Multiple sequence alignment - TraesCS3D01G092100

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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 TraesCS3D01G092100 chr3D 100.000 2534 0 0 1 2534 46484795 46487328 0.000000e+00 4680
1 TraesCS3D01G092100 chr3D 89.642 2568 203 34 1 2531 46523966 46526507 0.000000e+00 3210
2 TraesCS3D01G092100 chr3B 92.641 2582 121 26 1 2534 72714445 72717005 0.000000e+00 3651
3 TraesCS3D01G092100 chr3B 86.821 1510 126 33 1 1483 72921465 72922928 0.000000e+00 1618
4 TraesCS3D01G092100 chr3B 91.887 1060 74 5 1480 2531 72923088 72924143 0.000000e+00 1471
5 TraesCS3D01G092100 chr3A 92.335 2544 129 31 1 2512 57903718 57906227 0.000000e+00 3557
6 TraesCS3D01G092100 chr3A 91.882 1047 80 5 1391 2434 57981158 57980114 0.000000e+00 1458
7 TraesCS3D01G092100 chr3A 83.944 573 61 16 329 898 57915669 57916213 1.040000e-143 520
8 TraesCS3D01G092100 chr3A 91.121 214 16 3 1 212 57915306 57915518 1.150000e-73 287
9 TraesCS3D01G092100 chr3A 93.333 90 5 1 2442 2531 57975401 57975313 5.690000e-27 132
10 TraesCS3D01G092100 chr5A 75.815 1472 321 30 909 2367 143659792 143658343 0.000000e+00 713
11 TraesCS3D01G092100 chr5B 75.747 1472 321 32 909 2367 141149021 141147573 0.000000e+00 708
12 TraesCS3D01G092100 chr5D 76.003 1396 300 30 985 2367 128643430 128642057 0.000000e+00 689
13 TraesCS3D01G092100 chr6D 75.855 1375 292 30 994 2343 53175718 53174359 0.000000e+00 664
14 TraesCS3D01G092100 chr7A 75.839 1370 281 34 994 2336 631984736 631986082 0.000000e+00 651
15 TraesCS3D01G092100 chr7B 75.802 1372 278 37 994 2336 591461942 591463288 0.000000e+00 645
16 TraesCS3D01G092100 chr6B 75.447 1397 303 28 994 2365 120132595 120131214 0.000000e+00 643
17 TraesCS3D01G092100 chr7D 75.729 1372 279 36 994 2336 548231394 548232740 7.640000e-180 640
18 TraesCS3D01G092100 chr1B 75.175 1430 311 33 994 2397 4597252 4595841 3.560000e-178 634
19 TraesCS3D01G092100 chr1B 75.254 1378 285 42 995 2336 46830010 46828653 2.790000e-169 604


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 TraesCS3D01G092100 chr3D 46484795 46487328 2533 False 4680.0 4680 100.0000 1 2534 1 chr3D.!!$F1 2533
1 TraesCS3D01G092100 chr3D 46523966 46526507 2541 False 3210.0 3210 89.6420 1 2531 1 chr3D.!!$F2 2530
2 TraesCS3D01G092100 chr3B 72714445 72717005 2560 False 3651.0 3651 92.6410 1 2534 1 chr3B.!!$F1 2533
3 TraesCS3D01G092100 chr3B 72921465 72924143 2678 False 1544.5 1618 89.3540 1 2531 2 chr3B.!!$F2 2530
4 TraesCS3D01G092100 chr3A 57903718 57906227 2509 False 3557.0 3557 92.3350 1 2512 1 chr3A.!!$F1 2511
