Multiple sequence alignment - TraesCS6A01G120700

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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 TraesCS6A01G120700 chr6A 100.000 3196 0 0 1 3196 92574978 92578173 0.000000e+00 5903
1 TraesCS6A01G120700 chr6D 95.398 3216 125 11 1 3196 77171544 77174756 0.000000e+00 5097
2 TraesCS6A01G120700 chr6B 93.381 3203 164 22 1 3196 149875729 149878890 0.000000e+00 4697
3 TraesCS6A01G120700 chr6B 72.901 786 161 32 903 1665 87999734 87998978 1.150000e-54 224


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 TraesCS6A01G120700 chr6A 92574978 92578173 3195 False 5903 5903 100.000 1 3196 1 chr6A.!!$F1 3195
1 TraesCS6A01G120700 chr6D 77171544 77174756 3212 False 5097 5097 95.398 1 3196 1 chr6D.!!$F1 3195
2 TraesCS6A01G120700 chr6B 149875729 149878890 3161 False 4697 4697 93.381 1 3196 1 chr6B.!!$F1 3195
3 TraesCS6A01G120700 chr6B 87998978 87999734 756 True 224 224 72.901 903 1665 1 chr6B.!!$R1 762

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
282 285 1.405821 CCTGAACCGTCTACAGCTAGG 59.594 57.143 0.00 0.0 0.00 3.02 F
893 911 1.748403 CACCGATCGATGACCCCAT 59.252 57.895 18.66 0.0 35.29 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1245 1278 1.375908 GACGACCATTGGCTGCTGA 60.376 57.895 1.54 0.0 0.00 4.26 R
2835 2874 0.841961 CAAGGATGCTCATGGGAGGA 59.158 55.000 0.00 0.0 46.09 3.71 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
69 70 2.812358 TACACACACACTTCGCAGAT 57.188 45.000 0.00 0.00 35.04 2.90
183 184 4.221703 GGATGGATATCTGTTCTCACCGAT 59.778 45.833 2.05 0.00 33.68 4.18
282 285 1.405821 CCTGAACCGTCTACAGCTAGG 59.594 57.143 0.00 0.00 0.00 3.02
417 420 3.526534 CCTTTGCCAAGTCTAGTCTAGC 58.473 50.000 1.60 5.38 0.00 3.42
418 421 3.196685 CCTTTGCCAAGTCTAGTCTAGCT 59.803 47.826 1.60 0.00 0.00 3.32
420 423 5.451242 CCTTTGCCAAGTCTAGTCTAGCTAG 60.451 48.000 15.01 15.01 46.59 3.42
459 476 7.604657 TGTTTAATTTGGGTTTCCATACAGT 57.395 32.000 0.00 0.00 43.63 3.55
464 481 4.708576 TTGGGTTTCCATACAGTACACA 57.291 40.909 0.00 0.00 43.63 3.72
541 558 5.509163 GGCGCCAGAACATATATATACGGAT 60.509 44.000 24.80 0.00 0.00 4.18
746 764 7.029563 CCAAATTTAGGAAGATTGAAACGGAG 58.970 38.462 0.00 0.00 0.00 4.63
749 767 8.581253 AATTTAGGAAGATTGAAACGGAGATT 57.419 30.769 0.00 0.00 0.00 2.40
822 840 2.430382 TTCTCACTCGACGCCAACCC 62.430 60.000 0.00 0.00 0.00 4.11
893 911 1.748403 CACCGATCGATGACCCCAT 59.252 57.895 18.66 0.00 35.29 4.00
1515 1549 2.672996 ATGCACAACTGGGGCGTC 60.673 61.111 0.00 0.00 0.00 5.19
