Multiple sequence alignment - TraesCS7A01G429300

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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 TraesCS7A01G429300 chr7A 100.000 3286 0 0 1 3286 623453380 623450095 0.000000 6069.0
1 TraesCS7A01G429300 chr7D 94.914 3323 95 25 1 3286 540850414 540847129 0.000000 5132.0
2 TraesCS7A01G429300 chr7D 96.970 33 0 1 85 116 242701781 242701813 0.002000 54.7
3 TraesCS7A01G429300 chr7B 94.813 3316 106 34 1 3286 584309537 584306258 0.000000 5110.0
4 TraesCS7A01G429300 chr7B 97.297 37 0 1 81 116 233174226 233174262 0.000010 62.1
5 TraesCS7A01G429300 chr4A 97.222 36 0 1 82 116 380623711 380623676 0.000035 60.2
6 TraesCS7A01G429300 chr3A 100.000 28 0 0 89 116 203095452 203095425 0.006000 52.8
7 TraesCS7A01G429300 chr2A 100.000 28 0 0 89 116 644985062 644985089 0.006000 52.8
8 TraesCS7A01G429300 chr1D 100.000 28 0 0 89 116 174587419 174587446 0.006000 52.8
9 TraesCS7A01G429300 chr1A 100.000 28 0 0 89 116 358239652 358239625 0.006000 52.8


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 TraesCS7A01G429300 chr7A 623450095 623453380 3285 True 6069 6069 100.000 1 3286 1 chr7A.!!$R1 3285
1 TraesCS7A01G429300 chr7D 540847129 540850414 3285 True 5132 5132 94.914 1 3286 1 chr7D.!!$R1 3285
2 TraesCS7A01G429300 chr7B 584306258 584309537 3279 True 5110 5110 94.813 1 3286 1 chr7B.!!$R1 3285

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
386 413 0.401979 ATATCAGAGTGGGGGTGGGG 60.402 60.0 0.00 0.0 0.00 4.96 F
1111 1152 0.969894 CGGCCGATTTCCCTCTATCT 59.030 55.0 24.07 0.0 0.00 1.98 F
1842 1885 0.110056 CTTGCGTCAGGTGCATGAAC 60.110 55.0 0.00 0.0 42.84 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1842 1885 0.681733 ACCCTGTATAGCCGATGCAG 59.318 55.000 7.17 7.17 45.26 4.41 R
2247 2293 1.704641 GGGTTTCTTTCCCTGCTGTT 58.295 50.000 0.00 0.00 41.58 3.16 R
2915 2978 2.957680 TGGCTTGTTTCTTGAGCATTGA 59.042 40.909 0.00 0.00 38.14 2.57 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
24 25 5.047164 TGCAATCATGTGATTAACAAAGGCT 60.047 36.000 7.84 0.00 43.61 4.58
25 26 5.290158 GCAATCATGTGATTAACAAAGGCTG 59.710 40.000 7.84 0.00 43.61 4.85
26 27 6.623486 CAATCATGTGATTAACAAAGGCTGA 58.377 36.000 7.84 0.00 43.61 4.26
80 81 2.203070 AGGGATCGAACATGCCGC 60.203 61.111 0.00 0.00 34.46 6.53
