Multiple sequence alignment - TraesCS3D01G052300

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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 TraesCS3D01G052300 chr3D 100.000 3071 0 0 1 3071 21792058 21795128 0.000000e+00 5672.0
1 TraesCS3D01G052300 chr3D 85.647 1491 142 38 945 2410 21888387 21889830 0.000000e+00 1502.0
2 TraesCS3D01G052300 chr3A 94.046 2704 116 18 2 2678 31558206 31560891 0.000000e+00 4060.0
3 TraesCS3D01G052300 chr3A 85.705 1490 142 38 938 2410 31603448 31604883 0.000000e+00 1506.0
4 TraesCS3D01G052300 chr3A 94.798 346 15 2 2727 3071 31561054 31561397 1.250000e-148 536.0
5 TraesCS3D01G052300 chr3A 81.193 436 33 28 446 868 31603060 31603459 3.850000e-79 305.0
6 TraesCS3D01G052300 chr3A 97.222 36 1 0 2673 2708 31561026 31561061 9.190000e-06 62.1
7 TraesCS3D01G052300 chr3B 94.027 2344 88 30 1 2327 37969758 37972066 0.000000e+00 3506.0
8 TraesCS3D01G052300 chr3B 83.581 1748 176 56 513 2229 38793585 38795252 0.000000e+00 1535.0
9 TraesCS3D01G052300 chr3B 84.339 1143 112 33 1292 2410 38212450 38213549 0.000000e+00 1057.0
10 TraesCS3D01G052300 chr3B 84.339 1143 112 33 1292 2410 38309783 38310882 0.000000e+00 1057.0
11 TraesCS3D01G052300 chr3B 96.500 400 11 2 2673 3071 37972611 37973008 0.000000e+00 658.0
12 TraesCS3D01G052300 chr3B 95.263 380 14 1 2303 2678 37972097 37972476 1.580000e-167 599.0
13 TraesCS3D01G052300 chr3B 85.000 300 37 5 446 745 38211166 38211457 6.440000e-77 298.0
14 TraesCS3D01G052300 chr3B 85.000 300 37 5 446 745 38308609 38308900 6.440000e-77 298.0
15 TraesCS3D01G052300 chrUn 84.351 1457 146 34 981 2413 336370761 336369363 0.000000e+00 1352.0
16 TraesCS3D01G052300 chrUn 84.283 1457 147 34 981 2413 336373427 336372029 0.000000e+00 1347.0
17 TraesCS3D01G052300 chrUn 84.293 1146 113 33 1292 2413 341538639 341537537 0.000000e+00 1057.0
18 TraesCS3D01G052300 chrUn 84.293 1146 113 33 1292 2413 341541149 341540047 0.000000e+00 1057.0
19 TraesCS3D01G052300 chrUn 84.818 303 38 5 446 748 336371594 336371300 6.440000e-77 298.0
20 TraesCS3D01G052300 chrUn 84.818 303 38 5 446 748 336374260 336373966 6.440000e-77 298.0
21 TraesCS3D01G052300 chr5A 86.584 1051 115 15 979 2022 665443632 665444663 0.000000e+00 1136.0
22 TraesCS3D01G052300 chr4B 86.648 1056 105 21 979 2022 616967491 616968522 0.000000e+00 1136.0
23 TraesCS3D01G052300 chr4D 85.538 1051 117 15 979 2022 484620759 484621781 0.000000e+00 1066.0
24 TraesCS3D01G052300 chr7D 90.964 166 10 1 889 1054 460319605 460319445 5.160000e-53 219.0


