Multiple sequence alignment - TraesCS3B01G131600

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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 TraesCS3B01G131600 chr3B 100.000 2420 0 0 1 2420 113929391 113931810 0.000000e+00 4470
1 TraesCS3B01G131600 chr3B 84.150 347 48 6 714 1057 116390560 116390218 1.790000e-86 329
2 TraesCS3B01G131600 chr3B 82.659 346 53 6 714 1056 116438025 116437684 1.410000e-77 300
3 TraesCS3B01G131600 chr3B 91.837 147 6 3 667 807 113929813 113929667 1.470000e-47 200
4 TraesCS3B01G131600 chr3B 91.837 147 6 3 277 423 113930197 113930057 1.470000e-47 200
5 TraesCS3B01G131600 chr3B 73.668 319 60 17 714 1028 182203232 182203530 4.260000e-18 102
6 TraesCS3B01G131600 chr3A 93.091 2475 88 26 1 2420 80101787 80104233 0.000000e+00 3546
7 TraesCS3B01G131600 chr3A 81.556 347 55 7 714 1056 82744567 82744226 6.590000e-71 278
8 TraesCS3B01G131600 chr3A 91.429 140 10 1 670 807 80102230 80102091 8.830000e-45 191
9 TraesCS3B01G131600 chr3A 75.235 319 55 18 714 1028 79875911 79875613 1.950000e-26 130
10 TraesCS3B01G131600 chr3A 75.329 304 56 14 728 1028 79905458 79905171 7.020000e-26 128
11 TraesCS3B01G131600 chr3D 95.000 1580 38 14 1 1546 68072999 68071427 0.000000e+00 2442
12 TraesCS3B01G131600 chr3D 96.214 1083 26 4 1171 2251 68071402 68070333 0.000000e+00 1759
13 TraesCS3B01G131600 chr3D 84.348 345 49 5 714 1056 71116343 71116002 1.390000e-87 333
14 TraesCS3B01G131600 chr3D 97.059 170 5 0 2251 2420 68070298 68070129 1.090000e-73 287
15 TraesCS3B01G131600 chr3D 91.216 148 6 2 667 807 68072548 68072695 6.830000e-46 195
16 TraesCS3B01G131600 chr2B 96.059 203 4 2 1811 2011 557352276 557352076 6.450000e-86 327


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 TraesCS3B01G131600 chr3B 113929391 113931810 2419 False 4470 4470 100.000 1 2420 1 chr3B.!!$F1 2419
1 TraesCS3B01G131600 chr3A 80101787 80104233 2446 False 3546 3546 93.091 1 2420 1 chr3A.!!$F1 2419
2 TraesCS3B01G131600 chr3D 68070129 68072999 2870 True 1496 2442 96.091 1 2420 3 chr3D.!!$R2 2419