83 84 2.325857 GATCGAACATGCCGCAGC 59.674 61.111 0.00 0.00 40.48 5.25
97 98 2.978565 CAGCAGCACAGCAGCAGT 60.979 61.111 9.01 0.00 43.44 4.40
99 100 1.375652 AGCAGCACAGCAGCAGTAG 60.376 57.895 9.01 0.00 43.44 2.57
167 178 2.436417 GAAGGCCTTGCAACTCACATA 58.564 47.619 26.25 0.00 0.00 2.29
168 179 2.119801 AGGCCTTGCAACTCACATAG 57.880 50.000 0.00 0.00 0.00 2.23
169 180 1.630369 AGGCCTTGCAACTCACATAGA 59.370 47.619 0.00 0.00 0.00 1.98
170 181 1.740025 GGCCTTGCAACTCACATAGAC 59.260 52.381 0.00 0.00 0.00 2.59
205 221 5.622180 GGAGGTTTACTTTTCTTCAGAGGT 58.378 41.667 0.00 0.00 0.00 3.85
276 302 2.033757 AAGGACAGCAGCAGCAGG 59.966 61.111 3.17 0.00 45.49 4.85
385 412 2.260822 CTATATCAGAGTGGGGGTGGG 58.739 57.143 0.00 0.00 0.00 4.61
386 413 0.401979 ATATCAGAGTGGGGGTGGGG 60.402 60.000 0.00 0.00 0.00 4.96
616 644 1.594862 GCCAACGATCTCAAATCCTCG 59.405 52.381 0.00 0.00 37.17 4.63
636 664 1.372128 CTTTTGCCTCGTTGCTGCC 60.372 57.895 0.00 0.00 0.00 4.85
637 665 2.753931 CTTTTGCCTCGTTGCTGCCC 62.754 60.000 0.00 0.00 0.00 5.36
656 684 1.820056 CTGCATCCTGCTCCTGCTG 60.820 63.158 0.34 0.00 45.31 4.41
825 863 3.450457 TCCAGATTCCAGAGCTTCTTCTC 59.550 47.826 0.00 0.00 0.00 2.87
925 963 2.203394 AGTGCCCTTGCTGGTGTG 60.203 61.111 0.00 0.00 38.71 3.82
937 975 2.032071 GGTGTGTGGAGGTTCCCG 59.968 66.667 0.00 0.00 35.03 5.14
988 1026 3.820467 AGGAGAGTGAAGATGCGAGATAG 59.180 47.826 0.00 0.00 0.00 2.08
1111 1152 0.969894 CGGCCGATTTCCCTCTATCT 59.030 55.000 24.07 0.00 0.00 1.98
1135 1176 5.065602 TCTGCAGTCAAGCATGTGATAATTC 59.934 40.000 14.67 0.00 44.68 2.17
1136 1177 4.701171 TGCAGTCAAGCATGTGATAATTCA 59.299 37.500 0.00 0.00 40.11 2.57
1140 1181 7.132863 CAGTCAAGCATGTGATAATTCATCTG 58.867 38.462 0.00 0.00 34.46 2.90
1185 1226 8.560355 AAACTCTGGTTGCAGTTTAAAATTTT 57.440 26.923 8.75 8.75 40.35 1.82
1239 1280 1.614413 GGTGACGAGTCTGACCTTTCT 59.386 52.381 3.76 0.00 0.00 2.52
1240 1281 2.818432 GGTGACGAGTCTGACCTTTCTA 59.182 50.000 3.76 0.00 0.00 2.10
1499 1540 3.054875 TGGAACATGATGAGGTCTTCAGG 60.055 47.826 0.00 6.11 39.68 3.86
1541 1582 9.702726 AGTTTTGTTATTCATAATTCATCGTCG 57.297 29.630 0.00 0.00 0.00 5.12
1568 1609 8.892723 CATAAAGCACCAGATTTACAAGACATA 58.107 33.333 0.00 0.00 38.31 2.29
1573 1614 9.935241 AGCACCAGATTTACAAGACATATATAG 57.065 33.333 0.00 0.00 0.00 1.31
1605 1646 4.853924 TTGGGAAAGATCAAAAGTGAGC 57.146 40.909 0.00 0.00 40.63 4.26
