Multiple sequence alignment - TraesCS3D01G250500

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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 TraesCS3D01G250500 chr3D 100.000 3393 0 0 1 3393 350798178 350794786 0.000000e+00 6266.0
1 TraesCS3D01G250500 chr3D 83.448 145 12 8 3234 3373 580620895 580621032 1.280000e-24 124.0
2 TraesCS3D01G250500 chr3B 92.677 3100 137 39 1 3086 449208535 449205512 0.000000e+00 4385.0
3 TraesCS3D01G250500 chr3B 80.000 230 30 12 3172 3393 12154632 12154853 4.530000e-34 156.0
4 TraesCS3D01G250500 chr3B 84.906 106 11 5 3289 3393 378334316 378334215 5.990000e-18 102.0
5 TraesCS3D01G250500 chr3A 94.630 2011 58 19 862 2857 468533632 468531657 0.000000e+00 3070.0
6 TraesCS3D01G250500 chr3A 89.855 552 36 5 2855 3393 468519191 468518647 0.000000e+00 691.0
7 TraesCS3D01G250500 chr3A 80.769 494 56 23 333 800 468539504 468539024 1.940000e-92 350.0
8 TraesCS3D01G250500 chr3A 78.298 235 26 13 10 244 468539750 468539541 9.880000e-26 128.0
9 TraesCS3D01G250500 chr3A 82.524 103 15 3 3292 3393 527385876 527385976 1.680000e-13 87.9
10 TraesCS3D01G250500 chrUn 80.435 230 29 12 3172 3393 36494786 36494565 9.740000e-36 161.0
11 TraesCS3D01G250500 chr2D 83.929 168 20 6 3231 3393 11277684 11277519 1.630000e-33 154.0
12 TraesCS3D01G250500 chr7A 89.720 107 9 2 3289 3393 157199997 157200103 5.910000e-28 135.0
13 TraesCS3D01G250500 chr6D 76.577 222 35 15 3157 3369 397340843 397340630 4.630000e-19 106.0


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 TraesCS3D01G250500 chr3D 350794786 350798178 3392 True 6266 6266 100.0000 1 3393 1 chr3D.!!$R1 3392
1 TraesCS3D01G250500 chr3B 449205512 449208535 3023 True 4385 4385 92.6770 1 3086 1 chr3B.!!$R2 3085
2 TraesCS3D01G250500 chr3A 468531657 468533632 1975 True 3070 3070 94.6300 862 2857 1 chr3A.!!$R2 1995
3 TraesCS3D01G250500 chr3A 468518647 468519191 544 True 691 691 89.8550 2855 3393 1 chr3A.!!$R1 538
4 TraesCS3D01G250500 chr3A 468539024 468539750 726 True 239 350 79.5335 10 800 2 chr3A.!!$R3 790

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
855 881 0.326238 TAGGGAAACGAGGGGAGCAT 60.326 55.0 0.00 0.00 0.00 3.79 F
951 977 1.538047 TTCAGCAAAGGTCTCCATGC 58.462 50.0 7.99 7.99 38.38 4.06 F
2122 2156 0.255890 ACCTGTTCACCTGCAACTGT 59.744 50.0 0.00 0.00 0.00 3.55 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1969 2003 0.321919 TAGCAGGAAAGCAGCACTGG 60.322 55.000 0.00 0.0 36.85 4.00 R
2281 2315 1.001815 CAGCCGGCCATAAAAATACCG 60.002 52.381 26.15 0.0 43.44 4.02 R
