Multiple sequence alignment - TraesCS5D01G180700

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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 TraesCS5D01G180700 chr5D 100.000 3796 0 0 447 4242 281019865 281016070 0.000000e+00 7011.0
1 TraesCS5D01G180700 chr5D 100.000 238 0 0 1 238 281020311 281020074 1.400000e-119 440.0
2 TraesCS5D01G180700 chr5A 92.074 2435 72 18 1489 3857 370261190 370263569 0.000000e+00 3315.0
3 TraesCS5D01G180700 chr5A 96.562 960 30 1 531 1490 370260162 370261118 0.000000e+00 1587.0
4 TraesCS5D01G180700 chr5A 88.932 515 44 5 970 1475 32987294 32987804 1.300000e-174 623.0
5 TraesCS5D01G180700 chr5A 91.606 274 22 1 1489 1761 32987900 32988173 1.110000e-100 377.0
6 TraesCS5D01G180700 chr5A 93.525 139 9 0 4100 4238 370264072 370264210 1.550000e-49 207.0
7 TraesCS5D01G180700 chr5A 92.683 123 9 0 3975 4097 370263910 370264032 1.210000e-40 178.0
8 TraesCS5D01G180700 chr5A 96.078 102 1 3 1 101 370259523 370259622 3.390000e-36 163.0
9 TraesCS5D01G180700 chr5A 91.667 108 6 2 3740 3846 370263566 370263671 3.420000e-31 147.0
10 TraesCS5D01G180700 chr5A 91.667 84 3 2 3893 3976 370263669 370263748 3.470000e-21 113.0
11 TraesCS5D01G180700 chr5B 93.470 1562 57 20 2361 3910 318988308 318986780 0.000000e+00 2278.0
12 TraesCS5D01G180700 chr5B 96.740 1043 33 1 447 1489 318990250 318989209 0.000000e+00 1736.0
13 TraesCS5D01G180700 chr5B 94.686 828 25 2 1489 2297 318989136 318988309 0.000000e+00 1267.0
14 TraesCS5D01G180700 chr5B 95.890 219 3 5 1 216 318990900 318990685 2.430000e-92 350.0
15 TraesCS5D01G180700 chr6B 87.109 543 59 4 640 1181 668517748 668517216 4.690000e-169 604.0
16 TraesCS5D01G180700 chr6B 90.441 272 22 2 1491 1762 250783672 250783405 5.220000e-94 355.0
17 TraesCS5D01G180700 chr6B 86.982 169 13 2 1316 1475 250783940 250783772 9.370000e-42 182.0
18 TraesCS5D01G180700 chr2B 87.037 540 57 6 640 1178 765035041 765035568 7.850000e-167 597.0
19 TraesCS5D01G180700 chr2B 90.441 272 22 2 1491 1762 564975312 564975579 5.220000e-94 355.0
20 TraesCS5D01G180700 chr2B 86.982 169 13 2 1316 1475 564975044 564975212 9.370000e-42 182.0
21 TraesCS5D01G180700 chr3B 86.556 543 59 6 640 1178 39527941 39528473 1.700000e-163 586.0
22 TraesCS5D01G180700 chr2D 86.323 446 58 3 697 1142 454712916 454713358 2.290000e-132 483.0
23 TraesCS5D01G180700 chr2D 91.513 271 19 2 1491 1761 454713625 454713891 1.860000e-98 370.0
