Multiple sequence alignment - TraesCS3A01G248500

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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 TraesCS3A01G248500 chr3A 100.000 2771 0 0 1 2771 466483454 466480684 0.000000e+00 5118
1 TraesCS3A01G248500 chr1A 98.266 2191 38 0 581 2771 307487543 307485353 0.000000e+00 3836
2 TraesCS3A01G248500 chr1A 92.701 548 40 0 1 548 331279648 331280195 0.000000e+00 791
3 TraesCS3A01G248500 chr6A 93.639 2201 115 8 571 2765 171564141 171566322 0.000000e+00 3265
4 TraesCS3A01G248500 chr5D 83.342 1933 301 14 847 2771 453126849 453124930 0.000000e+00 1766
5 TraesCS3A01G248500 chr5D 96.843 792 25 0 1980 2771 74468499 74469290 0.000000e+00 1325
6 TraesCS3A01G248500 chr5D 83.224 1371 218 7 1404 2771 350301069 350302430 0.000000e+00 1247
7 TraesCS3A01G248500 chr5D 90.876 548 49 1 1 548 552348951 552348405 0.000000e+00 734
8 TraesCS3A01G248500 chr5D 90.528 549 50 2 1 549 510611042 510610496 0.000000e+00 725
9 TraesCS3A01G248500 chr1B 82.565 1778 295 9 999 2771 327336369 327334602 0.000000e+00 1552
10 TraesCS3A01G248500 chr1B 92.518 548 41 0 1 548 593501741 593501194 0.000000e+00 785
11 TraesCS3A01G248500 chr2A 95.803 548 23 0 1 548 655520031 655520578 0.000000e+00 885
12 TraesCS3A01G248500 chr2A 95.803 548 22 1 1 548 523877672 523878218 0.000000e+00 883
13 TraesCS3A01G248500 chr4A 93.248 548 37 0 1 548 147580057 147580604 0.000000e+00 808
14 TraesCS3A01G248500 chr4A 84.354 147 23 0 2457 2603 68787481 68787335 8.000000e-31 145
15 TraesCS3A01G248500 chr4D 91.788 548 44 1 1 548 280777128 280776582 0.000000e+00 761
16 TraesCS3A01G248500 chr3D 91.636 550 43 2 1 548 29164203 29163655 0.000000e+00 758


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 TraesCS3A01G248500 chr3A 466480684 466483454 2770 True 5118 5118 100.000 1 2771 1 chr3A.!!$R1 2770
1 TraesCS3A01G248500 chr1A 307485353 307487543 2190 True 3836 3836 98.266 581 2771 1 chr1A.!!$R1 2190
2 TraesCS3A01G248500 chr1A 331279648 331280195 547 False 791 791 92.701 1 548 1 chr1A.!!$F1 547
3 TraesCS3A01G248500 chr6A 171564141 171566322 2181 False 3265 3265 93.639 571 2765 1 chr6A.!!$F1 2194
4 TraesCS3A01G248500 chr5D 453124930 453126849 1919 True 1766 1766 83.342 847 2771 1 chr5D.!!$R1 1924
5 TraesCS3A01G248500 chr5D 74468499 74469290 791 False 1325 1325 96.843 1980 2771 1 chr5D.!!$F1 791
6 TraesCS3A01G248500 chr5D 350301069 350302430 1361 False 1247 1247 83.224 1404 2771 1 chr5D.!!$F2 1367