3368 3425 0.532862 AATATGCGAGCGGGGACTTG 60.533 55.000 0.00 0.0 0.00 3.16 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
23 24 3.764466 CGCTCGAGCCACTCCCTT 61.764 66.667 30.66 0.00 37.91 3.95
75 76 4.988598 CGTCCAACGGCTGGCTGT 62.989 66.667 0.69 0.69 45.98 4.40
102 103 1.689243 GATTGCTTTGGGATGGGGGC 61.689 60.000 0.00 0.00 0.00 5.80
150 152 6.479660 CCAATGTAACATTGTTTCAAGCACTT 59.520 34.615 12.06 0.76 0.00 3.16
199 201 4.139786 TCCTTGCCAATCTGATCTTATGC 58.860 43.478 0.00 0.00 0.00 3.14
253 255 5.446143 TGGTTCATAACATGTTTGACACC 57.554 39.130 17.78 22.58 0.00 4.16
272 274 6.045072 ACACCTAAAATGTCGTGGATAGAA 57.955 37.500 0.00 0.00 0.00 2.10
280 282 8.964476 AAAATGTCGTGGATAGAATACATCTT 57.036 30.769 0.00 0.00 39.71 2.40
281 283 8.594881 AAATGTCGTGGATAGAATACATCTTC 57.405 34.615 0.00 0.00 39.71 2.87
282 284 6.961360 TGTCGTGGATAGAATACATCTTCT 57.039 37.500 0.00 0.00 39.71 2.85
315 317 6.963805 GCTGTATCTTTGTCAATCTAAAGTGC 59.036 38.462 0.00 0.00 35.82 4.40
319 321 9.118236 GTATCTTTGTCAATCTAAAGTGCAAAC 57.882 33.333 0.00 0.00 35.82 2.93
364 366 2.576615 GGGTGTTGCTGAGTCTCTTTT 58.423 47.619 0.65 0.00 0.00 2.27
417 419 9.300681 CCTGCATTATAAGATGAAAAGGGATAA 57.699 33.333 0.00 0.00 0.00 1.75
429 431 7.630242 TGAAAAGGGATAAGCTATCTGTTTG 57.370 36.000 0.00 0.00 35.52 2.93
431 433 5.975988 AAGGGATAAGCTATCTGTTTGGA 57.024 39.130 0.00 0.00 35.52 3.53
442 444 5.163713 GCTATCTGTTTGGAGCTCGAAAATT 60.164 40.000 23.27 11.91 32.04 1.82
500 520 3.565482 GCAACAGTTTGATTGAGGAGTGA 59.435 43.478 0.00 0.00 34.24 3.41
545 565 3.935828 GAGAAGTTGTGGCTGTTATCCTC 59.064 47.826 0.00 0.00 0.00 3.71
546 566 3.584848 AGAAGTTGTGGCTGTTATCCTCT 59.415 43.478 0.00 0.00 0.00 3.69
565 585 8.845413 ATCCTCTCTTGTTCATATCTTAATGC 57.155 34.615 0.00 0.00 0.00 3.56
566 586 7.795047 TCCTCTCTTGTTCATATCTTAATGCA 58.205 34.615 0.00 0.00 0.00 3.96
718 744 7.886629 AATATGAAATGACATACCACAAGCT 57.113 32.000 0.00 0.00 35.91 3.74
722 748 5.121611 TGAAATGACATACCACAAGCTTACG 59.878 40.000 0.00 0.00 0.00 3.18
744 770 4.577283 CGACCACTTAACCTCTTCCAAAAA 59.423 41.667 0.00 0.00 0.00 1.94
855 881 0.326238 TAGGGAAACGAGGGGAGCAT 60.326 55.000 0.00 0.00 0.00 3.79
946 972 5.757850 TCTTTCTTTTCAGCAAAGGTCTC 57.242 39.130 0.00 0.00 42.18 3.36
951 977 1.538047 TTCAGCAAAGGTCTCCATGC 58.462 50.000 7.99 7.99 38.38 4.06
993 1019 9.840427 ACATTTGATTTTCTATAAGTTCAACGG 57.160 29.630 0.00 0.00 0.00 4.44
1411 1438 3.087370 ACTTGGAGGAAAATGCCTACC 57.913 47.619 0.00 0.00 38.17 3.18
1452 1483 9.494479 CATGCTGTCAACATATTTTACTTGTAG 57.506 33.333 0.00 0.00 0.00 2.74
1453 1484 8.615878 TGCTGTCAACATATTTTACTTGTAGT 57.384 30.769 0.00 0.00 0.00 2.73