24 TraesCS5D01G180700 chr2D 86.391 169 13 6 1316 1475 454713358 454713525 4.360000e-40 176.0
25 TraesCS5D01G180700 chr1A 90.809 272 21 2 1491 1762 335107774 335108041 1.120000e-95 361.0
26 TraesCS5D01G180700 chr1A 86.982 169 13 2 1316 1475 335107506 335107674 9.370000e-42 182.0
27 TraesCS5D01G180700 chr1B 89.916 119 7 3 1643 1761 137429765 137429878 9.500000e-32 148.0
28 TraesCS5D01G180700 chr3D 88.462 52 6 0 2261 2312 9066300 9066351 3.540000e-06 63.9


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 TraesCS5D01G180700 chr5D 281016070 281020311 4241 True 3725.500000 7011 100.000000 1 4242 2 chr5D.!!$R1 4241
1 TraesCS5D01G180700 chr5A 370259523 370264210 4687 False 815.714286 3315 93.465143 1 4238 7 chr5A.!!$F2 4237
2 TraesCS5D01G180700 chr5A 32987294 32988173 879 False 500.000000 623 90.269000 970 1761 2 chr5A.!!$F1 791
3 TraesCS5D01G180700 chr5B 318986780 318990900 4120 True 1407.750000 2278 95.196500 1 3910 4 chr5B.!!$R1 3909
4 TraesCS5D01G180700 chr6B 668517216 668517748 532 True 604.000000 604 87.109000 640 1181 1 chr6B.!!$R1 541
5 TraesCS5D01G180700 chr6B 250783405 250783940 535 True 268.500000 355 88.711500 1316 1762 2 chr6B.!!$R2 446
6 TraesCS5D01G180700 chr2B 765035041 765035568 527 False 597.000000 597 87.037000 640 1178 1 chr2B.!!$F1 538
7 TraesCS5D01G180700 chr2B 564975044 564975579 535 False 268.500000 355 88.711500 1316 1762 2 chr2B.!!$F2 446
8 TraesCS5D01G180700 chr3B 39527941 39528473 532 False 586.000000 586 86.556000 640 1178 1 chr3B.!!$F1 538
9 TraesCS5D01G180700 chr2D 454712916 454713891 975 False 343.000000 483 88.075667 697 1761 3 chr2D.!!$F1 1064
10 TraesCS5D01G180700 chr1A 335107506 335108041 535 False 271.500000 361 88.895500 1316 1762 2 chr1A.!!$F1 446

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
27 28 0.107312 TAGCCGTTACGCTCCTCTCT 60.107 55.0 0.0 0.0 40.39 3.10 F
1061 1270 0.107945 GCGGAGATGAAGAAGGCTGT 60.108 55.0 0.0 0.0 0.00 4.40 F
1707 2011 0.108138 AGCATCGGCACACTTAGGAC 60.108 55.0 0.0 0.0 44.61 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1838 2160 2.158885 TCCATCGATCCAAATACGGCAA 60.159 45.455 0.0 0.0 0.0 4.52 R
2664 3011 0.967380 CAAATGACACCAGCCTCCCC 60.967 60.000 0.0 0.0 0.0 4.81 R
3263 3614 2.167487 ACTTGGTGCCGTGTTCATTTTT 59.833 40.909 0.0 0.0 0.0 1.94 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
