Multiple sequence alignment - TraesCS1A01G057800

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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 TraesCS1A01G057800 chr1A 100.000 2690 0 0 1 2690 38358265 38360954 0.000000e+00 4968
1 TraesCS1A01G057800 chr1A 81.783 785 110 25 949 1713 37466614 37467385 6.320000e-176 627
2 TraesCS1A01G057800 chr1B 94.351 1788 73 16 1 1774 58539166 58540939 0.000000e+00 2717
3 TraesCS1A01G057800 chr1B 94.589 924 49 1 1768 2690 58540965 58541888 0.000000e+00 1428
4 TraesCS1A01G057800 chr1B 84.319 778 104 13 967 1737 58752942 58753708 0.000000e+00 745
5 TraesCS1A01G057800 chr1B 81.646 790 116 22 949 1721 57782649 57783426 1.760000e-176 628
6 TraesCS1A01G057800 chr1B 81.360 794 113 22 945 1721 58031466 58032241 4.920000e-172 614
7 TraesCS1A01G057800 chr1D 93.835 1249 50 12 536 1774 38654810 38656041 0.000000e+00 1855
8 TraesCS1A01G057800 chr1D 97.180 922 26 0 1769 2690 38656068 38656989 0.000000e+00 1559
9 TraesCS1A01G057800 chr1D 79.008 1210 210 32 949 2130 38250316 38251509 0.000000e+00 787
10 TraesCS1A01G057800 chr1D 93.333 495 13 5 1 494 38654213 38654688 0.000000e+00 713
11 TraesCS1A01G057800 chr1D 85.064 703 87 13 1041 1737 39651489 39652179 0.000000e+00 701
12 TraesCS1A01G057800 chr1D 81.392 790 118 23 949 1721 38294076 38294853 3.800000e-173 617


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 TraesCS1A01G057800 chr1A 38358265 38360954 2689 False 4968.000000 4968 100.000000 1 2690 1 chr1A.!!$F2 2689
1 TraesCS1A01G057800 chr1A 37466614 37467385 771 False 627.000000 627 81.783000 949 1713 1 chr1A.!!$F1 764
2 TraesCS1A01G057800 chr1B 58539166 58541888 2722 False 2072.500000 2717 94.470000 1 2690 2 chr1B.!!$F4 2689
3 TraesCS1A01G057800 chr1B 58752942 58753708 766 False 745.000000 745 84.319000 967 1737 1 chr1B.!!$F3 770
4 TraesCS1A01G057800 chr1B 57782649 57783426 777 False 628.000000 628 81.646000 949 1721 1 chr1B.!!$F1 772
5 TraesCS1A01G057800 chr1B 58031466 58032241 775 False 614.000000 614 81.360000 945 1721 1 chr1B.!!$F2 776
6 TraesCS1A01G057800 chr1D 38654213 38656989 2776 False 1375.666667 1855 94.782667 1 2690 3 chr1D.!!$F4 2689
7 TraesCS1A01G057800 chr1D 38250316 38251509 1193 False 787.000000 787 79.008000 949 2130 1 chr1D.!!$F1 1181
8 TraesCS1A01G057800 chr1D 39651489 39652179 690 False 701.000000 701 85.064000 1041 1737 1 chr1D.!!$F3 696
9 TraesCS1A01G057800 chr1D 38294076 38294853 777 False 617.000000 617 81.392000 949 1721 1 chr1D.!!$F2 772

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
256 269 1.076044 CCTTCGGCCCCCATCATTT 60.076 57.895 0.0 0.0 0.0 2.32 F
1390 1497 1.598130 AACCCAGCAACACGAGAGC 60.598 57.895 0.0 0.0 0.0 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1538 1654 0.744414 CGTGGAACCGGCAGATGAAT 60.744 55.0 0.00 0.0 0.00 2.57 R
2287 2442 0.393267 TAGTAAACCGGGGCACATGC 60.393 55.0 6.32 0.0 41.14 4.06 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
52 53 1.686587 TCTGAAAACACTGCTCCTCGA 59.313 47.619 0.00 0.00 0.00 4.04