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
917 959 3.884037 ATCACTTCCCATAACATCCCC 57.116 47.619 0.0 0.0 0.0 4.81 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2328 2810 2.353889 TGGTCGAGCGTCATACTACTTC 59.646 50.0 10.46 0.0 0.0 3.01 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
78 87 7.000472 ACAAATGCATTATGTAGCTATCTGGT 59.000 34.615 13.39 0.00 0.00 4.00
283 320 9.018582 CCAGGATCCATTATTCTCCTTTTAATC 57.981 37.037 15.82 0.00 35.95 1.75
439 481 6.742109 TCATCTGCTCCTTTTTGAAGAAAAG 58.258 36.000 4.66 4.66 37.08 2.27
443 485 5.351458 TGCTCCTTTTTGAAGAAAAGAAGC 58.649 37.500 13.35 13.35 39.04 3.86
596 638 9.172820 CAATTTCGTATCAACATTGGTGATATG 57.827 33.333 27.38 27.38 34.55 1.78
602 644 7.643764 CGTATCAACATTGGTGATATGTTTTCC 59.356 37.037 25.91 13.10 42.02 3.13
696 738 7.164122 TGAATTACTGCCAAATTTTATGCCAA 58.836 30.769 0.00 0.00 0.00 4.52
917 959 3.884037 ATCACTTCCCATAACATCCCC 57.116 47.619 0.00 0.00 0.00 4.81
1169 1211 2.098117 GGGAAATCATTGAGAACCAGCG 59.902 50.000 0.00 0.00 0.00 5.18
1376 1818 1.863155 ATCCCCACCACCCATGTCAC 61.863 60.000 0.00 0.00 0.00 3.67
1479 1921 5.951747 AGCAACAAAATATACCACATGGAGT 59.048 36.000 4.53 0.00 38.94 3.85
1519 1961 2.860679 TGATGGTGTACCTACCCCTCTA 59.139 50.000 2.32 0.00 40.09 2.43
1549 1991 2.520260 GCATCCCCACATGGCCTC 60.520 66.667 3.32 0.00 0.00 4.70
1566 2008 2.560542 GCCTCAGAGAAGACAAGACTCA 59.439 50.000 0.00 0.00 33.69 3.41
1656 2098 3.853831 ATGCAAGATTTGTGATCGCAA 57.146 38.095 17.57 17.57 0.00 4.85
1668 2110 4.565022 TGTGATCGCAAGTTCAACTCATA 58.435 39.130 6.47 0.00 46.62 2.15
1845 2287 3.994392 TCGCAAGTGGAGAAAGTCATTAC 59.006 43.478 0.00 0.00 39.48 1.89
1992 2434 7.986085 AATTAGTGGACTCATATATGGTTGC 57.014 36.000 12.78 6.05 0.00 4.17
2068 2512 7.640597 TCAATGAAGGTTCGTTAGATCTAGA 57.359 36.000 2.02 0.00 34.81 2.43
2139 2586 9.400638 CCGTTTCAAAATAGTTTGCTATGTAAA 57.599 29.630 10.71 2.85 43.30 2.01
2144 2591 9.891828 TCAAAATAGTTTGCTATGTAAAGTGTG 57.108 29.630 10.71 0.00 43.30 3.82
2145 2592 9.891828 CAAAATAGTTTGCTATGTAAAGTGTGA 57.108 29.630 2.29 0.00 37.89 3.58
2148 2595 6.500684 AGTTTGCTATGTAAAGTGTGATGG 57.499 37.500 0.00 0.00 0.00 3.51
2232 2679 3.449018 GTGGACTGACACATACTCCTCAT 59.551 47.826 0.00 0.00 40.99 2.90
2367 2849 4.279420 CGACCACCATTCTCTCTATCATCA 59.721 45.833 0.00 0.00 0.00 3.07
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
102 111 9.093458 GGAATATATTGGGAATTCATGGAAACT 57.907 33.333 7.93 0.00 32.42 2.66
218 227 9.236006 GAGAGAGAGAGAGAGCAAGAAATATAT 57.764 37.037 0.00 0.00 0.00 0.86
219 228 8.439971 AGAGAGAGAGAGAGAGCAAGAAATATA 58.560 37.037 0.00 0.00 0.00 0.86
220 229 7.293073 AGAGAGAGAGAGAGAGCAAGAAATAT 58.707 38.462 0.00 0.00 0.00 1.28
222 231 5.513233 AGAGAGAGAGAGAGAGCAAGAAAT 58.487 41.667 0.00 0.00 0.00 2.17