27 28 0.107312 TAGCCGTTACGCTCCTCTCT 60.107 55.000 0.00 0.00 40.39 3.10
39 40 0.861155 TCCTCTCTATCCCCTCCCAC 59.139 60.000 0.00 0.00 0.00 4.61
91 92 0.685660 CTATTTACTCCCCCTCCGCC 59.314 60.000 0.00 0.00 0.00 6.13
610 818 3.011885 CCTCCGTCTCCTCCTCCT 58.988 66.667 0.00 0.00 0.00 3.69
816 1024 1.308128 TGATGGGATCCTGGTGCCT 60.308 57.895 12.58 0.00 0.00 4.75
1059 1268 1.686052 CTAGCGGAGATGAAGAAGGCT 59.314 52.381 0.00 0.00 0.00 4.58
1061 1270 0.107945 GCGGAGATGAAGAAGGCTGT 60.108 55.000 0.00 0.00 0.00 4.40
1232 1441 6.934645 CCTTTTTACTGTGACAGAGGATGTAA 59.065 38.462 20.97 4.18 44.17 2.41
1254 1463 7.807433 TGTAATTTGATCTCCACAATTTGAACG 59.193 33.333 2.79 0.00 0.00 3.95
1397 1606 7.304479 AGAAGATCAAGAGGGATCAGAGATTA 58.696 38.462 6.01 0.00 44.89 1.75
1707 2011 0.108138 AGCATCGGCACACTTAGGAC 60.108 55.000 0.00 0.00 44.61 3.85
1838 2160 6.981762 TTGTTCATTTGCAAAAATGTCAGT 57.018 29.167 17.19 0.00 40.20 3.41
2108 2431 2.047274 GCGCAACTACTGGAGCCA 60.047 61.111 0.30 0.00 0.00 4.75
2173 2496 5.061853 ACTATCAAATAGCTGTCATGCCTG 58.938 41.667 0.00 0.00 36.30 4.85
2199 2522 9.150348 GGATATGTTACCTTTTTGAAATGGTTG 57.850 33.333 16.24 0.00 41.93 3.77
2297 2620 6.460953 GCTCAAAACTGGGACACTTATTTTGA 60.461 38.462 9.01 9.01 37.92 2.69
2300 2623 8.141268 TCAAAACTGGGACACTTATTTTGAATC 58.859 33.333 7.32 0.00 37.62 2.52
2599 2922 5.140747 ACTTGATAACTGAGAGTCGCTTT 57.859 39.130 0.00 0.00 0.00 3.51
2664 3011 7.254795 CCGTTGCCTTTCTATAAGAAATACCAG 60.255 40.741 2.76 0.00 42.66 4.00
3174 3525 7.767198 CCACGGAAATATCTAACTGGTTTCTTA 59.233 37.037 0.00 0.00 0.00 2.10
3205 3556 5.017490 CCCGTTACATAGATGAGGGAGTAT 58.983 45.833 0.00 0.00 39.71 2.12
3368 3721 3.518705 GAGAGGTGGCCTGATGATCATAT 59.481 47.826 8.54 0.00 31.76 1.78
3369 3722 4.692328 AGAGGTGGCCTGATGATCATATA 58.308 43.478 8.54 0.00 31.76 0.86
3376 3729 5.999600 TGGCCTGATGATCATATACAAAGTG 59.000 40.000 8.54 0.00 0.00 3.16
3586 3939 8.373048 TCGTTGATTCTTTGTGTACTTGTAAT 57.627 30.769 0.00 0.00 0.00 1.89
3614 3967 2.738846 CGTTGCTCAGATAGTGCTGTTT 59.261 45.455 0.00 0.00 37.61 2.83
3615 3968 3.181526 CGTTGCTCAGATAGTGCTGTTTC 60.182 47.826 0.00 0.00 37.61 2.78
3629 3982 6.630071 AGTGCTGTTTCTTTCTTTTTGCTAA 58.370 32.000 0.00 0.00 0.00 3.09
3630 3983 6.531594 AGTGCTGTTTCTTTCTTTTTGCTAAC 59.468 34.615 0.00 0.00 0.00 2.34
3631 3984 6.310224 GTGCTGTTTCTTTCTTTTTGCTAACA 59.690 34.615 0.00 0.00 0.00 2.41
