Multiple sequence alignment - TraesCS1A01G400700

Loading Multiple Alignment...

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 TraesCS1A01G400700 chr1A 100.000 2438 0 0 1 2438 564398607 564396170 0.000000e+00 4503
1 TraesCS1A01G400700 chr1D 91.492 1622 83 19 858 2438 470734418 470732811 0.000000e+00 2180
2 TraesCS1A01G400700 chr1D 85.533 553 39 15 56 578 470735507 470734966 7.670000e-150 540
3 TraesCS1A01G400700 chr1D 88.636 176 10 5 688 858 470734628 470734458 3.180000e-49 206
4 TraesCS1A01G400700 chr1B 89.487 1617 94 37 867 2438 654032176 654030591 0.000000e+00 1975
5 TraesCS1A01G400700 chr1B 81.984 494 32 23 80 524 654033836 654033351 1.380000e-97 366
6 TraesCS1A01G400700 chr1B 90.909 99 7 2 561 659 654033263 654033167 5.470000e-27 132
7 TraesCS1A01G400700 chr2D 87.976 657 73 6 1785 2438 25024781 25025434 0.000000e+00 771
8 TraesCS1A01G400700 chr2A 86.050 595 63 9 1785 2378 27499916 27500491 2.660000e-174 621


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 TraesCS1A01G400700 chr1A 564396170 564398607 2437 True 4503.000000 4503 100.000000 1 2438 1 chr1A.!!$R1 2437
1 TraesCS1A01G400700 chr1D 470732811 470735507 2696 True 975.333333 2180 88.553667 56 2438 3 chr1D.!!$R1 2382
2 TraesCS1A01G400700 chr1B 654030591 654033836 3245 True 824.333333 1975 87.460000 80 2438 3 chr1B.!!$R1 2358
3 TraesCS1A01G400700 chr2D 25024781 25025434 653 False 771.000000 771 87.976000 1785 2438 1 chr2D.!!$F1 653
4 TraesCS1A01G400700 chr2A 27499916 27500491 575 False 621.000000 621 86.050000 1785 2378 1 chr2A.!!$F1 593

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
346 393 0.316204 GGACGACGTGAGGGAAAAGA 59.684 55.0 4.58 0.0 0.0 2.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1613 2614 0.474184 ACCATCATCCGTTCATCCCC 59.526 55.0 0.0 0.0 0.0 4.81 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
48 49 2.684001 TGATAGTTTCACCGCCGATT 57.316 45.000 0.00 0.00 0.00 3.34
49 50 3.804786 TGATAGTTTCACCGCCGATTA 57.195 42.857 0.00 0.00 0.00 1.75
50 51 4.126208 TGATAGTTTCACCGCCGATTAA 57.874 40.909 0.00 0.00 0.00 1.40
51 52 4.116961 TGATAGTTTCACCGCCGATTAAG 58.883 43.478 0.00 0.00 0.00 1.85
52 53 2.467566 AGTTTCACCGCCGATTAAGT 57.532 45.000 0.00 0.00 0.00 2.24
53 54 2.073816 AGTTTCACCGCCGATTAAGTG 58.926 47.619 0.00 0.00 0.00 3.16
54 55 1.129811 GTTTCACCGCCGATTAAGTGG 59.870 52.381 0.00 0.00 40.87 4.00
61 62 3.375922 ACCGCCGATTAAGTGGTAATTTG 59.624 43.478 0.00 0.00 46.17 2.32
90 91 1.702886 CTCGTGTGTAGCACCAGAAG 58.297 55.000 0.00 0.00 44.97 2.85
94 95 1.466167 GTGTGTAGCACCAGAAGCATG 59.534 52.381 0.00 0.00 42.10 4.06
102 103 1.554160 CACCAGAAGCATGGAGAGAGT 59.446 52.381 9.37 0.00 43.57 3.24
