Multiple sequence alignment - TraesCS2A01G048500

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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 TraesCS2A01G048500 chr2A 100.000 2653 0 0 1 2653 18646898 18649550 0.000000e+00 4900
1 TraesCS2A01G048500 chr2A 86.773 1822 193 27 1 1797 18614230 18616028 0.000000e+00 1986
2 TraesCS2A01G048500 chr2A 86.458 1403 163 16 312 1694 18676052 18677447 0.000000e+00 1513
3 TraesCS2A01G048500 chr2A 86.770 257 31 3 12 266 18675793 18676048 1.550000e-72 283
4 TraesCS2A01G048500 chr2B 87.237 1998 202 32 1 1958 29055319 29057303 0.000000e+00 2228
5 TraesCS2A01G048500 chr2B 91.924 1263 87 11 687 1938 28998152 28999410 0.000000e+00 1753
6 TraesCS2A01G048500 chr2B 82.835 1841 236 40 1 1796 29980312 29978507 0.000000e+00 1576
7 TraesCS2A01G048500 chr2B 91.082 684 59 2 1969 2650 28999479 29000162 0.000000e+00 924
8 TraesCS2A01G048500 chr2B 89.898 683 64 5 1971 2650 29057349 29058029 0.000000e+00 874
9 TraesCS2A01G048500 chr2B 86.957 713 64 9 1969 2653 251377501 251376790 0.000000e+00 774
10 TraesCS2A01G048500 chr2B 85.841 678 62 13 1988 2653 153704480 153705135 0.000000e+00 689
11 TraesCS2A01G048500 chr2B 86.852 540 66 4 2115 2653 539701011 539700476 1.360000e-167 599
12 TraesCS2A01G048500 chr2B 84.768 604 75 9 672 1260 29871104 29870503 8.180000e-165 590
13 TraesCS2A01G048500 chr2B 86.905 420 44 6 1 413 28995809 28996224 6.690000e-126 460
14 TraesCS2A01G048500 chr2B 83.942 274 35 8 1 266 29871714 29871442 1.220000e-63 254
15 TraesCS2A01G048500 chr2D 95.464 948 36 6 1 945 17327118 17328061 0.000000e+00 1506
16 TraesCS2A01G048500 chr2D 96.483 853 28 2 1 851 17182785 17183637 0.000000e+00 1408
17 TraesCS2A01G048500 chr2D 92.573 929 49 6 882 1797 17184007 17184928 0.000000e+00 1315
18 TraesCS2A01G048500 chr2D 85.751 1158 127 22 672 1797 17238520 17239671 0.000000e+00 1190
19 TraesCS2A01G048500 chr2D 91.696 867 52 5 943 1796 17336729 17337588 0.000000e+00 1184
20 TraesCS2A01G048500 chr2D 89.550 555 44 4 1255 1796 17347191 17347744 0.000000e+00 691
21 TraesCS2A01G048500 chr2D 89.550 555 44 4 1255 1796 17356409 17356962 0.000000e+00 691
22 TraesCS2A01G048500 chr2D 84.820 639 73 14 2029 2648 95657222 95657855 2.900000e-174 621
23 TraesCS2A01G048500 chr2D 84.414 648 75 13 2016 2648 89906148 89906784 4.850000e-172 614
24 TraesCS2A01G048500 chr2D 95.498 311 8 1 943 1253 17346382 17346686 2.370000e-135 492
25 TraesCS2A01G048500 chr2D 95.498 311 8 1 943 1253 17355689 17355993 2.370000e-135 492
26 TraesCS2A01G048500 chr3D 89.527 697 52 8 1969 2653 418772630 418773317 0.000000e+00 863
27 TraesCS2A01G048500 chr3D 83.788 697 92 11 1971 2648 182426489 182425795 2.230000e-180 641
28 TraesCS2A01G048500 chr3D 80.713 477 53 21 1971 2442 100560667 100560225 4.230000e-88 335
29 TraesCS2A01G048500 chr3D 83.684 190 17 9 1793 1969 418772409 418772597 1.630000e-37 167
30 TraesCS2A01G048500 chr7D 88.323 668 60 5 1998 2653 129821490 129822151 0.000000e+00 785
31 TraesCS2A01G048500 chr7D 83.618 702 89 14 1971 2648 37001029 37001728 1.040000e-178 636