3632 3985 6.531240 TGCTGTTTCTTTCTTTTTGCTAACAG 59.469 34.615 0.00 0.00 42.35 3.16
3637 3990 8.921670 GTTTCTTTCTTTTTGCTAACAGAACAA 58.078 29.630 8.67 3.56 31.59 2.83
3678 4031 4.359706 GTTGAAGAACGGTGCTCATTTTT 58.640 39.130 0.00 0.00 0.00 1.94
3679 4032 3.963665 TGAAGAACGGTGCTCATTTTTG 58.036 40.909 0.00 0.00 0.00 2.44
3706 4059 0.874390 AGTTTGGCATGCACACGTAG 59.126 50.000 21.36 0.00 0.00 3.51
3736 4109 2.957402 TGCATCTTCCCAGTCAAGTT 57.043 45.000 0.00 0.00 0.00 2.66
3784 4158 4.732784 TGTCAAAGAACACTTGCAAGAAC 58.267 39.130 32.50 18.22 0.00 3.01
3823 4197 0.531974 GGTGTCTGTTGCCTTCGACA 60.532 55.000 0.00 0.00 35.40 4.35
3859 4233 3.731431 TGTGATGTAGAAGTATGGGGGT 58.269 45.455 0.00 0.00 0.00 4.95
3887 4261 3.510388 TTGATTGTTGCACGTTGGAAA 57.490 38.095 0.00 0.00 26.96 3.13
3931 4369 7.702772 GTGTGTATGTGGTTTTGTTTGTATTGA 59.297 33.333 0.00 0.00 0.00 2.57
3934 4372 9.823647 TGTATGTGGTTTTGTTTGTATTGATTT 57.176 25.926 0.00 0.00 0.00 2.17
3938 4376 8.669243 TGTGGTTTTGTTTGTATTGATTTTTCC 58.331 29.630 0.00 0.00 0.00 3.13
4005 4606 7.650504 TCAATGAGAAATGAGACAAAGCTTTTG 59.349 33.333 9.53 7.95 0.00 2.44
4038 4639 0.036306 AAACGAAGAAGCATCCGGGT 59.964 50.000 0.00 0.00 0.00 5.28
4052 4653 2.549082 TCCGGGTCCAACTAATAACCA 58.451 47.619 0.00 0.00 33.27 3.67
4053 4654 3.116959 TCCGGGTCCAACTAATAACCAT 58.883 45.455 0.00 0.00 33.27 3.55
4076 4677 5.447778 AGAAATTGAGATCATGGTGACCT 57.552 39.130 2.11 0.00 0.00 3.85
4077 4678 5.191426 AGAAATTGAGATCATGGTGACCTG 58.809 41.667 2.11 0.00 0.00 4.00
4089 4690 1.673920 GGTGACCTGTTGCGAGAAAAA 59.326 47.619 0.00 0.00 0.00 1.94
4114 4752 2.301870 TGGACCTAGACAAAACATCGCT 59.698 45.455 0.00 0.00 0.00 4.93
4127 4765 1.153409 ATCGCTGAGAGCTTGCTGG 60.153 57.895 0.00 0.00 39.60 4.85
4173 4811 4.831107 TCGTTCCATGAATGTTCTCATCA 58.169 39.130 0.00 0.00 33.66 3.07
4181 4819 4.498241 TGAATGTTCTCATCAGTTCGAGG 58.502 43.478 0.00 0.00 32.56 4.63
4183 4821 4.808414 ATGTTCTCATCAGTTCGAGGAA 57.192 40.909 0.00 0.00 33.18 3.36
4189 4827 2.005451 CATCAGTTCGAGGAAGGCAAG 58.995 52.381 0.00 0.00 0.00 4.01
4193 4831 2.525124 TTCGAGGAAGGCAAGGGCA 61.525 57.895 0.00 0.00 43.71 5.36
4202 4840 0.752658 AGGCAAGGGCACAAAAACTC 59.247 50.000 0.00 0.00 43.71 3.01
4210 4848 6.279882 CAAGGGCACAAAAACTCTTATGAAA 58.720 36.000 0.00 0.00 0.00 2.69
4238 4876 5.883673 TGTAGTGGGAACAATTATAGCCAAC 59.116 40.000 0.00 0.00 46.06 3.77