116 117 1.542030 AGAGAGTCGCAGAATGAACGT 59.458 47.619 0.00 0.00 39.69 3.99
141 147 0.388134 TACGAAGAACAGTCGCTGGC 60.388 55.000 10.80 3.72 42.27 4.85
144 150 3.883744 AAGAACAGTCGCTGGCCGG 62.884 63.158 7.41 7.41 35.51 6.13
168 174 3.484886 GCTGTCGTCCTACGTTGTACTAG 60.485 52.174 0.00 0.00 43.14 2.57
239 263 2.187946 CGGGGTGATGAGGTGCTC 59.812 66.667 0.00 0.00 0.00 4.26
240 264 2.362369 CGGGGTGATGAGGTGCTCT 61.362 63.158 0.00 0.00 0.00 4.09
273 300 5.627499 TTCATCTTCTTTTTCCGTCCATG 57.373 39.130 0.00 0.00 0.00 3.66
275 302 3.502123 TCTTCTTTTTCCGTCCATGGT 57.498 42.857 12.58 0.00 0.00 3.55
346 393 0.316204 GGACGACGTGAGGGAAAAGA 59.684 55.000 4.58 0.00 0.00 2.52
390 441 4.223125 GGGGCTGGCCATGGCATA 62.223 66.667 36.56 23.70 44.11 3.14
404 455 2.983433 GCATATCTGCGTGACAGCT 58.017 52.632 1.69 0.00 46.76 4.24
424 475 3.309954 GCTCTCGTGTCTTTTGTTTCAGT 59.690 43.478 0.00 0.00 0.00 3.41
429 480 2.096819 GTGTCTTTTGTTTCAGTCGCCA 59.903 45.455 0.00 0.00 0.00 5.69
433 484 4.623595 GTCTTTTGTTTCAGTCGCCAAAAA 59.376 37.500 0.00 0.00 36.63 1.94
461 512 1.404748 CACATGTCACACAAGGCAACA 59.595 47.619 0.00 0.00 41.41 3.33
476 527 6.040842 ACAAGGCAACACACTATTTTGAAGAT 59.959 34.615 0.00 0.00 41.41 2.40
477 528 7.230510 ACAAGGCAACACACTATTTTGAAGATA 59.769 33.333 0.00 0.00 41.41 1.98
478 529 7.145932 AGGCAACACACTATTTTGAAGATAC 57.854 36.000 0.00 0.00 41.41 2.24
479 530 6.021596 GGCAACACACTATTTTGAAGATACG 58.978 40.000 0.00 0.00 0.00 3.06
498 549 4.720530 ACGTACGGTGAAAATTGACTTC 57.279 40.909 21.06 0.00 0.00 3.01
641 744 8.962111 GTTGCAAAAGAAATTCTAGTCTTCTTG 58.038 33.333 0.00 11.11 38.94 3.02
700 1607 5.620738 AGCTAACAATGCTATCTTCTCCA 57.379 39.130 0.00 0.00 39.21 3.86
744 1651 6.613153 TTTTTCCTTCAAACTTCCTTCCAA 57.387 33.333 0.00 0.00 0.00 3.53
745 1652 6.806668 TTTTCCTTCAAACTTCCTTCCAAT 57.193 33.333 0.00 0.00 0.00 3.16
981 1949 0.605589 CCCACCCAAAAGACTCGTCC 60.606 60.000 0.00 0.00 0.00 4.79
1444 2433 2.261430 CTGCCACATCTAGCCTGCCA 62.261 60.000 0.00 0.00 0.00 4.92
1465 2458 4.384098 CCACCAGCCATGTATTCTCTGTTA 60.384 45.833 0.00 0.00 0.00 2.41
1466 2459 4.813161 CACCAGCCATGTATTCTCTGTTAG 59.187 45.833 0.00 0.00 0.00 2.34
1467 2460 4.471386 ACCAGCCATGTATTCTCTGTTAGT 59.529 41.667 0.00 0.00 0.00 2.24
1468 2461 5.661312 ACCAGCCATGTATTCTCTGTTAGTA 59.339 40.000 0.00 0.00 0.00 1.82
1469 2462 5.986135 CCAGCCATGTATTCTCTGTTAGTAC 59.014 44.000 0.00 0.00 0.00 2.73
1470 2463 6.183360 CCAGCCATGTATTCTCTGTTAGTACT 60.183 42.308 0.00 0.00 0.00 2.73
1537 2538 5.521372 TCGTTTTGATCGATCGACTACTCTA 59.479 40.000 22.06 8.21 32.30 2.43
1538 2539 5.616383 CGTTTTGATCGATCGACTACTCTAC 59.384 44.000 22.06 11.47 0.00 2.59
1539 2540 6.509837 CGTTTTGATCGATCGACTACTCTACT 60.510 42.308 22.06 0.00 0.00 2.57
