Multiple sequence alignment - TraesCS7A01G238000

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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 TraesCS7A01G238000 chr7A 100.000 2753 0 0 1 2753 211365438 211362686 0 5084
1 TraesCS7A01G238000 chr7A 97.649 638 15 0 2116 2753 4949338 4949975 0 1096
2 TraesCS7A01G238000 chr7A 97.649 638 15 0 2116 2753 120916332 120915695 0 1096
3 TraesCS7A01G238000 chr1A 97.062 2757 75 6 1 2753 94579882 94582636 0 4638
4 TraesCS7A01G238000 chr1A 96.928 1888 52 4 1 1887 94664949 94663067 0 3160
5 TraesCS7A01G238000 chr1A 97.538 731 17 1 2023 2753 94663076 94662347 0 1249
6 TraesCS7A01G238000 chr7D 96.662 2157 70 2 1 2155 382088787 382090943 0 3583
7 TraesCS7A01G238000 chr7D 96.247 2158 75 4 1 2155 626712205 626710051 0 3531
8 TraesCS7A01G238000 chr7D 95.831 2159 77 6 1 2155 307033661 307031512 0 3476
9 TraesCS7A01G238000 chr7D 95.039 2157 93 5 1 2155 307161909 307164053 0 3378
10 TraesCS7A01G238000 chr4D 96.293 2158 75 5 1 2155 123400505 123402660 0 3537
11 TraesCS7A01G238000 chr4D 96.054 2154 81 2 1 2150 134961998 134964151 0 3504
12 TraesCS7A01G238000 chr1D 95.970 2159 73 5 1 2155 275787598 275785450 0 3493
13 TraesCS7A01G238000 chr2A 96.748 1107 33 2 1650 2753 423418216 423417110 0 1842
14 TraesCS7A01G238000 chr3A 96.116 1107 39 2 1650 2753 227633804 227634909 0 1803
15 TraesCS7A01G238000 chr6A 97.962 638 13 0 2116 2753 289118161 289118798 0 1107
16 TraesCS7A01G238000 chrUn 97.806 638 14 0 2116 2753 406859804 406860441 0 1101
17 TraesCS7A01G238000 chr5A 97.806 638 14 0 2116 2753 300058356 300058993 0 1101


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 TraesCS7A01G238000 chr7A 211362686 211365438 2752 True 5084.0 5084 100.000 1 2753 1 chr7A.!!$R2 2752
1 TraesCS7A01G238000 chr7A 4949338 4949975 637 False 1096.0 1096 97.649 2116 2753 1 chr7A.!!$F1 637
2 TraesCS7A01G238000 chr7A 120915695 120916332 637 True 1096.0 1096 97.649 2116 2753 1 chr7A.!!$R1 637
3 TraesCS7A01G238000 chr1A 94579882 94582636 2754 False 4638.0 4638 97.062 1 2753 1 chr1A.!!$F1 2752
4 TraesCS7A01G238000 chr1A 94662347 94664949 2602 True 2204.5 3160 97.233 1 2753 2 chr1A.!!$R1 2752
5 TraesCS7A01G238000 chr7D 382088787 382090943 2156 False 3583.0 3583 96.662 1 2155 1 chr7D.!!$F2 2154
6 TraesCS7A01G238000 chr7D 626710051 626712205 2154 True 3531.0 3531 96.247 1 2155 1 chr7D.!!$R2 2154
7 TraesCS7A01G238000 chr7D 307031512 307033661 2149 True 3476.0 3476 95.831 1 2155 1 chr7D.!!$R1 2154
8 TraesCS7A01G238000 chr7D 307161909 307164053 2144 False 3378.0 3378 95.039 1 2155 1 chr7D.!!$F1 2154
9 TraesCS7A01G238000 chr4D 123400505 123402660 2155 False 3537.0 3537 96.293 1 2155 1 chr4D.!!$F1 2154
10 TraesCS7A01G238000 chr4D 134961998 134964151 2153 False 3504.0 3504 96.054 1 2150 1 chr4D.!!$F2 2149
11 TraesCS7A01G238000 chr1D 275785450 275787598 2148 True 3493.0 3493 95.970 1 2155 1 chr1D.!!$R1 2154
12 TraesCS7A01G238000 chr2A 423417110 423418216 1106 True 1842.0 1842 96.748 1650 2753 1 chr2A.!!$R1 1103
13 TraesCS7A01G238000 chr3A 227633804 227634909 1105 False 1803.0 1803 96.116 1650 2753 1 chr3A.!!$F1 1103
14 TraesCS7A01G238000 chr6A 289118161 289118798 637 False 1107.0 1107 97.962 2116 2753 1 chr6A.!!$F1 637
15 TraesCS7A01G238000 chrUn 406859804 406860441 637 False 1101.0 1101 97.806 2116 2753 1 chrUn.!!$F1 637
16 TraesCS7A01G238000 chr5A 300058356 300058993 637 False 1101.0 1101 97.806 2116 2753 1 chr5A.!!$F1 637