1935 1969 3.455910 AGGGCAGCATCTACATCAACTTA 59.544 43.478 0.00 0.00 0.00 2.24
2038 2072 1.596220 CGCCGAACATTCATGCATCAG 60.596 52.381 0.00 0.00 0.00 2.90
2139 2173 5.301045 TCTTCTACTTCCTTTGTTCTCGACA 59.699 40.000 0.00 0.00 36.19 4.35
2183 2217 1.197036 TGACGTCGATATGAGCGGATC 59.803 52.381 11.62 0.00 0.00 3.36
2192 2226 0.105453 ATGAGCGGATCAGTACCCCT 60.105 55.000 1.31 0.00 42.53 4.79
2210 2244 3.254903 CCCCTTCTTTTGTTCGGTTTAGG 59.745 47.826 0.00 0.00 0.00 2.69
2310 2344 1.227089 GTGATCGCCGCATCAGAGT 60.227 57.895 0.00 0.00 33.29 3.24
2317 2351 2.124983 CGCATCAGAGTGGTGGGG 60.125 66.667 0.00 0.00 37.72 4.96
2340 2374 4.380655 GGATGGTGGAGATAGTGTATACGC 60.381 50.000 8.42 8.42 0.00 4.42
2364 2398 5.502382 CGTTGTGTGGAAATATTCGAGATGG 60.502 44.000 0.00 0.00 0.00 3.51
2500 2535 1.535462 AGCAAGGAACCGAAATGAACG 59.465 47.619 0.00 0.00 0.00 3.95
2519 2554 7.361457 TGAACGGACTAGATTTAGATCCAAT 57.639 36.000 0.00 0.00 31.76 3.16
2574 2610 2.555547 GCTCGGCTGGCAAAGTTGT 61.556 57.895 1.08 0.00 0.00 3.32
2575 2611 1.234615 GCTCGGCTGGCAAAGTTGTA 61.235 55.000 1.08 0.00 0.00 2.41
2662 2698 0.465460 AGAAGGTTCGCCACAAAGCA 60.465 50.000 0.00 0.00 40.60 3.91
2663 2699 0.598065 GAAGGTTCGCCACAAAGCAT 59.402 50.000 0.00 0.00 40.60 3.79
2741 2780 9.638239 GCAGATAGGAACTGATTTTAGATCTAG 57.362 37.037 2.02 0.00 41.52 2.43
2835 2874 5.081315 ACAAGGATATGCTAGAGTACCCT 57.919 43.478 0.00 0.00 0.00 4.34
2841 2880 0.556747 TGCTAGAGTACCCTCCTCCC 59.443 60.000 0.00 0.00 38.58 4.30
2845 2884 1.319947 AGAGTACCCTCCTCCCATGA 58.680 55.000 0.00 0.00 38.58 3.07
2904 2943 1.885157 CACGCTCTAACGGTACCCA 59.115 57.895 6.25 0.00 37.37 4.51
2936 2975 1.797211 CTCGATACTGGGACGGCCTC 61.797 65.000 7.57 0.00 39.14 4.70
3012 3051 7.607991 CCCAACTTCTAAGAAAGCTTGATCTTA 59.392 37.037 16.23 16.23 37.16 2.10
3074 3114 5.072736 GGGCCCCTATAAAACTTAGCTCTAA 59.927 44.000 12.23 0.00 0.00 2.10
3087 3127 8.658840 AACTTAGCTCTAATCCCCTCTATAAG 57.341 38.462 0.00 0.00 0.00 1.73
3107 3147 1.452651 CGACGCTAGGGGTAGGTCA 60.453 63.158 11.95 0.00 0.00 4.02
3117 3157 1.338890 GGGTAGGTCAAGGGCCTCTC 61.339 65.000 6.46 0.00 37.54 3.20
3130 3170 2.486907 GGGCCTCTCTTCCATGATTCAG 60.487 54.545 0.84 0.00 0.00 3.02
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 6.040247 TCGTACATCATCGTCTTAAATTGCT 58.960 36.000 0.00 0.00 0.00 3.91
183 184 8.109634 AGGAAGGAAATAAATGAGCTAACTGAA 58.890 33.333 0.00 0.00 0.00 3.02
451 468 4.081142 TGAATCCTGGTGTGTACTGTATGG 60.081 45.833 0.00 0.00 0.00 2.74
459 476 2.356022 CCTGCATGAATCCTGGTGTGTA 60.356 50.000 0.00 0.00 0.00 2.90