1454 1485 9.713713 TGCTGTCAACATATTTTACTTGTAGTA 57.286 29.630 0.00 0.00 0.00 1.82
1593 1624 5.776208 TGTGTGTCAATACCTGGACTTACTA 59.224 40.000 0.00 0.00 35.11 1.82
1594 1625 6.439375 TGTGTGTCAATACCTGGACTTACTAT 59.561 38.462 0.00 0.00 35.11 2.12
1595 1626 6.979238 GTGTGTCAATACCTGGACTTACTATC 59.021 42.308 0.00 0.00 35.11 2.08
1864 1898 7.537596 TGTTCCACAATCCTGTTCATTTATT 57.462 32.000 0.00 0.00 31.64 1.40
1897 1931 8.685838 TTACTTCTGTAAAACCTACTTGCATT 57.314 30.769 0.00 0.00 35.90 3.56
1898 1932 7.582667 ACTTCTGTAAAACCTACTTGCATTT 57.417 32.000 0.00 0.00 0.00 2.32
1969 2003 7.437862 TGAAATACTCTTTGTTTTGTTCATGGC 59.562 33.333 0.00 0.00 0.00 4.40
2122 2156 0.255890 ACCTGTTCACCTGCAACTGT 59.744 50.000 0.00 0.00 0.00 3.55
2281 2315 1.693467 TCGTAACTGTGACGTGCATC 58.307 50.000 16.76 0.00 41.11 3.91
2326 2360 5.875359 GTCTTTCCTAATAGGGATATTGGCG 59.125 44.000 6.46 0.00 35.59 5.69
2567 2603 5.483937 TGGGAAAGCTGTAGAAAGTGAGATA 59.516 40.000 0.00 0.00 0.00 1.98
2648 2685 8.677148 ACGGTATGATTTTTAGCATTGAGTAT 57.323 30.769 0.00 0.00 0.00 2.12
2649 2686 9.120538 ACGGTATGATTTTTAGCATTGAGTATT 57.879 29.630 0.00 0.00 0.00 1.89
2650 2687 9.950680 CGGTATGATTTTTAGCATTGAGTATTT 57.049 29.630 0.00 0.00 0.00 1.40
2846 2890 6.936279 TCCCTACGAAAATCATCATATCTCC 58.064 40.000 0.00 0.00 0.00 3.71
2960 3004 2.620585 GCCTGCCCAATCTATTCAGAAC 59.379 50.000 0.00 0.00 33.50 3.01
2978 3022 7.323049 TCAGAACGGTTTTCATGTTTTTCTA 57.677 32.000 0.00 0.00 0.00 2.10
3004 3048 1.331756 GCCAATCTTGTCCGTATGCAG 59.668 52.381 0.00 0.00 0.00 4.41
3089 3133 5.510520 CCAGAAGAGTCATGGAGGTAATAGC 60.511 48.000 3.58 0.00 36.09 2.97
3109 3153 1.529438 CGTCGGTAGCACACACAAATT 59.471 47.619 0.00 0.00 0.00 1.82
3139 3183 1.040893 TGGCCGACCATCGTGTATCT 61.041 55.000 0.00 0.00 42.67 1.98
3140 3184 0.318784 GGCCGACCATCGTGTATCTC 60.319 60.000 0.00 0.00 38.40 2.75
3145 3189 3.058155 CCGACCATCGTGTATCTCTTAGG 60.058 52.174 0.00 0.00 38.40 2.69
3161 3215 0.320073 TAGGCCAACTCCGACAAACG 60.320 55.000 5.01 0.00 42.18 3.60
3170 3224 4.314096 CGACAAACGGACGTCTGT 57.686 55.556 24.31 24.31 38.46 3.41
3185 3239 5.844396 GGACGTCTGTTTTTACTGAATTTCG 59.156 40.000 16.46 0.00 0.00 3.46
3219 3273 6.038825 TGACGGTAAAATGAAGACACATGTTT 59.961 34.615 0.00 0.00 31.29 2.83
3221 3275 5.629020 CGGTAAAATGAAGACACATGTTTGG 59.371 40.000 0.00 0.00 31.29 3.28
3230 3284 0.599728 CACATGTTTGGTTTGGCCCG 60.600 55.000 0.00 0.00 36.04 6.13
3234 3288 2.522193 TTTGGTTTGGCCCGTCCC 60.522 61.111 0.00 0.00 36.04 4.46
3235 3289 4.958897 TTGGTTTGGCCCGTCCCG 62.959 66.667 0.00 0.00 36.04 5.14