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
470 476 0.404040 GGGCGGGGATAATCATTCCA 59.596 55.000 0.0 0.0 34.77 3.53 F
1049 1064 1.003118 CCATTTCAAGGGAGGACGACA 59.997 52.381 0.0 0.0 29.54 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1698 1714 1.428869 AATCCTGAGATTCCCCTCCG 58.571 55.000 0.00 0.00 38.36 4.63 R
2642 2664 1.067669 CAGATGAGAGATTCGGCGGAA 59.932 52.381 7.21 9.32 36.41 4.30 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 1.820519 GGGCTTTGCATCTGACATTCA 59.179 47.619 0.00 0.00 0.00 2.57
263 266 9.869667 ACTCTTCCACTGACTTATATATGTACT 57.130 33.333 1.48 0.00 0.00 2.73
470 476 0.404040 GGGCGGGGATAATCATTCCA 59.596 55.000 0.00 0.00 34.77 3.53
645 651 3.187211 GCTGCTCGCCTACATAGAC 57.813 57.895 0.00 0.00 0.00 2.59
855 870 1.320344 CCGAACCTCTGATCGACCCA 61.320 60.000 1.01 0.00 41.43 4.51
954 969 3.028366 GCGTCGGCTTGGAAGAAGC 62.028 63.158 0.00 0.00 42.30 3.86
1049 1064 1.003118 CCATTTCAAGGGAGGACGACA 59.997 52.381 0.00 0.00 29.54 4.35
1056 1071 1.705873 AGGGAGGACGACATACCATC 58.294 55.000 3.17 0.00 0.00 3.51
1131 1146 4.331717 CGTGCTAAAAATCCGGTACATTCT 59.668 41.667 0.00 0.00 0.00 2.40
1182 1197 7.136772 GCGACACTTCTGGTTTACTTATTTTT 58.863 34.615 0.00 0.00 0.00 1.94
1236 1252 6.670027 CCCCAGTAGTTCATATAGGAGCTATT 59.330 42.308 13.06 7.24 33.94 1.73
1237 1253 7.364232 CCCCAGTAGTTCATATAGGAGCTATTG 60.364 44.444 19.75 19.75 37.75 1.90
1238 1254 7.179338 CCCAGTAGTTCATATAGGAGCTATTGT 59.821 40.741 22.65 8.20 36.94 2.71
1322 1338 4.809426 AGTATTGCGCTATTTACCAGTGAC 59.191 41.667 10.14 0.00 0.00 3.67
1580 1596 9.069082 AGTACTTACTATGCATAGGACTACAAG 57.931 37.037 31.87 21.54 34.13 3.16
1698 1714 1.021920 GCTTCTCCTCCAAAGCGGAC 61.022 60.000 0.00 0.00 39.64 4.79
1781 1798 2.030371 GTTTTTCCCGGGTTTGGTACA 58.970 47.619 22.86 0.00 0.00 2.90
1804 1821 6.940298 ACAAAATCTGGATAAACTCCTTTCGA 59.060 34.615 0.00 0.00 45.21 3.71
2211 2233 2.770447 TGGTCTGGTTATAGCATCCCA 58.230 47.619 0.00 0.00 0.00 4.37
2446 2468 3.586892 CATAATGCACATGCCACAAACA 58.413 40.909 0.49 0.00 41.18 2.83
2592 2614 3.019564 GGCTAGGTCATTCATTGCTTGT 58.980 45.455 0.00 0.00 0.00 3.16
2642 2664 3.532232 TCTCCACAGGGACTTCCTACTAT 59.468 47.826 0.00 0.00 46.12 2.12
2683 2705 2.638363 GAGAAAGTAGGTCACCTGGGTT 59.362 50.000 6.61 0.00 34.61 4.11
2715 2737 4.967036 AGCATAGATAAGGCTGGAGTTTC 58.033 43.478 0.00 0.00 36.34 2.78
2719 2741 4.479786 AGATAAGGCTGGAGTTTCTGAC 57.520 45.455 0.00 0.00 0.00 3.51
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
38 39 0.546598 CCCGTAGAGGAAAGCCCAAT 59.453 55.000 0.00 0.00 45.00 3.16