32 TraesCS2A01G048500 chr7D 83.164 689 93 14 1971 2640 104586656 104587340 2.260000e-170 608
33 TraesCS2A01G048500 chr7D 86.207 145 16 2 1794 1934 615931272 615931128 1.270000e-33 154
34 TraesCS2A01G048500 chr1B 88.154 650 59 7 2014 2648 434337476 434338122 0.000000e+00 758
35 TraesCS2A01G048500 chr7B 80.112 890 139 27 1793 2648 594011171 594010286 1.730000e-176 628
36 TraesCS2A01G048500 chr5B 83.204 643 90 14 2014 2648 491632932 491632300 8.240000e-160 573
37 TraesCS2A01G048500 chr5D 82.948 563 80 7 1971 2518 241829627 241830188 6.600000e-136 494
38 TraesCS2A01G048500 chr1D 78.843 605 88 20 1792 2362 479390074 479389476 3.230000e-99 372
39 TraesCS2A01G048500 chr6D 88.406 138 12 3 1794 1927 403037202 403037339 2.110000e-36 163
40 TraesCS2A01G048500 chr4A 87.075 147 14 3 1792 1934 731920241 731920096 7.600000e-36 161
41 TraesCS2A01G048500 chr6A 87.050 139 14 2 1798 1932 602585165 602585027 1.270000e-33 154
42 TraesCS2A01G048500 chr6B 80.952 189 23 8 1793 1969 50502208 50502395 1.280000e-28 137


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 TraesCS2A01G048500 chr2A 18646898 18649550 2652 False 4900.000000 4900 100.000000 1 2653 1 chr2A.!!$F2 2652
1 TraesCS2A01G048500 chr2A 18614230 18616028 1798 False 1986.000000 1986 86.773000 1 1797 1 chr2A.!!$F1 1796
2 TraesCS2A01G048500 chr2A 18675793 18677447 1654 False 898.000000 1513 86.614000 12 1694 2 chr2A.!!$F3 1682
3 TraesCS2A01G048500 chr2B 29978507 29980312 1805 True 1576.000000 1576 82.835000 1 1796 1 chr2B.!!$R1 1795
4 TraesCS2A01G048500 chr2B 29055319 29058029 2710 False 1551.000000 2228 88.567500 1 2650 2 chr2B.!!$F3 2649
5 TraesCS2A01G048500 chr2B 28995809 29000162 4353 False 1045.666667 1753 89.970333 1 2650 3 chr2B.!!$F2 2649
6 TraesCS2A01G048500 chr2B 251376790 251377501 711 True 774.000000 774 86.957000 1969 2653 1 chr2B.!!$R2 684
7 TraesCS2A01G048500 chr2B 153704480 153705135 655 False 689.000000 689 85.841000 1988 2653 1 chr2B.!!$F1 665
8 TraesCS2A01G048500 chr2B 539700476 539701011 535 True 599.000000 599 86.852000 2115 2653 1 chr2B.!!$R3 538
9 TraesCS2A01G048500 chr2B 29870503 29871714 1211 True 422.000000 590 84.355000 1 1260 2 chr2B.!!$R4 1259
10 TraesCS2A01G048500 chr2D 17327118 17328061 943 False 1506.000000 1506 95.464000 1 945 1 chr2D.!!$F2 944
11 TraesCS2A01G048500 chr2D 17182785 17184928 2143 False 1361.500000 1408 94.528000 1 1797 2 chr2D.!!$F6 1796
12 TraesCS2A01G048500 chr2D 17238520 17239671 1151 False 1190.000000 1190 85.751000 672 1797 1 chr2D.!!$F1 1125
13 TraesCS2A01G048500 chr2D 17336729 17337588 859 False 1184.000000 1184 91.696000 943 1796 1 chr2D.!!$F3 853
14 TraesCS2A01G048500 chr2D 95657222 95657855 633 False 621.000000 621 84.820000 2029 2648 1 chr2D.!!$F5 619
15 TraesCS2A01G048500 chr2D 89906148 89906784 636 False 614.000000 614 84.414000 2016 2648 1 chr2D.!!$F4 632
16 TraesCS2A01G048500 chr2D 17346382 17347744 1362 False 591.500000 691 92.524000 943 1796 2 chr2D.!!$F7 853
17 TraesCS2A01G048500 chr2D 17355689 17356962 1273 False 591.500000 691 92.524000 943 1796 2 chr2D.!!$F8 853