1684 1725 5.389411 CGTTTGCAGTCATCAACGAGAATAA 60.389 40.000 12.52 0.00 0.00 1.40
1751 1792 5.447818 GCTGTTAACCTGCATAGTCATTCAC 60.448 44.000 13.56 0.00 37.89 3.18
1842 1885 0.110056 CTTGCGTCAGGTGCATGAAC 60.110 55.000 0.00 0.00 42.84 3.18
2034 2080 5.221342 GCACAGTACTCTGATACTAGGCAAT 60.221 44.000 1.86 0.00 43.76 3.56
2039 2085 7.231722 CAGTACTCTGATACTAGGCAATTACCT 59.768 40.741 1.99 1.99 43.76 3.08
2110 2156 5.459107 TCTTCGACGAAGAAACTTCAAGAAG 59.541 40.000 32.31 20.65 44.37 2.85
2247 2293 0.764369 ACCACACTGGCTCTTCTCCA 60.764 55.000 0.00 0.00 42.67 3.86
2286 2332 2.471818 CTTCTGGTCAGCATCGATGAG 58.528 52.381 29.20 19.13 0.00 2.90
2466 2515 3.383185 CGGAATTCTAGAGCTTCTCAGGT 59.617 47.826 5.23 0.00 32.06 4.00
2483 2532 1.212935 AGGTTGTCAAGCACAAGGACT 59.787 47.619 16.66 0.00 46.07 3.85
2572 2622 3.652869 TCCTCCCCATAATCCAGAATGAC 59.347 47.826 0.00 0.00 39.69 3.06
2647 2697 4.365514 TGTCCACCAATGCTCTAAAAGA 57.634 40.909 0.00 0.00 0.00 2.52
2661 2711 7.298122 TGCTCTAAAAGAAATTCTTGCTAACG 58.702 34.615 9.21 0.00 36.71 3.18
2769 2819 8.837099 AATAAATATGGGACCTTTTGTGATCA 57.163 30.769 0.00 0.00 0.00 2.92
2770 2820 8.837099 ATAAATATGGGACCTTTTGTGATCAA 57.163 30.769 0.00 0.00 0.00 2.57
2771 2821 7.552050 AAATATGGGACCTTTTGTGATCAAA 57.448 32.000 0.00 0.00 41.10 2.69
2772 2822 4.871933 ATGGGACCTTTTGTGATCAAAC 57.128 40.909 0.00 0.00 42.28 2.93
2773 2823 3.636679 TGGGACCTTTTGTGATCAAACA 58.363 40.909 0.00 0.00 42.28 2.83
2774 2824 3.383185 TGGGACCTTTTGTGATCAAACAC 59.617 43.478 0.00 0.00 42.28 3.32
2775 2825 3.243737 GGGACCTTTTGTGATCAAACACC 60.244 47.826 0.00 0.00 42.28 4.16
2776 2826 3.243737 GGACCTTTTGTGATCAAACACCC 60.244 47.826 0.00 0.00 42.28 4.61
2777 2827 3.370104 ACCTTTTGTGATCAAACACCCA 58.630 40.909 0.00 0.00 42.28 4.51
2778 2828 3.384467 ACCTTTTGTGATCAAACACCCAG 59.616 43.478 0.00 0.00 42.28 4.45
2779 2829 3.243839 CCTTTTGTGATCAAACACCCAGG 60.244 47.826 0.00 0.00 42.28 4.45
2780 2830 2.746279 TTGTGATCAAACACCCAGGT 57.254 45.000 0.00 0.00 39.69 4.00
2781 2831 2.746279 TGTGATCAAACACCCAGGTT 57.254 45.000 0.00 0.00 39.69 3.50
2861 2924 0.390492 GCCAAGCCAAAACTGCTCTT 59.610 50.000 0.00 0.00 38.34 2.85
2915 2978 9.520515 CTTATCCTGCTATTTAATATTGGGTGT 57.479 33.333 0.00 0.00 0.00 4.16
2982 3045 7.274250 GCAACATTAATCAATCAAGTTCCTGTC 59.726 37.037 0.00 0.00 0.00 3.51