4239 4877 4.929479 AGTGGGAACAATTATAGCCAACA 58.071 39.130 0.00 0.00 46.06 3.33
4240 4878 5.329399 AGTGGGAACAATTATAGCCAACAA 58.671 37.500 0.00 0.00 46.06 2.83
4241 4879 5.185056 AGTGGGAACAATTATAGCCAACAAC 59.815 40.000 0.00 0.00 46.06 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 1.542093 TTCAGGGGTGGGAGGGGATA 61.542 60.000 0.00 0.00 0.00 2.59
39 40 4.516698 CGTAATGAGATGGATTTTCAGGGG 59.483 45.833 0.00 0.00 0.00 4.79
91 92 1.081108 GGATTCGATCGGAGCGGAG 60.081 63.158 16.41 0.00 0.00 4.63
989 1198 4.776322 CCGCCATCACCTTCGCCA 62.776 66.667 0.00 0.00 0.00 5.69
1232 1441 5.476599 TCCGTTCAAATTGTGGAGATCAAAT 59.523 36.000 0.00 0.00 0.00 2.32
1254 1463 5.824904 ACAATAACAACATCAGCATCTCC 57.175 39.130 0.00 0.00 0.00 3.71
1397 1606 2.559668 CTGACCACCAACAATTGAGCAT 59.440 45.455 13.59 0.00 0.00 3.79
1838 2160 2.158885 TCCATCGATCCAAATACGGCAA 60.159 45.455 0.00 0.00 0.00 4.52
2108 2431 2.416244 TTCGAACAAGAGGCGACGCT 62.416 55.000 20.77 5.59 45.01 5.07
2173 2496 9.150348 CAACCATTTCAAAAAGGTAACATATCC 57.850 33.333 3.06 0.00 38.90 2.59
2254 2577 2.225727 GAGCTGGGGTTAGTTCAAAACG 59.774 50.000 0.00 0.00 36.23 3.60
2283 2606 4.335594 CCCTCCGATTCAAAATAAGTGTCC 59.664 45.833 0.00 0.00 0.00 4.02
2297 2620 7.504238 CAGCTATAAGATATACTCCCTCCGATT 59.496 40.741 0.00 0.00 0.00 3.34
2300 2623 6.358178 TCAGCTATAAGATATACTCCCTCCG 58.642 44.000 0.00 0.00 0.00 4.63
2339 2662 9.049523 GTTCTCACATAGAAGATCAATATGCAA 57.950 33.333 0.00 0.00 44.94 4.08
2393 2716 2.057922 ACTTCACAACCTCCATCCACT 58.942 47.619 0.00 0.00 0.00 4.00
2536 2859 7.277760 CGAATACATGTTCACTTTGGAGTATGA 59.722 37.037 2.30 0.00 33.90 2.15
2664 3011 0.967380 CAAATGACACCAGCCTCCCC 60.967 60.000 0.00 0.00 0.00 4.81
2903 3250 8.049117 AGAATAACTCAAAATGATACTGCCTCA 58.951 33.333 0.00 0.00 0.00 3.86
2944 3291 8.719648 CCTATATGACAAGAGCAAAATGAGATC 58.280 37.037 0.00 0.00 0.00 2.75
3174 3525 6.183360 CCTCATCTATGTAACGGGCAATTTTT 60.183 38.462 0.00 0.00 0.00 1.94
3263 3614 2.167487 ACTTGGTGCCGTGTTCATTTTT 59.833 40.909 0.00 0.00 0.00 1.94
3368 3721 5.938125 GGATACTTCTGCCTTTCACTTTGTA 59.062 40.000 0.00 0.00 0.00 2.41
3369 3722 4.762251 GGATACTTCTGCCTTTCACTTTGT 59.238 41.667 0.00 0.00 0.00 2.83
3586 3939 4.686091 GCACTATCTGAGCAACGCAATATA 59.314 41.667 0.00 0.00 32.44 0.86
3614 3967 9.651913 AATTTGTTCTGTTAGCAAAAAGAAAGA 57.348 25.926 0.00 0.00 40.01 2.52