18 TraesCS2A01G048500 chr3D 182425795 182426489 694 True 641.000000 641 83.788000 1971 2648 1 chr3D.!!$R2 677
19 TraesCS2A01G048500 chr3D 418772409 418773317 908 False 515.000000 863 86.605500 1793 2653 2 chr3D.!!$F1 860
20 TraesCS2A01G048500 chr7D 129821490 129822151 661 False 785.000000 785 88.323000 1998 2653 1 chr7D.!!$F3 655
21 TraesCS2A01G048500 chr7D 37001029 37001728 699 False 636.000000 636 83.618000 1971 2648 1 chr7D.!!$F1 677
22 TraesCS2A01G048500 chr7D 104586656 104587340 684 False 608.000000 608 83.164000 1971 2640 1 chr7D.!!$F2 669
23 TraesCS2A01G048500 chr1B 434337476 434338122 646 False 758.000000 758 88.154000 2014 2648 1 chr1B.!!$F1 634
24 TraesCS2A01G048500 chr7B 594010286 594011171 885 True 628.000000 628 80.112000 1793 2648 1 chr7B.!!$R1 855
25 TraesCS2A01G048500 chr5B 491632300 491632932 632 True 573.000000 573 83.204000 2014 2648 1 chr5B.!!$R1 634
26 TraesCS2A01G048500 chr5D 241829627 241830188 561 False 494.000000 494 82.948000 1971 2518 1 chr5D.!!$F1 547
27 TraesCS2A01G048500 chr1D 479389476 479390074 598 True 372.000000 372 78.843000 1792 2362 1 chr1D.!!$R1 570

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
150 152 1.205655 TCCTTGATCTCTTCAGCACCG 59.794 52.381 0.0 0.0 35.27 4.94 F
820 2586 3.099905 AGCTCAAGCCGCTATATGGATA 58.900 45.455 0.0 0.0 43.38 2.59 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1286 3912 0.539438 TTTCCATCTGTGGCACCACC 60.539 55.0 16.26 0.22 45.63 4.61 R
2451 5212 0.325602 ATACCCCTTCGTTTCCGCAA 59.674 50.0 0.00 0.00 0.00 4.85 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
31 32 7.324935 TGCAATTCGAGGTGTACTTATTTAGA 58.675 34.615 0.00 0.00 0.00 2.10
150 152 1.205655 TCCTTGATCTCTTCAGCACCG 59.794 52.381 0.00 0.00 35.27 4.94
286 297 3.947910 ACATTGGCCATGTTCTTGAAG 57.052 42.857 6.09 0.00 44.40 3.02
499 525 9.483489 TGAATCACTAGGGAAAACTATGTACTA 57.517 33.333 0.00 0.00 0.00 1.82
605 632 6.946009 ACCTGCTAATTACCACTTTGTGTAAT 59.054 34.615 0.00 0.00 0.00 1.89
817 2583 3.533606 ATAGCTCAAGCCGCTATATGG 57.466 47.619 2.95 0.00 45.95 2.74
820 2586 3.099905 AGCTCAAGCCGCTATATGGATA 58.900 45.455 0.00 0.00 43.38 2.59
851 2617 9.643693 AAAGTAAATTTCTTGATTGTGCCATAG 57.356 29.630 0.00 0.00 0.00 2.23
876 2644 9.822185 AGAGTAAAAGAAGGTAAACGTTTAAGA 57.178 29.630 21.67 0.00 0.00 2.10
926 3042 5.050499 GCCATCATTTCTCTACACAATCTCG 60.050 44.000 0.00 0.00 0.00 4.04
971 3091 4.100653 CCATGGTAGAGTGTCAGATGTGAT 59.899 45.833 2.57 0.00 34.36 3.06
1044 3165 9.088512 CACATCACACTAAGTTTATTCTCTACC 57.911 37.037 0.00 0.00 0.00 3.18
1286 3912 4.318593 GCGAACTATGAATCTCACGATACG 59.681 45.833 0.00 0.00 0.00 3.06
1553 4191 7.809806 TGAGATATGTATCATGTCGTCAATGTC 59.190 37.037 3.12 0.00 35.17 3.06
1664 4315 6.984474 TGGTTGAATTTACGGACTCTCATATC 59.016 38.462 0.00 0.00 0.00 1.63
1824 4488 3.890147 CTCTAGCAGACCCCGTATAAAGT 59.110 47.826 0.00 0.00 0.00 2.66
1887 4551 1.913951 AATGCTGCCCGATCAGACCA 61.914 55.000 7.86 0.00 36.19 4.02
1895 4559 0.948623 CCGATCAGACCACGCAAACA 60.949 55.000 0.00 0.00 0.00 2.83
1897 4561 1.225855 GATCAGACCACGCAAACACA 58.774 50.000 0.00 0.00 0.00 3.72