223 232 4.922206 AGAGAGAGAGAGAGAGCAAGAAA 58.078 43.478 0.00 0.00 0.00 2.52
226 235 3.209410 GGAGAGAGAGAGAGAGAGCAAG 58.791 54.545 0.00 0.00 0.00 4.01
227 236 2.092429 GGGAGAGAGAGAGAGAGAGCAA 60.092 54.545 0.00 0.00 0.00 3.91
229 238 1.202818 GGGGAGAGAGAGAGAGAGAGC 60.203 61.905 0.00 0.00 0.00 4.09
283 320 9.295214 CTCCTAGATATTGCATGAATAGTAACG 57.705 37.037 0.00 0.00 29.78 3.18
365 407 8.545472 AGATGGCAAGTATTAGTTTACCAGTTA 58.455 33.333 0.00 0.00 0.00 2.24
366 408 7.402862 AGATGGCAAGTATTAGTTTACCAGTT 58.597 34.615 0.00 0.00 0.00 3.16
367 409 6.958767 AGATGGCAAGTATTAGTTTACCAGT 58.041 36.000 0.00 0.00 0.00 4.00
368 410 7.865706 AAGATGGCAAGTATTAGTTTACCAG 57.134 36.000 0.00 0.00 0.00 4.00
452 494 5.416013 GGTCCAAGCTACTATTTGCTTCTTT 59.584 40.000 0.00 0.00 46.29 2.52
569 611 6.567687 TCACCAATGTTGATACGAAATTGT 57.432 33.333 0.00 0.00 0.00 2.71
596 638 4.998033 ACTCGATCTTGGAAGAAGGAAAAC 59.002 41.667 0.00 0.00 38.77 2.43
602 644 4.448537 AGTCACTCGATCTTGGAAGAAG 57.551 45.455 0.00 0.00 38.77 2.85
696 738 8.823220 ATTGGTAAACTAATACTTGCCATCTT 57.177 30.769 0.00 0.00 37.19 2.40
917 959 6.923508 TGTAGCGATAGTGTTTATTCTGATGG 59.076 38.462 0.00 0.00 39.35 3.51
1051 1093 2.104792 GTGCTGATAGGGCTACATTGGA 59.895 50.000 0.00 0.00 0.00 3.53
1099 1141 5.140454 GTTGGCCATGGATAAAGGAGTAAT 58.860 41.667 18.40 0.00 0.00 1.89
1169 1211 6.663944 AAGCTTGGTACGATAACATTTCTC 57.336 37.500 0.00 0.00 0.00 2.87
1355 1797 2.284515 GACATGGGTGGTGGGGATCC 62.285 65.000 1.92 1.92 0.00 3.36
1376 1818 3.446161 TGATGGTAGTGAGTTTACCTCGG 59.554 47.826 3.40 0.00 43.64 4.63
1479 1921 2.771372 TCAGTAGCATCATGGGTTAGCA 59.229 45.455 0.00 0.00 0.00 3.49
1549 1991 7.424803 CACCTATATGAGTCTTGTCTTCTCTG 58.575 42.308 0.00 0.00 0.00 3.35
1566 2008 2.441750 ACGACATTTGGGCCACCTATAT 59.558 45.455 5.23 0.00 37.76 0.86
1656 2098 6.126652 ACCATAGGCTTGATATGAGTTGAACT 60.127 38.462 0.00 0.00 33.30 3.01
1668 2110 1.915489 TGTGACCACCATAGGCTTGAT 59.085 47.619 0.00 0.00 0.00 2.57
2129 2576 6.653020 AGATTCCATCACACTTTACATAGCA 58.347 36.000 0.00 0.00 0.00 3.49
2139 2586 8.757982 AAAATATGCTAAGATTCCATCACACT 57.242 30.769 0.00 0.00 0.00 3.55
2140 2587 8.078596 GGAAAATATGCTAAGATTCCATCACAC 58.921 37.037 0.00 0.00 37.02 3.82
2141 2588 8.000709 AGGAAAATATGCTAAGATTCCATCACA 58.999 33.333 11.77 0.00 38.99 3.58
2142 2589 8.401490 AGGAAAATATGCTAAGATTCCATCAC 57.599 34.615 11.77 0.00 38.99 3.06
2146 2593 8.836413 CGTTTAGGAAAATATGCTAAGATTCCA 58.164 33.333 11.77 0.00 42.10 3.53
2147 2594 9.052759 TCGTTTAGGAAAATATGCTAAGATTCC 57.947 33.333 0.00 0.00 42.10 3.01
2328 2810 2.353889 TGGTCGAGCGTCATACTACTTC 59.646 50.000 10.46 0.00 0.00 3.01
2367 2849 3.319689 CACGTTGGTTCCATAGGGTTTTT 59.680 43.478 0.00 0.00 34.93 1.94


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

AutoCloner maintained by Alex Coulton.