7 TraesCS3A01G248500 chr5D 552348405 552348951 546 True 734 734 90.876 1 548 1 chr5D.!!$R3 547
8 TraesCS3A01G248500 chr5D 510610496 510611042 546 True 725 725 90.528 1 549 1 chr5D.!!$R2 548
9 TraesCS3A01G248500 chr1B 327334602 327336369 1767 True 1552 1552 82.565 999 2771 1 chr1B.!!$R1 1772
10 TraesCS3A01G248500 chr1B 593501194 593501741 547 True 785 785 92.518 1 548 1 chr1B.!!$R2 547
11 TraesCS3A01G248500 chr2A 655520031 655520578 547 False 885 885 95.803 1 548 1 chr2A.!!$F2 547
12 TraesCS3A01G248500 chr2A 523877672 523878218 546 False 883 883 95.803 1 548 1 chr2A.!!$F1 547
13 TraesCS3A01G248500 chr4A 147580057 147580604 547 False 808 808 93.248 1 548 1 chr4A.!!$F1 547
14 TraesCS3A01G248500 chr4D 280776582 280777128 546 True 761 761 91.788 1 548 1 chr4D.!!$R1 547
15 TraesCS3A01G248500 chr3D 29163655 29164203 548 True 758 758 91.636 1 548 1 chr3D.!!$R1 547

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
642 645 0.179056 GCGAATCCGGAATTCCTCCA 60.179 55.0 22.05 6.16 45.74 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 2066 1.398799 TTCCTCTCCTCCTCCTCCTT 58.601 55.0 0.0 0.0 0.0 3.36 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
116 117 2.027192 GTCCTGTGGCCAGAATTGTCTA 60.027 50.000 5.11 0.00 41.50 2.59
130 131 7.095910 CAGAATTGTCTAGCGATCTATTGGAT 58.904 38.462 0.00 0.00 32.71 3.41
187 188 1.613437 GGCAATACTTTGTGTGGTGCT 59.387 47.619 0.00 0.00 38.78 4.40
391 394 1.004044 CCAAGGAGCTTCACACTGGAT 59.996 52.381 0.00 0.00 0.00 3.41
475 478 3.228188 TCCAAGGTGCTTGATGTTCTT 57.772 42.857 0.00 0.00 43.42 2.52
491 494 1.442769 TCTTTGAAGATGCGCTGGAC 58.557 50.000 9.73 0.00 0.00 4.02
510 513 3.157217 GAGGAGATGACGGGCGCAT 62.157 63.158 10.83 0.00 0.00 4.73
550 553 5.914898 CCCCCGAAGAAGATTGTTTTAAT 57.085 39.130 0.00 0.00 0.00 1.40
551 554 5.891451 CCCCCGAAGAAGATTGTTTTAATC 58.109 41.667 0.00 0.00 0.00 1.75
552 555 5.448632 CCCCCGAAGAAGATTGTTTTAATCG 60.449 44.000 0.00 0.00 0.00 3.34
553 556 5.028375 CCCGAAGAAGATTGTTTTAATCGC 58.972 41.667 0.00 0.00 0.00 4.58
554 557 4.723862 CCGAAGAAGATTGTTTTAATCGCG 59.276 41.667 0.00 0.00 0.00 5.87
555 558 4.200366 CGAAGAAGATTGTTTTAATCGCGC 59.800 41.667 0.00 0.00 0.00 6.86
556 559 4.016113 AGAAGATTGTTTTAATCGCGCC 57.984 40.909 0.00 0.00 0.00 6.53
557 560 2.452006 AGATTGTTTTAATCGCGCCG 57.548 45.000 0.00 0.00 0.00 6.46
558 561 0.837605 GATTGTTTTAATCGCGCCGC 59.162 50.000 0.00 0.00 0.00 6.53
559 562 0.524604 ATTGTTTTAATCGCGCCGCC 60.525 50.000 2.28 0.00 0.00 6.13
