Multiple sequence alignment - TraesCS7B01G091700

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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 TraesCS7B01G091700 chr7B 100.000 2195 0 0 1 2195 105257446 105255252 0 4054
1 TraesCS7B01G091700 chr1D 95.374 2205 92 7 1 2195 254416213 254418417 0 3498
2 TraesCS7B01G091700 chr5D 94.557 2223 91 15 1 2195 503286449 503288669 0 3408
3 TraesCS7B01G091700 chr5D 94.397 2213 102 11 1 2194 120799019 120801228 0 3380
4 TraesCS7B01G091700 chr5D 93.964 2220 95 21 1 2195 6181795 6179590 0 3321
5 TraesCS7B01G091700 chr5D 93.823 1117 46 9 1102 2195 512409297 512408181 0 1659
6 TraesCS7B01G091700 chr6D 94.407 2217 89 17 1 2195 45512415 45510212 0 3374
7 TraesCS7B01G091700 chr5A 94.328 2204 112 12 1 2195 607200942 607198743 0 3365
8 TraesCS7B01G091700 chr5A 88.936 949 77 16 1097 2022 520661594 520662537 0 1146
9 TraesCS7B01G091700 chr1A 95.459 2026 75 13 186 2195 554457800 554459824 0 3216
10 TraesCS7B01G091700 chr2A 95.003 1641 67 6 1 1628 335831479 335829841 0 2562
11 TraesCS7B01G091700 chr2A 94.643 1176 53 6 1012 2177 334595896 334594721 0 1814
12 TraesCS7B01G091700 chr2B 95.192 1560 61 11 647 2195 474900137 474901693 0 2453
13 TraesCS7B01G091700 chr3B 96.107 1387 50 4 1 1383 101919897 101918511 0 2259
14 TraesCS7B01G091700 chr4D 91.933 1314 86 12 897 2195 207373081 207374389 0 1821
15 TraesCS7B01G091700 chr4B 93.133 1034 57 7 1172 2195 308683448 308682419 0 1504


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 TraesCS7B01G091700 chr7B 105255252 105257446 2194 True 4054 4054 100.000 1 2195 1 chr7B.!!$R1 2194
1 TraesCS7B01G091700 chr1D 254416213 254418417 2204 False 3498 3498 95.374 1 2195 1 chr1D.!!$F1 2194
2 TraesCS7B01G091700 chr5D 503286449 503288669 2220 False 3408 3408 94.557 1 2195 1 chr5D.!!$F2 2194
3 TraesCS7B01G091700 chr5D 120799019 120801228 2209 False 3380 3380 94.397 1 2194 1 chr5D.!!$F1 2193
4 TraesCS7B01G091700 chr5D 6179590 6181795 2205 True 3321 3321 93.964 1 2195 1 chr5D.!!$R1 2194
5 TraesCS7B01G091700 chr5D 512408181 512409297 1116 True 1659 1659 93.823 1102 2195 1 chr5D.!!$R2 1093
6 TraesCS7B01G091700 chr6D 45510212 45512415 2203 True 3374 3374 94.407 1 2195 1 chr6D.!!$R1 2194
7 TraesCS7B01G091700 chr5A 607198743 607200942 2199 True 3365 3365 94.328 1 2195 1 chr5A.!!$R1 2194
8 TraesCS7B01G091700 chr5A 520661594 520662537 943 False 1146 1146 88.936 1097 2022 1 chr5A.!!$F1 925
9 TraesCS7B01G091700 chr1A 554457800 554459824 2024 False 3216 3216 95.459 186 2195 1 chr1A.!!$F1 2009
10 TraesCS7B01G091700 chr2A 335829841 335831479 1638 True 2562 2562 95.003 1 1628 1 chr2A.!!$R2 1627
11 TraesCS7B01G091700 chr2A 334594721 334595896 1175 True 1814 1814 94.643 1012 2177 1 chr2A.!!$R1 1165
12 TraesCS7B01G091700 chr2B 474900137 474901693 1556 False 2453 2453 95.192 647 2195 1 chr2B.!!$F1 1548
13 TraesCS7B01G091700 chr3B 101918511 101919897 1386 True 2259 2259 96.107 1 1383 1 chr3B.!!$R1 1382
14 TraesCS7B01G091700 chr4D 207373081 207374389 1308 False 1821 1821 91.933 897 2195 1 chr4D.!!$F1 1298
15 TraesCS7B01G091700 chr4B 308682419 308683448 1029 True 1504 1504 93.133 1172 2195 1 chr4B.!!$R1 1023

