Multiple sequence alignment - TraesCS4A01G347000

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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 TraesCS4A01G347000 chr4A 100.000 2861 0 0 1 2861 625283133 625280273 0.000000e+00 5284.0
1 TraesCS4A01G347000 chr4A 87.490 1271 145 9 731 1998 625372987 625371728 0.000000e+00 1454.0
2 TraesCS4A01G347000 chr4A 84.729 1015 147 5 855 1863 625368253 625367241 0.000000e+00 1009.0
3 TraesCS4A01G347000 chr4A 89.889 722 68 4 731 1451 625322518 625321801 0.000000e+00 924.0
4 TraesCS4A01G347000 chr4A 84.302 860 130 5 990 1848 625265214 625264359 0.000000e+00 835.0
5 TraesCS4A01G347000 chr4A 86.667 210 18 7 742 951 625265421 625265222 1.030000e-54 224.0
6 TraesCS4A01G347000 chr5D 97.425 2874 58 6 1 2861 543816171 543819041 0.000000e+00 4883.0
7 TraesCS4A01G347000 chr5D 88.731 1269 132 4 731 1998 543771681 543772939 0.000000e+00 1541.0
8 TraesCS4A01G347000 chr5D 82.563 1147 155 29 742 1868 543830351 543831472 0.000000e+00 968.0
9 TraesCS4A01G347000 chr5D 89.751 722 62 4 731 1451 543803359 543804069 0.000000e+00 913.0
10 TraesCS4A01G347000 chr5D 86.104 770 77 14 1485 2229 543804067 543804831 0.000000e+00 802.0
11 TraesCS4A01G347000 chr5D 90.164 122 11 1 537 657 543801021 543801142 1.060000e-34 158.0
12 TraesCS4A01G347000 chr5D 80.100 201 32 7 1 197 336336866 336336670 2.970000e-30 143.0
13 TraesCS4A01G347000 chr5D 81.646 158 24 4 1 155 336241539 336241694 2.990000e-25 126.0
14 TraesCS4A01G347000 chr5D 94.737 38 2 0 4 41 542588574 542588537 3.080000e-05 60.2
15 TraesCS4A01G347000 chr5B 91.967 1718 79 18 410 2075 685692429 685690719 0.000000e+00 2353.0
16 TraesCS4A01G347000 chr5B 82.897 1146 156 23 742 1868 685658028 685656904 0.000000e+00 994.0
17 TraesCS4A01G347000 chr5B 90.960 177 15 1 861 1036 685608009 685608185 1.320000e-58 237.0
18 TraesCS4A01G347000 chr5B 80.597 201 27 4 1873 2066 685656852 685656657 8.260000e-31 145.0
19 TraesCS4A01G347000 chr1A 83.537 164 25 1 246 409 139560218 139560057 4.940000e-33 152.0
20 TraesCS4A01G347000 chr1A 82.941 170 23 6 243 410 589157294 589157459 6.390000e-32 148.0
21 TraesCS4A01G347000 chr1A 96.078 51 0 2 109 158 333501653 333501702 6.570000e-12 82.4
22 TraesCS4A01G347000 chr2D 82.927 164 25 2 246 409 600300534 600300694 8.260000e-31 145.0
23 TraesCS4A01G347000 chr2D 100.000 29 0 0 1 29 70482429 70482401 1.000000e-03 54.7
24 TraesCS4A01G347000 chr6B 82.738 168 20 8 246 410 609376664 609376825 1.070000e-29 141.0
25 TraesCS4A01G347000 chr2A 81.928 166 26 3 246 409 662973480 662973643 1.380000e-28 137.0
26 TraesCS4A01G347000 chr2A 81.928 166 26 3 246 409 663305252 663305415 1.380000e-28 137.0
27 TraesCS4A01G347000 chr1D 81.707 164 27 2 248 411 24096854 24097014 1.790000e-27 134.0
28 TraesCS4A01G347000 chr7D 81.065 169 29 2 243 410 94123051 94122885 6.430000e-27 132.0
29 TraesCS4A01G347000 chr1B 91.566 83 6 1 76 157 369544982 369545064 2.330000e-21 113.0
30 TraesCS4A01G347000 chr7A 75.258 194 40 7 2 195 70828948 70828763 5.080000e-13 86.1
31 TraesCS4A01G347000 chr4D 78.571 126 13 8 1 117 295426981 295427101 1.420000e-08 71.3
32 TraesCS4A01G347000 chr4D 100.000 29 0 0 1 29 28473045 28473073 1.000000e-03 54.7
33 TraesCS4A01G347000 chr7B 92.683 41 3 0 1 41 528755813 528755773 3.080000e-05 60.2