64 65 1.561643 TGCACAAAAAGGTTGGGACA 58.438 45.000 0.00 0.00 0.00 4.02
70 71 4.165180 AGGGGTTTATTGCACAAAAAGGTT 59.835 37.500 0.00 0.00 0.00 3.50
71 72 3.714280 AGGGGTTTATTGCACAAAAAGGT 59.286 39.130 0.00 0.00 0.00 3.50
263 266 5.072040 TCACTTTCTCGTATGAGCATTCA 57.928 39.130 7.11 0.00 42.26 2.57
277 280 2.370189 CAGACCCAGGAGTTCACTTTCT 59.630 50.000 0.00 0.00 0.00 2.52
371 377 2.898612 TGTAACCGTCACCTGTAATCCA 59.101 45.455 0.00 0.00 0.00 3.41
638 644 2.423898 CCCGGTCGCCTGTCTATGT 61.424 63.158 0.00 0.00 0.00 2.29
879 894 6.431543 ACTTACTGAATCTCGTCTTTCTCTCA 59.568 38.462 0.00 0.00 0.00 3.27
954 969 3.296943 CGCGGTTGTTCGTATTTCATTTG 59.703 43.478 0.00 0.00 0.00 2.32
981 996 7.598118 AGATGCATTCAAGTCGATCTATTACAG 59.402 37.037 0.00 0.00 0.00 2.74
1049 1064 7.822334 TCGACAAAACAGAAAGTATGATGGTAT 59.178 33.333 0.00 0.00 0.00 2.73
1056 1071 4.378459 GGGCTCGACAAAACAGAAAGTATG 60.378 45.833 0.00 0.00 0.00 2.39
1131 1146 5.319043 AGACTAGGATGGGAAACAAAACA 57.681 39.130 0.00 0.00 0.00 2.83
1182 1197 6.724441 TCATAGTGGAGAAGTCAAGACCTAAA 59.276 38.462 0.00 0.00 0.00 1.85
1191 1206 4.219115 GGGAGATCATAGTGGAGAAGTCA 58.781 47.826 0.00 0.00 0.00 3.41
1201 1216 5.144159 TGAACTACTGGGGAGATCATAGT 57.856 43.478 0.00 0.00 0.00 2.12
1236 1252 5.496556 ACCACGAATAGGAATGAAATGACA 58.503 37.500 0.00 0.00 0.00 3.58
1237 1253 6.436843 AACCACGAATAGGAATGAAATGAC 57.563 37.500 0.00 0.00 0.00 3.06
1238 1254 7.990314 TCATAACCACGAATAGGAATGAAATGA 59.010 33.333 0.00 0.00 32.88 2.57
1322 1338 7.557719 ACCAAAAGATCAGTCCAATAATACCAG 59.442 37.037 0.00 0.00 0.00 4.00
1580 1596 4.640647 GGAATACATCCTGTCTTTTCACCC 59.359 45.833 0.00 0.00 45.56 4.61
1698 1714 1.428869 AATCCTGAGATTCCCCTCCG 58.571 55.000 0.00 0.00 38.36 4.63
1814 1831 3.331889 AGCCAGAAAGAGAATTTCCTCCA 59.668 43.478 0.00 0.00 33.76 3.86
1863 1880 8.608185 TGATCTTCTTTAGGGGCAATTTAAAT 57.392 30.769 0.00 0.00 0.00 1.40
2211 2233 7.787623 ATTGACCAGAAAGGAATTGAGAAAT 57.212 32.000 0.00 0.00 41.22 2.17
2446 2468 4.973168 TCTGAGTGTGCTTCCACTTTATT 58.027 39.130 5.87 0.00 45.46 1.40
2592 2614 6.103997 AGAAGACAAAACGAATATAGCGGAA 58.896 36.000 0.00 0.00 0.00 4.30
2642 2664 1.067669 CAGATGAGAGATTCGGCGGAA 59.932 52.381 7.21 9.32 36.41 4.30
2683 2705 4.746702 GCCTTATCTATGCTGCTTTACCCA 60.747 45.833 0.00 0.00 0.00 4.51
2715 2737 5.394663 CCCTAGTAGACATCAACTTGGTCAG 60.395 48.000 0.00 0.00 37.04 3.51
2719 2741 3.197766 TGCCCTAGTAGACATCAACTTGG 59.802 47.826 0.00 0.00 38.06 3.61


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

AutoCloner maintained by Alex Coulton.