCAATAGATGTCCTG 60.306 52.174 0.00 0.00 30.91 3.86
2967 5599 1.067071 AGTTCTCCGGTTCCAACGATC 60.067 52.381 0.00 0.00 0.00 3.69
2983 5615 5.287992 CCAACGATCGGTTCTTTAGTACTTC 59.712 44.000 20.98 0.00 36.49 3.01
2984 5616 5.893897 ACGATCGGTTCTTTAGTACTTCT 57.106 39.130 20.98 0.00 0.00 2.85
2985 5617 5.638783 ACGATCGGTTCTTTAGTACTTCTG 58.361 41.667 20.98 0.00 0.00 3.02
2986 5618 5.182760 ACGATCGGTTCTTTAGTACTTCTGT 59.817 40.000 20.98 0.00 0.00 3.41
2987 5619 6.372659 ACGATCGGTTCTTTAGTACTTCTGTA 59.627 38.462 20.98 0.00 0.00 2.74
3014 6257 9.468532 GTAGTTTATTATTACTAACCACCTCGG 57.531 37.037 0.00 0.00 42.50 4.63
3016 6259 8.931568 AGTTTATTATTACTAACCACCTCGGAT 58.068 33.333 0.00 0.00 38.63 4.18
3017 6260 9.551734 GTTTATTATTACTAACCACCTCGGATT 57.448 33.333 0.00 0.00 38.63 3.01
3028 6271 3.313526 CCACCTCGGATTGCTATTTGAAG 59.686 47.826 0.00 0.00 36.56 3.02
3073 6316 6.271488 TCATTGCTTGAGAAAACTAATGGG 57.729 37.500 0.00 0.00 0.00 4.00
3078 6321 4.021981 GCTTGAGAAAACTAATGGGCAACT 60.022 41.667 0.00 0.00 0.00 3.16
3095 6338 6.042093 TGGGCAACTTATGTTTTTATTCCACA 59.958 34.615 0.00 0.00 33.52 4.17
3096 6339 7.102993 GGGCAACTTATGTTTTTATTCCACAT 58.897 34.615 0.00 0.00 33.52 3.21
3097 6340 7.277760 GGGCAACTTATGTTTTTATTCCACATC 59.722 37.037 0.00 0.00 33.52 3.06
3098 6341 8.034804 GGCAACTTATGTTTTTATTCCACATCT 58.965 33.333 0.00 0.00 33.52 2.90
3109 6352 3.931907 TTCCACATCTATCACCCAAGG 57.068 47.619 0.00 0.00 0.00 3.61
3112 6355 2.483714 CCACATCTATCACCCAAGGACG 60.484 54.545 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
511 1677 9.874205 TGAACTTCTTTTCAAACTTGATGAATT 57.126 25.926 0.00 0.0 36.72 2.17
665 1910 2.950877 CGATCTCACTGGTTCGCTC 58.049 57.895 0.00 0.0 0.00 5.03
770 2015 6.056997 TCTTTCCTTCCTATAGGATCCCTT 57.943 41.667 22.30 0.0 43.66 3.95
812 2057 1.946745 CGCAGGAAGGAAAGAGGATC 58.053 55.000 0.00 0.0 0.00 3.36
827 2072 0.461870 TCCGATCAATCCAACCGCAG 60.462 55.000 0.00 0.0 0.00 5.18
828 2073 0.461870 CTCCGATCAATCCAACCGCA 60.462 55.000 0.00 0.0 0.00 5.69
829 2074 0.179084 TCTCCGATCAATCCAACCGC 60.179 55.000 0.00 0.0 0.00 5.68
830 2075 2.138320 CATCTCCGATCAATCCAACCG 58.862 52.381 0.00 0.0 0.00 4.44
831 2076 3.397482 CTCATCTCCGATCAATCCAACC 58.603 50.000 0.00 0.0 0.00 3.77
859 2104 2.360801 CACCAGGATGTTCAAAAACCGT 59.639 45.455 0.00 0.0 34.28 4.83
1056 2323 3.499918 ACATCGGCTTCTTCTTCTTGTTG 59.500 43.478 0.00 0.0 0.00 3.33
1057 2324 3.744660 ACATCGGCTTCTTCTTCTTGTT 58.255 40.909 0.00 0.0 0.00 2.83
1058 2325 3.409026 ACATCGGCTTCTTCTTCTTGT 57.591 42.857 0.00 0.0 0.00 3.16
1059 2326 7.358765 CGAATATACATCGGCTTCTTCTTCTTG 60.359 40.741 2.58 0.0 36.68 3.02
1060 2327 6.642950 CGAATATACATCGGCTTCTTCTTCTT 59.357 38.462 2.58 0.0 36.68 2.52
1061 2328 6.153067 CGAATATACATCGGCTTCTTCTTCT 58.847 40.000 2.58 0.0 36.68 2.85
1135 2420 2.852180 CGCCCCATCGATCGTACCA 61.852 63.158 15.94 0.0 0.00 3.25
1159 2444 3.795688 TTCAGTGAGAGGGAAGCAATT 57.204 42.857 0.00 0.0 0.00 2.32
1748 3050 0.460987 CCAGATTCGAGTGTGCTCCC 60.461 60.000 0.00 0.0 38.49 4.30
1819 3127 0.954452 GAACCCAGGCTGACAACTTG 59.046 55.000 17.94 0.0 0.00 3.16
2120 3473 4.061596 GGCCTGACAGCAGACTATTATTC 58.938 47.826 0.00 0.0 45.17 1.75
2474 5106 7.551035 AGAGATCTGAAGAACATATTTGCAC 57.449 36.000 0.00 0.0 0.00 4.57
2541 5173 1.204146 AAGGAAGGCCTATCTGCGAA 58.796 50.000 5.16 0.0 46.28 4.70
2601 5233 3.630312 ACTTAAACACAACACAAGCCGAT 59.370 39.130 0.00 0.0 0.00 4.18
2787 5419 1.824230 ACAAGAAACAGCAAGCAACCA 59.176 42.857 0.00 0.0 0.00 3.67
2807 5439 0.112606 AACCTGACCGTCTGAGAGGA 59.887 55.000 3.35 0.0 0.00 3.71
2819 5451 1.614317 CCCAATCCCAGACAACCTGAC 60.614 57.143 0.00 0.0 45.78 3.51
2820 5452 0.698238 CCCAATCCCAGACAACCTGA 59.302 55.000 0.00 0.0 45.78 3.86
2872 5504 1.748493 TCTCTGGCAAAACACCACAAC 59.252 47.619 0.00 0.0 32.49 3.32
2924 5556 2.952702 GCCTAGGACTGACAGGACATCT 60.953 54.545 14.75 0.0 0.00 2.90
2930 5562 0.681564 ACTCGCCTAGGACTGACAGG 60.682 60.000 14.75 0.0 0.00 4.00
2933 5565 1.402613 GAGAACTCGCCTAGGACTGAC 59.597 57.143 14.75 0.0 0.00 3.51
2967 5599 8.038492 ACTACTACAGAAGTACTAAAGAACCG 57.962 38.462 0.00 0.0 39.80 4.44
3073 6316 8.986477 AGATGTGGAATAAAAACATAAGTTGC 57.014 30.769 0.00 0.0 38.17 4.17
3089 6332 3.199946 GTCCTTGGGTGATAGATGTGGAA 59.800 47.826 0.00 0.0 0.00 3.53


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

AutoCloner maintained by Alex Coulton.