1540 2541 6.528014 TTTGATCGATCGACTACTCTACTC 57.472 41.667 22.06 11.14 0.00 2.59
1541 2542 5.456548 TGATCGATCGACTACTCTACTCT 57.543 43.478 22.06 0.00 0.00 3.24
1563 2564 3.823873 TGCTGTAAATTTTCCACCGTGAT 59.176 39.130 0.00 0.00 0.00 3.06
1597 2598 5.737860 GGAAAAATTCCCAATCTGCTCAAT 58.262 37.500 0.00 0.00 44.30 2.57
1605 2606 7.664552 TTCCCAATCTGCTCAATATGATTTT 57.335 32.000 0.00 0.00 0.00 1.82
1607 2608 6.266103 TCCCAATCTGCTCAATATGATTTTCC 59.734 38.462 0.00 0.00 0.00 3.13
1613 2614 6.037500 TCTGCTCAATATGATTTTCCTCGTTG 59.962 38.462 0.00 0.00 0.00 4.10
1632 2634 0.474184 GGGGATGAACGGATGATGGT 59.526 55.000 0.00 0.00 0.00 3.55
1633 2635 1.597742 GGGATGAACGGATGATGGTG 58.402 55.000 0.00 0.00 0.00 4.17
1634 2636 1.134098 GGGATGAACGGATGATGGTGT 60.134 52.381 0.00 0.00 0.00 4.16
1636 2638 2.419990 GGATGAACGGATGATGGTGTGA 60.420 50.000 0.00 0.00 0.00 3.58
1637 2639 2.849294 TGAACGGATGATGGTGTGAA 57.151 45.000 0.00 0.00 0.00 3.18
1638 2640 3.348647 TGAACGGATGATGGTGTGAAT 57.651 42.857 0.00 0.00 0.00 2.57
1716 2759 1.006337 TCGTGCAAATGCTTTGGGC 60.006 52.632 6.97 6.55 40.94 5.36
1746 2789 0.545309 TGGGAGTGAAGGAGGACTGG 60.545 60.000 0.00 0.00 0.00 4.00
1778 2821 4.899239 GCCATGGAGGAGGCGACG 62.899 72.222 18.40 0.00 41.70 5.12
2111 3160 2.807045 GTGGACTGCACGAGCTCG 60.807 66.667 33.45 33.45 46.33 5.03
2306 3355 3.087253 CCGACCTACATGGGCCCA 61.087 66.667 30.92 30.92 42.31 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.684001 AATCGGCGGTGAAACTATCA 57.316 45.000 7.21 0.00 36.74 2.15
30 31 4.025979 CACTTAATCGGCGGTGAAACTATC 60.026 45.833 7.21 0.00 36.74 2.08
31 32 3.869246 CACTTAATCGGCGGTGAAACTAT 59.131 43.478 7.21 0.00 36.74 2.12
32 33 3.255725 CACTTAATCGGCGGTGAAACTA 58.744 45.455 7.21 0.00 36.74 2.24
33 34 2.073816 CACTTAATCGGCGGTGAAACT 58.926 47.619 7.21 0.00 36.74 2.66
34 35 1.129811 CCACTTAATCGGCGGTGAAAC 59.870 52.381 7.21 0.00 32.12 2.78
35 36 1.270947 ACCACTTAATCGGCGGTGAAA 60.271 47.619 7.21 0.00 32.12 2.69
36 37 0.322322 ACCACTTAATCGGCGGTGAA 59.678 50.000 7.21 0.00 32.12 3.18
37 38 1.184431 TACCACTTAATCGGCGGTGA 58.816 50.000 7.21 0.00 32.12 4.02
38 39 2.012937 TTACCACTTAATCGGCGGTG 57.987 50.000 7.21 6.66 0.00 4.94
39 40 2.994186 ATTACCACTTAATCGGCGGT 57.006 45.000 7.21 0.00 0.00 5.68
40 41 3.790789 GCAAATTACCACTTAATCGGCGG 60.791 47.826 7.21 0.00 29.39 6.13
41 42 3.359654 GCAAATTACCACTTAATCGGCG 58.640 45.455 0.00 0.00 29.39 6.46
42 43 3.129638 TGGCAAATTACCACTTAATCGGC 59.870 43.478 0.00 0.00 32.62 5.54
43 44 4.733523 GCTGGCAAATTACCACTTAATCGG 60.734 45.833 0.00 0.00 32.49 4.18
44 45 4.096382 AGCTGGCAAATTACCACTTAATCG 59.904 41.667 0.00 0.00 32.49 3.34
45 46 5.582689 AGCTGGCAAATTACCACTTAATC 57.417 39.130 0.00 0.00 32.49 1.75
