Multiple sequence alignment - TraesCS2B01G062300

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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 TraesCS2B01G062300 chr2B 100.000 1761 0 0 456 2216 29743786 29742026 0.000000e+00 3253.0
1 TraesCS2B01G062300 chr2B 78.719 874 158 12 456 1305 29722018 29721149 1.920000e-155 558.0
2 TraesCS2B01G062300 chr2B 78.128 919 157 25 456 1339 29737228 29736319 5.380000e-151 544.0
3 TraesCS2B01G062300 chr2B 78.972 642 108 17 710 1335 29731381 29730751 1.580000e-111 412.0
4 TraesCS2B01G062300 chr2B 100.000 66 0 0 1 66 29744241 29744176 2.990000e-24 122.0
5 TraesCS2B01G062300 chr2A 92.683 1640 104 11 456 2083 18858781 18860416 0.000000e+00 2350.0
6 TraesCS2B01G062300 chr2A 85.346 737 97 10 1370 2099 334910229 334910961 0.000000e+00 752.0
7 TraesCS2B01G062300 chr2A 78.446 914 145 22 456 1346 18909521 18910405 1.160000e-152 549.0
8 TraesCS2B01G062300 chr2A 81.250 656 94 14 688 1333 18903986 18904622 9.130000e-139 503.0
9 TraesCS2B01G062300 chr2D 93.611 767 43 5 610 1372 17456812 17457576 0.000000e+00 1140.0
10 TraesCS2B01G062300 chr2D 85.445 742 97 7 1370 2102 383573776 383573037 0.000000e+00 761.0
11 TraesCS2B01G062300 chr2D 85.389 746 93 10 1370 2102 474664548 474665290 0.000000e+00 760.0
12 TraesCS2B01G062300 chr2D 85.170 735 97 11 1370 2095 474685525 474684794 0.000000e+00 743.0
13 TraesCS2B01G062300 chr2D 80.132 906 147 21 456 1335 17497053 17497951 0.000000e+00 645.0
14 TraesCS2B01G062300 chr2D 94.928 138 7 0 456 593 17456618 17456755 1.330000e-52 217.0
15 TraesCS2B01G062300 chr3B 85.908 738 94 9 1370 2099 137609567 137610302 0.000000e+00 778.0
16 TraesCS2B01G062300 chr5D 82.955 880 109 18 1370 2211 118804682 118805558 0.000000e+00 756.0
17 TraesCS2B01G062300 chr1D 83.767 807 105 19 1370 2153 295400824 295400021 0.000000e+00 741.0
18 TraesCS2B01G062300 chr1D 80.508 118 11 3 2048 2153 113919463 113919580 1.820000e-11 80.5
19 TraesCS2B01G062300 chr7D 83.522 795 116 12 1370 2153 512061700 512062490 0.000000e+00 728.0


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 TraesCS2B01G062300 chr2B 29742026 29744241 2215 True 1687.5 3253 100.0000 1 2216 2 chr2B.!!$R4 2215
1 TraesCS2B01G062300 chr2B 29721149 29722018 869 True 558.0 558 78.7190 456 1305 1 chr2B.!!$R1 849
2 TraesCS2B01G062300 chr2B 29736319 29737228 909 True 544.0 544 78.1280 456 1339 1 chr2B.!!$R3 883
3 TraesCS2B01G062300 chr2B 29730751 29731381 630 True 412.0 412 78.9720 710 1335 1 chr2B.!!$R2 625