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 TraesCS4A01G347000 chr4A 625280273 625283133 2860 True 5284.000000 5284 100.0000 1 2861 1 chr4A.!!$R1 2860
1 TraesCS4A01G347000 chr4A 625367241 625372987 5746 True 1231.500000 1454 86.1095 731 1998 2 chr4A.!!$R4 1267
2 TraesCS4A01G347000 chr4A 625321801 625322518 717 True 924.000000 924 89.8890 731 1451 1 chr4A.!!$R2 720
3 TraesCS4A01G347000 chr4A 625264359 625265421 1062 True 529.500000 835 85.4845 742 1848 2 chr4A.!!$R3 1106
4 TraesCS4A01G347000 chr5D 543816171 543819041 2870 False 4883.000000 4883 97.4250 1 2861 1 chr5D.!!$F3 2860
5 TraesCS4A01G347000 chr5D 543771681 543772939 1258 False 1541.000000 1541 88.7310 731 1998 1 chr5D.!!$F2 1267
6 TraesCS4A01G347000 chr5D 543830351 543831472 1121 False 968.000000 968 82.5630 742 1868 1 chr5D.!!$F4 1126
7 TraesCS4A01G347000 chr5D 543801021 543804831 3810 False 624.333333 913 88.6730 537 2229 3 chr5D.!!$F5 1692
8 TraesCS4A01G347000 chr5B 685690719 685692429 1710 True 2353.000000 2353 91.9670 410 2075 1 chr5B.!!$R1 1665
9 TraesCS4A01G347000 chr5B 685656657 685658028 1371 True 569.500000 994 81.7470 742 2066 2 chr5B.!!$R2 1324