46 47 5.594317 CCTAGCTGGCAAATTACCACTTAAT 59.406 40.000 0.00 0.00 32.49 1.40
47 48 4.947388 CCTAGCTGGCAAATTACCACTTAA 59.053 41.667 0.00 0.00 32.49 1.85
48 49 4.523083 CCTAGCTGGCAAATTACCACTTA 58.477 43.478 0.00 0.00 32.49 2.24
49 50 3.356290 CCTAGCTGGCAAATTACCACTT 58.644 45.455 0.00 0.00 32.49 3.16
50 51 3.004752 CCTAGCTGGCAAATTACCACT 57.995 47.619 0.00 3.03 32.49 4.00
76 77 1.089920 CCATGCTTCTGGTGCTACAC 58.910 55.000 0.00 0.00 0.00 2.90
77 78 0.983467 TCCATGCTTCTGGTGCTACA 59.017 50.000 0.00 0.00 37.57 2.74
90 91 0.174389 TTCTGCGACTCTCTCCATGC 59.826 55.000 0.00 0.00 0.00 4.06
94 95 2.535331 GTTCATTCTGCGACTCTCTCC 58.465 52.381 0.00 0.00 0.00 3.71
102 103 1.333115 CGTGTACGTTCATTCTGCGA 58.667 50.000 0.00 0.00 34.11 5.10
116 117 2.662791 GCGACTGTTCTTCGTACGTGTA 60.663 50.000 16.05 1.33 38.77 2.90
141 147 2.799371 GTAGGACGACAGCTCCGG 59.201 66.667 0.00 0.00 32.45 5.14
144 150 0.240411 ACAACGTAGGACGACAGCTC 59.760 55.000 5.94 0.00 46.05 4.09
168 174 2.158957 TCCAGTGAATCCTCGCCATTAC 60.159 50.000 0.00 0.00 32.03 1.89
239 263 6.952935 AAAGAAGATGAAACGTAGCTGTAG 57.047 37.500 0.00 0.00 0.00 2.74
240 264 7.095355 GGAAAAAGAAGATGAAACGTAGCTGTA 60.095 37.037 0.00 0.00 0.00 2.74
305 344 1.222115 GCACCCACTCTTCGTGTCAC 61.222 60.000 0.00 0.00 42.20 3.67
340 387 2.131183 CCGATCGCCATCTCTCTTTTC 58.869 52.381 10.32 0.00 0.00 2.29
346 393 1.291588 GATGCCGATCGCCATCTCT 59.708 57.895 26.80 0.50 36.24 3.10
404 455 3.550275 CGACTGAAACAAAAGACACGAGA 59.450 43.478 0.00 0.00 0.00 4.04
433 484 6.158598 GCCTTGTGTGACATGTGAATATTTT 58.841 36.000 1.15 0.00 0.00 1.82
461 512 6.529125 CACCGTACGTATCTTCAAAATAGTGT 59.471 38.462 15.21 0.00 0.00 3.55
476 527 5.288015 TGAAGTCAATTTTCACCGTACGTA 58.712 37.500 15.21 0.00 30.03 3.57
477 528 4.121317 TGAAGTCAATTTTCACCGTACGT 58.879 39.130 15.21 0.00 30.03 3.57
478 529 4.718858 TGAAGTCAATTTTCACCGTACG 57.281 40.909 8.69 8.69 30.03 3.67
479 530 6.056428 AGTTGAAGTCAATTTTCACCGTAC 57.944 37.500 0.00 0.00 38.24 3.67
498 549 5.392811 GGGAGCAATCTTCATCTTCAAGTTG 60.393 44.000 0.00 0.00 0.00 3.16
548 622 9.302345 CGTAGTCTTGATAAGCAATCTTCTAAA 57.698 33.333 1.38 0.00 35.59 1.85
563 666 6.892658 ATAGCAGAAGATCGTAGTCTTGAT 57.107 37.500 5.47 0.00 38.51 2.57
603 706 7.475771 TTTCTTTTGCAACATAAACACCATC 57.524 32.000 0.00 0.00 0.00 3.51
604 707 8.449251 AATTTCTTTTGCAACATAAACACCAT 57.551 26.923 0.00 0.00 0.00 3.55
605 708 7.768120 AGAATTTCTTTTGCAACATAAACACCA 59.232 29.630 0.00 0.00 0.00 4.17
663 766 8.629986 GCATTGTTAGCTAAATATTTACATGCG 58.370 33.333 7.99 0.00 0.00 4.73
664 767 9.683069 AGCATTGTTAGCTAAATATTTACATGC 57.317 29.630 7.99 11.31 41.32 4.06
674 777 8.213679 TGGAGAAGATAGCATTGTTAGCTAAAT 58.786 33.333 7.99 0.00 46.55 1.40