4 TraesCS2B01G062300 chr2A 18858781 18860416 1635 False 2350.0 2350 92.6830 456 2083 1 chr2A.!!$F1 1627
5 TraesCS2B01G062300 chr2A 334910229 334910961 732 False 752.0 752 85.3460 1370 2099 1 chr2A.!!$F4 729
6 TraesCS2B01G062300 chr2A 18909521 18910405 884 False 549.0 549 78.4460 456 1346 1 chr2A.!!$F3 890
7 TraesCS2B01G062300 chr2A 18903986 18904622 636 False 503.0 503 81.2500 688 1333 1 chr2A.!!$F2 645
8 TraesCS2B01G062300 chr2D 383573037 383573776 739 True 761.0 761 85.4450 1370 2102 1 chr2D.!!$R1 732
9 TraesCS2B01G062300 chr2D 474664548 474665290 742 False 760.0 760 85.3890 1370 2102 1 chr2D.!!$F2 732
10 TraesCS2B01G062300 chr2D 474684794 474685525 731 True 743.0 743 85.1700 1370 2095 1 chr2D.!!$R2 725
11 TraesCS2B01G062300 chr2D 17456618 17457576 958 False 678.5 1140 94.2695 456 1372 2 chr2D.!!$F3 916
12 TraesCS2B01G062300 chr2D 17497053 17497951 898 False 645.0 645 80.1320 456 1335 1 chr2D.!!$F1 879
13 TraesCS2B01G062300 chr3B 137609567 137610302 735 False 778.0 778 85.9080 1370 2099 1 chr3B.!!$F1 729
14 TraesCS2B01G062300 chr5D 118804682 118805558 876 False 756.0 756 82.9550 1370 2211 1 chr5D.!!$F1 841
15 TraesCS2B01G062300 chr1D 295400021 295400824 803 True 741.0 741 83.7670 1370 2153 1 chr1D.!!$R1 783
16 TraesCS2B01G062300 chr7D 512061700 512062490 790 False 728.0 728 83.5220 1370 2153 1 chr7D.!!$F1 783

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
686 736 1.135575 CGAGCCAGAAAATTCCTGCAC 60.136 52.381 7.11 1.37 0.0 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1726 1822 1.683385 TCCCGAGTCATCACTATGCTG 59.317 52.381 0.0 0.0 30.63 4.41 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
38 39 2.512515 GGGATGCACACGAGGCTC 60.513 66.667 3.87 3.87 0.00 4.70
39 40 2.887568 GGATGCACACGAGGCTCG 60.888 66.667 33.42 33.42 46.93 5.03
40 41 2.887568 GATGCACACGAGGCTCGG 60.888 66.667 36.81 27.41 45.59 4.63
56 57 3.503363 GGCAGGCAGTAGCGCAAG 61.503 66.667 11.47 0.00 43.41 4.01
57 58 3.503363 GCAGGCAGTAGCGCAAGG 61.503 66.667 11.47 0.00 43.41 3.61
495 496 5.710513 TTATTTGATGGTGCAGATATGCC 57.289 39.130 10.32 0.91 0.00 4.40
536 542 9.630098 TGGAACTAGAAAAACGTATTAGTACTG 57.370 33.333 5.39 0.00 0.00 2.74
597 607 3.257127 TGCCCCTAACAACAATTTGCTAC 59.743 43.478 0.00 0.00 36.00 3.58
686 736 1.135575 CGAGCCAGAAAATTCCTGCAC 60.136 52.381 7.11 1.37 0.00 4.57
763 817 6.196724 GTGACGACGATTCTACAGATAAAAGG 59.803 42.308 0.00 0.00 0.00 3.11
822 888 4.467438 ACAAACCCATCCCATTGAAGAATC 59.533 41.667 0.00 0.00 0.00 2.52
