Multiple sequence alignment - TraesCS2D01G107600

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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 TraesCS2D01G107600 chr2D 100.000 3165 0 0 1 3165 59726099 59729263 0.000000e+00 5845.0
1 TraesCS2D01G107600 chr2D 86.680 2057 151 64 194 2220 60139709 60137746 0.000000e+00 2167.0
2 TraesCS2D01G107600 chr2D 92.167 600 31 7 1 592 59837994 59838585 0.000000e+00 833.0
3 TraesCS2D01G107600 chr2D 87.083 689 47 13 845 1524 59845414 59846069 0.000000e+00 741.0
4 TraesCS2D01G107600 chr2D 88.482 191 22 0 1325 1515 60015886 60015696 6.830000e-57 231.0
5 TraesCS2D01G107600 chr2D 80.753 239 43 2 1040 1276 60016134 60015897 1.940000e-42 183.0
6 TraesCS2D01G107600 chr2D 89.855 138 8 5 578 713 59839523 59839656 4.200000e-39 172.0
7 TraesCS2D01G107600 chr2D 75.824 364 52 24 866 1221 60108898 60108563 5.470000e-33 152.0
8 TraesCS2D01G107600 chr2D 90.826 109 8 2 739 847 59839951 59840057 9.150000e-31 145.0
9 TraesCS2D01G107600 chr2B 92.455 2399 112 39 1 2371 93110980 93113337 0.000000e+00 3363.0
10 TraesCS2D01G107600 chr2B 86.176 2040 172 64 206 2220 94035103 94033149 0.000000e+00 2104.0
11 TraesCS2D01G107600 chr2B 86.014 2052 159 69 206 2216 94225746 94223782 0.000000e+00 2082.0
12 TraesCS2D01G107600 chr2B 90.229 1351 86 18 935 2261 93440441 93441769 0.000000e+00 1722.0
13 TraesCS2D01G107600 chr2B 93.277 357 23 1 2550 2906 93127529 93127884 2.800000e-145 525.0
14 TraesCS2D01G107600 chr2B 87.919 447 33 10 183 627 93426172 93426599 1.010000e-139 507.0
15 TraesCS2D01G107600 chr2B 91.575 273 12 2 2892 3164 93129585 93129846 1.790000e-97 366.0
16 TraesCS2D01G107600 chr2B 78.435 575 101 12 1597 2152 94202752 94202182 1.400000e-93 353.0
17 TraesCS2D01G107600 chr2B 92.763 152 9 1 2363 2514 93127381 93127530 5.320000e-53 219.0
18 TraesCS2D01G107600 chr2B 87.719 171 21 0 2994 3164 93442704 93442874 1.930000e-47 200.0
19 TraesCS2D01G107600 chr2B 84.236 203 20 3 1 191 93425876 93426078 1.500000e-43 187.0
20 TraesCS2D01G107600 chr2B 76.033 363 53 25 866 1221 93934713 93934378 1.180000e-34 158.0
21 TraesCS2D01G107600 chr2B 91.228 57 3 1 888 942 93439256 93439312 3.390000e-10 76.8
22 TraesCS2D01G107600 chr2A 97.635 1607 33 5 1560 3165 59724410 59726012 0.000000e+00 2752.0
23 TraesCS2D01G107600 chr2A 87.595 1572 113 34 765 2325 60712035 60710535 0.000000e+00 1748.0
24 TraesCS2D01G107600 chr2A 97.722 878 18 1 691 1566 59723179 59724056 0.000000e+00 1509.0
25 TraesCS2D01G107600 chr2A 96.667 450 14 1 1 449 59721067 59721516 0.000000e+00 747.0
26 TraesCS2D01G107600 chr2A 87.946 589 41 8 1737 2325 60249051 60248493 0.000000e+00 667.0
27 TraesCS2D01G107600 chr2A 96.032 252 10 0 448 699 59721677 59721928 8.170000e-111 411.0
28 TraesCS2D01G107600 chr2A 80.321 249 38 8 1025 1266 59728433 59728189 9.020000e-41 178.0
29 TraesCS2D01G107600 chr7B 94.737 38 0 2 3073 3110 720976065 720976030 1.230000e-04 58.4
30 TraesCS2D01G107600 chr3A 100.000 28 0 0 3083 3110 728859269 728859296 6.000000e-03 52.8
31 TraesCS2D01G107600 chr1D 100.000 28 0 0 3083 3110 448602900 448602927 6.000000e-03 52.8