83 85 2.509336 CTTGTAGACCCTGGCGCG 60.509 66.667 0.00 0.00 0.00 6.86
84 86 4.752879 TTGTAGACCCTGGCGCGC 62.753 66.667 25.94 25.94 0.00 6.86
168 181 2.753029 GTGCTCTGGCCCTTCACT 59.247 61.111 0.00 0.00 37.74 3.41
218 231 2.042686 AACAAGCTGCACTGTGAGAA 57.957 45.000 12.86 0.00 0.00 2.87
256 269 1.076044 CCTTCGGCCCCCATCATTT 60.076 57.895 0.00 0.00 0.00 2.32
266 279 3.889538 GCCCCCATCATTTTTCTACTACC 59.110 47.826 0.00 0.00 0.00 3.18
287 300 1.819928 TACGCATGGTTGTGCTCAAT 58.180 45.000 4.26 0.00 42.88 2.57
330 343 2.759535 CAGATCTGAGCTCAGTTCCTCA 59.240 50.000 35.33 22.11 44.12 3.86
340 353 2.166459 CTCAGTTCCTCATCCACGCTAA 59.834 50.000 0.00 0.00 0.00 3.09
382 395 2.997315 CCTCCTGACCTGTCGCCA 60.997 66.667 0.00 0.00 0.00 5.69
419 432 3.244561 GGTCTGATTTCTGGTGAGTTCCA 60.245 47.826 0.00 0.00 36.00 3.53
432 445 3.438434 GTGAGTTCCATGCTTTCTCTTCC 59.562 47.826 0.00 0.00 0.00 3.46
510 541 1.838077 AGGGTGTGCTATGGTTAGGAC 59.162 52.381 0.00 0.00 44.56 3.85
640 736 4.818546 AGCATCCCTCGATTAAATGTCTTG 59.181 41.667 0.00 0.00 0.00 3.02
725 826 4.030216 ACACCAGAAACAATTTGTTCCCT 58.970 39.130 14.80 11.93 40.14 4.20
745 846 7.086685 TCCCTTGATTTGTCTAGGTAAAAGT 57.913 36.000 5.46 0.00 32.05 2.66
751 852 7.618137 TGATTTGTCTAGGTAAAAGTAGGTCC 58.382 38.462 0.00 0.00 0.00 4.46
763 864 2.363975 TAGGTCCGCGGCATCCTTT 61.364 57.895 30.16 16.68 0.00 3.11
791 892 6.791867 TGCAAAATCTAGCTAAGAGTAGGA 57.208 37.500 0.00 0.00 37.74 2.94
911 1012 5.104527 AGTTCGAATGGGATGAAGTTCCATA 60.105 40.000 0.00 0.00 40.09 2.74
929 1030 8.470002 AGTTCCATATCAACTATTTCCTTTTGC 58.530 33.333 0.00 0.00 32.08 3.68
1390 1497 1.598130 AACCCAGCAACACGAGAGC 60.598 57.895 0.00 0.00 0.00 4.09
1429 1536 4.373156 ACTTTTGTTGGGACTGATAGCT 57.627 40.909 0.00 0.00 0.00 3.32
1538 1654 2.107378 TGGTGGGCAAACTTGAGATGTA 59.893 45.455 0.00 0.00 0.00 2.29
1542 1658 4.458989 GTGGGCAAACTTGAGATGTATTCA 59.541 41.667 0.00 0.00 0.00 2.57
1686 1803 3.636764 GGTGTTTGAAGGTTTGGAGACAT 59.363 43.478 0.00 0.00 42.32 3.06
1738 1855 4.218200 CACCATTGACTTGCCATTTGACTA 59.782 41.667 0.00 0.00 0.00 2.59
1757 1874 2.561478 ATGCACCCGTGAGTAGTTTT 57.439 45.000 0.00 0.00 0.00 2.43
2111 2266 1.138661 GCCATGCTACTCAGAGCTTCT 59.861 52.381 0.00 0.00 43.27 2.85
2165 2320 2.630098 TGCTATCAGTGCCTCTATGACC 59.370 50.000 0.00 0.00 0.00 4.02
2414 2569 7.571919 ACATCTGTTTGTGGATAAGATCTCAT 58.428 34.615 0.00 0.00 0.00 2.90
2440 2595 6.522625 TTGTAGATAGAGCCTGATATCAGC 57.477 41.667 24.81 19.50 42.47 4.26
2455 2610 6.172630 TGATATCAGCTACTTGAGTTTGCAA 58.827 36.000 0.00 0.00 0.00 4.08
2467 2622 6.765989 ACTTGAGTTTGCAATACAACTCTACA 59.234 34.615 22.92 11.01 38.23 2.74
2569 2725 3.056821 TGTGGTACTGAAACTGGATCGAG 60.057 47.826 2.78 2.78 0.00 4.04
2624 2780 3.007506 CCCAACATGGCATATGCATGATT 59.992 43.478 30.15 21.74 44.36 2.57
2636 2792 6.258287 GCATATGCATGATTTTTAGTTGGCAA 59.742 34.615 22.84 0.00 41.59 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
52 53 0.184933 TACAAGTGGCTGTTGGGCTT 59.815 50.000 4.74 0.00 41.48 4.35
83 85 1.915769 AGGGAGGTCAGAGGTGTGC 60.916 63.158 0.00 0.00 0.00 4.57