560 563 2.277692 GTTTTAATCGCGCCGCCC 60.278 61.111 2.28 0.00 0.00 6.13
561 564 3.510675 TTTTAATCGCGCCGCCCC 61.511 61.111 2.28 0.00 0.00 5.80
642 645 0.179056 GCGAATCCGGAATTCCTCCA 60.179 55.000 22.05 6.16 45.74 3.86
650 653 3.201930 TCCGGAATTCCTCCATGATTTCA 59.798 43.478 22.05 0.00 45.74 2.69
679 682 4.952335 GTGTCCCCAATCTCAAATCAATCT 59.048 41.667 0.00 0.00 0.00 2.40
686 689 8.381636 CCCCAATCTCAAATCAATCTAGTAGAT 58.618 37.037 6.86 6.86 36.28 1.98
791 794 2.870411 AGTGCGTAGAAACTGAACCAAC 59.130 45.455 0.00 0.00 0.00 3.77
815 818 6.995091 ACAATCTCTTGTCTTGCTTAGTTTCT 59.005 34.615 0.00 0.00 41.86 2.52
900 904 1.539496 GGGTGCGCGATCCTTATACAA 60.539 52.381 12.10 0.00 0.00 2.41
933 937 0.380733 GCGTATTGGCCTTTAGGTGC 59.619 55.000 3.32 0.00 37.57 5.01
938 942 2.750237 GGCCTTTAGGTGCCGGTG 60.750 66.667 1.90 0.00 38.00 4.94
939 943 2.349755 GCCTTTAGGTGCCGGTGA 59.650 61.111 1.90 0.00 37.57 4.02
940 944 1.745489 GCCTTTAGGTGCCGGTGAG 60.745 63.158 1.90 0.00 37.57 3.51
941 945 1.078426 CCTTTAGGTGCCGGTGAGG 60.078 63.158 1.90 0.00 44.97 3.86
1152 1173 6.154706 AGCTAAAAGCAGTAGGAAAGCTACTA 59.845 38.462 1.22 0.00 45.56 1.82
1165 1186 7.302184 AGGAAAGCTACTATCTGATAGACCTT 58.698 38.462 26.93 20.51 36.68 3.50
1285 1306 3.008835 TCCATGATGAAGCAGGGAAAG 57.991 47.619 0.00 0.00 44.85 2.62
1463 1484 1.755380 AGGGGAGTTAATCGGAGAACG 59.245 52.381 1.29 0.00 43.58 3.95
1883 1908 4.225942 TGGATTCTGGAGAAGCAATAGTGT 59.774 41.667 6.95 0.00 41.81 3.55
1936 1961 3.637432 CGCAAAAATCTGCCTAACACAA 58.363 40.909 0.00 0.00 39.26 3.33
2041 2066 2.642807 AGGGGCAAGAAGCTAGTGTTTA 59.357 45.455 0.00 0.00 44.79 2.01
2066 2097 2.046292 GGAGGAGGAGAGGAAATCTGG 58.954 57.143 0.00 0.00 38.84 3.86
2367 2398 4.316025 TGAGGGGGAATTTTCGAAGAAT 57.684 40.909 0.00 0.00 45.90 2.40
2455 2486 7.196331 ACAAATATTAGAATTTGGAAGCGCTC 58.804 34.615 12.06 4.06 46.51 5.03
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 4.160439 GGATTCCCTGTCCATTTCCTTTTC 59.840 45.833 0.00 0.00 35.76 2.29
116 117 6.226787 CCAAGAACTAATCCAATAGATCGCT 58.773 40.000 0.00 0.00 32.47 4.93
130 131 6.299805 ACATCTATCAGTGCCAAGAACTAA 57.700 37.500 0.00 0.00 0.00 2.24
187 188 3.906720 CTTCCCAGGAAGGAATTCGTA 57.093 47.619 17.26 0.00 44.87 3.43
475 478 0.737367 CTCGTCCAGCGCATCTTCAA 60.737 55.000 11.47 0.00 41.07 2.69
491 494 4.933064 GCGCCCGTCATCTCCTCG 62.933 72.222 0.00 0.00 0.00 4.63
510 513 2.158813 GGGGGAAGCAGTATCGAAATCA 60.159 50.000 0.00 0.00 0.00 2.57
534 537 4.412207 GGCGCGATTAAAACAATCTTCTT 58.588 39.130 12.10 0.00 0.00 2.52