5 TraesCS3D01G092100 chr3A 57980114 57981158 1044 True 1458.0 1458 91.8820 1391 2434 1 chr3A.!!$R2 1043
6 TraesCS3D01G092100 chr3A 57915306 57916213 907 False 403.5 520 87.5325 1 898 2 chr3A.!!$F2 897
7 TraesCS3D01G092100 chr5A 143658343 143659792 1449 True 713.0 713 75.8150 909 2367 1 chr5A.!!$R1 1458
8 TraesCS3D01G092100 chr5B 141147573 141149021 1448 True 708.0 708 75.7470 909 2367 1 chr5B.!!$R1 1458
9 TraesCS3D01G092100 chr5D 128642057 128643430 1373 True 689.0 689 76.0030 985 2367 1 chr5D.!!$R1 1382
10 TraesCS3D01G092100 chr6D 53174359 53175718 1359 True 664.0 664 75.8550 994 2343 1 chr6D.!!$R1 1349
11 TraesCS3D01G092100 chr7A 631984736 631986082 1346 False 651.0 651 75.8390 994 2336 1 chr7A.!!$F1 1342
12 TraesCS3D01G092100 chr7B 591461942 591463288 1346 False 645.0 645 75.8020 994 2336 1 chr7B.!!$F1 1342
13 TraesCS3D01G092100 chr6B 120131214 120132595 1381 True 643.0 643 75.4470 994 2365 1 chr6B.!!$R1 1371
14 TraesCS3D01G092100 chr7D 548231394 548232740 1346 False 640.0 640 75.7290 994 2336 1 chr7D.!!$F1 1342
15 TraesCS3D01G092100 chr1B 4595841 4597252 1411 True 634.0 634 75.1750 994 2397 1 chr1B.!!$R1 1403
16 TraesCS3D01G092100 chr1B 46828653 46830010 1357 True 604.0 604 75.2540 995 2336 1 chr1B.!!$R2 1341

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
123 137 0.250338 AAACAGCTCCAACCTCGGTC 60.250 55.0 0.00 0.0 0.00 4.79 F
1254 1357 0.896923 GCCATGGCAATCAGTTGGAA 59.103 50.0 32.08 0.0 41.49 3.53 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1383 1486 0.105760 TGTTTGGTGTGGAGGCCAAT 60.106 50.000 5.01 0.00 43.38 3.16 R
2184 2480 2.818921 ACTTATGGCCTTGCAATCCAA 58.181 42.857 20.16 7.93 33.04 3.53 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
90 98 2.822399 CGGCGCCCTTTCCTCTAT 59.178 61.111 23.46 0.00 0.00 1.98
96 110 1.138266 CGCCCTTTCCTCTATTTCCGA 59.862 52.381 0.00 0.00 0.00 4.55
123 137 0.250338 AAACAGCTCCAACCTCGGTC 60.250 55.000 0.00 0.00 0.00 4.79
124 138 1.122019 AACAGCTCCAACCTCGGTCT 61.122 55.000 0.00 0.00 0.00 3.85
205 220 2.890311 TGGTTGATTGACACATGGAACC 59.110 45.455 0.00 0.00 0.00 3.62
207 222 3.157087 GTTGATTGACACATGGAACCCT 58.843 45.455 0.00 0.00 0.00 4.34
208 223 4.331968 GTTGATTGACACATGGAACCCTA 58.668 43.478 0.00 0.00 0.00 3.53
209 224 4.220693 TGATTGACACATGGAACCCTAG 57.779 45.455 0.00 0.00 0.00 3.02
210 225 3.587061 TGATTGACACATGGAACCCTAGT 59.413 43.478 0.00 0.00 0.00 2.57
283 343 3.319137 AGAATTAGTGTCGCTCAGCAA 57.681 42.857 0.00 0.00 0.00 3.91
286 346 4.697352 AGAATTAGTGTCGCTCAGCAAAAT 59.303 37.500 0.00 0.00 0.00 1.82
287 347 4.606457 ATTAGTGTCGCTCAGCAAAATC 57.394 40.909 0.00 0.00 0.00 2.17
320 380 4.265073 GTTCAGCAGGTGGATGTTATCTT 58.735 43.478 0.00 0.00 33.66 2.40