1898 4562 1.195448 GATCAGACCACGCAAACACAG 59.805 52.381 0.00 0.00 0.00 3.66
1931 4599 3.660111 GCGGGGCGTGGCATAATC 61.660 66.667 0.00 0.00 0.00 1.75
1958 4634 1.900016 GAAAACGCGGTTTCCCCCT 60.900 57.895 33.94 7.36 34.43 4.79
1959 4635 2.137425 GAAAACGCGGTTTCCCCCTG 62.137 60.000 33.94 0.00 34.43 4.45
2063 4796 2.403252 ACGATTCCAGCCAAACTAGG 57.597 50.000 0.00 0.00 0.00 3.02
2287 5041 4.430765 CGTCCTGTAGCCGCCGTT 62.431 66.667 0.00 0.00 0.00 4.44
2292 5049 3.620300 CTGTAGCCGCCGTTGTCGA 62.620 63.158 0.00 0.00 39.71 4.20
2313 5074 2.186602 TTGCCGGCAAGGATTCGGTA 62.187 55.000 37.30 12.35 44.97 4.02
2410 5171 1.889105 CGGACAATGCTGCGGCTAT 60.889 57.895 20.27 7.85 39.59 2.97
2553 5327 3.118629 TCTCATGTGTGTAGGAAGATGGC 60.119 47.826 0.00 0.00 0.00 4.40
2564 5338 3.438183 AGGAAGATGGCTGCTCATTTTT 58.562 40.909 0.00 1.43 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 6.595716 GCTGATATGTAGTTTCAAAGTCACCT 59.404 38.462 0.00 0.00 0.00 4.00
150 152 6.401367 GCAAATGATGAAACAAATAGTGTGGC 60.401 38.462 0.00 0.00 40.60 5.01
302 314 7.557358 TCCAAAAAGATTAGCAAGATCATAGCA 59.443 33.333 0.00 0.00 0.00 3.49
445 470 6.485171 ACTAGAACCAAGATTACCATTTGCT 58.515 36.000 0.00 0.00 0.00 3.91
515 542 6.265196 GCCACAATTCCCTTAATATGTCATCA 59.735 38.462 0.00 0.00 0.00 3.07
653 733 8.154203 TGGTCATTTGAGTTGTGTCTTATCTAA 58.846 33.333 0.00 0.00 0.00 2.10
662 742 4.985538 ACCTATGGTCATTTGAGTTGTGT 58.014 39.130 0.00 0.00 0.00 3.72
667 747 6.469410 TCGTTTAACCTATGGTCATTTGAGT 58.531 36.000 0.00 0.00 33.12 3.41
668 748 6.978343 TCGTTTAACCTATGGTCATTTGAG 57.022 37.500 0.00 0.00 33.12 3.02
887 2994 2.092323 GATGGCAGGGTGAAAACTACC 58.908 52.381 0.00 0.00 37.48 3.18
1044 3165 3.667497 TGGTTTGTACAGCTCTCTCTG 57.333 47.619 0.00 0.00 39.86 3.35
1286 3912 0.539438 TTTCCATCTGTGGCACCACC 60.539 55.000 16.26 0.22 45.63 4.61
1300 3926 1.089112 CATCAGACTGCGCATTTCCA 58.911 50.000 12.24 0.52 0.00 3.53
1553 4191 4.554363 CGGCCGGACTACGCAGAG 62.554 72.222 20.10 0.00 42.52 3.35
1835 4499 3.129113 ACCCGTATTTTGGCGGTTATTTC 59.871 43.478 0.00 0.00 45.91 2.17
1887 4551 1.096386 TTTACGGGCTGTGTTTGCGT 61.096 50.000 9.79 0.00 0.00 5.24
1895 4559 2.796735 CGCAAAAACTTTTACGGGCTGT 60.797 45.455 3.57 3.57 34.27 4.40
1897 4561 2.128367 CGCAAAAACTTTTACGGGCT 57.872 45.000 0.53 0.00 34.27 5.19
2113 4846 2.657237 CCGACGCAGGAGGAAGTT 59.343 61.111 0.00 0.00 0.00 2.66
2133 4869 1.812525 GATCTGCTCGTCTCTGGCA 59.187 57.895 0.00 0.00 34.66 4.92
2254 5008 1.641577 GACGAACCAGTACCTGCATC 58.358 55.000 0.00 0.00 0.00 3.91
2287 5041 2.331893 CCTTGCCGGCAAATCGACA 61.332 57.895 38.96 18.60 35.33 4.35
2292 5049 1.666209 CCGAATCCTTGCCGGCAAAT 61.666 55.000 38.96 28.66 36.62 2.32
2410 5171 1.079127 GCTTGGGCGTGCTAGAAGA 60.079 57.895 0.00 0.00 0.00 2.87
2451 5212 0.325602 ATACCCCTTCGTTTCCGCAA 59.674 50.000 0.00 0.00 0.00 4.85
2463 5224 3.603965 TGGAAACAACAACATACCCCT 57.396 42.857 0.00 0.00 37.44 4.79
2553 5327 4.512571 CCTTCCCAAAACAAAAATGAGCAG 59.487 41.667 0.00 0.00 0.00 4.24
2564 5338 6.310941 TCAATGTATTCTCCTTCCCAAAACA 58.689 36.000 0.00 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.