3282 3345 8.554528 CCATCACTCACATCATAAACAATAGAC 58.445 37.037 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.061441 TCTCAAACTCAGCCTTTGTTAATCA 58.939 36.000 0.00 0.00 31.63 2.57
24 25 0.892755 ACGCCCGTATCTCAAACTCA 59.107 50.000 0.00 0.00 0.00 3.41
25 26 1.557651 GACGCCCGTATCTCAAACTC 58.442 55.000 0.00 0.00 0.00 3.01
26 27 0.175073 GGACGCCCGTATCTCAAACT 59.825 55.000 0.00 0.00 0.00 2.66
83 84 1.232621 TTGCTACTGCTGCTGTGCTG 61.233 55.000 20.53 11.99 40.48 4.41
84 85 1.071987 TTGCTACTGCTGCTGTGCT 59.928 52.632 20.53 0.00 40.48 4.40
85 86 1.208614 GTTGCTACTGCTGCTGTGC 59.791 57.895 20.53 19.74 40.48 4.57
86 87 0.946528 TTGTTGCTACTGCTGCTGTG 59.053 50.000 20.53 12.07 40.48 3.66
87 88 0.947244 GTTGTTGCTACTGCTGCTGT 59.053 50.000 16.37 16.37 40.48 4.40
97 98 3.508012 ACAGGTTGTTGTTGTTGTTGCTA 59.492 39.130 0.00 0.00 0.00 3.49
99 100 2.666022 GACAGGTTGTTGTTGTTGTTGC 59.334 45.455 0.00 0.00 0.00 4.17
136 143 2.029918 GCAAGGCCTTCCTAACTTTGTG 60.030 50.000 17.29 0.97 43.40 3.33
152 163 2.959516 TCGTCTATGTGAGTTGCAAGG 58.040 47.619 0.00 0.00 0.00 3.61
167 178 0.038159 CCTCCGTTTGAGCTTCGTCT 60.038 55.000 0.00 0.00 39.98 4.18
168 179 0.319641 ACCTCCGTTTGAGCTTCGTC 60.320 55.000 0.00 0.00 39.98 4.20
169 180 0.106149 AACCTCCGTTTGAGCTTCGT 59.894 50.000 0.00 0.00 39.98 3.85
170 181 1.226746 AAACCTCCGTTTGAGCTTCG 58.773 50.000 0.00 0.00 40.74 3.79
205 221 0.179004 CCTGCCCACCAGTACAACAA 60.179 55.000 0.00 0.00 40.06 2.83
238 254 0.718343 GTAGTAGTCGTCGTCGCAGT 59.282 55.000 0.00 0.00 36.96 4.40
242 258 1.061711 CCTTGGTAGTAGTCGTCGTCG 59.938 57.143 0.00 0.00 38.55 5.12
616 644 1.372128 CAGCAACGAGGCAAAAGCC 60.372 57.895 0.00 0.00 35.83 4.35
825 863 1.450531 GCATGGGAGAATTGCGAGGG 61.451 60.000 0.00 0.00 0.00 4.30
1096 1137 3.320541 ACTGCAGAGATAGAGGGAAATCG 59.679 47.826 23.35 0.00 0.00 3.34
1111 1152 2.484742 ATCACATGCTTGACTGCAGA 57.515 45.000 23.35 0.00 46.71 4.26
1135 1176 2.938451 TCTACGATTTGCAAGGCAGATG 59.062 45.455 0.00 0.00 40.61 2.90
1136 1177 3.266510 TCTACGATTTGCAAGGCAGAT 57.733 42.857 0.00 0.00 40.61 2.90
1140 1181 6.322491 AGTTTAATTCTACGATTTGCAAGGC 58.678 36.000 0.00 0.00 0.00 4.35
1391 1432 2.910688 TGTCGTTCAAAAGCTCTCCT 57.089 45.000 0.00 0.00 0.00 3.69
1499 1540 5.886992 ACAAAACTACTTGTTACCTGTTGC 58.113 37.500 0.00 0.00 36.05 4.17