834 900 6.317391 CCCATTGAAGAATCTCCAACTTAGAC 59.683 42.308 0.00 0.00 0.00 2.59
1297 1382 4.576463 AGAAGTACTGCAGTGAAAGGTTTG 59.424 41.667 29.57 0.00 0.00 2.93
1351 1445 8.009974 CAGTAAAAGGTCGTGTATTTTCAAGAG 58.990 37.037 0.00 0.00 0.00 2.85
1424 1518 3.936453 TGTTAACGTGTGATATTGCTCCC 59.064 43.478 0.26 0.00 0.00 4.30
1563 1657 1.853963 AGTGGTCGGATAGCTCAAGT 58.146 50.000 0.00 0.00 0.00 3.16
1573 1667 3.879892 GGATAGCTCAAGTGTGGGATTTC 59.120 47.826 0.00 0.00 0.00 2.17
1613 1707 1.144276 GTTCTTAGGGCCCTCTCGC 59.856 63.158 32.80 12.69 0.00 5.03
1677 1772 0.327924 TCACAAGGATGCCGGAACAT 59.672 50.000 5.05 0.00 0.00 2.71
1696 1791 8.818057 CGGAACATAATAACGAGAAAGAAGAAT 58.182 33.333 0.00 0.00 0.00 2.40
1765 1861 3.775316 GGGAGGATAACGATACATCCCAT 59.225 47.826 15.14 0.00 43.67 4.00
1777 1874 5.447683 CGATACATCCCATGTTTTGTGAGTG 60.448 44.000 0.00 0.00 41.63 3.51
1794 1891 2.213499 AGTGTCACGAAGCAAAAGGAG 58.787 47.619 0.00 0.00 0.00 3.69
1805 1902 4.038271 AGCAAAAGGAGGATCACATGAA 57.962 40.909 0.00 0.00 36.25 2.57
1814 1911 4.766891 GGAGGATCACATGAAAACCAAAGA 59.233 41.667 0.00 0.00 36.25 2.52
2047 2159 0.675522 GGATCCGGAAGCGTTTTGGA 60.676 55.000 9.01 8.87 0.00 3.53
2050 2162 0.179040 TCCGGAAGCGTTTTGGAGTT 60.179 50.000 0.00 0.00 0.00 3.01
2078 2191 1.139455 GGGTTTCCGTGAATATCGGGA 59.861 52.381 4.58 0.00 46.82 5.14
2084 2197 6.875195 GGTTTCCGTGAATATCGGGAAATATA 59.125 38.462 14.50 0.00 45.71 0.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
2 3 4.735132 TCGCCGTGTGCTACTGCC 62.735 66.667 3.41 0.0 36.30 4.85
3 4 3.479269 GTCGCCGTGTGCTACTGC 61.479 66.667 0.00 0.0 38.05 4.40
4 5 3.172575 CGTCGCCGTGTGCTACTG 61.173 66.667 0.00 0.0 38.05 2.74
5 6 4.415332 CCGTCGCCGTGTGCTACT 62.415 66.667 0.00 0.0 38.05 2.57
17 18 2.880879 CTCGTGTGCATCCCGTCG 60.881 66.667 0.00 0.0 0.00 5.12
18 19 2.509336 CCTCGTGTGCATCCCGTC 60.509 66.667 0.00 0.0 0.00 4.79
19 20 4.760047 GCCTCGTGTGCATCCCGT 62.760 66.667 0.00 0.0 0.00 5.28
20 21 4.457496 AGCCTCGTGTGCATCCCG 62.457 66.667 0.00 0.0 0.00 5.14
21 22 2.512515 GAGCCTCGTGTGCATCCC 60.513 66.667 0.00 0.0 0.00 3.85
22 23 2.887568 CGAGCCTCGTGTGCATCC 60.888 66.667 5.82 0.0 34.72 3.51
23 24 2.887568 CCGAGCCTCGTGTGCATC 60.888 66.667 13.83 0.0 38.40 3.91
32 33 3.438017 CTACTGCCTGCCGAGCCTC 62.438 68.421 0.00 0.0 0.00 4.70
33 34 3.465403 CTACTGCCTGCCGAGCCT 61.465 66.667 0.00 0.0 0.00 4.58
39 40 3.503363 CTTGCGCTACTGCCTGCC 61.503 66.667 9.73 0.0 35.36 4.85
40 41 3.503363 CCTTGCGCTACTGCCTGC 61.503 66.667 9.73 0.0 35.36 4.85