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 TraesCS3D01G052300 chr3D 21792058 21795128 3070 False 5672.000000 5672 100.000000 1 3071 1 chr3D.!!$F1 3070
1 TraesCS3D01G052300 chr3D 21888387 21889830 1443 False 1502.000000 1502 85.647000 945 2410 1 chr3D.!!$F2 1465
2 TraesCS3D01G052300 chr3A 31558206 31561397 3191 False 1552.700000 4060 95.355333 2 3071 3 chr3A.!!$F1 3069
3 TraesCS3D01G052300 chr3A 31603060 31604883 1823 False 905.500000 1506 83.449000 446 2410 2 chr3A.!!$F2 1964
4 TraesCS3D01G052300 chr3B 37969758 37973008 3250 False 1587.666667 3506 95.263333 1 3071 3 chr3B.!!$F2 3070
5 TraesCS3D01G052300 chr3B 38793585 38795252 1667 False 1535.000000 1535 83.581000 513 2229 1 chr3B.!!$F1 1716
6 TraesCS3D01G052300 chr3B 38211166 38213549 2383 False 677.500000 1057 84.669500 446 2410 2 chr3B.!!$F3 1964
7 TraesCS3D01G052300 chr3B 38308609 38310882 2273 False 677.500000 1057 84.669500 446 2410 2 chr3B.!!$F4 1964
8 TraesCS3D01G052300 chrUn 341537537 341541149 3612 True 1057.000000 1057 84.293000 1292 2413 2 chrUn.!!$R2 1121
9 TraesCS3D01G052300 chrUn 336369363 336374260 4897 True 823.750000 1352 84.567500 446 2413 4 chrUn.!!$R1 1967
10 TraesCS3D01G052300 chr5A 665443632 665444663 1031 False 1136.000000 1136 86.584000 979 2022 1 chr5A.!!$F1 1043
11 TraesCS3D01G052300 chr4B 616967491 616968522 1031 False 1136.000000 1136 86.648000 979 2022 1 chr4B.!!$F1 1043
12 TraesCS3D01G052300 chr4D 484620759 484621781 1022 False 1066.000000 1066 85.538000 979 2022 1 chr4D.!!$F1 1043

