Multiple sequence alignment - TraesCS1A01G221500

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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 TraesCS1A01G221500 chr1A 100.000 2285 0 0 1 2285 390641673 390639389 0.000000e+00 4220
1 TraesCS1A01G221500 chr1D 94.924 1635 62 11 660 2285 310776145 310774523 0.000000e+00 2540
2 TraesCS1A01G221500 chr1D 94.286 665 35 2 1 662 310776932 310776268 0.000000e+00 1014
3 TraesCS1A01G221500 chr1B 92.555 1679 67 15 622 2285 420417562 420415927 0.000000e+00 2355
4 TraesCS1A01G221500 chr1B 91.200 250 18 3 336 583 420417807 420417560 1.010000e-88 337
5 TraesCS1A01G221500 chr2D 77.426 474 91 13 1638 2103 618301901 618302366 3.740000e-68 268
6 TraesCS1A01G221500 chr2B 77.704 453 90 8 1658 2103 754977203 754977651 1.350000e-67 267
7 TraesCS1A01G221500 chr5A 77.124 459 87 16 1638 2090 697052061 697052507 1.360000e-62 250
8 TraesCS1A01G221500 chr3D 76.754 456 81 18 1638 2090 108287757 108288190 4.910000e-57 231
9 TraesCS1A01G221500 chr4D 76.344 465 89 17 1638 2090 509095701 509096156 1.770000e-56 230
10 TraesCS1A01G221500 chr4B 76.923 364 50 19 1627 1986 658180133 658179800 2.330000e-40 176


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 TraesCS1A01G221500 chr1A 390639389 390641673 2284 True 4220 4220 100.0000 1 2285 1 chr1A.!!$R1 2284
1 TraesCS1A01G221500 chr1D 310774523 310776932 2409 True 1777 2540 94.6050 1 2285 2 chr1D.!!$R1 2284
2 TraesCS1A01G221500 chr1B 420415927 420417807 1880 True 1346 2355 91.8775 336 2285 2 chr1B.!!$R1 1949