41 42 2.046892 ACCTTGCGCTACTGCCTG 60.047 61.111 9.73 0.0 35.36 4.85
42 43 2.046892 CACCTTGCGCTACTGCCT 60.047 61.111 9.73 0.0 35.36 4.75
43 44 2.047274 TCACCTTGCGCTACTGCC 60.047 61.111 9.73 0.0 35.36 4.85
44 45 2.103042 CCTCACCTTGCGCTACTGC 61.103 63.158 9.73 0.0 0.00 4.40
45 46 2.103042 GCCTCACCTTGCGCTACTG 61.103 63.158 9.73 0.0 0.00 2.74
46 47 1.903877 ATGCCTCACCTTGCGCTACT 61.904 55.000 9.73 0.0 0.00 2.57
47 48 1.450312 ATGCCTCACCTTGCGCTAC 60.450 57.895 9.73 0.0 0.00 3.58
48 49 2.989639 ATGCCTCACCTTGCGCTA 59.010 55.556 9.73 0.0 0.00 4.26
495 496 1.600957 GTTCCATGCATCTGGACATCG 59.399 52.381 8.60 0.0 44.97 3.84
686 736 4.174009 ACGATCGACAATCTAAAGTGGTG 58.826 43.478 24.34 0.0 31.68 4.17
725 779 5.562506 TCGTCGTCACTAAGAAGATCATT 57.437 39.130 0.00 0.0 37.10 2.57
726 780 5.759506 ATCGTCGTCACTAAGAAGATCAT 57.240 39.130 0.00 0.0 37.10 2.45
763 817 9.523168 AGGGAGTTGATATACAGTAGTATTCTC 57.477 37.037 0.00 0.0 41.15 2.87
822 888 6.310711 GTGTTTTATCTCGGTCTAAGTTGGAG 59.689 42.308 0.00 0.0 0.00 3.86
834 900 6.548441 TTGGTTAGTTGTGTTTTATCTCGG 57.452 37.500 0.00 0.0 0.00 4.63
1297 1382 6.456501 AGCATCAGTCCCTTTATTCGTATAC 58.543 40.000 0.00 0.0 0.00 1.47
1400 1494 4.201783 GGAGCAATATCACACGTTAACACC 60.202 45.833 6.39 0.0 0.00 4.16
1445 1539 5.067936 AGTCCATCATACGGTAAGAAGTGAG 59.932 44.000 0.00 0.0 0.00 3.51
1573 1667 2.103373 TCTCTTCATTGTCGGAGGAGG 58.897 52.381 0.00 0.0 38.58 4.30
1635 1729 1.722034 AGTCACCTGTGTCTGACCAT 58.278 50.000 5.17 0.0 38.04 3.55
1696 1791 4.805192 CCGAAATCCTCGTTACCGATTTTA 59.195 41.667 0.00 0.0 46.65 1.52
1726 1822 1.683385 TCCCGAGTCATCACTATGCTG 59.317 52.381 0.00 0.0 30.63 4.41
1777 1874 1.878953 TCCTCCTTTTGCTTCGTGAC 58.121 50.000 0.00 0.0 0.00 3.67
1794 1891 8.306761 AGTAAATCTTTGGTTTTCATGTGATCC 58.693 33.333 0.00 0.0 0.00 3.36
2013 2125 4.323553 CGGATCCTCTCGGAACTATTTT 57.676 45.455 10.75 0.0 44.02 1.82
2065 2178 5.974108 ACCCTATATTTCCCGATATTCACG 58.026 41.667 0.00 0.0 0.00 4.35
2156 2283 9.893634 TGGTCTTTTTAGATCCGTTGATATTTA 57.106 29.630 0.00 0.0 0.00 1.40
2157 2284 8.801882 TGGTCTTTTTAGATCCGTTGATATTT 57.198 30.769 0.00 0.0 0.00 1.40
2159 2286 8.265055 TCTTGGTCTTTTTAGATCCGTTGATAT 58.735 33.333 0.00 0.0 0.00 1.63
2169 2312 5.843019 TCCACCTCTTGGTCTTTTTAGAT 57.157 39.130 0.00 0.0 46.60 1.98
2170 2313 5.621193 CTTCCACCTCTTGGTCTTTTTAGA 58.379 41.667 0.00 0.0 46.60 2.10


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

AutoCloner maintained by Alex Coulton.