675 778 7.564793 TGGAGAAGATAGCATTGTTAGCTAAA 58.435 34.615 7.99 0.00 46.55 1.85
678 781 5.620738 TGGAGAAGATAGCATTGTTAGCT 57.379 39.130 0.00 0.00 45.77 3.32
679 782 6.317391 AGTTTGGAGAAGATAGCATTGTTAGC 59.683 38.462 0.00 0.00 0.00 3.09
680 783 7.856145 AGTTTGGAGAAGATAGCATTGTTAG 57.144 36.000 0.00 0.00 0.00 2.34
721 1628 6.613153 TTGGAAGGAAGTTTGAAGGAAAAA 57.387 33.333 0.00 0.00 0.00 1.94
737 1644 9.745018 ATGGTAATTATCACTGATATTGGAAGG 57.255 33.333 0.00 0.00 0.00 3.46
739 1646 9.519191 CCATGGTAATTATCACTGATATTGGAA 57.481 33.333 2.57 0.00 0.00 3.53
740 1647 8.889445 TCCATGGTAATTATCACTGATATTGGA 58.111 33.333 12.58 9.82 0.00 3.53
744 1651 9.896645 GTGATCCATGGTAATTATCACTGATAT 57.103 33.333 25.50 4.20 41.93 1.63
745 1652 8.321353 GGTGATCCATGGTAATTATCACTGATA 58.679 37.037 28.79 2.97 43.72 2.15
760 1667 5.477984 TCTTTTCAGAAAAGGTGATCCATGG 59.522 40.000 28.05 4.97 46.11 3.66
832 1758 2.757155 TTTCGAGCGGTGCATCACGA 62.757 55.000 11.74 9.22 34.83 4.35
981 1949 0.321671 TCTTGGAAAGTCGGGAGCTG 59.678 55.000 0.00 0.00 46.34 4.24
1444 2433 4.471386 ACTAACAGAGAATACATGGCTGGT 59.529 41.667 0.00 0.00 0.00 4.00
1465 2458 7.052142 AGAGCAACTAACAAACAGTAGTACT 57.948 36.000 0.00 0.00 0.00 2.73
1466 2459 6.087820 CGAGAGCAACTAACAAACAGTAGTAC 59.912 42.308 0.00 0.00 0.00 2.73
1467 2460 6.147581 CGAGAGCAACTAACAAACAGTAGTA 58.852 40.000 0.00 0.00 0.00 1.82
1468 2461 4.982916 CGAGAGCAACTAACAAACAGTAGT 59.017 41.667 0.00 0.00 0.00 2.73
1469 2462 4.386049 CCGAGAGCAACTAACAAACAGTAG 59.614 45.833 0.00 0.00 0.00 2.57
1470 2463 4.202182 ACCGAGAGCAACTAACAAACAGTA 60.202 41.667 0.00 0.00 0.00 2.74
1537 2538 3.502211 CGGTGGAAAATTTACAGCAGAGT 59.498 43.478 18.71 0.00 33.18 3.24
1538 2539 3.502211 ACGGTGGAAAATTTACAGCAGAG 59.498 43.478 18.71 6.48 33.18 3.35
1539 2540 3.252215 CACGGTGGAAAATTTACAGCAGA 59.748 43.478 18.71 0.00 33.18 4.26
1540 2541 3.252215 TCACGGTGGAAAATTTACAGCAG 59.748 43.478 18.71 13.54 33.18 4.24
1541 2542 3.215151 TCACGGTGGAAAATTTACAGCA 58.785 40.909 18.71 0.00 33.18 4.41
1597 2598 4.165180 TCATCCCCAACGAGGAAAATCATA 59.835 41.667 0.00 0.00 41.22 2.15
1613 2614 0.474184 ACCATCATCCGTTCATCCCC 59.526 55.000 0.00 0.00 0.00 4.81
1638 2640 8.881743 GCTCCATAAATTAAAATTGCATCACAA 58.118 29.630 0.00 0.00 44.01 3.33
1658 2672 0.988832 TAAACAACTCCCGGCTCCAT 59.011 50.000 0.00 0.00 0.00 3.41
1716 2759 2.566833 TCACTCCCAATCACCAACTG 57.433 50.000 0.00 0.00 0.00 3.16
1723 2766 1.909302 GTCCTCCTTCACTCCCAATCA 59.091 52.381 0.00 0.00 0.00 2.57
1746 2789 2.295885 CATGGCCATGACCTCTTCTTC 58.704 52.381 37.84 0.00 41.20 2.87
1832 2881 4.592192 ACGCCGATGCCGATCCAG 62.592 66.667 0.00 0.00 38.22 3.86


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

AutoCloner maintained by Alex Coulton.