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
45 46 2.289195 CCATGGCAGCAATCTTTGTGTT 60.289 45.455 0.0 0.0 0.0 3.32 F
1036 1175 1.566298 ATCTGAAGTCCCCCAGCCAC 61.566 60.000 0.0 0.0 0.0 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1045 1184 0.321298 GTTGAGGCGGGCTTTACAGA 60.321 55.000 5.24 0.0 0.00 3.41 R
1856 2013 1.008538 CGCTGGCGAAACAAAAGCT 60.009 52.632 9.51 0.0 42.83 3.74 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
45 46 2.289195 CCATGGCAGCAATCTTTGTGTT 60.289 45.455 0.00 0.0 0.00 3.32
49 50 5.973899 TGGCAGCAATCTTTGTGTTAATA 57.026 34.783 0.00 0.0 0.00 0.98
63 64 9.979270 CTTTGTGTTAATAGTCAATAAGCTCAG 57.021 33.333 0.00 0.0 0.00 3.35
68 69 2.775911 AGTCAATAAGCTCAGCTGCA 57.224 45.000 9.47 0.0 39.62 4.41
76 77 5.747951 ATAAGCTCAGCTGCATTAACTTC 57.252 39.130 9.47 0.0 39.62 3.01
84 88 7.510549 TCAGCTGCATTAACTTCTTTAGTTT 57.489 32.000 9.47 0.0 44.73 2.66
91 95 9.515020 TGCATTAACTTCTTTAGTTTTGTCAAG 57.485 29.630 0.00 0.0 44.73 3.02
125 129 4.522022 CCTCTTTCACATGCTTCCTTCTTT 59.478 41.667 0.00 0.0 0.00 2.52
135 139 6.318144 ACATGCTTCCTTCTTTGATACATCAG 59.682 38.462 0.00 0.0 38.19 2.90
141 145 7.186570 TCCTTCTTTGATACATCAGATCACA 57.813 36.000 0.00 0.0 38.19 3.58
147 151 9.889128 TCTTTGATACATCAGATCACACAATTA 57.111 29.630 0.00 0.0 38.19 1.40
156 160 5.530543 TCAGATCACACAATTACACTTGCAA 59.469 36.000 0.00 0.0 0.00 4.08
212 216 9.010029 GTCTTTAGGAATTAAGAACCATTGTGA 57.990 33.333 0.00 0.0 32.59 3.58
398 402 2.289320 TGTGCTTGTGCTTTGGTGTTTT 60.289 40.909 0.00 0.0 40.48 2.43
466 471 8.546244 GTTTGTTAGGAAGTTTGTACTGTCTAC 58.454 37.037 0.00 0.0 34.01 2.59
496 501 2.378038 ACAGAACTGGTGTGCAATTGT 58.622 42.857 7.40 0.0 34.19 2.71
501 506 2.653726 ACTGGTGTGCAATTGTTGAGA 58.346 42.857 7.40 0.0 0.00 3.27
543 548 2.489938 TTATATCATGCGCCCTTCCC 57.510 50.000 4.18 0.0 0.00 3.97
607 612 5.304778 AGCATACACACACACAATTAGTCA 58.695 37.500 0.00 0.0 0.00 3.41
612 617 5.376625 ACACACACACAATTAGTCAAGGAT 58.623 37.500 0.00 0.0 0.00 3.24
637 642 6.061231 TCACATGTTGCTCTATAGACTACG 57.939 41.667 0.00 0.0 0.00 3.51
690 820 2.892852 ACTGGAATCATGTGGTGTTTGG 59.107 45.455 0.00 0.0 0.00 3.28
760 893 9.425248 TTCTAATGCTTAGGATTTGGATTCATT 57.575 29.630 3.97 0.0 34.00 2.57
914 1052 3.825908 AAGGGGGACTGCTATTTTTCA 57.174 42.857 0.00 0.0 0.00 2.69
915 1053 4.337264 AAGGGGGACTGCTATTTTTCAT 57.663 40.909 0.00 0.0 0.00 2.57
917 1055 4.026052 AGGGGGACTGCTATTTTTCATTG 58.974 43.478 0.00 0.0 0.00 2.82
918 1056 3.132824 GGGGGACTGCTATTTTTCATTGG 59.867 47.826 0.00 0.0 0.00 3.16
919 1057 3.769300 GGGGACTGCTATTTTTCATTGGT 59.231 43.478 0.00 0.0 0.00 3.67
920 1058 4.953579 GGGGACTGCTATTTTTCATTGGTA 59.046 41.667 0.00 0.0 0.00 3.25
921 1059 5.598417 GGGGACTGCTATTTTTCATTGGTAT 59.402 40.000 0.00 0.0 0.00 2.73
1036 1175 1.566298 ATCTGAAGTCCCCCAGCCAC 61.566 60.000 0.00 0.0 0.00 5.01
1045 1184 1.693640 CCCCAGCCACCTTCATCTT 59.306 57.895 0.00 0.0 0.00 2.40
1050 1192 2.237143 CCAGCCACCTTCATCTTCTGTA 59.763 50.000 0.00 0.0 0.00 2.74
1205 1350 2.791383 TTGTTTGCGATGTCAAAGGG 57.209 45.000 0.00 0.0 36.71 3.95
1206 1351 1.974265 TGTTTGCGATGTCAAAGGGA 58.026 45.000 0.00 0.0 36.71 4.20
1310 1462 6.373186 ACATATGATGCAATGTCAGTTCTG 57.627 37.500 10.38 0.0 30.54 3.02
1321 1473 6.293626 GCAATGTCAGTTCTGTGTAGTGAAAT 60.294 38.462 0.00 0.0 0.00 2.17
1336 1488 3.042887 GTGAAATTTTGTCGCTGTCACC 58.957 45.455 0.00 0.0 0.00 4.02
1350 1502 2.868583 CTGTCACCAAGCATAATCCTCG 59.131 50.000 0.00 0.0 0.00 4.63
1453 1607 6.471146 ACTGTCTATGCAAGAAGAGAAACAT 58.529 36.000 0.00 0.0 35.47 2.71
1594 1751 1.798813 CAGGACCGCACAAAGAACTAC 59.201 52.381 0.00 0.0 0.00 2.73
1751 1908 2.665603 GCCTTCTTCTCCAGCGGT 59.334 61.111 0.00 0.0 0.00 5.68
1871 2028 0.030101 CGGAAGCTTTTGTTTCGCCA 59.970 50.000 0.00 0.0 40.01 5.69
2107 2264 4.657824 CACGGCCCTCACGTCGTT 62.658 66.667 0.00 0.0 43.58 3.85