1538 1579 3.764885 AAATCTGGTGCTTTATGCGAC 57.235 42.857 0.00 0.00 46.63 5.19
1539 1580 4.257731 TGTAAATCTGGTGCTTTATGCGA 58.742 39.130 0.00 0.00 46.63 5.10
1540 1581 4.614555 TGTAAATCTGGTGCTTTATGCG 57.385 40.909 0.00 0.00 46.63 4.73
1541 1582 6.030228 GTCTTGTAAATCTGGTGCTTTATGC 58.970 40.000 0.00 0.00 43.25 3.14
1568 1609 7.982252 TCTTTCCCAATCTCAATGCTCTATAT 58.018 34.615 0.00 0.00 0.00 0.86
1573 1614 4.885907 TGATCTTTCCCAATCTCAATGCTC 59.114 41.667 0.00 0.00 0.00 4.26
1605 1646 9.831737 CTATTCTGGTATTTGAACTTTGAGTTG 57.168 33.333 0.00 0.00 38.80 3.16
1751 1792 6.202954 CAGAACAGTAGTAGTTGGTTTTCAGG 59.797 42.308 0.00 0.00 0.00 3.86
1842 1885 0.681733 ACCCTGTATAGCCGATGCAG 59.318 55.000 7.17 7.17 45.26 4.41
1975 2021 4.339748 AGCAGATTGACTAGTCTCTGACA 58.660 43.478 31.48 10.19 35.26 3.58
2034 2080 5.013568 TGAAGAAACGACTGTTCAGGTAA 57.986 39.130 4.82 0.00 37.31 2.85
2039 2085 5.504010 GCATTCTTGAAGAAACGACTGTTCA 60.504 40.000 12.10 0.00 37.82 3.18
2110 2156 3.304996 GCTTTCTGGTCTTCTTTCTTGGC 60.305 47.826 0.00 0.00 0.00 4.52
2247 2293 1.704641 GGGTTTCTTTCCCTGCTGTT 58.295 50.000 0.00 0.00 41.58 3.16
2286 2332 3.451141 TGCCAATTGGTTGTCAACTTC 57.549 42.857 25.19 5.48 38.31 3.01
2466 2515 2.159254 GCAAAGTCCTTGTGCTTGACAA 60.159 45.455 0.00 0.00 42.55 3.18
2572 2622 7.010923 GTCATTTCCTACTTGCTAATGTCTCTG 59.989 40.741 0.00 0.00 0.00 3.35
2647 2697 4.657075 CGGTGTACGTTAGCAAGAATTT 57.343 40.909 0.00 0.00 37.93 1.82
2685 2735 5.847515 GCAGATAAACAAAGCAAATGCAAAC 59.152 36.000 8.28 0.00 45.16 2.93
2747 2797 7.016072 TGTTTGATCACAAAAGGTCCCATATTT 59.984 33.333 0.00 0.00 45.65 1.40
2779 2829 7.011016 GCTGGCAATGTTTGGGTTATAAATAAC 59.989 37.037 4.57 4.57 41.38 1.89
2780 2830 7.044798 GCTGGCAATGTTTGGGTTATAAATAA 58.955 34.615 0.00 0.00 0.00 1.40
2781 2831 6.382570 AGCTGGCAATGTTTGGGTTATAAATA 59.617 34.615 0.00 0.00 0.00 1.40
2911 2974 3.988379 TGTTTCTTGAGCATTGACACC 57.012 42.857 0.00 0.00 0.00 4.16
2915 2978 2.957680 TGGCTTGTTTCTTGAGCATTGA 59.042 40.909 0.00 0.00 38.14 2.57
2959 3022 7.121759 CAGGACAGGAACTTGATTGATTAATGT 59.878 37.037 0.00 0.00 34.60 2.71
2982 3045 7.322664 ACAATAGTTCAACAAAATATGGCAGG 58.677 34.615 0.00 0.00 29.01 4.85
3121 3184 4.677514 CGAGGATTGCCATTTGTTTATGCA 60.678 41.667 0.00 0.00 36.29 3.96


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

AutoCloner maintained by Alex Coulton.