Multiple sequence alignment - TraesCS7B01G147200

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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 TraesCS7B01G147200 chr7B 100.000 3433 0 0 1 3433 192833408 192829976 0 6340
1 TraesCS7B01G147200 chr4B 96.447 3434 113 4 1 3433 173397508 173394083 0 5657
2 TraesCS7B01G147200 chr4B 96.040 3434 129 6 1 3433 199603021 199606448 0 5581
3 TraesCS7B01G147200 chr4B 95.868 3437 130 10 1 3433 629502193 629505621 0 5550
4 TraesCS7B01G147200 chr6B 95.489 3436 143 9 1 3433 9713706 9717132 0 5476
5 TraesCS7B01G147200 chr1B 95.230 3438 153 9 1 3433 413051775 413055206 0 5430
6 TraesCS7B01G147200 chr1B 93.821 3447 184 21 1 3433 164401143 164397712 0 5158
7 TraesCS7B01G147200 chr1B 93.523 3443 197 18 1 3433 256706746 256710172 0 5099


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 TraesCS7B01G147200 chr7B 192829976 192833408 3432 True 6340 6340 100.000 1 3433 1 chr7B.!!$R1 3432
1 TraesCS7B01G147200 chr4B 173394083 173397508 3425 True 5657 5657 96.447 1 3433 1 chr4B.!!$R1 3432
2 TraesCS7B01G147200 chr4B 199603021 199606448 3427 False 5581 5581 96.040 1 3433 1 chr4B.!!$F1 3432
3 TraesCS7B01G147200 chr4B 629502193 629505621 3428 False 5550 5550 95.868 1 3433 1 chr4B.!!$F2 3432
4 TraesCS7B01G147200 chr6B 9713706 9717132 3426 False 5476 5476 95.489 1 3433 1 chr6B.!!$F1 3432
5 TraesCS7B01G147200 chr1B 413051775 413055206 3431 False 5430 5430 95.230 1 3433 1 chr1B.!!$F2 3432
6 TraesCS7B01G147200 chr1B 164397712 164401143 3431 True 5158 5158 93.821 1 3433 1 chr1B.!!$R1 3432
7 TraesCS7B01G147200 chr1B 256706746 256710172 3426 False 5099 5099 93.523 1 3433 1 chr1B.!!$F1 3432