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
30 31 1.344438 TGATAGTCCGATGGCATGTCC 59.656 52.381 3.81 0.0 0.00 4.02 F
1660 3857 1.416401 CTGGGAGTGGCAATACCGTAT 59.584 52.381 12.23 0.0 43.94 3.06 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1850 4047 3.081804 CTCGCAAACCATTAACCTCCTT 58.918 45.455 0.0 0.0 0.0 3.36 R
2613 5602 0.688087 AGATCCCTTCGACTCACCCC 60.688 60.000 0.0 0.0 0.0 4.95 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
30 31 1.344438 TGATAGTCCGATGGCATGTCC 59.656 52.381 3.81 0.00 0.00 4.02
38 39 2.355197 CGATGGCATGTCCTGTTGTAA 58.645 47.619 3.81 0.00 35.26 2.41
154 155 3.417069 AATTTGAGATGTGACCGGTCA 57.583 42.857 33.23 33.23 37.24 4.02
170 171 2.433145 CACTGCTCATGGACGCGT 60.433 61.111 13.85 13.85 0.00 6.01
195 196 2.106534 TGTCCGCCGACGTTTGAA 59.893 55.556 0.00 0.00 42.37 2.69
259 260 5.447413 GCTTGCTAATTACTTCCTCCGTTTC 60.447 44.000 0.00 0.00 0.00 2.78
312 314 8.900781 ACTAGAGACTACATACGAAGCAAAATA 58.099 33.333 0.00 0.00 0.00 1.40
369 371 7.887381 ACATCCGAATATAGTCTTTCTAGTGG 58.113 38.462 0.00 0.00 31.67 4.00
373 375 8.794553 TCCGAATATAGTCTTTCTAGTGGAATC 58.205 37.037 0.00 0.00 33.53 2.52
496 500 1.562475 AGCCCTTATTAAGCCGGTCAA 59.438 47.619 1.90 0.00 0.00 3.18
696 2786 3.329814 TCTCTGCTTGCATATGGGATCAT 59.670 43.478 4.56 0.00 37.40 2.45
1411 3604 4.683832 CGAGGTACCCAAGAGTTTGATAG 58.316 47.826 8.74 0.00 36.36 2.08
1575 3771 3.992943 AGAACCAATGTTGTATCCGGA 57.007 42.857 6.61 6.61 33.97 5.14
1608 3805 5.588648 CACGGTTGTATCTGGGAATAACAAT 59.411 40.000 0.00 0.00 0.00 2.71
1647 3844 3.330701 ACAATACCATCACAACTGGGAGT 59.669 43.478 0.00 0.00 38.14 3.85
1660 3857 1.416401 CTGGGAGTGGCAATACCGTAT 59.584 52.381 12.23 0.00 43.94 3.06
1850 4047 2.426738 CTGGGAGCAACAAAGTTGTGAA 59.573 45.455 11.09 0.00 41.31 3.18
2000 4250 9.394767 ACATACTTGCTGACATAAATATCAACA 57.605 29.630 0.00 0.00 0.00 3.33
2104 4376 3.213506 CGTATCCTGATTGGGCATTTGA 58.786 45.455 0.00 0.00 36.20 2.69
2134 4406 6.364976 TGAATCACATAATGAGTTATACGCGG 59.635 38.462 12.47 0.00 41.91 6.46
2326 4806 7.104043 TGGTATAGTTTAACGAGCACTGTAT 57.896 36.000 0.00 0.00 0.00 2.29
2327 4807 7.549839 TGGTATAGTTTAACGAGCACTGTATT 58.450 34.615 0.00 0.00 0.00 1.89
2508 4988 1.228894 AAGGGAGCCGACTCAGACA 60.229 57.895 0.00 0.00 45.42 3.41
2613 5602 2.216046 ACACACACAGCTTGATGTCAG 58.784 47.619 3.37 0.00 0.00 3.51
2673 5662 6.772716 AGGGCTTTGTGTACATCCTAATAATG 59.227 38.462 0.00 0.00 0.00 1.90
2676 5665 7.416213 GGCTTTGTGTACATCCTAATAATGCAA 60.416 37.037 0.00 0.00 0.00 4.08
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
30 31 7.550551 ACACAGATCATCCTGTTATTACAACAG 59.449 37.037 9.63 9.63 44.32 3.16
38 39 4.847198 TGCAACACAGATCATCCTGTTAT 58.153 39.130 0.00 0.00 44.32 1.89
53 54 1.126113 CCTACGTGAACGATGCAACAC 59.874 52.381 10.26 0.00 43.02 3.32
154 155 2.125912 GACGCGTCCATGAGCAGT 60.126 61.111 28.61 0.00 0.00 4.40
195 196 4.019860 ACCGCATATAGCAAATCTGGATCT 60.020 41.667 0.00 0.00 46.13 2.75
290 292 8.321716 CAGTTATTTTGCTTCGTATGTAGTCTC 58.678 37.037 0.00 0.00 0.00 3.36
348 350 8.798402 AGATTCCACTAGAAAGACTATATTCGG 58.202 37.037 0.00 0.00 38.21 4.30
381 383 7.001099 TCCTTTCGTTCCTAAATACAAGTCT 57.999 36.000 0.00 0.00 0.00 3.24
400 402 5.338953 GGCCAATGTAAGGTAGTACTCCTTT 60.339 44.000 23.19 9.39 41.86 3.11
402 404 3.710165 GGCCAATGTAAGGTAGTACTCCT 59.290 47.826 0.00 3.16 36.81 3.69
496 500 1.081376 CGGAAGAGACGACGCACTT 60.081 57.895 0.00 0.00 0.00 3.16
696 2786 6.577103 CCAGTATGCAAGTAGAGAGATTGAA 58.423 40.000 0.00 0.00 31.97 2.69
1575 3771 3.246699 CAGATACAACCGTGTTGTCGTTT 59.753 43.478 20.78 8.93 39.30 3.60
1587 3784 7.773690 ACAGTATTGTTATTCCCAGATACAACC 59.226 37.037 0.00 0.00 32.28 3.77
1647 3844 3.302161 ACTACCAGATACGGTATTGCCA 58.698 45.455 1.57 0.00 40.74 4.92
1850 4047 3.081804 CTCGCAAACCATTAACCTCCTT 58.918 45.455 0.00 0.00 0.00 3.36
2134 4406 7.358066 TGTACGTATAGCTAGCTGACATTAAC 58.642 38.462 27.68 16.04 0.00 2.01
2484 4964 2.432510 CTGAGTCGGCTCCCTTCTTTAT 59.567 50.000 15.72 0.00 40.95 1.40
2508 4988 2.778187 GCTTCCTAAGCGTATCGACT 57.222 50.000 0.00 0.00 45.74 4.18
2534 5014 2.738213 AAGGCTCTTGCACGGACAGG 62.738 60.000 0.00 0.00 41.91 4.00
2592 5581 2.212652 TGACATCAAGCTGTGTGTGTC 58.787 47.619 18.23 18.23 40.84 3.67
2613 5602 0.688087 AGATCCCTTCGACTCACCCC 60.688 60.000 0.00 0.00 0.00 4.95


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

AutoCloner maintained by Alex Coulton.