84 86 0.542938 TCAGGGAGGTCAGAGGTGTG 60.543 60.000 0.00 0.00 0.00 3.82
85 87 0.191064 TTCAGGGAGGTCAGAGGTGT 59.809 55.000 0.00 0.00 0.00 4.16
86 88 0.901124 CTTCAGGGAGGTCAGAGGTG 59.099 60.000 0.00 0.00 0.00 4.00
87 89 0.787084 TCTTCAGGGAGGTCAGAGGT 59.213 55.000 0.00 0.00 0.00 3.85
88 90 1.944177 TTCTTCAGGGAGGTCAGAGG 58.056 55.000 0.00 0.00 0.00 3.69
196 209 1.945394 CTCACAGTGCAGCTTGTTTCT 59.055 47.619 0.00 0.00 0.00 2.52
330 343 1.407979 CGGTAGAGGTTTAGCGTGGAT 59.592 52.381 0.00 0.00 39.10 3.41
340 353 0.535797 GCTACTTGGCGGTAGAGGTT 59.464 55.000 17.61 0.00 40.98 3.50
419 432 6.127507 GGAAATTAAGCAGGAAGAGAAAGCAT 60.128 38.462 0.00 0.00 0.00 3.79
432 445 2.414559 CCAGCACACGGAAATTAAGCAG 60.415 50.000 0.00 0.00 0.00 4.24
510 541 6.818644 ACATACTAAATCAAGCACAGTGGTAG 59.181 38.462 5.48 0.95 0.00 3.18
543 639 6.656270 CCATTGGTAGCATTGCATTCTATCTA 59.344 38.462 11.91 0.00 0.00 1.98
544 640 5.475909 CCATTGGTAGCATTGCATTCTATCT 59.524 40.000 11.91 0.00 0.00 1.98
545 641 5.474532 TCCATTGGTAGCATTGCATTCTATC 59.525 40.000 11.91 0.00 0.00 2.08
640 736 6.710597 TGGGTTACTGAGATATGTACTCAC 57.289 41.667 0.00 0.00 39.10 3.51
653 750 8.988060 TCTGATGATTTACTAATGGGTTACTGA 58.012 33.333 0.00 0.00 0.00 3.41
725 826 8.098912 GGACCTACTTTTACCTAGACAAATCAA 58.901 37.037 0.00 0.00 0.00 2.57
745 846 1.906105 AAAAGGATGCCGCGGACCTA 61.906 55.000 33.48 12.18 32.06 3.08
751 852 1.616872 GCAACAAAAAGGATGCCGCG 61.617 55.000 0.00 0.00 32.73 6.46
763 864 7.510549 ACTCTTAGCTAGATTTTGCAACAAA 57.489 32.000 0.00 0.00 30.92 2.83
887 988 3.009033 TGGAACTTCATCCCATTCGAACT 59.991 43.478 0.00 0.00 38.82 3.01
961 1063 6.582295 CCTACTGACACGAAATGAAAATTTGG 59.418 38.462 0.00 0.00 0.00 3.28
1224 1330 3.243873 CGATTTCTCCATCATCTCGGGAA 60.244 47.826 0.00 0.00 0.00 3.97
1390 1497 7.042335 ACAAAAGTATCAGGAAGTATTCTCCG 58.958 38.462 0.00 0.00 46.56 4.63
1429 1536 3.925913 GCCAAAATAGTTGTACGACGGTA 59.074 43.478 7.62 0.00 0.00 4.02
1538 1654 0.744414 CGTGGAACCGGCAGATGAAT 60.744 55.000 0.00 0.00 0.00 2.57
1542 1658 2.047274 CACGTGGAACCGGCAGAT 60.047 61.111 7.95 0.00 0.00 2.90
1738 1855 2.561478 AAAACTACTCACGGGTGCAT 57.439 45.000 0.00 0.00 0.00 3.96
2165 2320 3.254411 TCAGCATCTAGAGCATAGGAACG 59.746 47.826 14.12 0.00 0.00 3.95
2287 2442 0.393267 TAGTAAACCGGGGCACATGC 60.393 55.000 6.32 0.00 41.14 4.06
2378 2533 5.752472 CCACAAACAGATGTAAACAATTGCA 59.248 36.000 5.05 0.00 35.56 4.08
2390 2545 8.447924 AATGAGATCTTATCCACAAACAGATG 57.552 34.615 0.00 0.00 0.00 2.90
2414 2569 7.875041 GCTGATATCAGGCTCTATCTACAAAAA 59.125 37.037 29.43 0.00 43.94 1.94
2440 2595 7.426929 AGAGTTGTATTGCAAACTCAAGTAG 57.573 36.000 23.98 0.00 39.03 2.57
2455 2610 5.962031 TCCCAGGTGTAATGTAGAGTTGTAT 59.038 40.000 0.00 0.00 0.00 2.29
2467 2622 5.787494 AGCATCATATAGTCCCAGGTGTAAT 59.213 40.000 0.00 0.00 0.00 1.89
2569 2725 5.106157 CCCTTGGTTCACAGAATACATTCAC 60.106 44.000 4.85 0.00 39.23 3.18
2624 2780 5.066634 TGTCATTCGAAGTTGCCAACTAAAA 59.933 36.000 11.10 6.14 41.91 1.52
2636 2792 3.074412 GTTGGGATGTGTCATTCGAAGT 58.926 45.455 3.35 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.