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 TraesCS2D01G107600 chr2D 59726099 59729263 3164 False 5845.000000 5845 100.000000 1 3165 1 chr2D.!!$F1 3164
1 TraesCS2D01G107600 chr2D 60137746 60139709 1963 True 2167.000000 2167 86.680000 194 2220 1 chr2D.!!$R2 2026
2 TraesCS2D01G107600 chr2D 59845414 59846069 655 False 741.000000 741 87.083000 845 1524 1 chr2D.!!$F2 679
3 TraesCS2D01G107600 chr2D 59837994 59840057 2063 False 383.333333 833 90.949333 1 847 3 chr2D.!!$F3 846
4 TraesCS2D01G107600 chr2B 93110980 93113337 2357 False 3363.000000 3363 92.455000 1 2371 1 chr2B.!!$F1 2370
5 TraesCS2D01G107600 chr2B 94033149 94035103 1954 True 2104.000000 2104 86.176000 206 2220 1 chr2B.!!$R2 2014
6 TraesCS2D01G107600 chr2B 94223782 94225746 1964 True 2082.000000 2082 86.014000 206 2216 1 chr2B.!!$R4 2010
7 TraesCS2D01G107600 chr2B 93439256 93442874 3618 False 666.266667 1722 89.725333 888 3164 3 chr2B.!!$F4 2276
8 TraesCS2D01G107600 chr2B 93127381 93129846 2465 False 370.000000 525 92.538333 2363 3164 3 chr2B.!!$F2 801
9 TraesCS2D01G107600 chr2B 94202182 94202752 570 True 353.000000 353 78.435000 1597 2152 1 chr2B.!!$R3 555
10 TraesCS2D01G107600 chr2B 93425876 93426599 723 False 347.000000 507 86.077500 1 627 2 chr2B.!!$F3 626
11 TraesCS2D01G107600 chr2A 60710535 60712035 1500 True 1748.000000 1748 87.595000 765 2325 1 chr2A.!!$R3 1560
12 TraesCS2D01G107600 chr2A 59721067 59726012 4945 False 1354.750000 2752 97.014000 1 3165 4 chr2A.!!$F1 3164
13 TraesCS2D01G107600 chr2A 60248493 60249051 558 True 667.000000 667 87.946000 1737 2325 1 chr2A.!!$R2 588