464 481 1.355381 TCAACCTGCATGAATCCTGGT 59.645 47.619 0.00 0.00 35.17 4.00
822 840 1.616159 CGGGGGTATTAATGGCCTTG 58.384 55.000 3.32 0.00 0.00 3.61
893 911 2.450243 GGGGTCAGAGGTGAGGGA 59.550 66.667 0.00 0.00 31.53 4.20
1057 1075 0.250727 TACAAAGGCCCACTGCTCAC 60.251 55.000 0.00 0.00 40.92 3.51
1234 1267 4.790962 CTGCTGATGCGCCTGGGT 62.791 66.667 4.18 0.00 43.34 4.51
1245 1278 1.375908 GACGACCATTGGCTGCTGA 60.376 57.895 1.54 0.00 0.00 4.26
1360 1394 3.880490 TGCATCATCCATTACGGTTAACC 59.120 43.478 15.13 15.13 35.57 2.85
1515 1549 1.669115 CTCCCCGAGTGCACAGTTG 60.669 63.158 21.04 2.72 0.00 3.16
1570 1604 3.507924 GGATTGCGCGTCCATGCA 61.508 61.111 22.45 0.00 39.81 3.96
1935 1969 2.779755 TTACACCCTTGCATCACGAT 57.220 45.000 0.00 0.00 0.00 3.73
2038 2072 7.023575 TGTCGACTCTAAAACTACGGAAATAC 58.976 38.462 17.92 0.00 0.00 1.89
2126 2160 1.734465 GCATCCCTGTCGAGAACAAAG 59.266 52.381 0.00 0.00 37.45 2.77
2139 2173 3.900892 CGTCGCGGTAGCATCCCT 61.901 66.667 6.13 0.00 45.49 4.20
2183 2217 2.812011 CCGAACAAAAGAAGGGGTACTG 59.188 50.000 0.00 0.00 0.00 2.74
2192 2226 6.762702 AGAAACCTAAACCGAACAAAAGAA 57.237 33.333 0.00 0.00 0.00 2.52
2310 2344 2.506644 ATCTCCACCATCCCCCACCA 62.507 60.000 0.00 0.00 0.00 4.17
2317 2351 4.380655 GCGTATACACTATCTCCACCATCC 60.381 50.000 3.32 0.00 0.00 3.51
2340 2374 5.492854 CATCTCGAATATTTCCACACAACG 58.507 41.667 0.00 0.00 0.00 4.10
2364 2398 5.692204 CCATAGTCATACGTGTCATCTTTCC 59.308 44.000 0.00 0.00 0.00 3.13
2500 2535 6.043243 TGGACCATTGGATCTAAATCTAGTCC 59.957 42.308 10.37 15.77 32.12 3.85
2504 2539 6.823286 TGTGGACCATTGGATCTAAATCTA 57.177 37.500 10.37 0.00 32.12 1.98
2519 2554 2.091610 TCCAACCAATCTTTGTGGACCA 60.092 45.455 0.00 0.00 39.62 4.02
2662 2698 2.306805 TCAGCCTTTCCTCACATGTGAT 59.693 45.455 28.00 8.71 39.13 3.06
2663 2699 1.699083 TCAGCCTTTCCTCACATGTGA 59.301 47.619 26.33 26.33 38.06 3.58
2741 2780 9.914923 CAAAATTTAGTTAGTCTTTTGGTTTGC 57.085 29.630 0.00 0.00 34.66 3.68
2835 2874 0.841961 CAAGGATGCTCATGGGAGGA 59.158 55.000 0.00 0.00 46.09 3.71
2904 2943 1.131638 TATCGAGCTTCCTGGCCAAT 58.868 50.000 7.01 0.00 0.00 3.16
3012 3051 0.804989 GAACTATTGGCTTGCACGCT 59.195 50.000 15.41 0.00 0.00 5.07
3087 3127 3.603671 CCTACCCCTAGCGTCGCC 61.604 72.222 14.86 0.00 0.00 5.54
3107 3147 1.904440 ATCATGGAAGAGAGGCCCTT 58.096 50.000 0.00 0.00 0.00 3.95
3117 3157 2.169352 ACCGAGGTCTGAATCATGGAAG 59.831 50.000 0.00 0.00 0.00 3.46
3130 3170 7.926555 TGAAGATGATAAAAATCTACCGAGGTC 59.073 37.037 0.00 0.00 33.17 3.85


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

AutoCloner maintained by Alex Coulton.