2210 2367 1.878775 CGGCTTGCCCTTGAAGAAG 59.121 57.895 6.02 0.0 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 5.917462 TGCAGCTGAGCTTATTGACTATTA 58.083 37.500 20.43 0.00 36.40 0.98
49 50 2.775911 TGCAGCTGAGCTTATTGACT 57.224 45.000 20.43 0.00 36.40 3.41
76 77 6.693315 TTCCTCCACTTGACAAAACTAAAG 57.307 37.500 0.00 0.00 0.00 1.85
125 129 8.260114 AGTGTAATTGTGTGATCTGATGTATCA 58.740 33.333 0.00 0.00 35.16 2.15
135 139 5.762045 ACTTGCAAGTGTAATTGTGTGATC 58.238 37.500 30.66 0.00 37.98 2.92
141 145 7.665561 AACAAAAACTTGCAAGTGTAATTGT 57.334 28.000 31.73 29.61 39.66 2.71
147 151 4.213059 CACCAAACAAAAACTTGCAAGTGT 59.787 37.500 31.73 24.63 39.66 3.55
156 160 5.242615 ACAAAATTGCCACCAAACAAAAACT 59.757 32.000 0.00 0.00 34.05 2.66
264 268 4.164981 ACAGGAGTACATTAAGGTGACCA 58.835 43.478 3.63 0.00 0.00 4.02
325 329 8.341173 GCTCAGAAGATACATTTGTTATCTTGG 58.659 37.037 8.91 2.95 39.73 3.61
334 338 7.783090 ACATACTGCTCAGAAGATACATTTG 57.217 36.000 3.60 0.00 0.00 2.32
466 471 5.231991 GCACACCAGTTCTGTAAAACAAATG 59.768 40.000 0.00 0.00 0.00 2.32
479 484 3.066621 TCTCAACAATTGCACACCAGTTC 59.933 43.478 5.05 0.00 0.00 3.01
535 540 0.826256 AAGGTTGTTTCGGGAAGGGC 60.826 55.000 0.00 0.00 0.00 5.19
543 548 5.351233 TGTGTTAGCATAAGGTTGTTTCG 57.649 39.130 0.00 0.00 0.00 3.46
607 612 8.310382 GTCTATAGAGCAACATGTGATATCCTT 58.690 37.037 1.64 0.00 0.00 3.36
612 617 7.660208 TCGTAGTCTATAGAGCAACATGTGATA 59.340 37.037 1.64 0.00 0.00 2.15
637 642 2.092429 TGAAGGGACAGGCACCAATATC 60.092 50.000 0.00 0.00 0.00 1.63
901 1039 8.970020 TGATGAATACCAATGAAAAATAGCAGT 58.030 29.630 0.00 0.00 0.00 4.40
904 1042 9.970395 TCATGATGAATACCAATGAAAAATAGC 57.030 29.630 0.00 0.00 0.00 2.97
914 1052 8.715190 TTCAATCCATCATGATGAATACCAAT 57.285 30.769 32.71 13.32 41.20 3.16
915 1053 8.715190 ATTCAATCCATCATGATGAATACCAA 57.285 30.769 32.71 18.68 41.20 3.67
917 1055 7.544566 GCAATTCAATCCATCATGATGAATACC 59.455 37.037 32.71 16.20 41.20 2.73
918 1056 8.085909 TGCAATTCAATCCATCATGATGAATAC 58.914 33.333 32.71 20.03 41.20 1.89
919 1057 8.184304 TGCAATTCAATCCATCATGATGAATA 57.816 30.769 32.71 19.32 41.20 1.75
920 1058 7.015195 TCTGCAATTCAATCCATCATGATGAAT 59.985 33.333 32.71 22.38 41.20 2.57
921 1059 6.322712 TCTGCAATTCAATCCATCATGATGAA 59.677 34.615 32.71 21.25 41.20 2.57
1036 1175 2.939103 CGGGCTTTACAGAAGATGAAGG 59.061 50.000 0.00 0.00 0.00 3.46
1045 1184 0.321298 GTTGAGGCGGGCTTTACAGA 60.321 55.000 5.24 0.00 0.00 3.41
1050 1192 1.966451 CGAAGTTGAGGCGGGCTTT 60.966 57.895 5.24 0.00 0.00 3.51
1205 1350 2.888863 CAGTCCCCTCTGCGACTC 59.111 66.667 0.00 0.00 37.23 3.36
1310 1462 4.844267 ACAGCGACAAAATTTCACTACAC 58.156 39.130 0.00 0.00 0.00 2.90
1321 1473 0.380378 GCTTGGTGACAGCGACAAAA 59.620 50.000 0.00 0.00 44.54 2.44
1336 1488 4.631377 TGTTTGACTCGAGGATTATGCTTG 59.369 41.667 18.41 0.00 0.00 4.01
1350 1502 9.788960 AAAATTTGAAACTCTACTGTTTGACTC 57.211 29.630 0.00 0.00 39.86 3.36
1406 1560 7.816941 GTCAAATGACGACAGCATGATTGCA 62.817 44.000 0.00 0.00 42.32 4.08
1407 1561 5.478976 GTCAAATGACGACAGCATGATTGC 61.479 45.833 0.00 0.00 41.18 3.56
1408 1562 4.093514 GTCAAATGACGACAGCATGATTG 58.906 43.478 0.00 0.00 35.71 2.67
1409 1563 4.346734 GTCAAATGACGACAGCATGATT 57.653 40.909 0.00 0.00 35.71 2.57
1424 1578 6.705302 TCTCTTCTTGCATAGACAGTCAAAT 58.295 36.000 2.66 0.00 30.90 2.32
1512 1669 7.915293 TCGTTTTTATAGGCAAAAGATCAGA 57.085 32.000 0.00 0.00 0.00 3.27
1594 1751 4.479993 CTGCTTCCTCGGCTGGGG 62.480 72.222 4.49 4.49 0.00 4.96
1751 1908 2.627945 GTCATGTACCCGAGCATCAAA 58.372 47.619 0.00 0.00 33.17 2.69
1853 2010 1.770957 CTGGCGAAACAAAAGCTTCC 58.229 50.000 0.00 0.00 0.00 3.46
1856 2013 1.008538 CGCTGGCGAAACAAAAGCT 60.009 52.632 9.51 0.00 42.83 3.74
2113 2270 4.143333 CCACCGTCGGCTACCTGG 62.143 72.222 12.28 7.37 0.00 4.45


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

AutoCloner maintained by Alex Coulton.