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
625 630 3.447944 AGGATTCGAACCTCTGAGTAACC 59.552 47.826 0.0 0.0 31.43 2.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1517 1556 1.134788 CCTTACCACACGGATCCACTC 60.135 57.143 13.41 0.0 35.59 3.51 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
130 131 5.659440 TCTTAAATTTCCACCCTCAATGC 57.341 39.130 0.00 0.00 0.00 3.56
163 164 7.438757 CGAGATGATCAATCTTGAAGTGAGAAT 59.561 37.037 0.00 0.00 46.34 2.40
377 380 5.934935 TCAACTCGAATACCAAAAGGAAC 57.065 39.130 0.00 0.00 0.00 3.62
378 381 5.369833 TCAACTCGAATACCAAAAGGAACA 58.630 37.500 0.00 0.00 0.00 3.18
625 630 3.447944 AGGATTCGAACCTCTGAGTAACC 59.552 47.826 0.00 0.00 31.43 2.85
697 702 9.469239 GTTTTATGCGACACTAATAAACACTAC 57.531 33.333 0.00 0.00 0.00 2.73
769 774 6.876257 GGAGGGATATTGTCTTGCTAGTATTG 59.124 42.308 0.00 0.00 0.00 1.90
776 781 9.884636 ATATTGTCTTGCTAGTATTGTACACAA 57.115 29.630 0.00 0.00 40.51 3.33
777 782 8.615878 ATTGTCTTGCTAGTATTGTACACAAA 57.384 30.769 0.00 0.00 39.55 2.83
1183 1193 0.953727 TGTTTGGCAAGCTGCTGTAG 59.046 50.000 15.19 0.00 44.28 2.74
1188 1198 0.523519 GGCAAGCTGCTGTAGGTTTC 59.476 55.000 1.35 3.24 44.32 2.78
1234 1244 7.160049 TGTATGCCAAATTGAATGATGTGTTT 58.840 30.769 0.00 0.00 0.00 2.83
1238 1248 9.887629 ATGCCAAATTGAATGATGTGTTTATTA 57.112 25.926 0.00 0.00 0.00 0.98
1365 1381 8.592809 ACAACAATAAATTTGGATCAGCCTTTA 58.407 29.630 0.00 0.00 37.63 1.85
1389 1411 1.541310 CCCCTGCACCTACGTTGAGA 61.541 60.000 0.00 0.00 0.00 3.27
1435 1467 6.605995 ACCACCTAACCCTATTTTTGCTATTC 59.394 38.462 0.00 0.00 0.00 1.75
1637 1679 8.660373 CAGTAGTGATATTCTTTGTTTCACTCC 58.340 37.037 7.11 0.00 44.27 3.85
1732 1782 9.834628 TTCTTATTGGATTTGTTTCGTACATTC 57.165 29.630 0.00 0.00 36.44 2.67
1892 1942 0.803768 CAGCCATCTCTCCACGTTCG 60.804 60.000 0.00 0.00 0.00 3.95
1924 1974 7.792364 AAGGTTTCCGTGATATGATATAGGA 57.208 36.000 1.26 1.26 0.00 2.94
1925 1975 7.979786 AGGTTTCCGTGATATGATATAGGAT 57.020 36.000 5.13 0.00 0.00 3.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
128 129 0.754472 TGATCATCTCGAGCCATGCA 59.246 50.000 7.81 0.12 0.00 3.96
130 131 3.927854 AGATTGATCATCTCGAGCCATG 58.072 45.455 7.81 7.69 37.79 3.66
163 164 8.609617 TTATTGAGGAAGAGTCAATCCTTCTA 57.390 34.615 16.19 8.86 46.04 2.10
410 415 3.888583 TCAAGCACATTCAGGATATGCA 58.111 40.909 0.00 0.00 38.79 3.96
463 468 7.736447 AAGTCTTAAGTCCAGTCAAATTGAG 57.264 36.000 1.63 0.00 0.00 3.02
585 590 1.960689 CCTTCCGTCCCACATTGTTTT 59.039 47.619 0.00 0.00 0.00 2.43
593 598 0.248289 TTCGAATCCTTCCGTCCCAC 59.752 55.000 0.00 0.00 0.00 4.61
617 622 1.202794 GGGTTTTGGTCCGGTTACTCA 60.203 52.381 0.00 0.00 0.00 3.41
755 760 9.582431 TCTATTTGTGTACAATACTAGCAAGAC 57.418 33.333 0.00 0.00 35.55 3.01
844 849 7.606073 TCAAATGAGAGTGGAATAAATTCGACA 59.394 33.333 16.81 0.46 44.64 4.35
876 881 9.981114 CAAACACAAAATACCTCCTTTTATTCT 57.019 29.630 0.00 0.00 0.00 2.40
882 887 5.212745 TCCCAAACACAAAATACCTCCTTT 58.787 37.500 0.00 0.00 0.00 3.11
1183 1193 7.764901 AGAGTACTAAAGATTTCATCGGAAACC 59.235 37.037 0.00 0.00 45.22 3.27
1188 1198 9.186323 CATACAGAGTACTAAAGATTTCATCGG 57.814 37.037 0.00 0.00 0.00 4.18
1325 1341 7.624360 TTTATTGTTGTAGCTACCCATTCAG 57.376 36.000 21.01 0.00 0.00 3.02
1365 1381 0.032416 ACGTAGGTGCAGGGGAGTAT 60.032 55.000 0.00 0.00 0.00 2.12
1389 1411 6.024893 TGGTTAGGTATTGTGTAGGTACCTT 58.975 40.000 22.11 2.80 44.34 3.50
1517 1556 1.134788 CCTTACCACACGGATCCACTC 60.135 57.143 13.41 0.00 35.59 3.51
1732 1782 3.073062 ACCCCCGGATTTTCTCATAGATG 59.927 47.826 0.73 0.00 0.00 2.90
1892 1942 1.600485 TCACGGAAACCTTTCGCTTTC 59.400 47.619 0.00 0.00 38.06 2.62
2098 2155 5.405935 AAATGCCCGCTAAAGAGAAAATT 57.594 34.783 0.00 0.00 0.00 1.82


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

AutoCloner maintained by Alex Coulton.