558 561 3.617143 GAGGGACCGAAAACGGGGG 62.617 68.421 13.05 0.00 0.00 5.40
559 562 2.046604 GAGGGACCGAAAACGGGG 60.047 66.667 13.05 0.00 0.00 5.73
560 563 2.433664 CGAGGGACCGAAAACGGG 60.434 66.667 13.05 0.00 0.00 5.28
561 564 3.116531 GCGAGGGACCGAAAACGG 61.117 66.667 7.12 7.12 0.00 4.44
562 565 3.475774 CGCGAGGGACCGAAAACG 61.476 66.667 0.00 0.00 0.00 3.60
563 566 2.356673 ACGCGAGGGACCGAAAAC 60.357 61.111 15.93 0.00 0.00 2.43
564 567 2.356553 CACGCGAGGGACCGAAAA 60.357 61.111 15.93 0.00 35.60 2.29
565 568 3.296836 TCACGCGAGGGACCGAAA 61.297 61.111 15.93 0.00 39.71 3.46
614 617 0.379669 TCCGGATTCGCGAACTCTAC 59.620 55.000 26.00 8.55 34.56 2.59
642 645 2.151202 GGGACACACACGTGAAATCAT 58.849 47.619 25.01 1.76 46.80 2.45
650 653 0.034896 GAGATTGGGGACACACACGT 59.965 55.000 0.00 0.00 42.67 4.49
679 682 5.425217 TGGACTGGAATTGCAAGATCTACTA 59.575 40.000 4.94 0.00 0.00 1.82
686 689 2.108075 TCCTTGGACTGGAATTGCAAGA 59.892 45.455 4.94 0.00 43.16 3.02
791 794 7.296660 CAGAAACTAAGCAAGACAAGAGATTG 58.703 38.462 0.00 0.00 0.00 2.67
815 818 3.195396 GTGGATTTGGGCTAAGATTTGCA 59.805 43.478 1.68 0.00 0.00 4.08
900 904 3.551846 CAATACGCCTAGGGATTTTGGT 58.448 45.455 11.72 0.00 0.00 3.67
952 956 1.077429 AAGAAATCCCCGCCTCTGC 60.077 57.895 0.00 0.00 0.00 4.26
953 957 0.464554 GGAAGAAATCCCCGCCTCTG 60.465 60.000 0.00 0.00 43.00 3.35
954 958 1.915983 GGAAGAAATCCCCGCCTCT 59.084 57.895 0.00 0.00 43.00 3.69
1065 1086 6.243148 TCTTATACCTTTCTTTTCCGCCTTT 58.757 36.000 0.00 0.00 0.00 3.11
1066 1087 5.812286 TCTTATACCTTTCTTTTCCGCCTT 58.188 37.500 0.00 0.00 0.00 4.35
1152 1173 5.207354 TCAGCTCTTGAAGGTCTATCAGAT 58.793 41.667 0.00 0.00 31.91 2.90
1165 1186 3.683365 TGCTACATGTTCAGCTCTTGA 57.317 42.857 18.88 0.00 38.63 3.02
1285 1306 3.554960 GGTCCATTGTTCAAAGCCTTTCC 60.555 47.826 0.00 0.00 0.00 3.13
1463 1484 2.041216 ACATCCAGTACCTTTCCAACCC 59.959 50.000 0.00 0.00 0.00 4.11
1556 1577 4.944619 AGTGTGAAGACTCTCATCAACA 57.055 40.909 0.00 0.00 0.00 3.33
1883 1908 2.415893 GCGTCGCTACCTTTACTACCAA 60.416 50.000 10.68 0.00 0.00 3.67
2041 2066 1.398799 TTCCTCTCCTCCTCCTCCTT 58.601 55.000 0.00 0.00 0.00 3.36
2066 2097 5.791336 ATGTTCCCTTTCTGAAAAAGGTC 57.209 39.130 13.86 11.29 44.05 3.85
2311 2342 6.945435 TCCATGTATTCAGCAAACCTTTTCTA 59.055 34.615 0.00 0.00 0.00 2.10
2367 2398 2.027285 TCCGTCAATCTCCATTCTTGCA 60.027 45.455 0.00 0.00 0.00 4.08


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

AutoCloner maintained by Alex Coulton.