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
582 1831 0.315568 GGCGACCTAGAGCATCGATT 59.684 55.0 0.0 0.0 42.67 3.34 F
796 3603 0.881118 CAAGTTGCACCATAACGGCT 59.119 50.0 0.0 0.0 39.03 5.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1430 5428 0.035317 TGCACATGGTCTCGAGCTTT 59.965 50.0 7.81 0.0 0.00 3.51 R
2607 7082 0.108585 GAGTCCACAGCTTTGGGTGA 59.891 55.0 18.76 0.0 42.91 4.02 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
65 81 1.227002 GACTAGTAGCCGGCACAGC 60.227 63.158 31.54 15.15 0.00 4.40
112 128 5.048434 TGCATGTCGTGGTCATTTGATTAAA 60.048 36.000 0.00 0.00 0.00 1.52
161 181 0.984230 TTCGAGCCAAGACCAATCCT 59.016 50.000 0.00 0.00 0.00 3.24
302 424 3.517901 CGGCCCAACCATCTTATCCTATA 59.482 47.826 0.00 0.00 39.03 1.31
413 537 2.918712 ATCTCAACCCATGATCGACC 57.081 50.000 0.00 0.00 37.44 4.79
458 745 8.093307 ACATTTTCTGAGATCTATATCGCATGT 58.907 33.333 0.00 0.00 40.54 3.21
461 748 9.794685 TTTTCTGAGATCTATATCGCATGTATC 57.205 33.333 0.00 0.00 40.54 2.24
499 786 0.970640 TGTACCAGTGCACCACGTAT 59.029 50.000 14.63 0.00 39.64 3.06
582 1831 0.315568 GGCGACCTAGAGCATCGATT 59.684 55.000 0.00 0.00 42.67 3.34
723 3524 4.950205 AGAAGAACTTAGTCACCCGAAA 57.050 40.909 0.00 0.00 0.00 3.46
796 3603 0.881118 CAAGTTGCACCATAACGGCT 59.119 50.000 0.00 0.00 39.03 5.52
1430 5428 2.076100 GTCATCGACAACATCAAGGCA 58.924 47.619 0.00 0.00 32.09 4.75
1581 5939 5.302823 GCTAATTTGCTCACCCTGGATATTT 59.697 40.000 4.53 0.00 0.00 1.40
1586 5944 4.016444 TGCTCACCCTGGATATTTGTTTC 58.984 43.478 0.00 0.00 0.00 2.78
1789 6165 4.415150 CACACCATCGGGCAGGCT 62.415 66.667 0.00 0.00 37.90 4.58
2266 6687 4.855340 CCCTTTCTTGGACCATAAGCTTA 58.145 43.478 8.99 8.99 0.00 3.09
2289 6710 6.992063 ATGAAAACAGGAGATGTGTCATAC 57.008 37.500 5.93 0.00 43.00 2.39
2607 7082 3.517901 TGACGATAATCTCCCAACAGGTT 59.482 43.478 0.00 0.00 36.75 3.50
2618 7093 1.402787 CAACAGGTTCACCCAAAGCT 58.597 50.000 0.00 0.00 37.46 3.74
2640 7115 1.003839 GACTCCCACGCATCCACAA 60.004 57.895 0.00 0.00 0.00 3.33
2704 7179 7.148306 GGCTCGGAAGATGACTTGTAAATTTTA 60.148 37.037 0.00 0.00 40.84 1.52
2852 7327 5.297547 ACATATTCGTTATTGATGTCGGCT 58.702 37.500 0.00 0.00 0.00 5.52
2938 9128 7.029563 GGAGCAAGTGTCGAATTAATTCATTT 58.970 34.615 24.23 9.00 36.61 2.32
3020 9405 7.976135 TCGTTAAGACTACTACTCTTTGTCT 57.024 36.000 0.00 0.00 39.35 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
65 81 2.223340 GCACATACAAATGGAAGGCGAG 60.223 50.000 0.00 0.00 37.43 5.03
112 128 3.521126 ACATGGACTGGTAGCTGATTTCT 59.479 43.478 5.76 0.00 0.00 2.52
161 181 0.248012 CATGCCAGCCATTCAGCAAA 59.752 50.000 0.00 0.00 38.99 3.68
302 424 7.736447 GATATCCATCGTCCTTCAAAATTCT 57.264 36.000 0.00 0.00 0.00 2.40
413 537 9.825972 GAAAATGTATGTGGTATTCCAATATCG 57.174 33.333 0.00 0.00 46.15 2.92
461 748 8.836268 TGGTACATTTTACTGGTAGTACTTTG 57.164 34.615 0.00 0.00 34.02 2.77
480 767 0.970640 ATACGTGGTGCACTGGTACA 59.029 50.000 17.98 2.31 31.34 2.90
499 786 2.076100 GATCATGGTTCTTCGTGCACA 58.924 47.619 18.64 0.81 0.00 4.57
638 1902 4.143284 CGTACGTGTGTGCAGCTTATTTTA 60.143 41.667 7.22 0.00 0.00 1.52
699 1965 3.760684 TCGGGTGACTAAGTTCTTCTACC 59.239 47.826 0.00 0.00 0.00 3.18
796 3603 5.661458 TGCAAAATTTTCCTGTTTTACGGA 58.339 33.333 0.00 0.00 0.00 4.69
805 3613 3.002144 CGTTGGGTTGCAAAATTTTCCTG 59.998 43.478 0.00 0.00 0.00 3.86
1420 5418 1.002430 TCTCGAGCTTTGCCTTGATGT 59.998 47.619 7.81 0.00 0.00 3.06
1430 5428 0.035317 TGCACATGGTCTCGAGCTTT 59.965 50.000 7.81 0.00 0.00 3.51
1581 5939 2.313317 ACTGTACCAGAGGACGAAACA 58.687 47.619 0.00 0.00 35.18 2.83
1586 5944 2.683867 CTCCTAACTGTACCAGAGGACG 59.316 54.545 0.00 0.00 32.06 4.79
1789 6165 0.397941 CCCTGAAGTTCTGGCACTGA 59.602 55.000 20.46 0.00 34.54 3.41
2266 6687 6.475504 TGTATGACACATCTCCTGTTTTCAT 58.524 36.000 0.00 0.00 39.62 2.57
2289 6710 1.134401 ACGAGGCCCTTGACATACATG 60.134 52.381 4.57 0.00 0.00 3.21
2607 7082 0.108585 GAGTCCACAGCTTTGGGTGA 59.891 55.000 18.76 0.00 42.91 4.02
2640 7115 1.949799 ACAAGATGCTCTCTCCAGGT 58.050 50.000 0.00 0.00 31.03 4.00
2704 7179 7.984617 TGCTTTTAACTAGGCAAAAGTTTCAAT 59.015 29.630 22.10 0.00 41.62 2.57
2852 7327 8.789762 CATCCATATTGCTTTCAATCTATCACA 58.210 33.333 0.00 0.00 41.68 3.58
2938 9128 7.415541 GCAGTAGATATTGCCTTTTGTGATCAA 60.416 37.037 0.00 0.00 33.42 2.57


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

AutoCloner maintained by Alex Coulton.