3379 3436 1.232119 CGTTTAAACAAGTCCCCGCT 58.768 50.000 18.07 0.00 0.00 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 0.609406 ACGCAGGAGCAGACTGTAGA 60.609 55.000 3.99 0.00 42.27 2.59
150 152 8.189119 AGGAACACCAATGAGCTTTATAAAAA 57.811 30.769 0.00 0.00 0.00 1.94
157 159 3.321968 GGAAAGGAACACCAATGAGCTTT 59.678 43.478 0.00 0.00 0.00 3.51
165 167 1.342474 TGGCAAGGAAAGGAACACCAA 60.342 47.619 0.00 0.00 0.00 3.67
253 255 9.698309 AGATGTATTCTATCCACGACATTTTAG 57.302 33.333 0.00 0.00 30.96 1.85
265 267 4.932200 CCGGCAAGAAGATGTATTCTATCC 59.068 45.833 0.00 0.00 38.59 2.59
272 274 1.765314 AGCTCCGGCAAGAAGATGTAT 59.235 47.619 0.00 0.00 41.70 2.29
280 282 1.195115 AAGATACAGCTCCGGCAAGA 58.805 50.000 0.00 0.00 41.70 3.02
281 283 1.667724 CAAAGATACAGCTCCGGCAAG 59.332 52.381 0.00 0.00 41.70 4.01
282 284 1.003118 ACAAAGATACAGCTCCGGCAA 59.997 47.619 0.00 0.00 41.70 4.52
315 317 5.650543 ACCACAAGAAGCTTAAAGTGTTTG 58.349 37.500 17.91 9.37 0.00 2.93
319 321 6.863126 CCATTAACCACAAGAAGCTTAAAGTG 59.137 38.462 14.41 14.41 0.00 3.16
321 323 6.389906 CCCATTAACCACAAGAAGCTTAAAG 58.610 40.000 0.00 0.00 0.00 1.85
364 366 4.411927 ACATGGGGTTATTTTGCTGTACA 58.588 39.130 0.00 0.00 0.00 2.90
377 379 0.482446 TGCAGGAAGAACATGGGGTT 59.518 50.000 0.00 0.00 44.10 4.11
383 385 8.985315 TTCATCTTATAATGCAGGAAGAACAT 57.015 30.769 0.00 0.00 32.00 2.71
429 431 3.596214 TGGTCTACAATTTTCGAGCTCC 58.404 45.455 8.47 0.00 0.00 4.70
431 433 4.832248 TCATGGTCTACAATTTTCGAGCT 58.168 39.130 0.00 0.00 0.00 4.09
442 444 7.016268 AGGAACTTTAGTTTCTCATGGTCTACA 59.984 37.037 0.00 0.00 39.61 2.74
474 477 2.364970 CCTCAATCAAACTGTTGCCCAA 59.635 45.455 0.00 0.00 34.50 4.12
545 565 7.239166 ACGTGCATTAAGATATGAACAAGAG 57.761 36.000 0.00 0.00 34.28 2.85
546 566 8.710835 TTACGTGCATTAAGATATGAACAAGA 57.289 30.769 0.00 0.00 34.28 3.02
565 585 5.910723 GTCAGGGTACAAAAATGTTTACGTG 59.089 40.000 0.00 0.00 0.00 4.49
566 586 5.008911 GGTCAGGGTACAAAAATGTTTACGT 59.991 40.000 0.00 0.00 0.00 3.57
718 744 3.896888 TGGAAGAGGTTAAGTGGTCGTAA 59.103 43.478 0.00 0.00 0.00 3.18
722 748 6.650427 ATTTTTGGAAGAGGTTAAGTGGTC 57.350 37.500 0.00 0.00 0.00 4.02
946 972 1.001268 GCTTGCATCTCATGAGCATGG 60.001 52.381 24.29 15.36 39.24 3.66
951 977 4.105486 CAAATGTGCTTGCATCTCATGAG 58.895 43.478 17.07 17.07 0.00 2.90
993 1019 9.556030 GAAAATACTTCAGTTAACATTAGTGCC 57.444 33.333 8.61 0.00 0.00 5.01
1454 1485 9.436957 AACAGAAACTACATATCGAAATGAACT 57.563 29.630 0.00 0.00 0.00 3.01
1571 1602 6.666113 TGATAGTAAGTCCAGGTATTGACACA 59.334 38.462 0.00 0.00 33.89 3.72
1572 1603 7.108841 TGATAGTAAGTCCAGGTATTGACAC 57.891 40.000 0.00 0.00 33.89 3.67