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
757 767 0.978907 GGACGGTTAGTTCTTCCCCA 59.021 55.0 0.0 0.0 0.00 4.96 F
1300 1318 0.181114 AGCAGTCCTGAAGTTGTGCA 59.819 50.0 0.0 0.0 33.24 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2321 2345 0.101759 ATGACTTGTACGCGGCGTAT 59.898 50.000 34.09 20.67 44.12 3.06 R
3196 3221 3.221956 CGCTTATACACGGCGCTC 58.778 61.111 6.90 0.00 42.28 5.03 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
73 74 7.465353 TGATAATCCTTTTGAATGCAGTCAA 57.535 32.000 24.54 24.54 35.72 3.18
141 142 2.224281 TGCTGTCAACCAGTAACTCAGG 60.224 50.000 0.00 0.00 43.55 3.86
237 240 7.753309 AAGGCATAGTAATAACAAACACACA 57.247 32.000 0.00 0.00 0.00 3.72
316 324 4.157289 CAGTCCCAATTCAGAAAGACCATG 59.843 45.833 0.00 0.00 0.00 3.66
523 533 7.068103 TGTTCAATTACACTTCAATCACCAGTT 59.932 33.333 0.00 0.00 0.00 3.16
755 765 2.038164 ACTTGGACGGTTAGTTCTTCCC 59.962 50.000 0.00 0.00 0.00 3.97
757 767 0.978907 GGACGGTTAGTTCTTCCCCA 59.021 55.000 0.00 0.00 0.00 4.96
936 954 1.112315 AAACCACCATTGCCGCTTCA 61.112 50.000 0.00 0.00 0.00 3.02
989 1007 2.594303 CAAAGCCCACAGTCGCCA 60.594 61.111 0.00 0.00 0.00 5.69
1005 1023 2.679092 CAGAGGAAGGCCATGGCA 59.321 61.111 36.56 0.00 44.11 4.92
1044 1062 0.746659 ATCATCATGCCGAGACGTCA 59.253 50.000 19.50 0.00 0.00 4.35
1050 1068 0.388649 ATGCCGAGACGTCAGACAAC 60.389 55.000 19.50 2.39 0.00 3.32
1074 1092 3.187700 GAGCAACCTCGTCGACATTAAT 58.812 45.455 17.16 0.00 0.00 1.40
1131 1149 1.201429 AAGGGGTTGAGCTCCACGAT 61.201 55.000 12.15 0.00 41.40 3.73
1185 1203 1.303888 AGACAAGGCCGACGAGGTA 60.304 57.895 0.00 0.00 43.70 3.08
1236 1254 2.032620 AGCTTTCGTAGGATCATCGGT 58.967 47.619 0.00 0.00 0.00 4.69
1291 1309 1.600638 CAGATGGCAGCAGTCCTGA 59.399 57.895 5.19 0.00 44.64 3.86
1300 1318 0.181114 AGCAGTCCTGAAGTTGTGCA 59.819 50.000 0.00 0.00 33.24 4.57
1433 1452 8.482128 TGAAAATTTAATCACACTTGTTTCCCT 58.518 29.630 0.00 0.00 0.00 4.20
2151 2175 1.503542 GACATTCAGCGCAAGTGGG 59.496 57.895 11.47 0.00 41.68 4.61
2256 2280 2.571212 ACAAGATCAACACGCAGGAAA 58.429 42.857 0.00 0.00 0.00 3.13
2321 2345 1.676529 GAGTACGCAGGAGTAGATGCA 59.323 52.381 0.00 0.00 42.68 3.96
2482 2506 3.702330 GTTTTACTTCCGCTTGTGCTTT 58.298 40.909 0.00 0.00 36.97 3.51
2666 2690 8.789825 TGTTAATCCATCATTTCAAAATTGGG 57.210 30.769 6.42 0.58 30.64 4.12
2735 2759 5.963176 ATCATGCAACTAATCACACAACA 57.037 34.783 0.00 0.00 0.00 3.33
2738 2762 6.747125 TCATGCAACTAATCACACAACATTT 58.253 32.000 0.00 0.00 0.00 2.32
3117 3142 6.935167 TGACAATGCTAGATACTTGAACTCA 58.065 36.000 0.00 0.00 0.00 3.41
3196 3221 3.691118 CACAGGTCAAGAGAGAGAGAGAG 59.309 52.174 0.00 0.00 0.00 3.20
3197 3222 3.587061 ACAGGTCAAGAGAGAGAGAGAGA 59.413 47.826 0.00 0.00 0.00 3.10
3369 3394 0.846693 AGCTATCTGGGCCGGAAAAT 59.153 50.000 21.02 5.57 0.00 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
783 793 2.967076 CAGTGCGTCGTGGCAACT 60.967 61.111 4.81 3.17 45.93 3.16
936 954 2.765699 AGGTTTGTGTGCAGTGGAAATT 59.234 40.909 0.00 0.00 0.00 1.82
989 1007 1.617536 TCTGCCATGGCCTTCCTCT 60.618 57.895 33.44 0.00 41.09 3.69
1005 1023 2.920912 TTGGCGGACGGTTCCTCT 60.921 61.111 0.00 0.00 40.23 3.69
1025 1043 0.746659 TGACGTCTCGGCATGATGAT 59.253 50.000 17.92 0.00 41.22 2.45
1074 1092 4.069232 CGCTTCTCGCCAGGGACA 62.069 66.667 0.00 0.00 34.21 4.02
1131 1149 1.309950 CGATCTCCAGCGTCTCCTTA 58.690 55.000 0.00 0.00 0.00 2.69
1218 1236 3.438297 ACACCGATGATCCTACGAAAG 57.562 47.619 0.00 0.00 0.00 2.62
1291 1309 1.792949 GAGTTCGTCGATGCACAACTT 59.207 47.619 10.05 0.00 0.00 2.66
1300 1318 0.603569 ACCAAGCAGAGTTCGTCGAT 59.396 50.000 0.00 0.00 0.00 3.59
1519 1540 5.056480 TCCAAATAGTAATCCAGTGCATCG 58.944 41.667 0.00 0.00 0.00 3.84
2151 2175 2.773993 TTTCCGGTGTATGGAACTCC 57.226 50.000 0.00 0.00 44.89 3.85
2256 2280 0.763035 GTCCCCCACAGTGTGTAGTT 59.237 55.000 21.48 0.00 0.00 2.24
2280 2304 0.403271 ATGAGGTTGTCTGGCAGCTT 59.597 50.000 10.34 0.00 0.00 3.74
2321 2345 0.101759 ATGACTTGTACGCGGCGTAT 59.898 50.000 34.09 20.67 44.12 3.06
2666 2690 6.018180 ACAACGTTCCATTCAGAAACTACTTC 60.018 38.462 0.00 0.00 0.00 3.01
2715 2739 7.410800 AAAATGTTGTGTGATTAGTTGCATG 57.589 32.000 0.00 0.00 0.00 4.06
2735 2759 6.772716 ACTGAGTTGTACTGACATGGAAAAAT 59.227 34.615 0.00 0.00 34.86 1.82
2738 2762 5.290493 ACTGAGTTGTACTGACATGGAAA 57.710 39.130 0.00 0.00 34.86 3.13
2799 2823 3.589988 ACGGACTGATGCTTCTTTGTAG 58.410 45.455 0.88 0.00 0.00 2.74
3196 3221 3.221956 CGCTTATACACGGCGCTC 58.778 61.111 6.90 0.00 42.28 5.03


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

AutoCloner maintained by Alex Coulton.