325 385 4.051922 GCAGGTGGATGTTATCTTCTACG 58.948 47.826 0.00 0.00 32.72 3.51
355 443 8.148999 AGTTATTATGTCCGTAGATTTCTTCCC 58.851 37.037 0.00 0.00 0.00 3.97
362 450 3.375299 CCGTAGATTTCTTCCCTGCTTTG 59.625 47.826 0.00 0.00 0.00 2.77
395 484 5.936372 GCAATTCCAGATATGTCTCTGCATA 59.064 40.000 0.00 0.00 41.12 3.14
467 556 9.993454 GATAAATAGGGTGGTACCTTAGTTAAG 57.007 37.037 14.36 0.00 41.44 1.85
620 715 5.957771 TGTCCAAAGGAGTATGCTAGAAT 57.042 39.130 0.00 0.00 33.13 2.40
621 716 6.313519 TGTCCAAAGGAGTATGCTAGAATT 57.686 37.500 0.00 0.00 33.13 2.17
622 717 6.721318 TGTCCAAAGGAGTATGCTAGAATTT 58.279 36.000 0.00 0.00 33.13 1.82
623 718 7.175104 TGTCCAAAGGAGTATGCTAGAATTTT 58.825 34.615 0.00 0.00 33.13 1.82
624 719 7.669722 TGTCCAAAGGAGTATGCTAGAATTTTT 59.330 33.333 0.00 0.00 33.13 1.94
671 766 2.303022 CAACTTCCTCAGGAGCACCTAA 59.697 50.000 1.02 0.00 45.94 2.69
685 780 2.763448 GCACCTAAGTCTCAGTCCTCAT 59.237 50.000 0.00 0.00 0.00 2.90
763 858 5.710513 TTCTGATTGGTTGTTTCTGGATG 57.289 39.130 0.00 0.00 0.00 3.51
765 860 3.499338 TGATTGGTTGTTTCTGGATGCT 58.501 40.909 0.00 0.00 0.00 3.79
766 861 3.256383 TGATTGGTTGTTTCTGGATGCTG 59.744 43.478 0.00 0.00 0.00 4.41
808 903 4.943705 GCAGTTTCAGATACTTGGGATGAA 59.056 41.667 0.00 0.00 0.00 2.57
840 943 9.367444 CTTCGATGTTGTTCCTTATTAGTAACT 57.633 33.333 0.00 0.00 0.00 2.24
860 963 8.495949 AGTAACTCATGAATTTTCACAAGTACG 58.504 33.333 0.00 0.00 40.49 3.67
861 964 7.490962 AACTCATGAATTTTCACAAGTACGA 57.509 32.000 0.00 0.00 40.49 3.43
864 967 8.656849 ACTCATGAATTTTCACAAGTACGATAC 58.343 33.333 0.00 0.00 40.49 2.24
930 1033 6.927936 TGCTATGCTTAACTCTGATTCTCATC 59.072 38.462 0.00 0.00 0.00 2.92
1072 1175 4.634883 CCAGGACAAGTGATCTGAATTCTG 59.365 45.833 7.05 6.50 0.00 3.02
1254 1357 0.896923 GCCATGGCAATCAGTTGGAA 59.103 50.000 32.08 0.00 41.49 3.53
1264 1367 2.151502 TCAGTTGGAAAACCAAGGCA 57.848 45.000 1.75 0.00 0.00 4.75
1359 1462 2.170607 TGGTCTTGGTTATCTAGCCTGC 59.829 50.000 0.00 0.00 0.00 4.85
1383 1486 2.217510 AGAAACTAGCGTCCCTCAGA 57.782 50.000 0.00 0.00 0.00 3.27
1387 1490 1.115467 ACTAGCGTCCCTCAGATTGG 58.885 55.000 0.00 0.00 0.00 3.16
1444 1548 0.311790 CGTGGCTGTTCATTGCAAGT 59.688 50.000 4.94 0.00 0.00 3.16
1531 1798 3.718434 TGGCTCTGTAGGATCATTGGAAT 59.282 43.478 0.00 0.00 0.00 3.01
2182 2478 1.174783 TTACTGGAGACACTCGAGCC 58.825 55.000 13.61 5.65 39.41 4.70
2183 2479 0.037734 TACTGGAGACACTCGAGCCA 59.962 55.000 13.61 10.42 39.41 4.75
2184 2480 0.613292 ACTGGAGACACTCGAGCCAT 60.613 55.000 13.61 0.00 39.41 4.40