1573 1604 7.563556 TGATGATAGTAAGTCCAGGTATTGACA 59.436 37.037 0.00 0.00 33.89 3.58
1632 1663 2.435805 TGTTCAGTATCCCCAGCTCATC 59.564 50.000 0.00 0.00 0.00 2.92
1636 1667 0.537188 CGTGTTCAGTATCCCCAGCT 59.463 55.000 0.00 0.00 0.00 4.24
1874 1908 7.284489 TGAAATGCAAGTAGGTTTTACAGAAGT 59.716 33.333 0.00 0.00 0.00 3.01
1897 1931 4.911514 AAGCGCTAAAAGAAAAGGTGAA 57.088 36.364 12.05 0.00 0.00 3.18
1898 1932 4.261447 GGAAAGCGCTAAAAGAAAAGGTGA 60.261 41.667 12.05 0.00 0.00 4.02
1969 2003 0.321919 TAGCAGGAAAGCAGCACTGG 60.322 55.000 0.00 0.00 36.85 4.00
2122 2156 2.225491 GCAGTTTGCCACGAATGAGTAA 59.775 45.455 0.00 0.00 37.42 2.24
2281 2315 1.001815 CAGCCGGCCATAAAAATACCG 60.002 52.381 26.15 0.00 43.44 4.02
2326 2360 4.154918 CACCCTATCAGAAGCAAACAGAAC 59.845 45.833 0.00 0.00 0.00 3.01
2516 2552 7.334844 TCTGTAGTGTTCATATCCTACACAG 57.665 40.000 11.82 0.00 43.46 3.66
2609 2646 5.097742 TCATACCGTCTGAACCAAATGAT 57.902 39.130 0.00 0.00 0.00 2.45
2658 2695 6.772716 AGGAAAAGAAACATTGCTTAGACTCA 59.227 34.615 0.00 0.00 0.00 3.41
2662 2699 7.581213 TCAAGGAAAAGAAACATTGCTTAGA 57.419 32.000 0.00 0.00 35.39 2.10
2665 2702 7.920160 TTTTCAAGGAAAAGAAACATTGCTT 57.080 28.000 0.28 0.00 36.73 3.91
2902 2946 2.295885 GATGTGGCTTCATCTTCCCTG 58.704 52.381 13.15 0.00 40.46 4.45
2960 3004 6.346518 GCCAACATAGAAAAACATGAAAACCG 60.347 38.462 0.00 0.00 0.00 4.44
3089 3133 1.144969 ATTTGTGTGTGCTACCGACG 58.855 50.000 0.00 0.00 0.00 5.12
3132 3176 3.491104 CGGAGTTGGCCTAAGAGATACAC 60.491 52.174 3.32 0.00 0.00 2.90
3139 3183 1.344065 TTGTCGGAGTTGGCCTAAGA 58.656 50.000 3.32 0.00 0.00 2.10
3140 3184 1.804748 GTTTGTCGGAGTTGGCCTAAG 59.195 52.381 3.32 0.00 0.00 2.18
3161 3215 5.844396 CGAAATTCAGTAAAAACAGACGTCC 59.156 40.000 13.01 0.00 0.00 4.79
3170 3224 6.469595 CACAAACGGACGAAATTCAGTAAAAA 59.530 34.615 0.00 0.00 0.00 1.94
3174 3228 4.209703 GTCACAAACGGACGAAATTCAGTA 59.790 41.667 0.00 0.00 0.00 2.74
3175 3229 3.001939 GTCACAAACGGACGAAATTCAGT 59.998 43.478 0.00 0.00 0.00 3.41
3199 3253 8.327429 CAAACCAAACATGTGTCTTCATTTTAC 58.673 33.333 0.00 0.00 0.00 2.01
3208 3262 1.412343 GGCCAAACCAAACATGTGTCT 59.588 47.619 0.00 0.00 38.86 3.41
3271 3325 7.380423 TTTTTCATTCTTGGGGGACAAAATA 57.620 32.000 0.00 0.00 38.91 1.40
3361 3418 1.196127 CGAGCGGGGACTTGTTTAAAC 59.804 52.381 11.54 11.54 0.00 2.01
3368 3425 0.532862 AATATGCGAGCGGGGACTTG 60.533 55.000 0.00 0.00 0.00 3.16
3372 3429 1.414919 AGTTTAATATGCGAGCGGGGA 59.585 47.619 0.00 0.00 0.00 4.81


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

AutoCloner maintained by Alex Coulton.