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
318 319 0.652592 CAGGGAATCGCGATCAACAC 59.347 55.0 23.92 17.28 0.0 3.32 F
977 4055 0.673985 GAACACCAGGCCAAGAAACC 59.326 55.0 5.01 0.00 0.0 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1806 5024 1.853963 ACTGCTTCTCCTGACCGTAT 58.146 50.000 0.00 0.0 0.0 3.06 R
2668 6002 6.599638 GCAAGATCTTAAACAATAGGGTGAGT 59.400 38.462 7.86 0.0 0.0 3.41 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
51 52 7.516198 AGAAAGAACAAAGTGCATGACTAAT 57.484 32.000 0.00 0.00 33.09 1.73
63 64 6.156949 AGTGCATGACTAATAAGAAGGAAGGA 59.843 38.462 0.00 0.00 30.86 3.36
132 133 4.159377 TGTTTTTCACATTCTCGGATGC 57.841 40.909 0.00 0.00 0.00 3.91
148 149 3.434641 CGGATGCATGACTATGACCAATC 59.565 47.826 2.46 0.00 36.36 2.67
305 306 8.933653 AGAAAATCCAAATAGTTTTTCAGGGAA 58.066 29.630 9.00 0.00 39.42 3.97
309 310 5.102313 CCAAATAGTTTTTCAGGGAATCGC 58.898 41.667 0.00 0.00 0.00 4.58
311 312 2.178912 AGTTTTTCAGGGAATCGCGA 57.821 45.000 13.09 13.09 0.00 5.87
318 319 0.652592 CAGGGAATCGCGATCAACAC 59.347 55.000 23.92 17.28 0.00 3.32
327 328 3.780902 TCGCGATCAACACATACAGAAT 58.219 40.909 3.71 0.00 0.00 2.40
336 337 5.344933 TCAACACATACAGAATTTCGACGAG 59.655 40.000 0.00 0.00 0.00 4.18
404 405 7.081349 CGTATGAGAATTTAAACAAACCAGCA 58.919 34.615 0.00 0.00 0.00 4.41
467 481 8.333235 ACAATTTACTCATTCCTGTGGGTTATA 58.667 33.333 0.00 0.00 34.02 0.98
653 3351 6.015918 TCCACCATCACTTCAAATTAACCAT 58.984 36.000 0.00 0.00 0.00 3.55
952 4030 1.085893 CAAGCACACAGACACACACA 58.914 50.000 0.00 0.00 0.00 3.72
974 4052 1.140312 AGAGAACACCAGGCCAAGAA 58.860 50.000 5.01 0.00 0.00 2.52
975 4053 1.494721 AGAGAACACCAGGCCAAGAAA 59.505 47.619 5.01 0.00 0.00 2.52
976 4054 1.609072 GAGAACACCAGGCCAAGAAAC 59.391 52.381 5.01 0.00 0.00 2.78
977 4055 0.673985 GAACACCAGGCCAAGAAACC 59.326 55.000 5.01 0.00 0.00 3.27
1352 4570 2.359975 CGCCACCAACTTCCCCTC 60.360 66.667 0.00 0.00 0.00 4.30
1806 5024 2.355837 GTGTTCTCGTGCTCGGCA 60.356 61.111 8.49 0.54 37.69 5.69
1986 5207 3.077556 GAGAAGAGGGGGCGAGCA 61.078 66.667 0.00 0.00 0.00 4.26
2124 5369 3.196901 GGTTCTCCTCCCTCTTTCTTCTC 59.803 52.174 0.00 0.00 0.00 2.87
2212 5474 4.614535 GCGTAGAACTCGTTCTTAAGTCCA 60.615 45.833 16.55 0.00 46.95 4.02
2668 6002 7.881751 GGATCTTGGATATGATTGAACATCTCA 59.118 37.037 0.00 0.00 0.00 3.27
2871 6345 7.667043 TTGAGTTATGTAACAATCTGACCAC 57.333 36.000 5.77 0.00 38.62 4.16
2883 6357 7.149569 ACAATCTGACCACATTGTTATTGAG 57.850 36.000 0.00 0.00 33.96 3.02
2976 6450 7.726216 TGAGCCATAAGAGATTTATTCGAAGA 58.274 34.615 3.35 0.00 0.00 2.87
2977 6451 8.204160 TGAGCCATAAGAGATTTATTCGAAGAA 58.796 33.333 3.35 1.66 45.90 2.52
2978 6452 8.964476 AGCCATAAGAGATTTATTCGAAGAAA 57.036 30.769 19.21 19.21 45.90 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 3.703001 TTCTTGCTAGGACCTTCCTTG 57.297 47.619 0.00 0.00 46.91 3.61
120 121 4.388165 GTCATAGTCATGCATCCGAGAATG 59.612 45.833 0.00 0.00 31.73 2.67
280 281 9.725019 ATTCCCTGAAAAACTATTTGGATTTTC 57.275 29.630 0.00 0.00 40.46 2.29
293 294 2.418628 TGATCGCGATTCCCTGAAAAAC 59.581 45.455 24.55 6.06 0.00 2.43
305 306 3.436700 TCTGTATGTGTTGATCGCGAT 57.563 42.857 23.97 23.97 0.00 4.58
309 310 6.178507 GTCGAAATTCTGTATGTGTTGATCG 58.821 40.000 0.00 0.00 0.00 3.69
311 312 5.867174 TCGTCGAAATTCTGTATGTGTTGAT 59.133 36.000 0.00 0.00 0.00 2.57
318 319 4.096311 ACGTCTCGTCGAAATTCTGTATG 58.904 43.478 0.00 0.00 33.69 2.39
327 328 7.536964 TGTTACAATAATAACGTCTCGTCGAAA 59.463 33.333 0.00 0.00 39.99 3.46
336 337 6.255887 AGCAGCTCTGTTACAATAATAACGTC 59.744 38.462 0.00 0.00 37.79 4.34
436 439 6.392354 CACAGGAATGAGTAAATTGTGCATT 58.608 36.000 0.00 0.00 32.36 3.56
467 481 6.590234 TGTAGTACAACATGATGTCTGTCT 57.410 37.500 12.36 9.36 34.75 3.41
653 3351 3.348119 TGGCGGCATATTTAGTTTGTGA 58.652 40.909 7.97 0.00 0.00 3.58
952 4030 1.352622 TTGGCCTGGTGTTCTCTGGT 61.353 55.000 3.32 0.00 0.00 4.00
974 4052 1.136891 GTTGCTTTTCTGTGGCTGGTT 59.863 47.619 0.00 0.00 0.00 3.67
975 4053 0.746659 GTTGCTTTTCTGTGGCTGGT 59.253 50.000 0.00 0.00 0.00 4.00
976 4054 0.032540 GGTTGCTTTTCTGTGGCTGG 59.967 55.000 0.00 0.00 0.00 4.85
977 4055 0.746063 TGGTTGCTTTTCTGTGGCTG 59.254 50.000 0.00 0.00 0.00 4.85
1806 5024 1.853963 ACTGCTTCTCCTGACCGTAT 58.146 50.000 0.00 0.00 0.00 3.06
2124 5369 8.281893 TCAACATATATCATGCATGTAACAACG 58.718 33.333 25.43 12.51 32.70 4.10
2329 5658 8.472413 AGAATGGAATTTATTGATGTGTCAAGG 58.528 33.333 0.00 0.00 41.68 3.61
2668 6002 6.599638 GCAAGATCTTAAACAATAGGGTGAGT 59.400 38.462 7.86 0.00 0.00 3.41
2883 6357 6.695278 TGCTGTTTACACTAAAACAAATCTGC 59.305 34.615 4.00 4.33 45.88 4.26
2978 6452 9.480053 CAAACACAGATGGTATTCAATCTTTTT 57.520 29.630 0.00 0.00 0.00 1.94
2998 6472 5.698832 TCTTACTTGTATGCATGCAAACAC 58.301 37.500 26.87 21.63 32.12 3.32


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

AutoCloner maintained by Alex Coulton.