2254 2550 3.830755 GCCCCATGCTTGATTAATCTCAT 59.169 43.478 16.24 12.89 36.87 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 98 3.541632 AGCTGTTTTCTTCAGTCGGAAA 58.458 40.909 0.00 0.00 34.44 3.13
96 110 2.952310 GGTTGGAGCTGTTTTCTTCAGT 59.048 45.455 0.00 0.00 35.60 3.41
123 137 4.527509 TCTGAAGTTGAGGAGCTAACAG 57.472 45.455 0.23 0.00 0.00 3.16
124 138 4.825422 CATCTGAAGTTGAGGAGCTAACA 58.175 43.478 0.23 0.00 0.00 2.41
205 220 7.317390 ACATAAAAATTACCCGCAAAACTAGG 58.683 34.615 0.00 0.00 0.00 3.02
207 222 7.039923 TGGACATAAAAATTACCCGCAAAACTA 60.040 33.333 0.00 0.00 0.00 2.24
208 223 6.160684 GGACATAAAAATTACCCGCAAAACT 58.839 36.000 0.00 0.00 0.00 2.66
209 224 5.927115 TGGACATAAAAATTACCCGCAAAAC 59.073 36.000 0.00 0.00 0.00 2.43
210 225 6.097915 TGGACATAAAAATTACCCGCAAAA 57.902 33.333 0.00 0.00 0.00 2.44
283 343 2.749621 GCTGAACCGACATCTTGGATTT 59.250 45.455 0.00 0.00 0.00 2.17
286 346 0.684535 TGCTGAACCGACATCTTGGA 59.315 50.000 0.00 0.00 0.00 3.53
287 347 1.081892 CTGCTGAACCGACATCTTGG 58.918 55.000 0.00 0.00 0.00 3.61
320 380 8.526218 CTACGGACATAATAACTACTCGTAGA 57.474 38.462 10.83 0.00 45.61 2.59
355 443 3.604875 ATTGCTGGGAAATCAAAGCAG 57.395 42.857 8.61 0.00 45.68 4.24
362 450 5.537674 ACATATCTGGAATTGCTGGGAAATC 59.462 40.000 4.08 0.00 0.00 2.17
395 484 6.323739 ACAAAGAACCCATAAGTCACACAATT 59.676 34.615 0.00 0.00 0.00 2.32
685 780 2.503765 TCGCATGAAAACCTCCTCCATA 59.496 45.455 0.00 0.00 0.00 2.74
719 814 9.952188 CAGAAATATGAGTCTACGAGATAACAA 57.048 33.333 0.00 0.00 0.00 2.83
840 943 8.541133 TGTATCGTACTTGTGAAAATTCATGA 57.459 30.769 0.00 0.00 39.73 3.07
930 1033 2.095364 GCAGAGCACTGGACAGAAATTG 60.095 50.000 13.26 0.00 43.62 2.32
1072 1175 0.234884 CGCTTCGACACAAGGGAAAC 59.765 55.000 0.00 0.00 38.33 2.78
1254 1357 2.664402 ACACAGAGATGCCTTGGTTT 57.336 45.000 0.00 0.00 0.00 3.27
1264 1367 5.453057 GGCAGTGAGATGATAACACAGAGAT 60.453 44.000 0.00 0.00 37.05 2.75
1359 1462 1.079503 GGGACGCTAGTTTCTTGCAG 58.920 55.000 0.00 0.71 32.19 4.41
1383 1486 0.105760 TGTTTGGTGTGGAGGCCAAT 60.106 50.000 5.01 0.00 43.38 3.16
1387 1490 2.514803 AGTTATGTTTGGTGTGGAGGC 58.485 47.619 0.00 0.00 0.00 4.70
1444 1548 3.777106 AATGTGGAGAGCAGAAAGACA 57.223 42.857 0.00 0.00 0.00 3.41
1531 1798 5.381174 TCGCACTTCTTTACTACAAGCTA 57.619 39.130 0.00 0.00 0.00 3.32
2182 2478 3.133362 ACTTATGGCCTTGCAATCCAATG 59.867 43.478 20.16 15.58 33.04 2.82
2183 2479 3.377573 ACTTATGGCCTTGCAATCCAAT 58.622 40.909 20.16 13.01 33.04 3.16
2184 2480 2.818921 ACTTATGGCCTTGCAATCCAA 58.181 42.857 20.16 7.93 33.04 3.53
2254 2550 3.695606 GGTCACAGAGCCGGAGCA 61.696 66.667 5.05 0.00 43.56 4.26


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

AutoCloner maintained by Alex Coulton.