3615 3968 9.906111 GAATTTGTTCTGTTAGCAAAAAGAAAG 57.094 29.630 0.00 0.00 40.01 2.62
3629 3982 5.479375 AGCCATCAATGAGAATTTGTTCTGT 59.521 36.000 0.00 0.00 0.00 3.41
3630 3983 5.962433 AGCCATCAATGAGAATTTGTTCTG 58.038 37.500 0.00 0.00 0.00 3.02
3631 3984 6.395629 CAAGCCATCAATGAGAATTTGTTCT 58.604 36.000 0.00 0.00 0.00 3.01
3632 3985 5.579511 CCAAGCCATCAATGAGAATTTGTTC 59.420 40.000 0.00 0.00 0.00 3.18
3637 3990 4.773674 TCAACCAAGCCATCAATGAGAATT 59.226 37.500 0.00 0.00 0.00 2.17
3678 4031 2.896044 TGCATGCCAAACTATCCAAACA 59.104 40.909 16.68 0.00 0.00 2.83
3679 4032 3.253230 GTGCATGCCAAACTATCCAAAC 58.747 45.455 16.68 0.00 0.00 2.93
3718 4071 1.200948 GCAACTTGACTGGGAAGATGC 59.799 52.381 0.00 0.00 40.57 3.91
3719 4072 2.486982 CAGCAACTTGACTGGGAAGATG 59.513 50.000 0.00 0.00 0.00 2.90
3753 4126 4.130118 AGTGTTCTTTGACATCCACTGAC 58.870 43.478 0.00 0.00 32.32 3.51
3784 4158 0.625849 ACCAAAGTGGGCCAGGATAG 59.374 55.000 15.87 4.04 43.37 2.08
3823 4197 3.392616 ACATCACAAAGGAGAACACCTCT 59.607 43.478 0.00 0.00 41.66 3.69
3859 4233 4.428209 ACGTGCAACAATCAATCACAAAA 58.572 34.783 0.00 0.00 35.74 2.44
3887 4261 1.946768 CACAGTCGACCCAACAAACAT 59.053 47.619 13.01 0.00 0.00 2.71
4034 4635 5.540400 TCTATGGTTATTAGTTGGACCCG 57.460 43.478 0.00 0.00 0.00 5.28
4052 4653 6.996879 CAGGTCACCATGATCTCAATTTCTAT 59.003 38.462 0.00 0.00 35.21 1.98
4053 4654 6.070021 ACAGGTCACCATGATCTCAATTTCTA 60.070 38.462 0.00 0.00 35.21 2.10
4065 4666 0.320683 CTCGCAACAGGTCACCATGA 60.321 55.000 0.00 0.00 0.00 3.07
4089 4690 4.695455 CGATGTTTTGTCTAGGTCCACATT 59.305 41.667 0.00 0.00 0.00 2.71
4097 4698 3.849911 TCTCAGCGATGTTTTGTCTAGG 58.150 45.455 0.00 0.00 0.00 3.02
4114 4752 1.181741 ACGTCTCCAGCAAGCTCTCA 61.182 55.000 0.00 0.00 0.00 3.27
4127 4765 4.082354 TCCTAGCCAAGAAGTTAACGTCTC 60.082 45.833 21.85 11.44 33.66 3.36
4173 4811 1.679898 CCCTTGCCTTCCTCGAACT 59.320 57.895 0.00 0.00 0.00 3.01
4181 4819 1.138859 AGTTTTTGTGCCCTTGCCTTC 59.861 47.619 0.00 0.00 36.33 3.46
4183 4821 0.752658 GAGTTTTTGTGCCCTTGCCT 59.247 50.000 0.00 0.00 36.33 4.75
4189 4827 6.454795 TGATTTCATAAGAGTTTTTGTGCCC 58.545 36.000 0.00 0.00 0.00 5.36
4202 4840 7.864108 TGTTCCCACTACATGATTTCATAAG 57.136 36.000 0.00 0.00 34.26 1.73
4210 4848 6.942576 GGCTATAATTGTTCCCACTACATGAT 59.057 38.462 0.00 0.00 0.00 2.45


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

AutoCloner maintained by Alex Coulton.